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A Preliminary Metagenome Analysis Based on a Combination of Protein Domains

Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
Japan Software Management Co, Ltd., Yokohama, Kanagawa 221-0056, Japan
Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Shiogama, Miyagi 985-0001, Japan
Hokkaido National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Kushiro, Hokkaido 085-0802, Japan
Research Center for Aquaculture Systems, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Minami-ise, Mie 516-0193, Japan
National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa 236-8648, Japan
Graduate School of Bioresorce and Bioenvironmental Sciences, Kyushu University, Fukuoka, Fukuoka 812-0053, Japan
School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
Authors to whom correspondence should be addressed.
The authors contributed to this work equally.
Proteomes 2019, 7(2), 19;
Received: 20 February 2019 / Revised: 17 April 2019 / Accepted: 26 April 2019 / Published: 29 April 2019
(This article belongs to the Special Issue Microbial Proteomics II)
PDF [3145 KB, uploaded 29 April 2019]


Metagenomic data have mainly been addressed by showing the composition of organisms based on a small part of a well-examined genomic sequence, such as ribosomal RNA genes and mitochondrial DNAs. On the contrary, whole metagenomic data obtained by the shotgun sequence method have not often been fully analyzed through a homology search because the genomic data in databases for living organisms on earth are insufficient. In order to complement the results obtained through homology-search-based methods with shotgun metagenomes data, we focused on the composition of protein domains deduced from the sequences of genomes and metagenomes, and we utilized them in characterizing genomes and metagenomes, respectively. First, we compared the relationships based on similarities in the protein domain composition with the relationships based on sequence similarities. We searched for protein domains of 325 bacterial species produced using the Pfam database. Next, the correlation coefficients of protein domain compositions between every pair of bacteria were examined. Every pairwise genetic distance was also calculated from 16S rRNA or DNA gyrase subunit B. We compared the results of these methods and found a moderate correlation between them. Essentially, the same results were obtained when we used partial random 100 bp DNA sequences of the bacterial genomes, which simulated raw sequence data obtained from short-read next-generation sequences. Then, we applied the method for analyzing the actual environmental data obtained by shotgun sequencing. We found that the transition of the microbial phase occurred because the seasonal change in water temperature was shown by the method. These results showed the usability of the method in characterizing metagenomic data based on protein domain compositions. View Full-Text
Keywords: protein domain; correlation coefficient; phylogenetic analysis; metagenomics; environmental DNA protein domain; correlation coefficient; phylogenetic analysis; metagenomics; environmental DNA

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Igarashi, Y.; Mori, D.; Mitsuyama, S.; Yoshitake, K.; Ono, H.; Watanabe, T.; Taniuchi, Y.; Sakami, T.; Kuwata, A.; Kobayashi, T.; Ishino, Y.; Watabe, S.; Gojobori, T.; Asakawa, S. A Preliminary Metagenome Analysis Based on a Combination of Protein Domains. Proteomes 2019, 7, 19.

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