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: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (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. D Haeseleer P, Gladden J, Allgaier M, Chain P, Tringe S, Malfatti S, et al. Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. PLoS ONE. 2013;8:e68465 pubmed publisher
    Thermophilic bacteria are a potential source of enzymes for the deconstruction of lignocellulosic biomass...
  2. Yeates T, Jorda J, Bobik T. The shells of BMC-type microcompartment organelles in bacteria. J Mol Microbiol Biotechnol. 2013;23:290-9 pubmed publisher
    ..This review updates our understanding of bacterial microcompartment shells, how they are assembled, and how they carry out their functions in molecular transport and enzyme organization. ..
  3. Kamada N, Núñez G. Regulation of the immune system by the resident intestinal bacteria. Gastroenterology. 2014;146:1477-88 pubmed publisher
    ..the interaction between the immune system and the microbiota, focusing on the role of resident intestinal bacteria in the development of immune responses...
  4. Kim S, Park S, Cha I, Min D, Kim J, Chung W, et al. Metabolic versatility of toluene-degrading, iron-reducing bacteria in tidal flat sediment, characterized by stable isotope probing-based metagenomic analysis. Environ Microbiol. 2014;16:189-204 pubmed publisher
    DNA stable isotope probing and metagenomic sequencing were used to assess the metabolic potential of iron-reducing bacteria involved in anaerobic aromatic hydrocarbon degradation in oil spill-affected tidal flats...
  5. Kantor R, Wrighton K, Handley K, Sharon I, Hug L, Castelle C, et al. Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. MBio. 2013;4:e00708-13 pubmed publisher
    ..These metagenomic analyses expand our view of a lifestyle apparently common across these candidate phyla. ..
  6. Vekeman B, Hoefman S, De Vos P, Spieck E, Heylen K. A generally applicable cryopreservation method for nitrite-oxidizing bacteria. Syst Appl Microbiol. 2013;36:579-84 pubmed publisher
    Nitrite-oxidizing bacteria are key members of the global nitrogen cycle but their study is hampered by their limited availability in culture, mostly due to laborious cultivation procedures and the lack of stable preservation methods...
  7. Delcour A. Electrophysiology of bacteria. Annu Rev Microbiol. 2013;67:179-97 pubmed publisher
    b>Bacteria secrete and harbor in their membranes a number of pore-forming proteins. Some of these are bona fide ion channels that may respond to changes in membrane tension, voltage, or pH...
  8. Campos J, Mourão J, Pestana N, Peixe L, Novais C, Antunes P. Microbiological quality of ready-to-eat salads: an underestimated vehicle of bacteria and clinically relevant antibiotic resistance genes. Int J Food Microbiol. 2013;166:464-70 pubmed publisher
    ..we analyzed the microbiological quality of Portuguese ready-to-eat salads (RTS) and their role in the spread of bacteria carrying acquired antibiotic resistance genes, food products scarcely considered in surveillance studies...
  9. Oshiki M, Awata T, Kindaichi T, Satoh H, Okabe S. Cultivation of planktonic anaerobic ammonium oxidation (anammox) bacteria using membrane bioreactor. Microbes Environ. 2013;28:436-43 pubmed
    Enrichment cultures of anaerobic ammonium oxidation (anammox) bacteria as planktonic cell suspensions are essential for studying their ecophysiology and biochemistry, while their cultivation is still laborious...

More Information

Publications97

  1. Lefèvre C, Bazylinski D. Ecology, diversity, and evolution of magnetotactic bacteria. Microbiol Mol Biol Rev. 2013;77:497-526 pubmed publisher
    Magnetotactic bacteria (MTB) are widespread, motile, diverse prokaryotes that biomineralize a unique organelle called the magnetosome...
  2. Venturi V, Fuqua C. Chemical signaling between plants and plant-pathogenic bacteria. Annu Rev Phytopathol. 2013;51:17-37 pubmed publisher
    Studies of chemical signaling between plants and bacteria in the past have been largely confined to two models: the rhizobial-legume symbiotic association and pathogenesis between agrobacteria and their host plants...
  3. Panda S, Zhang J, Tan N, Ho B, Ding J. Natural IgG antibodies provide innate protection against ficolin-opsonized bacteria. EMBO J. 2013;32:2905-19 pubmed publisher
    ..Here, we show for the first time that natural IgG recognizes a spectrum of bacteria through lectins like ficolin and mannose binding lectin (MBL)...
  4. Hu Y, Łukasik P, Moreau C, Russell J. Correlates of gut community composition across an ant species (Cephalotes varians) elucidate causes and consequences of symbiotic variability. Mol Ecol. 2014;23:1284-300 pubmed publisher
    ..is a likely cause, but only pollen-based diets had consistent effects, altering the abundance of two types of bacteria. Additional factors, such as host age, genetics, chance or natural selection, must therefore shape natural ..
  5. Fuerst J. The PVC superphylum: exceptions to the bacterial definition?. Antonie Van Leeuwenhoek. 2013;104:451-66 pubmed publisher
    The PVC superphylum is a grouping of distinct phyla of the domain bacteria proposed initially on the basis of 16S rRNA gene sequence analysis...
  6. Tang K, Zhang Y, Yu M, Shi X, Coenye T, Bossier P, et al. Evaluation of a new high-throughput method for identifying quorum quenching bacteria. Sci Rep. 2013;3:2935 pubmed publisher
    Quorum sensing (QS) is a population-dependent mechanism for bacteria to synchronize social behaviors such as secretion of virulence factors...
  7. Caldelari I, Chao Y, Romby P, Vogel J. RNA-mediated regulation in pathogenic bacteria. Cold Spring Harb Perspect Med. 2013;3:a010298 pubmed publisher
    Pathogenic bacteria possess intricate regulatory networks that temporally control the production of virulence factors, and enable the bacteria to survive and proliferate after host infection...
  8. Ashida H, Kim M, Sasakawa C. Exploitation of the host ubiquitin system by human bacterial pathogens. Nat Rev Microbiol. 2014;12:399-413 pubmed publisher
    ..These strategies enable bacterial pathogens to maximize effector function and obtain nutrients, thereby promoting bacterial proliferation. ..
  9. Moradigaravand D, Engelstädter J. The evolution of natural competence: disentangling costs and benefits of sex in bacteria. Am Nat. 2013;182:E112-26 pubmed publisher
    ..In finite populations, the recombining type is often favored through the Fisher-Muller effect. ..
  10. Neville B, Sheridan P, Harris H, Coughlan S, Flint H, Duncan S, et al. Pro-inflammatory flagellin proteins of prevalent motile commensal bacteria are variably abundant in the intestinal microbiome of elderly humans. PLoS ONE. 2013;8:e68919 pubmed publisher
    Some Eubacterium and Roseburia species are among the most prevalent motile bacteria present in the intestinal microbiota of healthy adults...
  11. Lui L, Xue X, Sui C, Brown A, Pritchard D, Halliday N, et al. Bacteria clustering by polymers induces the expression of quorum-sensing-controlled phenotypes. Nat Chem. 2013;5:1058-65 pubmed publisher
    b>Bacteria deploy a range of chemistries to regulate their behaviour and respond to their environment. Quorum sensing is one method by which bacteria use chemical reactions to modulate pre-infection behaviour such as surface attachment...
  12. Caza M, Kronstad J. Shared and distinct mechanisms of iron acquisition by bacterial and fungal pathogens of humans. Front Cell Infect Microbiol. 2013;3:80 pubmed publisher
    ..Hence, pathogenic bacteria and fungi have developed sophisticated strategies to gain access to iron from host sources...
  13. Altun O, Almuhayawi M, Ullberg M, Ozenci V. Clinical evaluation of the FilmArray blood culture identification panel in identification of bacteria and yeasts from positive blood culture bottles. J Clin Microbiol. 2013;51:4130-6 pubmed publisher
    ..evaluated the clinical performance of the FilmArray blood culture identification (BCID) panel, which includes 19 bacteria, five yeasts, and three antibiotic resistance genes...
  14. Ghyselinck J, Pfeiffer S, Heylen K, Sessitsch A, De Vos P. The effect of primer choice and short read sequences on the outcome of 16S rRNA gene based diversity studies. PLoS ONE. 2013;8:e71360 pubmed publisher
    ..The methodology followed can be extrapolated to other primers, allowing their evaluation prior to the experiment. ..
  15. Hamilton E, Kruger J, Schall W, Beal M, Manning S, Kaneene J. Acquisition and persistence of antimicrobial-resistant bacteria isolated from dogs and cats admitted to a veterinary teaching hospital. J Am Vet Med Assoc. 2013;243:990-1000 pubmed publisher
    To assess antimicrobial resistance among bacteria isolated from dogs and cats admitted to a veterinary teaching hospital (VTH), determine the incidence of acquisition of and frequency of persistent colonization by antimicrobial-resistant ..
  16. Hofbauer S, Gruber C, Pirker K, Sündermann A, Schaffner I, Jakopitsch C, et al. Transiently produced hypochlorite is responsible for the irreversible inhibition of chlorite dismutase. Biochemistry. 2014;53:3145-57 pubmed publisher
    ..We discuss the role of distal Arg173 by keeping hypochlorite in the reaction sphere for O-O bond formation. ..
  17. Singh R, Reddy C. Seaweed-microbial interactions: key functions of seaweed-associated bacteria. FEMS Microbiol Ecol. 2014;88:213-30 pubmed publisher
    Seaweed-associated bacteria play a crucial role in morphogenesis and growth of seaweeds (macroalgae) in direct and/or indirect ways...
  18. Fierer N, Ladau J, Clemente J, Leff J, Owens S, Pollard K, et al. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science. 2013;342:621-4 pubmed publisher
  19. Tajima K, Ohmori H, Tohno M, Ohtsu H, Tsukahara T, Aminov R. Segmented filamentous bacteria are a major group in terminal ileum of piglets. Anaerobe. 2013;23:109-11 pubmed publisher
    ..The majority of 1951 sequences retrieved (24.8%) displayed the closest similarity to segmented filamentous bacteria (SFB)...
  20. Eveleigh R, Meehan C, Archibald J, Beiko R. Being Aquifex aeolicus: Untangling a hyperthermophile's checkered past. Genome Biol Evol. 2013;5:2478-97 pubmed publisher
    ..this pattern is shown by only a minority of encoded proteins, and the Archaea, many lineages of thermophilic bacteria, and members of genus Clostridium and class Deltaproteobacteria also show strong connections to the Aquificae...
  21. Langille M, Zaneveld J, Caporaso J, McDonald D, Knights D, Reyes J, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013;31:814-21 pubmed publisher
  22. Brophy M, Nakashige T, Gaillard A, Nolan E. Contributions of the S100A9 C-terminal tail to high-affinity Mn(II) chelation by the host-defense protein human calprotectin. J Am Chem Soc. 2013;135:17804-17 pubmed publisher
    ..Within the S100 family, the S100A8/S100A9 heterooligomer is essential for providing high-affinity Mn(II) binding; the S100A7, S100A9(C3S), S100A12, and S100B homodimers do not exhibit such Mn(II)-binding capacity. ..
  23. Belkaid Y, Hand T. Role of the microbiota in immunity and inflammation. Cell. 2014;157:121-41 pubmed publisher
    ..This phenomenon is proposed to account for some of the dramatic rise in autoimmune and inflammatory disorders in parts of the world where our symbiotic relationship with the microbiota has been the most affected. ..
  24. Cole J, Wang Q, Fish J, Chai B, McGarrell D, Sun Y, et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014;42:D633-42 pubmed publisher
    ..In addition, most tools are now available as open source packages for download and local use by researchers with high-volume needs or who would like to develop custom analysis pipelines. ..
  25. Zhou X, Fang Z, Ruan Z, Wang M, Liu R, Tan M, et al. Aminoacylation and translational quality control strategy employed by leucyl-tRNA synthetase from a human pathogen with genetic code ambiguity. Nucleic Acids Res. 2013;41:9825-38 pubmed publisher
  26. Pande S, Merker H, Bohl K, Reichelt M, Schuster S, de Figueiredo L, et al. Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria. ISME J. 2014;8:953-62 pubmed publisher
    ..Together, our synthetic study approach reveals ecological principles that can help explain the widespread occurrence of obligate metabolic cross-feeding interactions in nature...
  27. Segata N, Börnigen D, Morgan X, Huttenhower C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun. 2013;4:2304 pubmed publisher
    ..PhyloPhlAn will thus be useful for both phylogenetic assessment and taxonomic quality control of newly sequenced genomes. The final phylogenies, conserved protein sequences and open-source implementation are available online. ..
  28. Garcia Migura L, Hendriksen R, Fraile L, Aarestrup F. Antimicrobial resistance of zoonotic and commensal bacteria in Europe: the missing link between consumption and resistance in veterinary medicine. Vet Microbiol. 2014;170:1-9 pubmed publisher
    ..Consequently, monitoring programs have been designed to monitor the occurrence of antimicrobial resistant bacteria. This study analyses the amount of antimicrobial agents used in nine European countries from 2005 to 2011, and ..
  29. Harshvardhan K, Jha B. Biodegradation of low-density polyethylene by marine bacteria from pelagic waters, Arabian Sea, India. Mar Pollut Bull. 2013;77:100-6 pubmed publisher
    Sixty marine bacteria isolated from pelagic waters were screened for their ability to degrade low-density polyethylene; among them, three were positive and able to grow in a medium containing polythene as the sole carbon source...
  30. Wang J, Morton M, Elliott C, Karoonuthaisiri N, Segatori L, Biswal S. Rapid detection of pathogenic bacteria and screening of phage-derived peptides using microcantilevers. Anal Chem. 2014;86:1671-8 pubmed publisher
  31. Avershina E, Storrø O, Øien T, Johnsen R, Pope P, Rudi K. Major faecal microbiota shifts in composition and diversity with age in a geographically restricted cohort of mothers and their children. FEMS Microbiol Ecol. 2014;87:280-90 pubmed publisher
    ..Taken together, the major age-affiliated population shift within gut microbiota suggests that there are important mechanisms for transmission and persistence of gut bacteria that remain unknown.
  32. Troxell B, Hassan H. Transcriptional regulation by Ferric Uptake Regulator (Fur) in pathogenic bacteria. Front Cell Infect Microbiol. 2013;3:59 pubmed publisher
    ..Oxygenation of the ancient world challenged bacteria to acquire the insoluble ferric iron (Fe(3+)) and later to defend against reactive oxygen species (ROS) generated ..
  33. Alenghat T, Osborne L, Saenz S, Kobuley D, Ziegler C, Mullican S, et al. Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis. Nature. 2013;504:153-7 pubmed publisher
    ..conditions can be influenced by host genetic and environmental factors, including signals derived from commensal bacteria. However, the mechanisms that integrate these diverse cues remain undefined...
  34. Jacob M, Soltwedel T, Boetius A, Ramette A. Biogeography of Deep-sea benthic bacteria at regional scale (LTER HAUSGARTEN, Fram Strait, Arctic). PLoS ONE. 2013;8:e72779 pubmed publisher
  35. Navas Molina J, Peralta Sánchez J, Gonzalez A, McMurdie P, Vázquez Baeza Y, Xu Z, et al. Advancing our understanding of the human microbiome using QIIME. Methods Enzymol. 2013;531:371-444 pubmed publisher
    ..We present examples of some of the types of analyses that are enabled by QIIME and discuss how other tools, such as phyloseq and R, can be applied to expand upon these analyses. ..
  36. Parte A. LPSN--list of prokaryotic names with standing in nomenclature. Nucleic Acids Res. 2014;42:D613-6 pubmed publisher
    ..bacterio.net) is a database that lists the names of prokaryotes (Bacteria and Archaea) that have been validly published in the International Journal of Systematic and Evolutionary ..
  37. Yilmaz P, Parfrey L, Yarza P, Gerken J, Pruesse E, Quast C, et al. The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic Acids Res. 2014;42:D643-8 pubmed publisher
    ..resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services...
  38. Cassini M, Pilloni A, Condo S, Vitali L, Pasquantonio G, Cerroni L. Periodontal bacteria in the genital tract: are they related to adverse pregnancy outcome?. Int J Immunopathol Pharmacol. 2013;26:931-9 pubmed
    One of the most important factors implicated in preterm birth (PTB) is acute genitourinary tract infection. The bacteria causing chronic periodontal inflammation include Gram-negative rods and anaerobes similar to those found in women ..
  39. Iida N, Dzutsev A, Stewart C, Smith L, Bouladoux N, Weingarten R, et al. Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment. Science. 2013;342:967-70 pubmed publisher
    ..contributes to development, progression, and treatment of cancer, but it remains unclear whether commensal bacteria affect inflammation in the sterile tumor microenvironment...
  40. Cornejo E, Abreu N, Komeili A. Compartmentalization and organelle formation in bacteria. Curr Opin Cell Biol. 2014;26:132-8 pubmed publisher
    ..Spore formation in Bacillus subtilis, outer membrane biogenesis in Gram-negative bacteria and protein diffusion barriers of Caulobacter crescentus will be used to demonstrate the physical, chemical, and ..
  41. Fleming E, Cetinić I, Chan C, Whitney King D, Emerson D. Ecological succession among iron-oxidizing bacteria. ISME J. 2014;8:804-15 pubmed publisher
    ..ochracea is abundant in waters that contain high concentrations of complex organic carbon, high Fe and Mn content and gentle redoxclines. Finally, these findings identify a largely unexplored relationship between FeOB and organic carbon...
  42. Chung S, Rosa C, Scully E, Peiffer M, Tooker J, Hoover K, et al. Herbivore exploits orally secreted bacteria to suppress plant defenses. Proc Natl Acad Sci U S A. 2013;110:15728-33 pubmed publisher
    ..Here, we demonstrate that Colorado potato beetle (Leptinotarsa decemlineata) larvae exploit bacteria in their oral secretions to suppress antiherbivore defenses in tomato (Solanum lycopersicum)...
  43. Huang J, Brumell J. Bacteria-autophagy interplay: a battle for survival. Nat Rev Microbiol. 2014;12:101-14 pubmed publisher
    ..organelles to lysosomes for degradation, but it has also been shown to combat infection with various pathogenic bacteria. In turn, bacteria have developed diverse strategies to avoid autophagy by interfering with autophagy signalling ..
  44. Glick B. Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiol Res. 2014;169:30-9 pubmed publisher
    ..One way to do this is through the increased use of plant growth-promoting bacteria; recently, scientists have developed a more profound understanding of the mechanisms employed by these bacteria ..
  45. Louwen R, Staals R, Endtz H, van Baarlen P, van der Oost J. The role of CRISPR-Cas systems in virulence of pathogenic bacteria. Microbiol Mol Biol Rev. 2014;78:74-88 pubmed publisher
    ..In this review, we describe recently reported cases of potential involvement of CRISPR-Cas systems in bacterial stress responses in general and bacterial virulence in particular...
  46. Roder C, Arif C, Bayer T, Aranda M, Daniels C, Shibl A, et al. Bacterial profiling of White Plague Disease in a comparative coral species framework. ISME J. 2014;8:31-9 pubmed publisher
    ..This suggests that while corals harbor distinct species-specific microbial assemblages, disease-specific bacterial abundance patterns exist that are maintained over coral species boundaries. ..
  47. Lemfack M, Nickel J, Dunkel M, Preissner R, Piechulla B. mVOC: a database of microbial volatiles. Nucleic Acids Res. 2014;42:D744-8 pubmed publisher
    ..Information on volatile emission from bacteria and fungi is presently scattered in the literature, and no public and up-to-date collection on mVOCs is available...
  48. Ghaz Jahanian M, Khodaparastan F, Berenjian A, Jafarizadeh Malmiri H. Influence of small RNAs on biofilm formation process in bacteria. Mol Biotechnol. 2013;55:288-97 pubmed publisher
    ..Some of the regulatory systems that produce common types of biofilms such as curli, PGA, cellulose and polysaccharides such as alginate, colonic acid, Psl and their involved sRNAs functions were also discussed. ..
  49. Binh C, Tong T, Gaillard J, Gray K, Kelly J. Common freshwater bacteria vary in their responses to short-term exposure to nano-TiO2. Environ Toxicol Chem. 2014;33:317-27 pubmed publisher
    ..possible ecological impacts of nano-TiO2, the authors used high-throughput screening to assess the responses of 4 bacteria representative of genera common in freshwater to short-term exposure (1-2?h) in 2 natural aqueous media (stream ..
  50. Goñi P, Fernández M, Rubio E. Identifying endosymbiont bacteria associated with free-living amoebae. Environ Microbiol. 2014;16:339-49 pubmed publisher
    The association between free-living amoebae and pathogenic bacteria is an issue that has gained great importance due to the environmental and health consequences that it implies...
  51. Wilks J, Beilinson H, Golovkina T. Dual role of commensal bacteria in viral infections. Immunol Rev. 2013;255:222-9 pubmed publisher
    With our abilities to culture and sequence the commensal bacteria that dwell on and within a host, we can now study the host in its entirety, as a supraorganism that must be navigated by the pathogen invader...
  52. Bravo D, Cailleau G, Bindschedler S, Simon A, Job D, Verrecchia E, et al. Isolation of oxalotrophic bacteria able to disperse on fungal mycelium. FEMS Microbiol Lett. 2013;348:157-66 pubmed publisher
    A technique based on an inverted Petri dish system was developed for the growth and isolation of soil oxalotrophic bacteria able to disperse on fungal mycelia...
  53. Vester J, Glaring M, Stougaard P. Improving diversity in cultures of bacteria from an extreme environment. Can J Microbiol. 2013;59:581-6 pubmed publisher
    ..The diversity and community dynamics in mixed cultures of bacteria from ikaite columns was investigated using denaturing gradient gel electrophoresis and pyrosequencing of 16S rDNA...
  54. van Teeseling M, de Almeida N, Klingl A, Speth D, Op den Camp H, Rachel R, et al. A new addition to the cell plan of anammox bacteria: "Candidatus Kuenenia stuttgartiensis" has a protein surface layer as the outermost layer of the cell. J Bacteriol. 2014;196:80-9 pubmed publisher
    Anammox bacteria perform anaerobic ammonium oxidation (anammox) and have a unique compartmentalized cell consisting of three membrane-bound compartments (from inside outwards): the anammoxosome, riboplasm, and paryphoplasm...
  55. Bassetti M, Merelli M, Temperoni C, Astilean A. New antibiotics for bad bugs: where are we?. Ann Clin Microbiol Antimicrob. 2013;12:22 pubmed publisher
    ..Therefore the management of antimicrobial resistance should also include fostering coordinated actions by all stakeholders, creating policy guidance, support for surveillance and technical assistance...
  56. Lau S, Tang B, Teng J, Chan T, Curreem S, Fan R, et al. Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry for identification of clinically significant bacteria that are difficult to identify in clinical laboratories. J Clin Pathol. 2014;67:361-6 pubmed publisher
    ..time-of-flight mass spectrometry (MALDI-TOF MS) has been evaluated for identification of various groups of bacteria, its application in bacteria that are 'difficult-to-identify' by phenotypic tests has been less well studied...
  57. Marathe N, Regina V, Walujkar S, Charan S, Moore E, Larsson D, et al. A treatment plant receiving waste water from multiple bulk drug manufacturers is a reservoir for highly multi-drug resistant integron-bearing bacteria. PLoS ONE. 2013;8:e77310 pubmed publisher
    The arenas and detailed mechanisms for transfer of antibiotic resistance genes between environmental bacteria and pathogens are largely unclear...
  58. Chun J, Rainey F. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol. 2014;64:316-24 pubmed publisher
    The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data...
  59. Edouard S, Raoult D. Use of the plaque assay for testing the antibiotic susceptibility of intracellular bacteria. Future Microbiol. 2013;8:1301-16 pubmed publisher
    ..and was later adapted for testing antibiotics susceptibility and to study virulence factors and motility of bacteria. Over time, the sensitivity and reproducibility of the technique has been improved...
  60. Chan P, Wong S, Lin S, Chen Y. Lysozyme-encapsulated gold nanocluster-based affinity mass spectrometry for pathogenic bacteria. Rapid Commun Mass Spectrom. 2013;27:2143-8 pubmed publisher
    ..Additionally, the emerging threat from antibiotic-resistant bacterial strains makes medical treatment even more difficult. Thus, rapid identification of infected bacterial strains is essential to assist diagnostics and medical treatment...
  61. Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, et al. Richness of human gut microbiome correlates with metabolic markers. Nature. 2013;500:541-6 pubmed publisher
    ..Our classifications based on variation in the gut microbiome identify subsets of individuals in the general white adult population who may be at increased risk of progressing to adiposity-associated co-morbidities. ..
  62. Tsaousoglou P, Nietzsche S, Cachovan G, Sculean A, Eick S. Antibacterial activity of moxifloxacin on bacteria associated with periodontitis within a biofilm. J Med Microbiol. 2014;63:284-92 pubmed publisher
    The activity of moxifloxacin was compared with ofloxacin and doxycycline against bacteria associated with periodontitis within a biofilm (single strain and mixed population) in vitro...
  63. David L, Maurice C, Carmody R, Gootenberg D, Button J, Wolfe B, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505:559-63 pubmed publisher
    ..Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses...
  64. Stieglmeier M, Mooshammer M, Kitzler B, Wanek W, Zechmeister Boltenstern S, Richter A, et al. Aerobic nitrous oxide production through N-nitrosating hybrid formation in ammonia-oxidizing archaea. ISME J. 2014;8:1135-46 pubmed publisher
    ..nitrous oxide (N2O) in the atmosphere and are generally attributed to the activity of nitrifying and denitrifying bacteria. However, the contribution of the recently discovered ammonia-oxidizing archaea (AOA) to N2O production from soil ..
  65. Tada Y, Grossart H. Community shifts of actively growing lake bacteria after N-acetyl-glucosamine addition: improving the BrdU-FACS method. ISME J. 2014;8:441-54 pubmed publisher
    In aquatic environments, community dynamics of bacteria, especially actively growing bacteria (AGB), are tightly linked with dissolved organic matter (DOM) quantity and quality...
  66. Ganesh S, Parris D, DeLong E, Stewart F. Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone. ISME J. 2014;8:187-211 pubmed publisher
    ..These results highlight an important role for surface attachment in shaping community metabolic potential and genome content in OMZ microorganisms. ..
  67. Lisher J, Giedroc D. Manganese acquisition and homeostasis at the host-pathogen interface. Front Cell Infect Microbiol. 2013;3:91 pubmed publisher
    Pathogenic bacteria acquire transition metals for cell viability and persistence of infection in competition with host nutritional defenses...
  68. Hu X, Wang C, Chen H, Ma J. Differences in the structure of the gut bacteria communities in development stages of the Chinese white pine beetle (Dendroctonus armandi). Int J Mol Sci. 2013;14:21006-20 pubmed publisher
    ..Analysis of PCR-amplified 16S rRNA gene fragments of bacteria from the guts of larvae, pupae, and male and female adults revealed bacterial communities of low complexity that ..
  69. Rubin B, Gibbons S, Kennedy S, Hampton Marcell J, Owens S, Gilbert J. Investigating the impact of storage conditions on microbial community composition in soil samples. PLoS ONE. 2013;8:e70460 pubmed publisher
    ..technologies have allowed scientists to probe increasingly complex biological systems, including the diversity of bacteria in the environment...
  70. Guo M, Yuan Q, Yang J. Ultraviolet reduction of erythromycin and tetracycline resistant heterotrophic bacteria and their resistance genes in municipal wastewater. Chemosphere. 2013;93:2864-8 pubmed publisher
    ..a major public health concern, but poorly understood about impact of disinfection on antibiotic resistant bacteria and antibiotic resistance genes...
  71. Ling Z, Liu X, Luo Y, Wu X, Yuan L, Tong X, et al. Associations between vaginal pathogenic community and bacterial vaginosis in Chinese reproductive-age women. PLoS ONE. 2013;8:e76589 pubmed publisher
  72. Kiliç S, White E, Sagitova D, Cornish J, Erill I. CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria. Nucleic Acids Res. 2014;42:D156-60 pubmed publisher
    ..umbc.edu) compiles data on experimentally validated, naturally occurring TF-binding sites across the Bacteria domain, placing a strong emphasis on the transparency of the curation process, the quality and availability of ..
  73. Cecchini D, Laville E, Laguerre S, Robe P, Leclerc M, Dore J, et al. Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria. PLoS ONE. 2013;8:e72766 pubmed publisher
    ..A functional metagenomic approach was used to explore the prebiotic breakdown potential of human gut bacteria, including non-cultivated ones...
  74. Lundberg D, Yourstone S, Mieczkowski P, Jones C, Dangl J. Practical innovations for high-throughput amplicon sequencing. Nat Methods. 2013;10:999-1002 pubmed publisher
    ..PCR clamps block amplification of contaminating sequences from a eukaryotic host, thereby substantially enriching microbial sequences without introducing bias. ..
  75. Nahid F, Khan A, Rehman S, Zahra R. Prevalence of metallo-?-lactamase NDM-1-producing multi-drug resistant bacteria at two Pakistani hospitals and implications for public health. J Infect Public Health. 2013;6:487-93 pubmed publisher
  76. Jing H, Xia X, Suzuki K, Liu H. Vertical profiles of bacteria in the tropical and subarctic oceans revealed by pyrosequencing. PLoS ONE. 2013;8:e79423 pubmed publisher
    Community composition of Bacteria in the surface and deep water layers were examined at three oceanic sites in the Pacific Ocean separated by great distance, i.e...
  77. Lozupone C, Li M, Campbell T, Flores S, Linderman D, Gebert M, et al. Alterations in the gut microbiota associated with HIV-1 infection. Cell Host Microbe. 2013;14:329-39 pubmed publisher
    ..S. individuals with carbohydrate-rich, protein- and fat-poor diets. By evaluating innate and adaptive immune responses to lysates from bacteria that differ with HIV, we explore the functional drivers of these compositional differences.
  78. Martín R, Miquel S, Ulmer J, Kechaou N, Langella P, Bermúdez Humarán L. Role of commensal and probiotic bacteria in human health: a focus on inflammatory bowel disease. Microb Cell Fact. 2013;12:71 pubmed publisher
    ..In addition, some food products contain live bacteria which transit through our gastrointestinal tract and could exert beneficial effects on our health (known as ..
  79. Ng V, Ke X, Lee A, Hedrick J, Yang Y. Synergistic co-delivery of membrane-disrupting polymers with commercial antibiotics against highly opportunistic bacteria. Adv Mater. 2013;25:6730-6 pubmed publisher
    ..g., doxycycline) shows high synergism towards difficult-to-kill bacteria P. aeruginosa...
  80. Kafil M, Bandani A, Kaltenpoth M, Goldansaz S, Alavi S. Role of symbiotic bacteria in the growth and development of the Sunn pest, Eurygaster integriceps. J Insect Sci. 2013;13:99 pubmed publisher
    ..Here, the contribution of symbiotic bacteria to the fitness of the bug was investigated by combining two different approaches to manipulate the host's ..
  81. Wu D, Jospin G, Eisen J. Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. PLoS ONE. 2013;8:e77033 pubmed publisher
    ..We report here the identification of PhyEco markers for different taxonomic levels including 40 for "all bacteria and archaea", 114 for "all bacteria (greatly expanding on the ?30 commonly used), and 100 s to 1000 s ..
  82. Dubinsky E, Conrad M, Chakraborty R, Bill M, Borglin S, Hollibaugh J, et al. Succession of hydrocarbon-degrading bacteria in the aftermath of the deepwater horizon oil spill in the gulf of Mexico. Environ Sci Technol. 2013;47:10860-7 pubmed publisher
    ..of dispersed oil and gas in the Gulf of Mexico that stimulated growth of psychrophilic, hydrocarbon degrading bacteria. We tracked succession of plume bacteria before, during and after the 83-day spill to determine the microbial ..
  83. Kaur B, Chakraborty D, Kumar B. Phenolic biotransformations during conversion of ferulic acid to vanillin by lactic acid bacteria. Biomed Res Int. 2013;2013:590359 pubmed publisher
    ..Phenolic biotransformations can occur during growth of lactic acid bacteria (LAB), and their production can be made feasible using specialized LAB strains that have been reported to produce ..
  84. Yang Y, Gao Y, Wang S, Xu D, Yu H, Wu L, et al. The microbial gene diversity along an elevation gradient of the Tibetan grassland. ISME J. 2014;8:430-40 pubmed publisher
  85. Lee C, Cho I, Jeong B, Lee S. Strategies to minimize antibiotic resistance. Int J Environ Res Public Health. 2013;10:4274-305 pubmed publisher
    ..g., handwashing). The problem of antibiotic resistance can be minimized only by concerted efforts of all members of society for ensuring the continued efficiency of antibiotics. ..
  86. Yu Q, Cho J, Shivapooja P, Ista L, Lopez G. Nanopatterned smart polymer surfaces for controlled attachment, killing, and release of bacteria. ACS Appl Mater Interfaces. 2013;5:9295-304 pubmed publisher
    ..was used to demonstrate the utility of nanopatterned PNIPAAm brushes to control biointerfacial interactions with bacteria. QAS was integrated into polymer-free regions of the substrate between nanopatterned PNIPAAm brushes...
  87. Siegismund D, Undisz A, Germerodt S, Schuster S, Rettenmayr M. Quantification of the interaction between biomaterial surfaces and bacteria by 3-D modeling. Acta Biomater. 2014;10:267-75 pubmed publisher
    It is general knowledge that bacteria/surface interactions depend on the surface topography. However, this well-known dependence has so far not been included in the modeling efforts...
  88. Rodrigo G, Landrain T, Shen S, Jaramillo A. A new frontier in synthetic biology: automated design of small RNA devices in bacteria. Trends Genet. 2013;29:529-36 pubmed publisher
    ..The automated design of RNA devices opens new possibilities for engineering fully synthetic regulatory systems that program new functions or reprogram dysfunctions in living cells. ..