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Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis
Deserts occupy one-third of the Earth’s terrestrial surface and represent a potentially significant reservoir of microbial biodiversity, yet the majority of desert microorganisms remain uncharacterized and are seen as “microbial dark matter”. Here, we introduce a multi-omics strategy, culturomics-ba...
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Published in: | NPJ biofilms and microbiomes 2023-09, Vol.9 (1), p.67-67, Article 67 |
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creator | Li, Shuai Lian, Wen-Hui Han, Jia-Rui Ali, Mukhtiar Lin, Zhi-Liang Liu, Yong-Hong Li, Li Zhang, Dong-Ya Jiang, Xian-Zhi Li, Wen-Jun Dong, Lei |
description | Deserts occupy one-third of the Earth’s terrestrial surface and represent a potentially significant reservoir of microbial biodiversity, yet the majority of desert microorganisms remain uncharacterized and are seen as “microbial dark matter”. Here, we introduce a multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, and shotgun metagenomic sequencing. The results showed that CBM captured a significant amount of taxonomic and functional diversity missed in direct sequencing by increasing the recovery of amplicon sequence variants (ASVs) and high/medium-quality metagenome-assembled genomes (MAGs). Importantly, CBM allowed the post hoc recovery of microbes of interest (e.g., novel or specific taxa), even those with extremely low abundance in the culture. Furthermore, strain-level analyses based on CBM and direct sequencing revealed that the desert soils harbored a considerable number of novel bacterial candidates (1941, 51.4%), of which 1095 (from CBM) were culturable. However, CBM would not exactly reflect the relative abundance of true microbial composition and functional pathways in the in situ environment, and its use coupled with direct metagenomic sequencing could provide greater insight into desert microbiomes. Overall, this study exemplifies the CBM strategy with high-resolution is an ideal way to deeply explore the untapped novel bacterial resources in desert soils, and substantially expands our knowledge on the microbial dark matter hidden in the vast expanse of deserts. |
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Here, we introduce a multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, and shotgun metagenomic sequencing. The results showed that CBM captured a significant amount of taxonomic and functional diversity missed in direct sequencing by increasing the recovery of amplicon sequence variants (ASVs) and high/medium-quality metagenome-assembled genomes (MAGs). Importantly, CBM allowed the post hoc recovery of microbes of interest (e.g., novel or specific taxa), even those with extremely low abundance in the culture. Furthermore, strain-level analyses based on CBM and direct sequencing revealed that the desert soils harbored a considerable number of novel bacterial candidates (1941, 51.4%), of which 1095 (from CBM) were culturable. However, CBM would not exactly reflect the relative abundance of true microbial composition and functional pathways in the in situ environment, and its use coupled with direct metagenomic sequencing could provide greater insight into desert microbiomes. Overall, this study exemplifies the CBM strategy with high-resolution is an ideal way to deeply explore the untapped novel bacterial resources in desert soils, and substantially expands our knowledge on the microbial dark matter hidden in the vast expanse of deserts.</description><identifier>ISSN: 2055-5008</identifier><identifier>EISSN: 2055-5008</identifier><identifier>DOI: 10.1038/s41522-023-00439-8</identifier><identifier>PMID: 37736746</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>631/326/2565/2134 ; 631/326/41/2142 ; Biodiversity ; Biomedical and Life Sciences ; Dark matter ; Deserts ; Genomes ; Life Sciences ; Medical Microbiology ; Metagenomics ; Microbial Ecology ; Microbial Genetics and Genomics ; Microbiology ; Microbiomes ; rRNA 16S</subject><ispartof>NPJ biofilms and microbiomes, 2023-09, Vol.9 (1), p.67-67, Article 67</ispartof><rights>The Author(s) 2023</rights><rights>The Author(s) 2023. 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Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Springer Nature Limited 2023</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c518t-faddc273ea74f6cc2e00f53b83e2bd4341f3920b9551c2060b9d5b049656ce613</citedby><cites>FETCH-LOGICAL-c518t-faddc273ea74f6cc2e00f53b83e2bd4341f3920b9551c2060b9d5b049656ce613</cites><orcidid>0000-0002-1233-736X ; 0000-0002-5767-2778</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2867134733/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2867134733?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25753,27924,27925,37012,37013,44590,53791,53793,75126</link.rule.ids></links><search><creatorcontrib>Li, Shuai</creatorcontrib><creatorcontrib>Lian, Wen-Hui</creatorcontrib><creatorcontrib>Han, Jia-Rui</creatorcontrib><creatorcontrib>Ali, Mukhtiar</creatorcontrib><creatorcontrib>Lin, Zhi-Liang</creatorcontrib><creatorcontrib>Liu, Yong-Hong</creatorcontrib><creatorcontrib>Li, Li</creatorcontrib><creatorcontrib>Zhang, Dong-Ya</creatorcontrib><creatorcontrib>Jiang, Xian-Zhi</creatorcontrib><creatorcontrib>Li, Wen-Jun</creatorcontrib><creatorcontrib>Dong, Lei</creatorcontrib><title>Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis</title><title>NPJ biofilms and microbiomes</title><addtitle>npj Biofilms Microbiomes</addtitle><description>Deserts occupy one-third of the Earth’s terrestrial surface and represent a potentially significant reservoir of microbial biodiversity, yet the majority of desert microorganisms remain uncharacterized and are seen as “microbial dark matter”. Here, we introduce a multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, and shotgun metagenomic sequencing. The results showed that CBM captured a significant amount of taxonomic and functional diversity missed in direct sequencing by increasing the recovery of amplicon sequence variants (ASVs) and high/medium-quality metagenome-assembled genomes (MAGs). Importantly, CBM allowed the post hoc recovery of microbes of interest (e.g., novel or specific taxa), even those with extremely low abundance in the culture. Furthermore, strain-level analyses based on CBM and direct sequencing revealed that the desert soils harbored a considerable number of novel bacterial candidates (1941, 51.4%), of which 1095 (from CBM) were culturable. However, CBM would not exactly reflect the relative abundance of true microbial composition and functional pathways in the in situ environment, and its use coupled with direct metagenomic sequencing could provide greater insight into desert microbiomes. Overall, this study exemplifies the CBM strategy with high-resolution is an ideal way to deeply explore the untapped novel bacterial resources in desert soils, and substantially expands our knowledge on the microbial dark matter hidden in the vast expanse of deserts.</description><subject>631/326/2565/2134</subject><subject>631/326/41/2142</subject><subject>Biodiversity</subject><subject>Biomedical and Life Sciences</subject><subject>Dark matter</subject><subject>Deserts</subject><subject>Genomes</subject><subject>Life Sciences</subject><subject>Medical Microbiology</subject><subject>Metagenomics</subject><subject>Microbial Ecology</subject><subject>Microbial Genetics and Genomics</subject><subject>Microbiology</subject><subject>Microbiomes</subject><subject>rRNA 16S</subject><issn>2055-5008</issn><issn>2055-5008</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNp9kk1v1DAQhiMEolXpH-BkiQuX0PFX4pwQWvFRqRIXOFuOPdn1ksSL7SD13-NsKko5cPJo_L7PWJ63ql5TeEeBq5skqGSsBsZrAMG7Wj2rLhlIWUsA9fyv-qK6TukIAFSKliv5srrgbcubVjSX1bIzp7xEP-9JPiCZvI2h92YkzsQfZDI5YyR-Jg4TxkxS8GMiS1r1dhmLMxRLqnuT0JEJs9njfG4RMzty8PtDHTGFcck-zKVnxvvk06vqxWDGhNcP51X1_dPHb7sv9d3Xz7e7D3e1lVTlejDOWdZyNK0YGmsZAgyS94oj653ggg68Y9B3UlLLoCmVkz2IrpGNxYbyq-p247pgjvoU_WTivQ7G63MjxL02MXs7okZDG-Suh2EAIaxRg2SWsc6BVLaMLaz3G-u09BM6i3OOZnwCfXoz-4Peh1-agqRNJ3ghvH0gxPBzwZT15JPFcTQzhiVpphpFGaPdKn3zj_QYllh-76xqKS-bXFVsU5WlpRRx-PMaCnpNid5SoktK9DklWhUT30zptK4d4yP6P67f8obAWw</recordid><startdate>20230922</startdate><enddate>20230922</enddate><creator>Li, Shuai</creator><creator>Lian, Wen-Hui</creator><creator>Han, Jia-Rui</creator><creator>Ali, Mukhtiar</creator><creator>Lin, Zhi-Liang</creator><creator>Liu, Yong-Hong</creator><creator>Li, Li</creator><creator>Zhang, Dong-Ya</creator><creator>Jiang, Xian-Zhi</creator><creator>Li, Wen-Jun</creator><creator>Dong, Lei</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><general>Nature Portfolio</general><scope>C6C</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-1233-736X</orcidid><orcidid>https://orcid.org/0000-0002-5767-2778</orcidid></search><sort><creationdate>20230922</creationdate><title>Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis</title><author>Li, Shuai ; 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Here, we introduce a multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, and shotgun metagenomic sequencing. The results showed that CBM captured a significant amount of taxonomic and functional diversity missed in direct sequencing by increasing the recovery of amplicon sequence variants (ASVs) and high/medium-quality metagenome-assembled genomes (MAGs). Importantly, CBM allowed the post hoc recovery of microbes of interest (e.g., novel or specific taxa), even those with extremely low abundance in the culture. Furthermore, strain-level analyses based on CBM and direct sequencing revealed that the desert soils harbored a considerable number of novel bacterial candidates (1941, 51.4%), of which 1095 (from CBM) were culturable. However, CBM would not exactly reflect the relative abundance of true microbial composition and functional pathways in the in situ environment, and its use coupled with direct metagenomic sequencing could provide greater insight into desert microbiomes. Overall, this study exemplifies the CBM strategy with high-resolution is an ideal way to deeply explore the untapped novel bacterial resources in desert soils, and substantially expands our knowledge on the microbial dark matter hidden in the vast expanse of deserts.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>37736746</pmid><doi>10.1038/s41522-023-00439-8</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0002-1233-736X</orcidid><orcidid>https://orcid.org/0000-0002-5767-2778</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | 631/326/2565/2134 631/326/41/2142 Biodiversity Biomedical and Life Sciences Dark matter Deserts Genomes Life Sciences Medical Microbiology Metagenomics Microbial Ecology Microbial Genetics and Genomics Microbiology Microbiomes rRNA 16S |
title | Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis |
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