An Overview

The surfaces of human intestinal mucosa and the adjacent lumenal contents are home to hundreds of billions of symbiotic microbes. While these organisms include members from all biological domains (Archaea, Bacteria and Eukarya, plus viruses), bacteria are the most abundant (up to 10¹¹ cells per gram), diverse (100 - >1000 species per healthy person) and functionally consequential to the human host. It is estimated that humans contain as many commensal bacterial cells as their own cells (Sender2016). The intricate interplay between the microbiome and host, and between the microorganisms themselves, has led to the belief the entire biological system as a whole is greater than the sum of its parts; in other words the system (human + bugs) could be described as a 'superorganism'.

The superorganism concept is probably best illustrated when considering the diversity of genes the biological system has access to. The collective variety of metabolic proteins produced by the microbiome far exceeds that of the host and this allows the system to adapt to changes in diet. This adaptive foraging approach tends to stabilise the microbiome ecosystem (Sonnenburg2005).

The microbiome plays an important role in supporting gut function. Microbes provide essential nutrients for the body and fuel for epithelial cells by metabolising glycoconjugates that would otherwise be excreted (Backhed2005, Johansson2011). The healthy microbiome also helps 'educate' the immune system early in life and continually supports the hosts ability to resist pathogenic bacteria that cause disease.

Individual species that reside in the gut tend to come from four major bacterial phyla, namely the Bacteroidetes (19%), Firmicutes (55%), Actinobacteria (10%) and Proteobacteria (12%), although individual bacteria from Verrucomicrobia (Akkermansia muciniphila), Desulfobacterota (Bilophila wadsworthia), Synergistetes, Fusobacteria and the Archaea Domain make important contributions as well (Table 1).

Table 1. A breakdown of the microbiome phyla found in the gut. Data is taken from the Pu.biome database and are somewhat subjective in terms of colonising propensity. Note, data represents organism occurrence, not abundance.

Species occurrence does not necessarily correspond to abundance: the Bacteroidetes/Firmicutes ratio, for example, can often be around parity, depending on the human population tested (Magne2020). In absolute numbers it has been found that individual Bacteroides species can typically reach the highest abundance levels (10¹¹ cells / gram). In 1991, Cummings and colleagues quantified the dominant taxa in human faeces and found Bacteroides were 5-10 times more prevalent than any other genus (Table 2), despite many taxa having undergone taxonomic revision since then (Cummings1991).

Table 2. Dominant taxa of the human gastrointestinal tract (from Cummings1991). Note that many species within these taxa have been reassigned to new families or genera. For example, many Peptostreptococcus strains have been reassigned to Anaerococcus, Finegoldia, Megasphaera, Parvimonas, Peptoniphilus and Slackia genera.

The Microbiome Tables

The microbiome tables are intended to help readers quickly filter the data associated with over 2600 organisms. An explanation about how best to use them can be found here. The tables focus on attributes that are related and a summary of the topics covered is outlined here. Each link under Microbes (left navigation) takes the reader to a summary page, with a glossary of terms and other information. From there, links to the relevant tables are provided above this information. The list below outlines the microbiome tables currently available (Table 3).

Table 3. A list of tables and the topics they cover.