The Inhabited Body book cover — a human silhouette composed of microbial organisms

The Inhabited Body

The Science of Our Microbial Selves

Dr Horst Herb

You have never been alone. From the moment of your birth, trillions of bacteria, fungi, viruses, and archaea have colonised every surface of your body. They train your immune system, digest your food, manufacture vitamins your own cells cannot produce, and communicate with your brain through chemical signals that influence your mood, your appetite, and possibly even your behaviour.

Your body is not just yours — it is an ecosystem, inhabited by a vast microbial community that shapes your health, your mood, and possibly even who you are.

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Volume 1 — The Other Us

The human microbiome is one of the most important discoveries in modern biology — not because these organisms are new, but because we have only recently developed the tools to see them and begin to understand what they are doing. And what they are doing turns out to be far more consequential than anyone suspected.

Meeting the Microbiome The real numbers, the myth of the "10:1 ratio," and why you are roughly half-microbe by cell count.
Built Together How viruses gave us the placenta, how a transposon built the immune system, and why 8% of your DNA is viral.
Your First Inheritance The birth canal, breastmilk, the first thousand days — how your microbiome is assembled across a lifetime.
Tools of Discovery From Petri dishes to shotgun metagenomics, gnotobiotic mice, and the AI tools we now need to make sense of what we are seeing.
The Body's Ecosystems The gut, the skin, the lungs, the mouth, the urogenital tract, the mycobiome, and the controversial brain microbiome.
The Immune Negotiation How microbes train the immune system from birth — and what happens when that lifelong dialogue breaks down.
The Gut–Brain Axis Microbial neurotransmitters, the vagus nerve, and the uncomfortable question of who is really in control.
Behavioural Modulation Can microbes shape food cravings, social behaviour, even the contours of free will? What the evidence supports, and what it does not.
Metabolism & Hormones Bile acids, the estrobolome, thyroid function, and the discovery that your microbes keep their own circadian clock.
The Viral Dimension The viral shield hidden in your mucus, and the eight per cent of your DNA you inherited from ancient infections.
Bacteriophages The most abundant biological entities on the planet — viruses that hunt bacteria — and the tripartite relationship between phages, bacteria, and you.

Written for a general readership with no specialist background required, the book follows the science wherever it leads — including the places where we are getting it wrong.

The Inhabited Body Volume 2 cover — a human silhouette dispersing into particles

Coming Next

When the Partnership Breaks

Volume 2 — Feeding, Fixing, and Fighting Your Microbiome

Everything we have mapped in Volume 1 is under assault. The ecosystem that evolved over hundreds of millions of years of host–microbe co-adaptation is being reshaped, in the span of a few generations, by forces it never encountered in its evolutionary history. Broad-spectrum antibiotics that carpet-bomb bacterial communities with the precision of a sledgehammer. Industrialised diets stripped of the complex fibres that feed the microbes we depend on. Caesarean sections and formula feeding that alter the founding communities a child acquires at birth. Environmental chemicals, food additives, and non-antibiotic drugs that disrupt microbial ecosystems in ways we are only beginning to catalogue.

Volume 2 begins with the damage — the collateral devastation of antibiotic therapy, the extinctions, the opportunistic blooms, the loss of colonisation resistance. Then it turns to the alternatives: phage therapy, the century-old idea whose time may finally have come. Diet, examined not through the lens of fad and marketing, but through the evidence for how specific nutrients feed specific microbial communities. Probiotics — the most commercially successful microbiome intervention and, as you will discover, one of the most poorly understood. Faecal microbiota transplantation — radical, unglamorous, and remarkably effective. And precision microbiome engineering — the frontier where synthetic biology meets ecology.

Volume 2 also confronts the diseases that microbiome disruption appears to drive or worsen: inflammatory bowel disease, metabolic syndrome, cancer — where the microbiome can determine whether immunotherapy succeeds or fails — and the neurological and psychiatric conditions where the gut–brain axis becomes clinically consequential. And it closes by asking the questions the science forces us to ask but cannot, by itself, answer. If the microbiome is part of who you are, what does it mean to alter it? If your microbes influence your mood, your appetite, and your behaviour, what happens to our concept of individual autonomy?

Antibiotics: Collateral Damage Why every antibiotic course is an ecological event, what is lost in the rubble, and what may not return.
Phage Therapy: The Comeback The century-old idea, written off by the antibiotic era, that may be returning just as antibiotics begin to fail.
Diet: Feeding the Ecosystem Fibre, fermentation, and the evidence behind the dietary advice that actually works — and the marketing that does not.
The Other Levers Sleep, exercise, stress, environment — the non-dietary factors that reshape your microbiome more than any pill.
Drugs Beyond Antibiotics Metformin, antidepressants, antacids — the medications that affect your microbes when no one was looking.
Probiotics: Promise, Hype, Hard Truths The most commercially successful microbiome intervention, and why the evidence rarely matches the marketing.
Faecal Microbiota Transplantation The unglamorous, remarkably effective therapy that cures most cases of recurrent C. difficile — and the regulatory tangle now reshaping it.
Precision Microbiome Engineering Defined consortia, engineered live bacteria, and the synthetic biology of the next generation of therapeutics.
Inflammatory & Autoimmune Disease Crohn's, ulcerative colitis, and the dysbiosis hypothesis — what the microbiome explains, and what it still cannot.
Metabolic Disease & Obesity Personalised glycaemic responses, the obesity-microbiota link, and the science behind tailored nutrition.
Cancer How specific bacteria promote some tumours, and how others determine whether modern immunotherapy will work at all.
Neurological & Psychiatric Disease Parkinson's, Alzheimer's, depression — where the gut–brain axis becomes clinically consequential and where it has been oversold.
The Microbiome as a Diagnostic Tool Stool tests, microbial biomarkers, and the gap between what the research can do and what the clinic actually offers.
Ethical, Social & Philosophical Questions Whose data, whose body, whose access, whose rules? The questions science forces us to ask but cannot answer alone.
Where Do We Go From Here? The next decade of microbiome research — and what it means to live well with our microbial selves.

The ecosystem is mapped. The players are introduced. Volume 2 is the story of what we do next.

Science Primer

New to biology? The companion primer covers the fundamentals — cells, DNA, viruses, fungi, and the tools scientists use to study what they can't see — in plain language, with no prerequisites.

Read the Primer
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