This article focuses on how bacteriophages (phages), antibiotic-resistance genes (ARGs), and disinfection practices intersect. Phages are considered to be the most abundant biological entities on Earth and they have the potential to transfer genes (including ARGs) among their bacterial hosts. In the urban water cycle, phages are used as indicators of fecal pollution and surrogates for human viral pathogens

The poly(ADP-ribose) polymerases (PARPs) family contains 17 members in humans, sharing a PARP domain to transfer ADP-ribose groups to target proteins to trigger ADP-ribosylation. The roles of PARPs have evolved from DNA damage repair to diverse biological processes, such as gene transcription, cellular stress response, etc. Recently, seminal studies have demonstrated the critical roles of PAPRs in

Despite the international guidelines on the containment of the coronavirus disease 2019 (COVID-19) pandemic, the European scientific community was not sufficiently prepared to coordinate scientific efforts. To improve preparedness for future pandemics, we have initiated a network of nine European-funded Cooperation in Science and Technology (COST) Actions that can help facilitate inter-, multi-, and

Although APOBEC3 degradation is the canonical function of HIV-1 Vif, this viral protein also induces potent cell cycle arrest through a newly defined mechanism. Here, we review recent advances in this area and propose that the scope of this activity may go beyond subversion of the host cell cycle.

The advent of inexpensive and rapid sequencing technologies has allowed bacterial whole-genome sequences to be generated at an unprecedented pace. This wealth of information has revealed an unanticipated degree of strain-to-strain genetic diversity within many bacterial species. Awareness of this genetic heterogeneity has corresponded with a greater appreciation of intraspecies variation in virulence

Enterobacter is a globally important pathogen. Here we clarify its taxonomy and review recent developments in its resistance to carbapenem and colistin, illustrating that Enterobacter has a large arsenal of mechanisms to grow under antimicrobial pressure. Further studies are required to decipher colistin heteroresistance and understand why certain Enterobacter lineages have emerged clinically.

Analyses of multiple whole-genome sequences from the same species have revealed that differences in gene content can be substantial, particularly in prokaryotes. Such variation has led to the recognition of pangenomes, the complete set of genes present in a species – consisting of core genes, present in all individuals, and accessory genes whose presence is variable. Questions now arise about how pangenomes

Recent emerging evidence has revealed that regulatory noncoding RNAs (microRNAs, circular RNAs) modulate host–microbe interactions and they have been proposed as potential biomarkers of the host’s response to microbiome-linked pathologies such as cancers, obesity, and neurodegenerative diseases. Interactions between microRNAs and circular RNAs, however, increase the complexity of the mechanisms that

Epigenetic modifications, including DNA methylation, stably alter gene expression without modifying genomic sequences. Recent evidence suggests that epigenetic regulation coupled with a long-term 'memory' effect plays a major role within bacterial persistence formation. Today, emerging high-resolution, single-molecule sequencing technologies allow an increased focus on DNA modifications as regulatory

The mammalian endocannabinoid system modulates gastrointestinal physiology and immunity via lipid hormones (endocannabinoids). Ellermann et al. have recently revealed the effect of the endocannabinoid, 2-arachidonoyl glycerol (2-AG) on intestinal infection. They show that 2-AG directly modulates bacterial function by antagonizing the provirulence receptor QseC, thereby protecting mice against enteric

Microbes constitute the very core of our existence. Long believed to be a nuisance and proponents of various diseases, latest research point toward their functions in processes that can prove beneficial for human survival and afford long-term protection from disease. The wide range of functions exhibited by a host of microbes implies diversity and heterogeneity at the level of the molecular machinery

Intricate gene regulatory networks control the transition between the planktonic and biofilm lifestyles in bacteria. New evidence from Mhatre et al. uncovers how various adaptive mutations that arose in a key gene at the nexus of signaling networks in Burkholderia cenocepacia led to the emergence of lineages with different ecological roles, enabling stable coexistence of multiple genotypes and increasing

Proteases are critical virulence determinants of Porphyromonas gingivalis, an emerging Alzheimer's disease, cancer, and arthritis pathogen and established agent of periodontitis. Transposon sequencing has been employed to define the core essential genome of this bacterium and genes conditionally essential in multiple environments – abscess formation; epithelial colonization; and cigarette smoke toxin

Physical forces have a profound influence on bacterial cell physiology and disease. A striking example is the formation of catch-bonds that reinforce under mechanical stress. While mannose-binding by the Escherichia coli FimH adhesin has long been the only thoroughly studied microbial catch-bond, it has recently become clear that proteins from other species, such as staphylococci, are also engaged

Antimicrobial resistance is a serious threat to global public health as antibiotics are losing effectiveness due to rapid development of resistance. The human immune system facilitates control and clearance of resistant bacterial populations during the course of antimicrobial therapy. Here we review current knowledge of mucosa-associated invariant T (MAIT) cells, an arm of the immune system on the

Pathogens usurp host pathways to generate a permissive environment for their propagation. The current spread of Severe Acute Respiratory Syndrome coronavirus-2 (SARS-CoV-2) infection presents the urgent need to understand the complex pathogen-host interplay for effective control of the virus. SARS-CoV-2 reorganizes the host cytoskeleton for efficient cell entry and controls host transcriptional processes

Toxin/antitoxin (TA) systems are present in nearly all bacterial and archaeal strains and consist of a toxin that reduces growth and an antitoxin that masks toxin activity. Currently there are six primary classes for TA systems based on the nature of the antitoxin and the way that the antitoxin inactivates the toxin. Here we show that there now are at least three additional and distinct TA systems

Camelid-derived and synthetic single-domain antibodies (sdAbs) are emerging as potent weapons against the novel coronavirus, SARS-CoV-2. SdAbs are small, compact, thermostable immunoglobulin elements capable of binding targets with sub-nanomolar affinities. By leveraging the power of phage- and yeast surface-display technologies, rare sdAbs can be isolated from highly diverse and complex antibody libraries

The appeal of using microbial inoculants to mediate plant traits and productivity in managed ecosystems has increased over the past decade, because microbes represent an alternative to fertilizers, pesticides, and direct genetic modification of plants. Using microbes bypasses many societal and environmental concerns because microbial products are considered a more sustainable and benign technology

Successful treatment of tuberculosis (TB) depends on the eradication of its causative agent Mycobacterium tuberculosis (Mtb) in the host. However, the emergence of phenotypically drug-resistant Mtb in the host environment tempers the ability of antibiotics to cure disease. Host immunity produces diverse microenvironmental niches that are exploited by Mtb to mobilize adaptation programs. Such differential

The gastrointestinal tract harbors an intrinsic neuronal network, the enteric nervous system (ENS). The ENS controls motility, fluid homeostasis, and blood flow, but also interacts with other components of the intestine such as epithelial and immune cells. Recent studies indicate that gut microbiota diversification, which occurs alongside postnatal ENS maturation, could be critical for the development

Potassium (K+) channels are highly conserved proteins found in all domains of life, that allow for selective movement of K+ ions across membranes. Despite their broad distribution, the physiological roles of individual members of this diverse channel family have only been thoroughly explored in eukaryotic systems, where they have critical functions in a variety of cellular processes. Recent studies

Latin binomials, popularised in the 18th century by the Swedish naturalist Linnaeus, have stood the test of time in providing a stable, clear, and memorable system of nomenclature across biology. However, relentless and ever-deeper exploration and analysis of the microbial world has created an urgent need for huge numbers of new names for Archaea and Bacteria. Manual creation of such names remains

Our capacity to investigate the biology of the major human and animal pathogen Staphylococcus aureus has been greatly enhanced by technological advances in transposon (Tn) mutagenesis. Here we provide a perspective on how these advances can further our understanding of pathogenesis and antibiotic resistance.

Despite the recent increase in knowledge concerning microorganisms, the processes determining their global distribution and functioning have not been disentangled. Microbial dormant stages are adapted to endure specific adverse conditions related to their dispersion path, suggesting that dispersion is not entirely a stochastic process. Long-term dormancy enhances microbial dispersion, promoting the

An increasing number of studies reveal that host–microbial interactome networks are coordinated, impacting human health and disease. Recently, several lines of evidence have revealed associations between the acquisition of a complex microbiota and adaptive immunity, supporting that host–microbiota symbiotic relationships have evolved as a means to maintain homeostasis where the role of the microbiota

The role of sex steroids in mammalian maturation is well established. Recently, it has been increasingly appreciated that sex steroids also play an important role in the propensity of adults to develop a myriad of diseases. The exposure and responsiveness of tissues to sex steroids varies among individuals and between the sexes, and this has been correlated with gender-specific differences in the composition

Bacteriophages (phages) are the most abundant biological entity in the human body, but until recently the role that phages play in human health was not well characterized. Although phages do not cause infections in human cells, phages can alter the severity of bacterial infections by the dissemination of virulence factors amongst bacterial hosts. Recent studies, made possible with advances in genome

Sigma (σ) factors are key regulatory proteins that control the transcription initiation in prokaryotes. In response to environmental or developmental cues, σ factors initiate the transcription of necessary genes responsible for maintaining a life-sustaining metabolic balance. Due to the significant role of σ factors in bacterial metabolism, their rational engineering for commercial metabolite production

Chikungunya virus (CHIKV) is an arthropod-borne virus that has re-emerged recently and has spread to previously unaffected regions, resulting in millions of infections worldwide. The genus Alphavirus, in the family Togaviridae, contains several members with a similar potential for epidemic emergence. In order for CHIKV to replicate in targeted cell types it is essential for the virus to enter these

Virtual conferences can offer significant benefits but require considerable planning and creativity to be successful. Here we describe the successes and failures of a hybrid in-person/virtual conference model. The COVID-19 epidemic presents the scientific community with an opportunity to pioneer novel models that effectively engage virtual participants to advance conference goals.

Males are disproportionately affected by severe disease and death from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. In their recent article, Takahashi et al. found sex differences in immune responses to SARS-CoV-2 and the predictors of disease progression. These findings contribute to elucidating the mechanisms that underlie the male bias in severe disease and death from

Candida auris, a multidrug-resistant fungal pathogen, is responsible for the recent global outbreaks in hospitalized and long-term care patients with significant mortality. A new study by Bruno et al. delineates innate host immune responses against C. auris and identifies critical roles for fungal mannans and mannoproteins.

Following emergence of the coronavirus disease 2019 (COVID-19) pandemic, a surge in the life-threatening illness now termed ‘multisystem inflammatory syndrome in children’ (MIS-C) has raised questions about the unique effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in children and adolescents. Two important new studies by Consiglio et al. and Gruber et al. have begun to shine

The ongoing COVID-19 pandemic has piqued public interest in the properties, evolution, and emergence of viruses. Here, we discuss how these basic questions have surprisingly remained disputed despite being increasingly within the reach of scientific analysis. We review recent data-driven efforts that shed light into the origin and evolution of viruses and explain factors that resist the widespread

Antibody tests for detecting past infection with SARS-CoV-2 have many uses for public health decision making, but demand has largely come from individual consumers. This review focuses on individual relevance of antibody tests: their accuracy in detecting prior infection, what past SARS-CoV-2 infection can currently infer about future immunity or possible medical sequelae, and the potential future

Motility allows many microbes to traverse their environment to find nutrient sources or escape unfavorable environments. However, some microbes are nonmotile and are restricted to their immediate conditions. Intriguingly, sporadic reports have demonstrated that many nonmotile microbes can utilize the motility machinery of other microbes in their vicinity. This form of transportation, called hitchhiking

Most prokaryotic cells are encased in a surface layer (S-layer) consisting of a paracrystalline array of repeating lattice-forming proteins. S-layer proteins populate a vast and diverse sequence space, performing disparate functions in prokaryotic cells, including cellular defense, cell-shape maintenance, and regulation of import and export of materials. This article highlights recent advances in the

Ancient microbes invented biochemical mechanisms and assembled core metabolic pathways on an anoxic Earth. Molecular oxygen appeared far later, forcing microbes to devise layers of defensive tactics that fend off the destructive actions of both reactive oxygen species (ROS) and oxygen itself. Recent work has pinpointed the enzymes that ROS attack, plus an array of clever protective strategies that

Protein lipidation, the covalent attachment of a lipid moiety to a target protein, plays a critical role in many cellular processes in eukaryotic cells. Bacterial pathogens secrete various effectors to subvert the host signaling pathway as a mechanism of microbial pathogenesis. An increasing number of effectors from diverse bacterial pathogens function as cysteine proteases to cause irreversible delipidation

Prokaryotic taxonomic assignments are shifting to genome-based algorithms. A recent study (Parks et al., 2020) has advanced genome-based taxonomy by constructing reference databases, computing average nucleotide identity and assigning tentative placeholder species names. However, prokaryotic taxonomy should be carefully curated and updated in a timely fashion; this requires coordinated efforts of prokaryotic

In certain niches, microbes encounter environmental challenges that are temporally linked. In such cases, microbial fitness is enhanced by the evolution of anticipatory responses where the initial challenge simultaneously activates pre-emptive protection against the second impending challenge. The accumulation of anticipatory responses in domesticated yeasts, which have been termed 'adaptive prediction'

In the past two decades, amyloids, typically associated with human diseases, have been described to play various functional roles in nearly all life forms. The structural and functional diversity of microbial 'functional amyloids' has dramatically increased in recent years, expanding the canonical definition of these assembled molecules. Here, we provide a broad review of the current understanding

In prokaryotes, transcription–translation coupling is thought to guarantee the synthesis of high-quality mRNAs and surveil foreign genes. Surprisingly, Johnson et al. show that translation is uncoupled from transcription in Bacillus subtilis, arguing that bacteria utilize very diverse gene expression strategies to meet their unique regulatory needs.

The cnidarian–dinoflagellate symbiosis is of huge importance as it underpins the success of coral reefs, yet we know very little about how the host cnidarian and its dinoflagellate endosymbionts communicate with each other to form a functionally integrated unit. Here, we review the current knowledge of interpartner molecular signaling in this symbiosis, with an emphasis on lipids, glycans, reactive

The outer membrane (OM) is a defining feature of Gram-negative bacteria that serves as a permeability barrier and provides rigidity to the cell. Critical to OM function is establishing and maintaining an asymmetrical bilayer structure with phospholipids in the inner leaflet and the complex glycolipid lipopolysaccharide (LPS) in the outer leaflet. Cells ensure this asymmetry by regulating the biogenesis

Cell entry and egress are essential steps in the viral life cycle that govern pathogenesis and spread. Mammalian orthoreoviruses (reoviruses) are nonenveloped viruses implicated in human disease that serve as tractable models for studies of pathogen–host interactions. In this review we discuss the function of intracellular vesicular transport systems in reovirus entry, trafficking, and egress and comment

Humanity’s ongoing struggle with new, re-emerging and endemic infectious diseases serves as a frequent reminder of the need to understand host–pathogen interactions. Recent advances in genomics have dramatically advanced our understanding of how genetics contributes to host resistance or susceptibility to bacterial infection. Here we discuss current trends in defining host–bacterial interactions at

The toxin-producing bacterium Bacillus cereus is an important and neglected human pathogen and a common cause of food poisoning. Several toxins have been implicated in disease, including the pore-forming toxins hemolysin BL (HBL) and nonhemolytic enterotoxin (NHE). Recent work revealed that HBL binds to the mammalian surface receptors LITAF and CDIP1 and that both HBL and NHE induce potassium efflux

The molecular evolution of the adaptive response at the host–pathogen interface has been frequently referred to as an 'arms race' between the host and bacterial pathogens. The innate immune system employs multiple strategies to starve microbes of metals. Pathogens, in turn, develop successful strategies to maintain access to bioavailable metal ions under conditions of extreme restriction of transition

Bacteria have evolved systems dedicated to interbacterial competition. Here we highlight defenses utilized by Gram-negative cells against type VI secretion system (T6SS)-wielding competitors, including physical barriers, genetically encoded antidotes, and stress responses. Further investigation of specific and general defenses will reveal the interbacterial selective pressures impacting bacterial survival

Nonulosonic acids (NulOs) are a diverse family of 9-carbon α-keto acid sugars that are involved in a wide range of functions across all branches of life. The family of NulOs includes the sialic acids as well as the prokaryote-specific NulOs. Select bacteria biosynthesize the sialic acid N-acetylneuraminic acid (Neu5Ac), and the ability to produce this sugar and its subsequent incorporation into cell-surface

As a result of increased reef degradation, restoration efforts are now being widely applied on coral reefs. However, outplanted coral survival in restoration zones varies substantially, and coral mortality can be a significant limitation to the success of restoration efforts. With reef restoration now occurring within, and adjacent to, nationally preserved and managed marine parks, the potential risks

The molecular interplay between cellular host factors and viral proteins is a continuous process throughout the viral life cycle determining virus host range and pathogenesis. The hepatitis E virus (HEV) is a long-neglected RNA virus and the major causative agent of acute viral hepatitis in humans worldwide. However, the mechanisms of liver pathology and clinical disease remain poorly understood for

Host organisms utilize nutritional immunity to limit the availability of nutrients essential to an invading pathogen. Nutrients may include amino acids, nucleotide bases, and transition metals, the essentiality of which varies among pathogens. The mammalian macrophage protein Slc11a1 (previously Nramp1) mediates resistance to several intracellular pathogens. Slc11a1 is proposed to restrict growth of

As plastic debris in the environment continues to increase, an emerging concern is the potential for microplastic to act as vectors for pathogen transport. With aquaculture the fastest growing food sector, and microplastic contamination of shellfish increasingly demonstrated, understanding any risk of pathogen transport associated with microplastic is important for this industry. However, there remains

The microbiome research field is rapidly evolving, but the required biobanking infrastructure is currently fragmented and not prepared for the biobanking of microbiomes. The rapid advancement of technologies requires an urgent assessment of how biobanks can underpin research by preserving microbiome samples and their functional potential.

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

Modified nucleotides in tRNA are critical components of the translation apparatus, but their importance in the process of translational regulation had until recently been greatly overlooked. Two breakthroughs have recently allowed a fuller understanding of the importance of tRNA modifications in bacterial physiology. One is the identification of the full set of tRNA modification genes in model organisms