title: Development of HuMiChip for functional profiling of human microbiomes.
abstract: Understanding the diversity, composition, structure, function, and dynamics of human microbiomes in individual human hosts is crucial to reveal human-microbial interactions, especially for patients with microbially mediated disorders, but challenging due to the high diversity of the human microbiome. Here we have developed a functional gene-based microarray for profiling human microbiomes (HuMiChip) with 36,802 probes targeting 50,007 protein coding sequences for 139 key functional gene families. Computational evaluation suggested all probes included are highly specific to their target sequences. HuMiChip was used to analyze human oral and gut microbiomes, showing significantly different functional gene profiles between oral and gut microbiome. Obvious shifts of microbial functional structure and composition were observed for both patients with dental caries and periodontitis from moderate to advanced stages, suggesting a progressive change of microbial communities in response to the diseases. Consistent gene family profiles were observed by both HuMiChip and next generation sequencing technologies. Additionally, HuMiChip was able to detect gene families at as low as 0.001% relative abundance. The results indicate that the developed HuMiChip is a useful and effective tool for functional profiling of human microbiomes.
authors.affiliation: Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America.
authors.forename: Qichao
authors.initials: Q
authors.lastname: Tu
authors.affiliation: Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America.
authors.forename: Zhili
authors.initials: Z
authors.lastname: He
authors.affiliation: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.
authors.forename: Yanfei
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America.
authors.forename: Ye
authors.initials: Y
authors.lastname: Deng
authors.affiliation: Chinese Academy of Sciences, Qingdao Institute of Bioenergy and Bioprocess Technology, Qingdao, Shandong, China.
authors.forename: Lu
authors.initials: L
authors.lastname: Lin
authors.affiliation: Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America.
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Hemme
authors.affiliation: Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America.
authors.forename: Tong
authors.initials: T
authors.lastname: Yuan
authors.affiliation: Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America.
authors.forename: Joy D
authors.initials: JD
authors.lastname: Van Nostrand
authors.affiliation: Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America.
authors.forename: Liyou
authors.initials: L
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
authors.forename: Xuedong
authors.initials: X
authors.lastname: Zhou
authors.affiliation: UCLA School of Dentistry, University of California Los Angeles, Los Angeles, California, United States of America.
authors.forename: Wenyuan
authors.initials: W
authors.lastname: Shi
authors.affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.
authors.forename: Lanjuan
authors.initials: L
authors.lastname: Li
authors.affiliation: Chinese Academy of Sciences, Qingdao Institute of Bioenergy and Bioprocess Technology, Qingdao, Shandong, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Xu
authors.affiliation: Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America; Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
mesh_terms: D041981:Gastrointestinal Tract / Q000382:microbiology*; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation; D006801:Humans; D054892:Metagenome; D064307:Microbiota; D009055:Mouth / Q000382:microbiology*; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation*