Benjamin E. Wolfe
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View article: Spatial Metabolomics Reveals the Role of Penicillic Acid in Cheese Rind Microbiome Disruption by a Spoilage Fungus
Spatial Metabolomics Reveals the Role of Penicillic Acid in Cheese Rind Microbiome Disruption by a Spoilage Fungus Open
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 …
View article: Fungi shape genome evolution of bacteria even in the absence of major growth phenotypes
Fungi shape genome evolution of bacteria even in the absence of major growth phenotypes Open
Studies of microbial interactions often emphasize large, easily measurable growth differences and short-term ecological outcomes spanning just a few generations. However, more subtle interactions, such as those without obvious phenotypes, …
View article: Pairwise interactions and serial bottlenecks help explain species composition in a multi-species microbial community
Pairwise interactions and serial bottlenecks help explain species composition in a multi-species microbial community Open
Characterizing the processes that drive microbial community assembly remains a key challenge in ecology. Several recent studies have argued that pairwise interactions may be insufficient to explain co-occurrence patterns in complex microbi…
View article: Genomics and synthetic community experiments uncover the key metabolic roles of acetic acid bacteria in sourdough starter microbiomes
Genomics and synthetic community experiments uncover the key metabolic roles of acetic acid bacteria in sourdough starter microbiomes Open
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 funct…
View article: Genomics and synthetic community experiments uncover the key metabolic roles of acetic acid bacteria in sourdough starter microbiomes
Genomics and synthetic community experiments uncover the key metabolic roles of acetic acid bacteria in sourdough starter microbiomes Open
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 funct…
View article: Is resilience a unifying concept for the biological sciences?
Is resilience a unifying concept for the biological sciences? Open
There is increasing interest in applying resilience concepts at different scales of biological organization to address major interdisciplinary challenges from cancer to climate change. It is unclear, however, whether resilience can be a un…
View article: Death caps (<i>Amanita phalloides</i>) frequently establish from sexual spores, but individuals can grow large and live for more than a decade in invaded forests
Death caps (<i>Amanita phalloides</i>) frequently establish from sexual spores, but individuals can grow large and live for more than a decade in invaded forests Open
Summary Global change is reshaping Earth's biodiversity, but the changing distributions of nonpathogenic fungi remain largely undocumented, as do mechanisms enabling invasions. The ectomycorrhizal Amanita phalloides is native to Europe and…
View article: Microbiome Assembly in Fermented Foods
Microbiome Assembly in Fermented Foods Open
For thousands of years, humans have enjoyed the novel flavors, increased shelf-life, and nutritional benefits that microbes provide in fermented foods and beverages. Recent sequencing surveys of ferments have mapped patterns of microbial d…
View article: Bacterial–fungal interactions promote parallel evolution of global transcriptional regulators in a widespread <i>Staphylococcus</i> species
Bacterial–fungal interactions promote parallel evolution of global transcriptional regulators in a widespread <i>Staphylococcus</i> species Open
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…
View article: <i>Penicillium</i> molds impact the transcriptome and evolution of the cheese bacterium <i>Staphylococcus equorum</i>
<i>Penicillium</i> molds impact the transcriptome and evolution of the cheese bacterium <i>Staphylococcus equorum</i> Open
The observation that Penicillium molds can inhibit the growth of Staphylococcus was a catalyst for the antibiotic revolution. Considerable attention has been paid to purified Penicillium metabolites that inhibit bacteria, but little is kno…
View article: A phylogenomic perspective on interspecific competition
A phylogenomic perspective on interspecific competition Open
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…
View article: LaeA-Regulated Fungal Traits Mediate Bacterial Community Assembly
LaeA-Regulated Fungal Traits Mediate Bacterial Community Assembly Open
Cheese rinds are economically important microbial communities where fungi can impact food quality and aesthetics. The specific mechanisms by which fungi can regulate bacterial community assembly in cheeses, other fermented foods, and micro…
View article: Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms
Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms Open
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 extra…
View article: Metabolomics of bacterial–fungal pairwise interactions reveal conserved molecular mechanisms
Metabolomics of bacterial–fungal pairwise interactions reveal conserved molecular mechanisms Open
Bacterial–fungal interactions (BFIs) were explored in pairwise co-cultures of species from the cheese rind microbiome, revealing that fungi are key contributors to small molecule mediate BFIs and are important contributors to microbiomes.
View article: Species interactions promote parallel evolution of global transcriptional regulators in a widespread<i>Staphylococcus</i>species
Species interactions promote parallel evolution of global transcriptional regulators in a widespread<i>Staphylococcus</i>species Open
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…
View article: Deciphering the Microbiome: Integrating Theory, New Technologies, and Inclusive Science
Deciphering the Microbiome: Integrating Theory, New Technologies, and Inclusive Science Open
The diversity and functional significance of microbiomes have become increasingly clear through the extensive sampling of Earth's many habitats and the rapid adoption of new sequencing technologies. However, much remains unknown about what…
View article: Microbial Diversity and Interaction Specificity in Kombucha Tea Fermentations
Microbial Diversity and Interaction Specificity in Kombucha Tea Fermentations Open
Through an integration of metagenomic and experimental approaches, our work reveals the diversity and nature of interactions among key taxa in kombucha microbiomes through the construction of synthetic microbial pairs. Manipulation of thes…
View article: Chronic stress and captivity alter the cloacal microbiome of a wild songbird
Chronic stress and captivity alter the cloacal microbiome of a wild songbird Open
There are complex interactions between an organism's microbiome and its response to stressors, often referred to as the ‘gut–brain axis’; however, the ecological relevance of this axis in wild animals remains poorly understood. Here, we us…
View article: Microbial War and Peace in Cheese Rind Microbiomes
Microbial War and Peace in Cheese Rind Microbiomes Open
In this talk, Benjamin Wolfe will explore how microbes compete and cooperate in cheese rind microbiomes.From fungal highways on wheels of Saint Nectaire to antibiotic producing fungi in cheddar, we'll learn about the ecology and chemistry …
View article: Defining the role of the polyasparagine repeat domain of the S. cerevisiae transcription factor Azf1p
Defining the role of the polyasparagine repeat domain of the S. cerevisiae transcription factor Azf1p Open
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 p…
View article: American artisan cheese quality and spoilage: A survey of cheesemakers' concerns and needs
American artisan cheese quality and spoilage: A survey of cheesemakers' concerns and needs Open
Production of artisan cheeses, including surface-ripened cheeses, has increased in the United States over the past 2 decades. Although many of these cheesemakers report unique quality and spoilage problems during production, a systematic a…
View article: Decision letter: Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition
Decision letter: Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition Open
Article Figures and data Abstract Introduction Results Discussion Materials and methods Appendix 1 Data availability References Decision letter Author response Article and author information Metrics Abstract The ratio of microbial populati…
View article: Defining the role of the polyasparagine repeat domain of the<i>S. cerevisiae</i>transcription factor Azf1p
Defining the role of the polyasparagine repeat domain of the<i>S. cerevisiae</i>transcription factor Azf1p Open
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 p…
View article: The diversity and function of sourdough starter microbiomes
The diversity and function of sourdough starter microbiomes Open
Humans have relied on sourdough starter microbial communities to make leavened bread for thousands of years, but only a small fraction of global sourdough biodiversity has been characterized. Working with a community-scientist network of b…
View article: Dietary vitamin K is remodeled by gut microbiota and influences community composition
Dietary vitamin K is remodeled by gut microbiota and influences community composition Open
Vitamins have well-established roles in bacterial metabolism. Menaquinones (MKn, n = prenyl units in sidechain) are bacterially produced forms of vitamin K produced by the gut microbiota and consumed in the diet. Little is known about the …
View article: The diversity and function of sourdough starter microbiomes
The diversity and function of sourdough starter microbiomes Open
ASVs tables, taxonomy, metadata
View article: Author response: The diversity and function of sourdough starter microbiomes
Author response: The diversity and function of sourdough starter microbiomes Open
Article Figures and data Abstract eLife digest Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Humans have relied on sourdou…