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
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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    • "Sandri et al. (2014) 348Zhou et al., 2015). Diet is the main driver of shifts 355 in rumen bacterial communities and this effect has been extensively studied (Kong et al., 2010; 356 Pitta et al., 2010; de Menezes et al., 2011), however, much less in known about the shifts inKong et al., 2010; Pitta et 363 al., 2010; Peng et al., 2015). There is a diverse array of biological functions associated with 364 bacteria from the phylum Bacteroidetes; the most prevailing function being polysaccharide 365 degradation (Thomas et al., 2011). "
    [Show abstract] [Hide abstract] ABSTRACT: Rumen bacteria form a dynamic, complex symbiotic relationship with their host, degrading forages to provide volatile fatty acids (VFA) and other substrates as energy to the animal. The objectives were to characterize rumen bacteria in three genetic lines of primiparous dairy cattle, Holstein (HO, n = 7), Jersey (JE, n = 8), and HO x JE crossbreeds (CB, n = 7) across a lactation (3, 93, 183, and 273 days in milk (DIM)) and correlate these factors with VFA, bacterial cell membrane fatty acids (FA), and animal production (i.e., milk yield). This study employed llumina MiSeq (v. 3) to investigate rumen bacterial communities and gas chromatography/mass spectroscopy to identify bacterial membrane FA. Lactation stage had a prominent effect on rumen bacterial communities, whereas genetics had a lesser effect on rumen bacteria. The FA composition of bacterial cell membranes was affected by both lactation stage and genetics. Few correlations existed between VFA and bacterial communities, however, moderate correlations occurred between milk yield, protein percentage, fat yield, and rumen bacterial communities. Positive correlations were found between branched-chain FA (BCFA) in bacterial cell membranes and bacteria genera. In conclusion, bacterial communities and their FA compositions are more affected by stage of lactation than by genetics of dairy cow.
    No preview · Article · Mar 2016 · FEMS Microbiology Ecology
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    • "Target organism Target gene T a (°C) Primer conc. (nM) Reference Protozoa 18S rRNA 55 600 [30] Methanogens mcrA 60 900 [31] Domain bacteria 16S rRNA 50 500 [32] Fibrobacter succinogenes 16S rRNA 58 200 [32] Ruminococcus albus 16S rRNA 55 500 [33] Ruminobacter amylophilus 16S rRNA 60 500 [32] Prevotella bryantii 16S rRNA 61 500 [32] Selenomonas ruminantium 16S rRNA 59 500 [32] Clostridium aminophilum 16S rRNA 56 400 [14, 34] doi:10.1371/journal.pone.0150115.t002where C, FS, P, and ST denote the treatment factors of sample class, forage source, period, and sampling time, respectively. "
    [Show abstract] [Hide abstract] ABSTRACT: This study examined ruminal microbial community composition alterations during initial adaption to and following incubation in a rumen simulation system (Rusitec) using grass or corn silage as substrates. Samples were collected from fermenter liquids at 0, 2, 4, 12, 24, and 48 h and from feed residues at 0, 24, and 48 h after initiation of incubation (period 1) and on day 13 (period 2). Microbial DNA was extracted and real-time qPCR was used to quantify differences in the abundance of protozoa, methanogens, total bacteria, Fibrobacter succinogenes, Ruminococcus albus, Ruminobacter amylophilus, Prevotella bryantii, Selenomonas ruminantium, and Clostridium aminophilum. We found that forage source and sampling time significantly influenced the ruminal microbial community. The gene copy numbers of most microbial species (except C. aminophilum) decreased in period 1; however, adaption continued through period 2 for several species. The addition of fresh substrate in period 2 led to increasing copy numbers of all microbial species during the first 2-4 h in the fermenter liquid except protozoa, which showed a postprandial decrease. Corn silage enhanced the growth of R. amylophilus and F. succinogenes, and grass silage enhanced R. albus, P. bryantii, and C. aminophilum. No effect of forage source was detected on total bacteria, protozoa, S. ruminantium, or methanogens or on total gas production, although grass silage enhanced methane production. This study showed that the Rusitec provides a stable system after an adaption phase that should last longer than 48 h, and that the forage source influenced several microbial species.
    Full-text · Article · Feb 2016 · PLoS ONE
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    • "At genus level, Clostridium , Ruminococcus and Butyrivibrio were the most represented Firmicutes. They are potent cellulose degraders as well as have the ability to digest pectin and hence are important component in the rumen dietary fiber utilization [44]. Bacteroidetes and Firmicutes population in the rumen and gut collectively involve in the conversion of organic matter to simpler forms [45, 46]. "
    [Show abstract] [Hide abstract] ABSTRACT: The rumen microbiota functions as an effective system for conversion of dietary feed to microbial proteins and volatile fatty acids. In the present study, metagenomic approach was applied to elucidate the buffalo rumen microbiome of Jaffrabadi buffalo adapted to varied dietary treatments with the hypothesis that the microbial diversity and subsequent in the functional capacity will alter with diet change and enhance our knowledge of effect of microbe on host physiology. Eight adult animals were gradually adapted to an increasing roughage diet (4 animals each with green and dry roughage) containing 50:50 (J1), 75:25 (J2) and 100:0 (J3) roughage to concentrate proportion for 6 weeks. Metagenomic sequences of solid (fiber adherent microbiota) and liquid (fiber free microbiota) fractions obtained using Ion Torrent PGM platform were analyzed using MG-RAST server and CAZymes approach. Taxonomic analysis revealed that Bacteroidetes was the most abundant phylum followed by Firmicutes, Fibrobacter and Proteobacteria. Functional analysis revealed protein (25-30 %) and carbohydrate (15-20 %) metabolism as the dominant categories. Principal component analysis demonstrated that roughage proportion, fraction of rumen and type of forage affected rumen microbiome at taxonomic as well as functional level. Rumen metabolite study revealed that rumen fluid nitrogen content reduced in high roughage diet fed animals and pathway analysis showed reduction in the genes coding enzymes involved in methanogenesis pathway. CAZyme annotation revealed the abundance of genes encoding glycoside hydrolases (GH), with the GH3 family most abundant followed by GH2 and GH13 in all samples. Results reveals that high roughage diet feed improved microbial protein synthesis and reduces methane emission. CAZyme analysis indicated the importance of microbiome in feed component digestion for fulfilling energy requirements of the host. The findings help determine the role of rumen microbes in plant polysaccharide breakdown and in developing strategies to maximize productivity in ruminants.
    Full-text · Article · Dec 2015 · BMC Genomics
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