Improving saliva shotgun metagenomics by chemical host DNA depletion

Microbiome

Jon G. Sanders¹  Rob Knight¹  Karsten Zengler¹  Clarisse A. Marotz¹  Cristal Zuniga¹  Livia S. Zaramela¹ 

[1] Department of Pediatrics, University of California San Diego;

关键词: Microbiome;    Host depletion;    Microbial enrichment;    Propidium monoazide;    Shotgun sequencing;    Saliva;   

DOI  :  10.1186/s40168-018-0426-3

来源: DOAJ

【 摘 要 】

Abstract Background Shotgun sequencing of microbial communities provides in-depth knowledge of the microbiome by cataloging bacterial, fungal, and viral gene content within a sample, providing an advantage over amplicon sequencing approaches that assess taxonomy but not function and are taxonomically limited. However, mammalian DNA can dominate host-derived samples, obscuring changes in microbial populations because few DNA sequence reads are from the microbial component. We developed and optimized a novel method for enriching microbial DNA from human oral samples and compared its efficiency and potential taxonomic bias with commercially available kits. Results Three commercially available host depletion kits were directly compared with size filtration and a novel method involving osmotic lysis and treatment with propidium monoazide (lyPMA) in human saliva samples. We evaluated the percentage of shotgun metagenomic sequencing reads aligning to the human genome, and taxonomic biases of those not aligning, compared to untreated samples. lyPMA was the most efficient method of removing host-derived sequencing reads compared to untreated sample (8.53 ± 0.10% versus 89.29 ± 0.03%). Furthermore, lyPMA-treated samples exhibit the lowest taxonomic bias compared to untreated samples. Conclusion Osmotic lysis followed by PMA treatment is a cost-effective, rapid, and robust method for enriching microbial sequence data in shotgun metagenomics from fresh and frozen saliva samples and may be extensible to other host-derived sample types.

【 授权许可】

Unknown