Gupta Mridula, Cilkiz Mustafa, Ibrahim Mohamed M A, Athrey Giridhar
Department of Poultry Science, Texas A&M University, 2472 TAMU, College Station, TX 77843, USA.
Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA.
Microorganisms. 2025 Mar 30;13(4):789. doi: 10.3390/microorganisms13040789.
Circadian rhythms are innate biological systems that control everyday behavior and physiology. Furthermore, bilateral interaction between the host's circadian rhythm and the gut microbes influences a variety of health ramifications, including metabolic diseases, obesity, and mental health including GALT physiology and the microbiome population. Therefore, we are studying the correlation between differential gene expression in the chicken brain and microbiota abundance during circadian rhythms. To understand this, we raised freshly hatched chicks under two photoperiod treatments: normal photoperiod (NP = 12/12 LD) and extended photoperiod (EP 23/1 LD). The chicks were randomly assigned to one of two treatments. After 21 days of circadian entrainment, the chicks were euthanized at nine time points spaced six hours apart over 48 h to characterize the brain transcriptomes. Each sample's RNA was extracted, and 36 mRNA libraries were generated and sequenced using Illumina technology, followed by data processing, count data generation, and differential gene expression analysis. We generated an average of 17.5 million reads per library for 237.9 M reads. When aligned to the Galgal6 reference genome, 11,867 genes had detectable expression levels, with a common dispersion value of 0.105. To identify the genes that follow 24 h rhythms, counts per million data were performed in DiscoRhythm. We discovered 577 genes with Cosinor and 417 with the JTK cycle algorithm that exhibit substantial rhythms. We used weighted gene co-expression network analysis (WGCNA) to analyze the correlation between differentially expressed genes and microbiota abundance. The most enriched pathways included aldosterone-regulated sodium reabsorption, endocrine and other factor-regulated calcium reabsorption, GABAergic synapse, oxidative phosphorylation, serotonergic synapse, dopaminergic synapse and circadian entrainment. This study builds on our previous study, and adds new findings about the specific interactions and co-regulation of the brain transcriptome and the gut microbiota. The interaction between gut microbiota and host gene expression highlights the potential benefits of microbiome-modulation approaches to improve gut health and performance in poultry.
昼夜节律是控制日常行为和生理的内在生物系统。此外，宿主昼夜节律与肠道微生物之间的双向相互作用会影响多种健康后果，包括代谢疾病、肥胖以及心理健康，其中包括肠道相关淋巴组织（GALT）生理学和微生物群落。因此，我们正在研究昼夜节律期间鸡大脑中差异基因表达与微生物群丰度之间的相关性。为了理解这一点，我们在两种光周期处理下饲养刚孵化的雏鸡：正常光周期（NP = 12/12 LD）和延长光周期（EP 23/1 LD）。雏鸡被随机分配到两种处理之一。在昼夜节律同步21天后，在48小时内每隔6小时的九个时间点对雏鸡实施安乐死，以表征大脑转录组。提取每个样本的RNA，使用Illumina技术生成并测序36个mRNA文库，随后进行数据处理、计数数据生成和差异基因表达分析。我们每个文库平均产生1750万条读数，共计2.379亿条读数。当与Galgal6参考基因组比对时，11867个基因具有可检测的表达水平，共同离散值为0.105。为了鉴定遵循24小时节律的基因，在DiscoRhythm中进行了每百万数据计数。我们发现577个基因符合Cosinor算法，417个基因符合JTK周期算法，它们表现出显著的节律。我们使用加权基因共表达网络分析（WGCNA）来分析差异表达基因与微生物群丰度之间的相关性。最富集的途径包括醛固酮调节的钠重吸收、内分泌和其他因子调节的钙重吸收、GABA能突触、氧化磷酸化、5-羟色胺能突触、多巴胺能突触和昼夜节律同步。本研究建立在我们之前研究的基础上，并增加了关于大脑转录组与肠道微生物群的特定相互作用和共同调节的新发现。肠道微生物群与宿主基因表达之间的相互作用突出了微生物群调节方法在改善家禽肠道健康和性能方面的潜在益处。
