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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Food and Feed Safety Research » Research » Publications at this Location » Publication #321265

Title: Spatial and temporal changes in the broiler chicken cecal and fecal microbiomes and correlations of bacterial taxa with cytokine gene expression

item OAKLEY, BRIAN - Western University Of Health Sciences
item Kogut, Michael - Mike

Submitted to: Frontiers in Veterinary Infectious Diseases
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/4/2016
Publication Date: 2/19/2016
Publication URL:
Citation: Oakley, B.B., Kogut, M.H. 2016. Spatial and temporal changes in the broiler chicken cecal and fecal microbiomes and correlations of bacterial taxa with cytokine gene expression. Frontiers in Veterinary Infectious Diseases. doi: 10.3389/fvets.2016.00011.

Interpretive Summary: The development of the immune response in baby chicks is by the animal's gut. This is because the gut is exposed to not only nutrients, but also many bacteria that live in the gut. What has been found over the last 20 years is that bacteria that do not cause disease, but normally grow in the gut can work together to make the baby animals immune system work better and prevent the bad germs from growing. This paper shows that the growth of specific bacteria control specific components of the baby chick's local immune environment in the gut. This paper would be beneficial to chicken growers, microbiologists, and nutritionists, and will help make better animal feeds that encourage the growth of the normal bacteria in the gut and help the development of a healthy immune system.

Technical Abstract: To better understand the ecology of the poultry gastrointestinal (GI) microbiome and its interactions with the host, we compared GI bacterial communities by sample type (fecal or cecal), time (1, 3, and 6 weeks post-hatch), and pen (1, 2, 3, or 4), and measured serum levels of the cytokines IL18, IL1-B, and IL6, IL10, and TGF-B4. The microbiome was characterized by sequencing of 16S rRNA gene amplicons, and immune responses were measured by a panel of quantitative-PCR assays targeting mRNAs. Significant differences were observed in the microbiome by GI location (fecal versus cecal) and bird age as determined by permutational MANOVA and phylogenetic hypothesis tests. At 1 wk post-hatch, bacterial genera significantly over-represented in fecal versus cecal samples included Gallibacterium and Lactobacillus, while the genus Bacteroides was significantly more abundant in the cecum. By 6 wk post-hatch, Clostridium and Caloramator (also a Clostridiales) sequence types had increased significantly in the cecum and Lactobacillus remained over-represented in fecal samples. In the ceca, the relative abundance of sequences classified as Clostridium increased by ca. 10-fold each, with a sampling period from 0.1% at 1 wk, to 1% at 3 wk, and 18% at 6 wk. Increasing community complexity through time were observed in a variety of ecological metrics. IL18 and IL-1B increased to maximum mean expression levels 1.5 fold greater at wk 3 than wk 1, while IL6 decreased to 0.8-fold and 0.5-fold expression at 3 wk and 6 wk post-hatch respectively, relative to wk 1. Expression of pro-inflammatory cytokines was generally negatively correlated with the relative abundance of various members of the phylum Firmicutes and positively correlated with Proteobacteria. Correlations of the microbiome with immune responses highlights the importance of the GI microbiome for bird health and productivity and may be a successful high-throughput strategy to identify bacterial taxa with specific immune-modulatory properties.