Skip to Main Content
 

Global Search Box

 
 
 

ETD Abstract Container

Abstract Header

An Integrated Study on Chicken Gut Microbiome Associated with Diets and Feed Utilization Using Microarray and Illumina Sequencing

Abstract Details

2014, Doctor of Philosophy, Ohio State University, Animal Sciences.
The gastrointestinal (GI) tract of chicken harbors a complex bacterial community which contributes to the wellbeing of animal host in a wide range of aspects, especially nutrition and disease resistance. The overall objective of the studies presented here was to better understand the role gut microbiome plays in host growth performance and disease resistance by investigating the diversity of gut microbiome and identifying bacteria with different relative abundance in chickens with different feed utilization efficiencies and fed with different diets. In the first study (Chapter 3), the relationship between gut microbiome and host feed utilization efficiency was investigated. Poultry Intestinal Tract Chip version 2 (PITChip2), a poultry specific phylogenetic microarray, was used to characterize gut microbiome structures in 24 male Cobb 500 broiler chickens with low feed conversion ratio (FCR) and 24 chickens with high FCR. No clear separation in the gut microbiome structure was observed between good- and bad-performance chickens. One hundred phylotypes were found to correlate with bird performance, with five of them were more abundant in good-performance low FCR chickens. These five phylotypes may serve as indicators of feed utilization efficiency in chicken and also as potential probiotic candidates or targets of enhancement by prebiotics to improve growth performance of broilers. In the second study (Chapter 4), PITChip3 was developed. It has 1,204 customized oligonucleotide probes designed based on the V1-V3 region of bacterial 16S rRNA and are able to detect 62 genus-level phylotypes, 662 species-level phylotypes, and 34 pathogens. The utility of PITChip3 was tested using cecal content samples of broilers fed either corn-based or wheat-based diet. Clear separations between chickens fed with different diets and between chickens at two different ages were observed. Eighteen species-level phylotypes were further identified with different relative abundance in chickens fed different diets. Such difference in gut microbiome revealed by PITChip3 may help to better understand the interactions between gut microbiome and diet and the benefits and risk associated with the two common diets. In the last study (Chapter 5), the difference in gut microbiome between chickens fed with corn- or wheat-based diet was further investigated using Illumina sequencing. Two hundred 1-day-old straight run Cobb 500 broiler chicks were randomly assigned to one of two dietary treatments. At 14 and 35 days of age, ileal mucosa and cecal content were collected and metagenomic DNA was extracted. Illumina MiSeq platform was used to sequence the V1-V3 hypervariable region of bacterial 16S rRNA gene. No clear difference in microbial diversity between the two dietary treatments was observed. Three phylotypes that have different relative abundance in 14-day-old chickens fed with the two different diets were identified. Further studies on the phylotypes identified may help to find non-antibiotic alternatives to enhance growth and protect chickens from disease such as necrotic enteritis (NE). Taken together, these studies expanded our knowledge on the potential role gut microbiome plays in host growth performance and disease resistance, and established a poultry specific phylogenetic microarray which can serve as a powerful tool for the study of poultry gut microbiome.
Zhongtang Yu (Advisor)
Michael Lilburn (Committee Member)
Thaddeus Ezeji (Committee Member)
Hua Wang (Committee Member)
184 p.

Recommended Citations

Citations

  • Pan, D. (2014). An Integrated Study on Chicken Gut Microbiome Associated with Diets and Feed Utilization Using Microarray and Illumina Sequencing [Doctoral dissertation, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1417694886

    APA Style (7th edition)

  • Pan, Deng. An Integrated Study on Chicken Gut Microbiome Associated with Diets and Feed Utilization Using Microarray and Illumina Sequencing. 2014. Ohio State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1417694886.

    MLA Style (8th edition)

  • Pan, Deng. "An Integrated Study on Chicken Gut Microbiome Associated with Diets and Feed Utilization Using Microarray and Illumina Sequencing." Doctoral dissertation, Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1417694886

    Chicago Manual of Style (17th edition)