Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy national laboratories, managed by the Department of Energy's (DOE) Office of Science. The main campus of the laboratory is in Richland, Washington.
The human microbiome is the aggregate of all microbiota that reside on or within human tissues and biofluids along with the corresponding anatomical sites in which they reside, including the skin, mammary glands, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, biliary tract, and gastrointestinal tract. Types of human microbiota include bacteria, archaea, fungi, protists, and viruses. Though micro-animals can also live on the human body, they are typically excluded from this definition. In the context of genomics, the term human microbiome is sometimes used to refer to the collective genomes of resident microorganisms; however, the term human metagenome has the same meaning.
The Joint Genome Institute (JGI) is a scientific user facility for integrative genomic science at Lawrence Berkeley National Laboratory. The mission of the JGI is to advance genomics research in support of the United States Department of Energy's (DOE) missions of energy and the environment. It is one of three national scientific user facilities supported by the Office of Biological and Environmental Research (BER) within the Department of Energy's Office of Research. These BER facilities are part of a more extensive network of 28 national scientific user facilities that operate at the DOE national laboratories.
Jeffrey Ivan Gordon is a biologist and the Dr. Robert J. Glaser Distinguished University Professor and Director of the Center for Genome Sciences and Systems Biology at Washington University in St. Louis. He is internationally known for his research on gastrointestinal development and how gut microbial communities affect normal intestinal function, shape various aspects of human physiology including our nutritional status, and affect predisposition to diseases. He is a member of the National Academy of Sciences, the American Academy of Arts and Sciences, the Institute of Medicine of the National Academies, and the American Philosophical Society.
The Human Microbiome Project (HMP) was a United States National Institutes of Health (NIH) research initiative to improve understanding of the microbiota involved in human health and disease. Launched in 2007, the first phase (HMP1) focused on identifying and characterizing human microbiota. The second phase, known as the Integrative Human Microbiome Project (iHMP) launched in 2014 with the aim of generating resources to characterize the microbiome and elucidating the roles of microbes in health and disease states. The program received $170 million in funding by the NIH Common Fund from 2007 to 2016.
Microbiota are the range of microorganisms that may be commensal, mutualistic, or pathogenic found in and on all multicellular organisms, including plants. Microbiota include bacteria, archaea, protists, fungi, and viruses, and have been found to be crucial for immunologic, hormonal, and metabolic homeostasis of their host.
The Earth Microbiome Project (EMP) is an initiative founded by Janet Jansson, Jack Gilbert and Rob Knight in 2010 to collect natural samples and to analyze the microbial community around the globe.
A microbiome is the community of microorganisms that can usually be found living together in any given habitat. It was defined more precisely in 1988 by Whipps et al. as "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity". In 2020, an international panel of experts published the outcome of their discussions on the definition of the microbiome. They proposed a definition of the microbiome based on a revival of the "compact, clear, and comprehensive description of the term" as originally provided by Whipps et al., but supplemented with two explanatory paragraphs. The first explanatory paragraph pronounces the dynamic character of the microbiome, and the second explanatory paragraph clearly separates the term microbiota from the term microbiome.
David Arnold Relman is an American microbiologist and the Thomas C. and Joan M. Merigan Professor in Medicine, and in Microbiology & Immunology at the Stanford University School of Medicine. His research focuses on the human microbiome and microbial ecosystem—for which he was a pioneer in the use of modern molecular methods, as well as on pathogen discovery and the genomics of host response.
B. Brett Finlay, is a Canadian microbiologist well known for his contributions to understanding how microbes cause disease in people and developing new tools for fighting infections, as well as the role the microbiota plays in human health and disease. Science.ca describes him as one of the world's foremost experts on the molecular understanding of the ways bacteria infect their hosts. He also led the SARS Accelerated Vaccine Initiative (SAVI) and developed vaccines to SARS and a bovine vaccine to E. coli O157:H7. His current research interests focus on pathogenic E. coli and Salmonella pathogenicity, and the role of the microbiota in infections, asthma, and malnutrition. He is currently the UBC Peter Wall Distinguished Professor and a Professor in the Michael Smith Laboratories, Microbiology and Immunology, and Biochemistry and Molecular Biology, and Co-director and Senior Fellow for the CIFAR Humans and Microbes program. He is also co-author of the book Let Them Eat Dirt: Saving Your Child from an Oversanitized World and The Whole-Body Microbiome: How to Harness Microbes - Inside and Out - For Lifelong Health. Finlay is the author of over 500 publications in peer-reviewed journals and served as editor of several professional publications for many years.
Pharmacomicrobiomics, proposed by Prof. Marco Candela for the ERC-2009-StG project call, and publicly coined for the first time in 2010 by Rizkallah et al., is defined as the effect of microbiome variations on drug disposition, action, and toxicity. Pharmacomicrobiomics is concerned with the interaction between xenobiotics, or foreign compounds, and the gut microbiome. It is estimated that over 100 trillion prokaryotes representing more than 1000 species reside in the gut. Within the gut, microbes help modulate developmental, immunological and nutrition host functions. The aggregate genome of microbes extends the metabolic capabilities of humans, allowing them to capture nutrients from diverse sources. Namely, through the secretion of enzymes that assist in the metabolism of chemicals foreign to the body, modification of liver and intestinal enzymes, and modulation of the expression of human metabolic genes, microbes can significantly impact the ingestion of xenobiotics.
Emily P. Balskus is an American chemical biologist, enzymologist, microbiologist, and biochemist born in Cincinnati, Ohio in 1980. She has been on the faculty of the Chemistry and Chemical Biology department of Harvard University since 2011 and is currently the Morris Kahn Professor. She has published more than 80 peer-reviewed papers and three book chapters. Since 2012 she has been invited to give over 170 lectures, has held positions on various editorial boards, and served as a reviewer for ACS and Nature journals among others. Balskus also currently serves as a consultant for Novartis, Kintai Therapeutics, and Merck & Co.
Abigail A. Salyers was a microbiologist who pioneered the field of human microbiome research. Her work on the bacterial phylum Bacteroidetes and its ecology led to a better understanding of antibiotic resistance and mobile genetic elements. At a time where the prevailing paradigm was focused on E. coli as a model organism, Salyers emphasized the importance of investigating the breadth of microbial diversity. She was one of the first to conceptualize the human body as a microbial ecosystem. Over the course of her 40 year career, she was presented with numerous awards for teaching and research and an honorary degree from ETH Zurich, and served as president of the American Society for Microbiology.
Jennifer B. H. Martiny is an American ecologist who is a professor at the University of California, Irvine. Her research considers microbial diversity in marine and terrestrial ecosystems. In 2020 she was elected a Fellow of the American Association for the Advancement of Science.
Regina Lamendella is an American Professor of Microbiology. She is best known for the use of omics for applied studies of microbiology in natural waterways and the guts of animals, including humans.
Emma Allen-Vercoe is a British-Canadian Molecular biologist who is a Professor and Canada Research Chair at the University of Guelph. Her research considers the gut microbiome and microbial therapeutics to treat Escherichia coli.
Maria Gloria Dominguez-Bello is a Venezuelan-American microbial ecologist that has worked on adaptations of gut fermentation organs in animals, gastric colonization by bacteria, assembly of the microbiota in early life, effect of practices that reduce microbiota transmission and colonization in humans, and effect of urbanization. She is the Henry Rutgers Professor of Microbiome and Health at Rutgers University, New Brunswick. She is the Director of the New Jersey Institute for Food, Nutrition, and Health. Her lab at Rutgers collaborates in multidisciplinary science, integrating microbiology, immunology, pediatrics, nutrition, anthropology, environmental engineering and architecture/urban studies, and microbial ecology.
A. Murat Eren (Meren) is a computer scientist known for his work on microbial ecology and developing novel, open-source, computational tools for analysis of large data sets.
Jennifer Pett-Ridge is an American biologist who is a senior staff scientist at the Lawrence Livermore National Laboratory. She also serves as an adjunct professor at the University of California, Merced. Her research makes use of systems biology and geochemistry to uncover function in microbial communities. She was awarded a 2021 United States Department of Energy Ernest Orlando Lawrence Award.
Ashley L. Shade is the Director of Research at the Institute of Ecology and the Environment within Le Centre National de la Recherche Scientifique. Shade is an associate professor at Michigan State University in the Department of Microbiology and Molecular Genetics and Department of Plant, Soil and Microbial Sciences. She is best known for her work in microbial ecology and plant-microbe interactions.
