Positive Interactions in the Coral Macro and Microbiome.
Abstract Researchers now recognize the importance of the coral microbiome, but they often overlook other species that live on corals and influence coral-microbe interactions. These 'interstitial associates' should be incorporated into the metaorganism concept for insights into how facilitations between associates, corals, and their microbiomes can be leveraged in ecology and restoration. PMID: 32663460 [PubMed - as supplied by publisher] (Source: Trends in Microbiology)
Source: Trends in Microbiology - July 15, 2020 Category: Microbiology Authors: Ainsworth TD, Renzi JJ, Silliman BR Tags: Trends Microbiol Source Type: research

Biofilm Matrixome: Extracellular Components in Structured Microbial Communities.
Abstract Biofilms consist of microbial communities embedded in a 3D extracellular matrix. The matrix is composed of a complex array of extracellular polymeric substances (EPS) that contribute to the unique attributes of biofilm lifestyle and virulence. This ensemble of chemically and functionally diverse biomolecules is termed the 'matrixome'. The composition and mechanisms of EPS matrix formation, and its role in biofilm biology, function, and microenvironment are being revealed. This perspective article highlights recent advances about the multifaceted role of the 'matrixome' in the development, physical-chemica...
Source: Trends in Microbiology - July 15, 2020 Category: Microbiology Authors: Karygianni L, Ren Z, Koo H, Thurnheer T Tags: Trends Microbiol Source Type: research

Shigella sonnei.
PMID: 32663462 [PubMed - as supplied by publisher] (Source: Trends in Microbiology)
Source: Trends in Microbiology - July 15, 2020 Category: Microbiology Authors: Torraca V, Holt K, Mostowy S Tags: Trends Microbiol Source Type: research

Between a Rock and a Soft Place: The Role of Viruses in Lithification of Modern Microbial Mats.
Abstract Stromatolites are geobiological systems formed by complex microbial communities, and fossilized stromatolites provide a record of some of the oldest life on Earth. Microbial mats are precursors of extant stromatolites; however, the mechanisms of transition from mat to stromatolite are controversial and are still not well understood. To fully recognize the profound impact that these ecosystems have had on the evolution of the biosphere requires an understanding of modern lithification mechanisms and how they relate to the geological record. We propose here viral mechanisms in carbonate precipitation, leadi...
Source: Trends in Microbiology - July 9, 2020 Category: Microbiology Authors: White RA, Visscher PT, Burns BP Tags: Trends Microbiol Source Type: research

Two Dietary Metabolites Fuel Salmonella Colonization.
Abstract Nguyen et al. used transposon sequencing analysis and competitive colonization assays to describe how aspartate/malate can trigger initial Salmonella Typhimurium gut-lumen colonization in mice, providing insight into the significance of certain key metabolites beyond the realm of Salmonella life. Metabolite-driven diagnostic and anti-infective strategies for preventing salmonellosis could rapidly emerge from this work. PMID: 32653110 [PubMed - as supplied by publisher] (Source: Trends in Microbiology)
Source: Trends in Microbiology - July 8, 2020 Category: Microbiology Authors: Jepsen S, Jiang S Tags: Trends Microbiol Source Type: research

Challenges of Studying the Human Virome - Relevant Emerging Technologies.
Abstract In this review we provide an overview of current challenges and advances in bacteriophage research within the growing field of viromics. In particular, we discuss, from a human virome study perspective, the current and emerging technologies available, their limitations in terms of de novo discoveries, and possible solutions to overcome present experimental and computational biases associated with low abundance of viral DNA or RNA. We summarize recent breakthroughs in metagenomics assembling tools and single-cell analysis, which have the potential to increase our understanding of phage biology, diversity, ...
Source: Trends in Microbiology - July 1, 2020 Category: Microbiology Authors: Khan Mirzaei M, Xue J, Costa R, Ru J, Schulz S, Taranu ZE, Deng L Tags: Trends Microbiol Source Type: research

Pangolins Harbor SARS-CoV-2-Related Coronaviruses.
Abstract The pandemic of coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has posed a severe threat to global public health. Yet, the origin of SARS-CoV-2 remains mysterious. Several recent studies (e.g., Lam et al.,Xiao et al.) identified SARS-CoV-2-related viruses in pangolins, providing novel insights into the evolution and diversity of SARS-CoV-2-related viruses. PMID: 32544437 [PubMed - in process] (Source: Trends in Microbiology)
Source: Trends in Microbiology - June 18, 2020 Category: Microbiology Authors: Han GZ Tags: Trends Microbiol Source Type: research

Sutterella Species, IgA-degrading Bacteria in Ulcerative Colitis.
Abstract Recent reports link Sutterella with gastrointestinal diseases, the most intriguing being therapeutic failure in ulcerative colitis (UC). Sutterella does not appear to induce substantial inflammation; rather, it has a capacity to degrade IgA. This activity, however, is not conserved, presenting a key target to deciphering the influence of Sutterella on the host. PMID: 32544438 [PubMed - in process] (Source: Trends in Microbiology)
Source: Trends in Microbiology - June 18, 2020 Category: Microbiology Authors: Kaakoush NO Tags: Trends Microbiol Source Type: research

Microbial Effector Proteins - A Journey through the Proteolytic Landscape.
uml;n S Abstract In the evolutionary arms race between pathogens and plants, pathogens evolved effector molecules that they secrete into the host to subvert plant cellular responses in a process termed the effector-targeted pathway (ETP). During recent years the repertoire of ETPs has increased and mounting evidence indicates that the proteasome and autophagy pathways are central hubs of microbial effectors. Both degradation pathways are implicated in a broad array of cellular responses and thus constitute an attractive target for effector proteins to have a broader impact on the host. In this article we first sum...
Source: Trends in Microbiology - June 18, 2020 Category: Microbiology Authors: Langin G, Gouguet P, Üstün S Tags: Trends Microbiol Source Type: research

A Gaseous Milieu: Extending the Boundaries of the Rhizosphere.
ant P Abstract Plant root activities shape microbial community functioning in the soil, making the rhizosphere the epicenter of soil biogeochemical processes. With this opinion article, we argue to rethink the rhizosphere boundaries: as gases can diffuse several centimeters away from the roots into the soil, the portion of soil influenced by root activities is larger than the strictly root-adhering soil. Indeed, gases are key drivers of biogeochemical processes due to their roles as energy sources or communication molecules, which has the potential to modify microbial community structure and functioning. In order ...
Source: Trends in Microbiology - June 18, 2020 Category: Microbiology Authors: de la Porte A, Schmidt R, Yergeau É, Constant P Tags: Trends Microbiol Source Type: research

Avoidance of Self during CRISPR Immunization.
Abstract The battle between microbes and their viruses is ancient and ongoing. Clustered regularly interspaced short palindromic repeat (CRISPR) immunity, the first and, to date, only form of adaptive immunity found in prokaryotes, represents a flexible mechanism to recall past infections while also adapting to a changing pathogenic environment. Critical to the role of CRISPR as an adaptive immune mechanism is its capacity for self versus non-self recognition when acquiring novel immune memories. Yet, CRISPR systems vary widely in both how and to what degree they can distinguish foreign from self-derived genetic m...
Source: Trends in Microbiology - June 18, 2020 Category: Microbiology Authors: Weissman JL, Stoltzfus A, Westra ER, Johnson PLF Tags: Trends Microbiol Source Type: research

Defective Interfering Particles of Negative-Strand RNA Viruses.
Abstract Viral defective interfering particles (DIPs) were intensely studied several decades ago but research waned leaving open many critical questions. New technologies and other advances led to a resurgence in DIP studies for negative-strand RNA viruses. While DIPs have long been recognized, their exact contribution to the outcome of acute or persistent viral infections has remained elusive. Recent studies have identified defective viral genomes (DVGs) in human infections, including respiratory syncytial virus and influenza, and growing evidence indicates that DVGs influence disease severity and may contribute ...
Source: Trends in Microbiology - June 18, 2020 Category: Microbiology Authors: Ziegler CM, Botten JW Tags: Trends Microbiol Source Type: research

Local and Universal Action: The Paradoxes of Indole Signalling in Bacteria.
Abstract Indole is a signalling molecule produced by many bacterial species and involved in intraspecies, interspecies, and interkingdom signalling. Despite the increasing volume of research published in this area, many aspects of indole signalling remain enigmatic. There is disagreement over the mechanism of indole import and export and no clearly defined target through which its effects are exerted. Progress is hindered further by the confused and sometimes contradictory body of indole research literature. We explore the reasons behind this lack of consistency and speculate whether the discovery of a new, pulse ...
Source: Trends in Microbiology - June 18, 2020 Category: Microbiology Authors: Zarkan A, Liu J, Matuszewska M, Gaimster H, Summers DK Tags: Trends Microbiol Source Type: research

Evolution of Lantibiotic Salivaricins: New Weapons to Fight Infectious Diseases.
Abstract Lantibiotic salivaricins are polycyclic peptides containing lanthionine and/or β-methyllanthionine residues produced by certain strains of Streptococcus salivarius, which almost exclusively reside in the human oral cavity. The importance of these molecules stems from their antimicrobial activity towards relevant oral pathogens which has so far been applied through the development of salivaricin-producing probiotic strains. However, salivaricins may also prove to be of great value in the development of new and novel antibacterial therapies in this era of emerging antibiotic resistance. In this review,...
Source: Trends in Microbiology - June 18, 2020 Category: Microbiology Authors: Barbour A, Wescombe P, Smith L Tags: Trends Microbiol Source Type: research

Aspergillus fumigatus.
PMID: 32544445 [PubMed - in process] (Source: Trends in Microbiology)
Source: Trends in Microbiology - June 18, 2020 Category: Microbiology Authors: Wassano NS, Goldman GH, Damasio A Tags: Trends Microbiol Source Type: research

Cross-Regulations between Bacterial Toxin-Antitoxin Systems: Evidence of an Interconnected Regulatory Network?
Abstract Toxin-antitoxin (TA) systems are ubiquitous among bacteria and include stable toxins whose toxicity can be counteracted by RNA or protein antitoxins. They are involved in multiple functions that range from stability maintenance for mobile genetic elements to stress adaptation. Bacterial chromosomes frequently have multiple homologues of TA system loci, and it is unclear why there are so many of them. In this review we focus on cross-regulations between TA systems, which occur between both homologous and nonhomologous systems, from similar or distinct types, whether encoded from plasmids or chromosomes. In...
Source: Trends in Microbiology - June 12, 2020 Category: Microbiology Authors: Riffaud C, Pinel-Marie ML, Felden B Tags: Trends Microbiol Source Type: research

Wall Teichoic Acid in Staphylococcus aureus Host Interaction.
Abstract Staphylococcus aureus is a major opportunistic human pathogen that frequently causes disease in community and hospital settings. Nasal colonization is an important risk factor for developing invasive disease. Cell wall-associated glycopolymers called wall teichoic acids (WTAs) contribute to efficient nasal colonization by S. aureus. In addition, WTAs are key targets of the host immune system due to their accessibility and high abundance on the S. aureus cell surface. In this review we discuss the new insights into interactions between the host and S. aureus WTA and the implications of these interactions f...
Source: Trends in Microbiology - June 12, 2020 Category: Microbiology Authors: van Dalen R, Peschel A, van Sorge NM Tags: Trends Microbiol Source Type: research

The Role of Integrative and Conjugative Elements in Antibiotic Resistance Evolution.
Abstract Mobile genetic elements (MGEs), such as plasmids and integrative and conjugative elements (ICEs), are main drivers for the spread of antibiotic resistance (AR). Coevolution between bacteria and plasmids shapes the transfer and stability of plasmids across bacteria. Although ICEs outnumber conjugative plasmids, the dynamics of ICE-bacterium coevolution, ICE transfer rates, and fitness costs are as yet largely unexplored. Conjugative plasmids and ICEs are both transferred by type IV secretion systems, but ICEs are typically immune to segregational loss, suggesting that the evolution of ICE-bacterium associa...
Source: Trends in Microbiology - June 11, 2020 Category: Microbiology Authors: Botelho J, Schulenburg H Tags: Trends Microbiol Source Type: research

Double-Membrane Vesicles as Platforms for Viral Replication.
ena M Abstract Viruses, as obligate intracellular parasites, exploit cellular pathways and resources in a variety of fascinating ways. A striking example of this is the remodelling of intracellular membranes into specialized structures that support the replication of positive-sense ssRNA (+RNA) viruses infecting eukaryotes. These distinct forms of virus-induced structures include double-membrane vesicles (DMVs), found during viral infections as diverse and notorious as those of coronaviruses, enteroviruses, noroviruses, or hepatitis C virus. Our understanding of these DMVs has evolved over the past 15 years thanks...
Source: Trends in Microbiology - June 11, 2020 Category: Microbiology Authors: Wolff G, Melia CE, Snijder EJ, Bárcena M Tags: Trends Microbiol Source Type: research

Countering Counter-Defense to Antiviral RNAi.
Abstract RNA interference (RNAi) is a powerful host defense mechanism against viruses. As a counter-defense, many viruses encode suppressors of RNAi, which - in plants - has provoked counter-counter-defense strategies. Recently, a mechanism was proposed in Drosophila (Zhang et al.) wherein a long noncoding RNA senses a virus-encoded RNAi suppressor to activate an innate immune response. PMID: 32534913 [PubMed - as supplied by publisher] (Source: Trends in Microbiology)
Source: Trends in Microbiology - June 10, 2020 Category: Microbiology Authors: Betting V, Van Rij RP Tags: Trends Microbiol Source Type: research

Carriage of Colibactin-producing Bacteria and Colorectal Cancer Risk.
Abstract Colibactin is a genotoxic molecule, produced primarily by Escherichia coli. Colibactin causes DNA damage that may lead to colorectal cancer. Here we review recent advances in the study of colibactin and propose a focus on patients with inflammatory bowel diseases (IBD) who have higher levels of colibactin-producing bacteria in their intestines. PMID: 32507544 [PubMed - as supplied by publisher] (Source: Trends in Microbiology)
Source: Trends in Microbiology - June 4, 2020 Category: Microbiology Authors: Dubinsky V, Dotan I, Gophna U Tags: Trends Microbiol Source Type: research

Correction of the cover caption of Trends in Microbiology 28/6 (June 2020).
Authors: PMID: 32505535 [PubMed - as supplied by publisher] (Source: Trends in Microbiology)
Source: Trends in Microbiology - June 3, 2020 Category: Microbiology Tags: Trends Microbiol Source Type: research

New Paradigms of Pilus Assembly Mechanisms in Gram-Positive Actinobacteria.
Abstract Adhesive pili in Gram-positive bacteria represent a variety of extracellular multiprotein polymers that mediate bacterial colonization of specific host tissues and associated pathogenesis. Pili are assembled in two distinct but coupled steps, an orderly crosslinking of pilin monomers and subsequent anchoring of the polymer to peptidoglycan, catalyzed by two transpeptidase enzymes - the pilus-specific sortase and the housekeeping sortase. Here, we review this biphasic assembly mechanism based on studies of two prototypical models, the heterotrimeric pili in Corynebacterium diphtheriae and the heterodimeric...
Source: Trends in Microbiology - June 1, 2020 Category: Microbiology Authors: Ramirez NA, Das A, Ton-That H Tags: Trends Microbiol Source Type: research

Anti-CRISPR Proteins in Archaea.
-Álvarez L Abstract Anti-CRISPR (Acr) proteins are natural inhibitors of CRISPR-Cas immune systems. To date, Acrs inhibiting types I, II, III, V, and VI CRISPR-Cas systems have been characterized. While most known Acrs are derived from bacterial phages and prophages, very few have been characterized in the domain Archaea, despite the nearly ubiquitous presence of CRISPR-Cas in archaeal cells. Here we summarize the discovery and characterization of the archaeal Acrs with the representatives encoded by a model archaeal virus, Sulfolobus islandicus rod-shaped virus 2 (SIRV2). AcrID1 inhibits subtype I-D CRISPR...
Source: Trends in Microbiology - June 1, 2020 Category: Microbiology Authors: Peng X, Mayo-Muñoz D, Bhoobalan-Chitty Y, Martínez-Álvarez L Tags: Trends Microbiol Source Type: research

AIDS-Related Mycoses: Updated Progress and Future Priorities.
coses Abstract Serious fungal infections continue to devastate people living with HIV and remain a leading cause of infection-related deaths in this population, second only to tuberculosis. The third AIDS-related mycoses workshop updated progress in the field over the last 3 years and highlighted six key action points for the future. PMID: 32396822 [PubMed - as supplied by publisher] (Source: Trends in Microbiology)
Source: Trends in Microbiology - May 13, 2020 Category: Microbiology Authors: Hoving JC, Brown GD, Gómez BL, Govender NP, Limper AH, May RC, Meya DB, Working Group from the Workshop on AIDS-related Mycoses Tags: Trends Microbiol Source Type: research

Phagocytosis in a Shape-shifting Bacterium.
ld JM Abstract Phagocytosis - cell ingestion - is an important process confined to eukaryotes. Or is it? Shiratori et al. have discovered the existence of phagocytosis in a planctomycete bacterium, raising new questions about the significance of phagotrophy beyond the realm of eukaryotic life. PMID: 32396823 [PubMed - as supplied by publisher] (Source: Trends in Microbiology)
Source: Trends in Microbiology - May 13, 2020 Category: Microbiology Authors: Gallot-Lavallée L, Archibald JM Tags: Trends Microbiol Source Type: research

The Microbiome Sets the Stage for Cholera.
Abstract Interactions between the eukaryotic host, microbiome members, and invading pathogens help to shape disease outcomes. Using the Drosophila model, Fast et al. identified that Vibrio cholerae acts to inhibit epithelial renewal through complex interactions between the type VI secretion system of V. cholerae and the microbial community of the fly. PMID: 32396824 [PubMed - as supplied by publisher] (Source: Trends in Microbiology)
Source: Trends in Microbiology - May 13, 2020 Category: Microbiology Authors: Sokol NS, Newton ILG Tags: Trends Microbiol Source Type: research

Assessing the Potential for Staphylococcus aureus to Evolve Resistance to XF-73.
PMID: 32396825 [PubMed - as supplied by publisher] (Source: Trends in Microbiology)
Source: Trends in Microbiology - May 13, 2020 Category: Microbiology Authors: MacLean RC Tags: Trends Microbiol Source Type: research

Redox Partners: Function Modulators of Bacterial P450 Enzymes.
Abstract The superfamily of cytochrome P450 monooxygenases (P450s) is widespread in all kingdoms of life. Functionally versatile P450s are extensively involved in diverse anabolic and catabolic processes. P450s require electrons to be transferred by redox partners (RPs) for O2 activation and substrate monooxygenation. Unlike monotonic eukaryotic cytochrome P450 reductases, bacterial RP systems are more diverse and complicated. Recent studies have demonstrated that the type, the amount, the combination, and the mode of action of bacterial RPs can affect not only the catalytic rate and product distribution but also ...
Source: Trends in Microbiology - May 13, 2020 Category: Microbiology Authors: Li S, Du L, Bernhardt R Tags: Trends Microbiol Source Type: research

Genomic and Postgenomic Diversity of Fungal Plant Biomass Degradation Approaches.
uml; MR Abstract Plant biomass degradation by fungi is a widely studied and applied field of science, due to its relevance for the global carbon cycle and many biotechnological applications. Before the genome era, many of the in-depth studies focused on a relatively small number of species, whereas now, many species can be addressed in detail, revealing the large variety in the approach used by fungi to degrade plant biomass. This variation is found at many levels and includes genomic adaptation to the preferred biomass component, but also different approaches to degrade this component by diverse sets of activitie...
Source: Trends in Microbiology - May 13, 2020 Category: Microbiology Authors: de Vries RP, Mäkelä MR Tags: Trends Microbiol Source Type: research

The Long-Term Relationship between Microbial Metabolism and Greenhouse Gases.
Abstract The production and consumption of the potent greenhouse gases, nitrous oxide and methane, are largely controlled by microorganisms that have long been assigned to defined functional guilds. However, our understanding of how microbial and biogeochemical processes interact to control the flux of these gases has expanded in recent years. The consumption and production of nitrous oxide and methane are functionally intertwined and engage a range of other biogeochemically active molecules from oxic to anoxic ecosystems. Abiotic processes, such as reaction of nitrogen oxides with metals, have a strong influence ...
Source: Trends in Microbiology - May 13, 2020 Category: Microbiology Authors: Stein LY Tags: Trends Microbiol Source Type: research

Pseudomonas putida.
PMID: 32396829 [PubMed - as supplied by publisher] (Source: Trends in Microbiology)
Source: Trends in Microbiology - May 13, 2020 Category: Microbiology Authors: Volke DC, Calero P, Nikel PI Tags: Trends Microbiol Source Type: research

Herpes Simplex Virus-1 in the Brain: The Dark Side of a Sneaky Infection.
Abstract Herpes simplex virus-1 (HSV-1) establishes latency preferentially in sensory neurons of peripheral ganglia. A variety of stresses can induce recurrent reactivations of the virus, which spreads and then actively replicates to the site of primary infection (usually the lips or eyes). Viral particles produced following reactivation can also reach the brain, causing a rare but severe form of diffuse acute infection, namely herpes simplex encephalitis. Most of the time, this infection is clinically asymptomatic. However, it was recently correlated with the production and accumulation of neuropathological bioma...
Source: Trends in Microbiology - May 5, 2020 Category: Microbiology Authors: Marcocci ME, Napoletani G, Protto V, Kolesova O, Piacentini R, Li Puma DD, Lomonte P, Grassi C, Palamara AT, De Chiara G Tags: Trends Microbiol Source Type: research

Genetic Regulation of Metal Ion Homeostasis in Staphylococcus aureus.
Abstract The acquisition of metal ions and the proper maturation of holo-metalloproteins are essential processes for all organisms. However, metal ion homeostasis is a double-edged sword. A cytosolic accumulation of metal ions can lead to mismetallation of proteins and cell death. Therefore, maintenance of proper concentrations of intracellular metals is essential for cell fitness and pathogenesis. Staphylococcus aureus, like all bacterial pathogens, uses transcriptional metalloregulatory proteins to aid in the detection and the genetic response to changes in metal ion concentrations. Herein, we review the mechani...
Source: Trends in Microbiology - May 4, 2020 Category: Microbiology Authors: Price EE, Boyd JM Tags: Trends Microbiol Source Type: research

Label or Concept - What Is a Pathobiont?
Abstract An increasing number of microorganisms are classified as 'pathobionts' (i.e., organisms that can cause harm under certain circumstances) but there exist no universally used criteria for this definition. In particular, the term is often used for categorizing disease-associated taxa without proof of 'causality'. This creates confusion and distracts from explicitly searching for beneficial functions of these organisms that they may in fact have. Here, we discuss why this term in its current use, and its apparent simplicity, may obscure the complexity of microbe-host and microbe-microbe interactions that defi...
Source: Trends in Microbiology - May 3, 2020 Category: Microbiology Authors: Jochum L, Stecher B Tags: Trends Microbiol Source Type: research

Strategies to Facilitate Translational Advances from Microbiome Surveys.
Abstract Manipulating the microbiome has enormous potential to treat important human diseases. Microbiome surveys are often used to identify potential therapeutic targets by finding associations between microbial elements and disease status. We argue that many reported associations between the microbiome and disease are incompatible with translational research because they are insufficiently specific. We encourage the clear specification of manipulable microbial elements that can be tested in follow-up randomized experiments, and we provide multiple examples of specific and nonspecific microbial elements. PMI...
Source: Trends in Microbiology - April 18, 2020 Category: Microbiology Authors: Willis AD, Minot SS Tags: Trends Microbiol Source Type: research

Bridging Bacteria and the Gut: Functional Aspects of Type IV Pili.
Abstract Cell-surface-located proteinaceous appendages, such as flagella and fimbriae or pili, are ubiquitous in bacterial communities. Here, we focus on conserved type IV pili (T4P) produced by bacteria in the intestinal tract, one of the most densely populated human ecosystems. Computational analysis revealed that approximately 30% of known intestinal bacteria are predicted to produce T4P. To rationalize how T4P allow intestinal bacteria to interact with their environment, other microbiota members, and host cells, we review their established role in gut commensals and pathogens with respect to adherence, motilit...
Source: Trends in Microbiology - April 18, 2020 Category: Microbiology Authors: Ligthart K, Belzer C, de Vos WM, Tytgat HLP Tags: Trends Microbiol Source Type: research

The crAss-like Phage Group: How Metagenomics Reshaped the Human Virome.
Abstract Metagenomics is currently the primary means for identifying new viruses. One of the most impactful metagenomic discoveries is that of crAssphage, the most abundant human-associated virus that is found in about 50% of human gut viromes where it can comprise up to 90% of the virus sequences. Although initial genome analysis of crAssphage failed to detect related phages, or functionally annotate most of the genes, subsequent reanalysis with powerful computational methods and larger databases led to the identification of an expansive group of crAss-like phages. The functions of most crAssphage proteins were p...
Source: Trends in Microbiology - April 18, 2020 Category: Microbiology Authors: Koonin EV, Yutin N Tags: Trends Microbiol Source Type: research

Plastic Circuits: Regulatory Flexibility in Fine Tuning Pathogen Success.
Abstract Bacterial pathogens employ diverse fitness and virulence mechanisms to gain an advantage in competitive niches. These lifestyle-specific traits require integration into the regulatory network of the cell and are often controlled by pre-existing transcription factors. In this review, we highlight recent advances that have been made in characterizing this regulatory flexibility in prominent members of the Enterobacteriaceae. We focus on the direct global interactions between transcription factors and their target genes in pathogenic Escherichia coli and Salmonella revealed using chromatin immunoprecipitatio...
Source: Trends in Microbiology - April 18, 2020 Category: Microbiology Authors: O'Boyle N, Turner NCA, Roe AJ, Connolly JPR Tags: Trends Microbiol Source Type: research

The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries.
Abstract Protein secretion is important for many biotic and abiotic interactions. The evolution of protein secretion systems of bacteria, and related nanomachines, occurred by the co-option of machineries for motility, conjugation, injection, or adhesion. Some of these secretion systems emerged many times, whereas others are unique. In most cases, their evolution occurred by successive rounds of gene accretion, deletion, and horizontal transfer, resulting in machines that can be very different from the original ones. The frequency with which such co-option processes occurred seems to depend on the complexity of th...
Source: Trends in Microbiology - April 18, 2020 Category: Microbiology Authors: Denise R, Abby SS, Rocha EPC Tags: Trends Microbiol Source Type: research

Contact-Dependent Interbacterial Antagonism Mediated by Protein Secretion Machines.
Abstract To establish and maintain an ecological niche, bacteria employ a wide range of pathways to inhibit the growth of their microbial competitors. Some of these pathways, such as those that produce antibiotics or bacteriocins, exert toxicity on nearby cells in a cell contact-independent manner. More recently, however, several mechanisms of interbacterial antagonism requiring cell-to-cell contact have been identified. This form of microbial competition is mediated by antibacterial protein toxins whose delivery to target bacteria uses protein secretion apparatuses embedded within the cell envelope of toxin-produ...
Source: Trends in Microbiology - April 18, 2020 Category: Microbiology Authors: Klein TA, Ahmad S, Whitney JC Tags: Trends Microbiol Source Type: research

Microbiome in Colorectal Cancer: How to Get from Meta-omics to Mechanism?
Abstract Mounting evidence from metagenomic analyses suggests that a state of pathological microbial imbalance or dysbiosis is prevalent in the gut of patients with colorectal cancer. Several bacterial taxa have been identified of which representative isolate cultures interact with human cancer cells in vitro and trigger disease pathways in animal models. However, how the complex interrelationships in dysbiotic communities may be involved in cancer pathogenesis remains a crucial question. Here, we provide a survey of current knowledge of the gut microbiome in colorectal cancer. Moving beyond observational studies,...
Source: Trends in Microbiology - April 18, 2020 Category: Microbiology Authors: Ternes D, Karta J, Tsenkova M, Wilmes P, Haan S, Letellier E Tags: Trends Microbiol Source Type: research

Unveiling the Origin and Transmission of 2019-nCoV.
Abstract A novel coronavirus has caused thousands of human infections in China since December 2019, raising a global public health concern. Recent studies (Huang et al., Chan et al., and Zhou et al.) have provided timely insights into its origin and ability to spread among humans, informing infection prevention and control practices. PMID: 32155431 [PubMed - in process] (Source: Trends in Microbiology)
Source: Trends in Microbiology - March 12, 2020 Category: Microbiology Authors: Xu Y Tags: Trends Microbiol Source Type: research

Novel Outlook in Microbial Ecology: Nonmutualistic Interspecies Electron Transfer.
, Hamelin J Abstract Recent advances in microbial electrochemical technologies have revealed the existence of numerous and highly diverse microorganisms able to exchange electrons with electrodes. This diversity could reflect the capacity of microorganisms to release and/or retrieve electrons with each other in natural environments. So far, this interspecies electron transfer has been studied with a special focus on syntrophy and was successfully demonstrated for several couples of species. In this article we argue that electron exchange between microbes exists beyond syntrophy or mutualism and could also promote ...
Source: Trends in Microbiology - March 12, 2020 Category: Microbiology Authors: Moscoviz R, Quéméner ED, Trably E, Bernet N, Hamelin J Tags: Trends Microbiol Source Type: research

Tracing the Origin of Invasive Fungal Infections.
Abstract Invasive fungal infections are a major cause of mortality in immunocompromised patients. By using high-resolution sequencing, Zhai et al. provide insight into translocation of Candida strains from the gut mycobiota to the bloodstream of transplanted patients. Microbiota-driven diagnostic methods could rapidly emerge for preventing deadly fungal infections. PMID: 32044130 [PubMed - as supplied by publisher] (Source: Trends in Microbiology)
Source: Trends in Microbiology - February 7, 2020 Category: Microbiology Authors: Papon N, Bougnoux ME, d'Enfert C Tags: Trends Microbiol Source Type: research

Flexibility and Adaptability of Quorum Sensing in Nature.
Abstract Quorum sensing (QS), a type of chemical communication, allows bacteria to sense and coordinate activities in natural biofilm communities using N-acyl homoserine lactones (AHLs) as one type of signaling molecule. For AHL-based communication to occur, bacteria must produce and recognize the same signals, which activate similar genes in different species. Our current understanding of AHL-QS suggests that signaling between species would arise randomly, which is not probable. We propose that AHL-QS signaling is a mutable and adaptable process, within limits. AHLs are highly-conserved signals, however, their co...
Source: Trends in Microbiology - January 27, 2020 Category: Microbiology Authors: Prescott RD, Decho AW Tags: Trends Microbiol Source Type: research

Towards Predicting Progression to Severe Dengue.
Abstract There is an urgent need for prognostic assays to predict progression to severe dengue infection, which is a major global threat. While the majority of symptomatic dengue patients experience an acute febrile illness, 5-20% progress to severe infection associated with significant morbidity and mortality. Early monitoring and administration of supportive care reduce mortality and clinically usable biomarkers to predict severe dengue are needed. Here, we review recent discoveries of gene sets, anti-dengue antibody properties, and inflammatory markers with potential utility as predictors of disease progression...
Source: Trends in Microbiology - January 22, 2020 Category: Microbiology Authors: Robinson M, Einav S Tags: Trends Microbiol Source Type: research

Improving Risk-Benefit in Faecal Transplantation through Microbiome Screening.
Abstract Faecal microbiota transplantation (FMT) has been shown to be effective in the treatment of a growing number of conditions, and its clinical use continues to rise. However, recent cases of antibiotic-resistant pathogen transmission through FMT, resulting in at least one case of fatal sepsis, highlight the need to reevaluate current donor screening practices. Commensal gut microbes profoundly influence infection risk but are not routinely assessed in donor stool. Extending the assessment of donor material beyond pathogen populations to include the composition and structure of the wider faecal microbiota has...
Source: Trends in Microbiology - January 15, 2020 Category: Microbiology Authors: Papanicolas LE, Gordon DL, Wesselingh SL, Rogers GB Tags: Trends Microbiol Source Type: research

The Microbiologist's Guide to Membrane Potential Dynamics.
Abstract All cellular membranes have the functionality of generating and maintaining the gradients of electrical and electrochemical potentials. Such potentials were generally thought to be an essential but homeostatic contributor to complex bacterial behaviors. Recent studies have revised this view, and we now know that bacterial membrane potential is dynamic and plays signaling roles in cell-cell interaction, adaptation to antibiotics, and sensation of cellular conditions and environments. These discoveries argue that bacterial membrane potential dynamics deserve more attention. Here, we review the recent studie...
Source: Trends in Microbiology - January 14, 2020 Category: Microbiology Authors: Benarroch JM, Asally M Tags: Trends Microbiol Source Type: research

The Evolutionary Genomics of Host Specificity in Staphylococcus aureus.
Abstract Staphylococcus aureus is an important human bacterial pathogen that has a cosmopolitan host range, including livestock, companion and wild animal species. Genomic and epidemiological studies show that S. aureus has jumped between host species many times over its evolutionary history. These jumps have involved the dynamic gain and loss of host-specific adaptive genes, usually located on mobile genetic elements. The same functional elements are often consistently gained in jumps into a particular species. Further sampling of diverse animal species is likely to uncover an even broader host range and greater ...
Source: Trends in Microbiology - January 13, 2020 Category: Microbiology Authors: Matuszewska M, Murray GGR, Harrison EM, Holmes MA, Weinert LA Tags: Trends Microbiol Source Type: research