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Host DNA depletion efficiency of microbiome DNA enrichment methods in infected tissue samples.
J Microbiol Methods. 2020 03; 170:105856.JM

Abstract

Shotgun metagenomic sequencing or metagenomic whole genome sequencing is a genome-wide sequencing approach to explore bacterial communities directly from their habitat or sites of infection. However, host DNA contamination in metagenomic sequencing overwhelm low biomass of microbial signals and decrease sensitivity for microbial detection. In this study, we evaluated the host DNA depletion efficiency of four different microbiome DNA enrichment methods (NEBNext Microbiome DNA Enrichment kit, Molzym Ultra-Deep Microbiome Prep, QIAamp DNA Microbiome kit and Zymo HostZERO microbial DNA kit) in diabetic foot infection (DFI) tissue samples using quantitative real-time PCR and their effect on bacterial community composition by 16S ribosomal RNA amplicon sequencing. The host DNA depletion ratio (18S/16S rRNA), the percentage of bacterial DNA component and the microbial community profile of DFI were compared before (control) and after each microbiome DNA enrichment method. There was a significant difference in the 18S/16S rRNA ratio among different microbiome DNA enrichment methods (p <.001). QIAamp and HostZERO method reduced 18S/16S rRNA ratio by 32 and 57 fold than control method respectively. The percentage of bacterial DNA component increased more than ten-fold in QiaAmp (71.0 ± 2.7%) and HostZERO (79.9 ± 3.1%) method respectively than those in control method without host DNA depletion (6.7 ± 0.1%). It demonstrated the host DNA contamination was efficiently depleted and bacterial DNA was effectively enriched in HostZERO and QIAamp methods, attesting to the efficacy of these two methods in shotgun metagenomic sequencing studies. Overall, bacterial community composition of DFI samples was similar between control and microbiome enriched DNA samples.

Authors+Show Affiliations

Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia. Electronic address: f.sadeghpour1989@gmail.com.QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia. Electronic address: Martha.Zakrzewski@qimrberghofer.edu.au.Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia. Electronic address: karen.vickery@mq.edu.au.Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia. Electronic address: helen.hu@mq.edu.au.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32007505

Citation

Heravi, Fatemah Sadeghpour, et al. "Host DNA Depletion Efficiency of Microbiome DNA Enrichment Methods in Infected Tissue Samples." Journal of Microbiological Methods, vol. 170, 2020, p. 105856.
Heravi FS, Zakrzewski M, Vickery K, et al. Host DNA depletion efficiency of microbiome DNA enrichment methods in infected tissue samples. J Microbiol Methods. 2020;170:105856.
Heravi, F. S., Zakrzewski, M., Vickery, K., & Hu, H. (2020). Host DNA depletion efficiency of microbiome DNA enrichment methods in infected tissue samples. Journal of Microbiological Methods, 170, 105856. https://doi.org/10.1016/j.mimet.2020.105856
Heravi FS, et al. Host DNA Depletion Efficiency of Microbiome DNA Enrichment Methods in Infected Tissue Samples. J Microbiol Methods. 2020;170:105856. PubMed PMID: 32007505.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Host DNA depletion efficiency of microbiome DNA enrichment methods in infected tissue samples. AU - Heravi,Fatemah Sadeghpour, AU - Zakrzewski,Martha, AU - Vickery,Karen, AU - Hu,Honghua, Y1 - 2020/01/30/ PY - 2019/11/23/received PY - 2020/01/28/revised PY - 2020/01/28/accepted PY - 2020/2/3/pubmed PY - 2020/2/3/medline PY - 2020/2/3/entrez KW - 16S rRNA sequencing, microbiome KW - DNA extraction KW - Diabetic foot infection KW - Host DNA depletion KW - Metagenomic whole genome sequencing KW - Microbiome DNA enrichment KW - Shotgun metagenomic sequencing SP - 105856 EP - 105856 JF - Journal of microbiological methods JO - J Microbiol Methods VL - 170 N2 - Shotgun metagenomic sequencing or metagenomic whole genome sequencing is a genome-wide sequencing approach to explore bacterial communities directly from their habitat or sites of infection. However, host DNA contamination in metagenomic sequencing overwhelm low biomass of microbial signals and decrease sensitivity for microbial detection. In this study, we evaluated the host DNA depletion efficiency of four different microbiome DNA enrichment methods (NEBNext Microbiome DNA Enrichment kit, Molzym Ultra-Deep Microbiome Prep, QIAamp DNA Microbiome kit and Zymo HostZERO microbial DNA kit) in diabetic foot infection (DFI) tissue samples using quantitative real-time PCR and their effect on bacterial community composition by 16S ribosomal RNA amplicon sequencing. The host DNA depletion ratio (18S/16S rRNA), the percentage of bacterial DNA component and the microbial community profile of DFI were compared before (control) and after each microbiome DNA enrichment method. There was a significant difference in the 18S/16S rRNA ratio among different microbiome DNA enrichment methods (p <.001). QIAamp and HostZERO method reduced 18S/16S rRNA ratio by 32 and 57 fold than control method respectively. The percentage of bacterial DNA component increased more than ten-fold in QiaAmp (71.0 ± 2.7%) and HostZERO (79.9 ± 3.1%) method respectively than those in control method without host DNA depletion (6.7 ± 0.1%). It demonstrated the host DNA contamination was efficiently depleted and bacterial DNA was effectively enriched in HostZERO and QIAamp methods, attesting to the efficacy of these two methods in shotgun metagenomic sequencing studies. Overall, bacterial community composition of DFI samples was similar between control and microbiome enriched DNA samples. SN - 1872-8359 UR - https://www.unboundmedicine.com/medline/citation/32007505/Host_DNA_depletion_efficiency_of_microbiome_DNA_enrichment_methods_in_infected_tissue_samples_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0167-7012(19)31069-3 DB - PRIME DP - Unbound Medicine ER -
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