Open Access

Non-contiguous finished genome sequence and description of Fenollaria massiliensis gen. nov., sp. nov., a new genus of anaerobic bacterium

  • Isabelle Pagnier1,
  • Olivier Croce1,
  • Catherine Robert1,
  • Didier Raoult1 and
  • Bernard La Scola1Email author
Standards in Genomic Sciences20149:9030704

https://doi.org/10.4056/sigs.3957647

Published: 15 June 2014

Abstract

Fenollaria massiliensis strain 9401234T, is the type strain of Fenollaria massiliensis gen. nov., sp. nov., a new species within a new genus Fenollaria. This strain, whose genome is described here, was isolated from an osteoarticular sample. F. massiliensis strain 9401234T is an obligate anaerobic Gram-negative bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1.71 Mbp long genome exhibits a G+C content of 34.46% and contains 1,667 protein-coding and 30 RNA genes, including 3 rRNA genes.

Keywords

Fenollaria massiliensis genome

Introduction

Fenollaria massiliensis strain 9401234T (= CSUR P127 = DSM 26367), is the type strain of Fenollaria massiliensis sp. nov., and the first member of the new genus Fenollaria gen. nov. This bacterium is a Gram-negative, anaerobic, non spore-forming, indole positive bacillus that was isolated from an osteoarticular sample, during a study prospecting anaerobic isolates from deep samples [1].

Traditionally, definition of a new bacterial species or genus has relied on the application of the “gold standard” methods of DNA-DNA hybridization and G+C content determination [2]. 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 rRNA sequences with cutoff [3], together with phenotypic characteristics. Recently, a number of new bacterial genera and species have been described using high throughput genome sequencing and mass spectrometric analyses, which allows access to a wealth of genetic and proteomic information [4,5]. We propose a new bacterial genus and species using a whole genome sequence and a MALDI-TOF spectrum, and the main characteristics of the organism, as we have previously done [612].

Here we present a summary classification and a set of features for F. massiliensis gen. nov., sp. nov. strain 9401234T (= CSUR P127= DSM 26367) together with the description of the complete genomic sequencing and annotation. These characteristics support the circumscription of a novel genus, Fenollaria gen. nov., within the Clostridiales Family XI Incertae sedis, with Fenollaria massiliensis gen. nov., sp. nov, as the type species.

Clostridiales Family XI Incertae sedis was created in 2009 [13], and currently comprises 11 genera, including Anaerococcus, Peptoniphilus and Tissierella. It is a heterogeneous group that includes anaerobic and morphologically variable bacteria. This group is defined mainly on the basis of phylogenetic analyses of 16S rRNA sequences and its members have no precise taxonomic or phylogenetic affiliation. Based on the 16S rRNA comparison, the species most closely related to Fenollaria massiliensis is Sporobacterium olearium [14], which is the sole representative of the genus Sporobacterium. S. olearium is a Gram-positive rod with terminal spores. The most closely related validly named species is Tissierella creatinini, which belongs to the genus Tissierella sp [15]. It was first described in 1986 and is represented by three species, among which the type species is T. praecuta, a strictly anaerobic Gram-negative, non spore-forming bacterium.

Classification and features

An osteoarticular sample was collected from a patient as part of a study analyzing emerging anaerobic infectious agents by MALDI-TOF and 16S rRNA gene sequencing. The specimen was sampled in Marseille and preserved at −80°C after collection. Strain 9401234T (Table 1) was isolated in February 2009, by anaerobic cultivation on 5% sheep blood-enriched Columbia agar (BioMerieux, Marcy l’Etoile, France). Based on the 16S rRNA sequencing, this strain exhibited 87% sequence similarity with Tissierella creatinini [26]. In the inferred phylogenetic tree, it forms a distinct lineage within the Clostridiales Family XI Incertae sedis (Figure 1). Those similarity values are lower than the recommended threshold to delineate a new genus without carrying out DNA-DNA hybridization [3].
Figure 1.

Phylogenetic tree highlighting the position of Fenollaria massiliensis strain 9401234T relative to other type strains within the Clostridiales Family XI Incertae sedis. 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 [27]. Numbers at the nodes are bootstrap values obtained by repeating the analysis 500 times to generate a majority consensus tree. The scale bar represents a 2% nucleotide sequence divergence.

Table 1.

Classification and general features of Fenollaria massiliensis strain 9401234T according to the MIGS recommendations [16]

MIGS ID

Property

Term

Evidence codea

 

Current classification

Domain Bacteria

TAS [17]

 

Phylum Firmicutes

TAS [1820]

 

Class Clostridia

TAS [21,22]

 

Order Clostridiales

TAS [23,24]

 

Family XI Incertae sedis

TAS [13]

 

Genus Fenollaria

IDA

 

Species Fenollaria massiliensis

IDA

 

Type strain 9401234T

IDA

 

Gram stain

Negative

IDA

 

Cell shape

Rod-shaped

IDA

 

Motility

Non motile

IDA

 

Sporulation

Non spore-forming

IDA

 

Temperature range

Mesophile

IDA

 

Optimum temperature

37°C

IDA

MIGS-6.3

Salinity

Weak growth on BHI agar + 1% NaCl

IDA

MIGS-22

Oxygen requirement

Anaerobic

IDA

 

Carbon source

Unknown

NAS

 

Energy source

Unknown

NAS

MIGS-6

Habitat

Human

IDA

MIGS-15

Biotic relationship

Free living

IDA

MIGS-14

Pathogenicity

Unknown

NAS

 

Biosafety level

2

 
 

Isolation

Osteoarticular sample

 

MIGS-4

Geographic location

France

IDA

MIGS-5

Sample collection time

February 2009

IDA

MIGS-4.1

Latitude

43.296482

IDA

MIGS-4.1

Longitude

5.36978

IDA

MIGS-4.3

Depth

Surface

IDA

MIGS-4.4

Altitude

0 above see 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 [25]. 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.

Growth at different temperatures was tested; no growth occurred at 23°C, 25°C, 28°C and 50°C, but did occur between 32° and 37°C. Optimal growth was observed at 37°C.

Colonies are punctiform, grey, smooth, and round when grown on blood-enriched Columbia agar (Biomerieux), under anaerobic conditions using GENbag anaer (BioMérieux). Growth was achieved anaerobically, on blood-enriched Columbia agar and in TS broth medium after 72h. They also were grown under anaerobic conditions on BHI agar supplemented with 1% NaCl. Growth did not occur under microaerophilic conditions and in the presence of air, with 5% CO2.. Gram staining showed rod-shaped non spore-forming Gram-negative bacilli (Figure 2). Cells were non-motile. Cells grown in TS broth medium have a mean length of 1.555 µm (min = 1.167µm; max = 2.948µm), and a mean width of 0.772 µm (min = 0.602 µm; max = 1.014 µm), as determined using electron microscopic observation after negative staining (Figure 3).
Figure 2.

Gram stain of F. massiliensis strain 9401234T

Figure 3.

Transmission electron micrograph of F. massiliensis strain 9401234T, taken using a Morgani 268D (Philips) at an operating voltage of 60kV. The scale bar represents 500 nm.

Strain 9401234T exhibited neither catalase nor oxidase activities. Using the API 20A system, a positive reaction was observed only for indole, and weakly for gelatinase. Using the API Zym system, a positive reaction was observed for leucine arylamidase and valine arylamidase regarding the proteases, and for Naphtol phosphatase. API RapidID 32A confirmed the positivity for indole and leucine arylamidase, and was also positive for arginine arylamidase, and weakly positive for pyrrolidonyl arylamidase, tyrosine arylamidase, glycine arylamidase, histidine arylamidase and serine arylamidase. Regarding antibiotic susceptibility, F. massiliensis was susceptible to penicillin G, amoxicillin, cefotetan, imipenem, metronidazole, and vancomycin. When compared to the species Tissierela creatinini, Sporobacterium olearium, and Anaerococcus prevotii, within the Clostridiales Family XI Incertae sedis, F. massiliensis exhibits the phenotypic characteristics details in Table 2.
Table 2.

Differential characteristics of Fenollaria massiliensis gen. nov., sp. nov., strain 9401234T, Tissierela creatinini strain DSM 9508T [26], Sporobacterium olearium strain SR1T [14] and Anaerococcus prevotii strain [28].

Properties

F. massilliensis

T. creatinini

S. olearium

A. prevotii

Cell diameter (µm)

0.6-1/1.2-2.9

1/3.5

0.4-0.8/5-10

0.6/0.9

Gram stain

Negative

Positive

Positive

Positive

Salt requirement

+

0-30g NaCl/l

na

Motility

+

+

Endospore formation

+

Optimal growth temperature

37°C

37°C

37–40°C

37°C

Phosphatase

Naphtholphosphatase

Na

na

Indole

+

na

Gelatinase

+

na

na

Urease

na

+

Utilization of

    

D-Glucose

+

D-mannose

na

+

Habitat

Human

Environment

Environment

Human

Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) MS protein analysis was carried out as previously described [29]. 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 Daltonik GmbH, Germany). Ten distinct deposits were done for strain JC122T from ten 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 ten 9401234T 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 5,697 bacteria in the Biotyper 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 compared with the spectra in database. The output score enabled the identification of 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; a score < 1.7 was not significant. For strain 9401234T, the obtained score was 1.04, which is not significant, suggesting that our isolate was not a member of a known genus. We added the spectrum from strain 9401234T (Figure 4) to our database. A dendrogram was constructed with the MALDI Biotyper software, comparing the reference spectrum of strain 9401234T with reference spectra of 29 bacterial species, all belonging to the order of Clostridiales (Figure 5). In this dendrogram, strain 9401234T appears in a separate clade between the genus Peptoniphilus and Acidaminococcus (Figure 5).
Figure 4.

Reference mass spectrum from F. massiliensis strain 9401234T. Spectra from 10 individual colonies were compared and a reference spectrum was generated.

Figure 5.

Dendrogram based on the comparison of the F. massiliensis strain 9401234T MALDI-TOF reference spectrum, and 29 other species of the order of Clostridiales.

Genome sequencing and annotation

Genome project history

The organism was selected for sequencing on the basis of its phylogenetic position, 16S rRNA similarity to other members of the Clostridiales Family XI Incertae sedis, and its isolation from an osteoarticular clinical sample. It is the first genome of the new genus Fenollaria (Genbank accession numbers are CALI02000001-CALI02000010) and consists of 11 contigs. Table 3 shows the project information and its association with MIGS version 2.0 compliance.
Table 3.

Project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

Non-contiguous finished

MIGS-28

Libraries used

One 454 PE 3-kb library

MIGS-29

Sequencing platforms

454 GS FLX Titanium

MIGS-31.2

Sequencing coverage

19.7

MIGS-30

Assemblers

Newbler 2.6

MIGS-32

Gene calling method

Prodigal 2.5

 

Genbank ID

CALI02000001-CALI02000010

 

Genbank Date of Release

October 9, 2013

MIGS-13

Source material identifier

DSM 26367

 

Project relevance

Study of anaerobic isolates from clinical samples

Growth conditions and DNA isolation

F. massiliensis sp. nov., gen. nov. strain 9401234T, CSUR P127 = DSM 26367, was grown on blood agar medium at 37°C under anaerobic conditions. Ten petri dishes were spread and resuspended in 5×100µl 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) using 2×20 seconds cycles. DNA was then treated with 2.5 µg/µL lysozyme (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 were measured by the Quant-it Picogreen kit (Invitrogen) on the Genios_Tecan fluorometer at 135 ng/µl.

Genome sequencing and assembly

This project was loaded twice on a one-quarter region for the paired end application on PTP Picotiter plates. DNA (5µg) was mechanically fragmented on a Hydroshear device (Digilab, Holliston, MA, USA) with an enrichment size at 3–4kb. The DNA fragmentation was visualized through an Agilent 2100 BioAnalyzer on a DNA LabChip 7500 with an optimal size of 4.2 kb. The library was constructed according to the 454_Titanium paired end protocol and manufacturer recommendations. Circularization and nebulization were performed and generated a pattern with an maximum at 686 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 with a RNA 6000 Pico chip at 1,820 pg/µL. The library concentration equivalence was calculated as 4.87E+09 molecules/µL. The library was stored at −20°C.

The paired end library was clonal amplified with 1cpb in 3 emPCR reactions with the GS Titanium SV emPCR Kit (Lib-L) v2. The yield of the emPCR was 10.5% 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 run was performed overnight and then analyzed on the cluster through the gsRunBrowser and gsAssembler_Roche.

The 454 sequencing generated 119,791 reads (38,34 Mb) and was assembled into contigs and scaffolds using Newbler version 2.6 (Roche) and SSPACE software v1.0 [30] combined with GapFiller V1.10 [31]. A sequence consisting of 6,257,638 reads generated from a SOLiD version 4 with a library constructed through an insert size of 150 bp and a 85 bp (50bp and 35bp) in a paired-end sequencing (Life Technologies) helped to improve the genome assembly using CLC Genomics Workbench v4.7.2 (CLC bio, Aarhus, Denmark). Finally, the available genome consists of 8 scaffolds and 11 contigs.

Genome annotation

Non-coding genes and miscellaneous features were predicted using RNAmmer [32], ARAGORN [33], Rfam [34] and signalP [35]. Open Reading Frames (ORFs) were predicted using Prodigal [36] with default parameters but the predicted ORFs were excluded if they were spanning a sequencing GAP region. The functional annotation was achieved using BLASTP [37] against the GenBank database [23] and the Clusters of Orthologous Groups (COG) database.

Genome properties

The genome of Fenollaria massiliensis sp. nov. strain 9401234T is estimated at 1.71 Mb long with a G+C content of 36.47% (Figure 6 and Table 4). A total of 1,667 protein-coding and 30 RNA genes, including 3 rRNA genes, 26 tRNA and 1 tmRNA were found. The majority of the protein-coding genes (70.8%) were assigned a putative function while the remaining ones were annotated as hypothetical proteins. The properties and the statistics of the genome are summarized in Table 4 and Table 5.
Figure 6.

Graphical circular map of the genome. From outside to the center: scaffolds are in grey (unordered), genes on forward strand (colored by COG categories), genes on reverse strand (colored by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content (black/grey), and GC skew (purple/olive).

Table 4.

Genome statistics

Attribute

Value

% of Total*

Genome size (bp)

1,709,674

100

DNA coding region (bp)

1,554,900

90.9

DNA G+C content (bp)

589,201

34.46

Total genes

1697

100

rRNA genes

3

0.18

tRNA genes

26

1.53

tmRNA

1

0.06

Protein-coding genes

1667

98.23

Genes with function prediction

1180

70.8

Genes assigned to COGs

1744

98.44

* 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

172

9.86

Translation

A

4

0.23

RNA processing and modification

K

109

6.25

Transcription

L

132

7.57

Replication, recombination and repair

B

4

0.23

Chromatin structure and dynamics

D

36

2.06

Cell cycle control, mitosis and meiosis

Y

1

0.06

Nuclear structure

V

86

4.93

Defense mechanisms

T

51

2.92

Signal transduction mechanisms

M

81

4.64

Cell wall/membrane biogenesis

N

14

0.8

Cell motility

Z

2

0.11

Cytoskeleton

W

0

0

Extracellular structures

U

36

2.06

Intracellular trafficking and secretion

O

68

3.9

Posttranslational modification, protein turnover, chaperones

C

98

5.62

Energy production and conversion

G

72

4.13

Carbohydrate transport and metabolism

E

111

6.36

Amino acid transport and metabolism

F

54

3.1

Nucleotide transport and metabolism

H

73

4.19

Coenzyme transport and metabolism

I

30

1.72

Lipid transport and metabolism

P

104

5.96

Inorganic ion transport and metabolism

Q

11

0.63

Secondary metabolites biosynthesis, transport and catabolism

R

204

11.7

General function prediction only

S

191

10.95

Function unknown

-

26

1.49

Not in COGs

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

Insights into the genome sequence

There is a lack of closely related genomes because Fenollaria gen. nov. is a new genus. However, we made some comparisons against Peptoniphilus sp. oral taxon 386 str. F0131 (accession number NZ_GL349422), which is relatively close to Fenollaria based on 16S rRNA and for which the completed genome is available in public databases.

The draft genome sequence of F. massiliensis has a slightly bigger size compared to the Peptoniphilus sp.(1.71 Mbp and 1.47 Mbp, respectively). The G+C content is slightly higher than Peptoniphilus sp. (34 and 31%, respectively). Fenollaria massiliensis gen. nov. encodes more genes (1,697 genes against 1,463 genes), however the number of genes per Mb is similar (1,007 – 1,004).

Table 6 presents the difference of gene number (in percentage) for each COG categories between Peptoniphilus sp. oral taxon 386 str. F0131 and Fenollaria massiliensis sp. nov.
Table 6.

Percentage of genes associated with the 25 general COG functional categories for Fenollaria massiliensis and Peptoniphilus sp. oral taxon 386 str. F0131.

Code

COG description

F. massiliensis

Peptoniphilus sp.

%Difference

J

Translation

9.86

10.01

1.5

A

RNA processing and modification

0.23

0.71

208.7

K

Transcription

6.25

6.52

4.3

L

Replication, recombination and repair

7.57

6.85

−9.5

B

Chromatin structure and dynamics

0.23

0.39

69.6

D

Cell cycle control, mitosis and meiosis

2.06

2.0

−2.9

Y

Nuclear structure

0.06

0

−100

V

Defense mechanisms

4.93

2.84

−42.4

T

Signal transduction mechanisms

2.92

2.97

1.7

M

Cell wall/membrane biogenesis

4.64

4.2

−9.5

N

Cell motility

0.8

1.1

37.5

Z

Cytoskeleton

0.11

0.19

72.7

W

Extracellular structures

0

0

0

U

Intracellular trafficking and secretion

2.06

2.84

37.9

O

Posttranslational modification, protein turnover, chaperones

3.9

4.26

9.2

C

Energy production and conversion

5.62

5.62

0

G

Carbohydrate transport and metabolism

4.13

2.65

−35.8

E

Amino acid transport and metabolism

6.36

7.56

18.9

F

Nucleotide transport and metabolism

3.1

3.94

27.1

H

Coenzyme transport and metabolism

4.19

2.78

−33.7

I

Lipid transport and metabolism

1.72

2.97

72.7

P

Inorganic ion transport and metabolism

5.96

4.78

−19.8

Q

Secondary metabolites biosynthesis, transport and catabolism

0.63

1.36

115.9

R

General function prediction only

11.7

11.56

−1.2

S

Function unknown

10.95

11.89

8.6

-

Not in COGs

1.49

1.29

8.6

Some COGs contain significantly more genes as “RNA processing and modification” (+208,7%) or “Secondary metabolites biosynthesis, transport and catabolism” (+115,9%), whereas others contain less genes as “Nuclear structure” (−100%) or “Defense mechanisms” (−42,4%).

Conclusion

On the basis of phenotypic, phylogenetic and genomic analyses, we formally propose the creation of Fenollaria massiliensis gen. nov., sp. nov. that contains the strain 9401234T. This bacterium was found in Marseille, France.

Description of Fenollaria gen. nov.

Fenollaria (Fe.nol.la’ria. N.L. gen. n. Fenollaria of F. Fenollar, expert microbiologist in Whipple’s disease and osteo-articular infections)

Gram negative rods. Obligate anaerobic. Non motile, non spore forming. Positive for indole. Negative for catalase and oxidase. Weakly positive gelatinase. Positive for leucine arylamidase, valine arylamidase, arginine arylamidase and for Naphtol phosphatase. Weakly positive for pyrrolidonyl arylamidase, tyrosine arylamidase, glycine arylamidase, histidine arylamidase and serine arylamidase. Habitat: human. Type species: Fenollaria massiliensis

Description of Fenollaria massiliensis gen. nov. sp.nov.

Fenollaria massiliensis (ma.si.li.en’.sis. L. fem. adj. massiliensis, of Massilia, the Latin name of Marseille where was isolated F. massiliensis).

Gram negative, catalase negative, oxidase negative and obligate anaerobic. Cells are non-spore forming, non motile rods, with a mean length of 1,555 µm, and a mean width of 772 µm. Colonies are punctiform, very small, grey, smooth, and round on blood-enriched Columbia agar under anaerobic conditions. Optimal growth under anaerobic conditions, at 37°C (range from 32°C to 37°C). Cells are positive for leucine arylamidase, valine arylamidase, arginine arylamidase and for Naphtol phosphatase. Cells are weakly positive for pyrrolidonyl arylamidase, tyrosine arylamidase, glycine arylamidase, histidine arylamidase and serine arylamidase. Susceptible to penicillin G, amoxicillin, cefotetan, imipenem, metronidazole and vancomycin. The potential pathogenicity of the type strain 9401234T is unknown.

The type strain is 9401234T (= CSUR P127 = DSM 26367); it was isolated from an osteoarticular sample of a patient in Marseille (France). The G+C content of the genome is 34.46 mol%. A partial 16S rRNA gene sequence was deposited in GenBank with the accession number HM587321. The whole genome shotgun sequence of F. massiliensis strain 9401234T (= CSUR P127 = DSM 26367) has been deposited in GenBank under accession numbers CALI02000001-CALI02000010.

Authors’ Affiliations

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

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