title: Optimized DNA extraction and metagenomic sequencing of airborne microbial communities.
abstract: Metagenomic sequencing has been widely used for the study of microbial communities from various environments such as soil, ocean, sediment and fresh water. Nonetheless, metagenomic sequencing of microbial communities in the air remains technically challenging, partly owing to the limited mass of collectable atmospheric particulate matter and the low biological content it contains. Here we present an optimized protocol for extracting up to tens of nanograms of airborne microbial genomic DNA from collected particulate matter. With an improved sequencing library preparation protocol, this quantity is sufficient for downstream applications, such as metagenomic sequencing for sampling various genes from the airborne microbial community. The described protocol takes ∼12 h of bench time over 2-3 d, and it can be performed with standard molecular biology equipment in the laboratory. A modified version of this protocol may also be used for genomic DNA extraction from other environmental samples of limited mass or low biological content.
authors.affiliation: School of Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China.
authors.forename: Wenjun
authors.initials: W
authors.lastname: Jiang
authors.affiliation: School of Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Liang
authors.affiliation: State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, Tsinghua University, Beijing, China.
authors.forename: Buying
authors.initials: B
authors.lastname: Wang
authors.affiliation: Center of Biomedical Analysis, School of Life Sciences, Tsinghua University, Beijing, China.
authors.forename: Jianhuo
authors.initials: J
authors.lastname: Fang
authors.affiliation: Center of Biomedical Analysis, School of Life Sciences, Tsinghua University, Beijing, China.
authors.forename: Jidong
authors.initials: J
authors.lastname: Lang
authors.affiliation: Center of Biomedical Analysis, School of Life Sciences, Tsinghua University, Beijing, China.
authors.forename: Geng
authors.initials: G
authors.lastname: Tian
authors.affiliation: State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, Tsinghua University, Beijing, China.
authors.forename: Jingkun
authors.initials: J
authors.lastname: Jiang
authors.affiliation: School of Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China.
authors.forename: Ting F
authors.initials: TF
authors.lastname: Zhu
mesh_terms: D000391:Air Microbiology; D001671:Biochemistry / Q000295:instrumentation / Q000379:methods*; D002681:China; D004247:DNA / Q000302:isolation & purification*; D004784:Environmental Monitoring / Q000295:instrumentation / Q000379:methods*; D004867:Equipment Design; D054892:Metagenome; D059013:Microbial Consortia / Q000235:genetics*; D052638:Particulate Matter; D011786:Quality Control; D017422:Sequence Analysis, DNA; D057188:Workflow
chemical_list: D052638:Particulate Matter; D004247:DNA