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Rosindell J, Manson K, Gumbs R, Pearse WD, Steel M. Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage. Syst Biol 2024; 73:158-182. [PMID: 38102727 PMCID: PMC11129585 DOI: 10.1093/sysbio/syad072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023] Open
Abstract
Phylogenetic metrics are essential tools used in the study of ecology, evolution and conservation. Phylogenetic diversity (PD) in particular is one of the most prominent measures of biodiversity and is based on the idea that biological features accumulate along the edges of phylogenetic trees that are summed. We argue that PD and many other phylogenetic biodiversity metrics fail to capture an essential process that we term attrition. Attrition is the gradual loss of features through causes other than extinction. Here we introduce "EvoHeritage", a generalization of PD that is founded on the joint processes of accumulation and attrition of features. We argue that while PD measures evolutionary history, EvoHeritage is required to capture a more pertinent subset of evolutionary history including only components that have survived attrition. We show that EvoHeritage is not the same as PD on a tree with scaled edges; instead, accumulation and attrition interact in a more complex non-monophyletic way that cannot be captured by edge lengths alone. This leads us to speculate that the one-dimensional edge lengths of classic trees may be insufficiently flexible to capture the nuances of evolutionary processes. We derive a measure of EvoHeritage and show that it elegantly reproduces species richness and PD at opposite ends of a continuum based on the intensity of attrition. We demonstrate the utility of EvoHeritage in ecology as a predictor of community productivity compared with species richness and PD. We also show how EvoHeritage can quantify living fossils and resolve their associated controversy. We suggest how the existing calculus of PD-based metrics and other phylogenetic biodiversity metrics can and should be recast in terms of EvoHeritage accumulation and attrition.
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Affiliation(s)
- James Rosindell
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand
| | - Kerry Manson
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand
| | - Rikki Gumbs
- EDGE of Existence Programme, Zoological Society of London, Regent’s Park, London NW1 4RY, UK
| | - William D Pearse
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
| | - Mike Steel
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand
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Pereira H, Chakarov N, Hoffman JI, Rinaud T, Ottensmann M, Gladow KP, Tobias B, Caspers BA, Maraci Ö, Krüger O. Early-life factors shaping the gut microbiota of Common buzzard nestlings. Anim Microbiome 2024; 6:27. [PMID: 38745254 DOI: 10.1186/s42523-024-00313-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Exploring the dynamics of gut microbiome colonisation during early-life stages is important for understanding the potential impact of microbes on host development and fitness. Evidence from model organisms suggests a crucial early-life phase when shifts in gut microbiota can lead to immune dysregulation and reduced host condition. However, our understanding of gut microbiota colonisation in long-lived vertebrates, especially during early development, remains limited. We therefore used a wild population of common buzzard nestlings (Buteo buteo) to investigate connections between the early-life gut microbiota colonisation, environmental and host factors. RESULTS We targeted both bacterial and eukaryotic microbiota using the 16S and 28S rRNA genes. We sampled the individuals during early developmental stages in a longitudinal design. Our data revealed that age significantly affected microbial diversity and composition. Nest environment was a notable predictor of microbiota composition, with particularly eukaryotic communities differing between habitats occupied by the hosts. Nestling condition and infection with the blood parasite Leucocytozoon predicted microbial community composition. CONCLUSION Our findings emphasise the importance of studying microbiome dynamics to capture changes occurring during ontogeny. They highlight the role of microbial communities in reflecting host health and the importance of the nest environment for the developing nestling microbiome. Overall, this study contributes to understanding the complex interplay between microbial communities, host factors, and environmental variables, and sheds light on the ecological processes governing gut microbial colonisation during early-life stages.
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Affiliation(s)
- Hugo Pereira
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany.
| | - Nayden Chakarov
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Department of Evolutionary Population Genetics, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Tony Rinaud
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Meinolf Ottensmann
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Kai-Philipp Gladow
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Busche Tobias
- Medical School East Westphalia-Lippe & Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, NRW, Germany
| | - Barbara A Caspers
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Öncü Maraci
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Oliver Krüger
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
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Murtaza N, Nawaz M, Yaqub T, Mehmood AK. Impact of Limosilactobacillus fermentum probiotic treatment on gut microbiota composition in sahiwal calves with rotavirus diarrhea: A 16S metagenomic analysis study". BMC Microbiol 2024; 24:114. [PMID: 38575861 PMCID: PMC10993544 DOI: 10.1186/s12866-024-03254-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/08/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Diarrhea poses a major threat to bovine calves leading to mortality and economic losses. Among the causes of calf diarrhea, bovine rotavirus is a major etiological agent and may result in dysbiosis of gut microbiota. The current study was designed to investigate the effect of probiotic Limosilactobacillus fermentum (Accession No.OR504458) on the microbial composition of rotavirus-infected calves using 16S metagenomic analysis technique. Screening of rotavirus infection in calves below one month of age was done through clinical signs and Reverse Transcriptase PCR. The healthy calves (n = 10) were taken as control while the infected calves (n = 10) before treatment was designated as diarrheal group were treated with Probiotic for 5 days. All the calves were screened for the presence of rotavirus infection on each day and fecal scoring was done to assess the fecal consistency. Infected calves after treatment were designated as recovered group. Fecal samples from healthy, recovered and diarrheal (infected calves before sampling) were processed for DNA extraction while four samples from each group were processed for 16S metagenomic analysis using Illumina sequencing technique and analyzed via QIIME 2. RESULTS The results show that Firmicutes were more abundant in the healthy and recovered group than in the diarrheal group. At the same time Proteobacteria was higher in abundance in the diarrheal group. Order Oscillospirales dominated healthy and recovered calves and Enterobacterials dominated the diarrheal group. Alpha diversity indices show that diversity indices based on richness were higher in the healthy group and lower in the diarrheal group while a mixed pattern of clustering between diarrheal and recovered groups samples in PCA plots based on beta diversity indices was observed. CONCLUSION It is concluded that probiotic Limosilactobacillus Fermentum N-30 ameliorate the dysbiosis caused by rotavirus diarrhea and may be used to prevent diarrhea in pre-weaned calves after further exploration.
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Affiliation(s)
- Nadeem Murtaza
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Muhammad Nawaz
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan.
| | - Tahir Yaqub
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Asim Khalid Mehmood
- Department of Veterinary Surgery and Pet Sciences, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
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De-la-Vega-Camarillo E, Hernández-García JA, Villa-Tanaca L, Hernández-Rodríguez C. Unlocking the hidden potential of Mexican teosinte seeds: revealing plant growth-promoting bacterial and fungal biocontrol agents. FRONTIERS IN PLANT SCIENCE 2023; 14:1247814. [PMID: 37860235 PMCID: PMC10582567 DOI: 10.3389/fpls.2023.1247814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/15/2023] [Indexed: 10/21/2023]
Abstract
The bacterial component of plant holobiont maintains valuable interactions that contribute to plants' growth, adaptation, stress tolerance, and antagonism to some phytopathogens. Teosinte is the grass plant recognized as the progenitor of modern maize, domesticated by pre-Hispanic civilizations around 9,000 years ago. Three teosinte species are recognized: Zea diploperennis, Zea perennis, and Zea mays. In this work, the bacterial diversity of three species of Mexican teosinte seeds was explored by massive sequencing of 16S rRNA amplicons. Streptomyces, Acinetobacter, Olivibacter, Erwinia, Bacillus, Pseudomonas, Cellvibrio, Achromobacter, Devosia, Lysobacter, Sphingopyxis, Stenotrophomonas, Ochrobactrum, Delftia, Lactobacillus, among others, were the bacterial genera mainly represented. The bacterial alpha diversity in the seeds of Z. diploperennis was the highest, while the alpha diversity in Z. mays subsp. mexicana race was the lowest observed among the species and races. The Mexican teosintes analyzed had a core bacteriome of 38 bacterial genera, including several recognized plant growth promoters or fungal biocontrol agents such as Agrobacterium, Burkholderia, Erwinia, Lactobacillus, Ochrobactrum, Paenibacillus, Pseudomonas, Sphingomonas, Streptomyces, among other. Metabolic inference analysis by PICRUSt2 of bacterial genera showed several pathways related to plant growth promotion (PGP), biological control, and environmental adaptation. The implications of these findings are far-reaching, as they highlight the existence of an exceptional bacterial germplasm reservoir teeming with potential plant growth promotion bacteria (PGPB). This reserve holds the key to cultivating innovative bioinoculants and formidable fungal antagonistic strains, thereby paving the way for a more sustainable and eco-friendly approach to agriculture. Embracing these novel NGS-based techniques and understanding the profound impact of the vertical transference of microorganisms from seeds could revolutionize the future of agriculture and develop a new era of symbiotic harmony between plants and microbes.
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Affiliation(s)
| | | | | | - César Hernández-Rodríguez
- Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
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Xu Z, Chen J, Li Y, Shekarriz E, Wu W, Chen B, Liu H. High Microeukaryotic Diversity in the Cold-Seep Sediment. MICROBIAL ECOLOGY 2023; 86:2003-2020. [PMID: 36973438 DOI: 10.1007/s00248-023-02212-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 03/22/2023] [Indexed: 06/18/2023]
Abstract
Microeukaryotic diversity, community structure, and their regulating mechanisms remain largely unclear in chemosynthetic ecosystems. Here, using high-throughput sequencing data of 18S rRNA genes, we explored microeukaryotic communities from the Haima cold seep in the northern South China Sea. We compared three distinct habitats: active, less active, and non-seep regions, with vertical layers (0-25 cm) from sediment cores. The results showed that seep regions harbored more abundant and diverse parasitic microeukaryotes (e.g., Apicomplexa and Syndiniales) as indicator species, compared to nearby non-seep region. Microeukaryotic community heterogeneity was larger between habitats than within habitat, and greatly increased when considering molecular phylogeny, suggesting the local diversification in cold-seep sediments. Microeukaryotic α-diversity at cold seeps was positively increased by metazoan richness and dispersal rate of microeukaryotes, while its β-diversity was promoted by heterogeneous selection mainly from metazoan communities (as potential hosts). Their combined effects led to the significant higher γ-diversity (i.e., total diversity in a region) at cold seeps than non-seep regions, suggesting cold-seep sediment as a hotspot for microeukaryotic diversity. Our study highlights the importance of microeukaryotic parasitism in cold-seep sediment and has implications for the roles of cold seep in maintaining and promoting marine biodiversity.
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Affiliation(s)
- Zhimeng Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jiawei Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yingdong Li
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Erfan Shekarriz
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Wenxue Wu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Bingzhang Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
| | - Hongbin Liu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China.
- CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Sanya, China.
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Sułowicz S, Borymski S, Dulski M, Nowak A, Bondarczuk K, Markowicz A. Nanopesticide risk assessment based on microbiome profiling - Community structure and functional potential as biomarkers in captan@ZnO 35-45 nm and captan@SiO 220-30 nm treated orchard soil. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131948. [PMID: 37392645 DOI: 10.1016/j.jhazmat.2023.131948] [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: 05/10/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/03/2023]
Abstract
Nanoformulation should minimise the usage of pesticides and limit their environmental footprint. The risk assessment of two nanopesticides with fungicide captan as an active organic substance and ZnO35-45 nm or SiO220-30 nm as nanocarriers was evaluated using the non-target soil microorganisms as biomarkers. The first time for that kind of nanopesticides next-generation sequencing (NGS) of bacterial 16 S rRNA and fungal ITS region and metagenomics functional predictions (PICRUST2) was made to study structural and functional biodiversity. During a 100-day microcosm study in soil with pesticide application history, the effect of nanopesticides was compared to pure captan and both nanocarriers. Nanoagrochemicals affected microbial composition, especially Acidobacteria-6 class, and alpha diversity, but the observed effect was generally more substantial for pure captan. As for beta diversity, the negative impact was detected only in response to captan and still observed on day 100. Fungal community in the orchard soil showed only a decrease in phylogenetic diversity in captan set-up since day 30. PICRUST2 analysis confirmed several times lower impact of nanopesticides considering the abundance of functional pathways and genes encoding enzymes. Furthermore, the overall data indicated that using SiO220-30 nm as a nanocarrier speeds up a recovery process compared to ZnO35-45 nm.
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Affiliation(s)
- Sławomir Sułowicz
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland.
| | - Sławomir Borymski
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland
| | - Mateusz Dulski
- University of Silesia, Institute of Materials Engineering, Silesian Center for Education and Interdisciplinary Research, 75 Pulku Piechoty 1A, 41-500 Chorzow, Poland
| | - Anna Nowak
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland
| | - Kinga Bondarczuk
- Centre for Bioinformatics and Data Analysis, Medical University of Białystok, Jerzego Waszyngtona 13A, 15-269 Białystok, Poland
| | - Anna Markowicz
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland
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Li J, Chai G, Xiao Y, Li Z. The impacts of ocean acidification, warming and their interactive effects on coral prokaryotic symbionts. ENVIRONMENTAL MICROBIOME 2023; 18:49. [PMID: 37287087 DOI: 10.1186/s40793-023-00505-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/19/2023] [Indexed: 06/09/2023]
Abstract
BACKGROUND Reef-building corals, the foundation of tropical coral reefs, are vulnerable to climate change e.g. ocean acidification and elevated seawater temperature. Coral microbiome plays a key role in host acclimatization and maintenance of the coral holobiont's homeostasis under different environmental conditions, however, the response patterns of coral prokaryotic symbionts to ocean acidification and/or warming are rarely known at the metatranscriptional level, particularly the knowledge of interactive and persistent effects is limited. Using branching Acropora valida and massive Galaxea fascicularis as models in a lab system simulating extreme ocean acidification (pH 7.7) and/or warming (32 °C) in the future, we investigated the changes of in situ active prokaryotic symbionts community and gene expression of corals under/after (6/9 d) acidification (A), warming (H) and acidification-warming (AH) by metatranscriptome analysis with pH8.1, 26 °C as the control. RESULTS A, H and AH increased the relative abundance of in situ active pathogenic bacteria. Differentially expressed genes (DEGs) involved in virulence, stress resistance, and heat shock proteins were up-regulated. Many DEGs involved in photosynthesis, carbon dioxide fixation, amino acids, cofactors and vitamins, auxin synthesis were down-regulated. A broad array of new DEGs involved in carbohydrate metabolism and energy production emerged after the stress treatment. Different response patterns of prokaryotic symbionts of massive G. fascicularis and branching A. valida were suggested, as well as the interactive effects of combined AH and persistent effects. CONCLUSIONS The metatranscriptome-based study indicates that acidification and/or warming might change coral's in situ active prokaryotic microbial diversity and functional gene expression towards more pathogenic and destabilized coral-microbes symbioses, particularly combined acidification and warming show interactive effects. These findings will aid in comprehension of the coral holobiont's ability for acclimatization under future climate change.
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Affiliation(s)
- Jinlong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Guangjun Chai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Yilin Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
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Rofael SAD, Brown J, Lipman MCI, Lowe DM, Spratt D, Quaderi S, Hurst JR, McHugh TD. Impact of prophylactic and 'rescue pack' antibiotics on the airway microbiome in chronic lung disease. BMJ Open Respir Res 2023; 10:10/1/e001335. [PMID: 37085283 PMCID: PMC10124267 DOI: 10.1136/bmjresp-2022-001335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 03/24/2023] [Indexed: 04/23/2023] Open
Abstract
The management of many chronic lung diseases involves multiple antibiotic prescriptions either to treat acute exacerbations or as prophylactic therapy to reduce the frequency of exacerbations and improve patients' quality of life. AIM To investigate the effects of antibiotics on the homeostasis of bacterial communities in the airways, and how this may contribute to antimicrobial resistance (AMR) among respiratory pathogens and microbiota. METHODS Within an observational cohort study, sputum was collected from 84 patients with chronic obstructive pulmonary disease and/or bronchiectasis at stable state: 47 were receiving antibiotic prophylaxis therapy. V3-V4 16S-rRNA sequencing on Illumina MiSeq, quantitative PCR for typical respiratory pathogens, bacteriology cultures and antimicrobial susceptibility testing of sputum isolates, resistome analysis on a subset of 17 sputum samples using MinION metagenomics sequencing were performed. FINDING The phylogenetic α-diversity and the total bacterial density in sputum were significantly lower in patients receiving prophylactic antibiotics (p=0.014 and 0.029, respectively). Antibiotic prophylaxis was associated with significantly lower relative abundance of respiratory pathogens such as Pseudomonas aeruginosa, Moraxella catarrhalis and members of family Enterobacteriaceae in the airway microbiome, but not Haemophilus influenzae and Streptococcus pneumoniae. No major definite directional shifts in the microbiota composition were identified with prophylactic antibiotic use at the cohort level. Surveillance of AMR and resistome analysis revealed a high frequency of resistance to macrolide and tetracycline in the cohort. AMR expressed by pathogenic bacterial isolates was associated with antibiotics prescribed as 'rescue packs' for prompt initiation of self-treatment of exacerbations (Spearman's rho=0.408, p=0.02). CONCLUSIONS Antibiotic prophylactic therapy suppresses recognised pathogenic bacteria in the sputum of patients with chronic lung disease. The use of antibiotic rescue packs may be driving AMR in this cohort rather than prophylactic antibiotics.
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Affiliation(s)
- Sylvia A D Rofael
- UCL Centre for Clinical Microbiology, Division of Infection & Immunity, University College London, London, UK
- Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - James Brown
- UCL Respiratory, Divison of Medicine, University College London, London, UK
- Respiratory Medicine, Royal Free NHS Foundation Trust, London, UK
| | - Marc C I Lipman
- UCL Respiratory, Divison of Medicine, University College London, London, UK
- Respiratory Medicine, Royal Free NHS Foundation Trust, London, UK
| | - David M Lowe
- Institute for Immunity and Transplantation, Divison of Infection and Immunity, University College London, London, UK
| | - David Spratt
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, UK
| | - Shumonta Quaderi
- UCL Respiratory, Divison of Medicine, University College London, London, UK
- Respiratory Medicine, Royal Free NHS Foundation Trust, London, UK
| | - John R Hurst
- UCL Respiratory, Divison of Medicine, University College London, London, UK
- Respiratory Medicine, Royal Free NHS Foundation Trust, London, UK
| | - Timothy D McHugh
- UCL Centre for Clinical Microbiology, Division of Infection & Immunity, University College London, London, UK
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Zu K, Zhang C, Chen F, Zhang Z, Ahmad S, Nabi G. Latitudinal gradients of angiosperm plant diversity and phylogenetic structure in China’s nature reserves. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
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10
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Intestinal Microbiota of Anser fabalis Wintering in Two Lakes in the Middle and Lower Yangtze River Floodplain. Animals (Basel) 2023; 13:ani13040707. [PMID: 36830494 PMCID: PMC9952484 DOI: 10.3390/ani13040707] [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: 01/06/2023] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
The intestinal microbiota of migratory birds participate in the life activities of the host and are affected by external environmental factors. The difference in habitat environment provides diversity in external environmental selection pressure for the same overwintering waterfowl, which may be reflected in their intestinal microbiota. Caizi lake and Shengjin Lake in the Middle and Lower Yangtze River Floodplain are the main habitats for migratory waterfowl in winter, especially the Anser fabalis (A. fabalis). It is important to explore the changes in intestinal microbiota composition and function of A. fabalis in the early overwintering period to clarify the effect of habitat size and protection status on intestinal microbiota. In this study, the composition and structural characteristics of the intestinal microbiota of A. fabalis in Shengjin Lake (SL) and Caizi Lake (CL) were preliminarily explored in order to obtain data for the migratory birds. In both SL and CL groups, 16S rRNA amplicon sequencing analysis showed that Firmicutes was the dominant bacterial phylum, but the relative abundance showed significant differences. Lactobacillus was the most abundant genus in both SL and CL groups. At the species level, the abundance of L. aviaries was the highest, with a relative abundance in both SL and CL groups of more than 34%. When comparing the average relative abundance of the 15 most abundant genera, it was found that Subdoligranulum, Exiguobacterium, and Terrisporobacter had higher abundances in the intestinal microbiota of CL A. fabalis, while Streptococcus and Rothia had higher abundances in the intestinal microbiota of SL A. fabalis. There was only a positive correlation between Bacteroidota and Proteobacteria in the intestinal microbiota flora of SL A. fabalis, and the species were closely related. At the same time, there were positive and negative correlations between Firmicutes and Actinomycetes. However, CL is mainly associated with a positive correlation between Firmicutes and Actinomycetes, and there are also a small number of connections between Firmicutes. PICRUSt1 prediction analysis revealed that the Clusters of Orthologous Groups (COG) functions of SL and CL involve energy production and transformation, amino acid transport and metabolism, carbohydrate transport and metabolism, and transcription. Understanding the changes in intestinal microbiota in Aves during the overwintering period is of great importance to explore the adaptation mechanism of migratory Aves to the overwintering environment. This work provides basic data for an A. fabalis intestinal microbiota study.
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Stefani F, Beguin J, Paré D, Morency MJ, Martineau C, Fortin JA, Thiffault N, Séguin A. Does wood mulch trigger microbially mediated positive plant-soil feedback in degraded boreal forest sites? A post hoc study. FRONTIERS IN PLANT SCIENCE 2023; 14:1122445. [PMID: 37206972 PMCID: PMC10191178 DOI: 10.3389/fpls.2023.1122445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/15/2023] [Indexed: 05/21/2023]
Abstract
Introduction Reforestation of degraded lands in the boreal forest is challenging and depends on the direction and strength of the plant-soil feedback (PSF). Methods Using a gradient in tree productivity (null, low and high) from a long-term, spatially replicated reforestation experiment of borrow pits in the boreal forest, we investigated the interplay between microbial communities and soil and tree nutrient stocks and concentrations in relation to a positive PSF induced by wood mulch amendment. Results Three levels of mulch amendment underlie the observed gradient in tree productivity, and plots that had been amended with a continuous layer of mulch 17 years earlier showed a positive PSF with trees up to 6 m tall, a closed canopy, and a developing humus layer. The average taxonomic and functional composition of the bacterial and fungal communities differed markedly betweenlow- and high-productivity plots. Trees in high-productivity plots recruited a specialized soil microbiome that was more efficient at nutrient mobilization and acquisition. These plots showed increases in carbon (C), calcium (Ca), nitrogen (N), potassium (K), and phosphorus (P) stocks and as well as bacterial and fungal biomass. The soil microbiome was dominated by taxa from the fungal genus Cortinarius and the bacterial family Chitinophagaceae, and a complex microbial network with higher connectivity and more keystone species supported tree productivity in reforested plots compared to unproductive plots. Discussion Therefore, mulching of plots resulted in a microbially mediated PSF that enhances mineral weathering and non-symbiotic N fixation, and in turn helps transform unproductive plots into productive plots to ensure rapid restoration of the forest ecosystem in a harsh boreal environment.
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Affiliation(s)
- Franck Stefani
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- *Correspondence: Franck Stefani, ; David Paré,
| | - Julien Beguin
- Institut de recherche sur les forêts, Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, QC, Canada
| | - David Paré
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
- *Correspondence: Franck Stefani, ; David Paré,
| | - Marie-Josée Morency
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Christine Martineau
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - J. André Fortin
- Université Laval, Faculté de foresterie, de géographie et de géomatique, Département des sciences du bois et de la forêt, Québec, QC, Canada
| | - Nelson Thiffault
- Natural Resources Canada, Canadian Forest Service, Canadian Wood Fibre Centre, Québec, QC, Canada
| | - Armand Séguin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
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12
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Changes in Phylogenetic and Functional Diversity of Ciliates along the Course of a Mediterranean Karstic River. Microorganisms 2022; 10:microorganisms10122493. [PMID: 36557746 PMCID: PMC9783291 DOI: 10.3390/microorganisms10122493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/04/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Ciliates are a group of phagotrophic protists found in a wide variety of ecosystems. This study builds on recent studies of ciliates in the Krka river and investigates changes in the phylogenetic and functional diversity of ciliates in biofilm to predict the phylogenetic and functional structure of ciliates in other karstic rivers. Biofilm samples were collected from four representative locations: upstream (Krka spring), midstream (Marasovine), and downstream (Roški slap, Skradinski buk) of the Krka river to test for differences in phylogenetic and functional diversity of ciliates in relation to location and positioning on tufa stones (light/dark-exposed side of tufa stone). Our results showed that Krka spring had higher phylogenetic species variability, lower phylogenetic diversity, and lower functional richness than Skradinski buk, suggesting phylogenetic overdispersal at Krka spring. This could be due to environmental filtering, competitive exclusion, or a combination of these factors. As the first study of its kind in the Mediterranean, our results shed light on the phylogenetic and functional diversity of ciliates in karst ecosystems and provide a basis for future ecological and conservation efforts.
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13
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Deng Y, Borewicz K, van Loo J, Olabarrieta MZ, Kokou F, Sipkema D, Verdegem MCJ. In-Situ Biofloc Affects the Core Prokaryotes Community Composition in Gut and Enhances Growth of Nile Tilapia (Oreochromis niloticus). MICROBIAL ECOLOGY 2022; 84:879-892. [PMID: 34609532 PMCID: PMC9622544 DOI: 10.1007/s00248-021-01880-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/20/2021] [Indexed: 05/03/2023]
Abstract
Biofloc technology is commonly applied in intensive tilapia (Oreochromis niloticus) culture to maintain water quality, supply the fish with extra protein, and improve fish growth. However, the effect of dietary supplementation of processed biofloc on the gut prokaryotic (bacteria and archaea) community composition of tilapia is not well understood. In this study one recirculating aquaculture system was used to test how biofloc, including in-situ biofloc, dietary supplementation of ex-situ live or dead biofloc, influence fish gut prokaryotic community composition and growth performance in comparison to a biofloc-free control treatment. A core gut prokaryotic community was identified among all treatments by analyzing the temporal variations in gut prokaryotes. In-situ produced biofloc significantly increased the prokaryotic diversity in the gut by reducing the relative abundance of dominant Cetobacterium and increasing the relative abundance of potentially beneficial bacteria. The in-situ biofloc delivered a unique prokaryotic community in fish gut, while dietary supplementation of tilapias with 5% and 10% processed biofloc (live or dead) only changed the relative abundance of minor prokaryotic taxa outside the gut core microbiota. The modulatory effect of in-situ biofloc on tilapia gut microbiota was associated with the distinct microbial community in the biofloc water and undisturbed biofloc. The growth-promoting effect on tilapia was only detected in the in-situ biofloc treatment, while dietary supplementation of processed biofloc had no effect on fish growth performance as compared to the control treatment.
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Affiliation(s)
- Yale Deng
- Aquaculture and Fisheries Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Klaudyna Borewicz
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
- Trouw Nutrition R&D, 3811 MH, Amersfoort, The Netherlands
| | - Joost van Loo
- Aquaculture and Fisheries Group, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Fotini Kokou
- Aquaculture and Fisheries Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Marc C J Verdegem
- Aquaculture and Fisheries Group, Wageningen University and Research, Wageningen, The Netherlands.
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14
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Prasad R, Patton MJ, Floyd JL, Fortmann S, DuPont M, Harbour A, Wright J, Lamendella R, Stevens BR, Oudit GY, Grant MB. Plasma Microbiome in COVID-19 Subjects: An Indicator of Gut Barrier Defects and Dysbiosis. Int J Mol Sci 2022; 23:9141. [PMID: 36012406 PMCID: PMC9409329 DOI: 10.3390/ijms23169141] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 12/16/2022] Open
Abstract
The gut is a well-established route of infection and target for viral damage by SARS-CoV-2. This is supported by the clinical observation that about half of COVID-19 patients exhibit gastrointestinal (GI) complications. We aimed to investigate whether the analysis of plasma could provide insight into gut barrier dysfunction in patients with COVID-19 infection. Plasma samples of COVID-19 patients (n = 146) and healthy individuals (n = 47) were collected during hospitalization and routine visits. Plasma microbiome was analyzed using 16S rRNA sequencing and gut permeability markers including fatty acid binding protein 2 (FABP2), peptidoglycan (PGN), and lipopolysaccharide (LPS) in both patient cohorts. Plasma samples of both cohorts contained predominately Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria. COVID-19 subjects exhibit significant dysbiosis (p = 0.001) of the plasma microbiome with increased abundance of Actinobacteria spp. (p = 0.0332), decreased abundance of Bacteroides spp. (p = 0.0003), and an increased Firmicutes:Bacteroidetes ratio (p = 0.0003) compared to healthy subjects. The concentration of the plasma gut permeability marker FABP2 (p = 0.0013) and the gut microbial antigens PGN (p < 0.0001) and LPS (p = 0.0049) were significantly elevated in COVID-19 patients compared to healthy subjects. These findings support the notion that the intestine may represent a source for bacteremia and contribute to worsening COVID-19 outcomes. Therapies targeting the gut and prevention of gut barrier defects may represent a strategy to improve outcomes in COVID-19 patients.
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Affiliation(s)
- Ram Prasad
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | - Michael John Patton
- Hugh Kaul Precision Medicine Institute, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jason Levi. Floyd
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | - Seth Fortmann
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | - Mariana DuPont
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | - Angela Harbour
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | | | | | - Bruce R. Stevens
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL 32611, USA
| | - Gavin Y. Oudit
- Division of Cardiology, Department of Medicine, University of Alberta, Mazankowski Alberta Heart Institute, Edmonton, AB T6G 2B7, Canada
| | - Maria B. Grant
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
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15
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Peanuts as a nighttime snack enrich butyrate-producing bacteria compared to an isocaloric lower-fat higher-carbohydrate snack in adults with elevated fasting glucose: A randomized crossover trial. Clin Nutr 2022; 41:2169-2177. [DOI: 10.1016/j.clnu.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/28/2022] [Accepted: 08/05/2022] [Indexed: 11/18/2022]
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16
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Ricci S, Pacífico C, Castillo-Lopez E, Rivera-Chacon R, Schwartz-Zimmermann HE, Reisinger N, Berthiller F, Zebeli Q, Petri RM. Progressive microbial adaptation of the bovine rumen and hindgut in response to a step-wise increase in dietary starch and the influence of phytogenic supplementation. Front Microbiol 2022; 13:920427. [PMID: 35935232 PMCID: PMC9354822 DOI: 10.3389/fmicb.2022.920427] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/27/2022] [Indexed: 01/08/2023] Open
Abstract
Microbial composition and activity in the gastrointestinal tract (GIT) of cattle has important implications for animal health and welfare, driving the focus of research toward ways to modify their function and abundance. However, our understanding of microbial adaption to nutritional changes remains limited. The aim of this study was to examine the progressive mechanisms of adaptation in the rumen and hindgut of cattle receiving increasing amounts of starch with or without dietary supplementation of a blended phytogenic feed additive (PFA; containing menthol, thymol and eugenol). We used 16S rRNA gene amplicon sequencing to assess the microbial composition and predicted metabolic pathways in ruminal solid and liquid digesta, and feces. Furthermore, we employed targeted liquid chromatography-mass spectrometry methods to evaluate rumen fluid metabolites. Results indicated a rapid microbial adaptation to diet change, starting on the second day of starch feeding for the particle associated rumen liquid (PARL) microbes. Solid rumen digesta- and feces-associated microbes started changing from the following day. The PARL niche was the most responsive to dietary changes, with the highest number of taxa and predicted pathways affected by the increase in starch intake, as well as by the phytogenic supplementation. Despite the differences in the microbial composition and metabolic potential of the different GIT niches, all showed similar changes toward carbohydrate metabolism. Metabolite measurement confirmed the high prevalence of glucose and volatile fatty acids (VFAs) in the rumen due to the increased substrate availability and metabolic activity of the microbiota. Families Prevotellaceae, Ruminococcaceae and Lachnospiraceae were found to be positively correlated with carbohydrate metabolism, with the latter two showing wide-ranging predicted metabolic capabilities. Phytogenic supplementation affected low abundant taxa and demonstrated the potential to prevent unwanted implications of feeding high-concentrate diet, such as reduction of microbial diversity. The inclusion of 50% concentrate in the diet caused a major shift in microbial composition and activity in the GIT of cattle. This study demonstrated the ability of microorganisms in various GIT niches to adjust differentially, yet rapidly, to changing dietary conditions, and revealed the potential beneficial effects of supplementation with a PFA during dietary adaptation.
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Affiliation(s)
- Sara Ricci
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Vienna, Austria
- *Correspondence: Sara Ricci
| | - Cátia Pacífico
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Vienna, Austria
| | - Ezequias Castillo-Lopez
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Vienna, Austria
| | - Raul Rivera-Chacon
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Vienna, Austria
| | - Heidi E. Schwartz-Zimmermann
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Franz Berthiller
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Qendrim Zebeli
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Vienna, Austria
| | - Renee M. Petri
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
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17
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Aalto NJ, Schweitzer HD, Krsmanovic S, Campbell K, Bernstein HC. Diversity and Selection of Surface Marine Microbiomes in the Atlantic-Influenced Arctic. Front Microbiol 2022; 13:892634. [PMID: 35910621 PMCID: PMC9329088 DOI: 10.3389/fmicb.2022.892634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
Arctic marine environments are experiencing rapid changes due to the polar amplification of global warming. These changes impact the habitat of the cold-adapted microbial communities, which underpin biogeochemical cycles and marine food webs. We comparatively investigated the differences in prokaryotic and microeukaryotic taxa between summer surface water microbiomes sampled along a latitudinal transect from the ice-free southern Barents Sea and into the sea-ice-covered Nansen Basin to disentangle the dominating community (ecological) selection processes driving phylogenetic diversity. The community structure and richness of each site-specific microbiome were assessed in relation to the physical and biogeochemical conditions of the environment. A strong homogeneous deterministic selection process was inferred across the entire sampling transect via a phylogenetic null modeling approach. The microbial species richness and diversity were not negatively influenced by northward decreasing temperature and salinity. The results also suggest that regional phytoplankton blooms are a major prevalent factor in governing the bacterial community structure. This study supports the consideration that strong homogeneous selection is imposed across these cold-water marine environments uniformly, regardless of geographic assignments within either the Nansen Basin or the Barents Sea.
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Affiliation(s)
- Nerea J. Aalto
- Faculty of Biosciences, Fisheries, and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
- The Arctic Centre for Sustainable Energy, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Hannah D. Schweitzer
- Faculty of Biosciences, Fisheries, and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
- The Arctic Centre for Sustainable Energy, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Stina Krsmanovic
- Faculty of Biosciences, Fisheries, and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Karley Campbell
- Faculty of Biosciences, Fisheries, and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Hans C. Bernstein
- Faculty of Biosciences, Fisheries, and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
- The Arctic Centre for Sustainable Energy, UiT—The Arctic University of Norway, Tromsø, Norway
- *Correspondence: Hans C. Bernstein
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18
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Gold MS, Quinn PJ, Campbell DE, Peake J, Smart J, Robinson M, O’Sullivan M, Vogt JK, Pedersen HK, Liu X, Pazirandeh-Micol E, Heine RG. Effects of an Amino Acid-Based Formula Supplemented with Two Human Milk Oligosaccharides on Growth, Tolerability, Safety, and Gut Microbiome in Infants with Cow's Milk Protein Allergy. Nutrients 2022; 14:nu14112297. [PMID: 35684099 PMCID: PMC9182596 DOI: 10.3390/nu14112297] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 12/04/2022] Open
Abstract
This open-label, non-randomized, multicenter trial (Registration: NCT03661736) aimed to assess if an amino acid-based formula (AAF) supplemented with two human milk oligosaccharides (HMO) supports normal growth and is well tolerated in infants with a cow's milk protein allergy (CMPA). Term infants aged 1-8 months with moderate-to-severe CMPA were enrolled. The study formula was an AAF supplemented with 2'-fucosyllactose (2'-FL) and lacto-N-neotetraose (LNnT). Infants were fed the study formula for 4 months and were offered to remain on the formula until 12 months of age. Tolerance and safety were assessed throughout the trial. Out of 32 infants (mean age 18.6 weeks; 20 (62.5%) male), 29 completed the trial. During the 4-month principal study period, the mean weight-for-age Z score (WAZ) increased from -0.31 at the baseline to +0.28 at the 4-months' follow-up. Linear and head growth also progressed along the WHO child growth reference, with a similar small upward trend. The formula was well tolerated and had an excellent safety profile. When comparing the microbiome at the baseline to the subsequent visits, there was a significant on-treatment enrichment in HMO-utilizing bifidobacteria, which was associated with a significant increase in fecal short-chain fatty acids. In addition, we observed a significant reduction in the abundance of fecal Proteobacteria, suggesting that the HMO-supplemented study formula partially corrected the gut microbial dysbiosis in infants with CMPA.
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Affiliation(s)
- Michael S. Gold
- Department of Allergy & Immunology, Women’s and Children’s Hospital, University of Adelaide, Adelaide, SA 5006, Australia;
- Correspondence:
| | - Patrick J. Quinn
- Department of Allergy & Immunology, Women’s and Children’s Hospital, University of Adelaide, Adelaide, SA 5006, Australia;
| | - Dianne E. Campbell
- Department of Allergy & Clinical Immunology, Children’s Hospital at Westmead, University of Sydney, Sydney, NSW 2145, Australia;
| | - Jane Peake
- Queensland Paediatric Immunology and Allergy Service, Queensland Children’s Hospital, University of Queensland, South Brisbane, QLD 4101, Australia;
| | - Joanne Smart
- Paediatric Allergy Services, Epworth Hospital, Richmond, VIC 3121, Australia;
| | - Marnie Robinson
- Melbourne Allergy Centre & Children’s Specialists Medical Group, Parkville, VIC 3152, Australia;
| | - Michael O’Sullivan
- Department of Immunology, Perth Children’s Hospital, Nedlands, WA 6009, Australia
| | | | | | - Xiaoqiu Liu
- Biostatistics and Data Science Division, The George Institute for Global Health, University of New South Wales, Sydney, NSW 2042, Australia;
| | | | - Ralf G. Heine
- Nestlé Health Science, CH-1800 Vevey, Switzerland; (E.P.-M.); (R.G.H.)
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19
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Dissanayake DSB, Holleley CE, Sumner J, Melville J, Georges A. Lineage diversity within a widespread endemic Australian skink to better inform conservation in response to regional-scale disturbance. Ecol Evol 2022; 12:e8627. [PMID: 35342559 PMCID: PMC8928872 DOI: 10.1002/ece3.8627] [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: 09/22/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 11/07/2022] Open
Abstract
Much attention is paid in conservation planning to the concept of a species, to ensure comparability across studies and regions when classifying taxa against criteria of endangerment and setting priorities for action. However, various jurisdictions now allow taxonomic ranks below the level of species and nontaxonomic intraspecific divisions to be factored into conservation planning—subspecies, key populations, evolutionarily significant units, or designatable units. Understanding patterns of genetic diversity and its distribution across the landscape is a key component in the identification of species boundaries and determination of substantial geographic structure within species. A total of 12,532 reliable polymorphic SNP loci were generated from 63 populations (286 individuals) covering the distribution of the Australian eastern three‐lined skink, Bassiana duperreyi, to assess genetic population structure in the form of diagnosable lineages and their distribution across the landscape, with particular reference to the recent catastrophic bushfires of eastern Australia. Five well‐supported diagnosable operational taxonomic units (OTUs) existed within B. duperreyi. Low levels of divergence of B. duperreyi between mainland Australia and Tasmania (no fixed allelic differences) support the notion of episodic exchange of alleles across Bass Strait (ca 60 m, 25 Kya) during periods of low sea level during the Upper Pleistocene rather than the much longer period of isolation (1.7 My) indicated by earlier studies using mitochondrial sequence variation. Our study provides foundational work for the detailed taxonomic re‐evaluation of this species complex and the need for biodiversity assessment to include an examination of cryptic species and/or cryptic diversity below the level of species. Such information on lineage diversity within species and its distribution in the context of disturbance at a regional scale can be factored into conservation planning regardless of whether a decision is made to formally diagnose new species taxonomically and nomenclaturally.
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Affiliation(s)
- Duminda S B Dissanayake
- Institute for Applied Ecology University of Canberra Canberra Australian Capital Territory Australia.,Australian National Wildlife Collection CSIRO Canberra Australian Capital Territory Australia
| | - Clare E Holleley
- Institute for Applied Ecology University of Canberra Canberra Australian Capital Territory Australia.,Australian National Wildlife Collection CSIRO Canberra Australian Capital Territory Australia
| | - Joanna Sumner
- Department of Sciences Museums Victoria Carlton Gardens Victoria Australia
| | - Jane Melville
- Department of Sciences Museums Victoria Carlton Gardens Victoria Australia
| | - Arthur Georges
- Institute for Applied Ecology University of Canberra Canberra Australian Capital Territory Australia
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20
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Dietary Intake Mediates Ethnic Differences in Gut Microbial Composition. Nutrients 2022; 14:nu14030660. [PMID: 35277019 PMCID: PMC8840192 DOI: 10.3390/nu14030660] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 11/16/2022] Open
Abstract
Background: The human gut microbiome (GM) has been observed to vary by race/ethnicity. Objective: Assess whether racial/ethnic GM variation is mediated by differences in diet. Design: Stool samples collected from 2013 to 2016 from 5267 healthy Multiethnic Cohort participants (age 59−98) were analyzed using 16S rRNA gene sequencing to estimate the relative abundance of 152 bacterial genera. For 63 prevalent genera (>50% in each ethnic group), we analyzed the mediation of GM differences among African Americans, Japanese Americans, Latinos, Native Hawaiians, and Whites by overall diet quality (Healthy Eating Index score (HEI-2015)) and intake amounts of 14 component foods/nutrients assessed from 2003 to 2008. For each significant mediation (p < 1.3 × 10−5), we determined the percent of the total ethnicity effect on genus abundance mediated by the dietary factor. Results: Ethnic differences in the abundance of 12 genera were significantly mediated by one or more of eight dietary factors, most frequently by overall diet quality and intakes of vegetables and red meat. Lower vegetable intake mediated differences in Lachnospira (36% in African Americans, 39% in Latinos) and Ruminococcus-1 (−35% in African Americans, −43% in Latinos) compared to Native Hawaiians who consumed the highest amount. Higher red meat intake mediated differences in Lachnospira (−41%) and Ruminococcus-1 (36%) in Native Hawaiians over African Americans, who consumed the least. Dairy and alcohol intakes appeared to mediate and counterbalance the difference in Bifidobacterium between Whites and Japanese Americans. Conclusions: Overall diet quality and component food intakes may contribute to ethnic differences in GM composition and to GM-related racial/ethnic health disparities.
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21
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Bhatti UA, Yu Z, Hasnain A, Nawaz SA, Yuan L, Wen L, Bhatti MA. Evaluating the impact of roads on the diversity pattern and density of trees to improve the conservation of species. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:14780-14790. [PMID: 34622403 DOI: 10.1007/s11356-021-16627-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Roadside trees alter biotic and abiotic factors of plants diversity in an ecosystem. Rows of plants grow along the roadside due to the interplay between the arrival of propagule and seedling establishment, which depends on the road's specifications, land pattern, and road administration and protection practices. A field study was conducted to measure the roadside tree diversity in the city of Karachi (Pakistan). A total of 180 plots, divided into three primary road groups, were surveyed. The highest quantity of tree biomass per unit area was found on wide roads, followed by medium roads. On narrow roads, the least biomass was detected. A single species or a limited number of species dominated the tree community. Conocarpus erectus was the most dominant non-native species on all types of sidewalks or roadsides, followed by Guaiacum officinale. A total of 76 species (32 non-natives and 44 natives) that were selectively spread along the roadsides of the city were studied. There was a significant difference in phylogenetic diversity (PD), phylogenetic mean pairwise distance (MPD), and phylogenetic mean nearest taxon distance (MNTD) among wide, medium, and narrow roads. Management practices have a significant positive correlation with diversity indices. Our study identified patterns of diversity in roadside trees in Karachi. It provides the basis for future planning for plant protection, such as the protection of plant species, the maintenance of plant habitats, and the coordination of plant management in Karachi.
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Affiliation(s)
- Uzair Aslam Bhatti
- School of Geography, Nanjing Normal University, Nanjing, 210014, People's Republic of China.
| | - Zhaoyuan Yu
- School of Geography, Nanjing Normal University, Nanjing, 210014, People's Republic of China
- Key Laboratory of Virtual Geographic Environment, Ministry of Education, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing, People's Republic of China
| | - Ahmad Hasnain
- School of Geography, Nanjing Normal University, Nanjing, 210014, People's Republic of China
| | | | - Linwang Yuan
- School of Geography, Nanjing Normal University, Nanjing, 210014, People's Republic of China
- Key Laboratory of Virtual Geographic Environment, Ministry of Education, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing, People's Republic of China
| | - Luo Wen
- School of Geography, Nanjing Normal University, Nanjing, 210014, People's Republic of China
- Key Laboratory of Virtual Geographic Environment, Ministry of Education, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing, People's Republic of China
| | - Mughair Aslam Bhatti
- School of Geography, Nanjing Normal University, Nanjing, 210014, People's Republic of China
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22
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Luo G, Jin T, Zhang H, Peng J, Zuo N, Huang Y, Han Y, Tian C, Yang Y, Peng K, Fei J. Deciphering the diversity and functions of plastisphere bacterial communities in plastic-mulching croplands of subtropical China. JOURNAL OF HAZARDOUS MATERIALS 2022; 422:126865. [PMID: 34449345 DOI: 10.1016/j.jhazmat.2021.126865] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/22/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
Considering the inhomogeneity of plastisphere and surrounding soil, it is plausible that the microbial community colonizing it also varies, affecting soil services and sustainability. Herein, we analyzed the soil and film residue from fifty-five plastic-mulching croplands in the subtropical areas of China. Based on the outcomes of this analysis, we explored the diversity and functions of the associated bacterial communities. Alpha-diversity and phylogenetic diversity of the plastisphere bacterial community was significantly lower than the surrounding soil. The average net relatedness and net nearest taxa indices of samples were less than zero. Four phyla and twenty genera were enriched in the plastisphere compared to the surrounding soil. Ecological networks of the plastisphere community showed multiple nodes, but fewer interactions, and the members of Bradyrhizobium, Rhodospirillaceae, and Bacillus were indicated as the hub species. Predicted pathways related to human disease, as well as the metabolisms of cofactors, vitamins, amino acids, and xenobiotic biodegradation, were reinforced in the plastisphere, and meanwhile, accompanied by an increase in abundance of genes related to carbon, nitrogen, and phosphorus cycles. These results demonstrated the diversity and functions of the plastisphere microbiome and highlighted the necessity for exploring the ecological and health risks of plastic residue in croplands.
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Affiliation(s)
- Gongwen Luo
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China; Key laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Tuo Jin
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China; Rural Energy and Environment Agency, Ministry of Agriculture and Rural affairs, Beijing 100125, China
| | - Huiru Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China
| | - Jianwei Peng
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China.
| | - Ning Zuo
- Resource Protection and Utilization Station, Hunan Agriculture and Rural Affairs Department, Changsha 410005, China
| | - Ying Huang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China
| | - Yongliang Han
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China
| | - Chang Tian
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China
| | - Yong Yang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China
| | - Kewei Peng
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China
| | - Jiangchi Fei
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China.
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23
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Gut Microbiota Composition across Normal Range Prostate-Specific Antigen Levels. J Pers Med 2021; 11:jpm11121381. [PMID: 34945854 PMCID: PMC8703440 DOI: 10.3390/jpm11121381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/13/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022] Open
Abstract
Animal studies have shown the interaction between androgens and the gut microbiome directly and indirectly; however, limited evidence from human studies is available. To evaluate the association between prostate-specific antigen (PSA) levels within the normal range, reflective of androgen receptor activity, and the gut microbiota composition, a cross-sectional analysis was performed in 759 Korean men aged between 25 and 78 years with normal PSA levels of ≤4.0 ng/mL. We evaluated the biodiversity of gut microbiota as well as the taxonomic and functional signatures associated with PSA levels using 16S rRNA gene sequencing data. PSA levels within the normal range were categorized into three groups: lowest quartile (G1), interquartile range (G2, reference), and highest quartile (G3). The G3 group had higher microbial richness than the G2 group, although it was dominated by a few bacteria. An increase in Escherichia/Shigella abundance and a reduction in Megamonas abundance in the G3 group were also detected. A U-shaped relationship was observed between the three groups across most analyses, including biodiversity, taxonomic composition, and inferred pathways in the gut microbiota. This study showed different microbiota patterns across PSA levels within the normal range. Further studies are required to elucidate the role of microbiota in regulating PSA levels.
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24
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Park E, Yun KE, Kim MH, Kim J, Chang Y, Ryu S, Kim HL, Kim HN, Jung SC. Correlation between Gut Microbiota and Six Facets of Neuroticism in Korean Adults. J Pers Med 2021; 11:1246. [PMID: 34945718 PMCID: PMC8704006 DOI: 10.3390/jpm11121246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022] Open
Abstract
A person high in neuroticism is more likely to experience anxiety, stress, worry, fear, anger, and depression. Previous studies have shown that the gut microbiota can influence personality and mental disorders, including stress, anxiety, and depression, through the gut-brain axis. Here, we investigated the correlations between the sub-facet of neuroticism and gut microbiota using the Revised NEO Personality Inventory and the 16S rRNA gene sequencing data 784 adults. We found that the high anxiety and vulnerability group showed significantly lower richness in microbial diversity than a group with low anxiety and vulnerability. In beta diversity, there was a significant difference between the low and high groups of anxiety, self-consciousness, impulsiveness, and vulnerability. In taxonomic compositions, Haemophilus belonging to Gammaproteobacteria was correlated with the Neuroticism domain as well as N1 anxiety and N6 vulnerability facets. The high N1 anxiety and N6 vulnerability group was correlated with a low abundance of Christensenellaceae belonging to Firmicutes Clostridia. High N4 self-consciousness was correlated with a low abundance of Alistipes and Sudoligranulum. N5 impulsiveness was correlated with a low abundance of Oscillospirales. Our findings will contribute to uncovering the potential link between the gut microbiota and neuroticism, and the elucidation of the correlations of the microbiome-gut-brain axis with behavioral changes and psychiatric cases in the general population.
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Affiliation(s)
- Eunkyo Park
- Department of Biochemistry, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.P.); (H.-L.K.)
| | - Kyung Eun Yun
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 04514, Korea; (K.E.Y.); (M.-H.K.); (J.K.); (Y.C.); (S.R.)
| | - Mi-Hyun Kim
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 04514, Korea; (K.E.Y.); (M.-H.K.); (J.K.); (Y.C.); (S.R.)
| | - Jimin Kim
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 04514, Korea; (K.E.Y.); (M.-H.K.); (J.K.); (Y.C.); (S.R.)
| | - Yoosoo Chang
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 04514, Korea; (K.E.Y.); (M.-H.K.); (J.K.); (Y.C.); (S.R.)
- Department of Occupational and Environmental Medicine, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 03181, Korea
- Department of Clinical Research Design and Evaluation, SAIHST, Sungkyunkwan University, Seoul 06355, Korea
| | - Seungho Ryu
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 04514, Korea; (K.E.Y.); (M.-H.K.); (J.K.); (Y.C.); (S.R.)
- Department of Occupational and Environmental Medicine, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 03181, Korea
- Department of Clinical Research Design and Evaluation, SAIHST, Sungkyunkwan University, Seoul 06355, Korea
| | - Hyung-Lae Kim
- Department of Biochemistry, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.P.); (H.-L.K.)
| | - Han-Na Kim
- Department of Clinical Research Design and Evaluation, SAIHST, Sungkyunkwan University, Seoul 06355, Korea
- Medical Research Institute, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 03181, Korea
| | - Sung-Chul Jung
- Department of Biochemistry, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.P.); (H.-L.K.)
- Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 07804, Korea
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25
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Assessing spatial patterns of phylogenetic diversity of Mexican mammals for biodiversity conservation. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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26
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Ali Z, Shahzadi I, Majeed A, Malik HMT, Waseem S, Ahmed I, Anis RA, Saeed S, Anees M. Comparative analysis of the serum microbiome of HIV infected individuals. Genomics 2021; 113:4015-4021. [PMID: 34637930 DOI: 10.1016/j.ygeno.2021.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/02/2021] [Accepted: 10/07/2021] [Indexed: 11/15/2022]
Abstract
HIV infects the CD4 cells which marks the suppression of our immune system. DNA from serum of healthy, treated and untreated HIV infected individuals was extracted. The DNA was subjected to 16S metagenomic sequencing and analyzed using QIIME2 pipeline. 16S sequencing analysis showed serum microbiome was dominated by Firmicutes, Proteobacteria, Bacteroidota and Actinobacteria. Treated HIV infection showed highest abundance of Firmicutes (66.40%) significantly higher than untreated HIV infection (35.88%) and control (41.89%). Bacilli was most abundant class in treated (63.59%) and second most abundant in untreated (34.53%) while control group showed highest abundance of class Gamma-proteobacteria (45.86%). Untreated HIV infection group showed Enterococcus (10.72%) and Streptococcus (6.599%) as the most abundant species. Untreated HIV infection showed significantly higher (p = 0.0039) species richness than treated and control groups. An altered serum microbiome of treated HIV infection and higher microbial abundance in serum of untreated HIV infection was observed.
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Affiliation(s)
- Zain Ali
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Iram Shahzadi
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Aqsa Majeed
- Alpha Genomics (Pvt) Ltd., Islamabad, Pakistan
| | | | | | - Ibrar Ahmed
- Alpha Genomics (Pvt) Ltd., Islamabad, Pakistan
| | - Riffat Aysha Anis
- Institute of Diet and Nutritional Sciences, University of Lahore, Islamabad Campus, Pakistan
| | - Sadia Saeed
- Institute of Biochemistry and Biotechnology, University of Arid Agriculture, Rawalpindi, Pakistan
| | - Mariam Anees
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan.
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27
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Coons AK, Busch K, Lenz M, Hentschel U, Borchert E. Biogeography rather than substrate type determines bacterial colonization dynamics of marine plastics. PeerJ 2021; 9:e12135. [PMID: 34603853 PMCID: PMC8445087 DOI: 10.7717/peerj.12135] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/18/2021] [Indexed: 01/04/2023] Open
Abstract
Since the middle of the 20th century, plastics have been incorporated into our everyday lives at an exponential rate. In recent years, the negative impacts of plastics, especially as environmental pollutants, have become evident. Marine plastic debris represents a relatively new and increasingly abundant substrate for colonization by microbial organisms, although the full functional potential of these organisms is yet to be uncovered. In the present study, we investigated plastic type and incubation location as drivers of marine bacterial community structure development on plastics, i.e., the Plastisphere, via 16S rRNA amplicon analysis. Four distinct plastic types: high-density polyethylene (HDPE), linear low-density polyethylene (LDPE), polyamide (PA), polymethyl methacrylate (PMMA), and glass-slide controls were incubated for five weeks in the coastal waters of four different biogeographic locations (Cape Verde, Chile, Japan, South Africa) during July and August of 2019. The primary driver of the coastal Plastisphere composition was identified as incubation location, i.e., biogeography, while substrate type did not have a significant effect on bacterial community composition. The bacterial communities were consistently dominated by the classes Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia, irrespective of sampling location or substrate type, however a core bacterial Plastisphere community was not observable at lower taxonomic levels. Overall, this study sheds light on the question of whether bacterial communities on plastic debris are shaped by the physicochemical properties of the substrate they grow on or by the marine environment in which the plastics are immersed. This study enhances the current understanding of biogeographic variability in the Plastisphere by including biofilms from plastics incubated in the previously uncharted Southern Hemisphere.
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Affiliation(s)
- Ashley K Coons
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Schleswig-Holstein, Germany
| | - Kathrin Busch
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Schleswig-Holstein, Germany
| | - Mark Lenz
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Schleswig-Holstein, Germany
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Schleswig-Holstein, Germany.,Christian-Albrechts-University Kiel, Kiel, Schleswig-Holstein, Germany
| | - Erik Borchert
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Schleswig-Holstein, Germany
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28
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Ge Y, Meng X, Heino J, García‐Girón J, Liu Y, Li Z, Xie Z. Stochasticity overrides deterministic processes in structuring macroinvertebrate communities in a plateau aquatic system. Ecosphere 2021. [DOI: 10.1002/ecs2.3675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Yihao Ge
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
- University of Chinese Academy of Sciences Beijing China
| | - Xingliang Meng
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Jani Heino
- Freshwater Centre Finnish Environment Institute Paavo Havaksen Tie 3P.O. Box 413 Oulu FI‐90014 Finland
| | - Jorge García‐Girón
- Group for Limnology and Environmental Biotechnology Area of Ecology Universidad de León Campus de Vegazana León Spain
| | - Yang Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
- University of Chinese Academy of Sciences Beijing China
| | - Zhengfei Li
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Zhicai Xie
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
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29
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Xie G, Kong X, Kang J, Su N, Luo G, Fei J. Community-level dormancy potential regulates bacterial beta-diversity succession during the co-composting of manure and crop residues. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 772:145506. [PMID: 33571759 DOI: 10.1016/j.scitotenv.2021.145506] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/17/2021] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
This study aimed to disclose the bacterial diversity succession during the co-composting of manure and crop residues and to provide new insight into the role of community-level dormancy potential in diversity succession. Illumina sequencing and PICRUSt-estimated metagenomes were used for this purpose. The bacterial richness and phylogenetic diversity decreased in the early and middle stages of composting and were maintained to a stable status in the late stage. Both composting phases and raw materials impacted the aforementioned alpha diversity significantly, while the composting phases had a greater (80%-94%) impact than the raw materials (1%-18%). Bacterial beta-diversity succession exhibited selectivity as the composting proceeded, and the dominant taxa changed into salt- and heat-resistant genera such as Bacillus, Glycomyces, and Halocella. Meanwhile, Georgenia, Actinomadura, and Ruminofilibacter were identified as the dominant predictor taxa of bacterial community succession in composting. Roughly, the abundance of genes underlying dormancy strategies, including sporulation factors (spo0A gene), toxin-antitoxin systems (dinJ/yafP, mazF/E, hipA/O, and relA/E genes), and resuscitation-promoting factors (rpfC gene), increased as composting proceeded and reached the highest in the thermophilic or maturation phases. Co-occurring relationships between bacterial communities and genes underlying dormancy strategies in different composting phases comprised multiple associations dominated by positive edges (50%-97%). The stability in genes underlying dormancy strategies and aggregate dormancy potential had a positive linear correlation with that in bacterial beta diversity (R2 = 0.26-0.42; P < 0.05), but not related significantly to that in richness and phylogenetic diversity. This study highlighted the importance of understanding how community-level dormancy strategies mediated microbial succession in composting to better predict compost maturity and product quality.
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Affiliation(s)
- Guixian Xie
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China
| | - Xiaoliang Kong
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China
| | - Jialu Kang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China
| | - Ning Su
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China
| | - Gongwen Luo
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China.
| | - Jiangchi Fei
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha 410128, China
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30
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Casaro MB, Thomas AM, Mendes E, Fukumori C, Ribeiro WR, Oliveira FA, Crisma AR, Murata GM, Bizzarro B, Sá-Nunes A, Setubal JC, Mayer MPA, Martins FS, Vieira AT, Antiorio ATFB, Tavares-de-Lima W, Camara NOS, Curi R, Dias-Neto E, Ferreira CM. A probiotic has differential effects on allergic airway inflammation in A/J and C57BL/6 mice and is correlated with the gut microbiome. MICROBIOME 2021; 9:134. [PMID: 34112246 PMCID: PMC8194189 DOI: 10.1186/s40168-021-01081-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
The phenotypes of allergic airway diseases are influenced by the interplay between host genetics and the gut microbiota, which may be modulated by probiotics. We investigated the probiotic effects on allergic inflammation in A/J and C57BL/6 mice. C57BL/6 mice had increased gut microbiota diversity compared to A/J mice at baseline. Acetate producer probiotics differentially modulated and altered the genus abundance of specific bacteria, such as Akkermansia and Allistipes, in mouse strains. We induced airway inflammation followed by probiotic treatment and found that only A/J mice exhibited decreased inflammation, and the beneficial effects of probiotics in A/J mice were partially due to acetate production. To understand the relevance of microbial composition colonization in the development of allergic diseases, we implanted female C57BL/6 mice with A/J embryos to naturally modulate the microbial composition of A/J mice, which increased gut microbiota diversity and reduced eosinophilic inflammation in A/J. These data demonstrate the central importance of microbiota to allergic phenotype severity. Video Abstract.
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Affiliation(s)
- Mateus B Casaro
- Department of Pharmaceutics Sciences, Institute of Environmental, Chemistry and Pharmaceutical Sciences, Universidade Federal de São Paulo, R. São Nicolau, 210, Diadema, SP, 09913-03, Brazil
| | - Andrew M Thomas
- Department CIBIO, University of Trento, Trento, Italy
- Medical Genomics Laboratory, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil
- Department of Biochemistry, Institute of Chemistry, Universidade de São Paulo, São Paulo, Brazil
| | - Eduardo Mendes
- Department of Pharmaceutics Sciences, Institute of Environmental, Chemistry and Pharmaceutical Sciences, Universidade Federal de São Paulo, R. São Nicolau, 210, Diadema, SP, 09913-03, Brazil
| | - Claudio Fukumori
- Department of Pharmaceutics Sciences, Institute of Environmental, Chemistry and Pharmaceutical Sciences, Universidade Federal de São Paulo, R. São Nicolau, 210, Diadema, SP, 09913-03, Brazil
| | - Willian R Ribeiro
- Department of Pharmaceutics Sciences, Institute of Environmental, Chemistry and Pharmaceutical Sciences, Universidade Federal de São Paulo, R. São Nicolau, 210, Diadema, SP, 09913-03, Brazil
| | - Fernando A Oliveira
- Center for Mathematics, Computing and Cognition (CMCC), Federal University of ABC - UFABC, São Bernardo do Campo, SP, Brazil
| | - Amanda R Crisma
- Department of Clinical Analyses, Universidade Federal do Paraná, Curitiba, Brazil
| | - Gilson M Murata
- Department of Medical Clinic, Faculty of Medicine, University of São Paulo, São Paulo, 01246-903, Brazil
| | - Bruna Bizzarro
- Department of Immunology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Anderson Sá-Nunes
- Department of Immunology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Joao C Setubal
- Department of Biochemistry, Institute of Chemistry, Universidade de São Paulo, São Paulo, Brazil
| | - Marcia P A Mayer
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Flaviano S Martins
- Department of Microbiology, Institute of Biological Sciences, Federal Universidade de Minas Gerais, Belo Horizonte, Brazil
| | - Angélica T Vieira
- Department of Biochemistry and Immunology, Biological Science Institute, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Ana T F B Antiorio
- Department of Pathology, School of Veterinary Medicine and Animal Science, Universidade de São Paulo, São Paulo, Brazil
| | - Wothan Tavares-de-Lima
- Department of Pharmacology, Institute of Biomedical Sciences I, Universidade de São Paulo, São Paulo, Brazil
| | - Niels O S Camara
- Department of Immunology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Rui Curi
- Interdisciplinary Post-Graduate Program in Health Sciences, Cruzeiro do Sul University, São Paulo, Brazil
| | - Emmanuel Dias-Neto
- Medical Genomics Laboratory, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil
- Laboratory of Neurosciences (LIM-27), Institute of Psychiatry, Medical School, Universidade de São Paulo, São Paulo, Brazil
| | - Caroline M Ferreira
- Department of Pharmaceutics Sciences, Institute of Environmental, Chemistry and Pharmaceutical Sciences, Universidade Federal de São Paulo, R. São Nicolau, 210, Diadema, SP, 09913-03, Brazil.
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31
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Therdtatha P, Song Y, Tanaka M, Mariyatun M, Almunifah M, Manurung NEP, Indriarsih S, Lu Y, Nagata K, Fukami K, Ikeda T, Lee YK, Rahayu ES, Nakayama J. Gut Microbiome of Indonesian Adults Associated with Obesity and Type 2 Diabetes: A Cross-Sectional Study in an Asian City, Yogyakarta. Microorganisms 2021; 9:897. [PMID: 33922321 PMCID: PMC8147061 DOI: 10.3390/microorganisms9050897] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/15/2021] [Accepted: 04/20/2021] [Indexed: 02/07/2023] Open
Abstract
Indonesia is a developing country facing the national problem of the growing obesity and diabetes in its population due to recent drastic dietary and lifestyle changes. To understand the link between the gut microbiome, diet, and health of Indonesian people, fecal microbiomes and metabolomes of 75 Indonesian adults in Yogyakarta City, including obese people (n = 21), type 2 diabetes (T2D) patients (n = 25), and the controls (n = 29) were characterized together with their dietary and medical records. Variations of microbiomes showed a triangular distribution in the principal component analysis, driven by three dominant bacterial genera, namely Bacteroides, Prevotella, and Romboutsia. The Romboutsia-driven microbiome, characterized by low bacterial diversity and high primary bile acids, was associated with fat-driven obesity. The Bacteroides-driven microbiome, which counteracted Prevotella but was associated with Ruminococcaceae concomitantly increased with high-carbohydrate diets, showed positive correlation with T2D indices but negative correlation with body mass index. Notably, Bacteroides fragilis was increased in T2D patients with a decrease in fecal conjugated bile acids, particularly tauroursodeoxycholic acid (TUDCA), a farnesoid X receptor (FXR) antagonist with anti-diabetic activity, while these features disappeared in patients administered metformin. These results indicate that the gut microbiome status of Indonesian adults is differently associated with obesity and T2D under their varied dietary habits.
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Affiliation(s)
- Phatthanaphong Therdtatha
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; (P.T.); (Y.S.); (M.T.)
| | - Yayi Song
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; (P.T.); (Y.S.); (M.T.)
| | - Masaru Tanaka
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; (P.T.); (Y.S.); (M.T.)
| | - Mariyatun Mariyatun
- Faculty of Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (M.M.); (M.A.); (N.E.P.M.); (S.I.); (E.S.R.)
| | - Maisaroh Almunifah
- Faculty of Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (M.M.); (M.A.); (N.E.P.M.); (S.I.); (E.S.R.)
| | - Nancy Eka Putri Manurung
- Faculty of Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (M.M.); (M.A.); (N.E.P.M.); (S.I.); (E.S.R.)
| | - Siska Indriarsih
- Faculty of Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (M.M.); (M.A.); (N.E.P.M.); (S.I.); (E.S.R.)
| | - Yi Lu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (Y.L.); (K.N.)
| | - Koji Nagata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (Y.L.); (K.N.)
| | - Katsuya Fukami
- Material Management Center of Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan;
| | - Tetsuo Ikeda
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan;
- Endoscopy and Endoscopic Surgery, Fukuoka Dental College, 2-15-1 Tamura, Sawara-ku, Fukuoka 814-0193, Japan
| | - Yuan-Kun Lee
- Department of Microbiology and Immunology, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore;
| | - Endang Sutriswati Rahayu
- Faculty of Agricultural Technology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (M.M.); (M.A.); (N.E.P.M.); (S.I.); (E.S.R.)
| | - Jiro Nakayama
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; (P.T.); (Y.S.); (M.T.)
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Möhrle K, Reyes-Aldana HE, Kollmann J, Teixeira LH. Suppression of an Invasive Native Plant Species by Designed Grassland Communities. PLANTS 2021; 10:plants10040775. [PMID: 33920882 PMCID: PMC8071313 DOI: 10.3390/plants10040775] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 11/27/2022]
Abstract
Grassland biodiversity is declining due to climatic change, land-use intensification, and establishment of invasive plant species. Excluding or suppressing invasive species is a challenge for grassland management. An example is Jacobaea aquatica, an invasive native plant in wet grasslands of Central Europe, that is causing problems to farmers by being poisonous, overabundant, and fast spreading. This study aimed at testing designed grassland communities in a greenhouse experiment, to determine key drivers of initial J. aquatica suppression, thus dismissing the use of pesticides. We used two base communities (mesic and wet grasslands) with three plant traits (plant height, leaf area, seed mass), that were constrained and diversified based on the invader traits. Native biomass, community-weighted mean trait values, and phylogenetic diversity (PD) were used as explanatory variables to understand variation in invasive biomass. The diversified traits leaf area and seed mass, PD, and native biomass significantly affected the invader. High native biomass permanently suppressed the invader, while functional traits needed time to develop effects; PD effects were significant at the beginning of the experiment but disappeared over time. Due to complexity and temporal effects, community weighted mean traits proved to be moderately successful for increasing invasion resistance of designed grassland communities.
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Affiliation(s)
- Kathrin Möhrle
- Restoration Ecology, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; (J.K.); (L.H.T.)
- Bavarian State Research Centre for Agriculture, Institute for Crop Science and Plant Breeding, 85354 Freising, Germany
- Correspondence:
| | - Hugo E. Reyes-Aldana
- Department of River Ecology, Helmholtz Center for Environmental Research—UFZ, 39114 Magdeburg, Germany;
| | - Johannes Kollmann
- Restoration Ecology, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; (J.K.); (L.H.T.)
- Norwegian Institute of Bioeconomy Research, P.O. Box 115, 1431 Ås, Norway
| | - Leonardo H. Teixeira
- Restoration Ecology, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; (J.K.); (L.H.T.)
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Prasad R, Patton MJ, Floyd JL, Vieira CP, Fortmann S, DuPont M, Harbour A, Jeremy CS, Wright J, Lamendella R, Stevens BR, Grant MB. Plasma microbiome in COVID-19 subjects: an indicator of gut barrier defects and dysbiosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33851159 DOI: 10.1101/2021.04.06.438634] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The gut is a well-established route of infection and target for viral damage by SARS-CoV-2. This is supported by the clinical observation that about half of COVID-19 patients exhibit gastrointestinal ( GI ) symptoms. We asked whether the analysis of plasma could provide insight into gut barrier dysfunction in patients with COVID-19 infection. Plasma samples of COVID-19 patients (n=30) and healthy control (n=16) were collected during hospitalization. Plasma microbiome was analyzed using 16S rRNA sequencing, metatranscriptomic analysis, and gut permeability markers including FABP-2, PGN and LPS in both patient cohorts. Almost 65% (9 out 14) COVID-19 patients showed abnormal presence of gut microbes in their bloodstream. Plasma samples contained predominately Proteobacteria, Firmicutes, and Actinobacteria . The abundance of gram-negative bacteria ( Acinetobacter, Nitrospirillum, Cupriavidus, Pseudomonas, Aquabacterium, Burkholderia, Caballeronia, Parabhurkholderia, Bravibacterium, and Sphingomonas ) was higher than the gram-positive bacteria ( Staphylococcus and Lactobacillus ) in COVID-19 subjects. The levels of plasma gut permeability markers FABP2 (1282±199.6 vs 838.1±91.33; p=0.0757), PGN (34.64±3.178 vs 17.53±2.12; p<0.0001), and LPS (405.5±48.37 vs 249.6±17.06; p=0.0049) were higher in COVID-19 patients compared to healthy subjects. These findings support that the intestine may represent a source for bacteremia and may contribute to worsening COVID-19 outcomes. Therapies targeting the gut and prevention of gut barrier defects may represent a strategy to improve outcomes in COVID-19 patients.
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Handsley-Davis M, Skelly E, Johnson NW, Kapellas K, Lalloo R, Kroon J, Weyrich LS. Biocultural Drivers of Salivary Microbiota in Australian Aboriginal and Torres Strait Islander Children. FRONTIERS IN ORAL HEALTH 2021; 2:641328. [PMID: 35047996 PMCID: PMC8757737 DOI: 10.3389/froh.2021.641328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/15/2021] [Indexed: 11/13/2022] Open
Abstract
Australian Aboriginal and Torres Strait Islander children experience unacceptably high rates of dental caries compared to their non-Indigenous Australian counterparts. Dental caries significantly impacts the quality of life of children and their families, particularly in remote communities. While many socioeconomic and lifestyle factors impact caries risk, the central role of the oral microbiota in mediating dental caries has not been extensively investigated in these communities. Here, we examine factors that shape diversity and composition of the salivary microbiota in Aboriginal and Torres Strait Islander children and adolescents living in the remote Northern Peninsula Area (NPA) of Far North Queensland. We employed 16S ribosomal RNA amplicon sequencing to profile bacteria present in saliva collected from 205 individuals aged 4–17 years from the NPA. Higher average microbial diversity was generally linked to increased age and salivary pH, less frequent toothbrushing, and proxies for lower socioeconomic status (SES). Differences in microbial composition were significantly related to age, salivary pH, SES proxies, and active dental caries. Notably, a feature classified as Streptococcus sobrinus increased in abundance in children who reported less frequent tooth brushing. A specific Veillonella feature was associated with caries presence, while features classified as Actinobacillus/Haemophilus and Leptotrichia were associated with absence of caries; a Lactobacillus gasseri feature increased in abundance in severe caries. Finally, we statistically assessed the interplay between dental caries and caries risk factors in shaping the oral microbiota. These data provide a detailed understanding of biological, behavioral, and socioeconomic factors that shape the oral microbiota and may underpin caries development in this group. This information can be used in the future to improve tailored caries prevention and management options for Australian Aboriginal and Torres Strait Islander children and communities.
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Affiliation(s)
- Matilda Handsley-Davis
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Australian Research Council Centre of Excellence in Australian Biodiversity and Heritage, University of Wollongong, Wollongong, NSW, Australia
| | - Emily Skelly
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Newell W. Johnson
- Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia
- School of Dentistry and Oral Health, Griffith University, Gold Coast, QLD, Australia
- Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, United Kingdom
- Newell W. Johnson
| | - Kostas Kapellas
- Indigenous Oral Health Unit, Australian Research Centre for Population Oral Health, Adelaide Dental School, University of Adelaide, Adelaide, SA, Australia
| | - Ratilal Lalloo
- School of Dentistry, University of Queensland, Brisbane, QLD, Australia
| | - Jeroen Kroon
- School of Dentistry and Oral Health, Griffith University, Gold Coast, QLD, Australia
| | - Laura S. Weyrich
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Australian Research Council Centre of Excellence in Australian Biodiversity and Heritage, University of Wollongong, Wollongong, NSW, Australia
- microARCH Laboratory, Department of Anthropology and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States
- *Correspondence: Laura S. Weyrich
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Rabelo-Ruiz M, Teso-Pérez C, Peralta-Sánchez JM, Ariza JJ, Martín-Platero AM, Casabuena-Rincón Ó, Vázquez-Chas P, Guillamón E, Aguinaga-Casañas MA, Maqueda M, Valdivia E, Baños A, Martínez-Bueno M. Allium Extract Implements Weaned Piglet's Productive Parameters by Modulating Distal Gut Microbiota. Antibiotics (Basel) 2021; 10:antibiotics10030269. [PMID: 33800152 PMCID: PMC8001633 DOI: 10.3390/antibiotics10030269] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/24/2021] [Accepted: 03/04/2021] [Indexed: 02/01/2023] Open
Abstract
Antimicrobial resistance (AMR) has risen as a global threat for human health. One of the leading factors for this emergence has been the massive use of antibiotics growth-promoter (AGPs) in livestock, enhancing the spread of AMR among human pathogenic bacteria. Thus, several alternatives such as probiotics, prebiotics, or phytobiotics have been proposed for using in animal feeding to maintain or improve productive levels while diminishing the negative effects of AGPs. Reducing the use of antibiotics is a key aspect in the pig rearing for production reasons, as well as for the production of high-quality pork, acceptable to consumers. Here we analyze the potential use of Allium extract as an alternative. In this study, weaned piglets were fed with Allium extract supplementation and compared with control and antibiotic (colistin and zinc oxide) treated piglets. The effects of Allium extract were tested by analyzing the gut microbiome and measuring different productive parameters. Alpha diversity indices decreased significantly in Allium extract group in caecum and colon. Regarding beta diversity, significant differences between treatments appeared only in caecum and colon. Allium extract and antibiotic piglets showed better values of body weight (BW), average daily weight gain (ADG), and feed conversion ratio (FCR) than control group. These results indicate that productive parameters can be implemented by modifying the gut microbiota through phytobiotics such as Allium extract, which will drive to drop the use of antibiotics in piglet diet.
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Affiliation(s)
- Miguel Rabelo-Ruiz
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain; (C.T.-P.); (J.M.P.-S.); (A.M.M.-P.); (M.M.); (E.V.); (M.M.-B.)
- Correspondence:
| | - Claudia Teso-Pérez
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain; (C.T.-P.); (J.M.P.-S.); (A.M.M.-P.); (M.M.); (E.V.); (M.M.-B.)
| | - Juan Manuel Peralta-Sánchez
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain; (C.T.-P.); (J.M.P.-S.); (A.M.M.-P.); (M.M.); (E.V.); (M.M.-B.)
| | - Juan José Ariza
- Departamento de Microbiología y Biotecnología, DMC Research Center, Camino de Jayena s/n, 18620 Granada, Spain; (J.J.A.); (E.G.); (M.A.A.-C.); (A.B.)
| | - Antonio Manuel Martín-Platero
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain; (C.T.-P.); (J.M.P.-S.); (A.M.M.-P.); (M.M.); (E.V.); (M.M.-B.)
| | - Óscar Casabuena-Rincón
- IMASDE AGROALIMENTARIA S.L., 28224 Pozuelo de Alarcón, Madrid, Spain; (Ó.C.-R.); (P.V.-C.)
| | - Patricia Vázquez-Chas
- IMASDE AGROALIMENTARIA S.L., 28224 Pozuelo de Alarcón, Madrid, Spain; (Ó.C.-R.); (P.V.-C.)
| | - Enrique Guillamón
- Departamento de Microbiología y Biotecnología, DMC Research Center, Camino de Jayena s/n, 18620 Granada, Spain; (J.J.A.); (E.G.); (M.A.A.-C.); (A.B.)
| | - María Arántzazu Aguinaga-Casañas
- Departamento de Microbiología y Biotecnología, DMC Research Center, Camino de Jayena s/n, 18620 Granada, Spain; (J.J.A.); (E.G.); (M.A.A.-C.); (A.B.)
| | - Mercedes Maqueda
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain; (C.T.-P.); (J.M.P.-S.); (A.M.M.-P.); (M.M.); (E.V.); (M.M.-B.)
| | - Eva Valdivia
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain; (C.T.-P.); (J.M.P.-S.); (A.M.M.-P.); (M.M.); (E.V.); (M.M.-B.)
- Instituto de Biotecnología, Universidad de Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain
| | - Alberto Baños
- Departamento de Microbiología y Biotecnología, DMC Research Center, Camino de Jayena s/n, 18620 Granada, Spain; (J.J.A.); (E.G.); (M.A.A.-C.); (A.B.)
| | - Manuel Martínez-Bueno
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain; (C.T.-P.); (J.M.P.-S.); (A.M.M.-P.); (M.M.); (E.V.); (M.M.-B.)
- Instituto de Biotecnología, Universidad de Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain
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Salmonella Genomics and Population Analyses Reveal High Inter- and Intraserovar Diversity in Freshwater. Appl Environ Microbiol 2021; 87:AEM.02594-20. [PMID: 33397693 DOI: 10.1128/aem.02594-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/21/2020] [Indexed: 01/04/2023] Open
Abstract
Freshwater can support the survival of the enteric pathogen Salmonella, though temporal Salmonella diversity in a large watershed has not been assessed. At 28 locations within the Susquehanna River basin, 10-liter samples were assessed in spring and summer over 2 years. Salmonella prevalence was 49%, and increased river discharge was the main driver of Salmonella presence. The amplicon-based sequencing tool, CRISPR-SeroSeq, was used to determine serovar population diversity and detected 25 different Salmonella serovars, including up to 10 serovars from a single water sample. On average, there were three serovars per sample, and 80% of Salmonella-positive samples contained more than one serovar. Serovars Give, Typhimurium, Thompson, and Infantis were identified throughout the watershed and over multiple collections. Seasonal differences were evident: serovar Give was abundant in the spring, whereas serovar Infantis was more frequently identified in the summer. Eight of the ten serovars most commonly associated with human illness were detected in this study. Crucially, six of these serovars often existed in the background, where they were masked by a more abundant serovar(s) in a sample. Serovars Enteritidis and Typhimurium, especially, were masked in 71 and 78% of samples where they were detected, respectively. Whole-genome sequencing-based phylogeny demonstrated that strains within the same serovar collected throughout the watershed were also very diverse. The Susquehanna River basin is the largest system where Salmonella prevalence and serovar diversity have been temporally and spatially investigated, and this study reveals an extraordinary level of inter- and intraserovar diversity.IMPORTANCE Salmonella is a leading cause of bacterial foodborne illness in the United States, and outbreaks linked to fresh produce are increasing. Understanding Salmonella ecology in freshwater is of importance, especially where irrigation practices or recreational use occur. As the third largest river in the United States east of the Mississippi, the Susquehanna River is the largest freshwater contributor to the Chesapeake Bay, and it is the largest river system where Salmonella diversity has been studied. Rainfall and subsequent high river discharge rates were the greatest indicators of Salmonella presence in the Susquehanna and its tributaries. Several Salmonella serovars were identified, including eight commonly associated with foodborne illness. Many clinically important serovars were present at a low frequency within individual samples and so could not be detected by conventional culture methods. The technologies employed here reveal an average of three serovars in a 10-liter sample of water and up to 10 serovars in a single sample.
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Rabelo-Ruiz M, Ariza-Romero JJ, Zurita-González MJ, Martín-Platero AM, Baños A, Maqueda M, Valdivia E, Martínez-Bueno M, Peralta-Sánchez JM. Allium-Based Phytobiotic Enhances Egg Production in Laying Hens through Microbial Composition Changes in Ileum and Cecum. Animals (Basel) 2021; 11:448. [PMID: 33572138 PMCID: PMC7915398 DOI: 10.3390/ani11020448] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/21/2021] [Accepted: 02/05/2021] [Indexed: 12/19/2022] Open
Abstract
Phytobiotics (bioactive compounds extracted from plants) are one of the explored alternatives to antibiotics in poultry and livestock due to their antimicrobial activity and its positive effects on gut microbiota and productive properties. In this study, we supplemented a product based on garlic and onion compounds in the diet to laying hens at the beginning of their productive life (from 16 to 20 weeks post-hatching). The experimental group showed a significant increase in the number of eggs laid and in their size, produced in one month compared to the control. This increase in production was accompanied by microbiota changes in the ileum and cecum by means of high throughput sequencing analyses. These bacterial shifts in the ileum were mainly the result of compositional changes in the rare biosphere (unweighted UniFrac), while in the cecum, treatment affected both majority and minority bacterial groups (weighted and unweighted UniFrac). These changes in the microbiota suggest an improvement in food digestibility. The relative abundance of Lactococcus in the ileum and Lactobacillus in the cecum increased significantly in the experimental group. The relative abundance of these bacterial genera are known to have positive effects on the hosts. These results are very promising for the use of these compounds in poultry for short periods.
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Affiliation(s)
- Miguel Rabelo-Ruiz
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain; (M.R.-R.); (A.M.M.-P.); (M.M.); (E.V.); (M.M.-B.)
| | - Juan José Ariza-Romero
- Departamento de Microbiología y Biotecnología, DMC Research Center, Camino de Jayena s/n, 18620 Granada, Spain; (J.J.A.-R.); (M.J.Z.-G.); (A.B.)
| | - María Jesús Zurita-González
- Departamento de Microbiología y Biotecnología, DMC Research Center, Camino de Jayena s/n, 18620 Granada, Spain; (J.J.A.-R.); (M.J.Z.-G.); (A.B.)
- Área de Endocrinología Molecular y Celular, Fundación Instituto de Investigación Sanotaria de Santiago de Compostela (FIDIS), Complejo Hospitalario Universitario De Santiago (CHUS), Servicio Gallego de Salud (SERGAS), 15706 Santiago de Compostela, Spain
| | - Antonio Manuel Martín-Platero
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain; (M.R.-R.); (A.M.M.-P.); (M.M.); (E.V.); (M.M.-B.)
| | - Alberto Baños
- Departamento de Microbiología y Biotecnología, DMC Research Center, Camino de Jayena s/n, 18620 Granada, Spain; (J.J.A.-R.); (M.J.Z.-G.); (A.B.)
| | - Mercedes Maqueda
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain; (M.R.-R.); (A.M.M.-P.); (M.M.); (E.V.); (M.M.-B.)
| | - Eva Valdivia
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain; (M.R.-R.); (A.M.M.-P.); (M.M.); (E.V.); (M.M.-B.)
- Instituto de Biotecnología, Universidad de Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain
| | - Manuel Martínez-Bueno
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain; (M.R.-R.); (A.M.M.-P.); (M.M.); (E.V.); (M.M.-B.)
- Instituto de Biotecnología, Universidad de Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain
| | - Juan Manuel Peralta-Sánchez
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain; (M.R.-R.); (A.M.M.-P.); (M.M.); (E.V.); (M.M.-B.)
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Rohana H, Azrad M, Nitzan O, Adler A, Binyamin D, Koren O, Peretz A. Characterization of Clostridioides difficile Strains, the Disease Severity, and the Microbial Changes They Induce. J Clin Med 2020; 9:jcm9124099. [PMID: 33353133 PMCID: PMC7766075 DOI: 10.3390/jcm9124099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Clostridioides difficile infection (CDI) is a major nosocomial disease. The characteristics of different strains, the disease severity they cause, their susceptibility to antibiotics, and the changes they inflict on gut microbiome, have not been comprehensively studied in Israel. METHODS A severity score was calculated for 70 patients. Stool samples were tested for toxins presence using a special kit. Bacteria were isolated, identified by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and antibiotic susceptibility tests were performed for several antibiotics. Strains were classified by Multi-locus sequence typing (MLST), and changes in gut microbiome were tested. RESULTS ST04 (22.5%) and ST37 (12.7%) were the most frequent strains. Clade (phylogenetic lineage) 1 was the most (81.4%) prevalent. We found significant associations between ST and age (p = 0.024) and between ST and moxifloxacin susceptibility (p = 0.001). At the clade level, we found significant associations with binary toxin gene occurrence (p = 0.002), and with susceptibility to both metronidazole and vancomycin (p = 0.024, 0.035, respectively). Differences in intestine microbiome were affected by age, clades' distribution and STs. CONCLUSIONS By defining the characteristics of the different strains and clades, clinicians can choose medical interventions based on the predicted response or disease severity associated with each strain, enabling new advances in the field of personalized medicine.
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Affiliation(s)
- Hanan Rohana
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel; (H.R.); (O.N.); (D.B.); (O.K.)
| | - Maya Azrad
- Baruch Padeh Medical Center, Clinical Microbiology Laboratory, Poriya, Tiberias 1528001, Israel;
| | - Orna Nitzan
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel; (H.R.); (O.N.); (D.B.); (O.K.)
- Baruch Padeh Medical Center, Unit of Infectious Diseases, Poriya, Tiberias 1528001, Israel
| | - Amos Adler
- Tel Aviv Sourasky Medical Centre, Microbiology Laboratory, Tel Aviv 6423906, Israel;
- The Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dana Binyamin
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel; (H.R.); (O.N.); (D.B.); (O.K.)
| | - Omry Koren
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel; (H.R.); (O.N.); (D.B.); (O.K.)
| | - Avi Peretz
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel; (H.R.); (O.N.); (D.B.); (O.K.)
- Baruch Padeh Medical Center, Clinical Microbiology Laboratory, Poriya, Tiberias 1528001, Israel;
- Correspondence: ; Tel.: +972-4-665-2322
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Pittner S, Bugelli V, Benbow ME, Ehrenfellner B, Zissler A, Campobasso CP, Oostra RJ, Aalders MCG, Zehner R, Lutz L, Monticelli FC, Staufer C, Helm K, Pinchi V, Receveur JP, Geißenberger J, Steinbacher P, Amendt J. The applicability of forensic time since death estimation methods for buried bodies in advanced decomposition stages. PLoS One 2020; 15:e0243395. [PMID: 33296399 PMCID: PMC7725292 DOI: 10.1371/journal.pone.0243395] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/19/2020] [Indexed: 12/11/2022] Open
Abstract
Estimation of the postmortem interval in advanced postmortem stages is a challenging task. Although there are several approaches available for addressing postmortem changes of a (human) body or its environment (ecologically and/or biochemically), most are restricted to specific timeframes and/or individual and environmental conditions. It is well known, for instance, that buried bodies decompose in a remarkably different manner than on the ground surface. However, data on how established methods for PMI estimation perform under these conditions are scarce. It is important to understand whether and how postmortem changes are affected under burial conditions, if corrective factors could be conceived, or if methods have to be excluded for respective cases. We present the first multi-methodological assessment of human postmortem decomposition carried out on buried body donors in Europe, at the Amsterdam Research Initiative for Sub-surface Taphonomy and Anthropology (ARISTA) in the Netherlands. We used a multidisciplinary approach to investigate postmortem changes of morphology, skeletal muscle protein decomposition, presence of insects and other necrophilous animals as well as microbial communities (i.e., microbiomes) from August to November 2018 associated with two complete body exhumations and eight partial exhumations. Our results clearly display the current possibilities and limitations of methods for PMI estimation in buried remains and provide a baseline for future research and application.
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Affiliation(s)
- Stefan Pittner
- Dept. of Forensic Medicine, University of Salzburg, Salzburg, Austria
| | - Valentina Bugelli
- Dept. of Medicine and Health Sciences, University of Florence, Florence, Italy
| | - M. Eric Benbow
- Dept. of Entomology, Michigan State University, East Lansing, Michigan, United States of America
- Dept. of Osteopathic Medical Specialties, Michigan State University, East Lansing, Michigan, United States of America
- Ecology, Evolutionary Biology and Behavior Program, Michigan State University, East Lansing, Michigan, United States of America
| | | | - Angela Zissler
- Dept. of Biosciences, University of Salzburg, Salzburg, Austria
| | - Carlo P. Campobasso
- Dept. of Experimental Medicine, University L. Vanvitelli of Campania, Naples, Italy
| | - Roelof-Jan Oostra
- Dept. of Medical Biology, Amsterdam UMC – location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Maurice C. G. Aalders
- Dept. of Biomedical Engineering and Physics, Amsterdam UMC – location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Richard Zehner
- Institute of Legal Medicine, Goethe-University Frankfurt, Frankfurt, Germany
| | - Lena Lutz
- Institute of Legal Medicine, Goethe-University Frankfurt, Frankfurt, Germany
| | | | - Christian Staufer
- Dept. of Forensic Medicine, University of Salzburg, Salzburg, Austria
| | - Katharina Helm
- Dept. of Forensic Medicine, University of Salzburg, Salzburg, Austria
| | - Vilma Pinchi
- Dept. of Medicine and Health Sciences, University of Florence, Florence, Italy
| | - Joseph P. Receveur
- Dept. of Entomology, Michigan State University, East Lansing, Michigan, United States of America
| | | | | | - Jens Amendt
- Institute of Legal Medicine, Goethe-University Frankfurt, Frankfurt, Germany
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Sau L, Olmstead CM, Cui LJ, Chen A, Shah RS, Kelley ST, Thackray VG. Alterations in Gut Microbiota Do Not Play a Causal Role in Diet-independent Weight Gain Caused by Ovariectomy. J Endocr Soc 2020; 5:bvaa173. [PMID: 33324864 PMCID: PMC7724750 DOI: 10.1210/jendso/bvaa173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Indexed: 01/03/2023] Open
Abstract
Acute estrogen deficiency in women can occur due to many conditions including hyperprolactinemia, chemotherapy, GnRH agonist treatment, and removal of hormone replacement therapy. Ovariectomized (OVX) rodent models, often combined with a high-fat diet (HFD), have been used to investigate the effects of decreased estrogen production on metabolism. Since evidence suggests that gut microbes may facilitate the protective effect of estrogen on metabolic dysregulation in an OVX + HFD model, we investigated whether the gut microbiome plays a role in the diet-independent weight gain that occurs after OVX in adult female mice. 16S rRNA gene sequence analysis demonstrated that OVX was not associated with changes in overall gut bacterial biodiversity but was correlated with a shift in beta diversity. Using differential abundance analysis, we observed a difference in the relative abundance of a few bacterial taxa, such as Turicibacter, 3 to 5 weeks after OVX, which was subsequent to the weight gain that occurred 2 weeks postsurgery. A cohousing study was performed to determine whether exposure to a healthy gut microbiome was protective against the development of the metabolic phenotype associated with OVX. Unlike mouse models of obesity, HFD maternal-induced metabolic dysregulation, or polycystic ovary syndrome, cohousing OVX mice with healthy mice did not improve the metabolic phenotype of OVX mice. Altogether, these results indicate that changes in the gut microbiome are unlikely to play a causal role in diet-independent, OVX-induced weight gain (since they occurred after the weight gain) and cohousing with healthy mice did not have a protective effect.
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Affiliation(s)
- Lillian Sau
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California, USA
| | | | - Laura J Cui
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California, USA
| | - Annie Chen
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California, USA
| | - Reeya S Shah
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Varykina G Thackray
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California, USA
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Telmadarrehei T, Tang JD, Raji O, Rezazadeh A, Narayanan L, Shmulsky R, Jeremic D. A Study of the Gut Bacterial Community of Reticulitermes virginicus Exposed to Chitosan Treatment. INSECTS 2020; 11:E681. [PMID: 33049915 PMCID: PMC7601259 DOI: 10.3390/insects11100681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/28/2020] [Accepted: 10/05/2020] [Indexed: 01/04/2023]
Abstract
A thorough understanding of microbial communities in the gut of lower termites is needed to develop target-specific and environmentally benign wood protection systems. In this study, the bacterial community from Reticulitermes virginicus was examined by Illumina sequencing of 16S ribosomal RNA (rRNA) spanning the V3 and V4 regions. Prior to library preparation, the termites were subjected to five treatments over an 18-day period: three groups were fed on wood treated with 0.5% chitosan, 25% acetic acid, or water, the fourth group was taken directly from the original collection log, and the fifth group was starved. Metagenomic sequences were analyzed using QIIME 2 to understand the treatments' effects on the dynamics of the gut bacteria. Four dominant phyla were detected: Bacteroidetes (34.4% of reads), Firmicutes (20.6%), Elusimicrobia (15.7%), and Proteobacteria (12.9%). A significant effect of chitosan treatment was observed in two phyla; Firmicutes abundance was significantly lower with chitosan treatment when compared to other groups, while Actinobacteria was lower in unexposed and starved termites. The results suggest that chitosan treatment not only affects the structure of the microbial community in the gut, but other treatments such as starving also cause shifts in termite gut communities.
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Affiliation(s)
- Telmah Telmadarrehei
- Department of Sustainable Bioproducts, Mississippi State University, 201 Locksley Way, Starkville, MS 39759, USA; (O.R.); (L.N.); (R.S.); (D.J.)
| | - Juliet D. Tang
- Forest Products Laboratory, USDA Forest Service, 201 Lincoln Green, Starkville, MS 39759, USA;
| | - Olanrewaju Raji
- Department of Sustainable Bioproducts, Mississippi State University, 201 Locksley Way, Starkville, MS 39759, USA; (O.R.); (L.N.); (R.S.); (D.J.)
- Department of Chemical Engineering and Applied Science, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
| | - Amir Rezazadeh
- Institute of Food and Agriculture Science, University of Florida, 8400 Picos Road, Ste. 101, Fort Pierce, FL 34945, USA;
| | - Lakshmi Narayanan
- Department of Sustainable Bioproducts, Mississippi State University, 201 Locksley Way, Starkville, MS 39759, USA; (O.R.); (L.N.); (R.S.); (D.J.)
| | - Rubin Shmulsky
- Department of Sustainable Bioproducts, Mississippi State University, 201 Locksley Way, Starkville, MS 39759, USA; (O.R.); (L.N.); (R.S.); (D.J.)
| | - Dragica Jeremic
- Department of Sustainable Bioproducts, Mississippi State University, 201 Locksley Way, Starkville, MS 39759, USA; (O.R.); (L.N.); (R.S.); (D.J.)
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An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists. Life (Basel) 2020; 10:life10090185. [PMID: 32911871 PMCID: PMC7555798 DOI: 10.3390/life10090185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 01/02/2023] Open
Abstract
High-throughput DNA sequencing (HTS) has changed our understanding of the microbial composition present in a wide range of environments. Applying HTS methods to air samples from different environments allows the identification and quantification (relative abundance) of the microorganisms present and gives a better understanding of human exposure to indoor and outdoor bioaerosols. To make full use of the avalanche of information made available by these sequences, repeated measurements must be taken, community composition described, error estimates made, correlations of microbiota with covariates (variables) must be examined, and increasingly sophisticated statistical tests must be conducted, all by using bioinformatics tools. Knowing which analysis to conduct and which tools to apply remains confusing for bioaerosol scientists, as a litany of tools and data resources are now available for characterizing microbial communities. The goal of this review paper is to offer a guided tour through the bioinformatics tools that are useful in studying the microbial ecology of bioaerosols. This work explains microbial ecology features like alpha and beta diversity, multivariate analyses, differential abundances, taxonomic analyses, visualization tools and statistical tests using bioinformatics tools for bioaerosol scientists new to the field. It illustrates and promotes the use of selected bioinformatic tools in the study of bioaerosols and serves as a good source for learning the “dos and don’ts” involved in conducting a precise microbial ecology study.
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Stefani F, Dupont S, Laterrière M, Knox R, Ruan Y, Hamel C, Hijri M. Similar Arbuscular Mycorrhizal Fungal Communities in 31 Durum Wheat Cultivars ( Triticum turgidum L. var. durum) Under Field Conditions in Eastern Canada. FRONTIERS IN PLANT SCIENCE 2020; 11:1206. [PMID: 32849748 PMCID: PMC7431883 DOI: 10.3389/fpls.2020.01206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/24/2020] [Indexed: 06/11/2023]
Abstract
Wheat is among the important crops harnessed by humans whose breeding efforts resulted in a diversity of genotypes with contrasting traits. The goal of this study was to determine whether different old and new cultivars of durum wheat (Triticum turgidum L. var. durum) recruit specific arbuscular mycorrhizal (AM) fungal communities from indigenous AM fungal populations of soil under field conditions. A historical set of five landraces and 26 durum wheat cultivars were field cultivated in a humid climate in Eastern Canada, under phosphorus-limiting conditions. To characterize the community of AMF inhabiting bulk soil, rhizosphere, and roots, MiSeq amplicon sequencing targeting the 18S rRNA gene (SSU) was performed on total DNAs using a nested PCR approach. Mycorrhizal colonization was estimated using root staining and microscope observations. A total of 317 amplicon sequence variants (ASVs) were identified as belonging to Glomeromycota. The core AM fungal community (i.e., ASVs present in > 50% of the samples) in the soil, rhizosphere, and root included 29, 30, and 29 ASVs, respectively. ASVs from the genera Funneliformis, Claroideoglomus, and Rhizophagus represented 37%, 18.6%, and 14.7% of the sequences recovered in the rarefied dataset, respectively. The two most abundant ASVs had sequence homology with the 18S sequences from well-identified herbarium cultures of Funneliformis mosseae BEG12 and Rhizophagus irregularis DAOM 197198, while the third most abundant ASV was assigned to the genus Paraglomus. Cultivars showed no significant difference of the percentage of root colonization ranging from 57.8% in Arnautka to 84.0% in AC Navigator. Cultivars were generally associated with similar soil, rhizosphere, and root communities, but the abundance of F. mosseae, R. irregularis, and Claroideoglomus sp. sequences varied in Eurostar, Golden Ball, and Wakooma. Although these results were obtained in one field trial using a non-restricted pool of durum wheat and at the time of sampling, that may have filtered the community in biotopes. The low genetic variation between durum wheat cultivars for the diversity of AM symbiosis at the species level suggests breeding resources need not be committed to leveraging plant selective influence through the use of traditional methods for genotype development.
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Affiliation(s)
- Franck Stefani
- Ottawa Research and Development Centre of Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sarah Dupont
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, Canada
| | - Mario Laterrière
- Quebec Research and Development Centre of Agriculture and Agri-Food Canada, Quebec, QC, Canada
| | - Ron Knox
- Swift Current Research and Development Centre of Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Centre of Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Chantal Hamel
- Quebec Research and Development Centre of Agriculture and Agri-Food Canada, Quebec, QC, Canada
| | - Mohamed Hijri
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, Canada
- AgroBioSciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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Debelius JW, Huang T, Cai Y, Ploner A, Barrett D, Zhou X, Xiao X, Li Y, Liao J, Zheng Y, Huang G, Adami HO, Zeng Y, Zhang Z, Ye W. Subspecies Niche Specialization in the Oral Microbiome Is Associated with Nasopharyngeal Carcinoma Risk. mSystems 2020; 5:e00065-20. [PMID: 32636333 PMCID: PMC7343305 DOI: 10.1128/msystems.00065-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/18/2020] [Indexed: 12/24/2022] Open
Abstract
Oral health and changes in the oral microbiome have been associated with both local and systemic cancer. Poor oral hygiene is a known risk factor for nasopharyngeal carcinoma (NPC), a virally associated head and neck cancer endemic to southern China. We explored the relationship between NPC and the oral microbiome using 16S rRNA sequencing in a study of 499 NPC patients and 495 population-based age and sex frequency-matched controls from an area of endemicity of Southern China. We found a significant reduction in community richness in cases compared to that in controls. Differences in the overall microbial community structure between cases and controls could not be explained by other potential confounders; disease status explained 5 times more variation in the unweighted UniFrac distance than the next most explanatory variable. In feature-based analyses, we identified a pair of coexcluding Granulicatella adiacens amplicon sequence variants (ASVs) which were strongly associated with NPC status and differed by a single nucleotide. The G. adiacens variant an individual carried was also associated with the overall microbial community based on beta diversity. Co-occurrence analysis suggested the two G. adiacens ASVs sit at the center of two coexcluding clusters of closely related organisms. Our results suggest there are differences in the oral microbiomes between NPC patients and healthy controls, and these may be associated with both a loss of microbial diversity and niche specialization among closely related commensals.IMPORTANCE The relationship between oral health and the risk of nasopharyngeal carcinoma (NPC) was previously established. However, the role of oral microbiome has not been evaluated in the disease in a large epidemiological study. This paper clearly establishes a difference in the oral microbiomes between NPC patients and healthy controls which cannot be explained by other confounding factors. It furthermore identifies a pair of closely related coexcluding organisms associated with the disease, highlighting the importance of modern methods for single-nucleotide resolution in 16S rRNA sequence characterization. To the best of our knowledge, this is one of the first examples of cancer-associated niche specialization of the oral microbiome.
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Affiliation(s)
- Justine W Debelius
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Tingting Huang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Yonglin Cai
- Department of Cancer Prevention Center, Wuzhou Red Cross Hospital, Wuzhou, People's Republic of China
- Wuzhou Health System Key Laboratory for Nasopharyngeal Carcinoma Etiology and Molecular Mechanism, Wuzhou, People's Republic of China
| | - Alexander Ploner
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Donal Barrett
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Xiaoying Zhou
- Life Science Institute, Guangxi Medical University, Nanning, People's Republic of China
- Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education, Nanning, People's Republic of China
| | - Xue Xiao
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Yancheng Li
- Department of Cancer Prevention Center, Wuzhou Red Cross Hospital, Wuzhou, People's Republic of China
- Wuzhou Health System Key Laboratory for Nasopharyngeal Carcinoma Etiology and Molecular Mechanism, Wuzhou, People's Republic of China
| | - Jian Liao
- Cangwu Institute for Nasopharyngeal Carcinoma Control and Prevention, Wuzhou, People's Republic of China
| | - Yuming Zheng
- Department of Cancer Prevention Center, Wuzhou Red Cross Hospital, Wuzhou, People's Republic of China
- Wuzhou Health System Key Laboratory for Nasopharyngeal Carcinoma Etiology and Molecular Mechanism, Wuzhou, People's Republic of China
| | - Guangwu Huang
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Hans-Olov Adami
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Clinical Effectiveness Research Group, Institute of Health, University of Oslo, Oslo, Norway
| | - Yi Zeng
- State Key Laboratory for Infectious Diseases Prevention and Control, Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Zhe Zhang
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Weimin Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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Sułowicz S, Bondarczuk K, Ignatiuk D, Jania JA, Piotrowska-Seget Z. Microbial communities from subglacial water of naled ice bodies in the forefield of Werenskioldbreen, Svalbard. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 723:138025. [PMID: 32213417 DOI: 10.1016/j.scitotenv.2020.138025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 03/16/2020] [Accepted: 03/16/2020] [Indexed: 06/10/2023]
Abstract
We assessed the structure of microbial communities in the subglacial drainage system of the Werenskioldbreen glacier, Svalbard, which consists of three independent channels. Dome-shaped naled ice bodies that had been forming and releasing subglacial water in the glacial forefield during accumulations season were used to study glacial microbiome. We tested the hypothesis that the properties of the water transported by these channels are site-dependent and influence bacterial diversity. We therefore established the phylogenetic structure of the subglacial microbial communities using next generation sequencing (NGS) of the 16S rRNA gene and performed bioinformatics analyses. A total of 1409 OTUs (operational taxonomic units) belonged to 40 phyla; mostly Proteobacteria, Gracilibacteria, Bacteroidetes, Actinobacteria and Parcubacteria were identified. Sites located on the edge of Werenskioldbreen forefield (Angell, Kvisla) were mainly dominated by Betaproteobacteria. In the central site (Dusan) domination of Epsilonproteobacteria class was observed. Gracilibacteria (GN02) and Gammaproteobacteria represented the dominant taxa only in the sample Kvisla 2. Principal Coordinate Analysis (PCoA) of beta diversity revealed that phylogenetic profiles grouped in three different clusters according to the sampling site. Moreover, higher similarity of bacterial communities from Angell and Kvisla compared to Dusan was confirmed by cluster analysis and Venn diagrams. The highest alpha index values was measured in Dusan. Richness and phylogenetic diversity indices were significantly (p < .05) and positively correlated with pH values of subglacial water and negatively with concentration of Cl-, Br-, and NO3- anions. These anions negatively impacted the values of richness indices but positively correlated with abundance of some microbial phyla. Our results indicated that subglacial water from naled ice bodies offer the possibility to study the glacial microbiome. In the studied subglacial water, the microbial community structure was sampling site specific and dependent on the water properties, which in turn were probably influenced by the local bedrock composition.
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Affiliation(s)
- Sławomir Sułowicz
- University of Silesia in Katowice, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland.
| | - Kinga Bondarczuk
- Medical University of Bialystok, Centre for Bioinformatics and Data Analysis, Waszyngtona 13a, 15-269 Bialystok, Poland
| | - Dariusz Ignatiuk
- University of Silesia in Katowice, Faculty of Natural Sciences, Institute of Earth Sciences, Bedzinska 60, 41-205 Sosnowiec, Poland; Svalbard Integrated Arctic Earth Observing System (SIOS), SIOS Knowledge Centre, Svalbard Science Centre, P.O. Box 156, N-9171 Longyearbyen, Svalbard, Norway
| | - Jacek A Jania
- University of Silesia in Katowice, Faculty of Natural Sciences, Institute of Earth Sciences, Bedzinska 60, 41-205 Sosnowiec, Poland
| | - Zofia Piotrowska-Seget
- University of Silesia in Katowice, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland
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McCabe RA, Receveur JP, Houtz JL, Thomas KL, Benbow ME, Pechal JL, Wallace JR. Characterizing the microbiome of ectoparasitic louse flies feeding on migratory raptors. PLoS One 2020; 15:e0234050. [PMID: 32497084 PMCID: PMC7271990 DOI: 10.1371/journal.pone.0234050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/17/2020] [Indexed: 01/04/2023] Open
Abstract
Louse flies (Diptera: Hippoboscidae) are obligate ectoparasites that often cause behavioral, pathogenic, and evolutionary effects on their hosts. Interactions between ectoparasites and avian hosts, especially migrating taxa, may influence avian pathogen spread in tropical and temperate ecosystems and affect long-term survival, fitness and reproductive success. The purpose of this study was to characterize the vector-associated microbiome of ectoparasitic louse flies feeding on migrating raptors over the fall migration period. Surveys for louse flies occurred during fall migration (2015-2016) at a banding station in Pennsylvania, United States; flies were collected from seven species of migrating raptors, and we sequenced their microbial (bacteria and archaea) composition using high-throughput targeted amplicon sequencing of the 16S rRNA gene (V4 region). All louse flies collected belonged to the same species, Icosta americana. Our analysis revealed no difference in bacterial communities of louse flies retrieved from different avian host species. The louse fly microbiome was dominated by a primary endosymbiont, suggesting that louse flies maintain a core microbial structure despite receiving blood meals from different host species. Thus, our findings highlight the importance of characterizing both beneficial and potentially pathogenic endosymbionts when interpreting how vector-associated microbiomes may impact insect vectors and their avian hosts.
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Affiliation(s)
- Rebecca A. McCabe
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Québec, Canada
- * E-mail: (RAM); (JRW)
| | - Joseph P. Receveur
- Department of Entomology, Michigan State University, East Lansing, Michigan, United States of America
| | - Jennifer L. Houtz
- Department of Biology, Millersville University, Millersville, Pennsylvania, United States of America
| | - Kayli L. Thomas
- Department of Biology, Millersville University, Millersville, Pennsylvania, United States of America
| | - M. Eric Benbow
- Department of Entomology, Michigan State University, East Lansing, Michigan, United States of America
| | - Jennifer L. Pechal
- Department of Entomology, Michigan State University, East Lansing, Michigan, United States of America
| | - John R. Wallace
- Department of Biology, Millersville University, Millersville, Pennsylvania, United States of America
- * E-mail: (RAM); (JRW)
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Park SK, Kim HN, Choi CH, Im JP, Cha JM, Eun CS, Kim TO, Kang SB, Bang KB, Kim HG, Jung Y, Yoon H, Han DS, Lee CW, Ahn K, Kim HL, Park DI. Differentially Abundant Bacterial Taxa Associated with Prognostic Variables of Crohn's Disease: Results from the IMPACT Study. J Clin Med 2020; 9:E1748. [PMID: 32516912 PMCID: PMC7357029 DOI: 10.3390/jcm9061748] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/30/2020] [Accepted: 06/02/2020] [Indexed: 12/18/2022] Open
Abstract
Limited studies have examined the intestinal microbiota composition in relation to Crohn's disease (CD) prognosis. We analyzed the differences in microbial communities and relevant metabolic pathways associated with prognostic variables in patients with CD. We applied 16S rRNA gene sequencing to analyze a cohort of 1110 CD and healthy control (HC) fecal samples. We categorized patients with CD into good (CD-G), intermediate (CD-I) and poor (CD-P) prognosis groups, according to the history of using biologics and intestinal resection. Microbiota α-diversity decreased more in CD-P than CD-G and CD-I. Microbiota ß-diversity in CD-P differed from that in CD-G and CD-I. Thirteen genera and 10 species showed differential abundance between CD-G and CD-P groups. Escherichia coli (p = 0.001) and species Producta (p = 0.01) and genera Lactobacillus (p = 0.003) and Coprococcus (p = 0.01) consistently showed differences between CD-G and CD-P groups after adjusting for confounding variables. Functional profiling suggested that the microbial catabolic pathways and pathways related to enterobacterial common antigen and lipopolysaccharide biosynthesis were better represented in the CD-P group than in the CD-G group, and E. coli were the top contributors to these pathways. CD prognosis is associated with altered microbiota composition and decreased diversity, and E. coli might be causally involved in CD progression, and may have adapted to live in inflammatory environments.
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Affiliation(s)
- Soo-kyung Park
- Division of Gastroenterology, Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea;
- Medical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea; (H.-N.K.); (C.-W.L.)
- Inflammatory Bowel Disease Study Group of the Korean Association for the Study of Intestinal Diseases, Seoul 06193, Korea; (C.H.C.); (J.P.I.); (T.-O.K.); (H.Y.)
| | - Han-Na Kim
- Medical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea; (H.-N.K.); (C.-W.L.)
- Department of Clinical Research Design and Evaluation, SAIHST, Sungkyunkwan University, Seoul 03063, Korea
| | - Chang Hwan Choi
- Inflammatory Bowel Disease Study Group of the Korean Association for the Study of Intestinal Diseases, Seoul 06193, Korea; (C.H.C.); (J.P.I.); (T.-O.K.); (H.Y.)
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul 06973, Korea
| | - Jong Pil Im
- Inflammatory Bowel Disease Study Group of the Korean Association for the Study of Intestinal Diseases, Seoul 06193, Korea; (C.H.C.); (J.P.I.); (T.-O.K.); (H.Y.)
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jae Myung Cha
- Department of Internal Medicine, Kyung Hee University Hospital at Gang Dong, Kyung Hee University School of Medicine, Seoul 02447, Korea;
| | - Chang Soo Eun
- Department of Internal Medicine, Hanyang University Guri Hospital, Guri 11923, Korea; (C.S.E.); (D.-S.H.)
| | - Tae-Oh Kim
- Inflammatory Bowel Disease Study Group of the Korean Association for the Study of Intestinal Diseases, Seoul 06193, Korea; (C.H.C.); (J.P.I.); (T.-O.K.); (H.Y.)
- Division of Gastroenterology, Department of Internal Medicine, Inje University Haeundae Paik Hospital, Busan 48108, Korea
| | - Sang-Bum Kang
- Division of Gastroenterology, Department of Internal medicine, Daejeon St. Mary’s Hospital, The Catholic University of Korea, Daejeon 34943, Korea;
| | - Ki Bae Bang
- Department of Internal Medicine, Dankook University College of Medicine, Cheonan 31116, Korea;
| | - Hyun Gun Kim
- Division of Gastroenterology, Department of Internal Medicine, Soonchunhyang University College of Medicine, Seoul Hospital, Seoul 04401, Korea;
| | - Yunho Jung
- Division of Gastroenterology, Department of Internal Medicine, Soonchunhyang University College of Medicine, Cheonan Hospital, Cheonan 31151, Korea;
| | - Hyuk Yoon
- Inflammatory Bowel Disease Study Group of the Korean Association for the Study of Intestinal Diseases, Seoul 06193, Korea; (C.H.C.); (J.P.I.); (T.-O.K.); (H.Y.)
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Dong-Soo Han
- Department of Internal Medicine, Hanyang University Guri Hospital, Guri 11923, Korea; (C.S.E.); (D.-S.H.)
| | - Chil-Woo Lee
- Medical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea; (H.-N.K.); (C.-W.L.)
| | - Kwangsung Ahn
- Functional Genome Institute, PDXen Biosystems Inc., Daejeon 34129, Korea;
| | - Hyung-Lae Kim
- Department of Biochemistry, School of Medicine, Ewha Womans University, Seoul 07804, Korea;
| | - Dong Il Park
- Division of Gastroenterology, Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea;
- Medical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea; (H.-N.K.); (C.-W.L.)
- Inflammatory Bowel Disease Study Group of the Korean Association for the Study of Intestinal Diseases, Seoul 06193, Korea; (C.H.C.); (J.P.I.); (T.-O.K.); (H.Y.)
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Ghosh A, Thakur M, Singh SK, Sharma LK, Chandra K. Gut microbiota suggests dependency of Arunachal Macaque (Macaca munzala) on anthropogenic food in Western Arunachal Pradesh, Northeastern India: Preliminary findings. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Sharma S, Lee M, Reinmann CS, Pumneo J, Cutright TJ, Senko JM. Impact of acid mine drainage chemistry and microbiology on the development of efficient Fe removal activities. CHEMOSPHERE 2020; 249:126117. [PMID: 32088465 DOI: 10.1016/j.chemosphere.2020.126117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 02/02/2020] [Accepted: 02/03/2020] [Indexed: 06/10/2023]
Abstract
Coal mine derived acid mine drainage (AMD) is formed when oxygenated water infiltrates mine voids and oxidizes FeS phases, generating acidic fluid rich in heavy metals, polluting thousands of miles of streams. Existing remediation options are cost-prohibitive and difficult to sustain. In some cases, AMD flows over previously pristine soil in thin sheets over terrestrial surface, enhancing AMD aeration and Fe(II) oxidizing activities, leading to oxidative Fe(II) precipitation from AMD, without any human intervention. Since robust Fe(II) biooxidation occurs in the mixture of intruding AMD and pristine soil, understanding the effects of chemically variant AMD can be exploited for effective Fe(II) removal. We hypothesized that chemistry and microbiology of AMD intruding pristine soil on surface would influence the development of Fe(II) oxidizing capabilities. Therefore, to investigate the response of pristine soil to the addition of AMD varying in chemical and microbial characteristics, we mixed soil with a near-neutral and moderately acidic AMD, in separate incubations. Incubations with near-neutral AMD developed microbial Fe(II) oxidation activities after 10 days. However, Fe(II) oxidation in moderately acidic AMD incubations was mostly abiotic. 16S rRNA gene sequences and metabolic functional prediction (Tax4Fun) analysis of near-neutral AMD and soil mixture indicated development of taxonomically different communities capable of activities similar to microorganisms in a mine void. In conclusion, results indicate that AMD chemistry and microbiology affects development of Fe(II) biooxidation. Therefore, understanding of the effect of AMD chemistry on the development of FeOB activities in soil can be exploited to design site-specific and sustainable solutions.
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Affiliation(s)
- Shagun Sharma
- Department of Biology, The University of Akron, Akron, OH, USA; Integrated Bioscience Program, The University of Akron, Akron, OH, USA.
| | - Matthew Lee
- Department of Geosciences, The University of Akron, Akron, OH, USA
| | - Casey S Reinmann
- Department of Geosciences, The University of Akron, Akron, OH, USA
| | - Jenna Pumneo
- Department of Biology, The University of Akron, Akron, OH, USA
| | - Teresa J Cutright
- Department of Civil Engineering, The University of Akron, Akron, OH, USA
| | - John M Senko
- Department of Biology, The University of Akron, Akron, OH, USA; Integrated Bioscience Program, The University of Akron, Akron, OH, USA; Department of Geosciences, The University of Akron, Akron, OH, USA
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50
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Yun KE, Kim J, Kim MH, Park E, Kim HL, Chang Y, Ryu S, Kim HN. Major Lipids, Apolipoproteins, and Alterations of Gut Microbiota. J Clin Med 2020; 9:jcm9051589. [PMID: 32456223 PMCID: PMC7290464 DOI: 10.3390/jcm9051589] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/14/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023] Open
Abstract
The gut microbiota has been linked to blood lipids. However, the relationship between the gut microbiome and other lipid markers like apolipoproteins A1 (apoA1) and B (apoB) as well as classical lipid markers in Asians remain unclear. Here, we examined the associations between gut microbial diversity and taxonomic compositions with both apolipoproteins and lipid markers in a large number of Korean patients. The fecal 16S rRNA gene sequencing data from 1141 subjects were analyzed and subjects were categorized into control group (G0) or abnormal group (G1) according to blood lipid measurements. The microbial diversity and several taxa of the gut microbiota were significantly associated with triglyceride, apoA1, and apoB levels, but not with total cholesterol, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol levels. The alpha diversity of the gut microbiota was inversely associated with high triglyceride level. Interestingly, G1 of apoA1 showed increased microbial richness and distinct microbial community compared with G0 of apoA1. A high abundance of Fusobacteria and low abundance of Oscillospira were found in the hypertriglyceridemia group. In this large-scale study, we identified associations of gut microbiota with apolipoproteins and classical lipid markers, indicating that the gut microbiota may be an important target for regulating blood lipids.
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Affiliation(s)
- Kyung Eun Yun
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 04514, Korea; (K.E.Y.); (J.K.); (M.-h.K.); (Y.C.); (S.R.)
| | - Jimin Kim
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 04514, Korea; (K.E.Y.); (J.K.); (M.-h.K.); (Y.C.); (S.R.)
| | - Mi-hyun Kim
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 04514, Korea; (K.E.Y.); (J.K.); (M.-h.K.); (Y.C.); (S.R.)
| | - Eunkyo Park
- Department of Biochemistry, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.P.); (H.-L.K.)
| | - Hyung-Lae Kim
- Department of Biochemistry, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.P.); (H.-L.K.)
| | - Yoosoo Chang
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 04514, Korea; (K.E.Y.); (J.K.); (M.-h.K.); (Y.C.); (S.R.)
- Department of Occupational and Environmental Medicine, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 03181, Korea
- Department of Clinical Research Design and Evaluation, SAIHST, Sungkyunkwan University, Seoul 03063, Korea
| | - Seungho Ryu
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 04514, Korea; (K.E.Y.); (J.K.); (M.-h.K.); (Y.C.); (S.R.)
- Department of Occupational and Environmental Medicine, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 03181, Korea
- Department of Clinical Research Design and Evaluation, SAIHST, Sungkyunkwan University, Seoul 03063, Korea
| | - Han-Na Kim
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 04514, Korea; (K.E.Y.); (J.K.); (M.-h.K.); (Y.C.); (S.R.)
- Department of Clinical Research Design and Evaluation, SAIHST, Sungkyunkwan University, Seoul 03063, Korea
- Medical Research Institute, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 03181, Korea
- Correspondence: ; Tel.: +82-2-2001-1978
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