Traditional and Next Generation Probiotics: A Review
DOI:
https://doi.org/10.55006/biolsciences.2026.6206Keywords:
NGPs (Next Generation probiotics), Probiotics, NGPs isolation techniques, Metagenomics, Isolation techniques of NGPsAbstract
Human microbiota consists of millions and trillions of micro-organisms like Firmicutes (Bacillota) and Bacteroidota including Faecalibacterium prausnitziithat thrives strictly anaerobically in the colon, regulate inflammation via butyrate-production. Bifidobacterium, produce lactic acid, break down fibers, and support infant gut health via human milk oligosaccharides. Other significant phyla include Actinomycetota, Pseudomonadota, and Verrucomicrobiota. Use of antibiotics and other disease conditions alter this microbiota of gut. Hence probiotics are used to flourish and maintain the microenvironment. This review paper focuses on isolation of various species of lactic acid bacteria including the newer strains developed till now. NGPs (Next Generation Probiotics) including Akkermansia muciniphila and engineered Escherichia coli variants, target precise conditions like metabolic syndrome and inflammation via advanced genomic modifications. Various isolation and identification techniques have also been explained like PAGE (Polyacrylamide Gel Electrophoresis), DGGE (Denaturing Gradient Gel Electrophoresis) and Culturomics. Post-2024 research highlights phage-assisted isolation to enrich rare taxa and machine learning-optimized media formulations for fastidious growers. Studies from 2025 report >90% success in isolating Akkermansia muciniphila variants using mucus-mimicking media, enhancing NGP yields for metabolic disorders. These methods prioritize scalability for clinical translation. Key hurdles include maintaining anaerobiosis, strain stability, and regulatory validation. Future techniques may leverage CRISPR-based tagging and organ-on-chip models for in situ isolation. Overall, NGP isolation has shifted from empirical culturing to precision microbiome engineering, promising personalized biotherapeutics.
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References
1. Palm NW, de Zoete MR, Flavell RA. Immune-microbiota interactions in health and disease. Clin Immunol. 2015;159(2):122-127. doi:10.1016/j.clim.2015.05.014.
2. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The Human Microbiome Project. Nature. 2007;449(7164):804-810. doi:10.1038/nature06244.
3. Plaza-Diaz J, Ruiz-Ojeda FJ, Gil-Campos M, Gil A. Mechanisms of action of probiotics. Adv Nutr. 2019;10(Suppl 1):S49-S66. doi:10.1093/advances/nmy063.
4. Rillera R, Dixit P, Dawoodi S, Dawoodi I. Gastrointestinal problem among Indian adults: evidence from longitudinal aging study in India 2017-18. Front Public Health. 2022;10:911354. doi:10.3389/fpubh.2022.911354.
5. Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol. 2009;9(5):313-323. doi:10.1038/nri2515.
6. Gibson MK, Crofts TS, Dantas G. Antibiotics and the developing infant gut microbiota and resistome. Curr Opin Microbiol. 2015;27:51-56. doi:10.1016/j.mib.2015.07.007.
7. Ferreira-Halder CV, Faria AVS, Andrade SS. Action and function of Faecalibacterium prausnitziiin health and disease. Best Pract Res Clin Gastroenterol. 2017;31(6):643-648. doi:10.1016/j.bpg.2017.09.011.
8. Miquel S, Martín R, Rossi O, Bermúdez-Humarán LG, Chatel JM, Sokol H, et al. Faecalibacterium prausnitziiand human intestinal health. Curr Opin Microbiol. 2013;16(3):255-261. doi:10.1016/j.mib.2013.06.003.
9. Ye WY, Cai Y. Akkermansia muciniphila: a microbial guardian against oxidative stress-gut microbiota crosstalk and clinical prospects. J Transl Med. 2025;23:Article number unavailable. doi:10.1186/s12967-025-07149-z.
10. Castaño-Rodríguez N, Mitchell HM, Kaakoush NO. NAFLD, Helicobacter species and the intestinal microbiome. Best Pract Res Clin Gastroenterol. 2017;31(6):657-668. doi:10.1016/j.bpg.2017.09.008.
11. Yang Z, Liu X, Wu Y, Peng J, Wei H. Effect of the microbiome on intestinal innate immune development in early life and the potential strategy of early intervention. Front Immunol. 2022;13:936300. doi:10.3389/fimmu.2022.936300.
12. Duncan SH, Sabater C. Emerging probiotics: future therapeutics for human gut health. FEMS Microbiol Ecol. 2025;101(5):fiaf077. doi:10.1093/femsec/fiaf077.
13. Li Y, Yao Y, Zhang Z, Gan Y. Research status and development trends of probiotics in clinical applications. Front Nutr. 2025;12:1650883. doi:10.3389/fnut.2025.1650883.
14. Zhang X, Wu Y, Jiang Y, Fan J, Dong Y, Fang S, et al. High-potency multi-strain probiotic formulations for safety and improvement of gastrointestinal function and intestinal health: a randomized controlled clinical trial. Front Nutr. 2025;12:1696243. doi:10.3389/fnut.2025.1696243.
15. Al-Fakhrany OM, Elekhnawy E. Next-generation probiotics: the upcoming biotherapeutics. Mol Biol Rep. 2024;51:Article number unavailable. doi:10.1007/s11033-024-09398-5.
16. Hossain MS, Mondal C, Rifa RJ, Ahamed MI, Rahman MM, Rahman T, et al. Isolation and characterization of lactic acid bacteria from Heteropneustes fossilis for probiotic applications in aquaculture. Sci Rep. 2026;16:35791. doi:10.1038/s41598-026-35791-0.
17. Tiwari A, Krisnawati DI, Susilowati E, Mutalik C, Kuo TR. Next-generation probiotics and chronic diseases: a review of current research and future directions. J Agric Food Chem. 2024;72:27679-27700. doi:10.1021/acs.jafc.4c08702.
18. Mu C, Yang Y, Luo Z, Zhu W. Temporal microbiota changes of high-protein diet intake in a rat model. Anaerobe. 2017;47:218-225. doi:10.1016/j.anaerobe.2017.06.003.
19. Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B, et al. Expert consensus document: the International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol. 2014;11(8):506-514. doi:10.1038/nrgastro.2014.66.
20. O'Callaghan A, van Sinderen D. Bifidobacteria and their role as members of the human gut microbiota. Front Microbiol. 2016;7:925. doi:10.3389/fmicb.2016.00925.
21. Swanson KS, Gibson GR, Hutkins R, Reimer RA, Reid G, Verbeke K, et al. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of synbiotics. Nat Rev Gastroenterol Hepatol. 2020;17(11):687-701. doi:10.1038/s41575-020-0344-2.
22. Wei J, Ding W, Song K, Zhang Y, Luo Q, Qi C. Next-generation probiotics and engineered BEVs for precision therapeutics in osteoporosis. Front Nutr. 2025;12:1581971. doi:10.3389/fnut.2025.1581971.
23. Binda C, Lopetuso LR, Rizzatti G, Gibiino G, Cennamo V, Gasbarrini A. Actinobacteria: a relevant minority for the maintenance of gut homeostasis. Dig Liver Dis. 2018;50(5):421-428. doi:10.1016/j.dld.2018.02.012.
24. Mahdizade Ari M, Dadgar L, Elahi Z, Ghanavati R, Taheri B. Genetically engineered microorganisms and their impact on human health. Int J Clin Pract. 2024;2024:6638269. doi:10.1155/2024/6638269.
25. Liu W, Bao Q, Jirimutu, Qing M, Siriguleng, Chen X, et al. Isolation and identification of lactic acid bacteria from Tarag in Eastern Inner Mongolia of China by 16S rRNA sequences and DGGE analysis. Microbiol Res. 2012;167(2):110-115. doi:10.1016/j.micres.2011.05.001.
26. Kumar Murali S, Mansell TJ. Next generation probiotics: engineering live biotherapeutics. Trends Biotechnol. 2024;42(2):150-162. doi:10.1016/j.tibtech.2023.07.003.
27. Cai W, Ran Y, Li Y, Wang B, Zhou L. Intestinal microbiome and permeability in patients with autoimmune hepatitis. Best Pract Res Clin Gastroenterol. 2017;31(6):669-673. doi:10.1016/j.bpg.2017.09.013.
28. Mande SS, Mohammed MH, Ghosh TS. Classification of metagenomic sequences: methods and challenges. Brief Bioinform. 2012;13(6):669-681. doi:10.1093/bib/bbs054.
29. Dawood DH, Darwish MS, El-Awady AA, Mohamed AH, Zaki AA, Taher MA. Chemical characterization of Cassia fistula polysaccharide (CFP) and its potential application as a prebiotic in synbiotic preparation. RSC Adv. 2021;11(22):13329-13340. doi:10.1039/d1ra00380a.
30. Shehata HR, Newmaster SG. The power of DNA-based methods in probiotic authentication. Front Microbiol. 2023;14:1158440. doi:10.3389/fmicb.2023.1158440.
31. Li M, Yao X, Zhang M, Hu B. Artificial intelligence for microbial isolation and cultivation: progress and challenges. Microorganisms. 2026;14(3):654. doi:10.3390/microorganisms14030654.
32. Loo KY, Thong JYH, Tan LTH, Letchumanan V, Chan KG, Lee LH, et al. A current overview of next-generation probiotics and their prospects in health and disease management. Prog Microbes Mol Biol. 2024;7(1):a0000457. doi:10.36877/pmmb.a0000457.
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