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Dang K, Ma Y, Liang H, Fan Z, Guo S, Li Z, Li H, Zhang S. Distinct planting patterns exert legacy effects on the networks and assembly of root-associated microbiomes in subsequent crops. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174276. [PMID: 38936715 DOI: 10.1016/j.scitotenv.2024.174276] [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: 04/20/2024] [Revised: 06/13/2024] [Accepted: 06/23/2024] [Indexed: 06/29/2024]
Abstract
Soil legacy effects from previous crops can significantly influence plant-soil interactions in crop rotations. However, the microbial mechanism underlying this effect in subsequent root-associated compartments remains unclear. We investigated the effects of planting patterns (four-year continuous maize [MM], three-year winter wheat and one-year maize rotation [WM], and three-year potato and one-year maize rotation [PM]) on the microbial composition and structure of root-associated compartments, the effect of distinct crops on subsequent microbial co-occurrence patterns, and the assembly mechanism by which the root-associated compartments (bulk soil, rhizosphere, and roots) in subsequent crops regulate the microbiome habitat. Compared with MM, the relative abundance of Acidobacteria in WM was 29.7 % lower, whereas that of Bacteroidota in PM was 37.9 % higher in all three compartments. The co-occurrence patterns of the microbial communities exhibited varied responses to different planting patterns. Indicator taxon analysis revealed less shared and specific species in the root bacterial and fungal networks. The planting pattern elicited specific responses from modules within bacterial and fungal co-occurrence networks in all three compartments. Moreover, the planting patterns and root-associated compartments collectively drove the assembly process of root-associated microorganisms. The neutral model showed that, compared with MM, the stochasticity of bacterial assembly decreased under WM and PM but increased for fungal assembly. WM and PM increased the relative effects of the homogenized dispersal of fungal assemblies in roots. We conclude that previous crops exhibit marked legacy effects in the root-associated microbiome. Therefore, soil heritage should not be ignored when discussing microbiome recruitment strategies and co-occurrence patterns in subsequent crops.
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Affiliation(s)
- Ke Dang
- The Research Center of Soil and Water Conservation and Ecological Environment, Chinese Academy of Sciences and Ministry of Education, Yangling, Shaanxi 712100, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi 712100, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yifan Ma
- Dryland Agriculture Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China
| | - Haofeng Liang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zihan Fan
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shuqing Guo
- The Research Center of Soil and Water Conservation and Ecological Environment, Chinese Academy of Sciences and Ministry of Education, Yangling, Shaanxi 712100, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi 712100, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhe Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hongbing Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Suiqi Zhang
- The Research Center of Soil and Water Conservation and Ecological Environment, Chinese Academy of Sciences and Ministry of Education, Yangling, Shaanxi 712100, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi 712100, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Ghannoum MA, Elshaer M, Al-Shakhshir H, Retuerto M, McCormick TS. A Probiotic Amylase Blend Positively Impacts Gut Microbiota Modulation in a Randomized, Placebo-Controlled, Double-Blind Study. Life (Basel) 2024; 14:824. [PMID: 39063578 PMCID: PMC11277872 DOI: 10.3390/life14070824] [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: 05/10/2024] [Revised: 06/21/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024] Open
Abstract
The present study was performed to determine if ingesting a blend of probiotics plus amylase would alter the abundance and diversity of gut microbiota in subjects consuming the blend over a 6-week period. 16S and ITS ribosomal RNA (rRNA) sequencing was performed on fecal samples provided by subjects who participated in a clinical study where they consumed either a probiotic amylase blend (Bifidobacterium breve 19bx, Lactobacillus acidophilus 16axg, Lacticaseibacillus rhamnosus 18fx, and Saccharomyces boulardii 16mxg, alpha amylase (500 SKB (Alpha-amylase-Dextrinizing Units)) or a placebo consisting of rice oligodextrin. The abundance and diversity of both bacterial and fungal organisms was assessed at baseline and following 6 weeks of probiotic amylase blend or placebo consumption. In the subjects consuming the probiotic blend, the abundance of Saccharomyces cerevisiae increased 200-fold, and its prevalence increased (~20% to ~60%) (p ≤ 0.05), whereas the potential pathogens Bacillus thuringiensis and Macrococcus caseolyticus decreased more than 150- and 175-fold, respectively, after probiotic-amylase blend consumption. We also evaluated the correlation between change in microbiota and clinical features reported following probiotic amylase consumption. Nine (9) species (seven bacterial and two fungal) were significantly (negatively or positively) associated with the change in 32 clinical features that were originally evaluated in the clinical study. Oral supplementation with the probiotic-amylase blend caused a marked increase in abundance of the beneficial yeast S. cerevisiae and concomitant modulation of gut-dwelling commensal bacterial organisms, providing the proof of concept that a beneficial commensal organism can re-align the gut microbiota.
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Affiliation(s)
- Mahmoud A. Ghannoum
- Department of Dermatology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Dermatology, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Mohammed Elshaer
- Department of Dermatology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Dermatology, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Hilmi Al-Shakhshir
- Department of Dermatology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Mauricio Retuerto
- Department of Dermatology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Thomas S. McCormick
- Department of Dermatology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Dermatology, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
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3
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Yan Z, Hao T, Yan Y, Zhao Y, Wu Y, Tan Y, Bi Y, Cui Y, Yang R, Zhao Y. Quantitative and dynamic profiling of human gut core microbiota by real-time PCR. Appl Microbiol Biotechnol 2024; 108:396. [PMID: 38922447 PMCID: PMC11208268 DOI: 10.1007/s00253-024-13204-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 05/05/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024]
Abstract
The human gut microbiota refers to a diverse community of microorganisms that symbiotically exist in the human intestinal system. Altered microbial communities have been linked to many human pathologies. However, there is a lack of rapid and efficient methods to assess gut microbiota signatures in practice. To address this, we established an appraisal system containing 45 quantitative real-time polymerase chain reaction (qPCR) assays targeting gut core microbes with high prevalence and/or abundance in the population. Through comparative genomic analysis, we selected novel species-specific genetic markers and primers for 31 of the 45 core microbes with no previously reported specific primers or whose primers needed improvement in specificity. We comprehensively evaluated the performance of the qPCR assays and demonstrated that they showed good sensitivity, selectivity, and quantitative linearity for each target. The limit of detection ranged from 0.1 to 1.0 pg/µL for the genomic DNA of these targets. We also demonstrated the high consistency (Pearson's r = 0.8688, P < 0.0001) between the qPCR method and metagenomics next-generation sequencing (mNGS) method in analyzing the abundance of selected bacteria in 22 human fecal samples. Moreover, we quantified the dynamic changes (over 8 weeks) of these core microbes in 14 individuals using qPCR, and considerable stability was demonstrated in most participants, albeit with significant individual differences. Overall, this study enables the simple and rapid quantification of 45 core microbes in the human gut, providing a promising tool to understand the role of gut core microbiota in human health and disease. KEY POINTS: • A panel of original qPCR assays was developed to quantify human gut core microbes. • The qPCR assays were evaluated and compared with mNGS using real fecal samples. • This method was used to dynamically profile the gut core microbiota in individuals.
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Affiliation(s)
- Ziheng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Tongyu Hao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yanfeng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yanting Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yafang Tan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yujing Bi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
- Beijing Key Laboratory of POCT for Bioemergency and Clinic, Beijing, 100071, China.
| | - Yong Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
- Beijing Key Laboratory of POCT for Bioemergency and Clinic, Beijing, 100071, China.
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Seyoum Y, Greffeuille V, Kouadio DKD, Kuong K, Turpin W, M'Rabt R, Chochois V, Fortin S, Perignon M, Fiorentino M, Berger J, Burja K, Ponce MC, Chamnan C, Wieringa FT, Humblot C. Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice. Nat Commun 2024; 15:5204. [PMID: 38890302 PMCID: PMC11189458 DOI: 10.1038/s41467-024-49093-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/21/2024] [Indexed: 06/20/2024] Open
Abstract
Faecal microbiota plays a critical role in human health, but its relationship with nutritional status among schoolchildren remains under-explored. Here, in a double-blinded cluster-randomized controlled trial on 380 Cambodian schoolchildren, we characterize the impact of six months consumption of two types of rice fortified with different levels of vitamins and minerals on pre-specified outcomes. We investigate the association between the faecal microbiota (16SrRNA sequencing) and age, sex, nutritional status (underweight, stunting), micronutrient status (iron, zinc and vitamin A deficiencies, anaemia, iron deficient anaemia, hemoglobinopathy), inflammation (systemic, gut), and parasitic infection. We show that the faecal microbiota is characterised by a surprisingly high proportion of Lactobacillaceae. We discover that deficiencies in specific micronutrients, such as iron and vitamin A, correlate with particular microbiota profiles, whereas zinc deficiency shows no such association. The nutritional intervention with the two rice treatments impacts both the composition and functions predicted from compositional analysis in different ways. (ClinicalTrials.gov (Identifier: NCT01706419)).
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Affiliation(s)
- Yohannes Seyoum
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Valérie Greffeuille
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Dorgeles Kouakou Dje Kouadio
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Khov Kuong
- Department of Fisheries Post-Harvest Technologies and Quality Control, Ministry of Agriculture, Forestry and Fisheries, Phnom Penh, Cambodia
| | - Williams Turpin
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, ON, Canada
- Division of Gastroenterology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Rachida M'Rabt
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Vincent Chochois
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Sonia Fortin
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Marlène Perignon
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
- MoISA, Univ Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Marion Fiorentino
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
- SESSTIM, INSERM, IRD, Aix Marseille Univ, Marseille, France
| | - Jacques Berger
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Kurt Burja
- United Nations World Food Programme, Phnom Penh, Cambodia
| | - Maiza Campos Ponce
- Section Infectious Diseases, department of Health Sciences, Faculty of Earth and Life Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Chhoun Chamnan
- Department of Fisheries Post-Harvest Technologies and Quality Control, Ministry of Agriculture, Forestry and Fisheries, Phnom Penh, Cambodia
| | - Frank T Wieringa
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Christèle Humblot
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France.
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Tian Y, Li P, Chen X, He J, Tian M, Zheng Z, Hu R, Fu Z, Yi Z, Li J. R3 strain and Fe-Mn modified biochar reduce Cd absorption capacity of roots and available Cd content of soil by affecting rice rhizosphere and endosphere key flora. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 278:116418. [PMID: 38696873 DOI: 10.1016/j.ecoenv.2024.116418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/04/2024]
Abstract
Microorganisms have a significant role in regulating the absorption and transportation of Cd in the soil-plant system. However, the mechanism by which key microbial taxa play a part in response to the absorption and transportation of Cd in rice under Cd stress requires further exploration. In this study, the cadmium-tolerant endophytic bacterium Herbaspirillum sp. R3 (R3) and Fe-Mn-modified biochar (Fe-Mn) were, respectively, applied to cadmium-contaminated rice paddies to investigate the effects of key bacterial taxa in the soil-rice system on the absorption and transportation of Cd in rice under different treatments. The results showed that both R3 and Fe-Mn treatments considerably decreased the content of cadmium in roots, stems and leaves of rice at the peak tillering stage by 17.24-49.28% in comparison to the control (CK). The cadmium content reduction effect of R3 treatment is better than that of Fe-Mn treatment. Further analysis revealed that the key bacterial taxa in rice roots under R3 treatment were Sideroxydans and Actinobacteria, and that their abundance showed a substantial positive correlation and a significant negative correlation with the capacity of rice roots to assimilate Cd from the surroundings, respectively. The significant increase in soil pH under Fe-Mn treatment, significant reduction in the relative abundances of Acidobacteria, Verrucomicrobia, Subdivision3 genera incertae sedis, Sideroxydans, Geobacter, Gp1, and Gp3, and the significant increase in the relative abundance of Thiobacillus among the soil bacterial taxa may be the main reasons for the decrease in available Cd content of the soil. In addition, both the R3 and Fe-Mn treatments showed some growth-promoting effects on rice, which may be related to their promotion of transformations of soil available nutrients. This paper describes the possible microbial mechanisms by which strain R3 and Fe-Mn biochar reduce Cd uptake in rice, providing a theoretical basis for the remediation of Cd contamination in rice and soil by utilizing key microbial taxa.
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Affiliation(s)
- Yunhe Tian
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Peng Li
- Hunan Soil and Fertilizer Institute, Hunan Academy of Agricultural Sciences, 410125, China
| | - Xinyu Chen
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Jing He
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Meijie Tian
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Zhongyi Zheng
- College of Education, Hunan Agricultural University, Changsha 410128, China
| | - Ruiwen Hu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China; State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zhiqiang Fu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Zhenxie Yi
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
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Haghebaert M, Laroche B, Sala L, Mondot S, Doré J. A mechanistic modelling approach of the host-microbiota interactions to investigate beneficial symbiotic resilience in the human gut. J R Soc Interface 2024; 21:20230756. [PMID: 38900957 DOI: 10.1098/rsif.2023.0756] [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: 12/18/2023] [Accepted: 04/11/2024] [Indexed: 06/22/2024] Open
Abstract
The health and well-being of a host are deeply influenced by the interactions with its gut microbiota. Contrasted environmental conditions, such as diseases or dietary habits, play a pivotal role in modulating these interactions, impacting microbiota composition and functionality. Such conditions can also lead to transitions from beneficial to detrimental symbiosis, viewed as alternative stable states of the host-microbiota dialogue. This article introduces a novel mathematical model exploring host-microbiota interactions, integrating dynamics of the colonic epithelial crypt, microbial metabolic functions, inflammation sensitivity and colon flows in a transverse section. The model considers metabolic shifts in epithelial cells based on butyrate and hydrogen sulfide concentrations, innate immune pattern recognition receptor activation, microbial oxygen tolerance and the impact of antimicrobial peptides on the microbiota. Using the model, we demonstrated that a high-protein, low-fibre diet exacerbates detrimental interactions and compromises beneficial symbiotic resilience, underscoring a destabilizing effect towards an unhealthy state. Moreover, the proposed model provides essential insights into oxygen levels, fibre and protein breakdown, and basic mechanisms of innate immunity in the colon and offers a crucial understanding of factors influencing the colon environment.
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Affiliation(s)
- Marie Haghebaert
- University Paris-Saclay, INRAE, MaIAGE , Jouy-en-Josas 78350, France
- University Paris-Saclay, INRIA, MUSCA , Palaiseau 91120, France
| | - Béatrice Laroche
- University Paris-Saclay, INRAE, MaIAGE , Jouy-en-Josas 78350, France
- University Paris-Saclay, INRIA, MUSCA , Palaiseau 91120, France
| | - Lorenzo Sala
- University Paris-Saclay, INRAE, MaIAGE , Jouy-en-Josas 78350, France
- University Paris-Saclay, INRIA, MUSCA , Palaiseau 91120, France
| | - Stanislas Mondot
- Micalis Institute, INRAE, AgroParisTech, University Paris-Saclay , Jouy-en-Josas 78350, France
| | - Joël Doré
- Micalis Institute, INRAE, AgroParisTech, University Paris-Saclay , Jouy-en-Josas 78350, France
- University Paris-Saclay, MGP, INRAE , Jouy-en-Josas 78350, France
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7
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Annunziato A, Vacca M, Cristofori F, Dargenio VN, Celano G, Francavilla R, De Angelis M. Celiac Disease: The Importance of Studying the Duodenal Mucosa-Associated Microbiota. Nutrients 2024; 16:1649. [PMID: 38892582 PMCID: PMC11174386 DOI: 10.3390/nu16111649] [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: 05/02/2024] [Revised: 05/24/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
There is increasing evidence indicating that changes in both the composition and functionality of the intestinal microbiome are closely associated with the development of several chronic inflammatory diseases, with celiac disease (CeD) being particularly noteworthy. Thanks to the advent of culture-independent methodologies, the ability to identify and quantify the diverse microbial communities residing within the human body has been significantly improved. However, in the context of CeD, a notable challenge lies in characterizing the specific microbiota present on the mucosal surfaces of the intestine, rather than relying solely on fecal samples, which may not fully represent the relevant microbial populations. Currently, our comprehension of the composition and functional importance of mucosa-associated microbiota (MAM) in CeD remains an ongoing field of research because the limited number of available studies have reported few and sometimes contradictory results. MAM plays a crucial role in the development and progression of CeD, potentially acting as both a trigger and modulator of the immune response within the intestinal mucosa, given its proximity to the epithelial cells and direct interaction. According to this background, this review aims to consolidate the existing literature specifically focused on MAM in CeD. By elucidating the complex interplay between the host immune system and the gut microbiota, we aim to pave the way for new interventions based on novel therapeutic targets and diagnostic biomarkers for MAM in CeD.
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Affiliation(s)
- Alessandro Annunziato
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/a, 70126 Bari, Italy; (A.A.); (G.C.); (M.D.A.)
| | - Mirco Vacca
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/a, 70126 Bari, Italy; (A.A.); (G.C.); (M.D.A.)
| | - Fernanda Cristofori
- Interdisciplinary Department of Medicine, Pediatric Section, Children’s Hospital ‘Giovanni XXIII’, University of Bari Aldo Moro, 70126 Bari, Italy; (F.C.); (V.N.D.); (R.F.)
| | - Vanessa Nadia Dargenio
- Interdisciplinary Department of Medicine, Pediatric Section, Children’s Hospital ‘Giovanni XXIII’, University of Bari Aldo Moro, 70126 Bari, Italy; (F.C.); (V.N.D.); (R.F.)
| | - Giuseppe Celano
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/a, 70126 Bari, Italy; (A.A.); (G.C.); (M.D.A.)
| | - Ruggiero Francavilla
- Interdisciplinary Department of Medicine, Pediatric Section, Children’s Hospital ‘Giovanni XXIII’, University of Bari Aldo Moro, 70126 Bari, Italy; (F.C.); (V.N.D.); (R.F.)
| | - Maria De Angelis
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/a, 70126 Bari, Italy; (A.A.); (G.C.); (M.D.A.)
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8
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Figueiredo CC, Monteiro HF, Cunha F, Bisinotto DZ, Ruiz AR, Duarte GA, Ge Y, Lima FS, Mohamadzadeh M, Galvão KN, Bisinotto RS. Shifts in uterine microbiome associated with pregnancy outcomes at first insemination and clinical cure in dairy cows with metritis. Sci Rep 2024; 14:11864. [PMID: 38789554 PMCID: PMC11126406 DOI: 10.1038/s41598-024-61704-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Objectives were to assess differences in uterine microbiome associated with clinical cure and pregnancy outcomes in dairy cows treated for metritis. Cows with metritis (reddish-brownish, watery, and fetid vaginal discharge) were paired with cows without metritis based on parity and days postpartum. Uterine contents were collected through transcervical lavage at diagnosis, five days later following antimicrobial therapy (day 5), and at 40 days postpartum. Uterine microbiome was assessed by sequencing the V4 hypervariable region of the 16S rRNA gene. Although alpha-diversity based on Chao1, Shannon, and inverse Simpson indexes at diagnosis did not differ between cows with and without metritis, disease was associated with differences in beta-diversity. Prevalence of Porphyromonas, Bacteroides, and Veillonella was greater in cows with metritis. Streptococcus, Sphingomonas, and Ureaplasma were more prevalent in cows without metritis. Differences in beta-diversity between cows with and without metritis persisted on day 5. Uterine microbiome was not associated with clinical cure. Richness and alpha-diversity, but not beta-diversity, of uterine microbiome 40 days postpartum were associated with metritis and pregnancy. No relationship between uterine microbiome and pregnancy outcomes was observed. Results indicate that factors other than changes in intrauterine bacterial community underlie fertility loss and clinical cure in cows with metritis.
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Affiliation(s)
- Caio C Figueiredo
- Department of Large Animal Clinical Sciences, D. H. Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, 32610, USA
- Department of Veterinary Clinical Sciences, Washington State University, Pullman, 99164, USA
| | - Hugo F Monteiro
- Department of Population Health and Reproduction, University of California, Davis, 95616, USA
| | - Federico Cunha
- Department of Large Animal Clinical Sciences, D. H. Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, 32610, USA
| | - Danilo Z Bisinotto
- Department of Large Animal Clinical Sciences, D. H. Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, 32610, USA
| | - Angel Revilla Ruiz
- Department of Animal Sciences, University of Florida, Gainesville, 32611, USA
| | - Gustavo A Duarte
- Department of Animal Sciences, University of Florida, Gainesville, 32611, USA
| | - Yong Ge
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health, San Antonio, 78229, USA
| | - Fábio S Lima
- Department of Population Health and Reproduction, University of California, Davis, 95616, USA
| | - Mansour Mohamadzadeh
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health, San Antonio, 78229, USA
| | - Klibs N Galvão
- Department of Large Animal Clinical Sciences, D. H. Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, 32610, USA
| | - Rafael S Bisinotto
- Department of Large Animal Clinical Sciences, D. H. Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, 32610, USA.
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9
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Marques TC, Monteiro HF, Melo DB, Coelho WM, Salman S, Marques LR, Leão KM, Machado VS, Menta P, Dubey D, Sun F, Lima FS. Effect of rumen-protected choline on dairy cow metabolism, immunity, lactation performance, and vaginal discharge microbiome. J Dairy Sci 2024; 107:2864-2882. [PMID: 38101729 DOI: 10.3168/jds.2023-23850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 11/12/2023] [Indexed: 12/17/2023]
Abstract
Rumen-protected choline (RPC) promotes benefits in milk production, immunity, and health in dairy cows by optimizing lipid metabolism during transition period management and early lactation. However, the RPC success in dairy cows depends on choline bioavailability, which is affected by the type of protection used in rumen-protected choline. Therefore, our objectives were to determine the effects of a novel RPC on dry matter intake (DMI), identify markers of metabolism and immunity, and evaluate lactation performance. Dry Holstein (n = 48) cows at 245 ± 3 d of gestation were blocked by parity and assigned to control or RPC treatment within each block. Cows enrolled in the RPC treatment received 15 g/d of CholiGEM (Kemin Industries, Cavriago RE, Italy) from 21 d prepartum and 30 g/d of CholiGEM from calving to 21 d postpartum. During the transition period, DMI was measured daily, and blood was sampled weekly for energy-related metabolites such as β-hydroxybutyrate (BHB), glucose, and nonesterified fatty acids (NEFA), as well as immune function markers such as haptoglobin (Hp) and lipopolysaccharide-binding protein (LPB). Vaginal discharge samples were collected at the calving and 7 d postpartum and stored in microcentrifuge tubes at -80°C until 16S rRNA sequencing. The main responses of body condition score, body weight, DMI, milk yield, milk components, and immune function markers were analyzed using the GLIMMIX procedure of SAS with the effects of treatment, time, parity, and relevant covariates added to the models. The relative abundance of microbiome α-diversity was evaluated by 3 indexes (Chao1, Shannon, and Simpson) and β-diversity by principal coordinate analysis and permutational multivariate ANOVA. We found no differences in DMI in the pre- and postpartum periods. Cows fed RPC increased the yields of energy- and 3.5% fat-corrected milk and fat yield in primiparous and multiparous cows, with an interaction between treatment and parity for these lactation variables. However, we found no differences in milk protein and lactose up to 150 DIM between treatments. Glucose, NEFA, and BHB had no differences between the treatments. However, RPC decreased BHB numerically (control = 1.07 ± 0.13 vs. RPC = 0.63 ± 0.13) in multiparous on the third week postpartum and tended to reduce the incidence of subclinical ketosis (12.7% vs. 4.2%). No effects for Hp and LPB were found in cows fed RPC. Chao1, Shannon, and Simpson indexes were lower at calving in the RPC treatment than in the Control. However, no differences were found 7 d later for Chao1, Shannon, and Simpson indexes. The vaginal discharge microbiome was altered in cows fed RPC at 7 d postpartum. Fusobacterium, a common pathogen associated with metritis, was reduced in cows fed RPC. Rumen-protected choline enhanced lactation performance and health and altered the vaginal discharge microbiome which is a potential proxy for uterine healthy in dairy cows. The current study's findings corroborate that RPC is a tool to support adaptation to lactation and shed light on opportunities for further research in reproductive health.
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Affiliation(s)
- T C Marques
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616; Department of Animal Science, Instituto Federal Goiano, Rio Verde, Goias 75901-970, Brazil
| | - H F Monteiro
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616
| | - D B Melo
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616
| | - W M Coelho
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616
| | - S Salman
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616
| | - L R Marques
- Department of Animal Science, Instituto Federal Goiano, Rio Verde, Goias 75901-970, Brazil
| | - K M Leão
- Department of Animal Science, Instituto Federal Goiano, Rio Verde, Goias 75901-970, Brazil
| | - V S Machado
- Department of Veterinary Sciences, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409
| | - P Menta
- Department of Veterinary Sciences, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409
| | - D Dubey
- Kemin Europa NV, Herentals 2640, Belgium
| | - F Sun
- Kemin Industries Inc., Des Moines, IA 50317
| | - F S Lima
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616.
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10
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Sha H, Lu J, Chen J, Xiong J. Rationally designed probiotics prevent shrimp white feces syndrome via the probiotics-gut microbiome-immunity axis. NPJ Biofilms Microbiomes 2024; 10:40. [PMID: 38605016 PMCID: PMC11009345 DOI: 10.1038/s41522-024-00509-5] [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: 10/03/2023] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
Increasing evidence infers that some complex diseases are attributed to co-infection with multiple pathogens, such as shrimp white feces syndrome (WFS); however, there is a lack of experimental evidence to validate such causal link. This deficiency further impedes rational design of probiotics to elicit desired benefits to shrimp WFS resistance. Herein, we validated the causal roles of Vibrio fluvialis, V. coralliilyticus and V. tubiashii (in a ratio of 7:2:1) in shrimp WFS etiology, which fully satisfied Koch's postulates. Correspondingly, we precisely designed four antagonistic strains: Ruegeria lacuscaerulensis, Nioella nitratireducens, Bacillus subtilis and Streptomyces euryhalinus in a ratio of 4:3:2:1, which efficiently guarded against WFS. Dietary supplementation of the probiotics stimulated beneficial gut populations, streptomycin, short chain fatty acids, taurine metabolism potentials, network stability, tight junction, and host selection, while reducing turnover rate and average variation degree of gut microbiota, thereby facilitating ecological and mechanical barriers against pathogens. Additionally, shrimp immune pathways, such as Fcγ R-mediated phagocytosis, Toll-like receptor and RIG-I-like receptor signaling pathways conferring immune barrier, were activated by probiotics supplementation. Collectively, we establish an updated framework for precisely validating co-infection with multiple pathogens and rationally designing antagonistic probiotics. Furthermore, our findings uncover the underlying beneficial mechanisms of designed probiotics from the probiotics-gut microbiome-host immunity axis.
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Affiliation(s)
- Haonan Sha
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Insititute of Plant Virology, Ningbo University, Ningbo, 315211, China.
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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11
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Ahrens AP, Hyötyläinen T, Petrone JR, Igelström K, George CD, Garrett TJ, Orešič M, Triplett EW, Ludvigsson J. Infant microbes and metabolites point to childhood neurodevelopmental disorders. Cell 2024; 187:1853-1873.e15. [PMID: 38574728 DOI: 10.1016/j.cell.2024.02.035] [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: 04/07/2023] [Revised: 11/22/2023] [Accepted: 02/28/2024] [Indexed: 04/06/2024]
Abstract
This study has followed a birth cohort for over 20 years to find factors associated with neurodevelopmental disorder (ND) diagnosis. Detailed, early-life longitudinal questionnaires captured infection and antibiotic events, stress, prenatal factors, family history, and more. Biomarkers including cord serum metabolome and lipidome, human leukocyte antigen (HLA) genotype, infant microbiota, and stool metabolome were assessed. Among the 16,440 Swedish children followed across time, 1,197 developed an ND. Significant associations emerged for future ND diagnosis in general and for specific ND subtypes, spanning intellectual disability, speech disorder, attention-deficit/hyperactivity disorder, and autism. This investigation revealed microbiome connections to future diagnosis as well as early emerging mood and gastrointestinal problems. The findings suggest links to immunodysregulation and metabolism, compounded by stress, early-life infection, and antibiotics. The convergence of infant biomarkers and risk factors in this prospective, longitudinal study on a large-scale population establishes a foundation for early-life prediction and intervention in neurodevelopment.
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Affiliation(s)
- Angelica P Ahrens
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL 32603, USA
| | - Tuulia Hyötyläinen
- School of Science and Technology, Örebro University, Örebro 702 81, Sweden
| | - Joseph R Petrone
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL 32603, USA
| | - Kajsa Igelström
- Department of Biomedical and Clinical Sciences, Division of Neurobiology, Linköping University, Linköping 58185, Sweden
| | - Christian D George
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL 32603, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Matej Orešič
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro 702 81, Sweden; Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; Department of Life Technologies, University of Turku, Turku 20014, Finland
| | - Eric W Triplett
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL 32603, USA.
| | - Johnny Ludvigsson
- Crown Princess Victoria Children's Hospital and Division of Pediatrics, Department of Biomedical and Clinical Sciences, Linköping University, Linköping 58185, Sweden
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12
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Xiao D, Tang Y, Zhang W, Hu P, Wang K. Lithology and niche habitat have significant effect on arbuscular mycorrhizal fungal abundance and their interspecific interactions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170774. [PMID: 38340853 DOI: 10.1016/j.scitotenv.2024.170774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/02/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
The chemical properties of bedrock play a crucial role in shaping the communities of soil and root-associated arbuscular mycorrhizal fungi (AMF). We investigate AMF community composition and diversity in bulk soil, rhizosphere soil, and roots in karst and non-karst forests. Chemical properties of bedrock of the calcium oxide (CaO) and ratio of calcium oxide and magnesium oxide (Ca/Mg), soil pH, and exchangeable Ca2+ were higher in karst carbonate rocks compared to non-karst clastic rocks. Conversely, bedrock phosphorus content (P-rock), silicon dioxide (SiO2) content, and tree diversity exhibited an opposing trend. AMF abundance was higher in non-karst clastic rocks than in karst carbonate rocks. Stronger interspecific interactions among AMF taxa occurred in the bulk soil and rhizosphere soil of non-karst clastic rocks compared to karst carbonate rocks. AMF abundance and diversity were higher in rhizosphere soil and roots, attributed to increasing nutrient availability when compared to the bulk soil. A more complex network within AMF taxa was observed in rhizosphere soil and roots compared to bulk soil due to an increase in AMF abundance and diversity in rhizosphere soil and roots. Comparing non-karst clastic rocks, karst carbonate rocks increased soil nitrogen (N) and P levels, which can be attributed to the elevated content of soil Ca2+ and Mg2+ content, facilitated by the high CaO content and Ca/Mg ratio in the bedrock of karst forests. However, the thicker soil layer exhibited higher soil nutrient storage, resulting in greater tree diversity in non-karst forests. These findings suggest that high tree richness may increase root biomass and secretion of root exudates in non-karst regions, thereby enhancing the abundance of AMF and their interspecies interactions. Consequently, the diverse bedrock properties that drive variations in soil properties, nutrients, and plant diversity can impact AMF communities, ultimately promoting plant growth and contributing to vegetation recovery.
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Affiliation(s)
- Dan Xiao
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 44547100, China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, China
| | - Yixin Tang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 44547100, China; Wuhan Geomatics Institute, Wuhan 430022, China
| | - Wei Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 44547100, China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, China.
| | - Peilei Hu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 44547100, China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, China
| | - Kelin Wang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 44547100, China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, China.
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13
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Manrique P, Montero I, Fernandez-Gosende M, Martinez N, Cantabrana CH, Rios-Covian D. Past, present, and future of microbiome-based therapies. MICROBIOME RESEARCH REPORTS 2024; 3:23. [PMID: 38841413 PMCID: PMC11149097 DOI: 10.20517/mrr.2023.80] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 06/07/2024]
Abstract
Technological advances in studying the human microbiome in depth have enabled the identification of microbial signatures associated with health and disease. This confirms the crucial role of microbiota in maintaining homeostasis and the host health status. Nowadays, there are several ways to modulate the microbiota composition to effectively improve host health; therefore, the development of therapeutic treatments based on the gut microbiota is experiencing rapid growth. In this review, we summarize the influence of the gut microbiota on the development of infectious disease and cancer, which are two of the main targets of microbiome-based therapies currently being developed. We analyze the two-way interaction between the gut microbiota and traditional drugs in order to emphasize the influence of gut microbial composition on drug effectivity and treatment response. We explore the different strategies currently available for modulating this ecosystem to our benefit, ranging from 1st generation intervention strategies to more complex 2nd generation microbiome-based therapies and their regulatory framework. Lastly, we finish with a quick overview of what we believe is the future of these strategies, that is 3rd generation microbiome-based therapies developed with the use of artificial intelligence (AI) algorithms.
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14
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Shin JH, Tillotson G, MacKenzie TN, Warren CA, Wexler HM, Goldstein EJC. Bacteroides and related species: The keystone taxa of the human gut microbiota. Anaerobe 2024; 85:102819. [PMID: 38215933 DOI: 10.1016/j.anaerobe.2024.102819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/14/2024]
Abstract
Microbial communities play a significant role in maintaining ecosystems in a healthy homeostasis. Presently, in the human gastrointestinal tract, there are certain taxonomic groups of importance, though there is no single species that plays a keystone role. Bacteroides spp. are known to be major players in the maintenance of eubiosis in the human gastrointestinal tract. Here we review the critical role that Bacteroides play in the human gut, their potential pathogenic role outside of the gut, and their various methods of adapting to the environment, with a focus on data for B. fragilis and B. thetaiotaomicron. Bacteroides are anaerobic non-sporing Gram negative organisms that are also resistant to bile acids, generally thriving in the gut and having a beneficial relationship with the host. While they are generally commensal organisms, some Bacteroides spp. can be opportunistic pathogens in scenarios of GI disease, trauma, cancer, or GI surgery, and cause infection, most commonly intra-abdominal infection. B. fragilis can develop antimicrobial resistance through multiple mechanisms in large part due to its plasticity and fluid genome. Bacteroidota (formerly, Bacteroidetes) have a very broad metabolic potential in the GI microbiota and can rapidly adapt their carbohydrate metabolism to the available nutrients. Gastrointestinal Bacteroidota species produce short-chain fatty acids such as succinate, acetate, butyrate, and occasionally propionate, as the major end-products, which have wide-ranging and many beneficial influences on the host. Bacteroidota, via bile acid metabolism, also play a role in in colonization-resistance of other organisms, including Clostridioides difficile, and maintenance of gut integrity.
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Affiliation(s)
- Jae Hyun Shin
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
| | | | | | - Cirle A Warren
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
| | - Hannah M Wexler
- GLAVAHCS, Los Angeles, CA, USA; David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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15
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Gul F, Herrema H, Davids M, Keating C, Nasir A, Ijaz UZ, Javed S. Gut microbial ecology and exposome of a healthy Pakistani cohort. Gut Pathog 2024; 16:5. [PMID: 38254227 PMCID: PMC10801943 DOI: 10.1186/s13099-024-00596-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Pakistan is a multi-ethnic society where there is a disparity between dietary habits, genetic composition, and environmental exposures. The microbial ecology of healthy Pakistani gut in the context of anthropometric, sociodemographic, and dietary patterns holds interest by virtue of it being one of the most populous countries, and also being a Lower Middle Income Country (LMIC). METHODS 16S rRNA profiling of healthy gut microbiome of normo-weight healthy Pakistani individuals from different regions of residence is performed with additional meta-data collected through filled questionnaires. The current health status is then linked to dietary patterns through [Formula: see text] test of independence and Generalized Linear Latent Variable Model (GLLVM) where distribution of individual microbes is regressed against all recorded sources of variability. To identify the core microbiome signature, a dynamic approach is used that considers into account species occupancy as well as consistency across assumed grouping of samples including organization by gender and province of residence. Fitting neutral modeling then revealed core microbiome that is selected by the environment. RESULTS A strong determinant of disparity is by province of residence. It is also established that the male microbiome is better adapted to the local niche than the female microbiome, and that there is microbial taxonomic and functional diversity in different ethnicities, dietary patterns and lifestyle habits. Some microbial genera, such as, Megamonas, Porphyromonas, Haemophilus, Klebsiella and Finegoldia showed significant associations with consumption of pickle, fresh fruits, rice, and cheese. Our analyses suggest current health status being associated with the diet, sleeping patterns, employment status, and the medical history. CONCLUSIONS This study provides a snapshot of the healthy core Pakistani gut microbiome by focusing on the most populous provinces and ethnic groups residing in predominantly urban areas. The study serves a reference dataset for exploring variations in disease status and designing personalized dietary and lifestyle interventions to promote gut health, particularly in LMICs settings.
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Affiliation(s)
- Farzana Gul
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 45550, Pakistan
| | - Hilde Herrema
- Department of Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| | - Mark Davids
- Department of Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| | - Ciara Keating
- School of Biodiversity, One Health & Veterinary Medicine, Graham Kerr Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Arshan Nasir
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 45550, Pakistan
- Moderna, Inc., Cambridge, MA, USA
| | - Umer Zeeshan Ijaz
- Water & Environment Research Group, Mazumdar-Shaw Advanced Research Centre, University of Glasgow, Glasgow, G11 6EW, UK.
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, L69 7BE, UK.
- National University of Ireland, Galway, University Road, Galway, H91 TK33, Ireland.
| | - Sundus Javed
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 45550, Pakistan.
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16
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Elisa Heesemann Rosenkilde C, Olsen Lützhøft D, Vazquez-Uribe R, Otto Alexander Sommer M. Heterologous expression and antimicrobial potential of class II bacteriocins. Gut Microbes 2024; 16:2369338. [PMID: 38899682 PMCID: PMC11195462 DOI: 10.1080/19490976.2024.2369338] [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: 12/22/2023] [Accepted: 06/12/2024] [Indexed: 06/21/2024] Open
Abstract
Gut bacteria are known to produce bacteriocins to inhibit the growth of other bacteria. Consequently, bacteriocins have attracted increased attention as potential microbiome-editing tools. In this study we examine the inhibitory spectrum of 75 class II bacteriocins against 48 representative gut microbiota species. The bacteriocins were heterologously expressed in Escherichia coli and evaluated in vitro, ex vivo and in vivo. In vitro assays revealed 22 bacteriocins to inhibit at least one species and showed selective inhibition patterns against species implicated in certain disorders and diseases. Three bacteriocins were selected for ex vivo assessment on mouse feces. Based on 16S rRNA sequencing of the cultivated feces we showed that the two bacteriocins: Actifencin (#13) and Bacteroidetocin A (#22) selectively inhibited the growth of Lactobacillus and Bacteroides, respectively. The probiotic: E. coli Nissle 1917 was engineered to express these two bacteriocins in mice. However, the selective inhibitory patterns found in the in vitro and ex vivo experiments could not be observed in vivo. Our study describes a methodology for heterologous high throughput bacteriocin expression and screening and elucidates the inhibitory patterns of class II bacteriocins on the gut microbiota.
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Affiliation(s)
| | - Ditte Olsen Lützhøft
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ruben Vazquez-Uribe
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Morten Otto Alexander Sommer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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17
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Das S, Özkurt E, Joishy TK, Mukherjee AK, Hildebrand F, Khan MR. A single dietary factor, daily consumption of a fermented beverage, can modulate the gut bacteria and fecal metabolites within the same ethnic community. mSystems 2023; 8:e0074523. [PMID: 37882544 PMCID: PMC10734539 DOI: 10.1128/msystems.00745-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/20/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Our study investigated how a traditional drink called Apong, made from fermented rice, affects the gut and health of the Mishing community in India. We compared two groups of people who drink Apong to a group of people who do not drink it. To accomplish this, we studied the gut bacteria, fecal metabolites, and blood samples of the participants. It was found that the people who drank Apong had higher blood pressure but lower blood sugar and protein levels than people who did not drink it. We also found that the gut microbiome composition of people who drank Apong was different from those who did not drink it. Moreover, people who drank Apong had lower levels of isovaleric acid in their feces. Overall, this study shows that a traditional drink like Apong can affect the gut bacteria of a community.
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Affiliation(s)
- Santanu Das
- Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India
- Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, Assam, India
| | - Ezgi Özkurt
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
- Digital Biology, Earlham Institute, Norwich, United Kingdom
| | - Tulsi Kumari Joishy
- Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India
| | - Ashis K. Mukherjee
- Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India
| | - Falk Hildebrand
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
- Digital Biology, Earlham Institute, Norwich, United Kingdom
| | - Mojibur R. Khan
- Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India
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18
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Zhang J, Shu Z, Lv S, Zhou Q, Huang Y, Peng Y, Zheng J, Zhou Y, Hu C, Lan S. Fermented Chinese Herbs Improve the Growth and Immunity of Growing Pigs through Regulating Colon Microbiota and Metabolites. Animals (Basel) 2023; 13:3867. [PMID: 38136904 PMCID: PMC10740985 DOI: 10.3390/ani13243867] [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: 11/18/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
(1) Background: the development of new antibiotic substitutes to promote pig growth and health has become an important way to solve the current dilemma and promote the pig industry. (2) Methods: to assess the effects of a fermented Chinese herbal (FCH) formula on the growth and immunity of growing pigs, 100 Duroc × Landrace × Yorshire three-way crossed growing pigs were randomly divided into control and treatment groups that were fed a basal diet, and a basal diet with 1% (group A), 2% (group B), and 3% (group C) FCH formulas, respectively. A sixty-day formal experiment was conducted, and their growth and serum indices, colonic microbiota, and metabolites were analyzed. (3) Results: the daily gain of growing pigs in groups A, B, and C increased by 7.93%, 17.68%, and 19.61%, respectively, and the feed-to-gain ratios decreased by 8.33%, 15.00%, and 14.58%, respectively. Serum immunity and antioxidant activities were significantly increased in all treatment groups. Particularly, adding a 2% FCH formula significantly changed the colon's microbial structure; the Proteobacteria significantly increased and Firmicutes significantly decreased, and the metabolite composition in the colon's contents significantly changed. (4) Conclusions: these results indicate that the FCH formula is a good feed additive for growing pigs, and the recommended addition ratio was 3%.
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Affiliation(s)
- Junhao Zhang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Zhiheng Shu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Sixiao Lv
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Qingwen Zhou
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Yuanhao Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Yingjie Peng
- Guangdong Chuangzhan Bona Agricultural Technology Co., Ltd., Guangning 526339, China;
| | - Jun Zheng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Yi Zhou
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Chao Hu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
| | - Shile Lan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Z.S.); (S.L.); (Q.Z.); (Y.H.); (J.Z.); (Y.Z.)
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Bhattacharjee P, Karim KA, Khan Z. Harnessing the Microbiome: A Comprehensive Review on Advancing Therapeutic Strategies for Rheumatic Diseases. Cureus 2023; 15:e50964. [PMID: 38249228 PMCID: PMC10800157 DOI: 10.7759/cureus.50964] [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] [Accepted: 12/22/2023] [Indexed: 01/23/2024] Open
Abstract
Rheumatic diseases are a group of disorders that affect the joints, muscles, and bones. These diseases, such as rheumatoid arthritis, lupus, and psoriatic arthritis, can cause pain, stiffness, and swelling, leading to reduced mobility and disability. Recent studies have identified the microbiome, the diverse community of microorganisms that live in and on the human body, as a potential factor in the development and progression of rheumatic diseases. Harnessing the microbiome offers a promising new avenue for developing therapeutic strategies for these debilitating conditions. There is growing interest in the role of oral and gut microbiomes in the management of rheumatoid arthritis and other autoimmune disease. Microbial metabolites have immunomodulatory properties that could be exploited for rheumatic disorders. A wide range of microorganisms are present in the oral cavity and are found to be vulnerable to the effects of the environment. The physiology and ecology of the microbiota become intimately connected with those of the host, and they critically influence the promotion of health or progression toward disease. This article aims to provide a comprehensive overview of the current state of knowledge on oral and gut microbiome and its potential future role in the management of rheumatic diseases. This article will also discuss newer treatment strategies such as bioinformatic analyses and fecal transplantation.
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Affiliation(s)
- Priyadarshini Bhattacharjee
- Acute Medicine, Cambridge University Hospital NHS Foundation Trust, Cambridge, GBR
- School of Clinical Medicine, University of Cambridge, Cambridge, GBR
| | - Karim Arif Karim
- Medicine and Surgery, Kamuzu University of Health Sciences, Blantyre, MWI
| | - Zahid Khan
- Acute Medicine, Mid and South Essex NHS Foundation Trust, Southend-on-Sea, GBR
- Cardiology, Bart's Heart Centre, London, GBR
- Cardiology and General Medicine, Barking, Havering and Redbridge University Hospitals NHS Trust, London, GBR
- Cardiology, Royal Free Hospital, London, GBR
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20
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Chen Y, Xu Y, Ma Y, Lin J, Ruan A. Microbial community structure and its driving mechanisms in the Hangbu estuary of Chaohu Lake under different sedimentary areas. ENVIRONMENTAL RESEARCH 2023; 238:117153. [PMID: 37726029 DOI: 10.1016/j.envres.2023.117153] [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: 07/25/2023] [Revised: 09/02/2023] [Accepted: 09/13/2023] [Indexed: 09/21/2023]
Abstract
Estuaries are known for their high ecological diversity and biological productivity. Sediment microorganisms, as crucial components of estuarine ecosystems, play a pivotal role in reflecting the intricate and dynamic ecological niches. However, our research on microbial community characteristics in estuarine ecosystems under different sedimentary types remains limited. In this study, we collected a total of 27 samples from three sampling sites at Hangbu estuary in Chaohu Lake, and three sedimentary areas were classified based on the overlying water flow conditions and sediment particle properties to elucidate their microbial community structure, environmental drivers, assembly processes, and co-occurrence network characteristics. Our results showed significant differences in microbial community composition and diversity among three sedimentary areas. Redundancy analysis indicated that the differences in microbial community composition at the OTU level among the three sedimentary areas were mainly determined by nitrate-nitrogen, temperature, and water content. Phylogenetic bin-based null model analysis revealed that temperature was a key factor influencing deterministic processes among the three sedimentary areas, while stochastic processes predominantly governed the assembly of microbial communities. In addition, co-occurrence network analysis demonstrated that the network in the hydraulically driven sedimentary area of the lake, consisting mainly of medium and fine silt, had the highest complexity, stability, and cohesion, but was missing potential keystone taxa. The remaining two sedimentary areas had 5 and 8 potential keystone taxa, respectively. Overall, our study proposes the delineation of sedimentary types and comprehensively elucidates the microbial community characteristics under different sedimentary areas, providing a new perspective for studying sediment microbial community structure and helping future scholars systematically study ecological dynamics in estuaries.
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Affiliation(s)
- Yang Chen
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Yaofei Xu
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Yunmei Ma
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Jie Lin
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Aidong Ruan
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China.
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Wang C, Zhao M, Xie J, Wang H, Gu Z, Sun F. Colon-Targeted Release of Gel Microspheres Loaded with Antioxidative Fullerenol for Relieving Radiation-Induced Colon Injury and Regulating Intestinal Flora. Adv Healthc Mater 2023; 12:e2301758. [PMID: 37657180 DOI: 10.1002/adhm.202301758] [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: 06/09/2023] [Revised: 08/15/2023] [Indexed: 09/03/2023]
Abstract
Radiation-induced colitis is a serious clinical problem worldwide. However, the current treatment options for this condition have limited efficacy and can cause side effects. To address this issue, colon-targeted fullerenol@pectin@chitosan gel microspheres (FPCGMs) are developed, which can aggregate on colon tissue for a long time, scavenge free radicals generated in the process of radiation, and regulate intestinal flora to mitigate damage to colonic tissue. First, FPCGMs exhibit acid resistance and colon-targeted release properties, which reduce gastrointestinal exposure and extend the local colonic drug residence time. Second, fullerenol, which has a superior scavenging ability and chemical stability, reduces oxidative stress in colonic epithelial cells. Based on this, it is found that FPCGMs significantly reduce inflammation in colonic tissue, mitigated damage to tight junctions of colonic epithelial cells, and significantly relieved radiation-induced colitis in mice. Moreover, 16S ribosomal DNA (16S rDNA) sequencing results show that the composition of the intestinal flora is optimized after FPCGMs are utilized, indicating that the relative abundance of probiotics increases while harmful bacteria are inhibited. These findings suggest that it is a promising candidate for treating radiation-induced colitis.
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Affiliation(s)
- Chengyan Wang
- Department of Pharmacy, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Maoru Zhao
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, Institute of High Energy Physics and National Center for Nanoscience and Technology of China, Chinese Academy of Sciences, Beijing, 100049, China
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiani Xie
- School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, China
| | - Hongping Wang
- Department of Pharmacy, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Zhanjun Gu
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, Institute of High Energy Physics and National Center for Nanoscience and Technology of China, Chinese Academy of Sciences, Beijing, 100049, China
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fengjun Sun
- Department of Pharmacy, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, 400038, China
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Kakakhel MA, Narwal N, Kataria N, Johari SA, Zaheer Ud Din S, Jiang Z, Khoo KS, Xiaotao S. Deciphering the dysbiosis caused in the fish microbiota by emerging contaminants and its mitigation strategies-A review. ENVIRONMENTAL RESEARCH 2023; 237:117002. [PMID: 37648194 DOI: 10.1016/j.envres.2023.117002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/01/2023]
Abstract
The primary barrier to nutrient absorption in fish is the intestinal epithelium, followed by a community of microorganisms known as the gut microbiota, which can be thought of as a hidden organ. The gastrointestinal microbiota of fish plays a key role in the upholding of overall health by maintaining the homeostasis and disease resistance of the host. However, emerging contaminants as the result of anthropogenic activities have significantly led to disruptions and intestinal dysbiosis in fish. Which probably results in fish mortalities and disrupts the balance of an ecosystem. Therefore, we comprehensively seek to compile the effects and consequences of emerging contaminations on fish intestinal microbiota. Additionally, the mitigation strategies including prebiotics, probiotics, plant-based diet, and Biofloc technology are being outlined. Biofloc technology (BFT) can treat toxic materials, i.e., nitrogen components, and convert them into a useful product such as proteins and demonstrated promising elevating technique for the fish intestinal bacterial composition. However, it remains unclear whether the bacterial isolate is primarily responsible for the BFT's removal of nitrate and ammonia and the corresponding removal mechanism. To answer this, real time polymerase chain reaction (RT-PCR) with metagenomics, transcriptomics, and proteomics techniques probably provides a possible solution.
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Affiliation(s)
- Mian Adnan Kakakhel
- Hubei International Science and Technology Cooperation Base of Fish Passage, Three Gorges University, Yichang, 443002, Hubei, China; College of Hydraulic & Environmental Engineering, Three Gorges University, Yichang, 443002, Hubei, China
| | - Nishita Narwal
- University School of Environment Management, Guru Gobind Singh Indraprastha University, New Delhi, 110078, India
| | - Navish Kataria
- Department of Environmental Sciences, J.C. Bose University of Science and Technology, YMCA, Faridabad, Haryana, 121006, India
| | - Seyed Ali Johari
- Department of Fisheries, Faculty of Natural Resources, University of Kurdistan, Sanandaj, Kurdistan, Iran
| | - Syed Zaheer Ud Din
- International School for Optoelectronic Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Zewen Jiang
- Hubei International Science and Technology Cooperation Base of Fish Passage, Three Gorges University, Yichang, 443002, Hubei, China; College of Hydraulic & Environmental Engineering, Three Gorges University, Yichang, 443002, Hubei, China
| | - Kuan Shiong Khoo
- Department of Chemical Engineering and Materials Science, Yuan Ze University, Taoyuan, Taiwan
| | - Shi Xiaotao
- Hubei International Science and Technology Cooperation Base of Fish Passage, Three Gorges University, Yichang, 443002, Hubei, China; College of Hydraulic & Environmental Engineering, Three Gorges University, Yichang, 443002, Hubei, China.
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23
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Venice F, Vizzini A, Danti R, Della Rocca G, Mello A. Responses of a soil fungal community to severe windstorm damages in an old silver fir stand. Front Microbiol 2023; 14:1246874. [PMID: 38029204 PMCID: PMC10668432 DOI: 10.3389/fmicb.2023.1246874] [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: 07/06/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023] Open
Abstract
Forests are increasingly threatened by climate change and the Anthropocene seems to have favored the emergence and adaptation of pathogens. Robust monitoring methods are required to prevent biodiversity and ecosystems losses, and this imposes the choice of bioindicators of habitat health. Fungal communities are increasingly recognized as fundamental components in nearly all natural and artificial environments, and their ecosystem services have a huge impact in maintaining and restoring the functionality of ecosystems. We coupled metabarcoding and soil analyses to infer the dynamics of a fungal community inhabiting the old silver fir stand in Vallombrosa (Italy), which is known to be afflicted by both Armillaria and Annosum root rot. The forest was affected in 2015, by a windstorm which caused a partial falling and uprooting of trees. The remaining stand, not affected by the windstorm, was used as a comparison to infer the consequences of the ecosystem disturbance. We demonstrated that the abundance of pathogens alone is not able to explain the soil fungal differences shown by the two areas. The fungal community as a whole was equally rich in the two areas, even if a reduction of the core ectomycorrhizal mycobiome was observed in the wind-damaged area, accompanied by the increase of wood saprotrophs and arbuscular mycorrhizas. We hypothesize a reshaping of the fungal community and a potentially ongoing re-generation of its functionalities. Our hypothesis is driven by the evidence that key symbiotic, endophytic, and saprotrophic guilds are still present and diversified in the wind-damaged area, and that dominance of single taxa or biodiversity loss was not observed from a mycological point of view. With the present study, we aim at providing evidence that fungal communities are fundamental for the monitoring and the conservation of threatened forest ecosystems.
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Affiliation(s)
- Francesco Venice
- Institute for Sustainable Plant Protection (IPSP) - SS Turin - National Research Council (CNR), Turin, Italy
- Department of Life Sciences and System Biology, University of Turin, Turin, Italy
| | - Alfredo Vizzini
- Institute for Sustainable Plant Protection (IPSP) - SS Turin - National Research Council (CNR), Turin, Italy
- Department of Life Sciences and System Biology, University of Turin, Turin, Italy
| | - Roberto Danti
- Institute for Sustainable Plant Protection (IPSP) - National Research Council (CNR), Sesto Fiorentino (FI), Italy
| | - Gianni Della Rocca
- Institute for Sustainable Plant Protection (IPSP) - National Research Council (CNR), Sesto Fiorentino (FI), Italy
| | - Antonietta Mello
- Institute for Sustainable Plant Protection (IPSP) - SS Turin - National Research Council (CNR), Turin, Italy
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24
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Krishnamurthy HK, Pereira M, Bosco J, George J, Jayaraman V, Krishna K, Wang T, Bei K, Rajasekaran JJ. Gut commensals and their metabolites in health and disease. Front Microbiol 2023; 14:1244293. [PMID: 38029089 PMCID: PMC10666787 DOI: 10.3389/fmicb.2023.1244293] [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: 06/22/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose of review This review comprehensively discusses the role of the gut microbiome and its metabolites in health and disease and sheds light on the importance of a holistic approach in assessing the gut. Recent findings The gut microbiome consisting of the bacteriome, mycobiome, archaeome, and virome has a profound effect on human health. Gut dysbiosis which is characterized by perturbations in the microbial population not only results in gastrointestinal (GI) symptoms or conditions but can also give rise to extra-GI manifestations. Gut microorganisms also produce metabolites (short-chain fatty acids, trimethylamine, hydrogen sulfide, methane, and so on) that are important for several interkingdom microbial interactions and functions. They also participate in various host metabolic processes. An alteration in the microbial species can affect their respective metabolite concentrations which can have serious health implications. Effective assessment of the gut microbiome and its metabolites is crucial as it can provide insights into one's overall health. Summary Emerging evidence highlights the role of the gut microbiome and its metabolites in health and disease. As it is implicated in GI as well as extra-GI symptoms, the gut microbiome plays a crucial role in the overall well-being of the host. Effective assessment of the gut microbiome may provide insights into one's health status leading to more holistic care.
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Affiliation(s)
| | | | - Jophi Bosco
- Vibrant America LLC., San Carlos, CA, United States
| | | | | | | | - Tianhao Wang
- Vibrant Sciences LLC., San Carlos, CA, United States
| | - Kang Bei
- Vibrant Sciences LLC., San Carlos, CA, United States
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25
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Zhang S, Han Y, Schofield W, Nicosia M, Karell PE, Newhall KP, Zhou JY, Musich RJ, Pan S, Valujskikh A, Sangwan N, Dwidar M, Lu Q, Stappenbeck TS. Select symbionts drive high IgA levels in the mouse intestine. Cell Host Microbe 2023; 31:1620-1638.e7. [PMID: 37776865 DOI: 10.1016/j.chom.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/14/2023] [Accepted: 09/01/2023] [Indexed: 10/02/2023]
Abstract
Immunoglobulin A (IgA) is an important factor in maintaining homeostasis at mucosal surfaces, yet luminal IgA levels vary widely. Total IgA levels are thought to be driven by individual immune responses to specific microbes. Here, we found that the prebiotic, pectin oligosaccharide (pec-oligo), induced high IgA levels in the small intestine in a T cell-dependent manner. Surprisingly, this IgA-high phenotype was retained after cessation of pec-oligo treatment, and microbiome transmission either horizontally or vertically was sufficient to retain high IgA levels in the absence of pec-oligo. Interestingly, the bacterial taxa enriched in the overall pec-oligo bacterial community differed from IgA-coated microbes in this same community. Rather, a group of ethanol-resistant microbes, highly enriched for Lachnospiraceae bacterium A2, drove the IgA-high phenotype. These findings support a model of intestinal adaptive immunity in which a limited number of microbes can promote durable changes in IgA directed to many symbionts.
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Affiliation(s)
- Shanshan Zhang
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Gastroenterology, Qilu Hospital, Shandong University, Jinan 250000, P.R. China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Yi Han
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - Michael Nicosia
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Paul E Karell
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kevin P Newhall
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Julie Y Zhou
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ryan J Musich
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Siyi Pan
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Anna Valujskikh
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Naseer Sangwan
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Mohammed Dwidar
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Qiuhe Lu
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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Cláudia-Ferreira A, Barbosa DJ, Saegeman V, Fernández-Rodríguez A, Dinis-Oliveira RJ, Freitas AR. The Future Is Now: Unraveling the Expanding Potential of Human (Necro)Microbiome in Forensic Investigations. Microorganisms 2023; 11:2509. [PMID: 37894167 PMCID: PMC10608847 DOI: 10.3390/microorganisms11102509] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/24/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
The relevance of postmortem microbiological examinations has been controversial for decades, but the boom in advanced sequencing techniques over the last decade is increasingly demonstrating their usefulness, namely for the estimation of the postmortem interval. This comprehensive review aims to present the current knowledge about the human postmortem microbiome (the necrobiome), highlighting the main factors influencing this complex process and discussing the principal applications in the field of forensic sciences. Several limitations still hindering the implementation of forensic microbiology, such as small-scale studies, the lack of a universal/harmonized workflow for DNA extraction and sequencing technology, variability in the human microbiome, and limited access to human cadavers, are discussed. Future research in the field should focus on identifying stable biomarkers within the dominant Bacillota and Pseudomonadota phyla, which are prevalent during postmortem periods and for which standardization, method consolidation, and establishment of a forensic microbial bank are crucial for consistency and comparability. Given the complexity of identifying unique postmortem microbial signatures for robust databases, a promising future approach may involve deepening our understanding of specific bacterial species/strains that can serve as reliable postmortem interval indicators during the process of body decomposition. Microorganisms might have the potential to complement routine forensic tests in judicial processes, requiring robust investigations and machine-learning models to bridge knowledge gaps and adhere to Locard's principle of trace evidence.
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Affiliation(s)
- Ana Cláudia-Ferreira
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
| | - Daniel José Barbosa
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
| | - Veroniek Saegeman
- Department of Infection Control and Prevention, University Hospitals Leuven, 3000 Leuven, Belgium;
| | - Amparo Fernández-Rodríguez
- Microbiology Laboratory, Biology Service, Institute of Toxicology and Forensic Sciences, 28232 Madrid, Spain;
| | - Ricardo Jorge Dinis-Oliveira
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
- Department of Public Health and Forensic Sciences, and Medical Education, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Ana R. Freitas
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
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Zhu S, Cai Y, Li Y, Xiong J, Lei Y, Sun Y. Effects of temporal and spatial scales on soil yeast communities in the peach orchard. Front Microbiol 2023; 14:1226142. [PMID: 37795290 PMCID: PMC10546340 DOI: 10.3389/fmicb.2023.1226142] [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: 05/20/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023] Open
Abstract
Shihezi Reclamation Area is located at the southern edge of the Junggar Basin, with natural, soil, and climatic conditions unique to the production of peaches. In turn, peach orchards have accumulated rich microbial resources. As an important taxon of soil fungi, the diversity and community structure changes of yeast in the soil of peach orchards on spatial and temporal scales are still unknown. Here, we aimed to investigate the changes in yeast diversity and community structure in non-rhizosphere and rhizosphere soils of peach trees of different ages in the peach orchard and the factors affecting them, as well as the changes in the yeast co-occurrence network in the peach orchard at spatial and temporal scales. High-through put sequencing results showed that a total of 114 yeast genera were detected in all soil samples, belonging to Ascomycota (60 genera) and Basidiomycota (54 genera). The most dominant genus, Cryptococcus, was present in greater than 10% abundance in each sample. Overall, the differences in yeast diversity between non-rhizosphere and rhizosphere soil of peach trees at 3, 8 and 15 years were not significant. Principal coordinate analysis (PCoA) showed that differences in yeast community structure were more pronounced at the temporal scale compared to the spatial scale. The results of soil physical and chemical analysis showed that the 15-year-old peach rhizosphere soil had the lowest pH, while the OM, TN, and TP contents increased significantly. Redundancy analysis showed that soil pH and CO were key factors contributing to changes in soil yeast community structure in the peach orchard at both spatial and temporal scales. The results of co-occurrence network analysis showed that the peach orchard soil yeast network showed synergistic effects as a whole, and the degree of interactions and connection tightness of the 15-year-old peach orchard soil yeast network were significantly higher than the 3- and 8-year-old ones on the time scale. The results reveal the distribution pattern and mechanism of action of yeast communities in peach orchard soils, which can help to develop effective soil management strategies and improve the stability of soil microecology, thus promoting crop growth.
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Affiliation(s)
- ShanShan Zhu
- Department of Plant Protection, College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - YanLi Cai
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Yang Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Jie Xiong
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - YongHui Lei
- Department of Plant Protection, College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - YanFei Sun
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
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Hu B, Shi Y, Lu C, Chen H, Zeng Y, Deng J, Zhang L, Lin Q, Li W, Chen Y, Zhong F, Xia X. Raspberry polyphenols alleviate neurodegenerative diseases: through gut microbiota and ROS signals. Food Funct 2023; 14:7760-7779. [PMID: 37555470 DOI: 10.1039/d3fo01835k] [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: 08/10/2023]
Abstract
Neurodegenerative diseases are neurological disorders that become more prevalent with age, usually caused by damage or loss of neurons or their myelin sheaths, such as Alzheimer's disease and epilepsy. Reactive oxygen species (ROS) are important triggers for neurodegenerative disease development, and mitigation of oxidative stress caused by ROS imbalance in the human body is important for the treatment of these diseases. As a widespread delicious fruit, the raspberry is widely used in the field of food and medicine because of its abundant polyphenols and other bioactive substances. Polyphenols from a wide variety of raspberry sources could alleviate neurodegenerative diseases. This review aims to summarize the current roles of these polyphenols in maintaining neurological stability by regulating the composition and metabolism of the intestinal flora and the gut-brain axis signal transmission. Especially, we discuss the therapeutic effects on neurodegenerative diseases of raspberry polyphenols through intestinal microorganisms and ROS signals, by means of summary and analysis. Finally, methods of improving the digestibility and utilization of raspberry polyphenols are proposed, which will provide a potential way for raspberry polyphenols to guarantee the health of the human nervous system.
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Affiliation(s)
- Boyong Hu
- National Engineering Research Center of Rice and Byproduct Deep Processing, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
| | - Yi Shi
- National Engineering Research Center of Rice and Byproduct Deep Processing, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
| | - Chunyue Lu
- National Engineering Research Center of Rice and Byproduct Deep Processing, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
| | - Haixin Chen
- National Engineering Research Center of Rice and Byproduct Deep Processing, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
| | - Yuqing Zeng
- National Engineering Research Center of Rice and Byproduct Deep Processing, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
| | - Jing Deng
- National Engineering Research Center of Rice and Byproduct Deep Processing, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
| | - Lin Zhang
- National Engineering Research Center of Rice and Byproduct Deep Processing, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
| | - Qinlu Lin
- National Engineering Research Center of Rice and Byproduct Deep Processing, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
| | - Wen Li
- National Engineering Research Center of Rice and Byproduct Deep Processing, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
| | - Yuan Chen
- School of Life Science, Huizhou University, Huizhou 516007, China
| | - Feifei Zhong
- National Engineering Research Center of Rice and Byproduct Deep Processing, Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
- Changsha Institute for Food and Drug Control, Changsha 410016, Hunan, China
| | - Xu Xia
- Huaihua Academy of Agricultural Sciences, Huaihua 418000, Hunan, China
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Morgan EW, Dong F, Annalora AJ, Murray IA, Wolfe T, Erickson R, Gowda K, Amin SG, Petersen KS, Kris-Etherton PM, Marcus CB, Walk ST, Patterson AD, Perdew GH. Contribution of Circulating Host and Microbial Tryptophan Metabolites Toward Ah Receptor Activation. Int J Tryptophan Res 2023; 16:11786469231182510. [PMID: 37441265 PMCID: PMC10334013 DOI: 10.1177/11786469231182510] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand activated transcription factor that plays an integral role in homeostatic maintenance by regulating cellular functions such as cellular differentiation, metabolism, barrier function, and immune response. An important but poorly understood class of AHR activators are compounds derived from host and bacterial metabolism of tryptophan. The commensal bacteria of the gut microbiome are major producers of tryptophan metabolites known to activate the AHR, while the host also produces AHR activators through tryptophan metabolism. We used targeted mass spectrometry-based metabolite profiling to determine the presence and metabolic source of these metabolites in the sera of conventional mice, germ-free mice, and humans. Surprisingly, sera concentrations of many tryptophan metabolites are comparable between germ-free and conventional mice. Therefore, many major AHR-activating tryptophan metabolites in mouse sera are produced by the host, despite their presence in feces and mouse cecal contents. Here we present an investigation of AHR activation using a complex mixture of tryptophan metabolites to examine the biological relevance of circulating tryptophan metabolites. AHR activation is rarely studied in the context of a mixture at relevant concentrations, as we present here. The AHR activation potentials of individual and pooled metabolites were explored using cell-based assays, while ligand binding competition assays and ligand docking simulations were used to assess the detected metabolites as AHR agonists. The physiological and biomedical relevance of the identified metabolites was investigated in the context of a cell-based model for rheumatoid arthritis. We present data that reframe AHR biology to include the presence of a mixture of ubiquitous tryptophan metabolites, improving our understanding of homeostatic AHR activity and models of AHR-linked diseases.
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Affiliation(s)
- Ethan W Morgan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, USA
| | - Fangcong Dong
- Department of Veterinary and Biomedical Sciences and the Center for Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, University Park, USA
| | - Andrew J Annalora
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA
| | - Iain A Murray
- Department of Veterinary and Biomedical Sciences and the Center for Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, University Park, USA
| | - Trenton Wolfe
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, USA
| | - Reece Erickson
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, USA
| | - Krishne Gowda
- Department of Pharmacology Penn State College of Medicine, Hershey, USA
| | - Shantu G Amin
- Department of Pharmacology Penn State College of Medicine, Hershey, USA
| | - Kristina S Petersen
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, USA
| | - Penny M Kris-Etherton
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, USA
| | - Craig B Marcus
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA
| | - Seth T Walk
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences and the Center for Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, University Park, USA
| | - Gary H Perdew
- Department of Veterinary and Biomedical Sciences and the Center for Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, University Park, USA
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Ternák G, Márovics G, Sümegi K, Bánfai Z, Büki G, Magyari L, Szabó A, Melegh B. Down-Syndrome-Related Maternal Dysbiosis Might Be Triggered by Certain Classes of Antibiotics: A New Insight into the Possible Pathomechanisms. Antibiotics (Basel) 2023; 12:1029. [PMID: 37370348 DOI: 10.3390/antibiotics12061029] [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: 05/03/2023] [Revised: 05/24/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Down syndrome (DS) is a leading human genomic abnormality resulting from the trisomy of chromosome 21. The genomic base of the aneuploidy behind this disease is complex, and this complexity poses formidable challenges to understanding the underlying molecular basis. In the spectrum of the classic DS risk factor associations, the role of nutrients, vitamins, and, in general, the foodborne-associated background, as part of the events ultimately leading to chromosome nondisjunction, has long been recognized as a well-established clinical association. The integrity of the microbiome is a basic condition in these events, and the dysbiosis may be associated with secondary health outcomes. The possible association of DS development with maternal gut microbiota should therefore require more attention. We have hypothesized that different classes of antibiotics might promote or inhibit the proliferation of different microbial taxa; and hence, we might find associations between the use of the different classes of antibiotics and the prevalence of DS through the modification of the microbiome. As antibiotics are considered major disruptors of the microbiome, it could be hypothesized that the consumption/exposure of certain classes of antibiotics might be associated with the prevalence of DS in European countries (N = 30). By utilizing three different statistical methods, comparisons have been made between the average yearly antibiotic consumption (1997-2020) and the estimated prevalence of people living with DS for the year 2019 as a percentage of the population in European countries. We have found strong statistical correlations between the consumption of tetracycline (J01A) and the narrow-spectrum, beta-lactamase-resistant penicillin (J01CF) and the prevalence of DS.
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Affiliation(s)
- Gábor Ternák
- Institute of Migration Health, Medical School, University of Pécs, Szigeti út 12., H-7624 Pécs, Hungary
| | - Gergely Márovics
- Department of Public Health Medicine, Medical School, University of Pécs, Szigeti út 12., H-7624 Pécs, Hungary
| | - Katalin Sümegi
- Department of Medical Genetics, Medical School, University of Pécs, Szigeti út 12., H-7624 Pécs, Hungary
- Department of Biochemistry and Chemistry, Medical School, University of Pécs, Szigeti út 12., H-7624 Pécs, Hungary
| | - Zsolt Bánfai
- Department of Medical Genetics, Medical School, University of Pécs, Szigeti út 12., H-7624 Pécs, Hungary
| | - Gergely Büki
- Department of Medical Genetics, Medical School, University of Pécs, Szigeti út 12., H-7624 Pécs, Hungary
| | - Lili Magyari
- Department of Medical Genetics, Medical School, University of Pécs, Szigeti út 12., H-7624 Pécs, Hungary
| | - András Szabó
- Department of Medical Genetics, Medical School, University of Pécs, Szigeti út 12., H-7624 Pécs, Hungary
| | - Béla Melegh
- Department of Medical Genetics, Medical School, University of Pécs, Szigeti út 12., H-7624 Pécs, Hungary
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Singh S, Keating C, Ijaz UZ, Hassard F. Molecular insights informing factors affecting low temperature anaerobic applications: Diversity, collated core microbiomes and complexity stability relationships in LCFA-fed systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 874:162420. [PMID: 36842571 DOI: 10.1016/j.scitotenv.2023.162420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/31/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
Fats, oil and grease, and their hydrolyzed counterparts-long chain fatty acids (LCFA) make up a large fraction of numerous wastewaters and are challenging to degrade anaerobically, more so, in low temperature anaerobic digestion (LtAD) systems. Herein, we perform a comparative analysis of publicly available Illumina 16S rRNA datasets generated from LCFA-degrading anaerobic microbiomes at low temperatures (10 and 20 °C) to comprehend the factors affecting microbial community dynamics. The various factors considered were the inoculum, substrate and operational characteristics, the reactor operation mode and reactor configuration, and the type of nucleic acid sequenced. We found that LCFA-degrading anaerobic microbiomes were differentiated primarily by inoculum characteristics (inoculum source and morphology) in comparison to the other factors tested. Inoculum characteristics prominently shaped the species richness, species evenness and beta-diversity patterns in the microbiomes even after long term operation of continuous reactors up to 150 days, implying the choice of inoculum needs careful consideration. The generalised additive models represented through beta diversity contour plots revealed that psychrophilic bacteria RBG-13-54-9 from family Anaerolineae, and taxa WCHB1-41 and Williamwhitmania were highly abundant in LCFA-fed microbial niches, suggesting their role in anaerobic treatment of LCFAs at low temperatures of 10-20 °C. Overall, we showed that the following bacterial genera: uncultured Propionibacteriaceae, Longilinea, Christensenellaceae R7 group, Lactivibrio, candidatus Caldatribacterium, Aminicenantales, Syntrophus, Syntrophomonas, Smithella, RBG-13-54-9, WCHB1-41, Trichococcus, Proteiniclasticum, SBR1031, Lutibacter and Lentimicrobium have prominent roles in LtAD of LCFA-rich wastewaters at 10-20 °C. This study provides molecular insights of anaerobic LCFA degradation under low temperatures from collated datasets and will aid in improving LtAD systems for treating LCFA-rich wastewaters.
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Affiliation(s)
- Suniti Singh
- Cranfield Water Science Institute, Cranfield University, College Way, Bedfordshire MK43 0AL, UK.
| | - Ciara Keating
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK.
| | - Umer Zeeshan Ijaz
- Infrastructure and Environment Research Division, James Watt School of Engineering, University of Glasgow, UK; Department of Molecular and Clinical Cancer Medicine, University of Liverpool, UK; College of Science and Engineering, NUI Galway, Ireland.
| | - Francis Hassard
- Cranfield Water Science Institute, Cranfield University, College Way, Bedfordshire MK43 0AL, UK; Institute for Nanotechnology and Water Sustainability, University of South Africa, UNISA Science Campus, 1710 Roodepoort, Johannesburg, South Africa.
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Tian CM, Yang MF, Xu HM, Zhu MZ, Zhang Y, Yao J, Wang LS, Liang YJ, Li DF. Emerging role of bacterial outer membrane vesicle in gastrointestinal tract. Gut Pathog 2023; 15:20. [PMID: 37106359 PMCID: PMC10133921 DOI: 10.1186/s13099-023-00543-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/30/2023] [Indexed: 04/29/2023] Open
Abstract
Bacteria form a highly complex ecosystem in the gastrointestinal (GI) tract. In recent years, mounting evidence has shown that bacteria can release nanoscale phospholipid bilayer particles that encapsulate nucleic acids, proteins, lipids, and other molecules. Extracellular vesicles (EVs) are secreted by microorganisms and can transport a variety of important factors, such as virulence factors, antibiotics, HGT, and defensive factors produced by host eukaryotic cells. In addition, these EVs are vital in facilitating communication between microbiota and the host. Therefore, bacterial EVs play a crucial role in maintaining the GI tract's health and proper functioning. In this review, we outlined the structure and composition of bacterial EVs. Additionally, we highlighted the critical role that bacterial EVs play in immune regulation and in maintaining the balance of the gut microbiota. To further elucidate progress in the field of intestinal research and to provide a reference for future EV studies, we also discussed the clinical and pharmacological potential of bacterial EVs, as well as the necessary efforts required to understand the mechanisms of interaction between bacterial EVs and gut pathogenesis.
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Affiliation(s)
- Cheng-Mei Tian
- Department of Emergency, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China
| | - Mei-Feng Yang
- Department of Hematology, Yantian District People's Hospital, Shenzhen, Guangdong, China
| | - Hao-Ming Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Min-Zheng Zhu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Yuan Zhang
- Department of Medical Administration, Huizhou Institute of Occupational Diseases Control and Prevention, Huizhou, Guangdong, China
| | - Jun Yao
- Department of Gastroenterology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), No.1017, Dongmen North Road, Luohu District, Shenzhen, 518020, People's Republic of China.
| | - Li-Sheng Wang
- Department of Gastroenterology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), No.1017, Dongmen North Road, Luohu District, Shenzhen, 518020, People's Republic of China.
| | - Yu-Jie Liang
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, No.1080, Cuizu Road, Luohu District, Shenzhen, 518020, People's Republic of China.
| | - De-Feng Li
- Department of Gastroenterology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), No.1017, Dongmen North Road, Luohu District, Shenzhen, 518020, People's Republic of China.
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da Cunha LL, Monteiro HF, Figueiredo CC, Canisso IF, Bicalho RC, Cardoso FC, Weimer BC, Lima FS. Characterization of rumen microbiome and metabolome from oro-esophageal tubing and rumen cannula in Holstein dairy cows. Sci Rep 2023; 13:5854. [PMID: 37041192 PMCID: PMC10090163 DOI: 10.1038/s41598-023-33067-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/06/2023] [Indexed: 04/13/2023] Open
Abstract
Less invasive rumen sampling methods, such as oro-esophageal tubing, became widely popular for exploring the rumen microbiome and metabolome. However, it remains unclear if such methods represent well the rumen contents from the rumen cannula technique. Herein, we characterized the microbiome and metabolome in the rumen content collected by an oro-esophageal tube and by rumen cannula in ten multiparous lactating Holstein cows. The 16S rRNA gene was amplified and sequenced using the Illumina MiSeq platform. Untargeted metabolome was characterized using gas chromatography of a time-of-flight mass spectrometer. Bacteroidetes, Firmicutes, and Proteobacteria were the top three most abundant phyla representing ~ 90% of all samples. Although the pH of oro-esophageal samples was greater than rumen cannula, we found no difference in alpha and beta-diversity among their microbiomes. The overall metabolome of oro-esophageal samples was slightly different from rumen cannula samples yet more closely related to the rumen cannula content as a whole, including its fluid and particulate fractions. Enrichment pathway analysis revealed a few differences between sampling methods, such as when evaluating unsaturated fatty acid pathways in the rumen. The results of the current study suggest that oro-esophageal sampling can be a proxy to screen the 16S rRNA rumen microbiome compared to the rumen cannula technique. The variation introduced by the 16S rRNA methodology may be mitigated by oro-esophageal sampling and the possibility of increasing experimental units for a more consistent representation of the overall microbial population. Studies should consider an under or over-representation of metabolites and specific metabolic pathways depending on the sampling method.
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Affiliation(s)
- Lais L da Cunha
- Department of Forage Plants and Agrometeorology, Faculty of Agronomy, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Hugo F Monteiro
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Caio C Figueiredo
- Department of Large Animal Clinical Sciences, D. H. Barron Reproductive, and Perinatal Biology Research Program, University of Florida, Gainesville, 32610, USA
- Department of Veterinary Clinical Sciences, Washington State University, Pullman, 99164, USA
| | - Igor F Canisso
- Department of Veterinary Clinical Medicine, University of Illinois, Urbana, IL, USA
| | - Rodrigo C Bicalho
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY, USA
| | - Felipe C Cardoso
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
| | - Bart C Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Fabio S Lima
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA.
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Kann S, Eberhardt K, Hinz R, Schwarz NG, Dib JC, Aristizabal A, Mendoza GAC, Hagen RM, Frickmann H, Barrantes I, Kreikemeyer B. The Gut Microbiome of an Indigenous Agropastoralist Population in a Remote Area of Colombia with High Rates of Gastrointestinal Infections and Dysbiosis. Microorganisms 2023; 11:625. [PMID: 36985199 PMCID: PMC10052337 DOI: 10.3390/microorganisms11030625] [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: 01/25/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
An Indigenous agropastoralist population called the Wiwa from the Sierra Nevada de Santa Marta, in North-East Colombia, shows high rates of gastrointestinal infections. Chronic gut inflammatory processes and dysbiosis could be a reason, suggesting an influence or predisposing potential of the gut microbiome composition. The latter was analyzed by 16S rRNA gene amplicon next generation sequencing from stool samples. Results of the Wiwa population microbiomes were associated with available epidemiological and morphometric data and compared to control samples from a local urban population. Indeed, locational-, age-, and gender-specific differences in the Firmicutes/Bacteriodetes ratio, core microbiome, and overall genera-level microbiome composition were shown. Alpha- and ß-diversity separated the urban site from the Indigenous locations. Urban microbiomes were dominated by Bacteriodetes, whereas Indigenous samples revealed a four times higher abundance of Proteobacteria. Even differences among the two Indigenous villages were noted. PICRUSt analysis identified several enriched location-specific bacterial pathways. Moreover, on a general comparative scale and with a high predictive accuracy, we found Sutterella associated with the abundance of enterohemorrhagic Escherichia coli (EHEC), Faecalibacteria associated with enteropathogenic Escherichia coli (EPEC) and helminth species Hymenolepsis nana and Enterobius vermicularis. Parabacteroides, Prevotella, and Butyrivibrio are enriched in cases of salmonellosis, EPEC, and helminth infections. Presence of Dialister was associated with gastrointestinal symptoms, whereas Clostridia were exclusively found in children under the age of 5 years. Odoribacter and Parabacteroides were exclusively identified in the microbiomes of the urban population of Valledupar. In summary, dysbiotic alterations in the gut microbiome in the Indigenous population with frequent episodes of self-reported gastrointestinal infections were confirmed with epidemiological and pathogen-specific associations. Our data provide strong hints of microbiome alterations associated with the clinical conditions of the Indigenous population.
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Affiliation(s)
- Simone Kann
- Department for Research and Development, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Kirsten Eberhardt
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
- Division of Hygiene and Infectious Diseases, Institute of Hygiene and Environment, 20539 Hamburg, Germany
| | - Rebecca Hinz
- SYNLAB Medizinisches Versorgungszentrum Hamburg GmbH, 22083 Hamburg, Germany
| | | | - Juan Carlos Dib
- Department of Medicine, Fundación Universidad de Norte, Baranquilla 080001, Colombia
| | | | | | - Ralf Matthias Hagen
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56070 Koblenz, Germany
| | - Hagen Frickmann
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 20359 Hamburg, Germany
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany
| | - Israel Barrantes
- Research Group Translational Bioinformatics, Institute for Biostatistics and Informatics in Medicine und Aging Research, University Medicine Rostock, 18057 Rostock, Germany
| | - Bernd Kreikemeyer
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany
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35
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Bach L, Ram A, Ijaz UZ, Evans TJ, Haydon DT, Lindström J. The Effects of Smoking on Human Pharynx Microbiota Composition and Stability. Microbiol Spectr 2023; 11:e0216621. [PMID: 36786634 PMCID: PMC10101099 DOI: 10.1128/spectrum.02166-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/16/2023] [Indexed: 02/15/2023] Open
Abstract
The oral microbiota is essential to the health of the host, yet little is known about how it responds to disturbances. We examined the oropharyngeal microbiota of 30 individuals over 40 weeks. As the oropharynx is an important gateway to pathogens, and as smoking is associated with increased incidence and severity of respiratory infections, we compared the microbiota of smokers and nonsmokers to shed light on its potential for facilitating infections. We hypothesized that decreased species diversity, decreased community stability, or increased differences in community structure could facilitate invading pathogens. We found that smoking is associated with reduced alpha diversity, greater differences in community structure, and increased environmental filtering. The effects of short-term perturbations (antibiotic use and participants exhibiting cold symptoms) were also investigated. Antibiotic use had a negative effect on alpha diversity, irrespective of smoking status, and both antibiotic use and cold symptoms were associated with highly unique bacterial communities. A stability analysis of models built from the data indicated that there were no differences in local or global stability in the microbial communities of smokers, compared to nonsmokers, and that their microbiota are equally resistant to species invasions. Results from these models suggest that smoker microbiota are perturbed but characterized by alternative stable states that are as stable and invasion-resistant as are the microbiota of nonsmokers. Smoking is unlikely to increase the risk of infectious disease through the altered composition and ecological function of the microbiota; this is more likely due to the effects of smoking on the local and systemic immune system. IMPORTANCE Smoking is associated with an increased risk of respiratory infections. Hypothetically, the altered community diversity of smokers' pharyngeal microbiota, together with changes in their ecological stability properties, could facilitate their invasion by pathogens. To address this question, we analyzed longitudinal microbiota data of baseline healthy individuals who were either smokers or nonsmokers. While the results indicate reduced biodiversity and increased species turnover in the smokers' pharyngeal microbiota, their ecological stability properties were not different from those of the microbiota of nonsmokers, implying, in ecological terms, that the smokers' microbial communities are not less resistant to invasions. Therefore, the study suggests that the increased propensity of respiratory infections that is seen in smokers is more likely associated with changes in the local and systemic immune system than with ecological changes in the microbial communities.
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Affiliation(s)
- Lydia Bach
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, United Kingdom
| | - Asha Ram
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, United Kingdom
| | - Umer Z. Ijaz
- School of Science and Engineering, University of Glasgow, United Kingdom
| | - Thomas J. Evans
- School of Infection and Immunity, Glasgow Biomedical Research Centre, University of Glasgow, United Kingdom
| | - Daniel T. Haydon
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, United Kingdom
| | - Jan Lindström
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, United Kingdom
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36
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Morgan EW, Dong F, Annalora A, Murray IA, Wolfe T, Erickson R, Gowda K, Amin SG, Petersen KS, Kris-Etherton PM, Marcus C, Walk ST, Patterson AD, Perdew GH. Contribution of circulating host and microbial tryptophan metabolites towards Ah receptor activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525691. [PMID: 36747842 PMCID: PMC9900944 DOI: 10.1101/2023.01.26.525691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand activated transcription factor that plays an integral role in homeostatic maintenance by regulating cellular functions such as cellular differentiation, metabolism, barrier function, and immune response. An important but poorly understood class of AHR activators are compounds derived from host and bacterial metabolism of tryptophan. The commensal bacteria of the gut microbiome are major producers of tryptophan metabolites known to activate the AHR, while the host also produces AHR activators through tryptophan metabolism. We used targeted mass spectrometry-based metabolite profiling to determine the presence and metabolic source of these metabolites in the sera of conventional mice, germ-free mice, and humans. Surprisingly, sera concentrations of many tryptophan metabolites are comparable between germ-free and conventional mice. Therefore, many major AHR-activating tryptophan metabolites in mouse sera are produced by the host, despite their presence in feces and mouse cecal contents. AHR activation is rarely studied in the context of a mixture at relevant concentrations, as we present here. The AHR activation potentials of individual and pooled metabolites were explored using cell-based assays, while ligand binding competition assays and ligand docking simulations were used to assess the detected metabolites as AHR agonists. The physiological and biomedical relevance of the identified metabolites was investigated in the context of cell-based models for cancer and rheumatoid arthritis. We present data here that reframe AHR biology to include the presence of ubiquitous tryptophan metabolites, improving our understanding of homeostatic AHR activity and models of AHR-linked diseases.
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Structure and Function Analysis of Cultivated Meconopsis integrifolia Soil Microbial Community Based on High-Throughput Sequencing and Culturability. BIOLOGY 2023; 12:biology12020160. [PMID: 36829439 PMCID: PMC9952792 DOI: 10.3390/biology12020160] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/14/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023]
Abstract
(1) Background: The structure, function, and community interactions of soil microbial communities of cultivated Meconopsis integrifolia were characterized by studying this alpine flower and traditional endangered Tibetan medicine. (2) Methods: Soil bacteria and fungi were studied based on high-throughput sequencing technology. Bacteria were isolated using culturomics and functionally identified as IAA-producing, organic phosphorus-dissolving, inorganic phosphorus-dissolving, and iron-producing carriers. (3) Results: The dominant bacterial phyla were found to be Proteobacteria and Acidobacteria, and unclassified_Rhizobiales was the most abundant genus. Ascomycota and Mortierellomycota were the dominant fungal phyla. The bacteria were mainly carbon and nitrogen metabolizers, and the fungi were predominantly Saprotroph-Symbiotroph. The identified network was completely dominated by positive correlations, but the fungi were more complex than the bacteria, and the bacterial keystones were unclassified_Caulobacteraceae and Pedobacter. Most of the keystones of fungi belonged to the phyla Ascomycetes and Basidiomycota. The highest number of different species of culturable bacteria belonged to the genus Streptomyces, with three strains producing IAA, 12 strains solubilizing organic phosphorus, one strain solubilizing inorganic phosphorus, and nine strains producing iron carriers. (4) Conclusions: At the cost of reduced ecological stability, microbial communities increase cooperation toward promoting overall metabolic efficiency and enabling their survival in the extreme environment of the Tibetan Plateau. These pioneering results have value for the protection of endangered Meconopsis integrifolia under global warming and the sustainable utilization of its medicinal value.
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Bauer-Estrada K, Sandoval-Cuellar C, Rojas-Muñoz Y, Quintanilla-Carvajal MX. The modulatory effect of encapsulated bioactives and probiotics on gut microbiota: improving health status through functional food. Food Funct 2023; 14:32-55. [PMID: 36515144 DOI: 10.1039/d2fo02723b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The gut microbiota can be a determining factor of the health status of the host by its association with some diseases. It is known that dietary intake can modulate this microbiota through the consumption of compounds like essential oils, unsaturated fatty acids, non-digestible fiber, and probiotics, among others. However, these kinds of compounds can be damaged in the gastrointestinal tract as they pass through it to reach the intestine. This is due to the aggressive and changing conditions of this tract. For this reason, to guarantee that compounds arrive in the intestine at an adequate concentration to exert a modulatory effect on the gut microbiota, encapsulation should be sought. In this paper, we review the current research on compounds that modulate the gut microbiota, the encapsulation techniques used to protect the compounds through the gastrointestinal tract, in vitro models of this tract, and how these encapsulates interact with the gut microbiota. Finally, an overview of the regulatory status of these encapsulates is presented. The key findings are that prebiotics are the best modulators of gut microbiota fermentation metabolites. Also, probiotics promote an increase of beneficial gut microorganisms, which in some cases promotes their fermentation metabolites as well. Spray drying, freeze drying, and electrodynamics are notable encapsulation techniques that permit high encapsulation efficiency, high viability, and, together with wall materials, a high degree of protection against gastrointestinal conditions, allowing controlled release in the intestine and exerting a modulatory effect on gut microbiota.
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Pittaluga AM, Yang F, Gaffney JR, Embree M, Relling AE. Effect of supplementation with ruminal probiotics on growth performance, carcass characteristics, plasma metabolites, methane emissions, and the associated rumen microbiome changes in beef cattle. J Anim Sci 2023; 101:skac308. [PMID: 36592753 PMCID: PMC9831096 DOI: 10.1093/jas/skac308] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/16/2022] [Indexed: 01/04/2023] Open
Abstract
To evaluate the effect of supplementing beef cattle with a ruminal probiotic consisting of native rumen microbes (NRM; Chordicoccus furentiruminis, Prevotella albensis, and Succinivibrio dextrinosolvens) on methane (CH4) emissions, growth performance, carcass characteristics, and plasma metabolites, Angus × SimAngus-crossbred steers (n = 32; 8 per pen) and heifers (n = 48; 12 per pen) with an initial body weight (BW) of 353 ± 64 kg were used in randomized complete block design. Cattle were blocked by sex and BW and randomly assigned to 1 of 2 treatments (2 pens per treatment). Treatments consisted of diets offered for ad libitum intake with (NRM) or without (CON) the inclusion of the ruminal probiotic. Cattle were fed a growing diet for 49 d followed by a ground corn-based diet for 124 ± 27 d until reaching the targeted final BW (635 kg for steers and 590 kg for heifers). Methane emissions were estimated using the GreenFeed system (n = 12 per treatment) prior to trial commencement (baseline; period 1), and on three (2, 3, and 4), and two (5 and 6) different sampling periods throughout the growing and finishing stage, respectively. All data were analyzed using the PROC MIXED procedure of SAS. For CH4 production (g/d), there was a tendency for an NRM supplementation × period interaction (P = 0.07) where cattle-fed diets with NRM had lower production of methane in periods 3 and 4. Including NRM in the diet decreased CH4 yield (g/kg of dry matter intake (DMI)) by 20%. For CH4 emission intensity (g/kg of average daily gain (ADG)), an interaction (P < 0.01) of NRM supplementation × period occurred. In periods 2 and 3, cattle-fed diets with NRM inclusion had lower CH4 emission intensity than CON cattle. During the 84-d period when all cattle were still on the finishing diet, feeding NRM increased (P = 0.02) ADG and tended to increase (P = 0.10) DMI. At the end of the 84-d period, cattle-fed NRM tended to be heavier (P = 0.06) than CON cattle. Cattle supplemented with NRM required less (P = 0.04) days on feed to reach the targeted final BW. No differences (P ≤ 0.11) were detected for gain-to-feed ratio and carcass characteristics. Cattle-fed NRM had greater abundance of uncultured rumen bacteria that may improve rumen digestion when fed a high grain diet and potentially promote the reduction of enteric CH4 production. Results from this study suggest that daily administration of NRM may be a strategy to mitigate methanogenesis and improve the growth performance of beef cattle.
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Affiliation(s)
| | - Fan Yang
- Native Microbials, Inc., San Diego, CA 92121, USA
| | | | | | - Alejandro E Relling
- Department of Animal Sciences/Interdisciplinary PhD Program in Nutrition, The Ohio State University, Columbus 43210, USA
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Berlin P, Barrantes I, Reiner J, Schröder E, Vollmar B, Bull J, Kreikemeyer B, Lamprecht G, Witte M. Dysbiosis and reduced small intestinal function are required to induce intestinal insufficiency in mice. Am J Physiol Gastrointest Liver Physiol 2023; 324:G10-G23. [PMID: 36346150 PMCID: PMC9799149 DOI: 10.1152/ajpgi.00201.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Extensive bowel resection can lead to short bowel syndrome and intestinal failure. Resection-induced dysbiosis may be related to the specific anatomic site of resection and influences the disease progression. Although patients with end-jejunostomy are at high risk for intestinal failure, preservation of the ileocecal valve and colon counteracts this risk. The present study investigated the role of the cecum in maintaining microbial homeostasis after different types of small bowel resection. Male C57BL6/J mice were anesthetized by intraperitoneal injection of ketamine-xylazine and received extended ileocecal resection (extended ICR), limited ileocecal resection (limited ICR), or mid-small bowel resection (SBR). Stool samples were collected before surgery and between postoperative days 2-7, for 16S rRNA gene sequencing. Only extended ICR, but neither limited ICR nor SBR, induced intestinal insufficiency. α-Diversity was reduced in both ICR variants but not after SBR. All resections resulted in an increase in Proteobacteria. Pathobionts, such as Clostridia, Shigella, and Enterococcus, increased after SBR while Muribaculaceae, Lactobacillus, and Lachnospiraceae decreased. Limited ICR resulted in an increase of members of the Clostridium sensu stricto group, Terrisporobacter and Enterococcus and a decrease of Muribaculaceae. The increase of Enterococcus was even more pronounced after extended ICR while Muribaculaceae and Akkermansia were dramatically reduced. Both ICR variants caused a decrease in steroid biosynthesis and glycosaminoglycan degradation-associated pathways, suggesting altered bile acid transformation and mucus utilization.NEW & NOTEWORTHY Resection-induced dysbiosis affects disease progression in patients with short bowel syndrome. Severe dysbiosis occurs after removal of the ileocecal valve, even in the absence of short bowel conditions, and is associated with the loss of Muribaculaceae and Akkermansia and an increase of Clostridium and Enterococcus. The preservation of the cecum should be considered in surgical therapy, and dysbiosis should be targeted based on its specific anatomical signature to improve postoperative bacterial colonization.
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Affiliation(s)
- Peggy Berlin
- 1Division of Gastroenterology, Department of Medicine II, Rostock University Medical Center, Rostock, Germany
| | - Israel Barrantes
- 2Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Johannes Reiner
- 1Division of Gastroenterology, Department of Medicine II, Rostock University Medical Center, Rostock, Germany
| | - Emma Schröder
- 1Division of Gastroenterology, Department of Medicine II, Rostock University Medical Center, Rostock, Germany
| | - Brigitte Vollmar
- 3Rudolf-Zenker-Institute for Experimental Surgery, Rostock University Medical Center, Rostock, Germany
| | - Jana Bull
- 4Institute for Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Bernd Kreikemeyer
- 4Institute for Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Georg Lamprecht
- 1Division of Gastroenterology, Department of Medicine II, Rostock University Medical Center, Rostock, Germany
| | - Maria Witte
- 5Department of General, Visceral, Thoracic, Vascular and Transplant Surgery, Rostock University Medical Center, Rostock, Germany
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The gut microbiota and depressive symptoms across ethnic groups. Nat Commun 2022; 13:7129. [PMID: 36473853 PMCID: PMC9726934 DOI: 10.1038/s41467-022-34504-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/27/2022] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome is thought to play a role in depressive disorders, which makes it an attractive target for interventions. Both the microbiome and depressive symptom levels vary substantially across ethnic groups. Thus, any intervention for depression targeting the microbiome requires understanding of microbiome-depression associations across ethnicities. Analysing data from the HELIUS cohort, we characterize the gut microbiota and its associations with depressive symptoms in 6 ethnic groups (Dutch, South-Asian Surinamese, African Surinamese, Ghanaian, Turkish, Moroccan; N = 3211), living in the same urban area. Diversity of the gut microbiota, both within (α-diversity) and between individuals (β-diversity), predicts depressive symptom levels, taking into account demographic, behavioural, and medical differences. These associations do not differ between ethnic groups. Further, β-diversity explains 29%-18% of the ethnic differences in depressive symptoms. Bacterial genera associated with depressive symptoms belong to mulitple families, prominently including the families Christensenellaceae, Lachnospiraceae, and Ruminococcaceae. In summary, the results show that the gut microbiota are linked to depressive symptom levels and that this association generalizes across ethnic groups. Moreover, the results suggest that ethnic differences in the gut microbiota may partly explain parallel disparities in depression.
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Talapko J, Včev A, Meštrović T, Pustijanac E, Jukić M, Škrlec I. Homeostasis and Dysbiosis of the Intestinal Microbiota: Comparing Hallmarks of a Healthy State with Changes in Inflammatory Bowel Disease. Microorganisms 2022; 10:microorganisms10122405. [PMID: 36557658 PMCID: PMC9781915 DOI: 10.3390/microorganisms10122405] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota, which represent a community of different microorganisms in the human intestinal tract, are crucial to preserving human health by participating in various physiological functions and acting as a metabolic organ. In physiological conditions, microbiota-host partnership exerts homeostatic stability; however, changes in intestinal microbiota composition (dysbiosis) are an important factor in the pathogenesis of inflammatory bowel disease and its two main disease entities: ulcerative colitis and Crohn's disease. The incidence and prevalence of these inflammatory conditions have increased rapidly in the last decade, becoming a significant problem for the healthcare system and a true challenge in finding novel therapeutic solutions. The issue is that, despite numerous studies, the etiopathogenesis of inflammatory bowel disease is not completely clear. Based on current knowledge, chronic intestinal inflammation occurs due to altered intestinal microbiota and environmental factors, as well as a complex interplay between the genetic predisposition of the host and an inappropriate innate and acquired immune response. It is important to note that the development of biological and immunomodulatory therapy has led to significant progress in treating inflammatory bowel disease. Certain lifestyle changes and novel approaches-including fecal microbiota transplantation and nutritional supplementation with probiotics, prebiotics, and synbiotics-have offered solutions for dysbiosis management and paved the way towards restoring a healthy microbiome, with only minimal long-term unfavorable effects.
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Affiliation(s)
- Jasminka Talapko
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Crkvena 21, 31000 Osijek, Croatia
| | - Aleksandar Včev
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Crkvena 21, 31000 Osijek, Croatia
| | - Tomislav Meštrović
- University Centre Varaždin, University North, 42000 Varaždin, Croatia
- Institute for Health Metrics and Evaluation and the Department of Health Metrics Sciences, University of Washington, Seattle, WA 98195, USA
- Correspondence: (T.M.); (I.Š.)
| | - Emina Pustijanac
- Faculty of Natural Sciences, Juraj Dobrila University of Pula, 52100 Pula, Croatia
| | - Melita Jukić
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Crkvena 21, 31000 Osijek, Croatia
- General Hospital Vukovar, Županijska 35, 32000 Vukovar, Croatia
| | - Ivana Škrlec
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Crkvena 21, 31000 Osijek, Croatia
- Correspondence: (T.M.); (I.Š.)
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Wortelboer K, Koopen AM, Herrema H, de Vos WM, Nieuwdorp M, Kemper EM. From fecal microbiota transplantation toward next-generation beneficial microbes: The case of Anaerobutyricum soehngenii. Front Med (Lausanne) 2022; 9:1077275. [PMID: 36544495 PMCID: PMC9760881 DOI: 10.3389/fmed.2022.1077275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
The commensal gut microbiota is important for human health and well-being whereas deviations of the gut microbiota have been associated with a multitude of diseases. Restoration of a balanced and diverse microbiota by fecal microbiota transplantation (FMT) has emerged as a potential treatment strategy and promising tool to study causality of the microbiota in disease pathogenesis. However, FMT comes with logistical challenges and potential safety risks, such as the transfer of pathogenic microorganisms, undesired phenotypes or an increased risk of developing disease later in life. Therefore, a more controlled, personalized mixture of cultured beneficial microbes might prove a better alternative. Most of these beneficial microbes will be endogenous commensals to the host without a long history of safe and beneficial use and are therefore commonly referred to as next-generation probiotics (NGP) or live biotherapeutic products (LBP). Following a previous FMT study within our group, the commensal butyrate producer Anaerobutyricum spp. (previously named Eubacterium hallii) was found to be associated with improved insulin-sensitivity in subjects with the metabolic syndrome. After the preclinical testing with Anaerobutyricum soehngenii in mice models was completed, the strain was produced under controlled conditions and several clinical studies evaluating its safety and efficacy in humans were performed. Here, we describe and reflect on the development of A. soehngenii for clinical use, providing practical guidance for the development and testing of NGPs and reflecting on the current regulatory framework.
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Affiliation(s)
- Koen Wortelboer
- Department of Experimental Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes and Metabolism, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, Metabolism and Nutrition, Amsterdam, Netherlands
- Department of Pharmacy, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Annefleur M. Koopen
- Amsterdam Cardiovascular Sciences, Diabetes and Metabolism, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, Metabolism and Nutrition, Amsterdam, Netherlands
- Department of Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Hilde Herrema
- Department of Experimental Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes and Metabolism, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, Metabolism and Nutrition, Amsterdam, Netherlands
| | - Willem M. de Vos
- Department of Experimental Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Max Nieuwdorp
- Department of Experimental Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes and Metabolism, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, Metabolism and Nutrition, Amsterdam, Netherlands
- Department of Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Diabetes Center, Department of Internal Medicine, Amsterdam UMC, Location VUMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - E. Marleen Kemper
- Department of Pharmacy, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, Netherlands
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Guo Y, Bei Q, Dzomeku BM, Martin K, Rasche F. Genetic diversity and community composition of arbuscular mycorrhizal fungi associated with root and rhizosphere soil of the pioneer plant Pueraria phaseoloides. IMETA 2022; 1:e51. [PMID: 38867903 PMCID: PMC10989906 DOI: 10.1002/imt2.51] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/22/2022] [Accepted: 08/10/2022] [Indexed: 06/14/2024]
Abstract
The pioneering plant Pueraria phaseoloides had a strong modulation effect on arbuscular mycorrhizal fungi (AMF) communities. Irrespective of geographical location, community composition of AMF in rhizosphere soil differed from that of the root. Co-occurrence network analysis revealed two AMF keystone species in rhizosphere soil (Acaulospora) and roots (Rhizophagus) of P. phaseoloides.
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Affiliation(s)
- Yaqin Guo
- Department of Agronomy in the Tropics and Subtropics, Institute of Agricultural Sciences in the Tropics (Hans‐Ruthenberg‐Institute)University of HohenheimStuttgartGermany
| | - Qicheng Bei
- Department of Soil EcologyHelmholtz Center for Environmental Research ‐ UFZLeipzigGermany
| | | | - Konrad Martin
- Department of Agronomy in the Tropics and Subtropics, Institute of Agricultural Sciences in the Tropics (Hans‐Ruthenberg‐Institute)University of HohenheimStuttgartGermany
| | - Frank Rasche
- Department of Agronomy in the Tropics and Subtropics, Institute of Agricultural Sciences in the Tropics (Hans‐Ruthenberg‐Institute)University of HohenheimStuttgartGermany
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Luo J, Gu S, Guo X, Liu Y, Tao Q, Zhao HP, Liang Y, Banerjee S, Li T. Core Microbiota in the Rhizosphere of Heavy Metal Accumulators and Its Contribution to Plant Performance. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:12975-12987. [PMID: 36067360 DOI: 10.1021/acs.est.1c08832] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Persistent microbial symbioses can confer greater fitness to their host under unfavorable conditions, but manipulating such beneficial interactions necessitates a mechanistic understanding of the consistently important microbiomes for the plant. Here, we examined the phylogenetic profiles and plant-beneficial traits of the core microbiota that consistently inhabits the rhizosphere of four divergent Cd hyperaccumulators and an accumulator. We evidenced the existence of a conserved core rhizosphere microbiota in each plant distinct from that in the non-hyperaccumulating plant. Members of Burkholderiaceae and Sphingomonas were the shared cores across hyperaccumulators and accumulators. Several keystone taxa in the rhizosphere networks were part of the core microbiota, the abundance of which was an important predictor of plant Cd accumulation. Furthermore, an inoculation experiment with synthetic communities comprising isolates belonging to the shared cores indicated that core microorganisms could facilitate plant growth and metal tolerance. Using RNA-based stable isotope probing, we discovered that abundant core taxa overlapped with active rhizobacteria utilizing root exudates, implying that the core rhizosphere microbiota assimilating plant-derived carbon may provide benefits to plant growth and host phenotype such as Cd accumulation. Our study suggests common principles underpinning hyperaccumulator-microbiome interactions, where plants consistently interact with a core set of microbes contributing to host fitness and plant performance. These findings lay the foundation for harnessing the persistent root microbiomes to accelerate the restoration of metal-disturbed soils.
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Affiliation(s)
- Jipeng Luo
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shaohua Gu
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, 100091 Beijing, China
| | - Xinyu Guo
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuankun Liu
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qi Tao
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - He-Ping Zhao
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Liang
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, North Dakota 58108-6050, United States
| | - Tingqiang Li
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
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Keystone taxa: an emerging area of microbiome research for future disease diagnosis and health safety in human. Microbiol Res 2022. [DOI: 10.1016/j.micres.2022.127203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Crisafi F, Smedile F, Yakimov MM, Aulenta F, Fazi S, La Cono V, Martinelli A, Di Lisio V, Denaro R. Bacterial biofilms on medical masks disposed in the marine environment: a hotspot of biological and functional diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155731. [PMID: 35533867 DOI: 10.1016/j.scitotenv.2022.155731] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/30/2022] [Accepted: 05/02/2022] [Indexed: 05/06/2023]
Abstract
The present paper was aimed at investigating the role of disposable medical masks as a substrate for microbial biofilm growth and for the selection of specific microbial traits in highly impacted marine environments. In this view, we have immerged masks in a coastal area affected by a continuous input of artisanal fishery wastes and hydrocarbons pollution caused by intense maritime traffic. Masks maintained one month in the field were colonized by a bacterial community significantly different from that detected in the natural matrices from the same areas (seawater and sediments). The masks served as a viable substrate for the growth and enrichment of phototrophic microorganisms (Oxyphotobacteria), as well as Ruminococcaceae, Gracilibacteria, and Holophageae. In a follow-up investigation, masks previously colonized in the field were transferred in lab-scale microcosms which were supplemented with hydrocarbons and which contained also a piece of a virgin mask. After one month, a shift in the community composition, likely triggered by hydrocarbons addition, was observed in the previously colonized mask, with signatures characteristic of hydrocarbon-degrading microbial groups. Such hydrocarbon-degrading bacteria were also found to colonize the virgin mask. Remarkably, SEM micrographs provided indications of the occurrence of morphological modifications of the surface components of the virgin masks colonized by hydrocarbonoclastic bacteria. Overall, for the first time, we have demonstrated the potential risk for human and animal health determined by the uncorrected disposal of masks which are suitable substrates for pathogens colonization, permanence and spreading. Moreover, we have herein strengthened the knowledge on the role of hydrocarbon-degrading bacteria in the colonization and modification of fossil-based plastics in marine environment.
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Affiliation(s)
- F Crisafi
- Institute of Polar Sciences, National Research Council (ISP-CNR), Spianata San Raineri, 86, 98121 Messina, Italy
| | - F Smedile
- Institute of Polar Sciences, National Research Council (ISP-CNR), Spianata San Raineri, 86, 98121 Messina, Italy
| | - M M Yakimov
- Institute of Polar Sciences, National Research Council (ISP-CNR), Spianata San Raineri, 86, 98121 Messina, Italy
| | - F Aulenta
- Water Research Institute, National Research Council (IRSA-CNR), Via Salaria km 29, 300, 00015 Monterotondo, Rome, Italy
| | - S Fazi
- Water Research Institute, National Research Council (IRSA-CNR), Via Salaria km 29, 300, 00015 Monterotondo, Rome, Italy
| | - V La Cono
- Institute of Polar Sciences, National Research Council (ISP-CNR), Spianata San Raineri, 86, 98121 Messina, Italy
| | - A Martinelli
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - V Di Lisio
- Donostia International Physics Center, Paseo Manuel de Lardizabal, 4, 20018 Donostia-San Sebastian, Spain
| | - R Denaro
- Water Research Institute, National Research Council (IRSA-CNR), Via Salaria km 29, 300, 00015 Monterotondo, Rome, Italy.
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Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties. THE ISME JOURNAL 2022; 16:2144-2159. [PMID: 35717467 PMCID: PMC9381525 DOI: 10.1038/s41396-022-01255-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 04/30/2022] [Accepted: 05/25/2022] [Indexed: 11/08/2022]
Abstract
AbstractMicrobe–microbe interactions in the human gut are influenced by host-derived glycans and diet. The high complexity of the gut microbiome poses a major challenge for unraveling the metabolic interactions and trophic roles of key microbes. Synthetic minimal microbiomes provide a pragmatic approach to investigate their ecology including metabolic interactions. Here, we rationally designed a synthetic microbiome termed Mucin and Diet based Minimal Microbiome (MDb-MM) by taking into account known physiological features of 16 key bacteria. We combined 16S rRNA gene-based composition analysis, metabolite measurements and metatranscriptomics to investigate community dynamics, stability, inter-species metabolic interactions and their trophic roles. The 16 species co-existed in the in vitro gut ecosystems containing a mixture of complex substrates representing dietary fibers and mucin. The triplicate MDb-MM’s followed the Taylor’s power law and exhibited strikingly similar ecological and metabolic patterns. The MDb-MM exhibited resistance and resilience to temporal perturbations as evidenced by the abundance and metabolic end products. Microbe-specific temporal dynamics in transcriptional niche overlap and trophic interaction network explained the observed co-existence in a competitive minimal microbiome. Overall, the present study provides crucial insights into the co-existence, metabolic niches and trophic roles of key intestinal microbes in a highly dynamic and competitive in vitro ecosystem.
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49
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Wu Q, Guo Z, Zhou Z, Jin M, Li Q, Zhou X. Recent advances in bioactive peptides from cereal-derived Foodstuffs. Int J Food Sci Nutr 2022; 73:875-888. [PMID: 35896503 DOI: 10.1080/09637486.2022.2104226] [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: 10/16/2022]
Abstract
Cereal-derived proteins account for a major part of human dietary protein consumption. Natural bioactive peptides (NBPs) from these proteins involve a variety of physiological activities and play an important role in the promotion of human health. This review focuses on the characteristics of NBPs obtained from cereals, and the commonly used methods for preparation, separation, purification, and identification. We also discussed the biological functions of cereal-derived NBPs (CNBPs), including the activities of antioxidant, immunomodulatory, antimicrobial, and regulation of hyperglycaemia and hypertension. The paper summarised the latest progress in the research and application of CNBPs and analysed the prospects for the development and application of several protein by-products, providing an important way to improve the added value of protein by-products in cereal processing.
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Affiliation(s)
- Qin Wu
- School of Agriculture and Biology, and Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhijian Guo
- School of Agriculture and Biology, and Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zerong Zhou
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, Wuhan, P. R. China
| | - Mengyuan Jin
- School of Agriculture and Biology, and Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Qizhang Li
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, School of Food and Biological Engineering, Hubei University of Technology, Wuhan, P. R. China
| | - Xuanwei Zhou
- School of Agriculture and Biology, and Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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50
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Gradisteanu Pircalabioru G, Liaw J, Gundogdu O, Corcionivoschi N, Ilie I, Oprea L, Musat M, Chifiriuc MC. Effects of the Lipid Profile, Type 2 Diabetes and Medication on the Metabolic Syndrome—Associated Gut Microbiome. Int J Mol Sci 2022; 23:ijms23147509. [PMID: 35886861 PMCID: PMC9318871 DOI: 10.3390/ijms23147509] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 02/08/2023] Open
Abstract
Metabolic syndrome (MetSyn) is a major health problem affecting approximately 25% of the worldwide population. Since the gut microbiota is highly connected to the host metabolism, several recent studies have emerged to characterize the role of the microbiome in MetSyn development and progression. To this end, our study aimed to identify the microbiome patterns which distinguish MetSyn from type 2 diabetes mellitus (T2DM). We performed 16S rRNA amplicon sequencing on a cohort of 70 individuals among which 40 were MetSyn patients. The microbiome of MetSyn patients was characterised by reduced diversity, loss of butyrate producers (Subdoligranulum, Butyricicoccus, Faecalibacterium prausnitzii) and enrichment in the relative abundance of fungal populations. We also show a link between the gut microbiome and lipid metabolism in MetSyn. Specifically, low-density lipoproteins (LDL) and high-density lipoproteins (HDL) display a positive effect on gut microbial diversity. When interrogating the signature of gut microbiota in a subgroup of patients harbouring both MetSyn and T2DM conditions, we observed a significant increase in taxa such as Bacteroides, Clostridiales, and Erysipelotrichaceae. This preliminary study shows for the first time that T2DM brings unique signatures of gut microbiota in MetSyn patients. We also highlight the impact of metformin treatment on the gut microbiota. Metformin administration was linked to changes in Prevotellaceae, Rickenellaceae, and Clostridiales. Further research focusing on the microbiome-metabolome patterns is needed to clarify the exact association of various gut microbial communities with the progression of T2DM and the occurrence of various complications in MetSyn patients.
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Affiliation(s)
| | - Janie Liaw
- Faculty of Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK;
| | - Ozan Gundogdu
- Faculty of Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK;
- Correspondence: (G.G.P.); (O.G.)
| | - Nicolae Corcionivoschi
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast BT9 5PX, UK;
- Faculty of Bioengineering of Animal Resources, Banat University of Agricultural Sciences and Veterinary Medicine—King Michael I of Romania, 300645 Timisoara, Romania
| | | | - Luciana Oprea
- National Institute of Endocrinology C.I. Parhon, 011863 Bucharest, Romania; (L.O.); (M.M.)
| | - Madalina Musat
- National Institute of Endocrinology C.I. Parhon, 011863 Bucharest, Romania; (L.O.); (M.M.)
- Department of Endocrinology, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Mariana-Carmen Chifiriuc
- Research Institute of University of Bucharest (ICUB), 300645 Bucharest, Romania;
- Romanian Academy, 010071 Bucharest, Romania
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