Harnessing the Intragenomic Variability of RRNA Operons to Improve Differentiation of Vibrio Species

Overview

Journal Sci Rep

Specialty Science

Date 2024 Apr 30

PMID 38688963

Authors

Amaia Leunda-Esnaola

Evgeni Bunin

Pablo Arrufat

Peter B Pearman

Vladimir R Kaberdin

Affiliations

Soon will be listed here.

Abstract

Although the 16S rRNA gene is frequently used as a phylogenetic marker in analysis of environmental DNA, this marker often fails to distinguish closely related species, including those in the genus Vibrio. Here, we investigate whether inclusion and analysis of 23S rRNA sequence can help overcome the intrinsic weaknesses of 16S rRNA analyses for the differentiation of Vibrio species. We construct a maximum likelihood 16S rRNA gene tree to assess the use of this gene to identify clades of Vibrio species. Within the 16S rRNA tree, we identify the putative informative bases responsible for polyphyly, and demonstrate the association of these positions with tree topology. We demonstrate that concatenation of 16S and 23S rRNA genes increases the number of informative nucleotide positions, thereby overcoming ambiguities in 16S rRNA-based phylogenetic reconstructions. Finally, we experimentally demonstrate that this approach considerably improves the differentiation and identification of Vibrio species in environmental samples.

Citing Articles

Screening of Lipid-Reducing Activity and Cytotoxicity of the Exometabolome from Cyanobacteria.

Luz R, Cordeiro R, Goncalves V, Vasconcelos V, Urbatzka R Mar Drugs. 2024; 22(9).

PMID: 39330293 PMC: 11433081. DOI: 10.3390/md22090412.

References

Ma F, Wang C, Zhang Y, Chen J, Xie R, Sun Z . Development of Microbial Indicators in Ecological Systems. Int J Environ Res Public Health. 2022; 19(21). PMC: 9654993. DOI: 10.3390/ijerph192113888. View

Jesser K, Noble R . Vibrio Ecology in the Neuse River Estuary, North Carolina, Characterized by Next-Generation Amplicon Sequencing of the Gene Encoding Heat Shock Protein 60 (). Appl Environ Microbiol. 2018; 84(13). PMC: 6007114. DOI: 10.1128/AEM.00333-18. View

Moi I, Leow A, Mohamad Ali M, Rahman R, Bakar Salleh A, Sabri S . Polyunsaturated fatty acids in marine bacteria and strategies to enhance their production. Appl Microbiol Biotechnol. 2018; 102(14):5811-5826. DOI: 10.1007/s00253-018-9063-9. View

Grimes D . The Vibrios: Scavengers, Symbionts, and Pathogens from the Sea. Microb Ecol. 2020; 80(3):501-506. DOI: 10.1007/s00248-020-01524-7. View

Sanches-Fernandes G, Sa-Correia I, Costa R . Vibriosis Outbreaks in Aquaculture: Addressing Environmental and Public Health Concerns and Preventive Therapies Using Gilthead Seabream Farming as a Model System. Front Microbiol. 2022; 13:904815. PMC: 9309886. DOI: 10.3389/fmicb.2022.904815. View

Vezzulli L, Colwell R, Pruzzo C . Ocean warming and spread of pathogenic vibrios in the aquatic environment. Microb Ecol. 2013; 65(4):817-25. DOI: 10.1007/s00248-012-0163-2. View

Mohd Yazid S, Daud H, Azmai M, Mohamad N, Mohd Nor N . Estimating the Economic Loss Due to Vibriosis in Net-Cage Cultured Asian Seabass (): Evidence From the East Coast of Peninsular Malaysia. Front Vet Sci. 2021; 8:644009. PMC: 8531722. DOI: 10.3389/fvets.2021.644009. View

Ogayar E, Larranaga I, Lomba A, Kaberdin V, Arana I, Orruno M . Efficiency and specificity of CARD-FISH probes in detection of marine vibrios. Environ Microbiol Rep. 2021; 13(6):928-933. DOI: 10.1111/1758-2229.13015. View

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P . The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2012; 41(Database issue):D590-6. PMC: 3531112. DOI: 10.1093/nar/gks1219. View

10.

Stoddard S, Smith B, Hein R, Roller B, Schmidt T . rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development. Nucleic Acids Res. 2014; 43(Database issue):D593-8. PMC: 4383981. DOI: 10.1093/nar/gku1201. View

11.

Yarza P, Yilmaz P, Pruesse E, Glockner F, Ludwig W, Schleifer K . Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol. 2014; 12(9):635-45. DOI: 10.1038/nrmicro3330. View

12.

Gutacker M, Conza N, Benagli C, Pedroli A, Bernasconi M, Permin L . Population genetics of Vibrio vulnificus: identification of two divisions and a distinct eel-pathogenic clone. Appl Environ Microbiol. 2003; 69(6):3203-12. PMC: 161503. DOI: 10.1128/AEM.69.6.3203-3212.2003. View

13.

Maiden M, Bygraves J, Feil E, Morelli G, Russell J, Urwin R . Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A. 1998; 95(6):3140-5. PMC: 19708. DOI: 10.1073/pnas.95.6.3140. View

14.

Glaeser S, Kampfer P . Multilocus sequence analysis (MLSA) in prokaryotic taxonomy. Syst Appl Microbiol. 2015; 38(4):237-45. DOI: 10.1016/j.syapm.2015.03.007. View

15.

Thompson F, Gevers D, Thompson C, Dawyndt P, Naser S, Hoste B . Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis. Appl Environ Microbiol. 2005; 71(9):5107-15. PMC: 1214639. DOI: 10.1128/AEM.71.9.5107-5115.2005. View

16.

Cano-Gomez A, Hoj L, Owens L, Andreakis N . Multilocus sequence analysis provides basis for fast and reliable identification of Vibrio harveyi-related species and reveals previous misidentification of important marine pathogens. Syst Appl Microbiol. 2011; 34(8):561-5. DOI: 10.1016/j.syapm.2011.09.001. View

17.

Johnson J, Spakowicz D, Hong B, Petersen L, Demkowicz P, Chen L . Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun. 2019; 10(1):5029. PMC: 6834636. DOI: 10.1038/s41467-019-13036-1. View

18.

Johansen J, Mares J, Pietrasiak N, Bohunicka M, Zima Jr J, Stenclova L . Highly divergent 16S rRNA sequences in ribosomal operons of Scytonema hyalinum (Cyanobacteria). PLoS One. 2017; 12(10):e0186393. PMC: 5658200. DOI: 10.1371/journal.pone.0186393. View

19.

Martijn J, Lind A, Schon M, Spiertz I, Juzokaite L, Bunikis I . Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon. Environ Microbiol. 2019; 21(7):2485-2498. PMC: 6849856. DOI: 10.1111/1462-2920.14636. View

20.

Hoffmann M, Brown E, Feng P, Keys C, Fischer M, Monday S . PCR-based method for targeting 16S-23S rRNA intergenic spacer regions among Vibrio species. BMC Microbiol. 2010; 10:90. PMC: 2856557. DOI: 10.1186/1471-2180-10-90. View