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. 2016 Sep 1;4(5):e00959-16. doi: 10.1128/genomeA.00959-16

Draft Genome Sequence of Criibacterium bergeronii gen. nov., sp. nov., Strain CCRI-22567T, Isolated from a Vaginal Sample from a Woman with Bacterial Vaginosis

Andrée F Maheux a,b,*, Ève Bérubé a, Dominique K Boudreau a, Frédéric Raymond a,c, Jacques Corbeil a,b,c,d, Paul H Roy a, Maurice Boissinot a,b,✉, Rabeea F Omar a,b,✉
PMCID: PMC5009990  PMID: 27587833

Abstract

Criibacterium bergeronii gen. nov., sp. nov., CCRI-22567 is the type strain of the new genus Criibacterium. The strain was isolated from a woman with bacterial vaginosis. The genome assembly comprised 2,384,460 bp, with 34.4% G+C content. This is the first genome announcement of a strain belonging to the genus Criibacterium.

GENOME ANNOUNCEMENT

Criibacterium bergeronii gen. nov., sp. nov., CCRI-22567T was isolated from a vaginal clinical swab harvested from a woman presenting a bacterial vaginosis (BV; Nugent score of 9) during a clinical study conducted in Spring 2014 at Centre Hospitalier Universitaire de Québec (Québec City, Canada). The isolated colony was subjected to PCR and DNA sequencing of the 16S rRNA gene for species identification. Comparative 16S rRNA gene sequence analysis showed that the closest cultured relative of strain CCRI-22567T was Eubacterium yurii subsp. schtika ATCC 43716T (88.0%) (1). The two closest organisms with an available draft genome were compared to strain CCRI-22567T for genomic relatedness assessment. The genomic average nucleotide identity by BLAST (ANIb) (2) obtained with Eubacterium yurii subsp. margaretiae ATCC 43715 (accession no. NZ_AEES01000000) is 68.5% and 67.4% with Filifactor alocis ATCC 35896 (accession no. NC_016630). This indicates that strain CCRI-22567T represents a novel species of a new genus in the Peptostreptococcaceae family (3, 4). The role of this new bacterium in BV remains unclear, since Gardnerella vaginalis, Bacteroides fragilis, and Mobiluncus curtisii (all species consistent with BV) were also isolated from the same vaginal swab.

Criibacterium bergeronii is a rod-shaped strictly anaerobic bacterium and the only cultured member of the genus Criibacterium. It grows on blood agar in 48 to 72 h at 35°C incubated under an anaerobic atmosphere, as previously described (5), forming pinpoint <1-mm translucent flat colonies. Genomic DNA was isolated by using BioSprint 15 DNA blood kit (Qiagen) automated with a KingFisher mL instrument (Thermo Fisher Scientific). Whole-genome sequencing of strain CCRI-22567T was performed on an Illumina HiSeq 2500 using SBS version 4 to sequence a 126-bp paired-end library (Nextera XT; Illumina). A total of 7,787,976 reads were assembled de novo in 19 contigs using Ray software (version 2.3.0) (6). The total genome length is 2,384,460 bp (N50, 321,664 bp), with an average G+C content of 34.4%. The draft genome sequence was annotated using NCBI GenBank annotation pipeline (version 3.3) and RAST annotation server (version 2.0). A total of 2,324 features were identified, including 9 rRNAs and 52 tRNAs. Of the 2,173 putative coding sequences, 914 were assigned as hypothetical proteins. A comparison of the 16S rRNA gene sequence with microbiome projects available in GenBank NR database also suggests that Criibacterium bergeronii is present on sebaceous parts of the skin (7). The complete genome sequence will help understand its ecological association with human microbiota.

Criibacterium bergeronii. (Cri.i.bac.te′ri.um. N. L. n. Cri from CRI, the abbreviation of Centre de Recherche en Infectiologie; N. L. neut. n. bacterium from Gr. n. bakterion a small rod; N. L. neut. n. Criibacterium a small rod isolated at CRI). bergeronii (ber.ge.ron′ii N. L. masc. gen. bergeronii of Bergeron, named after Professor Michel G. Bergeron (CM, OQ, MD, FRCPC, FCAHS, FIDSA), infectious diseases specialist, serial entrepreneur, Founder and former Director of Centre de Recherche en Infectiologie de l’Université Laval in Québec City [Québec], Canada [8]).

Accession number(s).

The whole-genome shotgun project of Criibacterium bergeronii CCRI-22567T has been deposited at DDBJ/EMBL/GenBank under the accession no. MBEW00000000. The version described in this paper is version MBEW01000000.

ACKNOWLEDGMENTS

We thank Mark T. Riley (Department of Foreign Languages, California State University, Sacramento, CA) and Hubert W. Hawkins (Manquin, VA, USA) for their help verifying the Latin name formation of our new bacteria.

Funding Statement

This research received no specific grant from any funding agency.

Footnotes

Citation Maheux AF, Bérubé È, Boudreau DK, Raymond F, Corbeil J, Roy PH, Boissinot M, Omar RF. 2016. Draft genome sequence of Criibacterium bergeronii gen. nov., sp. nov., strain CCRI-22567T, isolated from a vaginal sample from a woman with bacterial vaginosis. Genome Announc 4(5):e00959-16. doi:10.1128/genomeA.00959-16.

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