The Noyes Lab

The Noyes lab received a $3.7M NIH R01 grant along with long-time collaborator Dr. Christina Boucher at University of Florida. The grant will allow continued development of real-time detection and characterization of the resistome, advancing methods in molecular biology, bioinformatics and statistics.

Chris Dean and Ilya Slizovskiy successfully defended their PhDs within 2 weeks of one another, marking a big milestone for the Noyes Lab. Ilya and Chris had job offers before graduation. Chris will be joining the Cancer Institute of Singapore as a Bioinformatics Researcher, and Ilya will be joining Purdue University in a tenure-track Assistant Professor. A huge congratulations and best wishes for the next step!

The Noyes lab received a $3.5M grant to study bovine coronavirus within cattle, with collaborators from University of Liverpool, Mississippi State University, and Texas A&M University. This multi-year project is funded through a program called "Ecology and Evolution of Infectious Diseases", with funding from NSF, NIH, USDA, with the BBSRC in the UK. To read more about the project, read this article in Ag Week.

Omar, Mariana and Aaron advanced to PhD candidacy by passing their preliminary examinations. Congratulations, all!

Omar was announced as being one of the the 2023-2024 cohort fellows for the Global Food Ventures (GFV) as part of Minnesota’s Discovery, Research, and InnoVation Economy (MnDRIVE) partnership. He will be searching for effective solutions to issues surrounding food insecurity and population growth. 

Mariana received best poster award at SafePork 2023

Noelle gave a keynote talk at the annual Conference of Research Workers in Animal Diseases in January 2023, titled “Conducting research during a global pandemic: musings of an early career scientist.”

The Noyes Laboratory received ~$1M in funding from NIH to investigate the microbiome of swine workers. Dr. Montserrate Torremorell and Dr. Ilya Slizovskiy are collaborators on the project. The project is part of the Upper Midwest Agricultural Safety and Health Center (UMASH).

Drs. Montse Torremorell and Noyes received a grant from the Swine Health Information Center to investigate new technologies for multi-virus detection in field samples collected on swine farms.

Dr. Noyes will be collaborating on new research funded by the German Research Foundation with Dr. Claudia Guldimann at Zürich University. The project will investigate the microbiome and resistome of animal hospitals.

The Foundation for Food and Agriculture Research (FFAR) and the American Association of Veterinary Medical Colleges (AAVMC) has selected Jared Young as one of the 2022 FFAR Vet Fellows. Congratulations on being selected for this highly competitive fellowship opportunity, Jared!

Primary Investigator, Whitney Knauer and other collaborators including Luciano Caixeta, Noelle Noyes, and Maxim Cheeran were selected as a 2022 Multistate Grant awardee. Together they will be looking into the effect of pair housing on dairy calves during the pre-weaning period on immune function, nasal microbiome, and the stress response to weaning and social mixing.

At the College of Veterinary Medicine (CVM) Points of Pride Research Day,  Dr. Noyes was awarded with the 2022 Mark of Excellence Award. This annual event celebrates those in the CVM field and all the contributions being made to the advancement of biomedical sciences and veterinary medicine.

Gerardo and Mariana both won awards at the College of Veterinary Medicine (CVM) Points of Pride Research Day. Congratulations!

Gerardo was awarded the Samuel Maheswaran Graduate Fellowship.

Mariana received the William R. and Deanna E. Pritchard Fellowship.

Among several other students, Gerardo and Mariana were announced as being two of the the 2022-2023 cohort fellows for the Global Food Ventures (GFV) as part of Minnesota’s Discovery, Research, and InnoVation Economy (MnDRIVE) partnership. They will be searching for effective solutions to issues surrounding food insecurity and population growth. Congratulations to both!

Noelle Noyes was one of the professors awarded the McKnight Land-Grant Professorship. This Professorship Program has the goal of advancing assistant professors careers. Congratulations to all 2022 award recipients!

The Noyes Lab will be offering two workshop on metagenomic analysis in Summer 2022:

• A one-day workshop at #Microbe2022. Learn more information here!

• A 3-day short course at ISVEE16. Register and learn more information here!

Ilya, PhD student in the Veterinary Population Medicine Department, was the recipient of both the USDA FSIS PhD Fellowship and the UMN Doctoral Dissertation Fellowship. Congratulations!

Thanks to funding from the National Cattleman’s Beef Association, Dr. Noyes and Tara Gaire will be researching the utility of sequencing technologies and data for food safety and public health applications as they relate to beef.

Thanks to the National Science Foundation, Dr. Noyes will be collaborating with Dr. Boucher and Dr. Kahveci to solve the bait learning problem for large-scale DNA enrichment. 

Thomas Wehri, an Animal Sciences student, was accepted into the Veterinary Food Animals Scholars Track (VetFAST) 2021 cohort. Congratulations, Thomas!

The Noyes Lab welcomed several new members to the team in Fall 2021. We are delighted to have Gerardo R. Diaz, Aaron Asmus, Mariana Meneguzzi, and Omar Jimenez-Lopez contributing to the team! Learn more about each of them here.

With financial support from the National Pork Board, the Noyes Lab will train a graduate student in next-generation sequencing and data analysis, including bioinformatics and advanced statistical analysis.

​The Noyes Lab received $1M in funding from USDA to investigate whether different diets and commingling strategies influence AMR persistence after swine receive metaphylactic antibiotics for disease control and prevention. This work is only possible with the close partnership of stakeholders in the swine industry and the scientific collaboration with Dr. Randall Singer and Dr. Maria Pieters.

The Noyes Lab welcomed two new lab members for a great end to 2020 -- we are happy to have Tara Gaire and Peter Ferm joining us!

​The Noyes Lab received USDA Hatch funding to extend its custom bait enrichment technique to the swine virome. The goal is to develop a resource that will allow for full-genome sequencing of multiple viral targets from a single sample. Especially exciting is to work with Dr. Montse Torremorell on this project!

​Chris Dean, current PhD student in our lab, was awarded a prize for a microbiome article that he wrote for the eOrganics newsletter. As part of this award, Chris will present his work at the upcoming ASA, CSSA & SSSA Annual Meeting.  Congratulations Chris!

The Noyes Laboratory received a COVID-19 Rapid Response Grant from the University of Minnesota to aid in the development of molecular and bioinformatic methods for pan-virome analysis of SARS-COV-2 and co-circulating viruses.

Thanks to the Minnesota Beef Council who awarded Noelle and collaborators (Goldsmith, Caixeta and Webb) with a grant, the team investigated the impact of pre-feedlot management strategies on the rumen microbiome, sustainability, food safety and calf health and performance during feedlot transition.

​Blake Jorgenson successfully defended his Capstone Thesis as part of the Bioinformatics and Computational Biology program at UMN, and was awarded his Masters degree. Blake worked on the microbiome and resistome dynamics of the rumen and was an integral member of The Noyes Lab -- he will be missed! We look forward to following Blake's career as he pursues opportunities in industry.  Congratulations Blake!

​Breanna Shi, incoming doctoral student, received the UMN Graduate School's Diversity of Views and Experiences (DOVE) Fellowship for the 2020-2021 academic year. This highly competitive award will support Breanna's professional and academic goals as she starts her PhD program in the Noyes Lab. Congratulations Breanna!

The Noyes Lab received funding from the Minnesota Beef Council to develop a "Pathways Report" for the Minnesota beef sector. This report will include a description of the innovative and diverse pathways by which Minnesota beef calves are marketed, including a "deep dive" on backgrounding and pre-conditioning strategies. A unique aspect of this work will be its integration with rumen microbiome characterization of calves at various points along these diverse pathways. 

Dr. Carissa Odland, MS student, has received the prestigious Bob Morrison Graduate student Fellowship, awarded in honor of the late Dr. Bob Morrison. This fellowship will support Carissa as she completes her Master's Degree in the Veterinary Medicine Program under the advisement of Dr. Noyes and Dr. Davies. Dr. Odland also works full-time for Pipestone Veterinary Services, supporting swine producers throughout Minnesota and beyond. Congratulations Carissa on this very deserved award!

The Noyes Lab is partnering with researchers at three other institutions to provide support for more targeted antimicrobial treatment of metritis in dairy cows.  Led by Dr. Vinicius Machado at Texas Tech University, the cross-disciplinary project includes collaborators Dr. Michael Ballou at Texas Tech, Dr. Klibs Galvão at University of Florida, and Dr. Fabio Lima at University of Illinois.  We are excited to launch this exciting USDA-funded effort with such a great team!

With the grant provided by the Cattlemen’s Beef Association, the Dr. Noyes and Luciano Caixeta conducted a rapid bioinformatic analysis of existing metagenomic data for evidence for rumen protozoal associations with AMR and mobilization genes.

Thanks to the CVM Signature Programs who provided funding, Dr. Noyes will be part of a team looking at microbial population dynamics of salmonid aquaculture in traditional systems and aquaculture systems.

Dr. Noyes and a few others (Kaufman, and Nair) explained the answer to the following question: “How does an analytic approach impact pathogen population structure when analyzing whole genome sequence data?” A thanks goes out to the Foundation for Meat and Poultry Research Education as they are the ones who provided the grant!

Chris was selected to attend the 2nd "Speeding Up Science" Hackathon, hosted by Drs. Titus Brown and Holly Bik at UCDavis and UCRiverside.  Chris received funding to attend this 3-day workshop focused on use of Jupyter notebooks to increase accessibility and reproducibility of multi-omis data analysis.  You can find out more on Twitter: #SpeedingUpScience. Congratulations Chris!

The Laboratory will be assessing nursery exposures to antimicrobial drugs and the subsequent impacts it has on the resistance of market-ready pigs and their pre-retail pork products. This research has been funded by a grant provided by the National Pork Board.

The USDA Agriculture Food Research Initiative awarded Noelle Noyes and Randy Singer with a grant to assist with resistome fingerprinting. Together they worked on the development of a highly discriminative method for tracking and source attribution of antimicrobial resistance in environmental systems.

​October was a banner month for Ilya, who received First Place in Emerging and Zoonotic Diseases for his poster presentation at the UMN College of Veterinary Medicine Points of Pride Research Day, as well as a grad student travel award to attend the 100th Anniversary of the Conference for Research Workers in Animal Diseases.  Congratulations Ilya!

​Zhang presented his work on Haemophilus parasuis at the 2019 Allen D. Leman Swine Conference.  Zhang's abstract was selected as an oral research update, and Zhang did a great job communicating this important research to Leman participants.  Great job Zhang!

​It's been just a couple short months with wonderful Meera Nair working as a post-doc in the Noyes Lab, and while we are sad to see her go, we are so happy to report that Meera accepted a position as Assistant Clinical Professor of Veterinary Microbiology at the Animal Diagnostic Lab at Pennsylvania State University!  Meera will continue to collaborate with us on various ongoing projects as she makes the transition to faculty.  Congratulations Meera on this next step in your career, and we wish you all the best in your move and in your new position.

VMED PhD student Ilya Slizovskiy received funding from the Midwest Center for Occupational Health and Safety Pilot Project Research Training Program to conduct a pilot study on dynamics of swine worker microbiomes and resistomes before, during and after their shifts; and to understand how showering impacts these dynamics.  Congratulations Ilya!

The rumen contains a vast and complex microscopic community.  With funding from NCBA, the Noyes Lab will use existing rumen metagenomic data and advanced bioinformatic and statistical methods to generate hypotheses about how protozoa, bacteria and AMR genes interact within the rumen.  This amazing organ could hold immense potential for AMR control within beef production, and this rapid computational project will help to identify where that potential may be hiding and how it could be leveraged.

Image Credit: ProgressiveDairy.com, Kristen Phillips

With funding from USDA NIFA, The Noyes Lab -- along with co-investigator Dr. Randy Singer -- will probe the potential of resistome data to improve environmental AMR tracking.   The multi-year project will involve computational developments related to resistome data, as well as generation of an open-source soil benchmarking dataset for future research focused on environmental AMR. 

With funding from the UMN College of Veterinary Medicine Signature Programs, Drs. Alex Primus and Noelle Noyes will launch a project to characterize the microbiome of recirculating aquaculture systems (RAS).  This partnership aims to provide stakeholders in aquaculture production with foundational information about important microbial ecological dynamics within these emerging systems.

The Noyes Lab has recently welcomed lots of great new people to the team, including: PhD students Ilya Slizovskiy and Britta Wass; post-docs Meera Nair and Enrique Doster; BICB MS student Blake Jorgenson; Veterinary Summer Scholar Carol Baumann; and undergraduate student Thomas Wehri.  Please visit our "People" page to learn more about all of these great people.  We are so excited to welcome this new cohort of extremely talented and dedicated individuals!  Welcome to the team!

We are excited to launch a project funded by the Foundation for Meat and Poultry Research and Education that aims to understand the impact of various WGS analysis approaches.  This data-heavy project will be conducted in collaboration with Dr. Jamie Kaufman at IBM Research.  We look forward to a productive project and thank our funders! 

​April marked the official start of the second phase of a project funded by the National Pork Board, which aims to evaluate the impact of antimicrobial use in pigs with PRRS -- including health and welfare of the pigs, antimicrobial resistance (AMR), and food safety. The project involves longitudinal sampling of the same pigs from pre-weaning to post-harvest; use of metagenomic and culture-based methods; and environmental sampling of the brand-new pig facility.  We are very excited to be partnering with veterinary-scientists at Pipestone Veterinary Services, including Dr. Carissa Odland, Dr. Scott Dee and Dr. Joel Nerem.

​Chris Dean, PhD student in the BICB program and The Noyes Lab, received a prestigious summer internship at IBM Research.  Chris will spend his summer at the Almaden branch in San Jose, California, working closely with IBM scientists from diverse fields.  Congratulations Chris!

​Ilya Slizovskiy, VMED PhD student in The Noyes Lab, received an award from the Association for Veterinary Epidemiology and Preventive Medicine for his oral presentation at the 2018 Conference for Research Workers in Animal Diseases.  Ilya's talk was titled "Characterizing Risks of Mobilizing Antibiotic Resistance in Beef Production: A Metagenomics-Network Approach".  Congratulations Ilya!

PLoS has launched its much-anticipated Microbiome Channel -- a great resource for curated and exciting scientific literature on the microbiome.  Noelle has been working with the PLoS channel team and a great group of co-editors to put together the first list of featured content and Editor's picks.  The channel will be updated every two weeks, so be sure to check back for the latest hand-picked microbiome papers.  And of course, we welcome recommendations for papers to be included in the next update!

Thanks to funding from the National Institutes of Health, The Noyes Lab is partnering with Dr. Christina Boucher and Dr. Mattia Prosperi to develop novel computational and molecular methods for detecting and quantifying antimicrobial resistance genes in metagenomic datasets.

The Noyes Lab launched a USDA NIFA-funded project in September.  The multi-year, multi-regional project aims to identify and then exploit microbiome dynamics associated with protection from mastitis in dairy heifers.  A large part of the project is focused on expanding the reach of microbiome research, both through educational and outreach-based content to producers, extension specialists and agricultural researchers.  Our awesome collaborators on this project include Luciano Caixeta and Bradley Heins at University of Minnesota; Vinicius Machado at Texas Tech University; Pablo Pinedo at Colorado State University; and Alice Formiga at Oregon State University.  

The Noyes Lab will be teaming up with Henning Sørum at Norwegian University of Life Sciences and Katrine Lekang at University of Oslo in a project that aims to develop new metrics for quantifying selection pressures on the resistome.  The team also includes University of Minnesota researchers Alex Primus, Tiffany Wolf and Kim VanderWaal.  We look forward to building this transatlantic partnership, with the generous support of the Norwegian Centennial Chair.

​The IBM Distinguished Speaker Series hosted Noelle at Almaden Research.  She spoke about The Noyes Lab's work on antimicrobial resistance in livestock production.  There was an extended Q&A, and Noelle was able to spend several days working with the IBM food safety team on joint research questions.  Thanks to IBM for a wonderful visit!

Noelle spoke about antimicrobial resistance in livestock production at the One Health Session of the 2018 Annual Conference of the Consortium of Universities in Global Health.  It was a lively, interactive session and many great ideas were exchanged.  Many thanks to the session organizers; Dean Hendricks for her invitation; and to Colorado State University's College of Veterinary Medicine and Biomedical Sciences for financial support!