Nazipi Bushi Seven, Lund Marie B, Sandfeld Tobias, Nørskov Sanne Sadolin, Fruergaard Simon, Glasius Marianne, Bilde Trine, Schramm Andreas
Department of Biology - Section for Microbiology, Aarhus University, Aarhus, Denmark.
Department of Chemistry, Aarhus University, Aarhus, Denmark.
Appl Environ Microbiol. 2025 Feb 19;91(2):e0132524. doi: 10.1128/aem.01325-24. Epub 2025 Jan 8.
Antimicrobial resistance is an ever-increasing problem for human health, and with only a few novel antimicrobials discovered in recent decades, an extraordinary effort is needed to circumvent this crisis. A promising source of new microbial-derived antimicrobial compounds resides in the large fraction of microbes that are not readily cultured by standard cultivation. It has previously been shown that nests of the social spider contain a diverse bacterial community, where only a small fraction of the microbes could be recovered by standard cultivation. To improve the recovery of the bacterial diversity cultured from nests, we modified the previously described isolation chip (iChip) to fit the natural arid environment of nests. Here we provide a comprehensive analysis of the modified iChip's performance. We found that the modified iChip improved the overall culturability, performed equally or better at recovering the bacterial diversity from individual nests, and improved the recovery of rare isolates compared to standard cultivation. Furthermore, we show that the modified iChip can be used in the field. In addition, we observed that the nests contain volatile organic compounds (VOCs) that could serve as substrate for the selective enrichment of rare and iChip-specific isolates. Our modified iChip can be applied for cultivation in a broad range of arid habitats that can be exploited for future drug discovery.IMPORTANCEThe demand for novel antimicrobial compounds is an ever-increasing problem due to the rapid spread of antibiotic-resistant microbes. Therefore, exploring new habitats for microbial-derived antimicrobial compounds is crucial. The nest microbiome of remains largely unexplored and could potentially serve as a new source of antimicrobial compounds. To access the nest's microbial diversity, we designed a modified iChip for cultivation inside spider nests and tested its applications in both field and laboratory settings. Our study shows that the iChip's ability to recover abundant genera was comparable or superior to standard cultivation, while the recovery of rare (low-abundant genera) was higher. We argue that these low-abundant and iChip-specific isolates are enriched from naturally occurring nest volatile organic compounds (VOCs) during iChip incubation.
抗菌耐药性对人类健康而言是一个日益严重的问题，近几十年来仅发现了少数新型抗菌药物，因此需要付出巨大努力来规避这一危机。新的微生物源抗菌化合物的一个有前景的来源存在于很大一部分难以通过标准培养方法培养的微生物中。此前已有研究表明，群居蜘蛛的巢穴中含有多样的细菌群落，其中只有一小部分微生物能够通过标准培养方法被分离出来。为了提高从巢穴中培养出的细菌多样性，我们对之前描述的隔离芯片（iChip）进行了改进，使其适合巢穴的自然干旱环境。在此，我们对改进后的iChip的性能进行了全面分析。我们发现，改进后的iChip提高了整体可培养性，在从单个巢穴中恢复细菌多样性方面表现相当或更好，并且与标准培养相比，提高了稀有菌株的回收率。此外，我们证明改进后的iChip可在野外使用。另外，我们观察到巢穴中含有挥发性有机化合物（VOCs），这些化合物可作为选择性富集稀有和iChip特异性菌株的底物。我们改进后的iChip可应用于广泛的干旱栖息地培养，有望用于未来的药物发现。重要性由于抗生素耐药微生物的迅速传播，对新型抗菌化合物的需求是一个日益严重的问题。因此，探索微生物源抗菌化合物的新栖息地至关重要。群居蜘蛛的巢穴微生物群在很大程度上尚未被探索，有可能成为抗菌化合物的新来源。为了获取巢穴中的微生物多样性，我们设计了一种改进的iChip用于在蜘蛛巢穴内培养，并在野外和实验室环境中测试了其应用。我们的研究表明，iChip在恢复丰富菌属方面的能力与标准培养相当或更优，而稀有（低丰度菌属）的回收率更高。我们认为，这些低丰度和iChip特异性菌株是在iChip培养过程中从自然存在的巢穴挥发性有机化合物（VOCs）中富集而来的。
