Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale

Abstract

Operational Taxonomic Units (OTUs), usually defined as clusters of similar 16S/18S rRNA sequences, are the most widely used basic diversity units in large-scale characterizations of microbial communities. However, it remains unclear how well the various proposed OTU clustering algorithms approximate ‘true’ microbial taxa. Here, we explore the ecological consistency of OTUs – based on the assumption that, like true microbial taxa, they should show measurable habitat preferences (niche conservatism). In a global and comprehensive survey of available microbial sequence data, we systematically parse sequence annotations to obtain broad ecological descriptions of sampling sites. Based on these, we observe that sequence-based microbial OTUs generally show high levels of ecological consistency. However, different OTU clustering methods result in marked differences in the strength of this signal. Assuming that ecological consistency can serve as an objective external benchmark for cluster quality, we conclude that hierarchical complete linkage clustering, which provided the most ecologically consistent partitions, should be the default choice for OTU clustering. To our knowledge, this is the first approach to assess cluster quality using an external, biologically meaningful parameter as a benchmark, on a global scale.

Next Generation Sequencing and Microbial Community Associated With Eukaryotes Including Parasitic Heliminths: A Review Article.

“…The commonly employed ecological and NGS term explanation in the microbiota research field is illustrated in Figure 21 and Table 3. Clusters of 16S/18S small subunit (SSU) rRNA gene similarity, are used as theory-agnostic approximations of microbial taxa [40] Microbiome…”

Needs assessment for emerging oral microbiome knowledge in dental hygiene education

“…A unifying taxonomy theory for bacteria including the genetic characteristics (phylogenetics) and bacterial habitat remains controversial. [6, 7]…”

“…It has a cluster of unique sequences for a species despite lateral gene transfer of other sections. [6] Researchers used statistical algorithms to classify the small subunits (SSU) of rRNA as OTUs. Global datasets of bacterial rRNA sequences exist.…”

“…The approach is considered theory-agnostic, but the algorithms for OTU clusters have been shown to also have high levels of ecological consistency. [6]…”

Interações entre fungos micorrízicos arbusculares e a microbiota de solos

“…Figura 2 -Unidades taxonômicas operacionais (OTUs) das amostras de solo com inoculação das diluições microbianas (10 -1 , 10 -3 e 10 -6 ) das comunidades microbianas 'A' e 'B' e solo estéril (SE) sem microbiota inoculada, durante a condução do experimento As OTUs são compostas por agrupamentos com sequências similares de determinado gene ou região, considerados como uma unidade de diversidade básica que se aproxima dos táxons microbianos que compõem a comunidade (SCHMIDT et al, 2014). Esta unidade pode ser vista por dois critérios: quanto à filogenia destas espécies, pois representam grupos monofiléticos de organismos, ou relacionado a fatores ecológicos que causam diferenciação e especiação dos grupos formados (GEVERS et al, 2005;COHAN, 2006;KOEPPEL et al, 2008;HUNT et al, 2008;VOS, 2011;PREHEIM et al, 2013).…”