Host genetics and microbiome associations through the lens of genome wide association studies.
Abstract Recent studies indicate that the gut microbiome is partially heritable, motivating the need to investigate microbiome-host genome associations via microbial genome-wide association studies (mGWAS). Existing mGWAS demonstrate that microbiome-host genotype associations are typically weak and are spread across multiple variants, similar to associations often observed in genome-wide association studies (GWAS) of complex traits. Here we reconsider mGWAS by viewing them through the lens of GWAS, and demonstrate that there are striking similarities between the challenges and pitfalls faced by the two study desig...
Source: Current Opinion in Microbiology - June 14, 2018 Category: Microbiology Authors: Weissbrod O, Rothschild D, Barkan E, Segal E Tags: Curr Opin Microbiol Source Type: research

Go with the flow or solitary confinement: a look inside the single-cell toolbox for isolation of rare and uncultured microbes.
Abstract With the vast majority of the microbial world still considered unculturable or undiscovered, microbiologists not only require more fundamental insights concerning microbial growth requirements but also need to implement miniaturized, versatile and high-throughput technologies to upscale current microbial isolation strategies. In this respect, single-cell-based approaches are increasingly finding their way to the microbiology lab. A number of recent studies have demonstrated that analysis and separation of free microbial cells by flow-based sorting as well as physical stochastic confinement of individual c...
Source: Current Opinion in Microbiology - June 13, 2018 Category: Microbiology Authors: Huys GR, Raes J Tags: Curr Opin Microbiol Source Type: research

Recent advances in activating silent biosynthetic gene clusters in bacteria.
Abstract The explosion of microbial genome sequences has shown that bacteria harbor an immense, largely untapped potential for the biosynthesis of diverse natural products, which have traditionally served as an important source of pharmaceutical compounds. Most of the biosynthetic genes that can be detected bioinformatically are only weakly expressed, or not at all, under standard laboratory growth conditions. Herein we review three recent approaches that have been developed for inducing these so-called silent biosynthetic gene clusters: insertion of constitutively active promoters using CRISPR-Cas9, high-throughp...
Source: Current Opinion in Microbiology - June 5, 2018 Category: Microbiology Authors: Mao D, Okada BK, Wu Y, Xu F, Seyedsayamdost MR Tags: Curr Opin Microbiol Source Type: research

A decade of genome sequencing has revolutionized studies of experimental evolution.
Abstract Genome sequencing has revolutionized studies using experimental evolution of microbes because it readily provides comprehensive insight into the genetic bases of adaptation. In this perspective we discuss applications of sequencing-based technologies used to study evolution in microbes, including genomic sequencing of isolated evolved clones and mixed evolved populations, and also the use of sequencing methods to follow the fate of introduced variations, whether neutral barcodes or variants introduced by genome editing. Collectively, these sequencing-based approaches have vastly advanced the examination o...
Source: Current Opinion in Microbiology - June 4, 2018 Category: Microbiology Authors: Bruger EL, Marx CJ Tags: Curr Opin Microbiol Source Type: research

Engineering enzymatic assembly lines for the production of new antimicrobials.
Abstract A large portion of natural products are biosynthesized by the polyketide synthase and non-ribosomal peptide synthetase enzymatic assembly lines. Recent advancements in the study of these megasynthases has led to many new examples that demonstrate the production of non-natural natural products. The field is likely nearing the ability to design and build new biosynthetic pathways de novo. We discuss the various recent approaches taken towards this goal, focusing on the installation of new substrates, the swapping of enzymatic domains and modules, and the impact of metabolic engineering and synthetic biology...
Source: Current Opinion in Microbiology - May 3, 2018 Category: Microbiology Authors: Kalkreuter E, Williams GJ Tags: Curr Opin Microbiol Source Type: research

Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria.
Abstract Klebsiella pneumoniae is an opportunistic bacterial pathogen known for its high frequency and diversity of antimicrobial resistance (AMR) genes. In addition to being a significant clinical problem in its own right, K. pneumoniae is the species within which several new AMR genes were first discovered before spreading to other pathogens (e.g. carbapenem-resistance genes KPC, OXA-48 and NDM-1). Whilst K. pneumoniae's contribution to the overall AMR crisis is impossible to quantify, current evidence suggests it has a wider ecological distribution, significantly more varied DNA composition, greater AMR gene di...
Source: Current Opinion in Microbiology - April 30, 2018 Category: Microbiology Authors: Wyres KL, Holt KE Tags: Curr Opin Microbiol Source Type: research

Bursting onto the scene? Exploring stochastic mRNA production in bacteria.
Abstract Recent large-scale measurements of gene expression variability (or noise) in E. coli have led to the unexpected conclusion that the variability is in large part dictated by and increasing with the mean level of expression. Here we review the evidence for this apparent universal trend in variability, as well as for the related idea that transcription is fundamentally bursty. We examine recently proposed mechanisms for burstiness and universality and argue that they do not explain important features of observed data. Finally, we discuss potential limitations and pitfalls in the interpretation of experimenta...
Source: Current Opinion in Microbiology - April 26, 2018 Category: Microbiology Authors: Jones D, Elf J Tags: Curr Opin Microbiol Source Type: research

Editorial overview: The new microscopy.
PMID: 29702349 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - April 24, 2018 Category: Microbiology Authors: Briegel A, Uphoff S Tags: Curr Opin Microbiol Source Type: research

Microbial interactions trigger the production of antibiotics.
Abstract Since the discovery of penicillin, antibiotics have been instrumental in treating infectious diseases. However, emerging antibiotic multi-resistance coinciding with a nearly exhausted drug pipeline is a major concern for the future of the therapy of infections. A novel approach for the discovery of antibiotics relies on the analysis of microbial consortia in their ecological context, taking into account the potential natural role of antibiotics. Co-cultivations of microorganisms have been successfully applied for the isolation of unknown secondary metabolites including antibiotics, and, thus, open new ave...
Source: Current Opinion in Microbiology - April 24, 2018 Category: Microbiology Authors: Netzker T, Flak M, Krespach MK, Stroe MC, Weber J, Schroeckh V, Brakhage AA Tags: Curr Opin Microbiol Source Type: research

Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms.
Abstract Natural products produced by microorganisms represent the main source of bioactive molecules. The development of high-throughput (omics) techniques have importantly contributed to the renaissance of new antibiotic discovery increasing our understanding of complex mechanisms controlling the expression of biosynthetic gene clusters (BGCs) encoding secondary metabolites. In this context this review highlights recent progress in the use and integration of 'omics' approaches with focuses on genomics, transcriptomics, proteomics metabolomics meta-omics and combined omics as powerful strategy to discover new ant...
Source: Current Opinion in Microbiology - April 12, 2018 Category: Microbiology Authors: Palazzotto E, Weber T Tags: Curr Opin Microbiol Source Type: research

Microbiology catches the cryo-EM bug.
Abstract Over the past few years, the advances in technology and methods that have revolutionized cryo-EM are allowing for key insights in a variety of areas in biology, and microbiology is no exception. A wide range of important macromolecular assemblies in prokaryotic and eukaryotic cells, as well as intact viruses, have now become accessible to investigation by new methods in 3D electron microscopy. We focus here on selected examples that illustrate this breadth, and review the application of methods in single particle cryo-EM and cryo-electron tomography to progress in the structural biology of CRISPR systems,...
Source: Current Opinion in Microbiology - April 12, 2018 Category: Microbiology Authors: Earl LA, Falconieri V, Subramaniam S Tags: Curr Opin Microbiol Source Type: research

Self-resistance mechanisms to DNA-damaging antitumor antibiotics in actinobacteria.
Abstract Streptomyces and few other Actinobacteria naturally produce compounds currently used in chemotherapy for being cytotoxic against various types of tumor cells by damaging the DNA structure and/or inhibiting DNA functions. DNA-damaging antitumor antibiotics belong to different classes of natural compounds that are structurally unrelated such as anthracyclines, bleomycins, enediynes, mitomycins, and prodiginines. By targeting a ubiquitous molecule and housekeeping functions, these compounds are also cytotoxic to their producer. How DNA-damaging antitumor antibiotics producing actinobacteria avoid suicide is ...
Source: Current Opinion in Microbiology - April 8, 2018 Category: Microbiology Authors: Tenconi E, Rigali S Tags: Curr Opin Microbiol Source Type: research

To B or not to B: a tale of unorthodox chromosomes.
PMID: 29579575 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - March 23, 2018 Category: Microbiology Authors: Soyer JL, Balesdent MH, Rouxel T, Dean RA Tags: Curr Opin Microbiol Source Type: research

Rational engineering of synthetic microbial systems: from single cells to consortia.
Abstract One promise of synthetic biology is to provide solutions for biomedical and industrial problems by rational design of added functionality in living systems. Microbes are at the forefront of this biological engineering endeavor due to their general ease of handling and their relevance in many potential applications from fermentation to therapeutics. In recent years, the field has witnessed an explosion of novel regulatory tools, from synthetic orthogonal transcription factors to posttranslational mechanisms for increased control over the behavior of synthetic circuits. Tool development has been paralleled ...
Source: Current Opinion in Microbiology - March 22, 2018 Category: Microbiology Authors: Bittihn P, Din MO, Tsimring LS, Hasty J Tags: Curr Opin Microbiol Source Type: research

Fluorescence imaging host pathogen interactions: fifteen years benefit of hindsight ….
Fluorescence imaging host pathogen interactions: fifteen years benefit of hindsight…. Curr Opin Microbiol. 2018 Mar 19;43:193-198 Authors: Aulner N, Danckaert A, Fernandes J, Nicola MA, Roux P, Salles A, Tinevez JY, Shorte SL Abstract We consider in review current state-of-the-art fluorescence microscopy for investigating the host-pathogen interface. Our perspective is honed from years with literally thousands of microbiologists using the variety of imaging technologies available within our dedicated BSL2/BSL3 optical imaging research service facilities at the Institut Pasteur Paris founded fro...
Source: Current Opinion in Microbiology - March 19, 2018 Category: Microbiology Authors: Aulner N, Danckaert A, Fernandes J, Nicola MA, Roux P, Salles A, Tinevez JY, Shorte SL Tags: Curr Opin Microbiol Source Type: research

Cross-kingdom RNA trafficking and environmental RNAi-nature's blueprint for modern crop protection strategies.
Abstract In plants, small RNA (sRNA)-mediated RNA interference (RNAi) is critical for regulating host immunity against bacteria, fungi, oomycetes, viruses, and pests. Similarly, sRNAs from pathogens and pests also play an important role in modulating their virulence. Strikingly, recent evidence supports that some sRNAs can travel between interacting organisms and induce gene silencing in the counter party, a mechanism termed cross-kingdom RNAi. Exploiting this new knowledge, host-induced gene silencing (HIGS) by transgenic expression of pathogen gene-targeting double-stranded (ds)RNA has the potential to become an...
Source: Current Opinion in Microbiology - March 14, 2018 Category: Microbiology Authors: Cai Q, He B, Kogel KH, Jin H Tags: Curr Opin Microbiol Source Type: research

Resource allocation and metabolism: the search for governing principles.
Abstract Elucidating strategies of resource allocation and metabolism is crucial for a better understanding of microbial phenotypes. In particular, uncovering the governing principles underlying these processes would be a crucial step for achieving a central aim of systems microbiology, which is to quantitatively predict phenotypes of microbial cells or entire populations in diverse conditions. Here, some of the key concepts for understanding cellular resource allocation and metabolism that have been suggested over the past years are reviewed. In particular, recent experimental studies that have shown how phenotyp...
Source: Current Opinion in Microbiology - March 12, 2018 Category: Microbiology Authors: Basan M Tags: Curr Opin Microbiol Source Type: research

Healthy scents: microbial volatiles as new frontier in antibiotic research?
Abstract Microorganisms represent a large and still resourceful pool for the discovery of novel compounds to combat antibiotic resistance in human and animal pathogens. The ability of microorganisms to produce structurally diverse volatile compounds has been known for decades, yet their biological functions and antimicrobial activities have only recently attracted attention. Various studies revealed that microbial volatiles can act as infochemicals in long-distance cross-kingdom communication as well as antimicrobials in competition and predation. Here, we review recent insights into the natural functions and mode...
Source: Current Opinion in Microbiology - March 12, 2018 Category: Microbiology Authors: Avalos M, van Wezel GP, Raaijmakers JM, Garbeva P Tags: Curr Opin Microbiol Source Type: research

Antifungal drug resistance: evolution, mechanisms and impact.
Abstract Microorganisms have a remarkable capacity to evolve resistance to antimicrobial agents, threatening the efficacy of the limited arsenal of antimicrobials and becoming a dire public health crisis. This is of particular concern for fungal pathogens, which cause devastating invasive infections with treatment options limited to only three major classes of antifungal drugs. The paucity of antifungals with clinical utility is in part due to close evolutionary relationships between these eukaryotic pathogens and their human hosts, which limits the unique targets to be exploited therapeutically. This review highl...
Source: Current Opinion in Microbiology - March 12, 2018 Category: Microbiology Authors: Revie NM, Iyer KR, Robbins N, Cowen LE Tags: Curr Opin Microbiol Source Type: research

RiPP antibiotics: biosynthesis and engineering potential.
Abstract The threat of antibiotic resistant bacterial infections continues to underscore the need for new treatment options. Historically, small molecule metabolites from microbes have provided a rich source of antibiotic compounds, and as a result, significant effort has been invested in engineering the responsible biosynthetic pathways to generate novel analogs with attractive pharmacological properties. Unfortunately, biosynthetic stringency has limited the capacity of non-ribosomal peptide synthetases and polyketide synthases from producing substantially different analogs in large numbers. Another class of nat...
Source: Current Opinion in Microbiology - March 10, 2018 Category: Microbiology Authors: Hudson GA, Mitchell DA Tags: Curr Opin Microbiol Source Type: research

Genome engineering for microbial natural product discovery.
Abstract The discovery and development of microbial natural products (MNPs) have played pivotal roles in the fields of human medicine and its related biotechnology sectors over the past several decades. The post-genomic era has witnessed the development of microbial genome mining approaches to isolate previously unsuspected MNP biosynthetic gene clusters (BGCs) hidden in the genome, followed by various BGC awakening techniques to visualize compound production. Additional microbial genome engineering techniques have allowed higher MNP production titers, which could complement a traditional culture-based MNP chasing...
Source: Current Opinion in Microbiology - March 3, 2018 Category: Microbiology Authors: Choi SS, Katsuyama Y, Bai L, Deng Z, Ohnishi Y, Kim ES Tags: Curr Opin Microbiol Source Type: research

Complexity-aware simple modeling.
mad H Abstract Mathematical models continue to be essential for deepening our understanding of biology. On one extreme, simple or small-scale models help delineate general biological principles. However, the parsimony of detail in these models as well as their assumption of modularity and insulation make them inaccurate for describing quantitative features. On the other extreme, large-scale and detailed models can quantitatively recapitulate a phenotype of interest, but have to rely on many unknown parameters, making them often difficult to parse mechanistically and to use for extracting general principles. We dis...
Source: Current Opinion in Microbiology - February 26, 2018 Category: Microbiology Authors: Gómez-Schiavon M, El-Samad H Tags: Curr Opin Microbiol Source Type: research

Microfluidics and single-cell microscopy to study stochastic processes in bacteria.
Abstract Bacteria have molecules present in low and fluctuating numbers that randomize cell behaviors. Understanding these stochastic processes and their impact on cells has, until recently, been limited by the lack of single-cell measurement methods. Here, we review recent developments in microfluidics that enable following individual cells over long periods of time under precisely controlled conditions, and counting individual fluorescent molecules in many cells. We showcase discoveries that were made possible using these devices in various aspects of microbiology, such as antibiotic tolerance/persistence, cell-...
Source: Current Opinion in Microbiology - February 26, 2018 Category: Microbiology Authors: Potvin-Trottier L, Luro S, Paulsson J Tags: Curr Opin Microbiol Source Type: research

Priming the tuberculosis drug pipeline: new antimycobacterial targets and agents.
Abstract Claiming close to two million lives each year, tuberculosis is now the leading cause of death from an infectious disease. The rise in number of Mycobacterium tuberculosis (Mtb) strains resistant to existing TB drugs has underscored the urgent need to develop new antimycobacterials with novel mechanisms of action. To meet this need, a drug pipeline has been established that is populated with new and repurposed drugs. Recent advances in identifying molecules with inhibitory activity against Mtb under conditions modelled on those encountered during infection, and in elucidating their mechanisms of action, ha...
Source: Current Opinion in Microbiology - February 23, 2018 Category: Microbiology Authors: Evans JC, Mizrahi V Tags: Curr Opin Microbiol Source Type: research

Marine microbes in 4D-using time series observation to assess the dynamics of the ocean microbiome and its links to ocean health.
Abstract Microbial observation is of high relevance in assessing marine phenomena of scientific and societal concern including ocean productivity, harmful algal blooms, and pathogen exposure. However, we have yet to realise its potential to coherently and comprehensively report on global ocean status. The ability of satellites to monitor the distribution of phytoplankton has transformed our appreciation of microbes as the foundation of key ecosystem services; however, more in-depth understanding of microbial dynamics is needed to fully assess natural and anthropogenically induced variation in ocean ecosystems. Whi...
Source: Current Opinion in Microbiology - February 21, 2018 Category: Microbiology Authors: Buttigieg PL, Fadeev E, Bienhold C, Hehemann L, Offre P, Boetius A Tags: Curr Opin Microbiol Source Type: research

Metabolic heterogeneity in clonal microbial populations.
Abstract In the past decades, numerous instances of phenotypic diversity were observed in clonal microbial populations, particularly, on the gene expression level. Much less is, however, known about phenotypic differences that occur on the level of metabolism. This is likely explained by the fact that experimental tools probing metabolism of single cells are still at an early stage of development. Here, we review recent exciting discoveries that point out different causes for metabolic heterogeneity within clonal microbial populations. These causes range from ecological factors and cell-inherent dynamics in consta...
Source: Current Opinion in Microbiology - February 21, 2018 Category: Microbiology Authors: Takhaveev V, Heinemann M Tags: Curr Opin Microbiol Source Type: research

Bioinformatic prediction of plant-pathogenicity effector proteins of fungi.
Abstract Effector proteins are important virulence factors of fungal plant pathogens and their prediction largely relies on bioinformatic methods. In this review we outline the current methods for the prediction of fungal plant pathogenicity effector proteins. Some fungal effectors have been characterised and are represented by conserved motifs or in sequence repositories, however most fungal effectors do not generally exhibit high conservation of amino acid sequence. Therefore various predictive methods have been developed around: general properties, structure, position in the genomic landscape, and detection of ...
Source: Current Opinion in Microbiology - February 17, 2018 Category: Microbiology Authors: Jones DA, Bertazzoni S, Turo CJ, Syme RA, Hane JK Tags: Curr Opin Microbiol Source Type: research

Stimulus sensing and signal processing in bacterial chemotaxis.
Abstract Motile bacteria use chemotaxis to migrate towards environments that are favorable for growth and survival. The signaling pathway that mediates this behavior is largely conserved among prokaryotes, with Escherichia coli chemotaxis system being one of the simplest and the best studied. At the core of this pathway are the arrays of clustered chemoreceptors that detect, amplify and integrate various stimuli. Recent work provided deeper understanding of spatial organization and signal processing by these clusters and uncovered the variety of sensory mechanisms used to detect environmental stimuli. Moreover, st...
Source: Current Opinion in Microbiology - February 16, 2018 Category: Microbiology Authors: Bi S, Sourjik V Tags: Curr Opin Microbiol Source Type: research

Expanding horizons of cryo-tomography to larger volumes.
Abstract The three dimensional ultrastructure of cells and tissues comes to light with tomography. There is an inherent tension between representing molecular detail at the highest possible resolution, on one hand, and visualizing spatial relations between large organelles or even neighboring cells in large volumes, on the other. Together with its advantages for pristine sample preservation, cryo-tomography brings particular constraints. A major challenge has been the restriction to specimens thinner than the typical cell. New imaging modalities are now available to extend cryo-tomography to thicker specimens: cry...
Source: Current Opinion in Microbiology - February 15, 2018 Category: Microbiology Authors: Elbaum M Tags: Curr Opin Microbiol Source Type: research

The soil microbiome-from metagenomics to metaphenomics.
Abstract Soil microorganisms carry out important processes, including support of plant growth and cycling of carbon and other nutrients. However, the majority of soil microbes have not yet been isolated and their functions are largely unknown. Although metagenomic sequencing reveals microbial identities and functional gene information, it includes DNA from microbes with vastly varying physiological states. Therefore, metagenomics is only predictive of community functional potential. We posit that the next frontier lies in understanding the metaphenome, the product of the combined genetic potential of the microbiom...
Source: Current Opinion in Microbiology - February 15, 2018 Category: Microbiology Authors: Jansson JK, Hofmockel KS Tags: Curr Opin Microbiol Source Type: research

Cereal powdery mildew effectors: a complex toolbox for an obligate pathogen.
Abstract Cereal powdery mildews are major pathogens of cultivated monocot crops, and all are obligate biotrophic fungi that can only grow and reproduce on living hosts. This lifestyle is combined with extreme host specialization where every mildew subspecies (referred to as forma specialis) can only infect one plant species. Recently there has been much progress in our understanding of the possible roles effectors play in this complex host-pathogen interaction. Here, we review current knowledge on the origin, evolution, and mode of action of cereal mildew effectors, with a particular focus on recent advances in th...
Source: Current Opinion in Microbiology - February 15, 2018 Category: Microbiology Authors: Bourras S, Praz CR, Spanu PD, Keller B Tags: Curr Opin Microbiol Source Type: research

The birth and death of effectors in rapidly evolving filamentous pathogen genomes.
oll D Abstract Plant pathogenic fungi and oomycetes are major risks to food security due to their evolutionary success in overcoming plant defences. Pathogens produce effectors to interfere with host defences and metabolism. These effectors are often encoded in rapidly evolving compartments of the genome. We review how effector genes emerged and were lost in pathogen genomes drawing on the links between effector evolution and chromosomal rearrangements. Some new effectors entered pathogen genomes via horizontal transfer or introgression. However, new effector functions also arose through gene duplication or from p...
Source: Current Opinion in Microbiology - February 15, 2018 Category: Microbiology Authors: Fouché S, Plissonneau C, Croll D Tags: Curr Opin Microbiol Source Type: research

Show me the way: rust effector targets in heterologous plant systems.
Abstract For years, the study of rust fungal effectors has been impeded by the lack of molecular genetic tools in rust pathosystems. The recent use of heterologous plants to perform effector screens (effectoromics)-including effector localisation (cellular targets) and protein interactors (molecular targets) in plant cells-has changed the game. These screens revealed that many candidate effectors from various rust fungi target specific plant cell compartments, including chloroplasts, and associate with specific plant protein complexes. Such information represents unparalleled opportunities to understand how effect...
Source: Current Opinion in Microbiology - February 14, 2018 Category: Microbiology Authors: Lorrain C, Petre B, Duplessis S Tags: Curr Opin Microbiol Source Type: research

Phytophthora sojae effectors orchestrate warfare with host immunity.
Abstract Phytophthora sojae is one of the most damaging plant pathogens of soybean. To aid establishment of a compatible interaction with its host, P. sojae deploys many secreted effectors. These effectors act either in the apoplastic space to cope with hostile conditions or inside of host cells to reprogram host physiology favoring pathogen growth. Effectors have been used as molecular probes, which revealed in Phytophthora that effectors execute their virulence function via manipulating host targets. In addition, recent studies have discovered 'pseudo-effectors' in Phytophthora that act as decoys to shield virul...
Source: Current Opinion in Microbiology - February 14, 2018 Category: Microbiology Authors: Wang Y, Wang Y Tags: Curr Opin Microbiol Source Type: research

Fungal effectors at the crossroads of phytohormone signaling.
Abstract Phytohormone networks are crucial for maintaining the delicate balance between growth and biotic stress responses in plants. Jasmonic acid, salicylic acid, ethylene, and the associated signaling crosstalk are important for pathogen defense; whereas gibberellin and cytokinin function in growth and development in plants. Plant pathogenic fungi have evolved remarkable strategies to manipulate and/or hijack such phytohormone signaling cascades for their own benefit, thus leading to susceptibility and disease in host plants. Interestingly, these hormones are also targeted by fungal endosymbionts and mutualists...
Source: Current Opinion in Microbiology - February 13, 2018 Category: Microbiology Authors: Shen Q, Liu Y, Naqvi NI Tags: Curr Opin Microbiol Source Type: research

Just the surface: advances in the discovery and characterization of necrotrophic wheat effectors.
Abstract For many years pathogens of wheat have remained poorly understood. Hindered by an inaccessible host and the obligate nature of many of the pathogens, our understanding of these interactions has been limited compared to other more amenable pathosystems. However, breakthroughs over recent years have shed new light on diseases of wheat, particularly those caused by the genetically tractable necrotrophic pathogens. We now understand that many of the necrotrophic fungal pathogens do interact with wheat in a strict gene-for-gene relationship, and that pathogen and host partners in these interactions have now be...
Source: Current Opinion in Microbiology - February 13, 2018 Category: Microbiology Authors: McDonald MC, Solomon PS Tags: Curr Opin Microbiol Source Type: research

Exploring the function of bacterial chemotaxis.
Abstract Bacterial chemotaxis is a classical subject: our knowledge of its molecular pathway has grown very detailed, and experimental observations, as well as mathematical models of the dynamics of chemotactic populations, have a history of several decades. This should not lead to the conclusion that only minor details are left to be understood. Indeed, it is believed that bacterial chemotaxis is under selection for efficiency, yet the underlying functional forces remain largely unknown. These aspects are discussed here by the presentation of illustrative examples related to the role of adaptation and signal inte...
Source: Current Opinion in Microbiology - February 13, 2018 Category: Microbiology Authors: Wong-Ng J, Celani A, Vergassola M Tags: Curr Opin Microbiol Source Type: research

Extracellular vesicles - new players in cell-cell communication in aquatic environments.
Abstract Communication between microorganisms in aquatic environments can influence ecosystem function and determine the structure and composition of microbial populations. This microbial cross talk can be mediated by excretion of specialized metabolites or extracellular vesicles (EVs). Recently it has become apparent that cells across all domains of life produce EVs that may convey specific targeted signals that can modulate cell fate, morphology and susceptibility to viruses. The vast majority of knowledge about EVs is derived from studies of mammalian tissues, parasitic host-pathogen interactions and model bact...
Source: Current Opinion in Microbiology - February 12, 2018 Category: Microbiology Authors: Schatz D, Vardi A Tags: Curr Opin Microbiol Source Type: research

Editorial overview: Bacterial cell regulation: from genes to complex environments.
PMID: 29444492 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - February 11, 2018 Category: Microbiology Authors: Veening JW, Tamayo R Tags: Curr Opin Microbiol Source Type: research

Microbiomes in extremely acidic environments: functionalities and interactions that allow survival and growth of prokaryotes at low pH.
Abstract Extremely acidic environments have global distribution and can have natural or, increasingly, anthropogenic origins. Extreme acidophiles grow optimally at pH 3 or less, have multiple strategies for tolerating stresses that accompany high levels of acidity and are scattered in all three domains of the tree of life. Metagenomic studies have expanded knowledge of the diversity of extreme acidophile communities, their ecological networks and their metabolic potentials, both confirmed and inferred. High resolution compositional and functional profiling of these microbiomes have begun to reveal spatial diversit...
Source: Current Opinion in Microbiology - February 6, 2018 Category: Microbiology Authors: Quatrini R, Johnson DB Tags: Curr Opin Microbiol Source Type: research

Microscopy of fungal biofilms.
Abstract Fungal biofilms are heterogeneous, surface-associated colonies comprised of filamentous hyphae (chains of elongated cells), pseudohyphal cells, yeast-form cells, and various forms of extracellular matrix. When grown on a substratum under liquid culture medium, the microbial fungus Candida albicans forms dense biofilms that range in thickness from 100 to 600μm. Apical hyphae in the medium and invasive hyphae in the substratum may add greatly to the thickness and complexity of the biofilm. Because of the heterogeneity of the structure, and the large refractive index differences between cell walls, cytopl...
Source: Current Opinion in Microbiology - January 31, 2018 Category: Microbiology Authors: Lagree K, Desai JV, Finkel JS, Lanni F Tags: Curr Opin Microbiol Source Type: research

Correlative microscopy for structural microbiology.
Abstract Understanding how microbes utilize their environment is aided by visualizing them in their natural context at high resolution. Correlative imaging enables efficient targeting and identification of labelled viral and bacterial components by light microscopy combined with high resolution imaging by electron microscopy. Advances in genetic and bioorthogonal labelling, improved workflows for targeting and image correlation, and large-scale data collection are increasing the applicability of correlative imaging methods. Furthermore, developments in mass spectroscopy and soft X-ray imaging are expanding the cor...
Source: Current Opinion in Microbiology - January 29, 2018 Category: Microbiology Authors: Howes SC, Koning RI, Koster AJ Tags: Curr Opin Microbiol Source Type: research

Endolithic microbial habitats as refuges for life in polyextreme environment of the Atacama Desert.
Abstract The extremely harsh conditions of hyperarid deserts are a true challenge for microbial life. Microorganisms thriving in such polyextreme environments are fascinating as they can tell us more about life, its strategies and its boundaries than other groups of organisms. The Atacama Desert (North Chile) holds two world records of extreme environmental characteristics: the lowest rainfall and greatest surface ultraviolet radiation and total solar irradiance ever measured on Earth. Despite these limiting conditions for life, we recently identified several remarkable examples of endolithic habitats colonized by...
Source: Current Opinion in Microbiology - January 22, 2018 Category: Microbiology Authors: Wierzchos J, Casero MC, Artieda O, Ascaso C Tags: Curr Opin Microbiol Source Type: research

Designer microbiomes for environmental, energy and health biotechnology.
Abstract Biotechnology conventionally uses pure strains of microorganisms to realize a desired conversion. The design of functional microbiomes is becoming a powerful alternative for when an aseptic environment is not an option, either for economic reasons or if the environment is intrinsically open. Rapid technological developments in combined -omics approaches is enabling the engineering and optimization of highly complex microbiomes. This review outlines emerging principles of design and provides examples of successful approaches and interventions in wastewater treatment, bioenergy production and the human inte...
Source: Current Opinion in Microbiology - January 20, 2018 Category: Microbiology Authors: Strous M, Sharp C Tags: Curr Opin Microbiol Source Type: research

Modeling the multi-scale mechanisms of macromolecular resource allocation.
Abstract As microbes face changing environments, they dynamically allocate macromolecular resources to produce a particular phenotypic state. Broad 'omics' data sets have revealed several interesting phenomena regarding how the proteome is allocated under differing conditions, but the functional consequences of these states and how they are achieved remain open questions. Various types of multi-scale mathematical models have been used to elucidate the genetic basis for systems-level adaptations. In this review, we outline several different strategies by which microbes accomplish resource allocation and detail how ...
Source: Current Opinion in Microbiology - January 20, 2018 Category: Microbiology Authors: Yang L, Yurkovich JT, King ZA, Palsson BO Tags: Curr Opin Microbiol Source Type: research

How yeast coordinates metabolism, growth and division.
Abstract All cells, especially single cell organisms, need to adapt their metabolism, growth and division coordinately to the available nutrients. This coordination is mediated by extensive cross-talk between nutrient signaling, metabolism, growth, and the cell division cycle, which is only gradually being uncovered: Nutrient signaling not only controls entry into the cell cycle at the G1/S transition, but all phases of the cell cycle. Metabolites are even sensed directly by cell cycle regulators to prevent cell cycle progression in absence of sufficient metabolic fluxes. In turn, cell cycle regulators such as the...
Source: Current Opinion in Microbiology - January 12, 2018 Category: Microbiology Authors: Ewald JC Tags: Curr Opin Microbiol Source Type: research

Lessons from simple marine models on the bacterial regulation of eukaryotic development.
Abstract Molecular cues from environmental bacteria influence important developmental decisions in diverse marine eukaryotes. Yet, relatively little is understood about the mechanisms underlying these interactions, in part because marine ecosystems are dynamic and complex. With the help of simple model systems, including the choanoflagellate Salpingoeca rosetta, we have begun to uncover the bacterial cues that shape eukaryotic development in the ocean. Here, we review how diverse bacterial cues-from lipids to macromolecules-regulate development in marine eukaryotes. It is becoming clear that there are networks of ...
Source: Current Opinion in Microbiology - January 10, 2018 Category: Microbiology Authors: Woznica A, King N Tags: Curr Opin Microbiol Source Type: research

Sphingolipids in host-microbial interactions.
Abstract Sphingolipids, a lipid class characterized by a long-chain amino alcohol backbone, serve vital structural and signaling roles in eukaryotes. Though eukaryotes produce sphingolipids, this capacity is phylogenetically highly restricted in Bacteria. Intriguingly, bacterial species commonly associated in high abundance with eukaryotic hosts include sphingolipid producers, such as the Bacteroidetes in the mammalian gut. To date, a role for bacterial sphingolipids in immune system maturation has been described, but their fate and impact in host physiology and metabolism remain to be elucidated. The structural c...
Source: Current Opinion in Microbiology - January 9, 2018 Category: Microbiology Authors: Heaver SL, Johnson EL, Ley RE Tags: Curr Opin Microbiol Source Type: research

Probing the mechanistic principles of bacterial cell division with super-resolution microscopy.
Abstract Bacterial cell division takes place almost entirely below the diffraction limit of light microscopy, making super-resolution microscopy ideally suited to interrogating this process. I review how super-resolution microscopy has advanced our understanding of bacterial cell division. I discuss the mechanistic implications of these findings, propose physical models for cell division compatible with recent data, and discuss key outstanding questions and future research directions. PMID: 29324330 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - January 8, 2018 Category: Microbiology Authors: Holden S Tags: Curr Opin Microbiol Source Type: research

Native metals, electron bifurcation, and CO2 reduction in early biochemical evolution.
Abstract Molecular hydrogen is an ancient source of energy and electrons. Anaerobic autotrophs that harness the H2/CO2 redox couple harbour ancient biochemical traits that trace back to the universal common ancestor. Aspects of their physiology, including the abundance of transition metals, radical reaction mechanisms, and their main exergonic bioenergetic reactions, forge links between ancient microbes and geochemical reactions at hydrothermal vents. The midpoint potential of H2 however requires anaerobes that reduce CO2 with H2 to use flavin based electron bifurcation-a mechanism to conserve energy as low potent...
Source: Current Opinion in Microbiology - January 6, 2018 Category: Microbiology Authors: Sousa FL, Preiner M, Martin WF Tags: Curr Opin Microbiol Source Type: research