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Sargsian S, Mondragón-Palomino O, Lejeune A, Ercelen D, Jin WB, Varghese A, Lim YAL, Guo CJ, Loke P, Cadwell K. Functional characterization of helminth-associated Clostridiales reveals covariates of Treg differentiation. MICROBIOME 2024; 12:86. [PMID: 38730492 PMCID: PMC11084060 DOI: 10.1186/s40168-024-01793-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 03/10/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND Parasitic helminths influence the composition of the gut microbiome. However, the microbiomes of individuals living in helminth-endemic regions are understudied. The Orang Asli, an indigenous population in Malaysia with high burdens of the helminth Trichuris trichiura, display microbiotas enriched in Clostridiales, an order of spore-forming obligate anaerobes with immunogenic properties. We previously isolated novel Clostridiales that were enriched in these individuals and found that a subset promoted the Trichuris life cycle. In this study, we aimed to further characterize the functional properties of these bacteria. RESULTS Clostridiales isolates were profiled for their ability to perform 57 enzymatic reactions and produce short-chain fatty acids (SCFAs) and hydrogen sulfide, revealing that these bacteria were capable of a range of activities associated with metabolism and host response. Consistent with this finding, monocolonization of mice with individual isolates identified bacteria that were potent inducers of regulatory T-cell (Treg) differentiation in the colon. Comparisons between variables revealed by these studies identified enzymatic properties correlated with Treg induction and Trichuris egg hatching. CONCLUSION We identified Clostridiales species that are sufficient to induce high levels of Tregs. We also identified a set of metabolic activities linked with Treg differentiation and Trichuris egg hatching mediated by these newly isolated bacteria. Altogether, this study provides functional insights into the microbiotas of individuals residing in a helminth-endemic region. Video Abstract.
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Affiliation(s)
- Shushan Sargsian
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Octavio Mondragón-Palomino
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alannah Lejeune
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Defne Ercelen
- Department of Medicine, Division of Gastroenterology and Hepatology, New York University Langone Health, New York, NY, 10016, USA
| | - Wen-Bing Jin
- Weill Cornell Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Cornell University, New York, NY, 10021, USA
| | - Alan Varghese
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Yvonne A L Lim
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, 50603, Malaysia
| | - Chun-Jun Guo
- Weill Cornell Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Cornell University, New York, NY, 10021, USA
| | - P'ng Loke
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Ken Cadwell
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
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Tan Y, Liang J, Lai M, Wan S, Luo X, Li F. Advances in synthetic biology toolboxes paving the way for mechanistic understanding and strain engineering of gut commensal Bacteroides spp. and Clostridium spp. Biotechnol Adv 2023; 69:108272. [PMID: 37844770 DOI: 10.1016/j.biotechadv.2023.108272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
The gut microbiota plays a significant role in influencing human immunity, metabolism, development, and behavior by producing a wide range of metabolites. While there is accumulating data on several microbiota-derived small molecules that contribute to host health and disease, our knowledge regarding the molecular mechanisms underlying metabolite-mediated microbe-host interactions remains limited. This is primarily due to the lack of efficient genetic tools for most commensal bacteria, especially those belonging to the dominant phyla Bacteroides spp. and Clostridium spp., which hinders the application of synthetic biology to these gut commensal bacteria. In this review, we provide an overview of recent advances in synthetic biology tools developed for the two dominant genera, as well as their applications in deciphering the mechanisms of microbe-host interactions mediated by microbiota-derived small molecules. We also discuss the potential biomedical applications of engineering commensal bacteria using these toolboxes. Finally, we share our perspective on the future development of synthetic biology tools for a better understanding of small molecule-mediated microbe-host interactions and their engineering for biomedical purposes.
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Affiliation(s)
- Yang Tan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China.
| | - Jing Liang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Mingchi Lai
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Sai Wan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Fuli Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China.
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Johnstone MA, Holman MA, Self WT. Inhibition of selenoprotein synthesis is not the mechanism by which auranofin inhibits growth of Clostridioides difficile. Sci Rep 2023; 13:14733. [PMID: 37679389 PMCID: PMC10484987 DOI: 10.1038/s41598-023-36796-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 06/12/2023] [Indexed: 09/09/2023] Open
Abstract
Clostridioides difficile infections (CDIs) are responsible for a significant number of antibiotic-associated diarrheal cases. The standard-of-care antibiotics for C. difficile are limited to fidaxomicin and vancomycin, with the recently obsolete metronidazole recommended if both are unavailable. No new antimicrobials have been approved for CDI since fidaxomicin in 2011, despite varying rates of treatment failure among all standard-of-care drugs. Drug repurposing is a rational strategy to generate new antimicrobials out of existing therapeutics approved for other indications. Auranofin is a gold-containing anti-rheumatic drug with antimicrobial activity against C. difficile and other microbes. In a previous report, our group hypothesized that inhibition of selenoprotein biosynthesis was auranofin's primary mechanism of action against C. difficile. However, in this study, we discovered that C. difficile mutants lacking selenoproteins are still just as sensitive to auranofin as their respective wild-type strains. Moreover, we found that selenite supplementation dampens the activity of auranofin against C. difficile regardless of the presence of selenoproteins, suggesting that selenite's neutralization of auranofin is not because of compensation for a chemically induced selenium deficiency. Our results clarify the findings of our original study and may aid drug repurposing efforts in discovering the compound's true mechanism of action against C. difficile.
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Affiliation(s)
- Michael A Johnstone
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 4110 Libra Drive, Orlando, FL, 32816, USA
| | - Matthew A Holman
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 4110 Libra Drive, Orlando, FL, 32816, USA
| | - William T Self
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 4110 Libra Drive, Orlando, FL, 32816, USA.
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4
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Mi F, Wang X, Zheng W, Wang J, Lin T, Sun M, Su M, Li H, Ye H. Effects of Different Preparation Methods on Microbiota Composition of Fecal Suspension. Mol Biotechnol 2023; 65:871-880. [PMID: 36315335 DOI: 10.1007/s12033-022-00590-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/20/2022] [Indexed: 05/23/2023]
Abstract
Fecal microbiota transplantation is an emerging disease-modifying therapy. The viability of the microbiome in feces and its successful transfer depends on the preparation of fecal microbiota suspension. However, currently, no standard operation procedure is proposed for fecal suspension preparation. This study aims to compare the effect of different preparation methods on the composition of fecal microbiota composition in the rat. Four methods were used to collect the fecal suspension from fresh rat fecal (Group A), including stirring with normal saline (Group B), stirring with normal saline and then standing (Group C), stirring with normal saline and filtered with gauze (Group D), and stirring with normal saline and centrifuged (Group E). 16S ribosomal RNA gene (16S rDNA) sequencing technology was used to analyze the microbiota diversity and composition of each group of samples. Compared with fresh feces, the bacterial richness of the fecal suspension obtained by the four methods was significantly decreased (P < 0.05). The structural similarity with fresh fecal microbiota from high to low is groups B, D, C, and E. All four methods changed the microbiota structure to varying degrees, thus may affect the effect of FMT. In conclusion, choosing different methods to prepare fecal suspensions may help to better optimize the application of FMT.
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Affiliation(s)
- Fangxia Mi
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315046, Zhejiang, People's Republic of China
| | - Xinxue Wang
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315046, Zhejiang, People's Republic of China
| | - Wentao Zheng
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315046, Zhejiang, People's Republic of China
| | - Jian Wang
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315046, Zhejiang, People's Republic of China
| | - Tong Lin
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315046, Zhejiang, People's Republic of China
| | - Mengxia Sun
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315046, Zhejiang, People's Republic of China
| | - Mingli Su
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315046, Zhejiang, People's Republic of China
| | - Hong Li
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315046, Zhejiang, People's Republic of China
| | - Hua Ye
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315046, Zhejiang, People's Republic of China.
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Romero-Rodríguez A, Ruiz-Villafán B, Martínez-de la Peña CF, Sánchez S. Targeting the Impossible: A Review of New Strategies against Endospores. Antibiotics (Basel) 2023; 12:antibiotics12020248. [PMID: 36830159 PMCID: PMC9951900 DOI: 10.3390/antibiotics12020248] [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: 12/05/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
Endospore-forming bacteria are ubiquitous, and their endospores can be present in food, in domestic animals, and on contaminated surfaces. Many spore-forming bacteria have been used in biotechnological applications, while others are human pathogens responsible for a wide range of critical clinical infections. Due to their resistant properties, it is challenging to eliminate spores and avoid the reactivation of latent spores that may lead to active infections. Furthermore, endospores play an essential role in the survival, transmission, and pathogenesis of some harmful strains that put human and animal health at risk. Thus, different methods have been applied for their eradication. Nevertheless, natural products are still a significant source for discovering and developing new antibiotics. Moreover, targeting the spore for clinical pathogens such as Clostridioides difficile is essential to disease prevention and therapeutics. These strategies could directly aim at the structural components of the spore or their germination process. This work summarizes the current advances in upcoming strategies and the development of natural products against endospores. This review also intends to highlight future perspectives in research and applications.
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Affiliation(s)
- Alba Romero-Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
- Correspondence:
| | - Beatriz Ruiz-Villafán
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Claudia Fabiola Martínez-de la Peña
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72592, Mexico
| | - Sergio Sánchez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
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Mertaoja A, Nowakowska MB, Mascher G, Heljanko V, Groothuis D, Minton NP, Lindström M. CRISPR-Cas9-Based Toolkit for Clostridium botulinum Group II Spore and Sporulation Research. Front Microbiol 2021; 12:617269. [PMID: 33584620 PMCID: PMC7873358 DOI: 10.3389/fmicb.2021.617269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/05/2021] [Indexed: 01/05/2023] Open
Abstract
The spores of Clostridium botulinum Group II strains pose a significant threat to the safety of modern packaged foods due to the risk of their survival in pasteurization and their ability to germinate into neurotoxigenic cultures at refrigeration temperatures. Moreover, spores are the infectious agents in wound botulism, infant botulism, and intestinal toxemia in adults. The identification of factors that contribute to spore formation is, therefore, essential to the development of strategies to control related health risks. Accordingly, development of a straightforward and versatile gene manipulation tool and an efficient sporulation-promoting medium is pivotal. Our strategy was to employ CRISPR-Cas9 and homology-directed repair (HDR) to replace targeted genes with mutant alleles incorporating a unique 24-nt "bookmark" sequence that could act as a single guide RNA (sgRNA) target for Cas9. Following the generation of the sporulation mutant, the presence of the bookmark allowed rapid generation of a complemented strain, in which the mutant allele was replaced with a functional copy of the deleted gene using CRISPR-Cas9 and the requisite sgRNA. Then, we selected the most appropriate medium for sporulation studies in C. botulinum Group II strains by measuring the efficiency of spore formation in seven different media. The most effective medium was exploited to confirm the involvement of a candidate gene in the sporulation process. Using the devised sporulation medium, subsequent comparisons of the sporulation efficiency of the wild type (WT), mutant and "bookmark"-complemented strain allowed the assignment of any defective sporulation phenotype to the mutation made. As a strain generated by complementation with the WT gene in the original locus would be indistinguishable from the parental strain, the gene utilized in complementation studies was altered to contain a unique "watermark" through the introduction of silent nucleotide changes. The mutagenesis system and the devised sporulation medium provide a solid basis for gaining a deeper understanding of spore formation in C. botulinum, a prerequisite for the development of novel strategies for spore control and related food safety and public health risk management.
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Affiliation(s)
- Anna Mertaoja
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Maria B. Nowakowska
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Gerald Mascher
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Viivi Heljanko
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Daphne Groothuis
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Nigel P. Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Miia Lindström
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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García-Bayona L, Coyne MJ, Hantman N, Montero-Llopis P, Von SS, Ito T, Malamy MH, Basler M, Barquera B, Comstock LE. Nanaerobic growth enables direct visualization of dynamic cellular processes in human gut symbionts. Proc Natl Acad Sci U S A 2020; 117:24484-24493. [PMID: 32938803 PMCID: PMC7533675 DOI: 10.1073/pnas.2009556117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mechanistic studies of anaerobic gut bacteria have been hindered by the lack of a fluorescent protein system to track and visualize proteins and dynamic cellular processes in actively growing bacteria. Although underappreciated, many gut "anaerobes" are able to respire using oxygen as the terminal electron acceptor. The oxygen continually released from gut epithelial cells creates an oxygen gradient from the mucus layer to the anaerobic lumen [L. Albenberg et al., Gastroenterology 147, 1055-1063.e8 (2014)], with oxygen available to bacteria growing at the mucus layer. Here, we show that Bacteroides species are metabolically and energetically robust and do not mount stress responses in the presence of 0.10 to 0.14% oxygen, defined as nanaerobic conditions [A. D. Baughn, M. H. Malamy, Nature 427, 441-444 (2004)]. Taking advantage of this metabolic capability, we show that nanaerobic growth provides sufficient oxygen for the maturation of oxygen-requiring fluorescent proteins in Bacteroides species. Type strains of four different Bacteroides species show bright GFP fluorescence when grown nanaerobically versus anaerobically. We compared four different red fluorescent proteins and found that mKate2 yields the highest red fluorescence intensity in our assay. We show that GFP-tagged proteins can be localized in nanaerobically growing bacteria. In addition, we used time-lapse fluorescence microscopy to image dynamic type VI secretion system processes in metabolically active Bacteroides fragilis The ability to visualize fluorescently labeled Bacteroides and fluorescently linked proteins in actively growing nanaerobic gut symbionts ushers in an age of imaging analyses not previously possible in these bacteria.
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Affiliation(s)
- Leonor García-Bayona
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Michael J Coyne
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Noam Hantman
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
| | | | - Salena S Von
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Takeshi Ito
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Michael H Malamy
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111
| | - Marek Basler
- Biozentrum, University of Basel, CH 4056 Basel, Switzerland
| | - Blanca Barquera
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Laurie E Comstock
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115;
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Kwon SW, Paari KA, Malaviya A, Jang YS. Synthetic Biology Tools for Genome and Transcriptome Engineering of Solventogenic Clostridium. Front Bioeng Biotechnol 2020; 8:282. [PMID: 32363182 PMCID: PMC7181999 DOI: 10.3389/fbioe.2020.00282] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 03/17/2020] [Indexed: 12/18/2022] Open
Abstract
Strains of Clostridium genus are used for production of various value-added products including fuels and chemicals. Development of any commercially viable production process requires a combination of both strain and fermentation process development strategies. The strain development in Clostridium sp. could be achieved by random mutagenesis, and targeted gene alteration methods. However, strain improvement in Clostridium sp. by targeted gene alteration method was challenging due to the lack of efficient tools for genome and transcriptome engineering in this organism. Recently, various synthetic biology tools have been developed to facilitate the strain engineering of solventogenic Clostridium. In this review, we consolidated the recent advancements in toolbox development for genome and transcriptome engineering in solventogenic Clostridium. Here we reviewed the genome-engineering tools employing mobile group II intron, pyrE alleles exchange, and CRISPR/Cas9 with their application for strain development of Clostridium sp. Next, transcriptome engineering tools such as untranslated region (UTR) engineering and synthetic sRNA techniques were also discussed in context of Clostridium strain engineering. Application of any of these discussed techniques will facilitate the metabolic engineering of clostridia for development of improved strains with respect to requisite functional attributes. This might lead to the development of an economically viable butanol production process with improved titer, yield and productivity.
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Affiliation(s)
- Seong Woo Kwon
- Department of Agricultural Chemistry and Food Science Technology, Division of Applied Life Science (BK21 Plus Program), Institute of Agriculture & Life Science (IALS), Gyeongsang National University, Jinju, South Korea
| | | | - Alok Malaviya
- Applied and Industrial Biotechnology Laboratory (AIBL), Department of Life Sciences, CHRIST (Deemed to be University), Bengaluru, India
| | - Yu-Sin Jang
- Department of Agricultural Chemistry and Food Science Technology, Division of Applied Life Science (BK21 Plus Program), Institute of Agriculture & Life Science (IALS), Gyeongsang National University, Jinju, South Korea
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