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  • 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.

  • Aerobic organisms

    Organisms that require oxygen to survive.

  • Amplicon

    A piece of DNA (or RNA) that is the source and/or product of a replication process that greatly increases the amount of (ie., amplifies) that DNA or RNA. The amplification can be done experimentally using methods such as polymerase chain reaction (PCR) or it can occur naturally through gene duplication.

  • Amplicon Sequencing

    Determination of the nucleotide sequence of amplicons.

  • Anaerobic organisms

    Organisms that live an anoxic environment – one which lacks oxygen. While most
    living things require oxygen to survive, oxygen can be toxic to anaerobic organisms.

  • Anoxic

    The absence of oxygen.

  • Archaea

    Single-celled organisms, prokaryotes, that are thought to be modern descendants of an
    ancient lineage of bacteria that evolved around sulfur-rich deep-sea vents.

  • Bacteria

    Microscopic, single-celled microorganisms, prokaryotes, that have some biochemical and
    structural features different from those of animal and plant cells.

  • Bacteriophage

    A virus that infects and replicates within bacteria and archaea.

  • Biome

    A self-contained eco-system.

  • Calprotectin (Fecal Calprotectin)

    A calcium- and zinc-binding protein that is abundant in neutrophils; measurement of calprotectin in the stool is used to indicate the migration of neutrophils to the intestinal mucosa, which occurs during intestinal inflammation.

  • Chemosensitivity

    Susceptibility of a disease-causing bacterium or cancer cell to the action of a chemical agent.

  • Clade

    A clade consists of an organism and all of its descendants. It’s useful to think of a clade as being one “branch” on the tree of life, where the common ancestor is the place that the branch split from the main trunk. Because clades are a way of thinking about “branches of the tree of life,” a clade can only contain organisms that do share a common ancestor. A clade also contains all descendants of that branch, excluding none.

  • Colony Forming Units (CFU)

    A unit used in microbiology to estimate the number of viable bacteria or fungal cells in a sample. Viable is defined as the ability to multiply under the controlled conditions.

  • Commensal

    A relationship between two or more species such that they coexist, and one derives benefit from the relationship without harm or obvious benefit to the other.

  • Conventionalization

    A method in which germ-free animals (particularly mice) are inoculated with gut microbiota to populate the gastrointestinal tract. 

  • Cytokines

    A broad category of small proteins that are important in cell signaling and are produced by a range of cells, including immune cells. Cytokines include chemokines, interferons (IF), interleukins (IL), lymphokines, and tumor necrosis factors (TNF), but generally not hormones or growth factors.

  • Dysbiosis

     An imbalance between the organisms present in a person’s natural microbiota, especially in the gut.  Dysbiosis is thought to contribute to a range of conditions of ill health.

  • Ecosystem

    A biological community of interacting organisms and their physical environment.

  • Endogenous

    Growing or originating from within an organism

  • Enteroids

    Epithelial structures that contain crypt- and villus-like domains reminiscent of normal gut epithelium.

  • Epigenetics

    the study of phenotypic changes that are heritable and do not involve alterations in the DNA sequence.

  • Eukaryotes

    Organisms whose bodies are made up of eukaryotic cells, which are cells that contain a nucleus and organelles and are enclosed by a plasma membrane; protists, fungi, plants and animals are eukaryotes.

  • Fluorescence in situ hybridization (FISH)

    A technique that uses single-stranded DNA probes and fluorescence microscopy to detect and localize specific DNA sequences on chromosomes.

  • Genome

    The complete set of genetic information in an organism. In bacteria, this includes the chromosome(s) and plasmids.

  • Genotype

    The sets of genes or the entire genome of an organism.

  • Genus

    A taxonomic category that ranks above species and below family. It is denoted by a capitalized, italicized Latin name, such as Escherichia.

  • Gnotobiotic

    Describes laboratory mice that are in sterile (germ-free) conditions or 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.

  • Gram-negative bacteria

    Bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial classification. Gram-negative bacteria generally have a cytoplasmic membrane and include most of the bacteria normally found in the gastrointestinal tract that can be responsible for disease.

  • Gram-positive bacteria

    Bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their cell wall. These bacteria have a thick peptidoglycan layer that retains the stain.

  • Gut

    Gut refers to the entire digestive tract, starting with the mouth and ending with the anus.

  • Hereditary colorectal cancer

    The two main types of inherited colorectal cancer are Familial Adenomatous Polyposis (FAP) and Lynch Syndrome, also referred to as hereditary nonpolyposis colorectal cancer (HNPCC).

  • Homeostasis

    An organism’s process of maintaining a stable internal environment suitable for sustaining life.

  • Homolog

    One of two or more genes that are very similar in sequence as a result of derivation from the same ancestral gene.

  • Immunohistochemistry

    An experimental method used to selectively identify proteins in cells of a tissue using labelled antibodies that specifically bind to that protein.

  • Immunophenotype

    A process that uses antibodies to identify cells based on the types of antigens or markers on the surface of the cells.

  • Infection

    The invasion of the body or a part of the body by a pathogenic agent, such as a microorganism or virus. 

  • Innate immune system

    Immunity that is present at birth and does not have to be learned through exposure to an invader; thus it provides an immediate response to foreign invaders. 

  • Kingdom

    All of life, thought to come from a single origin, can be broken down into lower levels of classification, such as a kingdom or phylum. Each consecutive level represents a more related group of organisms.

  • Loci

    The position of a gene or mutation on a chromosome.

  • Metabolite

    An intermediate or end-product 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. The term metabolite is usually restricted to small molecules.

  • Metabolome

    The complete set of metabolites present in a cell, tissue, or other biological sample.

  • Metabolomics

    The analytical approaches used to determine the metabolite profile(s) of any given cell, tissue, or other biological sample. The set of all metabolites present in such a sample is called the metabolome.

  • Metagenome

    The collection of genomes and genes from the members of a microbiota. This collection is obtained through shotgun sequencing of DNA extracted from a sample (metagenomics) followed by assembly or mapping to a reference database.

  • Metagenomics

    The study of genetic material recovered directly from environmental samples, which contain complex microbial communities. The study examines the genomic composition of an entire organism, including each of the microbes that exist within it.

  • Metaproteomics

    Large-scale characterization of the all proteins of environmental or clinical samples at a given point in time.

  • Microbes

    A microscopic living organism. Examples of microorganisms include bacteria, archaea, algae, protozoa, and microscopic animals such as the dust mite.

  • Microbiome

    The microbiome is the genetic material of all the microbes (microbiota)- bacteria, fungi, protozoa and viruses - that live on and inside the human body. The bacteria in the microbiome help digest our food, regulate our immune system, protect against other bacteria that cause disease, and produce vitamins including B vitamins B12, thiamine and riboflavin, and Vitamin K, which is needed for blood coagulation. The microbiome is essential for human development, immunity and nutrition.

  • Microbiota

    The entire population of microorganisms that colonizes a location or organism. Microbiota are communities of commensal, symbiotic, and/or pathogenic microorganisms, which include bacteria, archaea, protists, fungi, and viruses. Microbiota have been found to be crucial for immunologic, hormonal, and metabolic homeostasis of their host.

  • Murine

    Murine, referring to mice or related rodents, primarily refers to mouse models in laboratory research.  There are many genetically modified strains of mice that are available to researchers.

  • Mutualist

    A microorganism that derives some benefit from its host and in return confers some benefit.

  • Next Gen Sequencing

    A term, short for next generation sequencing, that refers to modern very high-throughput DNA sequencing technology.

  • Organoid

    A three-dimensional cluster of cells that is derived from and resembles a particular organ and can be used to study the biology of that organ.

  • Oxidative stress

    A situation when there are more free radicals produced than the cell can neutralize with antioxidants causing damage to cellular components such as proteins, lipids, or nucleic acids.

  • Parasite

    A microorganism that derives some benefit from its host but in the process does harm to its host.

  • Pathogenic

    Capable of causing disease to an organism.

  • Pathogens

    Organisms that causes harm or disease.

  • Phage

    Short for bacteriophage, which is a general term for viruses that infect and replicate in bacteria and archea.

  • Phenotype

    An observable characteristic of an organism that is manifested on a molecular, cellular or population level. A phenotype of a cell varies over time and with changing physicochemical conditions.

  • Phylum

    A taxonomic category that ranks above class and below kingdom, such as Proteobacteria.

  • Plasmids

    Extra-chromosomal DNA molecules that can replicate autonomously within a bacterial cell.

  • Polymerase Chain Reaction

    A method widely used in molecular biology to rapidly make millions to billions of copies of a specific DNA sample, allowing scientists to start with a very small sample of DNA and amplify it to study it in detail.

  • Prokaryote

    Prokaryotes are unicellular organisms that consist of a single prokaryotic cell. Prokaryotic cells are simple cells that do not have a true nucleus or other cell organelles. Bacteria and Archaea are the two domains of life that are prokaryotes.

  • Proteases

    Enzymes that break down proteins and are involved in many biological functions, including digestion of eaten/swallowed proteins, protein catabolism, and cell signaling.

  • Proteasome

    A protein complex that degrades unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds. Enzymes that help such reactions are called proteases.

  • Proteomics

    The large-scale study of proteins.

  • Protists

    A group of loosely connected, mostly unicellular eukaryotic organisms that are not plants, animals or fungi.

  • Reactive oxygen species

    Reactive oxygen species (ROS) are unstable oxygen-containing molecules that easily react with other molecules in the cell and can cause cellular damage. Examples include peroxides, superoxide, hydroxyl radical, among others.

  • Ribozymes

    RNA molecule capable of acting like an enzyme, which catalyzes a chemical reaction.

  • RNA seq

    An experimental method that uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment, analyzing the continuously changing cellular transcriptome.

  • Sequencing

    The process of determining the order of nucleotides within an organism’s genetic material (DNA or RNA). This technique is generally used to identify genes from organisms and determine species categories using the genes for specific types of RNA.

  • Short chain fatty acids

    A variety of byproducts formed when gut bacteria digest fiber and polysaccharides. They can be used by the host as an energy source but have many different roles. They contain less than 6 carbon atoms. Examples include butyric acid (butyrate), propionic acid (propionate), and acetic acid (acetate).

  • Shotgun Sequencing

     A method used for sequencing entire chromosomes and entire genomes based on producing random fragments of DNA that are then assembled by computers. It is named by analogy to the rapidly expanding, random firing pattern of a shotgun. 

  • Single cell genomics

    Sequencing and analysis of the genome from a single cell.

  • Species

    A group of organisms that share a genetic heritage, can interbreed, and create offspring that are also fertile. It is denoted by a small case, italicized Latin name such as coli.

  • Supernatant

    The usually clear liquid overlying material deposited by settling, precipitation, or centrifugation.

  • Symbiotic

    A relationship between species that is beneficial to both.

  • Taxonomic classification

    Classification of microbes that is reported as phyla, genus, species, and strain. The microbiota is dominated by two bacterial phyla: gram-negative and gram-positive.

  • Taxonomy

    The branch of biology that classifies all living things. All living organisms are classified by a hierarchy called taxonomic rankings. The categories included in this hierarchy go as follows: domain, kingdom, phylum, class, order, family, genus, and finally, the smallest, species.

  • Transcriptome

    Is the full range of messenger RNA, or mRNA, molecules expressed by an organism or by a cell or tissue type. 

  • Transmissibility

    The ease with which a microorganism(s) can spread from a source to a host.

  • Transmission

    The transfer of a microorganism(s) from a source to a host.

  • Virome

    Refers to the collection of nucleic acids, both RNA and DNA, that make up the viral community associated with an ecosystem. The composition of the human virome includes viruses that infect human cells and bacteriophages that infect a broad array of bacteria that inhabit us. 

  • Virus

    A small infectious agent that can replicate only inside the cells of another organism, utilizing parts of the host's cellular machinery to reproduce and release the replicated nucleic acid chains to infect more cells.

  • Whole Genome Sequencing (WGS)

    WGS is the process of determining the complete DNA sequence of an organisms's genome (or genetic makeup) at a single time. This includes sequencing the chromosomal as well as extra-chromosomal DNA (such as mitochondrial DNA).

  • Xenobiotic

    Refers to foreign compounds that are neither produced nor naturally found in a host. The intestinal bacteria participate in the metabolism of xenobiotic chemicals.

  • Zonulin

    A protein that modulates the permeability of tight junctions between cells of the wall of the digestive tract.