Microbiome Application Data

The human microbiome is diverse, and your standards should be too. That’s why as part of our commitment to empowering researcher with cutting-edge tools, ATCC has developed a portfolio of microbiome standards for use in a broad range of applications ranging from method optimization to data interpretation.

The robust applicability of these controls combined with the ATCC commitment to authentication and characterization make ATCC Microbiome Standards the ideal tool for standardizing data from a wide range of sources and generating consensus among microbiome applications and analyses. Check out our application data below to see how the experts are using standards to improve reproducibility in microbiome research, or download our application data document below to view our full set of data.

Application Data

Microbiome Research Solutions

Optimization at each step of your microbiome workflow is essential for the validity and reproducibility of data. Explore our complete set of application data to discover how the experts are improving reproducibility in microbiome research.

Download the full application data

Improve Assay Consistency

When performing your microbiome research, the tools and protocols you choose can significantly affect your results. By using microbiome standards combined with the One Codex data analysis module in your research, you can compare the performance and overall accuracy of your methods and ensure the validity of your results.

Compare DNA Extraction Kits

Compare DNA Extraction Kits figure

Figure 1. The whole cell mock microbial communities can be used to compare different DNA extraction kits. Here, we show a proof-of-concept study. Total DNA from two aliquots of the whole cell microbiome standards was extracted using two commercial extraction kits. Following extraction, the genomic DNA was analyzed using shotgun genomic sequencing analysis on the Illumina® MiSeq® platform, and the resulting data were analyzed using the ATCC bioinformatics tool in One Codex.

Compare Sequencing Methods

Compare Sequencing Methods figure

Figure 2. The genomic DNA mock microbial communities can be used to compare 16S rRNA and shotgun metagenomics assays. (A, B) Here, we show a proof-of-concept study. The performance and overall accuracy of the quantitative genomic DNA mock microbial communities were tested using the Illumina® MiSeq® platform, and the resulting data were analyzed using the ATCC bioinformatics tool in One Codex.

Compare Sequencing Platforms

Compare Sequencing Platforms figure

Figure 3. Evaluation of different sequencing platforms with ATCC Microbiome Standards. (A) The Gut Microbiome Standards (ATCC® MSA-1006™ and MSA-2006™) were analyzed via shotgun sequencing on the Nanopore MinION platform. Results showed that one hour sequencing was enough to identify all organisms in the mix with sufficient genome coverage (read length N50 > 5kb and average coverage = 5x). (B) Comparison of 16S rRNA (full-length amplicon) and shotgun data on the PacBio Sequel Platform with the 20 organism staggered genomic DNA mix (ATCC® MSA-1003™). Results showed concordance between 16S rRNA (100% false negative) and Shotgun (100% false negative) analysis, which highlight a full-amplicon 16S analysis using a long-read platform to reduce 16S primers biases and improve taxonomic resolution. (C) 16S rRNA (V1V2) metagenomics profiling of 20 organism even genomic DNA mix (ATCC® MSA-1002™) on the Ion Torrent Ion PGM platform. Results showed all organisms were detected in the mix (100% true positive).

Back to top

Validate your assay

Evaluating the accuracy and reproducibility of your methods and ensuring standardization across your microbiome research is essential. To address these needs, ATCC has developed two microbiome spike-in standards that comprise an even mix of genomic DNA or whole cells of three genetically engineered bacterial strains that contain a unique synthetic DNA tag that can be detected via 16S rRNA profiling and shotgun metagenomics sequencing assays. These microbiome standards offer a valuable way to evaluate the accuracy and reproducibility of microbiome next-generation sequencing data analysis.

Spike-in Standards figure

Figure 4. Detection and measurement of three unique synthetic tags from the Spike-in Standards. (A) Percent of recovered reads of individual tags showed that synthetic tags can be identified and quantified by using three commercial primer sets that target the variable regions of the 16S rRNA gene. (B) Percent of genome copies (ddPCR) and percent of reads (shotgun) of individual tags detected in the Whole Cell Spike-in standards.

Back to top

Perform Community Profiling

Although there is already a wealth of knowledge on the human microbiome, much of it still remains an enigma. ATCC is committed to supporting this incredible field of research by creating the cutting-edge site-specific standards needed for studies on the mycobiome, virome, or the oral, skin, gut, and vaginal microbiomes. These standards are ideal for use as controls in microbial profiling of mixed populations or for research on how microbial communities affect human health and disease.

Explore The Human Microbiome

Genomic DNA mock microbial communities analyzed

Figure 5. Genomic DNA mock microbial communities analyzed via 16S rRNA and shotgun metagenomics sequencing methods. Genomic DNA Mixes representing the (A) oral genomic mix (ATCC® MSA-1004™), (B) skin genomic mix (ATCC® MSA-1005™), (C) gut genomix mix (ATCC® MSA-1006™), and (D) vaginal genomix mix (ATCC® MSA-1007™) were analyzed via shotgun metagenomics and 16S rRNA sequencing. Data analyses were performed on the One Codex platform.

Explore The Virome

Composition of genomic DNA and whole cell virome standards

Figure 6. Composition of genomic DNA and whole cell virome standards. (A) ATCC Virome Standards comprise genomic nucleic acids or whole cells prepared from fully sequenced, characterized, and authenticated viral strains that are selected on the basis of genomic size, DNA or RNA genome, envelope/non-envelop, and other special features. (B) The genome copy number for each virus in the virome mixture was determined by using individual digital PCR assays. The variation observed in ATCC® MSA-2008™ could be attributed to extraction efficiency.

Explore The Mycobiome

Mycobiome standards can be used with both internal transcribed spacer (ITS) and shotgun metagenomic sequencing assays

Figure 7. Mycobiome standards can be used with both internal transcribed spacer (ITS) and shotgun metagenomic sequencing assays. The Mycobiome Genomic DNA Mix (ATCC® MSA-1010™) was analyzed by (A) ITS and (B) shotgun metagenomic assays using the Illumina platform, and data were analyzed using OneCodex platform. ITS analysis could profile all the fungi in the mix to genus level where as shotgun metagenomic assay could identify all fungi to the species level. The results also demonstrated run-to-run reproducibility when performing both sequencing assays.

Back to top

Illumina, MiniSeq, MiSeq, NextSeq, and HiSeq are trademarks or registered trademarks of Illumina. Ion Torrent is a trademark of Thermo Fisher Scientific. MinION is a trademark of Oxford Nanopore Technologies. PacBio is a trademark of Pacific Biosciences.