John F. Brooks II - Circadian clock regulation at the host-microbe interface
Dr. John F. Brooks II
Assistant Professor, Princeton University
Bio Dr. John F. Brooks II completed his undergraduate work at the University of Michigan, Ann Arbor. After, he obtained his Ph.D. at Northwestern University, in the laboratory of Dr. Mark Mandel, where he became interested in understanding how animals form and maintain symbiotic associations with bacteria. To understand this question, he studied a unique animal model, in which the Hawaiian bobtail squid Euprymna scolopes forms an exclusive partnership with the bacteria, Vibrio fischeri. His thesis work examined how this symbiotic association forms, by systematically identifying the genes necessary for this interaction in a high-throughput screen. After his graduate work, he decided to pursue a postdoctoral fellowship with Dr. Lora Hooper at the University of Texas, Southwestern Medical Center. Here, Dr. Brooks, continued the study of animal-bacterial partnerships, by examining how the microorganisms that colonize the mammalian gastrointestinal tract, collectively known as the gut microbiota, regulate immunity. Dr. Brooks has made mechanistic discoveries on how the gut microbiota regulate animal immunity in coordination with a biological timer, known as the clock. As an Assistant Professor at Princeton University, his lab will continue to understand how the circadian clock, which couples physiological processes and gene expression programs to environmental light cycles, influences host-microbe dynamics at the intestinal epithelial barrier.
Symposium Talk Title The Microbiota Coordinates Diurnal Rhythms in Intestinal Innate immunity with the Host Circadian Clock
Abstract Environmental light cycles entrain circadian feeding behaviors in animals that produce rhythms in exposure to foodborne bacteria. It remains unclear whether there are corresponding immunological rhythms that anticipate this microbial exposure. Here, we show that the intestinal microbiota generates diurnal rhythms in innate immunity that synchronize with host feeding rhythms. Rhythmic expression of select antimicrobial proteins was driven by daily rhythms in epithelial attachment by segmented filamentous bacteria (SFB), a member of the mouse intestinal microbiota. Rhythmic SFB attachment was driven by the circadian clock through control of host feeding rhythms. Mechanistically, rhythmic SFB attachment activated an immunological circuit involving type 3 innate lymphoid cells (ILC3). This circuit triggered oscillations in epithelial STAT3 expression that produced rhythmic antimicrobial protein expression and caused resistance to intestinal bacterial infection to vary across the day-night cycle. Thus, host feeding rhythms are synchronized with rhythms in intestinal innate immunity that anticipate exogenous microbial exposure.
Learn more about Dr. Brooks and his research HERE.
Sophie Helaine - Salmonella persisters during infection
Dr. Sophie Helaine
Assistant Professor, Harvard Medical School Microbiology Dept
Bio I graduated from Universite Paris 5, France and moved to London in 2007 at Imperial College London for my postdoc. I obtained an MRC Career Development Award in 2015 to launch my independent career. In August 2019, I moved my lab from Imperial College London, UK and I joined the Department of Microbiology in Harvard Medical School. My lab studies the molecular mechanisms of bacterial persistence during infection.
Symposium Talk Title Salmonella persisters during infection
Abstract My lab studies the molecular mechanisms of bacterial persistence during infection. Bacterial persistence, characterized by chronic and relapsing infections, is a major threat to human health as these infections cause considerable morbidity and frequently require multiple courses of antibiotics. Such long-lasting infections are caused by a variety of bacterial pathogens including Mycobacterium tuberculosis, Salmonella, Pseudomonas and pathogenic Escherichia coli. We developed single cell reporters to track Salmonella growth history during macrophage and murine infections. It revealed the presence of non-growing bacteria in infected host cells, which had been hypothesized for decades but had remained elusive. Interaction between Salmonella and host macrophages has then proven to be a powerful and relevant model to study persister biology since we showed that the bacteria specifically respond to engulfment by the host defence cells by forming high proportions of persisters. I will present our characterization of how persisters survive antibiotics in this challenging environment.
Learn more about Dr. Helain and her research HERE.
Libusha Kelly - Phage ecology in the human body
Dr. Libusha Kelly
Associate Professor, Albert Einstein College of Medicine Department of Systems and Computational Biology and Department of Microbiology and Immunology; 2021–2022 Hrdy Fellow, Harvard Radcliffe Institute
Photo credit: HRI/Tony Rinaldo
Bio Libusha Kelly investigates how microbial communities impact human health and global ocean processes. Her lab’s work has discovered new, widespread viruses of bacteria (bacteriophages, or ‘phages’) in the oceans and has characterized the impact of microbial enzymes and metabolites in drug metabolism in the human body. She is an associate professor of Systems and Computational Biology and of microbiology and immunology at Albert Einstein College of Medicine. Kelly is the 2021-2022 Harvard Radcliffe Institute (HRI) Hrdy Fellow; at HRI she is working to illuminate the ecology of vaginal microbes in bacterial vaginosis (BV), the most common gynecological disorder in women of childbearing age, and in health.
Kelly completed a BA in human biology at Stanford University, a PhD in computational biology with Andrej Sali at the University of California, San Francisco, and postdoctoral work with Sallie W. Chisholm at the Massachusetts Institute of Technology. She was a visiting scientist at the National Library of Medicine and a member of the inaugural 2021 class of Google Cloud Research Innovators. Her research has been funded in part by the National Institutes of Health, the National Science Foundation, and the US Department of Defense.
Symposium Talk Title Phage ecology in the human body
Abstract Why do we have such a limited ability to translate basic research on the microbiome into the clinic? While the microbiome is strongly associated with numerous, physiologically diverse, diseases in humans, in most cases we lack a mechanistic understanding of how microbiomes reflect, or contribute to, disease. Our lab studies cryptic mediators of microbiome ecology, including chemical-chemical interactions and the functional role of phages, killers and manipulators of microbial metabolism. In this talk I will bring ground-breaking work on phages in marine environments into the context of the human body. I will discuss potential mechanisms of phage involvement in the occurrence and treatment of bacterial vaginosis, the most common gynecological condition in women of childbearing age. Our work must contend with vaginal microbiome diversity and microdiversity and identify how differences across populations present both challenges and opportunities for identifying fundamental features that define a healthy vaginal microbiome and those that presage a shift into a non-health-promoting state. We develop novel artificial intelligence/machine learning approaches for alignment-free discovery and classification of phages, and interrogate new paradigms for studying health and disease in the microbiome.
Karla J.F. Satchell - MARTX toxins: M is for multifunctional!
Karla J.F. Satchell, Ph.D.
Anne Stewart Youmans Professor of Microbiology, Northwestern University, Feinberg School of Medicine
PI & Co-Director, Center for Structural Genomics of Infectious Diseases
Bio Dr. Karla Satchell (nee Karla Fullner) earned her B.S. in Biology at Pacific Lutheran University in Tacoma WA in 1988 and completed a Ph.D. in Microbiology in 1996 at the University of Washington in Seattle. She conduct post-doctoral training at the University of Pittsburgh and at Harvard Medical School. During her post-doc, Dr. Satchell discovered a novel toxin now known as a representative of a large family of Multifunctional-Autoprocessing RTX toxins, or simply MARTX. Since joining the faculty at the Northwestern University Feinberg School of Medicine in Chicago in 2000, Dr. Satchell has continued to conduct research on the MARTX toxin of Vibrio cholerae, building a diverse program including biochemical and cell biology studies on the mechanism of action of the toxin and the role of the toxin in infection using mouse models. She has since 2008 expanded her research program to include studies of MARTX toxins of other pathogens, including Vibrio vulnificus, a bacterium that causes severe sepsis from seafood consumption. Her most recent work utilizes structure biology to understand the mechanism of a protease that cleaves oncogenic Ras. She recently showed this protease can be redirected to reduce tumorigenesis. In 2017, Dr. Satchell became the principal investigator of a multi-site center in high throughput structure determination for microbial pathogens. Her group in the center partners with infectious diseases researchers to support their programs with structural biology, particularly on topics of pathogenesis of antimicrobial resistant pathogens and mechanisms of antimicrobial resistance. In 2020, the center shifted to structural biology of SARS-CoV-2 and she built a research program on the viral methyltransferases and serum responses to COVID-19 infection. Across all the areas of research, she has published more than 100 research articles. In recognition of her work, she was the recipient of a Burroughs Wellcome Investigators in Pathogenesis of Infectious Diseases Award in 2006. She has been elected as a fellow for the American Academy of Microbiology and the American Association for the Advancement of Science. She is also active in teaching of graduate students and in 2016 was awarded the Driskill Dean’s Award for Excellence in Teaching.
Symposium Talk Title Vibrio MARTX Toxins: M is for Multifunctional! Integration of cell signaling by bacterial toxins.
Abstract Bacteria often coordinate secreted virulence factors to fine-tune the host response during infection. These coordinated events can include toxins counteracting or amplifying effects of another toxin. Multifunctional-autoprocessing repeats-in toxin (MARTX) toxins are large, secreted proteins that are a unique hybrid of secreted toxins and multi-effector delivery systems. Similar to many bacterial protein toxins, MARTX toxins are secreted from the bacteria and then form a pore in the host cell plasma membrane. At the membrane, the toxin translocates multiple cis-carried effector domains into the target cell cytosol. However, distinct from single function toxins that direct just one effector domain into cells, MARTX toxins have been found to carry up to 5 effector domains, selected from 10 known effector domains. An important feature of these toxins is that all the effectors linked together in a single polypeptide are delivered simultaneously to the same cell, at the same time, at equal molar ratio of 1:1:1:1:1. These have thus been dubbed “Cluster Bombs”. The impact on cell signaling as multiple effectors entering the same cell raising questions on how the multifunctionality impacts cell signaling, toxicity, and virulence. This talk will focus on MARTX toxins of Vibrio cholerae and Vibrio vulnificus, and how the action of actin depolymeration stimulates inflammation, but how other toxin effectors quash this signaling to create massive damage without sending out warning signals.
Learn more about Dr. Satchell and her research HERE.
Karthik Anantharaman - Viruses in microbiomes
Dr. Karthik Anantharaman
Assistant Professor, Department of Bacteriology, University of Wisconsin-Madison
Bio Karthik Anantharaman, Ph.D., is an assistant professor in the Department of Bacteriology at the University of Wisconsin-Madison, where his laboratory studies microbial and viral ecology. Anantharaman grew up in Mumbai, India and earned his B. Tech in Civil Engineering at the National Institute of Technology-Karnataka, India in 2007. Afterwards, he obtained his Ph.D in Earth and Environmental Sciences studying the microbiology of hydrothermal vents from the University of Michigan in 2014 under the supervision of Dr. Gregory Dick. During his postdoctoral training with Dr. Jillian Banfield at the University of California-Berkeley, he studied the microbial biogeochemistry of the terrestrial subsurface using high-resolution metagenomics. Anantharaman is the recipient of several awards, including the NSF CAREER, the NIH Outstanding Investigator Award, and the ASM Early Career Award for Environmental Research.
Anantharaman’s interdisciplinary research program uses a combination of computational, laboratory and field-based experiments to understand the microbial and viral processes that underpin biogeochemical transformations in marine and freshwater environments, and in human health. With increasing recognition that viruses and phage are integral components of all microbiomes, Anantharaman and his group are developing and applying state-of-the-art computational approaches and model systems to enable the study of viral ecology and interactions in nature.
Symposium Talk Title (Re)defining the roles of viruses in microbiomes
Abstract Viruses that infect microbes (typically referred to as bacteriophages, or phages) are amongst the most abundant biological entities in all ecosystems. By infecting and lysing microbial populations, phages can affect community composition and function which can directly impact ecosystems, biogeochemistry, and human health and disease. Increasing use of sequencing approaches such as metagenomics has allowed the generation of massive quantities of ‘viral dark matter’ from microbiomes, which refers to viruses, viral genomes, and proteins which are poorly characterized. In this talk, I will describe our newly developed computational toolbox to characterize phage ecology in microbiomes from genomic data. Our approaches allow for the study of phage at multiple resolutions and enable prediction of phage-microbe metabolic interactions at the scale of entire communities in human and environmental systems
Learn more about Dr. Anantharaman and his research HERE.
Otto X. Cordero - How the ocean digests complex organic matter
Dr. Otto X. Cordero
Associate Professor, Department of Civil & Environmental Engineering, Massachusetts Institute of Technology
Bio Otto X. Cordero received a B.S. in computer and electrical engineering from the Polytechnic University of Ecuador, an M.Sc. in artificial intelligence from Utrecht University, and a Ph.D. in theoretical biology, also from Utrecht University. His main research focus is the ecology and evolution of natural microbial collectives. The Cordero lab is interested in understanding how social and ecological interactions at micro-scales impact the global productivity, stability and evolutionary dynamics of microbial ecosystems.
Symposium Talk Title How the ocean digests complex organic matter: an eco-evo perspective
Abstract Just as microbes in our guts digest the complex fibers we eat, marine bacteria break down and digest the complex forms of organic matter that phyto- and zoo-plankton produce in the surface ocean. This biological process is key for life on the planet, as it returns carbon back to the atmosphere and balances the elemental cycles that sustain life. Complex organic matter is made up of long polymer chains packed in matrices, which cannot be directly absorbed by cells. Instead, bacteria need to first excrete enzymes that digest polymers into smaller, soluble molecules, a process that triggers a surprising cascade of microbial interactions that determine the mode and tempo of carbon consumption. In this talk I will focus on three key type of interactions that define this process: the transfer of carbon between different species of bacteria occupying well-defined metabolic guilds, the awakening of dormant viruses in the genomes of polymer degraders, and the emergence of cooperative, multicellular cell structures within which polymer-degrading organisms divide metabolic labor. Throughout my talk, I will highlight how studying these natural, polymer-degrading ecosystems can inform emerging efforts in microbiome engineering.
Learn more about Dr. Cordero and his research HERE.
Wally Fulweiler - All the nitrogen fixation we cannot see
Dr. Robinson W. ("Wally") Fulweiler
Professor, Department of Earth and Environment & Department of Biology, Boston University
Bio I am ecosystems ecologist and biogeochemist by training. I head a laboratory at Boston University where our research is focused on answering fundamental questions about energy flow and biogeochemical cycling of nutrients (nitrogen, phosphorus, and silica), carbon, and oxygen in a variety of environments. I am especially interested in how anthropogenic activities affect the ecology and elemental cycling of ecosystems on a variety of scales, from local nutrient loading to global climate change. Our latest research is centered on the transformations of elements across the land-ocean continuum, the ultimate fate of nitrogen in the marine environment, the impact of climate change on benthic-pelagic coupling, and the role of coastal systems in greenhouse gas budgets.
I earned my MS (2003) and my Ph.D. (2007) in Oceanography from the Graduate School of Oceanography at the University of Rhode Island following which I completed postdoctoral research at Louisiana State University. In 2008 I started at Boston University and founded my lab. I was awarded tenure in the Department of Earth and Environment and the Department of Biology in 2014, and was promoted to Professor in the spring of 2021. My professional honors include a Sloan Fellowship in 2012, the Cronin award from the Coastal Estuarine Research Federation in 2013, and the Metcalf Cup and Prize in 2019 - BU's highest teaching and mentoring award. In addition to my scientific endeavors, I am a passionate advocate for women and parents, especially mothers, in science. My goal is to create an equitable scientific community where individuals do not simply survive but thrive.
Symposium Talk Title All the nitrogen fixation we cannot see – building the case for the importance and the why of coastal sediment nitrogen fixation
Abstract Nitrogen fixation is an essential process in the global nitrogen cycling providing biologically usable nitrogen to the biosphere. While much work has focused on quantifying the rates and importance of nitrogen in terrestrial and ocean environments, nitrogen fixation is coastal marine sediments is largely unconstrained. There are a variety of reasons for this – e.g., it is logistically challenging and expensive to measure, some widely used methodologies introduce significant error, and the paradigm has long been that nitrogen fixation is simply not an important process in these environments. Research over the last two decades however demonstrate that heterotrophic nitrogen fixation frequently occurs in coastal sediments – from brackish to euhaline habitats. Further, nitrogen fixation rates can be on par with and even exceed rates of sediment denitrification. Despite mounting evidence these data are often met with skepticism – why would microbes, seemingly bathed in ammonium, conduct this energetically expensive process? In contrast to this viewpoint, I argue that sediments are ideal environments for nitrogen fixation. In this seminar I will discuss what we currently know about heterotrophic nitrogen fixation in coastal marine environments. I will also present four possible reasons for its occurrence in coastal sediments. Finally, I will describe the potential role nitrogen fixation plays in coastal nitrogen cycle and ecosystem function.
Learn more about Dr. Fulweiler and her research HERE.
Andrea Giometto - Evolutionary adaptation to range expansion
Dr. Andrea Giometto
Assistant Professor, Cornell University
Bio Andrea Giometto received a bachelor’s degree in Physics and a master’s degree in Theoretical Physics from Padua University. He completed his Ph.D. in Civil and Environmental Engineering at the École Polytechnique Fédérale de Lausanne (EPFL) in 2015. From 2015 to 2020, he was a Postdoctoral Fellow in the Department of Physics and in the Department of Molecular and Cellular Biology at Harvard University, where he investigated the spatiotemporal dynamics of microbial populations. He joined the faculty of the School of Civil and Environmental Engineering at Cornell University in the Summer of 2020.
Symposium Talk Title Evolutionary adaptation of non-motile cells to range expansion
Abstract Dense populations of non-motile microbes expand by cell growth and division while interacting mechanically with neighboring cells. Recent experimental and theoretical results have shown that mechanical forces among dividing cells in microbial colonies reduce the power of natural selection, prolonging the survival of deleterious mutations and reducing the rate at which beneficial mutations expand in these populations. These interactions also favor the maintenance of genetic diversity in colonies growing in time-varying environments. However, evolutionary adaptations may change the way in which cells interact mechanically with each other, which in turn may lead to changes to the effectiveness of natural selection. To investigate this possibility, we performed an evolutionary experiment in which we repeatedly selected cells at the front of Saccharomyces cerevisiae colonies and started new range expansions with them. We found that the imposed selection for faster expansion led to marked changes in cell shape that altered the mechanical interaction between neighboring cells, favoring faster expansion of the colony, but also increasing genetic drift, thereby further reducing the effectiveness of natural selection. Pathogenic strains of yeast are often elongated, a cell shape that is thought to promote invasiveness into tissues of plants and animals. Our results suggest that such elongated cell shapes may have emerged from selection for spatial expansion on surfaces.
Learn more about Dr. Giometto and his research HERE.
Science Art Features
Ellie Jameson - Drawn Phage and Bacteria
Dr. Ellie Jameson
Lecturer of Environmental Virology, Bangor University School of Natural Sciences
Bio I am an environmental microbiologist who researches the functional role of bacteriophages (phages for short - viruses that infect bacteria). I carried out a PhD at Plymouth Marine Laboratory studying cyanobacteria and their phages in the Atlantic Ocean. I subsequently went on to investigate biotechnological applications of microbes at the Universities of Bangor and Exeter. This led on to me starting my own lab at the University of Warwick where I lead research on phages, particularly on their characterisation, antibiofilm properties, roles and applications in diverse environments from clinical settings to soils. I have supplied phages for phage therapy in patients with antimicrobial resistant bacterial infections.
Alongside the science I have developed my own Sci-Art to communicate my science and that of other scientists. This has involved producing art for book covers, figures, posters, graphical abstracts and a quarterly cartoon for the Phage journal. I have recently taken up a position at Bangor University where I works on both medical and environmental applications of phages. My research encompasses many aspects of phage biology with the has focused on understanding fundamental phage biology, with the ambition of applying phages for the safe, reliable control of problematic bacteria in clinical and agricultural settings.
Research & Sci-Art Interests My research into bacteriophages (phages for short - viruses that infect bacteria) is exciting and has led to scientific advances in my chosen field of research. I am also a keen artist, and in 2019 started sharing my art through twitter. This began as a few drawings and paintings of bacteria. I had more positive feedback than I expected, which inspired me to carry on and take part in Inktober – doing one ink drawing every day for the month of October and posting it online. I enjoyed the challenge of fitting a microbial drawing to each prompt word. It has also encouraged me to understand and read about areas of microbiology I was unfamiliar with to ensure the explanatory text that accompanies them is accurate. The drawings are based on real science, with some artistic licence to reach a broader audience and make them visually appealing.
Sci-Art has been a fantastic springboard to make me well known to phage researchers. It has led to working with individuals, Universities and companies to better communicate scientific ideas to a wider audience. Sci-Art has helped me to think more broadly and promote my own science and publications. Much as well-written articles help to communicate the essence of research and guide readers to understand the science; bold, cohesive Sci-Art can improve interpretation and complement the science. The Sci-Art community has been welcoming giving me a creative outlet and it has improved communication of my research.
Bryan Mounce - Crocheted Viruses
Dr. Bryan Mounce
Assistant Professor, Loyola University Chicago, Department of Microbiology & Immunology
Bio Originally from small-town western Wisconsin, Bryan grew up with an interest in math, science, and creative arts. Bryan pursued BS degrees in mathematics and genetics at UW-Madison and a PhD in microbiology and immunology at the Medical College of Wisconsin. During his PhD, Bryan developed an interest in fiber arts and making small creatures out of yarn, which blossomed into more science-themed crochet and knitting during his postdoctoral fellowship at the Institut Pasteur in Paris, where he worked on emerging RNA viruses. Now with his independent laboratory at Loyola University Chicago, Bryan continues to create science-themed fiber art, including crocheted viruses.
Research & Sci-Art Interests In the Mounce laboratory, we focus on host-pathogen interactions, with specific interests in how RNA viruses interface with cellular metabolism. We use a number of different virus models, including enteroviruses, alphaviruses, and bunyaviruses, to investigate how these viruses use polyamines, small positively-charged molecules found in all cells. We're endlessly intrigued by how viruses use and manipulate polyamines to replicate within cells, and we're also interested in how polyamines help cells survive and fight off virus infection.
My yarn creations reflect our interest in pathogens, with an approach of making these pathogens more approachable to a broader audience. Originally, I made yarn viruses to share with friends at conferences, and when they became quite popular, I branched into other creations, including pipets, vaccines, antibodies, and bacteria. Science and even these pathogens can be beautiful, and I try to reflect this by making the little yarn creations more approachable, with bright colors and cartoonish eyes. I hope to continue challenging my creativity and developing more patterns and creations to communicate science to more and show how great virology research is.
Azul Pinochet-Barros - Science Photography
Dr. Azul Pinochet-Barros
Postdoctoral Fellow in the Kaçar Lab, NASA Center for Early Life & Evolution & Department of Bactriology, University of Wisconsin-Madison
Bio Azul Pinochet-Barros is an astrobiologist originally from Spain. Having previously studied metal homeostasis in present-day microbes, she now looks to understand how past metal usage has impacted the evolution of early life on Earth.
Research & Sci-Art Interests Azul Pinochet-Barros is an astrobiologist studying early Earth biology through the resurrection of ancient genes in present-day microbial systems. Specifically, she studies how metal conditions in the early Earth could have shaped the emergence of life as we know it via the evolution of key metalloenzymes like nitrogenase. This work not only informs us on the requirements of life on our home planet, Earth, but can also guide us to a better understanding of what life might potentially need in worlds beyond our own.
Azul's science photography centers on a variety of scientific themes, particularly microbiology and astronomy. She focuses on specific elements in her imagery and casts them in an abstract light. This dream-like lens enhances that fundamental sense of awe and wonder that drives science forward, from tiny microbes to the vast cosmos. In her 2018 interview with MUSÉE MAGAZINE she says: "I happen to think that people, to a greater or lesser extent, always seek out science and art because, as humans, we are naturally curious beings who are inherently attracted to aesthetic form. With this in mind, I wish to communicate science, the scientific experience, and ultimately in this way tap into my audience’s sense of awe and curiosity. If I can do this, it not only validates my worldview, but also sets the stage for the public to engage more with the scientific community."