Correction: Fecal microbiome of periparturient dairy cattle and associations with the onset of Salmonella shedding.
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ABSTRACT:
SUBMITTER: PLOS ONE Staff
PROVIDER: S-EPMC6373964 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Non-typhoidal Salmonella enterica is a zoonotic pathogen with critical importance in animal and public health. The persistence of Salmonella on farms affects animal productivity and health, and represents a risk for food safety. The intestinal microbiota plays a fundamental role in the colonization and invasion of this ubiquitous microorganism. To overcome the colonization resistance imparted by the gut microbiome, Salmonella uses invasion strategies and the host inflammatory response to survive, proliferate, and establish infections with diverse clinical manifestations. Cattle serve as reservoirs of Salmonella, and periparturient cows have high prevalence of Salmonella shedding; however, little is known about the association between the gut microbiome and the onset of Salmonella shedding during the periparturient period. Thus, the objective of this study was to assess the association between changes in bacterial communities and the onset of Salmonella shedding in cattle approaching parturition. In a prospective cohort study, fecal samples from 98 dairy cows originating from four different farms were collected at four time points relative to calving (-3 wks, -1 wk, +1 wk, +3 wks). All 392 samples were cultured for Salmonella. Sequencing of the V4 region of the 16S rRNA gene using the Illumina platform was completed to evaluate the fecal microbiome in a selected sample subset. Analyses of microbial composition, diversity, and structure were performed according to time points, farm, and Salmonella onset status. Individual cow fecal microbiomes, predominated by Bacteroidetes, Firmicutes, Spirochaetes, and Proteobacteria phyla, significantly changed before and after parturition. Microbial communities from different farms were distinguishable based on multivariate analysis. Although there were significant differences in some bacterial taxa between Salmonella positive and negative samples, our results did not identify differences in the fecal microbial diversity or structure for cows with and without the onset of Salmonella shedding. These data suggest that determinants other than the significant changes in the fecal microbiome influence the periparturient onset of Salmonella shedding in dairy cattle.
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Project description:Fecal microbiome of periparturient dairy cattle and associations with the onset of Salmonella shedding
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Project description:Pork meat is estimated to be responsible for 10-20% of human salmonellosis cases in Europe. Control strategies at the farm could reduce contamination at the slaughterhouse. One of the targeted sectors of production is maternity, where sows could be Salmonella reservoirs. The aim of this study was to assess the dynamics of shedding of Salmonella in terms of variation in both shedding prevalence and strains excreted during gestation in Quebec's maternity sector. The evolution of the fecal microbiota of these sows during gestation was also assessed to detect bacterial populations associated with these variations. A total of 73 sows both at the beginning and the end of the gestation were randomly selected and their fecal matter was analyzed. Salmonella detection was conducted using a method that includes two selective enrichment media (MSRV and TBG). Nine isolates per positive samples were collected. Among the 73 sows tested, 27 were shedding Salmonella. Sows in the first third of their gestation shed Salmonella significantly more frequently (21/27) than those in the last third (6/46) (?2P < 0.05). The shedding status of 19 of the sows that were previously sampled in the first third of their gestation was followed, this time in the last third of their gestation, which confirmed reduction of shedding. Using 16S rRNA gene sequencing and qPCR, significant differences between the fecal flora of sows at the beginning and the end of the gestation, shedding Salmonella or not and with different parity number were detected. Using MaAsLin, multiple OTUs were found to be associated with the time of gestation, the status of Salmonella excretion and parity number. Some of the identified taxa could be linked to the reduction of the shedding of Salmonella at the end of gestation. In this study, we showed that the level of Salmonella shedding was variable during gestation with significantly higher shedding at the beginning rather than at the end of gestation. We also observed for the first time a significant change in the microbiota during sow gestation and identified interesting taxa which could be linked to a reduced Salmonella shedding.
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Project description:In the United States Salmonella enterica subsp. enterica serotypes Kentucky and Cerro are frequently isolated from asymptomatic dairy cows. However, factors that contribute to colonization of the bovine gut by these two serotypes have not been identified. To investigate associations between Salmonella status and bacterial diversity, as well as the diversity of the microbial community in the dairy cow hindgut, the bacterial and archaeal communities of fecal samples from cows on a single dairy farm were determined by high-throughput sequencing of 16S rRNA gene amplicons. Fecal grab samples were collected from two Salmonella-positive cows and two Salmonella-negative cows on five sampling dates (n = 20 cows), and 16S rRNA gene amplicons from these samples were sequenced on the Illumina MiSeq platform. A high level of alpha (within) and beta diversity (between) samples demonstrated that microbial profiles of dairy cow hindguts are quite diverse. To determine whether Salmonella presence, sampling year, or sampling date explained a significant amount of the variation in microbial diversity, we performed constrained ordination analyses (distance based RDA) on the unifrac distance matrix produced with QIIME. Results indicated that there was not a significant difference in the microbial diversity associated with Salmonella presence (P > 0.05), but there were significant differences between sampling dates and years (Pseudo-F = 2.157 to 4.385, P < 0.05). Based on these data, it appears that commensal Salmonella infections with serotypes Cerro and Kentucky in dairy cows have little or no association with changes in the abundance of major bacterial groups in the hindgut. Rather, our results indicated that temporal dynamics and other undescribed parameters associated with them were the most influential drivers of the differences in microbial diversity and community structure in the dairy cow hindgut.
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Project description:Q fever is a worldwide zoonotic disease reported in humans and many animal species including cattle. The aims of this study were to evaluate the prevalence of Coxiella (C.) burnetii shedding in Polish dairy cattle herds and to identify the pathogen's genotypes and sequence types (STs) using multiple-locus variable number tandem repeat analysis (MLVA) and multispacer sequence typing (MST) methods. The presence of C. burnetii DNA was detected using a commercial real-time PCR kit, targeting the IS1111 element. Overall, 1,439 samples from 279 herds were tested including: 897 individual milk specimens, 101 bulk tank milk samples, 409 genital tract swabs and 32 placentas. Furthermore, 30 consumer milk samples, including 10 from vending machines and 77 dairy products were also analyzed. C. burnetii shedding was confirmed in 31.54% of tested cattle herds as well as in 69.16% of consumer milk and dairy products. Among real-time PCR-positive samples, 49 specimens obtained from 49 cattle herds and 8 samples of purchased dairy products were selected for genotyping. Overall, five previously known MLVA genotypes (I, J, BG, BE, and NM) and three new ones (proposed as PL1, PL2, and PL3) were identified. Two MST sequence types were recorded: ST16 and a novel sequence (ST61). The new genotypes and sequence types need further research particularly into their pathogenicity to humans.
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Project description:Whole genome shotgun data from dairy catttle
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Project description:Cattle are primary reservoirs of Escherichia coli O157:H7, a causative agent of severe human infections. To facilitate analyses of the communities in which this pathogen is found, we sequenced the fecal metagenomes of 10 dairy cows shedding E. coli O157:H7 and added them to the public domain.
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Project description:Due to insufficient dry matter intake and heightened nutrient requirements in early lactation, periparturient dairy cows mobilize adipose and muscle tissues to bridge energy and amino acid gaps, respectively. Our objective was to evaluate the relationship between the relative muscle thickness of late pregnant cows and their early lactation performance. At 35 d before expected calving (BEC), longissimus dorsi muscle thickness (LDT) was measured in forty-one multiparous Holstein cows via ultrasound. Tissue mobilization was evaluated via ultrasound images of LDT and backfat thickness (BFT) at 21 and 7 d BEC as well as at 0, 10, 30, and 60 DIM. Plasma concentrations of 3-methylhistidine (3-MH), creatinine (CRE), non-esterified fatty acids (NEFA), and β-hydroxybutyrate (BHB) were evaluated weekly. Milk yield and milk component data were collected through 60 DIM. Cattle were assigned post hoc to high-muscle (HM; n = 20; LDT > 4.49 cm) or low-muscle (LM; n = 21; ≤4.37 cm) groups, with mean LDT at 35 d BEC greater in HM (5.05 ± 0.49) than in LM (3.52 ± 0.65) animals. Between 35 and 21 d BEC, LM cows gained LDT, whereas HM cows gained BFT. HM cows mobilized more muscle from 21 d BEC to 30 DIM, as reflected by a greater loss of LDT, greater 3-MH concentrations (532 vs. 438 ± 30 ng/mL), and a greater 3-MH:CRE ratio (0.164 vs. 0.131 ± 0.008) in the first three weeks postpartum. The LDT and BFT at 21 d BEC were related to the amount of respective tissue mobilized through 30 DIM (R2 = 0.37 and 0.88, respectively). Although calves born to HM cattle were larger (45.2 vs. 41.8 ± 0.7 kg), HM cows produced less milk (38.8 vs. 41.6 ± 0.8 kg/d) with a tendency towards higher fat content (4.33 vs. 4.05 ± 0.12%), likely related to the mobilization of more backfat from 0 to 60 DIM (1.78 vs. 0.68 ± 0.34 mm), compared to LM cattle. These findings suggest that a cow's metabolic status, as measured by LDT and BFT prepartum, may influence the metabolic strategy the animal uses to meet energy and amino acid requirements in late gestation and early lactation.
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Project description:Antimicrobial resistance is a global public health concern, and livestock play a significant role in selecting for resistance and maintaining such reservoirs. Here we study the succession of dairy cattle resistome during early life using metagenomic sequencing, as well as the relationship between resistome, gut microbiota, and diet. In our dataset, the gut of dairy calves serves as a reservoir of 329 antimicrobial resistance genes (ARGs) presumably conferring resistance to 17 classes of antibiotics, and the abundance of ARGs declines gradually during nursing. ARGs appear to co-occur with antibacterial biocide or metal resistance genes. Colostrum is a potential source of ARGs observed in calves at day 2. The dynamic changes in the resistome are likely a result of gut microbiota assembly, which is closely associated with diet transition in dairy calves. Modifications in the resistome may be possible via early-life dietary interventions to reduce overall antimicrobial resistance.
| S-EPMC6765000 | biostudies-literature
Project description:The current study aimed to investigate whether bovine non-coding RNA play a role in regulating E. coli O157 shedding through studying miRNAomes of the whole gastrointestinal tract including duodenum, proximal jejunum, distal jejunum, cecum, spiral colon, descending colon and rectum. The number of miRNAs detected in each intestinal region ranged from 390 ± 13 to 413 ± 49. Compared between SS and NS, the number of differentially expressed (DE) miRNAs ranged from one to eight, and through the whole gut, seven miRNAs were up-regulated and seven were down-regulated in SS. The distal jejunum and rectum were the regions where the most DE miRNAs were identified (8 and 7, respectively). Functional analysis indicated that the bta-miR-378b, bta-miR-2284j and bta-miR-2284d which were down-regulated in both distal jejunum and rectum of SS, the bta-miR-2887 which was down-regulated in rectum of SS, as well as the bta-miR-211 and bta-miR-29d-3p which were up-regulated in rectum of SS were potentially regulatory to host immune functions, including hematological system development and immune cell trafficking. Our findings suggest that the alternation of miRNA expression in the gut of SS may lead to differential regulation in immune functions involved in E. coli O157 super-shedding in cattle.
2018-10-30 | GSE121916 | GEO