Gut bacteria
The gut microbiome explained in simple words
The gut microbiome is the community of bacteria, fungi and other microbes that live in your digestive tract, mostly in the large intestine. An adult carries roughly as many bacterial cells as human cells. These microbes digest fibre, make vitamins and other useful compounds, train the immune system and keep harmful organisms out. A healthy microbiome is varied and stable, and what you eat is the strongest influence on it that is within your control.
In short
- “Microbiome”, “microbiota” and “gut flora” are used for the same thing in everyday speech: the microbes that live in the gut.
- Most of them live in the large intestine and feed on the fibre you cannot digest.
- There is no single healthy microbiome. People in different parts of India carry different dominant bacteria, shaped by what they eat.
- Diet changes gut bacteria within days. A course of antibiotics can change them for months.
What is the gut microbiome?
Your digestive tract is home to several kinds of microbe:
- Bacteria, which make up most of the community
- Archaea, some of which make methane gas
- Fungi, mainly yeasts
- Viruses, most of which infect bacteria and not human cells
There are few microbes in the stomach, because of its acid. Their numbers rise along the small intestine and are highest in the large intestine.
Where gut microbes live. Most of them live in the large intestine and feed on the fibre you cannot digest.
An average adult carries about 38 trillion bacteria, roughly the same as the number of human cells in the body. Together they weigh about 200 grams.
Strictly, “microbiota” means the microbes and “microbiome” means the microbes together with their genes. “Gut flora” is the older word.
What do gut bacteria do?
They digest what you cannot
Gut bacteria ferment fibre into short-chain fatty acids. One of these, butyrate, is the main fuel of the cells that line the colon.
They make useful compounds
These include vitamin K and several B vitamins. They also process bile acids and plant compounds.
They train the immune system
A large share of the body’s immune cells sit in the gut wall. From birth, gut bacteria teach them what to attack and what to tolerate.
They keep harmful organisms out
Resident bacteria occupy the space and use up the nutrients, leaving little room for others.
They signal to the rest of the body
Through nerves, hormones and immune messengers, they influence the liver, metabolism and the brain. See the gut-brain axis explained.
What does a healthy microbiome look like?
A healthy gut community is:
- Varied: it contains many different kinds of bacteria
- Stable: it stays broadly the same from month to month
- Resilient: it recovers after a disturbance such as an infection
- Productive: it makes plenty of short-chain fatty acids from fibre
It does not have one fixed composition. In a study of 110 healthy Indian adults, people from north-central India, who ate a largely plant-based diet, carried mostly Prevotella. People from southern India, who ate a mixed diet, carried more Bacteroides, Ruminococcus and Faecalibacterium. Both groups were healthy. A second project sampled about 1,000 adults at 14 locations across India to map this variation.
For this reason, a “normal range” drawn from one population does not carry over neatly to another.
What shapes and changes the microbiome?
- Birth and early life: how a baby is born and fed, and antibiotics in infancy
- Diet: the strongest everyday influence. In one study, gut bacteria shifted within days of a change in diet.
- Antibiotics: after a short course, most bacteria return within one to two months. In one study, nine common species were still missing after six months.
- Other medicines: long-term acid-blockers are linked with lower diversity
- Gut infections
- Sleep, stress, physical activity and age
How do I know if my gut bacteria are out of balance?
No symptom proves it. Bloating, gas and a changed bowel habit that begin after antibiotics or a gut infection suggest it, but the same symptoms have many other causes.
An imbalance is called dysbiosis. It is a description, not a diagnosis. See gut dysbiosis and gut microbiome testing.
What helps the microbiome?
- A wide variety of plant foods, with fibre increased in steps
- Fermented foods such as curd and buttermilk
- Regular sleep and daily movement
- Antibiotics only when they are needed
See how to improve your gut microbiome and an Indian diet for the gut microbiome.
For those who want the longer version: my lecture on gut health, the microbiome and the gut lining.
When should I see a doctor?
See a doctor for bowel symptoms that last more than three to four weeks, and promptly for blood in the stool, weight loss, fever or symptoms that wake you at night. These need a diagnosis, not a gut-bacteria plan.
Questions patients ask me
What is the difference between gut microbiome, gut microbiota and gut flora?
In everyday use, none. Strictly, microbiota means the microbes themselves, and microbiome means the microbes together with their genes. Gut flora is an older term for the same community.
How many bacteria live in the gut?
About 38 trillion in an average adult, which is roughly the same as the number of human cells in the body.
What are some names of good gut bacteria?
Names that appear on reports include Bifidobacterium, Faecalibacterium, Roseburia and Akkermansia, which are linked with fibre fermentation and a healthy gut lining. No bacterium is good in every amount and setting. Variety and balance matter more than any single name.
Is the gut microbiome linked to immunity, weight and mood?
Yes, to all three, though for weight and mood most of the evidence shows association and not cause. See gut bacteria and body weight and the gut microbiome and mental health.
Sources
This page is written for patients and is based on the guidelines and studies below. It is for education and does not replace a consultation.
- Revised estimates of human and bacterial cell numbers in the body. Sender R et al. PLoS Biol. 2016. PubMed 27541692
- Review of the microbiota in immunity and inflammation. Belkaid Y, Hand TW. Cell. 2014. PubMed 24679531
- Multi-omics study of the Indian gut microbiome. Dhakan DB et al. Gigascience. 2019. PubMed 30698687
- Pan-India profile of the human gut microbiome. Dubey AK et al. Sci Data. 2018. PubMed 30375992
- Study of how quickly diet changes the gut microbiome. David LA et al. Nature. 2014. PubMed 24336217
- Study of gut bacteria recovery in healthy adults after antibiotics. Palleja A et al. Nat Microbiol. 2018. PubMed 30349083
- Study of acid-blocking medicines and the gut microbiome. Imhann F et al. Gut. 2016. PubMed 26657899
- Review of the microbiota-gut-brain axis. Cryan JF et al. Physiol Rev. 2019. PubMed 31460832