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Barac A, Vujovic A, Peric J, Tulic I, Stojanovic M, Stjepanovic M. Rethinking Aspergillosis in the Era of Microbiota and Mycobiota. Mycopathologia 2024; 189:49. [PMID: 38864956 DOI: 10.1007/s11046-024-00853-2] [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: 10/10/2023] [Accepted: 04/09/2024] [Indexed: 06/13/2024]
Abstract
Aspergillosis encompasses a wide range of clinical conditions based on the interaction between Aspergillus and the host. It ranges from colonization to invasive aspergillosis. The human lung provides an entry door for Aspergillus. Aspergillus has virulence characteristics such as conidia, rapid growth at body temperature, and the production of specific proteins, carbohydrates, and secondary metabolites that allow A. fumigatus to infiltrate the lung's alveoli and cause invasive aspergillosis. Alveolar epithelial cells play an important role in both fungus clearance and immune cell recruitment via cytokine release. Although the innate immune system quickly clears conidia in immunocompetent hosts, A. fumigatus has evolved multiple virulence factors in order to escape immune response such as ROS detoxifying enzymes, the rodlet layer, DHN-melanin and toxins. Bacterial co-infections or interactions can alter the immune response, impact Aspergillus growth and virulence, enhance biofilm formation, confound diagnosis, and reduce treatment efficacy. The gut microbiome's makeup influences pulmonary immune responses generated by A. fumigatus infection and vice versa. The real-time PCR for Aspergillus DNA detection might be a particularly useful tool to diagnose pulmonary aspergillosis. Metagenomics analyses allow quick and easy detection and identification of a great variety of fungi in different clinical samples, although optimization is still required particularly for the use of NGS techniques. This review will analyze the current state of aspergillosis in light of recent discoveries in the microbiota and mycobiota.
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Affiliation(s)
- Aleksandra Barac
- Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, Belgrade, Serbia.
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.
| | - Ankica Vujovic
- Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Jovan Peric
- Center for Anesthesiology and Resuscitation, University Clinical Center of Serbia, Belgrade, Serbia
| | - Ivan Tulic
- Clinic for Orthopedic Surgery and Traumatology, University Clinical Center of Serbia, Belgrade, Serbia
| | - Maja Stojanovic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
- Clinic for Allergology and Clinical Immunology, University Clinical Center of Serbia, Belgrade, Serbia
| | - Mihailo Stjepanovic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
- Clinic for Pulmonology, University Clinical Center of Serbia, Belgrade, Serbia
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Wu Y, Huang L, Li M, Cui X, Zhu J, Zhan Q, Wang C. Association between the lung microbiome and perioperative prognosis in lung transplant recipients. J Appl Microbiol 2024; 135:lxae089. [PMID: 38573839 DOI: 10.1093/jambio/lxae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/29/2024] [Accepted: 04/03/2024] [Indexed: 04/06/2024]
Abstract
RATIONALE Studies have confirmed that the lung microbiome of lung transplant recipients is altered and serves as a prognostic indicator for long-term mortality. Other studies reported that the lung microbiome affects host immunity and the transcriptome. However, the lung microbiome composition at the early post-transplant period following lung transplantation is unclear, and the relationship of the lung microbiome with pulmonary immunity and the host transcriptome is also not well understood. OBJECTIVES We hypothesize that changes in the lung microbiome composition in the early post-transplant period may have a predictive value for perioperative outcomes following lung transplantation and that the lung microbiome is correlated with pulmonary immunity and the host transcriptome. Thus, this prospective study aimed at observing the lung microbiome composition in the early post-transplant period and the impact of the lung microbiome on pulmonary cytokines and the host transcriptome. Our findings will help us gain a comprehensive understanding of the distribution and significance of the lung microbiome in the early post-transplant period. METHODS An observational study was conducted to identify the lung microbiome and the host transcriptome characteristics using next-generation sequencing. Luminex was employed for quantifying alveolar cytokines. Spearman's correlation analysis was utilized to assess the impact of the lung microbiome on pulmonary immunity and differentially expressed genes in patients who died perioperatively after lung transplantation. RESULTS Patients with poor perioperative outcomes showed an increase in Mycoplasma and Arcobacter, a decrease of Gemella, and increased interleukin (IL)-10, IL-1β, and tumor necrosis factor (TNF)-α concentration. The lung microbiome correlates with lung immunity in lung transplant recipients. In the death group, the function of differentially expressed genes is associated with cell apoptosis, and promoting TNF production is upregulated. The lung microbiome is related to differentially expressed genes between the two groups. CONCLUSIONS The lung microbiome and cytokines can be considered as potential biomarkers for early prognosis in lung transplant recipients. The lung microbiome is associated with both lung immunity and differentially expressed genes in lung transplant recipients.
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Affiliation(s)
- Yuhan Wu
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Harbin Medical University, Harbin 150086, China
- Harbin Medical University, Harbin 150086, China
| | - Linna Huang
- Department of Respiratory and Critical Care Medicine, China-Japan Friendship Hospital, Beijing 100029, China
| | - Min Li
- Department of Respiratory and Critical Care Medicine, China-Japan Friendship Hospital, Beijing 100029, China
| | - Xiaoyang Cui
- Department of Respiratory and Critical Care Medicine, China-Japan Friendship Hospital, Beijing 100029, China
| | - Jun Zhu
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Harbin Medical University, Harbin 150086, China
- Harbin Medical University, Harbin 150086, China
| | - Qingyuan Zhan
- Department of Respiratory and Critical Care Medicine, China-Japan Friendship Hospital, Beijing 100029, China
| | - Chen Wang
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Harbin Medical University, Harbin 150086, China
- Harbin Medical University, Harbin 150086, China
- Department of Respiratory and Critical Care Medicine, China-Japan Friendship Hospital, Beijing 100029, China
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Baldi S, Fabbrizzi A, Di Gloria L, Pallecchi M, Nannini G, D'Ambrosio M, Luceri C, Bartolucci G, Ramazzotti M, Fontana G, Mannini C, Lavorini F, Amedei A. First Exploration of the Altered Microbial Gut-Lung Axis in the Pathogenesis of Human Refractory Chronic Cough. Lung 2024; 202:107-118. [PMID: 38526572 PMCID: PMC11009740 DOI: 10.1007/s00408-024-00681-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/04/2024] [Indexed: 03/26/2024]
Abstract
PURPOSE Cough represents a natural mechanism that plays an important defensive role in the respiratory tract, but in some conditions, it may become persistent, nonproductive, and harmful. In general, refractory chronic cough (RCC) occurs in about 20% of individuals; hence, we aimed to assess the presence of altered gut-lung communication in RCC patients through a compositional and functional characterization of both gut (GM) and oral microbiota (OM). METHODS 16S rRNA sequencing was used to characterize both GM and OM composition of RCC patients and healthy controls (HC). PICRUST2 assessed functional changes in microbial communities while gas chromatography was used to evaluate fecal short-chain fatty acid levels and serum-free fatty acid (FFA) abundances. RESULTS In comparison with HC, RCC patients reported increased saliva alpha-diversity and statistically significant beta-diversity in both GM and OM. Also, a, respectively, significant increased or reduced Firmicutes/Bacteroidota ratio in stool and saliva samples of RCC patients has been shown, in addition to a modification of the abundances of several taxa in both GM and OM. Moreover, a potential fecal over-expression of lipopolysaccharide biosynthesis and lipoic acid metabolism pathways and several differences in serum FFA levels have been reported in RCC patients than in HC. CONCLUSION Since differences in both GM and OM of RCC patients have been documented, these findings could provide new information about RCC pathogenesis and also pave the way for the development of novel nutritional or pharmacological interventions for the management of RCC through the restoration of eubiotic gut-lung communication.
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Affiliation(s)
- Simone Baldi
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134, Florence, Italy
| | - Alessio Fabbrizzi
- Department of Respiratory Physiopathology, Palagi Hospital, 50122, Florence, Italy
| | - Leandro Di Gloria
- Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Florence, 50134, Florence, Italy
| | - Marco Pallecchi
- Department of Neuroscience, Psychology, Drug Research and Child Health NEUROFARBA, University of Florence, 50139, Florence, Italy
| | - Giulia Nannini
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134, Florence, Italy
| | - Mario D'Ambrosio
- Department of Neuroscience, Psychology, Drug Research and Child Health NEUROFARBA, University of Florence, 50139, Florence, Italy
- Enteric Neuroscience Program, Department of Medicine, Section of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Cristina Luceri
- Department of Neuroscience, Psychology, Drug Research and Child Health NEUROFARBA, University of Florence, 50139, Florence, Italy
| | - Gianluca Bartolucci
- Department of Neuroscience, Psychology, Drug Research and Child Health NEUROFARBA, University of Florence, 50139, Florence, Italy
| | - Matteo Ramazzotti
- Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Florence, 50134, Florence, Italy
| | - Giovanni Fontana
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134, Florence, Italy
| | - Claudia Mannini
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134, Florence, Italy
| | - Federico Lavorini
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134, Florence, Italy.
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134, Florence, Italy.
- SOD of Interdisciplinary Internal Medicine, Azienda Ospedaliera Universitaria Careggi (AOUC), 50134, Florence, Italy.
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Lian Q, Song X, Yang J, Wang L, Xu P, Wang X, Xu X, Yang B, He J, Ju C. Alterations of lung microbiota in lung transplant recipients with pneumocystis jirovecii pneumonia. Respir Res 2024; 25:125. [PMID: 38486264 PMCID: PMC10941442 DOI: 10.1186/s12931-024-02755-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 03/04/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Increasing evidence revealed that lung microbiota dysbiosis was associated with pulmonary infection in lung transplant recipients (LTRs). Pneumocystis jirovecii (P. jirovecii) is an opportunistic fungal pathogen that frequently causes lethal pneumonia in LTRs. However, the lung microbiota in LTRs with P. jirovecii pneumonia (PJP) remains unknow. METHODS In this prospective observational study, we performed metagenomic next-generation sequencing (mNGS) on 72 bronchoalveolar lavage fluid (BALF) samples from 61 LTRs (20 with PJP, 22 with PJC, 19 time-matched stable LTRs, and 11 from LTRs after PJP recovery). We compared the lung microbiota composition of LTRs with and without P. jirovecii, and analyzed the related clinical variables. RESULTS BALFs collected at the episode of PJP showed a more discrete distribution with a lower species diversity, and microbiota composition differed significantly compared to P. jirovecii colonization (PJC) and control group. Human gammaherpesvirus 4, Phreatobacter oligotrophus, and Pseudomonas balearica were the differential microbiota species between the PJP and the other two groups. The network analysis revealed that most species had a positive correlation, while P. jirovecii was correlated negatively with 10 species including Acinetobacter venetianus, Pseudomonas guariconensis, Paracandidimonas soli, Acinetobacter colistiniresistens, and Castellaniella defragrans, which were enriched in the control group. The microbiota composition and diversity of BALF after PJP recovery were also different from the PJP and control groups, while the main components of the PJP recovery similar to control group. Clinical variables including age, creatinine, total protein, albumin, IgG, neutrophil, lymphocyte, CD3+CD45+, CD3+CD4+ and CD3+CD8+ T cells were deeply implicated in the alterations of lung microbiota in LTRs. CONCLUSIONS This study suggests that LTRs with PJP had altered lung microbiota compared to PJC, control, and after recovery groups. Furthermore, lung microbiota is related to age, renal function, nutritional and immune status in LTRs.
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Affiliation(s)
- Qiaoyan Lian
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Organ transplantation, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, Guangdong, P.R. China
| | - Xiuling Song
- Vision Medicals Co., Ltd, 510700, Guangzhou, Guangdong, P.R. China
| | - Juhua Yang
- Vision Medicals Co., Ltd, 510700, Guangzhou, Guangdong, P.R. China
| | - Lulin Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Organ transplantation, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, Guangdong, P.R. China
| | - Peihang Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Organ transplantation, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, Guangdong, P.R. China
| | - Xiaohua Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Organ transplantation, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, Guangdong, P.R. China
| | - Xin Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Organ transplantation, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, Guangdong, P.R. China
- Department of Thoracic Surgery, the First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, Guangdong, P.R. China
| | - Bin Yang
- Vision Medicals Co., Ltd, 510700, Guangzhou, Guangdong, P.R. China
| | - Jianxing He
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Organ transplantation, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, Guangdong, P.R. China.
- Department of Thoracic Surgery, the First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, Guangdong, P.R. China.
| | - Chunrong Ju
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Organ transplantation, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, Guangdong, P.R. China.
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Aerts R, Feys S, Mercier T, Lagrou K. Microbiological Diagnosis of Pulmonary Aspergillus Infections. Semin Respir Crit Care Med 2024; 45:21-31. [PMID: 38228164 DOI: 10.1055/s-0043-1776777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
As microbiological tests play an important role in our diagnostic algorithms and clinical approach towards patients at-risk for pulmonary aspergillosis, a good knowledge of the diagnostic possibilities and especially their limitations is extremely important. In this review, we aim to reflect critically on the available microbiological diagnostic modalities for diagnosis of pulmonary aspergillosis and formulate some future prospects. Timely start of adequate antifungal treatment leads to a better patient outcome, but overuse of antifungals should be avoided. Current diagnostic possibilities are expanding, and are mainly driven by enzyme immunoassays and lateral flow device tests for the detection of Aspergillus antigens. Most of these tests are directed towards similar antigens, but new antibodies towards different targets are under development. For chronic forms of pulmonary aspergillosis, anti-Aspergillus IgG antibodies and precipitins remain the cornerstone. More studies on the possibilities and limitations of molecular testing including targeting resistance markers are ongoing. Also, metagenomic next-generation sequencing is expanding our future possibilities. It remains important to combine different test results and interpret them in the appropriate clinical context to improve performance. Test performances may differ according to the patient population and test results may be influenced by timing, the tested matrix, and prophylactic and empiric antifungal therapy. Despite the increasing armamentarium, a simple blood or urine test for the diagnosis of aspergillosis in all patient populations at-risk is still lacking. Research on diagnostic tools is broadening from a pathogen focus on biomarkers related to the patient and its immune system.
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Affiliation(s)
- Robina Aerts
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Simon Feys
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Medical Intensive Care Unit, University Hospitals Leuven, Leuven, Belgium
| | - Toine Mercier
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Oncology-Hematology, AZ Sint-Maarten, Mechelen, Belgium
| | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Laboratory Medicine and National Reference Center for Mycosis, University Hospitals Leuven, Leuven, Belgium
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McDaneld TG, Eicher SD, Dickey A, Kritchevsky JE, Bryan KA, Chitko-McKown CG. Probiotics in milk replacer affect the microbiome of the lung in neonatal dairy calves. Front Microbiol 2024; 14:1298570. [PMID: 38249465 PMCID: PMC10797021 DOI: 10.3389/fmicb.2023.1298570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/04/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction Probiotics have been investigated for their many health benefits and impact on the microbiota of the gut. Recent data have also supported a gut-lung axis regarding the bacterial populations (microbiomes) of the two locations; however, little research has been performed to determine the effects of oral probiotics on the microbiome of the bovine respiratory tract. We hypothesized that probiotic treatment would result in changes in the lung microbiome as measured in lung lavage fluid. Our overall goal was to characterize bacterial populations in the lungs of calves fed probiotics in milk replacer and dry rations from birth to weaning. Methods A group of 20 dairy calves was split into two treatment groups: probiotic (TRT; N = 10, milk replacer +5 g/d probiotics; Bovamine Dairy, Chr. Hansen, Inc., Milwaukee, WI) and control (CON; N = 10, milk replacer only). On day 0, birth weight was obtained, and calves were provided colostrum as per the dairy SOP. On day 2, probiotics were added to the milk replacer of the treated group and then included in their dry ration. Lung lavages were performed on day 52 on five random calves selected from each treatment group. DNA was extracted from lavage fluid, and 16S ribosomal RNA (rRNA) gene hypervariable regions 1-3 were amplified by PCR and sequenced using next-generation sequencing (Illumina MiSeq) for the identification of the bacterial taxa present. Taxa were classified into both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs). Results Overall, the evaluation of these samples revealed that the bacterial genera identified in the lung lavage samples of probiotic-fed calves as compared to the control calves were significantly different based on the OTU dataset (p < 0.05) and approached significance for the ASV dataset (p < 0.06). Additionally, when comparing the diversity of taxa in lung lavage samples to nasal and tonsil samples, taxa diversity of lung samples was significantly lower (p < 0.05). Discussion In conclusion, analysis of the respiratory microbiome in lung lavage samples after probiotic treatment provides insight into the distribution of bacterial populations in response to oral probiotics and demonstrates that oral probiotics affect more than the gut microbiome.
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Affiliation(s)
- Tara G. McDaneld
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Susan D. Eicher
- Livestock Behavior Research Unit, USDA, ARS, West Lafayette, IN, United States
| | - Aaron Dickey
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Janice E. Kritchevsky
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States
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Dumoulin E, Thornton CS, MacGregor JH, Tremblay A, Chan C, MacEachern PR, Kelly MM, Somayaji R, Parkins MD, Mody CH. Combined medical-interventional approaches for the management of complex fungal balls: a case series as a viable alternative in non-surgical patients. Ther Adv Respir Dis 2024; 18:17534666241255203. [PMID: 38785071 PMCID: PMC11119499 DOI: 10.1177/17534666241255203] [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: 10/24/2023] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Intracavitary pulmonary aspergilloma is a persistent and life-threatening infection that carries a mortality rate of up to 15%. It occurs when Aspergillus species gain entry to an existing lung cavity. In the absence of definitive treatment, patients may succumb to severe complications such as massive hemoptysis, cachexia, or secondary infections. Aspergillomas often show limited response to antifungal medications, mainly due to insufficient drug concentrations within the cavities. Surgery is frequently the preferred treatment option, but it poses significant risks, and many individuals are ineligible due to underlying health issues. We present the most extensive non-surgical fungal ball cohort to date, managed using an innovative multimodal strategy that combines antifungal therapy before and after bronchoscopic debulking. This was a cross-sectional observational study. For those who cannot undergo surgery, our medical center has pioneered a multimodal approach to aspergilloma resection. This approach combines bronchoscopic endoscopy with antifungal therapy and has been applied successfully to more than 18 patients that are presented in this series. The median age of the cohort was 58 years (range: 32-73), with an equal sex distribution. The mean percent predicted FEV1 was 65.3%. The mean follow-up duration was 3.6 years (range: 0.5-10 years). The cohort receiving antifungals systematically prior to debridement showed a reduction of the pre-existing cavity (40.38 mm versus 34.02 mm, p = 0.021). Across the 18 patients during the follow-up period, 94% remained recurrence-free (defined by symptoms and radiology). Our study fills a critical knowledge gap regarding the significance of initiating antifungal treatment before bronchoscopic debulking and presents a viable approach in these cases for which there is a current unmet therapeutic need.
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Affiliation(s)
- Elaine Dumoulin
- Department of Medicine, Cumming School of Medicine, University of Calgary, Pulmonary Diagnostics, South Health Campus, 4448 Front Street SE, Calgary, AB T3M 1M4, Canada
| | - Christina S. Thornton
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, CanadaDepartment of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - John H. MacGregor
- Department of Radiology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Alain Tremblay
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Chrystal Chan
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Paul R. MacEachern
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Margaret M. Kelly
- Deptartment of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ranjani Somayaji
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, CanadaDepartment of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Michael D. Parkins
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, CanadaDepartment of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Christopher H. Mody
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, CanadaDepartment of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
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Dellière S, Aimanianda V. Humoral Immunity Against Aspergillus fumigatus. Mycopathologia 2023; 188:603-621. [PMID: 37289362 PMCID: PMC10249576 DOI: 10.1007/s11046-023-00742-0] [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: 03/07/2023] [Accepted: 04/27/2023] [Indexed: 06/09/2023]
Abstract
Aspergillus fumigatus is one the most ubiquitous airborne opportunistic human fungal pathogens. Understanding its interaction with host immune system, composed of cellular and humoral arm, is essential to explain the pathobiology of aspergillosis disease spectrum. While cellular immunity has been well studied, humoral immunity has been poorly acknowledge, although it plays a crucial role in bridging the fungus and immune cells. In this review, we have summarized available data on major players of humoral immunity against A. fumigatus and discussed how they may help to identify at-risk individuals, be used as diagnostic tools or promote alternative therapeutic strategies. Remaining challenges are highlighted and leads are given to guide future research to better grasp the complexity of humoral immune interaction with A. fumigatus.
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Affiliation(s)
- Sarah Dellière
- Institut Pasteur, Immunobiology of Aspergillus, Université de Paris Cité, 75015, Paris, France.
- Laboratoire de Parasitologie-Mycologie, AP-HP, Hôpital Saint-Louis, 75010, Paris, France.
| | - Vishukumar Aimanianda
- Institut Pasteur, Immunobiology of Aspergillus, Université de Paris Cité, 75015, Paris, France.
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Mirhakkak MH, Chen X, Ni Y, Heinekamp T, Sae-Ong T, Xu LL, Kurzai O, Barber AE, Brakhage AA, Boutin S, Schäuble S, Panagiotou G. Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome. Nat Commun 2023; 14:4369. [PMID: 37474497 PMCID: PMC10359302 DOI: 10.1038/s41467-023-39982-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/03/2023] [Indexed: 07/22/2023] Open
Abstract
Aspergillus fumigatus, an opportunistic human pathogen, frequently infects the lungs of people with cystic fibrosis and is one of the most common causes of infectious-disease death in immunocompromised patients. Here, we construct 252 strain-specific, genome-scale metabolic models of this important fungal pathogen to study and better understand the metabolic component of its pathogenic versatility. The models show that 23.1% of A. fumigatus metabolic reactions are not conserved across strains and are mainly associated with amino acid, nucleotide, and nitrogen metabolism. Profiles of non-conserved reactions and growth-supporting reaction fluxes are sufficient to differentiate strains, for example by environmental or clinical origin. In addition, shotgun metagenomics analysis of sputum from 40 cystic fibrosis patients (15 females, 25 males) before and after diagnosis with an A. fumigatus colonization suggests that the fungus shapes the lung microbiome towards a more beneficial fungal growth environment associated with aromatic amino acid availability and the shikimate pathway. Our findings are starting points for the development of drugs or microbiome intervention strategies targeting fungal metabolic needs for survival and colonization in the non-native environment of the human lung.
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Affiliation(s)
- Mohammad H Mirhakkak
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany
| | - Xiuqiang Chen
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany
| | - Yueqiong Ni
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany
| | - Thorsten Heinekamp
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany
| | - Tongta Sae-Ong
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany
| | - Lin-Lin Xu
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany
| | - Oliver Kurzai
- Institute for Hygiene and Microbiology, University of Würzburg, 97080, Würzburg, Germany
- Research Group Fungal Septomics, Leibniz Institute of Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany
- National Reference Center for Invasive Fungal Infections (NRZMyk), Leibniz Institute of Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany
| | - Amelia E Barber
- Junior Research Group Fungal Informatics, Institute of Microbiology, Friedrich-Schiller-University Jena, 07745, Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, 07745, Jena, Germany
| | - Sebastien Boutin
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23562, Lübeck, Germany
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, 69120, Heidelberg, Germany
| | - Sascha Schäuble
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany.
| | - Gianni Panagiotou
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany.
- Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong, China.
- Friedrich Schiller University, Faculty of Biological Sciences, Jena, 07745, Germany.
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10
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Xie G, Hu Q, Cao X, Wu W, Dai P, Guo W, Wang O, Wei L, Ren R, Li Y. Clinical identification and microbiota analysis of Chlamydia psittaci- and Chlamydia abortus- pneumonia by metagenomic next-generation sequencing. Front Cell Infect Microbiol 2023; 13:1157540. [PMID: 37434780 PMCID: PMC10331293 DOI: 10.3389/fcimb.2023.1157540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/29/2023] [Indexed: 07/13/2023] Open
Abstract
Introduction Recently, the incidence of chlamydial pneumonia caused by rare pathogens such as C. psittaci or C. abortus has shown a significant upward trend. The non-specific clinical manifestations and the limitations of traditional pathogen identification methods determine that chlamydial pneumonia is likely to be poorly diagnosed or even misdiagnosed, and may further result in delayed treatment or unnecessary antibiotic use. mNGS's non-preference and high sensitivity give us the opportunity to obtain more sensitive detection results than traditional methods for rare pathogens such as C. psittaci or C. abortus. Methods In the present study, we investigated both the pathogenic profile characteristics and the lower respiratory tract microbiota of pneumonia patients with different chlamydial infection patterns using mNGS. Results More co-infecting pathogens were found to be detectable in clinical samples from patients infected with C. psittaci compared to C. abortus, suggesting that patients infected with C. psittaci may have a higher risk of mixed infection, which in turn leads to more severe clinical symptoms and a longer disease course cycle. Further, we also used mNGS data to analyze for the first time the characteristic differences in the lower respiratory tract microbiota of patients with and without chlamydial pneumonia, the impact of the pattern of Chlamydia infection on the lower respiratory tract microbiota, and the clinical relevance of these characteristics. Significantly different profiles of lower respiratory tract microbiota and microecological diversity were found among different clinical subgroups, and in particular, mixed infections with C. psittaci and C. abortus resulted in lower lung microbiota diversity, suggesting that chlamydial infections shape the unique lung microbiota pathology, while mixed infections with different Chlamydia may have important effects on the composition and diversity of the lung microbiota. Discussion The present study provides possible evidences supporting the close correlation between chlamydial infection, altered microbial diversity in patients' lungs and clinical parameters associated with infection or inflammation in patients, which also provides a new research direction to better understand the pathogenic mechanisms of pulmonary infections caused by Chlamydia.
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Affiliation(s)
- Gongxun Xie
- Department of Pathology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
| | - Qing Hu
- Department of Pathology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
| | - Xuefang Cao
- Institute of Innovative Applications, MatriDx Biotechnology Co., Ltd, Hangzhou, Zhejiang, China
| | - Wenjie Wu
- Institute of Innovative Applications, MatriDx Biotechnology Co., Ltd, Hangzhou, Zhejiang, China
| | - Penghui Dai
- Department of Pathology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
| | - Wei Guo
- Department of Pathology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
| | - Ouxi Wang
- Institute of Innovative Applications, MatriDx Biotechnology Co., Ltd, Hangzhou, Zhejiang, China
| | - Liang Wei
- Institute of Innovative Applications, MatriDx Biotechnology Co., Ltd, Hangzhou, Zhejiang, China
| | - Ruotong Ren
- Institute of Innovative Applications, MatriDx Biotechnology Co., Ltd, Hangzhou, Zhejiang, China
- Foshan Branch, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yanchun Li
- Department of Pathology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
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11
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Tejeda-Garibay S, Hoyer KK. Coccidioidomycosis and Host Microbiome Interactions: What We Know and What We Can Infer from Other Respiratory Infections. J Fungi (Basel) 2023; 9:586. [PMID: 37233297 PMCID: PMC10219296 DOI: 10.3390/jof9050586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/25/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
Between 70 and 80% of Valley fever patients receive one or more rounds of antibiotic treatment prior to accurate diagnosis with coccidioidomycosis. Antibiotic treatment and infection (bacterial, viral, fungal, parasitic) often have negative implications on host microbial dysbiosis, immunological responses, and disease outcome. These perturbations have focused on the impact of gut dysbiosis on pulmonary disease instead of the implications of direct lung dysbiosis. However, recent work highlights a need to establish the direct effects of the lung microbiota on infection outcome. Cystic fibrosis, chronic obstructive pulmonary disease, COVID-19, and M. tuberculosis studies suggest that surveying the lung microbiota composition can serve as a predictive factor of disease severity and could inform treatment options. In addition to traditional treatment options, probiotics can reverse perturbation-induced repercussions on disease outcomes. The purpose of this review is to speculate on the effects perturbations of the host microbiome can have on coccidioidomycosis progression. To do this, parallels are drawn to aa compilation of other host microbiome infection studies.
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Affiliation(s)
- Susana Tejeda-Garibay
- Quantitative and Systems Biology, Graduate Program, University of California Merced, Merced, CA 95343, USA
| | - Katrina K. Hoyer
- Department of Molecular and Cell Biology, University California Merced, Merced, CA 95343, USA
- Health Sciences Research Institute, University of California Merced, Merced, CA 95343, USA
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12
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Rozaliyani A, Antariksa B, Nurwidya F, Zaini J, Setianingrum F, Hasan F, Nugrahapraja H, Yusva H, Wibowo H, Bowolaksono A, Kosmidis C. The Fungal and Bacterial Interface in the Respiratory Mycobiome with a Focus on Aspergillus spp. Life (Basel) 2023; 13:life13041017. [PMID: 37109545 PMCID: PMC10142979 DOI: 10.3390/life13041017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The heterogeneity of the lung microbiome and its alteration are prevalently seen among chronic lung diseases patients. However, studies to date have primarily focused on the bacterial microbiome in the lung rather than fungal composition, which might play an essential role in the mechanisms of several chronic lung diseases. It is now well established that Aspergillus spp. colonies may induce various unfavorable inflammatory responses. Furthermore, bacterial microbiomes such as Pseudomonas aeruginosa provide several mechanisms that inhibit or stimulate Aspergillus spp. life cycles. In this review, we highlighted fungal and bacterial microbiome interactions in the respiratory tract, with a focus on Aspergillus spp.
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Affiliation(s)
- Anna Rozaliyani
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Budhi Antariksa
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Fariz Nurwidya
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Jamal Zaini
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Findra Setianingrum
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Firman Hasan
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Husna Nugrahapraja
- Life Science and Biotechnology, Bandung Institute of Technology, Bandung 40312, Indonesia
| | - Humaira Yusva
- Magister Program of Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Heri Wibowo
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Anom Bowolaksono
- Department of Biology, Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Indonesia, Depok 16424, Indonesia
| | - Chris Kosmidis
- Manchester Academic Health Science Centre, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M23 9LT, UK
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13
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Bloodworth JC, Hoji A, Wolff G, Mandal RK, Schmidt NW, Deshane JS, Morrow CD, Kloepfer KM, Cook-Mills JM. Dysbiotic lung microbial communities of neonates from allergic mothers confer neonate responsiveness to suboptimal allergen. FRONTIERS IN ALLERGY 2023; 4:1135412. [PMID: 36970065 PMCID: PMC10036811 DOI: 10.3389/falgy.2023.1135412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 02/17/2023] [Indexed: 03/12/2023] Open
Abstract
In humans and animals, offspring of allergic mothers have increased responsiveness to allergens. This is blocked in mice by maternal supplementation with α-tocopherol (αT). Also, adults and children with allergic asthma have airway microbiome dysbiosis with increased Proteobacteria and may have decreased Bacteroidota. It is not known whether αT alters neonate development of lung microbiome dysbiosis or whether neonate lung dysbiosis modifies development of allergy. To address this, the bronchoalveolar lavage was analyzed by 16S rRNA gene analysis (bacterial microbiome) from pups of allergic and non-allergic mothers with a basal diet or αT-supplemented diet. Before and after allergen challenge, pups of allergic mothers had dysbiosis in lung microbial composition with increased Proteobacteria and decreased Bacteroidota and this was blocked by αT supplementation. We determined whether intratracheal transfer of pup lung dysbiotic microbial communities modifies the development of allergy in recipient pups early in life. Interestingly, transfer of dysbiotic lung microbial communities from neonates of allergic mothers to neonates of non-allergic mothers was sufficient to confer responsiveness to allergen in the recipient pups. In contrast, neonates of allergic mothers were not protected from development of allergy by transfer of donor lung microbial communities from either neonates of non-allergic mothers or neonates of αT-supplemented allergic mothers. These data suggest that the dysbiotic lung microbiota is dominant and sufficient for enhanced neonate responsiveness to allergen. Importantly, infants within the INHANCE cohort with an anti-inflammatory profile of tocopherol isoforms had an altered microbiome composition compared to infants with a pro-inflammatory profile of tocopherol isoforms. These data may inform design of future studies for approaches in the prevention or intervention in asthma and allergic disease early in life.
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Affiliation(s)
- Jeffery C. Bloodworth
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Aki Hoji
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Garen Wolff
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
- Division of Pulmonary, Allergy and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Rabindra K. Mandal
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Nathan W. Schmidt
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Jessy S. Deshane
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Casey D. Morrow
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Kirsten M. Kloepfer
- Division of Pulmonary, Allergy and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Joan M. Cook-Mills
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
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14
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Ao Z, Xu H, Li M, Liu H, Deng M, Liu Y. Clinical characteristics, diagnosis, outcomes and lung microbiome analysis of invasive pulmonary aspergillosis in the community-acquired pneumonia patients. BMJ Open Respir Res 2023; 10:e001358. [PMID: 36828645 PMCID: PMC9972439 DOI: 10.1136/bmjresp-2022-001358] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 01/06/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Invasive pulmonary aspergillosis (IPA) remains underestimated in patients with community-acquired pneumonia (CAP). This study aims to describe clinical features and outcomes of IPA in CAP patients, assess diagnostic performance of metagenomic next-generation sequencing (mNGS) for IPA and analyse lung microbiome via mNGS data. METHODS This retrospective cohort study included CAP patients from 22 April 2019 to 30 September 2021. Clinical and microbiological data were analysed. Diagnostic performance of mNGS was compared with traditional detection methods. The lung microbiome detected by mNGS was characterised and its association with clinical features was evaluated. MAIN RESULTS IPA was diagnosed in 26 (23.4%) of 111 CAP patients. Patients with IPA displayed depressed immunity, higher hospital mortality (30.8% vs 11.8%) and intensive care unit mortality (42.1% vs 17.5%) compared with patients without IPA. The galactomannan (GM) antigen test had the highest sensitivity (57.7%) in detecting the Aspergillus spp, followed by mNGS (42.3%), culture (30.8%) and smear (7.7%). The mNGS, culture and smear had 100% specificity, while GM test had 92.9% specificity. The microbial structure of IPA significantly differed from non-IPA patients (p<0.001; Wilcoxon test). Nineteen different species were significantly correlated with clinical outcomes and laboratory biomarkers, particularly for Streptococcus salivarius, Prevotella timonensis and Human betaherpesvirus 5. CONCLUSIONS Our results reveal that patients with Aspergillus infection tend to have a higher early mortality rate. The mNGS may be suggested as a complement to routine microbiological test in diagnosis of patients at risk of Aspergillus infection. The lung microbiota is associated with inflammatory, immune and metabolic conditions of IPA, and thus influences clinical outcomes.
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Affiliation(s)
- Zhi Ao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Huan Xu
- Department of Scientific Affairs, Vision Medicals for Infection Diseases, Guangzhou, China
| | - Mengqi Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Huifang Liu
- Department of Scientific Affairs, Vision Medicals for Infection Diseases, Guangzhou, China
| | - Min Deng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuliang Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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15
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Guohui J, Kun W, Dong T, Ji Z, Dong L, Dong W, Jingyu C. Microbiosis in lung allotransplantation and xenotransplantation: State of the art and future perspective. HEALTH CARE SCIENCE 2022; 1:119-128. [PMID: 38938886 PMCID: PMC11080722 DOI: 10.1002/hcs2.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/10/2022] [Accepted: 08/03/2022] [Indexed: 06/29/2024]
Abstract
The respiratory tract is known to harbor a microbial community including bacteria, viruses, and fungi. New techniques contribute enormously to the identification of unknown or culture-independent species and reveal the interaction of the community with the host immune system. The existing respiratory microbiome and substantial equilibrium of the transplanted microbiome from donor lung grafts provide an extreme bloom of dynamic changes in the microenvironment in lung transplantation (LT) recipients. Dysbiosis in grafts are not only related to the modified microbial components but also involve the kinetics of the host-graft "talk," which signifies the destination of graft allograft injury, acute rejection, infection, and chronic allograft dysfunction development in short- and long-term survival. Microbiome-derived factors may contribute to lung xenograft survival when using genetically multimodified pig-derived organs. Here, we review the most advanced knowledge of the dynamics and resilience of microbial communities in transplanted lungs with various pretransplant indications. Conceptual and analytical points of view have been illustrated along the time series, gaining insight into the microbiome and lung grafts. Future endeavors on precise tools, sophisticated models, and novel targeted regimens are needed to improve the long-term survival in these patients.
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Affiliation(s)
- Jiao Guohui
- Center for Medical Device Evaluation, NMPABeijingChina
| | - Wu Kun
- Center for Medical Device Evaluation, NMPABeijingChina
| | - Tian Dong
- Department of Thoracic Surgery, West China HospitalSichuan UniversityChengduChina
| | - Zhang Ji
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical UniversityWuxiChina
| | - Liu Dong
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical UniversityWuxiChina
| | - Wei Dong
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical UniversityWuxiChina
| | - Chen Jingyu
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical UniversityWuxiChina
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16
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Costantini C, Nunzi E, Romani L. From the nose to the lungs: the intricate journey of airborne pathogens amidst commensal bacteria. Am J Physiol Cell Physiol 2022; 323:C1036-C1043. [PMID: 36036448 PMCID: PMC9529274 DOI: 10.1152/ajpcell.00287.2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The recent COVID-19 pandemic has dramatically brought the pitfalls of airborne pathogens to the attention of the scientific community. Not only viruses but also bacteria and fungi may exploit air transmission to colonize and infect potential hosts and be the cause of significant morbidity and mortality in susceptible populations. The efforts to decipher the mechanisms of pathogenicity of airborne microbes have brought to light the delicate equilibrium that governs the homeostasis of mucosal membranes. The microorganisms already thriving in the permissive environment of the respiratory tract represent a critical component of this equilibrium and a potent barrier to infection by means of direct competition with airborne pathogens or indirectly via modulation of the immune response. Moving down the respiratory tract, physicochemical and biological constraints promote site-specific expansion of microbes that engage in cross talk with the local immune system to maintain homeostasis and promote protection. In this review, we critically assess the site-specific microbial communities that an airborne pathogen encounters in its hypothetical travel along the respiratory tract and discuss the changes in the composition and function of the microbiome in airborne diseases by taking fungal and SARS-CoV-2 infections as examples. Finally, we discuss how technological and bioinformatics advancements may turn microbiome analysis into a valuable tool in the hands of clinicians to predict the risk of disease onset, the clinical course, and the response to treatment of individual patients in the direction of personalized medicine implementation.
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Affiliation(s)
- Claudio Costantini
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Emilia Nunzi
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Luigina Romani
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
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17
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Cai L, Gao P, Wang Z, Dai C, Ning Y, Ilkit M, Xue X, Xiao J, Chen C. Lung and gut microbiomes in pulmonary aspergillosis: Exploring adjunctive therapies to combat the disease. Front Immunol 2022; 13:988708. [PMID: 36032147 PMCID: PMC9411651 DOI: 10.3389/fimmu.2022.988708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Species within the Aspergillus spp. cause a wide range of infections in humans, including invasive pulmonary aspergillosis, chronic pulmonary aspergillosis, and allergic bronchopulmonary aspergillosis, and are associated with high mortality rates. The incidence of pulmonary aspergillosis (PA) is on the rise, and the emergence of triazole-resistant Aspergillus spp. isolates, especially Aspergillus fumigatus, limits the efficacy of mold-active triazoles. Therefore, host-directed and novel adjunctive therapies are required to more effectively combat PA. In this review, we focus on PA from a microbiome perspective. We provide a general overview of the effects of the lung and gut microbiomes on the growth of Aspergillus spp. and host immunity. We highlight the potential of the microbiome as a therapeutic target for PA.
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Affiliation(s)
- Liuyang Cai
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, China
- Basic School of Medicine, Second Military Medical University (Naval Medical University), Shanghai, China
| | - Peigen Gao
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, China
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zeyu Wang
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, China
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chenyang Dai
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, China
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ye Ning
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, China
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey
| | - Xiaochun Xue
- Department of Pharmacy, 905th Hospital of People’s Liberation Army of China (PLA) Navy, Shanghai, China
- *Correspondence: Xiaochun Xue, ; Jinzhou Xiao, ; Chang Chen,
| | - Jinzhou Xiao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- *Correspondence: Xiaochun Xue, ; Jinzhou Xiao, ; Chang Chen,
| | - Chang Chen
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, China
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Xiaochun Xue, ; Jinzhou Xiao, ; Chang Chen,
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18
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Rhodes LD, Emmons CK, Wisswaesser G, Wells AH, Hanson MB. Bacterial microbiomes from mucus and breath of southern resident killer whales ( Orcinus orca). CONSERVATION PHYSIOLOGY 2022; 10:coac014. [PMID: 35492424 PMCID: PMC9041426 DOI: 10.1093/conphys/coac014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 02/07/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Opportunities to assess odontocete health are restricted due to their limited time at the surface, relatively quick movements and large geographic ranges. For endangered populations such as the southern resident killer whales (SKRWs) of the northeast Pacific Ocean, taking advantage of non-invasive samples such as expelled mucus and exhaled breath is appealing. Over the past 12 years, such samples were collected, providing a chance to analyse and assess their bacterial microbiomes using amplicon sequencing. Based on operational taxonomic units, microbiome communities from SRKW and transient killer whales showed little overlap between mucus, breath and seawater from SRKW habitats and six bacterial phyla were prominent in expelled mucus but not in seawater. Mollicutes and Fusobacteria were common and abundant in mucus, but not in breath or seawater, suggesting these bacterial classes may be normal constituents of the SRKW microbiome. Out of 134 bacterial families detected, 24 were unique to breath and mucus, including higher abundances of Burkholderiaceae, Moraxellaceae and Chitinophagaceae. Although there were multiple bacterial genera in breath or mucus that include pathogenic species (e.g. Campylobacter, Hemophilus, Treponema), the presence of these bacteria is not necessarily evidence of disease or infection. Future emphasis on genotyping mucus samples to the individual animal will allow further assessment in the context of that animal's history, including body condition index and prior contaminants burden. This study is the first to examine expelled mucus from cetaceans for microbiomes and demonstrates the value of analysing these types of non-invasive samples.
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Affiliation(s)
- Linda D Rhodes
- Corresponding author: Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Boulevard East, Seattle, WA 98112, USA.
| | - Candice K Emmons
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Boulevard East, Seattle, WA 98112, USA
| | - GabrielS Wisswaesser
- Lynker Technologies, under contract to Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Boulevard East, Seattle, WA 98112, USA
| | - Abigail H Wells
- Lynker Technologies, under contract to Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Boulevard East, Seattle, WA 98112, USA
| | - M Bradley Hanson
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Boulevard East, Seattle, WA 98112, USA
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A High-Risk Profile for Invasive Fungal Infections Is Associated with Altered Nasal Microbiota and Niche Determinants. Infect Immun 2022; 90:e0004822. [PMID: 35311544 DOI: 10.1128/iai.00048-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It is becoming increasingly clear that the communities of microorganisms that populate the surfaces exposed to the external environment, termed microbiota, are key players in the regulation of pathogen-host cross talk affecting the onset as well as the outcome of infectious diseases. We have performed a multicenter, prospective, observational study in which nasal and oropharyngeal swabs were collected for microbiota predicting the risk of invasive fungal infections (IFIs) in patients with hematological malignancies. Here, we demonstrate that the nasal and oropharyngeal microbiota are different, although similar characteristics differentiate high-risk from low-risk samples at both sites. Indeed, similar to previously published results on the oropharyngeal microbiota, high-risk samples in the nose were characterized by low diversity, a loss of beneficial bacteria, and an expansion of potentially pathogenic taxa, in the presence of reduced levels of tryptophan (Trp). At variance with oropharyngeal samples, however, low Trp levels were associated with defective host-derived kynurenine production, suggesting reduced tolerance mechanisms at the nasal mucosal surface. This was accompanied by reduced levels of the chemokine interleukin-8 (IL-8), likely associated with a reduced recruitment of neutrophils and impaired fungal clearance. Thus, the nasal and pharyngeal microbiomes of hematological patients provide complementary information that could improve predictive tools for the risk of IFI in hematological patients.
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Palmieri F, Koutsokera A, Bernasconi E, Junier P, von Garnier C, Ubags N. Recent Advances in Fungal Infections: From Lung Ecology to Therapeutic Strategies With a Focus on Aspergillus spp. Front Med (Lausanne) 2022; 9:832510. [PMID: 35386908 PMCID: PMC8977413 DOI: 10.3389/fmed.2022.832510] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
Fungal infections are estimated to be the main cause of death for more than 1.5 million people worldwide annually. However, fungal pathogenicity has been largely neglected. This is notably the case for pulmonary fungal infections, which are difficult to diagnose and to treat. We are currently facing a global emergence of antifungal resistance, which decreases the chances of survival for affected patients. New therapeutic approaches are therefore needed to face these life-threatening fungal infections. In this review, we will provide a general overview on respiratory fungal infections, with a focus on fungi of the genus Aspergillus. Next, the immunological and microbiological mechanisms of fungal pathogenesis will be discussed. The role of the respiratory mycobiota and its interactions with the bacterial microbiota on lung fungal infections will be presented from an ecological perspective. Finally, we will focus on existing and future innovative approaches for the treatment of respiratory fungal infections.
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Affiliation(s)
- Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- *Correspondence: Fabio Palmieri,
| | - Angela Koutsokera
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Eric Bernasconi
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Christophe von Garnier
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Niki Ubags
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
- Niki Ubags,
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Hu Y, Jiang Y, Liu S, Shen J, An Y. Phenotypes, Lung Microbiota and Cytokine Responses in Pneumonia After Hematopoietic Stem Cell Transplantation. J Inflamm Res 2021; 14:6055-6065. [PMID: 34824541 PMCID: PMC8610763 DOI: 10.2147/jir.s338914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/12/2021] [Indexed: 12/15/2022] Open
Abstract
Objective We aim to identify phenotypes of hematopoietic stem cell transplantation (HSCT) patients with pneumonia, discover relations of microbiota composition, cytokine profile, and outcomes between phenotypes. Specific cytokines will be evaluated for their role in lung injury in a murine model. Methods HSCT patients with pneumonia were included, and clustering of variables including cytokine levels provided the phenotypes. Outcomes were compared between phenotypes. Analysis of lung microbiota identified marker species of phenotypes. In the murine model, marker species-related cytokine regulations and the role of cytokines in lung injury were evaluated. Results Seventy-two patients were included, and two phenotypes were identified, namely "reactive" (N=21) and "nonreactive" (N=51) phenotype. Compared to their counterparts, patients with nonreactive phenotype had lower serum IL-6, IL-8, less severe inflammation, worse outcomes and more viruses as marker species in lung microbiota. The animal study validated the pathogens specific cytokine responses that presented in the human study and the potential protective role of IL-6 in these patients. Conclusion HSCT patients with pneumonia can be clustered into two phenotypes with different marker species and outcomes: the "nonreactive" phenotype and the "reactive" phenotype. Serum cytokine levels were different between the two phenotypes, which indicate the existence of the pathogen-related cytokine responses. For patients with the "nonreactive" phenotype, IL-6 therapy may improve their prognosis, which should be further tested in clinical studies.
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Affiliation(s)
- Yan Hu
- Department of Respiratory and Critical Care Medicine, Peking University International Hospital, Beijing, People's Republic of China
| | - Yanwen Jiang
- Department of Respiratory and Critical Care Medicine, Peking University International Hospital, Beijing, People's Republic of China
| | - Shuang Liu
- Department of Respiratory and Critical Care Medicine, Peking University International Hospital, Beijing, People's Republic of China
| | - Jiawei Shen
- Department of Critical Care Medicine, Peking University People's Hospital, Beijing, People's Republic of China
| | - Youzhong An
- Department of Critical Care Medicine, Peking University People's Hospital, Beijing, People's Republic of China
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Liang T, Liu F, Liu L, Zhang Z, Dong W, Bai S, Ma L, Kang L. Effects of Helicobacter pylori Infection on the Oral Microbiota of Reflux Esophagitis Patients. Front Cell Infect Microbiol 2021; 11:732613. [PMID: 34604113 PMCID: PMC8482873 DOI: 10.3389/fcimb.2021.732613] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/11/2021] [Indexed: 12/12/2022] Open
Abstract
The human oral microbiota plays a vital role in maintaining metabolic homeostasis. To explore the relationship between Helicobacter pylori (Hp) and reflux esophagitis, we collected 86 saliva samples from reflux esophagitis patients (RE group) and 106 saliva samples from healthy people (C group) for a high-throughput sequencing comparison. No difference in alpha diversity was detected between the RE and the C groups, but beta diversity of the RE group was higher than the C group. Bacteroidetes was more abundant in the RE group, whereas Firmicutes was more abundant in the C group. The linear discriminant analysis effect size analysis demonstrated that the biomarkers of the RE group were Prevotella, Veillonella, Leptotrichia, and Actinomyces, and the biomarkers of the C group were Lautropia, Gemella, Rothia, and Streptococcus. The oral microbial network structure of the C group was more complex than that of the RE group. Second, to explore the effect of Hp on the oral microbiota of RE patients, we performed the 14C-urea breath test on 45 of the 86 RE patients. We compared the oral microbiota of 33 Hp-infected reflux esophagitis patients (REHpp group) and 12 non-Hp-infected reflux esophagitis patients (REHpn group). No difference in alpha diversity was observed between the REHpn and REHpp groups, and beta diversity of the REHpp group was significantly lower than that of the REHpn group. The biomarkers in the REHpp group were Veillonella, Haemophilus, Selenomonas, Megasphaera, Oribacterium, Butyrivibrio, and Campylobacter; and the biomarker in the REHpn group was Stomatobaculum. Megasphaera was positively correlated with Veillonella in the microbial network of the REHpp group. The main finding of this study is that RE disturbs the human oral microbiota, such as increased beta diversity. Hp infection may inhibit this disorderly trend.
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Affiliation(s)
- Tian Liang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China.,Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Fang Liu
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China.,Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Lijun Liu
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China.,Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Zhiying Zhang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China.,Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Wenxue Dong
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China.,Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Su Bai
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China.,Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Lifeng Ma
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China.,Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Longli Kang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China.,Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
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