scholarly journals Gut microbiome of an unindustrialized population have characteristic enrichment of SNPs in species and functions with the succession of seasons

2018 ◽  
Author(s):  
Jiyue Qin ◽  
Chongyang Tan ◽  
Kang Ning
Keyword(s):  
Gut Microbiome ◽  
Seasonal Changes ◽  
Community Dynamics ◽  
Wet Season ◽  
Human Gut ◽  
Microbial Community Dynamics ◽  
Species Abundances ◽  
Genome Level ◽  
Specific Species

AbstractMost studies investigating human gut microbiome dynamics are conducted in modern populations. However, unindustrialized populations are arguably better subjects in answering human-gut microbiome coevolution questions due to their lower exposure to antibiotics and higher dependence on natural resources. Hadza hunter-gatherers in Tanzania have been found to exhibit high biodiversity and seasonal patterns in their gut microbiome composition at family level, where some taxa disappear in one season and reappear at later time. However, such seasonal changes have previously been profiled only according to species abundances, with genome-level variant dynamics unexplored. As a result it is still elusive how microbial communities change at the genome-level under environmental pressures caused by seasonal changes. Here, a strain-level SNP analysis of Hadza gut metagenome is performed for 40 Hadza fecal samples collected in three seasons. First, we benchmarked three SNP calling tools based on simulated sequencing reads, and selected VarScan2 that has highest accuracy and sensitivity after a filtering step. Second, we applied VarScan2 on Hadza gut microbiome, with results showing that: with more SNP presented in wet season in general, eight prevalent species have significant SNP enrichments in wet season of which only three species have relatively high abundances. This indicates that SNP characteristics are independent of species abundances, and provides us a unique lens towards microbial community dynamics. Finally, we identify 83 genes with the most characteristic SNP distributions between wet season and dry season. Many of these genes are from Ruminococcus obeum, and mainly from metabolic pathways like carbon metabolism, pyruvate metabolism and glycolysis, as shown by KEGG annotation. This implies that the seasonal changes might indirectly impact the mutational patterns for specific species and functions for gut microbiome of an unindustrialized population, indicating the role of these variants in their adaptation to the changing environment and diets.ImportanceBy analyzing the changes of SNP enrichments in different seasons, we have found that SNP characteristics are independent of species abundances, and could provide us a unique lens towards microbial community dynamics at the genomic level. Many of the genes in microbiome also presented characteristic SNP distributions between wet season and dry season, indicating the role of variants in specific species in their adaptation to the changing environment for an unindustrialized population.

scholarly journals The seasonal changes of the gut microbiome of the population living in traditional lifestyles are represented by characteristic species-level and functional-level SNP enrichment patterns

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xue Zhu ◽  
Jiyue Qin ◽  
Chongyang Tan ◽  
Kang Ning
Keyword(s):  
Gut Microbiome ◽  
Seasonal Changes ◽  
Dry Season ◽  
Urban Setting ◽  
Snp Analysis ◽  
Wet Season ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Genome Level ◽  
Prevalent Species

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.

What is the role of cyclic di-GMP signaling within the human gut microbiome?

2014 ◽  
Vol 1 (1) ◽  
Author(s):  
Rachel M. Rudlaff ◽  
Christopher M. Waters
Keyword(s):  
Gut Microbiome ◽  
Diguanylate Cyclase ◽  
Human Gut ◽  
Base Pairs ◽  
Metagenomic Dna ◽  
Human Gut Microbiome ◽  
Commensal Species ◽  
Stool Samples ◽  
Specific Species

AbstractThere is currently little understanding of the role of the bacterial second messenger cyclic di-GMP (c-di-GMP) in the human gut microbiome. C-di-GMP is synthesized by highly conserved diguanylate cyclase (DGC) enzymes and degraded by highly conserved phosphodiesterase (PDE) enzymes. To begin to assess the prevalence of c-di-GMP signaling in the gut microbiome, we found on average 1.0 DGC and 0.8 PDE enzymes per million base pairs of metagenomic DNA derived from stool samples. Specific species encoding substantial numbers of GGDEF and EAL domains were the commensal species

Role of dietary fiber in the recovery of the human gut microbiome and its metabolome

2021 ◽  
Author(s):  
Ceylan Tanes ◽  
Kyle Bittinger ◽  
Yuan Gao ◽  
Elliot S. Friedman ◽  
Lisa Nessel ◽  
...  
Keyword(s):  
Dietary Fiber ◽  
Gut Microbiome ◽  
Human Gut ◽  
Human Gut Microbiome

Active and total microbial community dynamics and the role of functional genes bamA and mcrA during anaerobic digestion of phenol and p-cresol

2018 ◽  
Vol 264 ◽  
pp. 290-297 ◽  
Author(s):  
Oscar Franchi ◽  
Patricia Bovio ◽  
Eduardo Ortega-Martínez ◽  
Francisca Rosenkranz ◽  
Rolando Chamy
Keyword(s):  
Microbial Community ◽  
Anaerobic Digestion ◽  
Community Dynamics ◽  
Functional Genes ◽  
Microbial Community Dynamics

Global and temporal state of the human gut microbiome in health and disease

2021 ◽  
Author(s):  
Saeed Shoaie ◽  
Sunjae Lee ◽  
Mathieu Almeida ◽  
Gholamreza Bidkhori ◽  
Nicolas Pons ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Integrative Analysis ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Health And Disease ◽  
One Year ◽  
The Stability ◽  
Clinical Phenotyping ◽  
Sampling Times

Abstract The role of gut microbiota in humans is of great interest, and metagenomics provided the possibilities for extensively analysing bacterial diversity in health and disease. Here we explored the human gut microbiome samples across 19 countries, performing compositional, functional and integrative analysis. To complement these data and analyse the stability of the microbiome, we followed 86 healthy Swedish individuals over one year, with four sampling times and extensive clinical phenotyping. The integrative analysis of temporal microbiome changes shows the existence of two types of species with a tendency to vary in abundance with time, here called outflow and inflow species. Importantly, the former tends to be enriched in disease, while the latter is enriched in health. We suggest that the decrease of disease-associated outflow and the increase of health-associated inflow species with time may be a fundamental albeit previously unrecognized aspect of the homeostasis maintenance in a healthy microbiome.

Role of Human Gut Microbiome in Health and Disease

2021 ◽  
pp. 101-112
Author(s):  
Nazar Reehana ◽  
Mohamed Yousuff Mohamed Imran ◽  
Nooruddin Thajuddin ◽  
D. Dhanasekaran
Keyword(s):  
Gut Microbiome ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Health And Disease

scholarly journals Seasonal and Sexual Differences in the Microbiota of the Hoopoe Uropygial Secretion

Genes ◽  
2018 ◽  
Vol 9 (8) ◽  
pp. 407 ◽  
Author(s):  
Sonia Rodríguez-Ruano ◽  
Manuel Martín-Vivaldi ◽  
Juan Peralta-Sánchez ◽  
Ana García-Martín ◽  
Ángela Martínez-García ◽  
...  
Keyword(s):  
Breeding Season ◽  
Community Dynamics ◽  
Quantitative Polymerase Chain Reaction ◽  
Infection Risk ◽  
Uropygial Gland ◽  
Molecular Fingerprinting ◽  
Microbial Community Dynamics ◽  
High Infection ◽  
Uropygial Secretion

The uropygial gland of hoopoe nestlings and nesting females hosts bacterial symbionts that cause changes in the characteristics of its secretion, including an increase of its antimicrobial activity. These changes occur only in nesting individuals during the breeding season, possibly associated with the high infection risk experienced during the stay in the hole-nests. However, the knowledge on hoopoes uropygial gland microbial community dynamics is quite limited and based so far on culture-dependent and molecular fingerprinting studies. In this work, we sampled wild and captive hoopoes of different sex, age, and reproductive status, and studied their microbiota using quantitative polymerase chain reaction (qPCR), fluorescence in situ hybridization (FISH) and pyrosequencing. Surprisingly, we found a complex bacterial community in all individuals (including non-nesting ones) during the breeding season. Nevertheless, dark secretions from nesting hoopoes harbored significantly higher bacterial density than white secretions from breeding males and both sexes in winter. We hypothesize that bacterial proliferation may be host-regulated in phases of high infection risk (i.e., nesting). We also highlight the importance of specific antimicrobial-producing bacteria present only in dark secretions that may be key in this defensive symbiosis. Finally, we discuss the possible role of environmental conditions in shaping the uropygial microbiota, based on differences found between wild and captive hoopoes.

scholarly journals Interplay between severities of COVID-19 and the gut microbiome: implications of bacterial co-infections?

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Jyoti Chhibber-Goel ◽  
Sreehari Gopinathan ◽  
Amit Sharma
Keyword(s):  
Gut Microbiome ◽  
Distress Syndrome ◽  
Recovery Period ◽  
Gastrointestinal Symptoms ◽  
Human Gut ◽  
Immune Reactions ◽  
Effective Immune Response ◽  
Disease Prognosis ◽  
Nasal Swabs

AbstractCOVID-19 is an acute respiratory distress syndrome and is often accompanied by gastrointestinal symptoms. The SARS-CoV-2 has been traced not only in nasopharyngeal and mid-nasal swabs but also in stool and rectal swabs of COVID-19 patients. The gut microbiota is important for an effective immune response as it ensures that unfavorable immune reactions in lungs and other vital organs are regulated. The human gut-lung microbiota interplay provides a framework for therapies in the treatment and management of several pulmonary diseases and infections. Here, we have collated data from COVID-19 studies, which suggest that bacterial co-infections as well as the gut-lung cross talk may be important players in COVID-19 disease prognosis. Our analyses suggests a role of gut microbiome in pathogen infections as well as in an array of excessive immune reactions during and post COVID-19 infection recovery period.

Reproductive effort and seasonality associated with male-biased parasitism in Gracilinanus agilis (Didelphimorphia: Didelphidae) infected by Eimeria spp. (Apicomplexa: Eimeriidae) in the Brazilian cerrado

Parasitology ◽  
2015 ◽  
Vol 142 (8) ◽  
pp. 1086-1094 ◽  
Author(s):  
A. L. S. STRONA ◽  
M. LEVENHAGEM ◽  
N. O. LEINER
Keyword(s):  
Seasonal Changes ◽  
Spatial Organization ◽  
Reproductive Effort ◽  
Brazilian Cerrado ◽  
Mating Season ◽  
Wet Season ◽  
Differential Host ◽  
Future Studies ◽  
Eimeria Spp

SUMMARYThe aggregation of parasites among hosts is associated with differential host exposure and susceptibility to parasites, which varies according to host gender, body size, reproductive status and environmental factors. We evaluated the role of these factors on infestation by Eimeria spp. (Eimeriidae) in the agile gracile mouse opossum (Gracilinanus agilis), a semelparous didelphid inhabiting neotropical savannahs. Eimeria spp. abundance and prevalence among G. agilis were associated with the breeding status of individuals and to a lesser extent to climatic season, with both sexes presenting higher Eimeria spp. burdens during late breeding/wet season. On the other hand, male-biased parasitism was restricted to dry/mating season. We suggest that male spatial organization and diet may account for increased parasite burdens within this sex, although future studies should evaluate the role of physiological differences associated with androgen hormones. Finally, a rapid increase in Eimeria spp. loads among females during the late breeding/wet season seems associated with seasonal changes in susceptibility, due to breeding costs related to semelparity, and exposure to infective propagules, while male-die off seems to explain maintenance of higher Eimeria spp. burdens within this sex in the same period.

scholarly journals Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations

Metabolites ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 55
Author(s):  
Santosh Lamichhane ◽  
Partho Sen ◽  
Marina Amaral Alves ◽  
Henrique C. Ribeiro ◽  
Peppi Raunioniemi ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Gut Microbiome ◽  
Systemic Circulation ◽  
Water Soluble ◽  
Lipid Homeostasis ◽  
Microbial Lipids ◽  
Human Gut ◽  
Polar Metabolites ◽  
Health And Disease

Various studies aiming to elucidate the role of the gut microbiome-metabolome co-axis in health and disease have primarily focused on water-soluble polar metabolites, whilst non-polar microbial lipids have received less attention. The concept of microbiota-dependent lipid biotransformation is over a century old. However, only recently, several studies have shown how microbial lipids alter intestinal and circulating lipid concentrations in the host, thus impacting human lipid homeostasis. There is emerging evidence that gut microbial communities play a particularly significant role in the regulation of host cholesterol and sphingolipid homeostasis. Here, we review and discuss recent research focusing on microbe-host-lipid co-metabolism. We also discuss the interplay of human gut microbiota and molecular lipids entering host systemic circulation, and its role in health and disease.

Sign in / Sign up

Export Citation Format

Share Document