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Non-contiguous finished genome sequence and description of Kurthia massiliensis sp. nov.

Roux V, El Karkouri K, Lagier JC, Robert C, Raoult D - Stand Genomic Sci (2012)

Bottom Line: K. massiliensis is a Gram-positive aerobic rod.Here we describe the features of this organism, together with the complete genome sequence and annotation.The 3,199,090 bp long genome contains 3,240 protein-coding genes and 86 RNA genes, including between 3 and 4 rRNA genes.

View Article: PubMed Central - PubMed

Affiliation: Aix Marseille Université, URMITE, Faculté de médecine, Aix-Marseille Université

ABSTRACT
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 complete genome sequence and annotation. The 3,199,090 bp long genome contains 3,240 protein-coding genes and 86 RNA genes, including between 3 and 4 rRNA genes.

No MeSH data available.


Related in: MedlinePlus

Reference mass spectrum from K. massiliensis strain JC30T. Spectra from 24 individual colonies were compared and a reference spectrum was generated.
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f6: Reference mass spectrum from K. massiliensis strain JC30T. Spectra from 24 individual colonies were compared and a reference spectrum was generated.

Mentions: Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) MS protein analysis was carried out. Briefly, a pipette tip was used to pick one isolated bacterial colony from a culture agar plate, and to spread it as a thin film on a MALDI-TOF target plate (Bruker Daltonics). Twelve distinct deposits were made for strain JC30T from twelve isolated colonies and the manipulation was repeated another day. After air-drying, 1.5 µl matrix solution (saturated solution of α-cyanohydroxycinnaminic acid in 50% aqueous acetonitrile containing 2.5% trifluoroacetic acid) per spot was applied. MALDI-TOF MS was conducted using the Microflex LT spectrometer (Bruker Daltonics). All spectra were recorded in linear, positive ion mode. The acceleration voltage was 20 kV. Spectra were collected as a sum of 240 shots across a spot. Preprocessing and identification steps were performed using the manufacturer’s parameters. The JC30T spectra were imported into the MALDI BioTyper software (version 3.0, Bruker) and analyzed by standard pattern matching (with default parameter settings) against the main spectra of 4,108 bacteria including those from K. gibsonii, K. sibirica and K. zopfii, used as reference data, in the BioTyper database. A score enabled the identification, or not, from the tested species: a score > 2.3 with a validly published species enabled the identification at the species level, a score > 1.7 but < 2 enabled the identification at the genus level; and a score < 1.7 did not enable any identification. For strain JC30T, none of the obtained scores was > 1, thus suggesting that our isolate was not a member of a known species. We incremented our database with the spectrum from strain JC30T (Figure 6). The spectrum was made available online in our free-access URMS database [29].


Non-contiguous finished genome sequence and description of Kurthia massiliensis sp. nov.

Roux V, El Karkouri K, Lagier JC, Robert C, Raoult D - Stand Genomic Sci (2012)

Reference mass spectrum from K. massiliensis strain JC30T. Spectra from 24 individual colonies were compared and a reference spectrum was generated.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3569394&req=5

f6: Reference mass spectrum from K. massiliensis strain JC30T. Spectra from 24 individual colonies were compared and a reference spectrum was generated.
Mentions: Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) MS protein analysis was carried out. Briefly, a pipette tip was used to pick one isolated bacterial colony from a culture agar plate, and to spread it as a thin film on a MALDI-TOF target plate (Bruker Daltonics). Twelve distinct deposits were made for strain JC30T from twelve isolated colonies and the manipulation was repeated another day. After air-drying, 1.5 µl matrix solution (saturated solution of α-cyanohydroxycinnaminic acid in 50% aqueous acetonitrile containing 2.5% trifluoroacetic acid) per spot was applied. MALDI-TOF MS was conducted using the Microflex LT spectrometer (Bruker Daltonics). All spectra were recorded in linear, positive ion mode. The acceleration voltage was 20 kV. Spectra were collected as a sum of 240 shots across a spot. Preprocessing and identification steps were performed using the manufacturer’s parameters. The JC30T spectra were imported into the MALDI BioTyper software (version 3.0, Bruker) and analyzed by standard pattern matching (with default parameter settings) against the main spectra of 4,108 bacteria including those from K. gibsonii, K. sibirica and K. zopfii, used as reference data, in the BioTyper database. A score enabled the identification, or not, from the tested species: a score > 2.3 with a validly published species enabled the identification at the species level, a score > 1.7 but < 2 enabled the identification at the genus level; and a score < 1.7 did not enable any identification. For strain JC30T, none of the obtained scores was > 1, thus suggesting that our isolate was not a member of a known species. We incremented our database with the spectrum from strain JC30T (Figure 6). The spectrum was made available online in our free-access URMS database [29].

Bottom Line: K. massiliensis is a Gram-positive aerobic rod.Here we describe the features of this organism, together with the complete genome sequence and annotation.The 3,199,090 bp long genome contains 3,240 protein-coding genes and 86 RNA genes, including between 3 and 4 rRNA genes.

View Article: PubMed Central - PubMed

Affiliation: Aix Marseille Université, URMITE, Faculté de médecine, Aix-Marseille Université

ABSTRACT
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 complete genome sequence and annotation. The 3,199,090 bp long genome contains 3,240 protein-coding genes and 86 RNA genes, including between 3 and 4 rRNA genes.

No MeSH data available.


Related in: MedlinePlus