Characterizing Gene-Level Adaptations in the Gut Microbiome During Viral Infections: The Role of a Fucoidan-Rich Extract

The gut microbiome plays a crucial role in modulating immune responses during acute viral infections. This study examined the effects of a Fucoidan-rich extract from Saccharina latissima on gut microbiota composition, intestinal inflammation, and microbial functional gene content in participants infected with Dengue or Oropouche virus. Fecal samples were collected at baseline, day 28, and day 90 from 90 healthy adults, some of whom contracted the virus during the study period. Functional gene analysis was conducted using two approaches—the Kruskal-Wallis H test and Linear Discriminant Analysis Effect Size—applied to ortholog-level data normalized by read count and gene copy number. Infected participants exhibited significantly lower Lachnospiraceae-to-Enterobacteriaceae (LE) ratios, indicating increased intestinal inflammation. High-dose Fucoidan treatment led to a significant reduction in the LE ratio (p = 0.006), suggesting a strong anti-inflammatory effect. Microbiome analysis revealed a shift from dysbiosis to a more balanced composition by the end of the study, characterized by increased abundances of Akkermansia muciniphila, Bifidobacterium adolescentis, and B. longum, along with decreased pro-inflammatory taxa such as Fusobacterium. Genetic analysis provided distinct yet complementary insights into the microbiome’s functional responses to infection and therapeutic modulation by Fucoidan. These findings highlight the therapeutic potential of high-dose Fucoidan in reducing gut inflammation and promoting microbiome recovery following viral infections.