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Complete genome sequence of Citrobacter werkmanii strain BF-6 isolated from industrial putrefaction - PubMed

  • ️Sun Jan 01 2017

Complete genome sequence of Citrobacter werkmanii strain BF-6 isolated from industrial putrefaction

Gang Zhou et al. BMC Genomics. 2017.

Abstract

Background: In our previous study, Citrobacter werkmanii BF-6 was isolated from an industrial spoilage sample and demonstrated an excellent ability to form biofilms, which could be affected by various environmental factors. However, the genome sequence of this organism has not been reported so far.

Results: We report the complete genome sequence of C. werkmanii BF-6 together with the description of the genome features and its annotation. The size of the complete chromosome is 4,929,789 bp with an average coverage of 137×. The chromosome exhibits an average G + C content of 52.0%, and encodes 4570 protein coding genes, 84 tRNA genes, 25 rRNA operons, 3 microsatellite sequences and 34 minisatellite sequences. A previously unknown circular plasmid designated as pCW001 was also found with a length of 212,549 bp and a G + C content of 48.2%. 73.5%, 75.6% and 92.6% of the protein coding genes could be assigned to GO Ontology, KEGG Pathway, and COG (Clusters of Orthologous Groups) categories respectively. C. werkmanii BF-6 and C. werkmanii NRBC 105721 exhibited the closest evolutionary relationships based on 16S ribosomal RNA and core-pan genome assay. Furthermore, C. werkmanii BF-6 exhibits typical bacterial biofilm formation and development. In the RT-PCR experiments, we found that a great number of biofilm related genes, such as bsmA, bssR, bssS, hmsP, tabA, csgA, csgB, csgC, csgD, csgE, and csgG, were involved in C. werkmanii BF-6 biofilm formation.

Conclusions: This is the first complete genome of C. werkmanii. Our work highlights the potential genetic mechanisms involved in biofilm formation and paves a way for further application of C. werkmanii in biofilms research.

Keywords: Biofilm formation; Citrobacter werkmanii; Complete genome; Evolutionary relationships; RT-PCR.

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Figures

Fig. 1
Fig. 1

Circular representation of the complete genome of C. werkmanii BF-6 (a) and the plasmid pCW001 (b) displaying their relevant features, respectively. a From the inner- to the outermost circle: circle 1, GC skew (positive GC skew in green and negative GC skew in purple); circle 2, GC content; circle 3, sRNA; circle 4, rRNA; circle 5, tRNA; circle 6, genes on reverse strand; circle 7, genes on forward strand; circle 8, all annotated genes; circle 9, genome size. b The circular map of pCW001 was visualized in CGView. The features are the following from center to outside: GC skew, GC content, genes on reverse strand, genes on forward strand, all annotated genes, and plasmid size

Fig. 2
Fig. 2

Dendrogram indicating the phylogenetic relationship of C. werkmanii BF-6 with other Citrobacter sp. a 16 s ribosomal RNA phylogeny. This figure was constructed using MEGA 6.0 based on the Neighbor-Joining method. Bootstrap values (expressed as percentages of 1000 replicates) are shown at branch points; (b) Whole-genome phylogeny based on core-pan genome analysis

Fig. 3
Fig. 3

Analysis of the core and pan genome of Citrobacter sp. Dilution curve of bacterial core (a) and pan (b) genes. Heatmap was depicted after core gene deletion with the coverage cutoff >0.5 (c)

Fig. 4
Fig. 4

CLSM images of C. werkmanii BF-6 biofilms grown on glass slides and stained with SYTO9 and PI. A1, A2, A3: 2 days; B1, B2, B3: 4 days; C1, C2, C3: 6 days. Scale bar = 50 μm

Fig. 5
Fig. 5

Schematic representation of the curli assembly protein gene cluster and other biofilm-formation related genes on the chromosome of C. werkmanii BF-6 (a), and their relative expression levels in the 2-day old biofilms as determined by qRT-PCR (b). All assays were performed in triplicate; mean values and standard deviations are shown

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References

    1. Werkman CH, Gillen GF. Bacteria producing trimethylene glycol. J Bacteriol. 1932;23:167–182. - PMC - PubMed
    1. Lipsky BA, Hook EW, Smith AA, Plorde JJ. Citrobacter infections in humans: experience at the Seattle veterans administration medical center and a review of the literature. Rev Infect Dis. 1980;2:746–760. doi: 10.1093/clinids/2.5.746. - DOI - PubMed
    1. Hodges G, Degener C, Barnes W. Clinical significance of Citrobacter isolates. Am J Clin Pathol. 1978;70:37–40. doi: 10.1093/ajcp/70.1.37. - DOI - PubMed
    1. Arens S, Verhaegen J, Verbist L. Differentiation and susceptibility of Citrobacter isolates from patients in a university hospital. Clin Microbiol Infect. 1997;3:53–57. doi: 10.1111/j.1469-0691.1997.tb00251.x. - DOI - PubMed
    1. Katzenellenbogen E, Kocharova NA, Korzeniowska-Kowal A, Bogulska M, Rybka J, Gamian A, Kachala VV, Shashkov AS, Knirel YA. Structure of the glycerol phosphate-containing O-specific polysaccharide and serological studies on the lipopolysaccharides of Citrobacter werkmanii PCM 1548 and PCM 1549 (serogroup O14) FEMS Immunol Med Microbiol. 2008;54:255–262. doi: 10.1111/j.1574-695X.2008.00477.x. - DOI - PubMed

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