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      Yeast culture dietary supplementation modulates gut microbiota, growth and biochemical parameters of grass carp

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          Summary

          Gut microbiota contributes positively to the physiology of their host. Some feed additives have been suggested to improve livestock health and stimulate growth performance by modulating gut bacteria species. Here, we fed grass carp with 0 (control), 8% (Treat1), 10% (Treat2), 12% (Treat3) and 16% (Treat4) of yeast culture (YC) for 10 weeks. The gut microbiota was analysed by 16S rRNA gene V3‐4 region via an Illumina MiSeq platform. PCoA test showed that gut bacterial communities in the control and Treat3 formed distinctly separate clusters. Although all the groups shared a large size of OTUs as a core microbiota community, a strong distinction existed at genus level. Treat3 contained the highest proportion of the beneficial bacteria and obviously enhanced the capacity of amino acid, lipid metabolism and digestive system. In addition, Treat3 significantly improved the fish growth and increased the liver and serum T‐SOD activities while dramatically decreased the liver GPT and GOT. Collectively, these findings demonstrate the beneficial effects of YC feeding on gut microbiota, growth and biochemical parameters and Treat3 might be the optimal supplementation amount for grass carp, which opens up the possibility that a new feed additive can be developed for healthy aquaculture.

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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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            Antibiotics and antibiotic resistance in water environments.

            Antibiotic-resistant organisms enter into water environments from human and animal sources. These bacteria are able to spread their genes into water-indigenous microbes, which also contain resistance genes. On the contrary, many antibiotics from industrial origin circulate in water environments, potentially altering microbial ecosystems. Risk assessment protocols for antibiotics and resistant bacteria in water, based on better systems for antibiotics detection and antibiotic-resistance microbial source tracking, are starting to be discussed. Methods to reduce resistant bacterial load in wastewaters, and the amount of antimicrobial agents, in most cases originated in hospitals and farms, include optimization of disinfection procedures and management of wastewater and manure. A policy for preventing mixing human-originated and animal-originated bacteria with environmental organisms seems advisable.
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              Responses of Gut Microbiota and Glucose and Lipid Metabolism to Prebiotics in Genetic Obese and Diet-Induced Leptin-Resistant Mice

              OBJECTIVE To investigate deep and comprehensive analysis of gut microbial communities and biological parameters after prebiotic administration in obese and diabetic mice. RESEARCH DESIGN AND METHODS Genetic (ob/ob) or diet-induced obese and diabetic mice were chronically fed with prebiotic-enriched diet or with a control diet. Extensive gut microbiota analyses, including quantitative PCR, pyrosequencing of the 16S rRNA, and phylogenetic microarrays, were performed in ob/ob mice. The impact of gut microbiota modulation on leptin sensitivity was investigated in diet-induced leptin-resistant mice. Metabolic parameters, gene expression, glucose homeostasis, and enteroendocrine-related L-cell function were documented in both models. RESULTS In ob/ob mice, prebiotic feeding decreased Firmicutes and increased Bacteroidetes phyla, but also changed 102 distinct taxa, 16 of which displayed a >10-fold change in abundance. In addition, prebiotics improved glucose tolerance, increased L-cell number and associated parameters (intestinal proglucagon mRNA expression and plasma glucagon-like peptide-1 levels), and reduced fat-mass development, oxidative stress, and low-grade inflammation. In high fat–fed mice, prebiotic treatment improved leptin sensitivity as well as metabolic parameters. CONCLUSIONS We conclude that specific gut microbiota modulation improves glucose homeostasis, leptin sensitivity, and target enteroendocrine cell activity in obese and diabetic mice. By profiling the gut microbiota, we identified a catalog of putative bacterial targets that may affect host metabolism in obesity and diabetes.
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                Author and article information

                Contributors
                wangwm@mail.hzau.edu.cn
                Journal
                Microb Biotechnol
                Microb Biotechnol
                10.1111/(ISSN)1751-7915
                MBT2
                Microbial Biotechnology
                John Wiley and Sons Inc. (Hoboken )
                1751-7915
                26 March 2018
                May 2018
                : 11
                : 3 ( doiID: 10.1111/mbt2.2018.11.issue-3 )
                : 551-565
                Affiliations
                [ 1 ] College of Fisheries Key Lab of Freshwater Animal Breeding, Ministry of Agriculture Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education Huazhong Agricultural University 430070 Wuhan China
                [ 2 ] Laboratorio de Biotecnología Genómica Centro de Biotecnología Genómica Instituto Politécnico Nacional Boulevard del Maestro esquina Elías Piña, Colonia Narciso Mendoza 88710 Ciudad Reynosa Tamaulipas Mexico
                [ 3 ] Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province 41500 Changde China
                [ 4 ]Present address: College of Fisheries Huazhong Agricultural University Wuhan 430070 China
                Author notes
                [*] [* ]For correspondence. E‐mail wangwm@ 123456mail.hzau.edu.cn ; Tel. +86‐27‐8728 4292; Fax +86‐27‐8728 4292.
                Author information
                http://orcid.org/0000-0003-0811-1808
                Article
                MBT213261
                10.1111/1751-7915.13261
                5902330
                29578305
                d24eb82d-6d9f-49d3-89d2-a1e32a6cce26
                © 2018 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 30 August 2017
                : 04 February 2018
                : 16 February 2018
                Page count
                Figures: 7, Tables: 2, Pages: 15, Words: 8527
                Funding
                Funded by: Central Public‐interest Scientific Institution Basal Research Fund, CAFS
                Award ID: 2017HY‐XKQ0205
                Funded by: Fundament Research Funds for the Central Universities
                Award ID: 2662015PY019
                Funded by: National Science Foundation for Post‐doctoral Scientists of China
                Award ID: 2016M600600
                Funded by: project of the International Scientific and Technology Cooperation Program of Wuhan City
                Award ID: 2015030809020365
                Categories
                Research Article
                Research Articles
                Custom metadata
                2.0
                mbt213261
                May 2018
                Converter:WILEY_ML3GV2_TO_NLMPMC version:version=5.3.4 mode:remove_FC converted:16.04.2018

                Biotechnology
                Biotechnology

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