[ { "key": "EZKSJ4N3", "version": 26, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/EZKSJ4N3", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/EZKSJ4N3", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/719545/items/QETD284T", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1079081, "username": "hewilson86", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/hewilson86", "type": "text/html" } } } }, "data": { "key": "EZKSJ4N3", "version": 26, "parentItem": "QETD284T", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2016-11-01T18:41:53Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/15294817", "note": "", "contentType": "", "charset": "", "tags": [], "relations": {}, "dateAdded": "2016-11-01T18:42:10Z", "dateModified": "2016-11-01T18:42:10Z" } }, { "key": "QETD284T", "version": 26, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/QETD284T", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/QETD284T", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1079081, "username": "hewilson86", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/hewilson86", "type": "text/html" } } }, "creatorSummary": "Yu and Morrison", "parsedDate": "2004-08-01", "numChildren": 1 }, "data": { "key": "QETD284T", "version": 26, "itemType": "journalArticle", "title": "Comparisons of Different Hypervariable Regions of rrs Genes for Use in Fingerprinting of Microbial Communities by PCR-Denaturing Gradient Gel Electrophoresis", "creators": [ { "creatorType": "author", "firstName": "Zhongtang", "lastName": "Yu" }, { "creatorType": "author", "firstName": "Mark", "lastName": "Morrison" } ], "abstractNote": "Denaturing gradient gel electrophoresis (DGGE) has become a widely used tool to examine microbial diversity and community structure, but no systematic comparison has been made of the DGGE profiles obtained when different hypervariable (V) regions are amplified from the same community DNA samples. We report here a study to make such comparisons and establish a preferred choice of V region(s) to examine by DGGE, when community DNA extracted from samples of digesta is used. When the members of the phylogenetically representative set of 218 rrs genes archived in the RDP II database were compared, the V1 region was found to be the most variable, followed by the V9 and V3 regions. The temperature of the lowest-melting-temperature (Tm(L)) domain for each V region was also calculated for these rrs genes, and the V1 to V4 region was found to be most heterogeneous with respect to Tm(L). The average Tm(L) values and their standard deviations for each V region were then used to devise the denaturing gradients suitable for separating 95% of all the sequences, and the PCR-DGGE profiles produced from the same community DNA samples with these conditions were compared. The resulting DGGE profiles were substantially different in terms of the number, resolution, and relative intensity of the amplification products. The DGGE profiles of the V3 region were best, and the V3 to V5 and V6 to V8 regions produced better DGGE profiles than did other multiple V-region amplicons. Introduction of degenerate bases in the primers used to amplify the V1 or V3 region alone did not improve DGGE banding profiles. Our results show that DGGE analysis of gastrointestinal microbiomes is best accomplished by the amplification of either the V3 or V1 region of rrs genes, but if a longer amplification product is desired, then the V3 to V5 or V6 to V8 region should be targeted.", "publicationTitle": "Applied and Environmental Microbiology", "publisher": "", "place": "", "date": "08/01/2004", "volume": "70", "issue": "8", "section": "", "partNumber": "", "partTitle": "", "pages": "4800-4806", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Appl. Environ. Microbiol.", "DOI": "10.1128/AEM.70.8.4800-4806.2004", "citationKey": "", "url": "http://aem.asm.org/content/70/8/4800", "accessDate": "2016-11-01T18:41:51Z", "PMID": "", "PMCID": "", "ISSN": "0099-2240, 1098-5336", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "aem.asm.org", "callNumber": "", "rights": "", "extra": "PMID: 15294817", "tags": [], "collections": [ "QXMQHQ98" ], "relations": {}, "dateAdded": "2016-11-01T18:42:10Z", "dateModified": "2016-11-01T18:42:10Z" } }, { "key": "6DKGTPBE", "version": 25, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/6DKGTPBE", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/6DKGTPBE", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1079081, "username": "hewilson86", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/hewilson86", "type": "text/html" } } }, "creatorSummary": "Castelino et al.", "parsedDate": "2015", "numChildren": 0 }, "data": { "key": "6DKGTPBE", "version": 25, "itemType": "journalArticle", "title": "The skin microbiome in psoriatic arthritis: methodology development and pilot data", "creators": [ { "creatorType": "author", "firstName": "Madhura", "lastName": "Castelino" }, { "creatorType": "author", "firstName": "Stephen", "lastName": "Eyre" }, { "creatorType": "author", "firstName": "John", "lastName": "Moat" }, { "creatorType": "author", "firstName": "Graeme", "lastName": "Fox" }, { "creatorType": "author", "firstName": "Paul", "lastName": "Martin" }, { "creatorType": "author", "firstName": "Umer", "lastName": "Ijaz" }, { "creatorType": "author", "firstName": "Christopher", "lastName": "Quince" }, { "creatorType": "author", "firstName": "Pauline", "lastName": "Ho" }, { "creatorType": "author", "firstName": "Mathew", "lastName": "Upton" }, { "creatorType": "author", "firstName": "Anne", "lastName": "Barton" } ], "abstractNote": "", "publicationTitle": "The Lancet", "publisher": "", "place": "", "date": "02/2015", "volume": "385", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "S27", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1016/S0140-6736(15)60342-7", "citationKey": "", "url": "http://linkinghub.elsevier.com/retrieve/pii/S0140673615603427", "accessDate": "2016-11-01T18:19:56Z", "PMID": "", "PMCID": "", "ISSN": "01406736", "archive": "", "archiveLocation": "", "shortTitle": "The skin microbiome in psoriatic arthritis", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "QXMQHQ98" ], "relations": {}, "dateAdded": "2016-11-01T18:19:56Z", "dateModified": "2016-11-01T18:19:56Z" } }, { "key": "M7TTQD9U", "version": 24, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/M7TTQD9U", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/M7TTQD9U", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1079081, "username": "hewilson86", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/hewilson86", "type": "text/html" } } }, "creatorSummary": "Jo et al.", "parsedDate": "2016-03", "numChildren": 2 }, "data": { "key": "M7TTQD9U", "version": 24, "itemType": "journalArticle", "title": "Research Techniques Made Simple: Bacterial 16S Ribosomal RNA Gene Sequencing in Cutaneous Research", "creators": [ { "creatorType": "author", "firstName": "Jay-Hyun", "lastName": "Jo" }, { "creatorType": "author", "firstName": "Elizabeth A.", "lastName": "Kennedy" }, { "creatorType": "author", "firstName": "Heidi H.", "lastName": "Kong" } ], "abstractNote": "Skin serves as a protective barrier and also harbors numerous microorganisms collectively comprising the skin microbiome. As a result of recent advances in sequencing (next-generation sequencing), our understanding of microbial communities on skin has advanced substantially. In particular, the 16S ribosomal RNA gene sequencing technique has played an important role in efforts to identify the global communities of bacteria in healthy individuals and patients with various disorders in multiple topographical regions over the skin surface. Here, we describe basic principles, study design, and a workflow of 16S ribosomal RNA gene sequencing methodology, primarily for investigators who are not familiar with this approach. This article will also discuss some applications and challenges of 16S ribosomal RNA sequencing as well as directions for future development.", "publicationTitle": "Journal of Investigative Dermatology", "publisher": "", "place": "", "date": "March 2016", "volume": "136", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "e23-e27", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Journal of Investigative Dermatology", "DOI": "10.1016/j.jid.2016.01.005", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/pii/S0022202X16003481", "accessDate": "2016-11-01T18:18:43Z", "PMID": "", "PMCID": "", "ISSN": "0022-202X", "archive": "", "archiveLocation": "", "shortTitle": "Research Techniques Made Simple", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "QXMQHQ98", "SDVF8A4M" ], "relations": {}, "dateAdded": "2016-11-01T18:18:43Z", "dateModified": "2016-11-01T18:18:43Z" } }, { "key": "6P7HI5PM", "version": 23, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/6P7HI5PM", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/6P7HI5PM", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/719545/items/M7TTQD9U", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1079081, "username": "hewilson86", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/hewilson86", "type": "text/html" } } } }, "data": { "key": "6P7HI5PM", "version": 23, "parentItem": "M7TTQD9U", "itemType": "attachment", "linkMode": "linked_url", "title": "ScienceDirect Full Text PDF", "accessDate": "2016-11-01T18:18:43Z", "url": "http://www.sciencedirect.com/science/article/pii/S0022202X16003481/pdfft?md5=cd5dec22187ba1f75f3e3c24aad2974a&pid=1-s2.0-S0022202X16003481-main.pdf", "note": "", "contentType": "application/pdf", "charset": "", "tags": [], "relations": {}, "dateAdded": "2016-11-01T18:18:43Z", "dateModified": "2016-11-01T18:18:43Z" } }, { "key": "2S96PVSK", "version": 23, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/2S96PVSK", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/2S96PVSK", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/719545/items/M7TTQD9U", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1079081, "username": "hewilson86", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/hewilson86", "type": "text/html" } } } }, "data": { "key": "2S96PVSK", "version": 23, "parentItem": "M7TTQD9U", "itemType": "attachment", "linkMode": "linked_url", "title": "ScienceDirect Snapshot", "accessDate": "2016-11-01T18:18:43Z", "url": "http://www.sciencedirect.com/science/article/pii/S0022202X16003481", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2016-11-01T18:18:43Z", "dateModified": "2016-11-01T18:18:43Z" } }, { "key": "GM8STCK5", "version": 22, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/GM8STCK5", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/GM8STCK5", "type": "text/html" } }, "meta": { "createdByUser": { "id": 3382206, "username": "clarissebetancourt", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/clarissebetancourt", "type": "text/html" } } }, "creatorSummary": "Wang et al.", "parsedDate": "2015-01-21", "numChildren": 2 }, "data": { "key": "GM8STCK5", "version": 22, "itemType": "journalArticle", "title": "Application of metagenomics in the human gut microbiome", "creators": [ { "creatorType": "author", "firstName": "Wei-Lin", "lastName": "Wang" }, { "creatorType": "author", "firstName": "Shao-Yan", "lastName": "Xu" }, { "creatorType": "author", "firstName": "Zhi-Gang", "lastName": "Ren" }, { "creatorType": "author", "firstName": "Liang", "lastName": "Tao" }, { "creatorType": "author", "firstName": "Jian-Wen", "lastName": "Jiang" }, { "creatorType": "author", "firstName": "Shu-Sen", "lastName": "Zheng" } ], "abstractNote": "There are more than 1000 microbial species living in the complex human intestine. The gut microbial community plays an important role in protecting the host against pathogenic microbes, modulating immunity, regulating metabolic processes, and is even regarded as an endocrine organ. However, traditional culture methods are very limited for identifying microbes. With the application of molecular biologic technology in the field of the intestinal microbiome, especially metagenomic sequencing of the next-generation sequencing technology, progress has been made in the study of the human intestinal microbiome. Metagenomics can be used to study intestinal microbiome diversity and dysbiosis, as well as its relationship to health and disease. Moreover, functional metagenomics can identify novel functional genes, microbial pathways, antibiotic resistance genes, functional dysbiosis of the intestinal microbiome, and determine interactions and co-evolution between microbiota and host, though there are still some limitations. Metatranscriptomics, metaproteomics and metabolomics represent enormous complements to the understanding of the human gut microbiome. This review aims to demonstrate that metagenomics can be a powerful tool in studying the human gut microbiome with encouraging prospects. The limitations of metagenomics to be overcome are also discussed. Metatranscriptomics, metaproteomics and metabolomics in relation to the study of the human gut microbiome are also briefly discussed.", "publicationTitle": "World Journal of Gastroenterology : WJG", "publisher": "", "place": "", "date": "2015-1-21", "volume": "21", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "803-814", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "World J Gastroenterol", "DOI": "10.3748/wjg.v21.i3.803", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299332/", "accessDate": "2016-10-25T00:09:50Z", "PMID": "", "PMCID": "", "ISSN": "1007-9327", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "PMID: 25624713\nPMCID: PMC4299332", "tags": [], "collections": [ "ZWBMSEA9" ], "relations": {}, "dateAdded": "2016-10-25T00:09:50Z", "dateModified": "2016-10-25T00:09:50Z" } }, { "key": "THE2Q7DT", "version": 22, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/THE2Q7DT", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/THE2Q7DT", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/719545/items/GM8STCK5", "type": "application/json" } }, "meta": { "createdByUser": { "id": 3382206, "username": "clarissebetancourt", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/clarissebetancourt", "type": "text/html" } } } }, "data": { "key": "THE2Q7DT", "version": 22, "parentItem": "GM8STCK5", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed Central Full Text PDF", "accessDate": "2016-10-25T00:09:50Z", "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299332/pdf/WJG-21-803.pdf", "note": "", "contentType": "application/pdf", "charset": "", "tags": [], "relations": {}, "dateAdded": "2016-10-25T00:09:50Z", "dateModified": "2016-10-25T00:09:50Z" } }, { "key": "AADA5X6Q", "version": 22, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/AADA5X6Q", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/AADA5X6Q", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/719545/items/GM8STCK5", "type": "application/json" } }, "meta": { "createdByUser": { "id": 3382206, "username": "clarissebetancourt", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/clarissebetancourt", "type": "text/html" } } } }, "data": { "key": "AADA5X6Q", "version": 22, "parentItem": "GM8STCK5", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed Central Link", "accessDate": "2016-10-25T00:09:50Z", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299332/", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2016-10-25T00:09:50Z", "dateModified": "2016-10-25T00:09:50Z" } }, { "key": "Q4S5SX95", "version": 21, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/Q4S5SX95", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/Q4S5SX95", "type": "text/html" } }, "meta": { "createdByUser": { "id": 3386681, "username": "abateman9162", "name": "Ashley Bateman", "links": { "alternate": { "href": "https://www.zotero.org/abateman9162", "type": "text/html" } } }, "creatorSummary": "Oh et al.", "parsedDate": "2016-05", "numChildren": 0 }, "data": { "key": "Q4S5SX95", "version": 21, "itemType": "journalArticle", "title": "Temporal Stability of the Human Skin Microbiome.", "creators": [ { "creatorType": "author", "firstName": "Julia", "lastName": "Oh" }, { "creatorType": "author", "firstName": "Allyson L", "lastName": "Byrd" }, { "creatorType": "author", "firstName": "Morgan", "lastName": "Park" }, { "creatorType": "author", "firstName": "Heidi H.", "lastName": "NISC Comparative Sequencing Program" }, { "creatorType": "author", "firstName": "Heidi H", "lastName": "Kong" }, { "creatorType": "author", "firstName": "Julia A", "lastName": "Segre" }, { "creatorType": "author", "firstName": "G.I.", "lastName": "Perez-Perez" }, { "creatorType": "author", "firstName": "A. De", "lastName": "Souza" }, { "creatorType": "author", "firstName": "B.", "lastName": "Strober" }, { "creatorType": "author", "firstName": "Z.", "lastName": "Gao" }, { "creatorType": "author", "firstName": "M.", "lastName": "Bihan" }, { "creatorType": "author", "firstName": "K.", "lastName": "Li" }, { "creatorType": "author", "firstName": "B.A.", "lastName": "Methé" }, { "creatorType": "author", "firstName": "M.J.", "lastName": "Blaser" }, { "creatorType": "author", "firstName": "Y.", "lastName": "Belkaid" }, { "creatorType": "author", "firstName": "J.A.", "lastName": "Segre" }, { "creatorType": "author", "firstName": "J.G.", "lastName": "Caporaso" }, { "creatorType": "author", "firstName": "C.L.", "lastName": "Lauber" }, { "creatorType": "author", "firstName": "E.K.", "lastName": "Costello" }, { "creatorType": "author", "firstName": "D.", "lastName": "Berg-Lyons" }, { "creatorType": "author", "firstName": "A.", "lastName": "Gonzalez" }, { "creatorType": "author", "firstName": "J.", "lastName": "Stombaugh" }, { "creatorType": "author", "firstName": "D.", "lastName": "Knights" }, { "creatorType": "author", "firstName": "P.", "lastName": "Gajer" }, { "creatorType": "author", "firstName": "J.", "lastName": "Ravel" }, { "creatorType": "author", "firstName": "N.", "lastName": "Fierer" }, { "creatorType": "author", "firstName": "et", "lastName": "Al" }, { "creatorType": "author", "firstName": "S.", "lastName": "Conlan" }, { "creatorType": "author", "firstName": "L.A.", "lastName": "Mijares" }, { "creatorType": "author", "firstName": "J.", "lastName": "Becker" }, { "creatorType": "author", "firstName": "R.W.", "lastName": "Blakesley" }, { "creatorType": "author", "firstName": "G.G.", "lastName": "Bouffard" }, { "creatorType": "author", "firstName": "S.", "lastName": "Brooks" }, { "creatorType": "author", "firstName": "H.", "lastName": "Coleman" }, { "creatorType": "author", "firstName": "J.", "lastName": "Gupta" }, { "creatorType": "author", "firstName": "N.", "lastName": "Gurson" }, { "creatorType": "author", "firstName": "M.", "lastName": "Park" }, { "creatorType": "author", "firstName": "NISC Comparative Sequencing", "lastName": "Program" }, { "creatorType": "author", "firstName": "et", "lastName": "Al" }, { "creatorType": "author", "firstName": "E.K.", "lastName": "Costello" }, { "creatorType": "author", "firstName": "C.L.", "lastName": "Lauber" }, { "creatorType": "author", "firstName": "M.", "lastName": "Hamady" }, { "creatorType": "author", "firstName": "N.", "lastName": "Fierer" }, { "creatorType": "author", "firstName": "J.I.", "lastName": "Gordon" }, { "creatorType": "author", "firstName": "R.", "lastName": "Knight" }, { "creatorType": "author", "firstName": "R.C.", "lastName": "Edgar" }, { "creatorType": "author", "firstName": "J.J.", "lastName": "Faith" }, { "creatorType": "author", "firstName": "J.L.", "lastName": "Guruge" }, { "creatorType": "author", "firstName": "M.", "lastName": "Charbonneau" }, { "creatorType": "author", "firstName": "S.", "lastName": "Subramanian" }, { "creatorType": "author", "firstName": "H.", "lastName": "Seedorf" }, { "creatorType": "author", "firstName": "A.L.", "lastName": "Goodman" }, { "creatorType": "author", "firstName": "J.C.", "lastName": "Clemente" }, { "creatorType": "author", "firstName": "R.", "lastName": "Knight" }, { "creatorType": "author", "firstName": "A.C.", "lastName": "Heath" }, { "creatorType": "author", "firstName": "R.L.", "lastName": "Leibel" }, { "creatorType": "author", "firstName": "et", "lastName": "Al" }, { "creatorType": "author", "firstName": "K.", "lastName": "Findley" }, { "creatorType": "author", "firstName": "J.", "lastName": "Oh" }, { "creatorType": "author", "firstName": "J.", "lastName": "Yang" }, { "creatorType": "author", "firstName": "S.", "lastName": "Conlan" }, { "creatorType": "author", "firstName": "C.", "lastName": "Deming" }, { "creatorType": "author", "firstName": "J.A.", "lastName": "Meyer" }, { "creatorType": "author", "firstName": "D.", "lastName": "Schoenfeld" }, { "creatorType": "author", "firstName": "E.", "lastName": "Nomicos" }, { "creatorType": "author", "firstName": "M.", "lastName": "Park" }, { "creatorType": "author", "firstName": "H.H.", "lastName": "Kong" }, { "creatorType": "author", "firstName": "J.A.", "lastName": "Segre" }, { "creatorType": "author", "firstName": "NIH Intramural Sequencing Center Comparative Sequencing", "lastName": "Program" }, { "creatorType": "author", "firstName": "G.E.", "lastName": "Flores" }, { "creatorType": "author", "firstName": "J.G.", "lastName": "Caporaso" }, { "creatorType": "author", "firstName": "J.B.", "lastName": "Henley" }, { "creatorType": "author", "firstName": "J.R.", "lastName": "Rideout" }, { "creatorType": "author", "firstName": "D.", "lastName": "Domogala" }, { "creatorType": "author", "firstName": "J.", "lastName": "Chase" }, { "creatorType": "author", "firstName": "J.W.", "lastName": "Leff" }, { "creatorType": "author", "firstName": "Y.", "lastName": "Vázquez-Baeza" }, { "creatorType": "author", "firstName": "A.", "lastName": "Gonzalez" }, { "creatorType": "author", "firstName": "R.", "lastName": "Knight" }, { "creatorType": "author", "firstName": "et", "lastName": "Al" }, { "creatorType": "author", "firstName": "E.A.", "lastName": "Franzosa" }, { "creatorType": "author", "firstName": "K.", "lastName": "Huang" }, { "creatorType": "author", "firstName": "J.F.", "lastName": "Meadow" }, { "creatorType": "author", "firstName": "D.", "lastName": "Gevers" }, { "creatorType": "author", "firstName": "K.P.", "lastName": "Lemon" }, { "creatorType": "author", "firstName": "J.M.", "lastName": "Bohannan" }, { "creatorType": "author", "firstName": "C.", "lastName": "Huttenhower" }, { "creatorType": "author", "firstName": "P.", "lastName": "Gajer" }, { "creatorType": "author", "firstName": "R.M.", "lastName": "Brotman" }, { "creatorType": "author", "firstName": "G.", "lastName": "Bai" }, { "creatorType": "author", "firstName": "J.", "lastName": "Sakamoto" }, { "creatorType": "author", "firstName": "U.M.", "lastName": "Schütte" }, { "creatorType": "author", "firstName": "X.", "lastName": "Zhong" }, { "creatorType": "author", "firstName": "S.S.", "lastName": "Koenig" }, { "creatorType": "author", "firstName": "L.", "lastName": "Fu" }, { "creatorType": "author", "firstName": "Z.S.", "lastName": "Ma" }, { "creatorType": "author", "firstName": "X.", "lastName": "Zhou" }, { "creatorType": "author", "firstName": "et", "lastName": "Al" }, { "creatorType": "author", "firstName": "S.", "lastName": "Greenblum" }, { "creatorType": "author", "firstName": "R.", "lastName": "Carr" }, { "creatorType": "author", "firstName": "E.", "lastName": "Borenstein" }, { "creatorType": "author", "firstName": "E.A.", "lastName": "Grice" }, { "creatorType": "author", "firstName": "E.A.", "lastName": "Grice" }, { "creatorType": "author", "firstName": "J.A.", "lastName": "Segre" }, { "creatorType": "author", "firstName": "E.A.", "lastName": "Grice" }, { "creatorType": "author", "firstName": "H.H.", "lastName": "Kong" }, { "creatorType": "author", "firstName": "S.", "lastName": "Conlan" }, { "creatorType": "author", "firstName": "C.B.", "lastName": "Deming" }, { "creatorType": "author", "firstName": "J.", "lastName": "Davis" }, { "creatorType": "author", "firstName": "A.C.", "lastName": "Young" }, { "creatorType": "author", "firstName": "G.G.", "lastName": "Bouffard" }, { "creatorType": "author", "firstName": "R.W.", "lastName": "Blakesley" }, { "creatorType": "author", "firstName": "P.R.", "lastName": "Murray" }, { "creatorType": "author", "firstName": "E.D.", "lastName": "Green" }, { "creatorType": "author", "firstName": "NISC Comparative Sequencing", "lastName": "Program" }, { "creatorType": "author", "firstName": "et", "lastName": "Al" }, { "creatorType": "author", "firstName": "G.D.", "lastName": "Hannigan" }, { "creatorType": "author", "firstName": "J.S.", "lastName": "Meisel" }, { "creatorType": "author", "firstName": "A.S.", "lastName": "Tyldsley" }, { "creatorType": "author", "firstName": "Q.", "lastName": "Zheng" }, { "creatorType": "author", "firstName": "B.P.", "lastName": "Hodkinson" }, { "creatorType": "author", "firstName": "A.J.", "lastName": "SanMiguel" }, { "creatorType": "author", "firstName": "S.", "lastName": "Minot" }, { "creatorType": "author", "firstName": "F.D.", "lastName": "Bushman" }, { "creatorType": "author", "firstName": "E.A.", "lastName": "Grice" }, { "creatorType": "author", "firstName": "Human Microbiome Project", "lastName": "Consortium" }, { "creatorType": "author", "firstName": "D.", "lastName": "Kang" }, { "creatorType": "author", "firstName": "B.", "lastName": "Shi" }, { "creatorType": "author", "firstName": "M.C.", "lastName": "Erfe" }, { "creatorType": "author", "firstName": "N.", "lastName": "Craft" }, { "creatorType": "author", "firstName": "H.", "lastName": "Li" }, { "creatorType": "author", "firstName": "H.H.", "lastName": "Kong" }, { "creatorType": "author", "firstName": "J.", "lastName": "Oh" }, { "creatorType": "author", "firstName": "C.", "lastName": "Deming" }, { "creatorType": "author", "firstName": "S.", "lastName": "Conlan" }, { "creatorType": "author", "firstName": "E.A.", "lastName": "Grice" }, { "creatorType": "author", "firstName": "M.A.", "lastName": "Beatson" }, { "creatorType": "author", "firstName": "E.", "lastName": "Nomicos" }, { "creatorType": "author", "firstName": "E.C.", "lastName": "Polley" }, { "creatorType": "author", "firstName": "H.D.", "lastName": "Komarow" }, { "creatorType": "author", "firstName": "P.R.", "lastName": "Murray" }, { "creatorType": "author", "firstName": "NISC Comparative Sequence", "lastName": "Program" }, { "creatorType": "author", "firstName": "et", "lastName": "Al" }, { "creatorType": "author", "firstName": "S.", "lastName": "Lax" }, { "creatorType": "author", "firstName": "D.P.", "lastName": "Smith" }, { "creatorType": "author", "firstName": "J.", "lastName": "Hampton-Marcell" }, { "creatorType": "author", "firstName": "S.M.", "lastName": "Owens" }, { "creatorType": "author", "firstName": "K.M.", "lastName": "Handley" }, { "creatorType": "author", "firstName": "N.M.", "lastName": "Scott" }, { "creatorType": "author", "firstName": "S.M.", "lastName": "Gibbons" }, { "creatorType": "author", "firstName": "P.", "lastName": "Larsen" }, { "creatorType": "author", "firstName": "B.D.", "lastName": "Shogan" }, { "creatorType": "author", "firstName": "S.", "lastName": "Weiss" }, { "creatorType": "author", "firstName": "et", "lastName": "Al" }, { "creatorType": "author", "firstName": "H.", "lastName": "Li" }, { "creatorType": "author", "firstName": "A.", "lastName": "Liaw" }, { "creatorType": "author", "firstName": "M.", "lastName": "Wiener" }, { "creatorType": "author", "firstName": "T.D.", "lastName": "Lieberman" }, { "creatorType": "author", "firstName": "K.B.", "lastName": "Flett" }, { "creatorType": "author", "firstName": "I.", "lastName": "Yelin" }, { "creatorType": "author", "firstName": "T.R.", "lastName": "Martin" }, { "creatorType": "author", "firstName": "A.J.", "lastName": "McAdam" }, { "creatorType": "author", "firstName": "G.P.", "lastName": "Priebe" }, { "creatorType": "author", "firstName": "R.", "lastName": "Kishony" }, { "creatorType": "author", "firstName": "J.", "lastName": "Liu" }, { "creatorType": "author", "firstName": "R.", "lastName": "Yan" }, { "creatorType": "author", "firstName": "Q.", "lastName": "Zhong" }, { "creatorType": "author", "firstName": "S.", "lastName": "Ngo" }, { "creatorType": "author", "firstName": "N.J.", "lastName": "Bangayan" }, { "creatorType": "author", "firstName": "L.", "lastName": "Nguyen" }, { "creatorType": "author", "firstName": "T.", "lastName": "Lui" }, { "creatorType": "author", "firstName": "M.", "lastName": "Liu" }, { "creatorType": "author", "firstName": "M.C.", "lastName": "Erfe" }, { "creatorType": "author", "firstName": "N.", "lastName": "Craft" }, { "creatorType": "author", "firstName": "et", "lastName": "Al" }, { "creatorType": "author", "firstName": "Z.S.", "lastName": "Ma" }, { "creatorType": "author", "firstName": "A.", "lastName": "McKenna" }, { "creatorType": "author", "firstName": "M.", "lastName": "Hanna" }, { "creatorType": "author", "firstName": "E.", "lastName": "Banks" }, { "creatorType": "author", "firstName": "A.", "lastName": "Sivachenko" }, { "creatorType": "author", "firstName": "K.", "lastName": "Cibulskis" }, { "creatorType": "author", "firstName": "A.", "lastName": "Kernytsky" }, { "creatorType": "author", "firstName": "K.", "lastName": "Garimella" }, { "creatorType": "author", "firstName": "D.", "lastName": "Altshuler" }, { "creatorType": "author", "firstName": "S.", "lastName": "Gabriel" }, { "creatorType": "author", "firstName": "M.", "lastName": "Daly" }, { "creatorType": "author", "firstName": "M.A.", "lastName": "DePristo" }, { "creatorType": "author", "firstName": "S.", "lastName": "Naik" }, { "creatorType": "author", "firstName": "N.", "lastName": "Bouladoux" }, { "creatorType": "author", "firstName": "C.", "lastName": "Wilhelm" }, { "creatorType": "author", "firstName": "M.J.", "lastName": "Molloy" }, { "creatorType": "author", "firstName": "R.", "lastName": "Salcedo" }, { "creatorType": "author", "firstName": "W.", "lastName": "Kastenmuller" }, { "creatorType": "author", "firstName": "C.", "lastName": "Deming" }, { "creatorType": "author", "firstName": "M.", "lastName": "Quinones" }, { "creatorType": "author", "firstName": "L.", "lastName": "Koo" }, { "creatorType": "author", "firstName": "S.", "lastName": "Conlan" }, { "creatorType": "author", "firstName": "et", "lastName": "Al" }, { "creatorType": "author", "firstName": "J.", "lastName": "Oh" }, { "creatorType": "author", "firstName": "A.F.", "lastName": "Freeman" }, { "creatorType": "author", "firstName": "M.", "lastName": "Park" }, { "creatorType": "author", "firstName": "R.", "lastName": "Sokolic" }, { "creatorType": "author", "firstName": "F.", "lastName": "Candotti" }, { "creatorType": "author", "firstName": "S.M.", "lastName": "Holland" }, { "creatorType": "author", "firstName": "J.A.", "lastName": "Segre" }, { "creatorType": "author", "firstName": "H.H.", "lastName": "Kong" }, { "creatorType": "author", "firstName": "NISC Comparative Sequencing", "lastName": "Program" }, { "creatorType": "author", "firstName": "J.", "lastName": "Oh" }, { "creatorType": "author", "firstName": "A.L.", "lastName": "Byrd" }, { "creatorType": "author", "firstName": "C.", "lastName": "Deming" }, { "creatorType": "author", "firstName": "S.", "lastName": "Conlan" }, { "creatorType": "author", "firstName": "H.H.", "lastName": "Kong" }, { "creatorType": "author", "firstName": "J.A.", "lastName": "Segre" }, { "creatorType": "author", "firstName": "NISC Comparative Sequencing", "lastName": "Program" }, { "creatorType": "author", "firstName": "A.Y.", "lastName": "Peleg" }, { "creatorType": "author", "firstName": "D.A.", "lastName": "Hogan" }, { "creatorType": "author", "firstName": "E.", "lastName": "Mylonakis" }, { "creatorType": "author", "firstName": "T.C.", "lastName": "Scharschmidt" }, { "creatorType": "author", "firstName": "M.A.", "lastName": "Fischbach" }, { "creatorType": "author", "firstName": "S.", "lastName": "Schloissnig" }, { "creatorType": "author", "firstName": "M.", "lastName": "Arumugam" }, { "creatorType": "author", "firstName": "S.", "lastName": "Sunagawa" }, { "creatorType": "author", "firstName": "M.", "lastName": "Mitreva" }, { "creatorType": "author", "firstName": "J.", "lastName": "Tap" }, { "creatorType": "author", "firstName": "A.", "lastName": "Zhu" }, { "creatorType": "author", "firstName": "A.", "lastName": "Waller" }, { "creatorType": "author", "firstName": "D.R.", "lastName": "Mende" }, { "creatorType": "author", "firstName": "J.R.", "lastName": "Kultima" }, { "creatorType": "author", "firstName": "J.", "lastName": "Martin" }, { "creatorType": "author", "firstName": "et", "lastName": "Al" }, { "creatorType": "author", "firstName": "S.", "lastName": "Tomida" }, { "creatorType": "author", "firstName": "L.", "lastName": "Nguyen" }, { "creatorType": "author", "firstName": "B.H.", "lastName": "Chiu" }, { "creatorType": "author", "firstName": "J.", "lastName": "Liu" }, { "creatorType": "author", "firstName": "E.", "lastName": "Sodergren" }, { "creatorType": "author", "firstName": "G.M.", "lastName": "Weinstock" }, { "creatorType": "author", "firstName": "H.", "lastName": "Li" }, { "creatorType": "author", "firstName": "J.C.", "lastName": "Yue" }, { "creatorType": "author", "firstName": "M.K.", "lastName": "Clayton" }, { "creatorType": "author", "firstName": "A.", "lastName": "Zhu" }, { "creatorType": "author", "firstName": "S.", "lastName": "Sunagawa" }, { "creatorType": "author", "firstName": "D.R.", "lastName": "Mende" }, { "creatorType": "author", "firstName": "P.", "lastName": "Bork" } ], "abstractNote": "Biogeography and individuality shape the structural and functional composition of the human skin microbiome. To explore these factors' contribution to skin microbial community stability, we generated metagenomic sequence data from longitudinal samples collected over months and years. Analyzing these samples using a multi-kingdom, reference-based approach, we found that despite the skin's exposure to the external environment, its bacterial, fungal, and viral communities were largely stable over time. Site, individuality, and phylogeny were all determinants of stability. Foot sites exhibited the most variability; individuals differed in stability; and transience was a particular characteristic of eukaryotic viruses, which showed little site-specificity in colonization. Strain and single-nucleotide variant-level analysis showed that individuals maintain, rather than reacquire, prevalent microbes from the environment. Longitudinal stability of skin microbial communities generates hypotheses about colonization resistance and empowers clinical studies exploring alterations observed in disease states.", "publicationTitle": "Cell", "publisher": "", "place": "", "date": "May 2016", "volume": "165", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "854–66", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1016/j.cell.2016.04.008", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/27153496 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4860256", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1097-4172", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "PMID: 27153496", "tags": [], "collections": [ "SDVF8A4M" ], "relations": { "owl:sameAs": "http://zotero.org/groups/713267/items/DFR3SMUG" }, "dateAdded": "2016-10-09T22:00:35Z", "dateModified": "2016-10-09T22:00:35Z" } }, { "key": "KXTKBSN3", "version": 19, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/KXTKBSN3", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/KXTKBSN3", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1079081, "username": "hewilson86", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/hewilson86", "type": "text/html" } } }, "creatorSummary": "Rinke et al.", "parsedDate": "2016-09-22", "numChildren": 0 }, "data": { "key": "KXTKBSN3", "version": 19, "itemType": "journalArticle", "title": "Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics", "creators": [ { "creatorType": "author", "firstName": "Christian", "lastName": "Rinke" }, { "creatorType": "author", "firstName": "Serene", "lastName": "Low" }, { "creatorType": "author", "firstName": "Ben J.", "lastName": "Woodcroft" }, { "creatorType": "author", "firstName": "Jean-Baptiste", "lastName": "Raina" }, { "creatorType": "author", "firstName": "Adam", "lastName": "Skarshewski" }, { "creatorType": "author", "firstName": "Xuyen H.", "lastName": "Le" }, { "creatorType": "author", "firstName": "Margaret K.", "lastName": "Butler" }, { "creatorType": "author", "firstName": "Roman", "lastName": "Stocker" }, { "creatorType": "author", "firstName": "Justin", "lastName": "Seymour" }, { "creatorType": "author", "firstName": "Gene W.", "lastName": "Tyson" }, { "creatorType": "author", "firstName": "Philip", "lastName": "Hugenholtz" } ], "abstractNote": "", "publicationTitle": "PeerJ", "publisher": "", "place": "", "date": "2016-09-22", "volume": "4", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "e2486", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.7717/peerj.2486", "citationKey": "", "url": "https://peerj.com/articles/2486", "accessDate": "2016-10-05T18:12:06Z", "PMID": "", "PMCID": "", "ISSN": "2167-8359", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "QXMQHQ98" ], "relations": {}, "dateAdded": "2016-10-05T18:44:26Z", "dateModified": "2016-10-05T18:44:26Z" } }, { "key": "M7QNXTU6", "version": 20, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/M7QNXTU6", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/M7QNXTU6", "type": "text/html" } }, "meta": { "createdByUser": { "id": 3386681, "username": "abateman9162", "name": "Ashley Bateman", "links": { "alternate": { "href": "https://www.zotero.org/abateman9162", "type": "text/html" } } }, "creatorSummary": "Tridico et al.", "parsedDate": "2014-01", "numChildren": 0 }, "data": { "key": "M7QNXTU6", "version": 20, "itemType": "journalArticle", "title": "Metagenomic analyses of bacteria on human hairs: a qualitative assessment for applications in forensic science.", "creators": [ { "creatorType": "author", "firstName": "Silvana R", "lastName": "Tridico" }, { "creatorType": "author", "firstName": "Dáithí C", "lastName": "Murray" }, { "creatorType": "author", "firstName": "Jayne", "lastName": "Addison" }, { "creatorType": "author", "firstName": "Kenneth P", "lastName": "Kirkbride" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Bunce" } ], "abstractNote": "BACKGROUND: Mammalian hairs are one of the most ubiquitous types of trace evidence collected in the course of forensic investigations. However, hairs that are naturally shed or that lack roots are problematic substrates for DNA profiling; these hair types often contain insufficient nuclear DNA to yield short tandem repeat (STR) profiles. Whilst there have been a number of initial investigations evaluating the value of metagenomics analyses for forensic applications (e.g. examination of computer keyboards), there have been no metagenomic evaluations of human hairs-a substrate commonly encountered during forensic practice. This present study attempts to address this forensic capability gap, by conducting a qualitative assessment into the applicability of metagenomic analyses of human scalp and pubic hair. RESULTS: Forty-two DNA extracts obtained from human scalp and pubic hairs generated a total of 79,766 reads, yielding 39,814 reads post control and abundance filtering. The results revealed the presence of unique combinations of microbial taxa that can enable discrimination between individuals and signature taxa indigenous to female pubic hairs. Microbial data from a single co-habiting couple added an extra dimension to the study by suggesting that metagenomic analyses might be of evidentiary value in sexual assault cases when other associative evidence is not present. CONCLUSIONS: Of all the data generated in this study, the next-generation sequencing (NGS) data generated from pubic hair held the most potential for forensic applications. Metagenomic analyses of human hairs may provide independent data to augment other forensic results and possibly provide association between victims of sexual assault and offender when other associative evidence is absent. Based on results garnered in the present study, we believe that with further development, bacterial profiling of hair will become a valuable addition to the forensic toolkit.", "publicationTitle": "Investigative genetics", "publisher": "", "place": "", "date": "January 2014", "volume": "5", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "16", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1186/s13323-014-0016-5", "citationKey": "", "url": "http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4266914&tool=pmcentrez&rendertype=abstract", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "2041-2223", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "PMID: 25516795", "tags": [], "collections": [ "SDVF8A4M" ], "relations": {}, "dateAdded": "2016-10-04T17:18:26Z", "dateModified": "2016-10-04T17:18:26Z" } }, { "key": "8QK7T8ZC", "version": 20, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/8QK7T8ZC", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/8QK7T8ZC", "type": "text/html" } }, "meta": { "createdByUser": { "id": 3386681, "username": "abateman9162", "name": "Ashley Bateman", "links": { "alternate": { "href": "https://www.zotero.org/abateman9162", "type": "text/html" } } }, "creatorSummary": "Nayfach and Pollard", "parsedDate": "2016", "numChildren": 0 }, "data": { "key": "8QK7T8ZC", "version": 20, "itemType": "journalArticle", "title": "Toward Accurate and Quantitative Comparative Metagenomics", "creators": [ { "creatorType": "author", "firstName": "Stephen", "lastName": "Nayfach" }, { "creatorType": "author", "firstName": "Katherine S.", "lastName": "Pollard" } ], "abstractNote": "Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized.", "publicationTitle": "Cell", "publisher": "", "place": "", "date": "2016", "volume": "166", "issue": "5", "section": "", "partNumber": "", "partTitle": "", "pages": "1103–1116", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1016/j.cell.2016.08.007", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "00928674", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "QXMQHQ98" ], "relations": {}, "dateAdded": "2016-10-04T17:18:19Z", "dateModified": "2016-10-04T17:18:19Z" } }, { "key": "73W3EPAZ", "version": 20, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/73W3EPAZ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/73W3EPAZ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 3386681, "username": "abateman9162", "name": "Ashley Bateman", "links": { "alternate": { "href": "https://www.zotero.org/abateman9162", "type": "text/html" } } }, "creatorSummary": "Mathieu et al.", "parsedDate": "2013-06", "numChildren": 0 }, "data": { "key": "73W3EPAZ", "version": 20, "itemType": "journalArticle", "title": "Life on Human Surfaces: Skin Metagenomics", "creators": [ { "creatorType": "author", "firstName": "Alban", "lastName": "Mathieu" }, { "creatorType": "author", "firstName": "Tom O.", "lastName": "Delmont" }, { "creatorType": "author", "firstName": "Timothy M.", "lastName": "Vogel" }, { "creatorType": "author", "firstName": "Patrick", "lastName": "Robe" }, { "creatorType": "author", "firstName": "Renaud", "lastName": "Nalin" }, { "creatorType": "author", "firstName": "Pascal", "lastName": "Simonet" }, { "creatorType": "editor", "firstName": "Stefan", "lastName": "Bereswill" } ], "abstractNote": "", "publicationTitle": "PLoS ONE", "publisher": "", "place": "", "date": "June 2013", "volume": "8", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "e65288", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1371/journal.pone.0065288", "citationKey": "", "url": "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065288", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1932-6203", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "SDVF8A4M" ], "relations": {}, "dateAdded": "2016-10-04T17:18:16Z", "dateModified": "2016-10-04T17:18:16Z" } }, { "key": "FDQZGAD6", "version": 20, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/FDQZGAD6", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/FDQZGAD6", "type": "text/html" } }, "meta": { "createdByUser": { "id": 3386681, "username": "abateman9162", "name": "Ashley Bateman", "links": { "alternate": { "href": "https://www.zotero.org/abateman9162", "type": "text/html" } } }, "creatorSummary": "Grice", "parsedDate": "2015-10", "numChildren": 0 }, "data": { "key": "FDQZGAD6", "version": 20, "itemType": "journalArticle", "title": "The intersection of microbiome and host at the skin interface: genomic- and metagenomic-based insights", "creators": [ { "creatorType": "author", "firstName": "Elizabeth A.", "lastName": "Grice" } ], "abstractNote": "", "publicationTitle": "Genome Research", "publisher": "", "place": "", "date": "October 2015", "volume": "25", "issue": "10", "section": "", "partNumber": "", "partTitle": "", "pages": "1514–1520", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1101/gr.191320.115", "citationKey": "", "url": "http://genome.cshlp.org/lookup/doi/10.1101/gr.191320.115", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1088-9051", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "SDVF8A4M" ], "relations": {}, "dateAdded": "2016-10-04T17:18:14Z", "dateModified": "2016-10-04T17:18:14Z" } }, { "key": "EXRP9N3E", "version": 20, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/EXRP9N3E", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/EXRP9N3E", "type": "text/html" } }, "meta": { "createdByUser": { "id": 3386681, "username": "abateman9162", "name": "Ashley Bateman", "links": { "alternate": { "href": "https://www.zotero.org/abateman9162", "type": "text/html" } } }, "creatorSummary": "Franzosa et al.", "parsedDate": "2015-05", "numChildren": 0 }, "data": { "key": "EXRP9N3E", "version": 20, "itemType": "journalArticle", "title": "Identifying personal microbiomes using metagenomic codes", "creators": [ { "creatorType": "author", "firstName": "Eric A.", "lastName": "Franzosa" }, { "creatorType": "author", "firstName": "Katherine", "lastName": "Huang" }, { "creatorType": "author", "firstName": "James F.", "lastName": "Meadow" }, { "creatorType": "author", "firstName": "Dirk", "lastName": "Gevers" }, { "creatorType": "author", "firstName": "Katherine P.", "lastName": "Lemon" }, { "creatorType": "author", "firstName": "Brendan J. M.", "lastName": "Bohannan" }, { "creatorType": "author", "firstName": "Curtis", "lastName": "Huttenhower" } ], "abstractNote": "Community composition within the human microbiome varies across individuals, but it remains unknown if this variation is sufficient to uniquely identify individuals within large populations or stable enough to identify them over time. We investigated this by developing a hitting set-based coding algorithm and applying it to the Human Microbiome Project population. Our approach defined body site-specific metagenomic codes: sets of microbial taxa or genes prioritized to uniquely and stably identify individuals. Codes capturing strain variation in clade-specific marker genes were able to distinguish among 100s of individuals at an initial sampling time point. In comparisons with follow-up samples collected 30-300 d later, ∼30% of individuals could still be uniquely pinpointed using metagenomic codes from a typical body site; coincidental (false positive) matches were rare. Codes based on the gut microbiome were exceptionally stable and pinpointed \\textgreater80% of individuals. The failure of a code to match its owner at a later time point was largely explained by the loss of specific microbial strains (at current limits of detection) and was only weakly associated with the length of the sampling interval. In addition to highlighting patterns of temporal variation in the ecology of the human microbiome, this work demonstrates the feasibility of microbiome-based identifiability-a result with important ethical implications for microbiome study design. The datasets and code used in this work are available for download from huttenhower.sph.harvard.edu/idability.", "publicationTitle": "Proceedings of the National Academy of Sciences", "publisher": "", "place": "", "date": "May 2015", "volume": "112", "issue": "22", "section": "", "partNumber": "", "partTitle": "", "pages": "201423854", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1073/pnas.1423854112", "citationKey": "", "url": "http://www.pnas.org/content/112/22/E2930.abstract", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0027-8424", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "PMID: 25964341", "tags": [], "collections": [ "QXMQHQ98" ], "relations": {}, "dateAdded": "2016-10-04T17:18:09Z", "dateModified": "2016-10-04T17:18:09Z" } }, { "key": "KW3W9UP3", "version": 20, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/KW3W9UP3", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/KW3W9UP3", "type": "text/html" } }, "meta": { "createdByUser": { "id": 3386681, "username": "abateman9162", "name": "Ashley Bateman", "links": { "alternate": { "href": "https://www.zotero.org/abateman9162", "type": "text/html" } } }, "creatorSummary": "Fitz-Gibbon et al.", "parsedDate": "2013", "numChildren": 0 }, "data": { "key": "KW3W9UP3", "version": 20, "itemType": "journalArticle", "title": "Propionibacterium Acnes Strain Populations in the Human Skin Microbiome Associated with Acne", "creators": [ { "creatorType": "author", "firstName": "S", "lastName": "Fitz-Gibbon" }, { "creatorType": "author", "firstName": "S", "lastName": "Tomida" }, { "creatorType": "author", "firstName": "BH", "lastName": "Chiu" } ], "abstractNote": "", "publicationTitle": "Journal of Investigative \\ldots", "publisher": "", "place": "", "date": "2013", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1038/jid.2013.21.This", "citationKey": "", "url": "http://www.nature.com/jid/journal/vaop/naam/abs/jid201321a.html", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "SDVF8A4M" ], "relations": {}, "dateAdded": "2016-10-04T17:18:01Z", "dateModified": "2016-10-04T17:18:01Z" } }, { "key": "NMFDRAII", "version": 20, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/NMFDRAII", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/NMFDRAII", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/719545/items/I23VD67F", "type": "application/json" } }, "meta": { "createdByUser": { "id": 3386681, "username": "abateman9162", "name": "Ashley Bateman", "links": { "alternate": { "href": "https://www.zotero.org/abateman9162", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "NMFDRAII", "version": 20, "parentItem": "I23VD67F", "itemType": "note", "note": "

Ashkaan disagrees with a lot of points in this paper. Good for lab discussion sometime?

", "tags": [], "relations": {}, "dateAdded": "2016-10-04T17:17:55Z", "dateModified": "2016-10-04T17:17:55Z" } }, { "key": "I23VD67F", "version": 20, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/I23VD67F", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/I23VD67F", "type": "text/html" } }, "meta": { "createdByUser": { "id": 3386681, "username": "abateman9162", "name": "Ashley Bateman", "links": { "alternate": { "href": "https://www.zotero.org/abateman9162", "type": "text/html" } } }, "creatorSummary": "Faust et al.", "parsedDate": "2015-06", "numChildren": 1 }, "data": { "key": "I23VD67F", "version": 20, "itemType": "journalArticle", "title": "Metagenomics meets time series analysis: unraveling microbial community dynamics", "creators": [ { "creatorType": "author", "firstName": "Karoline", "lastName": "Faust" }, { "creatorType": "author", "firstName": "Leo", "lastName": "Lahti" }, { "creatorType": "author", "firstName": "Didier", "lastName": "Gonze" }, { "creatorType": "author", "firstName": "Willem M", "lastName": "de Vos" }, { "creatorType": "author", "firstName": "Jeroen", "lastName": "Raes" } ], "abstractNote": "The recent increase in the number of microbial time series studies offers new insights into the stability and dynamics of microbial communities, from the world's oceans to human microbiota. Dedicated time series analysis tools allow taking full advantage of these data. Such tools can reveal periodic patterns, help to build predictive models or, on the contrary, quantify irregularities that make community behavior unpredictable. Microbial communities can change abruptly in response to small perturbations, linked to changing conditions or the presence of multiple stable states. With sufficient samples or time points, such alternative states can be detected. In addition, temporal variation of microbial interactions can be captured with time-varying networks. Here, we apply these techniques on multiple longitudinal datasets to illustrate their potential for microbiome research.", "publicationTitle": "Current Opinion in Microbiology", "publisher": "", "place": "", "date": "June 2015", "volume": "25", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "56–66", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1016/j.mib.2015.04.004", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/pii/S1369527415000478", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "13695274", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "QXMQHQ98" ], "relations": {}, "dateAdded": "2016-10-04T17:17:55Z", "dateModified": "2016-10-04T17:17:55Z" } }, { "key": "ER3WZX4J", "version": 18, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/ER3WZX4J", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/ER3WZX4J", "type": "text/html" } }, "meta": { "createdByUser": { "id": 3386681, "username": "abateman9162", "name": "Ashley Bateman", "links": { "alternate": { "href": "https://www.zotero.org/abateman9162", "type": "text/html" } } }, "creatorSummary": "Darling et al.", "parsedDate": "2014-01", "numChildren": 0 }, "data": { "key": "ER3WZX4J", "version": 18, "itemType": "journalArticle", "title": "PhyloSift: phylogenetic analysis of genomes and metagenomes", "creators": [ { "creatorType": "author", "firstName": "Aaron E.", "lastName": "Darling" }, { "creatorType": "author", "firstName": "Guillaume", "lastName": "Jospin" }, { "creatorType": "author", "firstName": "Eric", "lastName": "Lowe" }, { "creatorType": "author", "firstName": "Frederick a.", "lastName": "Matsen" }, { "creatorType": "author", "firstName": "Holly M.", "lastName": "Bik" }, { "creatorType": "author", "firstName": "Jonathan a.", "lastName": "Eisen" } ], "abstractNote": "", "publicationTitle": "PeerJ", "publisher": "", "place": "", "date": "January 2014", "volume": "2", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "e243", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.7717/peerj.243", "citationKey": "", "url": "https://peerj.com/articles/243", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "2167-8359", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "accepted 19 december 2013" }, { "tag": "bayes factor" }, { "tag": "community" }, { "tag": "forensics" }, { "tag": "metagenomics" }, { "tag": "microbial diversity" }, { "tag": "phylogenetics" }, { "tag": "published 9 january 2014" }, { "tag": "submitted 21 march 2013" } ], "collections": [ "QXMQHQ98" ], "relations": {}, "dateAdded": "2016-10-04T17:10:52Z", "dateModified": "2016-10-04T17:10:52Z" } }, { "key": "JK8J2PUB", "version": 18, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/JK8J2PUB", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/JK8J2PUB", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1079081, "username": "hewilson86", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/hewilson86", "type": "text/html" } } }, "creatorSummary": "Bowers et al.", "parsedDate": "2015", "numChildren": 1 }, "data": { "key": "JK8J2PUB", "version": 18, "itemType": "journalArticle", "title": "Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community", "creators": [ { "creatorType": "author", "firstName": "Robert M.", "lastName": "Bowers" }, { "creatorType": "author", "firstName": "Alicia", "lastName": "Clum" }, { "creatorType": "author", "firstName": "Hope", "lastName": "Tice" }, { "creatorType": "author", "firstName": "Joanne", "lastName": "Lim" }, { "creatorType": "author", "firstName": "Kanwar", "lastName": "Singh" }, { "creatorType": "author", "firstName": "Doina", "lastName": "Ciobanu" }, { "creatorType": "author", "firstName": "Chew Yee", "lastName": "Ngan" }, { "creatorType": "author", "firstName": "Jan-Fang", "lastName": "Cheng" }, { "creatorType": "author", "firstName": "Susannah G.", "lastName": "Tringe" }, { "creatorType": "author", "firstName": "Tanja", "lastName": "Woyke" } ], "abstractNote": "The rapid development of sequencing technologies has provided access to environments that were either once thought inhospitable to life altogether or that contain too few cells to be analyzed using genomics approaches. While 16S rRNA gene microbial community sequencing has revolutionized our understanding of community composition and diversity over time and space, it only provides a crude estimate of microbial functional and metabolic potential. Alternatively, shotgun metagenomics allows comprehensive sampling of all genetic material in an environment, without any underlying primer biases. Until recently, one of the major bottlenecks of shotgun metagenomics has been the requirement for large initial DNA template quantities during library preparation.", "publicationTitle": "BMC Genomics", "publisher": "", "place": "", "date": "2015", "volume": "16", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "856", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "BMC Genomics", "DOI": "10.1186/s12864-015-2063-6", "citationKey": "", "url": "http://dx.doi.org/10.1186/s12864-015-2063-6", "accessDate": "2016-10-03T19:55:26Z", "PMID": "", "PMCID": "", "ISSN": "1471-2164", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "BioMed Central", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Library preparation protocol", "type": 1 }, { "tag": "Low biomass", "type": 1 }, { "tag": "Low input", "type": 1 }, { "tag": "Metagenome", "type": 1 }, { "tag": "Microbiome", "type": 1 } ], "collections": [ "QXMQHQ98", "SDVF8A4M" ], "relations": {}, "dateAdded": "2016-10-03T19:55:43Z", "dateModified": "2016-10-03T19:55:43Z" } }, { "key": "JN26Q4R3", "version": 15, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/JN26Q4R3", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/JN26Q4R3", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/719545/items/JK8J2PUB", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1079081, "username": "hewilson86", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/hewilson86", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "JN26Q4R3", "version": 15, "parentItem": "JK8J2PUB", "itemType": "note", "note": "Pages 1-12 in PDF", "tags": [], "relations": {}, "dateAdded": "2016-10-03T19:55:43Z", "dateModified": "2016-10-03T19:55:43Z" } }, { "key": "7B34RVKP", "version": 11, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/7B34RVKP", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/7B34RVKP", "type": "text/html" } }, "meta": { "createdByUser": { "id": 3386681, "username": "abateman9162", "name": "Ashley Bateman", "links": { "alternate": { "href": "https://www.zotero.org/abateman9162", "type": "text/html" } } }, "creatorSummary": "Zolfo et al.", "parsedDate": "2016-09", "numChildren": 0 }, "data": { "key": "7B34RVKP", "version": 11, "itemType": "journalArticle", "title": "MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples.", "creators": [ { "creatorType": "author", "firstName": "Moreno", "lastName": "Zolfo" }, { "creatorType": "author", "firstName": "Adrian", "lastName": "Tett" }, { "creatorType": "author", "firstName": "Olivier", "lastName": "Jousson" }, { "creatorType": "author", "firstName": "Claudio", "lastName": "Donati" }, { "creatorType": "author", "firstName": "Nicola", "lastName": "Segata" } ], "abstractNote": "Metagenomic characterization of microbial communities has the potential to become a tool to identify pathogens in human samples. However, software tools able to extract strain-level typing information from metagenomic data are needed. Low-throughput molecular typing schema such as Multilocus Sequence Typing (MLST) are still widely used and provide a wealth of strain-level information that is currently not exploited by metagenomic methods. We introduce MetaMLST, a software tool that reconstructs the MLST loci of microorganisms present in microbial communities from metagenomic data. Tested on synthetic and spiked-in real metagenomes, the pipeline was able to reconstruct the MLST sequences with \\textgreater98.5% accuracy at coverages as low as 1×. On real samples, the pipeline showed higher sensitivity than assembly-based approaches and it proved successful in identifying strains in epidemic outbreaks as well as in intestinal, skin and gastrointestinal microbiome samples.", "publicationTitle": "Nucleic acids research", "publisher": "", "place": "", "date": "September 2016", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "gkw837", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1093/nar/gkw837", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/27651451", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1362-4962", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "PMID: 27651451", "tags": [], "collections": [ "SDVF8A4M" ], "relations": {}, "dateAdded": "2016-09-29T03:36:01Z", "dateModified": "2016-09-29T03:36:01Z" } }, { "key": "J325RMP8", "version": 18, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/J325RMP8", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/J325RMP8", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1079081, "username": "hewilson86", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/hewilson86", "type": "text/html" } } }, "creatorSummary": "Burke and Darling", "parsedDate": "2016-09-20", "numChildren": 0 }, "data": { "key": "J325RMP8", "version": 18, "itemType": "journalArticle", "title": "A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq", "creators": [ { "creatorType": "author", "firstName": "Catherine M.", "lastName": "Burke" }, { "creatorType": "author", "firstName": "Aaron E.", "lastName": "Darling" } ], "abstractNote": "", "publicationTitle": "PeerJ", "publisher": "", "place": "", "date": "2016-09-20", "volume": "4", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "e2492", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.7717/peerj.2492", "citationKey": "", "url": "https://peerj.com/articles/2492", "accessDate": "2016-09-28T17:53:53Z", "PMID": "", "PMCID": "", "ISSN": "2167-8359", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "QXMQHQ98", "SDVF8A4M" ], "relations": {}, "dateAdded": "2016-09-28T17:54:22Z", "dateModified": "2016-09-28T17:54:22Z" } }, { "key": "PUNKB4GP", "version": 9, "library": { "type": "group", "id": 719545, "name": "MetagenomicsBIOBE", "links": { "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/719545/items/PUNKB4GP", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/metagenomicsbiobe/items/PUNKB4GP", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/719545/items/E54WMPI8", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1079081, "username": "hewilson86", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/hewilson86", "type": "text/html" } } } }, "data": { "key": "PUNKB4GP", "version": 9, "parentItem": "E54WMPI8", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed Central Link", "accessDate": "2016-09-27T21:46:14Z", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518434/", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2016-09-27T21:46:14Z", "dateModified": "2016-09-27T21:46:14Z" } } ]