Nature Café:
Modulating the Microbiome
to Treat Disease                                      
                                                                        

Ami Bhatt is a Professor at Stanford University in the Departments of Medicine (Hematology; Blood & Marrow Transplantation) and Genetics.  A physician scientist with a strong interest in microbial genomics and metagenomics, she received her MD and PhD from the University of California, San Francisco (Alpha Omega Alpha), followed by residency, chief residency and hematology/oncology fellowship training at Brigham and Women’s Hospital and the Dana-Farber Cancer Center at Harvard Medical School.  She joined the faculty at Stanford University in 2014 after completing a post-doctoral fellowship focused on genomics at the Broad Institute of Harvard and MIT.

Prof. Bhatt’s laboratory develops and applies novel molecular and computational tools to study strain level dynamics of the human microbiome, to understand how microbial genomes change over time and predict the functional output of microbiomes. She is keenly interested to understand how microbes use microproteins to “talk” to one another and to human cells, and to leverage this understanding to improve health and treat diseases. Her work is actively being translated from bench to bedside; for example, enzymes that her lab mined from microbes are now being developed these as human genome editing/engineering tools in a start-up company that she co-founded.

She has received multiple awards including the Chen Award of Excellence from the Human Genome Organisation (HUGO), the Distinguished Investigator Award from the Paul Allen Foundation, and the Sloan Foundation Fellowship; she is also an elected member of the American Society of Clinical Investigation and the 2024 American Society of Hematology William Dameshek Prize winner. She has disseminated her distinguished research globally, delivering more than 175 invited presentations. A committed mentor, she has served as the primary research advisor to a diverse cohort of over 60 undergraduate, medical, PhD, and post-doctoral scholars.

Dr. Bhatt is also leading efforts to ensure equity and global access in research and medicine. She carries out research with the H3Africa Genomics Consortium, volunteers for the nonprofit she co-founded in 2012, Global Oncology, and serves as the Director for Global Oncology for Stanford’s Center for Innovation in Global Health. She is working to improve collaboration and exchange between scholars at Stanford and those in South Asia, Africa, and beyond. She continues to practice medicine, caring for patients with hematological disorders. Outside of work, she enjoys strumming on the guitar and making her pour over coffee with scientific precision.

Kenya Honda, M.D., Ph.D., is a professor at Keio University School of Medicine and a Team Leader at RIKEN IMS. His research focuses on the interplay between the human host and endogenous microbiota. His group has made key contributions to understanding not only which microorganisms contribute to disease and how, but also which microorganisms are considered beneficial and could be used for treatment of disease. Notable achievements include identifying microbiota members that induce TH17 cells, Treg cells, TH1 cells, and CD8 T cells, as well as bile acid metabolizing microbes unique to centenarians.

He has been recognized as a Highly Cited Researcher by Clarivate Analytics from 2014 to 2023 and was awarded the Carlos J. Finlay UNESCO Prize for Microbiology in 2020. He is a scientific co-founder of Vedanta Bioscience and a scientific advisor of 4Bio Capital. Additionally, he serves on the advisory boards of Gut Microbes, Cell Host & Microbe, Nature Reviews Gastroenterology & Hepatology, and Current Opinion in Microbiology, and the Scientific Advisory Board of Science Translational Medicine.

Dr. Purna Kashyap is practicing gastroenterologist and Professor of Medicine and Physiology, the Bernard and Edith Waterman Director of the Microbiome program, and Director of the germ-free mouse facility in the Center for Individualized Medicine at Mayo Clinic, Rochester, MN. The NIH funded Gut Microbiome laboratory led by Dr. Kashyap is focused on delineating the complex interactions between diet, gut microbiome, and host gastrointestinal physiology.  The laboratory uses germ-free mouse models in conjunction with measures of gastrointestinal physiology in vitro and in vivo to investigate effects of gut microbial products on host gastrointestinal function. In parallel, they use a systems approach incorporating multi-omics, patient metadata, and physiologic tissue responses in human studies, to aid in discovery of novel microbial drivers of disease.

The overall goal of the program is to develop novel microbiota-targeted therapies. Dr. Kashyap has published nearly 100 peer reviewed articles including journals like Cell, Cell Host Microbe, Science Translational Medicine, Nature Communications, and Gastroenterology. He was inducted to American Society of Clinical Investigation in 2021. He has previously served on the scientific advisory board of American Gastroenterology Association Gut Microbiome Center, and on the council of American Neurogastroenterology and Motility Society. He now serves on the council and the research committee of AGA, in an editorial role for Gut Microbes and as an ad hoc reviewer on NIH study sections.

Dr. Marie-Claire Arrieta is an Associate Professor and Research Excellence Chair at the Cumming School of Medicine, University of Calgary. Her research focuses on the interactions between the early-life gut microbiome and infant development, using clinical and experimental approaches to understand mechanisms underlying host microbiome interactions. Dr. Arrieta’s contributions have been widely recognized, including the Canadian Institutes of Health Research (CIHR) Sick Kids New Investigator Award and the Killam Emerging Research Leader Award. Additionally, she was invited to join the College of New Scholars of the Royal Society of Canada, which honors exceptional early-career scholars across all fields.

Dr. Arrieta is also co-author of the best-selling book Let Them Eat Dirt and is actively involved in science communication and medical education on the microbiome.

Fredrik Bäckhed is professor of molecular medicine and has a PhD in infectious biology from Karolinska Institutet. He undertook post-doctoral training with Jeffrey Gordon at Washington University, St Louis, where he discovered that the gut microbiota can affect energy metabolism and contribute to the regulation of fat storage and obesity.

Fredrik Bäckhed and his research group combine clinically oriented research with gnotobiotic mouse models to understand the role of the gut microbiota in health and metabolic diseases.

During his postdoctoral training in Jeffrey Gordon's group at Washington University, St Louis, Fredrik Bäckhed identified the gut microbiota as a factor that controls fat storage in the host. At the Wallenberg Laboratory for Cardiovascular and Metabolic Research, his group focuses on improving our understanding of how the gut microbiota contributes to cardiometabolic diseases. His studies have shown, for example, that the gut microbiota is altered in individuals with prediabetes and untreated type 2 diabetes. His research also aims to identify "next generation" probiotics aimed at preventing the onset of metabolic diseases.

One goal is to use the knowledge gained to develop new microbiota-based therapies. A key finding towards this goal was the group’s identification of microbial metabolites as potential regulators of cardiometabolic diseases. Fredrik Bäckhed recently received the prestigious ERC Advanced Grant to translate this discovery into treatment. The idea is to prevent bacterial production of a metabolite that contributes to fibrosis in the heart, liver and other organs, and thereby reduce the risk of heart failure and the liver disease metabolic dysfunction-associated steatohepatitis (MASH, previously NASH).

João received his medical training at the Federal University in Rio de Janeiro, Brazil,  where he also earned a PhD degree, studying mechanisms of tolerance to self-antigens in autoimmune diseases. In 2009, he was named a Pew Latin American Fellow in the Biomedical Sciences, moving to the United States to pursue studies on T cell antigen recognition and in vivo dynamics of the immune responses with Ron Germain, at the National Institutes of Health. João was the senior editor for immunology and translational medicine at Cell from 2013-2017 and in December, 2017, he was appointed Chief Editor of Nature Medicine, where he leads a team of editors and journalists covering news, opinion and research across the entire landscape of translational and clinical research. He has given talks about medicine, science and publishing in many international conferences, and has championed efforts to raise ethical standards and transparency in the reporting of translational and clinical research. João cares about supporting young investigators, creating opportunities to make scientific publishing more inclusive, and harnessing the potential of scientific research to reduce health inequalities globally. Since 2021, he has served as a member of the International Committee of Medical Journal Editors (ICMJE).

Ami Bhatt is a Professor at Stanford University in the Departments of Medicine (Hematology; Blood & Marrow Transplantation) and Genetics.  A physician scientist with a strong interest in microbial genomics and metagenomics, she received her MD and PhD from the University of California, San Francisco (Alpha Omega Alpha), followed by residency, chief residency and hematology/oncology fellowship training at Brigham and Women’s Hospital and the Dana-Farber Cancer Center at Harvard Medical School.  She joined the faculty at Stanford University in 2014 after completing a post-doctoral fellowship focused on genomics at the Broad Institute of Harvard and MIT.

Prof. Bhatt’s laboratory develops and applies novel molecular and computational tools to study strain level dynamics of the human microbiome, to understand how microbial genomes change over time and predict the functional output of microbiomes. She is keenly interested to understand how microbes use microproteins to “talk” to one another and to human cells, and to leverage this understanding to improve health and treat diseases. Her work is actively being translated from bench to bedside; for example, enzymes that her lab mined from microbes are now being developed these as human genome editing/engineering tools in a start-up company that she co-founded.

She has received multiple awards including the Chen Award of Excellence from the Human Genome Organisation (HUGO), the Distinguished Investigator Award from the Paul Allen Foundation, and the Sloan Foundation Fellowship; she is also an elected member of the American Society of Clinical Investigation and the 2024 American Society of Hematology William Dameshek Prize winner. She has disseminated her distinguished research globally, delivering more than 175 invited presentations. A committed mentor, she has served as the primary research advisor to a diverse cohort of over 60 undergraduate, medical, PhD, and post-doctoral scholars.

Dr. Bhatt is also leading efforts to ensure equity and global access in research and medicine. She carries out research with the H3Africa Genomics Consortium, volunteers for the nonprofit she co-founded in 2012, Global Oncology, and serves as the Director for Global Oncology for Stanford’s Center for Innovation in Global Health. She is working to improve collaboration and exchange between scholars at Stanford and those in South Asia, Africa, and beyond. She continues to practice medicine, caring for patients with hematological disorders. Outside of work, she enjoys strumming on the guitar and making her pour over coffee with scientific precision.

Kenya Honda, M.D., Ph.D., is a professor at Keio University School of Medicine and a Team Leader at RIKEN IMS. His research focuses on the interplay between the human host and endogenous microbiota. His group has made key contributions to understanding not only which microorganisms contribute to disease and how, but also which microorganisms are considered beneficial and could be used for treatment of disease. Notable achievements include identifying microbiota members that induce TH17 cells, Treg cells, TH1 cells, and CD8 T cells, as well as bile acid metabolizing microbes unique to centenarians.

He has been recognized as a Highly Cited Researcher by Clarivate Analytics from 2014 to 2023 and was awarded the Carlos J. Finlay UNESCO Prize for Microbiology in 2020. He is a scientific co-founder of Vedanta Bioscience and a scientific advisor of 4Bio Capital. Additionally, he serves on the advisory boards of Gut Microbes, Cell Host & Microbe, Nature Reviews Gastroenterology & Hepatology, and Current Opinion in Microbiology, and the Scientific Advisory Board of Science Translational Medicine.

Dr. Purna Kashyap is practicing gastroenterologist and Professor of Medicine and Physiology, the Bernard and Edith Waterman Director of the Microbiome program, and Director of the germ-free mouse facility in the Center for Individualized Medicine at Mayo Clinic, Rochester, MN. The NIH funded Gut Microbiome laboratory led by Dr. Kashyap is focused on delineating the complex interactions between diet, gut microbiome, and host gastrointestinal physiology.  The laboratory uses germ-free mouse models in conjunction with measures of gastrointestinal physiology in vitro and in vivo to investigate effects of gut microbial products on host gastrointestinal function. In parallel, they use a systems approach incorporating multi-omics, patient metadata, and physiologic tissue responses in human studies, to aid in discovery of novel microbial drivers of disease.

The overall goal of the program is to develop novel microbiota-targeted therapies. Dr. Kashyap has published nearly 100 peer reviewed articles including journals like Cell, Cell Host Microbe, Science Translational Medicine, Nature Communications, and Gastroenterology. He was inducted to American Society of Clinical Investigation in 2021. He has previously served on the scientific advisory board of American Gastroenterology Association Gut Microbiome Center, and on the council of American Neurogastroenterology and Motility Society. He now serves on the council and the research committee of AGA, in an editorial role for Gut Microbes and as an ad hoc reviewer on NIH study sections.

Dr. Marie-Claire Arrieta is an Associate Professor and Research Excellence Chair at the Cumming School of Medicine, University of Calgary. Her research focuses on the interactions between the early-life gut microbiome and infant development, using clinical and experimental approaches to understand mechanisms underlying host microbiome interactions. Dr. Arrieta’s contributions have been widely recognized, including the Canadian Institutes of Health Research (CIHR) Sick Kids New Investigator Award and the Killam Emerging Research Leader Award. Additionally, she was invited to join the College of New Scholars of the Royal Society of Canada, which honors exceptional early-career scholars across all fields.

Dr. Arrieta is also co-author of the best-selling book Let Them Eat Dirt and is actively involved in science communication and medical education on the microbiome.

Fredrik Bäckhed is professor of molecular medicine and has a PhD in infectious biology from Karolinska Institutet. He undertook post-doctoral training with Jeffrey Gordon at Washington University, St Louis, where he discovered that the gut microbiota can affect energy metabolism and contribute to the regulation of fat storage and obesity.

Fredrik Bäckhed and his research group combine clinically oriented research with gnotobiotic mouse models to understand the role of the gut microbiota in health and metabolic diseases.

During his postdoctoral training in Jeffrey Gordon's group at Washington University, St Louis, Fredrik Bäckhed identified the gut microbiota as a factor that controls fat storage in the host. At the Wallenberg Laboratory for Cardiovascular and Metabolic Research, his group focuses on improving our understanding of how the gut microbiota contributes to cardiometabolic diseases. His studies have shown, for example, that the gut microbiota is altered in individuals with prediabetes and untreated type 2 diabetes. His research also aims to identify "next generation" probiotics aimed at preventing the onset of metabolic diseases.

One goal is to use the knowledge gained to develop new microbiota-based therapies. A key finding towards this goal was the group’s identification of microbial metabolites as potential regulators of cardiometabolic diseases. Fredrik Bäckhed recently received the prestigious ERC Advanced Grant to translate this discovery into treatment. The idea is to prevent bacterial production of a metabolite that contributes to fibrosis in the heart, liver and other organs, and thereby reduce the risk of heart failure and the liver disease metabolic dysfunction-associated steatohepatitis (MASH, previously NASH).