Abstract
Strain FF10T (= CSUR P1489 = DSM 100884) was isolated from the oral cavity of a lizard (Varanus niloticus) in Dakar, Senegal. Here we used a polyphasic study including phenotypic and genomic analyses to describe the strain FF10T. Results support strain FF10T being a Gram-positive coccus, facultative anaerobic bacterium, catalase-negative, non-motile and non-spore forming. The sequenced genome counts 2.46 Mb with one chromosome but no plasmid. It exhibits a G+C content of 40.4% and contains 2471 protein-coding and 45 RNA genes. On the basis of these data, we propose the creation of Streptococcus varani sp. nov.
Keywords: Culturomics, genome, Streptococcus varani, taxonogenomics, Varanus niloticus
Introduction
The genus Streptococcus contains 113 recognized species and 22 subspecies (http://www.bacterio.net/streptococcus.html) as of 5 February 2016. These species are Gram-positive cocci, chain-forming, facultative anaerobes and catalase negative [1]. Many of them are associated with human or animal hosts. Previous studies have reported that a large number of Streptococcus species colonize the oral cavities of humans and animals [2]. Among oral streptococci isolated from animals, we note: Streptococcus ursoris isolated from the oral cavities of bears [1], Streptococcus orisratti isolated from the surface of the lower molars of Sprague-Dawley rats [3], Streptococcus oriloxodontae isolated from the oral cavities of elephants [4], and Streptococcus mutans isolated from dental plaque [5].
Recently, with next-generation sequencing technology able to sequence whole genomes in a short time, and mass spectrometric analysis of bacteria, we have had easy access to genetic and proteomic information [6]. Therefore, we propose a polyphasic approach combining genomic properties in combination with matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) spectra and phenotypic characteristics to describe new bacterial species. The strain FF10T (= CSUR P1489 = DSM 100884) was isolated from the oral cavity of the Nile monitor (Varanus niloticus) in Dakar, Senegal.
Here, we present a summary classification and a set of features for Streptococcus varani sp. nov. strain FF10T (= CSUR P1489 = DSM 100884), including the description of its complete genome and annotation. These characteristics support the circumscription of the species S. varani.
Classification and Features of the Strain
Strain identification
In 2014, a sample was collected from the oral cavity of a lizard reptile named ‘Nile monitor’ (Varanus niloticus) in Dakar, Senegal, and stored at –80°C. In October 2014, the strain FF10T (Table 1) was isolated from this sample by cultivation on 5% sheep blood-enriched Columbia agar (BioMérieux, Marcy l'Etoile, France) at 37°C with 5% CO2.
Table 1.
Classification and general features of Streptococcus varani strain FF10T
| Property | Term | References |
|---|---|---|
| Classification | Domain Bacteria | [25] |
| Phylum Firmicutes | [26], [27] | |
| Class Bacilli | [28], [29] | |
| Order Lactobacillales | [29], [30] | |
| Family Streptococcaceae | [31], [32] | |
| Genus Streptococcus | [31], [33], [34] | |
| Species Streptococcus varani | ||
| Type strain FF10T | ||
| Gram stain | Positive | |
| Cell shape | Cocci | |
| Motility | Non-motile | |
| Sporulation | Non-spore forming | |
| Temperature range | Mesophile | |
| Optimum temperature | 37°C | |
| Carbon source | Unknown | |
| Habitat | Lizard | |
| Salinity | Unknown | |
| Oxygen requirement | Facultative anaerobe | |
| Biotic relationship | Free living | |
| Pathogenicity | Unknown | |
| Geographic location | Dakar | |
| Sample collection | October 22, 2014 | |
| Latitude | 13.7167 | |
| Longitude | –16.4167 | |
| Altitude | 51 m above sea level |
To identify the strain, MALDI-TOF MS protein analysis was performed as previously described [7] using a Microflex spectrometer (Bruker Daltonics, Leipzig, Germany). The 12 FF10T spectra were imported into the MALDI BioTyper software (version 2.0, Bruker) and analysed by standard pattern matching (with default parameter settings) against the main spectra of 6252 bacteria. From the resulting scores, the tested species may or may not be identified compared with the instrument's database; a score ≥ 2 with a validly published species enables identification at the species level; a score ≥ 1.7 and < 2 allows identification at the genus level; and a score < 1.7 does not enable any identification. For strain FF10T, the scores obtained were lower than 1.306, suggesting that our strain was not a member of any known species. The reference mass spectrum of S. varani strain FF10T was added to our database (Fig. 1). A gel view comparing the spectrum of strain FF10T with those of other Streptococcaceae species is shown in Fig. 2. The bacterium was identified using 16S rRNA PCR coupled with sequencing, as previously described [8]. Strain FF10T exhibited 96% 16S rRNA sequence similarity with Streptococcus minor strain DSM 17118 (GenBank accession number: AY232832), the phylogenetically closest bacterial species with standing in nomenclature-validated Streptococcus species (Fig. 3). This value was lower than the 98.7% 16S rRNA gene sequence threshold recommended by Stackebrandt and Ebers to delineate a new species without carrying out DNA–DNA hybridization [9]. Streptococcus varani strain FF10T 16S rRNA accession number from GenBank Sequence Database is LN810501.
Fig. 1.
Reference mass spectrum from Streptococcus varani sp. nov. strain FF10T. Spectra from 12 individual colonies were compared and a reference spectrum was generated.
Fig. 2.
Gel view comparing Streptococcus varani sp. nov. strain FF10T spectra with other members of the Streptococcus genus. The gel view displays the raw spectra of loaded spectrum files arranged in a pseudo-gel like look. The x-axis records the m/z value. The left y-axis displays the running spectrum number originating from subsequent spectra loading. The peak intensity is expressed by a Grey-scale scheme code. The colour bar and the right y-axis indicate the relation between the colour in which a peak is displayed and the peak intensity in arbitrary units. Displayed species are indicated on the left.
Fig. 3.
Phylogenetic tree showing the position of Streptococcus varani sp. nov. strain FF10T relative to other type strains within the genus Streptococcus. The strains and their corresponding GenBank accession numbers for 16S rRNA genes are in parenthesis. The tree was constructed by the neighbour joining method with Kimura two-parameter model and 1000 bootstrap replications using the MEGA6 software and rooted by using Lactococcus lactis (EU723831) strain as the out-group.
Growth characterization
Different growth temperatures (25°C, 30°C, 37°C, 45°C and 56°C) were tested. Growth was obtained between 25 and 37°C, with optimal growth at 37°C. Growth of the strain was tested also under anaerobic and microaerophilic conditions using GENbag anaer and GENbag microaer systems, respectively (bioMérieux), and under aerobic conditions, with or without 5% CO2. Strain growth was observed under anaerobic and microaerophilic conditions but optimal growth was observed under aerobic conditions. Colonies were translucent and yellow with a regular surface, haemolytic on 5% sheep blood-enriched Columbia agar (bioMérieux), and approximately 1 mm in diameter. A motility test was negative. Cells were Gram-positive cocci, unable to form spores (Fig. 4), and with mean diameter of 0.6 μm (range 0.4–0.8 μm) and mean length of 1.3 μm (range 0.7–1.9 μm) (Fig. 5).
Fig. 4.
Gram staining of Streptococcus varani sp. nov. strain FF10T.
Fig. 5.
Transmission electron microscopy of Streptococcus varani sp. nov. strain FF10T, using a TECNAI G20 (FEI) at an operating voltage of 200 keV. The scale bar represents 500 nm.
Biochemical characterization and antibiotic susceptibility
This bacterium, FF10T, exhibits neither catalase nor oxidase activities. Using an API ZYM strip (bioMérieux), positive reactions were observed for alkaline phosphatase, esterase, esterase-lipase, lipase, leucine arylamidase, acid phosphatase, β-glucosidase, β-galactosidase, α-mannosidase, and α-fucosidase. Negative reactions were noted for cystine arylamidase, valine arylamidase, trypsin, α-chymotrypsin, α-glucosidase, α-galactosidase, β-glucuronidase, naphthol-AS-BI-phosphohydrolase, and N-acetyl-β-glucosaminidase. Using an API 20 NE strip (bioMérieux), positive reactions were observed only for the esculin hydrolysis test whereas negative reactions were observed for nitrate reduction, urease, indole production, arginine dihydrolase, glucose fermentation, arabinose, mannose, mannitol, N-acetyl-glucosamine, maltose, gluconate, caprate, adipate, malate, citrate, phenyl-acetate assimilation, and gelatine hydrolysis.
Using API 50 CH strip (bioMérieux), negative reactions were observed for the fermentation of glycerol, erythritol, d-arabinose, l-arabinose, d-ribose, d-xylose, l-xylose, d-adonitol, methyl-β-d-xylopyranoside, d-galactose, d-glucose, d-fructose, d-mannose, l-sorbose, l-rhamnose, dulcitol, inositol, d-mannitol, d-sorbitol, methyl-αd-xylopyranoside, methyl-αd-glucopyranoside, N-acetylglucosamine, amygdalin, arbutin, salicin, d-cellobiose, d-maltose, d-lactose, d-mellibiose, d-saccharose, d-trehalose, inulin, d-melezitose, d-raffinose, amidon, glycogen, xylitol, gentiobiose, d-turanose, d-lyxose, d-tagatose, d-fucose, l-fucose, d-arabitol, l-arabitol, potassium gluconate, potassium 2-ketogluconate and potassium-5-ketogluconate.
Streptococcus varani strain FF10T was susceptible to penicillin, amoxicillin, amoxicillin/clavulanic acid, ticarcillin, ceftriaxone, cefalotin, imipenem, gentamicin, kanamycin, trimethoprim/sulfamethoxazole, erythromycin, doxycycline, metronidazole, vancomycin and rifampicin, but resistant to ciprofloxacin, nitrofurantoin and colistin.
The differential phenotypic characteristics with other Streptococcus species (S. minor [10], Streptococcus plurextorum [11], S. ursoris [1] and S. orisratti [3]) are summarized in Table 2.
Table 2.
Differential characteristics of Streptococcus varani sp. nov. strain FF10T with other strains (Streptococcus minor[8], Streptococcus plurextorum[9], Streptococcus ursoris[1] and Streptococcus orisratti[3])
| Characteristics | S. varani | S. minor | S. plurextorum | S. ursoris | S. orisratti |
|---|---|---|---|---|---|
| Cell diameter (μm) | 0.4–0.8 | <1 | na | 0.5–0.7 | na |
| Oxygen requirement | Facultative anaerobic | Microaerobic | Facultative anaerobic | Facultative anaerobic | Facultative anaerobic |
| Gram stain | + | + | + | + | + |
| Motility | – | na | – | na | – |
| Endospore formation | – | na | na | – | na |
| Production of: | |||||
| Alkaline phosphatase | + | – | – | – | – |
| Acid phosphatase | + | + | + | + | + |
| Catalase | – | na | – | + | – |
| Oxidase | – | na | – | na | na |
| Nitrate reductase | – | na | na | na | na |
| Urease | – | – | – | – | na |
| α-galactosidase | – | W | + | + | – |
| β-galactosidase | + | – | + | – | – |
| β-glucuronidase | – | – | + | – | – |
| α-glucosidase | – | na | – | + | na |
| β-glucosidase | + | na | – | + | na |
| Esterase | + | na | – | na | na |
| Esterase lipase | + | na | – | na | na |
| Naphthol-AS-BI-phosphohydrolase | – | na | – | + | + |
| N-acetyl-β-glucosaminidase | – | na | – | – | na |
| Utilization of: | |||||
| Gluconate | – | – | DP | na | na |
| d-ribose | – | – | – | + | – |
| d-xylose | – | – | – | – | na |
| d-fructose | – | + | + | + | + |
| d-glucose | – | + | + | + | + |
| d-mannose | – | + | – | + | + |
| d-lactose | – | + | + | + | + |
| d-maltose | – | + | + | + | + |
| dl-arabinose | – | – | – | – | – |
| Habitat | Lizard | Dog, cat and calf | Pigs | Bears | Rats |
+, positive; –, negative; DP, delayed production; W, weak reaction; na, not available.
Genome Description
Genome sequencing and assembly
The DNA was extracted using the phenol/chloroform method as previously described [12]. Genomic DNA (gDNA) of S. varani FF10T was sequenced on the MiSeq Technology (Illumina Inc., San Diego, CA, USA) using the mate-pair strategy. The gDNA was bar-coded in order to be mixed with 11 other projects with the Nextera Mate Pair sample prep kit (Illumina). The gDNA was quantified by a Qubit assay with the high sensitivity kit (Thermo Fisher Scientific, Waltham, MA, USA) to 62.4 mg/L. The mate-pair library was prepared with 1.5 μg of genomic DNA using the Nextera mate-pair Illumina guide. The gDNA sample was simultaneously fragmented and tagged with a mate-pair junction adapter. The fragmentation pattern was validated on an Agilent 2100 BioAnalyzer (Agilent Technologies Inc., Santa Clara, CA, USA) with a DNA 7500 LabChip. The DNA fragments ranged from 1.5 kb up to 11 kb with optimal size of 5.8 kb. No size selection was performed and 591 ng of tagmented fragments were circularized. The circularized DNA was mechanically sheared to small fragments, optimally at 697 bp, on the Covaris device S2 in T6 tubes (Covaris, Woburn, MA, USA). The library profile was visualized on a High Sensitivity Bioanalyzer LabChip (Agilent Technologies Inc.) and the final concentration library was measured at 75.52 nmol/L. The libraries were normalized at 2 nM and pooled. After a denaturation step and dilution at 15 pM, the pool of libraries was loaded onto the reagent cartridge and then onto the instrument along with the flow cell. Automated cluster generation and sequencing were performed in a single 39-h run in a 2 × 251-bp.
Total information of 5.9 Gb was obtained from a 624 K/mm2 cluster density with a cluster passing quality control filters of 96.33% (12 040 000 clusters). Within this run, the index representation for S. varani FF10T was determined to 5.26%. The 610 160 paired reads were filtered according to the read qualities. These reads were trimmed then assembled.
Genome Annotation and Genome Analysis
Open reading frames (ORFs) were predicted using Prodigal (http://prodigal.ornl.gov/) with default parameters. However, the predicted ORFs were excluded if they spanned a sequencing gap region. The predicted bacterial protein sequences were searched against GenBank [13] and Clusters of Orthologous Groups (COG) databases using BLASTP. The tRNAs and rRNAs were predicted using the tRNAScan-SE [14] and RNAmmer [15] tools, respectively. Signal peptides and numbers of transmembrane helices were predicted using SignalP [16], and TMHMM [17], respectively. Mobile genetic elements were predicted using PHAST [14] and RAST [18]. ORFans were identified if their BLASTP E-value was lower than 1e-03 for alignment length >80 amino acids. If alignment lengths were <80 amino acids, we used an E-value of 1e-05. Such parameter thresholds have already been used in previous work to define ORFans. Artemis [19] and DNA Plotter [20] were used for data management and visualization of genomic features, respectively. The Mauve alignment tool (version 2.3.1) was used for multiple genomic sequence alignment [21].
The mean level of nucleotide sequence similarity at the genome level between S. varani and other bacteria (S. orisratti (ARCG01000001.1), S. tigurinus (AORU01000001.1), Streptococcus parasanguinis (CP002843.1), Streptococcus agalactiae (AEQQ01000001.1), S. plurextorum (AUIO01000001.1), S. minor (AQYB01000001.1), Streptococcus oralis (ADMV01000001.1), Streptococcus pyogenes (AE004092.2), Streptococcus vestibularis (AEVI01000001.1), Streptococcus peroris (AEVF01000001.1) and Lactococcus lactis (NC_002662.1)) was estimated using the Average Genomic Identity of gene Sequences (AGIOS) home-made software [22]. Overall, this software combines the functionality of other software programs: Proteinortho [23] (detects orthologous proteins between genomes compared two by two, then retrieves the corresponding genes) and the Needleman–Wunsch global alignment algorithm (determines the mean percentage of nucleotide sequence identity among orthologous ORFs).
Genome properties
The genome is 2 460 376 bp long with 40.4% GC content (Table 3). It is composed of 16 contigs (Fig. 6). Of the 2516 predicted genes, 2471 were protein-coding genes, and 45 were RNAs (one gene is 5S rRNA, one gene is 16S rRNA, one gene is 23S rRNA, 42 genes are tRNA genes). No genes were identified as ORFans (0.0%). The remaining genes were annotated as hypothetical proteins (293 genes ≥ 11.64%). Table 4 distributes the genes into COG functional categories. The genome sequence has been deposited in GenBank under accession number GCA_001375655.
Table 3.
Nucleotide content and gene count levels of the genome
| Attribute | Value | % of totala |
|---|---|---|
| Genome size (bp) | 2 460 376 | 100 |
| DNA coding (bp) | 2 170 614 | 88.2 |
| DNA G+C (bp) | 993 991 | 40.4 |
| Total genes | 2516 | 100 |
| Protein coding genes | 2471 | 98.21 |
| RNA genes | 45 | 1.78 |
| Genes with function prediction | 1852 | 73.60 |
| Genes assigned to COGs | 1746 | 69.39 |
| Genes with signal peptides | 118 | 4.68 |
| Genes with transmembrane helices | 565 | 22.45 |
| Genes associated with resistant genes | 0 | 0 |
| Genes associated with PKS or NRPS | 5 | 0.19 |
| ORFans genes | 0 | 0 |
| CRISPRs repeats | 0 | 0 |
| Genes associated with Pfam-A domains | 2264 | 89.98 |
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.
Fig. 6.
Graphical circular map of the chromosome. From outside to the centre. Genes on the forward strand coloured by COG categories (only genes assigned to COG), genes on the reverse strand coloured by COG categories (only gene assigned to COG), RNA genes (tRNAs green, rRNAs red), GC content, and GC skew.
Table 4.
Number of genes associated with the 25 general COG functional categoriesa
| Code | Value | % | Description |
|---|---|---|---|
| J | 144 | 8.18 | Translation |
| A | 0 | 0 | RNA processing and modification |
| K | 101 | 5.74 | Transcription |
| L | 91 | 5.17 | Replication, recombination and repair |
| B | 0 | 0 | Chromatin structure and dynamics |
| D | 23 | 1.31 | Cell cycle control, mitosis and meiosis |
| Y | 0 | 0 | Nuclear structure |
| V | 37 | 2.10 | Defence mechanisms |
| T | 41 | 2.33 | Signal transduction mechanisms |
| M | 83 | 4.71 | Cell wall/membrane biogenesis |
| N | 5 | 0.28 | Cell motility |
| Z | 0 | 0 | Cytoskeleton |
| W | 0 | 0 | Extracellular structures |
| U | 20 | 1.13 | Intracellular trafficking and secretion |
| O | 54 | 3.07 | Post-translational modification, protein turnover, chaperones |
| C | 37 | 2.10 | Energy production and conversion |
| G | 111 | 6.30 | Carbohydrate transport and metabolism |
| E | 145 | 8.24 | Amino acid transport and metabolism |
| F | 69 | 3.92 | Nucleotide transport and metabolism |
| H | 42 | 2.39 | Coenzyme transport and metabolism |
| I | 35 | 1.99 | Lipid transport and metabolism |
| P | 71 | 4.03 | Inorganic ion transport and metabolism |
| Q | 13 | 74 | Secondary metabolites biosynthesis, transport and catabolism |
| R | 156 | 8.86 | General function prediction only |
| S | 154 | 8.75 | Function unknown |
| — | 328 | 18.64 | Not in COGs |
The total is based on the total number of protein-coding genes in the annotated genome.
Comparison with other genomes
The draft genome of S. varani (2.46 Mb) is larger than those of S. agalactiae (2.11 Mb), S. minor (1.93 Mb), S. oralis (1.90 Mb), S. orisratti (2.41 Mb), S. parasanguinis (2.15 Mb), S. peroris (1.63Mb), S. plurextorum (2.10 Mb), S. pyogenes (1.85 Mb), S. tigurinus (2.18 Mb), S. vestibularis (1.84 Mb). The G+C content of S. varani (40.40%) is lower than those of S. minor (41.10%), S. oralis (44.40%), S. parasanguinis (41.70%), S. plurextorum (41.10) but higher than those of S. agalactiae (35.30%), S. orisratti (38.50%), S. peroris (39.10%), S. pyogenes (38.50%), S. tigurinus (40.30%) and S. vestibularis (39.60%).
Similarly, the protein-coding genes of S. varani (2471) are larger than those of S. agalactiae, S. minor, S. oralis, S. orisratti, S. parasanguinis, S. peroris, S. plurextorum, S. pyogenes, S. tigurinus and S. vestibularis (2139, 1903, 1795, 2319, 1982, 1608, 2081, 1776, 2146 and 1812, respectively). The gene content of S. varani (2516) is larger than that of S. agalactiae, S. minor, S. oralis, S. orisratti, S. parasanguinis, S. peroris, S. plurextorum, S. pyogenes, S. tigurinus and S. vestibularis (2164, 1948, 1830, 2348, 2055, 1641, 2116, 1854, 2197 and 1838, respectively). However, the COG category gene distribution is similar in all genomes compared (Fig. 7). Among species with standing in nomenclature, AGIOS values ranged from 81.54 between S. peroris and S. oralis to 65.60 between L. lactis and S. varani (Table 5). To evaluate the genomic similarity among the strains, we determined two parameters, dDDH, which exhibits high correlation with DDH [24], and AGIOS [22], which was designed to be independent of DDH (Table 6).
Fig. 7.
Distribution of predicted genes of Streptococcus varani strain FF10T and 11 other closely related species into COG categories.
Table 5.
The numbers of orthologous protein shared between genomes (upper right)a
| S. varani | S. minor | S. agalactiae | S. oralis | S. orisratti | S. parasanguinis | S. peroris | S. plurextorum | S. pyogenes | S. tigurinus | S. vestibularis | L. lactis | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Streptococcus varani | 2471 | 476 | 1079 | 1016 | 1133 | 1067 | 975 | 1044 | 972 | 1089 | 983 | 952 |
| Streptococcus minor | 76.99 | 1903 | 997 | 1000 | 1089 | 1045 | 962 | 1024 | 930 | 1023 | 989 | 902 |
| Streptococcus agalactiae | 69.62 | 69.74 | 2139 | 982 | 1082 | 1030 | 936 | 1020 | 1022 | 1036 | 1008 | 915 |
| Streptococcus oralis | 70.91 | 70.91 | 69.62 | 1795 | 1035 | 1149 | 1171 | 994 | 911 | 1261 | 1031 | 887 |
| Streptococcus orisratti | 71.00 | 70.83 | 73.03 | 70.46 | 2319 | 1110 | 1001 | 1059 | 976 | 1092 | 1066 | 930 |
| Streptococcus parasanguinis | 70.27 | 70.37 | 69.26 | 74.95 | 69.97 | 1982 | 1101 | 1061 | 959 | 1156 | 1068 | 915 |
| Streptococcus peroris | 70.79 | 70.69 | 70.31 | 81.54 | 70.73 | 75.43 | 1608 | 950 | 870 | 1170 | 978 | 845 |
| Streptococcus plurextorum | 70.19 | 70.31 | 70.95 | 70.04 | 72.20 | 69.49 | 70.12 | 2081 | 951 | 1031 | 966 | 856 |
| Streptococcus pyogenes | 70.19 | 70.00 | 74.23 | 70.10 | 73.04 | 69.97 | 70.59 | 71.26 | 1176 | 932 | 903 | 840 |
| Streptococcus tigurinus | 70.58 | 70.52 | 69.82 | 93.01 | 70.27 | 74.91 | 81.42 | 69.96 | 69.92 | 2146 | 1051 | 892 |
| Streptococcus vestibularis | 70.47 | 70.45 | 71.67 | 71.82 | 72.94 | 72.11 | 72.00 | 71.56 | 72.05 | 71.69 | 1812 | 892 |
| Lactococcus lactis | 65.60 | 65.36 | 66.90 | 66.33 | 66.46 | 66.03 | 66.70 | 65.63 | 66.68 | 66.09 | 66.63 | 2650 |
Average percentage similarity of nucleotides corresponding to orthologous protein shared between genomes (lower left) and numbers of proteins per genome (bold).
Table 6.
Pairwise comparison of Streptococcus varani with eight other species using GGDC, formula 2 (DDH estimates based on identities / HSP length)a
|
S. varani |
S. minor |
S. agalactiae |
S. oralis |
S. orisratti |
S. parasanguis |
S. peroris |
S. plurextorum |
S. pyogenes |
S. tigurinus |
S. vestibularis |
|
|---|---|---|---|---|---|---|---|---|---|---|---|
| Streptococcus varani | 100% ± 00 | 24.7% ± 2.57 | 25.7% ± 2.53 | 25.0% ± 2.57 | 22.4% ± 2.60 | 25.8% ± 2.56 | 22.7% ± 2.57 | 25.2% ± 2.60 | 26.3% ± 2.72 | 25.3% ± 2.59 | 23.1% ± 2.59 |
| Streptococcus minor | 100% ± 00 | 23.4% ± 2.53 | 25.0% ± 2.57 | 23.2% ± 2.58 | 24.8% ± 2.73 | 25.0% ± 3.01 | 22.7% ± 2.58 | 27.4% ± 2.59 | 49.8% ± 3.14 | 25.4% ± 2.64 | |
| Streptococcus agalactiae | 100% ± 00 | 25.0% ± 2.57 | 22.4% ± 2.60 | 25.8% ± 2.56 | 22.7% ± 2.57 | 25.2% ± 2.60 | 26.3% ± 2.72 | 25.3% ± 2.59 | 23.1% ± 2.59 | ||
| Streptococcus oralis | 100% ± 00 | 23.2% ± 2.58 | 24.8% ± 2.73 | 25.0% ± 3.01 | 22.7% ± 2.58 | 27.4% ± 2.59 | 49.8% ± 3.14 | 25.4% ± 2.64 | |||
| Streptococcus orisratti | 100% ± 00 | 24.9% ± 2.57 | 23.5% ± 2.59 | 25% ± 2.61 | 23.2% ± 2.61 | 22.6% ± 2.58 | 23.5% ± 2.60 | ||||
| Streptococcus parasanguis | 100% ± 00 | 26..3% ± 2.77 | 23.1% ± 2.58 | 27.6% ± 2.59 | 24.5% ± 2.72 | 27.4% ± 2.68 | |||||
| Streptococcus peroris | 100% ± 00 | 24.9% ± 2.57 | 25.8% ± 2.59 | 24.9% ± 3.01 | 25.9% ± 2.65 | ||||||
| Streptococcus plurextorum | 100% ± 00 | 23.8% ± 2.60 | 21.9% ± 2.58 | 23.3% ± 2.58 | |||||||
| Streptococcus pyogenes | 100% ± 00 | 25.9% ± 2.59 | 24.7% ± 2.61 | ||||||||
| Streptococcus tigurinus | 100% ± 00 | 26% ± 2.64 | |||||||||
| Streptococcus vestibularis | 100% ± 00 |
The confidence intervals indicate the inherent uncertainty in estimating DDH values from intergenomic distances based on models derived from empirical test data sets (which are always limited in size). These results are in accordance with the 16S rRNA (Fig. 3) and phylogenomic analyses as well as the GGDC results.
Conclusion
On the basis of phenotypic, phylogenetic and genomic analyses, we formally propose the creation of Streptococcus varani sp. nov. that contains the strain FF10T. This bacterial strain has been isolated from the oral cavities of a lizard (Varanus niloticus) in Dakar, Senegal.
Description of Streptococcus varani sp. nov. strain FF10T
Streptococcus varani (va.ra'ni. NL. gen. n. varani, from Varanus, the Latin name from the lizard which the type strain was isolated) is a non-motile, non-spore forming, facultative anaerobe, and Gram-positive coccus. Growth is obtained between 25°C and 37°C, with optimal growth at 37°C. The colonies are translucent and yellow with a regular surface, haemolytic on 5% sheep blood-enriched Columbia agar, and approximately 1 mm in diameter. Cells have mean diameter of 0.6 μm and mean length of 1.3 μm. Streptococcus varani strain FF10T exhibits positive reactions for alkaline phosphatase, esterase, esterase-lipase, lipase, leucine arylamidase, acid phosphatase, β-glucosidase, β-galactosidase, α-mannosidase, α-fucosidase, and for the esculin hydrolysis test. Streptococcus varani strain FF10T is sensitive to penicillin, amoxicillin, amoxicillin/clavulanic acid, ticarcillin, ceftriaxone, cefalotin, imipenem, gentamicin, kanamycin, trimethoprim/sulfamethoxazole, erythromycin, doxycycline, metronidazole, vancomycin and rifampicin, but resistant to ciprofloxacin, nitrofurantoin and colistin. The G+C content of the genome is 40.4%. The 16S rRNA gene sequence and whole-genome shotgun sequence of strain FF10T are deposited in GenBank under accession numbers LN810501 and GCA_001375655, respectively. The type strain FF10T (= CSUR P1489 = DSM 100884) was isolated from the oral cavity of a lizard (Varanus niloticus) in Dakar, Senegal.
Authors' Contributions
SB, JR, and MB performed the genomic analyses and drafted the manuscript. CIL and CBE performed the phenotypic characterization of the bacterium and drafted the manuscript. OM participated in its design and helped to draft the manuscript. PB helped to draft the manuscript. DR conceived the study and helped to draft the manuscript. PEF and FF conceived the study, participated in its design and coordination and helped to draft the manuscript. All authors read and approved the final manuscript.
Transparency Declaration
The authors declare no conflict of interest.
Acknowledgements
The authors thank the Xegen Company (www.xegen.fr) for automating the genomic annotation process. This study was funded by the Fondation Méditerranée Infection. We also thank Claudia Andrieu for administrative assistance.
References
- 1.Shinozaki-Kuwahara N., Takada K., Hirasawa M. Streptococcus ursoris sp. nov., isolated from the oral cavities of bears. Int J Syst Evol Microbiol. 2015;61:40–44. doi: 10.1099/ijs.0.019638-0. [DOI] [PubMed] [Google Scholar]
- 2.Facklam R. What happened to the streptococci: overview of taxonomic and nomenclature changes. Clin Microbiol Rev. 2002;15:613–630. doi: 10.1128/CMR.15.4.613-630.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Zhu H., Willcox M.D.P., Knox K.W. A new species of oral Streptococcus isolated from Sprague-Dawley rats, Streptococcus orisratti sp. nov. Int J Syst Evol Microbiol. 2000;50:55–61. doi: 10.1099/00207713-50-1-55. [DOI] [PubMed] [Google Scholar]
- 4.Shinozaki-Kuwahara N., Saito M., Hirasawa M., Takada K. Streptococcus oriloxodontae sp. nov., isolated from the oral cavities of elephants. Int J Syst Evol Microbiol. 2014;64:3755–3759. doi: 10.1099/ijs.0.064048-0. [DOI] [PubMed] [Google Scholar]
- 5.Hamada S., Slade H. Biology, immunology, and cariogenicity of Streptococcus mutans. Microbiol Rev. 1980;44:331–384. doi: 10.1128/mr.44.2.331-384.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Welker M., Moore E.R. Applications of whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in systematic microbiology. Syst Appl Microbiol. 2011;34:2–11. doi: 10.1016/j.syapm.2010.11.013. [DOI] [PubMed] [Google Scholar]
- 7.Seng P., Drancourt M., Gouriet F., La Scola B., Fournier P.E., Rolain J.M. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin In-fect Dis. 2009;49:543–551. doi: 10.1086/600885. [DOI] [PubMed] [Google Scholar]
- 8.Mourembou G., Rathored J., Lekana-Douki J.B., Ndjoyi-Mbiguino A., Fenollar F., Michelle C. Non-contiguous finished genome sequence and description of Kallipyga gabonensis sp. nov. New Microbes New Infect. 2015;9:15–23. doi: 10.1016/j.nmni.2015.11.007. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Stackebrandt E., Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today. 2006;33:152–155. [Google Scholar]
- 10.Vancanneyt M., Devriese L., Haesebrouck F., Baele M., Lefebvre K., Snauwaert C. Streptococcus minor sp. nov., from faecal samples and tonsils of domestic animals. Int J Syst Evol Microbiol. 2004;54:449–452. doi: 10.1099/ijs.0.02818-0. [DOI] [PubMed] [Google Scholar]
- 11.Vela A., Casamayor A., Sanchez Del Rey V., Dominguez L., Fernandez-Garayzabal J. Streptococcus plurextorum sp. nov., isolated from pigs. Int J Syst Evol Microbiol. 2009;59:504–508. doi: 10.1099/ijs.0.65636-0. [DOI] [PubMed] [Google Scholar]
- 12.Lagier J.C., Bibi F., Ramasamy D., Azhar E.I., Robert C., Yasir M. BASE, EBSCOhost; 2014. Non contiguous-finished genome sequence and description of Clostridium jeddahense sp. nov. (accessed November 24, 2015) [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Benson D.A., Karsch-Mizrachi I., Clark K., Lipman D.J., Ostell J., Sayers E.W. GenBank. Nucl Acids Res. 2012;40:D48–D53. doi: 10.1093/nar/gkr1202. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Lowe T.M., Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucl Acids Res. 1997;25:955–964. doi: 10.1093/nar/25.5.955. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15.Lagesen K., Hallin P., Rodland E.A., Staerfeldt H.H., Rognes T., Ussery D.W. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucl Acids Res. 2007;35:3100–3108. doi: 10.1093/nar/gkm160. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16.Bendtsen J.D., Nielsen H., von Heijne G., Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol. 2004;340:783–795. doi: 10.1016/j.jmb.2004.05.028. [DOI] [PubMed] [Google Scholar]
- 17.Krogh A., Larsson B., von Heijne G., Sonnhammer E.L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001;305:567–580. doi: 10.1006/jmbi.2000.4315. [DOI] [PubMed] [Google Scholar]
- 18.Zhou Y., Liang Y., Lynch K.H., Dennis J.J., Wishart D.S. PHAST: a fast phage search tool. Nucl Acids Res. 2011;39:W347–W352. doi: 10.1093/nar/gkr485. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 19.Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M.A. Artemis: sequence visualization and annotation. Bioinformatics. 2000;16:944–945. doi: 10.1093/bioinformatics/16.10.944. [DOI] [PubMed] [Google Scholar]
- 20.Carver T., Thomson N., Bleasby A., Berriman M., Parkhill J. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics. 2009;25:119–120. doi: 10.1093/bioinformatics/btn578. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 21.Darling A.C., Mau B., Blattner F.R., Perna N.T. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004;14:1394–1403. doi: 10.1101/gr.2289704. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 22.Ramasamy D., Mishra A.K., Lagier J.C., Padhmanabhan R., Rossi-Tamisier M., Sentausa E. A polyphasic strategy incorporating genomic data for the taxonomic description of new bacterial species. Int J Syst Evol Microbiol. 2014;64:384–391. doi: 10.1099/ijs.0.057091-0. [DOI] [PubMed] [Google Scholar]
- 23.Lechner M., Findeiss S., Steiner L., Marz M., Stadler P.F., Prohaska S.J. Proteinortho: detection of (co)orthologs in large-scale analysis. BMC Bioinformatics. 2011;12:124. doi: 10.1186/1471-2105-12-124. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 24.Auch A.F., Von Jan M., Klenk H.P., Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci. 2010;2:117–134. doi: 10.4056/sigs.531120. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 25.Woese C.R., Kandler O., Wheelis M.L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA. 1990;87:4576–4579. doi: 10.1073/pnas.87.12.4576. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 26.Gibbons N.E., Murray R.G.E. Proposals Concerning the Higher Taxa of Bacteria. Int J Syst Bacteriol. 1978;28:1–6. [Google Scholar]
- 27.Murray R.G.E. The Higher Taxa, or, a Place for Everything...? In: Holt J.G., editor. Bergey's Manual of Systematic Bacteriology. First Edition. Volume 1. The Williams and Wilkins Co.; Baltimore, MD: 1984. pp. 31–34. [Google Scholar]
- 28.Euzéby J. List of new names and new combinations previously effectively, but not validly, published. List no. 132. Int J Syst Evol Microbiol. 2010;60:469–472. doi: 10.1099/ijs.0.2008/000679-0. [DOI] [PubMed] [Google Scholar]
- 29.Ludwig W., Schleifer K.H., Whitman W.B. Class I. Bacilli class nov. In: De Vos P., Garrity G., Jones D., Krieg N.R., Ludwig W., Rainey F.A., Schleifer K.H., Whitman W.B., editors. Bergey's Manual of Systematic Bacteriology. Second Edition. Volume 3. Springer-Verlag; New York: 2009. pp. 19–20. [Google Scholar]
- 30.Ludwig W., Schleifer K.H., Whitman W.B. Order II. Lactobacillales ord. nov. In: De Vos P., Garrity G., Jones D., Krieg N.R., Ludwig W., Rainey F.A., Schleifer K.H., Whitman W.B., editors. Bergey's Manual of Systematic Bacteriology. Second Edition. Volume 3. Springer-Verlag; New York: 2009. p. 464. [Google Scholar]
- 31.Skerman V.B.D., McGowan V., Sneath P.H.A. Approved Lists of Bacterial Names. Int J Syst Bacteriol. 1980;30:225–420. [Google Scholar]
- 32.Deibel R.H., Seeley H.W. Family II. Streptococcaceae. In: Buchanan R.E., Gibbons N.E., editors. Bergey's Manual of Determinative Bacteri-ology. Eighth Edition. The Williams and Wilkins Co.; Baltimore, MD: 1974. pp. 490–515. [Google Scholar]
- 33.Rosenbach FJ. In: Bergmann JF (ed), Microorganismen bei den Wund-Infections-Krankheiten des Menschen., Wiesbaden; 1884, p. 1–122.
- 34.Deibel R.H., Seeley H.W. Genus I. Streptococcus Rosenbach 1884, 22. In: Buchanan R.E., Gibbons N.E., editors. Bergey's Manual of Determinative Bacteriology. Eighth Edition. The Williams and Wilkins Co.; Baltimore: 1974. pp. 490–509. [Google Scholar]