Determining Microbiome Contributions Starts with Sample Collection

Get full value from multiomics data by considering the specimen source

A journey of a thousand miles begins with a single step‘ – from Tao Te Ching, Lao Tzu




Getting full value from specimens starts with getting sample collection right. By dictating collection and storage parameters and relying on an experienced partner to manage handling and logistics, a diverse population can be sampled while minimizing the variability over time and sites. Such controlled sample collection provides the foundation of large-scale databases that can be used for mining trends in methods and patients’ conditions through anonymized studies.

Prospective specimen collection in well-designed, controlled, longitudinal study designs valuably instills consistency of data for analysis and for its potential use in metadata studies. By integrating patient metadata with the individual’s microbiome composition to compare with these massive databases, clinical study investigators can give biomarkers new life through the added value of connecting safe and effective treatment to a patient’s likelihood to respond – the goal of precision medicine.

Among the many concerted efforts in the era of precision medicine (post-2015) has been mapping the interplay between various systems in the body to determine a therapeutic regimen. The immune system’s interaction with the body’s microbiomes for autoimmune diseases such as inflammatory bowel disease (IBD), multiple sclerosis (MS), psoriasis, and atopic dermatitis are of particular interest.

As high-content precision analytical tools, such as metagenomics, metabolomics, and wearable technologies, are being applied to mapping the interaction of the gut and skin microbiota with the immune system, therapeutics and consumer goods developers and medical providers are likewise adopting precision medicine methods to understand the specific roles of gut and skin microbiota on autoimmune diseases.


Measuring Gut Inflammation

Research has shown that the gut microbiome is a key regulator of the immune system, mediated via a direct gut-immune axis and/or indirectly through their respective axes with the brain [1,2]. These axes (direct or indirect) serve as key nexus for communications between tissues and organs in a bidirectional manner and play pivotal roles in systemic homeostasis. Naturally, inflammation originating in the digestive can manifest into the autoimmune responses that are hallmarks of inflammatory diseases [3].

Precision analysis of the microbiota population mix and associated metagenomics is an area of intensive research for assessing the causes of inflammation. Hypotheses about the cause of inflammation have pointed to a compromised mucosal gut lining, which normally harbors the microbiome’s interaction with the immune system. Recent efforts have been focused on assays (including shotgun metagenomic sequencing and metabolomics) to identify markers that might connect the functional metabolic potential of the microbiome with autoimmune diseases (e.g., IBD) through related symptom biomarkers [4-6].


Assays and Biomarkers for Gut Inflammation

More common and accessible means of measuring the inflammation of the gut is through multi-sample biomarker studies (e.g., blood + stool, blood + urine, or blood + skin) and imaging technologies (including endoscopy and enteroscopy), each set providing a different perspective that can be interpreted in a larger context of symptoms, provided the specimens are attached to patient-reported outcomes.

I recently experienced first-hand a journey into gut-related clinical biomarkers when a flag was raised in a blood test. Subsequently, I was asked to provide a stool swipe sample and had an endoscopy (to check for celiac disease, which proved negative). During the interval between the blood and stool tests and the endoscopy, I went gluten-free and undertook an elimination diet (removing certain food types systematically). Eventually, the condition was resolved without medical intervention. Incidental to this episode, I was starting on medication for my thyroid (Synthroid), however, I am unaware if these were related. I was fortunate in my case (no inflammation-induced pain), but I once again recognized the power of using a palette of tests to make, confirm, or refute a diagnosis.

Biomarkers derived from samples tested for irritable bowel disease include serum C-reactive protein and fecal calprotectin, as well as antibody-based assays for serum leucine-rich glycoprotein and urinary prostaglandin E major metabolite [7]; for celiac disease, markers include RNA and DNA assays as well as inflammatory markers, e.g., anti-TG2 IgA, anti-TG2 IgG, Anti-Deamidated gliadin peptides (DGP) IgG, anti-EMA IgA, anti-TG3, anti-TG6, and several interleukin cytokines (e.g., IL-15, 21, 2, 8, 10, 17A, 1a, 1b, et al.). [4-6] These markers are not definitive; they are used when symptoms are reported. A positive assay result is typically confirmed with an endoscopy, enteroscopy examination, or similar clinical confirmatory tests.


Understanding how therapies impact the microbiota: responder vs nonresponder

Biomarkers play a role in monitoring treatment response and providing data to healthcare providers on possible options. The key is to consider a combination of imaging and markers to determine the treatment that is best suited for an individual, the domain of precision medicine and precision nutrition.

A wide variety of therapeutic drugs (e.g., steroids and anti-inflammatory biologics) are available for those who suffer from chronic inflammations (e.g., IBD or Crohn’s Disease). These treatments come with inherent safety-efficacy profiles that vary from individual to individual, and thus developers and doctors need to identify patient characteristics that suggest the highest likelihood of an individual’s response to therapy. An area of recent interest is the impact of therapies for inflammatory conditions on the body’s microbiomes (changing population mix) and, conversely, the impact of the microbiome on drug safety or efficacy (e.g., too rapidly metabolized). In either case, the impact may present as abdominal pain, back pain, nausea, or diarrhea, among others. 

While the goal now is to find quantitative biomarkers in various sample types to determine the best therapies, it is worth noting that patient data (e.g., patient-reported symptoms and outcomes, medical records, family history) is paramount for biomarker utility. In general, biomarkers result from an arduous process of linking quantitative clinical results to qualitative symptoms (stomach pains, nausea, bloating, etc.). With the advent of large patient databases, dedicated researchers can pool data and mine the database to formulate hypotheses, design tests, and validate markers that can be used in approved diagnostic assays.


All Studies Start with Sample Collection

For many individuals and circumstances, at-home collection is necessary; for these cases, any problem of at-home collection is obviated with mobile phlebotomy and related specialists who can provide devices and instruction for different sample collection techniques. Furthermore, mobile phlebotomy supports the collection of simultaneous specimen collection, providing the means for scientists to integrate circulating or systemic markers with microbiota-specific tissues (e.g., stool or skin tapes). 

Sanguine Biosciences has designed, built, and validated robust operations to monitor sample quality and establish a trackable chain of custody needed for the privacy and security of the study participants. The chain’s integrity is critical since data is analyzed, and passed along to different institutions, users, care providers, and affiliated professionals along the patient’s journey.

To borrow from Ed Yong in his monumental read, I Contain Multitudes: The Microbes Within Us and a Grander View of Life, “Every one of us is a zoo in our own right – a colony enclosed within a single body. A multi-species collective. An entire world.” We each have our own unique fingerprint that holds the key to unlocking our own health. The tools are becoming available for precisely measuring that fingerprint. It all starts with a good sample. 


For more information on sample collection and analysis services, visit our page:

Procure Human Biospecimens Prospectively | Sanguine Bio


By: Tom Fare, Ph.D.; Geocyte 



[1] The Gut-Brain Axis in Inflammatory Bowel Disease-Current and Future Perspectives, Günther C, Rothhammer V, Karow M, Neurath M, Winner B., Int J Mol Sci. 2021 Aug 18;22(16):8870. doi: 10.3390/ijms22168870.

[2] Gut–Skin Axis: Current Knowledge of the Interrelationship between Microbial Dysbiosis and Skin Conditions, Britta De Pessemier, Lynda Grine, Melanie Debaere, Aglaya Maes, Bernhard Paetzold, and Chris Callewaert, Microorganisms. 2021 Feb; 9(2): 353. doi: 10.3390/microorganisms9020353

[3] The Gut–Brain Axis, Emeran A. Mayer, Karina Nance, and Shelley Chen, Annual Review of Medicine, Vol. 73:439-453 (January 2022)

[4] Molecular Biomarkers for Celiac Disease: Past, Present and Future, Ramírez-Sánchez AD, Tan IL, Gonera-de Jong BC, Visschedijk MC, Jonkers I, Withoff S. Int J Mol Sci. 2020 Nov 12;21(22):8528. doi: 10.3390/ijms21228528.

[5] Metabolomic Analysis in Inflammatory Bowel Disease: A Systematic Review, Gallagher K, Catesson A, Griffin JL, Holmes E, Williams HRT,  J Crohns Colitis. 2021 May 4;15(5):813-826. doi: 10.1093/ecco-jcc/jjaa227.

[6] Metabolomics in Autoimmune Diseases: Focus on Rheumatoid Arthritis, Systemic Lupus Erythematous, and Multiple Sclerosis, Yoon N, Jang AK, Seo Y, Jung BH, Metabolites. 2021 Nov 29;11(12):812. doi: 10.3390/metabo11120812. PMID: 34940570; PMCID: PMC8708401.

[7] C-Reactive Protein, Fecal Calprotectin, and Stool Lactoferrin for Detection of Endoscopic Activity in Symptomatic Inflammatory Bowel Disease Patients: A Systematic Review and Meta-Analysis, Mosli MH, Zou G, Garg SK, Feagan SG, MacDonald JK, Chande N, Sandborn WJ, Feagan BG., Am J Gastroenterol. 2015 Jun;110(6):802-19; quiz 820. doi: 10.1038/ajg.2015.120. Epub 2015 May 12. PMID: 25964225.