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: 1.92). 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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    • "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 · 2.14 Impact Factor
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    • "Our relative quantification of microbiota also showed an increase of genus Prevotella in the bacterial community with unfortified DDGS. Similarly, Callaway et al. (2010) reported increased Prevotella in the rumen with increasing DDGS levels in a basal feedlot diet. However, only the increase of Prevotella was not sufficient to entirely explain the current results of protein degradation. "
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    ABSTRACT: The role of dried distillers grains plus solubles (DDGS) and associative effects of different levels of grape seed meal (GSM) fortified in DDGS, used as both protein and energy sources in the diet, on ruminal fermentation and microbiota were investigated using rumen-simulation technique. All diets consisted of hay and concentrate mixture with a ratio of 48:52 [dry matter (DM) basis], but were different in the concentrate composition. The control diet contained soybean meal (13.5% of diet DM) and barley grain (37%), whereas DDGS treatments, unfortified DDGS (19.5% of diet DM), or DDGS fortified with GSM, either at 1, 5, 10, or 20% were used entirely in place of soybean meal and part of barley grain at a 19.5 to 25% inclusion level. All diets had similar DM, organic matter, and crude protein contents, but consisted of increasing neutral detergent fiber and decreasing nonfiber carbohydrates levels with DDGS-GSM inclusion. Compared with the soy-based control diet, the unfortified DDGS treatment elevated ammonia concentration (19.1%) of rumen fluid associated with greater crude protein degradation (∼19.5%). Methane formation decreased with increasing GSM fortification levels (≥5%) in DDGS by which the methane concentration significantly decreased by 18.9 to 23.4 and 12.8 to 17.6% compared with control and unfortified DDGS, respectively. Compared with control, unfortified DDGS decreased butyrate proportion, and GSM fortification in the diet further decreased this variable. The proportions of genus Prevotella and Clostridium cluster XIVa were enhanced by the presence of DDGS without any associative effect of GSM fortification. The abundance of methanogenic archaea was similar, but their composition differed among treatments; whereas Methanosphaera spp. remained unchanged, proportion of Methanobrevibacter spp. decreased in DDGS-based diets, being the lowest with 20% GSM inclusion. The abundance of Ruminococcus flavefaciens, anaerobic fungi, and protozoa were decreased by the GSM inclusion. As revealed by principal component analysis, these variables were the microorganisms associated with the methane formation. Grape seed meal fortification level in the diet decreased DM and organic matter degradation, but this effect was more related to a depression of nonfiber carbohydrates degradation. It can be concluded that DDGS fortified with GSM can favorably modulate ruminal fermentation. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.
    Journal of Dairy Science 01/2015; 98(4). DOI:10.3168/jds.2014-8751 · 2.55 Impact Factor
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    • "To determine the identity of bacteria in the remaining sequences, sequences were denoised, assembled into clusters and queried using a distributed BLASTn.NET algorithm (Dowd et al., 2005) against a bacterial database derived from the National Centre for Biotechnology Information (NCBI). The BLASTn outputs were compiled and validated using taxonomic distance methods as described previously (Dowd et al., 2008; Callaway et al., 2010). "
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    ABSTRACT: This study investigates the influence of pipe characteristics on the bacteriological composition of material mobilised from a drinking water distribution system (DWDS) and the impact of biofilm removal on water quality. Hydrants in a single UK Distribution Management Area (DMA) with both polyethylene and cast iron pipe sections were subjected to incremental increases in flow to mobilise material from the pipe walls. Turbidity was monitored during these operations and water samples were collected for physico-chemical and bacteriological analysis. DNA was extracted from the material mobilised into the bulk water before and during flushing. Bacterial tag-encoded 454 pyrosequencing was then used to characterize the bacterial communities present in this material. Turbidity values were high in the samples from cast iron pipes. Iron, aluminium, manganese and phosphate concentrations were found to correlate to observed turbidity. The bacterial community composition of the material mobilised from the pipes was significantly different between plastic and cast iron pipe sections (p < 0.5). High relative abundances of Alphaproteobacteria (23.3%), Clostridia (10.3%) and Actinobacteria (10.3%) were detected in the material removed from plastic pipes. Sequences related to Alphaproteobacteria (22.8%), Bacilli (16.6%), and Gammaproteobacteria (1.4%) were predominant in the samples obtained from cast iron pipes. The highest species richness and diversity were found in the samples from material mobilised from plastic pipes. Spirochaeta spp., Methylobacterium spp. Clostridium spp. and Desulfobacterium spp., were the most represented genera in the material obtained prior to and during the flushing of the plastic pipes. In cast iron pipes a high relative abundance of bacteria able to utilise different iron and manganese compounds were found such as Lysinibacillus spp., Geobacillus spp. and Magneto-bacterium spp.
    Water Research 05/2014; 54:100–114. DOI:10.1016/j.watres.2014.01.049 · 5.32 Impact Factor