Streptococcus pneumoniae
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2016 Career Development Grants for Postdoctoral Women Recipients
- Publication Date : December 2016
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The ASM Membership Board is pleased to announce the recipients of the 2016 Career Development Grants for Postdoctoral Women:
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Ancient Resistome
- Authors: Abiola Olumuyiwa Olaitan, Jean-Marc Rolain
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Citation: Olaitan A, Rolain J. 2016. Ancient resistome. 4(4): doi:10.1128/microbiolspec.PoH-0008-2015
- DOI 10.1128/microbiolspec.PoH-0008-2015
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Abstract:
Antibiotic resistance is an ancient biological mechanism in bacteria, although its proliferation in our contemporary world has been amplified through antimicrobial therapy. Recent studies conducted on ancient environmental and human samples have uncovered numerous antibiotic-resistant bacteria and resistance genes. The resistance genes that have been reported from the analysis of ancient bacterial DNA include genes coding for several classes of antibiotics, such as glycopeptides, β-lactams, tetracyclines, and macrolides. The investigation of the resistome of ancient bacteria is a recent and emerging field of research, and technological advancements such as next-generation sequencing will further contribute to its growth. It is hoped that the knowledge gained from this research will help us to better understand the evolution of antibiotic resistance genes and will also be used in drug design as a proactive measure against antibiotic resistance.
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Reflections on Rockefeller University Contributions to Microbiology—Yesterday, Today, and Tomorrow
- Author: Stanley Maloy
- Publication Date : August 2015
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Author: Stanley MaloyAbstract:
When the Rockefeller Institute for Medical Research was founded in 1901, infectious diseases were the most serious threat to human health—typhoid fever, tuberculosis, and diphtheria killed many people around the world, primarily poorer people but not sparing the affluent. In fact, the death of John Rockefeller's grandson of scarlet fever that year is said to have been the stimulus for the creation of the Rockefeller Institute.
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Introductory Immunology: Begin the Journey
- Author: Narveen Jandu
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Citation: Jandu N. 2015. Introductory immunology: begin the journey. 16(1):94-95 doi:10.1128/jmbe.v16i1.899
- DOI 10.1128/jmbe.v16i1.899
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Abstract:
Review of: Primer to the Immune Response, 2nd ed.; Tak Mak, Mary Saunders, and Bradley Jett; (2014). Elsevier Inc., London, UK. 702 pages.
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Escherich and Escherichia
- Author: Herbert C. Friedmann
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Citation: Friedmann H. 2014. Escherich and Escherichia, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0025-2013
- DOI 10.1128/ecosalplus.ESP-0025-2013
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Abstract:
The purpose of this essay is threefold: to give an outline of the life and the various achievements of Theodor Escherich, to provide a background to his discovery of what he called Bacterium coli commune (now Escherichia coli), and to indicate the enormous impact of studies with this organism, long before it became the cornerstone of research in bacteriology and in molecular biology.
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General Approaches to Identification of Aerobic Gram-Positive Cocci
- Author: Kathryn L. Ruoff
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Source: Manual of Clinical Microbiology, 10th Edition , pp 304-307
Publication Date :
January 2011
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Abstract:
Majority of aerobic, or facultatively aerobic, gram-positive cocci isolated from clinical specimens are distributed among the genera Staphylococcus, Streptococcus, and Enterococcus. This chapter provides tables containing organisms with similar cellular morphologies, either "streptococcal," consisting of gram-positive cocci or coccobacilli arranged primarily in pairs and/or chains, or "staphylococcal," signifying that cells appear as cocci arranged in pairs, tetrads, clusters, and irregular groups. The commonly isolated aerobic gram-positive cocci (staphylococci, streptococci, enterococci) can usually be accurately identified by determining a few basic phenotypic traits (cellular morphology, catalase reaction, and production of pyrrolidonyl arylamidase [PYR]). The chapter highlights the fact that it is increasingly difficult to identify some of the less frequently isolated organisms solely on the basis of phenotypic traits, as new genera and species of aerobic gram-positive cocci are described and characterized. Basic phenotypic tests can usually suggest a possible identity for strains of infrequently encountered aerobic gram-positive cocci, but evaluation with a larger battery of phenotypic tests or molecular identification methods is often valuable, if not indispensible, for accurate identification. Nucleic acid probe tests and amplification methods for identification of some of the commonly isolated aerobic gram-positive cocci are commercially available and designed for use in medium to large-volume clinical microbiology laboratories. The chapter concludes by emphasizing that the comparison of 16S rRNA gene sequences is the most useful method for molecular characterization of the aerobic gram-positive cocci of clinical interest, although sequence comparison of other genes may also be helpful for identification.
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Aerococcus, Abiotrophia, and Other Aerobic Catalase-Negative, Gram-Positive Cocci
- Author: Kathryn L. Ruoff
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Source: Manual of Clinical Microbiology, 10th Edition , pp 365-376
Publication Date :
January 2011
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Abstract:
The aerobic catalase-negative gram-positive cocci included in this chapter form a taxonomically diverse group of bacteria that are isolated infrequently as opportunistic agents of infection. The genera Abiotrophia and Granulicatella accommodate organisms previously known as nutritionally variant or satelliting streptococci. Most of the genera described here are catalase-negative facultative anaerobes, but Aerococcus viridans are classified as a microaerophile that grows poorly, if at all, under anaerobic conditions. Some strains of Aerococcus may exhibit weakly positive catalase reactions due to nonheme catalase activity. Commercially available identification kits or systems offering a more comprehensive array of phenotypic tests are improving in their ability to identify many of the organisms discussed in the chapter. Serologic response to the organisms described in this chapter has not been extensively investigated. Antimicrobial susceptibility studies on the organisms mentioned in the chapter have generally employed dilution testing methods. The lack of standardized methods and interpretive criteria and the relatively small collections of isolates for some of the genera discussed in the chapter make it difficult to accurately assess antimicrobial susceptibility patterns. Efforts to identify the gram-positive cocci included in the chapter should be made only when isolates are considered to be clinically significant, since the organisms may also appear in clinical cultures as contaminants or constituents of the normal microbiota. More extensive phenotypic testing using commercially available identification systems and molecular methods should be employed for definitive identification.
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Systems for Detection and Identification of Bacteria and Yeasts *
- Authors: Cathy A. Petti, Melvin P. Weinstein, Karen C. Carroll
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Source: Manual of Clinical Microbiology, 10th Edition , pp 15-26
Publication Date :
January 2011
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Abstract:
Traditionally, the detection and identification of bacteria were based on conventional tube-based biochemical reactions, and their results were compared to historical charts of expected biochemical reactions. Automation in microbiology first occurred in the early 1970s with the introduction of semiautomated blood culture instruments, followed by instrumented systems for identification and susceptibility testing of bacteria. This chapter reviews the systems used for the detection of bacteria and yeasts from blood and provides an overview of technologies for microorganism identification. The volume of blood obtained for culture is one of the most important variables in the detection of bloodstream infections (BSIs). The chapter describes the identification of microorganisms by nonphenotypic methods from instrument-flagged blood culture bottles, and from pure culture. The approximate turnaround time of the fluorescence in situ hybridization (FISH) procedure is 2.5 to 3 h (without batch testing), compared with >18 to 24 h for identification of bacteria and yeasts by conventional methods. The selection of DNA targets to identify bacteria and fungi relies on the concept that some genes have conserved segments flanked by variable regions. The technology is based on analyzing the protein composition of a bacterial cell, with ribosomal proteins comprising most bacterial proteins being detected. Another technique to characterize bacteria is the application of electrospray ionization-mass spectrometry to analyze products of multilocus, broad-range PCR (PCR/ESI-MS).
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Antibacterial Agents
- Authors: Joseph D. C. Yao, Robert C. Moellering
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Source: Manual of Clinical Microbiology, 10th Edition , pp 1043-1081
Publication Date :
January 2011
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Abstract:
Antimicrobial chemotherapy has played a vital role in the treatment of human infectious diseases since the discovery of penicillin in the 1920s. Hundreds of antimicrobial agents have been developed or synthesized to date, and a broad number and variety of agents are currently available for clinical use. However, the sheer numbers and continuing development of agents make it difficult for clinicians to keep up with progress in the field. This chapter provides an overview of the antibacterial agents currently marketed in the United States, with major emphasis on their mechanisms of action, spectra of activity, important pharmacologic parameters, and toxicities. The major antibacterial action of penicillins is derived from their ability to inhibit a number of bacterial enzymes, namely penicillin-binding proteins (PBPs), that are essential for peptidoglycan synthesis. Cephalosporins are generally very well tolerated. The monobactams are β-lactams with various side chains affixed to a monocyclic nucleus. Since the first aminoglycoside, streptomycin, was introduced, this class of antibiotic has played a vital role in the treatment of serious gram-negative infections. The currently available aminoglycosides are derived from Micromonospora spp. or from Streptomyces spp. Tetracyclines are broad-spectrum bacteriostatic antibiotics with the hydronaphthacene nucleus, which contains four fused rings. Glycylcyclines are a group of semisynthetic tetracycline derivatives containing a glycylamido substitution at position 9. Streptogramins are natural cyclic peptides produced by Streptomyces spp. They are a unique class of antibiotics in which each member is a combination of at least two structurally unrelated components, groups A and B streptogramins.
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Susceptibility Testing Instrumentation and Computerized Expert Systems for Data Analysis and Interpretation
- Authors: Sandra S. Richter, Mary Jane Ferraro
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Source: Manual of Clinical Microbiology, 10th Edition , pp 1144-1154
Publication Date :
January 2011
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Abstract:
Commercial antimicrobial susceptibility testing (AST) systems were introduced into clinical microbiology laboratories during the 1980s and have been used in the majority of laboratories since the 1990s. Manual and semiautomated broth microdilution systems are utilized for small volumes of susceptibility testing, while larger laboratories often choose an automated broth microdilution system. The AST systems include data management software that may be interfaced with a laboratory information system (LIS) and offer various levels of expert system and epidemiological analyses. This chapter focuses primarily on commercial susceptibility testing systems currently available in the United States. It discusses advantages and disadvantages of automated systems. Reports of AST performance for detecting problematic resistance phenotypes are also discussed. Expert systems to assist in the critical review of AST results are available for all commercial susceptibility systems currently marketed in the United States. Most expert systems use a rules-based approach focusing on AST results for one drug at a time without considering results for other agents tested simultaneously. Factors to consider when selecting an AST system include cost, performance, work flow, data management capabilities, and manufacturer technical support. Future advances in the development of AST systems may increase their clinical impact with the incorporation of molecular techniques that dramatically shorten the time required for results.
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Applications of Fluorescence In Situ Hybridization in Diagnostic Microbiology
- Authors: Stefan Juretschko, Thomas R. Fritsche
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Source: Molecular Microbiology , pp 3-19
Publication Date :
January 2011
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Abstract:
The presence of a sufficient number of target molecules is critical in detecting conferred fluorescence of probe-target hybrids and permits direct visualization of intact organisms by epifluorescence microscopy. This direct approach to visualization of organisms using fluorescence in situ hybridization (FISH) simultaneously provides information on phylogenetic relationships of organisms, their spatial distribution in the sample matrix, their relative abundance, and their relative physiologic activity. An incubator, a water bath, and an epifluorescence microscope are essential, with the microscope being most critical for successful FISH performance. The main goal in designing specific probes is to find a suitable and unique region within the 16S or 23S rRNA that permits discrimination of target from nontarget organisms. Once a probe has been designed and confirmed to be specific for the motif desired by using the appropriate databases, it must be evaluated against a series of reference organisms. In case of a low number of ribosomes, the simultaneous application of two fluorescence-monolabeled probes targeting two different regions of rRNA with the same specificity would theoretically result in a twofold amplification of signal intensity when applied to the test samples. The chapter talks about expanded techniques combined with FISH. FISH, based upon either DNA or PNA oligonucleotide probes, is a rapid diagnostic method capable of challenging traditional culture techniques for the direct and accurate identification not only of nonfastidious pathogens but also of fastidious, slow-growing, and difficult-to-cultivate organisms.
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DNA Probes for Culture Confirmation and Direct Detection of Bacterial and Fungal Infections: a Review of Current Technologies and Assays
- Authors: Julie Kingery, Karen C. Carroll
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Source: Molecular Microbiology , pp 21-30
Publication Date :
January 2011
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Abstract:
This chapter focuses on nonamplified nucleic acid probes and their current uses in the clinical laboratory. DNA probes are pieces of nucleic acid that are labeled in some way and are designed to seek out and bind to stretches of DNA or RNA that have sequences that are complementary to the probe. In hybridization reactions, a double-stranded DNA molecule is denatured to single strands. Several formats for the hybridization reactions exist: solid phase; in solution (liquid phase); in situ; or by use of a Southern hybridization procedure after gel electrophoresis. In sandwich hybridization assays, one probe is attached to a solid support such as a nitrocellulose filter in single-stranded form and ‘‘captures’’ homologous nucleic acids in liquid samples; a second probe, which recognizes a contiguous area of the nucleic acid, carries the reporter molecule such as a radioisotope or biotin. The target and probe nucleic acids are free to move in solution, maximizing chances that complementary sequences will bind. Southern hybridization involves using purified DNA that is cleaved with restriction endonucleases. There are numerous methods for detecting the binding of probe to target nucleic acid. Commercially available DNA probes used for culture confirmation of bacteria, mycobacteria, and fungi are discussed in the chapter. Of the assays discussed in the chapter, probes for the detection of mycobacteria have had the greatest clinical impact. The chapter describes the utility of nonamplified probes for the diagnosis of sexually transmitted diseases, vaginal infections, and streptococcal pharyngitis.
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Identification of Bacteria by DNA Target Sequencing in a Clinical Microbiology Laboratory
- Authors: Rosemary C. She, Keith E. Simmon, Cathy A. Petti
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Source: Molecular Microbiology , pp 479-489
Publication Date :
January 2011
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Abstract:
Nucleic acid sequencing of various bacterial genes and other DNA targets has been used for determining the phylogeny of bacteria and for their identification. A brief overview of nucleic acid sequencing is shown in this chapter. DNA targets have conserved regions flanking variable regions that can be used to differentiate closely related bacterial species. The routine use of sequencing can greatly enhance the ability of the clinical microbiology laboratory to identify bacteria on many levels. Of consideration in the routine use of DNA target sequencing is the need for technical expertise and its cost. The chapter addresses preparation of DNA from pure culture. Certain conventional methods such as latex agglutination assays are quicker, simpler, and less expensive than DNA target sequencing for the identification of beta-hemolytic streptococci. Basic conventional methods perform well in identifying common isolates, such as Bacteroides fragilis group, Peptostreptococcus spp., and most Clostridium spp. DNA target sequencing can provide more accurate identifications, especially since databases from conventional methods often are not current and do not reflect the tremendous genetic diversity within anaerobic taxa. For agents of bioterrorism, i.e., Bacillus anthracis, Brucella spp., Clostridium botulinum, Francisella tularensis, and Yersinia pestis, 16S rRNA sequencing has varying utility. Molecular studies have enhanced our knowledge about the taxonomical diversity among bacteria and allowed better definition of the epidemiology of bacterial infections.
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Color Plates
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Source: Molecular Microbiology
Publication Date :
January 2011
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No descriptions available.
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Index
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Source: Molecular Microbiology
Publication Date :
January 2011
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No descriptions available.
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Genomes of Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis
- Authors: Hervé Tettelin, Mogens Kilian
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Source: Oral Microbial Communities , pp 37-42
Publication Date :
January 2011
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Abstract:
This chapter talks about the closest relatives of Streptococcus mitis that are the commensals S. oralis, S. infantis, and, in particular, the important pathogen Streptococcus pneumoniae and the still relatively unknown Streptococcus pseudopneumoniae. The genetic diversity among S. mitis strains may have important consequences in the oral cavity. Draft genomes display an artificially high total number of genes and number of paralogs due to sequencing errors and gaps leading to gene fragmentation, as well as low-quality redundant sequences at contig ends. The verification results in the conclusion that this observation is not due to the fact that (i) all but one of the non-S. pneumoniae genomes studied are draft genomes, and (ii) gene prediction standards differ among sequencing centers. First, the closed S. mitis B6 genome displays a higher coding percentage. Second, the coding density was measured in three unpublished draft S. pneumoniae genomes obtained from three different sequencing centers, and the average coding percentage was 84.9%. The previous observation that virtually every independent isolate of S. mitis represents a distinct species according to traditional taxonomic principles is supported by our multigenome analysis. The significant sharing of core genes between S. mitis and S. pneumoniae reinforces the conclusion that S. pneumoniae is one lineage of the S. mitis complex.
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Competence-Stimulating Peptides in Oral Bacterial Signaling: Possible Implications in a Community Life
- Authors: Fernanda Cristina Petersen, Anne Aamdal Scheie
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Source: Oral Microbial Communities , pp 235-246
Publication Date :
January 2011
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Abstract:
The first studies focusing on the competence-stimulating peptide (CSP) system were prompted by investigations to understand competence development for natural transformation. CSP signals and regulatory pathways are found in most oral streptococci. The molecular mechanisms involved in CSP signaling have been described in more detail for Streptococcus pneumoniae than for other streptococci. The CSP autoinducing system is remarkably closely related to well-characterized bacteriocin autoinducing systems. Genetic competence and bacteriocin production appear to be closely linked in streptococci. It is possible, that the mechanisms involved in competence for genetic transformation are somehow uncoupled with the stress response to spectinomycin. The absence of one of the two components of the histidine kinase/response regulator ComDE impairs the increased biofilm formed in the presence of CSP, supporting the specificity of the response. The possible contribution of lysis and DNA binding to the CSP effect on biofilm formation is supported by the findings that mutants of Staphylococcus mutans deficient in the DNA binding and uptake machinery form less biofilm and that degradation of extracellular DNA reduces biofilm formation in streptococci. In the multicellular communities found in the oral cavity, natural interference with autoinducing signaling systems such as the CSP signaling pathway might be a natural scenario, depending on how the bacteria are structurally distributed in biofilms. Present efforts to sequence microbes commonly colonizing humans will certainly provide important tools to deepen our understanding of the interactions between microorganisms in complex communities, and the human responses to these communities.
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Heterotypic Streptococcus gordonii-Porphyromonas gingivalis Communities: Formation, Gene Regulation, and Development
- Authors: Masae Kuboniwa, Richard J. Lamont
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Source: Oral Microbial Communities , pp 313-329
Publication Date :
January 2011
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Abstract:
The composition of oral biofilm communities, and their pathogenic potential, may depend on interspecies binding and communication interactions. Multivalent coadhesive interactions characterize the binding of Porphyromonas gingivalis to oral streptococci such as Streptococcus gordonii and drive subsequent development of heterotypic S. gordonii-P. gingivalis communities. Gene regulation by two-component systems (TCSs) is a common mechanism used by bacteria to modulate cell behavior in response to environmental changes. Following the initial binding interaction between P. gingivalis and S. gordonii, adherent P. gingivalis cells undergo a programmatic phenotypic shift in order to prepare for community living. P. gingivalis produces autoinducer 2 (AI-2) and responds both to homologous signal and to AI-2 from other organisms such as S. gordonii and Actinobacillus actinomycetemcomitans. The expression of GTF, Rgg, and exo-β;-D-fructosidase (fructanase) is downregulated in the absence of LuxS, whereas expression of tagatose 1,6-diphosphate aldolase is elevated. Contact with S. cristatus propagates a signal in P. gingivalis that causes downregulation of fimA expression. Signaling is mediated by arginine deiminase (ArcA) on the surface of Streptococcus cristatus. Biofilms tend to be polymicrobial in nature, and the subgingival plaque biofilm is an exemplar of this situation, with as many as 200 species present in any one individual.
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INDEX
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Source: Oral Microbial Communities
Publication Date :
January 2011
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No descriptions available.
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Index
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Source: Pathogens and Toxins in Foods
Publication Date :
January 2010
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No descriptions available.
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