Research Article Gastrointestinal Bacterial and Methanogenic Archaea Diversity Dynamics Associated with Condensed Tannin-Containing Pine Bark Diet in Goats Using 16S rDNA Amplicon Pyrosequencing Byeng R. Min, 1 Sandra Solaiman, 1 Raymon Shange, 1 and Jong-Su Eun 2 1 Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, USA 2 Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA Correspondence should be addressed to Byeng R. Min; minb@mytu.tuskegee.edu Received 16 July 2013; Revised 4 September 2013; Accepted 4 September 2013; Published 2 January 2014 Academic Editor: Isabel S´ a-Correia Copyright © 2014 Byeng R. Min et al. is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Eighteen Kiko-cross meat goats (=6) were used to collect gastrointestinal (GI) bacteria and methanogenic archaea for diversity measures when fed condensed tannin-containing pine bark (PB). ree dietary treatments were tested: control diet (0% PB and 30% wheat straw (WS); 0.17% condensed tannins (CT) dry matter (DM)); 15% PB and 15% WS (1.6% CT DM), and 30% PB and 0% WS (3.2% CT DM). A 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing technique was used to characterize and elucidate changes in GI bacteria and methanogenic archaea diversity among the diets. Proteobacteria was the most dominant phylum in goats with mean relative abundance values ranging from 39.7 (30% PB) to 46.5% (control) and 47.1% (15% PB). Other phyla individually accounted for fewer than 25% of the relative abundance observed. Predominant methanogens were Methanobrevibacter (75, 72, and 49%), Methanosphaera (3.3, 2.3, and 3.4%), and Methanobacteriaceae (1.2, 0.6, and 0.7%) population in control, 15, and 30% PB, respectively. Among methanogens, Methanobrevibacter was linearly decreased ( = 0.05) with increasing PB supplementation. ese results indicate that feeding PB selectively altered bacteria and methanogenic archaeal populations in the GI tract of goats. 1. Introduction Studies on gastrointestinal (GI) microorganisms have tradi- tionally depended on the use of anaerobic cultivation tech- niques [1] which only can detect an estimated 11% of the total bacterial populations present in the rumen [2]. Molecular methodologies developed over the past decade now enable researchers to examine the diversity of the gut microflora independent of cultural methods. Bacterial diversities within the GI tract of humans [3, 4] and rumen of beef cattle [5, 6] have been investigated in recent years as a result of development of 16S rDNA-based analysis, yet similar data on the microbiomes of bacteria and methanogenic archaea diversity in the lower GI tract of meat goats are limited. In addition, there is no clear information on the prevalence of methanogenic and microbial populations in the hindgut of animals other than human and swine. Plant tannins (condensed (CT) and hydrolysable tannins) are polyphenolic compounds of relatively high molecular weight with the capacity to form complexes mainly with pro- teins due to the presence of a large number of phenolic hydroxyl groups [7]. ey are ubiquitously spread in nutri- tionally important forage trees, shrubs, legumes, cereals, and tree barks. e effects of tannins on ruminant production have been extensively published in the past, and among them beneficial effects of tannins on animal production system have been much focused, with particular interest in their positive effects on protein metabolism, prevention of frothy bloat, and modification on rumen microbial population [7]. Microbial population changes in the gut when animals were fed CT-containing diets were reported using a 16S PCR technique in sheep [8] and rat [9]. In addition, the use of rapid sequencing technologies combined with molecular methods is becoming a prevalent standard for evaluating Hindawi Publishing Corporation International Journal of Microbiology Volume 2014, Article ID 141909, 11 pages http://dx.doi.org/10.1155/2014/141909