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The continued emergence of pathogens, whether novel, re-emerging, or engineered, poses a persistent global biosecurity and public health challenge. Recent outbreaks, including COVID-19, Lassa fever, Marburg virus, mpox, and avian influenza, underscore the urgent need for robust systems that enable rapid surveillance, early diagnosis, and timely countermeasures before widespread human transmission occurs. In this article, we focus on early detection technologies and systematically evaluate current diagnostic and sensing modalities. We highlight sequencing and spectroscopy as two complementary approaches capable of providing broad, agnostic detection and rich biological insight. Our analysis emphasizes that scientific innovation alone is insufficient: effective preparedness alsomore » requires improved data curation, integration, and sharing to build AI-ready resources that accelerate future responses. We argue for coordinated advances in both technological capabilities and supporting infrastructure to enable the rapid identification and characterization of emerging pathogens and to fully leverage modern science against evolving infectious threats.« less

Viruses are found across all ecosystems and infect every type of organism on Earth. Traditional culture-based methods have proven insufficient to explore this viral diversity at scale, driving the development of viromics, the sequence-based analysis of uncultivated viruses. Viromics approaches have been particularly useful for studying viruses of microorganisms, which can act as crucial regulators of microbiomes across ecosystems. They have already revealed the broad geographic distribution of viral communities and are progressively uncovering the expansive genetic and functional diversity of the global virome. Moving forward, large-scale viral ecogenomics studies combined with new experimental and computational approaches to identify virusmore » activity and host interactions will enable a more complete characterization of global viral diversity and its effects.« less

Pectin is a complex plant heteropolysaccharide whose structure and function differ depending on its source. In animal feed, breaking down pectin is essential, as its presence increases feed viscosity and reduces nutrient absorption. Soybean meal, a protein-rich poultry feed ingredient, contains significant amounts of pectin, the structure of which remains unclear. Consequently, the enzyme activities required to degrade soybean meal pectin and how they interact are still open questions. In this study, we produced 15 recombinant fungal carbohydrate-active enzymes (CAZymes) identified from fungal secretomes acting on pectin. After observing that these enzymes were not active on soybean meal pectin whenmore » used alone, we developed a semi-miniaturized method to evaluate their effect as multi-activity cocktails. We designed and tested 12 enzyme pools, containing up to 15 different CAZymes, using several hydrolysis markers. Thanks to our multiactivity enzymatic approach combined with a Pearson correlation matrix, we identified 10 fungal CAZymes efficient on soybean meal pectin, 9 of which originate from Talaromyces versatilis. Based on enzyme specificity and linkage analysis, we propose a structural model for soybean meal pectin. Our findings underscore the importance of combining CAZymes to improve the degradation of agricultural co-products.« less

Abstract Expressing plant metabolic pathways in microbial platforms is an efficient, cost‐effective solution for producing many desired plant compounds. As eukaryotic organisms, yeasts are often the preferred platform. However, expression of plant enzymes in a yeast frequently leads to failure because the enzymes are poorly adapted to the foreign yeast cellular environment. Here, we first summarize the current engineering approaches for optimizing performance of plant enzymes in yeast. A critical limitation of these approaches is that they are labour‐intensive and must be customized for each individual enzyme, which significantly hinders the establishment of plant pathways in cellular factories. In responsemore » to this challenge, we propose the development of a cost‐effective computational pipeline to redesign plant enzymes for better adaptation to the yeast cellular milieu. This proposition is underpinned by compelling evidence that plant and yeast enzymes exhibit distinct sequence features that are generalizable across enzyme families. Consequently, we introduce a data‐driven machine learning framework designed to extract ‘yeastizing’ rules from natural protein sequence variations, which can be broadly applied to all enzymes. Additionally, we discuss the potential to integrate the machine learning model into a full design‐build‐test cycle.« less

ABSTRACT In the wild, C. elegans are emersed in environments teeming with a veritable menagerie of microorganisms. The C. elegans cuticular surface serves as a barrier and first point of contact with their microbial environments. In this study, we identify microbes from C. elegans natural habitats that associate with its cuticle, constituting a simple “skin microbiome.” We rear our animals on a modified CeMbio, mCeMbio, a consortium of ecologically relevant microbes. We first combine standard microbiological methods with an adapted micro skin-swabbing tool to describe the skin-resident bacteria on the C. elegans surface. Furthermore, we conduct 16S rRNA gene sequencingmore » studies to identify relative shifts in the proportion of mCeMbio bacteria upon surface-sterilization, implying distinct skin- and gut-microbiomes. We find that some strains of bacteria, including Enterobacter sp. JUb101 , are primarily found on the nematode skin, while others like Stenotrophomonas indicatrix JUb19 and Ochrobactrum vermis MYb71 are predominantly found in the animal’s gut. Finally, we show that this skin microbiome promotes host cuticle integrity in harsh environments. Together, we identify a skin microbiome for the well-studied nematode model and propose its value in conferring host fitness advantages in naturalized contexts. IMPORTANCE The genetic model organism C. elegans has recently emerged as a tool for understanding host–microbiome interactions. Nearly all of these studies either focus on pathogenic or gut-resident microbes. Little is known about the existence of native, nonpathogenic skin microbes or their function. We demonstrate that members of a modified C. elegans model microbiome, mCeMbio, can adhere to the animal's cuticle and confer protection from noxious environments. We combine a novel micro-swab tool, the first 16S microbial sequencing data from relatively unperturbed C. elegans , and physiological assays to demonstrate microbially mediated protection of the skin. This work serves as a foundation to explore wild C. elegans skin microbiomes and use C. elegans as a model for skin research.« less

Abstract Background Protists, single-celled eukaryotic organisms, are critical to food web ecology, contributing to primary productivity and connecting small bacteria and archaea to higher trophic levels. Lake Mendota is a large, eutrophic natural lake that is a Long-Term Ecological Research site and among the world’s best-studied freshwater systems. Metagenomic samples have been collected and shotgun sequenced from Lake Mendota for the last 20 years. Here, we analyze this comprehensive time series to infer changes to the structure and function of the protistan community and to hypothesize about their interactions with bacteria. Results Based on small subunit rRNA genes extracted frommore » the metagenomes and metagenome-assembled genomes of microeukaryotes, we identify shifts in the eukaryotic phytoplankton community over time, which we predict to be a consequence of reduced zooplankton grazing pressures after the invasion of a invasive predator (the spiny water flea) to the lake. The metagenomic data also reveal the presence of the spiny water flea and the zebra mussel, a second invasive species to Lake Mendota, prior to their visual identification during routine monitoring. Furthermore, we use species co-occurrence and co-abundance analysis to connect the protistan community with bacterial taxa. Correlation analysis suggests that protists and bacteria may interact or respond similarly to environmental conditions. Cryptophytes declined in the second decade of the timeseries, while many alveolate groups (e.g., ciliates and dinoflagellates) and diatoms increased in abundance, changes that have implications for food web efficiency in Lake Mendota. Conclusions We demonstrate that metagenomic sequence-based community analysis can complement existing efforts to monitor protists in Lake Mendota based on microscopy-based count surveys. We observed patterns of seasonal abundance in microeukaryotes in Lake Mendota that corroborated expectations from other systems, including high abundance of cryptophytes in winter and diatoms in fall and spring, but with much higher resolution than previous surveys. Our study identified long-term changes in the abundance of eukaryotic microbes and provided context for the known establishment of an invasive species that catalyzes a trophic cascade involving protists. Our findings are important for decoding potential long-term consequences of human interventions, including invasive species introduction.« less

The rapidly warming Arctic has transitioned to thinner sea ice which fractures, producing leads. Few studies have investigated Arctic sea spray aerosol (SSA) produced from open ocean, leads, and melt ponds, which vary in salinity and organic and microbial community composition. A marine aerosol reference tank was deployed aboard an icebreaker to the Arctic Ocean during August–September 2018 to study SSA generated from locally collected surface waters. Aerosol generation experiments were carried out using water collected from the marginal ice zone, a human-made hole in sea ice near the North Pole, and both lead and melt pond water during anmore » ice floe drift period. Salinity, chlorophyll a, organic carbon, nitrogen, and microbial community composition were measured. Eukaryotic plankton and bacterial abundance were elevated in experimental water from the marginal ice zone, but the relative contributions from major eukaryotic taxonomic groups varied little across the experiments. The chemical composition of individual SSA particles was analyzed using Raman microspectroscopy and computer-controlled scanning electron microscopy with energy-dispersive X-ray spectroscopy. Individual sea salt aerosol, primary organic aerosol, and mineral dust particles were observed. Sea salt aerosol constituted 44–95% of individual submicrometer and 68–100% of supermicrometer particles, by number, generated during each experiment. Carbon was detected in 85%, by number, of the individual sea salt particles, with visible organic coatings. Carbohydrates were detected in 72% of particles, by number, with smaller contributions from long-chain fatty acids (13%) and siliceous material (15%). SSA generated from melt pond water contained only long-chain fatty acids and siliceous material. Quantification of the ice-nucleating activity showed that locally produced SSA may define the High Arctic background ice-nucleating particle population, but cannot account for the peak atmospheric concentrations observed. As the Arctic warms, the increasing SSA emissions have a complex dependence on changing biological and physical processes.« less

Abstract Petroleum‐based plastics levy significant environmental and economic costs that can be alleviated with sustainably sourced, biodegradable, and bio‐based polymers such as polyhydroxyalkanoates (PHAs). However, industrial‐scale production of PHAs faces barriers stemming from insufficient product yields and high costs. To address these challenges, we must look beyond the current suite of microbes for PHA production and investigate non‐model organisms with versatile metabolisms. In that vein, we assessed PHA production by the photosynthetic purple non‐sulfur bacteria (PNSB) Rhodomicrobium vannielii and Rhodomicrobium udaipurense. We show that both species accumulate PHA across photo‐heterotrophic, photo‐hydrogenotrophic, photo‐ferrotrophic, and photo‐electrotrophic growth conditions, with either ammonium chloridemore » (NH ₄ Cl) or dinitrogen gas (N ₂ ) as nitrogen sources. Our data indicate that nitrogen source plays a significant role in dictating PHA synthesis, with N ₂ fixation promoting PHA production during photoheterotrophy and photoelectrotrophy but inhibiting production during photohydrogenotrophy and photoferrotrophy. We observed the highest PHA titres (up to 44.08 mg/L, or 43.61% cell dry weight) when cells were grown photoheterotrophically on sodium butyrate with N ₂ , while production was at its lowest during photoelectrotrophy (as low as 0.04 mg/L, or 0.16% cell dry weight). We also find that photohydrogenotrophically grown cells supplemented with NH ₄ Cl exhibit the highest electron yields – up to 58.89% – while photoheterotrophy demonstrated the lowest (0.27%–1.39%). Finally, we highlight superior electron conversion and PHA production compared to a related PNSB, Rhodopseudomonas palustris TIE‐1. This study illustrates the value of studying non‐model organisms like Rhodomicrobium for sustainable PHA production and indicates future directions for exploring PNSB metabolisms.« less

Introduction.Simethicone is an over-the-counter product that is frequently used by clinicians during endoscopic procedures to reduce foaming and improve visualization. Published studies have found simethicone residue on endoscopes after cleaning and disinfecting the devices as per the manufacturer’s instructions. Some literature suggests that simethicone residue may reduce disinfection efficacy and increase the risk of patient infections. Gap Statement.However, there appears to be a lack of direct evidence in the literature to either disprove this or correlate simethicone presence with an increased microbial risk. Aim: Research was conducted to evaluate thein vitroimpact of simethicone on disinfection efficacy. Methodology.Bacteria were grown inmore » a microtitre plate assay in the presence of a range of simethicone concentrations and then treated with a disinfectant. Bacterial growth was assessed by spotting each microtitre well onto an agar plate. Results.The results demonstrated that, under the conditions tested, simethicone did not reduce the efficacy of Cidex ortho-phthalaldehyde disinfectant, which demonstrated at least a 6-log unit reduction in bacterial viability. Additional experiments showed that direct exposure to 66 mg ml⁻¹of simethicone reduced bacterial viability. Conclusion.These results indicate that simethicone may not reduce the bactericidal efficacy of disinfectant during reprocessing, under certain conditions.« less

Abstract Soil microorganisms are pivotal in the global carbon cycle, but the viruses that affect them and their impact on ecosystems are less understood. In this study, we explored the diversity, dynamics, and ecology of soil viruses through 379 metagenomes collected annually from 2010 to 2017. These samples spanned the seasonally thawed active layer of a permafrost thaw gradient, which included palsa, bog, and fen habitats. We identified 5051 virus operational taxonomic units (vOTUs), doubling the known viruses for this site. These vOTUs were largely ephemeral within habitats, suggesting a turnover at the vOTU level from year to year. Whilemore » the diversity varied by thaw stage and depth‐related patterns were specific to each habitat, the virus communities did not significantly change over time. The abundance ratios of virus to host at the phylum level did not show consistent trends across the thaw gradient, depth, or time. To assess potential ecosystem impacts, we predicted hosts in silico and found viruses linked to microbial lineages involved in the carbon cycle, such as methanotrophy and methanogenesis. This included the identification of viruses of Candidatus Methanoflorens, a significant global methane contributor. We also detected a variety of potential auxiliary metabolic genes, including 24 carbon‐degrading glycoside hydrolases, six of which are uniquely terrestrial. In conclusion, these long‐term observations enhance our understanding of soil viruses in the context of climate‐relevant processes and provide opportunities to explore their role in terrestrial carbon cycling.« less