Functional gene arrays-based analysis of fecal microbiomes in patients with liver cirrhosis
Human gut microbiota plays an important role in the pathogenesis of cirrhosis complications. Although the phylogenetic diversity of intestinal microbiota in patients with liver cirrhosis has been examined in several studies, little is known about their functional composition and structure. To charac...
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| Veröffentlicht in: | BMC genomics 2014-09, Vol.15 (1), p.753-753, Article 753 |
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| creator | Chen, Yanfei Qin, Nan Guo, Jing Qian, Guirong Fang, Daiqiong Shi, Ding Xu, Min Yang, Fengling He, Zhili Van Nostrand, Joy D Yuan, Tong Deng, Ye Zhou, Jizhong Li, Lanjuan |
| description | Human gut microbiota plays an important role in the pathogenesis of cirrhosis complications. Although the phylogenetic diversity of intestinal microbiota in patients with liver cirrhosis has been examined in several studies, little is known about their functional composition and structure.
To characterize the functional gene diversity of the gut microbiome in cirrhotic patients, we recruited a total of 42 individuals, 12 alcoholic cirrhosis patients, 18 hepatitis B virus (HBV)-related cirrhosis patients, and 12 normal controls. We determined the functional structure of these samples using a specific functional gene array, which is a combination of GeoChip for monitoring biogeochemical processes and HuMiChip specifically designed for analyzing human microbiomes. Our experimental data showed that the microbial community functional composition and structure were dramatically distinctive in the alcoholic cirrhosis. Various microbial functional genes involved in organic remediation, stress response, antibiotic resistance, metal resistance, and virulence were highly enriched in the alcoholic cirrhosis group compared to the control group and HBV-related cirrhosis group. Cirrhosis may have distinct influences on metabolic potential of fecal microbial communities. The abundance of functional genes relevant to nutrient metabolism, including amino acid metabolism, lipid metabolism, nucleotide metabolism, and isoprenoid biosynthesis, were significantly decreased in both alcoholic cirrhosis group and HBV-related cirrhosis group. Significant correlations were observed between functional gene abundances and Child-Pugh scores, such as those encoding aspartate-ammonia ligase, transaldolase, adenylosuccinate synthetase and IMP dehydrogenase.
Functional gene array was utilized to study the gut microbiome in alcoholic and HBV-related cirrhosis patients and controls in this study. Our array data indicated that the functional composition of fecal microbiomes was heavily influenced by cirrhosis, especially by alcoholic cirrhosis. This study provides new insights into the functional potentials and activity of gut microbiota in cirrhotic patients with different etiologies. |
| doi_str_mv | 10.1186/1471-2164-15-753 |
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To characterize the functional gene diversity of the gut microbiome in cirrhotic patients, we recruited a total of 42 individuals, 12 alcoholic cirrhosis patients, 18 hepatitis B virus (HBV)-related cirrhosis patients, and 12 normal controls. We determined the functional structure of these samples using a specific functional gene array, which is a combination of GeoChip for monitoring biogeochemical processes and HuMiChip specifically designed for analyzing human microbiomes. Our experimental data showed that the microbial community functional composition and structure were dramatically distinctive in the alcoholic cirrhosis. Various microbial functional genes involved in organic remediation, stress response, antibiotic resistance, metal resistance, and virulence were highly enriched in the alcoholic cirrhosis group compared to the control group and HBV-related cirrhosis group. Cirrhosis may have distinct influences on metabolic potential of fecal microbial communities. The abundance of functional genes relevant to nutrient metabolism, including amino acid metabolism, lipid metabolism, nucleotide metabolism, and isoprenoid biosynthesis, were significantly decreased in both alcoholic cirrhosis group and HBV-related cirrhosis group. Significant correlations were observed between functional gene abundances and Child-Pugh scores, such as those encoding aspartate-ammonia ligase, transaldolase, adenylosuccinate synthetase and IMP dehydrogenase.
Functional gene array was utilized to study the gut microbiome in alcoholic and HBV-related cirrhosis patients and controls in this study. Our array data indicated that the functional composition of fecal microbiomes was heavily influenced by cirrhosis, especially by alcoholic cirrhosis. This study provides new insights into the functional potentials and activity of gut microbiota in cirrhotic patients with different etiologies.</description><identifier>ISSN: 1471-2164</identifier><identifier>EISSN: 1471-2164</identifier><identifier>DOI: 10.1186/1471-2164-15-753</identifier><identifier>PMID: 25179593</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Adult ; Aged ; Alcohol ; Alcohols - adverse effects ; Amino acids ; Analysis ; Antibiotic resistance ; Antibiotics ; BASIC BIOLOGICAL SCIENCES ; Biodiversity ; Biosynthesis ; Biotechnology & Applied Microbiology ; Carbohydrates ; Care and treatment ; Cluster Analysis ; Colleges & universities ; Complications and side effects ; Data processing ; Deoxyribonucleic acid ; Development and progression ; Disease ; DNA ; Drug resistance in microorganisms ; End-stage liver disease ; Feces - microbiology ; Female ; Gene-Environment Interaction ; Genes ; Genetic aspects ; Genetic Variation ; Genetics & Heredity ; Genomics ; Hepatitis B virus ; Humans ; Hybridization ; Intestines ; Laboratories ; Liver cirrhosis ; Liver Cirrhosis - etiology ; Male ; Medical diagnosis ; Medical research ; Medicine, Experimental ; Metabolism ; Metagenome - drug effects ; Metagenomics - methods ; Microarray ; Microbial activity ; Microbial communities ; Microbiota ; Middle Aged ; Phylogeny ; Physiological aspects ; Statistical analysis</subject><ispartof>BMC genomics, 2014-09, Vol.15 (1), p.753-753, Article 753</ispartof><rights>COPYRIGHT 2014 BioMed Central Ltd.</rights><rights>2014 Chen et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.</rights><rights>Chen et al.; licensee BioMed Central Ltd. 2014</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-b645t-ad852069e19a8f6c6b2c18b2d1e382779172a6df327240df8e1a1df04d56f75d3</citedby><cites>FETCH-LOGICAL-b645t-ad852069e19a8f6c6b2c18b2d1e382779172a6df327240df8e1a1df04d56f75d3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4171554/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4171554/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25179593$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/servlets/purl/1626437$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Chen, Yanfei</creatorcontrib><creatorcontrib>Qin, Nan</creatorcontrib><creatorcontrib>Guo, Jing</creatorcontrib><creatorcontrib>Qian, Guirong</creatorcontrib><creatorcontrib>Fang, Daiqiong</creatorcontrib><creatorcontrib>Shi, Ding</creatorcontrib><creatorcontrib>Xu, Min</creatorcontrib><creatorcontrib>Yang, Fengling</creatorcontrib><creatorcontrib>He, Zhili</creatorcontrib><creatorcontrib>Van Nostrand, Joy D</creatorcontrib><creatorcontrib>Yuan, Tong</creatorcontrib><creatorcontrib>Deng, Ye</creatorcontrib><creatorcontrib>Zhou, Jizhong</creatorcontrib><creatorcontrib>Li, Lanjuan</creatorcontrib><creatorcontrib>Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)</creatorcontrib><creatorcontrib>Univ. of Oklahoma, Norman, OK (United States)</creatorcontrib><title>Functional gene arrays-based analysis of fecal microbiomes in patients with liver cirrhosis</title><title>BMC genomics</title><addtitle>BMC Genomics</addtitle><description>Human gut microbiota plays an important role in the pathogenesis of cirrhosis complications. Although the phylogenetic diversity of intestinal microbiota in patients with liver cirrhosis has been examined in several studies, little is known about their functional composition and structure.
To characterize the functional gene diversity of the gut microbiome in cirrhotic patients, we recruited a total of 42 individuals, 12 alcoholic cirrhosis patients, 18 hepatitis B virus (HBV)-related cirrhosis patients, and 12 normal controls. We determined the functional structure of these samples using a specific functional gene array, which is a combination of GeoChip for monitoring biogeochemical processes and HuMiChip specifically designed for analyzing human microbiomes. Our experimental data showed that the microbial community functional composition and structure were dramatically distinctive in the alcoholic cirrhosis. Various microbial functional genes involved in organic remediation, stress response, antibiotic resistance, metal resistance, and virulence were highly enriched in the alcoholic cirrhosis group compared to the control group and HBV-related cirrhosis group. Cirrhosis may have distinct influences on metabolic potential of fecal microbial communities. The abundance of functional genes relevant to nutrient metabolism, including amino acid metabolism, lipid metabolism, nucleotide metabolism, and isoprenoid biosynthesis, were significantly decreased in both alcoholic cirrhosis group and HBV-related cirrhosis group. Significant correlations were observed between functional gene abundances and Child-Pugh scores, such as those encoding aspartate-ammonia ligase, transaldolase, adenylosuccinate synthetase and IMP dehydrogenase.
Functional gene array was utilized to study the gut microbiome in alcoholic and HBV-related cirrhosis patients and controls in this study. Our array data indicated that the functional composition of fecal microbiomes was heavily influenced by cirrhosis, especially by alcoholic cirrhosis. This study provides new insights into the functional potentials and activity of gut microbiota in cirrhotic patients with different etiologies.</description><subject>Adult</subject><subject>Aged</subject><subject>Alcohol</subject><subject>Alcohols - adverse effects</subject><subject>Amino acids</subject><subject>Analysis</subject><subject>Antibiotic resistance</subject><subject>Antibiotics</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>Biodiversity</subject><subject>Biosynthesis</subject><subject>Biotechnology & Applied Microbiology</subject><subject>Carbohydrates</subject><subject>Care and treatment</subject><subject>Cluster Analysis</subject><subject>Colleges & universities</subject><subject>Complications and side effects</subject><subject>Data processing</subject><subject>Deoxyribonucleic acid</subject><subject>Development and progression</subject><subject>Disease</subject><subject>DNA</subject><subject>Drug resistance in microorganisms</subject><subject>End-stage liver disease</subject><subject>Feces - microbiology</subject><subject>Female</subject><subject>Gene-Environment Interaction</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic Variation</subject><subject>Genetics & Heredity</subject><subject>Genomics</subject><subject>Hepatitis B virus</subject><subject>Humans</subject><subject>Hybridization</subject><subject>Intestines</subject><subject>Laboratories</subject><subject>Liver cirrhosis</subject><subject>Liver Cirrhosis - etiology</subject><subject>Male</subject><subject>Medical diagnosis</subject><subject>Medical research</subject><subject>Medicine, Experimental</subject><subject>Metabolism</subject><subject>Metagenome - drug effects</subject><subject>Metagenomics - methods</subject><subject>Microarray</subject><subject>Microbial activity</subject><subject>Microbial communities</subject><subject>Microbiota</subject><subject>Middle Aged</subject><subject>Phylogeny</subject><subject>Physiological aspects</subject><subject>Statistical analysis</subject><issn>1471-2164</issn><issn>1471-2164</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNptkstv1DAQxiMEog-4c0IRXMohJbbjRy6VqhWFSpWQeJw4WI4z3nWV2IvtFPa_x9stS4NWPtga_-absb8pileoPkdIsPeo4ajCiDUVohWn5ElxvA89fXQ-Kk5ivK1rxAWmz4sjTBFvaUuOix9Xk9PJeqeGcgkOShWC2sSqUxH6UuXwJtpYelMa0JkZrQ6-s36EWFpXrlWy4FIsf9m0Kgd7B6HUNoSVz1kvimdGDRFePuynxferD98Wn6qbzx-vF5c3VccamirVC4pr1gJqlTBMsw5rJDrcIyACc94ijhXrDcEcN3VvBCCFelM3PWWG056cFhc73fXUjdDr3FBQg1wHO6qwkV5ZOb9xdiWX_k42iCNKmyzwZifgY7IyaptAr7R3DnSSiGHWEJ6hxQ66f_3BKvMb7Ue5dUBuHZCIymxQVjl76DX4nxPEJEcbNQyDcuCnmDHGRC7HcUbf_ofe-ilkR-4pQgRrBPlHLdUA0jrjc3G9FZWXlLSUcYZFps4PUHn1kB31DozN8VnCu1lCZhL8Tks1xSivv36Zs_WOzaMRYwCz_xRUy-2cHvqG148t2yf8HUzyB9AN4Yw</recordid><startdate>20140902</startdate><enddate>20140902</enddate><creator>Chen, Yanfei</creator><creator>Qin, Nan</creator><creator>Guo, Jing</creator><creator>Qian, Guirong</creator><creator>Fang, Daiqiong</creator><creator>Shi, Ding</creator><creator>Xu, Min</creator><creator>Yang, Fengling</creator><creator>He, Zhili</creator><creator>Van Nostrand, Joy D</creator><creator>Yuan, Tong</creator><creator>Deng, Ye</creator><creator>Zhou, Jizhong</creator><creator>Li, Lanjuan</creator><general>BioMed Central Ltd</general><general>BioMed Central</general><general>Springer</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>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7U7</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</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>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7T7</scope><scope>OIOZB</scope><scope>OTOTI</scope><scope>5PM</scope></search><sort><creationdate>20140902</creationdate><title>Functional gene arrays-based analysis of fecal microbiomes in patients with liver cirrhosis</title><author>Chen, Yanfei ; Qin, Nan ; Guo, Jing ; Qian, Guirong ; Fang, Daiqiong ; Shi, Ding ; Xu, Min ; Yang, Fengling ; He, Zhili ; Van Nostrand, Joy D ; Yuan, Tong ; Deng, Ye ; Zhou, Jizhong ; Li, Lanjuan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-b645t-ad852069e19a8f6c6b2c18b2d1e382779172a6df327240df8e1a1df04d56f75d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Adult</topic><topic>Aged</topic><topic>Alcohol</topic><topic>Alcohols - adverse effects</topic><topic>Amino acids</topic><topic>Analysis</topic><topic>Antibiotic resistance</topic><topic>Antibiotics</topic><topic>BASIC BIOLOGICAL SCIENCES</topic><topic>Biodiversity</topic><topic>Biosynthesis</topic><topic>Biotechnology & Applied Microbiology</topic><topic>Carbohydrates</topic><topic>Care and treatment</topic><topic>Cluster Analysis</topic><topic>Colleges & universities</topic><topic>Complications and side effects</topic><topic>Data processing</topic><topic>Deoxyribonucleic acid</topic><topic>Development and progression</topic><topic>Disease</topic><topic>DNA</topic><topic>Drug resistance in microorganisms</topic><topic>End-stage liver disease</topic><topic>Feces - microbiology</topic><topic>Female</topic><topic>Gene-Environment Interaction</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genetic Variation</topic><topic>Genetics & Heredity</topic><topic>Genomics</topic><topic>Hepatitis B virus</topic><topic>Humans</topic><topic>Hybridization</topic><topic>Intestines</topic><topic>Laboratories</topic><topic>Liver cirrhosis</topic><topic>Liver Cirrhosis - 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Hybrid</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BMC genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chen, Yanfei</au><au>Qin, Nan</au><au>Guo, Jing</au><au>Qian, Guirong</au><au>Fang, Daiqiong</au><au>Shi, Ding</au><au>Xu, Min</au><au>Yang, Fengling</au><au>He, Zhili</au><au>Van Nostrand, Joy D</au><au>Yuan, Tong</au><au>Deng, Ye</au><au>Zhou, Jizhong</au><au>Li, Lanjuan</au><aucorp>Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)</aucorp><aucorp>Univ. of Oklahoma, Norman, OK (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Functional gene arrays-based analysis of fecal microbiomes in patients with liver cirrhosis</atitle><jtitle>BMC genomics</jtitle><addtitle>BMC Genomics</addtitle><date>2014-09-02</date><risdate>2014</risdate><volume>15</volume><issue>1</issue><spage>753</spage><epage>753</epage><pages>753-753</pages><artnum>753</artnum><issn>1471-2164</issn><eissn>1471-2164</eissn><abstract>Human gut microbiota plays an important role in the pathogenesis of cirrhosis complications. Although the phylogenetic diversity of intestinal microbiota in patients with liver cirrhosis has been examined in several studies, little is known about their functional composition and structure.
To characterize the functional gene diversity of the gut microbiome in cirrhotic patients, we recruited a total of 42 individuals, 12 alcoholic cirrhosis patients, 18 hepatitis B virus (HBV)-related cirrhosis patients, and 12 normal controls. We determined the functional structure of these samples using a specific functional gene array, which is a combination of GeoChip for monitoring biogeochemical processes and HuMiChip specifically designed for analyzing human microbiomes. Our experimental data showed that the microbial community functional composition and structure were dramatically distinctive in the alcoholic cirrhosis. Various microbial functional genes involved in organic remediation, stress response, antibiotic resistance, metal resistance, and virulence were highly enriched in the alcoholic cirrhosis group compared to the control group and HBV-related cirrhosis group. Cirrhosis may have distinct influences on metabolic potential of fecal microbial communities. The abundance of functional genes relevant to nutrient metabolism, including amino acid metabolism, lipid metabolism, nucleotide metabolism, and isoprenoid biosynthesis, were significantly decreased in both alcoholic cirrhosis group and HBV-related cirrhosis group. Significant correlations were observed between functional gene abundances and Child-Pugh scores, such as those encoding aspartate-ammonia ligase, transaldolase, adenylosuccinate synthetase and IMP dehydrogenase.
Functional gene array was utilized to study the gut microbiome in alcoholic and HBV-related cirrhosis patients and controls in this study. Our array data indicated that the functional composition of fecal microbiomes was heavily influenced by cirrhosis, especially by alcoholic cirrhosis. This study provides new insights into the functional potentials and activity of gut microbiota in cirrhotic patients with different etiologies.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>25179593</pmid><doi>10.1186/1471-2164-15-753</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | BMC genomics, 2014-09, Vol.15 (1), p.753-753, Article 753 |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; SpringerLink Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; PubMed Central Open Access; Springer Nature OA Free Journals |
| subjects | Adult Aged Alcohol Alcohols - adverse effects Amino acids Analysis Antibiotic resistance Antibiotics BASIC BIOLOGICAL SCIENCES Biodiversity Biosynthesis Biotechnology & Applied Microbiology Carbohydrates Care and treatment Cluster Analysis Colleges & universities Complications and side effects Data processing Deoxyribonucleic acid Development and progression Disease DNA Drug resistance in microorganisms End-stage liver disease Feces - microbiology Female Gene-Environment Interaction Genes Genetic aspects Genetic Variation Genetics & Heredity Genomics Hepatitis B virus Humans Hybridization Intestines Laboratories Liver cirrhosis Liver Cirrhosis - etiology Male Medical diagnosis Medical research Medicine, Experimental Metabolism Metagenome - drug effects Metagenomics - methods Microarray Microbial activity Microbial communities Microbiota Middle Aged Phylogeny Physiological aspects Statistical analysis |
| title | Functional gene arrays-based analysis of fecal microbiomes in patients with liver cirrhosis |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-16T07%3A29%3A46IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Functional%20gene%20arrays-based%20analysis%20of%20fecal%20microbiomes%20in%20patients%20with%20liver%20cirrhosis&rft.jtitle=BMC%20genomics&rft.au=Chen,%20Yanfei&rft.aucorp=Lawrence%20Berkeley%20National%20Laboratory%20(LBNL),%20Berkeley,%20CA%20(United%20States)&rft.date=2014-09-02&rft.volume=15&rft.issue=1&rft.spage=753&rft.epage=753&rft.pages=753-753&rft.artnum=753&rft.issn=1471-2164&rft.eissn=1471-2164&rft_id=info:doi/10.1186/1471-2164-15-753&rft_dat=%3Cgale_pubme%3EA539567628%3C/gale_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1563386483&rft_id=info:pmid/25179593&rft_galeid=A539567628&rfr_iscdi=true |