Skip to main content
Download PDF

Non-contiguous finished genome sequence and description of Bacteroides neonati sp. nov., a new species of anaerobic bacterium

Standards in Genomic Sciences volume 9, pages 794–806 (2014)Cite this article

Abstract

Bacteroides neonati strain MS4T, is the type strain of Bacteroides neonati sp. nov., a new species within the genus Bacteroides. This strain, whose genome is described here, was isolated from a premature neonate stool sample. B. neonati strain MS4T is an obligate anaerobic Gram-negative bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5.03 Mbp long genome exhibits a G+C content of 43.53% and contains 4,415 protein-coding and 91 RNA genes, including 9 rRNA genes.

Introduction

Bacteroides neonati strain MS4T (= CSUR P 1500= DSM 26805), is the type strain of Bacteroides neonati sp. nov., and a new member of the genus Bacteroides. This bacterium is a Gram-negative, anaerobic, non spore-forming, indole positive bacillus that was isolated from a preterm neonate stool sample, during a study prospecting stool samples from patients with necrotizing enterocolitis and controls [unpublished].

To define a new bacterial species or genus, the “gold standard” method is the DNA-DNA hybridization and G+C content determination [1]. However, those methods are expensive, and poorly reproducible. The development of PCR and sequencing methods led to new ways of classifying bacterial species, using in particular 16S rDNA sequences with an internationally-validated cutoff value [2]. More recently, new bacterial genera and species are described using high throughput genome sequencing and mass spectrometric analyses, which allow access to a wealth of genetic and proteomic information [3,4]. We propose the description of a new bacterial species, using genome sequences, MALDI-TOF spectra, and the main phenotypic characteristics, as previously done [5–22].

Here we present a summary classification and a set of features for B. neonati sp. nov. strain MS4T (= CSUR P 1500= DSM 26805) together with a description of the complete genomic sequencing and annotation. These characteristics support the circumscription of a novel species, B. neonati sp. nov., within the Bacteroides genus.

The Bacteroidaceae family is currently comprised of 3 genera: Acetomicrobium, Anaerorhabdus and Bacteroides. It is a heterogeneous family, grouping anaerobic and morphologically variable bacteria, and it is defined mainly on the basis of phylogenetic analyses of 16S rDNA sequences. The most closely related species to Bacteroides neonati sp. nov. is Bacteroides graminisolvens [23] followed by Bacteroides intestinalis [24]. Bacteroides neonati is a strictly anaerobic Gram negative, non spore-forming bacterium.

Classification and features

A stool sample was collected from a patient during a case-control study analyzing the fecal microbiota of premature neonates with necrotizing enterocolitis, using MALDI-TOF and 16S rRNA gene sequencing [unpublished]. After collection in Marseille, the specimen was preserved at −80°C. Strain MS4T (Table 1) was isolated in October 2012, by anaerobic cultivation on 5% sheep blood-enriched Columbia agar (BioMerieux, Marcy l’Etoile, France). This strain exhibited a 94% nucleotide sequence similarity with Bacteroides graminisolvens [23] and a 94% nucleotide sequence similarity with Bacteroides intestinalis [24]. Those similarity values are lower than the threshold recommended to delineate a new species without carrying out DNA-DNA hybridization [38]. In the inferred phylogenetic tree, it forms a distinct lineage close to Bacteroides graminisolvens (Figure 1).

Figure 1.
figure 1

Phylogenetic tree highlighting the position of Bacteroides neonati MS4T relative to other type strains within the genus Bacteroides. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained using the maximum-likelihood method within the MEGA 4 software [39]. Numbers at the nodes are bootstrap values obtained by repeating the analysis 500 times the analysis to generate a majority consensus tree. The scale bar represents a 2% nucleotide sequence divergence.

Full size image
Table 1. Classification and general features of Bacteroides neonati strain MS4T according to the MIGS recommendations [25]
Full size table

Seven different growth temperatures (23°C, 25°C, 28°C, 32°C, 35°C, 37°C, 50°C) were tested; no growth occurred at 50°C, growth occurred between 23° and 37°C, and optimal growth was observed at 37°C.

Colonies are punctiform, medium-sized, grey, shiny and round on blood-enriched Columbia agar under anaerobic conditions using GENbag anaer (BioMérieux). Bacteria were grown on blood-enriched Columbia agar (Biomerieux) and in Trypticase-soy TS broth medium, under anaerobic conditions using GENbag anaer (BioMérieux). They also were grown under anaerobic conditions on BHI agar and on BHI agar supplemented with 1% NaCl. Growth was achieved only anaerobically on blood-enriched Columbia agar and weakly on BHI agar as well as BHI agar supplemented with 1% NaCl after 72h incubation. Gram staining showed plump non spore-forming Gram-negative bacilli (Figure 2). The motility test was negative. Cells grow anaerobically in TS broth medium have a mean wide of 0.681 µm (min = 0.323 µm; max = 0.878 µm) and a mean length of 2.165 µm (min = 1.402; max = 2.951), as determined using electron microscopic observation after negative staining (Figure 3).

Figure 2.
figure 2

Gram staining of B. neonati strain MS4T

Full size image
Figure 3.
figure 3

Transmission electron micrograph of B. neonati strain MS4T, using a Morgani 268D (Philips) at an operating voltage of 60kV. The scale bar represents 1,000 nm.

Full size image

Strain MS4T exhibited catalase activity but no oxidase activities. Using API 20A, a positive reaction could be observed only weekly for Gelatinase. Using Api Zym, a positive reaction was observed for alkaline phosphatase (40 nmol of hydrolyzed substrata), acid phosphatase (40 nmol), naphtolphosphohydrolase (20 nmol), esterase (20 nmol), esterase lipase (5 nmol), alpha-galactosidase (5 nmol), beta-galactosidase (20 nmol), beta-glucuronidase (30 nmol), beta-glucosidase (5 nmol), N-acetyl-beta-glucosaminidase (40 nmol) and alpha-fucosidase (5 nmol). Using Api rapid id 32A, a positive reaction was observed for alpha-galactosidase, alpha-glucosidase, N-acetyl-beta-glucosaminidase and alpha-fucosidase. Regarding antibiotic susceptibility, Bacteroides neonati was susceptible to clavulanate-amoxicillin, imipenem and metronidazole. When compared to the representative species within the genus Bacteroides, B. neonati exhibits the phenotypic characteristics detailed in Table 2 [40].

Table 2. Differential characteristics of Bacteroides neonati sp. nov., strain MS4T, B. graminisolvens strain DSM 19988T, and B. intestinalis strain DSM 17397T.
Full size table

Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) MS protein analysis was carried out as previously described [41]. A pipette tip was used to pick one isolated bacterial colony from a culture agar plate, and to spread it as a thin film on a MTP 384 MALDI-TOF target plate (Bruker Daltonics, Germany). Ten distinct depos-its were done for strain MS4T from ten isolated colonies. Each smear was overlaid with 2 µL of matrix solution (saturated solution of alpha-cyano-4-hydroxycinnamic acid) in 50% acetoni-trile, 2.5% tri-fluoracetic acid, and allowed to dry for five 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 set-tings: ion source 1 (ISI), 20kV; IS2, 18.5 kV; lens, 7 kV). A spectrum was obtained after 675 shots at a variable laser power. The time of acquisition was between 30 seconds and 1 minute per spot. The ten MS4T spectra were imported into the MALDI Bio Typer software (version 2.0, Bruker) and ana-lyzed by standard pattern matching (with default parameter settings) against the main spectra of 6,335 bacteria, in the Bio Typer database. The method of identification includes the m/z from 3,000 to 15,000 Da. For every spectrum, 100 peaks at most were taken into account and com-pared with the spectra in database. A score ena-bled the identification, or not, from the tested spe-cies: a score > 2 with a validated species enabled the identification at the species level; a score > 1.7 but < 2 enabled the identification at the genus lev-el; and a score < 1.7 did not enable any identifica-tion. For strain MS4T, the best-obtained score was 1.345, which is not significant, suggesting that our isolate was not a member of a known genus. The reference spectrum from strain MS4T (Figure 4) was added to our database. A dendrogram was constructed with the MALDI Bio Typer software (version 2.0, Bruker), comparing the reference spectrum of strain MS4 with reference spectra of 26 bacterial species, all belonging to the order of Bacteroidetes. In this dendrogram, strain MS4T ap-pears as a separated branch within the genus Bacteroides (Figure 5).

Figure 4.
figure 4

Reference mass spectrum from B. neonati strain MS4T. Spectra from 10 individual colonies were compared and a reference spectrum was generated.

Full size image
Figure 5.
figure 5

Dendrogram based on the comparison of the B. neonati strain MS4T MALDI-TOF reference spectrum, and 72 other species of the genus of Bacteroides.

Full size image

Genome sequencing and annotation

Genome project history

The organism was selected for sequencing because it was isolated from a premature neonate stool sample as part of a study prospecting stool samples from patients with necrotizing enterocolitis.

The Genbank accession number is HG726019 – HG726036 and consists of 18 scaffolds with a total of 35 contigs. Table 3 shows the project information and its compliance with MIGS version 2.0 standards.

Table 3. Project information
Full size table

Growth conditions and DNA isolation

Bacteroides neonati strain MS4T (= CSUR P 1500= DSM 26805), was grown on blood agar medium at 37°C under anaerobic conditions. Eight petri dishes were spread and resuspended in 5 ×100µl of G2 buffer. A first mechanical lysis was performed using glass powder in the Fastprep-24 Sample Preparation system (MP Biomedicals, USA) with 2×20 second bursts. DNA was then incubated with lysozyme (30 minutes at 37°C) and extracted on a BioRobot EZ 1 Advanced XL (Qiagen). The DNA was then concentrated and purified on a Qiamp kit (Qiagen). The yield and the concentration were measured by the Quant-it Picogreen kit (Invitrogen) on the Genios_Tecan fluorometer at 15.7ng/µl.

Genome sequencing and assembly

A 3 kb paired end library was pyrosequenced on the 454 Roche Titanium. This project was loaded on a 1/4 region on PTP Picotiterplates. 5 µg of DNA was mechanically fragmented with a Hydroshear device (Digilab, Holliston, MA, USA) with an enrichment size at 3–4kb. The DNA fragmentation was visualized with an Agilent 2100 BioAnalyzer on a DNA labchip 7500 with an average size of 3.2 kb. The library was constructed according to the 454 Titanium paired end protocol supplied by the manufacturer. Circularization and nebulization were performed and generated a pattern with an optimal at 604 bp. After PCR amplification through 15 cycles followed by double size selection, the single stranded paired end library was then quantified on the Agilent 2100 BioAnalyzer on a RNA pico 6,000 labchip at 91pg/µL. The library concentration equivalence was calculated at 2.76 × 108 molecules/µL. The library was stored at −20°C until used.

The library was clonally amplified with 0.5 and 1 cpb in 2 emPCR reactions in each condition with the GS Titanium SV emPCR Kit (Lib-L) v2. The yield of the emPCR was 10.46 and 11.53%, respectively, according to the quality expected by the range of 5 to 20% from the Roche procedure. 790,000 beads were loaded on the GS Titanium PicoTiterPlates PTP Kit 70×75 sequenced with the GS Titanium Sequencing Kit XLR70

The 454 sequencing generated 811,269 reads (180 Mb, coverage of 27.0) assembled into contigs and scaffolds using Newbler version 2.8 (Roche, 454 Life Sciences) and Mira assembler v3.2 [42]. The obtained contigs were combined using the Opera software v1.2 [43] in tandem with GapFiller V1.10 [44] to reduce the set. Finally, some manual refinements using CLC Genomics software v4.7.2 (CLC bio, Aarhus, Denmark) were made. The genome consists of 35 contigs in18 scaffolds.

Genome annotation

Non-coding genes and miscellaneous features were predicted using RNAmmer [45], ARAGORN [46], Rfam [47], PFAM [48]. Open Reading Frames (ORFs) were predicted using Prodigal [49] with default parameters but the predicted ORFs were excluded if they spanned a sequencing GAP region. The functional annotation was achieved using BLASTP [50] against the GenBank database [51] and the Clusters of Orthologous Groups (COGs) database [52,53].

Genome properties

The genome of B. neonati strain MS4T is estimated to be 5.03 Mb long with a G+C content of 43.53% (Figure 6 and Table 4). A total of 4,415 protein-coding and 91 RNA genes, including 9 rRNA genes, 65 tRNA, 1 tmRNA and 39 miscellaneous other RNA were founded. The majority of the protein-coding genes were assigned a putative function (69.26%) while the remaining ones were annotated as hypothetical proteins. The properties and the statistics of the genome are summarized in Table 4. The distribution of genes into COG functional categories is presented in Table 5.

Figure 6.
figure 6

Circular representation of the Bacteroides neonati chromosome. Circles from the center to the outside: GC skew (green/purple), GC content (black), tRNA (dark red), rRNA (purple), tmRNA (blue), miscellaneous RNA (deep blue) on forward strand, genes on forward strand colored by COGs categories, scaffolds in alternative grays, genes on reverse strand colored by COGs, tRNA (dark red), rRNA (purple), tmRNA (blue), miscellaneous RNA (deep blue) on reverse strand.

Full size image
Table 4. Nucleotide content and gene count levels of the genome
Full size table
Table 5. Number of genes associated with the 25 general COG functional categories.
Full size table

Insights into the genome sequence

We made some brief comparisons against Bacteroides intestinalis DSM 17393 (ABJL00000000) that is currently the closest available sequenced genome. This genome is composed of 8 contigs (ABJL02000001-ABJL02000008).

The draft genome sequence of Bacteroides neonati has a smaller size compared to the Bacteroides intestinalis (respectively, 5.03 Mb against 6.05 Mb). The G+C content is very close to Bacteroides intestinalis (respectively, 43.53% and 42.8%). Bacteroides neonati has slightly fewer genes (4,506 genes against 4,984 genes), and a higher ratio of genes per Mb (895.82 genes/Mb against 823.8 genes/Mb).

Table 6 presents the difference of gene number (in percentage) related to each COG category between Bacteroides neonati and Bacteroides intestinalis. The proportion of COG is highly similar between the two species. The maximum difference is related to the COG “Carbohydrate Metabolism and transportation” which does not exceed 2.28%.

Table 6. Percentage of genes associated with the 25 general COG functional categories for B. neonati and B. intestinalis DSM 20548.
Full size table

Conclusion

On the basis of phenotypic, phylogenetic and genomic analysis, we formally propose the creation of Bacteroides neonati that contains the strain MS4T. This bacterium has been found in Marseille, France.

Description of Bacteroides neonati sp. nov.

Bacteroides neonati (neo.na’ti L. gen. masc. n. neonati, because this new species has been first isolated from a preterm neonate stool sample)is a Gram-negative bacillus; Obligate anaerobic; Non-spore-forming bacterium; Grows on axenic medium at 37°C in anaerobic atmosphere; Negative for indole; Non motile; The G+C content of the genome is 43.53%. The type strain is MS4T (= CSUR P 1500 = DSM 26805).

References

  1. 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.

    Chapter  Google Scholar 

  2. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155.

    Google Scholar 

  3. 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

    Article  CAS  PubMed  Google Scholar 

  4. 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

    Article  CAS  PubMed  Google Scholar 

  5. Kokcha S, Michra 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  6. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. 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

    Article  CAS  Google Scholar 

  8. Lagier JC, Armougom F, Mishra AK, Nguyen 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  9. Michra AK, Lagier JC, Robert C, Raoult D, Fournier PE. Non-contiguous-finished genome sequence and description of Clostridium senegalenses sp. nov. Stand Genomic Sci 2012; 6:386–395. PubMed

    Google Scholar 

  10. Michra AK, Lagier JC, Robert C, Raoult D, Fournier PE. Non-contiguous-finished genome sequence and description of Peptinophilus timonensis sp. nov. Stand Genomic Sci 2012; 7:1–11. PubMed

    Google Scholar 

  11. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  12. 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; 10.4056/sigs.3086474. PubMed

    PubMed Central  CAS  PubMed  Google Scholar 

  13. Roux V, El Karkouri K, Lagier JC, Robert C, Raoult D. Non-contiguous finished genome sequence and description of Kurthia massiliensis sp. nov. Stand Genomic Sci 2012; 7:221–232. PubMed http://dx.doi.org/10.4056/sigs.3206554

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  14. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  15. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  16. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  17. Lagier JC, El Karkouri K, Rivet R, Couderc C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Senegalemassilia anaerobia sp. nov. Stand Genomic Sci 2013; 7:343–356. PubMed http://dx.doi.org/10.4056/sigs.3246665

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. Mishra AK, Hugon P, Lagier JC, 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  19. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. Lagier JC, El 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  21. Hugon P, Ramasamy D, Lagier JC, Rivet R, Couderc C, 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  22. Mishra AK, Hugon P, Robert C, Couderc 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

    PubMed Central  CAS  PubMed  Google Scholar 

  23. Nishiyama T, Ueki A, Kaku N, Watanabe K, Ueki K. Bacteroides graminisolvens sp. nov., a xylanolytic anaerobe isolated from a methanogenic reactor treating cattle waste. Int J Syst Evol Microbiol 2009; 59:1901–1907. PubMed http://dx.doi.org/10.1099/ijs.0.008268-0

    Article  CAS  PubMed  Google Scholar 

  24. Bakir MA, Kitahara M, Sakamoto M, Matsumoto M, Benno Y. Bacteroides intestinalis sp. nov., isolated from human feces. Int J Syst Evol Microbiol 2006; 56:151–154. PubMed http://dx.doi.org/10.1099/ijs.0.63914-0

    Article  PubMed  Google Scholar 

  25. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  26. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eukarya. Proc Natl Acad Sci USA 1990; 87:4576–4579. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  27. Editor L. Validation List No. 143. Int J Syst Evol Microbiol 2012; 62:1–4.

    Article  Google Scholar 

  28. 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 

  29. 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 

  30. 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 

  31. Skerman VBD, Sneath PHA. Approved list of bacterial names. Int J Syst Bact 1980; 30:225–420. http://dx.doi.org/10.1099/00207713-30-1-225

    Article  Google Scholar 

  32. Pribram E. Klassification der Schizomyceten. Klassifikation der Schizomyceten (Bakterien), Franz Deuticke, Leipzig, 1933, p. 1–143.

    Google Scholar 

  33. 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 

  34. 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 

  35. 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

    Article  CAS  Google Scholar 

  36. 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

    Article  Google Scholar 

  37. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  38. Schloss PD, Handelsman J. Status of the microbial census. Microbiol Mol Biol Rev 2004; 68:686–691. PubMed http://dx.doi.org/10.1128/MMBR.68.4.686-691.2004

    Article  PubMed Central  PubMed  Google Scholar 

  39. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007; 24:1596–1599. PubMed http://dx.doi.org/10.1093/molbev/msm092

    Article  CAS  PubMed  Google Scholar 

  40. Murdoch DA. Gram-positive anaerobic cocci. Clin Microbiol Rev 1998; 11:81–120. PubMed

    PubMed Central  CAS  PubMed  Google Scholar 

  41. Seng P, Drancourt M, Gouriet F, La Scola B, 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

    Article  CAS  PubMed  Google Scholar 

  42. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WEG, Wetter T, Suhai S. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 2004; 14:1147–1159. PubMed http://dx.doi.org/10.1101/gr.1917404

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  43. Gao S, Sung WK, Nagarajan N. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. J Comput Biol 2011; 18:1681–1691. PubMed http://dx.doi.org/10.1089/cmb.2011.0170

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  44. Boetzer M, Pirovano W. Toward almost closed genomes with GapFiller. Genome Biol 2012; 13:R56. PubMed http://dx.doi.org/10.1186/gb-2012-13-6-r56

    Article  PubMed Central  PubMed  Google Scholar 

  45. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  46. Laslett D, Canback B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 2004; 32:11–16. PubMed http://dx.doi.org/10.1093/nar/gkh152

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  47. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nucleic Acids Res 2003; 31:439–441. PubMed http://dx.doi.org/10.1093/nar/gkg006

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  48. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, et al. The Pfam protein families database. Nucleic Acids Res 2012; 40:D290–D301. PubMed http://dx.doi.org/10.1093/nar/gkr1065

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  49. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. PubMed http://dx.doi.org/10.1186/1471-2105-11-119

    Article  PubMed Central  PubMed  Google Scholar 

  50. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421. PubMed http://dx.doi.org/10.1186/1471-2105-10-421

    Article  PubMed Central  PubMed  Google Scholar 

  51. Benson DA, Karsch-Mizrachi I, Clark K, Lipman DJ, Ostell J, Sayers EW. Gen Bank. Nucleic Acids Res 2012; 40:D48–D53. PubMed http://dx.doi.org/10.1093/nar/gkr1202

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  52. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genomoe-scale analysis of protein functions and evolution. Nucleic Acids Res 2000; 28:33–36. PubMed http://dx.doi.org/10.1093/nar/28.1.33

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  53. Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science 1997; 278:631–637. PubMed http://dx.doi.org/10.1126/science.278.5338.631

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Facultés de Médecine et de Pharmacie, Aix-Marseille Université, France

    Nadim Cassir, Olivier Croce, Isabelle Pagnier, Samia Benamar, Carine Couderc, Catherine Robert, Didier Raoult & Bernard La Scola

Authors
  1. Nadim Cassir
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Olivier Croce
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Isabelle Pagnier
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Samia Benamar
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Carine Couderc
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Catherine Robert
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Didier Raoult
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Bernard La Scola
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Bernard La Scola.

Rights and permissions

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Cassir, N., Croce, O., Pagnier, I. et al. Non-contiguous finished genome sequence and description of Bacteroides neonati sp. nov., a new species of anaerobic bacterium. Stand in Genomic Sci 9, 794–806 (2014). https://doi.org/10.4056/sigs.5159098

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.4056/sigs.5159098

Keywords

Environmental Microbiome

ISSN: 2524-6372