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Suggested Citation:"Appendix D: Glossary." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
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Appendix D

Glossary

Adaptive immune system: A collective term given to a group of highly specialized, systematic cells and processes that prevent vertebrates from certain death by pathogenic infections. (Alberts B, et al. 2002. Molecular Biology of the Cell, 4th Edition. New York: Garland Science.)

Anoxic: An absence or deficiency of oxygen reaching the tissues. (The Oxford English Dictionary)

Archaea: One of the three main branches of evolutionary descent (Archaea, Eukaryota, and Bacteria), archaea are single-celled organisms once classified as extremophiles (being found in harsh environments such as hot springs and salt lakes), yet recent evidence shows that archaea are widely distributed in nature. (IOM [Institute of Medicine]. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press.)

Axenic: Free of all microorganisms, including those that are typically found in the gut (thus truly germ free). Axenic mice (for example) are produced by hysterectomy rederivation and must be maintained in isolators under very strict handling procedures to keep them germ-free. (The Jackson Laboratory: https://www.jax.org/news-and-insights/jax-blog/2013/may/the-difference-between-germ-free-andspecific-pathogen-free-mice. Accessed March 2, 2018.)

Bacteria: Microscopic, single-celled organisms that have some biochemical and structural features different from those of animal and plant cells. (IOM. 2014. Microbial Ecology in States of Health and Disease: Workshop Summary. Washington, DC: The National Academies Press.)

Commensal/commensalism: Two (or more) species coexist, one deriving benefit from the relationship without harm or obvious benefit to the other. (IOM. 2014. Microbial Ecology in States of Health and Disease: Workshop Summary. Washington, DC: The National Academies Press.)

Suggested Citation:"Appendix D: Glossary." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×

Commensal organism: An organism that derives benefits from its association with humans or animals without causing harm (NASEM [National Academies of Sciences, Engineering, and Medicine]. 2017. Microbiomes of the Built Environment: A Research Agenda for Indoor Microbiology, Human Health, and Buildings. Washington, DC: The National Academies Press. doi: https://doi.org/10.17226/23647.)

Conventionalization: A method in which germ-free animals (particularly mice) are inoculated with gut microbiota to populate the gastrointestinal tract. (Cho I, Blaser MJ. 2012. The human microbiome: At the interface of health and disease. Nat Rev Genet 13:260-270.)

Ecosystem: A biological community of interacting organisms and their physical environment. (The Oxford English Dictionary)

Effector strain: Molecules that either facilitate infection (virulence factors or toxins) or that trigger host defense (avirulence factors or elicitors). (Kamoun S. 2006. A catalogue of the effector secretome of plant pathogenic oomycetes. Annu Rev Phytopathol 44:41-60.)

Endogenous: Growing or originating from within an organism. (The Oxford English Dictionary)

Enteroids: Epithelial structures that contain crypt- and villus-like domains reminiscent of normal gut epithelium. Commonly termed “enteroids” when derived from the small intestine and “colonoids” when derived from the colon, they are different from organoids that also contain mesenchymal tissue. (Mahe MM, et al. 2015. Establishment of human epithelial enteroids and colonoids from whole tissue and biopsy. J Vis Exp 97:e52483.)

Eukaryota: One of the three domains of life. The two other domains, Bacteria and Archaea, are prokaryotic and lack several features characteristic of eukaryotes (e.g., cells containing a nucleus surrounded by a membrane and with DNA bound together by proteins [histones] into chromosomes). Animals, plants, and fungi are all eukaryotic organisms. (IOM. 2014. Microbial Ecology in States of Health and Disease: Workshop Summary. Washington, DC: The National Academies Press.)

Genome: The complete set of genetic information in an organism. In bacteria, this includes the chromosome(s) and plasmids (extra-chromosomal DNA molecules that can replicate autonomously within a bacterial cell). (Ibid.)

Suggested Citation:"Appendix D: Glossary." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×

Genomics: The study of genes and their associated functions. (Ibid.)

Genotype: In a broad sense, the term genotype refers to the genetic makeup of an organism; in other words, it describes an organism’s complete set of genes. In a narrower sense, the term can be used to refer to the alleles, or variant forms of a gene, that are carried by an organism. (SciTable by Nature Education: https://www.nature.com/scitable/definition/genotype-234. Accessed March 2, 2018.)

Gnotobiotic: An animal that is colonized solely by known strains of bacteria or other microorganisms. The term also describes germ-free animals because the status of their microbial communities is known. (Cho I, Blaser MJ. 2012. The human microbiome: At the interface of health and disease. Nat Rev Genet 13:260-270.)

Gram negative: Refers to the inability of a microorganism to accept a certain stain. This ability is related to the cell wall composition of the microorganism and has been useful in classifying bacteria. (IOM. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press.)

Gram positive: Refers to the ability of a microorganism to accept a certain stain. This ability is related to the cell wall composition of the microorganism and has been useful in classifying bacteria. (IOM. 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press.)

Homolog: One of two or more genes that are similar in sequence as a result of derivation from the same ancestral gene. The term covers both orthologs and paralogs. (IOM. 2009. Microbial Evolution and Co-Adaptation: A Tribute to the Life and Scientific Legacies of Joshua Lederberg. Washington, DC: The National Academies Press.)

Immunophenotype/immunophenotyping: A process that uses antibodies to identify cells based on the types of antigens or markers on the surface of the cells. Immunophenotyping may also be used to separate cells into different groups based on the markers they have on the surface. (National Cancer Institute Dictionary of Cancer Terms: https://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=341450. Accessed March 2, 2018.)

Infection: The invasion of the body or a part of the body by a pathogenic agent, such as a microorganism or virus. Under favorable conditions, the agent develops or multiplies, with results that may produce injurious effects. (IOM. 2014. Microbial Ecology in States of Health and Disease: Workshop Summary. Washington, DC: The National Academies Press.)

Suggested Citation:"Appendix D: Glossary." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×

Innate immune system: Innate (natural) immunity is so named because it is present at birth and does not have to be learned through exposure to an invader. It thus provides an immediate response to foreign invaders. However, its components treat all foreign invaders in the same way. They recognize only a limited number of identifying substances (antigens) on foreign invaders. However, these antigens are present on many different invaders. Innate immunity, unlike acquired immunity, has no memory of the encounters, does not remember specific foreign antigens, and does not provide any ongoing protection against future infection. (Merck Manual: http://www.merckmanuals.com/home/immune-disorders/biologyof-the-immune-system/innate-immunity. Accessed March 2, 2018.)

Islet: A portion of tissue structurally distinct from surrounding tissues. (The Oxford English Dictionary)

Isobiotic: Colonized with only a defined set of microbes. (Stappenbeck TS, Virgin HW. 2016. Accounting for reciprocal host-microbiome interactions in experimental science. Nature 534:191-199.)

Isogenic: Organisms having the same or closely similar genotypes. (The Oxford English Dictionary)

Loci: The positions of a gene or mutation on a chromosome. (The Oxford English Dictionary)

Metabolites: Substances made or used when the body breaks down food, drugs or chemicals, or its own tissue (for example, fat or muscle tissue). This process, called metabolism, makes energy and the materials needed for growth, reproduction, and maintaining health. It also helps get rid of toxic substances. (National Cancer Institute Dictionary of Cancer Terms: https://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=462687. Accessed March 2, 2018.)

Metabolome: The census of all metabolites present in any given tissue, space, or sample. (Adapted from Marchesi JR, Ravel J. 2015. The vocabulary of microbiome research: A proposal. Microbiome 3(1):31. Cited in NASEM. 2017. Microbiomes of the Built Environment: A Research Agenda for Indoor Microbiology, Human Health, and Buildings. Washington, DC: The National Academies Press. doi: https://doi.org/10.17226/23647.)

Metabolomics: Systematic global analysis of nonpeptide small molecules, such as vitamins, sugars, hormones, fatty acids, and other metabolites. It is distinct from traditional analyses that target only individual metabolites or pathways. (NASEM. 2016. Genetically Engineered Crops: Experiences and Prospects. Washington, DC: The National Academies Press. doi: 10.17226/23395.)

Suggested Citation:"Appendix D: Glossary." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×

Metagenome: The collection of genomes and genes from the members of a microbiota or microbial community. (Marchesi JR, Ravel J. 2015. The vocabulary of microbiome research: A proposal. Microbiome 3(1):31.)

Metagenomics: A culture-independent method used for functional and sequence-based analysis of total environmental (community) DNA. (Adapted in part from IOM. 2014. Microbial Ecology in States of Health and Disease: Workshop Summary. Washington, DC: The National Academies Press.)

Metaproteomics: The large-scale characterization of the entire protein complement of environmental or clinical samples at a given point in time. (Marchesi JR, Ravel J. 2015. The vocabulary of microbiome research: A proposal. Microbiome 3(1):31.)

Microbe: A microscopic living organism, such as a bacterium, fungus, protozoan, or virus. (IOM. 2014. Microbial Ecology in States of Health and Disease: Workshop Summary. Washington, DC: The National Academies Press.)

Microbial community/microbiota: A collection of microorganisms existing in the same place at the same time. (Adapted from Ibid.)

Microbiome: The collection of all the organisms in or on a host, including viruses, bacteria, archaea, fungi, and protists. These organisms interact with each other and the host in a variety of complex and meaningful ways. (Presentation of HW Virgin)

Monocolonization: Inoculation of germ-free animals with one type of microbe. (Wiktionary)

Nonpathogenic: Refers to an organism or other agent that does not cause disease. (Adapted from Alberts B, et al. 2002. Molecular Biology of the Cell, 4th ed. New York: Garland Science.)

Operational Taxonomic Unit: OTUs, defined as clusters of 16S/18S small subunit (SSU) rRNA gene similarity, are used as theory-agnostic approximations of microbial taxa. (Schmidt TSB, Matias Rodrigues JF, von Mering C. 2014. Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale. PLoS Comput Biol. https://doi.org/10.1371/journal.pcbi.1003594.)

Organoid: An in vitro 3D cellular cluster derived exclusively from primary tissue, embryonic stem cells, or induced pluripotent stem cells, capable of self-renewal and self-organization, and exhibiting similar organ functionality as the tissue of origin. (Fatehullah A, Tan SH, Barker N. 2016. Organoids as an in vitro model of human development and disease. Nat Cell Biol 18:246-254.)

Suggested Citation:"Appendix D: Glossary." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×

Ortholog: One of two or more genes that are similar in sequence as a result of derivation from the same ancestral gene. The term covers both orthologs and paralogs. (IOM. 2009. Microbial Evolution and Co-adaptation: A Tribute to the Life and Scientific Legacies of Joshua Lederberg. Washington, DC: The National Academies Press.)

Pathogen/pathogenic: An organism or other agent that causes disease. (Alberts B, et al. 2002. Molecular Biology of the Cell, 4th ed. New York: Garland Science.)

Phenotype: The term phenotype refers to the observable physical properties of an organism; these include the organism’s appearance, development, and behavior. An organism’s phenotype is determined by its genotype, which is the set of genes the organism carries, as well as by environmental influences on these genes. (SciTable by Nature Education: https://www.nature.com/scitable/definition/phenotype-phenotypes-35. Accessed March 2, 2018.)

Proteomic: The large-scale characterization of the entire protein complement of a cell line, tissue, or organism. A more recent definition combined protein studies with analyses that have a genetic readout, such as mRNA analysis, genomics, and the yeast two-hybrid analysis. (Graves PR, Haystead TAJ. 2002. Molecular biologist’s guide to proteomics. Microbiol Mol Biol Rev 66(1):39-63.)

Protista Kingdom: Eukaryotic organisms that are unicellular and sometimes colonial or less often multicellular and that typically include the protozoans, most algae, and often some fungi (as slime molds). (Merriam-Webster Dictionary) (https://www.merriam-webster.com/dictionary/protist. Accessed March 2, 2018.)

Shotgun sequencing: Sequencing of a genome that has been fragmented into small pieces. (IOM. 2014. Microbial Ecology in States of Health and Disease: Workshop Summary. Washington, DC: The National Academies Press.)

Specific pathogen free (SPF): SPF mice are mice that are demonstrated to be free of a specific list of pathogens by routine testing. (The Jackson Laboratory: https://www.jax.org/news-and-insights/jax-blog/2013/may/the-difference-between-germ-free-and-specific-pathogen-free-mice. Accessed March 2, 2018.)

Symbiotic: Involving interaction between two different organisms living in close physical association. (The Oxford English Dictionary)

Taxa: A term used to refer to all the organisms that fall under a particular taxonomic criterion (such as kingdom, phylum, class, order, family, genus, species, or subspecies). (NASEM. 2017. Microbiomes of the Built Environment: A Research Agenda for Indoor Microbiology, Human Health, and Buildings. Washington, DC: The National Academies Press. https://doi.org/10.17226/23647.)

Suggested Citation:"Appendix D: Glossary." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×

Taxonomic/taxonomy: The systematic classification, identification, and nomenclature of organisms. (Adapted from Baron S, ed. 1996. Medical Microbiology, 4th ed. Galveston, TX: University of Texas Medical Branch at Galveston.)

Transcriptome: The transcriptome is the full range of messenger RNA, or mRNA, molecules expressed by an organism. The term can also be used to describe the array of mRNA transcripts produced in a particular cell or tissue type. (SciTable by Nature Education: https://www.nature.com/scitable/definition/transcriptome-296. Accessed March 2, 2018.)

Transmissibility: The ease with which a microorganism(s) can spread from a source to a host. (NASEM. 2017. Microbiomes of the Built Environment: A Research Agenda for Indoor Microbiology, Human Health, and Buildings. Washington, DC: The National Academies Press. https://doi.org/10.17226/23647.)

Transmission: The transfer of a microorganism(s) from a source to a host. (Adapted from Baron S, ed. 1996. Medical Microbiology, 4th ed. Galveston, TX: University of Texas Medical Branch at Galveston.)

Virome: The composition of the human virome includes viruses that infect human cells, ancient virus-derived elements inserted in our chromosomes, and bacteriophages that infect a broad array of bacteria that inhabit us. (Zou S, Caler L, Colombini-Hatch S, Glynn S, Srinivas P. 2016. Research on the human virome: Where are we and what is next. Microbiome 4:32.)

Virus: A small infectious agent that can replicate only inside the cells of another organism. Viruses are too small to be seen directly with a light microscope. They infect all types of organisms, from animals and plants to bacteria and archaea. (IOM. 2014. Microbial Ecology in States of Health and Disease: Workshop Summary. Washington, DC: The National Academies Press.)

Suggested Citation:"Appendix D: Glossary." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×
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Suggested Citation:"Appendix D: Glossary." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×
Page 93
Suggested Citation:"Appendix D: Glossary." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×
Page 94
Suggested Citation:"Appendix D: Glossary." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×
Page 95
Suggested Citation:"Appendix D: Glossary." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×
Page 96
Suggested Citation:"Appendix D: Glossary." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×
Page 97
Suggested Citation:"Appendix D: Glossary." National Academies of Sciences, Engineering, and Medicine. 2018. Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/24858.
×
Page 98
Animal Models for Microbiome Research: Advancing Basic and Translational Science: Proceedings of a Workshop Get This Book
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The surface of the human body and its mucous membranes are heavily colonized by microorganisms. Our understanding of the contributions that complex microbial communities make to health and disease is advancing rapidly. Most microbiome research to date has focused on the mouse as a model organism for delineating the mechanisms that shape the assembly and dynamic operations of microbial communities. However, the mouse is not a perfect surrogate for studying different aspects of the microbiome and how it responds to various environmental and host stimuli, and as a result, researchers have been conducting microbiome studies in other animals.

To examine the different animal models researchers employ in microbiome studies and to better understand the strengths and weaknesses of each of these model organisms as they relate to human and nonhuman health and disease, the Roundtable on Science and Welfare in Laboratory Animal Use of the National Academies of Sciences, Engineering, and Medicine convened a workshop in December 2016. The workshop participants explored how to improve the depth and breadth of analysis of microbial communities using various model organisms, the challenges of standardization and biological variability that are inherent in gnotobiotic animal-based research, the predictability and translatability of preclinical studies to humans, and strategies for expanding the infrastructure and tools for conducting studies in these types of models. This publication summarizes the presentations and discussions from the workshop.

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