Introduction
You assume that your body belongs entirely to you. In reality, human cells account for only ten percent of the physical form you inhabit.
Your body is only ten percent human by cell count, and your health depends entirely on the trillion-strong microbial ecosystem inside your gut.
Alanna Collen explores how your internal microbes control digestion, immunity, and mental health. When modern lifestyles damage this delicate ecosystem, you face chronic illness, obesity, and immune dysfunction.
This book examines how your microbes shape your daily existence and traces the modern forces that destroy them. You will discover how to restore your internal ecosystem to regain health.
- How do microbes dictate your weight and mental state?
- Why do modern medical practices endanger your internal ecosystem?
- What steps can you take to repair your microbiome?
1. The Hidden Organ
Humans possess surprisingly few genes compared to simpler organisms. During the Human Genome Project, senior research scientist Lee Rowen won a sweepstake by guessing the human gene count would be much lower than prevailing high estimates. She successfully predicted fewer than 50,000 genes.
The final count revealed just shy of 21,000 human genes. This is roughly the same as a roundworm, half the size of a rice plant, and smaller than a water flea. Mice carry 23,000 genes, wheat plants carry 26,000 genes, the worm C. elegans carries 20,500 genes, and the water flea carries 31,000 genes.
Human complexity relies on the cooperative genome of our microbial passengers.
Senior research scientist Lee Rowen made a winning bet of 41,440 and later 25,947 genes in the Cold Spring Harbor Laboratory Genesweep pool.
Microbial Cell Ratio
The human body hosts approximately 100 trillion microbes. Microbial cells outnumber human cells by a ten to one ratio.
These microbes include single-celled bacteria, viruses, fungi such as yeasts, and archaea. Together, their collective genomes form the microbiome, including 4.4 million microbial genes in the human microbiome.
The Appendix Safehouse
Long dismissed as a vestigial organ by Charles Darwin, the vermiform appendix is actually packed with specialized immune cells. It forms a biofilm that preserves and cultivates beneficial gut microbes during severe gastrointestinal infections.
This safehouse allows the gut to repopulate its normal microbiota after dangerous infections like dysentery, cholera, or giardiasis. Appendices range from 2 cm to 25 cm in length. 5 to 10 per cent of people get appendicitis. In a British hospital, there were 113 cases per year by 1918 compared to 3 or 4 prior to 1890.
In the 1950s, appendectomies became so common that men had a 1 in 8 chance and women a 1 in 4 chance of having their appendix removed during their lifetime.
2. The Rise of Twenty-First-Century Illnesses
As infectious diseases declined in the West, chronic conditions like allergies, obesity, and autism surged due to systemic changes in our environment.
Four major medical and public health innovations in the nineteenth and twentieth centuries doubled human life expectancy. Average global life expectancy rose from 31 years in 1900 to 66 years in 2005. These innovations defeated pathogens and transformed society from a two-generation to a four- or five-generation society.
Public Health History
Ignaz Semmelweis discovered that strict hand-washing with chlorinated lime drastically reduced childbed fever mortality in maternity wards. He stopped doctors from carrying fatal matter from autopsies to patients. Before germ theory, doctors operated under the incorrect theory of miasma. 32 per cent of women giving birth in hospital would subsequently die by the 1840s.
Jakob Kolletschka died of childbed fever after being accidentally cut by a student's scalpel during an autopsy. This event led Semmelweis to realize doctors were carrying death from the morgue to the maternity ward.
- Wash hands in a solution of chlorinated lime between conducting autopsies and examining patients
John Snow founded modern epidemiology by mapping cholera cases during an outbreak in London. He traced the source to a single contaminated water pump. During the Soho outbreak, a cholera sufferer could produce 20 litres of watery fluid per day.
During the 1854 Soho cholera outbreak, Snow realized victims had all drunk from the Broad Street pump. A group of monks who drank only beer made from the water remained completely unaffected.
- Ask three epidemiological questions: (1) Where are these diseases occurring? (2) Who are they affecting? and (3) When did they become a problem?
Demographics of Modern Sickness
As infectious diseases declined in the developed world, a new group of chronic twenty-first-century illnesses surged dramatically. These included allergies, autoimmune diseases, obesity, digestive disorders, and mental health conditions. By 1999, 30 per cent of American adults were classified as obese, and 20 per cent of children suffered from hay fever or eczema.
Twenty-first-century illnesses disproportionately strike the young, the privileged, and women with strong immune systems. Overall, 1 in 68 children are on the autistic spectrum, and 1 in 42 boys are affected.
Children of Somali immigrants who moved to Sweden or Toronto experienced autism rates three to four times higher than those in their home country. This proved that location and environment matter far more than race.
3. All Diseases Begin in the Gut
Human societies have undergone a rapid collective weight gain over the last sixty years. You cannot explain this trend through gluttony and sloth alone. Approximately one in three adults on Earth is overweight and one in nine is obese. On the island of Nauru, around 70 per cent of adults are obese and a further 23 per cent are overweight, making it the fattest nation on Earth.
Gut microbes extract calories, regulate metabolism, and influence weight gain far more than genetics or basal metabolic rates.
The Warbler Effect
Migratory garden warblers experience massive weight fluctuations that defy simple calculations of caloric intake and expenditure. Juvenile garden warblers double their weight from 17 g to 37 g in just a couple of weeks before migration without consuming enough extra food to account for it. Captive birds do the same without migrating.
Microbial Calorie Extraction
Gut microbes determine how many calories an animal extracts from its food. Experiments by Fredrik Bäckhed and Peter Turnbaugh showed that germ-free mice colonized with microbiota from obese subjects gained significantly more weight despite eating the same amount of food. Peter Turnbaugh showed that mice colonized with an obese microbiota extracted 2 per cent more calories from their food, gaining weight without eating extra.
The gut bacterium Akkermansia muciniphila supports the protective mucus layer of the gut and correlates inversely with human obesity. Patrice Cani found that supplementing mice with Akkermansia lowered lipopolysaccharide levels, restored healthy fat cell formation, and reduced weight. Gastric bypass surgery alters the gut microbiota into a lean phenotype, increasing Akkermansia populations by 10,000 times.
4. The Gut-Brain Axis
Gut bacteria communicate directly with the brain, altering stress responses, mood, and potentially triggering neurological disorders like autism.
Natural selection favors microbes that manipulate hosts because these behavioral changes help the microbe spread to new hosts or complete its life cycle. Trematode worm larvae burrow into tadpole limb buds, causing extra legs to grow. This makes the deformed frogs easy prey for herons, allowing the parasites to enter the bird's digestive tract.
Microbial Behavior Manipulation
The gut-brain-microbiota connection plays a vital role in regulating the brain's response to stress, particularly during early-life development. In 2004, Nobuyuki Sudo and Yoichi Chida conducted an experiment comparing germ-free mice to mice with normal gut microbes. Germ-free mice produced stress hormone concentrations twice as high as normal mice when placed in a tube.
Colonizing them with even a single bacterial species, Bifidobacterium infantis, prevented this overreaction if done early enough. The parasite Toxoplasma gondii alters human personality traits, increases risk-taking, and is associated with various psychiatric conditions. Studies in Prague and Turkey found that drivers involved in road traffic accidents were three to four times more likely to be infected with Toxoplasma than control groups.
Probiotics and Mood
Ingesting beneficial bacteria can improve mood and reduce anxiety by protecting blood tryptophan levels and stimulating the vagus nerve. A French clinical trial gave fifty-five healthy volunteers a daily bar containing two strains of live bacteria or a placebo, finding that those who received the live bacteria scored happier, less anxious, and less angry.
Disruption of the gut microbiome via antibiotics can potentially trigger regressive-onset autism by allowing neurotoxin-producing bacteria to proliferate. Ellen Bolte researched medical literature as a computer programmer, hypothesized a gut-brain link for her son Andrew's autism, and eventually convinced pediatric gastroenterologist Dr. Richard Sandler to conduct an antibiotic trial that temporarily improved Andrew's symptoms. Dr. Derrick MacFabe injected minute quantities of propionate into the spinal fluid of rats, the animals immediately began spinning on the spot, running in circles, and ignoring cage-mates.
5. Immunity and the Old Friends Hypothesis
David Strachan analyzed health data from over 17,000 British children born in a single week in March 1958 and tracked them until age twenty-three. Only children were far more likely to suffer from hay fever compared to those with three or four siblings.
Modern immune dysfunction arises from a lack of beneficial microbes that train the immune system and induce regulatory T cells.
This hygiene hypothesis proposed that allergies stem from a lack of early childhood infections. Professor Agnes Wold subsequently proposed the Old Friends hypothesis in 1998 after observing that babies in high-allergy countries like Sweden had lower gut microbial diversity than babies in Pakistan.
The Hygiene Hypothesis
Beneficial microbes promote the creation of regulatory T cells, or T regs, which exert a calming influence over pro-inflammatory immune cells. Without these microbial trainers, your immune system overreacts to harmless substances.
Early childhood antibiotic use disrupts microbial composition and correlates with an increased risk of developing asthma, eczema, and hay fever. Researchers at the University of Bristol utilized the Children of the 90s project tracking children born to 14,000 pregnant women in the early nineties. Infants given antibiotics before age two had nearly double the risk of developing asthma by age eight.
Microbial Signalling
Professor Sarkis Mazmanian at the California Institute of Technology discovered the mechanism of polysaccharide A produced by Bacteroides fragilis. Specific commensal bacteria produce molecular passwords like polysaccharide A, or PSA, that actively suppress inflammation and calibrate your immune response.
These capsules are engulfed by immune cells in the large intestine, triggering the activation of T regs. When the gut microbiota falls out of balance, the immune system triggers the release of zonulin, a protein that loosens intestinal tight junctions and creates a leaky gut. Alessio Fasano at the Massachusetts General Hospital for Children discovered zonulin and its role in coeliac disease and Type 1 diabetes.
6. Collateral Damage from Antibiotics
Widespread antibiotic overuse and agricultural growth promoters decimate beneficial gut bacteria and trigger long-term chronic illness.
In the late 1940s, scientists discovered that small daily doses of antibiotics boost the growth of chickens, cattle, pigs, sheep, and turkeys by up to 50 percent. This subtherapeutic antibiotic therapy allows animals to reach slaughter weight faster and enables denser crowding. Farmers in the US and post-war public demand drove the widespread adoption of these methods to produce cheaper meat. Today, 70 per cent of America's antibiotics are used in livestock. Without growth promoters, farming would require 452 million extra chickens, 23 million cattle, and 12 million pigs.
Antibiotics are heavily overprescribed and widely consumed in developed nations, often unnecessarily for viral infections like colds and flu. The average British woman takes 70 courses of antibiotics in her lifetime, while the average man takes 50 courses. In 1998, 55 per cent of antibiotic prescriptions given in the US were unnecessary.
Broad-spectrum antibiotics cause collateral damage by destroying beneficial gut bacteria, leading to antibiotic resistance and opportunistic infections like Clostridium difficile. In the seventy years since penicillin, scientists have developed 20 additional classes of antibiotics. Clostridium difficile infections caused nearly 4,000 deaths in England in 2007 after patients were treated with antibiotics that decimated their normal gut microbiota.
Livestock Growth
Martin Blaser's research demonstrated that giving low doses of penicillin to mice disrupted their microbiota, altered metabolic hormones, and significantly increased fat mass. This effect amplified when combined with a high-fat diet. Female mice on penicillin and a high-fat diet gained 10 g of fat mass, compared to 5 g on a high-fat diet alone. French researchers found that heart valve patients treated with vancomycin and gentamycin gained excess weight and harbored high levels of the vancomycin-resistant bacterium Lactobacillus reuteri. Forty per cent of overweight children were given antibiotics in the first six months, versus 13 per cent of normal weight children.
Microbiota Recovery
A short course of broad-spectrum antibiotics can permanently or long-term alter the composition and diversity of your gut microbiota. Five days of ciprofloxacin causes a profound rapid impact. Swedish researchers tracked volunteers given a seven-day course of clindamycin and found that Bacteroides species failed to return to their original composition two years after treatment ended.
7. Diet and the Forgotten Organ
Traditional plant-rich diets feed beneficial gut microbes with dietary fibre, producing short-chain fatty acids that maintain intestinal integrity.
As populations shifted toward processed, low-fibre foods, beneficial bacteria like Akkermansia muciniphila lost their nourishment. This caused a thinning of the protective gut mucus layer and induced gut permeability. Bacterial molecules like lipopolysaccharide then entered the bloodstream to provoke chronic inflammation.
Ancestral Diets
Children in the rural village of Boulpon in Burkina Faso consume diets high in millet, sorghum, and vegetables. Their gut microbiotas are dominated by Bacteroidetes, specifically Prevotella and Xylanibacter.
Italian children eat under 2 per cent of their diet as fibre compared to over 6.5 per cent for children in Boulpon. Children in urban Florence eating a Western diet lack these beneficial genera entirely and exhibit microbiotas dominated by Firmicutes.
Rising rates of food sensitivities to gluten and lactose stem from microbiome dysbiosis and immune system overreaction. About 95 per cent of North and West Europeans can tolerate milk as adults because of rapidly evolved lactase persistence genes.
Microbial Signalling
When microbes break down dietary fibre in the large intestine, they release short-chain fatty acids like acetate, propionate, and butyrate. These compounds bind to G-Protein-coupled Receptor 43 on immune cells to signal them not to attack.
Specific species like Faecalibacterium prausnitzii, Roseburia intestinalis, and Eubacterium rectale convert smaller molecules into butyrate when fed with high-fibre diets. Butyrate turns up the volume on genes producing intestinal protein chains, plugging leaks and halting inflammation.
Patrice Cani demonstrated that supplementing high-fat diets with oligofructose or arabinoxylan in mice increased bifidobacteria and boosted Akkermansia abundance up to eightyfold.
8. From the Very First Breath
Passing a microbial community to offspring is a near-universal evolutionary ritual that enhances infant survival and digestive abilities. Stinkbug mothers smear the surface of their eggs with bacteria-laden faeces, and Kudzu bug mothers leave a bacteria-filled package near their eggs for the hatching nymphs to consume.
Maternal microbial inheritance through vaginal birth and breast milk oligosaccharides shapes the infant immune system for life.
Vaginal Birth Inoculation
The journey through the birth canal coats the newborn in maternal vaginal and faecal microbes, which act as specialized pioneers for digestion and pathogen defense. Babes delivered by C-section miss out on these maternal vaginal microbes and instead acquire skin microbes from their environment, correlating with increased risks of immune and metabolic disorders. In a study of young adult Brazilians, 15 per cent of those born by C-section were obese compared with 10 per cent of those born vaginally.
Rob Knight and Maria Gloria Dominguez-Bello initiated clinical trials where maternal vaginal microbes are transferred to C-section babies via gauze to normalize their developing gut microbiotas. You can follow their experimental protocol:
- Insert a small piece of gauze into the mother's vagina an hour before she goes into the operating theatre.
- Remove the gauze just before the first cut and place it in a sterile pot.
- Rub the newborn baby with the gauze first in its mouth, then across its face, and then over the remainder of its body.
Breast-milk Oligosaccharides
Human breast milk contains around 130 different kinds of oligosaccharides that humans lack enzymes to digest. These specialized complex carbohydrates bypass digestion to exclusively feed beneficial gut bacteria and block pathogens. Formula-feeding leads to higher microbial diversity in infants, including dangerous pathogens like Clostridium difficile, and increases the risks of various childhood diseases. While only one-fifth of exclusively breast-fed babies carry C. diff, nearly four-fifths of babies put straight onto formula carry the pathogen.
9. Microbial Restoration
Faecal microbiota transplantation and high-fibre diets can successfully repair damaged gut ecosystems and reverse chronic disease.
Antibiotics disrupt beneficial gut microbes, allowing Clostridium difficile to rampage through the intestine like a weed. A third of gut bacteria and many pathogens can form spores, packaging themselves in a thick protective layer that resists antibacterial cleaners, stomach acids, antibiotics, and temperature extremes.
Peggy Kan Hai suffered from severe C. diff infections and lost 20 percent of her body weight after receiving antibiotics and surgery for a necrotic foot. She experienced 30 episodes of diarrhoea a day. In America alone, a single year saw 30,000 deaths from C. diff infection.
Faecal Transplants
Faecal microbiota transplantation transfers stool from a healthy donor into a patient's gut, achieving high cure rates for recurrent C. diff infections and reversing metabolic syndrome symptoms. Professor Tom Borody's clinic carried out 5,000 transplants. Treating C. diff with a single faecal transplant has an 80 per cent cure rate, rising over 95 per cent with a second.
You can perform the procedure using these steps:
- Take stool from a healthy donor
- Mix stool with some saline
- Whisk the mixture in a kitchen blender
- Squit the suspension into the large intestine via a colonoscope
Organizations like OpenBiome pay $40 per stool donation and quiz 50 applicants to find a single eligible donor. They supply frozen samples to hospitals. Meanwhile, researchers created synthetic mixtures such as RePOOPulate containing 33 bacterial strains.
Modernizing Restoration
An individual can actively reshape and improve their gut microbiota diversity and specific beneficial bacterial populations by increasing daily fibre intake. The author increased her daily fibre intake from about 15 grams to around 60 grams. Her previous breakfast contained 2 grams of fibre, while her new breakfast contained 16 grams.
You can rebuild your forgotten organ with these dietary actions:
- Mix rolled oats, wheat, and barley with nuts, seeds, fresh berries, live unsweetened natural yogurt, and milk for breakfast
- Add a side of beans and a portion of mushrooms to meals, substitute white rice with brown rice, and replace pasta with lentils
- Add a quick bowl of microwaved frozen peas or steamed spinach to lunch
Society must treat antibiotics with the same caution as cancer chemotherapy. You can protect your microbiome and future health through deliberate personal and medical choices:
- Reserve Caesarean sections for mothers and babies who really need them, and let nature take its course with those who don't
- Create a birth plan that includes providing your baby with the seeds of a healthy microbiota by giving birth vaginally
- Adopt vaginal-swabbing techniques if a C-section is unavoidable
- Stock up on knowledge, support, and determination ahead of time to breast-feed
- Consider waiting a day or two to see if your illness gets better using common sense
- Ask the doctor how sure they are that the infection is bacterial, not viral
- Ask if antibiotics are likely to make you significantly better or help you recover significantly faster
- Ask what the risks are of not taking antibiotics and allowing your immune system to fight the infection itself
10 Key Ideas
- Human complexity relies on the cooperative genome of our microbial passengers rather than our surprisingly low count of just under 21,000 human genes.
- As infectious diseases declined in the West, chronic conditions like allergies, obesity, and autism surged due to systemic changes in our environment.
- Gut microbes extract calories, regulate metabolism, and influence weight gain far more than genetics or basal metabolic rates.
- Gut bacteria communicate directly with the brain, altering stress responses, mood, and potentially triggering neurological disorders like autism.
- Modern immune dysfunction arises from a lack of beneficial microbes that train the immune system and induce regulatory T cells.
- Widespread antibiotic overuse and agricultural growth promoters decimate beneficial gut bacteria and trigger long-term chronic illness.
- Traditional plant-rich diets feed beneficial gut microbes with dietary fibre, producing short-chain fatty acids that maintain intestinal integrity.
- Maternal microbial inheritance through vaginal birth and breast milk oligosaccharides shapes the infant immune system for life.
- Faecal microbiota transplantation and high-fibre diets can successfully repair damaged gut ecosystems and reverse chronic disease.
- Society must treat antibiotics with the same caution as cancer chemotherapy to protect our microbiome and future health through deliberate choices.