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Trends in Microbiology

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ISSN (Print) 0966-842X
Published by Elsevier

[2565 journals]

Rising to the challenge: new therapies for tuberculosis
- Abstract: Publication date: Available online 11 June 2013
  Source:Trends in Microbiology
  Author(s): Emily B. Wong , Keira A. Cohen , William R. Bishai
  The standard treatment for tuberculosis (TB) is lengthy, complex, and significantly toxic. Drug development for TB has stagnated for decades, but in recent years renewed commitment and coordinated research has generated a modest pipeline of new drugs that hold the potential to make treatment more effective, shorter, less complex, and less toxic in the near future. With a particular focus on bedaquiline (TMC207), the first anti-TB drug of a novel class to be approved by the US Food and Drug Administration (FDA) in 40 years, this review summarizes the recent evidence behind new developments in TB treatment. Novel drug classes, repurposed drugs, and host-directed therapies are reviewed. In parallel to these exciting developments in drug discovery, we propose that it is crucial to develop more rapid and comprehensive diagnostics that will allow the timely selection of the best regimen for individual patients.
  
  PubDate: 2013-06-15T05:17:55Z
Cooperation: another mechanism of viral evolution
- Abstract: Publication date: Available online 11 June 2013
  Source:Trends in Microbiology
  Author(s): Yuta Shirogane , Shumpei Watanabe , Yusuke Yanagi
  RNA viruses evolve rapidly under selection pressure as a result of the high error rates of viral RNA polymerase. ‘Cooperation’ between wild type and variant measles virus (MV) genomes through the heterooligomer formation of a viral protein has recently been shown to act as a mechanism of viral evolution. This type of cooperation between genomes producing a new phenotype may have implications for various aspects of evolution, including the expansion of viral tropism and host range, the emergence of segmented viral genomes, and the evolution of heteromultimeric molecules. It also lends support to the concept of the quasispecies acting as a unit of selection.
  
  PubDate: 2013-06-15T05:17:55Z
Interspecies transmission and emergence of novel viruses: lessons from bats and birds
- Abstract: Publication date: Available online 14 June 2013
  Source:Trends in Microbiology
  Author(s): Jasper Fuk-Woo Chan , Kelvin Kai-Wang To , Herman Tse , Dong-Yan Jin , Kwok-Yung Yuen
  As exemplified by coronaviruses and influenza viruses, bats and birds are natural reservoirs for providing viral genes during evolution of new virus species and viruses for interspecies transmission. These warm-blooded vertebrates display high species biodiversity, roosting and migratory behavior, and a unique adaptive immune system, which are favorable characteristics for asymptomatic shedding, dissemination, and mixing of different viruses for the generation of novel mutant, recombinant, or reassortant RNA viruses. The increased intrusion of humans into wildlife habitats and overcrowding of different wildlife species in wet markets and farms have also facilitated the interspecies transmission between different animal species.
  
  PubDate: 2013-06-15T05:17:55Z
Condensing the omics fog of microbial communities
- Abstract: Publication date: Available online 10 June 2013
  Source:Trends in Microbiology
  Author(s): Emilie E.L. Muller , Enrico Glaab , Patrick May , Nikos Vlassis , Paul Wilmes
  Natural microbial communities are ubiquitous, complex, heterogeneous, and dynamic. Here, we argue that the future standard for their study will require systematic omic measurements of spatially and temporally resolved unique samples in line with a discovery-driven planning approach. Resulting datasets will allow the generation of solid hypotheses about causal relationships and, thereby, will facilitate the discovery of previously unknown traits of specific microbial community members. However, to achieve this, solid wet lab, bioinformatic and statistical methodologies are required to have the promises of the emerging field of Eco-Systems Biology come to fruition.
  
  PubDate: 2013-06-11T02:16:47Z
How academic labs can approach the drug discovery process as a way to synergize with big pharma
- Abstract: Publication date: June 2013
  Source:Trends in Microbiology, Volume 21, Issue 6
  Author(s): Arianna Loregian , Giorgio Palù
  While the pharmaceutical industry is facing highly challenging times, the academic drug discovery sector has the potential to contribute meaningfully to the discovery of novel drug targets and to the development of new mode-of-action therapeutics against a range of diseases, including rare and neglected diseases.
  
  PubDate: 2013-06-02T20:44:13Z
Editorial Board
- Abstract: Publication date: June 2013
  Source:Trends in Microbiology, Volume 21, Issue 6
  
  PubDate: 2013-06-02T20:44:13Z
The HIV-1-containing macrophage compartment: a perfect cellular niche?
- Abstract: Publication date: Available online 2 June 2013
  Source:Trends in Microbiology
  Author(s): Joshua Tan , Quentin J. Sattentau
  Macrophages are a major target of HIV-1 infection and are believed to act as viral reservoirs and mediators of HIV-1-associated neurological damage. These pathological roles may be associated with the ability of the virus to assemble and accumulate in apparently intracellular compartments in macrophages. These so-called virus-containing compartments were initially thought to be late endosomes or multivesicular bodies, but it has since been shown that they are distinct structures that have complex three-dimensional morphology, a unique set of protein markers, and features such as a near-neutral pH and frequent connections to the extracellular milieu. These features appear to protect HIV-1 from hostile elements both within and outside the cell. This review discusses the cellular and molecular characteristics of HIV-1-containing compartments in macrophages and how they offer a safe haven for the virus, with important consequences for pathogenesis.
  
  PubDate: 2013-06-02T20:44:13Z
Innate immune detection of microbial nucleic acids
- Abstract: Publication date: Available online 29 May 2013
  Source:Trends in Microbiology
  Author(s): Claudia Gürtler , Andrew G. Bowie
  Detection of pathogen-derived nucleic acids by pattern recognition receptors (PRRs) is essential for the host to mount an appropriate immune response, which for viruses involves the induction of type I interferons (IFNs). By contrast, inappropriate activation of PRRs by self nucleic acids can lead to autoimmunity. Recent developments in PRR research have uncovered important new molecular details as to how Toll-like receptors (TLRs) and retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs) distinguish pathogen from self RNA, while the discovery of cytosolic DNA sensing pathways for IFN induction has revealed completely new innate signaling mechanisms, and also questions how innate immunity discriminates between self and non-self DNA, if at all.
  
  PubDate: 2013-05-30T05:13:02Z
Lose the battle to win the war: bacterial strategies for evading host inflammasome activation
- Abstract: Publication date: Available online 24 May 2013
  Source:Trends in Microbiology
  Author(s): Naomi Higa , Claudia Toma , Toshitsugu Nohara , Noboru Nakasone , Giichi Takaesu , Toshihiko Suzuki
  The inflammasome is composed of nucleotide-binding, oligomerization domain (NOD)-like receptor (NLR) proteins, and leads to caspase-1 activation and subsequent secretion of the proinflammatory cytokines interleukin 1β (IL-1β) and interleukin-18 (IL-18). After certain pathogenic bacteria infect host cells, such as macrophages, NLR-mediated inflammasome activation is triggered to form part of the host defenses against the invading pathogens. However, recent evidence has shown that bacteria have strategies for evading inflammasome activation in host cells. In this review, we focus on NLR-mediated inflammasome activation and bacterial evasion of the inflammasome as part of the battle between the host defenses and pathogens.
  
  PubDate: 2013-05-26T04:06:46Z
Probiotic strategies for treatment of respiratory diseases
- Abstract: Publication date: Available online 23 May 2013
  Source:Trends in Microbiology
  Author(s): Nabeetha A. Nagalingam , Emily K. Cope , Susan V. Lynch
  Recent advances in next-generation sequencing and phylogenetic microarray technologies have identified diverse, niche-specific microbial communities that comprise the human superorganism. Mucosal microbiome perturbation is a prominent feature of an increasing number of chronic inflammatory disorders, including respiratory diseases, and efforts are now focused on identifying novel microbe-based strategies to treat or manage these conditions. Considering the evidence for niche-specificity and the diversity of function that human microbial communities afford, the range of therapeutic species used to date in probiotic supplements is strikingly narrow and is limited to species typically of gastrointestinal origin. Although the field is still relatively nascent, the potential for identifying novel microbe-based therapeutics in the human microbiome is great. This article focuses primarily on the respiratory tract, its associated microbiome, potential interactions with the gastrointestinal microbiota, and the possibilities for microbiome-manipulation strategies in the treatment and prevention of respiratory disease.
  
  PubDate: 2013-05-26T04:06:46Z
The prospects and challenges of universal vaccines for influenza
- Abstract: Publication date: Available online 17 May 2013
  Source:Trends in Microbiology
  Author(s): Kanta Subbarao , Yumiko Matsuoka
  Vaccination is the most effective way to reduce the impact of epidemic as well as pandemic influenza. However, the licensed inactivated influenza vaccine induces strain-specific immunity and must be updated annually. When novel viruses appear, matched vaccines are not likely to be available in time for the first wave of a pandemic. Yet, the enormous diversity of influenza A viruses in nature makes it impossible to predict which subtype or strain will cause the next pandemic. Several recent scientific advances have generated renewed enthusiasm and hope for universal vaccines that will induce broad protection from a range of influenza viruses.
  
  PubDate: 2013-05-17T21:08:59Z
Caenorhabditis elegans reveals novel Pseudomonas aeruginosa virulence mechanism
- Abstract: Publication date: Available online 14 May 2013
  Source:Trends in Microbiology
  Author(s): Putri Dwi Utari , Wim J. Quax
  The susceptibility of Caenorhabditis elegans to different virulent phenotypes of Pseudomonas aeruginosa makes the worms an excellent model for studying host–pathogen interactions. Including the recently described liquid killing, five different killing assays are now available offering superb possibilities for performing high-throughput screens for novel antibiotics using a whole-body infection system.
  
  PubDate: 2013-05-17T21:08:59Z
The emerging world of the fungal microbiome
- Abstract: Publication date: Available online 17 May 2013
  Source:Trends in Microbiology
  Author(s): Gary B. Huffnagle , Mairi C. Noverr
  The study of the fungal microbiota (‘mycobiome’) is a new and rapidly emerging field that lags behind our understanding of the bacterial microbiome. Every human has fungi as part of their microbiota, but the total number of fungal cells is orders of magnitude smaller than that of the bacterial microbiota. However, the impact of the mycobiome on human health is significant, especially as a reservoir for blooms of pathogenic microbes when the host is compromised and as a potential cofactor in inflammatory diseases and metabolic disorders.
  
  PubDate: 2013-05-17T21:08:59Z
Phenol-soluble modulins, hellhounds from the staphylococcal virulence-factor pandemonium
- Abstract: Publication date: Available online 14 May 2013
  Source:Trends in Microbiology
  Author(s): Eleni Tsompanidou , Emma. L. Denham , Jan Maarten van Dijl
  Phenol-soluble modulins are secreted peptides with multiple functions in Staphylococcus aureus pathogenesis and spreading. Recent studies by Otto and coworkers show that these hellhounds of the staphylococcal virulence-factor pandemonium are unleashed through an essential ABC transporter, which represents an exciting new target for stopping the spread of this important pathogen.
  
  PubDate: 2013-05-17T21:08:59Z
Programmed cell death in bacteria and implications for antibiotic therapy
- Abstract: Publication date: Available online 14 May 2013
  Source:Trends in Microbiology
  Author(s): Yu Tanouchi , Anna Jisu Lee , Hannah Meredith , Lingchong You
  It is now well appreciated that programmed cell death (PCD) plays critical roles in the life cycle of diverse bacterial species. It is an apparently paradoxical behavior as it does not benefit the cells undergoing PCD. However, growing evidence suggests that PCD can be ‘altruistic’: the dead cells may directly or indirectly benefit survivors through generation of public goods. This property provides a potential explanation on how PCD can evolve as an extreme form of cooperation, although many questions remain to be addressed. From another perspective, as PCD plays a critical role in bacterial pathogenesis, it has been proposed as a potential target for new antibacterial therapy. To this end, understanding the population and evolutionary dynamics resulting from PCD and public goods production may be a key to the success of designing effective antibiotic treatment.
  
  PubDate: 2013-05-17T21:08:59Z
HIV among women and children in Pakistan
- Abstract: Publication date: May 2013
  Source:Trends in Microbiology, Volume 21, Issue 5
  Author(s): Muhammad A. Raees , Syed H. Abidi , Wajid Ali , Muhammad R. Khanani , Syed Ali
  The HIV epidemic in Pakistan has now transmitted to female spouses of HIV-positive injection drug users (IDUs) and bisexual men, and to preadolescent children through vertical transmission. Owing to sociocultural barriers, HIV-infected pregnant women and children do not have optimum access to treatment, hindering the prevention of HIV transmission.
  
  PubDate: 2013-05-05T10:24:08Z
Editorial Board
- Abstract: Publication date: May 2013
  Source:Trends in Microbiology, Volume 21, Issue 5
  
  PubDate: 2013-05-05T10:24:08Z
Interpreting infective microbiota: the importance of an ecological perspective
- Abstract: Publication date: Available online 16 April 2013
  Source:Trends in Microbiology
  Author(s): Geraint B. Rogers , Lucas R. Hoffman , Mary P. Carroll , Kenneth D. Bruce
  Complex microbiota are being reported increasingly across a range of chronic infections, including those of the cystic fibrosis airways. Such diversity fits poorly into classical models of sterile tissue infections, which generally involve one species, and where microbe–outcome associations usually imply causality. It has been suggested that microbiota at sites of infection could represent pathogenic entities, analogous to individual species. We argue that our ability to identify causality in microbiota–disease associations is, however, inherently confounded. Although particular microbiota may be associated with clinical outcomes, niche characteristics at sites of infection will shape microbiota composition through exerting selective pressures. Here, we suggest that ecological theory can inform clinical understanding.
  
  PubDate: 2013-04-20T01:47:25Z
Potential of protein kinase inhibitors for treating herpesvirus-associated disease
- Abstract: Publication date: Available online 19 April 2013
  Source:Trends in Microbiology
  Author(s): Renfeng Li , S. Diane Hayward
  Herpesviruses are ubiquitous human pathogens that establish lifelong persistent infections. Clinical manifestations range from mild self-limiting outbreaks such as childhood rashes and cold sores to the more severe and life-threatening outcomes of disseminated infection, encephalitis, and cancer. Nucleoside analog drugs that target viral DNA replication provide the primary means of treatment. However, extended use of these drugs can result in selection for drug-resistant strains, particularly in immunocompromised patients. In this review we will present recent observations about the participation of cellular protein kinases in herpesvirus biology and discuss the potential for targeting these protein kinases as well as the herpesvirus-encoded protein kinases as an anti-herpesvirus therapeutic strategy.
  
  PubDate: 2013-04-20T01:47:25Z
Editorial Board
- Abstract: April 2013
  Publication year: 2013
  Source:Trends in Microbiology, Volume 21, Issue 4
  
  PubDate: 2013-04-07T18:53:40Z
The uses of race and ethnicity in human microbiome research
- Abstract: April 2013
  Publication year: 2013
  Source:Trends in Microbiology, Volume 21, Issue 4
  
  Research on the human microbiome is beginning to address factors associated with between-group differences. Recognition of the social and political nature of traditional race and ethnicity categories will allow microbiome research to contribute to reduction of health disparities while avoiding attribution of causal inference to specific race and ethnicity categories.
  
  PubDate: 2013-04-07T18:53:40Z
Daily battle against body odor: towards the activity of the axillary microbiota
- Abstract: Available online 6 April 2013
  Publication year: 2013
  Source:Trends in Microbiology
  
  The microbial community of the human axilla plays a key role in the formation of axillary odor by biotransformation of odorless natural secretions into volatile odorous molecules. Culture-based microbiological and biochemical studies have allowed the characterization of the axillary microbiota, but the advent of next-generation culture-independent DNA sequencing approaches has provided an unprecedented depth of data regarding the taxonomic composition of the axillary microbiota and intra- and interindividual variation. However, the physiological activity of the microbiota of an individual and its variation under different environmental conditions remains largely unknown. Thus, metatranscriptomics represents a promising technique to identify specific metabolic activities in the axillary microbiota linked to individual differences in body odor.
  
  PubDate: 2013-04-07T18:53:40Z
Mechanisms of endospore inactivation under high pressure
- Abstract: Available online 26 March 2013
  Publication year: 2013
  Source:Trends in Microbiology
  
  It is well known that spore germination and inactivation can be achieved within a broad temperature and pressure range. The existing literature, however, reports contradictory results concerning the effectiveness of different pressure–temperature combinations and the underlying inactivation mechanism(s). Much of the published kinetic data are prone to error as a result of unstable process conditions or an incomplete investigation of the entire inactivation pathway. Here, we review this field of research, and also discuss an inactivation mechanism of at least two steps and propose an inactivation model based on current data. Further, spore resistance properties and matrix interactions are linked to spore inactivation effectiveness.
  
  PubDate: 2013-03-30T11:15:52Z
Fleas and smaller fleas: virotherapy for parasite infections
- Abstract: Available online 26 March 2013
  Publication year: 2013
  Source:Trends in Microbiology
  
  Bacteriophages are viruses of bacteria that are used for controlling bacterial food-borne pathogens and have been proposed for more extensive usage in infection control. Protists are now recognised to harbour viruses and virus-like particles. We propose that investigation of their prevalence in parasites be intensified. We also propose that such viruses might be considered for virotherapy to control certain parasite infections of man and animals.
  
  PubDate: 2013-03-30T11:15:52Z
Key host–pathogen interactions for designing novel interventions against Helicobacter pylori
- Abstract: Available online 23 March 2013
  Publication year: 2013
  Source:Trends in Microbiology
  
  Helicobacter pylori can persist in the stomach of infected individuals for life, in the face of chronic inflammation and low pH. Efforts to develop vaccines have largely failed and, in the wake of emerging antibiotic resistance, novel therapeutic approaches must be considered. This review will discuss recent salient findings of host factors that modulate inflammatory responses to H. pylori with the aim of harnessing this knowledge for developing novel therapeutics. In addition, new approaches to vaccine development will be reviewed. Ultimately, the development of efficacious therapeutic interventions will likely need to consider host–pathogen interactions to enhance host immunity and circumvent bacterial evasion strategies.
  Highlights ► Complex host–pathogen interactions determine Helicobacter pylori disease outcome. ► Novel therapies should target multiple molecules to increase efficacy. ► The best drugs or vaccines will also reduce inflammation associated with infection. ► Development of novel, immunomodulatory adjuvants will lead to improved vaccines.
  
  PubDate: 2013-03-23T06:32:43Z
Respiratory syncytial virus interaction with human airway epithelium
- Abstract: Available online 22 March 2013
  Publication year: 2013
  Source:Trends in Microbiology
  
  Although respiratory syncytial virus (RSV) is a major human respiratory pathogen, our knowledge of how it causes disease in humans is limited. Airway epithelial cells are the primary targets of RSV infection in vivo, so the generation and exploitation of RSV infection models based on morphologically and physiologically authentic well-differentiated primary human airway epithelial cells cultured at an air–liquid interface (WD-PAECs) provide timely developments that will help to bridge this gap. Here we review the interaction of RSV with WD-PAEC cultures, the authenticity of the RSV–WD-PAEC models relative to RSV infection of human airway epithelium in vivo, and future directions for their exploitation in our quest to understand RSV pathogenesis in humans.
  Highlights ► RSV is a major respiratory pathogen in infants that infects airway epithelium. ► WD-PAEC cultures are authentic surrogates of human airway epithelium. ► RSV infection of WD-PAECs reproduces several hallmarks of RSV infection in infants. ► Studying RSV–WD-PAEC interactions will illuminate novel therapeutic strategies.
  
  PubDate: 2013-03-23T06:32:43Z
Reactivation of latent HIV by histone deacetylase inhibitors
- Abstract: Available online 18 March 2013
  Publication year: 2013
  Source:Trends in Microbiology
  
  Latent HIV persists in CD4+ T cells in infected patients under antiretroviral therapy (ART). Latency is associated with transcriptional silencing of the integrated provirus and driven, at least in part, by histone deacetylases (HDACs), a family of chromatin-associated proteins that regulate histone acetylation and the accessibility of DNA to transcription factors. Remarkably, inhibition of HDACs is sufficient to reactivate a fraction of latent HIV in a variety of experimental systems. This basic observation led to the shock and kill idea that forcing the transcriptional activation of HIV might lead to virus expression, to virus- or host-induced cell death of the reactivated cells, and to the eradication of the pool of latently infected cells. Such intervention might possibly lead to a cure for HIV-infected patients. Here, we review the basic biology of HDACs and their inhibitors, the role of HDACs in HIV latency, and recent efforts to use HDAC inhibitors to reactivate latent HIV in vitro and in vivo.
  
  PubDate: 2013-03-20T05:08:09Z
Missing out on the biology of heterosexual HIV-1 transmission
- Abstract: Available online 13 March 2013
  Publication year: 2013
  Source:Trends in Microbiology
  
  Although unprotected heterosexual intercourse is recognized as the primary mechanism sustaining the global spread of HIV-1, many fundamental details surrounding transmission and establishment of primary HIV-1 infection remain unresolved. Unprotected intercourse induces widespread changes in female reproductive tissues linked to immediate removal of excess spermatozoa and preparation of the uterus for implantation. Concurrently, contact with semen may transiently increase susceptibility to HIV-1 by perturbing mucosal barrier function and triggering localized inflammation. In this manner, infectious HIV-1 in semen becomes an adventitious traveler on the pathway leading to normal human reproduction. This review summarizes key elements of male-to-female HIV-1 transmission and presents a rationalization for human-based studies to illuminate the biology of heterosexual HIV-1 transmission.
  Highlights ► There is convergence in the fundamental biological processes occurring in the female reproductive tract linking human reproduction and heterosexual HIV-1 transmission. ► Components of human semen directly impact on HIV-1 transmission. ► Pre-existing conditions in the female reproductive tract increase susceptibility to HIV-1 infection. ► Ex vivo human mucosal tissue systems allow direct study of HIV-1 transmission.
  
  PubDate: 2013-03-16T00:31:47Z
Bacterial contact-dependent growth inhibition
- Abstract: Available online 7 March 2013
  Publication year: 2013
  Source:Trends in Microbiology
  
  Bacteria cooperate to form multicellular communities and compete against one another for environmental resources. Here, we review recent advances in the understanding of bacterial competition mediated by contact-dependent growth inhibition (CDI) systems. Different CDI+ bacteria deploy a variety of toxins to inhibit neighboring cells and protect themselves from autoinhibition by producing specific immunity proteins. The genes encoding CDI toxin–immunity protein pairs appear to be exchanged between cdi loci and are often associated with other toxin-delivery systems in diverse bacterial species. CDI also appears to facilitate cooperative behavior between kin, suggesting that these systems may have other roles beyond competition.
  
  PubDate: 2013-03-07T19:17:03Z
Editorial Board
- Abstract: March 2013
  Publication year: 2013
  Source:Trends in Microbiology, Volume 21, Issue 3
  
  PubDate: 2013-03-03T16:55:11Z
A call for antibiotic alternatives research
- Abstract: March 2013
  Publication year: 2013
  Source:Trends in Microbiology, Volume 21, Issue 3
  
  The persistence and spread of antibiotic resistance, in conjunction with decreased profitability of new antibiotics, have created the dangerous prospect of ineffective therapies against bacterial diseases. National strategies aimed at discovery, development, and definition of the mechanisms of effective antibiotic alternatives, especially for agricultural applications, should be encouraged.
  
  PubDate: 2013-03-03T16:55:11Z
Treatment, promotion, commotion: antibiotic alternatives in food-producing animals
- Abstract: March 2013
  Publication year: 2013
  Source:Trends in Microbiology, Volume 21, Issue 3
  
  Alternatives to antibiotics are urgently needed in animal agriculture. The form these alternatives should take presents a complex problem due to the various uses of antibiotics in animal agriculture, including disease treatment, disease prevention, and growth promotion, and to the relative contribution of these uses to the antibiotic resistance problem. Numerous antibiotic alternatives, such as pre- and probiotics, have been proposed but show variable success. This is because a fundamental understanding of how antibiotics improve feed efficiency is lacking, and because an individual alternative is unlikely to embody all of the performance-enhancing functions of antibiotics. High-throughput technologies need to be applied to better understand the problem, and informed combinations of alternatives, including vaccines, need to be considered.
  Highlights ► Antibiotics need to be used more prudently both in human medicine and in animal agriculture. ► Antibiotics in agriculture are more likely to be replaced by multiple substitutes or combined approaches. ► High-throughput technologies could help to inform the design of antibiotic alternatives.
  
  PubDate: 2013-03-03T16:55:11Z
The limits for life under multiple extremes
- Abstract: Available online 27 February 2013
  Publication year: 2013
  Source:Trends in Microbiology
  
  Life on Earth is limited by physical and chemical extremes that define the ‘habitable space’ within which it operates. Aside from its requirement for liquid water, no definite limits have been established for life under any extreme. Here, we employ growth data published for 67 prokaryotic strains to explore the limitations for microbial life under combined extremes of temperature, pH, salt (NaCl) concentrations, and pressure. Our review reveals a fundamental lack of information on the tolerance of microorganisms to multiple extremes that impedes several areas of science, ranging from environmental and industrial microbiology to the search for extraterrestrial life.
  
  PubDate: 2013-02-28T13:07:24Z
The intestinal microbiota and host immune interactions in the critically ill
- Abstract: Available online 28 February 2013
  Publication year: 2013
  Source:Trends in Microbiology
  
  The gastrointestinal tract harbors a complex population of microbes that play a fundamental role in the development of the immune system and human health. Besides an important local contribution in the host defense against infections, it has become increasingly clear that intestinal bacteria also modulate immune responses at systemic sites. These new insights can be of profound clinical relevance especially for intensive care medicine where the majority of patients are treated with antibiotics, which have pervasive and long-term effects on the intestinal microbiota. Moreover, considerable progress has been made in defining the role of the intestinal microbiota in both health and disease. In this review, we highlight these aspects and focus on recent key findings addressing the role of intestinal microbiota in antimicrobial defense mechanisms and its impact on intestinal homeostasis in the critically ill.
  
  PubDate: 2013-02-28T13:07:24Z
Mycoplasmas and their host: emerging and re-emerging minimal pathogens
- Abstract: Available online 16 February 2013
  Publication year: 2013
  Source:Trends in Microbiology
  
  Commonly known as mycoplasmas, bacteria of the class Mollicutes include the smallest and simplest life forms capable of self replication outside of a host. Yet, this minimalism hides major human and animal pathogens whose prevalence and occurrence have long been underestimated. Owing to advances in sequencing methods, large data sets have become available for a number of mycoplasma species and strains, providing new diagnostic approaches, typing strategies, and means for comprehensive studies. A broader picture is thus emerging in which mycoplasmas are successful pathogens having evolved a number of mechanisms and strategies for surviving hostile environments and adapting to new niches or hosts.
  Highlights ► Emerging and re-emerging pathogenic mycoplasmas best exploit their minimal genome. ► Advances in genomics allow understanding of prevalence and evolution of mycoplasmas. ► Advances in genomics improve our understanding of mycoplasma infections.
  
  PubDate: 2013-02-20T05:46:16Z
Bacterial lifestyle shapes stringent response activation
- Abstract: Available online 16 February 2013
  Publication year: 2013
  Source:Trends in Microbiology
  
  Bacteria inhabit enormously diverse niches and have a correspondingly large array of regulatory mechanisms to adapt to often inhospitable and variable environments. The stringent response (SR) allows bacteria to quickly reprogram transcription in response to changes in nutrient availability. Although the proteins controlling this response are conserved in almost all bacterial species, recent work has illuminated considerable diversity in the starvation cues and regulatory mechanisms that activate stringent signaling proteins in bacteria from different environments. In this review, we describe the signals and genetic circuitries that control the stringent signaling systems of a copiotroph, a bacteriovore, an oligotroph, and a mammalian pathogen – Escherichia coli, Myxococcus xanthus, Caulobacter crescentus, and Mycobacterium tuberculosis, respectively – and discuss how control of the SR in these species is adapted to their particular lifestyles.
  
  PubDate: 2013-02-20T05:46:16Z
Streptococcus pneumoniae and reactive oxygen species: an unusual approach to living with radicals
- Abstract: Available online 13 February 2013
  Publication year: 2013
  Source:Trends in Microbiology
  
  Streptococcus pneumoniae, an aerotolerant anaerobe, is an important human pathogen that regularly encounters toxic oxygen radicals from the atmosphere and from the host metabolism and immune system. Additionally, S. pneumoniae produces large amounts of H2O2 as a byproduct of its metabolism, which contributes to its virulence but also has adverse effects on its biology. Understanding how S. pneumoniae defends against oxidative stress is far from complete, but it is apparent that it does not follow the current paradigm of having canonical enzymes to detoxify oxygen radicals or homologues of typical oxidative stress responsive global regulators. We will give an overview of how S. pneumoniae copes with oxygen radicals. Furthermore, we draw parallels with other pathogenic streptococcal species and provide future research perspectives.
  Highlights ► Repertoire of oxidative detoxification and repair mechanisms is unique for S. pneumoniae. ► Endogenous production of H2O2 shapes pneumococcal oxidative stress response. ► Regulation of oxidative stress resistance is largely unknown. ► Manganese and zinc are the main cations involved in oxidative stress.
  
  PubDate: 2013-02-16T02:09:21Z
Interferon-induced ISG15 pathway: an ongoing virus–host battle
- Abstract: Available online 14 February 2013
  Publication year: 2013
  Source:Trends in Microbiology
  
  ISG15 is an interferon (IFN)-induced ubiquitin-like protein that is conjugated to target proteins via the sequential action of three enzymes that are also induced by IFN. Unlike ubiquitin, which is highly conserved, the sequence of ISG15 varies between species. ISG15 conjugation inhibits many viruses, and free (unconjugated) ISG15 can also act as an antiviral protein. In this review, we focus on the antiviral role of ISG15 conjugation and on countermeasures employed by several viruses. The countermeasure by influenza B virus is unique in that it exhibits species specificity. Only the antiviral activity of human and non-human primate ISG15s can be blocked, providing one possible explanation for the restriction of influenza B virus to humans.
  Highlights ► ISG15 has antiviral activity and is conjugated to viral proteins during infection. ► Some viral proteins bind ISG15 to counter its antiviral activity. ► NS1B protein of influenza B virus binds only human and non-human primate ISG15s. ► Other viral proteins remove ISG15 from proteins to counter antiviral activity.
  
  PubDate: 2013-02-16T02:09:21Z
Eukaryotic virulence determinants utilize phosphoinositides at the ER and host cell surface
- Abstract: Available online 30 January 2013
  Publication year: 2013
  Source:Trends in Microbiology
  
  Similar to bacteria, eukaryotic pathogens may utilize common strategies of pathogenic secretion, because effector proteins from the oomycete Phytophthora infestans and virulence determinants from the human malaria parasite Plasmodium falciparum share a functionally equivalent host-cell-targeting motif (RxLR-dEER in P. infestans and RxLxE/D/Q in P. falciparum). Here we summarize recent studies that reveal that the malarial motif may function differently than previously envisioned. Binding of the lipid phosphatidylinositol 3-phosphate [PI(3)P] is a critical step in accessing the host for both pathogens, but occurs in different locations. Nanomolar affinity for PI(3)P by these short amino acid motifs suggests that a newly identified mechanism of phosphoinositide binding that unexpectedly occurs in secretory locations has been exploited for virulence by diverse eukaryotic pathogens.
  Highlights ► Eukaryotic pathogens use common strategies to target virulence proteins into host cells. ► Binding of the lipid PI(3)P is a critical step in virulence-related trafficking. ► The high PI(3)P affinity of effectors from pathogens defines them as novel lipid-interacting proteins.
  
  PubDate: 2013-02-01T16:40:26Z
Editorial Board
- Abstract: February 2013
  Publication year: 2013
  Source:Trends in Microbiology, Volume 21, Issue 2
  
  PubDate: 2013-02-01T16:40:26Z
Response to Sutcliffe et al.: regarding the International Committee on Systematics of Prokaryotes
- Abstract: Available online 11 January 2013
  Publication year: 2013
  Source:Trends in Microbiology
  
  PubDate: 2013-01-19T07:55:14Z
Development of intestinal microbiota in infants and its impact on health
- Abstract: Available online 14 January 2013
  Publication year: 2013
  Source:Trends in Microbiology
  
  Throughout the human lifetime, the intestinal microbiota performs vital functions, such as barrier function, metabolic reactions, trophic effects, and maturation of the host's innate and adaptive immune responses. Development of the intestinal microbiota in infants is characterized by rapid and large changes in microbial abundance, diversity, and composition. These changes are influenced by medical, cultural, and environmental factors such as mode of delivery, diet, familial environment, diseases, and therapies used. Thus, it is nearly impossible to define a universal standard for intestinal colonization and development of the intestinal microbiota. This review discusses recent data on the early colonization of the gut by microbial species, development of the intestinal microbiota, and its impact on health.
  Highlights ► A standard pattern for human intestinal microbiota colonization is unpredictable. ► Patients’ intestinal microbiota should be considered in designing personalized therapies. ► Microbiota colonization during the neonatal period is a key point for adult health. ► Limitation and rationalization of neonatal antibiotic treatments is urgently needed.
  
  PubDate: 2013-01-19T07:55:14Z
Emerging therapies for multidrug resistant Acinetobacter baumannii
- Abstract: Available online 11 January 2013
  Publication year: 2013
  Source:Trends in Microbiology
  
  The global emergence of multidrug resistant Acinetobacter baumannii has reduced the number of clinically available antibiotics that retain activity against this pathogen. For this reason, the development of novel prevention and treatment strategies for infections caused by A. baumannii is necessary. Several studies have begun to characterize nonantibiotic approaches that utilize novel mechanisms of action to achieve antibacterial activity. Recent advances in phage therapy, iron chelation therapy, antimicrobial peptides, prophylactic vaccination, photodynamic therapy, and nitric oxide (NO)-based therapies have all been shown to have activity against A. baumannii. However, before these approaches can be used clinically there are still limitations and remaining questions that must be addressed.
  
  PubDate: 2013-01-19T07:55:14Z
Influence of bacterial interactions on pneumococcal colonization of the nasopharynx
- Abstract: Available online 25 December 2012
  Publication year: 2012
  Source:Trends in Microbiology
  
  Streptococcus pneumoniae (the pneumococcus) is a common commensal inhabitant of the nasopharynx and a frequent etiologic agent in serious diseases such as pneumonia, otitis media, bacteremia, and meningitis. Multiple pneumococcal strains can colonize the nasopharynx, which is also home to many other bacterial species. Intraspecies and interspecies interactions influence pneumococcal carriage in important ways. Co-colonization by two or more pneumococcal strains has implications for vaccine serotype replacement, carriage detection, and pneumonia diagnostics. Interactions between the pneumococcus and other bacterial species alter carriage prevalence, modulate virulence, and affect biofilm formation. By examining these interactions, this review highlights how the bacterial ecosystem of the nasopharynx changes the nature and course of pneumococcal carriage.
  Highlights ► Streptococcus pneumoniae is a member of a complex microbial community in the nasopharynx. ► Co-colonization with ≥2 strains is common, facilitating recombination and affecting density. ► Interactions with other nasopharyngeal bacteria influence carriage prevalence and virulence. ► Interspecies quorum-sensing may regulate nasopharyngeal bacterial biofilm formation.
  
  PubDate: 2012-12-28T15:13:10Z
HIV Gag polyprotein: processing and early viral particle assembly
- Abstract: Available online 22 December 2012
  Publication year: 2012
  Source:Trends in Microbiology
  
  Over the past several decades, extensive research into the Gag polyprotein, the main structural protein of HIV-1 and all other retroviruses, has changed the way that we describe Gag's role within viral lifecycles. Initially thought of as a simple scaffold protein forming the viral core, Gag has demonstrated the ability to specifically recognize genomic RNA and both viral and host proteins as it traffics to the cell membrane. There, Gag forms higher ordered structures required for the correct assembly, budding, and maturation of new infectious particles.
  
  PubDate: 2012-12-24T10:54:16Z
Synthase-dependent exopolysaccharide secretion in Gram-negative bacteria
- Abstract: Available online 29 October 2012
  Publication year: 2012
  Source:Trends in Microbiology
  
  The biosynthesis and export of bacterial cell-surface polysaccharides is known to occur through several distinct mechanisms. Recent advances in the biochemistry and structural biology of several proteins in synthase-dependent polysaccharide secretion systems have identified key conserved components of this pathway in Gram-negative bacteria. These components include an inner-membrane-embedded polysaccharide synthase, a periplasmic tetratricopeptide repeat (TPR)-containing scaffold protein, and an outer-membrane β-barrel porin. There is also increasing evidence that many synthase-dependent systems are post-translationally regulated by the bacterial second messenger bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP). Here, we compare these core proteins in the context of the alginate, cellulose, and poly-β-d-N-acetylglucosamine (PNAG) secretion systems.
  
  PubDate: 2012-12-17T05:34:46Z
Pyocyanin effects on respiratory epithelium: relevance in Pseudomonas aeruginosa airway infections
- Abstract: Available online 7 November 2012
  Publication year: 2012
  Source:Trends in Microbiology
  
  Pseudomonas aeruginosa (PA) uses several virulence factors to establish chronic respiratory infections in bronchiectasis, chronic obstructive pulmonary disease, and cystic fibrosis (CF) patients. One of its toxins, pyocyanin (PYO), is a redox-active pigment that is required for full virulence in animal models and has been detected in patients’ airway secretions. PYO promotes virulence by interfering with several cellular functions in host cells including electron transport, cellular respiration, energy metabolism, gene expression, and innate immune mechanisms. This review summarizes recent advances in PYO biology with special attention to current views on its role in human airway infections and on its interactions with the first line of our airway defense, the respiratory epithelium.
  Highlights ► Pyocyanin (PYO) is a redox-active virulence factor of Pseudomonas aeruginosa. ► PYO promotes inflammatory responses by imposing oxidative stress on host cells. ► PYO is required for full virulence in several models of P. aeruginosa infection. ► PYO levels were correlated with declining lung function in cystic fibrosis.
  
  PubDate: 2012-12-17T05:34:46Z
Back to the future: revisiting HIV-1 lethal mutagenesis
- Abstract: Available online 27 November 2012
  Publication year: 2012
  Source:Trends in Microbiology
  
  The concept of eliminating HIV-1 infectivity by elevating the viral mutation rate was first proposed over a decade ago, even though the general concept had been conceived earlier for RNA viruses. Lethal mutagenesis was originally viewed as a novel chemotherapeutic approach for treating HIV-1 infection in which use of a viral mutagen would over multiple rounds of replication lead to the lethal accumulation of mutations, rendering the virus population noninfectious – known as the slow mutation accumulation model. There have been limitations in obtaining good efficacy data with drug leads, leaving some doubt on clinical translation. More recent studies of the apolipoprotein B mRNA editing complex 3 (APOBEC3) proteins as well as new progress in the use of nucleoside analogs for inducing lethal mutagenesis have helped to refocus attention on rapid induction of HIV-1 lethal mutagenesis in a single or limited number of replication cycles leading to a rapid mutation accumulation model.
  
  PubDate: 2012-12-17T05:34:46Z
A call to action for the International Committee on Systematics of Prokaryotes
- Abstract: Available online 11 December 2012
  Publication year: 2012
  Source:Trends in Microbiology
  
  PubDate: 2012-12-17T05:34:46Z
Chlamydia pneumoniae: modern insights into an ancient pathogen
- Abstract: Available online 5 December 2012
  Publication year: 2012
  Source:Trends in Microbiology
  
  Chlamydia pneumoniae is an enigmatic human and animal pathogen. Originally discovered in association with acute human respiratory disease, it is now associated with a remarkably wide range of chronic diseases as well as having a cosmopolitan distribution within the animal kingdom. Molecular typing studies suggest that animal strains are ancestral to human strains and that C. pneumoniae crossed from animals to humans as the result of at least one relatively recent zoonotic event. Whole genome analyses appear to support this concept – the human strains are highly conserved whereas the single animal strain that has been fully sequenced has a larger genome with several notable differences. When compared to the other, better known chlamydial species that is implicated in human infection, Chlamydia trachomatis, C. pneumoniae demonstrates pertinent differences in its cell biology, development, and genome structure. Here, we examine the characteristic facets of C. pneumoniae biology, offering insights into the diversity and evolution of this silent and ancient pathogen.
  
  PubDate: 2012-12-17T05:34:46Z