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Zhang L, Xu Y, Li H, Li B, Duan G, Zhu C. The role of probiotics in children with autism spectrum disorders: A study protocol for a randomised controlled trial. PLoS One 2022; 17:e0263109. [PMID: 35202432 PMCID: PMC8870536 DOI: 10.1371/journal.pone.0263109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 01/11/2022] [Indexed: 12/20/2022] Open
Abstract
Background Autism spectrum disorder (ASD) is a neurological and developmental condition that begins in infancy or earlier and lasts through the individual’s lifetime. The aetiology and mechanisms of ASD are not yet fully understood, and current treatment comprises mainly education and rehabilitation, without significant improvement in the core symptoms. Recent studies suggest that microbiota change in children with ASD after the ingestion of probiotics may improve the balance of microbiota and thus ASD symptoms. Objective The objectives of this study are to evaluate the efficacy of probiotics on the symptoms of children with ASD and the possible mechanisms involved. Methods This is a prospective controlled trial. A total of 160 children with ASD will be stratified and allocated to placebo and probiotics groups randomised according to the severity of their ASD symptoms. The probiotics group will be given probiotics supplements orally twice a day for 3 months and the control group will be given a placebo at the same amount, in addition to the baseline therapy of education and rehabilitation. All the children will be evaluated systematically by using different scales, questionnaires before, during, and after 3 months’ treatment, as well as 3 months after discontinuation. The potential impact of probiotics on immunity and inflammation, metabolism, and metagenome will also be investigated. Discussion Our previous study showed that the abundance of intestinal flora was greatly different in children with ASD, and that Bifidobacterium was associated with the severity of ASD. In the present study, we will investigate the impact of probiotics supplementation on the symptoms of Children with ASD, with the purpose of evaluating the possible therapeutic effects of additives on ASD and of providing a reference for clinical treatment. The results will help to disclose as yet unknown relationship between probiotics and ASD. Trial registration This study has been registered with Chinese Clinical Trial Registry (ChiCTR-2000037941).
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Affiliation(s)
- Lingling Zhang
- Henan Key Laboratory of Child Brain Injury and Henan Clinical Research Center for Child Neurological Disorders, Institute of Neuroscience and The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yiran Xu
- Henan Key Laboratory of Child Brain Injury and Henan Clinical Research Center for Child Neurological Disorders, Institute of Neuroscience and The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongwei Li
- Henan Key Laboratory of Child Brain Injury and Henan Clinical Research Center for Child Neurological Disorders, Institute of Neuroscience and The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bingbing Li
- Henan Key Laboratory of Child Brain Injury and Henan Clinical Research Center for Child Neurological Disorders, Institute of Neuroscience and The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guiqin Duan
- Center for Child Behavioral Development, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Changlian Zhu
- Henan Key Laboratory of Child Brain Injury and Henan Clinical Research Center for Child Neurological Disorders, Institute of Neuroscience and The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Göteborg, Sweden
- Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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Silamiķele L, Silamiķelis I, Ustinova M, Kalniņa Z, Elbere I, Petrovska R, Kalniņa I, Kloviņš J. Metformin Strongly Affects Gut Microbiome Composition in High-Fat Diet-Induced Type 2 Diabetes Mouse Model of Both Sexes. Front Endocrinol (Lausanne) 2021; 12:626359. [PMID: 33815284 PMCID: PMC8018580 DOI: 10.3389/fendo.2021.626359] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
Effects of metformin, the first-line drug for type 2 diabetes therapy, on gut microbiome composition in type 2 diabetes have been described in various studies both in human subjects and animals. However, the details of the molecular mechanisms of metformin action have not been fully understood. Moreover, there is a significant lack of information on how metformin affects gut microbiome composition in female mouse models, depending on sex and metabolic status in well controlled experimental setting. Our study aimed to examine metformin-induced alterations in gut microbiome diversity, composition, and functional implications of high-fat diet-induced type 2 diabetes mouse model, using, for the first time in mice study, the shotgun metagenomic sequencing that allows estimation of microorganisms at species level. We also employed a randomized block, factorial study design, and including 24 experimental units allocated to 8 treatment groups to systematically evaluate the effect of sex and metabolic status on metformin interaction with microbiome. We used DNA obtained from fecal samples representing gut microbiome before and after ten weeks-long metformin treatment. We identified 100 metformin-related differentially abundant species in high-fat diet-fed mice before and after the treatment, with most of the species relative abundances increased. In contrast, no significant changes were observed in control diet-fed mice. Functional analysis targeted to carbohydrate, lipid, and amino acid metabolism pathways revealed 14 significantly altered hierarchies. We also observed sex-specific differences in response to metformin treatment. Males experienced more pronounced changes in metabolic markers, while in females the extent of changes in gut microbiome representatives was more marked, indicated by 53 differentially abundant species with more remarkable Log fold changes compared to the combined-sex analysis. The same pattern manifested regarding the functional analysis, where we discovered 5 significantly affected hierarchies in female groups but not in males. Our results suggest that both sexes of animals should be included in future studies focusing on metformin effects on the gut microbiome.
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Affiliation(s)
| | | | | | | | | | | | | | - Jānis Kloviņš
- Latvian Biomedical Research and Study Centre, Riga, Latvia
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Blaustein RA, Michelitsch LM, Glawe AJ, Lee H, Huttelmaier S, Hellgeth N, Ben Maamar S, Hartmann EM. Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota. Microbiome 2021; 9:32. [PMID: 33517907 PMCID: PMC7849112 DOI: 10.1186/s40168-020-00983-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 12/16/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND While indoor microbiomes impact our health and well-being, much remains unknown about taxonomic and functional transitions that occur in human-derived microbial communities once they are transferred away from human hosts. Toothbrushes are a model to investigate the potential response of oral-derived microbiota to conditions of the built environment. Here, we characterize metagenomes of toothbrushes from 34 subjects to define the toothbrush microbiome and resistome and possible influential factors. RESULTS Toothbrush microbiomes often comprised a dominant subset of human oral taxa and less abundant or site-specific environmental strains. Although toothbrushes contained lower taxonomic diversity than oral-associated counterparts (determined by comparison with the Human Microbiome Project), they had relatively broader antimicrobial resistance gene (ARG) profiles. Toothbrush resistomes were enriched with a variety of ARGs, notably those conferring multidrug efflux and putative resistance to triclosan, which were primarily attributable to versatile environmental taxa. Toothbrush microbial communities and resistomes correlated with a variety of factors linked to personal health, dental hygiene, and bathroom features. CONCLUSIONS Selective pressures in the built environment may shape the dynamic mixture of human (primarily oral-associated) and environmental microbiota that encounter each other on toothbrushes. Harboring a microbial diversity and resistome distinct from human-associated counterparts suggests toothbrushes could potentially serve as a reservoir that may enable the transfer of ARGs. Video abstract.
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Affiliation(s)
- Ryan A. Blaustein
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | | | - Adam J. Glawe
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
| | - Hansung Lee
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
| | - Stefanie Huttelmaier
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
| | - Nancy Hellgeth
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
| | - Sarah Ben Maamar
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
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Mencía-Ares O, Cabrera-Rubio R, Cobo-Díaz JF, Álvarez-Ordóñez A, Gómez-García M, Puente H, Cotter PD, Crispie F, Carvajal A, Rubio P, Argüello H. Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms. Microbiome 2020; 8:164. [PMID: 33213522 PMCID: PMC7678069 DOI: 10.1186/s40168-020-00941-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/17/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the resistome, not only in the animals but also on the farm environment. Here, we evaluate the resistome footprint of an extensive pig farming system, maintained for decades, as compared to that of industrialized intensive pig farming by analyzing 105 fecal, environmental and slurry metagenomes from 38 farms. RESULTS Our results evidence a significantly higher abundance of antimicrobial resistance genes (ARGs) on intensive farms and a link between AMU and AMR to certain antimicrobial classes. We observed differences in the resistome across sample types, with a higher richness and dispersion of ARGs within environmental samples than on those from feces or slurry. Indeed, a deeper analysis revealed that differences among the three sample types were defined by taxa-ARGs associations. Interestingly, mobilome analyses revealed that the observed AMR differences between intensive and extensive farms could be linked to differences in the abundance of mobile genetic elements (MGEs). Thus, while there were no differences in the abundance of chromosomal-associated ARGs between intensive and extensive herds, a significantly higher abundance of integrons in the environment and plasmids, regardless of the sample type, was detected on intensive farms. CONCLUSIONS Overall, this study shows how AMU, production system, and sample type influence, mainly through MGEs, the profile and dispersion of ARGs in pig production. Video Abstract.
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Affiliation(s)
- Oscar Mencía-Ares
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
| | - Raúl Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
| | - José Francisco Cobo-Díaz
- Department of Food Hygiene and Technology, Faculty of Veterinary, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology, Faculty of Veterinary, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Manuel Gómez-García
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
| | - Héctor Puente
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, Co. Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
| | - Ana Carvajal
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain.
| | - Pedro Rubio
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
| | - Héctor Argüello
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
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Shen L, Shen K, Bai J, Wang J, Singla RK, Shen B. Data-driven microbiota biomarker discovery for personalized drug therapy of cardiovascular disease. Pharmacol Res 2020; 161:105225. [PMID: 33007417 DOI: 10.1016/j.phrs.2020.105225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 02/07/2023]
Abstract
Cardiovascular disease (CVD) is the most wide-spread disorder all over the world. The personalized and precision diagnosis, treatment and prevention of CVD is still a challenge. With the developing of metagenome sequencing technologies and the paradigm shifting to data-driven discovery in life science, the computer aided microbiota biomarker discovery for CVD is becoming reality. We here summarize the data resources, knowledgebases and computational models available for CVD microbiota biomarker discovery, and review the present status of the findings about the microbiota patterns associated with the therapeutic effects on CVD. The future challenges and opportunities of the translational informatics on the personalized drug usages in CVD diagnosis, prognosis and treatment are also discussed.
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Affiliation(s)
- Li Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Ke Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Jinwei Bai
- Library of West-China Hospital, Sichuan University, Chengdu 610041, China
| | - Jiao Wang
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Rajeev K Singla
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
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Nelson MT, Wolter DJ, Eng A, Weiss EJ, Vo AT, Brittnacher MJ, Hayden HS, Ravishankar S, Bautista G, Ratjen A, Blackledge M, McNamara S, Nay L, Majors C, Miller SI, Borenstein E, Simon RH, LiPuma JJ, Hoffman LR. Maintenance tobramycin primarily affects untargeted bacteria in the CF sputum microbiome. Thorax 2020; 75:780-790. [PMID: 32631930 PMCID: PMC7875198 DOI: 10.1136/thoraxjnl-2019-214187] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 05/15/2020] [Accepted: 05/28/2020] [Indexed: 01/16/2023]
Abstract
RATIONALE The most common antibiotic used to treat people with cystic fibrosis (PWCF) is inhaled tobramycin, administered as maintenance therapy for chronic Pseudomonas aeruginosa lung infections. While the effects of inhaled tobramycin on P. aeruginosa abundance and lung function diminish with continued therapy, this maintenance treatment is known to improve long-term outcomes, underscoring how little is known about why antibiotics work in CF infections, what their effects are on complex CF sputum microbiomes and how to improve these treatments. OBJECTIVES To rigorously define the effect of maintenance tobramycin on CF sputum microbiome characteristics. METHODS AND MEASUREMENTS We collected sputum from 30 PWCF at standardised times before, during and after a single month-long course of maintenance inhaled tobramycin. We used traditional culture, quantitative PCR and metagenomic sequencing to define the dynamic effects of this treatment on sputum microbiomes, including abundance changes in both clinically targeted and untargeted bacteria, as well as functional gene categories. MAIN RESULTS CF sputum microbiota changed most markedly by 1 week of antibiotic therapy and plateaued thereafter, and this shift was largely driven by changes in non-dominant taxa. The genetically conferred functional capacities (ie, metagenomes) of subjects' sputum communities changed little with antibiotic perturbation, despite taxonomic shifts, suggesting functional redundancy within the CF sputum microbiome. CONCLUSIONS Maintenance treatment with inhaled tobramycin, an antibiotic with demonstrated long-term mortality benefit, primarily impacted clinically untargeted bacteria in CF sputum, highlighting the importance of monitoring the non-canonical effects of antibiotics and other treatments to accurately define and improve their clinical impact.
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Affiliation(s)
- Maria T Nelson
- Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
- Medical Scientist Training Program, University of Washington School of Medicine, Seattle, Washington, United States
- Molecular and Cellular Biology, University of Washington School of Medicine, Seattle, Washington, United States
| | - Daniel J Wolter
- Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
- Pediatrics, Seattle Children's Hospital, Seattle, Washington, USA
| | - Alexander Eng
- Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Eli J Weiss
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Anh T Vo
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | | | - Hillary S Hayden
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Sumedha Ravishankar
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Gilbert Bautista
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Anina Ratjen
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | | | - Sharon McNamara
- Pediatrics, Seattle Children's Hospital, Seattle, Washington, USA
| | - Laura Nay
- Pediatrics, Seattle Children's Hospital, Seattle, Washington, USA
| | - Cheryl Majors
- Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Samuel I Miller
- Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States
| | - Elhanan Borenstein
- Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Richard H Simon
- Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - John J LiPuma
- Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Luke R Hoffman
- Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
- Pediatrics, Seattle Children's Hospital, Seattle, Washington, USA
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
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7
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Luan X, Zhang H, Tian Z, Yang M, Wen X, Zhang Y. Microbial community functional structure in an aerobic biofilm reactor: Impact of streptomycin and recovery. Chemosphere 2020; 255:127032. [PMID: 32417519 DOI: 10.1016/j.chemosphere.2020.127032] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/30/2020] [Accepted: 05/08/2020] [Indexed: 06/11/2023]
Abstract
Antibiotics can affect microbial community structure and promote antibiotic resistance. However, the course of microbial community recovery in wastewater treatment systems after antibiotic disturbance remains unclear. Herein, multiple molecular biology tools, including 16S amplicon sequencing, GeoChip 5.0, quantitative polymerase chain reaction (qPCR), and metagenomic sequencing, were used to investigate the year-long (352 d) recovery of the microbial community functional structure in an aerobic biofilm reactor. Nitrification was completely inhibited under 50 mg/L of streptomycin spiking (STM_50) due to the significant reduction of ammonia-oxidizing bacteria, but recovered to original pre-disturbance levels after streptomycin removal, indicating the high resilience of ammonia-oxidizing bacteria. Bacterial community richness and diversity decreased significantly under STM_50 (p < 0.05), but recovered to levels similar to those observed before disturbance after 352 d. In contrast, bacterial composition did not recover to the original structure. The carbon degradation and nitrogen cycling functional community significantly changed after recovery compared to that observed pre-disturbance (p < 0.05), thus indicating functional redundancy. Additionally, levels of aminoglycoside and total antibiotic resistance genes under STM_50 (relative abundance, 0.33 and 0.80, respectively) and after one year of recovery (0.12 and 0.29, respectively) were higher than the levels detected pre-disturbance (0.04 and 0.24, respectively). This study provides an overall depiction of the recovery of the microbial community functional structure after antibiotic exposure. Our findings give notice that recovery caused by antibiotic disturbance in the water environment should be taken more seriously, and that engineering control strategies should be implemented to prevent the antibiotic pollution of wastewater.
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Affiliation(s)
- Xiao Luan
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Zhe Tian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Yang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianghua Wen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Pan X, Lin L, Zhang W, Dong L, Yang Y. Metagenome sequencing to unveil the resistome in a deep subtropical lake on the Yunnan-Guizhou Plateau, China. Environ Pollut 2020; 263:114470. [PMID: 32247114 DOI: 10.1016/j.envpol.2020.114470] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Erhai Lake in the Yunnan-Guizhou Plateau, a typical subtropical deep lake, experienced long-time input of nutrients and pollutants, which provides beneficial conditions for evolution and spread of resistance genes. In this study, the profile of bacterial community, antibiotic and metal resistance genes in sediments of Erhai Lake were analyzed via high-thought sequencing of 16S rRNA and metagenomic DNA. Proteobacteria, Firmicutes, Nitrospirae, and Bacteroidetes were found to be the main composition of the bacterial community. Multidrug-, bacitracin-, macrolide-lincosamide-streptogramin (MLS)- and tetracycline resistance genes were the primary antibiotic resistance gene (ARG) types with high relative abundance, whereas Multi-metal-, and arsenic- resistance genes were the primary metal resistance gene (MRG) types. The effects of nitrogen and phosphorus on the abundance of ARGs and MRGs depended on the different types. Some specific ARG (fosmidomycin resistance genes) and MRG types (multi-metal resistance genes) also showed significant geographic distribution. Bacterial community was the main driver shaping the resistome. Nutrients also played an essential role in structuring the bacterial community and resistome in the sediments of Erhai Lake. This study sheds light on the distribution and fate of resistome under a high load of nitrogen and phosphorus in a deep lake.
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Affiliation(s)
- Xiong Pan
- Basin Water Environmental Research Department, Changjiang River Scientific Research Institute, Wuhan, 430014, China
| | - Li Lin
- Basin Water Environmental Research Department, Changjiang River Scientific Research Institute, Wuhan, 430014, China
| | - Weihong Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Lei Dong
- Basin Water Environmental Research Department, Changjiang River Scientific Research Institute, Wuhan, 430014, China
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
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9
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Zhang H, Zhang Q, Chen S, Zhang Z, Song J, Long Z, Yu Y, Fang H. Enterobacteriaceae predominate in the endophytic microbiome and contribute to the resistome of strawberry. Sci Total Environ 2020; 727:138708. [PMID: 32334231 DOI: 10.1016/j.scitotenv.2020.138708] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/11/2020] [Accepted: 04/13/2020] [Indexed: 05/21/2023]
Abstract
Antibiotic resistance genes (ARGs) harbored by plant microbiomes have been implicated as a potential risk to public health via food chain, especially directly edible fruits and vegetables. Here, we investigated the microbiome and antibiotic resistome in soil-strawberry ecosystem using shotgun metagenomic sequencing. The results showed that the enterobacterial population dominated the endophytes of strawberry fruits. Moreover, 85 subtypes of ARGs, including several clinically important ARGs, were detected in the strawberry fruit metagenomes. Additionally, host tracking analysis in combination with antibiotic-resistant bacterial isolate screening suggested that fruit-borne ARGs were mainly carried by members of the Enterobacteriaceae family. Unexpectedly, most of fruit-borne isolates were found to be resistant to several clinically important antimicrobials, e.g., erythromycin and cephalexin. Our findings provide broad insights into endophytic antibiotic resistomes of direct edible strawberry fruits and their potential hosts, and highlight the potential exposure risks of plant microbiomes to the human food chain.
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Affiliation(s)
- Houpu Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qianke Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Shiyu Chen
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zihan Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jiajin Song
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhengnan Long
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yunlong Yu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hua Fang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China; Key laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China; Key laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China.
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10
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Moon K, Jeon JH, Kang I, Park KS, Lee K, Cha CJ, Lee SH, Cho JC. Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes. Microbiome 2020; 8:75. [PMID: 32482165 PMCID: PMC7265639 DOI: 10.1186/s40168-020-00863-4] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/11/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Antibiotic resistance developed by bacteria is a significant threat to global health. Antibiotic resistance genes (ARGs) spread across different bacterial populations through multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages. ARGs carried by bacteriophages are considered especially threatening due to their prolonged persistence in the environment, fast replication rates, and ability to infect diverse bacterial hosts. Several studies employing qPCR and viral metagenomics have shown that viral fraction and viral sequence reads in clinical and environmental samples carry many ARGs. However, only a few ARGs have been found in viral contigs assembled from metagenome reads, with most of these genes lacking effective antibiotic resistance phenotypes. Owing to the wide application of viral metagenomics, nevertheless, different classes of ARGs are being continuously found in viral metagenomes acquired from diverse environments. As such, the presence and functionality of ARGs encoded by bacteriophages remain up for debate. RESULTS We evaluated ARGs excavated from viral contigs recovered from urban surface water viral metagenome data. In virome reads and contigs, diverse ARGs, including polymyxin resistance genes, multidrug efflux proteins, and β-lactamases, were identified. In particular, when a lenient threshold of e value of ≤ 1 × e-5 and query coverage of ≥ 60% were employed in the Resfams database, the novel β-lactamases blaHRV-1 and blaHRVM-1 were found. These genes had unique sequences, forming distinct clades of class A and subclass B3 β-lactamases, respectively. Minimum inhibitory concentration analyses for E. coli strains harboring blaHRV-1 and blaHRVM-1 and catalytic kinetics of purified HRV-1 and HRVM-1 showed reduced susceptibility to penicillin, narrow- and extended-spectrum cephalosporins, and carbapenems. These genes were also found in bacterial metagenomes, indicating that they were harbored by actively infecting phages. CONCLUSION Our results showed that viruses in the environment carry as-yet-unreported functional ARGs, albeit in small quantities. We thereby suggest that environmental bacteriophages could be reservoirs of widely variable, unknown ARGs that could be disseminated via virus-host interactions. Video abstract.
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Affiliation(s)
- Kira Moon
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Jeong Ho Jeon
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Ilnam Kang
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Kwang Seung Park
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggi-do, 17058, Republic of Korea.
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea.
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11
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Baćmaga M, Wyszkowska J, Kucharski J. Response of soil microorganisms and enzymes to the foliar application of Helicur 250 EW fungicide on Horderum vulgare L. Chemosphere 2020; 242:125163. [PMID: 31677518 DOI: 10.1016/j.chemosphere.2019.125163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/17/2019] [Accepted: 10/20/2019] [Indexed: 06/10/2023]
Abstract
The use of fungicides bears the risk of many undesirable outcomes that are manifested in, among other things, changes in the structure and activity of microorganisms. This study aimed at determining the effect of a Helicur 250 EW preparation, used to protect crops against fungal diseases, on the microbiological and biochemical activity of soil and on the development of Horderum vulgare L. The fungicide was sprayed on leaves of spring barley in the following doses (per active substance, i.e. tebuconazole, TEB): 0.046, 0.093, 0.139, 1.395, and 2.790 mg TEB plant-1. The following indices were analyzed in the study: index of microorganisms resistance (RS) to the effects of fungicide, microorganisms colony development index (CD), microorganisms ecophysiological diversity index (EP), genetic diversity of bacteria, enzymatic activity, and effect of the fungicide on spring barley development (IFH). The most susceptible to the effects of the fungicide turned out to be fungi. The metagenomic analysis demonstrated that the bacterial community differed in terms of structure and percentage contribution in the soil exposed to the fungicide from the control soil even at the Phylum level. However, Proteobacteria appeared to be the prevailing taxon in both soils. Bacillus arabhattai, B. soli, and B. simplex occurred exclusively in the control soil, whereas Ramlibacter tataounensis, Azospirillum palatum, and Kaistobacter terrae - exclusively in the soil contaminated with the fungicide. Helicur 250 EW suppressed activities of all soil enzymes except for arylsulfatase. In addition, it proved to be a strong inhibitor of spring barley growth and development.
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Affiliation(s)
- Małgorzata Baćmaga
- Department of Microbiology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 3, 10-727, Olsztyn, Poland
| | - Jadwiga Wyszkowska
- Department of Microbiology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 3, 10-727, Olsztyn, Poland.
| | - Jan Kucharski
- Department of Microbiology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 3, 10-727, Olsztyn, Poland
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12
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Yang X, Chen Y, Guo F, Liu X, Su X, He Q. Metagenomic analysis of the biotoxicity of titanium dioxide nanoparticles to microbial nitrogen transformation in constructed wetlands. J Hazard Mater 2020; 384:121376. [PMID: 31611016 DOI: 10.1016/j.jhazmat.2019.121376] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/30/2019] [Accepted: 09/30/2019] [Indexed: 05/23/2023]
Abstract
Extensive use of titanium dioxide nanoparticles (TiO2 NPs) in various products has increased the release of these particles into wastewater, posing potential environmental risks. As an ecological wastewater treatment facility, constructed wetland (CW) is an important sink of NPs. However, little is known about the effects of NPs on microbial nitrogen transformation and related genes in CWs. In this study, short-term (5 days) and long-term (60 days) exposure experiments were conducted to investigate the effect of TiO2 NPs (0, 1, and 50 mg/L) on microbial nitrogen removal in CWs. The results showed that nitrogen removal efficiency was decreased by 35%-51% after long-term exposure to TiO2 NPs. Metagenomic analysis further confirmed that TiO2 NPs declined the relative abundance of functional genes and those enzyme encoding genes involved in the nitrogen metabolism pathway and glycolysis metabolism process. Furthermore, our data proved that the indigent glycolysis metabolism process resulted in the shortage of electron (NADH) and energy sources (ATP), causing inefficient nitrogen removal. Overall, these results revealed that the accumulation of TiO2 NPs altered the genetic expression of biofilm in CWs, which had significant impacts on biological nitrogen transformation.
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Affiliation(s)
- Xiangyu Yang
- Key Laboratory of the Three Gorges Region's Eco-Environment, Ministry of Education, College of Environment and Ecology, Chongqing University, Campus B 83 Shabeijie, Shapingba, Chongqing 400044, China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing, 400044, China
| | - Yi Chen
- Key Laboratory of the Three Gorges Region's Eco-Environment, Ministry of Education, College of Environment and Ecology, Chongqing University, Campus B 83 Shabeijie, Shapingba, Chongqing 400044, China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing, 400044, China.
| | - Fucheng Guo
- Key Laboratory of the Three Gorges Region's Eco-Environment, Ministry of Education, College of Environment and Ecology, Chongqing University, Campus B 83 Shabeijie, Shapingba, Chongqing 400044, China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing, 400044, China
| | - Xiaobo Liu
- Key Laboratory of the Three Gorges Region's Eco-Environment, Ministry of Education, College of Environment and Ecology, Chongqing University, Campus B 83 Shabeijie, Shapingba, Chongqing 400044, China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing, 400044, China
| | - Xiaoxuan Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Qiang He
- Key Laboratory of the Three Gorges Region's Eco-Environment, Ministry of Education, College of Environment and Ecology, Chongqing University, Campus B 83 Shabeijie, Shapingba, Chongqing 400044, China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing, 400044, China
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13
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Almeida AR, Alves M, Domingues I, Henriques I. The impact of antibiotic exposure in water and zebrafish gut microbiomes: A 16S rRNA gene-based metagenomic analysis. Ecotoxicol Environ Saf 2019; 186:109771. [PMID: 31629904 DOI: 10.1016/j.ecoenv.2019.109771] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/30/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
In order to supply human demand for food, the aquaculture industry has been growing fast in the last years, being fish usually cultivated in overcrowded conditions. Hence, to prevent the rapidly disease spreading, antibiotics may be applied to both sick and healthy animals. Due to its broad spectrum, oxytetracycline (OTC) is one of the most used antibiotics in food-production. Yet, although useful to prevent infections, antibiotics may reshape aquatic animals' microbiome, disturbing hosts' welfare. However, the impact of this exposure to the organism microbiome and its surrounding environment is poorly understood. Then, the objective of this study was to analyze in detail the long-term effect of OTC in both zebrafish gut and water microbiomes. Zebrafish adults were exposed, via water, for two months to three concentrations of OTC (0, 10 and 10000 μg/L). Total DNA was extracted from gut and water samples and the V3-V4 region of the bacterial 16 S rRNA gene was sequenced using Illumina technology. Results of alpha and beta-diversity analyses revealed that long-term exposure to OTC impacted both zebrafish gut and water microbiomes. In water samples, effects were observed even at the lowest (10 μg/L) OTC concentration tested resulting in an increase in Deltaproteobacteria, namely the Myxococcales and Bdellovibrionales orders. On the other hand, effects on zebrafish gut were only observed at the highest concentration with the selection of Alphaproteobacteria and Actinobacteria classes. Although these classes are common in fish gut, the increase of Actinobacteria may represent a health problem since some genera like Gordonia are linked to some human infection disease. Nevertheless, in both gut and water, it was observed a decrease in Gamaproteobacteria, probably due to OTC mode of action. In silico functional metagenomic analysis revealed that OTC exposure selected general detoxification mechanisms. In addition, the abundance of functional genes involved in Quorum Sensing (QS) increased under OTC exposure suggesting that QS may help bacteria to survive OTC stress. Thus, future studies should consider post-exposure scenarios for a deeper analysis of the water and zebrafish gut resistome, since bacteria may react differently after exposure ceased.
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Affiliation(s)
- Ana Rita Almeida
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Marta Alves
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Inês Domingues
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Isabel Henriques
- CESAM & Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Calçada Martins de Freitas, 3000-456, Coimbra, Portugal.
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14
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Jia S, Wu J, Ye L, Zhao F, Li T, Zhang XX. Metagenomic assembly provides a deep insight into the antibiotic resistome alteration induced by drinking water chlorination and its correlations with bacterial host changes. J Hazard Mater 2019; 379:120841. [PMID: 31279312 DOI: 10.1016/j.jhazmat.2019.120841] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 04/09/2019] [Accepted: 06/26/2019] [Indexed: 05/21/2023]
Abstract
Chlorination can contribute to the enrichment of specific antibiotic resistance genes (ARGs) in drinking water, but the underlying molecular ecological mechanisms remain unknown, which may hinder the assessment and control of the resulting health risks. In this study, metagenomic assembly and Resfams annotation were used to profile the co-occurrence patterns of ARGs, mobile genetic elements (MGEs) and their bacterial hosts, as well as the correlations of potential pathogens with the antibiotic resistome, in a full-scale drinking water treatment and transportation system. Seven ARG types involved in different resistance mechanisms occurred in drinking water and chlorination enhanced the total abundance of the ARGs (p < 0.05). The ARGs encoding resistance-nodulation-cell division and ATP-binding cassette antibiotic efflux pumps predominated in all the samples and were primarily responsible for the ARG accumulation. After chlorination, the ARGs were primarily carried by predominant Sphingomonas, Polaromonas, Hyphomicrobium, Acidovorax, Pseudomonas and Fluviicola. Further, enrichment of the bacterial hosts and MGEs greatly contributed to alteration of the antibiotic resistome. Pseudomonas alcaligenes, carrying multiple ARGs, was identified as a potential pathogen in the chlorinated drinking water. These findings provide novel insights into the host-ARG relationship and the mechanism underlying the resistome alteration during drinking water chlorination.
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Affiliation(s)
- Shuyu Jia
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Jialu Wu
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Fuzheng Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Tong Li
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing 210023, China.
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15
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Yuan K, Yu K, Yang R, Zhang Q, Yang Y, Chen E, Lin L, Luan T, Chen W, Chen B. Metagenomic characterization of antibiotic resistance genes in Antarctic soils. Ecotoxicol Environ Saf 2019; 176:300-308. [PMID: 30947033 DOI: 10.1016/j.ecoenv.2019.03.099] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/01/2019] [Accepted: 03/25/2019] [Indexed: 05/20/2023]
Abstract
Antibiotic resistance genes (ARGs) are considered environmental pollutants. Comprehensive characterization of the ARGs in pristine environments is essential towards understanding the evolution of antibiotic resistance. Here, we analyzed ARGs in soil samples collected from relatively pristine Antarctica using metagenomic approaches. We identified 79 subtypes related to 12 antibiotic classes in Antarctic soils, in which ARGs related to multidrug and polypeptide were dominant. The characteristics of ARGs in Antarctic soils were significantly different from those in active sludge, chicken feces and swine feces, in terms of composition, abundance and potential transferability. ARG subtypes (e.g., bacA, ceoB, dfrE, mdtB, amrB, and acrB) were more abundant than others in Antarctic soils. Approximately 60% of the ARGs conferred antibiotic resistance via an efflux mechanism, and a low fraction of ARGs (∼16%) might be present on plasmids. Culturable bacterial consortiums isolated from Antarctic soils were consistently susceptible to most of the tested antibiotics frequently used in clinical therapies. The amrB and ceoB carried by culturable species did not express the resistance to aminoglycoside and fluoroquinolone at the levels of clinical concern. Our results suggest that the wide use of antibiotics may have contributed to developing higher antibiotic resistance and mobility.
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Affiliation(s)
- Ke Yuan
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ke Yu
- School of Environmental and Energy, Peking University Shenzhen Graduate School, Guangdong, 518055, China
| | - Ruiqiang Yang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center of Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Qinghua Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center of Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ying Yang
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Enzhong Chen
- Zhujiang Hospital of Southern Medical University, Guangzhou, 510282, China
| | - Lan Lin
- Zhujiang Hospital of Southern Medical University, Guangzhou, 510282, China
| | - Tiangang Luan
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510275, China; School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wen Chen
- School of Public Health, Sun Yat-sen University, Guangzhou, 510275, China
| | - Baowei Chen
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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Hu M, Sun W, Krumins V, Li F. Arsenic contamination influences microbial community structure and putative arsenic metabolism gene abundance in iron plaque on paddy rice root. Sci Total Environ 2019; 649:405-412. [PMID: 30176453 DOI: 10.1016/j.scitotenv.2018.08.388] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/26/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
Iron (Fe) plaque on rice roots contains a unique microbiota that connects the root and rhizosphere environments. However, the factors controlling the microbial community structure and function in Fe plaque are unknown. We performed Illumina sequencing of 16S rRNA gene amplicons and of total community DNA to compare the microbial community structure and metabolic potential of Fe plaques derived from arsenic (As)- and non-contaminated sites. Geobacter and Hydrogenophaga were identified as the genera that differed significantly in abundance between As-contaminated and control samples (P < 0.05). Significant differences were found between contaminated and control samples in the relative abundances of predicted As functional genes of the microbial community in Fe plaque, in which the relative abundances of the arsC (encoding As(V) reductase) and arsB genes (encoding As(III) efflux membrane protein) in Fe plaque from contaminated sites (YH and TP samples) were significantly higher than those from the control samples (P < 0.05). In addition, the As concentration in Fe plaque contributed significantly to the relative abundance of genes related to As metabolism and correlated most strongly with the abundance of arrB genes (encoding respiratory arsenate reductase, FeS subunit). These results suggest that As contamination influences the community structure and metabolic potential of Fe plaque-associated microorganisms and may help in understanding the environmental behavior of As at the interface of Fe plaque.
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Affiliation(s)
- Min Hu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, PR China
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, PR China; Department of Environmental Sciences, Rutgers University, New Brunswick 08901, USA
| | - Valdis Krumins
- Department of Environmental Sciences, Rutgers University, New Brunswick 08901, USA
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, PR China.
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Las Heras V, Clooney AG, Ryan FJ, Cabrera-Rubio R, Casey PG, Hueston CM, Pinheiro J, Rudkin JK, Melgar S, Cotter PD, Hill C, Gahan CGM. Short-term consumption of a high-fat diet increases host susceptibility to Listeria monocytogenes infection. Microbiome 2019; 7:7. [PMID: 30658700 PMCID: PMC6339339 DOI: 10.1186/s40168-019-0621-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/04/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND A westernized diet comprising a high caloric intake from animal fats is known to influence the development of pathological inflammatory conditions. However, there has been relatively little focus upon the implications of such diets for the progression of infectious disease. Here, we investigated the influence of a high-fat (HF) diet upon parameters that influence Listeria monocytogenes infection in mice. RESULTS We determined that short-term administration of a HF diet increases the number of goblet cells, a known binding site for the pathogen, in the gut and also induces profound changes to the microbiota and promotes a pro-inflammatory gene expression profile in the host. Host physiological changes were concordant with significantly increased susceptibility to oral L. monocytogenes infection in mice fed a HF diet relative to low fat (LF)- or chow-fed animals. Prior to Listeria infection, short-term consumption of HF diet elevated levels of Firmicutes including Coprococcus, Butyricicoccus, Turicibacter and Clostridium XIVa species. During active infection with L. monocytogenes, microbiota changes were further exaggerated but host inflammatory responses were significantly downregulated relative to Listeria-infected LF- or chow-fed groups, suggestive of a profound tempering of the host response influenced by infection in the context of a HF diet. The effects of diet were seen beyond the gut, as a HF diet also increased the sensitivity of mice to systemic infection and altered gene expression profiles in the liver. CONCLUSIONS We adopted a systems approach to identify the effects of HF diet upon L. monocytogenes infection through analysis of host responses and microbiota changes (both pre- and post-infection). Overall, the results indicate that short-term consumption of a westernized diet has the capacity to significantly alter host susceptibility to L. monocytogenes infection concomitant with changes to the host physiological landscape. The findings suggest that diet should be a consideration when developing models that reflect human infectious disease.
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Affiliation(s)
- Vanessa Las Heras
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Adam G Clooney
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Feargal J Ryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Pat G Casey
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Cara M Hueston
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jorge Pinheiro
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Justine K Rudkin
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Silvia Melgar
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Cormac G M Gahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- School of Microbiology, University College Cork, Cork, Ireland.
- School of Pharmacy, University College Cork, Cork, Ireland.
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Fajardo C, García-Cantalejo J, Botías P, Costa G, Nande M, Martin M. New insights into the impact of nZVI on soil microbial biodiversity and functionality. J Environ Sci Health A Tox Hazard Subst Environ Eng 2018; 54:157-167. [PMID: 30588856 DOI: 10.1080/10934529.2018.1535159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/05/2018] [Accepted: 10/09/2018] [Indexed: 06/09/2023]
Abstract
Nanoscale zero-valent iron (nZVI) is a strong reducing agent used for in situ remediation of soil. The impacts of nZVI (5-10% w/w) on the soil microbial biodiversity and functionality of two soils (Lufa 2.2 and 2.4) were assessed. Illumina MiSeq technology was used to evaluate the structure of soil microbiomes after 21 days of exposure. Proteobacteria, Verrucomicrobia, Firmicutes and Actinobacteria were the most abundant phyla in both soils. However, the dynamics of bacterial community composition following nZVI addition differed. nZVI exposure induced pronounced shifts in the microbial composition of soil 2.4, but not in soil 2.2; an increase in Verrucomicrobia abundance was the unique common taxonomic pattern observed in both soils. The PICRUSt approach was applied to predict the functional composition of each metagenome. Environmental information processing function (membrane transport) was decreased in both nZVI-spiked soils, although soil 2.4 samples were enriched in functions involved in cellular processes and metabolism. The effects of nZVI on autochthonous bacterial communities clearly varied with the soil type assessed; changes at the phylogenetic level appeared to be more abundant than those observed at the functional level, and thus, the overall effort of the soil ecosystem might involve the maintenance of functionality following nZVI exposure.
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Affiliation(s)
- Carmen Fajardo
- a Facultad de Farmacia , Universidad de Alcalá , Alcalá de Henares , Madrid , Spain
| | - Jesús García-Cantalejo
- b Genomics Facility , Universidad Complutense, Parque Científico (UCM-PCM) , Madrid , Spain
| | - Pedro Botías
- b Genomics Facility , Universidad Complutense, Parque Científico (UCM-PCM) , Madrid , Spain
| | - Gonzalo Costa
- c Facultad de Veterinaria , Universidad Complutense , Madrid , Spain
| | - Mar Nande
- c Facultad de Veterinaria , Universidad Complutense , Madrid , Spain
| | - Margarita Martin
- c Facultad de Veterinaria , Universidad Complutense , Madrid , Spain
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Fujimoto M, Carey DE, McNamara PJ. Metagenomics reveal triclosan-induced changes in the antibiotic resistome of anaerobic digesters. Environ Pollut 2018; 241:1182-1190. [PMID: 30029328 DOI: 10.1016/j.envpol.2018.06.048] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/15/2018] [Accepted: 06/16/2018] [Indexed: 06/08/2023]
Abstract
Triclosan (TCS) is a broad-spectrum antimicrobial used in a variety of consumer products. While it was recently banned from hand soaps in the US, it is still a key ingredient in a top-selling toothpaste. TCS is a hydrophobic micropollutant that is recalcitrant under anaerobic digestion thereby resulting in high TCS concentrations in biosolids. The objective of this study was to determine the impact of TCS on the antibiotic resistome and potential cross-protection in lab-scale anaerobic digesters using shotgun metagenomics. It was hypothesized that metagenomics would reveal selection for antibiotic resistance genes (ARGs) not previously found in pure culture studies or mixed-culture studies using targeted qPCR. In this study, four different levels of TCS were continuously fed to triplicate lab-scale anaerobic digesters to assess the effect of TCS levels on the antibiotic resistance gene profiles (resistome). Blasting metagenomic reads against antibiotic/metal resistance gene database (BacMet) revealed that ARG diversity and abundance changed along the TCS concentration gradient. While loss of bacterial diversity and digester function were observed in the digester treated with the highest TCS concentration, FabV, which is a known TCS resistance gene, increased in this extremely high TCS environment. The abundance of several other known ARG or metal resistance genes (MRGs), including corA and arsB, also increased as the concentrations of TCS increased. Analysis of other functional genes using SEED database revealed the increase of potentially key genes for resistance including different types of transporters and transposons. These results indicate that antimicrobials can alter the abundance of multiple resistance genes in anaerobic digesters even when function (i.e. methane production) is maintained. This study also suggests that enriched ARGs could be released into environments with biosolids land application.
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Affiliation(s)
- Masanori Fujimoto
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, USA; Soil and Water Sciences Department, University of Florida, Gainesville, FL, USA
| | - Daniel E Carey
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, USA; Brown & Caldwell, Charlotte, NC, USA
| | - Patrick J McNamara
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, USA.
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20
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Liu H, Liu M, Fu X, Zhang Z, Zhu L, Zheng X, Liu J. Astaxanthin Prevents Alcoholic Fatty Liver Disease by Modulating Mouse Gut Microbiota. Nutrients 2018; 10:nu10091298. [PMID: 30217037 PMCID: PMC6164583 DOI: 10.3390/nu10091298] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/07/2018] [Accepted: 09/10/2018] [Indexed: 02/06/2023] Open
Abstract
The development and progression of alcoholic fatty liver disease (AFLD) is influenced by the intestinal microbiota. Astaxanthin, a type of oxygenated carotenoid with strong antioxidant and anti-inflammatory properties, has been proven to relieve liver injury. However, the relationship between the gut microbiota regulation effect of astaxanthin and AFLD improvement remains unclear. The effects of astaxanthin on the AFLD phenotype, overall structure, and composition of gut microbiota were assessed in ethanol-fed C57BL/6J mice. The results showed that astaxanthin treatment significantly relieves inflammation and decreases excessive lipid accumulation and serum markers of liver injury. Furthermore, astaxanthin was shown to significantly decrease species from the phyla Bacteroidetes and Proteobacteria and the genera Butyricimonas, Bilophila, and Parabacteroides, as well as increase species from Verrucomicrobia and Akkermansia compared with the Et (ethanol)group. Thirteen phylotypes related to inflammation as well as correlated with metabolic parameters were significantly altered by ethanol, and then notably reversed by astaxanthin. Additionally, astaxanthin altered 18 and 128 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways involved in lipid metabolism and xenobiotic biodegradation and metabolism at levels 2 and 3, respectively. These findings suggest that Aakkermansia may be a potential target for the astaxanthin-induced alleviation of AFLD and may be a potential treatment for bacterial disorders induced by AFLD.
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Affiliation(s)
- Huilin Liu
- School of Life Sciences, Jilin University, Changchun 130012, China.
| | - Meihong Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China.
- National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun 130118, China.
| | - Xueqi Fu
- School of Life Sciences, Jilin University, Changchun 130012, China.
| | - Ziqi Zhang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Lingyu Zhu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Xin Zheng
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Jingsheng Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China.
- National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun 130118, China.
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21
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Li M, Zhang X, Yang H, Li X, Cui Z. Soil sustainable utilization technology: mechanism of flavonols in resistance process of heavy metal. Environ Sci Pollut Res Int 2018; 25:26669-26681. [PMID: 30003485 DOI: 10.1007/s11356-018-2485-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
The soil ecosystem is critical for agricultural production, affecting many aspects of human health. Soil has more unknown biodiversity and edaphic parameters than any other ecosystem especially when polluted. Metagenomics and metatranscriptomics were applied to research on toxicological characteristics of Pb and resistance mechanism of flavonols. Rhizosphere microorganisms-plants system, a unified system closely related to soil environment was taken as research object. Results emphasize gene expression changes in different test groups. Gene ontology enrichment and eggNOG showed that Pb has a toxic effect on gene and protein function which concentrated on ATPase and ATP-dependent activity. Differentially expressed genes in the flavonols group indicated that flavonols regulate amino acid transport and other transportation process related to Pb stress. Kegg analysis represents that Pb interferences energy production process via not only the upstream like glycolysis and tricarboxylic acid (TCA) circle but also oxidative phosphorylation process, which can also produce reactive oxygen species and impact the eliminating process. Flavonols have shown the ability in alleviating toxic effect of Pb and improving the resistance of plants. Flavonols can recover the electronic transmission and other process in TCA and oxidative phosphorylation via ascorbic acid-glutathione metabolism. Flavonols activated antioxidative process and non-specific immunity via vitamins B2-B6 metabolism.
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Affiliation(s)
- Min Li
- School of Environmental Science and Engineering, Shandong University, Jinan, 250100, China
| | - Xu Zhang
- School of Environmental Science and Engineering, Shandong University, Jinan, 250100, China.
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland.
| | - Huanhuan Yang
- School of Life Science, Shandong University, Jinan, 250100, China
| | - Xinxin Li
- School of Environmental Science and Engineering, Shandong University, Jinan, 250100, China
| | - Zhaojie Cui
- School of Environmental Science and Engineering, Shandong University, Jinan, 250100, China.
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22
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Whitfield-Cargile CM, Chamoun-Emanuelli AM, Cohen ND, Richardson LM, Ajami NJ, Dockery HJ. Differential effects of selective and non-selective cyclooxygenase inhibitors on fecal microbiota in adult horses. PLoS One 2018; 13:e0202527. [PMID: 30138339 PMCID: PMC6107168 DOI: 10.1371/journal.pone.0202527] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/03/2018] [Indexed: 01/15/2023] Open
Abstract
Non-steroidal anti-inflammatory drugs (NSAIDs) are routinely used in both veterinary and human medicine. Gastrointestinal injury is a frequent adverse event associated with NSAID use and evidence suggests that NSAIDs induce gastrointestinal microbial imbalance (i.e., dysbiosis) in both animals and people. It is unknown, however, whether cyclooxygenase (COX)-2-selective NSAIDs induce dysbiosis, or if this phenomenon occurs in horses administered any class of NSAIDs. Therefore, our objectives were to determine whether the composition and diversity of the fecal microbiota of adult horses were altered by NSAID use, and whether these effects differed between non-selective and COX-2-selective NSAIDs. Twenty-five adult horses were randomly assigned to 1 of 3 groups: control (n = 5); phenylbutazone (n = 10); or, firocoxib (n = 10). Treatments were administered for 10 days. Fecal samples were collected every 5 days for 25 days. DNA was extracted from feces and the 16S rRNA gene amplified and sequenced to determine the composition of the microbiota and the inferred metagenome. While the fecal microbiota profile of the control group remained stable over time, the phenylbutazone and firocoxib groups had decreased diversity, and alteration of their microbiota profiles was most pronounced at day 10. Similarly, there were clear alterations of the inferred metagenome at day 10 compared to all other days, indicating that use of both non-selective and selective COX inhibitors resulted in temporary alterations of the fecal microbiota and inferred metagenome. Dysbiosis associated with NSAID administration is clinically relevant because dysbiosis has been associated with several important diseases of horses including abdominal pain (colic), colitis, enteric infections, and laminitis.
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Affiliation(s)
- Canaan M. Whitfield-Cargile
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
| | - Ana M. Chamoun-Emanuelli
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Noah D. Cohen
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Lauren M. Richardson
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Nadim J. Ajami
- The Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, United States of America
| | - Hannah J. Dockery
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
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23
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Yang Y, Wang W. Benzyldimethyldodecyl ammonium chloride shifts the proliferation of functional genes and microbial community in natural water from eutrophic lake. Environ Pollut 2018; 236:355-365. [PMID: 29414358 DOI: 10.1016/j.envpol.2018.01.059] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 01/15/2018] [Accepted: 01/17/2018] [Indexed: 06/08/2023]
Abstract
Benzylalkyldimethylethyl ammonium compounds are pervasive in natural environments and toxic at high concentrations. The changes in functional genes and microbial diversity in eutrophic lake samples exposed to benzyldimethyldodecyl ammonium chloride (BAC) were assessed. BAC exerted negative effects on bacteria abundance, particularly at concentrations of 100 μg L-1 and higher. A significant increase in the number of the quaternary ammonium compound-resistant gene qacA/B was recorded within the 10 μg L-1 treatment after the first day of exposure. Not all antibiotic resistance genes increased in abundance as the concentrations of BAC increased; rather, gene abundances were dependent on the gene type, concentrations of BAC, and contact time. The nitrogen fixation-related gene nifH and ammonia monooxygenase gene amoA were inhibited by high concentrations of BAC after the first day, whereas an increase of the nitrite reductase gene nirK was stimulated by exposure. Microbial communities within higher treatment levels (1000 and 10 000 μg L-1) exhibited significantly different community composition compared to other treatment levels and the control. Selective enrichment of Rheinheimera, Pseudomonas, and Vogesella were found in the higher treatment levels, suggesting that these bacteria have some resistance or degradation capacity to BAC. Genes related with RNA processing and modification, transcription, lipid transport and metabolism, amino acid transport and metabolism, and cell motility of microbial community function were involved in the process exposed to the BAC stress.
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Affiliation(s)
- Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK
| | - Weibo Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
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24
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Marathe NP, Janzon A, Kotsakis SD, Flach CF, Razavi M, Berglund F, Kristiansson E, Larsson DGJ. Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste. Environ Int 2018; 112:279-286. [PMID: 29316517 DOI: 10.1016/j.envint.2017.12.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/21/2017] [Accepted: 12/24/2017] [Indexed: 05/28/2023]
Abstract
Evolution has provided environmental bacteria with a plethora of genes that give resistance to antibiotic compounds. Under anthropogenic selection pressures, some of these genes are believed to be recruited over time into pathogens by horizontal gene transfer. River sediment polluted with fluoroquinolones and other drugs discharged from bulk drug production in India constitute an environment with unprecedented, long-term antibiotic selection pressures. It is therefore plausible that previously unknown resistance genes have evolved and/or are promoted here. In order to search for novel resistance genes, we therefore analyzed such river sediments by a functional metagenomics approach. DNA fragments providing resistance to different antibiotics in E. coli were sequenced using Sanger and PacBio RSII platforms. We recaptured the majority of known antibiotic resistance genes previously identified by open shot-gun metagenomics sequencing of the same samples. In addition, seven novel resistance gene candidates (six beta-lactamases and one amikacin resistance gene) were identified. Two class A beta-lactamases, blaRSA1 and blaRSA2, were phylogenetically close to clinically important ESBLs like blaGES, blaBEL and blaL2, and were further characterized for their substrate spectra. The blaRSA1 protein, encoded as an integron gene cassette, efficiently hydrolysed penicillins, first generation cephalosporins and cefotaxime, while blaRSA2 was an inducible class A beta-lactamase, capable of hydrolyzing carbapenems albeit with limited efficiency, similar to the L2 beta-lactamase from Stenotrophomonas maltophilia. All detected novel genes were associated with plasmid mobilization proteins, integrons, and/or other resistance genes, suggesting a potential for mobility. This study provides insight into a resistome shaped by an exceptionally strong and long-term antibiotic selection pressure. An improved knowledge of mobilized resistance factors in the external environment may make us better prepared for the resistance challenges that we may face in clinics in the future.
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Affiliation(s)
- Nachiket P Marathe
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Anders Janzon
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Stathis D Kotsakis
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Carl-Fredrik Flach
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Mohammad Razavi
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Fanny Berglund
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden.
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25
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Udayangani RMC, Dananjaya SHS, Nikapitiya C, Heo GJ, Lee J, De Zoysa M. Metagenomics analysis of gut microbiota and immune modulation in zebrafish (Danio rerio) fed chitosan silver nanocomposites. Fish Shellfish Immunol 2017; 66:173-184. [PMID: 28479399 DOI: 10.1016/j.fsi.2017.05.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 04/21/2017] [Accepted: 05/03/2017] [Indexed: 05/27/2023]
Abstract
In this study, we evaluated the effects of chitosan silver nanocomposites (CAgNCs) supplemented diet on gut microbial community, goblet cell density, gut morphometry and mRNA expression of immune related and mucin encoding genes in zebrafish. Zebrafish gut microbiota analysis results clearly showed the reduction of phylum Proteobacteria. However, they remained as the major bacterial group in gut with CAgNCs supplemented diet, while the abundance of phylum Fusobacteria and phylum Bacteroidetes were increased notably compared to the control diet fed fish. Total goblet cell density was significantly increased at 30 and 60 days in CAgNCs supplemented group (1.6-fold and 2.0-fold, respectively) compared to the control group indicating enhanced immune function in the gut. CAgNCs supplementation has also increased villi height significantly in the zebrafish mid gut at the end of 30 (95.5 ± 3.7 μm) and 60 days (144.40 ± 4.8 μm) compared to control diet fed fish at 30 (86.90 ± 3.7 μm) and 60 days (96.2 ± 4.8 μm). Furthermore, mRNA expression of immune related genes such as TNF-α (6.2-fold), IL-10 (5.0-fold), IL-12 (9.2-fold), IRF-1 (5.2-fold), Defbl1 (3-fold), Lyz (5.1-fold) and mucin encoding genes were significantly upregulated (above 2-fold) compared to that of control group. The current study revealed that CAgNCs supplemented diet engenders promising effects on fish gut immunity by enhancing beneficial microbial populations, goblet cell density, villi length, and transcriptional regulation of immune related and mucin encoding genes.
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Affiliation(s)
- R M C Udayangani
- College of Veterinary Medicine and Research Institute of Veterinary Medicine, Chungnam National University, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - S H S Dananjaya
- College of Veterinary Medicine and Research Institute of Veterinary Medicine, Chungnam National University, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Chamilani Nikapitiya
- Department of Marine Life Sciences, School of Marine Biomedical Sciences, Jeju National University, Jeju Self-Governing Province 63243, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province 63243, Republic of Korea
| | - Gang-Joon Heo
- College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Jehee Lee
- Department of Marine Life Sciences, School of Marine Biomedical Sciences, Jeju National University, Jeju Self-Governing Province 63243, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province 63243, Republic of Korea
| | - Mahanama De Zoysa
- College of Veterinary Medicine and Research Institute of Veterinary Medicine, Chungnam National University, Yuseong-gu, Daejeon 34134, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province 63243, Republic of Korea.
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26
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Salam LB, Obayori SO, Nwaokorie FO, Suleiman A, Mustapha R. Metagenomic insights into effects of spent engine oil perturbation on the microbial community composition and function in a tropical agricultural soil. Environ Sci Pollut Res Int 2017; 24:7139-7159. [PMID: 28093673 DOI: 10.1007/s11356-017-8364-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/02/2017] [Indexed: 06/06/2023]
Abstract
Analyzing the microbial community structure and functions become imperative for ecological processes. To understand the impact of spent engine oil (SEO) contamination on microbial community structure of an agricultural soil, soil microcosms designated 1S (agricultural soil) and AB1 (agricultural soil polluted with SEO) were set up. Metagenomic DNA extracted from the soil microcosms and sequenced using Miseq Illumina sequencing were analyzed for their taxonomic and functional properties. Taxonomic profiling of the two microcosms by MG-RAST revealed the dominance of Actinobacteria (23.36%) and Proteobacteria (52.46%) phyla in 1S and AB1 with preponderance of Streptomyces (12.83%) and Gemmatimonas (10.20%) in 1S and Geodermatophilus (26.24%), Burkholderia (15.40%), and Pseudomonas (12.72%) in AB1, respectively. Our results showed that soil microbial diversity significantly decreased in AB1. Further assignment of the metagenomic reads to MG-RAST, Cluster of Orthologous Groups (COG) of proteins, Kyoto Encyclopedia of Genes and Genomes (KEGG), GhostKOALA, and NCBI's CDD hits revealed diverse metabolic potentials of the autochthonous microbial community. It also revealed the adaptation of the community to various environmental stressors such as hydrocarbon hydrophobicity, heavy metal toxicity, oxidative stress, nutrient starvation, and C/N/P imbalance. To the best of our knowledge, this is the first study that investigates the effect of SEO perturbation on soil microbial communities through Illumina sequencing. The results indicated that SEO contamination significantly affects soil microbial community structure and functions leading to massive loss of nonhydrocarbon degrading indigenous microbiota and enrichment of hydrocarbonoclastic organisms such as members of Proteobacteria and Actinobacteria.
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Affiliation(s)
- Lateef B Salam
- Microbiology Unit, Department of Biological Sciences, Al-Hikmah University, Ilorin, Kwara, Nigeria.
| | - Sunday O Obayori
- Department of Microbiology, Lagos State University, Ojo, Lagos, Nigeria
| | - Francisca O Nwaokorie
- Department of Medical Laboratory Science, College of Medicine, University of Lagos, Akoka, Lagos, Nigeria
| | - Aisha Suleiman
- Microbiology Unit, Department of Biological Sciences, Al-Hikmah University, Ilorin, Kwara, Nigeria
| | - Raheemat Mustapha
- Microbiology Unit, Department of Biological Sciences, Al-Hikmah University, Ilorin, Kwara, Nigeria
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Ly M, Jones MB, Abeles SR, Santiago-Rodriguez TM, Gao J, Chan IC, Ghose C, Pride DT. Transmission of viruses via our microbiomes. Microbiome 2016; 4:64. [PMID: 27912785 PMCID: PMC5134127 DOI: 10.1186/s40168-016-0212-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 11/24/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Bacteria inhabiting the human body have important roles in a number of physiological processes and are known to be shared amongst genetically-related individuals. Far less is known about viruses inhabiting the human body, but their ecology suggests they may be shared between close contacts. RESULTS Here, we report the ecology of viruses in the guts and mouths of a cohort and demonstrate that substantial numbers of gut and oral viruses were shared amongst genetically unrelated, cohabitating individuals. Most of these viruses were bacteriophages, and each individual had distinct oral and gut viral ecology from their housemates despite the fact that some of their bacteriophages were shared. The distribution of bacteriophages over time within households indicated that they were frequently transmitted between the microbiomes of household contacts. CONCLUSIONS Because bacteriophages may shape human oral and gut bacterial ecology, their transmission to household contacts suggests they could have substantial roles in shaping the microbiota within a household.
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Affiliation(s)
- Melissa Ly
- Department of Pathology, University of California, San Diego, 92093, USA
| | | | - Shira R Abeles
- Department of Medicine, University of California, San Diego, 92093, USA
| | | | - Jonathan Gao
- Department of Pathology, University of California, San Diego, 92093, USA
| | - Ivan C Chan
- Department of Pathology, University of California, San Diego, 92093, USA
| | | | - David T Pride
- Department of Pathology, University of California, San Diego, 92093, USA.
- Department of Medicine, University of California, San Diego, 92093, USA.
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28
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Abstract
The distribution of potential clinically relevant antibiotic resistance (AR) genes across soil, water, animal, plant and human microbiomes is not well understood. We aimed to investigate if there were differences in the distribution and relative abundances of resistance genes across a variety of ecological niches. All sequence reads (human, animal, water, soil, plant and insect metagenomes) from the MG-RAST database were downloaded and assembled into a local sequence database. We show that there are many reservoirs of the basic form of resistance genes e.g. blaTEM, but the human and mammalian gut microbiomes contain the widest diversity of clinically relevant resistance genes using metagenomic analysis. The human microbiomes contained a high relative abundance of resistance genes, while the relative abundances varied greatly in the marine and soil metagenomes, when datasets with greater than one million genes were compared. While these results reflect a bias in the distribution of AR genes across the metagenomes, we note this interpretation with caution. Metagenomics analysis includes limits in terms of detection and identification of AR genes in complex and diverse microbiome population. Therefore, if we do not detect the AR gene is it in fact not there or just below the limits of our techniques?
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Affiliation(s)
- David Fitzpatrick
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, W23 F2H6, Ireland
| | - Fiona Walsh
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, W23 F2H6, Ireland
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29
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Lyte M, Chapel A, Lyte JM, Ai Y, Proctor A, Jane JL, Phillips GJ. Resistant Starch Alters the Microbiota-Gut Brain Axis: Implications for Dietary Modulation of Behavior. PLoS One 2016; 11:e0146406. [PMID: 26745269 PMCID: PMC4706316 DOI: 10.1371/journal.pone.0146406] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/16/2015] [Indexed: 12/21/2022] Open
Abstract
The increasing recognition that the gut microbiota plays a central role in behavior and cognition suggests that the manipulation of microbial taxa through diet may provide a means by which behavior may be altered in a reproducible and consistent manner in order to achieve a beneficial outcome for the host. Resistant starch continues to receive attention as a dietary intervention that can benefit the host through mechanisms that include altering the intestinal microbiota. Given the interest in dietary approaches to improve health, the aim of this study was to investigate whether the use of dietary resistant starch in mice to alter the gut microbiota also results in a change in behavior. Forty-eight 6 week-old male Swiss-Webster mice were randomly assigned to 3 treatment groups (n = 16 per group) and fed either a normal corn starch diet (NCS) or diets rich in resistant starches HA7 diet (HA7) or octenyl-succinate HA7 diet (OS-HA7) for 6 week and monitored for weight, behavior and fecal microbiota composition. Animals fed an HA7 diet displayed comparable weight gain over the feeding period to that recorded for NCS-fed animals while OS-HA7 displayed a lower weight gain as compared to either NCS or HA7 animals (ANOVA p = 0.0001; NCS:HA7 p = 0.244; HA7:OS-HA7 p<0.0001; NCS:OS-HA7 p<0.0001). Analysis of fecal microbiota using 16s rRNA gene taxonomic profiling revealed that each diet corresponded with a unique gut microbiota. The distribution of taxonomic classes was dynamic over the 6 week feeding period for each of the diets. At the end of the feeding periods, the distribution of taxa included statistically significant increases in members of the phylum Proteobacteria in OS-HA7 fed mice, while the Verrucomicrobia increased in HA7 fed mice over that of mice fed OS-HA7. At the class level, members of the class Bacilli decreased in the OS-HA7 fed group, and Actinobacteria, which includes the genus Bifidobacteria, was enriched in the HA7 fed group compared to the control diet. Behavioral analysis revealed that animals demonstrated profound anxiety-like behavior as observed by performance on the elevated-plus maze with time spent by the mice in the open arm (ANOVA p = 0.000; NCS:HA7 p = 0.004; NCS:OS-HA7 p = 1.000; HA7:OS-HA7 p = 0.0001) as well as entries in the open arm (ANOVA p = 0.039; NCS:HA7 p = 0.041; HA7:OS-HA7 p = 0.221; NCS:OS-HA7 p = 1.000). Open-field behavior, a measure of general locomotion and exploration, revealed statistically significant differences between groups in locomotion as a measure of transitions across quadrant boundaries. Additionally, the open-field assay revealed decreased exploration as well as decreased rearing in HA7 and OS-HA7 fed mice demonstrating a consistent pattern of increased anxiety-like behavior among these groups. Critically, behavior was not correlated with weight. These results indicate that diets based on resistant starch can be utilized to produce quantifiable changes in the gut microbiota and should be useful to "dial-in" a specific microbiome that is unique to a particular starch composition. However, undesirable effects can also be associated with resistant starch, including lack of weight gain and increased anxiety-like behaviors. These observations warrant careful consideration when developing diets rich in resistant starch in humans and animal models.
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Affiliation(s)
- Mark Lyte
- Department of Immunotherapeutics and Biotechnology, School of Pharmacy, Texas Tech University Health Sciences Center, Abilene, Texas, 79606, United States of America
- Department of Veterinary Microbiology & Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Ashley Chapel
- School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, 79905, United States of America
| | - Joshua M. Lyte
- Department of Food Science and Human Nutrition, College of Human Sciences, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Yongfeng Ai
- Department of Food Science and Human Nutrition, College of Human Sciences, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Alexandra Proctor
- Department of Veterinary Microbiology & Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Jay-Lin Jane
- Department of Food Science and Human Nutrition, College of Human Sciences, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Gregory J. Phillips
- Department of Veterinary Microbiology & Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, 50011, United States of America
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Yin J, Zhang XX, Wu B, Xian Q. Metagenomic insights into tetracycline effects on microbial community and antibiotic resistance of mouse gut. Ecotoxicology 2015; 24:2125-2132. [PMID: 26423395 DOI: 10.1007/s10646-015-1540-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/16/2015] [Indexed: 06/05/2023]
Abstract
Antibiotics have been widely used for disease prevention and treatment of the human and animals, and for growth promotion in animal husbandry. Antibiotics can disturb the intestinal microbial community, which play a fundamental role in animals' health. Misuse or overuse of antibiotics can result in increase and spread of microbial antibiotic resistance, threatening human health and ecological safety. In this study, we used Illumina Hiseq sequencing, (1)H nuclear magnetic resonance spectroscopy and metagenomics approaches to investigate intestinal microbial community shift and antibiotic resistance alteration of the mice drinking the water containing tetracycline hydrochloride (TET). Two-week TET administration caused reduction of gut microbial diversity (from 194 to 89 genera), increase in Firmicutes abundance (from 24.9 to 39.8%) and decrease in Bacteroidetes abundance (from 69.8 to 51.2%). Metagenomic analysis showed that TET treatment affected the intestinal microbial functions of carbohydrate, ribosomal, cell wall/membrane/envelope and signal transduction, which is evidenced by the alteration in the metabolites of mouse serum. Meanwhile, in the mouse intestinal microbiota, TET treatment enhanced the abundance of antibiotic resistance genes (ARGs) (from 307.3 to 1492.7 ppm), plasmids (from 425.4 to 3235.1 ppm) and integrons (from 0.8 to 179.6 ppm) in mouse gut. Our results indicated that TET administration can disturb gut microbial community and physiological metabolism of mice, and increase the opportunity of ARGs and mobile genetic elements entering into the environment with feces discharge.
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Affiliation(s)
- Jinbao Yin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Road, Nanjing, 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Road, Nanjing, 210023, China.
| | - Bing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Road, Nanjing, 210023, China
| | - Qiming Xian
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Road, Nanjing, 210023, China.
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Wang WL, Xu SY, Ren ZG, Tao L, Jiang JW, Zheng SS. Application of metagenomics in the human gut microbiome. World J Gastroenterol 2015; 21:803-814. [PMID: 25624713 PMCID: PMC4299332 DOI: 10.3748/wjg.v21.i3.803] [Citation(s) in RCA: 202] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/30/2014] [Accepted: 11/11/2014] [Indexed: 02/06/2023] Open
Abstract
There are more than 1000 microbial species living in the complex human intestine. The gut microbial community plays an important role in protecting the host against pathogenic microbes, modulating immunity, regulating metabolic processes, and is even regarded as an endocrine organ. However, traditional culture methods are very limited for identifying microbes. With the application of molecular biologic technology in the field of the intestinal microbiome, especially metagenomic sequencing of the next-generation sequencing technology, progress has been made in the study of the human intestinal microbiome. Metagenomics can be used to study intestinal microbiome diversity and dysbiosis, as well as its relationship to health and disease. Moreover, functional metagenomics can identify novel functional genes, microbial pathways, antibiotic resistance genes, functional dysbiosis of the intestinal microbiome, and determine interactions and co-evolution between microbiota and host, though there are still some limitations. Metatranscriptomics, metaproteomics and metabolomics represent enormous complements to the understanding of the human gut microbiome. This review aims to demonstrate that metagenomics can be a powerful tool in studying the human gut microbiome with encouraging prospects. The limitations of metagenomics to be overcome are also discussed. Metatranscriptomics, metaproteomics and metabolomics in relation to the study of the human gut microbiome are also briefly discussed.
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Guo X, Liu S, Wang Z, Zhang XX, Li M, Wu B. Metagenomic profiles and antibiotic resistance genes in gut microbiota of mice exposed to arsenic and iron. Chemosphere 2014; 112:1-8. [PMID: 25048881 DOI: 10.1016/j.chemosphere.2014.03.068] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 03/13/2014] [Accepted: 03/16/2014] [Indexed: 05/18/2023]
Abstract
Iron (Fe) has been widely applied to treat arsenic (As)-contaminated water, and Fe could influence bioavailability and toxicity of As. However, little is known about the impact of As and/or Fe on gut microbiota, which plays important roles in host health. In this study, high-throughput sequencing and quantitative real time PCR were applied to analyze the impact of As and Fe on mouse gut microbiota. Co-exposure of As and Fe mitigated effects on microbial community to a certain extent. Correlation analysis showed the shifts in gut microbiota caused by As and/or Fe exposure might be important reason of changes in metabolic profiles of mouse. For antibiotic resistance genes (ARGs), co-exposure of As and Fe increased types and abundance of ARGs. But for high abundance ARGs, such as tetQ, tetO and tetM, co-exposure of As and Fe mitigated effects on their abundances compared to exposure to As and Fe alone. No obvious relationship between ARGs and mobile genetic elements were found. The changes in ARGs caused by metal exposure might be due to the alteration of gut microbial diversity. Our results show that changes of gut microbial community caused by As and/or Fe can influence host metabolisms and abundances of ARGs in gut, indicating that changes of gut microbiota should be considered during the risk assessment of As and/or Fe.
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Affiliation(s)
- Xuechao Guo
- State Key Lab of Pollutant Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Su Liu
- State Key Lab of Pollutant Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Zhu Wang
- State Key Lab of Pollutant Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Xu-xiang Zhang
- State Key Lab of Pollutant Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Mei Li
- State Key Lab of Pollutant Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Bing Wu
- State Key Lab of Pollutant Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China.
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Lu K, Abo RP, Schlieper KA, Graffam ME, Levine S, Wishnok JS, Swenberg JA, Tannenbaum SR, Fox JG. Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis. Environ Health Perspect 2014; 122:284-91. [PMID: 24413286 PMCID: PMC3948040 DOI: 10.1289/ehp.1307429] [Citation(s) in RCA: 372] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 01/09/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND The human intestine is host to an enormously complex, diverse, and vast microbial community-the gut microbiota. The gut microbiome plays a profound role in metabolic processing, energy production, immune and cognitive development, epithelial homeostasis, and so forth. However, the composition and diversity of the gut microbiome can be readily affected by external factors, which raises the possibility that exposure to toxic environmental chemicals leads to gut microbiome alteration, or dysbiosis. Arsenic exposure affects large human populations worldwide and has been linked to a number of diseases, including cancer, diabetes, and cardiovascular disorders. OBJECTIVES We investigated the impact of arsenic exposure on the gut microbiome composition and its metabolic profiles. METHODS We used an integrated approach combining 16S rRNA gene sequencing and mass spectrometry-based metabolomics profiling to examine the functional impact of arsenic exposure on the gut microbiome. RESULTS 16S rRNA gene sequencing revealed that arsenic significantly perturbed the gut microbiome composition in C57BL/6 mice after exposure to 10 ppm arsenic for 4 weeks in drinking water. Moreover, metabolomics profiling revealed a concurrent effect, with a number of gut microflora-related metabolites being perturbed in multiple biological matrices. CONCLUSIONS Arsenic exposure not only alters the gut microbiome community at the abundance level but also substantially disturbs its metabolic profiles at the function level. These findings may provide novel insights regarding perturbations of the gut microbiome and its functions as a potential new mechanism by which arsenic exposure leads to or exacerbates human diseases. CITATION Lu K, Abo RP, Schlieper KA, Graffam ME, Levine S, Wishnok JS, Swenberg JA, Tannenbaum SR, Fox JG. 2014. Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis. Environ Health Perspect 122:284-291; http://dx.doi.org/10.1289/ehp.1307429.
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Affiliation(s)
- Kun Lu
- Department of Biological Engineering
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Zhou A, He Z, Qin Y, Lu Z, Deng Y, Tu Q, Hemme CL, Van Nostrand JD, Wu L, Hazen TC, Arkin AP, Zhou J. StressChip as a high-throughput tool for assessing microbial community responses to environmental stresses. Environ Sci Technol 2013; 47:9841-9849. [PMID: 23889170 DOI: 10.1021/es4018656] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Microbial community responses to environmental stresses are critical for microbial growth, survival, and adaptation. To fill major gaps in our ability to discern the influence of environmental changes on microbial communities from engineered and natural environments, a functional gene-based microarray, termed StressChip, has been developed. First, 46 functional genes involved in microbial responses to environmental stresses such as changes to temperature, osmolarity, oxidative status, nutrient limitation, or general stress response were selected and curated. A total of 22,855 probes were designed, covering 79,628 coding sequences from 985 bacterial, 76 archaeal, and 59 eukaryotic species/strains. Probe specificity was computationally verified. Second, the usefulness of functional genes as indicators of stress response was examined by surveying their distribution in metagenome data sets. The abundance of individual stress response genes is consistent with expected distributions based on respective habitats. Third, the StressChip was used to analyze marine microbial communities from the Deepwater Horizon oil spill. That functional stress response genes were detected in higher abundance (p < 0.05) in oil plume compared to nonplume samples indicated shifts in community composition and structure, consistent with previous results. In summary, StressChip provides a new tool for accessing microbial community functional structure and responses to environmental changes.
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Affiliation(s)
- Aifen Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
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Lindström C, Xu J, Oste R, Holst O, Molin G. Oral administration of live exopolysaccharide-producing Pediococcus parvulus, but not purified exopolysaccharide, suppressed Enterobacteriaceae without affecting bacterial diversity in ceca of mice. Appl Environ Microbiol 2013; 79:5030-7. [PMID: 23770909 PMCID: PMC3754715 DOI: 10.1128/aem.01456-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/09/2013] [Indexed: 01/19/2023] Open
Abstract
Growing evidence indicates that the gut microbiota could have an important role in the development of diet- and lifestyle-induced diseases. It has been shown that modulation of the gut microbiota by means of probiotics and prebiotics could improve host health. An oat-based product fermented by the exopolysaccharide (EPS)-producing organism Pediococcus parvulus 2.6 has been reported to have a bifidogenic effect. To find out whether the effect could be attributed to the EPS or the bacterium, mice were fed a diet supplemented with 2% purified EPS or 10(8) CFU/g of live P. parvulus 2.6 for 6 weeks. Both supplementations altered the gut microbiota composition but in different directions. Purified EPS not only significantly lowered the microbial diversity (P < 0.001) but decreased the bifidobacterial population (P = 0.01). In contrast, the live EPS-producing bacterium P. parvulus 2.6 antagonized Enterobacteriaceae without disturbing the homeostasis of the cecal microbiota.
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Affiliation(s)
- Cecilia Lindström
- Division of Biotechnology, Department of Chemistry, Lund University, Lund, Sweden.
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Murphy P, Dal Bello F, O'Doherty J, Arendt EK, Sweeney T, Coffey A. Analysis of bacterial community shifts in the gastrointestinal tract of pigs fed diets supplemented with β-glucan from Laminaria digitata, Laminaria hyperborea and Saccharomyces cerevisiae. Animal 2013; 7:1079-87. [PMID: 23446108 DOI: 10.1017/s1751731113000165] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This study was designed to evaluate the effects of algal and yeast β-glucans on the porcine gastrointestinal microbiota, specifically the community of Lactobacillus, Bifidobacterium and coliforms. A total of 48 pigs were fed four diets over a 28-day period to determine the effect that each had on these communities. The control diet consisted of wheat and soya bean meal. The remaining three diets contained wheat and soya bean meal supplemented with β-glucan at 250 g/tonne from Laminaria digitata, Laminaria hyperborea or Saccharomyces cerevisiae. Faecal samples were collected from animals before feeding each diet and after the feeding period. The animals were slaughtered the following day and samples were collected from the stomach, ileum, caecum, proximal colon and distal colon. Alterations in Lactobacillus in the gastrointestinal tract (GIT) were analysed using denaturing gradient gel electrophoresis (DGGE) profiles generated by group-specific 16S rRNA gene PCR amplicons. Plate count analysis was also performed to quantify total coliforms. DGGE profiles indicated that all β-glucan diets provoked the emergence of a richer community of Lactobacillus. The richest community of lactobacilli emerged after feeding L. digitata (LD β-glucan). Plate count analysis revealed that the L. hyperborea (LH β-glucan) diet had a statistically significant effect on the coliform counts in the proximal colon in comparison with the control diet. β-glucan from L. digitata and S. cerevisiae also generally reduced coliforms but to a lesser extent. Nevertheless, the β-glucan diets did not significantly reduce levels of Lactobacillus or Bifidobacterium. DGGE analysis of GIT samples indicated that the three β-glucan diets generally promoted the establishment of a more varied range of Lactobacillus species in the caecum, proximal and distal colon. The LH β-glucan had the most profound reducing effect on coliform counts when compared with the control diet and diets supplemented with L. digitata and S. cerevisiae β-glucans.
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Affiliation(s)
- P Murphy
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
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Gatica J, Cytryn E. Impact of treated wastewater irrigation on antibiotic resistance in the soil microbiome. Environ Sci Pollut Res Int 2013; 20:3529-38. [PMID: 23378260 PMCID: PMC3646162 DOI: 10.1007/s11356-013-1505-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Accepted: 01/17/2013] [Indexed: 05/19/2023]
Abstract
The reuse of treated wastewater (TWW) for irrigation is a practical solution for overcoming water scarcity, especially in arid and semiarid regions of the world. However, there are several potential environmental and health-related risks associated with this practice. One such risk stems from the fact that TWW irrigation may increase antibiotic resistance (AR) levels in soil bacteria, potentially contributing to the global propagation of clinical AR. Wastewater treatment plant (WWTP) effluents have been recognized as significant environmental AR reservoirs due to selective pressure generated by antibiotics and other compounds that are frequently detected in effluents. This review summarizes a myriad of recent studies that have assessed the impact of anthropogenic practices on AR in environmental bacterial communities, with specific emphasis on elucidating the potential effects of TWW irrigation on AR in the soil microbiome. Based on the current state of the art, we conclude that contradictory to freshwater environments where WWTP effluent influx tends to expand antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes levels, TWW irrigation does not seem to impact AR levels in the soil microbiome. Although this conclusion is a cause for cautious optimism regarding the future implementation of TWW irrigation, we conclude that further studies aimed at assessing the scope of horizontal gene transfer between effluent-associated ARB and soil bacteria need to be further conducted before ruling out the possible contribution of TWW irrigation to antibiotic-resistant reservoirs in irrigated soils.
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Affiliation(s)
- Joao Gatica
- Institute of Soil, Water and Environmental Sciences, Volcani Center, Agricultural Research Organization, Bet Dagan, Israel
- Department of Agroecology and Plant Health, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, Volcani Center, Agricultural Research Organization, Bet Dagan, Israel
- P.O. Box 6, Bet Dagan, 50250 Israel
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Choi JJ, Eum SY, Rampersaud E, Daunert S, Abreu MT, Toborek M. Exercise attenuates PCB-induced changes in the mouse gut microbiome. Environ Health Perspect 2013; 121:725-30. [PMID: 23632211 PMCID: PMC3672930 DOI: 10.1289/ehp.1306534] [Citation(s) in RCA: 211] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 04/23/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND The gut microbiome, a dynamic bacterial community that interacts with the host, is integral to human health because it regulates energy metabolism and immune functions. The gut microbiome may also play a role in risks from environmental toxicants. OBJECTIVES We investigated the effects of polychlorinated biphenyls (PCBs) and exercise on the composition and structure of the gut microbiome in mice. METHODS After mice exercised voluntarily for 5 weeks, they were treated by oral gavage with a mixture of environmentally relevant PCB congeners (PCB153, PCB138, and PCB180; total PCB dose, 150 µmol/kg) for 2 days. We then assessed the microbiome by determination of 16S rRNA using microarray analysis. RESULTS Oral exposure to PCBs significantly altered the abundance of the gut microbiome in mice primarily by decreasing the levels of Proteobacteria. The activity level of the mice correlated with a substantial shift in abundance, biodiversity, and composition of the microbiome. Importantly, exercise attenuated PCB-induced changes in the gut microbiome. CONCLUSIONS Our results show that oral exposure to PCBs can induce substantial changes in the gut microbiome, which may then influence their systemic toxicity. These changes can be attenuated by behavioral factors, such as voluntary exercise.
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Affiliation(s)
- Jeong June Choi
- Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Miami, Florida 33136, USA
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Kim SW, Suda W, Kim S, Oshima K, Fukuda S, Ohno H, Morita H, Hattori M. Robustness of gut microbiota of healthy adults in response to probiotic intervention revealed by high-throughput pyrosequencing. DNA Res 2013; 20:241-53. [PMID: 23571675 PMCID: PMC3686430 DOI: 10.1093/dnares/dst006] [Citation(s) in RCA: 228] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 02/16/2013] [Indexed: 12/22/2022] Open
Abstract
Probiotics are live microorganisms that potentially confer beneficial outcomes to host by modulating gut microbiota in the intestine. The aim of this study was to comprehensively investigate effects of probiotics on human intestinal microbiota using 454 pyrosequencing of bacterial 16S ribosomal RNA genes with an improved quantitative accuracy for evaluation of the bacterial composition. We obtained 158 faecal samples from 18 healthy adult Japanese who were subjected to intervention with 6 commercially available probiotics containing either Bifidobacterium or Lactobacillus strains. We then analysed and compared bacterial composition of the faecal samples collected before, during, and after probiotic intervention by Operational taxonomic units (OTUs) and UniFrac distances. The results showed no significant changes in the overall structure of gut microbiota in the samples with and without probiotic administration regardless of groups and types of the probiotics used. We noticed that 32 OTUs (2.7% of all analysed OTUs) assigned to the indigenous species showed a significant increase or decrease of ≥10-fold or a quantity difference in >150 reads on probiotic administration. Such OTUs were found to be individual specific and tend to be unevenly distributed in the subjects. These data, thus, suggest robustness of the gut microbiota composition in healthy adults on probiotic administration.
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Affiliation(s)
- Seok-Won Kim
- Center for Omics and Bioinformatics, The Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8561, Japan
| | - Wataru Suda
- Center for Omics and Bioinformatics, The Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8561, Japan
| | - Sangwan Kim
- Center for Omics and Bioinformatics, The Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8561, Japan
| | - Kenshiro Oshima
- Center for Omics and Bioinformatics, The Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8561, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Mizukami 246-2, Kakuganji, Tsuruoka City, Yamagata 997-0052, Japan
- Laboratory for Epithelial Immunobiology, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama 230-0045, Japan
| | - Hiroshi Ohno
- Laboratory for Epithelial Immunobiology, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama 230-0045, Japan
| | - Hidetoshi Morita
- School of Veterinary Medicine, Azabu University, Fuchinobe 1-17-71, Chuo-ku, Sagamihara, Kanagawa 252-5201, Japan
| | - Masahira Hattori
- Center for Omics and Bioinformatics, The Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8561, Japan
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Noack J, Timm D, Hospattankar A, Slavin J. Fermentation profiles of wheat dextrin, inulin and partially hydrolyzed guar gum using an in vitro digestion pretreatment and in vitro batch fermentation system model. Nutrients 2013; 5:1500-10. [PMID: 23645025 PMCID: PMC3708332 DOI: 10.3390/nu5051500] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 03/29/2013] [Accepted: 04/18/2013] [Indexed: 12/20/2022] Open
Abstract
This study investigated the fermentation and microbiota profiles of three fibers, wheat dextrin (WD), partially hydrolyzed guar gum (PHGG), and inulin, since little is known about the effects of WD and PHGG on gut microbiota. A treatment of salivary amylase, pepsin, and pancreatin was used to better physiologic digestion. Fibers (0.5 g) were fermented in triplicate including a control group without fiber for 0, 4, 8, 12, and 24 h. Analysis of pH, gas volume, hydrogen and methane gases, and short chain fatty acid (SCFA) concentrations were completed at each time point. Quantitative polymerase chain reaction (qPCR) was used to measure Bifidobacteria and Lactobacillus CFUs at 24 h. WD produced the least gas during fermentation at 8, 12, and 24 h (P < 0.0001), while inulin produced the most by 8 h (P < 0.0001). Each fiber reached its lowest pH value at different time points with inulin at 8 h (mean ± SE) (5.94 ± 0.03), PHGG at 12 h (5.98 ± 0.01), and WD at 24 h (6.17 ± 0.03). All fibers had higher total SCFA concentrations compared to the negative control (P < 0.05) at 24 h. At 24 h, inulin produced significantly (P = 0.0016) more butyrate than WD with PHGG being similar to both. An exploratory microbial analysis (log10 CFU/µL) showed WD had CFU for Bifidobacteria (6.12) and Lactobacillus (7.15) compared with the control (4.92 and 6.35, respectively). Rate of gas production is influenced by fiber source and may affect tolerance in vivo. Exploratory microbiota data hint at high levels of Bifidobacteria for WD, but require more robust investigation to corroborate these findings.
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Affiliation(s)
- Jackie Noack
- Department of Food Science and Nutrition, University of Minnesota, 225 Food Science and Nutrition, 1334 Eckles Ave, St. Paul, MN 55108, USA; E-Mails: (J.N.); (D.T.)
| | - Derek Timm
- Department of Food Science and Nutrition, University of Minnesota, 225 Food Science and Nutrition, 1334 Eckles Ave, St. Paul, MN 55108, USA; E-Mails: (J.N.); (D.T.)
| | | | - Joanne Slavin
- Department of Food Science and Nutrition, University of Minnesota, 225 Food Science and Nutrition, 1334 Eckles Ave, St. Paul, MN 55108, USA; E-Mails: (J.N.); (D.T.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-612-624-7234; Fax: +1-612-625-5272
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Abstract
BACKGROUND Recent studies in animals have shown a mechanistic link between intestinal microbial metabolism of the choline moiety in dietary phosphatidylcholine (lecithin) and coronary artery disease through the production of a proatherosclerotic metabolite, trimethylamine-N-oxide (TMAO). We investigated the relationship among intestinal microbiota-dependent metabolism of dietary phosphatidylcholine, TMAO levels, and adverse cardiovascular events in humans. METHODS We quantified plasma and urinary levels of TMAO and plasma choline and betaine levels by means of liquid chromatography and online tandem mass spectrometry after a phosphatidylcholine challenge (ingestion of two hard-boiled eggs and deuterium [d9]-labeled phosphatidylcholine) in healthy participants before and after the suppression of intestinal microbiota with oral broad-spectrum antibiotics. We further examined the relationship between fasting plasma levels of TMAO and incident major adverse cardiovascular events (death, myocardial infarction, or stroke) during 3 years of follow-up in 4007 patients undergoing elective coronary angiography. RESULTS Time-dependent increases in levels of both TMAO and its d9 isotopologue, as well as other choline metabolites, were detected after the phosphatidylcholine challenge. Plasma levels of TMAO were markedly suppressed after the administration of antibiotics and then reappeared after withdrawal of antibiotics. Increased plasma levels of TMAO were associated with an increased risk of a major adverse cardiovascular event (hazard ratio for highest vs. lowest TMAO quartile, 2.54; 95% confidence interval, 1.96 to 3.28; P<0.001). An elevated TMAO level predicted an increased risk of major adverse cardiovascular events after adjustment for traditional risk factors (P<0.001), as well as in lower-risk subgroups. CONCLUSIONS The production of TMAO from dietary phosphatidylcholine is dependent on metabolism by the intestinal microbiota. Increased TMAO levels are associated with an increased risk of incident major adverse cardiovascular events. (Funded by the National Institutes of Health and others.).
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Affiliation(s)
- W H Wilson Tang
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland 44195, USA
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Dang H, Zhou H, Zhang Z, Yu Z, Hua E, Liu X, Jiao N. Molecular detection of Candidatus Scalindua pacifica and environmental responses of sediment anammox bacterial community in the Bohai Sea, China. PLoS One 2013; 8:e61330. [PMID: 23577216 PMCID: PMC3620062 DOI: 10.1371/journal.pone.0061330] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 03/08/2013] [Indexed: 11/18/2022] Open
Abstract
The Bohai Sea is a large semi-enclosed shallow water basin, which receives extensive river discharges of various terrestrial and anthropogenic materials such as sediments, nutrients and contaminants. How these terrigenous inputs may influence the diversity, community structure, biogeographical distribution, abundance and ecophysiology of the sediment anaerobic ammonium oxidation (anammox) bacteria was unknown. To answer this question, an investigation employing both 16S rRNA and hzo gene biomarkers was carried out. Ca. Scalindua bacteria were predominant in the surface sediments of the Bohai Sea, while non-Scalindua anammox bacteria were also detected in the Yellow River estuary and inner part of Liaodong Bay that received strong riverine and anthropogenic impacts. A novel 16S rRNA gene sequence clade was identified, putatively representing an anammox bacterial new candidate species tentatively named "Ca. Scalindua pacifica". Several groups of environmental factors, usually with distinct physicochemical or biogeochemical natures, including general marine and estuarine physicochemical properties, availability of anammox substrates (inorganic N compounds), alternative reductants and oxidants, environmental variations caused by river discharges and associated contaminants such as heavy metals, were identified to likely play important roles in influencing the ecology and biogeochemical functioning of the sediment anammox bacteria. In addition to inorganic N compounds that might play a key role in shaping the anammox microbiota, organic carbon, organic nitrogen, sulfate, sulfide and metals all showed the potentials to participate in the anammox process, releasing the strict dependence of the anammox bacteria upon the direct availability of inorganic N nutrients that might be limiting in certain areas of the Bohai Sea. The importance of inorganic N nutrients and certain other environmental factors to the sediment anammox microbiota suggests that these bacteria were active for the in situ N transforming process and maintained a versatile life style well adapted to the varying environmental conditions of the studied coastal ocean.
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Affiliation(s)
- Hongyue Dang
- State Key Laboratory of Heavy Oil Processing, Key Laboratory of Bioengineering and Biotechnology in Universities of Shandong, Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, China.
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Bajaj JS, Heuman DM, Sanyal AJ, Hylemon PB, Sterling RK, Stravitz RT, Fuchs M, Ridlon JM, Daita K, Monteith P, Noble NA, White MB, Fisher A, Sikaroodi M, Rangwala H, Gillevet PM. Modulation of the metabiome by rifaximin in patients with cirrhosis and minimal hepatic encephalopathy. PLoS One 2013; 8:e60042. [PMID: 23565181 PMCID: PMC3615021 DOI: 10.1371/journal.pone.0060042] [Citation(s) in RCA: 302] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 02/19/2013] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED Hepatic encephalopathy (HE) represents a dysfunctional gut-liver-brain axis in cirrhosis which can negatively impact outcomes. This altered gut-brain relationship has been treated using gut-selective antibiotics such as rifaximin, that improve cognitive function in HE, especially its subclinical form, minimal HE (MHE). However, the precise mechanism of the action of rifaximin in MHE is unclear. We hypothesized that modulation of gut microbiota and their end-products by rifaximin would affect the gut-brain axis and improve cognitive performance in cirrhosis. Aim To perform a systems biology analysis of the microbiome, metabolome and cognitive change after rifaximin in MHE. METHODS Twenty cirrhotics with MHE underwent cognitive testing, endotoxin analysis, urine/serum metabolomics (GC and LC-MS) and fecal microbiome assessment (multi-tagged pyrosequencing) at baseline and 8 weeks post-rifaximin 550 mg BID. Changes in cognition, endotoxin, serum/urine metabolites (and microbiome were analyzed using recommended systems biology techniques. Specifically, correlation networks between microbiota and metabolome were analyzed before and after rifaximin. RESULTS There was a significant improvement in cognition(six of seven tests improved, p<0.01) and endotoxemia (0.55 to 0.48 Eu/ml, p = 0.02) after rifaximin. There was a significant increase in serum saturated (myristic, caprylic, palmitic, palmitoleic, oleic and eicosanoic) and unsaturated (linoleic, linolenic, gamma-linolenic and arachnidonic) fatty acids post-rifaximin. No significant microbial change apart from a modest decrease in Veillonellaceae and increase in Eubacteriaceae was observed. Rifaximin resulted in a significant reduction in network connectivity and clustering on the correlation networks. The networks centered on Enterobacteriaceae, Porphyromonadaceae and Bacteroidaceae indicated a shift from pathogenic to beneficial metabolite linkages and better cognition while those centered on autochthonous taxa remained similar. CONCLUSIONS Rifaximin is associated with improved cognitive function and endotoxemia in MHE, which is accompanied by alteration of gut bacterial linkages with metabolites without significant change in microbial abundance. TRIAL REGISTRATION ClinicalTrials.gov NCT01069133.
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Affiliation(s)
- Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire Veterans Affairs Medical Center, Richmond, Virginia, United States of America.
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McDougall H. New research provides hope for personalized treatment of asthma. Biomark Med 2013; 7:198-199. [PMID: 23667940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
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Ling Z, Liu X, Chen W, Luo Y, Yuan L, Xia Y, Nelson KE, Huang S, Zhang S, Wang Y, Yuan J, Li L, Xiang C. The restoration of the vaginal microbiota after treatment for bacterial vaginosis with metronidazole or probiotics. Microb Ecol 2013; 65:773-780. [PMID: 23250116 DOI: 10.1007/s00248-012-0154-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 12/06/2012] [Indexed: 06/01/2023]
Abstract
Whether or not treatment with antibiotics or probiotics for bacterial vaginosis (BV) is associated with a change in the diversity of vaginal microbiota in women was investigated. One hundred fifteen women, consisting of 30 healthy subjects, 30 BV-positive control subjects, 30 subjects with BV treated with a 7-day metronidazole regimen, and 25 subjects with BV treated with a 10-day probiotics regimen, were analyzed to determine the efficacy and disparity of diversity and richness of vaginal microbiota using 454 pyrosequencing. Follow-up visits at days 5 and 30 showed a greater BV cure rate in the probiotics-treated subjects (88.0 and 96 %, respectively) compared to the metronidazole-treated subjects (83.3 and 70 %, respectively [p = 0.625 at day 5 and p = 0.013 at day 30]). Treatment with metronidazole reduced the taxa diversity and eradicated most of the BV-associated phylotypes, while probiotics only suppressed the overgrowth and re-established vaginal homeostasis gradually and steadily. Despite significant interindividual variation, the microbiota of the actively treated groups or participants constituted a unique profile. Along with the decrease in pathogenic bacteria, such as Gardnerella, Atopobium, Prevotella, Megasphaera, Coriobacteriaceae, Lachnospiraceae, Mycoplasma, and Sneathia, a Lactobacillus-dominated vaginal microbiota was recovered. Acting as vaginal sentinels and biomarkers, the relative abundance of Lactobacillus and pathogenic bacteria determined the consistency of the BV clinical and microbiologic cure rates, as well as recurrent BV. Both 7-day intravaginal metronidazole and 10-day intravaginal probiotics have good efficacy against BV, while probiotics maintained normal vaginal microbiota longer due to effective and steady vaginal microbiota restoration, which provide new insights into BV treatment.
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Affiliation(s)
- Zongxin Ling
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
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Park DY, Ahn YT, Park SH, Huh CS, Yoo SR, Yu R, Sung MK, McGregor RA, Choi MS. Supplementation of Lactobacillus curvatus HY7601 and Lactobacillus plantarum KY1032 in diet-induced obese mice is associated with gut microbial changes and reduction in obesity. PLoS One 2013; 8:e59470. [PMID: 23555678 PMCID: PMC3605452 DOI: 10.1371/journal.pone.0059470] [Citation(s) in RCA: 205] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 02/18/2013] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE To investigate the functional effects of probiotic treatment on the gut microbiota, as well as liver and adipose gene expression in diet-induced obese mice. DESIGN Male C57BL/6J mice were fed a high-fat diet (HFD) for 8 weeks to induce obesity, and then randomized to receive HFD+probiotic (Lactobacillus curvatus HY7601 and Lactobacillus plantarum KY1032, n = 9) or HFD+placebo (n = 9) for another 10 weeks. Normal diet (ND) fed mice (n = 9) served as non-obese controls. RESULTS Diet-induced obese mice treated with probiotics showed reduced body weight gain and fat accumulation as well as lowered plasma insulin, leptin, total-cholesterol and liver toxicity biomarkers. A total of 151,061 pyrosequencing reads for fecal microbiota were analyzed with a mean of 6,564, 5,274 and 4,464 reads for the ND, HFD+placebo and HFD+probiotic groups, respectively. Gut microbiota species were shared among the experimental groups despite the different diets and treatments. The diversity of the gut microbiota and its composition were significantly altered in the diet-induced obese mice and after probiotic treatment. We observed concurrent transcriptional changes in adipose tissue and the liver. In adipose tissue, pro-inflammatory genes (TNFα, IL6, IL1β and MCP1) were down-regulated in mice receiving probiotic treatment. In the liver, fatty acid oxidation-related genes (PGC1α, CPT1, CPT2 and ACOX1) were up-regulated in mice receiving probiotic treatment. CONCLUSIONS The gut microbiota of diet-induced obese mice appears to be modulated in mice receiving probiotic treatment. Probiotic treatment might reduce diet-induced obesity and modulate genes associated with metabolism and inflammation in the liver and adipose tissue.
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Affiliation(s)
- Do-Young Park
- Korea Yakult Co., Ltd., Yongin, Gyeonggi, Republic of Korea
| | - Young-Tae Ahn
- Korea Yakult Co., Ltd., Yongin, Gyeonggi, Republic of Korea
| | - Se-Hoon Park
- Korea Yakult Co., Ltd., Yongin, Gyeonggi, Republic of Korea
| | - Chul-Sung Huh
- Korea Yakult Co., Ltd., Yongin, Gyeonggi, Republic of Korea
- * E-mail: (CSH); (MSC)
| | - Sae-Rom Yoo
- Department of Food Science and Nutrition, Kyungpook National University, Buk-gu, Daegu, Republic of Korea
| | - Rina Yu
- Center for Food and Nutritional Genomics, Kyungpook National University, Daegu, Republic of Korea
- Department of Food Science and Nutrition, University of Ulsan, Ulsan, Republic of Korea
| | - Mi-Kyung Sung
- Center for Food and Nutritional Genomics, Kyungpook National University, Daegu, Republic of Korea
- Department of Food and Nutrition, Sookmyung Women’s University, Seoul, Republic of Korea
| | - Robin A. McGregor
- Center for Food and Nutritional Genomics, Kyungpook National University, Daegu, Republic of Korea
| | - Myung-Sook Choi
- Center for Food and Nutritional Genomics, Kyungpook National University, Daegu, Republic of Korea
- Department of Food Science and Nutrition, Kyungpook National University, Buk-gu, Daegu, Republic of Korea
- * E-mail: (CSH); (MSC)
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Xiao J, Zhang YF, Wang Y, An R, Wang XH. [Study on effect of different compatibility of saponins contained in banxia xiexin tang on intestinal bacterium metabolism]. Zhongguo Zhong Yao Za Zhi 2013; 38:611-617. [PMID: 23713292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
OBJECTIVE To compare the effect of intestinal flora on the metabolism of the Banxia Xiexin Tang (BXT) full prescription group, the sweet-nourishing group and saponins contained in single ingredients ginseng and liquorices. METHOD The anaerobic incubation technology for intestinal flora in vitro was adopted to incubate the BXT full prescription group, the sweet-nourishing group and extracting solution of the single ingredients, under anaerobic conditions at 37 degrees C. Samples of different incubating time points were collected. The high-speed separation and content determination of various prototypes and metabolites were conducted with LC-MS/MS method, and then their degradation rate K was calculated to observe the difference and characteristics in metabolism of different compatible groups. RESULT Intestinal flora could transform saponins into their metabolites. Having comparing spss one factor variance, we learned the difference in saponin metabolites of different compatible groups. As for the degradation rate of glycyrrhizic acid, the sweet-nourishing group > the full prescription group > the single prescription group (P < 0.05). Rb1 degraded the most slowly in the full prescription group. As for the degradation rate of Re, the single prescription group > the sweet-nourishing group > the full prescription group (P < 0.05). CONCLUSION The sweet-nourishing group and the sweet-nourishing group have different effect in inducing or inhibiting intestinal flora. The single prescription group shows in inhibition in metabolites of Rb1 and Rg1. Glycyrrhizic acid metabolites are promoted by glycyrrhetinic acid, which facilitates the efficacy of drug absorption. The compatibility of compounds has no impact on metabolites of Rb1 and Rg3.
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Affiliation(s)
- Juan Xiao
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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