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Metagenomic Sequencing

Service Overview
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Metagenomic SequencingIn metagenomics, genomes from environmental samples are analyzed without the prior isolation and cultivation of individual species; therefore, it is a powerful technique for studying microbial communities in their natural habitat, with a broad range of applications. At Novogene, our customers can rely on our expertise in NGS to help them explore the rich genetic repertoire of microbial communities, while also benefiting from our bioinformatics expertise to help identify the species, genes, and pathways represented in their samples. Novogene provides metagenomic sequencing service with Illumina HiSeq platform and assembly-first strategy, and our bioinformatics analyses provide gene predictions, function annotations, and taxonomic annotations. Our standard analysis package includes mPATH, heatmaps, PCA, cluster analysis, and other programs, generating high-quality, publication-ready data.

The Novogene Advantage

  • Highly experienced: We have completed over 400 metagenomic sequencing projects for our customers, and have published multiple metagenomic studies.
  • Outstanding service: We provide high-quality sequencing, an efficient standard workflow, and bioinformatics analyses at a cost-effective price.
  • Effective methodology: Our techniques enhance the generation of data from low-abundance species.
  • Comprehensive analysis: Expert bioinformatics analysis with three databases (KEGG, eggNOG, CAZy) provides comprehensive data on annotated genes and metabolic pathways.

Project Workflow

metagenomic sequencing project workflow

Sequencing Strategy

  • 350 bp insert DNA library
  • Illumina platform, paired-end 150 bp

Data Quality Guarantee

  • For each sample, 6Gb and 12Gb packages are offered, with Q30 ≥ 80%.

Sample Requirements

  • DNA amount: ≥ 1 μg
  • DNA concentration: ≥ 20 ng/μl
  • DNA volume: ≥ 20 μl
  • Purity: No degradation, no RNA contamination

Turnaround Time

  • Within 25 working days from verification of sample quality (without data analysis)
  • Additional 10 working days for data analysis

Recommended Sequencing Depth

  • Two strategies: 6 Gb raw data or 12 Gb raw data

Analysis Pipeline

metagenomic sequencing analysis pipeline

List of Analyses

  • Our standard analysis package includes gene prediction, function annotation, and taxonomic annotation, mPATH, heatmaps, PCA, Krona, cluster analysis, MetaStats, and OG-Taxa.
  • Our advanced analysis package includes MRPP, ANOSIM, NMDS (Non-metric Multidimensional Scaling), CCA/RAD, and LEfSe (LDA Effect Size).
Table. The following table shows sample data from metagenomic sequencing projects conducted by Novogene. The effective rate, comparing clean data to raw data, was very high, with an average of over 94%, indicating that the base calling was highly accurate.
Sample Insert Size (bp) Raw Data Clean Data Clean_Q20 Clean_Q30 Clean_ GC (%) Effective Rate (%)
Test1 300 5,491.78 5,273.46 94.06 88.54 52.17 96.03
Test2 300 5,263.63 5,004.54 94.20 88.82 51.13 95.08
Test3 300 5,471.88 5,090.86 93.74 87.90 54.05 93.04
Test4 300 5,337.27 5,142.07 93.81 88.21 50.45 96.34
Test5 300 5,781.12 5,700.68 95.97 91.90 42.47 98.61
Test6 300 4,325.69 4,259.49 94.20 88.62 50.23 98.47

Project Example

The following study utilized Novogene's expert metagenomic sequencing services. Gut microbiota dysbiosis contributes to the development of hypertension Microbiome 5:14 (2017) In this study, the relationship between gut microbiota dysbiosis and hypertension, a highly prevalent cardiovascular disease, was examined using Novogene’s comprehensive metagenomic sequencing service. There was significantly less richness and diversity in the gut microbiome of subjects with pre-hypertension and primary hypertension compared to those of healthy control subjects. Pre-hypertensive and hypertensive subjects also presented below average levels of bacteria associated with healthy-status, as well as increased disease-associated microbial functions. The microbiomes in pre-hypertensive and hypertensive subjects were revealed to be significantly similar, and the characteristic metabolic changes found in both conditions were strongly associated with gut microbiota dysbiosis. Further fecal transplantation experiments demonstrated the direct effects of the gut microbiome on blood pressure, with hypertension-associated microbiota causing elevated blood pressure in transplant recipient mice. This study illustrates how the comprehensive metagenomic sequencing solution offered by Novogene was able to support research into the underlying relationship between gut microbiota dysbiosis and hypertension development.
Figure. Gut microbiota genera strikingly different across groups

Examples of Publications Using Novogene’s Services

Journal Title
Environmental Science & Technology, 49:1095-1104 (2015) Prevalence of antibiotic resistance genes and bacterial pathogens in long-term manured greenhouse soils as revealed by metagenomic survey.
Chemical Engineering Journal, 277:116-123 (2015) Metagenomic insights into salinity effect on diversity and abundance of denitrifying bacteria and genes in an expanded granular sludge bed reactor treating high-nitrate wastewater.
Scientific Reports, 5:8605 (2015) Impacts of the Three Gorges Dam on microbial structure and potential function.
Water research, 76:43-52 (2015) Metagenomic insights into Cr (VI) effect on microbial communities and functional genes of an expanded granular sludge bed reactor treating high-nitrate wastewater.
Water Research, 98:261-269 (2016) Changes of resistome, mobilome and potential hosts of antibiotic resistance genes during the transformation of anaerobic digestion from mesophilic to thermophilic.
Microbiome, 5:14 (2017) Gut microbiota dysbiosis contributes to the development of hypertension.
Nature Communications, 9: 2020 (2018) Hypoxia induces senescence of bone marrow mesenchymal stem cells via altered gut microbiota.