Composition of the Gut Microbiota

Composition of the Gut Microbiota

It is estimated that up to 80% of the bacteria in the human gut cannot be cultivated by conventional techniques, largely because of their fastidious nutrient and anaerobic requirements and their complex dependence on one another.

Molecular techniques have significantly advanced our understanding of the constituent members of the human microbiome and have largely supplanted cultivation-based techniques for study of the gut microbiome.

The most diverse and abundant microbial communities generally occur in the oral cavity and distal GI tract and have been the focus of most studies, because they are most amenable to sampling. However, the relatively simple indigenous microbiota of the human esophagus, stomach, and small bowel are relatively unstudied, and these niches present the added challenge of trying to discern allochthonous bacteria (“passersby” from upstream niches that are likely irrelevant) from autochthonous microbes (representing stable, functionally relevant community “residents”). The oral cavity contains members of the phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria, which account for 99% of all phyla present.

It has been estimated that the microbes in our bodies collectively make up to 100 trillion cells, tenfold the number of human cells, and suggested that they encode 100-fold more unique genes than our own genome. The majority of microbes reside in the gut, have a profound influence on human physiology and nutrition, and are crucial for human life

the gut microbes contribute to energy harvest from food, and changes of gut microbiome may be associated with bowel diseases or obesity

Essentially all (99.1%) of the genes of our catalogue are of bacterial origin, the remainder being mostly archaeal, with only 0.1% of eukaryotic and viral origins.

To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, ~150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.