Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders Universitygrid.1014.4, South Australia, Australia.
Microbiol Spectr. 2022 Jun 29;10(3):e0229621. doi: 10.1128/spectrum.02296-21. Epub 2022 May 2.
Sponge microbiomes are typically profiled by analyzing the community DNA of whole tissues, which does not distinguish the taxa residing within sponge cells from extracellular microbes. To uncover the endosymbiotic microbiome, we separated the sponge cells to enrich the intracellular microbes. The intracellular bacterial community of sponge was initially assessed by amplicon sequencing, which indicated that it hosts three unique phyla not found in the extracellular and bulk tissue microbiomes. These three phyla account for 66% of the taxonomically known genera in the intracellular microbiome. The shotgun metagenomic analysis extended the taxonomic coverage to viruses and eukaryotes, revealing the most abundant signature taxa specific to the intracellular microbiome. Functional KEGG pathway annotation demonstrated that the endosymbiotic microbiome hosted the greatest number of unique gene orthologs. The pathway profiles distinguished the intra- and extracellular microbiomes from the tissue and seawater microbiomes. Carbohydrate-active enzyme analysis further discriminated each microbiome based on their representative and dominant enzyme families. One pathway involved in digestion system and family esterase had a consistently higher level in intracellular microbiome and could statistically differentiate the intracellular microbiome from the others, suggesting that triacylglycerol lipases could be the key functional component peculiar to the endosymbionts. The identified higher abundance of lipase-related eggNOG categories further supported the lipid-hydrolyzing metabolism of endosymbiotic microbiota. Pseudomonas members, reported as lipase-producing bacteria, were only in the endosymbiotic microbiome, meanwhile Pseudomonas also showed a greater abundance intracellularly. Our study aided a comprehensive sponge microbiome that demonstrated the taxonomic and functional specificity of endosymbiotic microbiota. Sponges host abundant microbial symbionts that can produce an impressive number of novel bioactive metabolites. However, knowledge on intracellular (endosymbiotic) microbiota is scarce. We characterize the composition and function of the endosymbiotic microbiome by separation of sponge cells and enrichment of intracellular microbes. We uncover a noteworthy number of taxa exclusively in the endosymbiotic microbiome. We unlock the unique pathways and enzymes of endosymbiotic taxa. This study achieves a more comprehensive sponge microbial community profile, which demonstrates the structural and functional specificity of the endosymbiotic microbiome. Our findings not only open the possibility to reveal the low abundant and the likely missed microbiota when directly sequencing the sponge bulk tissues, but also warrant future in-depth exploration within single sponge cells.
海绵微生物组通常通过分析整个组织的群落 DNA 进行分析，这不能区分存在于海绵细胞内的分类群和细胞外微生物。为了揭示内共生微生物组，我们分离了海绵细胞以富集细胞内微生物。通过扩增子测序初步评估了海绵细胞的细胞内细菌群落，结果表明它含有三个不在细胞外和组织宏基因组中发现的独特门。这三个门占细胞内微生物组中已知分类群的 66%。宏基因组分析扩展了病毒和真核生物的分类学覆盖范围，揭示了特定于细胞内微生物组的最丰富的标志性分类群。功能 KEGG 途径注释表明，内共生微生物组拥有最多数量的独特基因直系同源物。途径谱将内共生微生物组与细胞外微生物组和组织微生物组以及海水微生物组区分开来。碳水化合物活性酶分析进一步根据代表性和主要酶家族区分了每个微生物组。一条涉及消化系统和酯酶家族的途径在细胞内微生物组中的水平更高，并且可以从统计学上区分细胞内微生物组与其他微生物组，这表明三酰基甘油脂肪酶可能是内共生体特有的关键功能成分。鉴定出的更高丰度的与脂肪酶相关的 eggNOG 类别进一步支持了内共生微生物群的脂质水解代谢。已报道为产脂肪酶细菌的假单胞菌成员仅存在于内共生微生物组中，同时假单胞菌在细胞内的丰度也更高。我们的研究辅助了全面的海绵微生物组，该微生物组展示了内共生微生物组的分类和功能特异性。海绵宿主丰富的微生物共生体，可以产生数量可观的新型生物活性代谢物。然而，关于细胞内（内共生）微生物组的知识却很少。我们通过分离海绵细胞和富集细胞内微生物来描述内共生微生物组的组成和功能。我们发现了大量仅存在于内共生微生物组中的分类群。我们揭示了内共生分类群的独特途径和酶。这项研究实现了更全面的海绵微生物群落图谱，展示了内共生微生物组的结构和功能特异性。我们的研究结果不仅为直接测序海绵宏组织时揭示低丰度和可能错过的微生物群提供了可能性，而且还为未来在单个海绵细胞内进行深入探索提供了依据。
