ABSTRACT
The term operational taxonomic unit (OTU) is another central element in both numerical taxonomy (based on phenotypic data), for which an OTU typically represents an individual strain or group of isolates with similar phenotypic properties, and high-throughput sequencing-based studies, for which organisms are not directly observed. Here, an OTU is used to delineate groups of sequences/ reads above a given similarity threshold. Typically, a similarity level of 97% is used for delineating sequences at the species level when based on the 16S ribosomal RNA (rRNA) gene. This similarity value is a reasonable “working value,” but it is important to
7.1 Domains of life ...................................................................................... 127 7.1.1 Operational taxonomic units .................................................. 127 7.1.2 Members of the mice and rat microbiome ............................ 128
References ........................................................................................................ 131
bear in mind that many validly described bacterial species differ by much less than 3%.4,8,9
In mice and rats, as well as in humans, Bacteriodetes and Firmicutes are the most abundant phyla, in general accounting for 50-90% of the total prokaryotic gut microbiota. Other members of the core gut microbiome of mice and rats are Actinobacteria, Deferribacteres, Proteobacteria, Tenericutes, Verrucomicrobia, and the candidate phylum TM7 (Table 7.2). Rats tend to have a much more diverse gut microbiota than mice and humans, with two to three times as many OTUs detected.10,11 This should be kept in mind when planning studies involving gut microbiota characterization based on, for example, 16S rRNA gene amplicon sequencing, as the rat fecal microbiota in many cases has to be sequenced deeper to reach adequate coverage. Unicellular eukaryotes (yeast, fungi, blastocytes), Archea, and phages are all members of the rodent microbiota. However, they are ignored in the majority of studies, where focus is solely on the Bacteria. However, recent publications showing the involvement of unicellular eukaryotes in disease models (as well as human health and disease) and the influence of phages on microbiome composition has led to greater interest in these organisms.7,12-14
Table 7.1 Taxonomic Position of the Probiotic Strain Bifidobacterium animalis subsp. lactis BB-12
Level Example
Domain Bacteria Kingdom Bacteria Phylum Actinobacteria Class Actinobacteria Order Bifidobacteriales Family Bifidobacteriaceae Genus Bifidobacterium Species Bifidobacterium animalis Subspecies Bifidobacterium animalis subsp. lactis Strain Bifidobacterium animalis subsp. lactis BB-12
Ta bl
e 7.
