Open Access

Non-contiguous finished genome sequence and description of Alistipes ihumii sp. nov.

  • Anne Pfleiderer1,
  • Ajay Kumar Mishra1,
  • Jean-Christophe Lagier1,
  • Catherine Robert1,
  • Aurelia Caputo1,
  • Didier Raoult1, 2 and
  • Pierre-Edouard Fournier1Email author
Standards in Genomic Sciences20149:9031221

https://doi.org/10.4056/sigs.4698398

Published: 15 June 2014

Abstract

Alistipes ihumii strain AP11T sp. nov. is the type strain of A. ihumii sp. nov., a new species within the genus Alistipes. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old French Caucasian female, suffering from a severe restrictive form of anorexia nervosa since the age of 12 years. A. ihumii is a Gram-negative anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,753,264 bp long genome (one chromosome but no plasmid) contains 2,254 protein-coding and 47 RNA genes, including 3 rRNA genes.

Keywords

Alistipes ihumii genome culturomics taxono-genomics

Introduction

Alistipes ihumii strain AP11T (= CSUR P204 = DSM 26107) is the type strain of A. ihumii sp. nov. This bacterium is a Gram-negative, non-spore-forming, anaerobic and non-motile bacillus that was isolated from the stool of a 21-year-old French female suffering from anorexia nervosa, and is part of a “culturomics” study aiming at cultivating individually all species within human feces [13].

Prokaryotic taxonomy is episodically confronted with the advancement of methodological and conceptual innovations. The current classification methodology for prokaryotes is known as polyphasic taxonomy, and relies on a combination of phenotypic and genotypic characteristics [4]. The number of completely sequenced genomes is geometrically increasing with time, concurrently with the decrease in cost of such techniques. To date, more than 6,000 bacterial genomes have been published and approximately 25,000 genome sequencing projects have been announced [5]. We recently proposed to integrate genomic information in the taxonomic framework for the description of new bacterial species [627].

The genus Alistipes (Rautio et al. 2003) was created in 2003 [28] 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 [29]. This genus is currently comprised of five species with validly published names, including A. finegoldii, A. putredinis [28], A. indistinctus [30], A. onderdonkii and A. shahii [31], to which we added three proposed new species, A. senegalensis [8], A. timonensis [9] and A. obesi [22].

Here we present a summary classification and a set of features for a new Alistipes species, A. ihumii sp. nov. strain AP11T (= CSUR P204 = DSM 26107), together with the description of the complete genomic sequence and its annotation.

Classification and features

A stool sample was collected from a 21-year-old French Caucasian female suffering from severe restrictive form of anorexia nervosa since the age of 12 years. At the time of sample collection, she was hospitalized in our hospital for recent aggravation of her medical condition (BMI: 10.4 kg/m2). The patient gave an informed and signed consent. Both this study and the assent procedure were approved by the Ethics Committee of the Institut Fédératif de Recherche IFR48, Faculty of Medicine, Marseille, France under reference 09-022. Ten other potentially new bacterial species were isolated from this patient’s stool, all of which are currently being described. Microbial culturomics also enabled the isolation of several other new bacterial species from other stool specimens [627]. The fecal specimen was stored at −80°C immediately after collection. Strain AP11T was isolated in November 2011 after 2 days of inoculation in anaerobic blood culture bottle with the addition of 5mL of thioglycolate and further inoculation on Columbia agar (BioMerieux, Marcy l’Etoile, France).

This strain exhibited a 95% 16S rRNA sequence similarity with A. indistinctus [30], the phylogenetically closest Alistipes species with a validly published name (Table 1, Figure 1), and 92% with A. onderdonkii [28] and A. putredinis [31]. This value was in the range of 16S rRNA sequence identities among species within the genus Alistipes that range from 90 to 95%, and 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 [41].
Figure 1.

Phylogenetic tree highlighting the position of Alistipes ihumii strain AP11T relative to other type strains within the genus Alistipes. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained using the maximum-likelihood method within the MEGA software. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 500 times to generate a majority consensus tree. Bacteroides splanchnicus was used as the outgroup. The scale bar represents a 2% nucleotide sequence divergence.

Table 1.

Classification and general features of Alistipes ihumii strain AP11T according to the MIGS recommendations [32]

MIGS ID

Property

Term

Evidence codea

  

Domain Bacteria

TAS [33]

  

Phylum Bacteroidetes

TAS [34,35]

  

Class Bacteroidia

TAS [34,36]

  

Order Bacteroidales

TAS [34,37]

  

Family Rikenellaceae

TAS [34,38]

  

Genus Alistipes

TAS [28,39]

  

Species Alistipes ihumii

IDA

 

Current classification

Type strain AP11T

IDA

 

Gram stain

Negative

IDA

 

Cell shape

Rod

IDA

 

Motility

nonmotile

IDA

 

Sporulation

nonsporulating

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

 
 

Energy source

unknown

 

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 & Longitude

43.296482 & 5.36978

IDA

MIGS-4.3

Depth

surface

IDA

MIGS-4.4

Altitude

0 m above sea level

IDA

aEvidence 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 [40]. If the evidence is IDA, then the property was directly observed for a live isolate by one of the authors or an expert mentioned in the acknowledgements.

Different growth temperatures (25, 30, 37, 45°C) were tested. Growth was observed between 25 and 45°C, with optimal growth at 37°C after 24 hours of inoculation. Colonies were about 0.2 mm in diameter, transparent, and exhibited a ß-hemolytic activity on blood-enriched Columbia agar. Growth of the strain was tested on 5% sheep blood agar, under anaerobic and microaerophilic conditions using the GENbag anaer and GENbag microaer systems, respectively (BioMerieux), and under aerobic conditions with or without 5% CO2. Optimal growth of this strain was obtained anaerobically, weak growth was observed under microaerophilic conditions, and no growth was observed under aerobic atmosphere. The motility test was negative. Cells grown on agar are Gram-negative rods (Figure 2) and have mean diameter and length of 0.72 and 1.69 µm, respectively, as determined using electron microscopy (Figure 3). Strain AP11T exhibited oxidase but no catalase activities. Using API 50CH (BioMérieux), we observed that strain AP11T was asaccharolytic. Using API 32A (BioMérieux), positive reactions were obtained for α-glucosidase, β-glucosidase, N-acetyl-β-glucosaminidase, mannose and raffinose fermentation, alkaline phosphatase, leucyl glycine arylamidase, alanine arylamidase, and glutamyl glutamic acid arylamidase. Weak reactions were observed for α-galactosidase and glutamic acid decarboxilase. Negative reactions were obtained for urease, arginine dihydrolase, β-galactosidase, 6 phospho-β-galactosidase, α-arabinosidase, β-glucuronidase, α-fucosidase, nitrate reduction, indole production, arginine arylamidase, proline arylamidase, phenylalanine arylamidase, leucine arylamidase, pyroglutamic acid arylamidase, tyrosine arylamidase, glycine arylamidase, histidine arylamidase, and serine arylamidase. A. ihumii is susceptible to amoxicillin, imipenem, and clindamycin, but resistant to vancomycin. When compared with representative species from the genus Alistipes, strain AP11T exhibited the phenotypic differences detailed in Table 2.
Figure 2.

Gram stain of A. ihumii strain AP11T

Figure 3.

Transmission electron microscopy of A. ihumii strain AP11T, using a Morgani 268D (Philips) at an operating voltage of 60kV. The scale bar represents 500 nm.

Table 2.

Differential characteristics of Alistipes strains

Properties

A. ihumii

A. senegalensis

A. timonensis

A. putredinis

A. indistinctus

A. shahii

A. obesi

Cell diameter (µm)

0.72

0.56

0.62

0.40

0.60

0.15

0.44–0.76

Oxygen requirement

anaerobic

anaerobic

anaerobic

anaerobic

anaerobic

anaerobic

anaerobic

Pigment production

+

+

+

+

+

Gram stain

Salt requirement

na

+

Motility

+

Endospore formation

na

Production of

       

Alkaline phosphatase

na

na

na

+

w

+

+

Catalase

+

+

+

+

+

Oxidase

+

Nitrate reductase

na

na

Urease

na

na

+

β-galactosidase

w

+

+

+

N-acetyl-glucosamine

+

na

W

+

+

+

Indole

w

W

+

+

Activity for

       

Leucyl glycine arylamidase

+

+

+

+

+

+

Glutamic acid decarboxylase

w

na

+

+

Glycine arylamidase

+

+

na

Chymotrypsin

na

na

na

na

Acid from

       

L-Arabinose

na

na

na

+

na

na

Raffinose

+

na

+

+

Mannose

+

+

+

+

Mannitol

na

na

na

na

+

na

na

Sucrose

na

na

na

+

+

na

D-glucose

na

na

na

+

+

na

D-fructose

na

na

na

+

+

na

D-maltose

na

na

na

+

+

na

D-lactose

na

na

na

+

+

na

Hydrolysis of gelatin

na

na

na

+

+

na

G+C content (mol%)

57.90

58.40

58.82

55.3

55.2

57.20

58.60

Habitat

human gut

human gut

human gut

appendix of children

human gut

human gut

human gut

na = data not available; w = weak

Alistipes ihumii strain AP11T, A. senegalensis strain JC50T, A. timonensis strain JC136T, A. putredinis strain ATCC29800 T, A. indistinctus strain YIT12060T, A. shahii strain WAL 8301T, A. obesi strain ph8T and A. finegoldii AHN2437T

Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) MS protein analysis was carried out as previously described [42] using a Microflex spectrometer (Bruker Daltonics, Leipzig, Germany). Twelve individual colonies were deposited on a MTP 384 MALDI-TOF target plate (Bruker). The twelve AP11T 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 4,706 bacteria, including spectra from A. finegoldii, A. onderdonkii, A. shahii, A. senegalensis, A. obesi and A. timonensis, used as reference data in the BioTyper database. The output score enabled the presumptive identification and discrimination of the tested species from those in the database: a score ≥ 2 with a validated species identifies a strain at the species level; and a score < 1.7 indicates a species-level match was not made. For strain AP11T, no significant score was obtained, suggesting that our isolate was not a member of any known species (Figures 4 and 5). We added the spectrum from strain AP11T to our database.
Figure 4.

Reference mass spectrum from A. ihumii strain AP11T. Spectra from 12 individual colonies were compared and a reference spectrum was generated.

Figure 5.

Gel view comparing spectra from Alistipes ihumii strain AP11T and other members of the genus Alistipes (A. obesi, A. timonensis, A. senegalensis, A. shahii, A. onderdonkii and A. finegoldii). The Gel View displays the raw spectra of all loaded spectrum files arranged in a pseudo-gel like look, with each peak displayed as a band or bar. The peak intensity is reflected by the intensity of the gray color. The right y-axis shows the relationship between the shades of gray and the peak intensity in arbitrary units. The x-axis records the m/z value. The left y-axis displays the running spectrum number originating from subsequent spectra loading.

Genome sequencing information

Genome project history

The organism was selected for sequencing on the basis of its phylogenetic position and 16S rRNA similarity to other members of the 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 eighth sequenced genome from an Alistipes species and the first from Alistipes ihumii sp. nov. A summary of the project information is shown in Table 3. The Genbank accession number is CAPH00000000 and consists of 60 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

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

 

Genbank ID

CAPH00000000

 

Genbank Date of Release

November 28, 2012

 

Gold ID

Gi20720

MIGS-13

Project relevance

Study of the human gut microbiome

Growth conditions and DNA isolation

A. ihumii sp. nov. strain AP11T, (= CSURP204 = DSM 26107), was grown aerobically on 5% sheep blood agar medium at 37°C. Five Petri dishes were spread and resuspended in 3x100µl 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, MP Biomedicals, USA) for 2×20 seconds. DNA was treated with 2.5 µg/µL of lysozyme (30 minutes at 37°C) and extracted using the BioRobot EZ 1 Advanced XL (Qiagen). The DNA was concentrated and purified on a Qiamp kit (Qiagen). The yield and the concentration of DNA was 70.7 ng/µl as measured by using Quant-it Picogreen kit (Invitrogen) on the Genios Tecan fluorometer.

Genome sequencing and assembly

A 3kb paired-end sequencing strategy (Roche, Meylan, France) was used. DNA (5 µg) was mechanically fragmented for the paired-end sequencing, using a Covaris device (Covaris Inc., Woburn, MA, USA) with an enrichment size of 3–4 kb. The DNA fragmentation was visualized through an Agilent 2100 BioAnalyzer on a DNA Labchip 7500 which yielded an optimal size of 2.3 kb. The library was constructed using the 454 GS FLX Titanium paired-end rapid library protocol. Circularization and nebulization were performed which generated a pattern of optimal size of 457 bp. PCR amplification was performed for 17 cycles followed by double size selection. The single-stranded paired-end library was quantified using a Quant-it Ribogreen Kit (Invitrogen) and the Genios Tecan fluorometer. The library concentration equivalence was calculated as 1.94× 1010 molecules/µL. The library was stored at −20°C until further use.

The paired-end library was clonally amplified with 0.5 and 1 cpb in 2 emPCR reactions with the GS Titanium SV emPCR Kit (Lib-L) v2 (Roche). The yield of the shotgun emPCR reactions was 6.24 and 16.24% respectively for the two kinds of paired-end emPCR reactions according to the quality expected (range of 5 to 20%) from the Roche procedure. Two libraries were loaded on the GS Titanium PicoTiterPlates (PTP Kit 70x75, Roche) and pyrosequenced with the GS Titanium Sequencing Kit XLR70 and the GS FLX Titanium sequencer (Roche). The run was performed overnight and then analyzed on the cluster through the gsRunBrowser and Newbler assembler (Roche). A total of 260,838 passed filter wells were obtained and generated 96.3 Mb with an average length of 369 bp. The passed filter sequences were assembled using Newbler with 90% identity and 40 bp as overlap. The final assembly identified 9 scaffolds and 60 contigs (> 1,500 bp) and generated a genome size of 2.75 Mb which corresponds to a coverage of 35× genome equivalent.

Genome annotation

Open Reading Frames (ORFs) were predicted using Prodigal [44] 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 [45] and the Clusters of Orthologous Groups (COG) databases using BLASTP. The tRNAScan-SE tool [46] was used to find tRNA genes, whereas ribosomal RNAs were found by using RNAmmer [47] and BLASTn against the GenBank database. Lipoprotein signal peptides and numbers of transmembrane helices were predicted using SignalP [48] and TMHMM [49] respectively. ORFans were identified if their BLASTP E-value was lower than 1e−03 for alignment length greater than 80 amino acids. If alignment lengths were smaller than 80 amino acids, we used an E-value of 1e−05. Such parameter thresholds have already been used in previous works to define ORFans.

Orthologous gene sets composed of one gene from A. ihumii compared to each of A. obesi strain ph8T (GenBank accession number CAHA00000000), A. finegoldii strain AHN 2437 (CP003274), A. indistinctus strain YIT 12060 (ADLD00000000), A. putredinis strain DSM 17216 (ABFK00000000), A. senegalensis strain JC50T (CAHI00000000), A. shahii strain WAL 8301 (FP929032), and A. timonensis strain JC136T (CAEG00000000) were identified using the Proteinortho software (version 1.4) [50] using a 30% protein identity and an E-value of 1e−05. The average percentage of nucleotide sequence identity of each orthologous set was determined using the Needleman-Wunsch algorithm global alignment technique. Artemis [51] was used for data management and DNA Plotter [52] was used for visualization of genomic features. The Mauve alignment tool was used for multiple genomic sequence alignment and visualization [53].

Genome properties

The genome of A. ihumii strain AP11T is 2,753,264 bp long (1 chromosome, but no plasmid) with a 57.90% G + C content (Figure 6 and Table 4). Of the 2,301 predicted genes, 2,254 were protein-coding genes, and 47 were RNAs. One rRNA operon (one 16S rRNA, one 23S rRNA and one 5S rRNA) and 44 predicted tRNA genes were identified in the genome. A total of 1,465 genes (63.66%) were assigned a putative function. Two hundred thirty-seven genes were identified as ORFans (10.29%). The remaining genes were annotated as hypothetical proteins. The properties and the 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, the outer two circles show open reading frames oriented in the forward and reverse (colored by COG categories) directions, respectively. The third circle marks the rRNA gene operon (red) and tRNA genes (green). The fourth circle shows the G+C% content plot. The inner-most circle shows GC skew, purple and olive indicating negative and positive values, respectively.

Table 4.

Nucleotide content and gene count levels of the genome

Attribute

Value

% of totala

Genome size (bp)

2,753,264

 

DNA coding region (bp)

2,320,878

84.29

DNA G+C content (bp)

1,594,140

57.90

Number of replicons

1

 

Extrachromosomal elements

0

 

Total genes

2,301

100

RNA genes

47

2.04

rRNA operons

1

 

Protein-coding genes

2,254

97.95

Genes with function prediction

1,540

66.92

Genes assigned to COGs

1,465

63.66

Protein coding genes assigned Pfam domains

1,834

79.70

Genes with peptide signals

296

12.86

Genes with transmembrane helices

457

19.86

CRISPR repeats

1

 

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 5.

Number of genes associated with the 25 general COG functional categories

Code

Value

%agea

Description

J

143

6.34

Translation

A

0

0

RNA processing and modification

K

88

3.90

Transcription

L

113

5.01

Replication, recombination and repair

B

0

0

Chromatin structure and dynamics

D

19

0.84

Cell cycle control, mitosis and meiosis

Y

0

0

Nuclear structure

V

28

1.24

Defense mechanisms

T

38

1.69

Signal transduction mechanisms

M

161

7.14

Cell wall/membrane biogenesis

N

6

0.27

Cell motility

Z

0

0

Cytoskeleton

W

0

0

Extracellular structures

U

32

142

Intracellular trafficking and secretion

O

60

2.66

Posttranslational modification, protein turnover, chaperones

C

111

4.92

Energy production and conversion

G

106

4.70

Carbohydrate transport and metabolism

E

131

5.81

Amino acid transport and metabolism

F

52

2.31

Nucleotide transport and metabolism

H

75

3.33

Coenzyme transport and metabolism

I

49

2.17

Lipid transport and metabolism

P

72

3.19

Inorganic ion transport and metabolism

Q

21

0.93

Secondary metabolites biosynthesis, transport and catabolism

R

235

10.43

General function prediction only

S

91

4.04

Function unknown

-

790

35.05

Not in COGs

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

Genome comparison with other Alistipes species

Here, we compared the genome of A. ihumii strain AP11T to those of A. obesi strain ph8T (GenBank accession number CAHA00000000), A. finegoldii strain AHN 2437 (CP003274), A. indistinctus strain YIT 12060 (ADLD00000000), A. putredinis strain DSM 17216 (ABFK00000000), A. senegalensis strain JC50T (CAHI00000000), A. shahii strain WAL 8301 (FP929032), and A. timonensis strain JC136T (CAEG00000000). The draft genome of A. ihumii is larger than that of A. putredinis (2.75 and 2.55 Mb, respectively) but smaller than those of A. indistinctus, A. obesi, A. timonensis, A. finegoldii, A. shahii and A. senegalensis (2.85, 3.16, 3.49, 3.73, 3.76, and 4.01 Mb, respectively). The G+C content of A. ihumii is comparable to that of A. shahii (57.90 and 57.60%, respectively), lower than those of A. timonensis and A. senegalensis (58.8 and 58.4%, respectively) and higher than those of A. putredinis, A. indistinctus and A. finegoldii (53.30, 54.80 and 56.60%, respectively). A. ihumii has a smaller gene content than those of A. putredinis, A. indistinctus, A. obesi, A. timonensis, A. shahii, A. senegalensis, and A. finegoldii (2,301, 2,335, 2,342, 2,619, 2,709, 3,132, 3,161, and 3,231, respectively). The ratio of genes per MB of A. ihumii is higher than those of A. timonensis, A. senegalensis, A. indistinctus, and A. obesi (836, 776, 788, 821, and 828, respectively), comparable to that of A. shahii (833) and smaller than those of A. finegoldii and A. putredinis (866 and 915, respectively).

The average genomic nucleotide sequence identity between A. ihumii and other Alistipes species ranged from 70.23 to 74.37%, whereas values ranged from 69.70 to 90.98% among other Alistipes species (Table 6).
Table 6.

Numbers of orthologous proteins shared between genomes

 

AIH

ASE

AT

AS

AF

AP

AO

AIN

A. ihumii

2,254

1,190

1,164

958

1,150

1,055

1,130

1,147

A. senegalensis

71.16

3,161

1,764

1,739

1,660

1,277

1,405

1,218

A. timonensis

70.90

90.98

2,709

1,650

1,585

1,238

1,377

1,210

A. shahii

71.19

86.33

80.03

3,132

1,674

1,270

1,166

1,155

A. finegoldii

71.62

82.04

81.14

82.90

3,231

1,303

1,385

1,202

A. putrenidis

70.23

75.32

75.21

75.50

76.23

2,335

1,182

1,038

A. onderdonkii

71.26

76.42

76.23

77.06

76.31

74.45

2,619

1,137

A. indistinctus

74.37

70.02

70.05

70.00

69.91

69.70

69.91

2,342

Upper right triangle-numbers of orthologous proteins shared between genomes; Lower left triangle-average percentage of nucleotide identity between orthologous gene sets shared between genomes; bold-numbers of proteins per genome: AIH- A. ihumii, ASE- A. senegalensis, AT- A. timonensis, AS- A. shahii, AF- A. finegoldii, AP- A. putredinis, AO- A. obesi, AIN- A. indistinctus

However, the distribution of genes into COG categories was not entirely similar in all eight compared genomes (Figure 7).
Figure 7.

Distribution of functional classes of predicted genes in Alistipes ihumii (colored in green), A. senegalensis (pink), A. timonensis (yellow), A. shahii (brown), A. finegoldii (blue), A. putredinis (red), A. obesi (orange) and A. indistinctus (black) chromosomes according to the clusters of orthologous groups of proteins.

Conclusion

On the basis of phenotypic, phylogenetic and genomic analyses, we formally propose the creation of Alistipes ihumii sp. nov. that contains strain AP11T. This bacterial strain has been isolated from the fecal flora of a patient suffering from anorexia nervosa living in Marseille, France. Several other new bacterial species were also cultivated from this patient as well as fecal samples from other patients using microbial culturomics [627], thus suggesting that the human fecal flora from human remains partially unknown.

Description of Alistipes ihumii sp. nov.

Alistipes ihumii (i.hum.i’i. N.L. gen. n. ihumii, based on the acronym IHUMI, the Institut Hospitalo-Universitaire Méditerranée-Infection, where the type strain was isolated).

Colonies are 0.2 mm in diameter and are translucent on blood-enriched Columbia agar. Cells are rod-shaped with a mean diameter of 0.72 µm and a mean length of 1.69 µm. Optimal growth is achieved anaerobically. No growth is obtained aerobically but weak growth is observed in microaerophilic conditions. Growth occurs between 25°C and 45°C, with an optimal growth observed at 37°C.

Cells stain Gram-negative, are non motile and are asaccharolytic. Activities present are α-glucosidase, β-glucosidase, N-acetyl-β-glucosaminidase, mannose and rafinnose fermentation, alkaline phosphatase, leucyl glycine arylamidase, alanine arylamidase, and glutamyl glutamic acid arylamidase. Cells are negative for urease, arginine dihydrolase, β-galactosidase, 6-phospho-β-galactosidase, α-arabinosidase, β-glucuronidase, α-fucosidase, nitrate reduction, indole production, arginine arylamidase, proline arylamidase, phenylalanine arylamidase, leucine arylamidase, pyroglutamic acid arylamidase, tyrosine arylamidase, glycine arylamidase, histidine arylamidase, and serine arylamidase. Cells are susceptible to amoxicillin, imipenem, and clindamycin, but resistant to vancomycin. The G+C content of the genome is 57.90%. The 16S rRNA and genome sequences are deposited in Genbank under accession numbers JX101692 and CAPH00000000, respectively.

The type strain AP11T (= CSUR P204 = DSM 26107) was isolated from the fecal flora of a 21-year-old French Caucasian female suffering from severe anorexia nervosa.

Notes

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)
URMITE, UM63, 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. Dubourg G, Lagier JC, Armougom F, Robert C, Hamad I, Brouqui P. The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics. Eur J Clin Microbiol Infect Dis 2013; 2013:637–645.View ArticleGoogle Scholar
  3. Pfleiderer A, Lagier JC, Armougom F, Robert C, Vialettes B, Raoult D. Culturomics identified 11 new bacterial species from a single anorexia nervosa stool sample. [Epub ahead of print]. Eur J Clin Microbiol Infect Dis 2013.Google Scholar
  4. Tindall BJ, Rossello-Mora R, Busse HJ, Ludwig W, Kampfer 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
  5. Genome Online Database. http://www.genomesonline.org/cgi-bin/GOLD/index.cgi
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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.3206554PubMed CentralView ArticlePubMedGoogle Scholar
  15. 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
  16. 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
  17. Lagier JC, Ramasamy D, Rivet R, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Cellulomonas massiliensissp. nov. Stand Genomic Sci 2012; 7:258–270. PubMed http://dx.doi.org/10.4056/sigs.3316719PubMed CentralView ArticlePubMedGoogle Scholar
  18. 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.3246665PubMed CentralView ArticlePubMedGoogle Scholar
  19. 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.32766871PubMed CentralView ArticlePubMedGoogle Scholar
  20. 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
  21. 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.3396830PubMed CentralView ArticlePubMedGoogle Scholar
  22. 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.3336746PubMed CentralView ArticlePubMedGoogle Scholar
  23. 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. PubMedPubMed CentralPubMedGoogle Scholar
  24. 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
  25. 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
  26. Ramasamy D, Lagier JC, Nguyen TT, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of 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
  27. 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 Micrococcinae. Stand Genomic Sci 2013; 8:318–335. PubMed http://dx.doi.org/10.4056/sigs.3476977PubMed CentralView ArticlePubMedGoogle Scholar
  28. Rautio M, Eerola E, Väisänen-Tunkelrott ML, Molitoris D, Lawson P, Collins MD, Jousimies-Somer H. Reclassification of Bacteroides putredinis (Weinberg et al., 1937) in a new genus Alistipes gen. nov., as Alistipes putredinis comb. nov., and description of Alistipes finegoldii sp. nov., from human sources. Syst Appl Microbiol 2003; 26:182–188. PubMed http://dx.doi.org/10.1078/072320203322346029View ArticlePubMedGoogle Scholar
  29. Tyrrell KL, Warren YA, Citron DM, Goldstein EJC. Re-assessment of phenotypic identifications of Bacteroides putredinis to Alistipes species using molecular methods. Anaerobe 2011; 17:130–134. PubMed http://dx.doi.org/10.1016/j.anaerobe.2011.04.002View ArticlePubMedGoogle Scholar
  30. Nagai F, Morotomi M, Watanabe Y, Sakon H, Tanaka R. Alistipes indistinctus sp. nov. and Odoribacter laneus sp. nov., common members of the human intestinal microbiota isolated from faeces. Int J Syst Evol Microbiol 2009; 60:1296–1302. PubMed http://dx.doi.org/10.1099/ijs.0.014571-0View ArticlePubMedGoogle Scholar
  31. Song Y, Könönen E, Rautio M, Liu C, Bryk A, Eerola E, Finegold SM. Alistipes onderdonkii sp. nov. and Alistipes shahii sp. nov., of human origin. Int J Syst Evol Microbiol 2006; 56:1985–1990. PubMed http://dx.doi.org/10.1099/ijs.0.64318-0View ArticlePubMedGoogle Scholar
  32. 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 CentralView ArticlePubMedGoogle Scholar
  33. 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
  34. Validation List No. 143. Int J Syst Evol Microbiol 2012; 62:1–4. http://dx.doi.org/10.1099/ijs.0.039487-0
  35. 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
  36. 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
  37. 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
  38. Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB. Family III. Rikenellaceae fam. 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. 54.Google Scholar
  39. Validation List no. 94. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol 2003; 53:1701–1702. PubMed http://dx.doi.org/10.1099/ijs.0.03001-0
  40. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, 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
  41. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155.Google Scholar
  42. 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/10.1086/600885View ArticlePubMedGoogle 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. Prodigal. http://prodigal.ornl.gov
  45. GenBank database. http://www.ncbi.nlm.nih.gov/genbank
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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

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