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      Dynamic Alterations of the Distal Intestinal Microbiota, Transcriptome, and Metabolome of Hybrid Grouper by β -Conglycinin With Reconciliations by Sodium Butyrate in Feed

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      Frontiers in Marine Science
      Frontiers Media SA

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          Abstract

          Different doses of β-conglycinin produce different regulations on the intestinal health of aquatic animals, affecting the absorption of nutrients, indirectly changing water quality. Sodium butyrate (NaB) can effectively alleviate the negative effects caused by high-dose β-conglycinin. We investigated the positive response to low-dose (1.5%, bL) and negative response to high-dose (6.0%, bH) β-conglycinin and supplementation with NaB (6.0% β-conglycinin + 0.13% NaB, bHNaB) in terms of water pollutants, microbiota, transcriptome, and metabolome in hybrid grouper ( Epinephelus fuscoguttatus♀ × E. lanceolatus♂). The ammonia nitrogen, nitrite, total nitrogen, and total phosphorus contents were significantly higher in the water from bH than from FMb, bL, and bHNaB. Supplementing with NaB significantly reduced the ammonia nitrogen, nitrite, total nitrogen, and total phosphorus contents. Low-dose β-conglycinin increased the relative abundance of Pelagibacterium, Pediococcus, Staphylococcus, and Lactobacillus and promoted the “ribosome,” “peroxisome proliferator-activated receptor (PPAR) signaling” and “histidine metabolism.” High-dose β-conglycinin increased the relative abundance of pathogenic bacteria Ralstonia and Photobacterium and inhibited the “cell cycle” “PPAR signaling” and “starch and proline metabolism.” NaB supplementation at high-dose β-conglycinin reduced the Ralstonia and Photobacterium abundance and promoted the “cell cycle,” “linoleic acid metabolism,” and “ABC transporters.” Overall, these results reveal differences in the effects of high- and low-dose β-conglycinin, as well as NaB supplementation, on the utilization of proteins, carbohydrates, and lipids and on substance transport and signaling among distal intestinal cells of hybrid grouper. A total of 15 differential metabolite biomarkers were identified: FMb vs. bL contained 10-methylimidazole acetic acid, N-acetyl histamine, urocanic acid, creatinine, glutathione, taurine, nervonic acid, stearic acid, docosanoic acid, and D-serine; FMb vs. bH contained 4- L-fucose, sucrose, α,α-trehalose, and quercetin; and bH vs. bHNaB contained 4- N-acetyl histamine, urocanic acid, creatinine, and S-adenosylhomocysteine, respectively. Our study provides new insights into the regulation of intestinal health by β-conglycinin in aquatic animals and the protective mechanism of NaB.

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          Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

          The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
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            Fast gapped-read alignment with Bowtie 2.

            As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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              fastp: an ultra-fast all-in-one FASTQ preprocessor

              Abstract Motivation Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient. Results We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2–5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools. Availability and implementation The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.
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                Author and article information

                Journal
                Frontiers in Marine Science
                Front. Mar. Sci.
                Frontiers Media SA
                2296-7745
                July 19 2021
                July 19 2021
                : 8
                Article
                10.3389/fmars.2021.705332
                76aec14d-2553-487f-8f3d-2c6716be0578
                © 2021

                Free to read

                https://creativecommons.org/licenses/by/4.0/

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