SEA-PHAGES Logo

The official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program.

The SEA-PHAGES Program

SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester, discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses, but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses.

The program aims to increase undergraduate interest and retention in the biological sciences through immediate immersion in authentic, valuable, yet accessible research. By finding and naming their own bacteriophages, students develop a sense of project ownership and have a ready-made personal research project at a fraction of the cost of traditional apprentice-based research programs. Some of the positive effects of the SEA-PHAGES program have been reported here.

SEA-PHAGES is jointly administered by Graham Hatfull's group at the University of Pittsburgh and the Howard Hughes Medical Institute's Science Education division.

SEA-PHAGES IN THE NEWS

  • Thumbnail for  Steele commended by Nobel Prize winner for her work

    Steele commended by Nobel Prize winner for her work

    Barbara Phillips

    Archer County News | April 21, 2016

    It is not often that a freshman in college is approached and commended for research by a Nobel Prize winner, but that is exactly what happened to Archer City graduate, London Steele, now a freshman at Baylor University....read more

    Related institution: Baylor University

  • Thumbnail for Ibadan Bacteriophage Research Team: A SEA-PHAGES team with a difference

    Ibadan Bacteriophage Research Team: A SEA-PHAGES team with a difference

    Tolulope Oduselu and Olubusuyi Adewumi

    Capsid Tail | Nov. 20, 2020

    A team of 8 biomedical science researchers at the University of Ibadan, led by Prof. O. G. Ademowo, envisioned new opportunities to foster early career research participation for young undergraduate students. To achieve this goal, the University of Ibadan was enlisted as a cohort institution in the SEA-PHAGES project, an early-career research initiative of the Howard Hughes Medical Institute and the Graham Hatfull Research group at the University of Pittsburgh.read more

    Related institution: University of Ibadan

  • ‘Virus Hunters’ get hands dirty in UConn class

    Brett Donovan

    the Chronicle | Nov. 30, 2018

    University of Connecticut students involved in a unique learning experience are getting their hands dirty — literally.read more

    Related institution: University of Connecticut

  • Thumbnail for Invisible Friends

    Invisible Friends

    Story by Joel Smith; photos by Rajah Bose

    Gonzaga—The Magazine of Gonzaga University | Aug. 15, 2016

    They may have goofy names, but these students’ microscopic pets are serious science. A junior in college, Vina Tran already has a bona fide scientific discovery to her name. Go ahead and look her up on the Actino-bacteriophage Database, a compendium of biological findings maintained by the University of Pittsburgh....read more

    Related institution: Gonzaga University

  • Thumbnail for Bacteria-busting viruses discovered by student researchers

    Bacteria-busting viruses discovered by student researchers

    Dave Price

    Newport News | July 4, 2022

    "This is Oregon Coast Community College’s first year in the SEA PHAGES program, and I think it was pretty darn successful,” said Matthew Fisher, who teaches biology at OCCC and mentors students during the research project. “The goal is to find new phages, but it’s also about developing the next generation of scientists and getting them excited about doing science at OCCC."read more

    Related institution: Oregon Coast Community College

  • Thumbnail for Young Māori scientist discovers virus

    Young Māori scientist discovers virus

    Rukuwai Tipene-Allen

    Māori Television | April 22, 2018

    Young, Māori scientist Anezka Hoskins has discovered a new virus and is hopeful that it will spark curiosity amongst Māori to push boundaries of knowledge.read more

    Related institution: Massey University

  • Thumbnail for Durham Tech students present research at national symposium

    Durham Tech students present research at national symposium

    Charlton Budd

    Chapelboro.com | June 27, 2016

    Two Durham Tech students were given the chance to present their research at a national symposium earlier this month. Qina Mo and Peter Said presented their research describing the isolation and characterization of two viruses that infect bacteria at the 8th annual SEA-PHAGES Symposium...read more

    Related institution: Durham Technical Community College

  • Thumbnail for Freshman find

    Freshman find

    Kyrie O'Connor

    Houston Chronicle | Oct. 15, 2016

    Brian Blake Maxfeldt likes science just fine, but he didn't go to college expecting to make a discovery his first year. Nevertheless, Maxfeldt, who goes by Blake and graduated from Morton Ranch High School in Katy, discovered a virus that nobody had ever seen before.read more

    Related institution: LeTourneau University

  • Thumbnail for Students isolate potentially novel soil-dwelling viruses

    Students isolate potentially novel soil-dwelling viruses

    WPI News

    Phys.org | June 8, 2016

    After sifting through soil samples collected from across Massachusetts, then drilling down to analyze the DNA of viruses they found, a team of undergraduates at Worcester Polytechnic Institute (WPI) hit pay dirt—three potentially novel viruses.... read more

    Related institution: Worcester Polytechnic Institute

  • Columbia State students place first in scientific research at state academy

    Jay Powell

    Columbia Daily Herald | Feb. 3, 2021

    Columbia State Community College can now add another first-place accolade to its esteemed alumni, this time in the category of scientific research.read more

    Related institution: Columbia State Community College

  • Thumbnail for La Sierra freshmen discover new viruses through national research program

    La Sierra freshmen discover new viruses through national research program

    Darla Martin Tucker

    La Sierra News | June 15, 2017

    La Sierra University freshman Casey Jang was pleasantly surprised—she knew it was possible, but really didn’t expect to find, and then name, a virus that is new to science.read more

    Related institution: La Sierra University

  • Thumbnail for Going viral: C of I students attend HHMI symposium

    Going viral: C of I students attend HHMI symposium

    The College of Idaho—Student News | Aug. 4, 2015

    Jetblade. The name might sound like the newest Marvel superhero to hit the big screen, but it’s actually the newest bacterial virus analyzed by College of Idaho students....read more

    Related institution: College of Idaho

  • Thumbnail for First-years discover viruses, analyze DNA

    First-years discover viruses, analyze DNA

    Kate Nussenbaum

    The Brown Daily Herald | Feb. 10, 2012

    Sixteen first-years watched with excitement as their screens loaded the sequence of 59,625 nucleic acids that comprise the DNA of “Job42,” the virus a student in their class had discovered, isolated and named during the fall semester. “Each of them codes for something,” said Jordan Rego...read more

    Related institution: Brown University

  • UMass Inclusive Excellence Initiative Continues for Third Year

    University of Massachusetts Amherst News and Media Relations | Oct. 14, 2020

    Connor says, “We are delighted with our students’ progress and the power of SEA-PHAGES to excite and engage students in research regardless of their prior experience and background.” She adds, “Courses like SEA-PHAGES teach research skills as part of the curriculum, offering a much more inclusive approach to STEM fields and engaging students early in research experiences.”read more

    Related institution: University of Massachusetts Amherst

  • Thumbnail for Round Rock Cedar Ridge grad earns scientific honor

    Round Rock Cedar Ridge grad earns scientific honor

    Mike Schoeffel

    Austin American-Statesman | Feb. 28, 2017

    Isabel Delwel, a junior at the University of North Texas, was chosen to participate in the 2017 Howard Hughes Medical Institute Exceptional Research Opportunities Program. One of Delwel’s professor’s, Dr. Lee Hughes, encouraged Delwel to apply for a spot in the program.read more

    Related institution: University of North Texas

2022 MRA Workflow

2022 MRA Workflow
 

Purpose
The MRA workflow is designed to support you (SEA faculty) and your students publish MRAs describing phages that you and your students discover and characterize as part of the PHAGES project. Participation is this workflow is only a requirement for those who are offered a discounted publication fee, though we welcome any and all faculty to participate and/or use workflow resources. As always, we’re happy to work with you individually if you have any questions or concerns, so please do not hesitate to reach out. Please direct any MRA Workflow-related questions to Vic Sivanathan.

The workflow includes the following 4 components, which you should click to read more about:

  1. Timeline
  2. Writing Guidance
  3. Internal Review
  4. Publication Fees

1. Timeline:

This timeline was developed to enable the program to support as many faculty publish MRAs on an annual basis. This year, SEA faculty have identified ~ 100 genomes to be included in this workflow. We are grateful to our SEA Faculty on the SMART Team who will aim to get these genomes  QC’ed and in GenBank by the end of June. It is therefore critical that your annotations be submitted on time, by May 1. Those annotations submitted after May 1 may be delayed in their submission to GenBank.

  • Feb 15, 2022: Sign-up by this date to participate in this MRA workflow.
  • May 1, 2022:  Submit your annotated genome for QC by this date. Genomes will be QC’ed and submitted to GenBank by June 30, 2022.
  • July 15, 2022: Complete a Review-to-Improve analyses of the pre- and post-QC'ed annotations, then submit your manuscript for internal review by this date.
  • Oct 31, 2022: By this date, finalize your MRA manuscript based on feedback from internal review. Note that you can submit your manuscript for publication as soon as internal-review feedback has been incorporated.

Note: If your annotated genomes do not require QC, that is if you are an Expedited Submitter or a SMART member, or if you are writing an MRA for genomes already in GenBank, your abbreviated workflow is as follows:

  • Feb 15, 2022: Sign-up by this date to participate in this MRA workflow.
  • May 1, 2022: Submit your annotated genome and MRA manuscript to SEA for submission to GenBank and review, respectively, by this date.
  • Oct 31, 2022: By this date, finalize your MRA manuscript based on feedback from internal review. Note that you can submit your manuscript for publication as soon as internal-review feedback has been incorporated.

2. Guidance for Writing your MRA:

  1. Please use the SEA Faculty Resource on QUBES for “Writing Microbial Resource Annoucements (MRA)”.
    This resource includes 3 primary components:
    • A template MRA that describes the information required for each section of the MRA, how to locate this information, as well as sample text and links to sample publications.
    • A data collection sheet, which we recommend you and your students  use to gather and house all the information you will need for the MRA. You will need to submit this data sheet (or the same compilation of data for your phage in another format) along with your manuscript to facilitate internal review.
    • A faculty checklist, which you can use to make sure you have included in your manuscript all the requested information. You will also need to submit this checklist along with your manuscript for internal review.
      Note: The resource was recently updated (Feb 2022), so please download the most recent version.
  2. If you intend to publish on multiple phages, you can do so by writing a single manuscript describing multiple phages or writing multiple manuscripts. Phages need not be closely related (e.g. same cluster or same host) to be included in one publication. Suggestions for formatting the information for multiple phages are provided in the MRA Template. Please note, however, that this year each school is only eligible to be considered for one MRA at the discounted price of $150.
  3. We recommend you begin the process of writing your manuscript early in the semester. For example, the initial part of your manuscript will describe characteristics of the phage(s) that were uncovered as part of the Phage Discovery component of the course, and this information can be gathered and entered into the Data Collection Sheet even before you begin annotating the genome.

3. Internal Review
This year, the SEA Team will perform the internal review. Next year, we hope to formalize the review process and invite SEA faculty to participate as reviewers.

4. Publication Fee

The current regular publication fee is $800 for ASM members and $1,100 for non-members. This year, ASM will charge a discounted publication fee of $150 for a limited number of submissions from the SEA. Priority for the discounted rate will be based on the following criteria:

  • First, for faculty who do not have access to funds to cover publications fees and have not previously published an MRA.
  • Second, for faculty who do not have access to funds to cover publications fees but have previously published an MRA.
  • Third, for faculty who have access to funds to cover publications fees but have not previously published an MRA.
  • Fourth, for faculty who have access to funds to cover publications fees and have previously published an MRA.

The SEA Team will notify those selected and not selected for this discounted rate for 2022 by email.

 

Sequencing Status 2021-22

Below is a live spreadsheet showing the status of SEA-PHAGES sequencing samples for the 2021-22 academic year. Generally, samples are only listed after they're scheduled for a MiSeq run, so don't worry if the samples you sent haven't appeared yet.

CLICK HERE to open this in a new browser window.

 

Sequencing Information: 2021-22

It's getting towards that time of year again: time to send SEA-PHAGES DNA samples in to be sequenced at Pitt!

Contact Us/Questions

Please send any questions about the information below to Dan (dar78@pitt.edu) and Becky (rag4@pitt.edu).

Sample Submission Form

Please submit the information about the samples you are sending using this Google Form. This will help us keep track of samples, correct any spelling errors, and make sure your samples are accounted for. Please fill out a copy of this form for each sample you are submitting. The best time to fill it out is as you are getting your shipment packed, so that when your box arrives, we'll already have the information on your phages in our database.

If possible, please add a tracking number in the appropriate place on the form. Our shipping situation is still not 100% normal, and we want to make sure all packages are accounted for. Please note whether each sample is a "Priority" or "Backup" in the Notes field, along with any other info we should have.

https://docs.google.com/forms/d/e/1FAIpQLSfdhZpw1LHL42zxAotEVqhmrr8RBN9-kuPL_42ioYmuBU-4-Q/viewform

Quantity

Each SEA-PHAGES school may have two genomes sequenced per Bioinformatics section that it is teaching during the current academic year. Please indicate any order of preference, if you have one.

Deadlines

Semester Schools

Please send your genomic DNA so that it arrives in Pittsburgh by Thursday, December 2.

Quarter Schools

Please send your genomic DNA so that it arrives in Pittsburgh by Friday, January 7.

If you will have trouble meeting these deadlines for any reason, please contact us.

Guidelines for DNA

Buffer

Samples that are resuspended in TE are problematic, since the EDTA may interfere with enzymatic shearing of the DNA. You can resuspend your DNA in Elution Buffer (Tris), T(1/10)E, or in purified water.

Amount

We need a minimum of 4 µg (micrograms) of genomic DNA. If you're in the ballpark of this number but not quite there, contact Dan and Becky to see if it's okay.

Concentration

At least 40 ng/µl. Ideal is 100-300 ng/µl. If you're above 300 ng/µl please consider diluting to a workable concentration and workable volume. Shipping volumes less than 20 µl is not recommended. Keep in mind that spec-based quantifications (like Nanodrop) count all absorbance at 260 nm, not just genomic DNA, so they often overestimate the real concentration. Err on the high side of the amount of DNA you send.

Gel Picture

Please submit—either via email or in the shipping box—an image of the gDNA being run on an agarose gel. We use these to look for sample integrity (not already sheared/degraded) and purity (no RNA).

Labeling

Please clearly label the tubes you are sending with the name of the phage as it appears on PhagesDB. Don't label tubes using student's initials only, or other ambiguous names like "Phage1" or "PittPhage". If possible, put a small circular sticker on the top of the tube and write the phage name only on it.

Shipping

Please ship samples, as described below, for delivery to Pittsburgh on Mon-Thurs. We sometimes have issues with Friday deliveries, and don't want any samples to sit over the weekend.

Also, we are unable to receive samples from Nov 24 to Nov 28, and again from Dec 17 to Jan 3. Please avoid shipping during these times.

Packaging

We prefer standard microcentrifuge tubes, and strongly recommend wrapping the caps with Parafilm to prevent spilling or evaporation. The tubes can be packed into a 50 ml conical tube with some KimWipes to stabilize them during shipment. If shipping overnight (preferred), you can actually just send the samples at room temperature, as the DNA should be fine for 24 hours in transit. If shipping on a slower schedule, you should use cold packs. Aim for delivery to Pittsburgh on Tuesday-Friday. If shipping near holidays, please check with us about when we'll be around to receive samples.

You can include a packing slip with any information you think we should have about the enclosed phages.

Address

Attn: Becky Garlena
University of Pittsburgh
Langley Garage 120F
Langley Hall
Fifth and Ruskin Avenues
Pittsburgh, PA 15260
(412) 624 6976

Sequencing Additional Samples

For the past several years, the Genomics Sciences Laboratory at NC State has provided high-quality, for-cost sequencing services to schools in the SEA-PHAGES program who wish to sequence additional genomes beyond those allotted by the program. The charge is usually $250 per genome for sequencing. Contact Andy Baltzegar at dabaltze@ncsu.edu for pricing and details.

Archiving Samples

Just a note that archiving samples should be sent to the same address as above, and so if it's convenient to you, you can send DNA samples and archiving samples together in a single box.

Upcoming Events

Recent Events

Phage Discovery Workshop 15B

July 9, 2022 to July 15, 2022

Phage Discovery Workshop 15A

June 25, 2022 to July 1, 2022

Forum Activity