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Human gut microbiome viewed across age and geography.

Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI - Nature (2012)

Bottom Line: Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism.These distinctive features are evident in early infancy as well as adulthood.Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.

View Article: PubMed Central - PubMed

Affiliation: Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA.

ABSTRACT
Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.

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Differences in the functional profiles of fecal microbiomes in the three study populationsExamples of KEGG ECs that exhibited the largest differences, as determined by Random Forests and ShotgunFuntionalizeR analyses, in proportional representation between USA and Malawian/Amerindian populations. Shown are the relative abundances of genes encoding the indicated ECs (normalized by Z-score across all datasets). (a) UPGMA clustering of 10 USA, 10 Malawian and 6 Amerindian baby fecal microbiomes. (b) UPGMA clustering of 16 USA, 5 Malawian and 5 Amerindian adult fecal microbiomes.
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Figure 3: Differences in the functional profiles of fecal microbiomes in the three study populationsExamples of KEGG ECs that exhibited the largest differences, as determined by Random Forests and ShotgunFuntionalizeR analyses, in proportional representation between USA and Malawian/Amerindian populations. Shown are the relative abundances of genes encoding the indicated ECs (normalized by Z-score across all datasets). (a) UPGMA clustering of 10 USA, 10 Malawian and 6 Amerindian baby fecal microbiomes. (b) UPGMA clustering of 16 USA, 5 Malawian and 5 Amerindian adult fecal microbiomes.

Mentions: ShotgunFunctionalizeR, Random Forests and Spearman rank correlation analyses were all used to compare EC representation in fecal microbiomes as a function of predefined categories of geographic location and age. 476 ECs were identified as being significantly different in the USA versus Malawian and Amerindian breast-fed babies (p<0.0001, ShotgunFunctionalizeR; Table S8). The most prominent differences involved pathways related to vitamin biosynthesis and carbohydrate metabolism. Malawian and Amerindian babies had higher representation of ECs that were components of the vitamin B2 (riboflavin) biosynthetic pathway (Figs. 3a, S18). These differences were not evident in adults (Table S7). Riboflavin is found in human milk and in meat and dairy products. We did not measure the levels of these vitamins in mothers and in their breast milk in the sampled populations, although it is tempting to speculate the observed differences in baby microbiomes may represent an adaptive response to vitamin availability.


Human gut microbiome viewed across age and geography.

Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI - Nature (2012)

Differences in the functional profiles of fecal microbiomes in the three study populationsExamples of KEGG ECs that exhibited the largest differences, as determined by Random Forests and ShotgunFuntionalizeR analyses, in proportional representation between USA and Malawian/Amerindian populations. Shown are the relative abundances of genes encoding the indicated ECs (normalized by Z-score across all datasets). (a) UPGMA clustering of 10 USA, 10 Malawian and 6 Amerindian baby fecal microbiomes. (b) UPGMA clustering of 16 USA, 5 Malawian and 5 Amerindian adult fecal microbiomes.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3376388&req=5

Figure 3: Differences in the functional profiles of fecal microbiomes in the three study populationsExamples of KEGG ECs that exhibited the largest differences, as determined by Random Forests and ShotgunFuntionalizeR analyses, in proportional representation between USA and Malawian/Amerindian populations. Shown are the relative abundances of genes encoding the indicated ECs (normalized by Z-score across all datasets). (a) UPGMA clustering of 10 USA, 10 Malawian and 6 Amerindian baby fecal microbiomes. (b) UPGMA clustering of 16 USA, 5 Malawian and 5 Amerindian adult fecal microbiomes.
Mentions: ShotgunFunctionalizeR, Random Forests and Spearman rank correlation analyses were all used to compare EC representation in fecal microbiomes as a function of predefined categories of geographic location and age. 476 ECs were identified as being significantly different in the USA versus Malawian and Amerindian breast-fed babies (p<0.0001, ShotgunFunctionalizeR; Table S8). The most prominent differences involved pathways related to vitamin biosynthesis and carbohydrate metabolism. Malawian and Amerindian babies had higher representation of ECs that were components of the vitamin B2 (riboflavin) biosynthetic pathway (Figs. 3a, S18). These differences were not evident in adults (Table S7). Riboflavin is found in human milk and in meat and dairy products. We did not measure the levels of these vitamins in mothers and in their breast milk in the sampled populations, although it is tempting to speculate the observed differences in baby microbiomes may represent an adaptive response to vitamin availability.

Bottom Line: Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism.These distinctive features are evident in early infancy as well as adulthood.Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.

View Article: PubMed Central - PubMed

Affiliation: Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA.

ABSTRACT
Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.

Show MeSH