Open Access

Genome sequence and description of Alistipes senegalensis sp. nov.

  • Ajay Kumar Mishra1,
  • Gregory Gimenez1,
  • Jean-Christophe Lagier1,
  • Catherine Robert1,
  • Didier Raoult1 and
  • Pierre-Edouard Fournier1Email author
Standards in Genomic Sciences20126:6030304

https://doi.org/10.4056/sigs.2625821

Published: 30 July 2012

Abstract

Alistipes senegalensis strain JC50T is the type strain of A. senegalensis sp. nov., a new species within the Alistipes genus. This strain, whose genome is described here, was isolated from the fecal flora of an asymptomatic patient. A. senegalensis is an anaerobic Gram-negative rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,017,609 bp long genome (1 chromosome, but no plasmid) contains 3,113 protein-coding and 50 RNA genes, including 5 rRNA genes.

Keywords

Alistipes senegalensis genome

Introduction

Alistipes senegalensis strain JC50T (= CSUR P156= DSM 25460) is the type strain of A. senegalensis sp. nov. This bacterium was isolated from the stool of a healthy Senegalese patient as part of a “culturomics” study aiming at cultivating all species in human feces, individually.

Bacterial species definition is a matter of debate. This is notably due to the high cost, poor reproducibility and inter-laboratory comparability of the “gold standard” of DNA-DNA hybridization and G+C content determination [1]. In contrast, the development of PCR and sequencing methods, both of which are now widely available and cost-effective, has profoundly changed the way of classifying prokaryotes. Using 16S rRNA sequences with internationally-agreed upon cutoff values, despite variations among taxa, enabled the taxonomic classification or reclassification of hundreds of taxa [2]. More recently, high throughput genome sequencing and mass spectrometric analyses of bacteria have given unprecedented access to a wealth of genetic and proteomic information [3]. As a consequence, we propose to use a polyphasic approach [4] to describe new bacterial taxa that includes their genome sequence, MALDI-TOF spectrum and major phenotypic characteristics (habitat, Gram staining, culture and metabolic characteristics, and when applicable, pathogenicity). Here we present a summary classification and a set of features for A. senegalensis sp. nov. strain JC50T together with the description of the complete genomic sequencing and annotation. These characteristics support the creation of the A. senegalensis species.

The genus Alistipes (Rautio et al. 2003) was created in 2003 [5] and is composed of strictly anaerobic Gram-negative rods that resemble the Bacteroides fragilis group in that most species are bile-resistant and indole-positive; however, they are only weakly saccharolytic and most species produce light brown pigment only on laked rabbit blood agar [6]. The genus Alistipes contains five species namely A. finegoldii, A. putredinis [5], A. indistinctus [7], A. onderdonkii and A. shahii [8].

The natural habitat of the genus Alistipes is unknown but most of the species have mostly been isolated from blood samples, appendiceal tissue samples, perirectal and brain abscess material [9,10]. Predisposing factors to Alistipes sp. bacteremia include malignant neoplasms, recent gastrointestinal or obstetric-gynecologic surgery, intestinal obstruction, and use of cytotoxic agents or corticosteroids [9]. A 16S rRNA phylogenetic analysis revealed that A. senegalensis is closely related to A. shahii. To the best of our knowledge, our report is the first to report the isolation of Alistipes sp. from the normal fecal flora.

Classification and features

A stool sample was collected from a healthy 16-year-old male Senegalese volunteer patient living in Dielmo (rural villages in the Guinean-Sudanian zone in Senegal), who was included in a research protocol. The patient gave an informed and signed consent, and the agreement of the National Ethics Committee of Senegal and the local ethics committee of the IFR48 (Marseille, France) (agreement 09-022), were obtained. The fecal specimen was preserved at −80°C after collection and sent to Marseille. Strain JC50T (Table 1) was isolated in March 2011 by anaerobic cultivation on Schaedler agar with kanamycin and vancomycin (Becton Dickinson, Heidelberg, Germany).
Table 1.

Classification and general features of Alistipes senegalensis strain JC50T

MIGS ID

Property

Term

Evidence codea

 

Current classification

Domain Bacteria

TAS [11]

 

Phylum Bacteroidetes

TAS [12,13]

 

Class Bacteroidia

TAS [12,14]

 

Order Bacteroidales

TAS [12,15]

 

Family Rikenellaceae

TAS [12,16]

 

Genus Alistipes

TAS [12,17]

 

Species Alistipes senegalensis

IDA

 

Type strain JC50T

IDA

 

Gram stain

negative

IDA

 

Cell shape

bacilli

IDA

 

Motility

nonmotile

IDA

 

Sporulation

nonsporulating

IDA

 

Temperature range

mesophileic

IDA

 

Optimum temperature

37°C

IDA

MIGS-6.3

Salinity

growth in BHI medium + 1% NaCl

IDA

MIGS-22

Oxygen requirement

anaerobic

IDA

 

Carbon source

unknown

 
 

Energy source

unknown

 

MIGS-6

Habitat

human gut

IDA

MIGS-15

Biotic relationship

free living

IDA

MIGS-14

Pathogenicity

unknown

 
 

Biosafety level

2

 
 

Isolation

human feces

 

MIGS-4

Geographic location

Senegal

IDA

MIGS-5

Sample collection time

September 2010

IDA

MIGS-4.1

Latitude

14.49740

IDA

MIGS-4.2

Longitude

-14.452362

IDA

MIGS-4.3

Depth

surface

IDA

MIGS-4.4

Altitude

51 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 [18]. 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.

The strain exhibited 97.0%, 16S rRNA nucleotide sequence similarity with A. shahii, the phylogenetically-closest validly published Alistipes species.(Figure 1). Although the level of sequence similarity of the 16S rRNA gene sequence is not uniform across taxa, this value was lower than the 98.7% 16S rRNA gene sequence threshold recommended by Stackebrandt and Ebers to delineate a new species without carrying out DNA-DNA hybridization [19].
Figure 1.

Phylogenetic tree highlighting the position of Alistipes senegalensis strain JC50T relative to other type strains within the Alistipes genus. GenBank accession numbers are indicated in parentheses. The tree was inferred from the comparison of 16S rRNA gene sequence. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained using the maximum-likelihood method within the MEGA software. Numbers at the nodes are bootstrap values obtained by repeating 500 times the analysis to generate a majority consensus tree. Bacteroides splanchnicus was used as an outgroup. The scale bar represents a 2% nucleotide sequence divergence.

Different growth temperatures (25, 30, 37, 45°C) were tested; no growth occurred at 25°C and 45°C, growth occurred between 30 and 37°C, and optimal growth was observed at 37°C. Colonies were 0.2 to 0.3 mm in diameter on blood-enriched Columbia agar and Brain Heart Infusion (BHI) agar. Growth of the strain was tested under anaerobic and microaerophilic conditions using GENbag anaer and GENbag microaer systems, respectively (BioMérieux), and in the presence of air, with or without 5% CO2 and in aerobic conditions. The optimal growth of the strain was obtained anaerobically, with weak growth being observed under microaerophilic conditions, and no growth observed under aerobic conditions. Gram staining showed Gram negative bacilli. A motility test was negative. Cells grown on agar are Gram-negative rod-shaped bacteria (Figure 2) and have a mean diameter of 0.56 µm (Figure 3) by electron microscopy.
Figure 2.

Gram staining of A. senegalensis strain JC50T

Figure 3.

Transmission electron microscopy of A. senegalensis strain JC50T, using a Morgani 268D (Philips) at an operating voltage of 60kV.The scale bar represents 900 nm.

Strain JC50T exhibited a catalase activity but no oxidase activity. Using API Rapid ID 32A, a positive reaction was obtained for mannose fermentation, proline arylimidase, leucyl glycine arylamidase, alanine arylamidase. A weak reaction was obtained for indole production, α-galactosidase, β-galactosidase, β-glucuronidase, arginine arlyamidase and glycine arylamidase. A. senegalensis is susceptible to penicillin G, imipeneme, amoxicillin + clavulanic acid and clindamycin but resistant to metronidazole and vancomycin.

Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) MS protein analysis was carried out as previously described [20]. Briefly, a pipette tip was used to pick one isolated bacterial colony from a culture agar plate, and spread as a thin film on an MTP 384 MALDI-TOF target plate (Bruker Daltonics, Germany). Four distinct deposits were done for strain JC50T from four isolated colonies. Each smear was overlaid with 2µL of matrix solution (saturated solution of alpha-cyano-4-hydroxycinnamic acid) in 50% acetonitrile, 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 settings: 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 four JC50T spectra were imported into the MALDI Bio Typer software (version 2.0, Bruker) and analyzed by standard pattern matching (with default parameter settings) against the main spectra of 2,843 bacteria, including spectra from three validly published Alistipes species used as reference data, in the Bio Typer database. The method of identification included the m/z from 3,000 to 15,000 Da. For every spectrum, 100 peaks at most were taken into account and compared with the spectra in database. A score enabled the presumptive identification, or discrimination, from the tested species: 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 level; and a score < 1.7 did not enable any identification. Spectra were compared with the Bruker database that contained spectra from the three validated Alistipes species. No significant score was obtained, thus suggesting that our isolate was not a member of a known species. We incremented our database with the spectrum from strain JC50T (Figure 4).
Figure 4.

Reference mass spectrum from A. senegalensis strain JC50T. Spectra from 12 individual colonies were compared and a reference spectrum was generated.

Genome sequencing and annotation

Genome project history

The organism was selected for sequencing on the basis of its phylogenetic position and 16S rRNA similarity to other members of the Alistipes genus, and is part of a “culturomics” study of the human digestive flora aiming at isolating all bacterial species within human feces. It was the second genome of an Alistipes species and the first genome of Alistipes senegalensis sp. nov. A summary of the project information is shown in Table 2. The Genbank accession number is CAHI00000000 and consists of forty contigs. Table 2 shows the project information and its association with MIGS version 2.0 compliance [5].
Table 2.

Project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

High-quality draft

MIGS-28

Libraries used

One 454 paired end 3-kb library

MIGS-29

Sequencing platforms

454 GS FLX Titanium

MIGS-31.2

Fold coverage

35

MIGS-30

Assemblers

Newbler version 2.5.3

MIGS-32

Gene calling method

Prodigal

 

INSDC ID

2000019201

 

GenBank ID

CAHI00000000

 

Genbank Date of Release

January 31, 2012

 

Gold ID

Gi12116

 

NCBI project ID

82331

MIGS-13

Project relevance

Study of the human gut microbiome

Growth conditions and DNA isolation

A. senegalensis sp. nov. strain JC50T, CSUR P156, was grown on blood agar medium at 37°C. Twelve petri dishes were spread and resuspended in 6×100µl of G2 buffer (EZ1 DNA Tissue kit, Qiagen). A first mechanical lysis was performed by glass powder on the Fastprep-24 device (Sample Preparation system) from MP Biomedicals, USA during 2×20 seconds. DNA was then incubated for a lysozyme treatment (30 minutes at 37°C) and extracted through the BioRobot EZ 1 Advanced XL (Qiagen). The DNA was then concentrated and purified on a Qiamp kit (Qiagen). The yield and the concentration was measured by the Quant-it Picogreen kit (Invitrogen) on the Genios_Tecan fluorometer at 62.7 ng/µl.

Genome sequencing and assembly

This project was loaded twice on a 1/4 region for the paired end application and once on a 1/8 region for the shotgun on PTP Picotiterplates. The shotgun library was constructed with 500 ng of DNA as described by the manufacturer Roche with the GS Rapid library Prep kit. DNA (5µg) was mechanically fragmented on the Hydroshear device (Digilab, Holliston, MA, USA) with an enrichment size at 3–4kb. The DNA fragmentation was visualized through the Agilent 2100 BioAnalyzer on a DNA labchip 7500 with an optimal size of 3.563kb. The library was constructed according to the 454_Titanium paired end protocol and manufacturer. Circularization and nebulization were performed and generated a pattern with an optimal at 377 bp. After PCR amplification through 15 cycles followed by double size selection, the single stranded paired end library was then quantified on the Quant-it Ribogreen kit (Invitrogen) on the Genios_Tecan fluorometer at 215pg/µL. The library concentration equivalence was calculated as 10.5E+08 molecules/µL. The library was stocked at −20°C until use.

The shotgun library was clonally amplified with 3 cpb in 3emPCR reactions with the GS Titanium SV emPCR Kit (Lib-L) v2 leading to 13.93% yield of the emPCR. The paired end library was clonally amplified with 1cpb in 4 SV-emPCR reactions leading to 17.56% yield was in the range of 5 to 20% from the Roche procedure. 790,000 beads for a 1/4 Region and 340,000 beads for a 1/8 region were loaded on the GS Titanium PicoTiterPlates PTP Kit 70×75 sequenced with the GS Titanium Sequencing Kit XLR70.

The runs were performed overnight and then analyzed on the cluster through the gsRunBrowser _Roche. Data from 78.55 Mb of passed filter wells were generated with an average of length of 228 bp for the paired end library, and 51.3 Mb with an average length of 417 bp were obtained from the shotgun library. The global passed filter sequences were assembled on the gsAssembler_Roche with 90% identity and 40bp as overlap. The final assembly into 4 scaffolds and 40 large contigs (>1500bp) generated a genome size of 4.01 Mb.

Genome annotation

Open Reading Frames (ORFs) were predicted using Prodigal [21] with default parameters but the predicted ORFs were excluded if they were spanning a sequencing GAP region. The predicted bacterial protein sequences were searched against the GenBank database [22] and the Clusters of Orthologous Groups (COG) databases using BLASTP. The tRNAScanSE tool [23] was used to find tRNA genes, whereas ribosomal RNAs were found by using RNAmmer [24] and BLASTn against the NR database. ORFans were identified if their BLASTP E-value were 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. To estimate the mean level of nucleotide sequence similarity at the genome level between Alistipes species, we compared the ORFs only using BLASTN and the following parameters: a query coverage of ≥ 70% and a minimum nucleotide length of 100 bp.

Genome properties

The genome is 4,017,609 bp long (1 chromosome but no plasmid) with a 58.40% GC content (Figure 5 and Table 3). Of the 3,163 predicted genes, 3,113 were protein-coding genes, and 50 were RNAs. A total of 1,977 genes (62.50%) were assigned a putative function. Eighty-one genes were identified as ORFans (2.6%). The remaining genes were annotated as hypothetical proteins. The properties and statistics of the genome are summarized in Tables 3 and distribution of genes into COG functional categories is presented in Table 4.
Figure 5.

Graphical circular map of the chromosome. From outside to the center: Genes on the forward strand (colored by COG categories), genes on the reverse strand (colored by COG categories), RNA genes (tRNAs green, rRNAs red), GC content, and GC skew.

Table 3.

Nucleotide content and gene count levels of the genome

Attribute

Value

% of totala

Genome size (bp)

4,017,609

 

DNA coding region (bp)

3,670,587

91.36

DNA G+C content (bp)

2,3462,84

58.40

Total genes

3,163

100

RNA genes

50

1.58

Protein-coding genes

3,113

98.41

Genes with function prediction

1,977

62.50

Genes assigned to COGs

1,863

58.90

Genes with peptide signals

712

22.51

Genes with transmembrane helices

645

20.39

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

Table 4.

Number of genes associated with the 25 general COG functional categories

Code

Value

% agea

Description

J

140

4.49

Translation

A

0

0

RNA processing and modification

K

149

4.78

Transcription

L

136

4.37

Replication, recombination and repair

B

0

0

Chromatin structure and dynamics

D

18

0.58

Cell cycle control, mitosis and meiosis

Y

0

0

Nuclear structure

V

44

1.41

Defense mechanisms

T

89

2.85

Signal transduction mechanisms

M

166

5.33

Cell wall/membrane biogenesis

N

7

0.22

Cell motility

Z

0

0

Cytoskeleton

W

0

0

Extracellular structures

U

41

1.32

Intracellular trafficking and secretion

O

67

2.15

Posttranslational modification, protein turnover, chaperones

C

134

4.30

Energy production and conversion

G

222

7.13

Carbohydrate transport and metabolism

E

155

4.98

Amino acid transport and metabolism

F

54

1.73

Nucleotide transport and metabolism

H

73

2.34

Coenzyme transport and metabolism

I

45

1.45

Lipid transport and metabolism

P

138

4.43

Inorganic ion transport and metabolism

Q

18

0.58

Secondary metabolites biosynthesis, transport and catabolism

R

281

9.03

General function prediction only

S

112

3.60

Function unknown

-

1,250

32.89

Not in COGs

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

Comparison with the genomes from other Alistipes species

To date, the genome from Alistipes shahii strain WAL 8301 is the only genome from the Alistipes genus that has been sequenced. By comparison with A. shahaii, A. senegalensis exhibited a higher G+C content (57.2% vs 58.40%, respectively), a higher number of genes (2,616 vs 3,163) and a smaller number of genes with peptide signal (989 vs 712). Moreover, A. senegalensis had higher ratios of genes per Mb (696 vs 788) and a comparable number of genes assigned to COGs (58.9 vs 59.3). However, the distribution of genes into COG categories (Table 4) was highly similar in both genomes. In addition, A. senegalensis and A. shahaii shared a mean 89.9% (range 78.4-100%) sequence similarity at the genome level.

Conclusion

On the basis of phenotypic, phylogenetic and genomic analyses, we formally propose the creation of Alistipes senegalensis sp. nov. that contains the strain JC50T. This bacterium has been found in Senegal.

Description of Alistipes senegalensis sp. nov.

Alistipes senegalensis (se.ne.gal.e’n.sis. L. gen. masc. n. senegalensis, of Senegal, the country of origin of Alistipes senegalensis).

Colonies are 0.2 to 0.3 mm in diameter on blood-enriched Columbia agar and Brain Heart Infusion (BHI) agar. Cells are rod-shaped with a mean diameter of 0.56 µm. Optimal growth is achieved anaerobically. Weak growth is observed in microaerophilic conditions. No growth is observed in aerobic conditions. Growth occurred between 30–37°C, with optimal growth observed at 37°C, in BHI medium + 5% NaCl. Cells stain Gram negative and are non-motile. Catalase, α-galactosidase, β-galactosidase, β-glucuronidase, arginine arlyamidase, glycine arylamidase, proline arylimidase, leucyl glycine arylamidase, and alanine arylamidase activities are present. Mannose fermentation and indole production are also present. Oxidase activity is absent. Cells are susceptible to penicillin G, amoxicillin + clavulanic acid, imipeneme and clindamycin but resistant to metronidazole. The G+C content of the genome is 58.40%. The 16S rRNA and genome sequence are deposited in GenBank under accession numbers JF824804 and CAHI00000000, respectively.

The type strain JC50T (= CSUR P156 = DSM 25460) was isolated from the fecal flora of a healthy patient in Senegal.

Authors’ Affiliations

(1)
Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de médecine, Aix-Marseille Université

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Copyright

© The Author(s) 2012