Multi-Region 16S rRNA Sequencing Reveals Host-Specific Ecological Structure in Sponge Microbiomes
Host-associated microbiomes are often considered stable and host-specific, yet these conclusions frequently rely on single-region 16S rRNA gene profiling, which provides limited taxonomic resolution and may obscure ecologically relevant patterns. Here, we analyzed microbiomes from seven sponge species representing the four Porifera classes and both high-microbial-abundance (HMA) and low-microbial-abundance (LMA) sponges using a multi-region 16S rRNA gene approach with a sponge-enriched reference database.Our results show that sponge microbiomes combine a stable higher-level taxonomic composition with strong host-specific differentiation at fine scales, revealing ecological structures not captured by conventional approaches.HMA sponges shared the same dominant lineages but were significantly different at the amplicon sequence variant (ASV) level. In contrast, LMA sponges exhibited simplified, highly specialized communities, often dominated by a few highly abundant taxa.Significant temporal variation was observed only in HMA sponges, driven primarily by shifts in the relative abundance of core ASVs rather than by large-scale community turnover.