Metagenomic Analysis of the Human Distal Gut Microbiome

The gut microbiome is the collective genome of all microorganisms, which live in the human intestine. It consist of aproximately 10-100 trillion symbiotic microbial cells. In comparison to the human genome, the gut microbiome is at least 100 times larger. These microbes mostly inhabit the distal gut. They help humans process otherwise indigestible nutritiens and synthesize essential amino acids and vitamins. Although host-associated microbes are mostly acquired from the environment, the composition of the bacterial communities in the human gut is very different to the one of free-living microbial communitites. The vertebrate gut is an extreme environment. This suggest that the coevolution of vertebrates and their bacterial communities selected those, which are capable of surviving the unfavorable gut environment. The presence of bacteria in the human gut is therefore tightly regulated and up to date only two bacterial divisions present were described: the Bacteroidetes and Firmicutes and one methanogenic archaeon: Methanobrevibacter smithii.
==History==
First interest in the diversity of the human microbiome appeared in the 1680s, when Antonie va Leewenhoek compared his oral and fecal microbiota and found a significant difference.  ==Methods/ Tools for microbial analysis:==
===shotgun characterization of total DNA:===
===16s ribosomal RNA:===
rRNA is shared by every organism, by comparing its sequence, relationships between various organisms can be established. It is therefore used for creation of evolution trees.
===UniFrac:===
Method for comparing the differences between microbial communities. This algorithm measures the proportion of shared branch lengths on a phylogenetic tree between sampes (Ursell et al., 2012). When microbial communitites are highly similar, the result UniFrac scores are near 0, on the other hand bacterial communities that do not share any branch length - are therefore completely independent acquire a UniFrac score of 1. UniFrac has an ability to distinguish differeces between communities by utilizing only 10 sequence per sample.
==Human gut microbiome across age and geography==
The human gut microbiome represents one source of human genetic and metabolic diversity. The diversity among the microbiome of individuals is extereme, when compared to the genomic variation: whereas individuals are from 99,9% identical to one another in their genome, their microbiome can be from 80-90% different (Ursell et al, 2012). An individual's microbiota is therefore a highly variable and compartmentalized ecosystem. To inverstigate whether the human gut microbiome varies across age, Yutsunenko et al., 2012, collected bacterial V4 16S rRNA from 326 individuals of age 0-17 and 202 adults aged 18-70 years.These sequences were identified by UniFrac - a method measuring similarity among bacterial communities. They discovered, that after the a three-year period after birth, the phylogenetic composition of bacterial communities started to evolve towards a adult-like type. Also, differences between the composition of these bacterial communities were bigger among children than among adults. In addition to this, Yutsunenko et al. also discovered that the fecal microbiota varies significantly between different countries.
==Interactions between human microbes and the environment==
==Role of the gut microbiome in digestion and nutrition==