# Vitreoscilla massiliensis sp. nov., Isolated From the Stool of an Amazonian Patient

Sokhna Ndongo, Mossaab Maaloum, Magali Richez, Rachid Saile, Pierre-Edouard Fournier, Jean Christophe Lagier, Didier Raoult, Saber Khelaifia

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To cite this version:

Sokhna Ndongo, Mossaab Maaloum, Magali Richez, Rachid Saile, Pierre-Edouard Fournier, et al. Vitreoscilla massiliensis sp. nov., Isolated From the Stool of an Amazonian Patient. Current Microbiology, 2021, 78 (8), pp.3313-3320. 10.1007/s00284-021-02577-8. hal-03334108

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# *Vitreoscilla massiliensis* sp. nov., Isolated From the Stool of an Amazonian Patient

Sokhna Ndongo<fnref n="1" />,<fnref n="2" /> · Mossaab Maaloum<fnref n="1" />,<fnref n="3" />,<fnref n="4" /> · Magali Richez<fnref n="1" /> · Rachid Saile<fnref n="4" /> · Pierre-Edouard Fournier<fnref n="1" />,<fnref n="3" /> · Jean Christophe Lagier<fnref n="1" />,<fnref n="2" /> · Didier Raoult<fnref n="1" />,<fnref n="2" /> · Saber Khelaifia<fnref n="1" />,<fnref n="2" />

Received: 18 September 2020 / Accepted: 15 June 2021 / Published online: 24 June 2021
© The Author(s) 2021

## Abstract

Strain SN6T is a non-motile and non-spore-forming gram-negative bacterium which was isolated from the stool sample of an Amazonian patient. The optimum growth was observed at 37 °C, pH 7, and 0–5 g/l of NaCl. Based on the 16S rRNA gene sequence similarity, the strain SN6T exhibited 97.5% identity with *Vitreoscilla stercoraria* strain ATCC_15218 (L06174), the phylogenetically closest species with standing in nomenclature. The predominant fatty acid was hexadecenoic acid (31%). The genomic DNA G+C content of the strain SN6T was 49.4 mol %. After analysis of taxonogenomic data, phenotypic and biochemical characteristics, we concluded that strain SN6T represents a new species of the genus *Vitreoscilla* for which the name *Vitreoscilla massiliensis* sp.nov is proposed. The type strain is SN6T (=CSUR P2036 = LN870312 = DSM 100958).

## Abbreviations

<table><tr><td>CSUR</td><td>Collection de Souches de l'Unité des Rickettsies</td></tr><tr><td>DSM</td><td>Deutsche Sammlung von Mikroorganismen</td></tr><tr><td>FAME</td><td>Fatty acid methyl ester</td></tr><tr><td>GC/SM</td><td>Gaz chromatography/mass spectrometry</td></tr><tr><td>OrthoANI</td><td>Orthologous average nucleotide identity</td></tr><tr><td>COGs</td><td>Clusters of orthologous groups</td></tr><tr><td>NR BLAST</td><td>Non-redundant protein sequence basic local alignment search tool</td></tr><tr><td>ORF</td><td>Open reading frame</td></tr><tr><td>GGDC</td><td>Genome-to-genome distance calculator</td></tr></table>

## Introduction

This strain was isolated from the stool specimen of an obese Amazonian patient as part of the culturomics study [1] to search for microaerophilic bacteria from human gut. The genus *Vitreoscilla* was first described by Pringsheim in 1951, after having proposed the family *Vitreoscillaceae* in 1949. In 1986, Strohl et al. proposed three new species with validated names (*Vitreoscilla stercoraria*, *Vitreoscilla beggiatoides* and *Vitreoscilla filiformis*) of this genus [2]. In 2013, through the use of new-generation sequencing tools, the genus *Vitreoscilla* was placed in the *Neisseriaceae* family on the basis of its branching in the 16S rRNA gene tree [3]. Within its clade, members of the genus were the only ones capable of evolving in different habitats.

Since the use of the culturomic concept, the repertoire of bacteria isolated from the human digestive microbiota [4] has expanded considerably. The characterization of these new species is based on a ribosomal RNA sequencing coupled with a taxonogenomics description, a strategy combining a comparison of genomic analysis and phenotypic characteristics, including the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) spectrum. In the present study, we used this approach to facilitate the identification and the description of this novel species named *Vitreoscilla massiliensis* sp.nov.

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Saber Khelaifia
khelaifia_saber@yahoo.fr

<footnote n="1">¹ IHU-Méditerranée Infection, Marseille, France</footnote>

<footnote n="2">² IRD, MEPHI, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France</footnote>

<footnote n="3">³ IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Aix Marseille Univ, Marseille, France</footnote>

<footnote n="4">⁴ Laboratory of Biology and Health, Faculty of Sciences Ben M'sik, Hassan II University, Casablanca, Morocco</footnote>
## Materials and Methods

*Vitreoscilla massiliensis* SN6T was isolated by cultivation on 5% sheep blood agar under microaerophilic conditions at 37 °C for 48 h and the strain could not be identified by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

(MALDI-TOF MS). The bacterial spectrum obtained was incremented in our database and its comparison with those of BioTyper database spectra and our own collection did not allow for its identification. Sequencing of 16S rRNA gene of the strain SN6T showed a nucleotide sequence similarity of 97.5% with *V. stercoraria* strain (ATCC 15218) and *V. stercoraria* strain Göttingen 1488-6 (NR_025894.1), the phylogenetically closest species with standing in nomenclature (Fig. 1).

## Optimal Growth

Growth at various temperatures (28 °C, 37 °C, 42 °C, 45 °C) in different atmospheres (aerobic, microaerophilic using CampyGen from Thermo Scientific and anaerobic using AnaeroGenTM from bioMérieux) was tested by culture on Columbia agar (bioMérieux) after 48 h of incubation. The salinity acceptance limit of SN6T strain was investigated by culture on a home-made culture medium consisting of a Columbia agar culture medium (Sigma-Aldrich,

Saint-Quentin Fallavier, France) modified by adding (per liter) 5 g MgCl2 6H2O, 5 g MgSO4 7H2O, 2 g KCl, 1 g CaCl2 2H2O; 0.5 g NaBr, 0.5 g NaHCO3, and 2 g glucose with various NaCl concentrations 0, 5, 10, 25, 50, and 75 g/L. The pH range (6; 6.5; 7; 8.5) for growth was also determined and pH was adjusted by addition of HCl or NaOH.

## Biochemical and Chemotaxonomic Analysis

The abilities of the strain SN6T to use various substrates as sole carbon sources were evaluated using the API 20NE and API 50CH (bioMérieux) and the presence of some enzyme activities using APIZYM following the manufacturer's instructions. All tests were performed in duplicate. Susceptibility to antimicrobial agents was determined by the disk (i2a, Montpellier, France) diffusion method [5] on Mueller-Hinton agar in a Petri dish (BioMérieux) after 48 h of incubation at 37 °C under aerobic conditions. The interpretation of inhibition diameters to the manual measurement using a ruler was done using a Sirscan system© (i2a, Montpellier, France) according to the criteria proposed by the Comité de l'Antibiogramme of the French Society for Microbiology [6]. Cellular fatty acid methyl ester (FAME) analysis was performed by GC/MS. Two samples were prepared with approximately 65 mg of bacterial biomass per tube harvested from several culture plates. Fatty acid methyl esters were prepared as previously described by Sasser [7].

<figure><img src="image_4.png" /><figcaption>**Fig. 1** Phylogenetic tree showing the position of *Vitreoscilla massiliensis* SN6T relative to other phylogenetically close neighbors. Sequences were aligned using CLUSTALW, and phylogenetic inferences are obtained with kimura two-parameter models using the maximum-likelihood method within the MEGA software. Numbers</figcaption></figure>

at nodes are percentages of bootstrap values obtained by repeating analysis 1,000 times to generate majority consensus tree. Scale bar indicates 1% nucleotide sequence divergence. The scale bar represents 500 nm

<figure><img src="image_5.png" /></figure>
GC/MS analyses were carried out as previously described by Dione et al. [8]. Briefly, fatty acid methyl esters were separated using an Elite 5-MS column and monitored by mass spectrometry (Clarus 500—SQ 8 S, Perkin Elmer, Courtaboeuf, France). Spectral database search was performed using MS Search 2.0 operated with the Standard Reference Database 1A (NIST, Gaithersburg, USA) and the FAMEs mass spectral database (Wiley, Chichester, UK).

## Genome Sequencing and Assembly

DNA of strain SN6T was extracted on the EZ1 biorobot (Qiagen) with a EZ1 DNA tissues kit after pretreatment by a lysozyme incubation at 37 °C, as previously described [9]. Genomic DNA (gDNA) was quantified by a Qubit assay with the high-sensitivity kit (Life technologies, Carlsbad, CA, USA) and sequenced on the MiSeq Technology (IlluminaInc, San Diego, CA, USA) with the mate pair strategy, as previously described [9]. The gDNA was barcoded in order to be mixed with 11 other projects with the Nextera Mate Pair sample prep kit (Illumina). The assembly of the genome was carried out with the help of a pipeline that allowed the creation of an assembly with different softwares (Velvet [10], Spades [11] and Soap Denovo [12], on trimmed (MiSeq and Trimmomatic [13] softwares) or untrimmed data (only MiSeq software). For each of the six assemblies performed, GapCloser [12] was used to reduce gaps. Then, contamination with Phage Phix was identified (blastn against Phage Phix174 DNA sequence) and eliminated. Finally, scaffolds whose size was less than 800 bp were removed and scaffolds whose depth value was lower than 25% of the mean depth were removed (identified as possible contaminants). The best assembly was selected using different criteria (number of scaffolds, N50 and number of N). Spades gave the best assembly of this strain, with a depth coverage of 98.

## Genome Annotation and Comparison

We used Prodigal as predicting tool of open reading frames (ORFs) [14] with default parameters. The predicted ORFs were excluded if they spanned a sequencing gap region (contained N). Using BLASTP, predicted bacterial protein sequences were blasted against GenBank and clusters of orthologous groups (COG) databases, DNA G+C content was identified by The RAST Server [15], and the tRNAs and rRNAs were predicted using the tRNAScan-SE [16] and RNAmmer tools [17], respectively. SignalP was used for Signal peptides prediction [18], the number of transmembrane helices was predicted using TMHMM [19], 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. Artemis

[20] and DNA Plotter [21] were used for data management and visualization of genomic features, respectively. The Average Nucleotide identity at the genome level between *V. massiliensis* SN6 CZPV00000000.1, *V. stercoraria* ATCC_15218 (ARNN00000000.1), *V. filiformis* ATCC_43190 (CP022423.1), *Gulbenkiania mobilis* E4FC31 (LIVN00000000.1), *Chitinilyticum litopenaei* DSM_21440 (ATZJ00000000.1), *Chitinilyticum aquatile* c14 (AUMS00000000.1), *Chitinibacter tainanensis* BCRC_17254 (AUCN00000000.1), and *Snodgrassella alvi* wkB2_wkB2 (CP007446.1) was estimated using Orthologous Average nucleotide identity tool (OAT) [22].

## Results and Discussion

Based on the sequence similarity threshold values of the 16S rRNA gene that delineate a new species according to the recommendations of Stackebrandt and Ebers [23], the strain SN6T can, therefore, be classified as a new species of the genus *Vitreoscilla* and was accordingly named *V. massiliensis* SN6T [24].

## Biochemical and Chemotaxonomic Analyses

API ZYM tests show positive reactions for esterase, esterase lipase, leucine arylamidase, acid phophatase, and naphthol-AS-BI-phosphohydrolase. In API 50CH, no substrate fermentation was observed and in API 20NE assimilation of substrates was observed for L-arginine dihydrolase and potassium gluconate. Some phenotypic characteristics of SN6T with those of closely related species are presented in Table 1. The most abundant fatty acid is hexadecenoic acid (31%). Several hydroxyl fatty acids such as C₁₂:₀ 3-OH (4.5 ± 1.0) and C₁₄:₀ 3-OH (2.9 ± 0.1) are described. Other fatty acids such as 9-Hexadecenoic acid (22.0 ± 0.5), Dodecanoic acid (10.2 ± 0.6), 2-hexyl-cyclopropaneoctanoic acid (8.8 ± 0.4), Octadecenoic acid (8.0 ± 0.2), Pentadecanoic acid (5.5 ± 0.2), Tetradecanoic acid (3.3 ± 0.3), and Heptadecanoic acid (1.1 ± 0.1) were detected. The strain SN6T was resistant to Oxacillin and Metronidazole, but susceptible to other antibiotics tested.

## Genome Properties

The genome is 3,716,289 bp long with 49.4% GC content (Fig. 2, Table 2). It is composed of 10 scaffolds (composed of 13 contigs). Of the 3 716 predicted genes, 3 627 were protein-coding genes and 89 were RNAs (5 genes are 5S rRNA, 5 genes are 16S rRNA, 5 genes are 23S rRNA and 74 genes are TRNA genes). A total of 2,263 genes (62.3%) were assigned with putative function (by cogs or by NR blast). 475 genes were identified as ORFans (13.1%). The
<caption>**Table 1** Differential characteristics of *Vitreoscilla massiliensis* SN6<sup>T</sup>, *Vitreoscilla stercoraria* ATCC 15218, *Vitreoscilla filiformis* ATCC 15551, *Vitreoscilla beggiatoides* B23SS, *Gulbenkiania mobilis*</caption>

E4FC31, *Chitinibacter tainanensis* BCRC 17254, *Chitinilyticum litopenaei* DSM _21440_c1, and *Snodgrassella alvi* wkB2 wkB2

<table><thead><tr><th>Properties</th><th>V.massiliensis</th><th>V.stercoraria<sup>a</sup></th><th>V.filiformis<sup>b</sup></th><th>V.beggiatoides<sup>c</sup></th><th>G. mobilis<sup>d</sup></th><th>C.litopenaei<sup>e</sup></th><th>C.tainanensis<sup>f</sup></th><th>S. alvi<sup>g</sup></th></tr></thead><tbody><tr><td>Cell diameter (μm)</td><td>0.5</td><td>1.0</td><td>1.0–1.5</td><td>2.5–3</td><td>0.2–0.4</td><td>0.3–0.5</td><td>0.5–0.9</td><td>0.4</td></tr><tr><td>Oxygen requirement</td><td>Aerobic/Microaerophilic</td><td>Aerobic</td><td>Aerobic/Microaerophilic</td><td>Aerobic/Microaerophilic</td><td>Aerobic</td><td>Aerobic/Anaerobic</td><td>Aerobic</td><td>Microaerophilic</td></tr><tr><td>Motility</td><td>–</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>+</td><td>–</td></tr><tr><td>Endospore formation</td><td>–</td><td>Na</td><td>Na</td><td>Na</td><td>–</td><td>–</td><td>Na</td><td>Na</td></tr><tr><td>pH</td><td>7–7.5</td><td>7.5–7.7</td><td>7.5</td><td>7.5</td><td>5.5–9.0</td><td>7–11</td><td>5.5–9</td><td>6.0–6.5</td></tr><tr><td>NaCl % (w/v)</td><td>0–0.5</td><td>Na</td><td>0</td><td>0.5</td><td>1.0</td><td>0–0.75</td><td>Na</td><td>Na</td></tr><tr><td>Indole</td><td>–</td><td>Na</td><td>Na</td><td>Na</td><td>–</td><td>–</td><td>–</td><td>–</td></tr><tr><td>Production of Alkaline phosphatase</td><td>–</td><td>Na</td><td>Na</td><td>Na</td><td>Na</td><td>+</td><td>Na</td><td>Na</td></tr><tr><td>Catalase</td><td>–</td><td>–</td><td>–</td><td>–</td><td>+</td><td>+</td><td>+</td><td>+</td></tr><tr><td>Oxidase</td><td>–</td><td>–</td><td>+</td><td>+</td><td>+</td><td>–</td><td>+</td><td>–</td></tr><tr><td>Nitrate reduction</td><td>–</td><td>–</td><td>+</td><td>+</td><td>–</td><td>+</td><td>–</td><td>+</td></tr><tr><td>Urease</td><td>–</td><td>Na</td><td>Na</td><td>Na</td><td>–</td><td>–</td><td>–</td><td>+</td></tr><tr><td>β-galactosidase</td><td>–</td><td>Na</td><td>Na</td><td>Na</td><td>–</td><td>–</td><td>–</td><td>–</td></tr><tr><td>N-acetyl-glucosamine</td><td>–</td><td>Na</td><td>Na</td><td>Na</td><td>–</td><td>+</td><td>+</td><td>Na</td></tr><tr><td>Acid from L-Arabinose</td><td>+</td><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td></tr><tr><td>Trehalose</td><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td><td>+</td><td>–</td><td>Na</td></tr><tr><td>D-mannose</td><td>+</td><td>–</td><td>–</td><td>–</td><td>–</td><td>+</td><td>–</td><td>–</td></tr><tr><td>Mannitol</td><td>+</td><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td></tr><tr><td>D-glucose</td><td>+</td><td>–</td><td>+</td><td>–</td><td>–</td><td>+</td><td>–</td><td>–</td></tr><tr><td>D-fructose</td><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td><td>+</td><td>–</td><td>–</td></tr><tr><td>Maltose</td><td>+</td><td>–</td><td>–</td><td>–</td><td>–</td><td>+</td><td>–</td><td>–</td></tr><tr><td>D-lactose</td><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td><td>Na</td><td>Na</td></tr><tr><td>D-raffinose</td><td>–</td><td>Na</td><td>–</td><td>–</td><td>–</td><td>–</td><td>Na</td><td>Na</td></tr><tr><td>Habitat</td><td>Human gut</td><td>Dung of Cow</td><td>Freshwater sediments</td><td>Sandy sediments</td><td>Wastewater</td><td>Freshwater pond</td><td>Soil</td><td>Gut of Bees</td></tr></tbody></table>

Na not available

remaining genes were described as hypothetical proteins (744 genes ≥ 20.5%). A summary of the distribution of V. massiliensis genes into the different COGs categories is presented in Table 3.

## Genome Comparison

The draft genome sequence and the G+C content of V. massiliensis (3.71 MB and 49.4%) is larger than that of

<footnote><sup>a</sup>Data from Mayfield et al. [25]</footnote>

<footnote><sup>b,c</sup>Data from Strohl et al. [2]</footnote>

<footnote><sup>d</sup>Data from Vaz-Moreira et al. [26]</footnote>

<footnote><sup>e</sup>Data from Chang et al. [27]</footnote>

<footnote><sup>f</sup>Data from Chern et al. [28]</footnote>

<footnote><sup>g</sup>Data from Kwong et al. [29]</footnote>
<figure><img src="image_6.png" /><figcaption>**Fig. 2** Graphical circular map of the genome of *Vitreoscilla massiliensis* strain SN6T from outside to the center: genes on the forward strand colored by COG categories (only genes assigned to COG), genes on the reverse strand colored by COG categories (only gene assigned to COG), RNA genes (tRNAs green, rRNAs red), GC content, and GC skew (Color figure online)</figcaption></figure>

<table><caption>**Table 2** Nucleotide content and gene count levels of the genome</caption><thead><tr><th rowspan="2">Attribute</th><th colspan="2">Genome (total)</th></tr><tr><th>Value</th><th>% of total<sup>a</sup></th></tr></thead><tbody><tr><td>Size (bp)</td><td>3,716,289</td><td>100</td></tr><tr><td>G+C content (%)</td><td>1,836,063</td><td>49.42</td></tr><tr><td>Coding region (bp)</td><td>3,249,937</td><td>87.45</td></tr><tr><td>Total genes</td><td>3,716</td><td>100</td></tr><tr><td>RNA genes</td><td>89</td><td>2.39</td></tr><tr><td>Protein-coding genes</td><td>3,627</td><td>100</td></tr><tr><td>Genes with function prediction</td><td>2,263</td><td>62.39</td></tr><tr><td>Genes assigned to COGs</td><td>2,184</td><td>60.21</td></tr><tr><td>Genes with peptide signals</td><td>677</td><td>18.66</td></tr><tr><td>Genes with transmembrane helices</td><td>774</td><td>21.33</td></tr><tr><td>Genes associated to virulence</td><td>715</td><td>19.71</td></tr><tr><td>ORFn genes</td><td>475</td><td>13.09</td></tr><tr><td>Genes associated with PKS or NRPS</td><td>20</td><td>0.55</td></tr><tr><td>Genes associated to toxine/antitoxine</td><td>115</td><td>3.17</td></tr></tbody></table>

V. stercoraria (2.58 MB and 43.9% respectively). Also, the gene content of V. massiliensis is larger than that of (3,627 and 2,440 respectively). The distribution of genes into COG categories was similar in all 7 compared genomes (Fig. 3). All genomes were compared with V. massiliensis using Orthologous average nucleotide identity. The OrthoANI analysis showed that identity nucleotide value is

76.4% with V. stercoraria which is lower than 95% (Fig. 4). Likewise, we obtained similar results for the analysis of the digital DNA-DNA hybridization (dDDH) with 31.60% between V. massiliensis and V. stercoraria (Table 4).

## Conclusion

Based on the phenotypic characteristics, and phylogenetic and genomic analyses of strain SN6T, we suggest the creation of a new species within the *Vitreoscilla genus*, for which the name *V. massiliensis* sp. nov., is proposed.

## Description of *Vitreoscilla massiliensis* sp. nov.

*Vitreoscilla massiliensis* (mas.si.li.en'sis. L. fem. adj. massiliensis, of Massilia, the Latin name of Marseille where strain SN6T was first isolated).

Cells are Gram-negative (0.5 × 1.5–2 µm), non-motile, non-spore-forming, and often occur in a long chain under electron microscopy. *V. massiliensis* SN6T grows at 28–37 °C and pH 7–7.5 and does not grow above 0.5% salinity. *V. massiliensis* SN6T grows under microaerophilic atmosphere and a lower growth was observed under anerobic conditions. On agar plates, colonies were gray, smooth, and hemolytic with 0.5 to 1 mm in diameter after 48 h of incubation under aerobic conditions. They are catalase and oxidase negative. Tests were negative for urease, the reduction of nitrates, indole production, and fermentation of β-galactosidase. API 50CH shows that the carbohydrates provided by this panel were not used. *V. massiliensis* SN6T is susceptible to Vancomycin (0.5), Cefotaxime (0.94), Tobamycin (0.38 µg), Fosfomycin (16 µg), Teicoplanin (1.5 µg), Rifampicin (0.29 µg), Colistin (0.32 µg), Imipenem (0.23 µg), Erythromycin (0.25 µg), Ceftriaxone (0.32 µg), and resistant to Oxacillin and Metronidazole. Major fatty acids are hexadecanoic acid (C₁₆:₀), 9-hexadecenoic acid (C₁₆:₁n₇), and an unusual cylo fatty acid named 2-hexylcyclopropaneoctanoic acid (C₁₆:₀ 9,10-methylene). The DNA G+C content is about 49.4%.

The type strain is SN6T (=CSUR P2036 =LN870312 =DSM 100958) and was isolated from the stool specimen of an obese Amazonian patient.

**Acknowledgements** The authors thank the Xegen Company (http://www.xegen.fr/) for automating the genomic annotation process. They also thank Aurelia Caputo for submitting the genomic sequences to GenBank.

This work has benefited from the French State support, managed by the 'Agence Nationale pour la Recherche', including the "Programme d'Investissement d'avenir" under the reference Méditerranée Infection

<footnote><sup>a</sup>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</footnote>
<table><caption>**Table 3** Number of genes associated with the 25 general COG functional categories</caption><thead><tr><th>Code</th><th>Value</th><th>% of total</th><th>Description</th></tr></thead><tbody><tr><td>[J]</td><td>213</td><td>5.872622</td><td>Translation</td></tr><tr><td>[A]</td><td>1</td><td>0.027570996</td><td>Rna processing and modification</td></tr><tr><td>[K]</td><td>121</td><td>3.3360906</td><td>Transcription</td></tr><tr><td>[L]</td><td>88</td><td>2.4262476</td><td>Replication, recombination and repair</td></tr><tr><td>[B]</td><td>4</td><td>0.110283986</td><td>Chromatin structure and dynamics</td></tr><tr><td>[D]</td><td>32</td><td>0.8822719</td><td>Cell cycle control, mitosis and meiosis</td></tr><tr><td>[Y]</td><td>0</td><td>0</td><td>Nuclear structure</td></tr><tr><td>[V]</td><td>44</td><td>1.2131238</td><td>Defense mechanisms</td></tr><tr><td>[T]</td><td>85</td><td>2.3435347</td><td>Signal transduction mechanisms</td></tr><tr><td>[M]</td><td>140</td><td>3.8599393</td><td>Cell wall/membrane biogenesis</td></tr><tr><td>[N]</td><td>29</td><td>0.7995589</td><td>Cell motility</td></tr><tr><td>[Z]</td><td>0</td><td>0</td><td>Cytoskeleton</td></tr><tr><td>[W]</td><td>19</td><td>0.52384895</td><td>Extracellular structures</td></tr><tr><td>[U]</td><td>27</td><td>0.7444169</td><td>Intracellular trafficking and secretion</td></tr><tr><td>[O]</td><td>97</td><td>2.6743865</td><td>Post-translational modification, protein turnover, chaperones</td></tr><tr><td>[X]</td><td>77</td><td>2.1229665</td><td>Mobilome, prophages, transposons</td></tr><tr><td>[C]</td><td>177</td><td>4.8800664</td><td>Energy production and conversion</td></tr><tr><td>[G]</td><td>125</td><td>3.4463744</td><td>Carbohydrate transport and metabolism</td></tr><tr><td>[E]</td><td>287</td><td>7.9128757</td><td>Amino acid transport and metabolism</td></tr><tr><td>[F]</td><td>64</td><td>1.7645438</td><td>Nucleotide transport and metabolism</td></tr><tr><td>[H]</td><td>119</td><td>3.2809484</td><td>Coenzyme transport and metabolism</td></tr><tr><td>[I]</td><td>133</td><td>3.6669421</td><td>Lipid transport and metabolism</td></tr><tr><td>[P]</td><td>136</td><td>3.7496552</td><td>Inorganic ion transport and metabolism</td></tr><tr><td>[Q]</td><td>90</td><td>2.4813895</td><td>Secondary metabolites biosynthesis, transport and catabolism</td></tr><tr><td>[R]</td><td>234</td><td>6.4516125</td><td>General function prediction only</td></tr><tr><td>[S]</td><td>145</td><td>3.9977942</td><td>Function unknown</td></tr><tr><td></td><td>1443</td><td>39.784946</td><td>Not in COGs</td></tr></tbody></table>

<figure><img src="image_7.png" /><figcaption>**Fig. 3** Distribution of functional classes of predicted genes according to the clusters of orthologous groups of proteins</figcaption></figure>

<figure><img src="image_8.png" /></figure>
<figure><img src="image_9.png" /><figcaption>**Table 4** Pairwise comparison of *Vitreoscilla massiliensis* SN6T with other species using GGDC, formula 2(DNA-DNA hybridization estimates based on identities/HSP length)</figcaption></figure>

<table><thead><tr><th></th><th>C.tainanensis</th><th>C.aquatile</th><th>G.mobilis</th><th>S.alvi</th><th>C.litopenaei</th><th>V.stercoraria</th><th>V.filiformis</th></tr></thead><tbody><tr><td>V.massiliensis</td><td>23.20%<br>2.4±</td><td>30.00%<br>2.45±</td><td>29.40%<br>2.45±</td><td>26.80%<br>2.45±</td><td>30.80%<br>2.45±</td><td>21.50%<br>2.35±</td><td>28.30%<br>2.45±</td></tr><tr><td>C.tainanensis</td><td></td><td>18.80%<br>2.3±</td><td>19.30%<br>2.25±</td><td>31.10%<br>2.45±</td><td>19.20%<br>2.3±</td><td>19.70%<br>2.3±</td><td>26.30%<br>2.4±</td></tr><tr><td>C.aquatile</td><td></td><td></td><td>18.30%<br>2.25±</td><td>37.20%<br>2.5±</td><td>25.60%<br>2.45±</td><td>28.40%<br>2.45±</td><td>19.50%<br>2.3±</td></tr><tr><td>G.mobilis</td><td></td><td></td><td></td><td>29.30%<br>2.45±</td><td>18.7%<br>2.25±</td><td>31.20%<br>2.45±</td><td>18.50%<br>2.3±</td></tr><tr><td>S.alvi</td><td></td><td></td><td></td><td></td><td>33.8%<br>2.5±</td><td>24.00%<br>2.35±</td><td>29.60%<br>2.45±</td></tr><tr><td>C.litopenaei</td><td></td><td></td><td></td><td></td><td></td><td>32.9%<br>2.5±</td><td>18.40%<br>2.25±</td></tr><tr><td>V.stercoraria</td><td></td><td></td><td></td><td></td><td></td><td></td><td>31.60%<br>2.45±</td></tr></tbody></table>

V.massiliensis *Vitreoscilla massiliensis* SN6T, G.mobilis *Gulbenkiania mobilis* E4FC31, C.litopenaei *Chitinilyticum litopenaei* DSM_21440_c1, S.alvi *Snodgrassella alvi* wkB2 wkB2, C.tainanensis *Chitinibacter tainanensis* BCRC 17254, C.aquatile *Chitinilyticum aquatile* c14, V.stercoraria *Vitreoscilla stercoraria* ATCC 15218 and V.filiformis *Vitreoscilla filiformis* ATCC 15551
10-IAHU-03. This work was supported by Région Provence-Alpes-Côte d'Azur and European funding FEDER PRIMI.

**Author Contributions** SN, MM, and MR performed the experiments. SN and SK wrote the manuscript. SK, DR, RS, and PEF reviewed the drafts of the manuscript. SK, JCL, and DR are responsible for data interpretation.

## Declarations

**Conflict of interest** The authors have no conflicts of interest to declare.

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