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Seed 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

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.

What’s new!

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

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.

Kim Seed is an Assistant Professor at the University of California, Berkeley and her lab studies the interactions between bacteria and their viral predators (bacteriophages), and how these interactions impact human health and disease.

Kimberly seed

Education

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

Ph.D. Microbiology and Biotechnology, University of Alberta

Kåhrström C.T. 2013. Phages level the playing field. Nature Reviews Microbiology. 11: 300-301. (Link)

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. 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 current focus is towards an understanding of the molecular basis for the anti-phage activity of a group of mobile genetic elements in epidemic V. cholerae. You can find more on our website!

Box A.M., McGuffie, M.J., O’Hara, B.J., and Seed, K.D. 2015. Functional analysis of bacteriophage immunity through a type I-E CRISPR-Cas system in Vibrio cholerae and its application in bacteriophage genome engineering. Journal of Bacteriology. 10.1128/JB.00747-15. (Link)

Dalia, A.B., Seed, K.D., Calderwood, S.B., and Camilli, A. 2015. A globally distributed mobile genetic element inhibits natural transformation of Vibrio cholerae. PNAS. 112:10485-90. (Link)

Seed, K.D. 2014. Battling phages: how bacteria defend against viral attack. PLoS Pathogens. 11(6):e1004847. (Link)

Seed, K .D., Yen, M., Shapiro, B.J., Hilaire, I.J., Charles, R.C., Teng, J.E., Ivers, L.C., Boncy, J., Harris, J.B., and Camill, A. 2014. Evolutionary consequences of intra-patient phage predation on microbial populations. eLife. 3:e03497. (Link)

Notable Media coverage:

  • Research Highlight: Molloy S. 2014. In-house dining for phage. Nature Reviews Microbiology. 12 : 658. (Link)

Seed, K.D., Lazinski, D.W., Calderwood, S.B., and Camill, A. 2013. A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity. Nature. 494:489-491. (Link)

Notable Media coverage:

  • News and Views: Villion M., and Moineau S. 2013. Virology: Phages hijack a host’s defence. Nature. 494:433-434. (Link)
  • Research Highlight: Kåhrström C.T. 2013. Phages level the playing field. Nature Reviews Microbiology. 11: 300-301. (Link)
  • News article: A Virus That Steals A Bacterium’s Immune System And Uses It As A Weapon. Popular Science, March 4, 2013. (Link)
  • News article: The virus that learns. National Geographic Phenomena Blog, February 27, 2013. (Link)

Seed, K.D., Faruque, S.M., Mekalanos, J.J., Calderwood, S.B., Qadri, F., and Camilli, A. 2012. Phase variable O antigen biosynthetic genes control expression of the major protective antigen and bacteriophage receptor in Vibrio cholerae O1. PLoS Pathogens. 8:e1002917. (Link)

Seed, K.D., Bodi, K.L., Kropinski, A.M., Ackermann H.W., Calderwood, S.B., Qadri, F., and Camilli, A. 2011. Evidence of a dominant lineage of Vibrio cholerae-specific lytic bacteriophages shed by cholera patients over a 10-year period in Dhaka, Bangladesh. mBio. 2:e00334-10.(Link)

Complete list of publications generated by PubMed

Kimberly seed Education Postdoctoral Fellow, Department of Molecular Biology & Microbiology, Tufts University School of Medicine Ph.D. Microbiology and Biotechnology, University of