Taxonomic profiles based on standard amplicon
sequencing are composed of operational taxonomic
units (OTUs), which are often more specific than gen-
era but in most cases are less specific than species (BOX 1).
Recently, a new strategy has been proposed that uses a
sequence entropy-based approach to identify maximally
informative sites within the 16S rRNA gene to improve
OTU resolution19. This strategy, called oligotyping, is
advantageous for distinguishing closely related taxa
(such as those that differ by a single 16S rRNA nucleo-
tide) and has been used to study subspecies-level popu-
lation structure in the vaginal microbiome20 and to link
sewage samples to specific faecal pollution sources21.
In addition, a new, low-error approach to 16S rRNA
gene sequencing, known as low-error amplicon sequenc-
ing (LEA–seq), has been proposed and used to profile
stable carriage of host-specific strains in the human gut
microbiome22.