Kogawa Masato, Miyaoka Rimi, Hemmerling Franziska, Ando Masahiro, Yura Kei, Ide Keigo, Nishikawa Yohei, Hosokawa Masahito, Ise Yuji, Cahn Jackson K B, Takada Kentaro, Matsunaga Shigeki, Mori Tetsushi, Piel Jörn, Takeyama Haruko
Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-0072, Japan.
PNAS Nexus. 2022 Mar 2;1(1):pgab007. doi: 10.1093/pnasnexus/pgab007. eCollection 2022 Mar.
The production of bioactive metabolites is increasingly recognized as an important function of host-associated bacteria. An example is defensive symbiosis that might account for much of the chemical richness of marine invertebrates including sponges (Porifera), 1 of the oldest metazoans. However, most bacterial members of sponge microbiomes have not been cultivated or sequenced, and therefore, remain unrecognized. Unequivocally linking metabolic functions to a cellular source in sponge microbiomes is, therefore, a challenge. Here, we report an analysis pipeline of microfluidic encapsulation, Raman microscopy, and integrated digital genomics (MERMAID) for an efficient identification of uncultivated producers. We applied this method to the chemically rich bacteriosponge (sponge that hosts a rich bacterial community) , previously shown to contain 'Entotheonella' symbionts that produce most of the bioactive substances isolated from the sponge. As an exception, the antifungal aurantosides had remained unassigned to a source. Raman-guided single-bacterial analysis and sequencing revealed a cryptic, distinct multiproducer, ' Poriflexus aureus' from a new Chloroflexi lineage as the aurantoside producer. Its exceptionally large genome contains numerous biosynthetic loci and suggested an even higher chemical richness of this sponge than previously appreciated. This study highlights the importance of complementary technologies to uncover microbiome functions, reveals remarkable parallels between distantly related symbionts of the same host, and adds functional support for diverse chemically prolific lineages being present in microbial dark matter.
生物活性代谢产物的产生日益被认为是宿主相关细菌的一项重要功能。一个例子是防御性共生，这可能解释了包括海绵（多孔动物门）在内的许多海洋无脊椎动物丰富的化学物质组成，海绵是最古老的后生动物之一。然而，海绵微生物群中的大多数细菌成员尚未被培养或测序，因此仍未被识别。因此，明确将代谢功能与海绵微生物群中的细胞来源联系起来是一项挑战。在这里，我们报告了一种微流控封装、拉曼显微镜和整合数字基因组学（MERMAID）的分析流程，用于高效识别未培养的生产者。我们将这种方法应用于化学物质丰富的噬菌海绵（ hosting a rich bacterial community的海绵），此前已证明其含有“Entotheonella”共生体，这些共生体产生了从该海绵中分离出的大部分生物活性物质。作为一个例外，抗真菌的橙黄糖苷的来源尚未确定。拉曼引导的单细菌分析和测序揭示了一种来自新的绿弯菌门谱系的神秘、独特的多生产者“金黄色多孔弯曲菌”是橙黄糖苷的生产者。其异常大的基因组包含众多生物合成位点，表明这种海绵的化学物质丰富程度比之前认为的还要高。这项研究强调了互补技术在揭示微生物群功能方面的重要性，揭示了同一宿主的远缘共生体之间的显著相似之处，并为微生物暗物质中存在的多种化学丰富谱系提供了功能支持。
