The Impact of Microbiome and Microbiota-Derived Sodium Butyrate on Drosophila Transcriptome and Metabolome Revealed by Multi-Omics Analysis

Abstract

The host microbiome plays an important role in regulating physiology through microbiota-derived metabolites during host-microbiome interactions. However, molecular mechanism underly host-microbiome interactions remains to be explored. In this study, we used Drosophila as the model to investigate the influence of microbiome and microbiota-derived metabolite sodium butyrate on host transcriptome and metabolome. We established both a sterile Drosophila model and a conventional Drosophila model to demonstrate the role of sodium butyrate. Using multi-omics analysis, we found that microbiome and sodium butyrate could impact host gene expression patterns in both the sterile Drosophila model and the conventional Drosophila model. The analysis of gut microbial using 16S rRNA sequencing showed sodium butyrate treatment also influenced Drosophila bacterial structures. In addition, Drosophila metabolites identified by ultra-high performance liquid chromatography-MS/MS were shown to be affected by sodium butyrate treatment with lipids as the dominant changed components. Our integrative analysis of the transcriptome, the microbiome, and the metabolome data identified candidate transcripts that are coregulated by sodium butyrate. Taken together, our results reveal the impact of the microbiome and microbiota-derived sodium butyrate on host transcriptome and metabolome, and our work provides a better understanding of host-microbiome interactions at the molecular level with multi-omics data.

Gut Microbiota Dysbiosis Influences Metabolic Homeostasis in Spodoptera frugiperda

“…Gut microbes play important roles in insect growth, development, and many physiological processes of the individual to maintain host health through regulating gene expression ( Raymann et al, 2017 ; Schoeler and Caesar, 2019 ; Zhou et al, 2021 ). It has been shown that gut microbes are important in absorbing nutrition, protection from parasites and pathogens, modulation of immune responses, and communications with environment ( Engel and Moran, 2013 ; Jang and Kikuchi, 2020 ).…”

“…The dysbiosis of intestinal microbes can affect the metabolic process. In Drosophila , we have demonstrated the impact of microbiome and microbiota-derived sodium butyrate on host transcriptome and metabolome with multi-omics data ( Zhou et al, 2021 ). Our studies revealed that the changes in composition and diversity of insect’s gut microbial community can influence important physiological functions in the host through regulating gene expression.…”

RNA-Seq and 16S rRNA Analysis Revealed the Effect of Deltamethrin on Channel Catfish in the Early Stage of Acute Exposure

“…Bacterial DNA was purified using the TIANamp Bacteria DNA kit (Tiangen Biotech Inc., Beijing, China), following the manufacturer’s protocols. A region encompassing the V3–V4 hypervariable regions of the 16S rRNA gene was amplified using the primers 341F (CCTACGGGNGGCWGCAG) and 806R (GGACTACHVGGGTATCTAAT) ( 52 ). The PCR amplification system comprehended 20 μL, including 10 μL premixed Taq (Takara), 1 μL of each primer (10 μM), 2 μL gDNA, and 6 μL ddH 2 O.…”

How Gut Microbes Nurture Intestinal Stem Cells: A Drosophila Perspective

“…Epithelial injury causing exposure of crypt ISCs to butyrate suppresses ISC proliferation and mucosal wound healing via Foxo3 regulation [113]. In Drosophila, the addition of sodium butyrate in the diet can effectively extend viability and life span [114] and microbiota-derived sodium butyrate impacts the microbiota composition and host gene expression [115]. Sodium butyrate was found to induce Firmicutes and to suppress Proteobacteria, while at the gene expression level, it was shown to have an inhibitory effect in key biological processes such as cell proliferation [115].…”