Omics & gene networks

Unveiling region-specific gut transcriptomic responses in pigs fed increasing levels of Arthrospira platensis using RNAseq

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Abstract

Soybean meal is widely used as a primary protein source in pig nutrition; however, its production is associated with environmental concerns, including deforestation, soil degradation, and loss of biodiversity. Arthrospira platensis (AP), commonly known as Spirulina, is a protein-rich microalga with an advantageous amino acid profile and represents a promising and sustainable alternative protein source. This study investigated the effects of partial to complete replacement of soybean meal with AP on the gut gene expression of growing-finishing pigs. A total of 88 barrows and gilts were randomly assigned to one of four isoenergetic, isoproteic, and isoaminoacidic diets: a control diet containing 100% soybean meal (CTRL), and three experimental diets replacing 33%, 66%, or 100% (AP100) of soybean meal with AP. At slaughter (238 days of age), samples from the ileum and the colon were collected (15 pigs per diet per tissue), yielding 120 samples for whole-transcriptome analysis. Blood samples for biochemical analyses, histological specimens, and microbiota from both tissues were also collected to assess systemic and local health. RNA was extracted using the RNeasy Mini Kit (Qiagen), and libraries were prepared using the TruSeq Stranded mRNA Library Kit (Illumina). Sequencing on an Illumina HiSeq X platform generated 100-bp paired-end reads, with an average of 51 million raw reads per sample, and 98% retained after trimming. Mapping to the Sscrofa11.1 reference genome using STAR yielded 83% uniquely mapped reads (range: 61-96%). Differential expression (DE) analysis was conducted using the edgeR R package, comparing each AP diet with CTRL for each tissue. The main findings stem from the CTRL vs AP100 comparison, which revealed 20 DE genes in the ileum and 296 in the colon. Expression patterns differed between tissues: 19 of 20 DE genes in the ileum were downregulated, while 272 of 296 in the colon were upregulated. Functional gene set overrepresentation analysis using PANTHER and gene functional annotation using DAVID revealed that the AP100 diet in the ileum downregulated genes such as SPRED1, P2RY12 and MARCKS (immune signalling and inflammation), YOD1 and TBL1XR1 (protein degradation and stress), and NAA30 and ARL5B (protein stability and vesicle trafficking). In contrast, the colon showed upregulation of genes including NFKBID, GNLY and CIAO3 (inflammation and mucosal immune readiness), NUDT22 and SLC14A1 (epithelial stress and metabolic adaptation), and PIP5KL1 (immune signalling). These profiles suggest region-specific effects of the AP100 diet along the gut: reduced immune and stress responses in the ileum and enhanced mucosal defence and epithelial renewal in the colon. These findings support the potential of AP as a protein source in pig nutrition, capable of modulating the intestinal transcriptome of growing-finishing pigs and promoting intestinal immune and metabolic health through the regulation of inflammatory signalling.

Keywords: 2026

How to Cite:

Giannuzzi, D., Toscano, A., Don, G., Tono, V., Pegolo, S., Cecchinato, A., Schiavon, S. & Gallo, L., (2026) “Unveiling region-specific gut transcriptomic responses in pigs fed increasing levels of Arthrospira platensis using RNAseq”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285473. doi: https://doi.org/10.31274/wcgalp.23720

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