Abstract
A Gram-stain-negative, strictly aerobic, non-flagellated, oxidase- and catalase-positive, rod-shaped marine bacterium, designated strain DM8T, was isolated from the intestine of Trichiurus japonicus in Weihai, China. The strain optimally grew at 25–35℃, with 1.0–4.0% (w/v) NaCl and at pH 7.0–8.0. Its colonies were circular, slightly yellow, non-transparent, smooth, and approximately 0.8–1.5 mm in diameter, after being cultured for 48 h on marine agar 2216. Based on the result of phylogenetic analysis of 16S rRNA gene sequence, strain DM8T had close relationship with Oceanisphaera profunda SM1222T (96.9%) and the type strain DSM 15406 T of the type species Oceanisphaera litoralis (94.7%), respectively. Genome sequencing revealed a genome size of 3,109,059 bp and a G + C content of 46.9 mol%. It had Q-8 as the sole respiratory quinone and possessed C16:0, summed features 3 (C16:1ω7c/C16:1ω6c) and summed features 8 (C18:1ω7c/C18:1ω6c) as major fatty acids. The major polar lipid profile was composed of phosphatidylglycerol and phosphatidylethanolamine. Based on the phenotypic, chemotaxonomic characterizations, phylogenetic properties and genome analysis, strain DM8T should represent a novel species of the genus Oceanisphaera, for which the name Oceanisphaera pacifica sp. nov. is proposed. The type strain is DM8T (= KCTC 82764 T = MCCC 1K06133T).
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Abbreviations
- AAI:
-
Amino Acid Identity
- ANI:
-
Average Nucleotide Identity
- BD:
-
Becton Dickinson
- dDDH:
-
Digital DNA–DNA Hybridization
- DSMZ:
-
Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
- GGDC:
-
Genome-to-Genome Distance Calculator
- HPLC:
-
High Performance Liquid Chromatography
- KCTC:
-
Korean Collection for Type Cultures
- KEGG:
-
Kyoto Encyclopedia of Genes and Genomes
- MA:
-
Marine agar 2216
- MB:
-
Marine broth 2216
- MCCC:
-
Marine Culture Collection of China
- MEGA:
-
Molecular Evolutionary Genetics Analysis
- MIDI:
-
Microbial Identifcation System
- TLC:
-
Thin-Layer Chromatography
References
Angiuoli SV, Gussman A, Klimke W et al (2008) Toward an online repository of standard operating procedures (SOPs) for (Meta) genomic annotation. Omi A J Integr Biol 12:137–141. https://doi.org/10.1089/omi.2008.0017
Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29. https://doi.org/10.1038/75556
Aziz RK, Bartels D et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9:75. https://doi.org/10.1186/1471-2164-9-75
Baym M, Lieberman TD, Kelsic ED et al (2016) Spatiotemporal microbial evolution on antibiotic landscapes. Science 353:1147–1151. https://doi.org/10.1126/science.aag0822
Besemer J, Lomsadze A, Borodovsky M (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29:2607–2618. https://doi.org/10.1093/nar/29.12.2607
Bowman JP (2000) Description of Cellulophaga algicola sp nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 50:1861–1868. https://doi.org/10.1099/00207713-50-5-1861
Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B (2009) The carbohydrate-active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 37:D233–D238. https://doi.org/10.1093/nar/gkn663
Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH (2020) GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 36:1925–1927. https://doi.org/10.1093/bioinformatics/btz848
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
Galperin MY, Makarova KS, Wolf YI, Koonin EV (2015) Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 43:D261–D269. https://doi.org/10.1093/nar/gku1223
Garcia-Gutierrez E, Mayer MJ, Cotter PD, Narbad A (2019) Gut microbiota as a source of novel antimicrobials. Gut Microbes 10:1–21. https://doi.org/10.1080/19490976.2018.1455790
Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91. https://doi.org/10.1099/ijs.0.64483-0
Grissa I, Vergnaud G, Pourcel C (2007) CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35:W52–W57. https://doi.org/10.1093/nar/gkm360
Jebbar M, vonBlohn C, Bremer E (1997) Ectoine functions as an osmoprotectant in Bacillus subtilis and is accumulated via the ABC-transport system OpuC. Fems Microbiol Letters 154:325–330. https://doi.org/10.1111/j.1574-6968.1997.tb12663.x
Jia B, Raphenya AR, Alcock B et al (2017) CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 45:D566–D573. https://doi.org/10.1093/nar/gkw1004
Jorgensen JH, Turnidge JD (2015) Susceptibility test methods: dilution and disk difusion methods. In: Jorgensen JH, Carroll KC, Funke G et al (eds) Manual of clinical microbiology,11th edn. Wiley, New York, pp 1253–1273
Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M (2015) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 44:D457–D462. https://doi.org/10.1093/nar/gkv1070
Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chrom 5:2359–2367. https://doi.org/10.1080/01483918208067640
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054
Lapébie P, Lombard V, Drula E, Terrapon N, Henrissat B (2019) Bacteroidetes use thousands of enzyme combinations to break down glycans. Nat Commun. https://doi.org/10.1038/s41467-019-10068-5
Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H, Chun J (2017) ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 67:2053–2057. https://doi.org/10.1099/ijsem.0.001872
Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24:713–714. https://doi.org/10.1093/bioinformatics/btn025
Liu B, Pop M (2009) ARDB-antibiotic resistance genes database. Nucleic Acids Res 37:D443–D447. https://doi.org/10.1093/nar/gkn656
Matias PM, Pereira IAC, Soares CM, Carrondo MA (2005) Sulphate respiration from hydrogen in Desulfovibrio bacteria: a structural biology overview. Prog Biophys Mol Bio 89:292–329. https://doi.org/10.1016/j.pbiomolbio.2004.11.003
Medema MH, Blin K, Cimermancic P et al (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39:W339–W346. https://doi.org/10.1093/nar/gkr466
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60. https://doi.org/10.1186/1471-2105-14-60
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241. https://doi.org/10.1016/0167-7012(84)90018-6
Nayak SK (2010) Probiotics and immunity: a fish perspective. Fish Shellfish Immunol 29:2–14. https://doi.org/10.1016/j.fsi.2010.02.017
Neter E (1956) Bacterial Hemagglutination and Hemolysis. Bacteriol Rev 20:166–188. https://doi.org/10.1128/mmbr.20.3.166-188.1956
Price MN, Dehal PS (2010) Arkin AP (2010) fasttree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5(3):e9490. https://doi.org/10.1371/journal.pone.0009490
Qin QL, Xie BB, Zhang XY et al (2014) A Proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 196:2210–2215. https://doi.org/10.1128/jb.01688-14
Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131. https://doi.org/10.1073/pnas.0906412106
Richter M, Rosselló-Móra R, Glöckner FO, Peplies J (2016) JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32:929–931. https://doi.org/10.1093/bioinformatics/btv681
Romanenko LA, Schumann P, Zhukova NV, Rohde M, Mikhailov VV, Stackebrandt E (2003) Oceanisphaera litoralis gen. nov., sp nov., a novel halophilic bacterium from marine bottom sediments. Int J Syst Evol Microbiol 53:1885–1888. https://doi.org/10.1099/ijs.0.02774-0
Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI technical note 101. Microbial ID Inc, Newark
Semova I, Carten JD, Stombaugh J et al (2012) Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish. Cell Host Microbe 12:277–288. https://doi.org/10.1016/j.chom.2012.08.003
Smibert RM, Krieg NR (1994) Phenotypic characterisation. In: Gerhardt P, Murray R, Wood W, Krieg N (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654
Stincone P, Brandelli A (2020) Marine bacteria as source of antimicrobial compounds. Crit Rev Biotechnol 40:306–319. https://doi.org/10.1080/07388551.2019.1710457
Tindall BJ, Sikorski J, Smibert RA, Krieg NR (2007) Phenotypic characterization and the principles of comparative systematics. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al (eds) Methods for general and molecular bacteriology, 3rd edn. American Society for Microbiology, Washington, DC, pp 330–393
Trifinopoulos J, Lam-Tung N, von Haeseler A, Minh BQ (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res 44:W232–W235. https://doi.org/10.1093/nar/gkw256
Wang AR, Ran C, Ringø E, Zhou ZG (2018) Progress in fish gastrointestinal microbiota research. Rev Aquac 10:626–640. https://doi.org/10.1111/raq.12191
Xu XW, Wu YH, Wang CS, Oren A, Zhou PJ, Wu M (2007) Haloferax larsenii sp nov, an extremely halophilic archaeon from a solar saltern. Int J Syst Evol Microbiol 57:717–720. https://doi.org/10.1099/ijs.0.64573-0
Yoon SH, Ha SM, Kwon S et al (2017a) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617. https://doi.org/10.1099/ijsem.0.001755
Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017b) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286. https://doi.org/10.1007/s10482-017-0844-4
Acknowledgements
We thank Professor Zong-Jun Du, Shandong University, for kindly providing the type strain DSM 15406T of the type species Oceanisphaera litoralis.
Funding
This work was funded by the National Natural Science Foundation of China (32070002) and the National Science and Technology Fundamental Resources Investigation Program of China (2019FY100700).
Author information
Authors and Affiliations
Contributions
JHX and LFS: isolated the strain DM8T, analysed most of the data. JHX, BNZ, WJW and YG: performed the experiments. The initial draft of the paper was written by JHX. LHZ and QZ: conceived of the study, designed the study, critically revised the manuscript and co-corresponding the study. All authors read, discussed the results and revised the manuscript.
Corresponding authors
Ethics declarations
Conflict of interest
Authors declare that there is no conflict of interest.
Ethical approval
In this study, experiments were not performed on live vertebrates. Instead, freshly caught dead fish was used and this article does not contain any study with human participants or animal experiments by any of the authors.
Additional information
Communicated by Erko Stackebrandt.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Xue, JH., Shi, LF., Zhang, BN. et al. Oceanisphaera pacifica sp. nov., isolated from the intestine of Trichiurus japonicus. Arch Microbiol 204, 338 (2022). https://doi.org/10.1007/s00203-022-02928-4
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00203-022-02928-4