F E Dewhirst

The Forsyth Institute, Cambridge, Massachusetts, United States

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Publications (206)698.21 Total impact

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    ABSTRACT: During 1 year, experimentally naïve C57BL/6NCrl weanlings born to timed-pregnant dams from a single vendor demonstrated markedly increased mortality associated with runting, abnormal gait, and decreased activity. Gram-positive, aerobic, α-hemolytic, coccoid bacteria were isolated from the meninges (n = 16), blood (n = 1), and kidneys (n = 1) of clinically affected weanlings (n = 15); from the uterus (n = 1), meninges (n = 1), and oral cavity (n = 2) of 3 dams; and from the meninges and oral cavity of a clinically affected 86-d-old mouse in the same colony. Multifocal, necrosuppurative meningoencephalitis and ventriculitis with intralesional gram-positive coccoid bacteria were present in all but 2 affected animals. The bacterium also was isolated from the oral cavity of an asymptomatic timed-pregnant dam (1 of 23) from the same vendor and from 8 mice at the vendor's facility. All isolates (n = 25) were identified by using 2 semiautomated rapid-identification systems, one of which consistently identified the causative bacterium as Aerococcus viridans 2 (n = 12) or 3 (n = 13), with probabilities of 55.7% to 98.3%. The bacterium did not grow in 6.5% NaCl at 10 °C, thus suggesting a Streptococcus species. Partial 16S rRNA sequencing of 4 isolates suggested S. hyointestinalis (probability, 93.4%) and S. gallinaceus (99.5%). Full 16S rRNA sequences for 3 isolates identified the bacterium as a novel Streptococcus species most closely related to S. acidominimus strain LGM (96.5%) and Streptococcus species strain Smarlab 3301444 (96.3%) and for which we propose the name S. azizii.
    Comparative medicine 07/2015; 65(3):186-95. · 0.76 Impact Factor
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    ABSTRACT: Tannerella forsythia is an oral pathogen implicated in the development of periodontitis. Here, we report the draft genome sequence of the Tannerella forsythia strain ATCC 43037. The previously available genome of this designation (NCBI reference sequence NC_016610.1) was discovered to be derived from a different strain, FDC 92A2 (= ATCC BAA-2717). FOOTNOTES Address correspondence to Christina Schäffer, christina.schaeffer{at}boku.ac.at. Citation Friedrich V, Pabinger S, Chen T, Messner P, Dewhirst FE, Schäffer C. 2015. Draft genome sequence of Tannerella forsythia type strain ATCC 43037. Genome Announc 3(3):e00660-15. doi:10.1128/genomeA.00660-15. Received 15 May 2015. Accepted 18 May 2015. Published 11 June 2015.
    Genome Announcements 06/2015; 3(3):e00660-15. DOI:10.1128/genomeA.00660-15
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    ABSTRACT: Bacterial invasion into pulps of primary teeth can lead to infection and premature tooth loss in children. This pilot study aimed to explore whether the microbiota of carious exposures of dental pulps resembles that of carious dentin or that of infected root canals. Children with severe early childhood caries were studied. Children were consented and extent of caries, plaque, and gingivitis measured. Bacteria were sampled from carious lesion biofilms and vital carious exposures of pulps, and processed by anaerobic culture. Isolates were characterized from partial sequences of the 16S rRNA gene and identified by comparison with taxa in the Human Oral Microbiome Database (http://www.HOMD.org). The microbiotas of carious lesions and dental pulps were compared using univariate and multivariate approaches. The microbiota of cariously exposed pulps was similar in composition to that of carious lesion biofilms except that fewer species/taxa were identified from pulps. The major taxa identified belonged to the phyla Firmicutes (mainly streptococci) and Actinobacteria (mainly Actinomyces species). Actinomyces and Selenomonas species were associated with carious lesions whereas Veillonella species, particularly Veillonella dispar was associated with pulps. Other bacteria detected in pulps included Streptococcus mutans, Parascardovia denticolens, Bifidobacterium longum, and several Lactobacillus and Actinomyces species. By principal, component analysis pulp microbiotas grouped together, whereas those in caries biofilms were widely dispersed. We conclude that the microbiota of cariously exposed vital primary pulps is composed of a subset of species associated with carious lesions. Vital primary pulps had a dominant Firmicutes and Actinobacteria microbiota which contrasts with reports of endodontic infections which can harbor a gram-negative microbiota. The microbiota of exposed primary pulps may provide insight into bacterial species at the forefront of caries invasion in dentinal lesions that can invade into the pulp and the nature of species that need suppressing for successful pulp therapy.
    Journal of Oral Microbiology 02/2015; 7:25951. DOI:10.3402/jom.v7.25951
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    ABSTRACT: The human oral microbiome is known to play a significant role in human health and disease. While less well studied, the feline oral microbiome is thought to play a similarly important role. To determine roles oral bacteria play in health and disease, one first has to be able to accurately identify bacterial species present. 16S rRNA gene sequence information is widely used for molecular identification of bacteria and is also useful for establishing the taxonomy of novel species. The objective of this research was to obtain full 16S rRNA gene reference sequences for feline oral bacteria, place the sequences in species-level phylotypes, and create a curated 16S rRNA based taxonomy for common feline oral bacteria. Clone libraries were produced using "universal" and phylum-selective PCR primers and DNA from pooled subgingival plaque from healthy and periodontally diseased cats. Bacteria in subgingival samples were also cultivated to obtain isolates. Full-length 16S rDNA sequences were determined for clones and isolates that represent 171 feline oral taxa. A provisional curated taxonomy was developed based on the position of each taxon in 16S rRNA phylogenetic trees. The feline oral microbiome curated taxonomy and 16S rRNA gene reference set will allow investigators to refer to precisely defined bacterial taxa. A provisional name such as "Propionibacterium sp. feline oral taxon FOT-327" is an anchor to which clone, strain or GenBank names or accession numbers can point. Future next-generation-sequencing studies of feline oral bacteria will be able to map reads to taxonomically curated full-length 16S rRNA gene sequences. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.
    Veterinary Microbiology 12/2014; 175(2-4). DOI:10.1016/j.vetmic.2014.11.019 · 2.73 Impact Factor
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    Anuj Camanocha, Floyd E Dewhirst
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    ABSTRACT: Background and objective In addition to the well-known phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Spirochaetes, Fusobacteria, Tenericutes, and Chylamydiae, the oral microbiomes of mammals contain species from the lesser-known phyla or candidate divisions, including Synergistetes, TM7, Chlorobi, Chloroflexi, GN02, SR1, and WPS-2. The objectives of this study were to create phyla-selective 16S rDNA PCR primer pairs, create selective 16S rDNA clone libraries, identify novel oral taxa, and update canine and human oral microbiome databases. Design 16S rRNA gene sequences for members of the lesser-known phyla were downloaded from GenBank and Greengenes databases and aligned with sequences in our RNA databases. Primers with potential phylum level selectivity were designed heuristically with the goal of producing nearly full-length 16S rDNA amplicons. The specificity of primer pairs was examined by making clone libraries from PCR amplicons and determining phyla identity by BLASTN analysis. Results Phylum-selective primer pairs were identified that allowed construction of clone libraries with 96–100% specificity for each of the lesser-known phyla. From these clone libraries, seven human and two canine novel oral taxa were identified and added to their respective taxonomic databases. For each phylum, genome sequences closest to human oral taxa were identified and added to the Human Oral Microbiome Database to facilitate metagenomic, transcriptomic, and proteomic studies that involve tiling sequences to the most closely related taxon. While examining ribosomal operons in lesser-known phyla from single-cell genomes and metagenomes, we identified a novel rRNA operon order (23S-5S-16S) in three SR1 genomes and the splitting of the 23S rRNA gene by an I-CeuI-like homing endonuclease in a WPS-2 genome. Conclusions This study developed useful primer pairs for making phylum-selective 16S rRNA clone libraries. Phylum-specific libraries were shown to be useful for identifying previously unrecognized taxa in lesser-known phyla and would be useful for future environmental and host-associated studies.
    Journal of Oral Microbiology 10/2014; 6. DOI:10.3402/jom.v6.25468
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    ABSTRACT: Considerable progress has been made in understanding the roles of Helicobacter pylori in inflammation and gastric cancer; however, far less is known about the roles of enterohepatic Helicobacter spp. (EHS) in carcinogenesis and their zoonotic or pathogenic potential. We determined the prevalence of EHS infection in a cohort of geriatric rhesus monkeys in which intestinal adenocarcinoma (IAC) is common and investigated the association between EHS infection and IAC. The cohort consisted of 36 animals, 14 of which (age 26-35 years) had IAC. Of the 36 rhesus, 35 (97%) were positive for EHS using PCR or bacterial isolation from feces, colonic or tumor tissues. Only a single rhesus, which had IAC, was negative for EHS by all detection methods. The EHS identified by 16S rRNA sequencing in this study were comprised of three Helicobacter taxa: H. macacae (previously rhesus monkey taxon 1), Helicobacter sp. rhesus monkey taxon 2, previously described from strain MIT 99-5507 and Helicobacter sp. rhesus monkey taxon 4, related to H. fennelliae. Thirteen of 14 monkeys with IAC were positive for either H. macacae (7/13 (54%)), EHS rhesus monkey taxon 4 (4/13 (31%)) or a mixture of the two EHS (2/13 (15%)). These results indicate that EHS is prevalent among aged rhesus macaques with IAC. Using Helicobacter-genus specific florescence in situ hybridization, EHS was detected on the surface of colonic epithelia of infected monkeys. All Helicobacter isolates, including H. macacae, effectively adhered to, invaded, and significantly induced proinflammatory genes, including IL8, IL6, TNF-α, and iNOS, while down regulating genes involved in the function of inflammasomes, particularly IL-1β, CASPASE-1, NRLP3, NLRP6, and NLRC4 in the human colonic T84 cell line (p < 0.0001). These results suggest that EHS may represent an etiological agent mediating diarrhea, chronic inflammation, and possibly intestinal cancer in nonhuman primates, and may play a role in similar disease syndromes in humans. Down regulation of inflammasome function may represent an EHS strategy for long-term persistence in the host and play a role in inducing pathological changes in the host's lower bowel.
    Journal of Medical Microbiology 04/2014; DOI:10.1099/jmm.0.072462-0 · 2.27 Impact Factor
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    ABSTRACT: Objective: Rhesus macaques are often used as animal models for periodontitis. The purpose of this study was to determine the presence of naturally-occurring Porphyromonas gingivalis (Pg) and other periodontal pathogens in an elder population of macaques. Method: Fifty-one elder animals (9 to 18 years) with clinical signs of mild-moderate periodontitis were studied. Bacterial DNA was isolated from subgingival plaque from the deepest sites and PCR-amplified using Pg-specific 16S rDNA bacterial primers. Amplicons were excised and sequenced. DNA was also PCR-amplified using Bacteroidetes-specific or broad-range 16S rDNA bacterial primers. Full-sized amplicons (about 1500 bp) were cloned and sequenced for species identification. Microarrays (HOMIM) were run on DNA samples from 7 animals. Result: Based on PCR and subsequent sequence analyses with 100% 250 bp match, all 51 macaques were colonized with Pg. Based on sequence analysis of 330 clones, 48 of 108 bacterial taxa (44%) were unique to the macaque. The remaining taxa were considered human species. Putative periodontal pathogens detected included Pg, Filifactor alocis, Parvimonas micra, several Treponema phylotypes, a Desulfobulbus phylotype, and, most notably, a monkey version of Aggregatibacter actinomycetemcomitans. Interestingly, caries-associated species, Streptococcus mutans and Scardovia wiggsiae were also detected. HOMIM was comparable to sequence analysis confirming the presence of Pg in all animals tested. Conclusion: The presence of naturally occurring Pg and other human periodontal pathogens in the subgingival plaque of elder macaques validates that they serve as an excellent animal model for human periodontitis.
    AADR Annual Meeting & Exhibition 2014; 03/2014
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    ABSTRACT: Objectives: Of the 688 taxa currently in the Human Oral Microbiome Database (HOMD), 65% have been cultivated and 244 taxa (35%) are as-yet-uncultivated phylotypes. The goal of this study was to determine the prevalence of uncultivated taxa in various oral niches. Methods: Ten adults who had not taken antibiotics within the past 3 months were sampled at 9 oral sites each: supragingival, subgingival (4 deepest sites), cheek, palate, tongue, tonsils (throat sampled for two subjects without tonsils). Soft tissue sites were sampled using nylon brushes, hard tissue sites with scalers. DNA was purified from the clinical samples, PCR amplified using 16S rRNA V3V4 primers, purified, and sequenced using an Illumina Miseq instrument. The 16S rRNA reads were parsed, and BLASTN analyzed using HOMD RefSeq Version 13.2. Results: A total of 5,586,237 sequences (V3-V4 assembled overlapped paired reads) matched HOMD reference sequences at >98.5% BLASTN identity. The reads were identified to 481 HOMD taxa: 317 cultivated and 164 uncultivated phylotypes. The number of uncultivated taxa per sample ranged from 15-68 with a mean of 40.6. The total number of oral taxa/subject-site ranged from 91-251 with a mean of 182. The mean number of uncultivated taxa/individual sample at oral sites was as follows: cheek 45.9, palate 38.4, tongue 29.0, tonsils 46.3, throat 45.0, supragingival 39.8 and subgingival 39.6. Uncultivated taxa identified included 22 from the rare phyla: Chloroflexi, 1; Synergistetes genus Fretibacterium, 4; GNO2, 3; SR1, 3; and TM7, 11 taxa. Conclusion: In screening just 10 subjects, we identified subject-sites with 164/244 (67%) of the uncultivated taxa currently in HOMD. The majority of these uncultivated taxa are thought to be uncultivable using standard cultivation methods; however, this study shows they are readily available for study and attempted cultivation.
    AADR Annual Meeting & Exhibition 2014; 03/2014
  • T. CHEN, J. MCCAFFERTY, F.E. DEWHIRST
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    ABSTRACT: Objective: Next generation sequencing platforms such as those based on the Illumina or Roche 454, have become cost-effective and commonly applied to study human oral microbiome by deep 16S rRNA gene sequencing of microbial samples. New and existing bioinformatics software pipelines are being developed and modified for analyzing the sequence reads and interpreting the microbial richness and diversity of the samples. Different software and analyzing procedures may result in different conclusions even on the same dataset. In this report, we evaluated different software pipelines and proposed a comprehensive approach that is optimized specifically for analyzing the 16S rRNA short read sequences derived from human oral samples. Method: Bioinformatics programs were evaluated for the following stages of data analysis: 1) sequence quality filtering; 2) pair-ending sequence merging; 3) operational taxonomic unit (OTU) calling; 4) classification; and 5) diversity and richness estimation. Result: The human oral microbiome has been well-characterized and full length 16S rRNA gene sequences of most abundant species are available as references. Based on the evaluation of the current available software and pipeline, we propose the use of two-stage, open-ended reference-base OTU calling pipeline: 1) reference-based OTU calling using HOMD 16S rRNA references and taxonomy inferred from the HOMD taxonomy; 2) de-novo OTU calling of the reads not mapped in stage 1 and taxonomy inferred from non-HOMD references, such as GreenGene or Silva databases. Conclusion: The proposed two-stage approach for NGS 16S rRNA data is comprehensive in mapping the reads to known human oral taxa as well as in discovering novel taxa in the oral microbial samples.
    AADR Annual Meeting & Exhibition 2014; 03/2014
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    ABSTRACT: Objective: The Human Oral Microbiome Database (HOMD) is a public database providing comprehensive information on the prokaryotic species present in the human oral cavity. Our team maintains and curates the HOMD with up-to-date information on genomics, phylogeny, and taxonomy for prevalent human oral microbial species. We have also been developing bioinformatics tools that are integrated into the database for use by the research community. This report summarizes the latest content updates as well as newly available tools and features. Method: The HOMD was created with PHP, Perl, MySQL and Apache and is hosted on a cluster of computers and housed in the Forsyth Institute Data Center. The HOMD Genomic BLAST was constructed based on the NCBI BLAST+. The new HOMD Genome Browser was implemented based on the “JBrowse” system. Novel human oral taxa were created based on 16S rRNA reference sequences of recently described oral species or recognized phylotypes. New genomic sequences were obtained through the collaboration with the Human Microbiome Project (HMP) sequencing centers and from repositories world-wide. Result: Currently HOMD contains a total of 688 human oral taxa. Of these, 342 (49.7%) are validly described, 102 (14.8%) unnamed (but cultivated) and 244 (35.5%) known only as uncultivated phylotypes. The current version (13.2) of the 16S rRNA reference sequences contains 831 full length sequences representing prevalent human oral taxa. The HOMD Genomics database currently contains 1292 genomes, representing 325 oral taxa, with either static or dynamic annotations. Additional genomic sequences are being added frequently as they appear at NCBI and other sequence repositories. The HOMD Genomic BLAST and the HOMD JBrowse Genome Browser have also been implemented for searching and navigating among all the human oral microbes with available sequences. Conclusion: HOMD is a comprehensive bioinformatics resource for the scientific community. HOMD is available at http://www.homd.org.
    AADR Annual Meeting & Exhibition 2014; 03/2014
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    ABSTRACT: Objective: We examined the metatranscriptome of the bacterial community associated with early childhood caries (ECC) compared with caries-free-associated plaques to evaluate which gene activities and species were contributing to caries pathogenesis. Method: Incisor and molar plaque samples were taken from 2-6 year old children attending a community dental center serving mainly low-income families. RNA was purified from plaque samples of 10 children (ECC n=5, caries-free n=5), and sequenced on the Illumina MiSeq platform. Gene expression analysis was conducted by aligning sequences to the genome sequences in the Human Oral Microbiome Database (HOMD) and counting total hits to genes. The edgeR package was used identify and visualize gene expression levels between the two groups. Result: Multidimensional scaling gene counts grouped four of five children in each group by caries or caries-free disease status. Over and under expressed genes were detected, however, no expressed genes differed significantly between ECC or caries-free groups (FDR < 0.1). Species with over expressed genes in ECC compared with caries-free included for Streptococcus mutans, (p=0.008) with higher gene expression for Oribacterium sp HOT 078, Actinomyces HOT 176, Scardovia wiggsiae Selenomonas sputigena and Prevotella sp. HOT 317, but not significantly. Over expressed genes included those for L-lactate dehydrogenase, glucosyltransferase GtfG, surface antigen-related protein, glycogen phosphorylase and lantibiotic streptococcin A-FF22 precursor all in S. mutans. There were only modest gene expression increases in taxa detected more frequently in caries-free children, including Streptococcus oralis, Neisseria sicca, Catonell morbi, Cardiobacterium hominis Cardiobacterium valvarum, and Actinomyces sp HOT 848. Conclusion: We detected species with increased gene expression activity in the caries-associated microbiome, and linked activity to individual species. This is a promising approach to determine species and mechanisms active in dental caries progression.
    AADR Annual Meeting & Exhibition 2014; 03/2014
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    ABSTRACT: Routine necropsies of 27 asymptomatic juvenile chinchillas revealed a high prevalence of gastric ulcers with microscopic lymphoplasmacytic gastroenteritis and typhlocolitis. Polymerase chain reaction (PCR) analysis using Campylobacter genus-specific partial 16S rRNA primers revealed the presence of Campylobacter spp. DNA in the faeces of 12 of 27 animals (44.4%). Species-specific partial 16S rRNA PCR and sequencing confirmed that these animals were colonized with Campylobacter lanienae, a gram-negative, microaerophilic bacterium that was first identified on routine faecal screening of slaughterhouse employees and subsequently isolated from faeces of livestock. Campylobacter lanienae was isolated from the faeces of six PCR-positive animals and identified with species-specific PCR and full 16S rRNA sequencing. Phylogenetic analysis showed that these isolates clustered with C. lanienae strain NCTC 13004. PCR analysis of DNA extracted from gastrointestinal tissues revealed the presence of C. lanienae DNA in the caecum and colon of these chinchillas. Gastrointestinal lesions were scored and compared between C. lanienae-positive and C. lanienae-negative animals. There was no correlation between colonization status and lesion severity in the stomach, liver, duodenum, or colon. Possible routes of C. lanienae infection in chinchillas could include waterborne transmission and faecal–oral transmission from wild mice and rats or livestock. Based on these findings, the authors conclude that C. lanienae colonizes the lower bowel of chinchillas in the absence of clinical disease. This is the first report of C. lanienae in any rodent species. Campylobacter lanienae isolates from different mammalian species demonstrate heterogeneity by 16S rRNA sequence comparison. Analysis using rpoB suggests that isolates and clones currently identified as C. lanienae may represent multiple species or subspecies.
    Zoonoses and Public Health 03/2014; 61(8). DOI:10.1111/zph.12107 · 2.07 Impact Factor
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    ABSTRACT: Limited information is available about the effect of human immunodeficiency virus (HIV) and subsequent antiretroviral treatment on host-microbe interaction. This study aimed to determine the salivary microbial composition in 10 HIV-seropositive subjects, before and 6 months after highly active antiretroviral therapy (HAART), compared with that of 10 HIV-seronegative subjects. Both a conventional culture and two culture-independent analyses were used and consistently demonstrated differences in microbial composition among the three sets of samples. HIV(+) subjects had higher levels of total cultivable microbes, including oral streptococci, lactobacilli, S. mutans, and Candida, in saliva as compared to HIV(-) subjects. The total cultivable microbial level was significantly correlated with CD4(+) T cell counts. Denaturing gradient gel electrophoresis (DGGE), which compared the overall microbial profiles, showed distinct fingerprinting profiles for each group. Human oral microbe identification microarray (HOMIM), which compared the 16S rRNA genes, showed a clear separation among the three sample groups. Veillonella, Synergistetes, and Streptococcus, were present in all 30 saliva samples. Only minor changes or no changes were observed in the prevalence of Neisseria, Haemophilus, Gemella, Leptotrichia, Solobacterium, Parvimonas and RothiaI. Severn genera were detected only in HIV(-) samples, including Capnocytophaga, Slackia, Porphyromonas, Kingella, Peptostreptococcaceae, Lactobacillus, and Atopobium. The prevalence of Fusobacterium, Campylobacter, Prevotella, Capnocytophaga, Selenomonas, Actinomyces, and Atopobium was increased after therapy with HAART. In contrast, the prevalence of Aggregatibacter was significantly decreased after HAART. Findings of this study suggest that HIV infection and therapy with HAART could have a significant effect on salivary microbial colonization and composition.
    Journal of clinical microbiology 02/2014; 52(5). DOI:10.1128/JCM.02954-13 · 4.23 Impact Factor
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    Emerging Infectious Diseases 01/2014; 20(1):159-61. DOI:10.3201/eid2001.130675 · 7.33 Impact Factor
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    ABSTRACT: Helicobacter canis has been associated with hepatobiliary and gastrointestinal disease in dogs, cats, and humans. Infection has not been documented in other species. Sheep feces subjected to microaerobic culture. Isolates were characterized by genus-specific PCR, restriction fragment length polymorphism, biochemical profiling, and 16S rRNA sequence analysis. Helicobacter canis was isolated from sheep feces and confirmed by the above methods. These isolates are distinct from other sheep-origin enterohepatic Helicobacter species previously isolated. This study identifies sheep as H. canis reservoirs potentially important in zoonotic or foodborne transmission.
    Helicobacter 11/2013; 19(1). DOI:10.1111/hel.12097 · 2.99 Impact Factor
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    ABSTRACT: Objective: Around half of oral bacteria have yet to be cultured. The family Lachnospiraceae includes a major lineage of uncultivated bacteria, some of which are disease-associated. The aim of this study was to use colony hybridisation directed enrichment co-culture to isolate a representative of LachnospiraceaeHuman Oral Taxon (HOT) 500. Methods: Samples of subgingival plaque from pockets > 8 mm in depth were collected from subjects with periodontitis patients and used to inoculate hydroxyapatite-coated pegs immersed in Periodontitis Peg Medium broth (PPB) in the Calgary Biofilm Device (CBD). The CBD was incubated anaerobically and the medium changed every 3.5 days. PCR primers and oligonucleotide probes specific for LachnospiraceaeHOT 500 were designed and validated. Colony hybridisation with DIG-labelled probes was performed on Periodontitis Peg Medium agar plates (PPA) inoculated with biofilms harvested from CBD biofilms incubated anaerobically for 10 days. Hybridisation-positive areas of the plates were subcultured onto fresh media to enrich for the target. Results: Lachnospiraceae HOT 500-positive regions were seen on colony hybridisation blots from CBD culture plates and, after enrichment, a simple community was seen consisting of Veillonella parvula, Parvimonas micra and tiny colonies growing in close proximity to the Veillonella parvula colonies. 16S rRNA gene sequence analysis identified the tiny colonies, designated strain SP1_1, as be Lachnospiraceae HOT 500. SP1_1 was found to be entirely dependent on V. parvula for growth. Growth stimulation was also seen with Fusobacterium nucleatum and Propionibacterium acnes. The addition of V. parvulaculture sonicates allowed SP1_1 to be cultured in PPB. Conclusion: A strain representative of the previously uncultivated human oral taxon Lachnospiraceae 500 has been successfully cultured using a colony hybridisation directed enrichment approach. This abstract is based on research that was funded entirely or partially by an outside source: NIH-NIDCR DE016937 Keywords: Ecology, Microbiology and Periodontal organisms Presenting author's disclosure statement: ** MISSING DISCLOSURE **
    09/2013
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    ABSTRACT: Aggregatibacter actinomycetemcomitans (Aa)-induced localized aggressive periodontitis (LAP) in African-American adolescents has been documented but poorly understood. Two thousand and fifty-eight adolescents, ages 11-17, were screened for their periodontal status and the presence of Aa. Seventy-one Aa-negative and 63 Aa-positive, periodontally healthy subjects were enrolled, sampled, examined and radiographed yearly for 3 years. Pocket depth and attachment levels were recorded. Disease was characterized by bone loss (BL). Subgingival sites were sampled every 6-months to assess; 1) the role of Aa in BL, and 2) the association of Aa with other microbes in relationship to BL. Sixteen of 63 subjects with Aa developed BL (47 subjects with Aa had no BL). No Aa-negative subjects developed BL. Human Oral Microbe Identification Microarray (HOMIM) was used for subgingival microbial assessment. On a subject level, pooled data from Aa subjects remaining healthy had higher prevalence and level of Streptococcus and Actinomyces species while Aa subjects with BL had higher prevalence and levels of Parvimonas micra, Filifactor alocis, Aa, and Peptostreptococus sp. HOT-113. At vulnerable sites, Aa, Streptococcus parasanguinis and F. alocis were elevated prior to BL. By detecting the three organism consortia (vs. Aa alone) the specificity for detecting sites of future BL increased from 75% to 99% with a sensitivity of 89%. We conclude that detecting the presence of Aa, S. parasanguinis, and F. alocis indicates sites of future BL in LAP. A synergistic interaction of this consortium in LAP causation is possible and the subject of ongoing research.
    Journal of clinical microbiology 06/2013; 51(9). DOI:10.1128/JCM.00729-13 · 4.23 Impact Factor
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    ABSTRACT: Coeliac disease is characterized by intestinal inflammation caused by gluten, proteins which are widely contained in the Western diet. Mammalian digestive enzymes are only partly capable of cleaving gluten, and fragments remain that induce toxic responses in patients with coeliac disease. We found that the oral microbiome is a novel and rich source of gluten-degrading organisms. Here we report on the isolation and characterization of the cultivable resident oral microbes that are capable of cleaving gluten, with special emphasis on the immunogenic domains. Bacteria were obtained by a selective culturing approach and enzyme activities were characterized by: (i) hydrolysis of paranitroanilide-derivatized gliadin-derived tripeptide substrates; (ii) gliadin degradation in-gel (gliadin zymography); (iii) gliadin degradation in solution; (iv) proteolysis of the highly immunogenic α-gliadin-derived 33-mer peptide. For selected strains pH activity profiles were determined. The culturing strategy yielded 87 aerobic and 63 anaerobic strains. Species with activity in at least two of the four assays were typed as: Rothia mucilaginosa HOT-681, Rothia aeria HOT-188, Actinomyces odontolyticus HOT-701, Streptococcus mitis HOT-677, Streptococcus sp. HOT-071, Neisseria mucosa HOT-682 and Capnocytophaga sputigena HOT-775, with Rothia species being active in all four assays. Cleavage specificities and substrate preferences differed among the strains identified. The approximate molecular weights of the enzymes were ~75 kD (Rothia spp.), ~60 kD (A. odontolyticus) and ~150 kD (Streptococcus spp.). In conclusion, this study identified new gluten-degrading microorganisms in the upper gastrointestinal tract. A cocktail of the most active oral bacteria, or their isolated enzymes, may offer promising new treatment modalities for coeliac disease.
    Clinical Microbiology and Infection 04/2013; 9. DOI:10.1111/1469-0691.12249 · 5.20 Impact Factor
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    ABSTRACT: Objective: 2,058 children ages 11-17 years were screened for the presence of Aggregatibacter actinomycetemcomitans (Aa) and localized aggressive periodontitis (LAP). Goals were to determine; 1) the relationship of Aa to BL, and 2) the relationship of Aa to other subgingival bacteria. Methods: 134 periodontally healthy children (73 Aa-negative and 61 Aa-positives) were enrolled in a longitudinal study. Subjects were sampled, examined, and x-rayed every 6 months for 3 years. LAP was diagnosed by radiographic evidence of bone loss (BL). Results: 227 of 2,058 subjects had Aa at screening. 64 of 2058 had LAP by probe. 54 of 64 with LAP had Aa at screening (84.3%). 54 of 227 Aa carriers had LAP (23.7%). In the longitudinal study 16 of 61 Aa-positives developed LAP (26.2%). 39 of 134 enrolled had pockets. 33 of 39 with pockets had Aa (84.6%)}. 16 subjects who developed BL were Aa-positive. Cross-sectional and longitudinal data in relation to Aa and disease were similar. Assessment of over 200 organisms by HOMIM showed pooled samples from subjects with pockets had elevated levels of Parvimonas micra, Filofactor alocis, Aa and Peptostreptococcus DA014 compared to pooled samples from healthy subjects. Streptococcus mitis, S. sanguis, S. salivarius, Veillonella parvula, and others were lower when these two groups were compared. Aa, F. alocis and S. parasanguis I and II were elevated in sites 6 months prior to BL. By combining the prevalence and levels of Aa, F. alocis and S. parasanguis the specificity to detect BL was elevated to 99% while the specificity was 89%. Conclusions: 1) Detection of Aa improves the chances of detecting patients susceptible to LAP from 2% (ethnicity alone) to over 20% (ethnicity and Aa). 2) Aa is necessary but not sufficient to initiate LAP. 2) LAP requires a consortium of organisms including F. alocis and S. parasanguis.
    IADR/AADR/CADR General Session and Exhibition 2013; 03/2013
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    ABSTRACT: Previous studies have demonstrated that HIV-infected individuals are at greater risk for oral microbial infections compared with non-HIV-infected controls. Objective: To quantitatively and qualitatively compare salivary microbiota profiles using two culture-independent survey methods, denaturing gradient gel electrophoresis (DGGE) and the human oral microbe identification microarray (HOMIM). Methods: Stimulated whole saliva samples were collected from 10 HIV-infected individuals before and 6 month after highly active antiretroviral therapy (HAART), and from 10 non-HIV-infected individuals. Total bacterial genomic DNA was isolated from each salivary sample and targeted 16S rRNA genes were PCR amplified. DGGE profiles of the 16S rRNA genes were analyzed using BioNumerics (Applied Maths, NV). Meanwhile, the same DNA samples were processed by HOMIM hybridization and were analyzed using MeV program (Dana-Farber Cancer Ins. MA). Results: The DGGE profile showed differences in the microbial distribution among the three groups; HAART reduced the microbial diversity. HOMIM data analysis showed that, of the 425 target probes, 121 were detected in the saliva samples. HIV-infected samples clustered separately from the non-HIV-infected samples. Species and phylotypes identified as different among the three groups were: Actinomyces gerencseriae (p<0.001), Aggregatibacter segnis (p<0.01), Atopobium sp (p<0.01), Capnocytophaga granulosa sp (p<0.05), Fusobacterium nucleatum (p<0.05), Fusobacterium periodontiumI (p<0.01), Haemophilus parainfluenzae (p<0.05), Neisseria Cluster II (p<0.05), Prevotella sp (p<0.05), and Streptococcus australis (p<0.05). Conclusion: HIV infection and subsequent HAART can significantly affect the oral microbial colonization and the microbial diversity in the saliva. Supported by research grant U19 DE018385 from the NIDCR/NIH.
    IADR/AADR/CADR General Session and Exhibition 2013; 03/2013

Publication Stats

13k Citations
698.21 Total Impact Points

Institutions

  • 1991–2015
    • The Forsyth Institute
      • Department of Cytokine Biology
      Cambridge, Massachusetts, United States
  • 2002–2014
    • Harvard University
      • • Department of Oral Medicine, Infection, and Immunity
      • • Department of Developmental Biology
      Cambridge, Massachusetts, United States
    • North Carolina State University
      • College of Veterinary Medicine
      Raleigh, North Carolina, United States
    • University of Wuerzburg
      • Institute for Hygiene and Microbiology
      Würzburg, Bavaria, Germany
  • 2012
    • King's College London
      • Dental Institute
      London, ENG, United Kingdom
  • 2009–2012
    • Federal University of Rio de Janeiro
      • Institute of Biology
      Rio de Janeiro, Rio de Janeiro, Brazil
  • 2001–2010
    • Harvard Medical School
      Boston, Massachusetts, United States
  • 1993–2010
    • Massachusetts Institute of Technology
      • Division of Comparative Medicine
      Cambridge, MA, United States
  • 1994–2003
    • University of Massachusetts Boston
      Boston, Massachusetts, United States
    • Humboldt-Universität zu Berlin
      Berlín, Berlin, Germany
  • 2000
    • Virginia Commonwealth University
      • Department of Periodontics
      Richmond, VA, United States
  • 1999
    • Biomedical Research Institute, Rockville
      Maryland, United States
  • 1998
    • Beverly Hospital, Boston MA
      BVY, Massachusetts, United States
  • 1995
    • Melbourne Institute of Technology
      Melbourne, Victoria, Australia
    • University of Minnesota Duluth
      Duluth, Minnesota, United States