HuMiChip2 for strain level identification and functional profiling of human microbiomes

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• 作者：Qichao Tu ; Jiabao Li ; Zhou Shi ; Yanfei Chen…
• 关键词：HuMiChip2 ; Microbial ecological microarray ; Strain ; level identification ; Functional profiling ; Human microbiome
• 刊名：Applied Microbiology and Biotechnology
• 出版年：2017
• 出版时间：January 2017
• 年：2017
• 卷：101
• 期：1
• 页码：423-435
• 全文大小：
• 刊物类别：Chemistry and Materials Science
• 刊物主题：Microbiology; Microbial Genetics and Genomics; Biotechnology;
• 出版者：Springer Berlin Heidelberg
• ISSN：1432-0614
• 卷排序：101

文摘

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.