OTUs and ASVs Produce Comparable Taxonomic and Diversity from Shrimp Microbiota 16S Profiles Using Tailored Abundance Filters

Genes

Andrés Cota-Huízar¹  Bruno Gómez-Gil²  AlonsoA. Lopez-Zavala³  Fernanda Cornejo-Granados⁴  Adrian Ochoa-Leyva⁴  Rodrigo García-López⁴  RogerioR. Sotelo-Mundo⁵ 

[1] Camarones el Renacimiento S.P.R. de R.I. Justino Rubio 26, Colonia Ejidal, Higuera de Zaragoza, Sinaloa 81330, Mexico;Centro de Investigación en Alimentación y Desarrollo, A.C. Mazatlán, Sinaloa 82100, Mexico;Departamento de Ciencias Químico Biológicas, Universidad de Sonora (UNISON), Blvd., Rosales y Luis, Encinas, Hermosillo, Sonora 83000, Mexico;Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional, Autónoma de México (UNAM) Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico;Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Sonora 83304, Mexico;

关键词: shrimp microbiota;    16S profiling;    OTUs;    ASVs;    clustering methods;    denoising;   

DOI  :  10.3390/genes12040564

来源: DOAJ

【 摘 要 】

The interplay between shrimp immune system, its environment, and microbiota contributes to the organism’s homeostasis and optimal production. The metagenomic composition is typically studied using 16S rDNA profiling by clustering amplicon sequences into operational taxonomic units (OTUs) and, more recently, amplicon sequence variants (ASVs). Establish the compatibility of the taxonomy, α, and β diversity described by both methods is necessary to compare past and future shrimp microbiota studies. Here, we used identical sequences to survey the V3 16S hypervariable-region using 97% and 99% OTUs and ASVs to assess the hepatopancreas and intestine microbiota of L. vannamei from two ponds under standardized rearing conditions. We found that applying filters to retain clusters >0.1% of the total abundance per sample enabled a consistent taxonomy comparison while preserving >94% of the total reads. The three sets turned comparable at the family level, whereas the 97% identity OTU set produced divergent genus and species profiles. Interestingly, the detection of organ and pond variations was robust to the clustering method’s choice, producing comparable α and β-diversity profiles. For comparisons on shrimp microbiota between past and future studies, we strongly recommend that ASVs be compared at the family level to 97% identity OTUs or use 99% identity OTUs, both using tailored frequency filters.

【 授权许可】

Unknown