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Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence.

Morton ER, Lynch J, Froment A, Lafosse S, Heyer E, Przeworski M, Blekhman R, Ségurel L - PLoS Genet. (2015)

Bottom Line: Characterizing the fecal microbiota of Pygmy hunter-gatherers as well as Bantu individuals from both farming and fishing populations in Southwest Cameroon, we found that the gut parasite Entamoeba is significantly correlated with microbiome composition and diversity.We show that across populations, colonization by this protozoa can be predicted with 79% accuracy based on the composition of an individual's gut microbiota, and that several of the taxa most important for distinguishing Entamoeba absence or presence are signature taxa for autoimmune disorders.We also found gut communities to vary significantly with subsistence mode, notably with some taxa previously shown to be enriched in other hunter-gatherers groups (in Tanzania and Peru) also discriminating hunter-gatherers from neighboring farming or fishing populations in Cameroon.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Cell Biology, and Development, Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, Minnesota, United States of America.

ABSTRACT
The human gut microbiota is impacted by host nutrition and health status and therefore represents a potentially adaptive phenotype influenced by metabolic and immune constraints. Previous studies contrasting rural populations in developing countries to urban industrialized ones have shown that industrialization is strongly correlated with patterns in human gut microbiota; however, we know little about the relative contribution of factors such as climate, diet, medicine, hygiene practices, host genetics, and parasitism. Here, we focus on fine-scale comparisons of African rural populations in order to (i) contrast the gut microbiota of populations inhabiting similar environments but having different traditional subsistence modes and either shared or distinct genetic ancestry, and (ii) examine the relationship between gut parasites and bacterial communities. Characterizing the fecal microbiota of Pygmy hunter-gatherers as well as Bantu individuals from both farming and fishing populations in Southwest Cameroon, we found that the gut parasite Entamoeba is significantly correlated with microbiome composition and diversity. We show that across populations, colonization by this protozoa can be predicted with 79% accuracy based on the composition of an individual's gut microbiota, and that several of the taxa most important for distinguishing Entamoeba absence or presence are signature taxa for autoimmune disorders. We also found gut communities to vary significantly with subsistence mode, notably with some taxa previously shown to be enriched in other hunter-gatherers groups (in Tanzania and Peru) also discriminating hunter-gatherers from neighboring farming or fishing populations in Cameroon.

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(a) Comparison of alpha diversity for Entamoeba negative (Ent-) and positive (Ent+) individuals using the phylogenetic distance whole tree metric.(b) Comparison of beta diversity within Ent-, within Ent+, and between Ent- and Ent+ individuals based on unweighted UniFrac distances. P-values are based on Welch’s t-test.
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pgen.1005658.g003: (a) Comparison of alpha diversity for Entamoeba negative (Ent-) and positive (Ent+) individuals using the phylogenetic distance whole tree metric.(b) Comparison of beta diversity within Ent-, within Ent+, and between Ent- and Ent+ individuals based on unweighted UniFrac distances. P-values are based on Welch’s t-test.

Mentions: Furthermore, when looking at the microbial diversity of Ent+ versus Ent- individuals, we found that the presence of Entamoeba is associated with a significant increase in alpha (intra-host) diversity using the Phylogenetic Distance Whole Tree metric (p = 1.03E-06; Welch’s t-test; Fig 3a), as well as using the Shannon and Simpson indices (p = 0.001 and p = 0.025, respectively; Welch’s t-test; S6 Fig). Interestingly, although the alpha (intra-host) diversity of Ent+ individuals is significantly higher than Ent- individuals, the beta (inter-host) diversity (as estimated by both UniFrac distance metrics) reveals that gut communities across Ent+ individuals are more similar than across Ent- individuals (weighted and unweighted, p = 2.23E-06 and p < 2.2E-16; Welch’s t-test; Fig 3b and S7 Fig). This could suggest that, as alpha diversity increases, there are fewer potential stable states for individual gut communities, or that the presence of Entamoeba drives changes in the microbiome (directly or indirectly through effects on the immune system) that are dominant over other factors.


Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence.

Morton ER, Lynch J, Froment A, Lafosse S, Heyer E, Przeworski M, Blekhman R, Ségurel L - PLoS Genet. (2015)

(a) Comparison of alpha diversity for Entamoeba negative (Ent-) and positive (Ent+) individuals using the phylogenetic distance whole tree metric.(b) Comparison of beta diversity within Ent-, within Ent+, and between Ent- and Ent+ individuals based on unweighted UniFrac distances. P-values are based on Welch’s t-test.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664238&req=5

pgen.1005658.g003: (a) Comparison of alpha diversity for Entamoeba negative (Ent-) and positive (Ent+) individuals using the phylogenetic distance whole tree metric.(b) Comparison of beta diversity within Ent-, within Ent+, and between Ent- and Ent+ individuals based on unweighted UniFrac distances. P-values are based on Welch’s t-test.
Mentions: Furthermore, when looking at the microbial diversity of Ent+ versus Ent- individuals, we found that the presence of Entamoeba is associated with a significant increase in alpha (intra-host) diversity using the Phylogenetic Distance Whole Tree metric (p = 1.03E-06; Welch’s t-test; Fig 3a), as well as using the Shannon and Simpson indices (p = 0.001 and p = 0.025, respectively; Welch’s t-test; S6 Fig). Interestingly, although the alpha (intra-host) diversity of Ent+ individuals is significantly higher than Ent- individuals, the beta (inter-host) diversity (as estimated by both UniFrac distance metrics) reveals that gut communities across Ent+ individuals are more similar than across Ent- individuals (weighted and unweighted, p = 2.23E-06 and p < 2.2E-16; Welch’s t-test; Fig 3b and S7 Fig). This could suggest that, as alpha diversity increases, there are fewer potential stable states for individual gut communities, or that the presence of Entamoeba drives changes in the microbiome (directly or indirectly through effects on the immune system) that are dominant over other factors.

Bottom Line: Characterizing the fecal microbiota of Pygmy hunter-gatherers as well as Bantu individuals from both farming and fishing populations in Southwest Cameroon, we found that the gut parasite Entamoeba is significantly correlated with microbiome composition and diversity.We show that across populations, colonization by this protozoa can be predicted with 79% accuracy based on the composition of an individual's gut microbiota, and that several of the taxa most important for distinguishing Entamoeba absence or presence are signature taxa for autoimmune disorders.We also found gut communities to vary significantly with subsistence mode, notably with some taxa previously shown to be enriched in other hunter-gatherers groups (in Tanzania and Peru) also discriminating hunter-gatherers from neighboring farming or fishing populations in Cameroon.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Cell Biology, and Development, Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, Minnesota, United States of America.

ABSTRACT
The human gut microbiota is impacted by host nutrition and health status and therefore represents a potentially adaptive phenotype influenced by metabolic and immune constraints. Previous studies contrasting rural populations in developing countries to urban industrialized ones have shown that industrialization is strongly correlated with patterns in human gut microbiota; however, we know little about the relative contribution of factors such as climate, diet, medicine, hygiene practices, host genetics, and parasitism. Here, we focus on fine-scale comparisons of African rural populations in order to (i) contrast the gut microbiota of populations inhabiting similar environments but having different traditional subsistence modes and either shared or distinct genetic ancestry, and (ii) examine the relationship between gut parasites and bacterial communities. Characterizing the fecal microbiota of Pygmy hunter-gatherers as well as Bantu individuals from both farming and fishing populations in Southwest Cameroon, we found that the gut parasite Entamoeba is significantly correlated with microbiome composition and diversity. We show that across populations, colonization by this protozoa can be predicted with 79% accuracy based on the composition of an individual's gut microbiota, and that several of the taxa most important for distinguishing Entamoeba absence or presence are signature taxa for autoimmune disorders. We also found gut communities to vary significantly with subsistence mode, notably with some taxa previously shown to be enriched in other hunter-gatherers groups (in Tanzania and Peru) also discriminating hunter-gatherers from neighboring farming or fishing populations in Cameroon.

Show MeSH
Related in: MedlinePlus