Development of a phylogenetic microarray for comprehensive analysis of ruminal bacterial communities

Abstract

RumenBactArray can be a robust tool to comparatively analyse ruminal bacteria needed in nutritional studies of ruminant animals.

Analysis of the rumen bacteria and methanogenic archaea of yak (Bos grunniens) steers grazing on the Qinghai-Tibetan Plateau

“…In the present study, the microbial community of the yak rumen was predominated by phyla Bacteroidetes (59.06%) and Firmicutes (25.81%); such microbial distribution of the major phyla was similar to the rumen bacterial community structure of yaks in Sichuan (Chen et al, 2015) and other ruminants from the genus Bos (Jami and Mizrahi, 2012;Lee et al, 2012;Wu et al, 2012;Zened et al, 2013;Kim et al, 2014;Lin et al, 2015). However, some other studies had different reports.…”

Essential oils affect populations of some rumen bacteria in vitro as revealed by microarray (RumenBactArray) analysis

“…Samples were prepared, labeled, and then subjected to microarray hybridization as described previously (Kim et al, 2014 ). Briefly, nearly full-length 16S rRNA genes were amplified from each metagenomic DNA sample using the universal primer set 27F (5′-AGA GTT TGA TCM TGG CTC AG-3′) and T7/1492R (5′-TCT AAT ACG ACT CAC TAT AGG GGG YTA CCT TGT TAC GAC TT-3′) as described previously.…”

“…Microarray hybridization was performed using Agilent Technologies' Hybridization gasket slides as described previously (Kim et al, 2014 ). Briefly, the hybridization solution containing 6× SSPE, 0.01% Tween-20, 0.01 mg/ml acetylated bovine serum albumin (BSA), 10% formamide, and 150 ng labeled cRNA was incubated at 65°C for 5 min and then placed on ice for 5 min.…”

“…The microarray slides were scanned and the fluorescent images of the hybridized microarrays were analyzed as previously described (Kim et al, 2014 ). Briefly, the hybridization images were captured with a GenePix 4000B Scanner (Axon Instruments, Union City, CA).…”

“…They have been used in investigations of bacteria in various environments, such as soil, human gut, human feces, sludges, and lakes (Small et al, 2001 ; Adamczyk et al, 2003 ; Castiglioni et al, 2004 ; Palmer et al, 2006 ; Rajilic-Stojanovic et al, 2009 ; Kang et al, 2010 ). A phylochip specifically for comprehensive analysis of rumen bacterial communities was recently developed based on 16S rRNA gene sequence with operational taxonomic units (OTUs) calculated at 97% sequence similarity (Kim et al, 2014 ). This phylochip, referred to as RumenBactArray, has more than 1600 OTU-specific probes that allow detection and semi-quantification of rumen bacteria.…”