--- title: "Metagenomics" lang: en url: https://www.gereallife.com/en/services/metagenomics.html canonical: https://www.gereallife.com/en/services/metagenomics.html entity: Shanghai Gereallife Biotech Co., Ltd updated: 2026-11-02 --- # Metagenomics Shotgun Metagenomics — Species & Functional Gene Profiling Shotgun metagenomic sequencing requires no amplification or cultivation — total DNA from environmental samples is randomly sequenced, yielding microbial species composition and functional-gene information in a single experiment. After assembly, gene prediction and non-redundant gene-set construction, taxonomic and functional annotation (GO / KEGG / COG / CAZy / CARD) is completed, followed by community composition, diversity and differential analyses. 6 G Sequencing Data Volume SEQUENCING DATA 5 Functional Databases FUNCTIONAL DATABASES 8 Analysis Modules ANALYSIS MODULES ## Technical Specifications TECHNICAL SPECIFICATIONS | Item | Details | | --- | --- | | Sequencing Data Volume | 6 G / 10G | | Assembly | Assembly into contigs with MEGAHIT (succinct de Bruijn graph); N50, contig counts and length distributions reported | | Gene Prediction | Prodigal predicts prokaryotic and metagenomic ORFs, outputting gene sequences, protein sequences and GFF files | | Non-redundant Gene Set | MMseqs2 clustering at 95% identity and 90% alignment coverage for dereplication; gene abundance quantified by Bowtie2 mapping | | Taxonomic & Functional Annotation | Taxonomic annotation by DIAMOND against NCBI-NR; functional annotation across five databases — GO, KEGG, COG, CAZy and CARD (including antibiotic resistance ontology ARO) | ## Analysis Workflow ANALYSIS WORKFLOW 1 Data QC Raw · cleaned data 2 Assembly MEGAHIT · contigs 3 Gene Prediction Prodigal · ORF 4 Gene-set construction MMseqs2 · Bowtie2 5 Functional annotation NR / KEGG / CAZy 6 Composition analysis Venn · Bar · heatmap 7 Diversity analysis Alpha · Beta 8 Differential Analysis LEfSe · rank-sum tests ## Bioinformatics Analyses BIOINFORMATIC MODULES | Module | Core Methods & Metrics | Key Outputs | | --- | --- | --- | | Sequencing Statistics | Raw fastq (R1/R2) statistics: data volume, read counts, base counts, Q20/Q30 and GC content; base retention rate after adapter trimming and quality filtering | Raw and cleaned data statistics tables, base-quality and content distribution plots | | Assembly | MEGAHIT (succinct de Bruijn graph) assembles effective sequences per sample into contigs; N50, contig counts and length distributions reported | Assembly statistics tables, length distribution plots | | Gene Prediction | Prodigal predicts prokaryotic and metagenomic ORFs and coding regions, outputting gene sequences, protein sequences and GFF files | Gene sequence files, protein sequence files, GFF | | Non-redundant Gene Set | MMseqs2 clustering at 95% identity and 90% alignment coverage for dereplication; per-sample effective reads mapped to the gene set with Bowtie2 for abundance | Non-redundant gene set, gene abundance tables | | Taxonomic & Functional Annotation | DIAMOND against NCBI-NR for taxonomic annotation with abundance computed from domain to species; functional annotation across GO, KEGG, COG, CAZy and CARD (including ARO) | Annotation summary tables, per-database level abundance tables | | Composition analysis | Venn diagrams, community bar plots and abundance heatmaps at species (Species/Genus/Family, etc.) and function (KO/COG/CAZy/ARO/GO/Pathway) levels | Venn diagram, community bar plots, heatmap | | Diversity analysis | Alpha-diversity indices with intergroup boxplots; beta-diversity distance matrices, hierarchical clustering, PCA / PCoA / NMDS ordination and ANOSIM tests | Index boxplots, PCA / PCoA / NMDS plots, ANOSIM plots | | Differential Analysis | LEfSe (LDA) at species and functional levels; intergroup Wilcoxon rank-sum tests to screen differential taxa and functional units | LEfSe plots, LDA bar charts, differential test tables | ## Example Results SELECTED FIGURES FROM ACTUAL REPORTS Contig Length Distribution Length-interval distribution of assembled contigs per sample, with N50 and other assembly metrics. KEGG Functional Annotation Gene counts at KEGG level-2 pathways, colored by major categories such as metabolism and genetic information processing. CAZy Annotation Gene counts across the six functional modules (GH / GT / PL / CE / AA / CBM). Shared / Unique Species Venn Diagram Shared and unique species between Treat and Con groups. Species Composition Bar Plot (Genus) Genus-level relative abundance per sample, visualizing intergroup community-structure differences. Species Abundance Heatmap (Excerpt) Abundance distribution and hierarchical clustering of top species across samples; selected species shown. PCA (Species) Principal-component score plot showing inter-sample compositional differences and within-group clustering. PCoA (Species, Bray-Curtis) Principal coordinates analysis on species distance matrices; confidence ellipses show group structure. LEfSe LDA Bar Chart (Excerpt) Significantly different species between groups with LDA scores; colors distinguish groups; top items shown. ## Applications APPLICATIONS Microbiome Functional Potential Novel Gene & Pathway Discovery Resistance Genes & Environmental Monitoring Host–Microbe Interactions Metagenome-Assembled Genomes ## FAQ FAQ How long does a Metagenomics 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 Metagenomics? 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 ### Amplicon Sequencing Amplicon Sequencing ### 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