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Article(id=1226956558140097520, tenantId=1146029695717560320, journalId=1192105938417971205, issueId=1226956547847275311, articleNumber=null, orderNo=null, doi=10.13343/j.cnki.wsxb.20250166, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=research-article, receivedDate=1740844800000, receivedDateStr=2025-03-02, revisedDate=null, revisedDateStr=null, acceptedDate=1744732800000, acceptedDateStr=2025-04-16, onlineDate=1770458839210, onlineDateStr=2026-02-07, pubDate=1756915200000, pubDateStr=2025-09-04, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1770458839210, onlineIssueDateStr=2026-02-07, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1770458839210, creator=13701087609, updateTime=1770458839210, updator=13701087609, issue=Issue{id=1226956547847275311, tenantId=1146029695717560320, journalId=1192105938417971205, year='2025', volume='65', issue='9', pageStart='3821', pageEnd='4232', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1770458836757, creator=13701087609, updateTime=1770459153781, updator=13701087609, preIssue=null, nextIssue=null, ext={EN=IssueExt(id=1226957877613605816, tenantId=1146029695717560320, journalId=1192105938417971205, issueId=1226956547847275311, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1226957877613605817, tenantId=1146029695717560320, journalId=1192105938417971205, issueId=1226956547847275311, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null}, startPage=4211, endPage=4223, ext={EN=ArticleExt(id=1226956558551138325, articleId=1226956558140097520, tenantId=1146029695717560320, journalId=1192105938417971205, language=EN, title=Establishment and testing of a MALDI-TOF MS database for the identificationof Streptomyces, columnId=1226236834313847103, journalTitle=Acta Microbiologica Sinica, columnName=Data Paper, runingTitle=null, highlight=null, articleAbstract=

Streptomyces is a genus of diverse actinomycetes known for producing antibiotics, showcasing high value for research and development. However, the limited number of Streptomyces species included in commercial databases restricts the application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in the identification of Streptomyces. [Objective] To establish a MALDI-TOF MS database for the identification of Streptomyces based on the mining of whole genome sequencing data and test its accuracy. [Methods] By searching against a genome database, we selected all the genome-sequenced type strains of Streptomyces. Subsequently, the sequences of 12 ribosomal proteins were extracted from their genome sequences and theoretical MALDI mass/charge (m/z) values were calculated. Accordingly, a database was established based on the combination of 12 theoretically calculated m/z values, which can be used as the identification criteria for Streptomyces species. Finally, type strains were randomly collected for MALDI-TOF MS testing. To test the accuracy of the database construction method and comparison results, we matched the experimental m/z values with the theoretically calculated m/z values of the species in the database. [Results] We established a MALDI-TOF MS database including 615 Streptomyces species. The mass spectra of the tested strains were accurately matched with those of corresponding species in the database. In addition, we proposed a method for the identification of Streptomyces by database comparison. [Conclusion] The database established in this study laid a foundation for identifying Streptomyces based on MALDI-TOF MS.

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链霉菌种类繁多，以盛产抗生素而闻名，是极具研发价值的放线菌类群。然而，商业数据库中收录的链霉菌属菌种数量较少，这限制了基质辅助激光解吸电离飞行时间质谱(matrix-assisted laser desorption/ionization-time of flight mass spectrometry, MALDI-TOF MS)技术在链霉菌鉴定中的应用。 【目的】 基于全基因组测序数据挖掘，建立链霉菌属菌种的MALDI-TOF MS数据库，并测试其准确性。 【方法】 检索基因组数据库，提取已测序的链霉菌属菌种模式菌株的12种核糖体蛋白序列，并计算其理论MALDI质谱峰值，以这12个峰值的组合作为菌种鉴定依据建立数据库。收集模式菌株进行MALDI-TOF MS测试，将实测峰值与数据库中菌种的理论峰值进行比对，以测试建库方法及数据库比对结果的准确性。 【结果】 建立了包含链霉菌属615个菌种的MALDI-TOF MS数据库。测试菌株的质谱均实现了与数据库中目标菌种的准确匹配。本研究还提出了基于数据库比对的菌种鉴定方法。 【结论】 本研究建立的数据库为基于MALDI-TOF MS技术鉴定链霉菌奠定了基础。

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作者贡献声明

孙伟：项目提出，数据收集与分析，设计并完成实验，文章写作与修订；罗倩：数据分析，文章审阅；许杰：项目咨询，文章审阅；李雷：提供链霉菌属模式菌株，文章审阅；蒋海霞：文章审阅。

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refType=null, unstructuredReference=尹盼盼, 白雯静, 李海燕, 彭腾腾, 石晓峰. 基质辅助激光解吸电离飞行时间质谱在微生物鉴定中的研究进展[J]. 微生物学通报, 2023, 50(10): 4655-4666., articleTitle=基质辅助激光解吸电离飞行时间质谱在微生物鉴定中的研究进展, refAbstract=null), Reference(id=1226964057320768422, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, doi=null, pmid=null, pmcid=null, year=2023, volume=50, issue=10, pageStart=4655, pageEnd=4666, url=null, language=null, rfNumber=[1], rfOrder=1, authorNames=YIN PP, BAI WJ, LI HY, PENG TT, SHI XF, journalName=Microbiology China, refType=null, unstructuredReference=YIN PP, BAI WJ, LI HY, PENG TT, SHI XF. 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Nature Communications, 2019, 10: 2182., articleTitle=TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy, refAbstract=null), Reference(id=1226964062177771628, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, doi=null, pmid=null, pmcid=null, year=2022, volume=204, issue=9, pageStart=581, pageEnd=null, url=null, language=null, rfNumber=[19], rfOrder=27, authorNames=LI CJ, WANG M, ZHANG Z, ZHI XY, YANG LL, journalName=Archives of Microbiology, refType=null, unstructuredReference=LI CJ, WANG M, ZHANG Z, ZHI XY, YANG LL. Genome-based analyses reveal heterotypic synonyms of Streptomyces species and associated subspecies[J]. Archives of Microbiology, 2022, 204(9): 581., articleTitle=Genome-based analyses reveal heterotypic synonyms of Streptomyces species and associated subspecies, refAbstract=null), Reference(id=1226964062311989366, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, doi=null, pmid=null, pmcid=null, year=2020, volume=70, issue=6, pageStart=3924, pageEnd=3929, url=null, language=null, rfNumber=[20], rfOrder=28, authorNames=MADHAIYAN M, SARAVANAN VS, SEE-TOO WS, journalName=International Journal of Systematic and Evolutionary Microbiology, refType=null, unstructuredReference=MADHAIYAN M, SARAVANAN VS, SEE-TOO WS. Genome-based analyses reveal the presence of 12 heterotypic synonyms in the genus Streptomyces and emended descriptions of Streptomyces bottropensis, Streptomyces celluloflavus, Streptomyces fulvissimus, Streptomyces glaucescens, Streptomyces murinus, and Streptomyces variegatus [J]. International Journal of Systematic and Evolutionary Microbiology, 2020, 70(6): 3924-3929., articleTitle=Genome-based analyses reveal the presence of 12 heterotypic synonyms in the genus Streptomyces and emended descriptions of Streptomyces bottropensis, Streptomyces celluloflavus, Streptomyces fulvissimus, Streptomyces glaucescens, Streptomyces murinus, and Streptomyces variegatus, refAbstract=null)], funds=[Fund(id=1226964056926503823, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, awardId=JCZXSJA2023-04, language=EN, fundingSource=Decision-making Consultation Project of Shanghai Jiao Tong University(JCZXSJA2023-04), fundOrder=null, country=null), Fund(id=1226964057006195604, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, awardId=JCZXSJA2023-04, language=CN, fundingSource=上海交通大学决策咨询课题(JCZXSJA2023-04), fundOrder=null, country=null)], companyList=[AuthorCompany(id=1226964048848273838, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, xref=null, ext=[AuthorCompanyExt(id=1226964048856662448, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, companyId=1226964048848273838, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China), AuthorCompanyExt(id=1226964048860856754, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, companyId=1226964048848273838, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=上海交通大学 生命科学技术学院，上海)])], figs=[ArticleFig(id=1226964053743026947, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, language=EN, label=Figure 1, caption=MALDI-TOF MS spectra of Streptomyces test strains. A: S. venezuelae ATCC 10712T; B: S. griseus J1014T; C: S. avermitilis NRRL 8165T; D: S. albidoflavus J1074T; E: S. coelicolor M145T. Peaks that match ribosomal proteins are marked., figureFileSmall=VQcFYfxUs/dMfWmzpr+a3g==, figureFileBig=yrT/Ja1CM6n6P+5FsFnYsA==, tableContent=null), ArticleFig(id=1226964055177478926, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, language=CN, label=图1, caption=链霉菌属测试菌株的MALDI-TOF MS图谱, figureFileSmall=VQcFYfxUs/dMfWmzpr+a3g==, figureFileBig=yrT/Ja1CM6n6P+5FsFnYsA==, tableContent=null), ArticleFig(id=1226964055269753627, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, language=EN, label=Table 1, caption=

Twenty-three Streptomyces groups in which dDDH values of the members are above 70%

, figureFileSmall=null, figureFileBig=null, tableContent=
GroupOrganism AOrganism BdDDH value (%)
1S. pluricolorescens JCM 4602TS. rubiginosohelvolus JCM 4415T99.3
2S. asiaticus DSM 41761TS. cangkringensis DSM 41769T98.4
S. asiaticus DSM 41761TS. indonesiensis DSM 41759T98.9
S. asiaticus DSM 41761TS. rhizosphaericus DSM 41760T96.6
S. cangkringensis DSM 41769TS. indonesiensis DSM 41759T98.4
S. cangkringensis DSM 41769TS. rhizosphaericus DSM 41760T96.3
S. indonesiensis DSM 41759TS. rhizosphaericus DSM 41760T96.2
3S. peucetius NRRL WC-3868TS. rimosus ATCC 10970T80.0
4S. niger NRRL B-3857TS. olivaceiscleroticus JCM 4805T81.3
5S. libani JCM 4322TS. nigrescens DSM 40276T92.0
6S. antimycoticus NBRC 12839TS. mordarskii JCM 5052T75.6
7S. cuspidosporus JCM 4316TS. sparsogenes DSM 40356T77.8
8S. malaysiensis JCM 10672TS. solisilvae HNM0141T99.8
9S. collinus DSM 40129TS. violaceochromogenes JCM 4530T94.8
10S. daghestanicus JCM 4365TS. griseoviridis DSM 40229T96.0
S. daghestanicus JCM 4365TS. niveoruber JCM 4234T94.6
S. griseoviridis DSM 40229TS. niveoruber JCM 4234T94.6
11S. roseiscleroticus JCM 4823TS. ruber JCM 3131T100.0
12S. gancidicus JCM 4171TS. pseudogriseolus NRRL B-3288T94.2
S. gancidicus JCM 4171TS. rubiginosus JCM 4416T95.6
S. pseudogriseolus NRRL B-3288TS. rubiginosus JCM 4416T94.4
13S. griseoincarnatus JCM 4381TS. labedae JCM 9381T95.2
S. griseoincarnatus JCM 4381TS. tunisiensis JCM 17589T83.6
S. labedae JCM 9381TS. tunisiensis JCM 17589T83.6
14S. griseoluteus JCM 4765TS. recifensis NRRL B-3811T72.4
15S. finlayi JCM 4637TS. spiroverticillatus JCM 4609T99.9
16S. carpaticus JCM 6915TS. cheonanensis JCM 14549T87.3
S. carpaticus JCM 6915TS. harbinensis CGMCC 4.7047T87.7
S. cheonanensis JCM 14549TS. harbinensis CGMCC 4.7047T92.1
17S. bellus JCM 4292TS. coeruleorubidus JCM 4359T81.8
18S. thermogriseus JCM 11269TS. thermovulgaris NRRL B-12375T95.0
19S. canarius JCM 4733TS. olivaceoviridis JCM 4499T76.0
20S. graminearus JCM 6923TS. murinus NRRL B-2286T86.2
21S. griseoaurantiacus JCM 4763TS. jietaisiensis CGMCC 4.1859T90.4
22S. albaduncus CECT 3226TS. griseoloalbus JCM 4480T92.1
23S. calvus CECT 3271TS. virens JCM 9095T92.8
), ArticleFig(id=1226964055471080238, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, language=CN, label=表1, caption=

dDDH值大于70%的23组链霉菌属菌种

, figureFileSmall=null, figureFileBig=null, tableContent=
GroupOrganism AOrganism BdDDH value (%)
1S. pluricolorescens JCM 4602TS. rubiginosohelvolus JCM 4415T99.3
2S. asiaticus DSM 41761TS. cangkringensis DSM 41769T98.4
S. asiaticus DSM 41761TS. indonesiensis DSM 41759T98.9
S. asiaticus DSM 41761TS. rhizosphaericus DSM 41760T96.6
S. cangkringensis DSM 41769TS. indonesiensis DSM 41759T98.4
S. cangkringensis DSM 41769TS. rhizosphaericus DSM 41760T96.3
S. indonesiensis DSM 41759TS. rhizosphaericus DSM 41760T96.2
3S. peucetius NRRL WC-3868TS. rimosus ATCC 10970T80.0
4S. niger NRRL B-3857TS. olivaceiscleroticus JCM 4805T81.3
5S. libani JCM 4322TS. nigrescens DSM 40276T92.0
6S. antimycoticus NBRC 12839TS. mordarskii JCM 5052T75.6
7S. cuspidosporus JCM 4316TS. sparsogenes DSM 40356T77.8
8S. malaysiensis JCM 10672TS. solisilvae HNM0141T99.8
9S. collinus DSM 40129TS. violaceochromogenes JCM 4530T94.8
10S. daghestanicus JCM 4365TS. griseoviridis DSM 40229T96.0
S. daghestanicus JCM 4365TS. niveoruber JCM 4234T94.6
S. griseoviridis DSM 40229TS. niveoruber JCM 4234T94.6
11S. roseiscleroticus JCM 4823TS. ruber JCM 3131T100.0
12S. gancidicus JCM 4171TS. pseudogriseolus NRRL B-3288T94.2
S. gancidicus JCM 4171TS. rubiginosus JCM 4416T95.6
S. pseudogriseolus NRRL B-3288TS. rubiginosus JCM 4416T94.4
13S. griseoincarnatus JCM 4381TS. labedae JCM 9381T95.2
S. griseoincarnatus JCM 4381TS. tunisiensis JCM 17589T83.6
S. labedae JCM 9381TS. tunisiensis JCM 17589T83.6
14S. griseoluteus JCM 4765TS. recifensis NRRL B-3811T72.4
15S. finlayi JCM 4637TS. spiroverticillatus JCM 4609T99.9
16S. carpaticus JCM 6915TS. cheonanensis JCM 14549T87.3
S. carpaticus JCM 6915TS. harbinensis CGMCC 4.7047T87.7
S. cheonanensis JCM 14549TS. harbinensis CGMCC 4.7047T92.1
17S. bellus JCM 4292TS. coeruleorubidus JCM 4359T81.8
18S. thermogriseus JCM 11269TS. thermovulgaris NRRL B-12375T95.0
19S. canarius JCM 4733TS. olivaceoviridis JCM 4499T76.0
20S. graminearus JCM 6923TS. murinus NRRL B-2286T86.2
21S. griseoaurantiacus JCM 4763TS. jietaisiensis CGMCC 4.1859T90.4
22S. albaduncus CECT 3226TS. griseoloalbus JCM 4480T92.1
23S. calvus CECT 3271TS. virens JCM 9095T92.8
), ArticleFig(id=1226964055584326455, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, language=EN, label=Table 2, caption=

Eighteen Streptomyces groups in which dDDH values of the members are below 70%

, figureFileSmall=null, figureFileBig=null, tableContent=
GroupOrganism AOrganism BdDDH value (%)
1S. bikiniensis NRRL ISP-5581TS. cinereoruber ATCC 19740T60.7
2S. amritsarensis MTCC 11845TS. yangpuensis fd2-tbT46.6
3S. globisporus JCM 4378TS. pluricolorescens JCM 4602T65.8
4S. globisporus JCM 4378TS. rubiginosohelvolus JCM 4415T66.1
5S. bacillaris ATCC 15855TS. cavourensis JCM 4298T68.0
6S. globosus JCM 13859TS. toxytricini JCM 4421T57.1
7S. barkulensis RC 1831TS. pini PL19T67.3
8S. chrestomyceticus JCM 4735TS. monomycini NRRL B-24309T49.4
9S. chrestomyceticus JCM 4735TS. paromomycinus NBRC 15454T59.9
10S. monomycini NRRL B-24309TS. paromomycinus NBRC 15454T50.0
11S. catenulae NRRL B-2342TS. ramulosus JCM 4193T47.7
12S. antimycoticus NBRC 12839TS. yatensis JCM 13244T63.9
13S. mordarskii JCM 5052TS. yatensis JCM 13244T61.3
14S. cyaneochromogenes MK-45TS. shaanxiensis JCM 16925T63.3
15S. neyagawaensis JCM 4796TS. ossamyceticus NRRL B-3822T57.9
16S. neyagawaensis JCM 4796TS. torulosus NRRL B-3889T62.1
17S. harenosi PRKS01-65TS. leeuwenhoekii C34T56.8
18S. bangladeshensis JCM 14924TS. nogalater JCM 4799T36.6
), ArticleFig(id=1226964055697572672, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, language=CN, label=表2, caption=

dDDH值小于70%的18组链霉菌属菌种

, figureFileSmall=null, figureFileBig=null, tableContent=
GroupOrganism AOrganism BdDDH value (%)
1S. bikiniensis NRRL ISP-5581TS. cinereoruber ATCC 19740T60.7
2S. amritsarensis MTCC 11845TS. yangpuensis fd2-tbT46.6
3S. globisporus JCM 4378TS. pluricolorescens JCM 4602T65.8
4S. globisporus JCM 4378TS. rubiginosohelvolus JCM 4415T66.1
5S. bacillaris ATCC 15855TS. cavourensis JCM 4298T68.0
6S. globosus JCM 13859TS. toxytricini JCM 4421T57.1
7S. barkulensis RC 1831TS. pini PL19T67.3
8S. chrestomyceticus JCM 4735TS. monomycini NRRL B-24309T49.4
9S. chrestomyceticus JCM 4735TS. paromomycinus NBRC 15454T59.9
10S. monomycini NRRL B-24309TS. paromomycinus NBRC 15454T50.0
11S. catenulae NRRL B-2342TS. ramulosus JCM 4193T47.7
12S. antimycoticus NBRC 12839TS. yatensis JCM 13244T63.9
13S. mordarskii JCM 5052TS. yatensis JCM 13244T61.3
14S. cyaneochromogenes MK-45TS. shaanxiensis JCM 16925T63.3
15S. neyagawaensis JCM 4796TS. ossamyceticus NRRL B-3822T57.9
16S. neyagawaensis JCM 4796TS. torulosus NRRL B-3889T62.1
17S. harenosi PRKS01-65TS. leeuwenhoekii C34T56.8
18S. bangladeshensis JCM 14924TS. nogalater JCM 4799T36.6
), ArticleFig(id=1226964055810818889, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, language=EN, label=Table 3, caption=

The list of the match details of the MALDI-TOF MS peaks from five Streptomyces test strains

, figureFileSmall=null, figureFileBig=null, tableContent=
Strainm/z
S. venezuelae ATCC 10712T*4 389.575 168.176 305.076 423.036 598.736 816.726 816.726 936.338 329.508 659.568 830.779 120.00
0256 S. venezuelae ATCC 10712T#4 390.405 167.966 306.246 423.506 599.626 815.836 819.146 936.238 330.448 659.728 831.349 120.63
Err (ppm)-189.0540.63-185.53-73.17-134.86130.58-354.8814.42-112.84-18.48-64.54-69.07
S. griseus J1014T*4 390.235 095.916 304.066 465.026 575.896 819.236 860.706 860.708 331.388 728.648 888.559 277.00
0076 S. griseus DSM 40236T#4 390.405 095.906 306.246 465.546 576.596 819.146 859.856 862.158 331.438 729.868 888.399 279.77
Err (ppm)-38.721.96-345.69-80.43-106.4413.20123.91-211.30-6.00-139.7518.00-298.50
S. avermitilis NRRL 8165T*4 402.075 052.586 289.476 457.676 486.576 759.366 818.016 948.688 271.508 745.638 857.389 365.03
0276 S. avermitilis MA-4680T#4 402.375 052.886 290.246 458.556 488.436 759.726 819.146 949.178 272.408 746.848 859.399 365.87
Err (ppm)-68.15-59.37-122.41-136.25-286.66-53.26-165.71-70.51-108.80-138.34-226.88-89.69
S. albidoflavus J1074T*4 415.935 121.466 288.626 471.896 617.636 817.846 853.716 963.268 269.678 699.478 855.989 343.08
0490 S. albidoflavus DSM 40455T#4 416.395 121.986 290.246 473.526 619.616 819.146 854.916 963.198 271.468 701.808 859.399 344.76
Err (ppm)-104.16-101.52-257.54-251.80-299.11-190.64-175.0610.05-216.41-267.76-384.90-179.78
S. coelicolor M145T*4 402.475 166.266 290.066 442.466 508.026 758.286 818.266 891.948 271.458 640.848 857.919 411.99
0361 S. violaceoruber CGMCC 4.1801T#4 402.375 166.046 290.246 442.556 508.426 757.756 819.146 892.078 271.428 643.728 858.419 411.89
Err (ppm)22.7242.59-28.62-13.97-61.4678.43-129.05-18.863.63-333.19-167.0510.62
), ArticleFig(id=1226964055907287890, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, language=CN, label=表3, caption=

五个链霉菌属测试菌株的MALDI质谱峰匹配表

, figureFileSmall=null, figureFileBig=null, tableContent=
Strainm/z
S. venezuelae ATCC 10712T*4 389.575 168.176 305.076 423.036 598.736 816.726 816.726 936.338 329.508 659.568 830.779 120.00
0256 S. venezuelae ATCC 10712T#4 390.405 167.966 306.246 423.506 599.626 815.836 819.146 936.238 330.448 659.728 831.349 120.63
Err (ppm)-189.0540.63-185.53-73.17-134.86130.58-354.8814.42-112.84-18.48-64.54-69.07
S. griseus J1014T*4 390.235 095.916 304.066 465.026 575.896 819.236 860.706 860.708 331.388 728.648 888.559 277.00
0076 S. griseus DSM 40236T#4 390.405 095.906 306.246 465.546 576.596 819.146 859.856 862.158 331.438 729.868 888.399 279.77
Err (ppm)-38.721.96-345.69-80.43-106.4413.20123.91-211.30-6.00-139.7518.00-298.50
S. avermitilis NRRL 8165T*4 402.075 052.586 289.476 457.676 486.576 759.366 818.016 948.688 271.508 745.638 857.389 365.03
0276 S. avermitilis MA-4680T#4 402.375 052.886 290.246 458.556 488.436 759.726 819.146 949.178 272.408 746.848 859.399 365.87
Err (ppm)-68.15-59.37-122.41-136.25-286.66-53.26-165.71-70.51-108.80-138.34-226.88-89.69
S. albidoflavus J1074T*4 415.935 121.466 288.626 471.896 617.636 817.846 853.716 963.268 269.678 699.478 855.989 343.08
0490 S. albidoflavus DSM 40455T#4 416.395 121.986 290.246 473.526 619.616 819.146 854.916 963.198 271.468 701.808 859.399 344.76
Err (ppm)-104.16-101.52-257.54-251.80-299.11-190.64-175.0610.05-216.41-267.76-384.90-179.78
S. coelicolor M145T*4 402.475 166.266 290.066 442.466 508.026 758.286 818.266 891.948 271.458 640.848 857.919 411.99
0361 S. violaceoruber CGMCC 4.1801T#4 402.375 166.046 290.246 442.556 508.426 757.756 819.146 892.078 271.428 643.728 858.419 411.89
Err (ppm)22.7242.59-28.62-13.97-61.4678.43-129.05-18.863.63-333.19-167.0510.62
), ArticleFig(id=1226964056054088540, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, language=EN, label=Table 4, caption=

Genome-based comparison of Streptomycescoelicolor A3(2)

, figureFileSmall=null, figureFileBig=null, tableContent=
QuerySubjectdDDH value (%)Taxonomic status
S. coelicolor A3(2)Streptomyces anthocyanicus JCM 505894.2Synonym
S. coelicolor A3(2)Streptomyces coelescens JCM 473993.9Synonym
S. coelicolor A3(2)Streptomyces violaceolatus JCM 453193.7Synonym
S. coelicolor A3(2)Streptomyces violaceoruber CGMCC 4.180193.3Correct name
S. coelicolor A3(2)Streptomyces humiferus JCM 303792.4Synonym
S. coelicolor A3(2)Streptomyces rubrogriseus NBRC 1545570.2Correct name
), ArticleFig(id=1226964056150557535, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, language=CN, label=表4, caption=

测试菌株 Streptomycescoelicolor A3(2)的基因组比对结果

, figureFileSmall=null, figureFileBig=null, tableContent=
QuerySubjectdDDH value (%)Taxonomic status
S. coelicolor A3(2)Streptomyces anthocyanicus JCM 505894.2Synonym
S. coelicolor A3(2)Streptomyces coelescens JCM 473993.9Synonym
S. coelicolor A3(2)Streptomyces violaceolatus JCM 453193.7Synonym
S. coelicolor A3(2)Streptomyces violaceoruber CGMCC 4.180193.3Correct name
S. coelicolor A3(2)Streptomyces humiferus JCM 303792.4Synonym
S. coelicolor A3(2)Streptomyces rubrogriseus NBRC 1545570.2Correct name
), ArticleFig(id=1226964056309941099, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, language=EN, label=Table 5, caption=

MALDI-TOF MS database-based comparison of six strains isolated from a soil sample

, figureFileSmall=null, figureFileBig=null, tableContent=
QueryTop-hit type strainMatching number (Err≤±500 ppm)Matching number (Err≤±600 ppm)
S1-6Streptomyces virginiae NRRL ISP-5094T1112
S1-8Streptomyces thermocarboxydus JCM 10368T1212
S1-10Streptomyces lydicamycinicus TP-A0598T1112
S1-13Streptomyces wuyuanensis CGMCC 4.7042T1212
S1-16Streptomyces alboflavus NRRL B-2373T1212
S1-39Streptomyces violaceoruber CGMCC 4.1801T1112
), ArticleFig(id=1226964056414798702, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, language=CN, label=表5, caption=

六个土壤来源菌株的MALDI-TOF MS数据库比对结果

, figureFileSmall=null, figureFileBig=null, tableContent=
QueryTop-hit type strainMatching number (Err≤±500 ppm)Matching number (Err≤±600 ppm)
S1-6Streptomyces virginiae NRRL ISP-5094T1112
S1-8Streptomyces thermocarboxydus JCM 10368T1212
S1-10Streptomyces lydicamycinicus TP-A0598T1112
S1-13Streptomyces wuyuanensis CGMCC 4.7042T1212
S1-16Streptomyces alboflavus NRRL B-2373T1212
S1-39Streptomyces violaceoruber CGMCC 4.1801T1112
), ArticleFig(id=1226964056553210743, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, language=EN, label=Table 6, caption=

16S rRNA gene sequence comparison of six strains isolated from a soil sample

, figureFileSmall=null, figureFileBig=null, tableContent=
QueryTop-hit type strainSimilarity (%)Accession No.Taxonomic status
S1-6Streptomyces virginiae NRRL ISP-5094T99.71PV450548Correct name
S1-8Streptomyces thermocarboxydus DSM 44293T99.35PV450549Correct name
S1-10Streptomyces lydicamycinicus NBRC 110027T100.00PV450550Correct name
S1-13Streptomyces marianii ICN19T99.85PV450551Not correct name
Streptomyces wuyuanensis CGMCC 4.7042T99.50Correct name
S1-16Streptomyces alboflavus NRRL B-2373T99.71PV450552Correct name
S1-39Streptomyces anthocyanicus NBRC 14892T100.00PV450553Synonym
Streptomyces violaceoruber NBRC 12826T100.00Correct name
Streptomyces tricolor NBRC 15461T100.00Synonym
), ArticleFig(id=1226964056679039870, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226956558140097520, language=CN, label=表6, caption=

六个土壤来源菌株的16S rRNA基因序列比对结果

, figureFileSmall=null, figureFileBig=null, tableContent=
QueryTop-hit type strainSimilarity (%)Accession No.Taxonomic status
S1-6Streptomyces virginiae NRRL ISP-5094T99.71PV450548Correct name
S1-8Streptomyces thermocarboxydus DSM 44293T99.35PV450549Correct name
S1-10Streptomyces lydicamycinicus NBRC 110027T100.00PV450550Correct name
S1-13Streptomyces marianii ICN19T99.85PV450551Not correct name
Streptomyces wuyuanensis CGMCC 4.7042T99.50Correct name
S1-16Streptomyces alboflavus NRRL B-2373T99.71PV450552Correct name
S1-39Streptomyces anthocyanicus NBRC 14892T100.00PV450553Synonym
Streptomyces violaceoruber NBRC 12826T100.00Correct name
Streptomyces tricolor NBRC 15461T100.00Synonym
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链霉菌基质辅助激光解吸电离飞行时间质谱数据库的建立及测试分析
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孙伟 , 罗倩 , 许杰 , 李雷 , 蒋海霞
微生物学报 | 数据论文 2025,65(9): 4211-4223
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微生物学报 | 数据论文 2025, 65(9): 4211-4223
链霉菌基质辅助激光解吸电离飞行时间质谱数据库的建立及测试分析
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孙伟 , 罗倩, 许杰, 李雷, 蒋海霞
作者信息
  • 上海交通大学 生命科学技术学院，上海
Establishment and testing of a MALDI-TOF MS database for the identificationof Streptomyces
Wei SUN , Qian LUO, Jie XU, Lei LI, Haixia JIANG
Affiliations
  • School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
出版时间: 2025-09-04 doi: 10.13343/j.cnki.wsxb.20250166
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摘要
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链霉菌种类繁多，以盛产抗生素而闻名，是极具研发价值的放线菌类群。然而，商业数据库中收录的链霉菌属菌种数量较少，这限制了基质辅助激光解吸电离飞行时间质谱(matrix-assisted laser desorption/ionization-time of flight mass spectrometry, MALDI-TOF MS)技术在链霉菌鉴定中的应用。 【目的】 基于全基因组测序数据挖掘，建立链霉菌属菌种的MALDI-TOF MS数据库，并测试其准确性。 【方法】 检索基因组数据库，提取已测序的链霉菌属菌种模式菌株的12种核糖体蛋白序列，并计算其理论MALDI质谱峰值，以这12个峰值的组合作为菌种鉴定依据建立数据库。收集模式菌株进行MALDI-TOF MS测试，将实测峰值与数据库中菌种的理论峰值进行比对，以测试建库方法及数据库比对结果的准确性。 【结果】 建立了包含链霉菌属615个菌种的MALDI-TOF MS数据库。测试菌株的质谱均实现了与数据库中目标菌种的准确匹配。本研究还提出了基于数据库比对的菌种鉴定方法。 【结论】 本研究建立的数据库为基于MALDI-TOF MS技术鉴定链霉菌奠定了基础。

链霉菌  /  基质辅助激光解吸电离飞行时间质谱  /  数据库  /  模式菌株  /  核糖体蛋白质

Streptomyces is a genus of diverse actinomycetes known for producing antibiotics, showcasing high value for research and development. However, the limited number of Streptomyces species included in commercial databases restricts the application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in the identification of Streptomyces. [Objective] To establish a MALDI-TOF MS database for the identification of Streptomyces based on the mining of whole genome sequencing data and test its accuracy. [Methods] By searching against a genome database, we selected all the genome-sequenced type strains of Streptomyces. Subsequently, the sequences of 12 ribosomal proteins were extracted from their genome sequences and theoretical MALDI mass/charge (m/z) values were calculated. Accordingly, a database was established based on the combination of 12 theoretically calculated m/z values, which can be used as the identification criteria for Streptomyces species. Finally, type strains were randomly collected for MALDI-TOF MS testing. To test the accuracy of the database construction method and comparison results, we matched the experimental m/z values with the theoretically calculated m/z values of the species in the database. [Results] We established a MALDI-TOF MS database including 615 Streptomyces species. The mass spectra of the tested strains were accurately matched with those of corresponding species in the database. In addition, we proposed a method for the identification of Streptomyces by database comparison. [Conclusion] The database established in this study laid a foundation for identifying Streptomyces based on MALDI-TOF MS.

Streptomyces  /  matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS)  /  database  /  type strain  /  ribosomal protein
孙伟, 罗倩, 许杰, 李雷, 蒋海霞. 链霉菌基质辅助激光解吸电离飞行时间质谱数据库的建立及测试分析. 微生物学报, 2025 , 65 (9) : 4211 -4223 . DOI: 10.13343/j.cnki.wsxb.20250166
Wei SUN, Qian LUO, Jie XU, Lei LI, Haixia JIANG. Establishment and testing of a MALDI-TOF MS database for the identificationof Streptomyces[J]. Acta Microbiologica Sinica, 2025 , 65 (9) : 4211 -4223 . DOI: 10.13343/j.cnki.wsxb.20250166
正文
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基质辅助激光解吸电离飞行时间质谱(matrix-assisted laser desorption/ionization-time of flight mass spectrometry, MALDI-TOF MS)是一种软电离质谱技术，具有速度快、成本低和准确率高的特点，已广泛应用于医学诊断、环境监测和食品安全等领域的微生物鉴定[1-6]。该技术鉴定微生物的原理是采集待测菌株的蛋白质指纹图谱，与MALDI-TOF MS数据库中的菌株图谱比对，根据比对分值鉴定至属、种或株。菌种鉴定的准确性依赖于MALDI-TOF MS图谱数据库的完善性与可靠性。当前的商业数据库，如德国布鲁克的MALDI Biotyper数据库、法国梅里埃的VITEK MS数据库以及安图生物的本土微生物数据库均以收录病原微生物为主，存在菌种类别及数量不足，不能满足用户鉴定需求的问题[7]。对于不在商业数据库范围内，但具有重要研发价值的非病原微生物建立相应数据库，可拓展MALDI-TOF MS技术鉴定微生物的应用范围。
针对用户多样化的鉴定需求，质谱仪厂商提供了一套自建MALDI-TOF MS数据库方案，包括获得建库菌种的单菌落、甲酸提取法制备样本、仪器校正、图谱采集、数据评估和图谱入库等步骤。建库过程需要严格的质量控制[8]，建库人员需要掌握微生物学技术并经过质谱相关专业培训。因此自建数据库一般不予公开，或者需要购买使用，限制了自建库的共享。
早期研究表明，细菌MALDI-TOF MS图谱中以核糖体蛋白质的质谱峰为主[9-10]。本课题组在前期研究中基于放线菌全基因组测序数据注释出的核糖体蛋白质序列预测分子量，找出了放线菌MALDI-TOF MS图谱中常见的核糖体蛋白质信号，为识别核糖体蛋白质的质谱峰鉴定放线菌的方法建立提供了理论依据[11]。通过对伦茨氏菌属(Lentzea)和糖丝菌属(Saccharothrix) 2类稀有放线菌的研究发现，核糖体蛋白质的理论MALDI质谱峰值(mass/charge, m/z)组合可以作为菌种鉴定依据[12-13]，证实了基于全基因组测序数据挖掘建立MALDI-TOF MS数据库方案的可行性。
链霉菌(Streptomyces)属于放线菌门(Actinomycetota)放线菌纲(Actinomycetes)北里氏孢菌目(Kitasatosporales)链霉菌科(Streptomycetaceae)，广泛分布于土壤、淡水和海洋环境。链霉菌是放线菌门中最大的分支，许多种类的链霉菌能够产生抗生素、抗癌化合物、抗病毒化合物、免疫抑制剂、驱虫剂和除草剂等生物活性物质[14]，是极具研发价值的放线菌类群。在链霉菌多样性研究及天然产物资源勘探中，菌种鉴定是一项基础工作，最常用的鉴定方法仍是16S rRNA基因测序分析法[15]。由于商业数据库收录的链霉菌属菌种数量少，MALDI-TOF MS技术尚未应用于链霉菌鉴定。随着高通量测序技术的快速发展和测序成本的显著降低，公开基因组测序数据的链霉菌属菌种与日俱增，为基于全基因组测序数据挖掘建立链霉菌MALDI-TOF MS数据库创造了条件。前期研究发现，分子量小于10 kDa的12种核糖体蛋白质(L36、L34、L33、L32、L30、L28、S14-Z、L35、L29、S18、L27和S20)在放线菌MALDI-TOF MS图谱中以高信号强度稳定出现[12-13]。在对MALDI Biotyper数据库中链霉菌属菌种的MALDI-TOF MS图谱进行核糖体蛋白质信号注释时，同样发现这12种蛋白质的注释率高[11]。因此本研究以链霉菌属菌种模式菌株12种核糖体蛋白质的理论MALDI质谱峰值组合作为菌种鉴定依据，建立链霉菌MALDI-TOF MS数据库，并收集模式菌株进行测试分析，测试建库方法及数据库比对结果的准确性。
1 材料与方法
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1.1 链霉菌属入库菌种选取
以“Streptomyces”为检索词搜索原核生物标准命名名录(list of prokaryotic names with standing in nomenclature, LPSN) (https://lpsn.dsmz.de/)，获得有效发表并正确命名的链霉菌属菌种信息，包括菌种名称及模式菌株编号。以菌种名称为检索词搜索美国国家生物技术信息中心基因组数据库(National Center for Biotechnology Information, NCBI) (https://www.ncbi.nlm.nih.gov/datasets/genome/)，选取已公开模式菌株基因组测序数据的菌种入库。
1.2 入库菌种模式菌株核糖体蛋白质序列提取
以“ribosomal”为检索词，基因类型选择蛋白质编码基因，搜索入库菌种模式菌株的基因组组装报告，将检索到的核糖体蛋白质按序列长度排序，提取长度小于90个氨基酸、分子量小于10 kDa的12种核糖体蛋白质(L36、L34、L33、L32、L30、L28、S14-Z、L35、L29、S18、L27和S20)的序列。
1.3 核糖体蛋白质理论MALDI质谱峰值计算
链霉菌属于原核生物，蛋白质翻译后N-端的起始甲硫氨酸可能被切除。分析核糖体蛋白质序列第2个氨基酸，如符合切除规则[16]，用去除起始甲硫氨酸的序列计算分子量，否则用初始序列计算分子量。应用在线蛋白质基本性质分析工具ProtParam (https://web.expasy.org/protparam/)计算得到核糖体蛋白质分子量。
原核生物存在甲基化、乙酰化等翻译后修饰[17]。前期研究发现链霉菌属菌种核糖体蛋白质L33发生一个甲基化修饰，导致分子量增加14 Da[11]，计算L33的分子量需考虑这一情况。
蛋白质在基质辅助激光解吸电离下产生带1个电荷的阳离子[M+H]+，核糖体蛋白质的理论分子量换算为MALDI质谱峰值需考虑蛋白质结合1个质子后分子量增加1 Da的情况。
综上所述，考虑起始甲硫氨酸切除、L33的甲基化修饰和MALDI质子化3个因素后计算得到核糖体蛋白质的理论MALDI质谱峰值。
1.4 链霉菌MALDI-TOF MS数据库建立与分析
以入库菌种模式菌株12种核糖体蛋白质的理论MALDI质谱峰值组合作为各菌种鉴定依据，建立链霉菌MALDI-TOF MS数据库。
评估以12种核糖体蛋白质的理论质谱峰值组合区分菌种的能力。对于无法区分的组别，将组内菌种模式菌株的基因组序列提交模式菌株基因组服务器(type strain genome server, TYGS) (https://tygs.dsmz.de/)进行比对，获得组内菌种间的数字DNA-DNA杂交(digital DNA-DNA hybridization, dDDH)值，dDDH值>70%的菌种判定为相同菌种，dDDH值<70%的菌种判定为不同菌种[18]。
1.5 链霉菌属菌种模式菌株收集
随机收集5个链霉菌属菌种的模式菌株用于测试和分析，包括委内瑞拉链霉菌(Streptomyces venezuelae) ATCC 10712T、灰色链霉菌(Streptomyces griseus) J1014T、阿维菌素链霉菌(Streptomyces avermitilis) NRRL 8165T、微白黄链霉菌(Streptomyces albidoflavus) J1074T和天蓝色链霉菌(Streptomyces coelicolor) M145T，均由上海交通大学生命科学技术学院李雷副教授惠赠。
1.6 菌株MALDI-TOF MS测试与分析
制备ISP2固体培养基，28 ℃培养菌株2-3 d，用无菌竹签挑取单菌落涂抹到MALDI 384抛光不锈钢靶板上，室温自然干燥。在单菌落涂层上加入1 μL 10 mg/mL的α-氰基-4-羟基肉桂酸基质溶液，溶剂为乙腈:水:三氟乙酸(50:47.5:2.5，体积比)。室温自然干燥后放入质谱仪。
基质辅助激光解析高分辨飞行时间质谱仪购自布鲁克道尔顿公司(Bruker Daltonik GmbH)。使用控制软件flexControl 3.4采集质谱图，使用布鲁克细菌测试标准品校准方法。仪器测定参数：采集m/z范围为4 000-10 000；激光点击数为1 000；测定模式为阳离子线性模式。如单次采集的质谱峰强度低于104，通过累加模式使质谱峰强度达到104。使用分析软件flexAnalysis 3.4处理质谱图并标峰，导出峰列表。
基于质谱仪在线性模式下的测量精度，将蛋白质分子离子m/z的最大质量误差设为±500 ppm并按2种方法测试：(1) 将测试菌株的质谱峰值与其所属菌种模式菌株的12个理论峰值一一比对，检测其一致性，此方法测试建库方法的准确性；(2) 将测试菌株的质谱峰值与数据库菌种进行比对，找到匹配数最大的菌种，检测其是否为所属菌种，此方法测试数据库比对结果的准确性。
基于测试分析结果建立基于数据库比对的菌种鉴定方法。
1.7 16S rRNA基因测序分析法验证
按本研究建立的方法对上海辰山植物园土壤样品中分离出的放线菌菌株进行鉴定，选取鉴定至种的菌株委托苏州金唯智生物科技有限公司进行测试。基因组DNA提取、16S rRNA基因扩增和Sanger法测序均由苏州金唯智生物科技有限公司完成。菌株的16S rRNA基因序列提交至GenBank获得登录号并在EzBioCloud (https://www.ezbiocloud.net/)数据库进行比对和鉴定。对2种方法得到的鉴定结果进行比较和分析。
2 结果与分析
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2.1 链霉菌属入库菌种选取
截至2025年1月31日，原核生物标准命名名录收录的有效发表且正确命名的链霉菌属菌种共计738个，其中公开模式菌株基因组测序数据的菌种有626个。除去未注释基因组的2个、未核实来源的3个、基因组污染的4个以及未注释出L36的2个菌种，最终数据库1.0版本包含链霉菌属615个菌种[原始数据存储于国家微生物科学数据中心(http://nmdc.cn)，编号为NMDCX0002103]，覆盖率达83.3%。
2.2 入库菌种模式菌株核糖体蛋白质序列提取
链霉菌的核糖体蛋白质在序列长度上表现出高度保守性。需要注意的是，L32、L28和S18注释出不同长度的2套序列，L33注释出相同长度(54个氨基酸)的2套序列。基于前期研究结果[11]，L32提取长度为57个氨基酸的序列，L28提取长度为61个氨基酸的序列，S18提取长度为78个氨基酸的序列，L33提取以“MAATDV”起始的序列。
2.3 核糖体蛋白质理论MALDI质谱峰值计算
序列分析表明链霉菌的12种核糖体蛋白质中，L36不符合起始甲硫氨酸切除规则，采用初始序列计算理论分子量；另外11种核糖体蛋白质则用去除起始甲硫氨酸的序列计算理论分子量。L33在理论分子量基础上加14以匹配甲基化。转换为MALDI质谱峰值时，将所有分子量加1以匹配MALDI质子化。最终得到615个菌种模式菌株的核糖体蛋白质理论MALDI质谱峰值组合，其中606个菌种包含12个峰值的组合，另外9个菌种包含11个峰值的组合，这是由于1种核糖体蛋白质未注释所致[老鹳草链霉菌(Streptomyces geranii)缺少L33；银耳链霉菌(Streptomyces tremellae)、产褐色链霉菌(Streptomyces fuscigenes)、山土链霉菌(Streptomyces montanisoli)、白黄黑链霉菌(Streptomyces albiflaviniger)、新泽西链霉菌(Streptomyces novaecaesareae)和海南链霉菌(Streptomyces hainanensis)缺少L28；Streptomyces solicavernae缺少S18；杀病链霉菌(Streptomyces pathocidini)缺少S20]。
2.4 链霉菌MALDI-TOF MS数据库建立与分析
为便于数据分析和数据库检索，将每个模式菌株的理论MALDI质谱峰值按从小到大排列，入库菌种按最小峰值从小到大排列，峰值相同则按次小峰值从小到大排列，以此类推，对入库菌种排序并编号，建立链霉菌MALDI-TOF MS数据库1.0版本(https://biocore.sjtu.edu.cn/public/upload/20250430/%E9%93%BE%E9%9C%89%E8%8F%8CMALDI-TOF+MS%E6%95%B0%E6%8D%AE%E5%BA%93V1.0.xlsx)。数据库中537个菌种(占比87.3%)具有特征性峰值组合，可与其他菌种区分开。数据库中存在相同峰值组合的菌种共计34组78个(编号为NMDCX0002103)，这些组内的菌种间无法区分。
基于基因组指标的分类方法，如数字DNA-DNA杂交、平均核苷酸一致性和平均氨基酸一致性分析如今已成为主流分类方法[15]。近年来，基于基因组指标的研究发现链霉菌属菌种间存在异名同种现象，部分菌种名不再作为正确名称，而被定义为“Synonym”[19-20]。本研究对数据库中具有相同峰值组合的菌种进行基因组序列比对，发现23个组的组内菌种间dDDH值>70% (表1)，提示这些组的组内菌种应为异名同种，因此具有相同的峰值组合符合预期。18个组(30个种)的组内菌种间dDDH值<70% (表2)，提示这些组的组内菌种并非同种。经基因组序列比对验证后，数据库中无法区分的菌种实际为30个(占比4.9%，表2)，这些菌种无法鉴定到种，而数据库中约95%的菌种可以鉴定到种。
2.5 菌株MALDI-TOF MS测试与分析
本研究中5个测试菌株的MALDI-TOF MS图谱见图1，菌株的质谱峰列表原始数据存储于国家微生物科学数据中心(http://nmdc.cn)，编号为NMDCX0002103。
2.5.1 建库方法准确性测试
用菌种名“Streptomyces venezuelae”搜索数据库，找到0256 Streptomyces venezuelae ATCC 10712T。峰值比对表明，菌株质谱图中的11个峰值(图1A)与目标菌株的12个理论峰值匹配(表3)，m/z 6 816.72同时匹配6 815.83和6 819.14，峰值的最大质量误差为-354.88 ppm，实测值和理论值完全一致。
用菌种名“Streptomyces griseus”搜索数据库，找到0076 Streptomyces griseus DSM 40236T。峰值比对表明，菌株质谱图中的11个峰值(图1B)与目标菌株的12个理论峰值匹配(表3)，m/z 6 860.70同时匹配6 859.85和6 862.15，峰值的最大质量误差为-345.69 ppm，实测值和理论值完全一致。
用菌种名“Streptomyces avermitilis”搜索数据库，找到0276 Streptomyces avermitilis MA-4680T。峰值比对表明，菌株质谱图中的12个峰值(图1C)与目标菌株的12个理论峰值匹配(表3)，峰值的最大质量误差为-286.66 ppm，实测值和理论值完全一致。
用菌种名“Streptomyces albidoflavus”搜索数据库，找到0490 Streptomyces albidoflavus DSM 40455T。峰值比对表明，菌株质谱图中的11个峰值(图1D)与目标菌株的11个理论峰值匹配(表3)，峰值的最大质量误差为-384.90 ppm。由于缺少与m/z 6 963.19匹配的峰值，未实现实测值和理论值完全一致。进一步分析发现，线性模式分辨率低，质谱图中的高强度峰m/z 6 971.61遮盖了附近低强度的核糖体蛋白质峰，导致对质谱图标峰时未将其标注上。将质谱图局部放大后，肩峰m/z 6 963.26清晰可见(图1D)，因此菌株质谱实测值和理论值完全一致。
用菌种名“Streptomyces coelicolor”搜索数据库，未找到目标菌种。分析原因发现LPSN已将Streptomyces coelicolor定义为“Synonym”，菌种未入库。
对4个测试菌株的比对和分析表明了实测峰值与理论峰值的一致性，证实了本研究所用建库方法的准确性。
2.5.2 数据库比对结果准确性测试
基于m/z 4 389.57和5 168.17，将检索范围定位至0256-0257，进一步比对得出测试菌株与0256 Streptomyces venezuelae ATCC 10712T的匹配数最大，为12。
基于m/z 4 390.23和5 095.91，将检索范围定位至0064-0081，进一步比对得出测试菌株与0076 Streptomyces griseus DSM 40236T的匹配数最大，为12；与0077 Streptomyces anulatus JCM 4721T的匹配数为11。
基于m/z 4 402.07和5 052.58，将检索范围定位至0276-0277，进一步比对得出测试菌株与0276 Streptomyces avermitilis MA-4680T的匹配数最大，为12。
基于m/z 4 415.93和5 121.46，将检索范围定位至0484-0492，进一步比对得出测试菌株与0490 Streptomyces albidoflavus DSM 40455T的匹配数最大，为11；与0491 Streptomyces koyangensis VK-A60T的匹配数为10；与0489 Streptomyces diastaticus JCM 4128T的匹配数为9。
基于m/z 4 402.07和5 166.26，将检索范围定位至0358-0377，进一步比对得出测试菌株与0361 Streptomyces violaceoruber CGMCC 4.1801T的匹配数最大，为12。为确定S. coelicolor的分类地位，按金标准基因组测序比对法进行鉴定。将S. coelicolor A3(2)T的基因组序列(GCA 000203835.1)提交至模式菌株基因组服务器进行比对，鉴定结果为Streptomyces violaceoruber (表4)，与数据库比对结果一致。
对5个测试菌株的数据库比对找到匹配数最大的菌种，均与所属菌种一致，证实了数据库比对结果的准确性。非正确命名的菌种S. coelicolor也得到了准确鉴定。
2.5.3 基于数据库比对的鉴定方法建立
基于以上测试分析结果，数据库可用于链霉菌属已知菌种的检测和未知菌种的鉴定。检测已知菌种的方法：用菌种名搜索数据库，找到目标菌种模式菌株，进行理论峰值和实测峰值匹配，若12个理论峰值全匹配，则将待检菌株确定为目标菌种。鉴定未知菌种的方法：基于L36 (m/z范围为4 367.36-4 432.44)和L34 (m/z范围为5 036.88-5 248.15)的峰值缩小检索范围，从中找出匹配数最大的模式菌株，若匹配数为12，则将待检菌株鉴定为该模式菌株所属菌种。
2.6 16S rRNA基因测序分析法验证
数据库比对发现，与数据库菌种的最大匹配数为12和11的菌株共有6株(表5)，菌株质谱峰列表原始数据存储于国家微生物科学数据中心(http://nmdc.cn)，编号为NMDCX0002103。菌株S1-8、S1-13和S1-16与数据库菌种的最大匹配数为12，可鉴定至种。菌株S1-6、S1-10和S1-39与数据库菌种的最大匹配数为11，未匹配的1个峰值是由于质量轴偏移导致其超出允许最大误差(编号为NMDCX0002103)。前期研究发现质量轴偏移时可适当调整质量误差范围[11]，将最大误差设定为-600 ppm，3个菌株的最大匹配数均达到12，同样可鉴定至种。
六个菌株的16S rRNA基因序列比对结果见表6，其中5个菌株的比对结果与本研究建立方法的鉴定结果一致。鉴定结果不一致的菌株是S1-13，其16S rRNA基因序列相似度最高的是Streptomyces marianii ICN19T。进一步分析发现，LPSN中“Streptomyces marianii”为非有效发表种，提示这一结果并不准确。序列相似度第二高的是婺源链霉菌(Streptomyces wuyuanensis) CGMCC 4.7042T，鉴定结果一致。基于以上测试分析，本研究建立的基于数据库比对的菌种鉴定方法与16S rRNA基因测序分析法具有高度一致的鉴定结果。
3 讨论与结论
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本研究基于基因组测序数据挖掘建立了链霉菌MALDI-TOF MS数据库。建库过程不依赖仪器测试，避免了菌株培养、样本处理、上机测试、质量控制等图谱数据库构建环节，极大简化了建库流程，降低了建库成本。这套方法易于标准化，只要遵循蛋白质的翻译后加工、修饰规律，即可准确预测并计算得出目标菌种的一组核糖体蛋白质理论质谱峰值，这些数值不受菌株培养条件、样本处理方法、仪器测量精度等因素的影响而产生偏差。因此这套建库方案具备推广条件，可应用于其他细菌类群的MALDI-TOF MS数据库构建。
MALDI-TOF MS鉴定微生物的样本制备方法主要包括直接涂抹法、扩展的直接涂抹法和甲酸提取法。本研究发现，直接涂抹法对培养2-3 d的链霉菌单菌落(营养菌丝体)制备效果好，采集到的质谱图以核糖体蛋白质峰为主，杂峰少，这对得到准确的匹配数至关重要。直接涂抹法操作简单，15 min可完成1个样本制备，5 min可完成质谱采集。用到的靶板可以清洗后反复使用，制备过程仅消耗少量的基质和试剂，鉴定一个单菌落仅需1-2元。长期以来，链霉菌的菌种鉴定主要应用16S rRNA基因测序法，需要先挑取单菌落液体培养1-2 d，再收集菌体提取基因组DNA，PCR扩增16S rRNA基因和Sanger测序，一般又需要1-2 d。此外，一个链霉菌菌株16S rRNA基因全长测序的成本大概在40-50元。随着基因组测序技术的发展，基于基因组指标的鉴定方法能够更真实地反映类群间的进化关系，但基因组测序法周期长、成本高，限制了其在菌种鉴定中的应用。因此凭借显著的价格和速度优势，MALDI-TOF MS法鉴定链霉菌显示出很大的应用潜力。
布鲁克的MALDI Biotyper数据库(Bruker MBT DB7854)收录了457种放线菌，但其中仅有14种链霉菌。本研究建立的链霉菌MALDI-TOF MS数据库1.0版本包含615种链霉菌，达到了较高水平的覆盖程度，极大地补充了商业数据库。随着微生物基因组测序的推进，一些尚未测序的链霉菌属菌种的全基因组测序数据仍会公开。同时，国际系统与进化微生物学杂志(International Journal of Systematic and Evolutionary Microbiology, IJSEM)已经规定新种的发表必须提供全基因组序列。因此，通过补充新测序的菌种数据，可以继续扩充数据库。通过对更多未知菌株进行鉴定可以全面分析鉴定方法的准确度。本研究中数据库建立基于基因组测序数据、基因功能注释和手动计算，不排除个别序列错误和计算错误的可能。后续使用中，将对发现的错误数据及时进行更正，并定期发布更新完善的数据库版本，推动自建链霉菌数据库及鉴定方法的应用。
数据库是MALDI-TOF MS菌种鉴定技术的核心。鉴于构建标准图谱数据库的技术壁垒高，本研究对MALDI-TOF MS数据库构建方法进行了创新。基于微生物基因组数据挖掘构建数据库的方法不依赖仪器设备和配套软件，不需要培养入库菌株，具备一定系统分类学和生物信息学知识即可完成快速建库。通过数据库的开放共享有助于鉴定方法的推广。目前，国内很多高校和研究机构都购置了基质辅助激光解析飞行时间质谱仪，但设备的整体使用率不高。在相关部门鼓励大型仪器对外共享的背景下，很多机构提供送样测试服务，科研人员可通过送样测试得到待检菌株的质谱，再基于自建库或公开数据库比对完成菌种鉴定。
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2025年第65卷第9期
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doi: 10.13343/j.cnki.wsxb.20250166
  • 接收时间：2025-03-02
  • 首发时间：2026-02-07
  • 出版时间：2025-09-04
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  • 收稿日期：2025-03-02
  • 录用日期：2025-04-16
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Decision-making Consultation Project of Shanghai Jiao Tong University(JCZXSJA2023-04)
上海交通大学决策咨询课题(JCZXSJA2023-04)
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    上海交通大学 生命科学技术学院，上海
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2种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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