Xue Zhu1, Jiyue Qin1, Chongyang Tan1, Kang Ning2. 1. Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, Center for AI Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China. 2. Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, Center for AI Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China. ningkang@hust.edu.cn.
Abstract
BACKGROUND: Most 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. RESULTS: In 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. CONCLUSIONS: Eight 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.
BACKGROUND: Most studies investigating humangut 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. RESULTS: In 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. CONCLUSIONS: Eight 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.
Entities:
Keywords:
Gut microbiome; SNP enrichment; Seasonal change; Traditional lifestyle
Authors: E V Sokurenko; V Chesnokova; D E Dykhuizen; I Ofek; X R Wu; K A Krogfelt; C Struve; M A Schembri; D L Hasty Journal: Proc Natl Acad Sci U S A Date: 1998-07-21 Impact factor: 11.205
Authors: Rasnik K Singh; Hsin-Wen Chang; Di Yan; Kristina M Lee; Derya Ucmak; Kirsten Wong; Michael Abrouk; Benjamin Farahnik; Mio Nakamura; Tian Hao Zhu; Tina Bhutani; Wilson Liao Journal: J Transl Med Date: 2017-04-08 Impact factor: 5.531