Environment and host species identity shape gut microbiota diversity in sympatric herbivorous mammals

Gut microbiota in geographically isolated host populations are often distinct. These differences have been attributed to between-population differences in host behaviours, environments, genetics and geographical distance. However, which factors are most important remains unknown. Here, we fill this gap for baboons by leveraging information on 13 environmental variables from 14 baboon populations spanning a natural hybrid zone. Sampling across a hybrid zone allowed us to additionally test whether phylosymbiosis (codiversification between hosts and their microbiota) is detectable in admixed, closely related primates. We found little evidence of genetic effects: none of host genetic ancestry, host genetic relatedness nor genetic distance between host populations were strong predictors of baboon gut microbiota. Instead, gut microbiota were best explained by the baboons' environments, especially the soil's geologic history and exchangeable sodium. Indeed, soil effects were 15 times stronger than those of host–population F ST, perhaps because soil predicts which foods are present, or because baboons are terrestrial and consume soil microbes incidentally with their food. Our results support an emerging picture in which environmental variation is the dominant predictor of host-associated microbiomes. We are the first to show that such effects overshadow host species identity among members of the same primate genus.

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Predictable and host‐species specific humanization of the gut microbiota in captive primates

Molecular Ecology ◽

10.1111/mec.15994 ◽

2021 ◽

Author(s):

Jennifer L. Houtz ◽

Jon G. Sanders ◽

Anthony Denice ◽

Andrew H. Moeller

Keyword(s):

Gut Microbiota ◽

Host Species ◽

Species Specific

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Effects of Host Species Identity and Diet on the Biodiversity of the Microbiota in Puerto Rican Bats

Current Microbiology ◽

10.1007/s00284-021-02607-5 ◽

2021 ◽

Author(s):

Steven J. Presley ◽

Joerg Graf ◽

Ahmad F. Hassan ◽

Anna R. Sjodin ◽

Michael R. Willig

Keyword(s):

Puerto Rican ◽

Host Species ◽

Species Identity

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The plant secondary compound swainsonine reshapes gut microbiota in plateau pikas (Ochotona curzoniae)

Applied Microbiology and Biotechnology ◽

10.1007/s00253-021-11478-6 ◽

2021 ◽

Author(s):

Shien Ren ◽

Chao Fan ◽

Liangzhi Zhang ◽

Xianjiang Tang ◽

Haibo Fu ◽

...

Keyword(s):

Gut Microbiota ◽

Artificial Diet ◽

Alpha Diversity ◽

Term Treatment ◽

Short Term Treatment ◽

Ochotona Curzoniae ◽

Rdna Sequencing ◽

Long Term Treatment ◽

Significant Difference ◽

Herbivorous Mammals

Abstract Plants produce various plant secondary compounds (PSCs) to deter the foraging of herbivorous mammals. However, little is known about whether PSCs can reshape gut microbiota and promote gut homeostasis of hosts. Using 16S rDNA sequencing to investigate the effects of PSCs on the gut microbiota of small herbivorous mammals, we studied plateau pikas (Ochotona curzoniae) fed diets containing swainsonine (SW) extracted from Oxytropis ochrocephala. Our results showed that both long- and short-term treatment of a single artificial diet in the laboratory significantly reduced alpha diversity and significantly affected beta diversity, core bacteria abundance, and bacterial functions in pikas. After SW was added to the artificial diet, the alpha diversity significantly increased in the long-term treatment, and core bacteria (e.g., Akkermansiaceae) with altered relative abundances in the two treatments showed no significant difference compared with pikas in the wild. The complexity of the co-occurrence network structure was reduced in the artificial diet, but it increased after SW was added in both treatments. Further, the abundances of bacteria related to altered alanine, aspartate, and glutamate metabolism in the artificial diet were restored in response to SW. SW further decreased the concentration of short-chain fatty acids (SCFAs) in both treatments. Our results suggest that PSCs play a key role in regulating gut microbiota community and intestinal homeostasis, thereby maintaining host health. Key points • Swainsonine improves the intestinal bacterial diversity of plateau pikas. • Swainsonine promotes the recovery of core bacterial abundances in the gut of plateau pikas. • Swainsonine promotes the restoration of intestinal bacterial functions of plateau pikas.

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Selective estrogen receptor modulator lasofoxifene suppresses spondyloarthritis manifestation and affects characteristics of gut microbiota in zymosan-induced SKG mice

Scientific Reports ◽

10.1038/s41598-021-91320-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hyemin Jeong ◽

In Young Kim ◽

Eun-Kyung Bae ◽

Chan Hong Jeon ◽

Kwang-Sung Ahn ◽

...

Keyword(s):

Estrogen Receptor ◽

Gut Microbiota ◽

Small Animal ◽

Joint Inflammation ◽

Fecal Calprotectin ◽

Selective Estrogen Receptor Modulator ◽

Mineral Density ◽

Receptor Modulator ◽

Significant Difference ◽

Microbiota Diversity

AbstractAnkylosing spondylitis is a male-predominant disease and previous study revealed that estrogens have an anti-inflammatory effect on the spondyloarthritis (SpA) manifestations in zymosan-induced SKG mice. This study aimed to evaluate the effect of selective estrogen receptor modulator (SERM) lasofoxifene (Laso) on disease activity of SpA. Mice were randomized into zymosan-treated, zymosan + 17β-estradiol (E2)-treated, and zymosan + Laso-treated groups. Arthritis was assessed by 18F-fluorodeoxyglucose (18F-FDG) small-animal positron emission tomography/computed tomography and bone mineral density (BMD) was measured. Fecal samples were collected and 16S ribosomal RNA gene sequencing was used to determine gut microbiota differences. Both zymosan + E2-treated mice and zymosan + Laso-treated mice showed lower arthritis clinical scores and lower 18F-FDG uptake than zymosan-treated mice. BMD was significantly higher in zymosan + E2-treated mice and zymosan + Laso-treated mice than zymosan-treated mice, respectively. Fecal calprotectin levels were significantly elevated at 8 weeks after zymosan injection in zymosan-treated mice, but it was not significantly changed in zymosan + E2-treated mice and zymosan + Laso-treated mice. Gut microbiota diversity of zymosan-treated mice was significantly different from zymosan + E2-treated mice and zymosan + Laso-treated mice, respectively. There was no significant difference in gut microbiota diversity between zymosan + E2-treated mice and zymosan + Laso -treated mice. Laso inhibited joint inflammation and enhanced BMD in SKG mice, a model of SpA. Laso also affected the composition and biodiversity of gut microbiota. This study provides new knowledge regarding that selected SpA patients could benefit from SERM treatment.

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The Effects of Increasing Intake of Intact Wheat Fibre or Wheat Bran on Gut Microbiota Diversity: a Systematic Review

Proceedings of The Nutrition Society ◽

10.1017/s0029665120004802 ◽

2020 ◽

Vol 79 (OCE2) ◽

Author(s):

Angie Jefferson ◽

Katie Adolphus

Keyword(s):

Systematic Review ◽

Gut Microbiota ◽

Wheat Bran ◽

Bacterial Species ◽

Microbiota Composition ◽

Inclusion Criteria ◽

Breakfast Cereal ◽

High Fibre ◽

Microbiota Diversity ◽

Gut Microbiota Composition

AbstractThe influence on health of the human gut microbiota is increasingly recognised, however wheat fibre, consumed frequently in Western diets has traditionally been considered inert with regard to gut microbiota composition and metabolic activity. We undertook a systematic review (PRISMA methodology) of human intervention studies examining the effects of intact cereal fibres on gut microbiota composition among healthy adults.(1) Studies published in the past 20 years were identified on PubMed and Cochrane electronic databases. Inclusion criteria were: healthy adult participants, at least one intact cereal fibre (or its sub-fraction) and measurement of faecal microbiota related outcomes. Out of forty studies meeting inclusion criteria, seventeen manipulated wheat fibre/bran or its key constituent arabinoxylans (AXOS), and ten used a whole diet approach with predominantly wheat fibre. Results from these twenty seven wheat fibre papers are presented here. Eight studies provided wheat bran/fibre (ranging from 5.7g-21g/day wheat fibre or 13g-28g/day wheat bran). Three reported significant effects on gut microbiota abundance and/or diversity (both at phyla and species level) and one showed no effect. Six reported significant increases in fermentation metabolites and one reported no significant change. Ten studies manipulated whole day fibre intake (predominantly wheat but also permitting some oats, rye and rice). Wholegrain intake ranged from 80g-150 g per day and fibre from 13.7g–40 g per day. Six found significant increases in bacterial diversity and/or abundance and five showed significant increases in fermentation metabolites. Two identified that response to high fibre intervention is dependent on baseline gut microbiota richness - those with limited richness exhibiting greater microbiota change over time in response to fibre increase. Two reported no significant effects. Nine studies utilised manipulation of AXOS (2.2g–18.8 g per day) with five demonstrating significant increases in target bacterial species and six significant increases in fermentation metabolites. One reported no significant effect to faecal metabolites. This review supports a role for the wheat fibre found in everyday foods (such as bran breakfast cereal of high fibre breads) promoting both microbiota diversity and abundance. While the healthy microbiome is yet to be defined, consumption of a single daily serving of wheat bran fibre appears sufficient to effect gut microbiota fermentation (with demonstrable effects arising from as low as 6g/day), and promote species diversity, with potential benefit to health.However exploration of stability over longer time frames (> 12 weeks) is now required.

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Dysbiosis characteristics of gut microbiota in cerebral infarction patients

Translational Neuroscience ◽

10.1515/tnsci-2020-0117 ◽

2020 ◽

Vol 11 (1) ◽

pp. 124-133

Author(s):

Hao Li ◽

Xiaohui Zhang ◽

Dengdeng Pan ◽

Yongqiang Liu ◽

Xuebing Yan ◽

...

Keyword(s):

Gut Microbiota ◽

Cerebral Infarction ◽

Operating Characteristic ◽

National Institutes Of Health ◽

Diagnostic Model ◽

Healthy Controls ◽

Characteristic Analysis ◽

Rrna Sequencing ◽

Stool Samples ◽

Microbiota Diversity

AbstractObjectiveThe aim of this study is to investigate the dysbiosis characteristics of gut microbiota in patients with cerebral infarction (CI) and its clinical implications.MethodsStool samples were collected from 79 CI patients and 98 healthy controls and subjected to 16S rRNA sequencing to identify stool microbes. Altered compositions and functions of gut microbiota in CI and its correlation with clinical features were investigated. Random forest and receiver operating characteristic analysis were used to develop a diagnostic model.ResultsMicrobiota diversity and structure between CI patients and healthy controls were overall similar. However, butyrate-producing bacteria (BPB) were significantly reduced in CI patients, while lactic acid bacteria (LAB) were increased. Genetically, BPB-related functional genes were reduced in CI patients, whereas LAB-related genes were enhanced. The interbacterial correlations among BPB in CI patients were less prominent than those in healthy controls. Clinically, BPB was negatively associated with the National Institutes of Health Stroke Scale (NIHSS), while LAB was positively correlated with NIHSS. Both BPB and LAB played leading roles in the diagnostic model based on 47 bacteria.ConclusionsThe abundance and functions of BPB in CI patients were significantly decreased, while LAB were increased. Both BPB and LAB displayed promising potential in the assessment and diagnosis of CI.

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Diversity in the intestinal microbiota and the influence of delivery, dietary profile and nutritional status

Journal of Clinical Images and Medical Case Reports ◽

10.52768/2766-7820/1325 ◽

2021 ◽

Vol 2 (5) ◽

Author(s):

Franciele Valduga ◽

◽

Malena Rostirola Miri ◽

Daniela Signori ◽

Larissa Pereira da Costa ◽

...

Keyword(s):

Nutritional Status ◽

Gut Microbiota ◽

School Children ◽

Alpha Diversity ◽

Grape Juice ◽

Anthropometric Parameters ◽

Culture Methods ◽

Normal Delivery ◽

Significant Difference ◽

Microbiota Diversity

Objective: This research aimed to evaluate the nutritional status and influence on the dietary profile in the gut microbiota, in an attempt to identify possible effects of grape juice consumption among school children aged 6-10. Design: Anthropometric parameters (weight, height, Body Mass Index, waist circumference, triceps, and subscapular skinfold) weremeasured at baseline. A Food Frequency Questionnaire (FFQ) was carried out to evaluate the dietary profile. Feces were analyzed by culture methods and the alpha diversity was determined by the Shannon Index. Participants: 36 volunteer school children aged 6 to 10 years from two different cities in the South of Brazil. Main outcome measure: Gut microbiota diversity according to anthropometric parameters, nutrition profile and delivery patterns. Analysis: For statistical analysis, t or u test and correlation were used through the statistical software SPSS® version 22.0. Results: The volunteers presented a eutrophic nutritional status, but 41.7% in the City 2 were overweight. There was a significant difference in the consumption of polyphenols (p<0.003), microbiotadiversity, breastfeeding, and delivery patterns by city. However, the dietary profile does not include the portions of daily nutrients recommended in both cities. The volunteers from City 1 presented a greater alpha diversity, which may be related to higher micronutrient intake, breastfeeding, and predominant natural/vaginal delivery Conclusion: We observed that the normal delivery and the dietary profile seems to be important factors to the gut microbiota diversity in these children. Keywords: grape juice; dietary profile; gut microbiota.

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Correlation of Gut Firmicutes/Bacteroidetes Ratio with Fibrosis and Steatosis in Patients with Non-alcoholic Fatty Liver Disease

10.21203/rs.3.rs-23643/v1 ◽

2020 ◽

Author(s):

Chyntia Olivia Maurine Jasirwan ◽

Akhmadu Muradi ◽

Irsan Hasan ◽

Marcellus Simadibrata ◽

Ikhwan Rinaldi ◽

...

Keyword(s):

Liver Disease ◽

Gut Microbiota ◽

Fatty Liver ◽

Fatty Liver Disease ◽

Central Obesity ◽

Gastrointestinal Microbiota ◽

Alcoholic Fatty Liver ◽

Microbiota Diversity ◽

Alcoholic Fatty Liver Disease ◽

High Triglyceride

Abstract Background : We investigated the gut microbiota in patients with non-alcoholic fatty liver disease (NAFLD) and its correlation with fibrosis and steatosis as reflected in the controlled attenuation parameter and transient elastography valuesMethods : A cross-sectional study was performed on 37 patients with NAFLD at Cipto Mangunkusumo National General Hospital from December 2018 to March 2019. The gut microbiota was investigated in fecal samples with 16S RNA sequencing using the next-generation sequencing platform MiSeq (Illumina).Results : NAFLD was more common in patients with metabolic syndrome. Firmicutes, Bacteroidetes, and Proteobacteria were the predominant phyla. Bacteroides was more dominant than Prevotella, contrary to the results in previous studies on normal populations in Indonesia. Microbiota dysbiosis was observed in most samples. The gastrointestinal microbiota diversity was significantly decreased in patients with NAFLD with high triglyceride levels and central obesity. The Firmicutes/Bacteroidetes ratio correlated with steatosis and obesity, whereas some other species in the lower taxonomy were mostly correlated with steatosis and obesity without fibrosis. Proteobacteria is the only phylum strongly correlated with fibrosis in patients with normal body mass index.Conclusions : The gut microbiota diversity was decreased in patients with NAFLD with high triglyceride levels and central obesity, and certain gut microbes were correlated with fibrosis and steatosis.

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The Studies to correlation between gut microbiota diversity and functional erectile dysfunction

10.21203/rs.3.rs-454949/v1 ◽

2021 ◽

Author(s):

Qiang Geng ◽

Shaofeng Chen ◽

Yuan Sun ◽

Yu Zhao ◽

Zhong Li ◽

...

Keyword(s):

Erectile Dysfunction ◽

Gut Microbiota ◽

Alpha Diversity ◽

T Test ◽

Data Quality Control ◽

Sequencing Data ◽

Significant Difference ◽

Miseq Platform ◽

Group 3 ◽

Microbiota Diversity

Abstract Objective: To analyze the distribution of gut microbiota in the ED patients, and explore the relationship between the diversity of gut microbiota and psychogenic erectile dysfunction. Methods: 30 cases of patients with erectile dysfunction (ED) and 30 healthy persons (healthy donor, HD) stool specimen were collected, using Illumina's Miseq platform samples V3-V4 region sequences bacterial 16SrRNA gene Paired end (PE) 300 sequencing, sequencing results were analyzed differences in species composition and diversity. Analysis contains five modules: sequencing data quality control, OTU species clustering and annotation, alpha diversity, beta diversity and the use of T-test and the analysis of the LEfSe differences. Results: 1. The flora diversity in the group of ED than HD significantly different (P<0.01), ED group has a low bacterial diversity. 2. Between ED group and HD group, abundant bacteria (TOPlO) and core flora (90%) had no significant difference in the genus level; all bacteria flora (>1%) display, Alloprevotella groups genus presents differences, Alloprevotella only be identified in the HD group. 3. ED and HD groups present in well separated PCoA analysis, having a significant difference in the two kinds of microflora. 4.T-test shows six species were significantly different, in the ED group, Streptococcus and Subdoligranulum were increasing, and Prevotella, Prevotella sp.9, Blautia, Lachnospiraceae NK4A136 groups and Roseburia were decreasing. 5.LEfSe analysis revealed 24 species were significantly different between ED and HD groups. Conclusion: Gene sequencing was performed on the two groups of specimens and finding that microbial community structure and diversity had significant difference, suggesting that ED have low gut microbiota diversity.

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