Glossary of Terms
Accugenix Specific Terms
What does a confidence level of ‘Genus’, ‘Species’, ‘Family’ or ‘No match’ mean on a report?
Identification reports contain an identification and confidence level of species, genus, family/order/class (bacterial samples only) or no match (fungal samples only). We will assign the highest level of taxonomic information possible for each sample.
•A species level identification will be given a genus and species name, as well as a confidence level of ‘Species’ on the report.
•A genus level identification will receive the genus name of the organism, but a species designation could not be confidently assigned for this organism.
•A family, order or class confidence level indicates that, although the sample could not be assigned to a particular genus, the sequence for the sample provided sufficient information to determine the family, order or class to which the organism belongs. The bacteria that are most closely related to the unknown determine the level of classification that we are able to assign. This confidence level will only be assigned to bacterial identifications.
•A “no match” indicates that, while we were able to sequence the organism successfully, we could not confidently assign a Genus or Species level name based on our current ITS2 fungal library. Identification at the family/order/class level is generally not possible for fungi as the taxonomy is not as refined. Thus, this confidence level will only be assigned to fungal identifications.
•Bacterial samples submitted for ID will not be given a “no match” result. If we cannot make an ID due to a missing library entry or because the organism has never been described in the literature, we will search a public database (GenBank) for an identification.
I received a Customer Notification Form that a sample was “cancelled”. Can you further explain?
At Accugenix our focus is to exceed your expectations by providing exceptional quality, accuracy and reliable microbial testing services. Unlike other contract labs, when we are not able to obtain an identification, we do not charge processing fees. Sometimes, despite our best efforts, a small percentage of samples do not yield useful data. A Customer Notification Form indicates that we were unable to obtain high quality data from your sample. For more information see our Cancel Reasons Page.
Terms of General Use
Basic Local Alignment Search Tool, (BLAST) – an algorithm for comparing primary DNA sequence information. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold.
Distance measurement – a comparison of one sequence to another, expressed as a percentage of nucleotide differences between the two sequences. The sequences are aligned to minimize the absolute number of differences between the two sequences. Next the sequences are compared at every nucleotide position (pairwise comparison) and the percentage difference is calculated.
Environmental monitoring – an established program that demonstrates control of a manufacturing environment in compliance with current Good Manufacturing Practices (cGMPs), providing a baseline microbial profile of the facility and allowing for tracking and trending to source contaminations or excursions.
Fatty Acid – a long unbranched chain of carbon and hydrogen molecules that has a terminal carboxylic acid group.
Genome – an organism’s complete set of hereditary information, including both the genes and the non-coding sequences of the DNA/RNA.
Genotypic – an identification method using DNA sequence data or fragment analysis.
Library/Database – a reference database with known microbial entries used to compare against unknown microbial data for identifications.
Locus – (plural loci) the position of a gene or other significant sequence on a chromosome.
MALDI-TOF (matrix-assisted laser desorption/ionization-time of flight) – a mass spectrometry method for analysis of complex protein samples, results in a spectrum (plural spectra) of protein peaks.
MLST/SLST (multi or single-locus sequence typing) – a technique to characterize the evolutionary relatedness between isolates of microbial species using highly variable DNA sequences.
National Center for Biotechnology Information (NCBI) – a division of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health. The NCBI houses genome sequencing data in GenBank and an index of biomedical research articles in PubMed Central and PubMed, as well as other information relevant to biotechnology.
Neighbor joining phylogenetic tree – a clustering method for the creation of evolutionary trees based on sequence data, utilizing the distance between each pair of taxa (e.g., species or sequences) to form the tree.
Operon – a functioning unit of genomic DNA containing a cluster of genes the control of a single regulatory signal.
Phenotypic – an identification method using biochemical or physiological data.
Phylogenetic – the evolutionary relatedness between groups of organisms.
Phylogenetic tree (evolutionary tree) – a branching diagram showing the inferred evolutionary relationships between study organisms based upon similarities and differences in their genetic characteristics.
Polymerase Chain Reaction (PCR) – a method that results in millions of copies of a specific piece of DNA through a series of repetitive enzymatic reactions.
Polymorphic - (polymorphism) a base position in a DNA sequence that can be different nucleotides.
Polyphasic – a method consisting of two or more phases.
Proteotypic – a bacterial identification method that uses a ribosomal protein spectral fingerprint.
Restriction Enzyme (or restriction endonuclease) – an enzyme that cuts double-stranded or single-stranded DNA at specific recognition nucleotide sequences known as restriction sites. Example enzymes are EcoRI and PvuII used in Ribotyping.
rDNA – the DNA that encode for the ribosomal RNA subunits in an organisms.
rRNA – the RNA sequence transcribed from the rDNA and assembles into the ribosomal complex.
Ribosome – the organelle responsible for protein synthesis, consists of multiple RNAs and proteins assembled into a complex.
Ribotyping – a method of making a DNA fingerprint of the bacterial ribosomal DNA region for strain characterization.
