Glossary of terms
| Amplicon90 | DNA product of amplification events via PCR |
| Clone library91 | Library of DNA sequences from a source (eg, 16SrRNA gene amplicons from a tissue sample), inserted into a bacterial plasmid, then picked up by a host bacteria and plated out on a selection media, such that each colony of bacteria on the plate has the identical ‘cloned’ DNA fragment in its plasmid |
| Denaturing gradient gel electrophoresis92 | Method for separating RNA or DNA using an electric field applied to samples placed within a gel. As it applies to microbial ecology, when 16S rRNA amplicons are chemically denatured, they yield unique electrophoretic patterns (banding) that are determined by the nucleic content of each of the amplicons. It can be used to visualise variation in microbial diversity |
| Fluorescent in situ hybridisation93 | Technique to detect and localise the presence of specific DNA or RNA sequences using fluorescently labelled nucleic acid probes |
| Hypervariable region90 | A DNA sequence in a conserved gene where genomic changes between individuals or species are clustered |
| Human microbiome6 | The complete collection of microbiota that live inside and on humans |
| Microarray92 | A tool for analysing gene expression that consists of a small membrane or glass slide containing specific DNA sequences, or probes, arranged in a regular ‘array’ pattern, which hybridise to DNA or cDNA (targets) and are then detected/quantified by a chemiluminescent reaction |
| Metagenomics90 | The shotgun random sequencing of all DNA in a sample (host and microbe), which is then analysed, organised and identified using sequence databases and computational tools |
| Operational taxonomic unit90 | A grouping or clustering of items (eg, DNA sequences) into a ‘unit’, in which similarity within the unit is defined by set criteria (eg, 97% homology) |
| Primer91 | Short strand of nucleic acid that complements a stretch of nucleic acid in the target and can serve as a starting point for DNA synthesis by a DNA polymerase |
| 16S rRNA Phylochip26 | 16S rRNA-based DNA microarray that provides rapid profiling of bacterial populations identified and classified on the basis of >97% sequence similarity |
| Quantitative real-time PCR94 | Laboratory technique, using PCR, to amplify and simultaneously quantify a sequence of DNA or RNA |
| Sanger sequencing91 | DNA sequencing method developed by Sanger and coworkers in 1977 (‘chain-termination method’) that was used widely until the development of high-throughput sequencing methods in the last 5 years that markedly enhanced the speed of DNA sequencing |
| Shotgun sequencing95 | Method for DNA sequencing. DNA is broken up into random small segments that are then sequenced. A computer program can use overlapping reads to assemble the continuous sequence |
| Temperature gradient gel electrophoresis92 | Similar approach to denaturing gradient gel electrophoresis, except that temperature, rather than a chemical gradient, is used to denature the DNA |
| Terminal restriction fragment length polymorphism16 | Technique for profiling microbial communities based on the amplification of 16S rRNA with fluorescently labelled primers followed by restriction enzyme digestion and separation of fragments on an automated DNA sequencer. The result is an electropherogram which is an intensity plot representation of the electrophoresis, with ‘peaks’ corresponding to a specific restriction fragment in the sample and its height or area corresponding to its relative abundance |
| 16S Ribosomal RNA90 | A component of the 30S subunit of prokaryotic ribosomes. As this genetic information is highly conserved, it can be used to differentiate species of bacteria, based upon sequence differences, largely clustered in the hypervariable regions of the gene |
| 454-Pyrosequencing90 | A method of high-throughput DNA sequencing, developed by 454 Life Sciences that has markedly dropped the cost per bp and runtime of sequencing, while increasing output by orders of magnitude over Sanger sequencing |