The complete gut microbiome workflow, from sample to sequence

Step 2: benchmark your workflow with confidence

NEW: ZymoBIOMICS® gut microbiome standard

The new ZymoBIOMICS® gut microbiome standard provides an essential quality control tool for gut microbiome studies. Unlike generic mock communities, this standard has been specifically designed to mimic the complexity of the human gut microbiome, incorporating 21 microbial strains representing bacteria, fungi, and archaea.

Researchers can use the standard to evaluate extraction efficiency, assess sequencing bias, validate bioinformatics pipelines, and compare performance between operators, laboratories, or studies.

Why it matters

Recent international initiatives have highlighted substantial variability between microbiome laboratories when analysing identical samples, underscoring the growing need for robust reference materials and workflow controls (Anwar et al., 2025).

Key benefits

• 21-species gut-representative community
• Includes bacteria, archaea, and fungi
• Supports workflow validation and optimisation
• Ideal positive control for NGS-based gut microbiome projects
• Helps identify extraction and sequencing biases

Step 3: extract high-quality microbial DNA and RNA

ZymoBIOMICS® nucleic acid extraction kits

Differential lysis can dramatically skew microbial abundance profiles, particularly when Gram-positive organisms are underrepresented. The ZymoBIOMICS® extraction portfolio has become one of the most widely adopted solutions for microbiome research because it is specifically engineered to minimise extraction bias and maximise representative recovery of microbial nucleic acids.

Using validated mechanical lysis and optimised purification chemistries, ZymoBIOMICS kits help ensure accurate representation of both easy- and difficult-to-lyse organisms across the microbial community.

Advantages for gut microbiome research

• Proven low-bias microbial lysis
• Compatible with stool and other challenging sample types
• DNA and RNA workflow options available
• Ideal for metagenomics, 16S sequencing and multi-omics studies
• Benchmarked using ZymoBIOMICS standards

Step 4: generate sequencing-ready libraries in record time

Quick-16S™ library preparation kits

Library preparation is often one of the most labour-intensive stages of microbiome analysis, but Zymo's Quick-16S™ library preparation kits streamline the journey from extracted DNA to sequencing-ready libraries. The workflow uses quantitative PCR (qPCR)-based amplification and simplified clean-up steps to dramatically reduce hands-on time while maintaining high data quality. The latest workflow can prepare up to 96 samples with as little as 30 minutes of hands-on time.

Enhanced primer design improves phylogenetic coverage across bacterial and archaeal taxa, helping researchers achieve a more comprehensive view of microbial diversity.

Benefits

• Rapid workflow with minimal hands-on time
• Reduced PCR chimera formation
• Improved bacterial and archaeal coverage
• Suitable for high-throughput studies
• Compatible with leading sequencing platforms

Endometriosis is a chronic inflammatory disease where cells similar to those that line the womb grow elsewhere in the body. Research suggests that people with endometriosis may have differences in their gut and reproductive microbiome, although it remains unclear whether these changes are a cause or consequence of the disease. The microbiome may influence inflammation, pain, immune function, and hormone regulation, while endometriosis itself may alter the microbiome through chronic pain, stress, and lifestyle factors. The ENDO1000 project will investigate these relationships by analysing microbiome samples from participants to better understand how microbial communities are linked to symptoms, treatment responses, and long-term health outcomes.

This study of 135 patients with colorectal cancer examined the relationship between tumour-associated microbiota, tumour metabolism, and clinical outcomes following surgical resection. The authors identified distinct bacterial communities within tumours and found that a microbiota cluster containing the pathobionts Fusobacterium nucleatum and Granulicatella adiacens was associated with tumour tissue and, unexpectedly, predicted improved disease-free survival after surgery. In contrast, a cluster enriched in bacteria such as Faecalibacterium prausnitzii and Ruminococcus gnavus was associated with poorer outcomes. The findings suggest that the composition of the tumour microbiome may have prognostic value in colorectal cancer and could influence disease progression through interactions with the tumour microenvironment and host immune responses.

The UK Gut-Immunology-Brain Axis Network+ is a four-year research initiative that aims to uncover how interactions between the gut microbiome, immune system, and brain influence health, disease, and wellbeing. The network will bring together researchers from multiple disciplines to investigate the biological mechanisms linking gut health to mental health, brain ageing, dementia, neurodevelopment, and chronic inflammatory diseases, while also exploring how lifestyle factors such as diet, sleep, and stress affect these processes. Ultimately, the programme seeks to generate evidence-based strategies, therapies, and health recommendations to improve physical, cognitive, and mental health across the lifespan.