New aspects of RNA-based regulation by Hfq and its partner sRNAs.
Abstract Hfq, an RNA chaperone, promotes the pairing of small RNAs (sRNAs) to target mRNAs, mediating post-transcriptional regulation of mRNA stability and translation. This regulation contributes to bacterial adaptation during stress and pathogenesis. Recent advances in sequencing techniques demonstrate the presence of sRNAs encoded not only in intergenic regions but also from the 3' and 5' UTRs of mRNAs, expanding sRNA regulatory networks. Additional layers of regulation by Hfq and its associated RNAs continue to be found. Newly identified RNA sponges modulate the activity of some sRNAs. A subset of sRNAs are pr...
Source: Current Opinion in Microbiology - November 7, 2017 Category: Microbiology Authors: Kavita K, de Mets F, Gottesman S Tags: Curr Opin Microbiol Source Type: research

Regulation of microbial growth by turgor pressure.
Abstract Rapid changes in environmental osmolarity are a natural aspect of microbial lifestyles. The change in turgor pressure resulting from an osmotic shock alters the mechanical forces within the cell envelope, and can impact cell growth across a range of timescales, through a variety of mechanical mechanisms. Here, we first summarize measurements of turgor pressure in various organisms. We then review how the combination of microfluidic flow cells and quantitative image analysis has driven discovery of the diverse ways in which turgor pressure mechanically regulates bacterial growth, independent of the effect ...
Source: Current Opinion in Microbiology - November 7, 2017 Category: Microbiology Authors: Rojas ER, Huang KC Tags: Curr Opin Microbiol Source Type: research

Commensal Koch's postulates: establishing causation in human microbiota research.
Abstract Advances in high-throughput sequencing technologies and the development of sophisticated bioinformatics analysis methods, algorithms, and pipelines to handle the large amounts of data generated have driven the field of human microbiome research forward. This specialist knowledge has been crucial to thoroughly mine the human gut microbiota, particularly in the absence of methods for the routine cultivation of most enteric microorganisms. In recent years, however, significant efforts have been made to address the 'great plate count anomaly' and to overcome the barriers to cultivation of the fastidious and m...
Source: Current Opinion in Microbiology - November 4, 2017 Category: Microbiology Authors: Neville BA, Forster SC, Lawley TD Tags: Curr Opin Microbiol Source Type: research

CryoEM-based hybrid modeling approaches for structure determination.
Abstract Recent advances in cryo-electron microscopy (cryoEM) have dramatically improved the resolutions at which vitrified biological specimens can be studied, revealing new structural and mechanistic insights over a broad range of spatial scales. Bolstered by these advances, much effort has been directed toward the development of hybrid modeling methodologies for the construction and refinement of high-fidelity atomistic models from cryoEM data. In this brief review, we will survey the key elements of cryoEM-based hybrid modeling, providing an overview of available computational tools and strategies as well as s...
Source: Current Opinion in Microbiology - November 3, 2017 Category: Microbiology Authors: Cassidy CK, Himes BA, Luthey-Schulten Z, Zhang P Tags: Curr Opin Microbiol Source Type: research

Infection by bacteriophage lambda: an evolving paradigm for cellular individuality.
Abstract Since the earliest days of molecular biology, bacteriophage lambda has served to illuminate cellular function. Among its many roles, lambda infection is a paradigm for phenotypic heterogeneity among genetically identical cells. Early studies attributed this cellular individuality to random biochemical fluctuations, or 'noise'. More recently, however, attention has turned to the role played by deterministic hidden variables in driving single-cell behavior. Here, I briefly describe how studies in lambda are driving the shift in our understanding of cellular heterogeneity, allowing us to better appreciate th...
Source: Current Opinion in Microbiology - November 3, 2017 Category: Microbiology Authors: Golding I Tags: Curr Opin Microbiol Source Type: research

The mucormycete-host interface.
Abstract Mucormycosis is a fungal infection with fulminant angioinvasion leading to high morbidity and mortality in susceptible individuals. The major predisposing conditions are uncontrolled diabetes, neutropenia, malignancies, receipt of a transplant and traumatic injury [1]. Over the past decade, mucormycosis has become an emerging fungal infection due to the increase in patient groups presenting with these pre-disposing conditions and our medical advances in diagnosing the infection [2-4]. Yet, we currently lack clinical interventions to treat mucormycosis effectively. This in turn is due to a lack of understa...
Source: Current Opinion in Microbiology - November 3, 2017 Category: Microbiology Authors: Ibrahim AS, Voelz K Tags: Curr Opin Microbiol Source Type: research

How Toxoplasma and malaria parasites defy first, then exploit host autophagic and endocytic pathways for growth.
Abstract Infections caused by the apicomplexan parasites Plasmodium and Toxoplasma are wide-spread, life-threatening and therapeutically challenging. These pathogens are obligate intracellular microorganisms that invade mammalian cells by forming a self-made niche, the parasitophorous vacuole that is impervious to host lysosomal fusion. Shortly after invasion, a noncanonical xenophagic pathway resembling LC3-associated phagocytosis is activated by the host cell to control infections. However, Plasmodium and Toxoplasma have elaborated strategies to avoid clearance by the sentinel activities of the host autophagic s...
Source: Current Opinion in Microbiology - November 2, 2017 Category: Microbiology Authors: Coppens I Tags: Curr Opin Microbiol Source Type: research

Staphylococcal pathogenicity islands-movers and shakers in the genomic firmament.
Abstract The staphylococcal pathogenicity islands (SaPIs) are highly mobile 15kb genomic islands that carry superantigen genes and other virulence factors and are mobilized by helper phages. Helper phages counteract the SaPI repressor to induce the SaPI replication cycle, resulting in encapsidation in phage like particles, enabling high frequency transfer. The SaPIs split from a protophage lineage in the distant past, have evolved a variety of novel and salient features, and have become an invaluable component of the staphylococcal genome. This review focuses on recent studies describing three different mechanisms...
Source: Current Opinion in Microbiology - October 31, 2017 Category: Microbiology Authors: Novick RP, Ram G Tags: Curr Opin Microbiol Source Type: research

Big data in cryoEM: automated collection, processing and accessibility of EM data.
Abstract The scope and complexity of cryogenic electron microscopy (cryoEM) data has greatly increased, and will continue to do so, due to recent and ongoing technical breakthroughs that have led to much improved resolutions for macromolecular structures solved using this method. This big data explosion includes single particle data as well as tomographic tilt series, both generally acquired as direct detector movies of ∼10-100 frames per image or per tilt-series. We provide a brief survey of the developments leading to the current status, and describe existing cryoEM pipelines, with an emphasis on the scope o...
Source: Current Opinion in Microbiology - October 31, 2017 Category: Microbiology Authors: Baldwin PR, Tan YZ, Eng ET, Rice WJ, Noble AJ, Negro CJ, Cianfrocco MA, Potter CS, Carragher B Tags: Curr Opin Microbiol Source Type: research

Autophagy in apicomplexan parasites.
Abstract Autophagy is a highly conserved eukaryotic degradation process that permits the recycling of intracellular components. The molecular machinery and the functions of autophagy have been classically characterized in mammalian cells and yeast, but have long remained unexplored in less-studied eukaryotes. Apicomplexan parasites are early-diverging eukaryotes responsible for a number of important human and veterinary diseases. In light of recent investigations into autophagy function in two of these pathogens, Plasmodium and Toxoplasma, it seems their autophagy-related machinery could be involved in both a cano...
Source: Current Opinion in Microbiology - October 30, 2017 Category: Microbiology Authors: Besteiro S Tags: Curr Opin Microbiol Source Type: research

Molecular interactions governing host-specificity of blood stage malaria parasites.
Abstract Non-human primates harbor diverse species of malaria parasites, including the progenitors of Plasmodium falciparum and Plasmodium vivax. Cross-species transmission of some malaria parasites-most notably the macaque parasite, Plasmodium knowlesi-continues to this day, compelling the scientific community to ask whether these zoonoses could impede malaria control efforts by acting as a source of recurrent human infection. Host-restriction varies considerably among parasite species and is governed by both ecological and molecular variables. In particular, the efficiency of red blood cell invasion constitutes ...
Source: Current Opinion in Microbiology - October 30, 2017 Category: Microbiology Authors: Scully EJ, Kanjee U, Duraisingh MT Tags: Curr Opin Microbiol Source Type: research

Differentiation of the fungus Histoplasma capsulatum into a pathogen of phagocytes.
Abstract Mammalian body temperature triggers differentiation of the fungal pathogen Histoplasma capsulatum into yeast cells. The Drk1 regulatory kinase and an interdependent network of Ryp transcription factors establish the yeast state. Beyond morphology, the differentiation-dependent expression program equips yeasts for invasion and survival within phagosomes. Yeast cells produce α-glucan and the Eng1 endoglucanase which hide yeasts from immune detection. Secretion of yeast phase-specific Sod3 and CatB detoxify phagocyte-derived reactive oxygen molecules. Histoplasma cells adapt to iron and zinc limitation...
Source: Current Opinion in Microbiology - October 26, 2017 Category: Microbiology Authors: Shen Q, Rappleye CA Tags: Curr Opin Microbiol Source Type: research

Lung epithelium: barrier immunity to inhaled fungi and driver of fungal-associated allergic asthma.
Abstract Fungi are ubiquitous in the environment. The epithelium that lines our airways is the first point of contact with the frequent encounter of inhaled fungi. Consequently, the lung epithelium has evolved behaviors that instruct the earliest immune events to resist fungal penetration. Although the epithelium efficiently assists in immunity to invasive fungi, it also can be inappropriately triggered, to the detriment of the host, by normally innocuous fungi or fungal components. Thus, there is a tipping point of protective immunity against fungal pathogens versus inflammatory disease caused by an exuberant imm...
Source: Current Opinion in Microbiology - October 26, 2017 Category: Microbiology Authors: Wiesner DL, Klein BS Tags: Curr Opin Microbiol Source Type: research

Contact-dependent interbacterial toxins deliver a message.
Abstract Both Gram-negative and Gram-positive organisms harbor systems for delivering toxins to neighboring bacteria upon direct cell contact. These systems, typified by type VI secretion (T6S) and contact-dependent growth inhibition (CDI) systems, are defined by their ability to mediate interbacterial competition in vitro, while their biological roles have remained uncertain. Recent research into the mechanisms of toxin delivery and activity, as well as investigation of contact-dependent toxin function during relevant biological processes, has offered insight into how interbacterial competition might work outside...
Source: Current Opinion in Microbiology - October 24, 2017 Category: Microbiology Authors: Garcia EC Tags: Curr Opin Microbiol Source Type: research

Immune cell type 'fingerprints' at the basis of outcome diversity of human infection.
Abstract Despite the availability of antibiotics and immunization, infectious diseases remain a major cause of malignancy and death worldwide. Yet, it is well documented that for most infectious agents, clinical disease develops in only a small minority of infected individuals. There is, in fact, great heterogeneity in infection outcome, from complete clearance of the pathogen to severe illness. Understanding this variation remains elusive, despite its great potential to equip us with new tools for the treatment of infectious diseases. Here, we propose a novel perspective for studying this diversity in human infec...
Source: Current Opinion in Microbiology - October 16, 2017 Category: Microbiology Authors: Hen-Avivi S, Avraham R Tags: Curr Opin Microbiol Source Type: research

Antibiotic efficacy-context matters.
Abstract Antibiotic lethality is a complex physiological process, sensitive to external cues. Recent advances using systems approaches have revealed how events downstream of primary target inhibition actively participate in antibiotic death processes. In particular, altered metabolism, translational stress and DNA damage each contribute to antibiotic-induced cell death. Moreover, environmental factors such as oxygen availability, extracellular metabolites, population heterogeneity and multidrug contexts alter antibiotic efficacy by impacting bacterial metabolism and stress responses. Here we review recent studies ...
Source: Current Opinion in Microbiology - October 16, 2017 Category: Microbiology Authors: Yang JH, Bening SC, Collins JJ Tags: Curr Opin Microbiol Source Type: research

Systems proteomics approaches to study bacterial pathogens: application to Mycobacterium tuberculosis.
Abstract Significant developments and improvements in basic and clinical research notwithstanding, infectious diseases still claim at least 13 million lives annually. Classical research approaches have deciphered many molecular mechanisms underlying infection. Today it is increasingly recognized that multiple molecular mechanisms cooperate to constitute a complex system that is used by a given pathogen to interfere with the biochemical processes of the host. Therefore, systems-level approaches now complement the standard molecular biology techniques to investigate pathogens and their interactions with the human ho...
Source: Current Opinion in Microbiology - October 12, 2017 Category: Microbiology Authors: Banaei-Esfahani A, Nicod C, Aebersold R, Collins BC Tags: Curr Opin Microbiol Source Type: research

'Exploring' the regulation of Streptomyces growth and development.
Abstract The Streptomyces life cycle encompasses three well-established developmental stages: vegetative hyphae, aerial hyphae and spores. Many regulators governing the transitions between these life cycle stages have been identified, and recent work is shedding light on their specific functions. A new discovery has shown Streptomyces can deviate from this classic life cycle through a process termed 'exploration', where cells rapidly traverse solid surfaces. Exploration does not require any of the traditional developmental regulators, and therefore provides an exciting new context in which to uncover novel develop...
Source: Current Opinion in Microbiology - October 9, 2017 Category: Microbiology Authors: Jones SE, Elliot MA Tags: Curr Opin Microbiol Source Type: research

Heterogeneity of Salmonella-host interactions in infected host tissues.
Abstract Infected host tissues have complex anatomy, diverse cell types, and dynamic inflammation. Traditional infection biology approaches largely ignore this complex host environment and its impact on pathogens, but recent single-cell technologies unravel extensively heterogeneous host-pathogen interactions in vivo. Salmonella are major model pathogens in this field due to the availability of excellent mouse disease models and facile molecular biology. The results show how Salmonella stochastically vary their virulence, exploit differential nutrient availability, experience and respond to widely varying stresses...
Source: Current Opinion in Microbiology - October 5, 2017 Category: Microbiology Authors: Bumann D, Cunrath O Tags: Curr Opin Microbiol Source Type: research

Antibiotic efficacy in the complex infection environment.
Abstract Accurate prediction of antimicrobial efficacy is essential for successful treatment of bacterial infection. Beyond genetically encoded mechanisms of antibiotic resistance, the determinants of antibiotic susceptibility during infection remain poorly understood, and treatment failure is common. Traditional antibiotic susceptibility testing fails to account for extrinsic determinants of antibiotic susceptibility present in the complex infection environment and is therefore a poor predictor of antibiotic treatment outcome. Here we discuss how host-pathogen interaction, microbial interspecies interaction, and ...
Source: Current Opinion in Microbiology - October 5, 2017 Category: Microbiology Authors: Radlinski L, Conlon BP Tags: Curr Opin Microbiol Source Type: research

Transcription fidelity and its roles in the cell.
Abstract Accuracy of transcription is essential for productive gene expression, and the past decade has brought new understanding of the mechanisms ensuring transcription fidelity. The discovery of a new catalytic domain, the Trigger Loop, revealed that RNA polymerase can actively choose the correct substrates. Also, the intrinsic proofreading activity was found to proceed via a ribozyme-like mechanism, whereby the erroneous nucleoside triphosphate (NTP) helps its own excision. Factor-assisted proofreading was shown to proceed through an exchange of active centres, a unique phenomenon among proteinaceous enzymes. ...
Source: Current Opinion in Microbiology - September 29, 2017 Category: Microbiology Authors: Gamba P, Zenkin N Tags: Curr Opin Microbiol Source Type: research

Phage therapy as an alternative or complementary strategy to prevent and control biofilm-related infections.
Abstract The complex heterogeneous structure of biofilms confers to bacteria an important survival strategy. Biofilms are frequently involved in many chronic infections in consequence of their low susceptibility to antibiotics as well as resistance to host defences. The increasing need of novel and effective treatments to target these complex structures has led to a growing interest on bacteriophages (phages) as a strategy for biofilm control and prevention. Phages can be used alone, as a cocktail to broaden the spectra of activity, or in combination with other antimicrobials to improve their efficacy. Here, we su...
Source: Current Opinion in Microbiology - September 28, 2017 Category: Microbiology Authors: Pires DP, Melo L, Vilas Boas D, Sillankorva S, Azeredo J Tags: Curr Opin Microbiol Source Type: research

Fungal diversity at fragmented landscapes: synthesis and future perspectives.
Abstract Fungi are organisms with important roles in ecosystem functioning and services, but knowledge about how habitat fragmentation affect fungal diversity is biased by experimental approaches and it is spread in different trophic groups. We analyzed the empirical evidences of fungal diversity in fragmented landscapes, and proposed future perspectives for the study of these organisms under land use changes. Fungal diversity might be negatively affected by habitat fragmentation; however, this trend may differ in magnitude depending on fungal groups and their nutritional habits. In addition, due to the fact that ...
Source: Current Opinion in Microbiology - September 28, 2017 Category: Microbiology Authors: Grilli G, Longo S, Huais PY, Pereyra M, Verga EG, Urcelay C, Galetto L Tags: Curr Opin Microbiol Source Type: research

Bacterial nanotubes: a conduit for intercellular molecular trade.
Abstract Bacteria use elaborate molecular machines for intercellular contact-dependent interactions. We discuss a relatively less explored type of intercellular connections mediated by tubular membranous bridges, termed nanotubes. Increasing evidence suggests that nanotube structures mediate cytoplasmic molecular trade among neighboring cells of the same and different species. Further, nanotubes were found to facilitate both antagonistic and cooperative interspecies interactions, thereby allowing the emergence of new non-heritable phenotypes in multicellular bacterial communities. We propose that nanotube-mediated...
Source: Current Opinion in Microbiology - September 26, 2017 Category: Microbiology Authors: Baidya AK, Bhattacharya S, Dubey GP, Mamou G, Ben-Yehuda S Tags: Curr Opin Microbiol Source Type: research

Two's company: studying interspecies relationships with dual RNA-seq.
e J Abstract Organisms do not exist isolated from each other, but constantly interact. Cells can sense the presence of interaction partners by a range of receptors and, via complex regulatory networks, specifically react by changing the expression of many of their genes. Technological advances in next-generation sequencing over the recent years now allow us to apply RNA sequencing to two species at the same time (dual RNA-seq), and thus to directly study the gene expression of two interacting species without the need to physically separate cells or RNA. In this review, we give an overview over the latest studies i...
Source: Current Opinion in Microbiology - September 25, 2017 Category: Microbiology Authors: Wolf T, Kämmer P, Brunke S, Linde J Tags: Curr Opin Microbiol Source Type: research

Chemical genomics reveals mechanistic hypotheses for uncharacterized bioactive molecules in bacteria.
Abstract In an effort to combat the perpetual emergence of new antibiotic-resistant human pathogens, research in industry and academe aims to find new means of controlling infection. The discovery of new antimicrobial chemicals is not the bottleneck in an era where high-throughput screening rapidly uncovers new bioactive compounds. Rather, the rate-limiting step in antimicrobial discovery pipelines is identifying mechanisms of action (MOA) of bioactive molecules produced by these increasingly large-scale efforts. Chemical genomics has proven to be of high value in providing mechanistic hypotheses for novel bioacti...
Source: Current Opinion in Microbiology - September 25, 2017 Category: Microbiology Authors: French S, Ellis MJ, Coutts BE, Brown ED Tags: Curr Opin Microbiol Source Type: research

Using CRISPR-Cas systems as antimicrobials.
Abstract Although CRISPR-Cas systems naturally evolved to provide adaptive immunity in bacteria and archaea, Cas nucleases can be co-opted to target chromosomal sequences rather than invasive genetic elements. Although genome editing is the primary outcome of self-targeting using CRISPR-based technologies in eukaryotes, self-targeting by CRISPR is typically lethal in bacteria. Here, we discuss how DNA damage introduced by Cas nucleases in bacteria can efficiently and specifically lead to plasmid curing or drive cell death. Specifically, we discuss how various CRISPR-Cas systems can be engineered and delivered usin...
Source: Current Opinion in Microbiology - September 5, 2017 Category: Microbiology Authors: Bikard D, Barrangou R Tags: Curr Opin Microbiol Source Type: research

Type III CRISPR-Cas systems: when DNA cleavage just isn't enough.
Abstract Type III CRISPR-Cas systems have a unique targeting mechanism that requires the transcription of the DNA target and results in the degradation of not only the genome of the invader but also its transcripts. Here we discuss the most recent studies describing dual DNA and RNA targeting by these systems, as well as the implications of this complex molecular mechanism for immunity in vivo. PMID: 28865392 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - August 30, 2017 Category: Microbiology Authors: Pyenson NC, Marraffini LA Tags: Curr Opin Microbiol Source Type: research

Systems-level interference strategies to decipher host factors involved in bacterial pathogen interaction: from RNAi to CRISPRi.
hio C Abstract Bacterial pathogen-host cell interactions involve an intricate interplay of multiple components from both partners. Systems level surveys have been used widely to profile host requirements for pathogen infection. Functional genomics, and more specifically genome-wide perturbation screens, constitute attractive methodologies to assess such host infectomes. Although these strategies have successfully identified numerous critical host factors, they may have failed in generating the high-quality data required for systems level analysis. This is the case for most RNA interference (RNAi) setups with their...
Source: Current Opinion in Microbiology - August 28, 2017 Category: Microbiology Authors: Québatte M, Dehio C Tags: Curr Opin Microbiol Source Type: research

Emergent properties of bacterial chemotaxis pathway.
Abstract The chemotaxis pathway of Escherichia coli is the most studied sensory system in prokaryotes. The highly conserved general architecture of this pathway consists of two modules which mediate signal transduction and adaptation. The signal transduction module detects and amplifies changes in environmental conditions and rapidly transmits these signals to control bacterial swimming behavior. The adaptation module gradually resets the activity and sensitivity of the first module after initial stimulation and thereby enables the temporal comparisons necessary for bacterial chemotaxis. Recent experimental and th...
Source: Current Opinion in Microbiology - August 16, 2017 Category: Microbiology Authors: Colin R, Sourjik V Tags: Curr Opin Microbiol Source Type: research

Towards detecting regulatory protein-metabolite interactions.
Abstract New mapping approaches have greatly expanded our view on the cellular landscape of protein-metabolite interactions. These methods either identify proteins interacting with a selected metabolite or vice versa. By reviewing recent developments, we found that comprehensive mapping of the protein-metabolite interaction space can be achieved eventually using existing methods, amongst which proteomics techniques to assess cell wide protein property changes in response to metabolite treatment currently offer the highest potential. Since we expect major advances in mapping protein-metabolite interactions in the n...
Source: Current Opinion in Microbiology - August 12, 2017 Category: Microbiology Authors: Diether M, Sauer U Tags: Curr Opin Microbiol Source Type: research

Elucidation of host-pathogen protein-protein interactions to uncover mechanisms of host cell rewiring.
Abstract Infectious diseases are the result of molecular cross-talks between hosts and their pathogens. These cross-talks are in part mediated by host-pathogen protein-protein interactions (HP-PPI). HP-PPI play crucial roles in infections, as they may tilt the balance either in favor of the pathogens' spread or their clearance. The identification of host proteins targeted by viral or bacterial pathogenic proteins necessary for the infection can provide insights into their underlying molecular mechanisms of pathogenicity, and potentially even single out pharmacological intervention targets. Here, we review the avai...
Source: Current Opinion in Microbiology - August 11, 2017 Category: Microbiology Authors: Nicod C, Banaei-Esfahani A, Collins BC Tags: Curr Opin Microbiol Source Type: research

Dysbiotic Proteobacteria expansion: a microbial signature of epithelial dysfunction.
AJ Abstract A balanced gut microbiota is important for health, but the mechanisms maintaining homeostasis are incompletely understood. Anaerobiosis of the healthy colon drives the composition of the gut microbiota towards a dominance of obligate anaerobes, while dysbiosis is often associated with a sustained increase in the abundance of facultative anaerobic Proteobacteria, indicative of a disruption in anaerobiosis. The colonic epithelium is hypoxic, but intestinal inflammation or antibiotic treatment increases epithelial oxygenation in the colon, thereby disrupting anaerobiosis to drive a dysbiotic expansion of...
Source: Current Opinion in Microbiology - August 4, 2017 Category: Microbiology Authors: Litvak Y, Byndloss MX, Tsolis RM, Bäumler AJ Tags: Curr Opin Microbiol Source Type: research

Understanding the holobiont: the interdependence of plants and their microbiome.
Poole PS, Tkacz A Abstract The holobiont is composed by the plant and its microbiome. In a similar way to ecological systems of higher organisms, the holobiont shows interdependent and complex dynamics [1,2]. While plants originate from seeds, the microbiome has a multitude of sources. The assemblage of these communities depends on the interaction between the emerging seedling and its surrounding environment, with soil being the main source. These microbial communities are controlled by the plant through different strategies, such as the specific profile of root exudates and its immune system. Despite this control...
Source: Current Opinion in Microbiology - July 18, 2017 Category: Microbiology Authors: Sánchez-Cañizares C, Jorrín B, Poole PS, Tkacz A Tags: Curr Opin Microbiol Source Type: research

Eco-Aging: stem cells and microbes are controlled by aging antagonist FoxO.
Abstract The review highlights the dual role that the conserved master regulator FoxO has in aging by coordinating both stem cell proliferation and antimicrobial peptides, effector molecules of the innate immune system. As observed in non-senescent Hydra, continuously high activity of the transcription factor FoxO contributes to continuous stem cell proliferation and could support robust colonization of epithelia with a stable microbiome. The integration of research from stem cell biology, microbiology and ecology into aging concepts (Eco-Aging) acknowledges the multi-organismic nature of all living beings and pre...
Source: Current Opinion in Microbiology - July 11, 2017 Category: Microbiology Authors: Mortzfeld BM, Bosch TC Tags: Curr Opin Microbiol Source Type: research

A three-act play: pentachlorophenol threats to the cork oak forest soils mycobiome.
Abstract Atmospheric release of persistent organic pollutants (POPs) constitutes a silent threat through chronic contamination of soils at global scale; yet fundamental understanding of their occurrence, sources and fate is still largely lacking. Similar to a three act play, this review comprises Setup, Confrontation and Resolution. The first emphasises the eighty years of the history of pentachlorophenol (PCP) usage, only recently classified as POP. The second focus on active sources of PCP pollution, including inside cork oak forests in N.W. Tunisia; a threat partially neutralised by the soil microbial diversity...
Source: Current Opinion in Microbiology - July 10, 2017 Category: Microbiology Authors: Varela A, Martins C, Silva Pereira C Tags: Curr Opin Microbiol Source Type: research

Linking fungal-bacterial co-occurrences to soil ecosystem function.
Abstract Fungi and bacteria are major players in soil biogeochemical cycles, however, most studies linking soil processes to microbial function ignore the potential role of interactions between these groups. A small number of studies have used correlation network analyses to investigate fungal-bacterial co-occurrences in soil, and revealed differences, as well as overlaps, in the ecosystem roles of these groups. These results contradict the view that fungi and bacteria are two distinct functional groups which can be studied in isolation. A more comprehensive understanding of the interplay between soil properties, ...
Source: Current Opinion in Microbiology - July 7, 2017 Category: Microbiology Authors: de Menezes AB, Richardson AE, Thrall PH Tags: Curr Opin Microbiol Source Type: research

Microbial activity and the dynamics of ecosystem processes in forest soils.
Abstract Microbial activity in forest soils is driven by the dynamics of ecosystem processes, largely dependent on trees as the major primary producers. Diurnal variation of root activity, seasonality of photosynthate production or recalcitrance of decomposing plant biomass all affect microbial abundance, composition of their communities and activity. Due to low N content, fungi appear to be the major decomposers of complex plant biomass: litter and deadwood and to largely shape associated bacterial communities and their activity. On the other hand, bacteria are important in decomposition of fungal mycelia and N-c...
Source: Current Opinion in Microbiology - July 6, 2017 Category: Microbiology Authors: Baldrian P Tags: Curr Opin Microbiol Source Type: research

Known knowns, known unknowns and unknown unknowns in prokaryotic transposition.
Abstract Although the phenomenon of transposition has been known for over 60 years, its overarching importance in modifying and streamlining genomes took some time to recognize. In spite of a robust understanding of transposition of some TE, there remain a number of important TE groups with potential high genome impact and unknown transposition mechanisms and yet others, only recently identified by bioinformatics, yet to be formally confirmed as mobile. Here, we point to some areas of limited understanding concerning well established important TE groups with DDE Tpases, to address central gaps in our knowledge of ...
Source: Current Opinion in Microbiology - July 3, 2017 Category: Microbiology Authors: Siguier P, Gourbeyre E, Chandler M Tags: Curr Opin Microbiol Source Type: research

Inhibition of CRISPR-Cas systems by mobile genetic elements.
Abstract Clustered, regularly interspaced, short, palindromic repeats (CRISPR) loci, together with their CRISPR-associated (Cas) proteins, provide bacteria and archaea with adaptive immunity against invasion by bacteriophages, plasmids, and other mobile genetic elements. These host defenses impart selective pressure on phages and mobile elements to evolve countermeasures against CRISPR immunity. As a consequence of this pressure, phages and mobile elements have evolved 'anti-CRISPR' proteins that function as direct inhibitors of diverse CRISPR-Cas effector complexes. Some of these CRISPR-Cas complexes can be deplo...
Source: Current Opinion in Microbiology - June 29, 2017 Category: Microbiology Authors: Sontheimer EJ, Davidson AR Tags: Curr Opin Microbiol Source Type: research

Microbial influence on Drosophila biology.
Abstract Commensal bacteria profoundly affect the biology of their animal partners. Drosophila melanogaster has been broadly used to study microbiota effects on invertebrates, whose findings are frequently applicable to translational studies. The beneficial role of commensal microbes on Drosophila biology is extensively described, ranging from growth to metabolism, immunity and even behaviour. However, the mechanisms underlying these effects are not well understood. Studies continue to discover new layers of complexity in the host-bacteria partnership that constantly changes depending on a plethora of different va...
Source: Current Opinion in Microbiology - June 29, 2017 Category: Microbiology Authors: Martino ME, Ma D, Leulier F Tags: Curr Opin Microbiol Source Type: research

Conformational regulation of CRISPR-associated nucleases.
Abstract Adaptive immune systems in bacteria and archaea rely on small CRISPR-derived RNAs (crRNAs) to guide specialized nucleases to foreign nucleic acids. The activation of these nucleases is controlled by a series of molecular checkpoints that ensure precise cleavage of nucleic acid targets, while minimizing toxic off-target cleavage events. In this review, we highlight recent advances in understanding regulatory mechanisms responsible for controlling the activation of these nucleases and identify emerging regulatory themes conserved across diverse CRISPR systems. PMID: 28646675 [PubMed - as supplied by pu...
Source: Current Opinion in Microbiology - June 21, 2017 Category: Microbiology Authors: Jackson RN, van Erp PB, Sternberg SH, Wiedenheft B Tags: Curr Opin Microbiol Source Type: research

Harnessing the natural diversity and in vitro evolution of Cas9 to expand the genome editing toolbox.
Abstract In the past few years, the Cas9 endonuclease from the type II CRISPR-Cas bacterial antiviral defense system has revolutionized the genome editing field. Guided by an RNA molecule, Cas9 can be reprogrammed to target almost any DNA sequence: the only limitation being the short nucleotide sequence in the vicinity of the target, termed the PAM, which is characteristic for each Cas9 protein. Streptococcus pyogenes Cas9 which recognizes the NGG PAM is currently most widely used for genome manipulation. However, Cas9 orthologues and engineered Cas9 variants offer expanded genome targeting capabilities, improved ...
Source: Current Opinion in Microbiology - June 20, 2017 Category: Microbiology Authors: Karvelis T, Gasiunas G, Siksnys V Tags: Curr Opin Microbiol Source Type: research

From complex gut communities to minimal microbiomes via cultivation.
Abstract The mammalian gut microbiota is dominated by populations of bacteria, mostly strict anaerobes. Because these bacteria can influence the health of their host, it is important to investigate their diversity and functions, which can be done via culture-based or molecular approaches. In recent years, microbiologists have very often preferred the use of molecular techniques, as they do not limit the analysis to the fraction of communities that can be grown in the laboratory. In reality, cultivation and molecular methods are complementary, and we are now witnessing a period of unification. Obtaining strains tha...
Source: Current Opinion in Microbiology - June 15, 2017 Category: Microbiology Authors: Clavel T, Lagkouvardos I, Stecher B Tags: Curr Opin Microbiol Source Type: research

Toward a genetic tool development pipeline for host-associated bacteria.
Abstract Bacteria reside in externally accessible niches on and in multicellular organisms, often forming mutualistic relationships with their host. Recent studies have linked the composition of these microbial communities with alterations in the host's health, behavior, and development, yet the causative mediators of host-microbiota interactions remain poorly understood. Advances in understanding and engineering these interactions require the development of genetic tools to probe the molecular interactions driving the structure and function of microbial communities as well as their interactions with their host. T...
Source: Current Opinion in Microbiology - June 15, 2017 Category: Microbiology Authors: Waller MC, Bober JR, Nair NU, Beisel CL Tags: Curr Opin Microbiol Source Type: research

The CRISPR-Cas app goes viral.
Abstract If biology laboratories were smartphones, CRISPR-Cas would be the leading app. Nowadays, technology users rely on apps to communicate, get directions, entertain, and more. Likewise, many life scientists now rely on CRISPR-Cas systems to study the interactions between microbes and their viruses, to track strains as well as to modify and modulate genomes. Considering their high level of polymorphism, CRISPR arrays can increase the resolution of a microbial typing scheme. As dynamic systems, they allow the identification and the tracking of specific sequences, which is highly valuable for epidemiological stu...
Source: Current Opinion in Microbiology - June 14, 2017 Category: Microbiology Authors: Lemay ML, Horvath P, Moineau S Tags: Curr Opin Microbiol Source Type: research

Next-generation precision antimicrobials: towards personalized treatment of infectious diseases.
Abstract Antibiotics started to be used almost 90 years ago to eradicate life-threatening infections. The urgency of the problem required rapid, broad-spectrum elimination of infectious agents. Since their initial discovery, these antimicrobials have saved millions of lives. However, they are not exempt from side effects, which include the indiscriminate disruption of the beneficial microbiota. Recent technological advances have enabled the development of antimicrobials that can selectively target a gene, a cellular process, or a microbe of choice. These strategies bring us a step closer to developing personalized...
Source: Current Opinion in Microbiology - June 14, 2017 Category: Microbiology Authors: de la Fuente-Nunez C, Torres MD, Mojica FJ, Lu TK Tags: Curr Opin Microbiol Source Type: research

Host-microbiota interactions in Caenorhabditis elegans and their significance.
Abstract As a useful genetic model, C. elegans can facilitate investigation of the genetic underpinnings of host-microbiota interactions. However, decades of feeding it with Escherichia coli left a gap in our understanding of its interactions with microbes, hindering such use. This is changing, with recent studies characterizing the gut microbiota of worms in their natural habitats, comparing them to those in their environment, and evaluating the significance of gut and environmental commensals. This work defined a shared core gut microbiota significantly influenced by host genetics, and unraveled bacterial contri...
Source: Current Opinion in Microbiology - June 14, 2017 Category: Microbiology Authors: Shapira M Tags: Curr Opin Microbiol Source Type: research

CRISPR-based engineering of next-generation lactic acid bacteria.
Abstract The advent of CRISPR-based technologies has opened new avenues for the development of next-generation food microorganisms and probiotics with enhanced functionalities. Building off two decades of functional genomics studies unraveling the genetic basis for food fermentations and host-probiotic interactions, CRISPR technologies offer a wide range of opportunities to engineer commercially-relevant Lactobacillus and Bifidobacteria. Endogenous CRISPR-Cas systems can be repurposed to enhance gene expression or provide new features to improve host colonization and promote human health. Alternatively, engineered...
Source: Current Opinion in Microbiology - June 13, 2017 Category: Microbiology Authors: Hidalgo-Cantabrana C, O'Flaherty S, Barrangou R Tags: Curr Opin Microbiol Source Type: research

The scales of the zebrafish: host-microbiota interactions from proteins to populations.
Abstract The interactions between animal hosts and their associated microbiota can be studied at multiple spatial and conceptual scales, with each providing unique perspectives on the processes structuring host-microbe systems. Recently, zebrafish, Danio rerio, has emerged as a powerful model in which to study these interactions at many different scales. Controlled but simplified gnotobiotic experiments enable discovery of the molecules and cellular dynamics that shape host-microbe system development, whereas population level investigations of bacterial dispersal and transmission are beginning to reveal the proces...
Source: Current Opinion in Microbiology - June 12, 2017 Category: Microbiology Authors: Burns AR, Guillemin K Tags: Curr Opin Microbiol Source Type: research