Sampling fish gut microbiota - A genome-resolved metagenomic approach

Area of Science:

• Microbiology
• Genomics
• Aquatic Biology

Background:

• Functional metagenome studies in teleosts are limited by challenges in extracting high-quality microbial DNA from intestinal samples.
• The zebrafish gut microbiota's functional landscape remains understudied due to a lack of standardized sampling methods.

Purpose of the Study:

• To systematically evaluate four distinct sampling methods for zebrafish gut microbiota.
• To compare genome-resolved metagenomics and 16S metabarcoding for assessing sample types.
• To provide guidance on selecting optimal sampling strategies for teleost microbiome research.

Main Methods:

• Tested four zebrafish gut microbiota sampling methods: tank faeces, whole gut, intestinal content, and extruded gut material.
• Utilized genome-resolved metagenomics and 16S metabarcoding for comparative analysis.
• Included water samples as environmental controls to assess contamination impact.

Main Results:

• Significant differences were observed across sample types in bioinformatic processing, metagenome co-assemblies, and generated metagenome-assembled genomes (MAGs).
• Functional potential, MAG coverage, and population microdiversity varied by sampling method.
• Environmental contamination from water samples influenced data interpretation.

Conclusions:

• No single sampling method is universally optimal; the best choice depends on specific research goals.
• Understanding environmental influences and methodological variations is crucial for accurate fish microbiome analysis.
• This study offers a framework for designing effective functional metagenome studies on teleost microbiomes.