- Open Access
Genome sequence and description of Bacteroides timonensis sp. nov.
Standards in Genomic Sciencesvolume 9, pages1181–1197 (2014)
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.
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 . 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 . With the introduction of high-throughput sequencing techniques , 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) . This strategy combines phenotypic characteristics, notably the MALDI-TOF MS spectrum, and genomic analysis [8–37].
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 . Currently, it is one of the largest genera among the human gut microbiota , and consists of 91 species and 5 subspecies with validly published names . Bacteroides species are Gram-negative, non-spore-forming, non-motile and anaerobic rods that are generally isolated from the gastrointestinal tract of mammals . 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 .
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.
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 , and was in the 74. 8 to 98.7% range of 16S rRNA identity values observed among 41 Bacteroides species with validly published names .
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).
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.
Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) MS protein analysis was carried out as previously described . 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).
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 . 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 .
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.
Open Reading Frames (ORFs) were predicted using Prodigal  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  and Clusters of Orthologous Groups (COG) databases using BLASTP. The tRNAs and rRNAs were predicted using the tRNAScan-SE  and RNAmmer  tools, respectively. Signal peptides and numbers of transmembrane helices were predicted using SignalP  and TMHMM , respectively. Mobile genetic elements were predicted using PHAST  and RAST . 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  and DNA Plotter  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 .
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 . Briefly, this software uses the Proteinortho software  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).
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.
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).
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.
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. PubMed
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.0.016949-0
Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155.
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/10.1099/00207713-37-4-463
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.
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.2010.11.013
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.2776064
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.0.057091-0
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.2415480
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.2625821
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.2685971
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. PubMed
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.2956294
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.3056450
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. PubMed
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.3256677
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.3306717
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.3316719
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.3246665
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.32766871
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.3366764
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.3396830
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.3336746
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.3466975
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.3426906
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.3496989
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.3567059
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.4087826
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.4047997
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.4077819
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.4378121
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.3476977
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.4388124
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.4358060
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.4097825
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. PubMed
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.3807472
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.
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.1110591
List of Prokaryotic names with standing nomenclature (LPSN). http://www.bacterio.cict.fr.
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.
Finegold SM, George WL. 1989. Anaerobic Infections in Humans. San Diego: Academic Press.
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/nbt1360
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.87.12.4576
Validation List No. 143. Int J Syst Evol Microbiol 2012; 62:1–4. http://dx.doi.org/10.1099/ijs.0.039487-0
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.
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.
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.
Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225–420. http://dx.doi.org/10.1099/00207713-30-1-225
Pribram E. Klassification der Schizomyceten. Klassifikation der Schizomyceten (Bakterien), Franz Deuticke, Leipzig, 1933, p. 1–143.
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.
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.
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/10.1099/00207713-32-3-271
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/10.1099/00207713-39-1-85
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/10.1038/75556
16S Yourself database. (http://www.mediterranee-infection.com/article.php?larub=152&titre=16s-yourself).
Eggerth AH, Gagnon BH. The Bacteroides of Human Feces. J Bacteriol 1933; 25:389–413. PubMed
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.
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.0.63914-0
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.0.64998-0
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.
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/10.1099/00207713-26-2-230
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.1080029
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.0.64517-0
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.
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.1513795
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.0.64084-0
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/10.1086/600885
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/gkr1202
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/25.5.0955
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/gkm160
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.2004.05.028
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.2000.4315
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/gkr485
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/10.1186/1471-2164-9-75
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/16.10.944
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/btn578
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.2289704
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/10.1186/1471-2105-12-124
The authors thank the Xegen Company (www.xegen.fr) for automating the genomic annotation process. This study was funded by the Mediterranee-Infection Foundation.