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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » ESQRU » Research » Publications at this Location » Publication #365591

Research Project: Reduction of Invasive Salmonella enterica in Poultry through Genomics, Phenomics and Field Investigations of Small Multi-Species Farm Environments

Location: ESQRU

Title: Intestinal microbial ecology associated with metabolic efficiency in commercial broilers

Author
item Rothrock, Michael
item ELLESTAD, LAURA - University Of Georgia
item Guard, Jean

Submitted to: Poultry Science Association Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/30/2019
Publication Date: 7/15/2019
Citation: Rothrock Jr, M.J., Ellestad, L.E., Guard, J.Y. 2019. Intestinal microbial ecology associated with metabolic efficiency in commercial broilers. Poultry Science Association Meeting Abstract. 234.

Interpretive Summary: In the absence of antibiotic growth promoters, the broiler industry needs to develop new strategies to maintain broiler production efficiency. To better develop these strategies, a basic understanding of the microbiome effects on broiler feed efficiency is needed, with the hope that this knowledge can be leveraged to make production strategies more efficacious. There is a natural variation in metabolic efficiency as measured by feed conversion ratio [FCR; g feed intake (FI)/g body weight gain (BWG)] in a given population of broilers. The objective of this study was to identify microbiological constituents associated with high efficiency (low FCR) and low efficiency (high FCR) commercial broiler chickens. Male Ross 708 broilers (108 birds) were individually reared between post-hatch day (D) 7 and D35, and on D36, jejunum, ileum, duodenum, and cecum were collected from the six highest (HE) and lowest (LE) efficiency birds based on FCR for microbiome analysis (n=6). For phenotypic microbiome analysis, tissue samples were homogenized in tryptic soy broth (1:3 w/v dilution), filtered, normalized to a 1.0 OD600, and used to seed Biolog EcoPlates to assess the microbial communities’ ability to utilize 31 different C-sources. For genotypic microbiome analysis, genomic DNA was extracted from homogenized tissue samples using the QIAamp DNA Stool kit, and 16S rDNA sequencing was performed using the Illumina MiSeq platform and processed using the QIIME2 pipeline. There were definite differences between gastrointestinal tract segments, regardless of feed efficiency, with the cecal microbial loads being more than 1 log higher than duodenal samples and more than 3 logs greater than ileal and jejunal segments. EcoPlate data indicated that microbial respiration was significantly higher, according to a 1-tailed, paired t-test, in LE birds (p<0.0001) in cecal, duodenal, and jejunal segments, with metabolism of C-sources such as glycogen, '-D-lactose, glucose-1-phosphate, and '-hydroxyl-butyric acid differing between groups. Genotypic microbiome analysis showed that while gastrointestinal segment was the greatest driver of richness, diversity, and community structure within these samples, there were significant differences in taxa within each segment between HE and LE broilers, including those within the dominant Firmicutes and Bacteriodetes phyla. These data suggest that microbial signatures are associated with feed efficiency differences that can be linked on a genotypic and a phenotypic community-scale level. These microbial signatures need to be studied further, as they represent potential targets for future strategies to maintain or even improve current production efficiencies within the poultry industry.

Technical Abstract: In the absence of antibiotic growth promoters, the broiler industry needs to develop new strategies to maintain broiler production efficiency. To better develop these strategies, a basic understanding of the microbiome effects on broiler feed efficiency is needed, with the hope that this knowledge can be leveraged to make production strategies more efficacious. There is a natural variation in metabolic efficiency as measured by feed conversion ratio [FCR; g feed intake (FI)/g body weight gain (BWG)] in a given population of broilers. The objective of this study was to identify microbiological constituents associated with high efficiency (low FCR) and low efficiency (high FCR) commercial broiler chickens. Male Ross 708 broilers (108 birds) were individually reared between post-hatch day (D) 7 and D35, and on D36, jejunum, ileum, duodenum, and cecum were collected from the six highest (HE) and lowest (LE) efficiency birds based on FCR for microbiome analysis (n=6). For phenotypic microbiome analysis, tissue samples were homogenized in tryptic soy broth (1:3 w/v dilution), filtered, normalized to a 1.0 OD600, and used to seed Biolog EcoPlates to assess the microbial communities’ ability to utilize 31 different C-sources. For genotypic microbiome analysis, genomic DNA was extracted from homogenized tissue samples using the QIAamp DNA Stool kit, and 16S rDNA sequencing was performed using the Illumina MiSeq platform and processed using the QIIME2 pipeline. There were definite differences between gastrointestinal tract segments, regardless of feed efficiency, with the cecal microbial loads being more than 1 log higher than duodenal samples and more than 3 logs greater than ileal and jejunal segments. EcoPlate data indicated that microbial respiration was significantly higher, according to a 1-tailed, paired t-test, in LE birds (p<0.0001) in cecal, duodenal, and jejunal segments, with metabolism of C-sources such as glycogen, '-D-lactose, glucose-1-phosphate, and '-hydroxyl-butyric acid differing between groups. Genotypic microbiome analysis showed that while gastrointestinal segment was the greatest driver of richness, diversity, and community structure within these samples, there were significant differences in taxa within each segment between HE and LE broilers, including those within the dominant Firmicutes and Bacteriodetes phyla. These data suggest that microbial signatures are associated with feed efficiency differences that can be linked on a genotypic and a phenotypic community-scale level. These microbial signatures need to be studied further, as they represent potential targets for future strategies to maintain or even improve current production efficiencies within the poultry industry.