Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania

Abstract

Humans have co-speciated with their gut-resident microbes, but it is difficult to infer features of our ancestral microbiome. Here, we examine the microbiome profile of 350 stool samples collected longitudinally for over a year from the Hadza hunter-gatherers of Tanzania. The data reveal annual cyclic reconfiguration of the microbiome, in which some taxa become undetectable only to reappear in a subsequent season. Comparison of the Hadza dataset with data collected from 18 populations in 16 countries with varying lifestyles reveals that gut community membership corresponds to modernization: Notably, the taxa within the Hadza that are the most seasonally volatile similarly differentiate industrialized and traditional populations. These data indicate that some dynamic lineages of microbes have decreased in prevalence and abundance in modernized populations.

The social network of microorganisms — how auxotrophies shape complex communities

“…For example, nutrient availability in the rhizosphere or the human gut is highly dynamic and can vary on different timescales. Physiological variation in human host physiology can be dependent on the time of the day 54 (for example, sleep–wake cycles, food intake or changes in hormone levels), over different seasons 55 or over the course of a lifetime 56 . Although multiple studies have delineated the effect of the host diet on the composition of the microbiome 55,57 , little work has been done to mechanistically resolve the effect of a change in diet on the microbial interaction network.…”

“…Physiological variation in human host physiology can be dependent on the time of the day 54 (for example, sleep–wake cycles, food intake or changes in hormone levels), over different seasons 55 or over the course of a lifetime 56 . Although multiple studies have delineated the effect of the host diet on the composition of the microbiome 55,57 , little work has been done to mechanistically resolve the effect of a change in diet on the microbial interaction network. Mice subjected to a Western-like diet with a high fat and low fibre content over several generations showed a progressive loss of microbial diversity, which could not be recovered after the reintroduction of a high-fibre diet 58 .…”

US Immigration Westernizes the Human Gut Microbiome

“…Rural indigenous populations have been found to harbor substantial biodiversity in their gut microbiomes, including novel microbial taxa not found in industrialized populations (Clemente et al, 2015; Gomez et al, 2016; Obregon-Tito et al, 2015; Schnorr et al, 2014; Smits et al, 2017; Yatsunenko et al, 2012). This loss of indigenous microbes or “disappearing microbiota” (Blaser and Falkow, 2009) may be critical in explaining the rise of chronic diseases in the modern world.…”

Diet affects gut microbiota and modulates hospitalization risk differentially in an international cirrhosis cohort

“…Disease progression is accompanied by an increase in relative abundance of potentially pathogenic taxa belonging to Enterobacteriaceae whereas autochthonous taxa are lower . A major determinant of gut microbial composition is the diet, which is different between industrialized and other countries . However, a detailed evaluation of dietary influences on gut microbiota and their impact on gut microbiota and outcomes in cirrhosis is unclear, especially from a multicenter perspective.…”