Two community types occur in gut microbiota of large‐sample wild plateau pikas ( Ochotona curzoniae )

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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Population Stratification in the Gut Microbiota of Bali is Associated with Transitional Lifestyle

10.21203/rs.3.rs-40341/v1 ◽

2020 ◽

Author(s):

Clarissa Asha Febinia ◽

Safarina G. Malik ◽

Ratna Djuwita ◽

I Wayan Weta ◽

Desak Made Wihandani ◽

...

Keyword(s):

Gut Microbiota ◽

Additive Model ◽

Alpha Diversity ◽

Population Level ◽

Wilcoxon Test ◽

Abundance Pattern ◽

Unifrac Distance ◽

Transitional State ◽

Community Types ◽

The Impact

Abstract Background: Human living conditions, such as food availability and the built environment, contribute to environmental forces that influence gut microbiota composition. Understanding the impact of the environment on microbiota assembly and its association with human health has multiple potential applications. Indonesia is a densely populated country that has been undergoing a dramatic societal change for the past two decades. It is distinctive in that it occupies an archipelago that imposes diverse geographic and cultural boundaries. The relationship between diet, microbiota, and health is poorly known in Indonesians and represents a natural study for the interaction between ethnogeographic factors and nutrition in microbiota assembly. Results: Here we show the first comprehensive report of the gut microbiota in adults from Bali, Indonesia (n=41). Their microbiotas clustered into two distinct community types: a Prevotella-rich (Type-P) and a Bacteroides-rich (Type-B) community. The Type-P individuals had lower alpha diversity (p <0.001, Shannon) and more incidence of obesity. The two community types are significantly different in their inter-genus co-abundance pattern (p <0.001, ANOSIM, Wilcoxon test). Further analyses with diet and obesity data showed that the presence of two distinct community types in Bali is a significant confounder for identifying health markers. In a multi-country dataset (n=257), the Bali microbiota indicates a transitional state from a subsistent (Prevotella-dominant) to industrial (Bacteroides-dominant) society. The two largest axes in a Principal Coordinate Analysis of weighted UniFrac distance explained the majority of variance between samples across countries (49.1%). Microbial dissimilarity across populations is significantly associated with Prevotella and Bacteriodes abundance (p <0.001, Generalized Additive Model). Conclusion: Our data showed that lifestyle transitions have a strong influence on the frequency of microbiota community types in a population. The Bali microbiota is undergoing a shift towards a Bacteroides-dominant community which reflects the ongoing transition of nutrition, socio-economy, and lifestyle the society. Although enterotypes obscured the detection of health markers, our findings collectively suggest that enterotypes may be useful in future studies for informing population-level stratification in large heterogenetic datasets.

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Stratification of the Gut Microbiota Composition Landscape Across the Alzheimer's Disease Continuum in a Turkish Cohort

10.1101/2021.10.28.466378 ◽

2021 ◽

Author(s):

Suleyman Yildirim ◽

Ozkan Ufuk Nalbantoglu ◽

Abdulahad Bayraktar ◽

Fatma Betül Ercan ◽

Aycan Gundogdu ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Gut Microbiota ◽

Latent Dirichlet Allocation ◽

Intervention Studies ◽

Neurodegenerative Disorder ◽

Machine Learning Techniques ◽

Topological Data Analysis ◽

Allocation Model ◽

Community Types

Alzheimer's disease (AD) is a heterogeneous neurodegenerative disorder that spans over a continuum with multiple phases including preclinical, mild cognitive impairment, and dementia. Unlike most other chronic diseases there are limited number of human studies reporting on AD gut microbiota in the literature. These published studies suggest that the gut microbiota of AD continuum patients varies considerably throughout the disease stages, raising expectations for existence of multiple microbiota community types. However, the community types of AD gut microbiota were not systematically investigated before, leaving important research gap for diet-based intervention studies and recently initiated precision nutrition approaches aiming at stratifying patients into distinct dietary subgroups. Here, we comprehensively assessed the community types of gut microbiota across the AD continuum. We analyze 16S rRNA amplicon sequencing of stool samples from 27 mild cognitive patients, 47 AD, and 51 non-demented control subjects using tools compatible with compositional nature of microbiota. To characterize gut microbiota community types, we applied multiple machine learning techniques including partitioning around the medoid clustering, fitting probabilistic Dirichlet mixture model, Latent Dirichlet Allocation model, and performed topological data analysis for population scale microbiome stratification based on Mapper algorithm. These four distinct techniques all converge on Prevotella and Bacteroides partitioning of the gut microbiota across AD continuum while some methods provided fine scale resolution in partitioning the community landscape. The Signature taxa and neuropsychometric parameters together robustly classify the heterogenous groups within the cohort. Our results provide a framework for precision nutrition approaches and diet-based intervention studies targeting AD cohorts.

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Feasibility Study Examining the Association between Gut Microbiota and Immune Response to Seasonal Influenza Vaccination in Healthy Adults

10.26686/wgtn.17151044 ◽

2021 ◽

Author(s):

◽

Nicholas Shortt

Keyword(s):

Immune Response ◽

Randomised Controlled Trial ◽

Gut Microbiota ◽

Study Protocol ◽

Controlled Trial ◽

Host Immune Response ◽

Blood Samples ◽

Community Types ◽

Stool Samples ◽

Randomised Controlled

<p>Research into the effect of the gut microbiota on host immune response is continuing to shed new light on the underappreciated role of the microbiota in human health. Recent research using mice has shown that the microbiota is critical to the host immune response to influenza infection. Whilst there is great variation in the human gut microbiota, classifications called stool community types can be used to classify individuals based on the abundance of major bacterial taxa. The primary objective of this study was to investigate the feasibility of using the study protocol for a large randomised controlled trial. Healthy adult participants (n=125) aged 18 to 64 were recruited from the general population and vaccinated with the seasonal trivalent influenza vaccine. Participants were followed up over a period of six months, during which time, both stool and blood samples were collected. Blood samples were collected at Day Zero, Three, Seven, 28 and 180 to measure immune response. The immune response to vaccination was measured by HAI antibody titres at Day Zero and Day 28. Stool samples were collected at Day Zero and Day 28 to assign participants to one of the four stool community types and assess stability over time. Stool samples were assigned to stool community types using the proportions of major taxa present. The association between stool community type and either post vaccination HAI titre, seroconversion rates or seroprotection rates was also assessed. The results obtained in this study supported the feasibility of a large randomised controlled trial using the study protocol. The study demonstrated a high participant retention rate (97.6%; 95% CI = 93.1% to 99.5%), as well as high participant adherence to the study protocol and good success obtaining the required blood and stool samples.</p>

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Feasibility Study Examining the Association between Gut Microbiota and Immune Response to Seasonal Influenza Vaccination in Healthy Adults

10.26686/wgtn.17151044.v1 ◽

2021 ◽

Author(s):

◽

Nicholas Shortt

Keyword(s):

Immune Response ◽

Randomised Controlled Trial ◽

Gut Microbiota ◽

Study Protocol ◽

Controlled Trial ◽

Host Immune Response ◽

Blood Samples ◽

Community Types ◽

Stool Samples ◽

Randomised Controlled

<p>Research into the effect of the gut microbiota on host immune response is continuing to shed new light on the underappreciated role of the microbiota in human health. Recent research using mice has shown that the microbiota is critical to the host immune response to influenza infection. Whilst there is great variation in the human gut microbiota, classifications called stool community types can be used to classify individuals based on the abundance of major bacterial taxa. The primary objective of this study was to investigate the feasibility of using the study protocol for a large randomised controlled trial. Healthy adult participants (n=125) aged 18 to 64 were recruited from the general population and vaccinated with the seasonal trivalent influenza vaccine. Participants were followed up over a period of six months, during which time, both stool and blood samples were collected. Blood samples were collected at Day Zero, Three, Seven, 28 and 180 to measure immune response. The immune response to vaccination was measured by HAI antibody titres at Day Zero and Day 28. Stool samples were collected at Day Zero and Day 28 to assign participants to one of the four stool community types and assess stability over time. Stool samples were assigned to stool community types using the proportions of major taxa present. The association between stool community type and either post vaccination HAI titre, seroconversion rates or seroprotection rates was also assessed. The results obtained in this study supported the feasibility of a large randomised controlled trial using the study protocol. The study demonstrated a high participant retention rate (97.6%; 95% CI = 93.1% to 99.5%), as well as high participant adherence to the study protocol and good success obtaining the required blood and stool samples.</p>

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Sympatric Yaks and Plateau Pikas Promote Microbial Diversity and Similarity by the Mutual Utilization of Gut Microbiota

Microorganisms ◽

10.3390/microorganisms9091890 ◽

2021 ◽

Vol 9 (9) ◽

pp. 1890

Author(s):

Haibo Fu ◽

Liangzhi Zhang ◽

Chao Fan ◽

Wenjing Li ◽

Chuanfa Liu ◽

...

Keyword(s):

Gut Microbiota ◽

Microbial Diversity ◽

Horizontal Transmission ◽

Population Expansion ◽

Underlying Mechanism ◽

Degradation Pathways ◽

Plateau Pika ◽

Ochotona Curzoniae ◽

Heparin Sulfate ◽

Xenobiotic Biodegradation

Interactions between species provide the basis for understanding coexisting mechanisms. The plateau pika (Ochotona curzoniae) and the yak (Bos grunniens) are considered competitors because they have shared habitats and consumed similar food on the Qinghai–Tibetan Plateau for more than 1 million years. Interestingly, the population density of plateau pikas increases with yak population expansion and subsequent overgrazing. To reveal the underlying mechanism, we sequenced the fecal microbial 16S rDNA from both sympatric and allopatric pikas and yaks. Our results indicated that sympatry increased both gut microbial diversity and similarity between pikas and yaks. The abundance of Firmicutes, Proteobacteria, Cyanobacteria, and Tenericutes decreased, while that of Verrucomicrobia increased in sympatric pikas. As for sympatric yaks, Firmicutes, Bacteroidetes, and Spirochaetes significantly increased, while Cyanobacteria, Euryarchaeota, and Verrucomicrobia significantly decreased. In sympatry, plateau pikas acquired 2692 OTUs from yaks, and yaks obtained 453 OTUs from pikas. The predominant horizontally transmitted bacteria were Firmicutes, Bacteroidetes, Verrucomicrobia, and Proteobacteria. These bacteria enhanced the enrichment of pathways related to prebiotics and immunity for pikas, such as heparin sulfate, heparin, chitin disaccharide, chondroitin-sulfate-ABC, and chondroitin-AC degradation pathways. In yaks, the horizontally transmitted bacteria enhanced pathways related to hepatoprotection, xenobiotic biodegradation, and detoxification. Our results suggest that horizontal transmission is a process of selection, and pikas and yaks tend to develop reciprocity through the horizontal transmission of gut microbiota.

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