Synchronized shift of oral, faecal and urinary microbiotas in bats and natural infection dynamics during seasonal reproduction

Seasonal reproduction is a period of extreme physiological and behavioural changes, yet we know little about how it may affect host microbial communities (i.e. microbiota) and pathogen transmission. Here, we investigated shifts of the bacterial microbiota in saliva, urine and faeces during the seasonal reproduction of bats in South Africa, and test for an interaction in shedding patterns of both bacterial ( Leptospira ) and viral (adeno- and herpesviruses) agents. Based on a comparative approach in two cave-dwelling bat species and high-throughput sequencing of the 16S rRNA gene, we demonstrated a clear signature in microbiota changes over the reproduction season, consistent across the multiple body habitats investigated, and associated with the sex, age and reproductive condition of bats. We observed in parallel highly dynamic shedding patterns for both bacteria and viruses, but did not find a significant association between viral shedding and bacterial microbiota composition. Indeed, only Leptospira shedding was associated with alterations in both the diversity and composition of the urinary microbiota. These results illustrate how seasonal reproduction in bats substantially affects microbiota composition and infection dynamics, and have broad implications for the understanding of disease ecology in important reservoir hosts, such as bats.

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The Fecal Bacterial Microbiota in Horses with Equine Recurrent Uveitis

Animals ◽

10.3390/ani11030745 ◽

2021 ◽

Vol 11 (3) ◽

pp. 745

Author(s):

Michelle Martin de Bustamante ◽

Diego Gomez ◽

Jennifer MacNicol ◽

Ralph Hamor ◽

Caryn Plummer

Keyword(s):

Beta Diversity ◽

High Throughput Sequencing ◽

Illumina Miseq ◽

Diversity Indices ◽

Rrna Gene ◽

Linear Discriminant ◽

Alpha And Beta Diversity ◽

Bacterial Microbiota ◽

Healthy Control ◽

Equine Recurrent Uveitis

The objective of this study was to describe and compare the fecal bacterial microbiota of horses with equine recurrent uveitis (ERU) and healthy horses using next-generation sequencing techniques. Fecal samples were collected from 15 client-owned horses previously diagnosed with ERU on complete ophthalmic examination. For each fecal sample obtained from a horse with ERU, a sample was collected from an environmentally matched healthy control with no evidence of ocular disease. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. The relative abundance of predominant taxa, and alpha and beta diversity indices were calculated and compared between groups. The phyla Firmicutes, Bacteroidetes, Verrucomicrobia, and Proteobacteria predominated in both ERU and control horses, accounting for greater than 60% of sequences. Based on linear discriminant analysis effect size (LEfSe), no taxa were found to be enriched in either group. No significant differences were observed in alpha and beta diversity indices between groups (p > 0.05 for all tests). Equine recurrent uveitis is not associated with alteration of the gastrointestinal bacterial microbiota when compared with healthy controls.

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Bacterial microbiota similarity between predators and prey in a blue tit trophic network

The ISME Journal ◽

10.1038/s41396-020-00836-3 ◽

2021 ◽

Author(s):

Hélène Dion-Phénix ◽

Anne Charmantier ◽

Christophe de Franceschi ◽

Geneviève Bourret ◽

Steven W. Kembel ◽

...

Keyword(s):

Spatial Scales ◽

Trophic Levels ◽

Rrna Gene ◽

Microbiota Composition ◽

16S Rrna Gene Sequences ◽

Blue Tit ◽

Trophic Networks ◽

Bacterial Microbiota ◽

Trophic Network ◽

Blue Tits

AbstractTrophic networks are composed of many organisms hosting microbiota that interact with their hosts and with each other. Yet, our knowledge of the factors driving variation in microbiota and their interactions in wild communities is limited. To investigate the relation among host microbiota across a trophic network, we studied the bacterial microbiota of two species of primary producers (downy and holm oaks), a primary consumer (caterpillars), and a secondary consumer (blue tits) at nine sites in Corsica. To quantify bacterial microbiota, we amplified 16S rRNA gene sequences in blue tit feces, caterpillars, and leaf samples. Our results showed that hosts from adjacent trophic levels had a more similar bacterial microbiota than hosts separated by two trophic levels. Our results also revealed a difference between bacterial microbiota present on the two oak species, and among leaves from different sites. The main drivers of bacterial microbiota variation within each trophic level differed across spatial scales, and sharing the same tree or nest box increased similarity in bacterial microbiota for caterpillars and blue tits. This study quantifies host microbiota interactions across a three-level trophic network and illustrates how the factors shaping bacterial microbiota composition vary among different hosts.

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Comparative Analysis of Gut Microbiome between Captive and Wild Red Deer 1 (Cervus elaphus) in Inner Mongolia

10.21203/rs.3.rs-312376/v1 ◽

2021 ◽

Author(s):

Yue Sun ◽

Yanze Yu ◽

Jinhao Guo ◽

Linqiang Zhong ◽

Minghai Zhang

Keyword(s):

Cervus Elaphus ◽

Gut Microbiome ◽

Red Deer ◽

High Throughput Sequencing ◽

Intestinal Flora ◽

Rrna Gene ◽

Bacterial Microbiota ◽

Genetic Information Processing ◽

The Comparative Study ◽

Two Populations

Abstract The digestive tract of ruminants is the home of the gut microbiome ecosystem, which plays a huge role in the diagnosis of various health conditions and the analysis of physiological conditions in wild animals. Red deer is a second-class protected animal in China. In this study, we used microsatellite and high-throughput sequencing of the 16S rRNA gene in fecal samples of red deer to investigate differences in the gut bacterial microbiota were analyzed between wild and captive in winter. Our results revealed that proportions of bacterial taxa, alpha-and beta-diversities, and relative abundances of amplicon sequence variants in the gut bacterial microbiota of the two groups differed. Firmicutes (79.46%), Bacteroidetes (16%) and Tenericutes (1.25%) were the most predominant phyla in wild red deer. While in captive red deer, Firmicutes (62.5%) was the dominant phylum, followed by Bacteroidetes (29.1%) and Tenericutes.( 3.21%). The specific function and mechanism of Tenericutes in red deer need further study. The wild red deer had higher fecal bacterial diversity than the captive in farm. These differences were attributed to the enrichment of bacterial taxa involved in the digestion of the supplementary food and to different natural diets consumed in the forest. Also the dominant and differential microflora of intestinal microflora in various populations were mined and their related metabolic pathways. In terms of functional data, most of the genes annotated are related to metabolism. The second most commented gene is related to genetic information processing. The comparative study of the intestinal flora of the two populations can not only assess the health status of the two populations, but also provide important suggestions for the breeding of captive red deer and the protection of wild populations.

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Impact of Host Genetics on Caecal Microbiota Composition and on Salmonella Carriage in Chicken

10.21203/rs.3.rs-76645/v1 ◽

2020 ◽

Author(s):

Anaïs Cazals ◽

Jordi ESTELLÉ ◽

Nicolas BRUNEAU ◽

Jean-Luc COVILLE ◽

Pierrette MENANTEAU ◽

...

Keyword(s):

High Throughput Sequencing ◽

Genetic Selection ◽

Digital Pcr ◽

Taxonomic Composition ◽

Rrna Gene ◽

Microbiota Composition ◽

Experimental Conditions ◽

Host Genetics ◽

Abundant Otus ◽

Caecal Microbiota

Abstract Background Salmonella Enteritidis (SE) is one of the major causes of human foodborne intoxication through the consumption of contaminated poultry products. Genetic selection of animals more resistant to Salmonella carriage and the modulation of gut microbiota are two promising ways of decreasing individual Salmonella carriage. This study aims to identify the main genetic and microbial factors controlling the individual levels of Salmonella carriage in chickens (Gallus gallus) in controlled experimental conditions. Two-hundred and forty animals from the White Leghorn inbred lines, N and 61, were infected by SE at 7 days of age. After infection, animals were kept in isolators to reduce the recontamination of birds by Salmonella. Caecal contents were sampled at 12 days post-infection and used for DNA extraction. Microbiota DNA was used to measure individual counts of SE by digital PCR and to determine the bacterial taxonomic composition through a 16S rRNA gene high-throughput sequencing approach. Results Results confirmed that the N line is more resistant to Salmonella carriage than the 61 line, and that intra-line variability is higher for the 61 line. Furthermore, the 16S analysis showed strong significant differences in microbiota taxonomic composition between the two lines. Out of 617 Operational Taxonomic Units (OTUs), over 390 were differentially abundant between the two lines. Furthermore, within the 61 line, we found a difference in the microbiota taxonomic composition between high and low Salmonella carriers, with 39 differentially abundant OTUs. Finally, via metagenome functional prediction based on 16S data, we identified several metabolic pathways potentially associated to microbiota taxonomic differences (e.g. butyrate metabolism) between high and low carriers. Conclusions Overall, this study demonstrates that the caecal microbiota composition of the N and 61 lines is influenced by the host genetics, which could be one of the reasons why these lines differ for their Salmonella carriage in experimental infection conditions.

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Vaccination against the brown stomach worm, Teladorsagia circumcincta, followed by parasite challenge, induces inconsistent modifications in gut microbiota composition of lambs

Parasites & Vectors ◽

10.1186/s13071-021-04688-4 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

James Rooney ◽

Alba Cortés ◽

Riccardo Scotti ◽

Daniel R. G. Price ◽

Yvonne Bartley ◽

...

Keyword(s):

High Throughput Sequencing ◽

Sequence Data ◽

Rrna Gene ◽

Helminth Parasites ◽

Microbiota Composition ◽

Related Factors ◽

Experimental Conditions ◽

Teladorsagia Circumcincta ◽

Host Parasite

Abstract Background Growing evidence points towards a role of gastrointestinal (GI) helminth parasites of ruminants in modifying the composition of the host gut flora, with likely repercussions on the pathophysiology of worm infection and disease, and on animal growth and productivity. However, a thorough understanding of the mechanisms governing helminth-microbiota interactions and of their impact on host health and welfare relies on reproducibility and replicability of findings. To this aim, in this study, we analysed quantitative and qualitative fluctuations in the faecal microbiota composition of lambs vaccinated against, and experimentally infected with, the parasitic GI nematode Teladorsagia circumcincta over the course of two separate trials performed over two consecutive years. Methods Two trials were conducted under similar experimental conditions in 2017 and 2018, respectively. In each trial, lambs were randomly assigned to one of the following experimental groups: (i) vaccinated/infected, (ii) unvaccinated/infected and (iii) unvaccinated/uninfected. Faecal samples collected from individual animals were subjected to DNA extraction followed by high-throughput sequencing of the V3-V4 region of the bacterial 16S rRNA gene and bioinformatics and biostatistical analyses of sequence data. Results Substantial differences in the populations of bacteria affected by immunisation against and infection by T. circumcincta were detected when comparing data from the two trials. Nevertheless, the abundance of Prevotella spp. was significantly linked to helminth infection in both trials. Conclusions Despite the largely conflicting findings between the two trials, our data revealed that selected gut microbial populations are consistently affected by T. circumcincta infection and/or vaccination. Nevertheless, our study calls for caution when interpreting data generated from in vivo helminth-microbiome interaction studies that may be influenced by several intrinsic and extrinsic host-, parasite- and environment-related factors.

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The Effect of Holder Pasteurization on the Diversity of the Human Milk Bacterial Microbiota Using High-Throughput DNA Sequencing

Journal of Human Lactation ◽

10.1177/08903344211011946 ◽

2021 ◽

pp. 089033442110119

Author(s):

Igrid García-González ◽

Karina Corona-Cervantes ◽

Fernando Hernández-Quiroz ◽

Loan Edel Villalobos-Flores ◽

Flor Galván-Rodríguez ◽

...

Keyword(s):

Human Milk ◽

Bacterial Diversity ◽

High Throughput ◽

Rrna Gene ◽

Microbiota Composition ◽

Sequencing Data ◽

Cross Sectional ◽

Milk Samples ◽

Bacterial Microbiota ◽

Before And After

Background Human milk is the best food for infants; however, when breastfeeding is not possible, pasteurized milk from human milk banks is the best alternative. Little has been reported about variations in the bacterial microbiota composition of human milk after pasteurization. Research aim To characterize and compare the bacterial microbiota composition and diversity within human milk among Mexican mothers before and after the Holder pasteurization process. Methods: A cross-sectional, observational, and comparative design was used. The effect of the pasteurization process on the bacterial composition and diversity of human milk samples of donors ( N = 42) from a public milk bank was assessed before and after pasteurization by high throughput deoxyribonucleic acid sequencing of V3-16S rRNA gene libraries. Sequencing data were examined using the Quantitative Insights into Microbial Ecology software and Phyloseq in R environment. Results A varied community of bacteria was found in both raw and pasteurized human milk. The bacterial diversity of the milk samples was increased by the pasteurization, where some thermoduric bacteria of the phyla Proteobacteria, Firmicutes, and Actinobacteria were more abundant. The source tracker analysis indicated that at most 1.0% of bacteria may have come from another source, showing the safety of the process used to treat milk samples. Conclusion The pasteurization process increased the bacterial diversity. We selected taxa capable of surviving the process, which could proliferate after the treatment without being a risk for infants.

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The Bacterial Gut Microbiota of Adult Patients Infected, Colonized or Noncolonized by Clostridioides difficile

Microorganisms ◽

10.3390/microorganisms8050677 ◽

2020 ◽

Vol 8 (5) ◽

pp. 677 ◽

Cited By ~ 3

Author(s):

Monique J. T. Crobach ◽

Quinten R. Ducarmon ◽

Elisabeth M. Terveer ◽

Celine Harmanus ◽

Ingrid M. J. G. Sanders ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Microbiota Composition ◽

Clostridioides Difficile ◽

Bacterial Microbiota ◽

Differential Abundance Analysis ◽

Gut Microbiota Composition ◽

Eubacterium Hallii

Gut microbiota composition in patients with Clostridioides difficile colonization is not well investigated. We aimed to identify bacterial signatures associated with resistance and susceptibility to C. difficile colonization (CDC) and infection (CDI). Therefore, gut microbiota composition from patients with CDC (n = 41), with CDI (n = 41), and without CDC (controls, n = 43) was determined through 16S rRNA gene amplicon sequencing. Bacterial diversity was decreased in CDC and CDI patients (p < 0.01). Overall microbiota composition was significantly different between control, CDC, and CDI patients (p = 0.001). Relative abundance of Clostridioides (most likely C. difficile) increased stepwise from controls to CDC and CDI patients. In addition, differential abundance analysis revealed that CDI patients’ gut microbiota was characterized by significantly higher relative abundance of Bacteroides and Veillonella than CDC patients and controls. Control patients had significantly higher Eubacterium hallii and Fusicatenibacter abundance than colonized patients. Network analysis indicated that Fusicatenibacter was negatively associated with Clostridioides in CDI patients, while Veillonella was positively associated with Clostridioides in CDC patients. Bacterial microbiota diversity decreased in both CDC and CDI patients, but harbored a distinct microbiota. Eubacterium hallii and Fusicatenibacter may indicate resistance against C. difficile colonization and subsequent infection, while Veillonella may indicate susceptibility to colonization and infection by C. difficile.

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Impact of proanthocyanidin-rich apple intake on gut microbiota composition and polyphenol metabolomic activity in healthy mildly hypercholesterolemic subjects

Proceedings of The Nutrition Society ◽

10.1017/s002966512000436x ◽

2020 ◽

Vol 79 (OCE2) ◽

Author(s):

Athanasios Koutsos ◽

Maria M. Ulaszewska ◽

Kajetan Trošt ◽

Jan Stanstrup ◽

Letizia Mariani ◽

...

Keyword(s):

Gut Microbiota ◽

Phenolic Acids ◽

High Throughput Sequencing ◽

Daily Intake ◽

Rrna Gene ◽

Microbiota Composition ◽

Microbial Metabolites ◽

Potential Health ◽

Hypercholesterolemic Subjects ◽

Gut Microbiota Composition

AbstractApples are a rich source of polyphenols and fiber. Proanthocyanidins (PAs), the largest polyphenolic class in apples, can reach the colon almost intact where they interact with the gut microbiota producing simple phenolic acids. These metabolites have the potential to modulate gut microbiota composition and activity and impact on host physiology. A randomized, controlled, crossover, dietary intervention study was performed to determine the broad effects of whole apple intake on fecal gut microbiota composition and activity. Forty heathy mildly hypercholesterolemic volunteers (23 women, 17 men), with a mean BMI (± SD) 25.3 ± 3.7 kg/m2 and age 51 ± 11 years, consumed 2 apples/day (Renetta Canada, rich in PAs), or a sugar matched control apple beverage, for 8 weeks separated by a 4-week washout period in a random order. Fecal and 24-h urine samples were collected before and after each treatment. The broad effects of apple intake on fecal gut microbiota composition were explored by the high throughput sequencing (HTS) of 16S rRNA gene lllumina MiSeq sequencing (V3-V4 region). Sequencing data analysis was performed using the Quantitative Insight Into Microbial Ecology (QIIME) open-source pipeline version 1.9.1. Specific bacterial groups were also enumerated using the quantitative Fluorescence In Situ Hybridization (FISH). Furthermore, the potential formation of microbial polyphenol metabolites, after apple intake, was explored in urine using Liquid Chromatography (LC) High-Resolution Mass Spectrometry (HRMS) metabolomics. Preliminary analysis showed no changes in gut microbiota abundances measured by Illumina MiSeq, after correction for multiple testing. Apple intake significantly decreased Enterobacteriaceae population (P = 0.04) compared to the control beverage, as determined with FISH. Twenty-four polyphenol microbial metabolites were identified in higher concentrations in the apple group (P < 0.05) compared to the control, including valerolactones, valeric and phenolic acids. In conclusion, preliminary data suggest that the daily intake of 2 Renetta Canada apples significantly decreased Enterobacteriaceae population, a family known for its pathogenic members, in healthy mildly hypercholesterolemic subjects. Moreover, several polyphenol microbial metabolites were identified, suggesting that microbial activity is crucial and a prerequisite for the absorption of apple polyphenols, producing active metabolites with potential health benefits.

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DIVERSITY OF CULTURABLE BACTERIAL MICROBIOTA OF THE Eisenia foetida DIGESTIVE TRACT

Revista Fitotecnia Mexicana ◽

10.35196/rfm.2018.3.255-264 ◽

2018 ◽

Vol 41 (3) ◽

pp. 255-264 ◽

Cited By ~ 1

Author(s):

J. Abraham Pérez-Pérez ◽

David Espinosa-Victoria ◽

Hilda V. Silva-Rojas ◽

Lucía López-Reyes

Keyword(s):

Bacterial Diversity ◽

Digestive Tract ◽

Bacterial Species ◽

Brain Heart Infusion ◽

Rrna Gene ◽

Eisenia Foetida ◽

Bacterial Isolates ◽

Bacterial Microbiota ◽

Decomposition Of Organic Matter ◽

Earthworm Gut

Bacteria are an unavoidable component of the natural earthworm diet; thus, bacterial diversity in the earthworm gut is directly linked to decomposition of organic matter and development of the surrounding plants. The aim of this research was to isolate and to identify biochemically and molecularly the culturable bacterial microbiota of the digestive tract of Eisenia foetida. Earthworms were sourced from Instituto de Reconversión Productiva y Bioenergética (IRBIO) and Colegio de Postgraduados (COLPOS), México. Bacterial isolation was carried out on plates of Brain Heart Infusion (BHI) culture medium. Fifty six and 44 bacterial isolates were obtained from IRBIO and COLPOS, respectively. The population was composed of 44 Gram-negative and 56 Gram-positive isolates. Over 50 % of the bacterial isolates were rod-shaped cells. The 16S rRNA gene was sequenced and nine genera were identified in worms from IRBIO (Bacillus, Paenibacillus, Solibacillus, Staphylococcus, Arthrobacter, Pantoea, Stenotrophomonas, Acinetobacter and Aeromonas) and six in worms from COLPOS (Bacillus, Paenibacillus, Stenotrophomonas, Staphylococcus, Acinetobacter and Aeromonas). Bacillus was the predominant genus, with eight and six species in the oligochaetes from IRBIO and COLPOS, respectively. The most represented bacteria in the worms from both sites were Bacillus sp. and B. subtilis. The predominance of Bacillus was probably due to spore formation, a reproductive strategy that ensures survival and dispersion in the soil and oligochaetes digestive tract. The gut of E. foetida not only harbored bacterial species of agronomic importance but also species potentially pathogenic for humans (Staphylococcus warneri, Pantoea agglomerans and Stentrophomonas sp.). The larger bacterial diversity in worms from IRBIO could be due to their feeding on cattle manure, which is a rich source of bacteria.

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Gut Microbiome Changes in Captive Plateau Zokors (Eospalax baileyi)

Evolutionary Bioinformatics ◽

10.1177/1176934321996353 ◽

2021 ◽

Vol 17 ◽

pp. 117693432199635

Author(s):

Daoxin Liu ◽

Pengfei Song ◽

Jingyan Yan ◽

Haijing Wang ◽

Zhenyuan Cai ◽

...

Keyword(s):

Gut Microbiota ◽

Gut Microbiome ◽

High Throughput Sequencing ◽

Tibet Plateau ◽

Rrna Gene ◽

Diversity Analysis ◽

Bacterial Phyla ◽

In Captivity ◽

Relative Abundances ◽

Plateau Zokor

Wild-caught animals must cope with drastic lifestyle and dietary changes after being induced to captivity. How the gut microbiome structure of these animals will change in response receives increasing attention. The plateau zokor ( Eospalax baileyi), a typic subterranean rodent endemic to the Qinghai-Tibet plateau, spends almost the whole life underground and is well adapted to the environmental pressures of both plateau and underground. However, how the gut microbiome of the plateau zokor will change in response to captivity has not been reported to date. This study compared the microbial community structure and functions of 22 plateau zokors before (the WS group) and after being kept in captivity for 15 days (the LS group, fed on carrots) using the 16S rRNA gene via high-throughput sequencing technology. The results showed that the LS group retained 973 of the 977 operational taxonomic units (OTUs) in the WS group, and no new OTUs were found in the LS group. The dominant bacterial phyla were Bacteroides and Firmicutes in both groups. In alpha diversity analysis, the Shannon, Sobs, and ACE indexes of the LS group were significantly lower than those of the WS group. A remarkable difference ( P < 0.01) between groups was also detected in beta diversity analysis. The UPGMA clustering, NMDS, PCoA, and Anosim results all showed that the intergroup difference was significantly greater than the intragroup difference. And compared with the WS group, the intragroup difference of the gut microbiota in the LS group was much larger, which failed to support the assumption that similar diets should drive convergence of gut microbial communities. PICRUSt revealed that although some functional categories displayed significant differences between groups, the relative abundances of these categories were very close in both groups. Based on all the results, we conclude that as plateau zokors enter captivity for a short time, although the relative abundances of different gut microbiota categories shifted significantly, they can maintain almost all the OTUs and the functions of the gut microbiota in the wild. So, the use of wild-caught plateau zokors in gut microbial studies is acceptable if the time in captivity is short.

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