scholarly journals Rumen bacterial community of young and adult of reindeer (Rangifer tarandus) from Yamalo-Nenets Autonomous District of Russia

2020 ◽  
Vol 5 (1) ◽  
pp. 10-20 ◽  
Author(s):  
Kasim A. Laishev ◽  
Larisa A. Ilina ◽  
Valentina A. Filippova ◽  
Timur P. Dunyashev ◽  
Georgiy Yu. Laptev ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Rangifer Tarandus ◽  
Biological Diversity ◽  
Physiological State ◽  
Alpha Diversity ◽  
Operational Taxonomic Unit ◽  
Taxonomic Composition ◽  
Food Material ◽  
Alpha And Beta Diversity ◽  
Microbiome Composition

AbstractThe aim of the work was to compare the taxonomic composition of the rumen procariotic community in young and adult individuals of Nenets breed reindeer (Rangifer tarandus ) from the central part of the Yamal region by using the NGS method (next generation sequencing) and compare the microbiome composition of reindeer with the microbiome of their initial vegetation food material. The obtained data showed that the dominant position in microbial communities, like that of other ruminants, was occupied by representatives of phylum Firmicutes and Bacteroidetes, whose total share between observed groups did not differ significantly. The composition of the microbiome of the rumen of the investigated group of animals was completely different from the microbiome structure of the initial vegetation cover. Digestion of vegetation by reindeers resulted in complex transformation in the initial plant microbiome and an increase of biological diversity which was expressed in operational taxonomic unit (OTU) numbers increasing and changes in indexes of alpha-diversity parameters. According to the results of alpha- and beta- diversity of the rumen microbial communities, the greatest uniqueness was revealed for the microbiomes of the adults in comparison with calves and young. The presence of changes in the biodiversity indexes of the rumen microbiota in the reindeer, examined by us, confirm the opinion of the researchers that the microbial community may also reflect the physiological state of the animals. It has also been demonstrated that the presence of the phylum Verrucomicrobia, and the genera Stenotrophomonas, Pseudomonas, etc., may be specific to Nenets breed reindeer and have a pattern with their presence on various plants and lichens that are part of the reindeer diet. This is partially confirmed by data on plants microbiome taxonomy.

scholarly journals Diversity Indices of Plant Communities and Their Rhizosphere Microbiomes: An Attempt to Find the Connection

2021 ◽  
Vol 9 (11) ◽  
pp. 2339
Author(s):  
Aleksei O. Zverev ◽  
Arina A. Kichko ◽  
Aleksandr G. Pinaev ◽  
Nikolay A. Provorov ◽  
Evgeny E. Andronov
Keyword(s):  
Microbial Communities ◽  
Plant Communities ◽  
Plant Diversity ◽  
Beta Diversity ◽  
Mutual Influence ◽  
Plant Root ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Alpha And Beta Diversity ◽  
Highly Correlated

The rhizosphere community represents an “ecological interface” between plant and soil, providing the plant with a number of advantages. Despite close connection and mutual influence in this system, the knowledge about the connection of plant and rhizosphere diversity is still controversial. One of the most valuable factors of this uncertainty is a rough estimation of plant diversity. NGS sequencing can make the estimations of the plant community more precise than classical geobotanical methods. We investigate fallow and crop sites, which are similar in terms of environmental conditions and soil legacy, yet at the same time are significantly different in terms of plant diversity. We explored amplicons of both the plant root mass (ITS1 DNA) and the microbial communities (16S rDNA); determined alpha- and beta-diversity indices and their correlation, and performed differential abundance analysis. In the analysis, there is no correlation between the alpha-diversity indices of plants and the rhizosphere microbial communities. The beta-diversity between rhizosphere microbial communities and plant communities is highly correlated (R = 0.866, p = 0.01). ITS1 sequencing is effective for the description of plant root communities. There is a connection between rhizosphere communities and the composition of plants, but on the alpha-diversity level we found no correlation. In the future, the connection of alpha-diversities should be explored using ITS1 sequencing, even in more similar plant communities—for example, in different synusia.

scholarly journals Immune Gene Expression Covaries with Gut Microbiome Composition in Stickleback

mBio ◽  
2021 ◽  
Vol 12 (3) ◽  
Author(s):  
Lauren E. Fuess ◽  
Stijn den Haan ◽  
Fei Ling ◽  
Jesse N. Weber ◽  
Natalie C. Steinel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Microbial Communities ◽  
Gut Microbiome ◽  
Alpha Diversity ◽  
Host Immunity ◽  
Host Gene ◽  
Microbiota Composition ◽  
Host Gene Expression ◽  
Microbiome Composition ◽  
Immune Genes

ABSTRACT Commensal microbial communities have immense effects on their vertebrate hosts, contributing to a number of physiological functions, as well as host fitness. In particular, host immunity is strongly linked to microbiota composition through poorly understood bi-directional links. Gene expression may be a potential mediator of these links between microbial communities and host function. However, few studies have investigated connections between microbiota composition and expression of host immune genes in complex systems. Here, we leverage a large study of laboratory-raised fish from the species Gasterosteus aculeatus (three-spined stickleback) to document correlations between gene expression and microbiome composition. First, we examined correlations between microbiome alpha diversity and gene expression. Our results demonstrate robust positive associations between microbial alpha diversity and expression of host immune genes. Next, we examined correlations between host gene expression and abundance of microbial taxa. We identified 15 microbial families that were highly correlated with host gene expression. These families were all tightly correlated with host expression of immune genes and processes, falling into one of three categories—those positively correlated, negatively correlated, and neutrally related to immune processes. Furthermore, we highlight several important immune processes that are commonly associated with the abundance of these taxa, including both macrophage and B cell functions. Further functional characterization of microbial taxa will help disentangle the mechanisms of the correlations described here. In sum, our study supports prevailing hypotheses of intimate links between host immunity and gut microbiome composition. IMPORTANCE Here, we document associations between host gene expression and gut microbiome composition in a nonmammalian vertebrate species. We highlight associations between expression of immune genes and both microbiome diversity and abundance of specific microbial taxa. These findings support other findings from model systems which have suggested that gut microbiome composition and host immunity are intimately linked. Furthermore, we demonstrate that these correlations are truly systemic; the gene expression detailed here was collected from an important fish immune organ (the head kidney) that is anatomically distant from the gut. This emphasizes the systemic impact of connections between gut microbiota and host immune function. Our work is a significant advancement in the understanding of immune-microbiome links in nonmodel, natural systems.

scholarly journals Sputum Microbiome Composition in Patients With Squamous Cell Lung Carcinoma

2021 ◽  
Author(s):  
E. D. Baranova ◽  
V. G. Druzhinin ◽  
L. V. Matskova ◽  
P. S. Demenkov ◽  
V. P . Volobaev ◽  
...  
Keyword(s):  
Squamous Cell ◽  
Inflammatory Responses ◽  
Alpha Diversity ◽  
Taxonomic Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Cell Lung Carcinoma ◽  
Microbiome Composition ◽  
Β Diversity ◽  
Genome Damage

Abstract Recent findings indicate that the microbiome can have a significant impact on the development of lung cancer by inducing inflammatory responses, causing dysbiosis and generating genome damage. The aim of this study was to search for bacterial markers of squamous cell carcinoma (LUSC). In the study, the taxonomic composition of the sputum microbiome of 40 men with untreated LUSC was compared with 40 healthy controls. Next Generation sequencing of bacterial 16S rRNA genes was used to determine the taxonomic composition of the respiratory microbiome. There was no differences in alpha diversity between the LUSC and control groups. Meanwhile, differences in the structure of bacterial communities (β diversity) among patients and controls differed significantly in sputum samples (pseudo-F = 1.65; p = 0.026). Only Streptococcus, Bacillus, Gemella and Haemophilus were found to be significantly increased in patients with LUSC compared to the control subjects, while 19 bacterial genera were significantly reduced, indicating a decrease in beta diversity in the microbiome of patients with LUSC. From our study, Streptococcus (Streptococcus agalactiae) emerges as the most likely LUSC biomarker, but more research is needed to confirm this assumption.

scholarly journals Alpha and Beta-diversity of Microbial Communities Associated to Plant Disease Suppressive Functions of On-farm Green Composts

Agriculture ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 113 ◽  
Author(s):  
Catello Pane ◽  
Roberto Sorrentino ◽  
Riccardo Scotti ◽  
Marcella Molisso ◽  
Antonio Di Matteo ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Ecological Niches ◽  
Rrna Gene ◽  
Alpha And Beta Diversity ◽  
Length Polymorphisms ◽  
Differential Pattern ◽  
Curtis Dissimilarity ◽  
Underlying Mechanisms

Green waste composts are obtained from agricultural production chains; their suppressive properties are increasingly being developed as a promising biological control option in the management of soil-borne phytopathogens. The wide variety of microbes harbored in the compost ecological niches may regulate suppressive functions through not yet fully known underlying mechanisms. This study investigates alpha- and beta-diversity of the compost microbial communities, as indicators of the biological features. Our green composts displayed a differential pattern of suppressiveness over the two assayed pathosystems. Fungal and bacterial densities, as well as catabolic and enzyme functionalities did not correlate with the compost control efficacy on cress disease. Differences in the suppressive potential of composts can be better predicted by the variations in the community levels of physiological profiles indicating that functional alpha-diversity is more predictive than that which is calculated on terminal restriction fragments length polymorphisms (T-RFLPs) targeting the 16S rRNA gene. However, beta-diversity described by nMDS analysis of the Bray–Curtis dissimilarity allowed for separating compost samples into distinct functionally meaningful clusters and indicated that suppressiveness could be regulated by selected groups of microorganisms as major deterministic mechanisms. This study contributes to individuating new suitable characterization procedures applicable to the suppressive green compost chain.

scholarly journals Timed Feeding Protocols While Consuming a High Fat Diet Do Not Alter Gut Fungal Populations (OR23-06-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Marie van der Merwe ◽  
Sunita Sharma ◽  
Jade Caldwell ◽  
Nicholas Smith ◽  
Richard Bloomer ◽  
...  
Keyword(s):  
High Fat Diet ◽  
Metabolic Regulation ◽  
Alpha Diversity ◽  
Taxonomic Composition ◽  
Chow Diet ◽  
High Fat ◽  
Alpha And Beta Diversity ◽  
Fungal Populations ◽  
Timing Strategies

Abstract Objectives The gut microbiome participates in host metabolic regulation. While the vast majority of microbiome research has focused on bacterial populations, other microorganisms also colonize the mammalian intestine and likely play functionally important roles in host metabolism. The objective of current study was to characterize the role of dietary composition and timing strategies upon gut fungal populations. Methods C57BL/6 male mice were randomized to a Chow diet or a high-fat diet (HFD) for 6 weeks, followed by a switch from HFD to 1) Chow (sChow), 2) Purified High Fiber – Daniel Fast (DF), 3) HFD ad lib, 4) HFD time restricted (TRF), 5) HFD alternative day fasting (ADF), or 6) HFD 60% caloric restriction (CR) for an additional 8 weeks. Ileal, cecal and serial fecal samples were collected for next generation sequencing of ITS2 rRNA to examine the gut mycobiome. Results We observed dramatic reductions in alpha diversity in fecal fungal populations when animals consumed the HFD compared with Chow. HFD resulted in dramatic reduction in the relative abundance of the fungal order Saccharomyces, with a concomitant increases in the genus Candida and Hanseniaspora. In response to dietary switch from HFD to Chow, fungal taxonomic composition, alpha, and beta diversity transitioned to a population clustering more similarity with Chow by weeks 4 and 8 of intervention. After 8 weeks on the respective dietary interventions, alpha diversity of the ileal, cecal and fecal fungal population in mice consuming DF or various HFD fasting protocols remained similar to the HFD controls. Saccharomycetales remained the dominant genus present in HFD and DF groups. However, amongst these groups, the DF group (fecal sample) showed the greatest increase in Saccharomyces, but time-restricted feeding protocols also showed increased levels of Saccharomyces. Conclusions While fasting protocols on HFD are associated with improved metabolic outcomes, these data demonstrate that – similar to microbial populations within the microbiome – diet remains the largest driver of microorganism community composition. To our knowledge, this is the first investigation into the role of dietary timing strategies upon the gut fungal communities ever reported. Funding Sources University of Memphis. Children's Foundation Research Institute, Memphis.

scholarly journals Diet Modification and Not Timed Feeding Strategies Result in Intestinal Microbiome Alterations (P21-030-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Marie van der Merwe ◽  
Sunita Sharma ◽  
Jade Caldwell ◽  
Nicholas Smith ◽  
Richard Bloomer ◽  
...  
Keyword(s):  
High Fat Diet ◽  
Beta Diversity ◽  
Diversity Index ◽  
Alpha Diversity ◽  
Taxonomic Composition ◽  
Intestinal Microbiome ◽  
Feeding Strategies ◽  
High Fat ◽  
Microbiome Composition ◽  
Intestinal Length

Abstract Objectives Time-restricted feeding strategies have been shown to normalize obesity parameters, even under high fat feeding conditions. The objective of this study is to examine whether timed feeding alters parameters of gut health or intestinal microbiome composition. Methods C57BL/6 male mice were randomized to Chow or a high fat diet (HFD) for 6 weeks, followed by a switch from HFD to 1) Chow (sChow), 2) Purified Vegan – Daniel Fast (DF), 3) HFD ad lib, 4) HFD time restricted (TRF), 5) HFD alternative day fasting (ADF), or 6) HFD 60% caloric restriction (CR) for an additional 8 weeks. Results We observed that body mass gain was reduced for all intervention groups (P ≤ 0.0001). Small intestinal length and cecal weight were increased in Chow, sChow and DF (P ≤ 0.02), while total cecal short chain fatty acid (SCFA) concentration was non-significantly increased for all groups consuming the HFD. Proprionate was specifically increased in the Chow, sChow and DF groups (P ≤ 0.02). Chow fed microbiota remained stable in taxonomic composition and alpha diversity (Shannon diversity index) throughout the study. HF fed microbiota displayed lower alpha diversity along with reduced phylum levels of Bacteroidetes and increase Firmicutes. Animals switched from HF to Chow demonstrated a rapid transition in taxonomic composition, alpha, and beta diversity that initially resembled HF, but clustered closely with Chow by weeks 4 and 8 of intervention. After 8 weeks on the respective dietary protocols, alpha diversity of the DF was most similar to Chow fed animals and also resulted in the largest increase in Bacteriodetes and largest decrease in Firmicutes. Beta diversity (weighted UniFrac) showed Chow, sChow, and DF clustered together, while high fat fed groups (HF, CR, ADF, and TRF) clustered. Compared with HF controls, CR and TRF led to a relative increase in the classes Clostridia, Deferribacteres and Deltaproteobacteria. The taxonomic composition and alpha diversity of ADF fasting resembled HF under fed conditions, while ADF under fasting conditions more closely resembled CR and TRF. Conclusions In conclusion, timed feeding on a high fat diet did not result in significant changes in the microbiome, demonstrating that diet, and not fasting is the major determinant for microbiome composition. Funding Sources University of Memphis & Children's Foundation Research Institute, Memphis.

scholarly journals Contrasting resistance and resilience of the coupled oxic and anoxic components of an experimental microbial ecosystem

2021 ◽  
Author(s):  
Marcel Suleiman ◽  
Frank Pennekamp ◽  
Yves Choffat ◽  
Owen L. Petchey
Keyword(s):  
Microbial Communities ◽  
Oxygen Concentration ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Bottom Layer ◽  
Light Limitation ◽  
Delayed Response ◽  
Light Conditions ◽  
Alpha And Beta Diversity ◽  
The Impact

Understanding how microbial communities as key drivers of global biogeochemical cycles respond to environmental change remains a critical challenge in microbial ecology. In this study, we used phototrophic oxic-anoxic micro-ecosystems to understand how aerobic and anaerobic lake analog communities responded towards stressful light removal. Continuous oxygen measurements and four snapshots of full-length 16S rRNA sequencing were performed to detect responses of oxygen concentration, and of alpha and beta diversity. In the top layer, oxygen concentration decreased significantly under light limitation, but showed almost complete resilience after normal light conditions were restored, while the bottom layer remained anoxic throughout the experiment. Microbial communities, however, differed in their response behavior: alpha-diversity of the aerobic communities showed a delayed response after light conditions were restored, and their composition was not resilient during the duration of the experiment. In contrast, alpha-diversity of the anaerobic bottom water communities increased due to the stressor and was resilient. Beta-diversity changed significantly during light removal, showed resilience for the aerobic communities, but stayed significantly affected for the anaerobic communities. We conclude that whole-ecosystem responses and several time-points are needed to fully understand the impact of stressors on microbial ecosystems, since resistance/resilience can differ among and within abiotic and biotic ecosystem components.

scholarly journals Functional Diversity within Gut Microbiomes: Implications for Conserving Biodiversity

Conservation ◽  
2021 ◽  
Vol 1 (4) ◽  
pp. 311-326
Author(s):  
Cameron S. Dodd ◽  
Catherine E. Grueber
Keyword(s):  
Microbial Communities ◽  
Environmental Changes ◽  
Amplicon Sequencing ◽  
Taxonomic Composition ◽  
Conservation Strategies ◽  
Careful Study ◽  
Microbiome Composition ◽  
Functional Perspective ◽  
Functional Characterisation ◽  
Microbiome Research

Conservation research has historically been conducted at the macro level, focusing on animals and plants and their role in the wider ecosystem. However, there is a growing appreciation of the importance of microbial communities in conservation. Most microbiome research in conservation thus far has used amplicon sequencing methods to assess the taxonomic composition of microbial communities and inferred functional capabilities from these data. However, as manipulation of the microbiome as a conservation tool becomes more and more feasible, there is a growing need to understand the direct functional consequences of shifts in microbiome composition. This review outlines the latest advances in microbiome research from a functional perspective and how these data can be used to inform conservation strategies. This review will also consider some of the challenges faced when studying the microbiomes of wild animals and how they can be overcome by careful study design and sampling methods. Environmental changes brought about by climate change or direct human actions have the potential to alter the taxonomic composition of microbiomes in wild populations. Understanding how taxonomic shifts affect the function of microbial communities is important for identifying species most threatened by potential disruption to their microbiome. Preservation or even restoration of these functions has the potential to be a powerful tool in conservation biology and a shift towards functional characterisation of gut microbiome diversity will be an important first step.

scholarly journals MON-022 Dissecting the Interplay Between Diet and PCOS Pathology on Gut Microbiota in a PCOS Mouse Model

2020 ◽  
Vol 4 (Supplement_1) ◽  
Author(s):  
Valentina Rodriguez Paris ◽  
Nadeem O Kaakoush ◽  
Samantha M Solon-Biet ◽  
Melissa C Edwards ◽  
William L Ledger ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Beta Diversity ◽  
Polycystic Ovary ◽  
Cell Metabolism ◽  
Consensus Sequence ◽  
Alpha Diversity ◽  
Operational Taxonomic Unit ◽  
Intestinal Microbiome ◽  
Alpha And Beta Diversity

Abstract The gut microbiome has been implicated in the development of metabolic disorders such as obesity and type-2 diabetes, and more recently polycystic ovary syndrome (PCOS). PCOS is a heterogeneous disorder with reproductive, endocrine and metabolic irregularities, and clinical and animal studies have reported that PCOS causes a decrease in microbial diversity and composition. Diet is an important regulator of the gut microbiome, and a recent study identified that alterations in macronutrient balance impact gut microbial communities which correlate with different metabolic health outcomes (1). We have identified that macronutrient balance impacts the development of PCOS traits. Therefore, to investigate the interplay between macronutrient balance and a PCOS environment on the gut microbiome, we analyzed the intestinal microbiome from fecal pellets of control and DHT-induced PCOS mice exposed to 10 different diets that varied systematically in protein (P), carbohydrate (C) and fat (F) content. The amount of dietary P, C and F consumed significantly altered alpha and beta diversity of the gut microbiota of pooled control and PCOS mice (P<0.0001). Alpha diversity between control and PCOS mice on the same diet did not differ significantly, and hence was only affected by diet composition. However, beta diversity was significantly altered between control and PCOS mice (P<0.05). We performed DESeq2 analysis and identified an operational taxonomic unit (OTU) within Bacteroides (OTU3) to be the most differentially abundant OTU between control and PCOS mice, with a significant decrease in PCOS mice compared to controls (control: 7.88 and PCOS: 5.38; fold change = 1.464; P<0.0001). The consensus sequence of Bacteroides OTU3 was found to share 99.2% similarity to Bacteroides acidifaciens. B. acidifaciens is associated with obesity with elevated levels reported to prevent the onset of obesity (2). Thus, we then investigated the influence of P, C and F on the relative abundance of Bacteroides OTU3 and revealed an association with C consumption, with increasing levels of C leading to increased levels of Bacteroides OTU3 (Carb: r= 0.22, p=0.0028, q=0.015). These findings demonstrate that diet exerts a stronger influence over the gut microbiome than PCOS pathology. However, the hyperandrogenic PCOS environment does lead to changes in gut microbiota beta diversity, with a specific decrease in an obesity-associated (2) Bacteroides species in PCOS mice that is also responsive to levels of C consumption. Reference: (1) Holmes et al., Cell Metabolism. 2017; 25(1): 140-151. (2) Yang et al., Mucosal Immunology. 2017, 10 (1), 104-116.

scholarly journals The Gills of Reef Fish Support a Distinct Microbiome Influenced by Host-Specific Factors

2018 ◽  
Vol 84 (9) ◽  
Author(s):  
Zoe A. Pratte ◽  
Marc Besson ◽  
Rebecca D. Hollman ◽  
Frank J. Stewart
Keyword(s):  
Microbial Communities ◽  
Reef Fish ◽  
Alpha Diversity ◽  
Comprehensive Analysis ◽  
Content Type ◽  
Microbiome Composition ◽  
Pathogen Invasion ◽  
Host Individual ◽  
Waste Exchange ◽  
Key Sites

ABSTRACT Teleost fish represent the most diverse of the vertebrate groups and play important roles in food webs, as ecosystem engineers, and as vectors for microorganisms. However, the microbial ecology of fishes remains underexplored for most host taxa and for certain niches on the fish body. This is particularly true for the gills, the key sites of respiration and waste exchange in fishes. Here we provide a comprehensive analysis of the gill microbiome. We focus on ecologically diverse taxa from coral reefs around Moorea, sampling the gills and intestines of adults and juveniles representing 15 families. The gill microbiome composition differed significantly from that of the gut for both adults and juveniles, with fish-associated niches having lower alpha diversity values and higher beta diversity values than those for seawater, sediment, and alga-associated microbiomes. Of ∼45,000 operational taxonomic units (OTUs) detected across all samples, 11% and 13% were detected only in the gill and the intestine, respectively. OTUs most enriched in the gill included members of the gammaproteobacterial genus Shewanella and the family Endozoicimonaceae . In adult fish, both gill and intestinal microbiomes varied significantly among host species grouped by diet category. Gill and intestinal microbiomes from the same individual were more similar to one another than to gill and intestinal microbiomes from different individuals. These results demonstrate that distinct body sites are jointly influenced by host-specific organizing factors operating at the level of the host individual. The results also identify taxonomic signatures unique to the gill and the intestine, confirming fish-associated niches as distinct reservoirs of marine microbial diversity. IMPORTANCE Fish breathe and excrete waste through their gills. The gills are also potential sites of pathogen invasion and colonization by other microbes. However, we know little about the microbial communities that live on the gill and the factors shaping their diversity. Focusing on ecologically distinct types of coral reef fish, we provide a comprehensive analysis of the fish gill microbiome. By comparison to microbiomes of the gut and the surrounding environment, we identify microbes unique to the gill niche. These microbes may be targets for further studies to determine the contribution of the microbiome to waste exchange or host immunity. We also show that despite exhibiting a unique taxonomic signature, the gill microbiome is influenced by factors that also influence the gut microbiome. These factors include the specific identity of the host individual. These results suggest basic principles describing how association with fishes structures the composition of microbial communities.

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