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      The Effect of Disease and Season to Hepatopancreas and Intestinal Mycobiota of Litopenaeus vannamei

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          Increasing evidence has manifested that the gut bacterial microbiota of shrimps is closely related to the environmental factors, host developmental stage and health status like that of humans and animals does. These studies have provided an important guidance for improving shrimp culture benefits. In practice, aside from bacteria, eukaryotic microorganisms dominated by fungal microbiota (mycobiota), also play a key role in host growth, metabolism and homeostasis. However, little so far is known about the mycobiota in the digestive tract of shrimp. In this study, we used high-throughput sequencing of internal transcribed spacer 1 region to characterize the hepatopancreas and intestinal mycobiota of Pacific white shrimp and their connections with disease incidence and seasonal variation. The results showed that the hepatopancreas and intestinal mycobiota of Litopenaeus vannamei are dominated by the phyla Ascomycota and Basidiomycota, and the genera Alternaria, Tuber, Hortaea, Sarocladium, and Stagonospora. The fungal microbiota significantly varies under the influence of disease and seasonal variation. Sick shrimps had a higher level of potential pathogenic fungus, Candida in the intestine. Healthy shrimps had a higher abundance of the genera Didymella and Filobasidium in the gut, and Pyrenochaetopsis in the hepatopancreas. Of note, most of the fungi carried by Pacific white shrimps were pathogens to humans. This study has revealed the intestinal and hepatopancreas mycobiota of L. vannamei and the effects of diseases and seasonal variation to the mycobiota. Our study provides important guidance for Pacific white shrimp farming and sheds further insight on the fungal microbiota.

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          Most cited references 79

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at Contact: Supplementary information: Supplementary data are available at Bioinformatics online.
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            QIIME allows analysis of high-throughput community sequencing data.

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              Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.

              mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

                Author and article information

                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                24 April 2019
                : 10
                Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources , Guangzhou, China
                Author notes

                Edited by: Gustavo Henrique Goldman, University of São Paulo, Brazil

                Reviewed by: Man Kit Cheung, The Chinese University of Hong Kong, China; Maryam Dadar, Razi Vaccine and Serum Research Institute, Iran

                *Correspondence: Jinping Chen, chenjp@

                This article was submitted to Fungi and Their Interactions, a section of the journal Frontiers in Microbiology

                Copyright © 2019 Li, Jiang, Li, Zhang and Chen.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                Page count
                Figures: 6, Tables: 2, Equations: 0, References: 79, Pages: 13, Words: 0
                Original Research

                Microbiology & Virology

                litopenaeus vannamei, mycobiota, hepatopancreas, intestine, its amplicon


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