Elsevier

Anaerobe

Volume 10, Issue 3, June 2004, Pages 197-203
Anaerobe

Taxonomy/systematics
Subdoligranulum variabile gen. nov., sp. nov. from human feces

https://doi.org/10.1016/j.anaerobe.2004.01.004Get rights and content

Abstract

During studies on the microflora of human feces we have isolated a strictly anaerobic, non-spore-forming, Gram-negative staining organism which exhibits a somewhat variable coccus-shaped morphology. Comparative 16S ribosomal RNA gene sequencing studies show the unidentified organism is phylogenetically a member of the Clostridium leptum supra-generic rRNA cluster and displays a close affinity to some rDNA clones derived from human and pig feces. The nearest named relatives of the unidentified isolate corresponded to Faecalibacterium prausnitzii (formerly Fusobacterium prausnitzii) displaying a 16S rRNA sequence divergence of approximately 9%, with Anaerofilum agile and A. pentosovorans the next closest relatives of the unidentified bacterium (sequence divergence approximately 10%). Based on phenotypic and phylogenetic considerations, it is proposed that the unusual coccoid-shaped organism be classified as a new genus and species, Subdoligranulum variabile. The type strain of S. variabile is BI 114T (=CCUG 47106T=DSM 15176T).

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.

Section snippets

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.

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