This collection of microbes that live on and in you is called your microbiota, and over 4600 different bacterial species have been identified in the human gut alone. Most gut bacteria have never been cultured in the laboratory and we only know them from the sequences of their genes, found in stool samples.
Where else do they live?
Different types of bacteria prefer different parts of the body and although scientists have been studying the specialised bacteria that live in their favoured body niche for many years, the advances of DNA sequence analysis has revolutionised our ability to identify the many thousands of bacteria you share your body with.
The vast majority of bacteria are totally harmless, and indeed many are beneficial; you can even find bacteria called cyanobacteria that live on your head and photosynthesise just like plants - so while most of us enjoy a sunny day, those bacteria particularly thrive!
Others live elsewhere - on your teeth, tongue, skin and feet, in your knee and elbow crevices, bellybutton, vagina, penis, ears, nose and armpits. But it is the bacterial community that lives in our gut that are studied most, due to their intimate relationship with the largest internal human organ - your intestines.
A delicate balance
Our microbiota is beneficial in many ways: the bacteria occupy space that might otherwise be occupied by pathogens, some of them digest material we’ve eaten in our diet that we can’t digest for ourselves, and others produce molecules, such as vitamin K and some of the B vitamins, that we need but can’t make ourselves. These bacteria are called commensals, meaning that they live happily alongside us without causing problems, or symbionts, meaning that there is mutual benefit for both host and bacteria. Only if their environment is upset, such as by a wound that disrupts the skin, do some bacteria move to where they’re not normally found (i.e. inside the body) and give rise to infections. Bacteria that can do this are called opportunistic pathogens. One particular problem are the descendants of naturally occurring bacteria that have acquired the genes to make them antibiotic-resistant meaning they can withstand antibiotic treatment, resulting in untreatable infections.
Where did you first meet?
Of course, your personal community of bacteria haven’t always been living in and on you. Human babies are born without a microbiota and are initially infected with their mother’s microbes during birth and subsequent close contact with the people and objects around them. Within a few days after birth, babies have already acquired many more microbes from their environment, and this process is vital for health: seeding the gut with a healthy microbiota can prevent blood poisoning in babies. This early exposure teaches the immune system to tolerate our commensal microbes. Indeed, medical intervention may affect the composition of the microbiota and has been linked to an increase in allergic and autoimmune diseases. Most of the colonisation of the infant’s gut takes place orally and this can occur because infants lack the stomach acid that would normally kill the bacteria, allowing them to pass through the stomach unharmed. You continue to collect bacteria through life, and your microbiota changes; even the gut microbiota in astronauts living in the relatively clean environment of the international space station changes in their new surroundings.
You can’t thrive without them
Life without the microbes in the gut would mean we would obtain far fewer nutrients from the plants we eat in our diet. Our own bodies lack the ability to digest the main components of plant cell walls. And while we do benefit from the undigested plant material, known as fibre or roughage, our microbiome includes a family of bacteria that can digest plant celluloses, allowing us to access plant cell contents and gain a higher nutritional value from plants. Alongside these bacteria are others that provide us with additional nutrients as they feed on food in our gut, including short-chain fatty acids, which can be used both by our own cells and by bacteria themselves as an energy source. The microbiota is also a source of a molecule called indolepropionic acid (IPA), which is a metabolite of the amino acid tryptophan. IPA has been shown to be a neuroprotective antioxidant and is currently being examined in clinical trials as a treatment for Alzheimer’s disease. Besides these known benefits of the microbiome, studies are finding strong associations between profiles of gut microbes and ill-health - and research is ongoing to try to discover the causative factors.
They’re essential for movement
The gut moves food along in a series of muscular contractions called peristalsis. Peristalsis works better if the muscles contract against a gut with bulky contents and a significant amount of this bulk comes from the mass of bacteria and undigested plant material. Faeces generally consist of roughage, with up to 50% of the dry mass being live bacteria and fragments of dead bacteria. The identity of the bacteria in faeces broadly reflects the microbiota but may be supplemented by ingested bacteria that can’t colonise the gut, and by transient pathogens.
And a discussion of gut bacteria isn’t complete without mention of those species that feed happily on our food, producing gas as by-products - mostly those gases that occur in normal air, but in some individuals, a particular type of gut bacteria means they also produce methane.
As we deposit our microbiota into the sewage system, they, along with the nutrients remaining in the faeces now join another ecosystem of new bacteria and other micro-organisms that exploit the nutrients available from the sewage. And where there are bacteria, there are the virus-like phages that infect them! Isolating phages from effluents taken from human sewage allows a route to finding those phages that can infect and destroy pathogens - and that someday might find their way back into your body as a therapy.