(Illustration by Bryan Christie)

In 2007, the National Institutes of Health initiated the Human Microbiome Project, which is pursuing a census of all of the microorganisms that normally live in and on the human body.

According to their findings, 90% of the cells in the human body are bacterial, fungal, or otherwise non-human.

Most of these nonhuman cells live in the digestive tract, but they have also been found throughout our bodies and they differ widely.  For example, the left and right hands have their own distinct biota, and the microbiomes of men and women differ.

This distribution of microorganisms suggests that humans should start thinking of themselves as ecosystems as well as discrete individuals.

Only a fraction of the human microbiota has been identified.  There are millions of genes in our “extended genome”compared to the nearly 23,000 in the human genome.  We have just begun to understand the how bacteria work to perpetuate their own survival and also how they support or detract from our survival.



Metagenomics is a new approach which looks at how whole communities of bacteria develop and interact by taking a sample from the environment, pooling the DNA from all the different species present, fracturing it into a mixture of relatively short fragments and then sequencing the lot.

Metagenomics, bacteria rapidly and frequently share their DNA with other bacteria – even distantly related bacteria – through a process called horizontal gene transfer, a kind of microscopic “file sharing.”  This means that, essentially, there is no such thing as a single microbial species.  More novel organisms are created through genetic recombination than through mutation.

Valerie Brown, in an article in the Pacific Standard, suggests that the micro-biosphere is much more like a web, with information of all kinds, including genes, traveling in all directions simultaneously.

Bacterial Communication

And bacteria don’t just get together for “file sharing.”  There are many examples of coordinated action, such as “swarming,” in which a colony of bacteria moves as a unit across a surface, and the development of “fruiting bodies,” in which bacteria come together to form inert spores as a means of surviving severe environmental conditions. Group behavior has now been demonstrated so widely that many microbiologists view bacteria as multicellular organisms, much of whose activity — from gene swapping to swarming to biofilm construction — is mediated by a wide variety of chemical communications.

Bacteria use chemicals to talk to each other and to non-bacterial cells as well.  According to Herbert Levine, of the University of California, San Diego’s Center for Theoretical Biological Physics, in Trends in Microbiology bacteria “maintain linguistic communication,” enabling them to engage in intentional behavior both singly and in groups. In other words, they have “social intelligence.”


Some bacteria have been identified pretty clearly as beneficial and it is possible to buy and take supplements that provide infusions of these organisms, often referred to as “probiotics.”

What we eat feeds all of our micro-organisms, not just the ones with our human DNA.  In a sense, our human cells function a little bit like farmers inside us helping to guide the growth of the crops of microorganisms that we want and need, while weeding out the ones that are not beneficial

Just as we need to get much better at tending the larger ecology that we live in, so we need to get better at tending the smaller ecology that lives in us.