OMNImet®•GUT: An at-home collection and ambient temperature transport device for fecal metabolomics (MK-01844 - pdf)

• Convenient at-home collection of fecal samples for targeted and untargeted metabolomics
• Stabilization of the gut metabolomic profiles for 7 days at room temperature
• LC-MS/MS compatibility (including Metabolon’s Global Platform and SCFAs)
• Suitable for the collection and analysis of fecal samples from donors of any age, including infants

MK-01336: Chasing the human skin microbiome: developing an efficient and versatile device to collect microbial samples from a broad range of skin sites (pdf)

The human skin is a vast and diverse environment that harbours a rich microbiota composed of hundreds of bacterial species as well as fungal and viral taxa in lower relative abundance. The discrete regions of the human skin can be grouped into three main groups based on their physico-chemical properties: sebaceous, wet and dry. Previous studies have indicated that each of these sites tend to support different microbial species; for instance Cutibacterium acnes is primarily found on lipid-rich sebaceous sites. The skin surface is generally poor in nutrients and therefore it is only able to sustain a much lower microbial biomass than the gut or the oral cavity. Very low microbial abundance combined with a wide variety of collection sites makes skin microbiome sampling notoriously difficult, and no standardized reliable collection methods are available.

To this end, we developed a swab-based skin microbiome collection and stabilization device (P-189), and demonstrated that this prototype can consistently collect microbiome samples from sebaceous, wet and dry skin sites. Given the critical importance of DNA yields in skin microbiome studies, we developed an optimized processing pipeline for P-189 collected samples, and show that our collection device is able to reliably yield DNA in sufficient quantities for downstream analysis, including from traditionally very low yield dry skin sites. Taxonomic analysis of P-189 collected skin microbiome samples using 16S/ITS and shotgun sequencing revealed microbial profiles consistent with published data, indicating efficient capture of site-specific microbial taxa, with minimum background contamination. Lastly, we also tested the quantitative performance of our device, and determined that the P-189 prototype can successfully collect as little as 104 bacterial cells spiked on artificial skin. Taken together, our data indicates that the P-189 is a versatile collection device optimized for skin microbiome studies.

MK-00461: Identification of factors during microbiome assessment that consistently impact reproducibility, quality and value of collected sampless (pdf)

The evolved characterization of human-associated microbial communities has given scientists a new perspective on diseases of the GI tract. Metagenomic profiles associated with diabetes, inflammatory bowel disorders and obesity are showing diagnostic, prognostic and monitoring potential. These microbial communities are dynamic systems that have been shown to respond to dietary, environmental, and even seasonal changes. Considering this intrinsic complexity, successful identification and validation of biomarkers requires the execution of large, longitudinal population studies. The proper execution of such studies relies on capturing an accurate representation or ‘taking a snapshot’ of the donor’s biology at the point of collection and reliably reproducing it through the analytical pipeline.

MK-00464: Identification of factors impacting reproducibility and quality of microbiome profile analysis (pdf)

The evolved characterization of human-associated microbial communities has given scientists a new perspective on diseases of the GI tract. Metagenomic profiles associated with diabetes, inflammatory bowel disorders and obesity are showing diagnostic, prognostic and monitoring potential. These microbial communities are dynamic systems that have been shown to respond to dietary, environmental, and even seasonal changes. Considering this intrinsic complexity, successful identification and validation of biomarkers requires the execution of large, longitudinal population studies. The proper execution of such studies relies on capturing an accurate representation or ‘taking a snapshot’ of the donor’s biology at the point-of-collection and reliably reproducing it through the analytical pipeline.

MK-00629: Critical To Quality pre-analytical factors and their impact on microbiome analysis (pdf)

Since the completion of the Human Microbiome Project (HMP), the number of microbiome focused research programs, peer-reviewed publications and patents has grown exponentially. As a result, much progress has been made in understanding the complex relationship between host and microbiome. However, lack of standard procedures, reference materials and quality control metrics limits reproducibility and comparability of published results, which can lead to discordant data interpretation and false inferences. The microbiome field can only reach its translational potential when hypotheses are rigorously tested with optimized methods.

MK-00971: A validated study protocol to compare microbiome and mycobiome profiles of Inflammatory Bowel Disease patients in remission and active flare (pdf)

Several large cohort studies of the gut bacterial composition of patients with Inflammatory Bowel Disease (IBD) have been published in recent years. While these studies have provided intriguing insights into the disease and promising clues for treatment options, they are often challenged by low enrollment and compliance rates. Low rates are largely influenced by donor perception of self-collection of the severe diarrhea samples common for IBD patients in flare. In collaboration with Crohn’s and Colitis Canada we launched a research study with two aims: to adapt and improve current practices for stool collection, preservation, processing and analysis and to use these optimized methods to compare bacterial and fungal profile differences in IBD patients in remission to those in active flare.

MK-01051: Beyond bacteria - Characterization and analysis of the mycobiome and virome in human gut samples (pdf)

The human gut is inhabited by a tremendous variety of microorganisms that collectively form the gut microbiome. This diverse community is dominated by hundreds of bacterial species, while fungal, archaeal and viral species are also present but in lower relative abundance. The commensal bacterial species found in the human gut have been extensively characterized by 16S and whole genome sequencing (WGS), and bacterial dysbiosis has been linked to a number of human diseases such as IBD, IBS, colorectal cancer and obesity. In contrast, the mycobiome and virome remain largely uncharacterized, primarily because of their much lower abundance but also due to a lack of fully optimized protocols and curated reference databases. In the present study, we tested methodologies to characterize and analyze the mycobiome and virome of human gut samples collected in OMNIgene®•GUT kits (OM-200, DNA Genotek). Preliminary analysis suggests that OMNIgene•GUT gut sample collection devices are able to capture and stabilize the human gut mycobiome and virome as efficiently as the bacteriome. Using internal transcribed spacer (ITS) sequencing for mycobiome taxonomic analysis, we demonstrate that primer selection is paramount to increase identification of fungal species by decreasing biased and non-specific PCR amplification. In virome methodology testing, we were able to enrich endogenous and exogenous bacteriophages by 5 to 10-fold in DNA extracted from OMNIgene•GUT samples. Viral enrichment was achieved using a purification protocol designed to select viral DNA over bacterial DNA. Taken together, our preliminary data indicate that OMNIgene•GUT collected samples could be suitable for mycobiome and virome studies.