Gut Microbiome Biomarkers and Functional Diversity Within an Amazonian Semi-Nomadic Hunter–Gatherer Group

Abstract

Human groups that still maintain traditional modes of subsistence (hunter–gatherers and rural agriculturalists) represent human groups non-impacted by urban-industrialized lifestyles, and therefore their gut microbiome provides the basis for understanding the human microbiome evolution and its association with human health and disease. The Yanomami is the largest semi-nomadic hunter–gatherer group of the Americas, exploring different niches of the Amazon rainforest in Brazil and Venezuela. Here, based on shotgun metagenomic data, we characterized the gut microbiome of the Yanomami from Brazil and compared taxonomically and functionally with the Yanomami from Venezuela, with other traditional groups from the Amazon and an urban-industrialized group. Taxonomic biomarkers were identified to each South American traditional group studied, including each Yanomami group. Broader levels of functional categories poorly discriminated the traditional and urban-industrialized groups, but the stratification of these categories revealed clear segregation of these groups. The Yanomami/Brazil gut microbiome presented unique functional features, such as a higher abundance of gene families involved in regulation/cell signaling, motility/chemotaxis, and virulence, contrasting with the gut microbiomes from the Yanomami/Venezuela and the other groups. Our study revealed biomarkers, and taxonomic and functional features that distinguished the gut microbiome of Yanomami/Brazil and Yanomami/Venezuela individuals, despite their shared lifestyle, culture, and genetic background. These differences may be a reflection of the environmental and seasonal diversity of the niches they explore. Overall, their microbiome profiles are shared with South American and African traditional groups, probably due to their lifestyle. The unique features identified within the Yanomami highlight the bias imposed by underrepresented sampling, and factors such as variations over space and time (seasonality) that impact, mainly, the hunter–gatherers.

Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides

“…Survey of human metagenomic data sets. Available cohorts of human gut metagenomic sequence data (National Center for Biotechnology Information projects PRJNA422434 [87], PRJEB10878 [88], PRJEB12123 [89], PRJEB12124 [90], PRJEB15371 [91], PRJEB6997 [92], PRJDB3601 [93], PRJNA48479 [94], PRJEB4336 [95], PRJEB2054 [96], PRJNA392180 [51], and PRJNA527208 [97]) were searched for the presence of 1,3GUL nucleotide sequences from B. fluxus (12.5 kb), B. thetaiotaomicron (12.6 kb), and B. uniformis (14.5 kb) using the following workflow. Each 1,3GUL nucleotide sequence was used separately as a template, and then magic-blast v1.5.0 (98) was used to recruit raw Illumina reads from the available metagenomic data sets with an identity cutoff of 97%.…”

Extensive transfer of genes for edible seaweed digestion from marine to human gut bacteria

“…Available cohorts of human gut metagenomic sequence data (National Center for Biotechnology Information projects: PRJNA422434 45 , PRJEB10878 46 , PRJEB12123 47 , PRJEB12124 48 , PRJEB15371 49 , PRJEB6997 50 , PRJDB3601 51 , PRJNA48479 52 , PRJEB4336 53 , PRJEB2054 54 , PRJNA392180 55 , and PRJNA527208 56 were searched for the presence of CGN/POR/AGAR degrading PUL nucleotide sequences from Bt 37371 , Bo 12C04 , Bp 17135 , Bu NP1 , Bx 18-002P and Faecalicatena spp. using the following workflow: Each PUL nucleotide sequence was used separately as a template and then magic-blast v1.5.0 57 was used to recruit raw Illumina reads from the available metagenomic datasets with an identity cutoff of 97%.…”

Skin exposure to sunlight: a factor modulating the human gut microbiome composition

“…The microbiome of these traditional groups has been characterized by higher biodiversity and higher Firmicutes to Bacteroidetes ratio contrasting with urban groups ( Figure 1 ). 1 , 3 – 5 , 14 In Bosman et al’s study, Firmicutes increased after UVB exposure with the enrichment of Lachnospiraceae, Ruminococcus and Clostridiaeae families. 16 These Firmicutes families were also abundant in the traditional groups, and abundance of other Firmicutes families/genera was also observed.…”

“…In the past decade, numerous studies on the gut microbiome of different populations have taken into account a wide range of factors, such as human diet, age, sex, life stage (pregnancy, lactating, menopausal stage), social behavior (use of alcohol, antibiotics, tobacco), geography, environment, ethnicity, and diseases. [1][2][3][4][5][6][7][8][9][10][11][12][13][14] Most of these studies established a link of one or more of those factors and the gut microbiome composition. Therefore, the gut microbiome modulation is driven by a complex and dynamic network presenting a wide range of variables.…”

“…Our research group has been exploring the diversity of the gut microbiome and its functionality among urban and traditional populations, especially the Yanomami ethnicity. 14 These hunter-gatherers inhabit a vast area in the Amazon Region, located around the equator (0 – 4°N latitude) in distinct altitudes. Thus, they are exposed naturally to a high incidence of sunlight and ultraviolet radiation, and this region is devoid of air pollution, a factor that blocks the UVB light from sunlight.…”