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

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

机构地区：[1]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 [2]Lee Kong Chian School of Medicine,Nanyang Technology University,Singapore 639798,Singapore

出　　处：《Genomics, Proteomics & Bioinformatics》2023年第6期1195-1205,共11页基因组蛋白质组与生物信息学报（英文版）

基　　金：supported by the National Key R&D Program of China(Grant Nos.2020YFA0509200 and 2020YFA0509203);the RGC Theme-based Res Scheme Hong Kong,China(Grant No.T21-705/20-N);the RGC Collaborative Research Fund,China(Grant Nos.C4039-19GF and C7065-18GF);the RGC-GRF Hong Kong,China(Grant No.14163817);the Vice-Chancellor’s Discretionary Fund Chinese University of Hong Kong,China.

摘　　要：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 DNA was 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,increasing bacterial reads by 2.46±0.20 folds while reducing host reads by 6.80%±1.06%.Moreover,2.40 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 folds while decreasing host reads by 10.2%±0.83%.Similarly,significantly more bacterial 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 improves the sensitivity of shotgun metagenomic sequencing in bacteria 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.

关 键 词：Gut microbiota Colon tissue Host DNAdepletion Shotgun metagenomic sequencing 

分 类 号：Q811.4[生物学—生物工程]