scholarly journals An investigation of seasonal variations in the microbiota of milk, feces, bedding, and airborne dust

2020 ◽  
Vol 33 (11) ◽  
pp. 1858-1865 ◽  
Author(s):  
Thuong Thi Nguyen ◽  
Haoming Wu ◽  
Naoki Nishino
Keyword(s):  
Seasonal Variation ◽  
Dairy Cow ◽  
Dairy Farm ◽  
Amplicon Sequencing ◽  
Milk Composition ◽  
Fecal Microbiota ◽  
Cow Milk ◽  
Rrna Gene ◽  
Airborne Dust ◽  
The Relationship

Objective: The microbiota of dairy cow milk varies with the season, and this accounts in part for the seasonal variation in mastitis-causing bacteria and milk spoilage. The microbiota of the cowshed may be the most important factor because the teats of a dairy cow contact bedding material when the cow is resting. The objectives of the present study were to determine whether the microbiota of the milk and the cowshed vary between seasons, and to elucidate the relationship between the microbiota.Methods: We used 16S rRNA gene amplicon sequencing to investigate the microbiota of milk, feces, bedding, and airborne dust collected at a dairy farm during summer and winter.Results: The seasonal differences in the milk yield and milk composition were marginal. The fecal microbiota was stable across the two seasons. Many bacterial taxa of the bedding and airborne dust microbiota exhibited distinctive seasonal variation. In the milk microbiota, the abundances of Staphylococcaceae, Bacillaceae, Streptococcaceae, Microbacteriaceae, and Micrococcaceae were affected by the seasons; however, only Micrococcaceae had the same seasonal variation pattern as the bedding and airborne dust microbiota. Nevertheless, canonical analysis of principle coordinates revealed a distinctive group comprising the milk, bedding, and airborne dust microbiota.Conclusion: Although the milk microbiota is related to the bedding and airborne dust microbiota, the relationship may not account for the seasonal variation in the milk microbiota. Some major bacterial families stably found in the bedding and airborne dust microbiota, e.g., Staphylococcaceae, Moraxellaceae, Ruminococcaceae, and Bacteroidaceae, may have greater influences than those that varied between seasons.

506. The importance of machine milking rate in dairy cow management and breeding

1953 ◽  
Vol 20 (2) ◽  
pp. 138-145 ◽  
Author(s):  
F. H. Dodd ◽  
A. S. Foot
Keyword(s):  
Dairy Cows ◽  
Dairy Cow ◽  
Peak Flow ◽  
Milk Composition ◽  
Regression Coefficients ◽  
Partial Regression ◽  
Fat Percentage ◽  
Machine Milking ◽  
Lactation Length ◽  
The Relationship

An analysis has been carried out on the milk yield, milk composition and milking-rate records collected in one herd of dairy cows.It has been shown from the results of eighty-six heifers that for each pound per minute increase in inherent milking rate (i.e. peak flow) the standard lactation yield increases by 419 lb., the maximum daily yield by 0·9 lb., the lactation length by 8 days and the persistency index by 10 days, whilst the lactation solids-not-fat percentage decreases by 0·03 and the fat percentage by 0·04. All except the last coefficient were significant, although it was also shown that the relationship with solids-not-fat percentage was due to an interaction. Similarly, by the calculation of partial regression coefficients it was demonstrated that the relationship between milking rate and standard lactation yield was due to the effect of milking rate on maximum daily yield, lactation length and persistency.

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 Assessing the microbiota of recycled bedding sand on a Wisconsin dairy farm

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hannah E. Pilch ◽  
Andrew J. Steinberger ◽  
Donald C. Sockett ◽  
Nicole Aulik ◽  
Garret Suen ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Pathogenic Bacteria ◽  
Bacterial Community Composition ◽  
Dairy Farm ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Recycling System ◽  
Core Microbiota ◽  
Relative Abundances

Abstract Background Sand is often considered the preferred bedding material for dairy cows as it is thought to have lower bacterial counts than organic bedding materials and cows bedded on sand experience fewer cases of lameness and disease. Sand can also be efficiently recycled and reused, making it cost-effective. However, some studies have suggested that the residual organic material present in recycled sand can serve as a reservoir for commensal and pathogenic bacteria, although no studies have yet characterized the total bacterial community composition. Here we sought to characterize the bacterial community composition of a Wisconsin dairy farm bedding sand recycling system and its dynamics across several stages of the recycling process during both summer and winter using 16S rRNA gene amplicon sequencing. Results Bacterial community compositions of the sand recycling system differed by both seasons and stage. Summer samples had higher richness and distinct community compositions, relative to winter samples. In both summer and winter samples, the diversity of recycled sand decreased with time drying in the recycling room. Compositionally, summer sand 14 d post-recycling was enriched in operational taxonomic units (OTUs) belonging to the genera Acinetobacter and Pseudomonas, relative to freshly washed sand and sand from cow pens. In contrast, no OTUs were found to be enriched in winter sand. The sand recycling system contained an overall core microbiota of 141 OTUs representing 68.45% ± 10.33% SD of the total bacterial relative abundance at each sampled stage. The 4 most abundant genera in this core microbiota included Acinetobacter, Psychrobacter, Corynebacterium, and Pseudomonas. Acinetobacter was present in greater abundance in summer samples, whereas Psychrobacter and Corynebacterium had higher relative abundances in winter samples. Pseudomonas had consistent relative abundances across both seasons. Conclusions These findings highlight the potential of recycled bedding sand as a bacterial reservoir that warrants further study.

scholarly journals Differential Somatic Cell Count as a Marker for Changes of Milk Composition in Cows with Very Low Somatic Cell Count

Animals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 604 ◽  
Author(s):  
Alfonso Zecconi ◽  
Francesca Dell’Orco ◽  
Diego Vairani ◽  
Nicoletta Rizzi ◽  
Micaela Cipolla ◽  
...  
Keyword(s):  
Somatic Cell ◽  
Cell Count ◽  
Milk Fat ◽  
Somatic Cell Count ◽  
Milk Composition ◽  
Cow Milk ◽  
Udder Health ◽  
Lactating Cows ◽  
Accuracy Of Measurements ◽  
The Relationship

The recent availability of a high-throughput milk analyzer performing a partial differential somatic cell count (DSCC) opened new opportunities in investigations on bovine udder health. This analyzer has a potential limitation on the accuracy of measurements when the somatic cell count (SCC) is below 50,000 cells/mL, values characterizing a good proportion of lactating cows in many herds. We obtained data for cows below this threshold, assessed the repeatability of these measurements and investigated the relationship between DSCC and udder health, milk composition and yield. Overall, 3022 cow milk test records performed on a Fossomatic™ 7/DC (Foss A/S, Hillerød, Denmark) were considered; 901 of them had an SCC ≤ 50,000 cells/mL. These latter samples were analyzed by qPCR to identify the presence of bacteria. Overall, 20.75% of the samples (187) were positive. However, the health status did not have any significant association with DSCC. The analysis of the association of DSCC on milk fat, protein and casein showed a significant decrease in their proportions as the DSCC increased, whereas it was not observed for milk yield and lactose. Therefore, DSCC in very low SCC cows may be suggested as a marker to identify early changes in milk composition.

scholarly journals Gut Microbiota and Dietary Intake of Normal-Weight and Overweight Filipino Children

2020 ◽  
Vol 8 (7) ◽  
pp. 1015
Author(s):  
Maria Julia Golloso-Gubat ◽  
Quinten R. Ducarmon ◽  
Robby Carlo A. Tan ◽  
Romy D. Zwittink ◽  
Ed J. Kuijper ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Amplicon Sequencing ◽  
Developed Countries ◽  
Normal Weight ◽  
Rrna Gene ◽  
Overweight Children ◽  
Cross Sectional ◽  
Filipino Children ◽  
Overweight Group ◽  
The Relationship

Diet and body mass index (BMI) have been shown to affect the gut microbiota of children, but studies are largely performed in developed countries. Here, we conducted a cross-sectional investigation on the differences in the bacterial gut microbiota between normal-weight and overweight urban Filipino children, and determined the relationship between their energy, macronutrient and dietary fiber intakes, and their gut microbiota composition and diversity. Forty-three children (normal-weight, n = 32; overweight, n = 11) participated in the study. Energy and fiber intakes were collected using a semi-quantitative Food Frequency Questionnaire (FFQ). The gut microbiota was profiled using 16S rRNA gene amplicon sequencing of the V3–V4 region. The diet of the children was a mixture of traditional and Western patterns. There were no significant differences in energy, macronutrients and energy-adjusted fiber intakes between the normal-weight and overweight groups, but there were significantly more children meeting the recommended fiber intake in the overweight group. Alpha and beta bacterial diversities did not significantly differ between weight groups. Relative abundance of Bifidobacterium, Turicibacter and Clostridiaceae 1 were higher in the normal-weight than overweight children, and Lachnospira was higher in overweight children.

scholarly journals Fecal microbiome signatures of pancreatic cancer patients

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Elizabeth Half ◽  
Nirit Keren ◽  
Leah Reshef ◽  
Tatiana Dorfman ◽  
Ishai Lachter ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Early Detection ◽  
Screening Method ◽  
Amplicon Sequencing ◽  
Developed Countries ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Alcoholic Fatty Liver ◽  
Fecal Microbiome ◽  
Chinese Cohort

AbstractPancreatic cancer (PC) is a leading cause of cancer-related death in developed countries, and since most patients have incurable disease at the time of diagnosis, developing a screening method for early detection is of high priority. Due to its metabolic importance, alterations in pancreatic functions may affect the composition of the gut microbiota, potentially yielding biomarkers for PC. However, the usefulness of these biomarkers may be limited if they are specific for advanced stages of disease, which may involve comorbidities such as biliary obstruction or diabetes. In this study we analyzed the fecal microbiota of 30 patients with pancreatic adenocarcinoma, 6 patients with pre-cancerous lesions, 13 healthy subjects and 16 with non-alcoholic fatty liver disease, using amplicon sequencing of the bacterial 16S rRNA gene. Fourteen bacterial features discriminated between PC and controls, and several were shared with findings from a recent Chinese cohort. A Random Forest model based on the microbiota classified PC and control samples with an AUC of 82.5%. However, inter-subject variability was high, and only a small part of the PC-associated microbial signals were also observed in patients with pre-cancerous pancreatic lesions, implying that microbiome-based early detection of such lesions will be challenging.

scholarly journals Rabbit microbiota across the whole body revealed by 16S rRNA gene amplicon sequencing

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiaofen Hu ◽  
Fei Wang ◽  
Shanshan Yang ◽  
Xu Yuan ◽  
Tingyu Yang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Amplicon Sequencing ◽  
Whole Body ◽  
Rrna Gene ◽  
Microbial Function ◽  
Relationship Of ◽  
The Relationship ◽  
Microbial Samples

Abstract Background Rabbit can produce meat, fur and leather, and serves as an important biomedical animal model. Understanding the microbial community of rabbits helps to raise rabbits healthily and better support their application as animal models. Results In this study, we selected 4 healthy Belgium gray rabbits to collect the microbial samples from 12 body sites, including skin, lung, uterus, mouth, stomach, duodenum, ileum, jejunum, colon, cecum, cecal appendix and rectum. The microbiota across rabbit whole body was investigated via 16S rRNA gene amplicon sequencing. After quality control, 46 samples were retained, and 3,148 qualified ASVs were obtained, representing 23 phyla and 264 genera. Based on the weighted UniFrac distances, these samples were divided into the large intestine (Lin), stomach and small intestine (SSin), uterus (Uter), and skin, mouth and lung (SML) groups. The diversity of Lin microbiota was the highest, followed by those of the SSin, Uter and SML groups. In the whole body, Firmicutes (62.37%), Proteobacteria (13.44%) and Bacteroidota (11.84%) were the most predominant phyla. The relative abundance of Firmicutes in the intestinal tract was significantly higher than that in the non-intestinal site, while Proteobacteria was significantly higher in the non-intestinal site. Among the 264 genera, 35 were the core microbiota distributed in all body sites. Sixty-one genera were specific in the SML group, while 13, 8 and 1 were specifically found in the Lin, SSin and Uter groups, respectively. The Lin group had the most difference with other groups, there were average 72 differential genera between the Lin and other groups. The functional prediction analysis showed that microbial function within each group was similar, but there was a big difference between the intestinal tracts and the non-intestinal group. Notably, the function of microorganism in uterus and mouth were the most different from those in the gastrointestinal sites; rabbit’s coprophagy of consuming soft feces possibly resulted in little differences of microbial function between stomach and large intestinal sites. Conclusion Our findings improve the knowledge about rabbit microbial communities throughout whole body and give insights into the relationship of microbial communities among different body sites in health rabbits.

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.

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