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Yang Z, Ni J, Sun X, Cui Q, Zhang X, Zhang M, Zhu X, Wu Z, Tang C, Zhu J, Mao H, Liu K, Wang C, Xing C, Zhu J. The prevention effect of Limosilactobacillus reuteri on acute kidney injury by regulating gut microbiota. Microbiol Immunol 2024; 68:213-223. [PMID: 38747013 DOI: 10.1111/1348-0421.13130] [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: 09/12/2023] [Revised: 03/26/2024] [Accepted: 05/02/2024] [Indexed: 07/09/2024]
Abstract
Acute kidney injury (AKI) has considerably high morbidity and mortality but we do not have proper treatment for it. There is an urgent need to develop new prevention or treatment methods. Gut microbiota has a close connection with renal diseases and has become the new therapy target for AKI. In this study, we found the oral administration of the probiotic Limosilactobacillus reuteri had a prevention effect on the AKI induced by lipopolysaccharide (LPS). It reduced serum concentration of creatinine and urea nitrogen and protected the renal cells from necrosis and apoptosis. Meanwhile, L. reuteri improved the gut barrier function, which is destroyed in AKI, and modulated the gut microbiota and relevant metabolites. Compared with the LPS group, L. reuteri increased the proportion of Proteobacteria and reduced the proportion of Firmicutes, changing the overall structure of the gut microbiota. It also influenced the fecal metabolites and changed the metabolite pathways, such as tyrosine metabolism, pentose and glucuronate interconversions, galactose metabolism, purine metabolism, and insulin resistance. These results showed that L. reuteri is a potential therapy for AKI as it helps in sustaining the gut barrier integrity and modulating gut microbiota and related metabolites.
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Affiliation(s)
- Zhan Yang
- Huadong Medical Institute of Biotechniques, Nanjing, China
| | - Juan Ni
- Huadong Medical Institute of Biotechniques, Nanjing, China
- Department of Nephrology, The First Affiliated Hospital of Nanjing Medical University (Jiangsu Province Hospital), Nanjing, China
| | - Xuewei Sun
- Huadong Medical Institute of Biotechniques, Nanjing, China
- Binzhou Medical University, Yantai, China
| | - Qian Cui
- Air Force Hospital of Eastern Theater, Nanjing, China
| | - Xinrui Zhang
- Huadong Medical Institute of Biotechniques, Nanjing, China
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Mingyan Zhang
- Huadong Medical Institute of Biotechniques, Nanjing, China
- Jinling Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiaojing Zhu
- Department of Pathlogy, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zihan Wu
- Huadong Medical Institute of Biotechniques, Nanjing, China
| | | | - Jingfeng Zhu
- Department of Nephrology, The First Affiliated Hospital of Nanjing Medical University (Jiangsu Province Hospital), Nanjing, China
| | - Huijuan Mao
- Department of Nephrology, The First Affiliated Hospital of Nanjing Medical University (Jiangsu Province Hospital), Nanjing, China
| | - Kang Liu
- Department of Nephrology, The First Affiliated Hospital of Nanjing Medical University (Jiangsu Province Hospital), Nanjing, China
| | - Chunhui Wang
- Huadong Medical Institute of Biotechniques, Nanjing, China
| | - Changying Xing
- Department of Nephrology, The First Affiliated Hospital of Nanjing Medical University (Jiangsu Province Hospital), Nanjing, China
| | - Jin Zhu
- Huadong Medical Institute of Biotechniques, Nanjing, China
- Basic Medical College, Nanjing Medical University, Nanjing, China
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2
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Burbano DA, Kiattisewee C, Karanjia AV, Cardiff RAL, Faulkner ID, Sugianto W, Carothers JM. CRISPR Tools for Engineering Prokaryotic Systems: Recent Advances and New Applications. Annu Rev Chem Biomol Eng 2024; 15:389-430. [PMID: 38598861 DOI: 10.1146/annurev-chembioeng-100522-114706] [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] [Indexed: 04/12/2024]
Abstract
In the past decades, the broad selection of CRISPR-Cas systems has revolutionized biotechnology by enabling multimodal genetic manipulation in diverse organisms. Rooted in a molecular engineering perspective, we recapitulate the different CRISPR components and how they can be designed for specific genetic engineering applications. We first introduce the repertoire of Cas proteins and tethered effectors used to program new biological functions through gene editing and gene regulation. We review current guide RNA (gRNA) design strategies and computational tools and how CRISPR-based genetic circuits can be constructed through regulated gRNA expression. Then, we present recent advances in CRISPR-based biosensing, bioproduction, and biotherapeutics across in vitro and in vivo prokaryotic systems. Finally, we discuss forthcoming applications in prokaryotic CRISPR technology that will transform synthetic biology principles in the near future.
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Affiliation(s)
- Diego Alba Burbano
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Cholpisit Kiattisewee
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ava V Karanjia
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ryan A L Cardiff
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ian D Faulkner
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Widianti Sugianto
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - James M Carothers
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
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3
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Liu D, Yu L, Rong H, Liu L, Yin J. Engineering Microorganisms for Cancer Immunotherapy. Adv Healthc Mater 2024; 13:e2304649. [PMID: 38598792 DOI: 10.1002/adhm.202304649] [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: 12/28/2023] [Revised: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Cancer immunotherapy presents a promising approach to fight against cancer by utilizing the immune system. Recently, engineered microorganisms have emerged as a potential strategy in cancer immunotherapy. These microorganisms, including bacteria and viruses, can be designed and modified using synthetic biology and genetic engineering techniques to target cancer cells and modulate the immune system. This review delves into various microorganism-based therapies for cancer immunotherapy, encompassing strategies for enhancing efficacy while ensuring safety and ethical considerations. The development of these therapies holds immense potential in offering innovative personalized treatments for cancer.
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Affiliation(s)
- Dingkang Liu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing, 211198, China
| | - Lichao Yu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing, 211198, China
| | - Haibo Rong
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, Nanjing, 210009, China
| | - Lubin Liu
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, No. 120 Longshan Road, Chongqing, 401147, China
| | - Jun Yin
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing, 211198, China
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4
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de la Fuente J, Ghosh S. Evolution of tick vaccinology. Parasitology 2024:1-8. [PMID: 38586999 DOI: 10.1017/s003118202400043x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Ticks represent a major concern for society worldwide. Ticks are also difficult to control, and vaccines represent the most efficacious, safe, economically feasible and environmentally sustainable intervention. The evolution of tick vaccinology has been driven by multiple challenges such as (1) Ticks are difficult to control, (2) Vaccines control tick infestations by reducing ectoparasite fitness and reproduction, (3) Vaccine efficacy against multiple tick species, (4) Impact of tick strain genetic diversity on vaccine efficacy, (5) Antigen combination to improve vaccine efficacy, (6) Vaccine formulations and delivery platforms and (7) Combination of vaccines with transgenesis and paratransgenesis. Tick vaccine antigens evolved from organ protein extracts to recombinant proteins to chimera designed by vaccinomics and quantum vaccinomics. Future directions will advance in these areas together with other novel technologies such as multiomics, AI and Big Data, mRNA vaccines, microbiota-driven probiotics and vaccines, and combination of vaccines with other interventions in collaboration with regions with high incidence of tick infestations and tick-borne diseases for a personalized medicine approach.
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Affiliation(s)
- José de la Fuente
- SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, 13005 Ciudad Real, Spain
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Srikant Ghosh
- Entomology Laboratory, Parasitology Division, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, Bareilly, UP, India
- Eastern Regional Station- Indian Veterinary Research Institute, 37 Belgachia Road, Kolkata-700037, West Bengal, India
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5
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Tan J, Fu B, Zhao X, Ye L. Novel Techniques and Models for Studying the Role of the Gut Microbiota in Drug Metabolism. Eur J Drug Metab Pharmacokinet 2024; 49:131-147. [PMID: 38123834 DOI: 10.1007/s13318-023-00874-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
The gut microbiota, known as the second human genome, plays a vital role in modulating drug metabolism, significantly impacting therapeutic outcomes and adverse effects. Emerging research has elucidated that the microbiota mediates a range of modifications of drugs, leading to their activation, inactivation, or even toxication. In diverse individuals, variations in the gut microbiota can result in differences in microbe-drug interactions, underscoring the importance of personalized approaches in pharmacotherapy. However, previous studies on drug metabolism in the gut microbiota have been hampered by technical limitations. Nowadays, advances in biotechnological tools, such as microbially derived metabolism screening and microbial gene editing, have provided a deeper insight into the mechanism of drug metabolism by gut microbiota, moving us toward personalized therapeutic interventions. Given this situation, our review summarizes recent advances in the study of gut-microbiota-mediated drug metabolism and showcases techniques and models developed to navigate the challenges posed by the microbial involvement in drug action. Therefore, we not only aim at understanding the complex interaction between the gut microbiota and drugs and outline the development of research techniques and models, but we also summarize the specific applications of new techniques and models in researching gut-microbiota-mediated drug metabolism, with the expectation of providing new insights on how to study drug metabolism by gut microbiota.
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Affiliation(s)
- Jianling Tan
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Bingxuan Fu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xiaojie Zhao
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Ling Ye
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
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6
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Kamel M, Aleya S, Alsubih M, Aleya L. Microbiome Dynamics: A Paradigm Shift in Combatting Infectious Diseases. J Pers Med 2024; 14:217. [PMID: 38392650 PMCID: PMC10890469 DOI: 10.3390/jpm14020217] [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: 12/26/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024] Open
Abstract
Infectious diseases have long posed a significant threat to global health and require constant innovation in treatment approaches. However, recent groundbreaking research has shed light on a previously overlooked player in the pathogenesis of disease-the human microbiome. This review article addresses the intricate relationship between the microbiome and infectious diseases and unravels its role as a crucial mediator of host-pathogen interactions. We explore the remarkable potential of harnessing this dynamic ecosystem to develop innovative treatment strategies that could revolutionize the management of infectious diseases. By exploring the latest advances and emerging trends, this review aims to provide a new perspective on combating infectious diseases by targeting the microbiome.
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Affiliation(s)
- Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 11221, Egypt
| | - Sami Aleya
- Faculty of Medecine, Université de Bourgogne Franche-Comté, Hauts-du-Chazal, 25030 Besançon, France
| | - Majed Alsubih
- Department of Civil Engineering, King Khalid University, Guraiger, Abha 62529, Saudi Arabia
| | - Lotfi Aleya
- Laboratoire de Chrono-Environnement, Université de Bourgogne Franche-Comté, UMR CNRS 6249, La Bouloie, 25030 Besançon, France
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7
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de la Fuente J, Mazuecos L, Contreras M. Innovative approaches for the control of ticks and tick-borne diseases. Ticks Tick Borne Dis 2023; 14:102227. [PMID: 37419001 DOI: 10.1016/j.ttbdis.2023.102227] [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: 06/05/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 07/09/2023]
Abstract
Ticks and tick-borne diseases constitute a major threat for human and animal health worldwide. Vaccines for the control of tick infestations and transmitted pathogens still represents a challenge for science and health. Vaccines have evolved with antigens derived from inactivated pathogens to recombinant proteins and vaccinomics approaches. Recently, vaccines for the control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have shown the efficacy of new antigen delivery platforms. However, until now only two vaccines based on recombinant Bm86/Bm95 antigens have been registered and commercialized for the control of cattle-tick infestations. Nevertheless, recently new technologies and approaches are under consideration for vaccine development for the control of ticks and tick-borne pathogens. Genetic manipulation of tick commensal bacteria converted enemies into friends. Frankenbacteriosis was used to control tick pathogen infection. Based on these results, the way forward is to develop new paratransgenic interventions and vaccine delivery platforms for the control of tick-borne diseases.
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Affiliation(s)
- José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13005, Ciudad Real, Spain; Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, 74078, USA.
| | - Lorena Mazuecos
- SaBio, Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13005, Ciudad Real, Spain
| | - Marinela Contreras
- SaBio, Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13005, Ciudad Real, Spain
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8
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Merritt J, Kreth J. Illuminating the oral microbiome and its host interactions: tools and approaches for molecular microbiology studies. FEMS Microbiol Rev 2023; 47:fuac050. [PMID: 36549660 PMCID: PMC10719069 DOI: 10.1093/femsre/fuac050] [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: 08/18/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Advancements in DNA sequencing technologies within the last decade have stimulated an unprecedented interest in the human microbiome, largely due the broad diversity of human diseases found to correlate with microbiome dysbiosis. As a direct consequence of these studies, a vast number of understudied and uncharacterized microbes have been identified as potential drivers of mucosal health and disease. The looming challenge in the field is to transition these observations into defined molecular mechanistic studies of symbiosis and dysbiosis. In order to meet this challenge, many of these newly identified microbes will need to be adapted for use in experimental models. Consequently, this review presents a comprehensive overview of the molecular microbiology tools and techniques that have played crucial roles in genetic studies of the bacteria found within the human oral microbiota. Here, we will use specific examples from the oral microbiome literature to illustrate the biology supporting these techniques, why they are needed in the field, and how such technologies have been implemented. It is hoped that this information can serve as a useful reference guide to help catalyze molecular microbiology studies of the many new understudied and uncharacterized species identified at different mucosal sites in the body.
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Affiliation(s)
- Justin Merritt
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, OR, United States
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, United States
| | - Jens Kreth
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, OR, United States
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, United States
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9
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Arenas-Gómez CM, Garcia-Gutierrez E, Escobar JS, Cotter PD. Human gut homeostasis and regeneration: the role of the gut microbiota and its metabolites. Crit Rev Microbiol 2023; 49:764-785. [PMID: 36369718 DOI: 10.1080/1040841x.2022.2142088] [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: 02/01/2022] [Revised: 08/18/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022]
Abstract
The healthy human gut is a balanced ecosystem where host cells and representatives of the gut microbiota interact and communicate in a bidirectional manner at the gut epithelium. As a result of these interactions, many local and systemic processes necessary for host functionality, and ultimately health, take place. Impairment of the integrity of the gut epithelium diminishes its ability to act as an effective gut barrier, can contribute to conditions associated to inflammation processes and can have other negative consequences. Pathogens and pathobionts have been linked with damage of the integrity of the gut epithelium, but other components of the gut microbiota and some of their metabolites can contribute to its repair and regeneration. Here, we review what is known about the effect of bacterial metabolites on the gut epithelium and, more specifically, on the regulation of repair by intestinal stem cells and the regulation of the immune system in the gut. Additionally, we explore the potential therapeutic use of targeted modulation of the gut microbiota to maintain and improve gut homeostasis as a mean to improve health outcomes.
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Affiliation(s)
- Claudia Marcela Arenas-Gómez
- Vidarium-Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
- Dirección Académica, Universidad Nacional de Colombia, Sede de La Paz, La Paz 202017, Colombia
| | - Enriqueta Garcia-Gutierrez
- Teagasc Food Research Centre Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- VistaMilk SFI Research Centre, Moorepark, Fermoy, Ireland
| | - Juan S Escobar
- Vidarium-Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
| | - Paul D Cotter
- Teagasc Food Research Centre Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- VistaMilk SFI Research Centre, Moorepark, Fermoy, Ireland
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10
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Zhao Q, Chen Y, Huang W, Zhou H, Zhang W. Drug-microbiota interactions: an emerging priority for precision medicine. Signal Transduct Target Ther 2023; 8:386. [PMID: 37806986 PMCID: PMC10560686 DOI: 10.1038/s41392-023-01619-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 07/20/2023] [Accepted: 08/24/2023] [Indexed: 10/10/2023] Open
Abstract
Individual variability in drug response (IVDR) can be a major cause of adverse drug reactions (ADRs) and prolonged therapy, resulting in a substantial health and economic burden. Despite extensive research in pharmacogenomics regarding the impact of individual genetic background on pharmacokinetics (PK) and pharmacodynamics (PD), genetic diversity explains only a limited proportion of IVDR. The role of gut microbiota, also known as the second genome, and its metabolites in modulating therapeutic outcomes in human diseases have been highlighted by recent studies. Consequently, the burgeoning field of pharmacomicrobiomics aims to explore the correlation between microbiota variation and IVDR or ADRs. This review presents an up-to-date overview of the intricate interactions between gut microbiota and classical therapeutic agents for human systemic diseases, including cancer, cardiovascular diseases (CVDs), endocrine diseases, and others. We summarise how microbiota, directly and indirectly, modify the absorption, distribution, metabolism, and excretion (ADME) of drugs. Conversely, drugs can also modulate the composition and function of gut microbiota, leading to changes in microbial metabolism and immune response. We also discuss the practical challenges, strategies, and opportunities in this field, emphasizing the critical need to develop an innovative approach to multi-omics, integrate various data types, including human and microbiota genomic data, as well as translate lab data into clinical practice. To sum up, pharmacomicrobiomics represents a promising avenue to address IVDR and improve patient outcomes, and further research in this field is imperative to unlock its full potential for precision medicine.
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Affiliation(s)
- Qing Zhao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Yao Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Weihua Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China.
- The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, PR China.
- The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, PR China.
- Central Laboratory of Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, Changsha, 410013, PR China.
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11
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Pantazi AC, Balasa AL, Mihai CM, Chisnoiu T, Lupu VV, Kassim MAK, Mihai L, Frecus CE, Chirila SI, Lupu A, Andrusca A, Ionescu C, Cuzic V, Cambrea SC. Development of Gut Microbiota in the First 1000 Days after Birth and Potential Interventions. Nutrients 2023; 15:3647. [PMID: 37630837 PMCID: PMC10457741 DOI: 10.3390/nu15163647] [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: 06/16/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
The first 1000 days after birth represent a critical window for gut microbiome development, which is essential for immune system maturation and overall health. The gut microbiome undergoes major changes during this period due to shifts in diet and environment. Disruptions to the microbiota early in life can have lasting health effects, including increased risks of inflammatory disorders, autoimmune diseases, neurological disorders, and obesity. Maternal and environmental factors during pregnancy and infancy shape the infant gut microbiota. In this article, we will review how maintaining a healthy gut microbiome in pregnancy and infancy is important for long-term infant health. Furthermore, we briefly include fungal colonization and its effects on the host immune function, which are discussed as part of gut microbiome ecosystem. Additionally, we will describe how potential approaches such as hydrogels enriched with prebiotics and probiotics, gut microbiota transplantation (GMT) during pregnancy, age-specific microbial ecosystem therapeutics, and CRISPR therapies targeting the gut microbiota hold potential for advancing research and development. Nevertheless, thorough evaluation of their safety, effectiveness, and lasting impacts is crucial prior to their application in clinical approach. The article emphasizes the need for continued research to optimize gut microbiota and immune system development through targeted early-life interventions.
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Affiliation(s)
- Alexandru Cosmin Pantazi
- Pediatrics Department, Faculty of Medicine, “Ovidius” University, 900470 Constanta, Romania (A.L.B.)
- Pediatrics Department, County Clinical Emergency Hospital of Constanta, 900591 Constanta, Romania
| | - Adriana Luminita Balasa
- Pediatrics Department, Faculty of Medicine, “Ovidius” University, 900470 Constanta, Romania (A.L.B.)
- Pediatrics Department, County Clinical Emergency Hospital of Constanta, 900591 Constanta, Romania
| | - Cristina Maria Mihai
- Pediatrics Department, Faculty of Medicine, “Ovidius” University, 900470 Constanta, Romania (A.L.B.)
- Pediatrics Department, County Clinical Emergency Hospital of Constanta, 900591 Constanta, Romania
| | - Tatiana Chisnoiu
- Pediatrics Department, Faculty of Medicine, “Ovidius” University, 900470 Constanta, Romania (A.L.B.)
- Pediatrics Department, County Clinical Emergency Hospital of Constanta, 900591 Constanta, Romania
| | - Vasile Valeriu Lupu
- Pediatrics Department, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | | | - Larisia Mihai
- Pediatrics Department, Faculty of Medicine, “Ovidius” University, 900470 Constanta, Romania (A.L.B.)
- Pediatrics Department, County Clinical Emergency Hospital of Constanta, 900591 Constanta, Romania
| | - Corina Elena Frecus
- Pediatrics Department, Faculty of Medicine, “Ovidius” University, 900470 Constanta, Romania (A.L.B.)
- Pediatrics Department, County Clinical Emergency Hospital of Constanta, 900591 Constanta, Romania
| | | | - Ancuta Lupu
- Pediatrics Department, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Antonio Andrusca
- Pediatrics Department, Faculty of Medicine, “Ovidius” University, 900470 Constanta, Romania (A.L.B.)
- Pediatrics Department, County Clinical Emergency Hospital of Constanta, 900591 Constanta, Romania
| | - Constantin Ionescu
- Faculty of Medicine, “Ovidius” University, 900470 Constanta, Romania (S.I.C.)
| | - Viviana Cuzic
- Pediatrics Department, Faculty of Medicine, “Ovidius” University, 900470 Constanta, Romania (A.L.B.)
- Pediatrics Department, County Clinical Emergency Hospital of Constanta, 900591 Constanta, Romania
| | - Simona Claudia Cambrea
- Infectious Diseases Department, Faculty of Medicine, “Ovidius” University, 900470 Constanta, Romania
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12
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Javed MU, Hayat MT, Mukhtar H, Imre K. CRISPR-Cas9 System: A Prospective Pathway toward Combatting Antibiotic Resistance. Antibiotics (Basel) 2023; 12:1075. [PMID: 37370394 DOI: 10.3390/antibiotics12061075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/05/2023] [Accepted: 05/17/2023] [Indexed: 06/29/2023] Open
Abstract
Antibiotic resistance is rising to dangerously high levels throughout the world. To cope with this problem, scientists are working on CRISPR-based research so that antibiotic-resistant bacteria can be killed and attacked almost as quickly as antibiotic-sensitive bacteria. Nuclease activity is found in Cas9, which can be programmed with a specific target sequence. This mechanism will only attack pathogens in the microbiota while preserving commensal bacteria. This article portrays the delivery methods used in the CRISPR-Cas system, which are both viral and non-viral, along with its implications and challenges, such as microbial dysbiosis, off-target effects, and failure to counteract intracellular infections. CRISPR-based systems have a lot of applications, such as correcting mutations, developing diagnostics for infectious diseases, improving crops productions, improving breeding techniques, etc. In the future, CRISPR-based systems will revolutionize the world by curing diseases, improving agriculture, and repairing genetic disorders. Though all the drawbacks of the technology, CRISPR carries great potential; thus, the modification and consideration of some aspects could result in a mind-blowing technique to attain all the applications listed and present a game-changing potential.
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Affiliation(s)
| | | | - Hamid Mukhtar
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Kalman Imre
- Department of Animal Production and Veterinary Public Health, Faculty of Veterinary Medicine, University of Life Sciences "King Mihai I" from Timişoara, 300645 Timișoara, Romania
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13
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Singh P, Elhaj DAI, Ibrahim I, Abdullahi H, Al Khodor S. Maternal microbiota and gestational diabetes: impact on infant health. J Transl Med 2023; 21:364. [PMID: 37280680 PMCID: PMC10246335 DOI: 10.1186/s12967-023-04230-3] [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: 02/05/2023] [Accepted: 05/26/2023] [Indexed: 06/08/2023] Open
Abstract
Gestational diabetes mellitus (GDM) is a common complication of pregnancy that has been associated with an increased risk of obesity and diabetes in the offspring. Pregnancy is accompanied by tightly regulated changes in the endocrine, metabolic, immune, and microbial systems, and deviations from these changes can alter the mother's metabolism resulting in adverse pregnancy outcomes and a negative impact on the health of her infant. Maternal microbiomes are significant drivers of mother and child health outcomes, and many microbial metabolites are likely to influence the host health. This review discusses the current understanding of how the microbiota and microbial metabolites may contribute to the development of GDM and how GDM-associated changes in the maternal microbiome can affect infant's health. We also describe microbiota-based interventions that aim to improve metabolic health and outline future directions for precision medicine research in this emerging field.
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Affiliation(s)
- Parul Singh
- College of Health & Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
- Research Department, Sidra Medicine, Doha, Qatar
| | | | - Ibrahim Ibrahim
- Women's Department, Sidra Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Hala Abdullahi
- Women's Department, Sidra Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Souhaila Al Khodor
- College of Health & Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar.
- Research Department, Sidra Medicine, Doha, Qatar.
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14
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Pal R, Athamneh AI, Deshpande R, Ramirez JAR, Adu KT, Muthuirulan P, Pawar S, Biazzo M, Apidianakis Y, Sundekilde UK, de la Fuente-Nunez C, Martens MG, Tegos GP, Seleem MN. Probiotics: insights and new opportunities for Clostridioides difficile intervention. Crit Rev Microbiol 2023; 49:414-434. [PMID: 35574602 PMCID: PMC9743071 DOI: 10.1080/1040841x.2022.2072705] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/17/2022] [Accepted: 04/28/2022] [Indexed: 02/08/2023]
Abstract
Clostridioides difficile infection (CDI) is a life-threatening disease caused by the Gram-positive, opportunistic intestinal pathogen C. difficile. Despite the availability of antimicrobial drugs to treat CDI, such as vancomycin, metronidazole, and fidaxomicin, recurrence of infection remains a significant clinical challenge. The use of live commensal microorganisms, or probiotics, is one of the most investigated non-antibiotic therapeutic options to balance gastrointestinal (GI) microbiota and subsequently tackle dysbiosis. In this review, we will discuss major commensal probiotic strains that have the potential to prevent and/or treat CDI and its recurrence, reassess the efficacy of probiotics supplementation as a CDI intervention, delve into lessons learned from probiotic modulation of the immune system, explore avenues like genome-scale metabolic network reconstructions, genome sequencing, and multi-omics to identify novel strains and understand their functionality, and discuss the current regulatory framework, challenges, and future directions.
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Affiliation(s)
- Rusha Pal
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Ahmad I.M. Athamneh
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
| | | | - Jose A. R Ramirez
- ProbioWorld Consulting Group, James Cook University, 4811, Queensland, Australia
| | - Kayode T. Adu
- ProbioWorld Consulting Group, James Cook University, 4811, Queensland, Australia
- Cann Group, Walter and Eliza Hall Institute, La Trobe University, Victoria 3083, Australia
| | | | - Shrikant Pawar
- The Anlyan Center Yale Center for Genomic Analysis, Yale School of Medicine, New Haven CT USA
| | - Manuele Biazzo
- The Bioarte Ltd Laboratories at Life Science Park, San Gwann, Malta
| | | | | | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mark G. Martens
- Reading Hospital, Tower Health, West Reading, PA 19611, USA
- Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - George P. Tegos
- Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - Mohamed N. Seleem
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
- Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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15
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Guimarães VHD, Marinho BM, Motta-Santos D, Mendes GDRL, Santos SHS. Nutritional implications in the mechanistic link between the intestinal microbiome, renin-angiotensin system, and the development of obesity and metabolic syndrome. J Nutr Biochem 2023; 113:109252. [PMID: 36509338 DOI: 10.1016/j.jnutbio.2022.109252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/12/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
Obesity and metabolic disorders represent a significant global health problem and the gut microbiota plays an important role in modulating systemic homeostasis. Recent evidence shows that microbiota and its signaling pathways may affect the whole metabolism and the Renin-Angiotensin System (RAS), which in turn seems to modify microbiota. The present review aimed to investigate nutritional implications in the mechanistic link between the intestinal microbiome, renin-angiotensin system, and the development of obesity and metabolic syndrome components. A description of metabolic changes was obtained based on relevant scientific literature. The molecular and physiological mechanisms that impact the human microbiome were addressed, including the gut microbiota associated with obesity, diabetes, and hepatic steatosis. The RAS interaction signaling and modulation were analyzed. Strategies including the use of prebiotics, symbiotics, probiotics, and biotechnology may affect the gut microbiota and its impact on human health.
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Affiliation(s)
- Victor Hugo Dantas Guimarães
- Laboratory of Health Science, Postgraduate Program in Health Science, Universidade Estadual de Montes Claros (Unimontes), Montes Claros, Minas Gerais, Brazil
| | - Barbhara Mota Marinho
- Laboratory of Health Science, Postgraduate Program in Health Science, Universidade Estadual de Montes Claros (Unimontes), Montes Claros, Minas Gerais, Brazil
| | - Daisy Motta-Santos
- School of Physical Education, Physiotherapy, and Occupational Therapy - EEFFTO, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Gabriela da Rocha Lemos Mendes
- Food Engineering, Institute of Agricultural Sciences (ICA), Universidade Federal de Minas Gerais (UFMG), Montes Claros, Minas Gerais, Brazil
| | - Sérgio Henrique Sousa Santos
- Laboratory of Health Science, Postgraduate Program in Health Science, Universidade Estadual de Montes Claros (Unimontes), Montes Claros, Minas Gerais, Brazil; Food Engineering, Institute of Agricultural Sciences (ICA), Universidade Federal de Minas Gerais (UFMG), Montes Claros, Minas Gerais, Brazil.
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16
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Maloshenok LG, Abushinova GA, Ryazanova AY, Bruskin SA, Zherdeva VV. Visualizing the Nucleome Using the CRISPR–Cas9 System: From in vitro to in vivo. BIOCHEMISTRY (MOSCOW) 2023; 88:S123-S149. [PMID: 37069118 PMCID: PMC9940691 DOI: 10.1134/s0006297923140080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
One of the latest methods in modern molecular biology is labeling genomic loci in living cells using fluorescently labeled Cas protein. The NIH Foundation has made the mapping of the 4D nucleome (the three-dimensional nucleome on a timescale) a priority in the studies aimed to improve our understanding of chromatin organization. Fluorescent methods based on CRISPR-Cas are a significant step forward in visualization of genomic loci in living cells. This approach can be used for studying epigenetics, cell cycle, cellular response to external stimuli, rearrangements during malignant cell transformation, such as chromosomal translocations or damage, as well as for genome editing. In this review, we focused on the application of CRISPR-Cas fluorescence technologies as components of multimodal imaging methods for in vivo mapping of chromosomal loci, in particular, attribution of fluorescence signal to morphological and anatomical structures in a living organism. The review discusses the approaches to the highly sensitive, high-precision labeling of CRISPR-Cas components, delivery of genetically engineered constructs into cells and tissues, and promising methods for molecular imaging.
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Affiliation(s)
- Liliya G Maloshenok
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Gerel A Abushinova
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Alexandra Yu Ryazanova
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Sergey A Bruskin
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Victoria V Zherdeva
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
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17
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Elokil AA, Chen W, Mahrose K, Elattrouny MM, Abouelezz KFM, Ahmad HI, Liu HZ, Elolimy AA, Mandouh MI, Abdelatty AM, Li S. Early life microbiota transplantation from highly feed-efficient broiler improved weight gain by reshaping the gut microbiota in laying chicken. Front Microbiol 2022; 13:1022783. [PMID: 36466637 PMCID: PMC9715608 DOI: 10.3389/fmicb.2022.1022783] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/10/2022] [Indexed: 08/27/2023] Open
Abstract
Starting phase of laying chicken life is the building stone for rearing and production stages. Since, fecal microbial transplantation (FMT) regulates the gut microbial diversity and affects the productive performance of the bird. The aim of this study is to evaluate the effect of FMT from feed-efficient broiler chicken could program the diversity of gut microbiota and growth of recipient native slow growing egg-laying chicks. For this, a total of 150 (one-day-old) Jing Hong chicks were randomly assigned into two groups, each group consisted of 5 replicates (n = 15 bird/ replicate). The control group (CON) and FMT recipient birds (FMT) fed on basal diet, the FMT group received an oral daily dose of FMT prepared from Cobb-500 chickens. The FMT performed from the 1d to 28d of age, through the experimental period, feed intake and body weight were recorded weekly. At the end of a 28-day trial, carcass traits were assessed and cecal samples were collected for microbiome assessment via 16S rRNA-based metagenomic analysis to characterize the diversity and functions of microbial communities. The data were statistically analyzed using R software. Body weight and body weight gain increased, and FCR decreased (p = 0.01) in FMT group. The relative abundance of Firmicutes and the Firmicutes/Bacteroidetes (F/B) ratio were increased due to FMT administration (p = 0.01). A higher relative abundance of Lactobacillus, Lactococcus, and Bifidobacterium were presented in the FMT group. Meanwhile, Enterococcus, Helicobacter, and Bacteroides were more abundant in the CON group (p < 0.01). Kyoto encyclopedia of genes and genomes (KEGG) pathways for microbial functions regarding amino acid metabolism, secondary metabolites biosynthesis, carbohydrate metabolism, energy metabolism, and enzyme families, cofactors, and vitamins were significantly annotated in the FMT group. Overall, FMT administration from the donor of highly feed-efficient broilers improved weight gain by reshaping a distinct gut microbiome, which may be related to the metabolism and health in the recipients laying chicks, providing new insight on the application of the FMT technique for early life programming of laying chickens.
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Affiliation(s)
- Abdelmotaleb A. Elokil
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Animal Production Department, Faculty of Agriculture, Moshtohor, Benha University, Mushthar, Egypt
| | - Wei Chen
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Key Laboratory of Poultry Genetics and Breeding, Ministry of Agriculture, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangzhou, China
| | - Khalid Mahrose
- Animal and Poultry Production Department, Faculty of Technology and Development, Zagazig University, Zagazig, Egypt
| | - Mahmoud M. Elattrouny
- Animal Production Department, Faculty of Agriculture, Moshtohor, Benha University, Mushthar, Egypt
| | - Khaled F. M. Abouelezz
- Department of Poultry Production, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Hafiz Ishfaq Ahmad
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Hua-Zhen Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ahmed A. Elolimy
- Department of Animal Production, National Research Centre, Giza, Egypt
| | - Mahmoud I. Mandouh
- Department of Nutrition and Clinical Nutrition, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Alzahraa M. Abdelatty
- Department of Nutrition and Clinical Nutrition, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Shijun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
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18
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Bikard D. How has microbiology changed 200 years after Pasteur's birth? C R Biol 2022; 345:21-33. [PMID: 36852594 DOI: 10.5802/crbiol.85] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 11/11/2022]
Abstract
The last two centuries have seen major scientific and technological advances that have turned the field of microbiology upside down. If Louis Pasteur came out of his vault to celebrate his two hundredth birthday with us, would he recognize the field of study of which he was one of the founders? Are the objectives of the discipline still the same? What is the influence of new technologies on our scientific approach? What are the new horizons and future challenges?
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19
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Tiruvayipati S, Hameed DS, Ahmed N. Play the plug: How bacteria modify recognition by host receptors? Front Microbiol 2022; 13:960326. [PMID: 36312954 PMCID: PMC9615552 DOI: 10.3389/fmicb.2022.960326] [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: 06/02/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
The diverse microbial community that colonizes the gastrointestinal tract has remarkable effects on the host immune system and physiology resulting in homeostasis or disease. In both scenarios, the gut microbiota interacts with their host through ligand-receptor binding whereby the downstream signaling processes determine the outcome of the interaction as disease or the counteractive immune responses of the host. Despite several studies on microbe-host interactions and the mechanisms by which this intricate process happens, a comprehensive and updated inventory of known ligand-receptor interactions and their roles in disease is paramount. The ligands which originate as a result of microbial responses to the host environment contribute to either symbiotic or parasitic relationships. On the other hand, the host receptors counteract the ligand actions by mounting a neutral or an innate response. The varying degrees of polymorphic changes in the host receptors contribute to specificity of interaction with the microbial ligands. Additionally, pathogenic microbes manipulate host receptors with endogenous enzymes belonging to the effector protein family. This review focuses on the diversity and similarity in the gut microbiome-host interactions both in health and disease conditions. It thus establishes an overview that can help identify potential therapeutic targets in response to critically soaring antimicrobial resistance as juxtaposed to tardy antibiotic development research.
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Affiliation(s)
- Suma Tiruvayipati
- Infectious Diseases Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Dharjath S. Hameed
- Department of Chemical Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Niyaz Ahmed
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India
- *Correspondence: Niyaz Ahmed, ,
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20
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Ahmed E, Hens K. Microbiome in Precision Psychiatry: An Overview of the Ethical Challenges Regarding Microbiome Big Data and Microbiome-Based Interventions. AJOB Neurosci 2022; 13:270-286. [PMID: 34379050 DOI: 10.1080/21507740.2021.1958096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
There has been a spurt in both fundamental and translational research that examines the underlying mechanisms of the human microbiome in psychiatric disorders. The personalized and dynamic features of the human microbiome suggest the potential of its manipulation for precision psychiatry in ways to improve mental health and avoid disease. However, findings in the field of microbiome also raise philosophical and ethical questions. From a philosophical point of view, they may yet be another attempt at providing a biological cause for phenomena that ultimately cannot be so easily localized. From an ethical point of view, it is relevant that the human gut microbiome comprises data on the individual's lifestyle, disease history, previous medications, and mental health. Massive datasets of microbiome sequences are collected to facilitate comparative studies to identify specific links between the microbiome and mental health. Although this emerging research domain may show promise for psychiatric patients, it is surrounded by ethical challenges regarding patient privacy, health risks, effects on personal identity, and concerns about responsibility. This narrative overview displays the roles and advances of microbiome research in psychiatry and discusses the philosophical and ethical implications of microbiome big data and microbiome-based interventions for psychiatric patients. We also investigate whether these issues are really "new," or "old wine in new bottles."
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Affiliation(s)
- Eman Ahmed
- University of Antwerp.,Suez Canal University
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21
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Boix-Amorós A, Monaco H, Sambataro E, Clemente JC. Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease. Gut Microbes 2022; 14:2107866. [PMID: 36104776 PMCID: PMC9481095 DOI: 10.1080/19490976.2022.2107866] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We present an overview of recent experimental and computational advances in technology used to characterize the microbiome, with a focus on how these developments improve our understanding of inflammatory bowel disease (IBD). Specifically, we present studies that make use of flow cytometry and metabolomics assays to provide a functional characterization of microbial communities. We also describe computational methods for strain-level resolution, temporal series, mycobiome and virome data, co-occurrence networks, and compositional data analysis. In addition, we review novel techniques to therapeutically manipulate the microbiome in IBD. We discuss the benefits and drawbacks of these technologies to increase awareness of specific biases, and to facilitate a more rigorous interpretation of results and their potential clinical application. Finally, we present future lines of research to better characterize the relation between microbial communities and IBD pathogenesis and progression.
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Affiliation(s)
- Alba Boix-Amorós
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA
| | - Hilary Monaco
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA
| | - Elisa Sambataro
- Department of Biological Sciences, CUNY Hunter College, New York, NY, USA
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA,CONTACT Jose C. Clemente Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY10029USA
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22
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Torres MDT, de la Fuente-Nunez C. Molecular tools for probing the microbiome. Curr Opin Struct Biol 2022; 76:102415. [PMID: 35985169 DOI: 10.1016/j.sbi.2022.102415] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 11/19/2022]
Abstract
The microbiome plays essential roles in health and disease. Our understanding of the imbalances that can arise in the microbiome and their consequences is held back by a lack of technologies that selectively knock out members of these microbial communities. Antibiotics and fecal transplants, the existing methods for manipulating the microbiota of the gastrointestinal tract, are not sufficiently pinpointed to reveal how particular microbial genes, strains, or species affect human health. A toolset for the precise manipulation of the microbiome could significantly advance disease diagnosis and treatment. Here, we provide an overview of current and future strategies for the development of molecular tools that can be used to probe the microbiome without producing off-target effects.
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Affiliation(s)
- Marcelo Der Torossian Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA. https://twitter.com/mdt_torres
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA.
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23
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Jurburg SD, Eisenhauer N, Buscot F, Chatzinotas A, Chaudhari NM, Heintz-Buschart A, Kallies R, Küsel K, Litchman E, Macdonald CA, Müller S, Reuben RC, da Rocha UN, Panagiotou G, Rillig MC, Singh BK. Potential of microbiome-based solutions for agrifood systems. NATURE FOOD 2022; 3:557-560. [PMID: 37118595 DOI: 10.1038/s43016-022-00576-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Affiliation(s)
- Stephanie D Jurburg
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
- Institute of Biology, Leipzig University, Leipzig, Germany.
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle, Germany
| | - Antonis Chatzinotas
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Narendrakumar M Chaudhari
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Anna Heintz-Buschart
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle, Germany
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Rene Kallies
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Kirsten Küsel
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Elena Litchman
- Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USA
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
| | - Catriona A Macdonald
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Susann Müller
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Rine C Reuben
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Gianni Panagiotou
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
- The State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Kowloon, Hong Kong SAR, China
- Department of Medicine, The University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Matthias C Rillig
- Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia.
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia.
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Al KF, Chmiel JA, Stuivenberg GA, Reid G, Burton JP. Long-Duration Space Travel Support Must Consider Wider Influences to Conserve Microbiota Composition and Function. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081163. [PMID: 36013342 PMCID: PMC9409767 DOI: 10.3390/life12081163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 12/03/2022]
Abstract
The microbiota is important for immune modulation, nutrient acquisition, vitamin production, and other aspects for long-term human health. Isolated model organisms can lose microbial diversity over time and humans are likely the same. Decreasing microbial diversity and the subsequent loss of function may accelerate disease progression on Earth, and to an even greater degree in space. For this reason, maintaining a healthy microbiome during spaceflight has recently garnered consideration. Diet, lifestyle, and consumption of beneficial microbes can shape the microbiota, but the replenishment we attain from environmental exposure to microbes is important too. Probiotics, prebiotics, fermented foods, fecal microbiota transplantation (FMT), and other methods of microbiota modulation currently available may be of benefit for shorter trips, but may not be viable options to overcome the unique challenges faced in long-term space travel. Novel fermented food products with particular impact on gut health, immune modulation, and other space-targeted health outcomes are worthy of exploration. Further consideration of potential microbial replenishment to humans, including from environmental sources to maintain a healthy microbiome, may also be required.
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Affiliation(s)
- Kait F. Al
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 3K7, Canada; (K.F.A.); (J.A.C.); (G.A.S.); (G.R.)
| | - John A. Chmiel
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 3K7, Canada; (K.F.A.); (J.A.C.); (G.A.S.); (G.R.)
| | - Gerrit A. Stuivenberg
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 3K7, Canada; (K.F.A.); (J.A.C.); (G.A.S.); (G.R.)
| | - Gregor Reid
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 3K7, Canada; (K.F.A.); (J.A.C.); (G.A.S.); (G.R.)
- Department of Surgery, University of Western Ontario, London, ON N6A 4V2, Canada
- Lawson Health Research Institute, London, ON N6A 4V2, Canada
| | - Jeremy P. Burton
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 3K7, Canada; (K.F.A.); (J.A.C.); (G.A.S.); (G.R.)
- Department of Surgery, University of Western Ontario, London, ON N6A 4V2, Canada
- Lawson Health Research Institute, London, ON N6A 4V2, Canada
- Correspondence:
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25
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Segura Munoz RR, Mantz S, Martínez I, Li F, Schmaltz RJ, Pudlo NA, Urs K, Martens EC, Walter J, Ramer-Tait AE. Experimental evaluation of ecological principles to understand and modulate the outcome of bacterial strain competition in gut microbiomes. THE ISME JOURNAL 2022; 16:1594-1604. [PMID: 35210551 PMCID: PMC9122919 DOI: 10.1038/s41396-022-01208-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 12/03/2021] [Accepted: 02/01/2022] [Indexed: 01/07/2023]
Abstract
It is unclear if coexistence theory can be applied to gut microbiomes to understand their characteristics and modulate their composition. Through experiments in gnotobiotic mice with complex microbiomes, we demonstrated that strains of Akkermansia muciniphila and Bacteroides vulgatus could only be established if microbiomes were devoid of these species. Strains of A. muciniphila showed strict competitive exclusion, while B. vulgatus strains coexisted but populations were still influenced by competitive interactions. These differences in competitive behavior were reflective of genomic variation within the two species, indicating considerable niche overlap for A. muciniphila strains and a broader niche space for B. vulgatus strains. Priority effects were detected for both species as strains’ competitive fitness increased when colonizing first, which resulted in stable persistence of the A. muciniphila strain colonizing first and competitive exclusion of the strain arriving second. Based on these observations, we devised a subtractive strategy for A. muciniphila using antibiotics and showed that a strain from an assembled community can be stably replaced by another strain. By demonstrating that competitive outcomes in gut ecosystems depend on niche differences and are historically contingent, our study provides novel information to explain the ecological characteristics of gut microbiomes and a basis for their modulation.
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Affiliation(s)
- Rafael R Segura Munoz
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.,Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Sara Mantz
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Ines Martínez
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Fuyong Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada.,Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Robert J Schmaltz
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Karthik Urs
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada. .,Department of Biological Sciences, University of Alberta, Edmonton, Canada. .,APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork, Cork, Ireland.
| | - Amanda E Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA. .,Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.
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Abstract
Fermented foods (FFs) hold global attention because of their huge advantages. Their health benefits, palatability, preserved, tasteful, and aromatic properties impart potential importance in the comprehensive evaluation of FFs. The bioactive components, such as minerals, vitamins, fatty acids, amino acids, and other phytochemicals synthesized during fermentation, provide consumers with several health benefits. Fermentation of food is an ancient process that has met with many remarkable changes owing to the development of scientific technologies over the years. Initially, fermentation relied on back-slapping. Nowadays, starter cultures strains are specifically chosen for the type of fermentation process. Modern biotechnological methods are being implemented in the fermentation process to achieve the desired product in high quality. Respiratory and gastrointestinal tract infections are the most severe health issues affecting human beings of all age groups, especially children and older adults, during this COVID-19 pandemic period. Studies suggest that the consumption of probiotic Lactobacillus strains containing fermented foods protects the subjects from common infectious diseases (CIDs, which is classified as upper respiratory tract infections, lower respiratory tract infections and gastrointestinal infections) by improving the host’s immune system. Further studies are obligatory to develop probiotic-based functional FFs that are effective against CIDs. Presently, we are urged to find alternative, safe, and cost-effective prevention measures against CIDs. The current manuscript briefs the production of FFs, functional properties of FFs, and their beneficial effects against respiratory tract infections. It summarizes the outcomes of clinical trials using human subjects on the effects of supplementation of FFs.
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27
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Wachsmuth HR, Weninger SN, Duca FA. Role of the gut-brain axis in energy and glucose metabolism. Exp Mol Med 2022; 54:377-392. [PMID: 35474341 PMCID: PMC9076644 DOI: 10.1038/s12276-021-00677-w] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/01/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
The gastrointestinal tract plays a role in the development and treatment of metabolic diseases. During a meal, the gut provides crucial information to the brain regarding incoming nutrients to allow proper maintenance of energy and glucose homeostasis. This gut-brain communication is regulated by various peptides or hormones that are secreted from the gut in response to nutrients; these signaling molecules can enter the circulation and act directly on the brain, or they can act indirectly via paracrine action on local vagal and spinal afferent neurons that innervate the gut. In addition, the enteric nervous system can act as a relay from the gut to the brain. The current review will outline the different gut-brain signaling mechanisms that contribute to metabolic homeostasis, highlighting the recent advances in understanding these complex hormonal and neural pathways. Furthermore, the impact of the gut microbiota on various components of the gut-brain axis that regulates energy and glucose homeostasis will be discussed. A better understanding of the gut-brain axis and its complex relationship with the gut microbiome is crucial for the development of successful pharmacological therapies to combat obesity and diabetes.
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Affiliation(s)
| | | | - Frank A Duca
- School of Animal and Comparative Biomedical Sciences, College of Agricultural and Life Sciences, University of Arizona, Tucson, AZ, USA. .,BIO5, University of Arizona, Tucson, AZ, USA.
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28
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Cass SH, Ajami NJ, White MG. The Microbiome: the Link to Colorectal Cancer and Research Opportunities. Curr Treat Options Oncol 2022; 23:631-644. [PMID: 35254596 DOI: 10.1007/s11864-022-00960-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2022] [Indexed: 12/24/2022]
Abstract
OPINION STATEMENT In recent years, we have seen an increase in the study and interest of the role of the microbiome in the development of malignancies, their progression, and evasion of therapies. This has been particularly fruitful in the case of colorectal cancer; multiple investigators have described correlative observations as well as hypotheses strengthened in preclinical studies that have begun to elucidate the critical role the gut and tumoral microbiome plays in carcinogenesis. Furthermore, these landmark studies lay the groundwork in describing the microbiome's role in carcinogenesis and provide a rich field of future study. Here, we review contemporary understandings of these observations and proposed mechanisms behind them.
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Affiliation(s)
- Samuel H Cass
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Unit 1484 PO Box 301402, Houston, TX, 77230, USA
| | - Nadim J Ajami
- Program for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael G White
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Unit 1484 PO Box 301402, Houston, TX, 77230, USA. .,Department of Colon and Rectal Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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29
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Kahraman Ilıkkan Ö. Analysis of Probiotic Bacteria Genomes: Comparison of CRISPR/Cas Systems and Spacer Acquisition Diversity. Indian J Microbiol 2022; 62:40-46. [PMID: 35068602 PMCID: PMC8758818 DOI: 10.1007/s12088-021-00971-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 08/04/2021] [Indexed: 11/25/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes constitute an adaptive (acquired) defense system of bacteria and archaea. Here 72 probiotic bacteria genomes were investigated in terms of the presence of CRISPR/Cas systems and phage/plasmid invaders through spacer analysis. 49 CRISPR/Cas systems were detected within probiotic strains, namely,17 type II-A, 10 type I-C, 8 type I-E, 5 Type I-U (I-G), 4 type III-A, 2 type I-B, 1 type I-A, 1 type IV-B, and 1 type II-C. The predicted target of spacers was determined in 25 strains and consequently, three different spacer and target patterns were revealed. The diversity of CRISPR spacers provides insight and understanding to determine strain-specific invaders of probiotic bacteria as well as their relationships between strains. CRISPR systems were clarified in many studies for genomic characterization. However, recently, endogenous genome editing with CRISPR has provided an approach for various genome editing projects. Thus, in the future, producing strain-specific phage-resistant starter cultures or probiotics by endogenous genome editing methods according to phage/plasmid survey can be utilized for industrial and pharmaceutical applications. Therefore, this study intended a comprehensive investigation of CRISPR systems of probiotic bacteria. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12088-021-00971-1.
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Affiliation(s)
- Özge Kahraman Ilıkkan
- Kahramankazan Vocational School, Başkent University, Food Quality Control and Analysis Program, Ankara, Turkey
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30
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Paraphocaeicola brunensis gen. nov., sp. nov., Carrying Two Variants of nimB Resistance Gene from Bacteroides fragilis, and Caecibacteroides pullorum gen. nov., sp. nov., Two Novel Genera Isolated from Chicken Caeca. Microbiol Spectr 2022; 10:e0195421. [PMID: 35170999 PMCID: PMC8849064 DOI: 10.1128/spectrum.01954-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Three difficult-to-cultivate, strictly anaerobic strains, AN20T, AN421T, and AN502, were analyzed within a project studying possible probiotics for newly hatched chickens. Phylogenetic analyses showed that strains AN20T, AN421T, and AN502 formed two well-separated phylogenetic lineages in all phylogenetic and phylogenomic trees comprising members of the family Bacteroidaceae. Comparison to reference genomes of type species Bacteroides fragilis NCTC 9343T, Phocaeicola abscessus CCUG 55929T, and Capsularis zoogleoformans ATCC 33285T showed low relatedness based on the calculated genome-to-genome distance and orthologous average nucleotide identity. Analysis of fatty acid profiles showed iso-C15:0, anteiso-C15:0, C16:0, C18:1ω9c, and iso-C17:0 3OH as the major fatty acids for all three strains and additionally C16:0 3OH for AN421T and AN502. A specific combination of respiratory quinones different from related taxa was found in analyzed strains, MK-5 plus MK-11 in strain AN20T and MK-5 plus MK-10 in strains AN421T and AN502. Strains AN421T and AN502 harbor complete CRISPR loci with CRISPR array, type II-C, accompanied by a set of cas genes (cas9, cas1, and cas2) in close proximity. Interestingly, strain AN20T was found to harbor two copies of nimB gene with >95% similarity to nimB of B. fragilis, suggesting a horizontal gene transfer between these taxa. In summary, three isolates characterized in this study represent two novel species, which we proposed to be classified in two novel genera of the family Bacteroidaceae, for which the names Paraphocaeicola brunensis sp. nov. (AN20T = CCM 9041T = DSM 111154T) and Caecibacteroides pullorum sp. nov. (AN421T= CCM 9040T = DSM 111155T) are proposed. IMPORTANCE This study represents follow-up research on three difficult-to-cultivate anaerobic isolates originally isolated within a project focused on strains that are able to stably colonize newly hatched chickens, thus representing possible probiotics. This project is exceptional in that it successfully isolates several miscellaneous strains that required modified and richly supplemented anaerobic media, as information on many gut-colonizing bacteria is based predominantly on metagenomic studies. Superior colonization of newly hatched chickens by Bacteroides spp., Phocaeicola spp., or related taxa can be considered of importance for development of future probiotics. Although different experiments can also be performed with provisionally characterized isolates, precise taxonomical definition is necessary for subsequent broad communication. The aim of this study is therefore to thoroughly characterize these isolates that represent novel genera and precisely determine their taxonomic position among related taxa to facilitate further research and communication involving these strains.
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31
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Ramires LC, Santos GS, Ramires RP, da Fonseca LF, Jeyaraman M, Muthu S, Lana AV, Azzini G, Smith CS, Lana JF. The Association between Gut Microbiota and Osteoarthritis: Does the Disease Begin in the Gut? Int J Mol Sci 2022; 23:ijms23031494. [PMID: 35163417 PMCID: PMC8835947 DOI: 10.3390/ijms23031494] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/11/2022] [Accepted: 01/25/2022] [Indexed: 02/05/2023] Open
Abstract
Some say that all diseases begin in the gut. Interestingly, this concept is actually quite old, since it is attributed to the Ancient Greek physician Hippocrates, who proposed the hypothesis nearly 2500 years ago. The continuous breakthroughs in modern medicine have transformed our classic understanding of the gastrointestinal tract (GIT) and human health. Although the gut microbiota (GMB) has proven to be a core component of human health under standard metabolic conditions, there is now also a strong link connecting the composition and function of the GMB to the development of numerous diseases, especially the ones of musculoskeletal nature. The symbiotic microbes that reside in the gastrointestinal tract are very sensitive to biochemical stimuli and may respond in many different ways depending on the nature of these biological signals. Certain variables such as nutrition and physical modulation can either enhance or disrupt the equilibrium between the various species of gut microbes. In fact, fat-rich diets can cause dysbiosis, which decreases the number of protective bacteria and compromises the integrity of the epithelial barrier in the GIT. Overgrowth of pathogenic microbes then release higher quantities of toxic metabolites into the circulatory system, especially the pro-inflammatory cytokines detected in osteoarthritis (OA), thereby promoting inflammation and the initiation of many disease processes throughout the body. Although many studies link OA with GMB perturbations, further research is still needed.
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Affiliation(s)
- Luciano C. Ramires
- Department of Orthopaedics and Sports Medicine, Mãe de Deus Hospital, Porto Alegre 90110-270, RS, Brazil;
| | - Gabriel Silva Santos
- Department of Orthopaedics, The Bone and Cartilage Institute, Indaiatuba 13334-170, SP, Brazil; (G.A.); (J.F.L.)
- Correspondence: (G.S.S.); (L.F.d.F)
| | - Rafaela Pereira Ramires
- Department of Biology, Cellular, Molecular and Biomedical Science, Boise State University, 1910 W University Drive, Boise, ID 83725, USA;
| | - Lucas Furtado da Fonseca
- Department of Orthopaedics, The Federal University of São Paulo, São Paulo 04024-002, SP, Brazil
- Correspondence: (G.S.S.); (L.F.d.F)
| | - Madhan Jeyaraman
- Department of Orthopaedics, Faculty of Medicine, Sri Lalithambigai Medical College and Hospital, Dr MGR Educational and Research Institute, Chennai 600095, Tamil Nadu, India;
| | - Sathish Muthu
- Department of Orthopaedics, Government Medical College and Hospital, Dindigul 624304, Tamil Nadu, India;
| | - Anna Vitória Lana
- Department of Medicine, Max Planck University Center, Indaiatuba 13343-060, SP, Brazil;
| | - Gabriel Azzini
- Department of Orthopaedics, The Bone and Cartilage Institute, Indaiatuba 13334-170, SP, Brazil; (G.A.); (J.F.L.)
| | - Curtis Scott Smith
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 83703, USA;
| | - José Fábio Lana
- Department of Orthopaedics, The Bone and Cartilage Institute, Indaiatuba 13334-170, SP, Brazil; (G.A.); (J.F.L.)
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Clavel T, Horz H, Segata N, Vehreschild M. Next steps after 15 stimulating years of human gut microbiome research. Microb Biotechnol 2022; 15:164-175. [PMID: 34818454 PMCID: PMC8719818 DOI: 10.1111/1751-7915.13970] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 10/31/2021] [Indexed: 12/26/2022] Open
Abstract
Gut microbiome research has bloomed over the past 15 years. We have learnt a lot about the complex microbial communities that colonize our intestine. Promising avenues of research and microbiome-based applications are being implemented, with the goal of sustaining host health and applying personalized disease management strategies. Despite this exciting outlook, many fundamental questions about enteric microbial ecosystems remain to be answered. Organizational measures will also need to be taken to optimize the outcome of discoveries happening at an extremely rapid pace. This article highlights our own view of the field and perspectives for the next 15 years.
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Affiliation(s)
- Thomas Clavel
- Functional Microbiome Research GroupInstitute of Medical MicrobiologyRWTH University HospitalAachenGermany
| | - Hans‐Peter Horz
- Phage Biology Research GroupInstitute of Medical MicrobiologyRWTH University HospitalAachenGermany
| | | | - Maria Vehreschild
- Department of Internal Medicine, Infectious DiseasesUniversity Hospital FrankfurtGoethe University FrankfurtFrankfurt am MainGermany
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Ajilogba CF, Olanrewaju OS, Babalola OO. Improving Bambara Groundnut Production: Insight Into the Role of Omics and Beneficial Bacteria. FRONTIERS IN PLANT SCIENCE 2022; 13:836133. [PMID: 35310649 PMCID: PMC8929175 DOI: 10.3389/fpls.2022.836133] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/04/2022] [Indexed: 05/05/2023]
Abstract
With the rise in the world population, environmental hazards caused by chemical fertilizers, and a decrease in food supply due to global climate change, food security has become very pertinent. In addition, considerable parts of agriculture lands have been lost to urbanization. It has therefore been projected that at the present rate of population increase coupled with the other mentioned factors, available food will not be enough to feed the world. Hence, drastic approach is needed to improve agriculture output as well as human sustainability. Application of environmentally sustainable approach, such as the use of beneficial microbes, and improved breeding of underutilized legumes are one of the proposed sustainable ways of achieving food security. Microbiome-assisted breeding in underutilized legumes is an untapped area with great capabilities to improve food security. Furthermore, revolution in genomics adaptation to crop improvement has changed the approach from conventional breeding to more advanced genomic-assisted breeding on the host plant and its microbiome. The use of rhizobacteria is very important to improving crop yield, especially rhizobacteria from legumes like Bambara groundnut (BGN). BGN is an important legume in sub-Saharan Africa with high ability to tolerate drought and thrive well in marginalized soils. BGN and its interaction with various rhizobacteria in the soil could play a vital role in crop production and protection. This review focus on the importance of genomics application to BGN and its microbiome with the view of setting a potential blueprint for improved BGN breeding through integration of beneficial bacteria.
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Affiliation(s)
- Caroline Fadeke Ajilogba
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Science, North-West University, Mafikeng, South Africa
- Division of Agrometeorology, Agricultural Research Council, Natural Resources and Engineering, Pretoria, South Africa
| | - Oluwaseyi Samuel Olanrewaju
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Science, North-West University, Mafikeng, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Science, North-West University, Mafikeng, South Africa
- *Correspondence: Olubukola Oluranti Babalola,
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Innard N, Chong JPJ. The challenges of monitoring and manipulating anaerobic microbial communities. BIORESOURCE TECHNOLOGY 2022; 344:126326. [PMID: 34780902 DOI: 10.1016/j.biortech.2021.126326] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 11/03/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Mixed anaerobic microbial communities are a key component in valorization of waste biomass via anaerobic digestion. Similar microbial communities are important as soil and animal microbiomes and have played a critical role in shaping the planet as it is today. Understanding how individual species within communities interact with others and their environment is important for improving performance and potential applications of an inherently green technology. Here, the challenges associated with making measurements critical to assessing the status of anaerobic microbial communities are considered. How these measurements could be incorporated into control philosophies and augment the potential of anaerobic microbial communities to produce different and higher value products from waste materials are discussed. The benefits and pitfalls of current genetic and molecular approaches to measuring and manipulating anaerobic microbial communities and the challenges which should be addressed to realise the potential of this exciting technology are explored.
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Affiliation(s)
- Nathan Innard
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - James P J Chong
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK.
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Understanding the Role of the Gut Microbiome and Microbial Metabolites in Non-Alcoholic Fatty Liver Disease: Current Evidence and Perspectives. Biomolecules 2021; 12:biom12010056. [PMID: 35053205 PMCID: PMC8774162 DOI: 10.3390/biom12010056] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 12/11/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease worldwide. NAFLD begins as a relatively benign hepatic steatosis which can evolve to non-alcoholic steatohepatitis (NASH); the risk of cirrhosis and hepatocellular carcinoma (HCC) increases when fibrosis is present. NAFLD represents a complex process implicating numerous factors—genetic, metabolic, and dietary—intertwined in a multi-hit etiopathogenetic model. Recent data have highlighted the role of gut dysbiosis, which may render the bowel more permeable, leading to increased free fatty acid absorption, bacterial migration, and a parallel release of toxic bacterial products, lipopolysaccharide (LPS), and proinflammatory cytokines that initiate and sustain inflammation. Although gut dysbiosis is present in each disease stage, there is currently no single microbial signature to distinguish or predict which patients will evolve from NAFLD to NASH and HCC. Using 16S rRNA sequencing, the majority of patients with NAFLD/NASH exhibit increased numbers of Bacteroidetes and differences in the presence of Firmicutes, resulting in a decreased F/B ratio in most studies. They also present an increased proportion of species belonging to Clostridium, Anaerobacter, Streptococcus, Escherichia, and Lactobacillus, whereas Oscillibacter, Flavonifaractor, Odoribacter, and Alistipes spp. are less prominent. In comparison to healthy controls, patients with NASH show a higher abundance of Proteobacteria, Enterobacteriaceae, and Escherichia spp., while Faecalibacterium prausnitzii and Akkermansia muciniphila are diminished. Children with NAFLD/NASH have a decreased proportion of Oscillospira spp. accompanied by an elevated proportion of Dorea, Blautia, Prevotella copri, and Ruminococcus spp. Gut microbiota composition may vary between population groups and different stages of NAFLD, making any conclusive or causative claims about gut microbiota profiles in NAFLD patients challenging. Moreover, various metabolites may be involved in the pathogenesis of NAFLD, such as short-chain fatty acids, lipopolysaccharide, bile acids, choline and trimethylamine-N-oxide, and ammonia. In this review, we summarize the role of the gut microbiome and metabolites in NAFLD pathogenesis, and we discuss potential preventive and therapeutic interventions related to the gut microbiome, such as the administration of probiotics, prebiotics, synbiotics, antibiotics, and bacteriophages, as well as the contribution of bariatric surgery and fecal microbiota transplantation in the therapeutic armamentarium against NAFLD. Larger and longer-term prospective studies, including well-defined cohorts as well as a multi-omics approach, are required to better identify the associations between the gut microbiome, microbial metabolites, and NAFLD occurrence and progression.
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Meile S, Du J, Dunne M, Kilcher S, Loessner MJ. Engineering therapeutic phages for enhanced antibacterial efficacy. Curr Opin Virol 2021; 52:182-191. [PMID: 34952266 DOI: 10.1016/j.coviro.2021.12.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/22/2021] [Accepted: 12/04/2021] [Indexed: 12/18/2022]
Abstract
The alarming rise in antimicrobial resistance coupled with a lack of innovation in antibiotics has renewed interest in the development of alternative therapies to combat bacterial infections. Despite phage therapy demonstrating success in various individual cases, a comprehensive and unequivocal demonstration of the therapeutic potential of phages remains to be shown. The co-evolution of phages and their bacterial hosts resulted in several inherent limitations for the use of natural phages as therapeutics such as restricted host range, moderate antibacterial efficacy, and frequent emergence of phage-resistance. However, these constraints can be overcome by leveraging recent advances in synthetic biology and genetic engineering to provide phages with additional therapeutic capabilities, improved safety profiles, and adaptable host ranges. Here, we examine different ways phages can be engineered to deliver heterologous therapeutic payloads to enhance their antibacterial efficacy and discuss their versatile applicability to combat bacterial pathogens.
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Affiliation(s)
- Susanne Meile
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Jiemin Du
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Matthew Dunne
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Samuel Kilcher
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
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Donabedian P, Dawson E, Li Q, Chen J. Gut Microbes and Eye Disease. Ophthalmic Res 2021; 65:245-253. [PMID: 34915517 PMCID: PMC9198007 DOI: 10.1159/000519457] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 09/03/2021] [Indexed: 11/19/2022]
Abstract
Microbial symbionts in the gut are increasingly recognized as having important effects on health and disease, but have only recently begun to be linked to diseases of the eye. We review current research on the intestinal microbiota's relationship to ocular disease, focusing on autoimmune uveitis, diabetic retinopathy, age-related macular degeneration, and primary-open angle glaucoma. We discuss findings and limitations of this exciting new area of ophthalmology research and explore possible future disease-modifying treatments.
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Affiliation(s)
| | - Elizabeth Dawson
- College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Qiuhong Li
- Department of Ophthalmology, University of Florida, Gainesville, Florida, USA
| | - Jinghua Chen
- Department of Ophthalmology, University of Florida, Gainesville, Florida, USA
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Mannaa M, Han G, Seo YS, Park I. Evolution of Food Fermentation Processes and the Use of Multi-Omics in Deciphering the Roles of the Microbiota. Foods 2021; 10:2861. [PMID: 34829140 PMCID: PMC8618017 DOI: 10.3390/foods10112861] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/11/2021] [Accepted: 11/17/2021] [Indexed: 12/22/2022] Open
Abstract
Food fermentation has been practised since ancient times to improve sensory properties and food preservation. This review discusses the process of fermentation, which has undergone remarkable improvement over the years, from relying on natural microbes and spontaneous fermentation to back-slopping and the use of starter cultures. Modern biotechnological approaches, including genome editing using CRISPR/Cas9, have been investigated and hold promise for improving the fermentation process. The invention of next-generation sequencing techniques and the rise of meta-omics tools have advanced our knowledge on the characterisation of microbiomes involved in food fermentation and their functional roles. The contribution and potential advantages of meta-omics technologies in understanding the process of fermentation and examples of recent studies utilising multi-omics approaches for studying food-fermentation microbiomes are reviewed. Recent technological advances in studying food fermentation have provided insights into the ancient wisdom in the practice of food fermentation, such as the choice of substrates and fermentation conditions leading to desirable properties. This review aims to stimulate research on the process of fermentation and the associated microbiomes to produce fermented food efficiently and sustainably. Prospects and the usefulness of recent advances in molecular tools and integrated multi-omics approaches are highlighted.
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Affiliation(s)
- Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (M.M.); (G.H.)
- Department of Plant Pathology, Cairo University, Giza 12613, Egypt
| | - Gil Han
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (M.M.); (G.H.)
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (M.M.); (G.H.)
| | - Inmyoung Park
- School of Culinary Arts, Youngsan University, Busan 48015, Korea
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Prospect and Challenges for Sustainable Management of Climate Change-Associated Stresses to Soil and Plant Health by Beneficial Rhizobacteria. STRESSES 2021. [DOI: 10.3390/stresses1040015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Climate change imposes biotic and abiotic stresses on soil and plant health all across the planet. Beneficial rhizobacterial genera, such as Bacillus, Pseudomonas, Paraburkholderia, Rhizobium, Serratia, and others, are gaining popularity due to their ability to provide simultaneous nutrition and protection of plants in adverse climatic conditions. Plant growth-promoting rhizobacteria are known to boost soil and plant health through a variety of direct and indirect mechanisms. However, various issues limit the wider commercialization of bacterial biostimulants, such as variable performance in different environmental conditions, poor shelf-life, application challenges, and our poor understanding on complex mechanisms of their interactions with plants and environment. This study focused on detecting the most recent findings on the improvement of plant and soil health under a stressful environment by the application of beneficial rhizobacteria. For a critical and systematic review story, we conducted a non-exhaustive but rigorous literature survey to assemble the most relevant literature (sorting of a total of 236 out of 300 articles produced from the search). In addition, a critical discussion deciphering the major challenges for the commercialization of these bioagents as biofertilizer, biostimulants, and biopesticides was undertaken to unlock the prospective research avenues and wider application of these natural resources. The advancement of biotechnological tools may help to enhance the sustainable use of bacterial biostimulants in agriculture. The perspective of biostimulants is also systematically evaluated for a better understanding of the molecular crosstalk between plants and beneficial bacteria in the changing climate towards sustainable soil and plant health.
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Ossowicki A, Raaijmakers JM, Garbeva P. Disentangling soil microbiome functions by perturbation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:582-590. [PMID: 34231344 PMCID: PMC8518845 DOI: 10.1111/1758-2229.12989] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 05/24/2023]
Abstract
Soil biota contribute to diverse soil ecosystem services such as greenhouse gas mitigation, carbon sequestration, pollutant degradation, plant disease suppression and nutrient acquisition for plant growth. Here, we provide detailed insight into different perturbation approaches to disentangle soil microbiome functions and to reveal the underlying mechanisms. By applying perturbation, one can generate compositional and functional shifts of complex microbial communities in a controlled way. Perturbations can reduce microbial diversity, diminish the abundance of specific microbial taxa and thereby disturb the interactions within the microbial consortia and with their eukaryotic hosts. Four different microbiome perturbation approaches, namely selective heat, specific biocides, dilution-to-extinction and genome editing are the focus of this mini-review. We also discuss the potential of perturbation approaches to reveal the tipping point at which specific soil functions are lost and to link this change to key microbial taxa involved in specific microbiome-associated phenotypes.
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Affiliation(s)
- Adam Ossowicki
- Department of Microbial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Droevendaalsesteeg 10WageningenPB6708Netherlands
- Soil and Water Research Infrastructure (SoWa)Biology Centre CASČeské BudějoviceCzech Republic
| | - Jos M. Raaijmakers
- Department of Microbial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Droevendaalsesteeg 10WageningenPB6708Netherlands
- Institute of Biology, Leiden UniversityLeidenNetherlands
| | - Paolina Garbeva
- Department of Microbial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Droevendaalsesteeg 10WageningenPB6708Netherlands
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Lipid and Energy Metabolism of the Gut Microbiota Is Associated with the Response to Probiotic Bifidobacterium breve Strain for Anxiety and Depressive Symptoms in Schizophrenia. J Pers Med 2021; 11:jpm11100987. [PMID: 34683128 PMCID: PMC8539730 DOI: 10.3390/jpm11100987] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/26/2021] [Accepted: 09/29/2021] [Indexed: 12/13/2022] Open
Abstract
A recent meta-analysis found that probiotics have moderate-to-large beneficial effects on depressive symptoms in patients with psychiatric disorders. However, it remains unclear how the baseline gut microbiota before probiotic administration influences the host’s response to probiotics. Therefore, we aimed to determine whether the predicted functional profile of the gut microbiota influences the effectiveness of probiotic treatment in patients with schizophrenia. A total of 29 patients with schizophrenia consumed Bifidobacterium breve A-1 (synonym B. breve MCC1274) for 4 weeks. We considered patients who showed a 25% or more reduction in the Hospital Anxiety and Depression Scale total score at 4 weeks from baseline to be “responders” and those who did not to be “non-responders”. We predicted the gut microbial functional genes based on 16S rRNA gene sequences and applied the linear discriminant analysis effect size method to determine the gut microbial functional genes most likely to explain the differences between responders and non-responders at baseline. The results showed that lipid and energy metabolism was elevated at baseline in responders (n = 12) compared to non-responders (n = 17). These findings highlight the importance of assessing the gut microbial functional genes at baseline before probiotic therapy initiation in patients with psychiatric disorders.
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Teulière J, Bernard C, Bapteste E. Interspecific interactions that affect ageing: Age-distorters manipulate host ageing to their own evolutionary benefits. Ageing Res Rev 2021; 70:101375. [PMID: 34082078 DOI: 10.1016/j.arr.2021.101375] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/22/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023]
Abstract
Genetic causes for ageing are traditionally investigated within a species. Yet, the lifecycles of many organisms intersect. Additional evolutionary and genetic causes of ageing, external to a focal species/organism, may thus be overlooked. Here, we introduce the phrase and concept of age-distorters and its evidence. Age-distorters carry ageing interfering genes, used to manipulate the biological age of other entities upon which the reproduction of age-distorters relies, e.g. age-distorters bias the reproduction/maintenance trade-offs of cells/organisms for their own evolutionary interests. Candidate age-distorters include viruses, parasites and symbionts, operating through specific, genetically encoded interferences resulting from co-evolution and arms race between manipulative non-kins and manipulable species. This interference results in organismal ageing when age-distorters prompt manipulated organisms to favor their reproduction at the expense of their maintenance, turning these hosts into expanded disposable soma. By relying on reproduction/maintenance trade-offs affecting disposable entities, which are left ageing to the reproductive benefit of other physically connected lineages with conflicting evolutionary interests, the concept of age-distorters expands the logic of the Disposable Soma theory beyond species with fixed germen/soma distinctions. Moreover, acknowledging age-distorters as external sources of mutation accumulation and antagonistic pleiotropic genes expands the scope of the mutation accumulation and of the antagonistic pleiotropy theories.
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Affiliation(s)
- Jérôme Teulière
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Charles Bernard
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France.
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43
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Dahl GE, Connor EE. Grand Challenges to Livestock Physiology and Management. FRONTIERS IN ANIMAL SCIENCE 2021. [DOI: 10.3389/fanim.2021.689345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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de Steenhuijsen Piters WAA, Binkowska J, Bogaert D. Early Life Microbiota and Respiratory Tract Infections. Cell Host Microbe 2021; 28:223-232. [PMID: 32791114 DOI: 10.1016/j.chom.2020.07.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/02/2020] [Accepted: 07/07/2020] [Indexed: 12/18/2022]
Abstract
Over the last decade, it has become clear that respiratory and intestinal tract microbiota are related to pathogenesis of respiratory tract infections (RTIs). Host and environmental factors can drive respiratory microbiota maturation in early life, which in turn is related to consecutive susceptibility to RTIs. Moreover, during RTIs, including viral bronchiolitis, the local microbiome appears to play an immunomodulatory role through complex interactions, though causality has not yet been fully demonstrated. The microbiota is subsequently associated with recovery after RTIs and can be related to persistent or long-term sequelae. In this Review, we explore the epidemiological evidence supporting these associations and link to mechanistic insights. The long-term consequences of childhood RTIs and the comprehensive role of the microbiota at various stages in RTI pathogenesis call for early life preventative and therapeutic interventions to promote respiratory health.
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Affiliation(s)
- Wouter A A de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands; National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands
| | - Justyna Binkowska
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands; National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands; University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK.
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45
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Dougherty MW, Jobin C. Shining a Light on Colibactin Biology. Toxins (Basel) 2021; 13:346. [PMID: 34065799 PMCID: PMC8151066 DOI: 10.3390/toxins13050346] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/06/2021] [Accepted: 05/10/2021] [Indexed: 12/16/2022] Open
Abstract
Colibactin is a secondary metabolite encoded by the pks gene island identified in several Enterobacteriaceae, including some pathogenic Escherichia coli (E. coli) commonly enriched in mucosal tissue collected from patients with inflammatory bowel disease and colorectal cancer. E. coli harboring this biosynthetic gene cluster cause DNA damage and tumorigenesis in cell lines and pre-clinical models, yet fundamental knowledge regarding colibactin function is lacking. To accurately assess the role of pks+ E. coli in cancer etiology, the biological mechanisms governing production and delivery of colibactin by these bacteria must be elucidated. In this review, we will focus on recent advances in our understanding of colibactin's structural mode-of-action and mutagenic potential with consideration for how this activity may be regulated by physiologic conditions within the intestine.
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Affiliation(s)
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, FL 32610, USA;
- Department of Infectious Diseases and Inflammation, University of Florida, Gainesville, FL 32610, USA
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Łobocka M, Dąbrowska K, Górski A. Engineered Bacteriophage Therapeutics: Rationale, Challenges and Future. BioDrugs 2021; 35:255-280. [PMID: 33881767 PMCID: PMC8084836 DOI: 10.1007/s40259-021-00480-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2021] [Indexed: 12/20/2022]
Abstract
The current problems with increasing bacterial resistance to antibacterial therapies, resulting in a growing frequency of incurable bacterial infections, necessitates the acceleration of studies on antibacterials of a new generation that could offer an alternative to antibiotics or support their action. Bacteriophages (phages) can kill antibiotic-sensitive as well as antibiotic-resistant bacteria, and thus are a major subject of such studies. Their efficacy in curing bacterial infections has been demonstrated in in vivo experiments and in the clinic. Unlike antibiotics, phages have a narrow range of specificity, which makes them safe for commensal microbiota. However, targeting even only the most clinically relevant strains of pathogenic bacteria requires large collections of well characterized phages, whose specificity would cover all such strains. The environment is a rich source of diverse phages, but due to their complex relationships with bacteria and safety concerns, only some naturally occurring phages can be considered for therapeutic applications. Still, their number and diversity make a detailed characterization of all potentially promising phages virtually impossible. Moreover, no single phage combines all the features required of an ideal therapeutic agent. Additionally, the rapid acquisition of phage resistance by bacteria may make phages already approved for therapy ineffective and turn the search for environmental phages of better efficacy and new specificity into an endless race. An alternative strategy for acquiring phages with desired properties in a short time with minimal cost regarding their acquisition, characterization, and approval for therapy could be based on targeted genome modifications of phage isolates with known properties. The first example demonstrating the potential of this strategy in curing bacterial diseases resistant to traditional therapy is the recent successful treatment of a progressing disseminated Mycobacterium abscessus infection in a teenage patient with the use of an engineered phage. In this review, we briefly present current methods of phage genetic engineering, highlighting their advantages and disadvantages, and provide examples of genetically engineered phages with a modified host range, improved safety or antibacterial activity, and proven therapeutic efficacy. We also summarize novel uses of engineered phages not only for killing pathogenic bacteria, but also for in situ modification of human microbiota to attenuate symptoms of certain bacterial diseases and metabolic, immune, or mental disorders.
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Affiliation(s)
- Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Krystyna Dąbrowska
- Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences, Wrocław, Poland
| | - Andrzej Górski
- Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences, Wrocław, Poland
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Han P, Gu JQ, Li LS, Wang XY, Wang HT, Wang Y, Chang C, Sun JL. The Association Between Intestinal Bacteria and Allergic Diseases-Cause or Consequence? Front Cell Infect Microbiol 2021; 11:650893. [PMID: 33937097 PMCID: PMC8083053 DOI: 10.3389/fcimb.2021.650893] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/22/2021] [Indexed: 12/17/2022] Open
Abstract
The incidence of allergic disorders has been increasing over the past few decades, especially in industrialized countries. Allergies can affect people of any age. The pathogenesis of allergic diseases is complex and involves genetic, epigenetic, and environmental factors, and the response to medication is very variable. For some patients, avoidance is the sole effective therapy, and only when the triggers are identifiable. In recent years, the intestinal microbiota has emerged as a significant contributor to the development of allergic diseases. However, the precise mechanisms related to the effects of the microbiome on the pathogenesis of allergic diseases are unknown. This review summarizes the recent association between allergic disorders and intestinal bacterial dysbiosis, describes the function of gut microbes in allergic disease development from both preclinical and clinical studies, discusses the factors that influence gut microbial diversity and advanced techniques used in microbial analysis. Ultimately, more studies are required to define the host-microbial relationship relevant to allergic disorders and amenable to new therapeutic interventions.
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Affiliation(s)
- Pei Han
- Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Jian-Qing Gu
- Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li-Sha Li
- Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xue-Yan Wang
- Department of Allergy, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hong-Tian Wang
- Department of Allergy, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yan Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Christopher Chang
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, Davis, CA, United States
- Division of Pediatric Immunology and Allergy, Joe DiMaggio Children’s Hospital, Hollywood, FL, United States
| | - Jin-Lyu Sun
- Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Haskett TL, Tkacz A, Poole PS. Engineering rhizobacteria for sustainable agriculture. THE ISME JOURNAL 2021; 15:949-964. [PMID: 33230265 PMCID: PMC8114929 DOI: 10.1038/s41396-020-00835-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/29/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023]
Abstract
Exploitation of plant growth promoting (PGP) rhizobacteria (PGPR) as crop inoculants could propel sustainable intensification of agriculture to feed our rapidly growing population. However, field performance of PGPR is typically inconsistent due to suboptimal rhizosphere colonisation and persistence in foreign soils, promiscuous host-specificity, and in some cases, the existence of undesirable genetic regulation that has evolved to repress PGP traits. While the genetics underlying these problems remain largely unresolved, molecular mechanisms of PGP have been elucidated in rigorous detail. Engineering and subsequent transfer of PGP traits into selected efficacious rhizobacterial isolates or entire bacterial rhizosphere communities now offers a powerful strategy to generate improved PGPR that are tailored for agricultural use. Through harnessing of synthetic plant-to-bacteria signalling, attempts are currently underway to establish exclusive coupling of plant-bacteria interactions in the field, which will be crucial to optimise efficacy and establish biocontainment of engineered PGPR. This review explores the many ecological and biotechnical facets of this research.
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Affiliation(s)
- Timothy L. Haskett
- grid.4991.50000 0004 1936 8948Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
| | - Andrzej Tkacz
- grid.4991.50000 0004 1936 8948Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
| | - Philip S. Poole
- grid.4991.50000 0004 1936 8948Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
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Portable CRISPR-Cas9 N System for Flexible Genome Engineering in Lactobacillus acidophilus, Lactobacillus gasseri, and Lactobacillus paracasei. Appl Environ Microbiol 2021; 87:AEM.02669-20. [PMID: 33397707 DOI: 10.1128/aem.02669-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/10/2020] [Indexed: 12/18/2022] Open
Abstract
Diverse Lactobacillus strains are widely used as probiotic cultures in the dairy and dietary supplement industries, and specific strains, such as Lactobacillus acidophilus NCFM, have been engineered for the development of biotherapeutics. To expand the Lactobacillus manipulation toolbox with enhanced efficiency and ease, we present here a CRISPR (clustered regularly interspaced palindromic repeats)-SpyCas9D10A nickase (Cas9N)-based system for programmable engineering of L. acidophilus NCFM, a model probiotic bacterium. Successful single-plasmid delivery system was achieved with the engineered pLbCas9N vector harboring cas9 N under the regulation of a Lactobacillus promoter and a cloning region for a customized single guide RNA (sgRNA) and editing template. The functionality of the pLbCas9N system was validated in NCFM with targeted chromosomal deletions ranging between 300 bp and 1.9 kb at various loci (rafE, lacS, and ltaS), yielding 35 to 100% mutant recovery rates. Genome analysis of the mutants confirmed precision and specificity of the pLbCas9N system. To showcase the versatility of this system, we also inserted an mCherry fluorescent-protein gene downstream of the pgm gene to create a polycistronic transcript. The pLbCas9N system was further deployed in other species to generate a concurrent single-base substitution and gene deletion in Lactobacillus gasseri ATCC 33323 and an in-frame gene deletion in Lactobacillus paracasei Lpc-37, highlighting the portability of the system in phylogenetically distant Lactobacillus species, where its targeting activity was not interfered with by endogenous CRISPR-Cas systems. Collectively, these editing outcomes illustrate the robustness and versatility of the pLbCas9N system for genome manipulations in diverse lactobacilli and open new avenues for the engineering of health-promoting lactic acid bacteria.IMPORTANCE This work describes the development of a lactobacillus CRISPR-based editing system for genome manipulations in three Lactobacillus species belonging to the lactic acid bacteria (LAB), which are commonly known for their long history of use in food fermentations and as indigenous members of healthy microbiotas and for their emerging roles in human and animal commercial health-promoting applications. We exploited the established CRISPR-SpyCas9 nickase for flexible and precise genome editing applications in Lactobacillus acidophilus and further demonstrated the efficacy of this universal system in two distantly related Lactobacillus species. This versatile Cas9-based system facilitates genome engineering compared to conventional gene replacement systems and represents a valuable gene editing modality in species that do not possess native CRISPR-Cas systems. Overall, this portable tool contributes to expanding the genome editing toolbox of LAB for studying their health-promoting mechanisms and engineering of these beneficial microbes as next-generation vaccines and designer probiotics.
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50
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Khwatenge CN, Nahashon SN. Recent Advances in the Application of CRISPR/Cas9 Gene Editing System in Poultry Species. Front Genet 2021; 12:627714. [PMID: 33679892 PMCID: PMC7933658 DOI: 10.3389/fgene.2021.627714] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/19/2021] [Indexed: 12/28/2022] Open
Abstract
CRISPR/Cas9 system genome editing is revolutionizing genetics research in a wide spectrum of animal models in the genetic era. Among these animals, is the poultry species. CRISPR technology is the newest and most advanced gene-editing tool that allows researchers to modify and alter gene functions for transcriptional regulation, gene targeting, epigenetic modification, gene therapy, and drug delivery in the animal genome. The applicability of the CRISPR/Cas9 system in gene editing and modification of genomes in the avian species is still emerging. Up to date, substantial progress in using CRISPR/Cas9 technology has been made in only two poultry species (chicken and quail), with chicken taking the lead. There have been major recent advances in the modification of the avian genome through their germ cell lineages. In the poultry industry, breeders and producers can utilize CRISPR-mediated approaches to enhance the many required genetic variations towards the poultry population that are absent in a given poultry flock. Thus, CRISPR allows the benefit of accessing genetic characteristics that cannot otherwise be used for poultry production. Therefore CRISPR/Cas9 becomes a very powerful and robust tool for editing genes that allow for the introduction or regulation of genetic information in poultry genomes. However, the CRISPR/Cas9 technology has several limitations that need to be addressed to enhance its use in the poultry industry. This review evaluates and provides a summary of recent advances in applying CRISPR/Cas9 gene editing technology in poultry research and explores its potential use in advancing poultry breeding and production with a major focus on chicken and quail. This could aid future advancements in the use of CRISPR technology to improve poultry production.
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Affiliation(s)
- Collins N. Khwatenge
- Department of Biological Sciences, Tennessee State University, Nashville, IN, United States
- Department of Agriculture and Environmental Sciences, Tennessee State University, Nashville, TN, United States
| | - Samuel N. Nahashon
- Department of Agriculture and Environmental Sciences, Tennessee State University, Nashville, TN, United States
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