What is Microbiome?

The microbiota is a term used to describe the microbes (including bacteria, yeast, viruses, parasites, and fungi) that coexist in various sites of the human body¹. The collection of their microbial genes, referred to as the microbiome, outweighs the number of human genes by as much as 100 times². Research into the microbiome is a ground-breaking and fast-growing field. Recent discoveries have found that the human microbiome plays a role that directly affects multiple organ systems. The composition of microbiota present varies depending on the region of the body (i.e., oral cavity, lung, vagina, or skin). This is because of the differences in environmental factors and activity at each region, including pH, gene mutations, and interactions among other microbes¹. The disruption of the microbial composition and its functions, known as dysbiosis, is linked to various disease manifestations, such as metabolic, inflammatory, neurological, and gastrointestinal disorders³.

The gut microbiome, which consists of billions of microorganisms, is now recognized as playing a critical role in maintaining gut health, contributing to the maturation and function of the immune system, and influencing the homeostasis of other peripheral organs⁴. There is even evidence of bidirectional communication between the gut microbiota and the brain through gut-brain immunological mediators; this is known as the gut-brain axis⁵. Stool samples are non-invasive, accessible, and cost-effective specimens that can be easy to collect to provide insight about the gut microbiome. Microbial DNA is extracted, amplified, sequenced, and analyzed to gain a comprehensive understanding of gut health, which can be used to guide patients’ treatment.

Other components of the human microbiome could soon play crucial roles in patients’ health as well. Nasal microbial dysbiosis is actively being evaluated for possible association with neurological diseases. The microbes of this niche and their microbial metabolites are able to cross the blood-brain barrier, causing a variety of neurological diseases: Parkinson’s disease, Alzheimer’s disease, and multiple sclerosis, to name a few⁵. The nasal mucosal barrier plays a key role in preventing infection within the upper respiratory tract. A nasal swab sample, similar to those used to test for SARS-CoV-2 infection, is also a safe, accessible, and cost-effective method to assess the nasal microbiome. These assessments allow us to understand how changes on the microbiome level impact the progression of related disorders.

REFERENCES

1. Hou K., Wu ZX., Chen XY. et al. Microbiota in health and diseases. Sig Transduct Target Ther 7, 135 (2022). https://doi.org/10.1038/s41392-022-00974-4
2. Sender R., Fuchs S., Milo R. Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans. Cell 2016;164:337–40.
3. Microbiome in precision medicine.
4. Lathrop SK, Bloom SM, Rao SM, Nutsch K, Lio C-W, Santacruz N, et al. Peripheral education of the immune system by colonic commensal microbiota. Nature 2011;478:250–4.
5. Thangaleela S., Sivamaruthi B.S., Kesika P., Bharathi M., Chaiyasut C. Nasal Microbiota, Olfactory Health,Neurological Disorders and Aging—A Review. Microorganisms 2022, 10, 1405. https://doi.org/10.3390/microorganisms10071405

• DNA isolations – Blood or Bone Marrow specimens
  
  
  • All isolations include full quality control parameters measured.
    • Nanodrop concentration, 260/280
    • Fluorescent concentration (dsDNA)
      
      
  • Each sample that has DNA Isolation performed will have an accompanying Extraction Summary Report provided to the ordering entity.
    
    
  • The high-quality control parameters ensure that downstream processes (i.e., PCR, NGS, WGS, etc.) have optimal opportunity for success.
    
    
• Plasma Separation – Whole Blood specimens
  
  
• Sample Storage and/or Sample forwarding to reference laboratory for validated confirmatory testing
  
  
• ALTseq – Rapid Whole Genome Sequencing for Cancer
  
  
  • In the world of cancer, time is of the essence. Having access to rapid WGS to characterize the disease in a fraction of the time it takes to perform standard methodologies, such as Flow Cytometry, Cytogenetics, Fluorescent in situ Hybridization, and PCR, will be life-changing for cancer patients and their families. The sooner the detailed genomic characteristics of a patient’s disease can be identified, the faster they can begin customized, targeted, precision therapies to give them the best chance at survival.
  • TGen Clinical Laboratory will be utilizing the Illumina NovaSeq X Plus to perform the ALTseq Assay
  • The Illumina NovaSeq X Plus was released in the spring of 2023 and represents the next evolution of their flagship Sequencing by Synthesis (SBS) technology with the incorporation of XLEAP-SBS chemistry. Like many instruments from Illumina, this system is highly flexible with two different sequencing positions that can each independently sequence one of the compatible flow cell types (1.5B, 10B, 25B).
  • The flexibility provided by the NovaSeq X Plus will enable TCL to provide a rapid turnaround time of 48 hours from the moment the patient specimen comes into the lab until the time a report is available to the ordering physician.