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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: 3.57). 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.

    • "Saro et al., 2012; Anantasook et al., 2013). The quantitative influence of different forage types on the abundance of the microbial populations is less well known and has been mainly shown in mixed forage-based diets (Kong et al., 2010; Saro et al., 2012). Tree and shrub foliage are important supplements for (small) ruminants on low-quality grasslands or shrublands in many areas of Latin and Central America, Asia and Africa as well as in Southern Europe (Leng, 1997). "
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    ABSTRACT: In ruminants, feed is digested mainly in the reticulorumen but to some extent also in the hindgut, and the digestive processes are influenced by the diet. The aim of the study was to record changes in microbial population and fermentation along the digestive tract by considering defined rumen compartments, caecum and colon as assessed in goats fed two contrasting diets. Ten adult female Saanen goats were fed either on grass hay (‘grass’) or a 1:1:1 mixture of dried poplar, raspberry and chestnut leaves (‘browse’). After at least 20 days on feed and 12 h of fasting, the goats were euthanised and frozen in the natural resting position to allow sampling of contents from exactly defined gastrointestinal locations. Lyophilised rumen and hindgut contents were used for isolation of genomic DNA and microbial quantification via real-time PCR. In filtered rumen and hindgut fluid, pH and concentrations of ammonia and short-chain fatty acids (SCFA) were measured. The experiment demonstrated that, within the rumen, the dry matter content decreased from dorsal and central (132 g/kg) to the ventral compartment (62 g/kg) as expected. The abundances of total and fibrolytic bacteria, protozoa and methanogens as well as SCFA concentrations were similar in the cranial and caudal dorsal and central rumen, but were lower in the ventral rumen compartment. Additionally, SCFA concentration and pH close to the rumen wall in the central rumen compartment resembled those in the ventral rumen more closely than those in the other central rumen samples. The pH was lower in the dorsal and central (6.4) than in the ventral (7.5) rumen compartment. In the caecum and colon, respectively, the copy numbers of bacteria (3.8 and 6.2 × 1010/ml), protozoa (1.4 and 0.2 × 107/ml) and methanogens (4.0 and 3.5 × 108/ml) (means of all goats combined) were markedly lower than those found in the rumen even though SCFA concentrations were similar. For all variables measured, the differences within the rumen and along the digestive tract were more pronounced in the browse-fed compared to the grass-fed goats. Consistent with the higher nutritional quality of the browse, the concentration of fermentation end-products and nitrogen availability were higher in the rumen across all compartments in the browse-fed goats compared to the grass-fed goats (pH, 6.4 vs. 7.3; SCFA, 139 vs. 111 mmol/L; ammonia, 11.2 vs. 4.1 mmol/L; copy numbers of bacteria, 8.1 vs. 7.8 × 1010/ml; protozoa, 1.7 vs. 0.3 × 109/ml; methanogens, 2.4 vs. 1.3 × 109/ml). Different from that, the hindgut pH was higher and ammonia concentration was lower in browse-fed goats compared to grass-fed goats. The results demonstrated that, when collecting rumen digesta to study the microbial population and rumen fermentation, it is important to distinguish between dorsal/central and ventral rumen sampling points and to consider forage type and quality. However, it is not decisive to distinguish between caudal and cranial rumen regions, provided the sampling is not done in rumen wall proximity and not in close proximity to the oesophagus.
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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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