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Portrait of The human microbiome

Science · Medicine & the body

The human microbiome

Term coined 2001

Medicine — microbial ecology of the human body

The community of bacteria, archaea, fungi and viruses that live in and on the human body, together with their collective genes. Most of it lives in the large intestine, weighs around 200 grams in total, and contributes several million genes to a host that has only about twenty thousand of its own. Its residents ferment fibre the body cannot digest, make vitamin K and several B vitamins, crowd out invading pathogens and help train the developing immune system. The long-repeated claim that microbial cells outnumber human ones ten to one was revised in 2016 to a ratio closer to one to one.

How to spot them

  • ▸Roughly 38 trillion bacterial cells against about 30 trillion human ones — not ten to one
  • ▸Joshua Lederberg popularised the word in 2001
  • ▸The NIH's cataloguing project was launched in 2007
  • ▸Gut communities are dominated by Bacillota (Firmicutes) and Bacteroidota (Bacteroidetes)
  • ▸Faecal transplantation is its best-established clinical application

Key facts

Roughly 38 trillion bacterial cells set against about 30 trillion human ones (2016)

Sender, Fuchs and Milo's revised estimate, published in PLOS Biology

The long-repeated claim that we are outnumbered ten to one, corrected in 2016 (2016)

The old figure traced back to a back-of-envelope estimate from 1972

Joshua Lederberg's coinage of 2001 for the ecological community sharing our body space (2001)

He wanted a word for the organisms and their genes together

The NIH Common Fund project launched in 2007 to catalogue it, reporting in 2012 (2007)

The Human Microbiome Project, which sequenced samples from hundreds of healthy volunteers

Faecal transplantation for recurrent Clostridioides difficile infection

Restoring a wrecked gut community, with cure rates conventional antibiotics cannot match

About 200 grams of organisms, the great majority of them in the colon

Roughly the weight of an orange, and a few million genes

Its members manufacture vitamin K and several B vitamins on our behalf

A genuinely symbiotic contribution, alongside the fermentation of fibre

The vagus nerve, short-chain fatty acids and the axis linking the gut to mood

The gut–brain axis, the most speculative area of the field

Key ideas

  • It is better thought of as an extra organ than as passengers: it performs metabolic work the human genome simply cannot encode, above all the fermentation of dietary fibre into short-chain fatty acids such as butyrate.
  • Distinguish the microbiota, meaning the organisms themselves, from the microbiome, which strictly means the organisms plus their collective genetic material — though the words are often used interchangeably.
  • Colonisation resistance matters clinically: a healthy community physically and chemically excludes invaders, which is why wiping it out with broad-spectrum antibiotics opens the door to Clostridioides difficile.

Quick-fire facts

  • •Sender, Fuchs and Milo estimated in 2016 that a reference adult carries about 3.8 × 10^13 bacteria and about 3.0 × 10^13 human cells, a ratio near 1.3 to 1
  • •Most human cells by number are red blood cells, which lack nuclei
  • •The total mass of the bacteria is roughly 0.2 kg, most of it in the colon
  • •Joshua Lederberg popularised the term in 2001
  • •The NIH Human Microbiome Project began in 2007 and published its first major survey of healthy adults in 2012
  • •The collective microbial gene catalogue runs to millions of genes, against roughly 20,000 human protein-coding genes
  • •The dominant gut phyla are Bacillota (formerly Firmicutes) and Bacteroidota (formerly Bacteroidetes)
  • •Gut bacteria ferment indigestible fibre into short-chain fatty acids — acetate, propionate and butyrate — and synthesise vitamin K and B vitamins including folate and biotin
  • •Faecal microbiota transplantation is an established treatment for recurrent Clostridioides difficile infection
  • •Distinct communities occupy the gut, skin, mouth, nose and vagina; colonisation begins at birth and differs between vaginal and caesarean delivery
  • •Barry Marshall and Robin Warren won the 2005 Nobel Prize for showing that Helicobacter pylori causes peptic ulcers; Marshall drank a culture to prove it
  • •David Strachan proposed the hygiene hypothesis in 1989, linking reduced early microbial exposure to rising allergy

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