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Molecular Identification of Bacillus Isolated from Korean Water Deer ( Hydropotes inermis argyropus ) and Striped Field Mouse ( Apodemus agrarius ) Feces by Using an SNP-Based 16S Ribosomal Marker
Ambiguous, heterogeneous, endospore-forming species, notably , often produce fatal toxins that threaten human health. We identified from wild animal fecal samples ( = 80), including the Korean water deer ( = 25) and striped field mouse ( = 55). Using traditional culture-based methods, 25 animal feca...
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| Published in: | Animals (Basel) 2022-04, Vol.12 (8), p.979 |
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| container_title | Animals (Basel) |
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| creator | Rahman, Md-Mafizur Lim, Sang-Jin Park, Yung-Chul |
| description | Ambiguous, heterogeneous, endospore-forming
species, notably
, often produce fatal toxins that threaten human health. We identified
from wild animal fecal samples (
= 80), including the Korean water deer (
= 25) and striped field mouse (
= 55). Using traditional culture-based methods, 25 animal fecal samples (31.25%; 25/80) were found to be positive for
species, whereas using molecular techniques, 19 samples (23.75%; 19/80) were found to be positive for the same. In addition, we designed a
species-specific 16S ribosomal RNA (rRNA) gene marker and utilized it to identify 19 samples by means of PCR amplification and sequencing, using at least one colony from the 19
positive samples. The recovered sequences were matched to sequences of three
species (
,
and
) from the GenBank database. Moreover, the phylogenetic tree generated in this study established specific clades for the
group. In addition, to differentiate between
,
, and
, we designed a single nucleotide polymorphism (SNP)-based primer by identifying SNPs in the alignment of 16S rRNA gene sequences of
group strains. The SNPs were used to design primer sets for discrimination between highly similar species from the
group. The study could be used in surveillance of agricultural fresh-produce-associated
outbreaks, for accurate identification of each
species, and in the development of control measures. |
| doi_str_mv | 10.3390/ani12080979 |
| format | article |
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species, notably
, often produce fatal toxins that threaten human health. We identified
from wild animal fecal samples (
= 80), including the Korean water deer (
= 25) and striped field mouse (
= 55). Using traditional culture-based methods, 25 animal fecal samples (31.25%; 25/80) were found to be positive for
species, whereas using molecular techniques, 19 samples (23.75%; 19/80) were found to be positive for the same. In addition, we designed a
species-specific 16S ribosomal RNA (rRNA) gene marker and utilized it to identify 19 samples by means of PCR amplification and sequencing, using at least one colony from the 19
positive samples. The recovered sequences were matched to sequences of three
species (
,
and
) from the GenBank database. Moreover, the phylogenetic tree generated in this study established specific clades for the
group. In addition, to differentiate between
,
, and
, we designed a single nucleotide polymorphism (SNP)-based primer by identifying SNPs in the alignment of 16S rRNA gene sequences of
group strains. The SNPs were used to design primer sets for discrimination between highly similar species from the
group. The study could be used in surveillance of agricultural fresh-produce-associated
outbreaks, for accurate identification of each
species, and in the development of control measures.</description><identifier>ISSN: 2076-2615</identifier><identifier>EISSN: 2076-2615</identifier><identifier>DOI: 10.3390/ani12080979</identifier><identifier>PMID: 35454225</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>16S ribosomal RNA ; allele ; Animals ; Anthrax ; Apodemus agrarius ; Bacillus ; Bacillus amyloliquefaciens ; Bacillus anthracis ; Bacillus cereus ; Bacillus megaterium ; Bacillus thuringiensis ; Bacteria ; Deoxyribonucleic acid ; DNA ; Feces ; Food contamination & poisoning ; Global positioning systems ; GPS ; Health risks ; Hydropotes inermis argyropus ; Identification ; National parks ; Nucleotide sequence ; Nucleotides ; Pathogens ; Phylogenetics ; Phylogeny ; Polymerase chain reaction ; Polymorphism ; RNA polymerase ; rRNA 16S ; Single-nucleotide polymorphism ; Strains (organisms) ; Toxins ; Wildlife ; Zoonoses</subject><ispartof>Animals (Basel), 2022-04, Vol.12 (8), p.979</ispartof><rights>2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2022 by the authors. 2022</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c405t-548f7117daecf688bf849cba464c31074feaad8d40212102e6e3196f6d15cd1b3</citedby><cites>FETCH-LOGICAL-c405t-548f7117daecf688bf849cba464c31074feaad8d40212102e6e3196f6d15cd1b3</cites><orcidid>0000-0001-9108-3048 ; 0000-0003-4066-1957</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2652947837/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2652947837?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25751,27922,27923,37010,37011,44588,53789,53791,74896</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35454225$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Rahman, Md-Mafizur</creatorcontrib><creatorcontrib>Lim, Sang-Jin</creatorcontrib><creatorcontrib>Park, Yung-Chul</creatorcontrib><title>Molecular Identification of Bacillus Isolated from Korean Water Deer ( Hydropotes inermis argyropus ) and Striped Field Mouse ( Apodemus agrarius ) Feces by Using an SNP-Based 16S Ribosomal Marker</title><title>Animals (Basel)</title><addtitle>Animals (Basel)</addtitle><description>Ambiguous, heterogeneous, endospore-forming
species, notably
, often produce fatal toxins that threaten human health. We identified
from wild animal fecal samples (
= 80), including the Korean water deer (
= 25) and striped field mouse (
= 55). Using traditional culture-based methods, 25 animal fecal samples (31.25%; 25/80) were found to be positive for
species, whereas using molecular techniques, 19 samples (23.75%; 19/80) were found to be positive for the same. In addition, we designed a
species-specific 16S ribosomal RNA (rRNA) gene marker and utilized it to identify 19 samples by means of PCR amplification and sequencing, using at least one colony from the 19
positive samples. The recovered sequences were matched to sequences of three
species (
,
and
) from the GenBank database. Moreover, the phylogenetic tree generated in this study established specific clades for the
group. In addition, to differentiate between
,
, and
, we designed a single nucleotide polymorphism (SNP)-based primer by identifying SNPs in the alignment of 16S rRNA gene sequences of
group strains. The SNPs were used to design primer sets for discrimination between highly similar species from the
group. The study could be used in surveillance of agricultural fresh-produce-associated
outbreaks, for accurate identification of each
species, and in the development of control measures.</description><subject>16S ribosomal RNA</subject><subject>allele</subject><subject>Animals</subject><subject>Anthrax</subject><subject>Apodemus agrarius</subject><subject>Bacillus</subject><subject>Bacillus amyloliquefaciens</subject><subject>Bacillus anthracis</subject><subject>Bacillus cereus</subject><subject>Bacillus megaterium</subject><subject>Bacillus thuringiensis</subject><subject>Bacteria</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Feces</subject><subject>Food contamination & poisoning</subject><subject>Global positioning systems</subject><subject>GPS</subject><subject>Health risks</subject><subject>Hydropotes inermis argyropus</subject><subject>Identification</subject><subject>National parks</subject><subject>Nucleotide sequence</subject><subject>Nucleotides</subject><subject>Pathogens</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Polymerase chain reaction</subject><subject>Polymorphism</subject><subject>RNA polymerase</subject><subject>rRNA 16S</subject><subject>Single-nucleotide polymorphism</subject><subject>Strains (organisms)</subject><subject>Toxins</subject><subject>Wildlife</subject><subject>Zoonoses</subject><issn>2076-2615</issn><issn>2076-2615</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNpdUktvEzEQXiEQrUpP3JElLq2qgF_7uiC1paERDSBCxXE1a4-Dg3cd7F2k_D9-GE5TqhQfbGv8PUafJ8teMvpGiJq-hd4yTital_WT7JDTspjwguVP9-4H2XGMK5pWmQuWs-fZgchlLjnPD7M_c-9QjQ4CmWnsB2usgsH6nnhDLkBZ58ZIZtE7GFATE3xHPvqA0JPvqRLIe0zbCbne6ODXfsBIbI-hs5FAWG5SLdFPCfSaLIZg10ljatFpMvdjxEQ8X3uNXQLBMkCwd-gpqqTTbshttP0ykcni05fJBcTEZsWCfLWtj74DR-YQfmJ4kT0z4CIe359H2e306tvl9eTm84fZ5fnNREmaD5NcVqZkrNSAyhRV1ZpK1qoFWUglGC2lQQBdaUk544xyLFCwujCFZrnSrBVH2Wynqz2smnWwHYRN48E2dwUflg2EwSqHDeWqMhXlgkohhWDAkpneGghIdjRpvdtprce2Q61S9gHcI9HHL7390Sz976amgjHJk8DJvUDwv0aMQ5NCV-gc9JiybXiRvriuy3Lr9fo_6MqPoU9RbVG8lmUlyoQ626FU8DEGNA_NMNpsh63ZG7aEfrXf_wP232iJv_Lx0DU</recordid><startdate>20220410</startdate><enddate>20220410</enddate><creator>Rahman, Md-Mafizur</creator><creator>Lim, Sang-Jin</creator><creator>Park, Yung-Chul</creator><general>MDPI AG</general><general>MDPI</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0001-9108-3048</orcidid><orcidid>https://orcid.org/0000-0003-4066-1957</orcidid></search><sort><creationdate>20220410</creationdate><title>Molecular Identification of Bacillus Isolated from Korean Water Deer ( Hydropotes inermis argyropus ) and Striped Field Mouse ( Apodemus agrarius ) Feces by Using an SNP-Based 16S Ribosomal Marker</title><author>Rahman, Md-Mafizur ; Lim, Sang-Jin ; Park, Yung-Chul</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c405t-548f7117daecf688bf849cba464c31074feaad8d40212102e6e3196f6d15cd1b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>16S ribosomal RNA</topic><topic>allele</topic><topic>Animals</topic><topic>Anthrax</topic><topic>Apodemus agrarius</topic><topic>Bacillus</topic><topic>Bacillus amyloliquefaciens</topic><topic>Bacillus anthracis</topic><topic>Bacillus cereus</topic><topic>Bacillus megaterium</topic><topic>Bacillus thuringiensis</topic><topic>Bacteria</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Feces</topic><topic>Food contamination & poisoning</topic><topic>Global positioning systems</topic><topic>GPS</topic><topic>Health risks</topic><topic>Hydropotes inermis argyropus</topic><topic>Identification</topic><topic>National parks</topic><topic>Nucleotide sequence</topic><topic>Nucleotides</topic><topic>Pathogens</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Polymerase chain reaction</topic><topic>Polymorphism</topic><topic>RNA polymerase</topic><topic>rRNA 16S</topic><topic>Single-nucleotide polymorphism</topic><topic>Strains (organisms)</topic><topic>Toxins</topic><topic>Wildlife</topic><topic>Zoonoses</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Rahman, Md-Mafizur</creatorcontrib><creatorcontrib>Lim, Sang-Jin</creatorcontrib><creatorcontrib>Park, Yung-Chul</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>AUTh Library subscriptions: ProQuest Central</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>Animals (Basel)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Rahman, Md-Mafizur</au><au>Lim, Sang-Jin</au><au>Park, Yung-Chul</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Molecular Identification of Bacillus Isolated from Korean Water Deer ( Hydropotes inermis argyropus ) and Striped Field Mouse ( Apodemus agrarius ) Feces by Using an SNP-Based 16S Ribosomal Marker</atitle><jtitle>Animals (Basel)</jtitle><addtitle>Animals (Basel)</addtitle><date>2022-04-10</date><risdate>2022</risdate><volume>12</volume><issue>8</issue><spage>979</spage><pages>979-</pages><issn>2076-2615</issn><eissn>2076-2615</eissn><abstract>Ambiguous, heterogeneous, endospore-forming
species, notably
, often produce fatal toxins that threaten human health. We identified
from wild animal fecal samples (
= 80), including the Korean water deer (
= 25) and striped field mouse (
= 55). Using traditional culture-based methods, 25 animal fecal samples (31.25%; 25/80) were found to be positive for
species, whereas using molecular techniques, 19 samples (23.75%; 19/80) were found to be positive for the same. In addition, we designed a
species-specific 16S ribosomal RNA (rRNA) gene marker and utilized it to identify 19 samples by means of PCR amplification and sequencing, using at least one colony from the 19
positive samples. The recovered sequences were matched to sequences of three
species (
,
and
) from the GenBank database. Moreover, the phylogenetic tree generated in this study established specific clades for the
group. In addition, to differentiate between
,
, and
, we designed a single nucleotide polymorphism (SNP)-based primer by identifying SNPs in the alignment of 16S rRNA gene sequences of
group strains. The SNPs were used to design primer sets for discrimination between highly similar species from the
group. The study could be used in surveillance of agricultural fresh-produce-associated
outbreaks, for accurate identification of each
species, and in the development of control measures.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>35454225</pmid><doi>10.3390/ani12080979</doi><orcidid>https://orcid.org/0000-0001-9108-3048</orcidid><orcidid>https://orcid.org/0000-0003-4066-1957</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Animals (Basel), 2022-04, Vol.12 (8), p.979 |
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| language | eng |
| recordid | cdi_doaj_primary_oai_doaj_org_article_02c8f80230434331a1f84dfeaa3a64c0 |
| source | Publicly Available Content Database; PubMed Central |
| subjects | 16S ribosomal RNA allele Animals Anthrax Apodemus agrarius Bacillus Bacillus amyloliquefaciens Bacillus anthracis Bacillus cereus Bacillus megaterium Bacillus thuringiensis Bacteria Deoxyribonucleic acid DNA Feces Food contamination & poisoning Global positioning systems GPS Health risks Hydropotes inermis argyropus Identification National parks Nucleotide sequence Nucleotides Pathogens Phylogenetics Phylogeny Polymerase chain reaction Polymorphism RNA polymerase rRNA 16S Single-nucleotide polymorphism Strains (organisms) Toxins Wildlife Zoonoses |
| title | Molecular Identification of Bacillus Isolated from Korean Water Deer ( Hydropotes inermis argyropus ) and Striped Field Mouse ( Apodemus agrarius ) Feces by Using an SNP-Based 16S Ribosomal Marker |
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