Summary: The study of microorganisms such as fungi, bacteria, algae, archaea, and viruses.

Top Publications

  1. Gianoulis T, Raes J, Patel P, Bjornson R, Korbel J, Letunic I, et al. Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci U S A. 2009;106:1374-9 pubmed publisher
    ..g., temperature). Moreover, we identified covariation in amino acid transport and cofactor synthesis, suggesting that limiting amounts of cofactor can (partially) explain increased import of amino acids in nutrient-limited conditions. ..
  2. Sinkovics J. Horizontal gene transfers and cell fusions in microbiology, immunology and oncology (Review). Int J Oncol. 2009;35:441-65 pubmed
    ..Cell fusions and horizontal exchanges of genes are fundamental attributes and inherent characteristics of the living matter. ..
  3. O Malley M. What did Darwin say about microbes, and how did microbiology respond?. Trends Microbiol. 2009;17:341-7 pubmed publisher
    ..This limited response may be connected to today's assumptions about Darwin's neglect of microbes. ..
  4. La Scola B, Elkarkouri K, Li W, Wahab T, Fournous G, Rolain J, et al. Rapid comparative genomic analysis for clinical microbiology: the Francisella tularensis paradigm. Genome Res. 2008;18:742-50 pubmed publisher
    ..In the bioterrorism context, it allows the rapid detection of strain manipulation, including intentionally added virulence genes and genes that support antibiotic resistance. ..
  5. Loman N, Pallen M. XDR-TB genome sequencing: a glimpse of the microbiology of the future. Future Microbiol. 2008;3:111-3 pubmed publisher
  6. Georgiou A, Prgomet M, Toouli G, Callen J, Westbrook J. What do physicians tell laboratories when requesting tests? A multi-method examination of information supplied to the microbiology laboratory before and after the introduction of electronic ordering. Int J Med Inform. 2011;80:646-54 pubmed publisher
    ..1) To determine the quantity and importance of handwritten clinical information provided by physicians to the Microbiology Department of a hospital pathology service; and (2) to examine the impact of a Computerized Provider Order ..
  7. Watrous J, Dorrestein P. Imaging mass spectrometry in microbiology. Nat Rev Microbiol. 2011;9:683-94 pubmed publisher
    ..samples without the need for chemical tagging or antibodies, and are becoming increasingly useful for microbiology applications...
  8. Dworkin M. Sergei Winogradsky: a founder of modern microbiology and the first microbial ecologist. FEMS Microbiol Rev. 2012;36:364-79 pubmed publisher
    Sergei Winogradsky, was born in Russia in 1856 and was to become a founder of modern microbiology. After his Master's degree work on the nutrition and growth physiology of the yeast Mycoderma vini at the University of St...
  9. M ikanatha N, Dettinger L, Perry A, Rogers P, Reynolds S, Nachamkin I. Culturing stool specimens for Campylobacter spp., Pennsylvania, USA. Emerg Infect Dis. 2012;18:484-7 pubmed publisher
    ..Most (96.3%) routinely test for Campylobacter spp. In 17 (15.7%), a stool antigen test is the sole method for diagnosis. We recommend that laboratory practice guidelines for Campylobacter spp. testing be developed...

More Information


  1. Clark A, Kaleta E, Arora A, Wolk D. Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clin Microbiol Rev. 2013;26:547-603 pubmed publisher
    Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular ..
  2. Forterre P. In a world of microbes, where should microbiology stand?. Res Microbiol. 2008;159:74-80 pubmed publisher
  3. Stigi K, MacDonald J, Tellez Marfin A, Lofy K. Laboratory practices and incidence of non-O157 shiga toxin-producing Escherichia coli infections. Emerg Infect Dis. 2012;18:477-9 pubmed publisher
    ..Despite increased assay use, only half of processed stool specimens underwent Shiga toxin testing during 2010, suggesting substantial underdetection of non-O157 STEC infections. ..
  4. Ralebitso Senior T, Senior E, Di Felice R, Jarvis K. Waste gas biofiltration: advances and limitations of current approaches in microbiology. Environ Sci Technol. 2012;46:8542-73 pubmed publisher
    ..Finally, to negate discharge of fungal spores, and/or archaeal and/or bacterial cells, capture/destruction technologies are required to enable exploitation of the mineralization product CO(2). ..
  5. Medini D, Serruto D, Parkhill J, Relman D, Donati C, Moxon R, et al. Microbiology in the post-genomic era. Nat Rev Microbiol. 2008;6:419-30 pubmed publisher
    Genomics has revolutionized every aspect of microbiology. Now, 13 years after the first bacterial genome was sequenced, it is important to pause and consider what has changed in microbiology research as a consequence of genomics...
  6. Shuster M. Can genetics and genomics nursing competencies be successfully taught in a prenursing microbiology course?. CBE Life Sci Educ. 2011;10:216-21 pubmed publisher
    ..this study sought to assess the impact of incorporation of genetics and genomics content into a prenursing microbiology course...
  7. Mira A, Martín Cuadrado A, D Auria G, Rodriguez Valera F. The bacterial pan-genome:a new paradigm in microbiology. Int Microbiol. 2010;13:45-57 pubmed
    ..The pan-genome concept has important consequences for the way we understand bacterial evolution, adaptation, and population structure, as well as for more applied issues such as vaccine design or the identification of virulence genes. ..
  8. Lavigne J, Espinal P, Dunyach Remy C, Messad N, Pantel A, Sotto A. Mass spectrometry: a revolution in clinical microbiology?. Clin Chem Lab Med. 2013;51:257-70 pubmed
    ..This report emphasizes the (r)evolution of these technologies in clinical microbiology.
  9. Beylefeld A, Struwig M. A gaming approach to learning medical microbiology: students' experiences of flow. Med Teach. 2007;29:933-40 pubmed
    ..Faculty of Health Sciences at the University of the Free State to address students' negativity towards medical microbiology. The study population consisted of third-year medical students who had recently completed the Infections module ..
  10. Mullard A. Microbiology: the inside story. Nature. 2008;453:578-80 pubmed publisher
  11. Dinsdale E, Edwards R, Hall D, Angly F, Breitbart M, Brulc J, et al. Functional metagenomic profiling of nine biomes. Nature. 2008;452:629-32 pubmed publisher
  12. Markowitz V, Kyrpides N. Comparative genome analysis in the integrated microbial genomes (IMG) system. Methods Mol Biol. 2007;395:35-56 pubmed
    ..Genes can be further examined using gene neighborhoods and compared with sequence alignment tools. ..
  13. Lane N. Marine microbiology: origins of death. Nature. 2008;453:583-5 pubmed publisher
  14. Seifert K, Fenster A, Dilts J, Temple L. An investigative, cooperative learning approach to the general microbiology laboratory. CBE Life Sci Educ. 2009;8:147-53 pubmed publisher
    ..In the General Microbiology laboratory for juniors and seniors at James Madison University, these strategies were combined to make a ..
  15. Katawa G, Kpotsra A, Karou D, Eklou M, Tayi K, De Souza C. [Contribution to the establishment of quality assurance in five medical microbiology departments in Togo]. Bull Soc Pathol Exot. 2011;104:20-4 pubmed publisher
    ..This indicates a limited organization of such laboratories. The issue of this study showed that laboratories must be equipped, their technical organization should be improved and they must establish a program of equipment maintenance. ..
  16. Cohen Bacrie S, Ninove L, Nougairede A, Charrel R, Richet H, Minodier P, et al. Revolutionizing clinical microbiology laboratory organization in hospitals with in situ point-of-care. PLoS ONE. 2011;6:e22403 pubmed publisher
    Clinical microbiology may direct decisions regarding hospitalization, isolation and anti-infective therapy, but it is not effective at the time of early care. Point-of-care (POC) tests have been developed for this purpose.
  17. Bullman S, Lucey B, Sleator R. Molecular diagnostics: the changing culture of medical microbiology. Bioeng Bugs. 2012;3:1-7 pubmed publisher
  18. Martin J, Zenilman J, Lazarus G. Molecular microbiology: new dimensions for cutaneous biology and wound healing. J Invest Dermatol. 2010;130:38-48 pubmed publisher
    ..a concise description of infectious agents as defined by new molecular techniques and to summarize what is known about the microbiology of chronic wounds in order to relate them to the pathophysiology and therapy of chronic wounds.
  19. Novais R, Thorstenson Y. The evolution of Pyrosequencing® for microbiology: From genes to genomes. J Microbiol Methods. 2011;86:1-7 pubmed publisher
    ..In addition, we describe numerous applications in microbiology that have benefited from the pyrosequencing method.
  20. Luchnikov V, Lonov L, Stamm M. Self-rolled polymer tubes: novel tools for microfluidics, microbiology, and drug-delivery systems. Macromol Rapid Commun. 2011;32:1943-52 pubmed publisher
    ..The self-rolling approach is promising for the development of novel drug- and cell-delivery systems, as well as for tissue engineering. ..
  21. Kok J, Chen S, Dwyer D, Iredell J. Current status of matrix-assisted laser desorption ionisation-time of flight mass spectrometry in the clinical microbiology laboratory. Pathology. 2013;45:4-17 pubmed publisher
    ..matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS) into many clinical microbiology laboratories has revolutionised routine pathogen identification...
  22. Hannigan G, Grice E. Microbial ecology of the skin in the era of metagenomics and molecular microbiology. Cold Spring Harb Perspect Med. 2013;3:a015362 pubmed publisher
    ..Previously, dermatological microbiology research was dominated by culture-based techniques, but significant advances in genomic technologies have ..
  23. Budowle B, Schutzer S, Einseln A, Kelley L, Walsh A, Smith J, et al. Public health. Building microbial forensics as a response to bioterrorism. Science. 2003;301:1852-3 pubmed
  24. Emori T, Gaynes R. An overview of nosocomial infections, including the role of the microbiology laboratory. Clin Microbiol Rev. 1993;6:428-42 pubmed
    ..and Pseudomonas aeruginosa resistant to imipenem. The active involvement and cooperation of the microbiology laboratory are important to the infection control program, particularly in surveillance and the use of ..
  25. Ellis L, Hershberger C, Wackett L. The University of Minnesota Biocatalysis/Biodegradation database: microorganisms, genomics and prediction. Nucleic Acids Res. 2000;28:377-9 pubmed
  26. Ward G, Carey K, Westwood N. Using small molecules to study big questions in cellular microbiology. Cell Microbiol. 2002;4:471-82 pubmed
    ..article, we provide an overview of the methods and technical requirements and we discuss the potential of small molecule approaches to address important and often otherwise experimentally intractable problems in cellular microbiology.
  27. McKendrick M. The European Union of Medical Specialties core training curriculum in infectious diseases: overview of national systems and distribution of specialists. Clin Microbiol Infect. 2005;11 Suppl 1:28-32 pubmed
    ..The numbers of infection specialists (infectious diseases and microbiology) per million population show considerable variation...
  28. Ellis L, Roe D, Wackett L. The University of Minnesota Biocatalysis/Biodegradation Database: the first decade. Nucleic Acids Res. 2006;34:D517-21 pubmed
    ..The next decade should see the PPS, and the UM-BBD on which it is based, find increasing use by national and international government agencies, commercial organizations and educational institutions. ..
  29. Dunne W, Pinckard J, Hooper L. Clinical microbiology in the year 2025. J Clin Microbiol. 2002;40:3889-93 pubmed
  30. Saarela U, Kivinen T, Sarkkinen H. External failures as descriptor of quality in clinical microbiology laboratory services. Clin Chem Lab Med. 2005;43:54-63 pubmed
    ..customer feedback surveys to assess the quality of the laboratory services provided by an accredited clinical microbiology laboratory...
  31. Menzies D, Fanning A, Yuan L, FitzGerald J. Factors associated with tuberculin conversion in Canadian microbiology and pathology workers. Am J Respir Crit Care Med. 2003;167:599-602 pubmed
    The risk of occupational tuberculosis (TB) infection and associated factors was estimated among all microbiology and pathology technicians and compared with a sample of nonclinical personnel in 17 Canadian acute care hospitals...
  32. Fenselau C, Demirev P. Characterization of intact microorganisms by MALDI mass spectrometry. Mass Spectrom Rev. 2001;20:157-71 pubmed
    ..Optimally these analyses should be carried out in less than five minutes. Successful applications are discussed from biotechnology, cell biology, and the pharmaceutical industry. ..
  33. Donay J, Mathieu D, Fernandes P, Prégermain C, Bruel P, Wargnier A, et al. Evaluation of the automated phoenix system for potential routine use in the clinical microbiology laboratory. J Clin Microbiol. 2004;42:1542-6 pubmed
    ..the identification (ID) and antimicrobial susceptibility testing (AST) performances of the BD Phoenix Automated Microbiology System (Becton Dickinson Diagnostic Systems [BD], Pont de Claix, France)...
  34. Atlas R. Bioterrorism and biodefence research: changing the focus of microbiology. Nat Rev Microbiol. 2003;1:70-4 pubmed
    ..There are some concerns, however, that a large emphasis on this issue could skew the microbiology research agenda...
  35. Villanueva J. The development of microbiology in Spain. Int Microbiol. 2003;6:1-2 pubmed
  36. Baker N, Verran J. The future of microbiology laboratory classes--wet, dry or in combination?. Nat Rev Microbiol. 2004;2:338-42 pubmed
  37. Freeman R. Microbiology workload. J Clin Pathol. 2002;55:734 pubmed
  38. Dufrêne Y. Recent progress in the application of atomic force microscopy imaging and force spectroscopy to microbiology. Curr Opin Microbiol. 2003;6:317-23 pubmed
    Atomic force microscopy imaging and force spectroscopy have recently opened a range of novel applications in microbiology. During the past two years, rapid advances have been made using atomic force microscopy to visualize the surface ..
  39. Drews G. The roots of microbiology and the influence of Ferdinand Cohn on microbiology of the 19th century. FEMS Microbiol Rev. 2000;24:225-49 pubmed
    The beginning of modern microbiology can be traced back to the 1870s, and it was based on the development of new concepts that originated during the two preceding centuries on the role of microorganisms, new experimental methods, and ..
  40. Mermel L, Josephson S, Dempsey J, Parenteau S, Perry C, Magill N. Outbreak of Shigella sonnei in a clinical microbiology laboratory. J Clin Microbiol. 1997;35:3163-5 pubmed
    ..Covering faucet handles with paper towels during hand washing in the laboratory was protective. No further cases occurred after the laboratory was cleaned with a phenolic agent and a handle-free faucet was installed...
  41. Yuan S, Astion M, Schapiro J, Limaye A. Clinical impact associated with corrected results in clinical microbiology testing. J Clin Microbiol. 2005;43:2188-93 pubmed
    We developed a strategy to determine the clinical impact associated with errors in clinical microbiology testing...
  42. Kuypers M, Jørgensen B. The future of single-cell environmental microbiology. Environ Microbiol. 2007;9:6-7 pubmed
  43. Lichtfouse E. Compound-specific isotope analysis. Application to archaeology, biomedical sciences, biosynthesis, environment, extraterrestrial chemistry, food science, forensic science, humic substances, microbiology, organic geochemistry, soil science and sport. Rapid Commun Mass Spectrom. 2000;14:1337-44 pubmed
    ..After a brief glance at pioneering studies revealing isotopic breakthroughs at the molecular and intramolecular levels, this paper reviews selected applications of compound-specific isotope analysis in various scientific fields. ..
  44. Yanofsky C. Advancing our knowledge in biochemistry, genetics, and microbiology through studies on tryptophan metabolism. Annu Rev Biochem. 2001;70:1-37 pubmed
    ..Throughout my career I enjoyed the excitement of solving basic scientific problems. Most rewarding, however, was the feeling that I was helping young scientists experience the pleasure of performing creative research. ..
  45. Weibel D, DiLuzio W, Whitesides G. Microfabrication meets microbiology. Nat Rev Microbiol. 2007;5:209-18 pubmed
    ..methods for constructing systems and structures at micron or submicron scales that have applications in microbiology. These tools make it possible to manipulate individual cells and their immediate extracellular environments and ..
  46. Bouza E, San Juan R, Munoz P, Pascau J, Voss A, Desco M. A European perspective on intravascular catheter-related infections: report on the microbiology workload, aetiology and antimicrobial susceptibility (ESGNI-005 Study). Clin Microbiol Infect. 2004;10:838-42 pubmed
    ..a 1-day (22 October 2001), laboratory-based, point-prevalence survey based on a questionnaire completed by microbiology laboratories in European (European Union (EU) and non-EU) hospitals...
  47. Budowle B. Genetics and attribution issues that confront the microbial forensics field. Forensic Sci Int. 2004;146 Suppl:S185-8 pubmed
    ..Differences include: database size and composition, statistical interpretation methods, and confidence/uncertainty in the outcome of an interpretation. ..
  48. Isenberg H. Clinical microbiology: past, present, and future. J Clin Microbiol. 2003;41:917-8 pubmed
  49. Peterson L, Hamilton J, Baron E, Tompkins L, Miller J, Wilfert C, et al. Role of clinical microbiology laboratories in the management and control of infectious diseases and the delivery of health care. Clin Infect Dis. 2001;32:605-11 pubmed
    ..resources now threaten our ability to adequately manage threats of infectious diseases by placing clinical microbiology services and expertise distant from the patient and their infectious diseases physician...
  50. Ward N, Fraser C. How genomics has affected the concept of microbiology. Curr Opin Microbiol. 2005;8:564-71 pubmed
    Genomics influences multiple areas of microbiology, and thus affects key microbiological concepts...
  51. Román E, Valencia R, Fernández Merino J, Gallardo M. [Contribution of the microbiology laboratory to epidemiologic surveillance]. Enferm Infecc Microbiol Clin. 2003;21:387-8 pubmed
  52. Canton R. Role of the microbiology laboratory in infectious disease surveillance, alert and response. Clin Microbiol Infect. 2005;11 Suppl 1:3-8 pubmed
    ..clinical microbiology laboratories play a pivotal role in these programmes...
  53. Vergidis P, Karavasiou A, Paraschakis K, Bliziotis I, Falagas M. Bibliometric analysis of global trends for research productivity in microbiology. Eur J Clin Microbiol Infect Dis. 2005;24:342-6 pubmed
    ..the limited literature estimating the quantity and quality of worldwide research production in the field of microbiology, a bibliometric analysis was conducted for the period 1995-2003 using the PubMed and Journal Citation Reports ..