Events & Info

If you were wondering where is Maliheh and why is she slower in responding to emails then here is the reason. I was organizing a course that I designed titled "Multi-omics analyses of the microbial community, P000113” for PhD level students at SLU from March 3 to March 14. We had 16 enthusiastic students who made the whole process of teaching and course organization very rewarding for me. I specifically liked the last course activity where we discussed the projects that students designed using multi-omics. It was a great feeling to see them present and defend their ideas and incorporate all the feedback they received! 

In another exchange through our CUALITY project Suhyun visited us at SLU from March 6 to 16th which coincided with the course Maliheh organized titled "Multi-omics analyses of the microbial community, P000113” for PhD level students at SLU. Suhyun joined this course presenting a lecture on March 10 titled “High throughput cultivation the cumbersome golden standard”. It is always fun to listen to what new culture are coming out of their lab and what new experiments are planned. It is a privileged to have a community of culture enthusiast scientists around!

For our MULTIPHAGE project we performed a sampling campaign from January 20 to February 20. This sampling was a long-term big dream of mine and I was really happy that I could bring along my whole team to share this unique experience! We did an under ice sampling and had long sample processing days! Its amazing that it is during these long days that one has to be flexible and a team player I reflect a lot on why is it that I enjoy working on microbial interactions so much! 

We collected and processed 1.3 tons of water from the frozen lake Erken and collected some opportunistic samples as well. Now its time to process all these samples and I am looking forward to see what we can learn from these samples!

On January 7 2025, Lauren joined Bionomics as a PhD student and she will be involved in our MULTIPHAGE project! Lauren is not new to SLU but I had to stage a photo with her at our main building where we get the access card for new employees for the sake of consistency :) 

On December 13th, I ended my working days in 2024 on a high note by attending the Nobel lectures together with Vesna! It was inspiring to see how John Jumper as a young scientist could change the field so clearly in a short time. I loved listening to both talks and learning about aspects of their progress that one can not see in publications. 

To mark the end of 2024, a year we grew three times bigger and dived deep in lake samples and also the end of Fran's visit to Bionomics we tried escape rooms. The great mind team was more successful in escaping and they even achieved the record time for the day! This was a fun activity to increase our teamwork and desire for adventures just before the begging of our MULTIPHAGE sampling in January!

We collect samples every month from Lake Ekoln and use them to isolate bacteria and phages in culture. As it is getting colder access to the lake gets harder but nothing stops Vesna from getting that monthly sample! 

Zahra was sent to the Single-Cell RNA Sequencing Bioinformatics workshop organized by the Earlham Institute in Norwich, UK, from November 11 to 15, 2024. This course focused on the latest advancements in single-cell transcriptomics, covering topics like experimental design, single-cell technologies, bioinformatics, and spatial transcriptomics. This was a great opportunity to learn from experts in the field and gain practical knowledge on how to implement these tools in her research.

In the context of ur STINT project we visited the Inha University and Prof. Cho's lab this year from Nov 2-Nov 9. This time I was joined by Vesna and Vinicius. We have a lot to learn from the Cho lab about cultivation and microbial metabolism and discussed all of these in a meeting where we shared our ongoing works on cultivating freshwater microbes and listened to their work on isolation of novel taxa. Our visit coincided with Dr. Clifton to cho lab and we listened to his great talk about SAR11 proteins! It is always fun to hang out with Jang-Cheon, Yeongjong, Ilnam, Suhyun and rest of the lab!

Maliheh was invited to present at the Conference of the microbiological society of Korea MSK2024, October 29-November 1. This conference was at the beautiful Jeju Island! I presented in the session Microbiome and talked about multipartite parasitic interactions and their impact on gene flow and biogeochemical cycling of nutrients in lake ecosystems. I also presented our results in applying different methods in assigning phages to their bacterial host with high confidence. This conference was really inspiring, I reflected a lot on the talk of Prof. Rhee and about what he presented about the correlation between time and effort with quality and novelty of findings and how he showed major findings of his career in this time-novelty context. Another big highlight was that My dear collaborators Jang-Cheon and Yeonjong were celebrated with career awards! It is always fun to celebrate your friend's achievements! Also Jeju is a really memorable location it found its own spot in my heart. 

We now have a logo, Yay! 

Hoping that this can transfer across my infinite curiosity about multipartite parasitic interactions that is fueling the research in my lab! 

Soon I will write more about the concept behind this design. It is an infinity sign and more! 

Our MULTIPHAGE sampling and cultivation is ongoing. The beautiful colors of this autumn made today's sampling even more rewarding! 

It is always fun to have fellow phage-bacteria enthusiasts around! Fran is doing his PhD at the University of Alicante, Spain and he is visiting use here at Bionomics for 3 months as a part of his PhD stay abroad. We are looking into using metaHiC for connecting freshwater bacteria to their viruses and have lots of exciting conversations specifically when he presented his newly accepted manuscript and ongoing analyses at our team meeting!

Today, August 2nd 2024, is the last day we have Maryam in the Bionomics lab. She is moving on to her new academic adventure. This week I have been reflecting on my time together with Maryam a lot. Our journey started several years ago when I joined her PhD supervision team on January 2017; but I have known her even before that. I dived into my emails and I saw that the first email I have from her dates back to Nov 2012! I had a lecture at their course and she wrote to me asking for some resources on genome libraries. For her PhD thesis we explored the microbial response to oil spill in the Persian Gulf together and as our bond got deeper, our topic of collaboration also got deeper and we have been working on deep groundwater during her PostDoc. 

Over the last 6.5 years we have had weekly online meetings, we have been frustrated on our data and reviewer comments together, we have learned how to work with each other and inspire each other, and we have celebrated the publication of our work together. So many good memories to cherish! I will miss our weekly meetings and closely working together with you and most importantly you! Good that we still have a couple of ongoing submissions and revisions. You will always be a dear member of the Bionomics fam and I’m rooting for you! 

We are developing a time series for our favorite Lake, Lake Erken! Both for sequencing metagenomes and for cultivation! 

On July 1st, 2024 Vesna started her researcher/PostDoc position  in the Bionomics lab!

We had the pleasure of hosting Prof. Stephen Giovannoni (father of SAR11 cultures 🙂) for a visit to our group at SLU. These last 3 days (June 22-24, 2024) were filled with great discussions and lots of learning for me (Maliheh). We had a full room of students and researchers who wanted to hear more about SAR11. Thank you Steve for patiently discussing everything microbes with all of us and for generously sharing your knowledge and perspective!

On June 17th, 2024 (officiallyJune 3rd) Maryam started her short-term research assistant position  in the Bionomics lab!

Maliheh was invited to present at the GRC Marine Microbes, Linking Genes,Rates, and Biogeochemistry in Marine Microbiology from June 9th to 10th 2024.  The conference was at the beautiful Les Diablerets Conference Center. I presented in a session led by Prof. Rachel Foster titled "Microbial Regulation of Marine Nutrient Cycling". My presentation title was "Multipartite Parasitic Interactions in the Aquatic Food Web: Modulating Gene Exchange and Carbon Flow". This conference is supposed to be about unpublished data and it was so much fun to hear such amazing talks and hang out with enthusiastic scientists! I really took a lot out of this conference! The conference is supposed to be off the internet so all photos I post here are from the amazing location :) 

I attended the symposium organized by the Wenner-Gren foundation on "Embracing the Alphafold Revolution: Unraveling the Future of Structural Biology". This was a great opportunity to hear more about what Alphafold can and cannot do from the experts and immerse myself in a new but very influential topic, meet new people and get inspired about how I want to use the Alphafold capacity!

May 2024 has been really busy and lively! We had Vesna here for a week and we worked together on her paper about symbionts of diatoms. Katarina is here to finish her manuscript on cave microbes. Krzysztof 's stay with us at SLU is ending. So we had to take advantage of all these movements and the sunny days and hang out a bit!

Bionomics lab joined the SciLifeLab The Svedberg seminar on monday May 20th given by Prof. Tal Dagan from Kiel University, Germany. She gave a great presentation about "Multilevel drift and selection in the evolution of prokaryotic plasmids". Amazing research and insightful discussions!

On May 2nd, 2024 (officially May 1st) Vinicius started his PostDoc/Researcher position  in the Bionomics lab!

Jonna is doing her PhD at the University of Turku in Silke Van den Wyngaert's group. She visited us at SLU from March 18th to April 12th to work on her metabarcoding datasets. It was really nice having her around! In addition to working on her very interesting datasets and listening to all the interesting plans she has for her PhD, we had a long walk from Ultuna to the center together to hang out and discuss many things science and non-science as well as a group dinner where we ended up reflecting on why does one do a PhD. Maybe this is something we do for ourselves! 

Krzysztof will spend the whole spring semester with us at SLU and Katarina was here from February 7 to 23rd. It is always nice to have discussions with both of them and an excuse for a movie night at the MVM kitchen!

We had the opportunity to attend the Nobel Lectures at the Uppsala University on December 13th. We attended the lecture by Dr. Katalin Kariko (University of Szeged, Hungary and Perelman School of Medicine, University of Pennsylvania, USA); the Nobel Laureate in medicine and physiology. Her lecture was amazing and at the end Katalin shared a final note to students. I Don't remember it word by word to quote it here but the message I took home was to take care of your mental and physical health. Learn how to manage bad stress but also remember that there is a good type of stress that inspires you to wake up in the morning and chase what you want to achieve. Good stress is good and we need to learn how to manage our bad stress. 

On November 21st, 2023 Zahra started her PhD in the Bionomics lab!

Lead scientific organizer: Maliheh Mehrshad

Bringing all these people together to discuss the potential of big data in microbial ecology has been on my mind for a while! It was a great 2 days event where we heard cutting edge research from top notch researchers in the world and in Sweden. This event was organized via the support of Aquatic Microbiome Research Initiative  (AMRI) and specifically Caroline was a great support in organizing this mini-symposium in connection to the last AMRI day on November 8th. On the AMRI day we also had Francisco Rodrigues Valera as a keynote speaker. Here is a link to the AMRI webpage (hopefully the links will stay active after the initiative is no longer funded)

November 9th - BiD-in-ME DAY1

9:00-9:15 Maliheh Mehrshad 

Welcome to Big Data in Microbial ٍEcology

9:15 – 9:30 Maliheh Mehrshad

Big Data in Microbial Ecology: a data overview in the AMRI network

9:30 – 10:30 Shini Sunagawa

The Ocean Microbiome as a Treasure Trove for the Discovery of new Taxa, Enzymes and Bioactive Compounds

10:45 – 11:45 Carolina Whalby

AI as a tool in large-scale microscopy-based life science research

13:00 – 13:40 Anders Andersson

What microbes are there, what can they do, and what do they say about the environment? - How we address these questions with machine learning

13:40 – 14:40 Tove Fall

Operational aspects and scientific outcomes of the large-scale GUTSY project characterizing the microbiome in 9,819 participants

15:00 _ 16:00 Holger Villwock & Jonathan Thiry (SITES)

SITES and FAIR – an example on organizing distributed field based research data 

16:00 _ 16:45 Discussion session I: Where are we headed with the next data-driven wave in microbial ecology? 

16:45 _ 17:00 Maliheh Mehrshad, Discussion recap

November 10th - BiD-in-ME DAY2

9:00 – 10:00 Artem Babaian

Entering the Platinum Age of Virus Discovery: Why the next 5 years will shape Virology for the next 5 decades

10:00 – 10:40 Ulisses Nunez da Rocha

Genome-scale metabolic modelling of over 60 thousand genomes reveals phylogenetic conservation of r/K-strategies within the archaeal and bacterial phylogenetic trees

11:00 – 11:40 Amrei Binzer-Panchal (SLUBI)

Practical considerations and available support for big data science

13:00 – 13:40 Stefanie Prast-Nielsen

The intestinal microbiota, plasma bile acids and inflammation markers in inflammatory bowel disease

13:40 – 14:05 Mohamad Bahram

Recent insights into soil microbial biogeography

14:30 – 15:45 Discussion session II: How to preapare for the big data era as a microbial ecologist? 

15:45_ 16:00 Maliheh Mehrshad, Discussion recap and closing remarks

In combination with the Big Data in Microbial Ecology mini-symposium, Suhyun and Yeonjung also visited us in Uppsala. An aim of our STINT mobility grant is to meet the local microbial ecology researchers both in Sweden and in South Korea; and this mini-symposium was a perfect opportunity for that! We also had the chance to see the festival of light in Uppsala. It was great hosting Suhyun and Yeonjung in Uppsala again and I am looking forward to more possibilities to hang out in future! 

Maliheh attended the Local pangenome 2023 conference in Alicante, Spain. This event had an impressive line up of speakers and presentations were full of inspiring new findings! I presented a speed talk about my aims and plans for MULTIFAGE, my ERC-StG. I met people who are running very interesting research and got super inspired by all the interactions! It is always fun to be back to Alicante!

During the visit of our Japaneses partners via the Formas SDG networking grant to SLU, Maliheh organized a visit to the SLU fish hatchery station in Alvkarleby on September 4th. We were lucky because the dam was open and we could see amazing views of the running river! We saw how salmons are trapped, mainly because of their love for going upstream, and different stages before young fish are released. Grateful to the researchers based at the station for showing us around!

During the visit of our Japaneses partners via the Formas SDG networking grant to SLU, Maliheh organized a discussion and talk session on August 30th, 1-5 pm. We had interesting talks from different groups. Here is the program and titles of the talks:

13:30 - 14:00 Kenta Okamoto, Uppsala Unviersity,

Primordial and acquired structures of icosahedral viruses in evolution

14:00 - 14:30 Nhat Ton Nguyen, SLU

Aquaculture: Potential monitoring and early detection by portable sequencing

14:30 - 15:00 Yuji Tomaru, FRA

Ecological relationships between diatom and its infectious viruses

15:30 - 16:00 Nanako Nakashuma, Saga Unviersity

Detection of DNA molecules associated with DNA viruses infected to the diatom Chaetoceros tenuissimus

16:00 - 16:30 Kazuhiro Yoshida, Saga Unviersity

Low-Fe availability reduces the photosynthetic competency of ice algae upon discharge from sea ice

16:30 - 17:00 Closing Remark and Open Discussion

Through our FORMAS SDG networking grant our Japanese colleagues  visited us in Uppsala from August 24 to September 6th, 2023. They spent some days with Kenta at Uppsala University and some days with Maliheh at SLU. During their stay at SLU we showed them around the campus, our department and lab spaces. We also organized a talks/discussion session and visited a SLU fisheries station. We also had two days of workshop on metagenome analysis and demonstration of different analyses pipelines enabled by this method. We also discussed future collaboration plans and ideas!

During our STINT visit to South Korea, Cho lab organized a workshop with a great line up of speakers! This workshop was organized at the beautiful Konjiam Resort, close to Seoul. Here is the program for all these talks!

Microbial Ecological Study by Korea (Inha Univ)-Sweden Research Cooperation

October 4th

13:00 – 13:10 Jang-Cheon Cho, Inha University

Opening Remark&Introduction  

13:10 – 13:35 Stefan Bertilsson, SLU

New perspectives on pangenomes and intra-species diversity in freshwater bacteria

13:35 – 14:00 Yeonjung Lim, Inha University

Isolation and genomic study of marine SAR202 bacteria          

14:00 – 14:20 Maliheh Mehrshad, SLU

Understanding microbial parasitic interactions in the aquatic food web 

14:20 – 14:40 Rajeev Meora, Inha University

Metagenomic insights into the biofloc aquaculture system         

Recent Advances in Microbial Ecology

15:00 – 15:25 Martin Steinegger, Seoul National University

From protein sequence to structure   

15:25 – 15:50 Hwan Su Yoon, Sungkyunkwan University

Genome adaptation to extreme environments in red algae          

15:50 – 16:15 Sung-Keun Rhee, Chungbuk National University

Anaerobic growth of methanotrophs coupled with N2O reduction       

16:15 – 16:40 Woo Jun Sul, Chung-Ang University

Epigenetic Landscape of Marine Microbiome and Freshwater Antibiotic Resistome  

16:40 – 17:05 Mincheol Kim, Korea Polar Research Institute

Spatiotemporal dynamics of dissolved organic matter compounds and microbial communities in an Arctic glacier foreland along a 100-year-chronosequence         

17:05 – 17:25 Woojun Park, Korea University

Collective defense within the bloom-forming Microcystis aeruginosa phycosphere   

17:25 – 17:30 Closing remarks & photo time

October 5th

10:00 – 11:00 Discussion forum for future aspects in microbial ecology

11:00 - 13:00 Walk in Hwadam Forest

Maliheh and Lauren visited the Cho lab at Inha university, South Korea as a part of our CUALITY STINT project. This visit was a great experience. We learned a lot about high throughput cultivation and all the amazing research going on in the Cho lab. Stefan also joined us in the middle of this visit for some days. This visit was a combination of cultural and scientific journey!

Cho lab also organized a workshop in line with our STINT visit. In this workshop we got to hear about the microbial ecology research ongoing in different groups in the South Korea. 

From June 26th to July 7th, 2023, we went to catch a bloom in the Baltic Sea. Silke, Jonna, Lumi and I went to the Uto Island in Finland and sampled the development and collapse of a bloom. If you want to know more about this exciting sampling adventure check out this Twitter/X thread. 

Carlotta defended her thesis on June 14th 2023! She did a great job presenting her work and defending it during the discussion sessions! Here is a link to her thesis online. 

I joined her supervision team in the middle of her PhD and we did 2 really nice studies together. One is already published and the other one will be submitted soon. 

Carlotta organized a defense party and she cooked for the whole department. It was a very fun night and I am very proud of her academic journey!

At the first day of our visit to the Saga university we had a discussion session where Aliecha introduced our department and our campus at SLU and then Maliheh talked in detail about "Integrating high-throughput multi-omics analyses with experimental strategies to understand parasitic interactions in the aquatic food web". Anna talked about their methods and results in studying viral structures. Then Kazu presented his work on a time series samples from an undesirable bloom and organized a taste test so we can fully understand the difference between a good sea weed and a less optimal one. 

I should look in my emails and find the program and the talk titles. 

Maliheh and Aliecha traveled to Japan and visited Kimura Lab at Saga university. This visit was in the context of our Formas SDG networking grant. In this trip we were accompanied by our collaborators from Uppsala University (Kenta (PI), Anna, Diogo, and Han).  

During this visit we had several samplings including a sampling day at the Ariake Sea. No networking activity is better than putting everyone in the same boat and giving them tasks to do as a part of the sampling team! We also visited multiple fishery organizations and  learned a lot about sustainable methods used in these organizations. Maliheh saw mudskippers for the first time and tried so hard to take a good photo of them but they are sharp and immediately jump back into their nest.

We isolated phytoplankton from the samples we collected. We also did virus isolation experiments. We worked at the amazingly organized lab of Prof. Kimura and witnessed his skills in picking up phytoplankton cells under the microscope. 

Fun fact: Prof. Kimura had many unique and exquisite equipment in his lab that were specifically designed by him and his father to fully fit the needs of his lab!

Isabell and Connor (based at IOW in Germany) spent the first week of January 2023 in Uppsala! I showed them the RNA extraction protocol I have optimized for phytoplankton and their microbiome. We also tested some new kits and finally decided to use our optimized method to extract RNA from the experiment we ran in March 2022. It was a nice week and we got to spend long days in the lab and immerse ourselves in RNA extraction and measurement! 

Carolina visited Maliheh in December 2022. We worked together on getting Carolina started on working on her project studying the global deep groundwater microbial community. Carolina is based at the Dopson group in linnaeus university. 

You might wonder what it means to become a docent? Its an academic evaluation in Sweden. In most Swedish universities one would need to pass this evaluation in order to be able to be assigned as the main supervisor for PhD students. It evaluates a researcher's independence, research vision, pedagogy qualifications and vision, teaching experiences and skills, and supervision experiences. It goes through external evaluation and the final step is a lecture. I presented my lecture with the title of; yes you guessed it right, my favorite one "Integrating high-throughput genomic analyses with experimental strategies to understand parasitic interactions in the aquatic food web" on September 19th 2022. 

Here is the popular summary of my lecture

Maliheh was invited to present at the LRUA22 Long-Read Sequencing, Uppsala, October 31 – November 2, 2022. This meeting was happening in the iconic main building of the Uppsala university. The aim was to showcase how we can empower our research with long-read sequencing technologies. This meeting was right after a very intense deadline so it was fun to hang out with researchers from different fields who are using similar methods. Here is a link to the LRUA2022 program. 

Maliheh went to ISME18 in Lausanne, Switzerland. I presented my work on Limnohabitans phages and  met many people. Sarahi and I reflected on many things during this conference and shared our thoughts on one of them in this twitter thread.

Cho lab also joined the ISME18 and we had more time to hang out and meet the extended team!

For the first mobility visit in the context of our STINT mobility grant, Jang Cheon Cho and his lab visited us at SLU from August 7th to 12th. This visit was in connection to us attending the ISME18. We showed them around the lab and our SLU campus. We also visited the single cell facility and NGI at Scilife Lab. We also organized a brainstorming session where we talked about science, heard about ongoing projects in the Cho lab and discussed ideas for our CUALITY project and future collaborations. 

July is usually a calm month in Sweden when everyone leaves on summer break but those who stay know we get to really progress in the work front and at the same time have the most fun! I was in Uppsala this year and had a great time with Maryam (Maryam is based at the Dopson group in linnaeus university) and Katarina (based at the Institut Ruđer Bošković, Croatia) working on deep groundwater and cave microbial community! Both these papers will be submitted soon!

Maliheh and Silke (based at Turku University) visited Isabell at IOW from March 4 to 15th, 2022. We ran an experiment together to better understand different aspects of chytrid infection and its impact on the host and its associated microbiome. We pulled off late night lab work sessions and picked hundreds of infected and non-infected hosts under the microscope. Isabell and her team are hard at work to extract data from this experiment and its samples!

Lead scientific organizer: Maliheh Mehrshad

This virtual event was organized on November 17 and 18, 2021, as a part of our STINT grant. DICE is an abbreviation for Dynamic Interface of Cultivation and Environmental omics.  

We had a great list of speakers working at this interface in Bacteria, Archaea, viruses, and microeukaryotes. We had a discussion after each session where we brainstormed on the future of research at this interface. We had  157 registrations and a fluctuating number of attendees but on average 100 researchers were present at each time.