Host-specific Gut Microbiomes in Three Estuarine Crabs

Abstract

Crab-associated microbiomes play critical roles in host nutrition, immunity, and ecological adaptation, yet remain poorly characterized for many ecologically and economically important species. Here, we present the first high-throughput 16S rRNA gene sequencing analysis of gut microbiomes in three Indo-Pacific estuarine crabs: the crucifix crab (Charybdis feriata), red-spotted swimming crab (Portunus sanguinolentus), and giant mud crab (Scylla serrata). One individual from each crab species was sampled, and its gut microbiome was sequenced, yielding over 100,000 high-quality non-chimeric reads per sample with greater than 96% merge success, ensuring robust taxonomic resolution and balanced coverage across hosts. Phylum-level profiles revealed clear host-specific signatures: C. feriata and S. serrata were dominated by Firmicutes (48% and 45%, respectively), whereas P. sanguinolentus was strongly enriched in Actinobacteria (76%). Alpha diversity analyses showed that C. feriata exhibited the highest richness and evenness, S. serrata intermediate, and P. sanguinolentus the lowest. Beta diversity analysis confirmed significant host-specific separation among species (PERMANOVA, p < 0.05), with P. sanguinolentus clustering distinctly from the other two. The ecological interpretation suggests that Firmicutes-rich microbiomes facilitate fermentation and nutrient processing, whereas Actinobacteria dominance may reflect specialized metabolic or antimicrobial traits contributing to reduced diversity. Together, these results demonstrate statistically significant, host-specific gut microbiome differences among the three crab species and establish a baseline for future ecological and applied research in aquaculture and marine biotechnology.