Characterizing the Gut Microbiome of Broilers Raised under Conventional and No Antibiotics Ever (NAE) Practices
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ABSTRACT:
PROVIDER: PRJNA826471 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18745900_1.fastq.gz | Fastqsanger.gz | |||
| SRR18745900_2.fastq.gz | Fastqsanger.gz | |||
| SRR18746000_1.fastq.gz | Fastqsanger.gz | |||
| SRR18746000_2.fastq.gz | Fastqsanger.gz | |||
| SRR18746100_1.fastq.gz | Fastqsanger.gz |
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Project description:Meat from broilers raised without the use of antibiotics is becoming increasingly popular among consumers. Consequently, interest in the microbial profiling of chickens produced under nonconventional practices is growing, however, research on this topic is lacking. The current study was designed to characterize the dynamics of gut microbial populations of broilers raised under conventional and no antibiotics ever (NAE) practices. Four commercial farms (2 conventional and 2 NAE) were included in this study. On each farm, cecal (n = 224) and ileal (n = 224) contents were collected from birds at different stages during the grow out of a single flock and following transportation to the processing facility. Cecal microbiota was dominated by the genera Escherichia and Enterococcus upon hatching in both conventional and NAE flocks, shifting with time toward predominantly Faecalibacterium and Bacteroides. The composition of cecal microbial communities of NAE broilers was different than that of conventional chickens (P ≤ 0.05). Conventional broilers harbored a rich, but less diverse cecal microbiota than NAE, while the ileal microbiota was primarily populated with genera previously named Lactobacillus, which exhibited a higher abundance in NAE broilers (P ≤ 0.05). In both production systems, the microbiota followed a similar temporal succession that was more evident in the ceca. Transportation to the processing plant impacted the microbial composition of the ileum (P ≤ 0.05), characterized by an increase in the relative abundance of Psychrobacter. Finally, differential abundance analysis showed a positive correlation between Campylobacter and Enorma within the cecum microbiota, and a negative correlation with Salmonella.
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Project description:The specific antimicrobial resistance (AMR) decreases that can be expected from reducing antimicrobial (AM) use in U.S. beef production have not been defined. To address this data gap, feces were recovered from 36 lots of "raised without antibiotics" (RWA) and 36 lots of "conventional" (CONV) beef cattle. Samples (n = 719) were collected during harvest and distributed over a year. AMR was assessed by (i) the culture of six AM-resistant bacteria (ARB), (ii) quantitative PCR (qPCR) for 10 AMR genes (ARGs), (iii) a qPCR array of 84 ARGs, and (iv) metagenomic sequencing. Generally, AMR levels were similar, but some were higher in CONV beef cattle. The prevalence of third-generation cephalosporin-resistant (3GCr) Escherichia coli was marginally different between production systems (CONV, 47.5%; RWA, 34.8%; P = 0.04), but the seasonal effect (summer, 92.8%; winter, 48.3%; P < 0.01) was greater. Erythromycin-resistant (ERYr) Enterococcus sp. concentrations significantly differed between production systems (CONV, 1.91 log10 CFU/g; RWA, 0.73 log10 CFU/g; P < 0.01). Levels of aadA1, ant(6)-I, blaACI, erm(A), erm(B), erm(C), erm(F), erm(Q), tet(A), tet(B), tet(M), and tet(X) ARGs were higher (P < 0.05) in the CONV system. Aggregate abundances of all 43 ARGs detected by metagenomic sequencing and the aggregate abundances of ARGs in the aminoglycoside, β-lactam, macrolide-lincosamide-streptogramin B (MLS), and tetracycline AM classes did not differ (log2 fold change < 1.0) between CONV and RWA systems. These results suggest that further reductions of AM use in U.S. beef cattle production may not yield significant AMR reductions beyond MLS and tetracycline resistance.IMPORTANCE The majority of antimicrobial (AM) use in the United States is for food-animal production, leading to concerns that typical AM use patterns during "conventional" (CONV) beef cattle production in the United States contribute broadly to antimicrobial resistance (AMR) occurrence. In the present study, levels of AMR were generally similar between CONV and "raised without antibiotics" (RWA) cattle. Only a limited number of modest AMR increases was observed in CONV cattle, primarily involving macrolide-lincosamide-streptogramin B (MLS) and tetracycline resistance. Macrolides (tylosin) and tetracyclines (chlortetracycline) are administered in-feed for relatively long durations to reduce liver abscesses. To ensure judicious AM use, the animal health, economic, and AMR impacts of shorter duration in-feed administration of these AMs should be examined. However, given the modest AMR reductions observed, further reductions of AM use in U.S. beef cattle production may not yield significant AMR reductions beyond MLS and tetracycline resistance.
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Project description:Metagenomic investigations have the potential to provide unprecedented insights into microbial ecologies, such as those relating to antimicrobial resistance (AMR). We characterized the microbial resistome in livestock operations raising cattle conventionally (CONV) or without antibiotic exposures (RWA) using shotgun metagenomics. Samples of feces, wastewater from catchment basins, and soil where wastewater was applied were collected from CONV and RWA feedlot and dairy farms. After DNA extraction and sequencing, shotgun metagenomic reads were aligned to reference databases for identification of bacteria (Kraken) and antibiotic resistance genes (ARGs) accessions (MEGARes). Differences in microbial resistomes were found across farms with different production practices (CONV vs. RWA), types of cattle (beef vs. dairy), and types of sample (feces vs. wastewater vs. soil). Feces had the greatest number of ARGs per sample (mean = 118 and 79 in CONV and RWA, respectively), with tetracycline efflux pumps, macrolide phosphotransferases, and aminoglycoside nucleotidyltransferases mechanisms of resistance more abundant in CONV than in RWA feces. Tetracycline and macrolide-lincosamide-streptogramin classes of resistance were more abundant in feedlot cattle than in dairy cow feces, whereas the β-lactam class was more abundant in dairy cow feces. Lack of congruence between ARGs and microbial communities (procrustes analysis) suggested that other factors (e.g., location of farms, cattle source, management practices, diet, horizontal ARGs transfer, and co-selection of resistance), in addition to antimicrobial use, could have impacted resistome profiles. For that reason, we could not establish a cause-effect relationship between antimicrobial use and AMR, although ARGs in feces and effluents were associated with drug classes used to treat animals according to farms' records (tetracyclines and macrolides in feedlots, β-lactams in dairies), whereas ARGs in soil were dominated by multidrug resistance. Characterization of the "resistance potential" of animal-derived and environmental samples is the first step toward incorporating metagenomic approaches into AMR surveillance in agricultural systems. Further research is needed to assess the public-health risk associated with different microbial resistomes.
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Project description:Campylobacter is one of the main bacterial pathogens that cause campylobacteriosis in the United States. Poultry is considered a major reservoir for the transmission of Campylobacter to humans. This study aimed to determine the prevalence and molecular characteristics of Campylobacter in the no-antibiotics-ever (NAE) broilers. A total of 414 samples were collected, among which 160 retail chicken samples were purchased from grocery stores and 254 samples were collected from broiler farms located in Mississippi State. The overall prevalence of Campylobacter was 25.4%, and a significantly higher prevalence was observed in retail chicken than in the farm samples (36.3% versus 18.5%; P < 0.0001), respectively. The prevalence of Campylobacter was not different (P = 0.263) between conventional retail (40.0%) and NAE (31.4%) retail chicken. Campylobacter jejuni was the predominant species among the positive isolates, accounting for 78.1%. Among the 82 C. jejuni isolates, 52.4% of the isolates carried the gyrA gene followed by the tet(O) gene (14.6%), whereas toxin-producing genes cdtA, cdtB, and cdtC were carried by 43.9%, 46.3%, and 43.9%, respectively. However, none of these virulence genes were detected in C. jejuni isolated from litter samples. Among tested C. jejuni, 13.6% of the isolates were multidrug resistant. The highest resistance was observed against nalidixic acid (49.2%), followed by tetracycline (23.7%). Our study suggests that the prevalence of Campylobacter was higher in retail meat samples than in environmental samples obtained from farms, and there was no difference in Campylobacter prevalence among conventional and NAE retail chicken. IMPORTANCE The FDA antibiotic withdrawal policy has led to a shift in the production system, from conventional antibiotics fed birds to no antibiotics ever (NAE) raised birds. However, the impact of this shift to NAE on the prevalence and characteristics of Campylobacter has not been studied on the farm or in retail chicken meats. The objective of this study was to determine the current prevalence of Campylobacter and the distribution of their antimicrobial resistance and virulence genes in NAE-raised broilers. The findings of this study will help the industry to take necessary action to develop effective mitigation strategies for reducing Campylobacter contamination in NAE broilers.
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Project description:An experiment was conducted to investigate the effects of dietary inclusion of rye, a model ingredient to increase gut viscosity, between 14 and 28 days of age on immune competence related parameters and performance of broiler. A total number of 960 one-day-old male Ross 308 chicks were weighed and randomly allocated to 24 pens (40 birds per pen), and the birds in every 8 replicate pens were assigned to one of three experimental diets including graded levels, 0%, 5%, and 10% of rye. Tested immune competence related parameters were composition of the intestinal microbiota, genes expression in gut tissue, and gut morphology. The inclusion of 5% or 10% rye in the diet (d14-28) resulted in decreased performance and litter quality, but in increased villus height and crypt depth in the small intestine (jejunum) of the broilers. Relative bursa and spleen weights were not affected by dietary inclusion of rye. In the jejunum, no effects on number and size of goblet cells, and only trends on microbiota composition in the digesta were observed. Dietary inclusion of rye affected expression of genes involved in cell cycle processes of the jejunal enterocyte cells, thereby influencing cell growth, cell differentiation and cell survival, which in turn were consistent with the observed differences in the morphology of the gut wall. In addition, providing rye-rich diets to broilers affected the complement and coagulation pathways, which are parts of the innate immune system. These pathways are involved in eradicating invasive pathogens. Overall, it can be concluded that inclusion of 5% or 10% rye to the grower diet of broilers had limited effects on performance. Ileal gut morphology, microbiota composition of jejunal digesta, and gene expression profiles of jejunal tissue, however, were affected by dietary rye inclusion level, indicating that rye supplementation to broiler diets might affect immune competence of the birds.
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2015-05-31 | E-MTAB-1028 | biostudies-arrayexpress
Project description:Intestinal microflora composition of broilers
| PRJEB46416 | ENA