Autochthonous species are particular to a given niche. The autochthonous microorganisms that inhabit the GI tract may be defined as “… indigenous microorganisms that colonize particular regions of the tract early in life, multiply to high population levels soon after colonization … remain at those levels throughout the lives of healthy well-nourished animals … (and) should be found in essentially all individuals of a given animal species, irrespective of their geographical location” (Savage, 1972). L. ruminis is one of the few Lactobacillus species considered autochthonous to the mammalian intestines (Tannock et al., 2000; Tannock, 2004), a fact that is supported by the frequent isolation of this organism from several mammalian hosts.
The previously described 18 month study involving ten healthy New Zealanders was among the first to demonstrate that L. ruminis was stably present in the human GI tract over time (Tannock et al., 2000). A meta-analysis describing earlier research on the Lactobacillus composition and succession in the human GI tract, reported that L. ruminis was recovered from the stomach and the intestines of human adults and from the intestines of children aged 6 - 12 years (Reuter, 2001). A culture independent study of the faecal Lactobacillus community of 13 healthy adults from the Netherlands, similarly found that L. ruminis-like sequences were commonly recovered from the faecal and cecal DNA libraries, and that L. ruminis was found to dominate the Lactobacillus community of the sampled sites in two out of three of these adults over a period of twenty months as assessed by monitoring DGGE fingerprints (Heilig et al., 2002). L. ruminis was recovered from one of two
individuals that took part in a Spanish study that aimed to investigate the daily
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populations”, particularly of the lactic acid bacteria, present in human faeces over a fifteen day period (Delgado et al., 2004). Incidental isolations of L. ruminis from human faeces have also been reported (Kagkli et al., 2007; Taweechotipatr et al., 2009; Yun et al., 2005).
Several studies on animals lend similar support for the establishment of L.
ruminis as an autochthonous species of the mammalian intestine. L. ruminis was first
isolated from the bovine rumen (Sharpe et al., 1973), and 16S rRNA gene restriction fragment length polymorphism (RFLP) analysis and sequencing have identified this species as a dominant member of the Lactobacillus community of cows (Krause et al., 2003).
Several reports have described the isolation of L. ruminis from the porcine GI tract, in which it has been the dominant lactic acid bacterium present (Al Jassim, 2003; Yin & Zheng, 2005). In fact, 8 of 13 isolates that were among 60 pure cultures recovered from the intestines of 6 healthy pigs post-mortem were identified as L.
ruminis by morphological analyses and 16S rRNA gene sequencing. At least one L.
ruminis strain was recovered from each pig (Al Jassim, 2003). Another study
identified 10 L. ruminis isolates as part of a panel of 52 Lactobacillus-like isolates that were a subset of all the colonies recovered from the either the gut or faeces of five pigs (Yin & Zheng, 2005). Remarkably, in both of these studies, L. ruminis was the only Lactobacillus species detected. However, L. ruminis does not always become dominant in the Lactobacillus community of the porcine GI tract. In a comparative 16S rRNA gene analysis of the phylogenetic diversity of the luminal GI microbiota of 24 pigs of varying age, health and dietary status, L. ruminis was represented in the library by a single clone (Leser et al., 2002). A total of 4,270 clones, representing 375 phylotypes constituted the library. A subset of twenty-four
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OTUs represented the Lactobacillus species present in the porcine gut. Twenty-two of these twenty-four Lactobacillus OTUs represented lactobacilli of known identity, and L. amylovorus (191 clones), L. johnsonii (138 clones) and L. reuteri (91 clones) were most abundantly represented in the clone library (Leser et al., 2002).
Species of the L. salivarius clade form a significant component of the equine GI microbiota (Morita et al., 2009; Willing et al., 2009). Swarming L. ruminis (11 isolates) was the dominant Lactobacillus species identified during screening of 40 colonies isolated from healthy thoroughbreds on a forage-concentrate diet. Other species of the L. salivarius clade identified included L. salivarius (5 isolates), L. equi (3 isolates) and L. agilis (1 isolate). This is consistent with an earlier study which recovered L. salivarius clade species, specifically L. equi (4/37 isolates), L. salivarius (3/37 isolates), L. ruminis (3/37 isolates), L. agilis (2/37 isolates), L. hayakitensis (1/37 isolates) and L. saerimneri (1/37 isolates) from equine faeces (Morita et al., 2009). However, L. hayakitensis, L. equigenerosi and L. equi rather than L. ruminis, were identified as the prevalent Lactobacillus species present in the faeces of these nine horses by PCR-DGGE analysis and sequencing (Morita et al., 2009).
L. ruminis may also dominate the GI microbiota of domestic cats (Desai et al.,
2009; Ritchie et al., 2010). Although only 2 of 12 cats in one study were found to harbour L. ruminis, this species represented 21.95 % of the 364 clones in a 16S rRNA gene fragment library derived from the faeces of the 12 animals (Ritchie et al., 2010).
L. ruminis was found to dominate the faecal microbiotas of four outdoor cats,
representing 63 % (736/1166 high-quality, sequenced chaperonin cpn60 clones) of the “outdoor” clone library (Desai et al., 2009). L. ruminis occurred at a lower frequency (46/1075 high-quality, sequenced clones) in the “indoor” clone library from five indoor cats faecal microbiota (Desai et al., 2009).
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L. ruminis therefore has a broad host-range that includes but is not limited to,
humans and domesticated mammals. The identification and/or isolation of L. ruminis from the intestinal and faecal microbiotas of these animals appear to vary considerably from study to study. This variation may reflect different experimental approaches for the isolation and detection of the dominant and persistent species of a given microbial community, as well as for species assignment. Furthermore, local variation in diet and environment may impact on the abundance of these species in the intestinal microbiotas of target animals.
The enteric Lactobacillus population is a subdominant component of the human GI microbiota (Tannock et al., 2000). Because L. ruminis constitutes only a fraction of the enteric Lactobacillus community, it must therefore be considered as a minority species in the gut.