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High Throughput Identification of Antimicrobial Peptides from Fish Gastrointestinal Microbiota

1,†, 1,2,†, 1 and 1,2,3,*
BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: Steve Peigneur
Toxins 2017, 9(9), 266;
Received: 10 August 2017 / Revised: 25 August 2017 / Accepted: 28 August 2017 / Published: 30 August 2017
(This article belongs to the Special Issue Toxins in Drug Discovery and Pharmacology)
PDF [10587 KB, uploaded 30 August 2017]


Antimicrobial peptides (AMPs) are a group of small peptides, which are secreted by almost all creatures in nature. They have been explored in therapeutic and agricultural aspects as they are toxic to many bacteria. A considerable amount of work has been conducted in analyzing 16S and metagenomics of the gastrointestinal (GI) microbiome of grass carp (Ctenopharyngodon idellus). However, these datasets are still untapped resources. In this present study, a homologous search was performed to predict AMPs from our newly generated metagenome of grass carp. We identified five AMPs with high similarities to previously reported bacterial toxins, such as lantibiotic and class II bacteriocins. In addition, we observed that the top abundant genus in the GI microbiota of the grass carp was generally consistent with the putative AMP-producing strains, which are mainly from Lactobacillales. Furthermore, we constructed the phylogenetic relationship of these putative AMP-producing bacteria existing in the GI of grass carp and some popular commercial probiotics (commonly used for microecologics), demonstrating that they are closely related. Thus, these strains have the potential to be developed into novel microecologics. In a word, we provide a high-throughput way to discover AMPs from fish GI microbiota, which can be developed as alternative pathogen antagonists (toxins) for microecologics or probiotic supplements. View Full-Text
Keywords: antimicrobial peptide (AMP); fish gastrointestinal microbiota; high throughput identification; AMP-producing bacteria antimicrobial peptide (AMP); fish gastrointestinal microbiota; high throughput identification; AMP-producing bacteria

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Dong, B.; Yi, Y.; Liang, L.; Shi, Q. High Throughput Identification of Antimicrobial Peptides from Fish Gastrointestinal Microbiota. Toxins 2017, 9, 266.

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