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. See Ribosomal RNA (rRNA), http://en.wikipedia.org/wiki/16S_ribosomal_RNA (accessed July 27, 2012).

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.

Antimicrobial resistance: Most commonly, this refers to infectious microbes that have acquired the ability to survive exposures to clinically relevant concentrations 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



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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. See Ribosomal RNA (rRNA), http://en.wikipedia.org/wiki/16S_ribo- somal_RNA (accessed July 27, 2012). 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. 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 587

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588 THE SOCIAL BIOLOGY OF MICROBIAL COMMUNITIES susceptible than its counterparts to a specific antimicrobial compound (or com- bination thereof). Asymptomatic infection: An infection where the patient does not have any ap- parent symptoms (also known as a subclinical infection). 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. Biocontrol: Method of controlling pests (including insects, mites, weeds, and diseases) in plants that relies on predation, parasitism, herbivory, or other natural mechanisms. Biofilms: Bacterial communities that adhere to biotic or abiotic surfaces. These microorganisms are usually encased in an extracellular polysaccharide matrix that they themselves synthesize and may be found on essentially any environmental surface in which sufficient moisture is present. Colonization: Capacity of a bacterium to remain at a particular site and multiply there. Commensalism: Two (or more) species coexist, one deriving benefit from the relationship without harm or obvious benefit to the other. Conidia: Asexually produced fungal spores, formed on a conidophore. Most conidia are dispersed by the wind and can endure extremes of cold, heat, and dryness. When conditions are favorable, they germinate and grow into structural parts of the body of a fungus (American Heritage Science Dictionary. 2011. Houghton Mifflin Harcourt Publishing Company). 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 which project inward from two chains containing alternate links of deoxyribose and phosphate, and that in eukaryotes are localized chiefly in cell nuclei. Ecology: The scientific study of the relationship between living things and their environments.

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APPENDIX D 589 Emerging infectious diseases: Infections that are rapidly increasing in incidence or geographic range. Endosymbiont: An organism that lives inside another organism, most often for the benefit of the two (example: rhizobia [nitrogen-fixing soil bacteria] 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). Enterohemorrhagic Escherichia coli (EHEC): A strain of E. coli that causes hemorrhage in the intestines. The organism produces Shiga toxin, which damages bowel tissue, causing intestinal ischemia and colonic necrosis. Symptoms are stomach cramping and bloody diarrhea. An infectious dose may be as low as 10 organisms. Spread by contaminated beef, unpasteurized milk and juice, sprouts, lettuce, and salami, as well as contaminated water, the infection can be serious although there may be no fever. Treatment consists of antibiotics and maintenance of fluid and electrolyte balance. In advanced cases, surgical removal of portions of the bowel may be required. Enteropathogens: A microorganism that causes disease of the intestine. 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, Bacteria and Archaea, are prokaryotes and lack several features characteristic of eukary- otes (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. Genomics: The study of genes and their associated functions. Germ theory: The germ theory of disease proposes that specific microorganisms are the cause of particular diseases. Gram-negative bacteria: Refers to the inability of a microorganism to accept a certain stain. This inability is related to the cell wall composition of the microor- ganism and has been useful in classifying bacteria.

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590 THE SOCIAL BIOLOGY OF MICROBIAL COMMUNITIES Gram-positive bacteria: Refers to the ability of a microorganism to retain a cer- tain stain. This ability is related to the cell wall composition of the microorganism and has been useful in classifying bacteria. Hemolytic uremic syndrome (HUS): A rare disease that is marked by the for- mation of thrombi in the capillaries and arterioles especially of the kidney that is characterized clinically by hemolytic anemia, thrombocytopenia, and varying degrees of kidney failure and is precipitated by a variety of etiologic factors (such as infection with Escherichia coli or Shigella dysenteriae) and that primarily af- fects infants and young children. Heterotropic: An organism that cannot manufacture its own food and instead obtains its food and energy by taking in organic substances, usually plant or animal matter (American Heritage Science Dictionary. 2011. Houghton Mifflin Harcourt Publishing Company). 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. Hospital-acquired infections: Infections not present and without evidence of incubation at the time of admission to a health care setting. As a better reflec- tion of the diverse health care settings currently available to patients, the term health careassociated infections replaced old ones such as nosocomial, hospital- acquired, or hospital-onset infections. Host: Animal or plant that harbors or nourishes another organism. 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. Keystone species: A species whose presence and role within an ecosystem has a disproportionate effect on other organisms within the system. A keystone species is often a dominant predator whose removal allows a prey population to explode and often decreases overall diversity. Other kinds of keystone organisms are those--such as coral--that significantly alter the habitat around them and thus

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APPENDIX D 591 affect large numbers of other organisms (American Heritage Science Dictionary. 2011. Houghton Mifflin Harcourt Publishing Company). 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: (i) The parasite occurs in every case of the disease in question and under circumstances which can account for the pathological changes and clinical course of the disease. (ii) The parasite occurs in no other disease as a fortuitous and non- pathogenic parasite. (iii) After being fully isolated from the body and repeatedly grown in pure culture, the parasite can induce the disease anew (Fredricks and Relman, 1996; Koch, 1891; Rivers, 1937). Metagenomics: A culture-independent analysis method that involves obtain- ing DNA from communities of microorganisms, sequencing it in a "shotgun" fashion--i.e., fragmenting the organisms' genomes into small pieces that can be sequenced--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. Microbe: A microscopic living organism, such as a bacterium, fungus, proto- zoan, or virus. Microbial threat: Microbes that lead to disease in humans. 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). Mutualism: An interspecies relationship in which both (or all) members benefit. Mycelia: The mass of fine branching tubes (known as hyphae) that forms the main growing structure of a fungus. Myxobacteria: Any of numerous Gram-negative, rod-shaped saprophytic bacte- ria (deriving nourishment from dead or decaying organic matter) of the phylum Myxobacteria, typically found embedded in slime in which they form complex colonies and noted for their ability to move by gliding along surfaces without any known organ of locomotion. Obligate: One of the three domains of life. The two other domains, Bacteria and Archaea, are prokaryotes and lack several features characteristic of eukaryotes (e.g., cells containing a nucleus surrounded by a membrane and whose DNA is

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592 THE SOCIAL BIOLOGY OF MICROBIAL COMMUNITIES bound together by proteins (histones) into chromosomes). Animals, plants, and fungi are all eukaryotic organisms. Parasite: An organism that lives in or on and takes its nourishment from another organism. A parasite cannot live independently. Parasitic diseases include infec- tions by protozoa, helminths, and arthropods (http://www.medterms.com/script/ main/art.asp?articlekey=4769). Parasitism: One species inflicts harm upon the other. Pathogen: Organism capable of causing disease. Pathogenic: Capable of causing disease. Peptidogylcan: A polymer found in the cell walls of prokaryotes that consists of polysaccharide and peptide chains in a strong molecular network. Petri dish: A shallow, circular dish with a loose cover, usually made of transpar- ent glass and plastic, and used to grow cultures of microorganisms. Phagocytosis: The uptake of particulate material by a cell. The main mammalian phagocytes are neutrophils and macrophages. 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. Planktonic: Bacteria that are suspended or growing in a fluid environment as opposed to those attached to a surface. 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. Polymeric matrix: Cells in a biofilm secrete polymers of varying chemical com- position that form an extracellular polymeric substance (EPS) or a slime matrix that gives the biofilm stability and helps it to adhere to a surface. Although gen- erally assumed to be primarily composed of polysaccharides, the EPS can also contain proteins and nucleic acids (Hall-Stoodley et al. 2004. Bacterial biofilms:

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APPENDIX D 593 From the natural environments to infectious disease. Nature Reviews Microbiol- ogy 2:95-108). Proteomics: The analysis of the expression, localizations, functions, and inter- actiosn of the proteins expressed by the genetic material of an organism ( Ameri- can Heritage Science Dictionary. 2011. Houghton Mifflin Harcourt Publishing Company). Public health: The art and science of dealing with the protection and improve- ment of community health by organized community effort and including preven- tive medicine and sanitary and social health. Quorum sensing: Cell-cell communication system that allows bacteria to moni- tor population density and control of specific genes in a density dependent manner Resistance: See Antibiotic resistance. Ribonucleic acid (RNA): A biologically important type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA is very similar to DNA, but differs in a few important structural details: in the cell, RNA is usually single-stranded, while DNA is usually double-stranded; RNA nucleotides contain ribose while DNA contains deoxyribose (a type of ribose that lacks one oxygen atom); and RNA has the base uracil rather than thymine that is present in DNA. Ribosomal RNA (rRNA): A class of RNA molecules, coded in the nucleolar organizer that has an integral (but poorly understood) role in ribosome structure and function. RNA components of the subunits of the ribosomes. Salmonella: A group of bacteria that cause typhoid fever, food poisoning, and enteric fever from contaminated food products. Shiga toxinproducing Escherichia coli (STEC): A type of enterohemor- rhagic E. coli (EHEC) bacteria that can cause illness ranging from mild intestinal disease to severe kidney complications. Other types of enterohemorrhagic E. coli include the relatively important serotype E. coli O157:H7, and more than 100 other non-O157 strains. Shotgun metagenome: See Metagenomics. Superorganism: A social colony of individuals who, through division of la- bor, effective communication and self-organization, form a highly connected

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594 THE SOCIAL BIOLOGY OF MICROBIAL COMMUNITIES community that functions as if it were a single organism (http://en.wiktionary. org/wiki/superorganism [accessed July 27, 2012]). 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 organ- isms is the host and may or may not derive a benefit (American Heritage Science Dictionary. 2011. Houghton Mifflin Harcourt Publishing Company). Symbiosis: The close association between two or more organisms of different species, often but not necessarily benefiting each member (American Heritage Science Dictionary. 2011. Houghton Mifflin Harcourt Publishing Company). Tragedy of the commons: A dilemma arising from the situation in which mul- tiple individuals, acting independently and rationally consulting their own self- interest, will ultimately deplete a shared limited resource, even when it is clear that it is not in anyone's long-term interest for this to happen. This dilemma was described in an article written by ecologist Garrett Hardin and first published in the journal Science in 1968 (http://en.wikipedia.org/wiki/Tragedy_of_the_com- mons [accessed July 27, 2012]). tRNase: Abbreviation for transfer ribonuclease. Ribonucleases are a type of en- zyme that catalyzes the degradation of RNA into smaller components. Transfer RNA is a RNA that delivers the amino acids necessary for protein synthesis to the ribosomes. 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.