Browsing by Subject "16S rDNA"
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Item Establishment, identification, quantification of methanogenic archaea in chicken ceca and methanogenesis inhibition in in vitro chicken ceca by using nitrocompounds(Texas A&M University, 2006-08-16) Saengkerdsub, SuwatIn the first phase of this study, the diversity of methanogenic bacteria in avian ceca was found to be minimal. Based on 16S rDNA clone libraries, a common phylotype, designated CH101, ranged between 92.86 to 100 % of the total clones whereas less than 1% of the other phylotypes were found. On the basis of the sequence identity, all of the sequences, except sequence CH1270, are related from 98.97 to 99.45% to 16S rDNA Methanobrevibacter woesei GS. Sequence CH1270 is 97.62% homologous to the sequence identified to uncultured archaeon clone ConP1-11F. Clearly, the predominant methanogen found to reside in the chicken ceca was M. woesei. By using a MPN enumeration method, methanogen counts were found to be in the range of 6.38 to 8.23 log10 organisms per gram wet weight. The 16S rDNA copy number per gram wet weight in the samples was between log10 5.50 and 7.19. The second phase of the study was conducted to observe the effects of selected nitrocompounds and two different feedstuffs on in vitro methane production in chicken cecal contents and rumen fluid. Initially, one of the three nitrocompounds was added to incubations containing cecal contents from laying hens supplemented with either alfalfa or layer feed. Both feed materials influenced volatile fatty acids (VFA) production and also fostered methane production in the incubations although methane was lower (P < 0.05) in incubations with added nitrocompound, particularly nitroethane. Secondly, nitroethane was examined in incubations of bovine or ovine rumen fluid or cecal contents containing either alfalfa or layer feed. Unlike cecal contents, layer feed significantly (P < 0.05) supported in vitro methane production in incubations of both rumen fluids. The results show that nitroethane impedes methane production, especially in incubations of chicken cecal contents. The final phase of this study was carried out to determine the methanogenic establishment in the chicken ceca by the cultural method with the quantitative PCR. The results suggested that methanogens colonized in chicken ceca at a few days after birth. Litter and house flies could be potential sources for methanogenic colonization in broiler chicks.Item Molecular characterization of intestinal bacteria in healthy cats and a comparison of the fecal bacterial flora between healthy cats and cats with inflammatory bowel disease (IBD)(2009-05-15) Ritchie, Lauren ElizabethPast studies characterizing the feline intestinal microflora have used traditional bacterial culture techniques. However, in recent years it has been recognized that the majority of intestinal bacteria are non cultivable. Therefore, the aim of this study was to describe the microflora along the intestinal tract in healthy cats using comparative 16S ribosomal DNA (16S rDNA) analysis. Intestinal content from the stomach, duodenum, jejunum, ileum, and colon was collected from 4 healthy cats and one specific pathogen free cat (SPF) and the bacterial composition was identified by direct sequencing of bacterial 16S rDNA amplicons. A predominant anaerobic microflora was observed in all evaluated segments of the intestine. Fourteen different bacterial orders were identified with the majority of all sequences classified in the class Clostridiales. Six different Clostridium clusters were identified with the majority of sequences affiliated with Clostridium cluster I. Comparative 16S rDNA analysis was also used to evaluate differences in the fecal microflora between healthy cats (n=6), cats with histopathologically confirmed inflammatory bowel disease (IBD; n=6), and cats with intestinal neoplasia (n=3). Compared to the IBD group, cats in the control group showed a significantly higher number of sequences classified as Firmicutes, Bacteroidetes, and Actinobacteria (p<0.0001). The control group had a significantly higher proportion of clones affiliated with Clostridium cluster XI, and a significantly lower proportion affiliated with cluster I (both p<0.0001). In the neoplasia group, the majority of sequences were classified in the phylum Firmicutes (97.9%) and clones were predominately affiliated with Clostridium clusters I and XI. These data indicate that the feline intestinal microflora is highly diverse and is comprised predominantly of anaerobic bacteria. Further studies are warranted to evaluate the clinical significance of the observed differences in intestinal microflora between healthy cats and cats with gastrointestinal disease.