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One of the greatest impacts on the gastrointestinal microbiome is diet because the host and microbiome share the same food source. In addition, the effect of diet can diverge depending on the host genotype. Diets supplemented with phytochemicals found in peppers might cause shifts in the microbiome. Thus, understanding how these interactions occur can reveal potential health implications associated with such changes. This study aims to explore the gut microbiome of different Drosophila genetic backgrounds and the effects of dietary pepper treatments on its composition and structure. We analyzed the gut microbiomes of three Drosophila melanogaster genetic backgrounds (Canton-S, Oregon-RC, and Berlin-K) reared on control and pepper-containing diets (bell, serrano, and habanero peppers). Results of 16S rRNA gene sequencing revealed that the variability of Drosophila gut microbiome can be driven mainly by genetic factors. When the abundance of these communities is considered, pepper-containing diets also appear to have an effect. The most relevant change in microbial composition was the increment of Lactobacillaceae and Acetobacteraceae abundance in the pepper-containing diets in comparison with the controls in Oregon-RC and Berlin-K. Regression analysis demonstrated that this enhancement was associated with the content of phenolic compounds and carotenoids of the peppers utilized in this study; specifically, to the concentration of β-carotene, β-cryptoxanthin, myricetin, quercetin, and apigenin.
Pubmed ID: 32023882 RIS Download
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Software providing a set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.
View all literature mentionsSoftware platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
View all literature mentionsDatabase of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. It is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. Submissions are supported by a web-based Submission Portal. The database facilitates organization and classification of project data submitted to NCBI, EBI and DDBJ databases that captures descriptive information about research projects that result in high volume submissions to archival databases, ties together related data across multiple archives and serves as a central portal by which to inform users of data availability. BioProject records link to corresponding data stored in archival repositories. The BioProject resource is a redesigned, expanded, replacement of the NCBI Genome Project resource. The redesign adds tracking of several data elements including more precise information about a project''''s scope, material, and objectives. Genome Project identifiers are retained in the BioProject as the ID value for a record, and an Accession number has been added. Database content is exchanged with other members of the International Nucleotide Sequence Database Collaboration (INSDC). BioProject is accessible via FTP.
View all literature mentionsConversion Software Registry (CSR) has been designed for collecting information about software packages that are capable of file format conversions. The work is motivated by a community need for finding file format conversions inaccessible via current search engines and by the specific need to support systems that could actually perform conversions, such as the NCSA Polyglot. In addition, the value of CSR is in complementing the existing file format registries and introducing software quality information obtained by content-based comparisons of files before and after conversions. The contribution of this work is in the CSR data model design that includes file format extension based conversion, as well as software scripts, software quality measures and test file specific information for evaluating software quality. The CSR system serves as the source of information and a test bed for the system that can execute the conversions automatically by using the third party software, for example, NCSA Polyglot. The CSR system is a database with a web-based interface that provides services related to a) finding a conversion path between formats b) uploading information about the 3rd party software packages and file extensions, c) uploading files for testing, and finally d) uploading scripts in operating system (OS) specific scripting languages (Windows AutoHotKey, AppleScript and Perl) for automated conversions according to the idea of imposed code reuse used by NCSA Polyglot. In order to provide file format conversion services, CSR have included the following components into CSR related to software capable of conversions: input and output file formats (extensions), scripts operating on the software, validated files to be used for information loss measurements, as well as quantitative measures of the information loss for conversions. The CSR focuses: on software and finding the format conversion paths described by a number of software packages and unique input and output formats. The formats themselves are represented by extensions. While not always unique, extensions are often the only accessible information when the 3rd party software is installed (often listed under the File/Open menu in most packages). The CSR also contains information about the software, operating system, software interface and scripts to execute the software. The scripts are important for the automating conversions with the 3rd party software and can be implemented using AutoHotkey scripts (Windows), AppleScript (Mac) or one of a variety of scripting languages for Unix. The information loss due to file format conversions is measured externally by different techniques within the NCSA object-to-object comparison framework called Versus. The comparison is relevant to the software domain, for example for 3D applications surface area or spin images are used and the loss (0-100 range with 100 representing no loss) for a particular software-conversion pair is stored in the database. The information loss also represents edge weights to Input/Output (I/O) Graph, a simple workflow used for finding the shortest conversion path. The CSR is written as a web service. It consists of three main components: Query, Add, Edit. In the Query mode users can a) view list of all software packages with their conversion options, b) select subsets of software in the I/O-Graph, c) search the database by conversions, software, extensions, MIME and PUID. The I/O-Graph contains all information about installed applications and the conversions they allow. The JAVA applet front end is part of the CSR web visualization interface. Section Add allows users to add new software packages with their conversion capabilities and upload the software scripts to automate them. The last section, Edit is designed for adding detailed information about the software, extensions and for uploading the test files. CSR requires users to login for adding and editing. The web fields are auto completed to help search. Sponsors: This research was partially supported by a National Archive and Records Administration (NARA) supplement to NSF PACI cooperative agreement CA #SCI-9619019. Keywords: Software, Registry, Information, Conversion, Database, Tool
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data. QIMME analyzes and transforms raw sequencing data generated on Illumina or other platforms to publication quality graphics and statistics.
View all literature mentionsSoftware tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data.
View all literature mentionsOrdination methods, diversity analysis and other functions for community and vegetation ecologists.
View all literature mentionsSoftware for handling and analysis of high-throughput microbiome census data.
View all literature mentionsQuality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.
View all literature mentionsOpen source software R package for modeling and correcting Illumina sequenced amplicon errors. Fast and accurate sample inference from amplicon data with single nucleotide resolution.
View all literature mentionsDrosophila melanogaster with name Canton-S from BDSC.
View all literature mentionsThe SciCrunch Infrastructure was developed as a cooperative data platform to be used by diverse communities in making data more FAIR.
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