Table 1.
Geographical/racial variations in gut microbiome composition and diversity.
| S. No. | Populations studied | Diet/life-style/mode of subsistence | Important observations | Proposed dominating factors | References | ||
|---|---|---|---|---|---|---|---|
| Differential composition of GM (phylum/genus/family levels) | Predicted enrichment of genes/pathways | Any other pertaining remarks | |||||
| 1 | a) Native Africans (NAs) | Higher dietary intakes of animal proteins, fat and low fiber by AAs than NAs | a) Dominance of Prevotella and butyrate-producing groups | a) Genes for hydrogen sulfide production, saccharolytic fermentation, butyrogenesis and methanogenesis | Higher risk of colon cancer in AAs | Diet | O'Keefe et al., 2007; Ou et al., 2013 |
| b) African Americans (AAs) | b) Higher abundance of Bacteroides | b) Genes for secondary bile acid production | |||||
| 2 | a) Children of Burkina Faso (BF) from a rural African village | a) Diet: low in fat and animal protein, rich in starch, fiber, and plant polysaccharides, predominantly vegetarian | a) Higher abundance of Actinobacteria and Bacteroidetes, exclusive presence of Prevotella, Xylanibacter, Butyrivibrio, and Treponema | a) Genes for cellulose, xylan hydrolysis and short-chain fatty acids | Higher microbial richness and biodiversity in BF samples than in EU samples | Diet | De Filippo et al., 2010 |
| b) European children (EU) | b) Typical western diet high in animal protein, sugar, starch, and fat and low in fiber | b) Higher abundance of Firmicutes, Proteobacteria, and Enterobacteriaceae (Shigella and Escherichia) | |||||
| 3 | a) The Hadza—a hunter- gatherer community of Tanzania, Africa | a) Ancient foraging subsistence Diet: Game meat, honey, baobab, berries and tubers | a) Enriched in Succinivibrio sp. Ruminobacter, Spirochaetes (Treponema), Prevotella, unclassified Bacteroidetes, Firmicutes, Proteobacteria, and Clostridiales | a) Propionate producers | Higher levels of microbial richness and biodiversity in the Hadza than in Italian urban controls | Diet, Sex, Foraging vs. Western lifestyle | Schnorr et al., 2014 |
| b) Urban Italian adults from Bologna, Italy | b) Western life-style Diet: plant foods, fresh fruit, pasta, bread olive oil; dairy, poultry, fish, and red meat | b) Higher abundance of Bifidobacterium, Firmicutes (Blautia, Ruminococcus, and Faecalibacterium) | b) Butyrate producers | ||||
| 4. | a) Amerindian population of Venezuela | a) Ancient subsistence Diet: corn, cassava | a) High abundance of Prevotella and Enterococcaceae | 460 ECs including those involved in glutamate synthase, alpha-amylase etc. are enriched in non-US populations (a & b) 433 ECs including those involved in vitamin biosynthesis, xenobiotics metabolism, sugar catabolism, bile salt metabolism etc. are enriched in US population 445 ECs are differentially present in Malawian and Amerindian adults Higher representation of Urease (EC3.5.1.5) genes in (a & b) | Significant similarity of the gut microbiome among family members across life-style | Host genetics, age, food habits, geography, differential exposure to pets and livestock etc. | Yatsunenko et al., 2012 |
| b) Rural Malawian communities | b) Rural agricultural subsistence Diet: maize, fruits, vegetables, ground nut flour etc. | b) High abundance of Prevotella | |||||
| c) US metropolitan city dwellers | c) Western, urban, industrialized life-style, protein-rich diet | c) Enriched in Bacteroides 56 species-level OTUs are differentially present in Malawian and Amerindian adults 73 OTUs (23 for Prevotella) are over represented in non-US adults (a & b) | |||||
| 5. | a) The Matses from the Peruvian Amazon | a) Isolated hunter-gatherer community Diet: tubers, invasive plantains, fish, game meat | a) Higher abundance of Succinovibrio, Treponema, Cyanobacteria, Tenericutes, Prevotella, Firmicutes (Clostridium, Catenibacterium, Eubacterium, Lachnospira etc.), Proteobacteria, Spirochaetes and Euryarchaeota | 78 KEGG ortholog groups (KOs), mostly associated with metabolism and genetic information processing and 79 ECs (some involved in Tricarboxylic acid cycle) are enriched in Traditional groups (a & b). 20 KOs, mostly associated with membrane transport, and 12 ECs (3 related to Vitamin B1 and B12 biosynthesis) are enriched in urban population (c). | Higher microbial diversity in the Matses and Tunapuco populations than in the Norman population. | Dietary regimes and life-style | Obregon-Tito et al., 2015 |
| b) Tunapuco populations from the Andean highlands | b) Traditional agriculturalist group Diet: local agricultural products, homegrown small animals | b) Higher abundance of Succinovibrio, Treponema, Prevotella, Bacteroidetes, Proteobacteria and Spirochaetes. | |||||
| c) Residents of Norman, Oklahoma, US. | c) Urban-industrialized Western society Diet: canned fruits and vegetables, bread, dairy products, prepackaged western meals | c) Enriched in Actinobacteria (Bifidobacterium), Bacteroides and Firmicutes (Ruminococcus, Blautia, Dorea) | |||||
| 6. | a) Pygmy hunter-gatherers | a) Ancient foraging subsistence Diet: cassava, nuts occasional game meat | a) Higher frequencies of Proteobacteria, especially of Succinivibrio and Salmonella, depleted in Lachnospiraceae family | Only one pathway associated with bacterial invasion of epithelial cells, has been reported to differ significantly across all subsistence types, with the highest relative abundance in the hunter-gatherers and lowest in the farmers | Significant correlation of the microbiome diversity and composition with presence of the gut protozoa Entamoeba and the mode of subsistence | Parasitic load, dietary regime, subsistence mode | Morton et al., 2015 |
| b) Bantu farming populations | b) Rural agricultural subsistence Diet: locally grown cereals, vegetables, meat | b) Higher abundance of Firmicutes, especially of Ruminococcus, Treponema | |||||
| c) Bantu fishing populations All three populations were from Southwest Cameroon, Africa | c) Fishing population Diet: cassava, fish, meat, yogurt | c) Enriched in Bifidobacteria, Bacteroidales, depleted in Ruminococcus | |||||
| 7. | a) BaAka pygmies from the Central African Republic. | a) Ancient hunter-gatherer subsistence, no exposure to antibiotics or modern therapeutics Diet: wild game, fish, fibrous leaves, nuts and fruits. | a) High abundance of Prevotella, Clostridiaceae and Treponema, depleted in Bacteroidales | a) 14 pathways including those involved in pathogenicity, peptidoglycan biosynthesis, purine/pyrimidine metabolism etc. Increased abundance of virulence, amino acid, lipid and vitamin metabolism pathways | A gradual change in the microbial profiles from the BaAka → the Bantu → US Americans—consistent with their degree of traditional lifestyle | Diet, life-style, parasitic load, exposure to modern therapeutics | Gomez et al., 2016 |
| b) Bantu population from the Central African Republic. | b) Intermediate abundance of Prevotella, Clostridiaceae, and Treponema, relatively enriched in Rickenellaceae and Bacteroides. Bantu gut microbiome is dominated by Firmicutes | b) Traditional agriculturist group, partial exposure to western life-style and modern therapeutics Diet: flour-like products, goat meat | b) 22 pathways including transporters, secretion system, signal transduction mechanism etc. Increased abundance of carbohydrate and xenobiotics metabolism pathways | ||||
| c) US Americans (from HMP project) | c) Highly enriched in Rickenellaceae and Bacteroides | c) Typical modern western life-style and diet | c) 36 pathways including carbohydrate metabolism, xenobiotics metabolism, amino/nucleotide sugar metabolism etc. | ||||
EC, Enzyme commission numbers.