{"id":10,"date":"2025-10-24T15:53:40","date_gmt":"2025-10-24T06:53:40","guid":{"rendered":"https:\/\/bs-p.tokyo\/biz\/?page_id=10"},"modified":"2025-12-24T17:17:13","modified_gmt":"2025-12-24T17:17:13","slug":"bio-infomatics","status":"publish","type":"page","link":"https:\/\/bs-p.tokyo\/biz\/?page_id=10","title":{"rendered":"Bioinformatics"},"content":{"rendered":"\n<div class=\"wp-block-cover is-light\"><video class=\"wp-block-cover__video-background intrinsic-ignore\" autoplay muted loop playsinline src=\"https:\/\/bs-p.tokyo\/biz\/wp-content\/uploads\/sites\/2\/2025\/10\/banner_1200x400.mp4\" data-object-fit=\"cover\"><\/video><span aria-hidden=\"true\" class=\"wp-block-cover__background has-background-dim\" style=\"background-color:#FFF\"><\/span><div class=\"wp-block-cover__inner-container is-layout-constrained wp-block-cover-is-layout-constrained\">\n<h1 class=\"wp-block-heading has-text-align-left has-text-color has-link-color has-xxlarge-font-size wp-elements-f5570f9af323e8ea154ce69a0fb020ad\" style=\"color:#daede9\"><strong><em>Bio Informatics<\/em><\/strong><\/h1>\n<\/div><\/div>\n\n\n\n<h1 class=\"wp-block-heading\">16S rRNA Microbiome Analysis Support<\/h1>\n\n\n\n<p>We provide a comprehensive service from pipeline construction using Qiime2\/DADA2\/SILVA to quality control, taxonomy assignment, \u03b1\/\u03b2 diversity analysis, and visualization.<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Examples of applicable samples: Saliva, stool, environmental samples, etc.,&nbsp;capable of batch analysis of&nbsp;<strong>400 samples<\/strong><\/li>\n\n\n\n<li>Requirements definition \u2192 Analysis environment construction \u2192 Pipelining \u2192 Report\/reproduction procedure<\/li>\n<\/ul>\n\n\n\n<figure class=\"wp-block-image\"><img loading=\"lazy\" decoding=\"async\" width=\"1600\" height=\"400\" src=\"https:\/\/bs-p.tokyo\/biz\/wp-content\/uploads\/sites\/2\/2025\/10\/microbiome_overview_en_fixed.png\" alt=\"\" class=\"wp-image-172\" srcset=\"https:\/\/bs-p.tokyo\/biz\/wp-content\/uploads\/sites\/2\/2025\/10\/microbiome_overview_en_fixed.png 1600w, https:\/\/bs-p.tokyo\/biz\/wp-content\/uploads\/sites\/2\/2025\/10\/microbiome_overview_en_fixed-300x75.png 300w, https:\/\/bs-p.tokyo\/biz\/wp-content\/uploads\/sites\/2\/2025\/10\/microbiome_overview_en_fixed-1024x256.png 1024w, https:\/\/bs-p.tokyo\/biz\/wp-content\/uploads\/sites\/2\/2025\/10\/microbiome_overview_en_fixed-768x192.png 768w, https:\/\/bs-p.tokyo\/biz\/wp-content\/uploads\/sites\/2\/2025\/10\/microbiome_overview_en_fixed-1536x384.png 1536w\" sizes=\"auto, (max-width: 1600px) 100vw, 1600px\" \/><\/figure>\n\n\n\n<h2 class=\"wp-block-heading\">Key points of reference research (Japanese summary)<\/h2>\n\n\n\n<p>In Alzheimer&#8217;s disease (AD) model mice,&nbsp;<strong>a decrease in gut microbiota diversity, an increase in the Firmicutes\/Bacteroidetes ratio, and translocation of bacteria to the pancreas and other organs<\/strong>&nbsp;were observed.<br>Dietary supplementation with&nbsp;<strong>L-arginine and limonoids<\/strong>&nbsp;improved the diversity of the gut microbiota and tended to suppress inflammation, oxidative stress, and neurodegeneration in the liver, pancreas, and brain.<br>This research suggests that&nbsp;<strong>gut-pancreas-liver-brain interactions<\/strong>&nbsp;may be involved in AD pathology, supporting the hypothesis that correcting the gut environment may help slow the progression of neurodegeneration.<br>(Source: Minamisawa et al., 2021; PubMed\/MDPI)<\/p>\n\n\n\n<p>For details, please refer to the original paper.<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>PubMed Abstract: Minamisawa M. et al.,&nbsp;<a href=\"https:\/\/www.mdpi.com\/2075-1729\/12\/1\/34\"><em>Life<\/em>&nbsp;12(1):34<\/a>, 2021. <\/li>\n\n\n\n<li>MDPI article page (JS required): <a href=\"https:\/\/www.mdpi.com\/2075-1729\/12\/1\/34\">Life 12(1):34<\/a>. <\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Implementation details<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">environment construction<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Selection and assembly of analysis hardware<\/li>\n\n\n\n<li>Building Python\/Anaconda on Linux<\/li>\n\n\n\n<li>Creating a Qiime2 pipeline<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Quality control and pretreatment<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>FASTQ (paired-end) quality check by DADA2<\/li>\n\n\n\n<li>Cropping\/Filtering\/Denoising<\/li>\n\n\n\n<li>High-quality ASV table creation<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Annotation and analysis<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>SILVA DB construction and reference settings<\/li>\n\n\n\n<li>Taxonomy assignment<\/li>\n\n\n\n<li>\u03b1\/\u03b2 diversity analysis (Shannon, Faith PD \/ UniFrac, etc.)<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">visualization<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>taxonomy-bar-plot<\/li>\n\n\n\n<li>Heat map (relative abundance and indicator bacteria)<\/li>\n\n\n\n<li>Principal coordinate analysis (PCoA)<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Reproducibility and transferability<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Steps to reproduce fixed parameter version<\/li>\n\n\n\n<li>Semi-automation using Snakemake\/shell etc. (optional)<\/li>\n\n\n\n<li>Proposal for recalculating results\/comparing differences<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Report<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Clarification of analysis policy\/preprocessing conditions<\/li>\n\n\n\n<li>Interpretation of statistical tests and visualizations<\/li>\n\n\n\n<li>Proposal for next action (hypothesis \u2192 additional analysis)<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Strengths<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>On a scale of 400 samples ,&nbsp;<\/strong><strong>parameters were optimized stepwise<\/strong>&nbsp;while observing the results&nbsp;, and repeated analysis was carried out from different angles.<\/li>\n\n\n\n<li><strong>We provide more exploratory and flexible<\/strong>&nbsp;analysis than general contract services&nbsp;(going back and forth between hypothesis testing and visualization).<\/li>\n\n\n\n<li><strong>We provide comprehensive<\/strong>&nbsp;support from requirements definition to environment and pipeline construction and reporting&nbsp;.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Representative deliverables (examples)<\/h2>\n\n\n\n<figure class=\"wp-block-image\"><img decoding=\"async\" src=\"https:\/\/bs-p.tokyo\/biz\/wp-content\/uploads\/sites\/2\/2025\/10\/taxonomy_bar_plot_placeholder.png\" alt=\"\"\/><figcaption class=\"wp-element-caption\">Taxonomy Bar Plot (intergroup comparison\/composition ratio of major genera)<br><br><\/figcaption><\/figure>\n\n\n\n<figure class=\"wp-block-image\"><img decoding=\"async\" src=\"https:\/\/bs-p.tokyo\/biz\/wp-content\/uploads\/sites\/2\/2025\/10\/heatmap_placeholder.png\" alt=\"\"\/><figcaption class=\"wp-element-caption\">Heatmap (major taxa x samples, with clustering)<br><br><br><\/figcaption><\/figure>\n\n\n\n<figure class=\"wp-block-image\"><img decoding=\"async\" src=\"https:\/\/bs-p.tokyo\/biz\/wp-content\/uploads\/sites\/2\/2025\/10\/pcoa_placeholder.png\" alt=\"\"\/><figcaption class=\"wp-element-caption\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/bs-p.tokyo\/biz\/wp-content\/uploads\/sites\/2\/2025\/10\/pcoa_placeholder.png\" alt=\"\" width=\"750\" height=\"150\">PCoA (UniFrac distance)<\/figcaption><\/figure>\n\n\n\n<h2 class=\"wp-block-heading\">How to proceed<\/h2>\n\n\n\n<ol class=\"wp-block-list\">\n<li><strong>Requirements hearing<\/strong>&nbsp;: Objectives, hypotheses, and benchmark definition<\/li>\n\n\n\n<li><strong>Environment and data reception<\/strong>&nbsp;: Determine metadata format\/naming rules<\/li>\n\n\n\n<li><strong>Pretreatment\/QC<\/strong>&nbsp;: Tentative determination of DADA2 conditions \u2192 Small-scale test<\/li>\n\n\n\n<li><strong>Main analysis<\/strong>&nbsp;: taxonomy, diversity, visualization, statistics<\/li>\n\n\n\n<li><strong>Report<\/strong>&nbsp;: Result interpretation, parameters\/reproduction steps, next actions<\/li>\n<\/ol>\n\n\n\n<h2 class=\"wp-block-heading\">inquiry<\/h2>\n\n\n\n<p>Let us know your requirements and data situation, and we&#8217;ll propose the appropriate scope and implementation plan.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>16S rRNA Microbiome Analysis Support We provide a comprehensive service from pipeline construction using Qiime2\/DADA2\/SILVA to quality control, taxonomy assignment, \u03b1\/\u03b2 diversity analysis, and visualization. Key points of reference research (Japanese summary) In Alzheimer&#8217;s disease (AD) model mice,&nbsp;a decrease in gut microbiota diversity, an increase in the Firmicutes\/Bacteroidetes ratio, and translocation of bacteria to the&#8230;<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_kad_post_transparent":"default","_kad_post_title":"hide","_kad_post_layout":"normal","_kad_post_sidebar_id":"","_kad_post_content_style":"default","_kad_post_vertical_padding":"","_kad_post_feature":"","_kad_post_feature_position":"","_kad_post_header":false,"_kad_post_footer":false,"_kad_post_classname":"","footnotes":""},"class_list":["post-10","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/bs-p.tokyo\/biz\/index.php?rest_route=\/wp\/v2\/pages\/10","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/bs-p.tokyo\/biz\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/bs-p.tokyo\/biz\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/bs-p.tokyo\/biz\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/bs-p.tokyo\/biz\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=10"}],"version-history":[{"count":17,"href":"https:\/\/bs-p.tokyo\/biz\/index.php?rest_route=\/wp\/v2\/pages\/10\/revisions"}],"predecessor-version":[{"id":360,"href":"https:\/\/bs-p.tokyo\/biz\/index.php?rest_route=\/wp\/v2\/pages\/10\/revisions\/360"}],"wp:attachment":[{"href":"https:\/\/bs-p.tokyo\/biz\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=10"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}