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      Siamese Fighting Fish (Betta splendens Regan) Gut Microbiota Associated with Age and Gender

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      Fishes
      MDPI AG

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          Abstract

          The Siamese fighting fish (Betta splendens Regan) is a popular ornamental fish in Thailand. Growing research suggests that fish health is influenced by gut microbiota. Here, we investigated, for the first time, the differences in the gut microbiota profiles of healthy Siamese fighting fish during the young (8-week-old) and adult male and female (16-week-old and 24-week-old) life stages using 16S rRNA gene sequence analysis. The fish were raised in controlled water quality conditions and fed on Moina macrocopa. Profiling of gut microbial communities revealed significant differences in the overall bacterial profile between young and adult Siamese fighting fish. Bacterial diversity decreased in the 24-week-old adult fish. Proteobacteria was the most predominant bacterial phylum in the gut of both young and adult carnivorous betta fish, in which the abundance of its members varied with age. Plesiomonas was enriched in male fish aged 24 weeks, whereas Pseudomonas dominated the gut of 8-week-old fish. Moreover, differences in predicted functions of these Proteobacteria between the young and adult fish could be a key target for improving fish growth. These findings expand our understanding of the role of gut microbiota and its association with host factors.

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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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            FLASH: fast length adjustment of short reads to improve genome assemblies.

            Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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              Metagenomic biomarker discovery and explanation

              This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.
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                Author and article information

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                Journal
                Fishes
                Fishes
                MDPI AG
                2410-3888
                December 2022
                November 25 2022
                : 7
                : 6
                : 347
                Article
                10.3390/fishes7060347
                4d610f29-329a-47d7-8e20-0d53604a68b0
                © 2022

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

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