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Field guide · Fig. 1–5

Microbes 101

Trillions of microbes live in your gut. Here’s who they are, what they eat and make, and what researchers are still working out.

Fig. 1 · Who’s in there

A crowd you carry

Most of them live in your large intestine. Nearly all are bacteria; archaea are a small minority, and fungi a tiny fraction. No two guts hold quite the same mix.

  • ~38 trillion bacteria in an adult, almost all in the gut, against about 30 trillion of your own cells. Sender, Fuchs & Milo 2016 · PLoS Biol
  • 2,435species found in human guts, that you can look up here, each with its own page. Counted from our data · live
  • 9in 10 healthy people carry Faecalibacterium prausnitzii, one of the most common. Our analysis of GMrepo data · live
Fig. 2 · What they eat and make

Lunch for trillions

Much of what you eat is digested before it reaches them. What isn’t, mostly fiber, becomes their food, and what one microbe leaves, another eats.

WHAT REACHES THEMFiber and sugarsfrom plantsFrom yougut mucus, bileProteinthat escapes digestionGROUPS THAT BREAK IT DOWNFiber and sugar breakersMucus foragersBile acid freersProtein fermentersWHAT THEY LEAVEAcetate, lactate, succinateHydrogenFreed bile acidsIndoles, ammoniaGROUPS THAT USE THOSEButyrate makersPropionate makersHydrogen usersBile acid reshapersVitamin makersfound in many groupsLEFT FOR YOUButyratefuel for your colon’s liningPropionateMethane and other gasesSecondary bile acidsB vitamins, vitamin Ksome of it
A group of microbes. What their genomes can do, not what they’re doing in you.
See every metabolite and microbe →
Fig. 3 · Six to know

Six to know

Each one does a job you can see in its genes or in a lab, and each has its own page with everything we hold about it.

  • Bacillota
    Makes butyrate

    Faecalibacterium prausnitzii

    Makes butyrate, the main fuel for the cells lining your colon.

    • Lab-tested Makes butyrate when grown in a lab, taking up acetate as it grows (Duncan 2002).
    • Our analysis of GMrepo data Fewer people with Crohn’s disease carry it.
    Meet it →
  • Verrucomicrobiota
    Eats gut mucus

    Akkermansia muciniphila

    Eats mucin, the gel your gut lining makes.

    • Lab-tested Grows on mucin as its only source of carbon and nitrogen (Derrien 2004).
    • Tested in a trial In a 3-month pilot trial, insulin sensitivity (HOMA) was 29% higher on the pasteurised bacterium than on placebo (32 adults finished; Depommier 2019).
    • In a dish Early work: a protein on its surface signals to immune cells and tightened a layer of gut cells (Ottman 2017).
    • Seen in people Less of it in gut biopsies from people with Crohn’s or colitis than from people without (66 people; Png 2010).
    Meet it →
  • Pseudomonadota
    Makes vitamin K

    Escherichia coli

    A famous name, and mostly an ordinary resident. Some types cause diarrhoeal illness.

    • Lab-tested Genetic work in E. coli mapped how it makes menaquinone, a form of vitamin K (Young 1975).
    • Lab-tested Grows with or without oxygen.
    Meet it →
  • Actinomycetota
    First foods

    Bifidobacterium longum subsp. infantis

    Can break down the sugars in breast milk that babies can’t digest.

    • Genome analysis Carries a cluster of genes for breaking down breast-milk sugars (Sela 2008).
    • Seen in people In 903 children followed from 3 months old, Bifidobacterium was more common while they were getting breast milk (Stewart 2018).
    Meet it →
  • Actinomycetota
    Changes a medicine

    Eggerthella lenta

    Some strains turn digoxin, a heart medicine, into a form the body can’t use.

    • In a dish Strains with the cgr genes do it; strains without them don’t (Haiser 2013; Koppel 2018).
    • In animals In mice, more protein in the diet went with less of the drug changed (Haiser 2013).
    Meet it →
  • Bacillota
    Eats lactate

    Veillonella atypica

    Turns lactate, which builds up in hard exercise, into propionate.

    • Seen in people In 15 runners sampled around the 2015 Boston Marathon, Veillonella made up more of their stool bacteria after the race (Scheiman 2019).
    • In animals Mice given a strain from one of the runners ran about 13% longer on a treadmill before tiring (32 mice; Scheiman 2019).
    Meet it →
Fig. 4 · How to read what we show

Good or bad? It depends

Every fact on Probiome carries a tag. Here’s what each one means, so you can tell a finding from a hunch.

How far it’s been tested From an idea at the top to a trial in people at the bottom.
  • Proposed An idea from the authors or a review. Nothing tested yet.
  • In a dish Cells or microbes grown in a lab.
  • In animals Usually mice, often with human microbes.
  • Seen in people Found in people, alongside something else. An association, not a cause.
  • Tested in a trial People were given it and compared with people who weren’t.
What a microbe can do Facts about the microbe itself, not about you.
  • Genome analysis What its genes say it can do. Not what it’s doing in your gut.
  • Lab-tested Checked when it was grown in a lab: its shape, whether it needs oxygen.
  • Our analysis of GMrepo data Our own count across public gut samples: how many people carry it.
  • No good or bad microbes The same microbe can be a quiet regular in one gut and a problem in another, depending on the strain, what else lives there and what you eat.
  • “Can make” isn’t “makes” What a microbe’s genome can do and what it does in your gut aren’t the same. How much it makes depends on its neighbours and your food.
  • More common isn’t a cause When a microbe is more or less common in people with a condition, that’s an association. It doesn’t say which came first.
Fig. 5 · Where next

Keep exploring

Sources Sender 2016 · Hillman 2017 · Duncan 2002 · Belenguer 2006 · Roediger 1980 · Derrien 2004 · Depommier 2019 · Ottman 2017 · Png 2010 · Young 1975 · Kaper 2004 · Sela 2008 · Stewart 2018 · Haiser 2013 · Koppel 2018 · Scheiman 2019