Down-stream targets of TGFβ/BMP signaling in C. elegans exposed to microbiota CeMbio using RNAseq. Down-stream targets of TGFβ/BMP signaling in C. elegans exposed to microbiota CeMbio using RNAseq

Only recently, the natural gut microbiome of the model organism Caenorhabditis elegans has been described. C. elegans harbors a distinct gut microbiome that is shaped by environmental conditions, age, and host genotype. However, there is not much known about the genetic factors on the molecular level that the worm employs in order to keep its microbiota at bay. Previously, we have shown that TGFβ/BMP immune signaling is able to control the gut microbiome of C. elegans in particular in regards to Enterobacter species. We now aimed to identify the downstream targets of TGFβ/BMP immune signaling that implement the changes in microbiome composition. Hence, we exposed TGFβ mutants, dbl-1(nk3) and sma-3(e491), overexpression strain ctIs40 [dbl-1(+) + sur-5::GFP], and wild-type N2 to a synthetic microbiota community, CeMbio, and an E. coli OP50 control, and performed RNAseq. CeMbio is a collection of 12 diverse bacterial strains, previously isolated from wild C. elegans, C. elegans grown in microcosms, or substrates with C. elegans. Using the R packages edgeR and limma we are currently analyzing the data to understand the involvement of TGFβ/BMP signaling in host-microbiome interaction. Overall design: worm strains dbl-1(nk3), sma-3(e491), ctIs40 [dbl-1(+) + sur-5::GFP], and N2 exposed to either E. coli OP50 or CeMbio in 3 biological replicates

直至近年，模式生物秀丽隐杆线虫（Caenorhabditis elegans）的天然肠道菌群才得到系统解析。该线虫拥有独特的肠道菌群，其组成受环境条件、宿主年龄与宿主基因型共同调控。然而，学界对于该线虫在分子层面用以维持肠道菌群稳态的遗传因子仍知之甚少。此前我们的研究已证实，转化生长因子β/骨形态发生蛋白（TGFβ/BMP）免疫信号通路能够调控秀丽隐杆线虫的肠道菌群，尤其对肠杆菌属（Enterobacter）物种的定植具有显著影响。本研究旨在解析介导菌群组成改变的TGFβ/BMP免疫信号通路下游效应靶点。为此，我们将TGFβ通路突变体dbl-1(nk3)、sma-3(e491)，过表达菌株ctIs40 [dbl-1(+) + sur-5::GFP] 以及野生型N2线虫分别暴露于合成菌群群落CeMbio与大肠杆菌（E. coli）OP50对照环境中，并开展了RNA测序（RNAseq）。CeMbio是由12种不同细菌菌株组成的合成菌群，这些菌株此前均分离自野生秀丽隐杆线虫、实验室微宇宙培养的秀丽隐杆线虫或携带有秀丽隐杆线虫的底物。目前我们正借助R语言工具包edgeR与limma对测序数据进行分析，以阐明TGFβ/BMP信号通路在宿主-菌群互作中的作用机制。实验整体设计：将dbl-1(nk3)、sma-3(e491)、ctIs40 [dbl-1(+) + sur-5::GFP] 四种线虫品系与野生型N2分别暴露于大肠杆菌OP50或CeMbio环境，每组设置3次生物学重复。