- A molecular view of microbial diversity and the biosphere
N R Pace
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
Science 276:734-40. 1997
- Microbial diversity in the deep sea and the underexplored "rare biosphere"
Mitchell L Sogin
Josephine Bay Paul Center, Marine Biological Laboratory at Woods Hole, 7 MBL Street, Woods Hole, MA 02543, USA
Proc Natl Acad Sci U S A 103:12115-20. 2006
..Members of the rare biosphere are highly divergent from each other and, at different times in earth's history, may have had a profound impact on shaping planetary processes...
- Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness
Patrick D Schloss
Department of Plant Pathology, University of Wisconsin Madison, 1630 Linden Dr, Madison, WI 53706, USA
Appl Environ Microbiol 71:1501-6. 2005
..We anticipate that an equivalent extent of sampling for soil would require sampling more than 10,000 sequences, almost 100 times the size of typical sequence collections obtained from soil...
- Community structure and metabolism through reconstruction of microbial genomes from the environment
Gene W Tyson
Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA
Nature 428:37-43. 2004
..Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment...
- Metagenomics: application of genomics to uncultured microorganisms
Department of Plant Pathology, University of Wisconsin Madison, Madison, WI 53706, USA
Microbiol Mol Biol Rev 68:669-85. 2004
..The application of metagenomic sequence information will facilitate the design of better culturing strategies to link genomic analysis with pure culture studies...
- Mycobacterium ulcerans in mosquitoes captured during outbreak of Buruli ulcer, southeastern Australia
Paul D R Johnson
Infectious Disease Department, Austin Health, Melbourne, Victoria, Australia
Emerg Infect Dis 13:1653-60. 2007
..Forty-eight pools (5 species) were positive for insertion sequence IS2404 (maximum likelihood estimate 4.3/1,000), and we confirmed the presence of M. ulcerans in a subset of pools by detection of 3 additional PCR targets...
- BIPES, a cost-effective high-throughput method for assessing microbial diversity
Hong Wei Zhou
Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, Guangdong, China
ISME J 5:741-9. 2011
..As a laborsaving and cost-effective method, BIPES can be routinely used to analyze the microbial ecology of both environmental and human microbiomes...
- A major role for mammals in the ecology of Mycobacterium ulcerans
Janet A M Fyfe
Victorian Infectious Diseases Reference Laboratory, North Melbourne, Victoria, Australia
PLoS Negl Trop Dis 4:e791. 2010
..The purpose of this study was to investigate the environmental distribution of M. ulcerans in south-eastern Australia...
- Characterization of environmental sources of the human and animal pathogen Cryptococcus gattii in British Columbia, Canada, and the Pacific Northwest of the United States
Sarah E Kidd
School of Occupational and Environmental Hygiene, 364 2206 East Mall, Vancouver, University of British Columbia V6T 1Z3, Canada
Appl Environ Microbiol 73:1433-43. 2007
..Our findings indicate extensive colonization by C. gattii within British Columbia and highlight an expansion of the ecological niche of this pathogen...
- Nitrogenase gene diversity and microbial community structure: a cross-system comparison
Jonathan P Zehr
Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
Environ Microbiol 5:539-54. 2003
..The broad analysis of nitrogenase genes provides a basis for developing molecular assays and bioinformatics approaches for the study of nitrogen fixation in the environment...
- Environmental detection of octahaem cytochrome c hydroxylamine/hydrazine oxidoreductase genes of aerobic and anaerobic ammonium-oxidizing bacteria
Markus C Schmid
Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands
Environ Microbiol 10:3140-9. 2008
..We propose that OCC protein-encoding genes are suitable targets for molecular ecological studies on both aerobic and anaerobic ammonium-oxidizing bacteria...
- Ecology and transmission of Buruli ulcer disease: a systematic review
Richard W Merritt
Department of Entomology, Michigan State University, East Lansing, Michigan, USA
PLoS Negl Trop Dis 4:e911. 2010
..The application of these criteria to the transmission of M. ulcerans presents a significant challenge...
- Measuring the effect of enhanced cleaning in a UK hospital: a prospective cross-over study
Stephanie J Dancer
Department of Microbiology, Hairmyres Hospital, East Kilbride, UK
BMC Med 7:28. 2009
..This study aimed to evaluate the potential impact of one additional cleaner by using microbiological standards based on aerobic colony counts and the presence of Staphylococcus aureus including meticillin-resistant S. aureus...
- Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches
Institute of Marine Sciences, CSIC, Barcelona ES 08003, Spain
J Microbiol Methods 91:106-13. 2012
The incursion of High-Throughput Sequencing (HTS) in environmental microbiology brings unique opportunities and challenges...
- Development of a recA gene-based identification approach for the entire Burkholderia genus
George W Payne
Cardiff School of Biosciences, Main Building, Museum Avenue, PO Box 915, Cardiff University, Cardiff, Wales CF10 3TL, United Kingdom
Appl Environ Microbiol 71:3917-27. 2005
..cepacia complex strains recovered from clinical infection versus the natural environment, it did facilitate the identification of clonal strain types of B. cepacia, B. stabilis, and B. ambifaria capable of residing in both niches...
- Diverse circovirus-like genome architectures revealed by environmental metagenomics
College of Marine Science, University of South Florida, St Petersburg, FL 33701, USA
J Gen Virol 90:2418-24. 2009
..Investigating the complex community of ssDNA viruses in the environment can lead to the discovery of divergent species and help elucidate evolutionary links between ssDNA viruses...
- Diversity and seasonal dynamics of bacterial community in indoor environment
Environmental Health Department, National Public Health Institute, P, O, Box 95, 70701 Kuopio, Finland
BMC Microbiol 8:56. 2008
..The application of molecular methods previously utilised in other environments has resulted in a substantial increase in our awareness of microbial diversity...
- Use of the ITS primers, ITS1F and ITS4, to characterize fungal abundance and diversity in mixed-template samples by qPCR and length heterogeneity analysis
Daniel K Manter
USDA ARS, Soil Plant Nutrient Research Unit, Ft Collins, CO, United States
J Microbiol Methods 71:7-14. 2007
..Variability associated with the individual steps of the LH-qPCR analysis was also determined from environmental samples...
- Molecular epidemiology of clinical and environmental isolates of the Cryptococcus neoformans species complex reveals a high genetic diversity and the presence of the molecular type VGII mating type a in Colombia
Grupo de Microbiologia, Instituto Nacional de Salud, Bogota, Colombia
FEMS Yeast Res 6:625-35. 2006
..The data presented form part of the Colombian contribution to the ongoing global survey of the C. neoformans species complex...
- Experimental tests of the bacterial distance-decay relationship
Department of Zoology, University of Oxford, South Parks Road, Oxford, UK
ISME J 4:1357-65. 2010
- Simultaneous analysis of microbial identity and function using NanoSIMS
Cemagref, Unité de Recherche Hydrosystèmes et Bioprocédés, Parc de Tourvoie, BP 44, 92163 Antony cedex, France
Environ Microbiol 10:580-8. 2008
..The applicability of this new technique to the study of in situ ecophysiology of uncultured microorganisms within complex microbial communities is illustrated...
- Regional pattern of the molecular types of Cryptococcus neoformans and Cryptococcus gattii in Brazil
Molecular Mycology Research Laboratory, Center for Infectious Diseases and Microbiology, Westmead Hospital, Westmead Millennium Institute, Western Clinical School, University of Sydney, Sydney, Australia
Mem Inst Oswaldo Cruz 103:455-62. 2008
- Prevalence and risk factor analysis of livestock associated MRSA-positive pig herds in The Netherlands
E M Broens
Quantitative Veterinary Epidemiology Group, Wageningen Institute of Animal Sciences, Wageningen University, P O Box 338, 6700 AH Wageningen, The Netherlands
Prev Vet Med 102:41-9. 2011
..Herd size appeared to be a compilation of several factors, which made larger herds more often MRSA positive...
- Culture clash: challenging the dogma of microbial diversity
Stuart P Donachie
Department of Microbiology, University of Hawai i, Honolulu, HI, USA
ISME J 1:97-9. 2007
- Rubrobacter bracarensis sp. nov., a novel member of the genus Rubrobacter isolated from a biodeteriorated monument
Instituto de Recursos Naturales y Agrobiologia, IRNAS CSIC, Av Reina Mercedes 10, 41012 Sevilla, Spain
Syst Appl Microbiol 35:306-9. 2012
..These data clearly showed that the three strains could represent a new species, for which we propose the name Rubrobacter bracarensis sp. nov., with strain VF70612_S1(T) (=CECT 7924=DSMZ 24908) as the type strain...
- Microbes on building materials--evaluation of DNA extraction protocols as common basis for molecular analysis
Jörg D Ettenauer
VIBT BOKU, University of Natural Resources and Life Sciences, Department of Biotechnology, Muthgasse 11, A 1190 Vienna, Austria
Sci Total Environ 439:44-53. 2012
..Therefore, we suggest this method as a gold standard for quantification of indoor fungi and bacteria in building materials...
- What is on that keyboard? Detecting hidden environmental reservoirs of Clostridium difficile during an outbreak associated with North American pulsed-field gel electrophoresis type 1 strains
Donald M Dumford
Department of Medicine, University Hospitals of Cleveland, Cleveland, OH, USA
Am J Infect Control 37:15-9. 2009
..However, less information is available regarding the frequency of contamination of environmental surfaces outside of CDI isolation rooms...
- Replication, lies and lesser-known truths regarding experimental design in environmental microbiology
Jay T Lennon
W K Kellogg Biological Station Department of Microbiology and Molecular Genetics, Michigan State University, Hickory Corners, MI 49060, USA
Environ Microbiol 13:1383-6. 2011
..Here, I provide examples where unreplicated data can be used to test hypotheses and yield novel information in a statistically robust manner...
- Quantitative metagenomic analyses based on average genome size normalization
Jeremy A Frank
Department of Microbiology, University of Copenhagen, Sølvgade 83H, Copenhagen DK 1307, Denmark
Appl Environ Microbiol 77:2513-21. 2011
- Validation of a partial rpoB gene sequence as a tool for phylogenetic identification of aeromonads isolated from environmental sources
Centre Hospitalier du Bassin de Thau, Sete, France
Can J Microbiol 56:217-28. 2010
..hydrophila subsp. anaerogenes is similar to A. caviae and should be considered synonymous...
- Ammonia-oxidising archaea--physiology, ecology and evolution
Department of Genetics in Ecology, University of Vienna, Vienna, Austria
Adv Microb Physiol 57:1-41. 2010
- Evaluation of VNTR typing for the identification of Mycobacterium ulcerans in environmental samples from Victoria, Australia
Caroline J Lavender
Mycobacterium Reference Laboratory, Victorian Infectious Diseases Reference Laboratory, 10 Wreckyn Street, North Melbourne, Victoria, Australia
FEMS Microbiol Lett 287:250-5. 2008
..ulcerans being detected was indistinguishable from the strain causing disease in humans in that region...
- Protists are microbes too: a perspective
David A Caron
Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 0371, USA
ISME J 3:4-12. 2009
- DGGE/TGGE a method for identifying genes from natural ecosystems
Netherlands Institute for Sea Research NL 1790 AB Den Burg, The Netherlands
Curr Opin Microbiol 2:317-22. 1999
..of denaturing gradient gel electrophoresis(DGGE) and temperature gradient gel electrophoresis (TGGE) in environmental microbiology these techniques are now routinely used in many microbiological laboratories worldwide as molecular ..
- Phylogenetic comparison of the methanogenic communities from an acidic, oligotrophic fen and an anaerobic digester treating municipal wastewater sludge
Lisa M Steinberg
Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA 16802, USA
Appl Environ Microbiol 74:6663-71. 2008
..Diversity indices for the 16S rRNA gene library of the bog and both mcrA libraries were similar, but these indices indicated much lower diversity in the 16S digester library than in the other three libraries...
- A wide host-range metagenomic library from a waste water treatment plant yields a novel alcohol/aldehyde dehydrogenase
School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
Environ Microbiol 7:1917-26. 2005
..These observations show that the use of wide host-range vectors enhances the efficacy with which metagenomic libraries can be screened for genes that confer novel functions...
- Environmental proteomics: a paradigm shift in characterizing microbial activities at the molecular level
Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, P O Box 2008, MS 6026, Oak Ridge, TN 37831, USA
Microbiol Mol Biol Rev 73:62-70. 2009
..The review closes with a discussion of critical improvements in the area of integrating experimental mass spectrometry technologies with bioinformatics as well as improved sample handling...
- Comparison of the efficacy of a hydrogen peroxide dry-mist disinfection system and sodium hypochlorite solution for eradication of Clostridium difficile spores
National Reference Laboratory for Clostridium difficile, Hopital Saint Antoine, Assistance Publique Hopitaux de Paris, Paris
Infect Control Hosp Epidemiol 30:507-14. 2009
..To compare a hydrogen peroxide dry-mist system and a 0.5% hypochlorite solution with respect to their ability to disinfect Clostridium difficile-contaminated surfaces in vitro and in situ...
- Metagenomics: genomic analysis of microbial communities
Christian S Riesenfeld
Department of Plant Pathology, University of Wisconsin Madison, Wisconsin 53706, USA
Annu Rev Genet 38:525-52. 2004
..This review describes progress toward understanding the biology of uncultured Bacteria, Archaea, and viruses through metagenomic analyses...
- Identification of Mycobacterium ulcerans in the environment from regions in Southeast Australia in which it is endemic with sequence capture-PCR
Department of Microbiology, Monash University, Clayton, Victoria, Australia
Appl Environ Microbiol 66:3206-13. 2000
..ulcerans may be transmitted from a point environmental source and demonstrate the utility of magnetic bead sequence capture-PCR for identification of nonculturable microbial pathogens in the environment...
- IMG/M: a data management and analysis system for metagenomes
Victor M Markowitz
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA
Nucleic Acids Res 36:D534-8. 2008
..IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools. IMG/M is available at http://img.jgi.doe.gov/m...
- Metabolically active microbial communities of yellow and grey colonizations on the walls of Altamira Cave, Spain
M C Portillo
Instituto de Recursos Naturales y Agrobiologia, CSIC, Avda Reina Mercedes, Sevilla, Spain
J Appl Microbiol 104:681-91. 2008
..To determine the major components of total and metabolically active microbial communities of yellow and grey colonizations threatening the conservation of palaeolithic paintings in Altamira Cave (Spain)...
- Proteogenomics for environmental microbiology
CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols sur Ceze, France
Proteomics 13:2731-42. 2013
..They illustrate the advent of a new era of environmental microbiology where proteomics and genomics are intimately integrated to answer key biological questions.
- Multilocus sequence typing supports the hypothesis that Ochrobactrum anthropi displays a human-associated subpopulation
Faculte de Pharmacie, Laboratoire de Bacteriologie virologie, Universite Montpellier 1, 34093 Montpellier Cedex 5, France
BMC Microbiol 9:267. 2009
..To address this issue, we proposed a polyphasic approach consisting in Multi-Locus Sequence Typing (MLST), multi-locus phylogeny, genomic-based fingerprinting by pulsed-field gel electrophoresis (PFGE) and antibiotyping...
- Feasibility of removing surface deposits on stone using biological and chemical remediation methods
Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Universita degli Studi di Milano, Via Celoria 2, Milan, Italy
Microb Ecol 60:1-14. 2010
..The reported case study reveals that conservators can benefit from an integrated biotechnological approach aimed at the biocleaning of chemical alterations and the abatement of biodeteriogens...
- Gene cassettes encoding resistance to quaternary ammonium compounds: a role in the origin of clinical class 1 integrons?
Michael R Gillings
Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
ISME J 3:209-15. 2009
- Role of copper in reducing hospital environment contamination
A L Casey
University Hospitals Birmingham NHS Foundation Trust, The Queen Elizabeth Hospital, Edgbaston, Birmingham B15 2TH, UK
J Hosp Infect 74:72-7. 2010
..The use of copper-containing materials for surfaces in the hospital environment may therefore be a valuable adjunct for the prevention of HCAIs and requires further evaluation...
- Characterization of the microbial acid mine drainage microbial community using culturing and direct sequencing techniques
Ryan R Auld
Department of Chemistry and Biochemistry, Laurentian University, Canada
J Microbiol Methods 93:108-15. 2013
- Monitoring the colonization of monuments by bacteria: cultivation versus molecular methods
Instituto de Recursos Naturales y Agrobiologia, CSIC, Apartado 1052, Avenida Reina Mercedes, 10, 41012 Sevilla, Spain
Environ Microbiol 5:72-4. 2003
..The data suggest that plating leads to an overestimation of the number of spore-forming bacteria with respect to quiescent vegetative forms; the latter are less easily cultured, but are readily detected by culture-independent techniques...
- Microbial nitrogen cycles: physiology, genomics and applications
R W Ye
DuPont Experimental Station, Wilmington, Delaware 19880, USA
Curr Opin Microbiol 4:307-12. 2001
..Microbial nitrogen metabolism has industrial applications ranging from wastewater treatment to bioremediation and potential future use in biocatalysis for chemical production...
- Evaluating short-term changes in recreational water quality during a hydrograph event using a combination of microbial tracers, environmental microbiology, microbial source tracking and hydrological techniques: a case study in Southwest Wales, UK
Mark D Wyer
Centre for Research into Environment and Health, River Basin Dynamics and Hydrology Research Group, Institute of Geography and Earth Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion SY23 3DB, UK
Water Res 44:4783-95. 2010
..This integration of tracers and MST offers additional information on the movement and individual sources causing water quality impairment...
- The identification of microorganisms by fluorescence in situ hybridisation
Molecular Ecology Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D 28359, Bremen, Germany
Curr Opin Biotechnol 12:231-6. 2001
..Over the past year there have been a number of methodological developments in this area and new applications of FISH in microbial ecology and biotechnology have been reported...
- Molecular monitoring of the microbial dynamics occurring on historical limestone buildings during and after the in situ application of different bio-consolidation treatments
Institute of Applied Microbiology, Department of Biotechnology, Vienna Institute of Bio Technology VIBT, University of Natural Resources and Life Sciences, Muthgasse 11, A 1190 Vienna, Austria
Sci Total Environ 409:5337-52. 2011
..The treatments seem to activate no dangerous microorganisms and furthermore, to select the remainder of a homogeneous group of carbonatogenic bacteria on the stones after a long period of time...
- Survival of prototype strains of somatic coliphage families in environmental waters and when exposed to UV low-pressure monochromatic radiation or heat
Hee Suk Lee
Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
Water Res 45:3723-34. 2011
- PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip
Kristen M DeAngelis
Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Appl Environ Microbiol 77:6313-22. 2011
- Phylogeny and distribution of the soxB gene among thiosulfate-oxidizing bacteria
, , 24105, Kiel, Germany
FEMS Microbiol Lett 197:171-8. 2001
- Diversity and ecology of psychrophilic microorganisms
Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A 6020 Innsbruck, Austria
Res Microbiol 162:346-61. 2011
- Detection of Coxiella burnetii in complex matrices by using multiplex quantitative PCR during a major Q fever outbreak in The Netherlands
A de Bruin
National Institute for Public Health and the Environment RIVM, Centre for Infectious Disease Control CIb, Laboratory for Zoonoses and Environmental Microbiology, Bilthoven, The Netherlands
Appl Environ Microbiol 77:6516-23. 2011
..burnetii targets in one multiplex qPCR assay showed that complex veterinary and environmental matrices can be screened reliably for the presence of C. burnetii DNA during an outbreak...
- Promises and pitfalls of recent advances in chemical means of preventing the spread of nosocomial infections by environmental surfaces
Syed A Sattar
Centre for Research on Environmental Microbiology CREM, Faculty of Medicine, University of Ottawa, Ontario, Canada
Am J Infect Control 38:S34-40. 2010
- Immunoglobulin G antibodies against indoor dampness-related microbes and adult-onset asthma: a population-based incident case-control study
M S Jaakkola
Department of Occupational Medicine, Finnish Institute of Occupational Health, Helsinki, Finland
Clin Exp Immunol 129:107-12. 2002
..There was no evidence of a dose-response relation between the IgG antibody level and the risk of asthma. T. citrinoviride may play a role in the aetiology of adult-onset asthma or serve as an indicator of other causal factors...
- Escherichia coli and selected veterinary and zoonotic pathogens isolated from environmental sites in companion animal veterinary hospitals in southern Ontario
Colleen P Murphy
Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario
Can Vet J 51:963-72. 2010
..There is an environmental reservoir of pathogens in veterinary hospitals; therefore, additional studies are required to characterize risk factors associated with HAI in companion animals, including the role of the environment...
- Differential habitat use and niche partitioning by Pseudomonas species in human homes
Susanna K Remold
Department of Biology, University of Louisville, 137 Life Sciences Building, Louisville, KY 40292, USA
Microb Ecol 62:505-17. 2011
..Furthermore, niche partitioning driven by competition among Pseudomonas species may be contributing to the observed variability in habitat use by Pseudomonas in this system...
- Environmental isolates of Burkholderia pseudomallei in Ceará State, northeastern Brazil
Dione B Rolim
Postgraduate Program in Medical Science, Faculty of Medicine, Federal University of Ceara, Fortaleza, Ceara, Brazil
Appl Environ Microbiol 75:1215-8. 2009
..This study investigated two municipalities in Ceará state where melioidosis cases have been confirmed to occur. Burkholderia pseudomallei was isolated in 26 (4.3%) of 600 samples in the dry and rainy seasons...
- Global Pseudomonas aeruginosa biodiversity as reflected in a Belgian river
Jean Paul Pirnay
Laboratory of Microbial Interactions, Department of Molecular and Cellular Interactions, Flanders Interuniversity Institute of Biotechnology, Vrije Universiteit Brussel, B 1050 Brussels, Belgium
Environ Microbiol 7:969-80. 2005
..These findings illustrate the significance of river water as a reservoir and source of distribution of potentially pathogenic P. aeruginosa strains and could have repercussions on antinosocomial infection strategies...
- Comparison of sampling methods used for MRSA-classification of herds with breeding pigs
E M Broens
Quantitative Veterinary Epidemiology Group, Wageningen Institute of Animal Sciences, Wageningen University, PO Box 338, 6700 AH Wageningen, The Netherlands
Vet Microbiol 147:440-4. 2011
..Individual analysis of environmental wipes is highly recommended, as pooling 5 environmental samples resulted in a substantial reduction of the apparent prevalence...
- When metagenomics meets stable-isotope probing: progress and perspectives
Department of Biological Sciences, The University of Warwick, Coventry CV4 7AL, UK
Trends Microbiol 18:157-63. 2010
..The combination of DNA-SIP and metagenomics not only permits the detection of rare low-abundance species from metagenomic libraries but also facilitates the detection of novel enzymes and bioactive compounds...
- The search and destroy strategy prevents spread and long-term carriage of methicillin-resistant Staphylococcus aureus: results from the follow-up screening of a large ST22 (E-MRSA 15) outbreak in Denmark
National Center for Antimicrobials and Infection Control, Statens Serum Institut, Copenhagen, Denmark
Clin Microbiol Infect 16:1427-34. 2010
..At the end of follow-up, ten of 16 long-term carriers and the two household contacts were MRSA-negative. In conclusion, decolonization of MRSA carriers is possible, but should include treatment of household members and the environment...
- Cultivation gives context to the microbial ecologist
Department of Biology, Northeastern University, Boston, MA, USA
FEMS Microbiol Ecol 60:351-7. 2007
- Detection of Coxiella burnetii DNA on small-ruminant farms during a Q fever outbreak in the Netherlands
A de Bruin
National Institute for Public Health and the Environment RIVM, Centre for Infectious Disease Control CIb, Bilthoven, Netherlands
Appl Environ Microbiol 78:1652-7. 2012
..burnetii to humans...
- Influence of selective media on successful detection of Shiga toxin-producing Escherichia coli in food, fecal, and environmental samples
Hussein S Hussein
Department of Animal Biotechnology, University of Nevada Reno, Reno, Nevada
Foodborne Pathog Dis 5:227-44. 2008
..Future research should focus on identifying possible antibiotic combinations that effectively inhibit most background bacteria without affecting pathogenic STEC strains in the test sample...
- Validation of a nylon-flocked-swab protocol for efficient recovery of bacterial spores from smooth and rough surfaces
Institute of Microbiology and Archaea Center, University of Regensburg, Universitaetsstrasse 31, 93053 Regensburg, Germany
Appl Environ Microbiol 76:5148-58. 2010
..anthracis contamination for law enforcement and security efforts...
- Outbreak of Serratia marcescens in a neonatal intensive care unit: contaminated unmedicated liquid soap and risk factors
Unité d Hygiène Hospitalière, Pôle Microorganismes, CHU Pontchaillou, Rennes, France
J Hosp Infect 72:17-22. 2009
..Prompt intervention and strict adherence to alcoholic hand disinfection were the key factors that led to the successful control of this outbreak...
- Low-density macroarray targeting non-locus of enterocyte effacement effectors (nle genes) and major virulence factors of Shiga toxin-producing Escherichia coli (STEC): a new approach for molecular risk assessment of STEC isolates
French Food Safety Agency, Food Quality and Agro alimentary Processes Research Laboratory, avenue du General de Gaulle, F 94706 Maisons Alfort, France
Appl Environ Microbiol 76:203-11. 2010
..The presence of eae, ent/espL2, nleB, nleE, and nleH1-2 genes is a clear signature of STEC strains with high virulence for humans...
- Environmental contamination during a carbapenem-resistant Acinetobacter baumannii outbreak in an intensive care unit
Department of Microbiology and Clinical Microbiology, Cerrahpasa Medical Faculty, University of Istanbul 34303, Aksaray, Istanbul, Turkey
J Hosp Infect 52:259-62. 2002
..No bacteria were grown on repeat environmental cultures. Environmental contamination has an important reservoir role in outbreaks of A. baumannii in ICUs and must be eradicated in order to overcome such outbreaks...
- Expanding small-molecule functional metagenomics through parallel screening of broad-host-range cosmid environmental DNA libraries in diverse proteobacteria
Jeffrey W Craig
Howard Hughes Medical Institute, Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
Appl Environ Microbiol 76:1633-41. 2010
- Applications of real-time polymerase chain reaction for quantification of microorganisms in environmental samples
Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
Appl Microbiol Biotechnol 70:281-9. 2006
..The applications of qRT-PCR for the quantification of microorganisms in the environment are also summarized...
- Methanotrophs and copper
Jeremy D Semrau
Department of Civil and Environmental Engineering, The University of Michigan, Ann Arbor, MI, USA
FEMS Microbiol Rev 34:496-531. 2010
- Effect of oxygen on growth of Mycobacterium ulcerans in the BACTEC system
J C Palomino
Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
J Clin Microbiol 36:3420-2. 1998
..Application of this observation may improve rates of isolation of M. ulcerans in primary culture from clinical samples and promote isolation of the bacterium from environmental sources...
- Microbial monitoring of spacecraft and associated environments
M T La Duc
Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
Microb Ecol 47:150-8. 2004
..Each of the methods tested in this study has its advantages, and by coupling two or more of these techniques even more reliable information as to microbial burden is rapidly obtained...
- Isolation and characterization of metalloproteases with a novel domain structure by construction and screening of metagenomic libraries
Abteilung Genomische und Angewandte Mikrobiologie, Institut für Mikrobiologie und Genetik der Georg August Universität, Grisebachstr 8, 37077 Gottingen, Germany
Appl Environ Microbiol 75:2506-16. 2009
..The optimum pH and temperature of both proteases were 8.0 and 65 degrees C, respectively, when casein was used as substrate...
- Stable-isotope probing of nucleic acids: a window to the function of uncultured microorganisms
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
Curr Opin Biotechnol 14:296-302. 2003
..Investigations using labelled substrates, or which detect variations in the natural abundance of isotopes, have thus revealed the metabolic function of microorganisms without the need to isolate them in culture...
- Recovery of diverse genes for class 1 integron-integrases from environmental DNA samples
Michael R Gillings
Department of Biological Sciences, Genes to Geoscience Research Centre, Macquarie University, Sydney, NSW, Australia
FEMS Microbiol Lett 287:56-62. 2008
..IntI1 was common in environmental samples and exhibited previously unsuspected sequence diversity. The method allowed discrimination between clinical and environmental variants of intI1...
- Phylogenetic classification of short environmental DNA fragments
Center for Biotechnology CeBiTec, Bioinformatics Resource Facility BRF, Bielefeld University, D 33594 Bielefeld, Germany
Nucleic Acids Res 36:2230-9. 2008
..The algorithm was applied in a comparative study of three aquatic microbial samples obtained by 454 pyrosequencing. Profound differences in the taxonomic composition of these samples could be clearly revealed...
- Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria
Jeanette M Norton
Department of Plants, Soils and Biometeorology, Utah State University, Logan, UT 84322 4820, USA
Arch Microbiol 177:139-49. 2002
..Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00203-001-0369-z...
- Metagenomics--the key to the uncultured microbes
Wolfgang R Streit
Institut fur Mikrobiologie und Genetik, Universitat Gottingen, Grisebachstr 8, 37077, Gottingen, Germany
Curr Opin Microbiol 7:492-8. 2004
..Using the metagenome sequences to fully understand how complex microbial communities function and how microbes interact within these niches represents a major challenge for microbiologists today...
- Antibiotic exposure and room contamination among patients colonized with vancomycin-resistant enterococci
Tufts Medical Center, Tufts University, Boston, Massachusetts, USA
Infect Control Hosp Epidemiol 29:709-15. 2008
..To determine whether total and antianaerobic antibiotic exposure increases the risk of room contamination among vancomycin-resistant enterococci (VRE)-colonized patients...
- Microviridae goes temperate: microvirus-related proviruses reside in the genomes of Bacteroidetes
Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Institut Pasteur, Paris, France
PLoS ONE 6:e19893. 2011
- Visual and statistical comparison of metagenomes
Center for Bioinformatics ZBIT, Tubingen University, Sand 14, 72076 Tubingen, Germany
Bioinformatics 25:1849-55. 2009
..One major challenge is how to compare multiple datasets. Furthermore, there is a need for bioinformatics tools that can process many large datasets and are easy to use...
- Identification of bacterial plasmids based on mobility and plasmid population biology
Maria Pilar Garcillán-Barcia
Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria CSIC IDICAN, C Herrera Oria s n, Santander, Spain
FEMS Microbiol Rev 35:936-56. 2011
..We would like to propose that, by using an identification methodology based on plasmid mobility types, we can follow the propagation routes of most plasmids in ?-proteobacteria, as well as their cargo genes, in complex ecosystems...
- Seasonality of rDNA- and rRNA-derived archaeal communities and methanogenic potential in a boreal mire
Department of Biological and Environmental Sciences, General Microbiology, University of Helsinki, Helsinki, Finland
ISME J 2:1157-68. 2008
..Detection of mRNA of the methanogenic mcrA gene confirmed activity of methanogens in winter, accounting for previously reported winter CH(4) emissions...
- mcrA-targeted real-time quantitative PCR method to examine methanogen communities
Lisa M Steinberg
Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, 16802, USA
Appl Environ Microbiol 75:4435-42. 2009
..The TaqMan qPCR assays were successfully able to determine the environmental abundance of different phylogenetic groups of methanogens, including several groups with few or no cultivated members...
- Prokaryotic diversity--magnitude, dynamics, and controlling factors
Department of Microbiology, University of Bergen, Jahnebakken 5, N 5020 Bergen, Norway
Science 296:1064-6. 2002
..Hypotheses and models explaining such differences are under development and are beginning to offer promising insights into the mechanisms governing prokaryote diversity and ecosystem function...
- Evaluation of an automated ultraviolet radiation device for decontamination of Clostridium difficile and other healthcare-associated pathogens in hospital rooms
Michelle M Nerandzic
Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, Ohio, USA
BMC Infect Dis 10:197. 2010
..Environmental surfaces play an important role in transmission of healthcare-associated pathogens. There is a need for new disinfection methods that are effective against Clostridium difficile spores, but also safe, rapid, and automated...
- Crystal ball. The viriosphere: the greatest biological diversity on Earth and driver of global processes
Earth and Ocean Sciences, Microbiology and Immunology, University of British Columbia, BC, Canada
Environ Microbiol 7:481-2. 2005
- Exopolysaccharides from extremophiles: from fundamentals to biotechnology
Istituto di Chimica Biomolecolare ICB, CNR Via Campi Flegrei 34, 80078, Pozzuoli NA, Italy
Environ Technol 31:1145-58. 2010
..The commercial value of EPSs synthesized by microorganisms from extreme habitats has been established recently...
- MRSA CC398 in the pig production chain
E M Broens
Quantitative Veterinary Epidemiology Group, Wageningen Institute of Animal Sciences, Wageningen University, P O Box 338, 6700 AH Wageningen, The Netherlands
Prev Vet Med 98:182-9. 2011
..This underlined the need for the identification of additional risk factors for MRSA...
- Characterization of aerobic bacterial and fungal microbiota on surfaces of historic Scottish monuments
Maija Liisa Suihko
VTT Technical Research Centre of Finland, Espoo, Finland
Syst Appl Microbiol 30:494-508. 2007
..Using in situ microscopy diatom algae were also detected...
- Microbial contamination of spacecraft
D L Pierson
NASA Johnson Space Center, Houston, TX, USA
Gravit Space Biol Bull 14:1-6. 2001
..Equally important is a better understanding of the immune response and of human-microorganism-environment interactions during long-term space habitation...
- The environment as an unrecognized reservoir for community-associated methicillin resistant Staphylococcus aureus USA300: a case-control study
Anne Catrin Uhlemann
Division of Infectious Diseases, Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
PLoS ONE 6:e22407. 2011
..Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infections are spreading, but the source of infections in non-epidemic settings remains poorly defined...
- Asymptomatic carriage of Klebsiella pneumoniae producing extended-spectrum beta-lactamase by patients in a neurological early rehabilitation unit: management of an outbreak
Landesuntersuchungsamt für Chemie, Hygiene und Veterinärmedizin, St Jürgenstr 1, D 28205 Bremen, Germany
J Hosp Infect 48:207-13. 2001
..Disinfection of mucous membranes was difficult. Eventually the application of a nasal spray containing povidone-iodine proved to be successful...
- A Stenotrophomonas maltophilia multilocus sequence typing scheme for inferring population structure
Institute of Environmental Medicine and Hospital Epidemiology at the University Medical Centre Freiburg, Breisacher Str 115 b, 79106 Freiburg, Germany
J Bacteriol 191:2934-43. 2009