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MICROBIOLOGY (254 journals)                  1 2     

Showing 1 - 0 of 0 Journals sorted alphabetically
Acta Microbiologica et Immunologica Hungarica     Full-text available via subscription   (Followers: 5)
Addiction Genetics     Open Access   (Followers: 5)
Advances in Applied Microbiology     Full-text available via subscription   (Followers: 21)
Advances in Microbiology     Open Access   (Followers: 19)
Advances in Molecular Imaging     Open Access   (Followers: 1)
African Journal of Clinical and Experimental Microbiology     Open Access  
African Journal of Microbiology Research     Open Access   (Followers: 1)
Algorithms for Molecular Biology     Open Access   (Followers: 4)
American Journal of Infectious Diseases and Microbiology     Open Access   (Followers: 18)
American Journal of Microbiological Research     Open Access   (Followers: 2)
American Journal of Microbiology     Open Access   (Followers: 14)
American Journal of Molecular Biology     Open Access   (Followers: 2)
American Journal of Stem Cell Research     Open Access   (Followers: 3)
Annals of Clinical Microbiology and Antimicrobials     Open Access   (Followers: 7)
Annals of Microbiology     Hybrid Journal   (Followers: 9)
Annual Review of Microbiology     Full-text available via subscription   (Followers: 36)
Antimicrobial Agents and Chemotherapy     Hybrid Journal   (Followers: 22)
Antiviral Research     Hybrid Journal   (Followers: 7)
Applied and Environmental Microbiology     Hybrid Journal   (Followers: 43)
Applied Biochemistry and Microbiology     Hybrid Journal   (Followers: 17)
Applied Microbiology and Biotechnology     Hybrid Journal   (Followers: 61)
Aquatic Microbial Ecology     Hybrid Journal   (Followers: 3)
Archives of Microbiology     Hybrid Journal   (Followers: 8)
Avicenna Journal of Clinical Microbiology and Infection     Open Access   (Followers: 1)
Bangladesh Journal of Medical Microbiology     Open Access   (Followers: 1)
Beneficial Microbes     Full-text available via subscription   (Followers: 2)
Bio-Research     Full-text available via subscription   (Followers: 1)
BioArchitecture     Full-text available via subscription  
Bioethanol     Open Access  
Biomaterials Science     Full-text available via subscription   (Followers: 8)
BioMolecular Concepts     Hybrid Journal   (Followers: 2)
Biomolecular Detection and Quantification     Open Access  
Biomolecules     Open Access   (Followers: 1)
Biotechnology and Molecular Biology Reviews     Open Access   (Followers: 1)
BMC Microbiology     Open Access   (Followers: 10)
Brazilian Journal of Microbiology     Open Access   (Followers: 2)
Canadian Journal of Infectious Diseases and Medical Microbiology     Open Access   (Followers: 3)
Canadian Journal of Microbiology     Full-text available via subscription   (Followers: 4)
Cell Biology : Research & Therapy     Hybrid Journal   (Followers: 3)
Cell Host & Microbe     Full-text available via subscription   (Followers: 15)
Cell Medicine     Open Access   (Followers: 3)
Cell Regeneration     Open Access   (Followers: 1)
Cell Stem Cell     Full-text available via subscription   (Followers: 32)
CellBio     Open Access  
Cells     Open Access   (Followers: 2)
Cellular & Molecular Immunology     Hybrid Journal   (Followers: 12)
Cellular and Molecular Biology Letters     Open Access   (Followers: 1)
Cellular and Molecular Life Sciences (CMLS)     Hybrid Journal   (Followers: 7)
Cellular Microbiology     Hybrid Journal   (Followers: 7)
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: 20)
Clinical Microbiology Newsletter     Hybrid Journal   (Followers: 6)
Clinical Microbiology Reviews     Hybrid Journal   (Followers: 18)
Comparative Immunology, Microbiology and Infectious Diseases     Hybrid Journal   (Followers: 11)
Computational Molecular Bioscience     Open Access   (Followers: 1)
Critical Reviews in Microbiology     Hybrid Journal   (Followers: 11)
Current Clinical Microbiology Reports     Hybrid Journal   (Followers: 1)
Current Issues in Molecular Biology     Open Access   (Followers: 2)
Current Microbiology     Hybrid Journal   (Followers: 11)
Current Molecular Biology Reports     Hybrid Journal   (Followers: 1)
Current Molecular Imaging     Hybrid Journal  
Current Opinion in Microbiology     Hybrid Journal   (Followers: 30)
Current Tissue Engineering     Hybrid Journal   (Followers: 2)
Current Topics in Microbiology and Immunology     Hybrid Journal   (Followers: 11)
Diagnostic Microbiology and Infectious Disease     Hybrid Journal   (Followers: 8)
DNA Barcodes     Open Access  
Egyptian Journal of Biochemistry and Molecular Biology     Full-text available via subscription  
Emerging Microbes & Infections     Open Access   (Followers: 3)
Environmental Microbiology     Hybrid Journal   (Followers: 15)
Environmental Microbiology Reports     Hybrid Journal   (Followers: 4)
Enzyme and Microbial Technology     Hybrid Journal   (Followers: 14)
Epigenetics of Degenerative Diseases     Open Access   (Followers: 5)
European Journal of Clinical Microbiology & Infectious Diseases     Hybrid Journal   (Followers: 18)
European Journal of Microbiology and Immunology     Open Access   (Followers: 8)
Experimental and Molecular Pathology     Hybrid Journal   (Followers: 4)
Experimental Cell Research     Hybrid Journal   (Followers: 7)
Fems Microbiology Ecology     Hybrid Journal   (Followers: 8)
Fems Microbiology Letters     Hybrid Journal   (Followers: 19)
Fems Microbiology Reviews     Hybrid Journal   (Followers: 24)
Fermentation     Open Access   (Followers: 1)
Folia Histochemica et Cytobiologica     Open Access  
Folia Microbiologica     Hybrid Journal   (Followers: 1)
Food Microbiology     Hybrid Journal   (Followers: 16)
Frontiers in Cell and Developmental Biology     Open Access   (Followers: 3)
Frontiers in Cellular and Infection Microbiology     Open Access   (Followers: 3)
Frontiers in Cellular Neuroscience     Open Access   (Followers: 8)
Frontiers in Microbiology     Open Access   (Followers: 9)
Frontiers in Molecular Neuroscience     Open Access   (Followers: 4)
Future Microbiology     Hybrid Journal   (Followers: 4)
Future Virology     Hybrid Journal   (Followers: 7)
Gene Expression     Full-text available via subscription  
Genetica si Biologie Moleculara     Open Access  
Genetics and Molecular Research     Open Access   (Followers: 4)
Geomicrobiology Journal     Hybrid Journal   (Followers: 2)
Gut Microbes     Full-text available via subscription   (Followers: 8)
IAWA Journal     Hybrid Journal  
Indian Journal of Microbiology     Hybrid Journal   (Followers: 2)
Indian Journal of Pathology and Microbiology     Open Access   (Followers: 1)
Infection Ecology & Epidemiology     Open Access   (Followers: 3)
Inside the Cell     Open Access  
International Journal of Antimicrobial Agents     Hybrid Journal   (Followers: 7)
International Journal of Bacteriology     Open Access  
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: 12)
International Journal of Genetics and Molecular Biology     Open Access  
International Journal of Infection and Microbiology     Open Access   (Followers: 1)
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: 3)
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: 2)
Journal of Microbial & Biochemical Technology     Open Access   (Followers: 2)
Journal of Applied Biology & Biotechnology     Open Access   (Followers: 2)
Journal of Applied Microbiology     Hybrid Journal   (Followers: 14)
Journal of Bacteriology     Hybrid Journal   (Followers: 29)
Journal of Basic Microbiology     Hybrid Journal   (Followers: 3)
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: 1)
Journal of Brewing and Distilling     Open Access   (Followers: 1)
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: 30)
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: 4)
Journal of General and Molecular Virology     Open Access  
Journal of Genes and Cells     Open Access  
Journal of Global Antimicrobial Resistance     Hybrid Journal   (Followers: 2)
Journal of Industrial Microbiology and Biotechnology     Hybrid Journal   (Followers: 15)
Journal of Medical Microbiology     Full-text available via subscription   (Followers: 4)
Journal of Microbiological Methods     Hybrid Journal   (Followers: 2)
Journal of Microbiology     Hybrid Journal   (Followers: 8)
Journal of Microbiology and Antimicrobials     Open Access   (Followers: 2)
Journal of Microbiology Research     Open Access   (Followers: 4)
Journal of Micropalaeontology     Hybrid Journal   (Followers: 7)
Journal of Molecular Biochemistry     Open Access   (Followers: 3)
Journal of Molecular Biology Research     Open Access   (Followers: 3)
Journal of Molecular Microbiology and Biotechnology     Full-text available via subscription   (Followers: 13)
Journal of Molecular Psychiatry     Open Access   (Followers: 9)
Journal of Morphology     Hybrid Journal   (Followers: 5)
Journal of Pharmacy & Bioresources     Full-text available via subscription   (Followers: 3)
Journal of Plant Molecular Biology and Biotechnology     Open Access   (Followers: 8)
Journal of Plant Pathology & Microbiology     Open Access   (Followers: 1)
Journal of Proteome Science and Computational Biology     Open Access  
Journal of Rapid Methods and Automation In Microbiology     Hybrid Journal   (Followers: 5)
Journal of Regenerative Medicine and Tissue Engineering     Open Access   (Followers: 3)
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: 1)
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  
Medical Mycology     Open Access   (Followers: 5)
Memórias do Instituto Oswaldo Cruz     Open Access  
Methods in Molecular Biology     Hybrid Journal   (Followers: 24)
Microbes and Health     Open Access   (Followers: 1)
Microbes and Infection     Full-text available via subscription   (Followers: 5)
Microbial Biotechnology     Open Access   (Followers: 8)
Microbial Cell Factories     Open Access   (Followers: 7)
Microbial Drug Resistance     Hybrid Journal   (Followers: 4)
Microbial Ecology     Hybrid Journal   (Followers: 8)
Microbial Ecology in Health and Disease     Open Access  
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: 13)
Microbiology (SGM)     Full-text available via subscription   (Followers: 17)
Microbiology and Immunology     Hybrid Journal   (Followers: 10)
Microbiology and Molecular Biology Reviews     Hybrid Journal   (Followers: 23)
Microbiology Australia     Hybrid Journal  
Microbiology Discovery     Open Access   (Followers: 1)
Microbiology Indonesia     Open Access  
Microbiology Research     Open Access   (Followers: 7)
MicrobiologyOpen     Open Access   (Followers: 2)
Microbiome     Hybrid Journal   (Followers: 7)
Microbiome Science and Medicine     Open Access   (Followers: 2)
Microorganisms     Open Access   (Followers: 2)
MicroRNA     Hybrid Journal   (Followers: 1)
Molecular and Cellular Therapies     Open Access  
Molecular Biology and Genetic Engineering     Open Access   (Followers: 1)
Molecular Biology Research Communications     Open Access   (Followers: 1)
Molecular Genetics and Metabolism Reports     Open Access   (Followers: 2)
Molecular Genetics, Microbiology and Virology     Hybrid Journal   (Followers: 6)
Molecular Imaging     Open Access  
Molecular Imaging and Biology     Hybrid Journal   (Followers: 2)
Molecular Medicine     Open Access   (Followers: 3)
Molecular Medicine Reports     Full-text available via subscription   (Followers: 6)
Molecular Microbiology     Hybrid Journal   (Followers: 30)
Molecular Oral Microbiology     Partially Free   (Followers: 3)

        1 2     

Journal Cover Trends in Microbiology
  [SJR: 5.285]   [H-I: 150]   [34 followers]  Follow
   Full-text available via subscription Subscription journal  (Not entitled to full-text)
   ISSN (Print) 0966-842X
   Published by Elsevier Homepage  [3041 journals]
  • Lactobacillus iners: Friend or Foe?
    • Authors: Mariya I. Petrova; Gregor Reid; Mario Vaneechoutte; Sarah Lebeer
      Pages: 182 - 191
      Abstract: Publication date: March 2017
      Source:Trends in Microbiology, Volume 25, Issue 3
      Author(s): Mariya I. Petrova, Gregor Reid, Mario Vaneechoutte, Sarah Lebeer
      The vaginal microbial community is typically characterized by abundant lactobacilli. Lactobacillus iners, a fairly recently detected species, is frequently present in the vaginal niche. However, the role of this species in vaginal health is unclear, since it can be detected in normal conditions as well as during vaginal dysbiosis, such as bacterial vaginosis, a condition characterized by an abnormal increase in bacterial diversity and lack of typical lactobacilli. Compared to other Lactobacillus species, L. iners has more complex nutritional requirements and a Gram-variable morphology. L. iners has an unusually small genome (ca. 1 Mbp), indicative of a symbiotic or parasitic lifestyle, in contrast to other lactobacilli that show niche flexibility and genomes of up to 3–4 Mbp. The presence of specific L. iners genes, such as those encoding iron–sulfur proteins and unique σ-factors, reflects a high degree of niche specification. The genome of L. iners strains also encodes inerolysin, a pore-forming toxin related to vaginolysin of Gardnerella vaginalis. Possibly, this organism may have clonal variants that in some cases promote a healthy vagina, and in other cases are associated with dysbiosis and disease. Future research should examine this friend or foe relationship with the host.

      PubDate: 2017-03-05T14:42:40Z
      DOI: 10.1016/j.tim.2016.11.007
  • The Enigmatic Esx Proteins: Looking Beyond Mycobacteria
    • Authors: Meera Unnikrishnan; Chrystala Constantinidou; Tracy Palmer; Mark J. Pallen
      Pages: 192 - 204
      Abstract: Publication date: March 2017
      Source:Trends in Microbiology, Volume 25, Issue 3
      Author(s): Meera Unnikrishnan, Chrystala Constantinidou, Tracy Palmer, Mark J. Pallen
      Bacteria export proteins across membranes using a range of transport machineries. Type VII secretion systems (T7SSs), originally described in mycobacteria, are now known to be widespread across diverse bacterial phyla. Recent studies have characterized secretion components and mechanisms of type VII secretion in pathogenic and environmental bacteria. A variety of functions have been attributed to T7SS substrates, including interactions with eukaryotes and with other bacteria. Here, we evaluate the growing body of knowledge on T7SSs, with focus on the nonmycobacterial systems, reviewing their phylogenetic distribution, structure and function in diverse settings.

      PubDate: 2017-03-05T14:42:40Z
      DOI: 10.1016/j.tim.2016.11.004
  • Disentangling Interactions in the Microbiome: A Network Perspective
    • Authors: Mehdi Layeghifard; David M. Hwang; David S. Guttman
      Pages: 217 - 228
      Abstract: Publication date: March 2017
      Source:Trends in Microbiology, Volume 25, Issue 3
      Author(s): Mehdi Layeghifard, David M. Hwang, David S. Guttman
      Microbiota are now widely recognized as being central players in the health of all organisms and ecosystems, and subsequently have been the subject of intense study. However, analyzing and converting microbiome data into meaningful biological insights remain very challenging. In this review, we highlight recent advances in network theory and their applicability to microbiome research. We discuss emerging graph theoretical concepts and approaches used in other research disciplines and demonstrate how they are well suited for enhancing our understanding of the higher-order interactions that occur within microbiomes. Network-based analytical approaches have the potential to help disentangle complex polymicrobial and microbe–host interactions, and thereby further the applicability of microbiome research to personalized medicine, public health, environmental and industrial applications, and agriculture.

      PubDate: 2017-03-05T14:42:40Z
      DOI: 10.1016/j.tim.2016.11.008
  • Protecting from Envelope Stress: Variations on the Phage-Shock-Protein
    • Authors: Riccardo Manganelli; Maria Laura Gennaro
      First page: 242
      Abstract: Publication date: March 2017
      Source:Trends in Microbiology, Volume 25, Issue 3
      Author(s): Riccardo Manganelli, Maria Laura Gennaro
      During envelope stress, critical inner-membrane functions are preserved by the phage-shock-protein (Psp) system, a stress response that emerged from work with Escherichia coli and other Gram-negative bacteria. Reciprocal regulatory interactions and multiple effector functions are well documented in these organisms. Searches for the Psp system across phyla reveal conservation of only one protein, PspA. However, examination of Firmicutes and Actinobacteria reveals that PspA orthologs associate with non-orthologous regulatory and effector proteins retaining functions similar to those in Gram-negative counterparts. Conservation across phyla emphasizes the long-standing importance of the Psp system in prokaryotes, while inter- and intra-phyla variations within the system indicate adaptation to different cell envelope structures, bacterial lifestyles, and/or bacterial morphogenetic strategies.

      PubDate: 2017-03-05T14:42:40Z
      DOI: 10.1016/j.tim.2016.11.010
  • Rethinking Diet to Aid Human–Microbe Symbiosis
    • Authors: Muriel Derrien; Patrick Veiga
      Pages: 100 - 112
      Abstract: Publication date: February 2017
      Source:Trends in Microbiology, Volume 25, Issue 2
      Author(s): Muriel Derrien, Patrick Veiga
      The spread of the Western lifestyle has been accompanied by microbial changes thought to underlie the emergence of chronic, nontransmissible, immune-related diseases. The past decade has seen the unprecedented development of therapies for ‘replenishing’ the microbiota of sick individuals. However, functional and ecological solutions helping the host and the gut microbiota to cope with the ecological stressors of modern life are still lacking. In this review, we discuss how recent advances in gut microbiome science are leading to the identification of microbe-derived and health-relevant metabolites. These molecules will guide the selection of the next-generation of probiotics and dietary recommendations, which should also take the resident gut microbiota into account, to optimise efficacy. These solutions for maintaining a well-functioning gut ecosystem and promoting good health should be customised, palatable, and as widely accessible as possible.

      PubDate: 2017-01-30T06:04:36Z
      DOI: 10.1016/j.tim.2016.09.011
  • Meningococcal Biofilm Formation: Let's Stick Together
    • Authors: Jesús Arenas; Jan Tommassen
      Pages: 113 - 124
      Abstract: Publication date: February 2017
      Source:Trends in Microbiology, Volume 25, Issue 2
      Author(s): Jesús Arenas, Jan Tommassen
      Extracellular DNA (eDNA) is an essential constituent of the extracellular matrix of biofilms of many microorganisms. In spite of many studies, it has long remained unclear how exactly eDNA exerts its role in biofilm formation. Here, we describe recent advances that have been made in understanding biofilm formation in the human pathogen Neisseria meningitidis. Several cell-surface-exposed proteins have been identified that bind DNA and other negatively charged polymers, such as heparin, by electrostatic interactions. By virtue of these proteins, eDNA can act as an adhesive that binds the bacteria together. We provide examples that indicate that the mechanism of binding eDNA via DNA/heparin-binding proteins is a conserved feature in biofilms of many different microorganisms, including fungi.

      PubDate: 2017-01-30T06:04:36Z
      DOI: 10.1016/j.tim.2016.09.005
  • Chlamydial Plasmid-Dependent Pathogenicity
    • Authors: Guangming Zhong
      Pages: 141 - 152
      Abstract: Publication date: February 2017
      Source:Trends in Microbiology, Volume 25, Issue 2
      Author(s): Guangming Zhong
      Most Chlamydia species carry a 7.5kb plasmid encoding eight open reading frames conventionally called plasmid glycoproteins 1–8 or pGP1–8. Although the plasmid is not critical for chlamydial growth in vitro, its role in chlamydial pathogenesis is clearly demonstrated in the genital tracts of mice infected with Chlamydia muridarum, a model for investigating the human pathogen Chlamydia trachomatis. Plasmid-free C. trachomatis is also attenuated in both the mouse genital tract and nonhuman primate ocular tissue. Deficiency in pGP3 alone, which is regulated by pGP4, largely reproduced the in vivo but not in vitro phenotypes of the plasmid-free organisms, suggesting that pGP3 is a key in vivo virulence factor. The positive and negative regulations of some chromosomal genes by pGP4 and pGP5, respectively, may allow the plasmid to promote chlamydial adaptation to varied animal tissue environments. The focus of this review is to summarize the progress on the pathogenic functions of the plasmid-encoded open reading frames, which may motivate further investigation of the molecular mechanisms of chlamydial pathogenicity and development of medical utility of the chlamydial plasmid system.

      PubDate: 2017-01-30T06:04:36Z
      DOI: 10.1016/j.tim.2016.09.006
  • Architecture of a Species: Phylogenomics of Staphylococcus aureus
    • Authors: Paul J. Planet; Apurva Narechania; Liang Chen; Barun Mathema; Sam Boundy; Gordon Archer; Barry Kreiswirth
      Pages: 153 - 166
      Abstract: Publication date: February 2017
      Source:Trends in Microbiology, Volume 25, Issue 2
      Author(s): Paul J. Planet, Apurva Narechania, Liang Chen, Barun Mathema, Sam Boundy, Gordon Archer, Barry Kreiswirth
      A deluge of whole-genome sequencing has begun to give insights into the patterns and processes of microbial evolution, but genome sequences have accrued in a haphazard manner, with biased sampling of natural variation that is driven largely by medical and epidemiological priorities. For instance, there is a strong bias for sequencing epidemic lineages of methicillin-resistant Staphylococcus aureus (MRSA) over sensitive isolates (methicillin-sensitive S. aureus: MSSA). As more diverse genomes are sequenced the emerging picture is of a highly subdivided species with a handful of relatively clonal groups (complexes) that, at any given moment, dominate in particular geographical regions. The establishment of hegemony of particular clones appears to be a dynamic process of successive waves of replacement of the previously dominant clone. Here we review the phylogenomic structure of a diverse range of S. aureus, including both MRSA and MSSA. We consider the utility of the concept of the ‘core’ genome and the impact of recombination and horizontal transfer. We argue that whole-genome surveillance of S. aureus populations could lead to better forecasting of antibiotic resistance and virulence of emerging clones, and a better understanding of the elusive biological factors that determine repeated strain replacement.

      PubDate: 2017-01-30T06:04:36Z
      DOI: 10.1016/j.tim.2016.09.009
  • Are CDI Systems Multicolored, Facultative, Helping Greenbeards?
    • Authors: Elizabeth S. Danka; Erin C. Garcia; Peggy A. Cotter
      Abstract: Publication date: Available online 9 March 2017
      Source:Trends in Microbiology
      Author(s): Elizabeth S. Danka, Erin C. Garcia, Peggy A. Cotter
      Competitive and cooperative interactions between organisms, including bacteria, can significantly impact the composition of a community and the fitness of its members, as well as the fitness of their hosts when communities are living on or within other organisms. Understanding the underlying mechanisms is critical to the development of strategies to control microbiological communities that impact animal and plant health and also for understanding the evolution of social behaviors, which has been challenging for evolutionary biologists. Contact-dependent growth inhibition (CDI) is a phenomenon defined by the delivery of a protein toxin to the cytoplasm of neighboring bacteria upon cell–cell contact, resulting in growth inhibition or death unless a specific immunity protein is present. CDI was first described based on observations of interbacterial killing and has been assumed to function primarily as a means of eliminating competitor cells. However, recent molecular evidence indicates that multiple levels of specificity restrict CDI toxin delivery and activity to the same bacterial strain, and that CDI system proteins can mediate cooperative behaviors among ‘self’ cells, a phenomenon called contact-dependent signaling (CDS). Here we review these recent findings and discuss potential biological and evolutionary implications of CDI system-mediated interbacterial competition and cooperation.

      PubDate: 2017-03-10T15:45:46Z
      DOI: 10.1016/j.tim.2017.02.008
  • Interferon-I: The Pièce de Résistance of HIV-1 Transmission?
    • Authors: Damien C. Tully; Daniel T. Claiborne; Todd M. Allen
      Abstract: Publication date: Available online 9 March 2017
      Source:Trends in Microbiology
      Author(s): Damien C. Tully, Daniel T. Claiborne, Todd M. Allen
      Despite the extensive viral quasispecies that develops in an individual during the course of HIV-1 infection, transmission is typically established by a single donor viral variant. Recent studies now provide insight into the phenotypic properties influencing this selection process at transmission, including the contribution of resistance to type I interferons.

      PubDate: 2017-03-10T15:45:46Z
      DOI: 10.1016/j.tim.2017.02.010
  • Bioengineered 3D Models for Studying Human Cell–Tuberculosis
    • Authors: Sulayman Benmerzoug; Valerie F.J. Quesniaux
      Abstract: Publication date: Available online 8 March 2017
      Source:Trends in Microbiology
      Author(s): Sulayman Benmerzoug, Valerie F.J. Quesniaux
      In vivo animal models have intrinsic limitations for studying relationships between tuberculosis and its host and there is a need for alternative, in vitro cellular models. A microsphere-based 3D in vitro culture system of Mycobacterium tuberculosis-infected human blood mononuclear cells was reported to address specific aspects of host–pathogen interactions.

      PubDate: 2017-03-10T15:45:46Z
      DOI: 10.1016/j.tim.2017.02.009
  • Dual Immunity Concomitantly Suppresses HIV-1 Progression
    • Authors: Huma Qureshi; Jayanta Bhattacharya
      Abstract: Publication date: Available online 8 March 2017
      Source:Trends in Microbiology
      Author(s): Huma Qureshi, Jayanta Bhattacharya
      Broadly neutralizing antibodies (bnAbs) elicited in HIV-1+ elite neutralizers typically are unable to reduce viremia in the same individuals from whom they are isolated. A recent study reports the development of bnAbs in an elite controller that, along with the help of T cells, were associated with restricting HIV-1 progression.

      PubDate: 2017-03-10T15:45:46Z
      DOI: 10.1016/j.tim.2017.02.011
  • Genome Surfing As Driver of Microbial Genomic Diversity
    • Authors: Mallory J. Choudoir; Kevin Panke-Buisse; Cheryl P. Andam; Daniel H. Buckley
      Abstract: Publication date: Available online 7 March 2017
      Source:Trends in Microbiology
      Author(s): Mallory J. Choudoir, Kevin Panke-Buisse, Cheryl P. Andam, Daniel H. Buckley
      Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can result in genome surfing, a mechanism that can cause widespread increase in the pan-genome frequency of genes acquired by horizontal gene exchange. We explain that patterns of genetic diversity within Streptomyces are consistent with genome surfing, and we describe several predictions for testing this hypothesis both in Streptomyces and in other microorganisms.

      PubDate: 2017-03-10T15:45:46Z
      DOI: 10.1016/j.tim.2017.02.006
  • Critical Streptococcus suis Virulence Factors: Are They All Really
    • Authors: Mariela Segura; Nahuel Fittipaldi; Cynthia Calzas; Marcelo Gottschalk
      Abstract: Publication date: Available online 6 March 2017
      Source:Trends in Microbiology
      Author(s): Mariela Segura, Nahuel Fittipaldi, Cynthia Calzas, Marcelo Gottschalk
      Streptococcus suis is an important swine pathogen that can be transmitted to humans by contact with diseased animals or contaminated raw pork products. This pathogen possesses a coat of capsular polysaccharide (CPS) that confers protection against the immune system. Yet, the CPS is not the only virulence factor enabling this bacterium to successfully colonize, invade, and disseminate in its host leading to severe systemic diseases such as meningitis and toxic shock-like syndrome. Indeed, recent research developments, cautiously inventoried in this review, have revealed over 100 ‘putative virulence factors or traits’ (surface-associated or secreted components, regulatory genes or metabolic pathways), of which at least 37 have been claimed as being ‘critical’ for virulence. In this review we discuss the current contradictions and controversies raised by this explosion of virulence factors and the future directions that may be conceived to advance and enlighten research on S. suis pathogenesis.

      PubDate: 2017-03-10T15:45:46Z
      DOI: 10.1016/j.tim.2017.02.005
  • Collective Infectious Units in Viruses
    • Authors: Rafael
      Abstract: Publication date: Available online 3 March 2017
      Source:Trends in Microbiology
      Author(s): Rafael Sanjuán
      Increasing evidence indicates that viruses do not simply propagate as independent virions among cells, organs, and hosts. Instead, viral spread is often mediated by structures that simultaneously transport groups of viral genomes, such as polyploid virions, aggregates of virions, virion-containing proteinaceous structures, secreted lipid vesicles, and virus-induced cell–cell contacts. These structures increase the multiplicity of infection, independently of viral population density and transmission bottlenecks. Collective infectious units may contribute to the maintenance of viral genetic diversity, and could have implications for the evolution of social-like virus–virus interactions. These may include various forms of cooperation such as immunity evasion, genetic complementation, division of labor, and relaxation of fitness trade-offs, but also noncooperative interactions such as negative dominance and interference, potentially leading to conflict.

      PubDate: 2017-03-05T14:42:40Z
  • KSHV microRNAs: Tricks of the Devil
    • Authors: Jie Qin; Wan Li; Shou-Jiang Gao; Chun Lu
      Abstract: Publication date: Available online 2 March 2017
      Source:Trends in Microbiology
      Author(s): Jie Qin, Wan Li, Shou-Jiang Gao, Chun Lu
      Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiologic agent of Kaposi’s sarcoma (KS), a vascular tumor frequently found in immunodeficient individuals. KSHV encodes 12 pre-microRNAs (pre-miRNAs), which are processed into 25 mature microRNAs (miRNAs). KSHV miRNAs maintain KSHV latency, enhance angiogenesis and dissemination of the infected cells, and interfere with the host immune system by regulating viral and cellular gene expression, ultimately contributing to KS development. In this review, we briefly introduce the biogenesis of miRNAs and then describe the recent advances in defining the roles and mechanisms of action of KSHV miRNAs in KS development.

      PubDate: 2017-03-05T14:42:40Z
      DOI: 10.1016/j.tim.2017.02.002
  • Editorial Board and Contents
    • Abstract: Publication date: March 2017
      Source:Trends in Microbiology, Volume 25, Issue 3

      PubDate: 2017-03-05T14:42:40Z
  • Biofilms: Microbial Cities Wherein Flow Shapes Competition
    • Authors: Su Chuen Chew; Liang Yang
      Abstract: Publication date: Available online 1 March 2017
      Source:Trends in Microbiology
      Author(s): Su Chuen Chew, Liang Yang
      The phenotypic diversity in biofilms allows bacteria to adapt to changing environmental conditions. Stochastic gene expression and structural differentiation are believed to confer phenotypic diversity. However, two recent publications demonstrate how hydrodynamic flow and substrate topography can also alter the competitive outcomes of different bacterial phenotypes, increasing biofilm phenotypic variation.

      PubDate: 2017-03-05T14:42:40Z
      DOI: 10.1016/j.tim.2017.02.007
  • Streptomyces Exploration: Competition, Volatile Communication and New
           Bacterial Behaviours
    • Authors: Stephanie E. Jones; Marie A. Elliot
      Abstract: Publication date: Available online 27 February 2017
      Source:Trends in Microbiology
      Author(s): Stephanie E. Jones, Marie A. Elliot
      Streptomyces bacteria are prolific producers of specialized metabolites, and have a well studied, complex life cycle. Recent work has revealed a new type of Streptomyces growth termed ‘exploration’ – so named for the ability of explorer cells to rapidly traverse solid surfaces. Streptomyces exploration is stimulated by fungal interactions, and is associated with the production of an alkaline volatile organic compound (VOC) capable of inducing exploration by other streptomycetes. Here, we examine Streptomyces exploration from the perspectives of interkingdom interactions, pH-induced morphological switches, and VOC-mediated communication. The phenotypic diversity that can be revealed through microbial interactions and VOC exposure is providing us with insight into novel modes of microbial development, and an opportunity to exploit VOCs to stimulate desired microbial behaviours.

      PubDate: 2017-03-05T14:42:40Z
      DOI: 10.1016/j.tim.2017.02.001
  • Regulation Mechanisms of Viral IRES-Driven Translation
    • Authors: Kuo-Ming Lee; Chi-Jene Chen; Shin-Ru Shih
      Abstract: Publication date: Available online 24 February 2017
      Source:Trends in Microbiology
      Author(s): Kuo-Ming Lee, Chi-Jene Chen, Shin-Ru Shih
      Internal ribosome entry sites (IRESs) can be found in the mRNA of many viruses as well as in cellular genes involved in the stress response, cell cycle, and apoptosis. IRES-mediated translation can occur when dominant cap-dependent translation is inhibited, and viruses can take advantage of this to subvert host translation machinery. In this review, we focus on the four major types of IRES identified in RNA viruses, and outline their distinct structural properties and requirements of translational factors. We further discuss auxiliary host factors known as IRES trans-acting factors (ITAFs), which are involved in the modulation of optimal IRES activity. Currently known strategies employed by viruses to harness ITAFs and regulate IRES activity are also highlighted.

      PubDate: 2017-02-26T12:44:28Z
      DOI: 10.1016/j.tim.2017.01.010
  • Picking the Survivor! CRISPR Reveals HIV Dependency Factors
    • Authors: Kerstin Schott; Renate König
      Abstract: Publication date: Available online 21 February 2017
      Source:Trends in Microbiology
      Author(s): Kerstin Schott, Renate König
      A new study employs genome-wide loss-of-function CRISPR/Cas9 screening to identify three novel factors for HIV-1 entry. The factors represent promising targets for therapeutics as they are essential for HIV-1 infection, but dispensable for cell survival. The involved pathways were validated in primary CD4+ T cells, target cells for HIV-1.

      PubDate: 2017-02-26T12:44:28Z
      DOI: 10.1016/j.tim.2017.02.004
  • The Secrets of Acinetobacter Secretion
    • Authors: Brent S. Weber; Rachel L. Kinsella; Christian M. Harding; Mario F. Feldman
      Abstract: Publication date: Available online 16 February 2017
      Source:Trends in Microbiology
      Author(s): Brent S. Weber, Rachel L. Kinsella, Christian M. Harding, Mario F. Feldman
      Infections caused by the bacterial pathogen Acinetobacter baumannii are a mounting concern for healthcare practitioners as widespread antibiotic resistance continues to limit therapeutic treatment options. The biological processes used by A. baumannii to cause disease are not well defined, but recent research has indicated that secreted proteins may play a major role. A variety of mechanisms have now been shown to contribute to protein secretion by A. baumannii and other pathogenic species of Acinetobacter, including a type II secretion system (T2SS), a type VI secretion system (T6SS), autotransporter, and outer membrane vesicles (OMVs). In this review, we summarize the current knowledge of secretion systems in Acinetobacter species, and highlight their unique aspects that contribute to the pathogenicity and persistence of these emerging pathogens.

      PubDate: 2017-02-19T09:44:38Z
      DOI: 10.1016/j.tim.2017.01.005
  • Spatial and Temporal Control of Evolution through
           Replication–Transcription Conflicts
    • Authors: Houra Merrikh
      Abstract: Publication date: Available online 16 February 2017
      Source:Trends in Microbiology
      Author(s): Houra Merrikh
      Evolution could potentially be accelerated if an organism could selectively increase the mutation rate of specific genes that are actively under positive selection. Recently, a mechanism that cells can use to target rapid evolution to specific genes was discovered. This mechanism is driven by gene orientation-dependent encounters between DNA replication and transcription machineries. These encounters increase mutagenesis in lagging-strand genes, where replication–transcription conflicts are severe. Due to the orientation and transcription-dependent nature of this process, conflict-driven mutagenesis can be used by cells to spatially (gene-specifically) and temporally (only upon transcription induction) regulate the rate of gene evolution. Here, I summarize recent findings on this topic, and discuss the implications of increasing mutagenesis rates and accelerating evolution through active mechanisms.

      PubDate: 2017-02-19T09:44:38Z
      DOI: 10.1016/j.tim.2017.01.008
  • Evolutionary Constraints Shaping Streptococcus pyogenes–Host
    • Authors: Reid V. Wilkening; Michael J. Federle
      Abstract: Publication date: Available online 16 February 2017
      Source:Trends in Microbiology
      Author(s): Reid V. Wilkening, Michael J. Federle
      Research on the Gram-positive human-restricted pathogen Streptococcus pyogenes (Group A Streptococcus, GAS) has long focused on invasive illness, the most severe manifestations of GAS infection. Recent advances in descriptions of molecular mechanisms of GAS virulence, coupled with massive sequencing efforts to isolate genomes, have allowed the field to better understand the molecular and evolutionary changes leading to pandemic strains. These findings suggest that it is necessary to rethink the dogma involving GAS pathogenesis, and that the most productive avenues for research going forward may be investigations into GAS in its ‘normal’ habitat, the nasopharynx, and its ability to either live with its host in an asymptomatic lifestyle or as an agent of superficial infections. This review will consider these advances, focusing on the natural history of GAS, the evolution of pandemic strains, and novel roles for several key virulence factors that may allow the field to better understand their physiological role.

      PubDate: 2017-02-19T09:44:38Z
      DOI: 10.1016/j.tim.2017.01.007
  • Multidrug-Resistant Enterococcal Infections: New Compounds, Novel
           Antimicrobial Therapies?
    • Authors: Roel M. van Harten; Rob J.L. Willems; Nathaniel I. Martin; Antoni P.A. Hendrickx
      Abstract: Publication date: Available online 13 February 2017
      Source:Trends in Microbiology
      Author(s): Roel M. van Harten, Rob J.L. Willems, Nathaniel I. Martin, Antoni P.A. Hendrickx
      Over the past two decades infections due to antibiotic-resistant bacteria have escalated world-wide, affecting patient morbidity, mortality, and health care costs. Among these bacteria, Enterococcus faecium and Enterococcus faecalis represent opportunistic nosocomial pathogens that cause difficult-to-treat infections because of intrinsic and acquired resistance to a plethora of antibiotics. In recent years, a number of novel antimicrobial compound classes have been discovered and developed that target Gram-positive bacteria, including E. faecium and E. faecalis. These new antibacterial agents include teixobactin (targeting lipid II and lipid III), lipopeptides derived from nisin (targeting lipid II), dimeric vancomycin analogues (targeting lipid II), sortase transpeptidase inhibitors (targeting the sortase enzyme), alanine racemase inhibitors, lipoteichoic acid synthesis inhibitors (targeting LtaS), various oxazolidinones (targeting the bacterial ribosome), and tarocins (interfering with teichoic acid biosynthesis). The targets of these novel compounds and mode of action make them very promising for further antimicrobial drug development and future treatment of Gram-positive bacterial infections. Here we review current knowledge of the most favorable anti-enterococcal compounds along with their implicated modes of action and efficacy in animal models to project their possible future use in the clinical setting.

      PubDate: 2017-02-19T09:44:38Z
      DOI: 10.1016/j.tim.2017.01.004
  • Langerhans Cells: the ‘Yin and Yang’ of HIV Restriction and
    • Authors: Luzia Mayr; Bin Su; Christiane Moog
      Abstract: Publication date: Available online 9 February 2017
      Source:Trends in Microbiology
      Author(s): Luzia Mayr, Bin Su, Christiane Moog
      Langerhans cells are specialized sentinels present in the epidermis expressing Langerin, a specific C-type lectin receptor involved in HIV capture and destruction. Recently, the specific mechanism leading to this HIV restriction was discovered. Nevertheless, Langerhans cells can be infected and the way HIV escapes this restriction needs to be unraveled.

      PubDate: 2017-02-12T08:51:54Z
      DOI: 10.1016/j.tim.2017.01.009
  • RNA Chaperones Step Out of Hfq’s Shadow
    • Authors: Laetitia Attaiech; J.N. Mark Glover; Xavier Charpentier
      Abstract: Publication date: Available online 9 February 2017
      Source:Trends in Microbiology
      Author(s): Laetitia Attaiech, J.N. Mark Glover, Xavier Charpentier
      The stability and function of regulatory small RNAs (sRNAs) often require a specialized RNA-binding protein called an RNA chaperone. Recent findings show that proteins containing a ProQ/FinO domain constitute a new class of RNA chaperones that could play key roles in post-transcriptional gene regulation throughout bacterial species.

      PubDate: 2017-02-12T08:51:54Z
      DOI: 10.1016/j.tim.2017.01.006
  • Cultivation-Free Raman Spectroscopic Investigations of Bacteria
    • Authors: Björn Lorenz; Christina Wichmann; Stephan Stöckel; Petra Rösch; Jürgen Popp
      Abstract: Publication date: Available online 7 February 2017
      Source:Trends in Microbiology
      Author(s): Björn Lorenz, Christina Wichmann, Stephan Stöckel, Petra Rösch, Jürgen Popp
      Raman spectroscopy is currently advertised as a hot and ambitious technology that has all of the features needed to characterize and identify bacteria. Raman spectroscopy is rapid, easy to use, noninvasive, and it could complement established microbiological and biomolecular methods in the near future. To bring this vision closer to reality, ongoing research is being conducted on spectral fingerprinting. This can yield a wealth of information, from even single bacteria from various habitats which can be further improved by combining Raman spectroscopy with methods such as stable isotope probing to elucidate microbial interactions. In conjunction with extensive statistical analysis, Raman spectroscopy will allow identification of (non)pathogenic bacteria at different taxonomic levels.

      PubDate: 2017-02-12T08:51:54Z
      DOI: 10.1016/j.tim.2017.01.002
  • Editorial Board and Contents
    • Abstract: Publication date: February 2017
      Source:Trends in Microbiology, Volume 25, Issue 2

      PubDate: 2017-01-30T06:04:36Z
  • A New Way to Beat Intestinal Pathogens
    • Authors: Corrella S. Detweiler
      Abstract: Publication date: Available online 27 January 2017
      Source:Trends in Microbiology
      Author(s): Corrella S. Detweiler
      In the gastrointestinal tract, the tug of war for iron may provide a new way to vaccinate. Recent work shows that immunizing mice with siderophores (small molecules that microbes produce to capture iron) foils pathogen colonization and may instead allow a commensal to expand.

      PubDate: 2017-01-30T06:04:36Z
      DOI: 10.1016/j.tim.2017.01.003
  • Transcriptional Regulation of Antiviral Interferon-Stimulated Genes
    • Authors: Wenshi Wang; Lei Xu; Junhong Su; Maikel P. Peppelenbosch; Qiuwei Pan
      Abstract: Publication date: Available online 27 January 2017
      Source:Trends in Microbiology
      Author(s): Wenshi Wang, Lei Xu, Junhong Su, Maikel P. Peppelenbosch, Qiuwei Pan
      Interferon-stimulated genes (ISGs) are a group of gene products that coordinately combat pathogen invasions, in particular viral infections. Transcription of ISGs occurs rapidly upon pathogen invasion, and this is classically provoked via activation of the Janus kinase/signal transducer and activator of transcription (JAK–STAT) pathway, mainly by interferons (IFNs). However, a plethora of recent studies have reported a variety of non-canonical mechanisms regulating ISG transcription. These new studies are extremely important for understanding the quantitative and temporal differences in ISG transcription under specific circumstances. Because these canonical and non-canonical regulatory mechanisms are essential for defining the nature of host defense and associated detrimental proinflammatory effects, we comprehensively review the state of this rapidly evolving field and the clinical implications of recently acquired knowledge in this respect.

      PubDate: 2017-01-30T06:04:36Z
      DOI: 10.1016/j.tim.2017.01.001
  • Marine Bacterioplankton Seasonal Succession Dynamics
    • Authors: Carina Bunse; Jarone Pinhassi
      Abstract: Publication date: Available online 17 January 2017
      Source:Trends in Microbiology
      Author(s): Carina Bunse, Jarone Pinhassi
      Bacterioplankton (bacteria and archaea) are indispensable regulators of global element cycles owing to their unique ability to decompose and remineralize dissolved organic matter. These microorganisms in surface waters worldwide exhibit pronounced seasonal succession patterns, governed by physicochemical factors (e.g., light, climate, and nutrient loading) that are determined by latitude and distance to shore. Moreover, we emphasize that the effects of large-scale factors are modulated regionally, and over shorter timespans (days to weeks), by biological interactions including molecule exchanges, viral lysis, and grazing. Thus the interplay and scaling between factors ultimately determine the success of particular bacterial populations. Spatiotemporal surveys of bacterioplankton community composition provide the necessary frame for interpreting how the distinct metabolisms encoded in the genomes of different bacteria regulate biogeochemical cycles.

      PubDate: 2017-01-23T04:07:01Z
      DOI: 10.1016/j.tim.2016.12.013
  • Resource Reallocation in Bacteria by Reengineering the Gene Expression
    • Authors: Hidde de Jong; Johannes Geiselmann; Delphine Ropers
      Abstract: Publication date: Available online 16 January 2017
      Source:Trends in Microbiology
      Author(s): Hidde de Jong, Johannes Geiselmann, Delphine Ropers
      Bacteria have evolved complex regulatory networks to control the activity of transcription and translation, and thus the growth rate, over a range of environmental conditions. Reengineering RNA polymerase and ribosomes allows modifying naturally evolved regulatory networks and thereby profoundly reorganizing the manner in which bacteria allocate resources to different cellular functions. This opens new opportunities for our fundamental understanding of microbial physiology and for a variety of applications. Recent breakthroughs in genome engineering and the miniaturization and automation of culturing methods have offered new perspectives for the reengineering of the transcription and translation machinery in bacteria as well as the development of novel in vitro and in vivo gene expression systems. We review different examples from the unifying perspective of resource reallocation, and discuss the impact of these approaches for microbial systems biology and biotechnological applications.

      PubDate: 2017-01-23T04:07:01Z
      DOI: 10.1016/j.tim.2016.12.009
  • A Chiral Pentagonal Polyhedral Framework for Characterizing Virus Capsid
    • Authors: Aditya Raguram; V. Sasisekharan; Ram Sasisekharan
      Abstract: Publication date: Available online 13 January 2017
      Source:Trends in Microbiology
      Author(s): Aditya Raguram, V. Sasisekharan, Ram Sasisekharan
      Recent developments of rational strategies for the design of antiviral therapies, including monoclonal antibodies (mAbs), have naturally relied extensively on available viral structural information. As new strategies continue to be developed, it is equally important to continue to refine our understanding and interpretation of viral structural data. There are known limitations to the traditional (Caspar–Klug) theory for describing virus capsid structures that involves subdividing a capsid into triangular subunits. In this context, we describe a more general polyhedral framework for describing virus capsid structures that is able to account for many of these limitations, including a more thorough characterization of intersubunit interfaces. Additionally, our use of pentagonal subunits instead of triangular ones accounts for the intrinsic chirality observed in all capsids. In conjunction with the existing theory, the framework presented here provides a more complete picture of a capsid’s structure and therefore can help contribute to the development of more effective antiviral strategies.

      PubDate: 2017-01-16T02:47:25Z
      DOI: 10.1016/j.tim.2016.12.007
  • Can MALDI-TOF Mass Spectrometry Reasonably Type Bacteria?
    • Authors: Marlène Sauget; Benoît Valot; Xavier Bertrand; Didier Hocquet
      Abstract: Publication date: Available online 13 January 2017
      Source:Trends in Microbiology
      Author(s): Marlène Sauget, Benoît Valot, Xavier Bertrand, Didier Hocquet
      Bacterial typing is crucial to tackle the spread of bacterial pathogens but current methods are time-consuming and costly. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has been recently integrated into the microbiology laboratory workflow for a quick and low-cost microbial species identification. Independent research groups have successfully redirected the original function of this technology from their primary purpose to discriminate subgroups within pathogen species. However, identical bacterial subgroups could be identified by unrelated peaks by independent methods, thus limiting their robustness and exportability. We propose several guidelines that could improve the performance of MALDI-TOF MS-based typing methods for use as a first-line epidemiological tool.

      PubDate: 2017-01-16T02:47:25Z
      DOI: 10.1016/j.tim.2016.12.006
  • Step by Step, Cell by Cell: Quantification of the Bacterial Cell Cycle
    • Authors: Matteo Osella; Sander J. Tans; Marco Cosentino Lagomarsino
      Abstract: Publication date: Available online 13 January 2017
      Source:Trends in Microbiology
      Author(s): Matteo Osella, Sander J. Tans, Marco Cosentino Lagomarsino
      The Escherichia coli cell cycle is a classic, but we are still missing some of its essential aspects. The reason is that our knowledge is mostly based on population data, and our grasp of the behavior of single cells is still very limited. Today, new dynamic single-cell data promise to overcome this barrier. Existing data from single cells have already led to findings and hypotheses that challenge standard views, and have raised new questions. Here, we review these recent developments and propose that a systematic exploration of the correlation patterns between ‘cell-cycle intervals’ defined by key molecular events measured in many single cells could lead to a quantitative characterization of the cell cycle in terms of inherent stochasticity and homeostatic controls.

      PubDate: 2017-01-16T02:47:25Z
      DOI: 10.1016/j.tim.2016.12.005
  • The Role of Reactive Oxygen Species in Antibiotic-Mediated Killing of
    • Authors: Heleen Van Acker; Tom Coenye
      Abstract: Publication date: Available online 12 January 2017
      Source:Trends in Microbiology
      Author(s): Heleen Van Acker, Tom Coenye
      Recently, it was proposed that there is a common mechanism behind the activity of bactericidal antibiotics, involving the production of reactive oxygen species (ROS). However, the involvement of ROS in antibiotic-mediated killing has become the subject of much debate. In the present review, we provide an overview of the data supporting the ROS hypothesis; we also present data that explain the contradictory results often obtained when studying antibiotic-induced ROS production. For this latter aspect we will focus on the importance of taking the experimental setup into consideration and on the importance of some technical aspects of the assays typically used. Finally, we discuss the link between ROS production and toxin–antitoxin modules, and present an overview of implications for treatment.

      PubDate: 2017-01-16T02:47:25Z
      DOI: 10.1016/j.tim.2016.12.008
  • Ecology of the Oral Microbiome: Beyond Bacteria
    • Authors: Jonathon L. Baker; Batbileg Bor; Melissa Agnello; Wenyuan Shi; Xuesong He
      Abstract: Publication date: Available online 11 January 2017
      Source:Trends in Microbiology
      Author(s): Jonathon L. Baker, Batbileg Bor, Melissa Agnello, Wenyuan Shi, Xuesong He
      Although great strides have been made in understanding the complex bacterial community inhabiting the human oral cavity, for a variety of (mainly technical) reasons the ecological contributions of oral fungi, viruses, phages, and the candidate phyla radiation (CPR) group of ultrasmall bacteria have remained understudied. Several recent reports have illustrated the diversity and importance of these organisms in the oral cavity, while TM7x and Candida albicans have served as crucial paradigms for CPR species and oral fungi, respectively. A comprehensive understanding of the oral microbiota and its influence on host health and disease will require a holistic view that emphasizes interactions among different residents within the oral community, as well as their interaction with the host.

      PubDate: 2017-01-16T02:47:25Z
      DOI: 10.1016/j.tim.2016.12.012
  • The Peculiar Functions of the Bacterial Extracellular Matrix
    • Authors: Anna
      Abstract: Publication date: Available online 11 January 2017
      Source:Trends in Microbiology
      Author(s): Anna Dragoš, Ákos T. Kovács
      A biofilm is a common life form where bacterial cells crowd together surrounded by an extracellular matrix (ECM). Traditionally, the ECM is considered as a structural material that glues and shields the biofilm cells. Here we describe alternative functions of the ECM, highlighting how it benefits microbes beyond the biofilms. Next to protecting free-living cells, the ECM participates in signaling, migration, and genetic exchange either being freely shared with other species or being exclusive to siblings. Considering the structural and recently discovered functions of the ECM, we also attempt to revise its role in sociomicrobiology. In the light of recent findings, the canonical view on ECM as a passive structural material of biofilms should be revisited.

      PubDate: 2017-01-16T02:47:25Z
  • Predatory Bacteria: Moving from Curiosity Towards Curative
    • Authors: J. Tyson; R.E. Sockett
      Abstract: Publication date: Available online 9 January 2017
      Source:Trends in Microbiology
      Author(s): J. Tyson, R.E. Sockett
      In a world where infection-causing, pathogenic bacteria are evolving resistance to conventional antibiotics, new solutions are needed. One proposal is the use of predatory bacteria as living antibiotics. Two new papers show that predators are not harmful and can kill pathogens inside live animals, a very positive step forward.

      PubDate: 2017-01-16T02:47:25Z
      DOI: 10.1016/j.tim.2016.12.011
  • Helicobacter pylori: A Paradigm Pathogen for Subverting Host Cell Signal
    • Authors: Michael Naumann; Olga Sokolova; Nicole Tegtmeyer; Steffen Backert
      Abstract: Publication date: Available online 3 January 2017
      Source:Trends in Microbiology
      Author(s): Michael Naumann, Olga Sokolova, Nicole Tegtmeyer, Steffen Backert
      Helicobacter pylori colonizes the gastric mucosa in the human stomach and represents a major risk factor for peptic ulcer disease and gastric cancer. Here, we summarize our current knowledge of the complex impact of H. pylori on manipulating host signalling networks, that is, by the cag pathogenicity island (cagPAI)-encoded type IV secretion system (T4SS). We show that H. pylori infections reflect a paradigm for interspecies contact-dependent molecular communication, which includes the disruption of cell–cell junctions and cytoskeletal rearrangements, as well as proinflammatory, cell cycle-related, proliferative, antiapoptotic, and DNA damage responses. The contribution of these altered signalling cascades to disease outcome is discussed.

      PubDate: 2017-01-08T01:36:39Z
      DOI: 10.1016/j.tim.2016.12.004
  • The ‘Antibiotic Apocalypse’ – Scaremongering or
           Scientific Reporting?
    • Authors: Jonathan A .G. Cox; Tony Worthington
      Abstract: Publication date: Available online 23 December 2016
      Source:Trends in Microbiology
      Author(s): Jonathan A .G. Cox, Tony Worthington
      Antimicrobial resistance is dominating scientific media. We are warned of an impending ‘antibiotic apocalypse’, where mankind faces its biggest threat, untreatable microbes. However, the world is not ending. Scientists are responding to the threat; new knowledge and chemotherapeutics are being created to safeguard our future. The future is bright, not gloomy.

      PubDate: 2016-12-29T22:37:25Z
      DOI: 10.1016/j.tim.2016.11.016
  • Editorial Board and Contents
    • Abstract: Publication date: January 2017
      Source:Trends in Microbiology, Volume 25, Issue 1

      PubDate: 2016-12-22T22:00:25Z
  • Assessing the Risk of Antibiotic Resistance Transmission from the
           Environment to Humans: Non-Direct Proportionality between Abundance and
    • Authors: Manaia
      Abstract: Publication date: Available online 21 December 2016
      Source:Trends in Microbiology
      Author(s): Célia M. Manaia
      The past decade has witnessed a burst of study regarding antibiotic resistance in the environment, mainly in areas under anthropogenic influence. Therefore, impacts of the contaminant resistome, that is, those related to human activities, are now recognized. However, a key issue refers to the risk of transmission of resistance to humans, for which a quantitative model is urgently needed. This opinion paper makes an overview of some risk-determinant variables and raises questions regarding research needs. A major conclusion is that the risks of transmission of antibiotic resistance from the environment to humans must be managed under the precautionary principle, because it may be too late to act if we wait until we have concrete risk values.

      PubDate: 2016-12-22T22:00:25Z
  • Metal Oxide Reduction Linked to Anaerobic Methane Oxidation
    • Authors: Oluwatobi E. Oni; Michael W. Friedrich
      Abstract: Publication date: Available online 13 December 2016
      Source:Trends in Microbiology
      Author(s): Oluwatobi E. Oni, Michael W. Friedrich
      Microbial methanotrophy is important in mitigating methane emissions to the atmosphere. Geochemical evidence suggests the occurrence of anaerobic methane oxidation with metal oxides in natural environments. A study has now identified, for the first time, novel freshwater archaea of the order Methanosarcinales that can oxidize methane with Fe(III) and Mn(IV) minerals as electron acceptors.

      PubDate: 2016-12-14T20:56:44Z
      DOI: 10.1016/j.tim.2016.12.001
  • Herpesviruses and Their Host Cells: A Successful Liaison
    • Authors: Barbara Adler; Christine Sattler; Heiko Adler
      Abstract: Publication date: Available online 9 December 2016
      Source:Trends in Microbiology
      Author(s): Barbara Adler, Christine Sattler, Heiko Adler
      During a long history of coevolution, herpesviruses have reached a fine-tuned balance with their hosts, allowing them to successfully persist and spread to new hosts without causing too much damage. Only under certain circumstances, as in neonates or immunocompromised individuals, they may cause serious diseases. The delicate balance between herpesviruses and their hosts results from interactions of a great variety of viral and cellular factors which together shape the tropism for a particular host, tissue, or cell. Understanding these interactions will provide insight into the viral life cycle and cell biology in general. Moreover, it will also facilitate comprehension of herpesvirus pathogenesis, enabling the development of new strategies to combat herpesviruses in cases where they cause disease.

      PubDate: 2016-12-14T20:56:44Z
      DOI: 10.1016/j.tim.2016.11.009
  • Protecting from Envelope Stress: Variations on the Phage-Shock-Protein
    • Authors: Riccardo Manganelli; Maria Laura Gennaro
      Abstract: Publication date: Available online 4 December 2016
      Source:Trends in Microbiology
      Author(s): Riccardo Manganelli, Maria Laura Gennaro

      PubDate: 2016-12-07T19:58:42Z
      DOI: 10.1016/j.tim.2016.10.001
  • Defining the Core Microbiome in Corals’ Microbial Soup
    • Authors: Alejandra Hernandez-Agreda; Ruth D. Gates; Tracy D. Ainsworth
      Abstract: Publication date: Available online 3 December 2016
      Source:Trends in Microbiology
      Author(s): Alejandra Hernandez-Agreda, Ruth D. Gates, Tracy D. Ainsworth
      Corals are considered one of the most complex microbial biospheres studied to date, hosting thousands of bacterial phylotypes in species-specific associations. There are, however, substantial knowledge gaps and challenges in understanding the functional significance of bacterial communities and bacterial symbioses of corals. The ubiquitous nature of some bacterial interactions has only recently been investigated and an accurate differentiation between the healthy (symbiotic) and unhealthy (dysbiotic) microbial state has not yet been determined. Here we review the complexity of the coral holobiont, coral microbiome diversity, and recently proposed bacterial symbioses of corals. We provide insight into coupling the core microbiome framework with community ecology principals, and draw on the theoretical insights from other complex systems, to build a framework to aid in deciphering ecologically significant microbes within a corals' microbial soup.

      PubDate: 2016-12-07T19:58:42Z
      DOI: 10.1016/j.tim.2016.11.003
  • Microbiological Research Under the Nagoya Protocol: Facts and Fiction
    • Authors: Jörg Overmann; Amber Hartman Scholz
      Abstract: Publication date: Available online 22 November 2016
      Source:Trends in Microbiology
      Author(s): Jörg Overmann, Amber Hartman Scholz
      The Nagoya Protocol is based on concepts of biological diversity that are hardly applicable to microorganisms. Because of this incongruence, the Nagoya Protocol threatens future microbial research, potentially defeating its original purpose. Countries with appropriate regulations can promote science and their bioeconomy through international collaboration and simultaneously gain a competitive advantage.

      PubDate: 2016-11-23T17:05:46Z
      DOI: 10.1016/j.tim.2016.11.001
  • Colonization of Black Smokers by Hyperthermophilic Microorganisms
    • Authors: Reinhard Wirth
      Abstract: Publication date: Available online 18 November 2016
      Source:Trends in Microbiology
      Author(s): Reinhard Wirth
      Newly erupted black smokers (hydrothermal vent chimneys) are sterile during their formation, but they house hyperthermophiles in substantial amounts in later stages. No hard data exist on the mechanisms by which hyperthermophiles colonize newly erupted black smokers. Here I propose a scenario – based on various experimental data – for how hyperthermophiles colonize black smokers. Hyperthermophiles which are present in cold sea water in minute amounts are transferred by chance to the outside of black smokers and react within seconds to the high temperature by very fast movements. After reaching an optimal temperature region they scan the surface via a zigzag seek-movement and adhere via their flagella at a suitable place, building up biofilms.

      PubDate: 2016-11-23T17:05:46Z
      DOI: 10.1016/j.tim.2016.11.002
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