Limits...
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.

Show MeSH

Related in: MedlinePlus

Normalized relative abundance of KEGG metabolic pathways significantly associated with Entamoeba status in an ANOVA (q < 0.05 using the most abundant; ≤ 0.4% in at least one group) (left panel) and the relative contributions of each taxon for each pathway (right panel).
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4664238&req=5

pgen.1005658.g004: Normalized relative abundance of KEGG metabolic pathways significantly associated with Entamoeba status in an ANOVA (q < 0.05 using the most abundant; ≤ 0.4% in at least one group) (left panel) and the relative contributions of each taxon for each pathway (right panel).

Mentions: We used the KEGG (Kyoto Encyclopedia of Genes and Genomes) database [49] and the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) pipeline [50] to predict abundances of pathways across individuals (see S9 Fig). Many of these pathways are classified based on eukaryotic genes. However, homologues in prokaryotes could have related functions. Considering the 220 most abundant KEGG pathways (comprising ≥ 0.01% of all assigned reads in at least 4 individuals), we identified 19 pathways with significant differences in abundance between Ent+ and Ent- individuals (FDR q < 0.05 after Benjamini-Hochberg correction for the number of pathways tested; ANOVA; see Fig 4 and S6 Table). Of these 19, of particular interest are an increase in amoebiasis (q = 0.001), biosynthesis of the antibiotic tetracycline (q = 0.03), and yeast MAPK signaling pathways (q = 0.01) in Ent+ individuals. These changes are largely attributed to Clostridiales and Ruminococcaceae, which occur at significantly greater abundance in Ent+ individuals (6.53% vs. 4.53%, q = 0.044; and 29.58% vs. 16.34%, q < 0.0001, respectively, Fig 4). Interestingly, the Cellular Antigens pathway, potentially involved in host-microbe and microbe-microbe interactions, is more represented in the predicted metagenomes of Ent- individuals (q = 0.01; ANOVA). This pathway is predominantly attributed to members of the Enterobacteriaceae family, which was found to be twice as abundant in individuals lacking the parasite.


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)

Normalized relative abundance of KEGG metabolic pathways significantly associated with Entamoeba status in an ANOVA (q < 0.05 using the most abundant; ≤ 0.4% in at least one group) (left panel) and the relative contributions of each taxon for each pathway (right panel).
© Copyright Policy
Related In: Results  -  Collection

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

pgen.1005658.g004: Normalized relative abundance of KEGG metabolic pathways significantly associated with Entamoeba status in an ANOVA (q < 0.05 using the most abundant; ≤ 0.4% in at least one group) (left panel) and the relative contributions of each taxon for each pathway (right panel).
Mentions: We used the KEGG (Kyoto Encyclopedia of Genes and Genomes) database [49] and the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) pipeline [50] to predict abundances of pathways across individuals (see S9 Fig). Many of these pathways are classified based on eukaryotic genes. However, homologues in prokaryotes could have related functions. Considering the 220 most abundant KEGG pathways (comprising ≥ 0.01% of all assigned reads in at least 4 individuals), we identified 19 pathways with significant differences in abundance between Ent+ and Ent- individuals (FDR q < 0.05 after Benjamini-Hochberg correction for the number of pathways tested; ANOVA; see Fig 4 and S6 Table). Of these 19, of particular interest are an increase in amoebiasis (q = 0.001), biosynthesis of the antibiotic tetracycline (q = 0.03), and yeast MAPK signaling pathways (q = 0.01) in Ent+ individuals. These changes are largely attributed to Clostridiales and Ruminococcaceae, which occur at significantly greater abundance in Ent+ individuals (6.53% vs. 4.53%, q = 0.044; and 29.58% vs. 16.34%, q < 0.0001, respectively, Fig 4). Interestingly, the Cellular Antigens pathway, potentially involved in host-microbe and microbe-microbe interactions, is more represented in the predicted metagenomes of Ent- individuals (q = 0.01; ANOVA). This pathway is predominantly attributed to members of the Enterobacteriaceae family, which was found to be twice as abundant in individuals lacking the parasite.

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