Biology subjects

Lewis, J. A.

Publications and source records attributed to Lewis, J. A..

At least 19 recordsLinked to original sources

bioRxiv2026

Scalable generation of human stem cell-derived ureteric bud and collecting duct organoids in stirred bioreactors

Emerging efforts to engineer multicellular kidney tissues for drug discovery, disease modeling, and therapeutic repair require scalable generation of kidney organoids derived from human induced pluripotent stem cells (hiPSCs). Here, we report a method for generating kidney ureteric bud and collecting duct epithelial organoids in stirred tank bioreactors. We demonstrate that extracellular matrix microcarriers facilitate organoid expansion and are compatible with suspension bioreactor methods. The combination of cell-coated matrix microcarriers with stirred bioreactors promotes maturation marker expression compared to static controls comprising matrix-embedded organoids. Our method offers promise for generating epithelial organoids that serve as multicellular models and organ building blocks for scalable biofabrication.

bioengineering↗

bioRxiv2026

CypA is a molecular barrier to HIV emergence from Eastern chimpanzees

Of the two lineages of lentivirus that endemically infect chimpanzees, only one has served as a source of infections in hu-mans. Using HIV-CRISPR screening, we identify factors that limit the replication of lentivirus from Eastern chimpanzees. We find that CypA restricts nonzoonotic Eastern chimpanzee lentivirus due to a unique feature encoded in capsid. The ability of CypA to restrict lentivirus replication is surprising given that CypA is a host factor exploited by HIV to promote its replica-tion. The selective ability of CypA to restrict this virus provides a molecular explanation as to why lentivirus from Eastern Chimpanzees has never been observed to infect humans. Our work has important implications for understanding the origins of HIV-1 and the potential for novel zoonosis of primate lentiviruses.

microbiology↗

bioRxiv2026

Lenacapavir allosterically remodels the HIV-1 capsid

Lenacapavir (LEN) is a highly potent, long-acting HIV-1 capsid inhibitor that holds exceptional promise for pre-exposure prophylaxis. LEN causes the mature viral capsid to rupture and lose integrity, but the underlying mechanism has been unclear. Here, we show that LEN is an allosteric modulator of HIV-1 capsid structure that breaks the capsids fullerene cone architecture in two steps: loss of high-curvature declinations occurs early, followed by failure of the capsid body. At the molecular level, LEN alters the non-covalent bonding interactions between capsid subunits and reduces local lattice curvature. LEN also alters the material properties of the capsid, by increasing brittleness. These results provide molecular rationales for how LEN remodels HIV-1 capsid structure and impairs the replication capacity of the virus.

microbiology↗

bioRxiv2025

Surprising regulatory plasticity for the conserved HOG pathway in diverse Saccharomyces cerevisiae strains

Mitogen-activated protein kinases (MAPKs) display remarkable regulatory plasticity across evolution, ranging from highly specialized pathways to broadly responsive global signaling hubs. In the budding yeast Saccharomyces cerevisiae, the high-osmolarity glycerol (HOG) network has served as a paradigm for largely stress-specific MAPK signaling, where the Hog1 MAPK coordinates osmoadaptation. This stands in sharp contrast to Hog1 orthologs in other fungi and humans, which respond not only to osmotic stress, but also diverse stresses including UV, heat shock, oxidative stress, and pathogen signals. Whether the relative osmospecificity of S. cerevisiae Hog1 represents an ancestral feature or lineage-specific evolution remains unclear. The majority of foundational work on S. cerevisiae HOG signaling has been performed in laboratory strains that are known to be genetic and phenotypic outliers, and we have been leveraging wild S. cerevisiae strains to understand aspects of stress signaling that may have been lost in laboratory strains. Here, we examined the phenotypic effects of hog1{Delta} mutations in a commonly-used laboratory S. cerevisiae strain and diverse wild strains on stress cross protection and gene expression. Our findings demonstrate an expanded role in cross-stress protection for Hog1 in wild yeast strains compared to the laboratory strain. More strikingly, we identified a large number of Hog1-dependent genes for non-osmotic stresses in the wild strains that were completely absent in the lab strain. Notably, the Hog1 regulon in wild strains responding to non-osmotic stresses is largely distinct from the canonical osmotic stress response, which we show likely occurs through non-canonical cytoplasmic functions. These findings reveal surprising within-species plasticity for the highly conserved HOG network, suggesting that evolutionary transitions between specialist to generalist stress signaling may occur with relative ease.

genetics↗

bioRxiv2025

Embedding Perfusable Microchannel Networks in Photoclickable Bioresins via High-Resolution Digital Light Processing

Light-mediated 3D bioprinting methods hold great promise for the generation of biomimetic microvasculature networks for applications ranging from organ-on-chip models to vascularized tissue constructs. While printing microvascular channels ([≤]100 {micro}m in diameter) within large hydrogel volumes ([≥]1 cm3) is theoretically feasible, progress remains limited by the lack of suitable biocompatible photoresins. Here, we report the development of an optimized photoresin based on fish gelatin and photoclick crosslinking chemistry for bioprinting perfusable, embedded microvascular networks via high-resolution digital light processing (DLP). Specifically, our biocompatible matrix leverages the fast kinetics and negligible dark curing of thiol-norbornene crosslinking as well as the low viscosity and thermal stability of fish gelatin. Using pulsed illumination and a biocompatible radical scavenger (DMPO), we further minimize radical diffusion-induced blurring, enabling extended printing (>5 h). Finally, printing failures are reduced through the incorporation of a biocompatible surfactant (Poloxamer-188). Together, these advances open new avenues for printing perfusable biomimetic microvascular networks embedded in biocompatible hydrogel matrices.

bioengineering↗

bioRxiv2025

MIC*: A Framework for Interpretable Analysis of Ordinal Viability Data

Microbial survival assays frequently use ordered categorical (ordinal) scores, such as semi-quantitative viability scores across drug concentrations. While these ordinal data provide rich information about dose-response dynamics, they require appropriate statistical approaches for proper analysis. Proportional-odds (PO) ordinal regression is specifically designed for such data, modeling the ordered nature of scores while accommodating continuous variables such as concentration. However, despite its advantages, PO regression remains underutilized in microbiology because its cumulative log-odds outputs are abstract and biologically unintuitive. Consequently, researchers often resort to flawed alternatives: collapsing scores into binary outcomes (growth/no growth), treating scores as continuous values for t-tests or ANOVA, or applying nonparametric tests that ignore dose-response structure. Each approach sacrifices power or validity, risking unreliable conclusions. To allow researchers to better leverage the power of ordinal datasets, we introduce MIC*, a summary measure that translates PO regression results into biologically interpretable units. MIC* is defined as the treatment concentration where the predicted probability of "no viability" equals 0.5, and is thus conceptually related to the minimum inhibitory dose (MIC) widely used in antimicrobial research. MIC* retains the rigor of ordinal regression while providing more biologically intuitive effect size measures. The MIC* framework enables formal comparisons as absolute differences ({Delta}MIC*) or relative fold-changes ({Delta}log2MIC*), allowing for robust statistical comparisons between samples. Monte Carlo simulations demonstrate that MIC* yields robust estimates with superior power compared to conventional statistical methods, while case studies demonstrate practical utility. To ensure wide adoption, we provide a suite of open-source tools: a BLInded Scoring System (BLISS) for generating ordinal viability scores, and web-based (MICalculator) and R package (ordinalMIC) alternatives for performing complete MIC* analyses, thus reducing barriers to appropriate analysis of ordinal phenotypes in microbiology. ImportanceMicrobiologists routinely use visual scoring systems to assess cell viability for antimicrobial and stress resistance studies. However, current analysis approaches tend to be problematic, with researchers seeking simple approaches that either discard valuable information or violate important statistical assumptions. While rigorous and appropriate statistical approaches exist, they are rarely used in microbiology because they produce outputs that are non-intuitive and require specialized expertise to implement. Our MIC* framework overcomes these longstanding barriers by translating abstract outputs into an intuitive, concentration-based metric akin to the minimum inhibitory concentration (MIC) well Known to microbiologists. MIC* allows for biologically interpretable comparisons on both absolute ({Delta}MIC*) and relative ({Delta}log2MIC*) scales, allowing for facile between-sample comparisons. MIC* outperforms conventional statistical approaches, and we offer user-friendly software tools to enable broad adoption by the community.

microbiology↗

bioRxiv2025

Perfusable 3D models of ureteric bud and collecting duct tubules

Recent protocols have emerged to derive ureteric bud (UB) and collecting duct (CD) organoids directly from human induced pluripotent stem cells (hiPSCs). However, these 3D kidney tissues lack biophysical cues from luminal flow and a drainage outlet. To address these limitations, we have created perfusable 3D models of UB and CD tubules. UB organoids are first generated from hiPSCs followed by their dissociation into individual UB cells. Individual UB cells are then seeded onto a 3D perfusable channel embedded within an extracellular matrix composed of fragmented basement membrane matrix and collagen I, where they self-assemble into a confluent monolayer. During in vitro perfusion, these cells exhibit UB-like marker expression over several weeks, during which they undergo budding akin to early branching morphogenesis in developing kidneys. To further promote network formation, UB cells are bioprinted adjacent to a perfusable UB tubule, which form interconnections through luminal fusion. Finally, these 3D perfusable UB tubules are differentiated into collecting duct tubules under luminal flow. Our platform facilitates fundamental understanding of human collecting duct formation during renal development, while paving the way for using these physiologically relevant models for drug testing, disease modeling, and, ultimately, integration into bioprinted kidney tissues for therapeutic use.

bioengineering↗

bioRxiv2025

Dynamic global acetylation remodeling during the yeast heat shock response

All organisms experience stress and must rapidly respond to changing conditions. Thus, cells have evolved sophisticated rapid-response mechanisms such as post-translational protein modification to rapidly and reversibly modulate protein activity. One such post-translational modification is reversible lysine acetylation, where proteomic studies have identified thousands of acetylated proteins across diverse organisms. While the sheer size of the acetylome is striking, the function of acetylation for the vast majority of proteins remains largely obscure. Here, we show that global acetylation plays a previously unappreciated role in the heat shock response of Saccharomyces cerevisiae. We find that dysregulated acetylation renders cells heat sensitive, and moreover, that the acetylome is globally remodeled during heat shock over time. Using quantitative acetyl-proteomics, we identified [~]400 high-confidence acetyl marks across [~]200 proteins that significantly change in acetylation when cells are shifted to elevated temperature. Proteins with significant changes in lysine acetylation during heat shock strongly overlap with genes induced or repressed by stress. Thus, we hypothesize that protein acetylation augments the heat shock response by activating induced proteins and inactivating repressed proteins. Intriguingly, we find nearly 40 proteins with at least two acetyl marks that significantly change in the opposite directions. These proteins are strongly enriched for chaperones and ribosomal proteins, suggesting that these two key processes are coordinately regulated by protein acetylation during heat shock. Moreover, we hypothesize that the same type of activating and inactivating marks that exist on histones may be a general feature of proteins regulated by acetylation. Overall, this work has identified a new layer of post-translational regulation that likely augments the classic heat shock response.

genomics↗

bioRxiv2024

Diet driven differences in host tolerance are linked to shifts in global gene expression in a common avian host-pathogen system

As humans alter the landscape, wildlife have become increasingly dependent on anthropogenic resources, altering interactions between individuals and subsequently disease transmission dynamics. Further, nutritional quantity and quality greatly impact an individual hosts immune capacity and ability to mitigate damage caused by infectious disease. Thus, understanding the impact of dietary nutrition on immune function is critical for predicting disease severity and transmission as human activity both facilitates the dispersal of pathogens and alters dietary options for wildlife. Here, we use transcriptomics to explore the previously unstudied molecular mechanisms underpinning diet-driven differences in pathogen tolerance using a widespread avian bacterial pathogen, Mycoplasma gallisepticum (MG). MG is an ideal model for understanding the dietary drivers of disease as the human supplementation that wild birds commonly rely on, bird feeders, are also an important source for MG transmission. Significant diet-driven differences in the expression of many genes encoding immune response and translational machinery proteins are seen both in the absence of MG and during the recovery period. Prior to infection, protein-fed birds are more transcriptionally primed for infection than lipid-fed birds which translates to greater tolerance in protein-fed birds during the recovery period. Given the significant importance of human supplemented food in wildlife disease systems, the molecular mechanisms by which interactions between diet and infection emerge provide insight into the ecological and immunological consequences of human behavior and wildlife disease.

ecology↗

bioRxiv2024

Improved vectors for retron-mediated CRISPR-Cas9 genome editing in Saccharomyces cerevisiae

In vivo site-directed mutagenesis is a powerful genetic tool for testing the effects of specific alleles in their normal genomic context. While the budding yeast Saccharomyces cerevisiae possesses classical tools for site-directed mutagenesis, more efficient recent CRISPR-based approaches use Cas cutting combined with homologous recombination of a repair template that introduces the desired edit. However, current approaches are limited for fully prototrophic yeast strains, and rely on relatively low efficiency cloning of short gRNAs. We were thus motivated to simplify the process by combining the gRNA and its cognate repair template in cis on a single oligonucleotide. Moreover, we wished to take advantage of a new approach that uses an E. coli retron (EcRT) to amplify repair templates as multi-copy single-stranded (ms)DNA in vivo, which are more efficient templates for homologous recombination. To this end, we have created a set of plasmids that express Cas9-EcRT, allowing for co-transformation with the gRNA-repair template plasmid in a single step. Our suite of plasmids contains different antibiotic (Nat, Hyg, Kan) or auxotrophic (HIS3, URA3) selectable markers, allowing for editing of fully prototrophic wild yeast strains. In addition to classic galactose induction, we generated a {beta}-estradiol-inducible version of each plasmid to facilitate editing in yeast strains that grow poorly on galactose. The plasmid-based system results in >95% editing efficiencies for point mutations and >50% efficiencies for markerless deletions, in a minimum number of steps and time. We provide a detailed step-by-step guide for how to use this system.

genetics↗

bioRxiv2024

Embedding biomimetic vascular networks via coaxial sacrificial writing into functional tissue

Printing human tissue constructs replete with biomimetic vascular networks is of growing interest for tissue and organ engineering. While it is now possible to embed perfusable channels within acellular and densely cellular matrices, they lack either the branching or multilayer architecture of native vessels. Here, we report a generalizable method for printing hierarchical branching vascular networks within soft and living matrices. We embed biomimetic vessels into granular hydrogel matrices via coaxial embedded printing (co-EMB3DP) as well as into bulk cardiac tissues via coaxial sacrificial writing into functional tissues (co-SWIFT). Each method relies on an extended core-shell printhead that promote facile interconnections between printed branching vessels. Though careful optimization of multiple core-shell inks and matrices, we show that embedded biomimetic vessels can be coaxially printed, which possess a smooth muscle cell-laden shell that surrounds perfusable lumens. Upon seeding these vessels with a confluent layer of endothelial cells, they exhibit good barrier function. As a final demonstration, we construct biomimetic vascularized cardiac tissues composed of a densely cellular matrix of cardiac spheroids derived from human induced pluripotent stem cells. Importantly, these co-SWIFT cardiac tissues mature under perfusion, beat synchronously, and exhibit a cardio-effective drug response in vitro. This advance opens new avenues for the scalable biomanufacturing of organ-specific tissues for drug testing, disease modeling, and therapeutic use.

bioengineering↗

bioRxiv2023

Natural variation in yeast reveals multiple paths for acquiring higher stress resistance

BackgroundOrganisms frequently experience environmental stresses that occur in predictable patterns and combinations. For wild Saccharomyces cerevisiae yeast growing in natural environments, cells may experience high osmotic stress when they first enter broken fruit, followed by high ethanol levels during fermentation, and then finally high levels of oxidative stress resulting from respiration of ethanol. Yeast have adapted to these patterns by evolving sophisticated "cross protection" mechanisms, where mild primary doses of one stress can enhance tolerance to severe doses of a different secondary stress. For example, in many yeast strains, mild osmotic or mild ethanol stresses cross protect against severe oxidative stress, which likely reflects an anticipatory response important for high fitness in nature. ResultsDuring the course of genetic mapping studies aimed at understanding the mechanisms underlying natural variation in ethanol-induced cross protection against H2O2, we found that a key H2O2 scavenging enzyme, cytosolic catalase T (Ctt1p), was absolutely essential for cross protection in a wild oak strain. This suggested the absence of other compensatory mechanisms for acquiring H2O2 resistance in that strain background under those conditions. In this study, we found surprising heterogeneity across diverse yeast strains in whether CTT1 function was fully necessary for acquired H2O2 resistance. Some strains exhibited partial dispensability of CTT1 when ethanol and/or salt were used as mild stressors, suggesting that compensatory peroxidases may play a role in acquired stress resistance in certain genetic backgrounds. We leveraged global transcriptional responses to ethanol and salt stresses in strains with different levels of CTT1 dispensability, allowing us to identify possible regulators of these alternative peroxidases and acquired stress resistance in general. ConclusionsUltimately, this study highlights how superficially similar traits can have different underlying molecular foundations and provides a framework for understanding the diversity and regulation of stress defense mechanisms. Author SummaryOrganisms in nature frequently experience environmental stress in predictable patterns. For example, during the summer months in temperate climates, the warmth of the morning sun gradually gives way to high afternoon temperatures. Organisms that can anticipate these predictable patterns to mobilize stress defenses would have an advantage in nature. One way organisms anticipate future stress is through cross protection, where cells exposed to a mild dose of one stress gain the ability to survive an otherwise lethal dose of different stress. To better understand the molecular mechanisms that are responsible cross protection, we have been taking advantage of wild yeast strains that are either more resilient or more sensitive to stresses. During the course of this study, we found that strains with superficially similar levels of cross protection differ in the precise molecular mechanisms that underlie the trait. Our study suggests that different molecular strategies may be important for yielding similar stress resistances under different environmental constraints, and highlights the power of harnessing natural genetic diversity to understand the molecular mechanisms underlying differences in environmental responses.

genomics↗

bioRxiv2023

Immune Response of Transplanted Kidney Tissues Assembled from Organoid Building Blocks

The increasing scarcity of organs and the significant morbidity linked to dialysis requires the development of engineered kidney tissues from human-induced pluripotent stem cells. To accomplish this, integrative approaches that synergize scalable kidney organoid differentiation, tissue biomanufacturing, and comprehensive assessment of their immune response and host integration are essential. Here, we create engineered human kidney tissues composed of kidney organoid building blocks (OBBs) and transplant them into mice reconstituted with allogeneic human immune cells. We assess their host vascular integration, in vivo maturation, and their ability to trigger human immune responses. Tissue-infiltrating human immune cells are composed of effector T cells and innate cells. This immune infiltration leads to kidney tissue injury characterized by reduced microvasculature, enhanced kidney cell apoptosis, and a unique inflammatory gene signature comparable to kidney organ transplant rejection in humans. Upon treatment with the immunosuppressive agent Rapamycin, the induced immune response is greatly suppressed. Our model serves as a translational platform to study engineered kidney tissue immunogenicity and develop novel therapeutic targets for kidney rejection.

bioengineering↗

bioRxiv2023

A Hypothesis-Based Hop Microbiology Laboratory Module Testing the Plausibility of the Mythical Origin of the India Pale Ale (IPA)

As one of the most famous fermented drinks in the world, beer is an especially relatable topic for microbiology courses. Here, we describe a short and easily adaptable module based on the antibacterial properties of hops used in brewing. By the 15th century, beer recipes included hops (the flower of the Humulus lupulus plant) as a bittering agent and antimicrobial. By the 19th century, the highly-hopped Indian Pale Ale (IPA) became popular, and a modern myth has emerged that IPAs were invented to survive long ocean voyages such as from Britain to India. With that myth in mind, we designed a hypothesis-driven microbiology lab module that tests the plausibility of this brewing myth-- namely that highly-hopped beers possess enough antibacterial activity to prevent spoilage, while lowly-hopped beers do not. The overall design of the module is to test the antimicrobial properties of hops using petri plates containing varying concentrations of hop extract. The module includes hypothesis generation and testing related to bacterial physiology and morphology (hops are not equally effective against gram-positive and gram-negative bacteria), and to mechanisms of antimicrobial resistance (as beer spoilage bacteria have repeatedly evolved hop resistance). Pre and post assessment showed that students made significant gains in the learning objectives for the module, which encourages critical thinking and hypothesis testing by linking microbial physiology and antimicrobial resistance to an important and topical real-world application.

scientific communication and education↗

bioRxiv2022

The dynamic response to hypoosmotic stress reveals distinct stages of freshwater acclimation by a euryhaline diatom

The salinity gradient separating marine and freshwater environments is a major ecological divide, and the mechanisms by which most organisms adapt to new salinity environments are poorly understood. Diatoms are a lineage of ancestrally marine microalgae that have repeatedly colonized and diversified in freshwaters. Cyclotella cryptica is a euryhaline diatom that naturally tolerates a broad range of salinities, thus providing a powerful system for understanding the genomic mechanisms for mitigating and acclimating to low salinity. To understand how diatoms mitigate acute hypoosmotic stress, we abruptly shifted C. cryptica from seawater to freshwater and performed transcriptional profiling during the first 10 hours. Freshwater shock dramatically remodeled the transcriptome, with ~50% of the genome differentially expressed in at least one time point. The peak response occurred within 1 hour, with strong repression of genes involved in cell growth and osmolyte production, and strong induction of specific stress defense genes. Transcripts largely returned to baseline levels within 4-10 hours, with growth resuming shortly thereafter, suggesting that gene expression dynamics may be useful for predicting acclimation. Moreover, comparison to a transcriptomics study of C. cryptica following months-long acclimation to freshwater revealed little overlap between the genes and processes differentially expressed in cells exposed to acute stress versus fully acclimated conditions. Altogether, this study highlights the power of time-resolved transcriptomics to reveal fundamental insights into how cells dynamically respond to an acute environmental shift and provides new insights into how diatoms mitigate natural salinity fluctuations and have successfully diversified across freshwater habitats worldwide.

genomics↗

bioRxiv2020

The genome of the nonphotosynthetic diatom, Nitzschia sp.: Insights into the metabolic shift to heterotrophy and the rarity of loss of photosynthesis in diatoms

Although most of the tens of thousands of diatom species are obligate photoautotrophs, many mixotrophic species can also use extracellular organic carbon for growth, and a small number of obligate heterotrophs have lost photosynthesis entirely. We sequenced the genome of a nonphotosynthetic diatom, Nitzschia sp. strain Nitz4, to determine how carbon metabolism was altered in the wake of this rare and radical trophic shift in diatoms. Like other groups that have lost photosynthesis, the genomic consequences were most evident in the plastid genome, which is exceptionally AT-rich and missing photosynthesis-related genes. The relatively small (27 Mb) nuclear genome did not differ dramatically from photosynthetic diatoms in gene or intron density. Genome-based models suggest that central carbon metabolism, including a central role for the plastid, remains relatively intact in the absence of photosynthesis. All diatom plastids lack an oxidative pentose phosphate pathway (PPP), leaving photosynthesis as the main source of plastid NADPH. Consequently, nonphotosynthetic diatoms lack the primary source of NADPH required for essential biosynthetic pathways that remain in the plastid. Genomic models highlighted similarities between nonphotosynthetic diatoms and apicomplexan parasites for provisioning NADPH in their plastids. The ancestral absence of a plastid PPP might constrain loss of photosynthesis in diatoms compared to Archaeplastida, whose plastid PPP continues to produce reducing cofactors following loss of photosynthesis. Finally, Nitzschia possesses a complete {beta}-ketoadipate pathway. Previously known only from fungi and bacteria, this pathway may allow mixotrophic and heterotrophic diatoms to obtain energy through the degradation of abundant plant-derived aromatic compounds.

genomics↗

bioRxiv2019

Comparison of RNA Isolation Methods on RNA-Seq: Implications for Differential Expression and Meta-Analyses

Technical variation across different batches of RNA-seq experiments can clearly produce spurious signals of differential expression and reduce our power to detect true differences. Thus, it is important to identify major sources of these so-called \"batch effects\" to eliminate them from study design. Based on the different chemistries of \"classic\" phenol extraction of RNA compared to common commercial RNA isolation kits, we hypothesized that specific mRNAs may be preferentially extracted depending upon method, which could masquerade as differential expression in downstream RNA-seq analyses. We tested this hypothesis and found that phenol extraction preferentially isolated membrane-associated mRNAs, thus resulting in spurious signals of differential expression. Within a self-contained experimental batch (e.g. control versus treatment), the method of RNA isolation had little effect on the ability to identify differentially expressed transcripts. However, we suggest that researchers performing meta-analyses across different experimental batches strongly consider the RNA isolation methods for each experiment.

genomics↗

bioRxiv2019

A Wild Yeast Laboratory Activity: From Isolation to Brewing

Microbial fermentation is a common form of metabolism that has been exploited by humans to great benefit. Industrial fermentation currently produces a myriad of products ranging from biofuels to pharmaceuticals. About one third of the worlds food is fermented, and the brewing of fermented beverages in particular has an ancient and storied history. Because fermentation is so intertwined with our daily lives, the topic is easily relatable to students interested in real-world applications for microbiology. Here, we describe the curriculum for an inquiry-based laboratory course that combines yeast molecular ecology and brewing. The rationale for the course is to compare commercial Saccharomyces cerevisiae yeast strains, which have been domesticated through thousands of generations of selection, with wild yeast, where there is growing interest in their potentially unique brewing characteristics. Because wild yeast are so easy to isolate, identify, and characterize, this is a great opportunity to present key concepts in molecular ecology and genetics in a way that is relevant and accessible to students. We organized the course around three main modules: isolation and identification of wild yeast, phenotypic characterization of wild and commercial ale yeast strains, and scientific design of a brewing recipe and head-to-head comparison of the performance of a commercial and wild yeast strain in the brewing process. Pre and post assessment showed that students made significant gains in the learning objectives for the course, and students enjoyed connecting microbiology to a real-world application.

scientific communication and education↗