Gut microbiome-brain crosstalk in the early life of chicken reveals the circadian regulation of key metabolic and immune signaling processes

Background 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. Several studies have revealed how neurological components interact with GALT physiology and the microbiome population in the host. Keeping these factors in regard, we are studying the correlation between differential gene expression in the chicken brain and microbiota abundance during circadian rhythms. To study rhythmic oscillations in immune genes, 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 hours to characterize the brain transcriptomes. Each sample's RNA was extracted, and 36 mRNA libraries were created and sequenced using Illumina technology, followed by data processing, count data generation, and differential gene expression analysis. Results We generated an average of 17.5 million reads per library for 237933593.3 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-hr 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. Conclusions Photoperiods and robust 24-hr rhythms differentially influenced key neurochemical and mitochondrial pathways during early life. Furthermore, the interaction between gut microbiota and host gene expression highlights the role that specific microbial taxa (like Lactobacillus) may play in the early-life regulation of homeostasis and provides promising avenues for application.