The page numbers in this index refer to the printed version of this book. The link provided will take you to the beginning of that print page. You may need to scroll forward from that location to find the corresponding reference on your e-reader.
Note: NCDs refers to noncommunicable diseases.
acetylcholine, 246
air travel, NCD incident examples, 10–12
Akkermansia, 43–44, 183, 245, 274
allergies. See also food allergies
current prevalence vs. past, 108–109
immune system and, 108–109
modifying microbiome to control, 181–182
multiple (atopy), 108
sinus infections, rebiosis and, 216–218, 220
triggering asthma, 15
amasi, 268–269
amygdalin, 61
animals, rebiosis for, 222–226
antibiotics
amoxicillin overuse, 143
breast milk and, 55
controlling deadly diseases, 3
discussing complementary therapy, 259
game-changing impact, 2–3
healthy choices, 259
mitigating unintended side effects, 181
origins of using, 2–3
overreach causing NCDs, 142–148
poultry, food supply impact, 144–148
resistance from overuse, 144–148
second generation of, 3
side effects, 4–5, 142–143, 144, 181
vision of future use, 174
anxiety, microbes and, 246–247, 261
ASD. See autism spectrum disorders (ASDs)
Asperger’s syndrome, 75
asthma
allergies triggering, 15
animal-associated, 260
biology of, 134
C-section deliveries and, 163–164
H. pylori and, 118–119
microbiome status impacting, 137–140
multiple (comorbid) NCDs with, 133–136
as one of many NCDs, 9
urban living elevating risk, 156, 157–158
attention deficit hyperactivity disorder (ADHD), 74–75, 164, 171
autism spectrum disorders (ASDs)
increased needs and care, 75, 77–78, 135
microbiome status and, 70, 137–140, 247
multiple (comorbid) NCDs with, 133–136, 171
as one of many NCDs, 7, 9, 137
premature babies and, 68
sulfur compounds and, 195
travel challenges example, 12–13
autoimmune diseases, 71, 104–105, 134, 136, 144, 185, 240
baby, newborn. See also birth delivery mode; cesarean section deliveries
birth event importance, 53–54
breast milk importance. See breast milk
changes in microbiome, 54
early-life programming of NCDs, 128–129
healthy choices, 259
immune system development, 131–132
immune system functioning, 34–35
microbiome partnership, 56, 132
NCD epidemic and, 170–172
oxygen-hating bacteria and, 53–54
pets and, 260
placental/vaginal microbes and, 53–54, 55, 64
prebiotics for infants, 251–252
seeding/development of microbiome, 53–56, 259
skin-to-skin contact for microbes, 54
Bäckhed, Fredrik, 160–162
Bacteroides fragilis (B. fragilis), 70, 120, 185, 234
Bacteroidetes and Firmicutes, 41, 42, 53, 245, 261, 270
benzene, 115
Bifidobacterium, 54, 55, 161, 176, 223, 227, 233, 245, 250, 251, 262, 274
biology, new, emergence of, 6. See also disease, patterns of; immune system; microbiome; NCDs references; precision medicine; rebiosis; self-care
biology, old
biological purity misunderstanding, 1, 5
end of, 21–30
Human Genome Project and, 24–27
human mammalian genome misunderstanding, 1–2, 5, 6–7, 26–29
identity of humans and, 1–2
institutions impacting perceptions, 21–24
Koch’s postulates and, 2
mistaken fundamental concepts of, 1–2, 5
pillars of, 24
taxonomy and, 6–7
vaccines and, 3–4
birth defects. See also incompleteness of microbiome
definitions of, 67–68
genetic causes, 66
growing disabled population, 72
microbiome-based, 66–67, 69–72
birth delivery mode, 158–164. See also cesarean section deliveries
importance of, 158
microbiome comparison of modes, 160–162
microbiome impact, 158, 160–162, 164
NCDs, immune system and, 162–164
vaginal, 53–54, 55, 63–64, 160–162
brain fog, microbiome and, 261
brain, microbes and, 242–252
about: overview of, 242–244
balancing, to improve health, 248–249
chemicals to control brain and, 245–249
communication routes, 242–243
deaths/illnesses from neurological disorders, 249
food cravings and, 244–245, 261
gamma-aminobutyric acid (GABA) and, 246
pathogens, parasites and, 244
puppet master microbiome, 242–243
rebiosis for, 249–252
“second brain” gut and, 243–244
breast milk
antibiotics affecting, 55
composition affected by delivery method, 55, 162
future of prepping for baby, 173–174
importance of, 54–55
nurturing microbiome, 54–55, 251
prebiotics and, 251–252
providing food for microbes, 55
substitutes (formulas) for, 55, 251–252, 259
butyrate (butyric acid), 191, 193, 225, 246, 270
cancer. See also cancer treatment
asbestos and, 116–117
chronic inflammation and, 125–126, 129
dogs detecting, 192–193
E-nose detecting, 201–202
flame-retardant chemicals and, 165
microbiome status impacting, 137–140, 144
multiple NCDs and, 132–136
rogue immune responses and, 113
sulfur and deterrence of, 195
cancer treatment
drugs dependent on microbiome integrity, 140
near-term focus of precision medicine, 99
probiotics as part of, 175, 232
vision of future, 175
carboxymethylcellulose, 167
Carter, Jimmy, 106–107
cats, rebiosis for, 225–226
celiac disease, 9, 12, 77, 134–135, 164, 171
cesarean section deliveries
interfering with birth of human superorganism, 160
microbiome impact, 158, 160–162, 164
missed health risks of, 159–160
NCDs, immune system and, 162–164
origins and evolution of, 158–160
prevalence of, 159
study comparing microbiomes of vaginal deliveries to, 160–162
vaginal microbe seeding and, 53–54, 55, 64, 158, 160–162, 259
chemicals and drugs
biologic drugs for NCDs, 166
food emulsifiers, 167, 254–255
misdirected safety efforts, 164–168
NCDs from, 164–168
chicha, 269
Clostridium, 54, 161, 184–185, 193, 251, 257
colitis, ulcerative, 138, 182, 185
commensals, 33–34, 119–120, 151, 152, 238, 256
comorbid NCDs. See NCDs
competitive exclusion, 210, 223–224
coral reef microbiome model, 38–40
CRISPR, 238–241
Dawkins, Richard, 23, 24, 25, 28–29
death, what can kill us, 60–62, 249
depression
disease interconnections and, 135–136
microbiome status impacting, 137–140, 144, 247, 248, 261
probiotics helping, 175
diabetes
gene swaps/switches and, 92
microbiome status impacting, 137–140
multiple (comorbid) NCDs and, 124, 132–136
social fracturing and, 76–78
travel challenges and, 11
diet. See also fermented foods; prebiotics; probiotics; rebiosis
changing for better health, 215–220, 258
food cravings and, 244–245, 261
food emulsifier safety and, 167, 254–255
food revolution and, 148–152
interconnectedness with microbiome, 257–258
linking with microbiome recommendations, 176
microbiome-supportive vs. generally healthy, 269–270
refrigeration/transport technology and, 149–151
unprecedented changes in, 151–152
vision of future recommendations, 176
digoxin, microbiome and, 139–140
disabilities, 72–76
disease. See also NCDs references
avoiding, microbial-driven immune system education and, 109–112, 119–122, 220
complexity of health and, 4
flawed fundamentals of, 1–2
Koch’s postulates, 2
toxins and, 60–62, 121–122, 237
disease, patterns of, 123–140
about: overview of, 123
comorbid diseases, 124–127, 132–136
depression and, 135–136
finding common links, 124
naming diseases and, 123–124
pillars of NCDs. See NCDs, four pillars of
dogs, detecting microbes/diseases, 192–194
drugs and chemicals
cancer drugs dependent on microbiome, 140
future of safety determinations, 175
misdirected safety efforts, 164–168
paying attention to effects, 260
probiotics helping after taking, 213
Edinburgh, Scotland, urbanization of, 153–155
electronic nose (E-nose), 201–202
emulsifiers, food, 167, 254–255
enterotypes, microbial diversity and, 208, 229–234
environmental adaptations, 87–89
environmental microbes, 56–57, 59
epigenetics
defined, 84
famine examples, 91–93
healthiness and, 89–94
memory of ancestral traits and, 90–92
microbiome depletion warning, 93–94
switches controlling genes, 80, 84–87, 89–94, 102
ethnopharmacology, 36
evaluations, microbiome, 175–176, 179–180, 208–209. See also rebiosis
exercise, benefits of, 270–271
fecal microbial transplant (FMT), 184–185, 260
fermented foods, 262–270
amasi, 268–269
chicha, 269
fermentation process, 263
health benefits of, 263. See also specific fermented foods
history of, 263–264
kimchi, 266–267
kombucha, 267
kvass, 268
live probiotic bacteria and, 264–265
miso, 267–268
sauerkraut, 265–266
tempeh, 268
traditions of using, 263–264
types of foods, 263–264, 265–269
Firmicutes and Bacteroidetes, 41, 42, 53, 245, 261, 270
flame-retardant chemicals, 165
Fleming, Alexander, 271–272
FMT. See fecal microbial transplant
food allergies and intolerances
accommodations for, 16–17
antibiotic use and, 70–71
ASD and, 135
prevalence of, 107
rebiosis guidelines, 260
social adaptations/fracturing and, 76–80
food emulsifiers, 167, 254–255
formula (breast milk substitute), 55, 251–252, 259
gamma-aminobutyric acid (GABA), 246
gene swaps and switches, 79–94
about: overview of, 79–80
controlling switches, 85–87
defined, 80
developmental programming and, 89–94
electricity analogy for switches, 84–85
environmental adaptations and, 87–89
giraffes’ necks and, 87–89
horizontal gene transfers, 81–83
origins of genes and, 80–81
swaps, 80–84
switches, 80, 84–87, 89–94, 102
traits, phenotypes and, 84
genetically modified organisms (GMOs), 168, 255–256
genome, human. See also human superorganism
changing, 46–47
environmental vs. genetic effects, 64–65
mammalian. See genome, mammalian
microbial. See genome, microbial
mistaken belief of, 1–2, 5, 6–7, 26–29
overemphasis on male offspring and, 51–53
reality of kinship/inheritance, 47–53
second genome. See genome, microbial
genome, mammalian
changing, challenges of, 46–47
microbial compared to, 46–47
percent of human genes, 23, 47, 50, 52
genome, microbial
British royalty succession in light of, 49–51
changing, ease of, 47
mammalian compared to, 46–47
matrilineal origins of, 50–52
new perspective on family heritage, 47–53
percent of human genes, 23, 47, 48, 50, 52
as second genome, 46–47
shared by millions of people, 47
giraffes, necks of, 87–89
glyphosate, 256–257
health. See also brain, microbes and; rebiosis; self-care
about: overview of microbiome and, 27–28. See also human superorganism; superorganism ecology
birth delivery and. See birth delivery mode; cesarean section deliveries
complexity of, 4
developmental programming and, 89–94
losing microbial partners and, 44–45
microbial-driven immune system education and, 109–112, 119–122, 220
misdirected human safety efforts and, 164–168
redirecting precision medicine for, 97–102
heart disease
comorbid NCDs and, 132–133
developmental programming of, 89–90
digoxin treatment, microbiome and, 139–140
early-life programming of, 128
microbiome status impacting, 139–140
obesity and, 125–126
urban living increasing, 156
VSL#3 and, 182–183
Helicobacter pylori (H. pylori), 117–119
helminthic therapy, 33, 181–182
histamine, 246
horizontal gene transfers, 81–83
human leukocyte antigen (HLA) complex, 203–204
human superorganism, 46–65. See also genome references; superorganism ecology
about: overview of, 29–30
ancient microbes and, 57–59
death of, toxicology and, 60–62
fit of microbiome to, 62–65
Human Genome Project revealing, 26–28
interdependence with microbes, 32
new family rules, 47–53
origins of, 56–59
urban living impacting, 58
immune system, 103–122. See also noncommunicable diseases (NCDs)
about: overview of things going wrong, 103–104
asbestos, microbiome and, 114–117
attacking inappropriate things, 108–109, 113–114
at birth, 34–35
brain similarity to, 248–249
cells, pervasiveness/locations of, 107–108, 112–113
CRISPR, 238–241
critical windows of vulnerability, 109–110
C-section deliveries impacting, 162–164
developmental programming and, 89–94
development process, 109–112
education of, by microbiome, 109–112, 119–122, 220
H. pylori and, 117–119
inflammation and, 130–132
integral nature of, 113
macrophages and, 108, 111–112, 114, 116–117, 121–122, 131, 248
main location of cells, 112
microbiome importance, 110–112
misconceptions about, 112–114
peanut allergies and, 106–107, 108–109, 183
requiring microbial partners, 35
training, 117–119
incompleteness of microbiome, 66–78
atypical humans, disabilities and, 72–76
as birth defect, 69–72
birth defects overview and, 66–69
growing disabled population, 72
metabolite production and, 70
NCDs and, 70–72
inflammation
early-life NCD programming and, 128–129
at heart of NCDs, 130–132
immunity and, 130–132
microbes causing brain injury with, 247–248
modifying microbiome to control, 181–182
monitoring, vision of future, 175
necessary, useful functions, 129
oxidative damage from, 129
prebiotics reducing, 260
unhealthy, NCDs and, 129–132
irritable bowel syndrome (IBS), rebiosis for, 216–220
kimchi, 266–267
Koch’s postulates, 2
kombucha, 267
kvass, 268
Lactobacillus
in breast milk, 55
chicha with, 269
formula supplemented with, 251–252
kimchi with, 266–267
kvass with, 268
neuroactive metabolites and, 246
probiotics with, 42, 168, 174–175, 183, 211, 227, 258–259, 261–262, 273
in skin microbiome, 214–215
in vaginal microbiome, 200
Lamarck, Jean-Baptiste, 87–89
Linnaeus, Carl, 6
Lynn, Walter, 104
macrophages, 108, 111–112, 114, 116–117, 121–122, 131, 248
mammalian genome, human. See genome, human
mammalian-only human medicine, 168–169
Margulis, Lynn, 58–59
medicine. See also precision medicine
gap between biological knowledge and, 97–98
geriatric, vision of future, 176
mammalian-only, NCDs and, 168–169
personalized, 98
memory, microbe, self-defense and, 238–241
metabolites
breast milk providing, 55
controlling gene switches, 85–86, 93
detecting and analyzing, 180, 191, 197
exercise and, 270
fermented foods and, 264–265
fighting NCDs with, 177
food cravings and, 244–245
importance of, 189
microbiome balance/imbalance and, 70
neuroactive types, 246–252
microbes
ancient, examples and importance of, 57–59
antibiotics destroying, 5
Bacteroidetes and Firmicutes, 41, 42, 53, 245, 261, 270
billions in/on human body, 5, 41
diversity of, 230–234
dogs detecting, 192–194
of early humanoids, matching ours, 57–58
garden of, 42–45
groups of, influencing, 235–238
as human co-partner species, 6
memory and self-defense, 238–241
mood, anxiety and, 246–247
new biology emerging, 6
origins of humans and, 57–59
phyla of bacteria, 41
quorum sensing, 235–238
range of types/quantities in humans, 5, 41
site-specific variation of, 41–42
in space, 57
in wrong site, 42
microbiome. See also incompleteness of microbiome
affecting NCD status, 137–140
beauty of, 271–272
breathalyzer tests to evaluate, 176
depletion warning, 93–94
domains of species, 40–41
dysbiosis, 137–140, 215–220, 225–226
evaluations/analyses, 175–176, 179–180, 208–209
exercise and, 270–271
fit for mammalian self, 62–65
gatekeeping functions, 62–63, 93–94. See also immune system
geographic/cultural differences, 232–234
healthy humans and, 27–28
immunity and. See immune system
as “Medicine’s Next Frontier,” 172. See also precision medicine
as “missing organ,” 71–72
modifying. See fermented foods; prebiotics; probiotics; rebiosis; self-care
newborn baby partnership with, 56, 132
“normal,” 229–230
precision medicine and, 97–102
toxins, toxicology and, 60–62, 121–122, 237
urban living impacting, 58
microbiomics, vision of, 176
miso, 267–268
Missing Microbes (Blaser), 48, 118
mood, microbes and, 246–247, 261
mouth, microbiome of, 198–199
NCDs. See also immune system
babies and. See baby, newborn; birth delivery mode; cesarean section deliveries
causes of. See NCDs, causes of epidemic
celebrity cases, 170
changing microbiome for. See brain, microbes and; rebiosis; self-care
consequences of, 10
deaths, disabilities caused by, 9
disability challenges, 74
everyday impact of, 9–10
examples impacting daily life, 10–17
financial impact, 9
imbalanced ecological system causing, 8–9
immune system causing, 108–109, 113–114
impact and elusiveness of, 8–9
incompleteness of microbiome and, 70–72
indigenous people and, 231–232
list (partial) of, 137–138
managing microbiome to reduce NCDs, 120. See also fermented foods; microbiome; prebiotics; precision medicine; probiotics; rebiosis; self-care
microbiome status impacting, 137–140
from mother to child, 170–172
new challenges of, 7
patterns of. See disease, patterns of
pervasiveness of, 7–8, 104–105
social adaptations/fracturing and, 15–16, 76–78, 76–80
transferring to non-diseased recipient, 138–139
traveling under the radar, 104–105
NCDs, causes of epidemic, 141–169
about: overview of, 8–9, 141–142
antibiotic overreach, 142–148
birth delivery mode, 158–164
food revolution and diet, 148–152
mammalian-only human medicine, 168–169
misdirected human safety efforts, 164–168
from mother to child, 170–172
urbanization, 153–158
NCDs, four pillars of, 127–140
about: overview of, 127
early-life programming, 128–129
microbiome status affecting NCD status, 137–140
NCDs leading to more NCDs with age, 132–136
unhealthy inflammation, 129–132
neurotransmitters and neuromodulators, 245–249
norepinephrine, 268
Nurmi, Professor Esko, 222
obesity
air travel related problems, 13–14
coral destruction parallels, 40
C-section deliveries and, 15
cultural impact study, 231–232
depression and, 136
inflammation and, 125
microbiome and, 14–15, 44, 68–69, 137–140, 245
multiple (comorbid) NCDs and, 124–127
as one of many NCDs, 7, 13, 138
political and legal issues, 14
prevalence of, 13
risk factors and related diseases, 125–126
vaginal microbiome, 200–201
obsessive-compulsive disorder, probiotics for, 174–175
odors, from human microbiome. See also volatile organic compounds
electronic nose (E-nose) and, 201–202
flatulence, 194–195
foot microbiome, 198
mouth microbiome, 198–199
origins of, 198
penis microbiome, 201
scent detection and, 202–203
skin microbiome, 195–198
sources of, 194
urogenital microbiome, 199–201
oxidative damage, 129
paradigm shift, of medicine, 178. See also precision medicine; rebiosis
peanut allergies, 106–107, 108–109, 183
penis microbiome, 201
pets, infant antibodies and, 260
pets, rebiosis for, 222–226
poultry, antibiotics impacting, 144–148
poultry, rebiosis for, 222–225
prebiotics
antibiotics and, 174
benefits of, 269–270
for brain functioning, 249–252
foods acting as, 269
healthy choices, 260
importance of, 260
for infants, 251–252
past food supplies containing, 151
probiotics with (synbiotics), 213, 261
reducing inflammation, 260
skin microbiome and, 262
for stress resiliency, 250–251
tailoring to feed newly installed microbes, 176
vision of future use, 176
precision medicine, 170–186. See also rebiosis
about: overview of, 172
moving to superorganism medicine, 102, 178–180
as paradigm shift, 178
reality of, 177–178
redirecting, 97–102
treating patient as ecosystem, 172
vision of major shifts for, 173–178
pregnancy. See also baby, newborn; birth delivery mode; cesarean section deliveries
NCD epidemic and, 170–171
vision of future medicine for, 173
preventing disease, vision of future, 174
Prevotella, 200, 208, 233, 245
probiotics. See also fermented foods
about: overview of, 261–262
alone as therapeutic strategy, 182–183
alone vs. with diet change, 215–220, 258–259
bodily uses, 263
for brain functioning, 249–252
for cancer treatment, 175, 232
defined, 262
effectiveness of, 209–210
fecal microbial profile and, 213–214
fecal microbial transplant (FMT), 184–185, 260
for food cravings, 261
history of, 263
how they work, 210–211
as medical foods or supplements, 258–259
microbial diversity and, 230–234
for neurobehavioral conditions, 174–175
for obsessive-compulsive disorder, 174–175
options/choosing, 226–227, 258–259, 261–262
other medications and, 213
prebiotics with (synbiotics), 213, 261
for rebiosis, 209–211, 213–214
rebiosis targets, 214–215
resources for, 273–275
for skin microbiome, 262
source quality, 211
treatment examples, 182–183
vision of future use, 174–175
yogurt source effectiveness, 214, 250
quorum sensing, 235–238
rain forest microbiome model, 35–38
rebiosis, 205–227. See also brain, microbes and; fermented foods; prebiotics; probiotics; self-care
about: overview of superorganism makeover, 205–206; reset buttons and, 206
age and, 211–212
for animals/pets, 222–226
author’s personal experience, 216–220
benchmark for planning adjustments, 179–180
defined, 173
fecal microbial transplant (FMT), 184–185, 260
goal of, 180–181
IBS/gastrointestinal example, 216–220
isolated gut microbial chemicals for, 185–186
knowledge available for, 206–207
microbiome evaluations/analyses for, 175–176, 179–180, 208–209
possibilities of, 181
preventing disease with, 174
process options, 207–208
reasons for needing, 212–213
risk associated with, 220–221
tailoring treatments to adjust microbiome, 180–186
target locations, 214–215
ulcerative colitis example, 182
value of, 186
refrigeration, food transport/production and, 149–150
Relman, David, 32
risk, of rebiosis, 220–221
rural living, urban vs., 155, 157–158, 233
safety. See also toxins, humans and
government handling, 255–257
as microbiome priority, 253–257
misdirected efforts, 164–168
NCD epidemic and, 254–255
Salmonella, 198, 222, 223, 224–225
sauerkraut, 265–266
scents. See odors, from human microbiome; volatile organic compounds (VOCs)
self-care. See also fermented foods; prebiotics; probiotics; rebiosis
about: makeovers and, 205–206
enterotypes, microbial diversity and, 229–234
exercise for, 270–271
healthy choices, 257–261
influencing groups of microbes, 235–238
microbe memory, self-defense and, 238–241
“normal” microbiome and, 229–230
safety first, 253–257
taking ownership of, 228–229
The Selfish Gene (Dawkins), 23, 28–29
sinus infections, rebiosis helping, 216–218, 220
skin microbiome
copartners and odors, 195–198
mapping of, 197
microbe transfers from, 54
mosquito attraction and, 196–197
probiotics, prebiotics and, 262
as rebiosis target, 214–215
secreting glands and, 198
Staphylococcus aureus, 5, 55, 144, 236
stress, prebiotics for, 250–251
superorganism ecology, 31–45. See also human superorganism
commensals and, 33–34
coral reef model, 38–40
ecology defined, 31
garden of microbes, 40–45
losing microbial partners, 44–45
niche definitions and, 31–32
parasites and, 33
pop culture ecology and, 32–33
predominant species requirements and, 43
prevalence vs. importance of species, 43–44
rain forest model, 35–38
types of ecological interactions and, 33–34
weak links in health of, 42–45
superorganism makeover. See rebiosis
synbiotics, 213
taxonomy, 6–7
tempeh, 268
toxins, humans and. See also safety
benzene, 115
flame-retardant chemicals, 165
food emulsifiers, 167, 254–255
glyphosate, 256–257
government regulating, 255–257
gram-positive/gram-negative bacteria and, 121–122
natural toxins, 62
NCD epidemic and, 254–255
probiotics for, 210
safety first, 253–257
signals/biomarkers for, 237
what can kill us, 60–62
urbanization, impact on NCDs, 153–158, 233
urogenital microbiome, 199–201
vaginal birth. See baby, newborn; birth delivery mode
vaginal microbiome, 200–201, 262
Vetter, David, 73–74
viruses
antibiotics and, 143
bacterial spreading aided by, 82
epigenetics and, 93
immune system response, 112, 121, 132. See also immune system
microbe memory, self-defense and, 238–241
old view of treating, 2
rabies, 243
vaccines for (polio, etc.), 3–4, 26
volatile organic compounds (VOCs), 189–204. See also odors, from human microbiome
butyrate (butyric acid). See also butyrate
commercial value of, 190–191
defined, 190
dogs detecting, 192–194
evaluating microbiome with, 191
of farts, 190
functions of, 190
from humans, 189–190
industrial, 190
in perfumes, 190–191