title: Environment shapes the fecal microbiome of invasive carp species.
abstract: Although the common, silver, and bighead carps are native and sparsely distributed in Eurasia, these fish have become abundant and invasive in North America. An understanding of the biology of these species may provide insights into sustainable control methods. The animal-associated microbiome plays an important role in host health. Characterization of the carp microbiome and the factors that affect its composition is an important step toward understanding the biology and interrelationships between these species and their environments.
  
  
  
  We compared the fecal microbiomes of common, silver, and bighead carps from wild and laboratory environments using Illumina sequencing of bacterial 16S ribosomal RNA (rRNA). The fecal bacterial communities of fish were diverse, with Shannon indices ranging from 2.3 to 4.5. The phyla Proteobacteria, Firmicutes, and Fusobacteria dominated carp guts, comprising 76.7 % of total reads. Environment played a large role in shaping fecal microbial community composition, and microbiomes among captive fishes were more similar than among wild fishes. Although differences among wild fishes could be attributed to feeding preferences, diet did not strongly affect microbial community structure in laboratory-housed fishes. Comparison of wild- and lab-invasive carps revealed five shared OTUs that comprised approximately 40 % of the core fecal microbiome.
  
  
  
  The environment is a dominant factor shaping the fecal bacterial communities of invasive carps. Captivity alters the microbiome community structure relative to wild fish, while species differences are pronounced within habitats. Despite the absence of a true stomach, invasive carp species exhibited a core microbiota that warrants future study.
authors: Department of Fisheries, Wildlife, and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, Twin Cities, Saint Paul, MN, 55108, USA.
authors: Jessica J
authors: JJ
authors: Eichmiller
authors: Department of Soil, Water and Climate, Biotechnology Institute, University of Minnesota, Saint Paul, MN, 55108, USA.
authors: Matthew J
authors: MJ
authors: Hamilton
authors: Department of Soil, Water and Climate, Biotechnology Institute, University of Minnesota, Saint Paul, MN, 55108, USA.
authors: Christopher
authors: C
authors: Staley
authors: Department of Fisheries, Wildlife, and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, Twin Cities, Saint Paul, MN, 55108, USA. sadowsky@umn.edu.|Department of Soil, Water and Climate, Biotechnology Institute, University of Minnesota, Saint Paul, MN, 55108, USA. sadowsky@umn.edu.
authors: Michael J
authors: MJ
authors: Sadowsky
authors: Department of Fisheries, Wildlife, and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, Twin Cities, Saint Paul, MN, 55108, USA. soren003@umn.edu.
authors: Peter W
authors: PW
authors: Sorensen
mesh_terms: D000818:Animals; D001483:Base Sequence; D002347:Carps / Q000145:classification / Q000382:microbiology*; D004777:Environment; D005243:Feces / Q000382:microbiology*; D000068536:Bacillota / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D045182:Fusobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D058865:Introduced Species; D064307:Microbiota / Q000235:genetics*; D009656:North America; D020560:Proteobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017423:Sequence Analysis, RNA
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: 16SrRNA gene; Community structure; Fecal microbiome; Invasive carp; Microbiota