Taxonomy/systematicsSubdoligranulum variabile gen. nov., sp. nov. from human feces
Introduction
Phylogenetic analyses based upon comparative analyses of small-subunit (16S) rRNA are transforming our perception of the diversity of the human gut microflora. Although it has long been known that the human gastrointestinal tract comprises a great diversity of largely anaerobic bacteria, it is only with the advent of culture-independent studies, in particular 16S rDNA direct community analysis, that the true extent of this diversity has started to be uncovered (e.g. [1], [2]). These and other studies have shown that the great majority of species have so far escaped taxonomic description [1], [2], [3]. Although it is possible that many of these “hidden species” are non-culturable, it is highly likely that some others have in the past eluded description due to difficulties in recognizing them as distinct taxonomic entities. 16S rRNA gene sequencing is being used increasingly as a powerful tool for screening for potentially novel species diversity in a whole range of environments. Indeed this molecular diagnostic tool, used in concert with culture-based methods, has resulted in the description of many novel organisms from the human gut in recent years (e.g. [4], [5], [6], [7], [8]). During the course of an on-going study of the diversity of the human gut microflora, we have used the aforementioned approach to facilitate the identification of a hitherto unknown species within the Clostridium leptum rRNA supra-generic cluster. Based on the presented findings, we describe a new genus and species, Subdoligranulum variabile.
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Culture and biochemical characterization
Strain BI 114T was recovered from a fecal specimen of a 47-year-old female, in Hørsholm, Denmark. The organism was isolated on the commercially available Biolog Universal Anaerobe agar supplemented with 5%(v/v) defibrinated calfs blood (BUA+B) (Biolog Inc., Hayward, CA, USA) incubated anaerobically at 37°C under N2, CO2 and H2 (80:10:10%(v/v)) gas phase. The strain was also grown in liquid medium M2GSC (including rumen fluid) prepared according to Barcenilla et al. [9] and in Fastidious
Results and discussion
The unknown isolate recovered from human feces was strictly anaerobic, and failed to grow in 2% or 6% (v/v) oxygen. The colonies of the isolate on BUA+B agar gained a size of approximately 1 mm in diameter after 4–5 days incubation at 37°C. The colonies had a grayish-white appearance and were circular and concave. It was not possible to grow the strain on TPY or BHI agar. The cells stained Gram-negative and were non-motile and non-spore-forming. Fig. 1 shows a phase contrast micrograph of the
Acknowledgements
This work has been carried out with financial support from the Commission of the European Communities, specific RTD program “Quality of Life and Management of Living Resources”, QLK1-2000-108, “Microbe Diagnostics”. It does not necessarily reflect its views and in no way anticipates the Commission's future policy in this area.
References (28)
- et al.
Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis
FEMS Microbiol Lett
(2002) - et al.
Anaerostipes caccae gen. nov., sp. nov., a new saccharolytic, acetate-utilising, butyrate-producing bacterium from human faeces
Syst Appl Microbiol
(2002) - et al.
Ruminococcus luti sp. nov., isolated from a human faecal sample
Syst Appl Microbiol
(2002) - et al.
Clostridium bolteae sp. nov., isolated from human sources
Syst Appl Microbiol
(2003) - et al.
Clostridium hathewayi sp. nov., from human faeces
Syst Appl Microbiol
(2001) - et al.
Fusobacterium prausnitzii and related species represent a dominant group within the human fecal flora
Syst Appl Microbiol
(2001) - et al.
Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut
Appl Environ Microbiol
(1999) - et al.
Human colonic biota studied by ribosomal DNA sequence analysis
Appl Environ Microbiol
(1996) - et al.
Reclassification of Eubacterium formicigenerans (Holdeman & Moore) in the genus Dorea as Dorea formicigenerans comb. nov. and description of Dorea longicatena sp. nov. isolated from human faeces
Int J Syst Evol Microbiol
(2001) - et al.
Phylogenetic relationships of butyrate-producing bacteria from the human gut
Appl Environ Microbiol
(2000)