1
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Slowik AR, Hesketh H, Sait SM, De Fine Licht HH. Thermal ecology shapes disease outcomes of entomopathogenic fungi infecting warm-adapted insects. J Invertebr Pathol 2024; 204:108106. [PMID: 38621520 DOI: 10.1016/j.jip.2024.108106] [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: 10/05/2023] [Revised: 03/13/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
The thermal environment is a critical determinant of outcomes in host-pathogen interactions, yet the complexities of this relationship remain underexplored in many ecological systems. We examined the Thermal Mismatch Hypothesis (TMH) by measuring phenotypic variation in individual thermal performance profiles using a model system of two species of entomopathogenic fungi (EPF) that differ in their ecological niche, Metarhizium brunneum and M. flavoviride, and a warm-adapted model host, the mealworm Tenebrio molitor. We conducted experiments across ecologically relevant temperatures to determine the thermal performance curves for growth and virulence, measured as % survival, identify critical thresholds for these measures, and elucidate interactive host-pathogen effects. Both EPF species and the host exhibited a shared growth optima at 28 °C, while the host's growth response was moderated in sublethal pathogen infections that depended on fungus identity and temperature. However, variances in virulence patterns were different between pathogens. The fungus M. brunneum exhibited a broader optimal temperature range (23-28 °C) for virulence than M. flavoviride, which displayed a multiphasic virulence-temperature relationship with distinct peaks at 18 and 28 °C. Contrary to predictions of the TMH, both EPF displayed peak virulence at the host's optimal temperature (28 °C). The thermal profile for M. brunneum aligned more closely with that of T. molitor than that for M. flavoviride. Moreover, the individual thermal profile of M. flavoviride closely paralleled its virulence thermal profile, whereas the virulence thermal profile of M. brunneum did not track with its individual thermal performance. This suggests an indirect, midrange (23 °C) effect, where M. brunneum virulence exceeded growth. These findings suggest that the evolutionary histories and ecological adaptations of these EPF species have produced distinct thermal niches during the host interaction. This study contributes to our understanding of thermal ecology in host-pathogen interactions, underpinning the ecological and evolutionary factors that shape infection outcomes in entomopathogenic fungi. The study has ecological implications for insect population dynamics in the face of a changing climate, as well as practically for the use of these organisms in biological control.
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Affiliation(s)
- Anna R Slowik
- University of Copenhagen, Department of Plant and Environmental Sciences, Thorvaldsensvej 40, 1871 Frederiksberg C., Denmark; UK Centre for Ecology & Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, United Kingdom; School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom.
| | - Helen Hesketh
- UK Centre for Ecology & Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, United Kingdom.
| | - Steven M Sait
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom.
| | - Henrik H De Fine Licht
- University of Copenhagen, Department of Plant and Environmental Sciences, Thorvaldsensvej 40, 1871 Frederiksberg C., Denmark.
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2
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Barbosa M, Chalmers JD. Bronchiectasis. Presse Med 2023; 52:104174. [PMID: 37778637 DOI: 10.1016/j.lpm.2023.104174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023] Open
Abstract
Bronchiectasis is a final common pathway of a wide variety of underlying conditions including infectious, autoimmune, allergic, genetic and inflammatory conditions. Patients experience a chronic disease with variable clinical symptoms and course, but most experience cough, sputum production and recurrent exacerbations. Symptoms of bronchiectasis lead to poor quality of life and exacerbations are the major driver of morbidity and mortality. Patients are often chronically infected with bacteria with the most common being Pseudomonas aeruginosa and Haemophilus influenzae. Treatment of bronchiectasis includes standardised testing to identify the underlying cause with targeted treatment if immune deficiency, allergic bronchopulmonary aspergillosis or non-tuberculous mycobacterial infection, for example, are identified. Airway clearance is the mainstay of therapy for patients with symptoms of cough and sputum production. Frequently exacerbating patients may benefit from long term antibiotic or mucoactive therapies. Bronchiectasis is a heterogeneous disease and increasingly precision medicine approaches are advocated to target treatments most appropriately and to limit the emergence of antimicrobial resistance.
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Affiliation(s)
- Miguel Barbosa
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, Dundee, DD1 9SY, UK
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, Dundee, DD1 9SY, UK.
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3
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Fabbrini M, Scicchitano D, Candela M, Turroni S, Rampelli S. Connect the dots: sketching out microbiome interactions through networking approaches. MICROBIOME RESEARCH REPORTS 2023; 2:25. [PMID: 38058764 PMCID: PMC10696587 DOI: 10.20517/mrr.2023.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 12/08/2023]
Abstract
Microbiome networking analysis has emerged as a powerful tool for studying the complex interactions among microorganisms in various ecological niches, including the human body and several environments. This analysis has been used extensively in both human and environmental studies, revealing key taxa and functional units peculiar to the ecosystem considered. In particular, it has been mainly used to investigate the effects of environmental stressors, such as pollution, climate change or therapies, on host-associated microbial communities and ecosystem function. In this review, we discuss the latest advances in microbiome networking analysis, including methods for constructing and analyzing microbiome networks, and provide a case study on how to use these tools. These analyses typically involve constructing a network that represents interactions among microbial taxa or functional units, such as genes or metabolic pathways. Such networks can be based on a variety of data sources, including 16S rRNA sequencing, metagenomic sequencing, and metabolomics data. Once constructed, these networks can be analyzed to identify key nodes or modules important for the stability and function of the microbiome. By providing insights into essential ecological features of microbial communities, microbiome networking analysis has the potential to transform our understanding of the microbial world and its impact on human health and the environment.
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Affiliation(s)
- Marco Fabbrini
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna 40138, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
- Authors contributed equally
| | - Daniel Scicchitano
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
- Authors contributed equally
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
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The soil bacterial community regulates germination of Plasmodiophora brassicae resting spores rather than root exudates. PLoS Pathog 2023; 19:e1011175. [PMID: 36862655 PMCID: PMC9980788 DOI: 10.1371/journal.ppat.1011175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 02/03/2023] [Indexed: 03/03/2023] Open
Abstract
Clubroot, caused by Plasmodiophora brassicae, is a severe soil-borne disease that restricts the production of cruciferous crops worldwide. A better understanding of biotic and abiotic factors regulating germination of P. brassicae resting spores in the soil is significant for developing novel control methods. Previous studies reported that root exudates can trigger P. brassicae resting spore germination, thus enabling a targeted attack of P. brassicae on host plant roots. However, we found that native root exudates collected under sterile conditions from host or non-host plants cannot stimulate the germination of sterile spores, indicating that root exudates may not be direct stimulation factors. Instead, our studies demonstrate that soil bacteria are essential for triggering germination. Through 16s rRNA amplicon sequencing analysis, we found that certain carbon sources and nitrate can reshape the initial microbial community to an inducing community leading to the germination of P. brassicae resting spores. The stimulating communities significantly differed in composition and abundance of bacterial taxa compared to the non-stimulating ones. Several enriched bacterial taxa in stimulating community were significantly correlated with spore germination rates and may be involved as stimulation factors. Based on our findings, a multi-factorial 'pathobiome' model comprising abiotic and biotic factors is proposed to represent the putative plant-microbiome-pathogen interactions associated with breaking spore dormancy of P. brassicae in soil. This study presents novel views on P. brassicae pathogenicity and lays the foundation for novel sustainable control strategies of clubroot.
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Chen D, Sun W, Xiang S, Zou S. High-Throughput Sequencing Analysis of the Composition and Diversity of the Bacterial Community in Cinnamomum camphora Soil. Microorganisms 2021; 10:microorganisms10010072. [PMID: 35056523 PMCID: PMC8778364 DOI: 10.3390/microorganisms10010072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/26/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
Soil bacterial communities and root-associated microbiomes play important roles in the nutrient absorption and healthy growth of host plants. Cinnamomum camphora is an important timber and special economic forest tree species in Fujian Province. In this study, the high-throughput sequencing technique was used to analyze the composition, diversity, and function of the bacterial communities present in the soil from different samples and slope positions of C. camphora. The results of this analysis demonstrated that the related bacterial communities in C. camphora soil were mainly clustered based on sample type. Bacterial alpha diversity in the rhizosphere and bulk soil of C. camphora growing downhill was higher than that of C. camphora growing uphill. At the phylum level, Bacteroidetes, Proteobacteria, Chloroflexi, and Gemmatimonadetes were positively correlated with pH, available phosphorus, total phosphorus, available potassium, and total potassium, while Acidobacteria and Verrucomicrobia were negatively correlated with alkaline-hydrolyzable nitrogen. These results show that there were remarkable differences in the composition, diversity, and function of related bacterial communities between different sample types of C. camphora soil. The slope position had a marked effect on the bacterial communities in the rhizosphere and bulk soil, while the root endosphere remained unaffected.
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Affiliation(s)
- Deqiang Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (D.C.); (W.S.); (S.X.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Colleage of Landscape Architecture, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weihong Sun
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (D.C.); (W.S.); (S.X.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Colleage of Landscape Architecture, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuang Xiang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (D.C.); (W.S.); (S.X.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Colleage of Landscape Architecture, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuangquan Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (D.C.); (W.S.); (S.X.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Colleage of Landscape Architecture, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence:
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6
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Wang J, Chai J, Zhang L, Zhang L, Yan W, Sun L, Chen Y, Sun Y, Zhao J, Chang C. Microbiota Associations with Inflammatory Pathways in Asthma. Clin Exp Allergy 2021; 52:697-705. [PMID: 34962671 DOI: 10.1111/cea.14089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/17/2021] [Accepted: 12/25/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND The airway microbiota plays an important role in asthma pathophysiology. However, the relationship between the airway microbiota and asthma phenotypes is still poorly understood. OBJECTIVE We aimed to characterize the airway microbiota in asthma patients and determine its correlation with airway inflammatory phenotypes and other phenotypic characteristics. METHODS The microbial composition of induced sputum specimens collected from asthma patients was determined using 16S rDNA gene sequencing. RESULTS Patients with asthma had a higher abundance of bacterial taxa associated with Bacteroidetes, Fusobacteria, and Proteobacteria and a reduced abundance of Firmicutes and Actinobacteria compared to healthy controls. This study classified the asthma-associated lung microbiota into three community types based on DMM models, which were defined as three pulmotypes (P1, P2, and P3). The lungs of patients with pulmotype 3 (P3) were dominated by Faecalibacterium and Bacteroides, while patients with pulmotype 1 (P1) had a greater abundance of Pasteurellaceae, Streptococcus, and Rothia. P1 patients were older (p = 0.045) and had lower blood TGF levels (P=0.028). P3 patients had fewer eosinophils (P=0.016) and more neutrophils (P=0.039) in induced sputa than P1 patients. CONCLUSIONS Differences in asthma-associated airway microbiota pulmotypes are associated with and might influence asthma, particularly inflammatory phenotypes.
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Affiliation(s)
- Juan Wang
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Jianmin Chai
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, USA
| | - Linlin Zhang
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Lijiao Zhang
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Wei Yan
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Lina Sun
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Yahong Chen
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Yongchang Sun
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, USA
| | - Chun Chang
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital, Beijing, China
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7
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Taviani E, Pedro O. Impact of the aquatic pathobiome in low-income and middle-income countries (LMICs) quest for safe water and sanitation practices. Curr Opin Biotechnol 2021; 73:220-224. [PMID: 34492621 DOI: 10.1016/j.copbio.2021.08.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/10/2021] [Accepted: 08/18/2021] [Indexed: 11/03/2022]
Abstract
Microbial contamination of surface waters is of particular relevance in low-income and middle-income countries (LMICs) since they often represent the only available source of water for drinking and domestic use. In the recent years, a growing urbanization, profound demographic shifts and drastic climate events have greatly affected LMICs capacity to reach access to safe drinking water and sanitation practices, and to protect citizens' health from risks associated to the exposure and use of contaminated water. Detailed phylogenetic and microbiological information on the exact composition of pathogenic organisms in urban and peri-urban water is scarce, especially in rapidly changing settings of sub-Saharan Africa. In this review we aim to highlight how large-scale water pathobiome studies can support the LMICs challenge to global access to safe water and sanitation practices.
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Affiliation(s)
- Elisa Taviani
- Center for Biotechnology, University Eduardo Mondlane, Maputo, Mozambique.
| | - Olivia Pedro
- Center for Biotechnology, University Eduardo Mondlane, Maputo, Mozambique
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8
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Fan D, Sun J, Liu C, Wang S, Han J, Agathokleous E, Zhu Y. Measurement and modeling of hormesis in soil bacteria and fungi under single and combined treatments of Cd and Pb. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 783:147494. [PMID: 34088122 DOI: 10.1016/j.scitotenv.2021.147494] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/28/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Heavy metals are considered major environmental pollutants. Soil microorganisms represent a predominant component of soils ecosystems, yet there is little information regarding hormetic responses of soil microorganisms to single and combined exposures to heavy metals. In the present study, to explore and predict the hormetic response of soil microorganisms, dose-response relationships of bacterial and fungal populations to single and combined treatments of cadmium (Cd) and lead (Pb) were evaluated. The results revealed hormetic responses of bacterial and fungal populations to both single and combined Cd and Pb treatments. The maximum stimulation (Mmax; relative to control treatment with no metals) of bacterial and fungal populations was 40% at 2 mg Cd/kg and 60% at 160 mg Pb/kg. An enhanced Mmax occurred in bacterial (50%) and fungal (75%) populations in the presence of the binary mixtures of 0.6 mg Cd/kg + 160 mg Pb/kg and 4.0 mg Cd/kg + 200 mg Pb/kg, suggesting positive additivity. This study showed that the hormetic effects of the mixtures were related to the independent effect of Cd and Pb, but they could not be predicted by the single effect of Cd or Pb. These new findings of the hormetic response of soil microorganisms to single treatments of Cd and Pb and their binary mixtures can facilitate the determination and minimization of ecological risks in heavy metal-polluted soils.
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Affiliation(s)
- Diwu Fan
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Jinwei Sun
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Chenglei Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Shengyan Wang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Jiangang Han
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China; Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Evgenios Agathokleous
- Key Laboratory of Agrometeorology of Jiangsu Province, School of Applied Meteorology, Nanjing University of Information Science & Technology (NUIST), Nanjing, Jiangsu 210044, China
| | - Yongli Zhu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China; Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China.
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9
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Plants under the Attack of Allies: Moving towards the Plant Pathobiome Paradigm. PLANTS 2021; 10:plants10010125. [PMID: 33435275 PMCID: PMC7827841 DOI: 10.3390/plants10010125] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/03/2021] [Accepted: 01/07/2021] [Indexed: 12/28/2022]
Abstract
Plants are functional macrobes living in a close association with diverse communities of microbes and viruses as complex systems that continuously interact with the surrounding environment. The microbiota within the plant holobiont serves various essential and beneficial roles, such as in plant growth at different stages, starting from seed germination. Meanwhile, pathogenic microbes—differentiated from the rest of the plant microbiome based on their ability to damage the plant tissues through transient blooming under specific conditions—are also a part of the plant microbiome. Recent advances in multi-omics have furthered our understanding of the structure and functions of plant-associated microbes, and a pathobiome paradigm has emerged as a set of organisms (i.e., complex eukaryotic, microbial, and viral communities) within the plant’s biotic environment which interact with the host to deteriorate its health status. Recent studies have demonstrated that the one pathogen–one disease hypothesis is insufficient to describe the disease process in many cases, particularly when complex organismic communities are involved. The present review discusses the plant holobiont and covers the steady transition of plant pathology from the one pathogen–one disease hypothesis to the pathobiome paradigm. Moreover, previous reports on model plant diseases, in which more than one pathogen or co-operative interaction amongst pathogenic microbes is implicated, are reviewed and discussed.
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10
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Stressmann FA, Bernal-Bayard J, Perez-Pascual D, Audrain B, Rendueles O, Briolat V, Bruchmann S, Volant S, Ghozlane A, Häussler S, Duchaud E, Levraud JP, Ghigo JM. Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection. ISME JOURNAL 2020; 15:702-719. [PMID: 33077888 DOI: 10.1038/s41396-020-00807-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 09/30/2020] [Accepted: 10/05/2020] [Indexed: 02/08/2023]
Abstract
The long-known resistance to pathogens provided by host-associated microbiota fostered the notion that adding protective bacteria could prevent or attenuate infection. However, the identification of endogenous or exogenous bacteria conferring such protection is often hindered by the complexity of host microbial communities. Here, we used zebrafish and the fish pathogen Flavobacterium columnare as a model system to study the determinants of microbiota-associated colonization resistance. We compared infection susceptibility in germ-free, conventional and reconventionalized larvae and showed that a consortium of 10 culturable bacterial species are sufficient to protect zebrafish. Whereas survival to F. columnare infection does not rely on host innate immunity, we used antibiotic dysbiosis to alter zebrafish microbiota composition, leading to the identification of two different protection strategies. We first identified that the bacterium Chryseobacterium massiliae individually protects both larvae and adult zebrafish. We also showed that an assembly of 9 endogenous zebrafish species that do not otherwise protect individually confer a community-level resistance to infection. Our study therefore provides a rational approach to identify key endogenous protecting bacteria and promising candidates to engineer resilient microbial communities. It also shows how direct experimental analysis of colonization resistance in low-complexity in vivo models can reveal unsuspected ecological strategies at play in microbiota-based protection against pathogens.
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Affiliation(s)
- Franziska A Stressmann
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France.,Department of Chemical Analytics and Biogeochemistry, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany
| | - Joaquín Bernal-Bayard
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Apartado 1095, 41080, Sevilla, Spain
| | - David Perez-Pascual
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France
| | - Bianca Audrain
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France
| | - Olaya Rendueles
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France.,Microbial Evolutionary Genomics Laboratory, Institut Pasteur, UMR3525, 75015, Paris, France
| | - Valérie Briolat
- Macrophages and Development of Immunity Laboratory, Institut Pasteur, UMR3738 CNRS, 75015, Paris, France
| | - Sebastian Bruchmann
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - Stevenn Volant
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Amine Ghozlane
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Department of Clinical Microbiology, Rigshospitalet, 2100, Copenhagen, Denmark
| | - Eric Duchaud
- Unité VIM, INRAE, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Jean-Pierre Levraud
- Macrophages and Development of Immunity Laboratory, Institut Pasteur, UMR3738 CNRS, 75015, Paris, France
| | - Jean-Marc Ghigo
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France.
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Abstract
This article explores how to prevent and manage complications of dentoalveolar surgery. Many complications are avoidable. Surgical skills and knowledge of anatomy play an important role in prevention of complications. Prevention starts with detailed history and physical examination of the patient. Key to perioperative management of patients is risk assessment. Without a proper history and physical examination, the clinician is unable to assess the risk of performing surgery and anesthesia for each patient. Some illnesses and medications increase the risk of complications. The following complications are discussed: alveolar osteitis, displacement, fracture, hemorrhage, infection, nonhealing wound, oroantral communication, swelling, and trismus.
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Affiliation(s)
- Patrick J Louis
- Department of Oral and Maxillofacial Surgery, University of Alabama at Birmingham, 1919 7th Avenue South, SDB 419, Birmingham, AL 35294, USA.
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12
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Menetrey Q, Dupont C, Chiron R, Jumas-Bilak E, Marchandin H. High Occurrence of Bacterial Competition Among Clinically Documented Opportunistic Pathogens Including Achromobacter xylosoxidans in Cystic Fibrosis. Front Microbiol 2020; 11:558160. [PMID: 33013789 PMCID: PMC7513574 DOI: 10.3389/fmicb.2020.558160] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/14/2020] [Indexed: 12/12/2022] Open
Abstract
Cystic Fibrosis (CF) airways favor abnormal microbial development. Infections are considered as polymicrobial and competition can be observed between microorganisms. The current literature on bacterial competition in CF mostly consists of studies with limited numbers of strains, mainly focused on the major pathogens Pseudomonas aeruginosa (Pa) and Staphylococcus aureus (Sa) and does not give a comprehensive overview of the overall importance of bacterial interactions or the behavior of less often encountered emerging bacteria such as Achromobacter. In this context, we screened a panel of 39 strains from six CF patients, of either clinical or domestic environmental origin, distinguished according to genotype and belonging to four opportunistic pathogens, Pa (n = 15), Sa (n = 3), Stenotrophomonas maltophilia (Sm, n = 10) and Achromobacter xylosoxidans (Ax, n = 11). We investigated their capacity to compete in terms of growth, motility, and pigment production on agar media through 203 crossing experiments. Eleven strains selected via the initial screening results were further studied for competitive growth in liquid medium and biofilm formation. Competition was noted for 33% (67/203) of the pairs of strains with 85 modifications observed between monocultures and co-cultures, impacting growth (23.6%), motility (13.8%), and/or pigment production (6.1%). Under all conditions of the study (clinical, environmental strains; intra-, inter-patients; intra-, inter-species levels), competition was significantly more frequent among pairs of strains with at least one clinical strain. While Pa mainly outcompeted other species, in one patient with chronic colonization by Ax and sporadic colonization by Pa, we showed that some Ax inhibited the growth and pigmentation of Pa whereas biofilm formation was drastically reduced. Enlarging the panel of strains tested in competition assays gave new perspectives on the complex interactions taking place among the CF airway community. Indeed, the frequent occurrence of varied, strain-dependent interactions is revealed here. We report the first results of competition assays for Ax with the ability of certain strains to outcompete Pa. Our results are linked to the patient’s colonization history and question the importance of bacterial competitiveness in the colonization pattern of CF airways.
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Affiliation(s)
- Quentin Menetrey
- HydroSciences Montpellier, Univ Montpellier, CNRS, IRD, Montpellier, France
| | - Chloé Dupont
- HydroSciences Montpellier, Univ Montpellier, CNRS, IRD, Montpellier, France.,HydroSciences Montpellier, Univ Montpellier, CNRS, IRD, Laboratoire d'Ecologie Microbienne Hospitalière, CHU Montpellier, Montpellier, France
| | - Raphaël Chiron
- HydroSciences Montpellier, Univ Montpellier, CNRS, IRD, Montpellier, France.,HydroSciences Montpellier, Univ Montpellier, CNRS, IRD, Centre de Ressources et de Compétences de la Mucoviscidose, CHU Montpellier, Montpellier, France
| | - Estelle Jumas-Bilak
- HydroSciences Montpellier, Univ Montpellier, CNRS, IRD, Montpellier, France.,HydroSciences Montpellier, Univ Montpellier, CNRS, IRD, Laboratoire d'Ecologie Microbienne Hospitalière, CHU Montpellier, Montpellier, France
| | - Hélène Marchandin
- HydroSciences Montpellier, Univ Montpellier, CNRS, IRD, Montpellier, France.,HydroSciences Montpellier, Univ Montpellier, CNRS, IRD, Département de Microbiologie, CHU Nîmes, Nîmes, France
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13
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Strain Background, Species Frequency, and Environmental Conditions Are Important in Determining Pseudomonas aeruginosa and Staphylococcus aureus Population Dynamics and Species Coexistence. Appl Environ Microbiol 2020; 86:AEM.00962-20. [PMID: 32651205 DOI: 10.1128/aem.00962-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/04/2020] [Indexed: 01/09/2023] Open
Abstract
Bacterial communities in the environment and in infections are typically diverse, yet we know little about the factors that determine interspecies interactions. Here, we apply concepts from ecological theory to understand how biotic and abiotic factors affect interaction patterns between the two opportunistic human pathogens Pseudomonas aeruginosa and Staphylococcus aureus, which often cooccur in polymicrobial infections. Specifically, we conducted a series of short- and long-term competition experiments between P. aeruginosa PAO1 (as our reference strain) and three different S. aureus strains (Cowan I, 6850, and JE2) at three starting frequencies and under three environmental (culturing) conditions. We found that the competitive ability of P. aeruginosa strongly depended on the strain background of S. aureus, whereby P. aeruginosa dominated against Cowan I and 6850 but not against JE2. In the latter case, both species could end up as winners depending on conditions. Specifically, we observed strong frequency-dependent fitness patterns, including positive frequency dependence, where P. aeruginosa could dominate JE2 only when common (not when rare). Finally, changes in environmental (culturing) conditions fundamentally altered the competitive balance between the two species in a way that P. aeruginosa dominance increased when moving from shaken to static environments. Altogether, our results highlight that ecological details can have profound effects on the competitive dynamics between coinfecting pathogens and determine whether two species can coexist or invade each others' populations from a state of rare frequency. Moreover, our findings might parallel certain dynamics observed in chronic polymicrobial infections.IMPORTANCE Bacterial infections are frequently caused by more than one species, and such polymicrobial infections are often considered more virulent and more difficult to treat than the respective monospecies infections. Pseudomonas aeruginosa and Staphylococcus aureus are among the most important pathogens in polymicrobial infections, and their cooccurrence is linked to worse disease outcome. There is great interest in understanding how these two species interact and what the consequences for the host are. While previous studies have mainly looked at molecular mechanisms implicated in interactions between P. aeruginosa and S. aureus, here we show that ecological factors, such as strain background, species frequency, and environmental conditions, are important elements determining population dynamics and species coexistence patterns. We propose that the uncovered principles also play major roles in infections and, therefore, proclaim that an integrative approach combining molecular and ecological aspects is required to fully understand polymicrobial infections.
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14
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Wen Z, Yan C, Duan G, Li S, Wu FX, Wang J. A survey on predicting microbe-disease associations: biological data and computational methods. Brief Bioinform 2020; 22:5881365. [PMID: 34020541 DOI: 10.1093/bib/bbaa157] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 02/06/2023] Open
Abstract
Various microbes have proved to be closely related to the pathogenesis of human diseases. While many computational methods for predicting human microbe-disease associations (MDAs) have been developed, few systematic reviews on these methods have been reported. In this study, we provide a comprehensive overview of the existing methods. Firstly, we introduce the data used in existing MDA prediction methods. Secondly, we classify those methods into different categories by their nature and describe their algorithms and strategies in detail. Next, experimental evaluations are conducted on representative methods using different similarity data and calculation methods to compare their prediction performances. Based on the principles of computational methods and experimental results, we discuss the advantages and disadvantages of those methods and propose suggestions for the improvement of prediction performances. Considering the problems of the MDA prediction at present stage, we discuss future work from three perspectives including data, methods and formulations at the end.
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Affiliation(s)
- Zhongqi Wen
- Hunan Provincial Key Lab of Bioinformatics, School of Computer Science and Engineering at Central South University, Hunan, China
| | - Cheng Yan
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
| | - Guihua Duan
- School of Computer Science and Engineering, Central South University
| | - Suning Li
- Hunan Provincial Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
| | - Fang-Xiang Wu
- College of Engineering and the Department of Computer Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Jianxin Wang
- Hunan Provincial Key Lab of Bioinformatics, School of Computer Science and Engineering at Central South University, Hunan, China
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15
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Lu J, Zhang X, Qiu Q, Chen J, Xiong J. Identifying Potential Polymicrobial Pathogens: Moving Beyond Differential Abundance to Driver Taxa. MICROBIAL ECOLOGY 2020; 80:447-458. [PMID: 32307553 DOI: 10.1007/s00248-020-01511-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
It is now recognized that some diseases of aquatic animals are attributed to polymicrobial pathogens infection. Thus, the traditional view of "one pathogen, one disease" might mislead the identification of multiple pathogens, which in turn impedes the design of probiotics. To address this gap, we explored polymicrobial pathogens based on the origin and timing of increased abundance over shrimp white feces syndrome (WFS) progression. OTU70848 Vibrio fluvialis, OTU35090 V. coralliilyticus, and OTU28721 V. tubiashii were identified as the primary colonizers, whose abundances increased only in individuals that eventually showed disease signs but were stable in healthy subjects over the same timeframe. Notably, the random Forest model revealed that the profiles of the three primary colonizers contributed an overall 91.4% of diagnosing accuracy of shrimp health status. Additionally, NetShift analysis quantified that the three primary colonizers were important "drivers" in the gut microbiotas from healthy to WFS shrimp. For these reasons, the primary colonizers were potential pathogens that contributed to the exacerbation of WFS. By this logic, we further identified a few "drivers" commensals in healthy individuals, such as OUT50531 Demequina sediminicola and OTU_74495 Ruegeria lacuscaerulensis, which directly antagonized the three primary colonizers. The predicted functional pathways involved in energy metabolism, genetic information processing, terpenoids and polyketides metabolism, lipid and amino acid metabolism significantly decreased in diseased shrimp compared with those in healthy cohorts, in concordant with the knowledge that the attenuations of these functional pathways increase shrimp sensitivity to pathogen infection. Collectively, we provide an ecological framework for inferring polymicrobial pathogens and designing antagonized probiotics by quantifying their changed "driver" feature that intimately links shrimp WFS progression. This approach might generalize to the exploring disease etiology for other aquatic animals.
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Affiliation(s)
- Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Xuechen Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Qiongfen Qiu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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16
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Schippa S, Frassanito A, Marazzato M, Nenna R, Petrarca L, Neroni B, Bonfiglio G, Guerrieri F, Frasca F, Oliveto G, Pierangeli A, Midulla F. Nasal Microbiota in RSV Bronchiolitis. Microorganisms 2020; 8:microorganisms8050731. [PMID: 32414211 PMCID: PMC7284514 DOI: 10.3390/microorganisms8050731] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 12/26/2022] Open
Abstract
Respiratory Syncytial Virus (RSV) is the leading cause of bronchiolitis, and the severity may be influenced by the bacterial ecosystem. Our aim was to analyze the nasal microbiota from 48 infants affected by bronchiolitis from RSV virus and 28 infants with bronchiolitis but negative for the virus. Results showed a significantly lower biodiversity in the RSV-positive group with respect to the RSV-negative group, a specific microbial profile associated with the RSV-positive group different from that observed in the negative group, and significant modifications in the relative abundance of taxa in the RSV-positive group, as well as in the RSV-A group, with respect to the negative group. Furthermore, microbial network analyses evidenced, in all studied groups, the presence of two predominant sub-networks characterized by peculiar inter- and intra-group correlation patterns as well as a general loss of connectivity among microbes in the RSV-positive group, particularly in the RSV-A group. Our results indicated that infants with more severe bronchiolitis disease, caused by RSV-A infection, present significant perturbations of both the nasal microbiota structure and the microbial relationships. Patients with a milder bronchiolitis course (RSV-B-infected and patients who have cleared the virus) presented less severe alterations.
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Affiliation(s)
- Serena Schippa
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (M.M.); (B.N.); (G.B.)
- Correspondence: (S.S.); (A.F.); (A.P.); (F.M.)
| | - Antonella Frassanito
- Department of Maternal, Infantile and Urological Sciences, “Sapienza” University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (R.N.); (L.P.)
- Correspondence: (S.S.); (A.F.); (A.P.); (F.M.)
| | - Massimiliano Marazzato
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (M.M.); (B.N.); (G.B.)
| | - Raffaella Nenna
- Department of Maternal, Infantile and Urological Sciences, “Sapienza” University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (R.N.); (L.P.)
| | - Laura Petrarca
- Department of Maternal, Infantile and Urological Sciences, “Sapienza” University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (R.N.); (L.P.)
| | - Bruna Neroni
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (M.M.); (B.N.); (G.B.)
| | - Giulia Bonfiglio
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (M.M.); (B.N.); (G.B.)
| | - Francesca Guerrieri
- Cancer Research Center of Lyon (CRCL), UMR Inserm U1052/CNRS 5286, 69008 Lyon, France;
| | - Federica Frasca
- Virology Laboratory, Department of Molecular Medicine, “Sapienza” University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (F.F.); (G.O.)
| | - Giuseppe Oliveto
- Virology Laboratory, Department of Molecular Medicine, “Sapienza” University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (F.F.); (G.O.)
| | - Alessandra Pierangeli
- Virology Laboratory, Department of Molecular Medicine, “Sapienza” University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (F.F.); (G.O.)
- Correspondence: (S.S.); (A.F.); (A.P.); (F.M.)
| | - Fabio Midulla
- Department of Maternal, Infantile and Urological Sciences, “Sapienza” University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (R.N.); (L.P.)
- Correspondence: (S.S.); (A.F.); (A.P.); (F.M.)
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17
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Cuthbertson L, Walker AW, Oliver AE, Rogers GB, Rivett DW, Hampton TH, Ashare A, Elborn JS, De Soyza A, Carroll MP, Hoffman LR, Lanyon C, Moskowitz SM, O’Toole GA, Parkhill J, Planet PJ, Teneback CC, Tunney MM, Zuckerman JB, Bruce KD, van der Gast CJ. Lung function and microbiota diversity in cystic fibrosis. MICROBIOME 2020; 8:45. [PMID: 32238195 PMCID: PMC7114784 DOI: 10.1186/s40168-020-00810-3] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/20/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Chronic infection and concomitant airway inflammation is the leading cause of morbidity and mortality for people living with cystic fibrosis (CF). Although chronic infection in CF is undeniably polymicrobial, involving a lung microbiota, infection surveillance and control approaches remain underpinned by classical aerobic culture-based microbiology. How to use microbiomics to direct clinical management of CF airway infections remains a crucial challenge. A pivotal step towards leveraging microbiome approaches in CF clinical care is to understand the ecology of the CF lung microbiome and identify ecological patterns of CF microbiota across a wide spectrum of lung disease. Assessing sputum samples from 299 patients attending 13 CF centres in Europe and the USA, we determined whether the emerging relationship of decreasing microbiota diversity with worsening lung function could be considered a generalised pattern of CF lung microbiota and explored its potential as an informative indicator of lung disease state in CF. RESULTS We tested and found decreasing microbiota diversity with a reduction in lung function to be a significant ecological pattern. Moreover, the loss of diversity was accompanied by an increase in microbiota dominance. Subsequently, we stratified patients into lung disease categories of increasing disease severity to further investigate relationships between microbiota characteristics and lung function, and the factors contributing to microbiota variance. Core taxa group composition became highly conserved within the severe disease category, while the rarer satellite taxa underpinned the high variability observed in the microbiota diversity. Further, the lung microbiota of individual patient were increasingly dominated by recognised CF pathogens as lung function decreased. Conversely, other bacteria, especially obligate anaerobes, increasingly dominated in those with better lung function. Ordination analyses revealed lung function and antibiotics to be main explanators of compositional variance in the microbiota and the core and satellite taxa. Biogeography was found to influence acquisition of the rarer satellite taxa. CONCLUSIONS Our findings demonstrate that microbiota diversity and dominance, as well as the identity of the dominant bacterial species, in combination with measures of lung function, can be used as informative indicators of disease state in CF. Video Abstract.
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Affiliation(s)
- Leah Cuthbertson
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Alan W. Walker
- Rowett Institute, University of Aberdeen, Aberdeen, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | - Geraint B. Rogers
- South Australian Health and Medical Research Institute, Adelaide, Australia
- School of Medicine, Flinders University, Adelaide, Australia
| | - Damian W. Rivett
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK
| | - Thomas H. Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Alix Ashare
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Department of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH USA
| | - J. Stuart Elborn
- National Heart and Lung Institute, Imperial College London, London, UK
- Adult Cystic Fibrosis Department, Royal Brompton Hospital, London, UK
- School of Medicine, Dentistry and Biomedical Sciences, Institute for Health Sciences, Queen’s University Belfast, Belfast, UK
| | - Anthony De Soyza
- Institute of Cellular Medicine, NIHR Biomedical Research Centre for Ageing, Newcastle University, Newcastle, UK
- Department of Respiratory Medicine, Freeman Hospital, Newcastle, UK
| | - Mary P. Carroll
- Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Southampton, UK
| | - Lucas R. Hoffman
- Seattle Children’s Hospital, Seattle, WA USA
- Departments of Pediatrics and Microbiology, University of Washington, Seattle, WA USA
| | - Clare Lanyon
- Faculty of Health and Life Sciences, University of Northumbria, Newcastle, UK
| | - Samuel M. Moskowitz
- Department of Pediatrics, Massachusetts General Hospital and Harvard Medical School, Boston, USA
- Vertex Pharmaceuticals, Boston, MA USA
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Julian Parkhill
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Paul J. Planet
- Pediatric Infectious Disease Division, Children’s Hospital of Philadelphia, Philadelphia, PA USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY USA
| | | | | | - Jonathan B. Zuckerman
- Maine Medical Center, Portland, ME USA
- School of Medicine, Tufts University, Boston, MA USA
| | - Kenneth D. Bruce
- Institute of Pharmaceutical Science, King’s College London, London, UK
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18
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Soret P, Vandenborght LE, Francis F, Coron N, Enaud R, Avalos M, Schaeverbeke T, Berger P, Fayon M, Thiebaut R, Delhaes L. Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis. Sci Rep 2020; 10:3589. [PMID: 32108159 PMCID: PMC7046743 DOI: 10.1038/s41598-020-60015-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022] Open
Abstract
Lung infections play a critical role in cystic fibrosis (CF) pathogenesis. CF respiratory tract is now considered to be a polymicrobial niche and advances in high-throughput sequencing allowed to analyze its microbiota and mycobiota. However, no NGS studies until now have characterized both communities during CF pulmonary exacerbation (CFPE). Thirty-three sputa isolated from patients with and without CFPE were used for metagenomic high-throughput sequencing targeting 16S and ITS2 regions of bacterial and fungal rRNA. We built inter-kingdom network and adapted Phy-Lasso method to highlight correlations in compositional data. The decline in respiratory function was associated with a decrease in bacterial diversity. The inter-kingdom network revealed three main clusters organized around Aspergillus, Candida, and Scedosporium genera. Using Phy-Lasso method, we identified Aspergillus and Malassezia as relevantly associated with CFPE, and Scedosporium plus Pseudomonas with a decline in lung function. We corroborated in vitro the cross-domain interactions between Aspergillus and Streptococcus predicted by the correlation network. For the first time, we included documented mycobiome data into a version of the ecological Climax/Attack model that opens new lines of thoughts about the physiopathology of CF lung disease and future perspectives to improve its therapeutic management.
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Affiliation(s)
- Perrine Soret
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, F-33000, Bordeaux, France
- INRIA SISTM Team, F-33405, Talence, France
| | - Louise-Eva Vandenborght
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- Genoscreen Society, 59000, Lille, France
| | - Florence Francis
- CHU Bordeaux, Department of Public Health, F-33000, Bordeaux, France
| | - Noémie Coron
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
- CHU de Bordeaux: Laboratoire de Parasitologie-Mycologie, Univ. Bordeaux, F-33000, Bordeaux, France
| | - Raphael Enaud
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
- CHU de Bordeaux, CRCM Pédiatrique, CIC, 1401, Bordeaux, France
| | - Marta Avalos
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, F-33000, Bordeaux, France
- INRIA SISTM Team, F-33405, Talence, France
| | | | - Patrick Berger
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
| | - Michael Fayon
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
- CHU de Bordeaux, CRCM Pédiatrique, CIC, 1401, Bordeaux, France
| | - Rodolphe Thiebaut
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, F-33000, Bordeaux, France
- INRIA SISTM Team, F-33405, Talence, France
- CHU Bordeaux, Department of Public Health, F-33000, Bordeaux, France
| | - Laurence Delhaes
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France.
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France.
- CHU de Bordeaux: Laboratoire de Parasitologie-Mycologie, Univ. Bordeaux, F-33000, Bordeaux, France.
- CHU de Bordeaux, CRCM Pédiatrique, CIC, 1401, Bordeaux, France.
- University and CHU of Lille, F-59000, Lille, France.
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19
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Son JH, Kim JH, Chang HS, Park JS, Park CS. Relationship of Microbial Profile With Airway Immune Response in Eosinophilic or Neutrophilic Inflammation of Asthmatics. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2020; 12:412-429. [PMID: 32141256 PMCID: PMC7061157 DOI: 10.4168/aair.2020.12.3.412] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/12/2019] [Accepted: 12/07/2019] [Indexed: 01/24/2023]
Abstract
PURPOSE Different characteristics of airway microbiome in asthmatics may lead to differential immune responses, which in turn cause eosinophilic or neutrophilic airway inflammation. However, the relationships among these factors have yet to be fully elucidated. METHODS Microbes in induced sputum samples were subjected to sequence analysis of 16S rRNA. Airway inflammatory phenotypes were defined as neutrophils (>60%) and eosinophils (>3%), and inflammation endotypes were defined by levels of T helper (Th) 1 (interferon-γ), Th2 (interleukin [IL]-5 and IL-13), Th-17 (IL-17), and innate Th2 (IL-25, IL-33, and thymic stromal lymphopoietin) cytokines, inflammasomes (IL-1β), epithelial activation markers (granulocyte-macrophage colony-stimulating factor and IL-8), and Inflammation (IL-6 and tumor necrosis factor-α) cytokines in sputum supernatants was assessed by enzyme-linked immunosorbent assay. RESULTS The numbers of operational taxonomic units were significantly higher in the mixed (n = 21) and neutrophilic (n = 23) inflammation groups than in the paucigranulocytic inflammation group (n = 19; p < 0.05). At the species level, Granulicatella adiacens, Streptococcus parasanguinis, Streptococcus pneumoniae, Veillonella rogosae, Haemophilus parainfluenzae, and Neisseria perflava levels were significantly higher in the eosinophilic inflammation group (n = 20), whereas JYGU_s levels were significantly higher in the neutrophilic inflammation group compared to the other subtypes (p < 0.05). Additionally, IL-5 and IL-13 concentrations were correlated with the percentage of eosinophils (p < 0.05) and IL-13 levels were positively correlated with the read counts of Porphyromonas pasteri and V. rogosae (p < 0.05). IL-1β concentrations were correlated with the percentage of neutrophils (p < 0.05). had a tendency to be positively correlated with the read count of JYGU_s (p = 0.095), and was negatively correlated with that of S. pneumoniae (p < 0.05). CONCLUSIONS Difference of microbial patterns in airways may induce distinctive endotypes of asthma, which is responsible for the neutrophilic or eosinophilic inflammation in asthma.
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Affiliation(s)
- Ji Hye Son
- Department of Interdisciplinary Program in Biomedical Science Major, Graduate School, Soonchunhyang University, Asan, Korea
| | - Jung Hyun Kim
- Department of Internal Medicine, Korean Armed Forces Capital Hospital, Seongnam, Korea
| | - Hun Soo Chang
- Department of Interdisciplinary Program in Biomedical Science Major, Graduate School, Soonchunhyang University, Asan, Korea.
| | - Jong Sook Park
- Genome Research Center and Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea.
| | - Choon Sik Park
- Genome Research Center and Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
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20
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Amati F, Simonetta E, Gramegna A, Tarsia P, Contarini M, Blasi F, Aliberti S. The biology of pulmonary exacerbations in bronchiectasis. Eur Respir Rev 2019; 28:28/154/190055. [PMID: 31748420 DOI: 10.1183/16000617.0055-2019] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 06/11/2019] [Indexed: 12/21/2022] Open
Abstract
Bronchiectasis is a heterogeneous chronic disease. Heterogeneity characterises bronchiectasis not only in the stable state but also during exacerbations, despite evidence on clinical and biological aspects of bronchiectasis, exacerbations still remain poorly understood.Although the scientific community recognises that bacterial infection is a cornerstone in the development of bronchiectasis, there is a lack of data regarding other trigger factors for exacerbations. In addition, a huge amount of data suggest a primary role of neutrophils in the stable state and exacerbation of bronchiectasis, but the inflammatory reaction involves many other additional pathways. Cole's vicious cycle hypothesis illustrates how airway dysfunction, airway inflammation, infection and structural damage are linked. The introduction of the concept of a "vicious vortex" stresses the complexity of the relationships between the components of the cycle. In this model of disease, exacerbations work as a catalyst, accelerating the progression of disease. The roles of microbiology and inflammation need to be considered as closely linked and will need to be investigated in different ways to collect samples. Clinical and translational research is of paramount importance to achieve a better comprehension of the pathophysiology of bronchiectasis, microbiology and inflammation both in the stable state and during exacerbations.
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Affiliation(s)
- Francesco Amati
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Edoardo Simonetta
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Andrea Gramegna
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Paolo Tarsia
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Martina Contarini
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesco Blasi
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Aliberti
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy .,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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21
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Rogers GB, Taylor SL, Hoffman LR, Burr LD. The impact of CFTR modulator therapies on CF airway microbiology. J Cyst Fibros 2019; 19:359-364. [PMID: 31416774 DOI: 10.1016/j.jcf.2019.07.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/12/2022]
Abstract
Major historical advances in cystic fibrosis (CF) respiratory clinical care, including mechanical airway clearance and inhaled medications, have aimed to address the consequences of cystic fibrosis transmembrane conductance regulator (CFTR) dysfunction. In contrast, CFTR modulator therapies instead target the underlying protein defect that leads to CF lung disease. The extent to which these therapies might reduce susceptibility to chronic lung infections remains to be seen. However, by improving airway clearance, reducing the requirement for antibiotics, and in some cases, through direct antimicrobial effects, CFTR modulators are likely to result in substantial changes in CF airway microbiology. These changes could contribute substantially to the clinical benefit associated with modulator therapies, as well as providing an important indicator of treatment efficacy and residual pathophysiology. Indeed, the widespread introduction of modulator therapies might require us to re-consider our models of CF airway microbiology.
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Affiliation(s)
- Geraint B Rogers
- Infection and Immunity Theme, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia; SAHMRI Microbiome Research Laboratory, Flinders University School of Medicine, Adelaide, SA, Australia.
| | - Steven L Taylor
- Infection and Immunity Theme, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia; SAHMRI Microbiome Research Laboratory, Flinders University School of Medicine, Adelaide, SA, Australia
| | - Lucas R Hoffman
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, USA; Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Lucy D Burr
- Department of Respiratory Medicine, Mater Health Services, South Brisbane, QLD, Australia; Mater Research - University of Queensland, Aubigny Place, South Brisbane, QLD, Australia
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22
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Yu W, Wu JH, Zhang J, Yang W, Chen J, Xiong J. A meta-analysis reveals universal gut bacterial signatures for diagnosing the incidence of shrimp disease. FEMS Microbiol Ecol 2019; 94:5066164. [PMID: 30124839 DOI: 10.1093/femsec/fiy147] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 08/01/2018] [Indexed: 12/21/2022] Open
Abstract
Increasing evidence indicates that dysbiosis in the gut microbiota contributes to disease pathogenesis. However, whether certain taxa are universally indicative of diverse shrimp diseases is unclear thus far. We conducted a meta-analysis to explore the divergences in gut microbiota between healthy and diseased shrimp. The gut bacterial communities of healthy shrimp varied significantly (P < 0.05 in each comparison) over ontogenetic stages, and were distinct from the corresponding diseased cohorts at each life stage. Both phylogenetic-based mean nearest taxon distance analysis and multivariate dispersion testing revealed that shrimp disease weakened the relative importance of deterministic processes in governing the gut microbiota. Partitioning beta diversity analysis indicated that temporal turnover governed the gut microbiota as healthy shrimp aged, whereas this trend was retarded in disease cohorts, concurrent with an increased nestedness. After ruling out the age-discriminatory and disease-specific orders, a high diagnosed accuracy (85.9%) of shrimp health status was achieved by using the profiles of the 11 universal disease-discriminatory orders as independent variables. These findings improve current understanding of how disease alters the ecological processes that govern the shrimp gut microbiota assembly, and exemplifies the potential application of universal bacterial signatures to diagnose the incidence of diverse shrimp diseases, irrespective of causal pathogens.
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Affiliation(s)
- Weina Yu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, 315211, China
| | - Jer-Horng Wu
- Department of Environmental Engineering, National Cheng Kung University, Tainan, 70101, Taiwan (ROC)
| | - Jinjie Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Wen Yang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiong Chen
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, 315211, China
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23
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Hanada S, Pirzadeh M, Carver KY, Deng JC. Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia. Front Immunol 2018; 9:2640. [PMID: 30505304 PMCID: PMC6250824 DOI: 10.3389/fimmu.2018.02640] [Citation(s) in RCA: 293] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 10/26/2018] [Indexed: 12/18/2022] Open
Abstract
Influenza and other respiratory viral infections are the most common type of acute respiratory infection. Viral infections predispose patients to secondary bacterial infections, which often have a more severe clinical course. The mechanisms underlying post-viral bacterial infections are complex, and include multifactorial processes mediated by interactions between viruses, bacteria, and the host immune system. Studies over the past 15 years have demonstrated that unique microbial communities reside on the mucosal surfaces of the gastrointestinal tract and the respiratory tract, which have both direct and indirect effects on host defense against viral infections. In addition, antiviral immune responses induced by acute respiratory infections such as influenza are associated with changes in microbial composition and function (“dysbiosis”) in the respiratory and gastrointestinal tract, which in turn may alter subsequent immune function against secondary bacterial infection or alter the dynamics of inter-microbial interactions, thereby enhancing the proliferation of potentially pathogenic bacterial species. In this review, we summarize the literature on the interactions between host microbial communities and host defense, and how influenza, and other acute respiratory viral infections disrupt these interactions, thereby contributing to the pathogenesis of secondary bacterial infections.
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Affiliation(s)
- Shigeo Hanada
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, United States.,Toranomon Hospital, Tokyo, Japan
| | - Mina Pirzadeh
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, United States.,Veterans Affairs Healthcare System, Ann Arbor, MI, United States
| | - Kyle Y Carver
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, United States.,Veterans Affairs Healthcare System, Ann Arbor, MI, United States
| | - Jane C Deng
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, United States.,Veterans Affairs Healthcare System, Ann Arbor, MI, United States
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24
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Taylor SL, O'Farrell HE, Simpson JL, Yang IA, Rogers GB. The contribution of respiratory microbiome analysis to a treatable traits model of care. Respirology 2018; 24:19-28. [PMID: 30282116 DOI: 10.1111/resp.13411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/13/2018] [Accepted: 09/09/2018] [Indexed: 12/15/2022]
Abstract
The composition of the airway microbiome in patients with chronic airway diseases, such as severe asthma, chronic obstructive pulmonary disease (COPD), bronchiectasis and cystic fibrosis (CF), has the potential to inform a precision model of clinical care. Patients with these conditions share overlapping disease characteristics, including airway inflammation and airflow limitation. The clinical management of chronic respiratory conditions is increasingly moving away from a one-size-fits-all model based on primary diagnosis, towards care targeting individual disease traits, and is particularly useful for subgroups of patients who respond poorly to conventional therapies. Respiratory microbiome analysis is an important potential contributor to such a 'treatable traits' approach, providing insight into both microbial drivers of airways disease, and the selective characteristics of the changing lower airway environment. We explore the potential to integrate respiratory microbiome analysis into a treatable traits model of clinical care and provide a practical guide to the application and clinical interpretation of respiratory microbiome analysis.
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Affiliation(s)
- Steven L Taylor
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,SAHMRI Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Hannah E O'Farrell
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Jodie L Simpson
- Respiratory and Sleep Medicine, Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, NSW, Australia
| | - Ian A Yang
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Geraint B Rogers
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,SAHMRI Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
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25
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Quantitative assessment of individual populations within polymicrobial biofilms. Sci Rep 2018; 8:9494. [PMID: 29934504 PMCID: PMC6015014 DOI: 10.1038/s41598-018-27497-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/24/2018] [Indexed: 02/06/2023] Open
Abstract
Selecting appropriate tools providing reliable quantitative measures of individual populations in biofilms is critical as we now recognize their true polymicrobial and heterogeneous nature. Here, plate count, quantitative real-time polymerase chain reaction (q-PCR) and peptide nucleic acid probe-fluorescence in situ hybridization (PNA-FISH) were employed to quantitate cystic fibrosis multispecies biofilms. Growth of Pseudomonas aeruginosa, Inquilinus limosus and Dolosigranulum pigrum was assessed in dual- and triple-species consortia under oxygen and antibiotic stress. Quantification methods, that were previously optimized and validated in planktonic consortia, were not always in agreement when applied in multispecies biofilms. Discrepancies in culture and molecular outcomes were observed, particularly for triple-species consortia and antibiotic-stressed biofilms. Some differences were observed, such as the higher bacterial counts obtained by q-PCR and/or PNA-FISH (≤4 log10 cells/cm2) compared to culture. But the discrepancies between PNA-FISH and q-PCR data (eg D. pigrum limited assessment by q-PCR) demonstrate the effect of biofilm heterogeneity in method’s reliability. As the heterogeneity in biofilms is a reflection of a myriad of variables, tailoring an accurate picture of communities´ changes is crucial. This work demonstrates that at least two, but preferentially three, quantification techniques are required to obtain reliable measures and take comprehensive analysis of polymicrobial biofilm-associated infections.
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26
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Microbiota Composition in Upper Respiratory Tracts of Healthy Children in Shenzhen, China, Differed with Respiratory Sites and Ages. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6515670. [PMID: 30013985 PMCID: PMC6022278 DOI: 10.1155/2018/6515670] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 05/07/2018] [Accepted: 05/24/2018] [Indexed: 12/20/2022]
Abstract
The upper respiratory tract (URT) is home to various microbial commensals, which function as competitors to pathogens and help train the immune system. However, few studies have reported the normal microbiota carriage in the URT of healthy Chinese children. In this study, we performed a 16S rDNA gene sequencing analysis of 83 anterior nares (ANs), 60 nasopharynx (NP), and 97 oropharynx (OP) samples from 98 healthy children in Shenzhen, China (≤12 years of age). The microbiota in ANs and NP is the same at different ages and typical species in these sites include Moraxella, Staphylococcus, Corynebacterium, Streptococcus, and Dolosigranulum. By contrast, the OP is primarily colonized by Streptococcus, Prevotella, Neisseria, Veillonella, Rothia, Leptotrichia, and Haemophilus. Streptococcus and Rothia keep low abundance in OP microbiota of children ≤1 year old, whereas Prevotella, Neisseria, Haemophilus, and Leptotrichia amass significantly in individuals >1 year old. This work furnishes an important reference for understanding microbial dysbiosis in the URT of Chinese paediatric patients.
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27
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How can the cystic fibrosis respiratory microbiome influence our clinical decision-making? Curr Opin Pulm Med 2018; 23:536-543. [PMID: 28786882 DOI: 10.1097/mcp.0000000000000419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE OF REVIEW Almost 15 years have now passed since bacterial community profiling techniques were first used to analyse respiratory samples from people with cystic fibrosis. Since then, many different analytical approaches have been used to try to better understand the contribution of the cystic fibrosis lung microbiota to disease, with varying degrees of success. We examine the extent to which cystic fibrosis respiratory microbiome research has been successful in informing clinical decision-making, and highlight areas that we believe have the potential to yield important insight. RECENT FINDINGS Recent research on the cystic fibrosis lung microbiome can be broadly divided into efforts to better characterize microbiota composition, particularly relative to key clinical events, and attempts to understand the cystic fibrosis lung microbiology as an interactive microbial system. The latter, in particular, has led to the development of a number of models in which microbiome-mediated processes precipitate clinical events. SUMMARY Growing technological sophistication is enabling increasingly detailed microbiological data to be generated from cystic fibrosis respiratory samples. However, translating these data into clinically useful measures that accurately predict outcomes and guide treatments remains a formidable challenge. The development of systems biology approaches that enable the integration of complex microbiome and host-derived data provide an exciting opportunity to address this goal.
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28
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Kosoy M, Kosoy R. Complexity and biosemiotics in evolutionary ecology of zoonotic infectious agents. Evol Appl 2018; 11:394-403. [PMID: 29636794 PMCID: PMC5891042 DOI: 10.1111/eva.12503] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/01/2017] [Indexed: 02/02/2023] Open
Abstract
More is not automatically better. Generation and accumulation of information reflecting the complexity of zoonotic diseases as ecological systems do not necessarily lead to improved interpretation of the obtained information and understanding of these complex systems. The traditional conceptual framework for analysis of diseases ecology is neither designed for, nor adaptable enough, to absorb the mass of diverse sources of relevant information. The multidirectional and multidimensional approaches to analyses form an inevitable part in defining a role of zoonotic pathogens and animal hosts considering the complexity of their inter-relations. And the more data we have, the more involved the interpretation needs to be. The keyword for defining the roles of microbes as pathogens, animals as hosts, and environmental parameters as infection drivers is "functional importance." Microbes can act as pathogens toward their host only if/when they recognize the animal organism as the target. The same is true when the host recognizes the microbe as a pathogen rather than harmless symbiont based on the context of its occurrence in that host. Here, we propose conceptual tools developed in the realm of the interdisciplinary sciences of complexity and biosemiotics for extending beyond the currently dominant mindset in ecology and evolution of infectious diseases. We also consider four distinct hierarchical levels of perception guiding how investigators can approach zoonotic agents, as a subject of their research, representing differences in emphasizing particular elements and their relations versus more unified systemic approaches.
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Affiliation(s)
- Michael Kosoy
- Division of Vector‐Borne DiseasesCenters for Disease Control and PreventionFort CollinsCOUSA
- Global Health AsiaMahidol UniversityBangkokThailand
| | - Roman Kosoy
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNYUSA
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29
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Wang H, Zhang S, Pratush A, Ye X, Xie J, Wei H, Sun C, Hu Z. Acclimation of Culturable Bacterial Communities under the Stresses of Different Organic Compounds. Front Microbiol 2018. [PMID: 29520254 PMCID: PMC5827545 DOI: 10.3389/fmicb.2018.00225] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The phylogenetic diversity of bacterial communities in response to environmental disturbances such as organic pollution has been well studied, but little is known about the way in which organic contaminants influence the acclimation of functional bacteria. In the present study, tolerance assays for bacterial communities from the sediment in the Pearl River Estuary were conducted with the isolation of functional bacteria using pyrene and different estrogens as environmental stressors. Molecular ecological networks and phylogenetic trees were constructed using both 16S rRNA gene sequences of cultured bacterial strains and 16S rRNA gene-based pyrosequencing data to illustrate the successions of bacterial communities and their acclimations to the different organic compounds. A total of 111 bacterial strains exhibiting degradation and endurance capabilities in response to the pyrene estrogen-induced stress were successfully isolated and were mainly affiliated with three orders, Pseudomonadales, Vibrionales, and Rhodobacterales. Molecular ecological networks and phylogenetic trees showed various adaptive abilities of bacteria to the different organic compounds. For instance, some bacterial OTUs could be found only in particular organic compound-treated groups while some other OTUs could tolerate stresses from different organic compounds. Furthermore, the results indicated that some new phylotypes were emerged under stresses of different organic pollutions and these new phylotypes could adapt to the contaminated environments and contribute significantly to the microbial community shifts. Overall, this study demonstrated a crucial role of the community succession and the acclimation of functional bacteria in the adaptive responses to various environmental disturbances.
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Affiliation(s)
- Hui Wang
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Shuangfei Zhang
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Amit Pratush
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Xueying Ye
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Jinli Xie
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Huan Wei
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Chongran Sun
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Zhong Hu
- Department of Biology, College of Science, Shantou University, Shantou, China
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30
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Inflammatory phenotypes in patients with severe asthma are associated with distinct airway microbiology. J Allergy Clin Immunol 2018; 141:94-103.e15. [DOI: 10.1016/j.jaci.2017.03.044] [Citation(s) in RCA: 176] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 02/28/2017] [Accepted: 03/15/2017] [Indexed: 12/31/2022]
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31
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The lung microbiome. Emerg Top Life Sci 2017; 1:313-324. [PMID: 33525774 DOI: 10.1042/etls20170043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/31/2017] [Accepted: 09/29/2017] [Indexed: 12/17/2022]
Abstract
Historically, our understanding of lung microbiology has relied on insight gained through culture-based diagnostic approaches that employ selective culture conditions to isolate specific pathogens. The relatively recent development of culture-independent microbiota-profiling techniques, particularly 16S rRNA (ribosomal ribonucleic acid) gene amplicon sequencing, has enabled more comprehensive characterisation of the microbial content of respiratory samples. The widespread application of such techniques has led to a fundamental shift in our view of respiratory microbiology. Rather than a sterile lung environment that can become colonised by microbes during infection, it appears that a more nuanced balance exists between what we consider respiratory health and disease, mediated by mechanisms that influence the clearance of microbes from the lungs. Where airway defences are compromised, the ongoing transient exposure of the lower airways to microbes can lead to the establishment of complex microbial communities within the lung. Importantly, the characteristics of these communities, and the manner in which they influence lung pathogenesis, can be very different from those of their constituent members when viewed in isolation. The lung microbiome, a construct that incorporates microbes, their genetic material, and the products of microbial genes, is increasingly central to our understanding of the regulation of respiratory physiology and the processes that underlie lung pathogenesis.
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32
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Rogers GB. Inflammation, age and changing microbiology: the search for causation in the cystic fibrosis airways. Eur Respir J 2017; 50:50/5/1701935. [DOI: 10.1183/13993003.01935-2017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 09/25/2017] [Indexed: 01/06/2023]
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33
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Catozzi C, Sanchez Bonastre A, Francino O, Lecchi C, De Carlo E, Vecchio D, Martucciello A, Fraulo P, Bronzo V, Cuscó A, D’Andreano S, Ceciliani F. The microbiota of water buffalo milk during mastitis. PLoS One 2017; 12:e0184710. [PMID: 28926595 PMCID: PMC5604978 DOI: 10.1371/journal.pone.0184710] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/23/2017] [Indexed: 02/07/2023] Open
Abstract
The aim of this study was to define the microbiota of water buffalo milk during sub-clinical and clinical mastitis, as compared to healthy status, by using high-throughput sequencing of the 16S rRNA gene. A total of 137 quarter samples were included in the experimental design: 27 samples derived from healthy, culture negative quarters, with a Somatic Cell Count (SCC) of less than 200,000 cells/ml; 27 samples from quarters with clinical mastitis; 83 samples were collected from quarters with subclinical mastitis, with a SCC number greater of 200,000 cells/ml and/or culture positive for udder pathogens, without clinical signs of mastitis. Bacterial DNA was purified and the 16S rRNA genes were individually amplified and sequenced. Significant differences were found in milk samples from healthy quarters and those with sub-clinical and clinical mastitis. The microbiota diversity of milk from healthy quarters was richer as compared to samples with sub-clinical mastitis, whose microbiota diversity was in turn richer as compared to those from clinical mastitis. The core microbiota of water buffalo milk, defined as the asset of microorganisms shared by all healthy milk samples, includes 15 genera, namely Micrococcus, Propionibacterium, 5-7N15, Solibacillus, Staphylococcus, Aerococcus, Facklamia, Trichococcus, Turicibacter, 02d06, SMB53, Clostridium, Acinetobacter, Psychrobacter and Pseudomonas. Only two genera (Acinetobacter and Pseudomonas) were present in all the samples from sub-clinical mastitis, and no genus was shared across all in clinical mastitis milk samples. The presence of mastitis was found to be related to the change in the relative abundance of genera, such as Psychrobacter, whose relative abundance decreased from 16.26% in the milk samples from healthy quarters to 3.2% in clinical mastitis. Other genera, such as SMB53 and Solibacillus, were decreased as well. Discriminant analysis presents the evidence that the microbial community of healthy and clinical mastitis could be discriminated on the background of their microbiota profiles.
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Affiliation(s)
- Carlotta Catozzi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via Celoria 10, Milano, Italy
| | - Armand Sanchez Bonastre
- Molecular Genetics Veterinary Service (SVGM), Veterinary School, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Olga Francino
- Molecular Genetics Veterinary Service (SVGM), Veterinary School, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Cristina Lecchi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via Celoria 10, Milano, Italy
| | - Esterina De Carlo
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, National Reference Centre for Hygiene and Technologies of Water Buffalo Farming and Productions, Via delle Calabrie, Salerno, Italy
| | - Domenico Vecchio
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, National Reference Centre for Hygiene and Technologies of Water Buffalo Farming and Productions, Via delle Calabrie, Salerno, Italy
| | - Alessandra Martucciello
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, National Reference Centre for Hygiene and Technologies of Water Buffalo Farming and Productions, Via delle Calabrie, Salerno, Italy
| | - Pasquale Fraulo
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, National Reference Centre for Hygiene and Technologies of Water Buffalo Farming and Productions, Via delle Calabrie, Salerno, Italy
| | - Valerio Bronzo
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via Celoria 10, Milano, Italy
| | - Anna Cuscó
- Vetgenomics. Ed Eureka. PRUAB. Campus UAB, Bellaterra, Barcelona, Spain
| | - Sara D’Andreano
- Vetgenomics. Ed Eureka. PRUAB. Campus UAB, Bellaterra, Barcelona, Spain
| | - Fabrizio Ceciliani
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Via Celoria 10, Milano, Italy
- * E-mail:
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34
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Strong incidence of Pseudomonas aeruginosa on bacterial rrs and ITS genetic structures of cystic fibrosis sputa. PLoS One 2017; 12:e0173022. [PMID: 28282386 PMCID: PMC5345789 DOI: 10.1371/journal.pone.0173022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 02/14/2017] [Indexed: 11/20/2022] Open
Abstract
Cystic fibrosis (CF) lungs harbor a complex community of interacting microbes, including pathogens like Pseudomonas aeruginosa. Meta-taxogenomic analysis based on V5-V6 rrs PCR products of 52 P. aeruginosa-positive (Pp) and 52 P. aeruginosa-negative (Pn) pooled DNA extracts from CF sputa suggested positive associations between P. aeruginosa and Stenotrophomonas and Prevotella, but negative ones with Haemophilus, Neisseria and Burkholderia. Internal Transcribed Spacer analyses (RISA) from individual DNA extracts identified three significant genetic structures within the CF cohorts, and indicated an impact of P. aeruginosa. RISA clusters Ip and IIIp contained CF sputa with a P. aeruginosa prevalence above 93%, and of 24.2% in cluster IIp. Clusters Ip and IIIp showed lower RISA genetic diversity and richness than IIp. Highly similar cluster IIp RISA profiles were obtained from two patients harboring isolates of a same P. aeruginosa clone, suggesting convergent evolution in the structure of their microbiota. CF patients of cluster IIp had received significantly less antibiotics than patients of clusters Ip and IIIp but harbored the most resistant P. aeruginosa strains. Patients of cluster IIIp were older than those of Ip. The effects of P. aeruginosa on the RISA structures could not be fully dissociated from the above two confounding factors but several trends in these datasets support the conclusion of a strong incidence of P. aeruginosa on the genetic structure of CF lung microbiota.
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35
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Le Bars P, Matamoros S, Montassier E, Le Vacon F, Potel G, Soueidan A, Jordana F, de La Cochetière MF. The oral cavity microbiota: between health, oral disease, and cancers of the aerodigestive tract. Can J Microbiol 2017; 63:475-492. [PMID: 28257583 DOI: 10.1139/cjm-2016-0603] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many studies show that the human microbiome plays a critical role in the chronic pathologies of obesity, inflammatory bowel diseases, and diabetes. More recently, the interaction between cancer and the microbiome has been highlighted. Most studies have focused on the gut microbiota because it represents the most extensive bacterial community, and the body of evidence correlating it with gut syndromes is increasing. However, in the strict sense, the gastrointestinal (GI) tract begins in the oral cavity, and special attention should be paid to the specific flora of this cavity. This study reviewed the current knowledge about the various microbial ecosystems of the upper part of the GI tract and discussed their potential link to carcinogenesis. The overall composition of the microbial communities, as well as the presence or absence of "key species", in relation to carcinogenesis is addressed. Alterations in the oral microbiota can potentially be used to predict the risk of cancer. Molecular advances and the further monitoring of the microbiota will increase our understanding of the role of the microbiota in carcinogenesis and open new perspectives for future therapeutic and prophylactic modalities.
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Affiliation(s)
- Pierre Le Bars
- a UFR d'odontologie, UIC Odontologie, CHU hôtel-Dieu, Université de Nantes, 1, place Alexis Ricordeau, B.P. 84215, 44042 Nantes CEDEX 1, France
| | - Sébastien Matamoros
- b Walloon Excellence in Life Sciences and Biotechnology, Louvain Drug Research Institute, Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, 1, place de l'Université, 1348 Brussels, Belgium
| | - Emmanuel Montassier
- c EA 3826 Thérapeutiques cliniques et expérimentales des infections, Faculté de médecine, CHU hôtel-Dieu, Université de Nantes, 1, rue G. Veil, 44000 Nantes, France
| | - Françoise Le Vacon
- d Biofortis Innovation Services - Mérieux NutriSciences, 3, route de la Chatterie, 44800 Saint-Herblain, France
| | - Gilles Potel
- c EA 3826 Thérapeutiques cliniques et expérimentales des infections, Faculté de médecine, CHU hôtel-Dieu, Université de Nantes, 1, rue G. Veil, 44000 Nantes, France
| | - Assem Soueidan
- a UFR d'odontologie, UIC Odontologie, CHU hôtel-Dieu, Université de Nantes, 1, place Alexis Ricordeau, B.P. 84215, 44042 Nantes CEDEX 1, France
| | - Fabienne Jordana
- a UFR d'odontologie, UIC Odontologie, CHU hôtel-Dieu, Université de Nantes, 1, place Alexis Ricordeau, B.P. 84215, 44042 Nantes CEDEX 1, France
| | - Marie-France de La Cochetière
- c EA 3826 Thérapeutiques cliniques et expérimentales des infections, Faculté de médecine, CHU hôtel-Dieu, Université de Nantes, 1, rue G. Veil, 44000 Nantes, France
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Layeghifard M, Hwang DM, Guttman DS. Disentangling Interactions in the Microbiome: A Network Perspective. Trends Microbiol 2017; 25:217-228. [PMID: 27916383 PMCID: PMC7172547 DOI: 10.1016/j.tim.2016.11.008] [Citation(s) in RCA: 418] [Impact Index Per Article: 59.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/31/2016] [Accepted: 11/08/2016] [Indexed: 12/12/2022]
Abstract
Microbiota are now widely recognized as being central players in the health of all organisms and ecosystems, and subsequently have been the subject of intense study. However, analyzing and converting microbiome data into meaningful biological insights remain very challenging. In this review, we highlight recent advances in network theory and their applicability to microbiome research. We discuss emerging graph theoretical concepts and approaches used in other research disciplines and demonstrate how they are well suited for enhancing our understanding of the higher-order interactions that occur within microbiomes. Network-based analytical approaches have the potential to help disentangle complex polymicrobial and microbe-host interactions, and thereby further the applicability of microbiome research to personalized medicine, public health, environmental and industrial applications, and agriculture.
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Affiliation(s)
- Mehdi Layeghifard
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - David M Hwang
- Department of Pathology, University Health Network Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada; Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada.
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Clinical Insights into Pulmonary Exacerbations in Cystic Fibrosis from the Microbiome. What Are We Missing? Ann Am Thorac Soc 2016; 12 Suppl 2:S207-11. [PMID: 26595741 DOI: 10.1513/annalsats.201506-353aw] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pulmonary exacerbations account for much of the decrease in lung function and consequently most of the morbidity and mortality in patients with cystic fibrosis. These events are driven by an acute inflammatory response to infection. Recent technological advancements in molecular profiling techniques have allowed for a proliferation of microbiome studies of the lower airways of patients with cystic fibrosis. But these methods may not provide a comprehensive and unbiased measure of the lung microbiota in these patients and molecular profiles do not always translate to quantitative microbiology. Furthermore, these studies have not yet been able to provide much in the way of mechanistic insights into exacerbations or to guide patient therapy. We propose a model in which pulmonary exacerbations may be driven by an active subpopulation of the lung microbiota, which may represent only a small portion of the microbiota measured in a clinical sample. Methodology should be focused on the ultimate goal, which is to use the best available approaches to provide accurate quantitative measures of the microbiome to inform clinical decisions and provide rapid assessment of treatment efficacy. These strategies would be relevant to other chronic lung diseases such as chronic obstructive pulmonary disease and neutrophilic asthma.
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Redefining the Chronic-Wound Microbiome: Fungal Communities Are Prevalent, Dynamic, and Associated with Delayed Healing. mBio 2016; 7:mBio.01058-16. [PMID: 27601572 PMCID: PMC5013295 DOI: 10.1128/mbio.01058-16] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Chronic nonhealing wounds have been heralded as a silent epidemic, causing significant morbidity and mortality especially in elderly, diabetic, and obese populations. Polymicrobial biofilms in the wound bed are hypothesized to disrupt the highly coordinated and sequential events of cutaneous healing. Both culture-dependent and -independent studies of the chronic-wound microbiome have almost exclusively focused on bacteria, omitting what we hypothesize are important fungal contributions to impaired healing and the development of complications. Here we show for the first time that fungal communities (the mycobiome) in chronic wounds are predictive of healing time, associated with poor outcomes, and form mixed fungal-bacterial biofilms. We longitudinally profiled 100, nonhealing diabetic-foot ulcers with high-throughput sequencing of the pan-fungal internal transcribed spacer 1 (ITS1) locus, estimating that up to 80% of wounds contain fungi, whereas cultures performed in parallel captured only 5% of colonized wounds. The “mycobiome” was highly heterogeneous over time and between subjects. Fungal diversity increased with antibiotic administration and onset of a clinical complication. The proportions of the phylum Ascomycota were significantly greater (P = 0.015) at the beginning of the study in wounds that took >8 weeks to heal. Wound necrosis was distinctly associated with pathogenic fungal species, while taxa identified as allergenic filamentous fungi were associated with low levels of systemic inflammation. Directed culturing of wounds stably colonized by pathogens revealed that interkingdom biofilms formed between yeasts and coisolated bacteria. Combined, our analyses provide enhanced resolution of the mycobiome during impaired wound healing, its role in chronic disease, and impact on clinical outcomes. Wounds are an underappreciated but serious complication for a diverse spectrum of diseases. High-risk groups, such as persons with diabetes, have a 25% lifetime risk of developing a wound that can become chronic. The majority of microbiome research related to chronic wounds is focused on bacteria, but the association of fungi with clinical outcomes remains to be elucidated. Here we describe the dynamic fungal communities in 100 diabetic patients with foot ulcers. We found that communities are unstable over time, but at the first clinical presentation, the relative proportions of different phyla predict healing times. Pathogenic fungi not identified by culture reside in necrotic wounds and are associated with a poor prognosis. In wounds stably colonized by fungi, we identified yeasts capable of forming biofilms in concert with bacteria. Our findings illuminate the associations of the fungal mycobiome with wound prognosis and healing.
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39
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Advances, challenges, and directions in shrimp disease control: the guidelines from an ecological perspective. Appl Microbiol Biotechnol 2016; 100:6947-54. [PMID: 27333908 DOI: 10.1007/s00253-016-7679-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/07/2016] [Accepted: 06/11/2016] [Indexed: 12/23/2022]
Abstract
High-density aquaculture has led to increasing occurrences of diseases in shrimp. Thus, it is imperative to establish effective and quantitative strategies for preventing and predicting these diseases. Water quality indices and investigations of specific pathogen abundance provide only a qualitative evaluation of the risk of shrimp disease and can be inaccurate. To address these shortcomings, we introduced intestinal indicative assemblages as independent variables with which to quantitatively predict incidences of shrimp disease. Given the ignorance regarding the niches differences in the shrimp intestine throughout its developmental stages, the use of probiotics in aquaculture has had limited success. Therefore, we propose the exploration of effective probiotic bacteria from shrimp intestinal flora and the establishment of therapeutic strategies dependent on shrimp age. Following ecological selection principles, we hypothesize that the larval stage provides the best opportunity to establish a desired gut microbiota through preemptive colonization of the treated rearing water with known probiotics. To employ this strategy, however, substantial barriers must be overcome.
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40
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Pettigrew MM, Johnson JK, Harris AD. The human microbiota: novel targets for hospital-acquired infections and antibiotic resistance. Ann Epidemiol 2016; 26:342-7. [PMID: 26994507 PMCID: PMC4892961 DOI: 10.1016/j.annepidem.2016.02.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/26/2016] [Accepted: 02/26/2016] [Indexed: 12/14/2022]
Abstract
PURPOSE Hospital-acquired infections are increasing in frequency due to multidrug resistant organisms (MDROs), and the spread of MDROs has eroded our ability to treat infections. Health care professionals cannot rely solely on traditional infection control measures and antimicrobial stewardship to prevent MDRO transmission. We review research on the microbiota as a target for infection control interventions. METHODS We performed a literature review of key research findings related to the microbiota as a target for infection control interventions. These data are summarized and used to outline challenges, opportunities, and unanswered questions in the field. RESULTS The healthy microbiota provides protective functions including colonization resistance, which refers to the microbiota's ability to prevent colonization and/or expansion of pathogens. Antibiotic use and other exposures in hospitalized patients are associated with disruptions of the microbiota that may reduce colonization resistance and select for antibiotic resistance. Novel methods to exploit protective mechanisms provided by an intact microbiota may provide the key to preventing the spread of MDROs in the health care setting. CONCLUSIONS Research on the microbiota as a target for infection control has been limited. Epidemiologic studies will facilitate progress toward the goal of manipulating the microbiota for control of MDROs in the health care setting.
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Affiliation(s)
- Melinda M Pettigrew
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT.
| | - J Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD
| | - Anthony D Harris
- Department of Epidemiology, University of Maryland School of Medicine, Baltimore, MD
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41
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Sismaet HJ, Banerjee A, McNish S, Choi Y, Torralba M, Lucas S, Chan A, Shanmugam VK, Goluch ED. Electrochemical detection of Pseudomonas in wound exudate samples from patients with chronic wounds. Wound Repair Regen 2016; 24:366-72. [PMID: 26815644 PMCID: PMC4853203 DOI: 10.1111/wrr.12414] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/23/2016] [Indexed: 01/13/2023]
Abstract
In clinical practice, point-of-care diagnostic testing has progressed rapidly in the last decade. For the field of wound care, there is a compelling need to develop rapid alternatives for bacterial identification in the clinical setting, where it generally takes over 24 hours to receive a positive identification. Even new molecular and biochemical identification methods require an initial incubation period of several hours to obtain a sufficient number of cells prior to performing the analysis. Here we report the use of an inexpensive, disposable electrochemical sensor to detect pyocyanin, a unique, redox-active quorum sensing molecule released by Pseudomonas aeruginosa, in wound fluid from patients with chronic wounds enrolled in the WE-HEAL Study. By measuring the metabolite excreted by the cells, this electrochemical detection strategy eliminates sample preparation, takes less than a minute to complete, and requires only 7.5 μL of sample to complete the analysis. The electrochemical results were compared against 16S rRNA profiling using 454 pyrosequencing. Blind identification yielded 9 correct matches, 2 false negatives, and 3 false positives giving a sensitivity of 71% and specificity of 57% for detection of Pseudomonas. Ongoing enhancement and development of this approach with a view to develop a rapid point-of-care diagnostic tool is planned.
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Affiliation(s)
- Hunter J. Sismaet
- Department of Chemical Engineering, Northeastern University, 360 Huntington Ave, 313 Snell Engineering, Boston, MA 02115 USA
| | - Anirban Banerjee
- Division of Rheumatology, Ideas to Health Laboratory, The George Washington University, School of Medicine and Health Sciences, 701 Ross Hall, 2300 Eye Street, NW, Washington, DC 20037
| | - Sean McNish
- Division of Rheumatology, Ideas to Health Laboratory, The George Washington University, School of Medicine and Health Sciences, 701 Ross Hall, 2300 Eye Street, NW, Washington, DC 20037
| | - Yongwook Choi
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850
| | - Manolito Torralba
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850
| | - Sarah Lucas
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850
| | - Agnes Chan
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850
| | - Victoria K. Shanmugam
- Division of Rheumatology, Ideas to Health Laboratory, The George Washington University, School of Medicine and Health Sciences, 701 Ross Hall, 2300 Eye Street, NW, Washington, DC 20037
| | - Edgar D. Goluch
- Department of Chemical Engineering, Northeastern University, 360 Huntington Ave, 313 Snell Engineering, Boston, MA 02115 USA
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42
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Rogers GB, Wesselingh S. Precision respiratory medicine and the microbiome. THE LANCET RESPIRATORY MEDICINE 2015; 4:73-82. [PMID: 26700443 DOI: 10.1016/s2213-2600(15)00476-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 11/04/2015] [Accepted: 11/04/2015] [Indexed: 02/06/2023]
Abstract
A decade of rapid technological advances has provided an exciting opportunity to incorporate information relating to a range of potentially important disease determinants in the clinical decision-making process. Access to highly detailed data will enable respiratory medicine to evolve from one-size-fits-all models of care, which are associated with variable clinical effectiveness and high rates of side-effects, to precision approaches, where treatment is tailored to individual patients. The human microbiome has increasingly been recognised as playing an important part in determining disease course and response to treatment. Its inclusion in precision models of respiratory medicine, therefore, is essential. Analysis of the microbiome provides an opportunity to develop novel prognostic markers for airways disease, improve definition of clinical phenotypes, develop additional guidance to aid treatment selection, and increase the accuracy of indicators of treatment effect. In this Review we propose that collaboration between researchers and clinicians is needed if respiratory medicine is to replicate the successes of precision medicine seen in other clinical specialties.
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Affiliation(s)
- Geraint B Rogers
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia; SAHMRI Microbiome Research Laboratory Flinders University School of Medicine, Adelaide, SA, Australia.
| | - Steve Wesselingh
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia; SAHMRI Microbiome Research Laboratory Flinders University School of Medicine, Adelaide, SA, Australia
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Magalhães AP, Azevedo NF, Pereira MO, Lopes SP. The cystic fibrosis microbiome in an ecological perspective and its impact in antibiotic therapy. Appl Microbiol Biotechnol 2015; 100:1163-1181. [PMID: 26637419 DOI: 10.1007/s00253-015-7177-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/11/2015] [Accepted: 11/13/2015] [Indexed: 01/24/2023]
Abstract
The recent focus on the cystic fibrosis (CF) complex microbiome has led to the recognition that the microbes can interact between them and with the host immune system, affecting the disease progression and treatment routes. Although the main focus remains on the interactions between traditional pathogens, growing evidence supports the contribution and the role of emergent species. Understanding the mechanisms and the biological effects involved in polymicrobial interactions may be the key to improve effective therapies and also to define new strategies for disease control. This review focuses on the interactions between microbe-microbe and host-microbe, from an ecological point of view, discussing their impact on CF disease progression. There are increasing indications that these interactions impact the success of antimicrobial therapy. Consequently, a new approach where therapy is personalized to patients by taking into account their individual CF microbiome is suggested.
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Affiliation(s)
- Andreia P Magalhães
- CEB-Centre of Biological Engineering, LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Nuno F Azevedo
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, 4200-465, Porto, Portugal
| | - Maria O Pereira
- CEB-Centre of Biological Engineering, LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Susana P Lopes
- CEB-Centre of Biological Engineering, LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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Andréjak C, Delhaes L. [The lung microbiome in 2015: a window on chronic lung diseases]. Med Sci (Paris) 2015; 31:971-8. [PMID: 26576604 DOI: 10.1051/medsci/20153111011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Recent development of high-throughput sequencing methods has shown that the human respiratory tract (including lower airways) is not sterile as formerly thought, but composed of a previously unappreciated complex microbial community referred as the lung microbiome and composed of bacteria, viruses and fungi. However, many questions remain unresolved, especially in terms of lung microbiome role, its interactions with host but also with environmental pathogens. Although data are still limited, links have already been demonstrated between lung microbiome and chronic respiratory diseases (such as asthma, chronic obstructive pulmonary disease or cystic fibrosis). This lung microbiome appears to play an important role both in disease genesis and evolution, and consequently offers an emerging research field.
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Affiliation(s)
- Claire Andréjak
- Service de pneumologie et réanimation respiratoire, CHU d'Amiens, EA 4294, université de Picardie Jules Verne, 80000 Amiens, France
| | - Laurence Delhaes
- Centre d'immunologie et d'infectiologie de Lille (BDEEP), Inserm U1019, CNRS UMR 8204, Institut Pasteur de Lille, université de Lille Nord de France, 1, rue du Professeur Calmette, 59019 Lille Cedex, France - Laboratoire de parasitologie-mycologie, CHRU de Lille, faculté de médecine, université Lille2, Lille, France - Adresse actuelle : Service de parasitologie- Mycologie, CHU de Bordeaux, université de Bordeaux, France
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Rogers GB, Shaw D, Marsh RL, Carroll MP, Serisier DJ, Bruce KD. Republished: Respiratory microbiota: addressing clinical questions, informing clinical practice. Postgrad Med J 2015; 91:463-70. [PMID: 26304986 PMCID: PMC4552901 DOI: 10.1136/postgradmedj-2014-205826rep] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 06/23/2014] [Indexed: 12/30/2022]
Abstract
Over the last decade, technological advances have revolutionised efforts to understand the role played by microbes in airways disease. With the application of ever more sophisticated techniques, the literature has become increasingly inaccessible to the non-specialist reader, potentially hampering the translation of these gains into improvements in patient care. In this article, we set out the key principles underpinning microbiota research in respiratory contexts and provide practical guidance on how best such studies can be designed, executed and interpreted. We examine how an understanding of the respiratory microbiota both challenges fundamental assumptions and provides novel clinical insights into lung disease, and we set out a number of important targets for ongoing research.
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Affiliation(s)
- Geraint B Rogers
- SAHMRI Infection and Immunity Theme, School of Medicine, Flinders University, Adelaide, Australia
| | - Dominick Shaw
- Nottingham Respiratory Research Unit, University of Nottingham, Nottingham City Hospital, Nottingham, Notts, UK
| | - Robyn L Marsh
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mary P Carroll
- Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Southampton, UK
| | - David J Serisier
- Immunity, Infection, and Inflammation Program, Mater Research Institute, University of Queensland, and Translational Research Institute, Woolloongabba, Queensland, Australia
- Department of Respiratory Medicine, Mater Adult Hospital, South Brisbane, Australia
| | - Kenneth D Bruce
- King's College London, Institute of Pharmaceutical Science, London, UK
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46
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A novel microbiota stratification system predicts future exacerbations in bronchiectasis. Ann Am Thorac Soc 2015; 11:496-503. [PMID: 24592925 DOI: 10.1513/annalsats.201310-335oc] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RATIONALE Although airway microbiota composition correlates with clinical measures in non-cystic fibrosis bronchiectasis, these data are unlikely to provide useful prognostic information at the individual patient level. A system enabling microbiota data to be applied clinically would represent a substantial translational advance. OBJECTIVES This study aims to determine whether stratification of patients according to the predominant microbiota taxon can provide improved clinical insight compared with standard diagnostics. METHODS The presence of bacterial respiratory pathogens was assessed in induced sputum from 107 adult patients by culture, quantitative PCR, and, in 96 samples, by ribosomal gene pyrosequencing. Prospective analysis was performed on samples from 42 of these patients. Microbiological data were correlated with concurrent clinical measures and subsequent outcomes. MEASUREMENTS AND MAIN RESULTS Microbiota analysis defined three groups: Pseudomonas aeruginosa dominated (n = 26), Haemophilus influenzae dominated (n = 34), and other taxa dominated (n = 36). Patients with P. aeruginosa- and H. influenzae-dominated communities had significantly worse lung function, higher serum levels of C-reactive protein (CRP), and higher sputum levels of IL-8 and IL-1β. Predominance of P. aeruginosa, followed by Veillonella species, was the best predictor of future exacerbation frequency, with H. influenzae-dominated communities having significantly fewer episodes. Detection of P. aeruginosa was associated with poor lung function and exacerbation frequency, irrespective of analytical strategy. Quantitative PCR revealed significant correlations between H. influenzae levels and sputum IL-8, IL-1β, and serum CRP. Genus richness was negatively correlated with 24-hour sputum weight, age, serum CRP, sputum IL-1β, and IL-8. CONCLUSIONS Stratification of patients with non-cystic fibrosis bronchiectasis on the basis of predominant bacterial taxa is more clinically informative than either conventional culture or quantitative PCR-based analysis. Further investigation is now required to assess the mechanistic basis of these associations.
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47
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Chang AB, Marsh RL, Upham JW, Hoffman LR, Smith-Vaughan H, Holt D, Toombs M, Byrnes C, Yerkovich ST, Torzillo PJ, O'Grady KAF, Grimwood K. Toward making inroads in reducing the disparity of lung health in Australian indigenous and new zealand māori children. Front Pediatr 2015; 3:9. [PMID: 25741502 PMCID: PMC4327127 DOI: 10.3389/fped.2015.00009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/26/2015] [Indexed: 01/01/2023] Open
Affiliation(s)
- Anne B Chang
- Child Health Division, Menzies School of Health Research, Charles Darwin University , Darwin, NT , Australia ; Queensland Children's Medical Research Institute, Queensland University of Technology , Brisbane, QLD , Australia
| | - Robyn L Marsh
- Child Health Division, Menzies School of Health Research, Charles Darwin University , Darwin, NT , Australia
| | - John W Upham
- Department of Respiratory Medicine, Princess Alexandra Hospital , Brisbane, QLD , Australia ; School of Medicine, The University of Queensland , Brisbane, QLD , Australia
| | - Lucas R Hoffman
- Department of Pediatrics, University of Washington , Seattle, WA , USA ; Department of Microbiology, University of Washington , Seattle, WA , USA
| | - Heidi Smith-Vaughan
- Child Health Division, Menzies School of Health Research, Charles Darwin University , Darwin, NT , Australia
| | - Deborah Holt
- Child Health Division, Menzies School of Health Research, Charles Darwin University , Darwin, NT , Australia
| | - Maree Toombs
- Child Health Division, Menzies School of Health Research, Charles Darwin University , Darwin, NT , Australia ; Indigenous Health, Toowoomba Rural Clinical School, The University of Queensland , Toowoomba, QLD , Australia
| | - Catherine Byrnes
- Paediatric Department, University of Auckland & Starship Children's Hospital , Auckland , New Zealand
| | - Stephanie T Yerkovich
- Child Health Division, Menzies School of Health Research, Charles Darwin University , Darwin, NT , Australia ; School of Medicine, The University of Queensland , Brisbane, QLD , Australia ; Queensland Lung Transplant Service, The Prince Charles Hospital , Chermside, QLD , Australia
| | - Paul J Torzillo
- Nganampa Health Council, Alice Springs and Royal Prince Alfred Hospital, The University of Sydney , Sydney, NSW , Australia
| | - Kerry-Ann F O'Grady
- Queensland Children's Medical Research Institute, Queensland University of Technology , Brisbane, QLD , Australia
| | - Keith Grimwood
- Gold Coast University Hospital, Griffith University , Gold Coast, QLD , Australia
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48
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Abstract
The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of sequencing and genetic analysis of microbiome samples. Much of the analytical work for these sequences involves phylogenetics, at least indirectly, but methodology has developed in a somewhat different direction than for other applications of phylogenetics. In this article, I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work.
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Affiliation(s)
- Frederick A Matsen
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 91802, USA
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49
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Rogers GB, Shaw D, Marsh RL, Carroll MP, Serisier DJ, Bruce KD. Respiratory microbiota: addressing clinical questions, informing clinical practice. Thorax 2015; 70:74-81. [PMID: 25035125 PMCID: PMC4283665 DOI: 10.1136/thoraxjnl-2014-205826] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 06/23/2014] [Indexed: 12/23/2022]
Abstract
Over the last decade, technological advances have revolutionised efforts to understand the role played by microbes in airways disease. With the application of ever more sophisticated techniques, the literature has become increasingly inaccessible to the non-specialist reader, potentially hampering the translation of these gains into improvements in patient care. In this article, we set out the key principles underpinning microbiota research in respiratory contexts and provide practical guidance on how best such studies can be designed, executed and interpreted. We examine how an understanding of the respiratory microbiota both challenges fundamental assumptions and provides novel clinical insights into lung disease, and we set out a number of important targets for ongoing research.
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Affiliation(s)
- Geraint B Rogers
- SAHMRI Infection and Immunity Theme, School of Medicine, Flinders University, Adelaide, Australia
| | - Dominick Shaw
- Nottingham Respiratory Research Unit, University of Nottingham, Nottingham City Hospital, Nottingham, Notts, UK
| | - Robyn L Marsh
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mary P Carroll
- Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Southampton, UK
| | - David J Serisier
- Immunity, Infection, and Inflammation Program, Mater Research Institute, University of Queensland, and Translational Research Institute, Woolloongabba, Queensland, Australia
- Department of Respiratory Medicine, Mater Adult Hospital, South Brisbane, Australia
| | - Kenneth D Bruce
- King's College London, Institute of Pharmaceutical Science, London, UK
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De Schryver P, Vadstein O. Ecological theory as a foundation to control pathogenic invasion in aquaculture. THE ISME JOURNAL 2014; 8:2360-8. [PMID: 24892581 PMCID: PMC4260705 DOI: 10.1038/ismej.2014.84] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 03/20/2014] [Accepted: 04/18/2014] [Indexed: 01/02/2023]
Abstract
Detrimental host-pathogen interactions are a normal phenomenon in aquaculture animal production, and have been counteracted by prophylactic use of antibiotics. Especially, the youngest life stages of cultivated aquatic animals are susceptible to pathogen invasion, resulting in disease and mortality. To establish a more sustainable aquatic food production, there is a need for new microbial management strategies that focus on 'join them' and not the traditional 'beat them' approaches. We argue that ecological theory could serve as a foundation for developing sustainable microbial management methods that prevent pathogenic disease in larviculture. Management of the water microbiota in aquaculture systems according to ecological selection principles has been shown to decrease opportunistic pathogen pressure and to result in an improved performance of the cultured animals. We hypothesize that manipulation of the biodiversity of the gut microbiota can increase the host's resistance against pathogenic invasion and infection. However, substantial barriers need to be overcome before active management of the intestinal microbiota can effectively be applied in larviculture.
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Affiliation(s)
- Peter De Schryver
- Laboratory of Aquaculture and Artemia Reference Center, Ghent University, Ghent, Belgium
| | - Olav Vadstein
- Department of Biotechnology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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