Introduction to Shotgun Metagenomic Sequencing
Shotgun metagenomic sequencing provides information on the total genomic DNA from all organisms in a sample, avoiding the need for isolation and cultivation of microorganisms or amplification of target regions. This is crucial because it is believed that nearly 99% of all microorganisms cannot be cultivated in the laboratory. Unlike the targeted approach used in the 16S/18S/ITS amplicon sequencing, shotgun metagenomic sequencing uses next-generation sequencing (NGS) technology to provide not only information on the taxonomic annotations of each organism, but also the functional profiling, gene prediction and microbial interaction of the whole community.
With extensive experience and well-developed bioinformatics pipelines, our services can help you determine the genomes, functions, and variations of microorganisms from diverse samples. Novogene’s shotgun metagenomic sequencing service delivers high-quality data, publication-ready results, and personalized analysis to meet different research objectives. Novogene offers comprehensive metagenomics solutions, from the study of community structure and species classification to system evolution, gene function, and metabolic network of environmental microorganisms.
Applications of Shotgun Metagenomic Sequencing
From taxonomic profiling to functional analysis and metabolic networks, shotgun metagenomic sequencing can be used in many different research topics, including:
- Annotation of microbial composition and function
- Detection of microbes of interest related to human health, environmental recovery, and energy synthesis
- Deep investigation of the genetic makeup and metabolism of microbes for drug development
- Investigation of the microbe-host relationship, which can also be related to the development of new drugs
Benifits of Novogene Shotgun Metagenomic Sequencing
- Shotgun metagenomic sequencing can be used to sequence multiple microorganisms, all in a single run, without specific isolation and cultivation of microorganisms or the amplification of target regions for either prokaryotes or eukaryotes. The sequencing results provide complete information not only pertaining to microbial diversity, but also functional diversity in the sample.
- Novogene has extensive experience providing metagenomic sequencing services to help clients obtain information about many different sample types, including soil, fecal, and water. Our newly improved metagenome assembly pipeline gives us the ability to provide long-read assembly services. This exciting development has made it possible to achieve complete maps of certain bacteria and fungi for the purposes of taxonomy resolution and functional annotation.
- Quick shipment to our UK or German lab.
Microbial Metagenomics and Whole Genome Sequencing Service Flyer
In shotgun metagenomic sequencing, genomes from environmental samples are analysed, without the prior isolation and cultivation of individual species. Therefore, it is a powerful technique for studying microbial communities in their natural habitat. 16S/18S/ITS amplicon metagenomic sequencing is frequently used to identify and differentiate microbial species. Short (<500 bp) hypervariable regions of conserved genes are amplified by PCR and analysed using next generation sequencing (NGS) technology.
On-demand Webinar
Unfolding the Microbial World: A Journey through Sequencing Applications
The microbial world is teeming with an estimated one trillion species, only a fraction of which, approximately 155,000, have been sequenced so far. For researchers interested in the microbiome, the advent of next-generation sequencing (NGS) technologies and advanced data analysis methods presents an unparalleled opportunity to delve deeper into the intricacies of the microbial universe – whether you are interested in a single species or a microbial community. NGS serves as a pivotal tool, allowing us to dissect microbial communities, unravelling their complexities and unveiling their profound impact on diverse ecosystems.
In this webinar we will talk about myriad microbial sequencing options such as microbial whole genome sequencing, metagenomics, and metatranscriptomics. We will also discuss recent advances in the field such as the applications of long-read sequencing and highlight Novogene’s diverse microbial sequencing solutions to aid your research.
Learning Objectives:
- Explore sequencing options for individual microbial species or communities
- Discover recent advances in microbial sequencing technologies
- Understand workflow and analysis pipelines for microbial sequencing.
Long-read sequencing, the next era of genomics
In this webinar, guest speaker Thea Zieglar, Sequencing Application Sales Specialist at PacBio, and Shi-qi Ann, Deputy Product Marketing Director at Novogene, will guide you through HiFi long-read sequencing with the PacBio Revio.
Learning Objectives:
- Understand the principle and advantages of highly accurate long-read sequencing to explore the full spectrum of genetic variation
- Gain an overview of our most important applications, as well as possible options for whole genome sequencing, targeted sequencing, RNA sequencing and microbial genomics
- Understand how PacBio long-read sequencing of extended 16S amplicons enables identification of metagenome community members at higher taxonomic resolution than common methods
- Learn how Kinnex full-length RNA and single-cell RNA sequencing enables scientists to capture full-length isoforms, elucidating isoform diversity in development and disease.
Metagenomic Specifications: DNA Sample Requirements
| Sample Type | Amount | Volume | Concentration | Purity |
| Total DNA | ≥ 200 ng | ≥20 μL | ≥ 10 ng/μL | A260/280 = 1.8-2.0 |
Note: Sample amounts displayed are for reference only. Download the Service Specifications or Sample Requirements to learn more. For detailed information, please contact us with your customized requests.
Metagenomic Specifications: Sequencing and Analysis
| Sequencing Platform | Illumina NovaSeq X Plus |
| Read Length | Pair-end 150 bp |
| Recommended Sequencing Depth | ≥ 40 million read pairs per sample for species with reference genome |
| Standard Data Analysis |
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Note: Sequencing depths and analysis contents listed are for reference only. Download the Service Specifications to learn more. For detailed information, please contact us.
Project Workflow of Novogene Metagenomic Sequencing Services
In order to ensure the accuracy and reliability of the sequencing data, quality control (QC), consistent with our high scientific standards, is performed at each step of the procedure. The shotgun metagenomic sequencing workflow comprises these main steps: sample preparation and quantification, fragmentation and library preparation, library quality control, sequencing, and bioinformatics analysis.

Featured publications with Novogene Shotgun Metagenomic Sequencing service
Shotgun Metagenomic Sequencing is a flexible approach to obtain microbial genomes among environments (de novo assembly), as well as gene functions (function annotation), and how they interact with each other (pathway analysis). Here presents a list of academic publications that have used Novogene Shotgun Metagenomic Sequencing services.
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Cancer MedicineIssue Date: 13 January 2025IF: 2.9DOI: https://doi.org/10.1002/cam4.70589
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Host genetic regulation of human gut microbial structural variation
NATUREIssue Date: 3 January 2024IF: 64.8DOI: 10.1038/s41586-023-06893-w
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Synergy and oxygen adaptation for development of next-generation probiotics
NATUREIssue Date: 2 August 2023IF: 64.8DOI: 10.1038/s41586-023-06378-w
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Cell Host & MicrobeIssue Date: 20 January 2023IF: 31.316DOI: 10.2139/ssrn.4327346
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Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags
Nature MicrobiologyIssue Date: 19 March 2024IF: 28.3DOI: 10.1038/s41564-024-01634-9
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High-resolution metagenomic reconstruction of the freshwater spring bloom
MicrobiomeIssue Date: 26 January 2023IF: 16.837DOI: 10.1186/s40168-022-01451-4
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Nature CommunicationsIssue Date: 12 September 2023IF: 16.6DOI: 10.1038/s41467-023-41329-z
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Effects of spaceflight on the composition and function of the human gut microbiota
Gut MicrobesIssue Date: 2020 Jul 3IF: 7.740DOI: 10.1080/19490976.2019.1710091
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MicrobiomeIssue Date: 19 October 2018IF: 11.607DOI: 10.1186/s40168-018-0561-x
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Hypoxia induces senescence of bone marrow mesenchymal stem cells via altered gut microbiota
Nature CommunicationsIssue Date: 2018 May 22IF: 12.121DOI: 10.1038/s41467-018-04453-9
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Age-associated microbiome shows the giant panda lives on hemicelluloses, not on cellulose
ISME JournalIssue Date: 01 February 2018IF: 9.180DOI: 10.1038/s41396-018-0051-y
Core-pan Gene Rarefaction Curve

Heatmap for the Relation among samples

Venn Figures for Gene Number among samples

Gene Number & Abundance Clustering Heatmap in genus level

Anosim Analysis at Phylum Level

Linear Discriminant Analysis (LDA) & Cladogram

Kyoto Encyclopedia of Genes and Genomes (KEGG) Annotation

Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups (eggNOG) Annotation

PCA & NMDS Analysis Results based on relative abundance of gene functions

Comparison Plot for Metabolic Pathway of multi-samples

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