HOMPPD:一个全面的人类口腔宏蛋白质组序列数据库
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摘要
与宏基因组学相比,宏蛋白质组学可以系统地描绘微生物功能的动态变化,因此用其研究口腔微生物的组成和功能已成为一个新兴的领域。一个适当、完整的蛋白质组序列数据库在宏蛋白质组的数据分析中至关重要。在口腔宏蛋白质组研究中,常用的数据库为人类口腔微生物数据库(Human Oral Microbiome Database,HOMD),其中收录来自117个菌属和367个菌种的蛋白质组序列。但在近年来的口腔宏基因组研究中,已报道大量HOMD未收录的菌属。通过对宏基因组研究报道的95个菌属的蛋白质序列进行筛选和去冗余,然后与HOMD进行整合,构建一个更完整的人类口腔微生物蛋白质组数据库HOMPPD(Human Oral MetaProteome Plus Database);同时基于口腔微生物的高度个体化,提出对每个样本进行一次两步搜索的改进的两步检索法,最后利用已发表的唾液蛋白质组数据对其进行测试。通过整合,HOMPPD最终收录184个菌属和2 793个菌种的蛋白质组序列;测试结果表明,采用HOMPPD和改进的两步检索法可以鉴定到39个HOMD中未收录的新菌属和124个新菌种。新鉴定到的菌属主要分布在Proteobacteria、Firmicutes、Bacteroidetes三个门中。HOMPPD是目前为止收录蛋白质序列最全的口腔细菌蛋白质组数据库,使用其检索可以更加全面地鉴定唾液微生物的类群构成,其下载链接为ftp://111.198.139.72:4000//pub//metaproteomics//homppd.fasta。
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.
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.
引文
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[16] Nasidze I,Li Jing,Quinque D,et al.Global diversity in the human salivary microbiome[J].Genome Research,2009,19(4):636-643.
[17] Nasidze I,Li Jing,Schroeder R,et al.High Diversity of the Saliva Microbiome in Batwa Pygmies[J].PloS One,2011,6(8):e23352.
[18] Li Jing,Quinque D,Horz H P,et al.Comparative analysis of the human saliva microbiome from different climate zones:Alaska,Germany,and Africa[J].BMC Microbiology,2014,14(1):316.
[19] Zhang Xu,Ning Zhibin,Mayne J,et al.MetaPro-IQ:a universal metaproteomic approach to studying human and mouse gut microbiota [J].Microbiome,2016,4(1):31.
[20] Verma D,Garg PK,Dubey AK.Insights into the human oral microbiome[J].Archives of Microbiology,2018:1-16.
[21] Kilian M,Chapple I,Hannig M,et al.The oral microbiome——An update for oral healthcare professionals[J].British Dental Journal,2016,221(10):657.
[22] Cornejo OE,Lefébure T,Pavinski Bitar PD,et al.Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans[J].Molecular Biology and Evolution,2012,30(4):881-893.
[2] Hettich RL,Sharma R,Chourey K,et al.Microbial metaproteomics:identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities[J].Current Opinion in Microbiology,2012,15(3):373-380.
[3] 徐欣,何金枝,周学东.口腔微生物群落在口腔与全身疾病预警中的作用[J].华西口腔医学杂志,2015,33(6):555-560.
[4] 周学东,徐健,施文元.人类口腔微生物组学研究:现状、挑战及机遇[J].微生物学报,2017,57(6):806-821.
[5] Yang Fang,Zeng Xiaowei,Ning Kang,et al.Saliva microbiomes distinguish caries-active from healthy human populations[J].The ISME Journal,2012,6(1):1.
[6] Wang Jinfeng,Qi Ji,Zhao Hui,et al.Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease[J].Scientific Reports,2013,3(5):1843.
[7] Daniel B,Palle H,Allan B,et al.Comparative analysis of bacterial profiles in unstimulated and stimulated saliva samples[J].Journal of Oral Microbiology,2016,8(1):30112.
[8] Belda‐Ferre P,Williamson J,Simón‐Soro á,et al.The human oral metaproteome reveals potential biomarkers for caries disease[J].Proteomics,2015,15(20):3497-3507.
[9] Belstr■m D,Jersiechristensen R R,Lyon D,et al.Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls[J].PeerJ,2016,4(9):e2433.
[10] Cargile B J,Bundy J L,Stephenson J L.Potential for false positive identifications from large databases through tandem mass spectrometry[J].Journal of Proteome Research,2004,3(5):1082-1085.
[11] Cantarel B L,Erickson A R,VerBerkmoes N C,et al.Strategies for metagenomic-guided whole-community proteomics of complex microbial environments[J].PloS One,2011,6(11):e27173.
[12] Dewhirst F E,Chen Tuste,Izard J,et al.The human oral microbiome[J].Journal of Bacteriology,2010,192(19):5002-5017.
[13] Grassl N,Kulak N A,Pichler G,et al.Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome[J].Genome Medicine,2016,8(1):44.
[14] Jagtap P,Mcgowan T,Bandhakavi S,et al.Deep metaproteomic analysis of human salivary supernatant[J].Proteomics,2012,12(7):992-1001.
[15] Jagtap P,Goslinga J,Kooren J A,et al.A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies[J].Proteomics,2013,13(8):1352-1357.
[16] Nasidze I,Li Jing,Quinque D,et al.Global diversity in the human salivary microbiome[J].Genome Research,2009,19(4):636-643.
[17] Nasidze I,Li Jing,Schroeder R,et al.High Diversity of the Saliva Microbiome in Batwa Pygmies[J].PloS One,2011,6(8):e23352.
[18] Li Jing,Quinque D,Horz H P,et al.Comparative analysis of the human saliva microbiome from different climate zones:Alaska,Germany,and Africa[J].BMC Microbiology,2014,14(1):316.
[19] Zhang Xu,Ning Zhibin,Mayne J,et al.MetaPro-IQ:a universal metaproteomic approach to studying human and mouse gut microbiota [J].Microbiome,2016,4(1):31.
[20] Verma D,Garg PK,Dubey AK.Insights into the human oral microbiome[J].Archives of Microbiology,2018:1-16.
[21] Kilian M,Chapple I,Hannig M,et al.The oral microbiome——An update for oral healthcare professionals[J].British Dental Journal,2016,221(10):657.
[22] Cornejo OE,Lefébure T,Pavinski Bitar PD,et al.Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans[J].Molecular Biology and Evolution,2012,30(4):881-893.