Open Access

Non-contiguous finished genome sequence and description of Bacillus massilioanorexius sp. nov.

  • Ajay Kumar Mishra1,
  • Anne Pfleiderer1,
  • Jean-Christophe Lagier1,
  • Catherine Robert1,
  • Didier Raoult1 and
  • Pierre-Edouard Fournier1Email author
Standards in Genomic Sciences20138:8030465

https://doi.org/10.4056/sigs.4087826

Published: 30 July 2013

Abstract

Bacillus massilioanorexius strain AP8T sp. nov. is the type strain of B. massilioanorexius sp. nov., a new species within the genus Bacillus. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old Caucasian French female suffering from a severe form of anorexia nervosa since the age of 12 years. B. massilioanorexius is a Gram-positive aerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,616,135 bp long genome (one chromosome but no plasmid) contains 4,432 protein-coding and 87 RNA genes, including 8 rRNA genes.

Keywords

Bacillus massilioanorexius genome culturomics taxonogenomics

Introduction

Bacillus massilioanorexius strain AP8T (= CSUR P201 = DSM 26092) is the type strain of B. massilioanorexius sp. nov. This bacterium is a Gram-positive, non-spore-forming, aerobic and motile bacillus that was isolated from the stool of a 21-year-old Caucasian French female suffering from a severe form of anorexia nervosa since the age of 12 years and is part of a “culturomics” study aiming at cultivating all species within human feces individually [13]. This bacterium was one of the 11 new bacterial species isolated from this single stool sample [3].

The current classification of Bacteria and Archaea remains a subject of debate and currently relies on a combination of phenotypic and genotypic characteristics [4]. Genomic data has not yet been routinely incorporated into descriptions. However, as more than 6,000 bacterial genomes have been sequenced including 982 type strains [5,6] and another 15,000 genomic projects are ongoing including 2,120 type strains [5,6], we recently proposed to integrate genomic information in the description of new bacterial species [728].

The genus Bacillus (Cohn 1872) was created in 1872 [29]. It consists mainly of Gram-positive, motile, spore-forming bacteria classified within 251 species and 3 subspecies with validly published names [30]. Members of the genus Bacillus are ubiquitous bacteria isolated from various environments including soil, fresh and sea water and food. In humans, Bacillus species may be opportunists in immunocompromised patients [31] or pathogenic, such as B. anthracis [32] and B. cereus. However, in addition to these two species, various Bacillus species may be involved in a variety of aspecific human infections, including cutaneous, ocular, central nervous system or bone infections, pneumonia, endocarditis and bacteremia [33].

Here we present a summary classification and a set of features for B. massilioanorexius sp. nov. strain AP8T (= CSUR P201 = DSM 26092), together with the description of the complete genomic sequence and its annotation. These characteristics support the circumscription of the species B. massilioanorexius.

Classification and information

A stool sample was collected from a 21-year-old Caucasian French female suffering from a severe restrictive form of anorexia nervosa since the age of 12 years. She was hospitalized in the nutrition unit of our hospital for recent aggravation of her medical condition. At the time of hospitalization, her weight and height was 27.7 kg, and 1.63 m (BMI: 10.4 kg/m2) respectively. 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 (agreement 09-022). The fecal specimen was preserved at −80°C after collection. Strain AP8T (Table 1) was isolated in March 2012 by aerobic cultivation on Columbia agar (BioMerieux, Marcy l’Etoile, France) after one month of preincubation of the stool sample with addition of 5ml of sheep rumen in blood bottle culture. This strain exhibited a 97% nucleotide sequence similarity with B. simplex [34], the phylogenetically closest validated Bacillus species (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 [35].
Figure 1.

Phylogenetic tree highlighting the position of Bacillus massilioanorexius strain AP8T relative to a selection of type strains of validly published species of Bacillus genus. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained using the maximum-likelihood method within MEGA program. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 500 times to generate a majority consensus tree. Clostridium botulinum was used as outgroup. The scale bar represents a 2% nucleotide sequence divergence.

Table 1.

Classification and general features of Bacillus massilioanorexius strain AP8T

MIGS ID

Property

Term

Evidence codea

 

Current classification

Domain Bacteria

TAS [36]

 

Phylum Firmicutes

TAS [3739]

 

Class Bacilli

TAS [40,41]

 

Order Bacillales

TAS [42,43]

 

Family Bacillaceae

TAS [42,44]

 

Genus Bacillus

TAS [29,42,45]

 

Species Bacillus massilioanorexius

IDA

 

Type strain AP8T

IDA

 

Gram stain

Positive

IDA

 

Cell shape

Bacilli

IDA

 

Motility

Motile

IDA

 

Sporulation

Nonsporulating

IDA

 

Temperature range

Mesophile

IDA

 

Optimum temperature

37°C

IDA

MIGS-6.3

Salinity

Unknown

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

 

Pathogenicity

Unknown

 
 

Biosafety level

2

 

MIGS-14

Isolation

Human feces

 

MIGS-4

Geographic location

France

IDA

MIGS-5

Sample collection time

August 2011

IDA

 

Latitude

43.296482

IDA

MIGS-4.1

Longitude

5.36978

IDA

MIGS-4.3

Depth

Surface

IDA

MIGS-4.4

Altitude

0 m above sea level

IDA

Evidence 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 [46]. 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.

Different growth temperatures (25, 30, 37, 45°C) were tested. Growth was observed between 25 and 45°C, with optimal growth at 37°C after 24 hours of incubation. Colonies were 3 mm in diameter and 0.5 mm in thickness and gray in color with coarse appearance on blood-enriched Columbia agar. 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. Growth was obtained in all the above mentioned conditions except in anaerobic conditions, where weak growth was observed. Gram staining showed Gram-positive rods. The motility test was positive. Cells grown on agar are Gram-positive rods (Figure 2), have a mean diameter of 0.77 µm and a mean length of 2.27 µm in electron microscopy (Figure 3).
Figure 2.

Gram staining of B. massilioanorexius strain AP8T

Figure 3.

Transmission electron microscopy of B. massilioanorexius strain AP8T, using a Morgani 268D (Philips) at an operating voltage of 60kV. The scale bar represents 900 nm.

Strain AP8T exhibited catalase and oxidase activity. Substrates oxidation and assimilation were examined with an API 50CH strip (BioMerieux) at the optimal growth temperature. Positive reactions were observed for D-glucose, D-fructose, D-saccharose, ribose, mannose, mannitol and D-trehalose and weak reactions were observed for L-rhamnose, esculine, salicine, D-cellobiose and gentiobiose. Using an API 20E strip (BioMerieux, Marcy l’Etoile), positive reactions were observed for tryptophane deaminase, acetoin and gelatinase production. Negative reactions were found for urease and indole production.

B. massilioanorexius is susceptible to amoxicillin, rifampicin, ciprofloxacin, gentamicin, doxycycline and vancomycin but resistant to trimethoprim/sulfamethoxazole and metronidazole. When compared with representative species from the genus Bacillus, B. massilioanorexius strain AP8T exhibited the phenotypic differences detailed in Table 2.
Table 2.

Differential characteristics of Bacillus massilioanorexius strain AP8T, B. timonensis strain DSM 25372, B. amyloliquefaciens strain FZB42, B. massiliosenegalensis strain JC6T, B. mycoides strain DSM 2048 and B. thuringiensis strain BMB171

Properties

B. massilioanorexius

B. timonensis

B. amyloliquefaciens

B. massiliosenegalensis

B. mycoides

B. thuringiensis

Cell diameter (µm)

0.77

0.66

0.8

0.65

1.1

1.0

Oxygen requirement

aerobic

aerobic

aerobic

aerobic

facultative anaerobic

facultative anaerobic

Pigment production

+

Gram stain

+

+

+

+

+

Salt requirement

+

+

+

+

 

Motility

+

+

+

+

 

Endospore formation

+

+

+

+

+

Production of

      

Acid phosphatase

na

na

+

w

+

+

Catalase

+

+

+

+

+

Oxidase

+

+

+

+

Nitrate reductase

na

na

+

+

v

+

Urease

na

v

+

β-galactosidase

na

+

v

na

+

N-acetyl-glucosamine

na

+

+

+

+

+

Acid from

      

L-Arabinose

+

+

+

na

Ribose

+

+

+

+

Mannose

+

+

+

+

Mannitol

+

+

+

+

Sucrose

+

+

v

D-glucose

+

+

+

+

+

D-fructose

+

+

+

+

D-maltose

+

+

+

+

D-lactose

+

+

+

+

Hydrolysis of

      

Gelatin

+

+

+

+

Starch

na

na

+

na

+

+

G+C content (mol%)

34.10

37.30

46.48

37.6

35.21

35.18

Habitat

human gut

human gut

Soil

human gut

soil

soil

na = data not available; w = weak, v = variable reaction

Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) MS protein analysis was carried out as previously described [47] using a Microflex spectrometer (Brüker Daltonics, Leipzig, Germany). Twelve individual colonies were deposited on a MTP 384 MALDI-TOF target plate (Brüker). The twelve AP8T 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 3,769 bacteria, including 129 spectra from 98 validly named Bacillus species, used as reference data 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 AP8T, 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 B. massilioanorexius strain AP8T. Spectra from 12 individual colonies were compared and a reference spectrum was generated.

Figure 5.

Gel view comparing B. massilioanorexius sp. nov strain AP8T and other Bacillus species. The gel view displays the raw spectra of loaded spectrum files arranged in a pseudo-gel like look. 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 Gray scale scheme code. The color bar and the right y-axis indicate the relation between the color a peak is displayed with and the peak intensity in arbitrary units. Displayed species are indicated on the left.

Genome sequencing information

Genome project history

The organism was selected for sequencing on the basis of its phylogenetic position and 16S rRNA similarity to other members of the Bacillus genus, and is part of a “culturomics” study of the human digestive flora aiming at isolating all bacterial species within human feces. It was the twenty-seventh genome of a Bacillus species and the first genome of Bacillus massilioanorexius sp. nov. A summary of the project information is shown in Table 3. The Genbank accession number is CAPG00000000 and consists of 120 contigs. Table 3 shows the project information and its association with MIGS version 2.0 compliance [48].
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

31.34 ×

MIGS-30

Assemblers

Newbler version 2.5.3

MIGS-32

Gene calling method

Prodigal

 

Genbank ID

CAPG00000000

 

Genbank Date of Release

November 28, 2012

 

Gold ID

Gi20708

MIGS-13

Project relevance

Study of the human gut microbiome

Growth conditions and DNA isolation

Strain AP8T was grown aerobically in Columbia broth (BioMerieux, Marcy l’Etoile, France). Extraction of chromosomal DNA was performed by using 50 mL of 48–72 h culture of B. massilioanorexius, centrifuged at 4oC and 2000 × g for 20 min. Resuspension of cell pellets was done in 1 mL Tris/EDTA/NaCl [10mM Tris/HCl (pH7.0), 10 mM EDTA (pH8.0), and 300 mM NaCl] and re-centrifugation was done under the same conditions. The pellets were resuspended in 200µL TE/lysozyme [25 mM Tris/HCl (pH8.0), 10 mM EDTA (pH8.0), 10 mM NaCl, and 10 mg lysozyme/mL]. The sample was incubated at 37oC for 30 min and then 30 µL of 30% (w/v) sodium N-lauroyl-sarcosine (Sarcosyl) was added to it, incubated for 20 min at 65oC, followed by incubation for 5 min at 4oC. Purification of DNA with phenol/chloroform/isoamylalcohol (25:24:1) was followed by precipitation with ethanol. DNA concentration was 64.3 ng/µl as determined by Genios Tecan fluorometer, using the Quant-it Picogreen kit (Invitrogen).

Genome sequencing and assembly

A 3kb paired-end sequencing strategy (Roche, Meylan, France) was used. Five µg of DNA were mechanically fragmented on the Covaris device (KBioScience-LGC Genomics, Middlesex, UK) through miniTUBE-Red with an enrichment size at 3–4kb. The DNA fragmentation was visualized through the Agilent 2100 BioAnalyzer on a DNA labchip 7500 with an optimal size of 2.95 kb. The library was constructed according to the 454 GS FLX Titanium paired end protocol. Circularization and nebulization were performed which generated a pattern of 553 bp optimal size. PCR amplification was performed for 17 cycles followed by double size selection. The single stranded paired-end library was quantified using Quant-it Ribogreen kit (Invitrogen) with Genios Tecan fluorometer that yielded concentration of 556 pg/µL. The library concentration equivalence was calculated as 1.82E+09 molecules/µL. The library was stored at −20°C until further use.

The shotgun library was clonally amplified with 5cpb in 4 emPCR reactions and the 3kb paired-end library was amplified with lower cpb in 4 emPCR reactions at 1cpb and 2 emPCR at 0.5 cpb with the GS Titanium SV emPCR Kit (Lib-L) v2 (Roche). The yield of the shotgun emPCR reactions was 16.9 and 5.62% respectively for the two kinds of paired-end emPCR reactions according to the quality expected (range of 5 to 20%) from the Roche procedure. Two libraries were loaded on the GS Titanium PicoTiterPlates (PTP Kit 70x75, Roche) and pyrosequenced with the GS Titanium Sequencing Kit XLR70 and the GS FLX Titanium sequencer (Roche). The run was performed overnight and analyzed on the cluster through the gsRunBrowser and Newbler assembler (Roche). A total of 410,883 passed filter wells were obtained and generated 144.49 Mb with a length average of 344 bp. The passed filter sequences were assembled Using Newbler with 90% identity and 40 bp as overlap. The final assembly identified 20 scaffolds and 120 contigs and generated a genome size of 4.61Mb which corresponds to a coverage of 31.34 × genome equivalent.

Genome annotation

Open Reading Frames (ORFs) were predicted using Prodigal [49] with default parameters but the predicted ORFs were excluded if they were spanning a sequencing gap region. The predicted bacterial protein sequences were searched against the GenBank database [50] and the Clusters of Orthologous Groups (COG) databases using BLASTP. The tRNAScanSE tool [51] was used to find tRNA genes, whereas ribosomal RNAs were found by using RNAmmer [52] and BLASTn against the GenBank database. Lipoprotein signal peptides and the number of transmembrane helices were predicted using SignalP [53] and TMHMM [54] respectively. ORFans were identified if their BLASTP E-value was lower than 1e-03 for alignment length greater than 80 amino acids. If alignment lengths were smaller than 80 amino acids, we used an E-value of 1e-05. Such parameter thresholds have already been used in previous works to define ORFans. Ortholog sets composed of one gene from each of six genomes (B. massilioanorexius strain AP8T, B. timonensis strain DSM 25372 (GenBank accession number CAET00000000), B. amyloliquefaciens strain FZB42 (GenBank accession number NC_009725), B. massiliosenegalensis strain JC6T (GenBank accession number CAHJ00000000), B. mycoides strain DSM 2048 (GenBank accession number CM000742) and B. thuringiensis strain BMB171 (GenBank accession number CP001903),) were identified using the Proteinortho software (version 1.4) [55] using a 30% protein identity and 1e-05E-value. The average percentage of nucleotide sequence identity between corresponding orthologous sets were determined using the Needleman-Wunsch algorithm global alignment technique. Artemis [56] was used for data management and DNA Plotter [57] was used for visualization of genomic features. Mauve alignment tool was used for multiple genomic sequence alignment and visualization [58].

Genome properties

The genome of B. massiliensis strain AP8T is 4,616,135 bp long (1 chromosome, but no plasmid) with a 34.10% G + C content (Figure 6 and Table 4). Of the 4,519 predicted genes, 4,432 were protein-coding genes, and 87 were RNAs. Eight rRNA genes (one 16S rRNA, one 23S rRNA and six 5S rRNA) and 79 predicted tRNA genes were identified in the genome. A total of 3,290 genes (72.80%) were assigned a putative function. Three hundred fifty-four genes were identified as ORFans (7.98%). The remaining genes were annotated as hypothetical proteins. The properties and the statistics of the genome are summarized in Table 4 and Table 5. The distribution of genes into COGs functional categories is presented in Table 5.
Figure 6.

Graphical circular map of the chromosome. From the outside in, the outer two circles show open reading frames oriented in the forward and reverse directions (colored by COG categories), respectively. The third circle shows 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 and olive indicating negative and positive values, respectively.

Table 4.

Nucleotide content and gene count levels of the genome

Attribute

Value

% of totala

Genome size (bp)

4,616,135

 

DNA coding region (bp)

3,750,534

81.24

DNA G+C content (bp)

1,574,102

34.10

Number of replicons

1

 

Extrachromosomal elements

0

 

Total genes

4,519

100

RNA genes

87

1.92

rRNA operons

1

 

Protein-coding genes

4,432

98.07

Genes with function prediction

3,524

77.98

Genes assigned to COGs

3,290

72.80

Protein coding genes assigned Pfam domains

3,807

84.24

Genes with peptide signals

270

5.97

Genes with transmembrane helices

1,241

27.46

CRISPR repeats

2

 

aThe 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

Table 5.

Number of genes associated with the 25 general COG functional categories

Code

Value

%agea

Description

J

171

3.86

Translation

A

0

0

RNA processing and modification

K

335

7.56

Transcription

L

200

4.51

Replication, recombination and repair

B

1

0.02

Chromatin structure and dynamics

D

37

0.83

Cell cycle control, mitosis and meiosis

Y

0

0

Nuclear structure

V

76

1.71

Defense mechanisms

T

212

4.78

Signal transduction mechanisms

M

147

3.32

Cell wall/membrane biogenesis

N

70

1.58

Cell motility

Z

0

0

Cytoskeleton

W

0

0

Extracellular structures

U

48

1.08

Intracellular trafficking and secretion

O

121

2.73

Posttranslational modification, protein turnover, chaperones

C

245

5.53

Energy production and conversion

G

221

4.99

Carbohydrate transport and metabolism

E

405

9.14

Amino acid transport and metabolism

F

98

2.21

Nucleotide transport and metabolism

H

135

3.05

Coenzyme transport and metabolism

I

136

3.07

Lipid transport and metabolism

P

258

5.82

Inorganic ion transport and metabolism

Q

81

1.83

Secondary metabolites biosynthesis, transport and catabolism

R

527

11.89

General function prediction only

S

349

7.87

Function unknown

-

1,142

25.77

Not in COGs

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

Comparison with other Bacillus species genomes

Here, we compared the genome of B. massilioanorexius strain AP8T, B. timonensis strain DSM 25372, B. amyloliquefaciens strain FZB42, B. massiliosenegalensis strain JC6T, B. mycoides strain DSM 2048 and B. thuringiensis strain BMB171. The draft genome of B. massilioanorexius is larger in size than that of B. amyloliquefaciens (4.6 vs 3.9 Mb, respectively), similar in size than that of B. timonensis (4.6 Mb) and smaller in size than those of B. massiliosenegalensis, B. mycoides and B. thuringiensis (4.9, 5.5 and 5.6 Mb, respectively). The G+C content of B. massilioanorexius is lower than those of B. massiliosenegalensis, B. timonensis, B. amyloliquefaciens, B. mycoides and B. thuringiensis (34.10, 37.60, 37.30, 46.48, 35.21 and 35.18%, respectively). The gene content of B. massilioanorexius is larger than that of B. amyloliquefaciens (4,519 and 3,814, respectively) and fewer than those of B. massiliosenegalensis, B. timonensis, B. mycoides and B. thuringiensis (4,997, 4,684, 5,747 and 5,495, respectively). The ratio of genes per MB of B. massilioanorexius is greater than that of B. amyloliquefaciens (982 and 978, respectively), comparable to that of B. thuringiensis (982) and smaller to those of B. massiliosenegalensis, B. timonensis and B. mycoides (1,019, 1,018 and 1,044, respectively). However, the distribution of genes into COG categories was not entirely similar in all the three compared genomes (Figure 7). The nucleotide sequence identity ranged from 66.09 to 83.69% among Bacillus species, and from 66.09 to 70.10% between B. massilioanorexius and other Bacillus species, thus confirming its new species status. Table 6 summarizes the numbers of orthologous genes and the average percentage of nucleotide sequence identity between the different genomes studied.
Figure 7.

Distribution of functional classes of predicted genes in B. massilioanorexius (red), B. massiliosenegalensis (blue), B. timonensis (pink), B. amyloliquefaciens (yellow), B. mycoides (brown) and B. thuringiensis (green) chromosomes according to the clusters of orthologous groups of proteins.

Table 6.

Orthologous gene comparison and average nucleotide identity Bacillus species B. massilioanorexius1 with B. massiliosenegalensis2; B. timonensis3, B. thuringiensis4; B. mycoides5; B. amyloliquefaciens6†.

 

B. massilioanorexius

B. massiliosenegalensis

B. timonensis

B. huringiensis

B. mycoides

B. amyloliquefaciens

B. massilioanorexius

4,432

1,897

1,864

1,887

1,794

1,709

B. massiliosenegalensis

70.10

4,895

1,965

1,863

1,765

1,755

B. timonensis

69.84

70.33

4,610

1,864

1,762

1,742

B. thuringiensis

69.35

68.88

69.31

6,243

2,210

1,832

B. mycoides

69.41

69.11

69.41

83.69

5,885

1,719

B. amyloliquefaciens

66.09

67.02

67.12

66.35

66.57

3,823

Upper right, numbers of orthologous genes; lower left, mean nucleotide identities of orthologous genes. Bold numbers indicate the numbers of genes or each genome. 1Genbank accession number CAPG00000000, 2CAHJ00000000, 3CAET00000000, 4CP001903, 5CM000742, 6NC_009725

Conclusion

On the basis of phenotypic, phylogenetic and genomic analyses, we formally propose the creation of Bacillus massilioanorexius sp. nov. that contains the strain AP8T. The strain has been found in France.

Description of Bacillus massilioanorexius sp. nov.

Bacillus massilioanorexius (ma.si.li.o.a.no.rex’i.us. L. masc. adj. massilioanorexius, combination of Massilia, the Latin name of Marseille, France, where the type strain was isolated, and anorexia, the disease presented by the patient from whom the strain was cultivated).

Colonies were 3 mm in diameter and 0.5 mm in thickness, gray in color with a coarse appearance on blood-enriched Columbia agar. Cells are rod-shaped with a mean diameter of 0.77 µm. Optimal growth occurs aerobically, weak growth was observed under anaerobic conditions. Growth occurs between 25 and 45°C, with optimal growth observed at 37°C. Cells stain Gram-positive, are non-endospore forming and are motile. Cells are Gram-positive, catalase-positive, oxidase-positive. D-glucose, D-fructose, D-saccharose, D-trehalose, ribose, mannitol, mannose were used as carbon source. Positive reactions were observed for tryptophane deaminase, acetoin and gelatinase production. Weak reactions were obtained for L-rhamnose, esculine, salicine, D-cellobiose and gentiobiose. Cells are susceptible to amoxicillin, rifampicin, ciprofloxacin, gentamicin, doxycycline and vancomycin but resistant to trimethoprim/sulfamethoxazole and metronidazole.

The G+C content of the genome is 34.10%. The 16S rRNA and genome sequences are deposited in GenBank under accession numbers JX101689 and CAPG00000000, respectively. The type strain AP8T (= CSUR P201 = DSM 26092) was isolated from the fecal flora of a female suffering from anorexia nervosa in Marseille, France.

Notes

Declarations

Acknowledgements

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

Authors’ Affiliations

(1)
URMITE, Faculté de médecine, Aix-Marseille Université

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