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Pharmaceutics
Volume 17
Issue 12
10.3390/pharmaceutics17121603
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Article

Flavonifractor plautii as a Next-Generation Probiotic Enhancing the NGP F/P Index in a Simulated Human Gut Microbiome Ecosystem

by
Md Sarower Hossen Shuvo
1,2,†,
Sukyung Kim
2,3,†,
Sujin Jo
1,2,
Md Abdur Rahim
2,
Indrajeet Barman
1,2,
Mohammed Solayman Hossain
1,2,
Youjin Yoon
1,2,
Hanieh Tajdozian
1,2,
Izaz Ahmed
1,2,
Ali Atashi
1,2,
GangWon Jeong
3,
Ho-Seong Suh
3,
JiMin You
3,
Chaemin Sung
3,
Mijung Kim
2,3,
Hoonhee Seo
2,3,* and
Ho-Yeon Song
1,2,3,*
1
Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Chungnam, Republic of Korea
2
K-Microbiome Institute, Soonchunhyang University, 22 Soonchunhyang-ro, Sinchang-myeon, Asan 31538, Chungnam, Republic of Korea
3
Next-Generation Microbiome Training Center, Soonchunhyang University, 22 Soonchunhyang-ro, Sinchang, Asan 31538, Chungnam, Republic of Korea
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Pharmaceutics 2025, 17(12), 1603; https://doi.org/10.3390/pharmaceutics17121603
Submission received: 3 November 2025 / Revised: 7 December 2025 / Accepted: 10 December 2025 / Published: 12 December 2025
(This article belongs to the Section Drug Targeting and Design)
Versions Notes

Abstract

Background/Objectives: Traditionally consumed fermented foods and lactic acid bacteria (LAB)-based products have primarily been investigated for their nutritional and health-promoting benefits as dietary supplements. More recently, research has advanced toward exploring their therapeutic potential in pharmaceutical development. However, reliance on conventional LAB strains despite their established safety and efficacy has led to saturation at the strain level, underscoring the need for next-generation probiotics (NGPs) with novel therapeutic potential. In this context, we identified Flavonifractor plautii from human feces as a candidate NGP and investigated its effects on the human gut microbiota. Methods: Whole-genome sequencing revealed distinct genetic features that supported its uniqueness, and the strain was designated PMC93. A human gut microbial ecosystem simulator was used to administer F. plautii daily for one week, after which microbial community changes were evaluated using 16S rRNA gene-based metagenomic sequencing. Results: The administration did not induce significant changes in alpha or beta diversity, suggesting that F. plautii does not disrupt overall bacterial community structure, thereby supporting its microbial community safety. Taxonomic analysis demonstrated a significant increase in the Firmicutes-to-Proteobacteria ratio (NGP F/P index). The improvement surpassed that of conventional LAB treatments and was consistently maintained under supplementation with commonly encountered pharmaceutical compounds and nutrients. The shift was associated with an increase in short-chain fatty acid (SCFA)-producing beneficial taxa and a decrease in pro-inflammatory and potentially pathogenic groups. Functional outcomes, including elevated SCFA levels and downregulation of inflammation-related gene expression, further corroborated these compositional changes. The strain also demonstrated safety in in vivo models. Conclusions: Collectively, these findings suggest that strain PMC93 is a promising NGP candidate with substantial therapeutic potential for microbiota-associated health and disease modulation, particularly due to its ability to enhance the NGP F/P index.
Keywords: next-generation probiotics; Flavonifractor plautii PMC93; simulator of human intestinal microbial ecosystem; short-chain fatty acids; NGP F/P index; gastrointestinal microbiome next-generation probiotics; Flavonifractor plautii PMC93; simulator of human intestinal microbial ecosystem; short-chain fatty acids; NGP F/P index; gastrointestinal microbiome

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MDPI and ACS Style

Shuvo, M.S.H.; Kim, S.; Jo, S.; Rahim, M.A.; Barman, I.; Hossain, M.S.; Yoon, Y.; Tajdozian, H.; Ahmed, I.; Atashi, A.; et al. Flavonifractor plautii as a Next-Generation Probiotic Enhancing the NGP F/P Index in a Simulated Human Gut Microbiome Ecosystem. Pharmaceutics 2025, 17, 1603. https://doi.org/10.3390/pharmaceutics17121603

AMA Style

Shuvo MSH, Kim S, Jo S, Rahim MA, Barman I, Hossain MS, Yoon Y, Tajdozian H, Ahmed I, Atashi A, et al. Flavonifractor plautii as a Next-Generation Probiotic Enhancing the NGP F/P Index in a Simulated Human Gut Microbiome Ecosystem. Pharmaceutics. 2025; 17(12):1603. https://doi.org/10.3390/pharmaceutics17121603

Chicago/Turabian Style

Shuvo, Md Sarower Hossen, Sukyung Kim, Sujin Jo, Md Abdur Rahim, Indrajeet Barman, Mohammed Solayman Hossain, Youjin Yoon, Hanieh Tajdozian, Izaz Ahmed, Ali Atashi, and et al. 2025. "Flavonifractor plautii as a Next-Generation Probiotic Enhancing the NGP F/P Index in a Simulated Human Gut Microbiome Ecosystem" Pharmaceutics 17, no. 12: 1603. https://doi.org/10.3390/pharmaceutics17121603

APA Style

Shuvo, M. S. H., Kim, S., Jo, S., Rahim, M. A., Barman, I., Hossain, M. S., Yoon, Y., Tajdozian, H., Ahmed, I., Atashi, A., Jeong, G., Suh, H.-S., You, J., Sung, C., Kim, M., Seo, H., & Song, H.-Y. (2025). Flavonifractor plautii as a Next-Generation Probiotic Enhancing the NGP F/P Index in a Simulated Human Gut Microbiome Ecosystem. Pharmaceutics, 17(12), 1603. https://doi.org/10.3390/pharmaceutics17121603

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