Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches
Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different di...
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| Veröffentlicht in: | Systematic and applied microbiology 2018-07, Vol.41 (4), p.374-385 |
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| creator | Pandit, Ramesh J. Hinsu, Ankit T. Patel, Shriram H. Jakhesara, Subhash J. Koringa, Prakash G. Bruno, Fosso Psifidi, Androniki Shah, S.V. Joshi, Chaitanya G. |
| description | Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes. Different proportions of roughage rather than the type of roughage (dry or green) modulated microbiome composition and the expression of its gene pool. Fibre degrading bacteria (i.e. Clostridium, Ruminococcus, Eubacterium, Butyrivibrio, Bacillus and Roseburia) were higher in the solid fraction of rumen (P |
| doi_str_mv | 10.1016/j.syapm.2018.02.002 |
| format | Article |
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In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes. Different proportions of roughage rather than the type of roughage (dry or green) modulated microbiome composition and the expression of its gene pool. Fibre degrading bacteria (i.e. Clostridium, Ruminococcus, Eubacterium, Butyrivibrio, Bacillus and Roseburia) were higher in the solid fraction of rumen (P<0.01) compared to the liquid fraction, whereas bacteria considered to be utilizers of the degraded product (i.e. Prevotella, Bacteroides, Parabacteroides, Paludibacter and Victivallis) were dominant in the liquid fraction (P<0.05). Likewise, expression of fibre degrading enzymes and related carbohydrate binding modules (CBMs) occurred in the solid fraction. When metagenomic and metatranscriptomic data were compared, it was found that some genera and species were transcriptionally more active, although they were in low abundance, making an important contribution to fibre degradation and its further metabolism in the rumen. This study also identified some of the transcriptionally active genera, such as Caldicellulosiruptor and Paludibacter, whose potential has been less-explored in rumen. Overall, the comparison of metagenomic shotgun and metatranscriptomic sequencing appeared to be a much richer source of information compared to conventional metagenomic analysis.</description><identifier>ISSN: 0723-2020</identifier><identifier>EISSN: 1618-0984</identifier><identifier>DOI: 10.1016/j.syapm.2018.02.002</identifier><identifier>PMID: 29555111</identifier><language>eng</language><publisher>Germany: Elsevier GmbH</publisher><subject>Animal Feed - analysis ; Animals ; Bacteria - classification ; Bacteria - genetics ; Cattle ; Diet ; Fibre degrading enzymes ; Gir cattle ; Metagenome ; Metagenome - genetics ; Metagenomics - methods ; Metatranscriptome ; Microbiome ; Microbiota - genetics ; Rumen ; Rumen - microbiology</subject><ispartof>Systematic and applied microbiology, 2018-07, Vol.41 (4), p.374-385</ispartof><rights>2018 Elsevier GmbH</rights><rights>Copyright © 2018 Elsevier GmbH. All rights reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c404t-d83d7d287088a4a505d4be540320c1e6ed10242610fb360bf4eb74c0ffc2f3c23</citedby><cites>FETCH-LOGICAL-c404t-d83d7d287088a4a505d4be540320c1e6ed10242610fb360bf4eb74c0ffc2f3c23</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S072320201830081X$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65534</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29555111$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Pandit, Ramesh J.</creatorcontrib><creatorcontrib>Hinsu, Ankit T.</creatorcontrib><creatorcontrib>Patel, Shriram H.</creatorcontrib><creatorcontrib>Jakhesara, Subhash J.</creatorcontrib><creatorcontrib>Koringa, Prakash G.</creatorcontrib><creatorcontrib>Bruno, Fosso</creatorcontrib><creatorcontrib>Psifidi, Androniki</creatorcontrib><creatorcontrib>Shah, S.V.</creatorcontrib><creatorcontrib>Joshi, Chaitanya G.</creatorcontrib><title>Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches</title><title>Systematic and applied microbiology</title><addtitle>Syst Appl Microbiol</addtitle><description>Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes. Different proportions of roughage rather than the type of roughage (dry or green) modulated microbiome composition and the expression of its gene pool. Fibre degrading bacteria (i.e. Clostridium, Ruminococcus, Eubacterium, Butyrivibrio, Bacillus and Roseburia) were higher in the solid fraction of rumen (P<0.01) compared to the liquid fraction, whereas bacteria considered to be utilizers of the degraded product (i.e. Prevotella, Bacteroides, Parabacteroides, Paludibacter and Victivallis) were dominant in the liquid fraction (P<0.05). Likewise, expression of fibre degrading enzymes and related carbohydrate binding modules (CBMs) occurred in the solid fraction. When metagenomic and metatranscriptomic data were compared, it was found that some genera and species were transcriptionally more active, although they were in low abundance, making an important contribution to fibre degradation and its further metabolism in the rumen. This study also identified some of the transcriptionally active genera, such as Caldicellulosiruptor and Paludibacter, whose potential has been less-explored in rumen. Overall, the comparison of metagenomic shotgun and metatranscriptomic sequencing appeared to be a much richer source of information compared to conventional metagenomic analysis.</description><subject>Animal Feed - analysis</subject><subject>Animals</subject><subject>Bacteria - classification</subject><subject>Bacteria - genetics</subject><subject>Cattle</subject><subject>Diet</subject><subject>Fibre degrading enzymes</subject><subject>Gir cattle</subject><subject>Metagenome</subject><subject>Metagenome - genetics</subject><subject>Metagenomics - methods</subject><subject>Metatranscriptome</subject><subject>Microbiome</subject><subject>Microbiota - genetics</subject><subject>Rumen</subject><subject>Rumen - microbiology</subject><issn>0723-2020</issn><issn>1618-0984</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9UcFu1DAQtRCIbgtfgIR8LBIJY8fJeg8coIKCVMQFzpZjjxevEjvYTkW_iN_E2y0cOY3mzXvzNPMIecGgZcCGN4c23-llbjkw2QJvAfgjsmEDkw3spHhMNrDlXcOBwxk5z_kAwMRuYE_JGd_1fc8Y25DfX7xJcfSxaGrivMTsi4_hNd1jQLrEOFEdLPUlU_y1JMy5TqkP9NonanQpE9LL9zFXyHqz5lc0rTMGugaLiVrvHCYMhbqY9B4rgHXTmn3Y0xlLhUKcvbn3OPYl6ZBN8ks5wcuSojY_MD8jT5yeMj5_qBfk-8cP364-NTdfrz9fvbtpjABRGis7u7VcbkFKLXQPvRUj9gI6DobhgJYBF3xg4MZugNEJHLfCgHOGu87w7oJcnvZW458r5qJmnw1Okw4Y16zqs3vZccn7Su1O1PrAnBM6tSQ_63SnGKhjQuqg7hM6iqQCrmpCVfXywWAdZ7T_NH8jqYS3JwLWM289JpWNx2DQ-oSmKBv9fw3-ALnHpv0</recordid><startdate>201807</startdate><enddate>201807</enddate><creator>Pandit, Ramesh J.</creator><creator>Hinsu, Ankit T.</creator><creator>Patel, Shriram H.</creator><creator>Jakhesara, Subhash J.</creator><creator>Koringa, Prakash G.</creator><creator>Bruno, Fosso</creator><creator>Psifidi, Androniki</creator><creator>Shah, S.V.</creator><creator>Joshi, Chaitanya G.</creator><general>Elsevier GmbH</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>7X8</scope></search><sort><creationdate>201807</creationdate><title>Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches</title><author>Pandit, Ramesh J. ; Hinsu, Ankit T. ; Patel, Shriram H. ; Jakhesara, Subhash J. ; Koringa, Prakash G. ; Bruno, Fosso ; Psifidi, Androniki ; Shah, S.V. ; Joshi, Chaitanya G.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c404t-d83d7d287088a4a505d4be540320c1e6ed10242610fb360bf4eb74c0ffc2f3c23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Animal Feed - analysis</topic><topic>Animals</topic><topic>Bacteria - classification</topic><topic>Bacteria - genetics</topic><topic>Cattle</topic><topic>Diet</topic><topic>Fibre degrading enzymes</topic><topic>Gir cattle</topic><topic>Metagenome</topic><topic>Metagenome - genetics</topic><topic>Metagenomics - methods</topic><topic>Metatranscriptome</topic><topic>Microbiome</topic><topic>Microbiota - genetics</topic><topic>Rumen</topic><topic>Rumen - microbiology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Pandit, Ramesh J.</creatorcontrib><creatorcontrib>Hinsu, Ankit T.</creatorcontrib><creatorcontrib>Patel, Shriram H.</creatorcontrib><creatorcontrib>Jakhesara, Subhash J.</creatorcontrib><creatorcontrib>Koringa, Prakash G.</creatorcontrib><creatorcontrib>Bruno, Fosso</creatorcontrib><creatorcontrib>Psifidi, Androniki</creatorcontrib><creatorcontrib>Shah, S.V.</creatorcontrib><creatorcontrib>Joshi, Chaitanya G.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Systematic and applied microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Pandit, Ramesh J.</au><au>Hinsu, Ankit T.</au><au>Patel, Shriram H.</au><au>Jakhesara, Subhash J.</au><au>Koringa, Prakash G.</au><au>Bruno, Fosso</au><au>Psifidi, Androniki</au><au>Shah, S.V.</au><au>Joshi, Chaitanya G.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches</atitle><jtitle>Systematic and applied microbiology</jtitle><addtitle>Syst Appl Microbiol</addtitle><date>2018-07</date><risdate>2018</risdate><volume>41</volume><issue>4</issue><spage>374</spage><epage>385</epage><pages>374-385</pages><issn>0723-2020</issn><eissn>1618-0984</eissn><abstract>Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes. Different proportions of roughage rather than the type of roughage (dry or green) modulated microbiome composition and the expression of its gene pool. Fibre degrading bacteria (i.e. Clostridium, Ruminococcus, Eubacterium, Butyrivibrio, Bacillus and Roseburia) were higher in the solid fraction of rumen (P<0.01) compared to the liquid fraction, whereas bacteria considered to be utilizers of the degraded product (i.e. Prevotella, Bacteroides, Parabacteroides, Paludibacter and Victivallis) were dominant in the liquid fraction (P<0.05). Likewise, expression of fibre degrading enzymes and related carbohydrate binding modules (CBMs) occurred in the solid fraction. When metagenomic and metatranscriptomic data were compared, it was found that some genera and species were transcriptionally more active, although they were in low abundance, making an important contribution to fibre degradation and its further metabolism in the rumen. This study also identified some of the transcriptionally active genera, such as Caldicellulosiruptor and Paludibacter, whose potential has been less-explored in rumen. Overall, the comparison of metagenomic shotgun and metatranscriptomic sequencing appeared to be a much richer source of information compared to conventional metagenomic analysis.</abstract><cop>Germany</cop><pub>Elsevier GmbH</pub><pmid>29555111</pmid><doi>10.1016/j.syapm.2018.02.002</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Systematic and applied microbiology, 2018-07, Vol.41 (4), p.374-385 |
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| language | eng |
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| source | MEDLINE; Elsevier ScienceDirect Journals |
| subjects | Animal Feed - analysis Animals Bacteria - classification Bacteria - genetics Cattle Diet Fibre degrading enzymes Gir cattle Metagenome Metagenome - genetics Metagenomics - methods Metatranscriptome Microbiome Microbiota - genetics Rumen Rumen - microbiology |
| title | Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches |
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