Evaluation of the bacterial diversity in the rumen and feces of cattle fed diets containing levels of dried distiller’s grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)

Food and Feed Safety Research Unit, Southern Plains Agricultural Research Center, Agricultural Research Service, USDA, College Station, TX 77845, USA.
Journal of Animal Science (Impact Factor: 2.11). 12/2010; 88(12):3977-83. DOI: 10.2527/jas.2010-2900
Source: PubMed

ABSTRACT Dietary components and changes cause shifts in the gastrointestinal microbial ecology that can play a role in animal health and productivity. However, most information about the microbial populations in the gut of livestock species has not been quantitative. In the present study, we utilized a new molecular method, bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) that can perform diversity analyses of gastrointestinal bacterial populations. In the present study, cattle (n = 6) were fed a basal feedlot diet and were subsequently randomly assigned to 1 of 3 diets (n = 2 cows per diet). In each diet, 0, 25, or 50% of the concentrate portion of the ration was replaced with dried distillers grain (DDGS). Ruminal and fecal bacterial populations were different when animals were fed DDGS compared with controls; ruminal and fecal Firmicute:Bacteroidetes ratios were smaller (P = 0.07) in the 25 and 50% DDG diets compared with controls. Ruminal pH was decreased (P < 0.05) in ruminal fluid from cattle fed diets containing 50% compared with 0% DDGS. Using bTEFAP, the normal microbiota of cattle were examined using modern molecular methods to understand how diets affect gastrointestinal ecology and the gastrointestinal contribution of the microbiome to animal health and production.

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Available from: Paul Kononoff, Sep 10, 2015
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    • "The 98 sequences belonged to the dominion Bacterium, of which approximately 97.96% were related to the Bacteroidetes phylum and only 2.04% of the sequences to the Firmicutes phylum. The predominance of the phyla corroborates data given by several authors who reported that the most relevant identified phyla in bovine rumen are the Bacteroidetes and Firmicutes phyla (Callaway et al., 2010; Chen et al., 2011; Li et al., 2014). Most sequences (47.96%) of the Bacteroidetes phylum belonged to the genus Prevotella, or rather, gram-negative, obligatory anaerobic, non-sporulating bacteria, without any motility and shaped as pleomorphic rods (Shah & Collins, 1990). "
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    ABSTRACT: The bacterial diversity by 16S rDNA partial sequencing and scanning electron microscope (SEM) of the rumen microbiome was characterized. Three Nellore bovines, cannulated at the rumen, were utilized. Liquid and solid fractions from the rumen content were processed for the extraction of metagenomic DNA and later 16S rDNA amplicons were utilized to construct the WGA library for further clone sequencing. Data were analyzed by MEGA and MOTUR (University of Michigan) softwares. Approximately 97.96% of operation taxonomic units (OTUs) were related to Bacteriodetes phylum and 2.04% of sequences were affiliated to Firmicutes phylum. In the case of Bacteriodetes, the great part of sequences (47.96%) was attributed to Prevotella genus. Bacteroidetes phylum was predominant in rumen content and the Prevotella genus was the most abundant, including diverse species related to this taxon. The bacterial morphological diversity associated to plant fibers was detected by SEM and showed its role in plant biomass deconstruction beyond the detection of microbiological interactions that involved protozoa. Diversidade bacteriana em rúmen bovino por análise de sequências do 16S rDNA metagenômico e microscopia eletrônica de varredura RESUMO. O estudo foi realizado para caracterizar a diversidade bacteriana por meio do sequenciamento parcial do 16S rDNA total e microscopia eletrônica de varredura (MEV) do microbioma ruminal. Foram utilizados três bovinos da raça Nelore, canulados no rúmen. As frações líquidas e sólidas do conteúdo ruminal foram processadas para extração de DNA metagenômico. Em seguida, amplicons 16S rDNA foram utilizados na construção da biblioteca WGA para posterior sequenciamento dos clones. Os dados foram analisados pelos softwares MEGA e MOTHUR (The University of Michigan). Aproximadamente 97,96% das UTOs foram relacionadas ao filo Bacteroidetes e apenas 2,04% das sequências foram afiliadas ao filo Firmicutes. Para o filo Bacteroidetes, grande parte das sequências (47,96%) foi atribuída ao gênero Prevotella. O filo Bacteroidetes foi predominante no conteúdo ruminal e o gênero Prevotella foi o mais abundante, incluindo diversas espécies relacionadas a esse nível taxonômico. A diversidade morfológica bacteriana associada às fibras vegetais foi detectada por MEV, evidenciando seu papel na desconstrução da biomassa vegetal, além da detecção de interações microbiológicas que envolvem protozoários.
    Acta Scientiarum Animal Sciences 08/2015; 37(3):251-257. DOI:10.4025/actascianimsci.v37i3.26535
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    • "In accordance with other studies, Prevotella, which comprise a well-known xylan degrading group (Flynt and Bayer 2008; Dodd et al. 2010), is always the dominant bacterial genus found in the rumen microbiome, regardless the animal species, host diet, geographical location or approach used to assess the microbiome (Stevenson and Weimer 2007; Callaway et al. 2010; Purushe et al. 2010; Lee et al. 2012; Li et al. 2012; Pitta et al. 2010). In addition to Prevotellaceae, other bacterial families normally detected in the rumen of different animal species were detected in high relative abundance in the sheep rumen microbiome, which included Succinivibrionaceae (Succinivibrio genus) (Callaway et al. 2010; Lee et al. 2012), Ruminococcaceae (Ruminococcus genus) (Lee et al. 2012), Veillonellaceae (Succiniclasticum genus) (Callaway et al. 2010; Lee et al. 2012), Porphyromonadaceae (Paludibacter genus) (Pitta "
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    ABSTRACT: The rumen is a complex ecosystem enriched for microorganisms able to degrade biomass during the animal's digestion process. The recovery of new enzymes from naturally evolved biomass-degrading microbial communities is a promising strategy to overcome the inefficient enzymatic plant destruction in industrial production of biofuels. In this context, this study aimed to describe the bacterial composition and functions in the sheep rumen microbiome, focusing on carbohydrate-active enzymes (CAE). Here, we used phylogenetic profiling analysis (inventory of 16S rRNA genes) combined with metagenomics to access the rumen microbiome of four sheep and explore its potential to identify fibrolytic enzymes. The bacterial community was dominated by Bacteroidetes and Firmicutes, followed by Proteobacteria. As observed for other ruminants, Prevotella was the dominant genus in the microbiome, comprising more than 30 % of the total bacterial community. Multivariate analysis of the phylogenetic profiling data and chemical parameters showed a positive correlation between the abundance of Prevotellaceae (Bacteroidetes phylum) and organic matter degradability. A negative correlation was observed between Succinivibrionaceae (Proteobacteria phylum) and methane production. An average of 2 % of the shotgun metagenomic reads was assigned to putative CAE when considering nine protein databases. In addition, assembled contigs allowed recognition of 67 putative partial CAE (NCBI-Refseq) representing 12 glycosyl hydrolase families (Pfam database). Overall, we identified a total of 28 lignocellulases, 22 amylases and 9 other putative CAE, showing the sheep rumen microbiome as a promising source of new fibrolytic enzymes.
    Antonie van Leeuwenhoek 04/2015; 108(1). DOI:10.1007/s10482-015-0459-6 · 1.81 Impact Factor
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    • " difficulty of taxonomically defining unique spe cies of microbes . The relative abundance of an OTU or higher taxon ( genus , family , order , class , or phylum ) is typically expressed as a percentage of the total num ber of sequences obtained from a sample , with results from multiple samples being subsequently associated with dietary effects ( Callaway et al . , 2010 ; Hristov et al . , 2012 ; Petri et al . , 2013a ; Ellison et al . , 2014 ) . Although NGS technologies are powerful tools to catalog microbial and gene diversity ( including dis covery of novel genes ) , they do not accurately quantify those individual microbial groups or genes ( Roh et al . , 2010 ) . In nearly all of the studies repo"
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    ABSTRACT: Metagenomics and high-throughput sequencing have greatly expanded our knowledge of the rumen microbiome. Surveys of all 4 cellular microbial groups (bacteria, archaea, protozoa, and fungi) reveal profound diversity. Even so, evidence exists for core members to perform key degradative or fermentative roles for the host. Some core members are functionally similar yet taxonomically diverse, and noncore members are particularly diverse and probably vary among diets, animals, and over time after feeding. Gains in functional knowledge are being made and offer much potential not only to improve fiber digestibility, decrease methane emissions, and improve efficiency of nitrogen usage but also to help explain the differences in nutrient digestibility or feed efficiency among animals fed the same diet. Integrated research using metagenomics, bioinformatics, traditional ruminant nutrition, and statistical inferences have provided opportunities for ruminant nutritionists and rumen microbiologists to work synergistically to improve nutrient utilization efficiency while minimizing output of wastes and emissions of methane and ammonia. Examples we highlight include residual feed intake, rumen biohydrogenation of unsaturated fatty acids, and dietary inclusion of ionophores. However, there are still some quantitative limitations in approaches being used. This review addresses knowledge gained and current limitations and challenges that remain.
    Journal of Animal Science 04/2015; 93(4):1450. DOI:10.2527/jas.2014-8754 · 2.11 Impact Factor
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