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Noncontiguous finished genome sequence and description of Weeksella massiliensis sp. nov.

Sankar SA, Lo CI, Fall B, Sambe-Ba B, Mediannikov O, Diallo I, Labas N, Faye N, Wade B, Raoult D, Fournier PE, Fenollar F - New Microbes New Infect (2015)

Bottom Line: The sequenced genome is 2 562 781 bp with one chromosome but no plasmid.It exhibits a G + C content of 35.9% and contains 2390 protein-coding and 56 RNA genes, including a complete rRNA operon.On the basis of these data, we propose the creation of Weeksella massiliensis sp. nov.

View Article: PubMed Central - PubMed

Affiliation: )Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France.

ABSTRACT
Strain FF8(T) (= CSUR P860 = DSM 28259) was isolated in Dakar, Senegal, from the urine of a 65-year-old man with acute cystitis. This strain shows a similarity of sequence of 16S rRNA of 98.38% with Weeksella virosa, and its GenBank accession numbers are HG931340 and CCMH00000000. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis had a poor score, ranging from 1.32 to 1.56, that did not allow identification of the bacterium. Using a polyphasic study made of phenotypic and genomic analyses, strain FF8(T) was a Gram-negative, aerobic rod and a member of the family Flavobacteriaceae. The sequenced genome is 2 562 781 bp with one chromosome but no plasmid. It exhibits a G + C content of 35.9% and contains 2390 protein-coding and 56 RNA genes, including a complete rRNA operon. On the basis of these data, we propose the creation of Weeksella massiliensis sp. nov.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree showing position of Weeksella massiliensis strain FF8T relative to other type strains within family Flavobacteriaceae. Strains and their corresponding 16S rRNA GenBank accession numbers are: Bergeyella zoohelcum strain ATCC 43767, M93153 (GA: AGYA00000000); Chryseobacterium gleum strain ATCC 35910, M58772 (GA: ACKQ00000000); Chryseobacterium arthrosphaerae strain CC-VM-7, FN398101; Chryseobacterium culicis strain R4-1A, FN554975; Chryseobacterium taichungense strain CC-TWGS1-8T, AJ843132; Chryseobacterium taiwanense strain BCRC 17412, DQ318789 (GA: JWTA00000000); Chryseobacterium bovis strain H9, EF204446; Chryseobacterium formosense strain CC-H3-2, AY315443 (GA: JPRP00000000); Chryseobacterium scophthalmum strain LMG 13028, AJ271009; Chryseobacterium balustinum strain LMG 8329, AY468447; Chryseobacterium piscium strain LMG 23089T, AM040439; Epilithonimonas lactis strain H1, EF204460 (GA: JPLY00000000); Epilithonimonas tenaxstrain DSM 16811, AF493696 (GA: AUAA00000000); Elizabethkingia meningoseptica strain ATCC 13253T, AJ704540 (GA: BARD00000000); Elizabethkingia anophelis strain Ag1, EF426426 (GA: AHHG00000000); Soonwooa buanensis strain HM0024T, FJ713810; Ornithobacterium rhinotracheale strain DSM 15997, NR102940 (GA: CP003283); Moheibacter sediminis strain M0116, KF694750; Empedobacter brevis strain NBRC 14943, NR112974 (GA: ARNT00000000); W. massilliensis strain FF8T, HG931340 (GA: CCMH00000000); Weeksella virosa strain DSM 16922T, NR074495 (GA: CP002455); and Empedobacter falsenii strain NF 993T, AM084341. Sequences were aligned using MUSCLE [42], and phylogenetic tree inferred by maximum likelihood method with Kimura 2-parameter model from MEGA 6 software [43]. Numbers at nodes are percentages of bootstrap values obtained by repeating analysis 1000 times to generate majority consensus tree. E. falsenii was used as outgroup. Scale bar = rate of substitution per site of 0.1.
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fig1: Phylogenetic tree showing position of Weeksella massiliensis strain FF8T relative to other type strains within family Flavobacteriaceae. Strains and their corresponding 16S rRNA GenBank accession numbers are: Bergeyella zoohelcum strain ATCC 43767, M93153 (GA: AGYA00000000); Chryseobacterium gleum strain ATCC 35910, M58772 (GA: ACKQ00000000); Chryseobacterium arthrosphaerae strain CC-VM-7, FN398101; Chryseobacterium culicis strain R4-1A, FN554975; Chryseobacterium taichungense strain CC-TWGS1-8T, AJ843132; Chryseobacterium taiwanense strain BCRC 17412, DQ318789 (GA: JWTA00000000); Chryseobacterium bovis strain H9, EF204446; Chryseobacterium formosense strain CC-H3-2, AY315443 (GA: JPRP00000000); Chryseobacterium scophthalmum strain LMG 13028, AJ271009; Chryseobacterium balustinum strain LMG 8329, AY468447; Chryseobacterium piscium strain LMG 23089T, AM040439; Epilithonimonas lactis strain H1, EF204460 (GA: JPLY00000000); Epilithonimonas tenaxstrain DSM 16811, AF493696 (GA: AUAA00000000); Elizabethkingia meningoseptica strain ATCC 13253T, AJ704540 (GA: BARD00000000); Elizabethkingia anophelis strain Ag1, EF426426 (GA: AHHG00000000); Soonwooa buanensis strain HM0024T, FJ713810; Ornithobacterium rhinotracheale strain DSM 15997, NR102940 (GA: CP003283); Moheibacter sediminis strain M0116, KF694750; Empedobacter brevis strain NBRC 14943, NR112974 (GA: ARNT00000000); W. massilliensis strain FF8T, HG931340 (GA: CCMH00000000); Weeksella virosa strain DSM 16922T, NR074495 (GA: CP002455); and Empedobacter falsenii strain NF 993T, AM084341. Sequences were aligned using MUSCLE [42], and phylogenetic tree inferred by maximum likelihood method with Kimura 2-parameter model from MEGA 6 software [43]. Numbers at nodes are percentages of bootstrap values obtained by repeating analysis 1000 times to generate majority consensus tree. E. falsenii was used as outgroup. Scale bar = rate of substitution per site of 0.1.

Mentions: Strain FF8 exhibited a 98.38% 16S rRNA sequence similarity with Weeksella virosa strain DSM 16922T (GenBank accession number NR_074495), the phylogenetically closest bacterial species with standing in nomenclature. These values were lower than the 98.7% 16S rRNA gene sequence threshold recommended by Meier-Kolthoff et al., 2013, to delineate a new species within phylum Bacteroidetes[11], [12] without carrying out DDH [13]. A phylogenetic tree based on the 16S rRNA sequence highlights the position of Weeksella massiliensis strain FF8T among the family Flavobacteriaceae (Fig. 1). Different growth temperatures (25, 30, 37, 45 and 56°C) were tested. Growth was obtained between 25 and 37°C, with an optimal growth at 37°C. Growth of the strain was tested also under anaerobic and microaerophilic conditions using GENbag anaer and GENbag microaer systems, respectively (bioMérieux), and under aerobic conditions, with or without 5% CO2. Thus the optimal growth was observed under aerobic and microaerophilic conditions. No growth was observed under anaerobic conditions. The colonies were opaque, light yellow in color with a smooth surface, not haemolytic on 5% sheep's blood–enriched Columbia agar (bioMérieux) and approximately 2 mm in diameter. A motility test was negative. Cells are Gram-negative, non-spore-forming rods of regular shape with rounded ends (Fig. 2) and have mean diameter of 0.3 μm (range, 0.2–0.5 μm) and a mean length of 1.5 μm (range, 0.8–2.1 μm) (Fig. 3). Weeksella massiliensis strain FF8T does not grow on MacConkey agar [14].


Noncontiguous finished genome sequence and description of Weeksella massiliensis sp. nov.

Sankar SA, Lo CI, Fall B, Sambe-Ba B, Mediannikov O, Diallo I, Labas N, Faye N, Wade B, Raoult D, Fournier PE, Fenollar F - New Microbes New Infect (2015)

Phylogenetic tree showing position of Weeksella massiliensis strain FF8T relative to other type strains within family Flavobacteriaceae. Strains and their corresponding 16S rRNA GenBank accession numbers are: Bergeyella zoohelcum strain ATCC 43767, M93153 (GA: AGYA00000000); Chryseobacterium gleum strain ATCC 35910, M58772 (GA: ACKQ00000000); Chryseobacterium arthrosphaerae strain CC-VM-7, FN398101; Chryseobacterium culicis strain R4-1A, FN554975; Chryseobacterium taichungense strain CC-TWGS1-8T, AJ843132; Chryseobacterium taiwanense strain BCRC 17412, DQ318789 (GA: JWTA00000000); Chryseobacterium bovis strain H9, EF204446; Chryseobacterium formosense strain CC-H3-2, AY315443 (GA: JPRP00000000); Chryseobacterium scophthalmum strain LMG 13028, AJ271009; Chryseobacterium balustinum strain LMG 8329, AY468447; Chryseobacterium piscium strain LMG 23089T, AM040439; Epilithonimonas lactis strain H1, EF204460 (GA: JPLY00000000); Epilithonimonas tenaxstrain DSM 16811, AF493696 (GA: AUAA00000000); Elizabethkingia meningoseptica strain ATCC 13253T, AJ704540 (GA: BARD00000000); Elizabethkingia anophelis strain Ag1, EF426426 (GA: AHHG00000000); Soonwooa buanensis strain HM0024T, FJ713810; Ornithobacterium rhinotracheale strain DSM 15997, NR102940 (GA: CP003283); Moheibacter sediminis strain M0116, KF694750; Empedobacter brevis strain NBRC 14943, NR112974 (GA: ARNT00000000); W. massilliensis strain FF8T, HG931340 (GA: CCMH00000000); Weeksella virosa strain DSM 16922T, NR074495 (GA: CP002455); and Empedobacter falsenii strain NF 993T, AM084341. Sequences were aligned using MUSCLE [42], and phylogenetic tree inferred by maximum likelihood method with Kimura 2-parameter model from MEGA 6 software [43]. Numbers at nodes are percentages of bootstrap values obtained by repeating analysis 1000 times to generate majority consensus tree. E. falsenii was used as outgroup. Scale bar = rate of substitution per site of 0.1.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

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Show All Figures
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fig1: Phylogenetic tree showing position of Weeksella massiliensis strain FF8T relative to other type strains within family Flavobacteriaceae. Strains and their corresponding 16S rRNA GenBank accession numbers are: Bergeyella zoohelcum strain ATCC 43767, M93153 (GA: AGYA00000000); Chryseobacterium gleum strain ATCC 35910, M58772 (GA: ACKQ00000000); Chryseobacterium arthrosphaerae strain CC-VM-7, FN398101; Chryseobacterium culicis strain R4-1A, FN554975; Chryseobacterium taichungense strain CC-TWGS1-8T, AJ843132; Chryseobacterium taiwanense strain BCRC 17412, DQ318789 (GA: JWTA00000000); Chryseobacterium bovis strain H9, EF204446; Chryseobacterium formosense strain CC-H3-2, AY315443 (GA: JPRP00000000); Chryseobacterium scophthalmum strain LMG 13028, AJ271009; Chryseobacterium balustinum strain LMG 8329, AY468447; Chryseobacterium piscium strain LMG 23089T, AM040439; Epilithonimonas lactis strain H1, EF204460 (GA: JPLY00000000); Epilithonimonas tenaxstrain DSM 16811, AF493696 (GA: AUAA00000000); Elizabethkingia meningoseptica strain ATCC 13253T, AJ704540 (GA: BARD00000000); Elizabethkingia anophelis strain Ag1, EF426426 (GA: AHHG00000000); Soonwooa buanensis strain HM0024T, FJ713810; Ornithobacterium rhinotracheale strain DSM 15997, NR102940 (GA: CP003283); Moheibacter sediminis strain M0116, KF694750; Empedobacter brevis strain NBRC 14943, NR112974 (GA: ARNT00000000); W. massilliensis strain FF8T, HG931340 (GA: CCMH00000000); Weeksella virosa strain DSM 16922T, NR074495 (GA: CP002455); and Empedobacter falsenii strain NF 993T, AM084341. Sequences were aligned using MUSCLE [42], and phylogenetic tree inferred by maximum likelihood method with Kimura 2-parameter model from MEGA 6 software [43]. Numbers at nodes are percentages of bootstrap values obtained by repeating analysis 1000 times to generate majority consensus tree. E. falsenii was used as outgroup. Scale bar = rate of substitution per site of 0.1.
Mentions: Strain FF8 exhibited a 98.38% 16S rRNA sequence similarity with Weeksella virosa strain DSM 16922T (GenBank accession number NR_074495), the phylogenetically closest bacterial species with standing in nomenclature. These values were lower than the 98.7% 16S rRNA gene sequence threshold recommended by Meier-Kolthoff et al., 2013, to delineate a new species within phylum Bacteroidetes[11], [12] without carrying out DDH [13]. A phylogenetic tree based on the 16S rRNA sequence highlights the position of Weeksella massiliensis strain FF8T among the family Flavobacteriaceae (Fig. 1). Different growth temperatures (25, 30, 37, 45 and 56°C) were tested. Growth was obtained between 25 and 37°C, with an optimal growth at 37°C. Growth of the strain was tested also under anaerobic and microaerophilic conditions using GENbag anaer and GENbag microaer systems, respectively (bioMérieux), and under aerobic conditions, with or without 5% CO2. Thus the optimal growth was observed under aerobic and microaerophilic conditions. No growth was observed under anaerobic conditions. The colonies were opaque, light yellow in color with a smooth surface, not haemolytic on 5% sheep's blood–enriched Columbia agar (bioMérieux) and approximately 2 mm in diameter. A motility test was negative. Cells are Gram-negative, non-spore-forming rods of regular shape with rounded ends (Fig. 2) and have mean diameter of 0.3 μm (range, 0.2–0.5 μm) and a mean length of 1.5 μm (range, 0.8–2.1 μm) (Fig. 3). Weeksella massiliensis strain FF8T does not grow on MacConkey agar [14].

Bottom Line: The sequenced genome is 2 562 781 bp with one chromosome but no plasmid.It exhibits a G + C content of 35.9% and contains 2390 protein-coding and 56 RNA genes, including a complete rRNA operon.On the basis of these data, we propose the creation of Weeksella massiliensis sp. nov.

View Article: PubMed Central - PubMed

Affiliation: )Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France.

ABSTRACT
Strain FF8(T) (= CSUR P860 = DSM 28259) was isolated in Dakar, Senegal, from the urine of a 65-year-old man with acute cystitis. This strain shows a similarity of sequence of 16S rRNA of 98.38% with Weeksella virosa, and its GenBank accession numbers are HG931340 and CCMH00000000. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis had a poor score, ranging from 1.32 to 1.56, that did not allow identification of the bacterium. Using a polyphasic study made of phenotypic and genomic analyses, strain FF8(T) was a Gram-negative, aerobic rod and a member of the family Flavobacteriaceae. The sequenced genome is 2 562 781 bp with one chromosome but no plasmid. It exhibits a G + C content of 35.9% and contains 2390 protein-coding and 56 RNA genes, including a complete rRNA operon. On the basis of these data, we propose the creation of Weeksella massiliensis sp. nov.

No MeSH data available.


Related in: MedlinePlus