Open Access

Genome sequence and description of Bacteroides timonensis sp. nov.

  • Dhamodharan Ramasamy1,
  • Jean-Christophe Lagier1,
  • Morgane Rossi-Tamisier1,
  • Anne Pfleiderer1,
  • Caroline Michelle1,
  • Carine Couderc1,
  • Didier Raoult1, 2 and
  • Pierre-Edouard Fournier1Email author
Standards in Genomic Sciences20149:9031181

https://doi.org/10.4056/sigs.5389564

Published: 15 June 2014

Abstract

Bacteroides timonensis strain AP1T (= CSUR P194 = DSM 26083) is the type strain of B. timonensis sp. nov. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old French Caucasoid female who suffered from severe anorexia nervosa. Bacteroides timonensis is a Gram-negative, obligate anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 7,130,768 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 43.3% and contains 5,786 protein-coding and 59 RNA genes, including 2 rRNA genes.

Keywords

Bacteroides timonensis genome culturomics taxono-genomics

Introduction

Bacteroides timonensis strain AP1T (= CSUR P194 = DSM 26083) is the type strain of B. timonensis sp. nov. This bacterium was isolated from the stool sample of a 21-year-old French Caucasoid female in an effort of cultivating individually all bacterial species within human feces [1]. It is a Gram-negative, anaerobic, indole-positive rod-shaped bacillus.

The conventional genetic parameters used in the delineation of bacterial species include 16S rRNA sequence identity and phylogeny [2,3], genomic G + C content diversity and DNA-DNA hybridization (DDH) [4,5]. These tools have limitations, notably because their cutoff values vary across species or genera [6]. With the introduction of high-throughput sequencing techniques [7], a wealth of genomic data was made available for many bacterial species. We recently proposed to include genomic data in a polyphasic approach to describe new bacterial taxa (taxono-genomics) [8]. This strategy combines phenotypic characteristics, notably the MALDI-TOF MS spectrum, and genomic analysis [837].

Here, we present a summary classification and a set of features for B. timonensis sp. nov. strain AP1T (= CSUR P194 = DSM 26083) together with the description of the complete genome sequencing and annotation. These characteristics support the circumscription of the type species, B. timonensis.

The genus Bacteroides (Castellani and Chalmers 1919) was created in 1919 [38]. Currently, it is one of the largest genera among the human gut microbiota [39], and consists of 91 species and 5 subspecies with validly published names [40]. Bacteroides species are Gram-negative, non-spore-forming, non-motile and anaerobic rods that are generally isolated from the gastrointestinal tract of mammals [41]. They have symbiotic relationships with humans and play many beneficial roles on normal intestinal physiology and function. Several Bacteroides species are identified as opportunistic pathogens when isolated from anaerobic infections [42].

Classification and features

A stool sample was collected from 21-year-old French Caucasoid female who suffered from severe restrictive anorexia nervosa from the age of 12 years. At the time of sample collection, she had been hospitalized for recent aggravation of her medical condition (BMI: 10.4 kg/m2). The patient’s written consent and the agreement of the local ethics committee of the IFR48 (Marseille, France) were obtained under agreement number 09-022. The feces sample of this patient was stored at −80°C immediately after collection. Strain AP1T (Table 1) was isolated in November 2011 after 1 month of incubation in Columbia agar (BioMerieux, Marcy l’Etoile, France). Several other new bacterial species were isolated from this stool specimen using various culture conditions.
Table 1.

Classification and general features of Bacteroides timonensis strain AP1T according to the MIGS recommendations [43]

MIGS ID

Property

Term

Evidence codea

 

Current classification

Domain Bacteria

TAS [44]

  

Phylum Bacteroidetes

TAS [45,46]

  

Class Bacteroidia

TAS [45,47]

  

Order Bacteroidales

TAS [45,48]

  

Family Bacteroidaceae

TAS [49,50]

  

Genus Bacteroides

IDA [49,5154]

  

Species Bacteroides timonensis

IDA

  

Type strain AP1T

IDA

 

Gram stain

Negative

IDA

 

Cell shape

Rod

IDA

 

Motility

Non motile

IDA

 

Sporulation

Non sporulating

IDA

 

Temperature range

Mesophile

IDA

 

Optimum temperature

37°C

IDA

MIGS-6.3

Salinity

Unknown

IDA

MIGS-22

Oxygen requirement

Anaerobic

IDA

 

Carbon source

Unknown

IDA

 

Energy source

Unknown

IDA

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

November 2011

IDA

MIGS-4.1

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 [55]. 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.

When compared to sequences available in GenBank, the 16S rRNA gene sequence of B. timonensis strain AP1T (GenBank accession number JX041639) exhibited an identity of 97.00% with Bacteroides cellulosilyticus (Figure 1). This value was the highest similarity observed, but was lower than the 97.8% 16S rRNA gene sequence threshold recommended by Stackebrandt and Ebers (2006) to delineate a new species without carrying out DNA-DNA hybridization [3], and was in the 74. 8 to 98.7% range of 16S rRNA identity values observed among 41 Bacteroides species with validly published names [56].
Figure 1.

Phylogenetic tree highlighting the position of Bacteroides timonensis strain AP1T relative to other type strains within the Bacteroides genus. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences were obtained using the maximum-likelihood method within the MEGA software. Numbers at the nodes are percentages of bootstrap values obtained from 500 replicates. Prevotella melaninogenica was used as outgroup. The scale bar represents a 2% nucleotide sequence divergence.

Four different growth temperatures (25, 30, 37, 45°C) were tested; growth occurred between 25 and 37°C, but optimal growth was observed at 37°C, 24 hours after inoculation. No growth occurred at 45°C. Colonies were translucent and approximately 0.3 mm in diameter on 5% sheep blood-enriched Columbia agar (BioMerieux). Growth of the strain was tested in the same agar 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 observed under anaerobic and microaerophilic conditions, and only weakly with 5% CO2. No growth occurred under aerobic condition without CO2. Gram staining showed short Gram-negative rods unable to form spores (Figure 1). A motility test was negative. Cells grown on agar are translucent and exhibit a mean diameter of 0.88 µm in electron microscopy (Figure 2, Figure 3).
Figure 2.

Gram staining of B. timonensis strain AP1T

Figure 3.

Transmission electron microscopy of B. timonensis strain AP1T, made using a Morgani 268D (Philips) at an operating voltage of 60kV.The scale bar represents 200 nm

Strain AP1T exhibited catalase but no oxidase activity (Table 2). Using an API Rapid ID 32A strip (BioMerieux), positive reactions were obtained for arginine dihydrolase, α-galactosidase, β-galactosidase, α-glucosidase, β-glucosidase, α-arabinosidase, N-acetyl-β-glucosaminidase, glutamic acid decarboxylase, α-fucosidase, nitrate reduction, indole production, alkaline phosphatase, proline arylamidase, leucyl glycine arylamidase, alanine arylamidase, glutamyl glutamic acid arylamidase, and fermentation of mannose and raffinose. Weak activities were observed for glycine arylamidase and serine arylamidase. Negative reactions were obtained for urease, β-galctosidase-6-phosphatase, β-glucuronidase, arginine arylamidase, phenylalanine arylamidase, leucine arylamidase, pyroglutamic acid arylamidase, tyrosine arylamidase and histidine arylamidase. Using an API 50CH strip (Biomerieux), strain AP1T was asaccharolytic. B. timonensis is susceptible to amoxicillin-clavulanate, ceftriaxon, imipenem, trimethoprim-sulfamethoxazole, metronidazole and doxycycline but resistant to amoxicillin, vancomycin and gentamicin. By comparison with other Bacteroides species, B. timonensis differed in production of indole, nitrate reductase, β-galactosidase and acidification of sugars.
Table 2.

Differential characteristics of Bacteroides species [5767].

Properties

B. timonensis

B. cellulosyticus

B. intestinalis

B. fragilis

B. vulgatus

B. thetaiotaomicron

B. salanitronis

B. helcogenes

B. finegoldii

B. uniformis

Cell diameter (µm)

0.88

2–5

1–3

1.3

0.5–0.8

0.7–2

2–3

1–2

1–2

0.5–2

Oxygen requirement

anaerobic

anaerobic

anaerobic

anaerobic

anaerobic

anaerobic

anaerobic

anaerobic

anaerobic

anaerobic

Gram stain

+

Salt requirement

+

+

+

+

na

na

na

na

+

+

Motility

Endospore formation

+

na

Indole

+

+

+

+

+

Production of

          

Alkaline phosphatase

+

+

+

Na

+

+

+

na

+

na

Catalase

+

+

+

na

+

na

Oxidase

+

na

+

na

na

na

na

na

na

Nitrate reductase

+

na

na

+

Urease

na

na

na

na

na

β-galactosidase

+

+

na

+

+

+

+

+

N-acetyl-glucosamine

+

+

+

na

na

+

na

na

+

+

Acid from

          

L-Arabinose

w

+

+

+

+

Ribose

+

na

+

na

na

na

na

Mannose

+

+

+

+

+

+

+

+

+

Mannitol

Sucrose

+

+

+

+

+

+

+

+

+

D-glucose

+

+

+

+

+

+

+

+

+

D-fructose

+

+

+

+

+

 

+

na

na

D-maltose

+

+

+

+

+

+

+

+

+

D-lactose

w

+

+

+

+

+

+

+

+

Habitat

human gut

human gut

human gut

human gut

human gut

human gut

human gut

pig gut

human gut

human gut

Bacteroides timonensis strain AP1T, B. cellulosilyticus strain DSM 14838, B. intestinalis strain DSM 17393, B. fragilis strain YCH46, B. vulgatus strain ATCC 8482, B. thetaiotaomicron strain VPI-5482, B. salanitronis strain DSM 18170, B. helcogenes strain P 36–108, B. finegoldii strain DSM 17565 and B. uniformis strain ATCC 8492 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 [68]. Briefly, a pipette tip was used to pick one isolated bacterial colony from a culture agar plate and spread it as a thin film on a MTP 384 MALDI-TOF target plate (Bruker Daltonics, Leipzig, Germany). Twelve distinct deposits from twelve isolated colonies were performed for strain AP1T. Each smear was overlaid with 2 µL of matrix solution (saturated solution of alpha-cyano-4-hydroxycinnamic acid) in 50% acetonitrile, 2.5% tri-fluoracetic acid, and allowed to dry for 5 minutes. Measurements were performed with a Microflex spectrometer (Bruker). Spectra were recorded in the positive linear mode for the mass range of 2,000 to 20,000 Da (parameter settings: ion source 1 (ISI), 20kV; IS2, 18.5 kV; lens, 7 kV). A spectrum was obtained after 675 shots with variable laser power. The time of acquisition was between 30 seconds and 1 minute per spot. The twelve AP1T spectra were imported into the MALDI BioTyper software (version 2.0, Bruker) and analyzed by standard pattern matching (with default parameter settings) against the main spectra of 3,769 bacteria, including 129 spectra from 98 Bacteroides species. The method of identification included the m/z from 3,000 to 15,000 Da. For every spectrum, a maximum of 100 peaks were compared with spectra in database. The resulting score enabled the identification of tested species, or not: a score ≥ 2 with a validly published species enabled identification at the species level, a score ≥ 1.7 but < 2 enabled identification at the genus level, and a score < 1.7 did not enable any identification. No significant MALDI-TOF score was obtained for strain AP1T against the Bruker database, suggesting that our isolate was not a member of a known species. We added the spectrum from strain AP1T to our database (Figure 4). Finally, the gel view showed the spectral differences with other members of the genus Bacteroides (Figure 5).
Figure 4.

Reference mass spectrum from B. timonensis strain AP1T. Spectra from 12 individual colonies were compared and a reference spectrum was generated.

Figure 5.

Gel view comparing B. timonensis strain AP1T to other Bacteroides species. The gel view displays the raw spectra of loaded spectrum files 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 code. The grey scale bar on the right y-axis indicate the relation between the shade of grey a peak is displayed with and the peak intensity in arbitrary units. Displayed species are detailed in the left column.

Genome sequencing information

Genome project history

The organism was selected for sequencing on the basis of its phylogenetic position and 16S rRNA gene sequence similarity to members of the genus Bacteroides, and is part of a study of the human digestive flora aiming at isolating all bacterial species within human feces [1]. It was the ninety-ninth genome of a Bacteroides species and the first genome of B. timonensis sp. nov. The GenBank accession number is CBVI000000000 and consists of 211 contigs. Table 3 shows the project information and its association with MIGS version 2.0 compliance [43].
Table 3.

Project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

High-quality draft

MIGS-28

Libraries used

454 GS paired-end 3-kb library

MIGS-29

Sequencing platform

454 GS FLX Titanium

MIGS-31.2

Fold coverage

35.76

MIGS-30

Assemblers

gsAssembler

MIGS-32

Gene calling method

PRODIGAL

Growth conditions and DNA isolation

B. timonensis sp. nov., strain AP1T (= CSUR P194 = DSM 26083) was grown on 5% sheep blood-enriched Columbia agar (BioMerieux) at 37°C in anaerobic atmosphere. Bacteria grown on four Petri dishes were harvested and resuspended in 4x100µL of TE buffer. Then, 200µL of this suspension was diluted in 1ml TE buffer for lysis treatment that included a 30-minute incubation with 2.5 µg/µL lysozyme at 37°C, followed by an overnight incubation with 20 µg/µL proteinase K at 37°C. Extracted DNA was then purified using 3 successive phenol-chloroform extractions and ethanol precipitation at −20°C overnight. After centrifugation, the DNA was resuspended in 160 µL TE buffer. The yield and concentration was measured by the Quant-it Picogreen kit (Invitrogen) on the Genios-Tecan fluorometer at 88.6 ng/µl.

Genome sequencing and assembly

Five µg of DNA was mechanically fragmented on Covaris device (KBioScience-LGC Genomics, Teddington, UK) using miniTUBE-blue. The DNA fragmentation was visualized through an Agilent 2100 BioAnalyzer on a DNA labchip 7500 with an average size of 2.950kb. A 3 kb paired-end library was constructed according to the 454 GS FLX Titanium paired-end protocol (Roche). Circularization and nebulization were performed and generated a pattern with a mean size of 513 bp. After PCR amplification through 17 cycles followed by double size selection, the single stranded paired-end library was quantified with the Quant-it Ribogreen kit (Invitrogen) on the Genios Tecan fluorometer at 243 pg/µL. The library concentration equivalence was calculated as 8.69 × 108 molecules/µL. The library was stored at −20°C until further use.

The paired-end library was clonally amplified with 0.5cpb and 1cbp in 8 SV-emPCR reactions with the GS Titanium SV emPCR Kit (Lib-L) v2 (Roche). The yields of the emPCR reactions were 4.65 and 7.29% respectively, within the recommended range of 5 to 20% from the Roche procedure. Approximately 790,000 beads were loaded on a 1/4 region of a GS Titanium PicoTiterPlate PTP Kit 70×75 and sequenced with the GS Titanium Sequencing Kit XLR70 (Roche). The run was performed overnight and then analyzed on the cluster through the gsRunBrowser and Newbler assembler (Roche). A total of 802,249 passed filter wells were obtained and generated 255Mb with a length average of 314 bp. These sequences were assembled using Newbler (Roche) with 90% identity and 40bp as overlap. The final assembly identified 63 scaffolds and 211 large contigs (>1,500bp) generating a genome size of 7.13 Mb which corresponds to a coverage of 35.76× genome equivalent.

Genome annotation

Open Reading Frames (ORFs) were predicted using Prodigal [69] with default parameters. However, the predicted ORFs were excluded if they spanned a sequencing gap region. The predicted bacterial protein sequences were searched against the GenBank [70] and Clusters of Orthologous Groups (COG) databases using BLASTP. The tRNAs and rRNAs were predicted using the tRNAScan-SE [71] and RNAmmer [72] tools, respectively. Signal peptides and numbers of transmembrane helices were predicted using SignalP [73] and TMHMM [74], respectively. Mobile genetic elements were predicted using PHAST [75] and RAST [76]. 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. Artemis [77] and DNA Plotter [78] 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 [79].

To estimate the mean level of nucleotide sequence similarity at the genome level between B. timonensis and 9 other members of the genus Bacteroides (Table 6), we used the Average Genomic Identity Of gene Sequences (AGIOS) in-house software [8]. Briefly, this software uses the Proteinortho software [80] for the pairwise detection of orthologous proteins between 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. B. timonensis strain AP1T was compared to B. intestinalis strain DSM 17393 (GenBank accession number NZ_ABJL00000000), B. cellulosilyticus strain DSM 14838 (NZ_ACCH00000000), B. fragilis strain YCH46 (NC_006347), B. vulgatus strain ATCC 8482 (NC_009614), B. thetaiotaomicron strain VPI-5482 (NC_004663), B. salanitronis strain DSM 18170 (NC_015164), B. helcogenes strain P36-108 (NC_014933), B. finegoldii strain DSM 17565 (NZ_ABXI00000000) and B. uniformis strain ATCC 8492 (AAYH00000000).

Genome properties

The genome is 7,130,768 bp long (1 chromosome, but no plasmid) with a 43.3% G+C content (Figure 6 and Table 4). Of the 5,845 predicted genes, 5,786 were protein-coding genes and 59 were RNAs, including 1 complete rRNA operon. A total of 3,111 genes (53.22%) were assigned a putative function and 3,283 genes were identified as ORFans (56.16%). Strain AP1T possesses a variety of mobile genetic elements. These include 6 prophages of 13.70, 14.60, 10.51, 8.18, 9.91 and 12.79 Kb, respectively) and 91 transposable elements belonging to 18 transposon families that include the putative mobilization protein BF0133, the putative conjugative transposon mobilization protein BF0132, the hypothetical protein clustered with conjugative transposons BF0131, TraA-CTn, TraB-CTn, TraD-CTn, TraE-CTn, TraF-CTn, TraG-CTn, TraH-CTn, TraI-CTn, TraJ-CTn, TraK-CTn, TraL-CTn, TraM-CTn, TraN-CTn, TraO-CTn and TraQ-CTn. The properties and statistics of the genome are summarized in Tables 4 and 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: open reading frames oriented in the forward (colored by COG categories) direction, open reading frames oriented in the reverse (colored by COG categories) direction, RNA operon (red), and tRNAs (green), GC content plot, and GC skew (purple: negative values, olive: positive values)..

Table 4.

Nucleotide content and gene count levels of the genome

Attribute

Value

% of totala

Genome size (bp)

7,130,768

 

DNA coding region (bp)

6,434,142

90.23

DNA G+C content (bp)

3,087,622

43.30

Number of replicons

1

 

Extra chromosomal element

0

 

Total genes

5,845

100

RNA genes

59

1.01

Protein-coding genes

5,786

98.99

Genes with function prediction

3,111

53.22

Genes assigned to COGs

2,820

48.24

Genes with peptide signals

435

7.44

Genes with transmembrane helices

456

7.80

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

156

2.66

Translation

A

0

0

RNA processing and modification

K

234

4.00

Transcription

L

200

3.42

Replication, recombination and repair

B

0

0

Chromatin structure and dynamics

D

27

0.46

Cell cycle control, mitosis and meiosis

Y

0

0

Nuclear structure

V

107

1.83

Defense mechanisms

T

240

4.22

Signal transduction mechanisms

M

361

6.17

Cell wall/membrane biogenesis

N

5

0.08

Cell motility

Z

0

0

Cytoskeleton

W

0

0

Extracellular structures

U

65

1.11

Intracellular trafficking and secretion

O

89

1.52

Posttranslational modification, protein turnover, chaperones

C

168

2.87

Energy production and conversion

G

369

6.31

Carbohydrate transport and metabolism

E

212

3.62

Amino acid transport and metabolism

F

73

1.25

Nucleotide transport and metabolism

H

130

2.22

Coenzyme transport and metabolism

I

87

1.48

Lipid transport and metabolism

P

202

3.42

Inorganic ion transport and metabolism

Q

47

0.80

Secondary metabolites biosynthesis, transport and catabolism

R

518

8.86

General function prediction only

S

197

3.37

Function unknown

-

2966

51.26

Not in COGs

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

Genome comparison with other Bacteroides genomes

Here, we compare the genome of B. timonensis with those of B. intestinalis, DSM 17393, B. cellulosilyticus DSM 14838, B. fragilis YCH46, B. vulgatus ATCC 8482, B. thetaiotaomicron VPI-5482, B. salanitronis DSM 18170, B. helcogenes P 36–108, B. finegoldii DSM 17565 and B. uniformis ATCC 8492. The draft genome of B. timonensis (7.13Mb) is larger than all other studied genomes (Table 6A). It also exhibits a higher G+C content than all other genomes except B. salanitronis, B. helcogenes and B. uniformis (43.3, 46.4, 44.7 and 46.4%, respectively). B. timonensis has a higher gene content (5,786) than any other compared genome. The distribution of genes into COG categories was similar in all 10 compared genomes except in the N category (cell motility) for which B. fragilis, B. vulgatus, B. salanitronis, B. helcogenes and B. uniformis were underrepresented (Figure 7). In addition, B. timonensis shared 2,956, 3,081, 2,159, 2,099, 2,379, 1,721, 2,001, 2,039 and 2,268 orthologous genes with B. intestinalis, B. cellulosilyticus, B. fragilis, B. vulgatus, B. thetaiotaomicron, B. salanitronis, B. helcogenes, B. finegoldii and B. uniformis, respectively. Among compared genomes except B. timonensis, AGIOS values ranged from 70.16 between B. salitronis and B. cellulosilyticus to 88.16% between B. intestinalis and B. cellulosilyticus. When B. timonensis was compared to other species, AGIOS values ranged from 70.29 with B. salitronis to 93.61% with B. cellulosilyticus (Table 6B).
Figure 7.

Distribution of predicted genes of B. timonensis and 9 other Bacteroides species into COG categories. B. uni = B. uniformis, B. fin = B. finegoldii, B. hel = B. helcogenes, B. sal = B. salanitronis, B. the = B. thetaiotaomicron, B. vul = B. vulgatus, B. fra = B. fragilis, B. cel = B. cellulosilyticus, B. int = B. intestinalis, B. tim = B. timonensis.

Table 6A.

Genomic comparison of B. timonensis with 9 other Bacteroides species.

Species

Strain

Genome accession number

Genome size (Mb)

G+C content

B. timonensis

AP1

CBVI010000000

7.13

43.3

B. intestinalis

DSM 17393

NZ_ABJL00000000

6.05

42.8

B. cellulosilyticus

DSM 14838

NZ_ACCH00000000

6.87

42.7

B. fragilis

YCH46

NC_006347

5.28

43.2

B. vulgatus

ATCC 8482

NC_009614

5.16

42.2

B. thetaiotaomicron

VPI-5482

NC_004663

6.26

42.8

B. salanitronis

DSM 18170

NC_015164

4.24

46.4

B. helcogenes

P 36–108

NC_014933

4.0

44.7

B. finegoldii

DSM 17565

NZ_ABXI00000000

4.89

42.9

B. uniformis

ATCC 8492

AAYH00000000

4.72

46.4

Species, Strain, GenBank accession number, genome size and G+C content of all compared genomes.

Table 6B.

Genomic comparison of B. timonensis with 9 other Bacteroides species.

 

B. tim

B. int

B. cel

B. fra

B. vul

B. the

B. sal

B. hel

B. fin

B. uni

B. tim

5,786

2,956

3,081

2,159

2,099

2,379

1,721

2,001

2,039

2,268

B. int

87.73

4,911

2,967

2,085

2,036

2,361

1,667

1,963

2,066

2,278

B. cell

93.61

88.16

5,719

2,130

2,078

2,380

1,655

1,990

2,017

2,231

B. fra

73.76

74.43

73.92

4,184

1,927

2,174

1,517

1,893

1,880

1,995

B. vul

71.91

71.74

71.48

71.87

4,066

2,100

1,638

1,743

1,859

1,898

B. the

73.99

74.65

73.87

75.42

72.21

4,778

1,601

1,891

2,191

2,039

B. sal

70.29

70.65

70.16

70.35

72.18

70.50

3,553

1,466

1,580

1,584

B. hel

76.40

76.51

76.41

74.15

71.62

73.64

70.68

3,244

1,703

1,930

B. fin

74.28

75.01

74.45

75.72

72.22

81.24

70.77

73.99

4,485

1,920

B. uni

77.08

76.83

76.80

74.25

72.45

74.36

71.32

79.37

74.77

4,663

numbers of orthologous proteins shared between genomes (above diagonal), AGIOS values (below diagonal) and numbers of proteins per genome (bold numbers).

B. tim = B. timonensis, B. int = B. intestinalis, B. cel = B. cellulosilyticus, B. fra = B. fragilis, B. vul = B. vulgatus, B. the = B. thetaiotaomicron, B. sal = B. salanitronis, B. hel = B. helcogenes, B. uni = B. uniformis, B. fin = B. finegoldii.

Conclusion

On the basis of phenotypic, phylogenetic and genomic analyses (taxono-genomics), we formally propose the creation of Bacteroides timonensis sp. nov. that contains strain AP1T. This strain was isolated from the fecal flora of a 21-year-old woman who suffered from severe anorexia nervosa.

Description of B. timonensis sp. nov.

Bacteroides timonensis (tim.o.nen’sis. L. masc. adj. timonensis, of Timone, the name of the hospital where strain AP1T was first cultivated).

Colonies are translucent and 0.3 mm in diameter on blood-enriched Columbia agar. Cells are rod-shaped with a mean diameter of 0.88 µm. Optimal growth is achieved anaerobically, although the strain is able to grow under microaerophilic conditions, and weakly with 5% CO2. Growth occurs between 25°C and 37°C, with optimal growth at 37°C. Cells stain Gram-negative and are not motile. Positive reactions for catalase, arginine dihydrolase, α-galactosidase, β-galactosidase, α-glucosidase, β-glucosidase, α-arabinosidase, N-acetyl-β-glucosaminidase, glutamic acid decarboxylase, α-fucosidase, nitrate reduction, indole production, alkaline phosphatase, proline arylamidase, leucyl glycine arylamidase, alanine arylamidase, glutamyl glutamic acid arylamidase, and fermentation of mannose and raffinose.

Weak activities are observed for glycine arylamidase and serine arylamidase. Negative reactions are obtained for urease, β-galctosidase-6-phosphatase, β-glucuronidase, arginine arylamidase, phenylalanine arylamidase, leucine arylamidase, pyroglutamic acid arylamidase, tyrosine arylamidase and histidine arylamidase. Using an API 50CH strip (Biomerieux), strain AP1T is asaccharolytic. Cells are susceptible to susceptible to amoxicillin-clavulanate, ceftriaxone, imipenem, trimethoprim-sulfamethoxazole, metronidazole and doxycycline but resistant to amoxicillin, vancomycin and gentamicin.

The 16S rRNA and genome sequences are deposited in GenBank under accession numbers JX041639 and CBVI000000000, respectively. The G+C content of the genome is 43.3%. The habitat of the organism is the digestive tract. The type strain AP1T (= CSUR P194 = DSMZ 26083) was isolated from the fecal flora of a French Caucasoid female who suffered from a severe restrictive form of anorexia nervosa. This strain has been found in Marseille, France.

Declarations

Acknowledgements

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

Authors’ Affiliations

(1)
Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université
(2)
King Fahd Medical Research Center, King Abdul Aziz University

References

  1. Lagier JC, Armougom F, Million M, Hugon P, Pagnier I, Robert C, Bittar F, Fournous G, Gimenez G, Maraninchi M, et al. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 2012; 18:1185–1193. PubMedView ArticlePubMedGoogle Scholar
  2. Tindall BJ, Rosselló-Móra R, Busse HJ, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266. PubMed http://dx.doi.org/10.1099/ijs.0.016949-0View ArticlePubMedGoogle Scholar
  3. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155.Google Scholar
  4. Wayne LG, Brenner DJ, Colwell PR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematic. Int J Syst Bacteriol 1987; 37:463–464. http://dx.doi.org/10.1099/00207713-37-4-463View ArticleGoogle Scholar
  5. Rossello-Mora R. DNA-DNA Reassociation Methods Applied to Microbial Taxonomy and Their Critical Evaluation. In: Stackebrandt E (ed), Molecular Identification, Systematics, and population Structure of Prokaryotes. Springer, Berlin, 2006; p. 23–50.View ArticleGoogle Scholar
  6. Welker M, Moore ER. Applications of whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry in systematic microbiology. Syst Appl Microbiol 2011; 34:2–11. PubMed http://dx.doi.org/10.1016/j.syapm.2010.11.013View ArticlePubMedGoogle Scholar
  7. Kokcha S, Mishra AK, Lagier JC, Million M, Leroy Q, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Bacillus timonensis sp. nov. Stand Genomic Sci 2012; 6:346–355. PubMed http://dx.doi.org/10.4056/sigs.2776064PubMed CentralView ArticlePubMedGoogle Scholar
  8. Ramasamy D, Mishra AK, Lagier JC, Padhmanabhan R, Rossi-Tamisier M, Sentausa E, Raoult D, Fournier PE. A polyphasic strategy incorporating genomic data for the taxonomic description of new bacterial species. Int J Syst Evol Microbiol 2013; 64:384–391. PubMed http://dx.doi.org/10.1099/ijs.0.057091-0View ArticleGoogle Scholar
  9. Lagier JC, El Karkouri K, Nguyen TT, Armougom F, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Anaerococcus senegalensis sp. nov. Stand Genomic Sci 2012; 6:116–125. PubMed http://dx.doi.org/10.4056/sigs.2415480PubMed CentralView ArticlePubMedGoogle Scholar
  10. Mishra AK, Gimenez G, Lagier JC, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Alistipes senegalensis sp. nov. Stand Genomic Sci 2012; 6:304–314. http://dx.doi.org/10.4056/sigs.2625821View ArticleGoogle Scholar
  11. Lagier JC, Armougom F, Mishra AK, Ngyuen TT, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Alistipes timonensis sp. nov. Stand Genomic Sci 2012; 6:315–324. PubMed http://dx.doi.org/10.4056/sigs.2685971PubMed CentralView ArticlePubMedGoogle Scholar
  12. Mishra AK, Lagier JC, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Clostridium senegalense sp. nov. Stand Genomic Sci 2012; 6:386–395. PubMedPubMed CentralPubMedGoogle Scholar
  13. Mishra AK, Lagier JC, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Peptoniphilus timonensis sp. nov. Stand Genomic Sci 2012; 7:1–11. PubMed http://dx.doi.org/10.4056/sigs.2956294PubMed CentralView ArticlePubMedGoogle Scholar
  14. Mishra AK, Lagier JC, Rivet R, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Paenibacillus senegalensis sp. nov. Stand Genomic Sci 2012; 7:70–81. PubMed http://dx.doi.org/10.4056/sigs.3056450PubMed CentralView ArticlePubMedGoogle Scholar
  15. Lagier JC, Gimenez G, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov. Stand Genomic Sci 2012; 7:200–209. PubMedPubMed CentralPubMedGoogle Scholar
  16. Kokcha S, Ramasamy D, Lagier JC, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Brevibacterium senegalense sp. nov. Stand Genomic Sci 2012; 7:233–245. PubMed http://dx.doi.org/10.4056/sigs.3256677PubMed CentralView ArticlePubMedGoogle Scholar
  17. Ramasamy D, Kokcha S, Lagier JC, N’Guyen TT, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Aeromicrobium massilense sp. nov. Stand Genomic Sci 2012; 7:246–257. PubMed http://dx.doi.org/10.4056/sigs.3306717PubMed CentralView ArticlePubMedGoogle Scholar
  18. Lagier JC, Ramasamy D, Rivet R, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Cellulomonas massiliensis sp. nov. Stand Genomic Sci 2012; 7:258–270. PubMed http://dx.doi.org/10.4056/sigs.3316719PubMed CentralView ArticlePubMedGoogle Scholar
  19. Lagier JC, Karkouri K, Rivet R, Couderc C, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov. Stand Genomic Sci 2013; 7:343–356. PubMed http://dx.doi.org/10.4056/sigs.3246665PubMed CentralView ArticlePubMedGoogle Scholar
  20. Mishra AK, Hugon P, Nguyen TT, Robert C, Couderc C, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Peptoniphilus obesi sp. nov. Stand Genomic Sci 2013; 7:357–369. PubMed http://dx.doi.org/10.4056/sigs.32766871PubMed CentralView ArticlePubMedGoogle Scholar
  21. Mishra AK, Lagier JC, Nguyen TT, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Peptoniphilus senegalensis sp. nov. Stand Genomic Sci 2013; 7:370–381. PubMed http://dx.doi.org/10.4056/sigs.3366764PubMed CentralView ArticlePubMedGoogle Scholar
  22. Lagier JC, Karkouri K, Mishra AK, Robert C, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Enterobacter massiliensis sp. nov. Stand Genomic Sci 2013; 7:399–412. PubMed http://dx.doi.org/10.4056/sigs.3396830PubMed CentralView ArticlePubMedGoogle Scholar
  23. Hugon P, Ramasamy D, Rivet R, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Alistipes obesi sp. nov. Stand Genomic Sci 2013; 7:427–439. PubMed http://dx.doi.org/10.4056/sigs.3336746PubMed CentralView ArticlePubMedGoogle Scholar
  24. Hugon P, Mishra AK, Nguyen TT, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Brevibacillus massiliensis sp. nov. Stand Genomic Sci 2013; 8:1–14. PubMed http://dx.doi.org/10.4056/sigs.3466975PubMed CentralView ArticlePubMedGoogle Scholar
  25. Mishra AK, Hugon P, Nguyen TT, Raoult D, 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. PubMed http://dx.doi.org/10.4056/sigs.3426906PubMed CentralView ArticlePubMedGoogle Scholar
  26. Ramasamy D, Lagier JC, Gorlas A, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Bacillus massiliosenegalensis sp. nov. Stand Genomic Sci 2013; 8:264–278. PubMed http://dx.doi.org/10.4056/sigs.3496989PubMed CentralView ArticlePubMedGoogle Scholar
  27. Ramasamy D, Lagier JC, Nguyen TT, Raoult D, 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. PubMed http://dx.doi.org/10.4056/sigs.3567059PubMed CentralView ArticlePubMedGoogle Scholar
  28. Mishra AK, Pfleiderer A, Lagier JC, Robert C, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Bacillus massilioanorexius sp. nov. Stand Genomic Sci 2013; 8:465–479. PubMed http://dx.doi.org/10.4056/sigs.4087826PubMed CentralView ArticlePubMedGoogle Scholar
  29. Hugon P, Ramasamy D, Robert C, Couderc C, Raoult D, 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. PubMed http://dx.doi.org/10.4056/sigs.4047997PubMed CentralView ArticlePubMedGoogle Scholar
  30. Padmanabhan R, Lagier JC, Dangui NPM, Michelle C, Couderc C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Megasphaera massiliensis. Stand Genomic Sci 2013; 8:525–538. PubMed http://dx.doi.org/10.4056/sigs.4077819PubMed CentralView ArticlePubMedGoogle Scholar
  31. Mishra AK, Edouard S, Dangui NPM, Lagier JC, Caputo A, Blanc-Tailleur C, Ravaux I, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Nosocomiicoccus massiliensis sp. nov. Stand Genomic Sci 2013; 9:205–219. PubMed http://dx.doi.org/10.4056/sigs.4378121PubMed CentralView ArticlePubMedGoogle Scholar
  32. Mishra AK, Lagier JC, Robert C, Raoult D, Fournier PE. Genome sequence and description of Timonella senegalensis gen. nov., sp. nov., a new member of the suborder Micrococcineae. Stand Genomic Sci 2013; 8:318–335. PubMed http://dx.doi.org/10.4056/sigs.3476977PubMed CentralView ArticlePubMedGoogle Scholar
  33. Keita MB, Diene SM, Robert C, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Bacillus massiliogorillae sp. nov. Stand Genomic Sci 2013; 9:93–105. PubMed http://dx.doi.org/10.4056/sigs.4388124PubMed CentralView ArticlePubMedGoogle Scholar
  34. Mediannikov O, El Karkouri K, Robert C, Fournier PE, Raoult D. Non contiguous-finished genome sequence and description of Bartonella florenciae sp. nov. Stand Genomic Sci 2013; 9:185–196. PubMed http://dx.doi.org/10.4056/sigs.4358060PubMed CentralView ArticlePubMedGoogle Scholar
  35. Lo CI, Mishra AK, Padhmanabhan R, Samb Ba B, Gassama Sow A, Robert C, Couderc C, Faye N, Raoult D, Fournier PE, Fenollar F. Non contiguous-finished genome sequence and description of Clostridium dakarense sp. nov. Stand Genomic Sci 2013; 9:14–27. PubMed http://dx.doi.org/10.4056/sigs.4097825PubMed CentralView ArticlePubMedGoogle Scholar
  36. Mishra AK, Hugon P, Robert C, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Peptoniphilus grossensis sp. nov. Stand Genomic Sci 2012; 7:320–330. PubMedPubMed CentralPubMedGoogle Scholar
  37. Mediannikov O, El Karkouri K, Diatta G, Robert C, Fournier PE, Raoult D. Non contiguous-finished genome sequence and description of Bartonella senegalensis sp. nov. Stand Genomic Sci 2013; 8:279–289. PubMed http://dx.doi.org/10.4056/sigs.3807472PubMed CentralView ArticlePubMedGoogle Scholar
  38. Garrity GM, Holt JG. Taxonomic Outline of the Archaea and Bacteria. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 155–166.Google Scholar
  39. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA. Diversity of the human intestinal microbial flora. Science 2005; 308:1635–1638. PubMed http://dx.doi.org/10.1126/science.1110591PubMed CentralView ArticlePubMedGoogle Scholar
  40. List of Prokaryotic names with standing nomenclature (LPSN). http://www.bacterio.cict.fr.
  41. Smith CJ, Rocha ER, Paster BJ. 2005. The medically important Bacteroides spp. in health and disease. In The Prokaryotes, an evolving electronic resource for the microbiological community, Release 3.19 (18.3.2005) (http://141-150-157-117:8080/prokPUB/index.htm). Edited by M. Dworkin. New York: Springer.Google Scholar
  42. Finegold SM, George WL. 1989. Anaerobic Infections in Humans. San Diego: Academic Press.Google Scholar
  43. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541–547. PubMed http://dx.doi.org/10.1038/nbt1360PubMed CentralView ArticlePubMedGoogle Scholar
  44. Woese CR, Kandler O, 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. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576PubMed CentralView ArticlePubMedGoogle Scholar
  45. Validation List No. 143. Int J Syst Evol Microbiol 2012; 62:1–4. http://dx.doi.org/10.1099/ijs.0.039487-0
  46. Krieg NR, Ludwig W, Euzéby J, Whitman WB. Phylum XIV. Bacteroidetes phyl. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 4, Springer, New York, 2011, p. 25.Google Scholar
  47. Krieg NR. Class I. Bacteroidia class. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 4, Springer, New York, 2011, p. 25.Google Scholar
  48. Krieg NR. Order I. Bacteroidales ord. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 4, Springer, New York, 2011, p. 25.Google Scholar
  49. Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225–420. http://dx.doi.org/10.1099/00207713-30-1-225View ArticleGoogle Scholar
  50. Pribram E. Klassification der Schizomyceten. Klassifikation der Schizomyceten (Bakterien), Franz Deuticke, Leipzig, 1933, p. 1–143.Google Scholar
  51. Castellani A, Chalmers AJ. Genus Bacteroides Castellani and Chalmers, 1918. Manual of Tropical Medicine, Third Edition, Williams, Wood and Co., New York, 1919, p. 959–960.Google Scholar
  52. Holdeman LV, Moore WEC. Genus I. Bacteroides Castellani and Chalmers 1919, 959. In: Buchanan RE, Gibbons NE (eds), Bergey’s Manual of Determinative Bacteriology, Eighth Edition, The Williams and Wilkins Co., Baltimore, 1974, p. 385–404.Google Scholar
  53. Cato EP, Kelley RW, Moore WEC, Holdeman LV. Bacteroides zoogleoformans, Weinberg, Nativelle, and Prévot 1937) corrig. comb. nov.: emended description. Int J Syst Bacteriol 1982; 32:271–274. http://dx.doi.org/10.1099/00207713-32-3-271View ArticleGoogle Scholar
  54. Shah HN, Collins MD. Proposal to restrict the genus Bacteroides (Castellani and Chalmers) to Bacteroides fragilis and closely related species. Int J Syst Bacteriol 1989; 39:85–87. http://dx.doi.org/10.1099/00207713-39-1-85View ArticleGoogle Scholar
  55. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25–29. PubMed http://dx.doi.org/10.1038/75556PubMed CentralView ArticlePubMedGoogle Scholar
  56. 16S Yourself database. (http://www.mediterranee-infection.com/article.php?larub=152&titre=16s-yourself).
  57. Eggerth AH, Gagnon BH. The Bacteroides of Human Feces. J Bacteriol 1933; 25:389–413. PubMedPubMed CentralPubMedGoogle Scholar
  58. Shah HN. 1992. The genus Bacteroides and related taxa. In The Prokaryotes, 2nd edn, pp. 3593–3607. Edited by Balows A, Truper HG, Dworkin M, Harder M & Schleifer KH. New York: Springer.View ArticleGoogle Scholar
  59. Bakir MA, Kitahara M, Sakamoto M, Matsumoto M, Benno Y. Bacteroides intestinalis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2006; 56:151–154. PubMed http://dx.doi.org/10.1099/ijs.0.63914-0View ArticlePubMedGoogle Scholar
  60. Robert C, Chassard C, Lawson PA, Bernalier-Donadille A. Bacteroides cellulosilyticus sp. nov., a cellulolytic bacterium from the human gut microbial community. Int J Syst Evol Microbiol 2007; 57:1516–1520. PubMed http://dx.doi.org/10.1099/ijs.0.64998-0View ArticlePubMedGoogle Scholar
  61. Johnson JL. Taxonomy of the Bacteroides I. Deoxyribonucleic acid homologies among Bacteroides fragilis and other saccharolytic Bacteroides species. Int J Syst Evol Microbiol 1978; 28:245–256.Google Scholar
  62. Cato EP, Johnson JL. Reinstatement of species rank for Bacteroides fragilis, B. ovatus, B. distasonis, B. thetaiotaomicron, and B. vulgatus: Designation of Neotype Strains for Bacteroides fragilis (Veillon and Zuber) Castellani and Chalmers and Bacteroides thetaiotaomicron (Distaso) Castellani and Chalmers. Int J Syst Bacteriol 1976; 26:230–237. http://dx.doi.org/10.1099/00207713-26-2-230View ArticleGoogle Scholar
  63. Xu J, Bjursell MK, Himrod J, Deng S, Carmichael LK, Chiang HC, Hooper LV, Gordon JI. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 2003; 299:2074–2076. PubMed http://dx.doi.org/10.1126/science.1080029View ArticlePubMedGoogle Scholar
  64. Lan PT, Sakamoto M, Sakata S, Benno Y. Bacteroides barnesiaesp. nov., Bacteroides salanitronis sp. nov. and Bacteroides gallinarum sp. nov., isolated from chicken caecum. Int J Syst Evol Microbiol 2006; 56:2853–2859. PubMed http://dx.doi.org/10.1099/ijs.0.64517-0View ArticlePubMedGoogle Scholar
  65. Benno Y, Watabe J, Mitsuoka T. Bacteroides pyogenes sp. nov., Bacteroides suis sp. nov., and Bacteroides helcogenes sp. nov., New Species from Abscesses and Feces of Pigs. Syst Appl Microbio 1983; 14:396–407.View ArticleGoogle Scholar
  66. Pati A, Gronow S, Zeytun A, Lapidus A, Nolan M, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, et al. Complete genome sequence of Bacteroides helcogenes type strain (P 36–108). Stand Genomic Sci 2011; 4:45–53. PubMed http://dx.doi.org/10.4056/sigs.1513795PubMed CentralView ArticlePubMedGoogle Scholar
  67. Bakir MA, Kitahara M, Sakamoto M, Matsumoto M, Benno Y. Bacteroides finegoldii sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2006; 56:931–935. PubMed http://dx.doi.org/10.1099/ijs.0.64084-0View ArticlePubMedGoogle Scholar
  68. Seng P, Drancourt M, Gouriet F, La SB, Fournier PE, Rolain JM, 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. PubMed http://dx.doi.org/10.1086/600885View ArticlePubMedGoogle Scholar
  69. Prodigal. http://prodigal.ornl.gov/
  70. Benson DA, Karsch-Mizrachi I, Clark K, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res 2012; 40:D48–D53. PubMed http://dx.doi.org/10.1093/nar/gkr1202PubMed CentralView ArticlePubMedGoogle Scholar
  71. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964. PubMed http://dx.doi.org/10.1093/nar/25.5.0955PubMed CentralView ArticlePubMedGoogle Scholar
  72. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108. PubMed http://dx.doi.org/10.1093/nar/gkm160PubMed CentralView ArticlePubMedGoogle Scholar
  73. Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004; 340:783–795. PubMed http://dx.doi.org/10.1016/j.jmb.2004.05.028View ArticlePubMedGoogle Scholar
  74. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001; 305:567–580. PubMed http://dx.doi.org/10.1006/jmbi.2000.4315View ArticlePubMedGoogle Scholar
  75. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res 2011; 39:W347–W352. PubMed http://dx.doi.org/10.1093/nar/gkr485PubMed CentralView ArticlePubMedGoogle Scholar
  76. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75. PubMed http://dx.doi.org/10.1186/1471-2164-9-75PubMed CentralView ArticlePubMedGoogle Scholar
  77. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B. Artemis: sequence visualization and annotation. Bioinformatics 2000; 16:944–945. PubMed http://dx.doi.org/10.1093/bioinformatics/16.10.944View ArticlePubMedGoogle Scholar
  78. Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 2009; 25:119–120. PubMed http://dx.doi.org/10.1093/bioinformatics/btn578PubMed CentralView ArticlePubMedGoogle Scholar
  79. Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004; 14:1394–1403. PubMed http://dx.doi.org/10.1101/gr.2289704PubMed CentralView ArticlePubMedGoogle Scholar
  80. Lechner M, Findeib S, Steiner L, Marz M, Stadler PF, Prohaska SJ. Proteinortho: Detection of (Co-)orthologs in large-scale analysis. BMC Bioinformatics 2011; 12:124. PubMed http://dx.doi.org/10.1186/1471-2105-12-124PubMed CentralView ArticlePubMedGoogle Scholar

Copyright

© The Author(s) 2014