Analysis of bacterial diversity and genetic evolution of Lacticaseibacillus paracasei isolates in fermentation pit mud
Aims Since little is known about the genetic diversity of lactic acid bacteria (LAB) isolates from the fermentation pit mud (FPM), we sought to evaluate the bacterial structure, identify the LAB isolates and investigate the genotype and genetic diversity of the LAB isolates. Methods and Results Usin...
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| Veröffentlicht in: | Journal of applied microbiology 2022-09, Vol.133 (3), p.1821-1831 |
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| container_title | Journal of applied microbiology |
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| creator | Zhang, Zhendong Dong, Yun Xiang, Fanshu Wang, Yurong Hou, Qiangchuan Ni, Hui Cai, Wenchao Liu, Wenhui Yang, Shaoyong Guo, Zhuang |
| description | Aims
Since little is known about the genetic diversity of lactic acid bacteria (LAB) isolates from the fermentation pit mud (FPM), we sought to evaluate the bacterial structure, identify the LAB isolates and investigate the genotype and genetic diversity of the LAB isolates.
Methods and Results
Using high‐throughput MiSeq sequencing, we identified seven dominant bacterial genera in FPM. Lactobacillus had the highest abundance. We isolated 55 LAB strains. These isolates were all identified as Lacticaseibacillus paracasei. Using an extant multilocus sequence typing (MLST) scheme, isolates were assigned to 18 sequence types (STs) and three clonal complexes. ST1, the largest group, mainly comprised FPM isolates. Niche‐specific ST2 to ST18 only contained FPM isolates. Isolates could be divided into four lineages, with most assigned to Lineage 1. Only one FPM isolate was classified as L. paracasei subsp. paracasei. Other isolates could not be classified at the subspecies level using the seven MLST loci.
Conclusions
Lactobacilli account for a high proportion of bacteria in pit mud. Based on the traditional culture method, L. paracasei was the dominant species, and these isolates exhibit a high ethanol tolerance, high intraspecific diversity and specific genetic profiles.
Significance and Impact of the Study
The study described the characterization of FPM bacterial diversity, giving an insight into the genetic diversity of L. paracasei strains present in FPM. |
| doi_str_mv | 10.1111/jam.15672 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2687720218</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2709886270</sourcerecordid><originalsourceid>FETCH-LOGICAL-c3652-85309abfdb236d1ba72f11a819077f9a1c3a1739df936356c794c386d26862763</originalsourceid><addsrcrecordid>eNp10c9LwzAUB_AgCs7pwf8g4EUP3fJjTdrjGP5k4kXP5TVNJSNtZ5JO-t-btZ4Ec8kjfN7jkS9C15QsaDzLHTQLmgrJTtCMcpEmLNanY71KUiLZObrwfkcI5SQVM3RYt2AHbzzualyCCtoZsLgyB-28CQOGtsKfutXBKKwPne2D6doj3kZsFHhtYpuxtvd4Dw7GF2x8ZyFoj02La-0a3QYYG_cm4KavLtFZDdbrq997jj4e7t83T8n27fF5s94mKu7OkizlJIeyrkrGRUVLkKymFDKaEynrHKjiQCXPqzrngqdCyXyleCYqJjLBpOBzdDvN3bvuq9c-FI3xSlsLre56X0QnJSOMZpHe_KG7rnfxd6KSJM-OA0lUd5NSrvPe6brYO9OAGwpKimMCRUygGBOIdjnZb2P18D8sXtavU8cPIGGIOA</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2709886270</pqid></control><display><type>article</type><title>Analysis of bacterial diversity and genetic evolution of Lacticaseibacillus paracasei isolates in fermentation pit mud</title><source>Oxford University Press Journals All Titles (1996-Current)</source><source>Wiley Online Library Journals Frontfile Complete</source><creator>Zhang, Zhendong ; Dong, Yun ; Xiang, Fanshu ; Wang, Yurong ; Hou, Qiangchuan ; Ni, Hui ; Cai, Wenchao ; Liu, Wenhui ; Yang, Shaoyong ; Guo, Zhuang</creator><creatorcontrib>Zhang, Zhendong ; Dong, Yun ; Xiang, Fanshu ; Wang, Yurong ; Hou, Qiangchuan ; Ni, Hui ; Cai, Wenchao ; Liu, Wenhui ; Yang, Shaoyong ; Guo, Zhuang</creatorcontrib><description>Aims
Since little is known about the genetic diversity of lactic acid bacteria (LAB) isolates from the fermentation pit mud (FPM), we sought to evaluate the bacterial structure, identify the LAB isolates and investigate the genotype and genetic diversity of the LAB isolates.
Methods and Results
Using high‐throughput MiSeq sequencing, we identified seven dominant bacterial genera in FPM. Lactobacillus had the highest abundance. We isolated 55 LAB strains. These isolates were all identified as Lacticaseibacillus paracasei. Using an extant multilocus sequence typing (MLST) scheme, isolates were assigned to 18 sequence types (STs) and three clonal complexes. ST1, the largest group, mainly comprised FPM isolates. Niche‐specific ST2 to ST18 only contained FPM isolates. Isolates could be divided into four lineages, with most assigned to Lineage 1. Only one FPM isolate was classified as L. paracasei subsp. paracasei. Other isolates could not be classified at the subspecies level using the seven MLST loci.
Conclusions
Lactobacilli account for a high proportion of bacteria in pit mud. Based on the traditional culture method, L. paracasei was the dominant species, and these isolates exhibit a high ethanol tolerance, high intraspecific diversity and specific genetic profiles.
Significance and Impact of the Study
The study described the characterization of FPM bacterial diversity, giving an insight into the genetic diversity of L. paracasei strains present in FPM.</description><identifier>ISSN: 1364-5072</identifier><identifier>EISSN: 1365-2672</identifier><identifier>DOI: 10.1111/jam.15672</identifier><language>eng</language><publisher>Cambridge: Oxford University Press</publisher><subject>Bacteria ; bacterial diversity ; Dominant species ; Drug tolerance ; Ethanol ; Evolution ; Evolution & development ; Fermentation ; Genera ; Genetic analysis ; Genetic diversity ; Genotypes ; Lactic acid ; Lactic acid bacteria ; Lacticaseibacillus paracasei ; Lactobacilli ; Mud ; Multilocus sequence typing ; pit mud ; sequence type ; Strains (organisms)</subject><ispartof>Journal of applied microbiology, 2022-09, Vol.133 (3), p.1821-1831</ispartof><rights>2022 Society for Applied Microbiology.</rights><rights>Copyright © 2022 The Society for Applied Microbiology</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3652-85309abfdb236d1ba72f11a819077f9a1c3a1739df936356c794c386d26862763</citedby><cites>FETCH-LOGICAL-c3652-85309abfdb236d1ba72f11a819077f9a1c3a1739df936356c794c386d26862763</cites><orcidid>0000-0003-1603-6633 ; 0000-0003-0013-3500</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fjam.15672$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fjam.15672$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,27901,27902,45550,45551</link.rule.ids></links><search><creatorcontrib>Zhang, Zhendong</creatorcontrib><creatorcontrib>Dong, Yun</creatorcontrib><creatorcontrib>Xiang, Fanshu</creatorcontrib><creatorcontrib>Wang, Yurong</creatorcontrib><creatorcontrib>Hou, Qiangchuan</creatorcontrib><creatorcontrib>Ni, Hui</creatorcontrib><creatorcontrib>Cai, Wenchao</creatorcontrib><creatorcontrib>Liu, Wenhui</creatorcontrib><creatorcontrib>Yang, Shaoyong</creatorcontrib><creatorcontrib>Guo, Zhuang</creatorcontrib><title>Analysis of bacterial diversity and genetic evolution of Lacticaseibacillus paracasei isolates in fermentation pit mud</title><title>Journal of applied microbiology</title><description>Aims
Since little is known about the genetic diversity of lactic acid bacteria (LAB) isolates from the fermentation pit mud (FPM), we sought to evaluate the bacterial structure, identify the LAB isolates and investigate the genotype and genetic diversity of the LAB isolates.
Methods and Results
Using high‐throughput MiSeq sequencing, we identified seven dominant bacterial genera in FPM. Lactobacillus had the highest abundance. We isolated 55 LAB strains. These isolates were all identified as Lacticaseibacillus paracasei. Using an extant multilocus sequence typing (MLST) scheme, isolates were assigned to 18 sequence types (STs) and three clonal complexes. ST1, the largest group, mainly comprised FPM isolates. Niche‐specific ST2 to ST18 only contained FPM isolates. Isolates could be divided into four lineages, with most assigned to Lineage 1. Only one FPM isolate was classified as L. paracasei subsp. paracasei. Other isolates could not be classified at the subspecies level using the seven MLST loci.
Conclusions
Lactobacilli account for a high proportion of bacteria in pit mud. Based on the traditional culture method, L. paracasei was the dominant species, and these isolates exhibit a high ethanol tolerance, high intraspecific diversity and specific genetic profiles.
Significance and Impact of the Study
The study described the characterization of FPM bacterial diversity, giving an insight into the genetic diversity of L. paracasei strains present in FPM.</description><subject>Bacteria</subject><subject>bacterial diversity</subject><subject>Dominant species</subject><subject>Drug tolerance</subject><subject>Ethanol</subject><subject>Evolution</subject><subject>Evolution & development</subject><subject>Fermentation</subject><subject>Genera</subject><subject>Genetic analysis</subject><subject>Genetic diversity</subject><subject>Genotypes</subject><subject>Lactic acid</subject><subject>Lactic acid bacteria</subject><subject>Lacticaseibacillus paracasei</subject><subject>Lactobacilli</subject><subject>Mud</subject><subject>Multilocus sequence typing</subject><subject>pit mud</subject><subject>sequence type</subject><subject>Strains (organisms)</subject><issn>1364-5072</issn><issn>1365-2672</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><recordid>eNp10c9LwzAUB_AgCs7pwf8g4EUP3fJjTdrjGP5k4kXP5TVNJSNtZ5JO-t-btZ4Ec8kjfN7jkS9C15QsaDzLHTQLmgrJTtCMcpEmLNanY71KUiLZObrwfkcI5SQVM3RYt2AHbzzualyCCtoZsLgyB-28CQOGtsKfutXBKKwPne2D6doj3kZsFHhtYpuxtvd4Dw7GF2x8ZyFoj02La-0a3QYYG_cm4KavLtFZDdbrq997jj4e7t83T8n27fF5s94mKu7OkizlJIeyrkrGRUVLkKymFDKaEynrHKjiQCXPqzrngqdCyXyleCYqJjLBpOBzdDvN3bvuq9c-FI3xSlsLre56X0QnJSOMZpHe_KG7rnfxd6KSJM-OA0lUd5NSrvPe6brYO9OAGwpKimMCRUygGBOIdjnZb2P18D8sXtavU8cPIGGIOA</recordid><startdate>202209</startdate><enddate>202209</enddate><creator>Zhang, Zhendong</creator><creator>Dong, Yun</creator><creator>Xiang, Fanshu</creator><creator>Wang, Yurong</creator><creator>Hou, Qiangchuan</creator><creator>Ni, Hui</creator><creator>Cai, Wenchao</creator><creator>Liu, Wenhui</creator><creator>Yang, Shaoyong</creator><creator>Guo, Zhuang</creator><general>Oxford University Press</general><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7T7</scope><scope>7TM</scope><scope>7U7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-1603-6633</orcidid><orcidid>https://orcid.org/0000-0003-0013-3500</orcidid></search><sort><creationdate>202209</creationdate><title>Analysis of bacterial diversity and genetic evolution of Lacticaseibacillus paracasei isolates in fermentation pit mud</title><author>Zhang, Zhendong ; Dong, Yun ; Xiang, Fanshu ; Wang, Yurong ; Hou, Qiangchuan ; Ni, Hui ; Cai, Wenchao ; Liu, Wenhui ; Yang, Shaoyong ; Guo, Zhuang</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3652-85309abfdb236d1ba72f11a819077f9a1c3a1739df936356c794c386d26862763</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Bacteria</topic><topic>bacterial diversity</topic><topic>Dominant species</topic><topic>Drug tolerance</topic><topic>Ethanol</topic><topic>Evolution</topic><topic>Evolution & development</topic><topic>Fermentation</topic><topic>Genera</topic><topic>Genetic analysis</topic><topic>Genetic diversity</topic><topic>Genotypes</topic><topic>Lactic acid</topic><topic>Lactic acid bacteria</topic><topic>Lacticaseibacillus paracasei</topic><topic>Lactobacilli</topic><topic>Mud</topic><topic>Multilocus sequence typing</topic><topic>pit mud</topic><topic>sequence type</topic><topic>Strains (organisms)</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhang, Zhendong</creatorcontrib><creatorcontrib>Dong, Yun</creatorcontrib><creatorcontrib>Xiang, Fanshu</creatorcontrib><creatorcontrib>Wang, Yurong</creatorcontrib><creatorcontrib>Hou, Qiangchuan</creatorcontrib><creatorcontrib>Ni, Hui</creatorcontrib><creatorcontrib>Cai, Wenchao</creatorcontrib><creatorcontrib>Liu, Wenhui</creatorcontrib><creatorcontrib>Yang, Shaoyong</creatorcontrib><creatorcontrib>Guo, Zhuang</creatorcontrib><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Nucleic Acids Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of applied microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhang, Zhendong</au><au>Dong, Yun</au><au>Xiang, Fanshu</au><au>Wang, Yurong</au><au>Hou, Qiangchuan</au><au>Ni, Hui</au><au>Cai, Wenchao</au><au>Liu, Wenhui</au><au>Yang, Shaoyong</au><au>Guo, Zhuang</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Analysis of bacterial diversity and genetic evolution of Lacticaseibacillus paracasei isolates in fermentation pit mud</atitle><jtitle>Journal of applied microbiology</jtitle><date>2022-09</date><risdate>2022</risdate><volume>133</volume><issue>3</issue><spage>1821</spage><epage>1831</epage><pages>1821-1831</pages><issn>1364-5072</issn><eissn>1365-2672</eissn><abstract>Aims
Since little is known about the genetic diversity of lactic acid bacteria (LAB) isolates from the fermentation pit mud (FPM), we sought to evaluate the bacterial structure, identify the LAB isolates and investigate the genotype and genetic diversity of the LAB isolates.
Methods and Results
Using high‐throughput MiSeq sequencing, we identified seven dominant bacterial genera in FPM. Lactobacillus had the highest abundance. We isolated 55 LAB strains. These isolates were all identified as Lacticaseibacillus paracasei. Using an extant multilocus sequence typing (MLST) scheme, isolates were assigned to 18 sequence types (STs) and three clonal complexes. ST1, the largest group, mainly comprised FPM isolates. Niche‐specific ST2 to ST18 only contained FPM isolates. Isolates could be divided into four lineages, with most assigned to Lineage 1. Only one FPM isolate was classified as L. paracasei subsp. paracasei. Other isolates could not be classified at the subspecies level using the seven MLST loci.
Conclusions
Lactobacilli account for a high proportion of bacteria in pit mud. Based on the traditional culture method, L. paracasei was the dominant species, and these isolates exhibit a high ethanol tolerance, high intraspecific diversity and specific genetic profiles.
Significance and Impact of the Study
The study described the characterization of FPM bacterial diversity, giving an insight into the genetic diversity of L. paracasei strains present in FPM.</abstract><cop>Cambridge</cop><pub>Oxford University Press</pub><doi>10.1111/jam.15672</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0003-1603-6633</orcidid><orcidid>https://orcid.org/0000-0003-0013-3500</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Journal of applied microbiology, 2022-09, Vol.133 (3), p.1821-1831 |
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| source | Oxford University Press Journals All Titles (1996-Current); Wiley Online Library Journals Frontfile Complete |
| subjects | Bacteria bacterial diversity Dominant species Drug tolerance Ethanol Evolution Evolution & development Fermentation Genera Genetic analysis Genetic diversity Genotypes Lactic acid Lactic acid bacteria Lacticaseibacillus paracasei Lactobacilli Mud Multilocus sequence typing pit mud sequence type Strains (organisms) |
| title | Analysis of bacterial diversity and genetic evolution of Lacticaseibacillus paracasei isolates in fermentation pit mud |
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