The roles of zinc and copper sensing in fungal pathogenesis.
Abstract All organisms must secure essential trace nutrients, including iron, zinc, manganese and copper for survival and proliferation. However, these very nutrients are also highly toxic if present at elevated levels. Mammalian immunity has harnessed both the essentiality and toxicity of micronutrients to defend against microbial invasion-processes known collectively as 'nutritional immunity'. Therefore, pathogenic microbes must possess highly effective micronutrient assimilation and detoxification mechanisms to survive and proliferate within the infected host. In this review we compare and contrast the micronut...
Source: Current Opinion in Microbiology - June 18, 2016 Category: Microbiology Authors: Ballou ER, Wilson D Tags: Curr Opin Microbiol Source Type: research

Considerations and caveats in anti-virulence drug development.
Abstract As antibiotic resistance remains a major public health threat, anti-virulence therapy research is gaining interest. Hundreds of potential anti-virulence compounds have been examined, but very few have made it to clinical trials and none have been approved. This review surveys the current anti-virulence research field with a focus on the highly resistant and deadly ESKAPE pathogens, especially Pseudomonas aeruginosa. We discuss timely considerations and caveats in anti-virulence drug development, including target identification, administration, preclinical development, and metrics for success in clinical t...
Source: Current Opinion in Microbiology - June 16, 2016 Category: Microbiology Authors: Maura D, Ballok AE, Rahme LG Tags: Curr Opin Microbiol Source Type: research

Anti-biofilm peptides as a new weapon in antimicrobial warfare.
Abstract Microorganisms growing in a biofilm state are very resilient in the face of treatment by many antimicrobial agents. Biofilm infections are a significant problem in chronic and long-term infections, including those colonizing medical devices and implants. Anti-biofilm peptides represent a very promising approach to treat biofilm-related infections and have an extraordinary ability to interfere with various stages of the biofilm growth mode. Anti-biofilm peptides possess promising broad-spectrum activity in killing both Gram-positive and Gram-negative bacteria in biofilms, show strong synergy with conventio...
Source: Current Opinion in Microbiology - June 15, 2016 Category: Microbiology Authors: Pletzer D, Coleman SR, Hancock RE Tags: Curr Opin Microbiol Source Type: research

Gene silencing and sex determination by programmed DNA elimination in parasitic nematodes.
Abstract Maintenance of genome integrity is essential. However, programmed DNA elimination removes specific DNA sequences from the genome during development. DNA elimination occurs in unicellular ciliates and diverse metazoa ranging from nematodes to vertebrates. Two distinct groups of nematodes use DNA elimination to silence germline-expressed genes in the soma (ascarids) or for sex determination (Strongyloides spp.). Data suggest that DNA elimination likely evolved independently in these nematodes. Recent studies indicate that differential CENP-A deposition within chromosomes defines which sequences are retained...
Source: Current Opinion in Microbiology - June 14, 2016 Category: Microbiology Authors: Streit A, Wang J, Kang Y, Davis RE Tags: Curr Opin Microbiol Source Type: research

Innate immune evasion strategies of DNA and RNA viruses.
Abstract Upon infection, both DNA and RNA viruses can be sensed by pattern recognition receptors (PRRs) in the cytoplasm or the nucleus to activate antiviral innate immunity. Sensing of viral products leads to the activation of a signaling cascade that ultimately results in transcriptional activation of type I and III interferons, as well as other antiviral genes that together mediate viral clearance and inhibit viral spread. Therefore, in order for viruses to replicate and spread efficiently, they must inhibit the host signaling pathways that induce the innate antiviral immune response. In this review, we will hi...
Source: Current Opinion in Microbiology - June 8, 2016 Category: Microbiology Authors: Beachboard DC, Horner SM Tags: Curr Opin Microbiol Source Type: research

Dissecting endophytic lifestyle along the parasitism/mutualism continuum in Arabidopsis.
Abstract Mutualistic interactions between plants and fungi often occur in the rhizosphere, although examples exist where shoot-endophytes support host growth and increase resistance to pathogens and herbivores. Fungal endophytes which colonize their hosts without any visible disease symptoms have been recognized to be fundamental components of various ecosystems. Initial efforts have been taken to decipher the genetic basis of beneficial plant-fungus interactions and of lifestyle transitions. This review gives a short overview on well established experimental systems amenable to genetic manipulation and of known g...
Source: Current Opinion in Microbiology - June 6, 2016 Category: Microbiology Authors: Fesel PH, Zuccaro A Tags: Curr Opin Microbiol Source Type: research

Malaria vaccines and human immune responses.
Abstract Despite reductions in malaria episodes and deaths over the past decade, there is still significant need for more effective tools to combat this serious global disease. The positive results with the Phase III trial of RTS,S directed to the circumsporozoite protein of Plasmodium falciparum have established that a vaccine against malaria can provide partial protection to children in endemic areas, but its limited efficacy and relatively short window of protection mandate that new generations of more efficacious vaccines must be sought. Evidence shows that anti-parasite immune responses can control infection ...
Source: Current Opinion in Microbiology - June 2, 2016 Category: Microbiology Authors: Long CA, Zavala F Tags: Curr Opin Microbiol Source Type: research

Old dogs and new tricks in antimicrobial discovery.
Abstract The discovery of new antibiotics is crucial if we are to avoid a future in which simple infections once again lead to death. New antibiotics were traditionally discovered by analyzing extracts from cultured soil-derived microbes. However, in the last few years only a few new antibiotic classes have been identified using this method. Attempts to apply target-based screening approaches to antibiotic discovery have also proven to be unproductive. In this article, we describe how DNA sequencing and bioinformatic techniques are revolutionizing natural product discovery leading to new natural product antibiotic...
Source: Current Opinion in Microbiology - June 2, 2016 Category: Microbiology Authors: Butler MS, Blaskovich MA, Owen JG, Cooper MA Tags: Curr Opin Microbiol Source Type: research

Virulence factors in fungal pathogens of man.
Abstract Human fungal pathogens are a commonly underestimated cause of severe diseases associated with high morbidity and mortality. Like other pathogens, their survival and growth in the host, as well as subsequent host damage, is thought to be mediated by virulence factors which set them apart from harmless microbes. In this review, we describe and discuss commonly employed strategies for fungal survival and growth in the host and how these affect the host-fungus interactions to lead to disease. While many of these strategies require host-specific virulence factors, more generally any fitness factor which allows...
Source: Current Opinion in Microbiology - May 31, 2016 Category: Microbiology Authors: Brunke S, Mogavero S, Kasper L, Hube B Tags: Curr Opin Microbiol Source Type: research

Cell wall hydrolases and antibiotics: exploiting synergy to create efficacious new antimicrobial treatments.
Abstract Cell wall hydrolases (CWH) are enzymes that build, remodel and degrade peptidoglycan within bacterial cell walls and serve essential roles in cell-wall metabolism, bacteriophage adsorption and bacteriolysis, environmental niche expansion, as well as eukaryotic innate immune defense against bacterial infection. Some CWHs, when tested as recombinant purified proteins, have been shown to have bactericidal activities both as single agents and in combinations with other antimicrobials, displaying synergies in vitro and potent activities in animal models of infection greater than the single agents alone. We sum...
Source: Current Opinion in Microbiology - May 31, 2016 Category: Microbiology Authors: Wittekind M, Schuch R Tags: Curr Opin Microbiol Source Type: research

(+) RNA virus replication compartments: a safe home for (most) viral replication.
Abstract This review describes recent advances in our understanding of the mechanisms by which (+) RNA viruses establish their replication niche. PMID: 27253151 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - May 30, 2016 Category: Microbiology Authors: Shulla A, Randall G Tags: Curr Opin Microbiol Source Type: research

The oxadiazole antibacterials.
Abstract The oxadiazoles are a class of antibacterials discovered by in silico docking and scoring of compounds against the X-ray structure of a penicillin-binding protein. These antibacterials exhibit activity against Gram-positive bacteria, including against methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE). They show in vivo efficacy in murine models of peritonitis/sepsis and neutropenic thigh MRSA infection. They are bactericidal and orally bioavailable. The oxadiazoles show promise in treatment of MRSA infection. PMID: 27239942 [PubMed - as supplied by publish...
Source: Current Opinion in Microbiology - May 27, 2016 Category: Microbiology Authors: Janardhanan J, Chang M, Mobashery S Tags: Curr Opin Microbiol Source Type: research

Microbial interactions and community assembly at microscales.
Abstract In most environments, microbial interactions take place within microscale cell aggregates. At the scale of these aggregates (∼100μm), interactions are likely to be the dominant driver of population structure and dynamics. In particular, organisms that exploit interspecific interactions to increase ecological performance often co-aggregate. Conversely, organisms that antagonize each other will tend to spatially segregate, creating distinct micro-communities and increased diversity at larger length scales. We argue that, in order to understand the role that biological interactions play in microbial c...
Source: Current Opinion in Microbiology - May 24, 2016 Category: Microbiology Authors: Cordero OX, Datta MS Tags: Curr Opin Microbiol Source Type: research

The diversity of insect antiviral immunity: insights from viruses.
Abstract Insects represent over 70% of all animal species. Recent virome analyses reveal unprecedented genetic diversity of insect viruses, which appears to match that of their hosts. Thus, insect-virus interactions may provide information on a vast repertoire of antiviral immune mechanisms. Tapping into this diversity is challenging because of several constraints imposed by the uniqueness of each insect model. Nevertheless, it is clear that many conserved and divergent pathways participate in the control of viral infection in insects. Co-evolution between hosts and viruses favors the development of immune evasion...
Source: Current Opinion in Microbiology - May 24, 2016 Category: Microbiology Authors: Marques JT, Imler JL Tags: Curr Opin Microbiol Source Type: research

Extracellular vesicles are the Trojan horses of viral infection.
Abstract Extracellular vesicles have recently emerged as a novel mode of viral propagation exploited by both enveloped and non-enveloped viruses. In particular non-enveloped viruses utilize the hosts' production of extracellular vesicles to exit from cells non-lytically and to hide and manipulate the immune system. Moreover, challenging the long held idea that viruses behave as independent genetic units, extracellular vesicles enable multiple viral particles and genomes to collectively traffic in and out of cells, which can promote genetic cooperativity among viral quasispecies and enhance the fitness of the overa...
Source: Current Opinion in Microbiology - May 24, 2016 Category: Microbiology Authors: Altan-Bonnet N Tags: Curr Opin Microbiol Source Type: research

Optimization of a novel series of pyranopyridine RND efflux pump inhibitors.
Abstract The rise of multidrug resistant (MDR) Gram-negative pathogens complicates our ability to treat bacterial infections with antibiotics. MDR efflux pumps play a major role in the acquisition and expression of the MDR phenotype. The major MDR efflux pumps in Gram-negative pathogens are the resistance-nodulation-division (RND) superfamily pumps. Efflux pump inhibitors (EPIs) that target RND superfamily pumps could play an important role in the clinic as an adjunctive therapy to increase antibiotic efficacy, decrease resistance, and attenuate virulence in Gram-negative pathogens. Here, we review recent advances...
Source: Current Opinion in Microbiology - May 24, 2016 Category: Microbiology Authors: Aron Z, Opperman TJ Tags: Curr Opin Microbiol Source Type: research

Treatment of Gram-negative bacterial infections by potentiation of antibiotics.
Abstract Infections caused by antibiotic-resistant pathogens, particularly Gram-negative bacteria, represent significant treatment challenges for physicians resulting in high rates of morbidity and mortality. The outer membrane of Gram-negative bacteria acts as a permeability barrier to many compounds that would otherwise be effective antibacterial agents, including those effective against Gram-positive pathogens. Potentiator molecules disrupt this barrier allowing entry of otherwise impermeant molecules, thus providing a strategy to render multi-drug resistant pathogens susceptible to a broader range of antibioti...
Source: Current Opinion in Microbiology - May 24, 2016 Category: Microbiology Authors: Zabawa TP, Pucci MJ, Parr TR, Lister T Tags: Curr Opin Microbiol Source Type: research

Emerging roles for extracellular vesicles in parasitic infections.
Abstract Extracellular vesicles (EVs) are released by cells and contain a complex mixture of proteins, genetic information and lipids. EVs mediate cell:cell communication by transferring their molecular cargo between cells. EVs, initially discovered in mammalian systems, have been demonstrated to play critical role in immunology and cancer biology. More recently, EVs have been identified in a broad range of both unicellular and multicellular parasites. In this review we focus on the emerging roles for EVs in parasitic infections. Parasite-derived EVs can transfer virulence factors and drug-resistance markers, modi...
Source: Current Opinion in Microbiology - May 18, 2016 Category: Microbiology Authors: Marti M, Johnson PJ Tags: Curr Opin Microbiol Source Type: research

Using metabolomics to dissect host-parasite interactions.
Abstract Protozoan parasites have evolved diverse growth and metabolic strategies for surviving and proliferating within different extracellular and intracellular niches in their mammalian hosts. Metabolomic approaches, including high coverage metabolite profiling and (13)C/(2)H-stable isotope labeling, are increasingly being used to identify parasite metabolic pathways that are important for survival and replication in vivo. These approaches are highlighting new links between parasite carbon metabolism and the ability of different parasite stages to colonize specific niches or host cell types. They have also reve...
Source: Current Opinion in Microbiology - May 17, 2016 Category: Microbiology Authors: Kloehn J, Blume M, Cobbold SA, Saunders EC, Dagley MJ, McConville MJ Tags: Curr Opin Microbiol Source Type: research

Editorial overview: Remapping the body of the world: Exploring interactions at the interface of microbial ecology, biological engineering and information science.
uez M PMID: 27199093 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - May 16, 2016 Category: Microbiology Authors: Hallam SJ, Vásquez M Tags: Curr Opin Microbiol Source Type: research

The bright side of microbial dark matter: lessons learned from the uncultivated majority.
Abstract Microorganisms are the most diverse and abundant life forms on Earth. Yet, in many environments, only 0.1-1% of them have been cultivated greatly hindering our understanding of the microbial world. However, today cultivation is no longer a requirement for gaining access to information from the uncultivated majority. New genomic information from metagenomics and single cell genomics has provided insights into microbial metabolic cooperation and dependence, generating new avenues for cultivation efforts. Here we summarize recent advances from uncultivated phyla and discuss how this knowledge has influenced ...
Source: Current Opinion in Microbiology - May 16, 2016 Category: Microbiology Authors: Solden L, Lloyd K, Wrighton K Tags: Curr Opin Microbiol Source Type: research

The information science of microbial ecology.
Abstract A revolution is unfolding in microbial ecology where petabytes of 'multi-omics' data are produced using next generation sequencing and mass spectrometry platforms. This cornucopia of biological information has enormous potential to reveal the hidden metabolic powers of microbial communities in natural and engineered ecosystems. However, to realize this potential, the development of new technologies and interpretative frameworks grounded in ecological design principles are needed to overcome computational and analytical bottlenecks. Here we explore the relationship between microbial ecology and information...
Source: Current Opinion in Microbiology - May 13, 2016 Category: Microbiology Authors: Hahn AS, Konwar KM, Louca S, Hanson NW, Hallam SJ Tags: Curr Opin Microbiol Source Type: research

Gene expression in Kinetoplastids.
Abstract Kinetoplastid parasites adapt to different environments with wide-reaching control of gene expression, but transcription of nuclear protein-coding genes is polycistronic: there is no individual control of transcription initiation. Mature mRNAs are made by co-transcriptional trans splicing and polyadenylation, and competition between processing and nuclear degradation may contribute to regulation of mRNA levels. In the cytosol both the extent to which mRNAs are translated, and mRNA decay rates, vary enormously. I here highlight gaps in our knowledge: no measurements of transcription initiation or elongatio...
Source: Current Opinion in Microbiology - May 10, 2016 Category: Microbiology Authors: Clayton CE Tags: Curr Opin Microbiol Source Type: research

Antigenic variation in the intestinal parasite Giardia lamblia.
aacute;n HD Abstract Giardia lamblia trophozoites undergo antigenic variation, where one member of the Variant-specific Surface Protein (VSP) family is expressed on the surface of proliferating trophozoites and periodically replaced by another one. Two main questions have challenged researchers since antigenic switching was discovered in Giardia: What are the mechanisms involved? How are they influenced by other cellular processes or by the environment? Two molecular mechanisms have been proposed, both involving small non-coding RNAs. Here we postulate that (a) chromatin remodeling, triggered by environmental fact...
Source: Current Opinion in Microbiology - May 10, 2016 Category: Microbiology Authors: Gargantini PR, Serradell MD, Ríos DN, Tenaglia AH, Luján HD Tags: Curr Opin Microbiol Source Type: research

Protein trafficking in apicomplexan parasites: crossing the vacuolar Rubicon.
Abstract Although apicomplexans like the blood stages of Plasmodium and the actively replicating 'tachyzoite' stage of Toxoplasma infect very dissimilar host cells, recent studies suggest they share molecular commonalities amongst differences at the parasitophorous vacuolar membrane (PVM) surrounding these intracellular parasites. A protein translocation export (PTEX) complex in the PVM of Plasmodium, is functionally informed by findings in Toxoplasma. Lipids play a role in trafficking to and across the PVM. Toxoplasma exploit an orthologue of a plasmodial secretory aspartyl protease but substrate cleavage yields ...
Source: Current Opinion in Microbiology - May 4, 2016 Category: Microbiology Authors: Haldar K Tags: Curr Opin Microbiol Source Type: research

Life cycle specialization of filamentous pathogens - colonization and reproduction in plant tissues.
We present and discuss specific life cycle traits that facilitate exploration of plant tissues and underline the importance of increasing our insight into the biology of plant pathogens. PMID: 27153045 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - May 3, 2016 Category: Microbiology Authors: Haueisen J, Stukenbrock EH Tags: Curr Opin Microbiol Source Type: research

Editorial overview: The megaviromes.
e;o J PMID: 27143484 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - April 30, 2016 Category: Microbiology Authors: Raoult D, Abrahão J Tags: Curr Opin Microbiol Source Type: research

Transitions in individuality through symbiosis.
Abstract When a more complex, functionally integrated entity emerges from the association of simpler, initially independent entities, a major evolutionary transition has occurred. Transitions that result from the association of different species include the evolution of the eukaryotic cell and some obligate mutualisms. Recent studies are revolutionizing our understanding of how these intimate interspecific associations come to be, revealing how and to what extent each partner contributes to the relationship, and how partners mediate conflict. Here, we review work on the evolution of mutualistic symbioses in the co...
Source: Current Opinion in Microbiology - April 27, 2016 Category: Microbiology Authors: Estrela S, Kerr B, Morris JJ Tags: Curr Opin Microbiol Source Type: research

The role of giant viruses of amoebas in humans.
Abstract Since 2003, dozens of giant viruses that infect amoebas (GVA), including mimiviruses and marseilleviruses, have been discovered. These giants appear to be common in our biosphere. From the onset, their presence and possible pathogenic role in humans have been serendipitously observed or investigated using a broad range of technological approaches, including culture, electron microscopy, serology and various techniques based on molecular biology. The link between amoebal mimiviruses and pneumonia has been the most documented, with findings that fulfill several of the criteria considered as proof of viral d...
Source: Current Opinion in Microbiology - April 27, 2016 Category: Microbiology Authors: Colson P, Aherfi S, La Scola B, Raoult D Tags: Curr Opin Microbiol Source Type: research

Environmental sensing by African trypanosomes.
Abstract African trypanosomes, which divide their life cycle between mammals and tsetse flies, are confronted with environments that differ widely in temperature, nutrient availability and host responses to infection. In particular, since trypanosomes cannot predict when they will be transmitted between hosts, it is vital for them to be able to sense and adapt to their milieu. Thanks to technical advances, significant progress has been made in understanding how the parasites perceive external stimuli and react to them. There is also a growing awareness that trypanosomes use a variety of mechanisms to exchange info...
Source: Current Opinion in Microbiology - April 27, 2016 Category: Microbiology Authors: Roditi I, Schumann G, Naguleswaran A Tags: Curr Opin Microbiol Source Type: research

Endogenized viral sequences in mammals.
Abstract Reverse-transcribed RNA molecules compose a significant portion of the human genome. Many of these RNA molecules were retrovirus genomes either infecting germline cells or having done so in a previous generation but retaining transcriptional activity. This mechanism itself accounts for a quarter of the genomic sequence information of mammals for which there is data. We understand relatively little about the causes and consequences of retroviral endogenization. This review highlights functions ascribed to sequences of viral origin endogenized into mammalian genomes and suggests some of the most pressing qu...
Source: Current Opinion in Microbiology - April 26, 2016 Category: Microbiology Authors: Parrish NF, Tomonaga K Tags: Curr Opin Microbiol Source Type: research

Are you my symbiont? Microbial polymorphic toxins and antimicrobial compounds as honest signals of beneficial symbiotic defensive traits.
Abstract In defensive symbioses where microbes benefit their host by killing competitors, predators or parasites, natural selection should favor the transmission of microbes with the most beneficial defensive traits. During the initiation of symbiosis, the host's ability to accurately pre-assess a symbiont's beneficial traits would be a selective advantage. We propose that one mechanism by which a host could recognize and select a beneficial partner would be if the latter displayed an honest signal of its defensive or other symbiotic capabilities. As one example, we suggest that polymorphic toxins and their surfac...
Source: Current Opinion in Microbiology - April 26, 2016 Category: Microbiology Authors: Hillman K, Goodrich-Blair H Tags: Curr Opin Microbiol Source Type: research

The impact of Toxoplasma gondii on the mammalian genome.
JC Abstract Nobody doubts that infections have imposed specialisations on the mammalian genome. However sufficient information is usually missing to attribute a specific genomic modification to pressure from a specific pathogen. Recent studies on mechanisms of mammalian resistance against the ubiquitous protozoan parasite, Toxoplasma gondii, have shown that the small rodents presumed to be largely responsible for transmission of the parasite to its definitive host, the domestic cat, possess distinctive recognition proteins, and interferon-inducible effector proteins (IRG proteins) that limit the potential virulen...
Source: Current Opinion in Microbiology - April 26, 2016 Category: Microbiology Authors: Müller UB, Howard JC Tags: Curr Opin Microbiol Source Type: research

Interspecific hybridization impacts host range and pathogenicity of filamentous microbes.
Abstract Interspecific hybridization is widely observed within diverse eukaryotic taxa, and is considered an important driver for genome evolution. As hybridization fuels genomic and transcriptional alterations, hybrids are adept to respond to environmental changes or to invade novel niches. This may be particularly relevant for organisms that establish symbiotic relationships with host organisms, such as mutualistic symbionts, endophytes and pathogens. The latter group is especially well-known for engaging in everlasting arms races with their hosts. Illustrated by the increased identification of hybrid pathogens ...
Source: Current Opinion in Microbiology - April 23, 2016 Category: Microbiology Authors: Depotter JR, Seidl MF, Wood TA, Thomma BP Tags: Curr Opin Microbiol Source Type: research

Macrobiota - helminths as active participants and partners of the microbiota in host intestinal homeostasis.
Abstract Important insights have recently been gained in our understanding of the intricate relationship in the intestinal milieu between the vertebrate host mucosal immune response, commensal bacteria, and helminths. Helminths are metazoan worms (macrobiota) and trigger immune responses that include potent regulatory components capable of controlling harmful inflammation, protecting barrier function and mitigating tissue damage. They can secrete a variety of products that directly affect immune regulatory function but they also have the capacity to influence the composition of microbiota, which can also then impa...
Source: Current Opinion in Microbiology - April 23, 2016 Category: Microbiology Authors: Gause WC, Maizels RM Tags: Curr Opin Microbiol Source Type: research

Filamentous pathogen effectors interfering with small RNA silencing in plant hosts.
Abstract Filamentous eukaryotic pathogens including fungi and oomycetes are major threats of plant health. During the co-evolutionary arms race with the hosts, these pathogens have evolved a large repertoire of secreted virulence proteins, called effectors, to facilitate colonization and infection. Many effectors are believed to directly manipulate targeted processes inside the host cells; and a fundamental function of the effectors is to dampen immunity. Recent evidence suggests that the destructive oomycete pathogens in the genus Phytophthora encode RNA silencing suppressors. These effectors play an important vi...
Source: Current Opinion in Microbiology - April 19, 2016 Category: Microbiology Authors: Ye W, Ma W Tags: Curr Opin Microbiol Source Type: research

Marine protist associations and environmental impacts across trophic levels in the twilight zone and below.
Abstract Marine protists are integral to marine food webs and exhibit complex relationships with other microbial taxa. Phagotrophic protists contribute significantly to carbon turnover in the sunlit ocean and evidence suggests grazing in the dark ocean can be significant as well. New in situ sampling technologies hold great promise for more accurately accessing these impacts. The molecular signatures of parasitic protists comprise significant fractions of many high-throughput sequencing datasets, suggesting a major role in controlling populations of their host(s). The prokaryotic symbionts of free-living protists ...
Source: Current Opinion in Microbiology - April 16, 2016 Category: Microbiology Authors: Edgcomb VP Tags: Curr Opin Microbiol Source Type: research

Viral metabolic reprogramming in marine ecosystems.
Abstract Marine viruses often contain host-derived metabolic genes (i.e., auxiliary metabolic genes; AMGs), which are hypothesized to increase viral replication by augmenting key steps in host metabolism. Currently described AMGs encompass a wide variety of metabolic functions, including amino acid and carbohydrate metabolism, energy production, and iron-sulfur cluster assembly and modification, and their community-wide gene content and abundance vary as a function of environmental conditions. Here, we describe different AMGs classes, their hypothesized role in redirecting host carbon metabolism, and their ecologi...
Source: Current Opinion in Microbiology - April 15, 2016 Category: Microbiology Authors: Hurwitz BL, U'Ren JM Tags: Curr Opin Microbiol Source Type: research

Flexible genomic islands as drivers of genome evolution.
acute;rez M Abstract Natural prokaryotic populations are composed of multiple clonal lineages that are different in their core genomes in a range that varies typically between 95 and 100% nucleotide identity. Each clonal lineage also carries a complement of not shared flexible genes that can be very large. The compounded flexible genome provides polyclonal populations with enormous gene diversity that can be used to efficiently exploit resources. This has fundamental repercussions for interpreting individual bacterial genomes. They are better understood as parts rather than the whole. Multiple genomes are required...
Source: Current Opinion in Microbiology - April 14, 2016 Category: Microbiology Authors: Rodriguez-Valera F, Martin-Cuadrado AB, López-Pérez M Tags: Curr Opin Microbiol Source Type: research

Principles for designing synthetic microbial communities.
Abstract Advances in synthetic biology to build microbes with defined and controllable properties are enabling new approaches to design and program multispecies communities. This emerging field of synthetic ecology will be important for many areas of biotechnology, bioenergy and bioremediation. This endeavor draws upon knowledge from synthetic biology, systems biology, microbial ecology and evolution. Fully realizing the potential of this discipline requires the development of new strategies to control the intercellular interactions, spatiotemporal coordination, robustness, stability and biocontainment of syntheti...
Source: Current Opinion in Microbiology - April 13, 2016 Category: Microbiology Authors: Johns NI, Blazejewski T, Gomes AL, Wang HH Tags: Curr Opin Microbiol Source Type: research

Aquatic fungi: targeting the forgotten in microbial ecology.
Abstract Fungi constitute important and conspicuous components of aquatic microbial communities, but their diversity and functional roles remain poorly characterized. New methods and conceptual frameworks are required to accurately describe their ecological roles, involvement in global cycling processes, and utility for human activities, considering both cultivation-independent techniques as well as experiments in laboratory and in natural ecosystems. Here we highlight recent developments and extant knowledge gaps in aquatic mycology, and provide a conceptual model to expose the importance of fungi in aquatic food...
Source: Current Opinion in Microbiology - April 11, 2016 Category: Microbiology Authors: Grossart HP, Rojas-Jimenez K Tags: Curr Opin Microbiol Source Type: research

How clonal are bacteria over time?
Abstract Bacteria and archaea reproduce clonally (vertical descent), but exchange genes by recombination (horizontal transfer). Recombination allows adaptive mutations or genes to spread rapidly within (or even between) species, and reduces the burden of deleterious mutations. Clonality-defined here as the balance between vertical and horizontal inheritance-is therefore a key microbial trait, determining how quickly a population can adapt and the size of its gene pool. Here, I discuss whether clonality varies over time and if it can be considered a stable trait of a given population. I show that, in some cases, cl...
Source: Current Opinion in Microbiology - April 5, 2016 Category: Microbiology Authors: Shapiro BJ Tags: Curr Opin Microbiol Source Type: research

Public goods and metabolic strategies.
Abstract Microbial growth can be characterized by a limited set of macroscopic parameters such as growth rate, biomass yield and substrate affinity. Different culturing protocols for laboratory evolution have been developed to select mutant strains that have one specific macroscopic growth parameter improved. Some of those mutant strains display tradeoffs between growth parameters and changed metabolic strategies, for example, a shift from respiration to fermentation. Here we discuss recent studies suggesting that metabolic strategies and growth parameter tradeoffs originate from a common set of physicochemical an...
Source: Current Opinion in Microbiology - April 4, 2016 Category: Microbiology Authors: Bachmann H, Bruggeman FJ, Molenaar D, Branco Dos Santos F, Teusink B Tags: Curr Opin Microbiol Source Type: research

Deciphering and shaping bacterial diversity through CRISPR.
Abstract Phage and bacteria have engaged in a sustainable arms race, a seemingly endless conflict, since the beginning of time. CRISPR-Cas systems shape and generate environmental diversity through evolution of both predator and prey genomes. Indeed, the gain or loss of CRISPR-mediated immunity and genome maintenance can spark speciation in bacteria. Alternatively, turning CRISPR-Cas on the host by targeting chromosomal DNA has led to the development of next-generation smart antimicrobials and genetic screening and engineering technologies. Although the ability to target and cleave DNA in a sequence-specific manne...
Source: Current Opinion in Microbiology - April 2, 2016 Category: Microbiology Authors: Briner AE, Barrangou R Tags: Curr Opin Microbiol Source Type: research

DNA repair genes in the Megavirales pangenome.
Abstract The order 'Megavirales' represents a group of eukaryotic viruses with a large genome encoding a few hundred up to two thousand five hundred genes. Several members of Megavirales possess genes involved in major DNA repair pathways. Some of these genes were likely inherited from an ancient virus world and some others were derived from the genomes of their hosts. Here we examine molecular phylogenies of key DNA repair enzymes in light of recent hypotheses on the origin of Megavirales, and propose that the last common ancestors of the individual families of the order Megavirales already possessed DNA repair f...
Source: Current Opinion in Microbiology - April 1, 2016 Category: Microbiology Authors: Blanc-Mathieu R, Ogata H Tags: Curr Opin Microbiol Source Type: research

Persistent virus and addiction modules: an engine of symbiosis.
Abstract The giant DNA viruses are highly prevalent and have a particular affinity for the lytic infection of unicellular eukaryotic host. The giant viruses can also be infected by inhibitory virophage which can provide lysis protection to their host. The combined protective and destructive action of such viruses can define a general model (PD) of virus-mediated host survival. Here, I present a general model for role such viruses play in the evolution of host symbiosis. By considering how virus mixtures can participate in addiction modules, I provide a functional explanation for persistence of virus derived geneti...
Source: Current Opinion in Microbiology - March 31, 2016 Category: Microbiology Authors: Villarreal LP Tags: Curr Opin Microbiol Source Type: research

Updating strategies for isolating and discovering giant viruses.
Abstract Almost fifteen years ago, the discovery of Acanthamoeba polyphaga mimivirus, the first giant virus, changed how we define a virus. It was discovered incidentally in a process of isolating Legionella sp. from environmental samples in the context of pneumonia epidemics using a co-culture system with Acanthamoeba. Since then, much effort and improvement has been put into the original technique. In addition to the known families of Mimiviridae and Marseilleviridae, four new proposed families of giant viruses have been isolated: Pandoravirus, Pithovirus, Faustovirus and Mollivirus. Major improvements were base...
Source: Current Opinion in Microbiology - March 31, 2016 Category: Microbiology Authors: Khalil JY, Andreani J, La Scola B Tags: Curr Opin Microbiol Source Type: research

Giants among larges: how gigantism impacts giant virus entry into amoebae.
on EG Abstract The proposed order Megavirales comprises the nucleocytoplasmic large DNA viruses (NCLDV), infecting a wide range of hosts. Over time, they co-evolved with different host cells, developing various strategies to penetrate them. Mimiviruses and other giant viruses enter cells through phagocytosis, while Marseillevirus and other large viruses explore endocytosis and macropinocytosis. These differing strategies might reflect the evolution of those viruses. Various scenarios have been proposed for the origin and evolution of these viruses, presenting one of the most enigmatic issues to surround these micr...
Source: Current Opinion in Microbiology - March 31, 2016 Category: Microbiology Authors: Rodrigues RA, Abrahão JS, Drumond BP, Kroon EG Tags: Curr Opin Microbiol Source Type: research

Harnessing the power of microbial metabolism.
Abstract Microorganisms are rich repositories of genetic material encoding many activities of potential interest. Recent advances make identifying and exploiting the metabolic treasures of uncultured microbes an easier proposition. Improved expression vectors and metagenomic screening techniques make it easier to identify activities of interest. Synthetic biology and efficient genome editing techniques allow microbial genomes to be modified almost without restriction. Computational approaches based on organism-wide analysis of transcription, protein synthesis and metabolic fluxes make it possible to accurately pre...
Source: Current Opinion in Microbiology - March 26, 2016 Category: Microbiology Authors: Santero E, Floriano B, Govantes F Tags: Curr Opin Microbiol Source Type: research

A strange endocytobiont revealed as largest virus.
Abstract A lot of endocytobionts (or endosymbionts) have been discovered within free-living amoebae in recent years. In this article the results of a long lasting effort to derive valuable data about an extraordinary spore-like infectious microorganism (endocytobiont, endosymbiont) within host amoebae (Acanthamoeba sp.) recently isolated from the contact lens case of a patient with keratitis, are presented. It took some time until this endocytobiont could be attributed to the genus Pandoravirus following a publication of two other pandoraviruses isolated from aquatic environments. Consequently the molecular biolog...
Source: Current Opinion in Microbiology - March 23, 2016 Category: Microbiology Authors: Scheid P Tags: Curr Opin Microbiol Source Type: research