2016-08-28 13.23.32.jpg
2016-03-14 19.03.18.jpg
2016-07-10 19.08.21-2.jpg
2016-08-28 13.23.32.jpg

What's new!


July 2023

Long overdue update!

Welcome to our newest lab members, graduate student Marize Rizkalla and postdoc Yamini Mathur

Farewell and congratulations to recent PhD graduates Dr. Drew Dunham and Dr. Zoe Netter, we will miss you both!

Check out our dive into the RNA-RNA interactome between a phage and its satellite virus published in Molecular Microbiology led by Drew Dunham

Caroline Boyd determined how our favorite satellite virus PLE manipulates phage capsid assembly - check it out in eLife and read the Research Highlight in Nature Reviews Microbiology

Interested in phage (and satellite) genome evolution? Zach Barth and Drew Dunham investigated the role of homing endonucleases in this fascinating topic - check out the preprint here

We’ve always wondered how interactions between Vibrio cholerae and phages may be influenced by the gut environment. Zoe Netter discovered that changes to phage receptor availability in conditions relevant to the gut context can provide V. cholerae with transient protection from phage attack, read the preprint here

October 2022

Want to learn more about how a phage can fight back against the mobile elements that parasitize it? Check out Maria Nguyen’s paper “A phage weaponizes a satellite recombinase to subvert viral restriction”

June 2022

Welcome to our newest lab member, graduate student Tansu Bagdatli!

May 2022

Congratulations to Dr. Kristen LeGault who graduated and will be moving on to a postdoc this fall, we will miss you Dr. LeGault!

February 2022

Check out Angus Angermeyer’s paper “Evolutionary Sweeps of Subviral Parasites and Their Phage Host Bring Unique Parasite Variants and Disappearance of a Phage CRISPR-Cas System” in mBio!

January 2022

Kristen LeGault’s paper “A phage parasite deploys a nicking nuclease effector to inhibit viral host replication” is out in Nucleic Acids Research!

July 2021

The final version of Kristen LeGault’s paper “Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts” is out in Science!

Interested in our favorite phage ICP1? check out our review article led by PhD student Caroline Boyd “Bacteriophage ICP1: A persistent predator of Vibrio cholerae” in Annual Review of Virology!

Check out the final version of Zach Barth’s paper “A chimeric nuclease substitutes a phage CRISPR-Cas system to provide sequence specific immunity against subviral parasites” published in eLife!

The Seed lab is very excited to welcome staff research associate Jeannette Farnham to the lab!

May 2021

Check our latest work published in Nucleic Acids Research led by PhD student Zoe Netter

March 2021

The Seed lab is very excited to welcome postdoc Reid Oshiro to the lab!

June 2020

The lab has been awarded an R01 grant by NIAID! And we are so happy to back in the lab (albeit not all at once!)

April 2020

We are excited to welcome Kishen Patel from the Infectious Diseases and Immunity PhD program to the Seed lab!

Check our latest work published in eLife by postdoc Steph Hays “Dominant Vibrio cholerae phage exhibits lysis inhibition sensitive to disruption by a defensive phage satellite”

March 2020

Our latest preprint led by PhD student Zach Barth is posted “A family of viral satellites manipulates invading virus gene expression and affects cholera toxin mobilization”

Due to COVID-19 shelter in place restrictions we have stopped bench research in the Seed lab, and sadly that means we can’t send off our graduating undergraduate researchers properly! We will miss you Jordan and Peter!

October 2019

The Seed lab has new published papers out on PLE/ICP1 DNA replication: check them out in Nucleic Acids Research and Cell Host & Microbe

August 2019

The first grad student to graduate from the Seed lab - Amelia Mckitterick - has left for her next adventure as a postdoc at Harvard!

May 2019

Kim was named a Burroughs Wellcome Fund Investigator in the Pathogenesis of Infectious Disease

April 2019

We are excited to have Caroline Boyd from the Microbiology PhD program join the lab!

March 2019

Our latest paper on competition between MGEs was published in a special Phil Trans B issue on ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’

Check out Kim’s interview on Talking CRISPR

June 2018

Amelia's paper was published in Nature Communications "Anti-phage islands force their target phage to directly mediate island excision and spread" congratulations!

Angus and collaborators published comparative genomics of ICP1 isolates "Analysis of 19 Highly Conserved Vibrio cholerae Bacteriophages Isolated from Environmental and Patient Sources Over a Twelve-Year Period"

April 2018

We have two new Microbiology PhD students: Drew Dunham and Zoe Netter joined the lab! Drew was also recently awarded an NSF Fellowship.

October 2017

Welcome to Angus Angermeyer, our new Postdoc!

June 2017

Amelia was awarded a 2017 Kathleen L. Miller Fellowship from the Henry Wheeler Center for Emerging and Neglected Diseases (CEND), congratulations!

Our newest paper "A highly specific phage defense system is a conserved feature of the Vibrio cholerae mobilome" has been published in PLOS Genetics! Congrats to Brendan, Zach and Amelia!

We are excited to welcome our new postdoc Steph Hays to the lab!

May 2017

Our paper "Functional Analysis of Bacteriophage Immunity through a Type I-E CRISPR-Cas System in Vibrio cholerae and Its Application in Bacteriophage Genome Engineering" was awarded the Nestlé Phage Award of the American Society for Microbiology! Thank you to Division M and the American Society for Microbiology for this award, congrats to former lab members Allison Box, Matt McGuffie and Brendan O'Hara!

April 2017

Kristen LeGault has joined the lab! Kristen is in the Microbiology PhD program and was also recently awarded an NSF Fellowship!

February 2017

Kim was named a Chan Zuckerberg Biohub investigator!

September 2016

The lab has been awarded an R01 grant by NIAID!

Current Openings

- We are always seeking bright and energetic additions to our lab. If you are interested, Please email Dr. Seed a cover letter describing your research interests and qualifications, your CV and contact information for three references.

SCROLL DOWN

What's new!


July 2023

Long overdue update!

Welcome to our newest lab members, graduate student Marize Rizkalla and postdoc Yamini Mathur

Farewell and congratulations to recent PhD graduates Dr. Drew Dunham and Dr. Zoe Netter, we will miss you both!

Check out our dive into the RNA-RNA interactome between a phage and its satellite virus published in Molecular Microbiology led by Drew Dunham

Caroline Boyd determined how our favorite satellite virus PLE manipulates phage capsid assembly - check it out in eLife and read the Research Highlight in Nature Reviews Microbiology

Interested in phage (and satellite) genome evolution? Zach Barth and Drew Dunham investigated the role of homing endonucleases in this fascinating topic - check out the preprint here

We’ve always wondered how interactions between Vibrio cholerae and phages may be influenced by the gut environment. Zoe Netter discovered that changes to phage receptor availability in conditions relevant to the gut context can provide V. cholerae with transient protection from phage attack, read the preprint here

October 2022

Want to learn more about how a phage can fight back against the mobile elements that parasitize it? Check out Maria Nguyen’s paper “A phage weaponizes a satellite recombinase to subvert viral restriction”

June 2022

Welcome to our newest lab member, graduate student Tansu Bagdatli!

May 2022

Congratulations to Dr. Kristen LeGault who graduated and will be moving on to a postdoc this fall, we will miss you Dr. LeGault!

February 2022

Check out Angus Angermeyer’s paper “Evolutionary Sweeps of Subviral Parasites and Their Phage Host Bring Unique Parasite Variants and Disappearance of a Phage CRISPR-Cas System” in mBio!

January 2022

Kristen LeGault’s paper “A phage parasite deploys a nicking nuclease effector to inhibit viral host replication” is out in Nucleic Acids Research!

July 2021

The final version of Kristen LeGault’s paper “Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts” is out in Science!

Interested in our favorite phage ICP1? check out our review article led by PhD student Caroline Boyd “Bacteriophage ICP1: A persistent predator of Vibrio cholerae” in Annual Review of Virology!

Check out the final version of Zach Barth’s paper “A chimeric nuclease substitutes a phage CRISPR-Cas system to provide sequence specific immunity against subviral parasites” published in eLife!

The Seed lab is very excited to welcome staff research associate Jeannette Farnham to the lab!

May 2021

Check our latest work published in Nucleic Acids Research led by PhD student Zoe Netter

March 2021

The Seed lab is very excited to welcome postdoc Reid Oshiro to the lab!

June 2020

The lab has been awarded an R01 grant by NIAID! And we are so happy to back in the lab (albeit not all at once!)

April 2020

We are excited to welcome Kishen Patel from the Infectious Diseases and Immunity PhD program to the Seed lab!

Check our latest work published in eLife by postdoc Steph Hays “Dominant Vibrio cholerae phage exhibits lysis inhibition sensitive to disruption by a defensive phage satellite”

March 2020

Our latest preprint led by PhD student Zach Barth is posted “A family of viral satellites manipulates invading virus gene expression and affects cholera toxin mobilization”

Due to COVID-19 shelter in place restrictions we have stopped bench research in the Seed lab, and sadly that means we can’t send off our graduating undergraduate researchers properly! We will miss you Jordan and Peter!

October 2019

The Seed lab has new published papers out on PLE/ICP1 DNA replication: check them out in Nucleic Acids Research and Cell Host & Microbe

August 2019

The first grad student to graduate from the Seed lab - Amelia Mckitterick - has left for her next adventure as a postdoc at Harvard!

May 2019

Kim was named a Burroughs Wellcome Fund Investigator in the Pathogenesis of Infectious Disease

April 2019

We are excited to have Caroline Boyd from the Microbiology PhD program join the lab!

March 2019

Our latest paper on competition between MGEs was published in a special Phil Trans B issue on ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’

Check out Kim’s interview on Talking CRISPR

June 2018

Amelia's paper was published in Nature Communications "Anti-phage islands force their target phage to directly mediate island excision and spread" congratulations!

Angus and collaborators published comparative genomics of ICP1 isolates "Analysis of 19 Highly Conserved Vibrio cholerae Bacteriophages Isolated from Environmental and Patient Sources Over a Twelve-Year Period"

April 2018

We have two new Microbiology PhD students: Drew Dunham and Zoe Netter joined the lab! Drew was also recently awarded an NSF Fellowship.

October 2017

Welcome to Angus Angermeyer, our new Postdoc!

June 2017

Amelia was awarded a 2017 Kathleen L. Miller Fellowship from the Henry Wheeler Center for Emerging and Neglected Diseases (CEND), congratulations!

Our newest paper "A highly specific phage defense system is a conserved feature of the Vibrio cholerae mobilome" has been published in PLOS Genetics! Congrats to Brendan, Zach and Amelia!

We are excited to welcome our new postdoc Steph Hays to the lab!

May 2017

Our paper "Functional Analysis of Bacteriophage Immunity through a Type I-E CRISPR-Cas System in Vibrio cholerae and Its Application in Bacteriophage Genome Engineering" was awarded the Nestlé Phage Award of the American Society for Microbiology! Thank you to Division M and the American Society for Microbiology for this award, congrats to former lab members Allison Box, Matt McGuffie and Brendan O'Hara!

April 2017

Kristen LeGault has joined the lab! Kristen is in the Microbiology PhD program and was also recently awarded an NSF Fellowship!

February 2017

Kim was named a Chan Zuckerberg Biohub investigator!

September 2016

The lab has been awarded an R01 grant by NIAID!

Current Openings

- We are always seeking bright and energetic additions to our lab. If you are interested, Please email Dr. Seed a cover letter describing your research interests and qualifications, your CV and contact information for three references.

The Seed Lab

Our research centers on the interactions between bacteria and their viral predators (bacteriophages), and how these interactions impact human health and disease.

2016-03-14 19.03.18.jpg

What are Phage?


Phages are viruses that specifically infect bacteria and they are found wherever bacteria reside. Like all viruses, phages are obligate intracellular parasites: they are metabolically inert in their extracellular form and they need to hijack a bacterial host in order to replicate. Phages employ diverse strategies to exploit bacteria for their own replication, phages can attack and kill a target bacterium within minutes of infection, or they can establish long-term symbiotic relationships with their bacterial hosts. The interactions between bacteria and phages are central to the evolution of microbial communities, including those that contribute to our health (the microbiome) and those that cause disease.

What are Phage?


Phages are viruses that specifically infect bacteria and they are found wherever bacteria reside. Like all viruses, phages are obligate intracellular parasites: they are metabolically inert in their extracellular form and they need to hijack a bacterial host in order to replicate. Phages employ diverse strategies to exploit bacteria for their own replication, phages can attack and kill a target bacterium within minutes of infection, or they can establish long-term symbiotic relationships with their bacterial hosts. The interactions between bacteria and phages are central to the evolution of microbial communities, including those that contribute to our health (the microbiome) and those that cause disease.

 

Our lab investigates the impact of phages on the evolution and epidemiology of Vibrio cholerae, which is the causative agent of the severe diarrheal disease cholera. As a waterborne disease, cholera is a serious threat in areas of the world where sanitation is poor and access to safe drinking water is limited. Cholera is endemic in over 50 countries and also causes devastating epidemics; alarmingly, the incidence of cholera is steadily increasing and the global disease burden is currently estimated to be 3-5 million cases annually. 

2016-07-10 19.08.21-2.jpg

Our focus


Phages that specifically infect and kill V. cholerae are thought to modulate the inter-epidemic persistence of V. cholerae in the environment, thus impacting the occurrence and severity of outbreaks; however, uniquely, these phages also travel with V. cholerae into the human host and continue to prey on their bacterial host during infection. Therefore, phages have the unique potential to impact all aspects of the V. cholerae life cycle (including environmental persistence, infectivity and dissemination), on both a short and long-term evolutionary scale.

Our focus


Phages that specifically infect and kill V. cholerae are thought to modulate the inter-epidemic persistence of V. cholerae in the environment, thus impacting the occurrence and severity of outbreaks; however, uniquely, these phages also travel with V. cholerae into the human host and continue to prey on their bacterial host during infection. Therefore, phages have the unique potential to impact all aspects of the V. cholerae life cycle (including environmental persistence, infectivity and dissemination), on both a short and long-term evolutionary scale.

Principal Investigator

Dr. Kimberley Seed, Ph.D.

Associate Professor

Department of Plant and Microbial Biology

Education and Training

Postdoctoral Fellow, Department of Molecular Biology & Microbiology, Tufts University School of Medicine

Ph.D. Microbiology and Biotechnology, University of Alberta