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SKAN Research Trust, promoted by Indian entrepreneur Mr. Ashok Soota, and UK-based Quadram Institute Bioscience today announced that they will apply the cutting-edge TraDIS-Xpress platform to study the action of traditional medical compounds on bacteria, thereby aiding in the reformulation and development of novel antibacterial regimens. TraDIS-Xpress is Quadram’s proprietary genetic sequencing platform that is in the forefront of efforts to uncover new antimicrobial agents and develop better prebiotics and probiotics for health promotion. The joint study titled the Application of TraDIS-Xpress in Microbiology for Healthy Living will be led by Quadram Principal Investigator, Prof.  Mark Webber and SKAN’s Deputy Director, Dr Yogesh Shouche. The project is part of a larger Comprehensive Partnership Agreement between the two organisations that have ongoing international collaborations focused on gut health and developing gut microbial therapies to alleviate ageing and neurological diseases like Parkinsons. An important aspect of the international collaboration is sharing the latest technologies in the study of the gut microbiome to augment Indian research capabilities. As part of this study, SKAN researchers will be trained on the TraDIS Xpress platform at the Quadram Institute in Norwich Research Park. This will facilitate the generation of data from large Indian cohorts that will aid in the development of India-specific therapies. Such data generation is also expected to hasten the TraDIS-Xpress platform's development and amplify its applications' scope. Prof. Ian Charles, Director of Quadram Institute Bioscience, said, “I’m excited to see the cutting-edge genomic technology and expertise we have here in Quadram supporting our valued partners at the SKAN Research Trust to benefit the health of the people of India, and also further our fundamental understanding of the links between microbes and human wellbeing.” Mr. Ashok Soota, Chairman & Managing Trustee of SKAN, said, “The research on novel microbial therapies raises our collaboration with QIB to a whole new level. We are grateful to Ian Charles for including SKAN as a partner in this transformational initiative.” Prof. Mark Webber, Group Leader, Quadram Institute Bioscience, said, “This project highlights the potential of the TraDIS Xpress platform for identifying and understanding the genetic basis behind bacteria’s enormous capacity to adapt for survival. I’m looking forward to helping our colleagues in India deploy it to support their research.” Dr. Yogesh Shouche, Deputy Director, SKAN, said, “The three-year project will also study the mechanisms of drug resistance for key pathogens relevant to India and the action of selected food additives used in India on the growth of selected gut microbes.” About SKAN Research Trust SKAN is a Bengaluru-based not-for-profit medical research trust that leverages transformational technologies to develop new therapies for ageing and neurological ailments, cardiovascular diseases, diabetes remission and lifestyle related disorders. SKAN applies its expertise in gut microbiome, genomics, stem cells, molecular biology, biomarkers, immunotherapies, nutrition, and alternate therapies to uncover kinder and gentler treatment protocols for ailments. Bioinformatics at SKAN vigorously pursues cutting edge, artificial intelligence, machine learning and other advanced technologies to predict, pre-empt, diagnose, treat, and facilitate remission of medical disorders. The Mission statement of SKAN is "Transform the future of medicine.  Impacting millions of lives". About Quadram Institute Bioscience Quadram Institute Bioscience is a UK national science capability, strategically funded by the Biotechnology and Biological Sciences Research Council, and its mission is to deliver healthier lives through innovation in gut health, microbiology and food and its vision is focused on understanding how food and microbes interact to promote health and prevent disease. Interconnected research themes at the Quadram Institute on the Norwich Research Park, UK, deliver a pipeline of research in plants, microbiology, food, and health: microbes and food safety; the gut microbiome; and food innovation. About TraDIS-Xpress TraDIS-Xpress (transposon-directed insertion-site sequencing) is a high-resolution whole-genome assay that identifies which genes are likely to affect bacterial fitness in any given condition. This uses extremely dense, highly saturated mutant libraries to identify fitness differences at base pair resolution. TraDIS-Xpress improves upon conventional transposon mutagenesis approaches through the use of outward-facing promoters. This allows the investigation of how gene expression, as well as gene deletion, affects bacterial fitness under a given growth condition. Additionally, it allows the investigation of essential genes that cannot be inactivated and therefore cannot be assayed by other approaches.

UK-based Quadram Institute Bioscience and SKAN Research Trust, promoted by Indian entrepreneur Mr Ashok Soota have entered into a Comprehensive Partnership Agreement to collaborate on research programmes focused on gut health and developing therapies that alleviate ageing and neurological diseases. [caption id="attachment_28840" align="alignright" width="400"] Prof Ian Charles and Mr Ashok Soota signing the Comprehensive Partnership Agreement[/caption] Areas of interest in common:  The Quadram Institute Bioscience (QIB) and SKAN Research Trust direct considerable research resources towards addressing gut health and the gut-cardiovascular and gut-brain axes. Important areas on which QIB and SKAN will collaborate under the terms of the Comprehensive Partnership Agreement include: undertaking joint research projects in UK and India for the development of microbiome-based products that promote human health and treat neurological and age-related ailments; technology transfer between the organizations to augment cutting-edge Indian research capabilities; training of young Indian research scientists with Quadram Institute Bioscience and study of large Indian population cohorts to develop India-specific therapies that alleviate ageing and neurological diseases. Prof. Ian Charles, Director of Quadram Institute Bioscience, said, “Our agreement with SKAN Research Trust signals important new collaborations between scientists in the UK and India and underlines our global reach in terms of research into the gut microbiome, gut-brain axis and human health.” Mr Ashok Soota, Chairman & Managing Trustee of SKAN, said, “We are delighted to be collaborating with Quadram Institute Bioscience, one of the global leaders in the field of gut microbiome research, particularly the gut-brain axis. The first project QIB and SKAN will undertake in terms of the Comprehensive Partnership Agreement will be “Microbiome-based Therapies to Alleviate Symptoms of Parkinson’s Disease.” [caption id="attachment_28842" align="alignright" width="400"] (L-R) Prof Arjan Narbad, Prof Ian Charles, Mr Ashok Soota. Mr Davis Karedan (SKAN Chief Operating Officer/Trustee) & Dr Graeme Brown (Quadram Institute Bioscience Chief Business Officer)[/caption] Prof. Arjan Narbad, Professor of Translational Microbiome, Quadram Institute Bioscience, said, “This exciting new collaboration will accelerate our common research in modulation of the human gut microbiome for health benefits with particular focus on the Parkinson’s disease for which currently there is no cure.” Dr Yogesh Shouche, Group Head, Gut Microbiology Research Division of SKAN, said, “We look forward to gaining from Quadram Institute Bioscience’s expertise in gut health research. We at SKAN hope to add value to the project findings by bringing in cohorts exposed to different environment conditions and diets.” Prof Arjan Narbad, Group Leader, Translational Microbiome at QIB and Dr Yogesh Shouche, eminent gut microbiologist of SKAN will be the principal investigators of this research project. The India leg of the research project will commence once necessary approvals are secured from the Government of India. About SKAN Research Trust SKAN is a not-for-profit medical research trust focused on transformational technologies that will alter the future of medicine through the discovery of new therapies. SKAN’s areas of expertise include gut microbiome, human genomics, stem cells, and transformational artificial intelligence applied to areas of ageing and neurological ailments to achieve breakthrough therapies.

Professor Arjan Narbad from the Quadram Institute on the Norwich Research Park has received a prestigious award by China’s Jiangsu Province. The competitive award is presented to foreign nationals who have made significant contribution or formed successful collaborations with Jiangsu Province. Arjan was nominated by Jiangnan University, with whom he has helped to establish the UK-China Joint Centre for Probiotics Research. [caption id="attachment_17468" align="alignright" width="612"] Gareth Taylor, Prof. Chen Wei, Prof. Arjan Narbad, Bronte Zhang[/caption] The award was presented by Professor Chen Wei, the Vice President of Jiangnan University, in the presence of Gareth Taylor, Consul Science and Innovation, British Consulate-General Shanghai and Bronte Zhang, Senior Science and innovation Officer, British Consulate-General Shanghai. The award highlights the success of the long term collaboration between the Quadram Institute and Jiangnan University. The two organisations initiated the UK-China Joint Centre for Probiotics Research in 2016, supported by the Newton Fund. The centre builds on and strengthens efforts to understand the gut microbiome, the community of trillions of microorganisms that inhabit our gut. Both Jiangnan University and the Quadram Institute have major programmes to understand the links between the microbiome and health, and are investigating ways to maintain a healthy microbiome, through probiotics, diet or other interventions. The collaboration continues to bear fruit. A recent publication presented joint research that uncovered insights into the varying ability of different strains of probiotic bacteria to restore a healthy microbiome following antibiotic treatments. In population, Jiangsu is similar to Germany and its GDP per capita of is roughly double the average for the rest of China. Jiangsu ranks first in China’s provincial innovation rankings. This has attracted a number of UK universities to set up presence in Jiangsu, and UK industry are also establishing themselves in the province. AstraZeneca opened a large R&D and manufacturing facility in Wuxi, where Jiangnan University is located, and the UK’s Graphene Lighting Ltd built a factory in Nanjing.

"My road to science was nothing short of a roller coaster. I completed my PhD at the National Centre for Biological Sciences in India. My scientific pursuit to understand the most abundant entity on earth called bacteriophages - a virus that kills bacteria - began in UK at the University of Liverpool in 2020. Now at the Quadram Institute, I am investigating how the infant gut virome is formed and shaped. This August, I returned to Government Higher Secondary School in Koothanoor, Tamil Nadu, India, the village where I was born, for a science outreach event as part of the Invincible Invisibles project. This was supported by Mr. Uloganathan Paramasivam, my partner, from the design to the delivery of the event. Invincible Invisibles is a public engagement project I started during my time at the University of Liverpool, to inspire young people about the world of mighty and valiant microbes. The visit was a deeply meaningful experience sharing the excitement of microbiome science with the next generation in the very place where my own curiosity began. Sparking interest in the gut microbiome With funding support from the Centre for Microbial Interactions, we introduced students to the gut microbiome as a collective group of microbes including bacteriophages, bacteria, fungi and protozoa. We discussed how beneficial microbes support not just digestion, but also define our mood, memory, and learning. We discussed that our bodies are home to trillions of microbes and that the “good” bacteria in our gut can be nurtured by eating fibre-rich foods. I shared examples of fibre-rich foods from their own diet including greens, fruits, banana stem, millets, and pulses along to be eaten alongside with protein-rich foods diet and carbs. Many students shared that they plan to choose healthier food after the session, something that resonates deeply with our mission at the Quadram Institute. I’m grateful to have helped plant this important idea in young minds. Using paper microscopes to see microbes in yoghurt The most exciting part of my visit to the school was when students used paper microscopes, called foldscopes, to observe bacteria called lactobacilli in yogurt. In short, Lactobacilli help in breaking the milk sugar lactose into lactic acid, which thickens the milk and gives yogurt its tangy taste. For many students, it was their first time seeing a microbe and their reactions were priceless. It reminded me how powerful real-world experiences are, far beyond what can be learned through books alone. What moved me most was their curiosity beyond the classroom. They wanted to collect moss from damp walls, samples from fermented foods, and even soil to observe microbes from their own surroundings. Many asked if I could return next year to explore the microbial environment with them. Their eagerness to explore the microbial world around them was truly inspiring. Building interest in bacteriophages and beyond As part of my visit, we also discussed bacteriophages, which is my favourite part of the microbiome. In fact, the students immediately connected phages to the therapeutic potential of treating antibiotic-resistant bugs. This moment awed me the most. Overall, the visit to the village where I grew up reminded me that science engagement is most powerful when it’s personal, local, and hands-on. These students are ready - not just to learn, but to discover. And I hope that this is just the beginning of many such journeys into the invisible, invincible world of microbes for them and that some of them emerge as a great microbiologists."

[caption id="attachment_31713" align="aligncenter" width="781"] Scientists from Nepal and the JIDCuk charitable trust standing outside the National Animal Health Research Center (NAHRC) in Lalitpur, Nepal.[/caption] JIDCuk is a charity that supports the open access Journal of Infection in Developing Countries (JIDC) and otherwise invests in scientific research opportunities in low and middle income countries, led by local scientists. The charity was founded by Professor John Wain and Dr Gemma Langridge, Group leaders at the Quadram Institute and University of East Anglia. Since its inception, JIDCuk has contributed to funding the research of numerous individuals in various countries and has provided in-person training in Fiji and Nepal. As well as funding researchers from low and middle income countries (LMIC) in their home countries JIDCuk fosters international collaboration and supports the development of accessible software and diagnostics for use in LMICs. “We believe investing in masters students, PhD candidates, and scientists early in their careers is paramount for overcoming the hurdles preventing current scientists from building sustainable infrastructure in their home countries", says Professor John Wain. Facilitating Fiji's microbiology sequencing capability Some of the work done by those at JIDCuk has been facilitated by existing international collaborations, such as our strong links with Fiji National University and previous Quadram projects into water related diseases caused by microorganisms such as Salmonella. In August 2023, Quadram Institute researchers Professor John Wain and Dr Emma Waters led a training visit to the university in Fiji to develop the country’s microbiology sequencing capability. The trip was a great success, Emma and John facilitated the first use of Nanopore sequencing in Fiji and the trip was a great success, ands the training provided the skills and resources to help identify the cause of an infection outbreak in a hospital unit for premature babies. Nanopore training in Nepal In 2024, JIDCuk supported the establishment of an Oxford Nanopore Technologies MinION sequencing facility at the National Animal Health Research Center (NAHRC) in Lalitpur, Nepal. Dr Gemma Langridge, Dr Emma Waters and PhD student Alice Nisbet traveled to Nepal to conduct comprehensive in person training. The training covered both the science behind sequencing and and to delivered hands-on laboratory sessions for sequencing techniques. This training visit was facilitated by links made between the NAHRC, Dr Dipali Singh and ProfessorJohn Wain. The training in Nepal was a great success, equipping local scientists with the understanding and the skills to perform DNA sequencing independently. This has a wed investigation of pathogens affecting local animal populations and the study of associated antimicrobial resistance profiles. “The training was comprehensive and we are confident in our ability to undertake sequencing following the completion of the course. We look forward to ongoing communications with Dr Langridge, Miss Nisbet and colleagues at the Quadram Institute as we establish our sequencing capability at NAHRC," says Dr Doj Raj Khanal, Executive Director, NAHRC. Supporting postgraduate science across the globe As well as these activities, JIDCuk currently supports students in Nigeria, Zimbabwe, the Philippines and Nepal. The PhD candidate in Nigeria is researching Salmonella enterica serovar Typhi in Nigeria, while another a PhD candidate is researching Acinetobacter baumannii in Zimbabwe. Plus , a PhD candidate is investigating metagenomics of colorectal cancer in the Philippines. The charity is funding two Masters by Research projects in bioinformatics and machine learning at the Nepal Applied Mathematics and Informatics Institute for Research. These projects have been made possible by funding from the JIDCuk charitable trust and links between in-country institutions and the Quadram Institute, as well as collaborations with established researchers Dr Ben Evans and Dr Colin Cooper from the University of East Anglia who currently act as supervisors and contacts for some of the projects supported by JIDCuk. An open access online journal The JIDCuk charitable trust supports JIDC with its activities as an independent, online, open-access, science publication that promotes scientific development in lower income and middle income countries. JIDC publishes the latest research from these countries, striving to make the scientific publication process more accessible to scientists worldwide. Some Quadram Institute scientists have been involved with the peer review process for JIDC including John Wain, Alice Nisbet and Caroline Jarvis. This has been a valuable experience for UEA PhD students Alice Nisbet and Caroline Jarvis. Future plans for the charity JIDCuk also aims to expand its repertoire to provide equitable, accessible, open-source bioinformatics software for use in developing countries, alongside training on how to use the programmes. This ongoing project is led by Dr Claire Hill, Dr Lisa Crossman and collaborators at Theiagen Genomics. Dr Cailean Carter is leading a research project with JIDCuk, developing a diagnostic test with the specific aim of accessibility to lower and middle income countries. This project is currently focusing on Nepal, In the future, JIDCuk will continue to support masters students, PhD candidates, and scientists early in their careers in developing countries, and provide training to scientists in low-resource settings. Read more about the efforts of JIDCuk to bridge the scientific development gap between low-income and high-income countries on the JIDCuk website and follow the charity on Bluesky and LinkedIn.

“I am currently engaged in research on the gut microbiome of Parkinson’s disease (PD) patients, focusing on understanding microbial alterations associated with the disease and exploring strategies for microbiome modulation. I am scientist at the Indian organisation Scientific Knowledge for Ageing and Neurological Ailment Research Trust (SKAN-RT), currently visiting Professor Arjan Narbard’s group for one year as part of our ongoing collaboration. The link between the gut microbiome and Parkinson’s disease My motivation for choosing this project stems from the growing evidence linking and imbalance in gut microbiota to Parkinson’s disease (PD), a progressive neurodegenerative disorder characterised by both motor and non-motor symptoms. Specific bacterial communities and their metabolites appear linked to neuroinflammation and α-synuclein aggregation,  hallmarks of the disease. My work involves characterising the gut microbial composition in PD patients in UK and in the future I’ll be working with samples from the Indian population too. I am identifying key bacterial species focusing on sulphate reducing bacteria (SRB) contributing to disease progression, and investigating targeted interventions to restore microbial balance. During my visit I isolated many species of SRB including a novel species of Eubacterium callanderi from a Parkinson’s patient. By characterising these bacterial communities and their interactions, I hope to identify specific microbial dysbiosis patterns contributing to neurodegeneration. The potential of bacteriophages for Parkinson’s disease As part of this research, I am exploring bacteriophage therapy as a potential approach to selectively eliminate disease-causing bacteria with a focus on SRB species such as Desulfovibrio which have been implicated in Parkinsons disease. Bacteriophage therapy uses bacteriophages which are viruses that kill specific bacteria. With the rising threat of antimicrobial resistance there is an urgent need for innovative therapeutic strategies. Phage therapy offers a promising alternative to conventional antibiotics in targeting microbial imbalances associated with Parkinsons disease . I am currently isolating phages that selectively eliminate disease-causing bacteria while preserving beneficial microbiota. To achieve a comprehensive understanding of gut microbiota involvement in Parkinsons disease, I will integrate multi-omics approaches, including metagenomics, metabolomics, and transcriptomics. These techniques will allow for the identification of key microbial alterations, metabolic byproducts, and bacterial gene expression patterns associated with Parkinsons disease. Collaborating across the globe to develop therapies The Scientific Knowledge for Ageing and Neurological Ailment Research Trust (SKAN-RT) plays a central role in this research. SKAN-RT, an Indian research organisation dedicated to advancing scientific understanding in aging and neurological disorders, provides critical support in exploring the connection between gut microbiota and Parkinsons disease . In 2023 SKAN-RT began a collaboration with the Quadram Institute focused on gut health and developing therapies that alleviate ageing and neurological diseases. At the Quadram Institute, I have been using culturable approach and working on identifying sulphate reducing bacteria, with support from Dr Lizbeth Sayavedra and bacteriophage screening with the help of Dr Melinda Mayer. I’m coming towards the end of my one-year visit to the Quadram Institute. Its been a very rewarding experience where I have been exposed to advanced research in the area of gut microbiome. When I leave, I’ll continue working on the project in India and a colleague from SKAN-RT will visit the Quadram Institute to work onthe interaction between the bacteria I have isolated and human tissues. Through SKAN-RT’s extensive expertise in neurological research and microbiome modulation, this project is positioned to explore innovative therapeutic strategies with the potential to improve patient outcomes in neurodegenerative diseases. Career path to studying the gut microbiome Before I joined SKAN-RT, I pursued a Bachelor's and Master's degree in Biotechnology, where I developed a strong foundation in microbial research. During my Master's program, I worked on the effects of algal lectins on siderophore-producing bacteria. This research exposed me to the fascinating role of bacteria in iron acquisition and their potential applications, sparking my deep interest in bacterial physiology and interactions. Building on this interest, I enrolled in a Ph.D. program where my research focused on biofilm-forming bacteria and their diverse applications. This research further solidified my enthusiasm for applied microbiology and microbial biotechnology. I then transitioned into the field of bacteriophages and gut microbiome research. I joined the Scientific Knowledge for Ageing and Neurological Ailment Research Trust (SKAN-RT), to work on bacteriophage therapy and investigating the complex interactions between the gut microbiome and neurological disorders. This progression in my research journey reflects my continuous commitment to understanding microbial dynamics and their translational applications in health and disease." Yogesh Shouche, Director of Research at SKAN concludes, “SKAN’s research interest in ageing and neurodegenerative disorders aligns well with the science strategy of the Quadram Institute and we are excited about the work that Madhav has initiated and going forward we plan to this collaboration with further joint projects.”  

Antimicrobial resistance is a major threat to modern medicine, reducing our ability to prevent or cure disease. Antimicrobial resistance on the rise “I remember when I was a kid, I used to see people taking antibiotics like Septran DS.  It’s vanished from the market in most of the places in the world as there’s so much resistance in bacteria, meaning the treatment is no longer effective,” reflects Yasir. "E.coli bacteria are now resistant to third generation antibiotics like fluoroquinolones and cephalosporines. We need to find ways to reuse those antibiotics again,” highlights Sajid. He continues, “My PhD at the University of Copenhagen is working on E.coli and how E.coli has developed resistance to the antibiotics called sulfonamides and trimethoprim. These antibiotics are often used together to treat urinary tract infections.” “I’m studying the mechanisms of how these antibiotics targets the E.coli, with the aim of to find secondary drug targets for helper drugs that can be taken together with sulfonamides and trimethoprim. The aim is that we can resensitise the E. coli to sulfonamides and trimethoprim by using helper drugs and make these antibiotics effective again.” “As part of my PhD program, there is a mandatory component known as secondment, which requires me to immerse myself in a different research environment to broaden knowledge and skills relevant to my current project.” “Since I am investigating the molecular responses of E. coli to sulfonamides and trimethoprim by using TraDIS, I was eager to learn about TraDIS-Xpress, an advanced version of TraDIS. This led me to the Quadram Institute, where I could gain valuable insights into this innovative research approach.” TraDIS-Xpress training to track down target genes for helper drugs Here at the Quadram Institute, our researchers developed the TraDIS-Xpress method. The method introduces small pieces of DNA called transposons into bacterial genes to make a mutant library. The method tests how different transposon mutated genes affect bacterial survive in different conditions. TraDIS-Xpress allows researchers to understand the roles of different genes inside the bacteria and how important the genes are for the bacteria’s survival. Yasir highlights the difference between TraDIS and TraDIS-xpress, “In TraDIS, we can only investigate the roles of non-essential genes (genes that can be mutated) under stress conditions. However, with TraDIS-Xpress, we can also explore the roles of essential genes (genes that cannot be mutated) during stress. An essential gene is one that a bacteria needs to survive. If this gene isn’t there or switched on, then the bacteria dies.” “I got an email from Sajid, asking about a placement to learn more about TRADIS-Xpress. We first came in contact as Sajid had a question about data analysis couple of years back and he reached out to me as we often approached by different researchers across globe regarding TraDIS-Xpress” describes Yasir. He continues, “Luckily our availability matched and Sajid joined us at the Quadram Institute in October 2024 for a six-week placement to learn more about the TraDIS-Xpress method.” Sajid explains, “Before I came, I had read the paper about TraDIS-Xpress from the Quadram Institute team but I did not understand it fully. Coming here, helped me learned a lot more about the method and how it works in the lab.” “The method is helpful to my PhD project as I can find which genes are essential under certain sulfonamides and trimethoprim treatment.” Sajid highlights another strand of research he has carried out at the Quadram Institute, “We have also used phytochemicals to suppress E.coli and see how E. coli survives in the stress of thymol by using TraDIS-Xpress. Thymol is an essential oil that comes from the thyme plant and can be found in over-the-counter antibacterial and antifungal products." Sajid's second PhD Sajid explains his path to his current second PhD, “I am from Pakistan. I did my undergraduate in my home city at the University of Agriculture, Faisalabad. I studied veterinary studies there for five years.” “After that I did my masters at the same university in Public Health and Climate Change. Then I continued at the University of Faisalabad and started my PhD in 2018. In Pakistan I was doing a PhD on the bacteria Salmonella Typhi to investigate how S. Typhi survive in varying concentrations of metal ions like iron, copper, manganese and cobalt.” “In 2021 I got a scholarship from Punjab Education Endowment Fund (PEEF) to start a new PhD in Copenhagen. My supervisor M Imran Arshad suggested having a PhD from University of Copenhagen, Denmark would develop my research career and I could freeze my degree in Pakistan. At the time, I had finished my research and was writing my thesis so it was decided I can submit my thesis for the work I did in Pakistan, when I finish my PhD in Copenhagen.” Exchanging expertise Reflecting on his placement at the Quadram Institute Sajid says, “My experience at the Quadram Institute has been nothing short of exceptional. I thoroughly enjoyed my time here, as the facilities are truly state-of-the-art. The atmosphere is vibrant and inspiring, allowing me to engage deeply with my research. I've had the opportunity to learn a great deal and have been continuously impressed by the level of expertise and dedication among the staff.” “During my visit, I gained a comprehensive understanding of the fundamentals of TraDIS-Xpress, including its operational mechanisms and the underlying concepts that drive this innovative technique. This knowledge is highly valuable for my research and will undoubtedly enhance my ability to analyse the survival mechanisms of E. coli in the presence of various compounds.” “I would like to express my heartfelt gratitude to everyone at the Quadram Institute for their warm welcome and support. The kindness and humility of the staff have made my experience even more enriching. Special thanks to Yasir, who provided valuable assistance throughout my experiments, and to Professor Mark Webber, along with Keith, Ryan, and other group members for their guidance and encouragement. This experience has not only advanced my research skills but also fostered meaningful connections that I will cherish throughout my academic journey.” Yasir concludes, “It’s been great to have Sajid join us in the Webber group to learn more about TraDIS-Xpress. Our collaboration established by Sajid’s visit is ongoing and we will publish collaborative work together on how we can help tackle antibiotic resistance.”

At the Quadram Institute we have a team of bioinformaticians who support our scientists to analyse data on the DNA of microbes. In May they welcomed experts from South Korea and Switzerland to build international partnerships and share bioinformatics expertise. “We decided to organise a set of workshops at the Quadram Institute to bring together world-leading experts in large-scale analysis of microbial genomes to optimise bioinformatics tools and forge new collaborations,” explains Dr Andrea Telatin, Head of Bioinformatics. From phylogenetics to protein identification using AI A key aspect to analysing microbial genomes is making comparisons between the DNA of organisms, whether between different microbes or between bacteria, animals and fungi. The visiting research group from University of Lausanne in Switzerland are focused on making these comparisons through large-scale genomics across the tree of life. The group led by Dr Natasha Glover and Prof Christophe Dessimoz are responsible for the software ecosystem around a database which keeps up-to-date evolutionary information on almost 3,000 genomes from different organisms and growing, called the Orthologous Matrix (OMA) database. The University of Lausanne researchers were joined by Professor Martin Steinegger from Seoul National University. His group have developed popular microbial genomics tools, and they apply artificial intelligence to advance structural phylogenetics. “As the Head of Phylogenomics, I was aware how the two groups' methodologies can be applied to elucidating bacterial evolution. We were keen to invite them to the Quadram Institute to share expertise,” explains Dr Leo Martins from the Bioinformatics team at Quadram Institute. Dr Stefano Pascarelli from the University of Lausanne comments on arriving in Norwich, “For me, I was truly impressed by the level of science and support that is found at the Quadram Institute. I observed a great synergy of the research themes in cooperation with an enviable Bioinformatics core facility that explains the growing success within the Norwich Research Park.” Along with talks, the two-day visit included activities to foster collaboration and dialogue. “We had a round table discussion with all guests, where we talked about the future of bioinformatic databases, and how we can use them fully for microbial studies" says Leo. As well as our Bioinformatics team, researchers from across the Quadram Institute joined the workshops to learn and share their latest developments including Dr Dipali Singh who is using mathematical modelling and AI to study the prostate cancer microbiome and Dr Falk Hildebrand whose group investigates the diversity of microorganisms in the gut microbiome through metagenomics. Dipali says, “Having world-leading experts in genome analysis get together at the Quadram Institute was an incredible opportunity. I gained valuable insights and learned about new tools that will be useful for my research. I am excited about the prospect of collaborating with these experts in the future." Falk adds, "It was a fantastic opportunity to welcome some of the forerunners of bioinformatic research to the Quadram Institute. I enjoyed spending time with these researchers, some of whom's software I have been using for years. I learnt more about the development process and reasoning in these hugely influential software. Going forward I think our interactions and exchanges will lead to future collaborations. " Improving and extending the use of existing bioinformatic tools “It was a very successful activity. At the same time as the guests presented state-of-the-art methods for the kind of bioinformatic analysis we do at the institute, we provided guests with specific needs and challenges posed by bacterial genomes,” reflects Leo. Professor Martin Steinegger says, "Assigning functions labels to metagenomic open reading frames is one of the major challenges in advancing microbial research. With the advances of next-generation structure predictors like AlphaFold2 and extensive databases structural database, we have a unique opportunity to improve annotation.” Dr Irene Julca Chavez from the University of Lausanne highlights the benefits from both sides, “I believe this was a very good initiative. Currently, I work in comparative genomics, and our lab has many tools that assist with analysis in this field. However, the discussions with experts from different fields during the meetings at the Quadram Institute made us aware of the lack of resources for certain taxonomic groups, such as bacteria and viruses”. Dr Dave Moi, from the University of Lausanne continues, “With the new tools that are emerging today, we can start making progress on redefining the viral taxonomy, annotating proteins of unknown function and resolve difficult phylogenies of highly diverged protein families. Going forward at the Dessimoz lab, it looks like we're going to be integrating more and more of the structural perspective into our workflows and tools.” Future collaborations Along with discussions and work to develop existing bioinformatics tools the international workshop sparked ideas for future collaborations. “I think this experience will help us expand some lines of research in our group and promote new collaborations,” highlights Irene. Stefano continues, “Our trip to Norwich led to a fantastic exchange of ideas and knowledge that will possibly lead to exciting new developments. We convened towards the need of shifting the attention of our research towards scalable methods that employ the additional layer of information coming from protein 3D structures.” Leo from the Quadram Institute Bioinformatics team adds, “There are plenty of opportunities for future collaborations, both in terms of method and workflow development but also in terms of practical applications to our increasingly large data sets generated here.” Dr Natasha Glover from the University of Lausanne says, “There is significant potential for collaboration between our group and the Quadram Institute, particularly in developing a database and tools for tracking prokaryote-specific evolution. The future of genomic analysis looks promising, with recent advancements in structural genomics now enabling us to recognise homologous genes where sequence similarity fails.” Martin adds, “We see multiple ways to collaborate with researchers at the Quadram Institute to enhance metagenomic analysis using structural aligners like Foldseek and Foldseek-multimer, implement our metagenomic classifier Metabuli well as the structure predictor ColabFold.” Natasha Glover concludes, “This experience has reaffirmed the necessity and benefits of international exchanges in pushing the boundaries of genomics.” The workshop was funded through BBSRC's International Partnership Awards