Table_4_The Inducible Response of the Nematode Caenorhabditis elegans to Members of Its Natural Microbiota Across Development and Adult Life.XLSX

The biology of all organisms is influenced by the associated community of microorganisms. In spite of its importance, it is usually not well understood how exactly this microbiota affects host functions and what are the underlying molecular processes. To rectify this knowledge gap, we took advantage of the nematode Caenorhabditis elegans as a tractable, experimental model system and assessed the inducible transcriptome response after colonization with members of its native microbiota. For this study, we focused on two isolates of the genus Ochrobactrum. These bacteria are known to be abundant in the nematode’s microbiota and are capable of colonizing and persisting in the nematode gut, even under stressful conditions. The transcriptome response was assessed across development and three time points of adult life, using general and C. elegans-specific enrichment analyses to identify affected functions. Our assessment revealed an influence of the microbiota members on the nematode’s dietary response, development, fertility, immunity, and energy metabolism. This response is mainly regulated by a GATA transcription factor, most likely ELT-2, as indicated by the enrichment of (i) the GATA motif in the promoter regions of inducible genes and (ii) of ELT-2 targets among the differentially expressed genes. We compared our transcriptome results with a corresponding previously characterized proteome data set, highlighting a significant overlap in the differentially expressed genes, the affected functions, and ELT-2 target genes. Our analysis further identified a core set of 86 genes that consistently responded to the microbiota members across development and adult life, including several C-type lectin-like genes and genes known to be involved in energy metabolism or fertility. We additionally assessed the consequences of induced gene expression with the help of metabolic network model analysis, using a previously established metabolic network for C. elegans. This analysis complemented the enrichment analyses by revealing an influence of the Ochrobactrum isolates on C. elegans energy metabolism and furthermore metabolism of specific amino acids, fatty acids, and also folate biosynthesis. Our findings highlight the multifaceted impact of naturally colonizing microbiota isolates on C. elegans life history and thereby provide a framework for further analysis of microbiota-mediated host functions.

所有生物体的生物学特性均受其共生微生物群落的影响。尽管这一关联至关重要，但目前学界对该微生物群（microbiota）究竟如何调控宿主功能、其背后的分子机制仍知之甚少。为填补这一认知空白，本研究以秀丽隐杆线虫（Caenorhabditis elegans）作为易操作的实验模型系统，探究其在定植本土微生物群成员后的诱导转录组（transcriptome）响应。本研究聚焦于苍白杆菌属（Ochrobactrum）的两株分离株：这类细菌在该线虫的微生物群中丰度较高，且即便在胁迫条件下，也可定植并持续存在于线虫肠道内。我们通过覆盖线虫发育阶段及成虫期三个时间点的转录组分析，结合通用富集分析（enrichment analysis）与秀丽隐杆线虫特异性富集分析，以鉴定受影响的生物学功能。分析结果显示，该微生物群成员可影响线虫的饮食响应、发育、繁殖力、免疫及能量代谢。该转录响应主要受GATA转录因子（GATA transcription factor）调控，大概率为ELT-2，相关证据包括：(i) 诱导型基因（inducible genes）的启动子区域富集GATA基序，(ii) 差异表达基因（differentially expressed genes）中富集ELT-2的靶标基因。我们将本次转录组结果与此前已表征的蛋白质组（proteome）数据集进行比对，发现二者在差异表达基因、受影响的生物学功能及ELT-2靶标基因上均存在显著重叠。本研究进一步鉴定出86个核心基因集，这些基因在线虫发育及成虫阶段对微生物群成员的定植均呈现稳定的响应，其中包括多个C型凝集素样基因（C-type lectin-like genes），以及已知参与能量代谢或繁殖过程的基因。我们还借助此前已构建的秀丽隐杆线虫代谢网络模型（metabolic network model），通过代谢网络分析评估了诱导基因表达的后续效应。该分析进一步补充了富集分析的结果，揭示苍白杆菌分离株可影响线虫的能量代谢，以及特定氨基酸、脂肪酸的代谢与叶酸生物合成（folate biosynthesis）。本研究结果凸显了自然定植的微生物群分离株对秀丽隐杆线虫生活史的多维度影响，为后续解析微生物群介导的宿主功能提供了研究框架。