Avian

Faecal Microbiome Comparison of Two Goose Breeds Under Identical Rearing Conditions

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Abstract

Introduction. Microbiome profiling of faecal material is a robust method for characterising host-microbe relationships, comparing ecological communities, and identifying taxonomic biomarkers associated with phenotype. When experimental variables are strictly controlled, breed-specific signals may manifest as differences in diversity structure and the relative abundance of specific clades. This study compared the faecal microbiota of two goose breeds reared in Poland, Pomorska (POM) and White Kołuda® (KOL), to identify breed-specific differences in richness, diversity, and taxonomic composition. It was hypothesised that distinct ancestry and breeding histories could result in divergent microbiota despite identical rearing and feeding conditions. Materials and Methods. Faecal samples were collected rectally post-slaughter from eight birds per breed (n=16 total), and each pair of samples was pooled prior to analysis, resulting in two groups (POM n=4, KOL n=4). All birds were housed under identical environmental conditions. The V3-V8 regions of the 16S rRNA gene were amplified using universal primers 337F/1391R and sequenced with Oxford Nanopore native barcoding (1D). Taxonomic classification was performed using UBLAST. Low-abundance features were removed by filtering OTUs/ASVs with total counts less than 10 across all samples. Alpha diversity was assessed using the Chao1 index (richness) and the Shannon index (richness and evenness), and statistical significance was evaluated using the Wilcoxon test with Benjamini-Hochberg FDR correction. Beta diversity was assessed using principal coordinates analysis (PCoA) of Bray-Curtis dissimilarities, with PERMANOVA applied for group separation. For differential-abundance visualisation, counts were normalised using Total Sum Scaling (TSS). All calculations and visualisations were conducted in MicrobiomeAnalyst. Results. Alpha diversity: Chao1 richness did not differ significantly between breeds or at the Order, Family, or Genus taxonomy levels (p=0.551, FDR=0.9; Wilcoxon, p >0.05). Shannon metrics also did not indicate significant differences in richness or evenness (p=0.885; FDR=0.885; Wilcoxon, p >0.05). Beta diversity: ordination did not reveal distinct clustering by breed, and PERMANOVA detected no significant separation of community structure (F=0.406; R²=0.063; p=0.753), indicating that breed explained approximately 6% of variance. Exploratory taxonomic shifts: descriptive log₂ fold-change inspection of aggregated counts identified the largest directional effects. Differences at the genus level were not statistically significant; however, some differences between breeds were observed at the Order taxonomy level for Fusobacteriales, Deferribacterales, Elusimicrobiales, Enterobacterales, and Spirochaetales. As these fold-changes were derived from group-level aggregates, validation on per-sample data is required. Conclusions. Under identical husbandry conditions, the faecal microbiota of Pomorska and White Kołuda® geese did not differ significantly at the community level (alpha or beta diversity). However, exploratory patterns suggest candidate clades, such as Fusobacteriales and Deferribacterales, that may contribute to subtle breed-associated profiles. Larger cohorts with per-sample differential testing and phylogeny-aware methods are necessary to confirm breed-specific biomarkers.

Keywords: 2026

How to Cite:

Koseniuk, A., Połtowicz, K., Oczkowicz, M. & Kłos, K., (2026) “Faecal Microbiome Comparison of Two Goose Breeds Under Identical Rearing Conditions”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285015. doi: https://doi.org/10.31274/wcgalp.23624

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