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Dong J, Wang W, Zheng G, Wu N, Xie J, Xiong S, Tian P, Li J. In vitro digestion and fermentation behaviors of polysaccharides from Choerospondias axillaris fruit and its effect on human gut microbiota. Curr Res Food Sci 2024; 8:100760. [PMID: 38764977 PMCID: PMC11098719 DOI: 10.1016/j.crfs.2024.100760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/22/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Abstract
Choerospondias axillaris fruit has attracted more and more attention due to its various pharmacological activities, which are rich in polysaccharides. This study investigated the in vitro saliva-gastrointestinal digestion and fecal fermentation behaviors of polysaccharides from Choerospondias axillaris fruit (CAP), as well as its impact on human gut microbiota. The results showed that CAP could be partially degraded during the gastrointestinal digestion. The FT-IR spectra of the digested CAP didn't change significantly, however, the morphological feature of SEM changed to disordered flocculent and rod-like structures. 16S rRNA sequencing analysis found that after in vitro fermentation, CAP could increase the relative abundances of beneficial bacteria including Megasphaera, Megamonas and Bifidobacterium to produce short-chain fatty acids (SCFAs), while it can also reduce the abundances of harmful bacteria of Collinsella, Gemmiger, Klebsiella and Citrobacter, suggesting that CAP could modulate the composition and abundance of gut microbiota. These results implied that CAP can be developed as a potential prebiotic in the future.
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Affiliation(s)
- Jinjiao Dong
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Wenjun Wang
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Guodong Zheng
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Nansheng Wu
- Choerospondias Axillaris Research Institute, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jingjing Xie
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shiyi Xiong
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | | | - Jingen Li
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
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Samadi A, Kermanshahi Pour A, Beims RF, Xu CC. Delignified porous wood as biofilm support for 1,4-dioxane-degrading bacterial consortium. ENVIRONMENTAL TECHNOLOGY 2024; 45:2541-2557. [PMID: 36749305 DOI: 10.1080/09593330.2023.2178330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Delignified porous wood samples were used as carriers for biofilm formation of a bacterial consortium with the ability to degrade 1,4-dioxane (DX). The delignification treatment of the natural wood resulted in higher porosity, formation of macropores, increase in surface roughness and hydrophilicity of the treated wood pieces. These superior properties of two types of treated carriers (respectively, A and B) compared to the untreated wood resulted in 2.19 ± 0.52- and 2.66 ± 0.23-fold higher growth of biofilm. Moreover, analysis of the fatty acid profiles indicated an increase in proportion of the saturated fatty acids during the biofilm formation, characterising an enhancement in rigidity and hydrophobicity of the biofilms. DX initial concentration of 100 mg/L was completely degraded (detection limit 0.01 mg/L) in 24 and 32 h using the treated A and B woods, while only 25.84 ± 5.95% was removed after 32 h using the untreated wood. However, fitting the DX biodegradation data to the Monod model showed a lower maximum specific growth rate for biofilm (0.0276 ± 0.0018 1/h) versus planktonic (0.0382 ± 0.0024 1/h), because of gradual accumulation of inactive cells in the biofilm. Findings of this study can contribute to the knowledge of biofilm formation regarding the physical/chemical properties of biofilm carriers and be helpful to the ongoing research on bioremediation of DX.
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Affiliation(s)
- Aryan Samadi
- Biorefining and Remediation Laboratory, Department of Process Engineering and Applied Science, Dalhousie University, Halifax, Canada
| | - Azadeh Kermanshahi Pour
- Biorefining and Remediation Laboratory, Department of Process Engineering and Applied Science, Dalhousie University, Halifax, Canada
| | - Ramon Filipe Beims
- Department of Biochemical and Chemical Engineering, University of Western Ontario, London, Canada
| | - Chunbao Charles Xu
- Department of Biochemical and Chemical Engineering, University of Western Ontario, London, Canada
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3
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Liu X, Liu Y, Liu J, Zhang H, Shan C, Guo Y, Gong X, Cui M, Li X, Tang M. Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence. Neural Regen Res 2024; 19:833-845. [PMID: 37843219 PMCID: PMC10664138 DOI: 10.4103/1673-5374.382223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/19/2023] [Accepted: 06/17/2023] [Indexed: 10/17/2023] Open
Abstract
A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis. As a contributing factor, microbiota dysbiosis always occurs in pathological changes of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. High-throughput sequencing technology has helped to reveal that the bidirectional communication between the central nervous system and the enteric nervous system is facilitated by the microbiota's diverse microorganisms, and for both neuroimmune and neuroendocrine systems. Here, we summarize the bioinformatics analysis and wet-biology validation for the gut metagenomics in neurodegenerative diseases, with an emphasis on multi-omics studies and the gut virome. The pathogen-associated signaling biomarkers for identifying brain disorders and potential therapeutic targets are also elucidated. Finally, we discuss the role of diet, prebiotics, probiotics, postbiotics and exercise interventions in remodeling the microbiome and reducing the symptoms of neurodegenerative diseases.
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Affiliation(s)
- Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Chaofan Shan
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yinglu Guo
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Xun Gong
- Department of Rheumatology & Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Mengmeng Cui
- Department of Neurology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Xiubin Li
- Department of Neurology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
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Tan J, Fu B, Zhao X, Ye L. Novel Techniques and Models for Studying the Role of the Gut Microbiota in Drug Metabolism. Eur J Drug Metab Pharmacokinet 2024; 49:131-147. [PMID: 38123834 DOI: 10.1007/s13318-023-00874-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
The gut microbiota, known as the second human genome, plays a vital role in modulating drug metabolism, significantly impacting therapeutic outcomes and adverse effects. Emerging research has elucidated that the microbiota mediates a range of modifications of drugs, leading to their activation, inactivation, or even toxication. In diverse individuals, variations in the gut microbiota can result in differences in microbe-drug interactions, underscoring the importance of personalized approaches in pharmacotherapy. However, previous studies on drug metabolism in the gut microbiota have been hampered by technical limitations. Nowadays, advances in biotechnological tools, such as microbially derived metabolism screening and microbial gene editing, have provided a deeper insight into the mechanism of drug metabolism by gut microbiota, moving us toward personalized therapeutic interventions. Given this situation, our review summarizes recent advances in the study of gut-microbiota-mediated drug metabolism and showcases techniques and models developed to navigate the challenges posed by the microbial involvement in drug action. Therefore, we not only aim at understanding the complex interaction between the gut microbiota and drugs and outline the development of research techniques and models, but we also summarize the specific applications of new techniques and models in researching gut-microbiota-mediated drug metabolism, with the expectation of providing new insights on how to study drug metabolism by gut microbiota.
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Affiliation(s)
- Jianling Tan
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Bingxuan Fu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xiaojie Zhao
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Ling Ye
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
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González A, Fullaondo A, Odriozola A. Techniques, procedures, and applications in microbiome analysis. ADVANCES IN GENETICS 2024; 111:81-115. [PMID: 38908906 DOI: 10.1016/bs.adgen.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Microbiota is a complex community of microorganisms living in a defined environment. Until the 20th century, knowledge of microbiota was partial, as the techniques available for their characterization were primarily based on bacteriological culture. In the last twenty years, the development of DNA sequencing technologies, multi-omics, and bioinformatics has expanded our understanding of microorganisms. We have moved from mainly considering them isolated disease-causing agents to recognizing the microbiota as an essential component of host biology. These techniques have shown that the microbiome plays essential roles in various host phenotypes, influencing development, physiology, reproduction, and evolution. This chapter provides researchers with a summary of the primary concepts, sample collection, experimental techniques, and bioinformatics analysis commonly used in microbiome research. The main features, applications in microbiome studies, and their advantages and limitations are included in each section.
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Affiliation(s)
- Adriana González
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain.
| | - Asier Fullaondo
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Adrián Odriozola
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
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Koepper S, Clark KF, McClure JT, Revie CW, Stryhn H, Thakur KK. Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada. Front Microbiol 2023; 14:1245818. [PMID: 38029079 PMCID: PMC10658194 DOI: 10.3389/fmicb.2023.1245818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
The shell microbial community of lobsters-a key factor in the development of epizootic shell disease (ESD)-is still insufficiently researched in Atlantic Canada and many knowledge gaps remain. This study aimed to establish a baseline description and analysis of the shell microbiome of apparently healthy lobsters from four locations in the region. More than 180 lobster shell swab samples were collected from New Brunswick, Nova Scotia and Prince Edward Island (PEI). PacBio long-read 16S rDNA sequencing and bioinformatic analyses in QIIME2 identified the shell-associated bacteria. The shell microbiome of healthy lobsters consisted mainly of the bacterial classes Gammaproteobacteria, Saprospiria, Verrucomicrobiae, Alphaproteobacteria, Flavobacteriia, Acidimicrobiia and Planctomycetia. The microbial composition differed regionally and seasonally, with some classes showing decreased or increased relative abundances in the PEI samples as well as in the winter and spring samples in Nova Scotia. The core shell microbiome included potentially pathogenic as well as beneficial bacterial taxa, of which some were present only in certain regions. Bacterial taxa that have previously been associated with ESD were present on healthy lobsters in Atlantic Canada, but their frequency differed by location, sampling time, and moult stage. This study indicated that geographical and seasonal factors influenced the shell microbiome of apparently healthy lobsters more than host factors such as sex, size, and moult stage. Our results provide valuable reference microbial data from lobsters in a disease-free state.
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Affiliation(s)
- Svenja Koepper
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - K. Fraser Clark
- Department of Animal Sciences and Aquaculture, Faculty of Agriculture, Dalhousie University, Bible Hill, NS, Canada
| | - J. Trenton McClure
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Crawford W. Revie
- Department of Computer and Information Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Henrik Stryhn
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Krishna K. Thakur
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
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Paerl RW, Curtis NP, Bittner MJ, Cohn MR, Gifford SM, Bannon CC, Rowland E, Bertrand EM. Use and detection of a vitamin B1 degradation product yields new views of the marine B1 cycle and plankton metabolite exchange. mBio 2023; 14:e0006123. [PMID: 37377416 PMCID: PMC10470507 DOI: 10.1128/mbio.00061-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 04/17/2023] [Indexed: 06/29/2023] Open
Abstract
Vitamin B1 (thiamin) is a vital nutrient for most cells in nature, including marine plankton. Early and recent experiments show that B1 degradation products instead of B1 can support the growth of marine bacterioplankton and phytoplankton. However, the use and occurrence of some degradation products remains uninvestigated, namely N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine (FAMP), which has been a focus of plant oxidative stress research. We investigated the relevance of FAMP in the ocean. Experiments and global ocean meta-omic data indicate that eukaryotic phytoplankton, including picoeukaryotes and harmful algal bloom species, use FAMP while bacterioplankton appear more likely to use deformylated FAMP, 4-amino-5-aminomethyl-2-methylpyrimidine. Measurements of FAMP in seawater and biomass revealed that it occurs at picomolar concentrations in the surface ocean, heterotrophic bacterial cultures produce FAMP in the dark-indicating non-photodegradation of B1 by cells, and B1-requiring (auxotrophic) picoeukaryotic phytoplankton produce intracellular FAMP. Our results require an expansion of thinking about vitamin degradation in the sea, but also the marine B1 cycle where it is now crucial to consider a new B1-related compound pool (FAMP), as well as generation (dark degradation-likely via oxidation), turnover (plankton uptake), and exchange of the compound within the networks of plankton. IMPORTANCE Results of this collaborative study newly show that a vitamin B1 degradation product, N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine (FAMP), can be used by diverse marine microbes (bacteria and phytoplankton) to meet their vitamin B1 demands instead of B1 and that FAMP occurs in the surface ocean. FAMP has not yet been accounted for in the ocean and its use likely enables cells to avoid B1 growth deficiency. Additionally, we show FAMP is formed in and out of cells without solar irradiance-a commonly considered route of vitamin degradation in the sea and nature. Altogether, the results expand thinking about oceanic vitamin degradation, but also the marine B1 cycle where it is now crucial to consider a new B1-related compound pool (FAMP), as well as its generation (dark degradation-likely via oxidation), turnover (plankton uptake), and exchange within networks of plankton.
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Affiliation(s)
- Ryan W. Paerl
- Department of Marine, Earth, and Atmospheric Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Nathaniel P. Curtis
- Department of Marine, Earth, and Atmospheric Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Meriel J. Bittner
- Marine Biology Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Melanie R. Cohn
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Scott M. Gifford
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Elden Rowland
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Erin M. Bertrand
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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8
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Devi MB, Sarma HK, Mukherjee AK, Khan MR. Mechanistic Insights into Immune-Microbiota Interactions and Preventive Role of Probiotics Against Autoimmune Diabetes Mellitus. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10087-1. [PMID: 37171690 DOI: 10.1007/s12602-023-10087-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
Recent studies on genetically susceptible individuals and animal models revealed the potential role of the intestinal microbiota in the pathogenesis of type 1 diabetes (T1D) through complex interactions with the immune system. T1D incidence has been increasing exponentially with modern lifestyle altering normal microbiota composition, causing dysbiosis characterized by an imbalance in the gut microbial community. Dysbiosis has been suggested to be a potential contributing factor in T1D. Moreover, several studies have shown the potential role of probiotics in regulating T1D through various mechanisms. Current T1D therapies target curative measures; however, preventive therapeutics are yet to be proven. This review highlights immune microbiota interaction and the immense role of probiotics and postbiotics as important immunological interventions for reducing the risk of T1D.
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Affiliation(s)
- M Bidyarani Devi
- Molecular Biology and Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India
- Department of Biotechnology, Gauhati University, Guwahati, Assam, India
| | | | - Ashis K Mukherjee
- Molecular Biology and Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India
| | - Mojibur R Khan
- Molecular Biology and Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India.
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Handy MY, Sbardellati DL, Yu M, Saleh NW, Ostwald MM, Vannette RL. Incipiently social carpenter bees (Xylocopa) host distinctive gut bacterial communities and display geographical structure as revealed by full-length PacBio 16S rRNA sequencing. Mol Ecol 2023; 32:1530-1543. [PMID: 36239475 DOI: 10.1111/mec.16736] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 09/14/2022] [Accepted: 09/28/2022] [Indexed: 11/27/2022]
Abstract
The gut microbiota of bees affects nutrition, immunity and host fitness, yet the roles of diet, sociality and geographical variation in determining microbiome structure, including variant-level diversity and relatedness, remain poorly understood. Here, we use full-length 16S rRNA amplicon sequencing to compare the crop and gut microbiomes of two incipiently social carpenter bee species, Xylocopa sonorina and Xylocopa tabaniformis, from multiple geographical sites within each species' range. We found that Xylocopa species share a set of core taxa consisting of Bombilactobacillus, Bombiscardovia and Lactobacillus, found in >95% of all individual bees sampled, and Gilliamella and Apibacter were also detected in the gut of both species with high frequency. The crop bacterial community of X. sonorina comprised nearly entirely Apilactobacillus with occasionally abundant nectar bacteria. Despite sharing core taxa, Xylocopa species' microbiomes were distinguished by multiple bacterial lineages, including species-specific variants of core taxa. The use of long-read amplicons revealed otherwise cryptic species and population-level differentiation in core microbiome members, which was masked when a shorter fragment of the 16S rRNA (V4) was considered. Of the core taxa, Bombilactobacillus and Bombiscardovia exhibited differentiation in amplicon sequence variants among bee populations, but this was lacking in Lactobacillus, suggesting that some bacterial genera in the gut may be structured by different processes. We conclude that these Xylocopa species host a distinctive microbiome, similar to that of previously characterized social corbiculate apids, which suggests that further investigation to understand the evolution of the bee microbiome and its drivers is warranted.
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Affiliation(s)
- Madeline Y Handy
- Department of Entomology and Nematology, University of California Davis, Davis, California, USA
| | - Dino L Sbardellati
- Microbiology Graduate Group, University of California Davis, Davis, California, USA
| | - Michael Yu
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | - Nicholas W Saleh
- Entomology and Nematology Department, Fort Lauderdale Research and Education Center, University of Florida, Davie, Florida, USA
| | | | - Rachel L Vannette
- Department of Entomology and Nematology, University of California Davis, Davis, California, USA
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Tian J, Wang X, Zhang X, Chen X, Dong M, Rui X, Zhang Q, Jiang M, Li W. Artificial simulated saliva, gastric and intestinal digestion and fermentation in vitro by human gut microbiota of intrapolysaccharide from Paecilomyces cicadae TJJ1213. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2022.07.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Cuetero-Martínez Y, Flores-Ramírez A, De Los Cobos-Vasconcelos D, Aguirre-Garrido JF, López-Vidal Y, Noyola A. Removal of bacterial pathogens and antibiotic resistance bacteria by anaerobic sludge digestion with thermal hydrolysis pre-treatment and alkaline stabilization post-treatment. CHEMOSPHERE 2023; 313:137383. [PMID: 36436581 DOI: 10.1016/j.chemosphere.2022.137383] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 06/16/2023]
Abstract
Primary sludge (PS) is associated with public health and environmental risks, so regulations focus on reducing the pathogenic and heavy metal contents of the treated material (biosolids), intended for soil amendments and land reclamation. The regulations set limits for Escherichia coli (or fecal coliforms), Salmonella spp., helminth eggs and enterovirus. However, the potential risk due to antibiotic resistant bacteria (ARB) and other human potential pathogenic bacteria (HPB) are not considered. In this work, three sludge treatment processes, having in common an anaerobic digestion step, were applied to assess the removal of regulated bacteria (fecal coliforms, Salmonella spp), ARB and HPB. The treatment arrangements, fed with PS from a full-scale wastewater treatment plant were: 1) Mesophilic anaerobic digestion followed by alkaline stabilization post-treatment (MAD-CaO); 2) Thermophilic anaerobic digestion (TAD) and, 3) Pre-treatment (mild thermo-hydrolysis) followed by TAD (PT-TAD). The results address the identification, quantification (colony forming units) and taxonomic characterization of ARB resistant to β-lactams and vancomycin, as well as the taxonomic characterization of HPB by sequencing with PacBio. In addition, quantification based on culture media of fecal coliforms and Salmonella spp. is presented. The capabilities and limitations of microbiological and metataxonomomic analyses based on PacBio sequencing are discussed, emphasizing that they complement each other. Genus Aeromonas, Acinetobacter, Citrobacter, Enterobacter, Escherichia, Klebsiella, Ochrobactrum, Pseudomonas and Raoultella, among others, were found in the PS, which are of clinical or environmental importance, being either HPB, HPB-ARB, or non-pathogenic ARB with the potentiality of horizontal gene transfer. Based on the analysis of fecal coliforms and Salmonella spp., the three processes produced class A (highest) biosolids, suitable for unrestricted agriculture applications. Mild thermo-hydrolisis was effective in decreasing ARB cultivability, but it reappeared after the following TAD. O. intermedium (HPB-ARB) was enriched in MAD and TAD while Laribacter hongkongensis (HPB) did persist after the applied treatments.
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Affiliation(s)
- Yovany Cuetero-Martínez
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico; Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico
| | - Aarón Flores-Ramírez
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico
| | - Daniel De Los Cobos-Vasconcelos
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico
| | - José Félix Aguirre-Garrido
- Departamento de Ciencias Ambientales, Universidad Autónoma Metropolitana - Unidad Lerma, 52005 Lerma de Villada, Edo. Mex, Mexico
| | - Yolanda López-Vidal
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico
| | - Adalberto Noyola
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico.
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de Villalobos NF, Costa MC, Marín-Beltrán I. A community of marine bacteria with potential to biodegrade petroleum-based and biobased microplastics. MARINE POLLUTION BULLETIN 2022; 185:114251. [PMID: 36330933 DOI: 10.1016/j.marpolbul.2022.114251] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 09/30/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
The biodegradability conditions for both, petroleum-based plastics and bioplastics needs to be evaluated under environmentally realistic conditions. We assessed the biodegradability of low-density polyethylene and biobased polyethylene terephthalate microplastic films by a consortium of marine bacteria during 45 days. Bacterial growth and pH were higher in the samples inoculated with bacteria, compared to the controls. Fourier Infrared spectroscopy-Attenuated Total Reflectance and scanning electron microscopy indicated changes in the chemical functional groups, and the presence of fractures and biofilms in the surface of both plastics exposed to the bacterial community, respectively. The chemical oxygen demand further indicated signs of biodegradation of both polymers. Specific groups of bacteria showed preference for each type of microplastic. Overall, our results show signs of biodegradation, or at least biodeterioration and biofragmentation, of both types of plastics, when subjected to the selected bacterial community. Biobased PET was no more prone to biodegradation than conventional, petroleum-based LDPE.
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Affiliation(s)
- Nuria Fernández de Villalobos
- Centro de Ciências do Mar do Algarve, Universidade do Algarve, Campus de Gambelas, Building 7, 8005-139 Faro, Portugal
| | - Maria Clara Costa
- Centro de Ciências do Mar do Algarve, Universidade do Algarve, Campus de Gambelas, Building 7, 8005-139 Faro, Portugal; Faculdade de Ciências e Tecnologia, Universidade do Algarve, Faro, Portugal
| | - Isabel Marín-Beltrán
- Centro de Ciências do Mar do Algarve, Universidade do Algarve, Campus de Gambelas, Building 7, 8005-139 Faro, Portugal.
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González R, González D, Stambuk F, Ramírez F, Guzmán F, Mercado L, Rojas R, Henríquez C, Brokordt K, Schmitt P. A g-type lysozyme from the scallop Argopecten purpuratus participates in the immune response and in the stability of the hemolymph microbiota. FISH & SHELLFISH IMMUNOLOGY 2022; 123:324-334. [PMID: 35314329 DOI: 10.1016/j.fsi.2022.03.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/15/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Lysozymes are antimicrobial acid hydrolases widely distributed in nature. They are located inside the cells in lysosomes, or they are secreted to the extracellular space, where they can lyse the cell wall of certain species of bacteria via hydrolysis of the peptidoglycan. Thus, lysozymes are bacteriolytic enzymes and play a major biological role in biodefense, as these enzymes can act as antibacterial and immune-modulating agents. In this study, we characterized a g-type lysozyme from the scallop Argopecten purpuratus named ApGlys. The cDNA sequence comprises an open reading frame (ORF) of 600 nucleotides, codifying for a putative protein of 200 amino acids with a signal peptide of 18 amino acids. The deduced mature protein sequence displays a molecular weight of 20.07 kDa and an isoelectric point (pI) of 6.49. ApGlys deduced protein sequence exhibits conserved residues associated with catalytic activity and substrate fixation in other g-type lysozymes. The phylogenetic analysis revealed a high degree of identity of ApGlys with other mollusk g-type lysozymes, which form a restricted and separated clade from the vertebrate lysozymes. ApGlys transcripts were constitutively and highly expressed in the digestive gland, and it was induced in hemocytes and gills of scallops after an immune challenge. Furthermore, the ApGlys protein was located inside hemocytes of immunostimulated scallops, determined by immunofluorescence analysis. Finally, the transcript silencing of ApGlys by RNA interference led to an increase of total culturable bacteria from the scallop hemolymph. Furthermore, we detected a higher diversity of the bacterial community in ApGlys-silenced scallops and an imbalance of certain bacterial groups present in the hemolymph by 16S rDNA deep amplicon sequencing. Overall, our results showed that ApGlys is a new member of scallop lysozymes that is implicated in the immune response and in the microbial homeostasis of A. purpuratus hemolymph.
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Affiliation(s)
- Roxana González
- Laboratorio de Fisiología y Genética Marina (FIGEMA), Departamento de Acuicultura, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile; Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Daniel González
- Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Felipe Stambuk
- Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Felipe Ramírez
- Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Fanny Guzmán
- Núcleo Biotecnología Curauma. Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Luis Mercado
- Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Rodrigo Rojas
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile
| | - Carlos Henríquez
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Larrondo 1281, Coquimbo, Chile
| | - Katherina Brokordt
- Laboratorio de Fisiología y Genética Marina (FIGEMA), Departamento de Acuicultura, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile; Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Larrondo 1281, Coquimbo, Chile; Centro de Innovación Acuícola (AquaPacífico), Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
| | - Paulina Schmitt
- Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile.
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Aiyer H, Fofana B, Fraser T, Caldwell C, Mckenzie-Gopsill A, Mills A, Foster A. Choice of cover crop influences soil fungal and bacterial communities in Prince Edward Island, Canada. Can J Microbiol 2022; 68:465-482. [PMID: 35344680 DOI: 10.1139/cjm-2021-0360] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Soil fungal and bacterial communities play various roles in agroecosystems and are significantly influenced by agricultural management practices. Currently, little is known about the effects of selected cover crops on soil fungal and bacterial communities in no-till systems. In this study, eight cover crops, three mixed crops, and an unmanaged fallow control were evaluated over two years for their effects on the soil microbiome. ITS and 16S rRNA amplicon sequencing was performed to characterize fungal and bacterial communities in the soil during the cover crop growing season, and in the subsequent year. Fungal and bacterial alpha diversity significantly increased over time and were influenced in the subsequent growing season by choice of cover crops. Some fungal and bacterial trophic and functional groups were also affected by crop choice. Fungal pathotroph abundance was positively associated with oilseed radish, alfalfa, and phacelia, but negatively associated with sorghum-sudangrass. Beneficial symbiotrophic fungi and functional nitrification-related bacterial groups were also associated with sorghum-sudangrass and buckwheat. These findings suggest that choice of cover crops influences the soil microbial community composition and may impact plant health in the subsequent crops.
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Affiliation(s)
- Harini Aiyer
- Agriculture and Agri-Food Canada, 6337, Charlottetown Research and Development Centre, Charlottetown, Prince Edward Island, Canada.,Dalhousie University Faculty of Agriculture, 89611, Department of Plant, Food and Environmental Sciences, Truro, Nova Scotia, Canada;
| | - Bourlaye Fofana
- Agriculture and Agri-Food Canada, 6337, Charlottetown Research and Development Centre, Ottawa, Ontario, Canada;
| | - Tandra Fraser
- Agriculture and Agri-Food Canada, 6337, Charlottetown Research and Development Centre, Charlottetown, Prince Edward Island, Canada;
| | - Claude Caldwell
- Dalhousie University Faculty of Agriculture, 89611, Department of Plant, Food and Environmental Sciences, Truro, Nova Scotia, Canada;
| | - Andrew Mckenzie-Gopsill
- Agriculture and Agri-Food Canada, 6337, Charlottetown Research and Development Centre, Charlottetown, Prince Edward Island, Canada;
| | - Aaron Mills
- Agriculture and Agri-Food Canada, 6337, Charlottetown Research and Development Centre, Charlottetown, Prince Edward Island, Canada;
| | - Adam Foster
- Agriculture and Agri-Food Canada, 6337, Charlottetown Research and Development Centre, Charlottetown, Prince Edward Island, Canada;
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Han H, Safe S, Jayaraman A, Chapkin RS. Diet-Host-Microbiota Interactions Shape Aryl Hydrocarbon Receptor Ligand Production to Modulate Intestinal Homeostasis. Annu Rev Nutr 2021; 41:455-478. [PMID: 34633858 PMCID: PMC8667662 DOI: 10.1146/annurev-nutr-043020-090050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-activated basic-helix-loop-helix transcription factor that binds structurally diverse ligands and senses cues from environmental toxicants and physiologically relevant dietary/microbiota-derived ligands. The AhR is an ancient conserved protein and is widely expressed across different tissues in vertebrates and invertebrates. AhR signaling mediates a wide range of cellular functions in a ligand-, cell type-, species-, and context-specific manner. Dysregulation of AhR signaling is linked to many developmental defects and chronic diseases. In this review, we discuss the emerging role of AhR signaling in mediating bidirectional host-microbiome interactions. We also consider evidence showing the potential for the dietary/microbial enhancement ofhealth-promoting AhR ligands to improve clinical pathway management in the context of inflammatory bowel diseases and colon tumorigenesis.
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Affiliation(s)
- Huajun Han
- Program in Integrative Nutrition and Complex Diseases and Department of Nutrition, Texas A&M University, College Station, Texas 77843, USA;
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Stephen Safe
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
| | - Arul Jayaraman
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Robert S Chapkin
- Program in Integrative Nutrition and Complex Diseases and Department of Nutrition, Texas A&M University, College Station, Texas 77843, USA;
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, USA
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Yuan X, Chen R, Zhang Y, Lin X, Yang X. Gut microbiota: effect of pubertal status. BMC Microbiol 2020; 20:334. [PMID: 33143658 PMCID: PMC7640488 DOI: 10.1186/s12866-020-02021-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/26/2020] [Indexed: 12/13/2022] Open
Abstract
Background The make-up of gut microbiota at different puberty stages has not been reported. This cross-sectional study analyzed the bio-diversity of gut microbiota at different puberty stages. Result The subjects (aged 5–15 years) were divided into non-pubertal (n = 42, male%: 66.7%) or pubertal groups (n = 47, male%:44.68); in both groups, Firmicutes, Bacteroidetes and Proteobacteria were the dominant phylum. There was no difference of alpha- and beta-diversity among disparate puberty stages. Non-pubertal subjects had members of the order Clostridiales, family Clostridiaceae, genus Coprobacillus which were significantly more prevalent than puberty subjects. Also, the pubertal subjects had members of class Betaproteobacteria, order Burkholderiales which were significantly more prevalent than the non-pubertal subjects. Their relative abundance was independent of BMI-Z. In the pubertal subjects, the abundance of genus Adlercreutzia, Ruminococcus, Dorea, Clostridium and Parabacteroides was associated with the level of testosterone. Conclusions This is the first report of the diversity of gut microbiota at different puberty stages. The various species of gut microbiota changed gradually associated with puberty stages. Differences in gut microflora at different pubertal status may be related to androgen levels. Supplementary Information Supplementary information accompanies this paper at 10.1186/s12866-020-02021-0.
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Affiliation(s)
- Xin Yuan
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children's Hospital of Fujian Medical University, NO.145, 817 Middle Road, Fuzhou, 350005, China
| | - Ruimin Chen
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children's Hospital of Fujian Medical University, NO.145, 817 Middle Road, Fuzhou, 350005, China.
| | - Ying Zhang
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children's Hospital of Fujian Medical University, NO.145, 817 Middle Road, Fuzhou, 350005, China
| | - Xiangquan Lin
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children's Hospital of Fujian Medical University, NO.145, 817 Middle Road, Fuzhou, 350005, China
| | - Xiaohong Yang
- Department of Endocrinology, Genetics and Metabolism, Fuzhou Children's Hospital of Fujian Medical University, NO.145, 817 Middle Road, Fuzhou, 350005, China
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Shigeno Y, Kitahara M, Shime M, Benno Y. Phascolarctobacterium wakonense sp. nov., isolated from common marmoset (Callithrix jacchus) faeces. Int J Syst Evol Microbiol 2019; 69:1941-1946. [PMID: 31038451 DOI: 10.1099/ijsem.0.003407] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Two strictly anaerobic strains (MB11T and MB56) were isolated from common marmoset (Callithrixjacchus) faeces. Cells of the two strains were Gram-stain-negative, pleomorphic short (strain MB11T) or long (strain MB56) rods. Phylogenetic analysis based on 16S rRNA gene sequences revealed that both isolates were related to the genus Phascolarctobacterium. They had 16S rRNA gene sequences similarities lower than 93 % to previously described species, Phascolarctobacterium faecium ACM 3679T and Phascolarctobacterium succinatutens YIT 12067T, and 98.7 % between themselves. DNA-DNA hybridization values showed that strains MB11T and MB56 were the same species. The genomic DNA G+C content of strains MB11T and MB56 were 47.3-47.4 mol% and 47.7-48.0 mol%. The isolates had different enzymatic activities compared with P. succinatutens JCM 16074T and different major cellular fatty acids compared with P. faecium ACM 3679T. Substrate availability revealed that they utilized not only succinate, but also pyruvate. With pyruvate supplementation, they produced both propionate and acetate, while only propionate production occured with succinate. As suggested by the phylogenic and physiological properties of strains MB11T and MB56, we propose the name Phascolarctobacteriumwakonense sp. nov. with the type strain MB11T (=JCM 32899T=DSM 107697T).
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Affiliation(s)
- Yuko Shigeno
- Benno Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science Technology and Innovation Hab, Wako, Saitama 351-0198, Japan
| | - Maki Kitahara
- Benno Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science Technology and Innovation Hab, Wako, Saitama 351-0198, Japan
| | - Mari Shime
- Benno Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science Technology and Innovation Hab, Wako, Saitama 351-0198, Japan
| | - Yoshimi Benno
- Benno Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science Technology and Innovation Hab, Wako, Saitama 351-0198, Japan
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18
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He L, Liu Y, Guo Y, Xiao N, Tan Z. Influences of Aflatoxin B 1 on main intestinal bacteria communities and enzyme activities in mice. TOXIN REV 2019. [DOI: 10.1080/15569543.2018.1426611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Lu He
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Yawei Liu
- Medical College, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Yanfang Guo
- The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Nenqun Xiao
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Zhoujin Tan
- Medical College, Hunan University of Chinese Medicine, Changsha, Hunan, China
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Flannery J, Callaghan B, Sharpton T, Fisher P, Pfeifer J. Is adolescence the missing developmental link in Microbiome-Gut-Brain axis communication? Dev Psychobiol 2019; 61:783-795. [PMID: 30690712 DOI: 10.1002/dev.21821] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/12/2018] [Accepted: 11/26/2018] [Indexed: 12/21/2022]
Abstract
Gut microbial research has recently opened new frontiers in neuroscience and potentiated novel therapies for mental health problems (Mayer, et al., 2014). Much of our understanding of the gut microbiome's role in brain function and behavior, however, has been largely derived from research on nonhuman animals. Even less is known about how the development of the gut microbiome influences critical periods of neural and behavioral development, particularly adolescence. In this review, we first discuss why the gut microbiome has become increasingly relevant to developmental cognitive neuroscience and provide a synopsis of the known connections of the gut microbiome with social-affective brain function and behavior, specifically highlighting human developmental work when possible. We then focus on adolescence, a key period of neurobiological and social-affective development. Specifically, we review the links between the gut microbiome and six overarching domains of change during adolescence: (a) social processes, (b) motivation and behavior, (c) neural development, (d) cognition, (e) neuroendocrine function, and (f) physical health and wellness. Using a developmental science perspective, we summarize key changes across these six domains to underscore the promise for the gut microbiome to bidirectionally influence and transform adolescent development.
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20
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Trujillo-de Santiago G, Lobo-Zegers MJ, Montes-Fonseca SL, Zhang YS, Alvarez MM. Gut-microbiota-on-a-chip: an enabling field for physiological research. MICROPHYSIOLOGICAL SYSTEMS 2018; 2:7. [PMID: 33954286 PMCID: PMC8096182 DOI: 10.21037/mps.2018.09.01] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Overwhelming scientific evidence today confirms that the gut microbiota is a central player in human health. Knowledge about interactions between human gut microbiota and human health has evolved rapidly in the last decade, based on experimental work involving analysis of human fecal samples or animal models (mainly rodents). A more detailed and cost-effective description of this interplay is now being enabled by the use of in vitro systems (i.e., gut-microbiota-on-chip systems) that recapitulate key aspects of the interaction between microbiota and human cells. Here, we review recent examples of the design and use of pioneering on-chip platforms for the study of the cross-talk between representative members of human microbiota and human microtissues. In these systems, the combined use of state-of-the-art microfluidics, biomaterials, cell culture techniques, classical microbiology, and a touch of genetic expression profiling have converged for the development of gut-on-chip platforms capable of recreating key features of the interplay between human microbiota and host human tissues. We foresee that the integration of novel microfabrication techniques and stem cell technologies will further accelerate the development of more complex and physiologically relevant microbiota-on-chip platforms. In turn, this will foster the faster acquisition of knowledge regarding human microbiota and will enable important advances in the understanding of how to control or prevent disease.
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Affiliation(s)
- Grissel Trujillo-de Santiago
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey
- Departamento de Mecatrónica e Ingeniería Eléctrica, Campus Monterrey, CP 64849, Monterrey, Nuevo León, México
| | - Matías José Lobo-Zegers
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey
- Departamento de Mecatrónica e Ingeniería Eléctrica, Campus Monterrey, CP 64849, Monterrey, Nuevo León, México
| | - Silvia Lorena Montes-Fonseca
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, CP 31300, Chihuahua, México
| | - Yu Shrike Zhang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA, USA
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Feng G, Flanagan BM, Mikkelsen D, Williams BA, Yu W, Gilbert RG, Gidley MJ. Mechanisms of utilisation of arabinoxylans by a porcine faecal inoculum: competition and co-operation. Sci Rep 2018. [PMID: 29540852 PMCID: PMC5852058 DOI: 10.1038/s41598-018-22818-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Recent studies show that a single or small number of intestinal microbes can completely degrade complex carbohydrates. This suggests a drive towards competitive utilisation of dietary complex carbohydrates resulting in limited microbial diversity, at odds with the health benefits associated with a diverse microbiome. This study investigates the enzymatic metabolism of wheat and rye arabinoxylans (AX) using in vitro fermentation, with a porcine faecal inoculum. Through studying the activity of AX-degrading enzymes and the structural changes of residual AX during fermentation, we show that the AX-degrading enzymes are mainly cell-associated, which enables the microbes to utilise the AX competitively. However, potential for cross-feeding is also demonstrated to occur by two distinct mechanisms: (1) release of AX after partial degradation by cell-associated enzymes, and (2) release of enzymes during biomass turnover, indicative of co-operative AX degradation. This study provides a model for the combined competitive-co-operative utilisation of complex dietary carbohydrates by gut microorganisms.
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Affiliation(s)
- Guangli Feng
- ARC Centre of Excellence in Plant Cell Walls, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Bernadine M Flanagan
- ARC Centre of Excellence in Plant Cell Walls, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Deirdre Mikkelsen
- ARC Centre of Excellence in Plant Cell Walls, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Barbara A Williams
- ARC Centre of Excellence in Plant Cell Walls, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Wenwen Yu
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Robert G Gilbert
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Agriculture, Yangzhou University, Yangzhou, Jiangsu Province, 225009, China
| | - Michael J Gidley
- ARC Centre of Excellence in Plant Cell Walls, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
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Zhou M, He J, Shen Y, Zhang C, Wang J, Chen Y. New Frontiers in Genetics, Gut Microbiota, and Immunity: A Rosetta Stone for the Pathogenesis of Inflammatory Bowel Disease. BIOMED RESEARCH INTERNATIONAL 2017; 2017:8201672. [PMID: 28831399 PMCID: PMC5558637 DOI: 10.1155/2017/8201672] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/03/2017] [Accepted: 07/03/2017] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel disease (IBD), which encompasses ulcerative colitis (UC) and Crohn's disease (CD), is a complicated, uncontrolled, and multifactorial disorder characterized by chronic, relapsing, or progressive inflammatory conditions that may involve the entire gastrointestinal tract. The protracted nature has imposed enormous economic burdens on patients with IBD, and the treatment is far from optimal due to the currently limited comprehension of IBD pathogenesis. In spite of the exact etiology still remaining an enigma, four identified components, including personal genetic susceptibility, external environment, internal gut microbiota, and the host immune response, are responsible for IBD pathogenesis, and compelling evidence has suggested that IBD may be triggered by aberrant and continuing immune responses to gut microbiota in genetically susceptibility individuals. The past decade has witnessed the flourishing of research on genetics, gut microbiota, and immunity in patients with IBD. Therefore, in this review, we will comprehensively exhibit a series of novel findings and update the major advances regarding these three fields. Undoubtedly, these novel findings have opened a new horizon and shed bright light on the causality research of IBD.
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Affiliation(s)
- Mingxia Zhou
- Department of Gastroenterology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Jing He
- Department of General Surgery, Huashan Hospital of Fudan University, Shanghai 200040, China
| | - Yujie Shen
- Department of Gastroenterology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Cong Zhang
- Department of Gastroenterology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Jiazheng Wang
- Department of Gastroenterology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Yingwei Chen
- Department of Gastroenterology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
- Shanghai Institute for Pediatric Research, Shanghai 200092, China
- Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai 200092, China
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23
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Peachey LE, Jenkins TP, Cantacessi C. This Gut Ain’t Big Enough for Both of Us. Or Is It? Helminth–Microbiota Interactions in Veterinary Species. Trends Parasitol 2017; 33:619-632. [DOI: 10.1016/j.pt.2017.04.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/12/2017] [Accepted: 04/13/2017] [Indexed: 01/25/2023]
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Abstract
蔗糖酶-异麦芽糖酶(sucrase-isomaltase, SI)是蔗糖酶在肠道内最主要的存在形式, 是最丰富的肠道二糖酶, 其包含了所有的蔗糖酶活性, 大部分的异麦芽糖酶活性及60%-80%的麦芽糖酶活性. 蔗糖酶-异麦芽糖酶缺乏症(sucrase-isomaltase deficiency, SID)是由于该二糖酶缺乏导致二糖吸收不良, 肠道正常生理功能受损, 机体营养不良, 生长发育落后, 甚至产生危及生命的胃肠道症状. 其最主要的临床表现是腹泻. 临床上通过调整肠道SI活性来治疗腹泻, 并将SI活性用于临床诊断. 本文主要阐述SID与腹泻的关系、研究进程以及诊疗手段, 促进SI在药理方面的研究.
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Jin P, Wang K, Huang C, Nice EC. Mining the fecal proteome: from biomarkers to personalised medicine. Expert Rev Proteomics 2017; 14:445-459. [PMID: 28361558 DOI: 10.1080/14789450.2017.1314786] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Fecal proteomics has gained increased prominence in recent years. It can provide insights into the diagnosis and surveillance of many bowel diseases by both identifying potential biomarkers in stool samples and helping identify disease-related pathways. Fecal proteomics has already shown its potential for the discovery and validation of biomarkers for colorectal cancer screening, and the analysis of fecal microbiota by MALDI-MS for the diagnosis of a range of bowel diseases is gaining clinical acceptance. Areas covered: Based on a comprehensive analysis of the current literature, we introduce the range of sensitive and specific proteomics methods which comprise the current 'Proteomics Toolbox', explain how the integration of fecal proteomics with data processing/bioinformatics has been used for the identification of potential biomarkers for both CRC and other gut-related pathologies and analysis of the fecal microbiome, outline some of the current fecal assays in current clinical practice and introduce the concept of personalised medicine which these technologies will help inform. Expert commentary: Integration of fecal proteomics with other proteomics and genomics strategies as well as bioinformatics is paving the way towards personalised medicine, which will bring with it improved global healthcare.
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Affiliation(s)
- Ping Jin
- a Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology , the Affiliated Hospital of Hainan Medical College , Haikou , China.,b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Kui Wang
- b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Canhua Huang
- a Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology , the Affiliated Hospital of Hainan Medical College , Haikou , China.,b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Edouard C Nice
- b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
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Su JQ, Cui L, Chen QL, An XL, Zhu YG. Application of genomic technologies to measure and monitor antibiotic resistance in animals. Ann N Y Acad Sci 2016; 1388:121-135. [DOI: 10.1111/nyas.13296] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/04/2016] [Accepted: 10/18/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Qing-Lin Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Xin-Li An
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
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Hiippala K, Kainulainen V, Kalliomäki M, Arkkila P, Satokari R. Mucosal Prevalence and Interactions with the Epithelium Indicate Commensalism of Sutterella spp. Front Microbiol 2016; 7:1706. [PMID: 27833600 PMCID: PMC5080374 DOI: 10.3389/fmicb.2016.01706] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/12/2016] [Indexed: 12/25/2022] Open
Abstract
Sutterella species have been frequently associated with human diseases, such as autism, Down syndrome, and inflammatory bowel disease (IBD), but the impact of these bacteria on health still remains unclear. Especially the interactions of Sutterella spp. with the host are largely unknown, despite of the species being highly prevalent. In this study, we addressed the interaction of three known species of Sutterella with the intestinal epithelium and examined their adhesion properties, the effect on intestinal barrier function and the pro-inflammatory capacity in vitro. We also studied the relative abundance and prevalence of the genus Sutterella and Sutterella wadsworthensis in intestinal biopsies of healthy individuals and patients with celiac disease (CeD) or IBD. Our results show that Sutterella spp. are abundant in the duodenum of healthy adults with a decreasing gradient toward the colon. No difference was detected in the prevalence of Sutterella between the pediatric IBD or CeD patients and the healthy controls. Sutterella parvirubra adhered better than the two other Sutterella spp. to differentiated Caco-2 cells and was capable of decreasing the adherence of S. wadsworthensis, which preferably bound to mucus and human extracellular matrix proteins. Furthermore, only S. wadsworthensis induced an interleukin-8 production in enterocytes, which could be due to different lipopolysaccharide structures between the species. However, its pro-inflammatory activity was modest as compared to non-pathogenic Escherichia coli. Sutterella spp. had no effect on the enterocyte monolayer integrity in vitro. Our findings indicate that the members of genus Sutterella are widely prevalent commensals with mild pro-inflammatory capacity in the human gastrointestinal tract and do not contribute significantly to the disrupted epithelial homeostasis associated with microbiota dysbiosis and increase of Proteobacteria. The ability of Sutterella spp. to adhere to intestinal epithelial cells indicate that they may have an immunomodulatory role.
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Affiliation(s)
- Kaisa Hiippala
- Immunobiology Research Program, Faculty of Medicine, University of Helsinki Helsinki, Finland
| | - Veera Kainulainen
- Pharmacology, Faculty of Medicine, University of Helsinki Helsinki, Finland
| | - Marko Kalliomäki
- Department of Pediatrics, Turku University Central Hospital and Functional Foods Forum, University of Turku Turku, Finland
| | - Perttu Arkkila
- Department of Gastroenterology, Helsinki University Central Hospital Helsinki, Finland
| | - Reetta Satokari
- Immunobiology Research Program, Faculty of Medicine, University of Helsinki Helsinki, Finland
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Ultrafiltration and Microarray for Detection of Microbial Source Tracking Marker and Pathogen Genes in Riverine and Marine Systems. Appl Environ Microbiol 2016; 82:1625-1635. [PMID: 26729716 DOI: 10.1128/aem.02583-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 12/24/2015] [Indexed: 01/12/2023] Open
Abstract
Pathogen identification and microbial source tracking (MST) to identify sources of fecal pollution improve evaluation of water quality. They contribute to improved assessment of human health risks and remediation of pollution sources. An MST microarray was used to simultaneously detect genes for multiple pathogens and indicators of fecal pollution in freshwater, marine water, sewage-contaminated freshwater and marine water, and treated wastewater. Dead-end ultrafiltration (DEUF) was used to concentrate organisms from water samples, yielding a recovery efficiency of >95% for Escherichia coli and human polyomavirus. Whole-genome amplification (WGA) increased gene copies from ultrafiltered samples and increased the sensitivity of the microarray. Viruses (adenovirus, bocavirus, hepatitis A virus, and human polyomaviruses) were detected in sewage-contaminated samples. Pathogens such as Legionella pneumophila, Shigella flexneri, and Campylobacter fetus were detected along with genes conferring resistance to aminoglycosides, beta-lactams, and tetracycline. Nonmetric dimensional analysis of MST marker genes grouped sewage-spiked freshwater and marine samples with sewage and apart from other fecal sources. The sensitivity (percent true positives) of the microarray probes for gene targets anticipated in sewage was 51 to 57% and was lower than the specificity (percent true negatives; 79 to 81%). A linear relationship between gene copies determined by quantitative PCR and microarray fluorescence was found, indicating the semiquantitative nature of the MST microarray. These results indicate that ultrafiltration coupled with WGA provides sufficient nucleic acids for detection of viruses, bacteria, protozoa, and antibiotic resistance genes by the microarray in applications ranging from beach monitoring to risk assessment.
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Moore SA, Levy BH, Prematilake C, Dissanaike S. The Prediction Predicament: Rethinking Necrotizing Soft Tissue Infections Mortality. Surg Infect (Larchmt) 2015; 16:813-21. [PMID: 26258645 DOI: 10.1089/sur.2015.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Our study sought to identify independent risk factors predisposing patients with necrotizing soft tissue infections (NSTIs) to mortality from among laboratory values, demographic data, and microbiologic findings in a small population. To this end, a retrospective review was conducted of the medical records of all patients with NSTI who had been treated at our institution from 2003 to 2012 (n=134). METHODS Baseline demographics and comorbidities, clinical and laboratory values, hospital course, and the microbiologic characteristics of surgical incision cultures were recorded. Each variable was tested for association with survival status and all associated variables with p<0.15 were included in a logistic regression model to seek factors associated independently with mortality. RESULTS Surprisingly, no demographic or pre-existing condition proved to be a predictor of mortality. Two laboratory values had an inverse correlation to mortality: High C-reactive protein (CRP) and highest recorded CRP. Of surgical incisions that grew bacteria in culture, 33.6% were polymicrobial. Mortality rates were highest with Enterococcus-containing polymicrobial infections (50%), followed by those containing Pseudomonas (40%), and Streptococcus spp. (27%). Understanding why so many studies across the literature, now including our own, find such disparate results for correlation of NSTI mortality with patient data may lie in the fundamentally dynamic nature of the organisms involved. CONCLUSIONS This study suggests that no single factor present on admission is a robust predictor of outcome; it is likely that survival in NSTI is predicated upon a complex interaction of multiple host and microbial factors that do not lend themselves to reduction into a simple formula. It is also abundantly clear that the well-established principles of NSTI surgery should continue to be followed in all cases, with an emphasis on early debridement, irrespective of apparent severity of initial presentation.
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Affiliation(s)
- Samantha A Moore
- 1 Department of Surgery, Texas Tech University Health Sciences Center , Lubbock, Texas
| | - Brandon H Levy
- 1 Department of Surgery, Texas Tech University Health Sciences Center , Lubbock, Texas
| | - Chalani Prematilake
- 2 Department of Mathematics and Statistics, Texas Tech University , Lubbock, Texas
| | - Sharmila Dissanaike
- 1 Department of Surgery, Texas Tech University Health Sciences Center , Lubbock, Texas
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Sankar SA, Lagier JC, Pontarotti P, Raoult D, Fournier PE. The human gut microbiome, a taxonomic conundrum. Syst Appl Microbiol 2015; 38:276-86. [DOI: 10.1016/j.syapm.2015.03.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 01/16/2023]
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Patro JN, Ramachandran P, Lewis JL, Mammel MK, Barnaba T, Pfeiler EA, Elkins CA. Development and utility of the FDA 'GutProbe' DNA microarray for identification, genotyping and metagenomic analysis of commercially available probiotics. J Appl Microbiol 2015; 118:1478-88. [PMID: 25766767 DOI: 10.1111/jam.12795] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/27/2015] [Accepted: 03/05/2015] [Indexed: 10/23/2022]
Abstract
AIM Lactic acid bacteria are beneficial microbes added to many food products and dietary supplements for their purported health benefits. Proper identification of bacteria is important to assess safety as well as proper product labelling. A custom microarray (FDA GutProbe) was developed to verify accurate labelling in commercial dietary supplements. METHODS AND RESULTS Strain-specific attribution was achieved with GutProbe array which contains genes from the most commonly found species in probiotic supplements and food ingredients. Applied utility of the array was assessed with direct from product DNA hybridization to determine (i) if identification of multiple strains in one sample can be conducted and (ii) if any lot-to-lot variations exist with eight probiotics found on the US market. CONCLUSIONS GutProbe is a useful tool in identifying a mixture of microbials in probiotics and did reveal some product variations. In addition, the array is able to identify lot-to-lot differences in these products. These strain level attribution may be useful for routine monitoring of batch variation as part of a 'Good Manufacturing Practices' process. SIGNIFICANCE AND IMPACT OF THE STUDY The FDA GutProbe is an efficient and reliable platform to identify the presence of microbial ingredients and determining microbe differences in dietary supplements. The GutProbe is a fast, rapid method for direct community profiling or food matrix sampling.
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Affiliation(s)
- J N Patro
- Division of Molecular Biology, Center for Food Safety & Applied Nutrition, U.S. Food and Drug Administration, Muirkirk Rd Laurel, MD, USA
| | - P Ramachandran
- Division of Molecular Biology, Center for Food Safety & Applied Nutrition, U.S. Food and Drug Administration, Muirkirk Rd Laurel, MD, USA
| | - J L Lewis
- Division of Molecular Biology, Center for Food Safety & Applied Nutrition, U.S. Food and Drug Administration, Muirkirk Rd Laurel, MD, USA
| | - M K Mammel
- Division of Molecular Biology, Center for Food Safety & Applied Nutrition, U.S. Food and Drug Administration, Muirkirk Rd Laurel, MD, USA
| | - T Barnaba
- Division of Molecular Biology, Center for Food Safety & Applied Nutrition, U.S. Food and Drug Administration, Muirkirk Rd Laurel, MD, USA
| | - E A Pfeiler
- Division of Molecular Biology, Center for Food Safety & Applied Nutrition, U.S. Food and Drug Administration, Muirkirk Rd Laurel, MD, USA
| | - C A Elkins
- Division of Molecular Biology, Center for Food Safety & Applied Nutrition, U.S. Food and Drug Administration, Muirkirk Rd Laurel, MD, USA
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Firkins JL, Yu Z. RUMINANT NUTRITION SYMPOSIUM: How to use data on the rumen microbiome to improve our understanding of ruminant nutrition1,2. J Anim Sci 2015; 93:1450-70. [DOI: 10.2527/jas.2014-8754] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- J. L. Firkins
- Department of Animal Sciences, The Ohio State University, Columbus 43210
| | - Z. Yu
- Department of Animal Sciences, The Ohio State University, Columbus 43210
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High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. mBio 2015; 6:mBio.02288-14. [PMID: 25626903 PMCID: PMC4324309 DOI: 10.1128/mbio.02288-14] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one of the grand challenges of 21st century science. To address this challenge, over the past decade, numerous technologies have been developed for interrogating microbial communities, of which some are amenable to exploratory work (e.g., high-throughput sequencing and phenotypic screening) and others depend on reference genes or genomes (e.g., phylogenetic and functional gene arrays). Here, we provide a critical review and synthesis of the most commonly applied “open-format” and “closed-format” detection technologies. We discuss their characteristics, advantages, and disadvantages within the context of environmental applications and focus on analysis of complex microbial systems, such as those in soils, in which diversity is high and reference genomes are few. In addition, we discuss crucial issues and considerations associated with applying complementary high-throughput molecular technologies to address important ecological questions.
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Hermes G, Zoetendal E, Smidt H. Molecular ecological tools to decipher the role of our microbial mass in obesity. Benef Microbes 2015; 6:61-81. [DOI: 10.3920/bm2014.0016] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
After birth, our gastrointestinal (GI) tract is colonised by a highly complex assemblage of microbes, collectively termed the GI microbiota, that develops intimate interactions with our body. Recent evidence indicates that the GI microbiota and its products may contribute to the development of obesity and related diseases. This, coupled with the current worldwide epidemic of obesity, has moved microbiome research into the spotlight of attention. Although the main cause of obesity and its associated metabolic complications is excess caloric intake compared with expenditure, differences in GI tract microbial ecology between individuals might be an important biomarker, mediator or new therapeutic target. This can be investigated using a diverse set of complementary so called -omics technologies, such as 16S ribosomal RNA gene-targeted composition profiling, metabolomics, metagenomics, metatranscriptomics and metaproteomics. This review aims to describe the different molecular approaches and their contributions to our understanding of the role of the GI microbiota in host energy homeostasis. Correspondingly, we highlight their respective strengths, but also try to create awareness for their specific limitations. However, it is currently still unclear which bacterial groups play a role in the development of obesity in humans. This might partly be explained by the heterogeneity in genotype, lifestyle, diet and the complex ethology of obesity and its associated metabolic disorders (OAMD). Nevertheless, recent research on this matter has shown a conceptual shift by focusing on more homogenous subpopulations, through the use of both anthropometric (weight, total body fat) as well as biochemical variables (insulin resistance, hyperlipidaemia) to define categories. Combined with technological advances, recent data suggests that an OAMD associated microbiota can be characterised by a potential pro-inflammatory composition, with less potential for the production of short chain fatty acids and butyrate in particular.
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Affiliation(s)
- G.D.A. Hermes
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - E.G. Zoetendal
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - H. Smidt
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
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Michail S, Lin M, Frey MR, Fanter R, Paliy O, Hilbush B, Reo NV. Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease. FEMS Microbiol Ecol 2014; 91:1-9. [PMID: 25764541 DOI: 10.1093/femsec/fiu002] [Citation(s) in RCA: 202] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Obesity is becoming the new pediatric epidemic. Non-alcoholic fatty liver disease (NAFLD) is frequently associated with obesity and has become the most common cause of pediatric liver disease. The gut microbiome is the major metabolic organ and determines how calories are processed, serving as a caloric gate and contributing towards the pathogenesis of NAFLD. The goal of this study is to examine gut microbial profiles in children with NAFLD using phylogenetic, metabolomic, metagenomic and proteomic approaches. Fecal samples were obtained from obese children with or without NAFLD and healthy lean children. Stool specimens were subjected to 16S rRNA gene microarray, shotgun sequencing, mass spectroscopy for proteomics and NMR spectroscopy for metabolite analysis. Children with NAFLD had more abundant Gammaproteobacteria and Prevotella and significantly higher levels of ethanol, with differential effects on short chain fatty acids. This group also had increased genomic and protein abundance for energy production with a reduction in carbohydrate and amino acid metabolism and urea cycle and urea transport systems. The metaproteome and metagenome showed similar findings. The gut microbiome in pediatric NAFLD is distinct from lean healthy children with more alcohol production and pathways allocated to energy metabolism over carbohydrate and amino acid metabolism, which would contribute to development of disease.
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Affiliation(s)
- Sonia Michail
- Department of Pediatrics, Division of Gastroenterology, Hepatology, and Nutrition at Children's Hospital Los Angeles, 4650 Sunset Blvd. MS#78, Los Angeles, CA 90027, USA Keck School of Medicine at the University of Southern California, Los Angeles, CA 90089, USA
| | - Malinda Lin
- Department of Pediatrics, Division of Gastroenterology, Hepatology, and Nutrition at Children's Hospital Los Angeles, 4650 Sunset Blvd. MS#78, Los Angeles, CA 90027, USA Keck School of Medicine at the University of Southern California, Los Angeles, CA 90089, USA
| | - Mark R Frey
- Department of Pediatrics, Division of Gastroenterology, Hepatology, and Nutrition at Children's Hospital Los Angeles, 4650 Sunset Blvd. MS#78, Los Angeles, CA 90027, USA Keck School of Medicine at the University of Southern California, Los Angeles, CA 90089, USA
| | - Rob Fanter
- Department of Pediatrics, Division of Gastroenterology, Hepatology, and Nutrition at Children's Hospital Los Angeles, 4650 Sunset Blvd. MS#78, Los Angeles, CA 90027, USA Childrens Hospital Los Angeles Proteomics Core, 4650 Sunset Blvd. MS#78, Los Angeles, CA 90027, USA
| | - Oleg Paliy
- Department of Biochemistry & Molecular Biology, Boonshoft School of Medicine, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH 45435, USA
| | - Brian Hilbush
- Real time Genomics, 999 Bayhill Dr #101, San Bruno, CA 94066, USA
| | - Nicholas V Reo
- Department of Biochemistry & Molecular Biology, Boonshoft School of Medicine, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH 45435, USA
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McKENNEY EA, ASHWELL M, LAMBERT JE, FELLNER V. Fecal microbial diversity and putative function in captive western lowland gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas) and binturongs (Arctictis binturong). Integr Zool 2014; 9:557-69. [DOI: 10.1111/1749-4877.12112] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Erin A. McKENNEY
- Department of Animal Sciences; North Carolina State University; Raleigh North Carolina USA
| | - Melissa ASHWELL
- Department of Animal Sciences; North Carolina State University; Raleigh North Carolina USA
| | - Joanna E. LAMBERT
- Department of Anthropology; The University of Texas at San Antonio; Texas USA
| | - Vivek FELLNER
- Department of Animal Sciences; North Carolina State University; Raleigh North Carolina USA
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Rajilić-Stojanović M, de Vos WM. The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol Rev 2014; 38:996-1047. [PMID: 24861948 PMCID: PMC4262072 DOI: 10.1111/1574-6976.12075] [Citation(s) in RCA: 716] [Impact Index Per Article: 71.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/29/2014] [Accepted: 05/09/2014] [Indexed: 02/06/2023] Open
Abstract
The microorganisms that inhabit the human gastrointestinal tract comprise a complex ecosystem with functions that significantly contribute to our systemic metabolism and have an impact on health and disease. In line with its importance, the human gastrointestinal microbiota has been extensively studied. Despite the fact that a significant part of the intestinal microorganisms has not yet been cultured, presently over 1000 different microbial species that can reside in the human gastrointestinal tract have been identified. This review provides a systematic overview and detailed references of the total of 1057 intestinal species of Eukarya (92), Archaea (8) and Bacteria (957), based on the phylogenetic framework of their small subunit ribosomal RNA gene sequences. Moreover, it unifies knowledge about the prevalence, abundance, stability, physiology, genetics and the association with human health of these gastrointestinal microorganisms, which is currently scattered over a vast amount of literature published in the last 150 years. This detailed physiological and genetic information is expected to be instrumental in advancing our knowledge of the gastrointestinal microbiota. Moreover, it opens avenues for future comparative and functional metagenomic and other high-throughput approaches that need a systematic and physiological basis to have an impact.
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Affiliation(s)
- Mirjana Rajilić-Stojanović
- Department for Biotechnology and Biochemical Engineering, Faculty of Technology and Metallurgy, University of BelgradeBelgrade, Serbia
- Laboratory of Microbiology, Wageningen UniversityWageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen UniversityWageningen, The Netherlands
- Departments of Bacteriology and Immunology, and Veterinary Biosciences, University of HelsinkiHelsinki, Finland
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Kim M, Wang L, Morrison M, Yu Z. Development of a phylogenetic microarray for comprehensive analysis of ruminal bacterial communities. J Appl Microbiol 2014; 117:949-60. [DOI: 10.1111/jam.12598] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 06/22/2014] [Accepted: 07/12/2014] [Indexed: 12/14/2022]
Affiliation(s)
- M. Kim
- Department of Animal Sciences; The Ohio State University; Columbus OH USA
| | - L. Wang
- Department of Animal Sciences; The Ohio State University; Columbus OH USA
| | - M. Morrison
- Department of Animal Sciences; The Ohio State University; Columbus OH USA
- University of Queensland Diamantina Institute; Woolloongabba Qld Australia
| | - Z. Yu
- Department of Animal Sciences; The Ohio State University; Columbus OH USA
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Taverniti V, Guglielmetti S. Methodological issues in the study of intestinal microbiota in irritable bowel syndrome. World J Gastroenterol 2014; 20:8821-8836. [PMID: 25083056 PMCID: PMC4112874 DOI: 10.3748/wjg.v20.i27.8821] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 04/10/2014] [Accepted: 06/05/2014] [Indexed: 02/06/2023] Open
Abstract
Irritable bowel syndrome (IBS) is an intestinal functional disorder with the highest prevalence in the industrialized world. The intestinal microbiota (IM) plays a role in the pathogenesis of IBS and is not merely a consequence of this disorder. Previous research efforts have not revealed unequivocal microbiological signatures of IBS, and the experimental results are contradictory. The experimental methodologies adopted to investigate the complex intestinal ecosystem drastically impact the quality and significance of the results. Therefore, to consider the methodological aspects of the research on IM in IBS, we reviewed 29 relevant original research articles identified through a PubMed search using three combinations of keywords: “irritable bowel syndrome + microflora”, “irritable bowel syndrome + microbiota” and “irritable bowel syndrome + microbiome”. For each study, we reviewed the quality and significance of the scientific evidence obtained with respect to the experimental method adopted. The data obtained from each study were compared with all considered publications to identify potential inconsistencies and explain contradictory results. The analytical revision of the studies referenced in the present review has contributed to the identification of microbial groups whose relative abundance significantly alters IBS, suggesting that these microbial groups could be IM signatures for this syndrome. The identification of microbial biomarkers in the IM can be advantageous for the development of new diagnostic tools and novel therapeutic strategies for the treatment of different subtypes of IBS.
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Effects of wheat bran extract containing arabinoxylan oligosaccharides on gastrointestinal parameters in healthy preadolescent children. J Pediatr Gastroenterol Nutr 2014; 58:647-53. [PMID: 24368315 DOI: 10.1097/mpg.0000000000000285] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
OBJECTIVES We assessed whether wheat bran extract (WBE) containing arabinoxylan-oligosaccharides (AXOS) elicited a prebiotic effect and modulated gastrointestinal (GI) parameters in healthy preadolescent children upon consumption in a beverage. METHODS This double-blind randomized placebo-controlled crossover trial evaluated the effects of consuming WBE at 0 (control) or 5.0 g/day for 3 weeks in 29 healthy children (8-12 years). Fecal levels of microbiota, short-chain fatty acids, branched-chain fatty acids, ammonia, moisture, and fecal pH were assessed at the end of each treatment and at the end of a 1-week run-in (RI) period. In addition, the subjects completed questionnaires scoring distress severity of 3 surveyed GI symptoms. Finally, subjects recorded defecation frequency and stool consistency. RESULTS Nominal fecal bifidobacteria levels tended to increase after 5 g/day WBE consumption (P = 0.069), whereas bifidobacteria expressed as percentage of total fecal microbiota was significantly higher upon 5 g/day WBE intake (P = 0.002). Additionally, 5 g/day WBE intake induced a significant decrease in fecal content of isobutyric acid and isovaleric acid (P < 0.01), markers of protein fermentation. WBE intake did not cause a change in distress severity of the 3 surveyed GI symptoms (flatulence, abdominal pain/cramps, and urge to vomit) (P > 0.1). CONCLUSIONS WBE is well tolerated at doses up to 5 g/day in healthy preadolescent children. In addition, the intake of 5 g/day exerts beneficial effects on gut parameters, in particular an increase in fecal bifidobacteria levels relative to total fecal microbiota, and reduction of colonic protein fermentation.
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Shankar V, Hamilton MJ, Khoruts A, Kilburn A, Unno T, Paliy O, Sadowsky MJ. Species and genus level resolution analysis of gut microbiota in Clostridium difficile patients following fecal microbiota transplantation. MICROBIOME 2014; 2:13. [PMID: 24855561 PMCID: PMC4030581 DOI: 10.1186/2049-2618-2-13] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 03/12/2014] [Indexed: 05/26/2023]
Abstract
BACKGROUND Clostridium difficile is an opportunistic human intestinal pathogen, and C. difficile infection (CDI) is one of the main causes of antibiotic-induced diarrhea and colitis. One successful approach to combat CDI, particularly recurrent form of CDI, is through transplantation of fecal microbiota from a healthy donor to the infected patient. In this study we investigated the distal gut microbial communities of three CDI patients before and after fecal microbiota transplantation, and we compared these communities to the composition of the donor's fecal microbiota. We utilized phylogenetic Microbiota Array, high-throughput Illumina sequencing, and fluorescent in situ hybridization to profile microbiota composition down to the genus and species level resolution. RESULTS The original patients' microbiota had low diversity, was dominated by members of Gammaproteobacteria and Bacilli, and had low numbers of Clostridia and Bacteroidia. At the genus level, fecal samples of CDI patients were rich in members of the Lactobacillus, Streptococcus, and Enterobacter genera. In comparison, the donor community was dominated by Clostridia and had significantly higher diversity and evenness. The patients' distal gut communities were completely transformed within 3 days following fecal transplantation, and these communities remained stable in each patient for at least 4 months. Despite compositional differences among recipients' pre-treatment gut microbiota, the transplanted gut communities were highly similar among recipients post-transplantation, were indistinguishable from that of the donor, and were rich in members of Blautia, Coprococcus, and Faecalibacterium. In each case, the gut microbiota restoration led to a complete patient recovery and symptom alleviation. CONCLUSION We conclude that C. difficile infection can be successfully treated by fecal microbiota transplantation and that this leads to stable transformation of the distal gut microbial community from the one abundant in aerotolerant species to that dominated by members of the Clostridia.
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Affiliation(s)
- Vijay Shankar
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, 3640 Col. Glenn Hwy, Dayton, OH 45435, USA
| | - Matthew J Hamilton
- Department of Soil, Water, and Climate, Biotechnology Institute, and Microbial Plant and Genomics Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Avenue, St. Paul, MN 55108, USA
| | - Alexander Khoruts
- Division of Gastroenterology; Department of Medicine, Center for Immunology, University of Minnesota, Minneapolis, MN USA
| | - Amanda Kilburn
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, 3640 Col. Glenn Hwy, Dayton, OH 45435, USA
| | - Tatsuya Unno
- Department of Soil, Water, and Climate, Biotechnology Institute, and Microbial Plant and Genomics Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Avenue, St. Paul, MN 55108, USA
| | - Oleg Paliy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, 3640 Col. Glenn Hwy, Dayton, OH 45435, USA
| | - Michael J Sadowsky
- Department of Soil, Water, and Climate, Biotechnology Institute, and Microbial Plant and Genomics Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Avenue, St. Paul, MN 55108, USA
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Tu Q, He Z, Li Y, Chen Y, Deng Y, Lin L, Hemme CL, Yuan T, Van Nostrand JD, Wu L, Zhou X, Shi W, Li L, Xu J, Zhou J. Development of HuMiChip for functional profiling of human microbiomes. PLoS One 2014; 9:e90546. [PMID: 24595026 PMCID: PMC3942451 DOI: 10.1371/journal.pone.0090546] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 02/01/2014] [Indexed: 02/05/2023] Open
Abstract
Understanding the diversity, composition, structure, function, and dynamics of human microbiomes in individual human hosts is crucial to reveal human-microbial interactions, especially for patients with microbially mediated disorders, but challenging due to the high diversity of the human microbiome. Here we have developed a functional gene-based microarray for profiling human microbiomes (HuMiChip) with 36,802 probes targeting 50,007 protein coding sequences for 139 key functional gene families. Computational evaluation suggested all probes included are highly specific to their target sequences. HuMiChip was used to analyze human oral and gut microbiomes, showing significantly different functional gene profiles between oral and gut microbiome. Obvious shifts of microbial functional structure and composition were observed for both patients with dental caries and periodontitis from moderate to advanced stages, suggesting a progressive change of microbial communities in response to the diseases. Consistent gene family profiles were observed by both HuMiChip and next generation sequencing technologies. Additionally, HuMiChip was able to detect gene families at as low as 0.001% relative abundance. The results indicate that the developed HuMiChip is a useful and effective tool for functional profiling of human microbiomes.
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Affiliation(s)
- Qichao Tu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Zhili He
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Yan Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yanfei Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Ye Deng
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Lu Lin
- Chinese Academy of Sciences, Qingdao Institute of Bioenergy and Bioprocess Technology, Qingdao, Shandong, China
| | - Christopher L. Hemme
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Tong Yuan
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Joy D. Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Liyou Wu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Wenyuan Shi
- UCLA School of Dentistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Jian Xu
- Chinese Academy of Sciences, Qingdao Institute of Bioenergy and Bioprocess Technology, Qingdao, Shandong, China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
- Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
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43
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Zhang J, Zheng Y, Guo Z, Qiao J, Gesudu Q, Sun Z, Huo D, Huang W, Huo Q, Kwok L, Zhang H. The diversity of intestinal microbiota of Mongolians living in Inner Mongolia, China. Benef Microbes 2013; 4:319-328. [PMID: 24311315 DOI: 10.3920/bm2013.0028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2024]
Abstract
The Mongolian nationality has developed their unique lifestyle and dietary habit for thousands of years. However, by now, little research has been focused on Mongolian gut microbiota and how it is related to different dietary habits. In this study, denaturing gradient gel electrophoresis (DGGE) and quantitative polymerase chain reaction (qPCR) methods were applied to reveal the diversity of predominant gut bacteria of 48 healthy Mongolians recruited from Hohhot city and the Xilin Gol pasturing area in Inner Mongolia. Compared to similar studies of other nationalities, results from the present study have confirmed that the composition of Mongolian gut microbiota is highly similar at the phylum level (Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria) but variable at the genus level. Especially, the numbers of Phascolarctobacterium, Lactobacillus and Bifidobacterium are rather high. DGGE profiles of Lactobacillus and Bifidobacterium revealed that Lactobacillus casei, Bifidobacterium longum and Bifidobacterium animalis subsp. lactis were predominant in the gut of the Mongolian subjects studied. On the contrary, Lactobacillus helveticus was detected in every pasturing area Mongolian, but not in any of the Hohhot city Mongolians. qPCR results revealed that the numbers of Lactobacillus and Bifidobacterium of Xilin Gol Mongolians were significantly higher (P<0.05) than that of Hohhot Mongolians, whereas the numbers of Enterobacterium were significantly lower (P<0.05). In addition, by partial least squares discriminate analysis and cluster analysis of data generated from DGGE and qPCR experiments, a striking difference in the composition of intestinal microbiota of Mongolians living in Hohhot city and the Xilin Gol pasturing area has been found. This study clearly shows that diet affects the microbiota composition of Mongolians living in different circumstances, i.e. urban versus rural.
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Affiliation(s)
- J Zhang
- Key Laboratory of Dairy Biotechnology and Bioengineering, Education Ministry of P.R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda road, Hohhot 010018, China
| | - Y Zheng
- Key Laboratory of Dairy Biotechnology and Bioengineering, Education Ministry of P.R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda road, Hohhot 010018, China
| | - Z Guo
- Key Laboratory of Dairy Biotechnology and Bioengineering, Education Ministry of P.R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda road, Hohhot 010018, China
| | - J Qiao
- Key Laboratory of Dairy Biotechnology and Bioengineering, Education Ministry of P.R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda road, Hohhot 010018, China
| | - Q Gesudu
- Key Laboratory of Dairy Biotechnology and Bioengineering, Education Ministry of P.R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda road, Hohhot 010018, China
| | - Z Sun
- Key Laboratory of Dairy Biotechnology and Bioengineering, Education Ministry of P.R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda road, Hohhot 010018, China
| | - D Huo
- Key Laboratory of Dairy Biotechnology and Bioengineering, Education Ministry of P.R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda road, Hohhot 010018, China
| | - W Huang
- Key Laboratory of Dairy Biotechnology and Bioengineering, Education Ministry of P.R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda road, Hohhot 010018, China
| | - Q Huo
- Key Laboratory of Dairy Biotechnology and Bioengineering, Education Ministry of P.R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda road, Hohhot 010018, China
| | - L Kwok
- Key Laboratory of Dairy Biotechnology and Bioengineering, Education Ministry of P.R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda road, Hohhot 010018, China
| | - H Zhang
- Key Laboratory of Dairy Biotechnology and Bioengineering, Education Ministry of P.R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda road, Hohhot 010018, China
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44
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Shankar V, Agans R, Holmes B, Raymer M, Paliy O. Do gut microbial communities differ in pediatric IBS and health? Gut Microbes 2013; 4:347-52. [PMID: 23674073 PMCID: PMC3744519 DOI: 10.4161/gmic.24827] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Human gastrointestinal microbial communities are recognized as important determinants of the host health and disease status. We have recently examined the distal gut microbiota of two groups of children: healthy adolescents and those diagnosed with diarrhea-predominant irritable bowel syndrome (IBS). We have revealed the common core of phylotypes shared among all children, identified genera differentially abundant between two groups and surveyed possible relationships among intestinal microbial genera and phylotypes. In this article we explored the use of supervised and unsupervised ordination and classification methods to separate and classify child fecal samples based on their quantitative microbial profile. We observed sample separation according to the participant health status, and this separation could often be attributed to the abundance levels of several specific microbial genera. We also extended our original correlation network analysis of the relative abundances of bacterial genera across samples and determined possible association networks separately for healthy and IBS groups. Interestingly, the number of significant genus abundance associations was drastically lower among the IBS samples, which can potentially be attributed to the existence of multiple routes to microbiota disbalance in IBS or to the loss of microbial interactions during IBS development.
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Affiliation(s)
- Vijay Shankar
- Department of Biochemistry and Molecular Biology; Wright State University; Dayton, OH USA
| | - Richard Agans
- Department of Biochemistry and Molecular Biology; Wright State University; Dayton, OH USA
| | - Benjamin Holmes
- Department of Computer Sciences; Wright State University; Dayton, OH USA
| | - Michael Raymer
- Department of Computer Sciences; Wright State University; Dayton, OH USA
| | - Oleg Paliy
- Department of Biochemistry and Molecular Biology; Wright State University; Dayton, OH USA,Correspondence to: Oleg Paliy,
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45
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Donatin E, Buffet S, Leroy Q, Raoult D, Drancourt M. A DNA microarray for the versatile diagnosis of infectious diarrhea. APMIS 2013; 121:634-42. [PMID: 23758523 PMCID: PMC7159548 DOI: 10.1111/apm.12081] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/17/2012] [Indexed: 01/08/2023]
Abstract
Several bacteria, viruses, and parasites cause diarrhea as coinfecting pathogens. We designed a DNA microarray comprising 60‐bp probes spotted 194 times for the multiplex detection of 33 enteropathogenic bacteria and seven enteropathogenic viruses, and the archaeon Methanobrevibacter smithii was used as an internal positive control. Nine pathogen‐free stool specimens were used as negative controls. One of these control specimens was further spiked with Salmonella enterica as a positive control. The microarray was then tested with 40 pathological stool specimens, comprising S. enterica (n = 30), Campylobacter jejuni (n = 4), pathogenic Escherichia coli (n = 2), and adenovirus (n = 4). M. smithii was detected in 47/49 (95.9%) specimens, no pathogen was detected in negative controls and S. enterica was identified in the S. enterica‐spiked positive control. The overall specificity was 100% and the overall sensitivity was 97.5% because one S. enterica sample was missed by the microarray. The multiplexed detection of C. jejuni spiked into an adenovirus‐positive stool sample gave positive results, with fluorescence values of 14.3 and 9.1, respectively. These data indicate that using the protocol developed in this article, the DNA array allows for the multiplexed detection of some enteropathogens in stool samples.
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Affiliation(s)
- Emilie Donatin
- Aix Marseille Université, URMITE, UMR63 CNRS 7278, IRD 198, Inserm 1095, Marseille, France
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46
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El Kaoutari A, Armougom F, Gordon JI, Raoult D, Henrissat B. The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol 2013; 11:497-504. [PMID: 23748339 DOI: 10.1038/nrmicro3050] [Citation(s) in RCA: 1027] [Impact Index Per Article: 93.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Descriptions of the microbial communities that live on and in the human body have progressed at a spectacular rate over the past 5 years, fuelled primarily by highly parallel DNA-sequencing technologies and associated advances in bioinformatics, and by the expectation that understanding how to manipulate the structure and functions of our microbiota will allow us to affect health and prevent or treat diseases. Among the myriad of genes that have been identified in the human gut microbiome, those that encode carbohydrate-active enzymes (CAZymes) are of particular interest, as these enzymes are required to digest most of our complex repertoire of dietary polysaccharides. In this Analysis article, we examine the carbohydrate-digestive capacity of a simplified but representative mini-microbiome in order to highlight the abundance and variety of bacterial CAZymes that are represented in the human gut microbiota.
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Affiliation(s)
- Abdessamad El Kaoutari
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7257, Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
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47
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Chen X, D'Souza R, Hong ST. The role of gut microbiota in the gut-brain axis: current challenges and perspectives. Protein Cell 2013; 4:403-14. [PMID: 23686721 DOI: 10.1007/s13238-013-3017-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 04/01/2013] [Indexed: 12/22/2022] Open
Abstract
Brain and the gastrointestinal (GI) tract are intimately connected to form a bidirectional neurohumoral communication system. The communication between gut and brain, knows as the gut-brain axis, is so well established that the functional status of gut is always related to the condition of brain. The researches on the gut-brain axis were traditionally focused on the psychological status affecting the function of the GI tract. However, recent evidences showed that gut microbiota communicates with the brain via the gut-brain axis to modulate brain development and behavioral phenotypes. These recent findings on the new role of gut microbiota in the gut-brain axis implicate that gut microbiota could associate with brain functions as well as neurological diseases via the gut-brain axis. To elucidate the role of gut microbiota in the gut-brain axis, precise identification of the composition of microbes constituting gut microbiota is an essential step. However, identification of microbes constituting gut microbiota has been the main technological challenge currently due to massive amount of intestinal microbes and the difficulties in culture of gut microbes. Current methods for identification of microbes constituting gut microbiota are dependent on omics analysis methods by using advanced high tech equipment. Here, we review the association of gut microbiota with the gut-brain axis, including the pros and cons of the current high throughput methods for identification of microbes constituting gut microbiota to elucidate the role of gut microbiota in the gut-brain axis.
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Affiliation(s)
- Xiao Chen
- BDRD Research Institute, JINIS Biopharmaceuticals Inc, 948-9 Dunsan, Bongdong, Wanju, Chonbuk, 565-902, South Korea
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48
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Tottey W, Denonfoux J, Jaziri F, Parisot N, Missaoui M, Hill D, Borrel G, Peyretaillade E, Alric M, Harris HMB, Jeffery IB, Claesson MJ, O'Toole PW, Peyret P, Brugère JF. The human gut chip "HuGChip", an explorative phylogenetic microarray for determining gut microbiome diversity at family level. PLoS One 2013; 8:e62544. [PMID: 23690942 PMCID: PMC3656878 DOI: 10.1371/journal.pone.0062544] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 03/22/2013] [Indexed: 02/07/2023] Open
Abstract
Evaluating the composition of the human gut microbiota greatly facilitates studies on its role in human pathophysiology, and is heavily reliant on culture-independent molecular methods. A microarray designated the Human Gut Chip (HuGChip) was developed to analyze and compare human gut microbiota samples. The PhylArray software was used to design specific and sensitive probes. The DNA chip was composed of 4,441 probes (2,442 specific and 1,919 explorative probes) targeting 66 bacterial families. A mock community composed of 16S rRNA gene sequences from intestinal species was used to define the threshold criteria to be used to analyze complex samples. This was then experimentally verified with three human faecal samples and results were compared (i) with pyrosequencing of the V4 hypervariable region of the 16S rRNA gene, (ii) metagenomic data, and (iii) qPCR analysis of three phyla. When compared at both the phylum and the family level, high Pearson's correlation coefficients were obtained between data from all methods. The HuGChip development and validation showed that it is not only able to assess the known human gut microbiota but could also detect unknown species with the explorative probes to reveal the large number of bacterial sequences not yet described in the human gut microbiota, overcoming the main inconvenience encountered when developing microarrays.
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Affiliation(s)
- William Tottey
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Jeremie Denonfoux
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Faouzi Jaziri
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
- CNRS, UMR 6158, ISIMA/LIMOS, Aubière/Clermont-Ferrand, France
| | - Nicolas Parisot
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Mohiedine Missaoui
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
- CNRS, UMR 6158, ISIMA/LIMOS, Aubière/Clermont-Ferrand, France
| | - David Hill
- CNRS, UMR 6158, ISIMA/LIMOS, Aubière/Clermont-Ferrand, France
| | - Guillaume Borrel
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Eric Peyretaillade
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Monique Alric
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Hugh M. B. Harris
- Department of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Ian B. Jeffery
- Department of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Marcus J. Claesson
- Department of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Paul W. O'Toole
- Department of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Pierre Peyret
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
| | - Jean-François Brugère
- EA CIDAM 4678, Clermont-Université, Université d'Auvergne, Clermont-Ferrand, France
- * E-mail:
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Nylund L, Satokari R, Nikkilä J, Rajilić-Stojanović M, Kalliomäki M, Isolauri E, Salminen S, de Vos WM. Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease. BMC Microbiol 2013; 13:12. [PMID: 23339708 PMCID: PMC3563445 DOI: 10.1186/1471-2180-13-12] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 11/26/2012] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Deviations in composition and diversity of intestinal microbiota in infancy have been associated with both the development and recurrence of atopic eczema. Thus, we decided to use a deep and global microarray-based method to characterize the diversity and temporal changes of the intestinal microbiota in infancy and to define specific bacterial signatures associated with eczema. Faecal microbiota at 6 and 18 months of age were analysed from 34 infants (15 with eczema and 19 healthy controls) selected from a prospective follow-up study based on the availability of faecal samples. The infants were originally randomized to receive either Lactobacillus rhamnosus GG or placebo. RESULTS Children with eczema harboured a more diverse total microbiota than control subjects as assessed by the Simpson's reciprocal diversity index of the microarray profiles. Composition of the microbiota did not differ between study groups at age of 6 months, but was significantly different at age of 18 months as assessed by MCPP (p=0.01). At this age healthy children harboured 3 -fold greater amount of members of the Bacteroidetes (p=0.01). Microbiota of children suffering from eczema had increased abundance of the Clostridium clusters IV and XIVa, which are typically abundant in adults. Probiotic Lactobacillus rhamnosus GG supplementation in early infancy was observed to have minor long-term effects on the microbiota composition. CONCLUSION A diverse and adult-type microbiota in early childhood is associated with eczema and it may contribute to the perpetuation of eczema.
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Affiliation(s)
- Lotta Nylund
- Functional Foods Forum, University of Turku, Turku, FI-20014, Finland.
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50
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Quantitative profiling of gut microbiota of children with diarrhea-predominant irritable bowel syndrome. Am J Gastroenterol 2012; 107:1740-51. [PMID: 22986438 DOI: 10.1038/ajg.2012.287] [Citation(s) in RCA: 145] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
OBJECTIVES Human intestinal microbiota has a number of important roles in human health and is also implicated in several gastrointestinal disorders. The goal of this study was to determine the gut microbiota in two groups of pre- and adolescent children: healthy volunteers and children diagnosed with diarrhea predominant irritable bowel syndrome (IBS-D). METHODS Phylogenetic Microbiota Array was used to obtain quantitative measurements of bacterial presence and abundance in subjects ’ fecal samples. We utilized high-throughput DNA sequencing, quantitative PCR, and fluorescent in situ hybridization to confirm microarray findings. RESULTS Both sample groups were dominated by the phyla Firmicutes, Bacteroidetes, and Actinobacteria, which cumulatively constituted 91 % of overall sample composition on average. A core microbiome shared among analyzed samples encompassed 55 bacterial phylotypes dominated by genus Ruminococcus ; members of genera Clostridium , Faecalibacterium, Roseburia, Streptococcus , and Bacteroides were also present. Several genera were found to be differentially abundant in the gut of healthy and IBS groups: levels of Veillonella , Prevotella , Lactobacillus , and Parasporo bacterium were increased in children diagnosed with IBS, whereas members of Bifidobacterium and Verrucomicrobium were less abundant in those individuals. By calculating a nonparametric correlation matrix among abundances of different genera in all samples, we also examined potential associations among intestinal microbes. Strong positive correlations were found between abundances of Veillonella and both Haemophilus and Streptococcus , between Anaerovorax and Verrucomicrobium , and between Tannerella and Anaerophaga . CONCLUSIONS Although at the higher taxonomical level gut microbiota was similar between healthy and IBS-D children, specific differences in the abundances of several bacterial genera were revealed. Core microbiome in children was dominated by Clostridia. Putative relationships identified among microbial genera provide testable hypotheses of cross-species associations among members of human gut microbiota
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