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Trøseid M, Nielsen SD, Vujkovic-Cvijin I. Gut microbiome and cardiometabolic comorbidities in people living with HIV. MICROBIOME 2024; 12:106. [PMID: 38877521 PMCID: PMC11177534 DOI: 10.1186/s40168-024-01815-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/12/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Despite modern antiretroviral therapy (ART), people living with HIV (PLWH) have increased relative risk of inflammatory-driven comorbidities, including cardiovascular disease (CVD). The gut microbiome could be one of several driving factors, along with traditional risk factors and HIV-related risk factors such as coinfections, ART toxicity, and past immunodeficiency. RESULTS PLWH have an altered gut microbiome, even after adjustment for known confounding factors including sexual preference. The HIV-related microbiome has been associated with cardiometabolic comorbidities, and shares features with CVD-related microbiota profiles, in particular reduced capacity for short-chain fatty acid (SCFA) generation. Substantial inter-individual variation has so far been an obstacle for applying microbiota profiles for risk stratification. This review covers updated knowledge and recent advances in our understanding of the gut microbiome and comorbidities in PLWH, with specific focus on cardiometabolic comorbidities and inflammation. It covers a comprehensive overview of HIV-related and comorbidity-related dysbiosis, microbial translocation, and microbiota-derived metabolites. It also contains recent data from studies in PLWH on circulating metabolites related to comorbidities and underlying gut microbiota alterations, including circulating levels of the SCFA propionate, the histidine-analogue imidazole propionate, and the protective metabolite indole-3-propionic acid. CONCLUSIONS Despite recent advances, the gut microbiome and related metabolites are not yet established as biomarkers or therapeutic targets. The review gives directions for future research needed to advance the field into clinical practice, including promises and pitfalls for precision medicine. Video Abstract.
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Affiliation(s)
- Marius Trøseid
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.
- Section for Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway.
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Susanne Dam Nielsen
- Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen, 2200, Denmark
- Department of Surgical Gastroenterology and Transplantation, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, Copenhagen Oe, 2100, Denmark
| | - Ivan Vujkovic-Cvijin
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Karsh Division of Gastroenterology & Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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Conradie T, Caparros-Martin JA, Egan S, Kicic A, Koks S, Stick SM, Agudelo-Romero P. Exploring the Complexity of the Human Respiratory Virome through an In Silico Analysis of Shotgun Metagenomic Data Retrieved from Public Repositories. Viruses 2024; 16:953. [PMID: 38932245 PMCID: PMC11209621 DOI: 10.3390/v16060953] [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: 03/21/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Respiratory viruses significantly impact global morbidity and mortality, causing more disease in humans than any other infectious agent. Beyond pathogens, various viruses and bacteria colonize the respiratory tract without causing disease, potentially influencing respiratory diseases' pathogenesis. Nevertheless, our understanding of respiratory microbiota is limited by technical constraints, predominantly focusing on bacteria and neglecting crucial populations like viruses. Despite recent efforts to improve our understanding of viral diversity in the human body, our knowledge of viral diversity associated with the human respiratory tract remains limited. METHODS Following a comprehensive search in bibliographic and sequencing data repositories using keyword terms, we retrieved shotgun metagenomic data from public repositories (n = 85). After manual curation, sequencing data files from 43 studies were analyzed using EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion). Complete and high-quality contigs were further assessed for genomic and taxonomic characterization. RESULTS Viral contigs were obtained from 194 out of the 868 FASTQ files processed through EVEREST. Of the 1842 contigs that were quality assessed, 8% (n = 146) were classified as complete/high-quality genomes. Most of the identified viral contigs were taxonomically classified as bacteriophages, with taxonomic resolution ranging from the superkingdom level down to the species level. Captured contigs were spread across 25 putative families and varied between RNA and DNA viruses, including previously uncharacterized viral genomes. Of note, airway samples also contained virus(es) characteristic of the human gastrointestinal tract, which have not been previously described as part of the lung virome. Additionally, by performing a meta-analysis of the integrated datasets, ecological trends within viral populations linked to human disease states and their biogeographical distribution along the respiratory tract were observed. CONCLUSION By leveraging publicly available repositories of shotgun metagenomic data, the present study provides new insights into viral genomes associated with specimens from the human respiratory tract across different disease spectra. Further studies are required to validate our findings and evaluate the potential impact of these viral communities on respiratory tract physiology.
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Affiliation(s)
- Talya Conradie
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA 6009, Australia
- Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA 6150, Australia
| | | | - Siobhon Egan
- Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA 6150, Australia
- Centre for Computational and Systems Medicine, Health Future Institute, Murdoch University, Perth, WA 6150, Australia
| | - Anthony Kicic
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA 6009, Australia
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital for Children, Perth, WA 6009, Australia
- Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, Perth, WA 6009, Australia
- School of Population Health, Curtin University, Perth, WA 6102, Australia
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Stephen M. Stick
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital for Children, Perth, WA 6009, Australia
- Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, Perth, WA 6009, Australia
| | - Patricia Agudelo-Romero
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA 6009, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- European Virus Bioinformatics Centre, Friedrich-Schiller-Universitat Jena, 07737 Jena, Germany
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253
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Cuffaro F, Russo E, Amedei A. Endometriosis, Pain, and Related Psychological Disorders: Unveiling the Interplay among the Microbiome, Inflammation, and Oxidative Stress as a Common Thread. Int J Mol Sci 2024; 25:6473. [PMID: 38928175 PMCID: PMC11203696 DOI: 10.3390/ijms25126473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/29/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Endometriosis (EM), a chronic condition in endometrial tissue outside the uterus, affects around 10% of reproductive-age women, significantly affecting fertility. Its prevalence remains elusive due to the surgical confirmation needed for diagnosis. Manifesting with a range of symptoms, including dysmenorrhea, dyschezia, dysuria, dyspareunia, fatigue, and gastrointestinal discomfort, EM significantly impairs quality of life due to severe chronic pelvic pain (CPP). Psychological manifestations, notably depression and anxiety, frequently accompany the physical symptoms, with CPP serving as a key mediator. Pain stems from endometrial lesions, involving oxidative stress, neuroinflammation, angiogenesis, and sensitization processes. Microbial dysbiosis appears to be crucial in the inflammatory mechanisms underlying EM and associated CPP, as well as psychological symptoms. In this scenario, dietary interventions and nutritional supplements could help manage EM symptoms by targeting inflammation, oxidative stress, and the microbiome. Our manuscript starts by delving into the complex relationship between EM pain and psychological comorbidities. It subsequently addresses the emerging roles of the microbiome, inflammation, and oxidative stress as common links among these abovementioned conditions. Furthermore, the review explores how dietary and nutritional interventions may influence the composition and function of the microbiome, reduce inflammation and oxidative stress, alleviate pain, and potentially affect EM-associated psychological disorders.
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Affiliation(s)
- Francesca Cuffaro
- Division of Interdisciplinary Internal Medicine, Careggi University Hospital of Florence, 50134 Florence, Italy;
| | - Edda Russo
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy
| | - Amedeo Amedei
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), 50139 Florence, Italy
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Benz F, Camara-Wilpert S, Russel J, Wandera KG, Čepaitė R, Ares-Arroyo M, Gomes-Filho JV, Englert F, Kuehn JA, Gloor S, Mestre MR, Cuénod A, Aguilà-Sans M, Maccario L, Egli A, Randau L, Pausch P, Rocha EPC, Beisel CL, Madsen JS, Bikard D, Hall AR, Sørensen SJ, Pinilla-Redondo R. Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans. Cell Host Microbe 2024; 32:875-886.e9. [PMID: 38754416 DOI: 10.1016/j.chom.2024.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 03/05/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024]
Abstract
Plasmid-encoded type IV-A CRISPR-Cas systems lack an acquisition module, feature a DinG helicase instead of a nuclease, and form ribonucleoprotein complexes of unknown biological functions. Type IV-A3 systems are carried by conjugative plasmids that often harbor antibiotic-resistance genes and their CRISPR array contents suggest a role in mediating inter-plasmid conflicts, but this function remains unexplored. Here, we demonstrate that a plasmid-encoded type IV-A3 system co-opts the type I-E adaptation machinery from its host, Klebsiella pneumoniae (K. pneumoniae), to update its CRISPR array. Furthermore, we reveal that robust interference of conjugative plasmids and phages is elicited through CRISPR RNA-dependent transcriptional repression. By silencing plasmid core functions, type IV-A3 impacts the horizontal transfer and stability of targeted plasmids, supporting its role in plasmid competition. Our findings shed light on the mechanisms and ecological function of type IV-A3 systems and demonstrate their practical efficacy for countering antibiotic resistance in clinically relevant strains.
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Affiliation(s)
- Fabienne Benz
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Synthetic Biology, Paris 75015, France; Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France; Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Sarah Camara-Wilpert
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Jakob Russel
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Katharina G Wandera
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Rimvydė Čepaitė
- Life Sciences Center - European Molecular Biology Laboratory (LSC-EMBL) Partnership for Genome Editing Technologies, Vilnius University - Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Manuel Ares-Arroyo
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
| | | | - Frank Englert
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Johannes A Kuehn
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Silvana Gloor
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Mario Rodríguez Mestre
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Aline Cuénod
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland; Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Mònica Aguilà-Sans
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Lorrie Maccario
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland; Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Lennart Randau
- Department of Biology, Philipps Universität Marburg, Marburg, Germany; SYNMIKRO, Center for Synthetic Microbiology, Marburg, Germany
| | - Patrick Pausch
- Life Sciences Center - European Molecular Biology Laboratory (LSC-EMBL) Partnership for Genome Editing Technologies, Vilnius University - Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany; Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Jonas Stenløkke Madsen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - David Bikard
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Synthetic Biology, Paris 75015, France
| | - Alex R Hall
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Søren Johannes Sørensen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark.
| | - Rafael Pinilla-Redondo
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark.
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Wang B, Tan M, Li W, Xu Q, Jin L, Xie S, Wang C. Exploring the microbiota difference of bronchoalveolar lavage fluid between community-acquired pneumonia with or without COPD based on metagenomic sequencing: a retrospective study. BMC Pulm Med 2024; 24:278. [PMID: 38867204 PMCID: PMC11167785 DOI: 10.1186/s12890-024-03087-6] [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: 08/03/2023] [Accepted: 06/03/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Community-acquired pneumonia (CAP) patients with chronic obstructive pulmonary disease (COPD) have higher disease severity and mortality compared to those without COPD. However, deep investigation into microbiome distribution of lower respiratory tract of CAP with or without COPD was unknown. METHODS So we used metagenomic next generation sequencing (mNGS) to explore the microbiome differences between the two groups. RESULTS Thirty-six CAP without COPD and 11 CAP with COPD cases were retrieved. Bronchoalveolar lavage fluid (BALF) was collected and analyzed using untargeted mNGS and bioinformatic analysis. mNGS revealed that CAP with COPD group was abundant with Streptococcus, Prevotella, Bordetella at genus level and Cutibacterium acnes, Rothia mucilaginosa, Bordetella genomosp. 6 at species level. While CAP without COPD group was abundant with Ralstonia, Prevotella, Streptococcus at genus level and Ralstonia pickettii, Rothia mucilaginosa, Prevotella melaninogenica at species level. Meanwhile, both alpha and beta microbiome diversity was similar between groups. Linear discriminant analysis found that pa-raburkholderia, corynebacterium tuberculostearicum and staphylococcus hominis were more enriched in CAP without COPD group while the abundance of streptococcus intermedius, streptococcus constellatus, streptococcus milleri, fusarium was higher in CAP with COPD group. CONCLUSIONS These findings revealed that concomitant COPD have an mild impact on lower airway microbiome of CAP patients.
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Affiliation(s)
- Bingbing Wang
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Min Tan
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Wei Li
- Department of Geriatrics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Qinghua Xu
- Vision Medicals Center for Infectious Disease, Guangzhou, Guangdong, China
| | - Lianfeng Jin
- Vision Medicals Center for Infectious Disease, Guangzhou, Guangdong, China
| | - Shuanshuan Xie
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China.
| | - Changhui Wang
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China.
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Mies US, Hervé V, Kropp T, Platt K, Sillam-Dussès D, Šobotník J, Brune A. Genome reduction and horizontal gene transfer in the evolution of Endomicrobia-rise and fall of an intracellular symbiosis with termite gut flagellates. mBio 2024; 15:e0082624. [PMID: 38742878 PMCID: PMC11257099 DOI: 10.1128/mbio.00826-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
Bacterial endosymbionts of eukaryotic hosts typically experience massive genome reduction, but the underlying evolutionary processes are often obscured by the lack of free-living relatives. Endomicrobia, a family-level lineage of host-associated bacteria in the phylum Elusimicrobiota that comprises both free-living representatives and endosymbionts of termite gut flagellates, are an excellent model to study evolution of intracellular symbionts. We reconstructed 67 metagenome-assembled genomes (MAGs) of Endomicrobiaceae among more than 1,700 MAGs from the gut microbiota of a wide range of termites. Phylogenomic analysis confirmed a sister position of representatives from termites and ruminants, and allowed to propose eight new genera in the radiation of Endomicrobiaceae. Comparative genome analysis documented progressive genome erosion in the new genus Endomicrobiellum, which comprises all flagellate endosymbionts characterized to date. Massive gene losses were accompanied by the acquisition of new functions by horizontal gene transfer, which led to a shift from a glucose-based energy metabolism to one based on sugar phosphates. The breakdown of glycolysis and many anabolic pathways for amino acids and cofactors in several subgroups was compensated by the independent acquisition of new uptake systems, including an ATP/ADP antiporter, from other gut microbiota. The putative donors are mostly flagellate endosymbionts from other bacterial phyla, including several, hitherto unknown lineages of uncultured Alphaproteobacteria, documenting the importance of horizontal gene transfer in the convergent evolution of these intracellular symbioses. The loss of almost all biosynthetic capacities in some lineages of Endomicrobiellum suggests that their originally mutualistic relationship with flagellates is on its decline.IMPORTANCEUnicellular eukaryotes are frequently colonized by bacterial and archaeal symbionts. A prominent example are the cellulolytic gut flagellates of termites, which harbor diverse but host-specific bacterial symbionts that occur exclusively in termite guts. One of these lineages, the so-called Endomicrobia, comprises both free-living and endosymbiotic representatives, which offers the unique opportunity to study the evolutionary processes underpinning the transition from a free-living to an intracellular lifestyle. Our results revealed a progressive gene loss in energy metabolism and biosynthetic pathways, compensated by the acquisition of new functions via horizontal gene transfer from other gut bacteria, and suggest the eventual breakdown of an initially mutualistic symbiosis. Evidence for convergent evolution of unrelated endosymbionts reflects adaptations to the intracellular environment of termite gut flagellates.
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Affiliation(s)
- Undine S. Mies
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Vincent Hervé
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tom Kropp
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Katja Platt
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - David Sillam-Dussès
- Laboratory of Experimental and Comparative Ethology LEEC, UR 4443, University Sorbonne Paris Nord, Villetaneuse, France
| | - Jan Šobotník
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czechia
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Huang H, Li G, He Y, Chen J, Yan J, Zhang Q, Li L, Cai X. Cellular succinate metabolism and signaling in inflammation: implications for therapeutic intervention. Front Immunol 2024; 15:1404441. [PMID: 38933270 PMCID: PMC11200920 DOI: 10.3389/fimmu.2024.1404441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Succinate, traditionally viewed as a mere intermediate of the tricarboxylic acid (TCA) cycle, has emerged as a critical mediator in inflammation. Disruptions within the TCA cycle lead to an accumulation of succinate in the mitochondrial matrix. This excess succinate subsequently diffuses into the cytosol and is released into the extracellular space. Elevated cytosolic succinate levels stabilize hypoxia-inducible factor-1α by inhibiting prolyl hydroxylases, which enhances inflammatory responses. Notably, succinate also acts extracellularly as a signaling molecule by engaging succinate receptor 1 on immune cells, thus modulating their pro-inflammatory or anti-inflammatory activities. Alterations in succinate levels have been associated with various inflammatory disorders, including rheumatoid arthritis, inflammatory bowel disease, obesity, and atherosclerosis. These associations are primarily due to exaggerated immune cell responses. Given its central role in inflammation, targeting succinate pathways offers promising therapeutic avenues for these diseases. This paper provides an extensive review of succinate's involvement in inflammatory processes and highlights potential targets for future research and therapeutic possibilities development.
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Affiliation(s)
- Hong Huang
- Department of Rheumatology of First Hospital and Institute of Innovation and Applied Research in Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Gejing Li
- Department of Rheumatology of First Hospital and Institute of Innovation and Applied Research in Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Yini He
- Department of Rheumatology of First Hospital and Institute of Innovation and Applied Research in Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Jing Chen
- Department of Rheumatology of First Hospital and Institute of Innovation and Applied Research in Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Jianye Yan
- Department of Rheumatology of First Hospital and Institute of Innovation and Applied Research in Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Qin Zhang
- Department of Rheumatology of First Hospital and Institute of Innovation and Applied Research in Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Liqing Li
- Department of Rheumatology of First Hospital and Institute of Innovation and Applied Research in Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
- The Central Research Laboratory, Hunan Traditional Chinese Medical College, Zhuzhou, Hunan, China
| | - Xiong Cai
- Department of Rheumatology of First Hospital and Institute of Innovation and Applied Research in Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
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Comi G, Colautti A, Bernardi CEM, Stella S, Orecchia E, Coppola F, Iacumin L. Leuconostoc gelidum Is the Major Species Responsible for the Spoilage of Cooked Sausage Packaged in a Modified Atmosphere, and Hop Extract Is the Best Inhibitor Tested. Microorganisms 2024; 12:1175. [PMID: 38930557 PMCID: PMC11206102 DOI: 10.3390/microorganisms12061175] [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: 05/14/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Cooked sausages packaged in a modified atmosphere (MAP: 20% CO2, 70% N2, <0.2% O2) with evident yellow stains were analyzed. The aims of this work were to study the microbial cause of the spoilage and to evaluate different antimicrobial compounds to prevent it. Leuconostoc gelidum was identified as the primary cause of the yellow coating in spoiled cooked sausage, as confirmed by its intentional inoculation on slices of unspoiled sausage. Leuconostoc gelidum was the main bacteria responsible for the yellow coating in spoiled cooked sausage, as confirmed by its intentional inoculation on slices of unspoiled sausage. The yellow color was also evident during growth in the model system containing cooked sausage extract, but the colonies on MRS agar appeared white, demonstrating that the food substrate stimulated the production of the yellow pigment. The spoilage was also characterized by different volatile compounds, including ketones, ethanol, acetic acid, and ethyl acetate, found in the spoiled cooked sausage packages. These compounds explained the activity of Leuc. gelidum because they are typical of heterofermentative LAB, cultivated either on food substrates or in artificial broths. Leuc. gelidum also produced slight swelling in the spoiled packages. The efficacy of different antimicrobials was assessed in model systems composed of cooked sausage extract with the antimicrobials added at food product concentrations. The data showed that sodium lactate, sodium acetate, and a combination of sodium lactate and sodium diacetate could only slow the growth of the spoiler-they could not stop it from occurring. Conversely, hop extract inhibited Leuc. gelidum, showing a minimal inhibitory concentration (MIC) of approximately 0.008 mg CAE/mL in synthetic broth and 4 mg CAE/kg in cooked sausage slices. Adding hop extract at the MIC did not allow Leuc. gelidum growth and did not change the sensorial characteristics of the cooked sausages. To our knowledge, this is the first report of the antimicrobial activities of hop extracts against Leuc. gelidum either in vitro or in vivo.
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Affiliation(s)
- Giuseppe Comi
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Via Sondrio 2/a, 33100 Udine, Italy; (A.C.); (E.O.); (L.I.)
| | - Andrea Colautti
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Via Sondrio 2/a, 33100 Udine, Italy; (A.C.); (E.O.); (L.I.)
| | - Cristian Edoardo Maria Bernardi
- Department of Veterinary Medicine and Animal Sciences, University of Milan, Via dell’Università 6, 26900 Lodi, Italy; (C.E.M.B.); (S.S.)
| | - Simone Stella
- Department of Veterinary Medicine and Animal Sciences, University of Milan, Via dell’Università 6, 26900 Lodi, Italy; (C.E.M.B.); (S.S.)
| | - Elisabetta Orecchia
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Via Sondrio 2/a, 33100 Udine, Italy; (A.C.); (E.O.); (L.I.)
| | - Francesca Coppola
- Food Sciences Institute, National Research Council, Via Roma, 64, 83100 Avellino, Italy;
| | - Lucilla Iacumin
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Via Sondrio 2/a, 33100 Udine, Italy; (A.C.); (E.O.); (L.I.)
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Guo Q, Cheng Y, Li T, Huang J, Li J, Zhang Z, Qu Y. The Gut Microbiota Contributes to the Development of LPS-Induced Orchitis by Disrupting the Blood-Testosterone Barrier in Mice. Reprod Sci 2024:10.1007/s43032-024-01613-9. [PMID: 38858330 DOI: 10.1007/s43032-024-01613-9] [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: 01/13/2024] [Accepted: 05/29/2024] [Indexed: 06/12/2024]
Abstract
Orchitis is a frequent inflammatory reproductive disease that causes male infertility and a decline in sperm quality. Gut microbiota can regulate systemic and local inflammation, spermatogenesis and blood-testosterone barrier (BTB). In this study, we investigated correlation between gut microbiota and orchitis by establishing a mouse gut microbiota imbalance model induced by antibiotics (ABX) treatment and orchitis model induced by lipopolysaccharide (LPS) infection. Based on these two models, 16s rRNA sequencing and feces microbiota transplantation (FMT) experiments were combined to examine the function and regulatory mechanisms of the gut microbiota in host defense against orchitis. Compared with control mice, gut microbiota imbalance resulted in increasing inflammatory responses, modulating oxidative stress related enzyme activity, testosterone levels and the permeability of blood testosterone barrier, which are restored after FMT. Subsequently, we tested the relationship between the gut microbiota imbalance and testicular inflammation severity in orchitis. It was found that the ABX and LPS co-treated mice had more severe inflammatory responses, lower testosterone levels and greater permeability of the BTB than the LPS-treated mice, but these changes could be partially recovered by gut microbiota transplantation. In conclusion, these above results proved for the first time that gut microbiota is involved in the pathogenesis of orchitis, which laid a good foundation for the subsequent development of anti-orchitis drugs and probiotic targeting intestinal flora.
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Affiliation(s)
- Qing Guo
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
- Heilongjiang Key Laboratory of Efficient Utilization of Feed Resources and Nutrition Manipulation in Cold Region, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Ye Cheng
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
- Heilongjiang Key Laboratory of Efficient Utilization of Feed Resources and Nutrition Manipulation in Cold Region, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Tianfeng Li
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
- Heilongjiang Key Laboratory of Efficient Utilization of Feed Resources and Nutrition Manipulation in Cold Region, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Jiang Huang
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Jinchun Li
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
- Heilongjiang Key Laboratory of Efficient Utilization of Feed Resources and Nutrition Manipulation in Cold Region, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Zecai Zhang
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China.
| | - Yongli Qu
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China.
- Heilongjiang Key Laboratory of Efficient Utilization of Feed Resources and Nutrition Manipulation in Cold Region, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China.
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260
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Grant AR, Johnson KP, Stanley EL, Baldwin-Brown J, Kolenčík S, Allen JM. Rapid Targeted Assembly of the Proteome Reveals Evolutionary Variation of GC Content in Avian Lice. Bioinform Biol Insights 2024; 18:11779322241257991. [PMID: 38860163 PMCID: PMC11163934 DOI: 10.1177/11779322241257991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 05/02/2024] [Indexed: 06/12/2024] Open
Abstract
Nucleotide base composition plays an influential role in the molecular mechanisms involved in gene function, phenotype, and amino acid composition. GC content (proportion of guanine and cytosine in DNA sequences) shows a high level of variation within and among species. Many studies measure GC content in a small number of genes, which may not be representative of genome-wide GC variation. One challenge when assembling extensive genomic data sets for these studies is the significant amount of resources (monetary and computational) associated with data processing, and many bioinformatic tools have not been optimized for resource efficiency. Using a high-performance computing (HPC) cluster, we manipulated resources provided to the targeted gene assembly program, automated target restricted assembly method (aTRAM), to determine an optimum way to run the program to maximize resource use. Using our optimum assembly approach, we assembled and measured GC content of all of the protein-coding genes of a diverse group of parasitic feather lice. Of the 499 426 genes assembled across 57 species, feather lice were GC-poor (mean GC = 42.96%) with a significant amount of variation within and between species (GC range = 19.57%-73.33%). We found a significant correlation between GC content and standard deviation per taxon for overall GC and GC3, which could indicate selection for G and C nucleotides in some species. Phylogenetic signal of GC content was detected in both GC and GC3. This research provides a large-scale investigation of GC content in parasitic lice laying the foundation for understanding the basis of variation in base composition across species.
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Affiliation(s)
- Avery R Grant
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Edward L Stanley
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | | | - Stanislav Kolenčík
- Faculty of Mathematics, Natural Sciences, and Information Technologies, University of Primorska, Koper, Slovenia
| | - Julie M Allen
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
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261
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Zhang L, Cai M, Zhang X, Wang S, Pang L, Chen X, Zheng C, Sun Y, Liang Y, Guo S, Wei F, Zhang Y. Integrated analysis of microbiome and host transcriptome unveils correlations between lung microbiota and host immunity in bronchoalveolar lavage fluid of pneumocystis pneumonia patients. Microbes Infect 2024:105374. [PMID: 38849069 DOI: 10.1016/j.micinf.2024.105374] [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: 03/03/2024] [Revised: 05/29/2024] [Accepted: 06/02/2024] [Indexed: 06/09/2024]
Abstract
OBJECTIVE The lung microbiota of patients with pulmonary diseases is disrupted and impacts the immunity. The microbiological and immune landscape of the lungs in patients with pneumocystis pneumonia (PCP) remains poorly understood. METHODS Multi-omics analysis and machine learning were performed on bronchoalveolar lavage fluid to explore interaction between the lung microbiota and host immunity in PCP. Then we constructed a diagnostic model using differential genes with LASSO regression and validated by qPCR. The immune infiltration analysis was performed to explore the landscape of lung immunity in patients with PCP. RESULTS Patients with PCP showed a low alpha diversity of lung microbiota, accompanied by the elevated abundance of Firmicutes, and the differential expressed genes (DEGs) analysis displayed a downregulation of MAPK signaling. The MAPK10, TGFB1, and EFNA3 indicated a potential to predict PCP (AUC = 0.86). The lung immune landscape in PCP showed the lower levels of naïve CD4+ T cells and activated dendritic cells. The correlation analysis of the MAPK signaling pathway-related DEGs and the differential microorganisms at the level of phylum showed that the Firmicutes was negatively correlated with these DEGs. CONCLUSION We profiled the characteristics of lung microbiota and immune landscape in PCP, which may contribute to elucidating the mechanism of PCP.
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Affiliation(s)
- Ling Zhang
- Department of Respiratory and Critical Care Medicine, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China; Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Miaotian Cai
- Department of Respiratory and Critical Care Medicine, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Xin Zhang
- Department of Respiratory and Critical Care Medicine, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China; Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Sitong Wang
- Department of Respiratory and Critical Care Medicine, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Lijun Pang
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Xue Chen
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China; Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing Key Laboratory for HIV/AIDS Research, Beijing, 100069, China
| | - Caopei Zheng
- Department of Respiratory and Critical Care Medicine, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China; Laboratory for Clinical Medicine, Capital Medical University, China
| | - Yuqing Sun
- Department of Respiratory and Critical Care Medicine, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China; Laboratory for Clinical Medicine, Capital Medical University, China
| | - Ying Liang
- Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing Key Laboratory for HIV/AIDS Research, Beijing, 100069, China; Laboratory for Clinical Medicine, Capital Medical University, China
| | - Shan Guo
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Feili Wei
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China.
| | - Yulin Zhang
- Department of Respiratory and Critical Care Medicine, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China; Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing Key Laboratory for HIV/AIDS Research, Beijing, 100069, China; Laboratory for Clinical Medicine, Capital Medical University, China; Beijing Research Center for Respiratory Infectious Diseases, China.
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262
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Morsica G, Messina E, Bagaglio S, Galli L, Lolatto R, Sampaolo M, Barakat M, Israel RJ, Castagna A, Clementi N. Clinico-Virological Outcomes and Mutational Profile of SARS-CoV-2 in Adults Treated with Ribavirin Aerosol for COVID-19 Pneumonia. Microorganisms 2024; 12:1146. [PMID: 38930529 PMCID: PMC11205916 DOI: 10.3390/microorganisms12061146] [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: 04/09/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
The emergence of new SARS-CoV-2 variants can affect vaccine efficacy, laboratory diagnosis and the therapies already available, triggering interest in the search for antiviral agents for SARS-CoV-2 infections. Ribavirin (RBV) is a broad-spectrum antiviral with demonstrated in vitro activity against multiple viruses, including SARS-CoV-2. This retrospective study evaluated the dynamics and viral clearance of SARS-CoV-2 in hospitalised adult participants (PTs) with COVID-19 pneumonia who received an RBV aerosol within a compassionate use study. The impact of RBV on the clinical outcome and the mutational profile of SARS-CoV-2 was also assessed. The median RNA values measured in nine PTs included in this study decreased from baseline to discharge (at BL, threshold cycle (Ct) = 22.4, IQR 19.84-5.07; at discharge, Ct = 27.92, IQR 26.43-36.11), with a significant decline in the Ct value evaluated by Friedman rank ANOVA analysis, p = 0.032. Seven out of nine PTs experienced a clinical improvement, while two PTs deceased during hospitalisation. In PTs with a favourable outcome, the virus clearance rate at discharge was 28.6%. The cumulative clearance rate was 71.4% within 14 days from discharge. A mutational pattern after RBV was detected in three out of five PTs in whom whole-genome sequencing was available. Our findings suggest that RBV limits SARS-CoV-2 replication, possibly resulting in a favourable clinical outcome. Ribavirin may also contribute to the mutational spectrum of SARS-CoV-2.
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Affiliation(s)
- Giulia Morsica
- Unit of Infectious Diseases, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.M.); (S.B.); (L.G.); (R.L.); (A.C.)
| | - Emanuela Messina
- Unit of Infectious Diseases, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.M.); (S.B.); (L.G.); (R.L.); (A.C.)
| | - Sabrina Bagaglio
- Unit of Infectious Diseases, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.M.); (S.B.); (L.G.); (R.L.); (A.C.)
| | - Laura Galli
- Unit of Infectious Diseases, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.M.); (S.B.); (L.G.); (R.L.); (A.C.)
| | - Riccardo Lolatto
- Unit of Infectious Diseases, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.M.); (S.B.); (L.G.); (R.L.); (A.C.)
| | - Michela Sampaolo
- Laboratory of Microbiology and Virology, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (M.S.); (N.C.)
| | | | | | - Antonella Castagna
- Unit of Infectious Diseases, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.M.); (S.B.); (L.G.); (R.L.); (A.C.)
- Faculty of Medicine and Surgery, Vita-Salute University, 20132 Milan, Italy
| | - Nicola Clementi
- Laboratory of Microbiology and Virology, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (M.S.); (N.C.)
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
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263
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Rozani S, Lykoudis PM. The impact of intestinal and mammary microbiomes on breast cancer development: A review on the microbiota and oestrobolome roles in tumour microenvironments. Am J Surg 2024:115795. [PMID: 38853033 DOI: 10.1016/j.amjsurg.2024.115795] [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: 04/03/2024] [Revised: 05/24/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
Abstract
Microbiota affects carcinogenesis by altering energy equilibrium, increasing fat mass, synthesizing small signaling molecules, and formulating and regulating immune response and indigestible food ingredient, xenobiotic, and pharmaceutical compound metabolism. The intestinal microbiome can moderate oestrogen and other steroid hormone metabolisms, and secrete bioactive metabolites that are important for tumour microenvironment. Specifically, the breast tissue microbiome could become altered and lead to breast cancer development. The study of oestrobolome, the microbiomic component that metabolizes oestrogens, can contribute to better breast cancer understanding and subsequent treatment. Investigating oestrobolome-related oestrogen metabolism mechanisms in immune system regulation can shed light on how intestinal microorganisms regulate tumour microenvironment. Intestinal and regional breast microbiomes can determine treatment lines and serve as possible biomarkers for breast cancer. The aim of this study is to summarise current evidence on the role of microbiome in breast cancer progression with particular interest in therapeutic and diagnostic implementation.
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Affiliation(s)
- Sofia Rozani
- Faculty of Medicine, National and Kapodistrian University of Athens, Greece.
| | - Panagis M Lykoudis
- Faculty of Medicine, National and Kapodistrian University of Athens, Greece; Honorary Lecturer, Division of Surgery and Interventional Science, University College London (UCL), United Kingdom
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264
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Bennett GM, Kwak Y, Maynard R. Endosymbioses Have Shaped the Evolution of Biological Diversity and Complexity Time and Time Again. Genome Biol Evol 2024; 16:evae112. [PMID: 38813885 PMCID: PMC11154151 DOI: 10.1093/gbe/evae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Life on Earth comprises prokaryotes and a broad assemblage of endosymbioses. The pages of Molecular Biology and Evolution and Genome Biology and Evolution have provided an essential window into how these endosymbiotic interactions have evolved and shaped biological diversity. Here, we provide a current perspective on this knowledge by drawing on decades of revelatory research published in Molecular Biology and Evolution and Genome Biology and Evolution, and insights from the field at large. The accumulated work illustrates how endosymbioses provide hosts with novel phenotypes that allow them to transition between adaptive landscapes to access environmental resources. Such endosymbiotic relationships have shaped and reshaped life on Earth. The early serial establishment of mitochondria and chloroplasts through endosymbioses permitted massive upscaling of cellular energetics, multicellularity, and terrestrial planetary greening. These endosymbioses are also the foundation upon which all later ones are built, including everything from land-plant endosymbioses with fungi and bacteria to nutritional endosymbioses found in invertebrate animals. Common evolutionary mechanisms have shaped this broad range of interactions. Endosymbionts generally experience adaptive and stochastic genome streamlining, the extent of which depends on several key factors (e.g. mode of transmission). Hosts, in contrast, adapt complex mechanisms of resource exchange, cellular integration and regulation, and genetic support mechanisms to prop up degraded symbionts. However, there are significant differences between endosymbiotic interactions not only in how partners have evolved with each other but also in the scope of their influence on biological diversity. These differences are important considerations for predicting how endosymbioses will persist and adapt to a changing planet.
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Affiliation(s)
- Gordon M Bennett
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
- National Science Foundation Biological Integration Institute—INSITE, University of California, Merced, CA, USA
| | - Younghwan Kwak
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
- National Science Foundation Biological Integration Institute—INSITE, University of California, Merced, CA, USA
| | - Reo Maynard
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
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265
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Lyu W, Li DF, Li SY, Hu H, Zhou JY, Wang L. Gut microbiota modulation: a narrative review on a novel strategy for prevention and alleviation of ovarian aging. Crit Rev Food Sci Nutr 2024:1-13. [PMID: 38835159 DOI: 10.1080/10408398.2024.2361306] [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: 06/06/2024]
Abstract
The global rise in life expectancy corresponds with a delay in childbearing age among women. Ovaries, seen as the chronometers of female physiological aging, demonstrate features of sped up aging, evidenced by the steady decline in both the quality and quantity of ovarian follicles from birth. The multifaceted pathogenesis of ovarian aging has kindled intensive research interest from the biomedical and pharmaceutical sectors. Novel studies underscore the integral roles of gut microbiota in follicular development, lipid metabolism, and hormonal regulation, forging a nexus with ovarian aging. In this review, we outline the role of gut microbiota in ovarian function (follicular development, oocyte maturation, and ovulation), compile and present gut microbiota alterations associated with age-related ovarian aging. We also discuss potential strategies for alleviating ovarian aging from the perspective of gut microbiota, such as fecal microbiota transplantation and probiotics.
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Affiliation(s)
- Wei Lyu
- Clinical Medical Research Center, The Second Affiliated Hospital of Army Military Medical University, Chongqing, China
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA
| | - De-Feng Li
- Clinical Medical Research Center, The Second Affiliated Hospital of Army Military Medical University, Chongqing, China
| | - Shu-Ying Li
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Army Military Medical University, Chongqing, China
| | - Hua Hu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Army Military Medical University, Chongqing, China
| | - Jian-Yun Zhou
- Clinical Medical Research Center, The Second Affiliated Hospital of Army Military Medical University, Chongqing, China
| | - Ling Wang
- Clinical Medical Research Center, The Second Affiliated Hospital of Army Military Medical University, Chongqing, China
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA
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266
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Longan ER, Fay JC. The distribution of beneficial mutational effects between two sister yeast species poorly explains natural outcomes of vineyard adaptation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597243. [PMID: 38895255 PMCID: PMC11185594 DOI: 10.1101/2024.06.03.597243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Domesticated strains of Saccharomyces cerevisiae have adapted to resist copper and sulfite, two chemical stressors commonly used in winemaking. S. paradoxus, has not adapted to these chemicals despite being consistently present in sympatry with S. cerevisiae in vineyards. This contrast represents a case of apparent evolutionary constraints favoring greater adaptive capacity in S. cerevisiae. In this study, we used a comparative mutagenesis approach to test whether S. paradoxus is mutationally constrained with respect to acquiring greater copper and sulfite resistance. For both species, we assayed the rate, effect size, and pleiotropic costs of resistance mutations and sequenced a subset of 150 mutants isolated from our screen. We found that the distributions of mutational effects displayed by the two species were very similar and poorly explained the natural pattern. We also found that chromosome VIII aneuploidy and loss of function mutations in PMA1 confer copper resistance in both species, whereas loss of function mutations in REG1 were only a viable route to copper resistance in S. cerevisiae. We also observed a single de novo duplication of the CUP1 gene in S. paradoxus but none in S. cerevisiae. For sulfite, loss of function mutations in RTS1 and KSP1 confer resistance in both species, but mutations in RTS1 have larger average effects in S. paradoxus. Our results show that even when the distributions of mutational effects are largely similar, species can differ in the adaptive paths available to them. They also demonstrate that assays of the distribution of mutational effects may lack predictive insight concerning adaptive outcomes.
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Affiliation(s)
- Emery R. Longan
- University of Rochester, Department of Biology, Rochester, NY, 14620 USA
| | - Justin C. Fay
- University of Rochester, Department of Biology, Rochester, NY, 14620 USA
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267
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Baraille M, Buttet M, Grimm P, Milojevic V, Julliand S, Julliand V. Changes of faecal bacterial communities and microbial fibrolytic activity in horses aged from 6 to 30 years old. PLoS One 2024; 19:e0303029. [PMID: 38829841 PMCID: PMC11146703 DOI: 10.1371/journal.pone.0303029] [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] [Received: 01/10/2024] [Accepted: 04/17/2024] [Indexed: 06/05/2024] Open
Abstract
Horse owners and veterinarians report that from the age of 15, their horses can lose body condition and be more susceptible to diseases. Large intestinal microbiome changes may be involved. Indeed, microbiota is crucial for maintaining the condition and health of herbivores by converting fibres into nutrients. This study aimed to compare the faecal microbiome in horses aged from 6 to 30 years old (yo), living in the same environment and consuming the same diet, in order to assess whether the parameters changed linearly with age and whether there was a pivotal age category. Fifty horses were selected from the same environment and distributed across four age categories: 6-10 (n = 12), 11-15 (n = 11), 16-20 (n = 13), and 21-30 (n = 14) yo. All horses had no digestive problems, had teeth suitable for consuming their feed, and were up to date with their vaccination and deworming programmes. After three weeks of constant diet (ad libitum hay and 860 g of concentrate per day), one faecal sample per horse was collected on the same day. The bacterial communities' richness and intra-sample diversity were negatively correlated with age. There was a new distribution of non-beneficial and beneficial taxa, particularly in the 21-30 yo category. Although the faecal concentration of short-chain fatty acids remained stable, the acetate proportion was negatively correlated with age while it was the opposite for the proportions of butyrate, valerate, and iso-valerate. Additionally, the faecal pH was negatively correlated with age. Differences were more pronounced when comparing the 6-10 yo and 21-30 yo categories. The values of the parameters studied became more dispersed from the 16-20 yo category onwards, which appeared as a transitional moment, as it did not differ significantly from the younger and older categories for most of these parameters. Our data suggest that the microbiome changes with age. By highlighting the pivotal age of 16-20, this gives the opportunity to intervene before individuals reach extremes that could lead to pathological conditions.
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Affiliation(s)
- Marylou Baraille
- Institut Agro Dijon, Université de Bourgogne Franche–Comté, PAM UMR A 02.102, Dijon, France
- Lab To Field, Dijon, France
| | | | | | | | | | - Véronique Julliand
- Institut Agro Dijon, Université de Bourgogne Franche–Comté, PAM UMR A 02.102, Dijon, France
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268
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Arron HE, Marsh BD, Kell DB, Khan MA, Jaeger BR, Pretorius E. Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: the biology of a neglected disease. Front Immunol 2024; 15:1386607. [PMID: 38887284 PMCID: PMC11180809 DOI: 10.3389/fimmu.2024.1386607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/11/2024] [Indexed: 06/20/2024] Open
Abstract
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a chronic, debilitating disease characterised by a wide range of symptoms that severely impact all aspects of life. Despite its significant prevalence, ME/CFS remains one of the most understudied and misunderstood conditions in modern medicine. ME/CFS lacks standardised diagnostic criteria owing to variations in both inclusion and exclusion criteria across different diagnostic guidelines, and furthermore, there are currently no effective treatments available. Moving beyond the traditional fragmented perspectives that have limited our understanding and management of the disease, our analysis of current information on ME/CFS represents a significant paradigm shift by synthesising the disease's multifactorial origins into a cohesive model. We discuss how ME/CFS emerges from an intricate web of genetic vulnerabilities and environmental triggers, notably viral infections, leading to a complex series of pathological responses including immune dysregulation, chronic inflammation, gut dysbiosis, and metabolic disturbances. This comprehensive model not only advances our understanding of ME/CFS's pathophysiology but also opens new avenues for research and potential therapeutic strategies. By integrating these disparate elements, our work emphasises the necessity of a holistic approach to diagnosing, researching, and treating ME/CFS, urging the scientific community to reconsider the disease's complexity and the multifaceted approach required for its study and management.
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Affiliation(s)
- Hayley E. Arron
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
| | - Benjamin D. Marsh
- MRCPCH Consultant Paediatric Neurodisability, Exeter, Devon, United Kingdom
| | - Douglas B. Kell
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
- The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - M. Asad Khan
- Directorate of Respiratory Medicine, Manchester University Hospitals, Wythenshawe Hospital, Manchester, United Kingdom
| | - Beate R. Jaeger
- Long COVID department, Clinic St Georg, Bad Aibling, Germany
| | - Etheresia Pretorius
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
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269
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Liu S, Wang S, Zhang N, Li P. The oral microbiome and oral and upper gastrointestinal diseases. J Oral Microbiol 2024; 16:2355823. [PMID: 38835339 PMCID: PMC11149586 DOI: 10.1080/20002297.2024.2355823] [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: 01/16/2024] [Accepted: 05/10/2024] [Indexed: 06/06/2024] Open
Abstract
Background Microbiomes are essential components of the human body, and their populations are substantial. Under normal circumstances, microbiomes coexist harmoniously with the human body, but disturbances in this equilibrium can lead to various diseases. The oral microbiome is involved in the occurrence and development of many oral and gastrointestinal diseases. This review focuses on the relationship between oral microbiomes and oral and upper gastrointestinal diseases, and therapeutic strategies aiming to provide valuable insights for clinical prevention and treatment. Methods To identify relevant studies, we conducted searches in PubMed, Google Scholar, and Web of Science using keywords such as "oral microbiome," "oral flora, " "gastrointestinal disease, " without any date restrictions. Subsequently, the retrieved publications were subject to a narrative review. Results In this review, we found that oral microbiomes are closely related to oral and gastrointestinal diseases such as periodontitis, dental caries, reflux esophagitis, gastritis, and upper gastrointestinal tumors (mainly the malignant ones). Oral samples like saliva and buccal mucosa are not only easy to collect, but also display superior sample stability compared to gastrointestinal tissues. Consequently, analysis of the oral microbiome could potentially serve as an efficient preliminary screening method for high-risk groups before undergoing endoscopic examination. Besides, treatments based on the oral microbiomes could aid early diagnosis and treatment of these diseases. Conclusions Oral microbiomes are essential to oral and gastrointestinal diseases. Therapies centered on the oral microbiomes could facilitate the early detection and management of these conditions.
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Affiliation(s)
- Sifan Liu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University; State Key Laboratory for Digestive Health; National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Shidong Wang
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Nan Zhang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University; State Key Laboratory for Digestive Health; National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Peng Li
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University; State Key Laboratory for Digestive Health; National Clinical Research Center for Digestive Diseases, Beijing, China
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270
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Chen J, Lan H, Li C, Xie Y, Cheng X, Xia R, Ke C, Liang X. Gut microbial signatures of patients with diarrhea-predominant irritable bowel syndrome and their healthy relatives. J Appl Microbiol 2024; 135:lxae118. [PMID: 38849305 DOI: 10.1093/jambio/lxae118] [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: 09/19/2023] [Revised: 04/24/2024] [Accepted: 05/12/2024] [Indexed: 06/09/2024]
Abstract
AIMS Irritable bowel syndrome (IBS) is a prevalent gastrointestinal disorder, encompassing diarrhea-predominant irritable bowel syndrome (IBS-D). Here, we utilized 16S rDNA gene sequencing to identify potential microbial drivers of IBS-D. METHODS AND RESULTS A total of 30 healthy relatives and 27 patients with IBS-D were recruited. Clinical data and fecal samples were collected from patients and controls. 16S rDNA gene sequencing was performed to obtain fecal bacterial data. Differences in community composition were evaluated utilizing analysis of similarity (ANOSIM) using Bray-Curtis dissimilarity. The Wilcoxon rank sum test was used to compare differences in taxa and functional pathways. Finally, the key gut microbiota was identified using the random forest algorithm. Gut microbiota diversity, estimated through the Observe, Chao1, and abundance-based coverage estimator (ACE) indices, was significantly lower in the IBS-D patients than in the healthy relatives. ANOSIM analysis further confirmed significant differences in the composition of the gut microbiota between IBS-D patients and healthy relatives, with an R value of 0.106 and a P-value of 0.005. Notably, the IBS-D patients exhibited a significant enrichment of specific bacterial genera, including Fusicatenibacter, Streptococcus, and Klebsiella, which may possess potential pathogenic properties. In particular, the bacterial genus Klebsiella demonstrated a positive correlation with irritable bowel syndrome severity scoring system scores. Conversely, healthy subjects showed enrichment of bacterial genera such as Alistipes, Akkermansia, and Dialister, which may be beneficial bacteria in IBS-D. Utilizing the random forest model, we developed a discriminative model for IBS-D based on differential bacterial genera. This model exhibited impressive performance, with an area under the curve value of 0.90. Additionally, our analysis did not reveal any gender-specific differences in the microbiota community composition among IBS-D patients. CONCLUSIONS Our findings offer preliminary insights into the potential relationship between intestinal microbiota and IBS-D. The identification model for IBS-D, grounded in gut microbiota, holds promising prospects for improving early diagnosis of IBS-D.
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Affiliation(s)
- Jie Chen
- Department of Gastroenterology, Northern Jiangsu People's Hospital, Yangzhou 225001, China
| | - Haibo Lan
- Department of Constipation, Chengdu Anorectal Hospital, Chengdu 610000, China
| | - Chenmeng Li
- Department of Clinical Laboratory, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen 361003, China
| | - Yongli Xie
- Department of Endocrinology, Pingxiang People's Hospital, Pingxiang 337000, China
| | - Xianhui Cheng
- Xiamen Treatgut Biotechnology Co., Ltd, Xiamen 361101, China
| | - Rongmu Xia
- Xiamen Treatgut Biotechnology Co., Ltd, Xiamen 361101, China
- Department of Gastroenterology, The Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou 350003, China
| | - Chunlin Ke
- Department of Radiotherapy, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Xuyang Liang
- Department of Gastroenterology, The Affiliated Lianyungang Hospital of Xuzhou Medical University/The First People's Hospital of Lianyungang, Lianyungang 222061, China
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271
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Costa Silva A, Pina-Vaz T, Morgado A, Martins-Silva C, Antunes-Lopes T, Alturas Silva J. The Role of the Urobiome in Kidney Transplantation: A Systematic Review. Transplant Direct 2024; 10:e1643. [PMID: 38769976 PMCID: PMC11104728 DOI: 10.1097/txd.0000000000001643] [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: 02/12/2024] [Accepted: 02/29/2024] [Indexed: 05/22/2024] Open
Abstract
Background The urinary microbiome, also known as the urobiome, was traditionally considered sterile. However, emerging evidence suggests its presence in the urinary tract. Urobiome dysbiosis has been associated with various urologic conditions, making it a topic of interest also in kidney transplantation. This systematic review examines the evidence of urobiome changes in kidney transplant recipients (KTRs). Methods Systematic literature searches in the PubMed and SCOPUS databases. Results Of the 770 articles identified, 8 met the inclusion criteria. The urobiome showed reduced diversity in KTRs compared with healthy controls and patients on dialysis. Proteobacteria enrichment was associated with graft stability or spontaneous tolerance in KTRs without immunological events. Kidney interstitial fibrosis and tubular atrophy were associated with changes in resident urinary microbes and increased pathogenic bacteria. Additionally, KTRs with chronic allograft dysfunction had a higher prevalence of Corynebacterium. Conclusions The review highlights the importance of studying the urobiome in KTRs and its potential impact on transplant outcomes. The field remains largely unexplored, and further research is needed to establish consistent study designs and objectives. Future studies could lead to biomarker discovery, personalized therapies, and improved outcomes and graft survival in KTRs.
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Affiliation(s)
- Alberto Costa Silva
- Urology Department, University Hospital Center of São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Teresa Pina-Vaz
- Urology Department, University Hospital Center of São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Afonso Morgado
- Urology Department, University Hospital Center of São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Carlos Martins-Silva
- Urology Department, University Hospital Center of São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Tiago Antunes-Lopes
- Urology Department, University Hospital Center of São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - João Alturas Silva
- Urology Department, University Hospital Center of São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
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Paciência I, Sharma N, Hugg TT, Rantala AK, Heibati B, Al-Delaimy WK, Jaakkola MS, Jaakkola JJ. The Role of Biodiversity in the Development of Asthma and Allergic Sensitization: A State-of-the-Science Review. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:66001. [PMID: 38935403 PMCID: PMC11218706 DOI: 10.1289/ehp13948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 05/06/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Changes in land use and climate change have been reported to reduce biodiversity of both the environment and human microbiota. These reductions in biodiversity may lead to inadequate and unbalanced stimulation of immunoregulatory circuits and, ultimately, to clinical diseases, such as asthma and allergies. OBJECTIVE We summarized available empirical evidence on the role of inner (gut, skin, and airways) and outer (air, soil, natural waters, plants, and animals) layers of biodiversity in the development of asthma, wheezing, and allergic sensitization. METHODS We conducted a systematic search in SciVerse Scopus, PubMed MEDLINE, and Web of Science up to 5 March 2024 to identify relevant human studies assessing the relationships between inner and outer layers of biodiversity and the risk of asthma, wheezing, or allergic sensitization. The protocol was registered in PROSPERO (CRD42022381725). RESULTS A total of 2,419 studies were screened and, after exclusions and a full-text review of 447 studies, 82 studies were included in the comprehensive, final review. Twenty-nine studies reported a protective effect of outer layer biodiversity in the development of asthma, wheezing, or allergic sensitization. There were also 16 studies suggesting an effect of outer layer biodiversity on increasing asthma, wheezing, or allergic sensitization. However, there was no clear evidence on the role of inner layer biodiversity in the development of asthma, wheezing, and allergic sensitization (13 studies reported a protective effect and 15 reported evidence of an increased risk). CONCLUSIONS Based on the reviewed literature, a future systematic review could focus more specifically on outer layer biodiversity and asthma. It is unlikely that association with inner layer biodiversity would have enough evidence for systematic review. Based on this comprehensive review, there is a need for population-based longitudinal studies to identify critical periods of exposure in the life course into adulthood and to better understand mechanisms linking environmental exposures and changes in microbiome composition, diversity, and/or function to development of asthma and allergic sensitization. https://doi.org/10.1289/EHP13948.
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Affiliation(s)
- Inês Paciência
- Center for Environmental and Respiratory Health Research, Population Health, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Needhi Sharma
- University of California, San Diego, San Diego, California, USA
| | - Timo T. Hugg
- Center for Environmental and Respiratory Health Research, Population Health, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Aino K. Rantala
- Center for Environmental and Respiratory Health Research, Population Health, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Behzad Heibati
- Center for Environmental and Respiratory Health Research, Population Health, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | | | - Maritta S. Jaakkola
- Center for Environmental and Respiratory Health Research, Population Health, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Jouni J.K. Jaakkola
- Center for Environmental and Respiratory Health Research, Population Health, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Finnish Meteorological Institute, Helsinki, Finland
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273
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Zhao YJ, Li YM, Yang T, Lu Z. The Janus kinase/signal transducers and activators of transcription (JAK/STAT) pathway contributes to the defense against bacterial infection in the pea aphid. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 202:105915. [PMID: 38879296 DOI: 10.1016/j.pestbp.2024.105915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 04/03/2024] [Accepted: 04/14/2024] [Indexed: 06/29/2024]
Abstract
The Janus kinase/signal transducers and activators of transcription (JAK/STAT) signaling is activated by infections of bacteria, fungi, viruses and parasites and mediated cellular and humoral immune responses. In the pea aphid Acyrthosiphon pisum little is known about the function of JAK/STAT signaling in its immune system. In this study, we first showed that expression of genes in the JAK/STAT signaling, including the receptors Domeless1/2, Janus kinase (JAK) and transcriptional factor Stat92E, is up-regulated upon bacteria Escherichia coli and Staphylococcus aureus and fungus Beauveria bassiana infections. After knockdown of expression of these genes by means of dsRNA injection, the aphids harbored more bacteria and suffered more death after infected with E. coli and S. aureus, but showed no significant change after B. bassiana infection. Our study suggests the JAK/STAT signaling contributes to the defense against bacterial infection in the pea aphid.
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Affiliation(s)
- Yu-Jie Zhao
- College of Plant Protection, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yue-Ming Li
- College of Plant Protection, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ting Yang
- College of Plant Protection, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhiqiang Lu
- College of Plant Protection, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi 712100, China.
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274
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Contreras-Rodriguez O, Blasco G, Biarnés C, Puig J, Arnoriaga-Rodríguez M, Coll-Martinez C, Gich J, Ramió-Torrentà L, Motger-Albertí A, Pérez-Brocal V, Moya A, Radua J, Manuel Fernández-Real J. Unraveling the gut-brain connection: The association of microbiota-linked structural brain biomarkers with behavior and mental health. Psychiatry Clin Neurosci 2024; 78:339-346. [PMID: 38421082 DOI: 10.1111/pcn.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 03/02/2024]
Abstract
AIM The gut microbiota can influence human behavior. However, due to the massive multiple-testing problem, research into the relationship between microbiome ecosystems and the human brain faces drawbacks. This problem arises when attempting to correlate thousands of gut bacteria with thousands of brain voxels. METHODS We performed brain magnetic resonance imaging (MRI) scans on 133 participants and applied machine-learning algorithms (Ridge regressions) combined with permutation tests. Using this approach, we were able to correlate specific gut bacterial families with brain MRI signals, circumventing the difficulties of massive multiple testing while considering sex, age, and body mass index as confounding factors. RESULTS The relative abundance (RA) of the Selenomonadaceae, Clostridiaceae, and Veillonellaceae families in the gut was associated with altered cerebellar, visual, and frontal T2-mapping and diffusion tensor imaging measures. Conversely, decreased relative abundance of the Eubacteriaceae family was also linked to T2-mapping values in the cerebellum. Significantly, the brain regions associated with the gut microbiome were also correlated with depressive symptoms and attentional deficits. CONCLUSIONS Our analytical strategy offers a promising approach for identifying potential brain biomarkers influenced by gut microbiota. By gathering a deeper understanding of the microbiota-brain connection, we can gain insights into the underlying mechanisms and potentially develop targeted interventions to mitigate the detrimental effects of dysbiosis on brain function and mental health.
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Affiliation(s)
- Oren Contreras-Rodriguez
- Department of Radiology-Medical Imaging (IDI), Girona Biomedical Research Institute (IdIBGi), Dr. Josep Trueta University Hospital, Girona, Spain
- Department of Psychiatry and Legal Medicine, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Health Institute Carlos III (ISCIII), Madrid, Spain
- CIBERSAM, Madrid, Spain
| | - Gerard Blasco
- Department of Radiology-Medical Imaging (IDI), Girona Biomedical Research Institute (IdIBGi), Dr. Josep Trueta University Hospital, Girona, Spain
| | - Carles Biarnés
- Department of Radiology-Medical Imaging (IDI), Girona Biomedical Research Institute (IdIBGi), Dr. Josep Trueta University Hospital, Girona, Spain
| | - Josep Puig
- Radiology Department CDI, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Maria Arnoriaga-Rodríguez
- Department of Diabetes, Endocrinology, and Nutrition (UDEN), Girona Biomedical Research Institute (IdIBGi), Dr. Josep Trueta University Hospital, Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CB06/03/0010), Girona, Spain
| | - Clàudia Coll-Martinez
- Neuroimmunology and Multiple Sclerosis Unit, Department of Neurology, Dr. Josep Trueta University Hospital, Girona, Spain
| | - Jordi Gich
- Neuroimmunology and Multiple Sclerosis Unit, Department of Neurology, Dr. Josep Trueta University Hospital, Girona, Spain
| | - Lluís Ramió-Torrentà
- Neuroimmunology and Multiple Sclerosis Unit, Department of Neurology, Dr. Josep Trueta University Hospital, Girona, Spain
| | - Anna Motger-Albertí
- Department of Diabetes, Endocrinology, and Nutrition (UDEN), Girona Biomedical Research Institute (IdIBGi), Dr. Josep Trueta University Hospital, Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CB06/03/0010), Girona, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Vicente Pérez-Brocal
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), València, Spain
- CIBEResp, Madrid, Spain
| | - Andrés Moya
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), València, Spain
- CIBEResp, Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), The Spanish National Research Council (CSIC-UVEG), The University of Valencia, València, Spain
| | - Joaquim Radua
- Health Institute Carlos III (ISCIII), Madrid, Spain
- CIBERSAM, Madrid, Spain
- Imaging of Mood- and Anxiety-Related Disorders (IMARD) Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Department of Medicine, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - José Manuel Fernández-Real
- Health Institute Carlos III (ISCIII), Madrid, Spain
- Department of Diabetes, Endocrinology, and Nutrition (UDEN), Girona Biomedical Research Institute (IdIBGi), Dr. Josep Trueta University Hospital, Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CB06/03/0010), Girona, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
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275
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Vinayamohan PG, Poelstra J, Cheng TY, Goetz H, Renaud DL, Gomez DE, Habing G. Exploring the effects of transport duration on the fecal microbial communities of surplus dairy calves. J Dairy Sci 2024; 107:3863-3884. [PMID: 38216047 DOI: 10.3168/jds.2023-24002] [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: 07/23/2023] [Accepted: 12/03/2023] [Indexed: 01/14/2024]
Abstract
Transportation significantly affects the health and welfare of surplus dairy calves, largely due to the various stressors and pathogen exposures encountered during the process. Concurrently, an animal's microbiome is known to correlate with its health status, with stress-induced alterations in the microbiota potentially precipitating various diseases. This study aimed to compare the effects of transportation durations of 6, 12, or 16 h on the fecal microbiota in young surplus dairy calves. We used a randomized controlled design in which surplus dairy calves aged 1 to 19 d from 5 commercial dairy farms in Ontario were allocated into 1 of 3 transportation groups (6, 12, and 16 h of continuous transportation). Health assessments were conducted before, immediately after, and for 2 wk following transportation. Fecal samples were collected before, immediately after, and at 24 and 72 h after transportation and subjected to 16S rRNA sequencing. Alpha diversity metrics showed no significant differences between the 3 transportation groups at any of the sampling time points. Although β diversity metrics revealed no clustering by transportation groups, they indicated significant differences across sampling time points within each group. The overall analysis revealed a total of 22 phyla and 353 genera, with Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria being the most abundant phyla. Bacteroides, Escherichia/Shigella, Lactobacillus, Collinsella, and Bifidobacterium were the most abundant genera. The reduction in Fusobacteria abundance before and after transport was significantly larger in the 16-h transportation group when compared with the 6-h transportation group. We also identified several genus-level and amplicon sequence variation-level taxa that displayed significant differences in their abundances across various transportation groups, observed at all sampling time points investigated. This research identifies microbiota changes due to varying transportation durations in surplus dairy calves, providing a broad understanding of the microbial shifts in surplus dairy calves after transportation across varying durations. Although these variations may not directly correlate with overall calf health or indicate dysbiosis, these results emphasize the importance of further investigating transportation practices to enhance calf health and well-being. Further studies are warranted to elucidate the relationship between microbiota and calf health.
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Affiliation(s)
| | - Jelmer Poelstra
- Molecular and Cellular Imaging Center (MCIC), The Ohio State University, Wooster, OH 44691
| | - Ting-Yu Cheng
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210
| | - Hanne Goetz
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada, NIG 2W1
| | - David L Renaud
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada, NIG 2W1
| | - Diego E Gomez
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada, NIG 2W1
| | - Greg Habing
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210.
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276
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Paul B, Han Q, Xie L, Rashwan AK, Yahia ZO, Liu Q, Liu S, Xu Y, Chen W. Development and evaluation of guar gum-coated nano-nutriosomes for cyanidin-3-O-glucoside encapsulation. Int J Biol Macromol 2024; 271:132537. [PMID: 38821806 DOI: 10.1016/j.ijbiomac.2024.132537] [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: 01/27/2024] [Revised: 05/13/2024] [Accepted: 05/19/2024] [Indexed: 06/02/2024]
Abstract
Cyanidin-3-O-glucoside (C3G) is a type of water-soluble flavonoid compound that is abundantly found in fruits and vegetables. C3G possesses numerous biological activities, however, it is prone to breakdown under environmental conditions. To overcome these issues, we developed nano-nutriosome (NS) carriers created by vortex-mixing and probe-sonication techniques for C3G encapsulation in which the phospholipid and Nutriose® FB06 were chosen as carrier material, and guar gum (GG) as a coating material to formulate a unilamellar and multicompartment structure. This study aimed to develop and evaluate C3G-loaded nano-nutriosomes coated by GG (GG-C3G-NS) for improving physicochemical stability, antioxidant activity, cellular uptake, and controlled release properties. The C3G-NS and GG-C3G-NS are nanosized (143.47 to 154.13 nm), with high encapsulation efficiency (>93.31 %). The NS carriers successfully encapsulated C3G which was confirmed by transmission electron microscopy, differential scanning calorimetry, and Fourier transform infrared spectroscopy. C3G showed more stability in storage, thermal, pH, ionic, and oxidative conditions. Furthermore, the NS exhibited a better-controlled release of C3G in different food stimulant conditions and in vitro release study. Additionally, NS systems enhanced cellular uptake and showed no cytotoxicity. Overall, GG-NS could be a promising nanocarrier for improving the stability, controlled release, and antioxidant activity of bioactive compounds.
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Affiliation(s)
- Bolai Paul
- Department of Traditional Chinese Medicine, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China; Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Qiang Han
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Lianghua Xie
- Department of Traditional Chinese Medicine, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China; Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Ahmed K Rashwan
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Zineb Ould Yahia
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Qingying Liu
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Shiyu Liu
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Yang Xu
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Wei Chen
- Department of Traditional Chinese Medicine, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China; Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.
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277
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Cuevas-Zuviria B, Fraile A, García-Arenal F. An Agent-Based Model Shows How Mixed Infections Drive Multiyear Pathotype Dynamics in a Plant-Virus System. PHYTOPATHOLOGY 2024; 114:1276-1288. [PMID: 38330173 DOI: 10.1094/phyto-06-23-0214-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Mathematical models are widely used to understand the evolution and epidemiology of plant pathogens under a variety of scenarios. Here, we used this approach to analyze the effects of different traits intrinsic and extrinsic to plant-virus interactions on the dynamics of virus pathotypes in genetically heterogeneous plant-virus systems. For this, we propose an agent-based epidemiological model that includes epidemiologically significant pathogen life-history traits related to virulence, transmission, and survival in the environment and allows for integrating long- and short-distance transmission, primary and secondary infections, and within-host pathogen competition in mixed infections. The study focuses on the tobamovirus-pepper pathosystem. Model simulations allowed us to integrate pleiotropic effects of resistance-breaking mutations on different virus life-history traits into the net costs of resistance breaking, allowing for predictions on multiyear pathotype dynamics. We also explored the effects of two control measures, the use of host resistance and roguing of symptomatic plants, that modify epidemiological attributes of the pathogens to understand how their populations will respond to evolutionary pressures. One major conclusion points to the importance of pathogen competition within mixed-infected hosts as a component of the overall fitness of each pathogen that, thus, drives their multiyear dynamics.
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Affiliation(s)
- Bruno Cuevas-Zuviria
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
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278
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Geng J, Zhang W, Liang S, Xue N, Song W, Yang Y. Diversity and biogeography of bacterial community in the Ili River network varies locally and regionally. WATER RESEARCH 2024; 256:121561. [PMID: 38581986 DOI: 10.1016/j.watres.2024.121561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/28/2024] [Accepted: 03/30/2024] [Indexed: 04/08/2024]
Abstract
Microorganisms in rivers indeed play a crucial role in nutrient cycling within aquatic ecosystems. Understanding the assembly mechanisms of bacterial communities in river networks is essential for predicting their special composition and functional characteristics in natural rivers. This study employed 16S rRNA gene amplicon sequence variation (ASVs) to scrutinize the bacterial community within the uniquely topographical Ili River network. The bacterial community composition varied across the three tributaries with distinct sources and the mainstream. The confluence of various sources diminished the diversity of the bacterial community and altered the functionality of within mainstream. We suggest that strong dispersal limitation predominantly shaped the community at the regional scale (46.6 %), underscoring the significant contribution of headwater sites to bacterial community composition. Contrary to expectation, the bacterial resources in the mainstream were not enriched by the higher diversity in three tributaries. Instead, confluence disturbance potentially increased the undominated processes (36.7 %) and alter the bacterial community composition at the local scale of the mainstream. The intricate coalescence at the confluence could potentially be an intriguing causative factor. Our research indicates that the composition of bacterial communities within intricate river networks exhibits biogeographic patterns, simultaneously influenced by river confluence and geographical features, necessitating multi-scale analysis.
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Affiliation(s)
- Jun Geng
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, China
| | - Weihong Zhang
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, China
| | - Shuxin Liang
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; School of Ecology and Environment, Tibet University, Lhasa 850000, China
| | - Nana Xue
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi 830052, China
| | - Wenjuan Song
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083, China; Xinjiang Laboratory of Environmental Pollution and Ecological Remediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China.
| | - Yuyi Yang
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, China.
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279
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Martínez-García MÁ, Quintero-Tobar A, de Lope Quiñones S, Insenser M, Fernández-Durán E, Escobar-Morreale HF, Luque-Ramírez M. Obesity and polycystic ovary syndrome influence on intestinal permeability at fasting, and modify the effect of diverse macronutrients on the gut barrier. Food Res Int 2024; 186:114338. [PMID: 38729719 DOI: 10.1016/j.foodres.2024.114338] [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: 09/20/2023] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024]
Abstract
Women with the extremely prevalent polycystic ovary syndromegather multiple cardiovascular risk factors and chronic subclinical inflammation. Interactions between diet, adiposity, and gut microbiota modulate intestinal permeabilityand bacterial product translocation, and may contribute to the chronic inflammation process associated with the polycystic ovary syndrome. In the present study, we aimed to address the effects of obesity, functional hyperandrogenism, and diverse oral macronutrients on intestinal permeabilityby measuring circulating markers of gut barrier dysfunction and endotoxemia. Participants included 17 non-hyperandrogenic control women, 17 women with polycystic ovary syndrome, and 19 men that were submitted to glucose, lipid, and protein oral loads. Lipopolysaccharide-binding protein, plasma soluble CD14, succinate, zonulin family peptide, and glucagon-like peptide-2 were determined at fasting and after oral challenges. Macronutrient challenges induced diverse changes on circulating intestinal permeabilitybiomarkers in the acute postprancial period, with lipids and proteins showing the most unfavorable and favorable effects, respectively. Particularly, lipopolysaccharide-binding protein, zonulin family peptide, and glucagon-like peptide-2 responses were deregulated by the presence of obesity after glucose and lipid challenges. Obese subjects showed higher fasting intestinal permeabilitybiomarkers levels than non-obese individuals, except for plasma soluble CD14. The polycystic ovary syndromeexacerbated the effect of obesity further increasing fasting glucagon-like peptide-2, lipopolysaccharide-binding protein, and succinate concentrations. We observed specific interactions of the polycystic ovary syndromewith obesity in the postprandial response of succinate, zonulin family peptide, and glucagon-like peptide-2. In summary, obesity and polycystic ovary syndromemodify the effect of diverse macronutrients on the gut barrier, and alsoinfluence intestinal permeabilityat fasting,contributing to the morbidity of functional hyperandrogenism by inducing endotoxemia and subclinical chronic inflammation.
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Affiliation(s)
- M Ángeles Martínez-García
- Diabetes, Obesity and Human Reproduction Research Group, Department of Endocrinology & Nutrition, Hospital Universitario Ramón y Cajal & Universidad de Alcalá & Instituto Ramón y Cajal de Investigación Sanitaria IRYCIS & Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas CIBERDEM, Madrid, Spain
| | - Alejandra Quintero-Tobar
- Diabetes, Obesity and Human Reproduction Research Group, Department of Endocrinology & Nutrition, Hospital Universitario Ramón y Cajal & Universidad de Alcalá & Instituto Ramón y Cajal de Investigación Sanitaria IRYCIS & Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas CIBERDEM, Madrid, Spain
| | - Sara de Lope Quiñones
- Diabetes, Obesity and Human Reproduction Research Group, Department of Endocrinology & Nutrition, Hospital Universitario Ramón y Cajal & Universidad de Alcalá & Instituto Ramón y Cajal de Investigación Sanitaria IRYCIS & Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas CIBERDEM, Madrid, Spain
| | - María Insenser
- Diabetes, Obesity and Human Reproduction Research Group, Department of Endocrinology & Nutrition, Hospital Universitario Ramón y Cajal & Universidad de Alcalá & Instituto Ramón y Cajal de Investigación Sanitaria IRYCIS & Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas CIBERDEM, Madrid, Spain
| | - Elena Fernández-Durán
- Diabetes, Obesity and Human Reproduction Research Group, Department of Endocrinology & Nutrition, Hospital Universitario Ramón y Cajal & Universidad de Alcalá & Instituto Ramón y Cajal de Investigación Sanitaria IRYCIS & Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas CIBERDEM, Madrid, Spain
| | - Héctor Francisco Escobar-Morreale
- Diabetes, Obesity and Human Reproduction Research Group, Department of Endocrinology & Nutrition, Hospital Universitario Ramón y Cajal & Universidad de Alcalá & Instituto Ramón y Cajal de Investigación Sanitaria IRYCIS & Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas CIBERDEM, Madrid, Spain
| | - Manuel Luque-Ramírez
- Diabetes, Obesity and Human Reproduction Research Group, Department of Endocrinology & Nutrition, Hospital Universitario Ramón y Cajal & Universidad de Alcalá & Instituto Ramón y Cajal de Investigación Sanitaria IRYCIS & Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas CIBERDEM, Madrid, Spain.
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280
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Kamal H, Zafar MM, Razzaq A, Parvaiz A, Ercisli S, Qiao F, Jiang X. Functional role of geminivirus encoded proteins in the host: Past and present. Biotechnol J 2024; 19:e2300736. [PMID: 38900041 DOI: 10.1002/biot.202300736] [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: 12/26/2023] [Revised: 03/19/2024] [Accepted: 04/16/2024] [Indexed: 06/21/2024]
Abstract
During plant-pathogen interaction, plant exhibits a strong defense system utilizing diverse groups of proteins to suppress the infection and subsequent establishment of the pathogen. However, in response, pathogens trigger an anti-silencing mechanism to overcome the host defense machinery. Among plant viruses, geminiviruses are the second largest virus family with a worldwide distribution and continue to be production constraints to food, feed, and fiber crops. These viruses are spread by a diverse group of insects, predominantly by whiteflies, and are characterized by a single-stranded DNA (ssDNA) genome coding for four to eight proteins that facilitate viral infection. The most effective means to managing these viruses is through an integrated disease management strategy that includes virus-resistant cultivars, vector management, and cultural practices. Dynamic changes in this virus family enable the species to manipulate their genome organization to respond to external changes in the environment. Therefore, the evolutionary nature of geminiviruses leads to new and novel approaches for developing virus-resistant cultivars and it is essential to study molecular ecology and evolution of geminiviruses. This review summarizes the multifunctionality of each geminivirus-encoded protein. These protein-based interactions trigger the abrupt changes in the host methyl cycle and signaling pathways that turn over protein normal production and impair the plant antiviral defense system. Studying these geminivirus interactions localized at cytoplasm-nucleus could reveal a more clear picture of host-pathogen relation. Data collected from this antagonistic relationship among geminivirus, vector, and its host, will provide extensive knowledge on their virulence mode and diversity with climate change.
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Affiliation(s)
- Hira Kamal
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Muhammad Mubashar Zafar
- Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
| | - Abdul Razzaq
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Aqsa Parvaiz
- Department of Biochemistry and Biotechnology, The Women University Multan, Multan, Pakistan
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Fei Qiao
- Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
| | - Xuefei Jiang
- Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
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281
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Navaratna TA, Alansari N, Eisenberg AR, O'Malley MA. Anaerobic fungi contain abundant, diverse, and transcriptionally active Long Terminal Repeat retrotransposons. Fungal Genet Biol 2024; 172:103897. [PMID: 38750926 DOI: 10.1016/j.fgb.2024.103897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/14/2024] [Accepted: 05/10/2024] [Indexed: 05/20/2024]
Abstract
Long Terminal Repeat (LTR) retrotransposons are a class of repetitive elements that are widespread in the genomes of plants and many fungi. LTR retrotransposons have been associated with rapidly evolving gene clusters in plants and virulence factor transfer in fungal-plant parasite-host interactions. We report here the abundance and transcriptional activity of LTR retrotransposons across several species of the early-branching Neocallimastigomycota, otherwise known as the anaerobic gut fungi (AGF). The ubiquity of LTR retrotransposons in these genomes suggests key evolutionary roles in these rumen-dwelling biomass degraders, whose genomes also contain many enzymes that are horizontally transferred from other rumen-dwelling prokaryotes. Up to 10% of anaerobic fungal genomes consist of LTR retrotransposons, and the mapping of sequences from LTR retrotransposons to transcriptomes shows that the majority of clusters are transcribed, with some exhibiting expression greater than 104 reads per kilobase million mapped reads (rpkm). Many LTR retrotransposons are strongly differentially expressed upon heat stress during fungal cultivation, with several exhibiting a nearly three-log10 fold increase in expression, whereas growth substrate variation modulated transcription to a lesser extent. We show that some LTR retrotransposons contain carbohydrate-active enzymes (CAZymes), and the expansion of CAZymes within genomes and among anaerobic fungal species may be linked to retrotransposon activity. We further discuss how these widespread sequences may be a source of promoters and other parts towards the bioengineering of anaerobic fungi.
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Affiliation(s)
- Tejas A Navaratna
- Department of Chemical Engineering, UC Santa Barbara, United States; California NanoSystems Institute, United States
| | - Nabil Alansari
- Department of Chemical Engineering, UC Santa Barbara, United States
| | - Amy R Eisenberg
- Department of Chemical Engineering, UC Santa Barbara, United States; California NanoSystems Institute, United States
| | - Michelle A O'Malley
- Department of Chemical Engineering, UC Santa Barbara, United States; California NanoSystems Institute, United States; Department of Bioengineering, UC Santa Barbara, United States.
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282
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Penteado AB, de Oliveira Ribeiro G, Lima Araújo EL, Kato RB, de Melo Freire CC, de Araújo JMG, da Luz Wallau G, Salvato RS, de Jesus R, Bosco GG, Franz HF, da Silva PEA, de Souza Leal E, Goulart Trossini GH, de Lima Neto DF. Binding Evolution of the Dengue Virus Envelope Against DC-SIGN: A Combined Approach of Phylogenetics and Molecular Dynamics Analyses Over 30 Years of Dengue Virus in Brazil. J Mol Biol 2024; 436:168577. [PMID: 38642883 DOI: 10.1016/j.jmb.2024.168577] [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: 01/09/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
The Red Queen Hypothesis (RQH), derived from Lewis Carroll's "Through the Looking-Glass", postulates that organisms must continually adapt in response to each other to maintain relative fitness. Within the context of host-pathogen interactions, the RQH implies an evolutionary arms race, wherein viruses evolve to exploit hosts and hosts evolve to resist viral invasion. This study delves into the dynamics of the RQH in the context of virus-cell interactions, specifically focusing on virus receptors and cell receptors. We observed multiple virus-host systems and noted patterns of co-evolution. As viruses evolved receptor-binding proteins to effectively engage with cell receptors, cells countered by altering their receptor genes. This ongoing mutual adaptation cycle has influenced the molecular intricacies of receptor-ligand interactions. Our data supports the RQH as a driving force behind the diversification and specialization of both viral and host cell receptors. Understanding this co-evolutionary dance offers insights into the unpredictability of emerging viral diseases and potential therapeutic interventions. Future research is crucial to dissect the nuanced molecular changes and the broader ecological consequences of this ever-evolving battle. Here, we combine phylogenetic inferences, structural modeling, and molecular dynamics analyses to describe the epidemiological characteristics of major Brazilian DENV strains that circulated from 1990 to 2022 from a combined perspective, thus providing us with a more detailed picture on the dynamics of such interactions over time.
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MESH Headings
- Dengue Virus/genetics
- Dengue Virus/metabolism
- Receptors, Cell Surface/metabolism
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/chemistry
- Phylogeny
- Molecular Dynamics Simulation
- Humans
- Cell Adhesion Molecules/metabolism
- Cell Adhesion Molecules/genetics
- Cell Adhesion Molecules/chemistry
- Brazil
- Lectins, C-Type/metabolism
- Lectins, C-Type/genetics
- Lectins, C-Type/chemistry
- Evolution, Molecular
- Dengue/virology
- Host-Pathogen Interactions/genetics
- Protein Binding
- Viral Envelope/metabolism
- Receptors, Virus/metabolism
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Viral Envelope Proteins/genetics
- Viral Envelope Proteins/metabolism
- Viral Envelope Proteins/chemistry
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Affiliation(s)
- André Berndt Penteado
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil
| | - Geovani de Oliveira Ribeiro
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil; Department of Cellular Biology, University of Brasilia (UNB), Brasilia, Distrito Federal, Brazil
| | - Emerson Luiz Lima Araújo
- General Coordination of Attention to Communicable Diseases in Primary Care of the Department of Comprehensive Care Management of the Secretariat of Primary Health Care of the Ministry of Health (CDTAP/DGCI/SAPS-MS), Brazil
| | - Rodrigo Bentes Kato
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Caio Cesar de Melo Freire
- Department of Genetics and Evolution, Centre of Biological and Health Sciences, Federal University of Sao Carlos, PO Box 676, Washington Luis Road, km 235, São Carlos, SP 13565-905, Brazil
| | - Joselio Maria Galvão de Araújo
- Federal University of Rio Grande do Norte, Biosciences Center, Department of Microbiology and Parasitology, Campus Universitário, S/N Lagoa Nova 59078900, Natal, RN, Brazil
| | - Gabriel da Luz Wallau
- Department of Entomology and Bioinformatics Center of the Aggeu Magalhães Institute - FIOCRUZ - IAM, Brazil
| | - Richard Steiner Salvato
- Center for Scientific and Technological Development, State Center for Health Surveillance of Rio Grande do Sul, State Department of Health of Rio Grande do Sul, Porto Alegre, Brazil
| | - Ronaldo de Jesus
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Geraldine Goés Bosco
- University of São Paulo, Faculty of Philosophy Sciences and Letters of Ribeirão Preto. Av. Bandeirantes, 3900 Ribeirão Preto, SP, Brazil
| | - Helena Ferreira Franz
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Pedro Eduardo Almeida da Silva
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Elcio de Souza Leal
- Federal University of Pará, Faculty of Biotechnology, Institute of Biological Sciences, Rua Augusto Corrêa, Guamá, 04039-032 Belem, PA, Brazil
| | - Gustavo Henrique Goulart Trossini
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil
| | - Daniel Ferreira de Lima Neto
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil.
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283
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Tawfeeq MT, Voordeckers K, van den Berg P, Govers SK, Michiels J, Verstrepen KJ. Mutational robustness and the role of buffer genes in evolvability. EMBO J 2024; 43:2294-2307. [PMID: 38719995 PMCID: PMC11183146 DOI: 10.1038/s44318-024-00109-1] [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: 11/08/2023] [Revised: 03/19/2024] [Accepted: 04/17/2024] [Indexed: 06/19/2024] Open
Abstract
Organisms rely on mutations to fuel adaptive evolution. However, many mutations impose a negative effect on fitness. Cells may have therefore evolved mechanisms that affect the phenotypic effects of mutations, thus conferring mutational robustness. Specifically, so-called buffer genes are hypothesized to interact directly or indirectly with genetic variation and reduce its effect on fitness. Environmental or genetic perturbations can change the interaction between buffer genes and genetic variation, thereby unmasking the genetic variation's phenotypic effects and thus providing a source of variation for natural selection to act on. This review provides an overview of our understanding of mutational robustness and buffer genes, with the chaperone gene HSP90 as a key example. It discusses whether buffer genes merely affect standing variation or also interact with de novo mutations, how mutational robustness could influence evolution, and whether mutational robustness might be an evolved trait or rather a mere side-effect of complex genetic interactions.
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Affiliation(s)
- Mohammed T Tawfeeq
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Karin Voordeckers
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Pieter van den Berg
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | - Jan Michiels
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Kevin J Verstrepen
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium.
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284
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Hu Q, Luo J, Cheng F, Wang P, Gong P, Lv X, Wang X, Yang M, Wei P. Spatial profiles of the bacterial microbiota throughout the gastrointestinal tract of dairy goats. Appl Microbiol Biotechnol 2024; 108:356. [PMID: 38822843 PMCID: PMC11144141 DOI: 10.1007/s00253-024-13200-8] [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: 12/29/2023] [Revised: 05/19/2024] [Accepted: 05/22/2024] [Indexed: 06/03/2024]
Abstract
The gastrointestinal tract (GIT) is stationed by a dynamic and complex microbial community with functions in digestion, metabolism, immunomodulation, and reproduction. However, there is relatively little research on the composition and function of microorganisms in different GIT segments in dairy goats. Herein, 80 chyme samples were taken from ten GIT sites of eight Xinong Saanen dairy goats and then analyzed and identified the microbial composition via 16S rRNA V1-V9 amplicon sequencing. A total of 6669 different operational taxonomic units (OTUs) were clustered, and 187 OTUs were shared by ten GIT segments. We observed 264 species belonging to 23 different phyla scattered across ten GITs, with Firmicutes (52.42%) and Bacteroidetes (22.88%) predominating. The results revealed obvious location differences in the composition, diversity, and function of the GIT microbiota. In LEfSe analysis, unidentified_Lachnospiraceae and unidentified_Succinniclassicum were significantly enriched in the four chambers of stomach, with functions in carbohydrate fermentation to compose short-chain fatty acids. Aeriscardovia, Candidatus_Saccharimonas, and Romboutsia were significantly higher in the foregut, playing an important role in synthesizing enzymes, amino acids, and vitamins and immunomodulation. Akkermansia, Bacteroides, and Alistipes were significantly abundant in the hindgut to degrade polysaccharides and oligosaccharides, etc. From rumen to rectum, α-diversity decreased first and then increased, while β-diversity showed the opposite trend. Metabolism was the major function of the GIT microbiome predicted by PICRUSt2, but with variation in target substrates along the regions. In summary, GIT segments play a decisive role in the composition and functions of microorganisms. KEY POINTS: • The jejunum and ileum were harsh for microorganisms to colonize due to the presence of bile acids, enzymes, faster chyme circulation, etc., exhibiting the lowest α-diversity and the highest β-diversity. • Variability in microbial profiles between the three foregut segments was greater than four chambers of stomach and hindgut, with a higher abundance of Firmicutes dominating than others. • Dairy goats dominated a higher abundance of Kiritimatiellaeota than cows, which was reported to be associated with fatty acid synthesis.
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Affiliation(s)
- Qingyong Hu
- Shaanxi Provincial Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, People's Republic of China
| | - Jun Luo
- Shaanxi Provincial Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, People's Republic of China.
| | - Fei Cheng
- Shaanxi Provincial Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, People's Republic of China
| | - Ping Wang
- Shaanxi Provincial Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, People's Republic of China
| | - Ping Gong
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Husbandry Science, Urumqi Xinjiang, 830000, People's Republic of China
| | - Xuefeng Lv
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Husbandry Science, Urumqi Xinjiang, 830000, People's Republic of China
| | - Xinpei Wang
- Shaanxi Provincial Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, People's Republic of China
| | - Min Yang
- Shaanxi Provincial Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, People's Republic of China
| | - Pengbo Wei
- Shaanxi Provincial Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A & F University, Yangling, 712100, People's Republic of China
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285
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Suslov AV, Panas A, Sinelnikov MY, Maslennikov RV, Trishina AS, Zharikova TS, Zharova NV, Kalinin DV, Pontes-Silva A, Zharikov YO. Applied physiology: gut microbiota and antimicrobial therapy. Eur J Appl Physiol 2024; 124:1631-1643. [PMID: 38683402 DOI: 10.1007/s00421-024-05496-1] [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: 02/09/2024] [Accepted: 04/22/2024] [Indexed: 05/01/2024]
Abstract
The gut microbiota plays an important role in maintaining human health and in the pathogenesis of several diseases. Antibiotics are among the most commonly prescribed drugs and have a significant impact on the structure and function of the gut microbiota. The understanding that a healthy gut microbiota prevents the development of many diseases has also led to its consideration as a potential therapeutic target. At the same time, any factor that alters the gut microbiota becomes important in this approach. Exercise and antibacterial therapy have a direct effect on the microbiota. The review reflects the current state of publications on the mechanisms of intestinal bacterial involvement in the pathogenesis of cardiovascular, metabolic, and neurodegenerative diseases. The physiological mechanisms of the influence of physical activity on the composition of the gut microbiota are considered. The mechanisms of the common interface between exercise and antibacterial therapy will be considered using the example of several socially important diseases. The aim of the study is to show the physiological relationship between the effects of exercise and antibiotics on the gut microbiota.
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Affiliation(s)
- Andrey V Suslov
- Russian National Centre of Surgery, Avtsyn Research Institute of Human Morphology, Moscow, 117418, Russia
- Pirogov Russian National Research Medical University (RNRMU), Moscow, 117997, Russia
| | - Alin Panas
- N.V. Sklifosovsky Institute of Clinical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), St. Trubetskaya, 8, Bld. 2, Moscow, 119991, Russia
| | - Mikhail Y Sinelnikov
- Department of Oncology, Radiotherapy and Reconstructive Surgery, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119048, Russia
| | - Roman V Maslennikov
- Department of Internal Medicine, Gastroenterology and Hepatology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119435, Russia
| | - Aleksandra S Trishina
- N.V. Sklifosovsky Institute of Clinical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), St. Trubetskaya, 8, Bld. 2, Moscow, 119991, Russia
| | - Tatyana S Zharikova
- Department of Human Anatomy and Histology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, 125009, Russia
- Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Nataliya V Zharova
- Department of Human Anatomy and Histology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, 125009, Russia
| | - Dmitry V Kalinin
- Pathology Department, A.V. Vishnevsky National Medical Research Center of Surgery, Moscow, 115093, Russia
| | - André Pontes-Silva
- Postgraduate Program in Physical Therapy (PPGFT), Department of Physical Therapy (DFisio), Universidade Federal de São Carlos (UFSCar), São Carlos (SP), Brazil.
| | - Yury O Zharikov
- Department of Human Anatomy and Histology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, 125009, Russia
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286
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García Navas P, Ruíz Del Prado MY, Villoslada Blanco P, Recio Fernández E, Ruíz Del Campo M, Pérez Matute P. Composition of the microbiota in patients with growth hormone deficiency before and after treatment with growth hormone. An Pediatr (Barc) 2024; 100:404-411. [PMID: 38806303 DOI: 10.1016/j.anpede.2024.05.004] [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: 12/05/2023] [Accepted: 03/25/2024] [Indexed: 05/30/2024] Open
Abstract
INTRODUCTION Growth hormone (GH) and insulin-like growth factor-1 (IGF-1) have modulatory effects on bowel function and its microbiota. Our aim was to investigate whether low levels of GH and IGF-1 in patients with GH deficiency are associated with changes in gut physiology/integrity as well as in the composition of the gut microbiota. MATERIALS AND METHODS We conducted a case-control study in 21 patients with GH deficiency, at baseline and after 6 months of GH treatment, and in 20 healthy controls. We analysed changes in anthropometric and laboratory characteristics and bacterial translocation and studied the composition of the microbiome by means of massive 16S rRNA gene sequencing. RESULTS Growth hormone deficiency was accompanied by a significant increase in serum levels of sCD14, a marker of bacterial translocation (P < .01). This increase was reversed by GH treatment. We did not find any differences in the composition or α- or β-diversity of the gut microbiota after treatment or between cases and controls. CONCLUSIONS Our work is the first to demonstrate that the presence of GH deficiency is not associated with differences in gut microbiota composition in comparison with healthy controls, and changes in microbiota composition are also not found after 6 months of treatment. However, GH deficiency and low IGF-1 levels were associated with an increase in bacterial translocation, which had reversed after treatment.
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Affiliation(s)
- Patricia García Navas
- Sección de Endocrinología Infantil, Servicio de Pediatría, Hospital San Pedro, Logroño, La Rioja, Spain.
| | | | - Pablo Villoslada Blanco
- Unidad de Enfermedades Infecciosas, Microbiota y Metabolismo, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, La Rioja, Spain
| | - Emma Recio Fernández
- Unidad de Enfermedades Infecciosas, Microbiota y Metabolismo, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, La Rioja, Spain
| | - María Ruíz Del Campo
- Sección de Endocrinología Infantil, Servicio de Pediatría, Hospital San Pedro, Logroño, La Rioja, Spain
| | - Patricia Pérez Matute
- Unidad de Enfermedades Infecciosas, Microbiota y Metabolismo, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, La Rioja, Spain; Facultad de Ciencias de la Salud de la Universidad de La Rioja, Logroño, La Rioja, Spain
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287
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Zare H, Amiri Ardekani E, Tavakoli A, Bradley R, Tavakoli F, Pasalar M. Reporting of adverse effects of pomegranate in clinical studies: a systematic review. JOURNAL OF COMPLEMENTARY & INTEGRATIVE MEDICINE 2024; 21:154-166. [PMID: 37116077 DOI: 10.1515/jcim-2022-0247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
OBJECTIVES Numerous studies have shown the pharmacological effects of pomegranate, such as: anti-cancer, cholesterol-lowering, anti-diabetic, and antihypertensive features. Pomegranate consumption has also revealed some adverse effects. This systematic review aimed to explore the adverse effects of pomegranate reported in clinical studies. CONTENT The keywords "pomegranate", "Punica granatum", "side effect", "clinical trial", and "case report or case series" were searched for in valid databases. Reports about adverse effects of pomegranate were also collected from several international registries. SUMMARY This systematic review included a total of 66 clinical articles. Eleven articles have reported side effects of pomegranate. Twenty-one articles have recorded no side effects in the pomegranate group while 34 articles have not mentioned any side effects for this plant. The study also included 7 case report studies. The most common side effects included gastrointestinal problems, flu-like symptoms, and urinary problems. In case report studies, the most significant reported side effect was allergic reaction. OUTLOOK In summary, pomegranate and its extract seem to be safe according to the reported adverse effects. Meanwhile, conducting more robust controlled trials with pomegranate products and documentation of any probable side effect is warranted.
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Affiliation(s)
- Hamid Zare
- Department of Traditional Medicine, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ehsan Amiri Ardekani
- Department of Phytopharmaceuticals (Traditional Pharmacy), Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Iranian Association of Indigenous Knowledge, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Tavakoli
- Department of Traditional Medicine, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Research Center for Traditional Medicine and History of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ryan Bradley
- Helfgott Research Institute, National University of Natural Medicine, Portland, USA
| | - Fatemeh Tavakoli
- Research Center for Traditional Medicine and History of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Pasalar
- Research Center for Traditional Medicine and History of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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288
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Jaglan AB, Vashisth M, Sharma P, Verma R, Virmani N, Bera BC, Vaid RK, Singh RK, Anand T. Phage Mediated Biocontrol: A Promising Green Solution for Sustainable Agriculture. Indian J Microbiol 2024; 64:318-327. [PMID: 39011019 PMCID: PMC11246405 DOI: 10.1007/s12088-024-01204-x] [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: 07/21/2023] [Accepted: 01/06/2024] [Indexed: 07/17/2024] Open
Abstract
In the current scenario of growing world population, limited cultivable land resources, plant diseases, and pandemics are some of the major factors responsible for declining global food security. Along with meeting the food demand, the maintenance of food quality is also required to ensure healthy consumption and marketing. In agricultural fields, pest infestations and bacterial diseases are common causes of crop damage, leading to massive yield losses. Conventionally, antibiotics and several pesticides have been used to manage and control these plant pathogens. However, the overuse of antibiotics and pesticides has led to the emergence of resistant strains of pathogenic bacteria. The bacteriophages are the natural predators of bacteria and are host-specific in their action. Therefore, the use of bacteriophages for the biocontrol of pathogenic bacteria is serving as a sustainable and green solution in crop protection and production. In this review, we have discussed the important plant pathogens and their impact on plant health and yield loss. Further, we have abridged the role of bacteriophages in the protection of crops from bacterial disease by discussing various greenhouse and field trials. Finally, we have discussed the impact of bacteriophages on the plant microbiome, phage resistance, and legal challenges in the registration and commercial production of bacteriophage-based biopesticides. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-024-01204-x.
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Affiliation(s)
- Anu Bala Jaglan
- ICAR - National Research Centre on Equines, Hisar, Haryana 125001 India
- Department of Zoology and Aquaculture, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana 125004 India
| | - Medhavi Vashisth
- ICAR - National Research Centre on Equines, Hisar, Haryana 125001 India
| | - Priya Sharma
- ICAR - National Research Centre on Equines, Hisar, Haryana 125001 India
| | - Ravikant Verma
- Department of Zoology and Aquaculture, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana 125004 India
| | - Nitin Virmani
- ICAR - National Research Centre on Equines, Hisar, Haryana 125001 India
| | - Bidhan C Bera
- ICAR - National Research Centre on Equines, Hisar, Haryana 125001 India
| | - Rajesh K Vaid
- ICAR - National Research Centre on Equines, Hisar, Haryana 125001 India
| | - Raj K Singh
- Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122 India
| | - Taruna Anand
- ICAR - National Research Centre on Equines, Hisar, Haryana 125001 India
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289
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Droz JP, Couppié P, Fayette J. [Oncology in French Guiana: A challenge to win]. Bull Cancer 2024; 111:597-607. [PMID: 38749776 DOI: 10.1016/j.bulcan.2024.02.018] [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: 11/30/2023] [Revised: 02/15/2024] [Accepted: 02/22/2024] [Indexed: 06/10/2024]
Abstract
French Guiana is an equatorial, multicultural, overseas territory in South America. The region is unique: a wealthy country with a universal healthcare system, but significant poverty, which bears little resemblance to its neighbors Brazil and Suriname. Cancer is the second leading cause of death. The incidence of cancer is lower than in France, stages are generally more advanced and the prognosis worse. To date, oncology has been organized through a joint venture between local institutions and healthcare professionals and a cancer center in mainland France, in line with the recommendations of the Institut National du Cancer. The implementation of a medical project and a complete medical studies curriculum in French Guiana is a tremendous opportunity for the development of oncology. The main challenges are consolidating medical care for patients, quality control, genetic oncology, molecular biology, implementation of radiotherapy and nuclear medicine, clinical and translational research, and teaching programs. Working in oncology in French Guiana is exciting because of the scientific interest (particular characteristics of cancers, notably the role of viral or micro-organism-induced carcinogenesis, genetic factors in these populations with African and Asian roots, and the importance of a public health policy) and human interest (patients from different cultures; all of them bring original approaches to health and illness that need to be deciphered in order to offer quality care). This requires the support of healthcare professionals who are enthusiastic about this unique adventure.
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Affiliation(s)
- Jean-Pierre Droz
- Université Claude-Bernard Lyon-1, 43, boulevard du 11-Novembre-1918, 69100 Villeurbanne, France.
| | - Pierre Couppié
- Centre hospitalier de Cayenne, rue des Flamboyants, 97306 Cayenne, Guyane française; DFR Santé, université de Guyane, WMMX+5Q3, 97300 Cayenne, Guyane française
| | - Jérôme Fayette
- Centre hospitalier de Cayenne, rue des Flamboyants, 97306 Cayenne, Guyane française; Centre Léon-Bérard, 28, rue Laënnec, 69008 Lyon, France
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290
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Chen XR, Cui YZ, Li BZ, Yuan YJ. Genome engineering on size reduction and complexity simplification: A review. J Adv Res 2024; 60:159-171. [PMID: 37442424 PMCID: PMC11156615 DOI: 10.1016/j.jare.2023.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/25/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Genome simplification is an important topic in the field of life sciences that has attracted attention from its conception to the present day. It can help uncover the essential components of the genome and, in turn, shed light on the underlying operating principles of complex biological systems. This has made it a central focus of both basic and applied research in the life sciences. With the recent advancements in related technologies and our increasing knowledge of the genome, now is an opportune time to delve into this topic. AIM OF REVIEW Our review investigates the progress of genome simplification from two perspectives: genome size reduction and complexity simplification. In addition, we provide insights into the future development trends of genome simplification. KEY SCIENTIFIC CONCEPTS OF REVIEW Reducing genome size requires eliminating non-essential elements as much as possible. This process has been facilitated by advances in genome manipulation and synthesis techniques. However, we still need a better and clearer understanding of living systems to reduce genome complexity. As there is a lack of quantitative and clearly defined standards for this task, we have opted to approach the topic from various perspectives and present our findings accordingly.
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Affiliation(s)
- Xiang-Rong Chen
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
| | - You-Zhi Cui
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China.
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
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291
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Yang F, Li Q, Yin X. Metagenomic analysis of the effects of salinity on microbial community and functional gene diversity in glacial meltwater estuary, Ny-Alesund, Arctic. Braz J Microbiol 2024; 55:1587-1599. [PMID: 38647870 PMCID: PMC11153410 DOI: 10.1007/s42770-024-01298-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 03/05/2024] [Indexed: 04/25/2024] Open
Abstract
Due to the inflow of meltwater from the Midre Lovénbreen glacier upstream of Kongsfjorden, the nutrient concentration of Kongsfjorden change from the estuary to the interior of the fjord. Our objective was to explore the changes in bacterial community structure and metabolism-related genes from the estuary to fjord by metagenomic analysis. Our data indicate that glacial meltwater input has altered the physicochemical properties of the fjords, with a significant effect, in particular, on fjords salinity, thus altering the relative abundance of some specific bacterial groups. In addition, we suggest that the salinity of a fjord is an important factor affecting the abundance of genes associated with the nitrogen and sulfur cycles in the fjord. Changes in salinity may affect the relative abundance of microbial populations that carry metabolic genes, thus affecting the relative abundance of genes associated with the nitrogen and sulfur cycles.
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Affiliation(s)
- Fan Yang
- Management College, Ocean University of China, Qingdao, China
- Business College, Qingdao University, Qingdao, China
| | - Qinxin Li
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, China
| | - Xiaofei Yin
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.
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292
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Chu H, Wang L, Wang J, Zhang Y, Jin N, Liu F, Li Y. Genomic profile of eGFP-tagged senecavirus A subjected to serial plaque-to-plaque transfers. Microb Pathog 2024; 191:106661. [PMID: 38657711 DOI: 10.1016/j.micpath.2024.106661] [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: 03/26/2024] [Revised: 04/14/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024]
Abstract
Senecavirus A (SVA) belongs to the genus Senecavirus in the family Picornaviridae. This virus possesses a positive-sense, single-stranded RNA genome, approximately 7200 nt in length, composed of a single 5' untranslated region, encoding region and 3' untranslated region. In this study, a recombinant SVA tagged with enhanced green fluorescent protein (eGFP) sequence, rSVA-eGFP, was rescued from its cDNA clone using reverse genetics. The passage-5 (P5) rSVA-eGFP was totally subjected to 55 rounds of consecutive fluorescent plaque-to-fluorescent plaque (FP-FP) transfers, and one extra common passaging in vitro. The P61 viral stock was analyzed by next-generation sequencing. The result showed ten single-nucleotide mutations (SNMs) in the rSVA-eGFP genome, including nine transitions and only one transversion. The P61 progeny still showed a complete eGFP sequence, indicating no occurrence of copy-choice recombination within the eGFP region during serial FP-FP transfers. In other words, this progeny was genetically deficient in the recombination of eGFP sequence (RES), namely, an RES-deficient strain. Out of ten SNMs, three were missense mutations, leading to single-amino acid mutations (SAAMs): F15V in L protein, A74T in VP2, and E53R in 3D protein. The E53R was predicted to be spatially adjacent to the RNA channel of 3D protein, perhaps involved in the emergence of RES-deficient strain. In conclusion, this study uncovered a global landscape of rSVA-eGFP genome after serial FP-FP transfers, and moreover shed light on a putative SAAM possibly related to the RES-deficient mechanism.
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Affiliation(s)
- Huanhuan Chu
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China; College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ling Wang
- University Hospital, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jie Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Ningyi Jin
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China; Changchun Institute of Veterinary Medicine, Chinese Academy of Agricultural Sciences, Changchun, 130122, China.
| | - Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Yan Li
- Qingdao Center for Animal Disease Control & Prevention, Qingdao, 266199, China.
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293
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Garrett D, Teakle G, Collier R, Bell JR, Cerezo-Medina S, Morales-Hojas R. Genome assembly and transcriptomic analysis to elucidate the ability of Nasonovia ribisnigri to break host plant resistance. INSECT MOLECULAR BIOLOGY 2024; 33:228-245. [PMID: 38348538 DOI: 10.1111/imb.12894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/09/2024] [Indexed: 02/27/2024]
Abstract
Aphid genomic resources enable the study of complex life history traits and provide information on vector biology, host adaption and speciation. The currant-lettuce aphid (Nasonovia ribisnigri (Hemiptera: Aphididae) (Mosley)) is a cosmopolitan pest of outdoor lettuce (Lactuca sativa (Asterales: Asteraceae) (Linnaeus)). Until recently, the use of resistant cultivars was an effective method for managing N. ribisnigri. A resistant cultivar containing a single gene (Nr-locus), introduced in the 1980s, conferred complete resistance to feeding. Overreliance of this Nr-locus in lettuce resulted in N. ribisnigri's ability to break resistance mechanism, with first reports during 2003. Our work attempts to understand which candidate gene(s) are associated with this resistance-breaking mechanism. We present two de novo draft assembles for N. ribisnigri genomes, corresponding to both avirulent (Nr-locus susceptible) and virulent (Nr-locus resistant) biotypes. Changes in gene expression of the two N. ribisnigri biotypes were investigated using transcriptomic analyses of RNA-sequencing (RNA-seq) data to understand the potential mechanisms of resistance to the Nr-locus in lettuce. The draft genome assemblies were 94.2% and 91.4% complete for the avirulent and virulent biotypes, respectively. Out of the 18,872 differentially expressed genes, a single gene/locus was identified in N. ribisnigri that was shared between two resistant-breaking biotypes. This locus was further explored and validated in Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) experiments and has predicted localisations in both the cytoplasm and nucleus. This is the first study to provide evidence that a single gene/locus is likely responsible for the ability of N. ribisnigri to overcome the Nr-locus resistance in the lettuce host.
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Affiliation(s)
- Dion Garrett
- Rothamsted Insect Survey, Rothamsted Research, Harpenden, UK
- Warwick Crop Centre, Wellesbourne Campus, University of Warwick, Warwick, UK
| | - Graham Teakle
- Warwick Crop Centre, Wellesbourne Campus, University of Warwick, Warwick, UK
| | - Rosemary Collier
- Warwick Crop Centre, Wellesbourne Campus, University of Warwick, Warwick, UK
| | - James R Bell
- Rothamsted Insect Survey, Rothamsted Research, Harpenden, UK
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, UK
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294
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Liu L, Tang W, Wu S, Ma J, Wei K. Pulmonary succinate receptor 1 elevation in high-fat diet mice exacerbates lipopolysaccharides-induced acute lung injury via sensing succinate. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167119. [PMID: 38479484 DOI: 10.1016/j.bbadis.2024.167119] [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: 11/16/2023] [Revised: 02/23/2024] [Accepted: 03/06/2024] [Indexed: 04/05/2024]
Abstract
BACKGROUND Individuals with obesity have higher level of circulating succinate, which acts as a signaling factor that initiates inflammation. It is obscure whether succinate and succinate receptor 1 (SUCNR1) are involved in the process of obesity aggravating acute lung injury (ALI). METHODS The lung tissue and blood samples from patients with obesity who underwent lung wedgectomy or segmental resection were collected. Six-week-old male C57BL/6J mice were fed a high-fat diet for 12 weeks to induce obesity and lipopolysaccharides (LPS) were injected intratracheally (100 μg, 1 mg/ml) for 24 h to establish an ALI model. The pulmonary SUCNR1 expression and succinate level were measured. Exogenous succinate was supplemented to assess whether succinate exacerbated the LPS-induced lung injury. We next examined the cellular localization of pulmonary SUCNR1. Furthermore, the role of the succinate-SUCNR1 pathway in LPS-induced inflammatory responses in MH-s macrophages and obese mice was investigated. RESULT The pulmonary SUCNR1 expression and serum succinate level were significantly increased in patients with obesity and in HFD mice. Exogenous succinate supplementation significantly increased the severity of ALI and inflammatory response. SUCNR1 was mainly expressed on lung macrophages. In LPS-stimulated MH-s cells, knockdown of SUCNR1 expression significantly inhibited pro-inflammatory cytokines' expression, the increase of hypoxia-inducible factor-1α (HIF-1α) expression, inhibitory κB-α (IκB-α) phosphorylation, p65 phosphorylation and p65 translocation to nucleus. In obese mice, SUCNR1 inhibition significantly alleviated LPS-induced lung injury and decreased the HIF-1α expression and IκB-α phosphorylation. CONCLUSION The high expression of pulmonary SUCNR1 and serum succinate accumulation at least partly participate in the process of obesity aggravating LPS-induced lung injury.
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Affiliation(s)
- Ling Liu
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Wenjing Tang
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Siqi Wu
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Jingyue Ma
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Ke Wei
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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295
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Jain A, Jain K, Jhurani D, Mishra A, Mohapatra S, Sharma A, Manchanda V, Sankar MJ, Agarwal R. Umbilical Cord Blood IgA Levels and Bacterial Profile in Preterm Neonates Born with Maternal Risk Factors for Early-Onset Neonatal Sepsis. Indian J Pediatr 2024; 91:541-547. [PMID: 37523074 DOI: 10.1007/s12098-023-04708-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/19/2023] [Indexed: 08/01/2023]
Abstract
OBJECTIVES To investigate the IgA levels and bacterial profile in umbilical cord blood (UCB) samples of mothers with risk factors compared to those without risk factors; and to understand the link between UCB culture positivity and neonatal outcomes [early-onset sepsis (EOS) or death within 7 d of life]. METHODS This is a pilot prospective case-control study. Mothers with preterm deliveries (gestational age <34 wk) were enrolled in two groups- Cases: Those with antenatal risk factors (prolonged duration of rupture of membranes of ≥24 h or chorioamnionitis) and controls: Those without these two risk factors. Serum IgA levels was assayed and microbiological culture was tested in UCB samples. 16S sequencing to determine the UCB microbiome was performed in a subset of samples (n = 15). Neonates were followed-up for the occurrence of EOS or death until 7 d of life. RESULTS Forty-nine mothers as cases and 50 mothers as controls were consecutively enrolled. No significant difference was observed in the IgA levels (60.5 vs. 58.1 mg/L; p = 0.71), neonatal blood culture positivity (4.1% vs. 8.0%; p = 0.41) and UCB culture positivity (30.6% vs. 26.0%; p = 0.61) in the two groups. No difference was observed between the groups in occurrence of EOS or death within 7 d of life. Proteobacteria, Firmicutes and Actinobacteria were the most abundant phyla. Serratia, Bifidobacterium, Collinsella, Meganomas and Blautia being the most common genera. CONCLUSIONS Cord blood IgA concentration could not differentiate the neonates at-risk of infection due to its presence in both the groups.
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Affiliation(s)
- Ashish Jain
- Department of Neonatology, Central Health Service, Maulana Azad Medical College, (University of Delhi), Govt. of India, New Delhi, India
| | - Kajal Jain
- Department of Pediatrics, WHO Collaborating Centre for Education and Research in Newborn Health, Newborn Health Knowledge Centre, All India Institute of Medical Sciences, New Delhi, 110029, India.
| | - Divashree Jhurani
- Department of Pediatrics, WHO Collaborating Centre for Education and Research in Newborn Health, Newborn Health Knowledge Centre, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Asha Mishra
- Department of Gastroenterology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Sarita Mohapatra
- Department of Microbiology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Akash Sharma
- Department of Pediatrics, WHO Collaborating Centre for Education and Research in Newborn Health, Newborn Health Knowledge Centre, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Vikas Manchanda
- Department of Microbiology, Central Health Service, Maulana Azad Medical College, (University of Delhi), Govt. of India, New Delhi, India
| | - M Jeeva Sankar
- Department of Pediatrics, WHO Collaborating Centre for Education and Research in Newborn Health, Newborn Health Knowledge Centre, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Ramesh Agarwal
- Department of Pediatrics, WHO Collaborating Centre for Education and Research in Newborn Health, Newborn Health Knowledge Centre, All India Institute of Medical Sciences, New Delhi, 110029, India
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296
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Barton N, Sachdeva H. Limits to selection on standing variation in an asexual population. Theor Popul Biol 2024; 157:129-137. [PMID: 38643838 DOI: 10.1016/j.tpb.2024.04.001] [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: 05/12/2023] [Revised: 01/23/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024]
Abstract
We consider how a population of N haploid individuals responds to directional selection on standing variation, with no new variation from recombination or mutation. Individuals have trait values z1,…,zN, which are drawn from a distribution ψ; the fitness of individual i is proportional to [Formula: see text] . For illustration, we consider the Laplace and Gaussian distributions, which are parametrised only by the variance V0, and show that for large N, there is a scaling limit which depends on a single parameter NV0. When selection is weak relative to drift (NV0≪1), the variance decreases exponentially at rate 1/N, and the expected ultimate gain in log fitness (scaled by V0), is just NV0, which is the same as Robertson's (1960) prediction for a sexual population. In contrast, when selection is strong relative to drift (NV0≫1), the ultimate gain can be found by approximating the establishment of alleles by a branching process in which each allele competes independently with the population mean and the fittest allele to establish is certain to fix. Then, if the probability of survival to time t∼1/V0 of an allele with value z is P(z), with mean P¯, the winning allele is the fittest of NP¯ survivors drawn from a distribution ψP/P¯. The expected ultimate change is ∼2log(1.15NV0) for a Gaussian distribution, and ∼-12log0.36NV0-log-log0.36NV0 for a Laplace distribution. This approach also predicts the variability of the process, and its dynamics; we show that in the strong selection regime, the expected genetic variance decreases as ∼t-3 at large times. We discuss how these results may be related to selection on standing variation that is spread along a linear chromosome.
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Affiliation(s)
- Nick Barton
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria.
| | - Himani Sachdeva
- Department of Mathematics, University of Vienna, Vienna 1090, Austria
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297
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Sahle Z, Engidaye G, Shenkute Gebreyes D, Adenew B, Abebe TA. Fecal microbiota transplantation and next-generation therapies: A review on targeting dysbiosis in metabolic disorders and beyond. SAGE Open Med 2024; 12:20503121241257486. [PMID: 38826830 PMCID: PMC11143861 DOI: 10.1177/20503121241257486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 05/09/2024] [Indexed: 06/04/2024] Open
Abstract
The human microbiome, particularly the gut microbiome, has emerged as a central determinant of health and disease. Dysbiosis, an imbalance in the microbial composition of the gut, is associated with a variety of metabolic and other diseases, highlighting the potential for microbiota-targeted treatments. Fecal microbiota transplantation has received considerable attention as a promising therapy to modulate the gut microbiome and restore microbial homeostasis. However, challenges remain, including standardization, safety, and long-term efficacy. This review summarizes current knowledge on fecal microbiota transplantation and describes the next generation therapies targeting microbiome. This review looked at the mechanistic understanding of fecal microbiota transplantation and alternative strategies, elucidating their potential role in improving dysbiosis-associated metabolic disorders, such as obesity, and type 2 diabetes and others. Additionally, this review discussed the growing application of therapies targeting the gut microbiome. Insights from clinical trials, preclinical studies, and emerging technologies provide a comprehensive overview of the evolving landscape of microbiome-based interventions. Through a critical assessment of current advances and prospects, this review aims to highlight the therapeutic potential of targeting gut microbiome and pave the way for innovative approaches in precision medicine and personalized treatments.
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Affiliation(s)
- Zenawork Sahle
- Department of Medical Laboratory Science, Asrat Weldeyes Health Science Campus, Debre Berhan University, Debre Berhan, Ethiopia
| | - Getabalew Engidaye
- Department of Medical Laboratory Science, Asrat Weldeyes Health Science Campus, Debre Berhan University, Debre Berhan, Ethiopia
| | - Demissew Shenkute Gebreyes
- Department of Medical Laboratory Science, Asrat Weldeyes Health Science Campus, Debre Berhan University, Debre Berhan, Ethiopia
| | - Behailu Adenew
- Department of Medical Laboratory Science, Debre Berhan Compressive Specialized Hospital, Debre Berhan, Ethiopia
| | - Tsegahun Asfaw Abebe
- Department of Medical Laboratory Science, Asrat Weldeyes Health Science Campus, Debre Berhan University, Debre Berhan, Ethiopia
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298
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Otaru N, Kourouma L, Pugin B, Constancias F, Braegger C, Mansuy IM, Lacroix C. Transgenerational effects of early life stress on the fecal microbiota in mice. Commun Biol 2024; 7:670. [PMID: 38822061 PMCID: PMC11143345 DOI: 10.1038/s42003-024-06279-2] [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: 11/09/2023] [Accepted: 05/02/2024] [Indexed: 06/02/2024] Open
Abstract
Stress in early life can affect the progeny and increase the risk to develop psychiatric and cardiometabolic diseases across generations. The cross-generational effects of early life stress have been modeled in mice and demonstrated to be associated with epigenetic factors in the germline. While stress is known to affect gut microbial features, whether its effects can persist across life and be passed to the progeny is not well defined. Here we show that early postnatal stress in mice shifts the fecal microbial composition (binary Jaccard index) throughout life, including abundance of eight amplicon sequencing variants (ASVs). Further effects on fecal microbial composition, structure (weighted Jaccard index), and abundance of 16 ASVs are detected in the progeny across two generations. These effects are not accompanied by changes in bacterial metabolites in any generation. These results suggest that changes in the fecal microbial community induced by early life traumatic stress can be perpetuated from exposed parent to the offspring.
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Affiliation(s)
- Nize Otaru
- Nutrition Research Unit, University Children's Hospital Zürich, Zürich, Switzerland
- Department of Health Sciences and Technology, Laboratory of Food Biotechnology, ETH Zürich, Zürich, Switzerland
| | - Lola Kourouma
- Department of Health Science and Technology of the ETH Zurich, Laboratory of Neuroepigenetics, Brain Research Institute, Medical Faculty of the University of Zurich, and Institute for Neuroscience, Zurich, Switzerland
- Center for Neuroscience Zürich, ETH and University Zürich, Zurich, Switzerland
| | - Benoit Pugin
- Department of Health Sciences and Technology, Laboratory of Food Biotechnology, ETH Zürich, Zürich, Switzerland
| | - Florentin Constancias
- Department of Health Sciences and Technology, Laboratory of Food Biotechnology, ETH Zürich, Zürich, Switzerland
| | - Christian Braegger
- Nutrition Research Unit, University Children's Hospital Zürich, Zürich, Switzerland
| | - Isabelle M Mansuy
- Department of Health Science and Technology of the ETH Zurich, Laboratory of Neuroepigenetics, Brain Research Institute, Medical Faculty of the University of Zurich, and Institute for Neuroscience, Zurich, Switzerland.
- Center for Neuroscience Zürich, ETH and University Zürich, Zurich, Switzerland.
| | - Christophe Lacroix
- Department of Health Sciences and Technology, Laboratory of Food Biotechnology, ETH Zürich, Zürich, Switzerland.
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299
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Liu Y, Fu X, Wang Y, Liu J, Liu Y, Li C, Dong J. Exploring Barbronia species diversity and phylogenetic relationship within Suborder Erpobdelliformes (Clitellata: Annelida). PeerJ 2024; 12:e17480. [PMID: 38827288 PMCID: PMC11144392 DOI: 10.7717/peerj.17480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/07/2024] [Indexed: 06/04/2024] Open
Abstract
Background Barbronia, a genus of freshwater macrophagous leeches, belongs to Erpobdelliformes (Salifidae: Clitellata: Annelida), and B. weberi, a well-known leech within this genus, has a worldwide distribution. However, the systematics of Barbronia have not yet been adequately investigated, primarily due to a few molecular markers, and only 20 Barbronia sequences available in the GenBank database. This gap significantly limits our understanding of the Barbronia species identification, as well as the phylogenetic placement of the genus Barbronia within Salifidae. Methods Next-generation sequencing (NGS) was used to simultaneously capture the entire mitochondrial genome and the full-length 18S/28S rDNA sequences. The species boundary of Barbronia species was estimated using bGMYC and bPTP methods, based on all available Barbronia COI sequences. Uncorrected COI p-distance was calculated in MEGA. A molecular data matrix consisting of four loci (COI, 12S, 18S, and 28S rDNA) for outgroups (three Haemopis leeches) and 49 erpobdellid leeches, representing eight genera within the Suborder Erpobdelliformes was aligned using MAFFT and LocARNA. This matrix was used to reconstruct the phylogenetic relationship of Barbronia via Bayesian inference (BI) and the maximum likelihood (ML) method. Results The full lengths of the mitochondrial genome, 18S and 28S rDNAs of B. cf. gwalagwalensis, are 14847 bp, 1876 bp 1876 bp, and 2863 bp, respectively. Both bGMYC and bPTP results based on COI data are generally congruent, suggesting that the previously proposed taxa (B. arcana, B. weberi formosana, and B. wuttkei or Erpobdella wuttkei) are synonyms of B. weberi. The specimens listed in the B. gwalagwalensis group, however, are split into at least two Primary Species Hypotheses (PSHs). The p-distance of the first PSH is less than 1.3% but increased to 4.5% when including the secondary PSH (i.e., B. cf. gwalagwalensis). In comparison, the interspecific p-distance between the B. weberi group and the B. gwalagwalensis group ranged from 6.4% to 8.7%, and the intraspecific p-distance within the B. weberi group is less than 0.8%. Considering the species delimitation results and the sufficient large p-distance, the specimen sampled in China is treated as B. cf. gwalagwalensis. The monophyly of the four Erpobdelliformes families Salifidae, Orobdellidae, Gastrostomobdellidae sensu stricto and Erpobdellidae is well supported in ML and BI analysis based on a data of four markers. Within the Salifidae, a well-supported Barbronia is closely related to a clade containing Odontobdella and Mimobdella, and these three genera are sister to a clade consisted of Salifa and Linta. According to the results of this study, the strategy of simultaneous obtaining both whole mitochondria and nuclear markers from extensively sampled Salifids species using NGS is expected to fathom both the species diversity of B. gwalagwalensis and the evolutionary relationship of Salifidae.
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Affiliation(s)
- Yingkui Liu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
- School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
| | - Xinxin Fu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
| | - Yu Wang
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
| | - Jing Liu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
| | - Yong Liu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
- School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
| | - Chong Li
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
- School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
| | - Jiajia Dong
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
- School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
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300
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Prince Y, Davison GM, Davids SF, Erasmus RT, Kengne AP, Raghubeer S, Matsha TE. The effect of cigarette smoking on the oral microbiota in a South African population using subgingival plaque samples. Heliyon 2024; 10:e31559. [PMID: 38831830 PMCID: PMC11145493 DOI: 10.1016/j.heliyon.2024.e31559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 05/13/2024] [Accepted: 05/17/2024] [Indexed: 06/05/2024] Open
Abstract
Disturbances in the oral microbiota may be due to several mechanisms and factors, such as smoking. An imbalance in oral bacteria may result in changes to the innate immune system and the development of periodontal disease. This study aimed to investigate the distribution of oral microbiota in smokers and non-smokers in a South African population using subgingival plaque samples. From the 128 recruited participants, 57 were identified as smokers (serum cotinine: >15 ng/ml). Analysis of 16S rRNA gene sequencing demonstrated significant differences between the two groups with a reduced abundance of Actinobacteria in smokers. Fusobacterium and Campylobacter were found in higher abundance, while a lower abundance of Leptotrichia, Actinomyces, Corynebacterium, and Lautropia were observed. This study highlighted significant differences in the oral microbiota of smokers, indicating an abundance of anaerobic gram-negative bacteria. These findings suggest that smoking allows certain oral microorganisms to gain dominance, thereby predisposing individuals to periodontal disease development and progression.
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Affiliation(s)
- Yvonne Prince
- SAMRC/CPUT/Cardiometabolic Health Research Unit, Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Bellville, South Africa
| | - Glenda M. Davison
- SAMRC/CPUT/Cardiometabolic Health Research Unit, Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Bellville, South Africa
| | - Saarah F.G. Davids
- SAMRC/CPUT/Cardiometabolic Health Research Unit, Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Bellville, South Africa
| | - Rajiv T. Erasmus
- Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Andre P. Kengne
- Non-communicable Diseases Research Unit, South African Medical Research Council, Cape Town, South Africa
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Shanel Raghubeer
- SAMRC/CPUT/Cardiometabolic Health Research Unit, Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Bellville, South Africa
| | - Tandi E. Matsha
- SAMRC/CPUT/Cardiometabolic Health Research Unit, Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Bellville, South Africa
- Sefako Makgatho Health Sciences University, Ga-Rankuwa, South Africa
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