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Romero-Rodríguez A, Ruíz-Villafán B, Sánchez S, Paredes-Sabja D. Is there a role for intestinal sporobiota in the antimicrobial resistance crisis? Microbiol Res 2024; 288:127870. [PMID: 39173554 DOI: 10.1016/j.micres.2024.127870] [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: 06/04/2024] [Revised: 07/23/2024] [Accepted: 08/06/2024] [Indexed: 08/24/2024]
Abstract
Antimicrobial resistance (AMR) is a complex issue requiring specific, multi-sectoral measures to slow its spread. When people are exposed to antimicrobial agents, it can cause resistant bacteria to increase. This means that the use, misuse, and excessive use of antimicrobial agents exert selective pressure on bacteria, which can lead to the development of "silent" reservoirs of antimicrobial resistance genes. These genes can later be mobilized into pathogenic bacteria and contribute to the spread of AMR. Many socioeconomic and environmental factors influence the transmission and dissemination of resistance genes, such as the quality of healthcare systems, water sanitation, hygiene infrastructure, and pollution. The sporobiota is an essential part of the gut microbiota that plays a role in maintaining gut homeostasis. However, because spores are highly transmissible and can spread easily, they can be a vector for AMR. The sporobiota resistome, particularly the mobile resistome, is important for tracking, managing, and limiting the spread of antimicrobial resistance genes among pathogenic and commensal bacterial species.
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Affiliation(s)
- A Romero-Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Ciudad de México 04510, Mexico.
| | - B Ruíz-Villafán
- Laboratorio de Microbiología Industrial. Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - S Sánchez
- Laboratorio de Microbiología Industrial. Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - D Paredes-Sabja
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
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2
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Taiwo G, Morenikeji OB, Idowu M, Sidney T, Adekunle A, Cervantes AP, Peters S, Ogunade IM. Characterization of rumen microbiome and immune genes expression of crossbred beef steers with divergent residual feed intake phenotypes. BMC Genomics 2024; 25:245. [PMID: 38443809 PMCID: PMC10913640 DOI: 10.1186/s12864-024-10150-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
We investigated whole blood and hepatic mRNA expressions of immune genes and rumen microbiome of crossbred beef steers with divergent residual feed intake phenotype to identify relevant biological processes underpinning feed efficiency in beef cattle. Low-RFI beef steers (n = 20; RFI = - 1.83 kg/d) and high-RFI beef steers (n = 20; RFI = + 2.12 kg/d) were identified from a group of 108 growing crossbred beef steers (average BW = 282 ± 30.4 kg) fed a high-forage total mixed ration after a 70-d performance testing period. At the end of the 70-d testing period, liver biopsies and blood samples were collected for total RNA extraction and cDNA synthesis. Rumen fluid samples were also collected for analysis of the rumen microbial community. The mRNA expression of 84 genes related to innate and adaptive immunity was analyzed using pathway-focused PCR-based arrays. Differentially expressed genes were determined using P-value ≤ 0.05 and fold change (FC) ≥ 1.5 (in whole blood) or ≥ 2.0 (in the liver). Gene ontology analysis of the differentially expressed genes revealed that pathways related to pattern recognition receptor activity, positive regulation of phagocytosis, positive regulation of vitamin metabolic process, vascular endothelial growth factor production, positive regulation of epithelial tube formation and T-helper cell differentiation were significantly enriched (FDR < 0.05) in low-RFI steers. In the rumen, the relative abundance of PeH15, Arthrobacter, Moryella, Weissella, and Muribaculaceae was enriched in low-RFI steers, while Methanobrevibacter, Bacteroidales_BS11_gut_group, Bacteroides and Clostridium_sensu_stricto_1 were reduced. In conclusion, our study found that low-RFI beef steers exhibit increased mRNA expression of genes related to immune cell functions in whole blood and liver tissues, specifically those involved in pathogen recognition and phagocytosis regulation. Additionally, these low-RFI steers showed differences in the relative abundance of some microbial taxa which may partially account for their improved feed efficiency compared to high-RFI steers.
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Affiliation(s)
- Godstime Taiwo
- Division of Animal and Nutritional Science, West Virginia University, 26505, Morgantown, WV, USA
| | - Olanrewaju B Morenikeji
- Division of Biological and Health Sciences, University of Pittsburgh at Bradford, 300 Campus Drive, 16701, Bradford, PA, USA.
| | - Modoluwamu Idowu
- Division of Animal and Nutritional Science, West Virginia University, 26505, Morgantown, WV, USA
| | - Taylor Sidney
- Division of Animal and Nutritional Science, West Virginia University, 26505, Morgantown, WV, USA
| | - Ajiboye Adekunle
- Division of Animal and Nutritional Science, West Virginia University, 26505, Morgantown, WV, USA
| | | | - Sunday Peters
- Department of Animal Science, Berry College, Mount Berry, GA, USA
| | - Ibukun M Ogunade
- Division of Animal and Nutritional Science, West Virginia University, 26505, Morgantown, WV, USA.
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3
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Erdenebileg S, Son YJ, Kim M, Oidovsambuu S, Cha KH, Kwon J, Jung DS, Nho CW. Saposhnikovia divaricata root and its major components ameliorate inflammation and altered gut microbial diversity and compositions in DSS-induced colitis. Integr Med Res 2023; 12:100998. [PMID: 38024289 PMCID: PMC10630121 DOI: 10.1016/j.imr.2023.100998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Background The root of Saposhnikovia divaricata (Turcz.) Schischk is a well-known traditional medicinal plant, containing various bioactive compounds with anti-inflammatory, antioxidant, and analgesic properties. However, no scientific studies have validated its clinical use as an anti-inflammatory agent against inflammatory bowel disease (IBD). This study aimed to investigate whether the root extract of S. divaricata ameliorates IBD and induces gut microbial alteration, using a RAW 264.7 cell line and a DSS-induced colitis mouse model. Methods To investigate the anti-inflammatory effects and alleviation of IBD, using a methanol extract of Saposhnikovia divaricata (Turcz.) Schischk. root (MESD), RAW 264.7, murine macrophages and a dextran sodium sulfate (DSS)-induced colitis mouse model were employed. 16S rRNA gene sequencing was conducted to determine the alterations in the gut microbiota of mice with DSS-induced colitis. Results MESD significantly decreased nitric oxide (NO) and inflammatory cytokine levels in lipopolysaccharide (LPS)-induced RAW 264.7 cells in vitro. Oral administration of MESD reduced the expression of inflammatory cytokines in the colons of mice with DSS-induced colitis. Additionally, MESD inhibited the abundance of Clostridium sensu stricto 1 and enhanced the predicted functional pathways, including l-glutamate degradation VIII (to propanoic acid). Seven compounds with anti-inflammatory properties were isolated from the MESD. Among them, 3'-O-acetylhamaudol and 3'-O-angeloylhamaudol exhibited strong anti-inflammatory effects in vitro. Conclusion Overall, MESD may be a potential natural product for the treatment of IBD by lowering inflammatory cytokine levels and altering gut microbiota composition.
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Affiliation(s)
- Saruul Erdenebileg
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung, South Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology (UST), Daejeon, South Korea
| | - Yang-Ju Son
- Department of Food and Nutrition, Chung-Ang University, Anseong, South Korea
| | - Myungsuk Kim
- Natural Product Research Center, Korea Institute of Science and Technology (KIST), Gangneung, South Korea
| | - Sarangerel Oidovsambuu
- Natural Product Chemistry Laboratory, Institute of Chemistry and Chemical Technology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia
| | - Kwang Hyun Cha
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST), Gangneung, South Korea
| | - Jaeyoung Kwon
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST), Gangneung, South Korea
| | - Da Seul Jung
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung, South Korea
| | - Chu Won Nho
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung, South Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology (UST), Daejeon, South Korea
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Choi S, Kim EB. A comprehensive longitudinal study of gut microbiota dynamic changes in laying hens at four growth stages prior to egg production. Anim Biosci 2023; 36:1727-1737. [PMID: 37871901 PMCID: PMC10623045 DOI: 10.5713/ab.23.0271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/14/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023] Open
Abstract
OBJECTIVE The poultry industry is a primary source of animal protein worldwide. The gut microbiota of poultry birds, such as chickens and ducks, is critical in maintaining their health, growth, and productivity. This study aimed to identify longitudinal changes in the gut microbiota of laying hens from birth to the pre-laying stage. METHODS From a total of 80 Hy-Line Brown laying hens, birds were selected based on weight at equal intervals to collect feces (n = 20 per growth) and ileal contents (n = 10 per growth) for each growth stage (days 10, 21, 58, and 101). The V4 regions of the 16S rRNA gene were amplified after extracting DNA from feces and ileal contents. Amplicon sequencing was performed using Illumina, followed by analysis. RESULTS Microbial diversity increased with growth stages, regardless of sampling sites. Microbial community analysis indicated that Firmicutes, Proteobacteria, and Bacteroidetes were the dominant phyla in the feces and ileal. The abundance of Lactobacillus was highest on day 10, and that of Escherichia-shigella was higher on day 21 than those at the other stages at the genus level (for the feces and ileal contents; p<0.05). Furthermore, Turicibacter was the most abundant genus after changing feed (for the feces and ileal contents; p<0.05). The fecal Ruminococcus torques and ileal Lysinibacillus were negatively correlated with the body weights of chickens (p<0.05). CONCLUSION The gut microbiota of laying hens changes during the four growth stages, and interactions between microbiota and feed may be present. Our findings provide valuable data for understanding the gut microbiota of laying hens at various growth stages and future applied studies.
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Affiliation(s)
- Seojin Choi
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, 24341,
Korea
| | - Eun Bae Kim
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, 24341,
Korea
- Institute of Animal Life Science, Kangwon National University, Chuncheon, 24341,
Korea
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5
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Herrera G, Vega L, Camargo A, Patarroyo MA, Ramírez JD, Muñoz M. Acquisition site-based remodelling of Clostridium perfringens- and Clostridioides difficile-related gut microbiota. Comp Immunol Microbiol Infect Dis 2023; 102:102074. [PMID: 37832162 DOI: 10.1016/j.cimid.2023.102074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/21/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023]
Abstract
INTRODUCTION Clostridium perfringens is a gram-positive, anaerobic sporulating bacillus which can infect several hosts, thereby being considered the causative agent of many gut illnesses. Some studies have suggested that C. perfringens's virulence factors may negatively affect gut microbiota homeostasis by decreasing beneficial bacteria; however, studies have failed to evaluate the simultaneous presence of other pathogenic bacteria, such as C. difficile (another sporulating bacillus known to play a role in gut microbiota imbalance). Conscious of the lack of compelling data, this work has ascertained how such microorganisms' coexistence can be associated with a variation in gut microbiota composition, compared to that of C. perfringens colonisation. METHODS PCR was thus used for identifying C. perfringens and C. difficile in 98 samples. Amplicon-based sequencing of 16S- and 18S-rRNA genes' V4 hypervariable region from such samples was used for determining the microbiota's taxonomical composition and diversity. RESULTS Small differences were observed in bacterial communities' taxonomic composition and diversity; such imbalance was mainly associated with groups having hospital-acquired diarrhoea. CONCLUSION The alterations reported herein may have been influenced by C. difficile and diarrhoea acquisition site, despite C. perfringens' ability to cause alterations in microbiota due to its virulence factors. Our findings highlight the need for a holistic view of gut microbiota.
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Affiliation(s)
- Giovanny Herrera
- Centro de Investigaciones en Microbiología y Biotecnología -UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia
| | - Laura Vega
- Centro de Investigaciones en Microbiología y Biotecnología -UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia
| | - Anny Camargo
- Centro de Investigaciones en Microbiología y Biotecnología -UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; Health Sciences Faculty, Universidad de Boyacá, Tunja, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá D.C. 111321, Colombia; Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá D.C. 111321, Colombia; Health Sciences Division, Main Campus, Universidad Santo Tomás, Bogotá D.C. 110231, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología -UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología -UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia.
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Kiu R, Shaw AG, Sim K, Acuna-Gonzalez A, Price CA, Bedwell H, Dreger SA, Fowler WJ, Cornwell E, Pickard D, Belteki G, Malsom J, Phillips S, Young GR, Schofield Z, Alcon-Giner C, Berrington JE, Stewart CJ, Dougan G, Clarke P, Douce G, Robinson SD, Kroll JS, Hall LJ. Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains. Nat Microbiol 2023; 8:1160-1175. [PMID: 37231089 PMCID: PMC10234813 DOI: 10.1038/s41564-023-01385-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 04/17/2023] [Indexed: 05/27/2023]
Abstract
Clostridium perfringens is an anaerobic toxin-producing bacterium associated with intestinal diseases, particularly in neonatal humans and animals. Infant gut microbiome studies have recently indicated a link between C. perfringens and the preterm infant disease necrotizing enterocolitis (NEC), with specific NEC cases associated with overabundant C. perfringens termed C. perfringens-associated NEC (CPA-NEC). In the present study, we carried out whole-genome sequencing of 272 C. perfringens isolates from 70 infants across 5 hospitals in the United Kingdom. In this retrospective analysis, we performed in-depth genomic analyses (virulence profiling, strain tracking and plasmid analysis) and experimentally characterized pathogenic traits of 31 strains, including 4 from CPA-NEC patients. We found that the gene encoding toxin perfringolysin O, pfoA, was largely deficient in a human-derived hypovirulent lineage, as well as certain colonization factors, in contrast to typical pfoA-encoding virulent lineages. We determined that infant-associated pfoA+ strains caused significantly more cellular damage than pfoA- strains in vitro, and further confirmed this virulence trait in vivo using an oral-challenge C57BL/6 murine model. These findings suggest both the importance of pfoA+ C. perfringens as a gut pathogen in preterm infants and areas for further investigation, including potential intervention and therapeutic strategies.
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Affiliation(s)
- Raymond Kiu
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | | | - Kathleen Sim
- Faculty of Medicine, Imperial College London, London, UK
| | | | | | - Harley Bedwell
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Sally A Dreger
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Wesley J Fowler
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Emma Cornwell
- Faculty of Medicine, Imperial College London, London, UK
| | - Derek Pickard
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gusztav Belteki
- Neonatal Intensive Care Unit, The Rosie Hospital, Cambridge, UK
| | - Jennifer Malsom
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Sarah Phillips
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Gregory R Young
- Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle upon Tyne, UK
| | - Zoe Schofield
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | | | - Janet E Berrington
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Newcastle Neonatal Services, Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Newcastle Neonatal Services, Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Paul Clarke
- Norfolk and Norwich University Hospital, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Gillian Douce
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Stephen D Robinson
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - J Simon Kroll
- Faculty of Medicine, Imperial College London, London, UK
| | - Lindsay J Hall
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK.
- Norwich Medical School, University of East Anglia, Norwich, UK.
- Intestinal Microbiome, School of Life Sciences, ZIEL-Institute for Food & Health, Technical University of Munich, Freising, Germany.
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7
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Kusumawaty D, Augustine SMN, Aryani A, Effendi Y, Emran TB, Tallei TE. Configuration of gut bacterial community profile and their potential functionality in the digestive tract of the wild and cultivated Indonesian shortfin elver-phase eels ( Anguilla bicolor bicolor McClelland, 1844). 3 Biotech 2023; 13:153. [PMID: 37131968 PMCID: PMC10148933 DOI: 10.1007/s13205-023-03561-8] [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: 06/21/2022] [Accepted: 04/15/2023] [Indexed: 05/04/2023] Open
Abstract
This study aimed to explore the bacteria present in the digestive tracts of wild and cultivated Indonesian shortfin eel during the elver phase. The eel has high export potential due to its vitamin and micronutrient content, but slow growth and vulnerability to collapse in farm conditions hinder its cultivation. The microbiota in the eel's digestive tract is crucial for its health, particularly during the elver phase. This study used Next Generation Sequencing to analyze the community structure and diversity of bacteria in the eels' digestive tracts, focusing on the V3-V4 regions of the 16S rRNA gene. Mothur software was used for data analysis and PAST v.3.26 was used to calculate alpha diversity. The results showed that Proteobacteria (64.18%) and Firmicutes (33.55%) were the predominant phyla in the digestive tract of cultivated eels, while Bacteroidetes (54.16%), Firmicutes (14.71%), and Fusobacteria (10.56%) were predominant in wild eels. The most prevalent genera in cultivated and wild elver were Plesiomonas and Cetobacterium, respectively. The microbiota in the digestive tract of cultivated eels was diverse despite uneven distribution. The KEGG database analysis revealed that the primary function of the microbiome was to facilitate the eel's absorption of nutrients by contributing significantly to the metabolism of carbohydrates and amino acids. This study's findings can aid in assessing eel health and improving eel farming conditions.
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Affiliation(s)
- Diah Kusumawaty
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung, 40154 Indonesia
| | - Stella Melbournita Noor Augustine
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung, 40154 Indonesia
| | - Any Aryani
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung, 40154 Indonesia
| | - Yunus Effendi
- Department of Biology, Faculty of Science and Technology, Al-Azhar Indonesia University, Jakarta, 12110 Indonesia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381 Bangladesh
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, 95115 North Sulawesi Indonesia
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8
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Liu D, Tian Q, Liu K, Ren F, Liu G, Zhou J, Yuan L, Fang Z, Zou B, Wang S. Ginsenoside Rg3 Ameliorates DSS-Induced Colitis by Inhibiting NLRP3 Inflammasome Activation and Regulating Microbial Homeostasis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:3472-3483. [PMID: 36752740 DOI: 10.1021/acs.jafc.2c07766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Ulcerative colitis (UC) is a recurrent inflammatory disease without a specific cure or treatment for improvement. Here, we investigated the potential therapeutic effect and mechanism of ginsenoside Rg3 (Gin Rg3) on UC. We constructed an in vitro cellular inflammatory model and a dextran sulfate sodium (DSS)-induced UC mouse model. We also used Gin Rg3, MCC950 (NLRP3 inhibitor), MSU (NLRP3 activator), and fecal transplantation (FMT) to intervene the model. The results showed that Gin Rg3 inhibited NLRP3 inflammasome activation, pyroptosis, and apoptosis in vitro and in vivo. DSS-induced changes in the abundance of gut microbiota at the phylum or genus level were partially restored by Gin Rg3. Furthermore, gin Rg3 affected intestinal metabolism in mice by inhibiting the activation of NLRP3 inflammasome. The gut microbiota treated with Gin Rg3 was sufficient to alleviate DSS-induced UC. In summary, Gin Rg3 alleviated DSS-induced UC by inhibiting NLRP3 inflammasome activation and regulating gut microbiota homeostasis.
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Affiliation(s)
- Dongcai Liu
- General Surgery Department, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Qingquan Tian
- General Surgery Department FIVE, People's Hospital of Xiangxi Tujia and Miao Autonomous Prefecture, Jishou, Hunan 416000, China
| | - Kuijie Liu
- General Surgery Department, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Feng Ren
- General Surgery Department, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Ganglei Liu
- General Surgery Department, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Jingyu Zhou
- General Surgery Department, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Lianwen Yuan
- General Surgery Department, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Zhixue Fang
- Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410000, China
| | - Bing Zou
- General Surgery Department, Changsha Central Hospital, Nanhua University, Changsha, Hunan 410000, China
| | - Shalong Wang
- General Surgery Department, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
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9
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Wang X, Qu Y, Wang Y, Wang X, Xu J, Zhao H, Zheng D, Sun L, Tai G, Zhou Y, Cheng H. β-1,6-Glucan From Pleurotus eryngii Modulates the Immunity and Gut Microbiota. Front Immunol 2022; 13:859923. [PMID: 35585984 PMCID: PMC9108243 DOI: 10.3389/fimmu.2022.859923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/04/2022] [Indexed: 01/22/2023] Open
Abstract
Polysaccharides from Pleurotus eryngii exhibit a variety of biological activities. Here, we obtained a homogeneous branched β-1,6-glucan (APEP-A-b) from the fruiting bodies of P. eryngii and investigated its effect on immunity and gut microbiota. Our results showed that APEP-A-b significantly increases splenic lymphocyte proliferation, NK cell activity and phagocytic capacity of peritoneal cavity phagocytes. Furthermore, we found that the proportion of CD4+ and CD8+ T cells in lamina propria are significantly increased upon APEP-A-b treatment. Additionally, APEP-A-b supplementation demonstrated pronounced changes in microbiota reflected in promotion of relative abundances of species in the Lachnospiraceae and Rikenellaceae families. Consistently, APEP-A-b significantly increased the concentration of acetic and butyric acid in cecum contents. Overall, our results suggest that β-1,6-glucan from P. eryngii might enhance immunity by modulating microbiota. These results are important for the processing and product development of P. eryngii derived polysaccharides.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yifa Zhou
- *Correspondence: Yifa Zhou, ; Hairong Cheng,
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10
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Ahmed HA, El Bayomi RM, Hamed RI, Mohsen RA, El-Gohary FA, Hefny AA, Elkhawaga E, Tolba HMN. Genetic Relatedness, Antibiotic Resistance, and Effect of Silver Nanoparticle on Biofilm Formation by Clostridium perfringens Isolated from Chickens, Pigeons, Camels, and Human Consumers. Vet Sci 2022; 9:vetsci9030109. [PMID: 35324837 PMCID: PMC8949260 DOI: 10.3390/vetsci9030109] [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: 01/29/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 11/16/2022] Open
Abstract
In this study, we determined the prevalence and toxin types of antibiotic-resistant Clostridium perfringens in chicken, pigeons, camels, and humans. We investigated the inhibitory effects of AgNPs on biofilm formation ability of the isolates and the genetic relatedness of the isolates from various sources determined using RAPD-PCR. Fifty isolates were identified using PCR, and all the isolates were of type A. The cpe and cpb2 genes were detected in 12% and 56% of the isolates, respectively. The effect of AgNPs on biofilm production of six representative isolates indicated that at the highest concentration of AgNPs (100 µg/mL), the inhibition percentages were 80.8–82.8%. The RAPD-PCR patterns of the 50 C. perfringens isolates from various sources revealed 33 profiles and four clusters, and the discriminatory power of RAPD-PCR was high. Multidrug-resistant C. perfringens isolates are predominant in the study area. The inhibition of biofilm formation by C. perfringens isolates was dose-dependent, and RAPD-PCR is a promising method for studying the genetic relatedness between the isolates from various sources. This is the first report of AgNPs’ anti-biofilm activity against C. perfringens from chickens, pigeons, camels, and humans, to the best of our knowledge.
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Affiliation(s)
- Heba A. Ahmed
- Department of Zoonoses, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt
- Correspondence:
| | - Rasha M. El Bayomi
- Department of Food Control, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt;
| | - Rehab I. Hamed
- Reference Laboratory for Quality Control on Poultry Production, Department of Poultry Diseases, Animal Health Research Institute, Zagazig Branch, Agriculture Research Center (ARC), Zagazig 44516, Egypt;
| | - Rasha A. Mohsen
- Department of Bacteriology, Animal Health Research Institute, Mansoura Branch, Agriculture Research Center (ARC), Mansoura 12618, Egypt;
| | - Fatma A. El-Gohary
- Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt;
| | - Ahmed A. Hefny
- Veterinary Hospital, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt;
| | - Eman Elkhawaga
- Department of Food Hygiene, Animal Health Research Institute, Mansoura Branch, Agriculture Research Center (ARC), Mansoura 12618, Egypt;
| | - Hala M. N. Tolba
- Department of Avian and Rabbit Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt;
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11
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Simas AM, Kramer CD, Genco CA. Diet-Induced Non-alcoholic Fatty Liver Disease and Associated Gut Dysbiosis Are Exacerbated by Oral Infection. FRONTIERS IN ORAL HEALTH 2022; 2:784448. [PMID: 35141703 PMCID: PMC8820505 DOI: 10.3389/froh.2021.784448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/29/2021] [Indexed: 11/13/2022] Open
Abstract
Increasing evidence indicates that chronic inflammation due to periodontal disease is associated with progression of non-alcoholic fatty liver disease (NAFLD) caused by a Western diet. NAFLD has also been associated with oral infection with the etiological agent of periodontal disease, Porphyromonas gingivalis. P. gingivalis oral infection has been shown to induce cardiometabolic disease features including hepatic lipid accumulation while also leading to dysbiosis of the gut microbiome. However, the impact of P. gingivalis infection on the gut microbiota of mice with diet-induced NAFLD and the potential for those changes to mediate NAFLD progression has yet to be determined. In the current study, we have demonstrated that P. gingivalis infection induced sustained alterations of the gut microbiota composition and predicted functions, which was associated with the promotion of NAFLD in steatotic mice. Reduced abundance of short-chain fatty acid-producing microbiota was observed after both acute and chronic P. gingivalis infection. Collectively, our findings demonstrate that P. gingivalis infection produces a persistent change in the gut microbiota composition and predicted functions that promotes steatosis and metabolic disease.
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Affiliation(s)
- Alexandra M. Simas
- Gerald J. and Dorothy R. Friedman School of Nutrition and Science Policy, Graduate Program in Biochemical and Molecular Nutrition, Tufts University, Boston, MA, United States
- Department of Immunology, Tufts University School of Medicine, Boston, MA, United States
| | - Carolyn D. Kramer
- Department of Immunology, Tufts University School of Medicine, Boston, MA, United States
| | - Caroline A. Genco
- Department of Immunology, Tufts University School of Medicine, Boston, MA, United States
- Graduate Program in Immunology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, United States
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, United States
- *Correspondence: Caroline A. Genco
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12
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Dong L, Ariëns RM, America AH, Paul A, Veldkamp T, Mes JJ, Wichers HJ, Govers C. Clostridium perfringens suppressing activity in black soldier fly protein preparations. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111806] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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13
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Ma E, Maskarinec G, Lim U, Boushey CJ, Wilkens LR, Setiawan VW, Le Marchand L, Randolph TW, Jenkins IC, Curtis KR, Lampe JW, Hullar MA. Long-term association between diet quality and characteristics of the gut microbiome in the multiethnic cohort study. Br J Nutr 2021; 128:1-10. [PMID: 34369335 PMCID: PMC8825880 DOI: 10.1017/s0007114521002968] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
As past usual diet quality may affect gut microbiome (GM) composition, we examined the association of the Healthy Eating Index (HEI)-2015 assessed 21 and 9 years before stool collection with measures of fecal microbial composition in a subset of the Multiethnic Cohort. A total of 5936 participants completed a validated quantitative FFQ (QFFQ) at cohort entry (Q1, 1993-1996), 5280 at follow-up (Q3, 2003-2008) and 1685 also at a second follow-up (Adiposity Phenotype Study (APS), 2013-2016). All participants provided a stool sample in 2013-2016. Fecal microbial composition was obtained from 16S rRNA gene sequencing (V1-V3 regions). HEI-2015 scores were computed based on each QFFQ. Using linear regression adjusted for relevant covariates, we calculated associations of HEI-2015 scores with gut microbial diversity and 152 individual genera. The mean HEI-2015 scores increased from Q1 (67 (sd 10)) to Q3 (71 (sd 11)) and APS (72 (sd 10)). Alpha diversity assessed by the Shannon Index was significantly higher with increasing tertiles of HEI-2015. Of the 152 bacterial genera tested, seven (Anaerostipes, Coprococcus_2, Eubacterium eligens, Lachnospira, Lachnospiraceae_ND3007, Ruminococcaceae_UCG-013 and Ruminococcus_1) were positively and five (Collinsella, Parabacteroides, Ruminiclostridium_5, Ruminococcus gnavus and Tyzzerella) were inversely associated with HEI-2015 assessed in Q1, Q3 and APS. The estimates of change per unit of the HEI-2015 score associated with the abundance of these twelve genera were consistent across the three questionnaires. The quality of past diet, assessed as far as ∼20 years before stool collection, is equally predictive of GM composition as concurrently assessed diet, indicative of the long-term consistency of this relation.
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Affiliation(s)
- Erica Ma
- University of Hawai’i Cancer Center, Honolulu, HI
| | | | - Unhee Lim
- University of Hawai’i Cancer Center, Honolulu, HI
| | | | | | - V. Wendy Setiawan
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA
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14
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Egan M, Dempsey E, Ryan CA, Ross RP, Stanton C. The Sporobiota of the Human Gut. Gut Microbes 2021; 13:1-17. [PMID: 33406976 PMCID: PMC7801112 DOI: 10.1080/19490976.2020.1863134] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 02/04/2023] Open
Abstract
The human gut microbiome is a diverse and complex ecosystem that plays a critical role in health and disease. The composition of the gut microbiome has been well studied across all stages of life. In recent years, studies have investigated the production of endospores by specific members of the gut microbiome. An endospore is a tough, dormant structure formed by members of the Firmicutes phylum, which allows for greater resistance to otherwise inhospitable conditions. This innate resistance has consequences for human health and disease, as well as in biotechnology. In particular, the formation of endospores is strongly linked to antibiotic resistance and the spread of antibiotic resistance genes, also known as the resistome. The term sporobiota has been used to define the spore-forming cohort of a microbial community. In this review, we present an overview of the current knowledge of the sporobiota in the human gut. We discuss the development of the sporobiota in the infant gut and the perinatal factors that may have an effect on vertical transmission from mother to infant. Finally, we examine the sporobiota of critically important food sources for the developing infant, breast milk and powdered infant formula.
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Affiliation(s)
- Muireann Egan
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Eugene Dempsey
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland
| | - C. Anthony Ryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland
| | - R. Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Catherine Stanton
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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15
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Koo BS, Hwang EH, Kim G, Park JY, Oh H, Lim KS, Kang P, Lee HY, Jeong KJ, Mo I, Villinger F, Hong JJ. Prevalence and characterization of Clostridium perfringens isolated from feces of captive cynomolgus monkeys (Macaca fascicularis). Anaerobe 2020; 64:102236. [PMID: 32623046 DOI: 10.1016/j.anaerobe.2020.102236] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 01/13/2023]
Abstract
Clostridium perfringens is ubiquitous in the environment and the gastrointestinal tract of warm-blooded animals. While part of the gut microbiome, abnormal growth of C. perfringens causes histotoxic, neurologic, and enteric diseases in a variety of animal species, including humans, due to the production of toxins. There is extremely limited information on C. perfringens infection in non-human primates. Presently, 10 strains were successfully isolated from 126 monkeys and confirmed by molecular and biochemical analyses. All isolates were genotype A based on molecular analysis. Alpha toxin was identified in all isolates. Beta 2 toxin was detected in only three isolates. No other toxins, including enterotoxin, beta, iota, epsilon, and net B toxin, were identified in any isolate. All isolates were highly susceptible to β-lactam antibiotics. Double hemolysis and lecithinase activity were commonly observed in all strains. Biofilm formation, which can increase antibiotic resistance, was identified in 90% of the isolates. The data are the first report the prevalence and characteristics of C. perfringens isolated from captive cynomolgus monkeys.
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Affiliation(s)
- Bon-Sang Koo
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea
| | - Eun-Ha Hwang
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea
| | - Green Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea
| | - Joon-Young Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea
| | - Hanseul Oh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea
| | - Kyung Seob Lim
- Futuristic Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea
| | - Philyong Kang
- Futuristic Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea
| | - Hwal-Yong Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea
| | - Kang-Jin Jeong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea
| | - Inpil Mo
- College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Francois Villinger
- New Iberia Research Center, University of Louisiana Lafayette, Lafayette, LA, 70560, USA
| | - Jung Joo Hong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea.
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16
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Parajuli A, Hui N, Puhakka R, Oikarinen S, Grönroos M, Selonen VAO, Siter N, Kramna L, Roslund MI, Vari HK, Nurminen N, Honkanen H, Hintikka J, Sarkkinen H, Romantschuk M, Kauppi M, Valve R, Cinek O, Laitinen OH, Rajaniemi J, Hyöty H, Sinkkonen A. Yard vegetation is associated with gut microbiota composition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 713:136707. [PMID: 32019041 DOI: 10.1016/j.scitotenv.2020.136707] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 06/10/2023]
Abstract
Gut microbes play an essential role in the development and functioning of the human immune system. A disturbed gut microbiota composition is often associated with a number of health disorders including immune-mediated diseases. Differences in host characteristics such as ethnicity, living habit and diet have been used to explain differences in the gut microbiota composition in inter-continental comparison studies. As our previous studies imply that daily skin contact with organic gardening materials modify gut microflora, here we investigated the association between living environment and gut microbiota in a homogenous western population along an urban-rural gradient. We obtained stool samples from 48 native elderly Finns in province Häme in August and November 2015 and identified the bacterial phylotypes using 16S rRNA Illumina MiSeq sequencing. We assumed that yard vegetation and land cover classes surrounding homes explain the stool bacterial community in generalized linear mixed models. Diverse yard vegetation was associated with a reduced abundance of Clostridium sensu stricto and an increased abundance of Faecalibacterium and Prevotellaceae. The abundance of Bacteroides was positively and strongly associated with the built environment. Exclusion of animal owners did not alter the main associations. These results suggest that diverse vegetation around homes is associated with health-related changes in gut microbiota composition. Manipulation of the garden diversity, possibly jointly with urban planning, is a promising candidate for future intervention studies that aim to maintain gut homeostasis.
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Affiliation(s)
- Anirudra Parajuli
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Nan Hui
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland; School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Riikka Puhakka
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Sami Oikarinen
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Mira Grönroos
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Ville A O Selonen
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Nathan Siter
- School of Architecture, Tampere University of Technology, Tampere, Finland
| | - Lenka Kramna
- Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Marja I Roslund
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Heli K Vari
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Noora Nurminen
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Hanna Honkanen
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | | | | | - Martin Romantschuk
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | | | - Raisa Valve
- Division of Food and Nutrition Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Ondřej Cinek
- Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Olli H Laitinen
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Juho Rajaniemi
- School of Architecture, Tampere University of Technology, Tampere, Finland
| | - Heikki Hyöty
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Aki Sinkkonen
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland; Natural Resources Institute Finland, Turku, Finland.
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17
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Shaw AG, Cornwell E, Sim K, Thrower H, Scott H, Brown JCS, Dixon RA, Kroll JS. Dynamics of toxigenic Clostridium perfringens colonisation in a cohort of prematurely born neonatal infants. BMC Pediatr 2020; 20:75. [PMID: 32070310 PMCID: PMC7027286 DOI: 10.1186/s12887-020-1976-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 02/12/2020] [Indexed: 01/15/2023] Open
Abstract
Background Clostridium perfringens forms part of the human gut microbiota and has been associated with life-threatening necrotising enterocolitis (NEC) in premature infants. Whether specific toxigenic strains are responsible is unknown, as is the extent of diversity of strains in healthy premature babies. We investigated the C. perfringens carrier status of premature infants in the neonatal intensive care unit, factors influence this status, and the toxic potential of the strains. Methods C. perfringens was isolated by culture from faecal samples from 333 infants and their toxin gene profiles analysed by PCR. A survival analysis was used to identify factors affecting probability of carriage. Competitive growth experiments were used to explore the results of the survival analysis. Results 29.4% of infants were colonized with C. perfringens before they left hospital. Three factors were inversely associated with probability of carriage: increased duration of maternal milk feeds, CPAP oxygen treatment and antibiotic treatment. C. perfringens grew poorly in breast milk and was significantly outperformed by Bifidobacterium infantis, whether grown together or separately. Toxin gene screening revealed that infants carried isolates positive for collagenase, perfringolysin O, beta 2, beta, becA/B, netB and enterotoxin toxin genes, yet none were observed to be associated with the development of NEC. Conclusions Approximately a third of preterm infants are colonised 3 weeks after birth with toxin gene-carrying C. perfringens. We speculate that increased maternal breast milk, oxygen and antibiotic treatment creates an environment in the gut hostile to growth of C. perfringens. Whilst potentially toxigenic C. perfringens isolates were frequent, no toxin type was associated with NEC. Trial registration clinicaltrials.govNCT01102738, registered 13th April 2010.
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Affiliation(s)
- Alexander G Shaw
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
| | - Emma Cornwell
- Department of Medicine, Section of Paediatrics, Imperial College London, London, UK
| | - Kathleen Sim
- Department of Medicine, Section of Paediatrics, Imperial College London, London, UK
| | - Hannah Thrower
- Department of Medicine, Section of Paediatrics, Imperial College London, London, UK
| | - Hannah Scott
- Department of Medicine, Section of Paediatrics, Imperial College London, London, UK
| | | | - Ronald A Dixon
- School of Life Sciences, University of Lincoln, Lincoln, UK
| | - J Simon Kroll
- Department of Medicine, Section of Paediatrics, Imperial College London, London, UK
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18
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Kiu R, Caim S, Painset A, Pickard D, Swift C, Dougan G, Mather AE, Amar C, Hall LJ. Phylogenomic analysis of gastroenteritis-associated Clostridium perfringens in England and Wales over a 7-year period indicates distribution of clonal toxigenic strains in multiple outbreaks and extensive involvement of enterotoxin-encoding (CPE) plasmids. Microb Genom 2019; 5. [PMID: 31553300 PMCID: PMC6861862 DOI: 10.1099/mgen.0.000297] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Clostridium perfringens is a major enteric pathogen known to cause gastroenteritis in human adults. Although major outbreak cases are frequently reported, only limited whole-genome sequencing (WGS) based studies have been performed to understand the genomic epidemiology and virulence gene content of outbreak-associated C. perfringens strains. We performed phylogenomic analysis on 109 C. perfringens isolates (human and food) obtained from disease cases in England and Wales between 2011 and 2017. Initial findings highlighted the enhanced discriminatory power of WGS in profiling outbreak C. perfringens strains, when compared to the current Public Health England referencing laboratory technique of fluorescent amplified fragment length polymorphism analysis. Further analysis identified that isogenic C. perfringens strains were associated with nine distinct care-home-associated outbreaks over the course of a 5-year interval, indicating a potential common source linked to these outbreaks or transmission over time and space. As expected, the enterotoxin cpe gene was encoded in all but 4 isolates (96.3 %; 105/109), with virulence plasmids encoding cpe (particularly pCPF5603 and pCPF4969 plasmids) extensively distributed (82.6 %; 90/109). Genes encoding accessory virulence factors, such as beta-2 toxin, were commonly detected (46.7 %; 51/109), and genes encoding phage proteins were also frequently identified. Overall, this large-scale genomic study of gastroenteritis-associated C. perfringens suggested that three major cpe-encoding (toxinotype F) genotypes underlie these outbreaks: strains carrying (1) pCPF5603 plasmid, (2) pCPF4969 plasmid and (3) chromosomal-cpe strains. Our findings substantially expanded our knowledge on type F C. perfringens involved in human-associated gastroenteritis, with further studies required to fully probe the dissemination and regional reservoirs of this enteric pathogen, which may help devise effective prevention strategies to reduce the food-poisoning disease burden in vulnerable patients, such as the elderly.
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Affiliation(s)
- Raymond Kiu
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich NR4 7UQ, UK
| | - Shabhonam Caim
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich NR4 7UQ, UK
| | - Anais Painset
- Gastrointestinal Bacteria Reference Unit, Public Health England, London NW9 5EQ, UK
| | - Derek Pickard
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Craig Swift
- Gastrointestinal Bacteria Reference Unit, Public Health England, London NW9 5EQ, UK
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Alison E Mather
- Faculty of Medicine and Health Sciences, University of East Anglia, Norwich NR4 7TJ, UK.,Microbes in the Food Chain, Quadram Institute Bioscience, Norwich NR4 7UQ, UK
| | - Corinne Amar
- Gastrointestinal Bacteria Reference Unit, Public Health England, London NW9 5EQ, UK
| | - Lindsay J Hall
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich NR4 7UQ, UK
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19
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Characterization of Proximal Small Intestinal Microbiota in Patients With Suspected Small Intestinal Bacterial Overgrowth: A Cross-Sectional Study. Clin Transl Gastroenterol 2019; 10:e00073. [PMID: 31464691 PMCID: PMC6736222 DOI: 10.14309/ctg.0000000000000073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES The composition of the small intestinal microbiota has not yet been characterized thoroughly using culture-independent techniques. We compared small intestinal microbial communities in patients with and without small intestinal bacterial overgrowth (SIBO) using culture-dependent and culture-independent bacterial identification approaches. METHODS Small bowel aspirate and mucosal samples were collected from patients with suspected SIBO. The aspirates were cultured to diagnose SIBO, defined as ≥10 colony-forming units/mL coliform or ≥10 colony-forming units/mL upper aerodigestive tract bacteria. Bacteria in the aspirates and mucosa were identified using 16S rRNA gene sequencing. We compared small intestinal microbiome composition between groups with and without a culture-based SIBO diagnosis. RESULTS Analysis of the aspirate and mucosal microbial communities from 36 patients revealed decreased α-diversity but no differences in β-diversity in patients with SIBO compared with those without SIBO. There were no significant differences in the relative abundance of individual taxa from the aspirates or mucosa after adjustment for false discovery rate between patients with and without SIBO. Subgroup analysis revealed significant differences in mucosal β-diversity between the coliform and upper aerodigestive tract subgroups. Relative abundances of a mucosal Clostridium spp. (P = 0.05) and an aspirate Granulicatella spp. (P = 0.02) were higher in coliform SIBO vs non-SIBO subgroups. The microbial composition and relative abundance of multiple taxa significantly differed in the mucosal and aspirate specimens. DISCUSSION Culture-based results of small bowel aspirates do not correspond to aspirate microbiota composition but may be associated with species richness of the mucosal microbiota.
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20
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Pagliai G, Russo E, Niccolai E, Dinu M, Di Pilato V, Magrini A, Bartolucci G, Baldi S, Menicatti M, Giusti B, Marcucci R, Rossolini GM, Casini A, Sofi F, Amedei A. Influence of a 3-month low-calorie Mediterranean diet compared to the vegetarian diet on human gut microbiota and SCFA: the CARDIVEG Study. Eur J Nutr 2019; 59:2011-2024. [PMID: 31292752 DOI: 10.1007/s00394-019-02050-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/05/2019] [Indexed: 12/27/2022]
Abstract
PURPOSE We evaluated the effect of low-calorie mediterranean (MD) and vegetarian (VD) diets on gut microbiome (GM) composition and short-chain-fatty acids (SCFA) production. METHODS We performed next generation sequencing (NGS) of 16S rRNA and SCFA analysis on fecal samples of 23 overweight omnivores (16 F; 7 M) with low-to-moderate cardiovascular risk. They were randomly assigned to a VD or MD, each lasting 3 months, with a crossover study design. RESULTS Dietary interventions did not produce significant diversity in the GM composition at higher ranks (family and above), neither between nor within MD and VD, but they did it at genus level. MD significantly changed the abundance of Enterorhabdus, Lachnoclostridium and Parabacteroides, while VD significantly affected the abundance of Anaerostipes, Streptococcus, Clostridium sensu stricto, and Odoribacter. Comparison of the mean variation of each SCFA between MD and VD showed an opposite and statistically significant trend for propionic acid (+ 10% vs - 28%, respectively, p = 0.034). In addition, variations of SCFA were negatively correlated with changes of some inflammatory cytokines such as VEGF, MCP-1, IL-17, IP-10 and IL-12, only after MD. Finally, correlation analyses showed a potential relationship-modulated by the two diets-between changes of genera and changes of clinical and biochemical parameters. CONCLUSIONS A short-term dietary intervention with MD or VD does not induce major change in the GM, suggesting that a diet should last longer than 3 months for scratching the microbial resilience. Changes in SCFA production support their role in modulating the inflammatory response, thus mediating the anti-inflammatory and protective properties of MD.
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Affiliation(s)
- Giuditta Pagliai
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Edda Russo
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Elena Niccolai
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Monica Dinu
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Vincenzo Di Pilato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Alessandro Magrini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Gianluca Bartolucci
- Department of Neurosciences, Psychology, Drug Research and Child Health Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Viale Pieraccini 6, 50139, Florence, Italy
| | - Simone Baldi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Marta Menicatti
- Department of Neurosciences, Psychology, Drug Research and Child Health Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Viale Pieraccini 6, 50139, Florence, Italy
| | - Betti Giusti
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Atherothrombotic Diseases Unit, Careggi University Hospital, Florence, Italy
| | - Rossella Marcucci
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Atherothrombotic Diseases Unit, Careggi University Hospital, Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Alessandro Casini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Clinical Nutrition Unit, Careggi University Hospital, Florence, Italy
| | - Francesco Sofi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Clinical Nutrition Unit, Careggi University Hospital, Florence, Italy
- IRCCS Don Carlo Gnocchi Foundation, Florence, Italy
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.
- Department of Biomedicine, Careggi University Hospital, Florence, Italy.
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Yang WY, Lee Y, Lu H, Chou CH, Wang C. Analysis of gut microbiota and the effect of lauric acid against necrotic enteritis in Clostridium perfringens and Eimeria side-by-side challenge model. PLoS One 2019; 14:e0205784. [PMID: 31150394 PMCID: PMC6544216 DOI: 10.1371/journal.pone.0205784] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 05/09/2019] [Indexed: 12/21/2022] Open
Abstract
Gut microbiota has been demonstrated to be involved in intestinal nutrition, defense, and immunity, as well as participating in disease progression. This study was to investigate gut microbiota changes in chickens challenged with netB-positive Clostridium perfringens strain (CP1) and/or the predisposing Eimeria species (Eimeria) and fed diets with fishmeal supplementation. In addition, the effects of lauric acid, a medium-chain fatty acid (MCFA), on necrotic enteritis (NE) reduction and modulation of microbiota were evaluated. The results demonstrated that microbial communities in the jejunum were distinct from those in the cecum, and the microbial community change was more significant in jejunum. Challenge of CP1 in conjunction with Eimeria significantly reduced species diversity in jejunal microbiota, but cecal microbiota remained stable. In the jejunum, CP1 challenge increased the abundance of the genera of Clostridium sensu stricto 1, Escherichia Shigella, and Weissella, but significantly decreased the population of Lactobacillus. Eimeria infection on its own was unable to promote NE, demonstrating decrements of Clostridium sensu stricto 1 and Lactobacillus. Co-infection with CP1 and Eimeria reproduced the majority of NE lesions with significant increment of Clostridium sensu stricto 1 and reduction in Lactobacillus. The advance of changes on these two taxa increased the severity of NE lesions. Further analyses of metagenomeSeq, STAMP, and LEfSe consistently showed significant overgrowth of Clostridium sensu stricto 1 was associated with NE. The supplementation of lauric acid did not reduce NE incidence and severity but decreased the relative abundance of Escherichia Shigella. In conclusion, significant overgrowth of C. perfringens as well as other Clostridium species in Clostridium sensu stricto 1 with the decrement of Lactobacillus in the jejunum is the featured microbiota correlated with NE. Controlling proliferation of Clostridium sensu stricto 1 and manipulation of Lactobacillus in the jejunum should be the strategy to prevent NE.
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Affiliation(s)
- Wen-Yuan Yang
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, United States of America
| | - Yuejia Lee
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, United States of America
| | - Hsinyi Lu
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, United States of America
| | - Chung-Hsi Chou
- Zoonoses Research Center and School of Veterinary Medicine, National Taiwan University, Taipei City, Taiwan
| | - Chinling Wang
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, United States of America
- * E-mail:
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Tsuji H, Matsuda K, Nomoto K. Counting the Countless: Bacterial Quantification by Targeting rRNA Molecules to Explore the Human Gut Microbiota in Health and Disease. Front Microbiol 2018; 9:1417. [PMID: 30008707 PMCID: PMC6033970 DOI: 10.3389/fmicb.2018.01417] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 06/08/2018] [Indexed: 12/12/2022] Open
Abstract
Over the past decade, the advent of next-generation-sequencing tools has revolutionized our approach to understanding the human gut microbiota. However, numerical data on the gut bacterial groups-particularly low-cell-count microbiota, such as indigenous pathobionts, that are otherwise important components of the microbiota-are relatively limited and disparate. As a result, the comprehensive quantitative structure of the human gut microbiota still needs to be fully defined and standardized. With the aim of filling this knowledge gap, we have established a highly sensitive quantitative analytical system that is based on reverse transcription-quantitative PCR and targets microbial rRNA molecules. The system has already been validated in the precise, sensitive, and absolute quantification of more than 70 target bacterial groups belonging to various human gut bacterial clades, including predominant obligate and facultative anaerobes. The system demonstrates sensitivity several hundred times greater than that of other rRNA-gene-targeting methods. It is thus an efficient and valuable tool for exhaustive analysis of gut microbiota over a wide dynamic range. Using this system, we have to date quantified the gut microbiota of about 2,000 healthy Japanese subjects ranging in age from 1 day to over 80 years. By integrating and analyzing this large database, we came across several novel and interesting features of the gut microbiota, which we discuss here. For instance, we demonstrated for the first time that the fecal counts of not only the predominant bacterial groups but also those at lower cell counts conform to a logarithmically normal distribution. In addition, we revealed several interesting quantitative differences in the gut microbiota of people from different age groups and countries and with different diseases. Because of its high analytic sensitivity, the system has also been applied successfully to other body niches, such as in characterizing the vaginal microbiota, detecting septicemia, and monitoring bacterial translocation. Here, we present a quantitative perspective on the human gut microbiota and review some of the novel microbial insights revealed by employing this promising analytical approach.
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Affiliation(s)
- Hirokazu Tsuji
- Basic Research Department, Yakult Central Institute, Tokyo, Japan
| | - Kazunori Matsuda
- Yakult Honsha European Research Center for Microbiology ESV, Gent-Zwijnaarde, Belgium
| | - Koji Nomoto
- Basic Research Department, Yakult Central Institute, Tokyo, Japan
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Chacar S, Itani T, Hajal J, Saliba Y, Louka N, Faivre JF, Maroun R, Fares N. The Impact of Long-Term Intake of Phenolic Compounds-Rich Grape Pomace on Rat Gut Microbiota. J Food Sci 2017; 83:246-251. [PMID: 29227528 DOI: 10.1111/1750-3841.14006] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 10/24/2017] [Accepted: 11/12/2017] [Indexed: 12/22/2022]
Abstract
The aim of this work is to evaluate the impact on the rat microbiota of long-term feeding with phenolic compounds (PC) rich grape pomace extracts. Thirty, 2-mo-old rats, were divided into 5 groups. Four groups were treated with different concentrations of PC (2.5, 5, 10, and 20 mg/kg/d diluted in 0.1% DMSO), and 1 group received 0.1% Dimethyl Sulfoxide (DMSO) alone (control group). The daily treatment lasted 14 mo. Major phenolic compounds constituents were characterized by the high-performance liquid chromatography and free radical scavenging capacity was measured by means of the DPPH assay. Fecal samples from young rats (2-mo old), and rats daily fed with PC or DMSO were collected at 6 and 14 mo posttreatment. The gut microbiota composition was analyzed by quantitative polymerase chain reaction. Bifidobacterium was significantly higher in the groups PC 2.5 and PC 5 than in control and young rats. Lactobacillus decreased with time in all treated and untreated groups. Bacteroides, Clostridium leptum subgroup (Clostridium cluster IV), and Enterococcus were not significantly changed by PC at any concentration when compared to control; nevertheless, after 14 mo of treatment all concentrations of PC abolished the increase of Clostridium sensu stricto (cluster I) (Clostridium Cluster I) observed in the control group when compared to young rats. PC do modulate selectively rat gut microbiome to a healthier phenotype in long-term feeding rats, and could counteract the adverse outcomes of aging on gut bacterial population. PRACTICAL APPLICATION This research shows that phenolic-rich grape pomace extracts exhibiting a high antioxidant activity, selectively modulate rat gut microbiota to a healthier phenotype within age in a long-term feeding rats.
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Affiliation(s)
- Stéphanie Chacar
- Centre d'Analyses et de Recherche, UR GPF, Laboratoire SIM, Faculté des Sciences, Univ. Saint-Joseph, Beyrouth, Liban.,Laboratoire de recherche en Physiologie et Physiopathologie, LRPP, pôle technologie santé, Faculté de Médecine, Univ. Saint Joseph, Beyrouth, Liban.,Laboratoire Signalisation et Transports Ioniques Membranaires (STIM), ERL CNRS 7368, Univ. de Poitiers, France
| | - Tarek Itani
- Laboratoire Rodolphe Mérieux, pôle technologie santé, Faculté de Pharmacie, Univ. Saint Joseph, Beyrouth, Liban
| | - Joelle Hajal
- Laboratoire de recherche en Physiologie et Physiopathologie, LRPP, pôle technologie santé, Faculté de Médecine, Univ. Saint Joseph, Beyrouth, Liban
| | - Youakim Saliba
- Laboratoire de recherche en Physiologie et Physiopathologie, LRPP, pôle technologie santé, Faculté de Médecine, Univ. Saint Joseph, Beyrouth, Liban
| | - Nicolas Louka
- Centre d'Analyses et de Recherche, UR GPF, Laboratoire SIM, Faculté des Sciences, Univ. Saint-Joseph, Beyrouth, Liban
| | - Jean-François Faivre
- Laboratoire Signalisation et Transports Ioniques Membranaires (STIM), ERL CNRS 7368, Univ. de Poitiers, France
| | - Richard Maroun
- Centre d'Analyses et de Recherche, UR GPF, Laboratoire SIM, Faculté des Sciences, Univ. Saint-Joseph, Beyrouth, Liban
| | - Nassim Fares
- Laboratoire de recherche en Physiologie et Physiopathologie, LRPP, pôle technologie santé, Faculté de Médecine, Univ. Saint Joseph, Beyrouth, Liban
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Milani C, Duranti S, Bottacini F, Casey E, Turroni F, Mahony J, Belzer C, Delgado Palacio S, Arboleya Montes S, Mancabelli L, Lugli GA, Rodriguez JM, Bode L, de Vos W, Gueimonde M, Margolles A, van Sinderen D, Ventura M. The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota. Microbiol Mol Biol Rev 2017; 81:e00036-17. [PMID: 29118049 PMCID: PMC5706746 DOI: 10.1128/mmbr.00036-17] [Citation(s) in RCA: 987] [Impact Index Per Article: 141.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.
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Affiliation(s)
- Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Bottacini
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Eoghan Casey
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Jennifer Mahony
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Susana Delgado Palacio
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Silvia Arboleya Montes
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Juan Miguel Rodriguez
- Department of Nutrition, Food Science and Food Technology, Complutense University of Madrid, Madrid, Spain
| | - Lars Bode
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California-San Diego, La Jolla, California, USA
| | - Willem de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Department of Bacteriology & Immunology, RPU Immunobiology, University of Helsinki, Helsinki, Finland
| | - Miguel Gueimonde
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Abelardo Margolles
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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Valle Gottlieb MG, Closs VE, Junges VM, Schwanke CHA. Impact of human aging and modern lifestyle on gut microbiota. Crit Rev Food Sci Nutr 2017; 58:1557-1564. [PMID: 28085494 DOI: 10.1080/10408398.2016.1269054] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Human evolution and lifestyle changes caused by the agricultural and industrial revolutions have led to great advances in medicine and increased life expectancy, whilst also profoundly altering the ecological relationships and disease patterns of populations. Studies involving populations that still enjoy a rural way of life and with traits similar to the Paleolithic period reveal them to present a more robust, resistant and diverse gut microbiota, in comparison to highly industrialized civilizations. The human diet has expanded and broadened to include the consumption of high-calorie foods, particularly from animal sources such as game meat and eggs. For some time, authors have been alert to the fact that a modern lifestyle leads to reduced intake of beneficial bacteria, suggesting that nonpathogenic bacteria are being eradicated. Furthermore, therapeutic procedures, including the use of probiotics and prebiotics, have been proposed to lead to recovery of this microbiota, which is altered due to both the ageing process and lifestyle related aspects. Accordingly, this article aims to review the impact of human aging and modern lifestyle on gut microbiota, within an evolutionary, ecological, epidemiological and therapeutic context.
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Affiliation(s)
- Maria Gabriela Valle Gottlieb
- a Biomedical Gerontology Graduate Program, Institute of Geriatrics and Gerontology, Pontifical Catholic University of Rio Grande do Sul (IGG-PUCRS) , Porto Alegre - RS , Brazil
| | - Vera Elizabeth Closs
- a Biomedical Gerontology Graduate Program, Institute of Geriatrics and Gerontology, Pontifical Catholic University of Rio Grande do Sul (IGG-PUCRS) , Porto Alegre - RS , Brazil
| | - Vilma Maria Junges
- a Biomedical Gerontology Graduate Program, Institute of Geriatrics and Gerontology, Pontifical Catholic University of Rio Grande do Sul (IGG-PUCRS) , Porto Alegre - RS , Brazil
| | - Carla Helena Augustin Schwanke
- a Biomedical Gerontology Graduate Program, Institute of Geriatrics and Gerontology, Pontifical Catholic University of Rio Grande do Sul (IGG-PUCRS) , Porto Alegre - RS , Brazil
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Nagpal R, Tsuji H, Takahashi T, Nomoto K, Kawashima K, Nagata S, Yamashiro Y. Gut dysbiosis following C-section instigates higher colonisation of toxigenic Clostridium perfringens in infants. Benef Microbes 2017; 8:353-365. [PMID: 28504574 DOI: 10.3920/bm2016.0216] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Herein we investigated the intestinal carriage of α-toxigenic and enterotoxigenic Clostridium perfringens during infancy, focusing on its association with other gut microbes and mode of delivery and feeding. Faecal samples from 89 healthy term infants were collected at age 7 days, 1 month, 3 months, 6 months and 3 years. C. perfringens was quantified by qPCR; other gut bacteria were quantified by reverse-transcription-qPCR. Alpha-toxigenic C. perfringens was detected in 3.4% infants at day 7 but was present in 35-40% infants at subsequent time-points, with counts ranging from 103-107 cells/g faeces. Enterotoxigenic C. perfringens remained undetected at day 7 but was detected in 1.1, 4.5, 10.1 and 4.5% infants at 1 month, 3 months, 6 months and 3 years, respectively. Intriguingly, infants carrying α-toxigenic C. perfringens had lower levels of Bacteroides fragilis group, bifidobacteria, lactobacilli and organic acids as compared to non-carriers. Further analyses revealed that, compared to vaginally-born infants, caesarean-born infants had higher carriage of C. perfringens and lower levels of B. fragilis group, bifidobacteria, lactobacilli and faecal organic acids during first 6 months. Compared to formula-fed infants, breast-fed infants were slightly less often colonised with C. perfringens; and within caesarean-born infants, breast-fed infants had slightly lower levels of C. perfringens and higher levels of B. fragilis group, bifidobacteria, and lactobacilli than formula-fed infants. This study demonstrates the quantitative dynamics of toxigenic C. perfringens colonisation in infants during the early years of life. Caesarean-born infants acquire a somewhat perturbed microbiota, and breast-feeding might be helpful in ameliorating this dysbiosis. Higher carriage of toxigenic C. perfringens in healthy infants is intriguing and warrants further investigation of its sources and clinical significance in infants, particularly the caesarean-born who may represent a potential reservoir of this opportunistic pathogen and might be more prone to associated illnesses.
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Affiliation(s)
- R Nagpal
- 1 Laboratory for Probiotics Research (Yakult), Juntendo University, Graduate School of Medicine, Hongo 2-9-8-3F, Bunkyo-ku, Tokyo 113-0033, Japan
| | - H Tsuji
- 2 Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - T Takahashi
- 2 Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - K Nomoto
- 2 Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - K Kawashima
- 3 Gonohashi Obstetrics and Gynecology Hospital, 6 Chome-1-6 Kameido, Koto, Tokyo 136-0071, Japan
| | - S Nagata
- 4 Department of Pediatrics, School of Medicine, Tokyo Women's Medical University, 8-1 Kawadacho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Y Yamashiro
- 1 Laboratory for Probiotics Research (Yakult), Juntendo University, Graduate School of Medicine, Hongo 2-9-8-3F, Bunkyo-ku, Tokyo 113-0033, Japan
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Tagliabue A, Ferraris C, Uggeri F, Trentani C, Bertoli S, de Giorgis V, Veggiotti P, Elli M. Short-term impact of a classical ketogenic diet on gut microbiota in GLUT1 Deficiency Syndrome: A 3-month prospective observational study. Clin Nutr ESPEN 2017; 17:33-37. [DOI: 10.1016/j.clnesp.2016.11.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 11/20/2016] [Accepted: 11/25/2016] [Indexed: 01/20/2023]
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Novakova J, Vlkova E, Salmonova H, Pechar R, Rada V, Kokoska L. Anticlostridial agent 8-hydroxyquinoline improves the isolation of faecal bifidobacteria on modified Wilkins-Chalgren agar with mupirocin. Lett Appl Microbiol 2016; 62:330-5. [PMID: 26849418 DOI: 10.1111/lam.12552] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 01/05/2016] [Accepted: 01/30/2016] [Indexed: 12/30/2022]
Abstract
UNLABELLED The need for suitable selective cultivation media for the isolation of Bifidobacterium spp. continues to be a real concern in the field of intestinal microbiology. Isolation of bifidobacteria from human and animal faecal samples using selective agar plating may be problematic especially in samples with increased clostridial counts than bifidobacterial counts. Due to the absence of anticlostridial agents in existing selective media, clostridia can displace bifidobacteria resulting in incorrect estimation of their counts. Therefore, we supplemented the existing selective medium 'modified Wilkins Chalgren agar with mupirocin' (MWM) with 90 mg l(-1) of 8-hydroxyquinoline (8HQ), which was recently proved to act selectively against clostridia. The newly composed 'modified Wilkins-Chalgren agar with 8HQ' (MWMQ) was tested on pure bifidobacterial and clostridial strains, their mixtures, and using faecal samples of mammalian origin; its selectivity was evaluated by genus-specific identification of isolates. The results demonstrated that the presence of 8HQ in this agar eliminated the growth of nonbifidobacterial strains on MWMQ compared to that on MWM, whereas the recovery of bifidobacterial counts was at satisfactory levels. In conclusion, MWMQ could be recommended for bifidobacterial isolation from human and animal faeces especially when bifidobacteria are not numerically dominant and there are chances of clostridial contamination. SIGNIFICANCE AND IMPACT OF THE STUDY Routine isolation of bifidobacteria from mammalian faeces does not use a reliable selective agar with an anticlostridial agent. Overgrowth of clostridia may result in incorrect estimation of bifidobacterial counts. Thus, in order to improve the selectivity of existing media for bifidobacterial isolation, we chose the modified Wilkins-Chalgren agar with mupirocin and supplemented it with 8-hydroxyquinoline (8HQ), a molecule that shows anticlostridial activity without affecting the growth of bifidobacteria. This newly composed medium showed enhanced selectivity and specificity compared to the original medium and therefore, can be recommended for the isolation of bifidobacteria from mammal faeces.
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Affiliation(s)
- J Novakova
- Department of Quality of Agricultural Products, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - E Vlkova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - H Salmonova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - R Pechar
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - V Rada
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - L Kokoska
- Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
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Abstract
This Review summarizes mechanistic investigations in faecal microbiota transplantation (FMT), which has increasingly been adapted into clinical practice as treatment for Clostridium difficile infection (CDI) that cannot be eliminated with antibiotics alone. Administration of healthy donor faecal microbiota in this clinical situation results in its engraftment and restoration of normal gut microbial community structure and functionality. In this Review, we consider several main mechanisms for FMT effectiveness in treatment of CDI, including direct competition of C. difficile with commensal microbiota delivered by FMT, restoration of secondary bile acid metabolism in the colon and repair of the gut barrier by stimulation of the mucosal immune system. Some of these mechanistic insights suggest possibilities for developing novel, next-generation CDI therapeutics. FMT might also have potential applications for non-CDI indications. The gut can become a reservoir of other potential antibiotic-resistant pathogens under pressure of antibiotic treatments, and restoration of normal microbial community structure by FMT might be a promising approach to protect against infections with these pathogens as well. Finally, FMT could be considered for multiple chronic diseases that are associated with some form of dysbiosis. However, considerable research is needed to optimize the FMT protocols for such applications before their therapeutic promise can be evaluated.
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Affiliation(s)
- Alexander Khoruts
- Department of Medicine, Division of Gastroenterology, Center for Immunology and BioTechnology Institute, Medical Biosciences Building, 2101 6th Street South East, University of Minnesota, Minneapolis, Minnesota 55414, USA
| | - Michael J Sadowsky
- Department of Soil, Water, and Climate, BioTechnology Institute, and Microbial and Plant Genomics Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Avenue, St. Paul, Minnesota 55108, USA
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30
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Nagpal R, Ogata K, Tsuji H, Matsuda K, Takahashi T, Nomoto K, Suzuki Y, Kawashima K, Nagata S, Yamashiro Y. Sensitive quantification of Clostridium perfringens in human feces by quantitative real-time PCR targeting alpha-toxin and enterotoxin genes. BMC Microbiol 2015; 15:219. [PMID: 26482797 PMCID: PMC4615878 DOI: 10.1186/s12866-015-0561-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 10/08/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Clostridium perfringens is a widespread pathogen, but the precise quantification of this subdominant gut microbe remains difficult due to its low fecal count (particularly in asymptomatic subjects) and also due to the presence of abundant polymerase-inhibitory substances in human feces. Also, information on the intestinal carriage of toxigenic C. perfringens strains in healthy subjects is sparse. Therefore, we developed a sensitive quantitative real-time PCR assays for quantification of C. perfringens in human feces by targeting its α-toxin and enterotoxin genes. To validate the assays, we finally observed the occurrence of α-toxigenic and enterotoxigenic C. perfringens in the fecal microbiota of healthy Japanese infants and young adults. METHODS The plc-specific qPCR assay was newly validated, while primers for 16S rRNA and cpe genes were retrieved from literature. The assays were validated for specificity and sensitivity in pre-inoculated fecal samples, and were finally applied to quantify C. perfringens in stool samples from apparently healthy infants (n 124) and young adults (n 221). RESULTS The qPCR assays were highly specific and sensitive, with a minimum detection limit of 10(3) bacterial cells/g feces. Alpha-toxigenic C. perfringens was detected in 36% infants and 33% adults, with counts ranging widely (10(3)-10(7) bacterial cells/g). Intriguingly, the mean count of α-toxigenic C. perfringens was significantly higher in infants (6.0±1.5 log10 bacterial cells/g), as compared to that in adults (4.8±1.2). Moreover, the prevalence of enterotoxigenic C. perfringens was also found to be significantly higher in infants, as compared to that in adults. The mean enterotoxigenic C. perfringens count was 5.9±1.9 and 4.8±0.8 log10 bacterial cells/g in infants and adults, respectively. CONCLUSIONS These data indicate that some healthy infants and young adults carry α-toxigenic and enterotoxigenic C. perfringens at significant levels, and may be predisposed to related diseases. Thus, high fecal carriage of toxigenic C. perfringens in healthy children warrants further investigation on its potential sources and clinical significance in these subjects. In summary, we present a novel qPCR assay for sensitive and accurate quantification of α-toxigenic and enterotoxigenic C. perfringens in human feces, which should facilitate prospective studies of the gut microbiota.
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Affiliation(s)
- Ravinder Nagpal
- Probiotics Research Laboratory, Juntendo University Graduate School of Medicine, Tokyo, Japan.
| | | | | | - Kazunori Matsuda
- Yakult Honsha European Research Center for Microbiology, Ghent-Zwijnaarde, Belgium.
| | | | | | - Yoshio Suzuki
- Department of Sports Science, Juntendo University School of Health and Sports Sciences, Chiba, Japan.
| | | | - Satoru Nagata
- Department of Pediatrics, School of Medicine, Tokyo Women's Medical University, Tokyo, Japan.
| | - Yuichiro Yamashiro
- Probiotics Research Laboratory, Juntendo University Graduate School of Medicine, Tokyo, Japan.
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Vlková E, Salmonová H, Bunešová V, Geigerová M, Rada V, Musilová Š. A new medium containing mupirocin, acetic acid, and norfloxacin for the selective cultivation of bifidobacteria. Anaerobe 2015; 34:27-33. [DOI: 10.1016/j.anaerobe.2015.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/23/2015] [Accepted: 04/02/2015] [Indexed: 11/27/2022]
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The gut microbiota composition in dichorionic triplet sets suggests a role for host genetic factors. PLoS One 2015; 10:e0122561. [PMID: 25874766 PMCID: PMC4396853 DOI: 10.1371/journal.pone.0122561] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/22/2015] [Indexed: 12/11/2022] Open
Abstract
Monozygotic and dizygotic twin studies investigating the relative roles of host genetics and environmental factors in shaping gut microbiota composition have produced conflicting results. In this study, we investigated the gut microbiota composition of a healthy dichorionic triplet set. The dichorionic triplet set contained a pair of monozygotic twins and a fraternal sibling, with similar pre- and post-natal environmental conditions including feeding regime. V4 16S rRNA and rpoB amplicon pyrosequencing was employed to investigate microbiota composition, and the species and strain diversity of the culturable bifidobacterial population was also examined. At month 1, the monozygotic pair shared a similar microbiota distinct to the fraternal sibling. By month 12 however, the profile was more uniform between the three infants. Principal coordinate analysis (PCoA) of the microbiota composition revealed strong clustering of the monozygotic pair at month 1 and a separation of the fraternal infant. At months 2 and 3 the phylogenetic distance between the monozygotic pair and the fraternal sibling has greatly reduced and by month 12 the monozygotic pair no longer clustered separately from the fraternal infant. Pulse field gel electrophoresis (PFGE) analysis of the bifidobacterial population revealed a lack of strain diversity, with identical strains identified in all three infants at month 1 and 12. The microbiota of two antibiotic-treated dichorionic triplet sets was also investigated. Not surprisingly, in both triplet sets early life antibiotic administration appeared to be a major determinant of microbiota composition at month 1, irrespective of zygosity. By month 12, early antibiotic administration appeared to no longer exert such a strong influence on gut microbiota composition. We hypothesize that initially host genetics play a significant role in the composition of an individual’s gut microbiota, unless an antibiotic intervention is given, but by month 12 environmental factors are the major determinant.
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Gondalia S, Scholey A. Gastrointestinal microbiota, diet and brain functioning. MICROBIOLOGY AUSTRALIA 2015. [DOI: 10.1071/ma15008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Conlon MA, Bird AR. The impact of diet and lifestyle on gut microbiota and human health. Nutrients 2014; 7:17-44. [PMID: 25545101 PMCID: PMC4303825 DOI: 10.3390/nu7010017] [Citation(s) in RCA: 879] [Impact Index Per Article: 87.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 12/09/2014] [Indexed: 02/07/2023] Open
Abstract
There is growing recognition of the role of diet and other environmental factors in modulating the composition and metabolic activity of the human gut microbiota, which in turn can impact health. This narrative review explores the relevant contemporary scientific literature to provide a general perspective of this broad area. Molecular technologies have greatly advanced our understanding of the complexity and diversity of the gut microbial communities within and between individuals. Diet, particularly macronutrients, has a major role in shaping the composition and activity of these complex populations. Despite the body of knowledge that exists on the effects of carbohydrates there are still many unanswered questions. The impacts of dietary fats and protein on the gut microbiota are less well defined. Both short- and long-term dietary change can influence the microbial profiles, and infant nutrition may have life-long consequences through microbial modulation of the immune system. The impact of environmental factors, including aspects of lifestyle, on the microbiota is particularly poorly understood but some of these factors are described. We also discuss the use and potential benefits of prebiotics and probiotics to modify microbial populations. A description of some areas that should be addressed in future research is also presented.
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Affiliation(s)
- Michael A Conlon
- CSIRO Food and Nutrition Flagship, Kintore Ave, Adelaide, SA 5000, Australia.
| | - Anthony R Bird
- CSIRO Food and Nutrition Flagship, Kintore Ave, Adelaide, SA 5000, Australia.
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Rajilić-Stojanović M, de Vos WM. The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol Rev 2014; 38:996-1047. [PMID: 24861948 PMCID: PMC4262072 DOI: 10.1111/1574-6976.12075] [Citation(s) in RCA: 723] [Impact Index Per Article: 72.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/29/2014] [Accepted: 05/09/2014] [Indexed: 02/06/2023] Open
Abstract
The microorganisms that inhabit the human gastrointestinal tract comprise a complex ecosystem with functions that significantly contribute to our systemic metabolism and have an impact on health and disease. In line with its importance, the human gastrointestinal microbiota has been extensively studied. Despite the fact that a significant part of the intestinal microorganisms has not yet been cultured, presently over 1000 different microbial species that can reside in the human gastrointestinal tract have been identified. This review provides a systematic overview and detailed references of the total of 1057 intestinal species of Eukarya (92), Archaea (8) and Bacteria (957), based on the phylogenetic framework of their small subunit ribosomal RNA gene sequences. Moreover, it unifies knowledge about the prevalence, abundance, stability, physiology, genetics and the association with human health of these gastrointestinal microorganisms, which is currently scattered over a vast amount of literature published in the last 150 years. This detailed physiological and genetic information is expected to be instrumental in advancing our knowledge of the gastrointestinal microbiota. Moreover, it opens avenues for future comparative and functional metagenomic and other high-throughput approaches that need a systematic and physiological basis to have an impact.
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Affiliation(s)
- Mirjana Rajilić-Stojanović
- Department for Biotechnology and Biochemical Engineering, Faculty of Technology and Metallurgy, University of BelgradeBelgrade, Serbia
- Laboratory of Microbiology, Wageningen UniversityWageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen UniversityWageningen, The Netherlands
- Departments of Bacteriology and Immunology, and Veterinary Biosciences, University of HelsinkiHelsinki, Finland
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Abstract
Yogurt consumption has been associated with health benefits in different populations. Limited information, however, is available on nutritional and health attributes of yogurt in older adults. Yogurt is abundant in calcium, zinc, B vitamins, and probiotics; it is a good source of protein; and it may be supplemented with vitamin D and additional probiotics associated with positive health outcomes. Aging is accompanied by a wide array of nutritional deficiencies and health complications associated with under- and overnutrition, including musculoskeletal impairment, immunosenescence, cardiometabolic diseases, and cognitive impairment. Furthermore, yogurt is accessible and convenient to consume by the older population, which makes yogurt consumption a feasible approach to enhance older adults' nutritional status. A limited number of studies have specifically addressed the impact of yogurt on the nutritional and health status of older adults, and most are observational. However, those reported thus far and reviewed here are encouraging and suggest that yogurt could play a role in improving the nutritional status and health of older adults. In addition, these reports support further investigation into the role of yogurt in healthy and active aging.
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Affiliation(s)
- Naglaa Hani El-Abbadi
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
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