Current Opinion in Microbiology

Early life represents a critical window for metabolic, cognitive and immune system development, which is influenced by the maternal microbiome as well as the infant gut microbiome. Antibiotic exposure, mode of delivery and breastfeeding practices modulate the gut microbiome and the reservoir of antibiotic resistance genes (ARGs). Vertical and horizontal microbial gene transfer during early life and the mechanisms behind these transfers are being uncovered. In this review, we aim to provide an overview of the current knowledge on the transfer of antibiotic resistance in the mother-infant dyad through vertical and horizontal transmission and to highlight the main gaps and challenges in this area...

Archaea are members of a separate domain of life that have unique properties, such as the composition of their cell walls and the structure of their lipid bilayers. Consequently, archaeal viruses face different challenges to infect host cells in comparison with viruses of bacteria and eukaryotes. Despite their significant impact on shaping microbial communities, our understanding of infection processes of archaeal viruses remains limited. Several receptors used by archaeal viruses to infect cells have recently been identified...

Group A Streptococcus (GAS) has a fantastically wide tissue tropism in humans, manifesting as different diseases depending on the strain's virulence factor repertoire and the tissue involved. Activation of immune cells and pro-inflammatory signaling has historically been considered an exclusively host-protective response that a pathogen would seek to avoid. However, recent advances in human and animal models suggest that in some tissues, GAS will activate and manipulate specific pro-inflammatory pathways to promote growth, nutrient acquisition, persistence, recurrent infection, competition with other microbial species, dissemination, and transmission...

RNA modifications play essential roles in modulating RNA function, stability, and fate across all kingdoms of life. The entirety of the RNA modifications within a cell is defined as the epitranscriptome. While eukaryotic RNA modifications are intensively studied, understanding bacterial RNA modifications remains limited, and knowledge about bacteriophage RNA modifications is almost nonexistent. In this review, we shed light on known mechanisms of bacterial RNA modifications and propose how this knowledge might be extended to bacteriophages...

The composition of the vaginal microbiota is linked to numerous reproductive health problems, including increased susceptibility to infection, pregnancy complications, and impaired vaginal tissue repair; however, the mechanisms contributing to these adverse outcomes are not yet fully defined. In this review, we highlight recent clinical advancements associating vaginal microbiome composition and function with health outcomes. Subsequently, we provide a summary of emerging models employed to identify microbe-microbe interactions contributing to vaginal health, including metagenomic sequencing, multi-omics approaches, and advances in vaginal microbiota cultivation...

Vibrio cholerae (V. cholerae), the etiological agent of cholera, uses cholera toxin (CT) to cause severe diarrheal disease. Cholera is still a significant cause of mortality worldwide with about half of all cholera cases and deaths occurring in children under five. Owing to the lack of cost-effective vaccination and poor vaccine efficacy in children, there is a need for alternative preventative and therapeutic strategies. Recent advances in our knowledge of the interplay between CT-induced disease and host-pathogen metabolism have opened the door for investigating how modulation of intestinal metabolism by V...

Sensing small molecules is crucial for microorganisms to adapt their genetic programs to changes in their environment. Arrest peptides encoded by short regulatory open reading frames program the ribosomes that translate them to undergo translational arrest in response to specific metabolites. Ribosome stalling in turn controls the expression of downstream genes on the same messenger RNA by translational or transcriptional means. In this review, we present our current understanding of the mechanisms by which ribosomes translating arrest peptides sense different metabolites, such as antibiotics or amino acids, to control gene expression...

Chlamydia trachomatis is a common cause of sexually transmitted infections in humans with devastating sequelae. Understanding of disease on all scales, from molecular details to the immunology underlying pathology, is essential for identifying new ways of preventing and treating chlamydia. Infection models of various complexity are essential to understand all aspects of chlamydia pathogenesis. Cell culture systems allow for research into molecular details of infection, including characterization of the unique biphasic Chlamydia developmental cycle and the role of type-III-secreted effectors in modifying the host environment to allow for infection...

Microbial communities are capable of performing diverse functions with important bioindustrial and medical applications. One approach to improving a community function is to breed new communities by artificially selecting for those displaying high community function ('community selection'). Importantly, community selection can improve the function of interest without needing to understand how the function arises, just like in classical artificial selection of individuals. However, experimental studies of community selection have had varied and largely limited success...

Bacteria produce a wide range of specialized biopolymers that can be classified into polysaccharides, polyamides, and polyesters and are considered to fulfill storage functions. In this review, we highlight recent developments in the field linking metabolism of biopolymers to stress and signaling physiology of the producers and demonstrating that biopolymers contribute to bacterial stress resistance and shape structure and composition of microenvironments. While specialized biopolymers are currently the focus of much attention in biotechnology as innovative and biodegradable materials, our understanding about the regulation and functions of these valuable compounds for the producers, microbial communities, and our environment is still very limited...

Amino acid metabolism in Escherichia coli has long been studied and has established the basis for regulatory mechanisms at the transcriptional, posttranscriptional, and posttranslational levels. In addition to the classical signal transduction cascade involving posttranslational modifications (PTMs), novel PTMs in the two primary nitrogen assimilation pathways have recently been uncovered. The regulon of the master transcriptional regulator NtrC is further expanded by a small RNA derived from the 3´UTR of glutamine synthetase mRNA, which coordinates central carbon and nitrogen metabolism...

Bacteria can use fatty acids (FAs) from their environment as carbon and energy source. This catabolism is performed by the enzymes of the well-known β-oxidation machinery, producing reducing power and releasing acetyl-CoA that can feed the tricarboxylic acid cycle. FAs are extremely diverse: they can be saturated or (poly)unsaturated and are found in different sizes. The need to degrade such a wide variety of compounds may explain why so many seemingly homologous enzymes are found for each step of the β-oxidation cycle...

Inorganic phosphate (Pi) is a fundamental molecule crucial for numerous biological processes, such as ATP synthesis and phospholipid formation. To prevent cellular toxicity, Pi transport is often linked to counterion transport within the bacterium. This review discusses the multifaceted functions of the PhoU protein in bacterial regulation, focusing on its role in coordinating Pi transport with counterions, controlling polyphosphate accumulation, and regulating secondary metabolite biosynthesis and DNA repair...

The cell division cycle of T. gondii is driven by cyclically expressed ApiAP2 transcription factors (AP2s) that promote gene sets (regulons) associated with specific biological functions. AP2s drive other AP2s, thereby propelling the progressive gene expression waves defining the lytic cycle. AP2s can act as dimers by themselves, in combination with other AP2s (constitutive or cyclical) or in complexes with epigenetic factors. Exit from the cell cycle into either the extracellular state or differentiation into bradyzoites results in major changes in gene expression...

Fungal infections of the central nervous system (FI-CNS) are a problematic and important medical challenge considering that those most affected are immunocompromised. Individuals with systemic cryptococcosis (67-84%), candidiasis (3-64%), blastomycosis (40%), coccidioidomycosis (25%), histoplasmosis (5-20%), mucormycosis (12%), and aspergillosis (4-6%) are highly susceptible to develop CNS involvement, which often results in high mortality (15-100%) depending on the mycosis and the affected immunosuppressed population...

In response to environmental cues, bacteria produce intracellular nucleotide messengers to regulate a wide variety of cellular processes and physiology. Studies on individual nucleotide messengers, such as (p)ppGpp or cyclic (di)nucleotides, have established their respective regulatory themes. As research on nucleotide signaling networks expands, recent studies have begun to uncover various crosstalk mechanisms between (p)ppGpp and other nucleotide messengers, including signal conversion, allosteric regulation, and target competition...

Apicomplexan parasites are a large and diverse clade of protists responsible for significant diseases of humans and animals. Central to the ability of these parasites to colonize their host and evade immune responses is an expanded repertoire of gene-expression programs that requires the coordinated action of complex transcriptional networks. DNA-binding proteins and chromatin regulators are essential orchestrators of apicomplexan gene expression that often act in concert. Although apicomplexan genomes encode various families of putative DNA-binding proteins, most remain functionally and mechanistically unexplored...

Bacteria sense and respond to their environment, allowing them to maximize their survival and growth under changing conditions, such as oxygen levels. Direct oxygen-sensing proteins allow bacteria to rapidly sense concentration changes and adapt by regulating signaling pathways and/or cellular machinery. Recent work has identified roles for direct oxygen-sensing proteins in controlling second messenger levels and motility machinery, as well as effects on biofilm formation, virulence, and motility. In this review, we discuss recent progress in understanding O2 -dependent regulation of cyclic di-GMP signaling and motility and highlight the emerging importance in controlling bacterial physiology and behavior...

Proteins are an important part of our regular diet. During food processing, their amino acid composition can be chemically altered by the reaction of free amino groups with sugars - a process termed glycation. The resulting Maillard reaction products (MRPs) have low bioavailability and thus predominantly end up in the colon where they encounter our gut microbiota. In the following review, we summarize bacterial strategies to efficiently metabolize these non-canonical amino acids. A particular focus will be on the complex regulatory mechanisms that allow a tightly controlled expression of metabolic genes to successfully occupy the ecological niches that result from the chemical diversity of MRPs...

Throughout the golden age of antibiotic discovery, Streptomyces have been unsurpassed for their ability to produce bioactive metabolites. Yet, this success has been hampered by rediscovery. As we enter a new stage of biodiscovery, omics data and existing scientific repositories can enable informed choices on the biodiversity that may yield novel antibiotics. Here, we focus on the chemical potential of rare actinomycetes, defined as bacteria within the order Actinomycetales, but not belonging to the genus Streptomyces...