Abstract
Marseille-P9602T is a Chryseobacterium-like strain that we isolated from planarian Schmidtea mediterranea and characterized by taxono-genomic approach. We found that Marseille-P9602T strain exhibits a 16S rRNA gene sequence similarity of 98.76% with Chryseobacterium scophthalmum LMG 13028T strain, the closest phylogenetic neighbor. Marseille-P9602T strain was observed to be a yellowish-pigmented, Gram-negative, rod-shaped bacterium, growing in aerobic conditions and belonging to the Flavobacteriaceae family. The major fatty acids detected are 13-methyl-tetradecanoic acid (57%), 15-methylhexadecenoic acid (18%) and 12-methyl-tetradecanoic acid (8%). Marseille-P9602 strain size was found from genome assembly to be of 4,271,905 bp, with a 35.5% G + C content. The highest values obtained for Ortho-ANI and dDDH were 91.67% and 44.60%, respectively. Thus, hereby we unravel that Marseille-P9602 strain is sufficiently different from other closed related species and can be classified as a novel bacterial species, for which we propose the name of Chryseobacterium schmidteae sp. nov. Type strain is Marseille-P9602T (= CSUR P9602T = CECT 30295T).
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Introduction
Using genotypic, chemotaxonomic and phenotypic characteristics of members of Flavobacterium and weeksella genus allowed revising the classification of the novel Chryseobacterium genus1 with Chryseobacterium gleum type strain2. Several genus members were isolated from soil, plant, waste water, fish, sewage, sludge, lactic acid beverage, oil, contaminated soil, and clinical samples3,4,5,6,7,8,9,10,11,12. Some species of this genus such as Chryseobacterium indologenes, Chryseobacterium oranimense and Chryseobacterium gleum are responsible for human pathologies13,14; others are involved in the production of natural bioactive substances such as prebiotics, antioxidants, and proteases15,16,17. Chryseobacterium cells wereobserved to be gram-negative, non-motile, non-spore-forming rods, with parallel sides and rounded ends. Typically, these cells are 0.5 mm wide and 1 to 3 mm long1. All strains grow at 30 °C; most strains grow at 37 °C. Growth on solid media is typically pigmented (yellow to orange). Colonies were observed to be translucent (occasionally opaque), circular, convex, or low convex, smooth, and shiny, with entire edges1. In this study, we used the genomic and taxonomy strategy that combines phenotypic assays and genome sequencing18,19,20,21 to further characterize a Chryseobacterium-like bacterial strain isolated from planarian Schmidtea mediterranea species. S. mediterranea platyhelminth is a zoophage invertebrate living in freshwater like ponds, lakes, and rivers22. This flatworm is a model organism for regeneration, because of its unique capacity to regenerate after amputation23, as well as to investigate host–pathogen interaction24,25,26.
Materials and methods
Culture of Schmidtea mediterranea
S. mediterranea animals are asexual (clonal line ClW4), kept in laboratory for 10 years and fed with calf liver, maintained in filtered tap water at 19 °C as previously described27.
Isolation and identification of bacteria from Schmidtea mediterranea
Before experiments, animals were starved for two weeks, washed in sterile water and then one worm was inoculated in Buffered Charcoal Yeast Extract (BCYE) (Oxoid Deutschland GmbH, Wesel, Germany), Luria Bertani (LB) and 5% sheep blood-enriched Columbia agar (bioMérieux, Marcy l’étoile, France) and incubated at 19, 28 and 37 °C. Bacterial colonies were identified by MALDI-TOF-MS (Microflex spectrometer; Bruker Daltonics, Bremen, Germany)28, as previously described27. Briefly, a colony was likely identified at the species level for a score ≥ 2.0; probably identified for a score between 1.99 and 1.7, but not identified for a score < 1.7.
Sequencing, assembly, and annotation
First, using EZ1 automate and DNA tissue kit (Qiagen, Hilden, Germany), bacterial genomic DNA was extracted and then quantified using a Qubit assay (Life Technologies, Carlsbad, CA, USA) at 0.2 ng/µl. Second, bacterial genomic DNA was prepared and sequenced using Mate-Pair strategy with a Miseq sequencer (Illumina, San Diego, CA, USA)29. Next, sequencing reads were assembled using Spades software (Galaxy version 3.12.0 + galaxy1)30 and genomic annotation was obtained using Prokka (Rapid Prokaryotic Genome Annotation)31. Finally, taxonomic assignation was done by BLASTn search performed against nr database. A sequence similarity threshold of 98.65% by comparison with the phylogenetically closest species with standing in nomenclature was used to delineate a putative novel species32.
Phylogenetic analysis, and genomic comparison
Phylogenetic relationships were inferred from comparison of 16S rRNA gene sequences using MEGAX (version10.1) software33,34. Sequences were aligned using MUSCLE algorithm setup with default parameters, and numbers at the nodes were percentages of bootstrap values obtained by repeating the analysis 1000 times to generate a majority consensus tree. Only bootstrap values ≥ 50% were retained. For the Phylogenetic tree based on the core genes, we generated a core-gene alignment using Roary 3.13.035 with 70% identity. We obtained an alignment of 1535 core genes from which we inferred a phylogenetic tree using FastTree 2.1.1036. Degrees of genomic similarity were evaluated using the GGDC37 (http://ggdc.dsmz.de/ggdc.php#) and Orthologous Average Nucleotide Identity38 (https://www.ezbiocloud.net/tools/orthoani, OrthoANI Tool version 0.93.1) softwares. Comparison COG functional categories were carried out using Blast P (E-value 10-3, coverage 0.7 and identity percent 30%) against clusters of orthologous groups (COG) database.
Phenotypic characteristics
Growth of Marseille-P9602 strain and Chryseobacterium scophthalmum LMG 13028T strain (purchased to DSMZ) (ATCC 700,039 = CCM 4109 = CCUG 33,454 = CIP 104,199 = DSM 16,779 = MM1)1,39 was attempted at various temperatures such as 4, 19, 28, 30, 37 and 45 °C in 5% sheep blood-enriched Columbia agar (bioMérieux) under anaerobic atmosphere using GasPak EZ generators (Becton–Dickinson, Maryland, USA), as well under aerobic atmosphere. Strain ability to sporulate was investigated by thermal shock. Briefly, bacteria were exposed at80 °C temperature for 30 min and then bacterial growth was assessed for 4 days. The capacity to growth under various salinity (0, 20, 40, 50, 60, 80 and 100 g of NaCl/l) and pH conditions (5, 5.5, 6, 6.5, 7.5, 8.5, 9 and 10) was also investigated. Gram staining and motility of fresh colonies were observed using a DSM1000 photonic microscopy (Leica Microsystems, Nanterre, France) with an ocular of 10 × and 40 × objective lens. Bacterial structure was defined using a scanning electron microscopy (Hitachi SUV5000) (Hitachi High-Technologies Corporation, Tokyo, Japan). Enzymatic activities such as catalase and oxydase activities were analysed with a BBL DrySlide following manufacturer's instructions (Becton Dickinson, Le Pont de Claix, France). API strips (API ZYM40,41,42, API 20NE43,44, API 20E45,46 and API 50CH47,48,49,50, bioMérieux) were used to study strains biochemical characteristics.
Antibiotic susceptibility of Marseille-P9602 strain
Bacterial susceptibility to benzylpenicillin, amoxicillin, ampicillin, ceftriaxone, imipenem, ciprofloxacin, amikacin, gentamicin, streptomycin, daptomycin, doxycycline, metronidazole, rifampicin, fosfomycin, vancomycin and tigecycline was assessed using E-tests and a 0.5 McFarland concentration of Marseille-P9602 and LMG 13028T strains. MICs were read at the point of intersection between the developed elliptical zone of inhibition and the test strip. Interpretation of the MICs was carried out according to NCCLS recommendations for bacterial isolates grown aerobically51.
Analysis of cellular fatty acids of strain Marseille-P9602
Cellular fatty acid methyl ester (FAME) analysis was performed by GC/MS for both Marseille-P9602 and LMG 13028T strain. Fatty acid methyl esters were prepared as described by Sasser52 and GC/MS analysis was realized as previously described53. Briefly, Marseille-P9602 and LMG 13028T strains were inoculated in 5% sheep blood-enriched Columbia agar and incubated at 28 °C. 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).
Results and discussion
Phylogenetic analysis and genomic comparison
The gene 16S rRNA sequence from Marseille-P9602 strain was observed to be 1513 bp-long. A sequence similarity calculation using BLASTn search in the nr database indicated that the closest relatives of Marseille-P9602 strain are Chryseobacterium scophthalmum LMG 13028T strain1,39, Chryseobacterium piscium LMG 23089T strain54, C. balustinum NBRC 15053T strain1, C. indoltheticum LMG 4025T strain55, C. taihuense THMBM1T strain55, C. ureilyticum F-Fue-04IIIaaaaT strain7, C. aquaticum 10-46T strain6, C. lactis KC1864T strain8, C. soldanellicola NBRC 100864T strain9, C. formosense CC-H3-2T strain56,C. aureum 17S1E7T strain57, C. hominis NF802T strain58, C. timonianum G972T strain59 C. polytrichastri YG4-6T strain10, C. echinoideorum CC-CZW010T strain60, C. xinjiangense TSBY-67T strain61, C. endophyticum CC-YTH209T strain62, C. taiwanense BCRC 17412T strain63, C. vrystaatense R-23566T strain64, C. joostei LMG 18212T strain65, C. geocarposphaerae 91A-561T66, and C. gleum NBRC 15054T strain2, whose similarity values, coverage and accesssion strain numbers are shown in Table 1. Therefore, Marseille-P9602 strain belongs to Chryseobacterium genus1 within the Flavobacteriaceae family67 and the Bacteroidetes phylum68 (Table 2). The 16S rRNA-based phylogenetic tree showed that Marseille-P9602, C. scophthalmum LMG 13028T, C. piscium LMG 23089T and C. balustinum NBRC 15053T strains form a monophyletic group (Fig. 1A). Core genome tree showed that strains are different from each other (Fig. 1B). The genomic sequence from Marseille-P9602 strain was assembled into 56 contigs for a total size of 4,276,845 bp (Cover, 56x; N50, 151,068; L50, 9) with a 33.5% G + C content. A total of 3881 predicted protein-coding genes were identified, along with 9 rRNAs, 67 tRNAs, 1 tmRNA and 1 repeat region; and this genome was compared with other closely related Chryseobacterium genomes (Table 3). Based on the Digital DNA-DNA hybridization values (dDDH) obtained using GGDC software, Marseille-P9602 strain values ranged from 21.40% with C. aureum and C. lactis to 44.60% with C. scophthalmum (Table 3). These values were below the 70% threshold recognized for the delimitation of bacterial species. Ortho-ANI values of Marseille-P9602 strain ranged from 76.65% C. aureum to 91.67% with C. scophthalmum, which is lower than the 95% threshold used to distinguish species (Table 3). These values of genomic comparison showed that Marseille-P9602 strain is probably a novel species in the Chryseobacterium genus. The distribution of genes in COG functional categories is presented in Fig. 2 and Table 4. Few differences were observed between these species. In addition, by comparison of the genomes of Marseille-P9602 strain and of the 11 closest species, we highlighted 100 specific and unique genes to the Marseille-P9602 strain (Supplementary data S1). Taken together, these results confirm that Marseille-P9602 strain belongs to a separate Chryseobacterium species.
Phylogenetic tree and Core-genome. (A) Phylogenetic tree based on 16S rRNA sequence comparison highlighting the position of Marseille-P9602 strain relative to other closely related species. Only bootstrap values ≥ 50% were shown. (B) Core-genome-based phylogenetic relationships of Marseille-P9602 strain relative to other closely related species.
Functional annotation of predicted gene according to the COGs comparison of COGs of Marseille-P9602 species with phylogenetically related species of the genus Chryseobacterium. [A] RNA processing and modification; [B] Chromatin structure and dynamics; [C] Energy production and conversion; [D] Cell cycle control, cell division, chromosome partitioning; [E] Amino acid transport and metabolism;[F] Nucleotide transport and metabolism; [G] Carbohydrate transport and metabolism; [H] Coenzyme transport and metabolism; [I] Lipid transport and metabolism; [J] Translation, ribosomal structure, and biogenesis; [K] Transcription; [L] Replication, recombination, and repair; [M] Cell wall/membrane/envelope biogenesis; [N] Cell motility; [O] Posttranslational modification, protein turnover, chaperones; [P] Inorganic ion transport and metabolism; [Q] Secondary metabolites biosynthesis, transport, and catabolism; [R] General function prediction only; [S] Function unknown; [T] Signal transduction mechanisms; [U] Intracellular trafficking, secretion, and vesicular transport; [V] Defense mechanisms; [W] Extracellular structures; [X] Mobilome: prophages, transposons; [Y] nuclear structure [Z] Cytoskeleton.
Phenotypic analysis and biochemical characteristics
Marseille-P9602 strain was isolated on COS agar after 2 days at 28 °C in aerobic atmosphere at pH 7.5. We observed that Marseille-P9602 strain grows at temperatures ranging from 4 to 30 °C in aerobic atmosphere and at pH values ranging from 6.5 to 9 (Neutro-alkalophilic bacterium). In contrast, LMG 13028T strain grows at pH 6. Marseille-P9602 strain grows at salinity concentrations lower than 12 g of NaCl/l; however, in contrast, LMG 13028T strain needs a NaCl concentration lower than 25 g/l. After 4 days culture on COS agar, Marseille-P9602 strain colonies were observed to be yellowish, small (0.4 mm median diameter), circular with a convex shape and smooth. Bacterial cells (Fig. 3) are Gram-negative (Fig. 3A), rod-shaped, non-spore-forming bacilli and non-motile, but without any flagellum. Their mean length and width are 3.15 µm and 0.66 µm, respectively (Fig. 3B). Marseille-P9602 strain was found to be oxidase positive and catalase negative. Bacterial metabolism was characterized using API 50CHB/E, API 20NE, API Zym and API 20E strips (Table 5). Marseille-P9602 strain differs from C. scophthalmum, C. indoltheticum, C. piscium, and C. balustinum regarding catalase, α-glucosidase, inositol and urea.
Micrograph of Marseille-P9602 strain. (A) Micrograph of Marseille-P9602 strain after Gram staining, (B) Transmission electron microscopy micrograph of Marseille-P9602 strain.
Antibiotic susceptibility
Marseille-P9602 strain growth is inhibited by benzylpenicillin, amikacin, amoxicillin, ampicillin, gentamicin, ciprofloxacin ceftriaxone, streptomycin, doxycycline, tigecycline, rifampicin, and vancomycin; but not by daptomycin, fosfomycin, and metronidazole (Table 6). We noticed that amikacin inhibits the growth of Marseille-P9602, but not LMG 13028 T strain.
Cellular fatty acids analysis
The fatty acids 13-methyl-tetradecanoic acid (56.7%), 15-Methylhexadecenoic acid (18.1%), 12-methyl-tetradecanoic acid (7.5%), 3-methyl-butanoic acid (4.9%),3-hydroxy-15-methyl-Hexadecanoic acid (3.3%), Hexadecanoic acid (1.2%) and 11-methyl-Dodecanoic acid (1.2%) were detected in Marseille-P9602 strain. Trace (< 1%) of unsaturated and saturated fatty acids such as 15-methyl-Hexadecanoic acid, 9,12-Octadecadienoic acid, 12-methyl-Tridecanoic acid, Pentadecanoic acid, 9-Octadecenoic acid, 3-hydroxy-Hexadecanoic acid, Tetradecanoic acid, 9-Hexadecenoic acid, and Octadecanoic acid were detected. The fatty acid 3-hydroxy-13-methyl-Tetradecanoic was not detected in Marseille-P9602 strain, in contrast to C. scophthalmum, C. indoltheticum, C. piscium, and C. balustinum strains (Table 7).
Conclusion
Based on the results obtained by the taxono-genomic approach, we confirm that Marseille-P9602 strain belongs to a novel species from Chryseobacterium genus. We propose the name of Chryseobacterium schmidteae Marseille-P9602T strain. To date, this novel strain has never been identified in any other environment.
Species description
Chryseobacterium schmidteae (schmid.te'ae. N.L. gen. n. schmidteae of the planarian genus Schmidtea, from which Marseille-P9602 strain was isolated) is a bacterium belonging to the Flavobacteriaceae family within the Bacteroidetes phylum. Marseille-P9602T type-strain was isolated on 5% sheep blood-enriched Columbia agar after 2 days at 28 °C in aerobic atmosphere at pH 7.5 from the microbiota of planarian Schmidtea mediterranea. Colonies were observed to be small, circular, smooth, yellowish and convex. Cells were found to be Gram-negative, rod-shaped, non-motile and non-spore-forming bacilli with negative catalase and positive oxydase activities. The major fatty acids were found to be 13-methyl-tetradecanoic acid, 15-Methylhexadecenoic acid, 12-methyl-tetradecanoic acid, 3-methyl-butanoic acid, 3-hydroxy-15-methyl-Hexadecanoic acid, 3-hydroxy-13-methyl-Tetradecanoic acid, Hexadecanoic acid and 11-methyl-Dodecanoic acid. It was observed to be positive for alkaline phosphatase, esterase (C4), lipase (C14), leucine arylamidase, cystine arylamidase, α-chymotrypsin, acid phosphatase, naphthol-AS-BI-phosphohydrolase, β-glucosidase and α-fucosidase, but negative for valine arylamidase, esterase lipase (C8), α-galactosidase, β-galactosidase, α-glucosidase, N-acetyl-β-glucosaminidase, α-mannosidase, and β-glucuronidase activities. It assimilates glucose, mannose, d-fructose, l-sorbose, amygdalin, inositol, esculin ferric citrate, gentiobiose and d-trehalose, but not glycerol, maltose, erythritol, d-arabinose, l-arabinose, d-ribose, d-xylose, l-xylose, d-adonitol, methyl-β d-xylopyranoside, d-galactose, l-rhamnose, Dulcitol, d-mannitol, d-sorbitol, methyl-αd-mannopyranoside, methyl-αd-glucopyranoside, N-acetylglucosamine, arbutin, salicin, d-cellobiose, d-lactose, d-melibiose, d-saccharose, inulin, d-melezitose, d-raffinose, glycogen, xylitol, d-turanose, d-lyxose, d-tagatose, d-fucose, l-fucose, d-arabitol, l-arabitol, Starch, potassium gluconate, potassium 2-ketogluconate, potassium and 5-ketogluconate. Positive reactions were observed for l-tryptophan, natrium pyruvat, indole production, potassium nitrate, and gelatin, but no reaction was detected for l-lysin, l-ormithin, trinatrium citrate, natrium thiosulfate, l-arginine, urea, N-acetyl-glucosamine, capric acid, malic acid, trisodium citrate, adipic acid, and phenylacetic acid. The genome of Marseille-P9602T strain was found to be 4.271.905 bp-long with a 35.5% G + C content. The 16S rRNA gene and genome sequences were deposited in GenBank under the accession numbers LR797929 and CAESCJ000000000.1, respectively. Marseille-P9602T type-strain was deposited in the CSUR strain collections under the numbers CSUR P9602 and CECT 30295.
Nucleotide sequence accession number
16S rRNA gene sequence and genome sequence were deposited in GenBank under the accession numbers LR797929 and CAESCJ000000000.1, respectively. The raw data for the assembly were deposited in EMBL-EBI under the run accession ERR4143501 and the experiment accession ERX4110774.
Deposit in culture collections
Marseille-P9602T strain was deposited in the Collection de Souches de l'Unité des Rickettsies (CSUR) and Colección Española De Cultivos Tipo (CECT) strain collections under the numbers CSUR P9602 and CECT 30295, respectively.
Change history
31 August 2021
A Correction to this paper has been published: https://doi.org/10.1038/s41598-021-97051-7
References
Vandamme, P., Bernardet, J.-F., Segers, P., Kersters, K. & Holmes, B. NOTES: new perspectives in the classification of the Flavobacteria: description of chryseobacterium gen. nov., bergeyella gen. nov., and empedobacter nom. Rev.. Int. J. Syst. Evol. Microbiol. 44(4), 827–831. https://doi.org/10.1099/00207713-44-4-827 (1994).
Holmes, B., Owen, R. J., Steigerwalt, A. G. & Brenner, D. J. Flavobacterium Gleum, a new species found in human clinical specimens. Int. J. Syst. Evol. Microbiol. 34(1), 21–25. https://doi.org/10.1099/00207713-34-1-21 (1984).
Nguyen, N.-L., Kim, Y.-J., Hoang, V. A. & Yang, D.-C. Chryseobacterium ginsengisoli sp. nov., isolated from the rhizosphere of ginseng and emended description of chryseobacterium gleum. Int. J. Syst. Evol. Microbiol. 63(Pt 8), 2975–2980. https://doi.org/10.1099/ijs.0.045427-0 (2013).
del Montero-Calasanz, M. C. et al. Chryseobacterium oleae sp. nov., an efficient plant growth promoting bacterium in the rooting induction of olive tree (olea europaea l.) cuttings and emended descriptions of the genus chryseobacterium, c. daecheongense, c. gambrini, c. gleum, c. joostei, c. jejuense, c. luteum, c. shigense, c. taiwanense, c. ureilyticum and c. vrystaatense. Syst. Appl. Microbiol. 37(5), 342–350. https://doi.org/10.1016/j.syapm.2014.04.004 (2014).
Meng, D. et al. Chryseobacterium binzhouense sp. nov., isolated from activated sludge. Int. J. Syst. Evol. Microbiol. 70(1), 618–623. https://doi.org/10.1099/ijsem.0.003800 (2020).
Kim, K. K., Lee, K. C., Oh, H.-M. & Lee, J.-S. Chryseobacterium Aquaticum sp. nov., isolated from a water reservoir. Int. J. Syst. Evol. Microbiol. 58(Pt 3), 533–537. https://doi.org/10.1099/ijs.0.65491-0 (2008).
Herzog, P., Winkler, I., Wolking, D., Kämpfer, P. & Lipski, A. Chryseobacterium ureilyticum sp. nov., chryseobacterium gambrini sp. nov., chryseobacterium pallidum sp. nov. and chryseobacterium molle sp. nov., isolated from beer-bottling plants. Int. J. Syst. Evol. Microbiol. 58(Pt 1), 26–33. https://doi.org/10.1099/ijs.0.65362-0 (2008).
Holmes, B., Steigerwalt, A. G. & Nicholson, A. C. DNA-DNA Hybridization study of strains of chryseobacterium, elizabethkingia and empedobacter and of other usually indole-producing non-fermenters of CDC Groups IIc, IIe, IIh and IIi, Mostly from human clinical sources, and proposals of chryseobacterium bernardetii sp. nov., chryseobacterium carnis sp. nov., chryseobacterium lactis sp. nov., chryseobacterium nakagawai sp. nov. and chryseobacterium taklimakanense comb. nov. Int. J. Syst. Evol. Microbiol. 63(Pt 12), 4639–4662. https://doi.org/10.1099/ijs.0.054353-0 (2013).
Park, M. S. et al. Chryseobacterium soldanellicola sp. nov. and chryseobacterium taeanense sp. nov., isolated from roots of sand-dune plants. Int. J. Syst. Evol. Microbiol. 56(Pt 2), 433–438. https://doi.org/10.1099/ijs.0.63825-0 (2006).
Chen, X. Y. et al. Chryseobacterium polytrichastri sp. nov., isolated from a moss (polytrichastrum formosum), and emended description of the genus chryseobacterium. Antonie Van Leeuwenhoek 107(2), 403–410. https://doi.org/10.1007/s10482-014-0338-6 (2015).
Szoboszlay, S. et al. Chryseobacterium hungaricum sp. nov., isolated from hydrocarbon-contaminated soil. Int. J. Syst. Evol. Microbiol. 58(Pt 12), 2748–2754. https://doi.org/10.1099/ijs.0.65847-0 (2008).
Ilardi, P., Fernández, J. & Avendaño-Herrera, R. Chryseobacterium piscicola sp. nov., isolated from diseased salmonid fish. Int. J. Syst. Evol. Microbiol. 59(Pt 12), 3001–3005. https://doi.org/10.1099/ijs.0.007021-0 (2009).
Chen, F.-L. et al. Clinical and epidemiological features of chryseobacterium indologenes infections: analysis of 215 Cases. J. Microbiol. Immunol. Infect 46(6), 425–432. https://doi.org/10.1016/j.jmii.2012.08.007 (2013).
Jain, V. et al. Simultaneous Isolation of chryseobacterium gleum from bloodstream and respiratory tract: first case report from india. JMM Case Rep. 4(10), e005122. https://doi.org/10.1099/jmmcr.0.005122 (2017).
Chaudhari, P. N., Wani, K. S., Chaudhari, B. L. & Chincholkar, S. B. Characteristics of sulfobacin a from a soil isolate chryseobacterium gleum. Appl. Biochem. Biotechnol. 158(1), 231–241. https://doi.org/10.1007/s12010-008-8417-7 (2009).
Gandhi Pragash, M., Narayanan, K. B., Naik, P. R. & Sakthivel, N. Characterization of chryseobacterium aquaticum strain pupc1 producing a novel antifungal protease from rice rhizosphere soil. J. Microbiol. Biotechnol. 19(1), 99–107 (2009).
Kim, H.-S. et al. Identification and characterization of chryseobacterium wanjuense strain kj9c8 as a biocontrol agent of phytophthora blight of pepper. Crop Prot. 32, 129–137. https://doi.org/10.1016/j.cropro.2011.10.018 (2012).
Ramasamy, D. et al. A Polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int. J. Syst. Evol. Microbiol. 64(2), 384–391. https://doi.org/10.1099/ijs.0.057091-0 (2014).
Fournier, P.-E., Lagier, J.-C., Dubourg, G. & Raoult, D. From culturomics to taxonomogenomics: a need to change the taxonomy of prokaryotes in clinical microbiology. Anaerobe 36, 73–78. https://doi.org/10.1016/j.anaerobe.2015.10.011 (2015).
Morel, A.-S. et al. Complementarity between targeted real-time specific PCR and conventional broad-range 16S RDNA PCR in the syndrome-driven diagnosis of infectious diseases. Eur. J. Clin. Microbiol. Infect. Dis. 34(3), 561–570. https://doi.org/10.1007/s10096-014-2263-z (2015).
Diop, A. et al. Microbial culturomics unravels the halophilic microbiota repertoire of table salt: description of gracilibacillus massiliensis sp. nov.. Microb. Ecol. Health Dis. 27, 32049 (2016).
Vila-Farré, M. & Rink, C. J. The ecology of freshwater planarians. Methods Mol. Biol. 1774, 173–205. https://doi.org/10.1007/978-1-4939-7802-1_3 (2018).
Elliott, S. A. & Sánchez Alvarado, A. The history and enduring contributions of planarians to the study of animal regeneration. Wiley Interdiscip. Rev. Dev. Biol. 2(3), 301–326. https://doi.org/10.1002/wdev.82 (2013).
Abnave, P. et al. Screening in planarians identifies morn2 as a key component in lc3-associated phagocytosis and resistance to bacterial infection. Cell Host Microbe 16(3), 338–350. https://doi.org/10.1016/j.chom.2014.08.002 (2014).
Maciel, E. I., Jiang, C., Barghouth, P. G., Nobile, C. J. & Oviedo, N. J. The planarian schmidtea mediterranea is a new model to study host-pathogen interactions during fungal infections. Dev. Comp. Immunol. 93, 18–27. https://doi.org/10.1016/j.dci.2018.12.005 (2019).
Torre, C. & La, G. É. planaire : un ver immortel pour élucider la réponse immunitaire de l’homme. Med. Sci. (Paris) 31(1), 20–22. https://doi.org/10.1051/medsci/20153101006 (2015).
Kangale, L. J., Raoult, D., Fournier, G. E. & P-E, ,. Pedobacter schmidteae sp nov, a new bacterium isolated from the microbiota of the planarian schmidtea mediterranea. Sci. Rep. 10(1), 1–12. https://doi.org/10.1038/s41598-020-62985-x (2020).
Seng, P. et al. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin. Infect. Dis. 49(4), 543–551. https://doi.org/10.1086/600885 (2009).
Ravi, R. K., Walton, K. & Khosroheidari, M. MiSeq: A next generation sequencing platform for genomic analysis. Methods Mol. Biol. 1706, 223–232. https://doi.org/10.1007/978-1-4939-7471-9_12 (2018).
Bankevich, A. et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19(5), 455–477. https://doi.org/10.1089/cmb.2012.0021 (2012).
Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30(14), 2068–2069. https://doi.org/10.1093/bioinformatics/btu153 (2014).
Meier-Kolthoff, J. P., Göker, M., Spröer, C. & Klenk, H.-P. When should a DDH experiment be mandatory in microbial taxonomy?. Arch. Microbiol. 195(6), 413–418. https://doi.org/10.1007/s00203-013-0888-4 (2013).
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35(6), 1547–1549. https://doi.org/10.1093/molbev/msy096 (2018).
Tamura, K. & Nei, M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10(3), 512–526. https://doi.org/10.1093/oxfordjournals.molbev.a040023 (1993).
Page, A. J. et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31(22), 3691–3693. https://doi.org/10.1093/bioinformatics/btv421 (2015).
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5(3), e9490. https://doi.org/10.1371/journal.pone.0009490 (2010).
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. 2(1), 117–134. https://doi.org/10.4056/sigs.531120 (2010).
Lee, I., Ouk Kim, Y., Park, S.-C. & Chun, J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int. J. Syst. Evol. Microbiol. 66(2), 1100–1103. https://doi.org/10.1099/ijsem.0.000760 (2016).
Mudarris, M. et al. Flavobacterium scophthalmum sp. nov., a pathogen of turbot (scophthalmus maximus l.). Int. J. Syst. Bacteriol. 44(3), 447–453. https://doi.org/10.1099/00207713-44-3-447 (1994).
Unaogu, I. C., Gugnani, H. C., & Boiron, P. The enzymatic profile of some pathogenic aerobic actinomycetes as determined by api-zym method. /data/revues/11565233/00090004/235/2008.
Gruner, E., von Graevenitz, A. & Altwegg, M. The API ZYM system: a tabulated review from 1977 to date. J. Microbiol. Methods 16(2), 101–118. https://doi.org/10.1016/0167-7012(92)90030-8 (1992).
Humble, M. W., King, A. & Phillips, I. API ZYM: a simple rapid system for the detection of bacterial enzymes. J. Clin. Pathol. 30(3), 275–277. https://doi.org/10.1136/jcp.30.3.275 (1977).
Søgaard, P., Gahrn-Hansen, B., Zhou, H. P. & Frederiksen, W. An investigation of three commercial methods for rapid identification of non-enteric gram-negative rods. Application on pseudomonas paucimobilis and some other pseudomonas species. Acta Pathol. Microbiol. Immunol. Scand. B 94(5), 357–363. https://doi.org/10.1111/j.1699-0463.1986.tb03067.x (1986).
Mk, B., Da, B., Gl, C. & Jg, G. Comparison of five commercial methods for the identification of non- fermentative and oxydase positive fermentative gram negative bacilli. NZ J. Med. Lab. Technol. 42(1), 8–12 (1988).
Swanson, E. C. & Collins, M. T. Use of the API 20E system to identify veterinary enterobacteriaceae. J. Clin. Microbiol. 12(1), 10–14 (1980).
Smith, P. B., Tomfohrde, K. M., Rhoden, D. L. & Balows, A. API system: a multitube micromethod for identification of enterobacteriaceae. Appl. Microbiol. 24(3), 449–452 (1972).
Véron, M. & Le Minor, L. [Nutrition and taxonomy of “enterobacteriaceae” and related bacteria. III. Nutritional characters and differentiation of the taxonomic groups (author’s transl)]. Ann. Microbiol. Paris 126(2), 125–147 (1975).
Bergey, D. H., Krieg, N. R. & Holt, J. G. Bergey’s Manual of Systematic Bacteriology (Williams & Wilkins, 1984).
Rogosa, M. & Sharpe, M. E. An approach to the classification of the lactobacilli. J. Appl. Bacteriol. 22(3), 329–340 (1960).
Sharpe, M. E., Hill, L. R. & Lapage, S. P. Pathogenic lactobacilli. J. Med. Microbiol. 6(3), 281–286. https://doi.org/10.1099/00222615-6-3-281 (1973).
Jorgensen, J. H. & Turnidge, J. D. Susceptibility test methods: dilution and disk diffusion methods. In Manual of Clinical Microbiology, Eleventh Edition 1253–1273 (2015). https://doi.org/10.1128/9781555817381.ch71.
Sasser, M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl. 20, 1–6 (1990).
Dione, N. et al. Genome sequence and description of anaerosalibacter massiliensis sp. nov.. New Microbes New Infect. 10, 66–76. https://doi.org/10.1016/j.nmni.2016.01.002 (2016).
de Beer, H. et al. Chryseobacterium piscium sp. Nov., isolated from fish of the South Atlantic ocean off South Africa. Int. J. Syst. Evol. Microbiol. 56(Pt 6), 1317–1322. https://doi.org/10.1099/ijs.0.64014-0 (2006).
Wu, Y.-F., Wu, Q.-L. & Liu, S.-J. Chryseobacterium taihuense sp. nov., isolated from a eutrophic lake, and emended descriptions of the genus chryseobacterium, chryseobacterium taiwanense, chryseobacterium jejuense and chryseobacterium indoltheticum. Int. J. Syst. Evol. Microbiol. 63(Pt 3), 913–919. https://doi.org/10.1099/ijs.0.040337-0 (2013).
Young, C.-C., Kämpfer, P., Shen, F.-T., Lai, W.-A. & Arun, A. B. Chryseobacterium formosense sp. nov., isolated from the rhizosphere of lactuca sativa l. (Garden Lettuce). Int. J. Syst. Evol. Microbiol. 55(Pt 1), 423–426. https://doi.org/10.1099/ijs.0.63331-0 (2005).
Lee, J.-E., Hwang, E.-M., Cha, C.-J. & Kim, G.-B. Chryseobacterium aureum sp. nov., isolated from the Han river, Republic of Korea. Int. J. Syst. Evol. Microbiol. 69(6), 1628–1633. https://doi.org/10.1099/ijsem.0.003370 (2019).
Vaneechoutte, M. et al. Chryseobacterium hominis sp. Nov., to accommodate clinical isolates biochemically similar to CDC Groups II-h and II-c. Int. J. Syst. Evol. Microbiol. 57(Pt 11), 2623–2628. https://doi.org/10.1099/ijs.0.65158-0 (2007).
Abou Abdallah, R. et al. Description of Chryseobacterium timonianum sp. nov., isolated from a patient with pneumonia. Antonie Van Leeuwenhoek 110(9), 1121–1132. https://doi.org/10.1007/s10482-017-0885-8 (2017).
Lin, S.-Y. et al. Chryseobacterium echinoideorum sp. nov., isolated from sea urchins (tripneustes gratilla). Int. J. Syst. Evol. Microbiol. 65(11), 3985–3990. https://doi.org/10.1099/ijsem.0.000524 (2015).
Zhao, Q. et al. Chryseobacterium xinjiangense sp. nov., isolated from alpine permafrost. Int. J. Syst. Evol. Microbiol. 61(Pt 6), 1397–1401. https://doi.org/10.1099/ijs.0.024141-0 (2011).
Lin, S.-Y. et al. Chryseobacterium endophyticum sp. nov., isolated from a maize leaf. Int. J. Syst. Evol. Microbiol. 67(3), 570–575. https://doi.org/10.1099/ijsem.0.001656 (2017).
Tai, C.-J. et al. Chryseobacterium taiwanense sp. nov., isolated from soil in Taiwan. Int. J. Syst. Evol. Microbiol. 56(Pt 8), 1771–1776. https://doi.org/10.1099/ijs.0.64294-0 (2006).
de Beer, H. et al. Chryseobacterium vrystaatense sp. nov., isolated from raw chicken in a chicken-processing plant. Int. J. Syst. Evol. Microbiol. 55(Pt 5), 2149–2153. https://doi.org/10.1099/ijs.0.63746-0 (2005).
Hugo, C. J., Segers, P., Hoste, B., Vancanneyt, M. & Kersters, K. Chryseobacterium joostei sp. nov., isolated from the dairy environment. Int. J. Syst. Evol. Microbiol. 53(Pt 3), 771–777. https://doi.org/10.1099/ijs.0.02232-0 (2003).
Kämpfer, P., McInroy, J. A. & Glaeser, S. P. Chryseobacterium zeae sp. nov., chryseobacterium arachidis sp. nov., and chryseobacterium geocarposphaerae sp. nov. isolated from the rhizosphere environment. Antonie Van Leeuwenhoek 105(3), 491–500. https://doi.org/10.1007/s10482-013-0101-4 (2014).
Bernardet, J.-F. Flavobacteriaceae. In Bergey’s Manual of Systematics of Archaea and Bacteria 1–18 (American Cancer Society, 2015). https://doi.org/10.1002/9781118960608.fbm00069.
Krieg, N. R., Ludwig, W., Euzéby, J. P. & Whitman, W. B. Bacteroidetes Phyl. Nov. In Bergey’s Manual of Systematics of Archaea and Bacteria 1–2 (American Cancer Society, 2015). https://doi.org/10.1002/9781118960608.pbm00004.
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. U.S.A. 87(12), 4576–4579. https://doi.org/10.1073/pnas.87.12.4576 (1990).
Hahnke, R. L. et al. Genome-based taxonomic classification of bacteroidetes. Front. Microbiol. https://doi.org/10.3389/fmicb.2016.02003 (2016).
List of new names and new combinations previously effectively, but not validly, published. Int. J. Syst. Evol. Microbiol. 62(1), 1–4. https://doi.org/10.1099/ijs.0.039487-0. (2012).
Bernardet, J.-F. Flavobacteriia Class. Nov. In Bergey’s Manual of Systematics of Archaea and Bacteria 1 (American Cancer Society, 2015). https://doi.org/10.1002/9781118960608.cbm00012.
Bernardet, J.-F. Flavobacteriales Ord. Nov. In Bergey’s Manual of Systematics of Archaea and Bacteria 1–2 (American Cancer Society, 2015). https://doi.org/10.1002/9781118960608.obm00033.
Campbell, L. L. & Williams, O. B. A study of chitin-decomposing micro-organisms of marine origin. Microbiology 5(5), 894–905. https://doi.org/10.1099/00221287-5-5-894 (1951).
Acknowledgements
LJK is fellow of Méditerranée-Infection foundation. The study was funded by the Méditerranée-Infection foundation, the National Research Agency under the program “Investissements d’avenir”, reference ANR-10-IAHU-03 and by Région Provence Alpes Côte d’Azur and European funding FEDER IHUBIOTK. We also thank Aurelia Caputo (IHU- Méditerranée-Infection) for submitting the 16S rRNA and genomic sequences to GenBank. We thank Giovanna Mottola (Aix-Marseille University, INSERM, INRAE, C2VN and Laboratory of Biochemistry, Hôpital de La Timone, Marseille, France) for scientific English editing.
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L.J.K., isolated the bacterium, conceived, and realised the experiments, analysed the data, prepared figures, and drafted the manuscript. D.R., E.G. and P.E.F. designed the experiments, conceived the experiments, analysed the data, and drafted the manuscript, and finalized the manuscipt.
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The original online version of this Article was revised: The original version of this Article contained a repeated error, where the reference number of the CECT strain “30295” was incorrectly given as “30,295”.
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Kangale, L.J., Raoult, D., Ghigo, E. et al. Chryseobacterium schmidteae sp. nov. a novel bacterial species isolated from planarian Schmidtea mediterranea. Sci Rep 11, 11002 (2021). https://doi.org/10.1038/s41598-021-90562-3
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DOI: https://doi.org/10.1038/s41598-021-90562-3
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