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. Clear rules for collection and storage let researchers sample a diverse population while keeping variability across time and sites to a minimum. An experienced partner who manages handling and logistics makes that consistency possible at scale. This kind of controlled collection lays the foundation for large-scale databases. Researchers can then mine these databases for trends in methods and patient conditions through anonymized studies.

Prospective specimen collection, built into well-designed, controlled, longitudinal studies, keeps data consistent for analysis and for later use in metadata studies. When researchers combine patient metadata with an individual’s microbiome makeup and compare it against these large databases, they can give biomarkers new life. That connects safe, effective treatment to how likely a patient is to respond. That’s the goal of precision medicine.

Since 2015, precision medicine has focused heavily on mapping how different body systems interact to shape a therapeutic plan. Researchers are especially interested in how the immune system interacts with the body’s microbiomes in autoimmune diseases such as inflammatory bowel disease (IBD), multiple sclerosis (MS), psoriasis, and atopic dermatitis.

High-content precision tools like metagenomics, metabolomics, and wearable technology now map how gut and skin microbiota interact with the immune system. In response, therapeutics and consumer goods developers, along with medical providers, are adopting precision medicine methods to understand the specific role gut and skin microbiota play in autoimmune diseases.

Measuring Gut Inflammation

Research shows the gut microbiome plays a key role in regulating the immune system. It works through a direct gut-immune axis, and indirectly through its connections with the brain.[1,2] These axes act as communication hubs between tissues and organs, in both directions, keeping the whole body in balance. So it’s no surprise that inflammation starting in the digestive tract can turn into the autoimmune responses seen in inflammatory diseases.[3]

Precisely analyzing the mix of microbiota and its metagenomics is an area of intense research aimed at understanding what causes inflammation. One hypothesis points to a compromised mucosal gut lining, which normally hosts the microbiome’s interaction with the immune system. Recent work has focused on assays — including shotgun metagenomic sequencing and metabolomics. These assays aim to find markers that connect the microbiome’s functional metabolic potential to autoimmune diseases like IBD, through related symptom biomarkers.[4-6]

Assays and Biomarkers for Gut Inflammation

The most common and accessible ways to measure gut inflammation are multi-sample biomarker studies (for example, blood plus stool, blood plus urine, or blood plus skin). Imaging technologies, including endoscopy and enteroscopy, are also common. Each gives a different perspective, and each can be read in the larger context of a patient’s symptoms, as long as the specimens link back to patient-reported outcomes.

I went through a journey into gut-related clinical biomarkers firsthand, after a blood test raised a flag. I was then asked to provide a stool sample and had an endoscopy to check for celiac disease, which came back negative. Between the blood and stool tests and the endoscopy, I went gluten-free and tried an elimination diet, removing certain food types one at a time. Eventually, the condition resolved without medical intervention. Around the same time, I also started medication for my thyroid (Synthroid), though I don’t know if the two were related. I was fortunate I didn’t experience inflammation-induced pain. But the experience reminded me how powerful it is to use a full panel of tests to make, confirm, or rule out a diagnosis.

Biomarkers drawn from tested samples for irritable bowel disease include:

• Serum C-reactive protein
• Fecal calprotectin
• Antibody-based assays for serum leucine-rich glycoprotein
• Urinary prostaglandin E major metabolite[7]

For celiac disease, markers include RNA and DNA assays. Inflammatory markers are also used, such as anti-TG2 IgA, anti-TG2 IgG, anti-deamidated gliadin peptides (DGP) IgG, anti-EMA IgA, anti-TG3, anti-TG6, and several interleukin cytokines (including IL-15, 21, 2, 8, 10, 17A, 1a, and 1b).[4-6] These markers aren’t definitive on their own. Doctors use them when a patient reports symptoms, and they typically confirm a positive result with an endoscopy, enteroscopy, or similar clinical test.

Understanding How Therapies Impact the Microbiota: Responder vs. Nonresponder

Biomarkers help monitor treatment response and give healthcare providers data on possible options. The key is combining imaging and markers to figure out which treatment fits an individual best — the core of precision medicine and precision nutrition.

A wide range of therapeutic drugs, such as steroids and anti-inflammatory biologics, are available for people with chronic inflammation (like IBD or Crohn’s disease). Each carries its own safety and efficacy profile, which varies from person to person. So developers and doctors need to identify which patient characteristics suggest the highest likelihood of a good response.

One area of recent interest is how therapies for inflammatory conditions affect the body’s microbiome, by changing the population mix. In turn, researchers are studying how the microbiome affects a drug’s safety or efficacy, for example by metabolizing it too quickly. Either way, the impact may show up as abdominal pain, back pain, nausea, or diarrhea, among other symptoms.

The goal now is to find quantitative biomarkers in various sample types that point to the best therapies. But patient data — reported symptoms and outcomes, medical records, family history — remains essential to making biomarkers useful. Researchers generally build biomarkers through a long process of linking quantitative clinical results to qualitative symptoms, like stomach pain, nausea, and bloating. With large patient databases now available, researchers can pool data and mine it to form hypotheses, design tests, and validate markers that can go into approved diagnostic assays.

All Studies Start with Sample Collection

For many people and situations, at-home collection is necessary. Mobile phlebotomy and related specialists solve the problem of at-home collection by providing devices and instructions for different sample collection techniques. Mobile phlebotomy also supports simultaneous specimen collection, giving scientists a way to combine circulating or systemic markers with microbiota-specific tissues (such as stool or skin tapes).

Sanguine Biosciences has designed, built, and validated robust operations to monitor sample quality and maintain a trackable chain of custody. This protects the privacy and security of study participants. That chain’s integrity matters, since the data gets analyzed and passed along to different institutions, users, care providers, and affiliated professionals throughout the patient’s journey.

To borrow from Ed Yong in his book 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.” Each of us carries a unique fingerprint that holds the key to unlocking our own health, and the tools to measure that fingerprint precisely are finally becoming available. 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

References

[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) https://doi.org/10.1146/annurev-med-042320-014032.

[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.