Multi-Organ Metatranscriptomics Establishes Organ-Specific Functional Baselines in the Crested Ibis (Nipponia nippon)

The crested ibis (Nipponia nippon) is an iconic East Asian species on the International Union for Conservation of Nature's (IUCN) Red List, with recurrent stress-related sudden death reported in captivity and in the wild. However, the mechanisms underlying stress responses remain poorly characterized.

Using opportunistic post-mortem samples, we generated, to our knowledge, the first organ-resolved metatranscriptomic reference dataset for this species in a stress-associated context. Matched libraries from small intestine, liver, spleen, and lung were sequenced and processed using a unified pipeline; microbial transcriptional activity was quantified following host and rRNA removal and stringent detection criteria, enabling concurrent readouts of community composition and functional gene expression.

Transcriptional activity was intestine-centric, whereas liver, spleen, and lung harbored low-load communities with limited taxon sharing. The small intestine was dominated by the aquatic-associated Cetobacterium somerae (~54.8%), consistent with fish-based feeding, while Romboutsia was scarce, suggesting a weak butyrate-producing guild. Functionally, transcripts were enriched for small-molecule metabolism, nucleotide/cofactor turnover, central carbon conversion, and membrane/envelope-associated precursor pathways. Stratified pathway analysis further resolved uneven classified contributions: Paraclostridium bifermentans spanned the broadest classified pathway repertoire, Cetobacterium somerae contributed more strongly to nucleotide-linked functions, and Clostridium perfringens retained a more distinctive inositol-related branch. Antimicrobial resistance (AMR)-linked transcripts in the intestine were dominated by target-site mechanisms (elongation factor Tu (EF-Tu), RNA polymerase β' subunit (rpoC) and DNA gyrase subunit A (gyrA)) with a low-level ErmQ-associated macrolide-lincosamide-streptogramin (MLS) resistance signature, consistent with background expression of core targets.

This organ-resolved dataset provides a practical baseline for microbiome, pathogen, and resistance surveillance in captive crested ibis, and a reference for future comparisons among captive, wild, and reintroduced populations. AMR signals are best read as contextual markers rather than phenotypic resistance and can serve as auxiliary sentinels alongside composition and function. Overall, the dataset provides a reusable framework for health assessment and conservation planning.