HOMPPD:A Comprehensive Protein Sequence Database for Human Oral Metaproteomic Studies
Song Tingting1,2, Shao Chen2, Du Peng1,2, Zhang Benyu2, Zhu Weimin2* , Jiang Jizhi1*
1(School of life science, Hebei University, Baoding 071000, Hebei, China); 2(National Center for Protein Sciences - Beijing, Beijing Proteome Research Center, Institute of Lifeomics, Beijing 102206)
Abstract：Compared with metagenomics, metaproteomics has the advantage of characterizing not only the composition of environmental microbiome, but also their functional dynamics. Metaproteomic exploration of oral microbiome is an emerging approach for the studies of oral diseases. A comprehensive protein database with sufficient coverage of oral microbiome is an essential tool for the success of these studies. The Human Oral Microbiome Database (HOMD) that collects protein sequences from 117 genera and 367 species is a database used most frequently for oral metaproteomic analysis. It has been recently reported. However, a large collection of microorganisms are not yet included in HOMD, which will certainly limit the correct identification. In this study, protein sequences from 95 more genera reported by published oral metagenomic studies were collected and filtered. Redundant sequences from the same taxon were removed. The resulting sequences were then integrated with HOMD to construct the Human Oral MetaProteome Plus Database (HOMPPD). Due to the high individualization of oral microbiota, we proposed an improved two-step search method, that is, a two-step search for each sample. In order to evaluate the efficient identification of these newly included oral microorganisms, we then used our database to reanalyze public oral mass spectrometry raw data. Our results demonstrated that the constructed HOMPPD collected proteins sequence of 184 genera and 2793 species, 39 new oral genera and 124 new oral species were confidentially identified when searching HOMPPD, and that HOMPPD is a better tool for oral metaproteomics researches for its significantly more comprehensive oral microbiome coverage. HOMPPD is publicly available at ftp://111.198.139.72:4000//pub//metaproteomics//homppd.fasta.
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