scholarly journals The Equine Faecal Microbiota Undergoes Step-wise Compositional Changes in Accordance With Increasing Levels of Domestication

2021 ◽  
Author(s):  
Katie Bull ◽  
Gareth Davies ◽  
Timothy Patrick Jenkins ◽  
Laura Elizabeth Peachey
Keyword(s):  
Adult Female ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Faecal Microbiota ◽  
Microbial Composition ◽  
Faecal Samples ◽  
High Incidence ◽  
Life Threatening ◽  
Group Variation ◽  
The Uk

Abstract BackgroundChanges to the gut microbiota are associated with an increased incidence of disease in many species. This is particularly important during the process of domestication, where captive animals commonly suffer from gastrointestinal (GI) pathology. Horses are a prime example of a species which suffers from a high incidence of (often life-threatening) GI diseases in domesticated environments. We aimed to indentify the gut microbial changes which occur due to domestication in horses by profiling the faecal microbiota of adult female Exmoor ponies under three management conditions, representing increasing levels of domestication.MethodsFaecal samples were collected from 29 adult female Exmoor ponies in the South West of the UK; ponies were categorised as Feral (n=10), Semi-Feral (n=10) and Domesticated (n=9), based on their management conditions; thus controlling for age, gender and random effects between groups. Diet and medication were recorded and faecal samples taken to assess parasite infection. Faecal microbial composition was profiled via high-throughput sequencing of the bacterial 16S rRNA gene.ResultsDownstream biostatistical analysis indicated profound step-wise changes in global microbial community structure in the transition from Feral to Semi-Feral to Domesticated groups. A relatively high abundance of members of the phylum Proteobacteria and Tenericutes were associated with the Domesticated group; and higher levels of Methanobacteria were seen in the Feral group. The Semi-Feral group frequently had intermediate levels of these taxa; however, they also exhibited the greatest ‘within group’ variation in bacterial diversity and parasites burdens. Functional predictions revealed increased amino acid and lipid metabolism in the Domesticated group and increased energy metabolism in the Feral group; supporting a hypothesis that differences in diet was the key driver of gut microbial composition. ConclusionsIf assumed the Feral population has a more natural gut microbial phenotype, akin to that with which horses have evolved, these data can potentially be used to provide microbial signitures of balanced gut homeostasis in horses; which, in turn, will aid prevention of GI disease in domesticated horses.

scholarly journals Effects of steam-flaked grains on foals’ growth and faecal microbiota

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Xiao Bin Li ◽  
Xin Xin Huang ◽  
Chang Jiang Zang ◽  
Chen Ma ◽  
Kai Xu Chen ◽  
...  
Keyword(s):  
Body Weight ◽  
Growth Performance ◽  
Relative Abundance ◽  
Alpha Diversity ◽  
The Body ◽  
Rrna Gene ◽  
Faecal Microbiota ◽  
Microbial Composition ◽  
Faecal Samples ◽  
Health And Development

Abstract Background There is little objective information concerning the effect of steam-flaked grains on foal’s growth performance and faecal microbiota. To determine the effects of steam-flaked grains on foal’s growth performance and faecal microbiota, faecal samples were collection from 18 foals which had been fed either corn, oat or barley diets over the 60 days of the experiment. Body weight and conformation measurements were collected. Next-generation sequencing of the V3 + V4 region of the 16 S rRNA gene was used to assess the microbial composition of faeces. Alpha diversity, Venn graph, Relative abundance and beta diversity are presented. Results There was a significantly higher larger increase in the body weight of those foals fed barley compared to either corn or oats. There were also significant changes in the Alpha diversity of the gut microbiota. The Shannon and Simpson indices were significantly higher in the barley fed group than those fed corn or oats. The Chao1 index was significantly higher in the oat fed group than the corn or barley fed groups. There were significant changes in the relative abundance of bacteria in the microbiota in terms of phylum, family and genus. The histogram of LDA value distribution showed that the 12 statistically different biomarkers of the bacteria were present. Tax4Fun function annotation clustering heat map showed that functional information was detected from 26 species of bacteria in faecal samples from the foals. Conclusions Differences by starch sources were found in overall growth of the foals and in the faecal microbiota if either supplementary corn, oat or barley was fed. Further studies are required to determine the potential impact of the changes in the microbiota on the health and development of foals fed cereal starch of different sources.

scholarly journals Experimental infection with the hookworm, Necator americanus, is associated with stable gut microbial diversity in human volunteers with relapsing multiple sclerosis

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Timothy P. Jenkins ◽  
David I. Pritchard ◽  
Radu Tanasescu ◽  
Gary Telford ◽  
Marina Papaiakovou ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Experimental Infection ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Placebo Treatment ◽  
Sequencing Data ◽  
Faecal Microbiota ◽  
Microbial Composition ◽  
Necator Americanus ◽  
Human Volunteers

Abstract Background Helminth-associated changes in gut microbiota composition have been hypothesised to contribute to the immune-suppressive properties of parasitic worms. Multiple sclerosis is an immune-mediated autoimmune disease of the central nervous system whose pathophysiology has been linked to imbalances in gut microbial communities. Results In the present study, we investigated, for the first time, qualitative and quantitative changes in the faecal bacterial composition of human volunteers with remitting multiple sclerosis (RMS) prior to and following experimental infection with the human hookworm, Necator americanus (N+), and following anthelmintic treatment, and compared the findings with data obtained from a cohort of RMS patients subjected to placebo treatment (PBO). Bacterial 16S rRNA high-throughput sequencing data revealed significantly decreased alpha diversity in the faecal microbiota of PBO compared to N+ subjects over the course of the trial; additionally, we observed significant differences in the abundances of several bacterial taxa with putative immune-modulatory functions between study cohorts. Parabacteroides were significantly expanded in the faecal microbiota of N+ individuals for which no clinical and/or radiological relapses were recorded at the end of the trial. Conclusions Overall, our data lend support to the hypothesis of a contributory role of parasite-associated alterations in gut microbial composition to the immune-modulatory properties of hookworm parasites.

scholarly journals Bioconductor workflow for microbiome data analysis: from raw reads to community analyses

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1492 ◽  
Author(s):  
Ben J. Callahan ◽  
Kris Sankaran ◽  
Julia A. Fukuyama ◽  
Paul J. McMurdie ◽  
Susan P. Holmes
Keyword(s):  
High Throughput Sequencing ◽  
Linear Models ◽  
Reference Database ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Nonparametric Testing ◽  
Abundance Estimates ◽  
Taxonomic Markers ◽  
Microbiome Data ◽  
Microbiome Data Analysis

High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or microbial composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, including both parameteric and nonparametric methods. We provide examples of using the R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests, partial least squares and linear models as well as nonparametric testing using community networks and the ggnetwork package.

Fruit Consumption is Associated with Alterations in Microbial Composition and Lower Rates of Pouchitis

2019 ◽  
Vol 13 (10) ◽  
pp. 1265-1272 ◽  
Author(s):  
L Godny ◽  
N Maharshak ◽  
L Reshef ◽  
I Goren ◽  
L Yahav ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Intestinal Inflammation ◽  
Disease Recurrence ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Fruit Consumption ◽  
Entire Cohort ◽  
Faecal Samples ◽  
16S Rrna Gene Pyrosequencing ◽  
Microbial Analysis

Abstract Background Patients with ulcerative colitis [UC] who undergo proctocolectomy with an ileal pouch–anal anastomosis commonly develop pouch inflammation [pouchitis]. Pouchitis develops in a previously normal small intestine and may involve environmental factors. We explored whether diet and microbiota alterations contributed to the pathogenesis of pouchitis. Methods Patients were recruited and prospectively followed at a comprehensive pouch clinic. Pouch behaviour was clinically defined as a normal pouch [NP] or pouchitis. Patients completed Food Frequency Questionnaires [FFQs]. Faecal samples were analysed for microbial composition [16S rRNA gene pyrosequencing]. Results Nutritional evaluation was performed in 172 patients [59% females], and of these, faecal microbial analysis was performed in 75 patients (microbiota cohort: NP [n = 22], pouchitis [n = 53]). Of the entire cohort, a subgroup of 39 [22.6%] patients had NP at recruitment [NP cohort]. Of these, 5 [12.8%] developed pouchitis within a year. Patients at the lowest tertile of fruit consumption [<1.45 servings/day] had higher rates of pouchitis compared with those with higher consumption [30.8% vs 3.8%, log rank, p = 0.03]. Fruit consumption was correlated with microbial diversity [r = 0.35, p = 0.002] and with the abundance of several microbial genera, including Faecalibacterium [r = 0.29, p = 0.01], Lachnospira [r = 0.38, p = 0.001], and a previously uncharacterized genus from the Ruminococcaceae family [r = 0.25, p = 0.05]. Reduction in fruit consumption over time was associated with disease recurrence and with reduced microbial diversity [Δ = –0.8 ± 0.3, p = 0.008]. Conclusions Fruit consumption is associated with modification of microbial composition, and lower consumption was correlated with the development of pouchitis. Thus, fruit consumption may protect against intestinal inflammation via alteration of microbial composition.

scholarly journals Microbial Composition of Human Appendices from Patients following Appendectomy

mBio ◽  
2013 ◽  
Vol 4 (1) ◽  
Author(s):  
Caitriona M. Guinane ◽  
Amany Tadrous ◽  
Fiona Fouhy ◽  
C. Anthony Ryan ◽  
Eugene M. Dempsey ◽  
...  
Keyword(s):  
Human Health ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Evolutionary Development ◽  
Rrna Gene ◽  
Limited Data ◽  
Microbial Composition ◽  
Content Type ◽  
Study Results ◽  
Human Appendix

ABSTRACT The human appendix has historically been considered a vestige of evolutionary development with an unknown function. While limited data are available on the microbial composition of the appendix, it has been postulated that this organ could serve as a microbial reservoir for repopulating the gastrointestinal tract in times of necessity. We aimed to explore the microbial composition of the human appendix, using high-throughput sequencing of the 16S rRNA gene V4 region. Seven patients, 5 to 25 years of age, presenting with symptoms of acute appendicitis were included in this study. Results showed considerable diversity and interindividual variability among the microbial composition of the appendix samples. In general, however, Firmicutes was the dominant phylum, with the majority of additional sequences being assigned at various levels to Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria. Despite the large diversity in the microbiota found within the appendix, however, a few major families and genera were found to comprise the majority of the sequences present. Interestingly, also, certain taxa not generally associated with the human intestine, including the oral pathogens Gemella, Parvimonas, and Fusobacterium, were identified among the appendix samples. The prevalence of genera such as Fusobacterium could also be linked to the severity of inflammation of the organ. We conclude that the human appendix contains a robust and varied microbiota distinct from the microbiotas in other niches within the human microbiome. The microbial composition of the human appendix is subject to extreme variability and comprises a diversity of biota that may play an important, as-yet-unknown role in human health. IMPORTANCE There are currently limited data available on the microbial composition of the human appendix. It has been suggested, however, that it may serve as a “safe house” for commensal bacteria that can reinoculate the gut at need. The present study is the first comprehensive view of the microbial composition of the appendix as determined by high-throughput sequencing. We have determined that the human appendix contains a wealth of microbes, including members of 15 phyla. Important information regarding the associated bacterial diversity of the appendix which will help determine the role, if any, the appendix microbiota has in human health is presented.

scholarly journals Faecal bacterial composition in dairy cows shedding Mycobacterium avium subsp. paratuberculosis in faeces in comparison with nonshedding cows

2016 ◽  
Vol 62 (6) ◽  
pp. 538-541 ◽  
Author(s):  
Marija Kaevska ◽  
Petra Videnska ◽  
Karel Sedlar ◽  
Iva Bartejsova ◽  
Alena Kralova ◽  
...  
Keyword(s):  
Dairy Cows ◽  
Mycobacterium Avium ◽  
Mycobacterium Avium Subsp ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Bacterial Composition ◽  
Bacterial Populations ◽  
Faecal Samples ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
The 16S Rrna Gene

The aim of this study was to determine possible differences in the faecal microbiota of dairy cows infected with Mycobacterium avium subsp. paratuberculosis (Johne’s disease) in comparison with noninfected cows from the same herds. Faecal samples from cows in 4 herds were tested for M. avium subsp. paratuberculosis by real-time PCR, and faecal bacterial populations were analysed by 454 pyrosequencing of the 16S rRNA gene. The most notable differences between shedding and nonshedding cows were an increase in the genus Psychrobacter and a decrease in the genera Oscillospira, Ruminococcus, and Bifidobacterium in cows infected with M. avium subsp. paratuberculosis. The present study is the first to report the faecal microbial composition in dairy cows infected with M. avium subsp. paratuberculosis.

scholarly journals Dietary resistant and butyrylated starches have different effects on the faecal bacterial flora of azoxymethane-treated rats

2011 ◽  
Vol 105 (10) ◽  
pp. 1480-1485 ◽  
Author(s):  
Guy C. J. Abell ◽  
Claus T. Christophersen ◽  
Alexandra L. McOrist ◽  
Julie M. Clarke
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Flora ◽  
Epidemiological Studies ◽  
Rrna Gene ◽  
Maize Starch ◽  
Faecal Microbiota ◽  
Faecal Samples ◽  
Gradient Gel Electrophoresis ◽  
High Amylose ◽  
Bowel Health

Epidemiological studies have suggested that dietary fibre lowers the risk of colorectal cancer, which may be due to increased butyrate production from colonic fermentation of a type of fibre, resistant starch (RS). The present study investigated the effects of dietary RS and butyrylated RS on the faecal microbiota of rats treated with azoxymethane. A total of four groups of nine rats were fed diets containing either standard maize starch (low-amylose maize starch (LAMS), low RS), LAMS with 3 % tributyrin (LAMST), cooked 10 % high-amylose maize starch (HAMS, high RS) or cooked 10 % butyrylated HAMS (HAMSB). Faecal samples were examined by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments. Multivariate analysis demonstrated no differences between faecal microbiota before treatment but revealed differences in DGGE patterns between diet groups, with the exception of the two low-RS groups (LAMS and LAMST). Subsequent analysis identified eleven DGGE bands contributing significantly to the differentiation between diets. These phylotypes belonged to Clostridiales (five),Lactobacillus(one) and Bacteroidetes (five) lineages. Rats fed HAMS had increased concentration of propionate in their distal colonic digesta and developed faecal populations containingRuminococcus bromii-like bacteria. HAMSB increased propionate and butyrate concentrations in distal colonic digesta and was associated with the appearance of two non-butyrate-producing bacteria,Lactobacillus gasseriandParabacteroides distasonis.In conclusion, supplementation with specific dietary RS leads to changes in faecal microbiota profiles that may be associated with improved bowel health.

scholarly journals Interactions between Teladorsagia circumcincta Infections and Microbial Composition of Sheep with or without Successful Monepantel Treatment—A Preliminary Study

Ruminants ◽  
2021 ◽  
Vol 1 (1) ◽  
pp. 31-45
Author(s):  
Craig A. Watkins ◽  
Dave J. Bartley ◽  
Burcu Gündüz Ergün ◽  
Büşra Yıldızhan ◽  
Tracy Ross-Watt ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Terminal Ileum ◽  
Anthelmintic Resistance ◽  
Economic Losses ◽  
Faecal Microbiota ◽  
Microbial Composition ◽  
Teladorsagia Circumcincta ◽  
Faecal Samples ◽  
Resistant Strains ◽  
Preliminary Study

Nematodes are one of the main impactors on the health, welfare and productivity of farmed animals. Teladorsagia circumcincta are endemic throughout many sheep-producing countries, particularly in the northern hemisphere, and contribute to the pathology and economic losses seen on many farms. Control of these nematode infections is essential and heavily reliant on chemotherapy (anthelmintics), but this has been compromised by the development of anthelmintic resistance. In mammals, the composition of the intestinal microbiota has been shown to have a significant effect on overall health. The interactions between host, microbiota and pathogens are complex and influenced by numerous factors. In this study, comparisons between intestinal and faecal microbiota of sheep infected with sensitive or resistant strains of T. circumcincta, with or without monepantel administration were assessed. The findings from both faecal samples and terminal ileum mucosal scrapings showed clear differences between successfully treated animals and those sheep that were left untreated and/or those carrying resistant nematodes. Specifically, the potentially beneficial genus Bifidobacterium was identified as elevated in successfully treated animals. The detection of these and other biomarkers will provide the basis for new therapeutic reagents particularly relevant to the problems of emerging multidrug anthelmintic resistance.

scholarly journals Benchmarking DNA isolation kits used in analyses of the urinary microbiome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lisa Karstens ◽  
Nazema Y. Siddiqui ◽  
Tamara Zaza ◽  
Alecsander Barstad ◽  
Cindy L. Amundsen ◽  
...  
Keyword(s):  
Beta Diversity ◽  
High Throughput Sequencing ◽  
Dna Isolation ◽  
Urine Samples ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Alpha And Beta Diversity ◽  
Dna Yield ◽  
Urinary Microbiome ◽  
Buffer Control

AbstractThe urinary microbiome has been increasingly characterized using next-generation sequencing. However, many of the technical methods have not yet been specifically optimized for urine. We sought to compare the performance of several DNA isolation kits used in urinary microbiome studies. A total of 11 voided urine samples and one buffer control were divided into 5 equal aliquots and processed in parallel using five commercial DNA isolation kits. DNA was quantified and the V4 segment of the 16S rRNA gene was sequenced. Data were processed to identify the microbial composition and to assess alpha and beta diversity of the samples. Tested DNA isolation kits result in significantly different DNA yields from urine samples. DNA extracted with the Qiagen Biostic Bacteremia and DNeasy Blood & Tissue kits showed the fewest technical issues in downstream analyses, with the DNeasy Blood & Tissue kit also demonstrating the highest DNA yield. Nevertheless, all five kits provided good quality DNA for high throughput sequencing with non-significant differences in the number of reads recovered, alpha, or beta diversity.

scholarly journals The skin microbiome of cow-nose rays (Rhinoptera bonasus) in an aquarium touch-tank exhibit

2016 ◽  
Author(s):  
Patrick J Kearns ◽  
Jennifer L Bowen ◽  
Michael F Tlusty
Keyword(s):  
Microbial Community ◽  
New England ◽  
High Throughput Sequencing ◽  
Ventral Surface ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Microbial Composition ◽  
Human Interactions ◽  
Rhinoptera Bonasus ◽  
Public Aquarium

Public aquarium exhibits offer numerous educational opportunities for visitors while touch tank exhibits offer guests the ability to directly interact with marine life. However, despite the popularity of these exhibits, the effect of human interactions on the host-associated microbiome or the habitat microbiome remains unclear. Microbial communities, both host-associated and habitat associated can have great implications for host health and habitat function. To better understand the link between human interactions and the microbiome of a touch tank we used high-throughput sequencing of the 16S rRNA gene to analyze the microbial community on the dorsal and ventral surfaces of cow-nose rays (Rhinoptera bonasus) as well as its environment in a frequently visited touch tank exhibit at the New England Aquarium. Our analyses revealed a distinct microbial community associated with the skin of the ray that had lower diversity than the surrounding habitat. The ray skin was dominated by three orders: Burkholderiales (~55%), Flavobacteriales (~19%) and Pseudomonadales (~12%), suggesting a potentially important role of these taxa in ray health. Further, there was no difference between dorsal and ventral surface of the ray in terms of microbial composition or diversity, and a very low presence of common human-associated microbial taxa (<1.5%). Our results suggest that human contact has a minimal effect on the skin and habitat microbiome of the cow-nose ray and that the ray skin harbors a distinct and lower diversity microbial community than its environment.

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