Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract and can be classified into Crohn disease and ulcerative colitis[1]. IBD can cause symptoms like persistent diarrhea and abdominal pain. In China mainland alone, more than 2.5 million patients are suffering from IBD and this number is even larger in US (~3 million people)[2][3]. IBD has caused severe physical, emotional, and financial burden to patients, according to recent research [4]


To date, no exact cause of IBD is known, but scientists generally believe IBD is a result of immune system defect. The immune system of patients responds in a wrong way to environmental triggers, which leads to inflammation of the gastrointestinal tract[5]. IBD is usually diagnosed by methods like endoscopy and histopathology, which requires expertise and instruments that might not be accessible for many patients[4]. The current treatment of IBD includes medical treatment and surgical treatment. Although many drugs including aminosalicylate have been developed to fight against IBD, they failed to control symptoms for many patients and the patients eventually needs surgery. Surgery is a relatively effective way to cure IBD, but it requires well-trained doctors and good medical condition. Also, for Crohn’s disease, up to 60% of the patients will have recurrence within 10 years even after a successful surgery[4].

It is therefore of great translational significance to develop portable, fast IBD diagnostic methods and novel, non-surgical therapies with long-term effect. We here propose a biomarker-based diagnostic route and multi-probiotics therapy for IBD.

Diagnosis: Pro-LAC

It has been reported that several miRNA in blood can serve as the biomarker for IBD[6]. We designed a system called Proximity-Labelling Assisted and CRISPR-Cas Inspired RNA Targeting system (Pro-LAC). Under blue light illumination, IBD-related miRNA will be labelled by biotin probes specifically with the help of complementary guide RNA (gRNA). Combined with lateral flow assay, our proposed method will provide potential patients with a preliminary idea of whether they have IBD or not in an easy, portable, and fast way.

Fig.1 The progress of Pro-LAC specific RNA detection system

Therapy: Multi-probiotics Approach

IBD-related problems can be separated into three parts: the destruction of intestinal tract on its surface, the dysbacteriosis of the intestinal flora, and the intestinal metabolic disorder. We therefore proposed a combinatory treatment approach according to those three aspects: Treatment Protein Secretion for recovering intestinal tract surface, Microcin Regulation for maintaining intestinal flora fitness, and Bile acid Balance Regulation for regaining intestinal metabolic stability.

Treatment I: Treatment protein secretion

IBD patients have gut inflammation, and nitic oxide (NO) and thiosulfate have been reported as signal molecules that can be sensed by diagnostic bacteria[7]. We have designed an engineered E. coli strain Nissle 1917 to express secretion peptide-linked treatment protein (like trefoil factors, TFF)[8] under the control of NO or thiosulfate sensors. So when gut inflammation happens, NO/thiosulfate will be presented and detected by engineered Nissle 1917, resulting in secretion of the treatment protein into the intestinal tract to promote the wound healing.

Treatment II: Microcin regulation

IBD patients usually have dysbacteriosis of their intestinal flora, which means pathogenic bacteria will break the immunological equilibrium and therefore targeting the pathogenic bacteria became one of our choices to fight with IBD. Microcin is a class of peptide antibiotics from gram-negative bacteria[9] that can kill pathogenic bacteria for regaining the immunological equilibrium inside the intestinal tract of IBD patients. We engineered Nissle 1917 to encode gene clusters that can produce microcin constitutively and validated its bacteria inhibition ability in vitro.

Treatment III: Bile acid balance regulation

Bile acids are important signal molecules synthesized by the liver. Bile acids have two forms: conjugated and unconjugated, and the conversion from the first form to the second is catalyzed by bile salt hydrolase (BSH). The balance between conjugated and unconjugated bile acids is crucial to the metabolic equilibrium and IBD patients often suffered from bile acid dysmetabolism due to loss of BSH activity[10]. We therefore engineered our bacteria to express BSH in intestinal tract to recover the bile acid metabolic equilibrium of IBD patients, thus relieving related IBD symptoms.

Fig.2 Plasmid design of therapeutic molecules


In summary, we combined chemical biology and synthetic biology to develop a novel diagnosis and therapy for IBD. Especially for the treatment part, bacteria were engineered to express and/or secret lots of peptides/proteins to achieve an integrative treatment of IBD. Our effort exhibits the power of synthetic biology in promoting human health and provides a novel route for IBD diagnosis and treatment. We envision future works will further prove the translational feasibility of our approach, and together will currently existed methods, can relief millions of IBD patients from their suffering one day.

It is worth mentioning that the ongoing COVID-19 pandemic has posted great challenge to our project this year. Many human practices have been cancelled and we have team members whose experimental plans were disrupted by COVID-related issues. Nevertheless, we also got the chance to explore other possibilities like communicating science through online meetings and perfecting our models when some members are unable to involve in Wetlab experiments. We managed, as a team, to overcome the challenges and uncertainties along the way!


[2] Qiu, Y., Ren, W., Liu, Y., Chen, W. E., Pan, X. H., & Ren, J. J. (2020). Disease burden of inflammatory bowel disease in China from 1990 to 2017: Findings from the global burden of diseases 2017. EClinicalMedicine, 27, 100544.
[6] James, J. P., Riis, L. B., Malham, M., Høgdall, E., Langholz, E., & Nielsen, B. S. (2020). MicroRNA Biomarkers in IBD-Differential Diagnosis and Prediction of Colitis-Associated Cancer. International journal of molecular sciences, 21(21), 7893.
[7] Rottinghaus, A. G., Amrofell, M. B., & Moon, T. S. (2020). Biosensing in Smart Engineered Probiotics. Biotechnology journal, 15(10), e1900319.
[8] Praveschotinunt, P., Duraj-Thatte, A. M., Gelfat, I., Bahl, F., Chou, D. B., & Joshi, N. S. (2019). Engineered E. coli Nissle 1917 for the delivery of matrix-tethered therapeutic domains to the gut. Nature communications, 10(1), 5580.
[9] NICHOLAS C.K. HENG, RALPH W. JACK. (2006). Handbook of Biologically Active Peptides (Ch.13 – Microcins), Academic Press, 75-81.
[10] Lavelle, A., & Sokol, H. (2020). Gut microbiota-derived metabolites as key actors in inflammatory bowel disease. Nature reviews Gastroenterology & hepatology, 17(4), 223–237.

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