BackgroundSome genetic data has dual-use potential. Sharing pathogen data has shown tremendous value. For example therapeutic development and lineage tracking during the COVID pandemic. This data sharing is complicated by the fact that these data have the potential to be used for harm. The genome sequence of a pathogen can be used to enable malicious genetic engineering approaches or to recreate the pathogen from synthetic DNA. Standard data security methods can be applied to genetic data, but when data is shared between institutions, ensuring appropriate security can be difficult. Sensitive data that is shared internationally among a wide array of institutions can be especially difficult to control. Methods for securely storing and sharing genetic data with potential for dual-use are needed to mitigate this potential harm.ResultsHere we propose new methods that allow genetic data to be shared in a data format that prevents a nefarious actor from accessing sensitive aspects of the data. Our methods obfuscate raw sequence data by pooling reads from different samples. This approach can ensure that data is secure while stored and during electronic transfer. We demonstrate that by pooling raw sequence data from multiple samples of the same organism, the ability to fully reconstruct any individual sample is prevented. In the pooled data, most genomic information remains, but reads or mutations cannot be directly attributed to any individual sample. To further restrict access to information, regions of a genome can be removed from the reads.ConclusionOur methods obscure genomic information within raw sequence reads. This method can allow genetic data to be stored and shared while preventing a nefarious actor from being able to perfectly reconstruct an organism. Broad-scale sequence information remains, while fine scale details about specific samples are difficult or impossible to reconstruct. Our software is available at https://github.com/Geneinfosec-Inc/ReadMixer.

Effective clinical and public health decision-making during a pandemic depends on reliable and interoperable clinical diagnostic test results. To ensure trustworthy outcomes, we need widely available calibration standards harmonized to a shared scale. We present a “playbook” for an interlaboratory harmonization study that calibrates any available standards against a limited-availability standard issued by a global authority like the World Health Organization (WHO).

Aerosol sampling with next-generation sequencing was used to characterize microbial communities in a cafeteria and medical facility waiting room in Los Alamos, New Mexico, USA. We detected sequences from human, bacteria, archaea, fungi, other eukaryotes, and viruses, providing insights into the diversity of the aerosol microbiome.

The movement of bacteria on the hyphae of fungi and other mycelial-forming organisms is an important process that determines their ability to actively disperse in water-unsaturated habitats. However, direct observation and characterization of bacterial cell movement on mycelial networks have been difficult to achieve. In this study, we developed a new method that uses high-speed video recording to track the dispersal of individual fluorescently tagged cells of two closely related strains of Pseudomonas putida (UWC1 and KT2440) over the mycelial network of the oomycete Pythium ultimum. We found high intra-population heterogeneity and between-population differences in dispersal speeds for the two bacterial strains. The fitting of the speed distribution functions led to the separation of speeds into two ranges (fast/slow) at an intersection of the fitted curves. In the lower speed range, the UWC1 strain dispersed faster, while the KT2440 strain moved faster in the higher speed range. This finding helps explain conflicting competition outcomes revealed in previous studies and suggests that population mean speed alone does not capture key aspects of bacterial dispersal in mycelial networks. Our new method opens the possibility of studying bacterial dispersal, competition, and other social interactions in spatially heterogeneous environments, such as soils.

The phytopathogenic fungus Sclerotinia sclerotiorum has a wide host range and causes significant economic losses in crops worldwide. This pathogen uses oxalic acid as a virulence factor; for this reason, the degradation of this organic acid by oxalotrophic bacteria has been proposed as a biological control approach. However, previous studies on the potential role of oxalotrophy in biocontrol did not investigate the differential effect of oxalic acid consumption and the subsequent pH alkalinisation on fungal growth. In this study, confrontation experiments on different media using a wild-type (WT) strain of S. sclerotiorum and an oxalate-deficient mutant (strain Δoah) with the soil oxalotrophic bacteria Cupriavidus necator and Cupriavidus oxalaticus showed the combined effect of media composition on oxalic acid production, pH, and fungal growth control. Oxalotrophic bacteria were able to control S. sclerotiorum only in the medium in which oxalic acid was produced. However, the deficient Δoah mutant was also controlled, indicating that the consumption of oxalic acid is not the sole mechanism of biocontrol. WT S. sclerotiorum acidified the medium when inoculated alone, while for both fungi, the pH of the medium changed from neutral to alkaline in the presence of bacteria. Therefore, medium alkalinisation independent of oxalotrophy contributes to fungal growth control.

Aspergillus fungi are opportunistic pathogens that affect millions of people worldwide. Aspergilli produce organic acids to optimize the environmental pH and match the needs of their enzymatic machinery. In this study, we tested the hypothesis that this also occurs during infection. By producing oxalic acid (OA), Aspergillus would manipulate pH during lung infection and thus, interfering with this process could control the pathogen. To test this hypothesis, we assessed in silico the potential for OA production in a wide range of Aspergilli. A genetic marker for AO production was detected in most of the species including prevalent human pathogens. We tested OA production in vitro in four strains of A. niger and A. fumigatus, but only one of the A. niger strains produced OA consistently. For this fungal strain, oxalotrophic bacteria were able to control fungal growth via OA consumption. To translate this observation into a pre-clinical system, increasingly complex experiments were performed. In 3D-cell cultures, A. niger also secreted OA and modified pH and free Ca2+. Co-inoculation of the oxalotrophic bacterium inhibited the development of the fungus. However, biocontrol could not be replicated in Galleria mellonella, which is often used as an infection model. In contrast, the bacterium improved disease score and the absence of oxalate crystals in the lungs in the mouse model. This biocontrol interaction between oxalotrophic bacteria and A. niger represents a paradigm shift in the fight against opportunistic fungal pathogens, where the goal is to render the host environment less permissive to pathogen development. ### Competing Interest Statement The authors have declared no competing interest.

Morchella species have considerable significance in terrestrial ecosystems, exhibiting a range of ecological lifestyles along the saprotrophism-to-symbiosis continuum. However, the mitochondrial genomes of these ascomycetous fungi have not been thoroughly studied, thereby impeding a comprehensive understanding of their genetic makeup and ecological role. In this study, we analysed the mitogenomes of 30 Morchellaceae species, including yellow, black, blushing and false morels. These mitogenomes are either circular or linear DNA molecules with lengths ranging from 217 to 565 kbp and GC content ranging from 38% to 48%. Fifteen core protein-coding genes, 28–37 tRNA genes and 3–8 rRNA genes were identified in these Morchellaceae mitogenomes. The gene order demonstrated a high level of conservation, with the cox1 gene consistently positioned adjacent to the rnS gene and cob gene flanked by apt genes. Some exceptions were observed, such as the rearrangement of atp6 and rps3 in Morchella importuna and the reversed order of atp6 and atp8 in certain morel mitogenomes. However, the arrangement of the tRNA genes remains conserved. We additionally investigated the distribution and phylogeny of homing endonuclease genes (HEGs) of the LAGLIDADG (LAGs) and GIY-YIG (GIYs) families. A total of 925 LAG and GIY sequences were detected, with individual species containing 19–48HEGs. These HEGs were primarily located in the cox1, cob, cox2 and nad5 introns and their presence and distribution displayed significant diversity amongst morel species. These elements significantly contribute to shaping their mitogenome diversity. Overall, this study provides novel insights into the phylogeny and evolution of the Morchellaceae.

Morels are iconic macrofungi known for their culinary value and spring emergence. Molecular phylogenetic studies have hitherto failed to elucidate the evolution of the ecological lifestyles of true and false morels, impeding their capacity to resolve longstanding debates regarding the extent of their saprotrophy and the potential for biotrophic associations with plants. In this study, we examined the evolutionary history and molecular innovations of Morchellaceae by generating high-quality genomes from species encompassing all the major clades within this family. We used conserved single-copy orthologs to infer the evolutionary history of true and false morels and related truffles. The genome size, transposable element content, and polysaccharide-degrading enzyme gene content are consistent with an ectomycorrhizal lifestyle for the Morchellaceae truffles Leucangium carthusianum and Kalapuya brunnea, whereas the other clades, including all true morels (Morchella spp.), exhibited genomic signatures of saprotrophic habits characterized by a highly conserved set of genes encoding plant biomass-related degrading enzymes. Morchellaceae species were found to be predominantly heterothallic, with either the MAT1-1 or MAT1-2 loci; however, the occurrence of colocalized mating-type idiomorphs, indicative of homothallism, was observed in M. rufobrunnea, M. peruviana, L. carthusianum, and the outgroup taxon Gyromitra esculenta. This study revealed a wealth of largely undiscovered genomic traits, including saprotrophic potential within Morchellaceae and a lack of biotrophic markers, and contributes to our understanding of the intricate evolutionary trajectories of the modes of nutrition in soil fungi.

Morchella helvetica, sp. nov. (Morchella sect. Distantes) is a new species of true morels discovered in Switzerland. It is formally described in the present study using an integrative approach based on micro- and macromorphological characteristics, multilocus phylogenetics, and a brief description of its habitat. Molecular analyses clearly indicated that Morchella helvetica is a sister species to M. eximioides, M. angusticeps, and M. confusa. It can be distinguished by the two phylogenetic markers RNA polymerase II subunit 2 (RPB2) and translation elongation factor-1 alpha (TEF1-alpha). In addition, M. helvetica exhibits particular morphological features, notably the presence of pale hairs on the pileus, a mealy stipe, and darkening ridges when aging.

Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sample. These bioinformatic workflows produced consensus genomes with differences in single nucleotide polymorphisms, inclusion and exclusion of insertions, and/or deletions, despite using the same raw sequence as input datasets. Here, we compared and characterized such discrepancies and propose a specific suite of parameters and protocols that should be adopted across the field. Consistent results from bioinformatic workflows are fundamental to SARS-CoV-2 and future pathogen surveillance efforts, including pandemic preparation, to allow for a data-driven and timely public health response.

Bacteriophages play a crucial role in shaping bacterial communities, yet the mechanisms by which nonmotile bacteriophages interact with their hosts remain poorly understood. This knowledge gap is especially pronounced in structured environments like soil, where spatial constraints and air-filled zones hinder aqueous diffusion. In soil, hyphae of filamentous microorganisms form a network of 'fungal highways' (FHs) that facilitate the dispersal of other microorganisms. We propose that FHs also promote bacteriophage dissemination. Viral particles can diffuse in liquid films surrounding hyphae or be transported by infectable (host) or uninfectable (nonhost) bacterial carriers coexisting on FH networks. To test this, two bacteriophages that infect Pseudomonas putida DSM291 (host) but not KT2440 (nonhost) were used. In the absence of carriers, bacteriophages showed limited diffusion on 3D-printed abiotic networks, but diffusion was significantly improved in Pythium ultimum-formed FHs when the number of connecting hyphae exceeded 20. Transport by both host and nonhost carriers enhanced bacteriophage dissemination. Host carriers were five times more effective in transporting bacteriophages, particularly in FHs with over 30 connecting hyphae. This study enhances our understanding of bacteriophage dissemination in nonsaturated environments like soils, highlighting the importance of biotic networks and bacterial hosts in facilitating this process.

Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these statistical associations across kingdoms are more difficult to infer than intra-kingdom associations due to the nature of the data involved using standard network inference techniques. We quantify the challenges of cross-kingdom network inference from both a theoretical and practical viewpoint using synthetic and real-world microbiome data. We detail the theoretical issue presented by combining compositional data sets drawn from the same environment, e.g. 16S and ITS sequencing of a single set of samples, and survey common network inference techniques for their ability to handle this error. We then test these techniques for the accuracy and usefulness of their intra- and inter-kingdom associations by inferring networks from a set of simulated samples for which a ground-truth set of associations is known. We show that while two methods mitigate the error of cross-kingdom inference, there is little difference between techniques for key practical applications including identification of strong correlations and identification of possible keystone taxa (i.e. hub nodes in the network). Furthermore, we identify a signature of the error caused transkingdom network inference and demonstrate that it appears in networks constructed using real-world environmental microbiome data.

according to a composite reference method. FluIDx and the rapid tests detected 85.9% and 62.0% of the RSV positive samples, respectively. Similar sensitivities were recorded for the influenza B samples; whereas the influenza A samples were poorly detected, likely due to the utilization of an influenza A signature that did not accurately match currently circulating influenza A strains. Data for all pathogens were compiled and indicate that FluIDx is more sensitive than the rapid tests, detecting 74.2% (95% C.I. of 64.7-81.9%) of the positive samples in comparison to 53.6% (95% C.I. of 43.7-63.2%) for the rapid tests. The higher sensitivity of FluIDx was partially offset by a lower specificity, 77.3% versus 100.0%. Overall, these data suggest automated flow-through PCR-based instruments that perform multiplexed assays can successfully screen clinical samples for infectious diseases.

Diverse and complex microbiomes are found in virtually every environment on Earth. Bacteria and fungi often co-dominate environmental microbiomes, and there is growing recognition that bacterial-fungal interactions (BFI) have significant impacts on the functioning of their associated microbiomes, environments, and hosts. Investigating BFI in vitro remains a challenge, particularly when attempting to examine interactions at multiple scales of system complexity. Fabricated devices can provide control over both biotic composition and abiotic factors within an experiment to enable the characterization of diverse BFI phenotypes such as modulation of growth rate, production of biomolecules, and alterations to physical movements. Engineered devices ranging from microfluidic chips to simulated rhizosphere systems have been and will continue to be invaluable to BFI research, and it is anticipated that such devices will continue to be developed for diverse applications in the field. This will allow researchers to address specific questions regarding the nature of BFI and how they impact larger microbiome and environmental processes such as biogeochemical cycles, plant productivity, and overall ecosystem resilience. Devices that are currently used for experimental investigations of bacteria, fungi, and BFI are discussed herein along with some of the associated challenges and several recommendations for future device design and applications.

Download This Paper Open PDF in Browser Add Paper to My Library Share: Permalink Using these links will ensure access to this page indefinitely Copy URL Tripartite Interactions Between Morchella spp., Pseudomonas koreensis And Acanthamoeba castellanii Reveal a Beneficial Fungal-Amoebal Association iScience 19 Pages Posted: 27 Feb 2024 Publication Status: Under Review See all articles by Melissa CraveroMelissa CraveroUniversity of NeuchatelAaron J. RobinsonGovernment of the United States of America - Los Alamos National LaboratoryPatrick S. G. ChainGovernment of the United States of America - Los Alamos National LaboratorySaskia BindschedlerUniversity of NeuchatelPilar JunierUniversity of Neuchatel More... Abstract Interactions between Morchella and other soil organisms have rarely been investigated. In this study, we investigated interactions between Morchella and Pseudomonas koreensis under predatory pressure of Acanthamoeba castellanii. Our main hypothesis was that P. koreensis would evade predation by hiding in Morchella hyphae. We tested first whether A. castellanii could feed on P. koreensis and/or Morchella and evaluated the reciprocal impacts by conducting qualitative (observations) and quantitative (microbial growth) analyses. Amoebae could feed on bacteria but not on Morchella, and used the mycelium as fungal highways. Bacteria inhibited Morchella’s growth. It was therefore expected that predation of A. castellanii on P. koreensis would be beneficial to Morchella. This was confirmed by the results from the tripartite competition assay. In the presence of the amoeba, P. koreensis did not hide in fungal hyphae but on the contrary formed biofilms around Morchella hyphae, that were heavily grazed by A. castellanii. Suggested Citation: Suggested Citation Cravero, Melissa and Robinson, Aaron J. and Chain, Patrick S. G. and Bindschedler, Saskia and Junier, Pilar, Tripartite Interactions Between Morchella spp., Pseudomonas koreensis And Acanthamoeba castellanii Reveal a Beneficial Fungal-Amoebal Association. Available at SSRN: https://ssrn.com/abstract=4739399 This version of the paper has not been formally peer reviewed. Melissa Cravero University of Neuchatel ( email ) Aaron J. Robinson Government of the United States of America - Los Alamos National Laboratory ( email ) Los Alamos, NM 87545United States Patrick S. G. Chain Government of the United States of America - Los Alamos National Laboratory ( email ) Saskia Bindschedler University of Neuchatel ( email ) Pilar Junier (Contact Author) University of Neuchatel ( email ) Download This Paper Open PDF in Browser Please enable JavaScript to view the comments powered by Disqus. Click here to go to Cell.com Go to Cell.com Paper statistics Downloads 1 Abstract Views 11 30 References PlumX Metrics Cell Press Journals on Sneak Peek All Journals (9067) Cancer Cell (104) Cell (567) Cell Chemical Biology (141) Cell Genomics (18) Cell Host & Microbe (185) Cell Metabolism (143) Cell Press Community (115) Cell Reports (2086) Cell Reports Medicine (223) Cell Reports Methods (163) Cell Reports Physical Science (209) Cell Reports Sustainability (0) Cell Stem Cell (155) Cell Systems (84) Chem (154) Chem Catalysis (0) Current Biology (638) Developmental Cell (280) Device (0) Immunity (240) iScience (2162) Joule (299) Matter (143) Med (38) Molecular Cell (188) Neuron (390) One Earth (79) Patterns (119) Structure (139) Related eJournals Cell Press Follow Cell Press Subscribe to this free journal for more curated articles on this topic FOLLOWERS 20 PAPERS 9,067 Feedback Feedback to SSRN Feedback (required) Email (required) Submit If you need immediate assistance, call 877-SSRNHelp (877 777 6435) in the United States, or +1 212 448 2500 outside of the United States, 8:30AM to 6:00PM U.S. Eastern, Monday - Friday.

We present the complete genome sequence of the probiotic strain Lactobacillus acidophilus ATCC 9224. The genome sequence provides a valuable resource for investigating the phylogenetic evolution of this lineage and conducting comparative genomics with other Lactobacillus strains and species.

ABSTRACT Mucoromycota fungi and their Mollicutes-related endobacteria (MRE) are an ideal system for studying bacterial–fungal interactions and evolution due to the long-term and intimate nature of their interactions. However, methods for detecting MRE face specific challenges due to the poor representation of MRE in sequencing databases coupled with the high sequence divergence of their genomes, making traditional similarity searches unreliable. This has precluded estimations on the diversity of MRE associated with Mucoromycota. To determine the prevalence of previously undetected MRE in fungal genome sequences, we scanned 389 Mucoromycota genome assemblies available from the National Center for Biotechnology Information for the presence of MRE sequences using publicly available tools to map contigs from fungal assemblies to publicly available MRE genomes. We demonstrate a higher diversity of MRE genomes than previously described in Mucoromycota and a lack of cophylogeny between MRE and the majority of their fungal hosts. This supports the late invasion hypothesis regarding MRE acquisition across most of the examined fungal families. In contrast with other Mucoromycota lineages, MRE from the Gigasporaceae displayed some degree of cophylogeny with their hosts, which may indicate that horizontal transmission is restricted between members of this family or that transmission is strictly vertical. These results underscore the need for a refined process to capture sequencing data from potential fungal endosymbionts to discern their evolution and transmission. Screens of fungal genomes for MRE can help improve the quality of fungal genome assemblies while identifying new MRE lineages to further test hypotheses on their origin and evolution. IMPORTANCE Mollicutes-related endobacteria (MRE) are obligate intracellular bacteria found within Mucoromycota fungi. Despite their frequent detection, MRE roles in host functioning are still unknown. Comparative genomic investigations can improve our understanding of the impact of MRE on their fungal hosts by identifying similarities and differences in MRE genome evolution. However, MRE genomes have only been assembled from a small fraction of Mucoromycota hosts. Here, we demonstrate that MRE can be present yet undetected in publicly available Mucoromycota genome assemblies. We use these newfound sequences to assess the broader diversity of MRE and their phylogenetic relationships with respect to their hosts. We demonstrate that publicly available tools can be used to extract novel MRE sequences from assembled fungal genomes leading to insights on MRE evolution. This work contributes to a greater understanding of the fungal microbiome, which is crucial to improving knowledge on the dynamics and impacts of fungi in microbial ecosystems.

Accessible and easy-to-use standardized bioinformatics workflows are necessary to advance microbiome research from observational studies to large-scale, data-driven approaches. Standardized multi-omics data enables comparative studies, data reuse, and applications of machine learning to model biological processes. To advance broad accessibility of standardized multi-omics bioinformatics workflows, the National Microbiome Data Collaborative (NMDC) has developed the Empowering the Development of Genomics Expertise (NMDC EDGE) resource, a user-friendly, open-source web application (https://nmdc-edge.org). Here, we describe the design and main functionality of the NMDC EDGE resource for processing metagenome, metatranscriptome, natural organic matter, and metaproteome data. The architecture relies on three main layers (web application, orchestration, and execution) to ensure flexibility and expansion to future workflows. The orchestration and execution layers leverage best practices in software containers and accommodate high-performance computing and cloud computing services. Further, we have adopted a robust user research process to collect feedback for continuous improvement of the resource. NMDC EDGE provides an accessible interface for researchers to process multi-omics microbiome data using production-quality workflows to facilitate improved data standardization and interoperability.