Abstract：
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is routinely used as a rapid and cost-effective method for pathogen identification in clinical settings. In comparison, its performance in other microbiological fields, such as environmental microbiology, is still being tested, although isolates of environmental microbes are essential for in-depth in vivo studies of their biology, including biotechnological applications. We investigated the applicability of MALDI-TOF MS for the identification of bacterial isolates from a highly oligotrophic environment - Dinaric Karst caves, which likely harbor specific microorganisms. We cultured bacteria from the shell surface of the endemic mussel Congeria jalzici, one of the three known cave mussels in the world that lives in the Dinaric karst underground. The bacterial isolates were obtained by swabbing the shell surface of mussels living in microhabitats with different amounts of water: 10 air-exposed mussels, 10 submerged mussels, and 10 mussels in the hygropetric zone. A collection of 87 pure culture isolates was obtained, mostly belonging to the phylum Bacillota (72%), followed by Pseudomonadota (16%), Actinomycetota (11%), and Bacteroidota (1%). We compared the results of MALDI-TOF MS identification (Bruker databases DB-5989 and version 11, v11) with the results of 16S rDNA-based phylogenetic analysis, a standard procedure for bacterial identification. Identification to the genus level based on 16S rDNA was possible for all isolates and clearly outperformed the results from MALDI-TOF MS, although the updated MALDI-TOF MS database v11 gave better results than the DB-5989 version (85% versus 62%). However, identification to the species-level by 16S rDNA sequencing was achieved for only 17% of isolates, compared with 14% and 40% for the MALDI-TOF MS databases DB-5989 and v11 database, respectively. In conclusion, our results suggest that continued enrichment of MALDI-TOF MS libraries will result with this method soon becoming a rapid, accurate, and efficient tool for assessing the diversity of culturable bacteria from different environmental niches.
摘要：
基质辅助激光解吸电离飞行时间质谱（MALDI-TOFMS）通常用作临床环境中病原体鉴定的快速且经济有效的方法。相比之下,它在其他微生物领域的表现，如环境微生物学，仍在测试中，尽管环境微生物的分离对于深入体内研究其生物学至关重要，包括生物技术应用。我们研究了MALDI-TOFMS用于鉴定来自高度寡营养环境的细菌分离株-Dinaric喀斯特洞穴的适用性，可能藏有特定的微生物。我们从特有贻贝的壳表面培养细菌，生活在Dinaric岩溶地下的世界上三种已知的洞穴贻贝之一。通过用不同量的水擦拭生活在微生境中的贻贝的壳表面来获得细菌分离物：10个暴露于空气的贻贝，10个淹没的贻贝，和湿度区的10个贻贝。获得了87个纯培养分离株的集合，主要属于芽孢杆菌门(72%)，其次是Pseudomonadota（16％），放线菌（11%），和拟杆菌(1%)。我们比较了MALDI-TOFMS鉴定的结果（Bruker数据库DB-5989和版本11，v11）与基于16SrDNA的系统发育分析的结果，细菌鉴定的标准程序。基于16SrDNA的属水平鉴定对于所有分离株都是可能的，并且明显优于MALDI-TOFMS的结果，尽管更新的MALDI-TOFMS数据库v11的结果优于DB-5989版本(85%对62%).然而,通过16SrDNA测序鉴定到物种水平，只有17%的分离株实现了，与MALDI-TOFMS数据库DB-5989和v11数据库的14%和40%相比，分别。总之,我们的结果表明，MALDI-TOFMS文库的持续富集将导致该方法很快成为一种快速，准确,和评估来自不同环境生态位的可培养细菌多样性的有效工具。
