We are not alone in our body : a home to trillions of tiny friends and foes

Each one of us harbors ten times more microbial cells than our own human cells. These commensals (organisms that live with you) govern a range of functions in health, disease and our behaviour. Some of the functions they are involved in are food digestion, drug metabolism, regulating metabolic rate, immunity, memory, behavior and obesity. The human microbiome is the genetic make up of all these microbial colonisers in our bodies. This sea of microbes includes bacteria, fungi, viruses, archaea and protists. The genetic difference between any two of us is miniscule but the difference imparted by our microbial colonies can be vast. Due to its large impact in human health and survival, the National Institutes of Health (NIH) launched the Human Microbiome Project (HMP) in 2008 to characterize human microbiota and elucidate its role in health and disease. This project involved 300 scientists from over 80 organizations. Samples for their analysis came from both healthy and sick individuals and the data was made public link.

So, here begins my analysis:

There are 2906 different microorganisms found in the data which include 2873 bacteria, but only a few non-bacterial microbes that includes, 8 eukaryotes (fungi only enlisted here), 6 viruses and 2 archaea.

These enlisted 2906 microbes are distinctly found in 16 distinct human body sites, each one having its own specific home inside or on us. Each organ/body site with its microbes is like an ecosystem on its own, with microbial diversity varying from one another. As expected, our gut is home to a diversity of microbes where 742 different microbial species (among those listed in Human Microbiome Project) can be found. Over 25 feet long, our gut harbors around 100 trillion bacterial cells. It is considered to be one of the most ecologically rich and diverse habitats on the planet. Almost all of the health benefits we know of human microbiome comes from this population residing in our gut and thus more and more of the research is targeted towards gut microbiota. Unlike the gut, the liver and the lymph nodes show less diversity and density. Only pathogens, Fusobacterium necrophorum subsp. Funduliforme and Enterococcus faecalis TX4248 are reported to be present in the liver and the lymph nodes respectively.

Let us now consider location in the human body of the different domains – bacteria, archaea, eukarya. As expected from above, bacteria are present in all the 16 studied human body sites, with most presence in the gut while eukarya are present in blood, skin, unknown sites, wound and airways and archaea are present in gut and the location of viruses is mostly in unknown sites (I could not find any explanation of “unknown sites” beyond what the words already imply).

All living beings are named according to binomial nomenclature, which comprises two parts. The first is the name of the genus to which an organism belongs. In taxonomy, genus is a small group of closely related organisms. The second is specific name that is the organism’s species within the genus, this separates the species from the rest of the organisms belonging to the genus. For example the scientific name of human is Homo sapiens where Homo is the genus to which human belongs and sapiens identifies the human species within this genus.

According to the available HMP data, Staphylococcus is the most ubiquitous genus and is present in 11 of the studies body sites, followed by Streptococcus with it present in 10 sites. Most Staphylococcus species are harmless but some like Staphylococcus aureus, which reside on human skin, are opportunistic pathogens (that is, harms us when our body resistance is low) and cause skin infection, respiratory infection and food poisoning.

The data lists 242 different genus residing in or on the human body. Of these, Streptococcus is the most common genus with 268 listed species, followed by Staphylococcus with 260 species. Streptococcus includes both pathogenic and commensal (a long term symbiotic relationship with us) species. Some of the common diseases they are responsible for include pharyngitis, meningitis, pink eye, bacterial pneumonia.

Genus	No. of species
Streptococcus	268
Staphylococcus	260
Enterococcus	178
Corynebacterium	132
Propionibacterium	104
Lactobacillus	97
Clostridium	93
Prevotella	83
Bacteroides	73
Helicobacter	70

Human have 20500 genes and according to this data human harbor 4286967 additional microbial genes, which is 209 times more than our gene count. Streptomyces sp. HGB0020 with 8490 genes has maximum gene count among all the microbial colonizers.

The microbial mass in our body is about our brain’s mass. Just like any organ this also carries vital functions and hence according to many researchers, it is not wrong to call this as an additional organ. Also, it befalls on us to take care of this special organ by avoiding taking broad-spectrum antibiotics and eating a healthy diet.

The data and analysis can be found in my github repository