bacteria

Summary

Summary: One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophic (via chemical reaction) or phototrophic (via light reaction); for chemotrophs by their source of chemical energy: lithotrophic (from inorganic compounds) or organotrophic (from organic compounds); and by where they get their CARBON: heterotrophic (from organic sources) or autotrophic (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.

Top Publications

  1. pmc Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    Qiong Wang
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
    Appl Environ Microbiol 73:5261-7. 2007
  2. pmc Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
    T Z DeSantis
    Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A 3317, Berkeley, CA 94720, USA
    Appl Environ Microbiol 72:5069-72. 2006
  3. pmc Bacterial community variation in human body habitats across space and time
    Elizabeth K Costello
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Science 326:1694-7. 2009
  4. pmc Human gut microbiome viewed across age and geography
    Tanya Yatsunenko
    Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 486:222-7. 2012
  5. pmc Enterotypes of the human gut microbiome
    Manimozhiyan Arumugam
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 473:174-80. 2011
  6. pmc A human gut microbial gene catalogue established by metagenomic sequencing
    Junjie Qin
    BGI Shenzhen, Shenzhen 518083, China
    Nature 464:59-65. 2010
  7. pmc Diversity of the human intestinal microbial flora
    Paul B Eckburg
    Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Room S 169, 300 Pasteur Drive, Stanford CA 94305 5107, USA
    Science 308:1635-8. 2005
  8. pmc UniFrac: a new phylogenetic method for comparing microbial communities
    Catherine Lozupone
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Appl Environ Microbiol 71:8228-35. 2005
  9. pmc Linking long-term dietary patterns with gut microbial enterotypes
    Gary D Wu
    Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Science 334:105-8. 2011
  10. ncbi An obesity-associated gut microbiome with increased capacity for energy harvest
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University, St Louis, Missouri 63108, USA
    Nature 444:1027-31. 2006

Detail Information

Publications271 found, 100 shown here

  1. pmc Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    Qiong Wang
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
    Appl Environ Microbiol 73:5261-7. 2007
    ..It combines the RDP Classifier with a statistical test to flag taxa differentially represented between samples. The RDP Classifier and RDP Library Compare are available online at http://rdp.cme.msu.edu/...
  2. pmc Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
    T Z DeSantis
    Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A 3317, Berkeley, CA 94720, USA
    Appl Environ Microbiol 72:5069-72. 2006
    ..Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.
  3. pmc Bacterial community variation in human body habitats across space and time
    Elizabeth K Costello
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Science 326:1694-7. 2009
    ..To obtain an integrated view of the spatial and temporal distribution of the human microbiota, we surveyed bacteria from up to 27 sites in seven to nine healthy adults on four occasions...
  4. pmc Human gut microbiome viewed across age and geography
    Tanya Yatsunenko
    Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 486:222-7. 2012
    ..Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization...
  5. pmc Enterotypes of the human gut microbiome
    Manimozhiyan Arumugam
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 473:174-80. 2011
    ..For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers...
  6. pmc A human gut microbial gene catalogue established by metagenomic sequencing
    Junjie Qin
    BGI Shenzhen, Shenzhen 518083, China
    Nature 464:59-65. 2010
    ..We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.
  7. pmc Diversity of the human intestinal microbial flora
    Paul B Eckburg
    Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Room S 169, 300 Pasteur Drive, Stanford CA 94305 5107, USA
    Science 308:1635-8. 2005
    ..We discovered significant intersubject variability and differences between stool and mucosa community composition. Characterization of this immensely diverse ecosystem is the first step in elucidating its role in health and disease...
  8. pmc UniFrac: a new phylogenetic method for comparing microbial communities
    Catherine Lozupone
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Appl Environ Microbiol 71:8228-35. 2005
    ..of UniFrac by applying it to published 16S rRNA gene libraries from cultured isolates and environmental clones of bacteria in marine sediment, water, and ice...
  9. pmc Linking long-term dietary patterns with gut microbial enterotypes
    Gary D Wu
    Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Science 334:105-8. 2011
    ..Thus, alternative enterotype states are associated with long-term diet...
  10. ncbi An obesity-associated gut microbiome with increased capacity for energy harvest
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University, St Louis, Missouri 63108, USA
    Nature 444:1027-31. 2006
    ..These results identify the gut microbiota as an additional contributing factor to the pathophysiology of obesity...
  11. doi Metagenomic discovery of biomass-degrading genes and genomes from cow rumen
    Matthias Hess
    Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
    Science 331:463-7. 2011
    ..These data sets provide a substantially expanded catalog of genes and genomes participating in the deconstruction of cellulosic biomass...
  12. doi Accurate determination of microbial diversity from 454 pyrosequencing data
    Christopher Quince
    Department of Civil Engineering, Rankine Building, University of Glasgow, Glasgow, UK
    Nat Methods 6:639-41. 2009
    ..We pyrosequenced a known mixture of microbial 16S rDNA sequences extracted from a lake and found that without noise reduction the number of operational taxonomic units is overestimated but using PyroNoise it can be accurately calculated...
  13. pmc Regulatory RNAs in bacteria
    Lauren S Waters
    Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
    Cell 136:615-28. 2009
    b>Bacteria possess numerous and diverse means of gene regulation using RNA molecules, including mRNA leaders that affect expression in cis, small RNAs that bind to proteins or base pair with target RNAs, and CRISPR RNAs that inhibit the ..
  14. pmc An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
    Daniel McDonald
    Department of Chemistry and Biochemistry and Biofrontiers Institute, University of Colorado, Boulder, CO, USA
    ISME J 6:610-8. 2012
    ..The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/...
  15. pmc A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
    Dongying Wu
    DOE Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 462:1056-60. 2009
    ..basis of their evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage...
  16. pmc Phylogenetic identification and in situ detection of individual microbial cells without cultivation
    R I Amann
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, Germany
    Microbiol Rev 59:143-69. 1995
    The frequent discrepancy between direct microscopic counts and numbers of culturable bacteria from environmental samples is just one of several indications that we currently know only a minor part of the diversity of microorganisms in ..
  17. pmc Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
    Micah Hamady
    Department of Computer Science, University of Colorado, Boulder, CO, USA
    ISME J 4:17-27. 2010
    ..Together, these case studies point the way toward a broad range of applications and show some of the new features of Fast UniFrac...
  18. ncbi Microbial ecology: human gut microbes associated with obesity
    Ruth E Ley
    Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 444:1022-3. 2006
    Two groups of beneficial bacteria are dominant in the human gut, the Bacteroidetes and the Firmicutes...
  19. pmc Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
    J Gregory Caporaso
    Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA
    ISME J 6:1621-4. 2012
    ....
  20. pmc Evolution of mammals and their gut microbes
    Ruth E Ley
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Science 320:1647-51. 2008
    ....
  21. pmc Microbial cellulose utilization: fundamentals and biotechnology
    Lee R Lynd
    Chemical and Biochemical Engineering, Thayer School of Engineering and Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
    Microbiol Mol Biol Rev 66:506-77, table of contents. 2002
    ....
  22. pmc The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing
    Les Dethlefsen
    Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America
    PLoS Biol 6:e280. 2008
    ..The rapid return to the pretreatment community composition is indicative of factors promoting community resilience, the nature of which deserves future investigation...
  23. pmc Regulation by small RNAs in bacteria: expanding frontiers
    Gisela Storz
    Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 18 Library Drive, Bethesda, MD 20892 5430, USA
    Mol Cell 43:880-91. 2011
    Research on the discovery and characterization of small, regulatory RNAs in bacteria has exploded in recent years...
  24. pmc Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa
    Carlotta De Filippo
    Department of Preclinical and Clinical Pharmacology, University of Florence, 50139 Firenze, Italy
    Proc Natl Acad Sci U S A 107:14691-6. 2010
    ..001), with a unique abundance of bacteria from the genus Prevotella and Xylanibacter, known to contain a set of bacterial genes for cellulose and xylan ..
  25. ncbi Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis
    Seth Rakoff-Nahoum
    Howard Hughes Medical Institute and Section of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
    Cell 118:229-41. 2004
    ..It is thought that an inflammatory response to commensal bacteria is avoided due to sequestration of microflora by surface epithelia...
  26. pmc Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Biol Direct 6:38. 2011
    The CRISPR-Cas adaptive immunity systems that are present in most Archaea and many Bacteria function by incorporating fragments of alien genomes into specific genomic loci, transcribing the inserts and using the transcripts as guide RNAs ..
  27. ncbi Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria?
    Kim A Brogden
    Department of Periodontics and Dows Institute for Dental Research, College of Dentistry, The University of Iowa, Iowa City, Iowa 52242, USA
    Nat Rev Microbiol 3:238-50. 2005
    ..In this review the different models of antimicrobial-peptide-induced pore formation and cell killing are presented...
  28. ncbi Ecological and evolutionary forces shaping microbial diversity in the human intestine
    Ruth E Ley
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Cell 124:837-48. 2006
    ..The ecological rules that govern the shape of microbial diversity in the gut apply to mutualists and pathogens alike...
  29. doi RNA-guided genetic silencing systems in bacteria and archaea
    Blake Wiedenheft
    Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, Maryland 20815 6789, USA
    Nature 482:331-8. 2012
    ..repeat (CRISPR) are essential components of nucleic-acid-based adaptive immune systems that are widespread in bacteria and archaea...
  30. pmc Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing
    Susan M Huse
    Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
    PLoS Genet 4:e1000255. 2008
    ..This technique allows the cost-effective exploration of changes in microbial community structure, including the rare biosphere, over space and time and can be applied immediately to initiatives, such as the Human Microbiome Project...
  31. pmc Topographical and temporal diversity of the human skin microbiome
    Elizabeth A Grice
    Genetics and Molecular Biology Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
    Science 324:1190-2. 2009
    ..This topographical and temporal survey provides a baseline for studies that examine the role of bacterial communities in disease states and the microbial interdependencies required to maintain healthy skin...
  32. doi CRISPR-mediated adaptive immune systems in bacteria and archaea
    Rotem Sorek
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Annu Rev Biochem 82:237-66. 2013
    ..that relies on small RNAs for sequence-specific targeting of foreign nucleic acids was recently discovered in bacteria and archaea...
  33. pmc The influence of sex, handedness, and washing on the diversity of hand surface bacteria
    Noah Fierer
    Department of Ecology and Evolutionary Biology, University of Colorado, UCB 334, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 105:17994-9. 2008
    b>Bacteria thrive on and within the human body. One of the largest human-associated microbial habitats is the skin surface, which harbors large numbers of bacteria that can have important effects on health...
  34. pmc Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 108:4516-22. 2011
    ..The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution...
  35. doi CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation
    Devaki Bhaya
    Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305, USA
    Annu Rev Genet 45:273-97. 2011
    b>Bacteria and archaea have evolved defense and regulatory mechanisms to cope with various environmental stressors, including virus attack...
  36. pmc Examining the global distribution of dominant archaeal populations in soil
    Scott T Bates
    Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA
    ISME J 5:908-17. 2011
    ..This trend was coupled with a concurrent increase in known N-oxidizing bacteria, suggesting competitive interactions between these groups.
  37. doi Functional metagenomic profiling of nine biomes
    Elizabeth A Dinsdale
    Department of Biology, San Diego State University, San Diego, California 92182, USA
    Nature 452:629-32. 2008
    ....
  38. pmc Moving pictures of the human microbiome
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, CO 80309, USA
    Genome Biol 12:R50. 2011
    ..Here, we present the largest human microbiota time series analysis to date, covering two individuals at four body sites over 396 timepoints...
  39. pmc Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale
    Christian L Lauber
    Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, 80309, USA
    Appl Environ Microbiol 75:5111-20. 2009
    ....
  40. ncbi Quorum sensing: cell-to-cell communication in bacteria
    Christopher M Waters
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544 1014, USA
    Annu Rev Cell Dev Biol 21:319-46. 2005
    b>Bacteria communicate with one another using chemical signal molecules. As in higher organisms, the information supplied by these molecules is critical for synchronizing the activities of large groups of cells...
  41. doi Antibiotic resistance is ancient
    Vanessa M D'Costa
    Michael G DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada, L8N 3Z5
    Nature 477:457-61. 2011
    ..This history has been interpreted to mean that antibiotic resistance in pathogenic bacteria is a modern phenomenon; this view is reinforced by the fact that collections of microbes that predate the ..
  42. ncbi Archaea predominate among ammonia-oxidizing prokaryotes in soils
    S Leininger
    Department of Biology, University of Bergen, Jahnebakken 5, N 5020 Bergen, Norway
    Nature 442:806-9. 2006
    ..Our results indicate that crenarchaeota may be the most abundant ammonia-oxidizing organisms in soil ecosystems on Earth...
  43. doi Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance
    A P Magiorakos
    European Centre for Disease Prevention and Control, Stockholm, Sweden
    Clin Microbiol Infect 18:268-81. 2012
    ..different definitions for multidrug-resistant (MDR), extensively drug-resistant (XDR) and pandrug-resistant (PDR) bacteria are being used in the medical literature to characterize the different patterns of resistance found in healthcare-..
  44. ncbi 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
    ..the main diversity of life is microbial, distributed among three primary relatedness groups or domains: Archaea, Bacteria, and Eucarya...
  45. pmc CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea
    Luciano A Marraffini
    Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, Illinois 60208, USA
    Nat Rev Genet 11:181-90. 2010
    ..In many bacteria and most archaea, clustered, regularly interspaced short palindromic repeats (CRISPRs) are involved in a more ..
  46. pmc A catalog of reference genomes from the human microbiome
    Karen E Nelson
    Science 328:994-9. 2010
    ..Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented...
  47. doi Host-gut microbiota metabolic interactions
    Jeremy K Nicholson
    Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
    Science 336:1262-7. 2012
    ..A deeper understanding of these axes is a prerequisite for optimizing therapeutic strategies to manipulate the gut microbiota to combat disease and improve health...
  48. doi Ecology drives a global network of gene exchange connecting the human microbiome
    Chris S Smillie
    Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Nature 480:241-4. 2011
    ..For example, we observe 25-fold more HGT between human-associated bacteria than among ecologically diverse non-human isolates (P = 3.0 × 10(-270))...
  49. pmc The impact of the gut microbiota on human health: an integrative view
    Jose C Clemente
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA
    Cell 148:1258-70. 2012
    ..The constituents of the microbiota--bacteria, viruses, and eukaryotes--have been shown to interact with one another and with the host immune system in ways ..
  50. pmc The shared antibiotic resistome of soil bacteria and human pathogens
    Kevin J Forsberg
    Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA
    Science 337:1107-11. 2012
    ..termed PARFuMS), we provide evidence for recent exchange of antibiotic resistance genes between environmental bacteria and clinical pathogens...
  51. ncbi Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
    Falk Warnecke
    DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
    Nature 450:560-5. 2007
    ..Only recently have data supported any direct role for the symbiotic bacteria in the gut of the termite in cellulose and xylan hydrolysis...
  52. pmc Metagenomic analysis of the human distal gut microbiome
    Steven R Gill
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 312:1355-9. 2006
    ..Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes...
  53. pmc Metagenomic microbial community profiling using unique clade-specific marker genes
    Nicola Segata
    Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
    Nat Methods 9:811-4. 2012
    ..We validated our metagenomic phylogenetic analysis tool, MetaPhlAn, on terabases of short reads and provide the largest metagenomic profiling to date of the human gut. It can be accessed at http://huttenhower.sph.harvard.edu/metaphlan/...
  54. doi Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species
    Ok Sun Kim
    School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
    Int J Syst Evol Microbiol 62:716-21. 2012
    ..The database and its analytical functions can be found at http://eztaxon-e.ezbiocloud.net/...
  55. pmc Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
    Arthur Brady
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
    Nat Methods 6:673-6. 2009
    ..We also describe how combining Phymm with sequence alignment algorithms improves accuracy...
  56. pmc Development of the human infant intestinal microbiota
    Chana Palmer
    Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Biol 5:e177. 2007
    ..subunit ribosomal RNA (SSU rRNA) gene sequences of most currently recognized species and taxonomic groups of bacteria. We used this microarray, along with sequencing of cloned libraries of PCR-amplified SSU rDNA, to profile the ..
  57. pmc The human oral microbiome
    Floyd E Dewhirst
    Department of Molecular Genetics, The Forsyth Institute, 245 First St, Cambridge, MA 02142, USA
    J Bacteriol 192:5002-17. 2010
    ..including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are colonized by bacteria. The oral microbiome is comprised of over 600 prevalent taxa at the species level, with distinct subsets ..
  58. ncbi Antibiotic resistance of bacteria in biofilms
    P S Stewart
    Center for Biofilm Engineering and Department of Chemical Engineering, Montana State University, Bozeman, MT 59717 3980, USA
    Lancet 358:135-8. 2001
    b>Bacteria that adhere to implanted medical devices or damaged tissue can encase themselves in a hydrated matrix of polysaccharide and protein, and form a slimy layer known as a biofilm...
  59. pmc Interactions between the microbiota and the immune system
    Lora V Hooper
    The Howard Hughes Medical Institute and Department of Immunology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
    Science 336:1268-73. 2012
    ..At the same time, resident bacteria profoundly shape mammalian immunity...
  60. doi Genomics and evolution of heritable bacterial symbionts
    Nancy A Moran
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
    Annu Rev Genet 42:165-90. 2008
    ..In addition, insect symbionts provide some of the extremes of cellular genomes, including the smallest and the fastest evolving, raising new questions about the limits of evolution of life...
  61. pmc Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns
    Maria G Dominguez-Bello
    Department of Biology, University of Puerto Rico, San Juan, Puerto Rico 00931
    Proc Natl Acad Sci U S A 107:11971-5. 2010
    ..neonate is exposed for the first time to a wide array of microbes from a variety of sources, including maternal bacteria. Although prior studies have suggested that delivery mode shapes the microbiota's establishment and, subsequently,..
  62. pmc Biofilms: survival mechanisms of clinically relevant microorganisms
    Rodney M Donlan
    Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
    Clin Microbiol Rev 15:167-93. 2002
    ..In the future, treatments may be based on inhibition of genes involved in cell attachment and biofilm formation...
  63. ncbi Microbial biogeography: putting microorganisms on the map
    Jennifer B Hughes Martiny
    Department of Ecology and Evolutionary Biology, 80 Waterman Street, Box G W, Brown University, Providence, Rhode Island 02912, USA
    Nat Rev Microbiol 4:102-12. 2006
    ..However, recent studies also dispute the idea that 'everything is everywhere'. We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world...
  64. ncbi Consolidated bioprocessing of cellulosic biomass: an update
    Lee R Lynd
    Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755, USA
    Curr Opin Biotechnol 16:577-83. 2005
    ..Recent studies of the fundamental principles of microbial cellulose utilization support the feasibility of CBP...
  65. pmc Human oral, gut, and plaque microbiota in patients with atherosclerosis
    Omry Koren
    Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
    Proc Natl Acad Sci U S A 108:4592-8. 2011
    Periodontal disease has been associated with atherosclerosis, suggesting that bacteria from the oral cavity may contribute to the development of atherosclerosis and cardiovascular disease...
  66. ncbi Two-component signal transduction
    A M Stock
    Center for Advanced Biotechnology and Medicine and Howard Hughes Medical Institute, University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
    Annu Rev Biochem 69:183-215. 2000
    ..Thus detailed analyses of a relatively small number of representative proteins provide a foundation for understanding this large family of signaling proteins...
  67. pmc Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University, St Louis, MO 63108, USA
    Cell Host Microbe 3:213-23. 2008
    ..Our study illustrates how combining comparative metagenomics with gnotobiotic mouse models and specific dietary manipulations can disclose the niches of previously uncharacterized members of the gut microbiota...
  68. pmc Innate immunity and intestinal microbiota in the development of Type 1 diabetes
    Li Wen
    Section of Endocrinology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
    Nature 455:1109-13. 2008
    ..Together, these findings indicate that interaction of the intestinal microbes with the innate immune system is a critical epigenetic factor modifying T1D predisposition...
  69. pmc Shifting the genomic gold standard for the prokaryotic species definition
    Michael Richter
    Marine Microbiology Group, Institut Mediterrani d Estudis Avançats CSIC UIB, E 07190 Esporles, Spain
    Proc Natl Acad Sci U S A 106:19126-31. 2009
    ..Moreover, for taxonomic purposes, the analyses can be produced by simply randomly sequencing at least 20% of the genome of the query strains rather than obtaining their full sequence...
  70. pmc Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans
    Brian D Muegge
    Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA
    Science 332:970-4. 2011
    ..These results illustrate the value of characterizing vertebrate gut microbiomes to understand host evolutionary histories at a supraorganismal level...
  71. doi Drug discovery and natural products: end of an era or an endless frontier?
    Jesse W H Li
    Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
    Science 325:161-5. 2009
    ..Advances in rapid genetic sequencing, coupled with manipulation of biosynthetic pathways, may provide a vast resource for the future discovery of pharmaceutical agents...
  72. pmc Metagenomic biomarker discovery and explanation
    Nicola Segata
    Department of Biostatistics, 677 Huntington Avenue, Harvard School of Public Health, Boston, MA 02115, USA
    Genome Biol 12:R60. 2011
    ..We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/...
  73. doi Dissemination of NDM-1 positive bacteria in the New Delhi environment and its implications for human health: an environmental point prevalence study
    Timothy R Walsh
    Department of Infection, Immunity and Biochemistry, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
    Lancet Infect Dis 11:355-62. 2011
    Not all patients infected with NDM-1-positive bacteria have a history of hospital admission in India, and extended-spectrum β-lactamases are known to be circulating in the Indian community...
  74. pmc Dominant and diet-responsive groups of bacteria within the human colonic microbiota
    Alan W Walker
    Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, UK
    ISME J 5:220-30. 2011
    ..bromii (R-ruminococci) increased in most volunteers on the RS diet, accounting for a mean of 17% of total bacteria compared with 3.8% on the NSP diet, whereas the uncultured Oscillibacter group increased on the RS and WL diets...
  75. doi Antibiotic resistance of bacterial biofilms
    Niels Høiby
    Department of Clinical Microbiology 9301, Juliane Mariesvej 22, Rigshospitalet, 2100 Copenhagen, Denmark
    Int J Antimicrob Agents 35:322-32. 2010
    A biofilm is a structured consortium of bacteria embedded in a self-produced polymer matrix consisting of polysaccharide, protein and DNA...
  76. pmc Statistical methods for detecting differentially abundant features in clinical metagenomic samples
    James Robert White
    Applied Mathematics and Scientific Computation Program, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
    PLoS Comput Biol 5:e1000352. 2009
    ..g. SAGE). A web server implementation of our methods and freely available source code can be found at http://metastats.cbcb.umd.edu/...
  77. pmc Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach
    C Manichanh
    Unité d Ecologie et de Physiologie du Système Digestif, INRA UEPSD, 78350 Jouy en Josas, France
    Gut 55:205-11. 2006
    ..However, investigation of such a complex ecosystem is difficult, even with culture independent molecular approaches...
  78. pmc The diversity and biogeography of soil bacterial communities
    Noah Fierer
    Department of Biology and Nicholas School of the Environment and Earth Sciences, Duke University, Durham, NC 27708, USA
    Proc Natl Acad Sci U S A 103:626-31. 2006
    ..Our results suggest that microbial biogeography is controlled primarily by edaphic variables and differs fundamentally from the biogeography of "macro" organisms...
  79. pmc Obesity alters gut microbial ecology
    Ruth E Ley
    Center for Genomes Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 102:11070-5. 2005
    ..The sequences reported in this paper have been deposited in the GenBank database [accession nos. DQ 014552--DQ 015671 (mothers) and AY 989911--AY 993908 (offspring)]...
  80. pmc eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data
    Edward J Feil
    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
    J Bacteriol 186:1518-30. 2004
    ..pneumoniae and Staphylococcus aureus MLST databases, and the more complicated clonal complexes observed for Campylobacter jejuni and Neisseria meningitidis...
  81. doi CRISPR/Cas, the immune system of bacteria and archaea
    Philippe Horvath
    Danisco France SAS, BP10, F 86220 Dangé Saint Romain, France
    Science 327:167-70. 2010
    ..In many Bacteria and most Archaea, clustered regularly interspaced short palindromic repeats (CRISPR) form peculiar genetic loci, ..
  82. pmc Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
    Brian J Haas
    Genome Sequencing and Analysis Program, The Broad Institute, Cambridge, Massachusetts 02142, USA
    Genome Res 21:494-504. 2011
    ..Shotgun metagenomic sequences of our mock community appear to be devoid of 16S chimeras, supporting a role for shotgun metagenomics in validating novel organisms discovered in targeted sequence surveys...
  83. doi The microbial engines that drive Earth's biogeochemical cycles
    Paul G Falkowski
    Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal Sciences and Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ 08901, USA
    Science 320:1034-9. 2008
    ..A major challenge in the coming decades is to understand how these machines evolved, how they work, and the processes that control their activity on both molecular and planetary scales...
  84. ncbi Biofilms as complex differentiated communities
    P Stoodley
    Center for Biofilm Engineering, Montana State University, Bozeman 59717, USA
    Annu Rev Microbiol 56:187-209. 2002
    ..In a holistic sense both biofilm and planktonic phenotypes may be viewed as integrated components of prokaryote life...
  85. pmc Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria
    Matthew R Hepworth
    Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Nature 498:113-7. 2013
    ..RORγt(+)) ILCs was associated with dysregulated adaptive immune cell responses against commensal bacteria and low-grade systemic inflammation...
  86. pmc Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells
    Hsin Jung Wu
    Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
    Immunity 32:815-27. 2010
    ..Introduction of a single gut-residing species, segmented filamentous bacteria, into GF animals reinstated the lamina propria Th17 cell compartment and production of autoantibodies, and ..
  87. doi Bad bugs, no drugs: no ESKAPE! An update from the Infectious Diseases Society of America
    Helen W Boucher
    Division of Geographic Medicine and Infectious Diseases, Tufts University and Tufts Medical Center, Boston, Massachusetts 02111, USA
    Clin Infect Dis 48:1-12. 2009
    ..This report provides an update on potentially effective antibacterial drugs in the late-stage development pipeline, in the hope of encouraging such collaborative action...
  88. ncbi Persister cells, dormancy and infectious disease
    Kim Lewis
    Antimicrobial Discovery Center, Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, USA
    Nat Rev Microbiol 5:48-56. 2007
    ..Accumulating evidence suggests that these seemingly disparate phenomena result from the ability of bacteria to enter into a dormant (non-dividing) state...
  89. pmc Viruses in the faecal microbiota of monozygotic twins and their mothers
    Alejandro Reyes
    Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 466:334-8. 2010
    ..These results indicate that a predatory viral-microbial dynamic, manifest in a number of other characterized environmental ecosystems, is notably absent in the very distal intestine...
  90. doi Toxin-antitoxin systems in bacteria and archaea
    Yoshihiro Yamaguchi
    Department of Biochemistry, Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
    Annu Rev Genet 45:61-79. 2011
    Almost all bacteria and many archaea contain genes whose expression inhibits cell growth and may lead to cell death when overproduced, reminiscent of apoptotic genes in higher systems...
  91. pmc Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)
    Scot E Dowd
    USDA ARS Livestock Issues Research Unit, Lubbock, TX 79403, USA
    BMC Microbiol 8:125. 2008
    ..We have evaluated the microbiome from the feces of 20 commercial, lactating dairy cows...
  92. pmc Comparative genomics of defense systems in archaea and bacteria
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 41:4360-77. 2013
    ....
  93. doi Genome architecture and global gene regulation in bacteria: making progress towards a unified model?
    Charles J Dorman
    Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
    Nat Rev Microbiol 11:349-55. 2013
    ..Here, I discuss the proposal that, in addition to DNA topology and nucleoid-associated proteins, gene regulation is an important organizing principle of nucleoid architecture...
  94. doi Principles of c-di-GMP signalling in bacteria
    Regine Hengge
    Institut für Biologie Mikrobiologie, Freie Universitat Berlin, 14195 Berlin, Germany
    Nat Rev Microbiol 7:263-73. 2009
    ..This Review focuses on emerging principles of c-di-GMP signalling using selected systems in different bacteria as examples.
  95. doi Evolutionary microbial genomics: insights into bacterial host adaptation
    Christina Toft
    Department of Molecular Evolution, Uppsala University, 752 36 Uppsala, Sweden
    Nat Rev Genet 11:465-75. 2010
    Host-adapted bacteria include mutualists and pathogens of animals, plants and insects. Their study is therefore important for biotechnology, biodiversity and human health...
  96. pmc Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes
    Todd J Treangen
    Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, Paris, France
    PLoS Genet 7:e1001284. 2011
    ..Therefore, the study of the evolution of biology systems should explicitly account for the predominant role of horizontal gene transfer in the diversification of protein families...
  97. doi Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota
    Davide Bulgarelli
    Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
    Nature 488:91-5. 2012
    ..Notably, soil bacteria are able to multiply inside roots as benign endophytes and modulate plant growth and development, with ..
  98. pmc Microbial co-occurrence relationships in the human microbiome
    Karoline Faust
    Department of Structural Biology, VIB, Brussels, Belgium
    PLoS Comput Biol 8:e1002606. 2012
    ..Comparing phylogenetic versus functional similarities among bacteria, we show that dominant commensal taxa (such as Prevotellaceae and Bacteroides in the gut) often compete, while ..
  99. doi Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
    Mads Albertsen
    Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark
    Nat Biotechnol 31:533-8. 2013
    ..This approach will be an important addition to the standard metagenome toolbox and greatly improve access to genomes of uncultured microorganisms...
  100. pmc VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors
    Lihong Chen
    State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy Medical Sciences and Peking Union Medical College, Beijing 100176, China
    Nucleic Acids Res 40:D641-5. 2012
    ..of complete sequences of bacterial genomes and increasing sophisticated technologies for manipulating bacteria and bacterial genomes...
  101. pmc A guide to the natural history of freshwater lake bacteria
    Ryan J Newton
    Great Lakes WATER Institute, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA
    Microbiol Mol Biol Rev 75:14-49. 2011
    Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about the identity and ecology of functionally significant lake bacteria...

Research Grants84

  1. Variation in M. tuberculosis in response to host selection
    Sarah Fortune; Fiscal Year: 2009
    ..or epigenetically, during the course of infection and that this variation contributes to the ability of the bacteria to avoid clearance by the host immune response...
  2. CFI Pathogen Inactivation Technology
    Trevor P Castor; Fiscal Year: 2010
    ..In addition to viruses, bacteria and parasites such as Babesia spp. and Plasmodium spp...
  3. Anti-Inflammatory Glycosaminoglycan Ethers for Treatment of Periodontitis
    JUSTIN RODNEY SAVAGE; Fiscal Year: 2011
    ..show other activities that could also be beneficial in treating gingivitis, including prevention of gram-negative bacteria attachment, disruption of gram negative microbial biofilm formation, inhibition of cytokine secretion by LPS-..
  4. Periodontal Biomaterials with BITE (Biofilm Immunity via T-cell Enhancement)
    James D Bryers; Fiscal Year: 2012
    ..The development and progression of chronic periodontitis has been associated with specific Gram-negative bacteria in subgingival plaque...
  5. Optimized Growth Media to Detect Intracellular Bacteria Implicated in Chronic Dis
    PATRICIA MASCARELLI; Fiscal Year: 2011
    ..b>Bacteria of the genus Bartonella (a member of the Rickettsiales order) have been linked in the medical case series ..
  6. Metabolic Engineering of Bacteria for Cancer Immunotherapy by Gamma Delta T Cells
    Craig T Morita; Fiscal Year: 2013
    ..Early in the 1900's, Coley successfully used a mix of heat-killed Streptococcus and Serratia bacteria to treat a variety of sarcomas and other cancers...
  7. Regulation of B Cell Function by Membrane-Cytoskeletal Remodeling
    Neetu Gupta; Fiscal Year: 2012
    ..Public Health Relevance: B cells respond to environmental pathogens such as bacteria and viruses by secreting specific antibodies that clear infections...
  8. Inhibition of human neutrophil function by Francisella tularensis
    Lee Ann H Allen; Fiscal Year: 2012
    ..white blood cell in alveoli and bronchioles during acute infection (day 2-14), and engulf large numbers of bacteria in this locale, Ft are not killed and bacterial load increases markedly...
  9. Enterococcus faecalis, Colorectal Cancer, and Bystander Effects
    Mark M Huycke; Fiscal Year: 2012
    ..However, no studies have convincingly defined how bacteria might promote this common tumor...
  10. Group A Streptococcus responses to oxidative stress
    Ioannis Gryllos; Fiscal Year: 2010
    ..peroxide (H2O2) or to H2O2 combined with human neutrophil granule contents in wild type versus perR mutant bacteria will define PerR-dependent and independent GAS responses to ROS generated by NADPH oxidase and myeloperoxidase as ..
  11. Targeting superbugs: discovery and development of new broad-spectrum lipopeptides
    Jian Li; Fiscal Year: 2013
    ..implies a total lack of antibiotics for treatment of life-threatening infections caused by these Gram-negative bacteria. Research Design: Using a new structure-activity relationship (SAR)-based mechanistic model for polymyxins, novel ..
  12. Alternative Macrophage Activation Limits Immunopathology
    DEBROSKI R HERBERT; Fiscal Year: 2011
    ..Infection with diverse bacteria and viruses gives rise to classically activated macrophages (CAMF), which produce pro- inflammatory cytokines (e...
  13. TLR4 Inhibition to Reduce Cerebral Ischemia Reperfusion Injury
    LORI ANN HOLLE; Fiscal Year: 2011
    ..complex system evolved over 700 million years to protect uni- and multi- cellular organisms from infection with bacteria, fungi, viruses and other pathogens...
  14. Fatty acid related regulation of enteric infectious disease
    FREDRICK JON KULL; Fiscal Year: 2012
    ..In many cases, enteric disease is caused by the ingestion of pathogenic bacteria via contaminated food or water...
  15. A unique approach to identify markers for congenital syphilis and neurosyphilis
    Nikhat Parveen; Fiscal Year: 2010
    ..T. pallidum sequence revealed itself to be one of the smallest genomes (1.1Mb) among bacteria with a few potential surface proteins that can determine the spirochete's ability to colonize various ..
  16. Novel DNA-Launched Attenuated Vaccine for VEE Virus
    PETER M PUSHKO; Fiscal Year: 2012
    ..Recombinant i-DNA clones produced in bacteria contains CpG motifs that activate TLR9 and MyD88-dependent signaling pathways resulting in robust production of ..
  17. A novel peroxidase in vascular endothelium and the development of atherosclerosis
    Guangjie Cheng; Fiscal Year: 2012
    ..hydrogen peroxide reduction and play important roles in physiology, immunology and pathology such as killing of bacteria, modulation of cell signal transduction pathway and tissue damage...
  18. Global regulatory interactions in bacterial pathogenesis
    BRIAN AKERLEY; Fiscal Year: 2009
    b>Bacteria sense their environments within diverse locations in the host and respond by appropriately altering their cell surface structures to avoid immunity and promote colonization...
  19. Analysis of gene regulation of Vibrio cholerae during infection
    Jun Zhu; Fiscal Year: 2013
    ..It has become clear in recent years that bacteria actively sense their surroundings...
  20. Molecular Basis of E. coli Adhesins in Bladder Disorders
    Scott J Hultgren; Fiscal Year: 2013
    ..bacterial replication results in the formation of intracellular bacterial communities (IBC) comprised of 104-105 bacteria. IBCs are transient and upon IBC maturation bacteria disperse from the biomass, filament, and spread to ..
  21. Regulation of the Vibrio cholerae intestinal exit plan
    ANISIA J SILVA BENITEZ; Fiscal Year: 2010
    ..Therefore, detachment of hyper infective bacteria from the intestinal mucosa late in infection is a critical step of the cholera transmission chain...
  22. Arsenic Trioxide and Acute Myeloid Leukemia
    Yongkui Jing; Fiscal Year: 2012
    ..AML cells share lineage derivation with polymorphonuclear cells, which use NADPH oxidase generated ROS to kill bacteria. We showed that As2O3 treatment of AML cells increases the expression, without causing activation, of a crucial ..
  23. Biochemistry and Function of a Novel Bacterial Photosensory Two-Component System
    MELISSA MARKS; Fiscal Year: 2010
    ..The cellular signaling networks that control physiological and developmental transitions in bacteria largely use two-component signal transduction systems, consisting of histidine protein kinases and their cognate ..
  24. Anti-Inflammatory Glycosaminoglycan Ethers for Treatment of Periodontitis
    JUSTIN RODNEY SAVAGE; Fiscal Year: 2013
    ..Gingivitis and periodontitis are initiated by chronic infection of the gingival crevice with bacteria such as Porphryomonas gingivalis...
  25. Endotoxin, the airway transcriptome, and obstructive lung disease
    PEGGY SUE LAI; Fiscal Year: 2013
    ..Endotoxin is derived from gram negative bacteria, and has been associated with both asthma and COPD...
  26. Signaling by Cytoplasmic Tyrosine Kinases in Leukocytes
    Clifford A Lowell; Fiscal Year: 2013
    ..PUBLIC HEALTH RELEVANCE: Immune cells sense pathogens such as bacteria, fungi and viruses through a complex array of cellular receptors...
  27. Effect of diet & commensal bacteria on diabetes outcome in NOD mouse
    Li Wen; Fiscal Year: 2010
    ..Increasing evidence suggests that commensal bacteria act as one of the important environmental factors in allergy, inflammatory bowel disease and diabetes (type 1 and ..
  28. Characterization of new toxins (YmgD and YdfD) from E.coli, targeting cell wall
    Hisako Masuda; Fiscal Year: 2012
    DESCRIPTION (provided by applicant): Bacteria are generally considered to be a single cellular, free living organism, yet they carry toxin or suicidal genes on their genome...
  29. Mechanism Underlying Nitrite Sensitivity of Mucoid Pseudomonas in COPD
    Daniel J Hassett; Fiscal Year: 2013
    ..suffer from chronic obstructive pulmonary disease (COPD) that often suffer from airway infection by opportunistic bacteria, the most prevalent of which is Pseudomonas aeruginosa (PA)...
  30. Non-coding RNA engineers antibody diversity
    Uttiya Basu; Fiscal Year: 2011
    ..fluids of vertebrates, and are used by the immune system to identify and neutralize foreign antigens, such as bacteria and viruses...
  31. New therapeutics for the treatment of Acinetobactor baumannii infections.
    ALLEN BERNARD REITZ; Fiscal Year: 2013
    ..biofilms have been implicated in cystic fibrosis, periodontitis and urinary tract infections, due to the bacteria's ability to colonize indwelling medical devices. The rise in antibiotic resistant A...
  32. The Electricidal Effect, a Novel Anti-Biofilm Strategy
    Robin Patel; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Biofilm bacteria are estimated to cause two thirds of infections in modern clinical practice...
  33. Photodynamic Therapy of Localized Infections
    Michael R Hamblin; Fiscal Year: 2013
    ..by exploring the combination of PDT with traditional systemic antibiotics to prevent regrowth of bacteria after PDT...
  34. Role of the neurogenic inflammatory pathway in the genital tract immune response
    Roger G Rank; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): There are multiple mechanisms by which bacteria elicit an inflammatory response at mucosal sites;however, a pathway mediated by neuropeptides has received little attention but may be equally as ..
  35. In Vivo Function of TRAF6 As a Target of K63-Linked Polyubiquitination
    DEAN BALLARD; Fiscal Year: 2010
    ..many of the TLR-dependent immune responses to pathogen-associated molecular patterns (PAMPs) expressed by bacteria and viruses...
  36. MEMBRANES OF THE DENTAL PATHOGEN STREPTOCOCCUS MUTANS
    L Jeannine Brady; Fiscal Year: 2013
    ..the SRP pathway results in vulnerability to numerous stressors including acid, salt, and oxidative shock, but the bacteria generate a functional membrane and survive...
  37. Anti-Bacterial Innate Responses Enhance Paramyxovirus Replication
    Griffith D Parks; Fiscal Year: 2010
    ..There is increasing evidence that polymicrobial infections involving bacteria and paramyxoviruses are a significant factor in human patients with chronic bronchitis, sinusitis and otitis ..
  38. Mucosal Memory T Cells at the Vanguard of Human Host Defense
    Donna L Farber; Fiscal Year: 2010
    ..influenza, tuberculosis, respiratory syncytial virus (RSV), rotavirus, and numerous intestinal parasites and bacteria pose substantial threats to world health, and have eluded the generation of protective vaccines...
  39. Colitis Induced by immune responses to luminal bacteria-mouse
    Ryan B Sartor; Fiscal Year: 2012
    ..suggesting that defective innate responses can activate pathogenic adaptive immune responses to persistent bacteria. Commensal enteric bacteria antigen-specific effector T cells that cause chronic colitis in interleukin 10 ..
  40. FUNCTIONAL PROPERTIES OF HEMOGLOBINS AND MYOGLOBINS
    John S Olson; Fiscal Year: 2010
    ..binding, and NO dioxygenation;(b) insight into the evolution of globin structures and functions, from Archaea to Bacteria to Eucarya;and (c) a framework for inhibiting the activities of globins from pathogenic organisms (Candida ..
  41. Durable Visible Light-activated Antivral Coatings for Fabrics Used for Personal P
    JOSEF STEPHAN SCHNEIDER; Fiscal Year: 2011
    ..In the Phase I portion of this grant, we established efficacy against influenza virus and Staphylococcal bacteria in light intensities equivalent to typical hospital room lighting and >99...
  42. Optimization of Neoglycoside Antibiotics for Nosocomial Pathogens and Select Agen
    Arnold Louie; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Multi-drug resistance in Gram-negative bacteria is a common problem in infected patients in the ICU environment. With Pseudomonas aeruginosa and Acinetobacter spp...
  43. Therapeutics for Drug-Resistant Bacteria: Myxopyronins
    Richard H Ebright; Fiscal Year: 2013
    ....
  44. Enhanced Membrane Systems for Supplying Quality Drinking Water
    Andrew Feiring; Fiscal Year: 2013
    ..A variety of bacteria such as Salmonella, Campylobacter and toxigenic E...
  45. GI Endotoxin as an Environmental Trigger in an alpha-Synuclein Transgenic Mouse
    Robert L Nussbaum; Fiscal Year: 2012
    ..transgenic models will (1) cause changes in distribution and composition of gut flora and exposure to intestinal bacteria, (2) enhance the absorption of endotoxin leading to systemic inflammatory effects and neurological defects, and (..
  46. Epidemiology and Etiology of Hospitalized Pneumonia in Children
    Krow Ampofo; Fiscal Year: 2010
    ..It will lead to improved understanding of the spectrum of viruses and bacteria responsible for pneumonia will aid in appropriate choices of antimicrobial therapy...
  47. Mechanisms of innate immune response modulation by mechanical ventilation
    William A Altemeier; Fiscal Year: 2012
    ..mRNA levels of genes transcribed in response to lipopolysaccharide (LPS), a cell wall component of gram-negative bacteria, and D) inhibition of c-Jun amino-terminal kinase (JNK - a kinase activator of AP-1) is protective against other ..
  48. Ibis T-6,000 Biosensor System
    CYNTHIA SEARS; Fiscal Year: 2010
    ..with an extensive genomic database to permit high throughput, rapid and sensitive identification of microbes (bacteria, viruses, fungi) in original, complex human or animal specimens including respiratory secretions and feces...
  49. The role of novel, uncultivable bacteria in incident PID
    CATHERINE L contact HAGGERTY; Fiscal Year: 2011
    ..Less in known about the role of other mycoplasmal bacteria, including the newly differentiated Ureaplamsa urealyticum biovar 2 and Ureaplamsa parvum in PID...
  50. The Mucolipin TRP Ion Channels
    Haoxing Xu; Fiscal Year: 2013
    ..Using bacteria killing assays, we will determine whether TRPML1-deficient macrophages exhibit reduced bactericidal activity...
  51. 5500 QTRAP
    John W Turk; Fiscal Year: 2010
    ..Molecular bases of antimicrobial resistance and virulence in pathogenic Salmonella gram-negative bacteria (Dr. Eduardo Groisman, WU, and Dr. Yixin Shi, Univ...
  52. Inhibitors of isoprenoid synthesis for antibacterial therapy
    Donald T Moir; Fiscal Year: 2013
    ..Isoprenoids are essential for electron transport and cell wall biosynthesis in bacteria. Many bacterial species, including the Gr(-) nonfermenters, utilize an alternate isoprenoid synthesis pathway, ..
  53. Role of formyl peptide receptor variants in mucosal innate immune defense
    HEINI MARITA MIETTINEN; Fiscal Year: 2010
    ..system, and FPR function in response to bacterial peptides from different commensal and pathogenic mucosal bacteria will be examined by measuring cell signaling and chemotaxis...
  54. Fic-mediated Adenylylation
    CAROLYN ANN WORBY; Fiscal Year: 2013
    ..PfhB2 shares extensive amino acid sequence identity with IbpA. This suggests that there is a small family of bacteria that harbors these 4000 amino acid toxins...
  55. Biofilm Infections in Postsurgical, Trauma, and Critically Ill Patients
    Carol L Wells; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): A biofilm is a population of bacteria growing on a surface and surrounded by a complex extracellular polymeric substance composed of proteins, glycoproteins, glycolipids, polysaccharides, and DNA...
  56. Analogs of GTP as novel inhibitors of bacterial c-di-GMP-synthesizing enzymes
    George E Wright; Fiscal Year: 2010
    ..applicant): The bacterial second messenger c-di-GMP (cyclo-(GMP)2) is responsible for inducing certain pathogenic bacteria to form biofilms, complex structures of one or more bacterial strains that resist conventional antibiotics and ..
  57. Iowa Phase II Clinical Trials of Novel Therapies for Lung Diseases (U01
    Lakshmi Durairaj; Fiscal Year: 2012
    ..Xylitol, a 5-carbon sugar, can lower ASL salt concentration without providing a carbon-source for bacteria. Xylitol has been shown to prevent progression of dental caries, and decrease the incidence of acute otitis media...
  58. Pulmonary effects of biomass fuel indoor PM from rural India
    Shyam Biswal; Fiscal Year: 2013
    ..We will also determine whether exposure of macrophages to indoor PM suppresses phagocytosis of bacteria. Although an inhalation exposure model is more realistic, airway instillation has been demonstrated to be a very ..
  59. Anti-inflammatory effects of colitis-induced changes in commensal gut microbes
    JONATHAN JAMES HANSEN; Fiscal Year: 2013
    ..potentially debilitating intestina disorders thought to be due to overly-aggressive immune responses to normal bacteria that typically colonize the intestines...
  60. MIF AND THE HOST RESPONSE TO INFECTION
    RICHARD J BUCALA; Fiscal Year: 2013
    ..it may allow for the identification of patients at risk for lethal outcome from different pathogens, whether bacteria, viruses, or emerging infectious agents...
  61. Studies on the virulence of Fillifactor alocis
    Hansel M Fletcher; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Bacteria in the periodontal pocket can develop complex sessile communities that play a significant role in infection-induced periodontal disease...
  62. International Symposium on Proline Metabolism and Human Health
    Donald F Becker; Fiscal Year: 2010
    ..Proline has multifaceted biological and biochemical roles in a variety of organisms from bacteria to mammals...
  63. Effect of Neonatal Hyperoxia on Alveolar Development and Infection
    MICHAEL A O'REILLY; Fiscal Year: 2012
    ..subpopulation of alveolar epithelial Type II cells that selectively expresses genes that destroy RNA viruses and bacteria, and control asymmetric cell division of stem/progenitor cells...
  64. Triazole hypersensitivity in Candida albicans
    Neeraj Chauhan; Fiscal Year: 2009
    ..Two-component signal transduction proteins have been reported in bacteria and lower eukaryotes. To date they have not yet been identified in animals and are absent in the human genome...
  65. Bacteriolytic phage enzymes as novel antibacterials against Yersinia pestis
    Ian Molineux; Fiscal Year: 2009
    ..species have become resistant to current antibiotics and there is the potential use of Select Agents and other bacteria in bioterrorist attacks...
  66. Investigations of the role of house flies as vectors for bacterial pathogens
    Dana Nayduch; Fiscal Year: 2009
    ..aims to determine if house flies are important transmitters of bacterial disease agents, by examining the fate of bacteria within flies and concurrent expression of antibacterial humoral defenses. Adult house flies (Musca domestica L...
  67. REGULATION OF PYRIMIDINE GENE EXPRESSION IN BACTERIA
    CHARLES TURNBOUGH; Fiscal Year: 2001
    DESCRIPTION: The objective of this application is to elucidate new mechanisms of gene regulation in bacteria and to characterize the molecular interactions involved in the regulatory process...
  68. The effect of inter-species interactions on the virulence of Streptococcus mutans
    Bing yan Wang; Fiscal Year: 2009
    ..The long-term goal of the proposed studies is to characterize specific interactions of S. mutans with oral bacteria in the dental plaque biofilm. We hypothesize that it is not merely colonization by S...
  69. Use of Probiotic Conditioned Media to Protect Against Necrotizing Enterocolitis
    ERIKA CLAUD; Fiscal Year: 2009
    ..to test the hypothesis that conditioned media (CM) obtained by filtering the broth used to grow the probiotic bacteria Lactobacillus plantarum can decrease the incidence and severity of NEC by improving intestinal host defense ..
  70. ANTIBIOTIC SUSCEPTIBILITIES OF PERIODONTAL BACTERIA
    Clay Walker; Fiscal Year: 1993
    ..The predominant cultivable bacteria present before and after therapy have been characterized and identified...
  71. Peptide Derivatives to treat Urinary Tract Infections
    Laszlo Otvos; Fiscal Year: 2003
    The war between man and bacteria entered a new phase. With the rapid spread of antimicrobial resistant bacterial strains the currently used drug families start to fail and desperate calls for a new armory of agents are regularly voiced...
  72. Enhancement of antimicrobics by electrical current
    Robin Patel; Fiscal Year: 2007
    unreadable] DESCRIPTION (provided by applicant): Bacteria growing in biofilms cause a wide range of human infections...
  73. Click chemistry for novel antimicrobials against periodontal pathogens
    Valery V Fokin; Fiscal Year: 2010
    ..Gingivitis and periodontitis are primarily infectious diseases caused by misplaced bacteria in the periodontal region...
  74. Anaerobic Bacteria as Oncopathic Agents for Pancreatic Cancer
    Savio Woo; Fiscal Year: 2009
    ..However, intratumoral bacteria replication was inhibited by a rapid accumulation of host inflammatory cells that are bactericidal, which limited ..
  75. Development of targeted photodynamic therapy for treatment of dental caries
    Randal Eckert; Fiscal Year: 2010
    ..of over 600 different non-harmful/commensal microbial species together with a limited number of pathogenic bacteria, including the major etiological agent of dental caries, Streptococcus mutans, which ferments dietary sugars to ..
  76. COMPETITION FOR HEME AMONG PERIODONTAL BACTERIA
    GEOFFREY TOMPKINS; Fiscal Year: 1993
    Heme- and iron-scavenging systems are important virulence factors among a diversity of pathogenic bacteria. The current proposal, however, will examine bacterial heme acquisition from an ecological point of view, according to the ..
  77. Molecular Insight into Toxicant Degradation by Microbial Communities
    Gerben Zylstra; Fiscal Year: 2009
    ..it is well known that the biodiversity of microorganisms remains relatively untapped with more than 99% of all bacteria in the environment uncharacterized...
  78. Developing acid-activated antimicrobial peptides to control dental caries
    Maxwell Anderson; Fiscal Year: 2009
    ..different non-harmful/commensal microbial species together with a limited number of acid- producing (cariogenic) bacteria such as Streptococcus mutans and Lactobacillus species...
  79. 3rd ASM Conference on Cell-Cell Communication in Bacteria
    WILLIAM FUQUA; Fiscal Year: 2007
    unreadable] DESCRIPTION: ASM Conference on Cell-Cell Communication in Bacteria, Clay Fuqua and Heidi B. Kaplan, Co-Organizers...
  80. Methylerythritol Phosphate Pathway Inhibitors Targeting Gram-Negative Infections
    CHARLES TESTA; Fiscal Year: 2009
    ..a new class of antibiotics targeting an underexploited pathway essential for the viability of all Gram-negative bacteria, the methylerythritol phosphate (MEP) pathway...
  81. Detection of Antibiotic Resistance Genes in Bacterial Agents of Hospital-Acquired
    Andrew Levin; Fiscal Year: 2009
    ..These acute conditions are caused by infection with a range of Gram-positive and Gram-negative bacteria commonly found in the hospital environment...
  82. B27 BINDING BACTERIAL AND SELF PEPTIDES IN B27 ARTHRITIS
    R Scofield; Fiscal Year: 2000
    ..They are strongly associated with the presence of the HLA Class 1 allele B27 and infection with enteric bacteria such as Salmonella, Shigella, Campylobacter, Yersinia, and Klebsiella...
  83. AMPLIFIED IMMUNOASSAY OF BACTERIA AND RECOVERY
    SAGYPASH SADIEV; Fiscal Year: 1999
    A new technique for amplified immunoassay will be developed for sensitive measurement of bacteria under conditions which do not destroy them, coupled with the isolation of these bacteria from the immunoassay matrices...
  84. 2nd ASM Conference on Cell-Cell Communication
    Bonnie Bassler; Fiscal Year: 2004
    Only a few years ago, the exchange of chemical signals, or pheromones, between bacteria was considered the exception rather than the rule...