Gut microbial communities constitute a compartment of crucial importance in regulation of homeostasis of multiple host physiological functions as well as in resistance towards environmental pollutants. Many chemical contaminants were shown to constitute a major threat for gut bacteria. Changes in gut microbiome could lead to alteration of host health. The access to high-throughput sequencing platforms permitted a great expansion of this discipline in human health while data from ecotoxicological studies are scarce and particularly those related to aquatic pollution. The main purpose of this review is to summarize recent body of literature providing data obtained from microbial community surveys using high-throughput 16S rRNA sequencing technology applied to aquatic ecotoxicity. Effects of pesticides, PCBs, PBDEs, heavy metals, nanoparticles, PPCPs, microplastics and endocrine disruptors on gut microbial communities are presented and discussed. We pointed out difficulties and limits provided by actual methodologies. We also proposed ways to improve understanding of links between changes in gut bacterial communities and host fitness loss, along with further applications for this emerging discipline.

Recent studies suggest an association between particulate matter (PM) air pollution and gastrointestinal (GI) disease. In addition to direct deposition, PM can be indirectly deposited in oropharynx via mucociliary clearance and upon swallowing of saliva and mucus. Within the GI tract, PM may alter the GI epithelium and gut microbiome. Our goal was to determine the effect of PM on gut microbiota in a murine model of PM exposure via inhalation. C57BL/6 mice were exposed via inhalation to either concentrated ambient particles or filtered air for 8-h per day, 5-days a week, for a total of 3-weeks. At exposure's end, GI tract tissues and feces were harvested, and gut microbiota was analyzed. Alpha-diversity was modestly altered with increased richness in PM-exposed mice compared to air-exposed mice in some parts of the GI tract. Most importantly, PM-induced alterations in the microbiota were very apparent in beta-diversity comparisons throughout the GI tract and appeared to increase from the proximal to distal parts. Changes in some genera suggest that distinct bacteria may have the capacity to bloom with PM exposure. Exposure to PM alters the microbiota throughout the GI tract which maybe a potential mechanism that explains PM induced inflammation in the GI tract.

Intestines contain a large number of microorganisms that collectively play a vital role in regulating physiological and biochemical processes, including digestion, water balance, and immune function. In this study, we explored the effects of ammonia stress on intestinal inflammation, the antioxidant system, and the microbiome of the Asian clam (Corbicula fluminea). Exposure to varying ammonia concentrations (10 and 25 mg N/L) and exposure times (7 and 14 days) resulted in damage to C. fluminea intestinal tissue, according to histological analysis. Furthermore, intestinal inflammatory responses and damage to the antioxidant system were revealed through qPCR, ELISA, and biochemical analysis experiments. Inflammatory responses were more severe in the treatment group exposed to a lower concentration of ammonia. High-throughput 16S rDNA sequencing showed that ammonia stress under different conditions altered intestinal bacterial diversity and microbial community composition, particularly impacting the dominant phylum Proteobacteria and genus Aeromonas. These results indicate that ammonia stress can activate intestinal inflammatory reactions, damage the intestinal antioxidant system, and alter intestinal microbial composition, thereby impeding intestinal physiological function and seriously threatening the health of C. fluminea.

Aquatic animals under waterborne metal exposure are also very likely exposed to elevated dietary metals. This study quantified the simultaneous uptake of dietary and waterborne Cd in gastrointestinal tracts (GT) of marine yellowstripe goby using a dual stable isotope tracer method. The Cd spiked diet (10–100 μg g−1, 111Cd as tracers) were fed to the fish as a single meal, and then the fish were exposed to waterborne Cd (0–500 μg L−1, 113Cd as tracers) for 48 h, during which the time-course uptake of Cd in the stomach and intestine was determined. The findings revealed that the dietary Cd uptake mainly occurred within 12 h after feeding. The fish exposed to 500 μg L−1 waterborne Cd showed significantly lower Cd assimilation efficiency (2.07%) than the control group (3.48%) at the dietary Cd of 100 μg g−1. Moreover, during 4–12 h when there was chyme in the GT, the waterborne Cd uptake in the intestine was lowest but the stomach showed the highest waterborne Cd uptake rate. The uptake of dietary and waterborne Cd, and the relative importance of dietary vs waterborne Cd was positively correlated with the Cd concentration in the chyme. Overall, this research demonstrated that there was interaction between dietary and waterborne Cd uptake in the GT of marine fish. The simultaneous uptake of metal from two routes is far more complex than the situation of a single route of metal uptake, which should be evaluated in determining metal bioaccumulation and toxicity in both laboratory and field metal exposure scenario.