The human gut microbiome: are we our enterotypes?

Blood groups, finger prints, iris scans and DNA bar codes are several ways to distinguish or identify individual humans. According to Arumugam and colleagues (2011) we can now also be distinguished by the microbial communities in our faeces, our ‘enterotypes’. The human gut is one of the most densely populated ecosystems known, and although this ecosystem contains members of the three domains of life – bacteria, archaea and eucarya (Finegold et al., 1983) – it is dominated by bacteria. They are essential in digesting the food we eat and in keeping us healthy by stimulating our immune system and fighting off pathogenic bacteria. It is estimated that 1013–1014 microbes inhabit our gastrointestinal tract (GIT), with the greatest number residing in the distal gut, where they synthesize essential vitamins and process otherwise indigestible components of our diet such as plant polysaccharides (Backhed et al., 2005). Early studies used 16S ribosomal DNA (rDNA) analysis to type and enumerate the distal gut and faecal microbiota. More than 90% of the bacterial phylotypes present in the intestinal microbiota in healthy humans are members of only three bacterial divisions: the Bacteroidetes, the Firmicutes and the Actinobacteria (Zoetendal et al., 2006). Nevertheless, each healthy adult's gut appears to have a unique and relatively stable microbiota (Zoetendal et al., 1998; Turnbaugh et al., 2007), which is a reflection of the numerous different phylogenetic clusters among the Firmicutes, Clostridium clusters IV, IX and XIVa, including the predominant genera Clostridium, Eubacterium, Roseburia and Ruminococcus. Furthermore, the Actinobacteria that encompass mainly the genera Bifidobacterium and Atopobium also represent important members of the gut microbial community (Harmsen et al., 2002; Turroni et al., 2008). Notably, recent estimates of the diversity of the human gut microbial ecosystem indicate it may encompass more than 1000 species and a multitude of strains (Backhed et al., 2005; Blaut and Clavel, 2007; Rajilic‐Stojanovic et al., 2007). Microbiota composition studies in humans have discovered that aberrations in the microbiome composition is present in obese individuals (Ley et al., 2006; Turnbaugh et al., 2009) as well as in individuals with a variety of other diseases (Zoetendal et al., 2008). Since the largest part (∼80%) of gut microbes remains uncultured, metagenomics analysis has become fashionable in the past 5 years to estimate the types, relative abundance and genome content of microbes in various parts of the GIT. The first metagenomics analysis from just two faecal samples (Gill et al., 2006) led to early insight into enrichment of genes encoding specific metabolic pathways, including metabolism associated with glycans, amino acids and xenobiotics, but also methanogenesis and biosynthesis of vitamins and isoprenoids. However, this early study provided only a very fragmented view due to limitations in sample size, sequencing technology, number of bases sequenced and availability of suitable reference genomes of gut inhabitants.