Reveal your microbes, and i'll reveal your origins: geographical traceability via Scomber colias intestinal tract metagenomics

Abstract

The commercial demand for small pelagic fish, such as Atlantic chub mackerel (Scomber colias), renders them susceptible to provenance fraud. Scomber colias specimens intestinal tract bacteriome from five distinct fishing areas along the Portuguese Atlantic coastline were analyzed by 4th-generation sequencing. Bacteria diversity indices and differential abundance revealed dissimilarities in operational taxonomic unit (OTU) abundance among specimens from distinct fishing sites. Random forest-based model yielded an 85% accuracy rate in attributing sample provenance based on intestinal tract bacteriome OTU relative abundance. Further refinement of microbial features using Indicator Species Analysis, Linear Discriminant Analysis Effect Size (LEfSe) and OTU Gini scores enabled the identification of 3-5 bacterial OTU location biomarkers per fishing site. The intestinal tract bacteriome revealed sequences linked to pathogenic bacteria, particularly in specimens from Center-North and Center-South fishing areas. While this doesn't imply active pathogens, it highlights potential public health concerns and complements efforts to improve seafood microbiological quality and traceability.

Keywords: Atlantic Chub mackerel; Intestinal tract metagenomics; Provenance; Small pelagic fish species; Traceability.

Fig. 1

Location of the five sampling areas along the west and south coasts of Portugal

Fig. 2

Scomber colias total length (A), weight (B), and Fulton condition index (C) of the specimens collected from the five sampling areas along the Portuguese west and south coast (N = 30 replicates per site; letters denote statistically significant differences at p < 0.05)

Fig. 3

Rarefaction curves (A), alpha diversity (B), phylum relative abundance (C), and principal coordinate analysis (beta-diversity PCoA, D) Operational Taxonomic Units of the intestinal tract microbiome of the S. colias specimens captured at the five surveyed fishing areas (N = 30 replicates per site; asterisks denote significant differences at p < 0.05 (*), p < 0.01 (**), and p < 0.001 (***) using the Kruskal-Wallis test)

Fig. 4

Phylogenetic heat tree comparison between the intestinal tract microbiome of S. colias specimens captured in the five surveyed fishing areas (N = 30 replicates per site; colored branches denote significantly different abundance of a specific taxon at p < 0.05 through a Kruskal-Wallis test)

Fig. 5

Random Forest biplot (A) and model training and testing accuracy heatmaps (B) based on the S. colias intestinal tract microbiome OTU relative abundances assessed for the animals captured in the five surveyed fishing areas

Fig. 6

Scomber colias intestinal tract microbiome LEfSe (Linear Discriminant analysis Effect Size) Top 15 OTU Linear Discriminant (LDA) score features by site

Fig. 7

Scomber colias intestinal tract microbiome indicator species point biserial statistical value heatmap per phylum of the five fishing areas considered

Fig. 8

Scomber colias intestinal tract microbiome biomarker OTUs relative abundance and overall total OTU abundance were assessed for each sampling area

Fig. 9

The abundance of potentially pathogenic OTUs in the intestinal tract microbiome of S. colias in the five fishing areas considered