Integration of AI with Next - Generation Probiotics for Gut and Potential Health Benefits

Suman Upadhyaya, Saumya Tiwari, Satyndra Kumar Yadav, Neha Vishnoi and Rajesh Kumar*

Department of Environmental Microbiology, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar Raebareli road Lucknow, U.P, India

*Corresponding Author: Rajesh Kumar, Head and Dean, Department of Environmental Microbiology, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar Raebareli road Lucknow, U.P, India.

Received: October 15, 2025; Published: November 12, 2025

Abstract

The emerging discipline of microbiome research has significantly transformed our understanding of human health, particularly highlighting the potential of probiotics and fecal microbiota transplantation (FMT) as therapeutic interventions [1]. Although traditional probiotics have obvious benefits, their efficacy and mechanisms are yet unknown, and the long-term effects of FMT are still under investigation [2]. Advances in high-efficiency sequencing have gradually revealed gut microorganisms with obvious health benefits [3].

All of this is opening the path for next-generation probiotics (NGPs), which are designed via synthetic biology and bioinformatics to solve specific disease problems with greater stability and survival [4].

This review exposes our present knowledge on NGP stiffness, difficulties in administration, and their applications in avoiding and managing chronic illnesses like diabetes, obesity, and cardiovascular diseases [5]. We discuss the opportunities and challenges of including numerous NGP strains into therapeutic practice as well as explore their physiological aspects, safety profiles, and modalities of action, insisting on the need for further studies to guarantee their safety and improve their effectiveness [6]. NGPs have enormous potential to transform treatments/therapies and improve clinical outcomes that are microbiome-based.

 Keywords: Synthetic Biology; Microbe Based Therapies; Next-Generation Probiotics; Chronic Diseases

References

1. Lynch SV and Pedersen O. “The human intestinal microbiome in health and disease”. The New England Journal of Medicine 24 (2016): 2369-2379.
2. Hill C., et al. “The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic”. Nature Reviews Gastroenterology and Hepatology8 (2014): 506-514.
3. Zmora N., et al. “You are what you eat: diet, health and the gut microbiota”. Nature Reviews Gastroenterology and Hepatology1 (2019): 35-56.
4. O'Toole P W., et al. “Next-generation probiotics: The spectrum from probiotics to live biotherapeutics”. Nature Microbiology 2 (2017): 17057.
5. Zmora N., et al. “Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features”. Cell6 (2018): 1388-1405.e21.
6. Doron S and Snydman DR. “Risk and safety of probiotics”. Clinical Infectious Disease 60 (2015): S129-S134.
7. Cunningham M., et al. “Shaping the future of probiotics and prebiotics”. Nature Reviews Gastroenterology and Hepatology9 (2021): 649-660.
8. Zhao Y., et al. “Gut microbiota and obesity: From pathogenesis to therapeutic perspective”. Nature Reviews Endocrinology6 (2019): 329-344.
9. Qin J., et al. “A human gut microbial gene catalogue established by metagenomic sequencing”. Nature 7285 (2010): 59-65.
10. Lloyd-Price J., et al. “The healthy human microbiome”. Genome Medicine 8 (2017): 51.
11. FAO/WHO. “Guidelines for the evaluation of probiotics in food”. London, Ontario, Canada: Food and Agriculture Organization of the United Nations and World Health Organization Working Group Report (2002).
12. Canfora EE., et al. “Gut microbial metabolites in obesity, NAFLD and T2DM”. Nature Reviews Endocrinology 5 (2019): 261-273.
13. Zhang Y., et al. “Research trends and perspectives of next-generation probiotics in food and health”. Critical Reviews in Food Science and Nutrition3 716-732.
14. Xw Feng., et al. “Recent advancements in intestinal microbiota analyses: a review for non-microbiologists”. Current Medical Science 38 (2018): 949-961.
15. M Kumari., et al. “Probiotic metabolites as epigenetic targets in the prevention of colon cancer”. Nutrition Reviews7 (2020): 499-512.
16. Boesmans L., et al. “Butyrate producers as potential next-generation probiotics: Safety assessment of the administration of Butyricicoccus pullicaecorum to healthy volunteers”. Msystems 3 (2018): e00094-18.
17. Hu W., et al. “Biodiversity and physiological characteristics of novel Faecalibacterium prausnitzii strains isolated from human feces”. Microorganisms2 (2022): 297.
18. Duncan SH., et al. “Proposal of Roseburia faecis sp. nov., Roseburia hominis sp. nov. and Roseburia inulinivorans sp. nov., based on isolates from human faeces”. International Journal of Systematic and Evolutionary Microbiology10 (2006): 2437-2441.
19. Lopez-Siles M., et al. “Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth”. Applied Environment Microbiology2 (2012): 420-428.
20. Pham VT., et al. “Early colonization of functional groups of microbes in the infant gut”. Environment Microbiology7 (2016): 2246-2258.
21. Wu X., et al. “Roseburia intestinalis-derived flagellin ameliorates colitis by targeting miR-223-3p-mediated activation of NLRP3 inflammasome and pyroptosis”. Molecular Medicine Reports4 (2020): 2695-2704.
22. R El Hage., et al. “Emerging trends in “smart probiotics”: functional consideration for the development of novel health and industrial applications”. Frontiers in Microbiology 8 (2017): 1889.
23. LS Celiberto., et al. “The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota”. Clinical Microbiology Review1 (2015): 237-264.
24. Den H., et al. “Efficacy of probiotics on cognition, and biomarkers of inflammation and oxidative stress in adults with Alzheimer’s disease or mild cognitive impairment—A meta-analysis of randomized controlled trials”. Aging 12 (2020): 4010.
25. Hidalgo-Cantabrana C., et al. “CRISPR-Based Engineering of next-Generation Lactic Acid Bacteria”. Current Opinion on Microbiology 37 (2017): 79-87.
26. P Gauffin Cano., et al. “Bacteroides Uniformis CECT 7771 Ameliorates Metabolic and Immunological Dysfunction in Mice with High-Fat-Diet Induced Obesity”. (2012): e41079.
27. Cunningham M., et al. “Shaping the future of probiotics and prebiotics”. Trends in Microbiology 29 (8 (2021): 667-685.
28. Den H., et al. “Efficacy of probiotics on cognition, and biomarkers of inflammation and oxidative stress in adults with Alzheimer’s disease or mild cognitive impairment—A meta-analysis of randomized controlled trials”. Aging 12 (2020): 4010.
29. Yu AQ and Li L. “The potential role of probiotics in cancer prevention and treatment”. Nutritional Cancer 68 (2016): 535-544.
30. Tata K., et al. “Role of Animal Models in the Development of Bacteria-Based Live Therapeutics to Fight Cancer”. In Handbook of Animal Models and Its Uses in Cancer Research; Springer: Berlin/Heidelberg, Germany (2023): 133.
31. Aganja RP., et al. “Salmonella as a Promising Curative Tool against Cancer”. Pharmaceutics 14 (2022): 2100.
32. Sharma R., et al. “Psychobiotics: The next-generation probiotics for the brain”. Current Microbiology 78 (2021): 449-463.
33. Tillmann S., et al. “Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 affect one-carbon metabolism in depressive-like rats”. Neurogastroenterology and Motility (2017).
34. Liu YW., et al. “Effects of Lactobacillus plantarum PS128 on children with autism spectrum disorder in Taiwan: A randomized, double-blind, placebo-controlled trial”. Nutrients 11 (2019): 820.
35. Liu G. “Lactic acid bacteria feeding reversed the malformed eye structures and ameliorated gut microbiota profiles of Drosophila melanogaster Alzheimer’s disease model”. Journal of Applied Microbiology 132 (2022): 3155-3167.
36. Agostini S., et al. “A marketed fermented dairy product containing Bifidobacterium lactis CNCM I-2494 suppresses gut hypersensitivity and colonic barrier disruption induced by acute stress in rats”. Neurogastroenterology Motility 24 (2012): 376-e172.
37. Leylabadlo HE., et al. “The role of gut microbiota in the treatment of irritable bowel syndrome”. Reviews and Research in Medical Microbiology 33 (2022): e89-e104.
38. Kolacek S., et al. “Commercial probiotic products: a call for improved quality control. A position paper by the espghan working group for probiotics and prebiotics”. Journal of Pediatric Gastroenterology and Nutrition 65 (2017): 117-124.
39. Arora M and Baldi A. “Regulatory categories of probiotics across the globe: a review representing existing and recommended categorization”. Indian Journal of Medical Microbiology 33 (2015): S2-S10. doi: 10.4103/0255-0857.150868
40. da Cruz AG., et al. “Academic Press; 2021”. Probiotics and prebiotics in foods: challenges, innovations, and advances (2021): 23.
41. O’Toole P., et al. “Next-generation probiotics: the spectrum from probiotics to live biotherapeutics”. Nature Microbiology5 (2017).
42. Zhang H., et al. “Next-generation probiotics: microflora intervention to human diseases”. BioMed Research International 16 (2022): 5633403.
43. Efsa Panel on Dietetic Products, Allergies N., et al. “Guidance on the preparation and presentation of an application for authorisation of a novel food in the context of Regulation (EU) 2015/2283”. EFSA J 14 (2016).
44. Hui W., et al. “Fecal microbiota transplantation for treatment of recurrent C. difficile infection: an updated randomized controlled trial meta-analysis”. PLoS One (2019): 14.
45. MR Charbonneau., et al. “Developing a new class of engineered live bacterial therapeutics to treat human diseases”. Nature Communication 11 (2020): 1738.
46. Abavisani M., et al. “Deciphering the gut microbiome: The revolution of artificial intelligence in microbiota analysis and intervention”. Current Research on Biotechnology 7 (2024): 100211.
47. Zhang C., et al. “Artificial Intelligence in Microbiome Research: Opportunities and Challenges”. Frontiers in Microbiology 11 (2020): 527458.
48. Oh M and Zhang L. “DeepMicro: Deep representation learning for disease prediction based on microbiome data”. Scientific Report 10 (2020): 6026.

Citation

Citation: Rajesh Kumar., et al. “Integration of AI with Next - Generation Probiotics for Gut and Potential Health Benefits”.Acta Scientific Medical Sciences 9.12 (2025): 26-42.

Copyright

Copyright: © 2025 Rajesh Kumar., et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.