Integrative In Vitro and Clinical Analyses of Gut Microbiota Dysbiosis and Its Restoration in Chemotherapy and Obesity
항암치료와 비만에서의 장내 미생물 불균형 및 회복에 대한 통합적 시험관내 및 임상 분석
- 주제(키워드) 도움말 Gut microbiota , dysbiosis , phytochemicals , next-generation probiotics
- 발행기관 국립강릉원주대학교 일반대학원
- 지도교수 도움말 강윤한
- 발행년도 2025
- 학위수여년월 2026. 2
- 학위명 박사
- 학과 및 전공 도움말 일반대학원 KIST강릉분원학.연협동과정
- 실제URI http://www.dcollection.net/handler/kangnung/000000012271
- UCI I804:42001-000000012271
- 본문언어 영어
초록/요약 도움말
A balanced microbiota is widely recognized as a biomarker of a healthy gastrointestinal environment; however, its disruption, referred to as gut dysbiosis, is consistently associated with the development of metabolic diseases and complications from therapeutic medications. In this thesis, in vitro culture and 16S rRNA gene amplicon sequencing techniques were employed to elucidate the characteristics of gut dysbiosis induced by chemotherapy regimens and obesity. We further investigated the potential benefits of phytochemicals and next-generation probiotics in alleviating these two types of dysbiosis, respectively. Additionally, we characterized the longitudinal alterations in gut microbiota composition of overweight and obese patients undergoing weight management with Qsymia, an FDA-approved obesity medication. To address these objectives, this thesis is structured into several chapters that integrate literature review, experimental modelling, and clinical microbiome analysis. Chapter 1 provides a comprehensive literature review on gut dysbiosis in metabolic diseases, particularly obesity, and on chemotherapy-induced dysbiosis as a major gastrointestinal side effect. It also highlights up-to-date microbiota-targeted interventions, including probiotics, prebiotics, and phytochemicals, and discusses their impact on chemotherapy- and obesity-induced dysbiosis as well as overall intestinal health. Although the causes may differ, dysbiosis arising from these factors often shows common characteristics. These include mucosal barrier damage leading to gastrointestinal inflammation (mucositis) and impaired barrier integrity. A disrupted gut barrier allows bacterial translocation and toxin leakage into the bloodstream, which raises the risk of systemic infections. Microbiota-targeting therapies, including probiotics, particularly strains from the Lactobacillus and Bifidobacterium genera, and prebiotics such as polyphenols, saponins, and polysaccharides, have demonstrated potential to mitigate dysbiosis in these contexts. However, further studies are needed to clarify their mechanisms of action, optimal dosage, safety, and efficacy in alleviating intestinal damage associated with chemotherapy and obesity. Chapter 2 elucidates the direct effects of three chemotherapy treatments: gemcitabine, gemcitabine plus paclitaxel, and FOLFIRINOX (a chemotherapy regimen comprising Leucovorin, 5-fluorouracil, oxaliplatin, and irinotecan). We also investigated the ability of three phytochemicals (epigallocatechin-gallate, emodin, and ginsenoside Rg3) to restore the chemotherapy-induced dysbiosis. Chemotherapy, particularly gemcitabine-based treatments, reduced the fecal microbial diversity and the abundance of beneficial bacteria such as Limosilactobacillus and Bifidobacterium, while promoting the growth of the pathogenic Sutterella wadsworthensis in a dose-dependent manner. PICRUSt2 analysis linked these microbial shifts to changes in metabolic pathways, including increased biofilm formation and lipopolysaccharide biosynthesis. Phytochemicals, particularly emodin, restored microbial diversity and enhanced the abundance of beneficial, butyrate-producing bacteria. Chapter 3 investigates the characteristics of obesity-induced gut dysbiosis and further explores the impact of a multi-strain treatment consisting of three next-generation probiotics candidates—Phocaeicola vulgatus KBL981, Roseburia intestinalis KBL982, and Akkermansia muciniphila KBL983—on obesity-related gut dysbiosis. Changes in the short-chain fatty acids profile in obese fecal samples were also characterized. Findings indicated that the optimal next-generation probiotic mix restored microbial diversity and inhibited the growth of potentially harmful commensal and pathogenic species, including Dorea formicigenerans, Sutterella wadsworthensis, and Fusobacterium ulcerans. In addition, levels of metabolites, such as ethanol, butyrate, lysine, leucine, and formate, which were elevated in the obese group, were restored to levels similar to those in the normal group. Chapter 4 presents findings from a longitudinal pilot study on changes in gut microbiota during phentermine/topiramate-assisted weight loss in overweight and obese individuals. It highlights a longitudinal improvement in microbial diversity of the responder group (body weight loss ≥5%) following Qsymia treatment. In addition, an endpoint differential analysis suggested a different microbial profile between responders and non-responders within both the placebo and Qsymia groups. This difference arises from the differing mechanisms of action in the two responder groups: Qsymia responders lost weight through medication treatment, whereas placebo responders lost weight through lifestyle modifications. A further enterotype-stratified analysis of study participants revealed a strong association between enterotype 1 and greater weight loss. In conclusion, this thesis defines the characteristics of gut microbiota dysbiosis across different contexts. It also provides experimental evidence supporting the role of gut microbiota, particularly next-generation probiotics, and phytochemicals such as epigallocatechin gallate, emodin, and ginsenoside Rg3 in ameliorating dysbiosis markers, including microbiota diversity, composition, and functionality. These findings underscore the potential of microbiota-targeting therapies in the management of metabolic diseases, particularly obesity, as well as the mitigation of chemotherapy-related gastrointestinal side effects.
more목차 도움말
Chapter 1. Etiology of gut microbiota dysbiosis: Diseases, therapies, and microbiota-targeting interventions 1
1.1. Introduction 1
1.2. Chemotherapy-induced dysbiosis and phytochemical interventions 5
1.2.1. Probiotics and phytochemicals ameliorate chemotherapy side effects 7
1.2.2. Phytochemicals in cancer therapy: Mechanisms of side effect mitigation 15
1.3. Obesity-induced dysbiosis and microbiota-targeting interventions 17
1.3.1. Microbiome-targeting therapeutic options for obesity 19
1.4. Current research limitations and future research directions 25
Chapter 2. Synthetic microbiome and phytochemical interventions for chemotherapy-induced dysbiosis 27
2.1. Introduction 29
2.2. Materials and Methods 31
2.2.1. Collection of fecal samples and preparation of glycerol stocks 31
2.2.2. In vitro feces culture and chemotherapy treatment 32
2.2.3. Natural product-derived microbial recovery 33
2.2.4. 16S rRNA gene sequencing and data processing 34
2.2.5. Microbial community and statistical analysis 35
2.3. Results 37
2.3.1. Impact of chemotherapy on the microbiota composition and diversity 37
2.3.2. Gemcitabine exhibited stronger side effects on the microbial community, as revealed by differential analysis 40
2.3.3. Effect of chemotherapy on functional metabolic pathways 44
2.3.4. Natural products alleviated chemotherapy-induced microbial alterations 46
2.4. Discussion 50
Chapter 3. Fecal microbiome approaches for obesity dysbiosis and associated next-generation probiotics 56
3.1. Introduction 59
3.2. Materials and methods 62
3.2.1. Collection and processing of fecal samples 62
3.2.2. In vitro feces culture and multi-strain beneficial gut microbiota treatment 63
3.2.3. 16S Microbial Genome Sequencing 65
3.2.4. NMR-based metabolomics analysis 67
3.2.5. Microbiome data statistical analysis 68
3.3. Results 69
3.3.1. Dysbiotic features in feces culture from the obese group 69
3.3.2. Multi-strain beneficial gut microbiota ameliorate obesity-induced dysbiosis 72
3.3.3. Effect on short-chain fatty acids and metabolites content 73
3.3.4. Effect on Bacteroides, Roseburia, and Akkermansia abundance 77
3.3.5. Effect on microbiota composition and metabolic functions 80
3.4. Discussion 84
Chapter 4. Longitudinal characterization of gut microbiota changes during phentermine/topiramate-assisted weight loss 90
4.1. Introduction 92
4.2. Materials and methods 94
4.2.1. Recruitment of study participants 94
4.2.2. Qsymia clinical intervention 96
4.2.3. Anthropometric measurements and sample collection 97
4.2.4. 16S Microbial Genome Sequencing 98
4.2.5. Microbiome data analysis 99
4.3. Results 100
4.3.1. Anthropometric characteristics of the participants 100
4.3.2. Gut microbiota alterations in Qsymia-mediated weight loss patients 102
4.3.3. Association of enterotypes and microbiota composition with Qsymia-mediated weight loss 106
4.3.4. Longitudinal dynamics between gut microbiota and weight loss in enterotype 1 participants 109
4.4. Discussion 114
Chapter 5. General conclusion and future perspectives 120
Acknowledgement 122
Reference 124
