首页|High Sensitivity of Shotgun Metagenomic Sequencing in Colon Tissue Biopsy by Host DNA Depletion

High Sensitivity of Shotgun Metagenomic Sequencing in Colon Tissue Biopsy by Host DNA Depletion

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The high host genetic background of tissue biopsies hinders the application of shotgun metagenomic sequencing in characterizing the tissue microbiota.We proposed an optimized method that removed host DNA from colon biopsies and examined the effect on metagenomic analysis.Human or mouse colon biopsies were divided into two groups,with one group undergoing host DNA depletion and the other serving as the control.Host DNAs were removed through differential lysis of mammalian and bacterial cells before sequencing.The impact of host DNA depletion on microbiota was compared based on phylogenetic diversity analyses and regression analyses.Removing host DNA enhanced bacterial sequencing depth and improved species discovery,increas-ing bacterial reads by 2.46±0.20 fold while reducing host reads by 6.80％±1.06％.Moreover,3.40 times more of bacterial species were detected after host DNA depletion.This was confirmed from mouse colon tissues,increasing bacterial reads by 5.46±0.42 fold while decreasing host reads by 10.2％±0.83％.Similarly,significantly more species were detected in the mouse colon tissue upon host DNA depletion(P＜0.001).Furthermore,an increased microbial richness was evident in the host DNA-depleted samples compared with non-depleted controls in human colon biopsies and mouse colon tissues(P＜0.001).Our optimized method of host DNA depletion improved the sensitivity of shotgun metagenomic sequencing in bacterial detection in the biopsy,which may yield a more accurate taxonomic profile of the tissue microbiota and identify bacteria that are important for disease initiation or progression.

Gut microbiotaColon tissueHost DNA depletionShotgun metagenomic sequencing

Wing Yin Cheng、Wei-Xin Liu、Yanqiang Ding、Guoping Wang、Yu Shi、Eagle S.H.Chu、Sunny Wong、Joseph J.Y.Sung、Jun Yu

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State Key Laboratory of Digestive Disease,Institute of Digestive Disease and The Department of Medicine and Therapeutics,Li Ka Shing Institute of Health Sciences,Shenzhen Research Institute,The Chinese University of Hong Kong,Hong Kong Special Administrative Region 999077,China

Lee Kong Chian School of Medicine,Nanyang Technology University,Singapore 639798,Singapore

National Key R&D Program of ChinaNational Key R&D Program of ChinaRGC Themebased Res Scheme Hong KongRGC Collaborative Research FundRGC Collaborative Research FundRGC-GRF Hong KongVice-Chancellor's Discretionary Fund Chinese University of Hong Kong

2020YFA05092002020YFA0509203T21-705/20-NC4039-19GFC7065-18GF14163817

2023

10.1016/j.gpb.2022.09.003

基因组蛋白质组与生物信息学报(英文版)
中国科学院北京基因组研究所

基因组蛋白质组与生物信息学报(英文版)

CSTPCDCSCD
影响因子：0.495
ISSN：1672-0229
年,卷(期)：2023.6(6)
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