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Appendix D

Glossary

16S ribosomal RNA (rRNA): A component of the small subunit of prokaryotic ribosomes. Significant insights into species richness, structure, composition, and membership of microbial communities have been gained through analysis of small-subunit rRNA gene sequences; these sequences contain hypervariable regions that can provide species-specific signature sequences. PCR amplification with primers that hybridize to highly conserved regions in bacterial or archaeal 16S rRNA genes (or eukaryotic microbial 18S rRNA genes) followed by cloning and sequencing yields an initial description of species present in a microbial community.

Acquired immune deficiency syndrome: An infectious disease caused by the human immunodeficiency virus (HIV). There are two variants of the HIV virus, HIV-1 and HIV-2, both of which ultimately cause AIDS.

Antibiotic: Class of substances that can kill or inhibit the growth of some groups of microorganisms. Originally antibiotics were derived from natural sources (e.g., penicillin from molds), but many currently used antibiotics are semisynthetic and modified with additions of man-made chemical components. See Antimicrobial.

Antimicrobial: In this document, the term antimicrobial is used inclusively to refer to any agent (including an antibiotic) used to kill or inhibit the growth of microorganisms (bacteria, viruses, fungi, or parasites). This term applies whether the agent is intended for human, veterinary, or agricultural applications.



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Appendix D Glossary 16S ribosomal RNA (rRNA): A component of the small subunit of prokaryotic ribosomes. Significant insights into species richness, structure, composition, and membership of microbial communities have been gained through analysis of small-subunit rRNA gene sequences; these sequences contain hypervariable regions that can provide species-specific signature sequences. PCR amplification with primers that hybridize to highly conserved regions in bacterial or archaeal 16S rRNA genes (or eukaryotic microbial 18S rRNA genes) followed by clon- ing and sequencing yields an initial description of species present in a microbial community. Acquired immune deficiency syndrome: An infectious disease caused by the human immunodeficiency virus (HIV). There are two variants of the HIV virus, HIV-1 and HIV-2, both of which ultimately cause AIDS. Antibiotic: Class of substances that can kill or inhibit the growth of some groups of microorganisms. Originally antibiotics were derived from natural sources (e.g., penicillin from molds), but many currently used antibiotics are semisynthetic and modified with additions of man-made chemical components. See Antimicrobial. Antimicrobial: In this document, the term antimicrobial is used inclusively to refer to any agent (including an antibiotic) used to kill or inhibit the growth of microorganisms (bacteria, viruses, fungi, or parasites). This term applies whether the agent is intended for human, veterinary, or agricultural applications. 503

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504 MICROBIAL ECOLOGY IN STATES OF HEALTH AND DISEASE Antimicrobial resistance: Most commonly, this refers to infectious microbes that have acquired the ability to survive exposures to clinically relevant con- centrations of antimicrobial drugs that would kill otherwise sensitive organisms of the same strain. The phrase is also used to describe any pathogen that is less susceptible than its counterparts to a specific antimicrobial compound (or com- bination thereof). Archaea: Any of various single-celled prokaryotes genetically distinct from bacteria, often thriving in extreme environments. ATP: Short for adenosine triphosphate, an organic compound that serves as a source of energy for many metabolic processes. Bacteria: Microscopic, single-celled organisms that have some biochemical and structural features different from those of animal and plant cells. Biogeography: The study of biodiversity in space and time. Clostridium difficile: A bacterium that can cause symptoms ranging from d ­ iarrhea to life-threatening inflammation of the colon. Commensal relationship: An intimate, although generally benign, relationship between a resident microorganism and its host—probably the product of a long evolutionary interplay between the microorganism and the host. The relationship need not be symbiotic. See Commensalism. Commensalism: Two (or more) species coexist, one deriving benefit from the relationship without harm or obvious benefit to the other. Crohn’s disease: A type of inflammatory bowel disease (IBD), resulting in swell- ing and dysfunction of the intestinal tract, especially the small intestine. Disease: In medicine, disease is often viewed as an observable change of the normal network structure of a system resulting in damage to the system. Diversity: A measure of how much variety is present in a community, irrespec- tive of the identities of the organisms present; consists of richness and evenness. DNA (deoxyribonucleic acid): Any of various nucleic acids that are usually the molecular basis of heredity are constructed of a double helix held together by hydrogen bonds between purine and pyrimidine bases that project inward from two chains containing alternate links of deoxyribose and phosphate and that in eukaryotes are localized chiefly in cell nuclei.

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APPENDIX D 505 DNA sequencing: Determining the order of nucleotides in DNA. Dysbiosis: Most commonly refers to a disruption in the normal homeostatic and beneficial relationship between microbes and their host, including disrup- tions in microbial community structure and function. Alterations in microbial community structure, involving Bacteria, Archaea, and/or Eukarya, can occur in any body habitat but have been best described in the gut where they have been associated with a number of disease states including, for example, inflammatory bowel disease. Ecology: The scientific study of the relationship between living things and their environments. Emerging infectious diseases: Infections that are rapidly increasing in incidence or geographic range. Escherichia coli: A straight rod-shaped gram-negative bacterium that is used in public health as an indicator of fecal pollution (as of water or food) and in medi- cine and genetics as a research organism and that occurs in various strains that may live as harmless inhabitants of the human lower intestine or may produce a toxin causing intestinal illness. Eukaryotic: One of the three domains of life. The two other domains, ­ acteria B and Archaea, are prokaryotes and lack several features characteristic of ­ ukaryotes e (e.g., cells containing a nucleus surrounded by a membrane and whose DNA is bound together by proteins [histones] into chromosomes). Animals, plants, and fungi are all eukaryotic organisms. Evenness: The distribution of individuals across types. Fecal microbiota transplantation: An emerging therapy for the treatment of Clostridium difficile colitis. Also known as a stool transplant, it is the process of transplanting fecal bacteria from a healthy individual into a recipient patient suffering from a Clostridium difficile infection. Function: An activity or “behavior” associated with a community, e.g., nitrogen fixation or resistance to invasion. Gene transfer: The transfer of individual genes or their components, islands of genes, entire organisms, or communities of organisms from parent to offspring (vertical transfer) or between individuals not in a direct lineage (horizontal transfer).

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506 MICROBIAL ECOLOGY IN STATES OF HEALTH AND DISEASE Genome: The complete set of genetic information in an organism. In bacteria, this includes the chromosome(s) and plasmids (extra-chromosomal DNA mol- ecules that can replicate autonomously within a bacterial cell). Genomics: The study of genes and their associated functions. Glycan: A polysaccharide or oligosaccharide, especially one that is attached to a glucoconjugate, as a glycoprotein, glycolipid, and proteoglycan. Helicobacter pylori: A species of spiral or straight gram-negative bacteria with multiple sheathed flagella found in the gastric mucosa of humans and other animals and associated with gastric and peptic ulcers as well as gastric cancers. Host: Animal or plant that harbors or nourishes another organism. Host defense: The protection an organism is afforded against infections. Types 1. Nonimmunologic—e.g., mucocutaneous or integumental barriers, cilia, microvilli; mechanical—e.g., urinary outflow, vascular perfusion of tissues; native flora, which outcompete pathogens; 2. Immunologic—e.g., chemotaxis, ­ hagocytosis, p immunoglobulins, complement, T cell defense. Host–pathogen interactions: The interactions taking place between a pathogen and its host. By definition, all pathogens damage their host to some extent. Human Genome Project: An international scientific research project with a primary goal of determining the sequence of chemical base pairs that make up DNA, and of identifying and mapping the approximately 20,000–25,000 genes of the human genome from both a physical and functional standpoint. A working draft of the genome was announced in 2000 and a complete one in 2003, with further, more detailed analysis still being published. Human immunodeficiency virus: A retrovirus that causes AIDS by infecting helper T cells of the immune system. The most common serotype, HIV-1, is dis- tributed worldwide, while HIV-2 is primarily confined to West Africa. Human Microbiome Project: An international project aiming to characterize the microbial communities found at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract, and to analyze the role of these microbes in human health and disease. The Human Microbiome Project is one of several international efforts designed to take advantage of metagenomic analysis to study human health and expects to con- tinue the practice established by the Human Genome Project of international collaboration to generate a rich, comprehensive, and publicly available data set.

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APPENDIX D 507 Hyphae: The fine, branching tubes that make up the body (or mycelium) of a multicellular fungus. Immune system: A complex network of interacting cells, cell products, and cell-forming tissues that protects the body from pathogens and other foreign sub- stances, destroys infected and malignant cells, and removes cellular debris: the system includes the thymus, spleen, lymph nodes and lymph tissue, stem cells, white blood cells, antibodies, and lymphokines. 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, the results of which may produce injurious effects. Infection should not be confused with disease. Inflammatory bowel disease (IBD): A term covering a group of disorders in which the intestines become inflamed (red and swollen), probably as a result of an immune reaction of the body against its own intestinal tissue. IBD includes Crohn’s disease and ulcerative colitis. Invasion: An ecological event characterized by the establishment of a foreign organism in a new community and the persistence and spread of this organism. Koch’s postulates: Koch’s postulates must be satisfied in order to state that a particular microbe causes a specific infectious disease. They include the follow- ing: (1) The parasite occurs in every case of the disease in question and under circumstances that can account for the pathological changes and clinical course of the disease; (2) The parasite occurs in no other disease as a fortuitous and non- pathogenic parasite; (3) After being fully isolated from the body and repeatedly grown in pure culture, the parasite can induce the disease anew. Latency: Of an infection, a period in which the infection is present in the host without producing overt symptoms. The time that elapses between a stimulus and a response to it. Lysogeny: The biological process in which a bacterium is infected by a bacterio­ phage that integrates its DNA into that of the host such that the host is not destroyed. Metabolic syndrome: A name for a group of risk factors related to obesity— such as extra weight around the middle and upper parts of the body and insulin resistance—that occur together and increase the risk for coronary artery disease, stroke, and type 2 diabetes.

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508 MICROBIAL ECOLOGY IN STATES OF HEALTH AND DISEASE Metagenome: The sum of all genes and genetic elements and their modifications in the somatic and germ cells of a host plus all genes and genetic elements in all microorganisms that live on or in that host at a given time. The metagenome has transient elements (e.g., during infection with a pathogen) and more persistent elements (e.g., infection with latent eukaryotic virus; presence of commensal bacteria). Metagenomics: A culture-independent method used for functional and sequence- based analysis of total environmental (community) DNA (note that this is not the same as amplifying, cloning, and sequencing the 16S rRNA-encoding gene, al- though metagenomic sequences [e.g., generated via modern sequencing ­ ethods] m can be probed for 16S rRNA-encoding genes or other phylogenetic markers). Microbe: A microscopic living organism, such as a bacterium, fungus, proto- zoan, or virus. Microbiome: The gene complement of a community; the collective genomes of the microorganisms that reside in an environmental niche. Microbiota/community: A collection of microorganisms existing in the same place at the same time. Mucosal immunity: Nonsusceptibility to the pathogenic effects of foreign micro­ rganisms or antigenic substances as a result of antibody secretions of the o mucous membranes. Mucosal epithelia in the gastrointestinal, respiratory, and reproductive tracts produce a form of IgA that serves to protect these ports of entry into the body. Mutualism: An interspecies relationship in which both (or all) members benefit. Nash equilibrium: In game theory, a solution concept in which players in a game are aware of the strategies of the other players but do not deviate from their own, because they do not have anything to gain; it will be disadvantageous to deviate (to cheat). Operational taxonomic unit (OTU): Taxonomic level of sampling selected by the user to be used in a study, such as individuals, populations, species, genera, or bacterial strains. Opportunistic pathogen: An infectious microorganism that is normally a com- mensal or does not harm its host but can cause disease when the host’s resistance is low.

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APPENDIX D 509 Pan-genome: The set of all of the genes that are found in members of a single species. Parasite: An organism that diminishes the reproductive fitness of another organ- ism or benefits from another organism without reciprocity. Parasitism: A relationship between two organisms where one organism benefits at the expense of the other. Pathogen: In medicine, any organism that causes disease. In biological terms, a pathogen is a microorganism that has the inherent capacity to cross anatomical barriers and resist host defenses that ordinarily restrict most other microorganisms. Pathogenic: Capable of causing disease. Phylogenomic: The use of evolutionary information in the prediction of gene function. Phylogeny: The evolutionary development and history of a species or higher taxonomic grouping of organisms. Polymerase chain reaction (PCR): A scientific technique in molecular biol- ogy to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. Pure culture: Technique in which single cells of a particular microbial type are grown in isolation from other organisms. Pyrosequencing: A method of DNA sequencing based on the “sequencing by synthesis” principle. It differs from Sanger sequencing, in that it relies on the detection of pyrophosphate release on nucleotide incorporation, rather than chain termination with dideoxynucleotides. The sequence of solutions that pro- duce ­ hemiluminescent signals allows the determination of the sequence of the c template. Resilience: The rate at which a community recovers to its native structure fol- lowing a perturbation. Resistance: The ability of a community to resist change to its structure after an ecological challenge. See Antimicrobial resistance.

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510 MICROBIAL ECOLOGY IN STATES OF HEALTH AND DISEASE Rhizosphere: The region of the soil in contact with the roots of a plant. It is directly influenced by root secretions and associated soil microorganisms. Richness: Number of types (e.g., species) in a community. RNA (ribonucleic acid): Any of various nucleic acids that contain ribose and uracil as structural components and are associated with the control of cellular chemical activities. rRNA (ribosomal RNA): A nucleic acid found in all living cells. Plays a role in transferring information from DNA to the protein-forming system of the cell. More specifically, rRNA sits in the ribosome, decoding the mRNA into various amino acids and assisting in translation. Sanger sequencing: A method of DNA sequencing based on the selective incor- poration of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication. “Shotgun” sequencing: Sequencing of a genome that has been fragmented into small pieces. Similarity: A measure that determines the similarity of two or more communi- ties, typically based on shared members, total richness, and sometimes abundance of members. Staphylococcus aureus: A facultatively anaerobic, gram-positive coccus and is the most common cause of staph infections. It is frequently part of the skin flora found in the nose and on skin. Structure: The composition of the community and the abundance of individual members. Superorganism: A living system of a superior degree of complexity, consist- ing of many organisms; a collection of agents that can act in concert to produce phenomena governed by the collective. Symbiont: An organism in a symbiotic relationship. In cases in which a distinc- tion is made between the two interacting organisms, the symbiont is the smaller of the two and is always a beneficiary in the relationship, while the larger organisms is the host and may or may not derive a benefit. Syntrophic interactions: Interactions in which organisms do more together than alone.

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APPENDIX D 511 Temporal stability: The ability of a community to maintain its native structure. Torpor: The dormant, inactive state of a hibernating animal. Ulcerative colitis: A serious chronic inflammatory disease of the large intestine and rectum characterized by recurrent episodes of abdominal pain and fever and chills and profuse diarrhea. Vibrio fischeri: A gram-negative rod-shaped bacterium found globally in marine environments. V. fischeri has bioluminescent properties, and is found predomi- nantly in symbiosis with various marine animals, such as the bobtail squid. It is heterotrophic and moves by means of flagella. Virome: The sum of all viruses living in the tissues of the host or infecting organ- isms in the microbiome. Virulence: A quantitative estimate of the ability of one organism to harm another. Virulence factor: Intrinsic characteristic of an infectious bacterium that facili- tates its ability to cause disease. Virus: A small infectious agent that can only replicate inside the cells of another organism. Viruses are too small to be seen directly with a light microscope. Viruses infect all types of organisms, from animals and plants to bacteria and archaea. Yersinia pestis: A gram-negative rod-shaped bacterium belonging to the fam- ily Enterobacteriaceae. It is a facultative anaerobe that can infect humans and other animals. Human Y. pestis infection takes three main forms: pneumonic, ­ epticemic, and the notorious bubonic plagues. s

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