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Lu S, Wang C, Ma J, Wang Y. Metabolic mediators: microbial-derived metabolites as key regulators of anti-tumor immunity, immunotherapy, and chemotherapy. Front Immunol 2024; 15:1456030. [PMID: 39351241 PMCID: PMC11439727 DOI: 10.3389/fimmu.2024.1456030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Accepted: 08/27/2024] [Indexed: 10/04/2024] Open
Abstract
The human microbiome has recently emerged as a focal point in cancer research, specifically in anti-tumor immunity, immunotherapy, and chemotherapy. This review explores microbial-derived metabolites, emphasizing their crucial roles in shaping fundamental aspects of cancer treatment. Metabolites such as short-chain fatty acids (SCFAs), Trimethylamine N-Oxide (TMAO), and Tryptophan Metabolites take the spotlight, underscoring their diverse origins and functions and their profound impact on the host immune system. The focus is on SCFAs' remarkable ability to modulate immune responses, reduce inflammation, and enhance anti-tumor immunity within the intricate tumor microenvironment (TME). The review critically evaluates TMAO, intricately tied to dietary choices and gut microbiota composition, assessing its implications for cancer susceptibility, progression, and immunosuppression. Additionally, the involvement of tryptophan and other amino acid metabolites in shaping immune responses is discussed, highlighting their influence on immune checkpoints, immunosuppression, and immunotherapy effectiveness. The examination extends to their dynamic interaction with chemotherapy, emphasizing the potential of microbial-derived metabolites to alter treatment protocols and optimize outcomes for cancer patients. A comprehensive understanding of their role in cancer therapy is attained by exploring their impacts on drug metabolism, therapeutic responses, and resistance development. In conclusion, this review underscores the pivotal contributions of microbial-derived metabolites in regulating anti-tumor immunity, immunotherapy responses, and chemotherapy outcomes. By illuminating the intricate interactions between these metabolites and cancer therapy, the article enhances our understanding of cancer biology, paving the way for the development of more effective treatment options in the ongoing battle against cancer.
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Affiliation(s)
- Shan Lu
- Department of General Practice, The Second Hospital of Jilin University, Changchun, China
| | - Chunling Wang
- Medical Affairs Department, The Second Hospital of Jilin University, Changchun, China
| | - Jingru Ma
- Department of Clinical Laboratory, the Second Hospital of Jilin University, Changchun, China
| | - Yichao Wang
- Department of Obstetrics and Gynecology, the Second Hospital of Jilin University, Changchun, China
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Nilson R, Penumutchu S, Pagano FS, Belenky P. Metabolic changes associated with polysaccharide utilization reduce susceptibility to some β-lactams in Bacteroides thetaiotaomicron. mSphere 2024; 9:e0010324. [PMID: 39109911 PMCID: PMC11351048 DOI: 10.1128/msphere.00103-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/07/2024] [Indexed: 08/29/2024] Open
Abstract
Antibiotic therapy alters bacterial abundance and metabolism in the gut microbiome, leading to dysbiosis and opportunistic infections. Bacteroides thetaiotaomicron (Bth) is both a commensal in the gut and an opportunistic pathogen in other body sites. Past work has shown that Bth responds to β-lactam treatment differently depending on the metabolic environment both in vitro and in vivo. Studies of other bacteria show that an increase in respiratory metabolism independent of growth rate promotes susceptibility to bactericidal antibiotics. We propose that Bth enters a protected state linked to an increase in polysaccharide utilization and a decrease in the use of simple sugars. Here, we apply antibiotic susceptibility testing, transcriptomic analysis, and genetic manipulation to characterize this polysaccharide-mediated tolerance (PM tolerance) phenotype. We found that a variety of mono- and disaccharides increased the susceptibility of Bth to several different β-lactams compared to polysaccharides. Transcriptomics indicated a metabolic shift from reductive to oxidative branches of the tricarboxylic acid cycle on polysaccharides. Accordingly, supplementation with intermediates of central carbon metabolism had varying effects on PM tolerance. Transcriptional analysis also showed a decrease in the expression of the electron transport chain (ETC) protein NQR and an increase in the ETC protein NUO, when given fiber versus glucose. Deletion of NQR increased Bth susceptibility while deletion of NUO and a third ETC protein NDH2 had no effect. This work confirms that carbon source utilization modulates antibiotic susceptibility in Bth and that anaerobic respiratory metabolism and the ETC play an essential role.IMPORTANCEAntibiotics are indispensable medications that revolutionized modern medicine. However, their effectiveness is challenged by a large array of resistance and tolerance mechanisms. Treatment with antibiotics also disrupts the gut microbiome which can adversely affect health. Bacteroides are prevalent in the gut microbiome and yet are frequently involved in anaerobic infections. Thus, understanding how antibiotics affect these bacteria is necessary to implement proper treatment. Recent work has investigated the role of metabolism in antibiotic susceptibility in distantly related bacteria such as Escherichia coli. Using antibiotic susceptibility testing, transcriptomics, and genetic manipulation, we demonstrate that polysaccharides reduce β-lactam susceptibility when compared to monosaccharides. This finding underscores the profound impact of metabolic adaptation on the therapeutic efficacy of antibiotics. In the long term, this work indicates that modulation of metabolism could make Bacteroides more susceptible during infections or protect them in the context of the microbiome.
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Affiliation(s)
- Rachael Nilson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Francesco S. Pagano
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
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Kattel A, Aro V, Lahtvee P, Kazantseva J, Jõers A, Nahku R, Belouah I. Exploring the resilience and stability of a defined human gut microbiota consortium: An isothermal microcalorimetric study. Microbiologyopen 2024; 13:e1430. [PMID: 39115291 PMCID: PMC11307317 DOI: 10.1002/mbo3.1430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/08/2024] [Accepted: 07/20/2024] [Indexed: 08/11/2024] Open
Abstract
The gut microbiota significantly contributes to human health and well-being. The aim of this study was to evaluate the stability and resilience of a consortium composed of three next-generation probiotics (NGPs) candidates originally found in the human gut. The growth patterns of Akkermansia muciniphila, Bacteroides thetaiotaomicron, and Faecalibacterium prausnitzii were studied both individually and consortium. The growth kinetics of Akkermansia muciniphila (A. muciniphila), Bacteroides thetaiotaomicron (B. thetaiotaomicron), and Faecalibacterium prausnitzii (F. prausnitzii) were characterized both individually and in consortium using isothermal microcalorimetry and 16S ribosomal RNA next-generation sequencing. The consortium reached stability after three passages and demonstrated resilience to changes in its initial composition. The concentration of butyrate produced was nearly twice as high in the consortium compared to the monoculture of F. prausnitzii. The experimental conditions and methodologies used in this article are a solid foundation for developing further complex consortia.
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Affiliation(s)
- Anna Kattel
- Department of Chemistry and BiotechnologyTallinn University of TechnologyTallinnEstonia
- Bioprocess OptimizationCenter of Food and Fermentation TechnologiesTallinnEstonia
| | - Valter Aro
- Department of Chemistry and BiotechnologyTallinn University of TechnologyTallinnEstonia
- Cell BiologyUniversity of Tartu, Institute of TechnologyTartuEstonia
| | | | | | - Arvi Jõers
- Cell BiologyUniversity of Tartu, Institute of TechnologyTartuEstonia
| | - Ranno Nahku
- Bioprocess OptimizationCenter of Food and Fermentation TechnologiesTallinnEstonia
| | - Isma Belouah
- Bioprocess OptimizationCenter of Food and Fermentation TechnologiesTallinnEstonia
- Cell BiologyUniversity of Tartu, Institute of TechnologyTartuEstonia
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4
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Li YS, Jiang HC. Integrating molecular pathway with genome-wide association data for causality identification in breast cancer. Discov Oncol 2024; 15:254. [PMID: 38954227 PMCID: PMC11219684 DOI: 10.1007/s12672-024-01125-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 06/26/2024] [Indexed: 07/04/2024] Open
Abstract
OBJECTIVE The study purpose was to explore the causal association between pyruvate metabolism and breast cancer (BC), as well as the molecular role of key metabolic genes, by using bioinformatics and Mendelian randomization (MR) analysis. METHODS We retrieved and examined diverse datasets from the GEO database to ascertain differentially acting genes (DAGs) in BC via differential expression analysis. Following this, we performed functional and pathway enrichment analyses to ascertain noteworthy molecular functions and metabolic pathways in BC. Employing MR analysis, we established a causal association between pyruvate metabolism and the susceptibility to BC. Additionally, utilizing the DGIdb database, we identified potential targeted medications that act on genes implicated in the pyruvate metabolic pathway and formulated a competing endogenous RNA (ceRNA) regulatory network in BC. RESULTS We collected the datasets GSE54002, GSE70947, and GSE22820, and identified a total of 1127 DEGs between the BC and NC groups. GO and KEGG enrichment analysis showed that the molecular functions of these DEGs mainly included mitotic nuclear division, extracellular matrix, signaling receptor activator activity, etc. Metabolic pathways were mainly concentrated in PI3K-Akt signaling pathway, Cytokine-cytokine receptor binding and Pyruvate, Tyrosine, Propanoate and Phenylalanine metabolism, etc. In addition, MR analysis demonstrated a causal relationship between pyruvate metabolism and BC risk. Finally, we constructed a regulatory network between pathway genes (ADH1B, ACSS2, ACACB, ADH1A, ALDH2, and ADH1C) and targeted drugs, as well as a ceRNA (lncRNA-miRNA-mRNA) regulatory network for BC, further revealing their interactions. CONCLUSIONS Our research revealed a causal association between pyruvate metabolism and BC risk, found that ADH1B, ACSS2, ACACB, ADH1A, ALDH2, and ADH1C takes place an important part in the development of BC in the molecular mechanisms related to pyruvate metabolism, and identified some potential targeted small molecule drugs.
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Affiliation(s)
- Yan-Shuang Li
- Department of Breast Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, China
| | - Hong-Chuan Jiang
- Department of Breast Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, China.
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5
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Zhang X, Wang J, Liu Y, Wang H, Li B, Li Q, Wang Y, Zong Y, Wang J, Meng Q, Wu S, Hao R, Li X, Chen R, Chen H. In situ profiling reveals spatially metabolic injury in the initiation of polystyrene nanoplastic-derived intestinal epithelial injury in mice. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172037. [PMID: 38575003 DOI: 10.1016/j.scitotenv.2024.172037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
Despite increasing concerns regarding the harmful effects of plastic-induced gut injury, mechanisms underlying the initiation of plastic-derived intestinal toxicity remain unelucidated. Here, mice were subjected to long-term exposure to polystyrene nanoplastics (PS-NPs) of varying sizes (80, 200, and 1000 nm) at doses relevant to human dietary exposure. PS-NPs exposure did not induce a significant inflammatory response, histopathological damage, or intestinal epithelial dysfunction in mice at a dosage of 0.5 mg/kg/day for 28 days. However, PS-NPs were detected in the mouse intestine, coupled with observed microstructural changes in enterocytes, including mild villous lodging, mitochondrial membrane rupture, and endoplasmic reticulum (ER) dysfunction, suggesting that intestinal-accumulating PS-NPs resulted in the onset of intestinal epithelial injury in mice. Mechanistically, intragastric PS-NPs induced gut microbiota dysbiosis and specific bacteria alterations, accompanied by abnormal metabolic fingerprinting in the plasma. Furthermore, integrated data from mass spectrometry imaging-based spatial metabolomics and metallomics revealed that PS-NPs exposure led to gut dysbiosis-associated host metabolic reprogramming and initiated intestinal injury. These findings provide novel insights into the critical gut microbial-host metabolic remodeling events vital to nanoplastic-derived-initiated intestinal injury.
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Affiliation(s)
- Xianan Zhang
- School of Public Health, Capital Medical University, Beijing 100069, China; Yanjing Medical College, Capital Medical University, Beijing 101300, China
| | - Jing Wang
- School of Public Health, Capital Medical University, Beijing 100069, China
| | - Yuansheng Liu
- School of Public Health, Capital Medical University, Beijing 100069, China
| | - Hemin Wang
- School of Public Health, Capital Medical University, Beijing 100069, China
| | - Bin Li
- School of Public Health, Capital Medical University, Beijing 100069, China
| | - Qing Li
- School of Public Health, Capital Medical University, Beijing 100069, China
| | - Yi Wang
- School of Public Health, Capital Medical University, Beijing 100069, China
| | - Yuru Zong
- School of Public Health, Capital Medical University, Beijing 100069, China
| | - Jiajia Wang
- School of Public Health, Capital Medical University, Beijing 100069, China
| | - Qingtao Meng
- School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Laboratory of Allergic Diseases, Beijing Municipal Education Commission, Beijing 100069, China
| | - Shenshen Wu
- School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Laboratory of Allergic Diseases, Beijing Municipal Education Commission, Beijing 100069, China
| | - Rongzhang Hao
- School of Public Health, Capital Medical University, Beijing 100069, China
| | - Xiaobo Li
- School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Laboratory of Allergic Diseases, Beijing Municipal Education Commission, Beijing 100069, China.
| | - Rui Chen
- School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Laboratory of Allergic Diseases, Beijing Municipal Education Commission, Beijing 100069, China; Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China; Department of Occupational and Environmental Health, Fourth Military Medical University, Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, Xi'an 710032, China.
| | - Hanqing Chen
- School of Public Health, Capital Medical University, Beijing 100069, China; Department of Nutrition & Food Hygiene, Capital Medical University, Beijing 100069, China.
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Aya JV, Vega LC, Muñoz E, Muñoz M, López DF, Guzmán MP, Martínez DF, Cruz-Saavedra LB, Castillo AK, Quintero KJ, Gónzalez Soltero R, Cala MP, Ramírez JD. Divergent Gut Microbiota: Archaeal and Bacterial Signatures Unveil Unique Patterns in Colombian Cyclists Compared to Weightlifters and Non-Athletes. Adv Biol (Weinh) 2024; 8:e2400069. [PMID: 38548661 DOI: 10.1002/adbi.202400069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/11/2024] [Indexed: 06/16/2024]
Abstract
Engagement in physical activity, across various sports, promotes a diverse microbiota in active individuals. This study examines the gut microbiota of Colombian athletes, specifically weightlifters (n = 16) and road cyclists (n = 13), compared to non-athletes (n = 15). Using Kruskal-Wallis tests, the physical activity level of a group of non-athletic individuals and the sports experience of a group of professional athletes is analyzed. The median age of participants is 24 years, comprising 25 men and 19 women. The microbiota is collected using fecal samples. Participants provided these samples during their pre-competitive stage, specifically during the concentration phase occurring two weeks prior to national competitions. This timing is chosen to capture the microbial composition during a period of heightened physical preparation. Questionnaire responses and microbial composition assessments identify disparities among groups. Microbial composition analysis explores core microbiome, abundance, and taxonomy using Pavian, MicrobiomeAnalyst 2.0, and GraPhlAn. ANCOM-BC2 reveals differentially abundant species. Road cyclists exhibit decreased Bacteria and increased Archaea abundance. Phylum-level variations included Planctomycetes, Acidobacteria, and Proteobacteria, while Bacteroidetes prevailed. Key families influencing gut microbiota are Bacteroidaceae, Muribaculaceae, and Selenomonadaceae. Weightlifters exhibit unique viral and archaeal community connections, while cyclists showed specialized microbial interplay influenced by endurance exercise. Correlation network analysis emphasizes distinctive microbial interactions within athlete groups, shedding light on the impact of physical activities on gut microbiota and athlete health.
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Affiliation(s)
- J V Aya
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - L C Vega
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - E Muñoz
- Universidad Santo Tomás, Bogotá, Colombia
| | - M Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Molecular Epidemiology Laboratory, Instituto de Biotecnología-UN (IBUN), Universidad Nacional de Colombia, Bogotá, Colombia
| | - D F López
- Centro Latinoamericano de Nutrición (CELAN), Bogotá, Colombia
| | - M P Guzmán
- Centro Latinoamericano de Nutrición (CELAN), Bogotá, Colombia
| | - D F Martínez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - L B Cruz-Saavedra
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - A K Castillo
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - K J Quintero
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - R Gónzalez Soltero
- MAS Microbiota Group, Department of Health Sciences, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Spain
| | - M P Cala
- MetCore - Metabolomics Core Facility, Vice-Presidency for Research, Universidad de los Andes, Bogotá, Colombia
| | - J D Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
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7
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Hutchison ER, Yen MI, Peng HW, Davis CR, Vivas EI, Tallon MM, Bui TPN, de Vos WM, Yen CLE, Nieuwdorp M, Rey FE. The gut microbiome modulates the impact of Anaerobutyricum soehngenii supplementation on glucose homeostasis in mice. RESEARCH SQUARE 2024:rs.3.rs-4324489. [PMID: 38746233 PMCID: PMC11092834 DOI: 10.21203/rs.3.rs-4324489/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background There is growing interest in the development of next-generation probiotics to prevent or treat metabolic syndrome. Previous studies suggested that Anaerobutyricum soehngenii may represent a promising probiotic candidate. A recent human study showed that while A. soehngenii supplementation is well tolerated and safe, it resulted in variable responses among individuals with a subset of the subjects significantly benefiting from the treatment. We hypothesized that gut microbiome variation is linked to the heterogeneous responses to A. soehngenii treatment observed in humans. Results We colonized germ-free mice with fecal microbiota from human subjects that responded to A. soehngenii treatment (R65 and R55) and non-responder subjects (N96 and N40). Colonized mice were fed a high-fat diet (45% kcal from fat) to induce insulin resistance, and orally treated with either live A. soehngenii culture or heat-killed culture. We found that R65-colonized mice received a benefit in glycemic control with live A. soehngenii treatment while mice colonized with microbiota from the other donors did not. The glucose homeostasis improvements observed in R65-colonized mice were positively correlated with levels of cecal propionate, an association that was reversed in N40-colonized mice. To test whether the microbiome modulates the effects of propionate, R65- or N40-colonized mice were treated with tripropionin (TP, glycerol tripropionate), a pro-drug of propionate, or glycerol (control). TP supplementation showed a similar response pattern as that observed in live A. soehngenii treatment, suggesting that propionate may mediate the effects of A. soehngenii. We also found that TP supplementation to conventional mice reduces adiposity, improves glycemic control, and reduces plasma insulin compared to control animals supplemented with glycerol. Conclusions These findings highlight the importance of the microbiome on glycemic control and underscore the need to better understand personal microbiome-by-therapeutic interactions to develop more effective treatment strategies.
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Chang KC, Nagarajan N, Gan YH. Short-chain fatty acids of various lengths differentially inhibit Klebsiella pneumoniae and Enterobacteriaceae species. mSphere 2024; 9:e0078123. [PMID: 38305176 PMCID: PMC10900885 DOI: 10.1128/msphere.00781-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/04/2024] [Indexed: 02/03/2024] Open
Abstract
The gut microbiota is inextricably linked to human health and disease. It can confer colonization resistance against invading pathogens either through niche occupation and nutrient competition or via its secreted metabolites. Short-chain fatty acids (SCFA) are the primary metabolites in the gut as a result of dietary fiber fermentation by the gut microbiota. In this work, we demonstrate that the interaction of single-species gut commensals on solid media is insufficient for pathogen inhibition, but supernatants from monocultures of these commensal bacteria enriched in acetate confer inhibition against anaerobic growth of the enteric pathogen Klebsiella pneumoniae. The three primary SCFAs (acetate, propionate, and butyrate) strongly inhibit the intestinal commensal Escherichia coli Nissle as well as a panel of enteric pathogens besides K. pneumoniae at physiological pH of the cecum and ascending colon. This inhibition was significantly milder on anaerobic gut commensals Bacteroides thetaiotaomicron and Bifidobacterium adolescentis previously demonstrated to be associated with microbiota recovery after antibiotic-induced dysbiosis. We describe a general suppression of bacterial membrane potential by these SCFAs at physiological cecum and ascending colonic pH. Furthermore, the strength of bacterial inhibition increases with increasing alkyl chain length. Overall, the insights gained in this study shed light on the potential therapeutic use of SCFAs for conferring colonization resistance against invading pathogens in a dysbiotic gut.IMPORTANCERising antimicrobial resistance has made treatment of bacterial infections increasingly difficult. According to the World Health Organization, it has become a burgeoning threat to hospital and public health systems worldwide. This threat is largely attributed to the global rise of carbapenem-resistant Enterobacteriaceae in recent years, with common hospital-acquired pathogens growing increasingly resistant to last-line antibiotics. Antibiotics disrupt the homeostatic balance of the gut microbiota, resulting in the loss of colonization resistance against enteric pathogens. This work describes the ability of short-chain fatty acids (SCFAs) produced by gut microbiota to be effective against a wide panel of enteric pathogens without major impact on common gut commensal species. We also demonstrate a previously undescribed link between alkyl chain length and antibacterial effects of SCFAs. SCFAs, thus, hold promise as an alternative therapeutic option leveraging on the antimicrobial activity of these endogenously produced gut metabolites without disrupting gut microbiota homeostasis.
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Affiliation(s)
- Kai Chirng Chang
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Niranjan Nagarajan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yunn-Hwen Gan
- Department of Biochemistry, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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9
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Kellogg TD, Ceglia S, Mortzfeld BM, Zeamer AL, Foley SE, Ward DV, Bhattarai SK, McCormick BA, Reboldi A, Bucci V. Microbiota encoded fatty-acid metabolism expands tuft cells to protect tissues homeostasis during Clostridioides difficile infection in the large intestine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.574039. [PMID: 38352546 PMCID: PMC10862725 DOI: 10.1101/2024.01.29.574039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Metabolic byproducts of the intestinal microbiota are crucial in maintaining host immune tone and shaping inter-species ecological dynamics. Among these metabolites, succinate is a driver of tuft cell (TC) differentiation and consequent type 2 immunity-dependent protection against invading parasites in the small intestine. Succinate is also a growth enhancer of the nosocomial pathogen Clostridioides difficile in the large intestine. To date, no research has shown the role of succinate in modulating TC dynamics in the large intestine, or the relevance of this immune pathway to C. difficile pathophysiology. Here we reveal the existence of a three-way circuit between commensal microbes, C. difficile and host epithelial cells which centers around succinate. Through selective microbiota depletion experiments we demonstrate higher levels of type 2 cytokines leading to expansion of TCs in the colon. We then demonstrate the causal role of the microbiome in modulating colonic TC abundance and subsequent type 2 cytokine induction using rational supplementation experiments with fecal transplants and microbial consortia of succinate-producing bacteria. We show that administration of a succinate-deficient Bacteroides thetaiotaomicron knockout (Δfrd) significantly reduces the enhanced type 2 immunity in mono-colonized mice. Finally, we demonstrate that mice prophylactically administered with the consortium of succinate-producing bacteria show reduced C. difficile-induced morbidity and mortality compared to mice administered with heat-killed bacteria or the vehicle. This effect is reduced in a partial tuft cell knockout mouse, Pou2f3+/-, and nullified in the tuft cell knockout mouse, Pou2f3-/-, confirming that the observed protection occurs via the TC pathway. Succinate is an intermediary metabolite of the production of short-chain fatty acids, and its concentration often increases during dysbiosis. The first barrier to enteric pathogens alike is the intestinal epithelial barrier, and host maintenance and strengthening of barrier integrity is vital to homeostasis. Considering our data, we propose that activation of TC by the microbiota-produced succinate in the colon is a mechanism evolved by the host to counterbalance microbiome-derived cues that facilitate invasion by intestinal pathogens.
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Affiliation(s)
- Tasia D. Kellogg
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA, USA
- Immunology and Microbial Pathogenesis Program, UMass Chan Medical School, Worcester, MA, USA
| | - Simona Ceglia
- Immunology and Microbial Pathogenesis Program, UMass Chan Medical School, Worcester, MA, USA
- Department of Pathology, UMass Chan Medical School, Worcester, MA, USA
| | - Benedikt M. Mortzfeld
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA, USA
- Immunology and Microbial Pathogenesis Program, UMass Chan Medical School, Worcester, MA, USA
| | - Abigail L. Zeamer
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA, USA
| | - Sage E. Foley
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
- Current address: Transformational and Translational Immunology Discovery Department, AbbVie, Cambridge, MA, USA
| | - Doyle V. Ward
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA, USA
| | - Shakti K. Bhattarai
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA, USA
- Immunology and Microbial Pathogenesis Program, UMass Chan Medical School, Worcester, MA, USA
| | - Beth A. McCormick
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA, USA
- Immunology and Microbial Pathogenesis Program, UMass Chan Medical School, Worcester, MA, USA
| | - Andrea Reboldi
- Immunology and Microbial Pathogenesis Program, UMass Chan Medical School, Worcester, MA, USA
- Department of Pathology, UMass Chan Medical School, Worcester, MA, USA
| | - Vanni Bucci
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
- Program in Microbiome Dynamics, UMass Chan Medical School, Worcester, MA, USA
- Immunology and Microbial Pathogenesis Program, UMass Chan Medical School, Worcester, MA, USA
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Abstract
Microbial communities are shaped by positive and negative interactions ranging from competition to mutualism. In the context of the mammalian gut and its microbial inhabitants, the integrated output of the community has important impacts on host health. Cross-feeding, the sharing of metabolites between different microbes, has emergent roles in establishing communities of gut commensals that are stable, resistant to invasion, and resilient to external perturbation. In this review, we first explore the ecological and evolutionary implications of cross-feeding as a cooperative interaction. We then survey mechanisms of cross-feeding across trophic levels, from primary fermenters to H2 consumers that scavenge the final metabolic outputs of the trophic network. We extend this analysis to also include amino acid, vitamin, and cofactor cross-feeding. Throughout, we highlight evidence for the impact of these interactions on each species' fitness as well as host health. Understanding cross-feeding illuminates an important aspect of microbe-microbe and host-microbe interactions that establishes and shapes our gut communities.
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Affiliation(s)
- Elizabeth J Culp
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA.
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11
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Supplementation of Sulfide or Acetate and 2-Mercaptoethane Sulfonate Restores Growth of the Methanosarcina acetivorans Δ hdrABC Deletion Mutant during Methylotrophic Methanogenesis. Microorganisms 2023; 11:microorganisms11020327. [PMID: 36838292 PMCID: PMC9963511 DOI: 10.3390/microorganisms11020327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/03/2023] [Accepted: 01/21/2023] [Indexed: 01/31/2023] Open
Abstract
Methanogenic archaea are important organisms in the global carbon cycle that grow by producing methane gas. Methanosarcina acetivorans is a methanogenic archaeum that can grow using methylated compounds, carbon monoxide, or acetate and produces renewable methane as a byproduct. However, there is limited knowledge of how combinations of substrates may affect metabolic fluxes in methanogens. Previous studies have shown that heterodisulfide reductase, the terminal oxidase in the electron transport system, is an essential enzyme in all methanogens. Deletion of genes encoding the nonessential methylotrophic heterodisulfide reductase enzyme (HdrABC) results in slower growth rate but increased metabolic efficiency. We hypothesized that increased sulfide, supplementation of mercaptoethanesulfonate (coenzyme M, CoM-SH), or acetate would metabolically alleviate the effect of the ΔhdrABC mutation. Increased sulfide improved growth of the mutant as expected; however, supplementation of both CoM-SH and acetate together were necessary to reduce the effect of the ΔhdrABC mutation. Supplementation of CoM-SH or acetate alone did not improve growth. These results support our model for the role of HdrABC in methanogenesis and suggest M.acetivorans is more efficient at conserving energy when supplemented with acetate. Our study suggests decreased Hdr enzyme activity can be overcome by nutritional supplementation with sulfide or coenzyme M and acetate, which are abundant in anaerobic environments.
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12
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Dixon B, Ahmed WM, Felton T, Fowler SJ. Molecular phenotyping approaches for the detection and monitoring of carbapenem-resistant Enterobacteriaceae by mass spectrometry. J Mass Spectrom Adv Clin Lab 2022; 26:9-19. [PMID: 36105942 PMCID: PMC9464899 DOI: 10.1016/j.jmsacl.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Breanna Dixon
- Division of Immunology, Immunity to Infection and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, United Kingdom
| | - Waqar M Ahmed
- Division of Immunology, Immunity to Infection and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, United Kingdom
| | - Tim Felton
- Division of Immunology, Immunity to Infection and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
- NIHR Manchester Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Stephen J Fowler
- Division of Immunology, Immunity to Infection and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
- NIHR Manchester Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
- Corresponding author at: Education and Research Centre, Wythenshawe Hospital, Manchester M23 9LT, United Kingdom.
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13
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Liu C, Guo Y, Cheng Y, Qian H. A colon-targeted delivery system of torularhodin encapsulated in electrospinning microspheres, and its co-metabolic regulation mechanism of gut microbiota. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.108189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Adaptation and Resistance: How Bacteroides thetaiotaomicron Copes with the Bisphenol A Substitute Bisphenol F. Microorganisms 2022; 10:microorganisms10081610. [PMID: 36014027 PMCID: PMC9414779 DOI: 10.3390/microorganisms10081610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
Bisphenols are used in the process of polymerization of polycarbonate plastics and epoxy resins. Bisphenols can easily migrate out of plastic products and enter the gastrointestinal system. By increasing colonic inflammation in mice, disrupting the intestinal bacterial community structure and altering the microbial membrane transport system in zebrafish, bisphenols seem to interfere with the gut microbiome. The highly abundant human commensal bacterium Bacteroides thetaiotaomicron was exposed to bisphenols (Bisphenol A (BPA), Bisphenol F (BPF), Bisphenol S (BPS)), to examine the mode of action, in particular of BPF. All chemicals caused a concentration-dependent growth inhibition and the half-maximal effective concentration (EC50) corresponded to their individual logP values, a measure of their hydrophobicity. B. thetaiotaomicron exposed to BPF decreased membrane fluidity with increasing BPF concentrations. Physiological changes including an increase of acetate concentrations were observed. On the proteome level, a higher abundance of several ATP synthase subunits and multidrug efflux pumps suggested an increased energy demand for adaptive mechanisms after BPF exposure. Defense mechanisms were also implicated by a pathway analysis that identified a higher abundance of members of resistance pathways/strategies to cope with xenobiotics (i.e., antibiotics). Here, we present further insights into the mode of action of bisphenols in a human commensal gut bacterium regarding growth inhibition, and the physiological and functional state of the cell. These results, combined with microbiota-directed effects, could lead to a better understanding of host health disturbances and disease development based on xenobiotic uptake.
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Catlett JL, Carr S, Cashman M, Smith MD, Walter M, Sakkaff Z, Kelley C, Pierobon M, Cohen MB, Buan NR. Metabolic Synergy between Human Symbionts Bacteroides and Methanobrevibacter. Microbiol Spectr 2022; 10:e0106722. [PMID: 35536023 PMCID: PMC9241691 DOI: 10.1128/spectrum.01067-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/11/2022] [Indexed: 12/12/2022] Open
Abstract
Trophic interactions between microbes are postulated to determine whether a host microbiome is healthy or causes predisposition to disease. Two abundant taxa, the Gram-negative heterotrophic bacterium Bacteroides thetaiotaomicron and the methanogenic archaeon Methanobrevibacter smithii, are proposed to have a synergistic metabolic relationship. Both organisms play vital roles in human gut health; B. thetaiotaomicron assists the host by fermenting dietary polysaccharides, whereas M. smithii consumes end-stage fermentation products and is hypothesized to relieve feedback inhibition of upstream microbes such as B. thetaiotaomicron. To study their metabolic interactions, we defined and optimized a coculture system and used software testing techniques to analyze growth under a range of conditions representing the nutrient environment of the host. We verify that B. thetaiotaomicron fermentation products are sufficient for M. smithii growth and that accumulation of fermentation products alters secretion of metabolites by B. thetaiotaomicron to benefit M. smithii. Studies suggest that B. thetaiotaomicron metabolic efficiency is greater in the absence of fermentation products or in the presence of M. smithii. Under certain conditions, B. thetaiotaomicron and M. smithii form interspecies granules consistent with behavior observed for syntrophic partnerships between microbes in soil or sediment enrichments and anaerobic digesters. Furthermore, when vitamin B12, hematin, and hydrogen gas are abundant, coculture growth is greater than the sum of growth observed for monocultures, suggesting that both organisms benefit from a synergistic mutual metabolic relationship. IMPORTANCE The human gut functions through a complex system of interactions between the host human tissue and the microbes which inhabit it. These diverse interactions are difficult to model or examine under controlled laboratory conditions. We studied the interactions between two dominant human gut microbes, B. thetaiotaomicron and M. smithii, using a seven-component culturing approach that allows the systematic examination of the metabolic complexity of this binary microbial system. By combining high-throughput methods with machine learning techniques, we were able to investigate the interactions between two dominant genera of the gut microbiome in a wide variety of environmental conditions. Our approach can be broadly applied to studying microbial interactions and may be extended to evaluate and curate computational metabolic models. The software tools developed for this study are available as user-friendly tutorials in the Department of Energy KBase.
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Affiliation(s)
- Jennie L. Catlett
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Sean Carr
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Mikaela Cashman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Megan D. Smith
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Mary Walter
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Zahmeeth Sakkaff
- Department of Computer Science & Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Christine Kelley
- Department of Mathematics, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Massimiliano Pierobon
- Department of Computer Science & Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Myra B. Cohen
- Department of Computer Science & Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Computer Science, Iowa State University, Ames, Iowa, USA
| | - Nicole R. Buan
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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16
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Kim K, Choe D, Song Y, Kang M, Lee SG, Lee DH, Cho BK. Engineering Bacteroides thetaiotaomicron to produce non-native butyrate based on a genome-scale metabolic model-guided design. Metab Eng 2021; 68:174-186. [PMID: 34655791 DOI: 10.1016/j.ymben.2021.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 10/04/2021] [Accepted: 10/09/2021] [Indexed: 12/29/2022]
Abstract
Bacteroides thetaiotaomicron represents a major symbiont of the human gut microbiome that is increasingly viewed as a promising candidate strain for microbial therapeutics. Here, we engineer B. thetaiotaomicron for heterologous production of non-native butyrate as a proof-of-concept biochemical at therapeutically relevant concentrations. Since B. thetaiotaomicron is not a natural producer of butyrate, we heterologously expressed a butyrate biosynthetic pathway in the strain, which led to the production of butyrate at the final concentration of 12 mg/L in a rich medium. Further optimization of butyrate production was achieved by a round of metabolic engineering guided by an expanded genome-scale metabolic model (GEM) of B. thetaiotaomicron. The in silico knock-out simulation of the expanded model showed that pta and ldhD were the potent knock-out targets to enhance butyrate production. The maximum titer and specific productivity of butyrate in the pta-ldhD double knockout mutant increased by nearly 3.4 and 4.8 folds, respectively. To our knowledge, this is the first engineering attempt that enabled butyrate production from a non-butyrate producing commensal B. thetaiotaomicron. The study also highlights that B. thetaiotaomicron can serve as an effective strain for live microbial therapeutics in human.
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Affiliation(s)
- Kangsan Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Donghui Choe
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yoseb Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Minjeong Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Seung-Goo Lee
- Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Dae-Hee Lee
- Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea; KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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17
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Spyrou N, Vallianou N, Kadillari J, Dalamaga M. The interplay of obesity, gut microbiome and diet in the immune check point inhibitors therapy era. Semin Cancer Biol 2021; 73:356-376. [DOI: 10.1016/j.semcancer.2021.05.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 03/22/2021] [Accepted: 05/06/2021] [Indexed: 12/13/2022]
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