J. E. Stajich

Discovery of Mycodnaviridae, a clade of giant viruses that persistently infect zoosporic fungi

The paper discovers a new family of giant viruses, Mycodnaviridae, that infect zoosporic fungi and persistently infect them, expanding the known host range of Nucleocytoviricota.

Comparative genomics reveals intra and inter species variation in the pathogenic fungus Batrachochytrium dendrobatidis

This study compares the genomes of different lineages of the amphibian pathogen Batrachochytrium dendrobatidis to identify core and accessory genes and their impact on transcriptome analysis.

Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic Mycetohabitans spp.

This study identifies and characterizes Btl proteins in Mycetohabitans spp., showing sequence and functional diversity across strains and suggesting their role in bacterial-fungal symbiosis.

Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria

This paper investigates the gut microbiomes of herptiles, showing that Basidiobolus fungi are common and interact with bacteria, potentially shaping bacterial communities through horizontal gene transfer.

Metagenomics untangles metabolic adaptations of Antarctic endolithic 1 bacteria at the fringe of habitability

The paper analyzes metagenomic data from Antarctic endolithic microbiomes to identify metabolic strategies supporting life at extreme environmental limits.

Geographical Survey of the Mycobiome and Microbiome of Southern California Glassy-winged Sharpshooters

This study characterizes the mycobiome and microbiome of glassy-winged sharpshooters across Southern California and finds geographic and captivity-related differences, with mycobiome linked to insecticide resistance.

Mrs4 loss of function in fungi during adaptation to the cystic fibrosis lung

The paper identifies MRS4 mutations in fungi associated with cystic fibrosis lung infections, showing they confer a fitness advantage by enhancing iron acquisition in iron-limited environments.

Discovery of an endogenous DNA virus in the amphibian killing fungus and its association with pathogen genotype and virulence

The paper identifies a DNA virus in the amphibian-killing fungus Bd and links its presence to reduced host growth and increased virulence.

Cataloging Viral Diversity from Nonaxenic Terrestrial Cyanobacteria Cultures

The paper catalogs viral diversity from nonaxenic terrestrial cyanobacteria cultures, identifying 726 viral operational taxonomic units and predicting host associations.

Highly diverse and unknown viruses may enhance Antarctic endoliths' adaptability

The paper analyzes viral diversity in Antarctic rocks using metagenomics, revealing highly diverse and spatially structured virus communities that may influence bacterial adaptation and biogeochemistry.

Patterns and determinants of the global herbivorous mycobiome

The paper analyzes AGF diversity across 661 fecal samples from 34 herbivorous species, identifying 56 novel genera and showing that both stochastic and deterministic processes shape AGF communities, with hindgut fermenters having stronger host-specific associations.

Morphological and phylogenetic resolution of Conoideocrella luteorostrata (Hypocreales: Claviciptaceae), a potential biocontrol fungus for Fiorinia externa in United States Christmas tree production areas

This study characterizes Conoideocrella luteorostrata's morphology and phylogeny, confirming its pathogenicity against EHS and highlighting challenges in genus-level classification.

In host evolution of Exophiala dermatitidis in cystic fibrosis lung micro-environment

The paper analyzes genomic and phenotypic variation in Exophiala dermatitidis isolates from a CF patient over two years, identifying clades with distinct mutations and functional traits.

Phylogenomic analysis of the Neocallimastigomycota: Proposal of Caecomycetaceae fam. nov., Piromycetaceae fam. nov., and emended description of the families Neocallimastigaceae and Anaeromycetaceae

This paper uses phylogenomic analysis of transcriptomic data to reclassify anaerobic gut fungi into four families and emend existing ones, providing quantitative estimates for taxonomic ranks.

Divergent evolution of early terrestrial fungi reveals the evolution of Mucormycosis pathogenicity factors

This study investigates the divergent evolution of zygomycete fungi, identifying lineage-specific genomic elements and evolutionary relationships that contribute to Mucormycosis pathogenicity.

Population genetic analysis of Ophidiomyces ophidiicola, the causative agent of snake fungal disease, indicates recent introductions to the USA

This study analyzes the genomes of Ophidiomyces ophidiicola strains to determine the history of its introduction to the USA, finding recent introductions and expansions.

Host lung environment limits Aspergillus fumigatus germination through a SskA-dependent signaling response

The paper identifies a SskA-dependent signaling pathway that limits Aspergillus fumigatus germination in the host lung environment, enhancing disease initiation and inflammation.

Transcriptional regulatory features associated with Coccidioides immitis phase transition

This study uses csRNA-seq to identify transcriptional changes and regulatory elements during phase transition in Coccidioides immitis, revealing a WOPR homologue involved in pathogenicity.

Aspergillus fumigatus In-Host HOG pathway mutation for Cystic Fibrosis Lung Microenvironment Persistence

This paper identifies a unique Pbs2 MAPKK allele in Aspergillus fumigatus isolates from CF patients that enables lung persistence by enhancing osmotic stress response in low oxygen but reducing oxidative stress resistance in standard conditions.

A heterogeneously expressed gene family modulates biofilm architecture and hypoxic growth of Aspergillus fumigatus

This paper identifies a gene family in Aspergillus fumigatus that modulates biofilm architecture and hypoxic growth, with potential applications in clinical and industrial settings.

Strain specific persistence in the murine lung of Aspergillus fumigatus conidia causes an Allergic Broncho-Pulmonary Aspergillosis-like disease phenotype

This study identifies an A. fumigatus strain, W72310, that persists in the mouse lung and causes ABPA-like disease without significant hyphal growth.

Balancing positive and negative selection: in vivo evolution of Candida lusitaniae MRR1

The paper analyzes MRR1 allele evolution in Candida lusitaniae isolates from a chronic infection, revealing tradeoffs between high Mrr1 activity conferring antifungal resistance and hydrogen peroxide resistance.

Genome-scale phylogenetic analyses confirm Olpidium as the closest living zoosporic fungus to the non-flagellated, terrestrial fungi

The paper uses genome and transcriptome data from Olpidium to analyze its phylogenetic position relative to non-flagellated terrestrial fungi, finding it as the closest zoosporic relative.

Volatiles from Serratia marcescens, S. proteamaculans, and Bacillus subtilis Inhibit Growth of Rhizopus stolonifer and Other Fungi

This paper identifies volatile compounds from three bacteria that inhibit fungal growth and develops a pipeline to translate these profiles into candidate antifungal compounds.

A genome-scale phylogeny of Fungi; insights into early evolution, radiations, and the relationship between taxonomy and phylogeny

The paper constructs a genome-scale fungal phylogeny using 1,644 species and multiple data matrices, finding robust relationships and identifying taxonomic discrepancies.

Genomic insights into the host specific adaptation of the Pneumocystis genus and emergence of the human pathogen Pneumocystis jirovecii

The paper sequenced genomes of Pneumocystis species from different mammals to study host specificity and evolutionary adaptations, revealing insights into the emergence of the human pathogen P. jirovecii.

Antarctic cryptoendolithic bacterial lineages of pre-Cambrian origin as proxy for Mars colonization

The paper analyzes Antarctic cryptoendolithic bacterial communities to explore their evolutionary origins and potential as analogs for Martian life.

Evolutionary relationships among Massospora spp. (Entomophthorales), obligate pathogens of cicadas

This study investigates the evolutionary relationships and species boundaries of Massospora spp. using molecular phylogenetic analysis and morphology, revealing a monophyletic group with distinct lineages and potential synonymies.

Shallow Genome Sequencing for Phylogenomics of Mycorrhizal Fungi from Endangered Orchids

This study uses shallow genome sequencing to analyze phylogenetic relationships among mycorrhizal fungi associated with endangered orchids, identifying potential new species and taxonomic revisions.

Insights into the desert living skin microbiome: geography, soil depth, and crust type affect biocrust microbial communities and networks in Mojave Desert, USA

The paper examines how geography, soil depth, and crust type influence microbial communities and networks in Mojave Desert biocrusts, identifying key drivers of diversity and structure.