Human body encompasses a huge number of microorganisms, which constitute the human microbiome. These microbes are in active interactions with immune system and play important role in maintaining health. Traditional studies of human microbes mainly focused on infection-causing single pathogens and ignored impact from the whole microbial community. Metagenomic and metatranscriptomic next-generation sequencing (mNGS) has emerged as a promising technology that can not only be used for pan-pathogen detection but has also enabled the illustration of whole microbial composition and function. Here, I will demonstrate two applications of mNGS in monitoring human diseases: 1) In the first study, we have explored multiple components of blood cell-free DNA (cfDNA) from ICU patients using metagenomi...[ Read more ]

Human body encompasses a huge number of microorganisms, which constitute the human microbiome. These microbes are in active interactions with immune system and play important role in maintaining health. Traditional studies of human microbes mainly focused on infection-causing single pathogens and ignored impact from the whole microbial community. Metagenomic and metatranscriptomic next-generation sequencing (mNGS) has emerged as a promising technology that can not only be used for pan-pathogen detection but has also enabled the illustration of whole microbial composition and function. Here, I will demonstrate two applications of mNGS in monitoring human diseases: 1) In the first study, we have explored multiple components of blood cell-free DNA (cfDNA) from ICU patients using metagenomic sequencing. Both the human and microbial cfDNA fragments contain information about the disease condition. After integrating these multifaceted cfDNA information, we can achieve very good performance for diagnosis of sepsis and moderate results for prediction of clinical outcome at an early stage; 2) In the second project, we have revealed altered microbial composition and function, as well as high risk of secondary infections caused by pathogens other than SARS-CoV-2 in COVID-19 patients. By comparing the microbial features in different body sites, gut microbiome seems to be more directly affected by SARS-CoV-2 abundance as compared to that in the respiratory tract. Moreover, we didn’t observe restoration of microbial composition during the study period. The results suggest that SARS-CoV-2 infection could have a long-time effect on human microbiome, which deserves more attention for the management of COVID-19 patients.