Abstract
BackgroundMost studies investigating human gut microbiome dynamics are conducted on humans living in an urban setting. However, few studies have researched the gut microbiome of the populations living traditional lifestyles. These understudied populations are arguably better subjects in answering human-gut microbiome evolution because of their lower exposure to antibiotics and higher dependence on natural resources. Hadza hunter-gatherers in Tanzania have exhibited high biodiversity and seasonal patterns in their gut microbiome composition at the family level, where some taxa disappear in one season and reappear later. Such seasonal changes have been profiled, but the nucleotide changes remain unexplored at the genome level. Thus, it is still elusive how microbial communities change with seasonal changes at the genome level.ResultsIn this study, we performed a strain-level single nucleotide polymorphism (SNP) analysis on 40 Hadza fecal metagenome samples spanning three seasons. With more SNP presented in the wet season, eight prevalent species have significant SNP enrichment with the increasing number of SNP calling by VarScan2, among which only three species have relatively high abundances. Eighty-three genes have the most SNP distributions between the wet season and dry season. Many of these genes are derived from Ruminococcus obeum, and mainly participated in metabolic pathways including carbon metabolism, pyruvate metabolism, and glycolysis.ConclusionsEight prevalent species have significant SNP enrichments with the increasing number of SNP, among which only Eubacterium biforme, Eubacterium hallii and Ruminococcus obeum have relatively high species abundances. Many genes in the microbiomes also presented characteristic SNP distributions between the wet season and the dry season. This implies that the seasonal changes might indirectly impact the mutation patterns for specific species and functions for the gut microbiome of the population that lives in traditional lifestyles through changing the diet in wet and dry seasons, indicating the role of these variants in these species’ adaptation to the changing environment and diets.
Highlights
Most studies investigating human gut microbiome dynamics are conducted on humans living in an urban setting
Many genes in the microbiomes presented characteristic single nucleotide polymorphism (SNP) distributions between the wet season and the dry season. This implies that the seasonal changes might indirectly impact the mutation patterns for specific species and functions for the gut microbiome of the population that lives in traditional lifestyles through changing the diet in wet and dry seasons, indicating the role of these variants in these species’ adaptation to the changing environment and diets
A SNP list containing 10,786 sites from 5 major species residing in human gut (Faecalibacterium prausnitzii, Prevotella copri (3,507,873 bp), Methanobrevibacter smithii (1,853,160 bp), Eubacterium biforme (2,415, 920 bp), Treponema succinifaciens (2,731,853 bp)) was used to generate a mutated reference genome set (Materials and Methods)
Summary
Most studies investigating human gut microbiome dynamics are conducted on humans living in an urban setting. Hadza hunter-gatherers in Tanzania have exhibited high biodiversity and seasonal patterns in their gut microbiome composition at the family level, where some taxa disappear in one season and reappear later. Such seasonal changes have been profiled, but the nucleotide changes remain unexplored at the genome level. Unindustrialized populations living traditional lifestyles, with lower exposure to antibiotics and higher dependence on natural resources, are arguably better subjects in answering ancient human-gut microbiome relationship [6]. The Hadza gut microbial communities exhibit a high degree of biodiversity [8] and a pattern of seasonal cycling in microbiome composition, where some taxa (at the family level) disappear in one season and reappear at a later time [7]. It is unclear how microbial communities change at the genome level under environmental stressors caused by seasonal changes
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have