title: HuMiChip2 for strain level identification and functional profiling of human microbiomes.
abstract: With the massive data generated by the Human Microbiome Project, how to transform such data into useful information and knowledge remains challenging. Here, with currently available sequencing information (reference genomes and metagenomes), we have developed a comprehensive microarray, HuMiChip2, for strain-level identification and functional characterization of human microbiomes. HuMiChip2 was composed of 29,467 strain-specific probes targeting 2063 microbial strains/species and 133,924 sequence- and group-specific probes targeting 157 key functional gene families involved in various metabolic pathways and host-microbiome interaction processes. Computational evaluation of strain-specific probes suggested that they were not only specific to mock communities of sequenced microorganisms and metagenomes from different human body sites but also to non-sequenced microbial strains. Experimental evaluation of strain-specific probes using single strains/species and mock communities suggested a high specificity of these probes with their corresponding targets. Application of HuMiChip2 to human gut microbiome samples showed the patient microbiomes of alcoholic liver cirrhosis significantly (p < 0.05) shifted their functional structure from the healthy individuals, and the relative abundance of 21 gene families significantly (p < 0.1) differed between the liver cirrhosis patients and healthy individuals. At the strain level, five Bacteroides strains were significantly (p < 0.1) and more frequently detected in liver cirrhosis patients. These results suggest that the developed HuMiChip2 is a useful microbial ecological microarray for both strain-level identification and functional profiling of human microbiomes.
authors.affiliation: Department of Marine Sciences, Ocean College, Zhejiang University, Zhejiang, China.|Zhoushan Municipal Center for Disease Control and Prevention, Zhoushan, Zhejiang, China.|Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
authors.forename: Qichao
authors.initials: Q
authors.lastname: Tu
authors.affiliation: Chinese Academy of Sciences, Chengdu Institute of Biology, Chengdu, Sichuan, China.
authors.forename: Jiabao
authors.initials: J
authors.lastname: Li
authors.affiliation: Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
authors.forename: Zhou
authors.initials: Z
authors.lastname: Shi
authors.affiliation: The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China.
authors.forename: Yanfei
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Department of Marine Sciences, Ocean College, Zhejiang University, Zhejiang, China.
authors.forename: Lu
authors.initials: L
authors.lastname: Lin
authors.affiliation: College of Agriculture, Hunan Agricultural University, Changsha, Hunan, China.
authors.forename: Juan
authors.initials: J
authors.lastname: Li
authors.affiliation: Zhoushan Municipal Center for Disease Control and Prevention, Zhoushan, Zhejiang, China.
authors.forename: Hongling
authors.initials: H
authors.lastname: Wang
authors.affiliation: Zhoushan Municipal Center for Disease Control and Prevention, Zhoushan, Zhejiang, China.
authors.forename: Jianbo
authors.initials: J
authors.lastname: Yan
authors.affiliation: College of Agriculture, Hunan Agricultural University, Changsha, Hunan, China.
authors.forename: Qingming
authors.initials: Q
authors.lastname: Zhou
authors.affiliation: Chinese Academy of Sciences, Chengdu Institute of Biology, Chengdu, Sichuan, China.
authors.forename: Xiangzhen
authors.initials: X
authors.lastname: Li
authors.affiliation: The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China.
authors.forename: Lanjuan
authors.initials: L
authors.lastname: Li
authors.affiliation: Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA. jzhou@ou.edu.
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
authors.affiliation: Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA. zhili.he@ou.edu.
authors.forename: Zhili
authors.initials: Z
authors.lastname: He
mesh_terms: D006801:Humans; D008103:Liver Cirrhosis; D056186:Metagenomics / Q000379:methods*; D046228:Microarray Analysis / Q000379:methods*; D008828:Microbiological Techniques / Q000379:methods*; D064307:Microbiota; D009693:Nucleic Acid Hybridization / Q000379:methods*; D012680:Sensitivity and Specificity
keywords: Functional profiling; HuMiChip2; Human microbiome; Microbial ecological microarray; Strain-level identification