ZymoBIOMICS Gut Microbiome Standard

ZymoBIOMICS^® Gut Microbiome Standard

Reliable benchmarking for gut microbiome research

Generate more accurate and reproducible microbiome data with the ZymoBIOMICS® Gut Microbiome Standard. This defined microbial community is designed to support benchmarking, quality control and validation across DNA extraction, library preparation, sequencing and bioinformatic analysis. With known species composition and characterised relative abundances, researchers can confidently evaluate workflow performance and identify sources of variability.

Validate every step of your microbiome workflow

Microbiome studies often involve multiple processing steps, each of which can introduce bias. Using a defined reference standard allows researchers to compare results against expected values and verify that every stage of the workflow performs as intended.

The ZymoBIOMICS^® Gut Microbiome Standard can be used for:

Method development and optimisation
DNA extraction benchmarking
NGS workflow validation
Quality control between runs
Cross-laboratory comparisons
Bioinformatics pipeline verification

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A defined microbial community for meaningful comparisons

Unlike undefined biological samples, the ZymoBIOMICS^® Gut Microbiome Standard contains a precisely characterised microbial community with known species abundance. This enables direct evaluation of extraction efficiency, library preparation performance and sequencing accuracy.

The standard incorporates representatives from multiple microbial kingdoms, including bacteria and fungi, helping researchers assess workflow performance across diverse organism types.

Standard composition

Species	Theoretical composition (%)
Species	Genomic DNA	16S only	16S and 18S	Genome copy	Cell number
*Pseudomonas aeruginosa*	12	4.2	3.6	6.1	6.1
*Escherichia coli*	12	10.1	8.9	8.5	8.5
*Salmonella enterica*	12	10.4	9.1	8.7	8.8
*Lactobacillus fermentum*	12	18.4	16.1	21.6	21.9
*Enterococcus faecalis*	12	9.9	8.7	14.6	14.6
*Staphylococcus aureus*	12	15.5	13.6	15.2	15.3
*Listeria monocytogenes*	12	14.1	12.4	13.9	13.9
*Bacillus subtilis*	12	17.4	15.3	10.3	10.3
*Saccharomyces cerevisiae*	2	NA	9.3	0.57	0.29
*Cryptococcus neoformans*	2	NA	3.3	0.37	0.18

Key benefits

Representative gut microbiome composition

Contains 21 microbial strains selected to mimic the complexity of the human gut microbiome and provide a realistic benchmarking tool.

Optimised for microbiome sequencing workflows

Evaluate and validate extraction methods, sequencing platforms and data analysis pipelines using a well-defined reference sample.

Supports quality control

Monitor inter-run consistency, identify workflow variation and improve reproducibility across projects and laboratories.

Cross-kingdom microbial coverage

Includes bacterial, fungal and archaeal organisms for comprehensive workflow assessment.

Technical specifications

Parameter	Specification
Biosafety	BSL-1
Foreign microbial DNA	< 0.01%
Reference genomes	16S&18S rRNA genes https://s3.amazonaws.com/zymo-files/BioPool/D6331.refseq.zip
Relative abundance deviation	< 15%
Storage solution	2X DNA/RNA Shield^®
Total cell concentration	~3.94 × 10⁹ cells/ml