Shotgun metagenomics offers novel insights into taxonomic compositions, metabolic pathways and antibiotic resistance genes in fish gut microbiome

  • Anuj TyagiEmail author
  • Balwinder Singh
  • Naveen K. Billekallu Thammegowda
  • Niraj K. Singh
Original Paper


Gut microbiota of freshwater carp (Labeo rohita) was investigated by shotgun metagenomics to understand its taxonomic composition and functional capabilities. With the presence of 36 phyla, 326 families and 985 genera, the fish gut microbiota was found to be quite diverse in nature. However, at the phylum level, more than three-fourths of gut microbes belonged to Proteobacteria. Very low prevalence of commonly used probiotic bacteria (Bacillus, Lactobacillus, Streptococcus, and Lactococcus) in fish gut suggested the need to search for alternative probiotics for aquaculture use. Biosynthesis pathways were found to be the most dominant (51%) followed by degradation (39%), energy metabolism (4%) and fermentation (2%). In conformity with herbivorous feeding habit of L. rohita, gut microbiome also had pathways for the degradation of cellulose, hemicellulose, chitin, pectin, starch, and other complex carbohydrates. High prevalence of Actinobacteria and antibiotic biosynthesis pathways in the fish gut microbiome indicated its potential for bioprospecting of potentially novel natural antibiotics. Fifty-one different types of antibiotic resistance genes (ARGs) belonging to 15 antimicrobial resistance (AMR) gene families and conferring resistance against 24 antibiotic types were detected in fish gut. Some of the ARGs for multi-drug resistance were also found to be located on sequences of plasmid origin. The presence of pathogenic bacteria and ARGs on plasmid sequences suggested the potential risk due to horizontal gene transfer in the confined gut environment. The role of ARGs in fish gut microbiome needs further investigations.


Fish gut Microbial diversity Shotgun metagenomics Metabolic pathways Antibiotic resistance 



The authors are grateful to the Dean (College of Fisheries, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India) for all necessary support during this study. Funding support from Science and Engineering Research Board, Department of Science and Technology (DST-SERB) Young Scientist Start-Up Research Grant (YSS/2014/000269) to Anuj Tyagi has been utilized to carry this work and it is gratefully acknowledged.

Author contributions

AT conceived the study, performed the bioinformatics analysis and drafted the manuscript. BS collected and processed the samples. NKBT helped in sample collection, result interpretations, and manuscript drafting. NKS supported in data analysis and manuscript drafting. All authors contributed in final manuscript correction.

Compliance with ethical standards

Conflict of interest

No conflict of interest declared.

Ethical standards

No special permission was required for this study.

Supplementary material

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Aquatic Environment, College of FisheriesGuru Angad Dev Veterinary and Animal Sciences UniversityLudhianaIndia
  2. 2.School of Animal BiotechnologyGuru Angad Dev Veterinary and Animal Sciences UniversityLudhianaIndia

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