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      Effect of Dietary Tryptophan on Growth, Intestinal Microbiota, and Intestinal Gene Expression in an Improved Triploid Crucian Carp

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          Abstract

          Tryptophan (Trp) has received increasing attention in the maintenance of intestinal function. In this study, improved triploid crucian carp (ITCC) fed diets containing 6.35 g kg −1 Trp had higher average daily gain (ADG) and improved villus height (VH) and crypt depth (CD) in the intestine compared to the control group. To elucidate the potential mechanisms, we used RNA sequencing (RNA-seq) to investigate changes in the intestinal transcriptome and 16S rRNA gene sequencing to measure the intestinal microbiota in response to 6.35 g kg −1 Trp feeding in ITCC. Dietary Trp altered intestinal gene expression involved in nutrient transport and metabolism. Differentially expressed transcripts (DETs) were highly enriched in key pathways containing protein digestion and absorption and the AMPK signaling pathway. 16S rRNA sequencing showed that 6.35 g kg −1 Trp significantly increased the abundance of the genus Cetobacterium, and the Firmicutes/Bacteroidetes ratio at the phylum level ( P < 0.05). In addition, bacterial richness indices (Simpson index) significantly increased ( P < 0.05) community evenness in response to 6.35 g kg −1 Trp. In conclusion, appropriate dietary Trp improves the growth performance, and influences the intestinal flora of ITCC. This study might be helpful to guide the supply of dietary exogenous Trp in ITCC breeding.

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          Most cited references75

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          Cytoscape: a software environment for integrated models of biomolecular interaction networks.

          Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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            edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

            Summary: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data. Availability: The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org). Contact: mrobinson@wehi.edu.au
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              An obesity-associated gut microbiome with increased capacity for energy harvest.

              The worldwide obesity epidemic is stimulating efforts to identify host and environmental factors that affect energy balance. Comparisons of the distal gut microbiota of genetically obese mice and their lean littermates, as well as those of obese and lean human volunteers have revealed that obesity is associated with changes in the relative abundance of the two dominant bacterial divisions, the Bacteroidetes and the Firmicutes. Here we demonstrate through metagenomic and biochemical analyses that these changes affect the metabolic potential of the mouse gut microbiota. Our results indicate that the obese microbiome has an increased capacity to harvest energy from the diet. Furthermore, this trait is transmissible: colonization of germ-free mice with an 'obese microbiota' results in a significantly greater increase in total body fat than colonization with a 'lean microbiota'. These results identify the gut microbiota as an additional contributing factor to the pathophysiology of obesity.
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                Author and article information

                Contributors
                Journal
                Front Nutr
                Front Nutr
                Front. Nutr.
                Frontiers in Nutrition
                Frontiers Media S.A.
                2296-861X
                17 June 2021
                2021
                : 8
                : 676035
                Affiliations
                [1] 1CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences , Changsha, China
                [2] 2College of Animal Science and Technology, Henan Agricultural University , Zhengzhou, China
                [3] 3State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University , Changsha, China
                Author notes

                Edited by: Christophe Lacroix, ETH Zürich, Switzerland

                Reviewed by: Jun Wang, Shanghai Ocean University, China; Yongqing Hou, Wuhan Polytechnic University, China

                *Correspondence: Kang Xu xukang2020@ 123456163.com

                This article was submitted to Nutrition and Microbes, a section of the journal Frontiers in Nutrition

                †These authors have contributed equally to this work

                Article
                10.3389/fnut.2021.676035
                8247481
                34222302
                2b08127a-c40a-4ef7-bee0-fcb270853fd1
                Copyright © 2021 Fu, Liang, Li, Gao, Wang, Li, Xu and Hu.

                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.

                History
                : 04 March 2021
                : 20 May 2021
                Page count
                Figures: 8, Tables: 2, Equations: 0, References: 76, Pages: 12, Words: 8011
                Categories
                Nutrition
                Original Research

                tryptophan,improved triploid crucian carp,transcriptome,intestinal flora,16s rrna

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