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      Microbial community-based protein from soybean-processing wastewater as a sustainable alternative fish feed ingredient

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          Abstract

          As the global demand for food increases, aquaculture plays a key role as the fastest growing animal protein sector. However, existing aquafeeds contain protein ingredients that are not sustainable under current production systems. We evaluated the use of microbial community-based single cell protein (SCP), produced from soybean processing wastewater, as a partial fishmeal protein substitute in juvenile Asian seabass ( Lates calcarifer). A 24-day feeding trial was conducted with a control fishmeal diet and a 50% fishmeal replacement with microbial community-based SCP as an experimental group, in triplicate tanks containing 20 fish each. Both diets met the protein, essential amino acids (except for lysine), and fat requirements for juvenile Asian sea bass. The microbial composition of the SCP was dominated by the genera Acidipropionibacterium and Propioniciclava, which have potential as probiotics and producers of valuable metabolites. The growth performance in terms of percent weight gain, feed conversion ratio (FCR), specific growth rate (SGR), and survival were not significantly different between groups after 24 days. The experimental group had less variability in terms of weight gain and FCR than the control group. Overall, microbial community-based protein produced from soybean processing wastewater has potential as a value-added feed ingredient for sustainable aquaculture feeds.

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            DADA2: High resolution sample inference from Illumina amplicon data

            We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
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              Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

              Recent advances have made it possible to analyze high-throughput marker-gene sequencing data without resorting to the customary construction of molecular operational taxonomic units (OTUs): clusters of sequencing reads that differ by less than a fixed dissimilarity threshold. New methods control errors sufficiently such that amplicon sequence variants (ASVs) can be resolved exactly, down to the level of single-nucleotide differences over the sequenced gene region. The benefits of finer resolution are immediately apparent, and arguments for ASV methods have focused on their improved resolution. Less obvious, but we believe more important, are the broad benefits that derive from the status of ASVs as consistent labels with intrinsic biological meaning identified independently from a reference database. Here we discuss how these features grant ASVs the combined advantages of closed-reference OTUs—including computational costs that scale linearly with study size, simple merging between independently processed data sets, and forward prediction—and of de novo OTUs—including accurate measurement of diversity and applicability to communities lacking deep coverage in reference databases. We argue that the improvements in reusability, reproducibility and comprehensiveness are sufficiently great that ASVs should replace OTUs as the standard unit of marker-gene analysis and reporting.
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                Author and article information

                Contributors
                Diana_CHAN@tp.edu.sg
                swuertz@ntu.edu.sg
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                31 January 2024
                31 January 2024
                2024
                : 14
                : 2620
                Affiliations
                [1 ]GRID grid.59025.3b, ISNI 0000 0001 2224 0361, Singapore Centre for Environmental Life Sciences Engineering, , Nanyang Technological University, ; Singapore, 637551 Singapore
                [2 ]Aquaculture Innovation Centre, Temasek Polytechnic, ( https://ror.org/03k1z9s75) Singapore, 529757 Singapore
                [3 ]School of Civil and Environmental Engineering, Nanyang Technological University, ( https://ror.org/02e7b5302) Singapore, 639798 Singapore
                Article
                51737
                10.1038/s41598-024-51737-w
                10831065
                38297061
                304fcfdd-6659-45d1-b3c4-8c41ec8f2b6b
                © The Author(s) 2024

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 28 September 2023
                : 9 January 2024
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001381, National Research Foundation Singapore;
                Award ID: NRF-CRP21-2018-0006
                Funded by: FundRef http://dx.doi.org/10.13039/501100001459, Ministry of Education - Singapore;
                Award ID: Research Centre of Excellence Program
                Categories
                Article
                Custom metadata
                © Springer Nature Limited 2024

                Uncategorized
                environmental biotechnology,environmental sciences,environmental microbiology,next-generation sequencing,animal physiology

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