Trends in Microbiology

Collateral sensitivity and genetic vulnerability of antibiotic resistance

From feedbacks to functional teams in the rhizosphere Johnson and Marín’s paper presents functional team selection (FTS) as a major conceptual advance in plant–microbiome ecology. FTS explains how limiting resources and/or stress selects cooperative microbial teams that promote plant adaptation, integrating ecological feedback and evolutionary selection to predict when and where resilient plant–microbiome partnerships will arise.

From feedbacks to functional teams in the rhizosphere

Friend or foe? Contextualizing Bacteroides through the lens of niche remodeling The genus Bacteroides comprises canonical commensals of the gastrointestinal microbiota that maintain intestinal homeostasis and contribute to host health. Yet, emergent evidence has revealed that these same bacteria can also increase host susceptibility to infectious and noninfectious diseases, as well as directly drive intestinal inflammatory pathology. In this review we reconcile this duality with the paradigm that Bacteroides’ pathogenic potential scales with the degree to which it remodels its intestinal niches. Understanding the molecular and ecological mechanisms underlying this niche remodeling is essential to defining when Bacteroides acts as friend or foe. This review highlights recent advances that illuminate these context-dependent behaviors and their implications for gut health and disease.

Friend or foe? Contextualizing Bacteroides through the lens of niche remodeling

Type I interferons in tuberculosis pathogenesis and prevention Mycobacterium tuberculosis (Mtb) remains an epidemiological concern due to heterogeneous outcomes in tuberculosis (TB) pathology and the lack of mechanistic understanding of early immune events. Type I interferons (IFNs) in TB are generally described as pathological. However, evidence also suggests a protective role in vaccination and adjunctive to chemotherapy. Understanding Type I IFN signaling in Mtb–host interactions is therefore critical as it is among the earliest signatures of progressive infection. Crosstalk between Type I and II IFN signaling during TB may also be key to disease outcome. This review explores our current understanding of the role of Type I IFNs in Mtb infection and vaccination and offers the IFN type switching model, among others, to explain the duality of IFNs' function in TB.

Type I interferons in tuberculosis pathogenesis and prevention

Engagement and justice considerations in mitigation of antimicrobial resistance We are delighted by the response by Dobreva et al. to our original article, and by the detail they provide about the methods used to try and ensure epistemic justice in the WHO antimicrobial resistance (AMR) research priority setting process [1]. That regardless of the efforts made, the process still led to over-representation from the global North, as the authors themselves concluded, is evidence of the complexity of ensuring epistemic justice in relation to AMR [2].

Engagement and justice considerations in mitigation of antimicrobial resistance

Vibrio natriegens Vibrio natriegens is a Gram-negative, halophilic member of the Harveyi clade and Vibrio core group that inhabits marine and estuarine coastal waters and sediments. While generally considered nonpathogenic, this species shares this clade with serious human pathogens (e.g., Vibrio parahaemolyticus) and aquatic animal pathogens (e.g., Vibrio harveyi, Vibrio campbelllii, and Vibrio alginolyticus). Although it was discovered more than 65 years ago, most of our knowledge regarding this bacterium has been generated in the past decade.

Vibrio natriegens

PilY proteins: bimodular drivers of type IV pilus versatility Type IV pili (T4P) are dynamic surface fibers that mediate diverse bacterial activities, including adhesion, twitching motility, horizontal gene transfer, biofilm formation, and virulence. The PilY family of T4P-associated proteins are found across a wide range of bacterial species and are critical for key T4P functions. PilY proteins are characterized by a shared domain architecture which consists of a variable N-terminal region that mediates adhesion and a conserved C-terminal beta-propeller domain that facilitates pilus biogenesis. Given their surface exposure and roles in virulence, PilY family proteins represent an attractive target for novel therapeutic interventions, including small-molecule antivirulence therapies against pathogenic bacteria and potential as vaccine antigens. This review synthesizes our current understanding of PilY structure, localization, function, and evolutionary relationships across T4P systems.

PilY proteins: bimodular drivers of type IV pilus versatility

Microbial rhythms – a new target to promote health? Daily dynamics in the composition and function of the human gut microbiota have been recognized since 2014, yet the molecular mechanisms underlying these rhythms and their impact on human health remain unclear. Disrupted microbial oscillations are increasingly linked to metabolic diseases such as obesity and type 2 diabetes, and to inflammatory conditions in the gut and beyond. We propose advancing from observational studies to experimentally targeting microbial rhythms and clocks to uncover causal relationships. In vivo and in vitro models offer opportunities to uncover how signaling cues and dietary patterns influence microbial oscillations and, in turn, host metabolic and immune functions. Manipulating microbial rhythmicity independent of host physiology represents a new frontier for microbiota-based strategies to promote health and prevent diseases.

Microbial rhythms – a new target to promote health?

Advancing equity in antimicrobial resistance research and policy The recent article 'Tracing epistemic injustice in global antimicrobial resistance research' reasons that injustices in setting global research priorities – that is, who produces and uses antimicrobial resistance (AMR) knowledge, and valuing certain types of knowledge – have created ‘blind spots’ in research and policy on AMR [1]. Research and interventions relevant to low- and middle-income countries (LMICs) have been underprioritised, even though more than half of the 92 million people whose lives could be saved by 2050 through improved access to antibiotics and health care are in sub-Saharan Africa and South Asia [2].

Advancing equity in antimicrobial resistance research and policy

Localized glutamine leakage shapes root microbiome Root exudates are vital for guiding microbial dynamics in the rhizosphere. Nevertheless, the key component in root exudates responsible for defining the root microbiome has remained obscure. Tsai et al. recently offered insights into how Casparian strips prevent glutamine leakage from the vasculature, thereby shaping the root microbiome.

Localized glutamine leakage shapes root microbiome

Mycorrhizal networks transfer jasmonic acid to recruit pathogen-suppressors Common mycorrhizal networks (CMNs) formed by arbuscular mycorrhizal fungi interconnect neighbouring plants. New evidence from Zhang et al. demonstrates that CMNs transfer jasmonic acid from necrotrophic pathogen-infected to uninfected tomato plants, priming defence responses and recruiting disease-suppressive bacteria. These findings establish a key mechanistic link underlying CMN-mediated plant defence communication.

Mycorrhizal networks transfer jasmonic acid to recruit pathogen-suppressors

The pig that could save us: swine models in respiratory infections Respiratory infections kill millions and overwhelm the healthcare systems worldwide. Swine are powerful allies in this fight. They provide practical, human-like platforms to study pathogens, test vaccines/therapies, and strengthen pandemic readiness. Pig models, with the advent of genetic engineering tools, are closing translational gaps and revealing mechanisms that guide interventions effectively.

The pig that could save us: swine models in respiratory infections

The hitchhiker’s guide to cross-species DNA delivery Microbial hitchhikers are rewriting the rules of horizontal gene transfer. He, Patkowski, et al. reveal how phage satellites assemble chimeric infective particles that deliver DNA across species boundaries through ‘tail piracy’. This discovery reframes microbial innovation and provides a blueprint for next-generation biotechnologies, achieving what phage engineering has long pursued.

The hitchhiker’s guide to cross-species DNA delivery

Toward a Yanomami framework for ethical microbiome research This paper proposes an ethical framework for microbiome research with the Yanomami, an Indigenous Amazonian people, grounded in collaboration, reciprocity, and relational accountability. Key elements include dedicated funding for community-identified initiatives, sustained community-led ethical oversight, and meaningful benefit-sharing. This approach fosters trust and supports equitable, culturally aligned, and sustainable research collaboration.

Toward a Yanomami framework for ethical microbiome research

PurFect timing: revisiting purine metabolism for tuberculosis treatment Eradication of tuberculosis requires new drugs targeting novel pathways. Although purine metabolism represents an essential antitubercular target, concerns about host nucleobase rescue limited its exploration. New data demonstrate that nucleobase levels in human lung tissue are insufficient to confer rescue, renewing interest in this pathway for tuberculosis drug discovery.

PurFect timing: revisiting purine metabolism for tuberculosis treatment

Tackling the active antibiotic-resistant bacteria in soils Soils are critical reservoirs of antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB), serving as interfaces among human, animal, plant, and environmental microbiomes. While many studies have profiled soil ARGs, most rely on DNA-based methods that cannot distinguish total from metabolically active ARB, limiting risk assessment and mitigation. This review outlines soil ARG sources, their mobility, and potential transmission to plants and the food chain. We highlight advances in community- and single-cell-level approaches for characterizing active ARB and explore emerging mitigation strategies such as advanced waste treatment and bioremediation. This review aims to bridge the gap between ARG pollution and its risk mitigation, contributing to a comprehensive framework for tackling active ARB in soils.

Tackling the active antibiotic-resistant bacteria in soils

Methanobrevibacter smithii Methanobrevibacter smithii is one of the most prevalent and worldwide distributed archaea in the human gut. M. smithii is a strict anaerobe that obtains its energy through methanogenesis. In culture, it reduces CO2 to methane (CH4) using H2 as electron donor (i.e., CO2-reducing hydrogenotrophic methanogenesis) and to a lower extent, formate. Other potential methanogenic substrates, methanol and ethanol, are not used in culture, but genes involved in their utilization are upregulated when colonizing the mouse intestine.

Methanobrevibacter smithii

Argentine microbiology: between scientific legacy and systemic fragility Argentina’s microbiology, born from 19th-century public health challenges, built enduring institutions and contributed globally to the fight against infectious diseases, to agriculture, and to biotechnology. Yet chronic underfunding, political instability, and policy discontinuity have undermined progress. Revitalization requires a sustained strategy that fosters investment and collaboration, transforming historical strengths into lasting scientific and societal development.

Argentine microbiology: between scientific legacy and systemic fragility

Revisiting the order Nitrospirales: phylogeny, habitat range, metabolism Nitrification is a key process in the nitrogen cycle performed by several functional groups of chemolithoautotrophic microorganisms. The order Nitrospirales plays a central role in this process. Comprehensive genomic analysis conducted by Kop et al. revealed unexplored phylogenetic diversity, habitat range, and metabolic versatility within the order Nitrospirales.

Revisiting the order Nitrospirales: phylogeny, habitat range, metabolism

Cellulose biosynthesis and function in Streptomyces Cellulose, a ubiquitous polysaccharide with critical roles in life, provides structural integrity to cells in plants and aids biofilm formation in many bacteria. Although bacterial cellulose biosynthesis is well studied in certain groups, its diversity in other lineages remains underexplored. Recent insights from filamentous streptomycetes reveal that cellulose is directly incorporated into the cell wall at growing tips, likely protecting hyphae during growth. This review examines cellulose biosynthesis, regulation, and secretion mechanisms in Streptomyces, and highlights how its structural organization supports distinct cellular functions. We also discuss the evolutionary context of this system. Together, these insights broaden our understanding of bacterial cellulose diversity and suggest that cellulose biosynthesis has evolved convergently to support different lifestyles, growth modes, and morphogenetic strategies.

Cellulose biosynthesis and function in Streptomyces

Kiwa antiviral system: a membrane-embedded defense against phage Bacteria and viruses have coevolved for billions of years. Recently, Zhang et al. identified the Kiwa defense system as a membrane-embedded sensor that detects early phage invasion and coordinates antiviral response; it collaborates with RecBCD to neutralize phage inhibitors, illustrating how prokaryotic immunity networks employ redundancy and versatility against evolving threats.

Kiwa antiviral system: a membrane-embedded defense against phage

From structure to immunity: how skin shapes age-related vulnerability to Chikungunya virus infections Arboviral diseases are resurging globally, with Chikungunya virus (CHIKV) demonstrating a troubling capacity for large-scale outbreaks. In 2024, CHIKV re-emerged in Réunion Island with 47 500 cases and 12 deaths reported by May 2025. Notably, infants and the elderly were disproportionately affected, two age groups with distinct and underexplored vulnerabilities in immune defense, particularly at the skin. As the skin is the primary site of CHIKV inoculation and a key immunological barrier, age-dependent changes in the skin likely influence infection outcomes. Yet, it remains an overlooked target for intervention. This review explores how developmental and aging-associated alterations in the skin’s structure, immune composition, and the microbiome shape arboviral pathogenesis, with a particular emphasis on CHIKV, and guides research toward age-tailored interventions for vulnerable populations.

From structure to immunity: how skin shapes age-related vulnerability to Chikungunya virus infections

Mangrove microbiomes as hidden ecological gatekeepers Mangroves are known worldwide but their concealed network of microbiomes is poorly understood. Huang et al., on genomic indicators, Siblos and Tabugo's 16S rRNA sequencing of the mangrove microbiome, and Dechavez et al.’s culture-dependent survey collectively highlight the ecological significance of mangroves, their conservation potential, and their role as key ecological gatekeepers.

Mangrove microbiomes as hidden ecological gatekeepers

On target: antibodies against the neuraminidase active site While often overlooked in studies of influenza antibody responses, the virally encoded neuraminidase (NA) is emerging as an attractive vaccine target due to its comparably high sequence conservation. Recent studies by Jo et al., Lederhofer et al., and Lv et al. reveal a common theme of receptor mimicry mediated by structurally convergent antibodies.

On target: antibodies against the neuraminidase active site

Unraveling microbiome integration in soil transplant Little is known about the processes that drive microbial community merging and development in transplanted soils. A recent study by Causevic et al. disentangled the relative contribution of habitat filtering and microbiota taxa origin in shaping transplant outcomes, providing valuable insights for advancing microbial engineering.

Unraveling microbiome integration in soil transplant

Saccharolobus islandicus Saccharolobus islandicus (f. Sulfolobus islandicus) is a hyperthermophilic archaeon frequently isolated from oxic hot spring waters and sediments at 59–91°C and pH 2–4. It grows aerobically with a doubling time of 6–10 h under laboratory conditions (optimal: 76–78°C and pH 3–3.5) and forms single colonies on gelrite- or phytagel-solidified media. As a heterotrophic organism, S. islandicus exhibits broad metabolic versatility, owing to numerous transport systems encoded in its genome, which facilitate the uptake of diverse carbon and organic nitrogen sources.

Saccharolobus islandicus

How should health researchers advance health equity? This commentary outlines ways in which health researchers can advance health equity. We focus on often-overlooked areas, including identifying context-specific drivers of inequity, carefully selecting research questions and priorities, engaging stakeholders, including those whose voices are seldom heard, improving diversity and inclusiveness among study participants, and using equity-oriented study designs.

How should health researchers advance health equity?

Navigating trust and science: microbiome research in the Amazon Including Indigenous Peoples in microbiome research is both a scientific imperative and an ethical responsibility. Our long-standing partnership with the Matsés Peoples from the Peruvian Amazon provided scientific insights in microbial profiles that have coevolved with humans, studies only possible via trust-based ethical partnerships. Community-based participatory research (CBPR) is essential to navigate mistrust rooted in historical injustices. We present our experience implementing culturally informed protocols and equitable benefit-sharing as cornerstones of respectful, inclusive microbiome research with Peruvian Indigenous Peoples. This approach fosters sustainable research partnerships grounded in reciprocal trust and mutual benefit.

Navigating trust and science: microbiome research in the Amazon

Working together to tackle fungal disease across Latin America Fungal infections are a major contributor to human infectious diseases. To address this in Latin America, international groups formed the Fungal Disease Interest Group (FDIG). At the Brazil conference of the International Society for Human and Animal Mycoses (ISHAM), FDIG hosted a forum highlighting key challenges and priorities to advance fungal disease research, education, and public health across the region.

Working together to tackle fungal disease across Latin America

Microbial traits for volatile production and consumption are diverse and consequential. Here's why they are ripe for interpretation through a trait-based lens...

Led by UA PhD students Ledford and Geffre @parkergeffre.bsky.social in collab w/ LBNL team @elbrodie.bsky.social Marschmann Karaoz