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Microbial community structure in fermentation process of Shaoxing rice wine by Illumina-based metagenomic sequencing
BACKGROUND To understand the role of the community structure of microbes in the environment in the fermentation of Shaoxing rice wine, samples collected from a wine factory were subjected to Illumina‐based metagenomic sequencing. RESULTS De novo assembly of the sequencing reads allowed the character...
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| Published in: | Journal of the science of food and agriculture 2013-09, Vol.93 (12), p.3121-3125 |
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| Main Authors: | , , , , , , |
| Format: | Article |
| Language: | English |
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| container_end_page | 3125 |
| container_issue | 12 |
| container_start_page | 3121 |
| container_title | Journal of the science of food and agriculture |
| container_volume | 93 |
| creator | Xie, Guangfa Wang, Lan Gao, Qikang Yu, Wenjing Hong, Xutao Zhao, Lingyun Zou, Huijun |
| description | BACKGROUND
To understand the role of the community structure of microbes in the environment in the fermentation of Shaoxing rice wine, samples collected from a wine factory were subjected to Illumina‐based metagenomic sequencing.
RESULTS
De novo assembly of the sequencing reads allowed the characterisation of more than 23 thousand microbial genes derived from 1.7 and 1.88 Gbp of sequences from two samples fermented for 5 and 30 days respectively. The microbial community structure at different fermentation times of Shaoxing rice wine was revealed, showing the different roles of the microbiota in the fermentation process of Shaoxing rice wine. The gene function of both samples was also studied in the COG database, with most genes belonging to category S (function unknown), category E (amino acid transport and metabolism) and unclassified group.
CONCLUSION
The results show that both the microbial community structure and gene function composition change greatly at different time points of Shaoxing rice wine fermentation. © 2013 Society of Chemical Industry |
| doi_str_mv | 10.1002/jsfa.6058 |
| format | article |
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To understand the role of the community structure of microbes in the environment in the fermentation of Shaoxing rice wine, samples collected from a wine factory were subjected to Illumina‐based metagenomic sequencing.
RESULTS
De novo assembly of the sequencing reads allowed the characterisation of more than 23 thousand microbial genes derived from 1.7 and 1.88 Gbp of sequences from two samples fermented for 5 and 30 days respectively. The microbial community structure at different fermentation times of Shaoxing rice wine was revealed, showing the different roles of the microbiota in the fermentation process of Shaoxing rice wine. The gene function of both samples was also studied in the COG database, with most genes belonging to category S (function unknown), category E (amino acid transport and metabolism) and unclassified group.
CONCLUSION
The results show that both the microbial community structure and gene function composition change greatly at different time points of Shaoxing rice wine fermentation. © 2013 Society of Chemical Industry</description><identifier>ISSN: 0022-5142</identifier><identifier>EISSN: 1097-0010</identifier><identifier>DOI: 10.1002/jsfa.6058</identifier><identifier>PMID: 23553745</identifier><identifier>CODEN: JSFAAE</identifier><language>eng</language><publisher>Chichester, UK: John Wiley & Sons, Ltd</publisher><subject><![CDATA[Actinobacteria - classification ; Actinobacteria - isolation & purification ; Actinobacteria - metabolism ; Ascomycota - classification ; Ascomycota - isolation & purification ; Ascomycota - metabolism ; Categories ; China ; Communities ; Computational Biology ; Diet - ethnology ; DNA, Bacterial - isolation & purification ; DNA, Bacterial - metabolism ; DNA, Fungal - isolation & purification ; DNA, Fungal - metabolism ; Fermentation ; Fungi - classification ; Fungi - isolation & purification ; Fungi - metabolism ; Genes ; Gram-Negative Bacteria - classification ; Gram-Negative Bacteria - isolation & purification ; Gram-Negative Bacteria - metabolism ; Gram-Positive Bacteria - classification ; Gram-Positive Bacteria - isolation & purification ; Gram-Positive Bacteria - metabolism ; metagenome ; Metagenomics ; Microbiology ; microbiota ; Microorganisms ; Molecular Typing ; Mycological Typing Techniques ; Oryza - chemistry ; Oryza sativa ; Proteobacteria - classification ; Proteobacteria - isolation & purification ; Proteobacteria - metabolism ; Quality Control ; Rice ; Seeds - chemistry ; Sequencing ; Shaoxing rice wine ; Time Factors ; Vitaceae ; wheat Qu ; Wine - analysis ; Wine - microbiology ; Wines]]></subject><ispartof>Journal of the science of food and agriculture, 2013-09, Vol.93 (12), p.3121-3125</ispartof><rights>2013 Society of Chemical Industry</rights><rights>2013 Society of Chemical Industry.</rights><rights>Copyright John Wiley and Sons, Limited Sep 2013</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4898-8fe68bb6e04709af4261fb10c5fa7f9b7b84b54abaff92c265d2adeaf15b357d3</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27922,27923</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23553745$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Xie, Guangfa</creatorcontrib><creatorcontrib>Wang, Lan</creatorcontrib><creatorcontrib>Gao, Qikang</creatorcontrib><creatorcontrib>Yu, Wenjing</creatorcontrib><creatorcontrib>Hong, Xutao</creatorcontrib><creatorcontrib>Zhao, Lingyun</creatorcontrib><creatorcontrib>Zou, Huijun</creatorcontrib><title>Microbial community structure in fermentation process of Shaoxing rice wine by Illumina-based metagenomic sequencing</title><title>Journal of the science of food and agriculture</title><addtitle>J. Sci. Food Agric</addtitle><description>BACKGROUND
To understand the role of the community structure of microbes in the environment in the fermentation of Shaoxing rice wine, samples collected from a wine factory were subjected to Illumina‐based metagenomic sequencing.
RESULTS
De novo assembly of the sequencing reads allowed the characterisation of more than 23 thousand microbial genes derived from 1.7 and 1.88 Gbp of sequences from two samples fermented for 5 and 30 days respectively. The microbial community structure at different fermentation times of Shaoxing rice wine was revealed, showing the different roles of the microbiota in the fermentation process of Shaoxing rice wine. The gene function of both samples was also studied in the COG database, with most genes belonging to category S (function unknown), category E (amino acid transport and metabolism) and unclassified group.
CONCLUSION
The results show that both the microbial community structure and gene function composition change greatly at different time points of Shaoxing rice wine fermentation. © 2013 Society of Chemical Industry</description><subject>Actinobacteria - classification</subject><subject>Actinobacteria - isolation & purification</subject><subject>Actinobacteria - metabolism</subject><subject>Ascomycota - classification</subject><subject>Ascomycota - isolation & purification</subject><subject>Ascomycota - metabolism</subject><subject>Categories</subject><subject>China</subject><subject>Communities</subject><subject>Computational Biology</subject><subject>Diet - ethnology</subject><subject>DNA, Bacterial - isolation & purification</subject><subject>DNA, Bacterial - metabolism</subject><subject>DNA, Fungal - isolation & purification</subject><subject>DNA, Fungal - metabolism</subject><subject>Fermentation</subject><subject>Fungi - classification</subject><subject>Fungi - isolation & purification</subject><subject>Fungi - metabolism</subject><subject>Genes</subject><subject>Gram-Negative Bacteria - classification</subject><subject>Gram-Negative Bacteria - isolation & purification</subject><subject>Gram-Negative Bacteria - metabolism</subject><subject>Gram-Positive Bacteria - classification</subject><subject>Gram-Positive Bacteria - isolation & purification</subject><subject>Gram-Positive Bacteria - metabolism</subject><subject>metagenome</subject><subject>Metagenomics</subject><subject>Microbiology</subject><subject>microbiota</subject><subject>Microorganisms</subject><subject>Molecular Typing</subject><subject>Mycological Typing Techniques</subject><subject>Oryza - chemistry</subject><subject>Oryza sativa</subject><subject>Proteobacteria - classification</subject><subject>Proteobacteria - isolation & purification</subject><subject>Proteobacteria - metabolism</subject><subject>Quality Control</subject><subject>Rice</subject><subject>Seeds - chemistry</subject><subject>Sequencing</subject><subject>Shaoxing rice wine</subject><subject>Time Factors</subject><subject>Vitaceae</subject><subject>wheat Qu</subject><subject>Wine - analysis</subject><subject>Wine - microbiology</subject><subject>Wines</subject><issn>0022-5142</issn><issn>1097-0010</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><recordid>eNqN0ctu1DAUBmALgehQWPACyBIbNmltx7csqxEtRQMsOmiWlu0cFw-JU-xE7bw9iaZ0wQZWtnS-3xf9CL2l5IwSws73JdgzSYR-hlaUNKoihJLnaDXPWCUoZyfoVSl7QkjTSPkSnbBaiFpxsULjl-jz4KLtsB_6fkpxPOAy5smPUwYcEw6Qe0ijHeOQ8F0ePJSCh4BvftjhIaZbnKMHfB8TYHfA11039THZytkCLe5htLeQhj56XODXBMnPkdfoRbBdgTeP6yn6fvlxu_5Ubb5dXa8vNpXnutGVDiC1cxIIV6SxgTNJg6PEi2BVaJxymjvBrbMhNMwzKVpmW7CBClcL1dan6MPx3PnZ891lNH0sHrrOJhimYqhUqlFcc_VvyrlWlEnG_4NSKRshqJzp-7_ofphymv-8KM1rpkk9q3ePanI9tOYux97mg_nT0gzOj-A-dnB4mlNilvrNUr9Z6jefby4vls2cqI6JWEZ4eErY_NNIVSthdl-vzG631XS9pWZT_wZGRLKc</recordid><startdate>201309</startdate><enddate>201309</enddate><creator>Xie, Guangfa</creator><creator>Wang, Lan</creator><creator>Gao, Qikang</creator><creator>Yu, Wenjing</creator><creator>Hong, Xutao</creator><creator>Zhao, Lingyun</creator><creator>Zou, Huijun</creator><general>John Wiley & Sons, Ltd</general><general>John Wiley and Sons, Limited</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>7QF</scope><scope>7QL</scope><scope>7QQ</scope><scope>7QR</scope><scope>7SC</scope><scope>7SE</scope><scope>7SN</scope><scope>7SP</scope><scope>7SR</scope><scope>7ST</scope><scope>7T5</scope><scope>7T7</scope><scope>7TA</scope><scope>7TB</scope><scope>7TM</scope><scope>7U5</scope><scope>7U9</scope><scope>8BQ</scope><scope>8FD</scope><scope>C1K</scope><scope>F28</scope><scope>FR3</scope><scope>H8D</scope><scope>H8G</scope><scope>H94</scope><scope>JG9</scope><scope>JQ2</scope><scope>KR7</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>M7N</scope><scope>P64</scope><scope>SOI</scope><scope>7X8</scope><scope>RC3</scope></search><sort><creationdate>201309</creationdate><title>Microbial community structure in fermentation process of Shaoxing rice wine by Illumina-based metagenomic sequencing</title><author>Xie, Guangfa ; Wang, Lan ; Gao, Qikang ; Yu, Wenjing ; Hong, Xutao ; Zhao, Lingyun ; Zou, Huijun</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4898-8fe68bb6e04709af4261fb10c5fa7f9b7b84b54abaff92c265d2adeaf15b357d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Actinobacteria - 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Academic</collection><collection>Genetics Abstracts</collection><jtitle>Journal of the science of food and agriculture</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Xie, Guangfa</au><au>Wang, Lan</au><au>Gao, Qikang</au><au>Yu, Wenjing</au><au>Hong, Xutao</au><au>Zhao, Lingyun</au><au>Zou, Huijun</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Microbial community structure in fermentation process of Shaoxing rice wine by Illumina-based metagenomic sequencing</atitle><jtitle>Journal of the science of food and agriculture</jtitle><addtitle>J. Sci. Food Agric</addtitle><date>2013-09</date><risdate>2013</risdate><volume>93</volume><issue>12</issue><spage>3121</spage><epage>3125</epage><pages>3121-3125</pages><issn>0022-5142</issn><eissn>1097-0010</eissn><coden>JSFAAE</coden><abstract>BACKGROUND
To understand the role of the community structure of microbes in the environment in the fermentation of Shaoxing rice wine, samples collected from a wine factory were subjected to Illumina‐based metagenomic sequencing.
RESULTS
De novo assembly of the sequencing reads allowed the characterisation of more than 23 thousand microbial genes derived from 1.7 and 1.88 Gbp of sequences from two samples fermented for 5 and 30 days respectively. The microbial community structure at different fermentation times of Shaoxing rice wine was revealed, showing the different roles of the microbiota in the fermentation process of Shaoxing rice wine. The gene function of both samples was also studied in the COG database, with most genes belonging to category S (function unknown), category E (amino acid transport and metabolism) and unclassified group.
CONCLUSION
The results show that both the microbial community structure and gene function composition change greatly at different time points of Shaoxing rice wine fermentation. © 2013 Society of Chemical Industry</abstract><cop>Chichester, UK</cop><pub>John Wiley & Sons, Ltd</pub><pmid>23553745</pmid><doi>10.1002/jsfa.6058</doi><tpages>5</tpages></addata></record> |
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| subjects | Actinobacteria - classification Actinobacteria - isolation & purification Actinobacteria - metabolism Ascomycota - classification Ascomycota - isolation & purification Ascomycota - metabolism Categories China Communities Computational Biology Diet - ethnology DNA, Bacterial - isolation & purification DNA, Bacterial - metabolism DNA, Fungal - isolation & purification DNA, Fungal - metabolism Fermentation Fungi - classification Fungi - isolation & purification Fungi - metabolism Genes Gram-Negative Bacteria - classification Gram-Negative Bacteria - isolation & purification Gram-Negative Bacteria - metabolism Gram-Positive Bacteria - classification Gram-Positive Bacteria - isolation & purification Gram-Positive Bacteria - metabolism metagenome Metagenomics Microbiology microbiota Microorganisms Molecular Typing Mycological Typing Techniques Oryza - chemistry Oryza sativa Proteobacteria - classification Proteobacteria - isolation & purification Proteobacteria - metabolism Quality Control Rice Seeds - chemistry Sequencing Shaoxing rice wine Time Factors Vitaceae wheat Qu Wine - analysis Wine - microbiology Wines |
| title | Microbial community structure in fermentation process of Shaoxing rice wine by Illumina-based metagenomic sequencing |
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