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Hilliam Y, Armbruster CR, Rapsinski GJ, Marshall CW, Moore J, Koirala J, Krainz L, Gaston JR, Cooper VS, Lee SE, Bomberger JM. Cystic fibrosis pathogens persist in the upper respiratory tract following initiation of elexacaftor/tezacaftor/ivacaftor therapy. Microbiol Spectr 2024; 12:e0078724. [PMID: 38916354 PMCID: PMC11302335 DOI: 10.1128/spectrum.00787-24] [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: 03/26/2024] [Accepted: 06/06/2024] [Indexed: 06/26/2024] Open
Abstract
Elexacaftor/tezacaftor/ivacaftor (ETI) therapy has revolutionized the treatment of cystic fibrosis (CF) for most affected individuals but the effects of treatment on sinus microbiota are still unknown. Changes to the airway microbiota in CF are associated with disease state and alterations to the bacterial community after ETI initiation may require changes to clinical management regimens. We collected sinus swab samples from the middle meatus in an observational study of 38 adults with CF and chronic rhinosinusitis (CRS) from 2017 to 2021 and captured the initiation of ETI therapy. We performed 16S and custom amplicon sequencing to characterize the sinus microbiota pre- and post-ETI. Real-time quantitative PCR (RT-qPCR) was performed to estimate total bacterial abundance. Sinus samples from people with CF (pwCF) clustered into three community types, dependent on the dominant bacterial organism: a Pseudomonas-dominant, Staphylococcus-dominant, and mixed dominance cluster. Shannon's diversity index was low and not significantly altered post-ETI. Total bacterial load was not significantly lowered post-ETI. Pseudomonas spp. abundance was significantly reduced post-ETI, but eradication was not observed. Staphylococcus spp. became the dominant organism in most individuals post-ETI and we showed the presence of methicillin-resistant Staphylococcus aureus (MRSA) in the sinus both pre- and post-ETI. We also demonstrated that the sinus microbiome is predictive of the presence of Pseudomonas spp., Staphylococcus spp., and Serratia spp. in the sputum. Pseudomonas spp. and Staphylococcus spp., including MRSA, persist in the sinuses of pwCF after ETI therapy, indicating that these pathogens will continue to be important in CF airway disease management in the era of highly effective modulator therapies (HEMT).IMPORTANCEHighly effective modulator therapies (HEMT), such as elexacaftor/tezacaftor/ivacaftor (ETI), for cystic fibrosis (CF) have revolutionized patient care and quality of life for most affected individuals. The effects of these therapies on the microbiota of the airways are still unclear, though work has already been published on changes to microbiota in the sputum. Our study presents evidence for reduced relative abundance of Pseudomonas spp. in the sinuses following ETI therapy. We also show that Staphylococcus spp. becomes the dominant organism in the sinus communities of most individuals in this cohort after ETI therapy. We identified methicillin-resistant Staphylococcus aureus (MRSA) in the sinus microbiota both pre- and post-therapy. These findings demonstrate that pathogen monitoring and treatment will remain a vital part of airway disease management for people with cystic fibrosis (pwCF) in the era of HEMT.
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Affiliation(s)
- Yasmin Hilliam
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Catherine R. Armbruster
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Glenn J. Rapsinski
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - John Moore
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Junu Koirala
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Leah Krainz
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jordan R. Gaston
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Vaughn S. Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Stella E. Lee
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Jennifer M. Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Niu X, Dang Z, Hong M, Shi H, Ding L. Effects of Freshwater Acidification on the Gut Microbial Community of Trachemys scripta elegans. Animals (Basel) 2024; 14:1898. [PMID: 38998010 PMCID: PMC11240511 DOI: 10.3390/ani14131898] [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: 05/29/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024] Open
Abstract
Freshwater acidification (FA) has become a global environmental problem, posing a potential threat to freshwater ecosystems. The gut microbiota plays a crucial role in the host's response and adaptation to new environments. In this study, we investigated the changes in microbial communities in Red-eared slider (Trachemys scripta elegans) under acidic conditions to reveal the ecological impacts of acidification on freshwater turtles. The results showed that there were significant differences in β-diversity (p = 0.03), while there were no significant differences in the α-diversity of gut microbiota in T. s. elegans between the different levels of acidification (pH of 5.5, 6.5, 7.5). Both the Gut Microbiome Health Index (GMHI) and the Microbial Dysbiosis Index (MDI) exhibited significant differences when comparing environments with a pH of 5.5 to those with a pH of 6.5 (p < 0.01). A comparative analysis between pH levels of 5.5 and 6.5 also revealed substantial differences (p < 0.01). Likewise, a comparative analysis between pH levels of 6.5 and 7.5 also revealed substantial differences (p < 0.01). At the phylum level, Firmicutes, Fusobacteria, and Bacteroidota formed a major part of the gut microbial community, Fusobacteria showed significant differences in different acidity environments (p = 0.03). At the genus level, Cetobacterium, Turicibacter, unclassified Eubacteriaceae, and Anaerorhabdus_furcosa_group showed significant differences in different acidity environments. The pH reduced interactivity in the gut microbiota of T. s. elegans. In addition, LEfSe analysis and functional prediction revealed that the potentially_pathogenic and stress_tolerant functional characteristics also showed significant differences in different acidity environments. The findings underscore the pivotal role of the gut microbiota in T. s. elegans in response to freshwater acidification and provide a foundation for further exploration into the impacts of acidification on freshwater ecosystems.
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Affiliation(s)
| | | | - Meiling Hong
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China; (X.N.); (Z.D.); (H.S.)
| | | | - Li Ding
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China; (X.N.); (Z.D.); (H.S.)
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Zhu M, Tang Y. Response of sediment microbial communities to the flow effect of the triangular artificial reef: A simulation-based experimental study. MARINE ENVIRONMENTAL RESEARCH 2024; 198:106546. [PMID: 38795576 DOI: 10.1016/j.marenvres.2024.106546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/22/2024] [Accepted: 05/06/2024] [Indexed: 05/28/2024]
Abstract
Artificial reefs (ARs), as an important tool for habitat restoration, play significant impacts on benthic microbial ecosystems. This study utilized 16S rRNA gene sequencing technology and computational fluid dynamics (CFD) flow simulation to investigate the effects of flow field distribution around ARs on microbial community structure. The results revealed distinct regional distribution patterns of microbial communities affected by different hydrodynamic conditions. Flow velocity and flow regime of water in sediment-water interface shaped the microbial community structure. The diversity and richness in R-HF were significantly decreased compared to other five regions (p < 0.05). At the phyla and OUT levels, most abundant taxa (1>%) showed an enrichment trend in R-HB. However, more than half of differentially abundant taxa were enriched in R-HB, which was significantly correlated with organic matter (OM). Bugbase phenotypic predictions indicated a low abundance of the anaerobic phenotype in R-HF and a high abundance of the biofilm-forming phenotype in R-HB.
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Affiliation(s)
- Meiling Zhu
- College of Fisheries, Ocean University of China, Qingdao, 266003, PR China
| | - Yanli Tang
- College of Fisheries, Ocean University of China, Qingdao, 266003, PR China.
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Niu X, Lin L, Zhang T, An X, Li Y, Yu Y, Hong M, Shi H, Ding L. Comparison of the intestinal flora of wild and artificial breeding green turtles ( Chelonia mydas). Front Microbiol 2024; 15:1412015. [PMID: 38873159 PMCID: PMC11170157 DOI: 10.3389/fmicb.2024.1412015] [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: 04/04/2024] [Accepted: 05/06/2024] [Indexed: 06/15/2024] Open
Abstract
Gut microbes are pivotal reference indicators for assessing the health status of animals. Before introducing artificially bred species into the wild, examining their gut microbe composition is crucial to help mitigate potential threats posed to wild populations. However, gut microbiological trait similarities between wild and artificially bred green turtles remain unexplored. Therefore, this study compared the gut microbiological characteristics of wild and artificially bred green turtles (Chelonia mydas) through high-throughput Illumina sequencing technology. The α-diversity of intestinal bacteria in wild green turtles, as determined by Shannon and Chao indices, significantly surpasses that of artificial breeding green turtles (p < 0.01). However, no significant differences were detected in the fungal α-diversity between wild and artificially bred green turtles. Meanwhile, the β-diversity analysis revealed significant differences between wild and artificially bred green turtles in bacterial and fungal compositions. The community of gut bacteria in artificially bred green turtles had a significantly higher abundance of Fusobacteriota including those belonging to the Paracoccus, Cetobacterium, and Fusobacterium genera than that of the wild green turtle. In contrast, the abundance of bacteria belonging to the phylum Actinobacteriota and genus Nautella significantly decreased. Regarding the fungal community, artificially bred green turtles had a significantly higher abundance of Fusarium, Sterigmatomyces, and Acremonium and a lower abundance of Candida and Rhodotorula than the wild green turtle. The PICRUSt2 analyses demonstrated significant differences in the functions of the gut bacterial flora between groups, particularly in carbohydrate and energy metabolism. Fungal functional guild analysis further revealed that the functions of the intestinal fungal flora of wild and artificially bred green turtles differed significantly in terms of animal pathogens-endophytes-lichen parasites-plant pathogens-soil saprotrophs-wood saprotrophs. BugBase analysis revealed significant potential pathogenicity and stress tolerance variations between wild and artificially bred green turtles. Collectively, this study elucidates the distinctive characteristics of gut microbiota in wild and artificially bred green turtles while evaluating their health status. These findings offer valuable scientific insights for releasing artificially bred green turtles and other artificially bred wildlife into natural habitats.
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Affiliation(s)
- Xin Niu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha, China
| | - Liu Lin
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha, China
| | - Ting Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha, China
| | - Xiaoyu An
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha, China
| | - Yupei Li
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha, China
- Marine Protected Area Administration of Sansha City, Sansha, China
| | - Yangfei Yu
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha, China
- Marine Protected Area Administration of Sansha City, Sansha, China
| | - Meiling Hong
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha, China
| | - Haitao Shi
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha, China
| | - Li Ding
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha, China
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Dong WJ, Xu MD, Yang XW, Yang XM, Long XZ, Han XY, Cui LY, Tong Q. Rice straw ash and amphibian health: A deep dive into microbiota changes and potential ecological consequences. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171651. [PMID: 38490417 DOI: 10.1016/j.scitotenv.2024.171651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 03/05/2024] [Accepted: 03/09/2024] [Indexed: 03/17/2024]
Abstract
Rice straw is burned as a result of agricultural practices and technical limitations, generating significant volumes of ash that might have environmental and ecological consequences; however, the effects on organisms have not been researched. Amphibians depend on their gut and skin microbiomes. Ash exposure may cause inflammation and changes in microbial diversity and function in frogs' skin and gut microbiota due to its chemical composition and physical presence, but the implications remain unclear. Rana dybowskii were exposed to five aqueous extracts of ashes (AEA) concentrations for 30 days to study survival, metal concentrations, and microbial diversity, analyzing the microbiota of the cutaneous and gut microbiota using Illumina sequencing. Dominant elements in ash: K > Ca > Mg > Na > Al > Fe. In AEA, K > Na > Ca > Mg > As > Cu. Increased AEA concentrations significantly reduced frog survival. Skin microbiota alpha diversity varied significantly among all treatment groups, but not gut microbiota. Skin microbiota differed significantly across treatments via Bray-Curtis and weighted UniFrac; gut microbiota was only affected by Bray-Curtis. Skin microbiota varied significantly with AEA levels in Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes, while the gut microbiota's dominant phyla, Firmicutes, Bacteroidetes, and Proteobacteria, remained consistent across all groups. Lastly, the functional prediction showed that the skin microbiota had big differences in how it worked and looked, which were linked to different health and environmental adaptation pathways. The gut microbiota, on the other hand, had smaller differences. In conclusion, AEA exposure affects R. dybowskii survival and skin microbiota diversity, indicating potential health and ecological impacts, with less effect on gut microbiota.
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Affiliation(s)
- Wen-Jing Dong
- School of Biology and Agriculture, Jiamusi University, Jiamusi 154007, China
| | - Ming-da Xu
- School of Biology and Agriculture, Jiamusi University, Jiamusi 154007, China
| | - Xue-Wen Yang
- School of Biology and Agriculture, Jiamusi University, Jiamusi 154007, China
| | - Xiu-Mei Yang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Xin-Zhou Long
- School of Biology and Agriculture, Jiamusi University, Jiamusi 154007, China
| | - Xiao-Yun Han
- School of Biology and Agriculture, Jiamusi University, Jiamusi 154007, China
| | - Li-Yong Cui
- School of Biology and Agriculture, Jiamusi University, Jiamusi 154007, China
| | - Qing Tong
- School of Biology and Agriculture, Jiamusi University, Jiamusi 154007, China; College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China.
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Zemke AC, Hilliam Y, Stapleton AL, Kimple AJ, Goralski JL, Shaffer AD, Pilewski JM, Senior BA, Lee SE, Cooper VS. Elexacaftor-tezacaftor-ivacaftor decreases pseudomonas abundance in the sinonasal microbiome in cystic fibrosis. Int Forum Allergy Rhinol 2024; 14:928-938. [PMID: 37837613 PMCID: PMC11131353 DOI: 10.1002/alr.23288] [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: 07/13/2023] [Revised: 09/15/2023] [Accepted: 09/23/2023] [Indexed: 10/16/2023]
Abstract
BACKGROUND Chronic rhinosinusitis (CRS) is common in individuals with cystic fibrosis (CF) and is marked by chronic inflammation and episodes of infection that negatively impact quality of life. Several studies have shown that elexacaftor-tezacaftor-ivacaftor (ETI) improves symptoms and examination findings in CF-CRS. The current study determines the effect of ETI on the sinonasal microbiota in CF. METHODS Sinonasal samples were collected under endoscopic visualization before and after starting ETI. Samples were subjected to 16S amplicon sequencing and sequences were processed with the QIIME2 pipeline with subsequent analysis using the vegan R-package. RESULTS Twenty-nine individual baseline samples and 23 sample pairs pre-/post-ETI were available. At baseline, the cohort had samples dominated by Staphylococcus, and alpha diversity was lower than that of a published reference set of individuals without sinonasal disease. Individuals with prior sinus surgery had lower alpha diversity as measured by Shannon Index, Observed Richness, and Faith's phylogenetic diversity Index. Beta diversity differed between individuals with and without allergic rhinitis, with higher Staphylococcus abundance in those with allergic rhinitis. No change in alpha or beta diversity was seen after a median of 9 months on ETI. With ETI, the Pseudomonas genus and the genus containing Burkholderia decreased in samples containing these taxa at baseline. Pseudomonas abundance decreased with treatment as measured by qPCR. Core sinonasal microbiome members Staphylococcus, Corynebacterium, and Streptococcus were unchanged, while Moraxella increased with ETI. CONCLUSIONS Treatment with ETI leads to a reduction in Pseudomonas abundance within the sinonasal microbiome of individuals with Pseudomonas at baseline.
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Affiliation(s)
- Anna C Zemke
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yasmin Hilliam
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Amanda L Stapleton
- Department of Otolaryngology-Head & Neck Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Adam J Kimple
- Department of Otolaryngology-Head & Neck Surgery, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jennifer L Goralski
- Division of Pulmonary Diseases & CCM, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Amber D Shaffer
- Department of Otolaryngology-Head & Neck Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Joseph M Pilewski
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brent A Senior
- Department of Otolaryngology-Head & Neck Surgery, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Stella E Lee
- Department of Otolaryngology-Head & Neck Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Otolaryngology-Head & Neck Surgery, Department of Surgery, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Bano Y, Shrivastava A, Shukla P, Chaudhary AA, Khan SUD, Khan S. The implication of microbiome in lungs cancer: mechanisms and strategies of cancer growth, diagnosis and therapy. Crit Rev Microbiol 2024:1-25. [PMID: 38556797 DOI: 10.1080/1040841x.2024.2324864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 02/20/2024] [Indexed: 04/02/2024]
Abstract
Available evidence illustrates that microbiome is a promising target for the study of growth, diagnosis and therapy of various types of cancer. Lung cancer is a leading cause of cancer death worldwide. The relationship of microbiota and their products with diverse pathologic conditions has been getting large attention. The novel research suggests that the microbiome plays an important role in the growth and progression of lung cancer. The lung microbiome plays a crucial role in maintaining mucosal immunity and synchronizing the stability between tolerance and inflammation. Alteration in microbiome is identified as a critical player in the progression of lung cancer and negatively impacts the patient. Studies suggest that healthy microbiome is essential for effective therapy. Various clinical trials and research are focusing on enhancing the treatment efficacy by altering the microbiome. The regulation of microbiota will provide innovative and promising treatment strategies for the maintenance of host homeostasis and the prevention of lung cancer in lung cancer patients. In the current review article, we presented the latest progress about the involvement of microbiome in the growth and diagnosis of lung cancer. Furthermore, we also assessed the therapeutic status of the microbiome for the management and treatment of lung cancer.
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Affiliation(s)
- Yasmin Bano
- Department of Biotechnology, College of Life Sciences, Cancer Hospital and research Institute, Gwalior, India
- Centre for Genomics, Molecular and Human Genetics, Jiwaji University, Gwalior, India
| | - Abhinav Shrivastava
- Department of Biotechnology, College of Life Sciences, Cancer Hospital and research Institute, Gwalior, India
| | - Piyush Shukla
- Centre for Genomics, Molecular and Human Genetics, Jiwaji University, Gwalior, India
- Laboratory of Natural Products, Department of Rural Technology and Social Development, Guru Ghasidas University, Bilaspur, India
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Salah-Ud-Din Khan
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Shahanavaj Khan
- Department of Medical Lab Technology, Indian Institute of Health Technology (IIHT), Deoband, Saharanpur, UP, India
- Department of Health Sciences, Novel Global Community Educational Foundation, Hebersham, Australia
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Cauwenberghs E, De Boeck I, Spacova I, Van Tente I, Bastiaenssen J, Lammertyn E, Verhulst S, Van Hoorenbeeck K, Lebeer S. Positioning the preventive potential of microbiome treatments for cystic fibrosis in the context of current therapies. Cell Rep Med 2024; 5:101371. [PMID: 38232705 PMCID: PMC10829789 DOI: 10.1016/j.xcrm.2023.101371] [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: 07/14/2023] [Revised: 10/24/2023] [Accepted: 12/14/2023] [Indexed: 01/19/2024]
Abstract
Antibiotics and cystic fibrosis transmembrane conductance regulator (CFTR) modulators play a pivotal role in cystic fibrosis (CF) treatment, but both have limitations. Antibiotics are linked to antibiotic resistance and disruption of the airway microbiome, while CFTR modulators are not widely accessible, and structural lung damage and pathogen overgrowth still occur. Complementary strategies that can beneficially modulate the airway microbiome in a preventive way are highly needed. This could be mediated via oral probiotics, which have shown some improvement of lung function and reduction of airway infections and exacerbations, as a cost-effective approach. However, recent data suggest that specific and locally administered probiotics in the respiratory tract might be a more targeted approach to prevent pathogen outgrowth in the lower airways. This review aims to summarize the current knowledge on the CF airway microbiome and possibilities of microbiome treatments to prevent bacterial and/or viral infections and position them in the context of current CF therapies.
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Affiliation(s)
- Eline Cauwenberghs
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Ilke De Boeck
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Irina Spacova
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Ilke Van Tente
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Joke Bastiaenssen
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Elise Lammertyn
- Belgian CF Association, Driebruggenstraat 124, 1160 Brussels, Belgium; Cystic Fibrosis Europe, Driebruggenstraat 124, 1160 Brussels, Belgium
| | - Stijn Verhulst
- University of Antwerp, Laboratory of Experimental Medicine and Pediatrics, Universiteitsplein 1, 2610 Wilrijk, Belgium; Antwerp University Hospital, Department of Pediatric Pulmonology, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Kim Van Hoorenbeeck
- University of Antwerp, Laboratory of Experimental Medicine and Pediatrics, Universiteitsplein 1, 2610 Wilrijk, Belgium; Antwerp University Hospital, Department of Pediatric Pulmonology, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Sarah Lebeer
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium.
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Somayaji R, Thornton CS, Acosta N, Smith K, Clark J, Fatovich L, Thakrar MV, Parkins MD. Evaluating Sinus Microbiology by Transplant Status in Persons With Cystic Fibrosis: A Matched Cohort Study. OTO Open 2024; 8:e101. [PMID: 38317784 PMCID: PMC10840018 DOI: 10.1002/oto2.101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/31/2023] [Accepted: 12/02/2023] [Indexed: 02/07/2024] Open
Abstract
Objective Sinus disease is prevalent in persons with cystic fibrosis (PwCF) and may be a reservoir of airway infection in postlung transplant (pTx) patients. The microbial composition of cystic fibrosis sinuses and its associations with chronic rhinosinusitis (CRS) is relatively unexplored. We aimed to examine the sinus and lower airway microbiome and their associations with CRS in PwCF and pTxPwCF. Study Design Prospective single-centre study. Setting A total of 31 sex and age (±2 years) matched PwCF and pTxPwCF. Methods Demographic and clinical data along with sinus swabs and sputum were collected. CRS was assessed using Sinonasal Outcome Test-22 (SNOT-22) (patient reported outcome) and Lund-McKay (computed tomography sinus) scores. Samples underwent MiSeq Illumina sequencing of the universal 16S ribosomal RNA gene. Results A total of 31 PwCF (15 pTxPwCF) were included. Aggregate airways microbiome composition was dominated by Pseudomonas (46%), Haemophilus (14%), Staphylococcus (11%), Streptococcus (10%), and Fusobacterium (6%). α-diversity was significantly lower in post-Tx samples across both sputum and sinus samples (P = .005). β-diversity was significantly different between sputum (P = .004), but not sinus (P = .75) samples by transplant status. While there was a trend in higher β-diversity associated with lower SNOT-22 score at time of first visit, this did not reach significance (P = .05). Conclusion Sinus and airway microbiomes differed in PwCF and pTxPwCF, but the prevalent organisms remained consistent. Elucidating the relationship of the microbiome with clinical status to better understand when to intervene accordingly is needed to optimize sinus disease management in PwCF.
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Affiliation(s)
- Ranjani Somayaji
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of MedicineUniversity of CalgaryCalgaryCanada
- Department of Medicine, Cumming School of Medicine, Alberta Health ServicesUniversity of CalgaryCalgaryCanada
- Snyder Institute for Chronic DiseasesUniversity of CalgaryCalgaryCanada
- Department of Community Health Sciences, Cumming School of MedicineUniversity of CalgaryCalgaryCanada
| | - Christina S. Thornton
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of MedicineUniversity of CalgaryCalgaryCanada
- Department of Medicine, Cumming School of Medicine, Alberta Health ServicesUniversity of CalgaryCalgaryCanada
- Snyder Institute for Chronic DiseasesUniversity of CalgaryCalgaryCanada
| | - Nicola Acosta
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of MedicineUniversity of CalgaryCalgaryCanada
| | - Kristine Smith
- Department of Otolaryngology–Head and Neck surgeryUniversity of UtahSalt Lake CityUtahUSA
| | - Jessica Clark
- Department of Surgery, Otolaryngology–Head and Neck Surgery, Cumming School of MedicineUniversity of CalgaryCalgaryCanada
| | - Linda Fatovich
- Department of Medicine, Cumming School of Medicine, Alberta Health ServicesUniversity of CalgaryCalgaryCanada
| | - Mitesh V. Thakrar
- Department of Medicine, Cumming School of Medicine, Alberta Health ServicesUniversity of CalgaryCalgaryCanada
| | - Michael D. Parkins
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of MedicineUniversity of CalgaryCalgaryCanada
- Department of Medicine, Cumming School of Medicine, Alberta Health ServicesUniversity of CalgaryCalgaryCanada
- Snyder Institute for Chronic DiseasesUniversity of CalgaryCalgaryCanada
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10
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Chen D, Zhang Y, Feng Q. Hydrochemical characteristics and microbial community evolution of Pinglu River affected by regional abandoned coal mine drainage, Guizhou Province, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27403-5. [PMID: 37155109 DOI: 10.1007/s11356-023-27403-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/29/2023] [Indexed: 05/10/2023]
Abstract
Pinglu River in southwestern China was continuously polluted by acid mine drainage (AMD) from abandoned coal mines, and AMD has become a major source of recharge to the river (43.26% of total flow), resulting in structural changes in the physicochemical properties and microbial communities of river water and sediments. In this study, we collected abandoned coal mine drainage, river water, and river sediment samples for comprehensive analysis. Results indicated that the hydrochemical types of AMD from abandoned coal mines were mainly SO4-Ca·Mg. The pH of river water in Pinglu River decreased from upstream to downstream due to AMD, with the hydrochemical type gradually changing from SO4·HCO3-Ca·Mg to SO4-Ca·Mg. The variation of pH along the river sediments was less than that of water samples, which remained weakly alkaline. However, high-throughput sequencing revealed a gradual decrease in microbial diversity in river sediments from upstream to downstream. The core bacteria groups in the upstream sediments were mainly attributed to the phylum Proteobacteria and Actinobacteriota, mainly including Geobacter, Anaeromyxobacter, Marmoricola, and Phycicoccus. The relative abundance of Gaiella, MND1, and Pseudolabrys in sediment samples gradually increased with the confluence of AMD, and the differences in microbial communities may be attributed to pH, TOC, and TP. Results of phenotype prediction demonstrated that the relative abundance of anaerobic microorganisms in river sediment gradually decreased from upstream to downstream (from 24.77 to 12.46%), presumably due to the large amount of oligotrophic AMD converge.
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Affiliation(s)
- Di Chen
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, China University of Mining and Technology, No. 1 Daxue Street, Quanshan District, Xuzhou, 221116, People's Republic of China.
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, No. 1 Daxue Street, Quanshan District, Xuzhou, 221116, People's Republic of China.
| | - Yun Zhang
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, China University of Mining and Technology, No. 1 Daxue Street, Quanshan District, Xuzhou, 221116, People's Republic of China
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, No. 1 Daxue Street, Quanshan District, Xuzhou, 221116, People's Republic of China
| | - Qiyan Feng
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, China University of Mining and Technology, No. 1 Daxue Street, Quanshan District, Xuzhou, 221116, People's Republic of China
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, No. 1 Daxue Street, Quanshan District, Xuzhou, 221116, People's Republic of China
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11
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Tong Q, Dong WJ, Xu MD, Hu ZF, Guo P, Han XY, Cui LY. Characteristics and a comparison of the gut microbiota in two frog species at the beginning and end of hibernation. Front Microbiol 2023; 14:1057398. [PMID: 37206336 PMCID: PMC10191234 DOI: 10.3389/fmicb.2023.1057398] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 03/21/2023] [Indexed: 05/21/2023] Open
Abstract
Season has been suggested to contribute to variation in the gut microbiota of animals. The complicated relationships between amphibians and their gut microbiota and how they change throughout the year require more research. Short-term and long-term hypothermic fasting of amphibians may affect gut microbiota differently; however, these changes have not been explored. In this study, the composition and characteristics of the gut microbiota of Rana amurensis and Rana dybowskii during summer, autumn (short-term fasting) and winter (long-term fasting) were studied by high-throughput Illumina sequencing. Both frog species had higher gut microbiota alpha diversity in summer than autumn and winter, but no significant variations between autumn and spring. The summer, autumn, and spring gut microbiotas of both species differed, as did the autumn and winter microbiomes. In summer, autumn and winter, the dominant phyla in the gut microbiota of both species were Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. All animals have 10 OTUs (>90% of all 52 frogs). Both species had 23 OTUs (>90% of all 28 frogs) in winter, accounting for 47.49 ± 3.84% and 63.17 ± 3.69% of their relative abundance, respectively. PICRUSt2 analysis showed that the predominant functions of the gut microbiota in these two Rana were focused on carbohydrate metabolism, Global and overview maps, Glycan biosynthesis metabolism, membrane transport, and replication and repair, translation. The BugBase analysis estimated that among the seasons in the R. amurensis group, Facultatively_Anaerobic, Forms_Biofilms, Gram_Negative, Gram_Positive, Potentially_Pathogenic were significantly different. However, there was no difference for R. dybowskii. The research will reveal how the gut microbiota of amphibians adapts to environmental changes during hibernation, aid in the conservation of endangered amphibians, particularly those that hibernate, and advance microbiota research by elucidating the role of microbiota under various physiological states and environmental conditions.
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Affiliation(s)
- Qing Tong
- School of Biology and Agriculture, Jiamusi University, Jiamusi, China
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
- Hejiang Forestry Research Institute of Heilongjiang Province, Jiamusi, China
| | - Wen-jing Dong
- School of Biology and Agriculture, Jiamusi University, Jiamusi, China
| | - Ming-da Xu
- School of Biology and Agriculture, Jiamusi University, Jiamusi, China
| | - Zong-fu Hu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Peng Guo
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Xiao-yun Han
- School of Biology and Agriculture, Jiamusi University, Jiamusi, China
| | - Li-yong Cui
- Hejiang Forestry Research Institute of Heilongjiang Province, Jiamusi, China
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12
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Armbruster CR, Li K, Kiedrowski MR, Zemke AC, Melvin JA, Moore J, Atteih S, Fitch AC, DuPont M, Manko CD, Weaver ML, Gaston JR, Alcorn JF, Morris A, Methé BA, Lee SE, Bomberger JM. Low Diversity and Instability of the Sinus Microbiota over Time in Adults with Cystic Fibrosis. Microbiol Spectr 2022; 10:e0125122. [PMID: 36094193 PMCID: PMC9603634 DOI: 10.1128/spectrum.01251-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 08/10/2022] [Indexed: 12/30/2022] Open
Abstract
Chronic rhinosinusitis (CRS) is a common, yet underreported and understudied manifestation of upper respiratory disease in people with cystic fibrosis (CF). Recently developed standard of care guidelines for the management of CF CRS suggest treatment of upper airway disease may ameliorate lower airway disease. We sought to determine whether changes to sinus microbial community diversity and specific taxa known to cause CF lung disease are associated with increased respiratory disease and inflammation. We performed 16S rRNA gene sequencing, supplemented with cytokine analyses, microscopy, and bacterial culturing, on samples from the sinuses of 27 adults with CF CRS. At each study visit, participants underwent endoscopic paranasal sinus sampling and clinical evaluation. We identified key drivers of microbial community composition and evaluated relationships between diversity and taxa with disease outcomes and inflammation. Sinus community diversity was low, and the composition was unstable, with many participants exhibiting alternating dominance between Pseudomonas aeruginosa and staphylococci over time. Despite a tendency for dominance by these two taxa, communities were highly individualized and shifted composition during exacerbation of sinus disease symptoms. Exacerbations were also associated with communities dominated by Staphylococcus spp. Reduced microbial community diversity was linked to worse sinus disease and the inflammatory status of the sinuses (including increased interleukin-1β [IL-1β]). Increased IL-1β was also linked to worse sinus endoscopic appearance, and other cytokines were linked to microbial community dynamics. Our work revealed previously unknown instability of sinus microbial communities and a link between inflammation, lack of microbial community diversity, and worse sinus disease. IMPORTANCE Together with prior sinus microbiota studies of adults with CF chronic rhinosinusitis, our study underscores similarities between sinus and lower respiratory tract microbial community structures in CF. We show how community structure tracks with inflammation and several disease measures. This work strongly suggests that clinical management of CRS could be leveraged to improve overall respiratory health in CF. Our work implicates elevated IL-1β in reduced microbiota diversity and worse sinus disease in CF CRS, suggesting applications for existing therapies targeting IL-1β. Finally, the widespread use of highly effective cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy has led to less frequent availability of spontaneous expectorated sputum for microbiological surveillance of lung infections. A better understanding of CF sinus microbiology could provide a much-needed alternative site for monitoring respiratory infection status by important CF pathogens.
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Affiliation(s)
- Catherine R. Armbruster
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Megan R. Kiedrowski
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Anna C. Zemke
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jeffrey A. Melvin
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - John Moore
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Samar Atteih
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Adam C. Fitch
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Matthew DuPont
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Christopher D. Manko
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Madison L. Weaver
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jordon R. Gaston
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - John F. Alcorn
- Department of Pediatrics, Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alison Morris
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Barbara A. Methé
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Stella E. Lee
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Jennifer M. Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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13
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Antibiotics Drive Expansion of Rare Pathogens in a Chronic Infection Microbiome Model. mSphere 2022; 7:e0031822. [PMID: 35972133 PMCID: PMC9599657 DOI: 10.1128/msphere.00318-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chronic (long-lasting) infections are globally a major and rising cause of morbidity and mortality. Unlike typical acute infections, chronic infections are ecologically diverse, characterized by the presence of a polymicrobial mix of opportunistic pathogens and human-associated commensals. To address the challenge of chronic infection microbiomes, we focus on a particularly well-characterized disease, cystic fibrosis (CF), where polymicrobial lung infections persist for decades despite frequent exposure to antibiotics. Epidemiological analyses point to conflicting results on the benefits of antibiotic treatment yet are confounded by the dependency of antibiotic exposures on prior pathogen presence, limiting their ability to draw causal inferences on the relationships between antibiotic exposure and pathogen dynamics. To address this limitation, we develop a synthetic infection microbiome model representing CF metacommunity diversity and benchmark on clinical data. We show that in the absence of antibiotics, replicate microbiome structures in a synthetic sputum medium are highly repeatable and dominated by oral commensals. In contrast, challenge with physiologically relevant antibiotic doses leads to substantial community perturbation characterized by multiple alternate pathogen-dominant states and enrichment of drug-resistant species. These results provide evidence that antibiotics can drive the expansion (via competitive release) of previously rare opportunistic pathogens and offer a path toward microbiome-informed conditional treatment strategies. IMPORTANCE We develop and clinically benchmark an experimental model of the cystic fibrosis (CF) lung infection microbiome to investigate the impacts of antibiotic exposures on chronic, polymicrobial infections. We show that a single experimental model defined by metacommunity data can partially recapitulate the diversity of individual microbiome states observed across a population of people with CF. In the absence of antibiotics, we see highly repeatable community structures, dominated by oral microbes. Under clinically relevant antibiotic exposures, we see diverse and frequently pathogen-dominated communities, and a nonevolutionary enrichment of antimicrobial resistance on the community scale, mediated by competitive release. The results highlight the potential importance of nonevolutionary (community-ecological) processes in driving the growing global crisis of increasing antibiotic resistance.
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14
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Armbruster CR, Marshall CW, Garber AI, Melvin JA, Zemke AC, Moore J, Zamora PF, Li K, Fritz IL, Manko CD, Weaver ML, Gaston JR, Morris A, Methé B, DePas WH, Lee SE, Cooper VS, Bomberger JM. Adaptation and genomic erosion in fragmented Pseudomonas aeruginosa populations in the sinuses of people with cystic fibrosis. Cell Rep 2021; 37:109829. [PMID: 34686349 PMCID: PMC8667756 DOI: 10.1016/j.celrep.2021.109829] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/09/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022] Open
Abstract
Pseudomonas aeruginosa notoriously adapts to the airways of people with cystic fibrosis (CF), yet how infection-site biogeography and associated evolutionary processes vary as lifelong infections progress remains unclear. Here we test the hypothesis that early adaptations promoting aggregation influence evolutionary-genetic trajectories by examining longitudinal P. aeruginosa from the sinuses of six adults with CF. Highly host-adapted lineages harbored mutator genotypes displaying signatures of early genome degradation associated with recent host restriction. Using an advanced imaging technique (MiPACT-HCR [microbial identification after passive clarity technique]), we find population structure tracks with genome degradation, with the most host-adapted, genome-degraded P. aeruginosa (the mutators) residing in small, sparse aggregates. We propose that following initial adaptive evolution in larger populations under strong selection for aggregation, P. aeruginosa persists in small, fragmented populations that experience stronger effects of genetic drift. These conditions enrich for mutators and promote degenerative genome evolution. Our findings underscore the importance of infection-site biogeography to pathogen evolution.
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Affiliation(s)
- Catherine R Armbruster
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | | | - Arkadiy I Garber
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Jeffrey A Melvin
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Anna C Zemke
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - John Moore
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Paula F Zamora
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Ian L Fritz
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Christopher D Manko
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Madison L Weaver
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Jordan R Gaston
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Alison Morris
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Barbara Methé
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - William H DePas
- Department of Pediatrics, Children's Hospital of Pittsburgh and University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Stella E Lee
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA.
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA; Pittsburgh Center for Evolutionary Biology & Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| | - Jennifer M Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
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15
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Lucas SK, Feddema E, Boyer HC, Hunter RC. Diversity of cystic fibrosis chronic rhinosinusitis microbiota correlates with different pathogen dominance. J Cyst Fibros 2021; 20:678-681. [PMID: 33931358 PMCID: PMC8403624 DOI: 10.1016/j.jcf.2021.03.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 02/27/2021] [Accepted: 03/30/2021] [Indexed: 09/30/2022]
Abstract
Chronic rhinosinusitis (CRS) affects nearly all individuals with cystic fibrosis (CF) and is thought to serve as a reservoir for microbiota that subsequently colonize the lung. To better understand the microbial ecology of CRS, we generated a 16S rRNA gene sequencing profile of sinus mucus from CF-CRS patients. We show that CF-CRS sinuses harbor bacterial diversity not entirely captured by clinical culture. Culture data consistently identified the dominant organism in most patients, though lower abundance bacteria were not always identified. We also demonstrate that bacterial communities dominated by Staphylococcus spp. were significantly more diverse compared to those dominated by Pseudomonas spp. Diversity was not significantly associated with clinical factors or patient age, however, younger subjects yielded a much wider range of bacterial diversity. These data mirror bacterial community dynamics in the lung and provide additional insight into the role of sinus microbiota in chronic airway disease progression.
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Affiliation(s)
- Sarah K Lucas
- Department of Microbiology & Immunology, University of Minnesota, USA.
| | - Erin Feddema
- Department of Otolaryngology, Head and Neck Surgery, University of Minnesota, USA.
| | - Holly C Boyer
- Department of Otolaryngology, Head and Neck Surgery, University of Minnesota, USA.
| | - Ryan C Hunter
- Department of Microbiology & Immunology, University of Minnesota, USA.
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16
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Wagner Mackenzie B, Dassi C, Vivekanandan A, Zoing M, Douglas RG, Biswas K. Longitudinal analysis of sinus microbiota post endoscopic surgery in patients with cystic fibrosis and chronic rhinosinusitis: a pilot study. Respir Res 2021; 22:106. [PMID: 33849523 PMCID: PMC8045235 DOI: 10.1186/s12931-021-01697-w] [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: 10/19/2020] [Accepted: 03/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cystic fibrosis is a debilitating, autosomal recessive disease which results in chronic upper and lower airway infection and inflammation. In this study, four adult patients presenting with cystic fibrosis and chronic rhinosinusitis were recruited. Culture and molecular techniques were employed to evaluate changes in microbial profiles, host gene expression and antimicrobial resistance (AMR) in the upper respiratory tract over time. METHODS Swab samples from the sinonasal cavity were collected at the time of surgery and at follow-up clinics at regular time intervals for up to 18 months. Nucleic acids were extracted, and DNA amplicon sequencing was applied to describe bacterial and fungal composition. In parallel, RNA was used to evaluate the expression of 17 AMR genes and two inflammatory markers (interleukins 6 and 8) using custom qPCR array cards. Molecular results were compared with routine sinus and sputum culture reports within each patient. RESULTS Bacterial amplicon sequencing and swab culture reports from the sinonasal cavity were mostly congruent and relatively stable for each patient across time. The predominant species detected in patients P02 and P04 were Pseudomonas aeruginosa, Staphylococcus aureus in patient P03, and a mixture of Enterobacter and S. aureus in patient P01. Fungal profiles were variable and less subject specific than bacterial communities. Increased expressions of interleukins 6 and 8 were observed in all patients throughout the sampling period compared with other measured genes. The most prevalent AMR gene detected was ampC. However, the prevalence of AMR gene expression was low in all patient samples across varying time-points. CONCLUSIONS We observed a surprising degree of stability of sinonasal microbial composition, and inflammatory and AMR gene expression across all patients post sinus surgery.
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Affiliation(s)
- Brett Wagner Mackenzie
- Department of Surgery, The University of Auckland, 85 Park Road, Grafton, 1023, Auckland, New Zealand.
| | - Camila Dassi
- Department of Surgery, The University of Auckland, 85 Park Road, Grafton, 1023, Auckland, New Zealand
| | - Anitha Vivekanandan
- Department of Surgery, The University of Auckland, 85 Park Road, Grafton, 1023, Auckland, New Zealand
| | - Melissa Zoing
- Department of Surgery, The University of Auckland, 85 Park Road, Grafton, 1023, Auckland, New Zealand
| | - Richard G Douglas
- Department of Surgery, The University of Auckland, 85 Park Road, Grafton, 1023, Auckland, New Zealand
| | - Kristi Biswas
- Department of Surgery, The University of Auckland, 85 Park Road, Grafton, 1023, Auckland, New Zealand
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17
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Liu H, Bai M, Xu K, Zhou J, Zhang X, Yu R, Huang R, Yin Y. Effects of different concentrations of coated nano zinc oxide material on fecal bacterial composition and intestinal barrier in weaned piglets. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:735-745. [PMID: 32706118 DOI: 10.1002/jsfa.10686] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/02/2020] [Accepted: 07/24/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Coated nano zinc oxide (Cnz) is a new feed or food additive, which is a potential replacement for a pharmacological dose level of ZnO. This study evaluated the positive effects of different concentrations of Cnz on the intestinal bacterial core, enterobacterial composition and mucosal barrier function in a pig model. RESULTS Microbiota sequencing results showed that Cnz could significantly alter the intestinal microbiota composition and metabolism. Besides increasing the richness indices (ACE and Chao1), 10% Cnz could protect the intestinal mucosal barrier through increasing the expression of occludin and zonula occludens-1 in the small intestine, increase the abundance of Lachnospiraceae UCG-004 and decrease the abundance of Ruminococcus flavefaciens compared to high ZnO diet and 5% Cnz material. CONCLUSIONS Cnz material at 10% supplementation is more effective than a level of 5% Cnz in increasing intestinal barrier through affecting gut microbiota. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Hongnan Liu
- National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Key Laboratory of Agro-ecological Processes in Subtropical Region, Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Breeding of Livestock and Poultry, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Hangzhou King Techina Technology Company Academician Expert Workstation, Hangzhou King Techina Technology Co. Ltd, Hangzhou, China
- Anhui Tianyuanju E-commerce Co. Ltd, Fuyang, China
| | - Miaomiao Bai
- National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Key Laboratory of Agro-ecological Processes in Subtropical Region, Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Breeding of Livestock and Poultry, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Kang Xu
- National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Key Laboratory of Agro-ecological Processes in Subtropical Region, Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Breeding of Livestock and Poultry, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Jian Zhou
- National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Key Laboratory of Agro-ecological Processes in Subtropical Region, Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Breeding of Livestock and Poultry, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Xiaofeng Zhang
- Hangzhou King Techina Technology Company Academician Expert Workstation, Hangzhou King Techina Technology Co. Ltd, Hangzhou, China
| | - Rong Yu
- Hangzhou King Techina Technology Company Academician Expert Workstation, Hangzhou King Techina Technology Co. Ltd, Hangzhou, China
| | - Ruilin Huang
- National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Key Laboratory of Agro-ecological Processes in Subtropical Region, Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Breeding of Livestock and Poultry, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Yulong Yin
- National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Key Laboratory of Agro-ecological Processes in Subtropical Region, Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Breeding of Livestock and Poultry, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Hangzhou King Techina Technology Company Academician Expert Workstation, Hangzhou King Techina Technology Co. Ltd, Hangzhou, China
- College of Animal Science, South China Agricultural University, Guangzhou, China
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18
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Zhao CY, Hao Y, Wang Y, Varga JJ, Stecenko AA, Goldberg JB, Brown SP. Microbiome Data Enhances Predictive Models of Lung Function in People With Cystic Fibrosis. J Infect Dis 2020; 223:S246-S256. [PMID: 33330902 DOI: 10.1093/infdis/jiaa655] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Microbiome sequencing has brought increasing attention to the polymicrobial context of chronic infections. However, clinical microbiology continues to focus on canonical human pathogens, which may overlook informative, but nonpathogenic, biomarkers. We address this disconnect in lung infections in people with cystic fibrosis (CF). METHODS We collected health information (lung function, age, and body mass index [BMI]) and sputum samples from a cohort of 77 children and adults with CF. Samples were collected during a period of clinical stability and 16S rDNA sequenced for airway microbiome compositions. We use ElasticNet regularization to train linear models predicting lung function and extract the most informative features. RESULTS Models trained on whole-microbiome quantitation outperformed models trained on pathogen quantitation alone, with or without the inclusion of patient metadata. Our most accurate models retained key pathogens as negative predictors (Pseudomonas, Achromobacter) along with established correlates of CF disease state (age, BMI, CF-related diabetes). In addition, our models selected nonpathogen taxa (Fusobacterium, Rothia) as positive predictors of lung health. CONCLUSIONS These results support a reconsideration of clinical microbiology pipelines to ensure the provision of informative data to guide clinical practice.
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Affiliation(s)
- Conan Y Zhao
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA.,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA.,Emory + Children's Center for Cystic Fibrosis and Airway Disease Research, Atlanta, Georgia, USA
| | - Yiqi Hao
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yifei Wang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA.,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA.,Institute for Data Engineering and Science (IDEaS), Georgia Institute of Technology, Atlanta, Georgia, USA.,Emory + Children's Center for Cystic Fibrosis and Airway Disease Research, Atlanta, Georgia, USA
| | - John J Varga
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA.,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA.,Division of Pulmonary, Allergy/Immunology, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA.,Emory + Children's Center for Cystic Fibrosis and Airway Disease Research, Atlanta, Georgia, USA
| | - Arlene A Stecenko
- Division of Pulmonary, Allergy/Immunology, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA.,Emory + Children's Center for Cystic Fibrosis and Airway Disease Research, Atlanta, Georgia, USA
| | - Joanna B Goldberg
- Division of Pulmonary, Allergy/Immunology, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA.,Emory + Children's Center for Cystic Fibrosis and Airway Disease Research, Atlanta, Georgia, USA
| | - Sam P Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA.,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA.,Emory + Children's Center for Cystic Fibrosis and Airway Disease Research, Atlanta, Georgia, USA
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19
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Maestrali F, Pilan R, Athanazio R, Sparvoli L, Cortez R, Taddei C, Voegels R. Cystic fibrosis microbiome: analysis of nasal middle meatus and sputum in different lung disease stages. RHINOLOGY ONLINE 2020. [DOI: 10.4193/rhinol/20.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND: Culture independent methods of molecular detection of microbiome have shown the polymicrobial nature of respiratory infections in cystic fibrosis, with pathogenic agents undetectable in conventional culture methods. Composition and diversity of the airway microbiome are still poorly understood. METHODOLOGY: This study evaluated the airway microbiome in 31 adult cystic fibrosis patients via the analysis of 16S rRNA se- quences by next generation sequencing. RESULTS: Staphylococcus, Streptococcus and Corynebacterium were the most abundant genera in the middle meatus, and Pseudo- monas, Haemophilus and Prevotella were the most abundant in sputum. In patients with advanced disease (FEV1< 50%), there was an increase in the prevalence of Pseudomonas in both sample types when studied separately. In each patient, in a paired analysis, the sputum and middle meatus showed similar microbiome composition in mild or moderate disease (FEV1≥ 50%). In patients with severe lung disease, the relative abundance of Pseudomonas had a positive correlation in both collection sites. CONCLUSIONS: This is the first Brazilian study to evaluate the airway microbiome in cystic fibrosis patients. Our findings agree with those in the international literature and indicate the role of Pseudomonas in the sputum and middle meatus in patients with advanced disease.
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20
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Parallel Analysis of Cystic Fibrosis Sputum and Saliva Reveals Overlapping Communities and an Opportunity for Sample Decontamination. mSystems 2020; 5:5/4/e00296-20. [PMID: 32636336 PMCID: PMC7343308 DOI: 10.1128/msystems.00296-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Cystic fibrosis is an inherited disease characterized by chronic respiratory tract infection and progressive lung disease. Studies of cystic fibrosis lung microbiology often rely on expectorated sputum to reflect the microbiota present in the lower airways. Passage of sputum through the oropharynx during collection, however, contributes microbes present in saliva to the sample, which could confound interpretation of results. Using culture-independent DNA sequencing-based analyses, we characterized the bacterial communities in pairs of expectorated sputum and saliva samples to generate a model for “decontaminating” sputum in silico. Our results demonstrate that salivary contamination of expectorated sputum does not have a large effect on most sputum samples and that observations of high bacterial diversity likely accurately reflect taxa present in cystic fibrosis lower airways. Culture-independent studies of the cystic fibrosis (CF) airway microbiome typically rely on expectorated sputum to assess the microbial makeup of lower airways. These studies have revealed rich bacterial communities. There is often considerable overlap between taxa observed in sputum and those observed in saliva, raising questions about the reliability of expectorated sputum as a sample representing lower airway microbiota. These concerns prompted us to compare pairs of sputum and saliva samples from 10 persons with CF. Using 16S rRNA gene sequencing and droplet digital PCR (ddPCR), we analyzed 37 pairs of sputum and saliva samples, each collected from the same person on the same day. We developed an in silico postsequencing decontamination procedure to remove from sputum the fraction of DNA reads estimated to have been contributed by saliva during expectoration. We demonstrate that while there was often sizeable overlap in community membership between sample types, expectorated sputum typically contains a higher bacterial load and a less diverse community compared to saliva. The differences in diversity between sputum and saliva were more pronounced in advanced disease stage, owing to increased relative abundance of the dominant taxa in sputum. Our effort to model saliva contamination of sputum in silico revealed generally minor effects on community structure after removal of contaminating reads. Despite considerable overlap in taxa observed between expectorated sputum and saliva samples, the impact of saliva contamination on measures of lower airway bacterial community composition in CF using expectorated sputum appears to be minimal. IMPORTANCE Cystic fibrosis is an inherited disease characterized by chronic respiratory tract infection and progressive lung disease. Studies of cystic fibrosis lung microbiology often rely on expectorated sputum to reflect the microbiota present in the lower airways. Passage of sputum through the oropharynx during collection, however, contributes microbes present in saliva to the sample, which could confound interpretation of results. Using culture-independent DNA sequencing-based analyses, we characterized the bacterial communities in pairs of expectorated sputum and saliva samples to generate a model for “decontaminating” sputum in silico. Our results demonstrate that salivary contamination of expectorated sputum does not have a large effect on most sputum samples and that observations of high bacterial diversity likely accurately reflect taxa present in cystic fibrosis lower airways.
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21
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Voronina OL, Ryzhova NN, Kunda MS, Loseva EV, Aksenova EI, Amelina EL, Shumkova GL, Simonova OI, Gintsburg AL. Characteristics of the Airway Microbiome of Cystic Fibrosis Patients. BIOCHEMISTRY (MOSCOW) 2020; 85:1-10. [PMID: 32079513 DOI: 10.1134/s0006297920010010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Microbiota as an integral component of human body is actively investigated, including by massively parallel sequencing. However, microbiomes of lungs and sinuses have become the object of scientific attention only in the last decade. For patients with cystic fibrosis, monitoring the state of respiratory tract microorganisms is essential for maintaining lung function. Here, we studied the role of sinuses and polyps in the formation of respiratory tract microbiome. We identified Proteobacteria in the sinuses and samples from the lower respiratory tract (even in childhood). In some cases, they were accompanied by potentially dangerous basidiomycetes. The presence of polyps did not affect formation of the sinus microbiome. Proteobacteria are decisive in reducing the biodiversity of lung and sinus microbiomes, which correlated with the worsening of the lung function indicators. Soft mutations in the CFTR gene contribute to the formation of safer microbiome even in heterozygotes with class I mutations.
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Affiliation(s)
- O L Voronina
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, 123098, Russia.
| | - N N Ryzhova
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, 123098, Russia
| | - M S Kunda
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, 123098, Russia
| | - E V Loseva
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, 123098, Russia
| | - E I Aksenova
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, 123098, Russia
| | - E L Amelina
- Pulmonology Research Institute, Federal Medical-Biological Agency, Moscow, 115682, Russia
| | - G L Shumkova
- Pulmonology Research Institute, Federal Medical-Biological Agency, Moscow, 115682, Russia
| | - O I Simonova
- National Medical Research Center for Children's Health, Ministry of Health of Russia, Moscow, 119296, Russia
| | - A L Gintsburg
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, 123098, Russia
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22
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Mauch RM, Hentschel J, Aanaes K, Barucha A, Nolasco da Silva MT, Levy CE, Høiby N, Mainz JG. Antibody response against Pseudomonas aeruginosa and its relationship with immune mediators in the upper and lower airways of cystic fibrosis patients. Pediatr Pulmonol 2020; 55:959-967. [PMID: 32022432 DOI: 10.1002/ppul.24671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/19/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND The upper airways (UAW) are a niche and a reservoir of Pseudomonas aeruginosa strains that cause chronic infection of the lower airways (LAW) in cystic fibrosis (CF). Here, we assessed the role of anti-P. aeruginosa immunoglobulin A (IgA) and IgG antibodies in upper and lower airway infections in cystic fibrosis patients. METHODS Nasal lavage fluid and induced sputum samples of 40 CF patients were microbiologically cultured. We searched for correlations between anti-P. aeruginosa IgA and IgG levels, measured by enzyme-linked immunosorbent assay (optical density), and unspecific immune mediators in both specimens. RESULTS Anti-P. aeruginosa IgA (median optical density: 0.953 vs 0.298) and IgG (0.120 vs 0.059) were significantly higher in nasal lavage than in sputum, but not significantly different between patients with and without chronic P. aeruginosa infection in UAW. Matrix metallopeptidase-9 (MMP-9) in nasal lavage and neutrophil elastase (NE) in sputum were predictors of IgA in nasal lavage and IgA in sputum, respectively. IgA was a predictor of myeloperoxidase (MPO) in nasal lavage. Tissue inhibitor of metalloproteinases-1 (TIMP-1) was a predictor of IgG in sputum. IgG, TIMP-1, and NE in sputum were predictors of IgG in nasal lavage. CONCLUSION The anti-P. aeruginosa IgA response was more prominent in CF patients' UAW, indicating a lower degree of inflammatory responses. Proteases may play a role in the anti-P. aeruginosa humoral response in the upper and LAW, and anti-P. aeruginosa IgG may be involved in the crosstalk between upper and lower airways in cystic fibrosis patients.
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Affiliation(s)
- Renan M Mauch
- Center for Investigation in Pediatrics, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig, Leipzig, Germany
| | - Kasper Aanaes
- Department of Oto-Rhino-Laryngology, Rigshospitalet (Copenhagen University Hospital), Copenhagen, Denmark
| | - Anton Barucha
- Department of Pediatric Pulmonology/Cystic Fibrosis Center, Brandenburg Medical School (MHB) University, Klinikum Westbrandenburg, Brandenburg an der Havel, Germany
| | - Marcos T Nolasco da Silva
- Center for Investigation in Pediatrics, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil.,Department of Pediatrics, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Carlos E Levy
- Department of Clinical Pathology, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Niels Høiby
- Department of International Health, Immunology, and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jochen G Mainz
- Department of Pediatric Pulmonology/Cystic Fibrosis Center, Brandenburg Medical School (MHB) University, Klinikum Westbrandenburg, Brandenburg an der Havel, Germany.,Cystic Fibrosis Center for Children and Adults, Jena University Hospital, Jena, Germany
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23
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Ramírez-Labrada AG, Isla D, Artal A, Arias M, Rezusta A, Pardo J, Gálvez EM. The Influence of Lung Microbiota on Lung Carcinogenesis, Immunity, and Immunotherapy. Trends Cancer 2020; 6:86-97. [PMID: 32061309 DOI: 10.1016/j.trecan.2019.12.007] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 12/12/2019] [Indexed: 12/20/2022]
Abstract
Microbiota have emerged as key modulators of both the carcinogenic process and the immune response against cancer cells, and, thus, it seems to influence the efficacy of immunotherapy. While most studies have focused on analyzing the influence of gut microbiota, its composition substantially differs from that in the lung. Here, we describe how microbial life in the lungs is associated with host immune status in the lungs and, thus, how the identification of the microbial populations in the lower respiratory tract rather than in the gut might be key to understanding the lung carcinogenic process and to predict the efficacy of different treatments. Understanding the influence of lung microbiota on host immunity may identify new therapeutic targets and help to design new immunotherapy approaches to treat lung cancer.
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Affiliation(s)
- Ariel G Ramírez-Labrada
- Unidad de Nanotoxicología e Inmunotoxicología (UNATI), Instituto de Investigación Sanitaria Aragón (IIS Aragón), Centro de Investigación Biomédica de Aragón (CIBA), Zaragoza, Spain
| | - Dolores Isla
- Medical Oncology Department, Instituto de Investigación Sanitaria Aragón, Hospital Clinico Universitario Lozano Blesa, Zaragoza, Spain
| | - Angel Artal
- Medical Oncology Department, Instituto de Investigación Sanitaria Aragón (IIS Aragón), Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - Maykel Arias
- Instituto de Carboquímica ICB-CSIC, Zaragoza, Spain
| | - Antonio Rezusta
- Department of Microbiology, Hospital Universitario Miguel Servet, Zaragoza, Spain; Department of Microbiology, Preventive Medicine and Public Health, University of Zaragoza, Zaragoza, Spain
| | - Julián Pardo
- Department of Microbiology, Preventive Medicine and Public Health, University of Zaragoza, Zaragoza, Spain; Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain; Aragón I + D Foundation (ARAID), Government of Aragon, Zaragoza, Spain
| | - Eva M Gálvez
- Instituto de Carboquímica ICB-CSIC, Zaragoza, Spain.
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24
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Phenotype-Specific Therapeutic Effect of Rhodiola wallichiana var. cholaensis Combined with Dexamethasone on Experimental Murine Asthma and Its Comprehensive Pharmacological Mechanism. Int J Mol Sci 2019; 20:ijms20174216. [PMID: 31466312 PMCID: PMC6747379 DOI: 10.3390/ijms20174216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/17/2019] [Accepted: 08/26/2019] [Indexed: 12/14/2022] Open
Abstract
The heterogeneity of asthma involves complex pathogenesis leading to confusion regarding the choice of therapeutic strategy. In the clinic, asthma is commonly classified as having either eosinophilic asthma (EA) or non-eosinophilic asthma (NEA) phenotypes. Microbiota colonizing in airways has been demonstrated to induce distinct phenotypes of asthma and the resistance to steroids. Rhodiola wallichiana var. cholaensis (RWC) has the potential to alleviate asthmatic inflammation according to recent studies, but its pharmacological mechanisms remain unclarified. In our study, murine asthmatic phenotypes were established and treated with RWC and/or dexamethasone (DEX). Combined treatment with RWC and DEX could improve spirometry and airway hyperresponsiveness (AHR) in asthmatic phenotypes, alleviate steroid resistance in NEA, and reduce the inflammatory infiltration of the both phenotypes. The combined treatment increased Th1, regulated the imbalance of Th2/Th1, and decreased the related cytokines in EA. As for NEA, the combined treatment reduced Th17 and promoted the accumulation of regulatory T cells (Tregs) in lung. A microbiome study based on 16S rDNA sequencing technique revealed the significantly changed structure of the lower airway microbiota after combined treatment in NEA, with 4 distinct genera and 2 species identified. OPLS-DA models of metabolomics analysis based on UPLC-Q/TOF-MS technique identified 34 differentiated metabolites and 8 perturbed metabolic pathways. A joint multiomics study predicted that the colonized microbiota in airways might be associated with susceptibility of asthma and steroid resistance, which involved systematic and pulmonary metabolic perturbation. In summary, the pharmacological network of RWC included the complicated interaction mechanisms of immune regulation, microbiota change, and metabolic perturbation.
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25
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Mauch RM, Rossi CL, Nolasco da Silva MT, Bianchi Aiello T, Ribeiro JD, Ribeiro AF, Høiby N, Levy CE. Secretory IgA-mediated immune response in saliva and early detection of Pseudomonas aeruginosa in the lower airways of pediatric cystic fibrosis patients. Med Microbiol Immunol 2019; 208:205-213. [PMID: 30706137 DOI: 10.1007/s00430-019-00578-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/08/2019] [Indexed: 12/14/2022]
Abstract
Pseudomonas aeruginosa (Pa) detection in the paranasal sinuses may help to prevent or postpone bacterial aspiration to the lower airways (LAW) and chronic lung infection in cystic fibrosis (CF). We assessed the ability of an ELISA test for measurement of specific Pa secretory IgA (sIgA) in saliva (a potential marker of sinus colonization) to early detect changes in the Pa LAW status (indicated by microbiological sputum or cough swab culture and specific serum IgG levels) of 65 patients for three years, in different investigation scenarios. Increased sIgA levels were detected in saliva up to 22 months before changes in culture/serology. Patients who remained Pa-positive had significantly increased sIgA levels than patients who remained Pa-negative, both at the baseline (39.6 U/mL vs. 19.2 U/mL; p = 0.02) and at the end of the follow-up (119.4 U/mL vs. 25.2 U/mL; p < 0.001). No association was found between sIgA levels in saliva and emergence or recurrence of Pa in the LAW. A positive median sIgA result in the first year of follow-up implied up to 12.5-fold increased risk of subsequent Pa exposure in the LAW. Our test detected early changes in the P. aeruginosa LAW status and risk of exposure to P. aeruginosa in the LAW with two years in advance. Comparison with sinus culture is needed to assess the test's ability to identify CF patients in need of a sinus approach for Pa investigation, which could provide opportunities of Pa eradication before its aspiration to the lungs.
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Affiliation(s)
- Renan Marrichi Mauch
- Department of Clinical Pathology, School of Medical Sciences, University of Campinas, Rua Vital Brasil 251, 2nd floor, Cidade Universitária, Barão Geraldo, Campinas, SP, 13083-888, Brazil.,Center for Investigation in Pediatrics, School of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo 126, Campinas, SP, 13083-887, Brazil
| | - Claudio Lucio Rossi
- Department of Clinical Pathology, School of Medical Sciences, University of Campinas, Rua Vital Brasil 251, 2nd floor, Cidade Universitária, Barão Geraldo, Campinas, SP, 13083-888, Brazil
| | - Marcos Tadeu Nolasco da Silva
- Center for Investigation in Pediatrics, School of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo 126, Campinas, SP, 13083-887, Brazil
| | - Talita Bianchi Aiello
- Laboratory of Microbiology, Centro Médico de Campinas, Rua Dr. Edilberto Luís Pereira da Silva 929, Campinas, SP, 13083-190, Brazil
| | - José Dirceu Ribeiro
- Center for Investigation in Pediatrics, School of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo 126, Campinas, SP, 13083-887, Brazil
| | - Antônio Fernando Ribeiro
- Center for Investigation in Pediatrics, School of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo 126, Campinas, SP, 13083-887, Brazil
| | - Niels Høiby
- Clinical Microbiology Department, Rigshospitalet (Copenhagen University Hospital), Juliane Maries Vej 22, 2100, Copenhagen, Denmark.,Costerton Biofilm Centre, Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 24.1, 2200, Copenhagen, Denmark
| | - Carlos Emilio Levy
- Department of Clinical Pathology, School of Medical Sciences, University of Campinas, Rua Vital Brasil 251, 2nd floor, Cidade Universitária, Barão Geraldo, Campinas, SP, 13083-888, Brazil.
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26
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Oriano M, Terranova L, Teri A, Sottotetti S, Ruggiero L, Tafuro C, Marchisio P, Gramegna A, Amati F, Nava F, Franceschi E, Cariani L, Blasi F, Aliberti S. Comparison of different conditions for DNA extraction in sputum - a pilot study. Multidiscip Respir Med 2019; 14:6. [PMID: 30733864 PMCID: PMC6357456 DOI: 10.1186/s40248-018-0166-z] [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: 11/16/2018] [Accepted: 12/25/2018] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The analysis of microbiome in respiratory samples is a topic of great interest in chronic respiratory diseases. The method used to prepare sputum samples for microbiome analysis is very heterogeneous. The selection of the most suitable methodology for DNA extraction is fundamental to have the most representative data. The objective of this study was to compare different conditions for DNA extraction from sputum in adult patients with bronchiectasis. METHODS Five sputum samples from bronchiectasis patients were collected at the Policlinico Hospital in Milan, Italy. Eighteen conditions for DNA extraction were compared, including two enzyme-based (Roche and Zymo) and one beads-based (Mobio) technique. These techniques were tested with/without Dithiothreitol (DTT) and with/without lysostaphin (0.18 and 0.36 mg/mL) step. DNA was quantified, tested using Real-time PCR for 16S rDNA and S. aureus and, then, microbiome was evaluated. RESULTS Although 16S rDNA was similarly detected across all the different techniques, Roche kit gave the highest DNA yield. The lowest Ct values for Real-time PCR for S. aureus was identified when lysostaphin was added. Considering genera from microbiome, alpha diversity indices did not show any significant differences between techniques, while relative abundances were more similar in presence of DTT. CONCLUSIONS None of the conditions emerged to be superior to the others even if enzyme-based kits seem to be needed in order to have a higher extraction yield.
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Affiliation(s)
- Martina Oriano
- University of Milan, Department of Pathophysiology and Transplantation, Via Francesco Sforza 35, 20122 Milan, Italy
- University of Pavia, Department of Molecular Medicine, Pavia, Italy
| | - Leonardo Terranova
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Antonio Teri
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Cystic Fibrosis Microbiology Laboratory, Milan, Italy
| | - Samantha Sottotetti
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Cystic Fibrosis Microbiology Laboratory, Milan, Italy
| | - Luca Ruggiero
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Paediatric Highly Intensive Care Unit, Via della Commenda 9, 20122 Milan, Italy
| | - Camilla Tafuro
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Paediatric Highly Intensive Care Unit, Via della Commenda 9, 20122 Milan, Italy
| | - Paola Marchisio
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Paediatric Highly Intensive Care Unit, Via della Commenda 9, 20122 Milan, Italy
| | - Andrea Gramegna
- University of Milan, Department of Pathophysiology and Transplantation, Via Francesco Sforza 35, 20122 Milan, Italy
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Francesco Amati
- University of Milan, Department of Pathophysiology and Transplantation, Via Francesco Sforza 35, 20122 Milan, Italy
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Fabrizio Nava
- University of Milan, Department of Pathophysiology and Transplantation, Via Francesco Sforza 35, 20122 Milan, Italy
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Elisa Franceschi
- University of Milan, Department of Pathophysiology and Transplantation, Via Francesco Sforza 35, 20122 Milan, Italy
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Lisa Cariani
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Cystic Fibrosis Microbiology Laboratory, Milan, Italy
| | - Francesco Blasi
- University of Milan, Department of Pathophysiology and Transplantation, Via Francesco Sforza 35, 20122 Milan, Italy
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Stefano Aliberti
- University of Milan, Department of Pathophysiology and Transplantation, Via Francesco Sforza 35, 20122 Milan, Italy
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Via Francesco Sforza 35, 20122 Milan, Italy
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27
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Eiserich JP, Ott SP, Kadir T, Morrissey BM, Hayakawa KA, La Merrill MA, Cross CE. Quantitative assessment of cyanide in cystic fibrosis sputum and its oxidative catabolism by hypochlorous acid. Free Radic Biol Med 2018; 129:146-154. [PMID: 30213640 DOI: 10.1016/j.freeradbiomed.2018.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/07/2018] [Indexed: 02/06/2023]
Abstract
RATIONALE Cystic fibrosis (CF) patients are known to produce cyanide (CN-) although challenges exist in determinations of total levels, the precise bioactive levels, and specificity of its production by CF microflora, especially P. aeruginosa. Our objective was to measure total CN- levels in CF sputa by a simple and novel technique in P. aeruginosa positive and negative adult patients, to review respiratory tract (RT) mechanisms for the production and degradation of CN-, and to interrogate sputa for post-translational protein modification by CN- metabolites. METHODS Sputa CN- concentrations were determined by using a commercially available CN- electrode, measuring levels before and after addition of cobinamide, a compound with extremely high affinity for CN-. Detection of protein carbamoylation was measured by Western blot. MEASUREMENTS AND MAIN RESULTS The commercial CN- electrode was found to overestimate CN- levels in CF sputum in a highly variable manner; cobinamide addition rectified this analytical issue. Although P. aeruginosa positive patients tended to have higher total CN- values, no significant differences in CN- levels were found between positive and negative sputa. The inflammatory oxidant hypochlorous acid (HOCl) was shown to rapidly decompose CN-, forming cyanogen chloride (CNCl) and the carbamoylating species cyanate (NCO-). Carbamoylated proteins were found in CF sputa, analogous to reported findings in asthma. CONCLUSIONS Our studies indicate that CN- is a transient species in the inflamed CF airway due to multiple biosynthetic and metabolic processes. Stable metabolites of CN-, such as cyanate, or carbamoylated proteins, may be suitable biomarkers of overall CN- production in CF airways.
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Affiliation(s)
- Jason P Eiserich
- Department of Internal Medicine, Division of Pulmonary/Critical Care and Sleep Medicine, University of California, Davis, CA 95616, United States; Department of Physiology and Membrane Biology, University of California, Davis, CA 95616, United States
| | - Sean P Ott
- Department of Internal Medicine, Division of Pulmonary/Critical Care and Sleep Medicine, University of California, Davis, CA 95616, United States
| | - Tamara Kadir
- Department of Internal Medicine, Division of Pulmonary/Critical Care and Sleep Medicine, University of California, Davis, CA 95616, United States
| | - Brian M Morrissey
- Department of Internal Medicine, Division of Pulmonary/Critical Care and Sleep Medicine, University of California, Davis, CA 95616, United States
| | - Keri A Hayakawa
- Department of Internal Medicine, Division of Pulmonary/Critical Care and Sleep Medicine, University of California, Davis, CA 95616, United States
| | - Michele A La Merrill
- Department of Environmental Toxicology, University of California, Davis, CA 95616, United States
| | - Carroll E Cross
- Department of Internal Medicine, Division of Pulmonary/Critical Care and Sleep Medicine, University of California, Davis, CA 95616, United States; Department of Physiology and Membrane Biology, University of California, Davis, CA 95616, United States.
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28
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Yang HJ, LoSavio PS, Engen PA, Naqib A, Mehta A, Kota R, Khan RJ, Tobin MC, Green SJ, Schleimer RP, Keshavarzian A, Batra PS, Mahdavinia M. Association of nasal microbiome and asthma control in patients with chronic rhinosinusitis. Clin Exp Allergy 2018; 48:1744-1747. [PMID: 30126004 PMCID: PMC6265059 DOI: 10.1111/cea.13255] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/07/2018] [Accepted: 07/14/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Hyo J. Yang
- Medical College, Rush University, Chicago, Illinois
- Department of Internal Medicine, Allergy/Immunology Division, Rush University Medical Center, Chicago, Illinois
| | - Phillip S. LoSavio
- Department of Otorhinolaryngology – Head and Neck Surgery, Rush University Medical Center, Chicago, Illinois
| | - Phillip A. Engen
- Division of Gastroenterology, Internal Medicine Department, Rush University Medical Center, Chicago, Illinois
| | - Ankur Naqib
- DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois
| | - Arpita Mehta
- Department of Internal Medicine, Allergy/Immunology Division, Rush University Medical Center, Chicago, Illinois
| | - Raj Kota
- Department of Internal Medicine, Allergy/Immunology Division, Rush University Medical Center, Chicago, Illinois
| | - Rafsa J. Khan
- Department of Internal Medicine, Allergy/Immunology Division, Rush University Medical Center, Chicago, Illinois
| | - Mary C. Tobin
- Department of Internal Medicine, Allergy/Immunology Division, Rush University Medical Center, Chicago, Illinois
| | - Stefan J. Green
- DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois
| | - Robert P. Schleimer
- Division of Allergy and Immunology, Internal Medicine Department, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ali Keshavarzian
- Division of Gastroenterology, Internal Medicine Department, Rush University Medical Center, Chicago, Illinois
| | - Pete S. Batra
- Department of Otorhinolaryngology – Head and Neck Surgery, Rush University Medical Center, Chicago, Illinois
| | - Mahboobeh Mahdavinia
- Department of Internal Medicine, Allergy/Immunology Division, Rush University Medical Center, Chicago, Illinois
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Pletcher SD, Goldberg AN, Cope EK. Loss of Microbial Niche Specificity Between the Upper and Lower Airways in Patients With Cystic Fibrosis. Laryngoscope 2018; 129:544-550. [PMID: 30284279 DOI: 10.1002/lary.27454] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2018] [Indexed: 12/27/2022]
Abstract
OBJECTIVES/HYPOTHESIS To determine the relationship between mucosal-associated sinus and bronchial microbiota in cystic fibrosis (CF) patients compared to non-CF patients with chronic rhinosinusitis (CRS). STUDY DESIGN Case series. METHODS We examined the microbial composition of 52 paired sinus and bronchial brushings from 26 patients with CRS. Paired airway samples from nine subjects with CF were compared with samples from 17 non-CF-CRS disease control patients. The Illumina MiSeq platform was used to sequence the V4 region of the 16S rRNA gene. Sequences were analyzed using QIIME 1.9.0. RESULTS CF patients demonstrate increased severity of sinus inflammation (Lund-Mackay score 16.3 vs. 12.4, P = .023) and diminished diversity of microbial communities in both the sinuses (Shannon diversity 0.98 vs. 3.3, P = .009) and lungs (Shannon diversity 2.2 vs. 4.0, P = .042) relative to non-CF-CRS. Non-CF-CRS sinus and lung microbiota were distinct and clustered by niche (sinus vs. lung, P = .004). However, CF airway microbiota demonstrated a loss of niche specificity (sinus vs. lung, P = .492). Two CF patients underwent lung transplantation at 4.5 and 9 months prior to sampling. Sinus and lung samples from these two patients demonstrated distinct microbial communities. CONCLUSIONS Patients with CF undergoing surgery for CRS exhibit substantial bacterial community collapse in the sinuses and a loss of niche specificity between the upper and lower airways compared to non-CF patients with CRS. These results extend previous studies elucidating the lower airway microbiome in cystic fibrosis and provide support for the concept of microbial translocation in the cystic fibrosis airways. LEVEL OF EVIDENCE 4 Laryngoscope, 129:544-550, 2019.
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Affiliation(s)
- Steven D Pletcher
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, California
| | - Andrew N Goldberg
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, California
| | - Emily K Cope
- Pathogen and Microbiome Institute, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, U.S.A
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