Milk microbiome signatures of subclinical mastitis‐affected cattle analysed by shotgun sequencing
Aims: Metagenomic analysis of milk samples collected from Kankrej, Gir (Bos indicus) and crossbred (Bos taurus × B. indicus) cattle harbouring subclinical mastitis was carried out by next‐generation sequencing 454 GS‐FLX technology to elucidate the microbial community structure of cattle milk. Metho...
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| Veröffentlicht in: | Journal of applied microbiology 2012-04, Vol.112 (4), p.639-650 |
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| creator | Bhatt, V.D Ahir, V.B Koringa, P.G Jakhesara, S.J Rank, D.N Nauriyal, D.S Kunjadia, A.P Joshi, C.G |
| description | Aims: Metagenomic analysis of milk samples collected from Kankrej, Gir (Bos indicus) and crossbred (Bos taurus × B. indicus) cattle harbouring subclinical mastitis was carried out by next‐generation sequencing 454 GS‐FLX technology to elucidate the microbial community structure of cattle milk. Methods and Results: Milk samples from Kankrej, Gir and crossbred cattle were subjected to metagenomic profiling by pyrosequencing. The Metagenomic analysis produced 63·07, 11·09 and 7·87 million base pairs (Mb) of sequence data, assembled in 264 798, 56 114 and 36 762 sequences with an average read length of 238, 197 and 214 nucleotides in Kankrej, Gir and crossbred cattle, respectively. Phylogenetic and metabolic profiles by the web‐based tool MG‐RAST revealed that the members of Enterobacteriales were predominant in mastitic milk followed by Pseudomonadales, Bacillales and Lactobacillales. Around 56 different species with varying abundance were detected in the subclinically infected milk. Escherichia coli was found to be the most predominant species in Kankrej and Gir cattle followed by Pseudomonas aeruginosa, Pseudomonas mendocina, Shigella flexneri and Bacillus cereus. In crossbred cattle, Staphylococcus aureus followed by Klebsiella pneumoniae, Staphylococcus epidermidis and E. coli were detected in descending order. Metabolic profiling indicated fluoroquinolones, methicillin, copper, cobalt–zinc–cadmium as the groups of antibiotics and toxic compounds to which the organisms showed resistance. Sequences indicating potential of organisms exhibiting multidrug resistance against antibiotics and resistance to toxic compounds were also present. Interestingly, presence of bacteriophages against Staph. aureus, E. coli, Enterobacter and Yersinia species was also observed. Conclusions: The analysis identified potential infectious organisms in mastitis, resistance of organisms to antibiotics and chemical compounds and the natural resistance potential of dairy cows. Significance and Impact of the Study: The findings of this study may help in formulating strategies for the prevention and treatment of mastitis in dairy animals and consequently in reducing economic losses incurred because of it. |
| doi_str_mv | 10.1111/j.1365-2672.2012.05244.x |
| format | Article |
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Methods and Results: Milk samples from Kankrej, Gir and crossbred cattle were subjected to metagenomic profiling by pyrosequencing. The Metagenomic analysis produced 63·07, 11·09 and 7·87 million base pairs (Mb) of sequence data, assembled in 264 798, 56 114 and 36 762 sequences with an average read length of 238, 197 and 214 nucleotides in Kankrej, Gir and crossbred cattle, respectively. Phylogenetic and metabolic profiles by the web‐based tool MG‐RAST revealed that the members of Enterobacteriales were predominant in mastitic milk followed by Pseudomonadales, Bacillales and Lactobacillales. Around 56 different species with varying abundance were detected in the subclinically infected milk. Escherichia coli was found to be the most predominant species in Kankrej and Gir cattle followed by Pseudomonas aeruginosa, Pseudomonas mendocina, Shigella flexneri and Bacillus cereus. In crossbred cattle, Staphylococcus aureus followed by Klebsiella pneumoniae, Staphylococcus epidermidis and E. coli were detected in descending order. Metabolic profiling indicated fluoroquinolones, methicillin, copper, cobalt–zinc–cadmium as the groups of antibiotics and toxic compounds to which the organisms showed resistance. Sequences indicating potential of organisms exhibiting multidrug resistance against antibiotics and resistance to toxic compounds were also present. Interestingly, presence of bacteriophages against Staph. aureus, E. coli, Enterobacter and Yersinia species was also observed. Conclusions: The analysis identified potential infectious organisms in mastitis, resistance of organisms to antibiotics and chemical compounds and the natural resistance potential of dairy cows. Significance and Impact of the Study: The findings of this study may help in formulating strategies for the prevention and treatment of mastitis in dairy animals and consequently in reducing economic losses incurred because of it.</description><identifier>ISSN: 1364-5072</identifier><identifier>EISSN: 1365-2672</identifier><identifier>DOI: 10.1111/j.1365-2672.2012.05244.x</identifier><identifier>PMID: 22277077</identifier><language>eng</language><publisher>Oxford, UK: Blackwell Publishing Ltd</publisher><subject>Animals ; Anti-Bacterial Agents - pharmacology ; Anti-Bacterial Agents - therapeutic use ; antibiotic resistance ; Bacillus cereus ; Bacteria - classification ; Bacteria - drug effects ; Bacteria - genetics ; Bacteria - isolation & purification ; bacteriophages ; Biological and medical sciences ; Bos ; Bos indicus ; cadmium ; Cattle ; cobalt ; community structure ; copper ; crossbreds ; Crosses, Genetic ; dairy cows ; economics ; Enterobacter ; Escherichia coli ; Female ; fluoroquinolones ; Fundamental and applied biological sciences. Psychology ; High-Throughput Nucleotide Sequencing ; Klebsiella pneumoniae ; mastitis ; Mastitis, Bovine - drug therapy ; Mastitis, Bovine - genetics ; Mastitis, Bovine - microbiology ; metabolomics ; metagenomics ; methicillin ; MG-RAST ; Microbiology ; microbiome ; milk ; Milk - microbiology ; milk analysis ; multiple drug resistance ; next-generation sequencing ; nucleotides ; phylogeny ; Pseudomonadales ; Pseudomonas aeruginosa ; Pseudomonas mendocina ; Shigella flexneri ; Staphylococcus aureus ; Staphylococcus epidermidis ; subclinical mastitis ; toxicity ; Yersinia ; zebu ; zinc</subject><ispartof>Journal of applied microbiology, 2012-04, Vol.112 (4), p.639-650</ispartof><rights>2012 The Authors. Journal of Applied Microbiology © 2012 The Society for Applied Microbiology</rights><rights>2015 INIST-CNRS</rights><rights>2012 The Authors. Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5494-47200f8a92950ce5ca90f478b8b7cc46c7fe458cf668fe91f464b6c82f37d7093</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fj.1365-2672.2012.05244.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1365-2672.2012.05244.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,777,781,1412,27905,27906,45555,45556</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=25617686$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22277077$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Bhatt, V.D</creatorcontrib><creatorcontrib>Ahir, V.B</creatorcontrib><creatorcontrib>Koringa, P.G</creatorcontrib><creatorcontrib>Jakhesara, S.J</creatorcontrib><creatorcontrib>Rank, D.N</creatorcontrib><creatorcontrib>Nauriyal, D.S</creatorcontrib><creatorcontrib>Kunjadia, A.P</creatorcontrib><creatorcontrib>Joshi, C.G</creatorcontrib><title>Milk microbiome signatures of subclinical mastitis‐affected cattle analysed by shotgun sequencing</title><title>Journal of applied microbiology</title><addtitle>J Appl Microbiol</addtitle><description>Aims: Metagenomic analysis of milk samples collected from Kankrej, Gir (Bos indicus) and crossbred (Bos taurus × B. indicus) cattle harbouring subclinical mastitis was carried out by next‐generation sequencing 454 GS‐FLX technology to elucidate the microbial community structure of cattle milk. Methods and Results: Milk samples from Kankrej, Gir and crossbred cattle were subjected to metagenomic profiling by pyrosequencing. The Metagenomic analysis produced 63·07, 11·09 and 7·87 million base pairs (Mb) of sequence data, assembled in 264 798, 56 114 and 36 762 sequences with an average read length of 238, 197 and 214 nucleotides in Kankrej, Gir and crossbred cattle, respectively. Phylogenetic and metabolic profiles by the web‐based tool MG‐RAST revealed that the members of Enterobacteriales were predominant in mastitic milk followed by Pseudomonadales, Bacillales and Lactobacillales. Around 56 different species with varying abundance were detected in the subclinically infected milk. Escherichia coli was found to be the most predominant species in Kankrej and Gir cattle followed by Pseudomonas aeruginosa, Pseudomonas mendocina, Shigella flexneri and Bacillus cereus. In crossbred cattle, Staphylococcus aureus followed by Klebsiella pneumoniae, Staphylococcus epidermidis and E. coli were detected in descending order. Metabolic profiling indicated fluoroquinolones, methicillin, copper, cobalt–zinc–cadmium as the groups of antibiotics and toxic compounds to which the organisms showed resistance. Sequences indicating potential of organisms exhibiting multidrug resistance against antibiotics and resistance to toxic compounds were also present. Interestingly, presence of bacteriophages against Staph. aureus, E. coli, Enterobacter and Yersinia species was also observed. Conclusions: The analysis identified potential infectious organisms in mastitis, resistance of organisms to antibiotics and chemical compounds and the natural resistance potential of dairy cows. Significance and Impact of the Study: The findings of this study may help in formulating strategies for the prevention and treatment of mastitis in dairy animals and consequently in reducing economic losses incurred because of it.</description><subject>Animals</subject><subject>Anti-Bacterial Agents - pharmacology</subject><subject>Anti-Bacterial Agents - therapeutic use</subject><subject>antibiotic resistance</subject><subject>Bacillus cereus</subject><subject>Bacteria - classification</subject><subject>Bacteria - drug effects</subject><subject>Bacteria - genetics</subject><subject>Bacteria - isolation & purification</subject><subject>bacteriophages</subject><subject>Biological and medical sciences</subject><subject>Bos</subject><subject>Bos indicus</subject><subject>cadmium</subject><subject>Cattle</subject><subject>cobalt</subject><subject>community structure</subject><subject>copper</subject><subject>crossbreds</subject><subject>Crosses, Genetic</subject><subject>dairy cows</subject><subject>economics</subject><subject>Enterobacter</subject><subject>Escherichia coli</subject><subject>Female</subject><subject>fluoroquinolones</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Klebsiella pneumoniae</subject><subject>mastitis</subject><subject>Mastitis, Bovine - drug therapy</subject><subject>Mastitis, Bovine - genetics</subject><subject>Mastitis, Bovine - microbiology</subject><subject>metabolomics</subject><subject>metagenomics</subject><subject>methicillin</subject><subject>MG-RAST</subject><subject>Microbiology</subject><subject>microbiome</subject><subject>milk</subject><subject>Milk - microbiology</subject><subject>milk analysis</subject><subject>multiple drug resistance</subject><subject>next-generation sequencing</subject><subject>nucleotides</subject><subject>phylogeny</subject><subject>Pseudomonadales</subject><subject>Pseudomonas aeruginosa</subject><subject>Pseudomonas mendocina</subject><subject>Shigella flexneri</subject><subject>Staphylococcus aureus</subject><subject>Staphylococcus epidermidis</subject><subject>subclinical mastitis</subject><subject>toxicity</subject><subject>Yersinia</subject><subject>zebu</subject><subject>zinc</subject><issn>1364-5072</issn><issn>1365-2672</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpFkc1yFCEUhSlLy8SYV1A2lqtugeavFy5iyowmGbNIUrqjaAZGJnR3bOhyZucj-Ix5ktCZcWTDpe53LhwOABCjEuf1YVXiirOCcEFKgjApESOUlutn4HDfeP5U04IhQQ7AqxhXCOEKMf4SHBBChEBCHAIz9-EOtt4MfeP71sLol51O42Aj7B2MY2OC77zRAbY6Jp98fPjzVztnTbILaHRKwULd6bCJ-dxsYPzZp-XYwWh_jbYzvlu-Bi-cDtEe7_YjcHv2-eb0S3F5Nft6enJZGEZrWlBBEHJS16RmyFhmdI0cFbKRjTCGciOcpUwax7l0tsaOctpwI4mrxEKgujoC77dz74c-3x2Tan00NgTd2X6MquYSy-yaZfLNjhyb1i7U_eBbPWzUv3_JwLsdoGP27gadncT_HONYcMkz93HL_fbBbvZ9jNSUk1qpKQ41xaGmnNRTTmqtzk_mU5X1xVbvY7LrvV4Pd4qLSjD1_dtMXfw4m0mEP6l55t9uead7pZdDftPtdZ5Mp2yFrGn1CEDOoA0</recordid><startdate>201204</startdate><enddate>201204</enddate><creator>Bhatt, V.D</creator><creator>Ahir, V.B</creator><creator>Koringa, P.G</creator><creator>Jakhesara, S.J</creator><creator>Rank, D.N</creator><creator>Nauriyal, D.S</creator><creator>Kunjadia, A.P</creator><creator>Joshi, C.G</creator><general>Blackwell Publishing Ltd</general><general>Blackwell</general><scope>FBQ</scope><scope>BSCLL</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>7QL</scope><scope>7T7</scope><scope>7U7</scope><scope>8FD</scope><scope>C1K</scope><scope>F1W</scope><scope>FR3</scope><scope>H95</scope><scope>H97</scope><scope>L.G</scope><scope>P64</scope></search><sort><creationdate>201204</creationdate><title>Milk microbiome signatures of subclinical mastitis‐affected cattle analysed by shotgun sequencing</title><author>Bhatt, V.D ; Ahir, V.B ; Koringa, P.G ; Jakhesara, S.J ; Rank, D.N ; Nauriyal, D.S ; Kunjadia, A.P ; Joshi, C.G</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5494-47200f8a92950ce5ca90f478b8b7cc46c7fe458cf668fe91f464b6c82f37d7093</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Animals</topic><topic>Anti-Bacterial Agents - pharmacology</topic><topic>Anti-Bacterial Agents - therapeutic use</topic><topic>antibiotic resistance</topic><topic>Bacillus cereus</topic><topic>Bacteria - classification</topic><topic>Bacteria - drug effects</topic><topic>Bacteria - genetics</topic><topic>Bacteria - isolation & purification</topic><topic>bacteriophages</topic><topic>Biological and medical sciences</topic><topic>Bos</topic><topic>Bos indicus</topic><topic>cadmium</topic><topic>Cattle</topic><topic>cobalt</topic><topic>community structure</topic><topic>copper</topic><topic>crossbreds</topic><topic>Crosses, Genetic</topic><topic>dairy cows</topic><topic>economics</topic><topic>Enterobacter</topic><topic>Escherichia coli</topic><topic>Female</topic><topic>fluoroquinolones</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Klebsiella pneumoniae</topic><topic>mastitis</topic><topic>Mastitis, Bovine - drug therapy</topic><topic>Mastitis, Bovine - genetics</topic><topic>Mastitis, Bovine - microbiology</topic><topic>metabolomics</topic><topic>metagenomics</topic><topic>methicillin</topic><topic>MG-RAST</topic><topic>Microbiology</topic><topic>microbiome</topic><topic>milk</topic><topic>Milk - microbiology</topic><topic>milk analysis</topic><topic>multiple drug resistance</topic><topic>next-generation sequencing</topic><topic>nucleotides</topic><topic>phylogeny</topic><topic>Pseudomonadales</topic><topic>Pseudomonas aeruginosa</topic><topic>Pseudomonas mendocina</topic><topic>Shigella flexneri</topic><topic>Staphylococcus aureus</topic><topic>Staphylococcus epidermidis</topic><topic>subclinical mastitis</topic><topic>toxicity</topic><topic>Yersinia</topic><topic>zebu</topic><topic>zinc</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Bhatt, V.D</creatorcontrib><creatorcontrib>Ahir, V.B</creatorcontrib><creatorcontrib>Koringa, P.G</creatorcontrib><creatorcontrib>Jakhesara, S.J</creatorcontrib><creatorcontrib>Rank, D.N</creatorcontrib><creatorcontrib>Nauriyal, D.S</creatorcontrib><creatorcontrib>Kunjadia, A.P</creatorcontrib><creatorcontrib>Joshi, C.G</creatorcontrib><collection>AGRIS</collection><collection>Istex</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Toxicology Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Engineering Research Database</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 3: Aquatic Pollution & Environmental Quality</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><jtitle>Journal of applied microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Bhatt, V.D</au><au>Ahir, V.B</au><au>Koringa, P.G</au><au>Jakhesara, S.J</au><au>Rank, D.N</au><au>Nauriyal, D.S</au><au>Kunjadia, A.P</au><au>Joshi, C.G</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Milk microbiome signatures of subclinical mastitis‐affected cattle analysed by shotgun sequencing</atitle><jtitle>Journal of applied microbiology</jtitle><addtitle>J Appl Microbiol</addtitle><date>2012-04</date><risdate>2012</risdate><volume>112</volume><issue>4</issue><spage>639</spage><epage>650</epage><pages>639-650</pages><issn>1364-5072</issn><eissn>1365-2672</eissn><abstract>Aims: Metagenomic analysis of milk samples collected from Kankrej, Gir (Bos indicus) and crossbred (Bos taurus × B. indicus) cattle harbouring subclinical mastitis was carried out by next‐generation sequencing 454 GS‐FLX technology to elucidate the microbial community structure of cattle milk. Methods and Results: Milk samples from Kankrej, Gir and crossbred cattle were subjected to metagenomic profiling by pyrosequencing. The Metagenomic analysis produced 63·07, 11·09 and 7·87 million base pairs (Mb) of sequence data, assembled in 264 798, 56 114 and 36 762 sequences with an average read length of 238, 197 and 214 nucleotides in Kankrej, Gir and crossbred cattle, respectively. Phylogenetic and metabolic profiles by the web‐based tool MG‐RAST revealed that the members of Enterobacteriales were predominant in mastitic milk followed by Pseudomonadales, Bacillales and Lactobacillales. Around 56 different species with varying abundance were detected in the subclinically infected milk. Escherichia coli was found to be the most predominant species in Kankrej and Gir cattle followed by Pseudomonas aeruginosa, Pseudomonas mendocina, Shigella flexneri and Bacillus cereus. In crossbred cattle, Staphylococcus aureus followed by Klebsiella pneumoniae, Staphylococcus epidermidis and E. coli were detected in descending order. Metabolic profiling indicated fluoroquinolones, methicillin, copper, cobalt–zinc–cadmium as the groups of antibiotics and toxic compounds to which the organisms showed resistance. Sequences indicating potential of organisms exhibiting multidrug resistance against antibiotics and resistance to toxic compounds were also present. Interestingly, presence of bacteriophages against Staph. aureus, E. coli, Enterobacter and Yersinia species was also observed. Conclusions: The analysis identified potential infectious organisms in mastitis, resistance of organisms to antibiotics and chemical compounds and the natural resistance potential of dairy cows. Significance and Impact of the Study: The findings of this study may help in formulating strategies for the prevention and treatment of mastitis in dairy animals and consequently in reducing economic losses incurred because of it.</abstract><cop>Oxford, UK</cop><pub>Blackwell Publishing Ltd</pub><pmid>22277077</pmid><doi>10.1111/j.1365-2672.2012.05244.x</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Animals Anti-Bacterial Agents - pharmacology Anti-Bacterial Agents - therapeutic use antibiotic resistance Bacillus cereus Bacteria - classification Bacteria - drug effects Bacteria - genetics Bacteria - isolation & purification bacteriophages Biological and medical sciences Bos Bos indicus cadmium Cattle cobalt community structure copper crossbreds Crosses, Genetic dairy cows economics Enterobacter Escherichia coli Female fluoroquinolones Fundamental and applied biological sciences. Psychology High-Throughput Nucleotide Sequencing Klebsiella pneumoniae mastitis Mastitis, Bovine - drug therapy Mastitis, Bovine - genetics Mastitis, Bovine - microbiology metabolomics metagenomics methicillin MG-RAST Microbiology microbiome milk Milk - microbiology milk analysis multiple drug resistance next-generation sequencing nucleotides phylogeny Pseudomonadales Pseudomonas aeruginosa Pseudomonas mendocina Shigella flexneri Staphylococcus aureus Staphylococcus epidermidis subclinical mastitis toxicity Yersinia zebu zinc |
| title | Milk microbiome signatures of subclinical mastitis‐affected cattle analysed by shotgun sequencing |
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