mBio Table of Contents Volume 16, Issue 6

Volume 16 • Number 6 • June 2025
Current Issue

Editorial

Common challenges faced by early-career researchers in Latin American and small U.S. universities

The Spanish-speaking Latin America region (LATAM) entails low representation in international databases (1) despite exhibiting incredible microbial diversity and endemicity for numerous infectious agents that have been tackled by skilled local microbiologists. Many factors, such as the inability to pay article processing charges (APCs), force LATAM researchers to publish in low-impact national journals or not publish at all. Their publications represent less than 1% of articles in gold (charge an APC) and 25% in diamond open-access journals (no APC charge) (1), 2.64% of the yearly total biomedical and life science publications (2), and have fewer citations even when published in prestigious journals (3, 4). Some of these constraints, such as limited funding and a significant gap in the number of publications compared to research-intensive institutions, are shared with small U.S. universities (5). This disparity is evident with studies reporting that the top 25% of institutions produce 89% of scientific articles from the United States (6). Ironically, both LATAM and small U.S. universities share the strict requirement of high-impact publications for promotion.

Perspectives

mGem: Decoding transmicrobe messaging—the growing impact of extracellular vesicles

Alicia Rojas

https://doi.org/10.1128/mbio.03130-24

Extracellular vesicles (EVs) are membrane-enclosed nanoparticles containing proteins, lipids, and nucleic acids (1) with mRNA, miRNA, lcRNA, tRNA (1), and even active proteasome subunits (2). EVs may be classified according to their size or their mechanisms of origin, and over the years, this classification has become more intricate with the increased resolution of analytical tools, now allowing the description of exomeres as small as 30 nm (3). Virtually, every biological system or fluid releases or contains EVs, with examples found in unicellular bacteria (4–6), ticks (7–9), and helminths (10–12) or detected in tears (13–15), milk (16–18), and snake venoms (19–21).

Ecologically expanding the One Health framework to unify the microbiome sciences

https://doi.org/10.1128/mbio.03147-24

Microbiome research rapidly expanded in the last two decades, with nearly 200,000 peer-reviewed articles that use the word “microbiome” and significant microbial lineage discoveries reshaping the evolutionary tree of life. The unprecedented growth of microbial-focused biotech industries, projected to reach a $317 billion value by 2032 (1), further reflects the increasing recognition that microbial ecology and traits are fundamental drivers of global health. Despite these advancements, the field remains largely compartmentalized within subdisciplines, limiting our ability to develop system-agnostic insights and integrative theories that connect microbial ecology and evolutionary dynamics across systems.

Opinion/Hypothesis

An RNA ligase partner for the prokaryotic protein-only RNase P: insights into the functional diversity of RNase P from genome mining

https://doi.org/10.1128/mbio.00449-25

The maturation of tRNAs entails many processing and modification steps (1). Excision of the 5′ leader in precursor (pre) tRNAs is performed by RNase P. Isolation and characterization of bacterial RNase P revealed that the enzyme is a ribonucleoprotein (RNP) composed of a catalytic RNA and a protein cofactor (2). Subsequently, archaeal and eukaryotic RNase P were also shown to be RNPs powered by an RNA catalyst and aided by multiple protein subunits (3, 4). The discovery of a ribozyme in RNase P, along with examples of other catalytic RNAs, overturned the dogma that only proteins can function as biocatalysts, but it also spawned the notion that all RNase P variants must contain a catalytic RNA (5). This idea was disproved by the finding of RNA-free, protein-only RNase P (PRORP) in eukaryotes, and later of a bacterial/archaeal protein-only variant that was named homolog of Aquifex RNase P (HARP) (6–8). Unlike PRORPs that have so far not been found in the same subcellular compartment as the RNP version, HARP is present in some bacteria and archaea that also have the RNP form of RNase P (6–8). While the use of RNA- and protein-based active sites in RNase P to catalyze pre-tRNA cleavage represents a remarkable example of convergent evolution, the driving forces for and the payoffs from having these two guises in bacteria and archaea remain a mystery (8–10). Here, we sought to gain insights into the function of HARP inspired by the emerging picture.

Minireviews

Not gently down the stream: flow induces amyloid bonding in environmental and pathological fungal biofilms

Peter N. Lipke

https://doi.org/10.1128/mbio.00203-25

Evolutionary accumulation modeling in AMR: machine learning to infer and predict evolutionary dynamics of multi-drug resistance

https://doi.org/10.1128/mbio.00488-25

Anti-microbial resistance (AMR) occurs when pathogens (like bacteria) evolve resistance to the drugs we use to kill them. Multi-drug resistance (MDR) occurs when a pathogen evolves resistance to multiple groups of drugs (usually three or more clinically relevant drug types). AMR is a growing health issue across the globe, particularly in developing countries: in 2019 and 2021, 1.27 m and 1.14 m deaths, respectively, were attributable to bacterial AMR, with the highest rates in sub-Saharan Africa (1, 2). AMR results in large excess societal costs due to prolonged illness and hospitalizations, need for isolation and use of expensive reserve medicines, and patients’ loss of productivity (3–5). AMR is one of the World Health Organization’s top 10 threats to human health (6).

Candidalysin biology and activation of host cells

https://doi.org/10.1128/mbio.00603-24

Iron acquisition strategies in pathogenic fungi

https://doi.org/10.1128/mbio.01211-25

Iron is essential for various biological functions, including metabolism, DNA replication, transcription, and energy production through respiration (1). However, while iron is vital, soluble ferrous iron (Fe²+) is also easily oxidized and potentially cytotoxic (2). At elevated levels, iron can be extremely detrimental to cellular growth and viability, causing nonspecific oxidation and damaging nucleic acids, lipids, and proteins (3, 4). This necessitates that organisms carefully balance iron acquisition with regulation to prevent toxic accumulation (3). To manage this, microorganisms, including fungi, developed iron uptake and storage strategies. These systems have been extensively characterized in the fungus Saccharomyces cerevisiae (5, 6). Broadly, the uptake of iron can be split into reductive and non-reductive pathways; the reductive uptake system relies on the extracellular reduction of ferric salts and chelates, which are then taken up by a high-affinity, ferrous-specific oxidase/permease complex, while the non-reductive system employs siderophores to scavenge iron from extracellular sources (7, 8). Additionally, several pathogenic fungi have developed methods to scavenge iron from heme, further facilitating iron uptake in the human host (9, 10). This review explores the iron acquisition strategies in medically significant fungi and how these strategies may be exploited in drug development.

Energy metabolism in Trypanosoma cruzi: the validated and putative bioenergetic and carbon sources

https://doi.org/10.1128/mbio.02215-24

Cellular metabolism is essential for all living organisms to transduce energy for maintenance and proliferation. Its configuration varies across species and is shaped by evolutionary adaptations to environmental challenges. Pathogenic trypanosomatids, including Trypanosoma cruzi, Trypanosoma brucei, and Leishmania spp. (collectively called TriTryps), cause Chagas disease, human african trypanosomiasis, and leishmaniasis, respectively. These parasites exhibit remarkable metabolic adaptations, enabling them to survive in diverse biochemical environments within their vertebrate and invertebrate hosts. For T. cruzi, these environments range from the glucose-rich vertebrate blood and the host-cell cytoplasm, where the parasite needs to compete for nutrients with the host-cell enzymatic machinery, to the severely nutrient-depleted insect midgut (1–4). Since diverging from the last eukaryote common ancestor (5, 6), TriTryps have evolved unique metabolic and structural innovations. A key example is the glycosome, a microbody-like organelle first described in T. brucei in 1977, which compartmentalizes enzymes for glycolysis and glycerol metabolism (7). This organelle is also found in most trypanosomatids, including T. cruzi (8), originated from peroxisomes (reviewed in reference 9) and later was shown to house enzymes from the pentose-phosphate pathway, glycerol-phosphate shuttle, lipid metabolism, purine salvage, and pyrimidine biosynthesis, among others (7, 10–13). Additionally, TriTryps possess a single and unique mitochondrion with DNA organized in a structure called the kinetoplast (14–16) and alternative energy-transduction mechanisms when compared to those of their hosts. This “peculiar” metabolic configuration allows them to thrive in the dynamic nutrient environments of their hosts. This review summarizes the available data on the uptake , biosynthesis, and catabolism of metabolites (Fig. 1), which fuel T. cruzi’s energy metabolism, aiming to provide a comprehensive “bioenergetics cartography” of this parasite.

Observation

The AusAB non-ribosomal peptide synthetase of Staphylococcus aureus preferentially generates phevalin in host-mimicking media

https://doi.org/10.1128/mbio.00845-24

Research Articles

Evolution of carbapenemase activity in the class C β-lactamase ADC-1

https://doi.org/10.1128/mbio.00185-25

The inhibitory receptor LAG3 affects NK cell IFN-γ production through glycolysis and the PSAT1/STAT1/IFNG pathway

https://doi.org/10.1128/mbio.00230-25

The rules in co-infection of multiple viruses across diverse lineages in a fungal host

https://doi.org/10.1128/mbio.00262-25

Direct relationship between protein expression and progeny yield of herpes simplex virus 1

https://doi.org/10.1128/mbio.00280-25

Resistance to oxyimino-cephalosporins conferred by an alternative mechanism of hydrolysis by the Acinetobacter-derived cephalosporinase-33 (ADC-33), a class C β-lactamase present in carbapenem-resistant Acinetobacter baumannii (CRAb)

https://doi.org/10.1128/mbio.00287-25

Phylogenetic analysis of pathogenic algae reveals lineage-dependent patterns of phagocytosis

https://doi.org/10.1128/mbio.00498-25

An antisense oligomer conjugate with unpredicted bactericidal activity against Fusobacterium nucleatum

https://doi.org/10.1128/mbio.00524-25

Nascent flagellar basal bodies are immobilized by rod assembly in Bacillus subtilis

https://doi.org/10.1128/mbio.00530-25

Temperature controls LasR regulation of piv expression in Pseudomonas aeruginosa

https://doi.org/10.1128/mbio.00541-25

Persistent articular infection and host reactive response contribute to Brucella-induced spondyloarthritis in SKG mice

https://doi.org/10.1128/mbio.00542-25

Metformin as antiviral therapy protects hyperglycemic and diabetic patients

https://doi.org/10.1128/mbio.00634-25

Propionate serves as a degradable control agent of citrus canker by acidifying cytoplasm and depleting intracellular ATP in Xanthomonas citri

https://doi.org/10.1128/mbio.00642-25

Targeting CTP synthetase 1 to restore interferon induction and impede nucleotide synthesis in SARS-CoV-2 infection

https://doi.org/10.1128/mbio.00649-25

Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments

https://doi.org/10.1128/mbio.00705-25

Characterization of a consensus-designed trans-cinnamic acid decarboxylase for styrene biosynthesis

https://doi.org/10.1128/mbio.00714-25

Stress-dependent activation of the Listeria monocytogenes virulence program ensures bacterial resilience during infection

https://doi.org/10.1128/mbio.00719-25

Nitrogen cycling during an Arctic bloom: from chemolithotrophy to nitrogen assimilation

https://doi.org/10.1128/mbio.00749-25

SSR42 is a novel regulator of cytolytic activity in Staphylococcus aureus

https://doi.org/10.1128/mbio.00772-25

Tetrahymena ATG8 homologs, TtATG8A and TtATG8B, are responsible for mitochondrial degradation induced by starvation

https://doi.org/10.1128/mbio.00783-25

Flagellar motility and the mucus environment influence aggregation-mediated antibiotic tolerance of Pseudomonas aeruginosa in chronic lung infection

https://doi.org/10.1128/mbio.00831-25

Delta-catenin is required for cell proliferation in virus-positive Merkel cell carcinoma cell lines but not in human fibroblasts

https://doi.org/10.1128/mbio.00832-25

Unraveling the molecular mechanisms of DNA capture by the Com pilus in naturally transformable monoderm bacteria

https://doi.org/10.1128/mbio.00851-25

Comparative genomic analysis of trypanosomatid protists illuminates an extensive change in the nuclear genetic code

https://doi.org/10.1128/mbio.00885-25

A protective and broadly binding antibody class engages the influenza virus hemagglutinin head at its stem interface

https://doi.org/10.1128/mbio.00892-25

c-di-GMP is required for swarming in E. coli, producing colanic acid that acts as surfactant

https://doi.org/10.1128/mbio.00916-25

Microbial vitamin biosynthesis links gut microbiota dynamics to chemotherapy toxicity

https://doi.org/10.1128/mbio.00930-25

Characterization of the family-level Borreliaceae pan-genome and development of an episomal typing protocol

https://doi.org/10.1128/mbio.00943-25

Nocardia genomes are a large reservoir of diverse gene content, biosynthetic gene clusters, and species-specific genes

https://doi.org/10.1128/mbio.00947-25

Physiological roles of an Acinetobacter-specific σ factor

https://doi.org/10.1128/mbio.00968-25

β-Coronaviruses exploit ESCRT for virion assembly and egress

https://doi.org/10.1128/mbio.00979-25

Role of glucuronoxylomannan and steryl glucosides in protecting against cryptococcosis

https://doi.org/10.1128/mbio.00984-25

TcCARP3 modulates compartmentalized cAMP signals involved in osmoregulation, infection of mammalian cells, and colonization of the triatomine vector in the human pathogen Trypanosoma cruzi

https://doi.org/10.1128/mbio.00994-25

Inactivation of the Fusobacterium nucleatum Rnf complex reduces FadA-mediated amyloid formation and tumor development

https://doi.org/10.1128/mbio.01032-25

Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion

https://doi.org/10.1128/mbio.01046-25

Outer membrane tube formation by Francisella novicida involves extensive envelope modifications and is linked with type VI secretion and alterations to the host phagosomal membrane

https://doi.org/10.1128/mbio.01060-25

Comparative proteomics of biofilm development in Pseudoalteromonas tunicata discovers a distinct family of Ca²⁺-dependent adhesins

https://doi.org/10.1128/mbio.01069-25

Nuanced differences in adenylate cyclase toxin production, acylation, and secretion may contribute to the evolution of virulence in Bordetella species

https://doi.org/10.1128/mbio.01082-25

Giant transposons promote strain heterogeneity in a major fungal pathogen

https://doi.org/10.1128/mbio.01092-25

Malassezia in environmental studies is derived from human inputs

https://doi.org/10.1128/mbio.01142-25

GSNOR plays roles in growth, pathogenicity, and stress resistance by modulating mitochondrial protein COX6B S-nitrosylation in Colletotrichum gloeosporioides

https://doi.org/10.1128/mbio.01269-25

The archaeal class Nitrososphaeria is a key component of the reproductive microbiome in sponges during gametogenesis

https://doi.org/10.1128/mbio.02019-24

FapR regulates HssRS-mediated heme homeostasis in Bacillus anthracis

https://doi.org/10.1128/mbio.02057-24

Comparative analysis of replication and immune evasion among SARS-CoV-2 subvariants BA.2.86, JN.1, KP.2, and KP.3

https://doi.org/10.1128/mbio.03503-24

Programming virulent bacteriophages by developing a multiplex genome engineering method

https://doi.org/10.1128/mbio.03582-24

Widely dispersed clonal expansion of multi-fungicide-resistant Aspergillus fumigatus limits genomic epidemiology prospects

https://doi.org/10.1128/mbio.03652-24

Exploring protein N-glycosylation in ammonia-oxidizing Nitrososphaerota archaea through glycoproteomic analysis

https://doi.org/10.1128/mbio.03859-24

Identification of a series of pyrrolo-pyrimidine-based SARS-CoV-2 Mac1 inhibitors that repress coronavirus replication

https://doi.org/10.1128/mbio.03865-24

DENV2 and ZIKV modulate the feeding behavior of Aedes aegypti by altering the tyrosine-dopamine pathway

https://doi.org/10.1128/mbio.03968-24

Erratum

Erratum for Woo et al., “Acinetobacter baumannii OmpA hinders host autophagy via the CaMKK2-reliant AMPK-pathway”

https://doi.org/10.1128/mbio.01224-25

homepage mBio cover image — *Cover image*: Endoplasmic reticulum tubules (red) mark the fission site of the *Salmonella-*containing vacuole (green) at the center. (*See related article in May 2025, vol. 16,* *e00114-25*.) (Copyright © 2025 Chopra et al. CC-BY 4.0.)

Cover image: Endoplasmic reticulum tubules (red) mark the fission site of the Salmonella-containing vacuole (green) at the center. (See related article in May 2025, vol. 16, e00114-25.) (Copyright © 2025 Chopra et al. CC-BY 4.0.)

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Volume 16 • Number 6 • June 2025Current Issue