NOTES

PROLOGUE

1. N. E. Klepeis, W. C. Nelson, W. R. Ott, J. P. Robinson, A. M. Tsang, P. Switzer, J. V. Behar, S. C. Hern, and W. H. Engelmann, “The National Human Activity Pattern Survey (NHAPS): A Resource for Assessing Exposure to Environmental Pollutants,” Journal of Exposure Science and Environmental Epidemiology 11, no. 3 (2001): 231. Or see, for example, results for Canada: C. J. Matz, D. M. Stieb, K. Davis, M. Egyed, A. Rose, B. Chou, and O. Brion, “Effects of Age, Season, Gender and Urban-Rural Status on Time-Activity: Canadian Human Activity Pattern Survey 2 (CHAPS 2),” International Journal of Environmental Research and Public Health 11, no. 2 (2014): 2108–2124.

CHAPTER 1

1. Lesley Robertson, a microbiologist and historian, has been able to use microscopes like Leeuwenhoek’s to see many of the kinds of organisms he would have seen, including diatoms, Vorticella, Cyanobacteria, and various species of bacteria. The work requires patience, wonder, and a willingness to try each and every permutation of lighting and specimen preparation, as did Leeuwenhoek himself. See L. A. Robertson, “Historical Microbiology: Is It Relevant in the 21st Century?” FEMS Microbiology Letters 362, no. 9 (2015): fnv057.

2. By the time Leeuwenhoek was using microscopes, most of his income probably came from a minor role he performed as a city official. That job offered Leeuwenhoek the leisure time affluence can afford, the sort of leisure that can feed obsession.

3. Leeuwenhoek would have used these lenses, called thread counters, to examine the quality of flax, wool, and textiles. See L. Robertson, J. Backer, C. Biemans, J. van Doorn, K. Krab, W. Reijnders, H. Smit, and P. Willemsen, Antoni van Leeuwenhoek: Master of the Minuscule (Boston: Brill, 2016).

4. The book is now available online for free through Project Gutenberg and contains wonders both very big and very small (https://www.gutenberg.org/files/15491/15491-h/15491-h.htm).

5. Samuel Pepys called it “the most ingenious book that I ever read in my life.” See R. Hooke, Micrographia: Or Some Physiological Descriptions of Minute Bodies Made by Magnifying Glasses with Questions and Inquiries Thereupon (J. Martin and J. Allestrym, 1665).

6. At the time, it was not even believed that fleas reproduced; rather, people thought that fleas arose spontaneously from some perfect slurry of urine, dust, and their own feces. Leeuwenhoek documented the mating of the fleas (the smaller male dangling beneath the belly of the female). He documented the sperm and penis of the male (across his career he would document the sperm of more than thirty different animals, including his own). He found the eggs produced by the females. He sketched the eggs as they hatched, watched the larvae, and then saw their metamorphosis. He estimated that the process of sex, fertilization, eggs, and development could happen seven or eight times a year. He upped the ante, whether or not anyone happened to be paying attention. He did so all while carrying flea eggs with him wherever he went, in his bag, the way a child might carry a pet frog. See Robertson et al., Antoni van Leeuwenhoek.

7. De Graaf’s accompanying letter can be read in full here: M. Leeuwenhoek, “A Specimen of Some Observations Made by Microscope, Contrived by M. Leeuwenhoek in Holland, Lately Communicated by Dr. Regnerus de Graaf,” Philosophical Transactions of the Royal Society 8 (1673): 6037–6038.

8. Leeuwenhoek’s timing was good. Science had begun its shift from a focus on revisiting old texts and abstracted thought to a focus on observation. Inspired by the work of the French philosopher René Descartes, this new generation of scientists believed that through observation one could most effectively discover new truths.

9. A. R. Hall, “The Leeuwenhoek Lecture, 1988, Antoni Van Leeuwenhoek 1632–1723,” Notes and Records the Royal Society Journal of the History of Science 43, no. 2 (1989): 249–273.

10. Vacuoles are a remarkable storage device used by plant, animal, protist, fungal, and even bacterial cells. In vacuoles food can be stored. In vacuoles waste can be stored. In vacuoles conditions can be maintained that are different from those in the rest of the cell. In this way, vacuoles are perhaps most analogous to the clay vessels and reed baskets of early human civilizations; vacuoles are multipurpose containers used by different species and at different times for different things.

11. The town in which Leeuwenhoek lived, Delft, was the epicenter of the study of the home, albeit by painters, not by scientists. The painters of Delft focused on depicting the townscape and then also the interiors of rooms. They depicted key habitats Leeuwenhoek would explore. Pieter de Hooch painted many scenes of courtyards; Carel Fabritius most famously painted The Goldfinch in its cage, but he also painted a landscape of Delft. Then there was Johannes (or Jan) Vermeer. Vermeer painted the same three rooms again and again, depicting small groups of people frozen, each set of them, in a kind of still life.

12. The lot where Leeuwenhoek’s house once stood has never been excavated. It may contain lost microscopes, samples, or nearly anything else. This lot is now the site of a fancy coffee shop. Lesley Robertson and I tried to convince the owners to let us drill through their newly laid floor to search for artifacts of Leeuwenhoek’s life beneath their shop. They declined, so instead I spent the next days trying to look through their windows into the backyard, the yard where Leeuwenhoek spent oh-so-very-much time.

CHAPTER 2

1. The documentary, called The Fifth Kingdom: How Fungi Made the World, tells the story of fungi, their evolution, and its consequences. I was standing by the hot springs to speak about the evolution of fungi against a backdrop that was equal parts volcanism and microbes.

2. I suppose it is also possible that scientists can be frustrating! Though I think that the truth is the busy crew had their minds set on finding the perfect geyser and just forgot to count heads before driving off.

3. Geyser is actually an Icelandic word for “hot spring.” For Brock’s delightful autobiography, see: T. D. Brock, “The Road to Yellowstone—and Beyond,” Annual Review of Microbiology 49 (1995): 1–28.

4. The archaea, like bacteria, evolved billions of years ago. Archaea are, like bacteria, single-celled. And, like bacteria, they lack a nucleus. The similarities end there, though. The cells of archaea are more different from those of bacteria than our cells are from plant cells. Archaea were discovered in the middle 1900s. Archaea are diverse but are often (though not exclusively) found in extreme habitats. They are never parasites of humans (ever). They are often relatively slow growing. And they have an extraordinary diversity of metabolic capabilities. I love bacteria, find them endlessly fascinating and surprising. But the archaea are even better, a life-form as old as life itself that never causes harm, carries out fundamental ecological processes, is poorly studied, and, as we recently revealed, sometimes lives in places as immediate to your daily experience as your belly button. Leeuwenhoek missed them, which is to suggest that we are better than he was at navel gazing. J. Hulcr, A. M. Latimer, J. B. Henley, N. R. Rountree, N. Fierer, A. Lucky, M. D. Lowman, and R. R. Dunn, “A Jungle in There: Bacteria in Belly Buttons Are Highly Diverse, but Predictable,” PloS One 7, no. 11 (2012): e47712.

5. Chemolithotrophs, chemical eaters that oxidize inorganic compounds to obtain energy.

6. Every species, be it a bacterium or a monkey, is given a species name and a genus name. The genus reflects the broader group to which a species belongs. As humans, we belong to the species sapiens (knowing) of the genus Homo. We are Homo sapiens. Just where the edges of one species end and another’s begin is often fuzzy, even more so the boundaries of genera. In theory, one might argue that genera should tend to be named and grouped by scientists in such a way that a genus of primates and one of bacteria are about the same age. In practice, the ways in which scientists of different subfields decide how many species to include in a genus vary. The genera of bacteria tend to contain many species and be ancient (Thermus may well be tens of millions of years old, if not older). Genera of life-forms more like us tend to include fewer species and to be more recent; this difference is entirely a function of the preferences of microbiologists relative to, say, those of primatologists rather than differences between bacteria and primates themselves. The genus and species names of organisms are always italicized (as you will see in the text) unless a species has not yet been given a name, in which case the genus is italicized, but not the placeholder name of the species. For example, Thermus X1, where X1 means it is probably a new species but has not yet been given a species name. In most groups of organisms, apart from vertebrates and plants, many species bear these provisional names because no one has yet had a chance to name them formally even though their existence is known.

7. When Brock grew Thermus aquaticus, he was actually trying to grow a species he called simply “a pink bacteria” that lives in even hotter conditions. He was unable to grow the pink bacteria. Nor has anyone, it seems, been able to grow it since. For the first Thermus study, see T. D. Brock and H. Freeze, “Thermus aquaticus gen. n. and sp. n., a Nonsporulating Extreme Thermophile,” Journal of Bacteriology 98, no. 1 (1969): 289–297.

8. R. F. Ramaley and J. Hixson, “Isolation of a Nonpigmented, Thermophilic Bacterium Similar to Thermus aquaticus,” Journal of Bacteriology 103, no. 2 (1970): 527.

9. Economics would later borrow the term again, from ecology.

10. T. D. Boylen and K. L. Boylen, “Presence of Thermophilic Bacteria in Laundry and Domestic Hot-Water Heaters,” Applied Microbiology 25, no. 1 (1973): 72–76.

11. J. K. Kristjánsson, S. Hjörleifsdóttir, V. Th. Marteinsson, and G. A. Alfredsson, “Thermus scotoductus, sp. nov., a Pigment-Producing Thermophilic Bacterium from Hot Tap Water in Iceland and Including Thermus sp. X-1,” Systematic and Applied Microbiology 17, no. 1 (1994): 44–50.

12. Kristjánsson et al., “Thermus scotoductus, sp. nov.,” 44–50.

13. One of the key points Brock makes, again and again, in his writing is that although industry has continued to work with the extreme microbes that he and his colleagues discovered in the 1970s and 1980s, very few researchers have continued to study the ecology of these organisms in the wild. See Brock, “The Road to Yellowstone,” 1–28.

14. D. J. Opperman, L. A. Piater, and E. van Heerden, “A Novel Chromate Reductase from Thermus scotoductus SA-01 Related to Old Yellow Enzyme,” Journal of Bacteriology 190, no. 8 (2008): 3076–3082. Also, because microbes never cease to surprise, another new strain of this same species has recently been shown to be able grow as a chemotroph when the need arises. In the lingo of scientists, it is a mixotroph. S. Skirnisdottir, G. O. Hreggvidsson, O. Holst, and J. K. Kristjansson, “Isolation and Characterization of a Mixotrophic Sulfur-Oxidizing Thermus scotoductus,” Extremophiles 5, no. 1 (2001): 45–51.

15. For more on why so many bacteria are still unculturable, see S. Pande and C. Kost, “Bacterial Unculturability and the Formation of Intercellular Metabolic Networks,” Trends in Microbiology 25, no. 5 (2017): 349–361.

16. “High throughput” is a fancy way of saying that one can do a lot at once, in this case decode the sequences of many organisms at the same time. It is “high-throughput” sequencing in much the way that McDonald’s is high-throughput eating. And as for “next generation,” such techniques advance so quickly that “next-generation” approaches are now feeling, among the hip and cool, oh-so “last generation,” which was inevitable when the term was coined.

17. There are usually a few additional steps to help get rid of anything remaining in the sample that is not DNA. But this is the broad picture.

18. With time, the exploration spurred by the work of Brock and his colleagues and contemporaries led to the discovery of more thermophilic microbes—even hyperthermophilic microbes—and with them an entire library of their enzymes, each of which has slightly different abilities. A polymerase has been identified in Pyrococcus furiosus, for example, that works like Taq but that is even more stable at high temperatures.

19. The standard approach to sequencing does not identify organisms in such a way as to precisely match them up with named species. Instead, we get lists of life-forms grouped into their genera, Thermus 1, Thermus 2, and so on. Individual sequences are grouped into these names, these taxa, as a function of the similarity of their DNA sequences. Microbiologists call these taxa operational taxonomic units (OTUs) in recognition that they aren’t quite species. In some cases, a single OTU might really contain several species. In other cases, the reverse can be true (two OTUs belong in the same species). We are still at a phase in our naming of microbial life that all of this is a bit messy, so although OTUs are a highly imperfect way of grouping life, they provide a means of continuing to move forward while figuring out ways to reconcile new and old approaches to classifying life.

20. Recently, Regina Wilpiszeski used these techniques to search for additional thermophilic bacteria in hot water heaters, species in addition to Thermus scotoductus. When she did, she found a half dozen species of bacteria that are typically found only in hot springs, several of which are as yet uncultured and yet now nonetheless detectable.

CHAPTER 3

1. More than once I walked long and far enough to exhaust all three, only to have to pick my way back to the station through the moonlight. In a forest chock-a-block full of venomous snakes, that was dumb.

2. S. H. Messier, “Ecology and Division of Labor in Nasutitermes corniger: The Effect of Environmental Variation on Caste Ratios” (PhD diss., University of Colorado, 1996).

3. B. Guénard and R. R. Dunn, “A New (Old), Invasive Ant in the Hardwood Forests of Eastern North America and Its Potentially Widespread Impacts,” PLoS One 5, no. 7 (2010): e11614.

4. B. Guénard and J. Silverman, “Tandem Carrying, a New Foraging Strategy in Ants: Description, Function, and Adaptive Significance Relative to Other Described Foraging Strategies,” Naturwissenschaften 98, no. 8 (2011): 651–659.

5. T. Yashiro, K. Matsuura, B. Guenard, M. Terayama, and R. R. Dunn, “On the Evolution of the Species Complex Pachycondyla chinensis (Hymenoptera: Formicidae: Ponerinae), Including the Origin of Its Invasive Form and Description of a New Species,” Zootaxa 2685, no. 1 (2010): 39–50.

6. Only one paper has ever been written about this ant, in 1954. M. R. Smith and M. W. Wing, “Redescription of Discothyrea testacea Roger, a Little-Known North American Ant, with Notes on the Genus (Hymenoptera: Formicidae),” Journal of the New York Entomological Society 62, no. 2 (1954): 105–112. As for Katherine, I wasn’t sure what she was up to, so I checked. She now works as a zookeeper at the El Paso Zoo. Katherine’s interest in big cats ultimately proved more powerful than my power to distract.

7. This was work begun and led by Andrea Lucky, now an assistant professor at the University of Florida. A. Lucky, A. M. Savage, L. M. Nichols, C. Castracani, L. Shell, D. A. Grasso, A. Mori, and R. R. Dunn, “Ecologists, Educators, and Writers Collaborate with the Public to Assess Backyard Diversity in the School of Ants Project,” Ecosphere 5, no. 7 (2014): 1–23.

8. Long before we ever considered that one day we might be studying people’s belly buttons or homes, Noah and I worked together on a project about ambrosia beetles, led by Jiri Hulcr. Jiri was studying the fungi and bacteria these beetles carry with them from place to place and garden to feed their babies. But this connection also allowed Noah and me to begin to work together. See J. Hulcr, N. R. Rountree, S. E. Diamond, L. L. Stelinski, N. Fierer, and R. R. Dunn, “Mycangia of Ambrosia Beetles Host Communities of Bacteria,” Microbial Ecology 64, no. 3 (2012): 784–793.

9. Initially, these participants tended to be people we knew, but as our projects grew bigger, the scope of our engagement grew, and grew, and grew.

10. H. Holmes, The Secret Life of Dust: From the Cosmos to the Kitchen Counter, the Big Consequences of Small Things (Hoboken, NJ: Wiley, 2001).

11. Which meant Noah’s technician, Jessica Henley, would soon be clipping four thousand tips of four thousand cotton swabs into four thousand vials. Sorry, Jessica. Sorry, and thank you.

12. In some places, the life in our homes records exactly where we put our bodies. Consider a study done by Matt Colloff, an ecologist and mite biologist then at the University of Glasgow. Colloff decided to sample and study, night after night, his own bed. He set up devices to monitor the temperature and humidity of nine quadrats of his bed while he slept. The bed was, Colloff notes in the study, a fifteen-year-old double bed with a fifteen-year-old mattress. The devices collected data about his mattress every hour on the hour as he snoozed. He expected to find more mites where conditions were warmer and more humid. This didn’t seem to be the case. What he did discover was that wherever his body was, regardless of the temperature, there were also more mites. He found eighteen species of mites in total, including dust mites, but also predators of dust mites, all living beneath the spot on the bed where he slept, eating his body as it fell apart. One imagines that microbes, too, show a similar pattern, living in the greatest densities beneath those places we spend the most time. Colloff attributes the great diversity of his bed to the mattress’s age. See M. J. Colloff, “Mite Ecology and Microclimate in My Bed,” in Mite Allergy: A Worldwide Problem, ed. A. De Weck and A. Todt (Brussels: UCB Institute of Allergy, 1988), 51–54.

13. We later had a similar incident when studying the life in someone’s belly button. The participant, a journalist of some renown, had a belly button filled almost exclusively with food-associated bacteria. We have no explanation. Some of life’s mysteries are beyond the scope of science.

14. P. Zalar, M. Novak, G. S. De Hoog, and N. Gunde-Cimerman, “Dishwashers—a Man-Made Ecological Niche Accommodating Human Opportunistic Fungal Pathogens,” Fungal Biology 115, no. 10 (2011): 997–1007.

15. Strain 121, as the species was called, was originally found near deep hydrothermal sea vents, where water can reach 130 degrees Celsius. It would turn out to survive at temperatures far beyond what anyone had previously believed possible. Autoclaves are like pressure cookers, pressurized so that they can reach sustained temperatures around 121 degrees Celsius (250 degrees Fahrenheit) and in doing so kill all life, especially the bacteria that contaminate lab equipment. Strain 121 could survive and thrive for more than twenty-four hours in the autoclave. Most autoclave sterilization cycles only last an hour or two. See K. Kashefi and D. R. Lovley, “Extending the Upper Temperature Limit for Life,” Science 301, no. 5635 (2003): 934–934.

16. We later showed that this is less true for doors in apartments (which look like everything else in apartments). See R. R. Dunn, N. Fierer, J. B. Henley, J. W. Leff, and H. L. Menninger, “Home Life: Factors Structuring the Bacterial Diversity Found within and between Homes,” PLoS One 8, no. 5 (2013): e64133.

17. B. Fruth and G. Hohmann, “Nest Building Behavior in the Great Apes: The Great Leap Forward?” Great Ape Societies, ed. W. C. McGrew, L. F. Marchant, and T. Nishida (New York: Cambridge University Press, 1996), 225; D. Prasetyo, M. Ancrenaz, H. C. Morrogh-Bernard, S. S. Utami Atmoko, S. A. Wich, and C. P. van Schaik, “Nest Building in Orangutans,” Orangutans: Geographical Variation in Behavioral Ecology, ed. S. A. Wich, S. U. Atmoko, T. M. Setia, and C. P. van Schaik (Oxford: Oxford University Press, 2009), 269–277.

18. Three-toed sloths make the treacherous descent from the safety of their canopy perches down to the forest floor every three weeks or so to defecate. When they do, the moths living in their fur lay their eggs in the sloth dung. The moth larvae develop completely within the dung. When they are mature, they fly up to the canopy to take up residency in the sloth’s fur. An individual three-toed sloth can harbor between four and thirty-five moths. It has been suggested that the moths provide nutrients that help algae, also growing in the sloth’s fur, to flourish. The sloths then eat the algae to supplement their diet because the algae are richer in lipids than is the foliage. See J. N. Pauli, J. E. Mendoza, S. A. Steffan, C. C. Carey, P. J. Weimer, and M. Z. Peery, “A Syndrome of Mutualism Reinforces the Lifestyle of a Sloth,” Proceedings of the Royal Society B 281, no. 1778 (2014): 20133006.

19. See, for example, M. J. Colloff, “Mites from House Dust in Glasgow,” Medical and Veterinary Entomology 1, no. 2 (1987): 163–168.

20. The chimpanzees don’t go to the bathroom in their nests, they don’t appear to abandon much of their food, and they build a new nest most nights. All of this must help to keep the microbes and other life-forms associated with chimpanzee bodies from accumulating. See D. R. Samson, M. P. Muehlenbein, and K. D. Hunt, “Do Chimpanzees (Pan troglodytes schweinfurthii) Exhibit Sleep Related Behaviors That Minimize Exposure to Parasitic Arthropods? A Preliminary Report on the Possible Anti-vector Function of Chimpanzee Sleeping Platforms,” Primates 54, no. 1 (2013): 73–80. For Megan’s study, see M. S. Thoemmes, F. A. Stewart, R. A. Hernandez-Aguilar, M. Bertone, D. A. Baltzegar, K. P. Cole, N. Cohen, A. K. Piel, and R. R. Dunn, “Ecology of Sleeping: The Microbial and Arthropod Associates of Chimpanzee Beds,” Royal Society Open Science 5 (2018): 180382. doi:10.1098/rsos.180382.

21. H. De Lumley, “A Paleolithic Camp at Nice,” Scientific American 220, no. 5 (1969): 42–51.

22. It is hard to imagine that hominids moved into Europe more than 1.7 million years ago without the ability to build a shelter. The trouble is that the elements out of which the first homes would have been built—branches, leaves, and mud—don’t preserve well. But it doesn’t take many steps to go from building a nest, to building a wind shelter, to building a crude dome.

23. L. Wadley, C. Sievers, M. Bamford, P. Goldberg, F. Berna, and C. Miller, “Middle Stone Age Bedding Construction and Settlement Patterns at Sibudu, South Africa,” Science 334, no. 6061 (2011): 1388–1391.

24. J. F. Ruiz-Calderon, H. Cavallin, S. J. Song, A. Novoselac, L. R. Pericchi, J. N. Hernandez, Rafael Rios, et al., “Walls Talk: Microbial Biogeography of Homes Spanning Urbanization,” Science Advances 2, no. 2 (2016): e1501061.

25. We humans tend to kill off useful species in our houses and, at the same time, accidentally favor the bad ones. The termites in our homes do the opposite. Formosan termites (Coptotermes spp.), for example, can smell fungi on their bodies or in their nest by waving their antennae in the darkness of their chambers. They are also then able to clean individual fungal spores off of their bodies. Once fungal spores are encountered, the termites get rid of them by eating them. Termite guts effectively encapsulate the fungi in feces, which serves as an effective biocide, much as does the nacre of an oyster’s pearl around the tapeworm cyst it includes. The termites then build the walls of their nests with their feces, antimicrobial spit (their own), and soil. Inside those walls the fungi live on, trapped. By employing this collection of behaviors—detection, consumption, construction—these termites have created an environment that is largely devoid of their most serious foes while, at the same time, letting other species, including those they depend on for digestion, persist unharmed. See A. Yanagawa, F. Yokohari, and S. Shimizu, “Defense Mechanism of the Termite, Coptotermes formosanus Shiraki, to Entomopathogenic Fungi,” Journal of Invertebrate Pathology 97, no. 2 (2010): 165–170. Also see A. Yanagawa, F. Yokohari, and S. Shimizu, “Influence of Fungal Odor on Grooming Behavior of the Termite, Coptotermes formosanus,” Journal of Insect Science 10, no. 1 (2010): 141. Also see A. Yanagawa, N. Fujiwara-Tsujii, T. Akino, T. Yoshimura, T. Yanagawa, and S. Shimizu, “Musty Odor of Entomopathogens Enhances Disease-Prevention Behaviors in the Termite Coptotermes formosanus,” Journal of Invertebrate Pathology 108, no. 1 (2011): 1–6.

26. D. L. Pierson, “Microbial Contamination of Spacecraft,” Gravitational and Space Research 14, no. 2 (2007): 1–6.

27. For bacteria. We will return to the fungi. See Novikova, “Review of the Knowledge of Microbial Contamination,” 127–132. Also see N. Novikova, P. De Boever, S. Poddubko, E. Deshevaya, N. Polikarpov, N. Rakova, I. Coninx, and M. Mergeay, “Survey of Environmental Biocontamination on Board the International Space Station,” Research in Microbiology 157, no. 1 (2006): 5–12.

28. The longest-term study found dozens of genera of bacteria, the most common of which were armpit bacteria (Corynebacterium) and acne bacteria (Propionibacterium). See A. Checinska, A. J. Probst, P. Vaishampayan, J. R. White, D. Kumar, V. G. Stepanov, G. R. Fox, H. R. Nilsson, D. L. Pierson, J. Perry, and K. Venkateswaran, “Microbiomes of the Dust Particles Collected from the International Space Station and Spacecraft Assembly Facilities,” Microbiome 3, no. 1 (2015): 50.

29. S. Kelly, Endurance: A Year in Space, a Lifetime of Discovery (New York: Knopf, 2017), 387.

CHAPTER 4

1. First discussed in a paper by Ron Pulliam. See H. R. Pulliam, “Sources, Sinks, and Population Regulation,” American Naturalist 132 (1988): 652–661.

2. Dan Janzen has suggested some bacteria produce repulsive odors not as waste products but instead as a means of preventing their food from being eaten by us. They stink, he argues, in order to be able to eat in peace. Sometimes I have the idea that people next to me on planes are trying the same strategy. See D. H. Janzen, “Why Fruits Rot, Seeds Mold, and Meat Spoils,” American Naturalist 111, no. 980 (1977): 691–713.

3. Just which odors we perceive to be disgusting is a reflection of both our evolutionary past and our culture. Culture modulates the way in which we think about a particular odor (for example, how we feel about fish paste). Evolution, however, shaped whether the signals in our brain triggered by an odor are perceived as unpleasant. It is worth noting that these perceptions are always species specific. The same “miasmic” odors that repulse us trigger the opposite reaction in a dung beetle or a turkey vulture.

4. This wasn’t technically the story of the biology of a home, but when everyone gets their water from a common well in the city, the whole city and its biology spill over into the home.

5. One reason some cholera epidemics subside is because viruses (vibriophages) attack Vibrio cholerae. As Vibrio cholerae becomes abundant, so too do the vibriophages until they are so abundant that populations of Vibrio cholerae crash. Then populations of the vibriophages crash, which allows Vibrio cholerae populations to grow again. In the Ganges, the rise and fall of Vibrio cholerae and its virus are seasonal as are cholera cases. S. Mookerjee, A. Jaiswal, P. Batabyal, M. H. Einsporn, R. J. Lara, B. Sarkar, S. B. Neogi, and A. Palit, “Seasonal Dynamics of Vibrio cholerae and Its Phages in Riverine Ecosystem of Gangetic West Bengal: Cholera Paradigm,” Environmental Monitoring and Assessment 186, no. 10 (2014): 6241–6250.

6. Inasmuch as millions of people still die every year from cholera, the challenge is to ensure such systems are available to everyone. The challenge is no longer figuring out the cause of the disease or even how to stop it but figuring out how to get the solution, clean drinking water, to everyone in the world. The challenge is no longer prevention of a mystery ailment due to miasma but instead the hard-to-resolve dilemma of global inequality and geopolitics.

7. I. Hanski, Messages from Islands: A Global Biodiversity Tour (Chicago: University of Chicago Press, 2016).

8. As if a kind of premonition, Haahtela referenced just twenty-three papers in this article, two of them by Hanski. See T. Haahtela, “Allergy Is Rare Where Butterflies Flourish in a Biodiverse Environment,” Allergy 64, no. 12 (2009): 1799–1803.

9. United Nations, World Urbanization Prospects: The 2014 Revision. Highlights (New York: United Nations, 2014), https://esa.un.org/unpd/wup/publications/files/wup2014-highlights.pdf.

10. E. O. Wilson, Biophilia (Cambridge, MA: Harvard University Press, 1984).

11. See, for example, citations and discussion in M. R. Marselle, K. N. Irvine, A. Lorenzo-Arribas, and S. L. Warber, “Does Perceived Restorativeness Mediate the Effects of Perceived Biodiversity and Perceived Naturalness on Emotional Well-Being Following Group Walks in Nature?” Journal of Environmental Psychology 46 (2016): 217–232.

12. R. Louv, Last Child in the Woods: Saving Our Children from Nature-Deficit Disorder (Chapel Hill, NC: Algonquin Books, 2008).

13. D. P. Strachan, “Hay Fever, Hygiene, and Household Size,” BMJ 299, no. 6710 (1989): 1259.

14. L. Ruokolainen, L. Paalanen, A. Karkman, T. Laatikainen, L. Hertzen, T. Vlasoff, O. Markelova, et al., “Significant Disparities in Allergy Prevalence and Microbiota between the Young People in Finnish and Russian Karelia,” Clinical and Experimental Allergy 47, no. 5 (2017): 665–674.

15. L. von Hertzen, I. Hanski, and T. Haahtela, “Natural Immunity,” EMBO Reports 12, no. 11 (2011): 1089–1093.

16. This project would ultimately, despite being started amid favorable conditions, fall apart. Janzen was left to lead it with little in the way of funds and based on field work and taxonomy done by a handful of dedicated friends. See J. Kaiser, “Unique, All-Taxa Survey in Costa Rica ‘Self-Destructs,’” Science 276, no. 5314 (1997): 893. Needless to say, it isn’t done. It may well never be done.

17. The same effort in Raleigh, for instance, would be an incredibly onerous undertaking involving many hundreds, perhaps thousands, of multicellular species, to say nothing of the bacteria.

18. I. Hanski, L. von Hertzen, N. Fyhrquist, K. Koskinen, K. Torppa, T. Laatikainen, P. Karisola, et al., “Environmental Biodiversity, Human Microbiota, and Allergy Are Interrelated,” Proceedings of the National Academy of Sciences 109, no. 21 (2012): 8334–8339.

19. H. F. Retailliau, A. W. Hightower, R. E. Dixon, and J. R. Allen. “Acinetobacter calcoaceticus: A Nosocomial Pathogen with an Unusual Seasonal Pattern,” Journal of Infectious Diseases 139, no. 3 (1979): 371–375.

20. N. Fyhrquist, L. Ruokolainen, A. Suomalainen, S. Lehtimäki, V. Veckman, J. Vendelin, P. Karisola, et al., “Acinetobacter Species in the Skin Microbiota Protect against Allergic Sensitization and Inflammation,” Journal of Allergy and Clinical Immunology 134, no. 6 (2014): 1301–1309.

21. Fyhrquist et al., “Acinetobacter Species in the Skin Microbiota,” 1301–1309.

22. Ruokolainen et al., “Significant Disparities in Allergy Prevalence and Microbiota,” 665–674.

23. Fyhrquist et al., “Acinetobacter Species in the Skin Microbiota,” 1301–1309.

24. L. von Hertzen, “Plant Microbiota: Implications for Human Health,” British Journal of Nutrition 114, no. 9 (2015): 1531–1532.

25. We understand so little that the answer may yet be very complex. For example, Megan has also explored the prevalence of Gammaproteobacteria in traditional Himba houses in Namibia compared to houses in the United States. Hanski and colleagues predict that we should see more Gammaproteobacteria in the Himba houses, houses made of mud and dung, houses out in the bush, than in houses in the United States. Megan sees the reverse. If this stuff were easy, we would have already figured it out.

26. M. M. Stein, C. L. Hrusch, J. Gozdz, C. Igartua, V. Pivniouk, S. E. Murray, J. G. Ledford, et al., “Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children,” New England Journal of Medicine 375, no. 5 (2016): 411–421.

27. T. Haahtela, T. Laatikainen, H. Alenius, P. Auvinen, N. Fyhrquist, I. Hanski, L. Hertzen, et al., “Hunt for the Origin of Allergy—Comparing the Finnish and Russian Karelia,” Clinical and Experimental Allergy 45, no. 5 (2015): 891–901.

CHAPTER 5

1. J. Leja, “Rembrandt’s ‘Woman Bathing in a Stream,’” Simiolus: Netherlands Quarterly for the History of Art 24, no. 4 (1996): 321–327.

2. Although Noah and I had both forgotten, this would actually prove to be (a check through my email reveals) the second time we talked about doing a project on showerheads. The first time the project went nowhere. The email chain died. This email from Noah was then a bit of a resurrection of an earlier enthusiasm.

3. A more complete list of the invertebrates in Danish water includes seed shrimp, flatworms, Cyclops species, species of Tubifex, bristle worms, amphipods, and roundworms. See S. C. B. Christensen, “Asellus aquaticus and Other Invertebrates in Drinking Water Distribution Systems” (PhD diss., Technical University of Denmark, 2011). See also S. C. B. Christensen, E. Nissen, E. Arvin, and H. J. Albrechtsen, “Distribution of Asellus aquaticus and Microinvertebrates in a Non-chlorinated Drinking Water Supply System—Effects of Pipe Material and Sedimentation,” Water Research 45, no. 10 (2011): 3215–3224.

4. We know this thanks to work by Carlos Goller and North Carolina State University students. Carlos is now busy searching, one spigot to the next, for new varieties of these unusual bacteria. He has solicited the help of thousands of undergrads in this effort, thousands of undergrads whom he has asked to peer up into their faucets, searching for new life-forms. They have found not only Delftia acidovorans but also many other Delftia species, quite a few of which appear to be new to science.

5. Much as with the plaque on your teeth.

6. Biofilms allow microbes to hold fast, and they protect microbes from everyday dangers, such as those posed by humans. The concentration of antimicrobials required to kill bacteria in biofilms, for instance, is up to a thousand times greater than that required when they are free floating in the water, like plankton. See P. Araujo, M. Lemos, F. Mergulhão, L. Melo, and M. Simoes, “Antimicrobial Resistance to Disinfectants in Biofilms,” in Science against Microbial Pathogens: Communicating Current Research and Technological Advances, ed. A. Mendez-Vilas, 826–834 (Badajoz: Formatex, 2011).

7. L. G. Wilson, “Commentary: Medicine, Population, and Tuberculosis,” International Journal of Epidemiology 34, no. 3 (2004): 521–524.

8. K. I. Bos, K. M. Harkins, A. Herbig, M. Coscolla, N. Weber, I. Comas, S. A. Forrest, J. M. Bryant, S. R. Harris, V. J. Schuenemann, and T. J Campbell, “Pre-Columbian Mycobacterial Genomes Reveal Seals as a Source of New World Human Tuberculosis,” Nature 514, no. 7523 (2014): 494–497. Also see S. Rodriguez-Campos, N. H. Smith, M. B. Boniotti, and A. Aranaz, “Overview and Phylogeny of Mycobacterium tuberculosis Complex Organisms: Implications for Diagnostics and Legislation of Bovine Tuberculosis,” Research in Veterinary Science 97 (2014): S5–S19.

9. W. Hoefsloot, J. Van Ingen, C. Andrejak, K. Ängeby, R. Bauriaud, P. Bemer, N. Beylis, et al., “The Geographic Diversity of Nontuberculous Mycobacteria Isolated from Pulmonary Samples: An NTM-NET Collaborative Study,” European Respiratory Journal 42, no. 6 (2013): 1604–1613.

10. J. R. Honda, N. A. Hasan, R. M. Davidson, M. D. Williams, L. E. Epperson, P. R. Reynolds, and E. D. Chan, “Environmental Nontuberculous Mycobacteria in the Hawaiian Islands,” PLoS Neglected Tropical Diseases 10, no. 10 (2016): e0005068. See also an important early study on showerhead microbes: L. M. Feazel, L. K. Baumgartner, K. L. Peterson, D. N. Frank, J. K. Harris, and N. R. Pace, “Opportunistic Pathogens Enriched in Showerhead Biofilms,” Proceedings of the National Academy of Sciences 106, no. 38 (2009): 16393–16399.

11. By that I mean that I sent Lauren Nichols in my lab an email and asked her to do it. Lauren sent the email to Lea Shell. Lea and Lauren would eventually share the email with Julie Sheard (a graduate student in our group based in Denmark).

12. The tenth time being when he tried to enlist me to sample my own urethral microbiome. No thanks.

13. In general, in your water, the more conducive conditions are to growth, the fewer species seem to be present. Flowing cold water is the most diverse, followed by flowing warm water, followed by stagnant water, followed by the biofilms, which are the least diverse. See figure 4b in C. R. Proctor, M. Reimann, B. Vriens, and F. Hammes, “Biofilms in Shower Hoses,” Water Research 131 (2018): 274–286.

14. Modern universities are arranged into colleges (for example, my university has a College of Humanities and Social Sciences—CHASS—and a College of Agriculture and Life Sciences—CALS—as well as many others). Each college is run by a dean, just as each department is run by a head or a chair. But the dean does not act alone. She or he also has associate deans. The associate deans don’t act alone. They have assistant deans. In some places, not even the assistant deans act alone. Just as each flea has lesser fleas, so too does each dean have lesser deans, aka deanlets.

15. E. Ludes and J. R. Anderson, “‘Peat-Bathing’ by Captive White-Faced Capuchin Monkeys (Cebus capucinus),” Folia Primatologica 65, no. 1 (1995): 38–42.

16. P. Zhang, K. Watanabe, and T. Eishi, “Habitual Hot Spring Bathing by a Group of Japanese Macaques (Macaca fuscata) in Their Natural Habitat,” American Journal of Primatology 69, no. 12 (2007): 1425–1430.

17. Based on conversations with Hjalmar Kuehl at the Max Planck Institute in Leipzig. Kuehl and his colleagues have spent many hours watching chimpanzees.

18. Relative to hand washing and clean drinking water, bathing in a bath or in a shower has more to do with aesthetics and culture than it does with hygiene, to a point. When NASA was exploring the potential for extended space missions, they realized that the astronauts would need to spend long periods in the same piece of clothing. The astronauts were made to sit for days and then weeks, both in training and in real missions, without washing or changing their clothes. Their clothing deteriorated. Their skin developed boils. The sebum on their skin built into a dense layer and began to cake up. Which is to say, if you are washing your hands and keeping your bits clean, you don’t have to shower or bathe very often, but you should do it more often than astronauts do, or at least more often than those astronauts did. See the chapter “Houston, We Have a Fungus” in M. Roach, Packing for Mars: The Curious Science of Life in the Void (New York: W. W. Norton, 2011).

19. See, for example, W. A. Fairservis, “The Harappan Civilization: New Evidence and More Theory,” American Museum Novitates, no. 2055 (1961).

20. In what now seems like a very modern moment, the Roman emperor Commodus once staged a rigged battle between himself and an ostrich. The crowd was huge. The ostrich was tethered. Commodus was naked. Commodus proceeded to dispatch the ostrich and hold its head aloft to the senators sitting ringside, to great and thunderous applause, mostly. One of the senators, Dio, would go on to describe this moment as one of the most difficult in his life. It took incredible heroism for him to stifle his desire to giggle. He even took a laurel from the wreath he was wearing and put it in his mouth to keep from laughing aloud. See M. Beard, Laughter in Ancient Rome: On Joking, Tickling, and Cracking Up (Oakland: University of California Press, 2014).

21. G. G. Fagan, “Bathing for Health with Celsus and Pliny the Elder,” Classical Quarterly 56, no. 1 (2006): 190–207.

22. An excavation of a latrine at a Roman bath in Sagalassos in what was then Asia Minor and is now Turkey revealed eggs of roundworms (Ascaris spp.) as well as evidence of the protist Giardia duodenalis. F. S. Williams, T. Arnold-Foster, H. Y. Yeh, M. L. Ledger, J. Baeten, J. Poblome, and P. D. Mitchell, “Intestinal Parasites from the 2nd–5th Century AD Latrine in the Roman Baths at Sagalassos (Turkey),” International Journal of Paleopathology 19 (2017): 37–42.

23. In the early Renaissance, both in Italy and in northern Europe, paintings of nude men in water became popular. These scenes evoked earlier Roman and Greek depictions but were almost universally depictions of men swimming rather than men engaged in efforts to clean themselves. Among the exceptions is a print by Albrecht Dürer (1471–1528) in which Dürer depicts himself and three of his friends at a male bathhouse in Germany. Such bathhouses were used both for bathing oneself and for socializing, though perhaps as much the latter as the former as is suggested by the closing of bathhouses in Nuremberg just before Dürer’s print was made because of the perceived spread of syphilis therein. See S. S. Dickey, “Rembrandt’s ‘Little Swimmers’ in Context,” in Midwest Arcadia: Essays in Honor of Alison Kettering (2015), doi:10.18277/makf.2015.05.

24. One exception was that of the Vikings. The Vikings were ferocious raiders of other peoples whose military successes depended on their ferocity, their weapons, and their very fast boats. They were also farmers. These two characteristics seem to be well known (and well documented). What is less well known is that the Vikings were also very fashion conscious. They used lye soap to bleach their hair before sailing out to conquer an abbey (much as modern Danes, descendants of those Vikings, bleach theirs before getting on their bikes to ride through Copenhagen). They also used lye soap on the rest of their bodies and on their clothes. As a result, it is likely that the Vikings’ bodies and clothes had very different species than did those of their Dark Ages colleagues, including fewer body lice than, say, many an English queen.

25. F. Geels, “Co-evolution of Technology and Society: The Transition in Water Supply and Personal Hygiene in the Netherlands (1850–1930)—a Case Study in Multi-level Perspective,” Technology in Society 27, no. 3 (2005): 363–397.

26. Yes, bottled water contains bacteria too. Learn to love them. S. C. Edberg, P. Gallo, and C. Kontnick, “Analysis of the Virulence Characteristics of Bacteria Isolated from Bottled, Water Cooler, and Tap Water,” Microbial Ecology in Health and Disease 9, no. 2 (1996): 67–77. In some studies, bottled water has actually been found to contain a much higher density of bacteria than does tap water. J. A. Lalumandier and L. W. Ayers, “Fluoride and Bacterial Content of Bottled Water vs. Tap Water,” Archives of Family Medicine 9, no. 3 (2000): 246.

27. Ninety-four percent of all the liquid (non-ice) freshwater on Earth is groundwater. C. Griebler and M. Avramov, “Groundwater Ecosystem Services: A Review,” Freshwater Science 34, no. 1 (2014): 355–367.

28. The fates of viruses in a diverse aquifer are little better (some protists even break apart viruses and incorporate their amino acids into their cells).

29. For a great review of all the ways a pathogen can die in an aquifer, see J. Feichtmayer, L. Deng, and C. Griebler, “Antagonistic Microbial Interactions: Contributions and Potential Applications for Controlling Pathogens in the Aquatic Systems,” Frontiers in Microbiology 8 (2017).

30. In a growing number of places (and ever more in our ever drier future), the treatment facility processes waste water and turns it, via a variety of ecological and chemical processes, into tap water.

31. F. Rosario-Ortiz, J. Rose, V. Speight, U. Von Gunten, and J. Schnoor, “How Do You Like Your Tap Water?” Science 351, no. 6276 (2016): 912–914.

32. We have talked in the lab about doing a water tasting to see which of these factors matters most to how people enjoy what they drink (and even which microbes might imbue water with special flavors). We haven’t yet, but one could. Pause and savor the next water you drink. Think about whether it has a hint of being “aged in clay pipes” or even the “faint and fruity flavor of crustacean.”

33. L. M. Feazel, L. K. Baumgartner, K. L. Peterson, D. N. Frank, J. L. Harris, and N. R. Pace, “Opportunistic Pathogens Enriched in Showerhead Biofilms,” Proceedings of the National Academy of Sciences 106, no. 38 (2009): 16393–16399.

34. S. O. Reber, P. H. Siebler, N.C. Donner, J. T. Morton, D. G. Smith, J. M. Kopelman, K. R. Lowe, et al., “Immunization with a Heat-Killed Preparation of the Environmental Bacterium Mycobacterium vaccae Promotes Stress Resilience in Mice,” Proceedings of the National Academy of Sciences 113, no. 22 (2016): E3130–E3139.

CHAPTER 6

1. S. Nash, “The Plight of Systematists: Are They an Endangered Species?” October 16, 1989, https://www.the-scientist.com/?articles.view/articleNo/10690/title/The-Plight-Of-Systematists—Are-They-An-Endangered-Species-/. See also the more recent but similarly themed: L. W. Drew, “Are We Losing the Science of Taxonomy? As Need Grows, Numbers and Training Are Failing to Keep Up,” BioScience 61, no. 12 (2011): 942–946.

2. The analysis of these data was a herculean task requiring patience, coding, vision, and then a little more patience. It was a task carried out by Albert Barberán, now at the University of Arizona, Tucson. See A. Barberán, R. R. Dunn, B. J. Reich, K. Pacifici, E. B. Laber, H. L. Menninger, J. M. Morton, et al., “The Ecology of Microscopic Life in Household Dust,” Proceedings of the Royal Society B: Biological Sciences 282, no. 1814 (2015): 20151139. See also A. Barberán, J. Ladau, J. W. Leff, K. S. Pollard, H. L. Menninger, R. R. Dunn, and N. Fierer, “Continental-Scale Distributions of Dust-Associated Bacteria and Fungi,” Proceedings of the National Academy of Sciences 112, no. 18 (2015): 5756–5761. We would also ultimately be able to consider not just fungi but also mutualisms for which fungi are one of the key partners, including lichens. See E. A. Tripp, J. C. Lendemer, A. Barberán, R. R. Dunn, and N. Fierer, “Biodiversity Gradients in Obligate Symbiotic Organisms: Exploring the Diversity and Traits of Lichen Propagules across the United States,” Journal of Biogeography 43, no. 8 (2016): 1667–1678.

3. Because no one on our team is trained as a fungal systematist, we actually can’t name new species we find, even if we can grow them. Naming requires someone with Birgitte’s skills, and people with Birgitte’s skills tend to be very, very busy.

4. V. A. Robert and A. Casadevall, “Vertebrate Endothermy Restricts Most Fungi as Potential Pathogens,” Journal of Infectious Diseases 200, no. 10 (2009): 1623–1626.

5. Many of the fungal species whose DNA we found in homes were probably dead. They drifted in. They landed. They then died, unable to cope with the hostile conditions in our bedrooms and kitchens. These fungi can’t grow. They can’t produce new compounds, metabolites, that make us sick. They can’t produce more allergens. They are ghosts whose presence is detectable but of little consequence. Other species of fungi in homes are quiescent, hanging out as spores and waiting for the right conditions to grow, some perfect mélange of food and water or, in many cases, just the right amount of water.

6. N. S. Grantham, B. J. Reich, K. Pacifici, E. B. Laber, H. L. Menninger, J. B. Henley, A. Barberán, J. W. Leff, N. Fierer, and R. R. Dunn, “Fungi Identify the Geographic Origin of Dust Samples,” PLoS One 10, no. 4 (2015): e0122605.

7. Though even this seemingly simple statement comes with a caveat. In one Russian study, species of household fungi and human skin bacteria exposed on the exterior of the International Space Station (yes, the exterior!) survived for at least thirteen months. See V. M. Baranov, N. D. Novikova, N. A. Polikarpov, V. N. Sychev, M. A. Levinskikh, V. R. Alekseev, T. Okuda, M. Sugimoto, O. A. Gusev, and A. I. Grigor’ev, “The Biorisk Experiment: 13-Month Exposure of Resting Forms of Organism on the Outer Side of the Russian Segment of the International Space Station: Preliminary Results,” Doklady Biological Sciences 426, no. 1 (2009): 267–270. MAIK Nauka/Interperiodica.

8. For example, no cultures appear to have been done at the high temperatures necessary to grow thermophiles. Nor were any samples taken in such a way as to consider bacteria or fungi that are hard to culture for other reasons or even unculturable.

9. What was more, the fungi on Mir grew up to four times more rapidly than did their relatives on the ground. Why this might be remains a mystery. See N. D. Novikova, “Review of the Knowledge of Microbial Contamination of the Russian Manned Spacecraft,” Microbial Ecology 47, no. 2 (2004): 127–132. The fungi also seemed to have cycles of some sort, though just why this might be (far beyond the reach of Earth’s seasons) has not been explored. Novikova links these cycles to radiation levels experienced in the space station, but just why levels of radiation would affect the fungi in this way is unclear.

10. O. Makarov, “Combatting Fungi in Space,” Popular Mechanics, January 1, 2016, 42–46.

11. Novikova, “Review of the Knowledge of Microbial Contamination of the Russian Manned Spacecraft,” 127–132.

12. T. A. Alekhova, N. A. Zagustina, A. V. Aleksandrova, T. Y. Novozhilova, A. V. Borisov, and A. D. Plotnikov, “Monitoring of Initial Stages of the Biodamage of Construction Materials Used in Aerospace Equipment Using Electron Microscopy,” Journal of Surface Investigation: X-ray, Synchrotron and Neutron Techniques 1, no. 4 (2007): 411–416.

13. Also found on Mir was Botrytis, a pathogen of grapes; it may have hopped a ride, alive, in wine.

14. It is distinct from the other pink fungus in bathrooms, Serratia marcescens, which is more common in places that are always wet, such as toilet bowls. Serratia was also found on Mir. In both cases, the pink color of the fungi is due to compounds that protect them from UV rays, a kind of fungal sunscreen. Rhodotorula can also harvest nitrogen from the air, so is well suited to living in places that seem unlivable.

15 N. Novikova, P. De Boever, S. Poddubko, E. Deshevaya, N. Polikarpov, N. Rakova, I. Coninx, and M. Mergeay, “Survey of Environmental Biocontamination on Board the International Space Station,” Research in Microbiology 157, no. 1 (2016): 5–12.

16. These included three Candida taxa, Cryptococcus oeirensis, Penicillium concetricum, and brewer’s yeast (Saccharomyces cerevisiae). Also more common in houses with more people were Rhodotorula mucilaginosa and Cystofilobasidium capitatum, both of which are species that do well under stressful conditions such as those associated with bathrooms that are frequently cleaned.

17. Air conditioners were also associated with several other fungal species though, including the wood rot fungus Physisporinus vitreus, a pattern the mechanistic links of which deserve more study.

18. The more often you use your air-conditioning system, the more fungi build up in the AC unit. To avoid spreading these fungi through your house via the air conditioner, clean the filter with a vacuum or by hand washing with soap, which seems to help. Also, because AC units spread the most fungi in the first ten minutes after they are turned on, some scientists recommend opening your windows each time you turn your AC on. Or you can keep the AC off and open the windows, which has the added advantage of allowing a rich biodiversity of environmental bacteria to blow in. N. Hamada and T. Fujita, “Effect of Air-Conditioner on Fungal Contamination,” Atmospheric Environment 36, no. 35 (2002): 5443–5448.

19. I say “to my knowledge” because science projects often go up on the ISS and some of these might well contain cellulose and lignin. When he was a postdoc in my lab, Clint Penick worked with Eleanor Spicer Rice (my friend and neighbor) to collect pavement ants (Tetramorium sp.) that were later sent up to live on the ISS for a while. Those ants would have carried many North Carolinian fungi and bacteria with them, conceivably some able to break down cellulose and lignin.

20. In practice, there are multiple reasons it might have been rare in dust. It could be truly rare in homes. Or it could be rare for reasons having to do with the details of the science of sequencing. Neither of these phenomena would prove, however, to be the most interesting possibility.

21. She identified species of Chaetomium, Penicillium, Mucor, and Aspergillus.

22. Species of Mucor have been found not only in human homes but also in those of wasps, suggesting that the relationship of fungi to homes (including nests) may be far older than our species and date instead to the origin of wasp homes, tens of millions of years earlier. See A. A. Madden, A. M. Stchigel, J. Guarro, D. Sutton, and P. T. Starks, “Mucor nidicola sp. nov., a Fungal Species Isolated from an Invasive Paper Wasp Nest,” International Journal of Systematic and Evolutionary Microbiology 62, no. 7 (2012): 1710–1714. For a beautiful study of the evolution of the architecture of wasp nests, see R. L. Jeanne, “The Adaptiveness of Social Wasp Nest Architecture,” Quarterly Review of Biology 50, no. 3 (1975): 267–287.

23. Chaetomium was found growing on surfaces in Mir, but not in the air. Penicillium species were everywhere in Mir (in nearly 80 percent of samples). Mucor was in 1–2 percent of Mir samples. Aspergillus was in 40 percent of surface samples on Mir and 76.6 percent of air samples.

24. P. F. E. W. Hirsch, F. E. W. Eckhardt, and R. J. Palmer Jr., “Fungi Active in Weathering of Rock and Stone Monuments,” Canadian Journal of Botany 73, no. S1 (1995): 1384–1390.

25. Most termites cannot break down lignin but get around this problem by dragging with them, wherever they go, guts full of bacteria and protists that can do the job. In nature, the work of termites and their microbes is integral to the existence of forests and grasslands. Termites speed up decomposition in ways that make trees grow faster and grasses grow taller and more generally maintain healthy, functioning ecosystems. But when we build homes, we want to forestall these processes (and termites) for as long as we can, much as we try to do the same in keeping fruit or meat sound until we eat it.

26. Among them were Arthrinium phaeospermum, Aureobasidium pullulans, Cladosporium herbarum, species of Trichoderma, Alternaria tenuissima, species of Fusarium, species of Gliocladium, Rhodotorula mucilaginosa, and Trichosporon pullulans. Few of these fungi were present on the space station or on Mir, which is perhaps unsurprising given that not much on the space station is made of wood.

27. H. Kauserud, H. Knudsen, N. Högberg, and I. Skrede, “Evolutionary Origin, Worldwide Dispersal, and Population Genetics of the Dry Rot Fungus Serpula lacrymans,” Fungal Biology Reviews 26, nos. 2–3 (2012): 84–93.

28. Among them Penicillium, Chaetomium, and Ulocladium.

29. R. I. Adams, M. Miletto, J. W. Taylor, and T. D. Bruns, “Dispersal in Microbes: Fungi in Indoor Air Are Dominated by Outdoor Air and Show Dispersal Limitation at Short Distances,” ISME Journal 7, no. 7 (2013): 1262–1273.

30. D. L. Price and D. G. Ahearn, “Sanitation of Wallboard Colonized with Stachybotrys chartarum,” Current Microbiology 39, no. 1 (1999): 21–26.

31. They have also seen stories like that of Tyrone Hayes. Tyrone studies the effects of an herbicide on animals. He found that the herbicide harms animals. The result, as Rachel Aviv describes in the New Yorker, is that “its maker pursued him,” and not in a good way (see “A Valuable Reputation,” February 10, 2014, www.newyorker.com/magazine/2014/02/10/a-valuable-reputation).

32. Birgitte is fascinated by Chaetomium species. They have, as she told me in an email, always surrounded her. For example, she sent me a photo of her elementary school class from when she was a little girl. The photo was labeled with an arrow. The arrow pointed not to Birgitte but instead to the fungus Chaetomium elatum, growing on the paper on which the photo was mounted.

33. Interestingly, none of these species was found on the International Space Station or even on the much more fungal Mir.

34. M. Nikulin, K. Reijula, B. B. Jarvis, and E.-L. Hintikka, “Experimental Lung Mycotoxicosis in Mice Induced by Stachybotrys atra,” International Journal of Experimental Pathology 77, no. 5 (1996): 213–218.

35. I. Došen, B. Andersen, C. B. W. Phippen, G. Clausen, and K. F. Nielsen, “Stachybotrys Mycotoxins: From Culture Extracts to Dust Samples,” Analytical and Bioanalytical Chemistry 408, no. 20 (2016): 5513–5526.

36. Alternaria alternate, Aspergillus fumigatus, and Cladosporium herbarum are all among the species present in Birgitte’s study, present, too, on the space station. These fungi are all commonly associated with allergies.

37. A. Nevalainen, M. Täubel, and A. Hyvärinen, “Indoor Fungi: Companions and Contaminants,” Indoor Air 25, no. 2 (2015): 125–156.

38. C. M. Kercsmar, D. G. Dearborn, M. Schluchter, L. Xue, H. L. Kirchner, J. Sobolewski, S. J. Greenberg, S. J. Vesper, and T. Allan, “Reduction in Asthma Morbidity in Children as a Result of Home Remediation Aimed at Moisture Sources,” Environmental Health Perspectives 114, no. 10 (2006): 1574.

CHAPTER 7

1. Though probably mostly in defense. Most recent studies argue that cave bears were largely herbivorous. But, from the perspective of a small human, a big, pissed-off herbivorous bear trapped in a cave is, first and foremost, just a big, pissed-off bear.

2. It would be a great story if the camel crickets were named for Francois Camel, who led the boys to the cave. I’m happy to pretend this is true if you are. The truth, though, is that camel crickets are called camel crickets because their backs are arched, like a camel’s hump.

3. Camel crickets are no longer found in the French Pyrenees, which raises another question: Where did the early human who depicted this camel cricket see the camel cricket? One option is that the camel crickets used to live in the French Pyrenees, but no longer do. This is possible, but unlikely. Caves in France at the time would have been much colder than they are today, and the modern distribution of Troglophilus camel crickets does not include France. The crickets occur only much farther south. Another possibility is that the artist saw the camel cricket in a more southerly cave and was depicting it from memory. Or maybe the artist actually made the art elsewhere and carried it with him or her.

4. S. Hubbell, Broadsides from the Other Orders (New York: Random House, 1994).

5. The cascade of resources from cricket food to cricket predators can be complex and bizarre. See, for example, the special case of hairworms, which can take control of the body and will of a camel cricket. T. Sato, M. Arizono, R. Sone, and Y. Harada, “Parasite-Mediated Allochthonous Input: Do Hairworms Enhance Subsidized Predation of Stream Salmonids on Crickets?” Canadian Journal of Zoology 86, no. 3 (2008): 231–235. See also: Y. Saito, I. Inoue, F. Hayashi, and H. Itagaki, “A Hairworm, Gordius sp., Vomited by a Domestic Cat,” Nihon Juigaku Zasshi: The Japanese Journal of Veterinary Science 49, no. 6 (1987): 1035–1037.

6. She is also, as one of her reference letters pointed out, a very talented fiddle player. You can hear her playing here: https://youtu.be/aVXG5koU9G4.

7. The parade-like scene of the team entering houses was not without precedent. Linnaeus, the father of modern taxonomy who named many of the more common arthropod species found in houses, actually did have a band that paraded before him when he went on excursions. The drum that was played as they walked together has been preserved. See B. Jonsell, “Daniel Solander—the Perfect Linnaean; His Years in Sweden and Relations with Linnaeus,” Archives of Natural History 11, no. 3 (1984): 443–450.

8. Entomologists spend a lot of time looking at the genitalia of insects. This reality, combined with the unique ways in which entomologists show their love and appreciation, can lead to unusual circumstances. For example, my friend Dan Simberloff recently had a new species of louse from a swiftlet named in his honor. One cannot but be flattered by something like this, and yet one should also note that the characteristics that make this new louse species, Dennyus simberloffi, unique and distinguishable from its closest relatives are its unusually small genitalia and very wide head and anus. See D. Clayton, R. Price, and R. Page, “Revision of Dennyus (Collodennyus) Lice (Phthiraptera: Menoponidae) from Swiftlets, with Descriptions of New Taxa and a Comparison of Host–Parasite Relationships,” Systematic Entomology 21, no. 3 (1996): 179–204.

9. If there is an afterlife for entomologists, it involves being kept in a jar for a while until some overworked God decides whether or not they are in good enough condition to be pinned.

10. A. A. Madden, A. Barberán, M. A. Bertone, H. L. Menninger, R. R. Dunn, and N. Fierer, “The Diversity of Arthropods in Homes across the United States as Determined by Environmental DNA Analyses,” Molecular Ecology 25, no. 24 (2016): 6214–6224.

11. This relationship between wasp and aphid was first observed by Leeuwenhoek on an aphid just outside his house in Delft. See F. N. Egerton, “A History of the Ecological Sciences, Part 19: Leeuwenhoek’s Microscopic Natural History,” Bulletin of the Ecological Society of America 87 (2006): 47–58.

12. See, for example, E. Panagiotakopulu, “New Records for Ancient Pests: Archaeoentomology in Egypt,” Journal of Archaeological Science 28, no. 11 (2001): 1235–1246; E. Panagiotakopulu, “Hitchhiking across the North Atlantic—Insect Immigrants, Origins, Introductions and Extinctions,” Quaternary International 341 (2014): 59–68; E. Panagiotakopulu, P. C. Buckland, and B. J. Kemp, “Underneath Ranefer’s Floors—Urban Environments on the Desert Edge,” Journal of Archaeological Science 37, no. 3 (2010): 474–481; E. Panagiotakopulu and P. C. Buckland, “Early Invaders: Farmers, the Granary Weevil and Other Uninvited Guests in the Neolithic,” Biological Invasions 20, no. 1 (2018): 219–233.

13. A. Bain, “A Seventeenth-Century Beetle Fauna from Colonial Boston,” Historical Archaeology 32, no. 3 (1998): 38–48.

14. E. Panagiotakopulu, “Pharaonic Egypt and the Origins of Plague,” Journal of Biogeography 31, no. 2 (2004): 269–275.

15. For more on this story, see J. B. Johnson and K. S. Hagen, “A Neuropterous Larva Uses an Allomone to Attack Termites,” Nature 289 (5797): 506.

16. E. A. Hartop, B. V. Brown, R. Henry, and L. Disney, “Opportunity in Our Ignorance: Urban Biodiversity Study Reveals 30 New Species and One New Nearctic Record for Megaselia (Diptera: Phoridae) in Los Angeles (California, USA),” Zootaxa 3941, no. 4 (2015): 451–484.

17. E. A. Hartop, B. V. Brown, R. Henry, and L. Disney, “Flies from LA, the Sequel: A Further Twelve New Species of Megaselia (Diptera: Phoridae) from the BioSCAN Project in Los Angeles (California, USA),” Biodiversity Data Journal 4 (2016).

18. J. A. Feinberg, C. E. Newman, G. J. Watkins-Colwell, M. D. Schlesinger, B. Zarate, B. R. Curry, H. B. Shaffer, and J. Burger, “Cryptic Diversity in Metropolis: Confirmation of a New Leopard Frog Species (Anura: Ranidae) from New York City and Surrounding Atlantic Coast Regions,” PLoS One 9, no. 10 (2014): e108213; J. Gibbs, “Revision of the Metallic Lasioglossum (Dialictus) of Eastern North America (Hymenoptera: Halictidae: Halictini),” Zootaxa 3073 (2011): 1–216; D. Foddai, L. Bonato, L. A. Pereira, and A. Minelli, “Phylogeny and Systematics of the Arrupinae (Chilopoda Geophilomorpha Mecistocephalidae) with the Description of a New Dwarfed Species,” Journal of Natural History 37 (2003): 1247–1267, https://doi.org/10.1080/00222930210121672.

19. Y. Ang, G. Rajaratnam, K. F. Y. Su, and R. Meier, “Hidden in the Urban Parks of New York City: Themira lohmanus, a New Species of Sepsidae Described Based on Morphology, DNA Sequences, Mating Behavior, and Reproductive Isolation (Sepsidae, Diptera),” ZooKeys 698 (2017): 95.

20. In the book H. W. Greene, Tracks and Shadows: Field Biology as Art (Berkeley: University of California Press, 2013).

21. See I. Kant, Critique of Judgment. 1790, trans. W. S. Pluhar (Indianapolis: Hackett 212, 1987).

CHAPTER 8

1. Another characteristic of cave organisms is their ability to go long periods without food. One ethnographer found silverfish (a species of Lepisma, which we also found to be common in Raleigh) to be abundant in Zulu houses. Out of interest, he trapped one of these silverfish in a wine glass, and it lived for at least three months with nothing for nutrition but the dust beneath the glass. See L. Grout, Zulu-Land; or, Life among the Zulu-Kafirs of Natal and Zulu-Land, South Africa (London: Trübner & Co., 1860).

2. See A. J. De Jesús, A. R. Olsen, J. R. Bryce, and R. C. Whiting, “Quantitative Contamination and Transfer of Escherichia coli from Foods by Houseflies, Musca domestica L. (Diptera: Muscidae),” International Journal of Food Microbiology 93, no. 2 (2004): 259–262. See also N. Rahuma, K. S. Ghenghesh, R. Ben Aissa, and A. Elamaari, “Carriage by the Housefly (Musca domestica) of Multiple-Antibiotic-Resistant Bacteria That Are Potentially Pathogenic to Humans, in Hospital and Other Urban Environments in Misurata, Libya,” Annals of Tropical Medicine and Parasitology 99, no. 8 (2005): 795–802.

3. Evolutionary biologists call these “primary endosymbioses” to distinguish them from secondary endosymbioses in which the bacteria (the symbionts) are picked up later.

4. J. J. Wernegreen, S. N. Kauppinen, S. G. Brady, and P. S. Ward, “One Nutritional Symbiosis Begat Another: Phylogenetic Evidence That the Ant Tribe Camponotini Acquired Blochmannia by Tending Sap-Feeding Insects,” BMC Evolutionary Biology 9, no. 1 (2009): 292; R. Pais, C. Lohs, Y. Wu, J. Wang, and S. Aksoy, “The Obligate Mutualist Wigglesworthia glossinidia Influences Reproduction, Digestion, and Immunity Processes of Its Host, the Tsetse Fly,” Applied and Environmental Microbiology 74, no. 19 (2008): 5965–5974. Also see G. A. Carvalho, A. S. Corrêa, L. O. de Oliveira, and R. N. C. Guedes, “Evidence of Horizontal Transmission of Primary and Secondary Endosymbionts between Maize and Rice Weevils (Sitophilus zeamais and Sitophilus oryzae) and the Parasitoid Theocolax elegans,” Journal of Stored Products Research 59 (2014): 61–65. Also see A. Heddi, H. Charles, C. Khatchadourian, G. Bonnot, and P. Nardon, “Molecular Characterization of the Principal Symbiotic Bacteria of the Weevil Sitophilus oryzae: A Peculiar G+ C Content of an Endocytobiotic DNA,” Journal of Molecular Evolution 47, no. 1 (1998): 52–61.

5. C. M. Theriot and A. M. Grunden, “Hydrolysis of Organophosphorus Compounds by Microbial Enzymes,” Applied Microbiology and Biotechnology 89, no. 1 (2011): 35–43.

6. The species was Paenibacillus glucanolyticus SLM1. Stephanie and Amy isolated this species from old and abandoned black liquor storage tanks kept in the demonstration paper-pulping facility at North Carolina State University. Yes, the university has a demonstration paper-pulping facility.

7. And a strong belief in the ability of nature, particularly bacterial nature, to solve problems.

8. And one could also check the many non-arthropod invertebrates, such as microscopic nematodes. It is said that the microscopic worms, the nematodes, in homes are so dense that if you removed the structure of a home and could make the worms visible, you would see the home still, framed in the outline of serpentine bodies. This could be the case. Yet, we were able to find no studies of nematodes in homes, nor the tardigrades, nor many other major groups of organisms. These creatures are there, but have not yet been tallied, much less had their potential uses considered.

9. F. Sabbadin, G. R. Hemsworth, L. Ciano, B. Henrissat, P. Dupree, T. Tryfona, R. D. S. Marques, et al., “An Ancient Family of Lytic Polysaccharide Monooxygenases with Roles in Arthropod Development and Biomass Digestion,” Nature Communications 9, no. 1 (2018): 756.

10. T. D. Morgan, P. Baker, K. J. Kramer, H. H. Basibuyuk, and D. L. J. Quicke, “Metals in Mandibles of Stored Product Insects: Do Zinc and Manganese Enhance the Ability of Larvae to Infest Seeds?” Journal of Stored Products Research 39, no. 1 (2003): 65–75.

11. Coby Schal and Ayako Wada-Katsumata at North Carolina State University have also teamed up to study the subset of these brushes insects use to clean their antennae. They discovered that when insects such as carpenter ants (Camponotus pennsylvanicus), house flies, and German cockroaches clean their antennae, they are better able to smell. With dirty antennae, the world is dulled. See K. Böröczky, A. Wada-Katsumata, D. Batchelor, M. Zhukovskaya, and C. Schal, “Insects Groom Their Antennae to Enhance Olfactory Acuity,” Proceedings of the National Academy of Sciences 110, no. 9 (2013): 3615–3620.

12. E. L. Zvereva, “Peculiarities of Competitive Interaction between Larvae of the House Fly Musca domestica and Microscopic Fungi,” Zoologicheskii Zhurnal 65 (1986): 1517–1525. See also K. Lam, K. Thu, M. Tsang, M. Moore, and G. Gries, “Bacteria on Housefly Eggs, Musca domestica, Suppress Fungal Growth in Chicken Manure through Nutrient Depletion or Antifungal Metabolites,” Naturwissenschaften 96 (2009): 1127–1132.

13. D. A. Veal, Jane E. Trimble, and A. J. Beattie, “Antimicrobial Properties of Secretions from the Metapleural Glands of Myrmecia gulosa (the Australian Bull Ant),” Journal of Applied Microbiology 72, no. 3 (1992): 188–194.

14. C. A. Penick, O. Halawani, B. Pearson, S. Mathews, M. M. López-Uribe, R. R. Dunn, and A. A. Smith, “External Immunity in Ant Societies: Sociality and Colony Size Do Not Predict Investment in Antimicrobials,” Royal Society Open Science 5, no. 2 (2018): 171332.

15. I. Stefanini, L. Dapporto, J.-L. Legras, A. Calabretta, M. Di Paola, C. De Filippo, R. Viola, et al. “Role of Social Wasps in Saccharomyces cerevisiae Ecology and Evolution,” Proceedings of the National Academy of Sciences 109, no. 33 (2012): 13398–13403.

16. This work was made possible thanks to Anne Madden’s ability to know, find, listen to, and sniff out new and interesting yeasts and John Sheppard’s ability to brew beer. For more on this project, see www.pbs.org/newshour/bb/wing-wasp-scientists-discover-new-beer-making-yeast/.

17. A. Madden, MJ Epps, T. Fukami, R. E. Irwin, J. Sheppard, D. M. Sorger, and R. R. Dunn, “The Ecology of Insect–Yeast Relationships and Its Relevance to Human Industry,” Proceedings of the Royal Society B 285, no. 1875 (2018): 20172733.

18. E. Panagiotakopulu, “Dipterous Remains and Archaeological Interpretation,” Journal of Archaeological Science 31, no. 12 (2004): 1675–1684.

19. E. Panagiotakopulu, P. C. Buckland, P. M. Day, and C. Doumas, “Natural Insecticides and Insect Repellents in Antiquity: A Review of the Evidence,” Journal of Archaeological Science 22, no. 5 (1995): 705–710.

CHAPTER 9

1. R. E. Heal, R. E. Nash, and M. Williams, “An Insecticide-Resistant Strain of the German Cockroach from Corpus Christi, Texas,” Journal of Economic Entomology 46, no. 2 (1953).

2. As with fipronil, the active compound in some cockroach baits and also in some flea sprays/powders/pills. See G. L. Holbrook, J. Roebuck, C. B. Moore, M. G. Waldvogel, and C. Schal, “Origin and Extent of Resistance to Fipronil in the German Cockroach, Blattella germanica (L.) (Dictyoptera: Blattellidae),” Journal of Economic Entomology 96, no. 5 (2003): 1548–1558.

3. These pesticides were so potent that they posed risks to birds and children alike (particularly in the concentrations at which they were being used); they were the pesticides about which Rachel Carson wrote in her documentary Silent Spring. Yet they were not potent enough to kill all of the German cockroaches.

4. Yes, Pleasanton is the name of the place where one goes to study cockroaches and other pest species. In Pleasanton, Jules had already spent three years studying another pest, the cat flea (Ctenocephalides felis). Cat fleas were already present in human homes in ancient Amarna, Egypt. Jules discovered that cat flea larvae subsist on the bloody feces of their parents, supplemented, it seems, by microbes from the environment, microbes that add nutrition to the feces. See J. Silverman and A. G. Appel, “Adult Cat Flea (Siphonaptera: Pulicidae) Excretion of Host Blood Proteins in Relation to Larval Nutrition,” Journal of Medical Entomology 31, no. 2 (1993): 265–271.

5. Most of these common names for the cockroaches now bear little relation to what we have learned about their histories. The American cockroach, for instance, appears to be native to Africa. The Oriental cockroach also appears to have been African and may have traveled with the Phoenicians, then the Greeks, then nearly everyone else. See R. Schweid, The Cockroach Papers: A Compendium of History and Lore (Chicago: University of Chicago Press, 2015). For a classic, see J. A. G. Rehn, “Man’s Uninvited Fellow Traveler—the Cockroach,” Scientific Monthly 61 no. 145 (1945): 265–276.

6. These species are incredibly varied in their lifeways. Many species of wild cockroaches are diurnal, active during the day. They often feed on leaf litter in the forest. Quite a few live in the nests of ants and termites as guests. Some even produce a kind of mother’s milk on which their babies feed. Others pollinate flowers. What is more, recent studies have confirmed that termites are actually all a special branch of the cockroach evolutionary tree in which sociality evolved. Termites are social cockroaches. See R. R. Dunn, “Respect the Cockroach,” BBC Wildlife 27, no. 4 (2009): 60.

7. From the Greek Parthenos for “virgin” and genesis for “creation.”

8. The Surinam cockroach (Pycnoscelus surinamensis) has taken this to an extreme. No males of this species have ever been found in the wild. In lab colonies, males are sometimes born but are so dysfunctional they quickly die.

9. Of course there are some bad things German cockroaches do that we don’t. German cockroaches have been reported to eat nearly anything and everything that contains starch, including cereals, stamps, drapes, book bindings, and paste.

10. German cockroaches, unlike many other cockroach species, do not do well when alone. They suffer from what is called isolation syndrome, which to me sounds a lot like some mix of loneliness and modest existential despair. When left alone, their metamorphosis is delayed, as is their sexual maturation. Also, they start to behave unusually, as if they don’t know quite how to be a cockroach anymore. They are no longer interested in normal cockroach activities or even cockroach sex. There is a big literature on the loneliness of German cockroaches, but for a start, read M. Lihoreau, L. Brepson, and C. Rivault, “The Weight of the Clan: Even in Insects, Social Isolation Can Induce a Behavioural Syndrome,” Behavioural Processes 82, no. 1 (2009): 81–84.

11. Half of the fifty or so species of Blattella live in Asia.

12. It may have happened with the earliest agriculture in tropical Asia. But it may also have been much later.

13. The oldest specimen of the German cockroach is actually from Denmark, so we can blame the Danes, but my suspicion is that the German cockroach actually arrived in Europe much, much earlier. See T. Qian, “Origin and Spread of the German Cockroach, Blattella germanica” (PhD diss., National University of Singapore, 2016).

14. Though the cockroach gets a little comeuppance. When the name of the German cockroach is written out in full, it is actually Blattella germanica Linnaeus. Linnaeus is placed after the species name to indicate that Linnaeus was the one who bestowed the name. This convention, along with the convention of giving each species a genus name (Blattella) and a species name (germanica), was invented by Linnaeus. As a result, wherever the German cockroach goes, forever, Linnaeus will drag behind it, as is the case with bed bugs, house flies, black rats (Cimex lectularis Linnaeus, Musca domestica Linnaeus, and Rattus rattus Linnaeus, respectively), and many other indoor species.

15. P. J. A. Pugh, “Non‐indigenous Acari of Antarctica and the Sub‐Antarctic Islands,” Zoological Journal of the Linnaean Society 110, no. 3 (1994): 207–217.

16. Which of the other species of cockroach are found indoors depends greatly on the climate outside and on geography. Some cockroach species do better in tropical environments, others where it is cold.

17. L. Roth and E. Willis, The Biotic Association of Cockroaches, Smithsonian Miscellaneous Collections, vol. 141 (Washington, DC: Smithsonian Institution, 1960).

18. Qian, “Origin and Spread of the German Cockroach.”

19. J. Silverman and D. N. Bieman, “Glucose Aversion in the German Cockroach, Blattella germanica,” Journal of Insect Physiology 39, no. 11 (1993): 925–933.

20. These rates of reproduction tend to outpace the rate at which new cockroaches move among buildings, so much so that German cockroaches of one lineage might occupy one apartment building and those of another might occupy the next.

21. J. Silverman and R. H. Ross, “Behavioral Resistance of Field-Collected German Cockroaches (Blattodea: Blattellidae) to Baits Containing Glucose,” Environmental Entomology 23, no. 2 (1994): 425–430.

22. For example, see J. Silverman and D. N. Bieman, “High Fructose Insecticide Bait Compositions,” US Patent No. 5,547,955 (1996).

23. See S. B. Menke, W. Booth, R. R. Dunn, C. Schal, E. L. Vargo, and J. Silverman, “Is It Easy to Be Urban? Convergent Success in Urban Habitats among Lineages of a Widespread Native Ant,” PLoS One 5, no. 2 (2010): e9194.

24. See S. Lengyel, A. D. Gove, A. M. Latimer, J. D. Majer, and R. R. Dunn, “Ants Sow the Seeds of Global Diversification in Flowering Plants,” PLoS One 4, no. 5 (2009): e5480. Also see S. Lengyel, A. D. Gove, A. M. Latimer, J. D. Majer, and R. R. Dunn, “Convergent Evolution of Seed Dispersal by Ants, and Phylogeny and Biogeography in Flowering Plants: A Global Survey,” Perspectives in Plant Ecology, Evolution and Systematics 12, no. 1 (2010): 43–55. Also, for a quirky elaboration on this theme involving stick insects, see L. Hughes and M. Westoby, “Capitula on Stick Insect Eggs and Elaiosomes on Seeds: Convergent Adaptations for Burial by Ants,” Functional Ecology 6, no. 6 (1992): 642–648.

25. In Faust: A Tragedy, Johann Wolfgang von Goethe has a demon introduce himself as “The lord of rats and the eke of mice, Of flies and bed-bugs, frogs and lice.” Except for the frogs, this seems an apt title for the actions of natural selection in our modern homes. See J. W. Goethe, Faust: A Tragedy, trans. B. Taylor (Boston: Houghton Mifflin, 1898), 1:86.

26. V. Markó, B. Keresztes, M. T. Fountain, and J. V. Cross, “Prey Availability, Pesticides and the Abundance of Orchard Spider Communities,” Biological Control 48, no. 2 (2009): 115–124. Also see L. W. Pisa, V. Amaral-Rogers, L. P. Belzunces, J. M. Bonmatin, C. A. Downs, D. Goulson, D. P. Kreutzweiser, et al., “Effects of Neonicotinoids and Fipronil on Non-target Invertebrates,” Environmental Science and Pollution Research 22, no. 1 (2015): 68–102.

27. We aren’t the first species to imagine using predators in our homes to control pests. Many species that build nests benefit from other species that live in those nests. Some owls bring snakes to their nests to control the insects that eat their nestlings. Similarly, packrat nests often include pseudoscorpions that feed upon the mites that plague the packrats. See F. R. Gehlbach and R. S. Baldridge, “Live Blind Snakes (Leptotyphlops dulcis) in Eastern Screech Owl (Otus asio) Nests: A Novel Commensalism,” Oecologia 71, no. 4 (1987): 560–563. Also see O. F. Francke and G. A. Villegas-Guzmán, “Symbiotic Relationships between Pseudoscorpions (Arachnida) and Packrats (Rodentia),” Journal of Arachnology 34, no. 2 (2006): 289–298.

28. O. F. Raum, The Social Functions of Avoidances and Taboos among the Zulu, vol. 6 (Berlin: Walter de Gruyter, 1973). The practice was then copied by the Voortrekkers, Boer pastoralists who arrived in the Cape Town region of South Africa with the Dutch East India Company and then migrated north and east in “great treks” in response to grievances with the British colonial government.

29. J. J. Steyn, “Use of Social Spiders against Gastro-intestinal Infections Spread by House Flies,” South African Medical Journal 33 (1959).

30. J. Wesley Burgess, “Social spiders.” Scientific American 234, no. 3 (1976): 100–107. This very cool spider appears to use dead flies in its web as a surface and food to farm yeasts, which then, in turn, attract live flies. No one has yet identified or even studied the yeast. W. J. Tietjen, L. R. Ayyagari, and G. W. Uetz, “Symbiosis between Social Spiders and Yeast: The Role in Prey Attraction,” Psyche 94, nos. 1–2 (1987): 151–158.

31. Social spiders are confined in their distribution (French introduction attempts notwithstanding) and are not for everyone. Not to worry, there are other options. Jumping spiders in houses in Thailand eat up to 120 Aedes mosquitoes, vectors of deadly dengue fever, a day. See R. Weterings, C. Umponstira, and H. L. Buckley, “Predation on Mosquitoes by Common Southeast Asian House-Dwelling Jumping Spiders (Salticidae),” Arachnology 16, no. 4 (2014): 122–127. In Kenya, another spider that lives in houses preferentially feeds on the Anopheles mosquitoes that transmit malaria, particularly those that have already fed (and hence stand a higher chance of transmitting malaria). See R. R. Jackson and F. R. Cross, “Mosquito-Terminator Spiders and the Meaning of Predatory Specialization,” Journal of Arachnology 43, no. 2 (2015): 123–142. Also, see X. J. Nelson, R. R. Jackson, and G. Sune, “Use of Anopheles-Specific Prey-Capture Behavior by the Small Juveniles of Evarcha culicivora, a Mosquito-Eating Jumping Spider,” Journal of Arachnology 33, no. 2 (2005): 541–548. Also, see X. J. Nelson and R. R. Jackson, “A Predator from East Africa That Chooses Malaria Vectors as Preferred Prey,” PLoS One 1, no. 1 (2006): e132.

32. G. L. Piper, G. W. Frankie, and J. Loehr, “Incidence of Cockroach Egg Parasites in Urban Environments in Texas and Louisiana,” Environmental Entomology 7, no. 2 (1978): 289–293.

33. A. M. Barbarin, N. E. Jenkins, E. G. Rajotte, and M. B. Thomas, “A Preliminary Evaluation of the Potential of Beauveria bassiana for Bed Bug Control,” Journal of Invertebrate Pathology 111, no. 1 (2012): 82–85. And other labs are trying other fungi, be it on the common bed bug or its tropical relative, Cimex hemipterus. For example, see Z. Zahran, N. M. I. M. Nor, H. Dieng, T. Satho, and A. H. A. Majid, “Laboratory Efficacy of Mycoparasitic Fungi (Aspergillus tubingensis and Trichoderma harzianum) against Tropical Bed Bugs (Cimex hemipterus) (Hemiptera: Cimicidae),” Asian Pacific Journal of Tropical Biomedicine 7, no. 4 (2017): 288–293. Meanwhile, in Denmark, a parasitoid that attacks the pupae of house flies is being bred and released experimentally in stables in which dairy cattle are kept. This is being done in an attempt to control house flies as well as stable flies and to prevent their spillover into nearby homes. See H. Skovgård and G. Nachman, “Biological Control of House Flies Musca domestica and Stable Flies Stomoxys calcitrans (Diptera: Muscidae) by Means of Inundative Releases of Spalangia cameroni (Hymenoptera: Pteromalidae),” Bulletin of Entomological Research 94, no. 6 (2004): 555–567.

34. D. R. Nelsen, W. Kelln, and W. K. Hayes, “Poke but Don’t Pinch: Risk Assessment and Venom Metering in the Western Black Widow Spider, Latrodectus Hesperus,” Animal Behaviour 89 (2014): 107–114.

35. As for just how unlikely spiders are to bite, a recent case is illustrative. In Lenexa, Kansas, 2,055 brown recluse spiders (Loxosceles reclusa) were removed from an old house over a six-month period. No bites occurred in this or other houses with large populations of brown recluses. Thousands of spiders, but no bites. Meanwhile, most of the brown recluse bites reported in the United States occur in regions where the spider does not occur (which is to say these were not brown recluse bites and were very unlikely to even be spider bites). See R. S. Vetter and D. K. Barger, “An Infestation of 2,055 Brown Recluse Spiders (Araneae: Sicariidae) and No Envenomations in a Kansas Home: Implications for Bite Diagnoses in Nonendemic Areas,” Journal of Medical Entomology 39, no. 6 (2002): 948–951.

36. M. H. Lizée, B. Barascud, J.-P. Cornec, and L. Sreng, “Courtship and Mating Behavior of the Cockroach Oxyhaloa deusta [Thunberg, 1784] (Blaberidae, Oxyhaloinae): Attraction Bioassays and Morphology of the Pheromone Sources,” Journal of Insect Behavior 30, no. 5 (2017): 1–21.

37. Coby has identified this odor. He hasn’t yet figured out, though, how to make large quantities of it. When he does, stay clear of Coby, because if he spills any of the stuff on him, he will be like the Pied Piper of German cockroaches.

38. A. Wada-Katsumata, J. Silverman, and C. Schal, “Changes in Taste Neurons Support the Emergence of an Adaptive Behavior in Cockroaches,” Science 340 (2013): 972–975.

39. None of the disasters humanity has imagined—not nuclear war, not even the most extreme climate change—will end life. As Sean Nee has noted, all of the horrible things we have done to the planet, changes that disfavor many species, including those on which we depend, nonetheless favor a subset of unusual microbes. What deforestation, climate change, nuclear disaster, and the like tip us toward is a world in which the microbes, once again, more fully assert themselves, a world like that in the very beginning, a world of bountiful slime. See S. Nee, “Extinction, Slime, and Bottoms,” PLoS Biology 2, no. 8 (2004): e272.

CHAPTER 10

1. Here is part of Jim’s thesis, if you are curious: J. A. Danoff-Burg, “Evolving under Myrmecophily: A Cladistic Revision of the Symphilic Beetle Tribe Sceptobiini (Coleoptera: Staphylinidae: Aleocharinae),” Systematic Entomology 19, no. 1 (1994): 25–45.

2. The units evolutionary biologists use to consider the benefits of one species to another species and, in doing so, to decide whether a relationship is parasitic or mutualistic are always units of Darwinian fitness. One species benefits another if it makes the second species more likely to survive and have more offspring that survive. Maybe this amoral economics of natural selection is no longer what we should use to consider which species benefit us and which fail to do so. Perhaps a species that makes us happy and “well,” whatever “well” means, but that does not benefit our fitness is, in the modern world, still a mutualist.

3. J. McNicholas, A. Gilbey, A. Rennie, S. Ahmedzai, J.-A. Dono, and E. Ormerod, “Pet Ownership and Human Health: A Brief Review of Evidence and Issues,” BMJ 331, no. 7527 (2005): 1252–1254.

4. The parasite was first discovered in Tunis, Tunisia, by researchers from the Pasteur Institute. They found the parasite in a rodent called the common gundi (Ctenodactylus gundi). The gundis were being studied because they harbored Leishmania parasites. It was the Leishmania parasites that researchers were searching for when Toxoplasma gondii was found. Gundi appears to be the North African Arabic word for these rodents. The name Toxoplasma is from Greek, where toxo means “bow” and plasma means “shaped,” in reference to the bow shape of the parasite. The name Toxoplasma gondii, then, full of history, means something like bow-shaped parasite from the common gundi.

5. J. Hay, P. P. Aitken, and M. A. Arnott, “The Influence of Congenital Toxoplasma Infection on the Spontaneous Running Activity of Mice,” Zeitschrift für Parasitenkunde 71, no. 4 (1985): 459–462.

6. Indeed, virtually all, or perhaps even all, mammals that have so far been studied.

7. Of the phylum Apicomplexa, which also contains the malaria parasite, Plasmodium.

8. For the staying power of these parasites, see A. Dumètre and M. L. Dardé, “How to Detect Toxoplasma gondii Oocysts in Environmental Samples?” FEMS Microbiology Reviews 27, no. 5 (2003): 651–661.

9. And they are not alone. In work led by Amy Savage, we’ve found that litter boxes contain hundreds of unusual, poorly studied species.

10. In Europe, between 1 and 10 in 10,000 newborn babies are infected with Toxoplasma gondii. One to 2 percent will die or develop learning difficulties, and 4 to 27 percent develop retinal lesions that lead to vision impairment. See A. J. C. Cook, R. Holliman, R. E. Gilbert, W. Buffolano, J. Zufferey, E. Petersen, P. A. Jenum, W. Foulon, A. E. Semprini, and D. T. Dunn, “Sources of Toxoplasma Infection in Pregnant Women: European Multicentre Case-Control Study,” BMJ 321, no. 7254 (2000): 142–147.

11. The blood of forty-one of the participants was studied in more detail using more expensive immunological assays. Those assays confirmed the results of the simpler antigen test.

12. Which is to say that being infected by a brain-manipulating parasite might make you less likely to be a department head or dean. I would have thought the opposite.

13. K. Yereli, I. C. Balcioğlu, and A. Özbilgin, “Is Toxoplasma gondii a Potential Risk for Traffic Accidents in Turkey?” Forensic Science International 163, no. 1 (2006): 34–37.

14. J. Flegr and I. Hrdý, “Evolutionary Papers: Influence of Chronic Toxoplasmosis on Some Human Personality Factors,” Folia Parasitologica 41 (1994): 122–126.

15. J. Flegr, J. Havlícek, P. Kodym, M. Malý, and Z. Smahel, “Increased Risk of Traffic Accidents in Subjects with Latent Toxoplasmosis: A Retrospective Case-Control Study,” BMC Infectious Diseases 2, no. 1 (2002): 11.

16. The effect of mice on stored grains was great, so great that some of our modern grains are tough because tough grains were more likely to survive being eaten by mice. See C. F. Morris, E. P. Fuerst, B. S. Beecher, D. J. Mclean, C. P. James, and H. W. Geng, “Did the House Mouse (Mus musculus L.) Shape the Evolutionary Trajectory of Wheat (Triticum aestivum L.)?” Ecology and Evolution 3, no. 10 (2013): 3447–3454.

17. Early agriculturalists often inadvertently offered parasites to the afterlife. See M. L. C. Gonçalves, A. Araújo, and L. F. Ferreira, “Human Intestinal Parasites in the Past: New Findings and a Review,” Memórias do Instituto Oswaldo Cruz 98 (2003): 103–118.

18. J.-D. Vigne, J. Guilaine, K. Debue, L. Haye, and P. Gérard, “Early Taming of the Cat in Cyprus,” Science 304, no. 5668 (2004): 259.

19. J. P. Webster, “The Effect of Toxoplasma gondii and Other Parasites on Activity Levels in Wild and Hybrid Rattus norvegicus,” Parasitology 109, no. 5 (1994): 583–589.

20. See M. Berdoy, J. P. Webster, and D. W. Macdonald, “Parasite-Altered Behaviour: Is the Effect of Toxoplasma gondii on Rattus norvegicus Specific?” Parasitology 111, no. 4 (1995): 403–409.

21. E. Prandovszky, E. Gaskell, H. Martin, J. P. Dubey, J. P. Webster, and G. A. McConkey, “The Neurotropic Parasite Toxoplasma gondii Increases Dopamine Metabolism,” PloS One 6, no. 9 (2011): e23866.

22. See V. J. Castillo-Morales, K. Y. Acosta Viana, E. D. S. Guzmán-Marín, M. Jiménez-Coello, J. C. Segura-Correa, A. J. Aguilar-Caballero, and A. Ortega-Pacheco, “Prevalence and Risk Factors of Toxoplasma gondii Infection in Domestic Cats from the Tropics of Mexico Using Serological and Molecular Tests,” Interdisciplinary Perspectives on Infectious Diseases 2012 (2012): 529108.

23. E. F. Torrey and R. H. Yolken, “The Schizophrenia–Rheumatoid Arthritis Connection: Infectious, Immune, or Both?” Brain, Behavior, and Immunity 15, no. 4 (2001): 401–410.

24. J. P. Webster, P. H. L. Lamberton, C. A. Donnelly, E. F. Torrey, “Parasites as Causative Agents of Human Affective Disorders? The Impact of Anti-Psychotic, Mood-Stabilizer and Anti-Parasite Medication on Toxoplasma gondii’s Ability to Alter Host Behaviour,” Proceedings of the Royal Society B: Biological Sciences 273, no. 1589 (2006): 1023–1030.

25. D. W. Niebuhr, A. M. Millikan, D. N. Cowan, R. Yolken, Y. Li, and N. S. Weber, “Selected Infectious Agents and Risk of Schizophrenia among US Military Personnel,” American Journal of Psychiatry 165, no. 1 (2008): 99–106.

26. R. H. Yolken, F. B. Dickerson, and E. Fuller Torrey, “Toxoplasma and Schizophrenia,” Parasite Immunology 31, no. 11 (2009): 706–715.

27. C. Poirotte, P. M. Kappeler, B. Ngoubangoye, S. Bourgeois, M. Moussodji, and M. J. Charpentier, “Morbid Attraction to Leopard Urine in Toxoplasma-Infected Chimpanzees,” Current Biology 26, no. 3 (2016): R98–R99.

28. Thus, infection could explain the behavior of men with too many pet cats, but not that of women with too many cats. See J. Flegr, “Influence of Latent Toxoplasma Infection on Human Personality, Physiology and Morphology: Pros and Cons of the Toxoplasma–Human Model in Studying the Manipulation Hypothesis,” Journal of Experimental Biology 216, no. 1 (2013): 127–133.

29. Though not everywhere. In China, where until recently the keeping of cats as pets was rare, the prevalence of Toxoplasma gondii antibodies (and hence exposures) was also very low. It is in such countries where it may be easiest to study the consequences of infection with Toxoplasma gondii on particular maladies inasmuch as changes in infection status will be much easier to document. See E. F. Torrey, J. J. Bartko, Z. R. Lun, and R. H. Yolken, “Antibodies to Toxoplasma gondii in Patients with Schizophrenia: A Meta-Analysis,” Schizophrenia Bulletin 33, no. 3 (2007): 729–736. doi:10.1093/schbul/sbl050.

30. M. S. Thoemmes, D. J. Fergus, J. Urban, M. Trautwein, and R. R. Dunn, “Ubiquity and Diversity of Human-Associated Demodex Mites,” PLoS One 9, no. 8 (2014): e106265.

31. And, well, also, it wasn’t the only thing Meredith was working on during those years.

32. See, for example, F. J. Márquez, J. Millán, J. J. Rodriguez‐Liebana, I. Garcia‐Egea, and M. A. Muniain, “Detection and Identification of Bartonella sp. in Fleas from Carnivorous Mammals in Andalusia, Spain,” Medical and Veterinary Entomology 23, no. 4 (2009): 393–398.

33. A. C. Y. Lee, S. P. Montgomery, J. H. Theis, B. L. Blagburn, and M. L. Eberhard, “Public Health Issues Concerning the Widespread Distribution of Canine Heartworm Disease,” Trends in Parasitology 26, no. 4 (2010): 168–173.

34. R. S. Desowitz, R. Rudoy, and J. W. Barnwell, “Antibodies to Canine Helminth Parasites in Asthmatic and Nonasthmatic Children,” International Archives of Allergy and Immunology 65, no. 4 (1981): 361–366.

35. Nor is this effect of dogs on the species that live with us in our homes new. Jean-Bernard Huchet, the entomologist charged with ensuring the well-being of the mummies at the Musée de l’Homme in Paris, the guardian of their afterlives, recently dissected a dog mummy from the Egyptian site of El Deir (not far from Cairo in the Nile delta, 332 to 30 BCE). One of the dogs had date pits and figs in its stomach, indications that the dog depended on the fruit of the human settlement. The ears of the dog were also covered in brown dog ticks (Rhipicephalus sanguineus), a species that has now spread globally with the spread of dogs. The ticks were very likely to carry inside their bodies pathogens that could be vectored to humans; nearly a dozen different pathogens have been found in this species of tick. All of these species were to some extent brought into the cities and homes of Egyptians via the dogs. See J. B. Huchet, C. Callou, R. Lichtenberg, and F. Dunand, “The Dog Mummy, the Ticks and the Louse Fly: Archaeological Report of Severe Ectoparasitosis in Ancient Egypt,” International Journal of Paleopathology 3, no. 3 (2013): 165–175.

36. Among them species of Arthrobacter, Sphingomonas, and Agrobacterium.

37. A. A. Madden, A. Barberán, M. A. Bertone, H. L. Menninger, R. R. Dunn, and N. Fierer, “The Diversity of Arthropods in Homes across the United States as Determined by Environmental DNA Analyses,” Molecular Ecology 25, no. 24 (2016): 6214–6224; M. Leong, M. A. Bertone, A. M. Savage, K. M. Bayless, R. R. Dunn, and M. D. Trautwein, “The Habitats Humans Provide: Factors Affecting the Diversity and Composition of Arthropods in Houses,” Scientific Reports 7, no. 1 (2017): 15347.

38. C. Pelucchi, C. Galeone, J. F. Bach, C. La Vecchia, and L. Chatenoud, “Pet Exposure and Risk of Atopic Dermatitis at the Pediatric Age: A Meta-Analysis of Birth Cohort Studies,” Journal of Allergy and Clinical Immunology 132 (2013): 616–622.e7.

39. K. C. Lødrup Carlsen, S. Roll, K. H. Carlsen, P. Mowinckel, A. H. Wijga, B. Brunekreef, M. Torrent, et al., “Does Pet Ownership in Infancy Lead to Asthma or Allergy at School Age? Pooled Analysis of Individual Participant Data from 11 European Birth Cohorts,” PLoS One 7 (2012): e43214.

40. G. Wegienka, S. Havstad, H. Kim, E. Zoratti, D. Ownby, K. J. Woodcroft, and C. C. Johnson, “Subgroup Differences in the Associations between Dog Exposure During the First Year of Life and Early Life Allergic Outcomes,” Clinical and Experimental Allergy 47, no. 1 (2017): 97–105.

41. S. J. Song, C. Lauber, E. K. Costello, C. A. Lozupone, G. Humphrey, D. Berg-Lyons, J. G. Caporaso, et al., “Cohabiting Family Members Share Microbiota with One Another and with Their Dogs,” Elife 2 (2013): e00458; M. Nermes, K. Niinivirta, L. Nylund, K. Laitinen, J. Matomäki, S. Salminen, and E. Isolauri, “Perinatal Pet Exposure, Faecal Microbiota, and Wheezy Bronchitis: Is There a Connection?” ISRN Allergy 2013 (2013).

42. M. G. Dominguez-Bello, E. K. Costello, M. Contreras, M. Magris, G. Hidalgo, N. Fierer, and R. Knight, “Delivery Mode Shapes the Acquisition and Structure of the Initial Microbiota across Multiple Body Habitats in Newborns,” Proceedings of the National Academy of Sciences 107, no. 26 (2010): 11971–11975.

CHAPTER 11

1. Also called 52 or 52a.

2. Or at least any other microbe in those countries in which public health systems, waste treatment, and hand washing were well established. H. R. Shinefield, J. C. Ribble, M. Boris, and H. F. Eichenwald, “Bacterial Interference: Its Effect on Nursery-Acquired Infection with Staphylococcus aureus. I. Preliminary Observations on Artificial Colonization of Newborns,” American Journal of Diseases of Children 105 (1963): 646–654.

3. Based on the most recent estimates, just a few decades earlier. See P. R. McAdam, K. E. Templeton, G. F. Edwards, M. T. G. Holden, E. J. Feil, D. M. Aanensen, H. J. A. Bargawi, et al., “Molecular Tracing of the Emergence, Adaptation, and Transmission of Hospital-Associated Methicillin-Resistant Staphylococcus aureus,” Proceedings of the National Academy of Sciences 109, no. 23 (2012): 9107–9112.

4. They had previously suggested that the answer, in the case of such infections, was the detailed study of the biology of the pathogen. Now they were being called to task. See H. F. Eichenwald and H. R. Shinefield, “The Problem of Staphylococcal Infection in Newborn Infants,” Journal of Pediatrics 56, no. 5 (1960): 665–674.

5. Shinefield et al., “Bacterial Interference: Its Effect On Nursery-Acquired Infection,” 646–654.

6. H. R. Shinefield, J. C. Ribble, M. B. Eichenwald, and J. M. Sutherland, “V. An Analysis and Interpretation,” American Journal of Diseases of Children 105, no. 6 (1963): 683–688.

7. These were the very same bacteria my colleagues and I would later find dominated belly buttons. See J. Hulcr, A. M. Latimer, J. B. Henley, N. R. Rountree, N. Fierer, A. Lucky, M. D. Lowman, and R. R. Dunn, “A Jungle in There: Bacteria in Belly Buttons Are Highly Diverse, but Predictable,” PLoS One 7, no. 11 (2012): e47712.

8. It was also possible that other species of bacteria, such as species of Micrococcus or Corynebacterium, might help repel 80/81, but Eichenwald and Shinefield thought that the competition between related species would be more intense than that between less-related species. In this, skin microbes are like plant species in grasslands or forests. More closely related plants tend to be more ecologically similar and more likely to compete with and be able to exclude each other. See J. H. Burns and S. Y. Strauss, “More Closely Related Species Are More Ecologically Similar in an Experimental Test,” Proceedings of the National Academy of Sciences 108, no. 13 (2011): 5302–5307.

9. D. Janek, A. Zipperer, A. Kulik, B. Krismer, and A. Peschel, “High Frequency and Diversity of Antimicrobial Activities Produced by Nasal Staphylococcus Strains against Bacterial Competitors,” PLoS Pathogens 12, no. 8 (2016): e1005812.

10. Among ants, for example, a classic example of interference competition is when ants of the species Novomessor cockerelli interfere with the foraging of their competitors, species of Pogonomyrmex harvester ants, by plugging the nest entrances of the latter with stones.

11. One exception being René Dubos. H. L. Van Epps, “René Dubos: Unearthing Antibiotics,” Journal of Experimental Medicine 203, no. 2 (2006): 259.

12. Shinefield et al., “Bacterial Interference: Its Effect on Nursery-Acquired Infection,” 646–654.

13. This is work done by the extraordinary scientist with the superhero name, Paul Planet, and his collaborators. D. Parker, A. Narechania, R. Sebra, G. Deikus, S. LaRussa, C. Ryan, H. Smith, et al., “Genome Sequence of Bacterial Interference Strain Staphylococcus aureus 502A,” Genome Announcements 2, no. 2 (2014): e00284-14.

14. This same concept, that success is best predicted by the number of individuals introduced (or the number of attempts at introduction), also holds for other sorts of colonization. For example, one of the best predictors of whether an introduced ant species succeeds in establishing is how many times it was introduced. See A. V. Suarez, D. A. Holway, and P. S. Ward, “The Role of Opportunity in the Unintentional Introduction of Nonnative Ants,” Proceedings of the National Academy of Sciences of the United States of America 102, no. 47 (2005): 17032–17035.

15. Interestingly, in those few cases when 502A didn’t take, it was often because other Staphylococcus had already colonized the noses and belly buttons of the babies. See Shinefield et al., “Bacterial Interference: Its Effect on Nursery-Acquired Infection,” 646–654.

16. H. R. Shinefield, J. M. Sutherland, J. C. Ribble, and H. F. Eichenwald, “II. The Ohio Epidemic,” American Journal of Diseases of Children 105, no. 6 (1963): 655–662.

17. H. R. Shinefield, M. Boris, J. C. Ribble, E. F. Cale, and Heinz F. Eichenwald, “III. The Georgia Epidemic,” American Journal of Diseases of Children 105, no. 6 (1963): 663–673. Also see M. Boris, H. R. Shinefield, J. C. Ribble, H. F. Eichenwald, G. H. Hauser, and C. T. Caraway, “IV. The Louisiana Epidemic,” American Journal of Diseases of Children 105, no. 6 (1963): 674–682.

18. H. F. Eichenwald, H. R. Shinefield, M. Boris, and J. C. Ribble, “‘Bacterial Interference’ and Staphylococcic Colonization in Infants and Adults,” Annals of the New York Academy of Sciences 128, no. 1 (1965): 365–380.

19. D. Janek, A. Zipperer, A. Kulik, B. Krismer, and A. Peschel, “High Frequency and Diversity of Antimicrobial Activities Produced by Nasal Staphylococcus Strains against Bacterial Competitors,” PLoS Pathogens 12, no. 8 (2016): e1005812.

20. This is what Paul Planet thinks may be going on.

21. C. S. Elton, The Ecology of Invasions by Animals and Plants (London: Methuen & Co, 1958).

22. For the quote, see J. D. van Elsas, M. Chiurazzi, C. A. Mallon, D. Elhottovā, V. Krištůfek, and J. F. Salles, “Microbial Diversity Determines the Invasion of Soil by a Bacterial Pathogen,” Proceedings of the National Academy of Sciences 109, no. 4 (2012): 1159–1164. For a general review, see J. M. Levine, P. M. Adler, and S. G. Yelenik, “A Meta‐Analysis of Biotic Resistance to Exotic Plant Invasions,” Ecology Letters 7, no. 10 (2004): 975–989.

23. J. M. H. Knops, D. Tilman, N. M. Haddad, S. Naeem, C. E. Mitchell, J. Haarstad, M. E. Ritchie, et al., “Effects of Plant Species Richness on Invasion Dynamics, Disease Outbreaks, and Insect Abundances and Diversity,” Ecology Letters 2 (1999): 286–293.

24 J. D. van Elsas, M. Chiurazzi, C. A. Mallon, D. Elhottovā, V. Krištůfek, and J. F. Salles, “Microbial Diversity Determines the Invasion of Soil by a Bacterial Pathogen,” Proceedings of the National Academy of Sciences 109, no. 4 (2012): 1159–1164.

25. Nor were the results of van Elsas and his colleagues a fluke of choosing to work on E. coli. Results have been similar in studies considering the invasion of the soil around wheat roots by the bacterial species Pseudomonas aeruginosa. See A. Matos, L. Kerkhof, and J. L. Garland, “Effects of Microbial Community Diversity on the Survival of Pseudomonas aeruginosa in the Wheat Rhizosphere,” Microbial Ecology 49 (2005): 257–264.

26. We often look back on choices societies have made and wonder whether anyone sounded the alarm when a bad decision was being made. We are quick to suggest that decades, or centuries, or millennia ago, our antecedents didn’t know enough to choose more wisely. In this particular case, we did know enough. In 1965, Shinefield and Eichenwald clearly laid out the problems that would emerge were we to focus completely on antibiotics. See Shinefield et al., “V. An Analysis and Interpretation,” 683–688.

27. Fleming said, “There is the danger that the ignorant man may easily underdose himself and by exposing his microbes to non-lethal quantities of the drug make them resistant. Here is a hypothetical illustration. Mr. X. has a sore throat. He buys some penicillin and gives himself, not enough to kill the streptococci but enough to educate them to resist penicillin. He then infects his wife. Mrs. X gets pneumonia and is treated with penicillin. As the streptococci are now resistant to penicillin the treatment fails. Mrs. X dies. Who is primarily responsible for Mrs. X’s death? Why Mr. X whose negligent use of penicillin changed the nature of the microbe.”

28. M. Baym, T. D. Lieberman, E. D. Kelsic, R. Chait, R. Gross, I. Yelin, and R. Kishony, “Spatiotemporal Microbial Evolution on Antibiotic Landscapes,” Science 353, no. 6304 (2016): 1147–1151.

29. F. D. Lowy, “Antimicrobial Resistance: The Example of Staphylococcus aureus,” Journal of Clinical Investigation 111, no. 9 (2003): 1265.

30. E. Klein, D. L. Smith, and R. Laxminarayan, “Hospitalizations and Deaths Caused by Methicillin-Resistant Staphylococcus aureus, United States, 1999–2005,” Emerging Infectious Diseases 13, no. 12 (2007): 1840.

31. Just why the use of antibiotics leads cows and pigs to grow more quickly is not entirely understood.

32. S. S. Huang, E. Septimus, K. Kleinman, J. Moody, J. Hickok, T. R. Avery, J. Lankiewicz, et al., “Targeted versus Universal Decolonization to Prevent ICU Infection,” New England Journal of Medicine 368, no. 24 (2013): 2255–2265.

33. R. Laxminarayan, P. Matsoso, S. Pant, C. Brower, J.-A. Røttingen, K. Klugman, and S. Davies, “Access to Effective Antimicrobials: A Worldwide Challenge,” Lancet 387, no. 10014 (2016): 168–175. For more on policy solutions to the resistance challenge, see P. S. Jorgensen, D. Wernli, S. P. Carroll, R. R. Dunn, S. Harbarth, S. A. Levin, A. D. So, M. Schluter, and R. Laxminarayan, “Use Antimicrobials Wisely,” Nature 537, no. 7619 (2016); K. Lewis, “Platforms for Antibiotic Discovery,” Nature Reviews Drug Discovery 12 (2013): 371–387.

CHAPTER 12

1. D. E. Beasley, A. M. Koltz, J. E. Lambert, N. Fierer, and R. R. Dunn, “The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome,” PloS One 10, no. 7 (2015): e0134116.

2. G. Campbell-Platt, Fermented Foods of the World. A Dictionary and Guide (Oxford: Butterworth Heinemann, 1987).

3. Kimchi is much more diverse than are most other fermented foods. Not only can individual kimchi types contain tens or even hundreds of species (that differ from one person’s kimchi to another person’s kimchi, it seems) but also different types of kimchi have very different microbes. See E. J. Park, J. Chun, C. J. Cha, W. S. Park, C. O. Jeon, and J. W. Jin-Woo Bae, “Bacterial Community Analysis During Fermentation of Ten Representative Kinds of Kimchi with Barcoded Pyrosequencing,” Food Microbiology 30, no. 1 (2012): 197–204. In addition to Staphylococcus and Lactobacillus, common genera of bacteria in kimchi include Leuconostoc and a close relative of Leuconostoc, Weisella (both of which we find to be abundant in refrigerators), Enterobacter (a fecal microbe), and Pseudomonas.

4. Bacillus subtillus, the same bacterial species that makes feet stinky (and that was found in abundance on the International Space Station). For more on Korean fermentation, see J. K. Patra, G. Das, S. Paramithiotis, and H.S. Shin, “Kimchi and Other Widely Consumed Traditional Fermented Foods of Korea: A Review,” Frontiers in Microbiology 7 (2016).

5. I highly recommend viewing the 1903 documentary film Cheese Mites (produced by Charles Urban and directed by F. Martin Duncan), a film that highlights the beauty of an animal that can help turn one food into another. www.youtube.com/watch?v=wR2DystgByQ.

6. L. Manunza, “Casu Marzu: A Gastronomic Genealogy,” in Edible Insects in Sustainable Food Systems (Cham, Switzerland: Springer International, 2018).

7. For a nice description of the early history of bread and a tale of the quest to re-create ancient bread technology, see E. Wood, World Sourdoughs from Antiquity (Berkeley, CA: Ten Speed Press, 1996).

8. These breads were a kind of money, a ration, and, like beer, a unit of exchange. Bread baking was a way of turning a hard-to-work grain into an easy-to-store, -trade, -sell, or -eat food. See D. Samuel, “Bread Making and Social Interactions at the Amarna Workmen’s Village, Egypt,” World Archaeology 31, no. 1 (1999): 121–144.

9. Nor has the question even been very seriously studied. No one, for instance, has searched for ancient DNA in any of the many mummified breads that accompany Egyptian burials. Such burials have already told us so very much about daily life in antiquity. They have much more to tell, though I’m not sure this is the afterlife the Egyptians had in mind.

10. The details of this process vary. Some use only distilled water, others only rainwater. Bakers also vary in terms of the kind of flour they use, the temperature at which their starters are kept, and even whether other microbe-laden foods (including fruits) are added to the mix.

11. L. De Vuyst, H. Harth, S. Van Kerrebroeck, and F. Leroy, “Yeast Diversity of Sourdoughs and Associated Metabolic Properties and Functionalities,” International Journal of Food Microbiology 239 (2016): 26–34.

12. One study of bakeries found that even though the flour being used contained bacteria of the genus Enterobacter (a potentially pathogenic fecal microbe), these bacteria never established in the sourdough starter. They were killed, it seems, by the sourdough bacteria and the acid they had produced. In the same study, the bacteria were very diverse in the flour, the mixing bowl, and even the bread storage box—but not in the sourdough, where a simple, stable microbial garden grew.

13. When refrigerators and freezers were invented, they were a new, alternative way of storing food, but mostly they are less effective than is fermentation. When you buy food, all of your food is filled with microbes (even the vacuum-sealed food). When you put your food in the refrigerator, it slows down the feeding and reproduction of the microbes in the food. The “best by” label on the food in your fridge is essentially a measure of how long it takes those microbes in your food, even under cold conditions, to divide and metabolize enough to take over the food. This is what the “best by” label should really say: “Not totally thick with microbes until January 4,” though just how long you get actually depends on which microbes have colonized your food from your kitchen, hands, and breath each time you open the jar. In other words, “best by January 4” is a lie, but a good rule-of-thumb lie, one that helps us get through the day alive.

14. Sometimes these breads are made sour by adding a strain of Lactobacillus reuteri originally from rodent feces. If you don’t believe me, read M. S. W. Su, P. L. Oh, J. Walter, and M. G. Gänzle, “Intestinal Origin of Sourdough Lactobacillus reuteri Isolates as Revealed by Phylogenetic, Genetic, and Physiological Analysis,” Applied and Environmental Microbiology 78, no. 18 (2012): 6777–6780.

15. In doing so, Saccharomyces cerevisiae seems to only rarely be part of the starter community, though our picture is biased. It appears that once packaged yeast is used in a bakery, it easily becomes part of the indoor yeast community in the bakery (setting up shop on the mixers, in the flour, in the storage containers, and so on) and, in doing so, readily “contaminates” new starters. This doesn’t prevent the starters from doing their job, but it does reduce the diversity of starters, a more subtle element of the microbial homogenization set in motion by the industrial-scale production and use of Saccharomyces. See F. Minervini, A. Lattanzi, M. De Angelis, G. Celano, and M. Gobbetti, “House Microbiotas as Sources of Lactic Acid Bacteria and Yeasts in Traditional Italian Sourdoughs,” Food Microbiology 52 (2015): 66–76.

16. No guess as to what might have made Herman turn pink. It probably had nothing to do with the earthquake.

17. We wanted to avoid letting them feed the starters before we sampled because if they fed the starters in the kitchen (and they would), they would likely inadvertently introduce microbes from the kitchen into the starters. This would happen. It was unavoidable, but by sampling before it happened, we had our best chance of measuring the microbes unique to each baker’s efforts, body, and home.

18. We controlled for the big differences, but it took constant work. We even had to keep an eye out to make sure the bakers didn’t introduce other ingredients into the breads, ingredients they were desperate to add (and that seemed to appear miraculously from pockets and smocks): “But what about a little garlic? Just a little? How about some sesame!”

19. D. A. Jensen, D. R. Macinga, D. J. Shumaker, R. Bellino, J. W. Arbogast, and D. W. Schaffner, “Quantifying the Effects of Water Temperature, Soap Volume, Lather Time, and Antimicrobial Soap as Variables in the Removal of Escherichia coli ATCC 11229 from Hands,” Journal of Food Protection 80, no. 6 (2017): 1022–1031.

20. A. A. Ross, K. Muller, J. S. Weese, and J. Neufeld, “Comprehensive Skin Microbiome Analysis Reveals the Uniqueness of Human-Associated Microbial Communities among the Class Mammalia,” bioRxiv (2017): 201434.

21. N. Fierer, M. Hamady, C. L. Lauber, and R. Knight, “The Influence of Sex, Handedness, and Washing on the Diversity of Hand Surface Bacteria,” Proceedings of the National Academy of Sciences 105, no. 46 (2008): 17994–17999.

22. A. Döğen, E. Kaplan, Z. Öksüz, M. S. Serin, M. Ilkit, and G. S. de Hoog, “Dishwashers Are a Major Source of Human Opportunistic Yeast-Like Fungi in Indoor Environments in Mersin, Turkey,” Medical Mycology 51, no. 5 (2013): 493–498.