The gut microbiome and resistome of yellow perch (Perca flavescens) living in Minnesota lakes under varying anthropogenic pressure
Omar Jimenez-Lopez,
Tui Ray,
Christopher Dean,
Ilya Slizovskiy,
Jessica Deere,
Tiffany Wolf,
Seth Moore,
Alexander Primus,
Jennifer Høy-Petersen,
Silje Finstad,
Jakob Mo,
Henning Sørum,
Noelle Noyes
Affiliations
Omar Jimenez-Lopez
Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, MN, USA
Tui Ray
Shriners Children's Genomics Institute, FL, USA
Christopher Dean
Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, MN, USA
Ilya Slizovskiy
Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA; Purdue Applied Microbiome Sciences Program, Purdue University, West Lafayette, IN, USA
Jessica Deere
Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, MN, USA
Tiffany Wolf
Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, MN, USA
Seth Moore
Grand Portage Band of Lake Superior Chippewa, MN, USA
Alexander Primus
Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, MN, USA; Hubbs-SeaWorld Research Institute, CA, USA
Jennifer Høy-Petersen
Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, MN, USA; Shriners Children's Genomics Institute, FL, USA; Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA; Purdue Applied Microbiome Sciences Program, Purdue University, West Lafayette, IN, USA; Grand Portage Band of Lake Superior Chippewa, MN, USA; Hubbs-SeaWorld Research Institute, CA, USA; Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
Silje Finstad
Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, MN, USA; Shriners Children's Genomics Institute, FL, USA; Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA; Purdue Applied Microbiome Sciences Program, Purdue University, West Lafayette, IN, USA; Grand Portage Band of Lake Superior Chippewa, MN, USA; Hubbs-SeaWorld Research Institute, CA, USA; Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
Jakob Mo
Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, MN, USA; Shriners Children's Genomics Institute, FL, USA; Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA; Purdue Applied Microbiome Sciences Program, Purdue University, West Lafayette, IN, USA; Grand Portage Band of Lake Superior Chippewa, MN, USA; Hubbs-SeaWorld Research Institute, CA, USA; Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
Henning Sørum
Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, MN, USA; Shriners Children's Genomics Institute, FL, USA; Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA; Purdue Applied Microbiome Sciences Program, Purdue University, West Lafayette, IN, USA; Grand Portage Band of Lake Superior Chippewa, MN, USA; Hubbs-SeaWorld Research Institute, CA, USA; Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
Noelle Noyes
Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, MN, USA; Corresponding author at: 385D AnSci/VM 1988 Fitch Avenue, St. Paul, MN 55108, United States.
Anthropogenic activities can significantly impact wildlife in natural water bodies, affecting not only the host's physiology but also its microbiome. This study aimed to analyze the gut microbiome and antimicrobial resistance gene profile (i.e., the resistome) of yellow perch living in lakes subjected to different levels of anthropogenic pressure: wastewater effluent-impacted lakes and undeveloped lakes. Total DNA and RNA from gut content samples were extracted and sequenced for analysis. Results indicate that the gut resistome and microbiome of yellow perch differ between lakes, perhaps due to varying anthropogenic pressure. The resistome was predominated by macrolide resistance genes, particularly the MLS23S group, making up 53 % of resistome sequences from effluent-impacted lakes and 73 % from undeveloped lakes. The colistin resistance gene group (mcr) was detected in numerous samples, including variants associated with Aeromonas and the family Enterobacteriaceae. The gut microbiome across all samples was dominated by the phyla Proteobacteria, Firmicutes, and Actinobacteria, with the opportunistic pathogens Plesiomonas shigelloides and Aeromonas veronii more abundant in effluent-impacted lakes. Metagenomic analysis of wild fish samples offers valuable insights into the effects of anthropogenic pressures on microbial communities, including antimicrobial resistance genes, in water bodies.
