Comparison of methods for identification of microbial communities in book collections: Culture-dependent (sequencing and MALDI-TOF MS) and culture-independent (Illumina MiSeq)
Comparison of methods for identification of microbial communities in book collections: Culture-dependent (sequencing and MALDI-TOF MS) and culture-independent (Illumina MiSeq)
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DOI：
10.1016/j.ibiod.2017.02.015
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发表时间：
2018-07-01
影响因子：
4.8
通讯作者：
Pangallo, Domenico
中科院分区：
文献类型：
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作者：
Krakova, Lucia;Soltys, Katarina;Pangallo, Domenico
采用新方法的不同鉴定策略，即依赖于培养的(使用基质辅助激光解吸/电离飞行时间质谱仪，MALDI-TOF MS)和不依赖于培养的(使用Illumina MiSeq平台上的高通量测序)方法，首次被应用于分析图书样品恶化的微生物区系。我们比较了两种不同的微生物培养鉴定技术：DNA测序和MALDI-TOF MS，两种鉴定系统产生的结果几乎相同。DNA测序能够较好地鉴定所有回收的菌株，而MALDI-TOF MS不能正确识别竹青链霉菌和溶血杆菌，后者至少可以在属水平上进行鉴定。此外，用MALDI-TOF MS方法未鉴定出偏粘毛霉和麦穗粘毛霉。这种不一致是由于MALDI BioTyper参考数据库中没有不同种类的微生物造成的。Illumina高通量测序与非侵入性采样相结合，可以识别复杂的细菌和真菌群落。本研究提出了两种新的可供选择的鉴定方法(MALDI-TOF MS和Illumina MiSeq)在调查定植于档案物品的微生物区系方面取得了令人满意的效果。(C)2017爱思唯尔有限公司。保留所有权利。
Different identification strategies employing new methodologies, namely, culture-dependent (using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, MALDI-TOF MS) and culture-independent (using high-throughput sequencing on Illumina MiSeq platform) approaches, were applied for the first time to analysis of the deteriorating microflora of book samples. We compared two different identification techniques coupled to microbial cultivation: DNA sequencing and MALDI-TOF MS. The two identification systems produced almost the same results. DNA sequencing was able to better identify all the recovered isolates, while MALDI-TOF MS failed to properly recognize Streptomyces ambofaciens and Lysinibacillus fusrforrnis, the latter method permitting identification at least at genus level. In addition, the isolates Myxotrichum deflexum and Oidiodendron cerealis were not identified by the MALDI-TOF MS approach. This incongruence was caused by the absence of different kinds of microorganisms in the MALDI BioTyper reference database. The Illumina high-throughput sequencing coupled to non-invasive sampling allowed the identification of a complex bacterial and fungal community. The study presents the satisfactory performance of two novel alternative identification methods (MALDI-TOF MS and Illumina MiSeq) for the investigation of microflora colonizing archival items. (C) 2017 Elsevier Ltd. All rights reserved.