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Mills EP, Liu CC, Mironovich MA, Taylor CM, Luo M, Emelogu U, Scott EM, Leis ML, Carter RT, Camacho-Luna P, Lewin AC. Relationship between the bacterial ocular surface microbiota and outcomes for cats with feline herpesvirus type 1 ocular surface disease. Vet Ophthalmol 2024; 27:318-329. [PMID: 37876296 DOI: 10.1111/vop.13157] [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: 07/03/2023] [Revised: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 10/26/2023]
Abstract
OBJECTIVE Feline herpesvirus 1 (FHV-1) causes ocular surface disease in domestic cats. The purpose of this study was to assess the relationship between bacterial ocular surface microbiota and outcomes for cats with FHV-1 ocular surface disease. ANIMALS STUDIED Twenty-two shelter-housed cats with confirmed FHV-1 ocular surface disease. PROCEDURES Animals were grouped according to FHV-1 shedding and ocular clinical scores following intervention: worsened outcome (WorOut, n = 11) or improved outcome (ImpOut, n = 11). Scoring and conjunctival sampling were completed on Days 1 and 8 of twice daily antiviral treatment. Bacterial DNA was extracted and submitted for 16S rRNA gene sequencing. Real-time polymerase chain reaction was performed for selected bacterial species. Overall DNA concentration between groups was assessed. RESULTS Bacterial microbiota relative abundance composition was significantly different between ImpOut and WorOut groups (weighted UniFrac p = .006). Alpha diversity was significantly higher in the ImpOut group compared with the WorOut group (Shannon p = .042, Simpson's p = .022, Pielou's p = .037). Differences in the relative abundance of various phyla and species were detected between groups. Total DNA concentration was higher in the WorOut group compared with the ImpOut group (p = .04). Feline GAPDH (p = .001) and Bilophila wadsworthia (p = .024) copy number was significantly higher in the ImpOut group compared with the WorOut group. CONCLUSIONS The results highlight the important relationship between the bacterial ocular surface microbiota and FHV-1 infection outcomes in cats treated with antiviral medications. Low bacterial species diversity, higher overall DNA (presumed predominantly bacterial) load, and certain bacterial phyla/species were associated with poor outcomes for cats with FHV-1 ocular disease.
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Affiliation(s)
- Erinn P Mills
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Chin-Chi Liu
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Melanie A Mironovich
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Christopher M Taylor
- Department of Microbiology, Immunology, and Parasitology, Health Sciences Center, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Meng Luo
- Department of Microbiology, Immunology, and Parasitology, Health Sciences Center, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Ugochi Emelogu
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Erin M Scott
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Marina L Leis
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Renee T Carter
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Pilar Camacho-Luna
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Andrew C Lewin
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
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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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Pimenta AI, Bernardino RM, Pereira IAC. Role of sulfidogenic members of the gut microbiota in human disease. Adv Microb Physiol 2024; 85:145-200. [PMID: 39059820 DOI: 10.1016/bs.ampbs.2024.04.003] [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: 07/28/2024]
Abstract
The human gut flora comprises a dynamic network of bacterial species that coexist in a finely tuned equilibrium. The interaction with intestinal bacteria profoundly influences the host's development, metabolism, immunity, and overall health. Furthermore, dysbiosis, a disruption of the gut microbiota, can induce a variety of diseases, not exclusively associated with the intestinal tract. The increased consumption of animal protein, high-fat and high-sugar diets in Western countries has been implicated in the rise of chronic and inflammatory illnesses associated with dysbiosis. In particular, this diet leads to the overgrowth of sulfide-producing bacteria, known as sulfidogenic bacteria, which has been linked to inflammatory bowel diseases and colorectal cancer, among other disorders. Sulfidogenic bacteria include sulfate-reducing bacteria (Desulfovibrio spp.) and Bilophila wadsworthia among others, which convert organic and inorganic sulfur compounds to sulfide through the dissimilatory sulfite reduction pathway. At high concentrations, sulfide is cytotoxic and disrupts the integrity of the intestinal epithelium and mucus barrier, triggering inflammation. Besides producing sulfide, B. wadsworthia has revealed significant pathogenic potential, demonstrated in the ability to cause infection, adhere to intestinal cells, promote inflammation, and compromise the integrity of the colonic mucus layer. This review delves into the mechanisms by which taurine and sulfide-driven gut dysbiosis contribute to the pathogenesis of sulfidogenic bacteria, and discusses the role of these gut microbes, particularly B. wadsworthia, in human diseases.
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Affiliation(s)
- Andreia I Pimenta
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Raquel M Bernardino
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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Kushkevych I, Martínková K, Mráková L, Giudici F, Baldi S, Novak D, Gajdács M, Vítězová M, Dordevic D, Amedei A, Rittmann SKMR. Comparison of microbial communities and the profile of sulfate-reducing bacteria in patients with ulcerative colitis and their association with bowel diseases: a pilot study. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:79-89. [PMID: 38486888 PMCID: PMC10939707 DOI: 10.15698/mic2024.03.817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 03/17/2024]
Abstract
Considerable evidence has accumulated regarding the molecular relationship between gut microbiota (GM) composition and the onset (clinical presentation and prognosis of ulcerative colitis (UC)). In addition, it is well documented that short-chain fatty acid (SCFA)-producing bacteria may play a fundamental role in maintaining an anti-inflammatory intestinal homeostasis, but sulfate- and sulfite reducing bacteria may be responsible for the production of toxic metabolites, such as hydrogen sulfide and acetate. Hence, the present study aimed to assess the GM composition - focusing on sulfate-reducing bacteria (SRB) - in patients with severe, severe-active and moderate UC. Each one of the six enrolled patients provided two stool samples in the following way: one sample was cultivated in a modified SRB-medium before 16S rRNA sequencing and the other was not cultivated. Comparative phylogenetic analysis was conducted on each sample. Percentage of detected gut microbial genera showed considerable variation based on the patients' disease severity and cultivation in the SRB medium. In detail, samples without cultivation from patients with moderate UC showed a high abundance of the genera Bacteroides, Bifidobacterium and Ruminococcus, but after SRB cultivation, the dominant genera were Bacteroides, Klebsiella and Bilophila. On the other hand, before SRB cultivation, the main represented genera in patients with severe UC were Escherichia-Shigella, Proteus, Methanothermobacter and Methanobacterium. However, after incubation in the SRB medium Bacteroides, Proteus, Alistipes and Lachnoclostridium were predominant. Information regarding GM compositional changes in UC patients may aid the development of novel therapeutic strategies (e.g., probiotic preparations containing specific bacterial strains) to counteract the mechanisms of virulence of harmful bacteria and the subsequent inflammatory response that is closely related to the pathogenesis of inflammatory bowel diseases.
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Affiliation(s)
- Ivan Kushkevych
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Kristýna Martínková
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Lenka Mráková
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Francesco Giudici
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Simone Baldi
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - David Novak
- Department of Biochemistry, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Márió Gajdács
- Department of Oral Biology and Experimental Dental Research, Faculty of Dentistry, University of Szeged, 6720 Szeged, Hungary
| | - Monika Vítězová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Dani Dordevic
- Department of Plant Origin Food Sciences, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 612 42 Brno, Czech Republic
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Simon K.-M. R. Rittmann
- Department of Functional and Evolutionary Ecology, Archaea Physiology & Biotechnology Group, Universität Wien, 1030 Wien, Austria
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Lares-Michel M, Housni FE, Reyes-Castillo Z, Huertas JR, Aguilera-Cervantes VG, Michel-Nava RM. Sustainable-psycho-nutritional intervention programme for a sustainable diet (the 'NutriSOS' study) and its effects on eating behaviour, diet quality, nutritional status, physical activity, metabolic biomarkers, gut microbiota and water and carbon footprints in Mexican population: study protocol of an mHealth randomised controlled trial. Br J Nutr 2023; 130:1823-1838. [PMID: 36991478 PMCID: PMC10587386 DOI: 10.1017/s0007114523000843] [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: 09/27/2022] [Revised: 02/06/2023] [Accepted: 03/22/2023] [Indexed: 03/31/2023]
Abstract
Mexico is going through an environmental and nutritional crisis related to unsustainable dietary behaviours. Sustainable diets could solve both problems together. This study protocol aims to develop a three-stage, 15-week mHealth randomised controlled trial of a sustainable-psycho-nutritional intervention programme to promote Mexican population adherence to a sustainable diet and to evaluate its effects on health and environmental outcomes. In stage 1, the programme will be designed using the sustainable diets, behaviour change wheel and capability, opportunity, motivation, and behaviour (COM-B) models. A sustainable food guide, recipes, meal plans and a mobile application will be developed. In stage 2, the intervention will be implemented for 7 weeks, and a 7-week follow-up period in a young Mexican adults (18-35 years) sample, randomly divided (1:1 ratio) into a control group (n 50) and an experimental group (n 50), will be divided into two arms at week 8. Outcomes will include health, nutrition, environment, behaviour and nutritional-sustainable knowledge. Additionally, socio-economics and culture will be considered. Thirteen behavioural objectives will be included using successive approaches in online workshops twice a week. The population will be monitored using the mobile application consisting of behavioural change techniques. In stage 3, the effects of the intervention will be assessed using mixed-effects models on dietary intake and quality, nutritional status, physical activity, metabolic biomarkers (serum glucose and lipid profile), gut microbiota composition and dietary water and carbon footprints of the evaluated population. Improvements in health outcomes and a decrease in dietary water and carbon footprints are expected.
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Affiliation(s)
- Mariana Lares-Michel
- Institute of Nutrition and Food Technology ‘José Mataix Verdú’, Biomedical Research Center, University of Granada, Avenida del Conocimiento S/N. Parque Tecnológico de la Salud. Armilla, 18071Granada, Spain
- Instituto de Investigaciones en Comportamiento Alimentario y Nutrición (IICAN), University Center of the South, University of Guadalajara, Av. Enrique Arreola Silva 883, Col. Centro, 49000, Cd. Guzmán, Jalisco, Mexico
| | - Fatima Ezzahra Housni
- Instituto de Investigaciones en Comportamiento Alimentario y Nutrición (IICAN), University Center of the South, University of Guadalajara, Av. Enrique Arreola Silva 883, Col. Centro, 49000, Cd. Guzmán, Jalisco, Mexico
| | - Zyanya Reyes-Castillo
- Instituto de Investigaciones en Comportamiento Alimentario y Nutrición (IICAN), University Center of the South, University of Guadalajara, Av. Enrique Arreola Silva 883, Col. Centro, 49000, Cd. Guzmán, Jalisco, Mexico
| | - Jesús R. Huertas
- Institute of Nutrition and Food Technology ‘José Mataix Verdú’, Biomedical Research Center, University of Granada, Avenida del Conocimiento S/N. Parque Tecnológico de la Salud. Armilla, 18071Granada, Spain
| | - Virginia Gabriela Aguilera-Cervantes
- Instituto de Investigaciones en Comportamiento Alimentario y Nutrición (IICAN), University Center of the South, University of Guadalajara, Av. Enrique Arreola Silva 883, Col. Centro, 49000, Cd. Guzmán, Jalisco, Mexico
| | - Rosa María Michel-Nava
- Tecnológico Nacional de México, Campus Ciudad Guzmán, Avenida Tecnológico 100, Col. Centro, 49000Ciudad Guzmán, Mexico
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Tabatabaei M, Dehvari A, Geramizadeh B, Niakan MH. Probable Role of Bilophila wadsworthia in Appendicle Infection. MEDICAL LABORATORY JOURNAL 2020. [DOI: 10.29252/mlj.14.1.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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7
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Feng Z, Long W, Hao B, Ding D, Ma X, Zhao L, Pang X. A human stool-derived Bilophila wadsworthia strain caused systemic inflammation in specific-pathogen-free mice. Gut Pathog 2017; 9:59. [PMID: 29090023 PMCID: PMC5657053 DOI: 10.1186/s13099-017-0208-7] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/17/2017] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Bilophila wadsworthia is a major member of sulfidogenic bacteria in human gut, it was originally recovered from different clinical specimens of intra-abdominal infections and recently was reported potentially linked to different chronic metabolic disorders. However, there is still insufficient understanding on its detailed function and mechanism to date. METHODS A B. wadsworthia strain was isolated from fresh feces of a latent autoimmune diabetes in adults patient and we investigated its pathogenicity by oral administration to specific-pathogen-free mice. Tissue samples and serum were collected after sacrifice. Stool samples were collected at different time points to profile the gut microbiota. RESULTS Bilophila wadsworthia infection resulted in the reduction of body weight and fat mass, apparent hepatosplenomegaly and elevated serum inflammatory factors, including serum amyloid A and interleukin-6, while without significant change of the overall gut microbiota structure. CONCLUSIONS These results demonstrated that higher amount of B. wadsworthia caused systemic inflammatory response in SPF mice, which adds new evidence to the pathogenicity of this bacterium and implied its potential role to the chronic inflammation related metabolic diseases like diabetes.
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Affiliation(s)
- Zhou Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Wenmin Long
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Binhan Hao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Ding Ding
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Xiaoqing Ma
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Liping Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Xiaoyan Pang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
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Ursodeoxycholic Acid and Its Taurine- or Glycine-Conjugated Species Reduce Colitogenic Dysbiosis and Equally Suppress Experimental Colitis in Mice. Appl Environ Microbiol 2017; 83:AEM.02766-16. [PMID: 28115375 DOI: 10.1128/aem.02766-16] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/10/2017] [Indexed: 02/06/2023] Open
Abstract
The promising results seen in studies of secondary bile acids in experimental colitis suggest that they may represent an attractive and safe class of drugs for the treatment of inflammatory bowel diseases (IBD). However, the exact mechanism by which bile acid therapy confers protection from colitogenesis is currently unknown. Since the gut microbiota plays a crucial role in the pathogenesis of IBD, and exogenous bile acid administration may affect the community structure of the microbiota, we examined the impact of the secondary bile acid ursodeoxycholic acid (UDCA) and its taurine or glycine conjugates on the fecal microbial community structure during experimental colitis. Daily oral administration of UDCA, tauroursodeoxycholic acid (TUDCA), or glycoursodeoxycholic acid (GUDCA) equally lowered the severity of dextran sodium sulfate-induced colitis in mice, as evidenced by reduced body weight loss, colonic shortening, and expression of inflammatory cytokines. Illumina sequencing demonstrated that bile acid therapy during colitis did not restore fecal bacterial richness and diversity. However, bile acid therapy normalized the colitis-associated increased ratio of Firmicutes to Bacteroidetes Interestingly, administration of bile acids prevented the loss of Clostridium cluster XIVa and increased the abundance of Akkermansia muciniphila, bacterial species known to be particularly decreased in IBD patients. We conclude that UDCA, which is an FDA-approved drug for cholestatic liver disorders, could be an attractive treatment option to reduce dysbiosis and ameliorate inflammation in human IBD.IMPORTANCE Secondary bile acids are emerging as attractive candidates for the treatment of inflammatory bowel disease. Although bile acids may affect the intestinal microbial community structure, which significantly contributes to the course of these inflammatory disorders, the impact of bile acid therapy on the fecal microbiota during colitis has not yet been considered. Here, we studied the alterations in the fecal microbial abundance in colitic mice following the administration of secondary bile acids. Our results show that secondary bile acids reduce the severity of colitis and ameliorate colitis-associated fecal dysbiosis at the phylum level. This study indicates that secondary bile acids might act as a safe and effective drug for inflammatory bowel disease.
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Kolmeder CA, Salojärvi J, Ritari J, de Been M, Raes J, Falony G, Vieira-Silva S, Kekkonen RA, Corthals GL, Palva A, Salonen A, de Vos WM. Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults. PLoS One 2016; 11:e0153294. [PMID: 27070903 PMCID: PMC4829149 DOI: 10.1371/journal.pone.0153294] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 03/28/2016] [Indexed: 12/31/2022] Open
Abstract
Recent metagenomic studies have demonstrated that the overall functional potential of the intestinal microbiome is rather conserved between healthy individuals. Here we assessed the biological processes undertaken in-vivo by microbes and the host in the intestinal tract by conducting a metaproteome analysis from a total of 48 faecal samples of 16 healthy adults participating in a placebo-controlled probiotic intervention trial. Half of the subjects received placebo and the other half consumed Lactobacillus rhamnosus GG for three weeks (1010 cfu per day). Faecal samples were collected just before and at the end of the consumption phase as well as after a three-week follow-up period, and were processed for microbial composition and metaproteome analysis. A common core of shared microbial protein functions could be identified in all subjects. Furthermore, we observed marked differences in expressed proteins between subjects that resulted in the definition of a stable and personalized microbiome both at the mass-spectrometry-based proteome level and the functional level based on the KEGG pathway analysis. No significant changes in the metaproteome were attributable to the probiotic intervention. A detailed taxonomic assignment of peptides and comparison to phylogenetic microarray data made it possible to evaluate the activity of the main phyla as well as key species, including Faecalibacterium prausnitzii. Several correlations were identified between human and bacterial proteins. Proteins of the human host accounted for approximately 14% of the identified metaproteome and displayed variations both between and within individuals. The individually different human intestinal proteomes point to personalized host-microbiota interactions. Our findings indicate that analysis of the intestinal metaproteome can complement gene-based analysis and contributes to a thorough understanding of the activities of the microbiome and the relevant pathways in health and disease.
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Affiliation(s)
- Carolin A. Kolmeder
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- * E-mail:
| | - Jarkko Salojärvi
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Jarmo Ritari
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Mark de Been
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jeroen Raes
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium
- VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Gwen Falony
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium
- VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Sara Vieira-Silva
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium
- VIB, Center for the Biology of Disease, Leuven, Belgium
| | | | - Garry L. Corthals
- Translational Proteomics, Turku Center for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Airi Palva
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Anne Salonen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Bacteriology and Immunology, Immunobiology Research Program, University of Helsinki, Helsinki, Finland
| | - Willem M. de Vos
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Bacteriology and Immunology, Immunobiology Research Program, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
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Taurine serves as sole source of nitrogen for aerobic and anaerobic growth by Klebsiella sp. World J Microbiol Biotechnol 2008. [DOI: 10.1007/s11274-007-9550-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Krejcík Z, Denger K, Weinitschke S, Hollemeyer K, Paces V, Cook AM, Smits THM. Sulfoacetate released during the assimilation of taurine-nitrogen by Neptuniibacter caesariensis: purification of sulfoacetaldehyde dehydrogenase. Arch Microbiol 2008; 190:159-68. [PMID: 18506422 DOI: 10.1007/s00203-008-0386-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Revised: 04/28/2008] [Accepted: 05/05/2008] [Indexed: 11/25/2022]
Abstract
Taurine (2-aminoethanesulfonate) is a widespread natural product whose nitrogen moiety was recently shown to be assimilated by bacteria, usually with excretion of an organosulfonate via undefined novel pathways; other data involve transcriptional regulator TauR in taurine metabolism. A screen of genome sequences for TauR with the BLAST algorithm allowed the hypothesis that the marine gammaproteobacterium Neptuniibacter caesariensis MED92 would inducibly assimilate taurine-nitrogen and excrete sulfoacetate. The pathway involved an ABC transporter (TauABC), taurine:pyruvate aminotransferase (Tpa), a novel sulfoacetaldehyde dehydrogenase (SafD) and exporter(s) of sulfoacetate (SafE) (DUF81). Ten candidate genes in two clusters involved three sets of paralogues (for TauR, Tpa and SafE). Inducible Tpa and SafD were detected in cell extracts. SafD was purified 600-fold to homogeneity in two steps. The monomer had a molecular mass of 50 kDa (SDS-PAGE); data from gel filtration chromatography indicated a tetrameric native protein. SafD was specific for sulfoacetaldehyde with a K (m)-value of 0.12 mM. The N-terminal amino acid sequence of SafD confirmed the identity of the safD gene. The eight pathway genes were transcribed inducibly, which indicated expression of the whole hypothetical pathway. We presume that this pathway is one source of sulfoacetate in nature, where this compound is dissimilated by many bacteria.
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Affiliation(s)
- Zdenĕk Krejcík
- Department of Biology, The University, 78457, Constance, Germany
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Hydrogen as an energy source for the human pathogen Bilophila wadsworthia. Antonie van Leeuwenhoek 2007; 93:381-90. [PMID: 18066702 DOI: 10.1007/s10482-007-9215-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Accepted: 11/29/2007] [Indexed: 02/08/2023]
Abstract
The gram-negative anaerobic gut bacterium Bilophila wadsworthia is the third most common isolate in perforated and gangrenous appendicitis, being also found in a variety of other infections. This organism performs a unique kind of anaerobic respiration in which taurine, a major organic solute in mammals, is used as a source of sulphite that serves as terminal acceptor for the electron transport chain. We show here that molecular hydrogen, one of the major products of fermentative bacteria in the colon, is an excellent growth substrate for B. wadsworthia. We have quantified the enzymatic activities associated with the oxidation of H(2), formate and pyruvate for cells obtained in different growth conditions. The cell extracts present high levels of hydrogenase activity, and up to five different hydrogenases can be expressed by this organism. One of the hydrogenases appears to be constitutive, whereas the others show differential expression in different growth conditions. Two of the hydrogenases are soluble and are recognised by antibodies against a [FeFe] hydrogenase of a sulphate reducing bacterium. One of these hydrogenases is specifically induced during fermentative growth on pyruvate. Another two hydrogenases are membrane-bound and show increased expression in cells grown with hydrogen. Further work should be carried out to reveal whether oxidation of hydrogen contributes to the virulence of B. wadsworthia.
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