Assessing Adverse Effects of Pollutants on Host-Associated and Free-Living Microbiomes Using Omics

Tamara García-Barrera, University of Huelva; Maria Carmen Collado, Institute of Agrochemistry and Food Technology; Alexander Feckler, RPTU Kaiserslautern-Landau; Daniel Globish, Uppsala University

The session, “Assessing Adverse Effects of Pollutants on Host-Associated and Free-Living Microbiomes Using -Omics,” was held during the SETAC Europe 33rd Annual Meeting from 30 April–4 May in Dublin. This interdisciplinary session aimed at integrating researchers from environmental analysis, ecotoxicology and nutrition among others that work with different models including plants, animals and humans. The session focused on recent advances related to the impact of environmental pollutants on host-microbiota mutualisms that further affect behavior, development, immune response or nutrient processing. An important place was also given to -omics methodologies involving metataxonomics, metabolomics, metallomics and other meta-omics.

Environmental pollutants pose a growing concern due to an ever-increasing hazard to humans and other organisms. Recently, a great number of studies have pointed out the importance of microbiota-host mutualisms that impact the hosts’ behavior, development, immune response and nutrient processing. Moreover, microbial communities are likewise critical for water quality, soil fertility and ecosystem functioning. However, microbiota are sensitive to diet and environmental pollutants, such as trace elements, heavy metals, pesticides, persistent organic pollutants, nanomaterials and food additives. Despite significant advances in the field of microbiome research during recent years, we are still facing the challenge of predicting stress responses of complex microbial communities. Understanding the response of microbial communities to environmental pollutants is a rapidly growing scientific field, which can be evaluated by using -omic methodologies, such as metataxonomics, metabolomics, metallomics, metaproteomics, metatranscriptomics and metagenomics.

This interdisciplinary topic is also of interest to researchers from other fields, such as nutrition, environmental analysis and medicine, who are working on different model systems (e.g., humans, animals and plants). The main objective of this session was to present scientific and analytical advances related to this challenging field by integrating researchers with different backgrounds to delve into the microbiota–pollutant interactions as well as current methodologies that can be applied. We invited contributions dealing with but that were not limited to:

• Integrative -omic and meta-omic approaches to characterize the effects of pollutants (or nutrients) on host-associated and free-living microbiomes
• Stressors’ effects on human or environmental microbial diversity, especially those that contribute to ecosystem functioning or phenotypic endpoints of health
• Single or multiple stressor(s) across different environments or host species with the purpose to derive generalizable insights into microbiomes’ stress responses
• Identification of microbial indicators (e.g., taxa, keystone species or guilds) responsive to single or multiple stressors, highlighting community-level signatures of stressed microbiomes

Presented Works

Four platform presentations, three poster spotlight presentations and nine posters were presented during the session. The first oral presentation was given by Nicholas Creusot from the Platforme Bordeaux Metabolome (France), who presented “Meta-Metabolomics to Uncover Short Versus Long Term Response of Periphytic Microbiome to a Model Fungicide.” He highlighted that at environmentally relevant concentrations, the fungicide tebuconazole can trigger fast changes of biofilms’ meta-metabolome. This might lead to mid- or long-term changes of the whole community metabolism as noted for the enzymatic activities as well as structural changes, increasing the abundance of autotrophs. Afterwards, Phillip Ankley from the University of Saskatchewan (Canada) presented “Effects of Erythromycin on Juvenile Rainbow Trout Gut Microbiome.” He concluded that erythromycin caused perturbations of the juvenile rainbow trout microbiome that continued beyond exposure. These alterations lead to changes in predicted functional pathways performed by the gut microbiome. Erythromycin was eliminated and/or transformed quickly in juvenile fish, leading to elevated metabolite in plasma at day seven. Later, Gema Rodríguez Moro from the University of Huelva (Spain) presented “A combination of -omics approaches to evaluate the effects of metabolic disorders of the non-steroidal anti-inflammatory drug diclofenac in Mus musculus mice. Antagonism with Selenium.” She described that diclofenac exposure and supplementation with selenium in mice causes alterations in the gut microbiota composition and in the brain, testicular and gut metabolomes, and that the combination of -omic methodologies is needed to understand the xenobiotics–microbiota intertwined mechanisms in the organisms. Finally, Laura-Fabienne Fröhlich, Helmholtz Centre for Environmental Research (Germany), presented “A High-Throughput Approach to Explore the Transformation Potential of the Human Gut Microbiome for Xenobiotic Interaction and Internal Exposure.” She explained that their findings proved the applicability of the Simplified Human Intestinal Microbiota (SIHUMIx) in combination with non-targeted LC-HRMS in high-throughput screening for toxicant transformation in the microbiome. The prodrug sulfasalazine was found to be degraded, and one of the transformation products was quantified. Furthermore, biodegradation was observed, and transformation products were identified for multiple compounds after 24 hours.

The first spotlight poster was presented by Pedro Inostroza from the University of Gothenburg (Sweden) with the title “Structural Responses of Bacterial Communities from Water, Biofilm, and Sediments to Environmental Parameters with Particular Emphasis on Antibiotic Stress at River Basin Level.” Their study suggested that there were significant community changes due to nutrient and antibiotic pressure in distinct parts if the river basin was linked to different land uses. They recognized that the mixture of antibiotics was one of the main drivers shaping the structure of bacterial communities from different environmental compartments in the study. After that, Maria Carmen Collado from the Institute of Agrochemistry and Food Technology, National Research Council (Spain) presented “Breast Milk Elemental Profile is Associated with Postnatal Maternal Factors.” She highlighted that diet can shape the composition in relevant metals for infant nutrition. She also noted that other non-controllable variables, such as type of birth, were also found to determine elemental composition, and in turn, the elemental composition was related to the breast milk microbiota. Finally, Cecilio Parra Martínez from the University of Huelva (Spain) presented “Exploring the Effects of ‘Chemical Cocktails’ into Brain and Testicular Metabolomes. Intertwined Mechanisms with Gut Microbiota and Selenium.” He explained that untargeted testicular and brain metabolomics in mice combining GC-MS and UHPLC-QTOF-MS revealed important impairments caused by chemical cocktails of pollutants and that some of them were modulated, almost partially by selenium supplementation. Interestingly, novel associations were determined between brain and testicular metabolites and gut microbes suggesting an intertwined mechanism, but they also disappeared or changed after selenium supplementation.

The following posters were also presented during the session:

• Daniela Maria Pampanin, University of Stavanger (Norway): The Influence of Florfenicol Coated Fish Feed on the Gene Expression of the Atlantic Salmon (Salmo salar) Gastrointestinal Tract and its Microbiome
• Alexander Feckler, RPTU Kaiserslautern-Landau (Germany): Antimicrobial Effects on the Gut Microbiome of a Leaf-Shredding Amphipod
• Ilaria Bernardini, University of Padua (Italy): Consequences of the Fragrance Amyl Salicylate on the Mediterranean Mussel Mytilus galloprovincialis and on Host-Microbiota Interactions
• Nicola Montemurro, IDAEA-CSIC (Spain): Impact of Contaminants of Emerging Concern on Groundwater Microbial Communities
• Rut Fernandez-Torres, University of Seville, (Spain): Bioavailability of flumequine and diclofenac in a mice model exposed a “chemical cocktail.” Impact of antibiotic-induced depletion of gut microbiota and selenium supplementation
• Rut Fernandez-Torres, University of Seville (Spain): Impact of a metal-drug “chemical cocktail” on mice bile acids profile
• Abdullah Aleidan, UEA (United Kingdom): Metabarcoding of Multiple Microbial and Metazoan Taxa in Grossly Contaminated Estuaries Reveals Their Differential Sensitivity to Metal Toxicity
• Olga Pantos, ESR (New Zealand): Not Just Plastic: Understanding the Complex Micro-Environment of Wastewater Treatment Plant Microplastics and Their Role in Shaping the Plastisphere
• Daniel Globisch, Uppsala University (Sweden): Chemical Biology Tools to Discover Unknown Bioactive Microbiome Metabolites

Author’s contact: Tamara García-Barrera, [email protected]