Gut microbiome composition and diversity of wild-caught and hatchery-bred milkfish (Chanos chanos) fry

Abstract

Milkfish is the most produced finfish in the Philippines, with approximately 75 % of its fry sourced from hatcheries. Despite numerous studies on gut microbiota of wild and cultured fish species, the diversity and functional roles of the milkfish fry gut microbiome remain poorly understood. This study presents the first gut microbiome profiles of wild and hatchery-bred milkfish fry using 16S rRNA amplicon analysis. A total of 437 OTUs were recovered and significant differences in gut bacterial communities among fry from different sources was observed, indicating that habitat is a key determinant of gut microbiome diversity. The core gut microbiota analysis identified Vibrionaceae and Roseobacteraceae as the most common and abundant bacterial families across fry sources. However, Paenibacillaceae and Bacillaceae under Phylum Bacillota were dominant in wild fry sources, particularly Hamtic and Kirayan, whereas families belonging to Phyla Cyanobacteriota, and Thermodesulfobacteria were more prevalent in Dumagas and Kirayan hatchery fry sources. Functional predictions of the gut bacterial microbiome revealed 26 differentially abundant pathways between wild-caught and hatchery-bred fry, including those related to metabolism, organismal systems, cellular processes, environmental and genetic information processing. These findings highlight significant variations in gut microbiome composition, diversity, and functional potential across different sources of wild-caught and hatchery-bred fry. Understanding these source-specific microbial communities could provide insight into the development of interventions that can improve gut health and enhance milkfish hatchery practices. It can also generate information on ideal fry selection across local milkfish sources that will enhance larval productivity and survival in the succeeding nursery and grow-out culture stages.

Keywords: Gut microbiome; Hatchery-bred; Metagenome; Microbial diversity; Milkfish fry; Wild-caught.

Fig. 1

Sampling sites for the collection of wild and hatchery-bred milkfish fry. Wild-caught fry were collected from the Visayas (Hamtic and Kirayan) and Mindanao regions (Malita) of the Philippines. Hatchery-bred fry were collected from hatcheries in the Visayas (Retcem Hatchery in Dumangas and SEAFDEC Hatchery in Tigbauan) and Mindanao regions (ALT Hatchery at Panabo) of the Philippines. Note: Map lines delineate study areas and do not necessarily depict accepted national boundaries. Images were created using Google Earth.

Fig. 2

The top twelve abundant phyla are shown with the average relative abundance values. The remaining phyla and family composition are indicated as “Other”. The sample data are merged by group: Kirayan, Malita, and Hamtic (wild-caught group) and Tigbauan, Panabo, and Dumangas (hatchery-bred group).

Fig. 3

Venn diagram showing the differences and similarities of wild-caught (Wild) and hatchery-bred (Hatchery) C. chanos fry gut microbiome in the core bacterial families comprising 80% of the relative abundance values.

Fig. 4

Alpha diversity indices (Observed, Chao1, Shannon, and Inverse Simpson) of C. chanos wild-caught (Wild) and hatchery-bred (Hatchery) fry. The bottom whisker indicates the minimum value to the lower quartile while the top whisker indicates the upper quartile to the maximum value. The p-adjusted values obtained by the Wilcoxon Rank Sum Test on the comparison between the wild and hatchery groups are reflected for each alpha diversity measure (A). Principal Coordinate Analysis (PCoA) of Bray-Curtis dissimilarity exhibits beta diversity between wild and hatchery groups. The PERMANOVA p-values, found in the lower left side of the PCA indicate significant differences in the gut bacterial communities (B).

Fig. 5

The top twelve abundant phyla (A) and families (B) are shown with the average relative abundance values. The remaining phyla and family composition are indicated as “Other”. The sample data are merged by fry source (hatchery group – Dumangas, Hamtic, and Kirayan; wild group – Malita, Panabo, and Tigbauan).

Fig. 6

The gut bacteriome of wild-caught C. chanos fry sourced from Hamtic (A) and hatchery-bred fry from Tigbauan (B) visualized using the Krona Pie chart. Each chart represents the gut composition calculated as the average relative abundance for each family detected within each fry source.

Fig. 7

Alpha diversity indices (Observed, Chao1, Shannon, and Inverse Simpson) of C. chanos fry sources, Malita, Hamtic, and Kirayan (wild group) and Dumangas, Panabo, and Tigbauan (hatchery group). The bottom whisker indicates the minimum value to the lower quartile while the top whisker indicates the upper quartile to the maximum value. The p-adjusted values obtained by Kruskal-Wallis’s test are reflected for each alpha diversity measure while significant pairwise comparisons using Dunn’s post hoc test (p < 0.05) are indicated by an asterisk (A). Principal Coordinate Analysis (PCoA) of Bray-Curtis dissimilarity exhibits beta diversity across fry sources. The PERMANOVA p-value found in the lower left side of the PCoA indicates significant differences in the gut bacterial communities (B).

Fig. 8

Differentially abundant families between C. chanos fry gut from Hamtic wild fry and Panabo (A), Dumangas (B), and Tigbauan (C) hatchery fry sources. Only the top 10 bacterial taxa with the lowest adjusted p-values (p < 0.05) for each comparison are shown.

Fig. 9

Functional prediction of significant KEGG pathways (p adj < 0.05) between wild-caught hatchery-bred fry gut microbiota using PICRUSt2. A total of 26 pathways were statistically significant after the removal of pathways related to Human diseases, with pathways relating to (top) metabolism and (bottom) genetic and environmental information processing, cellular processes and organismal systems. The relative abundance (mean ± standard deviation for the three sources) of each KEGG pathway is shown as red (hatchery-bred fry sources) and blue (wild-caught fry sources) bar plots. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 10

Functional prediction of significant KEGG pathways (p adj < 0.05) in Hamtic wild fry and Tigbauan hatchery fry sources using PICRUSt2. Only the top 40 KEGG pathways with the lowest adjusted p-values (p adj < 0.05) for each of the pathway classes are shown. The relative abundance (mean ± standard deviation for the three replicates) of each pathway is shown as red (Hamtic wild-cauaght fry) and blue (Tigbauan hatchery-bred fry) bar plots. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)