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Title: HuMiChip: Development of a Functional Gene Array for the Study of Human Microbiomes

Abstract

Microbiomes play very important roles in terms of nutrition, health and disease by interacting with their hosts. Based on sequence data currently available in public domains, we have developed a functional gene array to monitor both organismal and functional gene profiles of normal microbiota in human and mouse hosts, and such an array is called human and mouse microbiota array, HMM-Chip. First, seed sequences were identified from KEGG databases, and used to construct a seed database (seedDB) containing 136 gene families in 19 metabolic pathways closely related to human and mouse microbiomes. Second, a mother database (motherDB) was constructed with 81 genomes of bacterial strains with 54 from gut and 27 from oral environments, and 16 metagenomes, and used for selection of genes and probe design. Gene prediction was performed by Glimmer3 for bacterial genomes, and by the Metagene program for metagenomes. In total, 228,240 and 801,599 genes were identified for bacterial genomes and metagenomes, respectively. Then the motherDB was searched against the seedDB using the HMMer program, and gene sequences in the motherDB that were highly homologous with seed sequences in the seedDB were used for probe design by the CommOligo software. Different degrees of specific probes, including gene-specific,more » inclusive and exclusive group-specific probes were selected. All candidate probes were checked against the motherDB and NCBI databases for specificity. Finally, 7,763 probes covering 91.2percent (12,601 out of 13,814) HMMer confirmed sequences from 75 bacterial genomes and 16 metagenomes were selected. This developed HMM-Chip is able to detect the diversity and abundance of functional genes, the gene expression of microbial communities, and potentially, the interactions of microorganisms and their hosts.« less

Authors:
; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
Physical Biosciences Division
OSTI Identifier:
1008326
Report Number(s):
LBNL-4326E-Poster
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Technical Report
Resource Relation:
Conference: 110th General Meeting of the American Society for Microbiology, San Diego, CA, May 23-27, 2010
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; 58 GEOSCIENCES; microbiomes, HMM-Chip, gene expression of microbial communities

Citation Formats

Tu, Q., Deng, Ye, Lin, Lu, Hemme, Chris L., He, Zhili, and Zhou, Jizhong. HuMiChip: Development of a Functional Gene Array for the Study of Human Microbiomes. United States: N. p., 2010. Web. doi:10.2172/1008326.
Tu, Q., Deng, Ye, Lin, Lu, Hemme, Chris L., He, Zhili, & Zhou, Jizhong. HuMiChip: Development of a Functional Gene Array for the Study of Human Microbiomes. United States. doi:10.2172/1008326.
Tu, Q., Deng, Ye, Lin, Lu, Hemme, Chris L., He, Zhili, and Zhou, Jizhong. Mon . "HuMiChip: Development of a Functional Gene Array for the Study of Human Microbiomes". United States. doi:10.2172/1008326. https://www.osti.gov/servlets/purl/1008326.
@article{osti_1008326,
title = {HuMiChip: Development of a Functional Gene Array for the Study of Human Microbiomes},
author = {Tu, Q. and Deng, Ye and Lin, Lu and Hemme, Chris L. and He, Zhili and Zhou, Jizhong},
abstractNote = {Microbiomes play very important roles in terms of nutrition, health and disease by interacting with their hosts. Based on sequence data currently available in public domains, we have developed a functional gene array to monitor both organismal and functional gene profiles of normal microbiota in human and mouse hosts, and such an array is called human and mouse microbiota array, HMM-Chip. First, seed sequences were identified from KEGG databases, and used to construct a seed database (seedDB) containing 136 gene families in 19 metabolic pathways closely related to human and mouse microbiomes. Second, a mother database (motherDB) was constructed with 81 genomes of bacterial strains with 54 from gut and 27 from oral environments, and 16 metagenomes, and used for selection of genes and probe design. Gene prediction was performed by Glimmer3 for bacterial genomes, and by the Metagene program for metagenomes. In total, 228,240 and 801,599 genes were identified for bacterial genomes and metagenomes, respectively. Then the motherDB was searched against the seedDB using the HMMer program, and gene sequences in the motherDB that were highly homologous with seed sequences in the seedDB were used for probe design by the CommOligo software. Different degrees of specific probes, including gene-specific, inclusive and exclusive group-specific probes were selected. All candidate probes were checked against the motherDB and NCBI databases for specificity. Finally, 7,763 probes covering 91.2percent (12,601 out of 13,814) HMMer confirmed sequences from 75 bacterial genomes and 16 metagenomes were selected. This developed HMM-Chip is able to detect the diversity and abundance of functional genes, the gene expression of microbial communities, and potentially, the interactions of microorganisms and their hosts.},
doi = {10.2172/1008326},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2010},
month = {5}
}