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At least 19 records

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DOE OSTI2025

Quorum-driven microbial consortium for Bioplastic production from agro-waste

Microbial consortia have high relevance in natural environments. Here we present the production of polyhydroxyalkanoates (PHA) from agro-industrial residues by a synthetic interkingdom consortium formed by the saprotrophic fungus Ophiostoma piceae CECT 20146, which encodes a wide range of lignocellulolytic enzymes, and a natural PHA producer, Pseudomonas putida KT2440. Two agro-industrial residues were utilized: Brewer's Spent Grain (BSG) as a carbon/nitrogen source and biofilm scaffold and waste cooking oil (WCO) as a carbon source for PHA synthesis. Through biochemistry, microscopy, and omics analyses, it is shown that P. putida accumulates up to 40.2% of intracellular PHA when the quorum sensing molecule, farnesol (naturally produced by O. piceae) is added, thanks to the increased proliferation of P. putida cells. An interactive Shiny application has also been developed for an easy visualization and comprehension of all the transcriptomics and metabolomics data: https://jgf-bioinformatics.shinyapps.io/Visualization_app/. These results support the increased PHA production of the consortium by an induction of gene phaG, which redirects intermediaries of the fatty acid biosynthesis to PHA precursors, and the repression of the PHA depolymerase phaZ in P. putida. The trophic interaction between microorganisms seems to rely on the citric acid produced by O. piceae and the glycerol liberated from WCO, which can both be consumed by P. putida. Bioreactor scale-up experiments allowed a 3.3-fold increase in the PHA concentration in the consortium (6.7 g·L-1) without pretreatment or sterilization of the substrates, laying the groundwork for the implementation of an industrial consolidated bioprocess (CBP).

Bacteria↗

DOE OSTI2026

Multi-omic characterization of a soil microbial consortium reveals critical role of succinate and glutamate metabolism during calcium carbonate precipitation

Microbially induced calcium carbonate precipitation (MICP) holds potential for use in soil stabilization and carbon sequestration, with the overall efficiency of the process being a major determinant for use in many environmental and civil engineering applications. While the biogeochemical pathways and enzymes driving MICP are known, the microbial metabolic networks and community dynamics underlying such precipitation remain poorly characterized. To address this gap, we developed a four-member consortium of soil bacteria (Curtobacterium flaccumfaciens, Rhodococcus qingshengii, Microbacterium sp., and Bacillus toyonensis), termed carbon storing consortium - A (CSC-A), that is capable of MICP. Prior work shows that MICP production is higher in CSC-A compared to the sum of carbonate produced by each member, suggesting carbonate production is driven by consortium dynamics. To that end we used a multi-omic integration approach of genomics, transcriptomics, and metabolomics to investigate potential inter-species interactions that may influence the MICP phenotype. Genomic life history characterizations identified evidence of niche specialization by B. toyonensis and Microbacterium, while metatranscriptomic analysis suggests R. qingshengii is a keystone species during growth in urea. By comparing individual species’ metabolomes to the metabolic profile of a shared well of precipitated metabolites, we identified over 200 metabolites predicted to be produced or consumed by CSC-A members. Integrating both data types to search the KEGG reactome highlighted a network centered around glutamine metabolism and branched chain amino acid biosynthesis under regulation during CSC-A growth in urea. Succinate metabolism was also a major node in this network and laboratory assays confirmed that increasing the amount of succinate in the growth medium leads to increased carbonate precipitation by CSC-A, a critical confirmation of our modeling approach. By isolating and identifying the interconnected metabolic components underlying MICP in CSC-A, we identified keystone taxa, metabolites, and pathways important for future optimization of the application of this consortia to carbonate precipitation.

carbon storing consortium - A (CSC-A)↗

DOE OSTI2025

Engineering microbial consortia for mixed plastic upcycling

Recent studies in developing processes using ‘single’ plastic waste for microbial conversion have demonstrated great promise in advancing a circular economy. However, chemical complexity and compositional variability of post-consumer ‘mixed’ plastic waste pose huge challenges to using it as a feedstock for biomanufacturing. Here, we present a process leveraging a synthetic microbial consortium, comprising Rhodococcus jostii strain PET and Acinetobacter baylyi ADP1, enabled by engineering the division of labor. The robust consortium synergistically and stably consumes diverse mixtures of oxygenated compounds, derived from the depolymerization of post-consumer, mixed plastic waste, regardless of the fluctuating plastic waste compositions. We evaluate the upcycling potential of the stable consortium by applying rational metabolic engineering to both specialists, enabling the funneling of these oxygenates into lycopene and lipids. This work highlights the potential of stable microbial consortia to valorize untapped, mixed plastic waste for sustainable biomanufacturing, offering a promising solution to global plastic pollution.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

A Novel Integrated Fermentation Process with Engineered Microbial Consortia for Butanol Production from Lignocellulose Sugars without CO 2 Emission

The goal of this project was to develop a synthetic microbial consortium consisting of a lactic acid bacterium, a carboxydotrophic acetogen, and a solventogenic clostridia for the production of n butanol, an advanced biofuel and industrial chemical, from lignocellulose sugars (mainly glucose and xylose) and formate (produced from CO 2 by electrochemical reduction) in an integrated bioprocess (biorefinery), which can provide an effective solution to the technical challenges in developing energy and carbon optimized synthesis for the bioeconomy and achieve the program objectives of ARPA-E. The project focused on the design, modeling and construction of synthetic microbial consortia consisting of three bacterial species to maximize carbon conversion and butanol production with a 100% theoretical product yield from glucose and zero or negative CO 2 emission.

09 BIOMASS FUELS↗

NASA NTRS1998

Perennial Antarctic lake ice: an oasis for life in a polar desert

The permanent ice covers of Antarctic lakes in the McMurdo Dry Valleys develop liquid water inclusions in response to solar heating of internal aeolian-derived sediments. The ice sediment particles serve as nutrient (inorganic and organic)-enriched microzones for the establishment of a physiologically and ecologically complex microbial consortium capable of contemporaneous photosynthesis, nitrogen fixation, and decomposition. The consortium is capable of physically and chemically establishing and modifying a relatively nutrient- and organic matter-enriched microbial "oasis" embedded in the lake ice cover.

NASA Center ARC↗

DOE OSTI2025

Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation

Soil moisture and porosity regulate microbial metabolism by influencing factors, such as system chemistry, substrate availability, and soil connectivity. However, accurately representing the soil environment and establishing a tractable microbial community that limits confounding variables is difficult. Here, we use a reduced-complexity microbial consortium grown in a glass bead porous media amended with chitin to test the effects of moisture and a structural matrix on microbial phenotypes. Leveraging metagenomes, metatranscriptomes, metaproteomes, and metabolomes, we saw that our porous media system significantly altered microbial phenotypes compared with the liquid incubations, denoting the importance of incorporating pores and surfaces for understanding microbial phenotypes in soils. These phenotypic shifts were mainly driven by differences in expression of Streptomyces and Ensifer, which included a significant decrease in overall chitin degradation between porous media and liquid. Our findings suggest that the success of Ensifer in porous media is likely related to its ability to repurpose carbon via the glyoxylate shunt amidst a lack of chitin degradation byproducts while potentially using polyhydroxyalkanoate granules as a C source. We also identified traits expressed by Ensifer and others, including motility, stress resistance, and carbon conservation, that likely influence the metabolic profiles observed across treatments. Together, these results demonstrate that porous media incubations promote structure-induced microbial phenotypes and are likely a better proxy for soil conditions than liquid culture systems. Furthermore, they emphasize that microbial phenotypes encompass not only the multi-enzyme pathways involved in metabolism but also include the complex interactions with the environment and other community members.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRSDate not supplied

Agent-based modeling of microbes in space

Space is tough on organisms. Microorganisms traveling to space experience stress from environmental features such as ionizing radiation and lack of normal microgravity; however, much remains unknown about the mechanisms by which those environmental features affect microbial physiology. Microbes experience changes in gravity not directly but rather through changes in their fluid environment, and deep-space particle radiation causes cell damage that is complex but rare. Computational modeling at the single-cell level (agent-based modeling) can allow us to probe the spatially heterogeneous processes that characterize space stresses, to gain insight into the relationships of microbial cells with their environments and with each other. Here we present two software packages for simulating microbial population dynamics in space conditions: CAMDLES and AMMPER. Microbes growing in liquid culture medium in the microgravity of an orbital space station experience a quiescent, poorly-mixed fluid environment. CAMDLES (CFD-DEM Artificial Microgravity Developments for Living Ecosystem Simulation) simultaneously simulates biological, chemical, and mechanical processes to predict microbial ecological dynamics in microgravity, and in the rotating culture vessels used to create an artificial microgravity environment in the lab. Initial results demonstrate that the growth of a cross-feeding microbial consortium, dependent on the exchange of soluble metabolites, is sensitive to the initial spatial distribution of cells, and grows differently in real versus artificial microgravity. Microbial populations exposed to deep-space radiation experience spatially and temporally heterogeneous damage from the traversal of high-energy particles. AMMPER (Agent-Based Model for Microbial Populations Exposed to Radiation) pairs a 3d model of energy deposition along a radiation particle track with a microbial population growth and damage model to predict the effects of localized radiation damage on population-level responses. It includes a user-friendly graphical interface. AMMPER results agree with experimental data indicating that indirect effects of radiation (reactive oxygen species generation, metabolic impairment) have a greater impact on microorganisms than direct effects (DNA damage).

Jessica A Lee↗

NASA NTRS2022

Agent-Based Modeling of Microbes in Space

Space is tough on organisms. Microorganisms traveling to space experience stress from environmental features such as ionizing radiation and lack of normal gravity, and much remains unknown about the mechanisms by which those environmental features affect microbial physiology. Microbes experience changes in gravity not directly but rather through changes in their fluid environment, and deep-space particle radiation causes cell damage that is complex but rare. Computational modeling at the single-cell level (agent-based modeling) can allow us to probe the spatially heterogeneous processes that characterize space stresses, to gain insight into the relationships of microbial cells with their environments and with each other. Here we present two software packages for simulating microbial population dynamics in space conditions: CAMDLES and AMMPER. Microbes growing in liquid culture medium in the microgravity of an orbital space station experience a quiescent, poorly-mixed fluid environment. CAMDLES (CFD-DEM Artificial Microgravity Developments for Living Ecosystem Simulation) simultaneously simulates biological, chemical, and mechanical processes to predict microbial ecological dynamics in microgravity, and in the rotating culture vessels used to create an artificial microgravity environment in the lab. Initial results demonstrate that the growth of a cross-feeding microbial consortium, dependent on the exchange of soluble metabolites, is sensitive to the initial spatial distribution of cells, and grows differently in real versus artificial microgravity. Microbial populations exposed to deep-space radiation experience spatially and temporally heterogeneous damage from the traversal of high-energy particles. AMMPER (Agent-Based Model for Microbial Populations Exposed to Radiation) pairs a 3d model of energy deposition along a radiation particle track with a microbial population growth and damage model to predict the effects of localized radiation damage on population-level responses. It includes a user-friendly graphical interface. AMMPER growth curves recapitulate experimental results, and allow comparison between direct effects (DNA damage) and indirect effects (reactive oxygen species generation, metabolic impairment) of radiation.

microbiology↗

DOE OSTI2025

Characterization and Stimulation of Selenium Reducing Microbial Consortia from Real Flue Gas Desulfurization Wastewater Biological Treatment System

Selenium is released into the environment via anthropogenic activities such as coal combustion. The U.S. Environmental Protection Agency’s Effluent Limitation Guideline (ELG) Rule limits the release of selenium species into U.S. waterways. To meet the ELG limit for selenium, coal-fired power plants must treat the wastewater produced by the flue gas desulfurization (FGD) systems. Selenium removal is of interest because small changes of the concentrations of selenium in the environment can cause detrimental ecological consequences. Biological treatment is used to remediate this wastewater, but little is known about the individual species in the microbial consortium that reduce toxic water-soluble selenium oxyanions to insoluble elemental selenium. To optimize current biological treatment capabilities of this water, the selenium-reducing capabilities must be leveraged. In order to do so, the selenium-reducing bacteria (SeRB) in biological treatment systems must be characterized. This study will be the first to characterize the microbial consortia from a real FGD WW biological treatment system and provide insights on how to better achieve selenium removal via biological treatment. This work will provide insights into the microorganisms predominantly responsible for the reduction of selenium oxyanions in FGD wastewater biological treatment systems, which can be used to better optimize more efficient biological treatment strategies of this industrial waste.

geomicrobiology↗

DOE OSTI2024

Biofilm mitigation in hybrid chemical-biological upcycling of waste polymers

Accumulation of plastic waste in the environment is a serious global issue. To deal with this, there is a need for improved and more efficient methods for plastic waste recycling. One approach is to depolymerize plastic using pyrolysis or chemical deconstruction followed by microbial-upcycling of the monomers into more valuable products. Microbial consortia may be able to increase stability in response to process perturbations and adapt to diverse carbon sources, but may be more likely to form biofilms that foul process equipment, increasing the challenge of harvesting the cell biomass. To better understand the relationship between bioprocess conditions, biofilm formation, and ecology within the bioreactor, in this study a previously-enriched microbial consortium (LS1_Calumet) was grown on (1) ammonium hydroxide-depolymerized polyethylene terephthalate (PET) monomers and (2) the pyrolysis products of polyethylene (PE) and polypropylene (PP). Bioreactor temperature, pH, agitation speed, and aeration were varied to determine the conditions that led to the highest production of planktonic biomass and minimal formation of biofilm. The community makeup and diversity in the planktonic and biofilm states were evaluated using 16S rRNA gene amplicon sequencing. Results showed that there was very little microbial growth on the liquid product from pyrolysis under all fermentation conditions. When grown on the chemically-deconstructed PET the highest cell density (0.69 g/L) with minimal biofilm formation was produced at 30°C, pH 7, 100 rpm agitation, and 10 sL/hr airflow. Results from 16S rRNAsequencing showed that the planktonic phase had higher observed diversity than the biofilm, and that Rhodococcus, Paracoccus, and Chelatococcus were the most abundant genera for all process conditions. Biofilm formation by Rhodococcus sp. And Paracoccus sp. Isolates was typically lower than the full microbial community and varied based on the carbon source. Ultimately, the results indicate that biofilm formation within the bioreactor can be significantly reduced by optimizing process conditions and using pure cultures or a less diverse community, while maintaining high biomass productivity. The results of this study provide insight into methods for upcycling plastic waste and how process conditions can be used to control the formation of biofilm in bioreactors.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Single nucleotide variants drive evolutionary phage-host arms race in anaerobic carbon dioxide-converting microbiome

Microbial bioconversions are shaped by environmental perturbations and the adaptation of resident microbiomes. Prokaryotes coexist with bacteriophages, yet their coevolutionary trajectories remain underexplored. Here, we investigate the effects of a cultivation vessel leak on an anaerobic consortium performing carbon dioxide reduction. Using time-series shotgun metagenomic sequencing, we reconstruct microbial and viral genomes to track community shifts. We further apply single-nucleotide variant profiling and CRISPR array analysis to monitor viral microdiversity and host defense mechanisms. After bioaugmentation restores bioconversion efficiency, the consortium undergoes pronounced restructuring, with new dominant taxa emerging from the rare biosphere. We identify patterns consistent with phage predation selectively removing certain species, while others exhibit resilience to infection. This shift aligns with a widespread viral outbreak and a transient increased frequency of single nucleotide variants in bacterial CRISPR–Cas defense genes. Expansion of CRISPR spacers further supports that CRISPR-mediated processes influence microbial resilience. Concurrently, phages infecting resilient hosts exhibited adaptive evolution, marked by high genetic heterogeneity. Selective pressure varies across their genomes, targeting infectivity genes and protospacer-adjacent motifs. These findings highlight a dynamic evolutionary arms race driven by the selection of beneficial genetic variants, providing a mechanistic framework for multi-omics investigations, and informing biotechnological applications, including phage-based microbiome manipulation.

Ghiotto, G↗

DOE OSTI2025

Scrambling Signal Modularity in Bottom-up Assembled Synthetic Pseudomonas Consortia Reveals Robust Information Transfer

There is immense potential in crafting synthetic microbial communities for application in human health, agriculture, the environment, and even biomanufacturing where an appropriately constructed consortium can be assembled with tremendous biosynthetic or degradative capabilities. In many of these cases, bacterial signaling serves as a form of intercellular information transfer that guides the collective’s behavior. Such communication is complex, as many signals, signal disruptors, microbial species, physical barriers, and spatiotemporal constraints may be involved. Here, in this work, we demonstrate that a multisignal pathway for molecular information transfer within a consortium of several Pseudomonas spp. can be scrambled (genetically and organizationally) while the original message is still effectively conveyed. Assembled from the bottom up, we have employed two types of signaling molecules (i) a redox active secondary metabolite (rhizospheric signal, phloroglucinol), and (ii) a bacterial quorum sensing signal (3-oxo-C12 acylhomoserine lactone, AI-1). These signals can be intraconverted and acted upon by designated community members. We show how the order in which the signals are received, transduced, and subsequently transmitted can be rearranged with minimal impact on the intended outcome. In the consortial context, we found this messaging structure can be remarkably robust. Inspired by rhizospheric molecular signaling mechanisms, this work provides a conceptual framework for designing signaling and information transfer processes within assembled communities.

Biological and medical sciences↗

DOE OSTI2024

BioHydrogen (BioH2) Consortium to Advance Fermentative H2 Production

The overall objective of this project is to develop a carbon-neutral, microbial dark fermentation technology to convert waste lignocellulosic biomass into H2 with a production cost less than $2/kg-H2 via strain engineering, bioprocess design for scale-up, and integrating fermentation with microbial electrolysis cell (MEC).

bioH2↗

NASA NTRS2002

Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology

A mesophilic toluene-degrading consortium (TDC) and an ethylbenzene-degrading consortium (EDC) were established under sulfate-reducing conditions. These consortia were first characterized by denaturing gradient gel electrophoresis (DGGE) fingerprinting of PCR-amplified 16S rRNA gene fragments, followed by sequencing. The sequences of the major bands (T-1 and E-2) belonging to TDC and EDC, respectively, were affiliated with the family Desulfobacteriaceae. Another major band from EDC (E-1) was related to an uncultured non-sulfate-reducing soil bacterium. Oligonucleotide probes specific for the 16S rRNAs of target organisms corresponding to T-1, E-1, and E-2 were designed, and hybridization conditions were optimized for two analytical formats, membrane and DNA microarray hybridization. Both formats were used to characterize the TDC and EDC, and the results of both were consistent with DGGE analysis. In order to assess the utility of the microarray format for analysis of environmental samples, oil-contaminated sediments from the coast of Kuwait were analyzed. The DNA microarray successfully detected bacterial nucleic acids from these samples, but probes targeting specific groups of sulfate-reducing bacteria did not give positive signals. The results of this study demonstrate the limitations and the potential utility of DNA microarrays for microbial community analysis.

Non-NASA Center↗

DOE OSTI2025

Community Dynamics Drive Calcium Carbonate Production in an Enriched Consortium of Soil Microbes

Recently, there has been a focus on using soil microbes as a means to store carbon in the soil in the form of calcium carbonate, outcomes of which include soil stabilization and biocementation. The molecular processes involved in microbially induced calcium carbonate formation are known, but there is still a significant knowledge gap regarding how community interactions, emergent processes that are distinct from the roles of individual members, may drive the formation of carbonate. To answer these questions, we describe the development and application of a consortium of soil microbes consisting of one species each of the Rhodococcus , Microbacterium , and Curtobacterium genera and two species from the Bacillus genus. We term these five species cultivated together carbon storing consortium A (CSC-A). Growth assays show that only a subset of CSC-A members produces CaCO 3 with Rhodococcus producing the most CaCO 3 but the complete CSC-A produces significantly higher amounts of CaCO 3 compared to the sum total carbonate produced by all member species. The development of CSC-A shows that CaCO 3 production may be as much a community process as it is the contribution of individual species, requiring us to move beyond single species analysis to fully understand carbonate formation by microbial communities in nature. CSC-A will allow the scientific community to ask and answer key questions about the molecular interactions surrounding inorganic carbon formation in soil, an important knowledge gap that must be filled if we wish to stabilize soils and harness microbial processes for materials production.

calcium carbonate↗

DOE OSTI2025

Cyanobacteria and Chloroflexota cooperate to structure light-responsive biofilms

Microbial mats are stratified communities often dominated by unicellular and filamentous phototrophs within an exopolymer matrix. It is challenging to quantify the dynamic responses of community members in situ as they experience steep gradients and rapid fluctuations of light. To address this, we developed a binary consortium using two representative isolates from hot spring mats: the unicellular oxygenic phototrophic cyanobacterium Synechococcus OS-B′ (Syn OS-B′) and the filamentous anoxygenic phototroph Chloroflexus MS-CIW-1 (Chfl MS-1). We quantified the motility of individual cells and entire colonies and demonstrated that Chfl MS-1 formed bundles of filaments that moved in all directions with no directional bias to light. Syn OS-B′ was slightly less motile but exhibited positive phototaxis. This binary consortium displayed cooperative behavior by moving further than either species alone and formed ordered arrays where both species aligned with the light source. No cooperative motility was observed when a nonmotile pilB mutant of Syn OS-B′ was used instead of Syn OS-B′. The binary consortium also produced more adherent biofilm than individual species, consistent with the close interspecies association revealed by electron microscopy. We propose that cyanobacteria and Chloroflexota cooperate in forming natural microbial mats by colonizing new niches and building robust biofilms.

Functional and Systems Biology↗

NASA NTRSDate not supplied

Differential Gene Expression in A Cross-Feeding Two-Species Model Microbial Community Under Simulated Microgravity and Deep-Space Radiation

A long-term goal of space biology is to understand interspecies microbial interactions in space. Presently, little is known about the combined effect of microgravity and ionizing radiation on bacterial community response when species are interdependent through exchange of metabolites in fluid medium (cross-feeding). Microgravity is expected to slow interspecies mass transfer and growth in cross-feeding communities in the low-shear, diffusion-limited environment, while ionizing radiation may influence stress response to direct (DNA damage) and indirect damage (ROS). Using a well-understood, two-species (Escherichia coli and Salmonella enterica) microbial community engineered to be a model for studying cross-feeding, we simulated galactic cosmic rays (GCRsim) and microgravity to test the hypothesis: exposure to ionizing radiation causes cell damage or stress, altering transcriptomic community responses in metabolically interdependent cells, which is exacerbated by microgravity. We expect to see differential gene expression between cross-feeding and non-cross-feeding communities. We measured GCRsim effects on growth and gene expression in well-mixed versus simulated-microgravity conditions and in cross-feeding and non-cross-feeding medium. Microbial cultures were inoculated into liquid medium in rotating wall vessels (RWV) with different rotation rates: 5 RPM (simulated microgravity) and 50 RPM (well-mixed). The E. coli-S. enterica consortium, under simulated microgravity, were exposed to 500 mGy of Simplified 5-ion Galactic Cosmic Ray Simulation for 2 hours at Brookhaven National Lab. We harvested samples 40 minutes after irradiation for extraction and sequencing (NASA GeneLab). Here we present the differential gene expression analysis results, which reveal altered transcriptomic community responses, even where growth rate differences are not observed. Gene expression of these actively metabolizing microbial communities in GCRsim may illuminate molecular mechanisms of microbial interactions in space. Understanding how microbial community gene expression, metabolism, and other cellular processes are influenced by spaceflight stressors can inform the use of microbes in human life support for low Earth orbit missions and beyond.

microgravity↗

DOE OSTI2024

Identification and characterization of a skin microbiome on Caenorhabditis elegans suggests environmental microbes confer cuticle protection

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 sequencing 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.

16S RNA↗