Biology subjects

Wolfe, B. E.

Publications and source records attributed to Wolfe, B. E..

11 recordsLinked to original sources

bioRxiv2026

Insights from sourdough redefine the domestication landscape of baker's yeast

While the domestication of plants and animals is widely recognized for its role in the rise of human civilization, humans have also cultivated microbes over millennia to produce food and beverages. One microbe in particular, Saccharomyces cerevisiae, is associated with a wide variety of human-fermentation environments, including wine, beer, and notably bread, such that it is often referred to as "bakers yeast." To better illuminate the domestication history of baking associated yeast, we isolated 38 Saccharomyces cerevisiae strains from sourdough starters donated by bakers throughout North America and compared them to thousands of S. cerevisiae isolates from a variety of wild and human-fermentation environments. We identified 6 major clades with two primary domestication hubs, Mediterranean liquid-state fermentation and Asian solid-state fermentation, diverging across Eurasia that gave rise to human-associated lineages. Population genomic analyses demonstrate that S. cerevisiae strains found in sourdough starters are genetically distinct from commercial baking strains and do not come from the surrounding wild environment. Our results show that sourdough yeast strains are closely related to each other and have shared ancestry with strains isolated from various Asian solid state grain fermentations such Japanese sake, Asian rice wines, Chinese distilled spirits (baijiu), and Chinese steamed bread (mantou). We found evidence of significant admixture throughout S. cerevisiae populations, including baking-associated lineages, likely facilitated by human activity. Pangenome gene content largely captures S. cerevisiae traditional genomic sequence-based population structure and reflects human cultural practices, with differences in gene content and copy number between baking associated strains and other groups. Overall, we show that many generalized hallmarks of domestication, such as genome contraction, loss of genetic diversity, and lack of niche expansion, are not universal features of S. cerevisiae domestication, and that baking-associated yeasts have a complex evolutionary history heavily shaped by human culture.

evolutionary biology↗

bioRxiv2025

Spatial Metabolomics Reveals the Role of Penicillic Acid in Cheese Rind Microbiome Disruption by a Spoilage Fungus

Microbial interactions in cheese rinds influence community structure, food safety, and product quality. But the chemical mechanisms that mediate microbial interactions in cheeses and other fermented foods are generally not known. Here, we investigate how the spoilage mold Aspergillus westerdijkiae chemically inhibits beneficial cheese-rind bacteria using a combination of omics technologies. In cheese rind community and co-culture experiments, A. westerdijkiae strongly inhibited most cheese rind community members. In co-culture with Staphylococcus equorum, A. westerdijkiae strongly affected bacterial gene expression, including upregulation of a putative bceAB gene cluster that is associated with resistance to antimicrobial compounds in other bacteria. Mass spectrometry imaging (MSI) revealed spatially localized production of secondary metabolites, including penicillic acid and ochratoxin B at the fungal-bacterial interface. Integration of LC-MS/MS and genome annotations confirmed the presence of additional bioactive metabolites, such as notoamides and circumdatins. Fungal metabolic responses varied by bacterial partner, suggesting species-specific chemical strategies. Notably, penicillic acid levels increased 2.5-fold during interaction with Brachybacterium, and experiments with purified penicillic acid showed inhibition of a range of cheese rind bacteria. These findings show that A. westerdijkiae deploys a context-dependent arsenal of mycotoxins and other metabolites, disrupting microbial community assembly in cheese rinds. IMPORTANCEThis study identifies the chemical mechanisms underlying the negative impacts of Aspergillus westerdijkiae on cheese rind development, revealing how specialized metabolites like penicillic acid and ochratoxin B influence rind bacterial communities. By integrating biosynthetic gene cluster (BGC) analyses with mass spectrometry, we demonstrate how chemical communication shapes microbial interactions, with possible implications for food safety and cheese quality. Understanding these interactions is essential for assessing the risks of fungal driven-spoilage and mycotoxin production in cheese rind maturation. Beyond cheese, these findings contribute to broader microbiome ecology, emphasizing how secondary metabolites mediate microbial competition in natural and fermented food environments.

microbiology↗

bioRxiv2025

Transposable elements facilitate the unintentional domestication of a cheese-associated Penicillium mold

Previous comparative and experimental evolution studies have suggested how fungi may rapidly adapt to new environments, but direct observation of in situ selection in fungal populations is rare due to challenges with tracking populations over human time scales. We monitored a population of Penicillium solitum over eight years in a cheese cave and documented a phenotypic shift from predominantly green to white strains. Diverse mutations in the alb1 gene, which encodes the first protein in the DHN-melanin biosynthesis pathway, explained the green to white shift. A similar phenotypic shift was recapitulated with an alb1 knockout and experimental evolution in laboratory populations. The most common genetic disruption of the alb1 genomic region was caused by putative transposable element insertions upstream of the gene. White strains had substantial downregulation in global transcription, with genetically distinct white strains possessing divergent shifts in expression of different biological processes. White strains outcompeted green strains in co-culture, but this competitive advantage was only observed in the absence of light, suggesting that loss of melanin is only adaptive in dark conditions. Our results illustrate how fermented food production by humans provides opportunities for relaxed selection of key fungal traits over short time scales. Unintentional domestication of microbes by cheesemakers may provide opportunities to generate new strains for innovation in traditional cheese production.

microbiology↗

bioRxiv2024

Genomics and synthetic community experiments uncover the key metabolic roles of acetic acid bacteria in sourdough starter microbiomes

While research on the sourdough microbiome has primarily focused on lactic acid bacteria (LAB) and yeast, recent studies have found that acetic acid bacteria (AAB) are also common members. However, the ecology, genomic diversity, and functional contributions of AAB in sourdough remain unknown. To address this gap, we sequenced 29 AAB genomes, including three that represent putatively novel species, from a collection of over 500 sourdough starters surveyed globally from community scientists. We found variation in metabolic traits related to carbohydrate utilization, nitrogen metabolism, and alcohol production, as well as in genes related to mobile elements and defense mechanisms. Sourdough AAB genomes did not cluster when compared to AAB isolated from other environments, although a subset of gene functions were enriched in sourdough isolates. The lack of a sourdough-specific genomic cluster may reflect a nomadic lifestyle of AAB. To assess the consequences of AAB on the emergent function of sourdough starter microbiomes, we constructed synthetic starter microbiomes, varying only the AAB strain included. All AAB strains increased acidification of synthetic sourdough starters relative to yeast and LAB by 18.5% on average. Different strains of AAB had distinct effects on the profile of synthetic starter volatiles. Taken together, our results begin to define the key ways in which AAB shape emergent properties of starters and suggest that differences in gene content resulting from intraspecies diversification can have community-wide consequences on emergent function. ImportanceThis study is the first comprehensive genomic and ecological study of acetic acid bacteria isolated from sourdough starters. By combining comparative genomics with manipulative experiments using synthetic microbiomes, we demonstrate that even strains with >97% ANI can shift important microbiome functions, underscoring the importance of species and strain diversity in microbial systems. We also show the utility of sourdough starters as a model system to understand the consequences of genomic diversity at the strain and species level on multispecies communities. These results are also relevant to industrial and home-bakers as we uncover the importance of AAB in shaping properties of sourdough starters that have direct impact on sensory notes and quality of sourdough bread.

microbiology↗

bioRxiv2023

A phylogenomic perspective on interspecific competition

Evolutionary processes may have substantial impacts on community assembly, but evidence for phylogenetic relatedness as a determinant of interspecific interaction strength remains mixed. In this perspective, we consider a possible role for discordance between gene trees and species trees in the interpretation of phylogenetic signal in studies of community ecology. Modern genomic data show that the evolutionary histories of many taxa are better described by a patchwork of histories that vary along the genome rather than a single species tree. If a subset of genomic loci harbor trait-related genetic variation, then the phylogeny at these loci may be more informative of interspecific trait differences than the genome background. We develop a simple method to detect loci harboring phylogenetic signal and demonstrate its application through a proof of principle analysis of Penicillium genomes and pairwise interaction strength. Our results show that phylogenetic signal that may be masked genome-wide could be detectable using phylogenomic techniques and may provide a window into the genetic basis for interspecific interactions. Data & code accessibilityData and code for this project are freely available in the repository linked below and will be permanently archived upon publication. Statement of authorshipNL, BEW, and LHU designed the research; NL performed experiments; NL and LHU performed computational analyses; NL, BEW, and LHU wrote the manuscript. Code repositoryhttps://github.com/uricchio/ILSComp

ecology↗

bioRxiv2023

Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms

Bacterial-fungal interactions (BFIs) can shape the structure of microbial communities, but the small molecules mediating these BFIs are often understudied. We explored various optimization steps for our microbial culture and chemical extraction protocols for bacterial-fungal co-cultures, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed that metabolomic profiles are mainly comprised of fungi derived features, indicating that fungi are the key contributors to small molecule mediated BFIs. LC-inductively coupled plasma MS (LC-ICP-MS) and MS/MS based dereplication using database searching revealed the presence of several known fungal specialized metabolites and structurally related analogues in these extracts, including siderophores such as desferrichrome, desferricoprogen, and palmitoylcoprogen. Among these analogues, a novel putative coprogen analogue possessing a terminal carboxylic acid motif was identified from Scopulariopsis spp. JB370, a common cheese rind fungus, and its structure was elucidated via MS/MS fragmentation. Based on these findings, filamentous fungal species appear to be capable of producing multiple siderophores with potentially different biological roles (i.e. various affinities for different forms of iron). These findings highlight that fungal species are important contributors to microbiomes via their production of abundant specialized metabolites and their role in complex communities should continue to be a priority.

microbiology↗

bioRxiv2022

Species interactions promote parallel evolution of global transcriptional regulators in a widespread Staphylococcus species

Experimental studies of microbial evolution have largely focused on monocultures of model organisms, but most microbes live in communities where interactions with other species may impact rates and modes of evolution. Using the cheese rind model microbial community, we determined how species interactions shape the evolution of the widespread food- and animal-associated bacterium Staphylococcus xylosus. We evolved S. xylosus for 450 generations alone or in co-culture with one of three microbes: the yeast Debaryomyces hansenii, the bacterium Brevibacterium aurantiacum, and the mold Penicillium solitum. We used the frequency of colony morphology mutants (pigment and colony texture phenotypes) and whole-genome sequencing of isolates to quantify phenotypic and genomic evolution after 15 weeks of the evolution. The yeast D. hansenii strongly promoted diversification of S. xylosus; by the end of the experiment, all populations co-cultured with the yeast were dominated by pigment and colony morphology mutant phenotypes. Populations of S. xylosus grown alone, with Brevibacterium, or with Penicillium did not evolve novel phenotypic diversity. Whole-genome sequencing of individual mutant isolates across all four treatments revealed numerous unique mutations in the operons for the SigB, Agr, and WalKR global regulators, but only in the D. hansenii treatment. Phenotyping and RNA-seq experiments demonstrated that these mutations altered pigment and biofilm production, spreading, stress tolerance, and metabolism of S. xylosus. Fitness experiments revealed trade-offs of these mutations across biotic environments caused by antagonistic pleiotropy, where beneficial mutations that evolved in the presence of the yeast Debaryomyces had strong negative fitness effects in other biotic environments. IMPORTANCESubstantial phenotypic and genomic variation exists within microbial species, but the ecological factors that shape this strain diversity are poorly characterized. We demonstrate that the biotic context of a widespread Staphylococcus species can impact the evolution of strain diversity. This work demonstrates the potential for microbes in food production environments to rapidly evolve to novel substrates and biotic environments. Our findings may also help understand how other Staphylococcus species may evolve in multispecies microbiomes.

microbiology↗

bioRxiv2022

Fungal antibiotics control bacterial community diversity in the cheese rind microbiome

Potent antimicrobial metabolites are produced by filamentous fungi in pure lab cultures, but their ecological functions in nature are often unknown. Using an antibiotic-producing Penicillium isolate and the cheese rind microbial community, we demonstrate that a fungal specialized metabolite can regulate the diversity of bacterial communities. Inactivation of the global regulator, LaeA, resulted in the loss of antibacterial activity in the Penicillium isolate. Cheese rind bacterial communities assembled with the laeA deletion strain had significantly higher bacterial abundances than the wild-type strain. RNA-sequencing and metabolite profiling demonstrated a striking reduction in the expression and production of the natural product pseurotin in the laeA deletion strain. Inactivation of a core gene in the pseurotin biosynthetic cluster restored bacterial community composition, demonstrating the role of pseurotins in mediating bacterial community assembly. Our discovery demonstrates how antibiotic production can drive the assembly of microbiomes and provides an ecological context for widespread fungal specialized metabolites.

microbiology↗

bioRxiv2021

Defining the role of the polyasparagine repeat domain of the S. cerevisiae transcription factor Azf1p

Across eukaryotes, homopolymeric repeats of amino acids are enriched in regulatory proteins such as transcription factors and chromatin remodelers. These domains play important roles in signaling, binding, prion formation, and functional phase separation. Azf1p is a prion-forming yeast transcription factor that contains two homorepeat domains, a polyglutamine and a polyasparagine domain. In this work, we report a new phenotype for Azf1p and identify a large set of genes that are regulated by Azf1p during growth in glucose. We show that the polyasparagine (polyN) domain plays a subtle role in transcription but is dispensable for Azf1p localization and prion formation. Genes upregulated upon deletion of the polyN domain are enriched in functions related to carbon metabolism and storage. This domain may therefore be a useful target for engineering yeast strains for fermentation applications and small molecule production. We also report that both the polyasparagine and polyglutamine domains vary in length across strains of S. cerevisiae and propose a model for how this variation may impact protein function.

molecular biology↗

bioRxiv2020

From iron to antibiotics: Identification of conserved bacterial-fungal interactions across diverse partners

Microbial interactions are major determinants in shaping microbiome structure and function. Although fungi are found across diverse microbiomes, the mechanisms through which fungi interact with other species remain largely uncharacterized. In this work, we explore the diversity of ways in which fungi can impact bacteria by characterizing interaction mechanisms across 16 different bacterial-fungal pairs, involving 8 different fungi and 2 bacteria (Escherichia coli and Pseudomonas psychrophila). Using random barcode transposon-site sequencing (RB-TnSeq), we identified a large number of bacterial genes and pathways important in fungal interaction contexts. Within each interaction, fungal partners elicit both antagonistic and beneficial effects. Using a panel of phylogenetically diverse fungi allowed us to identify interactions that were conserved across all species. Our data show that all fungi modulate the availability of iron and biotin, suggesting that these may represent conserved bacterial-fungal interactions. Several fungi also appear to produce previously uncharacterized antibiotic compounds. Generating a mutant in a master regulator of fungal secondary metabolite production showed that fungal metabolites are key shapers of bacterial fitness profiles during interactions. This work demonstrates a diversity of mechanisms through which fungi are able to interact with bacterial species. In addition to many species-specific effects, there appear to be conserved interaction mechanisms which may be important across microbiomes.

microbiology↗

bioRxiv2019

Strain-level diversity impacts cheese rind microbiome assembly and function

Taxa that are consistently found across microbial communities are often considered members of a core microbiome. One common assumption is that taxonomically identical core microbiomes will have similar dynamics and functions across communities. However, strain-level genomic and phenotypic variation of core taxa could lead to differences in how core microbiomes assemble and function. Using cheese rinds, we tested whether taxonomically identical core microbiomes isolated from distinct locations have similar assembly dynamics and functional outputs. We first isolated the same three bacterial species (Staphylococcus equorum, Brevibacterium auranticum, and Brachybacterium alimentarium) from nine cheeses produced in different regions of the United States and Europe. Comparative genomics identified distinct phylogenetic clusters and significant variation in genome content across the nine core microbiomes. When we assembled each core microbiome with initially identical compositions, community structure diverged over time resulting in communities with different dominant taxa. The core microbiomes had variable responses to abiotic (high salt) and biotic (the fungus Penicillium) perturbations, with some communities showing no response and others substantially shifting in composition. Functional differences were also observed across the nine core communities, with considerable variation in pigment production (light yellow to orange) and composition of volatile organic compound profiles emitted from the rinds (nutty to sulfury). Our work demonstrates that core microbiomes isolated from independent communities may not function in the same manner due to strain-level variation of core taxa. Strain-level diversity across core cheese rind microbiomes may contribute to variability in the aesthetics and quality of surface-ripened cheeses.

microbiology↗