The standard cultural framing of the human body tends to treat it as a self-contained biological unit composed of cells that are, in some structural sense, all human. The framing is, on close examination, considerably less accurate than the wider register has been treating it as. The more accurate framing is that the human body is, more specifically, a particular kind of ecosystem in which human cells coexist with an enormous population of non-human organisms, and in which the non-human organisms are doing more of the operational work than the cultural register has been giving them credit for.

The most striking single fact is the cell count. Recent estimates place the ratio of microbial cells to human cells in the average adult body at approximately 38 trillion bacteria to 30 trillion human cells. The earlier figure of ten microbes to one human cell, widely circulated for decades, has been revised downward by careful contemporary measurements. Either way, the structural fact remains. Roughly half of the cells currently inside any given adult body are not, in any meaningful sense, that adult’s own. They are bacteria, fungi, archaea, and various other microorganisms that have, across millions of years of co-evolution, established themselves as permanent residents of the various ecological niches the body provides.

The combined genetic material of these organisms, sometimes called the metagenome, contains by various estimates 100 to 150 times as many genes as the human genome itself. The microorganisms are, in some real way, doing genetic work at a scale that dwarfs anything the human cells alone could perform.

What the microorganisms are actually doing

The most obvious function the microorganisms perform is digestion. The bacteria in the human gut break down a considerable fraction of food that the human digestive system, operating alone, would not be able to process. They produce enzymes the body does not produce on its own. They convert complex carbohydrates, fibers, and various plant materials into smaller molecules the body can then absorb. The microorganisms are, in some real way, the structural reason that the human diet can include the range of foods it currently does.

The microorganisms also produce, as byproducts of their metabolic activity, a wide range of molecules the body uses for purposes other than digestion. The molecules include vitamins, including significant portions of the body’s vitamin K and several B vitamins. The molecules include short-chain fatty acids, which the body uses for energy and for the maintenance of the intestinal lining. The molecules include various signaling compounds the immune system uses to calibrate its responses.

The microorganisms also occupy ecological niches that, if vacated, would be available for less helpful organisms to colonize. The competitive presence of the established microbiome is, in some real way, one of the structural defenses the body has against infection by pathogenic organisms.

What the gut-brain axis research has been finding

The emerging research, conducted across the last fifteen years, has been documenting something considerably more interesting than the digestive-helper framing. The microorganisms are, in addition to their digestive work, influencing aspects of human functioning that the wider register has not, on the available evidence, previously associated with the gut.

The most studied of these is the gut-brain axis, the bidirectional communication system between the gut microbiome and the central nervous system. Research published in Gastroenterology has documented that this communication operates through several pathways, including the vagus nerve, the immune system, and the production of neurotransmitters and neuroactive compounds by bacteria themselves. The communication is bidirectional. The brain influences the gut. The gut, more interestingly for current purposes, influences the brain.

The same research has documented a specific finding that gives the wider claim its empirical weight. The enteroendocrine cells of the gut contain more than 90 percent of the body’s serotonin, the neurotransmitter most strongly associated with mood regulation. The synthesis and release of serotonin in these cells is, on the available evidence, directly modulated by short-chain fatty acids and bile acids produced by spore-forming gut bacteria. The implication is structural. The bacteria are producing, or modulating, a significant fraction of the body’s supply of one of its most important mood-regulating compounds. The bacteria are doing this continuously, without the conscious mind being aware of it.

What the human studies have shown

The findings have been accumulating across the last decade. A 2019 review in Frontiers in Genetics summarized the published human studies on gut microbiota in mood disorders. The review documented that microbial diversity and taxonomic composition were significantly altered in patients with depression and bipolar disorder compared with healthy controls. Short-chain fatty acid-producing bacterial genera were consistently decreased in patients with depressive episodes, while pro-inflammatory genera were increased. Specific bacteria, including reduced abundance of Faecalibacterium and increased abundance of Actinobacteria and Enterobacteriaceae, were consistently associated with mood disorders across multiple studies.

The findings have implications that the wider research community has been careful about overstating. The correlations do not, on the available evidence, establish causation. The altered microbial composition in depression could, in principle, be a consequence of the depression rather than a cause of it. The wider research is still working out which direction the causation runs, in which cases, through which mechanisms.

What is clearer, on the available evidence, is that the gut microbiome and the central nervous system are in continuous biochemical communication, that the communication influences mood regulation through documented mechanisms involving serotonin, short-chain fatty acids, and inflammatory pathways, and that disruptions to the microbiome correlate reliably with disruptions to mental health outcomes. The specific decision-making research, which has documented potential microbial influence on food preferences and certain behavioral patterns, is at an earlier stage and remains more speculative. The mood and sleep findings are, by current standards of the field, reasonably well-established.

What this implies for how we think about ourselves

The structural implication of all this, on close examination, is that the standard cultural framing of the self as a unified human entity is, in some real way, simply not accurate. The self is, more accurately, an ecosystem. The ecosystem contains roughly equal numbers of human and non-human cells. The non-human cells are doing considerable amounts of the work the wider register has been attributing to the human cells alone. The non-human cells are influencing, by mechanisms still being mapped, aspects of human experience the wider register has been treating as purely human in origin.

The mood one is having on any given Tuesday is, on the available evidence, partly the product of the current state of the gut microbiome. The sleep one had last night was, in part, modulated by the same population. The food cravings that arrived at three in the afternoon may have, in part, originated in microbial signaling rather than in any feature of the conscious mind. The wider register has tended to treat all of these as features of the singular self. The accurate framing is that they are, more specifically, features of an ecosystem in which the singular self is one component among many.

This is not, on close examination, a diminishment of the human. The human is still the host. The human is the operating environment within which the microbiome conducts its activities. The human is also, however, in some real way, not the only agent in the system. The other agents are present. The other agents are influencing the outputs. The other agents have, by virtue of their numerical preponderance and their genetic diversity, considerably more biochemical resources at their disposal than the human cells alone would have.

The acknowledgment this article wants to leave

The human body is, by every available measure, less unitary than the wider cultural register has been treating it as. The body is, more accurately, a particular kind of ecosystem in which human cells coexist with a vast population of microorganisms whose collective activity influences digestion, immune function, mood, sleep, and possibly certain kinds of decision-making in ways the research community is only beginning to map.

The mapping is not, on the available evidence, complete. The findings have been accumulating quickly enough that the wider scientific consensus on what the microbiome is doing has been shifting noticeably across the last decade. The findings will, in all likelihood, continue to accumulate. The implications, when the mapping is more complete, will be considerable. They include, among other things, the recognition that the various features of inner experience the wider register has been attributing to purely human causes are, in many cases, partly the product of populations of organisms that the human is, in some real way, hosting rather than being.

The hosting has been going on for as long as the human species has existed. The hosting is, in some real way, what the human is. The acknowledgment is small. The acknowledgment is, on close examination, a structural revision of the standard self-understanding that the wider cultural register has not yet adequately absorbed. The absorbing is, modestly, what articles like this one are calibrated to begin.