Quick fish sampling for disease diagnostics: Microbiome sampling guide

Interactions between microbes associated with the host, other organisms present in the system and the environment itself are increasingly recognised to contribute to aquatic animal diseases. Those microbiome assemblages and their functions are extremely diverse and poorly understood. They vary over time in water and between host tissues and organs. High-throughput sequencing technologies (multi-omics) and bioinformatics analysis of complex microbiomes can provide biological insights offering new opportunities for early detection of pathogens and disease mitigation strategies. Similarly, such approaches are being applied to study the effect of locally available ingredients for use in fish feeds and their impact on fist gut microbiome and the health of the pond environment—optimising the growing conditions on-farm. WorldFish and partners developed this quick guide for microbiome sampling from fish skin/gills mucus swabs, internal organs (e.g. gut) and water samples from ponds, hatcheries tanks, river, and canals.

A free online training course on microbiome sampling is also available on Learn.ink.


Publisher: WorldFish

Rights: Creative Commons Attribution-NonCommercial.


Quick fish sampling for disease diagnostics: Package of practices

Quality biological sampling is a fundamental requirement for all kinds of work on diagnosing diseases and screening for pathogens. Fish sampling requires specific techniques and skills to collect good biological samples for accurate disease diagnosis. This package of practices developed by WorldFish and partners provides advice on fish sampling protocols for routine disease diagnostics and outbreak investigations in tilapia, carp and catfish production systems. These sampling protocols provide guidance and training to project team members, researchers, resident veterinarians, extension officers and farmers tasked with collecting quality biological samples for laboratory diagnosis whenever disease outbreaks occur on farms or hatcheries. A free online introductory course on fish sampling for disease diagnostics is also available via Learn.ink.