Gut microbiota of aquatic organisms: A key endpoint for ecotoxicological studies

Environ Pollut. 2019 May;248:989-999. doi: 10.1016/j.envpol.2019.02.101. Epub 2019 Mar 2.


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.

Keywords: 16S; Aquatic environment; Ecotoxicology; Intestine; Microbiota; Pollutants.

Publication types

  • Review

MeSH terms

  • Amphibians / microbiology
  • Animals
  • Aquatic Organisms / microbiology
  • Bacteria / classification
  • Bacteria / drug effects*
  • Bacteria / genetics
  • Ecotoxicology
  • Endocrine Disruptors / toxicity*
  • Fishes / microbiology
  • Gastrointestinal Microbiome / drug effects*
  • Halogenated Diphenyl Ethers / toxicity*
  • Humans
  • Metals, Heavy / toxicity*
  • Microbiota / drug effects
  • Pesticides / toxicity*
  • Plastics / toxicity*
  • RNA, Ribosomal, 16S / genetics
  • Water Pollutants, Chemical / toxicity*


  • Endocrine Disruptors
  • Halogenated Diphenyl Ethers
  • Metals, Heavy
  • Pesticides
  • Plastics
  • RNA, Ribosomal, 16S
  • Water Pollutants, Chemical