Browsing by Author "Youmans, Bonnie P"

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    A consistent and predictable commercial broiler chicken bacterial microbiome in antibiotic-free production displays strong correlations with performance
    (2018-01-16) Johnson, Timothy J; Youmans, Bonnie P; Noll, Sally; Cardona, Carol; Evans, Nicholas; Kernezos, Peter; Ngunjiri, John; Abundo, Michael; Lee, Chang-Won; tjj@umn.edu; Johnson, Timothy J
    Defining the baseline bacterial microbiome is critical towards understanding its relationship with health and disease. In broiler chickens, numerous studies have aimed at defining the core microbiome, yet the core and its possible relationships with health and disease have been difficult to define due to lack of study power. Here, the most comprehensive microbiome-based effort to date in commercial broilers was undertaken. The primary goals of this study included understanding what constitutes core in the broiler gastrointestinal, respiratory, and barn environments; how these core players change across age, geography, and time; and which bacterial taxa correlate with enhanced bird performance in antibiotic-free flocks. Using 2,309 samples from 37 different commercial flocks within a vertically integrated broiler system, and metadata from 549 flocks within that system, the baseline bacterial microbiome was defined. The effects of age, sample type, flock, and successive flock cycles were compared, and results indicate a consistent, predictable, age-dependent bacterial microbiome, irrespective of flock. The tracheal bacterial microbiome of broilers was comprehensively defined for the first time, and interestingly, Lactobacillus was the dominant bacterial taxa in the trachea. Numerous bacterial taxa were identified which were strongly correlated with broiler chicken performance, across multiple tissues. While many positively correlated taxa were identified representing targets for future probiotic development, many negatively associated potential pathogens were identified in the absence of clinical disease, indicating subclinical dynamics occurring that impact performance. Overall, this work provides necessary baseline data for the development of effective antibiotic alternatives for sustainable poultry production.
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    The effects of different feed additives on bird performance and the gastrointestinal microbiome of Salmonella-challenged broilers
    (2018-01-16) Johnson, Timothy J; Evans, Nicholas; Karnezos, Peter; Sims, Michael; Youmans, Bonnie P; tjj@umn.edu; Johnson, Timothy J
    A 42-day, 60-unit floor pen (10 pens per treatment, 25 birds per pen) Salmonella challenge study was conducted to determine the effects of supplementing broiler diets with virginiamycin (VM); medium chain fatty acids (MCFA); MCFA plus lactic acid (MCFA+LA) and a phytogenic blend (PB). Effects were assessed on bird performance and ileal, cecal, and litter microbiomes in birds challenged with Salmonella Typhimurium. Treatments were compared with a non-inoculated control group (NIC) and a Salmonella-challenged group without feed additives (IC). At days 14, 28, and 42 of age, all bird weights and intake were measured, 20 birds from each treatment were euthanized, and the ceca and ilea of euthanized birds were collected along with grab litter samples from each pen. Bacterial profiling was performed using 16S rRNA amplicon sequencing. Subsequent analyses were performed for measurements of alpha and beta bacterial community diversity, taxonomic classifications, and assessments of bacterial taxa that were shifted as a result of different treatments. At 42 days, body weights and mortality adjusted feed conversions for the UIC were significantly better (P<0.1) than the IC and VM while the MCFA, MCFA+LA and PB treatments were similar to the negative UIC. The Salmonella challenge itself had significant (P<0.01) effects on the bacterial microbiome of all sample types, with the greatest effects observed in the cecal microbiome of the bird. The VM treatment counteracted the effects of the Salmonella challenge on the overall bacterial communities of all sample types (P<0.05). While none of the antibiotic alternative treatments had significant effects on overall bacterial community structure consistent over time, specific bacterial taxa were impacted by several treatments. These included Candidatus Arthromitus (segmented filamentous bacteria), Peptostreptococcus, and Clostridium species. Unique signature taxonomic effects were identified for each treatment type, demonstrating attributes of each feed additive type in contributing to unique effects on the bird microbiota. Overall, this work identifies microbiome modulations conferred by different antibiotic alternatives under a Salmonella challenge.