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Phylogenetic tree highlighting the position of Kurthia massiliensis strain JC30 T relative to other type strains within the genus Kurthia. Sequences were aligned using CLUSTALX, and phylogenetic inferences obtained using the neighbor-joining method within the MEGA 5 package [20]. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 1,000 times to generate a majority consensus tree. Solibacillus silvestris was used as outgroup. The scale bar represents 0.005 nucleotide change per nucleotide position. Surface colonies were observed on sheep blood agar (bioMérieux) after 24 h aerobic incubation at 37°C. The colonies of strain JC30 T were circular, greyish/yellowish, shiny, curved and smooth, 2-5 mm in diameter. Gram staining showed Grampositive coccobacilli (Figure 2). Different growth temperatures (25, 30, 37, 45, 50 and 55°C) were tested. Growth occurred between 25°C and 55°C, and optimal growth was observed between 25°C and 50°C. Growth of the strain was tested under aerobic atmosphere, in the presence of 5% CO 2 , and under anaerobic and microaerophilic atmospheres, which were created using GENbag anaer and GENbag microaer (bioMérieux), respectively. The strains were aerobic but also grew under microaerophilic conditions and in the presence of 5% CO 2. Growth does not occur under anaerobic conditions. NaCl tolerance of strain JC30 T was determined on Difco TM Brain Heart Infusion Agar plates (Becton Dickinson). The powder was supplemented with NaCl (Euromedex) to obtain the tested concentrations (0.5, 1, 2, 3, 5 10, 15%, w/v). Growth occurred between 0.5-5% NaCl but the optimum growth was between 0.5-3% NaCl. Growth in the range of pH 5.0-10.0 was tested using BBL TM Brain Heart Infusion (Becton Dickinson). pH tolerance revealed that growth could occur over a range of pH 6.0-9.0 with optimal growth between pH 7.09.0. The size and ultrastructure of cells were determined by negative staining transmission electron microscopy. The rods were 0.9-2.4 μm long and 0.6-1.8 μm wide (Figure 3). Peritrichous flagella were observed. Capsule presence was determined by India ink stain and after bacteria embedding in Epon 812 resin and observation by transmission
Source publication
Kurthia massiliensis strain JC30(T) sp. nov. is the type strain of K. massiliensis sp. nov., a new species within the genus Kurthia. This strain, whose genome is described here, was isolated from the fecal flora of a healthy patient. K. massiliensis is a Gram-positive aerobic rod. Here we describe the features of this organism, together with the co...
Context in source publication
Context 1
... JC30 (Table 1) was isolated in Standards in Genomic Sciences January 2011 by aerobic cultivation on 5% sheep blood-enriched Columbia agar (BioMerieux). This strain exhibited a 96.9% nucleotide sequence sim- ilarity with K. gibsonii, the phylogenetically closest validated Kurthia species (Figure 1). This value was lower than the 97% 16S rRNA gene sequence threshold to delineate a new species without car- rying out DNA-DNA hybridization recommended by the report of the ad hoc committee on reconcil- iation of approaches to bacterial systematics [2]. ...
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Citations
... The ecology of the few described species of Kurthia supports the cryptosporulant lifestyle of the genus. Kurthia strains have been isolated from diverse environments such as stool (Roux et al., 2012), biogas slurry (Ruan et al., 2014), medical samples (Roux et al., 2012), cigarettes (Rooney et al., 2005) and methanogenic bacterial complexes (Ruan et al., 2013). In metagenomic studies, the genus Kurthia has been found in snail gastrointestinal tracts (Pawar et al., 2012), restaurant kitchen cutting boards (Abdul-Mutalib et al., 2015) and soy sauce fermentation processes (Wei, Chao, et al., 2013;Wei, Wang, et al., 2013). ...
... The ecology of the few described species of Kurthia supports the cryptosporulant lifestyle of the genus. Kurthia strains have been isolated from diverse environments such as stool (Roux et al., 2012), biogas slurry (Ruan et al., 2014), medical samples (Roux et al., 2012), cigarettes (Rooney et al., 2005) and methanogenic bacterial complexes (Ruan et al., 2013). In metagenomic studies, the genus Kurthia has been found in snail gastrointestinal tracts (Pawar et al., 2012), restaurant kitchen cutting boards (Abdul-Mutalib et al., 2015) and soy sauce fermentation processes (Wei, Chao, et al., 2013;Wei, Wang, et al., 2013). ...
Endosporulation is a complex morphophysiological process resulting in a more resistant cellular structure that is produced within the mother cell and is called endospore. Endosporulation evolved in the common ancestor of Firmicutes, but is lost in descendant lineages classified as asporogenic. While Kurthia spp. is considered to comprise only asporogenic species, we show here that strain 11kri321, which was isolated from an oligotrophic geothermal reservoir, produces phase‐bright spore‐like structures. Phylogenomics of strain 11kri321 and other Kurthia strains reveals little similarity to genetic determinants of sporulation known from endosporulating Bacilli. However, morphological hallmarks of endosporulation were observed in two of the four Kurthia strains tested, resulting in spore‐like structures (cryptospores). In contrast to classic endospores, these cryptospores did not protect against heat or UV damage and successive sub‐culturing led to the loss of the cryptosporulating phenotype. Our findings imply that a cryptosporulation phenotype may have been prevalent and subsequently lost by lab culturing in other Firmicutes currently considered as an asporogenic genus. Cryptosporulation might thus represent an ancestral but unstable and adaptive developmental state in Firmicutes that is under selection under harsh environmental conditions.
... The identification strategy was based on MALDI-TOF followed by 16S rRNA amplification and sequencing for the misidentified strains because of previously unknown spectra or of new bacterial species (microbial culturomics) [9]. The first culturomics study, testing 32,500 colonies by MALDI-TOF, allowed to identify 340 bacterial species, with more than half of those being the first to be described from the human gut, and 31 new bacterial species for which the genome has been sequenced and a majority of these has been already described [10][11][12][13][14][15][16][17][18][19][20][21]. In addition, this culture approach has allowed in 2012 three world records in microbiology: the largest human bacterial genome (Microvirga massiliensis, 9.3 Mb), the largest human virus (Senegalvirus, 372 Kb), and the largest human archaeal genome (Methanomassiliicoccus luminyensis, 2.6 Mb) [9,22]. ...
... As mass spectrometry is used in routine bacteriological analyses, including in two previous culturomics studies [9,24] completed using 16S rRNA amplification and sequencing [28] for unidentified colonies, we are confident in the results of this study [27]. Genome sequencing has been performed as previously described [10][11][12][13][14][15][16][17][18][19][20][21]. In parallel, we conducted pyrosequencing of 16S rRNA amplicons targeting the hypervariable V6 region, previously described as a reference method for analyses of the human gut [9,23,36]. ...
The rebirth of bacterial culture has been highlighted successively by environmental microbiologists, the design of axenic culture for intracellular bacteria in clinical microbiology, and, more recently, by human gut microbiota studies. Indeed, microbial culturomics (large scale of culture conditions with the identification of colonies by MALDI-TOF or 16S rRNA) allowed to culture 32 new bacterial species from only four stool samples studied. We performed culturomics in comparison with pyrosequencing 16S rRNA targeting the V6 region on an anorexia nervosa stool sample because this clinical condition has never been explored before by culture, while its composition has been observed to be atypical by metagenomics. We tested 88 culture conditions generating 12,700 different colonies identifying 133 bacterial species , with 19 bacterial species never isolated from the human gut before, including 11 new bacterial species for which the genome has been sequenced. These 11 new bacterial species isolated from a single stool sample allow to extend more significantly the repertoire in comparison to the bacterial species validated by the rest of the world during the last 2 years. Pyrosequencing indicated a dramatic discrepancy with the culturomics results, with only 23 OTUs assigned to the species level overlapping (17 % of the culturomics results). Most of the sequences assigned to bacteria detected only by pyrosequencing belonged to Ruminococcaceae, Lachnospiraceae, and Erysipelotrichaceae constituted by strictly anaerobic species, indicating the future route for culturomics. This study revealed new bacterial species participating significantly to the extension of the gut microbiota repertoire, which is the first step before being able to connect the bacterial composition with the geographic or clinical status.
... In our laboratory, over the past 5 years, we isolated representative strains from 124 putative new bacterial species including The total is based on the total number of protein-coding genes in the annotated genome 39 strict anaerobes [4]. Of these, the names of 17 species have officially been validated [4,7,16,19,28]. The new bacterium described in this article, G. massiliensis gen. nov., sp. ...
The identification of human-associated bacteria is very important to control infectious diseases. In recent years, we diversified culture conditions in a strategy named culturomics, and isolated more than 100 new bacterial species and/or genera. Using this strategy, strain GM7, a strictly anaerobic gram-negative bacterium was recently isolated from a stool specimen of a healthy Gabonese patient. It is a motile coccobacillus without catalase and oxidase activities. The genome of Gabonibacter massiliensis is 3,397,022 bp long with 2880 ORFs and a G+C content of 42.09 %. Of the predicted genes, 2,819 are protein-coding genes, and 61 are RNAs. Strain GM7 differs from the closest genera within the family Porphyromonadaceae both genotypically and in shape and motility. Thus, we propose that strain GM7T (=CSUR P2336 = DSM 101039) is the type strain of the new genus Gabonibacter gen. nov. and the new species G. massiliensis gen. nov., sp. nov.
... Motility and morphology after Gram staining and after negative staining for transmission electron microscopy were observed. Observation by electron microscopy was done as previously described [26]. Briefly, strain Bisph2 was suspended and then washed in phosphate buffer and stained with 1% (w/v) phosphotungstic acid. ...
Enterobacter sp. strain Bisph2 was isolated from a sandy soil from Biskra, Algeria and exhibits glyphosate-degrading activity. Multilocus sequence analysis of the 16S rRNA, rpoB, hsp60, gyrB and dnaJ genes demonstrated that Bisph2 might be a member of a new species of the genus Enterobacter. Genomic sequencing of Bisph2 was used to better clarify the relationships among Enterobacter species. Annotation and analysis of the genome sequence showed that the 5.535.656bp genome of Enterobacter sp. Bisph2 consists in one chromosome and no detectable plasmid, has a 53.19% GC content and 78% of genes were assigned a putative function. The genome contains four prophages of which 3 regions are intact and no CRISPER was detected. The nucleotide sequence of this genome was deposited into DDBJ/EMBL/GenBank under the accession JXAF00000000.
... This polyphasic strategy combines phenotypic characteristics that may be obtained by most clinical microbiology laboratories wordwide, the matrix-assisted laser desorption/ionization timeof-flight mass spectrometry (MALDI-TOF) spectrum, and the analysis and comparison of the complete genome sequence. To date, taxonogenomics has enabled us to validly publish 13 bacterial names567891011121314151617181920. We current study assessed the characteristics of A. massiliensis sp. ...
Anaerosalibacter massiliensis sp. nov. strain ND1T (= CSUR P762 = DSM 27308) is the type strain of A. massiliensis sp. nov., a new species within the genus Anaerosalibacter. This strain, whose genome is described here, was isolated from the fecal flora of a 49-year-old healthy Brazilian male. Anaerosalibacter massiliensis is a Gram-positive, obligate anaerobic rod, member of the family Clostridiaceae. With the complete genome sequence and annotation, we describe here the features of this organism. The 3,197,911 bp long genome (one chromosome but no plasmid) contains 3,271 protein-coding and 62 RNA genes, including 6 rRNA genes.
... 153 and no. 155 Lagier et al. 2012aLagier et al. ,b,c,d, 2013aRamasamy et al. 2012;Roux et al. 2012;Hugon et al. 2013;Oren and Garrity 2014). ...
Microvirga massiliensis sp. nov. strain JC119(T) is a bacteria isolated in Marseille from a stool sample collected in Senegal. The 16S rRNA (JF824802) of M. massiliensis JC119(T) revealed 95% sequence identity with Microvirga lotononidis WSM3557(T) (HM362432). This bacterium is aerobic, gram negative, catalase positive, and oxidase negative. The draft genome of M. massiliensis JC119(T) comprises a 9,207,211-bp-long genome that is the largest bacterial genome of an isolate in humans. The genome exhibits a G+C content of 63.28% and contains 8685 protein-coding genes and 77 RNA genes, including 21 rRNA genes. Here, we describe the features of M. massiliensis JC119(T) , together with the genome sequence information and its annotation.
... As a result of the declining cost of sequencing, the number of sequenced bacterial genomes has rapidly grown; to date, almost 40 000 bacterial genomes have been sequenced (GOLD Database, https://gold.jgi.doe.gov/). Hence, we recently proposed to use genomic information together with phenotypic criteria for the description of new bacterial species [7][8][9][10][11][12][13][14][15][16][17][18][19][20]. ...
Nocardioides massiliensis sp. nov strain GD13T is the type strain of N. massiliensis sp. nov., a new species within the genus Nocardioides. This strain was isolated from the feces of a 62-year-old man admitted to intensive care for Guillain-Barre syndrome. Nocardioides massiliensis is a strictly aerobic Gram-positive rod. Herein, we describe the features of this bacterium, together with the complete genome sequence and annotation. The 4,006,620-bp long genome contains 4,132 protein-coding and 47 RNA genes.
... was isolated from the feces of a healthy adult. [7] They are not part of the normal flora, and in the majority of cases, they have not normally been regarded as pathogenic. [8] Kurthia infections rarely become systemic. ...
Context:
Zoonotic sexual transmission.
Aims:
Identification of unknown microorganisms causing sexually transmitted zoonotic infection was a common effort of clinicians and the laboratory.
Settings and design:
A male patient had recurring urethritis and balanitis after having repeated unprotected penetrative sexual intercourse with female piglets. He claimed allergy to metals and plastics. Routine microbiological tests were carried out.
Materials and methods:
Specimens from the urethra, glans, rectum, throat, urine, and blood were cultured. Subsequently, isolates were tested for their biochemical activity and antibiotic susceptibility.
Results:
Kurthia gibsonii was isolated from both urethra and glans. No other concomitant infection was detected. The patient was cured with oral cefuroxime for 15 days and topical gentamicin cream for 2 months.
Conclusion:
This is the first reported zoophilic infection by Kurthia spp. Fecal contamination of animals' genital tract was the possible source of infection. Immune disturbance of the patient might predispose to opportunistic Kurthia infection.
... Further identification was based on 16S rRNA gene PCR amplification and sequencing [13] . Observations by electron microscopy were done as previously described [24]. Briefly, the bacteria were suspended and then washed in phosphate buffer and stained with 1 % (w/v) phosphotungstic acid. ...
Gemmata massiliana is a new Planctomycetes bacterium isolated from a hospital water network in France, using a new culture medium. It is an aerobic microorganism with optimal growth at pH 8, at 30 °C and salinity ≤ 1.25 % NaCl. G. massiliana is resistant to β-lactam antibiotics, due to lack of peptidoglycan in its cell wall.G. massiliana shares a 97 % 16S rRNA gene sequence similarity with the nearest species, Gemmata obscuriglobus; and 99 % similarity with unnamed soil isolates. Its 9,249,437-bp genome consists in one chromosome and no detectable plasmid and has a 64.07 % G + C content, 32.94 % of genes encoding for hypothetical proteins. The genome contains an incomplete 19.6-kb phage sequence, 26 CRISPRs, 3 CAS and 15 clusters of secondary metabolites. G. massiliana genome increases knowledge of a poorly known world of bacteria.
Electronic supplementary material
The online version of this article (doi:10.1186/s40793-015-0103-0) contains supplementary material, which is available to authorized users.
... By using the availability of data in genomics through the development of new tools for sequencing DNA, we introduced a new taxonomic method for the description of new bacterial species. This concept, which we named taxonogenomics, includes their genomic features [7] and proteomic information obtained by MALDI-TOF analysis [8][9][10][11][12][13][14][15][16][17]. ...
Virgibacillus senegalensis SK-1T (CSUR P1101 = DSM 28585), is the type strain of V. senegalensis sp. nov. It is an aerobic, Gram positive, moderately halophilic, motile bipolar flagellum, isolated from a healthy Senegalese male. Here, we describe the genomic and phenotypic characteristics of this isolate. The 3,755,098 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 42.9 % and contains 3,738 protein-coding and 95 RNA genes.
