Individual gut microbiome is shaped by interactions with many environmental factors, which can be represented by their origins of geography. We reanalysed gut metagenome samples of healthy subjects and identified three distinct clusters of geography, (1) European countries, (2) non-westernized countries, and (3) other industrialized countries (i.e. China, Japan, and US). It is clearly suggesting that human gut microbiome can be uniquely determined by respective resident environment niche.
We also identified microbial species differentially enriched between westernized and non-westernized countries. For example, many Prevotella and Faecalibacterium spp. were highly enriched among non-westernized countries, whereas Bacteroides spp. and some Firmicutes, including Clostridium phoceensis, Anaerobutyricum hallii, and Anaerostipes hadrus, were highly enriched among westernized countries. Therefore, such clear distinctions suggest that our understanding of microbiome in health and disease needs to be in the scope of its own environmental niche, thereby necessitating the identification of “region-enriched” species of human gut microbiome.
To provide detailed enrichment of microbial species by geography, we performed comparative studies among healthy subjects from different countries and identified “region-enriched” species (i.e. MGS) by effect size 0.3 in more than six countries to compare. We found many non-westernized countries harbours a large number of unique sets of different region-enriched microbial species, whereas some industrialized countries, such as China, Japan, and US, harbours relatively fewer numbers of unique sets of region-enriched species. HGMA users can explore region-enriched species by countries by clicking the coloured countries of the World map on the top of the page and look into compositional and functional characteristics of respective species by clicking each species from the list of region-enriched species.