Culture-independent phylogenetic analysis of the faecal flora of the rat

Abstract

The dominant faecal flora of the rat was determined using randomly cloned 16S rDNA comparative sequence analysis. A total of 109 near full-length 16S rDNA clones were sequenced, representing 69 unique 16S rRNA phylotypes or operational taxonomic units (OTUs). Estimates of species richness indicated that approximately 338 species were present in the faeces, suggesting that only 20% of species were identified. Only two of 39 Gram-negative clones aligned with previously cultured species, the remainder fell into a separate lineage within the Bacteroides-Cytophaga phylum. Several clones within this new group were related to 16S rDNA sequences previously identified from mouse faeces. Lactobacilli were the most abundant Gram-positive species, representing 23% of the total clones but only 7% of OTUs. The remaining Gram-positive clones were distributed among the Clostridium coccoides group (9%), the Clostridium leptum subgroup (18%), and throughout the low GC Gram-positive bacteria (13%). The majority of OTUs (63/69 or 91%) were less than 97% homologous to previously cultured bacteria. Faecal samples were also cultured using a variety of anaerobic media. With the exception of the lactobacilli, the cultured isolates demonstrated low species diversity and poorly reflected the population, as defined through comparative sequence analysis.

Host-microbial symbiosis in the vertebrate gastrointestinal tract and the Lactobacillus reuteri paradigm

“…L. reuteri is found in the digestive tract of mammals such as humans, pigs, hamsters, mice, rats, dogs, sheep, cattle, and different birds (41). In pigs, rodents, and chickens, L. reuteri is one of the most abundant species present in the gut and can be detected in a large subset of animals (42)(43)(44)(45). In contrast, the prevalence of L. reuteri is much lower in humans, where the species is only occasionally found (46).…”

Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution

“…L. johnsonii was added as this species co-exists with L. reuteri in natural populations of the rodent forestomach (Salzman et al, 2002;Brooks et al, 2003). Each of the L. reuteri strains used in the experiment carried a distinct allele of the leuS gene, allowing their differentiation.…”

“…In rodents, pigs and chickens, L. reuteri is one of the dominant species in the GIT (Leser et al, 2002;Salzman et al, 2002;Brooks et al, 2003;Abbas Hilmi et al, 2007). In these animals, L. reuteri colonizes the surfaces of the stratified squamous epithelial lining of the proximal regions of the digestive tract (Tannock, 1992;Walter et al, 2007).…”

Analysis of the bacterial diversity in the fecal material of the endangered Yangtze finless porpoise, Neophocaena phocaenoides asiaeorientalis

“…Many cultivation independent studies have been conducted on human fecal material [14][15][16]. The bacterial diversity in the fecal material of other animals, such as polar bears (Ursus maritimus) [17], wolves (Canis lupus) [18], gorillas (Gorilla beringei) [19], rats [20] and cows [21], has been described. The bacterial diversity in ruminants, such as the Yah (Bos grunniens) [22], the Gayal (Bos frontalis) [23,24], and the Swamp buffalo (Bubalus bubalis) [24] has also been investigated.…”