Metagenomics approach to the study of the gut microbiome structure and function in zebrafish Danio rerio fed with gluten formulated diet.
In this study, we report the gut microbial composition and predictive functional profiles of zebrafish, Danio rerio, fed with a control formulated diet (CFD), and a gluten formulated diet (GFD) using a metagenomics approach and bioinformatics tools. The microbial communities of the GFD-fed D. rerio displayed heightened abundances of Legionellales, Rhizobiaceae, and Rhodobacter, as compared to the CFD-fed counterparts. Predicted metagenomics of microbial communities (PICRUSt) in GFD-fed D. rerio showed KEGG functional categories corresponding to bile secretion, secondary bile acid biosynthesis, and the metabolism of glycine, serine, and threonine. The CFD-fed D. rerio exhibited KEGG functional categories of bacteria-mediated cobalamin biosynthesis, which was supported by the presence of cobalamin synthesizers such as Bacteroides and Lactobacillus. Though these bacteria were absent in GFD-fed D. rerio, a comparable level of the cobalamin biosynthesis KEGG functional category was observed, which could be contributed by the compensatory enrichment of Cetobacterium. Based on these results, we conclude D. rerio to be a suitable alternative animal model for the use of a targeted metagenomics approach along with bioinformatics tools to further investigate the relationship between the gluten diet and microbiome profile in the gut ecosystem leading to gastrointestinal diseases and other undesired adverse health effects.
Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
Hyunmin
H
Koo
Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
Joseph A
JA
Hakim
Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
Mickie L
ML
Powell
Biomedical Informatics, Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL, USA.
Ranjit
R
Kumar
Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
Peter G
PG
Eipers
Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
Casey D
CD
Morrow
Heflin Center for Genomic Sciences, University of Alabama at Birmingham, Birmingham, AL, USA.
Michael
M
Crowley
Biomedical Informatics, Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA.
Elliot J
EJ
Lefkowitz
Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA. Electronic address: sawatts@uab.edu.
Stephen A
SA
Watts
Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA. Electronic address: abej@uab.edu.
Asim K
AK
Bej
D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000378:metabolism* / Q000472:pathogenicity; D001647:Bile Acids and Salts / Q000378:metabolism; D044822:Biodiversity; D019295:Computational Biology / Q000295:instrumentation; D004269:DNA, Bacterial / Q000302:isolation & purification; D004032:Diet; D017753:Ecosystem; D005767:Gastrointestinal Diseases / Q000382:microbiology; D000069196:Gastrointestinal Microbiome / Q000502:physiology*; D041981:Gastrointestinal Tract / Q000378:metabolism / Q000382:microbiology*; D005798:Genes, Bacterial; D005983:Glutens / Q000378:metabolism*; D005998:Glycine / Q000378:metabolism; D056186:Metagenomics / Q000379:methods*; D059013:Microbial Consortia; D023421:Models, Animal; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012694:Serine / Q000378:metabolism; D013912:Threonine / Q000378:metabolism; D014805:Vitamin B 12 / Q000096:biosynthesis; D015027:Zebrafish / Q000382:microbiology*
D001647:Bile Acids and Salts; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D013912:Threonine; D012694:Serine; D005983:Glutens; D014805:Vitamin B 12; D005998:Glycine
16S rRNA; NextGen sequencing; PICRUSt; Pathogens; QIIME