Asia

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.

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

Plant-based alternatives to dairy milk have gained huge popularity in recent years. European plant-based “milk” sector has grown by 36% between 2018 – 2020 to €1.6bn and sales in the UK are set to double by 2025. This growth in popularity of plant-based alternatives has been stimulated by consumers moving away from animal-derived protein to plant-derived protein. The term “milk” is legally restricted in the EU to products produced by ruminant animals, similar products from plants are referred to as dairy or milk alternatives. Many people make this change for environmental reasons. Plant-based dairy alternatives consume much less water, require less land and produce lower greenhouse gas emissions than cow’s milk. There is no doubt that plant-based alternatives are more environmentally friendly. Nutrients in plant-based milk alternatives compared to dairy milk Regarding nutrition and health, some people regard plant-based milk alternatives as healthier than dairy milk, but this depends on the reasons. Individuals who have an allergy or intolerance to dairy proteins or who are lactose intolerant benefit hugely from the existence of these plant-based products. However, for healthy individuals, dairy products are a rich source of readily absorbed, high quality protein, containing all the essential amino acids. Dairy milk is naturally rich in a range of minerals and vitamins. Plant-based milk alternatives can contain dietary fibre, but the protein quality is generally lower than dairy milk and may have to be fortified with minerals and vitamins. The digestion of protein in plant-based milk alternatives [caption id="attachment_25888" align="alignright" width="196"] Clots formed by soy milk alternative in the presence of pectin during simulated stomach digestion[/caption] Researchers at Quadram are interested in how the structure of the food we eat can affect digestion and nutritional impact. Professor Pete Wilde explains, “We use lab-based models which simulate the conditions of human digestion to understand these mechanisms in more detail. We have been interested in the past in how dairy proteins are digested and found that they can form clot-like structures in the stomach which can control how quickly they are digested. Slower protein digestion is known to make you feel fuller for longer.” “Therefore, we wondered if plant-based milk alternatives behaved the same way during digestion.” The Wilde group have a collaboration with Zhejiang Gongshanga University in China, where soy-based products have been established for many years. Together they are learning more about how soy-based milks alternatives are digested. “Interestingly we found that soy-based milk alternatives behave in a similar way to dairy milk. Soy-based milk also forms clots and helps you feel fuller for longer.” “The soy-based products are often stabilised by natural gums. We found that the type of gum used could change the rate at which the proteins were digested. This could help in developing tailored food products as slow protein digestion can reduce appetite and slow down muscle loss in the elderly. In contrast, rapidly digested protein can aid in muscle synthesis for sports nutrition.” The research team is exploring the digestion of other plant-based milk alternatives too.  “The protein component is important, as some plant proteins are not as easily digested as dairy protein. We are investigating the mechanisms underpinning the digestibility of plant proteins to understand how products from different sources behave, such as those from oats and almond.” Increasing absorption of nutrients in plant-based milk alternatives Currently plant-based milk alternatives are fortified with vitamins and minerals. However, some plant-based products contain antinutrients which can stop the absorption and uptake of nutrients such as calcium into our bodies. [caption id="attachment_25890" align="alignright" width="200"] Microscopy image of a clot structure showing protein (green) and fat (red).[/caption] “Our research is ongoing to understand how these plant-based alternatives can provide positive health benefits akin to dairy milk. Fortification with calcium, iodine and vitamins is relatively straightforward, but we must ensure that these nutrients are absorbed by the body”, highlights Professor Wilde. “The gums we have been studying can be used to help stabilise calcium and other minerals. We are researching how the components of plant-based alternatives can influence nutrient availability and help develop ways that ensure that the nutrients are absorbed.” Professor Wilde concludes, “We are looking at how we can make plant-based milk alternatives more nutritious, so that they meet the nutritional needs of those wishing to adopt a more sustainable diet.”