Eman spent time in the lab when she was a senior at the University of the Sciences Philadelphia (USP), and spent the Spring semester of 2020 working in the lab on an independent study project. Eman was new to bench research and spent her time getting acquainted with fundamental techniques in molecular microbiology. Unfortunately, this work was cut short by the COVID19 pandemic, and Eman was accepted into a Postbac program at WashU.

Wojtek joined the lab in November of 2019 as our first bona fide software developer. He came to us from the Sanger Institute, where he served as the primary developer of Wormbase paraSite. His role on our team is to advance our microbiomeDB project, and he works closely with the larger VEuPathDB team that is our (essential!) partner in this effort. Wojtek moved on to other software development projects with this larger team, but during his time with us he loaded large enteric disease datasets into microbiomeDB, built private user workspaces that allow users to directly upload and analyze their own data, developed an automated workflow that enables handling of shotgun metagenomic data, and built a new software tool (CORRAL) that allows investigators to identify microbial eukaryotes in complex metagenomic datasets.

Camila initially came to spend a year in the lab as a PhD student participating in Brazil’s ‘sandwich’ program. During this time, she fell in love with bioinformatics and returned after her PhD to start a postdoc jointly between our lab and the laboratory of Phil Scott. During her postdoc, she took the lead on advancing our understanding of the transcriptional response that drives skin pathology during cutaneous leishmaniasis. Her initial studies identified key biomarkers that predict patient outcomes even before the first treatment has begun, and more recently she demonstrated that localized skin infection with Leishmania elicits a chronic systemic inflammatory response in patients. Currently, she is working as a Research Associate in the Scott lab where she is integrating data from multiomic assays generated from leishmaniasis patients in Brazil.

Olivia is a PhD student in the lab and is a member of the Microbiology, Virology and Parasitology (MVP) Graduate group. Olivia’s project is focused on the development of genomic methods to study the skin-dwelling parasite, Leishmania braziliensis. In her first paper, she successful developed Selective Whole Genome Amplification (SWGA) for Leishmania species. This work constitutes a breakthrough for the leishmania research field since it allows researchers to amplify whole Leishmania genomes directly from patient material to carry out population genetic studies of this important pathogen, without the need to culture or enrich parasites. She continues to use SWGA to study the population genetics of Leishmania braziliensis across South America.

Alex completed his PhD in biology at UPenn, working in Dustin Brisson’s lab where he studied the population genetics of Trypanosoma cruzi in Peru. He was a postdoc with us from 2018-2020, during which time he instrumental in our studies of the microbiome in large animal models. He was the first to show that natural parasite infections are a dominant factor in shaping microbiome structure in humans and animals (preprint here), and his most recent work used pigs to understand the impact of pregnancy and pregnancy history (parity) on the microbiome and offspring colonization (see here). In addition, Alex played a key role in supporting and developing our transcriptomics course, and was one of the lead authors on this perspectives piece that lays out our approach for teaching bioinformatics to bench biologists and how our curriculum was adapted to improve virtual content during the COVID19 pandemic.

Elise was our lab manager and sequencing guru from 2019-2021, and she played a vital role in helping the lab survive and continue to operate during the worst of the COVID19 pandemic. She left the lab to pursue a PhD in Biology at the University of Syracuse.

Clara came to us straight out of her undergraduate studies at Smith College, where she worked in the laboratory of Dr. Laura Katz. After learning the ropes, Clara now manages the lab and handles all our high-throughput sequencing.

For nearly 20 years I have studied host-microbial interactions, with a primary focus on leveraging genomic and bioinformatic approaches to elucidate mechanisms that regulate inflammation and host defense during infection with zoonotic microbes. During my PhD in Judy Appleton’s lab at Cornell University’s Baker Institute for Animal Health, I studied the immune response during chronic infection with the parasitic helminth, Trichinella spiralis. This work led to the identification of the cytokines IL10 and TGF-β, and eosinophils, as critical regulators of inflammation and immunity to chronic helminth infection. As as postdoc in David Roos’ lab at UPenn, my work shifted from helminth to protozoan parasites, and I began to employ genome-wide transcriptional profiling and genetic screens to identify novel players involved signaling pathways that regulate both immunity and pathogenic inflammation. The results of these studies helped shed light on important immune effector mechanisms, ranging from IL27 signaling in Tregs, to identifying novel enhancers of STAT1 signaling, to reactive oxygen species production by infected monocytes, to TLR3-dependent type I interferon production. In January of 2013, I began a faculty position in the School of Veterinary Medicine at UPenn, were I Co-founded and continue to Co-direct the Center for Host-Microbial Interactions (CHMI). My primary research mission in this role is to develop interdisciplinary ‘One-health’ projects related to microbiology and infectious diseases. In parallel with my research program, I work to engage trainees at the University level in bioinformatics training for managing and analyzing genomic datasets.

Amanda is a PhD student in the Immunology Graduate Group (IGG) and spent her 1st rotation with us. The goal of Amanda’s project was to interrogate the host transcriptional response during infection-induced dysbiosis, and to identify the microbes or microbial factors associated with inflammation leading to sepsis. Amanda used an infection with Toxoplasma gondii to induce severe dysbiosis fand collected gut tissue, stool and created a microbial isolate collection from mice at 0, 2, 5, and 8 days post-infection. Amanda then worked to isolate RNA from these tissues and prepare sequence-ready libraries. The goal of this project is to try to use RNAseq to simultaneous profile host and microbial gene expression during dysbiosis. This data set will provide insight into microbial community structure AND function during dysbiosis, as well as profiling the host response…all from the same sample.

Jake is a PhD student in the Genomics and Computational Biology (GCB) graduate group and spent his 2nd rotation with us. He employed ‘hybrid’ (short + long read) genome assembly methods to generate one of the first complete genomes for Clostridium hiranonis, a bile-acid producing member of the gut microbiome that is implicated in maintaining gut health through the production of secondary bile acids. Jake then annotated this genome and used comparative genomic approaches to understand population genetics of C. hiranonis across animals and humans. Since there is only one other complete genome available for this organism, Jake turned to mining our shotgun metagenomic data from animal stool samples and identified ~20 samples for which the metagenomic reads provide at least 100x coverage of the C. hiranonis genome. He used contigs from the metagenome assembled genomes (MAGs) in his comparative analysis.