This Article
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Liu, W. T.
Right arrow Articles by Forney, L. J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Liu, W. T.
Right arrow Articles by Forney, L. J.
Agricola
Right arrow Articles by Liu, W. T.
Right arrow Articles by Forney, L. J.

 Previous Article  |  Next Article 

Appl. Environ. Microbiol., Nov 1997, 4516-4522, Vol 63, No. 11
Copyright © 1997, American Society for Microbiology

Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA

WT Liu, TL Marsh, H Cheng and LJ Forney
Department of Microbiology, Michigan State University, East Lansing 48824, USA.

A quantitative molecular technique was developed for rapid analysis of microbial community diversity in various environments. The technique employed PCR in which one of the two primers used was fluorescently labeled at the 5' end and was used to amplify a selected region of bacterial genes encoding 16S rRNA from total community DNA. The PCR product was digested with restriction enzymes, and the fluorescently labeled terminal restriction fragment was precisely measured by using an automated DNA sequencer. Computer-simulated analysis of terminal restriction fragment length polymorphisms (T-RFLP) for 1,002 eubacterial sequences showed that with proper selection of PCR primers and restriction enzymes, 686 sequences could be PCR amplified and classified into 233 unique terminal restriction fragment lengths or "ribotypes." Using T-RFLP, we were able to distinguish all bacterial strains in a model bacterial community, and the pattern was consistent with the predicted outcome. Analysis of complex bacterial communities with T-RFLP revealed high species diversity in activated sludge, bioreactor sludge, aquifer sand, and termite guts; as many as 72 unique ribotypes were found in these communities, with 36 ribotypes observed in the termite guts. The community T-RFLP patterns were numerically analyzed and hierarchically clustered. The pattern derived from termite guts was found to be distinctly different from the patterns derived from the other three communities. Overall, our results demonstrated that T-RFLP is a powerful tool for assessing the diversity of complex bacterial communities and for rapidly comparing the community structure and diversity of different ecosystems.


This article has been cited by other articles:

  • Pieper, R., Bindelle, J., Rossnagel, B., Van Kessel, A., Leterme, P. (2009). Effect of Carbohydrate Composition in Barley and Oat Cultivars on Microbial Ecophysiology and Proliferation of Salmonella enterica in an In Vitro Model of the Porcine Gastrointestinal Tract. Appl. Environ. Microbiol. 75: 7006-7016 [Abstract] [Full Text]  
  • Lee, O. O., Chui, P. Y., Wong, Y. H., Pawlik, J. R., Qian, P.-Y. (2009). Evidence for Vertical Transmission of Bacterial Symbionts from Adult to Embryo in the Caribbean Sponge Svenzea zeai. Appl. Environ. Microbiol. 75: 6147-6156 [Abstract] [Full Text]  
  • Johnson, M. C., Devine, A. A., Ellis, J. C., Grunden, A. M., Fellner, V. (2009). Effects of antibiotics and oil on microbial profiles and fermentation in mixed cultures of ruminal microorganisms. J DAIRY SCI 92: 4467-4480 [Abstract] [Full Text]  
  • Alvarado, P., Manjon, J. L. (2009). Selection of Enzymes for Terminal Restriction Fragment Length Polymorphism Analysis of Fungal Internally Transcribed Spacer Sequences. Appl. Environ. Microbiol. 75: 4747-4752 [Abstract] [Full Text]  
  • Lee, O. O., Wong, Y. H., Qian, P.-Y. (2009). Inter- and Intraspecific Variations of Bacterial Communities Associated with Marine Sponges from San Juan Island, Washington. Appl. Environ. Microbiol. 75: 3513-3521 [Abstract] [Full Text]  
  • Fullmer, S.C., Preshaw, P.M., Heasman, P.A., Kumar, P.S. (2009). Smoking Cessation Alters Subgingival Microbial Recolonization. JDR 88: 524-528 [Abstract] [Full Text]  
  • Ramette, A. (2009). Quantitative Community Fingerprinting Methods for Estimating the Abundance of Operational Taxonomic Units in Natural Microbial Communities. Appl. Environ. Microbiol. 75: 2495-2505 [Abstract] [Full Text]  
  • Wagner, A. O., Malin, C., Illmer, P. (2009). Application of Denaturing High-Performance Liquid Chromatography in Microbial Ecology: Fermentor Sludge, Compost, and Soil Community Profiling. Appl. Environ. Microbiol. 75: 956-964 [Abstract] [Full Text]  
  • Waldron, L. S., Ferrari, B. C., Gillings, M. R., Power, M. L. (2009). Terminal Restriction Fragment Length Polymorphism for Identification of Cryptosporidium Species in Human Feces. Appl. Environ. Microbiol. 75: 108-112 [Abstract] [Full Text]  
  • Cao, Y., Green, P. G., Holden, P. A. (2008). Microbial Community Composition and Denitrifying Enzyme Activities in Salt Marsh Sediments. Appl. Environ. Microbiol. 74: 7585-7595 [Abstract] [Full Text]  
  • Neulinger, S. C., Jarnegren, J., Ludvigsen, M., Lochte, K., Dullo, W.-C. (2008). Phenotype-Specific Bacterial Communities in the Cold-Water Coral Lophelia pertusa (Scleractinia) and Their Implications for the Coral's Nutrition, Health, and Distribution. Appl. Environ. Microbiol. 74: 7272-7285 [Abstract] [Full Text]  
  • Junier, P., Junier, T., Witzel, K.-P. (2008). TRiFLe, a Program for In Silico Terminal Restriction Fragment Length Polymorphism Analysis with User-Defined Sequence Sets. Appl. Environ. Microbiol. 74: 6452-6456 [Abstract] [Full Text]  
  • Sibley, C. D., Parkins, M. D., Rabin, H. R., Duan, K., Norgaard, J. C., Surette, M. G. (2008). A polymicrobial perspective of pulmonary infections exposes an enigmatic pathogen in cystic fibrosis patients. Proc. Natl. Acad. Sci. USA 105: 15070-15075 [Abstract] [Full Text]  
  • Hamberger, A., Horn, M. A., Dumont, M. G., Murrell, J. C., Drake, H. L. (2008). Anaerobic Consumers of Monosaccharides in a Moderately Acidic Fen. Appl. Environ. Microbiol. 74: 3112-3120 [Abstract] [Full Text]  
  • Chhour, K.-L., Hinds, L. A., Deane, E. M., Jacques, N. A. (2008). The microbiome of the cloacal openings of the urogenital and anal tracts of the tammar wallaby, Macropus eugenii. Microbiology 154: 1535-1543 [Abstract] [Full Text]  
  • Edmonds, J. W., Weston, N. B., Joye, S. B., Moran, M. A. (2008). Variation in Prokaryotic Community Composition as a Function of Resource Availability in Tidal Creek Sediments. Appl. Environ. Microbiol. 74: 1836-1844 [Abstract] [Full Text]  
  • Camacho, N., Espinoza, C., Rodriguez, C., Rodriguez, E. (2008). Isolates of Clostridium perfringens recovered from Costa Rican patients with antibiotic-associated diarrhoea are mostly enterotoxin-negative and susceptible to first-choice antimicrobials. J Med Microbiol 57: 343-347 [Abstract] [Full Text]  
  • Winderl, C., Anneser, B., Griebler, C., Meckenstock, R. U., Lueders, T. (2008). Depth-Resolved Quantification of Anaerobic Toluene Degraders and Aquifer Microbial Community Patterns in Distinct Redox Zones of a Tar Oil Contaminant Plume. Appl. Environ. Microbiol. 74: 792-801 [Abstract] [Full Text]  
  • Kuramitsu, H. K., He, X., Lux, R., Anderson, M. H., Shi, W. (2007). Interspecies Interactions within Oral Microbial Communities. Microbiol. Mol. Biol. Rev. 71: 653-670 [Abstract] [Full Text]  
  • Dekio, I., Sakamoto, M., Hayashi, H., Amagai, M., Suematsu, M., Benno, Y. (2007). Characterization of skin microbiota in patients with atopic dermatitis and in normal subjects using 16S rRNA gene-based comprehensive analysis. J Med Microbiol 56: 1675-1683 [Abstract] [Full Text]  
  • Reimers, C. E., Stecher, H. A. III, Westall, J. C., Alleau, Y., Howell, K. A., Soule, L., White, H. K., Girguis, P. R. (2007). Substrate Degradation Kinetics, Microbial Diversity, and Current Efficiency of Microbial Fuel Cells Supplied with Marine Plankton. Appl. Environ. Microbiol. 73: 7029-7040 [Abstract] [Full Text]  
  • Ashby, M. N., Rine, J., Mongodin, E. F., Nelson, K. E., Dimster-Denk, D. (2007). Serial Analysis of rRNA Genes and the Unexpected Dominance of Rare Members of Microbial Communities. Appl. Environ. Microbiol. 73: 4532-4542 [Abstract] [Full Text]  
  • Collins, R. E., Rocap, G. (2007). REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis. Nucleic Acids Res 35: W58-W62 [Abstract] [Full Text]  
  • Wu, J.-H., Liu, W.-T. (2007). Quantitative multiplexing analysis of PCR-amplified ribosomal RNA genes by hierarchical oligonucleotide primer extension reaction. Nucleic Acids Res 35: e82-e82 [Abstract] [Full Text]  
  • Thies, F. L., Konig, W., Konig, B. (2007). Rapid characterization of the normal and disturbed vaginal microbiota by application of 16S rRNA gene terminal RFLP fingerprinting. J Med Microbiol 56: 755-761 [Abstract] [Full Text]  
  • Buckley, D. H., Huangyutitham, V., Hsu, S.-F., Nelson, T. A. (2007). Stable Isotope Probing with 15N2 Reveals Novel Noncultivated Diazotrophs in Soil. Appl. Environ. Microbiol. 73: 3196-3204 [Abstract] [Full Text]  
  • Buckley, D. H., Huangyutitham, V., Hsu, S.-F., Nelson, T. A. (2007). Stable Isotope Probing with 15N Achieved by Disentangling the Effects of Genome G+C Content and Isotope Enrichment on DNA Density. Appl. Environ. Microbiol. 73: 3189-3195 [Abstract] [Full Text]  
  • Schwartz, E. (2007). Characterization of Growing Microorganisms in Soil by Stable Isotope Probing with H218O. Appl. Environ. Microbiol. 73: 2541-2546 [Abstract] [Full Text]  
  • Bent, S. J., Pierson, J. D., Forney, L. J., Danovaro, R., Luna, G. M., Dell'Anno, A., Pietrangeli, B. (2007). Measuring Species Richness Based on Microbial Community Fingerprints: the Emperor Has No Clothes. Appl. Environ. Microbiol. 73: 2399-2401 [Full Text]  
  • Dicksved, J., Floistrup, H., Bergstrom, A., Rosenquist, M., Pershagen, G., Scheynius, A., Roos, S., Alm, J. S., Engstrand, L., Braun-Fahrlander, C., von Mutius, E., Jansson, J. K. (2007). Molecular Fingerprinting of the Fecal Microbiota of Children Raised According to Different Lifestyles. Appl. Environ. Microbiol. 73: 2284-2289 [Abstract] [Full Text]  
  • Nakatsu, C. H. (2007). Soil Microbial Community Analysis Using Denaturing Gradient Gel Electrophoresis. Soil Sci. 71: 562-571 [Abstract] [Full Text]  
  • Thies, J. E. (2007). Soil Microbial Community Analysis using Terminal Restriction Fragment Length Polymorphisms. Soil Sci. 71: 579-591 [Abstract] [Full Text]  
  • Martin, K. J. (2007). Introduction to Molecular Analysis of Ectomycorrhizal Communities. Soil Sci. 71: 601-610 [Abstract] [Full Text]  
  • Liu, W.-T., Guo, H., Wu, J.-H. (2007). Effects of Target Length on the Hybridization Efficiency and Specificity of rRNA-Based Oligonucleotide Microarrays. Appl. Environ. Microbiol. 73: 73-82 [Abstract] [Full Text]  
  • Singh, B. K., Nazaries, L., Munro, S., Anderson, I. C., Campbell, C. D. (2006). Use of Multiplex Terminal Restriction Fragment Length Polymorphism for Rapid and Simultaneous Analysis of Different Components of the Soil Microbial Community{triangledown}. Appl. Environ. Microbiol. 72: 7278-7285 [Abstract] [Full Text]  
  • Ruan, Q., Dutta, D., Schwalbach, M. S., Steele, J. A., Fuhrman, J. A., Sun, F. (2006). Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors. Bioinformatics 22: 2532-2538 [Abstract] [Full Text]  
  • Moss, J. A., Nocker, A., Lepo, J. E., Snyder, R. A. (2006). Stability and Change in Estuarine Biofilm Bacterial Community Diversity. Appl. Environ. Microbiol. 72: 5679-5688 [Abstract] [Full Text]  
  • Pang, C. M., Liu, W.-T. (2006). Biological Filtration Limits Carbon Availability and Affects Downstream Biofilm Formation and Community Structure. Appl. Environ. Microbiol. 72: 5702-5712 [Abstract] [Full Text]  
  • Bhatia, M., Sharp, M., Foght, J. (2006). Distinct Bacterial Communities Exist beneath a High Arctic Polythermal Glacier. Appl. Environ. Microbiol. 72: 5838-5845 [Abstract] [Full Text]  
  • Rodriguez, C., Lang, L., Wang, A., Altendorf, K., Garcia, F., Lipski, A. (2006). Lettuce for Human Consumption Collected in Costa Rica Contains Complex Communities of Culturable Oxytetracycline- and Gentamicin-Resistant Bacteria. Appl. Environ. Microbiol. 72: 5870-5876 [Abstract] [Full Text]  
  • Danovaro, R., Luna, G. M., Dell'Anno, A., Pietrangeli, B. (2006). Comparison of Two Fingerprinting Techniques, Terminal Restriction Fragment Length Polymorphism and Automated Ribosomal Intergenic Spacer Analysis, for Determination of Bacterial Diversity in Aquatic Environments. Appl. Environ. Microbiol. 72: 5982-5989 [Abstract] [Full Text]  
  • Pratt, J. S., Sachen, K. L., Wood, H. D., Eaton, K. A., Young, V. B. (2006). Modulation of Host Immune Responses by the Cytolethal Distending Toxin of Helicobacter hepaticus.. Infect. Immun. 74: 4496-4504 [Abstract] [Full Text]  
  • Rogers, G. B., Carroll, M. P., Serisier, D. J., Hockey, P. M., Jones, G., Kehagia, V., Connett, G. J., Bruce, K. D. (2006). Use of 16S rRNA Gene Profiling by Terminal Restriction Fragment Length Polymorphism Analysis To Compare Bacterial Communities in Sputum and Mouthwash Samples from Patients with Cystic Fibrosis.. J. Clin. Microbiol. 44: 2601-2604 [Abstract] [Full Text]  
  • Ruan, Q., Steele, J. A., Schwalbach, M. S., Fuhrman, J. A., Sun, F. (2006). A dynamic programming algorithm for binning microbial community profiles. Bioinformatics 22: 1508-1514 [Abstract] [Full Text]  
  • Sanguin, H., Remenant, B., Dechesne, A., Thioulouse, J., Vogel, T. M., Nesme, X., Moenne-Loccoz, Y., Grundmann, G. L. (2006). Potential of a 16S rRNA-Based Taxonomic Microarray for Analyzing the Rhizosphere Effects of Maize on Agrobacterium spp. and Bacterial Communities.. Appl. Environ. Microbiol. 72: 4302-4312 [Abstract] [Full Text]  
  • Cordova-Kreylos, A. L., Cao, Y., Green, P. G., Hwang, H.-M., Kuivila, K. M., LaMontagne, M. G., Van De Werfhorst, L. C., Holden, P. A., Scow, K. M. (2006). Diversity, composition, and geographical distribution of microbial communities in california salt marsh sediments.. Appl. Environ. Microbiol. 72: 3357-3366 [Abstract] [Full Text]  
  • Frey, J. C., Rothman, J. M., Pell, A. N., Nizeyi, J. B., Cranfield, M. R., Angert, E. R. (2006). Fecal bacterial diversity in a wild gorilla.. Appl. Environ. Microbiol. 72: 3788-3792 [Abstract] [Full Text]  
  • Souza, V., Espinosa-Asuar, L., Escalante, A. E., Eguiarte, L. E., Farmer, J., Forney, L., Lloret, L., Rodriguez-Martinez, J. M., Soberon, X., Dirzo, R., Elser, J. J. (2006). From the Cover: An endangered oasis of aquatic microbial biodiversity in the Chihuahuan desert. Proc. Natl. Acad. Sci. USA 103: 6565-6570 [Abstract] [Full Text]  
  • Countway, P. D., Caron, D. A. (2006). Abundance and Distribution of Ostreococcus sp. in the San Pedro Channel, California, as Revealed by Quantitative PCR. Appl. Environ. Microbiol. 72: 2496-2506 [Abstract] [Full Text]  
  • Lepere, C., Boucher, D., Jardillier, L., Domaizon, I., Debroas, D. (2006). Succession and Regulation Factors of Small Eukaryote Community Composition in a Lacustrine Ecosystem (Lake Pavin). Appl. Environ. Microbiol. 72: 2971-2981 [Abstract] [Full Text]  
  • Mohanty, S. R., Bodelier, P. L. E., Floris, V., Conrad, R. (2006). Differential Effects of Nitrogenous Fertilizers on Methane-Consuming Microbes in Rice Field and Forest Soils. Appl. Environ. Microbiol. 72: 1346-1354 [Abstract] [Full Text]  
  • Fierer, N., Jackson, R. B. (2006). From the Cover: The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA 103: 626-631 [Abstract] [Full Text]  
  • Palmer, C., Bik, E. M., Eisen, M. B., Eckburg, P. B., Sana, T. R., Wolber, P. K., Relman, D. A., Brown, P. O. (2006). Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res 34: e5-e5 [Abstract] [Full Text]  
  • Penning, H., Conrad, R. (2006). Effect of Inhibition of Acetoclastic Methanogenesis on Growth of Archaeal Populations in an Anoxic Model Environment. Appl. Environ. Microbiol. 72: 178-184 [Abstract] [Full Text]  
  • Hullar, M. A. J., Kaplan, L. A., Stahl, D. A. (2006). Recurring Seasonal Dynamics of Microbial Communities in Stream Habitats. Appl. Environ. Microbiol. 72: 713-722 [Abstract] [Full Text]  
  • Dinoto, A., Suksomcheep, A., Ishizuka, S., Kimura, H., Hanada, S., Kamagata, Y., Asano, K., Tomita, F., Yokota, A. (2006). Modulation of Rat Cecal Microbiota by Administration of Raffinose and Encapsulated Bifidobacterium breve. Appl. Environ. Microbiol. 72: 784-792 [Abstract] [Full Text]  
  • Scupham, A. J, Presley, L. L., Wei, B., Bent, E., Griffith, N., McPherson, M., Zhu, F., Oluwadara, O., Rao, N., Braun, J., Borneman, J. (2006). Abundant and Diverse Fungal Microbiota in the Murine Intestine. Appl. Environ. Microbiol. 72: 793-801 [Abstract] [Full Text]  
  • Pinhassi, J., Simo, R., Gonzalez, J. M., Vila, M., Alonso-Saez, L., Kiene, R. P., Moran, M. A., Pedros-Alio, C. (2005). Dimethylsulfoniopropionate Turnover Is Linked to the Composition and Dynamics of the Bacterioplankton Assemblage during a Microcosm Phytoplankton Bloom. Appl. Environ. Microbiol. 71: 7650-7660 [Abstract] [Full Text]  
  • Coolen, M. J. L., Post, E., Davis, C. C., Forney, L. J. (2005). Characterization of Microbial Communities Found in the Human Vagina by Analysis of Terminal Restriction Fragment Length Polymorphisms of 16S rRNA Genes. Appl. Environ. Microbiol. 71: 8729-8737 [Abstract] [Full Text]  
  • Pett-Ridge, J., Firestone, M. K. (2005). Redox Fluctuation Structures Microbial Communities in a Wet Tropical Soil. Appl. Environ. Microbiol. 71: 6998-7007 [Abstract] [Full Text]  
  • Saikaly, P. E., Stroot, P. G., Oerther, D. B. (2005). Use of 16S rRNA Gene Terminal Restriction Fragment Analysis To Assess the Impact of Solids Retention Time on the Bacterial Diversity of Activated Sludge. Appl. Environ. Microbiol. 71: 5814-5822 [Abstract] [Full Text]  
  • Fairchild, A. S., Smith, J. L., Idris, U., Lu, J., Sanchez, S., Purvis, L. B., Hofacre, C., Lee, M. D. (2005). Effects of Orally Administered Tetracycline on the Intestinal Community Structure of Chickens and on tet Determinant Carriage by Commensal Bacteria and Campylobacter jejuni. Appl. Environ. Microbiol. 71: 5865-5872 [Abstract] [Full Text]  
  • Kuehl, C. J., Wood, H. D., Marsh, T. L., Schmidt, T. M., Young, V. B. (2005). Colonization of the Cecal Mucosa by Helicobacter hepaticus Impacts the Diversity of the Indigenous Microbiota. Infect. Immun. 73: 6952-6961 [Abstract] [Full Text]  
  • Steinberger, R. E., Holden, P. A. (2005). Extracellular DNA in Single- and Multiple-Species Unsaturated Biofilms. Appl. Environ. Microbiol. 71: 5404-5410 [Abstract] [Full Text]  
  • Crawford, R. L. (2005). Microbial Diversity and Its Relationship to Planetary Protection. Appl. Environ. Microbiol. 71: 4163-4168 [Full Text]  
  • Jampachaisri, K., Valinsky, L., Borneman, J., Press, S. J. (2005). Classification of oligonucleotide fingerprints: application for microbial community and gene expression analyses. Bioinformatics 21: 3122-3130 [Abstract] [Full Text]  
  • Kibe, R., Sakamoto, M., Yokota, H., Ishikawa, H., Aiba, Y., Koga, Y., Benno, Y. (2005). Movement and Fixation of Intestinal Microbiota after Administration of Human Feces to Germfree Mice. Appl. Environ. Microbiol. 71: 3171-3178 [Abstract] [Full Text]  
  • Rosch, C., Bothe, H. (2005). Improved Assessment of Denitrifying, N2-Fixing, and Total-Community Bacteria by Terminal Restriction Fragment Length Polymorphism Analysis Using Multiple Restriction Enzymes. Appl. Environ. Microbiol. 71: 2026-2035 [Abstract] [Full Text]  
  • Yu, C.-P., Ahuja, R., Sayler, G., Chu, K.-H. (2005). Quantitative Molecular Assay for Fingerprinting Microbial Communities of Wastewater and Estrogen-Degrading Consortia. Appl. Environ. Microbiol. 71: 1433-1444 [Abstract] [Full Text]  
  • Schloss, P. D., Handelsman, J. (2005). Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness. Appl. Environ. Microbiol. 71: 1501-1506 [Abstract] [Full Text]  
  • Besemer, K., Moeseneder, M. M., Arrieta, J. M., Herndl, G. J., Peduzzi, P. (2005). Complexity of Bacterial Communities in a River-Floodplain System (Danube, Austria). Appl. Environ. Microbiol. 71: 609-620 [Abstract] [Full Text]  
  • Miyamoto, T., Kawahara, M., Minamisawa, K. (2004). Novel Endophytic Nitrogen-Fixing Clostridia from the Grass Miscanthus sinensis as Revealed by Terminal Restriction Fragment Length Polymorphism Analysis. Appl. Environ. Microbiol. 70: 6580-6586 [Abstract] [Full Text]  
  • Rogers, G. B., Carroll, M. P., Serisier, D. J., Hockey, P. M., Jones, G., Bruce, K. D. (2004). Characterization of Bacterial Community Diversity in Cystic Fibrosis Lung Infections by Use of 16S Ribosomal DNA Terminal Restriction Fragment Length Polymorphism Profiling. J. Clin. Microbiol. 42: 5176-5183 [Abstract] [Full Text]  
  • Wong, M.-T., Tan, F. M., Ng, W. J., Liu, W.-T. (2004). Identification and occurrence of tetrad-forming Alphaproteobacteria in anaerobic-aerobic activated sludge processes. Microbiology 150: 3741-3748 [Abstract] [Full Text]  
  • Frias-Lopez, J., Klaus, J. S., Bonheyo, G. T., Fouke, B. W. (2004). Bacterial Community Associated with Black Band Disease in Corals. Appl. Environ. Microbiol. 70: 5955-5962 [Abstract] [Full Text]  
  • Cardinale, M., Brusetti, L., Quatrini, P., Borin, S., Puglia, A. M., Rizzi, A., Zanardini, E., Sorlini, C., Corselli, C., Daffonchio, D. (2004). Comparison of Different Primer Sets for Use in Automated Ribosomal Intergenic Spacer Analysis of Complex Bacterial Communities. Appl. Environ. Microbiol. 70: 6147-6156 [Abstract] [Full Text]  
  • Chen, C.-L., Macarie, H., Ramirez, I., Olmos, A., Ong, S. L., Monroy, O., Liu, W.-T. (2004). Microbial community structure in a thermophilic anaerobic hybrid reactor degrading terephthalate. Microbiology 150: 3429-3440 [Abstract] [Full Text]  
  • Donovan, S. E., Purdy, K. J., Kane, M. D., Eggleton, P. (2004). Comparison of Euryarchaea Strains in the Guts and Food-Soil of the Soil-Feeding Termite Cubitermes fungifaber across Different Soil Types. Appl. Environ. Microbiol. 70: 3884-3892 [Abstract] [Full Text]  
  • Ritalahti, K. M., Loffler, F. E. (2004). Populations Implicated in Anaerobic Reductive Dechlorination of 1,2-Dichloropropane in Highly Enriched Bacterial Communities. Appl. Environ. Microbiol. 70: 4088-4095 [Abstract] [Full Text]  
  • Sakamoto, M., Huang, Y., Ohnishi, M., Umeda, M., Ishikawa, I., Benno, Y. (2004). Changes in oral microbial profiles after periodontal treatment as determined by molecular analysis of 16S rRNA genes. J Med Microbiol 53: 563-571 [Abstract] [Full Text]  
  • Idris, R., Trifonova, R., Puschenreiter, M., Wenzel, W. W., Sessitsch, A. (2004). Bacterial Communities Associated with Flowering Plants of the Ni Hyperaccumulator Thlaspi goesingense. Appl. Environ. Microbiol. 70: 2667-2677 [Abstract] [Full Text]  
  • Devare, M. H., Jones, C. M., Thies, J. E. (2004). Effect of Cry3Bb Transgenic Corn and Tefluthrin on the Soil Microbial Community: Biomass, Activity, and Diversity. J. Environ. Qual. 33: 837-843 [Abstract] [Full Text]  
  • Steward, G. F., Jenkins, B. D., Ward, B. B., Zehr, J. P. (2004). Development and Testing of a DNA Macroarray To Assess Nitrogenase (nifH) Gene Diversity. Appl. Environ. Microbiol. 70: 1455-1465 [Abstract] [Full Text]  
  • Sliwinski, M. K., Goodman, R. M. (2004). Spatial Heterogeneity of Crenarchaeal Assemblages within Mesophilic Soil Ecosystems as Revealed by PCR-Single-Stranded Conformation Polymorphism Profiling. Appl. Environ. Microbiol. 70: 1811-1820 [Abstract] [Full Text]  
  • Broderick, N. A., Raffa, K. F., Goodman, R. M., Handelsman, J. (2004). Census of the Bacterial Community of the Gypsy Moth Larval Midgut by Using Culturing and Culture-Independent Methods. Appl. Environ. Microbiol. 70: 293-300 [Abstract] [Full Text]  
  • Stres, B., Mahne, I., Avgustin, G., Tiedje, J. M. (2004). Nitrous Oxide Reductase (nosZ) Gene Fragments Differ between Native and Cultivated Michigan Soils. Appl. Environ. Microbiol. 70: 301-309 [Abstract] [Full Text]  
  • Dunfield, K. E., Germida, J. J. (2003). Seasonal Changes in the Rhizosphere Microbial Communities Associated with Field-Grown Genetically Modified Canola (Brassica napus). Appl. Environ. Microbiol. 69: 7310-7318 [Abstract] [Full Text]  
  • Jeon, C. O., Park, W., Padmanabhan, P., DeRito, C., Snape, J. R., Madsen, E. L. (2003). Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment. Proc. Natl. Acad. Sci. USA 100: 13591-13596 [Abstract] [Full Text]  
  • Buchan, A., Newell, S. Y., Butler, M., Biers, E. J., Hollibaugh, J. T., Moran, M. A. (2003). Dynamics of Bacterial and Fungal Communities on Decaying Salt Marsh Grass. Appl. Environ. Microbiol. 69: 6676-6687 [Abstract] [Full Text]  
  • Kent, A. D., Smith, D. J., Benson, B. J., Triplett, E. W. (2003). Web-Based Phylogenetic Assignment Tool for Analysis of Terminal Restriction Fragment Length Polymorphism Profiles of Microbial Communities. Appl. Environ. Microbiol. 69: 6768-6776 [Abstract] [Full Text]  
  • Martiny, A. C., Jorgensen, T. M., Albrechtsen, H.-J., Arvin, E., Molin, S. (2003). Long-Term Succession of Structure and Diversity of a Biofilm Formed in a Model Drinking Water Distribution System. Appl. Environ. Microbiol. 69: 6899-6907 [Abstract] [Full Text]  
  • Schmitt-Wagner, D., Friedrich, M. W., Wagner, B., Brune, A. (2003). Axial Dynamics, Stability, and Interspecies Similarity of Bacterial Community Structure in the Highly Compartmentalized Gut of Soil-Feeding Termites (Cubitermes spp.). Appl. Environ. Microbiol. 69: 6018-6024 [Abstract] [Full Text]  
  • Bent, S. J., Gucker, C. L., Oda, Y., Forney, L. J. (2003). Spatial Distribution of Rhodopseudomonas palustris Ecotypes on a Local Scale. Appl. Environ. Microbiol. 69: 5192-5197 [Abstract] [Full Text]  
  • Engebretson, J. J., Moyer, C. L. (2003). Fidelity of Select Restriction Endonucleases in Determining Microbial Diversity by Terminal-Restriction Fragment Length Polymorphism. Appl. Environ. Microbiol. 69: 4823-4829 [Abstract] [Full Text]  
  • Rogers, G. B., Hart, C. A., Mason, J. R., Hughes, M., Walshaw, M. J., Bruce, K. D. (2003). Bacterial Diversity in Cases of Lung Infection in Cystic Fibrosis Patients: 16S Ribosomal DNA (rDNA) Length Heterogeneity PCR and 16S rDNA Terminal Restriction Fragment Length Polymorphism Profiling. J. Clin. Microbiol. 41: 3548-3558 [Abstract] [Full Text]  
  • Merrill, L., Richardson, J., Kuske, C. R., Dunbar, J. (2003). Fluorescent Heteroduplex Assay for Monitoring Bacillus anthracis and Close Relatives in Environmental Samples. Appl. Environ. Microbiol. 69: 3317-3326 [Abstract] [Full Text]  
  • Nikolcheva, L. G., Cockshutt, A. M., Barlocher, F. (2003). Determining Diversity of Freshwater Fungi on Decaying Leaves: Comparison of Traditional and Molecular Approaches. Appl. Environ. Microbiol. 69: 2548-2554 [Abstract] [Full Text]  
  • Egert, M., Friedrich, M. W. (2003). Formation of Pseudo-Terminal Restriction Fragments, a PCR-Related Bias Affecting Terminal Restriction Fragment Length Polymorphism Analysis of Microbial Community Structure. Appl. Environ. Microbiol. 69: 2555-2562 [Abstract] [Full Text]  
  • Sait, L., Galic, M., Strugnell, R. A., Janssen, P. H. (2003). Secretory Antibodies Do Not Affect the Composition of the Bacterial Microbiota in the Terminal Ileum of 10-Week-Old Mice. Appl. Environ. Microbiol. 69: 2100-2109 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»