Spirochaete genome identified in red abalone sample represents a novel genus Candidatus Haliotispira gen. nov. within the order Spirochaetales

Sharma, Sharu Paul; Purcell, Catherine M.; Hyde, John R.; Severin, Andrew J.

doi:10.1099/ijsem.0.006198

Spirochaete genome identified in red abalone sample represents a novel genus Candidatus Haliotispira gen. nov. within the order Spirochaetales

Journal Article · Fri Jan 05 00:00:00 EST 2024 · International Journal of Systematic and Evolutionary Microbiology

DOI:https://doi.org/10.1099/ijsem.0.006198· OSTI ID:2278902

^[1]; Purcell, Catherine M. ^[2]; Hyde, John R. ^[2]; ^[1]

Genome Informatics Facility, Iowa State University, Ames, Iowa, USA
NOAA Fisheries Southwest Fisheries Science Center, La Jolla, California, USA

A fully assembled spirochaete genome was identified as a contaminating scaffold in our red abalone ( Haliotis rufescens ) genome assembly. In this paper, we describe the analysis of this bacterial genome. The assembled spirochaete genome is 3.25 Mb in size with 48.5 mol% G+C content. The proteomes of 38 species were compared with the spirochaete genome and it was discovered to form an independent branch within the family Spirochaetaceae on the phylogenetic tree. The comparison of 16S rRNA sequences and average nucleotide identity scores between the spirochaete genome with known species of different families in Spirochaetia indicate that it is an unknown species. Further, the percentage of conserved proteins compared to neighbouring taxa confirm that it does not belong to a known genus within Spirochaetaceae . We propose the name Candidatus Haliotispira prima gen. nov., sp. nov. based on its taxonomic placement and origin. We also tested for the presence of this species in different species of abalone and found that it is also present in white abalone ( Haliotis sorenseni ). In addition, we highlight the need for better classification of taxa within the class Spirochaetia .

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Research Organization:: Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC)

Grant/Contract Number:: SC0014664

OSTI ID:: 2278902

Alternate ID(s):: OSTI ID: 2582465

Journal Information:: International Journal of Systematic and Evolutionary Microbiology, Journal Name: International Journal of Systematic and Evolutionary Microbiology Journal Issue: 1 Vol. 74; ISSN 1466-5026

Publisher:: Society for General MicrobiologyCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (44)

Spirochetes in gastropods from Lake Baikal and North American freshwaters: new multi-family, multi-habitat host records Sitnikova, Tatiana; Michel, Ellinor; Tulupova, Yulia Symbiosis, Vol. 56, Issue 3 https://doi.org/10.1007/s13199-012-0167-1	journal	April 2012
Genetic diversity in Treponema pallidum: Implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws Šmajs, David; Norris, Steven J.; Weinstock, George M. Infection, Genetics and Evolution, Vol. 12, Issue 2 https://doi.org/10.1016/j.meegid.2011.12.001	journal	March 2012
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega Sievers, Fabian; Wilm, Andreas; Dineen, David Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.75	journal	January 2011
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype Kim, Daehwan; Paggi, Joseph M.; Park, Chanhee Nature Biotechnology, Vol. 37, Issue 8 https://doi.org/10.1038/s41587-019-0201-4	journal	August 2019
Spirochetes isolated from arthropods constitute a novel genus Entomospira genus novum within the order Spirochaetales Graña-Miraglia, Lucía; Sikutova, Silvie; Vancová, Marie Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-74033-9	journal	October 2020
Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes Seshadri, R.; Myers, G. S. A.; Tettelin, H. Proceedings of the National Academy of Sciences, Vol. 101, Issue 15 https://doi.org/10.1073/pnas.0307639101	journal	April 2004
Fold and Function of the InlB B-repeat Ebbes, Maria; Bleymüller, Willem M.; Cernescu, Mihaela Journal of Biological Chemistry, Vol. 286, Issue 17 https://doi.org/10.1074/jbc.M110.189951	journal	April 2011
The MaSuRCA genome assembler Zimin, Aleksey V.; Marçais, Guillaume; Puiu, Daniela Bioinformatics, Vol. 29, Issue 21 https://doi.org/10.1093/bioinformatics/btt476	journal	August 2013
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Simão, Felipe A.; Waterhouse, Robert M.; Ioannidis, Panagiotis Bioinformatics, Vol. 31, Issue 19 https://doi.org/10.1093/bioinformatics/btv351	journal	June 2015
JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison Richter, Michael; Rosselló-Móra, Ramon; Oliver Glöckner, Frank Bioinformatics, Vol. 32, Issue 6 https://doi.org/10.1093/bioinformatics/btv681	journal	November 2015
Complex heatmaps reveal patterns and correlations in multidimensional genomic data Gu, Zuguang; Eils, Roland; Schlesner, Matthias Bioinformatics, Vol. 32, Issue 18 https://doi.org/10.1093/bioinformatics/btw313	journal	May 2016
Minimap2: pairwise alignment for nucleotide sequences Li, Heng Bioinformatics, Vol. 34, Issue 18 https://doi.org/10.1093/bioinformatics/bty191	journal	May 2018
An Annotated Genome for Haliotis rufescens (Red Abalone) and Resequenced Green, Pink, Pinto, Black, and White Abalone Species Masonbrink, Rick E.; Purcell, Catherine M.; Boles, Sara E. Genome Biology and Evolution, Vol. 11, Issue 2 https://doi.org/10.1093/gbe/evz006	journal	January 2019
Twelve years of SAMtools and BCFtools Danecek, Petr; Bonfield, James K.; Liddle, Jennifer GigaScience, Vol. 10, Issue 2 https://doi.org/10.1093/gigascience/giab008	journal	January 2021
STRIDE: Species Tree Root Inference from Gene Duplication Events Emms, David M.; Kelly, Steven Molecular Biology and Evolution, Vol. 34, Issue 12 https://doi.org/10.1093/molbev/msx259	journal	September 2017
Function of the crystalline style and first detection of laminarinase activity in freshwater mussels of the genus Anodonta Michl, S. C.; Windisch, W.; Geist, J. Journal of Molluscan Studies, Vol. 80, Issue 2 https://doi.org/10.1093/mollus/eyt053	journal	January 2014
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation Letunic, Ivica; Bork, Peer Nucleic Acids Research, Vol. 49, Issue W1 https://doi.org/10.1093/nar/gkab301	journal	April 2021
NCBI prokaryotic genome annotation pipeline Tatusova, Tatiana; DiCuccio, Michael; Badretdin, Azat Nucleic Acids Research, Vol. 44, Issue 14 https://doi.org/10.1093/nar/gkw569	journal	June 2016
Borrelia recurrentis Characterization and Comparison with Relapsing-Fever, Lyme-Associated, and Other Borrelia spp. Cutler, S. J.; Moss, J.; Fukunaga, M. International Journal of Systematic Bacteriology, Vol. 47, Issue 4 https://doi.org/10.1099/00207713-47-4-958	journal	October 1997
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes Kim, M.; Oh, H. -S.; Park, S. -C. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 2 https://doi.org/10.1099/ijs.0.059774-0	journal	February 2014
DNA–DNA hybridization values and their relationship to whole-genome sequence similarities Klappenbach, Joel A.; Goris, Johan; Vandamme, Peter International Journal of Systematic and Evolutionary Microbiology, Vol. 57, Issue 1 https://doi.org/10.1099/ijs.0.64483-0	journal	January 2007
Rejection of the name Borreliella and all proposed species comb. nov. placed therein Margos, Gabriele; Castillo-Ramirez, Santiago; Cutler, Sally International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 5 https://doi.org/10.1099/ijsem.0.004149	journal	May 2020
List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ Parte, Aidan C.; Sardà Carbasse, Joaquim; Meier-Kolthoff, Jan P. International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 11 https://doi.org/10.1099/ijsem.0.004332	journal	November 2020
A new family for ‘termite gut treponemes’: description of Breznakiellaceae fam. nov., Gracilinema caldarium gen. nov., comb. nov., Leadbettera azotonutricia gen. nov., comb. nov., Helmutkoenigia isoptericolens gen. nov., comb. nov., and Zuelzera stenostrepta gen. nov., comb. nov., and proposal of Rectinemataceae fam. nov. Brune, Andreas; Song, Yulin; Oren, Aharon International Journal of Systematic and Evolutionary Microbiology, Vol. 72, Issue 5 https://doi.org/10.1099/ijsem.0.005439	journal	May 2022
The Role of Lineage-Specific Gene Family Expansion in the Evolution of Eukaryotes Lespinet, O. Genome Research, Vol. 12, Issue 7 https://doi.org/10.1101/gr.174302	journal	July 2002
Lineage-Specific Gene Expansions in Bacterial and Archaeal Genomes Jordan, I. K. Genome Research, Vol. 11, Issue 4 https://doi.org/10.1101/gr.gr-1660r	journal	March 2001
XSEDE: Accelerating Scientific Discovery Towns, John; Cockerill, Timothy; Dahan, Maytal Computing in Science & Engineering, Vol. 16, Issue 5 https://doi.org/10.1109/MCSE.2014.80	journal	September 2014
Evidence for chemoautotrophic symbiosis in a Mediterranean cold seep clam (Bivalvia: Lucinidae): comparative sequence analysis of bacterial 16S rRNA, APS reductase and RubisCO genes Duperron, SÃ©bastien; Fiala-MÃ©dioni, Aline; Caprais, Jean-Claude FEMS Microbiology Ecology, Vol. 59, Issue 1 https://doi.org/10.1111/j.1574-6941.2006.00194.x	journal	January 2007
Novel spirochetes isolated from mosquitoes and black flies in the Czech Republic Šikutová, Silvie; Halouzka, Jiří; Mendel, Jan Journal of Vector Ecology, Vol. 35, Issue 1 https://doi.org/10.1111/j.1948-7134.2010.00057.x	journal	June 2010
Acetogenesis from H ₂ Plus CO ₂ by Spirochetes from Termite Guts Leadbetter, J. R.; Schmidt, T. M.; Graber, J. R. Science, Vol. 283, Issue 5402 https://doi.org/10.1126/science.283.5402.686	journal	January 1999
Porphyromonas gingivalis Vesicles Enhance Attachment, and the Leucine-Rich Repeat BspA Protein Is Required for Invasion of Epithelial Cells by "Tannerella forsythia" Inagaki, S.; Onishi, S.; Kuramitsu, H. K. Infection and Immunity, Vol. 74, Issue 9 https://doi.org/10.1128/IAI.00062-06	journal	August 2006
A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights Qin, Q. -L.; Xie, B. -B.; Zhang, X. -Y. Journal of Bacteriology, Vol. 196, Issue 12 https://doi.org/10.1128/JB.01688-14	journal	April 2014
PCR Amplification from Fixed Tissue Indicates Frequent Involvement of Brachyspira aalborgi in Human Intestinal Spirochetosis Mikosza, Andrew S. J.; La, Tom; Brooke, C. Josephine Journal of Clinical Microbiology, Vol. 37, Issue 6 https://doi.org/10.1128/JCM.37.6.2093-2098.1999	journal	June 1999
Anaerobic Spirochete from a Deep-Sea Hydrothermal Vent Harwood, C. S.; Jannasch, H. W.; Canale-Parola, E. Applied and Environmental Microbiology, Vol. 44, Issue 1 https://doi.org/10.1128/aem.44.1.234-237.1982	journal	July 1982
MUSCLE: a multiple sequence alignment method with reduced time and space complexity Edgar, Robert C. BMC Bioinformatics, Vol. 5, Issue 1, p. 113 https://doi.org/10.1186/1471-2105-5-113	journal	August 2004
Complete genome sequence and description of Salinispira pacifica gen. nov., sp. nov., a novel spirochaete isolated form a hypersaline microbial mat Ben Hania, Wajdi; Joseph, Manon; Schumann, Peter Standards in Genomic Sciences, Vol. 10, Issue 1 https://doi.org/10.1186/1944-3277-10-7	journal	January 2015
Gene family expansions and contractions are associated with host range in plant pathogens of the genus Colletotrichum Baroncelli, Riccardo; Amby, Daniel Buchvaldt; Zapparata, Antonio BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2917-6	journal	August 2016
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy Emms, David M.; Kelly, Steven Genome Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s13059-015-0721-2	journal	August 2015
JBrowse 2: a modular genome browser with views of synteny and structural variation Diesh, Colin; Stevens, Garrett J.; Xie, Peter Genome Biology, Vol. 24, Issue 1 https://doi.org/10.1186/s13059-023-02914-z	journal	April 2023
Characterization of the BspA and Pmp protein family of trichomonads Handrich, Maria R.; Garg, Sriram G.; Sommerville, Ewen W. Parasites & Vectors, Vol. 12, Issue 1 https://doi.org/10.1186/s13071-019-3660-z	journal	August 2019
A Spirochaete is suggested as the causative agent of Akoya oyster disease by metagenomic analysis Matsuyama, Tomomasa; Yasuike, Motoshige; Fujiwara, Atushi PLOS ONE, Vol. 12, Issue 8 https://doi.org/10.1371/journal.pone.0182280	journal	August 2017
The genus Borrelia reloaded Margos, Gabriele; Gofton, Alex; Wibberg, Daniel PLOS ONE, Vol. 13, Issue 12 https://doi.org/10.1371/journal.pone.0208432	journal	December 2018
Spirochetes in Crystalline Styles of Marine Bivalves: Group-Specific PCR Detection and 16S rRNA Sequence Analysis Husmann, Gunnar; Gerdts, Gunnar; Wichels, Antje Journal of Shellfish Research, Vol. 29, Issue 4 https://doi.org/10.2983/035.029.0409	journal	December 2010
Microbial community analysis in the gills of abalones suggested possible dominance of epsilonproteobacterium in Haliotis gigantea Mizutani, Yukino; Mori, Tetsushi; Miyazaki, Taeko PeerJ, Vol. 8 https://doi.org/10.7717/peerj.9326	journal	June 2020

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