Table 1

Glossary of terms

Amplicon90DNA product of amplification events via PCR
Clone library91Library 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 electrophoresis92Method 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 hybridisation93Technique to detect and localise the presence of specific DNA or RNA sequences using fluorescently labelled nucleic acid probes
Hypervariable region90A DNA sequence in a conserved gene where genomic changes between individuals or species are clustered
Human microbiome6The complete collection of microbiota that live inside and on humans
Microarray92A 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
Metagenomics90The 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 unit90A 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)
Primer91Short 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 Phylochip2616S rRNA-based DNA microarray that provides rapid profiling of bacterial populations identified and classified on the basis of >97% sequence similarity
Quantitative real-time PCR94Laboratory technique, using PCR, to amplify and simultaneously quantify a sequence of DNA or RNA
Sanger sequencing91DNA 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 sequencing95Method 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 electrophoresis92Similar approach to denaturing gradient gel electrophoresis, except that temperature, rather than a chemical gradient, is used to denature the DNA
Terminal restriction fragment length polymorphism16Technique 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 RNA90A 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-Pyrosequencing90A 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