Program

Conference Venue

The conference will be hosted in the new Agriculture and Natural Resources Building (2431 Joe Johnson Dr.) The poster sessions will be hosted in the arena in the Brehm Animal Science Building (2506 River Drive) adjacent to the ANR building. All speaker sessions will be hosted in room 101. Transportation between the hotels downtown and the venue will be provided by the conference, see Accommodations for more details.

Sunday (08/03)

9:00AM – 4:00PM (Room 124)

PHAGE GENOMICS IN THE AI ERA

A One-day Workshop on Phage Genomics: Automated Annotation, AI tools, and Manual Curation

“Embrace AI, but don’t mess with Grandma!”

For over a decade, The Evergreen Phage Meeting has been offering workshops on phage genomics, metagenomics, and other pertinent topics.

Every meeting featured one or more workshops displaying different tools and methods for phage genome annotation and analysis. A famous quote by Andrew Kropinski during these workshops is, “Don’t assign a function unless you can convince your grandma with clear evidence!” While the grandma rule has recently been a subject of debate, it has always been a unique element in phage meetings.

Does it still hold at the time of AI?

This workshop covers phage genome annotation, from sequence reads to publication-quality figures, and features newly developed AI-based tools by various groups. The workshop uses the BV-BRC platform as a starter, but walks you through how to implement other tools, and—more importantly—how to validate and reconcile various annotations. Emphasis is placed on specialty gene detection (e.g., virulence, antimicrobial resistance, lysis, and lysogeny). Even with AI getting smarter, visual inspection and “manual curation” remain crucial. Come and see for yourselves!

The workshop is suitable for beginner and intermediate users. No programming or command-line knowledge is necessary.

Bios:

Ramy Aziz is a professor of Microbiology and Immunology at Cairo University and is currently the Head of MARC Bioscience Research Laboratories in Egypt. He has been running tutorials and workshops at Evergreen since 2009.

Rebecca Wattam is an Associate Professor at The University of Virginia. She is a founding member and the outreach lead of the PATRIC resource center (now part of BV-BRC), and has conducted dozens of tutorials around the world on the use of online resources for biological discovery.

9:00AM – 12:00PM (Room 123)
Viromics Workshop:
Evelien Adriaenssens, Group Leader, Quadram Institute of Bioscience, Norwich, Great Britain

This workshop is for participants who want to learn the principles of viromics (viral metagenomics) bioinformatics analyses, particularly focused on the bacteriophage complement of the microbiome. The workshop will consist of a mixture of lecture and hands-on analyses. Hands-on analyses will be performed using a command-line interface and free software on a publicly available dataset. Experience in operating a command-line environment is ideal but the workshop will be open to interested participants from all backgrounds and levels of expertise.

1:00PM – 3:00PM (Room 123)
Overview of Phage Purification Techniques:
Tobi Nagel, Founder and President, Phages for Global Health

This workshop will include experts discussing their experiences using different technologies to purify phages for therapeutic use, such as tangential flow filtration, chromatography, and dialysis.

Monday (08/04)

9:00AM – 9:30AM
Introductory Remarks:
Ria Kaelin, Phagebiotics Research Foundation
Tom Denes, University of Tennessee

9:30AM – 10:30AM
“A role for phage in the proliferation of cyanobacteria”:

Steven Wilhelm is the Kenneth & Blaire Mossman Professor of the Department of Microbiology at the University of Tennessee. He completed his undergraduate and graduate work at the University of Western Ontario before postdoctoral stops at the University of Texas and the University of British Columbia. In 2016 he became a fellow of the American Academy of Microbiology as well as a Sustaining Fellow of the Association for the Sciences of Limnology & Oceanography (ASLO). In 2021 he was elected as a fellow of the American Association for the Advancement of Science and received the John R Martin Award for a paper making a significant contribution during the last thirty years from ASLO. In 2024 became a fellow of the Royal Society of Canada.

His group studies synergies between microbial communities and biogeochemical cycles in lakes and oceans. Lab members use biomolecular tools – DNA and RNA sequencing, metabolomics, and PCR-based quantitative analyses – to study viruses, bacteria, cyanobacteria and algae. Presently the group has a focused interest in harmful algal blooms, trace element constraints on marine productivity and on the interplay of between viruses, plasmids and transposable elements.

10:30AM – 10:50AM
Break: Coffee, Tea and Snacks

10:55AM – 11:20AM
“The push and pull of phages and plasmids in an ocean bacterium”:
Alison Buchan, University of Tennessee

11:20AM – 11:45AM
“Never Say Never Lyse Again: Bacterial Virus Exploitation of Physiologically Older Bacteria”
Steve Abedon, Ohio State University

Lunch: 12:00PM – 1:00PM at the UT Gardens

1:10PM – 1:35PM
“The magnificent, frustrating diversity of soil viruses”:
Joanne Emerson, University of California, Davis

1:35PM – 1:55PM
“Determining the potential of bacteriophages to evolve their host range”
Wallapat Phongtang, Friedrich Schiller University Jena, Germany

1:55PM – 2:15PM
“Precipitation and Phosphorus Reshape Viral Infections and Virion Stability in Soil Ecosystems”:
Gareth Trubl, Lawrence Livermore National Laboratory

2:15PM – 2:35PM
“Comparing Cultivation-Dependent and Metagenomic Approaches to Characterize Bacteriophage Diversity in Wastewater Systems”:
Archana Anand, San Francisco State University

2:35PM – 2:55PM
Break: Coffee, Tea and Snacks

3:00PM – 3:20PM
“A novel mobile genetic element with virus-like characteristics is widespread in the world’s oceans”
Paul Kirchberger, Oklahoma State University

3:20PM – 3:40PM
“A Culture-Independent Minicell-Based Approach for Characterising Host-Specific Bacteriophage Communities”:
Edouard Galyov, University of Leicester

3:40PM – 4:00PM
“Characterizing viral-host interaction networks in building plumbing and a full-scale drinking water distribution system”:
Bridget Hegarty, Case Western Reserve University

4:00PM – 4:15PM
“Sub-daily Bermuda Atlantic Time Series virus sampling reveals taxonomy, host, and functional differences at the population, but not community level”:
Alfonso Carrillo, Ohio State University

4:15PM – 4:40PM
“Single-cell transcriptomics of cyanophage-Synechococcus interactions in vitro and in situ”:
Katelyn A. Houghton, University of Tennessee

4:40PM
Announcements

Special Screening of “Last Chance to Save a Life“: 7:00PM at the Bijou Theater (see Activities)

Tuesday (08/05)

9:00AM – 10:00AM
“Elaborate mechanisms for immune nuclease evasion by a bacteriophage”:

Joseph Bondy-Denomy is a Professor in the Department of Microbiology & Immunology at the University of California, San Francisco. Prior to coming to UCSF, Joe was a PhD student with Alan Davidson at the University of Toronto and received his undergraduate degree in Biology from the University of Waterloo. The lab is focused on studying the interactions between bacteriophages and the defense systems encoded by host bacteria, specifically focused on the human pathogen Pseudomonas aeruginosa. The lab studies a mix of anti-phage defense systems and the cognate response from the phage, which includes inhibitor proteins (i.e. anti-CRISPR and anti-CBASS proteins). More recent work has broadened that interest to include unique mechanisms of CRISPR-Cas evasion, such as “phage nucleus” compartments. Work in the Bondy-Denomy lab has been funded by the NIH, DARPA, the Searle Scholars Program, the Vallee Foundation, and the Innovative Genomics Institute.

10:00AM – 10:25AM
“Environmental Osmolarity Influences CRISPR-Cas Ability to act as a Defense Mechanism”:
James Gurney, Georgia State University

10:25AM – 10:40AM
Break: Coffee and Tea

10:45AM – 11:05AM
“Structure, Function, and Regulation of Bacteriophage Lambda Terminase Holoenzyme”:
Nikolai S. Prokhorov, Indiana University

11:05AM – 11:25AM
“A Phage-Based Approach to Identify Antivirulence Inhibitors of Bacterial Type IV Pili”:
Tori Shimozono, Virginia Tech

11:25AM – 11:40AM
“Decoding Phage-Host Relationships and Infection Cycles via Longitudinal Metagenomics”:
Dinesh Kumar Kuppa Baskaran, University of Wisconsin-Madison

11:40AM – 11:55AM
“Prophages Reshape Metabolism, Stress Tolerance, Biofilm formation and phage defence in Enterotoxigenic Escherichia coli”:
Adrian Thaqi, Helmholtz Centre Munich, Technical University of Munich

Lunch: 12:00PM – 1:00PM at the UT Gardens

1:10PM – 1:35PM
“Phage taxonomy in the era of big data: what phages are in my microbiome?”:
Evelien Adriaenssens, Quadram Institute Bioscience

1:35PM – 2:00PM
“Staphylococcus aureus bacteriophage 80α: from head to tail”:
Terje Dokland, University of Alabama at Birmingham

2:00PM – 2:20PM
“Engineering Bacteriophage For Improved Biosensing and Therapeutics”:
David Parker, Carnegie Science

2:20PM – 2:35PM
“The consequences of superinfection of B. subtilis by SPbeta-like phages”:
Valentina A. Floccari, University of Ljubljana, Slovenia.

2:35PM – 2:50PM
Break: Coffee and Tea

2:55PM – 3:20PM
“The kinds of viruses you might like: understanding and leveraging phage-bacterial interactions in the mammalian gut”:
Brian Hsu, Virginia Tech

3:20PM – 3:40PM
“Next-Generation Proteomics for Quantitative Mapping of Mycobacteriophage D29–Bacteria Interactions Using SEC-DIA-MS”:
Shrestha Ghosh, Karolinska Institute, Sweden

3:40PM – 4:00PM
“A picobirnavirus from the human gut infects bacteria”:
Tianyu Gan, Washington University in St. Louis

4:00PM – 4:15PM
“Validation of Improved Physiological Classification of Escherichia coli Phages Through Comprehensive Receptor Analysis”:
Tomoyoshi Kaneko, Waseda University, Japan

4:15PM – 4:30PM
“‘Phollowing’ phage outbreaks within microbiomes and living animals using fluorescence microscopy”:
Lizett Ortiz de Ora, University of California, Irvine

4:30PM – 6:00PM

Location: Brehm Animal Science Arena (Animal Science Building, signs will point the way from the lecture hall to the poster room.)

Focus Topics: Ecology and Evolution and Phage Fundamentals

Food Provided: Cheese tray with crackers, pita chips and crostini, fresh garden crudité with dill ranch dip, and two drink tickets per attendee for wine (wine only for attendees 21 years of age or older)

Wednesday (08/06)

9:00AM – 9:20AM
“Phages That Heal, Phages That Signal: Resolving Efficacy and Immunity in CF Therapy”:
Dwayne Roach, San Diego State University

9:20AM – 9:40AM
“Single cell viral tagging of Faecalibacterium prausnitzii and uncultivated gut bacteria reveals rare bacteriophages associated with inflammatory bowel disease”:
Danielle Campbell, Washington University in St Louis School of Medicine

9:40AM – 10:00AM
“Establishing preclinical safety and efficacy profiles of bacteriophage Kara-mokiny 3 targeting Pseudomonas aeruginosa”:
Renee Ng, The Kids Research Institute Australia

10:00AM – 10:20AM
“WRAIR Phage Cocktails to Treat Drug-Resistant Pseudomonas aeruginosa Pulmonary Infection”:
Nino Mzhavia, Walter Reed Army Institute of Research

10:20AM – 10:35AM
Break: Coffee and Tea

10:40AM – 10:55AM
“Progress Towards Understanding the Mechanism of Action of Phage-Induced Immunity (PHI-II)”:
Haroldo Hernandez, Baylor College of Medicine

10:55AM – 11:15AM
“In-vitro proof of endolysin therapy for Group B Streptococcus treatment and prevention”:
Urmil M. Dave, University of Maryland

11:15AM – 11:30AM
“Investigation of phage resistance mechanism leads to discovery of antibiotic-induced sensitivity to phage”:
Rachel Lahowetz, Baylor College of Medicine

11:30AM – 11:45AM
“Dispatches from California: Evolving Phages, Synergizing Therapies, and Treating Our First Case”:
Katrine Whiteson, University of California Irvine

Lunch: 12:00PM – 12:55PM at the UT Gardens

1:05PM – 1:25PM
Tara Hicks, Bacteria Beyond Borders

1:25PM – 1:45PM
Tobi Nagel, Phages for Global Health

1:45PM – 2:05PM
“Clinical trial update”
Stacy Kolar, Armata Pharmaceuticals

2:05PM – 2:25PM
“Development and Clinical Progress of Engineered Phage Therapeutics at Locus Biosciences: Insights from the ELIMINATE Phase 2 Trial”
Ethan Baker, Locus Biosciences

2:25PM – 2:40PM
Break: Coffee, Tea and Snacks

2:45PM – 3:05PM
“Beyond the Bench: Founding, Funding, and Forging a Sustainable Phage Therapy Enterprise”
Anthony Maresso, TAILOR Labs – Baylor College of Medicine

3:05PM – 3:25PM
“Planning, Building, and Operating an Academic GMP Personalized Phage Manufacturing Facility”
Austen Terwilliger, TAILOR Labs – Baylor College of Medicine

3:25PM – 3:45PM
“High-performance genome annotation for a safer and fast-er-developing phage therapy”:
Antoine Culot, Rime Bioinformatics SAS, France

3:45PM – 4:45PM
Roundtable Discussion

Phage Gala: 6:30 PM – 9:30 PM at the Press Room (see Activities)

Thursday (08/07)

9:00AM – 9:30AM
“The Cost of Resistance: Multi-Omics Insights into Trade-Offs in Bacteriophage Insensitive Mutants of Erwinia amylovora and Salmonella Enteritidis”:
Hany Anany, Agriculture and Agri-Food Canada

9:30AM – 10:00AM
“Cell-free expression for biosynthesis and characterization of Salmonella enterica and Escherichia coli specific bacteriophages”:
Steven Bowden, University of Minnesota

10:00AM – 10:20AM
“Novel Phages Resulted from the Ethnomicrobiological Practice of Nunu Fermentation”:
Tsai-Tien Tseng, Kennesaw State University

10:20AM – 10:35AM
Break: Coffee and Tea

10:40AM – 11:15AM
“A Day in the Life of a Soil Phage”:
Mark Radosovich University of Tennessee

11:15AM – 11:45AM
“One-Pot, Modular, In Vitro Synthetic Genome Assembly Leveraging Uracil-DNA Glycosylase”:
Patrick Needham, Cornell University

Lunch: 12:00PM – 1:00PM at the UT Gardens

1:10PM – 1:30PM
“Nanomaterials for Antimicrobial and Antiviral Applications: From Surface Engineering to Selective Biocontrol”:
Jan Paczesny, Polish Academy of Sciences

1:30PM – 1:50PM
“Bacteriophage-based bioremediation to control antimicrobial resistant pathogens in wastewater”:
Hannah Pye, Quadram Institute Bioscience

1:50PM – 2:10PM
“The Fat and the Phage-ious: Synergistic Antimicrobials in Action”:
Sage Dunham, University of California Irvine

2:10PM – 2:25PM
“Environmental Phages Against MDR Acinetobacter baumannii: A Therapeutic Promise”:
Pooja Sachdeva, All India Institute Of Medical Science, New Delhi

2:25PM – 2:40PM
“Characterizing the disruption of intestinal bacterial and phage communities in pediatric patients with antibiotic-induced neutropenia”:
Haina Jin, Washington University in St. Louis

2:40PM – 2:55PM
“Pathogen-Phage Bioprospecting to Overcome Resistance”:
Camilla Do, Baylor College of Medicine

3:00PM – 4:25PM

Location: Brehm Animal Science Arena (Animal Science Building, signs and volunteers will point the way from the lecture hall to the poster room.)

Focus Topics: Phage Therapy, Non-profit and Industry, Food, Agriculture, and the Built Environment

Food Provided: Ice cream made by the University of Tennessee Creamery

Closing Remarks: 4:30PM – 5:10PM

Friday (08/08)

Optional Group Outing to Gatlinburg in the Great Smoky Mountains (See Activities)

Conference Venue

Sunday (08/03)

Monday (08/04)

Tuesday (08/05)

Wednesday (08/06)

Thursday (08/07)

Friday (08/08)

DEPARTMENT QUICK LINKS