Microbial community structure in gastrointestinal tracts of domestic animals: comparative analyses using rRNA-targeted oligonucleotide probes

Abstract

The microbial community structure of the gastrointestinal (GI) tracts of various domestic animals (bovine, ovine, caprine, and swine) was evaluated using oligonucleotide probes targeting the small subunit (SSU) ribosomal RNA (rRNA) of major microbial groups. Bacterial, eukaryotic, and archaeal rRNAs were estimated to account for approximately 60–90%, 3–30% and 0.5–3%, respectively, of the total rRNA present in the GI tracts of most of the animals examined in this study. The abundance of phylogenetically defined groups of methanogens and sulfate‐reducing bacteria (SRB) was also evaluated. Methanobacteriales were the predominant methanogens in the rumen of bovine and caprine, while Methanomicrobiales predominated in the ovine rumen. A dominant archaeal group could not be identified in other sampling locations of the GI tract of these ruminants and in the GI tract of pigs, using the available collection of group‐specific probes. Desulfovibrio species were the most abundant Gram‐negative SRB targeted by available probes in the GI tract of nearly all animals.

Diversity, abundance and novel 16S rRNA gene sequences of methanogens in rumen liquid, solid and epithelium fractions of Jinnan cattle

“…Such marked differences between these two studies are also likely to be explained, in part, by animal species and diet. Lin et al (1997) targeting the small subunit ribosomal RNA through oligonucleotide probes demonstrated that animal species and diet affected the quantity and dominance of methanogens in the rumen. The molecular diversity of methanogens also confirmed this (Wright et al, 2004 and.…”

Methanogenic System of a Small Lowland Stream Sitka, Czech Republic

“…Methanogenic archaea are ubiquitous in anoxic environments and require an extremely low redox potential to grow. They can be found both in moderate habitats such as rice paddies (Grosskopf et al 1998a,b), lakes (Jürgens et al 2000, Keough et al 2003) and lake sediments (Chan et al 2005), as well as in the gastrointestinal tract of animals (Lin et al 1997) and in extreme habitats such as hydrothermal vents (Jeanthon et al 1999), hypersaline habitats (Mathrani & Boone 1995) and permafrost soils (Kobabe et al 2004, Ganzert et al 2006. Rates of methane production and consumption in sediments are controlled by the relative availability of substrates for methanogenesis (especially acetate or hydrogen and carbon dioxide).…”

An <i>in vitro</i> study on the effect of sage, <i>Salvia officinalis</i> L., on rumen fermentation

“…Fluorescence in situ hybridization (FISH), as described by Pers-Kamczyc et al (2011), was used to quantify the methanogen population. The specific oligonucleotide probe (TibMolBiol, Poznań, Poland) was designed for all methanogens (Lin et al, 1997) and was complementary to 16S rRNA. Hybridization was done at 37°C in a hybridization buffer containing 0.9 M NaCl, 20 mM Tris-HCl, 38% formamide, and 0.1% sodium dodecyl sulphate (SDS) with 50 ng/well fluorescent dye Cy3 at the 5' end of the oligonucleotide probe.…”