Amplicon: Pieces of DNA formed as the products of natural or artificial amplification events. For example, they can be formed via polymerase chain reactions (PCRs) or ligase chain reactions (LCRs), as well as by natural gene duplication.
Animalcules: A microscopic or minute organism, such as an amoeba or paramecium, usually considered to be an animal.
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.
Antibiotic resistance: Property of bacteria that confers the capacity to inactivate or exclude antibiotics or a mechanism that blocks the inhibitory or killing effects of antibiotics.
Antimicrobial: 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.
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.
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Appendix D Glossary Amplicon: Pieces of DNA formed as the products of natural or artificial ampli- fication events. For example, they can be formed via polymerase chain reactions (PCRs) or ligase chain reactions (LCRs), as well as by natural gene duplication. Animalcules: A microscopic or minute organism, such as an amoeba or parame- cium, usually considered to be an animal. 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. Antibiotic resistance: Property of bacteria that confers the capacity to inactivate or exclude antibiotics or a mechanism that blocks the inhibitory or killing effects of antibiotics. Antimicrobial: 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. 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. 387
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388 THE SCIENCE AND APPLICATIONS OF MICROBIAL GENOMICS Astroviruses: Small, single-stranded, positive sense RNA viruses, 6 to 8 kb in length. They cause diarrhea in humans and other animals. Attaching and effacing Escherichia coli (AEEC): E. coli that produces Shiga toxin (verotoxin). Certain serotypes cause enteritis, colitis, and diarrhea in a number of different animal species by expressing a virulence factor protein called intimin that allows intimate attachment of the organism to the microvillus brush border of the enterocyte, forming a characteristic attaching and effacing lesion. Diagnosis is by the detection of the Shiga toxin and characteristic lesions. Bacteria: Microscopic, single-celled organisms that have some biochemical and structural features different from those of animal and plant cells. Bacteriophage: A virus that infects bacteria. Bundle-forming pilus: So named because of its tendency to aggregate into rope-like bundles. The bundle-forming pilus is a member of a family of pili produced by important pathogens of humans and domestic animals known as type IV fimbriae. Chemoautotrophic: Organisms that use energy derived from the oxidation of inorganic compounds to fix carbon. Contig: A group of overlapping clones representing regions of the genome; the contiguous sequence of DNA created by assembling these overlapping chromo- some fragments. Diarrheagenic Escherichia coli (DEC): Any of a number of E. coli bacteria that cause diarrhea. 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. 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. Duplicate read inferred sequencing error estimation (DRISEE): A new tool to estimate the amount of “noise” in metagenomic data sets.
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APPENDIX D 389 Earth Microbiome Project: An initiative to collect natural samples and to ana- lyze the microbial community around the globe. Emerging infection: Infections that are rapidly increasing in incidence or geo- graphic range. Enteroaggregative Escherichia coli (EAEC): A subgroup of diarrheagenic E. coli (DEC) that during the past decade has received increasing attention as a cause of watery diarrhea, which is often persistent. EAEC have been isolated from children and adults worldwide. 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, salami, and 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. Enteroinvasive Escherichia coli (EIEC): A strain of Escherichia coli that pen- etrates gut mucosa and multiplies in colon epithelial cells, resulting in shigellosis- like changes of the mucosa. This strain produces a severe diarrheal illness that can resemble shigellosis except for the absence of vomiting and shorter duration of illness. Enteropathogenic Escherichia coli (EPEC): Strains of E. coli that cause en- teritis by close association with enteric cells. This group includes attaching and effacing E. coli. Enterotoxigenic Escherichia coli (ETEC): A strain of E. coli that is a frequent cause of diarrhea in travelers. 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. Genetic fingerprinting: A method employed to determine differences in amino acid sequences between related proteins; relies upon the presence of a simple tandem-repetitive sequences that are scattered throughout the human genome.
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390 THE SCIENCE AND APPLICATIONS OF MICROBIAL GENOMICS Genome: The complete set of genetic information in an organism. In bacteria, this includes the chromosome(s) and plasmids (extrachromosomal DNA mol- ecules that can replicate autonomously within a bacterial cell). Genome metastructure: Organization of the genome with respect to where the various structural and functional components are located. Genomics: The study of genes and their associated functions. 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 micro organism and has been useful in classifying bacteria. Gram-positive bacteria: Refers to the ability of a microorganism to retain a certain stain. This ability is related to the cell wall composition of the microor ganism and has been useful in classifying bacteria. Highly active antiretroviral therapy (HAART): The name given to treatment regimens that aggressively suppress HIV replication and progression of HIV disease. The usual HAART regimen combines three or more anti-HIV drugs from at least two different classes. Horizontal gene transfer: Any process in which an organism incorporates ge- netic material from another organism without being the offspring of that organism. 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 (HIV): Retrovirus that causes AIDS by infect- ing helper T cells of the immune system. The most common serotype, HIV-1, is distributed worldwide, while HIV-2 is primarily confined to West Africa. Human Microbiome Project: A U.S. National Institutes of Health initiative with the goal of identifying and characterizing the microorganisms that are found in association with both healthy and diseased humans (i.e., their microbial flora). The ultimate goal of this and similar NIH-sponsored microbiome projects is to test how changes in the human microbiome are associated with human health or disease.
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APPENDIX D 391 Indel: An insertion or deletion of genetic material. Indel refers to the mutation class that includes both insertions, deletions, and the combination thereof, includ- ing insertion and deletion events that may be separated by many years. 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. Metagenomics Rapid Annotation using Subsystem Technology server (MG- RAST): A community resource providing an automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. Methicillin-resistant Staphylococcus aureus (MRSA): A type of staph bacteria that is resistant to certain antibiotics called beta-lactams. These antibiotics in- clude methicillin and other more common antibiotics such as oxacillin, penicillin, and amoxicillin. See Antibiotic resistance. Microbe: A microorganism or biologic agent that can replicate in humans (in- cluding bacteria, viruses, protozoa, fungi, and prions). Microbial threat: Microbes that lead to disease in humans. Multilocus sequence typing (MLST): A technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes. Approximately 450–500 bp internal fragments of each gene are used, as these can be accurately sequenced on both strands using an automated DNA sequencer. For each housekeeping gene, the different sequences present within a bacterial species are assigned as distinct alleles and, for each isolate, the alleles at each of the loci define the allelic profile or sequence type (ST). Mycobacterial interspersed repetitive unit (MIRU): Short tandem repeat structures found at multiple loci throughout the Mycobacterium tuberculosis genome that have been used for typing these pathogens. 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.
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392 THE SCIENCE AND APPLICATIONS OF MICROBIAL GENOMICS 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. Pathogen: Organism capable of causing disease. Pathogenic: Capable of causing disease. Phage: A virus that infects bacteria. Many phage have proved useful in the study of molecular biology and as vectors for the transfer of genetic information be- tween cells. Lytic phage (e.g., the T series phage that infect Escherichia coli [coli- phages]), 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. Phylogenetics: The study of evolutionary relationships among groups of organ- isms (e.g., species, populations) that is discovered through molecular sequencing data and morphological data matrices. 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. Principal coordinates analysis: A method to explore and to visualize similarities or dissimilarities of data. It starts with a similarity matrix or dissimilarity matrix (= distance matrix) and assigns for each item a location in a low-dimensional space, such as a 3-D graphics. Rare biosphere: Rare microbial species in the soil, ocean, and living creatures that were effectively cloaked from previous sampling methods by more abundant species. Resistance: See Antibiotic resistance. 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.
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APPENDIX D 393 More specifically, rRNA sits in the ribosome, decoding the mRNA into various amino acids and assisting in translation. Shiga toxin-producing Escherichia coli (STEC): A type of enterohemorrhagic E. coli (EHEC) bacteria that can cause illness ranging from mild intestinal dis- ease 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 sequencing: The sequencing of a large DNA segment by sequencing of randomly derived sub-segments, whose order and orientation within the large segment are unknown until the final assembly of overlapping sequences. Single nucleotide polymorphism (SNP): A DNA sequence variation occurring when a single nucleotide—A, T, C, or G—in the genome (or other shared se- quence) differs between members of a biological species or paired chromosomes in an individual. Staphylococcus aureus: A gram-positive bacteria that is the most common cause of staph infections. It is frequently part of the skin flora found in the nose and on skin. About 20 percent of the human population are long-term carriers of S. aureus. Sympatric speciation: Speciation in the absence of physical barriers to genetic exchange between incipient species. Taxon: A particular taxonomic grouping, such as a species, genus, family, order, class, phylum, or kingdom. Tuberculosis (TB): A potentially fatal contagious disease that can affect almost any part of the body but is mainly an infection of the lungs. It is caused by a bacterial microorganism, the tubercle bacillus or Mycobacterium tuberculosis. Vaccine: A vaccine is a biological preparation that improves immunity to a par- ticular disease. A vaccine typically contains an agent that resembles a disease- causing microorganism, and is often made from weakened or killed forms of the microbe or its toxins. Variable number tandem repeats (VNTRs): Short nucleotide sequences that are present in multiple copies at a particular locus in the genome. The number of repeats can vary from individual to individual, making analysis of VNTRs useful for subtyping of microorganisms.
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394 THE SCIENCE AND APPLICATIONS OF MICROBIAL GENOMICS Virulence factor: Intrinsic characteristic of an infectious bacteria that facilitates 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. Whole genome sequencing: A laboratory process that determines the complete DNA sequence of an organism’s genome at a single time. This entails sequenc- ing all of an organism’s chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast. Almost any biological sample containing a full copy of the DNA—even a very small amount of DNA or ancient DNA—can provide the genetic material necessary for whole genome sequencing.