Successional changes in the chicken cecal microbiome during 42 days of growth are independent of organic acid feed additives

Abstract

BackgroundPoultry remains a major source of foodborne bacterial infections. A variety of additives with presumed anti-microbial and/or growth-promoting effects are commonly added to poultry feed during commercial grow-out, yet the effects of these additives on the gastrointestinal microbial community (the GI microbiome) as the bird matures remain largely unknown. Here we compared temporal changes in the cecal microbiome to the effects of formic acid, propionic acid, and medium-chain fatty acids (MCFA) added to feed and/or drinking water.ResultsCecal 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 from each bird in combination with cultivation-based recovery of a Salmonella Typhimurium marker strain and quantitative-PCR targeting Clostridium perfringens. 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, but by 42d, 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 on the cecal microbiome as a whole. In contrast, temporal changes in the cecal microbiome were dramatic, highly significant, and consistent across treatments. At 7d, the cecal community was dominated by three genera (Flavonifractor, Pseudoflavonifractor, and a Lachnospiracea sequence type) that 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.ConclusionsOver the 42 d experiment, the cecal bacterial community changed significantly as measured by a variety of ecological metrics and increases in the complexity of co-occurrence networks. Management of poultry to improve animal health, nutrition, or food safety may need to consider the interactive effects of any treatments with the dramatic temporal shifts in the taxonomic composition of the cecal microbiome as described here.Electronic supplementary materialThe online version of this article (doi:10.1186/s12917-014-0282-8) contains supplementary material, which is available to authorized users.

Original XPCTM Effect on Salmonella Typhimurium and Cecal Microbiota from Three Different Ages of Broiler Chickens When Incubated in an Anaerobic In Vitro Culture System

“…Trial 1 revealed less variation while Trial 2 revealed significant increases ( P < 0.05) at 28 and 42 days compared to 14 days (data not shown). Increasing cecal microbiota complexity that directly relates to sampling age has been observed in previous studies on poultry intestinal microbiota characterization (Salanitro et al, 1974; Danzeisen et al, 2013; Oakley et al, 2014). Meimandipour et al (2011) provided evidence for this based on the variation in the production of SCFA observed in the ceca across various sampling ages.…”

“…What has been recognized in the current research along with previous work is that feed supplements, aside from vitamins (Luo et al, 2013), thus far appear to have little general impact on the composition of the cecal microbiome (Danzeisen et al, 2013; Oakley et al, 2014). …”

Campylobacter and Salmonella are prevalent in broiler farms in Kyushu, Japan: results of a 2-year distribution and circulation dynamics audit

“…These findings appear to be consistent with a previous study in which artificially inoculated Salmonella in the broiler caecal microbiome decreased from 21 to 42 days of age (Oakley et al . ). Furthermore, Salmonella isolation from caecal and environmental samples was highly correlated (Table S2).…”

“…; Oakley et al . ). To date, however, molecular epidemiological data to elucidate these temporal fluctuations for naturally contaminated broiler flocks in Japan have not been reported.…”

Developmental Dynamic Analysis of the Excreted Microbiome of Chickens Using Next-Generation Sequencing

“…A total of 9 and 13 classes, 11 and 17 orders, 18 and 40 families, and 30 and 87 genera were identified on days 1 and 35, respectively. Oakley et al [2014] analyzed the changes in the chicken cecal microbiome during 42 days of growth and reported that the cecal bacterial community changed significantly and taxonomic richness and diversity at the genus level increased through growth time. In a similar way, Danzeisen et al [2011] examined the effects of the growth promoter virginiamycin and tylosin on the broiler chicken cecal microbiome and metagenome.…”