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Kong YH, Teather R, Forster R.. Composition, spatial distribution, and diversity of the bacterial communities in the rumen of cows fed different forages. FEMS Microbiol Ecol 74: 612-622

Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
FEMS Microbiology Ecology (Impact Factor: 3.88). 09/2010; 74(3):612-22. DOI: 10.1111/j.1574-6941.2010.00977.x
Source: PubMed

ABSTRACT The species composition, distribution, and biodiversity of the bacterial communities in the rumen of cows fed alfalfa or triticale were investigated using 16S rRNA gene clone library analyses. The rumen bacterial community was fractionated and analyzed as three separate fractions: populations in the planktonic, loosely attached to rumen digesta particles, and tightly attached to rumen digesta particles. Six hundred and thirteen operational taxonomic units (OTUs) belonging to 32 genera, 19 families, and nine phyla of the domain Bacteria were identified from 1014 sequenced clones. Four hundred and fifty one of the 613 OTUs were identified as new species. These bacterial sequences were distributed differently among the three fractions in the rumen digesta of cows fed alfalfa or triticale. Chao 1 estimation revealed that, in both communities, the populations tightly attached to particulates were more diverse than the planktonic and those loosely attached to particulates. S-Libshuff detected significant differences in the composition between any two fractions in the rumen of cows with the same diet and between the communities fed alfalfa and triticale diets. The species richness estimated for the communities fed alfalfa and triticale is 1027 and 662, respectively. The diversity of the rumen bacterial community examined in this study is greater than previous studies have demonstrated and the differences in the community composition between two high-fiber diets have implications for sample selection for downstream metagenomics applications.

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    • "Our results show that the number of bacterial species present in the gut of the House Sparrow is large with 4,436 specieslevel OTUs (from the CD-Hit analysis). Our study described the presence of a higher number of bacteria in the gut of a wild bird than those reported by previous studies for the gut of birds, some mammals, and even humans [16] [22] [32] [34] [62]. Because the analysis we used not only eliminated sequences that include chimera, homopolymer sequences, and sequences created by errors of pyrosequencing [56], but also it removed some real bacterial sequences by its stringent criteria, we expect the total number of OTUs present in the House Sparrow's gut to be higher. "
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    • "The genes and the deduced proteins retrieved had varied degrees of similarity to genes previously found in typical ruminal bacteria such as Bacteroides and Prevotella species (27 to 99 % amino acid similarity). Prevotella is one of the most predominant bacterial genera found in the rumen, accounting for up to 20 % of the total bacteria found in sheep (Bekele et al. 2010), between 14 and 60 % in dairy cows (Kong et al. 2010; Stevenson and Weimer, 2007) and up to 90 % in steers (Huws et al. 2010; 2013). The publication of the P. ruminicola 23 and Prevotella bryantii B(1)4 genomes (Purushe et al. 2010) may explain why most of the fosmid sequences were similar to these entries as only limited information on other rumen bacteria is currently deposited. "
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    • "The genes and the deduced proteins retrieved had varied degrees of similarity to genes previously found in typical ruminal bacteria such as Bacteroides and Prevotella species (27 to 99 % amino acid similarity). Prevotella is one of the most predominant bacterial genera found in the rumen, accounting for up to 20 % of the total bacteria found in sheep (Bekele et al. 2010), between 14 and 60 % in dairy cows (Kong et al. 2010; Stevenson and Weimer, 2007) and up to 90 % in steers (Huws et al. 2010; 2013). The publication of the P. ruminicola 23 and Prevotella bryantii B(1)4 genomes (Purushe et al. 2010) may explain why most of the fosmid sequences were similar to these entries as only limited information on other rumen bacteria is currently deposited. "
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    ABSTRACT: Improving the health beneficial fatty acid content of meat and milk is a major challenge requiring an increased understanding of rumen lipid metabolism. In this study, we isolated and characterized rumen bacterial lipases/esterases using functional metagenomics. Metagenomic libraries were constructed from DNA extracted from strained rumen fluid (SRF), solid-attached bacteria (SAB) and liquid-associated rumen bacteria (LAB), ligated into a fosmid vector and subsequently transformed into an Escherichia coli host. Fosmid libraries consisted of 7,744; 8,448; and 7,680 clones with an average insert size of 30 to 35 kbp for SRF, SAB and LAB, respectively. Transformants were screened on spirit blue agar plates containing tributyrin for lipase/esterase activity. Five SAB and four LAB clones exhibited lipolytic activity, and no positive clones were found in the SRF library. Fosmids from positive clones were pyrosequenced and twelve putative lipase/esterase genes and two phospholipase genes retrieved. Although the derived proteins clustered into diverse esterase and lipase families, a degree of novelty was seen, with homology ranging from 40 to 78 % following BlastP searches. Isolated lipases/esterases exhibited activity against mostly short- to medium-chain substrates across a range of temperatures and pH. The function of these novel enzymes recovered in ruminal metabolism needs further investigation, alongside their potential industrial uses.
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