[ { "key": "E6XRIBZS", "version": 8, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/E6XRIBZS", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/E6XRIBZS", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/268269/items/CTGHN45C", "type": "application/json" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } } }, "data": { "key": "E6XRIBZS", "version": 8, "parentItem": "CTGHN45C", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2019-08-20T21:37:47Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/30746447", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2019-08-20T21:37:47Z", "dateModified": "2019-08-20T21:37:47Z" } }, { "key": "CTGHN45C", "version": 8, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/CTGHN45C", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/CTGHN45C", "type": "text/html" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } }, "creatorSummary": "Dominy et al.", "parsedDate": "2019-01", "numChildren": 1 }, "data": { "key": "CTGHN45C", "version": 8, "itemType": "journalArticle", "title": "Porphyromonas gingivalis in Alzheimer's disease brains: Evidence for disease causation and treatment with small-molecule inhibitors", "creators": [ { "creatorType": "author", "firstName": "Stephen S.", "lastName": "Dominy" }, { "creatorType": "author", "firstName": "Casey", "lastName": "Lynch" }, { "creatorType": "author", "firstName": "Florian", "lastName": "Ermini" }, { "creatorType": "author", "firstName": "Malgorzata", "lastName": "Benedyk" }, { "creatorType": "author", "firstName": "Agata", "lastName": "Marczyk" }, { "creatorType": "author", "firstName": "Andrei", "lastName": "Konradi" }, { "creatorType": "author", "firstName": "Mai", "lastName": "Nguyen" }, { "creatorType": "author", "firstName": "Ursula", "lastName": "Haditsch" }, { "creatorType": "author", "firstName": "Debasish", "lastName": "Raha" }, { "creatorType": "author", "firstName": "Christina", "lastName": "Griffin" }, { "creatorType": "author", "firstName": "Leslie J.", "lastName": "Holsinger" }, { "creatorType": "author", "firstName": "Shirin", "lastName": "Arastu-Kapur" }, { "creatorType": "author", "firstName": "Samer", "lastName": "Kaba" }, { "creatorType": "author", "firstName": "Alexander", "lastName": "Lee" }, { "creatorType": "author", "firstName": "Mark I.", "lastName": "Ryder" }, { "creatorType": "author", "firstName": "Barbara", "lastName": "Potempa" }, { "creatorType": "author", "firstName": "Piotr", "lastName": "Mydel" }, { "creatorType": "author", "firstName": "Annelie", "lastName": "Hellvard" }, { "creatorType": "author", "firstName": "Karina", "lastName": "Adamowicz" }, { "creatorType": "author", "firstName": "Hatice", "lastName": "Hasturk" }, { "creatorType": "author", "firstName": "Glenn D.", "lastName": "Walker" }, { "creatorType": "author", "firstName": "Eric C.", "lastName": "Reynolds" }, { "creatorType": "author", "firstName": "Richard L. M.", "lastName": "Faull" }, { "creatorType": "author", "firstName": "Maurice A.", "lastName": "Curtis" }, { "creatorType": "author", "firstName": "Mike", "lastName": "Dragunow" }, { "creatorType": "author", "firstName": "Jan", "lastName": "Potempa" } ], "abstractNote": "Porphyromonas gingivalis, the keystone pathogen in chronic periodontitis, was identified in the brain of Alzheimer's disease patients. Toxic proteases from the bacterium called gingipains were also identified in the brain of Alzheimer's patients, and levels correlated with tau and ubiquitin pathology. Oral P. gingivalis infection in mice resulted in brain colonization and increased production of Aβ1-42, a component of amyloid plaques. Further, gingipains were neurotoxic in vivo and in vitro, exerting detrimental effects on tau, a protein needed for normal neuronal function. To block this neurotoxicity, we designed and synthesized small-molecule inhibitors targeting gingipains. Gingipain inhibition reduced the bacterial load of an established P. gingivalis brain infection, blocked Aβ1-42 production, reduced neuroinflammation, and rescued neurons in the hippocampus. These data suggest that gingipain inhibitors could be valuable for treating P. gingivalis brain colonization and neurodegeneration in Alzheimer's disease.", "publicationTitle": "Science Advances", "publisher": "", "place": "", "date": "Jan 2019", "volume": "5", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "eaau3333", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Sci Adv", "DOI": "10.1126/sciadv.aau3333", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "2375-2548", "archive": "", "archiveLocation": "", "shortTitle": "Porphyromonas gingivalis in Alzheimer's disease brains", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "PMID: 30746447\nPMCID: PMC6357742", "tags": [], "collections": [], "relations": {}, "dateAdded": "2019-08-20T21:37:47Z", "dateModified": "2019-08-20T21:37:47Z" } }, { "key": "BSFJC9SJ", "version": 7, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/BSFJC9SJ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/BSFJC9SJ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } }, "creatorSummary": "Sanders et al.", "parsedDate": "1990-02", "numChildren": 0 }, "data": { "key": "BSFJC9SJ", "version": 7, "itemType": "journalArticle", "title": "Determination of guanine-plus-cytosine content of bacterial DNA by dual-laser flow cytometry", "creators": [ { "creatorType": "author", "firstName": "C A", "lastName": "Sanders" }, { "creatorType": "author", "firstName": "D M", "lastName": "Yajko" }, { "creatorType": "author", "firstName": "W", "lastName": "Hyun" }, { "creatorType": "author", "firstName": "R G", "lastName": "Langlois" }, { "creatorType": "author", "firstName": "P S", "lastName": "Nassos" }, { "creatorType": "author", "firstName": "M J", "lastName": "Fulwyler" }, { "creatorType": "author", "firstName": "W K", "lastName": "Hadley" } ], "abstractNote": "A dual-laser flow cytometer was used to analyse different species of bacteria for the molar percentage of guanine-plus-cytosine (% G + C) without the need for DNA extraction or purification. Ethanol-fixed bacterial cells were stained with a combination of DNA-specific fluorochromes, Hoechst 33258 and chromomycin A3, which bind to AT- and GC-rich regions of DNA, respectively. A linear relationship (r = 0.99) was demonstrated between the log of the ratio of chromomycin A3 to Hoechst 33258 fluorescence and the log of the % G + C as determined by thermal denaturation (Tm) or buoyant density centrifugation (Bd) methods. Linearity was maintained for all bacterial species tested over the range of 28-67% G + C. A standard curve was constructed using five strains whose % G + C had been determined by other methods. From the equation describing this line, the % G + C values of nine other strains with known DNA base composition, together with the five strains used to construct the curve, were calculated using the chromomycin A3 to Hoechst 33258 ratio and were in agreement with values obtained by Tm, Bd or HPLC. The reproducibility of flow cytometric analysis (mean error 0.7% G + C) compared well with the reproducibility of other methods. Mixtures containing two species were also analysed. Two cell populations could be discerned in mixtures containing two species which differed in base composition by as little as 4% G + C.(ABSTRACT TRUNCATED AT 250 WORDS)", "publicationTitle": "Journal of general microbiology", "publisher": "", "place": "", "date": "Feb 1990", "volume": "136", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "359-365", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Gen. Microbiol.", "DOI": "", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/2324706", "accessDate": "2012-05-15T19:31:33Z", "PMID": "", "PMCID": "", "ISSN": "0022-1287", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 2324706", "tags": [ { "tag": "Cytosine", "type": 1 }, { "tag": "DNA, Bacterial", "type": 1 }, { "tag": "Flow Cytometry", "type": 1 }, { "tag": "Guanine", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2014-06-05T20:17:18Z", "dateModified": "2014-06-05T20:17:18Z" } }, { "key": "KQSNZAC9", "version": 6, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/KQSNZAC9", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/KQSNZAC9", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/268269/items/5BZ7X2N4", "type": "application/json" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } } }, "data": { "key": "KQSNZAC9", "version": 6, "parentItem": "5BZ7X2N4", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2014-06-05T19:56:17Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/11940147", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-06-05T19:56:17Z", "dateModified": "2014-06-05T19:56:17Z" } }, { "key": "5BZ7X2N4", "version": 6, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/5BZ7X2N4", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/5BZ7X2N4", "type": "text/html" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } }, "creatorSummary": "Socransky et al.", "parsedDate": "2002-03", "numChildren": 1 }, "data": { "key": "5BZ7X2N4", "version": 6, "itemType": "journalArticle", "title": "Subgingival microbial profiles in refractory periodontal disease", "creators": [ { "creatorType": "author", "firstName": "Sigmund S", "lastName": "Socransky" }, { "creatorType": "author", "firstName": "Claire", "lastName": "Smith" }, { "creatorType": "author", "firstName": "Anne D", "lastName": "Haffajee" } ], "abstractNote": "BACKGROUND/AIM: The purpose of the present investigation was to examine subgingival microbial profiles associated with refractory periodontitis and to seek such profiles in periodontally healthy, periodontally well-maintained elder and untreated periodontitis subjects.\nMETHODS: 36 subjects were defined as refractory on the basis of further attachment loss after scaling and root planing, surgery and systemically administered antibiotics. A total of 890 subgingival plaque samples (mean/subject=24.7) were taken from the mesial aspect of each tooth in each subject at baseline and individually processed for their content of 40 subgingival taxa using checkerboard DNA-DNA hybridization. Cluster analysis was performed on mean within subject species counts using the chord coefficient and an average unweighted linkage sort. Significant differences among clusters for individual and complexes of species were sought using the Kruskal Wallis test. The microbial profiles of the refractory subjects were compared with those of 27 periodontally healthy subjects (n plaque samples=708), 35 periodontally well-maintained elder subjects (n plaque samples=801) and 115 untreated adult periodontitis subjects (n plaque samples=2871).\nRESULTS: 28 of 36 refractory subjects fell into 4 clusters with >29% similarity. 10 of 40 species and 4 of 7 complexes differed significantly among clusters. Profile (Cluster) I (n=4) was characterized by high proportions of \"yellow\" and \"green\" complex species, profile II (n=3) by low total counts and high proportions of \"orange\" and \"purple\" complex species, profile III (n=9) by high total counts and counts of Actinomyces and \"purple\" complex species, profile IV (n=12) by high proportions of \"red\" and \"orange\" complex species. The mean profiles of each cluster were subjected to cluster analysis with microbial data from 4380 (mean 24.7) baseline subgingival plaque samples from 27 periodontally healthy, 35 treated, well-maintained elders and 115 untreated adult periodontitis subjects. 12 clusters were formed with >41% similarity. 3 of the refractory profiles were detected in 3 cluster groups. Profile II in a cluster of 1 healthy, 1 elder and 4 untreated periodontitis subjects; profile III in a cluster of 1 healthy, 2 elder and 12 periodontitis subjects; Profile IV, with 1 healthy and 5 untreated periodontitis subjects. The profile not detected in non refractory subjects was dominated by Streptococcus species. 9 clusters did not harbor refractory profiles. 11.1% of healthy, 8.6% of elder and 18.3% of periodontitis subjects were in clusters exhibiting refractory microbial profiles.\nCONCLUSIONS: 4 subgingival microbial profiles were detected among refractory subjects. \"Refractory microbial profiles\" could be detected in subjects who had not yet exhibited refractory disease.", "publicationTitle": "Journal of clinical periodontology", "publisher": "", "place": "", "date": "Mar 2002", "volume": "29", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "260-268", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Clin. Periodontol.", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0303-6979", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 11940147", "tags": [ { "tag": "Actinobacillus", "type": 1 }, { "tag": "Adult", "type": 1 }, { "tag": "Aged", "type": 1 }, { "tag": "Bacterial Typing Techniques", "type": 1 }, { "tag": "Bacteroides", "type": 1 }, { "tag": "Chronic Disease", "type": 1 }, { "tag": "Cluster Analysis", "type": 1 }, { "tag": "DNA, Bacterial", "type": 1 }, { "tag": "Dental Plaque", "type": 1 }, { "tag": "Female", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Male", "type": 1 }, { "tag": "Middle Aged", "type": 1 }, { "tag": "Nucleic Acid Hybridization", "type": 1 }, { "tag": "Periodontitis", "type": 1 }, { "tag": "Porphyromonas gingivalis", "type": 1 }, { "tag": "Statistics, Nonparametric", "type": 1 }, { "tag": "Streptococcus", "type": 1 }, { "tag": "Treponema", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2014-06-05T19:56:17Z", "dateModified": "2014-06-05T19:56:17Z" } }, { "key": "BMGRB6WF", "version": 5, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/BMGRB6WF", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/BMGRB6WF", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/268269/items/FQV2DVDG", "type": "application/json" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } } }, "data": { "key": "BMGRB6WF", "version": 5, "parentItem": "FQV2DVDG", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2014-06-05T19:47:28Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/23134607", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-06-05T19:47:28Z", "dateModified": "2014-06-05T19:47:28Z" } }, { "key": "FQV2DVDG", "version": 5, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/FQV2DVDG", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/FQV2DVDG", "type": "text/html" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } }, "creatorSummary": "Hajishengallis and Lamont", "parsedDate": "2012-12", "numChildren": 1 }, "data": { "key": "FQV2DVDG", "version": 5, "itemType": "journalArticle", "title": "Beyond the red complex and into more complexity: the polymicrobial synergy and dysbiosis (PSD) model of periodontal disease etiology", "creators": [ { "creatorType": "author", "firstName": "G", "lastName": "Hajishengallis" }, { "creatorType": "author", "firstName": "R J", "lastName": "Lamont" } ], "abstractNote": "Recent advancements in the periodontal research field are consistent with a new model of pathogenesis according to which periodontitis is initiated by a synergistic and dysbiotic microbial community rather than by select 'periopathogens', such as the 'red complex'. In this polymicrobial synergy, different members or specific gene combinations within the community fulfill distinct roles that converge to shape and stabilize a disease-provoking microbiota. One of the core requirements for a potentially pathogenic community to arise involves the capacity of certain species, termed 'keystone pathogens', to modulate the host response in ways that impair immune surveillance and tip the balance from homeostasis to dysbiosis. Keystone pathogens also elevate the virulence of the entire microbial community through interactive communication with accessory pathogens. Other important core functions for pathogenicity require the expression of diverse molecules (e.g. appropriate adhesins, cognate receptors, proteolytic enzymes and proinflammatory surface structures/ligands), which in combination act as community virulence factors to nutritionally sustain a heterotypic, compatible and proinflammatory microbial community that elicits a non-resolving and tissue-destructive host response. On the basis of the fundamental concepts underlying this model of periodontal pathogenesis, that is, polymicrobial synergy and dysbiosis, we term it the PSD model.", "publicationTitle": "Molecular oral microbiology", "publisher": "", "place": "", "date": "Dec 2012", "volume": "27", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "409-419", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Mol Oral Microbiol", "DOI": "10.1111/j.2041-1014.2012.00663.x", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "2041-1014", "archive": "", "archiveLocation": "", "shortTitle": "Beyond the red complex and into more complexity", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 23134607 \nPMCID: PMC3653317", "tags": [ { "tag": "Bacteria", "type": 1 }, { "tag": "Host-Pathogen Interactions", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Immune Evasion", "type": 1 }, { "tag": "Inflammation Mediators", "type": 1 }, { "tag": "Microbial Consortia", "type": 1 }, { "tag": "Periodontitis", "type": 1 }, { "tag": "Symbiosis", "type": 1 }, { "tag": "Virulence", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2014-06-05T19:47:28Z", "dateModified": "2014-06-05T19:47:28Z" } }, { "key": "FRB4WX2F", "version": 4, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/FRB4WX2F", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/FRB4WX2F", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/268269/items/MSWW8MBX", "type": "application/json" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } } }, "data": { "key": "FRB4WX2F", "version": 4, "parentItem": "MSWW8MBX", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2014-06-05T19:45:35Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/23533413", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-06-05T19:45:35Z", "dateModified": "2014-06-05T19:45:35Z" } }, { "key": "MSWW8MBX", "version": 4, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/MSWW8MBX", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/MSWW8MBX", "type": "text/html" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } }, "creatorSummary": "Suzuki et al.", "parsedDate": "2013", "numChildren": 1 }, "data": { "key": "MSWW8MBX", "version": 4, "itemType": "journalArticle", "title": "Mixed red-complex bacterial infection in periodontitis", "creators": [ { "creatorType": "author", "firstName": "N", "lastName": "Suzuki" }, { "creatorType": "author", "firstName": "M", "lastName": "Yoneda" }, { "creatorType": "author", "firstName": "T", "lastName": "Hirofuji" } ], "abstractNote": "The red complex, which includes Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia (formerly Bacteroides forsythus), are recognized as the most important pathogens in adult periodontal disease. These bacteria are usually found together in periodontal pockets, suggesting that they may cause destruction of the periodontal tissue in a cooperative manner. This article discusses the interspecies pathogenic interactions within the red complex.", "publicationTitle": "International journal of dentistry", "publisher": "", "place": "", "date": "2013", "volume": "2013", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "587279", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Int J Dent", "DOI": "10.1155/2013/587279", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1687-8728", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 23533413 \nPMCID: PMC3606728", "tags": [], "collections": [], "relations": {}, "dateAdded": "2014-06-05T19:45:35Z", "dateModified": "2014-06-05T19:45:35Z" } }, { "key": "ZZ55JU7U", "version": 3, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/ZZ55JU7U", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/ZZ55JU7U", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/268269/items/DR65IGS6", "type": "application/json" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } } }, "data": { "key": "ZZ55JU7U", "version": 3, "parentItem": "DR65IGS6", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2014-06-05T19:43:58Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/24040571", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-06-05T19:43:58Z", "dateModified": "2014-06-05T19:43:58Z" } }, { "key": "DR65IGS6", "version": 3, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/DR65IGS6", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/DR65IGS6", "type": "text/html" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } }, "creatorSummary": "Shet et al.", "parsedDate": "2013-08", "numChildren": 1 }, "data": { "key": "DR65IGS6", "version": 3, "itemType": "journalArticle", "title": "Quantitative analysis of periodontal pathogens present in the saliva of geriatric subjects", "creators": [ { "creatorType": "author", "firstName": "Uttom K", "lastName": "Shet" }, { "creatorType": "author", "firstName": "Hee-Kyun", "lastName": "Oh" }, { "creatorType": "author", "firstName": "Hye-Jeong", "lastName": "Kim" }, { "creatorType": "author", "firstName": "Hyun-Ju", "lastName": "Chung" }, { "creatorType": "author", "firstName": "Young-Joon", "lastName": "Kim" }, { "creatorType": "author", "firstName": "Ok-Su", "lastName": "Kim" }, { "creatorType": "author", "firstName": "Hong-Ran", "lastName": "Choi" }, { "creatorType": "author", "firstName": "Ok-Jun", "lastName": "Kim" }, { "creatorType": "author", "firstName": "Hoi-Jeong", "lastName": "Lim" }, { "creatorType": "author", "firstName": "Seok-Woo", "lastName": "Lee" } ], "abstractNote": "PURPOSE: At present, information regarding periodontal disease in geriatric patients is scarce. The purpose of this study was to quantify the periodontal pathogens present in the saliva of Korean geriatric patients and assess the relationship between the bacterial levels and the periodontal condition.\nMETHODS: Six putative periodontal pathogens were quantified by using a real-time polymerase chain reaction assay in geriatric patient groups (>60 years) with mild chronic periodontitis (MCP), moderate chronic periodontitis (MoCP), and severe chronic periodontitis (SCP). The copy numbers of Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum, and Prevotella intermedia were measured.\nRESULTS: It was found that the bacterial copy numbers increased as the severity of the disease increased from MCP to SCP, except for P. intermedia. For P. intermedia, it was found that samples in the MCP group yielded the largest amount. It was also found that the quantities of P. gingivalis, T. forsythia, and T. denticola, the so-called \"red complex\" bacteria, were lower than those of F. nucleatum, A. actinomycetemcomitans, and P. intermedia in all of the samples.\nCONCLUSIONS: Collectively, the results of this study suggest that the levels of P. gingivalis, T. forsythia, F. nucleatum, and T. denticola present in saliva are associated with the severity of periodontal disease in geriatric patients.", "publicationTitle": "Journal of periodontal & implant science", "publisher": "", "place": "", "date": "Aug 2013", "volume": "43", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "183-190", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J Periodontal Implant Sci", "DOI": "10.5051/jpis.2013.43.4.183", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "2093-2278", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 24040571 \nPMCID: PMC3769597", "tags": [], "collections": [], "relations": {}, "dateAdded": "2014-06-05T19:43:58Z", "dateModified": "2014-06-05T19:43:58Z" } }, { "key": "CX6VTG8G", "version": 3, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/CX6VTG8G", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/CX6VTG8G", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/268269/items/4IHJV5VQ", "type": "application/json" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } } }, "data": { "key": "CX6VTG8G", "version": 3, "parentItem": "4IHJV5VQ", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2014-06-05T19:42:38Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/24744537", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-06-05T19:42:38Z", "dateModified": "2014-06-05T19:42:38Z" } }, { "key": "4IHJV5VQ", "version": 3, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/4IHJV5VQ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/4IHJV5VQ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } }, "creatorSummary": "Arora et al.", "parsedDate": "2014", "numChildren": 1 }, "data": { "key": "4IHJV5VQ", "version": 3, "itemType": "journalArticle", "title": "Microbial role in periodontitis: Have we reached the top? Some unsung bacteria other than red complex", "creators": [ { "creatorType": "author", "firstName": "Nupur", "lastName": "Arora" }, { "creatorType": "author", "firstName": "Ashank", "lastName": "Mishra" }, { "creatorType": "author", "firstName": "Samir", "lastName": "Chugh" } ], "abstractNote": "The microbial etiology of periodontal disease has been the focus of researchers for a long time. The search for the pathogens of periodontal diseases has been underway for more than 100 years, and continues up today. Despite the increasing knowledge about oral microbiota, we are not able to implicate any one particular organism that can be considered as a candidate pathogen. In fact the term \"candidate pathogen\" has lost its steam with a myriad of microorganisms being incriminated from time to time. Most studies of the bacterial etiology of periodontitis have used either culture-based or targeted deoxyribonucleic acid approaches and so it is likely that pathogens remain undiscovered. The advent of 16S cloning and sequencing has facilitated identification of several uncultivable bacteria in the oral cavity. The concept that not one single organism, but several organisms contained in the biofilm orchestrating in a medley of the show appears to be more plausible. The present review highlights some lesser known bacteria associated with periodontal destruction.", "publicationTitle": "Journal of Indian Society of Periodontology", "publisher": "", "place": "", "date": "1 2014", "volume": "18", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "9-13", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J Indian Soc Periodontol", "DOI": "10.4103/0972-124X.128192", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0972-124X", "archive": "", "archiveLocation": "", "shortTitle": "Microbial role in periodontitis", "language": "ENG", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 24744537 \nPMCID: PMC3988654", "tags": [], "collections": [], "relations": {}, "dateAdded": "2014-06-05T19:42:38Z", "dateModified": "2014-06-05T19:42:38Z" } }, { "key": "BQJ56J4P", "version": 2, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/BQJ56J4P", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/BQJ56J4P", "type": "text/html" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } }, "creatorSummary": "Gu et al.", "parsedDate": "2005-08", "numChildren": 1 }, "data": { "key": "BQJ56J4P", "version": 2, "itemType": "journalArticle", "title": "In situ and non-invasive detection of specific bacterial species in oral biofilms using fluorescently labeled monoclonal antibodies", "creators": [ { "creatorType": "author", "firstName": "Fang", "lastName": "Gu" }, { "creatorType": "author", "firstName": "Renate", "lastName": "Lux" }, { "creatorType": "author", "firstName": "Laurence", "lastName": "Du-Thumm" }, { "creatorType": "author", "firstName": "Ivy", "lastName": "Stokes" }, { "creatorType": "author", "firstName": "Jens", "lastName": "Kreth" }, { "creatorType": "author", "firstName": "Maxwell H", "lastName": "Anderson" }, { "creatorType": "author", "firstName": "David T", "lastName": "Wong" }, { "creatorType": "author", "firstName": "Lawrence", "lastName": "Wolinsky" }, { "creatorType": "author", "firstName": "Richard", "lastName": "Sullivan" }, { "creatorType": "author", "firstName": "Wenyuan", "lastName": "Shi" } ], "abstractNote": "Noninvasive in situ detection of suspected cariogenic bacterial species within dental biofilms could facilitate monitoring of the dynamic change of oral microbial flora and assist in the assessment of the treatment efficacy of therapeutic agents. In this study, we explore the possibility to use three well-characterized monoclonal antibodies (MAbs) against Streptococcus mutans, Actinomyces naeslundii, and Lactobacillus casei to identify these three important members of the oral microbial community in the complex environment of oral biofilms. These MAbs, which were conjugated to different fluorescent labels and visualized with confocal laser scanning microscopy (CLSM), proved to be an useful tool to identify the three species of interest (S. mutans, A. naeslundii, and L. casei) under various experimental conditions including in vitro and in vivo derived oral biofilms. Manifold addition of the MAbs on consecutive days did not alter the biofilm structure thus allowing monitoring of the same biofilm over extended time periods. Using this MAb-based method the effect of sucrose challenge on the biofilm composition and the distribution of S. mutans, A. naeslundii, and L. casei were examined. S. mutans was found to be the predominant species under the various biofilm conditions tested. These studies indicate that MAbs based bacterial detection with CLSM is a versatile tool which permits new insights into the ecology of oral biofilm development.", "publicationTitle": "Journal of microbiological methods", "publisher": "", "place": "", "date": "Aug 2005", "volume": "62", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "145-160", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Microbiol. Methods", "DOI": "10.1016/j.mimet.2005.02.013", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0167-7012", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 15935497", "tags": [ { "tag": "Actinomyces", "type": 1 }, { "tag": "Antibodies, Monoclonal", "type": 1 }, { "tag": "Antibody Specificity", "type": 1 }, { "tag": "Biofilms", "type": 1 }, { "tag": "Dental Plaque", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Lactobacillus casei", "type": 1 }, { "tag": "Microscopy, Confocal", "type": 1 }, { "tag": "Mouth", "type": 1 }, { "tag": "Saliva", "type": 1 }, { "tag": "Streptococcus mutans", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2014-06-05T19:38:08Z", "dateModified": "2014-06-05T19:38:08Z" } }, { "key": "HZR68V3I", "version": 2, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/HZR68V3I", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/HZR68V3I", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/268269/items/BQJ56J4P", "type": "application/json" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } } }, "data": { "key": "HZR68V3I", "version": 2, "parentItem": "BQJ56J4P", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2014-06-05T19:38:08Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/15935497", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-06-05T19:38:08Z", "dateModified": "2014-06-05T19:38:08Z" } }, { "key": "X82M545W", "version": 2, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/X82M545W", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/X82M545W", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/268269/items/ZAKEU6PE", "type": "application/json" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } } }, "data": { "key": "X82M545W", "version": 2, "parentItem": "ZAKEU6PE", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2014-06-05T19:37:58Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/14706749", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-06-05T19:37:58Z", "dateModified": "2014-06-05T19:37:58Z" } }, { "key": "ZAKEU6PE", "version": 2, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/ZAKEU6PE", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/ZAKEU6PE", "type": "text/html" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } }, "creatorSummary": "Thurnheer et al.", "parsedDate": "2004-01", "numChildren": 1 }, "data": { "key": "ZAKEU6PE", "version": 2, "itemType": "journalArticle", "title": "Multiplex FISH analysis of a six-species bacterial biofilm", "creators": [ { "creatorType": "author", "firstName": "T", "lastName": "Thurnheer" }, { "creatorType": "author", "firstName": "R", "lastName": "Gmür" }, { "creatorType": "author", "firstName": "B", "lastName": "Guggenheim" } ], "abstractNote": "Established procedures use different and seemingly incompatible experimental protocols for fluorescent in situ hybridization (FISH) with Gram-negative and Gram-positive bacteria. The aim of this study was to develop a procedure, based on FISH and confocal laser scanning microscopy (CLSM), for the analysis of the spatial organization of in vitro biofilms containing both Gram-negative and Gram-positive oral bacteria. Biofilms composed of the six oral species Actinomyces naeslundii, Candida albicans, Fusobacterium nucleatum, Streptococcus oralis, Streptococcus sobrinus, and Veillonella dispar were grown anaerobically for 64.5 h at 37 degrees C on hydroxyapatite disks preconditioned with saliva. Conditions for the simultaneous in situ hybridization of both Gram-negative and Gram-positive bacteria were sought by systematic variation of fixation and exposure to lysozyme. After fixation and permeabilization biofilms were labeled by FISH with 16S rRNA-targeted oligonucleotide probes ANA103 (for the detection of A. naeslundii), EUK116 (C. albicans), FUS664 (F. nucleatum), MIT447 and MIT588 (S. oralis), SOB174 (S. sobrinus), and VEI217 (V. dispar). Probes were used as 6-FAM, Cy3 or Cy5 conjugates, resulting in green, orange-red or deep-red fluorescence of target cells, respectively. Thus, with two independent triple-hybridizations with three probes carrying different fluorescence-tags, all six species could be visualized. Results show that the simultaneous investigation by FISH of complex biofilms composed of multiple bacterial species with differential Gram-staining properties is possible. In combination with the optical sectioning properties of CLSM the technique holds great promise for the analysis of spatial alterations in biofilm composition in response to environmental challenges.", "publicationTitle": "Journal of microbiological methods", "publisher": "", "place": "", "date": "Jan 2004", "volume": "56", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "37-47", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Microbiol. Methods", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0167-7012", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 14706749", "tags": [ { "tag": "Biofilms", "type": 1 }, { "tag": "Carbocyanines", "type": 1 }, { "tag": "DNA Probes", "type": 1 }, { "tag": "DNA, Bacterial", "type": 1 }, { "tag": "Dental Plaque", "type": 1 }, { "tag": "Fluoresceins", "type": 1 }, { "tag": "Fluorescent Dyes", "type": 1 }, { "tag": "Gram-Negative Bacteria", "type": 1 }, { "tag": "Gram-Positive Bacteria", "type": 1 }, { "tag": "In Situ Hybridization, Fluorescence", "type": 1 }, { "tag": "Microscopy, Confocal", "type": 1 }, { "tag": "Specimen Handling", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2014-06-05T19:37:58Z", "dateModified": "2014-06-05T19:37:58Z" } }, { "key": "BP6NJMU2", "version": 2, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/BP6NJMU2", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/BP6NJMU2", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/268269/items/BCSURQUN", "type": "application/json" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } } }, "data": { "key": "BP6NJMU2", "version": 2, "parentItem": "BCSURQUN", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2014-06-05T19:37:47Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/18402605", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-06-05T19:37:47Z", "dateModified": "2014-06-05T19:37:47Z" } }, { "key": "BCSURQUN", "version": 2, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/BCSURQUN", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/BCSURQUN", "type": "text/html" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } }, "creatorSummary": "Haffajee et al.", "parsedDate": "2008-06", "numChildren": 1 }, "data": { "key": "BCSURQUN", "version": 2, "itemType": "journalArticle", "title": "Microbial complexes in supragingival plaque", "creators": [ { "creatorType": "author", "firstName": "A D", "lastName": "Haffajee" }, { "creatorType": "author", "firstName": "S S", "lastName": "Socransky" }, { "creatorType": "author", "firstName": "M R", "lastName": "Patel" }, { "creatorType": "author", "firstName": "X", "lastName": "Song" } ], "abstractNote": "BACKGROUND/AIMS: To examine microbial communities in supragingival biofilm samples.\nMETHODS: Supragingival plaque samples were taken from 187 subjects at baseline (n = 4745). Fifty-five subjects provided supragingival plaque samples at 1-7 days after professional tooth cleaning (n = 1456); 93 subjects provided 8044 samples between 3 and 24 months post-therapy. All samples were individually analyzed for their content of 40 bacterial species using checkerboard DNA-DNA hybridization. Microbial associations among species were sought using cluster analysis and community ordination techniques for the three groups separately.\nRESULTS: Six complexes were formed for the baseline samples. Similar complexes were formed for the samples taken 3-24 months post-therapy. However, distinct changes were observed in microbial communities in samples taken during the 7 days of plaque redevelopment. The complexes related to clinical parameters of periodontal disease.\nCONCLUSION: There were specific microbial complexes in supragingival plaque that were similar to those found in subgingival plaque samples with a few minor differences. The relation of previously unclustered taxa to the complexes was also described.", "publicationTitle": "Oral microbiology and immunology", "publisher": "", "place": "", "date": "Jun 2008", "volume": "23", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "196-205", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Oral Microbiol. Immunol.", "DOI": "10.1111/j.1399-302X.2007.00411.x", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1399-302X", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 18402605", "tags": [ { "tag": "Actinomyces", "type": 1 }, { "tag": "Adult", "type": 1 }, { "tag": "Aged", "type": 1 }, { "tag": "Bacteria", "type": 1 }, { "tag": "Bacteroidaceae", "type": 1 }, { "tag": "Biofilms", "type": 1 }, { "tag": "Chronic Disease", "type": 1 }, { "tag": "Dental Plaque", "type": 1 }, { "tag": "Dental Scaling", "type": 1 }, { "tag": "Female", "type": 1 }, { "tag": "Follow-Up Studies", "type": 1 }, { "tag": "Gingival Hemorrhage", "type": 1 }, { "tag": "Gingivitis", "type": 1 }, { "tag": "Gram-Negative Bacteria", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Male", "type": 1 }, { "tag": "Middle Aged", "type": 1 }, { "tag": "Nucleic Acid Hybridization", "type": 1 }, { "tag": "Periodontal Attachment Loss", "type": 1 }, { "tag": "Periodontal Pocket", "type": 1 }, { "tag": "Periodontitis", "type": 1 }, { "tag": "Root Planing", "type": 1 }, { "tag": "Streptococcus", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2014-06-05T19:37:47Z", "dateModified": "2014-06-05T19:37:47Z" } }, { "key": "BT93HRKQ", "version": 2, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/BT93HRKQ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/BT93HRKQ", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/268269/items/V86A7MEP", "type": "application/json" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } } }, "data": { "key": "BT93HRKQ", "version": 2, "parentItem": "V86A7MEP", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2014-06-05T19:37:35Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/9495612", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-06-05T19:37:35Z", "dateModified": "2014-06-05T19:37:35Z" } }, { "key": "V86A7MEP", "version": 2, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/V86A7MEP", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/V86A7MEP", "type": "text/html" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } }, "creatorSummary": "Socransky et al.", "parsedDate": "1998-02", "numChildren": 1 }, "data": { "key": "V86A7MEP", "version": 2, "itemType": "journalArticle", "title": "Microbial complexes in subgingival plaque", "creators": [ { "creatorType": "author", "firstName": "S S", "lastName": "Socransky" }, { "creatorType": "author", "firstName": "A D", "lastName": "Haffajee" }, { "creatorType": "author", "firstName": "M A", "lastName": "Cugini" }, { "creatorType": "author", "firstName": "C", "lastName": "Smith" }, { "creatorType": "author", "firstName": "R L, Jr", "lastName": "Kent" } ], "abstractNote": "It has been recognized for some time that bacterial species exist in complexes in subgingival plaque. The purpose of the present investigation was to attempt to define such communities using data from large numbers of plaque samples and different clustering and ordination techniques. Subgingival plaque samples were taken from the mesial aspect of each tooth in 185 subjects (mean age 51 +/- 16 years) with (n = 160) or without (n = 25) periodontitis. The presence and levels of 40 subgingival taxa were determined in 13,261 plaque samples using whole genomic DNA probes and checkerboard DNA-DNA hybridization. Clinical assessments were made at 6 sites per tooth at each visit. Similarities between pairs of species were computed using phi coefficients and species clustered using an averaged unweighted linkage sort. Community ordination was performed using principal components analysis and correspondence analysis. 5 major complexes were consistently observed using any of the analytical methods. One complex consisted of the tightly related group: Bacteroides forsythus, Porphyromonas gingivalis and Treponema denticola. The 2nd complex consisted of a tightly related core group including members of the Fusobacterium nucleatum/periodonticum subspecies, Prevotella intermedia, Prevotella nigrescens and Peptostreptococcus micros. Species associated with this group included: Eubacterium nodatum, Campylobacter rectus, Campylobacter showae, Streptococcus constellatus and Campylobacter gracilis. The 3rd complex consisted of Streptococcus sanguis, S. oralis, S. mitis, S. gordonii and S. intermedius. The 4th complex was comprised of 3 Capnocytophaga species, Campylobacter concisus, Eikenella corrodens and Actinobacillus actinomycetemcomitans serotype a. The 5th complex consisted of Veillonella parvula and Actinomyces odontolyticus. A. actinomycetemcomitans serotype b, Selenomonas noxia and Actinomyces naeslundii genospecies 2 (A. viscosus) were outliers with little relation to each other and the 5 major complexes. The 1st complex related strikingly to clinical measures of periodontal disease particularly pocket depth and bleeding on probing.", "publicationTitle": "Journal of clinical periodontology", "publisher": "", "place": "", "date": "Feb 1998", "volume": "25", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "134-144", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Clin. Periodontol.", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0303-6979", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 9495612", "tags": [ { "tag": "Adult", "type": 1 }, { "tag": "Aged", "type": 1 }, { "tag": "Aged, 80 and over", "type": 1 }, { "tag": "Bacteria, Anaerobic", "type": 1 }, { "tag": "Bacterial Typing Techniques", "type": 1 }, { "tag": "Cluster Analysis", "type": 1 }, { "tag": "DNA Probes", "type": 1 }, { "tag": "DNA, Bacterial", "type": 1 }, { "tag": "Dental Plaque", "type": 1 }, { "tag": "Ecosystem", "type": 1 }, { "tag": "Female", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Male", "type": 1 }, { "tag": "Middle Aged", "type": 1 }, { "tag": "Periodontal Index", "type": 1 }, { "tag": "Periodontal Pocket", "type": 1 }, { "tag": "Periodontitis", "type": 1 }, { "tag": "Regression Analysis", "type": 1 }, { "tag": "Statistics, Nonparametric", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2014-06-05T19:37:35Z", "dateModified": "2014-06-05T19:37:35Z" } }, { "key": "UAV4PDI3", "version": 2, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/UAV4PDI3", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/UAV4PDI3", "type": "text/html" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } }, "creatorSummary": "Cugini et al.", "parsedDate": "2013", "numChildren": 1 }, "data": { "key": "UAV4PDI3", "version": 2, "itemType": "journalArticle", "title": "Porphyromonas gingivalis: keeping the pathos out of the biont", "creators": [ { "creatorType": "author", "firstName": "Carla", "lastName": "Cugini" }, { "creatorType": "author", "firstName": "Vanja", "lastName": "Klepac-Ceraj" }, { "creatorType": "author", "firstName": "Elze", "lastName": "Rackaityte" }, { "creatorType": "author", "firstName": "James E", "lastName": "Riggs" }, { "creatorType": "author", "firstName": "Mary E", "lastName": "Davey" } ], "abstractNote": "The primary goal of the human microbiome initiative has been to increase our understanding of the structure and function of our indigenous microbiota and their effects on human health and predisposition to disease. Because of its clinical importance and accessibility for in vivo study, the oral biofilm is one of the best-understood microbial communities associated with the human body. Studies have shown that there is a succession of select microbial interactions that directs the maturation of a defined community structure, generating the formation of dental plaque. Although the initiating factors that lead to disease development are not clearly defined, in many individuals there is a fundamental shift from a health-associated biofilm community to one that is pathogenic in nature and a central player in the pathogenic potential of this community is the presence of Porphyromonas gingivalis. This anaerobic bacterium is a natural member of the oral microbiome, yet it can become highly destructive (termed pathobiont) and proliferate to high cell numbers in periodontal lesions, which is attributed to its arsenal of specialized virulence factors. Hence, this organism is regarded as a primary etiologic agent of periodontal disease progression. In this review, we summarize some of the latest information regarding what is known about its role in periodontitis, including pathogenic potential as well as ecological and nutritional parameters that may shift this commensal to a virulent state. We also discuss parallels between the development of pathogenic biofilms and the human cellular communities that lead to cancer, specifically we frame our viewpoint in the context of 'wounds that fail to heal'.", "publicationTitle": "Journal of oral microbiology", "publisher": "", "place": "", "date": "2013", "volume": "5", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J Oral Microbiol", "DOI": "10.3402/jom.v5i0.19804", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "2000-2297", "archive": "", "archiveLocation": "", "shortTitle": "Porphyromonas gingivalis", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 23565326 \nPMCID: PMC3617648", "tags": [], "collections": [], "relations": {}, "dateAdded": "2014-06-05T19:37:24Z", "dateModified": "2014-06-05T19:37:24Z" } }, { "key": "P2PPRCTF", "version": 2, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/P2PPRCTF", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/P2PPRCTF", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/268269/items/UAV4PDI3", "type": "application/json" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } } }, "data": { "key": "P2PPRCTF", "version": 2, "parentItem": "UAV4PDI3", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2014-06-05T19:37:24Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/23565326", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-06-05T19:37:24Z", "dateModified": "2014-06-05T19:37:24Z" } }, { "key": "H53NPMXW", "version": 2, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/H53NPMXW", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/H53NPMXW", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/268269/items/4GUFF5CX", "type": "application/json" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } } }, "data": { "key": "H53NPMXW", "version": 2, "parentItem": "4GUFF5CX", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2014-06-05T19:37:14Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/22989070", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-06-05T19:37:14Z", "dateModified": "2014-06-05T19:37:14Z" } }, { "key": "4GUFF5CX", "version": 2, "library": { "type": "group", "id": 268269, "name": "saliva_bact", "links": { "alternate": { "href": "https://www.zotero.org/groups/saliva_bact", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/268269/items/4GUFF5CX", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/saliva_bact/items/4GUFF5CX", "type": "text/html" } }, "meta": { "createdByUser": { "id": 46158, "username": "fyshou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/fyshou", "type": "text/html" } } }, "creatorSummary": "Hendrickson et al.", "parsedDate": "2012", "numChildren": 1 }, "data": { "key": "4GUFF5CX", "version": 2, "itemType": "journalArticle", "title": "Proteomics of Streptococcus gordonii within a model developing oral microbial community", "creators": [ { "creatorType": "author", "firstName": "Erik L", "lastName": "Hendrickson" }, { "creatorType": "author", "firstName": "Tiansong", "lastName": "Wang" }, { "creatorType": "author", "firstName": "Brittany C", "lastName": "Dickinson" }, { "creatorType": "author", "firstName": "Sarah E", "lastName": "Whitmore" }, { "creatorType": "author", "firstName": "Christopher J", "lastName": "Wright" }, { "creatorType": "author", "firstName": "Richard J", "lastName": "Lamont" }, { "creatorType": "author", "firstName": "Murray", "lastName": "Hackett" } ], "abstractNote": "BACKGROUND: Streptococcus gordonii is one of several species that can initiate the formation of oral biofilms that develop into the complex multispecies microbial communities referred to as dental plaque. It is in the context of dental plaque that periodontal pathogens such as Porphyromonas gingivalis cause disease. We have previously reported a whole cell quantitative proteomics investigation of P. gingivalis in a model dental plaque community of S. gordonii, P. gingivalis, and Fusobacterium nucleatum. Here we report the adaptation of S. gordonii to the same model.\nRESULTS: 1122 S. gordonii proteins were detected in S. gordonii control samples, 915 in communities with F. nucleatum, 849 with P. gingivalis, and 649 with all three organisms. Quantitative comparisons showed extensive proteome changes in association with F. nucleatum or P. gingivalis individually or both P. gingivalis and F. nucleatum together. The changes were species specific, though the P. gingivalis interaction may be dominant, indicated by large differences between the proteomes with F. nucleatum or P. gingivalis but limited changes between communities with P. gingivalis or both P. gingivalis and F. nucleatum. The results were inspected manually and an ontology analysis conducted using DAVID. Extensive changes were seen in nutrition pathways with increases in energy metabolism and changes in the resulting byproducts, while the acid and sugar repressed PTS (phosphoenolpyruvate dependent phosphotransferase system) sugar transport systems showed decreases. These results were seen across all the multispecies samples, though with different profiles according to the partner species. F. nucleatum association decreased proteins for the metabolic end products acetate and ethanol but increased lactate, the primary source of acidity from streptococcal cultures. P. gingivalis containing samples had a reduction in levels of proteins for ethanol and formate but increased proteins for both acetate and lactate production. The communities also showed increases in exopolysaccharide synthesis, amino acid biosynthesis, and oxidative stress protection and decreases in adhesion and transporter proteins.\nCONCLUSION: This study showed that S. gordonii demonstrates species specific responses during interactions with F. nucleatum or P. gingivalis. Extensive changes were seen in energy metabolism and byproduct production implicating nutrient transfer as an important community interaction.", "publicationTitle": "BMC microbiology", "publisher": "", "place": "", "date": "2012", "volume": "12", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "211", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "BMC Microbiol.", "DOI": "10.1186/1471-2180-12-211", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1471-2180", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 22989070 \nPMCID: PMC3534352", "tags": [ { "tag": "Bacterial Proteins", "type": 1 }, { "tag": "Dental Plaque", "type": 1 }, { "tag": "Ecosystem", "type": 1 }, { "tag": "Fusobacterium nucleatum", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Microbial Interactions", "type": 1 }, { "tag": "Models, Biological", "type": 1 }, { "tag": "Porphyromonas gingivalis", "type": 1 }, { "tag": "Proteome", "type": 1 }, { "tag": "Streptococcus gordonii", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2014-06-05T19:37:14Z", "dateModified": "2014-06-05T19:37:14Z" } } ]