scholarly journals A cross-sectional study of the nasal and fecal microbiota of sows from different health status within six commercial swine farms

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12120
Author(s):  
Andreia G. Arruda ◽  
Loic Deblais ◽  
Vanessa L. Hale ◽  
Christopher Madden ◽  
Monique Pairis-Garcia ◽  
...  
Keyword(s):  
Health Status ◽  
Alpha Diversity ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Upper Respiratory Tract ◽  
Microbial Composition ◽  
Cross Sectional ◽  
Swine Farms ◽  
Nasal Microbiota

Background Cull sows are a unique population on swine farms, often representing poor producing or compromised animals, and even though recent studies have reported that the microbiome is associated with susceptibility to diseases, the microbiome of the cull sow population has not been explored. The main objective of this study was to investigate whether there were differences in fecal and upper respiratory tract microbiota composition for groups of sows of different health status (healthy, cull, and compromised/ clinical sows) and from different farms (1 to 6). Methods Six swine farms were visited once. Thirty individual fecal samples and nasal swabs were obtained at each farm and pooled by five across health status and farm. Samples underwent 16S rRNA gene amplicon sequencing and nasal and fecal microbiota were analyzed using QIIME2 v.2021.4. Results Overall, the diversity of the nasal microbiota was lower than the fecal microbiota (p < 0.01). No significant differences were found in fecal or nasal alpha diversity by sow’s health status or by farm. There were significant differences in nasal microbial composition by farm and health status (PERMANOVA, p < 0.05), and in fecal microbiota by farm (PERMANOVA, p < 0.05), but not by health status. Lastly, at the L7 level, there was one differentially abundant taxa across farms for each nasal and fecal pooled samples. Discussion This study provided baseline information for nasal and fecal microbiota of sows under field conditions, and results suggest that farm of origin can affect microbial diversity and composition. Furthermore, sow’s health status may have an impact on the nasal microbiota composition.

Alterations of gut microbiome in autoimmune hepatitis

Gut ◽  
2019 ◽  
Vol 69 (3) ◽  
pp. 569-577 ◽  
Author(s):  
Yiran Wei ◽  
Yanmei Li ◽  
Li Yan ◽  
Chunyan Sun ◽  
Qi Miao ◽  
...  
Keyword(s):  
Autoimmune Hepatitis ◽  
Gut Microbiome ◽  
Alpha Diversity ◽  
Disease Status ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Healthy Controls ◽  
Microbial Composition ◽  
Cross Sectional ◽  
Treatment Naïve

ObjectiveThe significance of the liver-microbiome axis has been increasingly recognised as a major modulator of autoimmunity. The aim of this study was to take advantage of a large well-defined corticosteroids treatment-naïve group of patients with autoimmune hepatitis (AIH) to rigorously characterise gut dysbiosis compared with healthy controls.DesignWe performed a cross-sectional study of individuals with AIH (n=91) and matched healthy controls (n=98) by 16S rRNA gene sequencing. An independent cohort of 28 patients and 34 controls was analysed to validate the results. All the patients were collected before corticosteroids therapy.ResultsThe gut microbiome of steroid treatment-naïve AIH was characterised with lower alpha-diversity (Shannon and observed operational taxonomic units, both p<0.01) and distinct overall microbial composition compared with healthy controls (p=0.002). Depletion of obligate anaerobes and expansion of potential pathobionts including Veillonella were associated with disease status. Of note, Veillonella dispar, the most strongly disease-associated taxa (p=8.85E–8), positively correlated with serum level of aspartate aminotransferase and liver inflammation. Furthermore, the combination of four patients with AIH-associated genera distinguished AIH from controls with an area under curves of approximately 0.8 in both exploration and validation cohorts. In addition, multiple predicted functional modules were altered in the AIH gut microbiome, including lipopolysaccharide biosynthesis as well as metabolism of amino acids that can be processed by bacteria to produce immunomodulatory metabolites.ConclusionOur study establishes compositional and functional alterations of gut microbiome in AIH and suggests the potential for using gut microbiota as non-invasive biomarkers to assess disease activity.

scholarly journals Nasal and gut microbiota for sows of different health status within six commercial swine farms from one swine production system

2019 ◽  
Author(s):  
Andréia Gonçalves Arruda ◽  
Loic Deblais ◽  
Vanessa Hale ◽  
Monique Pairis-Garcia ◽  
Vishal Srivastava ◽  
...  
Keyword(s):  
Health Status ◽  
Gut Microbiota ◽  
Beta Diversity ◽  
Animal Health ◽  
Alpha Diversity ◽  
Considerable Proportion ◽  
Upper Respiratory Tract ◽  
Fecal Samples ◽  
Cull Sows ◽  
Nasal Microbiota

AbstractSow culling is an essential practice in swine herds to optimize animal health and productivity; and cull sows represent a considerable proportion of the herd at any given time point. Even though recent studies have reported that the microbiome is associated with susceptibility to diseases, the microbiome in the cull sow population has not been explored. The main objective of this study was to investigate whether there were differences in abundance and diversity of microbes encountered in the gut and upper respiratory tract of sows of different health status (healthy, cull, and compromised cull sows) and different farms. Farms were visited once, 30 individual fecal and nasal swab samples were obtained per farm; and pooled across animals by health status and farm in pools of five. Genomic DNA was extracted and samples were subjected to MiSeq 16S rRNA sequencing using Illumina MiSeq. Diversity analyses were conducted using QIIME. Alpha diversity was analyzed using observed OTUs, PD Whole Tree, and Chao1; and beta diversity was assessed using weighted UniFrac. The mean number of OTUs was 3,846.97±9,078.87 and 28,747.92±14,090.50 for nasal and fecal pooled samples, respectively. Diversity of the nasal microbiota was low compared to the gut microbiota. For nasal samples, there was a difference in diversity between samples from farms 1-6 using the Chao1 metric (p = 0.0005); and weighted beta diversity values indicated clustering by health status. For fecal samples, there was no difference in diversity between compromised, cull, and healthy sows; or between samples from farms 1-6. Weighted PCoA analyses showed an influence of farm of origin on the diversity of pooled fecal samples. Finally, differences at the genus level were found in the fecal microbiota composition of sows of different health status and farm of origin; but not for nasal microbiota.

scholarly journals Gut Microbiota Composition and Metabolomic Profiles of Wild and Captive Chinese Monals (Lophophorus lhuysii) 

2020 ◽  
Author(s):  
Dandan Jiang ◽  
Xin He ◽  
Marc Valitutto ◽  
Li Chen ◽  
Qin Xu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
High Performance ◽  
Bird Species ◽  
Alpha Diversity ◽  
Integrated Approach ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Metabolomic Profile ◽  
Gut Microbiota Composition

Abstract Background：The Chinese monal (Lophophorus lhuysii) is an endangered bird species, with a wild population restricted to the mountains of southwest China, and only one known captive population in the world. We investigated the fecal microbiota and metabolome of wild and captive Chinese monals to explore differences and similarities in nutritional status and digestive characteristics. An integrated approach combining 16S ribosomal RNA (16S rRNA) gene sequencing and ultra-high performance liquid chromatography (UHPLC) based metabolomics were used to examine the fecal microbiota composition and the metabolomic profile of Chinese monals. Results: The results showed that the alpha diversity of gut microbes in the wild group were significantly higher than that in the captive group and the core bacterial taxa in the two groups showed remarkable differences at phylum, class, order, and family levels. Metabolomic profiling also revealed differences, mainly related to galactose, starch and sucrose metabolism, fatty acid, bile acid biosynthesis and bile secretion. Furthermore, strong correlations of metabolite types and bacterial genus were detected. Conclusions: There were remarkable differences in the gut microbiota composition and metabolomic profile between wild and captive Chinese monals. This study has established a baseline for a normal gut microbiota and metabolomic profile for wild Chinese monals, thus allowing us to evaluate if differences seen in captive organisms have an impact on their overall health and reproduction.

scholarly journals Sugar Beet Pectin Supplementation Did Not Alter Profiles of Fecal Microbiota and Exhaled Breath in Healthy Young Adults and Healthy Elderly

Nutrients ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 2193 ◽  
Author(s):  
Ran An ◽  
Ellen Wilms ◽  
Agnieszka Smolinska ◽  
Gerben D.A. Hermes ◽  
Ad A.M. Masclee ◽  
...  
Keyword(s):  
Young Adults ◽  
Sugar Beet ◽  
Healthy Aging ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Exhaled Breath ◽  
Microbiota Composition ◽  
Microbial Composition ◽  
Double Blind ◽  
Healthy Elderly

Aging is accompanied with increased frailty and comorbidities, which is potentially associated with microbiome perturbations. Dietary fibers could contribute to healthy aging by beneficially impacting gut microbiota and metabolite profiles. We aimed to compare young adults with elderly and investigate the effect of pectin supplementation on fecal microbiota composition, short chain fatty acids (SCFAs), and exhaled volatile organic compounds (VOCs) while using a randomized, double-blind, placebo-controlled parallel design. Fifty-two young adults and 48 elderly consumed 15 g/day sugar beet pectin or maltodextrin for four weeks. Fecal and exhaled breath samples were collected before and after the intervention period. Fecal samples were used for microbiota profiling by 16S rRNA gene amplicon sequencing, and for analysis of SCFAs by gas chromatography (GC). Breath was used for VOC analysis by GC-tof-MS. Young adults and elderly showed similar fecal SCFA and exhaled VOC profiles. Additionally, fecal microbiota profiles were similar, with five genera significantly different in relative abundance. Pectin supplementation did not significantly alter fecal microbiota, SCFA or exhaled VOC profiles in elderly or young adults. In conclusion, aside from some minor differences in microbial composition, healthy elderly and young adults showed comparable fecal microbiota composition and activity, which were not altered by pectin supplementation.

scholarly journals Gut microbiota composition and metabolomic profiles of wild and captive Chinese monals (Lophophorus lhuysii)

2020 ◽  
Vol 17 (1) ◽  
Author(s):  
Dandan Jiang ◽  
Xin He ◽  
Marc Valitutto ◽  
Li Chen ◽  
Qin Xu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
High Performance ◽  
Bird Species ◽  
Alpha Diversity ◽  
Integrated Approach ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Metabolomic Profile ◽  
Gut Microbiota Composition

Abstract Background The Chinese monal (Lophophorus lhuysii) is an endangered bird species, with a wild population restricted to the mountains in southwest China, and only one known captive population in the world. We investigated the fecal microbiota and metabolome of wild and captive Chinese monals to explore differences and similarities in nutritional status and digestive characteristics. An integrated approach combining 16S ribosomal RNA (16S rRNA) gene sequencing and ultra-high performance liquid chromatography (UHPLC) based metabolomics were used to examine the fecal microbiota composition and the metabolomic profile of Chinese monals. Results The results showed that the alpha diversity of gut microbes in the wild group were significantly higher than that in the captive group and the core bacterial taxa in the two groups showed remarkable differences at phylum, class, order, and family levels. Metabolomic profiling also revealed differences, mainly related to galactose, starch and sucrose metabolism, fatty acid, bile acid biosynthesis and bile secretion. Furthermore, strong correlations between metabolite types and bacterial genus were detected. Conclusions There were remarkable differences in the gut microbiota composition and metabolomic profile between wild and captive Chinese monals. This study has established a baseline for a normal gut microbiota and metabolomic profile for wild Chinese monals, thus allowing us to evaluate if differences seen in captive organisms have an impact on their overall health and reproduction.

scholarly journals Feeding Pre-weaned Calves With Waste Milk Containing Antibiotic Residues Is Related to a Higher Incidence of Diarrhea and Alterations in the Fecal Microbiota

2021 ◽  
Vol 8 ◽  
Author(s):  
Martina Penati ◽  
Giulia Sala ◽  
Filippo Biscarini ◽  
Antonio Boccardo ◽  
Valerio Bronzo ◽  
...  
Keyword(s):  
Alpha Diversity ◽  
Operational Taxonomic Unit ◽  
Fecal Microbiota ◽  
Resistant Bacteria ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
16S Rrna Gene Analysis ◽  
Gastrointestinal Health ◽  
Milk Substitute ◽  
Waste Milk

The cows receiving antibiotics for intra-mammary infection (IMI) produce milk that cannot be marketed. This is considered waste milk (WM), and a convenient option for farmers is using it as calf food. However, adding to the risk of selecting resistant bacteria, residual antibiotics might interfere with the gut microbiome development and influence gastrointestinal health. We assessed the longitudinal effect of unpasteurized WM containing residual cefalexin on calf intestinal health and fecal microbiota in an 8-week trial. After 3 days of colostrum, six calves received WM and six calves received bulk tank milk (BM) for 2 weeks. For the following 6 weeks, all 12 calves received milk substitute and starter feed. Every week for the first 2 weeks and every 2 weeks for the remaining 6 weeks, we subjected all calves to clinical examination and collected rectal swabs for investigating the fecal microbiota composition. Most WM calves had diarrhea episodes in the first 2 weeks of the trial (5/6 WM and 1/6 BM), and their body weight was significantly lower than that of BM calves. Based on 16S rRNA gene analysis, WM calves had a lower fecal microbiota alpha diversity than that in BM calves, with the lowest p-value at Wk4 (p &lt; 0.02), 2 weeks after exposure to WM. The fecal microbiota beta diversity of the two calf groups was also significantly different at Wk4 (p &lt; 0.05). Numerous significant differences were present in the fecal microbiota taxonomy of WM and BM calves in terms of relative normalized operational taxonomic unit (OTU) levels, affecting five phyla, seven classes, eight orders, 19 families, and 47 genera. At the end of the trial, when 6 weeks had passed since exposure to WM, the phyla Bacteroidetes, Firmicutes, and Saccharibacteria were lower, while Chlamydiae were higher in WM calves. Notably, WM calves showed a decrease in beneficial taxa such as Faecalibacterium, with a concomitant increase in potential pathogens such as Campylobacter, Pseudomonas, and Chlamydophila spp. In conclusion, feeding pre-weaned calves with unpasteurized WM containing antibiotics is related to a higher incidence of neonatal diarrhea and leads to significant changes in the fecal microbiota composition, further discouraging this practice in spite of its short-term economic advantages.

scholarly journals Altered Fecal Microbiota Signatures in Patients With Anxiety and Depression in the Gastrointestinal Cancer Screening: A Case-Control Study

2021 ◽  
Vol 12 ◽  
Author(s):  
Juan Zhu ◽  
Minjuan Li ◽  
Dantong Shao ◽  
Shanrui Ma ◽  
Wenqiang Wei
Keyword(s):  
Cancer Screening ◽  
Gastrointestinal Cancer ◽  
Large Scale ◽  
Alpha Diversity ◽  
Fecal Microbiota ◽  
Anxiety And Depression ◽  
Control Group ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Depression Group

Background: Increasing attention has been devoted to cancer screening and microbiota in recent decades, but currently there is less focus on microbiota characterization among screeners and its relationship to anxiety and depression.Methods: We characterized the microbial communities of fecal samples collected through the FOBT card from anxiety and depression screeners and paired controls in Henan, China (1:2, N = 69). DNA was extracted using the MOBIO PowerSoil kit. The V4 region of the 16S rRNA gene was sequenced using MiniSeq and processed using QIIME1. LEfSe was used to identify differentially abundant microbes, the Wilcoxon rank-sum test was used to test alpha diversity differences, and permutational multivariate analysis of variance was used to test for differences in beta diversity.Results: Similar fecal microbiota signatures in composition were found among screeners. The intestinal microbial environments by phylum were all composed primarily of Firmicutes, Bacteroidetes, and Proteobacteria, and the corresponding top genera were Faecalibacterium, Roseburia, and Prevotella. Compared with controls, the ranking of the top five genera in the anxiety and depression group changed, and the dominant genus was Prevotella in the anxiety and depression group and Faecalibacterium in the control group. There was a lower relative abundance of Gemmiger (1.4 vs. 2.3%, P = 0.025), Ruminococcus (0.6 vs. 0.8%, P = 0.037), and Veillonella (0.6 vs. 1.3%, P = 0.020). This may be linked to the lower alpha diversity in participants with anxiety and depression (Observed OTUs: 122.35 vs. 143.24; Chao1: 127.35 vs. 149.98), although no significant differences were observed. Distinct clustering in microbial composition between the two groups was detected for the Jaccard distance (P = 0.011).Conclusions: Our study showed differing microbial characterization among participants with anxiety and depression in the endoscopic screening of upper gastrointestinal cancer. Gemmiger, Ruminococcus, and Veillonella were informative and have potential clinical implications, which need to be confirmed by large-scale, prospective cohort studies and biological mechanism research.

scholarly journals Gut Microbiota Associations with Metabolic Health and Obesity Status in Older Adults

Nutrients ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 2364 ◽  
Author(s):  
Xiaozhong Zhong ◽  
Janas M. Harrington ◽  
Seán R. Millar ◽  
Ivan J. Perry ◽  
Paul W. O’Toole ◽  
...  
Keyword(s):  
Older Adults ◽  
Health Status ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Alpha Diversity ◽  
Metabolic Health ◽  
Rrna Gene ◽  
Phylogenetic Distance ◽  
Microbiota Composition ◽  
Gut Microbiota Composition

Emerging evidence links the gut microbiota with several chronic diseases. However, the relationships between metabolic syndrome (MetS), obesity and the gut microbiome are inconsistent. This study aimed to investigate associations between gut microbiota composition and diversity and metabolic health status in older adults (n = 382; median age = 69.91 [± 5 years], male = 50.79%) with and without obesity. Gut microbiome composition was determined by sequencing 16S rRNA gene amplicons. Results showed that alpha diversity and richness, as indicated by the Chao1 index (p = 0.038), phylogenetic diversity (p = 0.003) and observed species (p = 0.038) were higher among the metabolically healthy non-obese (MHNO) individuals compared to their metabolically unhealthy non-obese (MUNO) counterparts. Beta diversity analysis revealed distinct differences between the MHNO and MUNO individuals on the phylogenetic distance scale (R2 = 0.007, p = 0.004). The main genera contributing to the gut composition among the non-obese individuals were Prevotella, unclassified Lachnospiraceae, and unclassified Ruminococcaceae. Prevotella, Blautia, Bacteroides, and unclassified Ruminococcaceae mainly contributed to the variation among the obese individuals. Co-occurrence network analysis displayed different modules pattern among different metabolic groups and revealed groups of microbes significantly correlated with individual metabolic health markers. These findings confirm relationships between metabolic health status and gut microbiota composition particularly, among non-obese older adults.

scholarly journals Plasma Metabolites Related to Peripheral and Hepatic Insulin Sensitivity Are Not Directly Linked to Gut Microbiota Composition

Nutrients ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 2308
Author(s):  
Annefleur M. Koopen ◽  
Nicolien C. de Clercq ◽  
Moritz V. Warmbrunn ◽  
Hilde Herrema ◽  
Mark Davids ◽  
...  
Keyword(s):  
Insulin Sensitivity ◽  
Gut Microbiota ◽  
Prediction Models ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Plasma Metabolites ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Cross Sectional ◽  
Gut Microbiota Composition

Plasma metabolites affect a range of metabolic functions in humans, including insulin sensitivity (IS). A subset of these plasma metabolites is modified by the gut microbiota. To identify potential microbial–metabolite pathways involved in IS, we investigated the link between plasma metabolites, gut microbiota composition, and IS, using the gold-standard for peripheral and hepatic IS measurement in a group of participants with metabolic syndrome (MetSyn). In a cross-sectional study with 115 MetSyn participants, fasting plasma samples were collected for untargeted metabolomics analysis and fecal samples for 16S rRNA gene amplicon sequencing. A two-step hyperinsulinemic euglycemic clamp was performed to assess peripheral and hepatic IS. Collected data were integrated and potential interdependence between metabolites, gut microbiota, and IS was analyzed using machine learning prediction models. Plasma metabolites explained 13.2% and 16.7% of variance in peripheral and hepatic IS, respectively. Fecal microbiota composition explained 4.2% of variance in peripheral IS and was not related to hepatic IS. Although metabolites could partially explain the variances in IS, the top metabolites related to peripheral and hepatic IS did not significantly correlate with gut microbiota composition (both on taxonomical level and alpha-diversity). However, all plasma metabolites could explain 18.5% of the variance in microbial alpha-diversity (Shannon); the top 20 metabolites could even explain 44.5% of gut microbial alpha-diversity. In conclusion, plasma metabolites could partially explain the variance in peripheral and hepatic IS; however, these metabolites were not directly linked to the gut microbiota composition, underscoring the intricate relation between plasma metabolites, the gut microbiota, and IS in MetSyn

scholarly journals Analysis of the developing gut microbiota in young dairy calves—impact of colostrum microbiota and gut disturbances

2020 ◽  
Vol 53 (1) ◽  
Author(s):  
Bui Phan Thu Hang ◽  
Ewa Wredle ◽  
Johan Dicksved
Keyword(s):  
Average Daily Gain ◽  
Amplicon Sequencing ◽  
Fecal Microbiota ◽  
Dairy Calves ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Microbial Composition ◽  
Fecal Samples ◽  
Calf Health ◽  
Significant Difference

AbstractThe aim of this study was to characterize the colostrum and fecal microbiota in calves and to investigate whether fecal microbiota composition was related to colostrum microbiota or factors associated with calf health. Colostrum samples were collected in buckets after hand milking of 76 calving cows from 38 smallholder dairy farms. Fecal samples were taken directly from the rectum of 76 calves at birth and at 14 days age. The bacterial community structure in colostrum and feces was analyzed by terminal restriction fragment length polymorphism for all samples, and the microbial composition was determined by 16S rRNA gene amplicon sequencing for a subset of the samples (8 colostrum, 40 fecal samples). There was a significant difference in fecal microbiota composition between day 0 and day 14 samples, but no associations between the microbiota and average daily gain, birth weight, or transfer of passive immunity. At 14 days of age, Faecalibacterium and Butyricicoccus were prevalent in higher relative abundances in the gut of healthy calves compared to calves with diarrhea that had been treated with antimicrobials. Colostrum showed great variation in composition of microbiota but no association to fecal microbiota. This study provides the first insights into the composition of colostrum and fecal microbiota of young dairy calves in southern Vietnam and can form the basis for future more detailed studies.

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