1
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Sprotte S, Brinks E, Neve H, Franz CM. Complete genome sequence of the novel virulent phage PMBT24 infecting Enterocloster bolteae from the human gut. Heliyon 2024; 10:e28813. [PMID: 38655313 PMCID: PMC11035940 DOI: 10.1016/j.heliyon.2024.e28813] [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: 10/10/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
PMBT24, the first reported virulent bacteriophage infecting the anaerobic human gut bacterium Enterocloster bolteae strain MBT-21, was isolated from a municipal sewage sample and its genome was sequenced and analysed. Transmission electron microscopy revealed a phage with an icosahedral head and a long, non-contractile tail. The circularly permutated, 99,962-bp dsDNA genome of the pac-type phage has a mol% G + C content of 32.1 and comprises 173 putative ORFs. Using amino acid sequence-based phylogeny, phage PMBT24 showed similarity to other, hitherto non-published phage genomes in the databases. Our data suggested phage PMBT24 to present the type phage of a novel genus (proposed name Kielvirus) and novel family of phages (proposed name Kielviridae).
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Affiliation(s)
- Sabrina Sprotte
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Str. 1, 24103, Kiel, Germany
| | - Erik Brinks
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Str. 1, 24103, Kiel, Germany
| | | | - Charles M.A.P. Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Str. 1, 24103, Kiel, Germany
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2
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Ma W, Wang Y, Nguyen LH, Mehta RS, Ha J, Bhosle A, Mclver LJ, Song M, Clish CB, Strate LL, Huttenhower C, Chan AT. Gut microbiome composition and metabolic activity in women with diverticulitis. Nat Commun 2024; 15:3612. [PMID: 38684664 PMCID: PMC11059386 DOI: 10.1038/s41467-024-47859-4] [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: 12/06/2023] [Accepted: 04/11/2024] [Indexed: 05/02/2024] Open
Abstract
The etiopathogenesis of diverticulitis, among the most common gastrointestinal diagnoses, remains largely unknown. By leveraging stool collected within a large prospective cohort, we performed shotgun metagenomic sequencing and untargeted metabolomics profiling among 121 women diagnosed with diverticulitis requiring antibiotics or hospitalizations (cases), matched to 121 women without diverticulitis (controls) according to age and race. Overall microbial community structure and metabolomic profiles differed in diverticulitis cases compared to controls, including enrichment of pro-inflammatory Ruminococcus gnavus, 1,7-dimethyluric acid, and histidine-related metabolites, and depletion of butyrate-producing bacteria and anti-inflammatory ceramides. Through integrated multi-omic analysis, we detected covarying microbial and metabolic features, such as Bilophila wadsworthia and bile acids, specific to diverticulitis. Additionally, we observed that microbial composition modulated the protective association between a prudent fiber-rich diet and diverticulitis. Our findings offer insights into the perturbations in inflammation-related microbial and metabolic signatures associated with diverticulitis, supporting the potential of microbial-based diagnostics and therapeutic targets.
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Affiliation(s)
- Wenjie Ma
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Yiqing Wang
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Long H Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raaj S Mehta
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jane Ha
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Amrisha Bhosle
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lauren J Mclver
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mingyang Song
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lisa L Strate
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA.
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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3
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Liu DS, Wang XS, Zhong XH, Cao H, Zhang F. Sexual dimorphism in the gut microbiota and sexual dimorphism in chronic diseases: Association or causation? J Steroid Biochem Mol Biol 2024; 237:106451. [PMID: 38154505 DOI: 10.1016/j.jsbmb.2023.106451] [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: 10/20/2022] [Revised: 03/31/2023] [Accepted: 12/24/2023] [Indexed: 12/30/2023]
Abstract
Understanding the sexual dimorphism in diseases is essential to investigate the pathogenesis of some chronic diseases (e.g., autoimmune diseases, etc). The gut microbiota has been found to show a notable impact on the pathology of several chronic diseases in recent years. Intriguingly, the composition of the gut microbiota varies between sexes. Here, we reviewed 'facts and fiction' regarding sexual dimorphism in chronic diseases and sexual dimorphism in the gut microbiota respectively. The association and causative relationship between them aiming to elucidate the pathological mechanisms of sexual dimorphism in chronic diseases were further explored. The development of gender-special food products based on the sexual dimorphism in the gut microbiota were recommended, which would be beneficial to facilitating the personalized treatment.
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Affiliation(s)
- Dong-Song Liu
- Affiliated Hospital of Jiangnan University, Wuxi, China; Nantong University, Nantong, China
| | - Xue-Song Wang
- Affiliated Hospital of Jiangnan University, Wuxi, China; Nantong University, Nantong, China; Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Xiao-Hui Zhong
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Hong Cao
- Affiliated Hospital of Jiangnan University, Wuxi, China; Nantong University, Nantong, China; Wuxi School of Medicine, Jiangnan University, Wuxi, China.
| | - Feng Zhang
- Affiliated Hospital of Jiangnan University, Wuxi, China; Wuxi School of Medicine, Jiangnan University, Wuxi, China.
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Cai J, Yuan X, Kong Y, Hu Y, Li J, Jiang S, Dong C, Ding K. Chemical approaches for the stereocontrolled synthesis of 1,2-cis-β-D-rhamnosides. Chin J Nat Med 2023; 21:886-901. [PMID: 38143103 DOI: 10.1016/s1875-5364(23)60408-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Indexed: 12/26/2023]
Abstract
In carbohydrate chemistry, the stereoselective synthesis of 1,2-cis-glycosides remains a formidable challenge. This complexity is comparable to the synthesis of 1,2-cis-β-D-mannosides, primarily due to the adverse anomeric and Δ-2 effects. Over the past decades, to attain β-stereoselectivity in D-rhamnosylation, researchers have devised numerous direct and indirect methodologies, including the hydrogen-bond-mediated aglycone delivery (HAD) method, the synthesis of β-D-mannoside paired with C6 deoxygenation, and the combined approach of 1,2-trans-glycosylation and C2 epimerization. This review elaborates on the advancements in β-D-rhamnosylation and its implications for the total synthesis of tiacumicin B and other physiologically relevant glycans.
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Affiliation(s)
- Juntao Cai
- Henan Polysaccharide Research Center, Henan Key Laboratory of Chinese Medicine for Polysaccharides and Drugs Research, Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, China.
| | - Xin Yuan
- Henan Polysaccharide Research Center, Henan Key Laboratory of Chinese Medicine for Polysaccharides and Drugs Research, Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Yuanfang Kong
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Yulong Hu
- Henan Polysaccharide Research Center, Henan Key Laboratory of Chinese Medicine for Polysaccharides and Drugs Research, Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Jieming Li
- Henan Polysaccharide Research Center, Henan Key Laboratory of Chinese Medicine for Polysaccharides and Drugs Research, Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Shiqing Jiang
- Henan Polysaccharide Research Center, Henan Key Laboratory of Chinese Medicine for Polysaccharides and Drugs Research, Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, China; Department of Oncology, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou 450000, China.
| | - Chunhong Dong
- Henan Polysaccharide Research Center, Henan Key Laboratory of Chinese Medicine for Polysaccharides and Drugs Research, Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, China.
| | - Kan Ding
- Henan Polysaccharide Research Center, Henan Key Laboratory of Chinese Medicine for Polysaccharides and Drugs Research, Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, China; Carbohydrate-Based Drug Research Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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5
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Dorst KM, Widmalm G. NMR chemical shift prediction and structural elucidation of linker-containing oligo- and polysaccharides using the computer program CASPER. Carbohydr Res 2023; 533:108937. [PMID: 37734222 DOI: 10.1016/j.carres.2023.108937] [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: 08/02/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/23/2023]
Abstract
Carbohydrate structures containing alkyl groups as aglycones are useful for investigating enzyme activity and glycan-protein interactions. Moreover, linker-containing oligosaccharides with a spacer group are commonly used to print glycan microarrays or to prepare protein-conjugates as vaccine candidates. The structural accuracy of these synthesized glycans are essential for interpretation of results from biological experiments in which the compounds have been used and NMR spectroscopy can unravel and confirm their structures. An approach for efficient 1H and 13C NMR chemical shift assignments employed a parallel NOAH-10 measurement followed by NMR spin-simulation to refine the 1H NMR chemical shifts, as exemplified for a disaccharide with an azidoethyl group as an aglycone, the NMR chemical shifts of which have been used to enhance the quality of CASPER (http://www.casper.organ.su.se/casper/). The CASPER program has been further developed to aid characterization of linker-containing oligo- and polysaccharides, either by chemical shift prediction for comparison to experimental NMR data or as structural investigation of synthesized glycans based on acquired unassigned NMR data. The ability of CASPER to elucidate structures of linker-containing oligosaccharides is demonstrated and comparisons to assigned or unassigned NMR data show the utility of CASPER in supporting a proposed oligosaccharide structure. Prediction of NMR chemical shifts of an oligosaccharide, corresponding to the repeating unit of an O-antigen polysaccharide, having a linker as an aglycone and a non-natural substituent derivative thereof are presented to exemplify the diversity of structures handled. Furthermore, NMR chemical shift predictions of synthesized polysaccharides, corresponding to bacterial polysaccharides, containing a linker are described showing that in addition to oligosaccharide structures also polysaccharide structures having an aglycone spacer group can be analyzed by CASPER.
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Affiliation(s)
- Kevin M Dorst
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden.
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Gao C, Shao D, Wang C, Kuang Y, Lu J, Zeng D, He J, Qiu X. Long-term effect of caesarean section on the gut microbial taxonomical profile and metabolic function of children at pre-school age. Clin Transl Med 2023; 13:e1470. [PMID: 37929652 PMCID: PMC10626499 DOI: 10.1002/ctm2.1470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/07/2023] Open
Affiliation(s)
- Chang Gao
- Division of Birth Cohort StudyGuangzhou Women and Children's Medical Center, Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Dan‐Tong Shao
- Division of Birth Cohort StudyGuangzhou Women and Children's Medical Center, Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Cheng‐Rui Wang
- Division of Birth Cohort StudyGuangzhou Women and Children's Medical Center, Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Ya‐Shu Kuang
- Division of Birth Cohort StudyGuangzhou Women and Children's Medical Center, Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Jin‐Hua Lu
- Division of Birth Cohort StudyGuangzhou Women and Children's Medical Center, Guangzhou Medical UniversityGuangzhouGuangdongChina
- Department of Women's HealthGuangdong Provincial Key Clinical Specialty of Women and Child Health, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouGuangdongChina
| | - Ding‐Yuan Zeng
- Liuzhou Maternity and Child Healthcare HospitalAffiliated Women and Children's Hospital of Guangxi University of Science and TechnologyLiuzhouChina
| | - Jian‐Rong He
- Division of Birth Cohort StudyGuangzhou Women and Children's Medical Center, Guangzhou Medical UniversityGuangzhouGuangdongChina
- Department of Women's HealthGuangdong Provincial Key Clinical Specialty of Women and Child Health, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouGuangdongChina
| | - Xiu Qiu
- Division of Birth Cohort StudyGuangzhou Women and Children's Medical Center, Guangzhou Medical UniversityGuangzhouGuangdongChina
- Department of Women's HealthGuangdong Provincial Key Clinical Specialty of Women and Child Health, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouGuangdongChina
- Guangdong Provincial Clinical Research Center for Child HealthGuangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouGuangdongChina
- Provincial Key Laboratory of Research in Structure Birth Defect Disease and Department of Pediatric SurgeryGuangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouGuangdongChina
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7
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Magdy Wasfy R, Mbaye B, Borentain P, Tidjani Alou M, Murillo Ruiz ML, Caputo A, Andrieu C, Armstrong N, Million M, Gerolami R. Ethanol-Producing Enterocloster bolteae Is Enriched in Chronic Hepatitis B-Associated Gut Dysbiosis: A Case-Control Culturomics Study. Microorganisms 2023; 11:2437. [PMID: 37894093 PMCID: PMC10608849 DOI: 10.3390/microorganisms11102437] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) infection is a global health epidemic that causes fatal complications, leading to liver cirrhosis and hepatocellular carcinoma. The link between HBV-related dysbiosis and specific bacterial taxa is still under investigation. Enterocloster is emerging as a new genus (formerly Clostridium), including Enterocloster bolteae, a gut pathogen previously associated with dysbiosis and human diseases such as autism, multiple sclerosis, and inflammatory bowel diseases. Its role in liver diseases, especially HBV infection, is not reported. METHODS The fecal samples of eight patients with chronic HBV infection and ten healthy individuals were analyzed using the high-throughput culturomics approach and compared to 16S rRNA sequencing. Quantification of ethanol, known for its damaging effect on the liver, produced from bacterial strains enriched in chronic HBV was carried out by gas chromatography-mass spectrometry. RESULTS Using culturomics, 29,120 isolated colonies were analyzed by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-TOF); 340 species were identified (240 species in chronic HBV samples, 254 species in control samples) belonging to 169 genera and 6 phyla. In the chronic HBV group, 65 species were already known in the literature; 48 were associated with humans but had not been previously found in the gut, and 17 had never been associated with humans previously. Six species were newly isolated in our study. By comparing bacterial species frequency, three bacterial genera were serendipitously found with significantly enriched bacterial diversity in patients with chronic HBV: Enterocloster, Clostridium, and Streptococcus (p = 0.0016, p = 0.041, p = 0.053, respectively). However, metagenomics could not identify this enrichment, possibly concerning its insufficient taxonomical resolution (equivocal assignment of operational taxonomic units). At the species level, the significantly enriched species in the chronic HBV group almost all belonged to class Clostridia, such as Clostridium perfringens, Clostridium sporogenes, Enterocloster aldenensis, Enterocloster bolteae, Enterocloster clostridioformis, and Clostridium innocuum. Two E. bolteae strains, isolated from two patients with chronic HBV infection, showed high ethanol production (27 and 200 mM). CONCLUSIONS Culturomics allowed us to identify Enterocloster species, specifically, E. bolteae, enriched in the gut microbiota of patients with chronic HBV. These species had never been isolated in chronic HBV infection before. Moreover, ethanol production by E. bolteae strains isolated from the chronic HBV group could contribute to liver disease progression. Additionally, culturomics might be critical for better elucidating the relationship between dysbiosis and chronic HBV infection in the future.
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Affiliation(s)
- Reham Magdy Wasfy
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- MEPHI, IRD, Aix-Marseille Université, 13005 Marseille, France
| | - Babacar Mbaye
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- MEPHI, IRD, Aix-Marseille Université, 13005 Marseille, France
| | - Patrick Borentain
- Unité Hépatologie, Hôpital de la Timone, APHM, 13005 Marseille, France;
- Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
| | - Maryam Tidjani Alou
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- MEPHI, IRD, Aix-Marseille Université, 13005 Marseille, France
| | - Maria Leticia Murillo Ruiz
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- MEPHI, IRD, Aix-Marseille Université, 13005 Marseille, France
| | - Aurelia Caputo
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
| | - Claudia Andrieu
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
| | - Nicholas Armstrong
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- MEPHI, IRD, Aix-Marseille Université, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
| | - Rene Gerolami
- IHU Méditerranée Infection, 13005 Marseille, France (M.T.A.); (C.A.)
- MEPHI, IRD, Aix-Marseille Université, 13005 Marseille, France
- Unité Hépatologie, Hôpital de la Timone, APHM, 13005 Marseille, France;
- Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
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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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Sharma A, Gupta S, Paul K. Codon usage behavior distinguishes pathogenic Clostridium species from the non-pathogenic species. Gene 2023; 873:147394. [PMID: 37137382 DOI: 10.1016/j.gene.2023.147394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 05/05/2023]
Abstract
Genus Clostridium is of the largest genus in class Clostridia. It is comprised of spore-forming, anaerobic, gram-positive organisms. The members of this genus include human pathogens to free-living nitrogen fixing bacteria. In the present study, we have performed a comparison of the choice of preferred codons, codon usage patterns, dinucleotide and amino acid usage pattern of 76 species of Genus Clostridium. We found the pathogenic clostridium species to have smaller AT-rich genomes as compared to opportunistic and non-pathogenic clostridium species. The choice of preferred and optimal codons was also influenced by genomic GC/AT content of the respective clostridium species. The pathogenic clostridium species displayed a strict bias in the codon usage, employing 35 of the 61 codons encoding for 20 amino acids. Comparison of amino acid usage revealed an increased usage of amino acids with lower biosynthetic cost by pathogenic clostridium species as compared to opportunistic and non-pathogenic clostridium species. Smaller genome, strict codon usage bias and amino acid usage lead to lower protein energetic cost for the clostridial pathogens. Overall, we found the pathogenic members of genus Clostridium to prefer small, AT-rich codons to reduce biosynthetic costs and match the cellular environment of its AT-rich human host.
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Affiliation(s)
- Anuj Sharma
- Department of Biochemistry, DAV University, Jalandhar, Punjab 144012, India
| | - Shelly Gupta
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Punjab 144411, India
| | - Karan Paul
- Department of Biochemistry, DAV University, Jalandhar, Punjab 144012, India.
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10
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Frame NW, Allas MJ, Pequegnat B, Vinogradov E, Liao VCH, Al-Abdul-Wahid S, Arroyo L, Allen-Vercoe E, Lowary TL, Monteiro MA. Structure and synthesis of a vaccine and diagnostic target for Enterocloster bolteae, an autism-associated gut pathogen – Part II. Carbohydr Res 2023; 526:108805. [PMID: 37023666 DOI: 10.1016/j.carres.2023.108805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 03/25/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023]
Abstract
Enterocloster bolteae (formerly known as Clostridium bolteae) is a gastro-intestinal pathogenic bacterium often detected in the fecal microbiome of children in the autism spectrum. E. bolteae excretes metabolites that are thought to act as neurotoxins. This study is an update of our first E. bolteae investigation that discovered an immunogenic polysaccharide. Through a combination of chemical derivatizations/degradations, spectrometry and spectroscopy techniques, a polysaccharide composed of disaccharide repeating blocks comprised of 3-linked β-d-ribofuranose and 4-linked α-l-rhamnopyranose, [→3)-β-D-Ribf-(1 → 4)-α-L-Rhap-(1→]n, was identified. To confirm the structure, and to provide material for subsequent investigations, the chemical synthesis of a corresponding linker-equipped tetrasaccharide, β-D-Ribf-(1 → 4)-α-L-Rhap-(1 → 3)-β-D-Ribf-(1 → 4)-α-L-Rhap-(1→O(CH2)8N3, is also described. Research tools based on this immunogenic glycan structure can form the foundation for serotype classification, diagnostic/vaccine targets and clinical studies into the hypothesized role of E. bolteae in the onset/augmentation of autism related conditions in children.
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Affiliation(s)
- Nolan W Frame
- Department of Chemistry, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Mikel Jason Allas
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada; Institute of Biological Chemistry, Academia Sinica, Nangang, Taipei, 11529, Taiwan
| | - Brittany Pequegnat
- Department of Chemistry, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | | | - Victor C-H Liao
- Institute of Biological Chemistry, Academia Sinica, Nangang, Taipei, 11529, Taiwan
| | | | - Luis Arroyo
- Department of Clinical Studies, University of Guelph, N1G 2W1, Guelph, ON, Canada
| | - Emma Allen-Vercoe
- Department of Microbiology, University of Guelph, N1G 2W1, Guelph, ON, Canada
| | - Todd L Lowary
- Institute of Biological Chemistry, Academia Sinica, Nangang, Taipei, 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, 106, Taiwan.
| | - Mario A Monteiro
- Department of Chemistry, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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11
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Athanasopoulou K, Adamopoulos PG, Scorilas A. Unveiling the Human Gastrointestinal Tract Microbiome: The Past, Present, and Future of Metagenomics. Biomedicines 2023; 11:biomedicines11030827. [PMID: 36979806 PMCID: PMC10045138 DOI: 10.3390/biomedicines11030827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/26/2023] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
Over 1014 symbiotic microorganisms are present in a healthy human body and are responsible for the synthesis of vital vitamins and amino acids, mediating cellular pathways and supporting immunity. However, the deregulation of microbial dynamics can provoke diverse human diseases such as diabetes, human cancers, cardiovascular diseases, and neurological disorders. The human gastrointestinal tract constitutes a hospitable environment in which a plethora of microbes, including diverse species of archaea, bacteria, fungi, and microeukaryotes as well as viruses, inhabit. In particular, the gut microbiome is the largest microbiome community in the human body and has drawn for decades the attention of scientists for its significance in medical microbiology. Revolutions in sequencing techniques, including 16S rRNA and ITS amplicon sequencing and whole genome sequencing, facilitate the detection of microbiomes and have opened new vistas in the study of human microbiota. Especially, the flourishing fields of metagenomics and metatranscriptomics aim to detect all genomes and transcriptomes that are retrieved from environmental and human samples. The present review highlights the complexity of the gastrointestinal tract microbiome and deciphers its implication not only in cellular homeostasis but also in human diseases. Finally, a thorough description of the widely used microbiome detection methods is discussed.
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Affiliation(s)
- Konstantina Athanasopoulou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
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12
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Guo C, Che X, Briese T, Ranjan A, Allicock O, Yates RA, Cheng A, March D, Hornig M, Komaroff AL, Levine S, Bateman L, Vernon SD, Klimas NG, Montoya JG, Peterson DL, Lipkin WI, Williams BL. Deficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS. Cell Host Microbe 2023; 31:288-304.e8. [PMID: 36758522 PMCID: PMC10183837 DOI: 10.1016/j.chom.2023.01.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/10/2022] [Accepted: 01/04/2023] [Indexed: 02/11/2023]
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is characterized by unexplained debilitating fatigue, cognitive dysfunction, gastrointestinal disturbances, and orthostatic intolerance. Here, we report a multi-omic analysis of a geographically diverse cohort of 106 cases and 91 healthy controls that revealed differences in gut microbiome diversity, abundances, functional pathways, and interactions. Faecalibacterium prausnitzii and Eubacterium rectale, which are both recognized as abundant, health-promoting butyrate producers in the human gut, were reduced in ME/CFS. Functional metagenomics, qPCR, and metabolomics of fecal short-chain fatty acids confirmed a deficient microbial capacity for butyrate synthesis. Microbiome-based machine learning classifier models were robust to geographic variation and generalizable in a validation cohort. The abundance of Faecalibacterium prausnitzii was inversely associated with fatigue severity. These findings demonstrate the functional nature of gut dysbiosis and the underlying microbial network disturbance in ME/CFS, providing possible targets for disease classification and therapeutic trials.
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Affiliation(s)
- Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Amit Ranjan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Orchid Allicock
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Rachel A Yates
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Aaron Cheng
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Dana March
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Mady Hornig
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Anthony L Komaroff
- Division of General Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Nancy G Klimas
- Institute for Neuro-Immune Medicine, College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33314, USA; Miami VA Medical Center, Miami, FL 33125, USA
| | - Jose G Montoya
- Palo Alto Medical Foundation, Jack S. Remington Laboratory for Specialty Diagnostics of Toxoplasmosis, Palo Alto, CA 94301, USA
| | - Daniel L Peterson
- Sierra Internal Medicine at Incline Village, Incline Village, NV 89451, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Brent L Williams
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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13
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Yang X, Li J, Zhou Y, Zhang N, Liu J. Effect of stigma maydis polysaccharide on the gut microbiota and transcriptome of VPA induced autism model rats. Front Microbiol 2022; 13:1009502. [PMID: 36406395 PMCID: PMC9672813 DOI: 10.3389/fmicb.2022.1009502] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/17/2022] [Indexed: 07/27/2023] Open
Abstract
Stigma maydis polysaccharide (SMPS) is a plant polysaccharide that participates in immune regulation and gastrointestinal motility. Autism spectrum disorder (ASD) refers to a group of neurodevelopmental disorders, and ASD patients often present intestinal microflora imbalance problems; however, there is no effective treatment method. This study explores the effect of SMPS intervention on the gut microbiota in autism model rats as well as the potential action pathways. Female Wistar rats were intraperitoneally injected with sodium valproic acid (VPA) or normal saline at embryonic day 12.5 to establish an autism model or normal control in their offspring. The offspring prenatally exposed to VPA were randomly assigned to the VPA and the SMPS groups. The SMPS group was administered SMPS from E0.5 to postnatal day (PND) 21. We performed 16S rRNA and transcriptomics analyses to reveal the gut microbiota (GM) and differentially expressed genes in the autism model rats in response to SMPS intervention. SMPS intervention significantly improved the diversity and structure of the GM in autism model rats compared with the VPA rats. Moreover, the relative abundance of Prevotellaceae and Lachnospiraceae_NK4A136_group was increased after SMPS intervention. Transcriptome sequencing showed that 496 differentially expressed genes (DEGs) were identified after SMPS administration compared with the VPA group. Meanwhile, gene ontology (GO) enrichment analysis of DEGs was showed that the SMPS group had significant 653 GO terms. SMPS intervention had a major influence on oxidative phosphorylation, retrograde endocannabinoid signaling, thermogenesis, ribosome, protein digestion and absorption, renin-angiotensin system, calcium signaling pathway, glycosphingolipid biosynthesis-ganglio series, and propanoate metabolism pathways. Overall, this study suggests that SMPS interventions in early life may have an impact on gut microbiota, and then affect the transcriptomics levels of the hippocampal tissue in the VPA-induced autism model rats. It provides scientific evidence for the role of the microbe-gut-brain axis in ASD research.
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Affiliation(s)
- Xiaolei Yang
- Department of Preventive Medicine, School of Public Health, Qiqihar Medical University, Qiqihar, China
| | - Jiyuan Li
- Department of Preventive Medicine, School of Public Health, Qiqihar Medical University, Qiqihar, China
| | - Yang Zhou
- Department of Anorectal Surgery, The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, China
| | - Ning Zhang
- College of Pathology, Qiqihar Medical University, Qiqihar, China
| | - Jicheng Liu
- Research Institute of Medical and Pharmacy, Qiqihar Medical University, Qiqihar, China
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14
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Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups. Sci Rep 2022; 12:17034. [PMID: 36220843 PMCID: PMC9554176 DOI: 10.1038/s41598-022-21327-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 09/26/2022] [Indexed: 12/29/2022] Open
Abstract
Observational studies have shown that the composition of the human gut microbiome in children diagnosed with Autism Spectrum Disorder (ASD) differs significantly from that of their neurotypical (NT) counterparts. Thus far, reported ASD-specific microbiome signatures have been inconsistent. To uncover reproducible signatures, we compiled 10 publicly available raw amplicon and metagenomic sequencing datasets alongside new data generated from an internal cohort (the largest ASD cohort to date), unified them with standardized pre-processing methods, and conducted a comprehensive meta-analysis of all taxa and variables detected across multiple studies. By screening metadata to test associations between the microbiome and 52 variables in multiple patient subsets and across multiple datasets, we determined that differentially abundant taxa in ASD versus NT children were dependent upon age, sex, and bowel function, thus marking these variables as potential confounders in case-control ASD studies. Several taxa, including the strains Bacteroides stercoris t__190463 and Clostridium M bolteae t__180407, and the species Granulicatella elegans and Massilioclostridium coli, exhibited differential abundance in ASD compared to NT children only after subjects with bowel dysfunction were removed. Adjusting for age, sex and bowel function resulted in adding or removing significantly differentially abundant taxa in ASD-diagnosed individuals, emphasizing the importance of collecting and controlling for these metadata. We have performed the largest (n = 690) and most comprehensive systematic analysis of ASD gut microbiome data to date. Our study demonstrated the importance of accounting for confounding variables when designing statistical comparative analyses of ASD- and NT-associated gut bacterial profiles. Mitigating these confounders identified robust microbial signatures across cohorts, signifying the importance of accounting for these factors in comparative analyses of ASD and NT-associated gut profiles. Such studies will advance the understanding of different patient groups to deliver appropriate therapeutics by identifying microbiome traits germane to the specific ASD phenotype.
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15
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Biazzo M, Allegra M, Deidda G. Clostridioides difficile and neurological disorders: New perspectives. Front Neurosci 2022; 16:946601. [PMID: 36203814 PMCID: PMC9530032 DOI: 10.3389/fnins.2022.946601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/24/2022] [Indexed: 12/02/2022] Open
Abstract
Despite brain physiological functions or pathological dysfunctions relying on the activity of neuronal/non-neuronal populations, over the last decades a plethora of evidence unraveled the essential contribution of the microbial populations living and residing within the gut, called gut microbiota. The gut microbiota plays a role in brain (dys)functions, and it will become a promising valuable therapeutic target for several brain pathologies. In the present mini-review, after a brief overview of the role of gut microbiota in normal brain physiology and pathology, we focus on the role of the bacterium Clostridioides difficile, a pathogen responsible for recurrent and refractory infections, in people with neurological diseases, summarizing recent correlative and causative evidence in the scientific literature and highlighting the potential of microbiota-based strategies targeting this pathogen to ameliorate not only gastrointestinal but also the neurological symptoms.
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Affiliation(s)
- Manuele Biazzo
- The BioArte Limited, Life Sciences Park, San Gwann, Malta
- SienabioACTIVE, University of Siena, Siena, Italy
| | - Manuela Allegra
- Neuroscience Institute, National Research Council (IN-CNR), Padua, Italy
| | - Gabriele Deidda
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- *Correspondence: Gabriele Deidda
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16
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Liu X, Lin Y, Peng W, Zhang Z, Gao L, Zhou Y, Song Z, Wang Y, Xu P, Yu B, Sun H, Xie W, Li W. Direct Synthesis of 2,6-Dideoxy-β-glycosides and β-Rhamnosides with a Stereodirecting 2-(Diphenylphosphinoyl)acetyl Group. Angew Chem Int Ed Engl 2022; 61:e202206128. [PMID: 35695834 DOI: 10.1002/anie.202206128] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 12/11/2022]
Abstract
Anomeric stereocontrol is usually one of the major issues in the synthesis of complex carbohydrates, particularly those involving β-configured 2,6-dideoxyglycoside and d/l-rhamnoside moieties. Herein, we report that 2-(diphenylphosphinoyl)acetyl is highly effective as a remote stereodirecting group in the direct synthesis of these challenging β-glycosides under mild conditions. A deoxy-trisaccharide as a mimic of the sugar chain of landomycin E was prepared stereospecifically in high yield. The synthetic potential was also highlighted in the synthesis of Citrobacter freundii O-antigens composed of a [→4)-α-d-Manp-(1→3)-β-d-Rhap(1→4)-β-d-Rhap-(1→] repeating unit, wherein the convergent assembly up to a nonasaccharide was realized with a strongly β-directing trisaccharide donor. Variable-temperature NMR studies indicate the presence of intermolecular H-bonding between the donor and the bulky acceptor as direct spectral evidence in support of the concept of hydrogen-bond-mediated aglycone delivery.
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Affiliation(s)
- Xianglai Liu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Yetong Lin
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Wenyi Peng
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Zhaolun Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Longwei Gao
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Yueer Zhou
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Zhe Song
- Instrumental Analysis Center, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, Jiangsu 210009, China
| | - Yingjie Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Peng Xu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Biao Yu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Haopeng Sun
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Weijia Xie
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Wei Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
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17
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Liu X, Lin Y, Peng W, Zhang Z, Gao L, Zhou Y, Song Z, Wang Y, Xu P, Yu B, Sun H, Xie W, Li W. Direct Synthesis of 2,6‐Dideoxy‐β‐glycosides and β‐Rhamnosides with a Stereodirecting 2‐(Diphenylphosphinoyl)acetyl Group. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Xianglai Liu
- China Pharmaceutical University School of Pharmacy Department of Medicinal Chemistry CHINA
| | - Yetong Lin
- China Pharmaceutical University School of Pharmacy Department of Medicinal Chemistry CHINA
| | - Wenyi Peng
- China Pharmaceutical University School of Pharmacy Department of Medicinal Chemistry CHINA
| | - Zhaolun Zhang
- Shanghai Institute of Organic Chemistry State Key Laboratory of Bioorganic and Natural Products Chemistry CHINA
| | - Longwei Gao
- China Pharmaceutical University School of Pharmacy Department of Medicinal Chemistry CHINA
| | - Yueer Zhou
- China Pharmaceutical University School of Pharmacy Department of Medicinal Chemistry CHINA
| | - Zhe Song
- China Pharmaceutical University Instrumental Analysis Center CHINA
| | - Yingjie Wang
- Shanghai Institute of Organic Chemistry State Key Laboratory of Bioorganic and Natural Products Chemistry CHINA
| | - Peng Xu
- Shanghai Institute of Organic Chemistry State Key Laboratory of Bioorganic and Natural Products Chemistry CHINA
| | - Biao Yu
- Shanghai Institute of Organic Chemistry State Key Laboratory of Bioorganic and Natural Products Chemistry CHINA
| | - Haopeng Sun
- China Pharmaceutical University School of Pharmacy Department of Medicinal Chemistry CHINA
| | - Weijia Xie
- China Pharmaceutical University School of Pharmacy Department of Medicinal Chemistry CHINA
| | - Wei Li
- China Pharmaceutical University School of Pharmacy Department of Medicinal Chemistry 639 Longmian Avenue 211198 Nanjing CHINA
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18
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Davidson J, Gauthier-Signore C, Bishop KP, Wicks C, Monteiro MA, Roy PN, Auzanneau FI. ROESY and 13C NMR to distinguish between D- and L-rhamnose in the α-D-Man p-(1 → 4)-β-Rha p-(1 → 3) repeating motif. Org Biomol Chem 2022; 20:2964-2980. [PMID: 35333269 DOI: 10.1039/d2ob00131d] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Many children suffering from autism spectrum disorder (ASD) experience gastrointestinal (GI) conditions. Enterocloster bolteae has been regularly detected in the stool of individuals suffering from GI symptoms and autism. Literature has suggested that E. bolteae strains WAL 16351 and WAL 14578 produce an immunogenic capsular polysaccharide (CPS) comprised of disaccharide repeating units: α-D-Man-(1 → 4)-β-Rha-(1 → 3) that could be used for the development of an immunotherapeutic vaccine. Ambiguity in the configuration of rhamnose led to the synthesis of tri- and disaccharide analogues containing D-rhamnose and L-rhamnose, respectively. ROESY-NMR spectra showed that CH3-6 of rhamnose and H-2 of mannose in the L-Rha containing disaccharide gave correlation. No such correlation was seen between the CH3-6 of rhamnose and the H-2 of mannose in the D-Rha containing trisaccharide. Molecular dynamics studies on hexasaccharide containing L-Rha or D-Rha confirmed that these structures adopt conformations resulting in different distances between the C6-rhamnose and the H-2 mannose of the preceding residue. We also demonstrate that assignment of the absolute configuration of the rhamnosyl residue in the β-Rhap-(1 → 3)-D-Man linkage can be determined using the 13C chemical shift of C-2 in of D-Mannose. While β-D-Rha will lead to an upfield shift of C-2 due to γ-gauche interaction between H-1 Rha and H-2 Man, β-L-Rha will not. Our results provide insights to distinguish between D- and L-rhamnose in the α-D-Manp-(1 → 4)-β-Rhap-(1 → 3) repeating motif.
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Affiliation(s)
- Jeffrey Davidson
- Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
| | | | - Kevin P Bishop
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Christopher Wicks
- Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
| | - Mario A Monteiro
- Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
| | - Pierre-Nicholas Roy
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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19
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Wang L, Wang Y, Zhang P, Song C, Pan F, Li G, Peng L, Yang Y, Wei Z, Huang F. Gut microbiota changes in patients with spondyloarthritis: A systematic review. Semin Arthritis Rheum 2021; 52:151925. [PMID: 34844732 DOI: 10.1016/j.semarthrit.2021.11.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/30/2021] [Accepted: 11/04/2021] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Gut microbiota has been proposed as a pivotal role in the progression of Spondyloarthritis (SpA), however diverse results remain to be synthesized. We performed a systematic review to collect evidence on the characteristic of the gut microbiota in patients with SpA, as compared to controls. METHODS We systematically searched MEDLINE, EMBASE, Cochrane Database of Systematic Reviews, and Cochrane Central Register of Controlled Trials databases, through June 1, 2021 for studies that compared gut microbiota of cases with SpA versus healthy controls. RESULTS Of 3756 records identified, 28 studies from 23 articles were included in the analysis. Results of β-diversity showed SpA patients hold a significantly different microbial composition compared with controls. Several taxa-level differences of gut microbiota between SpA (and its subtypes) cases and controls were identified. Fourteen studies including only patients with ankylosing spondylitis (AS) reported increased amounts of Actinobacteria, Dialister, Streptococcus, and Clostridium bolteae, and decreased amounts of Bacteroidales and Parasutterella in AS cases versus controls in ≥ 3 studies. Dialister invisus was increased in axial-SpA cases versus controls in 3 studies. Bacteroides fragilis was increased in enthesitis-related arthritis (ERA) cases versus controls in 2 studies. For all SpA studies, Proteobacteria, Enterobacteriaceae, and Bacteroidaceae were increased, whereas Bacteroidetes, Bacteroidales, and Akkermansia were decreased in cases versus controls in ≥ 3 studies. Over 40% of the studies showed comparable data of both sex and age between cases and controls. CONCLUSION The microbial characteristics of SpA summarized in the systematic review laid the groundwork for evidence-based microbial treatment. The microbial variance among subtypes of SpA remains to be explored. Further studies are needed to elucidate how the altered microbiota participate in the pathogenesis of SpA.
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Affiliation(s)
- Lei Wang
- Department of Rheumatology and Immunology, The First Medical Center, Chinese PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China
| | - Yiwen Wang
- Department of Rheumatology and Immunology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Pei Zhang
- School of Medicine, Nankai University, Tianjin, China
| | - Chuan Song
- Department of Rheumatology and Immunology, The First Medical Center, Chinese PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China
| | - Fei Pan
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Gang Li
- Health Service Department of the Guard Bureau of the Joint Staff Department, Beijing, China
| | - Lihua Peng
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yunsheng Yang
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Zhimin Wei
- Health Service Department of the Guard Bureau of the Joint Staff Department, Beijing, China.
| | - Feng Huang
- Department of Rheumatology and Immunology, The First Medical Center, Chinese PLA General Hospital, Beijing, China.
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20
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Li YQ, Sun YH, Liang YP, Zhou F, Yang J, Jin SL. Effect of probiotics combined with applied behavior analysis in the treatment of children with autism spectrum disorder: a prospective randomized controlled trial. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2021; 23:1103-1110. [PMID: 34753541 PMCID: PMC8580031 DOI: 10.7499/j.issn.1008-8830.2108085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVES To study the effect of probiotics combined with applied behavior analysis (ABA) in the treatment of children with autism spectrum disorder (ASD). METHODS A total of 41 children with ASD who attended the Affiliated Hospital of Jiangsu University from May 2019 to December 2020 were enrolled and randomly divided into an observation group with 21 children and a control group with 20 children. The children in the observation group were given oral probiotics combined with ABA intervention, while those in the control group were given ABA intervention alone. The treatment outcomes were compared between the two groups. Autism Treatment Evaluation Checklist (ATEC) was used to evaluate the severity of behavioral symptoms in both groups before intervention and at 3 months after intervention. The fecal samples were collected to analyze the difference in intestinal flora between the two groups based on 16s rRNA high-throughput sequencing. RESULTS Before intervention, there was no significant difference in the ATEC score between the observation and control groups (P>0.05). At 3 months after intervention, both groups had a significant reduction in the ATEC score, and the observation group had a significantly lower ATEC score than the control group (P<0.05). Before intervention, there was no significant difference in the composition of intestinal flora between the observation and control groups. At 3 months after intervention, there was a significant difference in the composition of intestinal flora between the observation and control groups. Compared with the control group, the observation group had significantly higher relative abundances of Bifidobacterium, Lactobacillus, Coprobacillus, Ruminococcus, Prevotella, and Blautia (P<0.05) and significantly lower relative abundances of Shigella and Clostridium (P<0.05). CONCLUSIONS Probiotics may improve the effect of conventional ABA intervention in children with ASD by regulating intestinal flora.
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Affiliation(s)
- Yu-Qin Li
- Department of Pediatrics, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China (yqli1314@163. com)
| | - Ying-Hong Sun
- Department of Pediatrics, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China (yqli1314@163. com)
| | | | - Fan Zhou
- Department of Pediatrics, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China (yqli1314@163. com)
| | - Jie Yang
- Department of Pediatrics, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China (yqli1314@163. com)
| | - Sheng-Li Jin
- Department of Pediatrics, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China (yqli1314@163. com)
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21
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Ding X, Zhou J, Chai Y, Yan Z, Liu X, Dong Y, Mei X, Jiang Y, Lei H. A metagenomic study of the gut microbiome in PTB'S disease. Microbes Infect 2021; 24:104893. [PMID: 34710620 DOI: 10.1016/j.micinf.2021.104893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/29/2021] [Accepted: 10/10/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND There is an abundant link between the gut microbiota and human health and it plays a critical role in the clinic. It is recognized that microbial dysregulation contributes to the pathogenesis of tuberculosis (TB), but the underlying mechanisms remain unclear. In this study, we investigated the association of gut microbiome composition with TB as well as its possible roles in the development of this disease. METHODS Fecal samples were collected from 10 TB patients and 20 healthy control samples. DNA extracted from fecal samples was subjected to 16S rDNA gene sequencing analysis on the Illumina MiSeq platform. RESULTS Compared with healthy control samples, the gut microbiome of patients with TB was characterized by the decreased Alpha diversity. Perhaps, the decrease of microbial diversity which results in microbial dysregulation is the reason for clinical patients with more symptoms. The PTB group showed the most unique microbiota by higher abundance of Bifidobacteriaceae, Bifidobacteriales, Coriobacteriaceae, Coriobacteriales, Actinobacteria, Caulobacteraceae, Phyllobacteriaceae, Rhizobiales, Burkholderiaceae, Burkholderiaceae. Inflammatory status in PTB patients may be associated with the increased abundance of Clostridia and decreased abundance of Prevotella. We found that the abundance of Solobacterium and Actinobacteria was higher in the patients. There were 4 significant differences (p<0.05) in the two groups which belonged to four metabolic categories, including endocytosis, phosphotransferase system (PTS), toluene degradation, and amoebiasis. CONCLUSION We applied the approach of metagenomic sequencing to characterize the features of gut microbiota in PTB patients. The present study provided a detailed analysis of the characterization of the gut microbiota in patients based on the clinic. According to the metagenome analysis, our results indicated that the gut microbiota in PTB patients was significantly different from healthy control samples as characterized by the bacteria and metabolic pathway. The richness of the gut microbiota in patients was revealed. It was hypothesized that the above-mentioned changes of the gut microbiota could exert an impact on the development of PTB through the downstream regulation of the immune status of the host by way of the gut-lung axis.
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Affiliation(s)
- Xiudong Ding
- 8th Medical Center of PLA General Hospital, China
| | | | - Yinghui Chai
- 8th Medical Center of PLA General Hospital, China
| | - Zengkui Yan
- 8th Medical Center of PLA General Hospital, China
| | - Xin Liu
- 8th Medical Center of PLA General Hospital, China
| | - Yueming Dong
- 8th Medical Center of PLA General Hospital, China
| | - Xue Mei
- 8th Medical Center of PLA General Hospital, China
| | - Ying Jiang
- 8th Medical Center of PLA General Hospital, China.
| | - Hong Lei
- 8th Medical Center of PLA General Hospital, China.
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22
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Deidda G, Biazzo M. Gut and Brain: Investigating Physiological and Pathological Interactions Between Microbiota and Brain to Gain New Therapeutic Avenues for Brain Diseases. Front Neurosci 2021; 15:753915. [PMID: 34712115 PMCID: PMC8545893 DOI: 10.3389/fnins.2021.753915] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/16/2021] [Indexed: 12/12/2022] Open
Abstract
Brain physiological functions or pathological dysfunctions do surely depend on the activity of both neuronal and non-neuronal populations. Nevertheless, over the last decades, compelling and fast accumulating evidence showed that the brain is not alone. Indeed, the so-called "gut brain," composed of the microbial populations living in the gut, forms a symbiotic superorganism weighing as the human brain and strongly communicating with the latter via the gut-brain axis. The gut brain does exert a control on brain (dys)functions and it will eventually become a promising valuable therapeutic target for a number of brain pathologies. In the present review, we will first describe the role of gut microbiota in normal brain physiology from neurodevelopment till adulthood, and thereafter we will discuss evidence from the literature showing how gut microbiota alterations are a signature in a number of brain pathologies ranging from neurodevelopmental to neurodegenerative disorders, and how pre/probiotic supplement interventions aimed to correct the altered dysbiosis in pathological conditions may represent a valuable future therapeutic strategy.
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Affiliation(s)
- Gabriele Deidda
- The BioArte Limited, Life Sciences Park, San Gwann, Malta
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Manuele Biazzo
- The BioArte Limited, Life Sciences Park, San Gwann, Malta
- SienabioACTIVE, University of Siena, Siena, Italy
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23
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Cai J, Hu J, Qin C, Li L, Shen D, Tian G, Zou X, Seeberger PH, Yin J. Chemical Synthesis Elucidates the Key Antigenic Epitope of the Autism‐Related Bacterium
Clostridium bolteae
Capsular Octadecasaccharide. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Juntao Cai
- Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministry of Education School of Biotechnology Jiangnan University Lihu Avenue 1800 Wuxi Jiangsu Province 214122 P. R. China
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany
| | - Jing Hu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministry of Education School of Biotechnology Jiangnan University Lihu Avenue 1800 Wuxi Jiangsu Province 214122 P. R. China
- Wuxi School of Medicine Jiangnan University Lihu Avenue 1800 Wuxi Jiangsu Province 214122 P. R. China
| | - Chunjun Qin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministry of Education School of Biotechnology Jiangnan University Lihu Avenue 1800 Wuxi Jiangsu Province 214122 P. R. China
| | - Lingxin Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministry of Education School of Biotechnology Jiangnan University Lihu Avenue 1800 Wuxi Jiangsu Province 214122 P. R. China
| | - Dacheng Shen
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany
| | - Guangzong Tian
- Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministry of Education School of Biotechnology Jiangnan University Lihu Avenue 1800 Wuxi Jiangsu Province 214122 P. R. China
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany
| | - Xiaopeng Zou
- Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministry of Education School of Biotechnology Jiangnan University Lihu Avenue 1800 Wuxi Jiangsu Province 214122 P. R. China
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany
| | - Peter H. Seeberger
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany
| | - Jian Yin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministry of Education School of Biotechnology Jiangnan University Lihu Avenue 1800 Wuxi Jiangsu Province 214122 P. R. China
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24
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Cai J, Hu J, Qin C, Li L, Shen D, Tian G, Zou X, Seeberger PH, Yin J. Chemical Synthesis Elucidates the Key Antigenic Epitope of the Autism-Related Bacterium Clostridium bolteae Capsular Octadecasaccharide. Angew Chem Int Ed Engl 2020; 59:20529-20537. [PMID: 32734715 DOI: 10.1002/anie.202007209] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/13/2020] [Indexed: 12/20/2022]
Abstract
The gut pathogen Clostridium bolteae has been associated with the onset of autism spectrum disorder (ASD). To create vaccines against C. bolteae, it is important to identify exact protective epitopes of the immunologically active capsular polysaccharide (CPS). Here, a series of C. bolteae CPS glycans, up to an octadecasaccharide, was prepared. Key to achieving the total syntheses is a [2+2] coupling strategy based on a β-d-Rhap-(1→3)-α-d-Manp repeating unit that in turn was accessed by a stereoselective β-d-rhamnosylation. The 4,6-O-benzylidene-induced conformational locking is a powerful strategy for forming a β-d-mannose-type glycoside. An indirect strategy based on C2 epimerization of β-d-quinovoside was efficiently achieved by Swern oxidation and borohydride reduction. Sequential glycosylation, and regioselective and global deprotection produced the disaccharide and tetrasaccharide, up to the octadecasaccharide. Glycan microarray analysis of sera from rabbits immunized with inactivated C. bolteae bacteria revealed a humoral immune response to the di- and tetrasaccharide, but none of the longer sequences. The tetrasaccharide may be a key motif for designing glycoconjugate vaccines against C. bolteae.
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Affiliation(s)
- Juntao Cai
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Avenue 1800, Wuxi, Jiangsu Province, 214122, P. R. China.,Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Jing Hu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Avenue 1800, Wuxi, Jiangsu Province, 214122, P. R. China.,Wuxi School of Medicine, Jiangnan University, Lihu Avenue 1800, Wuxi, Jiangsu Province, 214122, P. R. China
| | - Chunjun Qin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Avenue 1800, Wuxi, Jiangsu Province, 214122, P. R. China
| | - Lingxin Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Avenue 1800, Wuxi, Jiangsu Province, 214122, P. R. China
| | - Dacheng Shen
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Guangzong Tian
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Avenue 1800, Wuxi, Jiangsu Province, 214122, P. R. China.,Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Xiaopeng Zou
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Avenue 1800, Wuxi, Jiangsu Province, 214122, P. R. China.,Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Jian Yin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Avenue 1800, Wuxi, Jiangsu Province, 214122, P. R. China
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25
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Huang R, Li F, Zhou Y, Zeng Z, He X, Fang L, Pan F, Chen Y, Lin J, Li J, Qiu D, Tian Y, Tan X, Song Y, Xu Y, Lai Y, Yi H, Gao Q, Fang X, Shi M, Zhou C, Huang J, He YT. Metagenome-wide association study of the alterations in the intestinal microbiome composition of ankylosing spondylitis patients and the effect of traditional and herbal treatment. J Med Microbiol 2020; 69:797-805. [PMID: 31778109 PMCID: PMC7451032 DOI: 10.1099/jmm.0.001107] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 10/23/2019] [Indexed: 01/07/2023] Open
Abstract
Introduction. Ankylosing spondylitis (AS) is a systemic progressive disease with an unknown etiology that may be related to the gut microbiome. Therefore, a more thorough understanding of its pathogenesis is necessary for directing future therapy.Aim. We aimed to determine the differences in intestinal microbial composition between healthy individuals and patients with AS who received and who did not receive treatment interventions. In parallel, the pathology of AS in each patient was analysed to better understand the link between AS treatment and the intestinal microbiota of the patients.Methodology. Sixty-six faecal DNA samples, including 37 from healthy controls (HCs), 11 from patients with untreated AS (NM), 7 from patients treated with nonsteroidal anti-inflammatory drugs (e.g. celecoxib; WM) and 11 from patients treated with Chinese herbal medicine (CHM), such as the Bushen-Qiangdu-Zhilv decoction, were collected and used in the drug effect analysis. All samples were sequenced using Illumina HiSeq 4000 and the microbial composition was determined.Results. Four species were enriched in the patients with AS: Flavonifractor plautii, Oscillibacter, Parabacteroides distasonis and Bacteroides nordii (HC vs. NM, P<0.05); only F. plautii was found to be significantly changed in the NM-HC comparison. No additional species were found in the HC vs. CHM analysis, which indicated a beneficial effect of CHM in removing the other three strains. F. plautii was found to be significantly increased in the comparison between the HC and WM groups, along with four other species (Clostridium bolteae, Clostridiales bacterium 1_7_47FAA, C. asparagiforme and C. hathewayi). The patients with AS harboured more bacterial species associated with carbohydrate metabolism and glycan biosynthesis in their faeces. They also had bacterial profiles less able to biodegrade xenobiotics or synthesize and transport vitamins.Conclusion. The gut microbiota of the patients with AS varied from that of the HCs, and the treatment had an impact on this divergence. Our data provide insight that could guide improvements in AS treatment.
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Affiliation(s)
- RunYue Huang
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
| | - Fang Li
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
| | - Yingyan Zhou
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
- Postdoctoral Mobile Research Station, Guangzhou 510006, PR China
| | - Zhenhua Zeng
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
| | - Xiaohong He
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
| | - Lihua Fang
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
| | - Feng Pan
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
| | - Yile Chen
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
| | - Jiehua Lin
- Nephropathy Center, The Affiliated Jiangmen TCM Hospital, Jinan University, Jiangmen 529000, PR China
| | - Jie Li
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
| | - Dongni Qiu
- Department of Traditional Chinese Medicine, Guangdong Armed Police Corps Hospital, Guangzhou 510507, PR China
| | - Yinping Tian
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
| | - Xi Tan
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
| | - Yanni Song
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
| | - Yongyue Xu
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
| | - Yonghui Lai
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
| | - Hao Yi
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
| | - Qiang Gao
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
| | - Xiaodong Fang
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
| | - Mingming Shi
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
| | - Chu Zhou
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
| | - Jinqun Huang
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
| | - Yi-Ting He
- The Second Affiliated Hospital, Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510120 or 510006, PR China
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26
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Galkin F, Mamoshina P, Aliper A, Putin E, Moskalev V, Gladyshev VN, Zhavoronkov A. Human Gut Microbiome Aging Clock Based on Taxonomic Profiling and Deep Learning. iScience 2020; 23:101199. [PMID: 32534441 PMCID: PMC7298543 DOI: 10.1016/j.isci.2020.101199] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 04/14/2020] [Accepted: 05/21/2020] [Indexed: 12/14/2022] Open
Abstract
The human gut microbiome is a complex ecosystem that both affects and is affected by its host status. Previous metagenomic analyses of gut microflora revealed associations between specific microbes and host age. Nonetheless there was no reliable way to tell a host's age based on the gut community composition. Here we developed a method of predicting hosts' age based on microflora taxonomic profiles using a cross-study dataset and deep learning. Our best model has an architecture of a deep neural network that achieves the mean absolute error of 5.91 years when tested on external data. We further advance a procedure for inferring the role of particular microbes during human aging and defining them as potential aging biomarkers. The described intestinal clock represents a unique quantitative model of gut microflora aging and provides a starting point for building host aging and gut community succession into a single narrative. DNNs are the most appropriate model to predict host age from gut microflora profiles Our DNN models reach MAE of 5.9 years in independent verification Feature importance analysis gives a starting point for anti-aging intervention design
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Affiliation(s)
- Fedor Galkin
- Deep Longevity Inc, Hong Kong Science and Technology Park, Hong Kong; Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Polina Mamoshina
- Deep Longevity Inc, Hong Kong Science and Technology Park, Hong Kong; Insilico Medicine Ltd, Hong Kong Science and Technology Park, Hong Kong
| | - Alex Aliper
- Insilico Medicine Ltd, Hong Kong Science and Technology Park, Hong Kong
| | - Evgeny Putin
- Insilico Medicine Ltd, Hong Kong Science and Technology Park, Hong Kong
| | - Vladimir Moskalev
- Insilico Medicine Ltd, Hong Kong Science and Technology Park, Hong Kong
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, MA, USA
| | - Alex Zhavoronkov
- Deep Longevity Inc, Hong Kong Science and Technology Park, Hong Kong; Insilico Medicine Ltd, Hong Kong Science and Technology Park, Hong Kong; Buck Institute for Research on Aging, Novato, CA, USA; Biogerontology Research Foundation, London, UK.
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27
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Ghosh TS, Das M, Jeffery IB, O'Toole PW. Adjusting for age improves identification of gut microbiome alterations in multiple diseases. eLife 2020; 9:50240. [PMID: 32159510 PMCID: PMC7065848 DOI: 10.7554/elife.50240] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 02/10/2020] [Indexed: 02/06/2023] Open
Abstract
Interaction between disease-microbiome associations and ageing has not been explored in detail. Here, using age/region-matched sub-sets, we analysed the gut microbiome differences across five major diseases in a multi-cohort dataset constituting more than 2500 individuals from 20 to 89 years old. We show that disease-microbiome associations display specific age-centric trends. Ageing-associated microbiome alterations towards a disease-like configuration occur in colorectal cancer patients, thereby masking disease signatures. We identified a microbiome disease response shared across multiple diseases in elderly subjects that is distinct from that in young/middle-aged individuals, but also a novel set of taxa consistently gained in disease across all age groups. A subset of these taxa was associated with increased frailty in subjects from the ELDERMET cohort. The relevant taxa differentially encode specific functions that are known to have disease associations.
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Affiliation(s)
- Tarini S Ghosh
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Mrinmoy Das
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Ian B Jeffery
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paul W O'Toole
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
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28
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Endo A, Hirano K, Ose R, Maeno S, Tochio T. Impact of kestose supplementation on the healthy adult microbiota in in vitro fecal batch cultures. Anaerobe 2020; 61:102076. [DOI: 10.1016/j.anaerobe.2019.102076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 01/06/2023]
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29
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Chen J, Wang Q, Wang A, Lin Z. Structural and Functional Characterization of the Gut Microbiota in Elderly Women With Migraine. Front Cell Infect Microbiol 2020; 9:470. [PMID: 32083024 PMCID: PMC7001586 DOI: 10.3389/fcimb.2019.00470] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 12/20/2019] [Indexed: 12/17/2022] Open
Abstract
Migraine is a very common, multifactorial, and recurrent central nervous system disorder that causes throbbing headache, photophobia, phonophobia, nausea, and disability. Migraine occurs more often in females, and its complex physiopathology is not yet fully understood. An increasing number of gastrointestinal disorders have been linked to the occurrence of migraine suggesting that gut microbiota might play a pivotal role in migraine through the gut–brain axis. In the present work, we performed a metagenome-wide association study (MWAS) to determine the relationship between gut microbiota and migraine by analyzing 108 shotgun-sequenced fecal samples obtained from elderly women who suffer from migraine and matched healthy controls. Notably, the alpha diversity was significantly decreased in the migraine group at species, genus, and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologous levels. Firmicutes, especially the “unfriendly” Clostridium spp., were significantly enriched in the migraine group. Conversely, the healthy controls held more beneficial microorganisms, such as Faecalibacterium prausnitzii, Bifidobacterium adolescentis, and Methanobrevibacter smithii. For functional modules, the migraine group was enriched in gut–brain modules (GBMs) including kynurenine degradation and γ-aminobutyric acid (GABA) synthesis. However, the healthy controls held higher gut metabolic modules (GMMs) including glycolysis, homoacetogenesis, and GBMs including quinolinic acid degradation and S-adenosyl methionine (SAM) synthesis. The differences in gut microbiota composition and function between the migraine and healthy groups provided new information as well as novel therapeutic targets and strategies for migraine treatment, which could help to improve the early diagnosis of the disease, as well as the long-term prognosis and the life quality of patients suffering from migraine.
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Affiliation(s)
- Juanjuan Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.,BGI-Shenzhen, Shenzhen, China
| | - Qi Wang
- BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | | | - Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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30
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Mathee K, Cickovski T, Deoraj A, Stollstorff M, Narasimhan G. The gut microbiome and neuropsychiatric disorders: implications for attention deficit hyperactivity disorder (ADHD). J Med Microbiol 2020; 69:14-24. [PMID: 31821133 PMCID: PMC7440676 DOI: 10.1099/jmm.0.001112] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/01/2019] [Indexed: 12/11/2022] Open
Abstract
Neuropsychiatric disorders (NPDs) such as depression, anxiety, bipolar disorder, autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD) all relate to behavioural, cognitive and emotional disturbances that are ultimately rooted in disordered brain function. More specifically, these disorders are linked to various neuromodulators (i.e. serotonin and dopamine), as well as dysfunction in both cognitive and socio-affective brain networks. Increasing evidence suggests that the gut environment, and particularly the microbiome, plays a significant role in individual mental health. Although the presence of a gut-brain communication axis has long been established, recent studies argue that the development and regulation of this axis is dictated by the gut microbiome. Many studies involving both animals and humans have connected the gut microbiome with depression, anxiety and ASD. Microbiome-centred treatments for individuals with these same NPDs have yielded promising results. Despite its recent rise and underlying similarities to other NPDs, both biochemically and symptomatically, connections between the gut microbiome and ADHD currently lag behind those for other NPDs. We demonstrate that all evidence points to the importance of, and dire need for, a comprehensive and in-depth analysis of the role of the gut microbiome in ADHD, to deepen our understanding of a condition that affects millions of individuals worldwide.
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Affiliation(s)
- Kalai Mathee
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Florida, USA
| | - Trevor Cickovski
- Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Florida, USA
| | - Alok Deoraj
- Department of Environmental and Occupational Health, Robert Stempel College of Public Health and Social Work, Florida International University, Florida, USA
| | - Melanie Stollstorff
- Department of Psychology, College of Arts, Science and Education, Florida International University, Florida, USA
| | - Giri Narasimhan
- Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Florida, USA
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Pequegnat B, Monteiro MA. Carbohydrate Scaffolds for the Study of the Autism-associated Bacterium, Clostridium bolteae. Curr Med Chem 2019; 26:6341-6348. [PMID: 30799780 PMCID: PMC7040508 DOI: 10.2174/0929867326666190225164527] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 10/03/2018] [Accepted: 11/08/2018] [Indexed: 12/23/2022]
Abstract
A large number of children in the autism spectrum disorder suffer from gastrointestinal (GI) conditions, such as constipation and diarrhea. Clostridium bolteae is a part of a set of pathogens being regularly detected in the stool samples of hosts affected by GI and autism symptoms. Accompanying studies have pointed out the possibility that such microbes affect behaviour through the production of neurotoxic metabolites in a so-called, gut-brain connection. As an extension of our Clostridium difficile polysaccharide (PS)-based vaccine research, we engaged in the discovery of C. bolteae surface carbohydrates. So far, studies revealed that C. bolteae produces a specific immunogenic PS capsule comprised of disaccharide repeating blocks of mannose (Manp) and rhamnose (Rhap) units: α-D-Manp-(1→[-4)-β-D-Rhap- (1→3)-α-D-Manp-(1→]n. For vaccinology and further immunogenic experiments, a method to produce C. bolteae PS conjugates has been developed, along with the chemical syntheses of the PS non-reducing end linkage, with D-Rha or L-Rha, α-D-Manp-(1→4)-α-D-Rhap- (1→O(CH2)5NH2 and α-D-Manp-(1→4)-α-L-Rhap-(1→O(CH2)5NH2, equipped with an aminopentyl linker at the reducing end for conjugation purposes. The discovery of C. bolteae PS immunogen opens the door to the creation of non-evasive diagnostic tools to evaluate the frequency and role of this microbe in autistic subjects and to a vaccine to reduce colonization levels in the GI tract, thus impeding the concentration of neurotoxins.
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Affiliation(s)
| | - Mario A Monteiro
- Department of Chemistry, University of Guelph, Guelph, ON, Canada
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Duration of Persistent Atrial Fibrillation Is Associated with Alterations in Human Gut Microbiota and Metabolic Phenotypes. mSystems 2019; 4:4/6/e00422-19. [PMID: 31822598 PMCID: PMC6906738 DOI: 10.1128/msystems.00422-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Atrial fibrillation was associated with a disordered gut microbiota in previous research. However, the gut microbiota signature of patients at different stages of atrial fibrillation remains largely unknown. We sought to determine whether the shift in the gut microbiota and metabolic profiles occurs early and remains stable or develops gradually during atrial fibrillation. We found that patients with persistent atrial fibrillation of <12 months and persistent atrial fibrillation of >12 months shared most of the common features of gut microbiota dysbiosis. However, some distinctive and progressive alterations in the gut microbiota and metabolic structure, which may contribute to the progression of atrial fibrillation, were identified. The present study provides a comprehensive description of the dysbiotic gut microbiota and metabolic profiles in patients of short and long persistent atrial fibrillation, and our findings may help identify therapeutic strategies targeting the gut microbiota to treat atrial fibrillation at an early stage. Atrial fibrillation (AF) has been shown to be associated with disordered gut microbiota (GM). The underlying factors governing persistent AF (psAF) are not well understood, and the association between AF duration and GM profiles remains to be characterized. Thus, the present study aimed at investigating the dysbiosis of GM in patients with short and long psAF duration and illuminating the relationship between the GM and psAF maintenance. Based on metagenomic sequencing and metabolomic analyses, we assessed the metabolic and GM signature in 12 patients with psAF of <12 months (Pers<12m), eight patients with psAF of >12 months (Pers>12m), and 20 controls. We found that the GM in patients with both Pers<12m and Pers>12m was significantly perturbed, with an elevated microbial diversity, distinct structure, and discrepant composition. Although Pers<12m and Pers>12m patients shared a large number of common bacteria with controls, including 84 genera and 404 species, certain bacteria were differently enriched at different AF durations. Furthermore, disturbance in gut microbial function and GM-linked metabolic alterations were detected in both the Pers<12m and Pers>12m groups. The connection of GM and metabolites with psAF is consistent with interaction and potential modulation of host metabolic pathways due to GM dysbiosis with AF persistence. Our results showed that patients of the Pers<12m and Pers>12m groups shared many common disordered GM and metabolic features, which might occur in early disease, while prolonged psAF duration was related to certain unique alterations. Preventative strategies targeting GM and microbial metabolites for early intervention to treat AF patients are highly warranted. IMPORTANCE Atrial fibrillation was associated with a disordered gut microbiota in previous research. However, the gut microbiota signature of patients at different stages of atrial fibrillation remains largely unknown. We sought to determine whether the shift in the gut microbiota and metabolic profiles occurs early and remains stable or develops gradually during atrial fibrillation. We found that patients with persistent atrial fibrillation of <12 months and persistent atrial fibrillation of >12 months shared most of the common features of gut microbiota dysbiosis. However, some distinctive and progressive alterations in the gut microbiota and metabolic structure, which may contribute to the progression of atrial fibrillation, were identified. The present study provides a comprehensive description of the dysbiotic gut microbiota and metabolic profiles in patients of short and long persistent atrial fibrillation, and our findings may help identify therapeutic strategies targeting the gut microbiota to treat atrial fibrillation at an early stage.
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Hu Y, Feng Y, Wu J, Liu F, Zhang Z, Hao Y, Liang S, Li B, Li J, Lv N, Xu Y, Zhu B, Sun Z. The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients. Front Cell Infect Microbiol 2019; 9:90. [PMID: 31001490 PMCID: PMC6456665 DOI: 10.3389/fcimb.2019.00090] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/14/2019] [Indexed: 11/13/2022] Open
Abstract
Cross talk occurs between the human gut and the lung through a gut-lung axis involving the gut microbiota. However, the signatures of the human gut microbiota after active Mycobacterium tuberculosis infection have not been fully understood. Here, we investigated changes in the gut microbiota in tuberculosis (TB) patients by shotgun sequencing the gut microbiomes of 31 healthy controls and 46 patients. We observed a dramatic changes in gut microbiota in tuberculosis patients as reflected by significant decreases in species number and microbial diversity. The gut microbiota of TB patients were mostly featured by the striking decrease of short-chain fatty acids (SCFAs)-producingbacteria as well as associated metabolic pathways. A classification model based on the abundance of three species, Haemophilus parainfluenzae, Roseburia inulinivorans, and Roseburia hominis, performed well for discriminating between healthy and diseased patients. Additionally, the healthy and diseased states can be distinguished by SNPs in the species of B. vulgatus. We present a comprehensive profile of changes in the microbiota in clinical TB patients. Our findings will shed light on the design of future diagnoses and treatments for M. tuberculosis infections.
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Affiliation(s)
- Yongfei Hu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuqing Feng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiannan Wu
- Translational Medicine Research Center, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Fei Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhiguo Zhang
- Department of Laboratory Medicine, Tuberculosis Control Institute in Changping District, Beijing, China
| | - Yanan Hao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shihao Liang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Boxing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Na Lv
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuhui Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Zhaogang Sun
- Translational Medicine Research Center, Beijing Chest Hospital, Capital Medical University, Beijing, China
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Azhari A, Azizan F, Esposito G. A systematic review of gut-immune-brain mechanisms in Autism Spectrum Disorder. Dev Psychobiol 2018; 61:752-771. [PMID: 30523646 DOI: 10.1002/dev.21803] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/10/2018] [Accepted: 10/09/2018] [Indexed: 12/13/2022]
Abstract
Despite decades of research, the etiological origins of Autism Spectrum Disorder (ASD) remain elusive. Recently, the mechanisms of ASD have encompassed emerging theories involving the gastrointestinal, immune, and nervous systems. While each of these perspectives presents its own set of supporting evidence, the field requires an integration of these modular concepts and an overarching view of how these subsystems intersect. In this systematic review, we have synthesized relevant evidences from the existing literature, evaluating them in an interdependent manner and in doing so, outlining their possible connections. Specifically, we first discussed gastrointestinal and immuno-inflammation pathways in-depth, exploring the relationships between microbial composition, bacterial metabolites, gut mucosa, and immune system constituents. Accounting for temporal differences in the mechanisms involved in neurodevelopment, prenatal and postnatal phases were further elucidated, where the former focused on maternal immune activation (MIA) and fetal development, while the latter addressed the role of immune dysregulation in contributing to atypical neurodevelopment. As autism remains, foremost, a neurodevelopmental disorder, this review presents an integration of disparate modules into a "Gut-Immune-Brain" paradigm. Existing gaps in the literature have been highlighted, and possible avenues for future research with an integrated physiological perspective underlying ASD have also been suggested.
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Affiliation(s)
- Atiqah Azhari
- Psychology Program, School of Social Sciences, Nanyang Technological University, Singapore, Singapore
| | - Farouq Azizan
- Psychology Program, School of Social Sciences, Nanyang Technological University, Singapore, Singapore
| | - Gianluca Esposito
- Psychology Program, School of Social Sciences, Nanyang Technological University, Singapore, Singapore.,Department of Psychology and Cognitive Science, University of Trento, Rovereto, TN, Italy
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35
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Veiga M, Costa EM, Silva S, Pintado M. Impact of plant extracts upon human health: A review. Crit Rev Food Sci Nutr 2018; 60:873-886. [PMID: 30501504 DOI: 10.1080/10408398.2018.1540969] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
With the increase in evidences directly linking diet and health, several foodstuffs, such as phenolic rich fruits and vegetables, have emerged as possessing potential health benefits. Plants, given their fiber and phenolic content (and their intrinsic biological potential), have long been considered as contributing to health promotion. Therefore, the present work aimed to review the existing evidences regarding the various potential benefits of plant extracts' and plant extract-based products' consumption, with emphasis on in vivo works and epidemiological studies whenever available. Overall, the information available supports that, while there are indications of the potential benefits of plant extracts' consumption, further human-based studies are still needed to establish a true cause-effect.
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Affiliation(s)
- Mariana Veiga
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Porto, Portugal
| | - Eduardo M Costa
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Porto, Portugal
| | - Sara Silva
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Porto, Portugal
| | - Manuela Pintado
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Porto, Portugal
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36
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Sinha T, Vich Vila A, Garmaeva S, Jankipersadsing SA, Imhann F, Collij V, Bonder MJ, Jiang X, Gurry T, Alm EJ, D’Amato M, Weersma RK, Scherjon S, Wijmenga C, Fu J, Kurilshikov A, Zhernakova A. Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles. Gut Microbes 2018; 10:358-366. [PMID: 30373468 PMCID: PMC6546312 DOI: 10.1080/19490976.2018.1528822] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Several gastrointestinal diseases show a sex imbalance, although the underlying (patho)physiological mechanisms behind this are not well understood. The gut microbiome may be involved in this process, forming a complex interaction with host immune system, sex hormones, medication and other environmental factors. Here we performed sex-specific analyses of fecal microbiota composition in 1135 individuals from a population-based cohort. The overall gut microbiome composition of females and males was significantly different (p = 0.001), with females showing a greater microbial diversity (p = 0.009). After correcting for the effects of intrinsic factors, smoking, diet and medications, female hormonal factors such as the use of oral contraceptives and undergoing an ovariectomy were associated with microbial species and pathways. Females had a higher richness of antibiotic-resistance genes, with the most notable being resistance to the lincosamide nucleotidyltransferase (LNU) gene family. The higher abundance of resistance genes is consistent with the greater prescription of the Macrolide-Lincosamide-Streptogramin classes of antibiotics to females. Furthermore, we observed an increased resistance to aminoglycosides in females with self-reported irritable bowel syndrome. These results throw light upon the effects of common medications that are differentially prescribed between sexes and highlight the importance of sex-specific analysis when studying the gut microbiome and resistome.
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Affiliation(s)
- Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sanzhima Garmaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Soesma A. Jankipersadsing
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Floris Imhann
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Valerie Collij
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marc Jan Bonder
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Xiaofang Jiang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas Gurry
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eric J. Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mauro D’Amato
- Gastrointestinal Genetics Unit, Biodonostia Health Research Institute, San Sebastian, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sicco Scherjon
- Department of Obstetrics and Gynecology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,Department of Immunology, K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,CONTACT Alexandra Zhernakova, Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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Wang Q, Li F, Liang B, Liang Y, Chen S, Mo X, Ju Y, Zhao H, Jia H, Spector TD, Xie H, Guo R. A metagenome-wide association study of gut microbiota in asthma in UK adults. BMC Microbiol 2018; 18:114. [PMID: 30208875 PMCID: PMC6134768 DOI: 10.1186/s12866-018-1257-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 09/04/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Asthma, one of the most common chronic respiratory disorders, is associated with the hyper-activation of the T-cell subset of adaptive immunity. The gut microbiota may be involved in the development of asthma through the production of short-chain fatty acids (SCFAs), exhibiting modulatory effects on Th. So, we performed a metagenome-wide association study (MWAS) of the fecal microbiota from individuals with asthma and healthy controls. And that was the first case to resolve the relationship between asthma and microbiome among UK adults. RESULTS The microbiota of the individuals with asthma consisted of fewer microbial entities than the microbiota of healthy individuals. Faecalibacterium prausnitzii, Sutterella wadsworthensis and Bacteroides stercoris were depleted in cases, whereas Clostridiums with Eggerthella lenta were over-represented in individuals with asthma. Functional analysis shows that the SCFAs might be altered in the microbiota of asthma patients. CONCLUSION In all, the adult human gut microbiome of asthma patients is clearly different from healthy controls. The functional and taxa results showed that the change of asthma patients might related to SCFAs.
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Affiliation(s)
- Qi Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.,BGI-Shenzhen, Shenzhen, 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Fei Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.,BGI-Shenzhen, Shenzhen, 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Bishan Liang
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Yuhu Liang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.,BGI-Shenzhen, Shenzhen, 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sijie Chen
- BGI-Shenzhen, Shenzhen, 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Xiaodong Mo
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.,BGI-Shenzhen, Shenzhen, 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yanmei Ju
- BGI-Shenzhen, Shenzhen, 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hui Zhao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.,BGI-Shenzhen, Shenzhen, 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huijue Jia
- BGI-Shenzhen, Shenzhen, 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China.,Macau University of Science and Technology, Taipa, Macau, 999078, China.,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, 518083, China
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | | | - Ruijin Guo
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China. .,Macau University of Science and Technology, Taipa, Macau, 999078, China.
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38
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Ssepuuya G, Wynants E, Verreth C, Crauwels S, Lievens B, Claes J, Nakimbugwe D, Van Campenhout L. Microbial characterisation of the edible grasshopper Ruspolia differens in raw condition after wild-harvesting in Uganda. Food Microbiol 2018; 77:106-117. [PMID: 30297041 DOI: 10.1016/j.fm.2018.09.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 01/01/2023]
Abstract
This research aimed at establishing the chemical intrinsic properties and the microbial quality of an edible grasshopper Ruspolia differens and the effect of its source (geographical area) in Uganda, trading point, swarming season and plucking on these parameters. The intrinsic properties of the grasshopper can support the growth of a wide variety of microorganisms. High counts of total aerobic microbes, Enterobacteriaceae, lactic acid bacteria, total aerobic spores, and yeasts and moulds were obtained. Metagenetic analyses yielded 1793 Operational Taxonomic Units (OTUs) belonging to 24 phyla. Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria and Proteobacteria were the most abundant phyla, while members of the genera Acinetobacter, Buttiauxella, Lactococcus, Staphylococcus and Undibacterium were the most abundant OTUs. A number of genera harbouring potential pathogens (Acinetobacter, Bacillus, Buttiauxella, Campylobacter, Clostridium, Staphylococcus, Pseudomonas and Neisseria) were identified. The geographical area, trading point, swarming season and plucking significantly influenced microbial counts and bacterial diversity. The high microbial counts predispose R. differens to fast microbial spoilage, while the presence of Clostridium and Campylobacter makes this grasshopper a potential source of food borne diseases. Further research should identify the specific spoilage microorganisms of R. differens and assess the characteristics of this grasshopper that support growth of food pathogens.
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Affiliation(s)
- Geoffrey Ssepuuya
- KU Leuven, Department of Microbial and Molecular Systems (M2S), Lab4Food, Technology Campus Geel, Kleinhoefstraat 4, B-2440, Geel, Belgium; KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, Belgium; Makerere University, Department of Food Technology and Nutrition, CAES, P. O. Box, 7062, Kampala, Uganda
| | - Enya Wynants
- KU Leuven, Department of Microbial and Molecular Systems (M2S), Lab4Food, Technology Campus Geel, Kleinhoefstraat 4, B-2440, Geel, Belgium; KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, Belgium
| | - Christel Verreth
- KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, Belgium; KU Leuven, Department of Microbial and Molecular Systems (M2S), Laboratory for Process Microbial Ecology and Bioinspirational Management (PME & BIM), Campus De Nayer, B-2860, Sint-Katelijne-Waver, Belgium
| | - Sam Crauwels
- KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, Belgium; KU Leuven, Department of Microbial and Molecular Systems (M2S), Laboratory for Process Microbial Ecology and Bioinspirational Management (PME & BIM), Campus De Nayer, B-2860, Sint-Katelijne-Waver, Belgium
| | - Bart Lievens
- KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, Belgium; KU Leuven, Department of Microbial and Molecular Systems (M2S), Laboratory for Process Microbial Ecology and Bioinspirational Management (PME & BIM), Campus De Nayer, B-2860, Sint-Katelijne-Waver, Belgium
| | - Johan Claes
- KU Leuven, Department of Microbial and Molecular Systems (M2S), Lab4Food, Technology Campus Geel, Kleinhoefstraat 4, B-2440, Geel, Belgium; KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, Belgium
| | - Dorothy Nakimbugwe
- Makerere University, Department of Food Technology and Nutrition, CAES, P. O. Box, 7062, Kampala, Uganda
| | - Leen Van Campenhout
- KU Leuven, Department of Microbial and Molecular Systems (M2S), Lab4Food, Technology Campus Geel, Kleinhoefstraat 4, B-2440, Geel, Belgium; KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, Belgium.
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Stanley D, Moore RJ, Wong CHY. An insight into intestinal mucosal microbiota disruption after stroke. Sci Rep 2018; 8:568. [PMID: 29330443 PMCID: PMC5766598 DOI: 10.1038/s41598-017-18904-8] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/19/2017] [Indexed: 12/12/2022] Open
Abstract
Recent work from our laboratory has provided evidence that indicates selective bacterial translocation from the host gut microbiota to peripheral tissues (i.e. lung) plays a key role in the development of post-stroke infections. Despite this, it is currently unknown whether mucosal bacteria that live on and interact closely with the host intestinal epithelium contribute in regulating bacterial translocation after stroke. Here, we found that the microbial communities within the mucosa of gastrointestinal tract (GIT) were significantly different between sham-operated and post-stroke mice at 24 h following surgery. The differences in microbiota composition were substantial in all sections of the GIT and were significant, even at the phylum level. The main characteristics of the stroke-induced shift in mucosal microbiota composition were an increased abundance of Akkermansia muciniphila and an excessive abundance of clostridial species. Furthermore, we analysed the predicted functional potential of the altered mucosal microbiota induced by stroke using PICRUSt and revealed significant increases in functions associated with infectious diseases, membrane transport and xenobiotic degradation. Our findings revealed stroke induces far-reaching and robust changes to the intestinal mucosal microbiota. A better understanding of the precise molecular events leading up to stroke-induced mucosal microbiota changes may represent novel therapy targets to improve patient outcomes.
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Affiliation(s)
- Dragana Stanley
- School of Health Medical and Applied Sciences, Central Queensland University, Bruce Highway, Rockhampton, Queensland, 4702, Australia
| | - Robert J Moore
- School of Science, RMIT University, Bundoora, Victoria, 3083, Australia.,Infection and Immunity Program, Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia
| | - Connie H Y Wong
- Centre for Inflammatory Diseases, Department of Medicine, School of Clinical Sciences, Monash University, Clayton, Victoria, 3168, Australia.
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40
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Feng Y, Stams AJM, de Vos WM, Sánchez-Andrea I. Enrichment of sulfidogenic bacteria from the human intestinal tract. FEMS Microbiol Lett 2017; 364:2966324. [PMID: 28158432 DOI: 10.1093/femsle/fnx028] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 01/30/2017] [Indexed: 01/16/2023] Open
Abstract
Hydrogen sulfide is formed in the human intestinal tract as the end product of the anaerobic microbial degradation of sulfur compounds present in mucus, bile or proteins. Since human gut microbial sulfur metabolism has been poorly characterized, we aimed to identify and isolate the microorganisms involved in sulfide formation. Fresh fecal samples from one healthy donor and one diagnosed with irritable bowel syndrome were used as inocula for enrichments that were supplemented with sulfate or sulfite as electron acceptors in combination with different electron donors. After two transfers, cultures with high sulfide production were selected and the phylogenetic composition of the enriched microbial communities was determined. Sulfite respiration and cysteine degradation were the dominant sulfidogenic processes, and the most abundant bacteria enriched belonged to Bilophila and Clostridium cluster XIVa. Different isolates were obtained and remarkably included a novel sulfite reducer, designated strain 2C. Strain 2C belongs to the Veillonellaceae family of Firmicutes phylum and showed limited (91%) 16S rRNA gene sequence similarity with that of known Sporomusa species and hence may represent a novel genus. This study indicates that bacteria that utilize sulfite and organic sulfur compounds rather than merely sulfate are relevant for human intestinal sulfur metabolism.
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Affiliation(s)
- Yuan Feng
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,Department of Bacteriology and Immunology, Faculty of Medicine University of Helsinki, 00014 Helsinki, Finland
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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41
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Stadlbauer V, Horvath A, Ribitsch W, Schmerböck B, Schilcher G, Lemesch S, Stiegler P, Rosenkranz AR, Fickert P, Leber B. Structural and functional differences in gut microbiome composition in patients undergoing haemodialysis or peritoneal dialysis. Sci Rep 2017; 7:15601. [PMID: 29142271 PMCID: PMC5688134 DOI: 10.1038/s41598-017-15650-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/31/2017] [Indexed: 01/28/2023] Open
Abstract
Complications of end-stage renal disease (ESRD) are critically related to inflammation. The gut microbiome is a key driver of inflammation. Since dialysis modalities may differently influence the gut microbiome, we aimed to compare the effects of haemodialysis (HD) and peritoneal dialysis (PD) on patients' gut microbiome composition and function. We therefore studied faecal microbiome composition and function as well as inflammation and gut permeability in 30 patients with ESRD (15 HD, 15 PD) and compared to 21 healthy controls. We found an increase in potentially pathogenic species and a decrease in beneficial species in patients on HD and to a lesser extend in patients on PD when compared to controls. These changes in taxonomic composition also resulted in differences in predicted metagenome functions of the faecal microbiome. In HD but not in PD, changes in microbiome composition were associated with an increase in c-reactive protein (CRP) but not with intestinal inflammation or gut permeability. In conclusion microbiome composition in ESRD differs from healthy controls but also between modes of dialysis. These differences are associated with systemic inflammation and cannot completely be explained by dialysis vintage. The mode of renal replacement therapy seems to be an important driver of dysbiosis in ESRD.
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Affiliation(s)
- Vanessa Stadlbauer
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria.
| | - Angela Horvath
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- Division of Transplantation Surgery, Department of Surgery, Medical University of Graz, Graz, Austria
| | - Werner Ribitsch
- Clinical Division of Nephrology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Bianca Schmerböck
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- Division of Transplantation Surgery, Department of Surgery, Medical University of Graz, Graz, Austria
- Center of Biomarker Research in Medicine (CBmed), Graz, Austria
| | - Gernot Schilcher
- Clinical Division of Nephrology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- Intensive Care Unit, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Sandra Lemesch
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Philipp Stiegler
- Division of Transplantation Surgery, Department of Surgery, Medical University of Graz, Graz, Austria
| | - Alexander R Rosenkranz
- Clinical Division of Nephrology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Peter Fickert
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Bettina Leber
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- Division of Transplantation Surgery, Department of Surgery, Medical University of Graz, Graz, Austria
- Center of Biomarker Research in Medicine (CBmed), Graz, Austria
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42
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Kelly JR, Minuto C, Cryan JF, Clarke G, Dinan TG. Cross Talk: The Microbiota and Neurodevelopmental Disorders. Front Neurosci 2017; 11:490. [PMID: 28966571 PMCID: PMC5605633 DOI: 10.3389/fnins.2017.00490] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/17/2017] [Indexed: 12/11/2022] Open
Abstract
Humans evolved within a microbial ecosystem resulting in an interlinked physiology. The gut microbiota can signal to the brain via the immune system, the vagus nerve or other host-microbe interactions facilitated by gut hormones, regulation of tryptophan metabolism and microbial metabolites such as short chain fatty acids (SCFA), to influence brain development, function and behavior. Emerging evidence suggests that the gut microbiota may play a role in shaping cognitive networks encompassing emotional and social domains in neurodevelopmental disorders. Drawing upon pre-clinical and clinical evidence, we review the potential role of the gut microbiota in the origins and development of social and emotional domains related to Autism spectrum disorders (ASD) and schizophrenia. Small preliminary clinical studies have demonstrated gut microbiota alterations in both ASD and schizophrenia compared to healthy controls. However, we await the further development of mechanistic insights, together with large scale longitudinal clinical trials, that encompass a systems level dimensional approach, to investigate whether promising pre-clinical and initial clinical findings lead to clinical relevance.
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Affiliation(s)
- John R Kelly
- Department of Psychiatry and Neurobehavioural Science, University College CorkCork, Ireland.,APC Microbiome Institute, University College CorkCork, Ireland
| | - Chiara Minuto
- Department of Psychiatry and Neurobehavioural Science, University College CorkCork, Ireland.,APC Microbiome Institute, University College CorkCork, Ireland
| | - John F Cryan
- APC Microbiome Institute, University College CorkCork, Ireland.,Department of Anatomy and Neuroscience, University College CorkCork, Ireland
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioural Science, University College CorkCork, Ireland.,APC Microbiome Institute, University College CorkCork, Ireland
| | - Timothy G Dinan
- Department of Psychiatry and Neurobehavioural Science, University College CorkCork, Ireland.,APC Microbiome Institute, University College CorkCork, Ireland
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Abstract
梭菌(Clostridium)是肠道内一大类正常的兼性厌氧细菌, 属于厚壁菌门, 能产生芽孢. 目前已经报道的梭菌有十几种, 其中有一些主要用于疾病的预防、诊断或治疗, 还有部分被证实与人类某些疾病的发生、发展、预后转归息息相关, 比如抗生素相关性腹泻、伪膜性结肠炎等疾病. 其主要包括有益的梭菌和有害的梭菌两大类, 主要来源于肠道和粪便. 本文总结了目前已报道的肠道梭菌种类、有害梭菌的致病机制及与药物疗效相关作用机制、益生梭菌的主要产物及基因的应用、微生态制剂研制等方面研究进展, 为肠道梭菌在疾病预防和治疗方面的进一步研究提供思路与依据.
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Dehoux P, Marvaud JC, Abouelleil A, Earl AM, Lambert T, Dauga C. Comparative genomics of Clostridium bolteae and Clostridium clostridioforme reveals species-specific genomic properties and numerous putative antibiotic resistance determinants. BMC Genomics 2016; 17:819. [PMID: 27769168 PMCID: PMC5073890 DOI: 10.1186/s12864-016-3152-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 10/11/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Clostridium bolteae and Clostridium clostridioforme, previously included in the complex C. clostridioforme in the group Clostridium XIVa, remain difficult to distinguish by phenotypic methods. These bacteria, prevailing in the human intestinal microbiota, are opportunistic pathogens with various drug susceptibility patterns. In order to better characterize the two species and to obtain information on their antibiotic resistance genes, we analyzed the genomes of six strains of C. bolteae and six strains of C. clostridioforme, isolated from human infection. RESULTS The genome length of C. bolteae varied from 6159 to 6398 kb, and 5719 to 6059 CDSs were detected. The genomes of C. clostridioforme were smaller, between 5467 and 5927 kb, and contained 5231 to 5916 CDSs. The two species display different metabolic pathways. The genomes of C. bolteae contained lactose operons involving PTS system and complex regulation, which contribute to phenotypic differentiation from C. clostridioforme. The Acetyl-CoA pathway, similar to that of Faecalibacterium prausnitzii, a major butyrate producer in the human gut, was only found in C. clostridioforme. The two species have also developed diverse flagella mobility systems contributing to gut colonization. Their genomes harboured many CDSs involved in resistance to beta-lactams, glycopeptides, macrolides, chloramphenicol, lincosamides, rifampin, linezolid, bacitracin, aminoglycosides and tetracyclines. Overall antimicrobial resistance genes were similar within a species, but strain-specific resistance genes were found. We discovered a new group of genes coding for rifampin resistance in C. bolteae. C. bolteae 90B3 was resistant to phenicols and linezolide in producing a 23S rRNA methyltransferase. C. clostridioforme 90A8 contained the VanB-type Tn1549 operon conferring vancomycin resistance. We also detected numerous genes encoding proteins related to efflux pump systems. CONCLUSION Genomic comparison of C. bolteae and C. clostridiofrome revealed functional differences in butyrate pathways and in flagellar systems, which play a critical role within human microbiota. Most of the resistance genes detected in both species were previously characterized in other bacterial species. A few of them were related to antibiotics inactive against Clostridium spp. Some were part of mobile genetic elements suggesting that these commensals of the human microbiota act as reservoir of antimicrobial resistances.
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Affiliation(s)
- Pierre Dehoux
- Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Jean Christophe Marvaud
- Faculté de Pharmacie, EA4043 “Unité Bactéries Pathogènes et Santé” (UBaPS), Université Paris Sud, Châtenay-Malabry Cedex, 92296 France
| | - Amr Abouelleil
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Ashlee M. Earl
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thierry Lambert
- Faculté de Pharmacie, EA4043 “Unité Bactéries Pathogènes et Santé” (UBaPS), Université Paris Sud, Châtenay-Malabry Cedex, 92296 France
- Antibacterial Agents Unit, Department of Microbiology, Institut Pasteur, Paris, France
| | - Catherine Dauga
- Department of Genomes and Genetics, Institut Pasteur, Paris, France
- International Group of Data Analysis, Centre for Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France
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45
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Lucchese G. Understanding Neuropsychiatric Diseases, Analyzing the Peptide Sharing between Infectious Agents and the Language-Associated NMDA 2A Protein. Front Psychiatry 2016; 7:60. [PMID: 27148089 PMCID: PMC4827103 DOI: 10.3389/fpsyt.2016.00060] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 03/29/2016] [Indexed: 11/13/2022] Open
Abstract
Language disorders and infections may occur together and often concur, to a different extent and via different modalities, in characterizing brain pathologies, such as schizophrenia, autism, epilepsies, bipolar disorders, frontotemporal neurodegeneration, and encephalitis, inter alia. The biological mechanism(s) that might channel language dysfunctions and infections into etiological pathways connected to neuropathologic sequelae are unclear. Searching for molecular link(s) between language disorders and infections, the present study explores the language-associated NMDA 2A subunit for peptide sharing with pathogens that have been described in concomitance with neuropsychiatric diseases. It was found that a vast peptide commonality links the human glutamate ionotropic receptor NMDA 2A subunit to infectious agents. Such a link expands to and interfaces with neuropsychiatric disorders in light of the specific allocation of NMDA 2A gene expression in brain areas related to language functions. The data hint at a possible pathologic scenario based on anti-pathogen immune responses cross-reacting with NMDA 2A in the brain.
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Affiliation(s)
- Guglielmo Lucchese
- Brain and Language Laboratory, Freie Universität Berlin , Berlin , Germany
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46
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Babb JA, Deligiannidis KM, Murgatroyd CA, Nephew BC. Peripartum depression and anxiety as an integrative cross domain target for psychiatric preventative measures. Behav Brain Res 2015; 276:32-44. [PMID: 24709228 PMCID: PMC4185260 DOI: 10.1016/j.bbr.2014.03.039] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 03/21/2014] [Accepted: 03/24/2014] [Indexed: 11/20/2022]
Abstract
Exposure to high levels of early life stress has been identified as a potent risk factor for neurodevelopmental delays in infants, behavioral problems and autism in children, but also for several psychiatric illnesses in adulthood, such as depression, anxiety, autism, and posttraumatic stress disorder. Despite having robust adverse effects on both mother and infant, the pathophysiology of peripartum depression and anxiety are poorly understood. The objective of this review is to highlight the advantages of using an integrated approach addressing several behavioral domains in both animal and clinical studies of peripartum depression and anxiety. It is postulated that a greater focus on integrated cross domain studies will lead to advances in treatments and preventative measures for several disorders associated with peripartum depression and anxiety.
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Affiliation(s)
- Jessica A Babb
- Department of Biomedical Sciences, Tufts University Cummings School of Veterinary Medicine, North Grafton, MA 01536, USA.
| | - Kristina M Deligiannidis
- Departments of Psychiatry and Obstetrics & Gynecology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | | | - Benjamin C Nephew
- Department of Biomedical Sciences, Tufts University Cummings School of Veterinary Medicine, North Grafton, MA 01536, USA.
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47
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Samsam M, Ahangari R, Naser SA. Pathophysiology of autism spectrum disorders: Revisiting gastrointestinal involvement and immune imbalance. World J Gastroenterol 2014; 20:9942-9951. [PMID: 25110424 PMCID: PMC4123375 DOI: 10.3748/wjg.v20.i29.9942] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 05/22/2014] [Accepted: 06/13/2014] [Indexed: 02/06/2023] Open
Abstract
Autism spectrum disorders (ASD) comprise a group of neurodevelopmental abnormalities that begin in early childhood and are characterized by impairment of social communication and behavioral problems including restricted interests and repetitive behaviors. Several genes have been implicated in the pathogenesis of ASD, most of them are involved in neuronal synaptogenesis. A number of environmental factors and associated conditions such as gastrointestinal (GI) abnormalities and immune imbalance have been linked to the pathophysiology of ASD. According to the March 2012 report released by United States Centers for Disease Control and Prevention, the prevalence of ASD has sharply increased during the recent years and one out of 88 children suffers now from ASD symptoms. Although there is a strong genetic base for the disease, several associated factors could have a direct link to the pathogenesis of ASD or act as modifiers of the genes thus aggravating the initial problem. Many children suffering from ASD have GI problems such as abdominal pain, chronic diarrhea, constipation, vomiting, gastroesophageal reflux, and intestinal infections. A number of studies focusing on the intestinal mucosa, its permeability, abnormal gut development, leaky gut, and other GI problem raised many questions but studies were somehow inconclusive and an expert panel of American Academy of Pediatrics has strongly recommended further investigation in these areas. GI tract has a direct connection with the immune system and an imbalanced immune response is usually seen in ASD children. Maternal infection or autoimmune diseases have been suspected. Activation of the immune system during early development may have deleterious effect on various organs including the nervous system. In this review we revisited briefly the GI and immune system abnormalities and neuropeptide imbalance and their role in the pathophysiology of ASD and discussed some future research directions.
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48
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Asano K, Yoshimura S, Nakane A. Alteration of intestinal microbiota in mice orally administered with salmon cartilage proteoglycan, a prophylactic agent. PLoS One 2013; 8:e75008. [PMID: 24040376 PMCID: PMC3767651 DOI: 10.1371/journal.pone.0075008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 08/08/2013] [Indexed: 12/20/2022] Open
Abstract
Proteoglycan (PG) extracted from salmon nasal cartilage has potential to be a prophylactic agent. Daily oral administration of the PG attenuates systemic inflammatory response in the experimental mouse models. In this study, we applied the culture-independent approach to investigate an alteration of intestinal microbiota composition in PG-administered mice. The results indicated that the population level of bacilli increased in the small and large intestine upon PG administration. On the other hand, the population level of clostridia decreased in the large intestine. The proportion of bacteria that are able to ferment saccharides and produce short-chain fatty acids increased in the small intestine and decreased in the large intestine. Importantly, population level of probiotic lactobacilli and bacteria exhibiting the immunomodulatory effect increased in the PG-administered mice. In addition, several disease-associated bacteria decreased upon PG administration. These results provided an understanding of the specific role of PG involved in host immune modulation and supported our hypothesis that daily oral administration of PG improves the overall balance in composition of the intestinal microbial community.
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Affiliation(s)
- Krisana Asano
- Department of Microbiology and Immunology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori, Japan
| | - Sayuri Yoshimura
- Department of Microbiology and Immunology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori, Japan
| | - Akio Nakane
- Department of Microbiology and Immunology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori, Japan
- * E-mail:
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49
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Borody TJ, Peattie D, Campbell J. Therapeutic Potential of the Human Gastrointestinal Microbiome. Drug Dev Res 2013. [DOI: 10.1002/ddr.21093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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