Current progress in microbiome biomarker discovery

Article by: Sanna Abbasi, PhD, and Charles Harkness

The human microbiome: defining microbiome biomarkers  

The microbiome, home to trillions of bacteria, fungi, and viruses, is comprised of 10-fold more cells than the human body.1 Potentially impacting the health and wellbeing of the host, these microbes directly interact with host cells and metabolic pathways. Researchers profiling the microbiome have begun identifying microbial signatures within healthy and disease states to elucidate biomarkers from the microbiome.  

Biomarkers are measurable substances whose presence or lack thereof can be used to predict or indicate disease. Given the medical relevance of biomarkers, many researchers are in constant search for new and specific markers that can quantify health states. Consequently, microbiome-based biomarkers may play an important role in disease prediction, pathogenesis, diagnosis, and treatment. Microbiome profiles and specific microbe biomarkers are being evaluated for their potential to provide clinically relevant information on disease states. 

Microbiome biomarkers may represent a new avenue for clinical diagnosis or treatment distinct from traditional biomarkers. Already, research efforts are underway to identify gut microbiome biomarkers within the context of Parkinson’s disease, inflammatory bowel disease, and colorectal cancer. 

  1. Parkinson’s disease


Parkinson’s disease is the second most common neurodegenerative disorder worldwide. Most often seen in people around age 60, the disease first affects the central nervous system before progressing to the motor system (e.g., tremors, muscle stiffness, impaired gait, etc.).1 Prior to presenting motor symptoms, roughly 80% of Parkinson’s disease patients also suffer from intestinal dysfunction (i.e., constipation) and studies conducted in mice have provided strong evidence that disease pathogenesis is modulated and may originate in the gastrointestinal tract.2,3 

The composition of the gut microbiome has been shown to influence neurological outcomes in patients through several mechanisms, including metabolite production.1 While emerging evidence has shown that gut microbiota dysbiosis—an imbalance of the gut microbial community including a loss of beneficial microbes and an increase in pathogenic ones—is involved in Parkinson’s disease, at present, no single microbe has been found to be responsible for causing the disease.4 Instead, several microbial species have been implicated. Compositional differences in the gut microbiome of healthy individuals compared to those with Parkinson’s disease have been well-documented.4 For example, in Parkinson’s disease patients: 

  • Lactobacillus, Akkermansia, Bifidobacterium, and Verrucomicrobiaceae seem to be increased. 
  • Roseburia, Faecalibacterium, Prevotella, Coprococcus, Prevotellaceae, and Blautia appear to be present at a lower abundance.

In terms of potential diagnostic biomarkers for Parkinson’s disease, one group led by Dr. Filip Scheperjans published a highly cited 2015 study that found that measuring the abundance of four specific bacterial families could be used to identify Parkinson’s disease patients.5 More recent case-control studies, including a 2020 publication by Qian and colleagues,6 have also attempted to capitalize on the identified gut microbial differences between healthy and diseased individuals. 

Thus far, the progress towards developing and implementing accurate diagnostic microbiome biomarkers for Parkinson’s disease is still in the early stages. A systematic review published by Boertien et al. in 2019 with principal investigator Dr. Filip Scheperjans, surveyed sixteen human case-control studies that had shown a connection between gut microbial changes and Parkinson’s disease.7 In this review, the authors described how some findings could be replicated while others could not and highlighted methodological differences and confounding variables (e.g., diet, treatment, etc.) in the study designs.7  

  1. Inflammatory bowel disease


Inflammatory bowel disease (IBD), which includes Crohn’s disease and ulcerative colitis, affected approximately 6 million people worldwide in 2017,8 with documented incidences increasing annually. IBD is a multi-factorial autoimmune disease with chronic and repetitive episodes of gastrointestinal tract inflammation and no cure.9,10 Like the research being done on Parkinson’s disease, the composition of the human gut microbiome also seems to be important as disruption has been associated with the development of IBD. Consistently, research by several groups has shown reduced gut microbial diversity in patients with IBD.10,11 

In 2021, a group of researchers from Madrid, Spain published a comprehensive systematic review where they collated 143 published studies on IBD and the microbiome.10 By assessing the studies, they saw several consistent trends including: 

  • Reduced species richness and diversity in the intestinal microbiome of IBD patients 
  • Reduced abundance of beneficial bacteria, and an increase in pathogenic bacteria in IBD patients 
  • Significant differences between remission and relapse IBD patients  
  • Considerable diversity in methodology and experimental design 
  1. Colorectal cancer


The third most diagnosed cancer type globally, colorectal cancer includes malignancies of the colon and rectum.12,13 Typically, colon cancer has been especially prevalent in developed countries, however, the incidence of this cancer has been increasing steadily worldwide.13 Unlike other cancers, colorectal cancer spreads slowly, providing an ample window of time for early screening and diagnosis.13 

Research into colorectal cancer patients versus healthy individuals has shown the gut microbiome to be altered between the two groups. Like studies on Parkinson’s disease and IBD, gut microbiota dysbiosis has been shown to convincingly modulate colorectal cancer development in several studies using animal models and/or human patients.14,15 Colorectal cancer patients have shown a reduction in bacterial diversity of their gut microbiome and several hypotheses have been put forward to explain how microbiota changes during carcinogenesis. These hypotheses include the “Alpha-Bug Hypothesis”, which indicates enterotoxigenic Bacteroides fragilis (ETBF) potential to promote cancer in the colon epithelium and the “Driver-Passenger Model” that classifies microbes into indigenous microbes that initiate colorectal cancer and opportunistic microbes which proliferate and mediate colorectal tumorigenesis.14

In their recent 2021 review, a group of researchers from Clermont-Ferrand, France focused on a specific potential microbial biomarker for colorectal cancer, a pathogenic strain of Escherichia coli that produces colibactin, a genotoxin.15 In their review, the researchers also highlighted two in-progress clinical trials underway to assess the prognostic value of colibactin-producing E. coli for colorectal cancer:  

  1. The METABIOTE project, assessing a prospective cohort of ~300 patients ( Identifier: NCT03843905) 
  2. The MICARE project, assessing a prospective cohort of ~220 patients ( Identifier: NCT04103567) 

Concluding remarks and takeaways 


Several similarities are evident from studies of the human gut microbiome and its role in the disease cases discussed here. First, although the microbiome consists of bacteria, fungi, and viruses, most of the research into the human gut microbiome in the context of the discussed diseases has only looked at bacteria. Second, shifts in the composition and abundance of gut microbiota seem to correlate with disease onset and/or pathogenesis, fueling the hope that it may be possible to identify clinical microbial biomarkers (most likely an index of several gut microbial species) to predict disease risk or determine treatment. For example, all three of the discussed cases have correlational evidence of reduced gut microbial diversity in diseased patients with an increase in potentially pathogenic bacteria and a decrease in beneficial bacteria. Third, several results from such studies have not been reproducible, in part due to methodological and design differences, a major limiting factor in our progress towards acquiring clinically relevant microbial biomarkers.

In the future, for the successful identification and implementation of microbial biomarkers, large multicenter cohort studies assessing treatment-naïve patients in longitudinal settings will be needed in conjunction with harmonized protocols.11 Other challenges to consider include the fact that the microbiome can change based on age, diet, lifestyle, and antibiotic treatment regimens. Consequently, the high microbial diversity between individuals represents a substantial hurdle in developing one-size-fits-all microbiome biomarkers for diseases. Despite the remaining challenges, research to date on the human gut microbiome shows strong promise as a potential source of clinical microbial biomarkers for several human diseases. 


  1. Yang D, Zhao D, Ali Shah SZ, Wu W, Lai M, Zhang X, Li J, Guan Z, Zhao H, Li W, Gao H, Zhou X, Yang L. (2019) The role of the gut microbiota in the pathogenesis of Parkinson’s disease. Front Neurol. doi: 10.3389/fneur.2019.01155 
  2. Sampson TR, Debelius JW, Thron T, Janssen S, Shastri GG, Ilhan ZE, Challis C, Schretter CE, Rocha S, Gradinaru V, Chesselet MF, Keshavarzian A, Shannon KM, Krajmalnik-Brown R, Wittung-Stafshede P, Knight R, Mazmanian SK. (2016) Gut microbiota regulate motor deficits and neuroinflammation in a model of Parkinson’s disease. Cell. doi: 10.1016/j.cell.2016.11.018 
  3. Dodiya HB, Forsyth CB, Voigt RM, Engen PA, Patel J, Shaikh M, Green SJ, Naqib A, Roy A, Kordower JH, Pahan K, Shannon KM, Keshavarzian A. (2020) Chronic stress-induced gut dysfunction exacerbates Parkinson’s disease phenotype and pathology in a rotenone-induced mouse model of Parkinson’s disease. Neurobiol Dis. doi: 10.1016/j.nbd.2018.12.012 
  4. Cabral GF, Schaan AP, Cavalcante GC, Sena-Dos-Santos C, de Souza TP, Souza Port’s NM, Dos Santos Pinheiro JA, Ribeiro-Dos-Santos Â, Vidal AF. (2021) Nuclear and mitochondrial genome, epigenome and gut microbiome: emerging molecular biomarkers for Parkinson’s disease. Int J Mol Sci. doi: 10.3390/ijms22189839 
  5. Scheperjans F, Aho V, Pereira PA, Koskinen K, Paulin L, Pekkonen E, Haapaniemi E, Kaakkola S, Eerola-Rautio J, Pohja M, Kinnunen E, Murros K, Auvinen P. (2015) Gut microbiota are related to Parkinson’s disease and clinical phenotype. Mov Disord. doi: 10.1002/mds.26069 
  6. Qian Y, Yang X, Xu S, Huang P, Li B, Du J, He Y, Su B, Xu LM, Wang L, Huang R, Chen S, Xiao Q. (2020) Gut metagenomics-derived genes as potential biomarkers of Parkinson’s disease. Brain. doi: 10.1093/brain/awaa201 
  7. Boertien JM, Pereira PAB, Aho VTE, Scheperjans F. (2019) Increasing comparability and utility of gut microbiome studies in Parkinson’s disease: a systematic review. J Parkinsons Dis. doi: 10.3233/JPD-191711 
  8. GBD 2017 Inflammatory Bowel Disease Collaborators. (2020) The global, regional, and national burden of inflammatory bowel disease in 195 countries and territories, 1990-2017: a systematic analysis for the Global Burden of Disease Study 2017. Lancet Gastroenterol Hepatol. doi: 10.1016/S2468-1253(19)30333-4 
  9. Fakhoury M, Negrulj R, Mooranian A, Al-Salami H. (2014) Inflammatory bowel disease: clinical aspects and treatments. J Inflamm Res. doi: 10.2147/JIR.S65979 
  10. Aldars-García L, Chaparro M, Gisbert JP. (2021) Systematic review: the gut microbiome and its potential clinical application in inflammatory bowel disease. Microorganisms. doi: 10.3390/microorganisms9050977 
  11. Ananthakrishnan AN. (2020) Microbiome-based biomarkers for IBD. Inflamm Bowel Dis. doi: 10.1093/ibd/izaa071 
  12. Arnold M, Sierra MS, Laversanne M, Soerjomataram I, Jemal A, Bray F. (2017) Global patterns and trends in colorectal cancer incidence and mortality. Gut. doi: 10.1136/gutjnl-2015-310912 
  13. Brenner H, Chen C. (2018) The colorectal cancer epidemic: challenges and opportunities for primary, secondary and tertiary prevention. Br J Cancer. doi: 10.1038/s41416-018-0264-x 
  14. Cheng Y, Ling Z, Li L. (2020) The intestinal microbiota and colorectal cancer. Front Immunol. doi: 10.3389/fimmu.2020.615056  
  15. Veziant J, Villéger R, Barnich N, Bonnet M. (2021) Gut microbiota as potential biomarker and/or therapeutic target to improve the management of cancer: focus on colibactin-producing Escherichia coli in colorectal cancer. Cancers (Basel). doi: 10.3390/cancers13092215 

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