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MICROBIOLOGY (263 journals)                  1 2 | Last

Showing 1 - 200 of 263 Journals sorted alphabetically
Acta Microbiologica et Immunologica Hungarica     Full-text available via subscription   (Followers: 4)
Acta Neurobiologiae Experimentalis     Open Access  
Addiction Genetics     Open Access   (Followers: 8)
Advances in Applied Microbiology     Full-text available via subscription   (Followers: 22)
Advances in Microbiology     Open Access   (Followers: 24)
Advances in Molecular Imaging     Open Access   (Followers: 1)
African Journal of Clinical and Experimental Microbiology     Open Access   (Followers: 1)
African Journal of Microbiology Research     Open Access   (Followers: 2)
Algorithms for Molecular Biology     Open Access   (Followers: 4)
American Journal of Current Microbiology     Open Access  
American Journal of Infectious Diseases and Microbiology     Open Access   (Followers: 24)
American Journal of Microbiological Research     Open Access   (Followers: 2)
American Journal of Molecular Biology     Open Access   (Followers: 2)
American Journal of Stem Cell Research     Open Access   (Followers: 5)
Annals of Clinical Microbiology and Antimicrobials     Open Access   (Followers: 9)
Annals of Microbiology     Hybrid Journal   (Followers: 10)
Annual Review of Microbiology     Full-text available via subscription   (Followers: 42)
Antimicrobial Agents and Chemotherapy     Hybrid Journal   (Followers: 25)
Antiviral Research     Hybrid Journal   (Followers: 8)
Applied and Environmental Microbiology     Hybrid Journal   (Followers: 46)
Applied Biochemistry and Microbiology     Hybrid Journal   (Followers: 16)
Applied Microbiology and Biotechnology     Hybrid Journal   (Followers: 63)
Aquatic Microbial Ecology     Hybrid Journal   (Followers: 5)
Archives of Microbiology     Hybrid Journal   (Followers: 8)
Avicenna Journal of Clinical Microbiology and Infection     Open Access   (Followers: 2)
Bangladesh Journal of Medical Microbiology     Open Access   (Followers: 3)
Beneficial Microbes     Full-text available via subscription   (Followers: 2)
Bio-Research     Full-text available via subscription   (Followers: 2)
BioArchitecture     Full-text available via subscription  
Bioethanol     Open Access  
Biomaterials Science     Full-text available via subscription   (Followers: 10)
BioMolecular Concepts     Hybrid Journal   (Followers: 2)
Biomolecular Detection and Quantification     Open Access  
Biomolecules     Open Access   (Followers: 2)
Biotechnology and Molecular Biology Reviews     Open Access   (Followers: 1)
BMC Microbiology     Open Access   (Followers: 12)
Brazilian Journal of Microbiology     Open Access   (Followers: 3)
Canadian Journal of Infectious Diseases and Medical Microbiology     Open Access   (Followers: 5)
Canadian Journal of Microbiology     Hybrid Journal   (Followers: 6)
Cell Biology : Research & Therapy     Hybrid Journal   (Followers: 5)
Cell Biology and Development     Open Access  
Cell Host & Microbe     Full-text available via subscription   (Followers: 21)
Cell Medicine     Open Access   (Followers: 5)
Cell Regeneration     Open Access   (Followers: 1)
Cell Stem Cell     Full-text available via subscription   (Followers: 38)
CellBio     Open Access  
Cells     Open Access   (Followers: 2)
Cellular & Molecular Immunology     Hybrid Journal   (Followers: 13)
Cellular and Molecular Biology Letters     Open Access   (Followers: 1)
Cellular and Molecular Life Sciences (CMLS)     Hybrid Journal   (Followers: 5)
Cellular Microbiology     Hybrid Journal   (Followers: 9)
Cheese: Chemistry, Physics and Microbiology     Full-text available via subscription   (Followers: 2)
Chimerism     Full-text available via subscription  
Clinical Microbiology and Infection     Hybrid Journal   (Followers: 22)
Clinical Microbiology Newsletter     Hybrid Journal   (Followers: 8)
Clinical Microbiology Reviews     Hybrid Journal   (Followers: 16)
Comparative Immunology, Microbiology and Infectious Diseases     Hybrid Journal   (Followers: 12)
Computational Molecular Bioscience     Open Access   (Followers: 2)
Critical Reviews in Microbiology     Hybrid Journal   (Followers: 14)
Current Clinical Microbiology Reports     Hybrid Journal   (Followers: 3)
Current Issues in Molecular Biology     Open Access   (Followers: 3)
Current Microbiology     Hybrid Journal   (Followers: 15)
Current Molecular Biology Reports     Hybrid Journal   (Followers: 1)
Current Opinion in Microbiology     Hybrid Journal   (Followers: 34)
Current Regenerative Medicine     Hybrid Journal  
Current Research in Microbiology     Open Access   (Followers: 18)
Current Tissue Engineering     Hybrid Journal   (Followers: 3)
Current Topics in Microbiology and Immunology     Hybrid Journal   (Followers: 12)
Diagnostic Microbiology and Infectious Disease     Hybrid Journal   (Followers: 9)
DNA Barcodes     Open Access  
Egyptian Journal of Biochemistry and Molecular Biology     Full-text available via subscription  
Emerging Microbes & Infections     Open Access   (Followers: 4)
Environmental Microbiology     Hybrid Journal   (Followers: 22)
Environmental Microbiology Reports     Hybrid Journal   (Followers: 7)
Enzyme and Microbial Technology     Hybrid Journal   (Followers: 13)
Epigenetics of Degenerative Diseases     Open Access   (Followers: 5)
Epigenomes     Open Access  
European Journal of Clinical Microbiology & Infectious Diseases     Hybrid Journal   (Followers: 20)
European Journal of Microbiology and Immunology     Open Access   (Followers: 8)
Experimental and Molecular Pathology     Hybrid Journal   (Followers: 4)
Experimental Cell Research     Hybrid Journal   (Followers: 5)
Fems Microbiology Ecology     Hybrid Journal   (Followers: 10)
Fems Microbiology Letters     Hybrid Journal   (Followers: 22)
Fems Microbiology Reviews     Hybrid Journal   (Followers: 27)
Fermentation     Open Access   (Followers: 1)
Folia Histochemica et Cytobiologica     Open Access  
Folia Microbiologica     Hybrid Journal   (Followers: 1)
Food Microbiology     Hybrid Journal   (Followers: 18)
Frontiers in Cell and Developmental Biology     Open Access   (Followers: 5)
Frontiers in Cellular and Infection Microbiology     Open Access   (Followers: 3)
Frontiers in Cellular Neuroscience     Open Access   (Followers: 8)
Frontiers in Microbiology     Open Access   (Followers: 15)
Frontiers in Molecular Neuroscience     Open Access   (Followers: 5)
Future Microbiology     Hybrid Journal   (Followers: 5)
Future Virology     Hybrid Journal   (Followers: 9)
Gene Expression     Full-text available via subscription   (Followers: 1)
Genetics and Molecular Research     Open Access   (Followers: 4)
Geomicrobiology Journal     Hybrid Journal   (Followers: 3)
Gut Microbes     Full-text available via subscription   (Followers: 9)
IAWA Journal     Hybrid Journal   (Followers: 1)
Indian Journal of Microbiology     Hybrid Journal   (Followers: 2)
Indian Journal of Pathology and Microbiology     Open Access   (Followers: 2)
Infection Ecology & Epidemiology     Open Access   (Followers: 5)
Inside the Cell     Open Access  
International Journal of Antimicrobial Agents     Hybrid Journal   (Followers: 10)
International Journal of Bioassays     Open Access   (Followers: 2)
International Journal of Biotechnology and Molecular Biology Research     Open Access   (Followers: 2)
International Journal of Food Microbiology     Hybrid Journal   (Followers: 13)
International Journal of Genetics and Molecular Biology     Open Access  
International Journal of Infection and Microbiology     Open Access   (Followers: 2)
International Journal of Medical Microbiology     Hybrid Journal   (Followers: 8)
International Journal of Molecular Medicine     Full-text available via subscription   (Followers: 5)
International Journal of Mycobacteriology     Open Access  
International Journal of Systematic and Evolutionary Microbiology     Full-text available via subscription   (Followers: 4)
International Journal of Virology and Molecular Biology     Open Access  
International Microbiology     Open Access   (Followers: 4)
Invertebrate Immunity     Open Access   (Followers: 1)
JMM Case Reports     Open Access  
Journal of Cell Science & Therapy     Open Access   (Followers: 1)
Journal of Microbial & Biochemical Technology     Open Access   (Followers: 2)
Journal of Applied Biology & Biotechnology     Open Access   (Followers: 3)
Journal of Applied Microbiology     Hybrid Journal   (Followers: 16)
Journal of Bacteriology     Hybrid Journal   (Followers: 28)
Journal of Basic Microbiology     Hybrid Journal   (Followers: 2)
Journal of Biochemistry and Molecular Biology Research     Open Access  
Journal of Biomolecular Structure and Dynamics     Hybrid Journal   (Followers: 2)
Journal of Bionanoscience     Full-text available via subscription  
Journal of Bone Marrow Research     Open Access   (Followers: 2)
Journal of Brewing and Distilling     Open Access   (Followers: 2)
Journal of Cell and Animal Biology     Open Access  
Journal of Cell Biology and Genetics     Open Access   (Followers: 2)
Journal of Clinical Microbiology     Hybrid Journal   (Followers: 31)
Journal of Clinical Pathology     Full-text available via subscription   (Followers: 10)
Journal of Extracellular Vesicles     Open Access   (Followers: 4)
Journal of Food Microbiology     Open Access   (Followers: 5)
Journal of General and Molecular Virology     Open Access   (Followers: 1)
Journal of Genes and Cells     Open Access   (Followers: 1)
Journal of Global Antimicrobial Resistance     Hybrid Journal   (Followers: 2)
Journal of Industrial Microbiology and Biotechnology     Hybrid Journal   (Followers: 16)
Journal of Medical Microbiology     Full-text available via subscription   (Followers: 5)
Journal of Microbiological Methods     Hybrid Journal   (Followers: 3)
Journal of Microbiology     Hybrid Journal   (Followers: 8)
Journal of Microbiology and Antimicrobials     Open Access   (Followers: 2)
Journal of Microbiology Research     Open Access   (Followers: 7)
Journal of Micropalaeontology     Hybrid Journal   (Followers: 3)
Journal of Molecular Biochemistry     Open Access   (Followers: 4)
Journal of Molecular Biology Research     Open Access   (Followers: 3)
Journal of Molecular Microbiology and Biotechnology     Full-text available via subscription   (Followers: 11)
Journal of Molecular Psychiatry     Open Access   (Followers: 8)
Journal of Morphology     Hybrid Journal   (Followers: 6)
Journal of Organic and Biomolecular Simulations     Open Access  
Journal of Pharmacy & Bioresources     Full-text available via subscription   (Followers: 3)
Journal of Plant Pathology & Microbiology     Open Access   (Followers: 1)
Journal of Proteome Science and Computational Biology     Open Access  
Journal of Regenerative Medicine and Tissue Engineering     Open Access   (Followers: 4)
Journal of The Academy of Clinical Microbiologists     Open Access  
Journal of the American Society of Brewing Chemists     Full-text available via subscription   (Followers: 2)
Journal of the Institute of Brewing     Free   (Followers: 3)
Journal of Tropical Microbiology and Biotechnology     Full-text available via subscription  
Jundishapur Journal of Microbiology     Open Access  
Letters In Applied Microbiology     Hybrid Journal   (Followers: 6)
Macrophage     Open Access  
MAP Kinase     Open Access   (Followers: 1)
Medical Mycology     Open Access   (Followers: 4)
Memórias do Instituto Oswaldo Cruz     Open Access  
Metagenomics     Unknown  
Methods in Molecular Biology     Hybrid Journal   (Followers: 19)
Microbes and Health     Open Access   (Followers: 1)
Microbes and Infection     Full-text available via subscription   (Followers: 6)
Microbial Biotechnology     Open Access   (Followers: 9)
Microbial Cell Factories     Open Access   (Followers: 8)
Microbial Drug Resistance     Hybrid Journal   (Followers: 4)
Microbial Ecology     Hybrid Journal   (Followers: 11)
Microbial Ecology in Health and Disease     Open Access   (Followers: 1)
Microbial Informatics and Experimentation     Open Access   (Followers: 1)
Microbial Pathogenesis     Hybrid Journal   (Followers: 7)
Microbial Risk Analysis     Full-text available via subscription  
Microbiologia Medica     Open Access   (Followers: 1)
Microbiological Research     Hybrid Journal   (Followers: 6)
Microbiology     Hybrid Journal   (Followers: 15)
Microbiology (SGM)     Full-text available via subscription   (Followers: 19)
Microbiology and Immunology     Hybrid Journal   (Followers: 10)
Microbiology and Molecular Biology Reviews     Hybrid Journal   (Followers: 24)
Microbiology Australia     Hybrid Journal  
Microbiology Discovery     Open Access   (Followers: 2)
Microbiology Indonesia     Open Access  
Microbiology Research     Open Access   (Followers: 7)
MicrobiologyOpen     Open Access   (Followers: 2)
Microbiome     Hybrid Journal   (Followers: 10)
Microbiome Science and Medicine     Open Access   (Followers: 3)
Microorganisms     Open Access   (Followers: 2)
MicroRNA     Hybrid Journal   (Followers: 1)
Molecular and Cellular Therapies     Open Access  
Molecular Biology and Genetic Engineering     Open Access   (Followers: 2)
Molecular Biology Research Communications     Open Access   (Followers: 1)
Molecular Genetics and Metabolism Reports     Open Access   (Followers: 3)
Molecular Genetics, Microbiology and Virology     Hybrid Journal   (Followers: 6)
Molecular Imaging     Open Access  
Molecular Imaging and Biology     Hybrid Journal   (Followers: 1)
Molecular Medicine     Open Access   (Followers: 3)

        1 2 | Last

Journal Cover Trends in Microbiology
  [SJR: 5.285]   [H-I: 150]   [38 followers]  Follow
   Full-text available via subscription Subscription journal
   ISSN (Print) 0966-842X
   Published by Elsevier Homepage  [3175 journals]
  • Not Just Antibiotics: Is Cancer Chemotherapy Driving Antimicrobial
    • Authors: Lito E. Papanicolas; David L. Gordon; Steve L. Wesselingh; Geraint B. Rogers
      Pages: 393 - 400
      Abstract: Publication date: May 2018
      Source:Trends in Microbiology, Volume 26, Issue 5
      Author(s): Lito E. Papanicolas, David L. Gordon, Steve L. Wesselingh, Geraint B. Rogers
      The global spread of antibiotic-resistant pathogens threatens to increase the mortality of cancer patients significantly. We propose that chemotherapy contributes to the emergence of antibiotic-resistant bacteria within the gut and, in combination with antibiotics, drives pathogen overgrowth and translocation into the bloodstream. In our model, these processes are mediated by the effects of chemotherapy on bacterial mutagenesis and horizontal gene transfer, the disruption of commensal gut microbiology, and alterations to host physiology. Clinically, this model manifests as a cycle of recurrent sepsis, with each episode involving ever more resistant organisms and requiring increasingly broad-spectrum antimicrobial therapy. Therapies that restore the gut microbiota following chemotherapy or antibiotics could provide a means to break this cycle of infection and treatment failure.

      PubDate: 2018-04-25T05:18:31Z
      DOI: 10.1016/j.tim.2017.10.009
  • Cable Bacteria Take a New Breath Using Long-Distance Electricity
    • Authors: Filip J.R. Meysman
      Pages: 411 - 422
      Abstract: Publication date: May 2018
      Source:Trends in Microbiology, Volume 26, Issue 5
      Author(s): Filip J.R. Meysman
      Recently, a new group of multicellular microorganisms was discovered, called ‘cable bacteria’, which are capable of generating and mediating electrical currents across centimetre-scale distances. By transporting electrons from cell to cell, cable bacteria can harvest electron donors and electron acceptors that are widely separated in space, thus providing them with a competitive advantage for survival in aquatic sediments. The underlying process of long-distance electron transport challenges some long-held ideas about the energy metabolism of multicellular organisms and entails a whole new type of electrical cooperation between cells. This review summarizes the current knowledge about these intriguing multicellular bacteria.

      PubDate: 2018-04-25T05:18:31Z
      DOI: 10.1016/j.tim.2017.10.011
  • Compartmentalized Antimicrobial Defenses in Response to Flagellin
    • Authors: Aneesh Vijayan; Martin Rumbo; Christophe Carnoy; Jean-Claude Sirard
      Pages: 423 - 435
      Abstract: Publication date: May 2018
      Source:Trends in Microbiology, Volume 26, Issue 5
      Author(s): Aneesh Vijayan, Martin Rumbo, Christophe Carnoy, Jean-Claude Sirard
      Motility is often a pathogenicity determinant of bacteria targeting mucosal tissues. Flagella constitute the machinery that propels bacteria into appropriate niches. Besides motility, the structural component, flagellin, which forms the flagella, targets Toll-like receptor 5 (TLR5) to activate innate immunity. The compartmentalization of flagellin-mediated immunity and the contribution of epithelial cells and dendritic cells in detecting flagellin within luminal and basal sides are highlighted here, respectively. While a direct stimulation of the epithelium mainly results in recruitment of immune cells and production of antimicrobial molecules, TLR5 engagement on parenchymal dendritic cells can contribute to the stimulation of innate lymphocytes such as type 3 innate lymphoid cells, as well as T helper cells. This review, therefore, illustrates how the innate and adaptive immunity to flagellin are differentially regulated by the epithelium and the dendritic cells in response to pathogens that either colonize or invade mucosa.

      PubDate: 2018-04-25T05:18:31Z
      DOI: 10.1016/j.tim.2017.10.008
  • A Call to Arms: Quest for a Cryptococcal Vaccine
    • Authors: Marley C. Caballero Van Dyke; Floyd L. Wormley
      Pages: 436 - 446
      Abstract: Publication date: May 2018
      Source:Trends in Microbiology, Volume 26, Issue 5
      Author(s): Marley C. Caballero Van Dyke, Floyd L. Wormley
      Cryptococcosis remains a significant cause of morbidity and mortality world-wide, particularly among AIDS patients. Yet, to date, there are no licensed vaccines clinically available to treat or prevent cryptococcosis. In this review, we provide a rationale to support continued investment in Cryptococcus vaccine research, potential challenges that must be overcome along the way, and a literature review of the current progress underway towards developing a vaccine to prevent cryptococcosis.

      PubDate: 2018-04-25T05:18:31Z
      DOI: 10.1016/j.tim.2017.10.002
  • 25 Years of Trends in Microbiology: Window to the Past and Future
    • Authors: Gail Teitzel
      Pages: 243 - 245
      Abstract: Publication date: April 2018
      Source:Trends in Microbiology, Volume 26, Issue 4
      Author(s): Gail Teitzel

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.02.005
  • Towards a Natural History of Soil Bacterial Communities
    • Authors: Jennifer B.H. Martiny; Kendra E. Walters
      Pages: 250 - 252
      Abstract: Publication date: April 2018
      Source:Trends in Microbiology, Volume 26, Issue 4
      Author(s): Jennifer B.H. Martiny, Kendra E. Walters
      Despite the enormous diversity of bacteria, a recent study reveals that soils are globally dominated by a small list of taxa. Characterizing the traits of these bacteria offers the potential for predicting functional differences among soil communities.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.02.010
  • Host Cell Targeting by Enteropathogenic Bacteria T3SS Effectors
    • Authors: Laurie Pinaud; Philippe J. Sansonetti; Armelle Phalipon
      Pages: 266 - 283
      Abstract: Publication date: April 2018
      Source:Trends in Microbiology, Volume 26, Issue 4
      Author(s): Laurie Pinaud, Philippe J. Sansonetti, Armelle Phalipon
      Microbial pathogens possess a diversity of weapons that disrupt host homeostasis and immune defenses, thus resulting in the establishment of infection. The best-characterized system mediating bacterial protein delivery into target eukaryotic cells is the type III secretion system (T3SS) expressed by Gram-negative bacteria, including the human enteric pathogens Shigella, Salmonella, Yersinia, and enteropathogenic/enterohemorragic Escherichia coli (EPEC/EHEC). The emerging global view is that these T3SS-bearing pathogens share similarities in their ability to target key cellular pathways such as the cell cytoskeleton, trafficking, cell death/survival, and the NF-κB and MAPK signaling pathways. In particular, multiple host proteins are targeted in a given pathway, and different T3SS effectors from various pathogens share functional similarities.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.01.010
  • Dynamic Fungal Cell Wall Architecture in Stress Adaptation and Immune
    • Authors: Alex Hopke; Alistair J.P. Brown; Rebecca A. Hall; Robert T. Wheeler
      Pages: 284 - 295
      Abstract: Publication date: April 2018
      Source:Trends in Microbiology, Volume 26, Issue 4
      Author(s): Alex Hopke, Alistair J.P. Brown, Rebecca A. Hall, Robert T. Wheeler
      Deadly infections from opportunistic fungi have risen in frequency, largely because of the at-risk immunocompromised population created by advances in modern medicine and the HIV/AIDS pandemic. This review focuses on dynamics of the fungal polysaccharide cell wall, which plays an outsized role in fungal pathogenesis and therapy because it acts as both an environmental barrier and as the major interface with the host immune system. Human fungal pathogens use architectural strategies to mask epitopes from the host and prevent immune surveillance, and recent work elucidates how biotic and abiotic stresses present during infection can either block or enhance masking. The signaling components implicated in regulating fungal immune recognition can teach us how cell wall dynamics are controlled, and represent potential targets for interventions designed to boost or dampen immunity.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.01.007
  • Achieving a Predictive Understanding of Antimicrobial Stress Physiology
           through Systems Biology
    • Authors: Sean G. Mack; Randi L. Turner; Daniel J. Dwyer
      Pages: 296 - 312
      Abstract: Publication date: April 2018
      Source:Trends in Microbiology, Volume 26, Issue 4
      Author(s): Sean G. Mack, Randi L. Turner, Daniel J. Dwyer
      The dramatic spread and diversity of antibiotic-resistant pathogens has significantly reduced the efficacy of essentially all antibiotic classes, bringing us ever closer to a postantibiotic era. Exacerbating this issue, our understanding of the multiscale physiological impact of antimicrobial challenge on bacterial pathogens remains incomplete. Concerns over resistance and the need for new antibiotics have motivated the collection of omics measurements to provide systems-level insights into antimicrobial stress responses for nearly 20 years. Although technological advances have markedly improved the types and resolution of such measurements, continued development of mathematical frameworks aimed at providing a predictive understanding of complex antimicrobial-associated phenotypes is critical to maximize the utility of multiscale data. Here we highlight recent efforts utilizing systems biology to enhance our knowledge of antimicrobial stress physiology. We provide a brief historical perspective of antibiotic-focused omics measurements, highlight new measurement discoveries and trends, discuss examples and opportunities for integrating measurements with mathematical models, and describe future challenges for the field.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.02.004
  • Antibacterial Weapons: Targeted Destruction in the Microbiota
    • Authors: Benoit Chassaing; Eric Cascales
      Pages: 329 - 338
      Abstract: Publication date: April 2018
      Source:Trends in Microbiology, Volume 26, Issue 4
      Author(s): Benoit Chassaing, Eric Cascales
      The intestinal microbiota plays an important role in health, particularly in promoting intestinal metabolic capacity and in maturing the immune system. The intestinal microbiota also mediates colonization resistance against pathogenic bacteria, hence protecting the host from infections. In addition, some bacterial pathogens deliver toxins that target phylogenetically related or distinct bacterial species in order to outcompete and establish within the microbiota. The most widely distributed weapons include bacteriocins, as well as contact-dependent growth inhibition and type VI secretion systems. In this review, we discuss important advances about the impact of such antibacterial systems on shaping the intestinal microbiota.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.01.006
  • Glycan Utilization and Cross-Feeding Activities by Bifidobacteria
    • Authors: Francesca Turroni; Christian Milani; Sabrina Duranti; Jennifer Mahony; Douwe van Sinderen; Marco Ventura
      Pages: 339 - 350
      Abstract: Publication date: April 2018
      Source:Trends in Microbiology, Volume 26, Issue 4
      Author(s): Francesca Turroni, Christian Milani, Sabrina Duranti, Jennifer Mahony, Douwe van Sinderen, Marco Ventura
      Bifidobacteria represent one of the first colonizers of the mammalian gut, where such colonization is facilitated by their saccharolytic capabilities. Genomic analyses of bifidobacteria have revealed intriguing genetic strategies employed by these bacteria to access a variety of dietary and host-produced glycans. Bifidobacterial genome evolution therefore represents a fascinating example of how their chromosomes were molded to contain a large number of genes involved in carbohydrate metabolism. One of the reasons as to why bifidobacteria are such dominant and prevalent members of the (early) microbiota is that they may access glycans in the gut through mutualistic cross-feeding or resource-sharing activities, which is indicative of ‘social behavior’ among bifidobacterial strains.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2017.10.001
  • The Archaellum: An Update on the Unique Archaeal Motility Structure
    • Authors: Sonja-Verena Albers; Ken F. Jarrell
      Pages: 351 - 362
      Abstract: Publication date: April 2018
      Source:Trends in Microbiology, Volume 26, Issue 4
      Author(s): Sonja-Verena Albers, Ken F. Jarrell
      Each of the three domains of life exhibits a unique motility structure: while Bacteria use flagella, Eukarya employ cilia, and Archaea swim using archaella. Since the new name for the archaeal motility structure was proposed, in 2012, a significant amount of new data on the regulation of transcription of archaella operons, the structure and function of archaellum subunits, their interactions, and cryo-EM data on in situ archaellum complexes in whole cells have been obtained. These data support the notion that the archaellum is evolutionary and structurally unrelated to the flagellum, but instead is related to archaeal and bacterial type IV pili and emphasize that it is a motility structure unique to the Archaea.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.01.004
  • Learning from Noise: How Observing Stochasticity May Aid Microbiology
    • Authors: Ariel Amir; Nathalie Q. Balaban
      Pages: 376 - 385
      Abstract: Publication date: April 2018
      Source:Trends in Microbiology, Volume 26, Issue 4
      Author(s): Ariel Amir, Nathalie Q. Balaban
      For many decades, the wedding of quantitative data with mathematical modeling has been fruitful, leading to important biological insights. Here, we review some of the ongoing efforts to gain insights into problems in microbiology – and, in particular, cell-cycle progression and its regulation – through observation and quantitative analysis of the natural fluctuations in the system. We first illustrate this idea by reviewing a classic example in microbiology – the Luria–Delbrück experiment – and discussing how, in that case, useful information was obtained by looking beyond the mean outcome of the experiment, but instead paying attention to the variability between replicates of the experiment. We then switch gears to the contemporary problem of cell cycle progression and discuss in more detail how insights into cell size regulation and, when relevant, coupling between the cell cycle and the circadian clock, can be gained by studying the natural fluctuations in the system and their statistical properties. We end with a more general discussion of how (in this context) the correct level of phenomenological model should be chosen, as well as some of the pitfalls associated with this type of analysis. Throughout this review the emphasis is not on providing details of the experimental setups or technical details of the models used, but rather, in fleshing out the conceptual structure of this particular approach to the problem. For this reason, we choose to illustrate the framework on a rather broad range of problems, and on organisms from all domains of life, to emphasize the commonality of the ideas and analysis used (as well as their differences).

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.02.003
  • Hepatitis B Virus
    • Authors: Chiaho Shih; Ching-Chun Yang; Gansukh Choijilsuren; Chih-Hsu Chang; An-Ting Liou
      Pages: 386 - 387
      Abstract: Publication date: April 2018
      Source:Trends in Microbiology, Volume 26, Issue 4
      Author(s): Chiaho Shih, Ching-Chun Yang, Gansukh Choijilsuren, Chih-Hsu Chang, An-Ting Liou
      This infographic about hepatitis B virus explores its replication cycle, natural history of infection and pathogenesis, and how this can be controlled and treated. Hepatitis B virus (HBV) is a common worldwide blood-borne pathogen. Chronic hepatitis B can progress to an inactive carrier state, and then, in some patients, give rise to cirrhosis and cancer of the liver, leading to death. An HBV surface-antigen vaccine is effective, but treatments are currently not curative. HBV replicates via reverse transcription. Its covalently closed circular (ccc) DNA in the nucleus encodes a pregenomic RNA (pgRNA), which can be encapsidated by HBV polymerase. Reverse transcription occurs in the capsids by using the pgRNA as a template for the synthesis of single-stranded linear and then partially double-stranded relaxed circular (rc) DNA. Capsids containing a mature rc DNA genome target to the nucleus for ccc DNA synthesis. Persistent HBV infection is caused mainly by ccc DNA and immune tolerance to HBV antigens in the liver. Unlike acute infection, chronic carriers contain only a low level of HBV core-antigen-specific T cell activity, contributing to the lack of viral clearance.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.01.009
  • Legionella Effectors Explored with INSeq: New Functional Insights
    • Authors: Monica Rolando; Carmen Buchrieser
      Pages: 169 - 170
      Abstract: Publication date: March 2018
      Source:Trends in Microbiology, Volume 26, Issue 3
      Author(s): Monica Rolando, Carmen Buchrieser
      Legionella pneumophila secretes over 300 effector proteins that manipulate host cells. This multiplicity of effectors hampers the characterization of their individual roles. Shames et al. report a new approach to solve the enigma of Legionella effector function by using INSeq to analyse effector functions in the context of infection.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.01.003
  • Life on Phosphite: A Metagenomics Tale
    • Authors: Yunuen Tapia-Torres; Gabriela Olmedo-Álvarez
      Pages: 170 - 172
      Abstract: Publication date: March 2018
      Source:Trends in Microbiology, Volume 26, Issue 3
      Author(s): Yunuen Tapia-Torres, Gabriela Olmedo-Álvarez
      Phosphite, a species of phosphorus in a P3+ oxidation state, is believed to have played an important role in the primordial Earth. Figueroa et al. used metagenomics to uncover anaerobic bacterial communities from waste water waste sludge that sustain life from energy provided by phosphite.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.01.002
  • A Delicate Connection: c-di-AMP Affects Cell Integrity by Controlling
           Osmolyte Transport
    • Authors: Fabian M. Commichau; Johannes Gibhardt; Sven Halbedel; Jan Gundlach; Jörg Stülke
      Pages: 175 - 185
      Abstract: Publication date: March 2018
      Source:Trends in Microbiology, Volume 26, Issue 3
      Author(s): Fabian M. Commichau, Johannes Gibhardt, Sven Halbedel, Jan Gundlach, Jörg Stülke
      Bacteria use second-messenger molecules to adapt to their environment. Several second messengers, among them cyclic di-AMP (c-di-AMP), have been discovered and intensively studied. Interestingly, c-di-AMP is essential for growth of Gram-positive bacteria such as Bacillus subtilis, Listeria monocytogenes, and Staphylococcus aureus. Many studies demonstrated that perturbation of c-di-AMP metabolism affects the integrity of the bacterial cell envelope. Therefore, it has been assumed that the nucleotide is essential for proper cell envelope synthesis. In this Opinion paper, we propose that the cell envelope phenotypes caused by perturbations of c-di-AMP metabolism can be interpreted differently: c-di-AMP might indirectly control cell envelope integrity by modulating the turgor, a physical variable that needs to be tightly adjusted. We also discuss open questions related to c-di-AMP metabolism that need to be urgently addressed by future studies.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2017.09.003
  • The Molecular Basis of Noncanonical Bacterial Morphology
    • Authors: Paul D. Caccamo; Yves V. Brun
      Pages: 191 - 208
      Abstract: Publication date: March 2018
      Source:Trends in Microbiology, Volume 26, Issue 3
      Author(s): Paul D. Caccamo, Yves V. Brun
      Bacteria come in a wide variety of shapes and sizes. The true picture of bacterial morphological diversity is likely skewed due to an experimental focus on pathogens and industrially relevant organisms. Indeed, most of the work elucidating the genes and molecular processes involved in maintaining bacterial morphology has been limited to rod- or coccal-shaped model systems. The mechanisms of shape evolution, the molecular processes underlying diverse shapes and growth modes, and how individual cells can dynamically modulate their shape are just beginning to be revealed. Here we discuss recent work aimed at advancing our knowledge of shape diversity and uncovering the molecular basis for shape generation in noncanonical and morphologically complex bacteria.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2017.09.012
  • Clinical Potential of Prefusion RSV F-specific Antibodies
    • Authors: Iebe Rossey; Jason S. McLellan; Xavier Saelens; Bert Schepens
      Pages: 209 - 219
      Abstract: Publication date: March 2018
      Source:Trends in Microbiology, Volume 26, Issue 3
      Author(s): Iebe Rossey, Jason S. McLellan, Xavier Saelens, Bert Schepens
      Human respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections in the very young. The RSV fusion protein (F) is essential for virus entry because it mediates viral and host membrane fusion. During this fusion process F is converted from a metastable prefusion conformation into an energetically favored postfusion state. Antibodies that target F can prevent viral entry and reduce disease caused by RSV. During recent years, many prefusion F-specific antibodies have been described. These antibodies typically have stronger RSV-neutralizing activity compared to those that also bind F in the postfusion conformation. Here, we describe how F-specific antibodies protect against RSV and why specifically targeting prefusion F could have great clinical potential.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2017.09.009
  • Antibiotic-Resistance Genes in Waste Water
    • Authors: Antti Karkman; Thi Thuy Do; Fiona Walsh; Marko P.J. Virta
      Pages: 220 - 228
      Abstract: Publication date: March 2018
      Source:Trends in Microbiology, Volume 26, Issue 3
      Author(s): Antti Karkman, Thi Thuy Do, Fiona Walsh, Marko P.J. Virta
      Waste water and waste water treatment plants can act as reservoirs and environmental suppliers of antibiotic resistance. They have also been proposed to be hotspots for horizontal gene transfer, enabling the spread of antibiotic resistance genes between different bacterial species. Waste water contains antibiotics, disinfectants, and metals which can form a selection pressure for antibiotic resistance, even in low concentrations. Our knowledge of antibiotic resistance in waste water has increased tremendously in the past few years with advances in the molecular methods available. However, there are still some gaps in our knowledge on the subject, such as how active is horizontal gene transfer in waste water and what is the role of the waste water treatment plant in the environmental resistome' The purpose of this review is to briefly describe some of the main methods for studying antibiotic resistance in waste waters and the latest research and main knowledge gaps on the issue. In addition, some future research directions are proposed.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2017.09.005
  • Oral Biofilms: Pathogens, Matrix, and Polymicrobial Interactions in
    • Authors: William H. Bowen; Robert A. Burne; Hui Wu; Hyun Koo
      Pages: 229 - 242
      Abstract: Publication date: March 2018
      Source:Trends in Microbiology, Volume 26, Issue 3
      Author(s): William H. Bowen, Robert A. Burne, Hui Wu, Hyun Koo
      Biofilms are microbial communities embedded within an extracellular matrix, forming a highly organized structure that causes many human infections. Dental caries (tooth decay) is a polymicrobial biofilm disease driven by the diet and microbiota–matrix interactions that occur on a solid surface. Sugars fuel the emergence of pathogens, the assembly of the matrix, and the acidification of the biofilm microenvironment, promoting ecological changes and concerted multispecies efforts that are conducive to acid damage of the mineralized tooth tissue. Here, we discuss recent advances in the role of the biofilm matrix and interactions between opportunistic pathogens and commensals in the pathogenesis of dental caries. In addition, we highlight the importance of matrix-producing organisms in fostering a pathogenic habitat where interspecies competition and synergies occur to drive the disease process, which could have implications to other infections associated with polymicrobial biofilms.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2017.09.008
  • Editorial Board and Contents
    • Abstract: Publication date: May 2018
      Source:Trends in Microbiology, Volume 26, Issue 5

      PubDate: 2018-04-25T05:18:31Z
  • The Expanding Diversity of RNA Viruses in Vertebrates
    • Authors: Wenqiang Wang; Guan-Zhu Han
      Abstract: Publication date: Available online 24 April 2018
      Source:Trends in Microbiology
      Author(s): Wenqiang Wang, Guan-Zhu Han
      The diversity of RNA viruses in vertebrates remains largely unexplored. The discovery of 214 novel vertebrate-associated RNA viruses will likely help us to understand the diversity and evolution of RNA viruses in vertebrates.

      PubDate: 2018-04-25T05:18:31Z
      DOI: 10.1016/j.tim.2018.04.003
  • Emerging Role of Retromer in Modulating Pathogen Growth
    • Authors: Cherilyn Elwell; Joanne Engel
      Abstract: Publication date: Available online 24 April 2018
      Source:Trends in Microbiology
      Author(s): Cherilyn Elwell, Joanne Engel
      Intracellular pathogens have developed elegant mechanisms to modulate host endosomal trafficking. The highly conserved retromer pathway has emerged as an important target of viruses and intravacuolar bacteria. Some pathogens require retromer function to survive. For others, retromer activity restricts intracellular growth; these pathogens must disrupt retromer function to survive. In this review, we discuss recent paradigm changes to the current model for retromer assembly and cargo selection. We highlight how the study of pathogen effectors has contributed to these fundamental insights, with a special focus on the biology and structure of two recently described bacterial effectors, Chlamydia trachomatis IncE and Legionella pneumophila RidL. These two pathogens employ distinct strategies to target retromer components and overcome restriction of intracellular growth imposed by retromer.

      PubDate: 2018-04-25T05:18:31Z
      DOI: 10.1016/j.tim.2018.04.001
  • Can Broadly Neutralizing Monoclonal Antibodies Lead to a Hepatitis C Virus
    • Authors: Valerie J. Kinchen; Andrea L. Cox; Justin R. Bailey
      Abstract: Publication date: Available online 24 April 2018
      Source:Trends in Microbiology
      Author(s): Valerie J. Kinchen, Andrea L. Cox, Justin R. Bailey
      While licensed vaccines elicit protective antibody responses against a variety of viral infections, an effective vaccine for hepatitis C virus (HCV) has remained elusive. The extraordinary genetic diversity of HCV and the ability of the virus to evade the immune response have hindered vaccine development efforts. However, recent studies have greatly expanded the number of well characterized broadly neutralizing human monoclonal antibodies (bNAbs) against HCV. These bNAbs target relatively conserved HCV epitopes, prevent HCV infection in animal models, and are associated with spontaneous clearance of human HCV infection. In this review, recent high-resolution bNAb epitope mapping and structural analysis of bNAb–epitope complexes that may serve as a guide for vaccine development are discussed along with major obstacles.

      PubDate: 2018-04-25T05:18:31Z
      DOI: 10.1016/j.tim.2018.04.002
  • Influenza Hemagglutinin Protein Stability, Activation, and Pandemic Risk
    • Authors: Charles J. Russell; Meng Hu; Faten A. Okda
      Abstract: Publication date: Available online 19 April 2018
      Source:Trends in Microbiology
      Author(s): Charles J. Russell, Meng Hu, Faten A. Okda
      For decades, hemagglutinin (HA) protein structure and its refolding mechanism have served as a paradigm for understanding protein-mediated membrane fusion. HA trimers are in a high-energy state and are functionally activated by low pH. Over the past decade, HA stability (or the pH at which irreversible conformational changes are triggered) has emerged as an important determinant in influenza virus host range, infectivity, transmissibility, and human pandemic potential. Here, we review HA protein structure, assays to measure its stability, measured HA stability values, residues and mutations that regulate its stability, the effect of HA stability on interspecies adaptation and transmissibility, and mechanistic insights into this process. Most importantly, HA stabilization appears to be necessary for adapting emerging influenza viruses to humans.

      PubDate: 2018-04-25T05:18:31Z
      DOI: 10.1016/j.tim.2018.03.005
  • Bat-Origin Coronaviruses Expand Their Host Range to Pigs
    • Authors: Liang Wang; Shuo Su; Yuhai Bi; Gary Wong; George F. Gao
      Abstract: Publication date: Available online 18 April 2018
      Source:Trends in Microbiology
      Author(s): Liang Wang, Shuo Su, Yuhai Bi, Gary Wong, George F. Gao
      Infections with bat-origin coronaviruses have caused severe illness in humans by ‘host jump’. Recently, novel bat-origin coronaviruses were found in pigs. The large number of mutations on the receptor-binding domain allowed the viruses to infect the new host, posing a potential threat to both agriculture and public health.

      PubDate: 2018-04-25T05:18:31Z
      DOI: 10.1016/j.tim.2018.03.001
  • Convergent Evolution in Intracellular Elements: Plasmids as Model
    • Authors: Anne-Kathrin Dietel; Martin Kaltenpoth; Christian Kost
      Abstract: Publication date: Available online 10 April 2018
      Source:Trends in Microbiology
      Author(s): Anne-Kathrin Dietel, Martin Kaltenpoth, Christian Kost
      Endosymbionts are organisms that live inside the cells of other species. This lifestyle is ubiquitous across the tree of life and is featured by unicellular eukaryotes, prokaryotes, and by extrachromosomal genetic elements such as plasmids. Given that all of these elements dwell in the cytoplasm of their host cell, they should be subject to similar selection pressures. Here we show that strikingly similar features have evolved in both bacterial endosymbionts and plasmids. Since host and endosymbiont are often metabolically tightly intertwined, they are difficult to disentangle experimentally. We propose that using plasmids as tractable model systems can help to solve this problem, thus allowing fundamental questions to be experimentally addressed about the ecology and evolution of endosymbiotic interactions.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.03.004
  • Editorial Board and Contents
    • Abstract: Publication date: April 2018
      Source:Trends in Microbiology, Volume 26, Issue 4

      PubDate: 2018-04-15T04:01:03Z
  • How Has Microbiology Changed over the Past 25 Years'
    • Abstract: Publication date: April 2018
      Source:Trends in Microbiology, Volume 26, Issue 4

      PubDate: 2018-04-15T04:01:03Z
  • Structure of Herpesvirus Capsid Sheds Light on Drug Discovery
    • Authors: Louis F. Taylor; Yan Yuan
      Abstract: Publication date: Available online 27 March 2018
      Source:Trends in Microbiology
      Author(s): Louis F. Taylor, Yan Yuan
      The atomic resolution structure of Kaposi’s sarcoma-associated herpesvirus (KSHV) capsid reveals that protein–protein interfaces (PPIs) are essential for its structural stability. This structural information guided a mutagenesis study that identified novel drug targets interrupting PPIs essential for capsid assembly.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.03.003
  • Mobilization of Bacteriocins during Competence in Streptococci
    • Authors: Charles Y. Wang; Suzanne Dawid
      Abstract: Publication date: Available online 24 March 2018
      Source:Trends in Microbiology
      Author(s): Charles Y. Wang, Suzanne Dawid
      Many streptococci have evolved the ability for natural genetic competence. Recent studies have uncovered regulatory links between competence and the production of antimicrobial peptides called bacteriocins in multiple streptococcal species. This reveals a broadly distributed strategy among streptococci to exploit bacteriocin-mediated killing during competence for adaptive gain.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.03.002
  • Community Assembly Processes of the Microbial Rare Biosphere
    • Authors: Xiu Jia; Francisco Dini-Andreote; Joana Falcão Salles
      Abstract: Publication date: Available online 14 March 2018
      Source:Trends in Microbiology
      Author(s): Xiu Jia, Francisco Dini-Andreote, Joana Falcão Salles
      Our planet teems with microorganisms that often present a skewed abundance distribution in a local community, with relatively few dominant species coexisting alongside a high number of rare species. Recent studies have demonstrated that these rare taxa serve as limitless reservoirs of genetic diversity, and perform disproportionate types of functions despite their low abundances. However, relatively little is known about the mechanisms controlling rarity and the processes promoting the development of the rare biosphere. Here, we propose the use of multivariate cut-offs to estimate rare species and phylogenetic null models applied to predefined rare taxa to disentangle the relative influences of ecoevolutionary processes mediating the assembly of the rare biosphere. Importantly, the identification of the factors controlling rare species assemblages is critical for understanding the types of rarity, how the rare biosphere is established, and how rare microorganisms fluctuate over spatiotemporal scales, thus enabling prospective predictions of ecosystem responses.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.02.011
  • Extracellular Vesicle RNA: A Universal Mediator of Microbial
    • Authors: James A. Tsatsaronis; Sandra Franch-Arroyo; Ulrike Resch; Emmanuelle Charpentier
      Abstract: Publication date: Available online 13 March 2018
      Source:Trends in Microbiology
      Author(s): James A. Tsatsaronis, Sandra Franch-Arroyo, Ulrike Resch, Emmanuelle Charpentier
      Both extracellular RNAs and extracellular vesicles (EVs) have recently garnered attention as novel mediators of intercellular communication in eukaryotes and prokaryotes alike. EVs not only permit export of RNA, but also facilitate delivery and trans-kingdom exchange of these and other biomolecules, for instance between microbes and their hosts. In this Opinion article, we propose that EV-mediated export of RNA represents a universal mechanism for interkingdom and intrakingdom communication that is conserved among bacterial, archaeal, and eukaryotic microbes. We speculate how microbes might use EV RNA to influence target cell gene expression or manipulate host immune responses.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.02.009
  • Within-Host Evolution of Human Influenza Virus
    • Authors: Katherine S. Xue; Louise H. Moncla; Trevor Bedford; Jesse D. Bloom
      Abstract: Publication date: Available online 10 March 2018
      Source:Trends in Microbiology
      Author(s): Katherine S. Xue, Louise H. Moncla, Trevor Bedford, Jesse D. Bloom
      The rapid global evolution of influenza virus begins with mutations that arise de novo in individual infections, but little is known about how evolution occurs within hosts. We review recent progress in understanding how and why influenza viruses evolve within human hosts. Advances in deep sequencing make it possible to measure within-host genetic diversity in both acute and chronic influenza infections. Factors like antigenic selection, antiviral treatment, tissue specificity, spatial structure, and multiplicity of infection may affect how influenza viruses evolve within human hosts. Studies of within-host evolution can contribute to our understanding of the evolutionary and epidemiological factors that shape influenza virus’s global evolution.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.02.007
  • Towards Understanding MCR-like Colistin Resistance
    • Authors: Jian Sun; Huimin Zhang; Ya-Hong Liu; Youjun Feng
      Abstract: Publication date: Available online 7 March 2018
      Source:Trends in Microbiology
      Author(s): Jian Sun, Huimin Zhang, Ya-Hong Liu, Youjun Feng
      Antibiotic resistance has become a global public health priority. Polymyxins, a family of cationic polypeptide antibiotics, act as a final line of refuge against severe infections by Gram-negative pathogens with pan-drug resistance. Unfortunately, this last-resort antibiotic has been challenged by the emergence and global spread of mobilized colistin resistance determinants (mcr). Given the fact that it has triggered extensive concerns worldwide, we present here an updated view of MCR-like colistin resistance. These studies provide a basic framework for understanding the molecular epidemiology and resistance mechanism of MCR-like genes. However, further large-scale epidemiology and functional studies are urgently needed to better understand the biology of this clinically important antibiotic resistance.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.02.006
  • Editorial Board and Contents
    • Abstract: Publication date: March 2018
      Source:Trends in Microbiology, Volume 26, Issue 3

      PubDate: 2018-04-15T04:01:03Z
  • Of Mice and Men....and Plants: Comparative Genomics of the Dual Lifestyles
           of Enteric Pathogens
    • Authors: Max Teplitski; Marcos de Moraes
      Abstract: Publication date: Available online 1 March 2018
      Source:Trends in Microbiology
      Author(s): Max Teplitski, Marcos de Moraes
      Outbreaks of gastrointestinal illness, linked to the consumption of fruits, vegetables, and sprouts, continue to capture the attention of the general public and scientists. The recurrence of these outbreaks, despite heightened producer and consumer awareness, combined with improved sanitation protocols and technology, can be explained by the hypothesis that enteric pathogens, such as nontyphoidal Salmonella spp. and enterovirulent Escherichia coli, have evolved to exploit plants as alternative hosts. This review explores the genetic and genomic context for this hypothesis. Even though gastroenteritis outbreaks associated with the consumption of produce have been caused by a limited number of strains or serovars, robust evidence in support of the polymorphism hypothesis is lacking. While some housekeeping genes with additional virulence functions in animal models contribute to the fitness of enterics within plants, canonical virulence determinants required for animal infections, such as the type III secretion system (T3SS) and effectors, by and large, are of little consequence in interactions with plants. Conversely, despite possessing some functions more commonly found in phytobacteria, human enteric pathogens do not appear to rely on the same strategies for plant colonization. Instead, it is likely that nontyphoidal Salmonella and enterovirulent E. coli have evolved a set of functions distinct from its virulence regulon and from those used by phytopathogens.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.02.008
  • Nitrospira
    • Authors: Holger Daims; Michael Wagner
      Abstract: Publication date: Available online 28 February 2018
      Source:Trends in Microbiology
      Author(s): Holger Daims, Michael Wagner
      In this infographic, the key metabolic functions of Nitrospira and the role that these bacteria play in nitrification and other processes in the environment is shown. Nitrospira plays pivotal roles in nitrification as an aerobic chemolithoautotrophic nitrite-oxidizing bacterium. These bacteria often occur in close association with ammonia-oxidizing bacteria or archaea that convert ammonia to nitrite, which is further oxidized to nitrate by Nitrospira. However, in ‘reciprocal feeding’ interactions, Nitrospira can also provide ammonia oxidizers with ammonia released from urea or cyanate, which is further nitrified as described above. Recently discovered Nitrospira members even catalyze both nitrification steps alone and are therefore called complete ammonia oxidizers or ‘comammox’ organisms. Some strains of Nitrospira utilize alternative substrates, such as H2 and formate, using oxygen or nitrate as terminal electron acceptor, and can exploit these energy sources concurrently with aerobic nitrite oxidation. This metabolic versatility enables Nitrospira to colonize a broad range of habitats and to sustain shifts in environmental conditions such as changing oxygen concentrations.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.02.001
  • The New Kid on the Block: A Specialized Secretion System during Bacterial
    • Authors: Cécile Morlot; Christopher D.A. Rodrigues
      Abstract: Publication date: Available online 20 February 2018
      Source:Trends in Microbiology
      Author(s): Cécile Morlot, Christopher D.A. Rodrigues
      The transport of proteins across the bacterial cell envelope is mediated by protein complexes called specialized secretion systems. These nanomachines exist in both Gram-positive and Gram-negative bacteria and have been categorized into different types based on their structural components and function. Interestingly, multiple studies suggest the existence of a protein complex in endospore-forming bacteria that appears to be a new type of specialized secretion system. This protein complex is called the SpoIIIA-SpoIIQ complex and is an exception to the categorical norm since it appears to be a hybrid composed of different parts from well-defined specialized secretion systems. Here we summarize and discuss the current understanding of this complex and its potential role as a specialized secretion system.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.01.001
  • Current Trends in Methylotrophy
    • Authors: Ludmila Chistoserdova; Marina G. Kalyuzhnaya
      Abstract: Publication date: Available online 19 February 2018
      Source:Trends in Microbiology
      Author(s): Ludmila Chistoserdova, Marina G. Kalyuzhnaya
      Methylotrophy is a field of study dealing with microorganisms capable of utilization of compounds devoid of carbon–carbon bonds (C1 compounds). In this review, we highlight several emerging trends in methylotrophy. First, we discuss the significance of the recent discovery of lanthanide-dependent alcohol dehydrogenases for understanding both the occurrence and the distribution of methylotrophy functions among bacteria, and then we discuss the newly appreciated role of lanthanides in biology. Next, we describe the detection of other methylotrophy pathways across novel bacterial taxa and insights into the evolution of methylotrophy. Further, data are presented on the occurrence and activity of aerobic methylotrophs in hypoxic and anoxic environments, questioning the prior assumptions on niche separation of aerobic and anaerobic methylotrophy. The concept of communal function in aerobic methane oxidation is also briefly discussed. Finally, we review recent research in engineering methylotrophs for biotechnological applications as well as recent progress in engineering synthetic methylotrophy.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.01.011
  • Phasevarions of Bacterial Pathogens: Methylomics Sheds New Light on Old
    • Authors: John M. Atack; Aimee Tan; Lauren O. Bakaletz; Michael P. Jennings; Kate L. Seib
      Abstract: Publication date: Available online 13 February 2018
      Source:Trends in Microbiology
      Author(s): John M. Atack, Aimee Tan, Lauren O. Bakaletz, Michael P. Jennings, Kate L. Seib
      A wide variety of bacterial pathogens express phase-variable DNA methyltransferases that control expression of multiple genes via epigenetic mechanisms. These randomly switching regulons – phasevarions – regulate genes involved in pathogenesis, host adaptation, and antibiotic resistance. Individual phase-variable genes can be identified in silico as they contain easily recognized features such as simple sequence repeats (SSRs) or inverted repeats (IRs) that mediate the random switching of expression. Conversely, phasevarion-controlled genes do not contain any easily identifiable features. The study of DNA methyltransferase specificity using Single-Molecule, Real-Time (SMRT) sequencing and methylome analysis has rapidly advanced the analysis of phasevarions by allowing methylomics to be combined with whole-transcriptome/proteome analysis to comprehensively characterize these systems in a number of important bacterial pathogens.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.01.008
  • Evolutionary Mechanisms Shaping the Maintenance of Antibiotic Resistance
    • Authors: Paulo Durão; Roberto Balbontín; Isabel Gordo
      Abstract: Publication date: Available online 10 February 2018
      Source:Trends in Microbiology
      Author(s): Paulo Durão, Roberto Balbontín, Isabel Gordo
      Antibiotics target essential cellular functions but bacteria can become resistant by acquiring either exogenous resistance genes or chromosomal mutations. Resistance mutations typically occur in genes encoding essential functions; these mutations are therefore generally detrimental in the absence of drugs. However, bacteria can reduce this handicap by acquiring additional mutations, known as compensatory mutations. Genetic interactions (epistasis) either with the background or between resistances (in multiresistant bacteria) dramatically affect the fitness cost of antibiotic resistance and its compensation, therefore shaping dissemination of antibiotic resistance mutations. This Review summarizes current knowledge on the evolutionary mechanisms influencing maintenance of resistance mediated by chromosomal mutations, focusing on their fitness cost, compensatory evolution, epistasis, and the effect of the environment on these processes.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2018.01.005
  • Antiviral Immunity and Virus-Mediated Antagonism in Disease Vector
    • Authors: Glady Hazitha Samuel; Zach N. Adelman; Kevin M. Myles
      Abstract: Publication date: Available online 31 January 2018
      Source:Trends in Microbiology
      Author(s): Glady Hazitha Samuel, Zach N. Adelman, Kevin M. Myles
      More than 100 pathogens, spanning multiple virus families, broadly termed ‘arthropod-borne viruses (arboviruses)’ have been associated with human and/or animal diseases. These viruses persist in nature through transmission cycles that involve alternating replication in susceptible vertebrate and invertebrate hosts. Collectively, these viruses are among the greatest burdens to global health, due to their widespread prevalence, and the severe morbidity and mortality they cause in human and animal hosts. Specific examples of mosquito-borne pathogens include Zika virus (ZIKV), West Nile virus (WNV), dengue virus serotypes 1–4 (DENV 1–4), Japanese encephalitis virus (JEV), yellow fever virus (YFV), chikungunya virus (CHIKV), and Rift Valley fever virus (RVFV). Interactions between arboviruses and the immune pathways of vertebrate hosts have been extensively reviewed. In this review we focus on the antiviral immune pathways present in mosquitoes. We also discuss mechanisms by which mosquito-borne viruses may antagonize antiviral pathways in disease vectors. Finally, we elaborate on the possibility that mosquito-borne viruses may be engaged in an evolutionary arms race with their invertebrate vector hosts, and the possible implications of this for understanding the transmission of mosquito-borne viruses.

      PubDate: 2018-04-15T04:01:03Z
      DOI: 10.1016/j.tim.2017.12.005
  • Do Archaea Need an Origin of Replication'
    • Authors: Lori M. Kelman; Zvi Kelman
      Abstract: Publication date: Available online 18 December 2017
      Source:Trends in Microbiology
      Author(s): Lori M. Kelman, Zvi Kelman
      Chromosomal DNA replication starts at a specific region called an origin of replication. Until recently, all organisms were thought to require origins to replicate their chromosomes. It was recently discovered that some archaeal species do not utilize origins of replication under laboratory growth conditions.

      PubDate: 2017-12-27T04:23:58Z
      DOI: 10.1016/j.tim.2017.12.001
  • End-in-Sight: Cell Polarization by the Polygamic Organizer PopZ
    • Authors: Matthieu Bergé; Patrick H. Viollier
      Abstract: Publication date: Available online 29 November 2017
      Source:Trends in Microbiology
      Author(s): Matthieu Bergé, Patrick H. Viollier
      Understanding how asymmetries in cellular constituents are achieved and how such positional information directs the construction of structures in a nonrandom fashion is a fundamental problem in cell biology. The recent identification of determinants that self-assemble into macromolecular complexes at the bacterial cell pole provides new insight into the underlying organizational principles in bacterial cells. Specifically, polarity studies in host-associated or free-living α-proteobacteria, a lineage of Gram-negative (diderm) bacteria, reveals that functional and cytological mono- and bipolarity is often conferred by the multivalent polar organizer PopZ, originally identified as a component of a polar chromosome anchor in the cell cycle model system Caulobacter crescentus. PopZ-dependent polarization appears to be widespread and also functional in obligate intracellular pathogens. Here, we discuss how PopZ polarization and the establishment of polar complexes occurs, and we detail the physiological roles of these complexes.

      PubDate: 2017-11-30T03:22:40Z
      DOI: 10.1016/j.tim.2017.11.007
  • Impact of HIV-1 Envelope Conformation on ADCC Responses
    • Authors: Jonathan Richard; Jérémie Prévost; Nirmin Alsahafi; Shilei Ding; Andrés Finzi
      Abstract: Publication date: Available online 20 November 2017
      Source:Trends in Microbiology
      Author(s): Jonathan Richard, Jérémie Prévost, Nirmin Alsahafi, Shilei Ding, Andrés Finzi
      HIV-1 envelope glycoproteins (Env) represent the only virus-specific antigen exposed at the surface of infected cells. In its unliganded form, Env from primary viruses samples a ‘closed’ conformation (State 1), which is preferentially recognized by broadly neutralizing antibodies (bNAbs). CD4 engagement drives Env into an intermediate ‘partially open’ (State 2) and then into the ‘open’ CD4-bound conformation (State 3). Emerging evidence suggests a link between Env conformation and Ab-dependent cellular cytotoxicity (ADCC). HIV-1-infected cells exposing Env in the CD4-bound conformation are susceptible to ADCC mediated by CD4-induced Abs and HIV+sera. Cells exposing State 1 Env are susceptible to ADCC mediated by bNAbs. Here, we discuss how Env conformation affects ADCC responses and in vitro measurements.

      PubDate: 2017-11-30T03:22:40Z
      DOI: 10.1016/j.tim.2017.10.007
  • Quorum-Sensing Systems as Targets for Antivirulence Therapy
    • Authors: Tom Defoirdt
      Abstract: Publication date: Available online 10 November 2017
      Source:Trends in Microbiology
      Author(s): Tom Defoirdt
      The development of novel therapies to control diseases caused by antibiotic-resistant pathogens is one of the major challenges we are currently facing. Many important plant, animal, and human pathogens regulate virulence by quorum sensing, bacterial cell-to-cell communication with small signal molecules. Consequently, a significant research effort is being undertaken to identify and use quorum-sensing-interfering agents in order to control diseases caused by these pathogens. In this review, an overview of our current knowledge of quorum-sensing systems of Gram-negative model pathogens is presented as well as the link with virulence of these pathogens, and recent advances and challenges in the development of quorum-sensing-interfering therapies are discussed.

      PubDate: 2017-11-19T02:50:28Z
      DOI: 10.1016/j.tim.2017.10.005
  • A Tale of Two Viruses: Does Heterologous Flavivirus Immunity Enhance Zika
    • Authors: Carlos A. Sariol; Mauricio L. Nogueira; Nikos Vasilakis
      Abstract: Publication date: Available online 6 November 2017
      Source:Trends in Microbiology
      Author(s): Carlos A. Sariol, Mauricio L. Nogueira, Nikos Vasilakis
      The rise of Zika virus (ZIKV) and its unusual clinical manifestations provided ground for speculative debate. The clinical severity of secondary dengue virus (DENV) infections is associated with antibody-dependent enhancement (ADE), and it was recently suggested that previous exposure to DENV may worsen ZIKV clinical outcomes. In this Opinion article we analyze the relationship among different flaviviruses and ADE. We discuss new evidence obtained in non-human primates and human cohorts demonstrating that there is no correlation to ADE when ZIKV infection occurs in the presence of pre-existing DENV immunity. We propose a redefinition of ADE in the context of complex immunological flavivirus interactions to provide a more objective perspective when translating in vitro or in vivo observations into the clinical setting.

      PubDate: 2017-11-19T02:50:28Z
      DOI: 10.1016/j.tim.2017.10.004
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