Exploring bile acids produced by gut microbesLawrence David, Assistant Professor
Molecular Genetics & Microbiology, Duke University, USA
How does having a diet made up of a diverse range of plant-based foods affect the gut microbiomes and health of infants? This is the question that Lawrence David intends to explore in Nicaragua using his grant.
Read more about this research here: https://www.nature.com/articles/d42473-022-00193-z
Lawrence David is an associate professor in Duke University’s Department of Molecular Genetics and Microbiology and interim director of the Duke Microbiome Center. His lab studies relationships between diet, the gut microbiome and human health. The lab is also interested in engineering new tools at the interface of nutrition and microbiology, including building genomic approaches for tracking food intake and microfluidic techniques for high-throughput assay of microbial metabolism. David was previously a junior fellow at the Harvard Society of Fellows, and he received a PhD in computational and systems biology from the Massachusetts Institute of Technology and a BS in biomedical engineering from Columbia University. He has been awarded innovator and investigator awards from the Burroughs Wellcome Fund, the Searle Scholars Program, the Arnold and Mabel Beckman Foundation, the Hartwell Foundation, the Alfred P. Sloan Foundation, and the Damon Runyon Foundation, and David has been named one of the ten scientists under 40 years old to watch by ScienceNews.
Exploring bile acids produced by gut microbes
Robert Quinn, Assistant Professor
Department of Biochemistry and Molecular Biology. Michigan State University, USA
Following on from his discovery of a special set of bile acids produced by the microbiome, Robert Quinn will use his grant to explore how they affect infant health.
Read more about this research here: https://www.nature.com/articles/d42473-022-00205-y
Robert Quinn’s career has spanned several microbiome fields, from fish and corals to lungs and guts. He received his undergraduate degree in microbiology from the University of Guelph in Ontario, Canada, and his PhD from the University of Louisiana at Lafayette, where he studied bacterial shell disease of the American lobster. Quinn was then inspired to focus more on human microbiomes and began a postdoc with Forest Rohwer at San Diego State University with a fellowship from a non-profit cystic fibrosis institute. His postdoctoral research focused on lung disease in cystic fibrosis, but working in the microbiome research hub of San Diego enabled him to expand his knowledge into other systems. He transitioned to the University of California San Diego under the mentorship of Pieter Dorrestein to learn advanced metabolomics methods. In his current faculty position at Michigan State University, Quinn and his team use microbial ecology theory and metabolomics to understand the dynamics of microbiomes in the cystic fibrosis lung, human gut and coral reefs.
Discovering how malnutrition stunts children’s growth via the microbiome
Bryan Gonzales, Assistant Professor
Group of Nutrition, Metabolism and Genomics Division of Human Nutrition and Health, Wageningen University The Netherlands
How does malnutrition affect infant growth via the availability of two key dietary nutrients produced by the gut microbiome? Bryan Gonzales will use his grant to explore this question in children in Malawi.
Read more about this research here: https://www.nature.com/articles/d42473-022-00191-1
Gerard Bryan Gonzales studied Food Technology at the University of the Philippines Mindanao. In 2010, he obtained an Erasmus Mundus Scholarship to study an MSc in food science at the University of Copenhagen (Denmark) and Universitat Autonoma de Barcelona (Spain). He then moved to Belgium to pursue a PhD in applied biological science (chemistry) at Ghent University, where he studied polyphenols using mass spectrometry. After a consulting stint with the World Health Organization Europe in Turkmenistan, he obtained a Research Foundation Flanders (FWO) Fellowship at Ghent University to work on the molecular mechanisms driving different phenotypes of childhood severe malnutrition, especially kwashiorkor, in collaboration with and funded by the Médecins Sans Frontiéres. During his postdoc, he was a visiting scientist at the Hospital for Sick Children (Toronto, Canada), Kenya Medical Research Institute–Wellcome Trust (Kilifi, Kenya), and the University of Cambridge (Cambridge, UK). In 2020, he joined Wageningen University as assistant professor in nutri-informatics and metabolism.
A pioneering microbiome model for the small intestinePurna Kashyap, Associate Professor of Medicine, Associate Professor of Physiology
Mayo Clinic College of Medicine, Rochester, MN
After creating the first humanized mouse model of the small intestine, Purna Kashyap will use his grant to explore links between the small-intestine microbiome and gastrointestinal disorders.
Read more about this research here: https://www.nature.com/articles/d42473-021-00237-w
Purna Kashyap is a consultant physician at the Mayo Clinic College of Medicine in Rochester in Minnesota, US. His research into functional gastrointestinal disorders is driven by direct experience of working with his patients, with the overarching goal of improving understanding of these complex, debilitating health conditions. He studies gut bacteria, dietary carbohydrates, and associated metabolites, and explores their influence on host physiology, with the aim of developing new biomarkers and targeted therapies for gastrointestinal disorders.
Deciphering the molecular language of the small intestineMarco Jost, Assistant Professor
Department of Microbiology, Harvard Medical School, Boston, MA
Marco Jost plans to use his grant to listen into communication between the small-intestine microbiome and host cells by using organoids of the small intestine.
Read more about this research here: https://www.nature.com/articles/d42473-021-00236-x
Marco Jost is an assistant professor in microbiology at Harvard Medical School in Boston, US, where he set up the Jost Lab in April 2021. His postdoc with Jonathan Weissman and Carol Gross at the University of California San Francisco involved developing tailored CRISPR screening techniques, which he used to begin exploring the gut microbiome in collaboration with Michael Fischbach and colleagues. The Jost Lab will use single-cell RNA sequencing and CRISPR technologies to improve understanding of molecular communications in the gut and how this influences physiology throughout the body.
Examining the influence of the small intestine on glucose responsesGuido Hooiveld, Assistant professor
Division of Human Nutrition and Health, Wageningen University, The Netherlands
Why do different people have different blood glucose responses to the same foods? Guido Hooiveld thinks part of the answer could lie in the small-intestine microbiota and will use his grant to explore these complex relationships.
Read more about this research here: https://www.nature.com/articles/d42473-021-00235-y
Guido Hooiveld is an assistant professor at the Division of Human Nutrition and Health at Wageningen University, The Netherlands. His specialisms include biochemistry, physiology and molecular biology. As a molecular nutritionist, he is interested in how the food we eat interacts on a molecular level with the microbiome, and how this in turn influences host responses and ultimately health. Previously, he focused on dietary lipids and their absorption in the body, before turning his attention to examining the differences in control of glucose responses in healthy and diseased states.
Role of gut commensal protists in immune-mediated food sensitivitiesReinhard Hinterleitner, Assistant Professor
Department of Immunology at the University of Pittsburgh School of Medicine
Immune-mediated food sensitivities that include food allergies and celiac disease are on the rise worldwide. Dendritic cells constantly sample food antigens from the intestinal lumen and establish oral tolerance to food antigens through the induction of regulatory T cells, which prevent the onset of immune-mediated food sensitivities.
Lack of certain microbial products due to altered intestinal microbial communities (dysbiosis) caused by modern lifestyle practices (e.g. high-fat, low-fiber diet, antibiotic overuse), enteric infections, and overexpression of inflammatory cytokines are thought to drive undesired proinflammatory responses that result in loss of oral tolerance to food antigens and set the stage for the development of immune-mediated food sensitivities.
This project will study how specific gut commensal microbes promote oral tolerance and protect from loss of oral tolerance which will provide the basis for microbe-based therapies to prevent the development food allergies and celiac disease.
Dr. Reinhard Hinterleitner is an Assistant Professor in the Department of Immunology at the University of Pittsburgh School of Medicine. He studied Biotechnology at the University of Applied Sciences in Vienna and received his PhD from the Medical University of Innsbruck, Austria. Supported by an Erwin Schrödinger Postdoctoral Fellowship, Reinhard joined the laboratory of Dr. Bana Jabri at the University of Chicago where he studied the role of enteric viral infections on oral tolerance in the context of celiac disease. Reinhard was appointed by the Department of Immunology at the University of Pittsburgh School of Medicine in 2018 as an Assistant Professor in the tenure track. His current research focuses on the cross talk between gut microbes and the host mucosal immune system in the context of food sensitivities and intestinal inflammation.
Read more about Reinhard Hinterleitner's work here: https://www.nature.com/articles/d42473-020-00310-w
Deciphering human antibody repertoires against the microbiome in health and diseaseEran Segal, Professor & Principal Investigator
Weizmann Institute of Science
Despite significant progress in understanding microbiota driven immunity in animal models, it is vastly unknown which antibody repertoires humans possess and how these responses affect health and disease. This project will apply a novel and broad approach to identify which epitopes of the microbiota are immunogenic and result in antibody generation.
Multidisciplinary immunology will be combined with machine learning methods to screen rationally designed libraries of 244,000 epitopes. Leveraging phage display and robotic automation, the interplay of individual antibody repertoires with clinical parameters and the microbiome will be systematically assessed in 1,000 individuals. These results alone will represent the largest systematic study to date of the interaction of the gut microbiota and the immune response in healthy humans. Furthermore, samples of inflammatory bowel disease (IBD) patients and autoimmune diseases (multiple sclerosis, MS) will be analysed for biomarker discovery, paving the way towards novel therapeutic approaches.
Eran Segal is a Professor at the Department of Computer Science and Applied Mathematics at the Weizmann Institute of Science, heading a lab with a multi-disciplinary team of computational biologists and experimental scientists in the area of Computational and Systems biology. His group has extensive experience in machine learning, computational biology, and analysis of heterogeneous high-throughput genomic data. His research focuses on Microbiome, Nutrition, Genetics, and their effect on health and disease. His aim is to develop personalized medicine based on big data from human cohorts.
Prof. Segal published over 150 publications, and received several awards and honors for his work, including the Overton prize, awarded annually by the International Society for Bioinformatics (ICSB) to one scientist for outstanding accomplishments in computational biology, and the Michael Bruno award. He was recently elected as an EMBO member and as a member of the young Israeli academy of science.
Before joining the Weizmann Institute, Prof. Segal held an independent research position at Rockefeller University, New York.
Read more about Eran Segal's work here: https://www.nature.com/articles/d42473-020-00313-7
Functionally characterizing IBD dysbiosis and harnessing gut bioactives to suppress IL-23 driven inflammationJakob Begun, Senior Lecturer & IBD Group Leader
Mater Medical Research Institute Limited
The microbiota impacts the entire body and contributes to both health and disease. Bacteria produce a broad array of biologically active chemicals that have direct impacts on host signalling pathways. These can promote health, as in the case of short-chain fatty acids (SCFAs) promoting mucus production and decreasing inflammation, or they can drive disease as in the case of tri-methylamine-N-oxide (TMAO) and cardiovascular disease. The gut microbiota has been implicated in inflammatory bowel disease (IBD), where dysbiosis is a dominant feature. But, the relationship between dysbiosis and inflammation remains unclear. After nearly twenty years of “omics” based investigation into the microbiota significant progress has been made in identifying the bacteria present in the microbiota, but the function of these bacteria remains largely a mystery.
To address this challenge, Dr Begun's team has developed a discovery pipeline to isolate and characterize secreted bioactives derived from cultured gut bacteria. The pipeline is based on optimized anaerobic growth conditions to culture a wide range of human microbial species. Bioactives produced by these isolates are then screened for pathway specific anti-inflammatory activity using high throughput reporter systems. The team has used this pipeline to successfully identify two NF-?B bioactives which have shown anti-inflammatory activity in pre-clinical animal models. The pipeline is easily adaptable, and this proposal will screen for bioactives that inhibit IL-23 induced STAT3 activity. This pathway has emerged as an effective target in IBD, psoriasis and arthritis, where approved therapeutics are already in use.
The project team will screen its collection of healthy stool bacterial isolates to identify bioactives that can inhibit IL-23. Additionally, it will determine the frequency of strains capable of supressing IL-23 signalling in healthy subjects and compare that with IBD patients. This will allow the team to begin to describe the functional dysbiosis in IBD patients.
A/Prof Jakob Begun obtained his MD and PhD in genetics at Harvard Medical School. His advanced training in Gastroenterology and Inflammatory Bowel Disease (IBD) was at Massachusetts General Hospital (MGH) where he developed a keen interest in the microbiome – immune system interactions. He is the director of IBD at the Mater Hospital Brisbane and IBD Group leader at the Mater Research Institute – University of Queensland. He runs a basic and translational laboratory investigating the interaction between innate immune functions of the gut and the microbial community. He also performs clinical research on the use of intestinal ultrasound in IBD, real world effectiveness of therapeutics, and identifying barriers of care for adolescents and young adults with IBD at the Mater Young Adult Health Centre. He is the chair of the Gastroenterological Society of Australia IBD Faculty.
Read more about Jakob Begun's work here: https://www.nature.com/articles/d42473-020-00312-8
In vivo long term evolution of a commensal in the gut microbiotaIsabel Gordo, Deputy Director of Science
Gulbenkian Science Institute, Portugal
Microbiota diversity is a key modulator of host health: a diverse gut microbiome is indicative of health and a microbiome exhibiting low diversity is typically associated with disease. How such microbiome diversity emerges and is maintained over the life of an individual host is one of the great mysteries that this project seeks to address.
Recent analysis of the Human Microbiome Project data suggests that within-host evolution of microbiota species can occur in the human gut over months or years. However, the limited sampling, difficulties with analyzing short read sequence data and lack of control of the initial conditions of strain colonization, makes it extraordinarily difficult to quantify rates of evolution. Furthermore, possible migration of strains from the environment raises uncertainty in establishing the relative contribution of mutation and horizontal gene transfer (HGT) to intra- and inter- species diversity in the gut.
Experimental evolution of bacteria model species colonizing the gut offers a powerful complementary approach to understand the emergence of strain diversity and its consequences for the function and structure of the gut microbiome. In this context the project team has developed a new in vivo long term experimental evolution (ivLTEE) mouse system, where the evolution of a commensal lineage within a rich ecosystem offers novel insights into the missing process of evolution within the microbiota. Using this unique experimental system together with dense time series sequencing, the researchers will characterize evolution in real time of a gut commensal throughout the adult life of laboratory mice.
Preliminary data identifies HGT as a key driver of evolutionary change in the initial stages of colonization under specific conditions. When direct competitors of a newly colonizing species reside in the gut, phage driven HGT generates new strains that acquire tens of genes from the resident microbiota. When these competitors are absent new mutations accumulate and new clones with an increased mutation rate (mutators) can emerge. Both HGT and mutation are identified as key evolutionary mechanism from comparative genomic studies. Yet, these have not only been hard to detect in real time but also their relative rates have been difficult to establish. This new ivLTEE offers exactly that possibility: quantification of the rate of long-term evolution via de novo mutation and HGT.
The spontaneous emergence and maintenance of hypermutators (rarely detected either in vitro or in vivo studies) in this complex ecosystem raises a conundrum: How can these be maintained? Will they be eliminated in the long term?; in other words: How does microbial genomic instability shape intra-species diversity in the gut ecosystem? Both the short and the possible long term maintenance of clones with mutation rates 1000-fold higher than the typical rate can have strong effects in modulating the level of antibiotic resistance (AMR) in the gut microbiome. Not only will the level of spontaneous AMR be higher, but also it may increase to dominant levels, under antibiotic treatment. The project will also address the role of mutators in modulating AMR levels. The originality of the plan lies on its focus to characterise and quantify evolutionary change within a host lifetime, with great precision.
Dr Isabel Gordo is a principal investigator at the Gulbenkian Science Institute, Portugal. She graduated in Physics and received a PhD in Evolutionary Genetics from the University of Edinburgh in 2002. Her PostDoctoral research was carried out at the Gulbenkian Science Institute where she then became leader of the Evolutionary Biology group in 2004. In 2010 she won an ERC Starting Grant and in 2015 a FCT Investigator Consolidator Grant.
She founded the Portuguese Society for Evolutionary Biology, has served as panel member of the European Research Council grants evaluation since 2014 and was elected an European Molecular Biology Organization member in 2017.
Her current research combines theoretical and empirical methods aiming at a better understanding of the major forces that shape diversity of bacteria and their resistance levels in the context of the gut microbiome. She uses Escherichia coli as a bacteria model and mice as a host model system.
Read more about Isabel Gordo's work here: https://www.nature.com/articles/d42473-019-00246-w
Drug-gut microbiota interactions: developing a pathway to personalized medicine in psychiatryNiall Hyland, Senior Lecturer (Associate Professor)
University College Cork, Ireland
The microbiome plays a key role in health and disease and there has been considerable interest in therapeutic targeting of the microbiome as well as mining this rich resource in drug discovery efforts. However, a growing body of evidence now suggests that the gut microbiota can itself influence the actions of a range of drugs both by directly metabolising them and indirectly by affecting host drug metabolism, the consequences of which can be either beneficial or potentially harmful. Nevertheless, such studies have not extended to psychotropic medications nor addressed whether the dysbiosis associated with psychiatric illness may underpin the clinical response to psychotropic drugs.
The project's objectives are to determine the impact of clinically diagnosed depression on microbial drug metabolism; to identify whether depression-associated dysbiosis affects host drug metabolism and drug pharmacokinetics in a humanized rat model of depression; and to develop a Physiologically based Pharmacokinetic (PbPK) model incorporating a microbiome-mediated drug metabolism compartment for predicting drug pharmacokinetics in patients.
Researchers will measure the drug-metabolising activity of the gut microbiome from patients with depression by preparing a stable cell-free extract of human faeces, fecalase. Using high performance liquid chromatography we will then determine whether fecalase from depressed subjects differentially affects the metabolism of psychotropic drugs. To better understand the impact of disease-driven dysbiosis on host drug metabolism and pharmacokinetics, in a humanised rat model of depression they will examine the expression of genes involved in host drug metabolism and the pharmacokinetic profile of psychotropic medications. Finally, through the incorporation of different types of data, including -omics, enzymatic and pharmacokinetic data in an integrated way they will develop an in silico model which can be tailored to the individual patient characteristics and provide reliable predictions of drug levels in these patients.
Dr Niall Hyland is a tenured Senior Lecturer in the Department of Physiology and Faculty in APC Microbiome Ireland at University College Cork, Ireland. He received a BSc (Hons) in Biomedical Sciences from the University of Ulster and PhD in Pharmacology from King’s College London. Niall was a visiting fellow at the Department of Pharmacology and Experimental Therapeutics, Louisiana State University Medical Center (1998-1999) and completed an AstraZeneca/Canadian Association of Gastroenterology/Canadian Institutes of Health Research-funded postdoctoral fellowship at the University of Calgary in Canada. He returned to Ireland in 2007 to take up a GlaxoSmithKline-supported senior postdoctoral position at APC Microbiome Ireland and was subsequently appointed Lecturer in Pharmacology in the School of Medicine in 2008 and Senior Lecturer in Physiology in 2018.
Niall’s laboratory investigates the interactions between the gut microbiome and host in the context of intestinal physiology and the gut-brain axis. Current collaborative projects are investigating microbial drug metabolism; the bladder microbiome; and the temporal changes in the gut microbiome during colon carcinogenesis. Dr Hyland has a H-Index of 22 and co-edited the book, The Gut-Brain Axis: Dietary, Probiotic, and Prebiotic Interventions on the Microbiota published by Elsevier/Academic Press.
Read more about Niall Hyland's work here: https://www.nature.com/articles/d42473-019-00247-9