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Obr M, Percipalle M, Chernikova D, Yang H, Thader A, Pinke G, Porley D, Mansky LM, Dick RA, Schur FKM. Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. Nat Struct Mol Biol 2024:10.1038/s41594-024-01390-8. [PMID: 39242978 DOI: 10.1038/s41594-024-01390-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/14/2024] [Indexed: 09/09/2024]
Abstract
Human T cell leukemia virus type 1 (HTLV-1) immature particles differ in morphology from other retroviruses, suggesting a distinct way of assembly. Here we report the results of cryo-electron tomography studies of HTLV-1 virus-like particles assembled in vitro, as well as derived from cells. This work shows that HTLV-1 uses a distinct mechanism of Gag-Gag interactions to form the immature viral lattice. Analysis of high-resolution structural information from immature capsid (CA) tubular arrays reveals that the primary stabilizing component in HTLV-1 is the N-terminal domain of CA. Mutagenesis analysis supports this observation. This distinguishes HTLV-1 from other retroviruses, in which the stabilization is provided primarily by the C-terminal domain of CA. These results provide structural details of the quaternary arrangement of Gag for an immature deltaretrovirus and this helps explain why HTLV-1 particles are morphologically distinct.
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Affiliation(s)
- Martin Obr
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
- Material and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord, Eindhoven, Netherlands
| | - Mathias Percipalle
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Darya Chernikova
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Huixin Yang
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
| | - Andreas Thader
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Gergely Pinke
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Dario Porley
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
| | - Robert A Dick
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Department of Pediatrics, Laboratory of Biochemical Pharmacology, Center for ViroScience and Cure, Emory University School of Medicine, Atlanta, GA, USA
| | - Florian K M Schur
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.
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Zhou C, Kuang M, Tao Y, Wang J, Luo Y, Fu Y, Chen Z, Liu Y, Li Z, Wu W, Wang L, Dou Y, Wang J, Hou Y. Nynrin preserves hematopoietic stem cell function by inhibiting the mitochondrial permeability transition pore opening. Cell Stem Cell 2024; 31:1359-1375.e8. [PMID: 38955185 DOI: 10.1016/j.stem.2024.06.007] [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: 11/21/2023] [Revised: 04/22/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024]
Abstract
Mitochondria are key regulators of hematopoietic stem cell (HSC) homeostasis. Our research identifies the transcription factor Nynrin as a crucial regulator of HSC maintenance by modulating mitochondrial function. Nynrin is highly expressed in HSCs under both steady-state and stress conditions. The knockout Nynrin diminishes HSC frequency, dormancy, and self-renewal, with increased mitochondrial dysfunction indicated by abnormal mPTP opening, mitochondrial swelling, and elevated ROS levels. These changes reduce HSC radiation tolerance and promote necrosis-like phenotypes. By contrast, Nynrin overexpression in HSCs diminishes irradiation (IR)-induced lethality. The deletion of Nynrin activates Ppif, leading to overexpression of cyclophilin D (CypD) and further mitochondrial dysfunction. Strategies such as Ppif haploinsufficiency or pharmacological inhibition of CypD significantly mitigate these effects, restoring HSC function in Nynrin-deficient mice. This study identifies Nynrin as a critical regulator of mitochondrial function in HSCs, highlighting potential therapeutic targets for preserving stem cell viability during cancer treatment.
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Affiliation(s)
- Chengfang Zhou
- Department of Radiological Medicine, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Mei Kuang
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yin Tao
- Department of Gynecology, The affiliated ZhuZhou Hospital (ZhuZhou Central Hospital), Xiangya Medical College of Central South University, Zhuzhou, Hunan 412007, China
| | - Jianming Wang
- Department of Radiological Medicine, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Yu Luo
- Department of Radiological Medicine, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Yinghao Fu
- Department of Radiological Medicine, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Zhe Chen
- Department of Radiological Medicine, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Yuanyuan Liu
- Department of Radiological Medicine, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Zhigang Li
- Department of Radiological Medicine, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Weiru Wu
- Department of Radiological Medicine, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Li Wang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, 1 Youyi Road, Yuzhong Qu, Chongqing 400016, China
| | - Ying Dou
- Department of Hematology, Children's Hospital of Chongqing Medical University, Chongqing 400014, China.
| | - Junping Wang
- State Key Laboratory of Trauma and Chemical Poisoning, Institute of Combined Injury, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China.
| | - Yu Hou
- Department of Radiological Medicine, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China; Department of Hematology, Children's Hospital of Chongqing Medical University, Chongqing 400014, China; Chongqing Key Laboratory of Hematology and Microenvironment, Chongqing Medical University, Chongqing 400016, China.
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Meng L, Liang L, Shi Y, Yin H, Li L, Xiao J, Huang N, Zhao A, Xia Y, Hou J. Biofilms in plastisphere from freshwater wetlands: Biofilm formation, bacterial community assembly, and biogeochemical cycles. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:134930. [PMID: 38901258 DOI: 10.1016/j.jhazmat.2024.134930] [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: 03/04/2024] [Revised: 05/10/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024]
Abstract
Microorganisms can colonize to the surface of microplastics (MPs) to form biofilms, termed "plastisphere", which could significantly change their physiochemical properties and ecological roles. However, the biofilm characteristics and the deep mechanisms (interaction, assembly, and biogeochemical cycles) underlying plastisphere in wetlands currently lack a comprehensive perspective. In this study, in situ biofilm formation experiments were performed in a park with different types of wetlands to examine the plastisphere by extrinsic addition of PVC MPs in summer and winter, respectively. Results from the spectroscopic and microscopic analyses revealed that biofilms attached to the MPs in constructed forest wetlands contained the most abundant biomass and extracellular polymeric substances. Meanwhile, data from the high-throughput sequencing showed lower diversity in plastisphere compared with soil bacterial communities. Network analysis suggested a simple and unstable co-occurrence pattern in plastisphere, and the null model indicated increased deterministic process of heterogeneous selection for its community assembly. Based on the quantification of biogeochemical cycling genes by high-throughput qPCR, the relative abundances of genes involving in carbon degradation, carbon fixation, and denitrification were significantly higher in plastisphere than those of soil communities. This study greatly enhanced our understanding of biofilm formation and ecological effects of MPs in freshwater wetlands.
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Affiliation(s)
- Liang Meng
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China; Key Laboratory of Environment Remediation and Ecological Health, Zhejiang University, Ministry of Education, Hangzhou 310058, China; Yangtze River Delta Urban Wetland Ecosystem National Field Scientific Observation and Research Station, Shanghai 201722, China
| | - Longrui Liang
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yansong Shi
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Haitao Yin
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Li Li
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jiamu Xiao
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Nannan Huang
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Angang Zhao
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yangrongchang Xia
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jingwen Hou
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai 200240, China.
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Shang F, Ding BY, Niu J, Lu JM, Xie XC, Li CZ, Zhang W, Pan D, Jiang RX, Wang JJ. microRNA maintains nutrient homeostasis in the symbiont-host interaction. Proc Natl Acad Sci U S A 2024; 121:e2406925121. [PMID: 39196627 PMCID: PMC11388328 DOI: 10.1073/pnas.2406925121] [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: 04/09/2024] [Accepted: 06/30/2024] [Indexed: 08/29/2024] Open
Abstract
Endosymbionts provide essential nutrients for hosts, promoting growth, development, and reproduction. However, the molecular regulation of nutrient transport from endosymbiont to host is not well understood. Here, we used bioinformatic analysis, RNA-Sequencing, luciferase assays, RNA immunoprecipitation, and in situ hybridization to show that a bacteriocyte-distributed MRP4 gene (multidrug resistance-associated protein 4) is negatively regulated by a host (aphid)-specific microRNA (miR-3024). Targeted metabolomics, microbiome analysis, vitamin B6 (VB6) supplements, 3D modeling/molecular docking, in vitro binding assays (voltage clamp recording and microscale thermophoresis), and functional complementation of Escherichia coli were jointly used to show that the miR-3024/MRP4 axis controls endosymbiont (Serratia)-produced VB6 transport to the host. The supplementation of miR-3024 increased the mortality of aphids, but partial rescue was achieved by providing an external source of VB6. The use of miR-3024 as part of a sustainable aphid pest-control strategy was evaluated by safety assessments in nontarget organisms (pollinators, predators, and entomopathogenic fungi) using virus-induced gene silencing assays and the expression of miR-3024 in transgenic tobacco. The supplementation of miR-3024 suppresses MRP4 expression, restricting the number of membrane channels, inhibiting VB6 transport, and ultimately killing the host. Under aphids facing stress conditions, the endosymbiont titer is decreased, and the VB6 production is also down-regulated, while the aphid's autonomous inhibition of miR-3024 enhances the expression of MRP4 and then increases the VB6 transport which finally ensures the VB6 homeostasis. The results confirm that miR-3024 regulates nutrient transport in the endosymbiont-host system and is a suitable target for sustainable pest control.
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Affiliation(s)
- Feng Shang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Bi-Yue Ding
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jinzhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jin-Ming Lu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Xiu-Cheng Xie
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Chuan-Zhen Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Wei Zhang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Deng Pan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Rui-Xu Jiang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
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Ferracci S, Manippa V, D'Anselmo A, Bolovon L, Guagnano MT, Brancucci A, Porcelli P, Conti C. The role of impulsivity and binge eating in outpatients with overweight or obesity: an EEG temporal discounting study. J Eat Disord 2024; 12:130. [PMID: 39227881 PMCID: PMC11373217 DOI: 10.1186/s40337-024-01080-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 08/07/2024] [Indexed: 09/05/2024] Open
Abstract
BACKGROUND Binge eating (BE) is associated with a range of cognitive control deficits related to impulsivity, including lower response inhibition, preference for immediate gratification, and maladaptive decision-making. The aim was to investigate whether impulsivity and BE may interact with the decision process and underlying brain activity in outpatients with overweight or obesity who are starting a treatment to achieve weight loss. METHODS A sample of 26 treatment-seeking outpatients with overweight or obesity was evaluated for impulsivity, BE, and temporal discounting rates. Impulsivity was measured with the Barratt Impulsiveness Scale (BIS-11), according to which two groups were composed: high BIS and low BIS; BE was assessed with the eating disorders module of the Structured Clinical Interview for DSM5-Research Version, according to which two groups were composed: with (BE group) or without BE (NBE group). Changes in subjective value of rewards were measured with the Temporal Discounting Task (TDt) where participants had to choice between sooner but smaller vs. later but larger monetary rewards. These choices were made in two differently delayed conditions ("Now" and "Not-now"). Brain rhythms were recorded through high-density electroencephalogram (hd-EEG) during the TDt. RESULTS Patients with BE reported more impulsive tendencies and perceived sooner rewards as more gratifying when both options were delayed (Not-now condition, p = 0.02). The reward choice in the TDt was accompanied by a general EEG alpha band desynchronization in parietal areas observed without differences between experimental conditions and patients groups. No effects were observed within the Now condition or in the other EEG bands. CONCLUSIONS The tendency to favor immediate rewards may constitute an obstacle to adhering to treatment plans and achieving weight loss goals for outpatients with overweight or obesity. Clinicians are therefore encouraged to include psychological factors, such as impulsivity and dysfunctional eating behaviors, when designing weight loss programs. By addressing these psychological aspects, clinicians can better support patients in overcoming barriers to adherence and achieving sustainable weight loss. TRIAL REGISTRATION This study was approved by the Ethics Committee of the Department of Psychological, Health, and Territorial Sciences of the University G. d'Annunzio of Chieti-Pescara (Prot. n. 254 of 03/14/2017).
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Affiliation(s)
- Sara Ferracci
- Department of Communication Sciences, Humanities and International Studies, University "Carlo Bo", Urbino, Italy
- Department of Psychological, Health and Territorial Sciences, University "G. d'Annunzio", Chieti, Italy
| | - Valerio Manippa
- Department of Education, Psychology and Communication, University "Aldo Moro", Bari, Italy
| | - Anita D'Anselmo
- Department of Psychological, Health and Territorial Sciences, University "G. d'Annunzio", Chieti, Italy
- Department of Medicine and Aging Sciences, University "G. d'Annunzio", Chieti, Italy
| | - Luca Bolovon
- Department of Psychological, Health and Territorial Sciences, University "G. d'Annunzio", Chieti, Italy
| | - Maria Teresa Guagnano
- Department of Medicine and Aging Sciences, University "G. d'Annunzio", Chieti, Italy
| | - Alfredo Brancucci
- Department of Motor, Human and Health Sciences, University "Foro Italico", Rome, Italy
| | - Piero Porcelli
- Department of Psychological, Health and Territorial Sciences, University "G. d'Annunzio", Chieti, Italy
| | - Chiara Conti
- Department of Psychological, Health and Territorial Sciences, University "G. d'Annunzio", Chieti, Italy.
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He Q, Ji L, Wang Y, Zhang Y, Wang H, Wang J, Zhu Q, Xie M, Ou W, Liu J, Tang K, Lu K, Liu Q, Zhou J, Zhao R, Cai X, Li N, Cao Y, Li T. Acetate enables metabolic fitness and cognitive performance during sleep disruption. Cell Metab 2024; 36:1998-2014.e15. [PMID: 39163862 DOI: 10.1016/j.cmet.2024.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 03/31/2024] [Accepted: 07/25/2024] [Indexed: 08/22/2024]
Abstract
Sleep is essential for overall health, and its disruption is linked to increased risks of metabolic, cognitive, and cardiovascular dysfunctions; however, the molecular mechanisms remain poorly understood. This study investigated how sleep disturbances contribute to metabolic imbalance and cognition impairment using a chronic sleep fragmentation (SF) mouse model. SF mice exhibited impaired cognition, glucose metabolism, and insulin sensitivity compared with controls. We identified increased acetate levels in hypothalamic astrocytes as a defensive response in SF mice. Through acetate infusion or astrocyte-specific Acss1 deletion to elevate acetate levels, we observed mitigated metabolic and cognitive impairments in SF mice. Mechanistically, acetate binds and activates pyruvate carboxylase, thereby restoring glycolysis and the tricarboxylic acid cycle. Among individuals most commonly affected by SF, patients with obstructive sleep apnea exhibited elevated acetate levels when coupled with type 2 diabetes. Our study uncovers the protective effect of acetate against sleep-induced metabolic and cognitive impairments.
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Affiliation(s)
- Qinqin He
- Department of Anesthesiology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, Sichuan, China; Laboratory of Mitochondrial Metabolism and Perioperative Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Liwei Ji
- Department of Anesthesiology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, Sichuan, China; Laboratory of Mitochondrial Metabolism and Perioperative Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Yanyan Wang
- Healthcare Innovation Research Laboratory, Institute of Nursing Research & National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yarong Zhang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Haiyan Wang
- Department of Anesthesiology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, Sichuan, China; Laboratory of Mitochondrial Metabolism and Perioperative Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Junyan Wang
- Department of Anesthesiology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, Sichuan, China; Laboratory of Mitochondrial Metabolism and Perioperative Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Qing Zhu
- Hypertension Center of People's Hospital of Xinjiang Uygur Autonomous Region, Xinjiang Hypertension Institute, NHC Key Laboratory of Hypertension Clinical Research, Key Laboratory of Xinjiang Uygur Autonomous Region "Hypertension Research Laboratory", Xinjiang Clinical Medical Research Center for Hypertension (Cardio-Cerebrovascular) Diseases, Urumqi, Xinjiang, China
| | - Maodi Xie
- Department of Anesthesiology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, Sichuan, China; Laboratory of Mitochondrial Metabolism and Perioperative Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Wei Ou
- Department of Anesthesiology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, Sichuan, China; Laboratory of Mitochondrial Metabolism and Perioperative Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Jun Liu
- Department of Otolaryngology-Head and Neck Surgery, the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, China
| | - Kuo Tang
- Laboratory of Mitochondrial Metabolism and Perioperative Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Kening Lu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Qingmei Liu
- Department of Anesthesiology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, Sichuan, China; Laboratory of Mitochondrial Metabolism and Perioperative Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Jian Zhou
- Laboratory of Mitochondrial Metabolism and Perioperative Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Rui Zhao
- Department of Anesthesiology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, Sichuan, China; Division of Gastrointestinal Surgery, Department of General Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Xintian Cai
- Hypertension Center of People's Hospital of Xinjiang Uygur Autonomous Region, Xinjiang Hypertension Institute, NHC Key Laboratory of Hypertension Clinical Research, Key Laboratory of Xinjiang Uygur Autonomous Region "Hypertension Research Laboratory", Xinjiang Clinical Medical Research Center for Hypertension (Cardio-Cerebrovascular) Diseases, Urumqi, Xinjiang, China
| | - Nanfang Li
- Hypertension Center of People's Hospital of Xinjiang Uygur Autonomous Region, Xinjiang Hypertension Institute, NHC Key Laboratory of Hypertension Clinical Research, Key Laboratory of Xinjiang Uygur Autonomous Region "Hypertension Research Laboratory", Xinjiang Clinical Medical Research Center for Hypertension (Cardio-Cerebrovascular) Diseases, Urumqi, Xinjiang, China.
| | - Yang Cao
- Department of Cardiology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| | - Tao Li
- Department of Anesthesiology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu, Sichuan, China; Laboratory of Mitochondrial Metabolism and Perioperative Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital of Sichuan University, Chengdu, Sichuan, China.
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Ryan MJ, Clemmer JS, Mathew RO, Faulkner JL, Taylor EB, Abais-Battad JM, Hollis F, Sullivan JC. Revisiting sex as a biological variable in hypertension research. J Clin Invest 2024; 134:e180078. [PMID: 39225093 PMCID: PMC11364402 DOI: 10.1172/jci180078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
Half of adults in the United States have hypertension as defined by clinical practice guidelines. Interestingly, women are generally more likely to be aware of their hypertension and have their blood pressure controlled with treatment compared with men, yet hypertension-related mortality is greater in women. This may reflect the fact that the female sex remains underrepresented in clinical and basic science studies investigating the effectiveness of therapies and the mechanisms controlling blood pressure. This Review provides an overview of the impact of the way hypertension research has explored sex as a biological variable (SABV). Emphasis is placed on epidemiological studies, hypertension clinical trials, the genetics of hypertension, sex differences in immunology and gut microbiota in hypertension, and the effect of sex on the central control of blood pressure. The goal is to offer historical perspective on SABV in hypertension, highlight recent studies that include SABV, and identify key gaps in SABV inclusion and questions that remain in the field. Through continued awareness campaigns and engagement/education at the level of funding agencies, individual investigators, and in the editorial peer review system, investigation of SABV in the field of hypertension research will ultimately lead to improved clinical outcomes.
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Affiliation(s)
- Michael J. Ryan
- Columbia VA Health Care System, Columbia, South Carolina, USA
- University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | - John S. Clemmer
- University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Roy O. Mathew
- Loma Linda VA Health Care System, Loma Linda, California, USA
| | | | - Erin B. Taylor
- University of Mississippi Medical Center, Jackson, Mississippi, USA
| | | | - Fiona Hollis
- University of South Carolina School of Medicine, Columbia, South Carolina, USA
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Türkoğlu İ, Sacinti KG, Panattoni A, Namazov A, Sanlier NT, Sanlier N, Cela V. Eating for Optimization: Unraveling the Dietary Patterns and Nutritional Strategies in Endometriosis Management. Nutr Rev 2024:nuae120. [PMID: 39225782 DOI: 10.1093/nutrit/nuae120] [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: 09/04/2024] Open
Abstract
Endometriosis is a chronic gynecological disorder affecting millions of women worldwide, causing chronic pelvic pain, dyspareunia, dysmenorrhea, and infertility, and severely impacting their quality of life. Treatment primarily involves hormonal therapies and surgical excision, but high recurrence rates and the economic burden are substantial. With these challenges, significant discussion surrounds the potential role of dietary patterns in managing endometriosis, making it necessary to bridge this critical gap. This review investigates the current scientific evidence on the dietary patterns (eg, Mediterranean, vegetarian, anti-inflammatory, low-fermentable oligosaccharides, disaccharides, monosaccharides, and polyols [low-FODMAP], and Western-style diets) associated with endometriosis and provides a concise, yet thorough, overview on the subject. In addition, antioxidants, microbiota, and artificial intelligence (AI) and their potential roles were also evaluated as future directions. An electronic-based search was performed in MEDLINE, Embase, Cochrane Library, CINAHL, ClinicalTrials.gov, Scopus, and Web of Science. The current data on the topic indicate that a diet based on the Mediterranean and anti-inflammatory diet pattern, rich in dietary fiber, omega-3 fatty acids, plant-based protein, and vitamins and minerals, has a positive influence on endometriosis, yielding a promising improvement in patient symptoms. Preclinical investigations and clinical trials indicate that dietary antioxidants and gut microbiota modulation present potential new approaches in managing endometriosis. Also, AI may offer a promising avenue to explore how dietary components interact with endometriosis. Ultimately, considering genetic and lifestyle factors, a healthy, balanced, personalized approach to diet may offer valuable insights on the role of diet as a means of symptom improvement, facilitating the utilization of nutrition for the management of endometriosis.
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Affiliation(s)
- İnci Türkoğlu
- Department of Nutrition and Dietetics, Hacettepe University School of Health Sciences, Ankara 06100, Turkey
| | - Koray Gorkem Sacinti
- Department of Obstetrics and Gynecology, Aksaray University Training and Research Hospital, Aksaray 68200, Turkey
- Division of Epidemiology, Department of Public Health, Hacettepe University Faculty of Medicine, Ankara 06100, Turkey
| | - Andrea Panattoni
- Division of Obstetrics and Gynecology, Department of Clinical and Reproductive Medicine, University of Pisa, Pisa 56126, Italy
| | - Ahmet Namazov
- Department of Obstetrics and Gynecology, Barzilai University Medical Center, Ashkelon 7830604, Israel
- Faculty of Health Sciences, Ben-Gurion University of Negev, Beer-Sheva 8410501, Israel
| | - Nazlı Tunca Sanlier
- Department of Obstetrics and Gynecology, Turkish Ministry of Health, Ankara City Hospital, Ankara 06800, Turkey
| | - Nevin Sanlier
- Department of Nutrition and Dietetics, Ankara Medipol University School of Health Sciences, Ankara 06050, Turkey
| | - Vito Cela
- Division of Obstetrics and Gynecology, Department of Clinical and Reproductive Medicine, University of Pisa, Pisa 56126, Italy
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Liwinski T, Auer MK, Schröder J, Pieknik I, Casar C, Schwinge D, Henze L, Stalla GK, Lang UE, von Klitzing A, Briken P, Hildebrandt T, Desbuleux JC, Biedermann SV, Holterhus PM, Bang C, Schramm C, Fuss J. Gender-affirming hormonal therapy induces a gender-concordant fecal metagenome transition in transgender individuals. BMC Med 2024; 22:346. [PMID: 39218875 PMCID: PMC11367877 DOI: 10.1186/s12916-024-03548-z] [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: 04/05/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Limited data exists regarding gender-specific microbial alterations during gender-affirming hormonal therapy (GAHT) in transgender individuals. This study aimed to investigate the nuanced impact of sex steroids on gut microbiota taxonomy and function, addressing this gap. We prospectively analyzed gut metagenome changes associated with 12 weeks of GAHT in trans women and trans men, examining both taxonomic and functional shifts. METHODS Thirty-six transgender individuals (17 trans women, 19 trans men) provided pre- and post-GAHT stool samples. Shotgun metagenomic sequencing was used to assess the changes in gut microbiota structure and potential function following GAHT. RESULTS While alpha and beta diversity remained unchanged during transition, specific species, including Parabacteroides goldsteinii and Escherichia coli, exhibited significant abundance shifts aligned with affirmed gender. Overall functional metagenome analysis showed a statistically significant effect of gender and transition (R2 = 4.1%, P = 0.0115), emphasizing transitions aligned with affirmed gender, particularly in fatty acid-related metabolism. CONCLUSIONS This study provides compelling evidence of distinct taxonomic and functional profiles in the gut microbiota between trans men and women. GAHT induces androgenization in trans men and feminization in trans women, potentially impacting physiological and health-related outcomes. TRIAL REGISTRATION Clinicaltrials.gov NCT02185274.
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Affiliation(s)
- Timur Liwinski
- Clinic for Adult Psychiatry, University Psychiatric Clinics, University of Basel, Wilhelm Klein-Strasse 27, Basel, CH-4002, Switzerland
| | - Matthias K Auer
- Medizinische Klinik and Poliklinik IV, Klinikum der Universität München, LMU München, Munich, Germany
- Institute of Forensic Psychiatry and Sex Research, Center for Translational Neuro- and Behavioral Sciences, University of Duisburg-Essen, Alfredstr. 68-72, Essen, 45130, Germany
| | - Johanna Schröder
- Department of Psychology, Institute for Clinical Psychology and Psychotherapy, Medical School Hamburg, Hamburg, Germany
| | - Ina Pieknik
- Institute of Forensic Psychiatry and Sex Research, Center for Translational Neuro- and Behavioral Sciences, University of Duisburg-Essen, Alfredstr. 68-72, Essen, 45130, Germany
| | - Christian Casar
- First Department of Medicine, University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Dorothee Schwinge
- First Department of Medicine, University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Lara Henze
- First Department of Medicine, University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Günter K Stalla
- Medizinische Klinik and Poliklinik IV, Klinikum der Universität München, LMU München, Munich, Germany
- Medicover Neuroendocrinology, Munich, Germany
| | - Undine E Lang
- Clinic for Adult Psychiatry, University Psychiatric Clinics, University of Basel, Wilhelm Klein-Strasse 27, Basel, CH-4002, Switzerland
| | - Alina von Klitzing
- Institute for Sex Research, Sexual Medicine and Forensic Psychiatry, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peer Briken
- Institute for Sex Research, Sexual Medicine and Forensic Psychiatry, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Hildebrandt
- Department of Gynecology and Obstetrics, CCC Erlangen EMN, Friedrich Alexander University, Erlangen, Germany
| | - Jeanne C Desbuleux
- Institute of Forensic Psychiatry and Sex Research, Center for Translational Neuro- and Behavioral Sciences, University of Duisburg-Essen, Alfredstr. 68-72, Essen, 45130, Germany
| | - Sarah V Biedermann
- Department of Psychiatry and Psychotherapy, Social and Emotional Neuroscience Group, Center for Psychosocial Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Paul-Martin Holterhus
- Division of Pediatric Endocrinology and Diabetes, Department of Children and Adolescent Medicine I, University Hospital of Schleswig-Holstein, Campus Kiel/Christian-Albrechts University of Kiel, Kiel, D-24105, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, University Hospital Schleswig-Holstein, Rosalind-Franklin-Str. 12, Kiel, 24105, Germany
| | - Christoph Schramm
- First Department of Medicine, University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Centre for Translational Immunology (HCTI), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Martin Zeitz Center for Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Johannes Fuss
- Institute of Forensic Psychiatry and Sex Research, Center for Translational Neuro- and Behavioral Sciences, University of Duisburg-Essen, Alfredstr. 68-72, Essen, 45130, Germany
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Wang Z, Xu M, Li Q, Lu S, Liu Z. Subchronic Chloroform Exposure Causes Intestinal Damage and Induces Gut Microbiota Disruption and Metabolic Dysregulation in Mice. ENVIRONMENTAL TOXICOLOGY 2024. [PMID: 39221872 DOI: 10.1002/tox.24417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 07/12/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Chloroform is a prevalent toxic environmental pollutant in urban settings, posing risks to human health through exposure via various mediums such as air and tap water. The gut microbiota plays a pivotal role in maintaining host health. However, there is a paucity of research elucidating the impact of chloroform exposure on the gut microbiota. In this investigation, 18 SPF Kunming female mice were stratified into three groups (n = 6) and subjected to oral gavage with chloroform doses equivalent to 0, 50, and 150 mg/kg of body weight over 30 days. Our findings demonstrate that subchronic chloroform exposure significantly perturbs hematological parameters in mice and induces histopathological alterations in cecal tissues, consequently engendering marked disparities in the functional composition of cecal microbiota and metabolic equilibrium of cecal contents. Ultimately, our investigation revealed a statistically robust correlation, exhibiting a high degree of significance, between the intestinal microbiome composition and the metabolites that were differentially expressed consequent to chloroform exposure.
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Affiliation(s)
- Zaishan Wang
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, China
| | - Meng Xu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, China
| | - Qiang Li
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, China
| | - Sihan Lu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, China
| | - Zhu Liu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, China
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61
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Jiang SS, Kang ZR, Chen YX, Fang JY. The gut microbiome modulate response to immunotherapy in cancer. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2634-7. [PMID: 39235561 DOI: 10.1007/s11427-023-2634-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 06/05/2024] [Indexed: 09/06/2024]
Abstract
Gut microbiota have been reported to play an important role in the occurrence and development of malignant tumors. Currently, clinical studies have identified specific gut microbiota and its metabolites associated with efficacy of immunotherapy in multiple types of cancers. Preclinical investigations have elucidated that gut microbiota modulate the antitumor immunity and affect the efficacy of cancer immunotherapy. Certain microbiota and its metabolites may favorably remodel the tumor microenvironment by engaging innate and/or adaptive immune cells. Understanding how the gut microbiome interacts with cancer immunotherapy opens new avenues for improving treatment strategies. Fecal microbial transplants, probiotics, dietary interventions, and other strategies targeting the microbiota have shown promise in preclinical studies to enhance the immunotherapy. Ongoing clinical trials are evaluating these approaches. This review presents the recent advancements in understanding the dynamic interplay among the host immunity, the microbiome, and cancer immunotherapy, as well as strategies for modulating the microbiome, with a view to translating into clinical applications.
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Affiliation(s)
- Shan-Shan Jiang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200001, China
| | - Zi-Ran Kang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200001, China
| | - Ying-Xuan Chen
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200001, China
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200001, China.
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62
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Nagraj AK, Shukla M, Kulkarni M, Patil P, Borgave M, Banerjee SK. Reversal of carbapenem resistance in Pseudomonas aeruginosa by camelid single domain antibody fragment (VHH) against the C4-dicarboxylate transporter. J Antibiot (Tokyo) 2024; 77:612-626. [PMID: 38886486 DOI: 10.1038/s41429-024-00748-w] [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: 11/25/2023] [Revised: 05/06/2024] [Accepted: 05/18/2024] [Indexed: 06/20/2024]
Abstract
Antimicrobial resistance is emerging as the new healthcare crisis necessitating the development of newer classes of drugs using non-traditional approaches. Pseudomonas aeruginosa, one of the most common pathogens involved in nosocomial infections, is extremely difficult to treat even with the last resort frontline drug, the carbapenems. As the pathogen has the ability to acquire resistance to new small-molecule antibiotics, being deployed, a novel biological approach has been tried using antibody fragments in combination with carbapenems and β-lactams as adjunct therapy for an enduring solution to the problem. In this study, we developed a camelid antibody fragment (VHH) library against P. aeruginosa and isolated a highly potent hit, PsC23. Mass spectrometry identified the target to be a component of the C4-dicarboxylate transporter that feeds metabolites to the glyoxylate shunt particularly under conditions of oxidative stress. PsC23 is bacteriostatic at a concentration of 1.66 µM (25 µg ml-1) and shows a synergistic effect with both the classes of drugs at an effective concentration of 100-200 nM (1.5-3.0 µg ml-1) when co administered with them. In combination with meropenem the VHH completely cleared the infection from a neutropenic mouse with a carbapenem-resistant P. aeruginosa systemic infection. Blocking the glyoxylate shunt by PsC23 resulted in disruption of energy transduction due to a respiratory shift to the oxygen-depleted TCA cycle causing inhibition of efflux and increased free radical generation from carbapenems and β-lactams exerting a strong bactericidal effect that reversed the resistance to multiple unrelated drugs.
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Affiliation(s)
| | | | | | - Pratik Patil
- AbGenics Life Sciences Pvt. Ltd, Pune, 411045, India
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Munley JA, Park G, Kelly LS, Kannan KB, Mankowski RT, Casadesus G, Chakrabarty P, Wallet SM, Maile R, Bible LE, Wang B, Moldawer LL, Mohr AM, Nagpal R, Efron PA. Persistence and Sexual Dimorphism of Gut Dysbiosis and Pathobiome after Sepsis and Trauma. Ann Surg 2024; 280:491-503. [PMID: 38864230 PMCID: PMC11392637 DOI: 10.1097/sla.0000000000006385] [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] [Indexed: 06/13/2024]
Abstract
OBJECTIVE To evaluate the persistence of intestinal microbiome dysbiosis and gut-plasma metabolomic perturbations following severe trauma or sepsis weeks after admission in patients experiencing chronic critical illness (CCI). SUMMARY Trauma and sepsis can lead to gut dysbiosis and alterations in the plasma and fecal metabolome. However, the impact of these perturbations and correlations between gut dysbiosis and the plasma metabolome in chronic critical illness have not been studied. METHODS A prospective observational cohort study was performed with healthy subjects, severe trauma patients, and patients with sepsis residing in an intensive care unit for 2 to 3 weeks. A high-throughput multi-omics approach was utilized to evaluate the gut microbial and gut-plasma metabolite responses in critically ill trauma and sepsis patients 14 to 21 days after intensive care unit admission. RESULTS Patients in the sepsis and trauma cohorts demonstrated strikingly depleted gut microbiome diversity, with significant alterations and specific pathobiome patterns in the microbiota composition compared to healthy subjects. Further subgroup analyses based on sex revealed resistance to changes in microbiome diversity among female trauma patients compared to healthy counterparts. Sex--specific changes in fecal metabolites were also observed after trauma and sepsis, while plasma metabolite changes were similar in both males and females. CONCLUSIONS Dysbiosis induced by trauma and sepsis persists up to 14 to 21 days after onset and is sex-specific, underscoring the implication of pathobiome and entero-septic microbial-metabolite perturbations in post-sepsis and posttrauma chronic critical illness. This indicates resilience to infection or injury in females' microbiome and should inform and facilitate future precision/personalized medicine strategies in the intensive care unit.
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Affiliation(s)
- Jennifer A Munley
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, FL
| | - Gwoncheol Park
- Department of Health, Nutrition and Food Sciences, The Gut Biome Lab, Florida State University, Tallahassee, FL
| | - Lauren S Kelly
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, FL
| | - Kolenkode B Kannan
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, FL
| | - Robert T Mankowski
- Division of Gerontology, Geriatrics and Palliative Care, Department of Medicine, University of Alabama, Birmingham, AL
| | - Gemma Casadesus
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, FL
| | - Paramita Chakrabarty
- Department of Neuroscience, University of Florida College of Medicine, Gainesville, FL
| | - Shannon M Wallet
- Department of Oral Biology, University of Florida College of Medicine, Gainesville, FL
| | - Robert Maile
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, FL
| | - Letitia E Bible
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, FL
| | - Bo Wang
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL
| | - Lyle L Moldawer
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, FL
| | - Alicia M Mohr
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, FL
| | - Ravinder Nagpal
- Department of Health, Nutrition and Food Sciences, The Gut Biome Lab, Florida State University, Tallahassee, FL
| | - Philip A Efron
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, FL
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Leveau JHJ. Re-Envisioning the Plant Disease Triangle: Full Integration of the Host Microbiota and a Focal Pivot to Health Outcomes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2024; 62:31-47. [PMID: 38684078 DOI: 10.1146/annurev-phyto-121423-042021] [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: 05/02/2024]
Abstract
The disease triangle is a structurally simple but conceptually rich model that is used in plant pathology and other fields of study to explain infectious disease as an outcome of the three-way relationship between a host, a pathogen, and their environment. It also serves as a guide for finding solutions to treat, predict, and prevent such diseases. With the omics-driven, evidence-based realization that the abundance and activity of a pathogen are impacted by proximity to and interaction with a diverse multitude of other microorganisms colonizing the same host, the disease triangle evolved into a tetrahedron shape, which features an added fourth dimension representing the host-associated microbiota. Another variant of the disease triangle emerged from the recently formulated pathobiome paradigm, which deviates from the classical "one pathogen" etiology of infectious disease in favor of a scenario in which disease represents a conditional outcome of complex interactions between and among a host, its microbiota (including microbes with pathogenic potential), and the environment. The result is a version of the original disease triangle where "pathogen" is substituted with "microbiota." Here, as part of a careful and concise review of the origin, history, and usage of the disease triangle, I propose a next step in its evolution, which is to replace the word "disease" in the center of the host-microbiota-environment triad with the word "health." This triangle highlights health as a desirable outcome (rather than disease as an unwanted state) and as an emergent property of host-microbiota-environment interactions. Applied to the discipline of plant pathology, the health triangle offers an expanded range of targets and approaches for the diagnosis, prediction, restoration, and maintenance of plant health outcomes. Its applications are not restricted to infectious diseases only, and its underlying framework is more inclusive of all microbial contributions to plant well-being, including those by mycorrhizal fungi and nitrogen-fixing bacteria, for which there never was a proper place in the plant disease triangle. The plant health triangle also may have an edge as an education and communication tool to convey and stress the importance of healthy plants and their associated microbiota to a broader public and stakeholdership.
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Affiliation(s)
- Johan H J Leveau
- Department of Plant Pathology, University of California, Davis, California, USA;
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Boyd A, El Dani M, Ajrouche R, Demontant V, Cheval J, Lacombe K, Cosson G, Rodriguez C, Pawlotsky JM, Woerther PL, Surgers L. Gut microbiome diversity and composition in individuals with and without extended-spectrum β-lactamase-producing Enterobacterales carriage: a matched case-control study in infectious diseases department. Clin Microbiol Infect 2024; 30:1154-1163. [PMID: 38527613 DOI: 10.1016/j.cmi.2024.03.016] [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: 11/21/2023] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 03/27/2024]
Abstract
OBJECTIVE Little is known about the effect of gut microbial and extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) carriage, particularly in the general population. The aim of this study was to identify microbiota signatures uniquely correlated with ESBL-E carriage. METHODS We conducted a case-control study among individuals seeking care at the Sexual Health Clinic or Department of Infectious and Tropical Diseases, Saint-Antoine Hospital, Paris, France. Using coarsened exact matching, 176 participants with ESBL-carriage (i.e. cases) were matched 1:1 to those without ESBL-carriage (i.e. controls) based on sexual group, ESBL-E prevalence of countries travelled in <12 months, number of sexual partners in <6 months, geographic origin, and any antibiotic use in <6 months. 16S rRNA gene amplicon sequencing was used to generate differential abundances at the genus level and measures of α- and β-diversity. RESULTS Participants were mostly men (83.2%, n = 293/352) and had a median age of 33 years (interquartile range: 27-44). Nine genera were found associated with ESBL-E carriage: Proteus (p < 0.0001), Carnobacterium (p < 0.0001), Enterorhabdus (p 0.0079), Catonella (p 0.017), Dermacoccus (p 0.017), Escherichia/Shigella (p 0.021), Kocuria (p 0.023), Bacillus (p 0.040), and Filifactor (p 0.043); however, differences were no longer significant after Benjamini-Hochberg correction (q > 0.05). There were no differences between those with versus without ESBL-E carriage in measures of α-diversity (Shannon Diversity Index, p 0.49; Simpson Diversity Index, p 0.54; and Chao1 Richness Estimator, p 0.16) or β-diversity (Bray-Curtis dissimilarity index, p 0.42). DISCUSSION In this large carefully controlled study, there is lacking evidence that gut microbial composition and diversity is any different between individuals with and without ESBL-E carriage.
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Affiliation(s)
- Anders Boyd
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique, Paris, France; Stichting HIV Monitoring, Amsterdam, The Netherlands; Public Health Service of Amsterdam, Infectious Diseases, Amsterdam, The Netherlands
| | - Mariam El Dani
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique, Paris, France; Clinical and Epidemiological Research Laboratory, Faculty of Pharmacy, Lebanese University, Hadat, Lebanon
| | - Roula Ajrouche
- Clinical and Epidemiological Research Laboratory, Faculty of Pharmacy, Lebanese University, Hadat, Lebanon; Institut National de Santé Publique, d'Épidémiologie Clinique et de Toxicologie-Liban (INSPECT-LB), Beirut, Lebanon
| | - Vanessa Demontant
- NGS Platform, Henri Mondor Hospital, APHP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Justine Cheval
- NGS Platform, Henri Mondor Hospital, APHP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Karine Lacombe
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique, Paris, France; GHU APHP. Sorbonne Université, Service des Maladies Infectieuses et Tropicales, Hôpital Saint-Antoine, Paris, France
| | - Guillaume Cosson
- GHU APHP. Sorbonne Université, Service des Maladies Infectieuses et Tropicales, Hôpital Saint-Antoine, Paris, France
| | - Christophe Rodriguez
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique Hôpitaux de Paris (APHP), Université Paris-Est-Créteil, Créteil, France; INSERM U955, Team "Viruses, Hepatology, Cancer", Créteil, France
| | - Jean-Michel Pawlotsky
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique Hôpitaux de Paris (APHP), Université Paris-Est-Créteil, Créteil, France; INSERM U955, Team "Viruses, Hepatology, Cancer", Créteil, France
| | - Paul-Louis Woerther
- NGS Platform, Henri Mondor Hospital, APHP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France; Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique Hôpitaux de Paris (APHP), Université Paris-Est-Créteil, Créteil, France; Université Paris-Est-Créteil (UPEC), EA 7380 Dynamic, Ecole nationale vétérinaire d'Alfort, USC Anses, Créteil, France
| | - Laure Surgers
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique, Paris, France; GHU APHP. Sorbonne Université, Service des Maladies Infectieuses et Tropicales, Hôpital Saint-Antoine, Paris, France.
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James D, Poveda C, Walton GE, Elmore JS, Linden B, Gibson J, Griffin BA, Robertson MD, Lewis MC. Do high-protein diets have the potential to reduce gut barrier function in a sex-dependent manner? Eur J Nutr 2024; 63:2035-2054. [PMID: 38662018 PMCID: PMC11377480 DOI: 10.1007/s00394-024-03407-w] [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: 12/05/2023] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
PURPOSE Impaired gut barrier function is associated with systemic inflammation and many chronic diseases. Undigested dietary proteins are fermented in the colon by the gut microbiota which produces nitrogenous metabolites shown to reduce barrier function in vitro. With growing evidence of sex-based differences in gut microbiotas, we determined whether there were sex by dietary protein interactions which could differentially impact barrier function via microbiota modification. METHODS Fermentation systems were inoculated with faeces from healthy males (n = 5) and females (n = 5) and supplemented with 0.9 g of non-hydrolysed proteins sourced from whey, fish, milk, soya, egg, pea, or mycoprotein. Microbial populations were quantified using fluorescence in situ hybridisation with flow cytometry. Metabolite concentrations were analysed using gas chromatography, solid phase microextraction coupled with gas chromatography-mass spectrometry and ELISA. RESULTS Increased protein availability resulted in increased proteolytic Bacteroides spp (p < 0.01) and Clostridium coccoides (p < 0.01), along with increased phenol (p < 0.01), p-cresol (p < 0.01), indole (p = 0.018) and ammonia (p < 0.01), varying by protein type. Counts of Clostridium cluster IX (p = 0.03) and concentration of p-cresol (p = 0.025) increased in males, while females produced more ammonia (p = 0.02), irrespective of protein type. Further, we observed significant sex-protein interactions affecting bacterial populations and metabolites (p < 0.005). CONCLUSIONS Our findings suggest that protein fermentation by the gut microbiota in vitro is influenced by both protein source and the donor's sex. Should these results be confirmed through human studies, they could have major implications for developing dietary recommendations tailored by sex to prevent chronic illnesses.
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Affiliation(s)
- Daniel James
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights Campus, Reading, RG6 6DZ, UK.
| | - Carlos Poveda
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights Campus, Reading, RG6 6DZ, UK
| | - Gemma E Walton
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights Campus, Reading, RG6 6DZ, UK
| | - J Stephen Elmore
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights Campus, Reading, RG6 6DZ, UK
| | - Brandon Linden
- Department of Nutrition, Food & Exercise Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - John Gibson
- Food and Feed Innovations, Woodstock, Newcastle Rd, Woore, N Shropshire, CW3 95N, UK
| | - Bruce A Griffin
- Department of Nutrition, Food & Exercise Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - M Denise Robertson
- Department of Nutrition, Food & Exercise Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Marie C Lewis
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights Campus, Reading, RG6 6DZ, UK
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Cui Y, Liu Y, Yang J, Duan H, Wang P, Guo L, Guo Y, Li S, Zhao Y, Wang J, Qi G, Guan J. Microencapsulated Lactobacillus plantarum promotes intestinal development through gut colonization of layer chicks. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2024; 18:1-16. [PMID: 38989011 PMCID: PMC11231655 DOI: 10.1016/j.aninu.2024.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 01/29/2024] [Accepted: 03/12/2024] [Indexed: 07/12/2024]
Abstract
The effects of Lactobacillus plantarum in microencapsulation (LPM) on intestinal development in layer chicks were investigated in this study, as well as the colonization of L. plantarum in the gut. A total of 480 healthy Hy-Line Brown layer chicks at 0 d old were randomly divided into 4 groups (8 replicates each treatment), and the diets of these birds were supplemented with nothing (control), L. plantarum (0.02 g/kg feed; 109 CFU/kg feed), LPM (1.0 g/kg feed; 109 CFU/kg feed) and wall material of LPM (WM; 0.98 g/kg feed), respectively. Compared to control, LPM improved growth performance and intestinal development of layer chicks, evidenced by significantly increased body weight, average daily gain, average daily feed intake, villus height, villus height/crypt depth, as well as weight and length of the duodenum, jejunum and ileum (P < 0.05). These results could be attributed to the increased colonization of L. plantarum in the gut, which was verified by significant increases in lactic acid content, viable counts in chyme and mucosa (P < 0.05), as well as a visible rise in number of strains labeled with fluorescein isothiocyanate. Meanwhile, the relative abundances of Lactobacillus and Bifidobacterium significantly increased in response to microencapsulated L. plantarum supplementation (P < 0.05), accompanied by the significant up-regulation of colonization related genes (P < 0.05), encoding solute carrier family, monocarboxylate transporter, activin A receptor, succinate receptor and secretogranin II. To sum up, microencapsulated L. plantarum supplementation promoted intestinal development, which could be attributed to the enhancement of L. plantarum colonization in the intestine through the mutual assistance of Bifidobacterium and interactions with colonization related transmembrane proteins.
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Affiliation(s)
- Yaoming Cui
- School of Biological Engineering, Henan University of Technology, Zhengzhou, Henan 450001, China
| | - Yanxia Liu
- School of Biological Engineering, Henan University of Technology, Zhengzhou, Henan 450001, China
| | - Jing Yang
- School of Biological Engineering, Henan University of Technology, Zhengzhou, Henan 450001, China
| | - Haitao Duan
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan 450046, China
| | - Peng Wang
- School of Biological Engineering, Henan University of Technology, Zhengzhou, Henan 450001, China
| | - Linna Guo
- School of Biological Engineering, Henan University of Technology, Zhengzhou, Henan 450001, China
| | - Yanjiao Guo
- School of Biological Engineering, Henan University of Technology, Zhengzhou, Henan 450001, China
| | - Suying Li
- School of Biological Engineering, Henan University of Technology, Zhengzhou, Henan 450001, China
| | - Yating Zhao
- School of Biological Engineering, Henan University of Technology, Zhengzhou, Henan 450001, China
| | - Jinrong Wang
- School of Biological Engineering, Henan University of Technology, Zhengzhou, Henan 450001, China
| | - Guanghai Qi
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junjun Guan
- School of Biological Engineering, Henan University of Technology, Zhengzhou, Henan 450001, China
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Lu S, Zhao Q, Guan Y, Sun Z, Li W, Guo S, Zhang A. The communication mechanism of the gut-brain axis and its effect on central nervous system diseases: A systematic review. Biomed Pharmacother 2024; 178:117207. [PMID: 39067168 DOI: 10.1016/j.biopha.2024.117207] [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: 05/13/2024] [Revised: 07/15/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024] Open
Abstract
Gut microbiota is involved in intricate and active metabolic processes the host's brain function, especially its role in immune responses, secondary metabolism, and symbiotic connections with the host. Gut microbiota can promote the production of essential metabolites, neurotransmitters, and other neuroactive chemicals that affect the development and treatment of central nervous system diseases. This article introduces the relevant pathways and manners of the communication between the brain and gut, summarizes a comprehensive overview of the current research status of key gut microbiota metabolites that affect the functions of the nervous system, revealing those adverse factors that affect typical communication between the brain-gut axis, and outlining the efforts made by researchers to alleviate these neurological diseases through targeted microbial interventions. The relevant pathways and manners of communication between the brain and gut contribute to the experimental design of new treatment plans and drug development. The factors that may cause changes in gut microbiota and affect metabolites, as well as current intervention methods are summarized, which helps improve gut microbiota brain dialogue, prevent adverse triggering factors from interfering with the gut microbiota system, and minimize neuropathological changes.
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Affiliation(s)
- Shengwen Lu
- Department of Pharmaceutical Analysis, GAP Center, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin 150040, China
| | - Qiqi Zhao
- Department of Pharmaceutical Analysis, GAP Center, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin 150040, China
| | - Yu Guan
- Department of Pharmaceutical Analysis, GAP Center, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin 150040, China
| | - Zhiwen Sun
- Department of Gastroenterology, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin 150040, China
| | - Wenhao Li
- School of Basic Medical Science of Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin 150040, China
| | - Sifan Guo
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China
| | - Aihua Zhang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan Medical University, Xueyuan Road 3, Haikou 571199, China; Graduate School, Heilongjiang University of Chinese Medicine, Harbin 150040, China; INTI International University, Nilai 71800, Malaysia.
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Araújo JR, Marques C, Rodrigues C, Calhau C, Faria A. The metabolic and endocrine impact of diet-derived gut microbiota metabolites on ageing and longevity. Ageing Res Rev 2024; 100:102451. [PMID: 39127442 DOI: 10.1016/j.arr.2024.102451] [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: 02/21/2024] [Revised: 07/16/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
Gut dysbiosis has been recently recognized as a hallmark of ageing. At this stage of life, gut microbiota becomes depleted from bacteria involved in the production of short-chain fatty acids (SCFA), indole and its derivative indole-3-propionic acid (IPA), metabolites shown to improve host glycemic control as well as insulin sensitivity and secretion. Moreover, gut microbiota becomes enriched in pathobiont bacteria involved in the production of imidazole propionate, phenols and trimethylamine, metabolites that promote host insulin resistance and atherosclerosis. The magnitude of these changes is much more pronounced in unhealthy than in healthy ageing. On the other hand, a distinct gut microbiota signature is displayed during longevity, the most prominent being an enrichment in both SCFA and IPA bacterial producers. This short Review discusses, in an innovative and integrative way, cutting-edge research on the composition of gut microorganisms and profile of metabolites secreted by them, that are associated with a healthy and unhealthy ageing pattern and with longevity. A detailed description of the positive or detrimental metabolic effects, in the ageing host, of diet-derived gut microbial metabolites is provided. Finally, microbiota-targeted interventions that counteract gut dysbiosis associated with ageing, are briefly outlined.
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Affiliation(s)
- João R Araújo
- Nutrition & Metabolism, CINTESIS@RISE, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa 1169-056, Portugal.
| | - Cláudia Marques
- Nutrition & Metabolism, CINTESIS@RISE, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa 1169-056, Portugal.
| | - Catarina Rodrigues
- Nutrition & Metabolism, CHRC, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa 1169-056, Portugal.
| | - Conceição Calhau
- Nutrition & Metabolism, CINTESIS@RISE, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa 1169-056, Portugal; Unidade Universitária Lifestyle Medicine José de Mello Saúde by NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa 1169-056, Portugal.
| | - Ana Faria
- Nutrition & Metabolism, CINTESIS@RISE, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa 1169-056, Portugal; Nutrition & Metabolism, CHRC, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa 1169-056, Portugal.
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70
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Castiglioni VG, Olmo-Uceda MJ, Martín S, Félix MA, González R, Elena SF. Experimental evolution of an RNA virus in Caenorhabditis elegans. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105623. [PMID: 38901623 DOI: 10.1016/j.meegid.2024.105623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/02/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024]
Abstract
The discovery of Orsay virus (OrV), the first virus infecting wild populations of Caenorhabditis elegans, has boosted studies of viral immunity pathways in this nematode. Considering the many advantages that C. elegans offers for fundamental research in host-pathogen interactions, this pathosystem has high potential to become a model system for experimental virus evolution studies. However, the evolutionary constraints - i.e, the balance between genetic variation, selection, drift and historical contingency- operating in this pathosystem have barely been explored. Here we describe for the first time an evolution experiment of two different OrV strains in C. elegans. Comparison of the two ancestral strains showed differences in infectivity and sequence, and highlighted the importance of consistently normalize viral inocula for meaningful comparisons among strains. After 10 serial passages of evolution, we report slight changes in infectivity and non-synonymous mutations fixed in the evolved viral populations. In addition, we observed numerous minor variants emerging in the viral population. These minor variants were not randomly distributed along the genome but concentrated in polymorphic genomic regions. Overall, our work established the grounds for future experimental virus evolution studies using Caenorhabditis nematodes.
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Affiliation(s)
- Victoria G Castiglioni
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, 46980 València, Spain
| | - María J Olmo-Uceda
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, 46980 València, Spain
| | - Susana Martín
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, 46980 València, Spain
| | - Marie-Anne Félix
- Institut de Biologie de l'École Normale Supérieure, CNRS, INSERM, 75005 Paris, France
| | - Rubén González
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, 46980 València, Spain; Institut de Biologie de l'École Normale Supérieure, CNRS, INSERM, 75005 Paris, France.
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, 46980 València, Spain; Santa Fe Institute, Sant Fe, NM 87501, USA.
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71
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Vosseberg J, van Hooff JJE, Köstlbacher S, Panagiotou K, Tamarit D, Ettema TJG. The emerging view on the origin and early evolution of eukaryotic cells. Nature 2024; 633:295-305. [PMID: 39261613 DOI: 10.1038/s41586-024-07677-6] [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: 11/02/2023] [Accepted: 06/05/2024] [Indexed: 09/13/2024]
Abstract
The origin of the eukaryotic cell, with its compartmentalized nature and generally large size compared with bacterial and archaeal cells, represents a cornerstone event in the evolution of complex life on Earth. In a process referred to as eukaryogenesis, the eukaryotic cell is believed to have evolved between approximately 1.8 and 2.7 billion years ago from its archaeal ancestors, with a symbiosis with a bacterial (proto-mitochondrial) partner being a key event. In the tree of life, the branch separating the first from the last common ancestor of all eukaryotes is long and lacks evolutionary intermediates. As a result, the timing and driving forces of the emergence of complex eukaryotic features remain poorly understood. During the past decade, environmental and comparative genomic studies have revealed vital details about the identity and nature of the host cell and the proto-mitochondrial endosymbiont, enabling a critical reappraisal of hypotheses underlying the symbiotic origin of the eukaryotic cell. Here we outline our current understanding of the key players and events underlying the emergence of cellular complexity during the prokaryote-to-eukaryote transition and discuss potential avenues of future research that might provide new insights into the enigmatic origin of the eukaryotic cell.
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Affiliation(s)
- Julian Vosseberg
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Jolien J E van Hooff
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Stephan Köstlbacher
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Kassiani Panagiotou
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Daniel Tamarit
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.
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Lippincott RA, O’Connor J, Neff CP, Lozupone C, Palmer BE. Deciphering HIV-associated inflammation: microbiome's influence and experimental insights. Curr Opin HIV AIDS 2024; 19:228-233. [PMID: 38884255 PMCID: PMC11305906 DOI: 10.1097/coh.0000000000000866] [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] [Indexed: 06/18/2024]
Abstract
PURPOSE OF REVIEW To review novel experimental approaches for studying host:microbe interactions and their role in intestinal and systemic inflammation in people living with HIV (PLWH). RECENT FINDINGS Inflammation in PLWH is impacted by interactions between the microbiome, the intestinal epithelium, and immune cells. This complex interplay is not fully understood and requires a variety of analytical techniques to study. Using a multiomic systems biology approach provides hypothesis generating data on host:microbe interactions that can be used to guide further investigation. The direct interactions between host cells and microbes can be elucidated using peripheral blood mononuclear cells (PBMCs), lamina propria mononuclear cells (LPMC's) or human intestinal organoids (HIO). Additionally, the broader relationship between the host and the microbiome can be explored using animal models such as nonhuman primates and germ-free and double humanized mice. SUMMARY To explore complex host:microbe relationships, hypotheses are generated and investigations are guided by multiomic data, while causal components are identified using in-vitro and in-vivo assays.
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Affiliation(s)
| | - John O’Connor
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | | | - Catherine Lozupone
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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Spence H, Mengoa-Fleming S, Sneddon AA, McNeil CJ, Waiter GD. Associations between sex, systemic iron and inflammatory status and subcortical brain iron. Eur J Neurosci 2024; 60:5069-5085. [PMID: 39113267 DOI: 10.1111/ejn.16467] [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: 01/12/2024] [Revised: 06/24/2024] [Accepted: 07/02/2024] [Indexed: 09/04/2024]
Abstract
Brain iron increases in several neurodegenerative diseases are associated with disease progression. However, the causes of increased brain iron remain unclear. This study investigates relationships between subcortical iron, systemic iron and inflammatory status. Brain magnetic resonance imaging (MRI) scans and blood plasma samples were collected from cognitively healthy females (n = 176, mean age = 61.4 ± 4.5 years, age range = 28-72 years) and males (n = 152, mean age = 62.0 ± 5.1 years, age range = 32-74 years). Regional brain iron was quantified using quantitative susceptibility mapping. To assess systemic iron, haematocrit, ferritin and soluble transferrin receptor were measured, and total body iron index was calculated. To assess systemic inflammation, C-reactive protein (CRP), neutrophil:lymphocyte ratio (NLR), macrophage colony-stimulating factor 1 (MCSF), interleukin 6 (IL6) and interleukin 1β (IL1β) were measured. We demonstrated that iron levels in the right hippocampus were higher in males compared with females, while iron in the right caudate was higher in females compared with males. There were no significant associations observed between subcortical iron levels and blood markers of iron and inflammatory status indicating that such blood measures are not markers of brain iron. These results suggest that brain iron may be regulated independently of blood iron and so directly targeting global iron change in the treatment of neurodegenerative disease may have differential impacts on blood and brain iron.
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Affiliation(s)
- Holly Spence
- Aberdeen Biomedical Imaging Centre, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Stephanie Mengoa-Fleming
- Aberdeen Biomedical Imaging Centre, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | | | - Christopher J McNeil
- Aberdeen Biomedical Imaging Centre, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Gordon D Waiter
- Aberdeen Biomedical Imaging Centre, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
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Laatri S, El Khayari S, Qriouet Z. Exploring the molecular aspect and updating evolutionary approaches to the DNA polymerase enzymes for biotechnological needs: A comprehensive review. Int J Biol Macromol 2024; 276:133924. [PMID: 39033894 DOI: 10.1016/j.ijbiomac.2024.133924] [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: 03/10/2024] [Revised: 07/07/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
DNA polymerases are essential enzymes that play a key role in living organisms, as they participate in the synthesis and maintenance of the DNA molecule. The intrinsic properties of these enzymes have been widely observed and studied to understand their functions, activities, and behavior, which has allowed their natural power in DNA synthesis to be exploited in modern biotechnology, to the point of making them true pillars of the field. In this context, the laboratory evolution of these enzymes, either by directed evolution or rational design, has led to the generation of a wide range of new DNA polymerases with novel properties, suitable for a variety of biotechnological needs. In this review, we examine DNA polymerases at the molecular level, their biotechnological use, and their evolutionary methods in relation to the novel properties sought, providing a chronological selection of evolved DNA polymerases cited in the literature that we consider to be of great interest. To our knowledge, this work is the first to bring together the molecular, functional and evolutionary aspects of the DNA polymerase enzyme. We believe it will be of great interest to researchers whose aim is to produce new lines of evolved DNA polymerases.
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Affiliation(s)
- Said Laatri
- Microbiology and Molecular Biology Laboratory, Faculty of Sciences, Mohammed V-Souissi University, Rabat 10100, Morocco.
| | | | - Zidane Qriouet
- Pharmacology and Toxicology Laboratory, Faculty of Medicine and Pharmacy, Mohammed V-Souissi University, Rabat 10100, Morocco
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Denkel LA, Gastmeier P. Gut microbiome and its role in the acquisition of extended-spectrum β-lactamase-producing Enterobacterales. Clin Microbiol Infect 2024; 30:1102-1104. [PMID: 38821175 DOI: 10.1016/j.cmi.2024.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/22/2024] [Accepted: 05/26/2024] [Indexed: 06/02/2024]
Affiliation(s)
- Luisa A Denkel
- Institute of Hygiene and Environmental Medicine, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany; National Reference Center for the Surveillance of Nosocomial Infections, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.
| | - Petra Gastmeier
- Institute of Hygiene and Environmental Medicine, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany; National Reference Center for the Surveillance of Nosocomial Infections, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
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76
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Bulnes R, Utay NS. Therapeutic microbiome modulation: new frontiers in HIV treatment. Curr Opin HIV AIDS 2024; 19:268-275. [PMID: 38874442 DOI: 10.1097/coh.0000000000000864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
PURPOSE OF REVIEW Dysbiosis may be a key driver of systemic inflammation, which increases the risk of non-AIDS events in people living with HIV (PLWH). Modulation of the microbiome to reverse this dysbiosis may be a novel approach to decrease inflammation and therefore morbidity and mortality in PLWH. RECENT FINDINGS Fecal microbiota transplantation (FMT), probiotics, prebiotics, synbiotics, postbiotics, and dietary modifications have the potential to modulate the microbiome. These interventions have been well tolerated in clinical trials to date. However, these interventions have not resulted in consistent or lasting changes to the microbiome or consistent changes in biomarkers of intestinal permeability, microbial translocation, inflammation, immune activation, or CD4 + T cell counts. Sustained engraftment may require prebiotics and/or dietary modifications added to either probiotics or FMT. SUMMARY Adequately powered randomized controlled trials are needed to elucidate whether microbiome modulation can be achieved and impact systemic inflammation in PLWH.
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Affiliation(s)
- Rene Bulnes
- Department of Internal Medicine, Division of Infectious Diseases and Geographic Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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Rodriguez-Ruiz JP, Lin Q, Van Heirstraeten L, Lammens C, Stewardson AJ, Godycki-Cwirko M, Coenen S, Goossens H, Harbarth S, Malhotra-Kumar S. Long-term effects of ciprofloxacin treatment on the gastrointestinal and oropharyngeal microbiome are more pronounced after longer antibiotic courses. Int J Antimicrob Agents 2024; 64:107259. [PMID: 38936492 DOI: 10.1016/j.ijantimicag.2024.107259] [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] [Revised: 06/04/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND Urinary tract infections (UTIs) are one of the main reasons for antibiotic prescriptions in primary care. Recent studies demonstrate similar clinical outcomes with short vs. long antibiotics courses. The aim of this study was to investigate the differential collateral effect of ciprofloxacin treatment duration on the gastrointestinal and oropharyngeal microbiome in patients presenting with uncomplicated UTI to primary care practices in Switzerland, Belgium and Poland. METHODS Stool and oropharyngeal samples were obtained from 36 treated patients and 14 controls at the beginning of antibiotic therapy, end of therapy and one month after the end of therapy. Samples underwent shotgun metagenomics. RESULTS At the end of therapy, patients treated with both short (≤7 days) and long (>7 days) ciprofloxacin courses showed similar changes in the gastrointestinal microbiome compared to non-treated controls. After one month, most changes in patients receiving short courses were reversed; however, long courses led to increased abundance of the genera Roseburia, Faecalicatena and Escherichia. Changes in the oropharynx were minor and reversed to baseline levels within one month. Ciprofloxacin resistance encoding mutations in gyrA/B and parC/E reads were observed in both short and long treatment groups but decreased to baseline levels after one month. An increased abundance of resistance genes was observed in the gastrointestinal microbiome after longer treatment, and correlated to increased prevalence of aminoglycoside, β-lactam, sulphonamide, and tetracycline resistance genes. CONCLUSION Collateral effects on the gastrointestinal community, including an increased prevalence of antimicrobial resistance genes, persists for up to at least one month following longer ciprofloxacin therapy. These data support the use of shorter antimicrobial treatment duration.
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Affiliation(s)
- J P Rodriguez-Ruiz
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Q Lin
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - L Van Heirstraeten
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - C Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - A J Stewardson
- Department of Infectious Diseases, The Alfred and Central Clinical School, Monash University, Melbourne, Australia
| | - M Godycki-Cwirko
- Centre for Family and Community Medicine, Medical University of Lodz, Lodz, Poland
| | - S Coenen
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - H Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - S Harbarth
- Infection Control Program & Division of Infectious Diseases, University of Geneva and Faculty of Medicine, Geneva
| | - S Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium.
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Ortiz AM, Brenchley JM. Untangling the role of the microbiome across the stages of HIV disease. Curr Opin HIV AIDS 2024; 19:221-227. [PMID: 38935047 PMCID: PMC11305932 DOI: 10.1097/coh.0000000000000870] [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] [Indexed: 06/28/2024]
Abstract
PURPOSE OF REVIEW The primate microbiome consists of bacteria, eukaryotes, and viruses that dynamically shape and respond to host health and disease. Understanding how the symbiotic relationship between the host and microbiome responds to HIV has implications for therapeutic design. RECENT FINDINGS Advances in microbiome identification technologies have expanded our ability to identify constituents of the microbiome and to infer their functional capacity. The dual use of these technologies and animal models has allowed interrogation into the role of the microbiome in lentiviral acquisition, vaccine efficacy, and the response to antiretrovirals. Lessons learned from such studies are now being harnessed to design microbiome-based interventions. SUMMARY Previous studies considering the role of the microbiome in people living with HIV largely described viral acquisition as an intrusion on the host:microbiome interface. Re-framing this view to consider HIV as a novel, albeit unwelcome, component of the microbiome may better inform the research and development of pre and postexposure prophylaxes.
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Affiliation(s)
- Alexandra M Ortiz
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, NIAID, NIH, Bethesda, Maryland, USA
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79
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Zou J, Kyndt T, Yu J, Zhou J. Plant-nematode battle: engagement of complex signaling network. Trends Parasitol 2024; 40:846-857. [PMID: 39142937 DOI: 10.1016/j.pt.2024.07.010] [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: 01/30/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 08/16/2024]
Abstract
Plant-parasitic nematodes (PPNs) are widely distributed and highly adaptable. To evade the invasion and infection of PPNs, plants initiate a series of defense responses. In turn, PPNs secrete effectors into the host tissues to suppress plant defense. In this ongoing battle between PPNs and plants, complex signal transduction processes are typically involved. This article aims to review the plant signaling network involved in host perception by the nematode, nematode perception, and downstream activation of plant defense signaling and how nematodes attempt to interfere with this network. Our goal is to establish a foundation for elucidating the signaling and regulatory mechanisms of plant-nematode interactions, and to provide insights and tools for developing PPN-resistant crops and technologies.
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Affiliation(s)
- Jinping Zou
- Department of Horticulture, Zhejiang Provincial Key Laboratory of Horticultural Crop Quality Regulation, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China; Key Laboratory of Horticultural Plants Growth, Development and Quality Improvement, Ministry of Agriculture and Rural Affairs of China, Yuhangtang Road 866, Hangzhou 310058, China
| | - Tina Kyndt
- Department Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
| | - Jingquan Yu
- Department of Horticulture, Zhejiang Provincial Key Laboratory of Horticultural Crop Quality Regulation, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China; Key Laboratory of Horticultural Plants Growth, Development and Quality Improvement, Ministry of Agriculture and Rural Affairs of China, Yuhangtang Road 866, Hangzhou 310058, China
| | - Jie Zhou
- Department of Horticulture, Zhejiang Provincial Key Laboratory of Horticultural Crop Quality Regulation, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China; Key Laboratory of Horticultural Plants Growth, Development and Quality Improvement, Ministry of Agriculture and Rural Affairs of China, Yuhangtang Road 866, Hangzhou 310058, China.
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Bustamante-Brito R, Vera-Ponce de León A, Rosenblueth M, Martínez-Romero E. Comparative genomics of the carmine cochineal symbiont Candidatus Dactylopiibacterium carminicum reveals possible protection to the host against viruses via CRISPR/Cas. Syst Appl Microbiol 2024; 47:126540. [PMID: 39068732 DOI: 10.1016/j.syapm.2024.126540] [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: 03/14/2024] [Revised: 06/25/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
We present new genomes from the bacterial symbiont Candidatus Dactylopiibacterium carminicum obtained from non-domesticated carmine cochineals belonging to the scale insect Dactylopius (Hemiptera: Coccoidea: Dactylopiidae). As Dactylopiibacterium has not yet been cultured in the laboratory, metagenomes and metatranscriptomics have been key in revealing putative symbiont functions. Dactylopiibacterium is a nitrogen-fixing beta-proteobacterium that may be vertically transmitted and shows differential gene expression inside the cochineal depending on the tissue colonized. Here we found that all cochineal species tested had Dactylopiibacterium carminicum which has a highly conserved genome. All Dactylopiibacterium genomes analyzed had genes involved in nitrogen fixation and plant polymer degradation. Dactylopiibacterium genomes resemble those from free-living plant bacteria, some found as endophytes. Notably, we found here a new putative novel function where the bacteria may protect the insect from viruses, since all Dactylopiibacterium genomes contain CRISPRs with a spacer matching nucleopolyhedrovirus that affects insects.
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Affiliation(s)
- Rafael Bustamante-Brito
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico
| | - Arturo Vera-Ponce de León
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico; Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Mónica Rosenblueth
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico
| | - Esperanza Martínez-Romero
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico.
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Guardamagna M, Meyer ML, Berciano-Guerrero MÁ, Mesas-Ruiz A, Cobo-Dols M, Perez-Ruiz E, Cantero Gonzalez A, Lavado-Valenzuela R, Barragán I, Oliver J, Garrido-Aranda A, Alvarez M, Rueda-Dominguez A, Queipo-Ortuño MI, Alba Conejo E, Benitez JC. Oncogene-addicted solid tumors and microbiome-lung cancer as a main character: a narrative review. Transl Lung Cancer Res 2024; 13:2050-2066. [PMID: 39263011 PMCID: PMC11384476 DOI: 10.21037/tlcr-24-216] [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: 03/06/2024] [Accepted: 07/03/2024] [Indexed: 09/13/2024]
Abstract
Background and Objective Lung cancer stands as the main cause of cancer-related deaths worldwide. With the advent of immunotherapy and the discovery of targetable oncogenic driver genes, although prognosis has changed in the last few years, survival rates remain dismal for most patients. This emphasizes the urgent need for new strategies that could enhance treatment in precision medicine. The role of the microbiota in carcinogenesis constitutes an evolving landscape of which little is known. It has been suggested these microorganisms may influence in responses, resistance, and adverse effects to cancer treatments, particularly to immune checkpoint blockers. However, evidence on the impact of microbiota composition in oncogene-addicted tumors is lacking. This review aims to provide an overview of the relationship between microbiota, daily habits, the immune system, and oncogene-addicted tumors, focusing on lung cancer. Methods A PubMed and Google Scholar search from 2013 to 2024 was conducted. Relevant articles were reviewed in order to guide our research and generate hypothesis of clinical applicability. Key Content and Findings Microbiota is recognized to participate in immune reprogramming, fostering inflammatory, immunosuppressive, or anti-tumor responses. Therefore, identifying the microbiota that impact response to treatment and modulating its composition by interventions such as dietary modifications, probiotics or antibiotics, could potentially yield better outcomes for cancer patients. Additionally, targeted therapies that modulate molecular signaling pathways may impact both immunity and microbiota. Understanding this intricate interplay could unveil new therapeutic strategies. Conclusions By comprehending how microbiota may influence efficacy of targeted therapies, even though current evidence is scarce, we may generate interesting hypotheses that could improve clinical practice.
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Affiliation(s)
- Mora Guardamagna
- Medical Oncology Department, Virgen de la Victoria University Hospital, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
- Department of Medicine and Dermatology, Medical School University of Málaga, Campus Teatinos, Málaga, Spain
- Department of Cancer Medicine, Institute Gustave Roussy, Villejuif, France
| | - May-Lucie Meyer
- The Tisch Cancer Institute, Mount Sinai Hospital, New York, NY, USA
| | - Miguel Ángel Berciano-Guerrero
- Medical Oncology Department, Virgen de la Victoria University Hospital, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
- Department of Medicine and Dermatology, Medical School University of Málaga, Campus Teatinos, Málaga, Spain
- Group of Translational Research in Cancer Immunotherapy, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
| | - Andres Mesas-Ruiz
- Medical Oncology Department, Virgen de la Victoria University Hospital, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
| | - Manuel Cobo-Dols
- Group of Translational Research in Cancer Immunotherapy, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
- Medical Oncology Department, Regional University Hospital, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
| | - Elisabeth Perez-Ruiz
- Group of Translational Research in Cancer Immunotherapy, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
- Medical Oncology Department, Regional University Hospital, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
| | - Alexandra Cantero Gonzalez
- Group of Translational Research in Cancer Immunotherapy, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
- Medical Oncology Department, Regional University Hospital, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
| | - Rocío Lavado-Valenzuela
- Medical Oncology Department, Virgen de la Victoria University Hospital, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
- Cancer Molecular Biology Laboratory, CIMES, Malaga, Spain
| | - Isabel Barragán
- Group of Translational Research in Cancer Immunotherapy, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
- Group of Pharmacoepigenetics, Department of Physiology and Pharmacology, Karolinska Institute, Solna, Sweden
| | - Javier Oliver
- Group of Translational Research in Cancer Immunotherapy, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
| | - Alicia Garrido-Aranda
- Medical Oncology Department, Virgen de la Victoria University Hospital, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
- Cancer Molecular Biology Laboratory, CIMES, Malaga, Spain
| | - Martina Alvarez
- Medical Oncology Department, Virgen de la Victoria University Hospital, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
- Cancer Molecular Biology Laboratory, CIMES, Malaga, Spain
| | - Antonio Rueda-Dominguez
- Medical Oncology Department, Virgen de la Victoria University Hospital, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
- Department of Medicine and Dermatology, Medical School University of Málaga, Campus Teatinos, Málaga, Spain
- Group of Translational Research in Cancer Immunotherapy, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
| | - María Isabel Queipo-Ortuño
- Medical Oncology Department, Virgen de la Victoria University Hospital, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
- Department of Surgical Specialties, Biochemical and Immunology, Faculty of Medicine, University of Málaga, Málaga, Spain
| | - Emilio Alba Conejo
- Medical Oncology Department, Virgen de la Victoria University Hospital, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
- Department of Medicine and Dermatology, Medical School University of Málaga, Campus Teatinos, Málaga, Spain
- Group of Translational Research in Cancer Immunotherapy, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
| | - Jose Carlos Benitez
- Medical Oncology Department, Virgen de la Victoria University Hospital, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
- Group of Translational Research in Cancer Immunotherapy, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
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Gharib E, Robichaud GA. From Crypts to Cancer: A Holistic Perspective on Colorectal Carcinogenesis and Therapeutic Strategies. Int J Mol Sci 2024; 25:9463. [PMID: 39273409 PMCID: PMC11395697 DOI: 10.3390/ijms25179463] [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: 07/29/2024] [Revised: 08/19/2024] [Accepted: 08/24/2024] [Indexed: 09/15/2024] Open
Abstract
Colorectal cancer (CRC) represents a significant global health burden, with high incidence and mortality rates worldwide. Recent progress in research highlights the distinct clinical and molecular characteristics of colon versus rectal cancers, underscoring tumor location's importance in treatment approaches. This article provides a comprehensive review of our current understanding of CRC epidemiology, risk factors, molecular pathogenesis, and management strategies. We also present the intricate cellular architecture of colonic crypts and their roles in intestinal homeostasis. Colorectal carcinogenesis multistep processes are also described, covering the conventional adenoma-carcinoma sequence, alternative serrated pathways, and the influential Vogelstein model, which proposes sequential APC, KRAS, and TP53 alterations as drivers. The consensus molecular CRC subtypes (CMS1-CMS4) are examined, shedding light on disease heterogeneity and personalized therapy implications.
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Affiliation(s)
- Ehsan Gharib
- Département de Chimie et Biochimie, Université de Moncton, Moncton, NB E1A 3E9, Canada
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada
| | - Gilles A Robichaud
- Département de Chimie et Biochimie, Université de Moncton, Moncton, NB E1A 3E9, Canada
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada
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83
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Zhao M, Tian J, Hou W, Yin L, Li W. Global research trends on the associations between the microbiota and lung cancer: a visualization bibliometric analysis (2008-2023). Front Microbiol 2024; 15:1416385. [PMID: 39282557 PMCID: PMC11392740 DOI: 10.3389/fmicb.2024.1416385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 08/19/2024] [Indexed: 09/19/2024] Open
Abstract
Numerous papers have been published on the microbiota in lung cancer in recent years. However, there is still a lack of bibliometric analysis of the microbiota in lung cancer in this field. Our paper did bibliometric analyses and elucidated the knowledge structure and study hotspots related to the microbiota in lung cancer patients. We screened publications reporting on the microbiota in lung cancer from 2008 to 2023 from the Web of Science Core Collection (WoSCC) database, and carried out bibliometric analyses by the application of the VOSviewers, CiteSpace and R package "bibliometrix." The 684 documents enrolled in the analysis were obtained from 331 institutions in 67 regions by 4,661 authors and were recorded in 340 journals. Annual papers are growing rapidly, and the countries of China, the United States and Italy are contributing the most to this area of research. Zhejiang University is the main research organization. Science and Cancer had significant impacts on this area. Zhang Yan had the most articles, and the Bertrand Routy had the most co-cited times. Exploring the mechanism of action of the lung and/or gut microbiota in lung cancer and therapeutic strategies involving immune checkpoint inhibitors in lung cancer are the main topics. Moreover, "gut microbiota," "immunotherapy," and "short-chain fatty acids" are important keywords for upcoming study hotspots. In conclusion, microbiota research offers promising opportunities in lung cancer, with pivotal studies exploring the mechanisms that link lung and gut microbiota to therapeutic strategies, particularly through immune checkpoint inhibitors. Moreover, the gut-lung axis emerges as a novel target for innovative treatments. Further research is essential to unravel the detailed mechanisms of this connection.
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Affiliation(s)
- Maoyuan Zhao
- Lung Cancer Center, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jie Tian
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wang Hou
- Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Liyuan Yin
- Lung Cancer Center, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Research Units of West China, Chinese Academy of Medical Sciences, West China Hospital, Chengdu, Sichuan, China
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Santolin L, Riedel SL, Brigham CJ. Synthetic biology toolkit of Ralstonia eutropha (Cupriavidus necator). Appl Microbiol Biotechnol 2024; 108:450. [PMID: 39207499 PMCID: PMC11362209 DOI: 10.1007/s00253-024-13284-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024]
Abstract
Synthetic biology encompasses many kinds of ideas and techniques with the common theme of creating something novel. The industrially relevant microorganism, Ralstonia eutropha (also known as Cupriavidus necator), has long been a subject of metabolic engineering efforts to either enhance a product it naturally makes (polyhydroxyalkanoate) or produce novel bioproducts (e.g., biofuels and other small molecule compounds). Given the metabolic versatility of R. eutropha and the existence of multiple molecular genetic tools and techniques for the organism, development of a synthetic biology toolkit is underway. This toolkit will allow for novel, user-friendly design that can impart new capabilities to R. eutropha strains to be used for novel application. This article reviews the different synthetic biology techniques currently available for modifying and enhancing bioproduction in R. eutropha. KEY POINTS: • R. eutropha (C. necator) is a versatile organism that has been examined for many applications. • Synthetic biology is being used to design more powerful strains for bioproduction. • A diverse synthetic biology toolkit is being developed to enhance R. eutropha's capabilities.
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Affiliation(s)
- Lara Santolin
- Technische Universität Berlin, Institute of Biotechnology, Chair of Bioprocess Engineering, Berlin, Germany
| | - Sebastian L Riedel
- Berliner Hochschule Für Technik, Department VIII - Mechanical Engineering, Event Technology and Process Engineering, Environmental and Bioprocess Engineering Laboratory, Berlin, Germany.
| | - Christopher J Brigham
- Department of Bioengineering, University of Massachusetts Dartmouth, North Dartmouth, MA, USA.
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85
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Shi X, Liu Y, Ma T, Jin H, Zhao F, Sun Z. Delivery mode and maternal gestational diabetes are important factors in shaping the neonatal initial gut microbiota. Front Cell Infect Microbiol 2024; 14:1397675. [PMID: 39268487 PMCID: PMC11390658 DOI: 10.3389/fcimb.2024.1397675] [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: 03/08/2024] [Accepted: 08/06/2024] [Indexed: 09/15/2024] Open
Abstract
Background The infant gut microbiome's establishment is pivotal for health and immune development. Understanding it unveils insights into growth, development, and maternal microbial interactions. Research often emphasizes gut bacteria, neglecting the phageome. Methods To investigate the influence of geographic or maternal factors (mode of delivery, mode of breastfeeding, gestational diabetes mellitus) on the gut microbiota and phages of newborns, we collected fecal samples from 34 pairs of mothers and their infants within 24 hours of delivery from three regions (9 pairs from Enshi, 7 pairs from Hohhot, and 18 pairs from Hulunbuir) using sterile containers. Gut microbiota analysis by Shotgun sequencing was subsequently performed. Results Our results showed that geographic location affects maternal gut microbiology (P < 0.05), while the effect on infant gut microbiology was not significant (P = 0.184). Among the maternal factors, mode of delivery had a significant (P < 0.05) effect on the newborn. Specific bacteria (e.g., Bacteroides, Escherichia spp., Phocaeicola vulgatus, Escherichia coli, Staphylococcus hominis, Veillonella spp.), predicted active metabolites, and bacteriophage vOTUs varied with delivery mode. Phocaeicola vulgatus significantly correlated with some metabolites and bacteriophages in the early infant gut (P < 0.05). In the GD group, a strong negative correlation of phage diversity between mother and infants was observed (R = -0.58, P=0.04). Conclusion In conclusion, neonatal early gut microbiome (including bacteria and bacteriophages) colonization is profoundly affected by the mode of delivery, and maternal gestational diabetes mellitus. The key bacteria may interact with bacteriophages to influence the levels of specific metabolites. Our study provides new evidence for the study of the infant microbiome, fills a gap in the analysis of the infant gut microbiota regarding the virome, and emphasizes the importance of maternal health for the infant initial gut virome.
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Affiliation(s)
- Xuan Shi
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Collaborative Innovation Center of Lactic Acid Bacteria and Fermented Dairy Products, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Yanfang Liu
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Collaborative Innovation Center of Lactic Acid Bacteria and Fermented Dairy Products, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Teng Ma
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Collaborative Innovation Center of Lactic Acid Bacteria and Fermented Dairy Products, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Hao Jin
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Collaborative Innovation Center of Lactic Acid Bacteria and Fermented Dairy Products, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Feiyan Zhao
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Collaborative Innovation Center of Lactic Acid Bacteria and Fermented Dairy Products, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Zhihong Sun
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Collaborative Innovation Center of Lactic Acid Bacteria and Fermented Dairy Products, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
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Yang KC, Tien WY, Cheng MF. Gut microbiota compositions in the carriers and noncarriers of third-generation cephalosporin-resistant Escherichia coli: A study among children in southern Taiwan. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2024:S1684-1182(24)00154-3. [PMID: 39261124 DOI: 10.1016/j.jmii.2024.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 08/13/2024] [Accepted: 08/26/2024] [Indexed: 09/13/2024]
Abstract
BACKGROUND Antimicrobial resistance, particularly in third-generation cephalosporin-resistant (3GC-R) Escherichia coli (E. coli), poses major global health challenges and has various clinical implications. Researchers have explored the relationship between extended-spectrum β-lactamase-producing E. coli and gut microbiota composition, which influence host health and disease susceptibility, in adults. In this study, we analyzed gut microbiota composition in Taiwanese children by the colonization status of 3GC-R E. coli. METHODS This cross-sectional study included children (age, 0-6 years) from Kaohsiung, Taiwan. Fecal samples were subjected to microbiological and gut microbiome (full-length 16S rRNA sequencing) analyses. The antimicrobial susceptibility of E. coli colonies isolated from the samples was tested. Furthermore, gut microbiota compositions and diversity indices were compared between 3GC-R E. coli carriers and noncarriers. RESULTS Approximately 46% of all children aged <6 years carried 3GC-R E. coli. The abundances of Drancourtella, Romboutsia, and Desulfovibrio (genus level) were higher in carriers than in noncarriers. By contrast, the abundances of Odoribacteraceae (family level) and Sutterella (genus level) were higher in noncarriers than in carriers. No significant between-group difference was observed in alpha diversity. However, a significant between-group difference was noted in beta diversity (unweighted UniFrac analysis). CONCLUSION This is the first study that investigated differences in the gut microbiota between healthy 3GC-R E. coli carriers and noncarriers in children, suggesting potential mechanisms involving altered utilization of short-chain fatty acids and elevated succinate levels contributing to increased colonization of 3GC-R E. coli. The other taxa identified in this study may contribute to colonization resistance in the pediatric population.
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Affiliation(s)
- Keng-Chin Yang
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Wan-Yu Tien
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Ming-Fang Cheng
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan; School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Kaohsiung Veterans General Hospital Tainan Branch, Tainan, Taiwan.
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87
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Flynn PJ, Moreau CS. Viral diversity and co-evolutionary dynamics across the ant phylogeny. Mol Ecol 2024:e17519. [PMID: 39192682 DOI: 10.1111/mec.17519] [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: 06/13/2024] [Revised: 07/25/2024] [Accepted: 08/15/2024] [Indexed: 08/29/2024]
Abstract
Knowledge of viral biodiversity within insects, particularly within ants, is extremely limited with only a few environmental viruses from invasive ant species identified to date. This study documents and explores the viral communities in ants. We comprehensively profile the metagenomes of a phylogenetically broad group of 35 ant species with varied ecological traits and report the discovery of 3710 novel and unique ant-associated viral genomes. These previously unknown viruses discovered within this study constitute over 95% of all currently described ant viruses, significantly increasing our knowledge of the ant virosphere. The identified RNA and DNA viruses fill gaps in insect-associated viral phylogenies and uncover evolutionary histories characterized by both frequent host switching and co-divergence. Many ants also host diverse bacterial communities, and we discovered that approximately one-third of these new ant-associated viruses are bacteriophages. Two ecological categories, bacterial abundance in the host and habitat degradation are both correlated with ant viral diversity and help to structure viral communities within ants. These data demonstrate that the ant virosphere is remarkably diverse phylogenetically and genomically and provide a substantial foundation for studies in virus ecology and evolution within eukaryotes. We highlight the importance of studying insect-associated viruses in natural ecosystems in order to more thoroughly and effectively understand host-microbe evolutionary dynamics.
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Affiliation(s)
- Peter J Flynn
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Corrie S Moreau
- Department of Entomology, Cornell University, Ithaca, New York, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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88
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Lammi C, Ottaviano E, Fiore G, Bollati C, d'Adduzio L, Fanzaga M, Ceccarani C, Vizzuso S, Zuccotti G, Borghi E, Verduci E. Effect of docosahexaenoic acid as an anti-inflammatory for Caco-2 cells and modulating agent for gut microbiota in children with obesity (the DAMOCLE study). J Endocrinol Invest 2024:10.1007/s40618-024-02444-w. [PMID: 39186221 DOI: 10.1007/s40618-024-02444-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024]
Abstract
PURPOSE Docosahexaenoic acid (DHA) is a long-chain omega-3 polyunsaturated fatty acid. We investigated the dual health ability of DHA to modulate gut microbiota in children with obesity and to exert anti-inflammatory activity on human intestinal Caco-2 cells. METHODS In a pilot study involving 18 obese children (8-14 years), participants received a daily DHA supplement (500 mg/day) and dietary intervention from baseline (T0) to 4 months (T1), followed by dietary intervention alone from 4 months (T1) to 8 months (T2). Fecal samples, anthropometry, biochemicals and dietary assessment were collected at each timepoint. At preclinical level, we evaluated DHA's antioxidant and anti-inflammatory effects on Caco-2 cells stimulated with Hydrogen peroxide (H2O2) and Lipopolysaccharides (LPS), by measuring also Inducible nitric oxide synthase (iNOS) levels and cytokines, respectively. RESULTS Ten children were included in final analysis. No major changes were observed for anthropometric and biochemical parameters, and participants showed a low dietary compliance at T1 and T2. DHA supplementation restored the Firmicutes/Bacteroidetes ratio that was conserved also after the DHA discontinuation at T2. DHA supplementation drove a depletion in Ruminococcaceae and Dialisteraceae, and enrichment in Bacteroidaceae, Oscillospiraceae, and Akkermansiaceae. At genus level, Allisonella was the most decreased by DHA supplementation. In Caco-2 cells, DHA decreased H2O2-induced reactive oxygen species (ROS) and nitric oxide (NO) production via iNOS pathway modulation. Additionally, DHA modulated proinflammatory (IL-1β, IL-6, IFN-γ, TNF-α) and anti-inflammatory (IL-10) cytokine production in LPS-stimulated Caco-2 cells. CONCLUSION An improvement in gut dysbiosis of children with obesity seems to be triggered by DHA and to continue after discontinuation. The ability to modulate gut microbiota, matches also with an anti-inflammatory effect of DHA on Caco-2 cells.
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Affiliation(s)
- C Lammi
- Department of Pharmaceutical Sciences, University of Milan, 20133, Milan, Italy
| | - E Ottaviano
- Department of Health Sciences, University of Milan, 20142, Milan, Italy
| | - G Fiore
- Department of Health Sciences, University of Milan, 20142, Milan, Italy.
- Department of Pediatrics, Vittore Buzzi Children's Hospital, University of Milan, Via Lodovico Castelvetro 32, 20154, Milan, Italy.
| | - C Bollati
- Department of Pharmaceutical Sciences, University of Milan, 20133, Milan, Italy
| | - L d'Adduzio
- Department of Pharmaceutical Sciences, University of Milan, 20133, Milan, Italy
| | - M Fanzaga
- Department of Pharmaceutical Sciences, University of Milan, 20133, Milan, Italy
| | - C Ceccarani
- Institute for Biomedical Technologies, CNR, Segrate, Italy
| | - S Vizzuso
- Department of Pediatrics, Vittore Buzzi Children's Hospital, University of Milan, Via Lodovico Castelvetro 32, 20154, Milan, Italy
| | - G Zuccotti
- Department of Pediatrics, Vittore Buzzi Children's Hospital, University of Milan, Via Lodovico Castelvetro 32, 20154, Milan, Italy
- Department of Biomedical and Clinical Sciences, University of Milan, 20157, Milan, Italy
| | - E Borghi
- Department of Health Sciences, University of Milan, 20142, Milan, Italy
| | - E Verduci
- Department of Health Sciences, University of Milan, 20142, Milan, Italy
- Metabolic Diseases Unit, Department of Paediatrics, Vittore Buzzi Children's Hospital, University of Milan, 20157, Milan, Italy
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89
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Puente-Sánchez F, Pascual-García A, Bastolla U, Pedrós-Alió C, Tamames J. Cross-biome microbial networks reveal functional redundancy and suggest genome reduction through functional complementarity. Commun Biol 2024; 7:1046. [PMID: 39181977 PMCID: PMC11344793 DOI: 10.1038/s42003-024-06616-5] [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: 06/26/2023] [Accepted: 07/23/2024] [Indexed: 08/27/2024] Open
Abstract
The structure of microbial communities arises from a multitude of factors, including the interactions of microorganisms with each other and with the environment. In this work, we sought to disentangle those drivers by performing a cross-study, cross-biome meta-analysis of microbial occurrence data in more than 5000 samples, applying a novel network clustering algorithm aimed to capture conditional taxa co-occurrences. We then examined the phylogenetic and functional composition of the resulting clusters, and searched for global patterns of assembly both at the community level and in the presence/absence of individual metabolic pathways.Our analysis highlighted the prevalence of functional redundancy in microbial communities, particularly between taxa that co-occur in more than one environment, pointing to a relationship between functional redundancy and environmental adaptation. In spite of this, certain pathways were observed in fewer taxa than expected by chance, suggesting the presence of auxotrophy, and presumably cooperation among community members. This hypothetical cooperation may play a role in genome reduction, since we observed a negative relationship between the size of bacterial genomes and the size of the community they belong to.Overall, our results suggest the microbial community assembly is driven by universal principles that operate consistently across different biomes and taxonomic groups.
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Affiliation(s)
- Fernando Puente-Sánchez
- Systems Biology Department, Centro Nacional de Biotecnología (CSIC), C/ Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain.
- Department of Aquatic Sciences and Assessment, Swedish University for Agricultural Sciences (SLU), Lennart Hjelms väg 9, 756 51, Uppsala, Sweden.
| | - Alberto Pascual-García
- Systems Biology Department, Centro Nacional de Biotecnología (CSIC), C/ Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Ugo Bastolla
- Computational Biology and Bioinformatics, Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid - CSIC), C/ Nicolás Cabrera 1, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Carlos Pedrós-Alió
- Systems Biology Department, Centro Nacional de Biotecnología (CSIC), C/ Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Javier Tamames
- Systems Biology Department, Centro Nacional de Biotecnología (CSIC), C/ Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
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90
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Pi Y, Fang M, Li Y, Cai L, Han R, Sun W, Jiang X, Chen L, Du J, Zhu Z, Li X. Interactions between Gut Microbiota and Natural Bioactive Polysaccharides in Metabolic Diseases: Review. Nutrients 2024; 16:2838. [PMID: 39275156 PMCID: PMC11397228 DOI: 10.3390/nu16172838] [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: 07/16/2024] [Revised: 08/16/2024] [Accepted: 08/22/2024] [Indexed: 09/16/2024] Open
Abstract
The gut microbiota constitutes a complex ecosystem, comprising trillions of microbes that have co-evolved with their host over hundreds of millions of years. Over the past decade, a growing body of knowledge has underscored the intricate connections among diet, gut microbiota, and human health. Bioactive polysaccharides (BPs) from natural sources like medicinal plants, seaweeds, and fungi have diverse biological functions including antioxidant, immunoregulatory, and metabolic activities. Their effects are closely tied to the gut microbiota, which metabolizes BPs into health-influencing compounds. Understanding how BPs and gut microbiota interact is critical for harnessing their potential health benefits. This review provides an overview of the human gut microbiota, focusing on its role in metabolic diseases like obesity, type II diabetes mellitus, non-alcoholic fatty liver disease, and cardiovascular diseases. It explores the basic characteristics of several BPs and their impact on gut microbiota. Given their significance for human health, we summarize the biological functions of these BPs, particularly in terms of immunoregulatory activities, blood sugar, and hypolipidemic effect, thus providing a valuable reference for understanding the potential benefits of natural BPs in treating metabolic diseases. These properties make BPs promising agents for preventing and treating metabolic diseases. The comprehensive understanding of the mechanisms by which BPs exert their effects through gut microbiota opens new avenues for developing targeted therapies to improve metabolic health.
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Affiliation(s)
- Yu Pi
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Miaoyu Fang
- Nutrilite Health Institute, Amway (Shanghai) Innovation & Science Co., Ltd., Shanghai 201203, China
| | - Yanpin Li
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Long Cai
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ruyi Han
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenjuan Sun
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xianren Jiang
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liang Chen
- Nutrilite Health Institute, Amway (Shanghai) Innovation & Science Co., Ltd., Shanghai 201203, China
| | - Jun Du
- Nutrilite Health Institute, Amway (Shanghai) Innovation & Science Co., Ltd., Shanghai 201203, China
| | - Zhigang Zhu
- Nutrilite Health Institute, Amway (Shanghai) Innovation & Science Co., Ltd., Shanghai 201203, China
| | - Xilong Li
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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91
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Wang X, Zheng M, Zhang Y, Gao Y, Jiang L, Huang S, Wang X, Su C, Niu W, Wu S, Bai Z. Prior carbapenem exposure increases the incidence of ventilator-associated pneumonia in critically Ill children. BMC Infect Dis 2024; 24:855. [PMID: 39179984 PMCID: PMC11342520 DOI: 10.1186/s12879-024-09735-w] [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: 10/24/2023] [Accepted: 08/07/2024] [Indexed: 08/26/2024] Open
Abstract
BACKGROUND Prior antibiotic exposure has been identified as a risk factor for VAP occurrence, making it a growing concern among clinical practitioners. But there is a lack of systematic research on the types of antibiotics and the duration of exposure that influence VAP occurrence in children at current. METHODS We retrospectively reviewed 278 children admitted to the Pediatric Intensive Care Unit (PICU) and underwent invasive mechanical ventilation (MV) between January 2020 and December 2022. Of these, 171 patients with MV duration ≥ 48 h were included in the study, with 61 of them developing VAP (VAP group) and the remaining 110 as the non-VAP group. We analyzed the relationship between early antibiotic exposure and VAP occurrence. RESULTS The incidence of VAP was 21.94% (61/278). The VAP group had significantly longer length of hospital stay (32.00 vs. 20.00 days, p<0.001), PICU stay(25.00 vs. 10.00 days, p<0.001), and duration of mechanical ventilation(16.00 vs. 6.00 days, p<0.001) compared to the non-VAP group. The mortality in the VAP group was significantly higher than that in the non-VAP group (36.07% vs. 21.82%, p = 0.044). The VAP group had a significantly higher rate of carbapenem exposure (65.57% vs. 41.82%, p = 0.003) and duration of usage (9.00 vs. 5.00 days, p = 0.004) than the non-VAP group. Vancomycin and/or linezolid exposure rates (57.38% vs. 40.00%, p = 0.029) and duration (8 vs. 4.5 days, p = 0.010) in the VAP group were significantly higher than that in the non-VAP group, either. Multivariate logistic regression analysis identified the use of carbapenem (≥ 7 days) (OR = 5.156, 95% CI: 1.881-14.137, p = 0.001), repeated intubation (OR = 3.575, 95% CI: 1.449-8.823, p = 0.006), and tracheostomy (OR = 5.767, 95% CI:1.686-19.729, p = 0.005) as the independent risk factors for the occurrence of VAP, while early intravenous immunoglobulin (IVIG) was a protective factor against VAP (OR = 0.426, 95% CI: 0.185-0.98, p = 0.045). CONCLUSION Prior carbapenem exposure (more than 7 days) was an independent risk factor for the occurrence of VAP. For critically ill children, reducing carbapenem use and duration as much as possible should be considered.
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Affiliation(s)
- Xuguo Wang
- Department of Pediatrics, The First People's Hospital of Lianyungang, Xuzhou Medical University Affiliated Hospital of Lianyungang (Lianyungang Clinical College of Nanjing Medical University), Lianyungang, 222000, China
- Pediatric Intensive Care Unit, Children's Hospital of Soochow University, Suzhou, 215000, Jiangsu, China
| | - Mutian Zheng
- Pediatric Intensive Care Unit, Children's Hospital of Soochow University, Suzhou, 215000, Jiangsu, China
| | - Yue Zhang
- Pediatric Intensive Care Unit, Children's Hospital of Soochow University, Suzhou, 215000, Jiangsu, China
| | - Yang Gao
- Department of Pediatrics, The First People's Hospital of Lianyungang, Xuzhou Medical University Affiliated Hospital of Lianyungang (Lianyungang Clinical College of Nanjing Medical University), Lianyungang, 222000, China
- Pediatric Intensive Care Unit, Children's Hospital of Soochow University, Suzhou, 215000, Jiangsu, China
| | - Leihua Jiang
- Department of Pediatrics, The First People's Hospital of Lianyungang, Xuzhou Medical University Affiliated Hospital of Lianyungang (Lianyungang Clinical College of Nanjing Medical University), Lianyungang, 222000, China
| | - Saihu Huang
- Department of Pediatrics, The First People's Hospital of Lianyungang, Xuzhou Medical University Affiliated Hospital of Lianyungang (Lianyungang Clinical College of Nanjing Medical University), Lianyungang, 222000, China
| | - Xue Wang
- Department of Infection Control, Children's Hospital of Soochow University, Suzhou, 215000, China
| | - Chunmei Su
- Department of Infection Control, Children's Hospital of Soochow University, Suzhou, 215000, China
| | - Wensi Niu
- Pediatric Intensive Care Unit, Children's Hospital of Soochow University, Suzhou, 215000, Jiangsu, China
- Children's Hospital of Wujiang District, Suzhou, 215200, China
| | - Shuiyan Wu
- Pediatric Intensive Care Unit, Children's Hospital of Soochow University, Suzhou, 215000, Jiangsu, China.
| | - Zhenjiang Bai
- Pediatric Intensive Care Unit, Children's Hospital of Soochow University, Suzhou, 215000, Jiangsu, China.
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92
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Pereira TJ, De Santiago A, Bik HM. Soil properties predict below-ground community structure, but not nematode microbiome patterns in semi-arid habitats. Mol Ecol 2024:e17501. [PMID: 39175265 DOI: 10.1111/mec.17501] [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: 01/02/2024] [Revised: 08/02/2024] [Accepted: 08/07/2024] [Indexed: 08/24/2024]
Abstract
Microbial and microeukaryotic communities are extremely abundant and diverse in soil habitats where they play critical roles in ecosystem functioning and services that are essential to soil health. Soil biodiversity is influenced by above-ground (vegetation) and below-ground factors (soil properties), which together create habitat-specific conditions. However, the compound effects of vegetation and soil properties on soil communities are less studied or often focused on one component of the soil biota. Here, we integrate metabarcoding (16S and 18S rRNA genes) and nematode morphology to assess the effects of habitat and soil properties shaping microbial and microeukaryotic communities as well as nematode-associated microbiomes. We show that both vegetation and soil properties (soil bulk density) were major factors structuring microbial and microeukaryotic communities in semi-arid soil habitats. Despite having lower nutrients and lower pH, denser soils displayed significantly higher alpha diversity than less dense soils across datasets. Nematode-associated microbiomes have lower microbial diversity, strongly differ from soil microbes and are more likely to respond to microscale variations among samples than to vegetation or soil bulk density. Consequently, different nematode lineages and trophic groups are likely to display similar associated microbiomes when sharing the same microhabitat. Different microbiome taxa were enriched within specific nematode lineages (e.g. Mycobacterium, Candidatus Cardinium) highlighting potentially new species-specific associations that may confer benefits to their soil nematode hosts. Our findings highlight the importance of exploring above- and below-ground effects to assess community structure in terrestrial habitats, and how fine-scale analyses are critical for understanding patterns of host-associated microbiomes.
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Affiliation(s)
- Tiago José Pereira
- Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Alejandro De Santiago
- Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Holly M Bik
- Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
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93
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Kim JC, Maeng J, Choi JW. The impact of appendectomy on the occurrence of alopecia areata: a retrospective cohort study. Clin Exp Dermatol 2024; 49:1062-1064. [PMID: 38499863 DOI: 10.1093/ced/llae097] [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: 12/10/2023] [Revised: 03/07/2024] [Accepted: 04/06/2024] [Indexed: 03/20/2024]
Abstract
We explore the association between appendectomy and a higher risk of alopecia areata (AA). Analysing data from 16 385 people who had undergone appendectomy and a matched control group we found a higher incidence of AA in the appendectomy group, with a hazard ratio of 2.27 highlighted by the analysis. This suggests that appendectomy may affect the gut microbiome and immune regulation, having an impact on hair health and highlighting the role of appendectomy in autoimmune diseases.
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Affiliation(s)
- Jin Cheol Kim
- Department of Dermatology, Ajou University School of Medicine, Suwon, Korea
| | - Jieun Maeng
- Department of Dermatology, Ajou University School of Medicine, Suwon, Korea
| | - Jee Woong Choi
- Department of Dermatology, Ajou University School of Medicine, Suwon, Korea
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94
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Garbuglia AR, Pauciullo S, Zulian V, Del Porto P. Update on Hepatitis C Vaccine: Results and Challenges. Viruses 2024; 16:1337. [PMID: 39205311 PMCID: PMC11359353 DOI: 10.3390/v16081337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Therapy against the Hepatitis C virus (HCV) has significantly improved with the introduction of direct-acting antiviral drugs (DAAs), achieving over 95% sustained virological response (SVR). Despite this, the development of an effective anti-HCV vaccine remains a critical challenge due to the low number of patients treated with DAAs and the occurrence of HCV reinfections in high-risk groups. Current vaccine strategies aim to stimulate either B-cell or T-cell responses. Vaccines based on E1 and E2 proteins can elicit broad cross-neutralizing antibodies against all major HCV genotypes, though with varying efficiencies and without full protection against infection. In humans, the neutralizing antibodies induced by such vaccines mainly target the AR3 region, but their levels are generally insufficient for broad neutralization. Various HCV proteins expressed through different viral vectors have been utilized to elicit T cell immune responses, showing sustained expansion of HCV-specific effector memory T cells and improved proliferation and polyfunctionality of memory T cells over time. However, despite these advancements, the frequency and effectiveness of T-cell responses remain limited.
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Affiliation(s)
- Anna Rosa Garbuglia
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (S.P.); (V.Z.)
| | - Silvia Pauciullo
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (S.P.); (V.Z.)
| | - Verdiana Zulian
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (S.P.); (V.Z.)
| | - Paola Del Porto
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00100 Rome, Italy;
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95
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Chen Y, Che X, Rong Y, Zhu J, Yu Y, Xu H, Sun Y, Chen H, Yan L, Chen L, Xu Y, Zhang J. Immunomodulation in Endometriosis: Investigating the interrelationship between VISTA expression and Escherichia.Shigella-Associated metabolites. Int Immunopharmacol 2024; 137:112366. [PMID: 38852526 DOI: 10.1016/j.intimp.2024.112366] [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: 04/02/2024] [Revised: 05/18/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024]
Abstract
AIMS Endometriosis is characterized by an abnormal immune microenvironment. Despite the extensive use of immune therapies, the application of immune checkpoint inhibitors in endometriosis lacks confidence due to the instability of preclinical research data. This study aims to elucidate the regulation of the immune inhibitory checkpoint VISTA and its effects on T cells from the perspective of microbiota and metabolism. MAIN METHODS We divided endometriosis patients into high and low groups based on the expression levels of VISTA in lesion tissues. We collected peritoneal fluid samples from these two groups and performed 16 s RNA sequencing and metabolomics analysis to investigate microbial diversity and differential metabolites. Through combined analysis, we identified microbial-associated metabolites and validated their correlation with VISTA and CD8 + T cells using ELISA and immunofluorescence. In vitro experiments were conducted to confirm the regulatory relationship among these factors. KEY FINDINGS Our findings revealed a distinct correlation between VISTA expression and the microbial colony Escherichia.Shigella. Moreover, we identified the metabolites LTD4-d5 and 2-n-Propylthiazolidine-4-carboxylic acid as being associated with both Escherichia.Shigella and VISTA expression. In vitro experiments confirmed the inhibitory effects of these metabolites on VISTA expression, while they demonstrated a positive regulation of CD8 + T cell infiltration into endometriotic lesions. SIGNIFICANCE This study reveals the connection between microbial diversity, metabolites, and VISTA expression in the immune microenvironment of endometriosis, providing potential targets for therapeutic interventions.
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Affiliation(s)
- Yichen Chen
- Women and Children's Hospital of Ningbo University, Ningbo, China
| | - Xuan Che
- Jiaxing University Affiliated Women and Children Hospital, Jiaxing, China
| | - Yishen Rong
- Women and Children's Hospital of Ningbo University, Ningbo, China; Ningbo University, Ningbo, China
| | - Jue Zhu
- Women and Children's Hospital of Ningbo University, Ningbo, China
| | - Yayuan Yu
- Jiaxing University Affiliated Women and Children Hospital, Jiaxing, China
| | - Hong Xu
- International Peace Maternity and Child Health Hospital, School of Medicine Shanghai Jiao Tong University, Shanghai, China
| | - Yuhui Sun
- Women and Children's Hospital of Ningbo University, Ningbo, China
| | - Huan Chen
- Women and Children's Hospital of Ningbo University, Ningbo, China; Ningbo University, Ningbo, China
| | - Lifeng Yan
- Women and Children's Hospital of Ningbo University, Ningbo, China
| | - Liang Chen
- Women and Children's Hospital of Ningbo University, Ningbo, China
| | - Yanan Xu
- Women and Children's Hospital of Ningbo University, Ningbo, China
| | - Jing Zhang
- Women and Children's Hospital of Ningbo University, Ningbo, China.
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96
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Siering O, Langbein M, Herrmann M, Wittwer K, von Messling V, Sawatsky B, Pfaller CK. Genetic diversity accelerates canine distemper virus adaptation to ferrets. J Virol 2024; 98:e0065724. [PMID: 39007615 PMCID: PMC11334482 DOI: 10.1128/jvi.00657-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/12/2024] [Indexed: 07/16/2024] Open
Abstract
RNA viruses adapt rapidly to new host environments by generating highly diverse genome sets, so-called "quasispecies." Minor genetic variants promote their rapid adaptation, allowing for the emergence of drug-resistance or immune-escape mutants. Understanding these adaptation processes is highly relevant to assessing the risk of cross-species transmission and the safety and efficacy of vaccines and antivirals. We hypothesized that genetic memory within a viral genome population facilitates rapid adaptation. To test this, we investigated the adaptation of the Morbillivirus canine distemper virus to ferrets and compared an attenuated, Vero cell-adapted virus isolate with its recombinant derivative over consecutive ferret passages. Although both viruses adapted to the new host, the reduced initial genetic diversity of the recombinant virus resulted in delayed disease onset. The non-recombinant virus gradually increased the frequencies of beneficial mutations already present at very low frequencies in the input virus. In contrast, the recombinant virus first evolved de novo mutations to compensate for the initial fitness impairments. Importantly, while both viruses evolved different sets of mutations, most mutations found in the adapted non-recombinant virus were identical to those found in a previous ferret adaptation experiment with the same isolate, indicating that mutations present at low frequency in the original virus stock serve as genetic memory. An arginine residue at position 519 in the carboxy terminus of the nucleoprotein shared by all adapted viruses was found to contribute to pathogenesis in ferrets. Our work illustrates the importance of genetic diversity for adaptation to new environments and identifies regions with functional relevance.IMPORTANCEWhen viruses encounter a new host, they can rapidly adapt to this host and cause disease. How these adaptation processes occur remains understudied. Morbilliviruses have high clinical and veterinary relevance and are attractive model systems to study these adaptation processes. The canine distemper virus is of particular interest, as it exhibits a broader host range than other morbilliviruses and frequently crosses species barriers. Here, we compared the adaptation of an attenuated virus and its recombinant derivative to that of ferrets. Pre-existing mutations present at low frequency allowed faster adaptation of the non-recombinant virus compared to the recombinant virus. We identified a common point mutation in the nucleoprotein that affected the pathogenesis of both viruses. Our study shows that genetic memory facilitates environmental adaptation and that erasing this genetic memory by genetic engineering results in delayed and different adaptation to new environments, providing an important safety aspect for the generation of live-attenuated vaccines.
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Affiliation(s)
- Oliver Siering
- Division of Veterinary Medicine, Paul-Ehrlich-Institute, Langen, Germany
| | - Mareike Langbein
- Division of Veterinary Medicine, Paul-Ehrlich-Institute, Langen, Germany
| | - Maike Herrmann
- Division of Veterinary Medicine, Paul-Ehrlich-Institute, Langen, Germany
| | - Kevin Wittwer
- Division of Veterinary Medicine, Paul-Ehrlich-Institute, Langen, Germany
| | | | - Bevan Sawatsky
- Division of Veterinary Medicine, Paul-Ehrlich-Institute, Langen, Germany
| | - Christian K. Pfaller
- Division of Veterinary Medicine, Paul-Ehrlich-Institute, Langen, Germany
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
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97
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Chansa O, Shantavasinkul PC, Monsuwan W, Sirivarasai J. Association between Gut Microbiota Profiles, Dietary Intake, and Inflammatory Markers in Overweight and Obese Women. Foods 2024; 13:2592. [PMID: 39200519 PMCID: PMC11353678 DOI: 10.3390/foods13162592] [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: 07/27/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 09/02/2024] Open
Abstract
Being overweight and obesity are significant global public health challenges due to their association with adipose tissue dysfunction, pro-inflammatory marker production, and alterations in gut microbiota composition. To explore the relationship between gut microbiota, dietary factors, and inflammatory markers in overweight or obese women, we conducted a cross-sectional study involving a healthy group (n = 20) and an overweight or obese group (n = 75). We collected data, including clinical, anthropometric, and dietary assessments, and carried out a blood biochemical analysis, the measurement of inflammatory biomarkers (hs-CRP, IL-6, and TNF-α), and the 16S rRNA gene sequencing of fecal samples. The gut microbiota analysis revealed notable differences in alpha and beta diversity between the two groups. Moreover, the abundance of gut microbiota in the overweight or obese group correlated positively with adiposity markers, blood pressure, lipid profiles, and inflammatory markers. These findings highlight significant changes in gut microbiota associated with obesity, potentially implicating pathways such as lipopolysaccharide biosynthesis. Understanding the role of the gut microbiome in obesity could reveal specific avenues for intervention.
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Affiliation(s)
- Orada Chansa
- Master of Science Program in Nutrition, Faculty of Medicine Ramathibodi Hospital, Institute of Nutrition, Mahidol University, Bangkok 10400, Thailand;
| | | | - Wutarak Monsuwan
- Nutrition Unit, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Jintana Sirivarasai
- Nutrition Unit, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
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98
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Juefeng Z, Fang L, Haiying Z, Liwei L, Jianming C. Integrated microbiome and metabolomic analysis of Spodoptera litura under Metarhizium flavoviride qc1401 stress. Int Microbiol 2024:10.1007/s10123-024-00574-y. [PMID: 39145832 DOI: 10.1007/s10123-024-00574-y] [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: 02/23/2024] [Revised: 05/07/2024] [Accepted: 08/01/2024] [Indexed: 08/16/2024]
Abstract
Metarhizium spp. have emerged as an alternative to chemical pesticides for protecting crops from insect pest. Here, we investigated midgut microbial community and metabolites of Spodoptera litura at three different timepoints after infection with Metarhizium flavoviride. The innate immune system of S. litura was activated with levels of polyphenol oxidase, carboxylesterase, multifunctional oxidase, and glutathione S-transferase activity significantly increasing. Exposure to the fungal pathogen also altered bacterial abundance and diversity in host's midgut, and these changes varied depending on the time elapsed since exposure. We identified more operational taxonomic units in the treated samples as compared to the control samples at all tested time points. A total of 372 metabolites were identified, and 88, 149, and 142 differentially accumulated metabolites (DAMs) were identified between the treatment and control groups at 3 timepoints after treatment, respectively. Based on the changes of DAMs in response to M. flavoviride infection at different timepoints and significantly enriched KEGG pathways, we speculated that "tyrosine metabolism," "galactose metabolism," "ATP-binding cassette transporters," "neuroactive ligand-receptor interaction," "purine metabolism," "arginine and proline metabolism," "beta-alanine metabolism," "lysosome," and "carbon metabolism" may participate in the metabolic-level defense response. An integrated pathway-level analysis of the 16S-rDNA and metabolomic data illustrated the connections and interdependencies between the metabolic responses of S. litura and the midgut microorganisms to M. flavoviride infection. This work emphasizes the value of integrated analyses of insect-pathogen interactions, provides a framework for future studies of critical microorganisms and metabolic determinants of these interactions, establishes a theoretical basis for the sustainable use of M. flavoviride.
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Affiliation(s)
- Zhang Juefeng
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China.
| | - Li Fang
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Zhong Haiying
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Liu Liwei
- Zhejiang Natural Museum, Hangzhou, Zhejiang, China
| | - Chen Jianming
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
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99
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Schartl M, Woltering JM, Irisarri I, Du K, Kneitz S, Pippel M, Brown T, Franchini P, Li J, Li M, Adolfi M, Winkler S, de Freitas Sousa J, Chen Z, Jacinto S, Kvon EZ, Correa de Oliveira LR, Monteiro E, Baia Amaral D, Burmester T, Chalopin D, Suh A, Myers E, Simakov O, Schneider I, Meyer A. The genomes of all lungfish inform on genome expansion and tetrapod evolution. Nature 2024:10.1038/s41586-024-07830-1. [PMID: 39143221 DOI: 10.1038/s41586-024-07830-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 07/15/2024] [Indexed: 08/16/2024]
Abstract
The genomes of living lungfishes can inform on the molecular-developmental basis of the Devonian sarcopterygian fish-tetrapod transition. We de novo sequenced the genomes of the African (Protopterus annectens) and South American lungfishes (Lepidosiren paradoxa). The Lepidosiren genome (about 91 Gb, roughly 30 times the human genome) is the largest animal genome sequenced so far and more than twice the size of the Australian (Neoceratodus forsteri)1 and African2 lungfishes owing to enlarged intergenic regions and introns with high repeat content (about 90%). All lungfish genomes continue to expand as some transposable elements (TEs) are still active today. In particular, Lepidosiren's genome grew extremely fast during the past 100 million years (Myr), adding the equivalent of one human genome every 10 Myr. This massive genome expansion seems to be related to a reduction of PIWI-interacting RNAs and C2H2 zinc-finger and Krüppel-associated box (KRAB)-domain protein genes that suppress TE expansions. Although TE abundance facilitates chromosomal rearrangements, lungfish chromosomes still conservatively reflect the ur-tetrapod karyotype. Neoceratodus' limb-like fins still resemble those of their extinct relatives and remained phenotypically static for about 100 Myr. We show that the secondary loss of limb-like appendages in the Lepidosiren-Protopterus ancestor was probably due to loss of sonic hedgehog limb-specific enhancers.
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Affiliation(s)
- Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany.
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria.
| | | | - Iker Irisarri
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum of Nature, Hamburg, Germany
| | - Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
| | - Susanne Kneitz
- Biochemistry and Cell Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Martin Pippel
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- DRESDEN-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Thomas Brown
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- DRESDEN-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
- Leibniz Institute for Zoo & Wildlife Research, Berlin, Germany
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Jing Li
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Ming Li
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Mateus Adolfi
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Sylke Winkler
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Zhuoxin Chen
- Department of Developmental & Cell Biology, University of California, Irvine, CA, USA
| | - Sandra Jacinto
- Department of Developmental & Cell Biology, University of California, Irvine, CA, USA
| | - Evgeny Z Kvon
- Department of Developmental & Cell Biology, University of California, Irvine, CA, USA
| | | | - Erika Monteiro
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | | | | | - Domitille Chalopin
- Institute of Cellular Biochemistry and Genetics, CNRS, University of Bordeaux, Bordeaux, France
| | - Alexander Suh
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
- School of Biological Sciences, University of East Anglia, Norwich, UK
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Eugene Myers
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center of Systems Biology Dresden, Dresden, Germany
| | - Oleg Simakov
- Department for Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
| | - Igor Schneider
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany.
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100
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Castells-Nobau A, Mayneris-Perxachs J, Fernández-Real JM. Unlocking the mind-gut connection: Impact of human microbiome on cognition. Cell Host Microbe 2024; 32:1248-1263. [PMID: 39146797 DOI: 10.1016/j.chom.2024.07.019] [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: 06/24/2024] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 08/17/2024]
Abstract
This perspective explores the current understanding of the gut microbiota's impact on cognitive function in apparently healthy humans and in individuals with metabolic disease. We discuss how alterations in gut microbiota can influence cognitive processes, focusing not only on bacterial composition but also on often overlooked components of the gut microbiota, such as bacteriophages and eukaryotes, as well as microbial functionality. We examine the mechanisms through which gut microbes might communicate with the central nervous system, highlighting the complexity of these interactions. We provide a comprehensive overview of the emerging field of microbiota-gut-brain interactions and its significance for cognitive health. Additionally, we summarize novel therapeutic strategies designed to promote cognitive resilience and reduce the risk of cognitive disorders, focusing on interventions that target the gut microbiota. An in-depth understanding of the microbiome-brain axis is imperative for developing innovative treatments aimed at improving cognitive health.
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Affiliation(s)
- Anna Castells-Nobau
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta Hospital, Girona, Spain; Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain; CIBER Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, Spain; Integrative Systems Medicine and Biology Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain
| | - Jordi Mayneris-Perxachs
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta Hospital, Girona, Spain; CIBER Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, Spain; Integrative Systems Medicine and Biology Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain
| | - José Manuel Fernández-Real
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta Hospital, Girona, Spain; Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain; CIBER Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, Spain; Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain.
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