Kaylynn (PennVet class of ‘21) spent the summer of 2018 in the lab as a NIH-BI research fellow. She was the first person in our lab to profile the microbiome in a large collection of stool samples generated by the PennVet Clinical Parasitology lab from dogs with defined parasite infections. Her data showed a clear role for natural parasite infections in shaping the microbiome, and really set the stage for future work in the lab leading to this paper.

Adri (PennVet class of ‘21) spent the summer of 2018 in the lab as a supported by a fellowship from Biomeme. She expanded our portable diagnostic capabilities by testing assays for equine strangles (Strep. equi equi). Her data showed some promise for being able to detect this pathogen, and set the stage for future work by additional summer vet students.

Ying joined our lab as a volunteer in 2017 and worked her way up to being a very skilled lab manager that handled much of our early high-throughput sequencing experiments.

Francislon spent a year in the lab (April 2017-2018) as part of the wonderful Brazilian ‘sandwich’ PhD program. During this time he contributed to the earliest stages of our microbiomeDB project. Even though only in the lab for a short time, his work was critical in building the core Shiny apps that are still used on our site for visualizing microbiome datasets. His work led to the first publication describing our database resource.

Ana was the first postdoc to join the lab and was instrumental in helping us gain momentum in our research endeavors and build a center that also supported research broadly across PennVet. She set up our sequencing operation, and worked closely with colleagues at PennVet and PennMed to kickstart many collaborations that would run for years. Ana was awarded a Morris Animal Foundation Fellowship, and her research focused on genome sequencing and comparative genomics of Staphyloccous species from animals and humans. Her work was the first to overturn the widely held view that Staphylococci used the mevalonate pathway for isoprenoid biosynthesis (an essential pathway for all of life), showing that this was only true for S. aureus, and that most – if not all – Staph associated with companion, agricultural and wildlife animals used a separate pathway to make isoprenoids. Her ‘One-health’ project paved the way for drug development for veterinary Staph species and highlighted a unique evolutionary aspect of Staphylococcus.

Jenn (PennVet class of ‘20) spent the summer of 2017 in the lab as a NIH-BI research fellow. She was the first person in the lab to begin using our Biomeme platform for portable QPCR detection of veterinary pathogens. Working with our colleagues at the Pennsylvania Diagnostic Lab Services (PADLS) at our large animal hospital, she optimized portable assays for important avian disease, including infectious bronchitis virus (IBV) and Mycobacterium gallinarium and septicum (Mg/Ms).

Elaine joined the lab as a visiting faculty member from Universidade de São Paulo in 2017. Over the course of about 7 months, Elaine set-up our slow-turning lateral vessel (STLV) bioreactor for creating a 3D culture system that would allow us to model host-bacterial interactions in vitro. She then used cultures generated in these STLVs to optimize immunofluorescence and confocal microscopy assays to study intestinal ‘organotypic’ cultures. When she wasn’t working on this project, Elaine also made important contributions to advancing our shotgun metagenomics work, contributing to this publication.

Sam spent the Spring semester of his senior year in our lab as part of her final project for the BIO376 course. During this time, Sam worked closely with another undergraduate in the lab to analyze the microbiome in pregnant sows. Although his time in the lab was relatively brief, he made important contributions to our study that described the impact of parity (pregnancy history) on the microbiome. After graduating from UPenn in 2017, Sam took a job at Memorial Sloan-Kettering Cancer Center (MSKCC), where studies the the impact of the microbiome on cancer immunotherapy. Sam hopes to pursue a graduate degree in bioinformatics.

Lydia spent the Spring semester of her senior year in our lab as part of her final project for the BIO376 course. During this time, Lyida worked closely with another undergraduate to analyze the microbiome in pregnant sows. Although her time in the lab was relatively brief, she made important contributions to our study that described the impact of parity (pregnancy history) on the microbiome. After graduating from UPenn in 2017, Lydia began working as a Clinical Research Coordinator in the Division of Gastroenterology at the Children’s Hospital of Philadelphia (CHOP).

Grace was a lab manager from 2015 to 2016, and she was instrumental in coordinating and organizing our stool biobank as several critical studies were gaining momentum in the lab. She left our lab to start veterinary school at Virginia Tech.