Community Board

The community board is a place for phage researchers and phage enthusiasts to share news and seek advice, collaborations, opportunities, and more. Every week we highlight the best community posts on our newsletter, Capsid & Tail.

Have a question or request for the phage community? Post it below and reach hundreds of phage enthusiasts spanning academia, industry, medicine, and beyond.

Showing 70 community posts

Request for feedback Viral TaxonomyNomenclature
Posted 5 days ago

Binomial nomenclature for virus species: a consultation

International Committee on Taxonomy of Viruses (ICTV)

Bas Dutilh

We are thinking about making virus taxonomy more consistent with the rest of biology by introducing binomial species nomenclature. You know: genus name & species epithet. Do you have an opinion about this? Let us know: Paper | ICTV Public Forum | Tweet thread

Seeking guidance ProteomicsProtocols
Posted 5 days ago

Seeking phage proteomics protocol

Ael Hardy

Has anyone successfully performed proteomics (LC-MS) on whole phage particles (not bands from SDS-PAGE gels)?

Looking for alternative protocols as the one I have been trying has given me a hard time. — @ael_hardy, via Twitter

Seeking guidance Marine phagesProtocolsPhage Isolation
Posted 6 days ago

Seeking optimised protocol for isolation of phages from seawater samples

I am working on isolation and characterisation of marine phages for anti-bio fouling activity. Our lab has assessed the influence of chlorine on different marine microorganisms as well as barnacles, and now we are looking into use of marine bacteriophage therapy for targeting the biofilms involved in microfouling which leads to macrofouling.

I am optimising a protocol for isolation of phages from marine water samples, but somewhere I am making mistakes, leading to negative results. Could anyone please share their optimised protocol for isolation of bacteriophages from sea water samples? Until now I have used a protocol which includes dilution of filtered sea water with 2X culture broth and overnight grown pure culture, but I am looking for an alternate protocol.

Please email me at atifbhu91@gmail.com if you can help.

Seeking opportunity Internship
Posted 16 days ago

PhD student seeking unpaid 3 month industry placement

Rebecca Quinn, University of Warwick

My name is Rebecca Quinn, I’m a PhD student at University of Warwick, researching phage genetics. I’m funded by the BBSRC, and under the direction of Dr Richard Puxty.

I have funding for a 3 month work placement/internship in Summer 2020 (there is date flexibility). The placement cannot be lab-based, but all other departments (HR, IT, marketing, etc) are suitable.

I have the right to work in the UK/EU, Canada, and the US and am location-flexible.

Please email me at rebecca.quinn@warwick.ac.uk if you know of any opportunities! Thanks.

Seeking guidance Protocols
Posted 21 days ago

Seeking phage titration methods & help

Emmanuel Nnadi, Plateau State University

We have been attempting to get the titre of our phage but don’t seem to know where we are getting it wrong. What’s your preferred protocol? We use the double-layer plaque assay and a McFarlands standard 1.0 for the culture. If you would love to share your protocol you may wish to email me at eennadi@gmail.com.

Phage meetup PhageSocialCollaboration
Posted a month ago

Boston PFU (Phage Fanatics United) First Meetup!

Boston PFU

The first meeting of Boston PFU (Phage Fanatics United) will be Thursday, Dec. 5, 2019 at the Countway Medical Library, Harvard Medical School. Find details and join the mailing list here! This is a social and general meeting, and is open to anyone interested in phages. Email bostonpfu@gmail.com with any questions.

Seeking opportunity Seeking opportunity
Posted a month ago

Seeking Post Doctoral Research Fellowship

My name is Dr. Adamu Kaikabo Ahmad, currently working at National Veterinary Research Institute Vom, Nigeria. I hold a degree in Veterinary Medicine, and Master degree in Veterinary Science. I obtained my PhD in Bacteriology and Food Safety in 2016. My PhD thesis was on phage therapy against colibacillosis in chickens, an infection caused by avian pathogenic Escherichia coli (APEC). I’ve isolated and characterized numerous phages against E. coli, Riemerella anatipestifer, Aeromonas hydrophila. Looking for a postdoctoral position. Contact karkafa@yahoo.co.uk.

Gauging interest Phage meetup
Posted a month ago

Boston phage meetup: gauging interest

Amelia McKitterick and Sian Owen, Boston, Massachussetts

Calling all phage enthusiasts in the Boston area! @implosian and I want to organize a meetup with other Boston phage peeps to share ideas and network etc. Trying to gauge interest, so let us know if you would want to participate!

Seeking guidance Phage cocktail
Posted 2 months ago

Questions about E. coli and phages

Michelle Yang

How are strain B and UPEC strains of E. coli similar?
How do you select phages for a phage cocktail?
Please email me at yang94m@gmail.com.

Seeking opportunity Phage TherapyMolecular phage studies
Posted 2 months ago

Seeking postdoctoral position

Dr. Soleimani

I am seeking a research position in phage therapy or molecular phage studies. I hold a Ph.D from Shahid Beheshti University, Tehran, Iran (Department of microbiology and microbial biotechnology, faculty of life sciences and biotechnology).

My thesis was entitled “Isolation of a lytic bacteriophage effective against Multidrug-resistant (MDR) Klebsiella pneumoniae and the potential of phage therapy against infection in a mouse model” under the supervision of Prof. Fereshteh Eftekhar. During my Ph.D. project, I have experienced almost all the necessary techniques and methods for phage study, phage therapy and lung infection studies in animal models. I am looking for a postdoc or research scientist position. Please contact me at mah.slmn@yahoo.com.

Seeking opportunity Phage TherapyMicrobiologyBiotech
Posted 2 months ago

Seeking PhD position

I have a master’s degree in microbiology. I defended my thesis with the title of ‘Isolation and Identification of Specific Viruses Isolated from the Microbial Corroded Place in the Petroleum Industry’ with the best grade. The title of one of my articles that is published in Anti-Corrosion Methods and Materials Journal is ‘Phage therapy of corrosion-producing bacterium Stenotrophomonas maltophilia using isolated lytic bacteriophages’.

I am keen to work in microbiology, bacteriophages (phage therapy) and biotechnology. Please email me at arezoopedramfar@yahoo.com if you are interested.

Seeking collaborators Phage IsolationSeeking collaborators
Posted 2 months ago

Seeking collaborators for phage characterization studies

Emmanuel Nnadi, Plateau State University, Bokkos, Nigeria

My lab started isolation of phages from hospital environment, so far we have isolated a phage effective against E.coli and working on phages against P. aeruginosa. As a small unfunded lab we are not able to characterize and store for very long because of electricity. So we are open to collaboration. Any lab willing to collaborate to store and characterize our phage and also open to further studies are welcome. Please email me at eennadi@gmail.com.

Seeking collaborators Phage BiocontrolBanana wilt
Posted 2 months ago

Looking to meet phage scientists, find companies offering EM services, and find out about phage conferences

Dr. Ritah Nakayinga, Kyambogo University, Uganda

Hello passionate phage scientists,
My name is Dr. Ritah Nakayinga and I will be starting phage research, early 2020, at Kyambogo University, Uganda. My research is funded by IDRC/OWSD. I will be developing an effective phage bio-control against the Banana wilt disease of the Banana crop and a major staple food crop in Uganda. I would like to network with phage scientists with similar research interests, get information about companies that offer affordable electron microscopy services and any upcoming future phage conferences in 2021. Reach me at: nakayingar@gmail.com.

Q&A Horizontal Gene TransferQ&A
Posted 2 months ago

Seeking method for detecting HGT in sequenced genomes

Dr. Heather Hendrickson

Does anyone have a robust and reliable method that they like for auto detecting HGT in completely sequence genomes? I was playing with HGTecor last week but it seems to be broken. Help? —@DrHHNZ | Tweet thread

Seeking opportunity Phage TherapyBiofilmsWound infections
Posted 2 months ago

Seeking postdoctoral position

Dr. Pallavali Roja Rani

I am seeking a post-doctoral position related to Bacteriophage therapy, Antibiotic Resistance and Biofilm studies. The main objective of my Ph.D. thesis was to study the predominant bacterial isolates of septic wound infections, isolation and characterization of bacteriophages against biofilms of multi drug resistant P. aeruginosa, S. aureus, K. pneumoniae, and E. coli, and application of respective bacteriophages and phage cocktails on the single & dual species biofilms of these predominant bacterial isolates of septic wound infections. Please email me at p.rojarani.virology@gmail.com if you know of any opportunities.

New Community Members Phage DirectoryNew Members
Posted 2 months ago

Welcome new Phage Directory members!

Between July 26 and Sep. 30, we welcomed:

  • 16 phage professionals
    Ael Hardy, Anna Dragos, Cesar de la Fuente, Christine Thompson, Fatma Abdelrahman, Francesca Hodges, Geoffrey Hutinet, Hardian Susilo Addy, Jared Schlechte, Jonas Van Belleghem, Karen Weynberg, Ligia Ayala Navarrete, Milan Bunata, Nayeem Bari, Sam Nugen, Tim Blower.

  • 4 phage research labs
    KeRis Terapi Bakteriofag, Blower Lab, Food Micro Lab, Nnadi Lab

  • 9 phage companies
    Bacteriophage & Drug Development Consultants, Cellexus, Clean Cells, Jafral, MB Pharma, PhagoMed Biopharma, PhagePro, SciPhage, Vetophage.

How can I join the community?

Sign up here!

Special Issue Special IssueResearch
Posted 2 months ago

Invitation to submit to "Phage Diversity for Research and Application” issue of Antibiotics

Dr. Christine Rohde

I recently accepted to serve as Guest Editor for the Special Issue “Phage Diversity for Research and Application” of the journal Antibiotics. I would be very pleased if you agreed to contribute a research paper, or a comprehensive review on any research aspect related to phage diversity. The deadline for manuscript submissions is 1 June 2020. The articles will be published upon acceptance, on an ongoing basis.

Antibiotics is a peer-reviewed open access journal on all aspects of antibiotics. It has an impact factor of 2.921 and is indexed in SCIE (Web of Science), Scopus, and PubMed. The Article Processing Charge of 1200 CHF applies to all papers accepted after peer review.

In order for us to plan this Special Issue, we kindly ask you to inform us as to whether you are interested in contributing to this issue.

Many thanks,
Christine Rohde

Seeking opportunity Phage TherapyPhage Genomics
Posted 3 months ago

Seeking job in phage research field

I am looking for jobs in the phage research field. I have almost fifteen years’ experience in phage research particularly on phage genomics and phage therapy in animal, insect and plant models. I have developed a phage based product. It is on the verge of commercialization now. Please contact me at mdas@tamu.edu if you know any possible opportunities.

Seeking opportunity Research opportunityPhD Project
Posted 3 months ago

Seeking graduate research position

I am Ritam Das, a third year undergraduate student studying Life Sciences at Acharya Narendra Dev College, University of Delhi. I’ve been actively working at the Anti-Mycobacterial Drug Discovery Lab of our college under the guidance of Dr. Urmi Bajpai since December 2018, wherein I am trying to isolate, purify and characterize Mycobacteriophages and phage-derived proteins. Currently, I’m looking for graduate programs (Masters/Masters-PhD integrated) at institutes working on bacteriophages. I wish to apply as a full-time student and to associate myself with a lab to explore phages and phage-derived enzybiotics as credible alternatives to antibiotics. Please contact me at ritamdas007@gmail.com if you know of possible opportunities.

Q&A Phage IsolationQ&A#PhageTwitter
Posted 3 months ago

Seeking community input on using multiple hosts to isolate phages

Anyone inoculate their samples for enriched isolation of phage with multiple hosts to save resources? —@BryanGibb2 | Tweet thread

Seeking opportunity Research opportunity
Posted 3 months ago

Seeking graduate research position

I am Uchenna Precious Nnadi, a graduate of Veterinary Medicine from the University of Nigeria, Nsukka. I am looking for a graduate mentor that will accept to supervise me to develop into a fantastic phage researcher and to provide impactful research and skill to my local community and country, thereby enabling me to grow into a great scientist that will meet local and global issues that relates to health. Please contact me at nnadi.ucheprecious@gmail.com if you know of possible opportunities.

Seeking guidance TEMQ&A#PhageTwitter
Posted 3 months ago

Seeking tips on imaging phage infection

Hoping to get some really cool #TEM images of cool #phages infecting #bacteria really soon. Anyone have any advice on imaging a phage infection? — @MotherOfPhage | Tweet thread

Seeking opportunity Clinical MicrobiologyPhage TherapyAnimal Model
Posted 3 months ago

Seeking postdoctoral research opportunity

Dr. Kübra Can

I am seeking a research position in phage therapy or moleculer phage studies. I hold a PhD from Istanbul University (Institute of Health Sciences, Medical Microbiology Department).

I have strong experience in clinical microbiology, bacteriophage therapy and animal disease models. I am interested in clinical microbiology and crosstalk between organs in mouse models. I am also eager to learn and implement new methods and NGS data analysis for future studies.

Please contact me at kubra.can@istanbul.edu.tr

Seeking opportunity Phage lysins
Posted 3 months ago

Seeking research exchange opportunity

Fatma Abdelrahman

My name is Fatma Abdelrahman and I have BSc in Microbiology from the Faculty of Science, Zagazig University, Egypt. I’m currently a research assistant at the Center of Microbiology and Phage Therapy, Zewail City of Science and Technology, Egypt. My first paper about phage encapsulation is here.

I am looking forward to obtaining an internship or research visit in the fields of phage therapy, phage lysins, other phage-derived enzymes or related topics. I’m planning to pursue my master degree on these topics and I have chosen it to be my future research area.

If there are no fully funded research grants, there are several local institutions which can aid in providing adequate grants upon being accepted.

Please contact me at fabdelrahman@zewailcity.edu.eg

Collaboration Request In vivo studiesResearch
Posted 3 months ago

Seeking collaborators for in vivo lung infection studies

Dr. Swapnil Ganesh Sanmukh

I am Dr. Swapnil Ganesh Sanmukh, presently working on my postdoctoral project (funded my MSCA-COFUND) entitled “Isolation of bacteriophages and lytic enzymes for targeted treatment of chronic bacterial lung infections”. I am looking forward to have collaborations for in-vivo studies. Please email me at swamukh1985in@rediffmail.com

Q&A #PhageTwitterQ&AMethods
Posted 3 months ago

Community Q&A: Removing phages from liquid?

Question:
Hello phage people, does anyone have an improved method to physically remove #phages from liquid broth? Thank you! — @PetrovicFabijan

A subset of the answers to date:

  • We use Amicon filters in my lab to concentrate phage and we’ve noticed that’s there’s a significant amount of phage in the filtrate with the 100 KDa membrane. To remove phage, a different cutoff might be more suitable. —@Z_Doust

  • High protein binding 0.1 um filters —@raw9371

Check the tweet thread for more answers as they come in!

Phage News Source FacebookPhage Community
Posted 3 months ago

The Phage Page on Facebook

Have you checked out The Phage Page on Facebook? Run by Prof. Gail Christie of Virginia Commonwealth University, this page is a fantastic place to find phage news, research and commentary. We get lots of our “What’s New” articles from Gail’s fantastically-curated page! This week, there’s been an especially large number of news items posted!

Group Chat What's AppPhage Research
Posted 4 months ago

New phage research What’s App group

Fatma Abdelrhman

Dear phage community,
I’ve created a What’s App group for scientists who work on phage and AMR, to gather them, benefit and share experience, knowledge, and research of phage worldwide. Please join and share the link (https://chat.whatsapp.com/F4gwFkwvHuxLXLuDtGGqLQ) if you like!

Q&A Phage storageMethods#BestOfPhageTwitter
Posted 4 months ago

Community Q&A: Storing phages?

Question

Any advice on how to store phages/ viruses? I know there are quite a few methods for long-time storage but I’d like to hear your advice. Thanks!
😀 — @LeptihnLab

A few of the answers:

“Easiest way that our lab uses is to make a high titre lysate. You can clean this via ultra-centrifugation into SM buffer, and store long term at 4C. Option to add 0.1 volume chloroform if concerned about sterility. Most phages will keep for decades using this approach […] See our methods paper on this” — @JeremyJBarr

“Will depend on phage and phage-host system. -80 glycerol stocks of phage - needs testing for phage. Or -80 stock of cells that are infected .Or in SM buffer @ 4 if above dont work .Some phage are sensitive to this as well. Can ad CHCl3 to lystates for storage -check CHCl3 first!” — @milja001

“One thing we do is use a modified version of Graham Hatfull’s (@GHatfull) approach for BRED where we extract the genome with phenol chloroform. Can be used later to electroporate back into the host if the phage is unstable. Works good for med genomes <90kbp” — @Phage4Lyfe

Check the tweet thread for more replies as they come in!

Survey SurveyStudent Project
Posted 4 months ago

Student project: Phage Field Expert Survey

California State University, San Marcos

Olympia Alvarez and Taehoon Ha

We are MPH graduate students from California State University, San Marcos, and this survey is for our capstone project on phage therapy. Due to the limited human clinical cases in the literature, we were advised to interview/survey phage experts in the field. The questions pertain to how/whether phage therapy is done in your area, and your thoughts and recommendations regarding phage therapy. We hope to collect responses between now and early/mid September.

Survey: https://www.surveymonkey.com/r/B6K8BK2

Q&A #BestOfPhageTwitter
Posted 4 months ago

Community Q&A: Extracting phage DNA from low titer lysate?

This week on #phagetwitter: “Anyone have a good protocol for DNA extractions from low titer phage lysates?”@FazzinoLisa

Check out the thread for many helpful answers and links!

Phage Request Phage RequestResearch
Posted 5 months ago

Seeking Acinetobacter and Pseudomonas phages for research

Noel-David Nogbou
Sefako Makgatho Health Sciences University
Pretoria, South Africa

Hello, I am looking for Acinetobacter baumannii bacteriophages and Pseudomonas aeruginosa phage OMKO1. This is for a research project. If you can help, please contact me at davnogbou2@gmail.com

Seeking guidance QuestionGenome sequencing
Posted 5 months ago

Question about phage genome sequencing

Amna Mian
University of Lahore
Lahore, Pakistan

I want to sequence my phage genomes. Could someone tell me where to send, and about the cost? Please email me at amnaafmian@gmail.com if you can help.

Q&A Bioinformatics
Posted 5 months ago

Community Q&A: Database of phage genomes for mapping / favorite mapping pipeline?

Here’s a great example of the phage community helping each other out on Twitter — thanks to Stephen Stockdale of APC Microbiome (@SteveStockyPhD) and Simon Roux of the Joint Genome Institute (@simroux_virus) for providing answers!

Here’s the question:

Does anyone know of a database of (putative) phage genomes that you can map reads against? Or your favorite pipeline for mapping reads to a set of references/contigs? Bonus points if it’s easy to use for people who don’t like coding (that’s me)!@ElysianTweets

The answers (so far):

If you are not comfortable downloading viral RefSeq, there is the complete reference viral database (RVDB)@SteveStockyPhD

Or Andrew Millard’s group @milja001 have an easy to download database@SteveStockyPhD

Or if you would like easy to download crAss-like phage sequences@SteveStockyPhD

If you have access to a server that will run alignments and process output (using Bowtie2 and Samtools), but are not comfortable with coding, I can send you some commands. — @SteveStockyPhD

And for mapping reads to genomes without the need to code, we have iVirus on @CyVerseOrg, with full protocols courtesy of Ben Bolduc from @Lab_Sullivan. — @simroux_virus

If you get help from someone in the phage community, or you see an example like this, send it to community@phage.directory — we’d love to feature it here!

Seeking opportunity Post DocResearch
Posted 6 months ago

Seeking phage research opportunity

Golestan University of Medical Sciences

Mahsa Yazdi Gorgan, Iran

I recently graduated with a Ph.D. in Microbiology from the University of Isfahan, Iran. My thesis was entitled “Isolation and characterization of lytic bacteriophages against some of the most common bacterial causes of urinary tract infections” under the supervision of Prof. Majid Bouzari. During my Ph.D. project, I learned almost all the necessary techniques and methods for phage study and gained useful experience in phages and phage therapy. I currently work as an independent researcher at the Department of Microbiology, Golestan University of Medical Sciences, Gorgan, Iran. I am looking for a postdoc or research scientist position to pursue my interest in phages and related topics. Please email me at mahsayazdi92@gmail.com if you have any openings or would like to discuss further!

Seeking opportunity Genome sequencingPhage characterization
Posted 6 months ago

PhD student seeking a phage lab for a funded 1-month internship

University of Constantine 1

Ibtihadj Souda Constantine, Algeria

I am Ibtihadj Souda, a PhD student at the University of Constantine 1 in Algeria working on isolation and characterization of new bacteriophages from wastewater in the Sahara Desert of Algeria (North Africa). Recently, I have been offered a fully funded scholarship from our university (to cover travel and accommodation), so I have an opportunity to spend a one-month internship at a laboratory to do molecular characterisation of the phages we have isolated. I would like to observe my phages by transmission electron microscopy and perform genome sequencing. The location of the lab can be anywhere, and the timing of the visit can be anytime from June-Dec 2019, but I need to submit an invitation letter by June 30, so I need to find a host lab as soon as possible. Please email me at ibtihege.souda@umc.edu.dz and we can discuss details! Thank you!

Event MeetupNetworking
Posted 6 months ago

Phage meetups and talks at ASM Microbe this weekend!

American Society for Microbiology

San Francisco, California

Phage Meetups

  • Friday, June 21, 5-6:30 PM: Division M phage meeting and award ceremony (Division M is the bacteriophage division of ASM); there will be food, drink and phage; room 306/307/308 South
  • Sunday, June 23, 5:30 PM: Adair Borges and others in the Bondy-Denomy lab are organizing an informal gathering for phage enthusiasts at a brewery near the conference venue (location TBA)! RSVP by commenting on Adair’s tweet.

Phage Talks

For more, check out (and add to) this Twitter thread!

  • Carski Award Lecture: Dr. Louise Temple (Saturday, 3:30 PM, S206, room 2018 West)
  • Dr. Paul Turner (Friday, 8:30 AM)
  • Dr. Graham Hatfull on SEA-PHAGES (Saturday, noon, S167)
  • Bacteriophage defense in the era of CRISPR (Sunday, 8:00 AM, S287)

Seeking a guest blogger!

If you’re attending ASM Microbe, we’re looking for a phage researcher to write a guest post for Capsid & Tail about insights/impressions from the conference! Email capsid@phage.directory if you’re interested, and we’ll send you more info! Looking for a draft to be written by mid-July.

Phage Request Research study
Posted 6 months ago

Seeking T4 and T7 phage

Universidad de Panamá

Ednner Emmanuel Victoria Blanco Panama City, Panama

I am seeking samples of T4 and T7 phage for research. Please email me at Ednner@gmail.com if you can help. Thank you!

Seeking references Research support
Posted 6 months ago

Seeking review articles on phage endolysins

Wuhan Institute of Virology

Fazal Mehmood Khan Wuhan, China

I am looking for recommended review articles on phage endolysins. Please send them to fazalmehmoodhu@hotmail.com. Thank you!

Seeking references Research support
Posted 6 months ago

Seeking references for phage gene loss/genetic drift

University of Warwick

Ellie Jameson

Can anyone help find a reference for gene loss and genetic drift in lab grown phage isolates? I’m sure there must be something published but my search terms aren’t hitting the right publications. (Reply or check out the responses to date on Twitter here).

Phage Request Research study
Posted 6 months ago

Seeking Propionibacterium freudenreichii phages

University of Copenhagen

Paulina Deptula Copenhagen, Denmark

Does anyone have access to phages infecting Propionibacterium freudenreichii? I’m trying to isolate my own, but in the meantime I’d like to start testing defence systems with any phage I can get. Please email me at paulina.deptula@helsinki.fi!

Phage Request Anticipating phage therapy need
Posted 6 months ago

Seeking groups who work with Legionella phages

IPATH

Steffanie Strathdee San Diego, California

Looking for #phage against #Legionella, in anticipation of an urgent request for #Phagetherapy for a patient in #HongKong whose family reached out @IPATH. If you have #bacteriophage against any Legionella strains, please DM me on Twitter at @chngin_the_wrld.

Phage Request Research study
Posted 6 months ago

Seeking Vibrio natriegens phages

University of South Florida

Mya Breitbart St. Petersburg, Florida

Looking for a lytic #phage capable of infecting Vibrio natrigens (for lab research, not therapy) - can anyone help? Needs to infect well in liquid culture, preferably a myovirus but any dsDNA phage will work. Please message me on Twitter at @virome_girl.

Phage Request Anticipating phage therapy need
Posted 6 months ago

Seeking groups who work with Legionella phages

PhageVax

Clark Tibbs Newark, Ohio

Ohio Department of Health director Amy Acton issued an order to the Mount Carmel Grove City hospital on May 31 to take immediate action to contain an outbreak of Legionnaire’s disease. If anyone knows of anyone working with Legionella phages, please get in touch with Clark Tibbs at cta@ee.net.

Workshop GenomicsViromics
Posted 6 months ago

Register now for the 2019 Evergreen Phage Bioinformatics Workshop

Evergreen International Phage Meeting

Betty Kutter & Evergreen Organizers Olympia, WA

The 2019 Evergreen Phage Bioinformatics Workshop will consist of three tracks: Genomics with Galaxy & WebApollo; Genomic annotation with PATRIC; and Viromics (metaviromics). Participants are invited to register for one of these tracks on Saturday (4 PM – 9PM, 4h of work, with a break for supper), and/or for one of these as repeated on Sunday (8:30 to- 12:00, 3 ½ h). Each track will consist of an introductory lecture followed by hands-on sessions where participants can work on example datasets.

Observers are also welcome in each of the 3 sessions. (Note: Participants need to work on their own laptops; no computers will be provided.

We will plan on having a van pool for people arriving Saturday morning. For people taking part in the Saturday workshop, there will be an extra $10 fee from Evergreen for using their facilities.

The 3 tracks are:

  1. Genomics – Annotation: with PATRIC (Ramy Aziz & PATRIC people): Phage annotation using RAST and PATRIC. This track is suitable for beginners.

  2. Genomics - Phage genomics: with Galaxy and WebApollo (Jason Gill): This track will cover the start-to-finish process of whole-phage genomics, including DNA sequencing, assembly, end determination, annotation, and comparative genomics using the user-friendly interfaces Galaxy and WebApollo. This is suitable for both beginner and intermediate users. There will be a limited number of participants for people doing their own genomes, but the 2 hour lecture is open to all, the hand-on portion can handle about 15 people working on their own genomes.

  3. Viromics – (Alejandro Reyes & Evelien Adriaenssens): introduction to sequence pre-processing, clean-up, and assembly using command-line tools; visualization of data. Suitable for users who know how to navigate a command-line environment.

Register here for the Genome Workshops!

And if you haven’t yet registered for the Evergreen phage conference itself (Aug 4-9), register here!

Seeking environmental samples Phage Isolation
Posted 6 months ago

Seeking soil samples for phage isolation

Center for Phage Technology

College Station, Texas

Howdy phage enthusiasts! The Center for Phage Technology is currently seeking out new environmental soil and water samples for phage isolation! Direct message the CPT on Twitter if there’s something you’d like to send! We’ll cover shipping and can even send you a kit to get started! #phage #science #savingtheworld #CitizenScience

Collaboration Request Phage Consortium
Posted 7 months ago

IBRC Community Update: New web design, a documentary, and new members welcome!

International Bacteriophage Research Consortium

The IBRC portal is inspired by the global antibiotic resistance situation & the promising potential phages offer as credible antimicrobial therapeutics.

Launched in October 2018, IBRC is a joint effort by Acharya Narendra Dev College (ANDC), University of Delhi, India and Open Health Systems Laboratory (OHSL), USA to build a consortium of scientists working on phages and lysins.

If you’re a phage scientist/scholar, a medical or industry professional, or a phage therapy supporter interested in joining the consortium, contact Dr. Urmi Bajpai at urmibajpai@andc.du.ac.in or at ibrc.pt2018@gmail.com, or tweet @phageconsortium.

To help promote AMR awareness, and prior to launching the IBRC, Dr. Bajpai created a short docu-drama film on AMR and phage therapy (10 min), which will be soon dubbed in other languages too. In it, you’ll hear from Pranav Johri of Vitalis Phage Therapy and Mzia Kutateladze, the director of Eliava Institute.

Phage Request ProphageSalmonella
Posted 7 months ago

Seeking temperature-inducible P22 prophage

José R Penadés

Glasgow, UK

Phage community, I need your help! I’m desperate looking for a P22 prophage that is inducible by temperature (P22 ts c2 29). It was published more than 50 years ago. If you know somebody that could have it, please, contact me at JoseR.Penades@glasgow.ac.uk! If not, please pass it on! It is really important! Thanks!

(Check out his twitter thread (@jrpenades) to see responses so far, or to add yours!)

Phage Request Phage typing Research study
Posted 7 months ago

Seeking phage typing collections

Michael Koeris

I’m looking for phage typing collections of Enterobacteriaciae (eg. E. coli, Klebsiella, Salmonella) to pursue capsular variant-phage type correlation studies. Please email me at mike@aresinnovation.com or tweet @mkoeris to get in touch!

Collaboration Request Sequencing
Posted 8 months ago

Seeking collaborator for phage and host sequencing

University of Haripur

Irshad Ul Haq, PhD, Assistant Professor,
Khyber Pakhtunkhwa, Pakistan

We are seeking help/collaboration on phage and host sequencing. We don’t have any resources to do the sequencing of these, and therefore would like to connect with someone who would want to collaborate. Please email me at irshadulhaq85@gmail.com.

Workshop Phage
Posted 8 months ago

Thank you to participants of the 2019 Latin America Phage Workshop

Ednner Emmanuel Victoria Blanco

Thank you to all the students from Latin America for participating in this 2019 phage course, and special thanks to Martin Loessner and Alejandro Reyes for the amazing lectures and workshop. Hope to see you all soon!

Phage Directory New VolunteersAnnouncement
Posted 8 months ago

Welcome, new volunteers!

Phage Directory

We have our first Phage Directory volunteer! Cathy Nguyen will be helping with Capsid & Tail’s What’s New and Jobs section. We also welcome our first guest writer this week, Lucy Furfaro!

If you’d like to help (or be kept up to date on other volunteer opportunities), email volunteer@phage.directory. If you’d like to contribute a guest article, email capsid@phage.directory for details.

Phage Hunt Phage TherapyVeterinary MedicineCanine
Posted 8 months ago

Seeking Pseudomonas phages for a canine ear infection

Phage Directory

Miami Beach, Florida

We are seeking Pseudomonas aeruginosa phages to treat a dog’s antibiotic-resistant ear infection. Please get in touch with us by email at staff@phage.directory if you are willing to test your phages on the dog’s strain, or to send phages on behalf of this dog.

Phage Directory Update
Posted 9 months ago

Many thanks for helping with the seaturtle

On New Year’s Eve, we got a request for Citrobacter phages to treat a sea turtle’s antibiotic-resistant shell infection. If you can help, please email staff@phage.directory!

Update:
THANK YOU to the labs of @GroseLab of BYU, @RandallJDeJong and @insectmicrobejr of Calvin College, @phage4lyfe of MSU, @BryanGibb2 of NYIT, and Ben Chan of Yale for offering to supply/test phages so far!

Thanks also to @chngin_the_wrld and @phagehunter of @ipath_ucsd for helping coordinate efforts!

Lastly, thanks to the 200+ people on Twitter who’ve helped spread the word about this turtle to 20,000+ people and counting!

Collaboration Request Phage BiocontrolPhage Therapy
Posted 9 months ago

Seeking collaborators and guidance for phage research

IZSLT

Raniero Lorenzetti
Rome, Italy

Our group is looking to begin isolating and characterizing phages, first against fish pathogens, mainly at the molecular level. In the future, we will seek to exploit phages to control many animal pathogens. We are seeking help and support from phage experts during the learning curve process. I would also be very grateful if a phage lab could host me as a visiting scientist for a few days, to help me get acquainted with the process of phage manipulation. Please contact me at raniero.lorenzetti@izslt.it to talk about this further.

Seeking environmental samples AMRPhage IsolationPhage Therapy
Posted 9 months ago

Seeking environmental samples for phage hunts!

IPATH

Steffanie Strathdee
San Diego, CA

Want to help #phagetherapy patients? Our collaboration between @IPATH & @TAMU_CPT needs environmental samples for #phagehunts! You can help by sending soil samples to @TAMU_CPT. Message Steffanie Strathdee (@chngin_the_wrld) on Twitter for details and may the #phage be with you! #AMR #superbugs #AntibioticResistance

Seeking opportunity Medical microbiologyPhage Therapy
Posted 9 months ago

Seeking postdoctoral opportunity in medical microbiology / phage therapy

Vellore Institute of Technology

Prasanth Manohar

I have completed my Ph.D. at Vellore Institute of Technology, Vellore, India. My research project deals with the characterization of bacteriophages infecting E. coli, K. pneumoniae and Enterobacter species. I have expertise in working with carbapenem-resistant clinical bacteria and studying the antibacterial activity of phages in vivo. In the future, I am looking forward to do my post-doctoral research in the field of Medical Microbiology, especially phage therapy. Please email me at prasanth.emsa1@gmail.com if you know of opportunities!

Seeking guidance Phage IsolationLab tips
Posted 10 months ago

Seeking tips on how to isolate P. larvae phages

Massey University

Heather Hendrickson
Auckland, New Zealand

Phage Friends! We need help! We have processed over 300 soil samples looking for phages on Paenibacillus larvae… (the bee pathogen) here in NZ. Have you ever looked SO HARD for a phage and not found one? Suggestions? Ideas? Sympathy? PLEASE? (Bonus: check out all the tips the phage community has already shared via Twitter!)

Phage Request Phage TherapyVeterinary Medicine
Posted a year ago

Update: Citrobacter phages for sea turtle

Phage Directory

We are still seeking Citrobacter phages to treat a sea turtle’s antibiotic-resistant shell infection. If you can help, please email staff@phage.directory!

Progress so far:
Good news! At least one phage active against the turtle’s Citrobacter strain has been found, and the FDA has given its approval to proceed with getting phages ready for this case.

Collaboration Request Phage Therapy
Posted a year ago

Seeking collaborators and guidance for new phage therapy center

Tribhuvan University

Gunaraj Dhungana
Kathmandu, Nepal

My name is Gunaraj Dhungana, I’m a Ph.D scholar from the central Department of Biotechnology, Tribhuvan University, Nepal. We have been working on the characterization and preparation of a phage bank to establish a phage therapy centre in Nepal. We are seeking collaborations and guidance to establish the centre. Please email me at grdhungana79@gmail.com if you are willing to offer advice or would like to talk about collaborating.

Seeking opportunity Phage PhD project
Posted a year ago

Seeking PhD opportunity

Silviane Miruka

I am a student seeking a PhD opportunity in a phage lab. I recently did a project for my master’s thesis titled “Molecular Detection of Pathogenic Staphylococcus aureus Using Phage Based Genetic Markers.” Please email me at silvianejoash@gmail.com or find me on Twitter @m_silviane if you know of any opportunities.

Seeking opportunity Phage PhD project
Posted a year ago

Seeking PhD opportunity

International Centre for Diarrhoeal Disease Research

Mahmuda Akter

I have been working at the International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b) and earned my M.S. degree from the University of Dhaka in Bangladesh. I was awarded joint funding from icddr,b and SIDA to isolate and characterize Shigella phages. I have isolated more than 100 Shigella phages, characterized their host ranges and sequenced some of these in collaboration with Martha Clokie and Nathan Brown. I have 10 publications as a co-author and have shared my data at two international meetings: VoM (2012) and Evergreen (2015). Please email me at mahmuda@icddrb.org if you know of opportunities.

Request for donations NonprofitLab SuppliesDonation Request
Posted a year ago

Seeking micropipette donations

Phages for Global Health

Tobi Nagel
Oakland, CA

Hi phage community! Do you have any old micropipettes that you’re ready to get rid of? If so, Phages for Global Health regularly needs micropipette donations for our laboratory training workshops in Africa. We could use any sizes 10 - 1000 uL. Please email me if you have any donations or questions: tobi@phagesforglobalhealth.org.

Seeking guidance BioinformaticsPhage GenomesMentorship
Posted a year ago

Seeking help with phage genome bioinformatics

Tribhuvan University

Gunaraj Dhungana
Kathmandu, Nepal

My name is Gunaraj Dhungana, I’m a Ph.D scholar from the central Department of Biotechnology, Tribhuvan University, Nepal. We have sequenced the whole genome of four lytic phages against carbapenem-resistant and colistin resistant clinical isolates like Klebsiella pneumoniae, Acinetobacter baumannii, Salmonella spp and Pseudomonas aeruginosa by next-generation sequencing using Illumina platform. I am searching for help/advice/mentorship with the bioinformatic analysis of sequenced data. Please email me at grdhungana79@gmail.com.

Seeking phage data BioinformaticsPhage GenomesAI
Posted a year ago

Seeking complete phage genome sequences with lytic/lysogenic labels

Piotr Tynecki

I’m working on a deep learning-based analysis of phage genomes considering their lytic/lysogenic potential. I’m looking for complete phage genome sequences in FASTA format with lytic/lysogenic labels that have been confirmed by domain experts. Email Piotr at piotr@tynecki.pl or tweet @ptynecki if you can help!

Phage Request Phage Immunity Systems
Posted a year ago

Seeking diverse Salmonella phages

Harvard Medical School

Sian Owen
Cambridge, MA

I’m a postdoc at Harvard Medical School researching a novel phage-immunity system in Salmonella enterica sv. Typhimurium. I’m looking for characterised (and ideally genome sequenced/published) phages infecting S. Typhimurium to test against the system. So far I have the phages P22, BTP1, det7, 9NA and FelixO1, but I would really like some more diverse Salmonella phages, particularly those that adsorb to non-LPS receptors. Note: other collaborators in this project are located in the UK, so I am looking for people who could send phages to either the US or the UK. Email Sian at sian@hms.harvard.edu if you can help!

Phage Directory Update
Posted a year ago

Welcome to Phage Directory, new labs!

Check out the 17 new labs we just added to Phage Directory! We just made our signup process faster, so if you’ve thought about signing up your lab, now’s the time!

Seeking opportunity AquaculturePhage PhD projectPhage Therapy
Posted a year ago

Seeking PhD opportunity

Pukyong National University

Muhammad Akmal

I am Muhammad Akmal, working as a Lecturer at the Department of Fisheries and Aquaculture, University of Veterinary and Animal Sciences, Lahore, Pakistan since July 2014, where I also received my Bachelors and Masters degrees in Fisheries and Aquaculture. I am now pursuing a second Masters in Fisheries Science at Pukyong National University, South Korea (ends Feb. 2019). Previously I worked on isolation and characterization of fish pathogenic Aeromonas hydrophila for the possible control of motile aeromonas septicemia in fish. Now I am searching for a PhD position in phage therapy-related aquaculture. I am open to any available opportunity where I can learn more about the phage therapy, especially in control of disease in aquaculture. Please email Rana at muhammad.akmal@uvas.edu.pk if you know of any opportunities.

Phage Hunt Phage TherapyVeterinary Medicine
Posted a year ago

Seeking Citrobacter phages for a sea turtle

Phage Directory

On New Year’s Eve, we got a request for Citrobacter phages to treat a sea turtle’s antibiotic-resistant shell infection. If you can help, please email staff@phage.directory!

Update:
THANK YOU to the labs of @GroseLab of BYU, @RandallJDeJong and @insectmicrobejr of Calvin College, @phage4lyfe of MSU, @BryanGibb2 of NYIT, and Ben Chan of Yale for offering to supply/test phages so far!

Thanks also to @chngin_the_wrld and @phagehunter of @ipath_ucsd for helping coordinate efforts!

Lastly, thanks to the 200+ people on Twitter who’ve helped spread the word about this turtle to 20,000+ people and counting!

Phage Directory
Posted a year ago

Community Board Intro

Phage Directory

Have a question or request for the phage community? Post it here and reach > 200 phage enthusiasts spanning academia, industry, medicine, and beyond. Feel free to be creative about what you might ask! (e.g. collaborations, advice, seeking opportunities)

Capsid & Tail

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