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


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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    • "Tag-encoded FLX amplicon pyrosequencing analyses used a Roche 454 FLX instrument with titanium reagents, and titanium procedures performed at the Research and Testing Laboratory (Lubbock, TX). Following sequencing, all failed sequence reads, low-quality sequence ends, tags, and primers were removed, and sequence collections depleted of non-bacterial ribosome sequences and those with degenerate base calls, homopolymers >5 bp in length, reads <200 bp, and chimeras (Gontcharova et al., 2010), as described (Bailey et al., 2011;Callaway et al., 2010;Finegold et al., 2010;Handl et al., 2011). OTU Picking PIBD-CC We used a naive Bayes classifier with confidence cutoff = 0.5 and RDP database (Cole et al., 2014) for OTUs assignments. "
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