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A molecular approach to understanding the interrelation between the microbiomes in the litter and intestines of commercial broiler chickens

Cressman, Michael David

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2009, Master of Science, Ohio State University, Animal Sciences.

Two studies were conducted to determine the effect of litter microbiome on the ontogeny of the intestinal microbiome in broilers over a 6-week growth cycle. In the first study, composite (10 random birds/replicate) ileal mucosa and cecal luminal samples from birds reared on both fresh pine shavings and 2-year old reused pine litter were collected at days 7, 14, 21, and 42. At the same times, litter subsamples were also collected and pooled from multiple locations (brood area, along the water and feed lines, and along the walls) within the broiler house. Microbiome DNA was extracted from all samples using the RBB+C method. Bacterial community profiles were compared among samples (ileum, cecum, or litter) based on each litter type using PCR-DGGE. DGGE banding patterns were analyzed using BioNumerics V.5.1 software, and compared among individual samples with UPGMA clustering analysis using the Dice similarity coefficient. The DGGE banding patterns were also analyzed using SAS and principal component analysis (PCA). All these analyses indicated the following: 1) The two litter types appeared to have very distinct microbiomes, with the reused litter having a greater bacterial diversity than the fresh litter; 2) the litter microbiome is more influential on the ileal than the cecal microbiome; 3) all samples (ileal, cecal and litter) exhibit temporal shifts in the bacterial community structure; and, 4) the intestinal microbiome of the chickens raised on the fresh litter becomes similar to that of chickens raised on reused litter by week six. In addition to microbiome structure, further analysis of the chemical composition of the litter and bird performance in subsequent trials is needed to better understand the relationship between the condition of litter and gastrointestinal health of the broiler chicken.

In the second study, a 16S rRNA gene clone library was constructed from microbiome DNA extracted from ileal mucosa and cecal lumen of young chicks (7 days of age) placed on fresh pine shavings or 2-year old reused litter, as well as the litter samples. All the recovered 16S rRNA gene sequences were identified by comparison with database sequences and analyzed using phylogenetic programs. As demonstrated in the 16S clone libraries, all samples had distinct microbiomes at day 7. The predominant genera were Lachnospiraceae Incertae Sedis (19.3%), Lactobacillus (18.1%), Enterococcus (3.4%), Faecalibacterium (3.4%), and Staphylococcus (3.2%). Although the co-occurrence of both Lactobacillus and Enterococcus species was seen between the fresh litter and the ileal clones of chicks placed on fresh pine shavings, very few co-occurrences were seen between the reused litter and ileal clones of chicks placed on reused litter. The majority of clones in the cecal library of chicks placed on reused litter were classified as belonging to Ruminococcaceae (60%), while the majority of clones in the cecal library of chicks placed on fresh pine shavings belonged to Lachnospiraceae (58%). Collective analysis of all 476 clones identified 138 operation taxonomic units (OTUs) corresponding to species (defined by 97% sequence identity). Less than 12% (16 OTUs) of these OTUs were ≥97% identical to known bacterial species, while another 4 OTUs (2.9%) were 95-96.9% identical. Another 6 OTUs (4.3%) were 90-94.9% identical to known bacterial species. The remaining 112 (81.2%) OTUs were <90% identical to any known bacterial species within the database. These results suggest that the microbiome in different litter can affect the intestinal microbiome differently, and the majority of the bacteria present in these microbiome remains to be identified.

Steven Moeller, PhD (Advisor)
Henry Zerby, PhD (Advisor)
Michael Lilburn, PhD (Committee Member)
Zhongtang Yu, PhD (Committee Member)
95 p.

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Citations

  • Cressman, M. D. (2009). A molecular approach to understanding the interrelation between the microbiomes in the litter and intestines of commercial broiler chickens [Master's thesis, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1243872965

    APA Style (7th edition)

  • Cressman, Michael. A molecular approach to understanding the interrelation between the microbiomes in the litter and intestines of commercial broiler chickens. 2009. Ohio State University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1243872965.

    MLA Style (8th edition)

  • Cressman, Michael. "A molecular approach to understanding the interrelation between the microbiomes in the litter and intestines of commercial broiler chickens." Master's thesis, Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1243872965

    Chicago Manual of Style (17th edition)