The effects of different feed additives on bird performance and the gastrointestinal microbiome of Salmonella-challenged broilers

Abstract

This dataset contain raw sequence data for 16S amplicon microbiome profiling of broilers challenged with Salmonella and fed several different intervention strategies. Files are tar archives containing zipped fastq raw data files for each sample. The metadata sheet described sample prefixes.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.USDA-AFRI Grant nos. 2016-67015-2491