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      Influence of sodium chlorate, ferulic acid, and essential oils on Escherichia coli and porcine fecal microbiota

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          Abstract

          The influence of sodium chlorate (SC), ferulic acid (FA), and essential oils (EO) was examined on the survivability of two porcine diarrhetic enterotoxigenic Escherichia coli (ETEC) strains (F18 and K88) and populations of porcine fecal bacteria. Fecal bacterial populations were examined by denaturing gradient gel electrophoresis (DGGE) and identification by 16S gene sequencing. The treatments were control (no additives), 10 mM SC, 2.5 mg FA /mL, a 1.5% vol/vol solution of an EO mixture as well as mixtures of EO + SC, EO + FA, and FA + SC at each of the aforementioned concentrations. EO were a commercial blend of oregano oil and cinnamon oil with water and citric acid. Freshly collected porcine feces in half-strength Mueller Hinton broth was inoculated with E. coli F18 (Trial 1) or E. coli K88 (Trial 2). The fecal-E. coli suspensions were transferred to crimp top tubes preloaded with the treatment compounds. Quantitative enumeration was at 0, 6, and 24 h. All treatments reduced (P < 0.05) the counts of E. coli F18 at 6 and 24 h. With the exception of similarity coefficient (%SC), all the other treatments reduced (P < 0.05) the K88 counts at 24 h. The most effective treatments to reduce the F18 and K88 CFU numbers were those containing EO. Results of DGGE revealed that Dice percentage similarity coefficients (%SC) of bacterial profiles among treatment groups varied from 81.3% to 100%SC. The results of gene sequencing showed that, except for SC at 24 h, all the other treatments reduced the counts of the family Enterobacteriaceae, while Lactobacillaceae and Ruminococcaceae increased and Clostridiaceae decreased in all treatments. In conclusion, all treatments were effective in reducing the ETEC, but EO mixture was the most effective. The porcine microbial communities may be influenced by the studied treatments.

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          Most cited references39

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          QIIME allows analysis of high-throughput community sequencing data.

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            Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

            A 16S rRNA gene database ( http://greengenes.lbl.gov ) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria .
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              Is Open Access

              An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

              Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a ‘taxonomy to tree' approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408 315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.
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                Author and article information

                Journal
                Journal of Animal Science
                Oxford University Press (OUP)
                0021-8812
                1525-3163
                March 2020
                March 01 2020
                February 17 2020
                March 2020
                March 01 2020
                February 17 2020
                : 98
                : 3
                Affiliations
                [1 ]Department of Animal Nutrition, College of Animal Science and Ecology, Universidad Autónoma de Chihuahua, Chihuahua, Mexico
                [2 ]United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, Food and Feed Safety Research Unit, College Station, TX
                [3 ]Bezoar Laboratories LLC, Bryan, TX
                [4 ]Department of Animal Nutrition, College of Medicine Veterinary and Animal Science, Universidad Autónoma de Tamaulipas, Tamaulipas, Mexico
                Article
                10.1093/jas/skaa059
                7072035
                32064520
                6c5f243a-e8dd-487f-8430-37372639c2d2
                © 2020

                https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model

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