Repository logo

Investigating the Potential Effects of Pollutants on the Rainbow Trout (Oncorhynchus mykiss) Gastrointestinal Microbiome



Journal Title

Journal ISSN

Volume Title





Degree Level



The gastrointestinal (GI) microbiome is an important aspect of organismal health with the ability to affect host nutrition, metabolic processes, and immune system development. Changes to the GI microbiome can affect any of these or other host functions and could result in negative effects on overall fish health. While it is known that low concentrations of pollutants can affect environmental microbes, little information is known about the effects of environmental contaminants on GI microbiota in fish. I conducted two studies to explore the potential effects of chemicals on the GI microbiome of fish. The pilot study aimed to develop a method to extract and analyse the microbiota within the GI tract of fish. It also compared the microbiomes of two phylogenetically distant fish species, lake sturgeon (Acipenser fulvescens) and rainbow trout (Oncorhynchus mykiss), under controlled conditions. The second study aimed to discover the effects of two common environmental contaminants, benzo(a)pyrene (BaP) and triclosan, on the GI microbiome in rainbow trout. In both experiments, DNA was extracted from intestinal contents of fish and GI microbiota were evaluated using next-generation sequencing techniques and downstream applications. The pilot study suggested GI microbial communities were more diverse in rainbow trout and were significantly different from those communities in lake sturgeon. Due to the similarities in rearing conditions and diet in the laboratory, microbial differences between the two species may indicate evolutionary differences. In the second study, the GI microbiomes of rainbow trout were compared after exposure to four different diets (solvent control, 5.09 mg/kg BaP, 40.7 mg/kg BaP and a mixture of 4.58 mg/kg BaP + 2.89 mg/kg triclosan) and sampled at each of three time points (exposure: one and 21 days; recovery: 28 days). Proteobacteria was dominant across all treatments and at all time points. Firmicutes, Tenericutes or Fusobacteria was the next most dominant phylum, depending on treatment and/or time. There were significant differences in both treatment and time. Composition was significantly different among treatment groups during each individual time, and time points differed for all treatments except the solvent control. Differences over time may be due to initial introduction of contaminants, followed by coping mechanisms, and recovery when exposure was removed. Together, these results suggest that fish species, chemical exposure, and duration of exposure all contribute to differences in the GI microbial composition of fish. Thus, the complexity of this system needs to be considered when identifying potential biomarkers of pollutant exposure in wild fish.



Lake Sturgeon, Rainbow Trout, Benzo(a)pyrene, Triclosan, Gastrointestinal Microbiome, 16S rRNA, Next-generation Sequencing



Master of Science (M.Sc.)


Toxicology Centre




Part Of