--- title: "Amplicon Sequencing" lang: en url: https://www.gereallife.com/en/services/amplicon.html canonical: https://www.gereallife.com/en/services/amplicon.html entity: Shanghai Gereallife Biotech Co., Ltd updated: 2026-11-02 --- 16S AMPLICON SEQUENCING # Amplicon Sequencing 16S / 18S / ITS Amplicon Sequencing — Microbial Diversity & Community Profiling Amplicon sequencing targets specific regions of microbial marker genes — 16S rRNA (bacteria/archaea), 18S (eukaryotic microbes) and ITS (fungi) — for high-throughput sequencing, profiling community structure without isolation or culture. After QC, OTU clustering and taxonomic annotation, we perform community composition, alpha/beta diversity and intergroup differential analyses, with PICRUSt2 functional prediction supported. PE250 Illumina MiSeq Paired-end PAIRED-END 250 bp 50,000 reads / sample READS PER SAMPLE 8 Analysis Modules ANALYSIS MODULES ## Technical Specifications TECHNICAL SPECIFICATIONS | Item | Details | | --- | --- | | Sequencing Platform | Illumina MiSeq PE250（16S / 18S / ITS） | | Analysis Strategy | OTU / ASV analysis, 50,000 reads per sample | | Taxonomy Databases | RDP classifier Bayesian algorithm; reference databases Silva 138 (16S/18S) and Unite 7.0 (ITS); community composition statistics across 7 ranks (domain to species) | | Functional Prediction | PICRUSt2 predicts functional abundance from marker genes (KEGG orthologs KO, EC enzyme classes) | | Standard Delivery | Raw data + analysis report | ## Analysis Workflow ANALYSIS WORKFLOW 1 Data QC PE merging · filtering 2 OTU Clustering Dereplication · chimera removal 3 Taxonomy Annotation RDP · Silva 138 4 Composition Venn · Bar · heatmap 5 Alpha Diversity Rarefaction · indices 6 Beta Diversity PCoA · NMDS 7 Differential Taxa LEfSe · rank-sum tests 8 Functional Prediction PICRUSt2 · KEGG ## Bioinformatics Analyses BIOINFORMATIC MODULES | Module | Core Methods & Metrics | Key Outputs | | --- | --- | --- | | Data QC | PE reads merged by overlap; sequences are quality-controlled, filtered and demultiplexed before clustering/denoising and taxonomic analysis | Filtering statistics table, base-quality distribution plots | | OTU Clustering | Non-redundant sequences extracted and singletons removed; OTUs clustered at 97% similarity with chimera removal during clustering | OTU abundance table, annotated OTU table, taxon statistics table | | Taxonomy Annotation | Taxonomic annotation with the RDP classifier Bayesian algorithm; Silva 138 (16S/18S) and Unite 7.0 (ITS) reference databases; composition statistics across 7 ranks (domain/kingdom/phylum/class/order/family/genus/species) | Absolute / relative abundance tables at each taxonomic rank | | Composition | Shared and unique OTU statistics between groups; community bar plots at each taxonomic level; abundance heatmap with two-way clustering of taxa and samples | Venn diagram, community bar plots, heatmap | | Alpha Diversity | Richness (Chao1/Ace), diversity (Shannon/Simpson), evenness (Pielou), phylogenetic diversity (PD) and coverage; rarefaction, Shannon-Wiener and rank-abundance curves | Three curve plots, intergroup boxplots of indices and test tables | | Beta Diversity | Inter-sample distance matrices (Bray-Curtis / Jaccard / UniFrac); UPGMA hierarchical clustering; PCA / PCoA / NMDS ordination; ANOSIM / adonis intergroup tests | Distance-matrix heatmap, clustering tree, PCA / PCoA / NMDS plots | | Differential Taxa Analysis | LEfSe linear discriminant analysis effect size (LDA scores); Wilcoxon rank-sum test for two groups and Kruskal test for multiple groups to identify significantly enriched taxa | LEfSe cladogram, LDA bar chart, differential test tables | | Functional Prediction | PICRUSt2 prediction of functional abundance from marker genes (KEGG orthologs KO, EC classes); PCoA of functional units; LEfSe and MetagenomeSeq differential analysis of KEGG / MetaCyc pathways | Functional abundance tables, functional PCoA plot, pathway LEfSe plots | ## Example Results SELECTED FIGURES FROM ACTUAL REPORTS Shared / Unique OTU Venn Diagram Shared and unique OTUs across KO / OE / WT groups; numbers in overlapping areas indicate shared features. Community Composition Bar Plot (Genus Level) Relative genus-level abundance per sample; low-abundance taxa grouped as 'other'. Taxon Abundance Heatmap (Genus Level) Abundance distribution of top genera across samples, with two-way hierarchical clustering of taxa and samples. Rarefaction Curve Observed taxa versus randomly sampled sequences, assessing whether sequencing depth is sufficient. Shannon-Wiener Curve Shannon diversity index at increasing sequencing depths; a plateau indicates sufficient data volume. Alpha Diversity Intergroup Boxplot Distribution and significance testing of the Ace richness index across groups, with significance markers. PCA (OTU Level) Principal-component score plot of community-structure differences, annotated with R² and test p-values. PCoA (Bray-Curtis) Principal coordinates analysis on distance matrices; confidence ellipses show intergroup structural differences. LEfSe Cladogram Taxonomic distribution of significantly different taxa between groups; colors indicate the enriched group. ## Applications APPLICATIONS Gut Microbiota Profiling Environmental Microbial Diversity Fermentation Microbiome Monitoring Plant Rhizosphere Microbiome Microbiome-Metabolome Integration ## FAQ FAQ How long does a Amplicon Sequencing project take? From sample QC approval, standard timelines are 3-6 weeks (library prep, sequencing and bioinformatics included); large cohorts or deep custom analyses follow the confirmed study plan. What if my samples fail QC? Failed QC is reported immediately with reasons, and we discuss resampling or plan adjustments with you — sequencing never proceeds without qualification. What bioinformatics is included? Can I add custom analyses? Standard delivery covers QC, mapping/assembly, quantification, differential and functional enrichment analyses. Custom deep-dive and multi-omics integrative analyses are supported on request. What samples do you need for Amplicon Sequencing? Total RNA ≥1 μg with RIN ≥7 (snap-frozen, dry ice); microbial and faecal samples ≥200 mg (sterile, −80 °C); whole blood for WGS ≥500 μL (EDTA only, never heparin). RNA integrity matters more than concentration. See Technical Resources → Sample Guide . ## Related Services RELATED SERVICES ### Eukaryotic RNA-seq Eukaryotic RNA-seq ### Metagenomics Metagenomics ### Whole Genome Sequencing Whole Genome Sequencing Delivery timing: sample shipping, customs declaration and similar steps may extend turnaround; actual project timelines prevail. ## Request a Quote or Study Design Tell us about your project — we reply within one business day (free assessment) Name Organization Phone or WeChat Service of interest Sample type, number of samples and aims (optional) Submit Used only for this enquiry; never shared. ## Start Your Multi-omics Project Free study design · Interactive execution · In-depth data interpretation HOTLINE 400-660-8826 EMAIL market@gereallife.com Official Channels OFFICIAL CHANNELS Official Account WECHAT OFFICIAL ACCOUNT WeChat Service CUSTOMER SERVICE Xiaohongshu XIAOHONGSHU Call us： 400-660-8826 Scan to chat on WeChat