(1) Background: Acidogenic Western-style diets disrupt gut bacteria promoting obesity-related diseases. Here, we investigated whether long-term feeding of alkalinized dietary casein as a protein source (ammonium hydroxide enhancement, AHE) modulates microbiome structure/functions under high-fat conditions, and normal diets, and whether these responses are sex-dimorphic. (2) Methods: C3H/HeJ mice (N = 256; equal sex distribution) received either control casein (CC), AHE casein (CCN), high-fat casein (HFC), or AHE high-fat casein (HFCN) diets from 6 to 18 months. Body mass and survival were tracked; fecal samples collected at 16 months were sequenced and underwent shotgun metagenomics. (3) Results: Diet and sex jointly shaped host metrics. AHE diets taxonomically showed an abundance of Verrucomicrobiota phyla predominating in most cohorts, notably Akkermansia muciniphila. Within Pseudomonadota, Christensenella was identified, along with other taxa associated with beneficial health outcomes, including Lactococcus lactis, Lactococcus cremoris, Pediococcus acidilactici, and families Lachnospiraceae/Oscillospiraceae. Additionally, sex- and diet-dependent advantageous enriched functions associated with AHE that enhanced electron transport, B-vitamin cofactor pathways, and mucosal/redox support were observed. (4) Conclusions: In the long term, pH-directed protein chemistry is a tractable lever for gut ecology during high-fat feeding, enriching and promoting the balance of beneficial taxa, providing a mechanistic bridge between dietary acid load and microbiome remodeling.

Pratylenchus penetrans (Ppen) is an economically important plant-parasitic nematode (PPN), which can be challenging to study in culture. There is great interest in potential control of Ppen through manipulation of its bacterial endosymbionts Wolbachia and 'Candidatus Cardinium'. With a broad host range of over 300 plant species, Ppen is a prime candidate for genomics and transcriptomics studies aimed at understanding parasitism and potential biological control approaches. However, these studies require the ability to culture large populations and establish isofemale lines in which host genotype diversity is minimized and maternally inherited endosymbiont status is uniform, particularly because endosymbiont prevalence is typically less than 100% in natural populations. Establishing aseptic isofemale lines has been traditionally challenging for Ppen due to the biology of this sexually reproducing migratory endoparasite. Here, we describe the development of an optimized reproducible protocol for establishing Ppen isofemale lines using surface-sterilized carrot discs and Pluronic F-127 gel, enabling pure, contamination-free cultures under laboratory conditions. Among various tested media, only carrot discs in Pluronic gel supported full development from juveniles to reproductive adults. This new method promises to facilitate numerous studies on both PPN-plant interactions and PPN-endosymbiont interactions and may prove particularly useful for genomic and transcriptomic and symbiont manipulation experiments.Copyright (c) 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Plant endophytic microbiomes play critical roles in plant health, productivity, and stress tolerance, however, their relationship with host genotype remains poorly understood. This study focused on endophytic microbiomes of six banana (Musa spp.) cultivars grown under shared environmental conditions to determine how genotype influences microbial diversity and structure. We used deep amplicon sequencing to investigate the endophytic microbiomes from above- and below-ground tissues of wild diploid cultivars Musa balbisiana, M. balbisiana “Thai Black”, and M. textilis, and domesticated triploid cultivars Dwarf Cavendish, Williams Hybrid, and hybrid FHIA-25, grown in sympatry. Across all samples, dominant genera included Pseudomonas, Acinetobacter, Enterobacter, Devosia, and Rhizobium, while 27.4% of ASVs were unclassified. Although many core taxa were shared, each cultivar and tissue harbored distinct low-abundance microbial taxa. Beta diversity analyses revealed that banana cultivar explained a small but significant proportion of community variation (Bray–Curtis R2 = 2.7%, p = 0.002; Weighted UniFrac R2 = 2.9%, p = 0.005), whereas tissue type and domestication contributed less to overall variation. PICRUSt2 predicted functional differences among endophytic communities across banana cultivars, with 49 pathways differing between wild and domesticated plants, including enrichment of lipid metabolism, biotin biosynthesis, and aromatic compound degradation in domesticated cultivars. However, because domestication status and ploidy differed among the selected cultivars, these effects could not be fully separated in the current study. Together, these results indicate that banana genotype influences endophytic microbiome composition and predicted function, although host genotype accounted for only a modest proportion of the observed variation, highlighting the importance of additional ecological and environmental factors in shaping plant-associated microbial communities.

Entomopathogenic nematodes (EPNs) of the genera Heterorhabditis and Steinernema are increasingly recognized as potent biological control agents due to their ability to infect and kill diverse insect pest taxa through a symbiotic partnership with insect-pathogenic bacteria. Over the last decades, substantial progress has been made in improving EPN field performance through advances in formulation and application methods, use of biodegradable polymers and nanocarriers, and elucidation of stress tolerance mechanisms. However, despite their proven efficacy, large-scale commercialization of EPNs remains limited by high production costs, formulation instability, and environmental constraints. While numerous reviews have separately addressed EPN biology, mass production, or field application independently, a critical and integrative synthesis linking molecular mechanisms, and formulation strategies remains lacking. This review synthesizes current understanding of EPN biology with emphasis on molecular mechanisms governing host localization, invasion, and immune suppression, as well as their biotic ecological interactions within soil environments. We also discuss advances in stress tolerance mechanisms, innovations in formulation, and outline future research priorities needed to develop ecologically resilient EPN-based biocontrol products. As agriculture shifts toward more regenerative and environmentally sustainable systems, a comprehensive understanding of EPN biology, full ecological potential of EPN-bacteria partnerships holds promise not only for effective pest suppression but also for advancing fundamental understanding of host-microbe interactions and ecosystem resilience.

Acinetobacter baumannii is a critical threat to immunocompromised patients, particularly those with burn injuries. Despite its clinical significance, little is known about how this bacterium adapts to the complex environment of burn patient blood, which differs significantly from that of healthy individuals. To address this, our methods included analyses of a blood-isolated strain of A. baumannii A118 grown ex vivo in whole blood from healthy volunteers (WBHV) and burn patients (WBBP). Transcriptomic analysis revealed host-specific expression patterns, including the downregulation of acinetobactin siderophore genes in WBBP—suggesting increased free iron levels—and the strong upregulation of nitrate/nitrite metabolism genes, indicating altered nitrogen availability in burn patients’ blood. Since serum makes up the majority of blood volume and contains key factors influencing bacterial physiology, we examined the transcriptomic response of A. baumannii to pooled human serum in an LB + 10% serum model at two different time points of growth, isolating the impact of soluble components free from immune cells and building on patterns seen in whole blood. Consistent with our ex vivo findings, we again observed dynamic regulation of the acinetobactin operon—this time in response to serum exposure: an initial upregulation of key iron uptake genes at early time points was followed by strong downregulation later, suggesting a transient iron starvation response that is modulated as intracellular iron accumulates, which can be supported by our ICP-MS results, revealing increased intracellular iron and other metal ions in serum-treated bacteria over time. To support additional serum-induced transcriptomic findings beyond acinetobactin, we used multiple experimental approaches: LC–MS/MS of outer membrane protein (OMP) extracts identified a serum-upregulated acinetobactin transporter; and phenotypic assays revealed that serum enhanced biofilm formation, increased twitching motility, elevated mortality in the Galleria mellonella infection model, and raised minimum inhibitory concentration (MIC) for multiple antibiotics. In conclusion, these findings expand our understanding of pathogen behavior in clinically relevant conditions and suggest that host-specific blood physiology—especially in burn patients—can shape the course of infection.

Acinetobacter baumannii is a major cause of bloodstream infections, yet its adaptation and survival mechanisms in human blood remain poorly understood. While previous studies focused on individual blood components, the impact of human whole blood on A. baumannii gene expression has not been explored. To address this, we used an ex vivo model where A. baumannii was grown in human whole blood from healthy volunteers (WBHV) and compared its gene expression to that in Luria-Bertani (LB) broth using RNA-seq. Our lab has previously employed a similar WBHV vs. LB comparison in Pseudomonas aeruginosa, validating this approach. Our results showed that ribosome biogenesis was the most upregulated pathway in WBHV, with 51 out of 55 ribosomal protein genes exhibiting increased expression. We then examined virulence related genes and found upregulation in iron and zinc acquisition systems (acinetobactin, znuABC) and biofilm/quorum sensing regulators, including the csu operon. Given these findings, we hypothesized that WBHV exposure enhances virulence. Using the Galleria mellonella infection model, we confirmed that A. baumannii caused higher larval mortality when grown in WBHV than when grown in LB. Upregulation of the csu operon, involved in pili assembly, led us to investigate twitching motility, where we observed a significant increase in WBHV. Additionally, since A. baumannii exhibits high drug resistance through the regulation of various outer membrane proteins (OMPs), we analyzed OMP expression in response to WBHV. SDS-PAGE and LC-MS/MS analysis identified three OMPs-Omp33-36, CarO, and OmpA-that were downregulated in WBHV. As these proteins mediate carbapenem uptake, we tested imipenem resistance using a minimum bactericidal concentration (MBC) assay and found that WBHV exposure increased A. baumannii's MBC to imipenem, suggesting reduced susceptibility. Our findings provide valuable insights into the adaptive mechanisms of A. baumannii in human whole blood, highlighting potential targets for combating its persistence and antibiotic resistance in bloodstream infections.

Wastewater treatment plants (WWTPs) are an understudied source of mercury methylating and demethylating microbes to downstream aquatic and terrestrial environments, where methylmercury production and subsequent bioaccumulation in the food web occur. To identify methylators and demethylators and evaluate their occurrence in WWTPs, metagenomic and metatranscriptomic analyses of raw sewage, activated sludge, and effluent samples from WWTPs across the globe were conducted. Results indicated that hgcA- and merB-carriers were widespread in WWTPs, with higher abundance in raw sewage and sludge compared to treated effluent. Bdellovibrionota were identified as merB-carriers, linking them to demethylation for the first time. Novel conserved motifs of hgcB and fused hgcAB were also identified. 30% of hgcA genes were colocalized with arsenic-resistance operons on the same contig, while all merB-carriers contained arsenic resistance genes (ars), though merB and arsR were not colocated. Antibiotic resistance genes were also present in the genomes of multiple hgcA- amd merB-carriers, including one sample where hgcA and the antiseptic/antibiotic resistant gene (qacG) were colocated on the same contig, suggesting possible coselection in environments containing antibiotics. Mobile genetic element-mediated horizontal gene transfer was identified as a mechanism facilitating the genetic transfer of hgcA. Overall, these findings highlight WWTPs as reservoirs of genes involved in mercury methylation and demethylation, with potential implications for mercury cycling in downstream environments.

Objectives: To characterize the genetic basis of azithromycin resistance in Escherichia coli and Salmonella collected within the EU harmonized antimicrobial resistance (AMR) surveillance programme in 2014-18 and the Danish AMR surveillance programme in 2016-19. Methods: WGS data of 1007 E. coli [165 azithromycin resistant (MIC > 16 mg/L)] and 269 Salmonella [29 azithromycin resistant (MIC > 16 mg/L)] were screened for acquired macrolide resistance genes and mutations in rplDV, 23S rRNA and acrB genes using ResFinder v4.0, AMRFinder Plus and custom scripts. Genotype-phenotype concordance was determined for all isolates. Transferability of mef(C)-mph(G)-carrying plasmids was assessed by conjugation experiments. Results: mph(A), mph(B), mef(B), erm(B) and mef(C)-mph(G) were detected in E. coli and Salmonella, whereas erm(C), erm(42), ere(A) and mph(E)-msr(E) were detected in E. coli only. The presence of macrolide resistance genes, alone or in combination, was concordant with the azithromycin-resistant phenotype in 69% of isolates. Distinct mph(A) operon structures were observed in azithromycin-susceptible (n = 50) and -resistant (n = 136) isolates. mef(C)-mph(G) were detected in porcine and bovine E. coli and in porcine Salmonella enterica serovar Derby and Salmonella enterica 1,4, [5],12:i:-, flanked downstream by ISCR2 or TnAs1 and associated with IncI gamma and IncFII plasmids. Conclusions: Diverse azithromycin resistance genes were detected in E. coli and Salmonella from food-producing animals and meat in Europe. Azithromycin resistance genes mef(C)-mph(G) and erm(42) appear to be emerging primarily in porcine E. coli isolates. The identification of distinct mph(A) operon structures in susceptible and resistant isolates increases the predictive power of WGS-based methods for in silico detection of azithromycin resistance in Enterobacterales.

Since the discovery of Wolbachia in plant-parasitic nematodes (PPNs), there has been increased interest in this earliest branching clade that may hold important clues to early transitions in Wolbachia function in the Ecdysozoa. However, due to the specialized skills and equipment of nematology and the difficulty in culturing most PPNs, these PPN-type Wolbachia remain undersampled and poorly understood. To date, there are few established laboratory methods for working with PPN-type Wolbachia strains, and most research has relied on chance discovery and comparative genomics. Here, we address this challenge by providing detailed methods to assist researchers with more efficiently collecting PPNs and screen these communities, populations, or single nematodes with a newly developed PPN-type Wolbachia-specific PCR assay. We provide an overview of the typical yields and outcomes of these methods, to facilitate further targeted cultivation or experimental methods, and finally we provide a short introduction to some of the specific challenges and solutions in following through with comparative or population genomics on PPN-type Wolbachia strains.

Studies have suggested that alkalinized foods may reduce the effects of the acidogenic Western diet in promoting obesity, metabolic syndrome, type 2 diabetes, cancer, and coronary heart disease. Indeed, a recent study in mice fed a high-fat diet containing dietary beef supplemented with ammonium hydroxide showed improvement in a suite of metabolic outcomes. However, the effects of dietary protein ammonium supplementation on the microbiome remain unknown. In this study, the effects of ammonium supplementation on beef protein towards microbiome taxa and function in a high-fat diet were analyzed. Fecal microbiomes were characterized using a shotgun metagenomic approach for 16-month-old male and female mice after long-term diet treatments. The results for ammoniated diets showed that several bacteria known to be associated with health benefits increased significantly, including Romboutsia, Oscillospiraceae, and Lactococcus cremoris. The beneficial mucin-degrader Akkermansia was especially abundant, with a high prevalence (~86%) in females. Concurrently, the phyla Actinomycetota (Actinobacteria) and Bacteroidota (Bacteroidetes) were significantly reduced. While sex was a confounding factor affecting microbiome responses to ammonium supplementation in dietary protein, it is worth noting that several putatively beneficial microbiome functions increased with ammonium supplementation, such as glycine betaine transport, xenobiotic detoxification, enhanced defense, and others. Conversely, many disease-associated microbiome functions reduced. Importantly, modifying protein pH alone via ammonium supplementation induced beneficial microbiota changes. Taken together, these results suggest that ammonium-supplemented proteins may mediate some negative microbiome-associated effects of high-fat/Western diets.

Bioinformatics sequence data mining can reveal hidden microbial symbionts that might normally be filtered and removed as contaminants. Data mining can be helpful to detect Wolbachia, a widespread bacterial endosymbiont in insects and filarial nematodes whose distribution in plant-parasitic nematodes (PPNs) remains underexplored. To date, Wolbachia has only been reported a few PPNs, yet nematode-infecting Wolbachia may have been widespread in the evolutionary history of the phylum based on evidence of horizontal gene transfers, suggesting there may be undiscovered Wolbachia infections in PPNs. The goal of this study was to more broadly sample PPN Wolbachia strains in tylenchid nematodes to enable further comparative genomic analyses that may reveal Wolbachia’s role and identify targets for biocontrol. Published whole-genome shotgun assemblies and their raw sequence data from 33 Meloidogyne spp. assemblies, seven Globodera spp. assemblies, and seven Heterodera spp. assemblies were analyzed to look for Wolbachia. No Wolbachia was found in Meloidogyne spp. and Globodera spp., but among seven genome assemblies for Heterodera spp., an H. schachtii assembly from the Netherlands was found to have a large Wolbachia-like sequence that, when re-assembled from reads, formed a complete, circular genome. Detailed analyses comparing read coverage, GC content, pseudogenes, and phylogenomic patterns clearly demonstrated that the H. schachtii Wolbachia represented a novel strain (hereafter, denoted wHet). Phylogenomic tree construction with PhyloBayes showed wHet was most closely related to another PPN Wolbachia, wTex, while 16S rRNA gene analysis showed it clustered with other Heterodera Wolbachia assembled from sequence databases. Pseudogenes in wHet suggested relatedness to the PPN clade, as did the lack of significantly enriched GO terms compared to PPN Wolbachia strains. It remains unclear whether the lack of Wolbachia in other published H. schachtii isolates represents the true absence of the endosymbiont from some hosts.

Mercury (Hg) methylation is a microbially mediated process that produces methylmercury (MeHg), a bioaccumulative neurotoxin. A highly conserved gene pair, hgcAB, is required for Hg methylation, which provides a basis for identifying Hg methylators and evaluating their genomic composition. In this study, we conducted a large-scale omics analysis in which 281 metagenomic freshwater and marine sediment samples from 46 geographic locations across the globe were queried. Specific objectives were to examine the prevalence of Hg methylators, to identify horizontal gene transfer (HGT) events involving hgcAB within Hg methylator communities, and to identify associations between hgcAB and microbial biochemical functions/genes. Hg methylators from the phyla Desulfobacterota and Bacteroidota were dominant in both freshwater and marine sediments while Firmicutes and methanogens belonging to Euryarchaeota were identified only in freshwater sediments. Novel Hg methylators were found in the Phycisphaerae and Planctomycetia classes within the phylum Planctomycetota, including potential hgcA-carrying anammox metagenome-assembled genomes (MAGs) from Candidatus Brocadiia. HGT of hgcA and hgcB were identified in both freshwater and marine methylator communities. Spearman’s correlation analysis of methylator genomes suggested that in addition to sulfide, thiosulfate, sulfite, and ammonia may be important parameters for Hg methylation processes in sediments. Overall, our results indicated that the biochemical drivers of Hg methylation vary between marine and freshwater sites, lending insight into the influence of environmental perturbances, such as a changing climate, on Hg methylation processes.

Microbiomes are critical to plants, promoting growth, elevating stress tolerance, and expanding the plant’s metabolic repertoire with novel defense pathways. However, generally microbiomes within plant tissues, which intimately interact with their hosts, remain poorly characterized. These endospheres have become a focus in banana (Musa spp.)—an important plant for study of microbiome-based disease protection. Banana is important to global food security, while also being critically threatened by pandemic diseases. Domestication and clonal propagation are thought to have depleted protective microbiomes, whereas wild relatives may hold promise for new microbiome-based biological controls. The goal was to compare metapangenomes enriched from 7 Musa genotypes, including wild and cultivated varieties grown in sympatry, to assess the host associations with root and leaf endosphere functional profiles. Density gradients successfully generated culture-free microbial enrichment, dominated by bacteria, with all together 24,325 species or strains distinguished, and 1.7 million metagenomic scaffolds harboring 559,108 predicted gene clusters. About 20

Introduction:Viruses generally cause disease, but some viruses may be beneficial as resident regulators of their hosts or host microbiomes. Plant-associated viruses can help plants survive by increasing stress tolerance or regulating endophytic communities. The goal of this study was to characterize endophytic virus communities in banana and plantain (Musa spp.) genotypes, including cultivated and wild species, to assess virome repertoires and detect novel viruses.Methods:DNA viral communities were characterized by shotgun sequencing of an enriched endosphere extract from leaves and roots or corm of 7 distinct Musa genotypes (M. balbisiana, Thai Black, M. textilis, M. sikkimensis, Dwarf Cavendish, Williams Hybrid, and FHIA-25 Hybrid).Results:Results showed abundant virus-like contigs up to 108,191 bp long with higher relative abundance in leaves than roots. Analyses predicted 733 phage species in 51 families, with little overlap in phage communities among plants. Phage diversity was higher in roots and in diploid wild hosts. Ackermanniviridae and Rhizobium phage were generally the most abundant taxa. A Rhizobium RR1-like phage related to a phage of an endophytic tumor-causing rhizobium was found, bearing a holin gene and a partial Shiga-like toxin gene, raising interest in its potential to regulate endophytic Rhizobiaceae. Klebsiella phages were of interest for possible protection against Fusarium wilt, and other phages were predicted with potential to regulate Erwinia, Pectobacterium, and Ralstonia-associated diseases. Although abundant phage-containing contigs were functionally annotated, revealing 1,038 predicted viral protein domains, gene repertoires showed high divergence from database sequences, suggesting novel phages in these banana cultivars. Plant DNA viruses included 56 species of Badnavirus and 26 additional non-Musa plant viruses with distributions that suggested a mixture of resident and transient plant DNA viruses in these samples.Discussion:Together, the disparate viral communities in these plants from a shared environment suggest hosts drive the composition of these virus communities. This study forms a first step in understanding the endophytic virome in this globally important food crop, which is currently threatened by fungal, bacterial, and viral diseases.

Wolbachia is a widespread endosymbiont of insects and filarial nematodes that profoundly influences host biology. Wolbachia has also been reported in rhizosphere hosts, where its diversity and function remain poorly characterized. The discovery that plant-parasitic nematodes (PPNs) host Wolbachia strains with unknown roles is of interest evolutionarily, ecologically, and for agriculture as a potential target for developing new biological controls. The goal of this study was to screen communities for PPN endosymbionts and analyze genes and genomic patterns that might indicate their role. Genome assemblies revealed 1 out of 16 sampled sites had nematode communities hosting a Wolbachia strain, designated wTex, that has highly diverged as one of the early supergroup L strains. Genome features, gene repertoires, and absence of known genes for cytoplasmic incompatibility, riboflavin, biotin, and other biosynthetic functions placed wTex between mutualist C + D strains and reproductive parasite A + B strains. Functional terms enriched in group L included protoporphyrinogen IX, thiamine, lysine, fatty acid, and cellular amino acid biosynthesis, while dN/dS analysis suggested the strongest purifying selection on arginine and lysine metabolism, and vitamin B6, heme, and zinc ion binding, suggesting these as candidate roles in PPN Wolbachia. Higher dN/dS pathways between group L, wPni from aphids, wFol from springtails, and wCfeT from cat fleas suggested distinct functional changes characterizing these early Wolbachia host transitions. PPN Wolbachia had several putative horizontally transferred genes, including a lysine biosynthesis operon like that of the mitochondrial symbiont Midichloria, a spirochete-like thiamine synthesis operon shared only with wCfeT, an ATP/ADP carrier important in Rickettsia, and a eukaryote-like gene that may mediate plant systemic acquired resistance through the lysine-to-pipecolic acid system. The Discovery of group L-like variants from global rhizosphere databases suggests diverse PPN Wolbachia strains remain to be discovered. These findings support the hypothesis of plant-specialization as key to shaping early Wolbachia evolution and present new functional hypotheses, demonstrating promise for future genomics-based rhizosphere screens.

Microbes interact in natural communities in a spatially structured manner, particularly in biofilms and polymicrobial infections. While next generation sequencing approaches provide powerful insights into diversity, metabolic capacity, and mutational profiles of these communities, they generally fail to recover in situ spatial proximity between distinct genotypes in the interactome. Hi‐C is a promising method that has assisted in analysing complex microbiomes, by creating chromatin cross‐links in cells, that aid in identifying adjacent DNA, to improve de novo assembly. This study explored a modified Hi‐C approach involving an initial lysis phase prior to DNA cross‐linking, to test whether adjacent cell chromatin can be cross‐linked, anticipating that this could provide a new avenue for study of spatial‐mutational dynamics in structured microbial communities. An artificial polymicrobial mixture of Pseudomonas aeruginosa, Staphylococcus aureus, and Escherichia coli was lysed for 1–18 h, then prepared for Hi‐C. A murine biofilm infection model was treated with sonication, mechanical lysis, or chemical lysis before Hi‐C. Bioinformatic analyses of resulting Hi‐C interspecies chromatin links showed that while microbial species differed from one another, generally lysis significantly increased links between species and increased the distance of Hi‐C links within species, while also increasing novel plasmid‐chromosome links. The success of this modified lysis‐Hi‐C protocol in creating extracellular DNA links is a promising first step toward a new lysis‐Hi‐C based method to recover genotypic microgeography in polymicrobial communities, with potential future applications in diseases with localized resistance, such as cystic fibrosis lung infections and chronic diabetic ulcers.

Interactions between insect symbionts and plant pathogens are dynamic and complex, sometimes involving direct antagonism or synergy and sometimes involving ecological and evolutionary leaps, as insect symbionts transmit through plant tissues or plant pathogens transition to become insect symbionts. Hemipterans such as aphids, whiteflies, psyllids, leafhoppers, and planthoppers are well-studied plant pests that host diverse symbionts and vector plant pathogens. The related hemipteran treehoppers (family Membracidae) are less well-studied but offer a potentially new and diverse array of symbionts and plant pathogenic interactions through their distinct woody plant hosts and ecological interactions with diverse tending hymenopteran taxa. To explore membracid symbiont-pathogen diversity and co-occurrence, this study performed shotgun metagenomic sequencing on 20 samples (16 species) of treehopper, and characterized putative symbionts and pathogens using a combination of rapid blast database searches and phylogenetic analysis of assembled scaffolds and correlation analysis. Among the 8.7 billion base pairs of scaffolds assembled were matches to 9 potential plant pathogens, 12 potential primary and secondary insect endosymbionts, numerous bacteriophages, and other viruses, entomopathogens, and fungi. Notable discoveries include a divergent Brenneria plant pathogen-like organism, several bee-like Bombella and Asaia strains, novel strains of Arsenophonus-like and Sodalis-like symbionts, Ralstonia sp. and Ralstonia-type phages, Serratia sp., and APSE-type phages and bracoviruses. There were several short Phytoplasma and Spiroplasma matches, but there was no indication of plant viruses in these data. Clusters of positively correlated microbes such as yeast-like symbionts and Ralstonia, viruses and Serratia, and APSE phage with parasitoid-type bracoviruses suggest directions for future analyses. Together, results indicate membracids offer a rich palette for future study of symbiont-plant pathogen interactions.

This report presents the draft genome sequences of two Campylobacter novaezeelandiae and four unclassified Campylobacter isolates from Canadian agricultural surface water. Phylogenomic analysis revealed that the six isolates formed unique clades, closely related to the disease-causing species C. jejuni , C. coli , and C. hepaticus .

Xiphinematobacter spp. are distinctly evolved intracellular symbionts in the phylum Verrucomicrobia , which includes the important human gut-associated microbe Akkermansia muciniphila and many highly abundant free-living soil microbes. Like Akkermansia sp., Xiphinematobacter sp. is obligately associated with the gut of its hosts, which in this case consists of a group of plant-parasitic nematodes that are among the top 10 most destructive species to global agriculture, by vectoring plant viruses.

Plant microbiomes are not only diverse, but also appear to host a vast pool of secondary metabolites holding great promise for bioactive natural products and drug discovery. Yet, most microbes within plants appear to be uncultivable, and for those that can be cultivated, their metabolic potential lies largely hidden through regulatory silencing of biosynthetic genes. The recent explosion of powerful interdisciplinary approaches, including multi-omics methods to address multi-trophic interactions and artificial intelligence-based computational approaches to infer distribution of function, together present a paradigm shift in high-throughput approaches to natural product discovery from plant-associated microbes. Arguably, the key to characterizing and harnessing this biochemical capacity depends on a novel, systematic approach to characterize the triggers that turn on secondary metabolite biosynthesis through molecular or genetic signals from the host plant, members of the rich 'in planta' community, or from the environment. This review explores breakthrough approaches for natural product discovery from plant microbiomes, emphasizing the promise of deep learning as a tool for endophyte bioprospecting, endophyte biochemical novelty prediction, and endophyte regulatory control. It concludes with a proposed pipeline to harness global databases (genomic, metabolomic, regulomic, and chemical) to uncover and unsilence desirable natural products.