Shotgun sequencing services

Shotgun metagenomic sequencing utilises next-generation sequencing to provide insights into the genetic diversity of microbial communities associated with hosts, their functional diversity, gene prediction and annotation, host-microbe interactions, and microbiota-related disease mechanisms. Because this method sequences the entire genome, it can determine not only the genus and species but also, in some cases, subspecies and strains. Additionally, it allows for the analysis of gene expression, function, and how these metabolic functions contribute to community fitness and host-microbe symbiosis.

What you can expect from Zymo’s shotgun services

Quick turnaround time
High quality data
Multi-kingdom strain level resolution
Proprietary algorithm reduces the risk of false positives
Microbiome standards included in every run
User-friendly analysis report

Comprehensive bioinformatics report

Zymo’s dedicated team excels in creating user-friendly and custom bioinformatic reports, ensuring the data is presented in a clear and understandable format, tailored to the client’s needs. The shotgun sequencing service report includes taxonomy analysis, alpha diversity bar plots, beta diversity analysis, gene family profiling, metabolic pathway analysis, antibiotics resistance gene and virulence gene profiling, and LEfSe biomarker discovery.

Sequencing accuracy and consistency

shotgun sequencing relative abundance

Zymo’s shotgun services are continuously monitored with their own highly-cited microbial community standards for batch-to-batch consistency. Their proprietary algorithm for shotgun sequencing is optimised to reduce the risk of false positives in taxonomy assignment and provide high confidence accuracy for sample profiling.

Shotgun sequencing technical specifications

Sequencing platform	Illumina NovaSeq 6000™, NextSeq 2000™, NovaSeq X™
Sample collection	Raw Sample Various sample collection devices provided upon request DNA sample (> 1 ng/μl by Fluorescence DNA quantification) Please ensure it is PCR inhibitor-free
Read length	2 x 150 bp
Taxonomy resolution	Bacteria and Archaea: strain level Fungi and viruses: species level
Accepted sample types	Extracted genomic DNA or raw samples
DNA extraction	ZymoBIOMICS 96 Magbead DNA (D4308) ZymoBIOMICS DNA Miniprep (D4300)
Library prep	Illumina DNA Prep (Formerly Nextera Flex) Unique Dual Indexing (UDI) included
Sequencing analysis	Kmer signature based analysis using Sourmash with antimicrobial resistance using Diamond and functional pathway analysis using Humann3
Reference database	Zymo uses pre-built databases supported by the SourMash development group covering Prokaryote, Eukaryote, Archaea, and Viral genomes compatible with GTDB and NCBI taxonomies.
Data visualisation	Taxonomy Profiling Taxa abundance bar plot and heatmap Alpha diversity boxplot Beta diversity PCoA plot Functional Profiling Antibiotics resistance identification Virulence gene identification Gene family profiling (UniRef) Metabolic pathway profiling (MetaCyc)
Statistical analysis	LEfSe analysis uncovers taxa/traits that are differentially distributed among defined sample groups.
Data storage	Raw sequencing data and analysis report are stored for up to 3 months