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 gastrointestinal tract, skin, mammary glands, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, and the biliary 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 Harvard T.H. Chan School of Public Health is the public health school of Harvard University, located in the Longwood Medical Area of Boston, Massachusetts. The school grew out of the Harvard-MIT School for Health Officers, the nation's first graduate training program in population health, which was founded in 1913 and then became the Harvard School of Public Health in 1922.
Gut microbiota, gut microbiome, or gut flora are the microorganisms, including bacteria, archaea, fungi, and viruses, that live in the digestive tracts of animals. The gastrointestinal metagenome is the aggregate of all the genomes of the gut microbiota. The gut is the main location of the human microbiome. The gut microbiota has broad impacts, including effects on colonization, resistance to pathogens, maintaining the intestinal epithelium, metabolizing dietary and pharmaceutical compounds, controlling immune function, and even behavior through the gut–brain axis.
Dysbiosis is characterized by a disruption to the microbiome resulting in an imbalance in the microbiota, changes in their functional composition and metabolic activities, or a shift in their local distribution. For example, a part of the human microbiota such as the skin flora, gut flora, or vaginal flora, can become deranged (unbalanced), when normally dominating species become underrepresented and species that normally are outcompeted or contained increase to fill the void. Similar to the human gut microbiome, diverse microbes colonize the plant rhizosphere, and dysbiosis in the rhizosphere, can negatively impact plant health. Dysbiosis is most commonly reported as a condition in the gastrointestinal tract or plant rhizosphere.
Microecology means microbial ecology or ecology of a microhabitat. It is a large field that includes many topics such as: evolution, biodiversity, exobiology, ecology, bioremediation, recycling, and food microbiology. It can also refer to a hybrid urban network at the scale of the neighbourhood. It is the study of the interactions between living organisms and their environment, and how these interactions affect the organisms and their environment. Additionally, it is a multidisciplinary area of study, combining elements of biology, chemistry, physics, mathematics and urban planning. It focuses on the study of the interactions between microorganisms and the environment they inhabit, their effects on the environment, and their effects on other organisms. Microecology also studies the effects of human activity on the environment and how this affects the growth and development of microorganisms or organic structures. Microecology has many applications in the fields of medicine, agriculture, biotechnology and design. It is also important for understanding the cycling of nutrients in the environment, and the behavior of microorganisms or actors in various environments.
Long-term close-knit interactions between symbiotic microbes and their host can alter host immune system responses to other microorganisms, including pathogens, and are required to maintain proper homeostasis. The immune system is a host defense system consisting of anatomical physical barriers as well as physiological and cellular responses, which protect the host against harmful microorganisms while limiting host responses to harmless symbionts. Humans are home to 1013 to 1014 bacteria, roughly equivalent to the number of human cells, and while these bacteria can be pathogenic to their host most of them are mutually beneficial to both the host and bacteria.
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.
Mucosal immunology is the study of immune system responses that occur at mucosal membranes of the intestines, the urogenital tract, and the respiratory system. The mucous membranes are in constant contact with microorganisms, food, and inhaled antigens. In healthy states, the mucosal immune system protects the organism against infectious pathogens and maintains a tolerance towards non-harmful commensal microbes and benign environmental substances. Disruption of this balance between tolerance and deprivation of pathogens can lead to pathological conditions such as food allergies, irritable bowel syndrome, susceptibility to infections, and more.
Skin immunity is a property of skin that allows it to resist infections from pathogens. In addition to providing a passive physical barrier against infection, the skin also contains elements of the innate and adaptive immune systems which allows it to actively fight infections. Hence the skin provides defense in depth against infection.
The gut–brain axis is the two-way biochemical signaling that takes place between the gastrointestinal tract and the central nervous system (CNS). The term "microbiota–gut–brain axis" highlights the role of gut microbiota in these biochemical signaling. Broadly defined, the gut–brain axis includes the central nervous system, neuroendocrine system, neuroimmune systems, the hypothalamic–pituitary–adrenal axis, sympathetic and parasympathetic arms of the autonomic nervous system, the enteric nervous system, vagus nerve, and the gut microbiota.
The altered Schaedler flora (ASF) is a community of eight bacterial species: two lactobacilli, one Bacteroides, one spiral bacterium of the Flexistipes genus, and four extremely oxygen sensitive (EOS) fusiform-shaped species. The bacteria are selected for their dominance and persistence in the normal microflora of mice, and for their ability to be isolated and grown in laboratory settings. Germ-free animals, mainly mice, are colonized with ASF for the purpose of studying the gastrointestinal (GI) tract. Intestinal mutualistic bacteria play an important role in affecting gene expression of the GI tract, immune responses, nutrient absorption, and pathogen resistance. The standardized microbial cocktail enabled the controlled study of microbe and host interactions, role of microbes, pathogen effects, and intestinal immunity and disease association, such as cancer, inflammatory bowel disease, diabetes, and other inflammatory or autoimmune diseases. Also, compared to germfree animals, ASF mice have fully developed immune system, resistance to opportunistic pathogens, and normal GI function and health, and are a great representation of normal mice.
Alessio Fasano is an Italian-born medical doctor, pediatric gastroenterologist and researcher. He currently holds many roles, including professor of pediatrics at Harvard Medical School and professor of nutrition at Harvard T.H. Chan School of Public Health, both in Boston. He serves as director of the Center for Celiac Research and Treatment at MassGeneral Hospital for Children (MGHfC) and co-director of the Harvard Medical School Celiac Research Program. In addition, he is director of the Mucosal Immunology and Biology Research Center at MGHfC, where he oversees a research program with approximately 50 scientists and staff researching a variety of acute and chronic inflammatory diseases, including cystic fibrosis, celiac disease, enteric infections and necrotizing enterocolitis. A common theme of these programs is the study of the emerging role of the gut microbiome in health and disease. Fasano is also the scientific director of the European Biomedical Research Institute of Salerno (EBRIS) in Italy. Along with these leadership positions, he is a practicing outpatient clinician in pediatric gastroenterology and nutrition and the division chief.
Curtis Huttenhower is a Professor of Computational Biology and Bioinformatics in the Department of Biostatistics, School of Public Health, Harvard University.
Michael Andrew Fischbach is an American chemist, microbiologist, and geneticist. He is an associate professor of Bioengineering and ChEM-H Faculty Fellow at Stanford University and a Chan Zuckerberg Biohub Investigator.
Eric J. Rubin is an American microbiologist, infectious disease specialist, and is currently the editor-in-chief of the New England Journal of Medicine. He is also an adjunct professor of immunology and infectious diseases and was formerly the Irene Heinz Given Professor and chair of the department of immunology and infectious diseases at the Harvard T.H. Chan School of Public Health. His research laboratory works on Mycobacterium tuberculosis, nontuberculous mycobacteria (NTMs), and the development and application of bacterial genetics tools to study the fundamental biology of these pathogenic organisms. He holds an M.D. from the School of Medicine as well as a Ph.D. from the Graduate School of Biomedical Sciences at Tufts University.
Yasmine Belkaid; is an immunologist, currently President of the Institut Pasteur. She has Algerian citizenship by her father and French citizenship by her mother, and she also holds US citizenship.
Sarah Merritt Fortune is an American immunologist. She is a Full Professor of Immunology and Infectious Diseases in the Department of Immunology and Infectious Diseases at the Harvard T.H. Chan School of Public Health.
Eran Elinav is an Israeli immunologist and microbiota researcher at the Weizmann Institute of Science and the DKFZ.
Dennis L. Kasper is an American microbiologist and immunologist, and the William Ellery Channing Professor of Medicine and Professor of Immunology at Harvard Medical School. He leads the Kasper Laboratory within the Blavatnik Institute in the Department of Immunology at Harvard Medical School. He was also executive dean for academic programs at Harvard Medical School and director of the Channing Laboratory Department of Medicine at Brigham and Women's Hospital.
Sidonia Făgărășan is a Romanian biological scientist who is a professor at the Riken Institute in Japan. Her research considers the molecular mechanisms that underpin processes in gut microbioata and the mucosal barrier. In 2020, she was awarded the Kobayashi Foundation Award.
