Potential role of rumen microbiota in altering average daily gain and feed efficiency in meat goats fed simple and mixed pastures using bacterial tag-encoded FLX amplicon pyrosequencing1.

Cost-effective and feasible production system of meat goats requires that grazed forages are converted to profitable goat meat product. However, there are studies as how altering forage type influences ruminal fermentation parameters and animal growth performance, and interact with microbiota in meat goats. Our objective for current study was to examine whether the comparative abundance of the Bacteroidetes (B) and Firmicutes (F) bacterial phyla in meat goats fed simple and mixed forages influenced average daily gain (ADG) and rumen fermentation parameters. In the present study, a molecular approach, bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) was applied to accomplish diversity analyses of rumen bacterial populations. Thirty-six Kiko-cross growing meat goats (body weight (BW) = 27.7 ± 2.83 kg) at approximately 7 mo of age were used in this study. Animals were randomly allocated to 3 pasture treatment groups (n = 12) as follows: 1) bermudagrass pasture (BG; Cynodon dactylon), 2) sunn hemp forage (SH; Crotalaria juncea), and 3) BG + SH forage combinations. There were 2 replicates per treatment and animals grazed these pastures for 45 d. Results indicated that treatments had similar initial BW, but final BW and ADG were higher (P < 0.01) for SH and BG + SH combinations than for BG alone. Animal ADG and rumen fermentation (acetate to propionate; A/P ratios) were highly correlated with the abundance of various bacterial populations within the rumen microbiome. There were linear decreases in percentage of Bacteroidetes (R2 = -0.84; P < 0.05) associated with decreasing ADG. In contrast, increased ADG was linearly associated with higher percentages of Firmicutes (R2 = 0.79; P < 0.05), F/B ratios (R2 = 0.88; P = 0.07), total VFA (R2 = 0.45; P < 0.05), and lower A/P ratio (R2 = -0.72; P < 0.01). This suggests that the substrates (diets) and bacterial community have the role in adapting host biological parameters in meat goats. The abundance examination of both Bacteroidetes and Firmicutes will be useful for exploring the structure of gut microbiota as an estimate of animal performance.

Gastrointestinal Bacterial and Methanogenic Archaea Diversity Dynamics Associated with Condensed Tannin-Containing Pine Bark Diet in Goats Using 16S rDNA Amplicon Pyrosequencing.

Eighteen Kiko-cross meat goats (n = 6) were used to collect gastrointestinal (GI) bacteria and methanogenic archaea for diversity measures when fed condensed tannin-containing pine bark (PB). Three 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 (P = 0.05) with increasing PB supplementation. These results indicate that feeding PB selectively altered bacteria and methanogenic archaeal populations in the GI tract of goats.

Distinct soil bacterial communities revealed under a diversely managed agroecosystem.

Land-use change and management practices are normally enacted to manipulate environments to improve conditions that relate to production, remediation, and accommodation. However, their effect on the soil microbial community and their subsequent influence on soil function is still difficult to quantify. Recent applications of molecular techniques to soil biology, especially the use of 16S rRNA, are helping to bridge this gap. In this study, the influence of three land-use systems within a demonstration farm were evaluated with a view to further understand how these practices may impact observed soil bacterial communities. Replicate soil samples collected from the three land-use systems (grazed pine forest, cultivated crop, and grazed pasture) on a single soil type. High throughput 16S rRNA gene pyrosequencing was used to generate sequence datasets. The different land use systems showed distinction in the structure of their bacterial communities with respect to the differences detected in cluster analysis as well as diversity indices. Specific taxa, particularly Actinobacteria, Acidobacteria, and classes of Proteobacteria, showed significant shifts across the land-use strata. Families belonging to these taxa broke with notions of copio- and oligotrphy at the class level, as many of the less abundant groups of families of Actinobacteria showed a propensity for soil environments with reduced carbon/nutrient availability. Orders Actinomycetales and Solirubrobacterales showed their highest abundance in the heavily disturbed cultivated system despite the lowest soil organic carbon (SOC) values across the site. Selected soil properties ([SOC], total nitrogen [TN], soil texture, phosphodiesterase [PD], alkaline phosphatase [APA], acid phosphatase [ACP] activity, and pH) also differed significantly across land-use regimes, with SOM, PD, and pH showing variation consistent with shifts in community structure and composition. These results suggest that use of pyrosequencing along with traditional analysis of soil physiochemical properties may provide insight into the ecology of descending taxonomic groups in bacterial communities.