Two new kits for microbiome profiling: fungal and combined bacterial + fungal

When your run profiles bacteria but ignores fungi, you are working with an incomplete picture from the start. We built two kits to close the gap: one dedicated to fungal profiling, one that allows bacterial ánd fungal analysis on the same sample but in two separate reactions.  

Fungi are not an edge case. In gut health research, environmental monitoring, food safety, and clinical diagnostics, fungal communities play a meaningful role alongside bacteria. Yet the vast majority of microbiome sequencing workflows target the bacterial 16S rRNA gene and stop there. The ITS region, the fungal equivalent of 16S, is still missing from most sequencing runs. That gap costs you real insight. And in a core lab environment where every sequencing run needs to earn its place, it also costs you efficiency. We designed two kits to address this: one for labs that need fungal profiling on their own, and one for labs that need both bacterial and fungal data from the same samples. 

The EasySeq™ ITS Microbiome Library Prep Kit enables reliable profiling of fungal communities using short-read next-generation sequencing. It targets the ITS2 region of the fungal rRNA operon, a region with high nucleotide heterogeneity that allows for accurate taxonomic classification and diversity analysis across a broad range of fungal species. 

The workflow is a one-tube, single reaction setup. Amplification, indexing, and adapter addition happen in one reaction, with no open-tube sample transfer. Pre-spotted, breakable Unique Dual Index plates keep each sample traceable with minimal waste. Up to 768 samples can be multiplexed per run. 

It works directly on DNA extracted from environmental, soil, feed, food, human, and animal-derived samples. No fungal culture is required. 

The EasySeq™ DuoBiome Library Prep Kit combines the EasySeq™ 16S and EasySeq™ ITS workflows in one kit format. It allows library preparation for both bacteria and fungi from the same samples, targeting the 16S V3-V4 region for bacteria and the ITS2 region for fungi, in two separate reactions that are later pooled equimolarly before sequencing. 

The separated reactions matter as bacterial and fungal loads can differ within the sample. Hence, the library prep requires different input amounts and PCR cycling conditions for complex input materials like fecal matter. Running them separately, then pooling after QC, means each library is optimized on its own terms. This ensures sensitive and reliable results from both 16S and ITS, without interference between the two targets. 

Both kits are built on the one-tube, single reaction library prep, using our proprietary and licensed Reverse Complement PCR technology. 

Standard ITS workflows require a significant PhiX spike-in to compensate for low-complexity regions in the amplicon. That spike-in does not generate useful data; it consumes sequencing capacity that could otherwise hold your samples. Over dozens of runs per year, the cumulative loss adds up. 

The EasySeq™ ITS workflow reduces that PhiX requirement substantially. The result is up to 45% more usable sequencing reads per run and 35% higher flow cell utilization compared to standard workflows. 

For a laboratory processing 20,000 samples per year on a mid-throughput short-read platform, the numbers look like this: 

*Based on 100,000 usable reads per sample

That translates directly into fewer sequence runs to handle the same annual volume: 23 runs instead of 40. At typical sequencing reagent costs, that difference amounts to approximately €27,000 in annual savings. At 100,000 samples per year, savings can exceed €140,000 annually. 

But there is a second benefit that often gets overlooked. 

When you run fewer sequences to process the same sample volume, you free up instrument time. That time does not sit idle; it becomes capacity for additional runs. For a lab director planning sequencing capacity for the next few years, that freed instrument time is budget without a line item. More data for less and more capacity for the same instrument. 

Both kits are designed for laboratories working across a wide range of sample types and research areas: 

• Environmental and soil microbiome research: characterize fungal diversity in complex materials
• Food and feed safety testing: detect and profile fungal contamination in production and supply chain samples
• Agricultural and veterinary microbiology: monitor fungal communities in plant and animal-derived materials
• Clinical and translational research: profile gut mycobiome in human cohort studies
• Water quality monitoring: fungal profiling in environmental water samples

The ITS kit is suited to labs with a pure fungal focus. The DuoBiome kit is the right choice when you need a complete bacterial and fungal picture from the same sample in one  workflow. 

Both kits are built on single reaction library prep, using our proprietary and licensed Reverse Complement PCR technology, which means in practice: 

• One-tube, single reaction workflow: amplification, indexing, and library preparation in a single closed-tube reaction, reducing hands-on time by more than 50% compared to conventional multi-step workflows
• Reduced contamination risk: the closed-tube setup eliminates open-tube transfer between PCR and indexing, which is where most amplicon contamination events occur
• Excellent abundance representation: Reverse Complement PCR kinetics improves target binding resulting in very consistent results. 

Compatibility with all major short-read sequencer platforms: no platform lock-in 

The most direct way to evaluate a library prep kit is to run it. Request a sample kit, test the EasySeq™ ITS Microbiome Library Prep Kit on your own samples, and compare the output against your current workflow.