Euphausiids (krill) are important contributors to marine biomass and key players in marine pelagic trophic webs. Euphausiid stomachs represent a specific niche for microbes that participate in the digestion of the host’s dietary components. Methods for the study of the diversity and function of these microorganisms remain complex. Bacterial ribosomal sequences obtained from lysates of stomachs are often overrepresented by organisms from the surrounding environment. Flow cytometry with cell sorting (FC-CS) have become a powerful technique to study microbial community structure but also for the study of population genomics of gut-associated bacteria. We compared the performance of the FC-CS-sequencing and total DNA extraction-sequencing to study the stomach microbiota of the Humboldt Current krill. Non-specific amplification was not retrieved in the polymerase chain reaction (PCR) from cells sorted, opposite to the observed using the DNA from the whole lysate. Sequences obtained from the whole stomach DNA were enriched in picocyanobacteria, whereas sequences retrieved from cells sorted belonged almost exclusively to Balneola sp. of the new phylum Balneolaeota. Our results suggest that the stomach-associated microbiota can be successfully characterized by FC-CS and sequencing by manual scraping of the stomach. The implementation of this technique might complement future studies on host-microbes interaction and their implications on the marine pelagic food web.

中文翻译：

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流式细胞术与细胞分选和测序作为研究洪堡流磷虾（Euphausiacea）胃微生物群的工具

磷虾（磷虾）是海洋生物量的重要贡献者，也是海洋中上层营养网的关键参与者。Euhausiid 的胃代表了参与消化宿主饮食成分的微生物的特定生态位。研究这些微生物的多样性和功能的方法仍然很复杂。从胃的裂解物中获得的细菌核糖体序列通常被来自周围环境的生物体过度代表。带细胞分选的流式细胞术 (FC-CS) 已成为研究微生物群落结构以及研究肠道相关细菌群体基因组学的强大技术。我们比较了 FC-CS 测序和总 DNA 提取测序的性能，以研究洪堡流磷虾的胃微生物群。在聚合酶链式反应 (PCR) 中未从分选的细胞中检索到非特异性扩增，这与使用来自整个裂解物的 DNA 观察到的相反。从整个胃 DNA 获得的序列富含 picocyanobacteria，而从分选的细胞中检索到的序列几乎完全属于 Balneola sp。的新门 Balneolaeota。我们的研究结果表明，胃相关微生物群可以通过 FC-CS 成功表征，并通过手动刮胃进行测序。该技术的实施可能会补充未来对宿主-微生物相互作用及其对海洋中上层食物网的影响的研究。从整个胃 DNA 获得的序列富含 picocyanobacteria，而从分选的细胞中检索到的序列几乎完全属于 Balneola sp。的新门 Balneolaeota。我们的研究结果表明，胃相关微生物群可以通过 FC-CS 成功表征，并通过手动刮胃进行测序。该技术的实施可能会补充未来对宿主-微生物相互作用及其对海洋中上层食物网的影响的研究。从整个胃 DNA 获得的序列富含 picocyanobacteria，而从分选的细胞中检索到的序列几乎完全属于 Balneola sp。的新门 Balneolaeota。我们的研究结果表明，胃相关微生物群可以通过 FC-CS 成功表征，并通过手动刮胃进行测序。该技术的实施可能会补充未来对宿主-微生物相互作用及其对海洋中上层食物网的影响的研究。