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Appendix C Glossary Adaptive immune response: Response of the vertebrate immune system to a specific antigen that typically generates immunological memory (Alberts, B., A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter. 2002. Molecular biology of the cell, fourth edition. New York: Garland Science). Affymetrix chip: A type of DNA microarray gene chip that contains up to 500,000 unique probes corresponding to tens of thousands of gene expression measurements (http://cnx.org/content/m12387/latest/). Anthropogenic: Caused or produced by humans. Archaea: Unique group of microorganisms classified as bacteria (Archaeobac- teria) but genetically and metabolically different from all other known bacteria. They appear to be living fossils, the survivors of an ancient group of organisms that bridged the gap in evolution between bacteria and the eukaryotes (multicellu- lar organisms) (http://www.medterms.com/script/main/art.asp?articlekey=2322). Asymptomatic carrier: An individual who serves as host for an infectious agent but who does not show any apparent signs of the illness; may serve as a source of infection for others (http://medical-dictionary.thefreedictionary. com/Asymptomatic+carrier). Bacteriocins: Bacterially produced, small, heat-stable peptides that are active against other bacteria and to which the producer has a specific immunity mecha- 0

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 APPENDIX C nism. Bacteriocins can have a narrow or broad target spectrum (http://www. nature.com/nrmicro/journal/v3/n10/glossary/nrmicro1273_glossary.html). Binary associations: A population of a single microbial phylotype associates with a host. Biofilm: A slime layer that develops naturally when bacteria congregate on sur- faces (http://publications.nigms.nih.gov/thenewgenetics/glossary.html). Bioluminescence: Light produced by a chemical reaction that originates in an organism (primarily a marine phenomenon). The causal organisms are almost always dinoflagellates, or single-cell algae, often numbering many hundreds per liter (http://www.lifesci.ucsb.edu/~biolum/). Clustered regularly interspaced short palindromic repeats (CRISPRs): Direct repeats found in the DNA of many bacteria and archaea. These repeats range in size from 23 to 47 base pairs and are separated by spacers of similar length. Spacers are usually unique in a genome. Some spacer sequences match sequences in phage genomes; it is proposed that these spacers derive from phage and subsequently help protect the cell from infection (http://crispr.u-psud.fr/ crispr/CRISPRHomePage.php?page=about). Commensals: Organisms in a mutually symbiotic relationship where both live peacefully together while not being completely dependent on one another (exam- ple: the gut microbiome) (http://www.bacteriamuseum.org/niches/evolution/ commensals.shtml). Consortial association: Populations of more than one phylotype of microbe liv- ing in association with a host animal. Cytoskeleton: The internal components of animal cells that give them structural strength and motility. The major components of cytoskeleton are the microfila- ments (of actin), microtubules (of tubulin) and intermediate filament systems in cells (http://www.mblab.gla.ac.uk/~julian/Dict.html). Emerging infections: Infections that are rapidly increasing in incidence or geo- graphic range. Endosymbiont: An organism that lives inside another organism, most often for the benefit of the two (example: rhizobia [nitrogen-fixing soil bacterial] that live within root nodules—rhizobia cannot independently fix nitrogen but need the plant as an energy source; in turn, rhizobia supply the plant host with ammonia and amino acids).

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 MICROBIAL EVOLUTION AND CO-ADAPTATION Extensively drug resistant tuberculosis (xDR TB): A relatively rare type of MDR TB. XDR TB is defined as tuberculosis that is resistant to isoniazid and rifampicin, plus resistant to any fluoroquinolone and at least one of three inject- able second-line drugs (i.e., amikacin, kanamycin, capreomycin) (http://www. cdc.gov/tb/pubs/tbfactsheets/mdrtb.htm). Generalized transduction: The ability of certain phages to transfer any gene in the donor bacterial chromosome to a recipient bacterium (http://www.ncbi.nlm. nih.gov/books/bv.fcgi?rid=iga.section.1363). Genus: A group of species with similar characteristics that are closely related (http://www.sedgwickmuseum.org/education/glossary.html#g). Gnotobiotic vertebrates: Organisms or environmental conditions that have been rendered free of bacteria or contaminants or into which a known microorganism or contaminant has been introduced for research purposes (http://www.answers. com/topic/gnotobiotics). 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. Hormesis: Showing different effects at low doses compared to high. Hydrothermal vent ecosystems: The community of organisms that thrives in the extreme heat and mineral-rich waters surrounding hydrothermal vents (geysers on the sea floor). Such organisms include tubeworms, vent crabs, heat worms, and ancient bacteria (http://www.ocean.udel.edu/deepsea/level-2/geology/vents. html). Innate immune response: Immune response (of both vertebrates and inverte- brates) to a pathogen that involves the preexisting defenses of the body, such as barriers formed by skin and mucosa, antimicrobial molecules and phagocytes. Such a response is not specific for the pathogen (http://www.ncbi.nlm.nih.gov/ books/bv.fcgi?rid=mboc4.glossary.4754). Interferon: One of a group of small antiviral proteins synthesized and secreted by cells following viral infection (http://www.portlandpress.com/pp/books/online/ glick/searchresdet.cfm?Term=interferon). International units: The quantity of a biologically active substance, such as a hormone or vitamin, required to produce a specific response (http://www.answers. com/topic/international-unit).

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 APPENDIX C Lamarckism: The theory that evolution is caused by inheritance of character changes acquired during the life of an individual, due to its behavior or to envi- ronmental influences (http://evolution.unibe.ch/teaching/GlossarE.htm). Leukocyte extravasation: The movement of leukocytes out of the circulatory system, via specific cell-cell contacts with endothelial cells lining the blood vessel, toward site of tissue damage or infection (http://en.wikipedia.org/wiki/Leukocyte_extravasation; http://www.whfreeman.com/kuby/content/anm/kb01an01.htm). Lymph nodes: Small bean-shaped organs scattered along the vessels of the lymphatic system. The lymph nodes produce white blood cells and filter bacteria and cancer cells that may travel through the system (http://www.everythingbio. com/glos/definition.php?word=Lymph+nodes). Lymphoid follicles: Specialized regions of secondary lymphoid organs critical for B-cell development (a type of lymphocyte that makes antibodies) and, thus, are critical for the functioning of the adaptive immune system (Sompayrac, L. M. 1991. How the immune system works, second edition. New York: Wiley-Blackwell). Macrophage: Phagocytic cell derived from blood monocytes, typically resi- dent in most tissues. It has both scavenger and antigen-presenting functions in immune responses (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4. glossary.4754). Malthusian fitness: A measure of reproductive potential based on the Malthusian Population Theory, which asserts that in biology, the viability of virtually any organism or species greatly exceeds the Earth’s capacity to support all its possible offspring. Consequently, species diversity is preserved through mechanisms that keep population sizes in check, such as predation (http://www.economyprofessor. com/economictheories/malthusian-population-theory.php). Metagenomics: A culture-independent analysis method that involves obtaining DNA from communities of microorganisms, sequencing it in a “shotgun” fashion, and characterizing genes and genomes comparisons with known gene sequences. With this information, researchers can gain insights into how members of the microbial community may interact, evolve, and perform complex functions in their habitats (Jurkowski, A., A. H. Reid, and J. B. Labov. 2007. Metagenomics: a call for bringing a new science into the classroom while it’s still new. CBE Life Sciences Education 6(4):260-265; National Research Council. 2007. The new sci- ence of metagenomics: revealing the secrets of our microbial planet. Washington, DC: The National Academies Press).

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 MICROBIAL EVOLUTION AND CO-ADAPTATION Methicillin-resistant Staphylococcus aureus (MRSA): A type of staph that is resistant to antibiotics called β-lactams. β-lactam antibiotics include methicillin and other more common antibiotics such as oxacillin, penicillin and amoxicillin (http://www.cdc.gov/ncidod/dhqp/ar_MRSA_ca_public.html#2). Microbiome: Term used to describe the collective genome of our indigenous microbes (microflora) (Hooper, L. V., and J. I. Gordon. 2001. Commensal host- bacterial relationships in the gut. Science 292(5519):1115-1118). Microcins: Bacteriocins that contain a smaller number of amino acids. Multidrug-resistant tuberculosis (MDR TB): Tuberculosis that is resistant to at least two of the best anti-TB drugs, isoniazid and rifampicin. These drugs are considered first-line drugs and are used to treat all persons with TB disease (http://www.cdc.gov/tb/pubs/tbfactsheets/mdrtb.htm). Neutrophil: Most common blood leukocyte; a short-lived phagocytic cell of the myeloid series, which is responsible for the primary cellular response to an acute inflammatory episode, and for general tissue homeostasis by removal of damaged material (http://www.mblab.gla.ac.uk/~julian/Dict.html). Pandemic: Disease outbreak occurring over a wide geographic area and affect- ing an exceptionally high proportion of the population (http://www2.merriam- webster.com/cgi-bin/mwmednlm?book=Medical&va=pandemic). Pathogen: A specific causative agent (such as a bacterium or virus) of dis- ease (http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical& va=pathogen). Pathogenicity: Pathogenicity reflects the ongoing evolution between a para- site and host, and disease is the product of a microbial adaptive strategy for survival. Pathogenicity islands: Large genomic regions encoding for virulence factors of pathogenic bacteria, present on the genomes of pathogenic strains but absent from the genomes of nonpathogenic members of the same or related species. (Hacker, J., and J. Kaper. 2000. Pathogenicity islands and the evolution of microbes. Annual Review of Microbiology 54:641-679). Peyer’s patches: Large aggregates of lymphoid tissue (similar to lymph nodes) located in the mucosa and extending into the submucosa of the small intes- tine. Peyer’s patches facilitate the generation of an immune response within the mucosa (http://www.microbiologybytes.com/iandi/2b.html).

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 APPENDIX C Phage(s): A virus that infects bacteria. Many phages have proved useful in the study of molecular biology and as vectors for the transfer of genetic information between cells. Lytic phage (e.g., the T series phage that infect Escherichia coli [coliphages]), invariably lyse a cell following infection; temperate phage (e.g., lambda bacteriophage) can also undergo a lytic cycle or can enter a lysogenic cycle, in which the phage DNA is incorporated into that of the host, awaiting a signal that initiates events leading to replication of the virus and lysis of the host cell (http://www.portlandpress.com/pp/books/online/glick/searchresdet.cfm? Term=bacteriophage). Phagocyte/phagocytic cell: A cell that is capable of phagocytosis, or the uptake of particulate material by a cell. The main mammalian phagocytes are neutrophils and macrophages (http://www.mblab.gla.ac.uk/~julian/Dict.html). Phylogenetic profiling: Phylogenetic profiling is a well established method for predicting functional relations and physical interactions between proteins (Pagel, P., P. Wong, and D. Frishman. 2004. A domain interaction map based on phylo- genetic profiling. Journal of Molecular Biology 344(5):1331-1346). Phylogenetics: The study of the relationships between organisms based on how closely they are related to each other (http://www.medterms.com/script/main/art. asp?articlekey=39615). Phylogenomics: The use of evolutionary information in the prediction of gene function (http://genome.cshlp.org/content/8/3/163.full.pdf+html). Phylum: In taxonomy and systematics, the highest level of classification below the kingdom (http://ec.europa.eu/research/biosociety/library/glossarylist_en.cfm). Pleiotropic: Producing more than one effect; having multiple phenotypic expres- sions (http://www.merriam-webster.com/dictionary/pleiotropic). Ribosomal RNA: A class of RNA molecules, coded in the nucleolar organizer, that has an integral (but poorly understood) role in ribosome structure and func- tion. RNA components of the subunits of the ribosomes (http://www.biochem. northwestern.edu/holmgren/Glossary/Definitions/Def-R/ribosomal_RNA.html). Serotype: The characterization of a microorganism based on the kinds and com- binations of constituent antigens present in that organism; a taxonomic subdivi- sion of bacteria based on the above.

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 MICROBIAL EVOLUTION AND CO-ADAPTATION Species: The basic unit of taxonomy. A species is defined as a group of individu- als that are genetically related and can interbreed to produce fertile young of the same kind (http://www.sedgwickmuseum.org/education/glossary.html). Transposons: Small, mobile DNA sequences that can replicate and insert copies at random sites within chromosomes. They have nearly identical sequences at each end, oppositely oriented (inverted) repeats, and code for the enzyme, trans- posase, that catalyses their insertion (http://www.mblab.gla.ac.uk/~julian/Dict. html). Vancomycin-intermediate or vancomycin-resistant Staphylococcus aureus (VISA/VRSA): VISA and VRSA are specific types of antimicrobial-resistant staph bacteria. While most staph bacteria are susceptible to the antimicrobial agent vancomycin some have developed resistance. VISA and VRSA cannot be treated successfully with vancomycin because these organisms are no longer susceptibile to vancomycin. However, to date, all VISA and VRSA isolates have been susceptible to other Food and Drug Administration (FDA)-approved drugs (http://www.cdc.gov/ncidod/dhqp/ar_visavrsa_FAQ.html). Virulence: The degree of pathogenicity of an organism as evidenced by the sever- ity of resulting disease and the organism’s ability to invade the host tissues. Virulence factors: The properties (i.e., gene products) that enable a microorgan- ism to establish itself on or within a host of a particular species and enhance its potential to cause disease. Virulence factors include bacterial toxins, cell surface proteins that mediate bacterial attachment, cell surface carbohydrates and pro- teins that protect a bacterium, and hydrolytic enzymes that may contribute to the pathogenicity of the bacterium (http://www.mgc.ac.cn/VFs/main.htm). Zoonotic: Infection that causes disease in human populations but can be perpetu- ated solely in nonhuman host animals (e.g., bubonic plague); may be enzootic or epizootic.