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.

scholarly journals Supplementation of a lacto-fermented rapeseed-seaweed blend promotes gut microbial- and gut immune-modulation in weaner piglets

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yan Hui ◽  
Paulina Tamez-Hidalgo ◽  
Tomasz Cieplak ◽  
Gizaw Dabessa Satessa ◽  
Witold Kot ◽  
...  
Keyword(s):  
Immune Modulation ◽  
Amplicon Sequencing ◽  
Saccharina Latissima ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Colon Mucosa ◽  
Weaned Piglets ◽  
Brown Macroalgae ◽  
Blood Concentrations ◽  
Significant Difference

Abstract Background The direct use of medical zinc oxide in feed will be abandoned after 2022 in Europe, leaving an urgent need for substitutes to prevent post-weaning disorders. Results This study investigated the effect of using rapeseed-seaweed blend (rapeseed meal added two brown macroalgae species Ascophylum nodosum and Saccharina latissima) fermented by lactobacilli (FRS) as feed ingredients in piglet weaning. From d 28 of life to d 85, the piglets were fed one of three different feeding regimens (n = 230 each) with inclusion of 0%, 2.5% and 5% FRS. In this period, no significant difference of piglet performance was found among the three groups. From a subset of piglets (n = 10 from each treatment), blood samples for hematology, biochemistry and immunoglobulin analysis, colon digesta for microbiome analysis, and jejunum and colon tissues for histopathological analyses were collected. The piglets fed with 2.5% FRS manifested alleviated intraepithelial and stromal lymphocytes infiltration in the gut, enhanced colon mucosa barrier relative to the 0% FRS group. The colon microbiota composition was determined using V3 and V1-V8 region 16S rRNA gene amplicon sequencing by Illumina NextSeq and Oxford Nanopore MinION, respectively. The two amplicon sequencing strategies showed high consistency between the detected bacteria. Both sequencing strategies indicated that inclusion of FRS reshaped the colon microbiome of weaned piglets with increased Shannon diversity. Prevotella stercorea was verified by both methods to be more abundant in the piglets supplied with FRS feed, and its abundance was positively correlated with colonic mucosa thickness but negatively correlated with blood concentrations of leucocytes and IgG. Conclusions FRS supplementation relieved the gut lymphocyte infiltration of the weaned piglets, improved the colon mucosa barrier with altered microbiota composition. Increasing the dietary inclusion of FRS from 2.5% to 5% did not lead to further improvements.

scholarly journals Comparative Analysis of Fecal Microbiota Composition Between Rheumatoid Arthritis and Osteoarthritis Patients

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 748 ◽  
Author(s):  
Jin-Young Lee ◽  
Mohamed Mannaa ◽  
Yunkyung Kim ◽  
Jehun Kim ◽  
Geun-Tae Kim ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Bacterial Species ◽  
Amplicon Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Stool Samples ◽  
Gut Microbiota Composition

The aim of this study was to investigate differences between the gut microbiota composition in patients with rheumatoid arthritis (RA) and those with osteoarthritis (OA). Stool samples from nine RA patients and nine OA patients were collected, and DNA was extracted. The gut microbiome was assessed using 16S rRNA gene amplicon sequencing. The structures and differences in the gut microbiome between RA and OA were analyzed. The analysis of diversity revealed no differences in the complexity of samples. The RA group had a lower Bacteroidetes: Firmicutes ratio than did the OA group. Lactobacilli and Prevotella, particularly Prevotella copri, were more abundant in the RA than in the OA group, although these differences were not statistically significant. The relative abundance of Bacteroides and Bifidobacterium was lower in the RA group. At the species level, the abundance of certain bacterial species was significantly lower in the RA group, such as Fusicatenibacter saccharivorans, Dialister invisus, Clostridium leptum, Ruthenibacterium lactatiformans, Anaerotruncus colihominis, Bacteroides faecichinchillae, Harryflintia acetispora, Bacteroides acidifaciens, and Christensenella minuta. The microbial properties of the gut differed between RA and OA patients, and the RA dysbiosis revealed results similar to those of other autoimmune diseases, suggesting that a specific gut microbiota pattern is related to autoimmunity.

scholarly journals Higher fiber complementary food alters Fecal microbiota composition and normalizes stool form in Malawian children: A randomized trial

2021 ◽  
Vol 21 (04) ◽  
pp. 17854-17875
Author(s):  
Edda Lungu ◽  
◽  
J Auger ◽  
A Piano ◽  
WJ Dahl ◽  
...  
Keyword(s):  
Dietary Intake ◽  
Bacterial Species ◽  
Amplicon Sequencing ◽  
Fecal Microbiota ◽  
Stool Frequency ◽  
Sub Saharan Africa ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Linear Discriminant ◽  
Stool Form

Dietary fiber favorably modulates gut microbiota and may be protective against diarrhea in sub-Saharan Africa where rates in infants and young children are high. Soybean hull is high in fiber and accessible in rural Africa; however, its use in complementary feeding has not been evaluated. The objective of this study was to determine the acceptability and feasibility of a soybean, soy hull fiber, and maize (SFM) blend food; the primary outcome was compliance to the feeding protocol. Secondary outcomes were stool form and frequency, fecal microbiota composition, growth and dietary intake. In a parallel, single-blind study, children 6-36 months of age from the Lilongwe district of Malawi were randomized to receive daily SFM (n=69) or maize only(n=10) porridge(phala) for 6 months. Anthropometrics were measured monthly, and compliance, stool frequency,and stool form, weekly. At baseline, 3-month,and 6-month (study end) time points, dietary intake (24-h recall) was assessed,and fecal samples were collected. Fecal DNA was analyzed by Real-Time polymerase chain reaction (PCR) for microbes of interest and 16S rRNA gene amplicon sequencing. Mothers accessed the acceptability and feasibility of the study foods at study end. Mothers reported excellent compliance to feeding the SFM porridge, rated it more acceptable than maize,and noted improved appetite, weight, and stool consistency of their children. Stool frequency at baseline (2±1 stools/d) was unchanged with intervention; however, there were significantly fewer diarrhea-type stools reported during study months 4-6 vs.1-3 for the SFM group, whereas no improvement was seen for the maize group. At study end, the fecal abundance ofAkkermansia muciniphila was enriched in children receiving the SFM, compared to maize (p<0.05), and a trend for increased Faecalibacterium prausnitzii (p=0.07) was seen. A comparison of fecal microbiota composition using linear discriminant analysis effect size (LEfSe)showed notable differences in numerous taxa in the SFM group compared to baseline, whereas the maize comparator exhibited fewer changes. Fiber intake was higher for the SFMgroup, compared to maize at 6 months (13.7±3.8 vs. 8.4±4.5 g/day, p<0.01). Weight-for-height and BMI-for-age Z-scores were significantly higher for the SFM group. In young Malawian children, feeding a blend of soybean, soy hulls and maize reduced diarrhea-type stools and increased the abundance of Akkermansia muciniphila, a bacterial species involved in maintaining intestinal health, and thus may provide a feasible means of improving wellness in children in resource-poor settings through the modulation of microbiota composition.

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 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.

scholarly journals Supplementation of a lacto-fermented rapeseed-seaweed blend promotes gut microbial- and gut immune-modulation in weaner piglets

2020 ◽  
Author(s):  
Yan Hui ◽  
Paulina Tamez-Hidalgo ◽  
Tomasz Cieplak ◽  
Gizaw Dabessa Satessa ◽  
Witold Kot ◽  
...  
Keyword(s):  
Basal Diet ◽  
Amplicon Sequencing ◽  
Saccharina Latissima ◽  
Blood Levels ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Colon Mucosa ◽  
Gut Health ◽  
Microbial Composition ◽  
Final Body Weight

AbstractThe direct use of medical zinc oxide (ZnO) in feed will be abandoned after 2022 in Europe, leaving an urgent need for substitutes to prevent post-weaning disorders. This study assessed whether rapeseed meal added two brown macroalagae species (Saccharina latissima and Ascophylum nodosum) and fermented using lactic acid bacteria (FRS) could improve piglet performance and gut health. The weaned piglets were fed one of three different feeding regimens (n = 230 each): basal diet, 2.5% and 5% FRS from day 28 of life to day 85. The piglets fed with 2.5% FRS presented superior phenotype with alleviated intraepithelial and stromal lymphocytes infiltration in the gut, enhanced colon mucosa barrier as well as numerically improvements of final body weight. Colon microbiota composition was determined using amplicon sequencing of the V3 and V1 – V8 region of the 16S rRNA gene using Illumina Nextseq and Oxford Nanopore MinION sequencing, respectively. The two amplicon sequencing strategies showed high consistence between the detected bacteria. Both sequencing technologies showed that the FRS fed piglets had a distinctly different microbial composition relative to the basal diet. Compared with piglets fed the basal diet, Prevotella stercorea was verified by both technologies to be more abundant in the FRS piglets, and positively correlated with colon mucosa thickness and negatively correlated with blood levels of leucocytes and IgG. In conclusion, FRS supplementation improved gut health of weaner piglets, and altered their gut microbiota composition. Increasing the dietary inclusion of FRS from 2.5% to 5% did not cause further improvements.

scholarly journals The vaginal and fecal microbiomes are related to pregnancy status in beef heifers

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Feilong Deng ◽  
Maryanna McClure ◽  
Rick Rorie ◽  
Xiaofan Wang ◽  
Jianmin Chai ◽  
...  
Keyword(s):  
Illumina Miseq ◽  
First Trimester ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Beef Heifers ◽  
Microbial Composition ◽  
Fecal Samples ◽  
Fecal Microbiome ◽  
Bovine Reproduction ◽  
Pregnancy Status

Abstract Background The greatest impact on profitability of a commercial beef operation is reproduction. However, in beef heifers, little is known about the vaginal and fecal microbiota with respect to their relationship with fertility. To this end, we followed heifers through gestation to examine the dynamics of vaginal and fecal microbial composition throughout pregnancy. Results Heifers were exposed to an estrus synchronization protocol, observed over a 12-day period, artificially inseminated 12 h to 18 h after observed estrus, and subsequently exposed to bulls for a 50-day breeding season. Vaginal samples were taken at pre-breeding (n = 72), during the first (n = 72), and second trimester (n = 72) for all individuals, and third trimester for individuals with confirmed pregnancies (n = 56). Fecal samples were taken at pre-breeding (n = 32) and during the first trimester (n = 32), including bred and open individuals. Next generation sequencing of the V4 region of the16S rRNA gene via the Illumina MiSeq platform was applied to all samples. Shannon indices and the number of observed bacterial features were the same in fecal samples. However, significant differences in vaginal microbiome diversity between gestation stages were observed. No differences in beta-diversity were detected in vaginal or fecal samples regarding pregnancy status, but such differences were seen with fecal microbiome over time. Random Forest was developed to identify predictors of pregnancy status in vaginal (e.g., Histophilus, Clostridiaceae, Campylobacter) and fecal (e.g., Bacteroidales, Dorea) samples. Conclusions Our study shows that bovine vaginal and fecal microbiome could be used as biomarkers of bovine reproduction. Further experiments are needed to validate these biomarkers and to examine their roles in a female’s ability to establish pregnancy.

scholarly journals Adults with Prader–Willi syndrome exhibit a unique microbiota profile

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Wendy J. Dahl ◽  
Jérémie Auger ◽  
Zainab Alyousif ◽  
Jennifer L. Miller ◽  
Thomas A. Tompkins
Keyword(s):  
Adult Population ◽  
Geographical Location ◽  
Gastrointestinal Transit ◽  
Amplicon Sequencing ◽  
Fecal Microbiota ◽  
Machine Learning Algorithms ◽  
Rrna Gene ◽  
Prader Willi Syndrome ◽  
Microbiota Composition ◽  
Gastrointestinal Transit Time

Abstract Objective Adults with Prader–Willi syndrome (PWS) require less energy intake to maintain body weight than the general adult population. This, combined with their altered gastrointestinal transit time, may impact microbiota composition. The aim of the study was to determine if the fecal microbiota composition of adults with PWS differed from non-affected adults. Using usual diet/non-interventional samples, fecal microbiota composition was analyzed using 16S rRNA gene amplicon sequencing and data from adults with PWS were merged with four other adult cohorts that differed by geographical location and age. QIIME 2™ sample-classifier, machine learning algorithms were used to cross-train the samples and predict from which dataset the taxonomic profiles belong. Taxa that most distinguished between all datasets were extracted and a visual inspection of the R library PiratePlots was performed to select the taxa that differed in abundance specific to PWS. Results Fecal microbiota composition of adults with PWS showed low Blautia and enhanced RF39 (phyla Tenericutes), Ruminococcaceae, Alistipes, Erysipelotrichacaea, Parabacteriodes and Odoribacter. Higher abundance of Tenericutes, in particular, may be a signature characteristic of the PWS microbiota although its relationship, if any, to metabolic health is not yet known.

scholarly journals Impact of Ambient Temperature Sample Storage on the Equine Fecal Microbiota

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 819
Author(s):  
Michelle Martin de Bustamante ◽  
Caryn Plummer ◽  
Jennifer MacNicol ◽  
Diego Gomez
Keyword(s):  
Ambient Temperature ◽  
Room Temperature ◽  
High Throughput Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Sample Storage ◽  
Sample Collection ◽  
Microbial Composition ◽  
Fecal Samples ◽  
Community Membership

Sample storage conditions are an important factor in fecal microbiota analyses in general. The objective of this study was to investigate the effect of sample storage at room temperature on the equine fecal microbiota composition. Fecal samples were collected from 11 healthy horses. Each sample was divided into 7 sealed aliquots. One aliquot was immediately frozen at −80 °C; the remaining aliquots were stored at room temperature (21 to 22 °C) with one transferred to the freezer at each of the following time points: 6, 12, 24, 48, 72 and 96 h. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. Fibrobacteraceae (Fibrobacter) and Ruminococcaceae (Ruminococcus) were enriched in samples from 0 h and 6 h, whereas taxa from the families Bacillaceae, Planococcaceae, Enterobacteriaceae and Moraxellaceae were enriched in samples stored at room temperature for 24 h or greater. Samples frozen within the first 12 h after collection shared similar community membership. The community structure was similar for samples collected at 0 h and 6 h, but it was significantly different between samples frozen at 0 h and 12 h or greater. In conclusion, storage of equine fecal samples at ambient temperature for up to 6 h before freezing following sample collection had minimal effect on the microbial composition. Longer-term storage at ambient temperature resulted in alterations in alpha-diversity, community membership and structure and the enrichment of different taxa when compared to fecal samples immediately frozen at −80 °C.

scholarly journals The Composition and Predictive Function of the Fecal Microbiota Differ Between Young and Adult Donkeys

2020 ◽  
Vol 11 ◽  
Author(s):  
Jingya Xing ◽  
Guiqin Liu ◽  
Xinzhuang Zhang ◽  
Dongyi Bai ◽  
Jie Yu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Community Composition ◽  
Age Groups ◽  
Fecal Microbiota ◽  
Microbial Colonization ◽  
Rrna Gene ◽  
Functional Prediction ◽  
Microbial Composition ◽  
Significant Difference ◽  
And Function

The community of microorganisms inhabiting the gastrointestinal tract of monogastric herbivores played critical roles in the absorption of nutrients and keeping the host healthy. However, its establishment at different age groups has not been quantitatively and functionally examined. The knowledge of microbial colonization and its function in the intestinal tract of different-age donkeys is still limited. By applying the V3–V4 region of the bacterial 16S rRNA gene and functional prediction on fecal samples from different-age donkeys, we characterized the gut microbiota during the different age groups. In contrast to the adult donkeys, the gut microbiota diversity and richness of the young donkeys showed significantly less resemblance. The microbial data showed that diversity and richness increased with age, but a highly individual variation of microbial composition was observed at month 1. Principal coordinate analysis (PCoA) revealed a significant difference across five time points in the feces. The abundance of Bacteroides, Lactobacillus, and Odoribacter tended to decrease, while the proportion of Streptococcus was significantly increased with age. For functional prediction, the relative abundance of pathways had a significant difference in the feces across different age groups, for example, Terpenoids and Polyketides and Folding, Sorting, and Degradation (P &lt; 0.05 or P &lt; 0.01). The analysis of beta diversity (PCoA and LEfSe) and microbial functions predicted with PICRUSt (NSTIs) clearly divided the donkeys into foals (≤3 months old) and adults (≥7 months old). Microbial community composition and structure had distinctive features at each age group, in accordance with functional stability of the microbiota. Our findings established a framework for understanding the composition and function of the fecal microbiota to differ between young and adult donkeys.

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