{"id":8579,"date":"2023-08-07T13:28:20","date_gmt":"2023-08-07T12:28:20","guid":{"rendered":"https:\/\/mbioworks.com\/?p=8579"},"modified":"2023-08-10T13:06:36","modified_gmt":"2023-08-10T12:06:36","slug":"biofilm-bacterial-diversity-on-drinking-water-plastic-bags","status":"publish","type":"post","link":"https:\/\/mbioworks.com\/?p=8579","title":{"rendered":"Biofilm Bacterial Diversity on Drinking Water Plastic Bags"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"8579\" class=\"elementor elementor-8579\">\n\t\t\t\t\t\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-27db53e elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"27db53e\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-5e8675f\" data-id=\"5e8675f\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-5364571 elementor-widget elementor-widget-text-editor\" data-id=\"5364571\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<style>\/*! elementor - v3.11.5 - 14-03-2023 *\/\n.elementor-widget-text-editor.elementor-drop-cap-view-stacked .elementor-drop-cap{background-color:#818a91;color:#fff}.elementor-widget-text-editor.elementor-drop-cap-view-framed .elementor-drop-cap{color:#818a91;border:3px solid;background-color:transparent}.elementor-widget-text-editor:not(.elementor-drop-cap-view-default) .elementor-drop-cap{margin-top:8px}.elementor-widget-text-editor:not(.elementor-drop-cap-view-default) .elementor-drop-cap-letter{width:1em;height:1em}.elementor-widget-text-editor .elementor-drop-cap{float:left;text-align:center;line-height:1;font-size:50px}.elementor-widget-text-editor .elementor-drop-cap-letter{display:inline-block}<\/style>\t\t\t\t<h5><b>Key Takeaways<\/b><\/h5>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-5657fce elementor-widget elementor-widget-text-editor\" data-id=\"5657fce\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<ul>\n<li>\n<p>A surface polishing tool designed for hard surfaces has been effectively modified to collect biofilm biomass from plastic bags.<\/p>\n<\/li>\n<li>\n<p>An average of &gt;80 K raw tags of 16S V3-V4 regions were generated from each sample.<\/p>\n<\/li>\n<li>\n<p>Inside each of these biofilms, there are over 300 bacterial species from ~30 phyla thriving, representing a vibrant microbial community with rich biodiversity.<\/p>\n<\/li>\n<\/ul>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-14bc6b9 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"14bc6b9\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-d34964f\" data-id=\"d34964f\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-de0ffe3 elementor-widget elementor-widget-text-editor\" data-id=\"de0ffe3\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h5><b>Biofilms on Plastic Bag<\/b><\/h5>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-37c5276 elementor-widget elementor-widget-image\" data-id=\"37c5276\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<style>\/*! elementor - v3.11.5 - 14-03-2023 *\/\n.elementor-widget-image{text-align:center}.elementor-widget-image a{display:inline-block}.elementor-widget-image a img[src$=\".svg\"]{width:48px}.elementor-widget-image img{vertical-align:middle;display:inline-block}<\/style>\t\t\t\t\t\t\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"675\" height=\"675\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/biofilm_bag.png\" class=\"attachment-full size-full wp-image-8584\" alt=\"\" srcset=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/biofilm_bag.png 675w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/biofilm_bag-300x300.png 300w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/biofilm_bag-150x150.png 150w\" sizes=\"auto, (max-width: 675px) 100vw, 675px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-14f212c elementor-widget elementor-widget-text-editor\" data-id=\"14f212c\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p><strong>Biofilms: Tiny Communities with a Big Impact<\/strong><\/p><p>Imagine a bustling city of microscopic residents, all living together in a sticky, protective neighborhood. These are biofilms \u2013 clusters of tiny organisms like bacteria, forming communities on various surfaces.\u00a0<\/p><p><strong>Why Do Biofilms Love Plastic Bags?<\/strong><\/p><p>Plastic is a bit like a cozy hideout for these microorganisms. Its smooth surface doesn&#8217;t bother them, and places like hospitals or labs, where plastic bags are often used, provide the perfect moisture they need to thrive. On top of that, plastic can contain bits of stuff that these tiny residents find delicious \u2013 like a little snack to keep them going.<\/p><p><strong>Fighting Back: Keeping Biofilms in Check<\/strong><\/p><p>Storing bags in dry areas and giving them regular clean-ups can help in preventing biofilms. Some scientists are working on making special plastic that biofilms don&#8217;t like, and adding special germ-fighting ingredients. Even using sunlight in a special way, called ultraviolet (UV) light, might help keep these biofilms from causing trouble.<\/p><p>By understanding these tiny communities and finding clever ways to stop them from forming, we&#8217;re taking a step towards a cleaner, safer world. To achieve this, the very first step is to investigate who these microbes residing on the plastic bag surfaces are.<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-e63edd0 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"e63edd0\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-bd2ab7d\" data-id=\"bd2ab7d\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-20c012f elementor-widget elementor-widget-text-editor\" data-id=\"20c012f\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h5><b>Study Design<\/b><\/h5>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-1aeb0f0 elementor-widget elementor-widget-image\" data-id=\"1aeb0f0\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"1125\" height=\"1125\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/sample_bag2.png\" class=\"attachment-full size-full wp-image-8613\" alt=\"\" srcset=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/sample_bag2.png 1125w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/sample_bag2-300x300.png 300w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/sample_bag2-1024x1024.png 1024w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/sample_bag2-150x150.png 150w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/sample_bag2-768x768.png 768w\" sizes=\"auto, (max-width: 1125px) 100vw, 1125px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-4475eaf elementor-widget elementor-widget-text-editor\" data-id=\"4475eaf\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>A thin layer of biofilm was collected from the surface of the bag at different locations (front side surface, back side surface, and inside the dispenser). The sampled plastic bag has been used for a year to store drinking water treated from untreated water sources. DNA was extracted and then PCR amplified on 16S rRNA genes, followed by high throughput sequencing of PCR products.\u00a0 Bioinformatic analysis reveals the composition of the microbial community of the biofilms.<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-a6dd7d0 elementor-widget elementor-widget-text-editor\" data-id=\"a6dd7d0\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h6><b>Collection of Biofilms<\/b><\/h6>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-d5c3f4d gallery-spacing-custom elementor-widget elementor-widget-image-gallery\" data-id=\"d5c3f4d\" data-element_type=\"widget\" data-widget_type=\"image-gallery.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<style>\/*! elementor - v3.11.5 - 14-03-2023 *\/\n.elementor-image-gallery .gallery-item{display:inline-block;text-align:center;vertical-align:top;width:100%;max-width:100%;margin:0 auto}.elementor-image-gallery .gallery-item img{margin:0 auto}.elementor-image-gallery .gallery-item .gallery-caption{margin:0}.elementor-image-gallery figure img{display:block}.elementor-image-gallery figure figcaption{width:100%}.gallery-spacing-custom .elementor-image-gallery .gallery-icon{padding:0}@media (min-width:768px){.elementor-image-gallery .gallery-columns-2 .gallery-item{max-width:50%}.elementor-image-gallery .gallery-columns-3 .gallery-item{max-width:33.33%}.elementor-image-gallery .gallery-columns-4 .gallery-item{max-width:25%}.elementor-image-gallery .gallery-columns-5 .gallery-item{max-width:20%}.elementor-image-gallery .gallery-columns-6 .gallery-item{max-width:16.666%}.elementor-image-gallery .gallery-columns-7 .gallery-item{max-width:14.28%}.elementor-image-gallery .gallery-columns-8 .gallery-item{max-width:12.5%}.elementor-image-gallery .gallery-columns-9 .gallery-item{max-width:11.11%}.elementor-image-gallery .gallery-columns-10 .gallery-item{max-width:10%}}@media (min-width:480px) and (max-width:767px){.elementor-image-gallery .gallery.gallery-columns-2 .gallery-item,.elementor-image-gallery .gallery.gallery-columns-3 .gallery-item,.elementor-image-gallery .gallery.gallery-columns-4 .gallery-item,.elementor-image-gallery .gallery.gallery-columns-5 .gallery-item,.elementor-image-gallery .gallery.gallery-columns-6 .gallery-item,.elementor-image-gallery .gallery.gallery-columns-7 .gallery-item,.elementor-image-gallery .gallery.gallery-columns-8 .gallery-item,.elementor-image-gallery .gallery.gallery-columns-9 .gallery-item,.elementor-image-gallery .gallery.gallery-columns-10 .gallery-item{max-width:50%}}@media (max-width:479px){.elementor-image-gallery .gallery.gallery-columns-2 .gallery-item,.elementor-image-gallery .gallery.gallery-columns-3 .gallery-item,.elementor-image-gallery .gallery.gallery-columns-4 .gallery-item,.elementor-image-gallery .gallery.gallery-columns-5 .gallery-item,.elementor-image-gallery .gallery.gallery-columns-6 .gallery-item,.elementor-image-gallery .gallery.gallery-columns-7 .gallery-item,.elementor-image-gallery .gallery.gallery-columns-8 .gallery-item,.elementor-image-gallery .gallery.gallery-columns-9 .gallery-item,.elementor-image-gallery .gallery.gallery-columns-10 .gallery-item{max-width:100%}}<\/style>\t\t<div class=\"elementor-image-gallery\">\n\t\t\t<div id='gallery-1' class='gallery galleryid-8579 gallery-columns-4 gallery-size-thumbnail'><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon landscape'>\n\t\t\t\t<a data-elementor-open-lightbox=\"no\" href='https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/2.jpg'><img loading=\"lazy\" decoding=\"async\" width=\"150\" height=\"150\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/2-150x150.jpg\" class=\"attachment-thumbnail size-thumbnail\" alt=\"\" \/><\/a>\n\t\t\t<\/div><\/figure><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon landscape'>\n\t\t\t\t<a data-elementor-open-lightbox=\"no\" href='https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/1.jpg'><img loading=\"lazy\" decoding=\"async\" width=\"150\" height=\"150\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/1-150x150.jpg\" class=\"attachment-thumbnail size-thumbnail\" alt=\"\" \/><\/a>\n\t\t\t<\/div><\/figure><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon landscape'>\n\t\t\t\t<a data-elementor-open-lightbox=\"no\" href='https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/5.jpg'><img loading=\"lazy\" decoding=\"async\" width=\"150\" height=\"150\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/5-150x150.jpg\" class=\"attachment-thumbnail size-thumbnail\" alt=\"\" \/><\/a>\n\t\t\t<\/div><\/figure><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon portrait'>\n\t\t\t\t<a data-elementor-open-lightbox=\"no\" href='https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/8.jpg'><img loading=\"lazy\" decoding=\"async\" width=\"150\" height=\"150\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/8-150x150.jpg\" class=\"attachment-thumbnail size-thumbnail\" alt=\"\" \/><\/a>\n\t\t\t<\/div><\/figure><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon portrait'>\n\t\t\t\t<a data-elementor-open-lightbox=\"no\" href='https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/3.jpg'><img loading=\"lazy\" decoding=\"async\" width=\"150\" height=\"150\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/3-150x150.jpg\" class=\"attachment-thumbnail size-thumbnail\" alt=\"\" \/><\/a>\n\t\t\t<\/div><\/figure><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon landscape'>\n\t\t\t\t<a data-elementor-open-lightbox=\"no\" href='https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/4.jpg'><img loading=\"lazy\" decoding=\"async\" width=\"150\" height=\"150\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/4-150x150.jpg\" class=\"attachment-thumbnail size-thumbnail\" alt=\"\" \/><\/a>\n\t\t\t<\/div><\/figure><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon portrait'>\n\t\t\t\t<a data-elementor-open-lightbox=\"no\" href='https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/6.jpg'><img loading=\"lazy\" decoding=\"async\" width=\"150\" height=\"150\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/6-150x150.jpg\" class=\"attachment-thumbnail size-thumbnail\" alt=\"\" \/><\/a>\n\t\t\t<\/div><\/figure><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon portrait'>\n\t\t\t\t<a data-elementor-open-lightbox=\"no\" href='https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/7.jpg'><img loading=\"lazy\" decoding=\"async\" width=\"150\" height=\"150\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/7-150x150.jpg\" class=\"attachment-thumbnail size-thumbnail\" alt=\"\" \/><\/a>\n\t\t\t<\/div><\/figure>\n\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-44d07f2 elementor-widget elementor-widget-text-editor\" data-id=\"44d07f2\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>The biofilms at the surface of the plastic bags were collected by removing the top layer (ca. 1 mm thick) of the plastic surfaces using a sanding method with a cordless hand-held multitool (Dremel 8220) mounted with metal spinners. The metal spinner tips were heat-sterilized for 3 hours at 180 \u00b0C before use. The body of the multitool was covered with a piece of sterile plastic bag to prevent contaminations from falling onto the sample bags. 800 uL of TE buffer was placed on the sanding area of the bag. After surface sanding for 15-30 seconds, the TE solution with fine plastic powders off the bag was collected for microbiome DNA extraction.<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-1a43486 elementor-widget elementor-widget-text-editor\" data-id=\"1a43486\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h6><b>Selection of 16S rRNA Gene Region for PCR<\/b><\/h6>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-3630c8b elementor-widget elementor-widget-image\" data-id=\"3630c8b\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"1254\" height=\"865\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/primers2.png\" class=\"attachment-full size-full wp-image-8628\" alt=\"\" srcset=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/primers2.png 1254w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/primers2-300x207.png 300w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/primers2-1024x706.png 1024w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/primers2-768x530.png 768w\" sizes=\"auto, (max-width: 1254px) 100vw, 1254px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c40c81a elementor-widget elementor-widget-text-editor\" data-id=\"c40c81a\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>Most commonly used primer set of V3-V4 was selected for 16S rRNA gene metagenomics. The length of PCR products was well covered by PE250 sequencing strategy.\u00a0<\/p><p>Reference:<\/p><p>Pan et al., 2023. Microbial Diversity Biased Estimation Caused by Intragenomic Heterogeneity and Interspecific Conservation of 16S rRNA Genes. Applied and Environmental Microbiology. 89:5.\u00a0\u00a0<a href=\"https:\/\/doi.org\/10.1128\/aem.02108-22\">https:\/\/doi.org\/10.1128\/aem.02108-22<\/a>.<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-fe07d43 elementor-widget elementor-widget-text-editor\" data-id=\"fe07d43\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h6><b>DNA Extraction, PCR, Sequencing and Bioinformatics<\/b><\/h6>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-840a6be elementor-widget elementor-widget-text-editor\" data-id=\"840a6be\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p><strong>DNA extraction<\/strong><\/p><p>Microbiome DNA was extracted using a FastPure Microbiome DNA Isolation Kit (Vazyme, Nanjing, China) according to the manufacturer\u2019s instructions. DNA quantity and quality were assessed with a nano-spectrophotometer at mBioWorks Copenhagen, Denmark.<\/p><p><strong>High-throughput 16S ribosomal RNA gene sequencing<\/strong><\/p><p>The hypervariable region V3-V4 of the bacterial 16S rRNA gene was amplified with the primer pair 5&#8242;- GYGCASCAGKCGMGAAW -3&#8242; and 5&#8242;- GGACTACVSGGGTATCTAAT -3&#8242;. Both the forward and reverse 16S primers were tailed with sample-specific Illumina index sequences to allow for deep NGS sequencing. The PCR was performed in a reaction mixture of DNA template 5-50 ng, 0.3 \u03bcL forward primer (10\u03bcM), 0.3 \u03bcL reverse primer (10\u03bcM), 5 \u03bcL KOD FX Neo Buffer, 2 \u03bcL dNTP (2 mM each), 0.2 \u03bcL KOD FX Neo polymerase (Toyobo Life Sciences, Shanghai), and finally ddH2O added to a total volume of 20 \u03bcL. After initial denaturation at 95 \u00b0C for 5 min, followed by 20 cycles of denaturation at 95 \u00b0C for 30 s, annealing at 50 \u00b0C for 30 s, and extension at 72 \u00b0C for 40 s, and a final step at 72 \u00b0C for 7 min. The amplified products were purified with an Omega DNA purification kit (Omega Inc., Norcross, GA, USA) and were quantified using Qsep-400 (BiOptic, Inc., New Taipei City, Taiwan). The amplicon library was paired-end sequenced (2\u00d7250) on an Illumina Novaseq 6000.<\/p><p><strong>Bioinformatic analysis<\/strong><\/p><p><span style=\"text-decoration: underline\">NGS data pre-treatment:<\/span> Raw data were first filtered by Trimmomatic (version 0.33) with parameters: window size of 50 bp and average Q-score within the window as min. 20. Identification and<\/p><p>removal of primer sequences were processed by Cutadapt (version 1.9.1) with a maximum mismatch set as 20% and minimum coverage of 80%. PE reads were assembled by USEARCH (version 10) with a minimum length of overlap of 10 bp, minimum similarity within the overlapping region as 90%, and maximum mismatch accepted as 5 bp. The chimera removal was done using UCHIME (version 8.1). If a fragment with over 80% similarity to the query sequence is found on both parents, this query sequence was defined as a chimera sequence. The high-quality reads generated were used in the following analysis.<\/p><p><span style=\"text-decoration: underline\">ASV analysis:<\/span> DADA2 method in QIIME2 (version 2020.06) was used to de-noise sequences, generating ASVs. The conservative threshold for OTU filtration is 0.005%. Each ASV was annotated using a combination of BLAST-based method and a Naive Bayes classifier-based method. The BALST-based annotation method was done with the Classify-consensus-blast functionality in QIIME2, which identifies the annotation with the highest consensus in N best hits (default: 3). Parameter setting: minimum similarity in sequence: 90%; minimum coverage: 90%; minimum consensus: 51%. The Naive Bayes classifier-based method is processed with the classify-sklearn plugin in QIIME. The classifier needs to be trained before use in order to \u201clearn\u201d which features can be used for classification. Parameter setting: the confidence of classifier set as 0.7. In general, feature sequences are firstly BLASTed against the reference database (Silva) using classify-consensus-blast. The sequences that could not be matched in the reference database were further classified by classify-sklearn.<\/p><p><span style=\"text-decoration: underline\">Alpha diversity: <\/span>Alpha diversity was calculated using QIIME2 (<a href=\"https:\/\/qiime2.org\/\">https:\/\/qiime2.org\/<\/a>), which reflects the species richness of individual samples and the species diversity. Chao1 and Ace index measure species richness, i.e. the number of species. Shannon and Simpson\u2019s indexes are used to measure species diversity, which are affected by species richness and community evenness in the sample community. In the case of the same species richness, the higher the evenness of each species in the community is, the higher the community diversity is. A larger Shannon index and a smaller Simpson index indicate that the species diversity of the sample is higher.<\/p><p><span style=\"text-decoration: underline\">Beta diversity:<\/span> Beta diversity analysis was processed using QIIME2 (<a href=\"https:\/\/qiime2.org\/\">https:\/\/qiime2.org\/<\/a>), with the aim to compare species diversity between different samples. There are four commonly used statistical algorithm to calculate the distance between samples in beta diversity analysis, that is binary Jaccard, Bray Curtis, weighted Unifrac, and unweighted Unifrac. These four algorithms can be classified into weighted (Bray-Curtis and Weighted Unifrac) and non-weighted (Jaccard and Unweighted Unifrac). The unweighted algorithm focuses on the existence of a species, while the weighted algorithm takes both existence and abundance into consideration.<\/p><p>The unweighted Pair-group Method with Arithmetic Mean (UPGMA) distance analysis method was used to construct a clustering tree based on the similarity between samples. Distance matrices were obtained by the four distance algorithms mentioned above. Hierarchical clustering of samples was performed by UPGMA in the R language tool to determine the similarity in species composition among samples.<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-eee49a9 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"eee49a9\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-bbafaef\" data-id=\"bbafaef\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-10213c8 elementor-widget elementor-widget-text-editor\" data-id=\"10213c8\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h5><b>Results<\/b><\/h5>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-fa6fb5d elementor-widget elementor-widget-text-editor\" data-id=\"fa6fb5d\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h6><b>Raw reads quality report<\/b><\/h6>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-3403b40 elementor-widget elementor-widget-text-editor\" data-id=\"3403b40\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>A typical read quality report generated with fastqc:<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-0056b9a elementor-widget elementor-widget-image\" data-id=\"0056b9a\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"2790\" height=\"1707\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/fastqc.png\" class=\"attachment-full size-full wp-image-8639\" alt=\"\" srcset=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/fastqc.png 2790w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/fastqc-300x184.png 300w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/fastqc-1024x627.png 1024w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/fastqc-768x470.png 768w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/fastqc-1536x940.png 1536w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/fastqc-2048x1253.png 2048w\" sizes=\"auto, (max-width: 2790px) 100vw, 2790px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-d1e4182 elementor-widget elementor-widget-text-editor\" data-id=\"d1e4182\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h6><b>Summary of raw data processing<\/b><\/h6>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-09daf00 elementor-widget elementor-widget-image\" data-id=\"09daf00\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"2961\" height=\"486\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/raw_data-1.png\" class=\"attachment-full size-full wp-image-8655\" alt=\"\" srcset=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/raw_data-1.png 2961w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/raw_data-1-300x49.png 300w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/raw_data-1-1024x168.png 1024w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/raw_data-1-768x126.png 768w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/raw_data-1-1536x252.png 1536w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/raw_data-1-2048x336.png 2048w\" sizes=\"auto, (max-width: 2961px) 100vw, 2961px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-f676a86 elementor-widget elementor-widget-text-editor\" data-id=\"f676a86\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h6><b>Length distribution of effective reads after data quality control<\/b><\/h6>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-01f57d6 elementor-widget elementor-widget-image\" data-id=\"01f57d6\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"1500\" height=\"621\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/length_distribution.png\" class=\"attachment-full size-full wp-image-8654\" alt=\"\" srcset=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/length_distribution.png 1500w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/length_distribution-300x124.png 300w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/length_distribution-1024x424.png 1024w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/length_distribution-768x318.png 768w\" sizes=\"auto, (max-width: 1500px) 100vw, 1500px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-6f2c2b7 elementor-widget elementor-widget-text-editor\" data-id=\"6f2c2b7\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h6><b>Number of reads confidently classified to the known taxonomic level<\/b><\/h6>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-9d2658a elementor-widget elementor-widget-image\" data-id=\"9d2658a\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"2981\" height=\"405\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/taxa_table.png\" class=\"attachment-full size-full wp-image-8659\" alt=\"\" srcset=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/taxa_table.png 2981w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/taxa_table-300x41.png 300w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/taxa_table-1024x139.png 1024w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/taxa_table-768x104.png 768w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/taxa_table-1536x209.png 1536w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/taxa_table-2048x278.png 2048w\" sizes=\"auto, (max-width: 2981px) 100vw, 2981px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-b7ed827 elementor-widget elementor-widget-text-editor\" data-id=\"b7ed827\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>The original feature table may contain those with extremely low abundance (reads number less than 2). After removing low abundance features, a summary of annotated the number of tags that are accurately annotated at each taxonomic level, including Kingdom, Phylum, Class, Order, Family, Genus, and Species, were shown here. Detailed classification can usually be found in the file named <strong><em>OTU_table_detail.xls<\/em><\/strong>.<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-094d3de elementor-widget elementor-widget-text-editor\" data-id=\"094d3de\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h6><b>Number of taxa confidently assigned to each level<\/b><\/h6>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-b38c14d elementor-widget elementor-widget-image\" data-id=\"b38c14d\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"2958\" height=\"396\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/taxa_level.png\" class=\"attachment-full size-full wp-image-8666\" alt=\"\" srcset=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/taxa_level.png 2958w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/taxa_level-300x40.png 300w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/taxa_level-1024x137.png 1024w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/taxa_level-768x103.png 768w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/taxa_level-1536x206.png 1536w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/taxa_level-2048x274.png 2048w\" sizes=\"auto, (max-width: 2958px) 100vw, 2958px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c169c05 elementor-widget elementor-widget-text-editor\" data-id=\"c169c05\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h6><b>\u00a0Taxonomic distribution<\/b><\/h6>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-2dafaff elementor-widget elementor-widget-image\" data-id=\"2dafaff\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"1500\" height=\"1065\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/phylum_class2.png\" class=\"attachment-full size-full wp-image-8672\" alt=\"\" srcset=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/phylum_class2.png 1500w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/phylum_class2-300x213.png 300w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/phylum_class2-1024x727.png 1024w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/phylum_class2-768x545.png 768w\" sizes=\"auto, (max-width: 1500px) 100vw, 1500px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-f2c3d38 elementor-widget elementor-widget-image\" data-id=\"f2c3d38\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"1500\" height=\"1091\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/order_family2.png\" class=\"attachment-full size-full wp-image-8674\" alt=\"\" srcset=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/order_family2.png 1500w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/order_family2-300x218.png 300w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/order_family2-1024x745.png 1024w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/order_family2-768x559.png 768w\" sizes=\"auto, (max-width: 1500px) 100vw, 1500px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-9428f7d elementor-widget elementor-widget-image\" data-id=\"9428f7d\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"1500\" height=\"981\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/genus_species.png\" class=\"attachment-full size-full wp-image-8675\" alt=\"\" srcset=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/genus_species.png 1500w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/genus_species-300x196.png 300w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/genus_species-1024x670.png 1024w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/genus_species-768x502.png 768w\" sizes=\"auto, (max-width: 1500px) 100vw, 1500px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-7c13b73 elementor-widget elementor-widget-text-editor\" data-id=\"7c13b73\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h6><b>Taxonomic abundance clustering\u00a0<\/b><\/h6>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-42eab88 elementor-widget elementor-widget-image\" data-id=\"42eab88\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"1500\" height=\"1081\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/pco.png\" class=\"attachment-full size-full wp-image-8682\" alt=\"\" srcset=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/pco.png 1500w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/pco-300x216.png 300w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/pco-1024x738.png 1024w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/pco-768x553.png 768w\" sizes=\"auto, (max-width: 1500px) 100vw, 1500px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-f91d0b8 elementor-widget elementor-widget-image\" data-id=\"f91d0b8\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"1456\" height=\"1047\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/fgs2.png\" class=\"attachment-full size-full wp-image-8687\" alt=\"\" srcset=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/fgs2.png 1456w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/fgs2-300x216.png 300w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/fgs2-1024x736.png 1024w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/fgs2-768x552.png 768w\" sizes=\"auto, (max-width: 1456px) 100vw, 1456px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-786a996 elementor-widget elementor-widget-text-editor\" data-id=\"786a996\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>The clustering heat map was generated at the level of phylum, class, order, family, genus, and species. The values shown on the heatmap are z-scores generated by the z-normalization of relative abundance. The color gradient from blue to red represents the relative abundance at each row and the color gradient (blue to red) represents the relative richness (low to high).<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-e2ba03d elementor-widget elementor-widget-text-editor\" data-id=\"e2ba03d\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h6><b>Alpha diversity indices<\/b><\/h6>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-68f6972 elementor-widget elementor-widget-image\" data-id=\"68f6972\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"2956\" height=\"389\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/alpha.png\" class=\"attachment-full size-full wp-image-8691\" alt=\"\" srcset=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/alpha.png 2956w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/alpha-300x39.png 300w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/alpha-1024x135.png 1024w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/alpha-768x101.png 768w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/alpha-1536x202.png 1536w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/alpha-2048x270.png 2048w\" sizes=\"auto, (max-width: 2956px) 100vw, 2956px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-ab5ad25 elementor-widget elementor-widget-text-editor\" data-id=\"ab5ad25\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h6><b>Rarefaction curve analysis<\/b><\/h6>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-4feb7e2 elementor-widget elementor-widget-image\" data-id=\"4feb7e2\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"2560\" height=\"1679\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/rarefraction-scaled.jpg\" class=\"attachment-full size-full wp-image-8698\" alt=\"\" srcset=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/rarefraction-scaled.jpg 2560w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/rarefraction-300x197.jpg 300w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/rarefraction-1024x671.jpg 1024w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/rarefraction-768x504.jpg 768w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/rarefraction-1536x1007.jpg 1536w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/rarefraction-2048x1343.jpg 2048w\" sizes=\"auto, (max-width: 2560px) 100vw, 2560px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-cd88209 elementor-widget elementor-widget-text-editor\" data-id=\"cd88209\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>The rarefaction curve is a plot of species counts that are detected from randomly sampled data. This curve is designed to evaluate whether a set of sequencing data is adequate to detect all species from a sample, which also reflects species diversity from the side. If the curve keeps climbing towards the end, it indicates that with more data included, more species will be detected, i.e. current sequencing depth is not sufficient. If the curve gradually becomes flat, it indicates that with more data included, a limited number of new species will be found, i.e. sequencing data is adequate to present the majority of the species in a sample.<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-56b9165 elementor-widget elementor-widget-text-editor\" data-id=\"56b9165\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h6><b>UPGMA clustering with taxonomic composition at the genus level<\/b><\/h6>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-8c7365d elementor-widget elementor-widget-image\" data-id=\"8c7365d\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"1500\" height=\"529\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/UPGMA.png\" class=\"attachment-full size-full wp-image-8705\" alt=\"\" srcset=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/UPGMA.png 1500w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/UPGMA-300x106.png 300w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/UPGMA-1024x361.png 1024w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/08\/UPGMA-768x271.png 768w\" sizes=\"auto, (max-width: 1500px) 100vw, 1500px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-d468920 elementor-widget elementor-widget-text-editor\" data-id=\"d468920\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>This diagram combines the UPGMA clustering tree and histogram of species composition. Sample clustering trees on the left were constructed based on a distance algorithm as detailed in the above method, which shows the similarity between samples. Taxonomic composition in the genus level was shown as a histogram placed on the right in order to visualize similarity in species abundance.<\/p><p>Sample hierarchical clustering tree: The samples closer (with shorter branch lengths) share a higher similarity in taxonomic compositions.<\/p><p>Taxonomic composition histogram: The area of each block indicates an abundance of genus in the corresponding sample.<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-8280837 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"8280837\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-1c5354f\" data-id=\"1c5354f\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-8238c43 elementor-widget elementor-widget-text-editor\" data-id=\"8238c43\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h5><b>Acknowledgement<\/b><\/h5>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-12547c5 elementor-widget elementor-widget-text-editor\" data-id=\"12547c5\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>We thank S. Bredgaard for preparing the plastic bags, and J. B. J\u00f8rgensen and C. F. Michelsen for sharing their insights and expertise.<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>Through 16S metagenomics, we reveal a remarkably high bacterial diversity within the surface biofilms of a commercial drinking water bag after one-year use. Additionally, we introduced an innovative method for collecting biofilm bacterial biomass that adheres strongly to plastic bags.<\/p>\n","protected":false},"author":2,"featured_media":8584,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[14],"tags":[64,77,76,67],"class_list":["post-8579","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-casestudy","tag-16s","tag-bacterial-diversity","tag-biofilm","tag-metagenomics"],"_links":{"self":[{"href":"https:\/\/mbioworks.com\/index.php?rest_route=\/wp\/v2\/posts\/8579","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/mbioworks.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/mbioworks.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/mbioworks.com\/index.php?rest_route=\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/mbioworks.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=8579"}],"version-history":[{"count":121,"href":"https:\/\/mbioworks.com\/index.php?rest_route=\/wp\/v2\/posts\/8579\/revisions"}],"predecessor-version":[{"id":8792,"href":"https:\/\/mbioworks.com\/index.php?rest_route=\/wp\/v2\/posts\/8579\/revisions\/8792"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/mbioworks.com\/index.php?rest_route=\/wp\/v2\/media\/8584"}],"wp:attachment":[{"href":"https:\/\/mbioworks.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=8579"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/mbioworks.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=8579"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/mbioworks.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=8579"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}