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Chiang-Ni C, Huang JY, Hsu CY, Lo YC, Chen YYM, Lai CH, Chiu CH. Genetic diversity, biofilm formation, and Vancomycin resistance of clinical Clostridium innocuum isolates. BMC Microbiol 2024; 24:353. [PMID: 39294587 PMCID: PMC11409672 DOI: 10.1186/s12866-024-03503-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 09/05/2024] [Indexed: 09/20/2024] Open
Abstract
BACKGROUND Clostridium innocuum, previously considered a commensal microbe, is a spore-forming anaerobic bacterium. C. innocuum displays inherent resistance to vancomycin and is associated with extra-intestinal infections, antibiotic-associated diarrhea, and inflammatory bowel disease. This study seeks to establish a multilocus sequence typing (MLST) scheme to explore the correlation between C. innocuum genotyping and its potential pathogenic phenotypes. METHODS Fifty-two C. innocuum isolates from Linkou Chang Gung Memorial Hospital (CGMH) in Taiwan and 60 sequence-available C. innocuum isolates from the National Center for Biotechnolgy Information Genome Database were included. The concentrated sequence of housekeeping genes in C. innocuum was determined by amplicon sequencing and used for MLST and phylogenetic analyses. The biofilm production activity of the C. innocuum isolates was determined by crystal violet staining. RESULTS Of the 112 C. innocuum isolates, 58 sequence types were identified. Maximum likelihood estimation categorized 52 CGMH isolates into two phylogenetic clades. These isolates were found to be biofilm producers, with isolates in clade I exhibiting significantly higher biofilm production than isolates in clade II. The sub-inhibitory concentration of vancomycin seemed to minimally influence biofilm production by C. innocuum isolates. Nevertheless, C. innocuum embedded in the biofilm structure demonstrated resistance to vancomycin treatments at a concentration greater than 256 µg/mL. CONCLUSIONS This study suggests that a specific genetic clade of C. innocuum produces a substantial amount of biofilm. Furthermore, this phenotype assists C. innocuum in resisting high concentrations of vancomycin, which may potentially play undefined roles in C. innocuum pathogenesis.
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Affiliation(s)
- Chuan Chiang-Ni
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, No. 259 Wen-Hwa 1st Road, Kwei-Shan, Taoyuan, 333323, Taiwan.
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan.
| | - Jing-Yi Huang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Yun Hsu
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, No. 259 Wen-Hwa 1st Road, Kwei-Shan, Taoyuan, 333323, Taiwan
| | - Yi-Chi Lo
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Ywan M Chen
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, No. 259 Wen-Hwa 1st Road, Kwei-Shan, Taoyuan, 333323, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Chih-Ho Lai
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, No. 259 Wen-Hwa 1st Road, Kwei-Shan, Taoyuan, 333323, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
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Liu PY, Liaw J, Soutter F, Ortiz JJ, Tomley FM, Werling D, Gundogdu O, Blake DP, Xia D. Multi-omics analysis reveals regime shifts in the gastrointestinal ecosystem in chickens following anticoccidial vaccination and Eimeria tenella challenge. mSystems 2024:e0094724. [PMID: 39287379 DOI: 10.1128/msystems.00947-24] [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: 08/14/2024] [Accepted: 08/27/2024] [Indexed: 09/19/2024] Open
Abstract
Coccidiosis, caused by Eimeria parasites, significantly impacts poultry farm economics and animal welfare. Beyond its direct impact on health, Eimeria infection disrupts enteric microbial populations leading to dysbiosis and increases vulnerability to secondary diseases such as necrotic enteritis, caused by Clostridium perfringens. The impact of Eimeria infection or anticoccidial vaccination on host gastrointestinal phenotypes and enteric microbiota remains understudied. In this study, the metabolomic profiles and microbiota composition of chicken caecal tissue and contents were evaluated concurrently during a controlled experimental vaccination and challenge trial. Cobb500 broilers were vaccinated with a Saccharomyces cerevisiae-vectored anticoccidial vaccine and challenged with 15,000 Eimeria tenella oocysts. Assessment of caecal pathology and quantification of parasite load revealed correlations with alterations to caecal microbiota and caecal metabolome linked to infection and vaccination status. Infection heightened microbiota richness with increases in potentially pathogenic species, while vaccination elevated beneficial Bifidobacterium. Using a multi-omics factor analysis, data on caecal microbiota and metabolome were integrated and distinct profiles for healthy, infected, and recovering chickens were identified. Healthy and recovering chickens exhibited higher vitamin B metabolism linked to short-chain fatty acid-producing bacteria, whereas essential amino acid and cell membrane lipid metabolisms were prominent in infected and vaccinated chickens. Notably, vaccinated chickens showed distinct metabolites related to the enrichment of sphingolipids, important components of nerve cells and cell membranes. Our integrated multi-omics model revealed latent biomarkers indicative of vaccination and infection status, offering potential tools for diagnosing infection, monitoring vaccination efficacy, and guiding the development of novel treatments or controls.IMPORTANCEAdvances in anticoccidial vaccines have garnered significant attention in poultry health management. However, the intricacies of vaccine-induced alterations in the chicken gut microbiome and its subsequent impact on host metabolism remain inadequately explored. This study delves into the metabolic and microbiotic shifts in chickens post-vaccination, employing a multi-omics integration analysis. Our findings highlight a notable synergy between the microbiome composition and host-microbe interacted metabolic pathways in vaccinated chickens, differentiating them from infected or non-vaccinated cohorts. These insights pave the way for more targeted and efficient approaches in poultry disease control, enhancing both the efficacy of vaccines and the overall health of poultry populations.
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Affiliation(s)
- Po-Yu Liu
- Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
- School of Medicine, College of Medicine, National Sun Yat-sen University, Kaohsiung, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Janie Liaw
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - José Jaramillo Ortiz
- Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
- Centre for Vaccinology and Regenerative Medicine, Royal Veterinary College, London, United Kingdom
| | - Fiona M Tomley
- Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Dirk Werling
- Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
- Centre for Vaccinology and Regenerative Medicine, Royal Veterinary College, London, United Kingdom
| | - Ozan Gundogdu
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Damer P Blake
- Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
- Centre for Vaccinology and Regenerative Medicine, Royal Veterinary College, London, United Kingdom
| | - Dong Xia
- Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
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3
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Liu C, Liu X, Li X. Causal relationship between gut microbiota and hidradenitis suppurativa: a two-sample Mendelian randomization study. Front Microbiol 2024; 15:1302822. [PMID: 38348190 PMCID: PMC10860757 DOI: 10.3389/fmicb.2024.1302822] [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: 09/27/2023] [Accepted: 01/08/2024] [Indexed: 02/15/2024] Open
Abstract
Background Accumulating evidence suggests that alterations in gut microbiota composition are associated with the hidradenitis suppurativa (HS). However, the causal association between gut microbiota and HS remain undetermined. Methods We performed a bidirectional two-sample Mendelian randomization (MR) analysis using genome-wide association study summary data of gut microbiota and hidradenitis suppurativa from the MiBioGen consortium which concluded 18,340 individuals analyzed by the MiBioGen Consortium, comprising 211 gut microbiota. HS data were acquired from strictly defined HS data collected by FinnGenbiobank analysis, which included 211,548 European ancestors (409 HS patients, 211,139 controls). The inverse variance weighted method (IVW), weighted median (WME), simple model, weighted model, weighted median, and MR-Egger were used to determine the changes of HS pathogenic bacterial taxa, followed by sensitivity analysis including horizontal pleiotropy analysis. The MR Steiger test evaluated the strength of a causal association and the leave-one-out method assessed the reliability of the results. Additionally, a reverse MR analysis was carried out to seek for possible reverse causality. Results By combining the findings of all the MR steps, we identified four causal bacterial taxa, namely, Family XI, Porphyromonadaceae, Clostridium innocuum group and Lachnospira. The risk of HS might be positively associated with a high relative abundance of Clostridium innocuum group (Odds ratio, OR 2.17, p = 0.00038) and Lachnospira (OR 2.45, p = 0.017) but negatively associated with Family XI (OR 0.67, p = 0.049) and Porphyromonadaceae (OR 0.29, p = 0.014). There were no noticeable outliers, horizontal pleiotropy, or heterogeneity. Furthermore, there was no proof of reverse causation found in the reverse MR study. Conclusion This study indicates that Clostridium innocuum group and Lachnospira might have anti-protective effect on HS, whereas Family XI and Porphyromonadaceae might have a protective effect on HS. Our study reveals that there exists a beneficial or detrimental causal effect of gut microbiota composition on HS and offers potentially beneficial methods for therapy and avoidance of HS.
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Affiliation(s)
- Chengling Liu
- Center of Burns and Plastic Surgery and Dermatology, The 924th Hospital of Joint Logistics Support Force of the PLA, Guilin, China
| | - Xingchen Liu
- Department of Pathology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xin Li
- Center of Burns and Plastic Surgery and Dermatology, The 924th Hospital of Joint Logistics Support Force of the PLA, Guilin, China
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Wu HY, Kuo CJ, Chou CH, Ho MW, Chen CL, Hsu TS, Chen YC, Chiang-Ni C, Chen YYM, Chiu CH, Lai CH. Clostridium innocuum, an emerging pathogen that induces lipid raft-mediated cytotoxicity. Virulence 2023; 14:2265048. [PMID: 37798913 PMCID: PMC10561569 DOI: 10.1080/21505594.2023.2265048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 09/25/2023] [Indexed: 10/07/2023] Open
Abstract
Clostridium innocuum is an emerging spore-forming anaerobe that is often observed in Clostridioides difficile-associated inflammatory bowel disease (IBD) exacerbations. Unlike C. difficile, C. innocuum neither produces toxins nor possesses toxin-encoding genetic loci, but is commonly found in both intestinal and extra-intestinal infections. Membrane lipid rafts are composed of dynamic assemblies of cholesterol and sphingolipids, allowing bacteria to gain access to cells. However, the direct interaction between C. innocuum and lipid rafts that confers bacteria the ability to disrupt the intestinal barrier and induce pathogenesis remains unclear. In this study, we investigated the associations among nucleotide-binding oligomerization domain containing 2 (NOD2), lipid rafts, and cytotoxicity in C. innocuum-infected gut epithelial cells. Our results revealed that lipid rafts were involved in C. innocuum-induced NOD2 expression and nuclear factor (NF)-κB activation, triggering an inflammatory response. Reducing cholesterol by simvastatin significantly dampened C. innocuum-induced cell death, indicating that the C. innocuum-induced pathogenicity of cells was lipid raft-dependent. These results demonstrate that NOD2 mobilization into membrane rafts in response to C. innocuum-induced cytotoxicity results in aggravated pathogenicity.
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Affiliation(s)
- Hui-Yu Wu
- Department of Microbiology and Immunology, Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Jung Kuo
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Chia-Huei Chou
- Department of Infectious Disease, China Medical University Hospital, Taichung, Taiwan
- Department of Infectious Disease, Department of Microbiology and Immunology, School of Medicine, China Medical University, Taichung, Taiwan
| | - Mao-Wang Ho
- Department of Infectious Disease, China Medical University Hospital, Taichung, Taiwan
- Department of Infectious Disease, Department of Microbiology and Immunology, School of Medicine, China Medical University, Taichung, Taiwan
| | - Chyi-Liang Chen
- Department of Microbiology and Immunology, Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Department of Pediatrics, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Tsui-Shan Hsu
- Department of Microbiology and Immunology, Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Ying-Chu Chen
- Department of Microbiology and Immunology, Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Chuan Chiang-Ni
- Department of Microbiology and Immunology, Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Department of Pediatrics, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Yi-Ywan M. Chen
- Department of Microbiology and Immunology, Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Department of Pediatrics, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Department of Microbiology and Immunology, Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Chang Gung Microbiota Therapy Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Department of Pediatrics, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Chih-Ho Lai
- Department of Microbiology and Immunology, Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
- Department of Infectious Disease, Department of Microbiology and Immunology, School of Medicine, China Medical University, Taichung, Taiwan
- Molecular Infectious Disease Research Center, Department of Pediatrics, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
- Department of Nursing, Asia University, Taichung, Taiwan
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Cobo F, Pérez-Carrasco V, Tarriño-León M, Aguilera-Franco M, García-Salcedo JA, Navarro-Marí JM. Bacteremia due to Clostridium innocuum: Analysis of four cases and literature review. Anaerobe 2023; 83:102771. [PMID: 37562537 DOI: 10.1016/j.anaerobe.2023.102771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/01/2023] [Accepted: 08/05/2023] [Indexed: 08/12/2023]
Abstract
Clostridium innocuum is a Gram-positive anaerobic spore-forming bacillus that has been identified as part of the normal intestinal microbiota. This bacterium has been rarely associated with human infections, and only few severe infections have been reported until now. In this work, we report on four patients with bacteremia due to C. innocuum, which were well identified by MALDI-TOF MS. Moreover, a review of the previous published cases of bacteremia due to this anaerobic bacterium has been performed.
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Affiliation(s)
- Fernando Cobo
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain.
| | - Virginia Pérez-Carrasco
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
| | - María Tarriño-León
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
| | - María Aguilera-Franco
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
| | - José A García-Salcedo
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
| | - José María Navarro-Marí
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
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Li Z, Gu M, Sun H, Chen X, Zhou J, Zhang Y. The Potential of Gut Microbiota in Prediction of Stroke-Associated Pneumonia. Brain Sci 2023; 13:1217. [PMID: 37626573 PMCID: PMC10452830 DOI: 10.3390/brainsci13081217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/10/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Stroke-associated pneumonia (SAP) is a common stroke complication, and the changes in the gut microbiota composition may play a role. Our study aimed to evaluate the predictive ability of gut microbiota for SAP. METHODS Acute ischemic stroke patients were prospectively enrolled and divided into two groups based on the presence or absence of SAP. The composition of gut microbiota was characterized by the 16S RNA Miseq sequencing. The gut microbiota that differed significantly between groups were incorporated into the conventional risk scores, the Acute Ischemic Stroke-Associated Pneumonia Score (AIS-APS), and the Age, Atrial fibrillation, Dysphagia, Sex, Stroke Severity Score (A2DS2). The predictive performances were assessed in terms of the area under the curve (AUC), the Net Reclassification Improvement (NRI), and the Integrated Discrimination Improvement (IDI) indices. RESULTS A total of 135 patients were enrolled, of whom 43 had SAP (31%). The short-chain fatty acids (SCFAs)-producing bacteria, such as Bacteroides, Fusicatenibacter, and Butyricicoccus, were decreased in the SAP group. The integrated models showed better predictive ability for SAP (AUC = 0.813, NRI = 0.333, p = 0.052, IDI = 0.038, p = 0.018, for AIS-APS; AUC = 0.816, NRI = 0.575, p < 0.001, IDI = 0.043, p = 0.007, for A2DS2) in comparison to the differential genera (AUC = 0.699) and each predictive score (AUCAISAPS = 0.777; AUCA2DS2 = 0.777). CONCLUSIONS The lower abundance of SCFAs-producing gut microbiota after acute ischemic stroke was associated with SAP and may play a role in SAP prediction.
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Affiliation(s)
- Zhongyuan Li
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, Nanjing 210006, China; (Z.L.); (X.C.)
| | - Mengmeng Gu
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, Nanjing 210006, China; (Z.L.); (X.C.)
| | - Huanhuan Sun
- Department of Neurology, Nanjing Yuhua Hospital, Nanjing 210039, China
| | - Xiangliang Chen
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, Nanjing 210006, China; (Z.L.); (X.C.)
| | - Junshan Zhou
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, Nanjing 210006, China; (Z.L.); (X.C.)
| | - Yingdong Zhang
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, No. 68, Changle Road, Nanjing 210006, China; (Z.L.); (X.C.)
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Kim S, Li H, Jin Y, Armad J, Gu H, Mani S, Cui JY. Maternal PBDE exposure disrupts gut microbiome and promotes hepatic proinflammatory signaling in humanized PXR-transgenic mouse offspring over time. Toxicol Sci 2023; 194:209-225. [PMID: 37267213 PMCID: PMC10375318 DOI: 10.1093/toxsci/kfad056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
Abstract
Developmental exposure to the persistent environmental pollutant, polybrominated diphenyl ethers (PBDEs), is associated with increased diabetes prevalence. The microbial tryptophan metabolite, indole-3-propionic acid (IPA), is associated with reduced risk of type 2 diabetes and lower-grade inflammation and is a pregnane X receptor (PXR) activator. To explore the role of IPA in modifying the PBDE developmental toxicity, we orally exposed humanized PXR-transgenic (hPXR-TG) mouse dams to vehicle, 0.1 mg/kg/day DE-71 (an industrial PBDE mixture), DE-71+IPA (20 mg/kg/day), or IPA, from 4 weeks preconception to the end of lactation. Pups were weaned at 21 days of age and IPA supplementation continued in the corresponding treatment groups. Tissues were collected at various ages until 6 months of age (n = 5 per group). In general, the effect of maternal DE-71 exposure on the gut microbiome of pups was amplified over time. The regulation of hepatic cytokines and prototypical xenobiotic-sensing transcription factor target genes by DE-71 and IPA was age- and sex-dependent, where DE-71-mediated mRNA increased selected cytokines (Il10, Il12p40, Il1β [both sexes], and [males]). The hepatic mRNA of the aryl hydrocarbon receptor (AhR) target gene Cyp1a2 was increased by maternal DE-71 and DE-71+IPA exposure at postnatal day 21 but intestinal Cyp1a1 was not altered by any of the exposures and ages. Maternal DE-71 exposure persistently increased serum indole, a known AhR ligand, in age- and sex-dependent manner. In conclusion, maternal DE-71 exposure produced a proinflammatory signature along the gut-liver axis, including gut dysbiosis, dysregulated tryptophan microbial metabolism, attenuated PXR signaling, and elevated AhR signaling in postweaned hPXR-TG pups over time, which was partially corrected by IPA supplementation.
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Affiliation(s)
- Sarah Kim
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105, USA
| | - Hao Li
- Departments of Medicine, Molecular Pharmacology, and Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Yan Jin
- Center for Translational Science, Florida International University, Port St. Lucie, Florida 34987-2352, USA
| | - Jasmine Armad
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105, USA
| | - Haiwei Gu
- Center for Translational Science, Florida International University, Port St. Lucie, Florida 34987-2352, USA
| | - Sridhar Mani
- Departments of Medicine, Molecular Pharmacology, and Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Julia Y Cui
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105, USA
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Bhattacharjee D, Flores C, Woelfel-Monsivais C, Seekatz AM. Diversity and Prevalence of Clostridium innocuum in the Human Gut Microbiota. mSphere 2023; 8:e0056922. [PMID: 36541771 PMCID: PMC9942572 DOI: 10.1128/msphere.00569-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Clostridia are a polyphyletic group of Gram-positive, spore-forming anaerobes in the Firmicutes phylum that significantly impact metabolism and functioning of the human gastrointestinal tract. Recently, Clostridia were divided into two separate classes, Clostridia and Erysipelotrichia, based on phenotypic and 16S rRNA gene-based differences. While Clostridia include many well-known pathogenic bacteria, Erysipelotrichia remain relatively uncharacterized, particularly regarding their role as a pathogen versus commensal. Despite wide recognition as a commensal, the erysipelotrichial species Clostridium innocuum has recently been associated with various disease states. To further understand the ecological and potential virulent role of C. innocuum, we conducted a genomic comparison across 38 C. innocuum isolates and 194 publicly available genomes. Based on colony morphology, we isolated multiple C. innocuum cultivars from the feces of healthy human volunteers (n = 5). Comparison of the 16S rRNA gene of our isolates against publicly available microbiota data sets in healthy individuals suggests a high prevalence of C. innocuum across the human population (>80%). Analysis of single nucleotide polymorphisms (SNPs) across core genes and average nucleotide identify (ANI) revealed the presence of four clades among all available genomes (n = 232 total). Investigation of carbohydrate and protein utilization pathways, including comparison against the carbohydrate-activating enzyme (CAZyme) database, demonstrated inter- and intraclade differences that were further substantiated in vitro. Collectively, these data indicate genetic variance within the C. innocuum species that may help clarify its role in human disease and health. IMPORTANCE Clostridia are a group of medically important anaerobes as both commensals and pathogens. Recently, a new class of Erysipelotrichia containing a number of reassigned clostridial species has emerged, including Clostridium innocuum. Recent studies have implicated C. innocuum as a potential causative agent of diarrhea in patients from whom Clostridioides difficile could not be isolated. Using genomic and in vitro comparison, this study sought to characterize C. innocuum in the healthy human gut. Our analyses suggest that C. innocuum is a highly prevalent and diverse species, demonstrating clade-specific differences in metabolism and potential virulence. Collectively, this study is the first investigation into a broader description of C. innocuum as a human gut inhabitant.
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Affiliation(s)
- Disha Bhattacharjee
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Clara Flores
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | | | - Anna M. Seekatz
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
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Association Studies on Gut and Lung Microbiomes in Patients with Lung Adenocarcinoma. Microorganisms 2023; 11:microorganisms11030546. [PMID: 36985120 PMCID: PMC10059697 DOI: 10.3390/microorganisms11030546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
Lung adenocarcinoma (LADC) is a prevalent type of lung cancer that is associated with lung and gut microbiota. However, the interactions between these microbiota and cancer development remain unclear. In this study, a microbiome study was performed on paired fecal and bronchoalveolar lavage fluid (BALF) samples from 42 patients with LADC and 64 healthy controls using 16S rRNA gene amplicon and shotgun metagenome sequencing, aiming to correlate the lung and gut microbiota with LADC. Patients with LADC had reduced α-diversity in the gut microbiome and altered β-diversity compared with healthy controls, and the abundances of Flavonifractor, Eggerthella, and Clostridium were higher in the gut microbiome of LADC patients. The increased abundance of microbial species, such as Flavonifractor plautii, was associated with advanced-stage LADC and a higher metastasis rate. Phylogenetically, Haemophilus parainfluenzae was the most frequently shared taxon in the lung and gut microbiota of LADC patients. Gut microbiome functional pathways involving leucine, propanoate, and fatty acids were associated with LADC progression. In conclusion, the low diversity of the gut microbiota and the presence of H. parainfluenzae in gut and lung microbiota were linked to LADC development, while an increased abundance of F. plautii and the enriched metabolic pathways could be associated with the progression of LADC.
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Cherny KE, Muscat EB, Balaji A, Mukherjee J, Ozer EA, Angarone MP, Hauser AR, Sichel JS, Amponsah E, Kociolek LK. Association Between Clostridium innocuum and Antibiotic-Associated Diarrhea in Adults and Children: A Cross-sectional Study and Comparative Genomics Analysis. Clin Infect Dis 2023; 76:e1244-e1251. [PMID: 35724319 PMCID: PMC10169446 DOI: 10.1093/cid/ciac483] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/03/2022] [Accepted: 06/09/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND A recent study from Taiwan suggested that Clostridium innocuum may be an unrecognized cause of antibiotic-associated diarrhea (AAD) and clinically indistinguishable from Clostridioides difficile infection. Our objective was to compare C. innocuum prevalence and strain between those with AAD and asymptomatic controls. METHODS In this cross-sectional study, we collected stool from 200 individuals with AAD and 100 asymptomatic controls. We evaluated the association between AAD and C. innocuum in stool using anaerobic culture and quantitative polymerase chain reaction (qPCR). To identify strain-specific associations with AAD, we performed whole-genome sequencing of C. innocuum isolates using Illumina MiSeq and constructed comparative genomics analyses. RESULTS C. innocuum was isolated from stool of 126/300 (42%) subjects and more frequently from asymptomatic controls than AAD subjects (50/100 [50%] vs 76/200 [38%], respectively; P = .047). C. innocuum isolation frequency was not associated with AAD in either the adult or pediatric subgroups. C. innocuum and C. difficile were frequently co-prevalent in individuals with and without diarrhea. There were no phylogenetic differences or accessory genome associations between C. innocuum isolates from AAD subjects and asymptomatic controls. CONCLUSIONS C. innocuum was frequently isolated and at a greater frequency in asymptomatic controls than those with AAD. We did not identify strain lineages or accessory genomic elements associated with AAD. These data highlight that differentiating C. innocuum-associated diarrhea from asymptomatic colonization, and differentiating diarrhea caused by C. difficile from C. innocuum, are clinical microbiology challenges that require additional investigation to identify host-specific factors and/or biomarkers that distinguish these conditions.
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Affiliation(s)
- Kathryn E Cherny
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Emily B Muscat
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Aakash Balaji
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Jayabrata Mukherjee
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Egon A Ozer
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Michael P Angarone
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Alan R Hauser
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Joseph S Sichel
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Emmanuel Amponsah
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Larry K Kociolek
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA.,Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
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11
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Zakia LS, MacNicol JL, Borges AS, Yu S, Boerlin P, Gomez DE, Surette MG, Arroyo LG. Fecal prevalence of Clostridium innocuum DNA in healthy horses and horses with colitis. Anaerobe 2023; 79:102681. [PMID: 36481352 DOI: 10.1016/j.anaerobe.2022.102681] [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: 09/16/2022] [Revised: 10/23/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022]
Abstract
This study compared the prevalence of C. innocuum DNA in the feces of healthy horses and horses with acute colitis. C. innocuum was identified in 22% (15/68) of colitis cases and 18% (12/68) of healthy horses (p = 0.416).
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Affiliation(s)
- Luiza S Zakia
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada.
| | - Jennifer L MacNicol
- Department of Animal Bioscience, Ontario Agricultural College, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada.
| | - Alexandre S Borges
- São Paulo State University (Unesp), School of Veterinary Medicine and Animal Science, Department of Veterinary Clinical Science, Walter Mauricio Correa Street, No Number, Botucatu, Sao Paulo, 18618-681, Brazil.
| | - Serena Yu
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada.
| | - Patrick Boerlin
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada.
| | - Diego E Gomez
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada.
| | - Michael G Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada.
| | - Luis G Arroyo
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada.
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12
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Chen YC, Le PH, Wang YH, Chuang TC, Yeh YM, Chiu CT, Chiu CH. Gut Colonization and Antibiotic-Associated Diarrhea by Clostridium innocuum in Children and Adults. Clin Infect Dis 2023; 76:369-371. [PMID: 36029096 DOI: 10.1093/cid/ciac696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/23/2022] [Indexed: 01/18/2023] Open
Affiliation(s)
- Yi-Ching Chen
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Puo-Hsien Le
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Yi-Hsin Wang
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Tzu-Chun Chuang
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Cheng-Tang Chiu
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan.,Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
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13
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Yu S, Ge X, Xu H, Tan B, Tian B, Shi Y, Dai Y, Li Y, Hu S, Qian J. Gut microbiome and mycobiome in inflammatory bowel disease patients with Clostridioides difficile infection. Front Cell Infect Microbiol 2023; 13:1129043. [PMID: 36814443 PMCID: PMC9940757 DOI: 10.3389/fcimb.2023.1129043] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/24/2023] [Indexed: 02/08/2023] Open
Abstract
Background Clostridium difficile infection (CDI) is common in patients with inflammatory bowel disease (IBD) and has been reported as a risk factor for poor outcome. However, gut microbiome and mycobiome of IBD patients with CDI have been barely investigated. This study aimed to assess the gut microbiome and mycobiome in IBD patients with CDI. Methods We collected fecal samples from patients with active IBD and concomitant CDI (IBD-CDI group, n=25), patients with active IBD and no CDI (IBD-only group, n=51), and healthy subjects (HC, n=40). Patients' characteristics including demographic data, disease severity, and medication history were collected. Metagenomic sequencing, taxonomic and functional analysis were carried out in the samples. Results We found that the bacterial alpha diversity of the IBD-CDI group was decreased. The bacterial and fungal beta diversity variations between IBD patients and HC were significant, regardless of CDI status. But the IBD-CDI group did not significantly cluster separately from the IBD-only group. Several bacterial taxa, including Enterococcus faecium, Ruminococcus gnavus, and Clostridium innocuum were overrepresented in the IBD-CDI group. Furthermore, IBD patients with CDI were distinguished by several fungal taxa, including overrepresentation of Saccharomyces cerevisiae. We also identified functional differences in IBD patients with CDI include enrichment of peptidoglycan biosynthesis. The network analysis indicated specific interactions between microbial markers in IBD-CDI patients. Conclusion IBD patients with CDI had pronounced microbial dysbiosis. Gut micro-ecological changes in IBD patients with CDI might provide insight into the pathological process and potential strategies for diagnosis and treatment in this subset of patients.
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Affiliation(s)
- Si Yu
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaomeng Ge
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hui Xu
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bei Tan
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bowen Tian
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yujie Shi
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yimin Dai
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yue Li
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- *Correspondence: Yue Li, ; Songnian Hu,
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Yue Li, ; Songnian Hu,
| | - Jiaming Qian
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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14
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Sgro M, Iacono G, Yamakawa GR, Kodila ZN, Marsland BJ, Mychasiuk R. Age matters: Microbiome depletion prior to repeat mild traumatic brain injury differentially alters microbial composition and function in adolescent and adult rats. PLoS One 2022; 17:e0278259. [PMID: 36449469 PMCID: PMC9710846 DOI: 10.1371/journal.pone.0278259] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/13/2022] [Indexed: 12/02/2022] Open
Abstract
Dysregulation of the gut microbiome has been shown to perpetuate neuroinflammation, alter intestinal permeability, and modify repetitive mild traumatic brain injury (RmTBI)-induced deficits. However, there have been no investigations regarding the comparative effects that the microbiome may have on RmTBI in adolescents and adults. Therefore, we examined the influence of microbiome depletion prior to RmTBI on microbial composition and metabolome, in adolescent and adult Sprague Dawley rats. Rats were randomly assigned to standard or antibiotic drinking water for 14 days, and to subsequent sham or RmTBIs. The gut microbiome composition and metabolome were analysed at baseline, 1 day after the first mTBI, and at euthanasia (11 days following the third mTBI). At euthanasia, intestinal samples were also collected to quantify tight junction protein (TJP1 and occludin) expression. Adolescents were significantly more susceptible to microbiome depletion via antibiotic administration which increased pro-inflammatory composition and metabolites. Furthermore, RmTBI induced a transient increase in 'beneficial bacteria' (Lachnospiraceae and Faecalibaculum) in only adolescents that may indicate compensatory action in response to the injury. Finally, microbiome depletion prior to RmTBI generated a microbiome composition and metabolome that exemplified a potentially chronic pathogenic and inflammatory state as demonstrated by increased Clostridium innocuum and Erysipelatoclostridium and reductions in Bacteroides and Clostridium Sensu Stricto. Results highlight that adolescents are more vulnerable to RmTBI compared to adults and dysbiosis prior to injury may exacerbate secondary inflammatory cascades.
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Affiliation(s)
- Marissa Sgro
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Giulia Iacono
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Glenn R. Yamakawa
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Zoe N. Kodila
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Benjamin J. Marsland
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Richelle Mychasiuk
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- * E-mail:
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15
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Vega L, Bohórquez L, Ramírez JD, Muñoz M. Do we need to change our perspective about gut biomarkers? A public data mining approach to identify differentially abundant bacteria in intestinal inflammatory diseases. Front Cell Infect Microbiol 2022; 12:918237. [PMID: 36478676 PMCID: PMC9719923 DOI: 10.3389/fcimb.2022.918237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/31/2022] [Indexed: 11/22/2022] Open
Abstract
Introduction The gut microbiome is involved in multiple processes that influence host physiology, and therefore, disruptions in microbiome homeostasis have been linked to diseases or secondary infections. Given the importance of the microbiome and the communities of microorganisms that compose it (microbiota), the term biomarkers were coined, which are bacteria correlated with disease states, diets, and the lifestyle of the host. However, a large field in the study of intestinal biomarkers remains unexplored because the bacterial communities associated with a given disease state have not been exactly defined yet. Methods Here, we analyzed public data of studies focused on describing the intestinal microbiota of patients with some intestinal inflammatory diseases together with their respective controls. With these analyses, we aimed to identify differentially abundant bacteria between the subjects with the disease and their controls. Results We found that frequently reported bacteria such as Fusobacterium, Streptococcus, and Escherichia/Shigella were differentially abundant between the groups, with a higher abundance mostly in patients with the disease in contrast with their controls. On the other hand, we also identified potentially beneficial bacteria such as Faecalibacterium and Phascolarctobacterium, with a higher abundance in control patients. Discussion Our results of the differentially abundant bacteria contrast with what was already reported in previous studies on certain inflammatory diseases, but we highlight the importance of considering more comprehensive approaches to redefine or expand the definition of biomarkers. For instance, the intra-taxa diversity within a bacterial community must be considered, as well as environmental and genetic factors of the host, and even consider a functional validation of these biomarkers through in vivo and in vitro approaches. With the above, these key bacterial communities in the intestinal microbiota may have potential as next-generation probiotics or may be functional for the design of specific therapies in certain intestinal diseases.
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Affiliation(s)
- Laura Vega
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Laura Bohórquez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia,Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia,*Correspondence: Marina Muñoz,
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16
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Arias-Borrego A, Selma-Royo M, Collado MC, Abril N, García-Barrera T. Impact of "chemical cocktails" exposure in shaping mice gut microbiota and the role of selenium supplementation combining metallomics, metabolomics, and metataxonomics. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129444. [PMID: 35999733 DOI: 10.1016/j.jhazmat.2022.129444] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/31/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Biological systems are exposed to a complex environment in which pollutants can interact through synergistic or antagonistic mechanisms, but limited information is available on the combined effects. To this end, conventional and antibiotic-treated (Abx) mice models were fed regular rodent or selenium (Se) supplemented diets and exposed to a "chemical cocktail" (CC) including metals and pharmaceuticals. Metallomics, metabolomics, and metataxomics were combined to delve into the impact on gut microbiota, plasma selenoproteome, metabolome, and arsenic metabolization. At the molecular level, Se decreased the concentration of the antioxidant glutathione peroxidase in plasma and increased the arsenic methylation rate, possibly favoring its excretion, but not in the Abx and also plasma metabolomes of Abx, and Abx-Se were not differentiated. Moreover, numerous associations were obtained between plasma selenoproteins and gut microbes. Se-supplementation partially antagonizes the gut microbiota alteration caused by Abx, and slightly by CC, but strongly altered profiles were observed in CC-Abx-Se, suggesting synergistic deleterious effects between pollutants, Abx and Se. Moreover, although CC and Abx changed gut microbiota, several common taxa were enriched in CC-Abx and control mice, indicating possible synergistic effects. Our results suggest a potential beneficial impact of supplementation, but mediated by gut microbes being reversed in their absence.
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Affiliation(s)
- A Arias-Borrego
- Research Center of Natural Resources, Health and the Environment (RENSMA). Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Fuerzas Armadas Ave., 21007 Huelva, Spain; Department of Analytical Chemistry, Faculty of Chemistry, University of Sevilla, 41012 Sevilla, Spain
| | - M Selma-Royo
- Institute of Agrochemistry and Food Technology (IATA-CSIC), Department of Biotechnology, Agustin Escardino 7, 46980 Paterna, Valencia, Spain
| | - M C Collado
- Institute of Agrochemistry and Food Technology (IATA-CSIC), Department of Biotechnology, Agustin Escardino 7, 46980 Paterna, Valencia, Spain
| | - N Abril
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain
| | - T García-Barrera
- Research Center of Natural Resources, Health and the Environment (RENSMA). Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Fuerzas Armadas Ave., 21007 Huelva, Spain.
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17
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Wang Y, An M, Zhang Z, Zhang W, Kulyar MFEA, Iqbal M, He Y, Li F, An T, Li H, Luo X, Yang S, Li J. Effects of Milk Replacer-Based Lactobacillus on Growth and Gut Development of Yaks' Calves: a Gut Microbiome and Metabolic Study. Microbiol Spectr 2022; 10:e0115522. [PMID: 35771011 PMCID: PMC9431445 DOI: 10.1128/spectrum.01155-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/08/2022] [Indexed: 01/01/2023] Open
Abstract
The gut microbiota and its metabolic activities are crucial for maintaining host homoeostasis and health, of which the role of probiotics has indeed been emphasized. The current study delves into the performance of probiotics as a beneficial managemental strategy, which further highlights their impact on growth performance, serologic investigation, gut microbiota, and metabolic profiling in yaks' calves. A field experiment was employed consisting of 2 by 3 factorial controls, including two development stages, namely, 21 and 42 days (about one and a half month), with three different feeding treatments. Results showed a positive impact of probiotic supplements on growth performance by approximately 3.16 kg (P < 0.01) compared with the blank control. Moreover, they had the potential to improve serum antioxidants and biochemical properties. We found that microorganisms that threaten health were enriched in the gut of the blank control with the depletion of beneficial bacteria, although all yaks were healthy. Additionally, the gut was colonized by a microbial succession that assembled into a more mature microbiome, driven by the probiotics strategy. The gut metabolic profiling was also changed significantly after the probiotic strategy, i.e., the concentrations of metabolites and the metabolic pattern, including enrichments in protein digestion and absorption, vitamin digestion and absorption, and biosynthesis of secondary metabolites. In summary, probiotics promoted gut microbiota/metabolites, developing precise interventions and achieving physiological benefits based on intestinal microecology. Hence, it is important to understand probiotic dietary changes to the gut microbiome, metabolome, and the host phenotype. IMPORTANCE The host microbiome is a composite of the trillion microorganisms colonizing host bodies. It can be impacted by various factors, including diet, environmental conditions, and physical activities. The yaks' calves have a pre-existing imbalance in the intestinal microbiota with an inadequate feeding strategy, resulting in poor growth performance, diarrhea, and other intestinal diseases. Hence, targeting gut microbiota might provide a new effective feeding strategy for enhancing performance and maintaining a healthy intestinal environment. Based on the current findings, milk replacer-based Lactobacillus feeding may improve growth performance and health in yaks' calves.
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Affiliation(s)
- Yaping Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Miao An
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhao Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Wenqian Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | | | - Mudassar Iqbal
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Yuanyuan He
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Feiran Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Tianwu An
- Sichuan Academy of Grassland Science, Chengdu, People’s Republic of China
| | - Huade Li
- Sichuan Academy of Grassland Science, Chengdu, People’s Republic of China
| | - Xiaolin Luo
- Sichuan Academy of Grassland Science, Chengdu, People’s Republic of China
| | - Shan Yang
- Sichuan Academy of Grassland Science, Chengdu, People’s Republic of China
| | - Jiakui Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- College of Animals Husbandry and Veterinary Medicine, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People’s Republic of China
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18
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Cherny KE, Balaji A, Mukherjee J, Goo YA, Hauser AR, Ozer E, Satchell KJF, Bachta KER, Kochan TJ, Mitra SD, Kociolek LK. Identification of Clostridium innocuum hypothetical protein that is cross-reactive with C. difficile anti-toxin antibodies. Anaerobe 2022; 75:102555. [PMID: 35367613 PMCID: PMC9197939 DOI: 10.1016/j.anaerobe.2022.102555] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 11/01/2022]
Abstract
OBJECTIVES Previously considered solely an opportunistic pathogen, Clostridium innocuum (CI) was recently reported in Taiwan to be an emerging cause of antibiotic-associated diarrhea and clinically indistinguishable from Clostridioides difficile (CD) infection. We previously identified CI culture supernatant being cross-reactive with commercial CD toxin enzyme immunoassays. We aimed to identify and characterize the cross-reacting protein and determine whether it functioned as a human toxin. METHODS We performed western blots using CI culture supernatants and CD anti-toxin antibodies and identified interacting bands. We identified protein(s) using tandem mass spectrometry and evaluated them by cytotoxicity assays. RESULTS CI, but not CD, was isolated from stool of 12 children and adults with diarrhea. Culture supernatant from 6/12 CI isolates, and an ATCC reference strain, tested positive for CD toxins (total 7/13 isolates) by commercial EIA. Using two of these isolates, we identified two ∼40 kDa hypothetical proteins, CI_01447 and CI_01448, and confirmed cross-reactivity with CD anti-toxin antibodies by enzyme immunoassay and Western blot. Whole-genome sequencing confirmed all 13 isolates contained both genes, which were highly conserved. We observed no cytopathic or cytotoxic effects to HeLa cells when treated with these proteins. We identified amino acid sequence similarity to the NlpC/P60 family of proteins. CONCLUSIONS Our findings do not suggest CI proteins CI_01448 and CI_01447, which cross-react with antibodies against CD toxins A and B, are toxic to HeLa cells. Further studies are needed to determine the function of these cross-reacting proteins and the potential virulence factors that could be responsible for CI diarrheal disease.
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Affiliation(s)
- K E Cherny
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA; Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
| | - A Balaji
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - J Mukherjee
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Y A Goo
- Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - A R Hauser
- Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - E Ozer
- Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - K J F Satchell
- Northwestern University, Feinberg School of Medicine, Chicago, IL, USA; Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - K E R Bachta
- Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - T J Kochan
- Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - S D Mitra
- Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - L K Kociolek
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA; Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
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19
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Skinner AM, Petrella L, Spandoni S, Serna-Perez F, Johnson S. Can Clostridium innocuum masquerade as Clostridioides difficile? Clin Infect Dis 2022; 75:1268-1269. [PMID: 35579505 DOI: 10.1093/cid/ciac377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Andrew M Skinner
- Department of Research and Medicine, Edward Hines Jr Veterans Administration Hospital, Hines, Illinois, USA.,Loyola University Medical Center, Department of Medicine, Maywood, Illinois, USA
| | - Laurica Petrella
- Department of Research and Medicine, Edward Hines Jr Veterans Administration Hospital, Hines, Illinois, USA
| | - Stacey Spandoni
- Department of Research and Medicine, Edward Hines Jr Veterans Administration Hospital, Hines, Illinois, USA
| | - Fidel Serna-Perez
- Department of Research and Medicine, Edward Hines Jr Veterans Administration Hospital, Hines, Illinois, USA
| | - Stuart Johnson
- Department of Research and Medicine, Edward Hines Jr Veterans Administration Hospital, Hines, Illinois, USA.,Loyola University Medical Center, Department of Medicine, Maywood, Illinois, USA
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20
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Petrov VA, Sharapov SZ, Shagam L, Nostaeva AV, Pezer M, Li D, Hanić M, McGovern D, Louis E, Rahmouni S, Lauc G, Georges M, Aulchenko YS. Association Between Human Gut Microbiome and N-Glycan Composition of Total Plasma Proteome. Front Microbiol 2022; 13:811922. [PMID: 35572712 PMCID: PMC9100934 DOI: 10.3389/fmicb.2022.811922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Being one of the most dynamic entities in the human body, glycosylation of proteins fine-tunes the activity of the organismal machinery, including the immune system, and mediates the interaction with the human microbial consortium, typically represented by the gut microbiome. Using data from 194 healthy individuals, we conducted an associational study to uncover potential relations between the gut microbiome and the blood plasma N-glycome, including N-glycome of immunoglobulin G. While lacking strong linkages on the multivariate level, we were able to identify associations between alpha and beta microbiome diversity and the blood plasma N-glycome profile. Moreover, for two bacterial genera, namely, Bilophila and Clostridium innocuum, significant associations with specific glycans were also shown. The study’s results suggest a non-trivial, possibly weak link between the total plasma N-glycome and the gut microbiome, predominantly involving glycans related to the immune system proteins, including immunoglobulin G. Further studies of glycans linked to microbiome-related proteins in well-selected patient groups are required to conclusively establish specific associations.
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Affiliation(s)
- Vyacheslav A. Petrov
- Unit of Animal Genomics, Grappe Interdisciplinaire de Génoprotéomique Appliquée-Institute, University of Liège, Liège, Belgium
- Central Research Laboratory, Ministry of Healthcare of Russian Federation, Federal State Budget Educational Institution of Higher Education, Siberian State Medical University, Tomsk, Russia
| | - Sodbo Zh. Sharapov
- Laboratory of Glycogenomics, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Lev Shagam
- Central Research Laboratory, Ministry of Healthcare of Russian Federation, Federal State Budget Educational Institution of Higher Education, Siberian State Medical University, Tomsk, Russia
| | - Arina V. Nostaeva
- Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University, Novosibirsk, Russia
| | | | - Dalin Li
- Cedars-Sinai Medical Center, The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, CA, United States
| | - Maja Hanić
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | - Dermot McGovern
- Cedars-Sinai Medical Center, The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, CA, United States
| | - Edouard Louis
- Laboratory of Translational Gastroenterology, Grappe Interdisciplinaire de Génoprotéomique Appliquée-Institute, University of Liège, Liège, Belgium
| | - Souad Rahmouni
- Central Research Laboratory, Ministry of Healthcare of Russian Federation, Federal State Budget Educational Institution of Higher Education, Siberian State Medical University, Tomsk, Russia
| | - Gordan Lauc
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Michel Georges
- Central Research Laboratory, Ministry of Healthcare of Russian Federation, Federal State Budget Educational Institution of Higher Education, Siberian State Medical University, Tomsk, Russia
| | - Yurii S. Aulchenko
- Laboratory of Glycogenomics, Institute of Cytology and Genetics, Novosibirsk, Russia
- *Correspondence: Yurii S. Aulchenko,
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21
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Chen YC, Kuo YC, Chen MC, Zhang YD, Chen CL, Le PH, Chiu CH. Case–Control Study of Clostridium innocuum Infection, Taiwan. Emerg Infect Dis 2022. [DOI: 10.3201/2803.204421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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22
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Le PH, Chiu CT, Yeh PJ, Pan YB, Chiu CH. Clostridium innocuum infection in hospitalised patients with inflammatory bowel disease. J Infect 2022; 84:337-342. [PMID: 34963635 DOI: 10.1016/j.jinf.2021.12.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 11/26/2021] [Accepted: 12/15/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Clostridium innocuum (CI) infection can lead to creeping fat in Crohn's disease and is associated with intestinal strictures. At present, no clinical study ever has evaluated the role of CI infection in inflammatory bowel disease (IBD). MATERIALS AND METHODS In this retrospective cohort study, we enrolled hospitalized IBD patients with culture results for both CI and Clostridioides difficile (CD) in a medical center between October 2019 and April 2021. They were divided into the CI (CI+/CD-), control (CI-/CD-), coinfection (CI+/CD+), and CD (CI-/CD+) groups. We analyzed the risk factors, clinical presentations, and outcomes by comparing the CI and control groups. RESULTS We enrolled a total of 90 patients, including 22, 39, 13, and 16 patients in the CI, control, coinfection, and CD groups. The incidence rates of CI (CI+) and CD (CD+) were 39% (35/90) and 32% (29/90), respectively. We analyzed the differences between CI and control groups. We identified the use of steroid (77.3% vs. 46.2%, P = 0.018) and 5-aminosalicylic acid (90.9% vs. 64.1%, P = 0.022) as risk factors of CI infection. Clinical analysis showed that more patients in CI group presented with bloody stool (77.3% vs. 51.3%, P = 0.046). Although CI group had significantly lower overall occurrence of intraabdominal abscess (0% vs. 17.9%, P = 0.042), it showed a lower clinical remission rate (50% vs. 87.5%, P = 0.044) and higher Mayo score at the end of follow-up (10 points vs. 3 points, P = 0.008) in ulcerative colitis. CONCLUSIONS CI infection may lead to a poorer clinical remission in ulcerative colitis. We should take it into consideration in IBD patents with active inflamamtion or refractory diarrhea with or without CD infection. Precise identification of CI is imperative to guide approproate antimicrobial therapy because of its intrinsic vancomycin resistance nature.
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Affiliation(s)
- Puo-Hsien Le
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan; Taiwan Association of the Study of Small Intestinal Disease, Taoyuan, Taiwan; Liver Research Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
| | - Cheng-Tang Chiu
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan; Taiwan Association of the Study of Small Intestinal Disease, Taoyuan, Taiwan
| | - Pai-Jui Yeh
- Division of Pediatric Gastroenterology, Department of Pediatrics, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
| | - Yu-Bin Pan
- Biostatistical Section, Clinical Trial Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Linkou Branch, 5, Fu-Hsin Street Guei-Shan District, Taoyuan 333, Taiwan; Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan.
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23
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Liu Q, Mak JWY, Su Q, Yeoh YK, Lui GCY, Ng SSS, Zhang F, Li AYL, Lu W, Hui DSC, Chan PK, Chan FKL, Ng SC. Gut microbiota dynamics in a prospective cohort of patients with post-acute COVID-19 syndrome. Gut 2022; 71:544-552. [PMID: 35082169 PMCID: PMC8814432 DOI: 10.1136/gutjnl-2021-325989] [Citation(s) in RCA: 269] [Impact Index Per Article: 134.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/06/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Long-term complications after COVID-19 are common, but the potential cause for persistent symptoms after viral clearance remains unclear. OBJECTIVE To investigate whether gut microbiome composition is linked to post-acute COVID-19 syndrome (PACS), defined as at least one persistent symptom 4 weeks after clearance of the SARS-CoV-2 virus. METHODS We conducted a prospective study of 106 patients with a spectrum of COVID-19 severity followed up from admission to 6 months and 68 non-COVID-19 controls. We analysed serial faecal microbiome of 258 samples using shotgun metagenomic sequencing, and correlated the results with persistent symptoms at 6 months. RESULTS At 6 months, 76% of patients had PACS and the most common symptoms were fatigue, poor memory and hair loss. Gut microbiota composition at admission was associated with occurrence of PACS. Patients without PACS showed recovered gut microbiome profile at 6 months comparable to that of non-COVID-19 controls. Gut microbiome of patients with PACS were characterised by higher levels of Ruminococcus gnavus, Bacteroides vulgatus and lower levels of Faecalibacterium prausnitzii. Persistent respiratory symptoms were correlated with opportunistic gut pathogens, and neuropsychiatric symptoms and fatigue were correlated with nosocomial gut pathogens, including Clostridium innocuum and Actinomyces naeslundii (all p<0.05). Butyrate-producing bacteria, including Bifidobacterium pseudocatenulatum and Faecalibacterium prausnitzii showed the largest inverse correlations with PACS at 6 months. CONCLUSION These findings provided observational evidence of compositional alterations of gut microbiome in patients with long-term complications of COVID-19. Further studies should investigate whether microbiota modulation can facilitate timely recovery from post-acute COVID-19 syndrome.
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Affiliation(s)
- Qin Liu
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong, Hong Kong SAR, China
| | - Joyce Wing Yan Mak
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Qi Su
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong, Hong Kong SAR, China
| | - Yun Kit Yeoh
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong, Hong Kong SAR, China
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Grace Chung-Yan Lui
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Susanna So Shan Ng
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Fen Zhang
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong, Hong Kong SAR, China
| | - Amy Y L Li
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Wenqi Lu
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong, Hong Kong SAR, China
| | - David Shu-Cheong Hui
- Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Paul Ks Chan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Francis K L Chan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong, Hong Kong SAR, China
| | - Siew C Ng
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Science, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong, Hong Kong SAR, China
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Chen YC, Kuo YC, Chen MC, Zhang YD, Chen CL, Le PH, Chiu CH. Case-Control Study of Clostridium innocuum Infection, Taiwan. Emerg Infect Dis 2022; 28:599-607. [PMID: 35195517 PMCID: PMC8888209 DOI: 10.3201/eid2803.204421] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Vancomycin-resistant Clostridium innocuum was recently identified as an etiologic agent for antibiotic-associated diarrhea in humans. We conducted a case–control study involving 152 C. innocuum-infected patients during 2014–2019 in Taiwan, using 304 cases of Clostridioides difficile infection (CDI) matched by diagnosis year, age (+2 years), and sex as controls. The baseline characteristics were similar between the 2 groups. C. innocuum–infected patients experienced more extraintestinal clostridial infection and gastrointestinal tract–related complications than did patients with CDI. The 30-day mortality rate among C. innocuum–infected patients was 14.5%, and the overall rate was 23.0%. Chronic kidney disease, solid tumor, intensive care unit admission, and shock status were 4 independent risk factors for death. C. innocuum identified from clinical specimens should be recognized as a pathogen requiring treatment, and because of its intrinsic vancomycin resistance, precise identification is necessary to guide appropriate and timely antimicrobial therapy.
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25
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Motamedi H, Fathollahi M, Abiri R, Kadivarian S, Rostamian M, Alvandi A. A worldwide systematic review and meta-analysis of bacteria related to antibiotic-associated diarrhea in hospitalized patients. PLoS One 2021; 16:e0260667. [PMID: 34879104 PMCID: PMC8654158 DOI: 10.1371/journal.pone.0260667] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/12/2021] [Indexed: 01/05/2023] Open
Abstract
INTRODUCTION Antibiotic-associated diarrhea (AAD) is a major hospital problem and a common adverse effect of antibiotic treatment. The aim of this study was to investigate the prevalence of the most important bacteria that cause AAD in hospitalized patients. MATERIALS AND METHODS PubMed, Web of Science and Scopus databases were searched using multiple relevant keywords and screening carried out based on inclusion/exclusion criteria from March 2001 to October 2021. The random-effects model was used to conduct the meta-analysis. RESULTS Of the 7,377 identified articles, 56 met the inclusion criteria. Pooling all studies, the prevalence of Clostridioides (Clostridium) difficile, Clostridium perfringens, Klebsiella oxytoca, and Staphylococcus aureus as AAD-related bacteria among hospitalized patients were 19.6%, 14.9%, 27%, and 5.2%, respectively. The prevalence of all four bacteria was higher in Europe compared to other continents. The highest resistance of C. difficile was estimated to ciprofloxacin and the lowest resistances were reported to chloramphenicol, vancomycin, and metronidazole. There was no or little data on antibiotic resistance of other bacteria. CONCLUSIONS The results of this study emphasize the need for a surveillance program, as well as timely public and hospital health measures in order to control and treat AAD infections.
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Affiliation(s)
- Hamid Motamedi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Matin Fathollahi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ramin Abiri
- Fertility and Infertility Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sepide Kadivarian
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mosayeb Rostamian
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amirhooshang Alvandi
- Medical Technology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Zhao TS, Xie LW, Cai S, Xu JY, Zhou H, Tang LF, Yang C, Fang S, Li M, Tian Y. Dysbiosis of Gut Microbiota Is Associated With the Progression of Radiation-Induced Intestinal Injury and Is Alleviated by Oral Compound Probiotics in Mouse Model. Front Cell Infect Microbiol 2021; 11:717636. [PMID: 34760714 PMCID: PMC8573182 DOI: 10.3389/fcimb.2021.717636] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/05/2021] [Indexed: 12/12/2022] Open
Abstract
The acute radiation-induced intestinal injury (RIII) has raised much concerns and is influenced by non-cytocidal radiation effects including the perturbations in gut microbiota. Although a number of studies have reported alteration in gut microbiota following radiation, little is known about its dynamic variation in the progression of acute RIII. In this study, mouse model were treated with total body irradiation (TBI) of 0, 4, 8 and 12 Gy, and the intestinal tissues and fecal samples were collected at 6 h, 3.5 d and 7 d post radiation. We found that the intestinal injuries were manifested in a radiation dose-dependent manner. Results from 16S rRNA gene sequencing demonstrated that the diversity of gut microbiota was not significantly affected at the prodromal stage of acute RIII, after 6 h of radiation. At the critical stage of acute RIII, after 3.5 d of radiation, the composition of gut microbiota was correlated with the radiation dose. The Pearson’s correlation analysis showed that the relative abundances of phylum Proteobacteria, genera Escherichia-Shigella and Eubacterium xylanophilum_group, and species Lactobacillus murinus exhibited linear correlations with radiation dose. At the recovery stage of acute RIII, after 7 d of radiation, the diversity of gut microbiota decreased as a whole, among which the relative abundance of phyla Proteobacteria and Bacteroides increased, while that of phylum Tenericutes and genus Roseburia decreased. The intra-gastric administration of compound probiotics for 14 days improved the survival duration of mice exposed to 9 Gy TBI, alleviated the intestinal epithelial injury and partially restored the diversity of gut microbiota. Our findings suggest that acute RIII is accompanied by the dysbiosis of gut microbiota, including its decreased diversity, reduced abundance of beneficial bacteria and increased abundance of pathogens. The gut microbiota cannot be used as sensitive biomarkers at the prodromal stage in acute RIII, but are potential biomarkers at the critical stage of acute RIII. The dysbiosis is persistent until the recovery stage of acute RIII, and interventions are needed to restore it. The administration of probiotics is an effective strategy to protect against acute RIII and subsequent dysbiosis.
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Affiliation(s)
- Tian-Shu Zhao
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Radiotherapy and Oncology, Soochow University, Suzhou, China
| | - Li-Wei Xie
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Radiotherapy and Oncology, Soochow University, Suzhou, China
| | - Shang Cai
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Radiotherapy and Oncology, Soochow University, Suzhou, China
| | - Jia-Yu Xu
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Radiotherapy and Oncology, Soochow University, Suzhou, China
| | - Hao Zhou
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University; Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Lin-Feng Tang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University; Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Chao Yang
- Department of Nucleus Radiation-Related Injury Treatment, PLA Rocket Force Characteristic Medical Center, Beijing, China
| | | | - Ming Li
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University; Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Ye Tian
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Radiotherapy and Oncology, Soochow University, Suzhou, China
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Uzal FA, Arroyo LG, Navarro MA, Gomez DE, Asín J, Henderson E. Bacterial and viral enterocolitis in horses: a review. J Vet Diagn Invest 2021; 34:354-375. [PMID: 34763560 DOI: 10.1177/10406387211057469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Enteritis, colitis, and enterocolitis are considered some of the most common causes of disease and death in horses. Determining the etiology of these conditions is challenging, among other reasons because different causes produce similar clinical signs and lesions, and also because some agents of colitis can be present in the intestine of normal animals. We review here the main bacterial and viral causes of enterocolitis of horses, including Salmonella spp., Clostridium perfringens type A NetF-positive, C. perfringens type C, Clostridioides difficile, Clostridium piliforme, Paeniclostridium sordellii, other clostridia, Rhodococcus equi, Neorickettsia risticii, Lawsonia intracellularis, equine rotavirus, and equine coronavirus. Diarrhea and colic are the hallmark clinical signs of colitis and enterocolitis, and the majority of these conditions are characterized by necrotizing changes in the mucosa of the small intestine, colon, cecum, or in a combination of these organs. The presumptive diagnosis is based on clinical, gross, and microscopic findings, and confirmed by detection of some of the agents and/or their toxins in the intestinal content or feces.
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Affiliation(s)
- Francisco A Uzal
- California Animal Health and Food Safety Laboratory, University of California-Davis, San Bernardino Laboratory, USA
| | - Luis G Arroyo
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Mauricio A Navarro
- California Animal Health and Food Safety Laboratory, University of California-Davis, San Bernardino Laboratory, USA.,Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Diego E Gomez
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Javier Asín
- California Animal Health and Food Safety Laboratory, University of California-Davis, San Bernardino Laboratory, USA
| | - Eileen Henderson
- California Animal Health and Food Safety Laboratory, University of California-Davis, San Bernardino Laboratory, USA
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Cherny KE, Muscat EB, Reyna ME, Kociolek LK. Clostridium innocuum: Microbiological and clinical characteristics of a potential emerging pathogen. Anaerobe 2021; 71:102418. [PMID: 34332070 DOI: 10.1016/j.anaerobe.2021.102418] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 10/20/2022]
Abstract
Clostridium innocuum is an anaerobic, gram-positive, spore-forming bacterium identified by Smith and King in 1962 after being isolated from a patient with an appendiceal abscess. Its name, C. innocuum, reflected its clinically "innocuous" nature based on observed lack of virulence in animal models of infection. Since that time, C. innocuum has been identified as both part of the normal intestinal flora and the cause of a rare, intrinsically vancomycin-resistant opportunistic infection in immunocompromised patients. More recently, reports from Taiwan suggest that C. innocuum, in addition to being a known extraintestinal pathogen, may also be a diarrheal pathogen that causes a C. difficile infection-like antibiotic-associated diarrheal illness. However, unanswered questions about the clinical relevance of C. innocuum remain. Here we review the microbiological and clinical characteristics of this emerging pathogen.
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Affiliation(s)
- Kathryn E Cherny
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA; Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - Emily B Muscat
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Megan E Reyna
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Larry K Kociolek
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA; Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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Abstract
We report the complete genome sequence of Clostridium innocuum ATCC 14501, which was isolated in 1962 from an appendiceal abscess. At that time, the isolated strain was designated C. innocuum, given its suspected lack of virulence, but recent reports suggest that C. innocuum is an emerging pathogen. We report the complete genome sequence of Clostridium innocuum ATCC 14501, which was isolated in 1962 from an appendiceal abscess. At that time, the isolated strain was designated C. innocuum, given its suspected lack of virulence, but recent reports suggest that C. innocuum is an emerging pathogen.
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Complete Genome Sequence of Clostridium innocuum Strain LC-LUMC-CI-001, Isolated from a Patient with Recurrent Antibiotic-Associated Diarrhea. Microbiol Resour Announc 2020; 9:9/28/e00365-20. [PMID: 32646898 PMCID: PMC7348016 DOI: 10.1128/mra.00365-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Here, we report the complete genome sequence of Clostridium innocuum strain LC-LUMC-CI-001. As recently as 2018, C. innocuum was generally considered a benign gastrointestinal microorganism. This strain was isolated from the stool of a patient with recurrent Clostridioides difficile infection-like illnesses. Here, we report the complete genome sequence of Clostridium innocuum strain LC-LUMC-CI-001. As recently as 2018, C. innocuum was generally considered a benign gastrointestinal microorganism. This strain was isolated from the stool of a patient with recurrent Clostridioides difficile infection-like illnesses.
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Chen R, Liu B, Wang X, Chen K, Zhang K, Zhang L, Fei C, Wang C, Yingchun L, Xue F, Gu F, Wang M. Effects of polysaccharide from Pueraria lobata on gut microbiota in mice. Int J Biol Macromol 2020; 158:S0141-8130(20)33067-1. [PMID: 32387359 DOI: 10.1016/j.ijbiomac.2020.04.201] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/16/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023]
Abstract
Polysaccharide was derived from Pueraria lobata (PPL) which was considered as one of the traditional Chinese medicinal and edible herbs. In the present study, PPL was administered in equal doses (12.5 mg/kg) to both normal mice and antibiotic-associated diarrhea (AAD) mice for two weeks, and was evaluated in terms of body weight, organ indices, gut structure, gut microbiota and short chain fatty acids. The results showed that normal mice treated with PPL not only reduced the isovaleric acid concentration (P < 0.05), but also significantly increased the abundance of beneficial bacteria, involving Oscillospira and Anaerotruncus (P < 0.05). In addition, PPL could relieve colonic pathological changes and gut microbiota dysbiosis caused by AAD. It indicated that PPL was a potential functional food ingredient by modulating gut microbiota.
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Affiliation(s)
- Rong Chen
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China
| | - Bo Liu
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China
| | - Xiaoyang Wang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China
| | - Kai Chen
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China
| | - Keyu Zhang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China
| | - Lifang Zhang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China
| | - Chenzhong Fei
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China
| | - Chunmei Wang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China
| | - Liu Yingchun
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China
| | - Feiqun Xue
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China
| | - Feng Gu
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China
| | - Mi Wang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China.
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Jiménez-Avalos JA, Arrevillaga-Boni G, González-López L, García-Carvajal ZY, González-Avila M. Classical methods and perspectives for manipulating the human gut microbial ecosystem. Crit Rev Food Sci Nutr 2020; 61:234-258. [PMID: 32114770 DOI: 10.1080/10408398.2020.1724075] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A healthy Human Gut Microbial Ecosystem (HGME) is a necessary condition for maintaining the orderly function of the whole body. Major alterations in the normal gut microbial composition, activity and functionality (dysbiosis) by an environmental or host-related disruptive event, can compromise metabolic, inflammatory, and neurological processes, causing disorders such as obesity, inflammatory bowel disease, colorectal cancer, and depressive episodes. The restore or the maintaining of the homeostatic balance of Gut Microbiota (GM) populations (eubiosis) is possible through diet, the use of probiotics, prebiotics, antibiotics, and even Fecal Microbiota Transplantation (FMT). Although these "classic methods" represent an effective and accepted way to modulate GM, the complexity of HGME requires new approaches to control it in a more appropriate way. Among the most promising emergent strategies for modulating GM are the use of engineered nanomaterials (metallic nanoparticles (NP), polymeric-NP, quantum dots, micelles, dendrimers, and liposomes); phagotherapy (i.e., phages linked with the CRISPR/Cas9 system), and the use of antimicrobial peptides, non-antibiotic drugs, vaccines, and immunoglobulins. Here we review the current state of development, implications, advantages, disadvantages, and perspectives of the different approaches for manipulating HGME.
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Affiliation(s)
- Jorge Armando Jiménez-Avalos
- Medical and Pharmaceutical Biotechnology Department, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara, Jalisco, Mexico
| | - Gerardo Arrevillaga-Boni
- Medical and Pharmaceutical Biotechnology Department, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara, Jalisco, Mexico
| | | | - Zaira Yunuen García-Carvajal
- Medical and Pharmaceutical Biotechnology Department, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara, Jalisco, Mexico
| | - Marisela González-Avila
- Medical and Pharmaceutical Biotechnology Department, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara, Jalisco, Mexico
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Mefferd CC, Bhute SS, Phan JR, Villarama JV, Do DM, Alarcia S, Abel-Santos E, Hedlund BP. A High-Fat/High-Protein, Atkins-Type Diet Exacerbates Clostridioides ( Clostridium) difficile Infection in Mice, whereas a High-Carbohydrate Diet Protects. mSystems 2020; 5:e00765-19. [PMID: 32047064 PMCID: PMC7018531 DOI: 10.1128/msystems.00765-19] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/29/2020] [Indexed: 02/06/2023] Open
Abstract
Clostridioides difficile (formerly Clostridium difficile) infection (CDI) can result from the disruption of the resident gut microbiota. Western diets and popular weight-loss diets drive large changes in the gut microbiome; however, the literature is conflicted with regard to the effect of diet on CDI. Using the hypervirulent strain C. difficile R20291 (RT027) in a mouse model of antibiotic-induced CDI, we assessed disease outcome and microbial community dynamics in mice fed two high-fat diets in comparison with a high-carbohydrate diet and a standard rodent diet. The two high-fat diets exacerbated CDI, with a high-fat/high-protein, Atkins-like diet leading to severe CDI and 100% mortality and a high-fat/low-protein, medium-chain-triglyceride (MCT)-like diet inducing highly variable CDI outcomes. In contrast, mice fed a high-carbohydrate diet were protected from CDI, despite the high levels of refined carbohydrate and low levels of fiber in the diet. A total of 28 members of the Lachnospiraceae and Ruminococcaceae decreased in abundance due to diet and/or antibiotic treatment; these organisms may compete with C. difficile for amino acids and protect healthy animals from CDI in the absence of antibiotics. Together, these data suggest that antibiotic treatment might lead to loss of C. difficile competitors and create a favorable environment for C. difficile proliferation and virulence with effects that are intensified by high-fat/high-protein diets; in contrast, high-carbohydrate diets might be protective regardless of the source of carbohydrate or of antibiotic-driven loss of C. difficile competitors.IMPORTANCE The role of Western and weight-loss diets with extreme macronutrient composition in the risk and progression of CDI is poorly understood. In a longitudinal study, we showed that a high-fat/high-protein, Atkins-type diet greatly exacerbated antibiotic-induced CDI, whereas a high-carbohydrate diet protected, despite the high monosaccharide and starch content. Our study results, therefore, suggest that popular high-fat/high-protein weight-loss diets may enhance CDI risk during antibiotic treatment, possibly due to the synergistic effects of a loss of the microorganisms that normally inhibit C. difficile overgrowth and an abundance of amino acids that promote C. difficile overgrowth. In contrast, a high-carbohydrate diet might be protective, despite reports on the recent evolution of enhanced carbohydrate metabolism in C. difficile.
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Affiliation(s)
| | - Shrikant S Bhute
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Jacqueline R Phan
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Jacob V Villarama
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Dung M Do
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Stephanie Alarcia
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Ernesto Abel-Santos
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
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Cobo F, Rodríguez-Granger J, Pérez-Zapata I, Sampedro A, Aliaga L, Navarro-Marí JM. Antimicrobial susceptibility and clinical findings of significant anaerobic bacteria in southern Spain. Anaerobe 2019; 59:49-53. [PMID: 31103531 DOI: 10.1016/j.anaerobe.2019.05.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/08/2019] [Accepted: 05/15/2019] [Indexed: 12/12/2022]
Abstract
The objectives of this study were to report on the antimicrobial susceptibility of 276 clinically significant anaerobic bacteria belonging to the major genera isolated between May 2017 and November 2018 in a tertiary hospital in Granada (Spain) and to describe key clinical features of the patients. Species identification was performed by MALDI-TOF MS. Antimicrobial susceptibility tests were performed against penicillin, amoxicillin-clavulanic, imipenem, meropenem, moxifloxacin, clindamycin, metronidazole, vancomycin, and piperacillin-tazobactam using the gradient diffusion technique and EUCAST breakpoints (except for moxifloxacin). The most frequent anaerobes were Bacteroides (29.7%; n = 82), Clostridioides difficile (15.9%, n = 44), Prevotella (10.8%, n = 30), and Propionibacterium (10.7%, n = 25). Metronidazole was not universally active against all genera tested, and some isolates showed resistance to this drug. Almost all tested anaerobes were susceptible to carbapenems and amoxicillin-clavulanate except for Clostridioides difficile (resistance rate of 94%) and Bacteroides (19%), respectively. High overall resistance rates to clindamycin were observed, especially for genera Finegoldia (54%), Bacteroides (49%), and Prevotella (40%). Resistance rates to carbapenems and amoxicillin-clavulanate were very low for the majority of tested genera but were high for Clostridioides difficile and Bacteroides spp., respectively. Resistance to clindamycin was very high, especially for Bacteroides, Finegoldia magna, Prevotella and Peptoniphilus. Routine antimicrobial susceptibility testing for anaerobes contributes information on the global situation and allows empirical therapies to be selected in accordance with local data on resistant strains.
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Affiliation(s)
- Fernando Cobo
- Department of Microbiology and Instituto Biosanitario, Virgen de las Nieves University Hospita, Granada, Spain.
| | - Javier Rodríguez-Granger
- Department of Microbiology and Instituto Biosanitario, Virgen de las Nieves University Hospita, Granada, Spain
| | - Inés Pérez-Zapata
- Department of Microbiology and Instituto Biosanitario, Virgen de las Nieves University Hospita, Granada, Spain
| | - Antonio Sampedro
- Department of Microbiology and Instituto Biosanitario, Virgen de las Nieves University Hospita, Granada, Spain
| | - Luis Aliaga
- Department of Medicine (University of Granada), Granada, Spain
| | - José María Navarro-Marí
- Department of Microbiology and Instituto Biosanitario, Virgen de las Nieves University Hospita, Granada, Spain
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35
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Charles MK, Wang Y, Zurberg T, Kinna J, Bryce E. Detecting Clostridioides (Clostridium) difficile using canine teams: What does the nose know? Infect Prev Pract 2019; 1:100005. [PMID: 34368671 PMCID: PMC8336037 DOI: 10.1016/j.infpip.2019.100005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 04/03/2019] [Indexed: 11/24/2022] Open
Abstract
Background Trained canines are capable of detecting Clostridioides (Clostridium) difficile (CD) in the environment; however, the primary odour of interest on which the dogs alert is unclear. Aim To evaluate the inter-rater reliability of two canine detection teams for their ability to discriminate between scent pads containing CD-toxin-positive and -negative odours and their ability to discriminate between clostridial strains. Methods During a six-month period, two canine teams were tested weekly for their ability to detect CD-toxin-positive odours and discriminate between these and -negative odours. To further determine the canines' discrimination capability, scent pads impregnated with odours from reference isolates representing common CD toxin types (including toxin-negative CD isolates) or from clinical isolates representing other clostridial species were used. Results A total of 264 samples were tested with an overall sensitivity of 94.7% (Team A) and 86.8% (Team B) and specificities of 96.9% and 98.7%, respectively. Inter-rater reliability was very good (Cohen's kappa 0.87). When challenged with toxin- and non-toxin-producing strains, the teams alerted on 96.3% of all CD isolate odours (including nontoxigenic strains) and 46.7% of closely related species. Conclusions The canine teams exhibited strong inter-rater reliability on both clinical faecal specimens and reference CD isolates (both toxin and non-toxin producing) but were challenged to discriminate between CD and closely related clostridial species. These findings strongly support the development of scent detection programmes provided dogs and their handlers are properly trained and used in the right context.
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Affiliation(s)
- M K Charles
- Division of Medical Microbiology and Infection Prevention, Vancouver Coastal Health and University of British Columbia Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Y Wang
- University of British Columbia Undergraduate Integrated Sciences Program, Vancouver, British Columbia, Canada
| | - T Zurberg
- Quality and Patient Safety Department, Vancouver Coastal Health, Vancouver, British Columbia, Canada
| | - J Kinna
- Quality and Patient Safety Department, Vancouver Coastal Health, Vancouver, British Columbia, Canada
| | - E Bryce
- Division of Medical Microbiology and Infection Prevention, Vancouver Coastal Health and University of British Columbia Faculty of Medicine, Vancouver, British Columbia, Canada
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36
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Gyssens IC. Animal models for research in human infectious diseases. CMI editorial policy. Clin Microbiol Infect 2019; 25:649-650. [PMID: 30986559 DOI: 10.1016/j.cmi.2019.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- I C Gyssens
- Department of Internal Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands; Faculty of Medicine, Research Group of Immunology and Biochemistry, Hasselt University, Hasselt, Belgium; CMI Editorial Office, UK.
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