Parasalinivibrio latis gen. nov., sp. nov., isolated from the distal gut of healthy farmed Asian Seabass (Lates calcarifer)
Asian Seabass ( Lates calcarifer ) is widely farmed as a sustainable source of protein for countries in the tropical Indo-West Pacific region. However, microbial species of the gut microbiome of healthy Asian Seabass remain largely uncharacterized and uncultured. Here, we analysed the microbial comp...
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| Veröffentlicht in: | Antonie van Leeuwenhoek 2025-01, Vol.118 (1), p.25-25, Article 25 |
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| creator | Er, Shuan Soh, Melissa Low, Adrian Seedorf, Henning |
| description | Asian Seabass (
Lates calcarifer
) is widely farmed as a sustainable source of protein for countries in the tropical Indo-West Pacific region. However, microbial species of the gut microbiome of healthy Asian Seabass remain largely uncharacterized and uncultured. Here, we analysed the microbial composition along the gastrointestinal tract of a farmed healthy Asian Seabass. We used different cultivation approaches to obtain isolates from the seabass intestinal tract and describe the isolation and characterization of a novel strain, TLL-SE01
T
. Analysis of the strain’s 16S rRNA gene indicates that the strain belongs to the family
Vibrionaceae
with
Photobacterium damselae
as its closest relative, albeit sharing only 94.8% (aligned region 1553 bp) nucleotide identity. Comparative genomic analysis with all validly published
Vibrionaceae
species with available genomes revealed average nucleotide identity (ANI) and DNA–DNA hybridisation (DDH) values of around 70% and 24% respectively to strain TLL-SE01
T
, which are well below proposed thresholds for species delineation (ANI, 95–96%; DDH, 70%). The alignment fraction and ANI genus demarcation boundaries for all genera in the
Vibrionaceae
family were determined for which strain TLL-SE01
T
is well below the calculated values, indicating that it belongs to a novel genus. Single- and core-gene phylogenetic analysis places strain TLL-SE01
T
in a monophyletic clade, further supporting its designation to a novel genus. Phenotypic comparison between strain TLL-SE01
T
and its close relatives indicated additional differences, such as growth response at different salt concentrations and different metabolic capabilities. Based on genotypic, phylogenetic and phenotypic differences to other
Vibrionaceae
species, we propose a novel species in a new genus,
Parasalinivibrio latis
gen. nov. sp. nov. and strain TLL-SE01
T
(= BCRC 81435
T
= JCM 36283
T
) as the type strain. |
| doi_str_mv | 10.1007/s10482-024-02036-x |
| format | Article |
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Lates calcarifer
) is widely farmed as a sustainable source of protein for countries in the tropical Indo-West Pacific region. However, microbial species of the gut microbiome of healthy Asian Seabass remain largely uncharacterized and uncultured. Here, we analysed the microbial composition along the gastrointestinal tract of a farmed healthy Asian Seabass. We used different cultivation approaches to obtain isolates from the seabass intestinal tract and describe the isolation and characterization of a novel strain, TLL-SE01
T
. Analysis of the strain’s 16S rRNA gene indicates that the strain belongs to the family
Vibrionaceae
with
Photobacterium damselae
as its closest relative, albeit sharing only 94.8% (aligned region 1553 bp) nucleotide identity. Comparative genomic analysis with all validly published
Vibrionaceae
species with available genomes revealed average nucleotide identity (ANI) and DNA–DNA hybridisation (DDH) values of around 70% and 24% respectively to strain TLL-SE01
T
, which are well below proposed thresholds for species delineation (ANI, 95–96%; DDH, 70%). The alignment fraction and ANI genus demarcation boundaries for all genera in the
Vibrionaceae
family were determined for which strain TLL-SE01
T
is well below the calculated values, indicating that it belongs to a novel genus. Single- and core-gene phylogenetic analysis places strain TLL-SE01
T
in a monophyletic clade, further supporting its designation to a novel genus. Phenotypic comparison between strain TLL-SE01
T
and its close relatives indicated additional differences, such as growth response at different salt concentrations and different metabolic capabilities. Based on genotypic, phylogenetic and phenotypic differences to other
Vibrionaceae
species, we propose a novel species in a new genus,
Parasalinivibrio latis
gen. nov. sp. nov. and strain TLL-SE01
T
(= BCRC 81435
T
= JCM 36283
T
) as the type strain.</description><identifier>ISSN: 0003-6072</identifier><identifier>ISSN: 1572-9699</identifier><identifier>EISSN: 1572-9699</identifier><identifier>DOI: 10.1007/s10482-024-02036-x</identifier><identifier>PMID: 39520647</identifier><language>eng</language><publisher>Cham: Springer International Publishing</publisher><subject>Animals ; Aquaculture ; Bacterial Typing Techniques ; Bass - microbiology ; Biomedical and Life Sciences ; Deoxyribonucleic acid ; Digestive system ; digestive tract ; DNA ; DNA, Bacterial - genetics ; family ; Gastrointestinal Microbiome ; Gastrointestinal system ; Gastrointestinal tract ; genes ; Genome, Bacterial ; Genomic analysis ; genomics ; genus ; Hybridization ; Intestinal microflora ; intestinal microorganisms ; intestines ; Lates calcarifer ; Life Sciences ; Medical Microbiology ; Microbiology ; Microbiomes ; Microorganisms ; monophyly ; New genera ; new genus ; New species ; Nucleotides ; Original Paper ; phenotype ; Photobacterium damselae ; Phylogenetics ; Phylogeny ; Plant Sciences ; Protein sources ; RNA, Ribosomal, 16S - genetics ; rRNA 16S ; Sequence Analysis, DNA ; Soil Science & Conservation ; species ; Strain analysis ; Vibrionaceae ; Vibrionaceae - classification ; Vibrionaceae - genetics ; Vibrionaceae - isolation & purification</subject><ispartof>Antonie van Leeuwenhoek, 2025-01, Vol.118 (1), p.25-25, Article 25</ispartof><rights>The Author(s), under exclusive licence to Springer Nature Switzerland AG 2024 Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.</rights><rights>2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.</rights><rights>Copyright Springer Nature B.V. Jan 2025</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c289t-7e0f91d9415da6cc1578bbb63a838bc5ccebc99b4a34c6dad9873a12dafc6faa3</cites><orcidid>0000-0003-0997-2490 ; 0000-0002-5763-0236 ; 0000-0002-5315-5474 ; 0000-0002-7578-9515</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10482-024-02036-x$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10482-024-02036-x$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27903,27904,41467,42536,51297</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39520647$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Er, Shuan</creatorcontrib><creatorcontrib>Soh, Melissa</creatorcontrib><creatorcontrib>Low, Adrian</creatorcontrib><creatorcontrib>Seedorf, Henning</creatorcontrib><title>Parasalinivibrio latis gen. nov., sp. nov., isolated from the distal gut of healthy farmed Asian Seabass (Lates calcarifer)</title><title>Antonie van Leeuwenhoek</title><addtitle>Antonie van Leeuwenhoek</addtitle><addtitle>Antonie Van Leeuwenhoek</addtitle><description>Asian Seabass (
Lates calcarifer
) is widely farmed as a sustainable source of protein for countries in the tropical Indo-West Pacific region. However, microbial species of the gut microbiome of healthy Asian Seabass remain largely uncharacterized and uncultured. Here, we analysed the microbial composition along the gastrointestinal tract of a farmed healthy Asian Seabass. We used different cultivation approaches to obtain isolates from the seabass intestinal tract and describe the isolation and characterization of a novel strain, TLL-SE01
T
. Analysis of the strain’s 16S rRNA gene indicates that the strain belongs to the family
Vibrionaceae
with
Photobacterium damselae
as its closest relative, albeit sharing only 94.8% (aligned region 1553 bp) nucleotide identity. Comparative genomic analysis with all validly published
Vibrionaceae
species with available genomes revealed average nucleotide identity (ANI) and DNA–DNA hybridisation (DDH) values of around 70% and 24% respectively to strain TLL-SE01
T
, which are well below proposed thresholds for species delineation (ANI, 95–96%; DDH, 70%). The alignment fraction and ANI genus demarcation boundaries for all genera in the
Vibrionaceae
family were determined for which strain TLL-SE01
T
is well below the calculated values, indicating that it belongs to a novel genus. Single- and core-gene phylogenetic analysis places strain TLL-SE01
T
in a monophyletic clade, further supporting its designation to a novel genus. Phenotypic comparison between strain TLL-SE01
T
and its close relatives indicated additional differences, such as growth response at different salt concentrations and different metabolic capabilities. Based on genotypic, phylogenetic and phenotypic differences to other
Vibrionaceae
species, we propose a novel species in a new genus,
Parasalinivibrio latis
gen. nov. sp. nov. and strain TLL-SE01
T
(= BCRC 81435
T
= JCM 36283
T
) as the type strain.</description><subject>Animals</subject><subject>Aquaculture</subject><subject>Bacterial Typing Techniques</subject><subject>Bass - microbiology</subject><subject>Biomedical and Life Sciences</subject><subject>Deoxyribonucleic acid</subject><subject>Digestive system</subject><subject>digestive tract</subject><subject>DNA</subject><subject>DNA, Bacterial - genetics</subject><subject>family</subject><subject>Gastrointestinal Microbiome</subject><subject>Gastrointestinal system</subject><subject>Gastrointestinal tract</subject><subject>genes</subject><subject>Genome, Bacterial</subject><subject>Genomic analysis</subject><subject>genomics</subject><subject>genus</subject><subject>Hybridization</subject><subject>Intestinal microflora</subject><subject>intestinal microorganisms</subject><subject>intestines</subject><subject>Lates calcarifer</subject><subject>Life Sciences</subject><subject>Medical Microbiology</subject><subject>Microbiology</subject><subject>Microbiomes</subject><subject>Microorganisms</subject><subject>monophyly</subject><subject>New genera</subject><subject>new genus</subject><subject>New species</subject><subject>Nucleotides</subject><subject>Original Paper</subject><subject>phenotype</subject><subject>Photobacterium damselae</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Plant Sciences</subject><subject>Protein sources</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>rRNA 16S</subject><subject>Sequence Analysis, DNA</subject><subject>Soil Science & Conservation</subject><subject>species</subject><subject>Strain analysis</subject><subject>Vibrionaceae</subject><subject>Vibrionaceae - classification</subject><subject>Vibrionaceae - genetics</subject><subject>Vibrionaceae - isolation & purification</subject><issn>0003-6072</issn><issn>1572-9699</issn><issn>1572-9699</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2025</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkV9rFDEUxYModl39Aj5IwJcKzpp_k0keS9FWWLCgPg83mWQ3ZXZmzZ0pLX55025roQ_iQ0jC_Z1zufcQ8pazFWes-YScKSMqJlQ5TOrq-hlZ8LoRldXWPicLxpisNGvEEXmFeFm-VpvmJTmSthZMq2ZBfl9ABoQ-DekquZxG2sOUkG7CsKLDeLX6SHH_8Eo4lmroaMzjjk7bQLuEE_R0M090jHQboJ-2NzRC3hXqBBMM9HsAB4j0eF2kSD30HnKKIX94TV5E6DG8ub-X5OeXzz9Oz6v1t7Ovpyfrygtjp6oJLFreWcXrDrT3ZULjnNMSjDTO194H5611CqTyuoPOmkYCFx1EryOAXJLjg-8-j7_mgFO7S-hD38MQxhlbyevizUxt_wMVplFalMUuyfsn6OU456EMcktppWrGTKHEgfJ5RMwhtvucdpBvWs7a2xTbQ4ptSbG9S7G9LqJ399azK4v8K3mIrQDyAGApDZuQH3v_w_YPHvCoPA</recordid><startdate>20250101</startdate><enddate>20250101</enddate><creator>Er, Shuan</creator><creator>Soh, Melissa</creator><creator>Low, Adrian</creator><creator>Seedorf, Henning</creator><general>Springer International Publishing</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7T7</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>7X8</scope><scope>7S9</scope><scope>L.6</scope><orcidid>https://orcid.org/0000-0003-0997-2490</orcidid><orcidid>https://orcid.org/0000-0002-5763-0236</orcidid><orcidid>https://orcid.org/0000-0002-5315-5474</orcidid><orcidid>https://orcid.org/0000-0002-7578-9515</orcidid></search><sort><creationdate>20250101</creationdate><title>Parasalinivibrio latis gen. nov., sp. nov., isolated from the distal gut of healthy farmed Asian Seabass (Lates calcarifer)</title><author>Er, Shuan ; Soh, Melissa ; Low, Adrian ; Seedorf, Henning</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c289t-7e0f91d9415da6cc1578bbb63a838bc5ccebc99b4a34c6dad9873a12dafc6faa3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2025</creationdate><topic>Animals</topic><topic>Aquaculture</topic><topic>Bacterial Typing Techniques</topic><topic>Bass - microbiology</topic><topic>Biomedical and Life Sciences</topic><topic>Deoxyribonucleic acid</topic><topic>Digestive system</topic><topic>digestive tract</topic><topic>DNA</topic><topic>DNA, Bacterial - genetics</topic><topic>family</topic><topic>Gastrointestinal Microbiome</topic><topic>Gastrointestinal system</topic><topic>Gastrointestinal tract</topic><topic>genes</topic><topic>Genome, Bacterial</topic><topic>Genomic analysis</topic><topic>genomics</topic><topic>genus</topic><topic>Hybridization</topic><topic>Intestinal microflora</topic><topic>intestinal microorganisms</topic><topic>intestines</topic><topic>Lates calcarifer</topic><topic>Life Sciences</topic><topic>Medical Microbiology</topic><topic>Microbiology</topic><topic>Microbiomes</topic><topic>Microorganisms</topic><topic>monophyly</topic><topic>New genera</topic><topic>new genus</topic><topic>New species</topic><topic>Nucleotides</topic><topic>Original Paper</topic><topic>phenotype</topic><topic>Photobacterium damselae</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Plant Sciences</topic><topic>Protein sources</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>rRNA 16S</topic><topic>Sequence Analysis, DNA</topic><topic>Soil Science & Conservation</topic><topic>species</topic><topic>Strain analysis</topic><topic>Vibrionaceae</topic><topic>Vibrionaceae - classification</topic><topic>Vibrionaceae - genetics</topic><topic>Vibrionaceae - isolation & purification</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Er, Shuan</creatorcontrib><creatorcontrib>Soh, Melissa</creatorcontrib><creatorcontrib>Low, Adrian</creatorcontrib><creatorcontrib>Seedorf, Henning</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><jtitle>Antonie van Leeuwenhoek</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Er, Shuan</au><au>Soh, Melissa</au><au>Low, Adrian</au><au>Seedorf, Henning</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Parasalinivibrio latis gen. nov., sp. nov., isolated from the distal gut of healthy farmed Asian Seabass (Lates calcarifer)</atitle><jtitle>Antonie van Leeuwenhoek</jtitle><stitle>Antonie van Leeuwenhoek</stitle><addtitle>Antonie Van Leeuwenhoek</addtitle><date>2025-01-01</date><risdate>2025</risdate><volume>118</volume><issue>1</issue><spage>25</spage><epage>25</epage><pages>25-25</pages><artnum>25</artnum><issn>0003-6072</issn><issn>1572-9699</issn><eissn>1572-9699</eissn><abstract>Asian Seabass (
Lates calcarifer
) is widely farmed as a sustainable source of protein for countries in the tropical Indo-West Pacific region. However, microbial species of the gut microbiome of healthy Asian Seabass remain largely uncharacterized and uncultured. Here, we analysed the microbial composition along the gastrointestinal tract of a farmed healthy Asian Seabass. We used different cultivation approaches to obtain isolates from the seabass intestinal tract and describe the isolation and characterization of a novel strain, TLL-SE01
T
. Analysis of the strain’s 16S rRNA gene indicates that the strain belongs to the family
Vibrionaceae
with
Photobacterium damselae
as its closest relative, albeit sharing only 94.8% (aligned region 1553 bp) nucleotide identity. Comparative genomic analysis with all validly published
Vibrionaceae
species with available genomes revealed average nucleotide identity (ANI) and DNA–DNA hybridisation (DDH) values of around 70% and 24% respectively to strain TLL-SE01
T
, which are well below proposed thresholds for species delineation (ANI, 95–96%; DDH, 70%). The alignment fraction and ANI genus demarcation boundaries for all genera in the
Vibrionaceae
family were determined for which strain TLL-SE01
T
is well below the calculated values, indicating that it belongs to a novel genus. Single- and core-gene phylogenetic analysis places strain TLL-SE01
T
in a monophyletic clade, further supporting its designation to a novel genus. Phenotypic comparison between strain TLL-SE01
T
and its close relatives indicated additional differences, such as growth response at different salt concentrations and different metabolic capabilities. Based on genotypic, phylogenetic and phenotypic differences to other
Vibrionaceae
species, we propose a novel species in a new genus,
Parasalinivibrio latis
gen. nov. sp. nov. and strain TLL-SE01
T
(= BCRC 81435
T
= JCM 36283
T
) as the type strain.</abstract><cop>Cham</cop><pub>Springer International Publishing</pub><pmid>39520647</pmid><doi>10.1007/s10482-024-02036-x</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0003-0997-2490</orcidid><orcidid>https://orcid.org/0000-0002-5763-0236</orcidid><orcidid>https://orcid.org/0000-0002-5315-5474</orcidid><orcidid>https://orcid.org/0000-0002-7578-9515</orcidid></addata></record> |
| fulltext | fulltext |
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| ispartof | Antonie van Leeuwenhoek, 2025-01, Vol.118 (1), p.25-25, Article 25 |
| issn | 0003-6072 1572-9699 1572-9699 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_3128746200 |
| source | MEDLINE; SpringerLink Journals |
| subjects | Animals Aquaculture Bacterial Typing Techniques Bass - microbiology Biomedical and Life Sciences Deoxyribonucleic acid Digestive system digestive tract DNA DNA, Bacterial - genetics family Gastrointestinal Microbiome Gastrointestinal system Gastrointestinal tract genes Genome, Bacterial Genomic analysis genomics genus Hybridization Intestinal microflora intestinal microorganisms intestines Lates calcarifer Life Sciences Medical Microbiology Microbiology Microbiomes Microorganisms monophyly New genera new genus New species Nucleotides Original Paper phenotype Photobacterium damselae Phylogenetics Phylogeny Plant Sciences Protein sources RNA, Ribosomal, 16S - genetics rRNA 16S Sequence Analysis, DNA Soil Science & Conservation species Strain analysis Vibrionaceae Vibrionaceae - classification Vibrionaceae - genetics Vibrionaceae - isolation & purification |
| title | Parasalinivibrio latis gen. nov., sp. nov., isolated from the distal gut of healthy farmed Asian Seabass (Lates calcarifer) |
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