Recent trend, biases and limitations of cultivation-based diversity studies of microbes
Abstract The current study attempts to analyze recent trends, biases and limitations of cultivation-based microbial diversity studies based on published, novel species in the past 6 years in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), an official publication of the...
Gespeichert in:
| Veröffentlicht in: | FEMS microbiology letters 2021-09, Vol.368 (17), p.1 |
|---|---|
| Hauptverfasser: | , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | |
|---|---|
| container_issue | 17 |
| container_start_page | 1 |
| container_title | FEMS microbiology letters |
| container_volume | 368 |
| creator | Prakash, Om Parmar, Mrinalini Vaijanapurkar, Manali Rale, Vinay Shouche, Yogesh S |
| description | Abstract
The current study attempts to analyze recent trends, biases and limitations of cultivation-based microbial diversity studies based on published, novel species in the past 6 years in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), an official publication of the International Committee on Systematics of Prokaryotes (ICSP) and the Bacteriology and Applied Microbiology (BAM) Division of the International Union of Microbiological Societies (IUMS). IJSEM deals with taxa that have validly published names under the International Code of Nomenclature of Prokaryotes (ICNP). All the relevant publications from the last 6 years were retrieved, sorted and analyzed to get the answers to What is the current rate of novel species description? Which country has contributed substantially and which phyla represented better in culturable diversity studies? What are the current limitations? Published data for the past 6 years indicate that 500–900 novel species are reported annually. China, Korea, Germany, UK, India and the USA are at the forefront while contributions from other nations are meager. Despite the recent development in culturomics tools the dominance of Proteobacteria, Bacteroidetes and Actinobacteria are still prevalent in cultivation, while the representation of archaea, obligate anaerobes, microaerophiles, synergistic symbionts, aerotolerant and other fastidious microbes is poor. Single strain-based taxonomic descriptions prevail and emphasis on objective-based cultivation for biotechnological and environmental significance is not yet conspicuous.
This article discusses the trends, biases and limitations of cultivation-based taxonomic studies of microorganisms based on past 6 years and mentions possible measures to break the current trends and reduce the biases and limitations in future. |
| doi_str_mv | 10.1093/femsle/fnab118 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_proqu</sourceid><recordid>TN_cdi_proquest_miscellaneous_2566255595</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A700321003</galeid><oup_id>10.1093/femsle/fnab118</oup_id><sourcerecordid>A700321003</sourcerecordid><originalsourceid>FETCH-LOGICAL-c458t-bfe32d878fa47e51137fee9cc955652dc49b9857040c41270f9bb20d396545963</originalsourceid><addsrcrecordid>eNqFkctrFjEUxYMotla3LmXAjUKnTTJ5TJalqC0UhKq4DHnclJSZ5HOSKfa_N20_rZWCBPLid05y70HoNcEHBKvhMMBcJjgMyVhCxidol3DJeqHE-PSv_Q56UcolxphRLJ6jnYExrpgUu-j7OThItasLJL_f2WgKlM4k301xjtXUmFPpcujcOtV4dXvubYN85-MVLCXW667U1Ue4xebolmyhvETPgpkKvNque-jbxw9fj0_6s8-fTo-PznrH-Fh7G2CgfpRjMEwCJ2SQAUA5pzgXnHrHlFUjl5hhxwiVOChrKfaDEryVIIY99O7Od7PkHyuUqudYHEyTSZDXoikXgnLOFW_o23_Qy7wuqf2uUZLTcVCc3lMXZgIdU8h1Me7GVB9JjAdK2tSog0eoNjy0DuQEIbb7B4L3DwSNqfCzXpi1FH365fxR89bKUhYIerPE2SzXmmB9k7q-S11vU2-CN9vKVjuD_4P_jvn-9bxu_mf2C8fQtW0</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2575283952</pqid></control><display><type>article</type><title>Recent trend, biases and limitations of cultivation-based diversity studies of microbes</title><source>MEDLINE</source><source>Oxford University Press Journals All Titles (1996-Current)</source><source>Alma/SFX Local Collection</source><creator>Prakash, Om ; Parmar, Mrinalini ; Vaijanapurkar, Manali ; Rale, Vinay ; Shouche, Yogesh S</creator><creatorcontrib>Prakash, Om ; Parmar, Mrinalini ; Vaijanapurkar, Manali ; Rale, Vinay ; Shouche, Yogesh S</creatorcontrib><description>Abstract
The current study attempts to analyze recent trends, biases and limitations of cultivation-based microbial diversity studies based on published, novel species in the past 6 years in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), an official publication of the International Committee on Systematics of Prokaryotes (ICSP) and the Bacteriology and Applied Microbiology (BAM) Division of the International Union of Microbiological Societies (IUMS). IJSEM deals with taxa that have validly published names under the International Code of Nomenclature of Prokaryotes (ICNP). All the relevant publications from the last 6 years were retrieved, sorted and analyzed to get the answers to What is the current rate of novel species description? Which country has contributed substantially and which phyla represented better in culturable diversity studies? What are the current limitations? Published data for the past 6 years indicate that 500–900 novel species are reported annually. China, Korea, Germany, UK, India and the USA are at the forefront while contributions from other nations are meager. Despite the recent development in culturomics tools the dominance of Proteobacteria, Bacteroidetes and Actinobacteria are still prevalent in cultivation, while the representation of archaea, obligate anaerobes, microaerophiles, synergistic symbionts, aerotolerant and other fastidious microbes is poor. Single strain-based taxonomic descriptions prevail and emphasis on objective-based cultivation for biotechnological and environmental significance is not yet conspicuous.
This article discusses the trends, biases and limitations of cultivation-based taxonomic studies of microorganisms based on past 6 years and mentions possible measures to break the current trends and reduce the biases and limitations in future.</description><identifier>ISSN: 1574-6968</identifier><identifier>ISSN: 0378-1097</identifier><identifier>EISSN: 1574-6968</identifier><identifier>DOI: 10.1093/femsle/fnab118</identifier><identifier>PMID: 34459476</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Anaerobes ; Analysis ; Archaea ; Archaea - genetics ; Bacteria - genetics ; Bacteriology ; Bias ; Biodiversity ; Biological diversity ; Biotechnology ; China ; Cultivation ; Germany ; Microbiology ; Microorganisms ; Nomenclature ; Prokaryotes ; Species ; Symbionts ; Systematics</subject><ispartof>FEMS microbiology letters, 2021-09, Vol.368 (17), p.1</ispartof><rights>The Author(s) 2021. Published by Oxford University Press on behalf of FEMS. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2021</rights><rights>The Author(s) 2021. Published by Oxford University Press on behalf of FEMS. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</rights><rights>COPYRIGHT 2021 Oxford University Press</rights><rights>The Author(s) 2021. Published by Oxford University Press on behalf of FEMS. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c458t-bfe32d878fa47e51137fee9cc955652dc49b9857040c41270f9bb20d396545963</citedby><cites>FETCH-LOGICAL-c458t-bfe32d878fa47e51137fee9cc955652dc49b9857040c41270f9bb20d396545963</cites><orcidid>0000-0002-6568-0567 ; 0000-0002-5055-5931</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,1578,27903,27904</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34459476$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Prakash, Om</creatorcontrib><creatorcontrib>Parmar, Mrinalini</creatorcontrib><creatorcontrib>Vaijanapurkar, Manali</creatorcontrib><creatorcontrib>Rale, Vinay</creatorcontrib><creatorcontrib>Shouche, Yogesh S</creatorcontrib><title>Recent trend, biases and limitations of cultivation-based diversity studies of microbes</title><title>FEMS microbiology letters</title><addtitle>FEMS Microbiol Lett</addtitle><description>Abstract
The current study attempts to analyze recent trends, biases and limitations of cultivation-based microbial diversity studies based on published, novel species in the past 6 years in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), an official publication of the International Committee on Systematics of Prokaryotes (ICSP) and the Bacteriology and Applied Microbiology (BAM) Division of the International Union of Microbiological Societies (IUMS). IJSEM deals with taxa that have validly published names under the International Code of Nomenclature of Prokaryotes (ICNP). All the relevant publications from the last 6 years were retrieved, sorted and analyzed to get the answers to What is the current rate of novel species description? Which country has contributed substantially and which phyla represented better in culturable diversity studies? What are the current limitations? Published data for the past 6 years indicate that 500–900 novel species are reported annually. China, Korea, Germany, UK, India and the USA are at the forefront while contributions from other nations are meager. Despite the recent development in culturomics tools the dominance of Proteobacteria, Bacteroidetes and Actinobacteria are still prevalent in cultivation, while the representation of archaea, obligate anaerobes, microaerophiles, synergistic symbionts, aerotolerant and other fastidious microbes is poor. Single strain-based taxonomic descriptions prevail and emphasis on objective-based cultivation for biotechnological and environmental significance is not yet conspicuous.
This article discusses the trends, biases and limitations of cultivation-based taxonomic studies of microorganisms based on past 6 years and mentions possible measures to break the current trends and reduce the biases and limitations in future.</description><subject>Anaerobes</subject><subject>Analysis</subject><subject>Archaea</subject><subject>Archaea - genetics</subject><subject>Bacteria - genetics</subject><subject>Bacteriology</subject><subject>Bias</subject><subject>Biodiversity</subject><subject>Biological diversity</subject><subject>Biotechnology</subject><subject>China</subject><subject>Cultivation</subject><subject>Germany</subject><subject>Microbiology</subject><subject>Microorganisms</subject><subject>Nomenclature</subject><subject>Prokaryotes</subject><subject>Species</subject><subject>Symbionts</subject><subject>Systematics</subject><issn>1574-6968</issn><issn>0378-1097</issn><issn>1574-6968</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqFkctrFjEUxYMotla3LmXAjUKnTTJ5TJalqC0UhKq4DHnclJSZ5HOSKfa_N20_rZWCBPLid05y70HoNcEHBKvhMMBcJjgMyVhCxidol3DJeqHE-PSv_Q56UcolxphRLJ6jnYExrpgUu-j7OThItasLJL_f2WgKlM4k301xjtXUmFPpcujcOtV4dXvubYN85-MVLCXW667U1Ue4xebolmyhvETPgpkKvNque-jbxw9fj0_6s8-fTo-PznrH-Fh7G2CgfpRjMEwCJ2SQAUA5pzgXnHrHlFUjl5hhxwiVOChrKfaDEryVIIY99O7Od7PkHyuUqudYHEyTSZDXoikXgnLOFW_o23_Qy7wuqf2uUZLTcVCc3lMXZgIdU8h1Me7GVB9JjAdK2tSog0eoNjy0DuQEIbb7B4L3DwSNqfCzXpi1FH365fxR89bKUhYIerPE2SzXmmB9k7q-S11vU2-CN9vKVjuD_4P_jvn-9bxu_mf2C8fQtW0</recordid><startdate>20210901</startdate><enddate>20210901</enddate><creator>Prakash, Om</creator><creator>Parmar, Mrinalini</creator><creator>Vaijanapurkar, Manali</creator><creator>Rale, Vinay</creator><creator>Shouche, Yogesh S</creator><general>Oxford University Press</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>ISR</scope><scope>3V.</scope><scope>7QL</scope><scope>7T7</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-6568-0567</orcidid><orcidid>https://orcid.org/0000-0002-5055-5931</orcidid></search><sort><creationdate>20210901</creationdate><title>Recent trend, biases and limitations of cultivation-based diversity studies of microbes</title><author>Prakash, Om ; Parmar, Mrinalini ; Vaijanapurkar, Manali ; Rale, Vinay ; Shouche, Yogesh S</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c458t-bfe32d878fa47e51137fee9cc955652dc49b9857040c41270f9bb20d396545963</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Anaerobes</topic><topic>Analysis</topic><topic>Archaea</topic><topic>Archaea - genetics</topic><topic>Bacteria - genetics</topic><topic>Bacteriology</topic><topic>Bias</topic><topic>Biodiversity</topic><topic>Biological diversity</topic><topic>Biotechnology</topic><topic>China</topic><topic>Cultivation</topic><topic>Germany</topic><topic>Microbiology</topic><topic>Microorganisms</topic><topic>Nomenclature</topic><topic>Prokaryotes</topic><topic>Species</topic><topic>Symbionts</topic><topic>Systematics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Prakash, Om</creatorcontrib><creatorcontrib>Parmar, Mrinalini</creatorcontrib><creatorcontrib>Vaijanapurkar, Manali</creatorcontrib><creatorcontrib>Rale, Vinay</creatorcontrib><creatorcontrib>Shouche, Yogesh S</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>FEMS microbiology letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Prakash, Om</au><au>Parmar, Mrinalini</au><au>Vaijanapurkar, Manali</au><au>Rale, Vinay</au><au>Shouche, Yogesh S</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Recent trend, biases and limitations of cultivation-based diversity studies of microbes</atitle><jtitle>FEMS microbiology letters</jtitle><addtitle>FEMS Microbiol Lett</addtitle><date>2021-09-01</date><risdate>2021</risdate><volume>368</volume><issue>17</issue><spage>1</spage><pages>1-</pages><issn>1574-6968</issn><issn>0378-1097</issn><eissn>1574-6968</eissn><abstract>Abstract
The current study attempts to analyze recent trends, biases and limitations of cultivation-based microbial diversity studies based on published, novel species in the past 6 years in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), an official publication of the International Committee on Systematics of Prokaryotes (ICSP) and the Bacteriology and Applied Microbiology (BAM) Division of the International Union of Microbiological Societies (IUMS). IJSEM deals with taxa that have validly published names under the International Code of Nomenclature of Prokaryotes (ICNP). All the relevant publications from the last 6 years were retrieved, sorted and analyzed to get the answers to What is the current rate of novel species description? Which country has contributed substantially and which phyla represented better in culturable diversity studies? What are the current limitations? Published data for the past 6 years indicate that 500–900 novel species are reported annually. China, Korea, Germany, UK, India and the USA are at the forefront while contributions from other nations are meager. Despite the recent development in culturomics tools the dominance of Proteobacteria, Bacteroidetes and Actinobacteria are still prevalent in cultivation, while the representation of archaea, obligate anaerobes, microaerophiles, synergistic symbionts, aerotolerant and other fastidious microbes is poor. Single strain-based taxonomic descriptions prevail and emphasis on objective-based cultivation for biotechnological and environmental significance is not yet conspicuous.
This article discusses the trends, biases and limitations of cultivation-based taxonomic studies of microorganisms based on past 6 years and mentions possible measures to break the current trends and reduce the biases and limitations in future.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>34459476</pmid><doi>10.1093/femsle/fnab118</doi><tpages>9</tpages><orcidid>https://orcid.org/0000-0002-6568-0567</orcidid><orcidid>https://orcid.org/0000-0002-5055-5931</orcidid></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1574-6968 |
| ispartof | FEMS microbiology letters, 2021-09, Vol.368 (17), p.1 |
| issn | 1574-6968 0378-1097 1574-6968 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_2566255595 |
| source | MEDLINE; Oxford University Press Journals All Titles (1996-Current); Alma/SFX Local Collection |
| subjects | Anaerobes Analysis Archaea Archaea - genetics Bacteria - genetics Bacteriology Bias Biodiversity Biological diversity Biotechnology China Cultivation Germany Microbiology Microorganisms Nomenclature Prokaryotes Species Symbionts Systematics |
| title | Recent trend, biases and limitations of cultivation-based diversity studies of microbes |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-25T18%3A28%3A25IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_proqu&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Recent%20trend,%20biases%20and%20limitations%20of%20cultivation-based%20diversity%20studies%20of%20microbes&rft.jtitle=FEMS%20microbiology%20letters&rft.au=Prakash,%20Om&rft.date=2021-09-01&rft.volume=368&rft.issue=17&rft.spage=1&rft.pages=1-&rft.issn=1574-6968&rft.eissn=1574-6968&rft_id=info:doi/10.1093/femsle/fnab118&rft_dat=%3Cgale_proqu%3EA700321003%3C/gale_proqu%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2575283952&rft_id=info:pmid/34459476&rft_galeid=A700321003&rft_oup_id=10.1093/femsle/fnab118&rfr_iscdi=true |