Open Access

Genome sequence and description of Nesterenkonia massiliensis sp. nov. strain NP1T

  • Sophie Edouard
  • , Senthil Sankar
  • , Nicole Prisca Makaya Dangui
  • , Jean-Christophe Lagier
  • , Caroline Michelle
  • , Didier Raoult,
  • and Pierre-Edouard Fournier
Corresponding author

DOI: 10.4056/sigs.5631022

Received: 01 April 2014

Accepted: 01 April 2014

Published: 15 June 2014

Abstract

Nesterenkonia massiliensis sp. nov., strain NP1T, is the type strain of Nesterenkonia massiliensis sp. nov., a new species within the genus Nesterenkonia. This strain, whose genome is described here, was isolated from the feces of a 32-year-old French woman suffering from AIDS and living in Marseille. Nesterenkonia massiliensis is a Gram-positive aerobic coccus. Here, we describe the features of this bacterium, together with the complete genome sequencing and annotation. The 2,726,371 bp long genome (one chromosome but no plasmid) contains 2,663 protein-coding and 51 RNA genes, including 1 rRNA operon.

Keywords:

Nesterenkonia massiliensisgenomeculturomicstaxono-genomics

Introduction

Nesterenkonia massiliensis strain NP1T (= CSUR P244 = DSM 26221) is the type strain of N. massiliensis sp. nov. This bacterium is a Gram-positive, non-spore-forming, aerobic and motile coccus that was isolated from the fecal flora of AIDS-infected French female living in Marseille, France, as part of a “culturomics” study aiming at cultivating as many of the bacterial species in human feces as possible [1,2].

Taking advantage of the availability of more than 12,000 bacterial genome sequences [3], we recently proposed to use genomic properties in combination with phenotypic characteristics for the taxonomic classification of Bacteria [4-34].

Herein, we present a summary classification and a set features for Nesterenkonia massiliensis sp. nov., strain NP1T (CSUR= P244 = DSM 26221), including the description of its complete genome and annotation. These characteristics support the circumscription of the species Nesterenkonia massiliensis.

The genus Nesterenkonia was first described by Stackebrandt et al. in 1995 [35]. This genus belongs to the family Micrococcaceae within the phylum Actinobacteria, and is most closely related to the genera Micrococcus, Arthrobacter and Kocuria [35]. The Nesterenkonia genus includes Gram-positive, non spore-forming, aerobic, mesophilic bacteria that may be halotolerant or halophilic. Currently, the genus Nesterenkonia includes 12 species with validly published names [36]. Members of the genus Nesterenkonia are ubiquitous bacteria, which have been isolated from various environments including hypersaline soil and lakes, soda lakes, sea food, and paper and cotton pulp mills [36-40]. However, prior to our study, Nesterenkonia species had not been reported in humans, with the exception of DNA sequences from Nesterenkonia sp. detected in the gut microbiota of patients with chronic kidney diseases [41].

Classification and features

A stool sample was collected from a Caucasian, AIDS-infected, 32-year-old French woman living in Marseille, France. The patient gave an informed and signed consent. This study and the assent procedure were approved by the Ethics Committee of the Institut Fédératif de Recherche IFR48, Faculty of Medicine, Marseille, France under agreement number 09-022. The fecal sample was preserved at -80°C after collection. Strain NP1T (Table 1) was first isolated in March 2012 by cultivation on Columbia agar (BioMerieux, Marcy l’Etoile, France) under aerobic conditions after 14 days of preincubation of the stool sample with addition of 5ml of sheep rumen in blood bottle culture. The strain exhibited a 96.7% 16S rRNA nucleotide sequence identity with N. alba [51], the phylogenetically most closely related Nesterenkonia species with standing in nomenclature (Figure 1). This value was lower than the 98.7% 16S rRNA gene sequence threshold recommended by Stackebrandt and Ebers to delineate a new species without carrying out DNA-DNA hybridization [52].

Table 1

Classification and general features of Nesterenkonia massiliensis strain NP1 T according to the MIGS recommendations [42].

MIGS ID

       Property

        Term

       Evidence codea

       Current classification

        Domain Bacteria

       TAS [43]

        Phylum Actinobacteria

       TAS [44]

        Class Actinobacteria

       TAS [45]

        Order Actinomycetales

       TAS [45-48]

        Family Micrococcaceae

       TAS [45-47,49]

        Genus Nesterenkonia

       TAS [35,39,45]

        Species Nesterenkonia massiliensis

       IDA

        Type strain: NP1

       IDA

       Gram stain

        Positive

       IDA

       Cell shape

        Cocci

       IDA

       Motility

        Motile

       IDA

       Sporulation

        Nonsporulating

       IDA

       Temperature range

        Mesophile

       IDA

       Optimum temperature

        Unknown

       IDA

MIGS-6.3

       Salinity

        Halophilic

       IDA

MIGS-22

       Oxygen requirement

        Aerobic

       IDA

       Carbon source

        Unknown

       NAS

       Energy source

        Unknown

       NAS

MIGS-6

       Habitat

        Human gut

       IDA

MIGS-15

       Biotic relationship

        Free living

       IDA

MIGS-14

       Pathogenicity

        Unknown

       Biosafety level

        2

       Isolation

        Human feces

MIGS-4

       Geographic location

        Marseille, France

       IDA

MIGS-5

       Sample collection time

        March 2012

       IDA

MIGS-4.1

       Latitude       Longitude

        43.296482        5.36978

       IDA

MIGS-4.3

       Depth

        Surface

       IDA

MIGS-4.4

       Altitude

        0 m above sea level

       IDA

aEvidence codes - IDA: Inferred from Direct Assay; TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [50]. If the evidence is IDA, then the property was directly observed for a live isolate by one of the authors or an expert mentioned in the acknowledgements.

Figure 1

Consensus phylogenetic tree highlighting the position of Nesterenkonia massiliensis strain NP1T relative to other type strains within the Nesterenkonia genus. Genbank accession numbers are indicated for each species. Sequences were aligned using CLUSTALW and phylogenetic inferences obtained using the maximum-likelihood method in the MEGA software package. Numbers at the nodes are percentages of bootstrap values from 500 replicates that support the node. Micrococcus luteus was used as the outgroup. The scale bar represents a 5% nucleotide sequence divergence.

Four different growth temperatures (25, 30, 37, 45°C) were tested. Growth was observed between 25 and 45°C on blood-enriched Columbia agar (BioMerieux), with optimal growth occurring at 37°C after 24 hours of incubation. Colonies were dark yellow and 1 mm in diameter. Growth of the strain was tested under anaerobic and microaerophilic conditions using GENbag anaer and GENbag microaer systems, respectively (BioMerieux), and under aerobic conditions, with or without 5% CO2. Optimal growth was obtained under aerobic conditions, but weak growth occurred in a microaerophilic atmosphere. No growth was observed under anaerobic conditions. Bacterial cells were Gram-positive (Figure 2), non-endospore-forming, and motile cocci. Cells grown on agar had a mean diameter and length of 0.67 μm and 1.4 μm, respectively (Figure 3).

Figure 2

Gram-stain of Nesterenkonia massiliensis strain NP1T

Figure 3

Transmission electron micrograph of N. massiliensis strain NP1T, made using a Morgani 268D (Philips) at an operating voltage of 60kV. The scale bar represents 500 nm.

Strain NP1T exhibited catalase but no oxidase activity. Using an API 20NE strip (BioMerieux), negative reactions were obtained for nitrate reduction, urease, indole production, glucose fermentation, arginine dihydrolase, β-galactosidase, glucose, arabinose, mannose, mannitol, N-acetyl-glucosamine, maltose, gluconate, caprate, adipate, malate, citrate, phenyl-acetate assimilation and cytochrome oxidase. Substrate oxidation and assimilation were examined with an API 50CH carbohydrate fermentation strip (BioMerieux) at 37°C. Positive reactions were observed for D-glucose, D-fructose, D-saccharose, ribose, mannose, mannitol, D-trehalose and L-rhamnose. No reaction was observed for esculin, salicin, D-cellobiose and gentiobiose. N. massiliensis is susceptible to amoxicillin, imipenem, rifampin, ciprofloxacin, gentamicin, doxycycline and vancomycin but resistant to trimethoprim/sulfamethoxazole and metronidazole. When compared with representative species from the genus Nesterenkonia, N. massiliensis strain NP1T differed in cell shape, colony color, motility, optimal growth temperature, and mannitol fermentation (Table 2).

Table 2

Differential characteristics of Nesterenkonia species*.

    N. massiliensis

    N. alba

     N. flava

     N. lacusekhoensis

Cell diameter (µm)

    0.7x1.4

    0.4-0.6 x 0.8-1.2

     0.6-0.8 x1.2- 1.4

     0.8-0.9 x 1-1.3

Oxygen requirement

    Aerobic

    Aerobic

     Aerobic

     Aerobic

Pigment production

    Dark Yellow

    White

     Yellow

     Bright yellow

Gram stain

    cocci

    Short rods

     Short rods

     Short rods

Optimal temperature (oC)

    37°C

    42

     40-42

     27-33.5

Salt requirementNaCl tolerance (%)

    0-3

    0-6

     0-10

     0-15

Motility

    +

    -

     -

     -

Endospore formation

    -

    -

     -

     -

H2S production

    -

    -

     -

     W

Indole production

    -

    -

     -

     -

ONPG test*

    NA

    +

     -

     NA

Citrate test

    NA

    -

     -

     W

Voges–Proskauer reaction

    NA

    -

     -

     -

Production of

Catalase

    +

    +

     +

     +

Oxidase

    -

    -

     -

     -

Nitrate reductase

    -

    -

     -

     -

Urease

    -

    -

     -

     NA

Β-galactosidase

    -

    NA

     -

     NA

Acid from

L-arabinose

    -

    +

     +

     NA

Mannose

    -

    -

     +

     +

Mannitol

    +

    NA

     -

     -

Sucrose

    +

     +

     +

D-glucose

    +

    +

     +

     +

D-fructose

    +

    -

     +

     +

D-maltose

    +

    +

     +

     +

D-lactose

    -

    -

     -

     -

D-Galactose

    -

    -

     -

     -

Trehalose

    -

    W

     -

     +

D-Xylose

    -

    -

     -

     -

Hydrolysis of:

Starch

    -

    -

     +

     -

Gelatin

    -

    +

     +

     -

G+C content (mol%)

    62.47

    60.2

     65.5

     66.1

Habitat

    Human gut, France

    Black liquor treatment system of a cotton pulp mill, China

     Paper mill effluent, China

     Hypersaline lake, East Antarctica

+, Positive; –, negative; W, weak reaction; NA, not available.

* N. massiliensis strain NPT, N. alba strain DSM 19423, N. flava strain JCM 14814T, N. lacusekhoensis strain DSM 12544

Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) MS protein analysis was carried out as previously described [53] using a Microflex spectrometer (Brüker Daltonics, Leipzig, Germany). Twelve individual NP1T colonies were deposited on a MTP 384 MALDI-TOF target plate (Brüker). The twelve spectra were imported into the MALDI BioTyper software (version 2.0, Brüker) and analyzed by standard pattern matching (with default parameter settings) against the main spectra of 4,706 bacteria, including 1 spectrum from N. lacusekhoensis, the only validly named Nesterenkonia species for which a spectrum was available in the BioTyper database. A score enabled the presumptive identification and discrimination of the tested species from those in a database: a score > 2 with a validated species enabled the identification at the species level; and a score < 1.7 did not enable any identification. For strain NP1T, no significant score was obtained, suggesting that our isolate was not a member of any known species (Figures 4 and 5).

Figure 4

Reference mass spectrum from Nesterenkonia massiliensis strain NP1T. Spectra from 12 individual colonies were compared and a reference spectrum was generated.

Figure 5

Gel view comparing N. massiliensis strain NP1T, N. lacusekhoensis and other species belonging to the family Micrococcaceae. The gel view displays the raw spectra of loaded spectrum files arranged as a pseudo-electrophoretic gel. The x-axis records the m/z value. The left y-axis displays the running spectrum number originating from subsequent spectra loading. The peak intensity is expressed by a grey scale scheme. The grey scale on the right y-axis indicates the relative peak intensity in arbitrary units. Species names are on the left.

Genome sequencing information

Genome project history

The organism was selected for sequencing on the basis of its phylogenetic position, 16S rDNA similarity and phenotypic differences with other members of the genus Nesterenkonia, and is part of a “culturomics” study aiming at isolating individually all bacterial species within the human gut flora [1]. It was the third genome of a Nesterenkonia species and the first genome of N. massiliensis sp. nov. A summary of the project information is shown in Table 3. The Genbank accession number is CBLL000000000 and consists of 141 contigs. Table 3 shows the project information and its association with MIGS version 2.0 compliance [42].

Table 3

Project information

MIGS ID

     Property

      Term

MIGS-31

     Finishing quality

      High-quality draft

MIGS-28

     Libraries used

      One 454 paired-end 3-kb library

MIGS-29

     Sequencing platforms

      454 GS FLX Titanium

MIGS-31.2

     Fold coverage

      22.63×

MIGS-30

     Assemblers

      Newbler version 2.5.3

MIGS-32

     Gene calling method

      Prodigal

     INSDC ID

      PRJEB668

     Genbank ID

      CBLL000000000

     Genebank Date of release

      August 20, 2013

     Gold ID

      Gi39432

MIGS-13

     Project relevance

      Study of human gut microbiome

Growth conditions and DNA isolation

N. massiliensis sp. nov strain NP1T, (= CSUR P244 = DSM 26221) was grown aerobically on sheep blood-enriched Columbia agar at 37°C. Two petri dishes were spread and the colonies resuspended in 6x100 µl of G2 buffer (EZI DNA Tissue Kit, Qiagen). A first mechanical lysis was performed with glass powder on the Fastprep-24 device (Sample Preparation system, MP Biomedicals, USA) using 2x20 second bursts. DNA was incubated with 2.5 µg/µL of lysozyme for 30 minutes at 37°C and extracted using the BioRobot EZ 1 Advanced XL (Qiagen).The DNA was then concentrated and purified on a Qiamp kit (Qiagen). The DNA concentration measured by the Quant-it Picogreen kit (Invitrogen) on the Genios Tecan fluorometer was 94 ng/µl.

Genome sequencing and assembly

DNA (5 µg) was mechanically fragmented with a Hydroshear device (Digilab, Holliston, MA, USA) with an enrichment size at 3-4 kb. The DNA fragmentation was visualized through the Agilent 2100 BioAnalyzer on a DNA labchip 7500 with an average size of 3.5 kb. The library was constructed using a 454 GS-FLX Titanium paired-end rapid library protocol. Circularization and nebulization generated a pattern with an average size of 390 bp. After 20 cycles of PCR amplification, the double stranded paired-end library was quantified using the Quant-it Ribogreen kit (Invitrogen) using a Genios Tecan fluorometer at 820 pg/µL. The library concentration equivalence was calculated as 3.86 x 109 molecules/µL. The library was stored at -20°C until further use.

The library was clonally amplified with 1 cpb in two emPCR reactions with the GS Titanium SV emPCR Kit (Lib-L) v2. The yield of the emPCR was 13.67%, within the range of 5 to 20% recommended for the Roche procedure. Approximately 656,601 beads were loaded for a ¼ region on the GS Titanium PicoTiterPlate (PTP Kit 70x75, Roche) and sequenced with the GS Titanium Sequencing Kit XLR70. The run was performed overnight and analyzed on the cluster through the gsRunBrowser and Newbler assemblers (Roche). A total of 176,833 passed filter wells were obtained and generated 60.9 Mb with an average of length of 345 bp. The passed filter sequences were assembled on Newbler with 90% identity and 40 bp as overlap. The final assembly identified 18 scaffolds and 141 large contigs (>1,500 bp), and generated a genome size of 2.69Mb which corresponds to a coverage of 22.63 genome equivalents.

Genome annotation

Open Reading Frames (ORFs) were predicted using Prodigal [54] with default parameters but the predicted ORFs were excluded if they spanned a sequencing gap region. The predicted bacterial protein sequences were searched against the GenBank database [55] and the Clusters of Orthologous Groups (COG) databases using BLASTP. The tRNAScanSE tool [56] was used to find tRNA genes, whereas ribosomal RNAs were found by using RNAmmer [57] and BLASTn against the GenBank database. Lipoprotein signal peptides and the number of transmembrane helices were predicted using SignalP [58] and TMHMM [59] respectively. ORFans were identified if their BLASTP E-value was lower than 1e-3 for alignment length greater than 80 amino acids. If alignment lengths were smaller than 80 amino acids, we used an E-value of 1e-5. Such parameter thresholds have already been used in previous works to define ORFans. Artemis [60] and DNA Plotter [61] were used for data management and visualization of genomic features, respectively. The Mauve alignment tool (version 2.3.1) was used for multiple genomic sequence alignment [62]. To estimate the mean level of nucleotide sequence similarity at the genome level, we used the Average Genomic Identity Of gene Sequences (AGIOS) home-made software [34]. Briefly, this software combines the Proteinortho software [63] for detecting orthologous proteins in pairwise comparisons of genomes, then retrieves the corresponding genes and determines the mean percentage of nucleotide sequence identity among orthologous ORFs using the Needleman-Wunsch global alignment algorithm. As only one genome was available for the genus Nesterenkonia, we used genomes from closely related genera for the calculation of AGIOS values. N. massiliensis strain NT1T was compared to Nesterenkonia alba strain DSM 19423 (GenBank accession number ATXP00000000), Micrococcus luteus strain NCTC2665 (CP001628), Kocuria rhizophila strain DSM 2048 (AP009152) and Arthrobacter arilaitensis strain RE117 (FQ311875).

Genome properties

The genome of N. massiliensis strain NP1T is 2,726,371bp long (1 chromosome, but no plasmid) with a 62.47% G+C content (Table 4, Figure 6, Figure 7). Of the 2,714 predicted genes, 2,663 were protein- coding genes, and 51 were RNAs. Three rRNA genes (one 16S rRNA, one 23S rRNA and one 5S rRNA) and 48 predicted tRNA genes were identified in the genome. A total of 1,962 genes (73.68%) were assigned a putative function. One hundred and ninety-nine genes were identified as ORFans (7.47%). The remaining genes were annotated as hypothetical proteins. The properties and the statistics of the genome are summarized in Table 4. The distribution of genes into COGs functional categories is presented in Table 5 and a comparison is presented in Table 6.

Table 4

Nucleotide content and gene count levels of the genome

Attribute

    Value

    % of totala

Genome size (bp)

    2,726,371

    100

DNA coding region (bp)

    2,473,018

    90.40

DNA G+C content (bp)

    1,703,271

    62.47

Total genes

    2714

    100

RNA genes

    51

    1.88

Protein-coding genes

    2663

    98.12

Genes with function prediction (Cogs + NR)

    1962

    73.68

Genes assigned to COGs

    1950

    73.23

Genes with peptide signals

    241

    9.05

Genes with transmembrane helices

    599

    22.49

a The total is based on either the size of the genome in base pairs or the total number of protein coding genes in the annotated genome.

Figure 6

Graphical circular map of the chromosome. From the outside in, the outer two circles show open reading frames oriented in the forward (colored by COG categories) and reverse (colored by COG categories) directions, respectively. The third circle marks the rRNA gene operon (red) and tRNA genes (green). The fourth circle shows the G+C% content plot. The inner-most circle shows GC skew, purple indicating negative values and olive, positive values.

Figure 7

Distribution of functional classes of predicted genes on the chromosomes of Nesterenkonia massiliensis (NM), Nesterenkonia alba (NA), Micrococcus luteus (ML), Kocuria rhizophila (KR) and Arthrobacter arilaitensis (AA) according to the COG category. For each genome, we indicated the percentage of each gene category.

Table 5

Number of genes associated with the 25 general COG functional categories

Code

    Value

    %agea

     Description

J

    149

    5,60

     Translation

A

    1

    0,04

     RNA processing and modification

K

    162

    6,08

     Transcription

L

    188

    7,06

     Replication, recombination and repair

B

    1

    0,04

     Chromatin structure and dynamics

D

    20

    0,75

     Cell cycle control, mitosis and meiosis

Y

    0

    0

     Nuclear structure

V

    36

    1,35

     Defense mechanisms

T

    78

    2,93

     Signal transduction mechanisms

M

    112

    4,21

     Cell wall/membrane biogenesis

N

    3

    0,11

     Cell motility

Z

    0

    0

     Cytoskeleton

W

    0

    0

     Extracellular structures

U

    29

    1,09

     Intracellular trafficking and secretion

O

    71

    2,67

     Posttranslational modification, protein turnover, chaperones

C

    129

    4,84

     Energy production and conversion

G

    148

    5,56

     Carbohydrate transport and metabolism

E

    239

    8,97

     Amino acid transport and metabolism

F

    67

    2,52

     Nucleotide transport and metabolism

H

    88

    3,30

     Coenzyme transport and metabolism

I

    73

    2,74

     Lipid transport and metabolism

P

    160

    6,01

     Inorganic ion transport and metabolism

Q

    48

    1,80

     Secondary metabolites biosynthesis, transport and catabolism

R

    293

    11,00

     General function prediction only

S

    142

    5,33

     Function unknown

_

    713

    26,77

     Not in COGs

aThe total is based on the total number of protein coding genes in the annotated genome

Table 6

Genomic comparison of N. massiliensis and 4 other members of the family Micrococcaceae.

    Nesterenkonia massilensis

    Nesterenkonia alba

    Micrococcus luteus

    Kocuria rhizophila

    Arthrobacter arilaitensis

Nesterenkonia massilensis

    2,663

    1,142

    1,132

    1,087

    1,208

Nesterenkonia alba

    75.61

    2,351

    1,046

    1,033

    1,116

Micrococcus luteus

    70.5

    1,046

    2,236

    1,152

    1,241

Kocuria rhizophila

    69.76

    69.96

    74.23

    2,357

    1,224

Arthrobacter arilaitensis

    68.57

    68.04

    69.35

    69.05

    3,436

Upper right, numbers of orthologous proteins shared between genomes; lower left, AGIOS values; bold numbers indicate the numbers of proteins per genome.

Genomic comparison

We compared the genome of N. massiliensis strain NP1T to those of N. alba strain DSM 19423, M. luteus strain NCTC2665, K. rhizophila strain DSM 2048 and A. arilaitensis strain RE117. The draft genome of N. massiliensis had a larger size than those of N. alba and M. luteus (2.72, 2.59 and 2.7 Mb, respectively) but was smaller than that of A. arilaitensis (3.92 Mb). The G+C content of N. massiliensis was lower than those of N. alba, M. luteus and K. rhizophila (62.4, 63.8, 73 and 71.2%, respectively) but higher than that of A. arilaitensis (59.3%). The gene content of N. massiliensis was larger than those of N. alba, M. luteus and K. rhizophila (2,714, 2,403, 2,345 and 2,414 genes, respectively) but smaller than that of A. arilaitensis (3,771). In addition, N. massiliensis shared 1,142, 1,132, 1,087 and 1,208 orthologous genes with N. alba, M. luteus and K. rhizophila, respectively. N. massiliensis exhibited an AGIOS value of 75.61% with N. alba, and 68.57 to 70.5 with other members of the family Micrococcaceae.

Conclusion

On the basis of phenotypic, phylogenetic and genomic analyses, we formally propose the creation of Nesterenkonia massiliensis sp. nov. that contains the strain NP1T. The strain has been isolated from the fecal flora of an AIDS-infected patient living in Marseille, France. Several other bacterial species were also cultivated from different fecal samples through diversification of culture conditions [4-34], thus suggesting that the human fecal flora of humans remains only partially known.

Description of Nesterenkonia massiliensis sp. nov.

Nesterenkonia massiliensis (mas.si.li.en′sis. L. gen. fem. n. massiliensis of Massilia, the Roman name of Marseille, France, where the type strain was isolated).

Grows between 25 and 45°C on blood-enriched Columbia agar (BioMerieux). Optimal growth obtained at 37°C in aerobic atmosphere. Weak growth in microaerophilic atmosphere. No growth under anaerobic condition. Colonies are dark yellow and 1 mm in diameter. Cells are Gram-positive, non-endospore-forming, and motile cocci, with a mean diameter and length of 0.67 μm and 1.4 μm, respectively. Catalase positive, oxidase negative. Negative reactions obtained for nitrate reduction, urease, indole production, glucose fermentation, arginine dihydrolase, β-galactosidase, glucose, arabinose, mannose, mannitol, N-acetyl-glucosamine, maltose, gluconate, caprate, adipate, malate, citrate, phenylacetate assimilation and cytochrome oxidase. Fermentation of D-glucose, D-fructose, D-saccharose, ribose, mannose, mannitol, D-trehalose and L-rhamnose. No reaction observed for esculin, salicin, D-cellobiose and gentiobiose. Cells are susceptible to amoxicillin, imipenem, rifampin, ciprofloxacin, gentamicin, doxycycline and vancomycin but resistant to trimethoprim/sulfamethoxazole and metronidazole.

The G+C content of the genome is 62.47%. The 16S rRNA and genome sequences are deposited in GenBank under accession numbers JX424770 and CBLL00000000, respectively. The habitat of the microorganism is the human digestive tract. The type strain NP1T (= CSUR P244 = DSM 26221) was isolated from the fecal flora of a 32-year-old French female suffering from AIDS.

Declarations

Acknowledgements

The authors thank the Xegen Company (Web Site) for automating the genomic annotation process. This study was funded by the Mediterranée-Infection Foundation.


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References

  1. Lagier JC, Armougom F, Million M, Hugon P, Pagnier I, Robert C, Bittar F, Fournous G, Gimenez G and Maraninchi M. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect. 2012; 18:1185-1193PubMed
  2. Dubourg G, Lagier JC, Armougom F, Robert C, Hamad I, Brouqui P and Raoult D. The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics. Eur J Clin Microbiol Infect. 2013; 32:637-645 View ArticlePubMed
  3. Database GOLD. Web Site
  4. Ramasamy D, Mishra AK, Lagier JC, Padhmanabhan R, Rossi-Tamisier M, Sentausa E, Raoult D and Fournier PE. A polyphasic strategy incorporating genomic data for the taxonomic description of new bacterial species. Int J Syst Evol Microbiol. 2014; (In press). View ArticlePubMed
  5. Roux V, Million M, Robert C, Magne A and Raoult D. Non-contiguous finished genome sequence and description of Oceanobacillus massiliensis sp. nov. Stand Genomic Sci. 2013; 9:370-384 View ArticlePubMed
  6. Kokcha S, Mishra AK, Lagier JC, Million M, Leroy Q, Raoult D and Fournier PE. Non contiguous-finished genome sequence and description of Bacillus timonensis sp. nov. Stand Genomic Sci. 2012; 6:346-355 View ArticlePubMed
  7. Lagier JC, El Karkouri K, Nguyen TT, Armougom F, Raoult D and Fournier PE. Non-contiguous finished genome sequence and description of Anaerococcus senegalensis sp. nov. Stand Genomic Sci. 2012; 6:116-125 View ArticlePubMed
  8. Mishra AK, Gimenez G, Lagier JC, Robert C, Raoult D and Fournier PE. Genome sequence and description of Alistipes senegalensis sp. nov. Stand Genomic Sci. 2012; 7:1-16 View ArticlePubMed
  9. Lagier JC, Armougom F, Mishra AK, Nguyen TT, Raoult D and Fournier PE. Non-contiguous finished genome sequence and description of Alistipes timonensis sp. nov. Stand Genomic Sci. 2012; 6:315-324 View ArticlePubMed
  10. Mishra AK, Lagier JC, Robert C, Raoult D and Fournier PE. Non-contiguous finished genome sequence and description of Clostridium senegalense sp. nov. Stand Genomic Sci. 2012; 6:386-395PubMed
  11. Mishra AK, Lagier JC, Robert C, Raoult D and Fournier PE. Non contiguous-finished genome sequence and description of Peptoniphilus timonensis sp. nov. Stand Genomic Sci. 2012; 7:1-11 View ArticlePubMed
  12. Mishra AK, Lagier JC, Rivet R, Raoult D and Fournier PE. Non-contiguous finished genome sequence and description of Paenibacillus senegalensis sp. nov. Stand Genomic Sci. 2012; 7:70-81 View ArticlePubMed
  13. Lagier JC, Gimenez G, Robert C, Raoult D and Fournier PE. Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov. Stand Genomic Sci. 2012; 7:200-209PubMed
  14. Roux V, El Karkouri K, Lagier JC, Robert C and Raoult D. Non-contiguous finished genome sequence and description of Kurthia massiliensis sp. nov. Stand Genomic Sci. 2012; 7:221-232 View ArticlePubMed
  15. Kokcha S, Ramasamy D, Lagier JC, Robert C, Raoult D and Fournier PE. Non-contiguous finished genome sequence and description of Brevibacterium senegalense sp. nov. Stand Genomic Sci. 2012; 7:233-245 View ArticlePubMed
  16. Ramasamy D, Kokcha S, Lagier JC, Nguyen TT, Raoult D and Fournier PE. Genome sequence and description of Aeromicrobium massiliense sp. nov. Stand Genomic Sci. 2012; 7:246-257 View ArticlePubMed
  17. Lagier JC, Ramasamy D, Rivet R, Raoult D and Fournier PE. Non contiguous-finished genome sequence and description of Cellulomonas massiliensis sp. nov. Stand Genomic Sci. 2012; 7:258-270 View ArticlePubMed
  18. Lagier JC, Elkarkouri K, Rivet R, Couderc C, Raoult D and Fournier PE. Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov. Stand Genomic Sci. 2013; 7:343-356 View ArticlePubMed
  19. Mishra AK, Hugon P, Lagier JC, Nguyen TT, Robert C, Couderc C, Raoult D and Fournier PE. Non contiguous-finished genome sequence and description of Peptoniphilus obesi sp. nov. Stand Genomic Sci. 2013; 7:357-369 View ArticlePubMed
  20. Mishra AK, Lagier JC, Nguyen TT, Raoult D and Fournier PE. Non contiguous-finished genome sequence and description of Peptoniphilus senegalensis sp. nov. Stand Genomic Sci. 2013; 7:370-381 View ArticlePubMed
  21. Lagier JC, El Karkouri K, Mishra AK, Robert C, Raoult D and Fournier PE. Non contiguous-finished genome sequence and description of Enterobacter massiliensis sp. nov. Stand Genomic Sci. 2013; 7:399-412 View ArticlePubMed
  22. Hugon P, Ramasamy D, Lagier JC, Rivet R, Couderc C, Raoult D and Fournier PE. Non contiguous-finished genome sequence and description of Alistipes obesi sp. nov. Stand Genomic Sci. 2013; 7:427-439 View ArticlePubMed
  23. Mishra AK, Hugon P, Robert C, Raoult D and Fournier PE. Non contiguous-finished genome sequence and description of Peptoniphilus grossensis sp. nov. Stand Genomic Sci. 2012; 7:320-330PubMed
  24. Mishra AK, Hugon P, Lagier JC, Nguyen TT, Couderc C, Raoult D and Fournier PE. Non contiguous-finished genome sequence and description of Enorma massiliensis gen. nov., sp. nov., a new member of the Family Coriobacteriaceae. Stand Genomic Sci. 2013; 8:290-305 View ArticlePubMed
  25. Ramasamy D, Lagier JC, Gorlas A, Raoult D and Fournier PE. Non contiguous-finished genome sequence and description of Bacillus massiliosenegalensis sp. nov. Stand Genomic Sci. 2013; 8:264-278 View ArticlePubMed
  26. Ramasamy D, Lagier JC, Nguyen TT, Raoult D and Fournier PE. Non contiguous-finished genome sequence and description of Dielma fastidiosa gen. nov., sp. nov., a new member of the Family Erysipelotrichaceae. Stand Genomic Sci. 2013; 8:336-351 View ArticlePubMed
  27. Mishra AK, Lagier JC, Robert C, Raoult D and Fournier PE. Genome sequence and description of Timonella senegalensis gen. nov., sp. nov., a new member of the suborder Micrococcinae. Stand Genomic Sci. 2013; 8:318-335 View ArticlePubMed
  28. Mishra AK, Pfleiderer A, Lagier JC, Robert C, Raoult D and Fournier PE. Non contiguous-finished genome sequence and description of Bacillus massilioanorexius sp. nov. Stand Genomic Sci. 2013; 8:465-479 View ArticlePubMed
  29. Hugon P, Mishra AK, Lagier JC, Nguyen TT, Couderc C, Raoult D and Fournier PE. Non-contiguous finished genome sequence and description of Brevibacillus massiliensis sp. nov. Stand Genomic Sci. 2013; 8:1-14 View ArticlePubMed
  30. Hugon P, Mishra AK, Robert C, Raoult D and Fournier PE. Non-contiguous finished genome sequence and description of Anaerococcus vaginalis. Stand Genomic Sci. 2012; 6:356-365 View ArticlePubMed
  31. Hugon P, Ramasamy D, Robert C, Couderc C, Raoult D and Fournier PE. Non-contiguous finished genome sequence and description of Kallipyga massiliensis gen. nov., sp. nov., a new member of the family Clostridiales Incertae Sedis XI. Stand Genomic Sci. 2013; 8:500-515 View ArticlePubMed
  32. Padhmanabhan R, Lagier JC, Dangui NPM, Michelle C, Couderc C, Raoult D and Fournier PE. Non-contiguous finished genome sequence and description of Megasphaera massiliensis. Stand Genomic Sci. 2013; 8:525-538 View ArticlePubMed
  33. Mishra AK, Edouard S, Dangui NPM, Lagier JC, Caputo A, Blanc-Tailleur C, Ravaux I, Raoult D and Fournier PE. Non-contiguous finished genome sequence and description of Nosocomiicoccus massiliensis sp. nov. Stand Genomic Sci. 2013; 9:205-219 View ArticlePubMed
  34. Mishra AK, Lagier JC, Pfleiderer A, Nguyen TT, Caputo A, Raoult D and Fournier PE. Non-contiguous finished genome sequence and description of Holdemania massiliensis sp. nov. Stand Genomic Sci. 2013; 9:395-409 View ArticlePubMed
  35. Stackebrandt E, Koch C, Gvozdiak O and Schumann P. Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend. Int J Syst Bacteriol. 1995; 45:682-692 View ArticlePubMed
  36. Govender L, Naidoo L and Setati ME. Nesterenkonia suensis sp. nov., a haloalkaliphilic actinobacterium isolated from a salt pan. Int J Syst Evol Microbiol. 2013; 63:41-46 View ArticlePubMed
  37. Collins MD, Lawson PA, Labrenz M, Tindall BJ, Weiss N and Hirsch P. Nesterenkonia lacusekhoensis sp. nov., isolated from hypersaline Ekho Lake, East Antarctica, and emended description of the genus Nesterenkonia. Int J Syst Evol Microbiol. 2002; 52:1145-1150 View ArticlePubMed
  38. Li WJ, Zhang YQ, Schumann P, Liu HY, Yu LY, Zhang YQ, Stackebrandt E, Xu LH and Jiang CL. Nesterenkonia halophila sp. nov., a moderately halophilic, alkalitolerant actinobacterium isolated from a saline soil. Int J Syst Evol Microbiol. 2008; 58:1359-1363 View ArticlePubMed
  39. Li WJ, Chen HH, Kim CJ, Zhang YQ, Park DJ, Lee JC, Xu LH and Jiang CL. Nesterenkonia sandarakina sp. nov. and Nesterenkonia lutea sp. nov., novel actinobacteria, and emended description of the genus Nesterenkonia. Int J Syst Evol Microbiol. 2005; 55:463-466 View ArticlePubMed
  40. Li WJ, Chen HH, Zhang YQ, Schumann P, Stackebrandt E, Xu LH and Jiang CL. Nesterenkonia halotolerans sp. nov. and Nesterenkonia xinjiangensis sp. nov., actinobacteria from saline soils in the west of China. Int J Syst Evol Microbiol. 2004; 54:837-841 View ArticlePubMed
  41. Vaziri ND, Wong J, Pahl M, Piceno YM, Yuan J, DeSantis TZ, Ni Z, Nguyen TH and Andersen GL. Chronic kidney disease alters intestinal microbial flora. Kidney Int. 2013; 83:308-315 View ArticlePubMed
  42. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ and Angiuoli SV. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008; 26:541-547 View ArticlePubMed
  43. Woese CR, Kandler O and Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA. 1990; 87:4576-4579 View ArticlePubMed
  44. Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 119-169.
  45. Stackebrandt E, Rainey FA and Ward-Rainey NL. Proposal for a New Hierarchic Classification System, Actinobacteria classis nov. Int J Syst Bacteriol. 1997; 47:479-491 View Article
  46. Zhi XY, Li WJ and Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol. 2009; 59:589-608 View ArticlePubMed
  47. Skerman VBD, McGowan V and Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol. 1980; 30:225-420 View Article
  48. Buchanan RE. Studies in the Nomenclature and Classification of the Bacteria: II. The Primary Subdivisions of the Schizomycetes. J Bacteriol. 1917; 2:155-164PubMed
  49. Pribram E. A Contribution to the classification of microorganisms. J Bacteriol. 1929; 18:361-394PubMed
  50. Ashburner M, Ball CA, Blake JA, Botstein D, But-ler H, Cherry JM, Davis AP, Dolinski K, Dwight SS and Eppig JT. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25:25-29 View ArticlePubMed
  51. Luo HY, Wang YR, Miao LH, Yang PL, Shi PJ, Fang CX, Yao B and Fan YL. Nesterenkonia alba sp. nov., an alkaliphilic actinobacterium isolated from the black liquor treatment system of a cotton pulp mill. Int J Syst Evol Microbiol. 2009; 59:863-868 View ArticlePubMed
  52. Stackebrandt E and Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today. 2006; 33:152-155
  53. Seng P, Drancourt M, Gouriet F, La Scola B, Fournier PE, Rolain JM and Raoult D. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis. 2009; 49:543-551 View ArticlePubMed
  54. Prodigal. Web Site
  55. Benson DA, Karsch-Mizrachi I, Clark K, Lipman DJ, Ostell J and Sayers EW. GenBank. Nucleic Acids Res. 2012; 40:D48-D53 View ArticlePubMed
  56. Lowe TM and Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997; 25:955-964 View ArticlePubMed
  57. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T and Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007; 35:3100-3108 View ArticlePubMed
  58. Bendtsen JD, Nielsen H, von Heijne G and Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol. 2004; 340:783-795 View ArticlePubMed
  59. Krogh A, Larsson B, von Heijne G and Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001; 305:567-580 View ArticlePubMed
  60. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA and Barrell B. Artemis: sequence visualization and annotation. Bioinformatics. 2000; 16:944-945 View ArticlePubMed
  61. Carver T, Thomson N, Bleasby A, Berriman M and Parkhill J. DNA Plotter: circular and linear interactive genome visualization. Bioinformatics. 2009; 25:119-120 View ArticlePubMed
  62. Darling AC, Mau B, Blattner FR and Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004; 14:1394-1403 View ArticlePubMed
  63. Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF and Prohaska SJ. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics. 2011; 12:124 View ArticlePubMed