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Alsayed AR, Abed A, Khader HA, Al-Shdifat LMH, Hasoun L, Al-Rshaidat MMD, Alkhatib M, Zihlif M. Molecular Accounting and Profiling of Human Respiratory Microbial Communities: Toward Precision Medicine by Targeting the Respiratory Microbiome for Disease Diagnosis and Treatment. Int J Mol Sci 2023; 24:4086. [PMID: 36835503 PMCID: PMC9966333 DOI: 10.3390/ijms24044086] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/05/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The wide diversity of microbiota at the genera and species levels across sites and individuals is related to various causes and the observed differences between individuals. Efforts are underway to further understand and characterize the human-associated microbiota and its microbiome. Using 16S rDNA as a genetic marker for bacterial identification improved the detection and profiling of qualitative and quantitative changes within a bacterial population. In this light, this review provides a comprehensive overview of the basic concepts and clinical applications of the respiratory microbiome, alongside an in-depth explanation of the molecular targets and the potential relationship between the respiratory microbiome and respiratory disease pathogenesis. The paucity of robust evidence supporting the correlation between the respiratory microbiome and disease pathogenesis is currently the main challenge for not considering the microbiome as a novel druggable target for therapeutic intervention. Therefore, further studies are needed, especially prospective studies, to identify other drivers of microbiome diversity and to better understand the changes in the lung microbiome along with the potential association with disease and medications. Thus, finding a therapeutic target and unfolding its clinical significance would be crucial.
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Affiliation(s)
- Ahmad R. Alsayed
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Anas Abed
- Pharmacological and Diagnostic Research Centre, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman 11931, Jordan
| | - Heba A. Khader
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan
| | - Laith M. H. Al-Shdifat
- Department of Pharmaceutical Chemistry and Pharmacognosy, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Luai Hasoun
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Mamoon M. D. Al-Rshaidat
- Laboratory for Molecular and Microbial Ecology (LaMME), Department of Biological Sciences, School of Sciences, The University of Jordan, Amman 11942, Jordan
| | - Mohammad Alkhatib
- Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Roma, Italy
| | - Malek Zihlif
- Department of Pharmacology, School of Medicine, The University of Jordan, Amman 11942, Jordan
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2
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Kim JG, Zhang A, Rauseo AM, Goss CW, Mudd PA, O'Halloran JA, Wang L. The salivary and nasopharyngeal microbiomes are associated with SARS-CoV-2 infection and disease severity. J Med Virol 2023; 95:e28445. [PMID: 36583481 PMCID: PMC9880756 DOI: 10.1002/jmv.28445] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/15/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022]
Abstract
Emerging evidence suggests the oral and upper respiratory microbiota may play important roles in modulating host immune responses to viral infection. As the host microbiome may be involved in the pathophysiology of coronavirus disease 2019 (COVID-19), we investigated associations between the oral and nasopharyngeal microbiome and COVID-19 severity. We collected saliva (n = 78) and nasopharyngeal swab (n = 66) samples from a COVID-19 cohort and characterized the microbiomes using 16S ribosomal RNA gene sequencing. We also examined associations between the salivary and nasopharyngeal microbiome and age, COVID-19 symptoms, and blood cytokines. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection status, but not COVID-19 severity, was associated with community-level differences in the oral and nasopharyngeal microbiomes. Salivary and nasopharyngeal microbiome alpha diversity negatively correlated with age and were associated with fever and diarrhea. Oral Bifidobacterium, Lactobacillus, and Solobacterium were depleted in patients with severe COVID-19. Nasopharyngeal Paracoccus was depleted while nasopharyngeal Proteus, Cupravidus, and Lactobacillus were increased in patients with severe COVID-19. Further analysis revealed that the abundance of oral Bifidobacterium was negatively associated with plasma concentrations of known COVID-19 biomarkers interleukin 17F and monocyte chemoattractant protein-1. Our results suggest COVID-19 disease severity is associated with the relative abundance of certain bacterial taxa.
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Affiliation(s)
- Josh G. Kim
- Department of Medicine, Division of Allergy and ImmunologyWashington University School of MedicineSt. LouisMissouriUSA
| | - Ai Zhang
- Department of Medicine, Division of Allergy and ImmunologyWashington University School of MedicineSt. LouisMissouriUSA
| | - Adriana M. Rauseo
- Department of Medicine, Division of Infectious DiseasesWashington University School of MedicineSt. LouisMissouriUSA
| | - Charles W. Goss
- Division of BiostatisticsWashington University School of MedicineSt. LouisMissouriUSA
| | - Philip A. Mudd
- Department of Emergency MedicineWashington University School of MedicineSt. LouisMissouriUSA
| | - Jane A. O'Halloran
- Department of Medicine, Division of Infectious DiseasesWashington University School of MedicineSt. LouisMissouriUSA
| | - Leyao Wang
- Department of Medicine, Division of Allergy and ImmunologyWashington University School of MedicineSt. LouisMissouriUSA
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3
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Lee HW, Baek MG, Choi S, Ahn YH, Bang JY, Sohn KH, Kang MG, Jung JW, Choi JH, Cho SH, Yi H, Kang HR. Peripheral blood transcriptomic clusters uncovered immune phenotypes of asthma. Respir Res 2022; 23:237. [PMID: 36076228 PMCID: PMC9461267 DOI: 10.1186/s12931-022-02156-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 08/01/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcriptomic analysis has been used to elucidate the complex pathogenesis of heterogeneous disease and may also contribute to identify potential therapeutic targets by delineating the hub genes. This study aimed to investigate whether blood transcriptomic clustering can distinguish clinical and immune phenotypes of asthmatics, and microbiome in asthmatics. METHODS Transcriptomic expression of peripheral blood mononuclear cells (PBMCs) from 47 asthmatics and 21 non-asthmatics was measured using RNA sequencing. A hierarchical clustering algorithm was used to classify asthmatics. Differentially expressed genes, clinical phenotypes, immune phenotypes, and microbiome of each transcriptomic cluster were assessed. RESULTS In asthmatics, three distinct transcriptomic clusters with numerously different transcriptomic expressions were identified. The proportion of severe asthmatics was highest in cluster 3 as 73.3%, followed by cluster 2 (45.5%) and cluster 1 (28.6%). While cluster 1 represented clinically non-severe T2 asthma, cluster 3 tended to include severe non-T2 asthma. Cluster 2 had features of both T2 and non-T2 asthmatics characterized by the highest serum IgE level and neutrophil-dominant sputum cell population. Compared to non-asthmatics, cluster 1 showed higher CCL23 and IL1RL1 expression while the expression of TREML4 was suppressed in cluster 3. CTSD and ALDH2 showed a significant positive linear relationship across three clusters in the order of cluster 1 to 3. No significant differences in the diversities of lung and gut microbiomes were observed among transcriptomic clusters of asthmatics and non-asthmatics. However, our study has limitations in that small sample size data were analyzed with unmeasured confounding factors and causal relationships or function pathways were not verified. CONCLUSIONS Genetic clustering based on the blood transcriptome may provide novel immunological insight, which can be biomarkers of asthma immune phenotypes. Trial registration Retrospectively registered.
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Affiliation(s)
- Hyun Woo Lee
- Department of Internal Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Min-Gyung Baek
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, Korea
| | - Sungmi Choi
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, Korea
| | - Yoon Hae Ahn
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-Gu, Seoul, 110-744, Korea
| | - Ji-Young Bang
- Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Kyoung-Hee Sohn
- Department of Internal Medicine, Kyung Hee University Hospital, Seoul, Korea
| | - Min-Gyu Kang
- Department of Internal Medicine, Chungbuk National University College of Medicine, Chungbuk National University Hospital, Cheongju, Korea
| | - Jae-Woo Jung
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Korea
| | - Jeong-Hee Choi
- Department of Pulmonology and Allergy, Allergy and Clinical Immunology Research Center, Hallym University College of Medicine, Chuncheon, Korea
| | - Sang-Heon Cho
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-Gu, Seoul, 110-744, Korea.,Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
| | - Hana Yi
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, Korea. .,School of Biosystems and Biomedical Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Korea.
| | - Hye-Ryun Kang
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-Gu, Seoul, 110-744, Korea. .,Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Korea. .,Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Korea.
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Avalos-Fernandez M, Alin T, Métayer C, Thiébaut R, Enaud R, Delhaes L. The respiratory microbiota alpha-diversity in chronic lung diseases: first systematic review and meta-analysis. Respir Res 2022; 23:214. [PMID: 35999634 PMCID: PMC9396807 DOI: 10.1186/s12931-022-02132-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/17/2022] [Indexed: 11/26/2022] Open
Abstract
Background While there seems to be a consensus that a decrease in gut microbiome diversity is related to a decline in health status, the associations between respiratory microbiome diversity and chronic lung disease remain a matter of debate. We provide a systematic review and meta-analysis of studies examining lung microbiota alpha-diversity in patients with asthma, chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF) or bronchiectasis (NCFB), in which a control group based on disease status or healthy subjects is provided for comparison. Results We reviewed 351 articles on title and abstract, of which 27 met our inclusion criteria for systematic review. Data from 24 of these studies were used in the meta-analysis. We observed a trend that CF patients have a less diverse respiratory microbiota than healthy individuals. However, substantial heterogeneity was present and detailed using random-effects models, which limits the comparison between studies. Conclusions Knowledge on respiratory microbiota is under construction, and for the moment, it seems that alpha-diversity measurements are not enough documented to fully understand the link between microbiota and health, excepted in CF context which represents the most studied chronic respiratory disease with consistent published data to link alpha-diversity and lung function. Whether differences in respiratory microbiota profiles have an impact on chronic respiratory disease symptoms and/or evolution deserves further exploration. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02132-4.
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Affiliation(s)
- Marta Avalos-Fernandez
- University of Bordeaux, Bordeaux Population Health Research Center, UMR U1219, INSERM, F-33000, Bordeaux, France. .,SISTM team Inria BSO, F-33405, Talence, France.
| | - Thibaud Alin
- University of Bordeaux, Bordeaux Population Health Research Center, UMR U1219, INSERM, F-33000, Bordeaux, France.,SISTM team Inria BSO, F-33405, Talence, France
| | - Clémence Métayer
- University of Bordeaux, Bordeaux Population Health Research Center, UMR U1219, INSERM, F-33000, Bordeaux, France.,SISTM team Inria BSO, F-33405, Talence, France
| | - Rodolphe Thiébaut
- University of Bordeaux, Bordeaux Population Health Research Center, UMR U1219, INSERM, F-33000, Bordeaux, France.,SISTM team Inria BSO, F-33405, Talence, France.,Pole of Public Health, University Hospital of Bordeaux, F-33000, Bordeaux, France
| | - Raphaël Enaud
- Cystic fibrosis centre (CRCM), Paediatrics Department, University Hospital of Bordeaux, F-33000, Bordeaux, France.,Parasitology-Mycology Department, University Hospital of Bordeaux, F-33000, Bordeaux, France
| | - Laurence Delhaes
- Cystic fibrosis centre (CRCM), Paediatrics Department, University Hospital of Bordeaux, F-33000, Bordeaux, France.,Parasitology-Mycology Department, University Hospital of Bordeaux, F-33000, Bordeaux, France.,University of Bordeaux, Bordeaux Cardio-Thoracic Research Center, U1045, INSERM, F-33000, Bordeaux, France
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5
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Logotheti M, Agioutantis P, Katsaounou P, Loutrari H. Microbiome Research and Multi-Omics Integration for Personalized Medicine in Asthma. J Pers Med 2021; 11:jpm11121299. [PMID: 34945771 PMCID: PMC8707330 DOI: 10.3390/jpm11121299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/13/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022] Open
Abstract
Asthma is a multifactorial inflammatory disorder of the respiratory system characterized by high diversity in clinical manifestations, underlying pathological mechanisms and response to treatment. It is generally established that human microbiota plays an essential role in shaping a healthy immune response, while its perturbation can cause chronic inflammation related to a wide range of diseases, including asthma. Systems biology approaches encompassing microbiome analysis can offer valuable platforms towards a global understanding of asthma complexity and improving patients' classification, status monitoring and therapeutic choices. In the present review, we summarize recent studies exploring the contribution of microbiota dysbiosis to asthma pathogenesis and heterogeneity in the context of asthma phenotypes-endotypes and administered medication. We subsequently focus on emerging efforts to gain deeper insights into microbiota-host interactions driving asthma complexity by integrating microbiome and host multi-omics data. One of the most prominent achievements of these research efforts is the association of refractory neutrophilic asthma with certain microbial signatures, including predominant pathogenic bacterial taxa (such as Proteobacteria phyla, Gammaproteobacteria class, especially species from Haemophilus and Moraxella genera). Overall, despite existing challenges, large-scale multi-omics endeavors may provide promising biomarkers and therapeutic targets for future development of novel microbe-based personalized strategies for diagnosis, prevention and/or treatment of uncontrollable asthma.
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Affiliation(s)
- Marianthi Logotheti
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece
| | - Panagiotis Agioutantis
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
| | - Paraskevi Katsaounou
- Pulmonary Dept First ICU, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, Ipsilantou 45-7, 10675 Athens, Greece;
| | - Heleni Loutrari
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
- Correspondence:
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6
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Fabbrizzi A, Nannini G, Lavorini F, Tomassetti S, Amedei A. Microbiota and IPF: hidden and detected relationships. SARCOIDOSIS VASCULITIS AND DIFFUSE LUNG DISEASES 2021; 38:e2021028. [PMID: 34744424 PMCID: PMC8552575 DOI: 10.36141/svdld.v38i3.11365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/02/2021] [Indexed: 12/23/2022]
Abstract
Lung microbiota (LM) is an interesting new way to consider and redesign pathogenesis and possible therapeutic approach to many lung diseases, such as idiopathic pulmonary fibrosis (IPF), which is an interstitial pneumonia with bad prognosis. Chronic inflammation is the basis but probably not the only cause of lung fibrosis and although the risk factors are not completely clear, endogenous factors (e.g. gastroesophageal reflux) and environmental factors like cigarette smoking, industrial dusts, and precisely microbial agents could contribute to the IPF development. It is well demonstrated that many bacteria can cause epithelial cell injuries in the airways through induction of a host immune response or by activating flogosis mediators following a chronic, low-level antigenic stimulus. This persistent host response could influence fibroblast responsiveness suggesting that LM may play a role in repetitive alveolar injury in IPF. We reviewed literature regarding not only bacteria but also the role of virome and mycobiome in IPF. In fact, some viruses such as hepatitis C virus or certain fungi could be etiological agents or co-factors in the IPF progress. We aim to illustrate how the cross-talk between different local microbiotas throughout specific axis and immune modulation governed by microorganisms could be at the basis of lung dysfunctions and IPF development. Finally, since the future direction of medicine will be personalized, we suggest that the analysis of LM could be a goal to research new therapies also in IPF.
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Affiliation(s)
- Alessio Fabbrizzi
- Department of Respiratory Physiopathology, Palagi Hospital, Florence, Italy
| | - Giulia Nannini
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - Federico Lavorini
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - Sara Tomassetti
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - Amedeo Amedei
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy.,SOD of Interdisciplinary Internal Medicine, Azienda Ospedaliera Universitaria Careggi (AOUC), Florence, Italy
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7
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Effect of chewing betel nut on the gut microbiota of Hainanese. PLoS One 2021; 16:e0258489. [PMID: 34648581 PMCID: PMC8516201 DOI: 10.1371/journal.pone.0258489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 09/28/2021] [Indexed: 12/12/2022] Open
Abstract
Betel nut chewing (BNC) is prevalent in South Asia and Southeast Asia. BNC can affect host health by modulating the gut microbiota. The aim of this study is to evaluate the effect of BNC on the gut microbiota of the host. Feces samples were obtained from 34 BNC individuals from Ledong and Lingshui, Hainan, China. The microbiota was analyzed by 16S rRNA gene sequencing. BNC decreased the microbial α-diversity. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the predominant phyla, accounting for 99.35% of the BNC group. The Firmicutes-to-Bacteroidetes ratio was significantly increased in the BNC group compared to a control group. The abundances of the families Aerococcaceae, Neisseriaceae, Moraxellaceae, Porphyromonadaceae, and Planococcaceae were decreased in the BNC/BNC_Male/BNC_Female groups compared to the control group, whereas the abundances of Coriobacteriaceae, Streptococcaceae, Micrococcaceae, Xanthomonadaceae, Coxiellaceae, Nocardioidaceae, Rhodobacteraceae, and Succinivibrionaceae were increased. In general, the gut microbiome profiles suggest that BNC may have positive effects, such as an increase in the abundance of beneficial microbes and a reduction in the abundance of disease-related microbes. However, BNC may also produce an increase in the abundance of disease-related microbes. Therefore, extraction of prebiotic components could increase the beneficial value of betel nut.
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8
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Zheng J, Wu Q, Zou Y, Wang M, He L, Guo S. Respiratory Microbiota Profiles Associated With the Progression From Airway Inflammation to Remodeling in Mice With OVA-Induced Asthma. Front Microbiol 2021; 12:723152. [PMID: 34526979 PMCID: PMC8435892 DOI: 10.3389/fmicb.2021.723152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/27/2021] [Indexed: 12/31/2022] Open
Abstract
Background The dysbiosis of respiratory microbiota plays an important role in asthma development. However, there is limited information on the changes in the respiratory microbiota and how these affect the host during the progression from acute allergic inflammation to airway remodeling in asthma. Objective An ovalbumin (OVA)-induced mouse model of chronic asthma was established to explore the dynamic changes in the respiratory microbiota in the different stages of asthma and their association with chronic asthma progression. Methods Hematoxylin and eosin (H&E), periodic acid-schiff (PAS), and Masson staining were performed to observe the pathological changes in the lung tissues of asthmatic mice. The respiratory microbiota was analyzed using 16S rRNA gene sequencing followed by taxonomical analysis. The cytokine levels in bronchoalveolar lavage fluid (BALF) specimens were measured. The matrix metallopeptidase 9 (MMP-9) and vascular endothelial growth factor (VEGF-A) expression levels in lung tissues were measured to detect airway remodeling in OVA-challenged mice. Results Acute allergic inflammation was the major manifestation at weeks 1 and 2 after OVA atomization stimulation, whereas at week 6 after the stimulation, airway remodeling was the most prominent observation. In the acute inflammatory stage, Pseudomonas was more abundant, whereas Staphylococcus and Cupriavidus were more abundant at the airway remodeling stage. The microbial compositions of the upper and lower respiratory tracts were similar. However, the dominant respiratory microbiota in the acute inflammatory and airway remodeling phases were different. Metagenomic functional prediction showed that the pathways significantly upregulated in the acute inflammatory phase and airway remodeling phase were different. The cytokine levels in BALF and the expression patterns of proteins associated with airway remodeling in the lung tissue were consistent with the metagenomic function results. Conclusion The dynamic changes in respiratory microbiota are closely associated with the progression of chronic asthma. Metagenomic functional prediction indicated the changes associated with acute allergic inflammation and airway remodeling.
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Affiliation(s)
- Jun Zheng
- Department of Traditional Chinese Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Wu
- Department of Traditional Chinese Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ya Zou
- Department of Emergency Medicine, Putuo Hospital, Shanghai University of Traditional Medicine, Shanghai, China
| | - Meifen Wang
- Department of Pediatrics, Sanmen People's Hospital, Taizhou, China
| | - Li He
- Department of Traditional Chinese Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Sheng Guo
- Department of Endocrine, Genetics and Metabolism, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
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Hartmann JE, Albrich WC, Dmitrijeva M, Kahlert CR. The Effects of Corticosteroids on the Respiratory Microbiome: A Systematic Review. Front Med (Lausanne) 2021; 8:588584. [PMID: 33777968 PMCID: PMC7988087 DOI: 10.3389/fmed.2021.588584] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Background: Since its discovery, the respiratory microbiome has been implicated in the pathogenesis of multiple pulmonary diseases. Even though corticosteroid treatments are widely prescribed for pulmonary diseases, their effects on the respiratory microbiome are still poorly understood. This systematic review summarizes the current understanding of the effects of corticosteroids on the microbiome of the airways. Research Question: How does treatment with corticosteroids impact the respiratory microbiome? Study Design and Methods: According to the PRISMA guidelines, Embase, Medline, and the Cochrane Central Register of Controlled Trials (CENTRAL) databases were systematically searched for all observational or randomized-controlled studies comparing the microbiome parameters of patients receiving corticosteroids to those of controls. The primary outcomes of interest were changes in the diversity, composition and total burden of the respiratory microbiome as assessed by culture-independent molecular methods. Results: Out of 1,943 identified reports, five studies could be included: two on patients with asthma, two on patients with chronic obstructive pulmonary disease and one on patients with chronic rhinosinusitis. The studies were highly heterogeneous with regards to the methods used and the populations investigated. Microbiome diversity increased with corticosteroids at least transiently in three studies and decreased in one study. The effects of corticosteroids on the composition of the respiratory microbiome were significant but without a clear shared direction. A significant increase in microbial burden after corticosteroids was seen in one study. Interpretation: Data on the effect of corticosteroids on the respiratory microbiome are still limited, with considerable heterogeneity between studies. However, available data suggest that corticosteroid treatment may have significant effects on the composition and possibly the diversity of the respiratory microbiome. Further research is needed to better understand the influence of corticosteroids on the respiratory microbiome and thus better target its widespread therapeutic use.
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Affiliation(s)
- Julia E. Hartmann
- Division of Infectious Diseases/Hospital Epidemiology, Kantonsspital St. Gallen, St.Gallen, Switzerland
| | - Werner C. Albrich
- Division of Infectious Diseases/Hospital Epidemiology, Kantonsspital St. Gallen, St.Gallen, Switzerland
| | - Marija Dmitrijeva
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Christian R. Kahlert
- Division of Infectious Diseases/Hospital Epidemiology, Kantonsspital St. Gallen, St.Gallen, Switzerland
- Division of Infectious Diseases/Hospital Epidemiology, Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland
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10
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Chen R, Wang L, Koch T, Curtis V, Yin-DeClue H, Handley SA, Shan L, Holtzman MJ, Castro M, Wang L. Sex effects in the association between airway microbiome and asthma. Ann Allergy Asthma Immunol 2020; 125:652-657.e3. [PMID: 32931909 DOI: 10.1016/j.anai.2020.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/02/2020] [Accepted: 09/04/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND Sex differences exist in asthma susceptibility and severity. Accumulating evidence has linked airway microbiome dysbiosis to asthma, and airway microbial communities have been found to differ by sex. However, whether sex modifies the link between airway microbiome and asthma has not been investigated. OBJECTIVE To evaluate sex effects in the association between airway microbiome and asthma. METHODS We analyzed induced sputum samples from 47 subjects (n = 23 patients with asthma and n = 24 normal controls) using 16S ribosomal RNA gene sequencing methods. The bacterial composition was analyzed for sex differences. Bacterial associations with asthma were assessed for each sex at the core taxa and genus levels. RESULTS The microbiome in induced sputum differed in women vs men at the community level. A total of 5 core bacterial taxa were found in all samples. No sex-specific core taxa were detected. The most abundant core taxon, Streptococcus salivarius, was significantly enriched in women than in men (P = .02). Within each sex, individuals with relatively lower abundance of S salivarius were more likely to have asthma (P = .006). For both sexes, increased Lactobacillus species were found in sputum samples of patients with patients compared with normal controls (adjusted P = .01). Haemophilus species were associated with asthma in men and not in women. CONCLUSION The airway microbiome differed by sex, and sex effects exist in the association of airway microbial markers and asthma. Future airway microbiome studies may yield better resolution if the context of specific sex is considered. The airway microbiome is a potential mechanism driving sex differences in asthma.
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Affiliation(s)
- Renjin Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Leran Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Tammy Koch
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Vanessa Curtis
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Huiqing Yin-DeClue
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri; Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri
| | - Liang Shan
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Michael J Holtzman
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Mario Castro
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, Kansas
| | - Leyao Wang
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri.
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11
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Luo J, Long Y. NTSHMDA: Prediction of Human Microbe-Disease Association Based on Random Walk by Integrating Network Topological Similarity. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:1341-1351. [PMID: 30489271 DOI: 10.1109/tcbb.2018.2883041] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Accumulating clinic evidences have demonstrated that the microbes residing in human bodies play a significantly important role in the formation, development, and progression of various complex human diseases. Identifying latent related microbes for disease could provide insight into human disease mechanisms and promote disease prevention, diagnosis, and treatment. In this paper, we first construct a heterogeneous network by connecting the disease similarity network and the microbe similarity network through known microbe-disease association network, and then develop a novel computational model to predict human microbe-disease associations based on random walk by integrating network topological similarity (NTSHMDA). Specifically, each microbe-disease association pair is regarded as a distinct relationship level and, thus, assigned different weights based on network topological similarity. The experimental results show that NTSHMDA outperforms some state-of-the-art methods with average AUCs of 0.9070, 0.8896 ± 0.0038 in the frameworks of Leave-one-out cross validation and 5-fold cross validation, respectively. In case studies, 9, 18, 38 and 9, 18, 45 out of top-10, 20, 50 candidate microbes are verified by recently published literatures for asthma and inflammatory bowel disease, respectively. In conclusion, NTSHMDA has potential ability to identify novel disease-microbe associations and can also provide valuable information for drug discovery and biological researches.
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12
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Li S, Xie M, Liu X. A Novel Approach Based on Bipartite Network Recommendation and KATZ Model to Predict Potential Micro-Disease Associations. Front Genet 2019; 10:1147. [PMID: 31803235 PMCID: PMC6873782 DOI: 10.3389/fgene.2019.01147] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/21/2019] [Indexed: 12/24/2022] Open
Abstract
Accumulating evidence indicates that the microbes colonizing human bodies have crucial effects on human health and the discovery of disease-related microbes will promote the discovery of biomarkers and drugs for the prevention, diagnosis, treatment, and prognosis of diseases. However clinical experiments of disease-microbe associations are time-consuming, laborious and expensive, and there are few methods for predicting potential microbe-disease association. Therefore, developing effective computational models utilizing the accumulated public data of clinically validated microbe-disease associations to identify novel disease-microbe associations is of practical importance. We propose a novel method based on the KATZ model and Bipartite Network Recommendation Algorithm (KATZBNRA) to discover potential associations between microbes and diseases. We calculate the Gaussian interaction profile kernel similarity of diseases and microbes based on validated disease-microbe associations. Then, we construct a bipartite graph and execute a bipartite network recommendation algorithm. Finally, we integrate the disease similarity, microbe similarity and bipartite network recommendation score to obtain the final score, which is used to infer whether there are some novel disease-microbe interactions. To evaluate the predictive power of KATZBNRA, we tested it with the walk length 2 using global leave-one-out cross validation (LOOV), two-fold and five-fold cross validations, with AUCs of 0.9098, 0.8463 and 0.8969, respectively. The test results also show that KATZBNRA is more accurate than two recent similar methods KATZHMDA and BNPMDA.
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Affiliation(s)
- Shiru Li
- College of Information Science and Engineering, Hunan Normal University, Changsha, China
| | - Minzhu Xie
- College of Information Science and Engineering, Hunan Normal University, Changsha, China
| | - Xinqiu Liu
- Hunan Vocational College of Engineering, Changsha, China
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13
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Long Y, Luo J. WMGHMDA: a novel weighted meta-graph-based model for predicting human microbe-disease association on heterogeneous information network. BMC Bioinformatics 2019; 20:541. [PMID: 31675979 PMCID: PMC6824056 DOI: 10.1186/s12859-019-3066-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/02/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND An increasing number of biological and clinical evidences have indicated that the microorganisms significantly get involved in the pathological mechanism of extensive varieties of complex human diseases. Inferring potential related microbes for diseases can not only promote disease prevention, diagnosis and treatment, but also provide valuable information for drug development. Considering that experimental methods are expensive and time-consuming, developing computational methods is an alternative choice. However, most of existing methods are biased towards well-characterized diseases and microbes. Furthermore, existing computational methods are limited in predicting potential microbes for new diseases. RESULTS Here, we developed a novel computational model to predict potential human microbe-disease associations (MDAs) based on Weighted Meta-Graph (WMGHMDA). We first constructed a heterogeneous information network (HIN) by combining the integrated microbe similarity network, the integrated disease similarity network and the known microbe-disease bipartite network. And then, we implemented iteratively pre-designed Weighted Meta-Graph search algorithm on the HIN to uncover possible microbe-disease pairs by cumulating the contribution values of weighted meta-graphs to the pairs as their probability scores. Depending on contribution potential, we described the contribution degree of different types of meta-graphs to a microbe-disease pair with bias rating. Meta-graph with higher bias rating will be assigned greater weight value when calculating probability scores. CONCLUSIONS The experimental results showed that WMGHMDA outperformed some state-of-the-art methods with average AUCs of 0.9288, 0.9068 ±0.0031 in global leave-one-out cross validation (LOOCV) and 5-fold cross validation (5-fold CV), respectively. In the case studies, 9, 19, 37 and 10, 20, 45 out of top-10, 20, 50 candidate microbes were manually verified by previous reports for asthma and inflammatory bowel disease (IBD), respectively. Furthermore, three common human diseases (Crohn's disease, Liver cirrhosis, Type 1 diabetes) were adopted to demonstrate that WMGHMDA could be efficiently applied to make predictions for new diseases. In summary, WMGHMDA has a high potential in predicting microbe-disease associations.
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Affiliation(s)
- Yahui Long
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China.
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14
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Niu YW, Qu CQ, Wang GH, Yan GY. RWHMDA: Random Walk on Hypergraph for Microbe-Disease Association Prediction. Front Microbiol 2019; 10:1578. [PMID: 31354672 PMCID: PMC6635699 DOI: 10.3389/fmicb.2019.01578] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/25/2019] [Indexed: 12/12/2022] Open
Abstract
Based on advancements in deep sequencing technology and microbiology, increasing evidence indicates that microbes inhabiting humans modulate various host physiological phenomena, thus participating in various disease pathogeneses. Owing to increasing availability of biological data, further studies on the establishment of efficient computational models for predicting potential associations are required. In particular, computational approaches can also reduce the discovery cycle of novel microbe-disease associations and further facilitate disease treatment, drug design, and other scientific activities. This study aimed to develop a model based on the random walk on hypergraph for microbe-disease association prediction (RWHMDA). As a class of higher-order data representation, hypergraph could effectively recover information loss occurring in the normal graph methodology, thus exclusively illustrating multiple pair-wise associations. Integrating known microbe-disease associations in the Human Microbe-Disease Association Database (HMDAD) and the Gaussian interaction profile kernel similarity for microbes, random walk was then implemented for the constructed hypergraph. Consequently, RWHMDA performed optimally in predicting the underlying disease-associated microbes. More specifically, our model displayed AUC values of 0.8898 and 0.8524 in global and local leave-one-out cross-validation (LOOCV), respectively. Furthermore, three human diseases (asthma, Crohn's disease, and type 2 diabetes) were studied to further illustrate prediction performance. Moreover, 8, 10, and 8 of the 10 highest ranked microbes were confirmed through recent experimental or clinical studies. In conclusion, RWHMDA is expected to display promising potential to predict disease-microbe associations for follow-up experimental studies and facilitate the prevention, diagnosis, treatment, and prognosis of complex human diseases.
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Affiliation(s)
- Ya-Wei Niu
- School of Mathematics, Shandong University, Jinan, China
| | - Cun-Quan Qu
- School of Mathematics, Shandong University, Jinan, China.,Data Science Institute, Shandong University, Jinan, China
| | - Guang-Hui Wang
- School of Mathematics, Shandong University, Jinan, China.,Data Science Institute, Shandong University, Jinan, China
| | - Gui-Ying Yan
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
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15
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Abdel-Aziz MI, Vijverberg SJH, Neerincx AH, Kraneveld AD, Maitland-van der Zee AH. The crosstalk between microbiome and asthma: Exploring associations and challenges. Clin Exp Allergy 2019; 49:1067-1086. [PMID: 31148278 PMCID: PMC6852296 DOI: 10.1111/cea.13444] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/17/2022]
Abstract
With the advancement of high‐throughput DNA/RNA sequencing and computational analysis techniques, commensal bacteria are now considered almost as important as pathological ones. Understanding the interaction between these bacterial microbiota, host and asthma is crucial to reveal their role in asthma pathophysiology. Several airway and/or gut microbiome studies have shown associations between certain bacterial taxa and asthma. However, challenges remain before gained knowledge from these studies can be implemented into clinical practice, such as inconsistency between studies in choosing sampling compartments and/or sequencing approaches, variability of results in asthma studies, and not taking into account medication intake and diet composition especially when investigating gut microbiome. Overcoming those challenges will help to better understand the complex asthma disease process. The therapeutic potential of using pro‐ and prebiotics to prevent or reduce risk of asthma exacerbations requires further investigation. This review will focus on methodological issues regarding setting up a microbiome study, recent developments in asthma bacterial microbiome studies, challenges and future therapeutic potential.
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Affiliation(s)
- Mahmoud I Abdel-Aziz
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Clinical Pharmacy, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Susanne J H Vijverberg
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Anne H Neerincx
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Aletta D Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.,Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Anke H Maitland-van der Zee
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Pediatric Respiratory Medicine, Amsterdam UMC, Emma Children's Hospital, Amsterdam, The Netherlands
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16
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Schmidt J, Krohn S, Buenger L, Zeller K, Schneider H, Treuheit M, Kaiser T, Ziebolz D, Berg T, Haak R. Molecular characterization of intact cell-derived and cell-free bacterial DNA from carious dentine samples. J Microbiol Methods 2019; 158:33-43. [DOI: 10.1016/j.mimet.2019.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 01/22/2023]
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17
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Peng LH, Yin J, Zhou L, Liu MX, Zhao Y. Human Microbe-Disease Association Prediction Based on Adaptive Boosting. Front Microbiol 2018; 9:2440. [PMID: 30356751 PMCID: PMC6189371 DOI: 10.3389/fmicb.2018.02440] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 09/24/2018] [Indexed: 12/13/2022] Open
Abstract
There are countless microbes in the human body, and they play various roles in the physiological process. There is growing evidence that microbes are closely associated with human diseases. Researching disease-related microbes helps us understand the mechanisms of diseases and provides new strategies for diseases diagnosis and treatment. Many computational models have been proposed to predict disease-related microbes, in this paper, we developed a model of Adaptive Boosting for Human Microbe-Disease Association prediction (ABHMDA) to reveal the associations between diseases and microbes by calculating the relation probability of disease-microbe pair using a strong classifier. Our model could be applied to new diseases without any known related microbes. In order to assess the prediction power of the model, global and local leave-one-out cross validation (LOOCV) were implemented. As shown in the results, the global and local LOOCV values reached 0.8869 and 0.7910, respectively. What's more, 10, 10, and 8 out of the top 10 microbes predicted to be most likely to be associated with Asthma, Colorectal carcinoma and Type 1 diabetes were all verified by relevant literatures or database HMDAD, respectively. The above results verify the superior predictive performance of ABHMDA.
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Affiliation(s)
- Li-Hong Peng
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Jun Yin
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Liqian Zhou
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Ming-Xi Liu
- Institutes of Science and Development, Chinese Academy of Sciences, Beijing, China
| | - Yan Zhao
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
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18
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Mathieu E, Escribano-Vazquez U, Descamps D, Cherbuy C, Langella P, Riffault S, Remot A, Thomas M. Paradigms of Lung Microbiota Functions in Health and Disease, Particularly, in Asthma. Front Physiol 2018; 9:1168. [PMID: 30246806 PMCID: PMC6110890 DOI: 10.3389/fphys.2018.01168] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/03/2018] [Indexed: 12/22/2022] Open
Abstract
Improvements in our knowledge of the gut microbiota have broadened our vision of the microbes associated with the intestine. These microbes are essential actors and protectors of digestive and extra-digestive health and, by extension, crucial for human physiology. Similar reconsiderations are currently underway concerning the endogenous microbes of the lungs, with a shift in focus away from their involvement in infections toward a role in physiology. The discovery of the lung microbiota was delayed by the long-held view that the lungs of healthy individuals were sterile and by sampling difficulties. The lung microbiota has a low density, and the maintenance of small numbers of bacteria seems to be a critical determinant of good health. This review aims to highlight how knowledge about the lung microbiota can change our conception of lung physiology and respiratory health. We provide support for this point of view with knowledge acquired about the gut microbiota and intestinal physiology. We describe the main characteristics of the lung microbiota and its functional impact on lung physiology, particularly in healthy individuals, after birth, but also in asthma. We describe some of the physiological features of the respiratory tract potentially favoring the installation of a dysbiotic microbiota. The gut microbiota feeds and matures the intestinal epithelium and is involved in immunity, when the principal role of the lung microbiota seems to be the orientation and balance of aspects of immune and epithelial responsiveness. This implies that the local and remote effects of bacterial communities are likely to be determinant in many respiratory diseases caused by viruses, allergens or genetic deficiency. Finally, we discuss the reciprocal connections between the gut and lungs that render these two compartments inseparable.
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Affiliation(s)
- Elliot Mathieu
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Unai Escribano-Vazquez
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Delphyne Descamps
- Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Claire Cherbuy
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Philippe Langella
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sabine Riffault
- Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Aude Remot
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Muriel Thomas
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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19
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Wu C, Gao R, Zhang D, Han S, Zhang Y. PRWHMDA: Human Microbe-Disease Association Prediction by Random Walk on the Heterogeneous Network with PSO. Int J Biol Sci 2018; 14:849-857. [PMID: 29989079 PMCID: PMC6036753 DOI: 10.7150/ijbs.24539] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 02/28/2018] [Indexed: 12/24/2022] Open
Abstract
Microorganisms resided in human body play a vital role in metabolism, immune defense, nutrition absorption, cancer control and protection against pathogen colonization. The changes of microbial communities can cause human diseases. Based on the known microbe-disease association, we presented a novel computational model employing Random Walking with Restart optimized by Particle Swarm Optimization (PSO) on the heterogeneous interlinked network of Human Microbe-Disease Associations (PRWHMDA) (see Figure 1). Based on the known human microbe-disease associations, we constructed the heterogeneous interlinked network with Cosine similarity. The extended random walk with restart (RWR) method was derived to get the potential microbe-disease associations. PSO was utilized to get the optimal parameters of RWR. To evaluate the prediction effectiveness, we performed leave one out cross validation (LOOCV) and 5-fold cross validation (CV), which got the AUC (The area under ROC curve) of 0.915 (LOOCV) and the average AUCs of 0.8875 ± 0.0046 (5-fold CV). Moreover, we carried out three case studies of asthma, inflammatory bowel disease (IBD) and type 1 diabetes (T1D) for the further evaluation. The result showed that 10, 10 and 9 of top-10 predicted microbes were verified by previously published experimental results, respectively. It is anticipated that PRWHMDA can be effective to identify the disease-related microbes and maybe helpful to disclose the relationship between microorganisms and their human host.
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Affiliation(s)
- Chuanyan Wu
- School of Control Science and Engineering, Shandong University, Jinan, 250061, China
| | - Rui Gao
- School of Control Science and Engineering, Shandong University, Jinan, 250061, China
| | - Daoliang Zhang
- School of Control Science and Engineering, Shandong University, Jinan, 250061, China
| | - Shiyun Han
- General Clinic, The No. 2 People's Hospital of Tianqiao, Jinan, 250032, China
| | - Yusen Zhang
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, China
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20
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Zou S, Zhang J, Zhang Z. A novel approach for predicting microbe-disease associations by bi-random walk on the heterogeneous network. PLoS One 2017; 12:e0184394. [PMID: 28880967 PMCID: PMC5589230 DOI: 10.1371/journal.pone.0184394] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/23/2017] [Indexed: 02/07/2023] Open
Abstract
Since the microbiome has a significant impact on human health and disease, microbe-disease associations can be utilized as a valuable resource for understanding disease pathogenesis and promoting disease diagnosis and prognosis. Accordingly, it is necessary for researchers to achieve a comprehensive and deep understanding of the associations between microbes and diseases. Nevertheless, to date, little work has been achieved in implementing novel human microbe-disease association prediction models. In this paper, we develop a novel computational model to predict potential microbe-disease associations by bi-random walk on the heterogeneous network (BiRWHMDA). The heterogeneous network was constructed by connecting the microbe similarity network and the disease similarity network via known microbe-disease associations. Microbe similarity and disease similarity were calculated by the Gaussian interaction profile kernel similarity measure; moreover, a logistic function was applied to regulate disease similarity. Additionally, leave-one-out cross validation and 5-fold cross validation were implemented to evaluate the predictive performance of our method; both cross validation methods performed well. The leave-one-out cross validation experiment results illustrate that our method outperforms other previously proposed methods. Furthermore, case studies on asthma and inflammatory bowel disease prove the favorable performance of our method. In conclusion, our method can be considered as an effective computational model for predicting novel microbe-disease associations.
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Affiliation(s)
- Shuai Zou
- School of Information Science and Engineering, Central South University, Changsha, Hunan, China
| | - Jingpu Zhang
- School of Information Science and Engineering, Central South University, Changsha, Hunan, China
| | - Zuping Zhang
- School of Information Science and Engineering, Central South University, Changsha, Hunan, China
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21
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Szemiako K, Śledzińska A, Krawczyk B. A new assay based on terminal restriction fragment length polymorphism of homocitrate synthase gene fragments for Candida species identification. J Appl Genet 2017; 58:409-414. [PMID: 28349380 PMCID: PMC5509809 DOI: 10.1007/s13353-017-0394-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 02/21/2017] [Accepted: 03/17/2017] [Indexed: 12/02/2022]
Abstract
Candida sp. have been responsible for an increasing number of infections, especially in patients with immunodeficiency. Species-specific differentiation of Candida sp. is difficult in routine diagnosis. This identification can have a highly significant association in therapy and prophylaxis. This work has shown a new application of the terminal restriction fragment length polymorphism (t-RFLP) method in the molecular identification of six species of Candida, which are the most common causes of fungal infections. Specific for fungi homocitrate synthase gene was chosen as a molecular target for amplification. The use of three restriction enzymes, DraI, RsaI, and BglII, for amplicon digestion can generate species-specific fluorescence labeled DNA fragment profiles, which can be used to determine the diagnostic algorithm. The designed method can be a cost-efficient high-throughput molecular technique for the identification of six clinically important Candida species.
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Affiliation(s)
- Kasjan Szemiako
- Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Anna Śledzińska
- Department of Therapy Monitoring and Pharmacogenetics, Medical University of Gdańsk, Gdańsk, Poland
| | - Beata Krawczyk
- Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland.
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