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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Poultry Microbiological Safety and Processing Research Unit » Research » Publications at this Location » Publication #299205
Title: Successional changes in the chicken cecal microbiome during 42 days of growth are independent of organic acid feed additives

Author
item Oakley, Brian
item Buhr, Richard - Jeff
item CASEY, RITZ - University Of Georgia
item BRIAN, KIEPPER - University Of Georgia
item Berrang, Mark
item Seal, Bruce
item Cox Jr, Nelson

Submitted to: BMC Veterinary Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/1/2013
Publication Date: 11/27/2014
Citation: Oakley, B., Buhr, R.J., Casey, R.W., Brian, K.W., Berrang, M.E., Seal, B.S., Cox Jr, N.A. 2014. Successional changes in the chicken cecal microbiome during 42 days of growth are independent of organic acid feed additives. BMC Veterinary Research. 10:282-288.

Interpretive Summary: Removing antibiotics from poultry feed will require testing alternative feed additives to see how they affect bacterial communities in the poultry gut. An important part of such testing is documenting natural background changes in the gut bacteria which occur as chickens mature and comparing these changes to the effects of the feed additives. In this study, formic acid, propionic acid and medium-chain fatty acids (MCFA) were added to feed and/or drinking water. Gastro-intestinal (G-I) bacterial communities were sampled from treated and untreated chickens at day of hatch, 7 d, 21 d, and 42 d after hatch. Next-generation DNA sequencing was used to compare the types of bacteria and their relative abundance across treatments and sampling times. The main conclusion of the study is that changes in the G-I bacterial communities as the birds matured were much more dramatic than the effects of the additives tested. By applying next-generation DNA sequencing for one of the first times to poultry G-I bacterial communities, a comprehensive census of the bacteria present at each time point were obtained. These data showed that nearly all of the bacteria present belonged to a group called the Clostridiales. Some bacteria belonging to the Clostridiales group provide important nutrients to the chicken, but others are recognized human and animal pathogens. Balancing the beneficial and harmful members of this group is important for optimizing poultry productivity, animal health, and food safety. The data provided by this study illustrate the importance of testing alternative feed additives and provide important benchmarks of the natural changes through time of poultry G-I bacteria.

Technical Abstract: Poultry remains a major source of foodborne infections in the U.S. and globally. A variety of additives with presumed anti-microbial and/or growth-promoting effects are commonly added to poultry feed, yet the effects of these additives on the ecology of the gastro-intestinal microbial community (the G-I microbiome) remain largely unknown. Here we compared temporal changes in the G-I microbiome to the effects of additives containing formic acid, propionic acid, and medium-chain fatty acids (MCFA) added to feed and/or drinking water. Cecal bacterial communities at day of hatch (n=5 birds), 7d (n=32), 21d (n=27), and 42d (n=36) post-hatch were surveyed using direct 454 sequencing of 16S rRNA gene amplicons in combination with cultivation-based recovery of a Salmonella Typhimurium marker strain and quantitative-PCR targeting Clostridium. Treatment effects on specific pathogens were generally non-significant. S. Typhimurium introduced by oral gavage at day of hatch was recovered by cultivation from nearly all birds sampled across treatments at 7d and 21d. By 42d post-hatch, S. Typhimurium was only recovered from ca. 25% of birds, regardless of treatment. Sequencing data also revealed non-significant treatment effects on genera containing known pathogens and generally non-significant effects on the cecal microbiome as a whole. In contrast, temporal changes were dramatic, highly significant, and consistent across treatments. At 7d, the cecal community was dominated by three genera (Dorea, Flavonifractor, Pseudoflavonifractor) which accounted for more than half of sequences. By 21d post-hatch, a single genus (Faecalibacterium) accounted for 23-55% of sequences, and the number of Clostridium 16S rRNA gene copies detected by quantitative-PCR reached a maximum. During the 42 d experiment, the cecal bacterial community was dominated by members of the Clostridiales but changed significantly according to a variety of ecological metrics and increases in network complexity. These dramatic temporal shifts in the taxonomic composition of the cecal microbiome have important ramifications for the management of poultry for productivity, animal health, and food safety.