1
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Seelbinder B, Lohinai Z, Vazquez-Uribe R, Brunke S, Chen X, Mirhakkak M, Lopez-Escalera S, Dome B, Megyesfalvi Z, Berta J, Galffy G, Dulka E, Wellejus A, Weiss GJ, Bauer M, Hube B, Sommer MOA, Panagiotou G. Candida expansion in the gut of lung cancer patients associates with an ecological signature that supports growth under dysbiotic conditions. Nat Commun 2023; 14:2673. [PMID: 37160893 PMCID: PMC10169812 DOI: 10.1038/s41467-023-38058-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 04/11/2023] [Indexed: 05/11/2023] Open
Abstract
Candida species overgrowth in the human gut is considered a prerequisite for invasive candidiasis, but our understanding of gut bacteria promoting or restricting this overgrowth is still limited. By integrating cross-sectional mycobiome and shotgun metagenomics data from the stool of 75 male and female cancer patients at risk but without systemic candidiasis, bacterial communities in high Candida samples display higher metabolic flexibility yet lower contributional diversity than those in low Candida samples. We develop machine learning models that use only bacterial taxa or functional relative abundances to predict the levels of Candida genus and species in an external validation cohort with an AUC of 78.6-81.1%. We propose a mechanism for intestinal Candida overgrowth based on an increase in lactate-producing bacteria, which coincides with a decrease in bacteria that regulate short chain fatty acid and oxygen levels. Under these conditions, the ability of Candida to harness lactate as a nutrient source may enable Candida to outcompete other fungi in the gut.
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Affiliation(s)
- Bastian Seelbinder
- Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology- Hans Knöll Institute, Jena, Germany
| | - Zoltan Lohinai
- National Koranyi Institute of Pulmonology, Budapest, Hungary
- Translational Medicine Institute, Semmelweis University, Budapest, Hungary
| | - Ruben Vazquez-Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Sascha Brunke
- Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Xiuqiang Chen
- Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology- Hans Knöll Institute, Jena, Germany
| | - Mohammad Mirhakkak
- Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology- Hans Knöll Institute, Jena, Germany
| | - Silvia Lopez-Escalera
- Chr. Hansen A/S, Human Health Innovation, Hoersholm, Denmark
- Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Balazs Dome
- National Koranyi Institute of Pulmonology, Budapest, Hungary
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
- Department of Thoracic Surgery, National Institute of Oncology-Semmelweis University, Budapest, Hungary
| | - Zsolt Megyesfalvi
- National Koranyi Institute of Pulmonology, Budapest, Hungary
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
- Department of Thoracic Surgery, National Institute of Oncology-Semmelweis University, Budapest, Hungary
| | - Judit Berta
- National Koranyi Institute of Pulmonology, Budapest, Hungary
| | | | - Edit Dulka
- County Hospital of Torokbalint, Torokbalint, Hungary
| | - Anja Wellejus
- Chr. Hansen A/S, Human Health Innovation, Hoersholm, Denmark
| | - Glen J Weiss
- Department of Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - Michael Bauer
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - Bernhard Hube
- Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Gianni Panagiotou
- Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology- Hans Knöll Institute, Jena, Germany.
- Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany.
- Department of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China.
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2
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Marfil-Sánchez A, Zhang L, Alonso-Pernas P, Mirhakkak M, Mueller M, Seelbinder B, Ni Y, Santhanam R, Busch A, Beemelmanns C, Ermolaeva M, Bauer M, Panagiotou G. An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness. Gut Microbes 2022; 13:1993598. [PMID: 34793277 PMCID: PMC8604395 DOI: 10.1080/19490976.2021.1993598] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Antibiotics are commonly used in the Intensive Care Unit (ICU); however, several studies showed that the impact of antibiotics to prevent infection, multi-organ failure, and death in the ICU is less clear than their benefit on course of infection in the absence of organ dysfunction. We characterized here the compositional and metabolic changes of the gut microbiome induced by critical illness and antibiotics in a cohort of 75 individuals in conjunction with 2,180 gut microbiome samples representing 16 different diseases. We revealed an "infection-vulnerable" gut microbiome environment present only in critically ill treated with antibiotics (ICU+). Feeding of Caenorhabditis elegans with Bifidobacterium animalis and Lactobacillus crispatus, species that expanded in ICU+ patients, revealed a significant negative impact of these microbes on host viability and developmental homeostasis. These results suggest that antibiotic administration can dramatically impact essential functional activities in the gut related to immune responses more than critical illness itself, which might explain in part untoward effects of antibiotics in the critically ill.
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Affiliation(s)
- Andrea Marfil-Sánchez
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Lu Zhang
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | | | - Mohammad Mirhakkak
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Melinda Mueller
- Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Bastian Seelbinder
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Yueqiong Ni
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Rakesh Santhanam
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Anne Busch
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany
| | - Christine Beemelmanns
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Maria Ermolaeva
- Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany,Maria Ermolaeva Stress Tolerance and Homeostasis, Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstraße 11, Jena 07745, Germany
| | - Michael Bauer
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany,Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany,Michael Bauer Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany,Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong, China,Lead Contact,CONTACT Gianni Panagiotou Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11A, Jena07745, Germany
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3
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Zoran T, Seelbinder B, White PL, Price JS, Kraus S, Kurzai O, Linde J, Häder A, Loeffler C, Grigoleit GU, Einsele H, Panagiotou G, Loeffler J, Schäuble S. Molecular Profiling Reveals Characteristic and Decisive Signatures in Patients after Allogeneic Stem Cell Transplantation Suffering from Invasive Pulmonary Aspergillosis. J Fungi (Basel) 2022; 8:jof8020171. [PMID: 35205926 PMCID: PMC8880021 DOI: 10.3390/jof8020171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 02/07/2023] Open
Abstract
Despite available diagnostic tests and recent advances, diagnosis of pulmonary invasive aspergillosis (IPA) remains challenging. We performed a longitudinal case-control pilot study to identify host-specific, novel, and immune-relevant molecular candidates indicating IPA in patients post allogeneic stem cell transplantation (alloSCT). Supported by differential gene expression analysis of six relevant in vitro studies, we conducted RNA sequencing of three alloSCT patients categorized as probable IPA cases and their matched controls without Aspergillus infection (66 samples in total). We additionally performed immunoassay analysis for all patient samples to gain a multi-omics perspective. Profiling analysis suggested LGALS2, MMP1, IL-8, and caspase-3 as potential host molecular candidates indicating IPA in investigated alloSCT patients. MMP1, IL-8, and caspase-3 were evaluated further in alloSCT patients for their potential to differentiate possible IPA cases and patients suffering from COVID-19-associated pulmonary aspergillosis (CAPA) and appropriate control patients. Possible IPA cases showed differences in IL-8 and caspase-3 serum levels compared with matched controls. Furthermore, we observed significant differences in IL-8 and caspase-3 levels among CAPA patients compared with control patients. With our conceptual work, we demonstrate the potential value of considering the human immune response during Aspergillus infection to identify immune-relevant molecular candidates indicating IPA in alloSCT patients. These human host candidates together with already established fungal biomarkers might improve the accuracy of IPA diagnostic tools.
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Affiliation(s)
- Tamara Zoran
- Department of Internal Medicine II, University Hospital Wuerzburg, 97080 Wuerzburg, Germany; (T.Z.); (S.K.); (C.L.); (G.U.G.); (H.E.)
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knoell Institute, 07745 Jena, Germany; (B.S.); (G.P.)
| | - Bastian Seelbinder
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knoell Institute, 07745 Jena, Germany; (B.S.); (G.P.)
| | - Philip Lewis White
- Public Health Wales, Microbiology Cardiff, UHW, Cardiff CF14 4XW, UK; (P.L.W.); (J.S.P.)
| | - Jessica Sarah Price
- Public Health Wales, Microbiology Cardiff, UHW, Cardiff CF14 4XW, UK; (P.L.W.); (J.S.P.)
| | - Sabrina Kraus
- Department of Internal Medicine II, University Hospital Wuerzburg, 97080 Wuerzburg, Germany; (T.Z.); (S.K.); (C.L.); (G.U.G.); (H.E.)
| | - Oliver Kurzai
- Research Group Fungal Septomics, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knoell Institute, 07745 Jena, Germany; (O.K.); (A.H.)
- Institute for Hygiene and Microbiology, Julius Maximilians University of Wuerzburg, Josef-Schneider-Straße 2/E1, 97080 Wuerzburg, Germany
| | - Joerg Linde
- Friedrich—Loeffler Institute, Institute of Bacterial Infections and Zoonoses, 07743 Jena, Germany;
| | - Antje Häder
- Research Group Fungal Septomics, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knoell Institute, 07745 Jena, Germany; (O.K.); (A.H.)
| | - Claudia Loeffler
- Department of Internal Medicine II, University Hospital Wuerzburg, 97080 Wuerzburg, Germany; (T.Z.); (S.K.); (C.L.); (G.U.G.); (H.E.)
| | - Goetz Ulrich Grigoleit
- Department of Internal Medicine II, University Hospital Wuerzburg, 97080 Wuerzburg, Germany; (T.Z.); (S.K.); (C.L.); (G.U.G.); (H.E.)
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Wuerzburg, 97080 Wuerzburg, Germany; (T.Z.); (S.K.); (C.L.); (G.U.G.); (H.E.)
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knoell Institute, 07745 Jena, Germany; (B.S.); (G.P.)
| | - Juergen Loeffler
- Department of Internal Medicine II, University Hospital Wuerzburg, 97080 Wuerzburg, Germany; (T.Z.); (S.K.); (C.L.); (G.U.G.); (H.E.)
- Correspondence: (J.L.); (S.S.)
| | - Sascha Schäuble
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knoell Institute, 07745 Jena, Germany; (B.S.); (G.P.)
- Correspondence: (J.L.); (S.S.)
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4
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Barber AE, Sae-Ong T, Kang K, Seelbinder B, Li J, Walther G, Panagiotou G, Kurzai O. Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection. Nat Microbiol 2021; 6:1526-1536. [PMID: 34819642 DOI: 10.1038/s41564-021-00993-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 10/08/2021] [Indexed: 12/25/2022]
Abstract
Aspergillus fumigatus is an environmental saprobe and opportunistic human fungal pathogen. Despite an estimated annual occurrence of more than 300,000 cases of invasive disease worldwide, a comprehensive survey of the genomic diversity present in A. fumigatus-including the relationship between clinical and environmental isolates and how this genetic diversity contributes to virulence and antifungal drug resistance-has been lacking. In this study we define the pan-genome of A. fumigatus using a collection of 300 globally sampled genomes (83 clinical and 217 environmental isolates). We found that 7,563 of the 10,907 unique orthogroups (69%) are core and present in all isolates and the remaining 3,344 show presence/absence of variation, representing 16-22% of the genome of each isolate. Using this large genomic dataset of environmental and clinical samples, we found an enrichment for clinical isolates in a genetic cluster whose genomes also contain more accessory genes, including genes coding for transmembrane transporters and proteins with iron-binding activity, and genes involved in both carbohydrate and amino-acid metabolism. Finally, we leverage the power of genome-wide association studies to identify genomic variation associated with clinical isolates and triazole resistance as well as characterize genetic variation in known virulence factors. This characterization of the genomic diversity of A. fumigatus allows us to move away from a single reference genome that does not necessarily represent the species as a whole and better understand its pathogenic versatility, ultimately leading to better management of these infections.
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Affiliation(s)
- Amelia E Barber
- Research Group Fungal Septomics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany.,Junior Research Group Fungal Informatics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Tongta Sae-Ong
- Research Group Systems Biology and Bioinformatics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Kang Kang
- Research Group Systems Biology and Bioinformatics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Bastian Seelbinder
- Research Group Systems Biology and Bioinformatics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.,School of Data Science, City University of Hong Kong, Hong Kong, China
| | - Grit Walther
- National Reference Center for Invasive Fungal Infections (NRZMyk), Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Gianni Panagiotou
- Research Group Systems Biology and Bioinformatics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany. .,Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong, China.
| | - Oliver Kurzai
- Research Group Fungal Septomics, Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany. .,National Reference Center for Invasive Fungal Infections (NRZMyk), Leibniz Institute of Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany. .,Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany.
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5
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Marfil-Sánchez A, Seelbinder B, Ni Y, Varga J, Berta J, Hollosi V, Dome B, Megyesfalvi Z, Dulka E, Galffy G, Weiss GJ, Panagiotou G, Lohinai Z. Gut microbiome functionality might be associated with exercise tolerance and recurrence of resected early-stage lung cancer patients. PLoS One 2021; 16:e0259898. [PMID: 34793492 PMCID: PMC8601557 DOI: 10.1371/journal.pone.0259898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/28/2021] [Indexed: 11/18/2022] Open
Abstract
Impaired exercise tolerance and lung function is a marker for increased mortality in lung cancer patients undergoing lung resection surgery. Recent data suggest that the gut-lung axis regulates systemic metabolic and immune functions, and microbiota might alter exercise tolerance. Here, we aimed to evaluate the associations between gut microbiota and outcomes in lung cancer patients who underwent lung resection surgery. We analysed stool samples, from 15 early-stage lung cancer patients, collected before and after surgical resection using shotgun metagenomic and Internal Transcribed Spacer (ITS) sequencing. We analysed microbiome and mycobiome associations with post-surgery lung function and cardiopulmonary exercise testing (CPET) to assess the maximum level of work achieved. There was a significant difference, between pre- and post-surgical resection samples, in microbial community functional profiles and several species from Alistipes and Bacteroides genus, associated with the production of SCFAs, increased significantly in abundance. Interestingly, an increase in VO2 coincides with an increase in certain species and the "GABA shunt" pathway, suggesting that treatment outcome might improve by enriching butyrate-producing species. Here, we revealed associations between specific gut bacteria, fungi, and their metabolic pathways with the recovery of lung function and exercise capacity.
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Affiliation(s)
- Andrea Marfil-Sánchez
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Bastian Seelbinder
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Yueqiong Ni
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Janos Varga
- National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Judit Berta
- National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Virag Hollosi
- National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Balazs Dome
- National Koranyi Institute of Pulmonology, Budapest, Hungary
- Department of Thoracic Surgery, National Institute of Oncology-Semmelweis University, Budapest, Hungary
- Division of Thoracic Surgery, Department of Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Zsolt Megyesfalvi
- National Koranyi Institute of Pulmonology, Budapest, Hungary
- Department of Thoracic Surgery, National Institute of Oncology-Semmelweis University, Budapest, Hungary
- Division of Thoracic Surgery, Department of Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Edit Dulka
- County Hospital of Torokbalint, Torokbalint, Hungary
| | | | - Glen J. Weiss
- MiRanostics Consulting, Oro Valley, Arizona, United States of America
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
- * E-mail:
| | - Zoltan Lohinai
- National Koranyi Institute of Pulmonology, Budapest, Hungary
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6
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Seelbinder B, Wallstabe J, Marischen L, Weiss E, Wurster S, Page L, Löffler C, Bussemer L, Schmitt AL, Wolf T, Linde J, Cicin-Sain L, Becker J, Kalinke U, Vogel J, Panagiotou G, Einsele H, Westermann AJ, Schäuble S, Loeffler J. Triple RNA-Seq Reveals Synergy in a Human Virus-Fungus Co-infection Model. Cell Rep 2020; 33:108389. [PMID: 33207195 DOI: 10.1016/j.celrep.2020.108389] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/30/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
High-throughput RNA sequencing (RNA-seq) is routinely applied to study diverse biological processes; however, when performed separately on interacting organisms, systemic noise intrinsic to RNA extraction, library preparation, and sequencing hampers the identification of cross-species interaction nodes. Here, we develop triple RNA-seq to simultaneously detect transcriptomes of monocyte-derived dendritic cells (moDCs) infected with the frequently co-occurring pulmonary pathogens Aspergillus fumigatus and human cytomegalovirus (CMV). Comparing expression patterns after co-infection with those after single infections, our data reveal synergistic effects and mutual interferences between host responses to the two pathogens. For example, CMV attenuates the fungus-mediated activation of pro-inflammatory cytokines through NF-κB (nuclear factor κB) and NFAT (nuclear factor of activated T cells) cascades, while A. fumigatus impairs viral clearance by counteracting viral nucleic acid-induced activation of type I interferon signaling. Together, the analytical power of triple RNA-seq proposes molecular hubs in the differential moDC response to fungal/viral single infection or co-infection that contribute to our understanding of the etiology and, potentially, clearance of post-transplant infections.
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Affiliation(s)
- Bastian Seelbinder
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), 07745 Jena, Germany
| | - Julia Wallstabe
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany
| | - Lothar Marischen
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany
| | - Esther Weiss
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany
| | - Sebastian Wurster
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany; The University of Texas MD Anderson Cancer Center, Department of Infectious Diseases, Infection Control and Employee Health, Houston, TX 77030, USA
| | - Lukas Page
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany
| | - Claudia Löffler
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany
| | - Lydia Bussemer
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany
| | - Anna-Lena Schmitt
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany
| | - Thomas Wolf
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), 07745 Jena, Germany
| | - Jörg Linde
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, 07743 Jena, Germany
| | - Luka Cicin-Sain
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Hannover-Braunschweig Site, 38124 Braunschweig, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH) Braunschweig, 38124 Braunschweig, Germany
| | - Jennifer Becker
- Institute for Experimental Infection Research, TWINCORE-Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH), 30625 Hannover, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE-Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH), 30625 Hannover, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), 07745 Jena, Germany; Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong S.A.R., China
| | - Hermann Einsele
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany
| | - Alexander J Westermann
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Sascha Schäuble
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), 07745 Jena, Germany
| | - Juergen Loeffler
- University Hospital Würzburg, Medical Hospital II, WÜ4i, 97080 Würzburg, Germany.
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7
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Seelbinder B, Chen J, Brunke S, Vazquez-Uribe R, Santhaman R, Meyer AC, de Oliveira Lino FS, Chan KF, Loos D, Imamovic L, Tsang CC, Lam RPK, Sridhar S, Kang K, Hube B, Woo PCY, Sommer MOA, Panagiotou G. Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria. Microbiome 2020; 8:133. [PMID: 32919472 PMCID: PMC7488854 DOI: 10.1186/s40168-020-00899-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/24/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND Antibiotic treatment has a well-established detrimental effect on the gut bacterial composition, but effects on the fungal community are less clear. Bacteria in the lumen of the gastrointestinal tract may limit fungal colonization and invasion. Antibiotic drugs targeting bacteria are therefore seen as an important risk factor for fungal infections and induced allergies. However, antibiotic effects on gut bacterial-fungal interactions, including disruption and resilience of fungal community compositions, were not investigated in humans. We analysed stool samples collected from 14 healthy human participants over 3 months following a 6-day antibiotic administration. We integrated data from shotgun metagenomics, metatranscriptomics, metabolomics, and fungal ITS2 sequencing. RESULTS While the bacterial community recovered mostly over 3 months post treatment, the fungal community was shifted from mutualism at baseline to competition. Half of the bacterial-fungal interactions present before drug intervention had disappeared 3 months later. During treatment, fungal abundances were associated with the expression of bacterial genes with functions for cell growth and repair. By extending the metagenomic species approach, we revealed bacterial strains inhibiting the opportunistic fungal pathogen Candida albicans. We demonstrated in vitro how C. albicans pathogenicity and host cell damage might be controlled naturally in the human gut by bacterial metabolites such as propionate or 5-dodecenoate. CONCLUSIONS We demonstrated that antibacterial drugs have long-term influence on the human gut mycobiome. While bacterial communities recovered mostly 30-days post antibacterial treatment, the fungal community was shifted from mutualism towards competition. Video abstract.
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Affiliation(s)
- Bastian Seelbinder
- Leibniz Institute for Natural Product Research and Infection Biology-Systems Biology and Bioinformatics, Hans Knöll Institute, Adolf-Reichwein-Straße 23, 07745, Jena, Germany
| | - Jiarui Chen
- Leibniz Institute for Natural Product Research and Infection Biology-Systems Biology and Bioinformatics, Hans Knöll Institute, Adolf-Reichwein-Straße 23, 07745, Jena, Germany
- Department of Medicine, State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong, SAR, China
| | - Sascha Brunke
- Leibniz Institute for Natural Product Research and Infection Biology-Microbial Pathogenicity Mechanisms, Hans Knöll Institute, Adolf-Reichwein-Straße 23, 07745, Jena, Germany
| | - Ruben Vazquez-Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Lyngby, Denmark
| | - Rakesh Santhaman
- Leibniz Institute for Natural Product Research and Infection Biology-Systems Biology and Bioinformatics, Hans Knöll Institute, Adolf-Reichwein-Straße 23, 07745, Jena, Germany
| | - Anne-Christin Meyer
- Leibniz Institute for Natural Product Research and Infection Biology-Microbial Pathogenicity Mechanisms, Hans Knöll Institute, Adolf-Reichwein-Straße 23, 07745, Jena, Germany
| | - Felipe Senne de Oliveira Lino
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Lyngby, Denmark
| | - Ka-Fai Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Daniel Loos
- Leibniz Institute for Natural Product Research and Infection Biology-Systems Biology and Bioinformatics, Hans Knöll Institute, Adolf-Reichwein-Straße 23, 07745, Jena, Germany
| | - Lejla Imamovic
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Lyngby, Denmark
| | - Chi-Ching Tsang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Rex Pui-Kin Lam
- Emergency Medicine Unit, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Siddharth Sridhar
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kang Kang
- Leibniz Institute for Natural Product Research and Infection Biology-Systems Biology and Bioinformatics, Hans Knöll Institute, Adolf-Reichwein-Straße 23, 07745, Jena, Germany
| | - Bernhard Hube
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Lyngby, Denmark
| | - Patrick Chiu-Yat Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong
| | - Morten Otto Alexander Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Lyngby, Denmark.
| | - Gianni Panagiotou
- Leibniz Institute for Natural Product Research and Infection Biology-Systems Biology and Bioinformatics, Hans Knöll Institute, Adolf-Reichwein-Straße 23, 07745, Jena, Germany.
- Department of Medicine, State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong, SAR, China.
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8
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Zoran T, Weber M, Springer J, White PL, Bauer J, Schober A, Löffler C, Seelbinder B, Hünniger K, Kurzai O, Scherag A, Schäuble S, Morton CO, Einsele H, Linde J, Löffler J. Treatment with etanercept and low monocyte concentration contribute to the risk of invasive aspergillosis in patients post allogeneic stem cell transplantation. Sci Rep 2019; 9:17231. [PMID: 31754120 PMCID: PMC6872713 DOI: 10.1038/s41598-019-53504-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 10/29/2019] [Indexed: 12/16/2022] Open
Abstract
Invasive aspergillosis (IA) is a life-threatening complication among allogeneic hematopoietic stem cell transplant (alloSCT) recipients. Despite well known risk factors and different available assays, diagnosis of invasive aspergillosis remains challenging. 103 clinical variables from patients with hematological malignancies and subsequent alloSCT were collected. Associations between collected variables and patients with (n = 36) and without IA (n = 36) were investigated by applying univariate and multivariable logistic regression. The predictive power of the final model was tested in an independent patient cohort (23 IA cases and 25 control patients). Findings were investigated further by in vitro studies, which analysed the effect of etanercept on A. fumigatus-stimulated macrophages at the gene expression and cytokine secretion. Additionally, the release of C-X-C motif chemokine ligand 10 (CXCL10) in patient sera was studied. Low monocyte concentration (p = 4.8 × 10−06), severe GvHD of the gut (grade 2–4) (p = 1.08 × 10−02) and etanercept treatment of GvHD (p = 3.5 × 10−03) were significantly associated with IA. Our studies showed that etanercept lowers CXCL10 concentrations in vitro and ex vivo and down-regulates genes involved in immune responses and TNF-alpha signaling. Our study offers clinicians new information regarding risk factors for IA including low monocyte counts and administration of etanercept. After necessary validation, such information may be used for decision making regarding antifungal prophylaxis or closely monitoring patients at risk.
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Affiliation(s)
- Tamara Zoran
- University Hospital Würzburg, Medical Hospital II, WÜ4i, Würzburg, Germany.,Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Michael Weber
- Friedrich Löffler Institute, Institute of Molecular Pathogenesis, Jena, Germany.,Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Jan Springer
- University Hospital Würzburg, Medical Hospital II, WÜ4i, Würzburg, Germany
| | | | - Joachim Bauer
- University Hospital Würzburg, Medical Hospital II, WÜ4i, Würzburg, Germany
| | - Annika Schober
- University Hospital Würzburg, Medical Hospital II, WÜ4i, Würzburg, Germany
| | - Claudia Löffler
- University Hospital Würzburg, Medical Hospital II, WÜ4i, Würzburg, Germany
| | - Bastian Seelbinder
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Kerstin Hünniger
- Septomics Research Centre, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany.,Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Oliver Kurzai
- Septomics Research Centre, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany.,Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - André Scherag
- Institute of Medical Statistics, Computer and Data Sciences, University Hospital, Jena, Germany
| | - Sascha Schäuble
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - C Oliver Morton
- Western Sydney University, School of Science and Health, Campbelltown, NSW, 2560, Australia
| | - Hermann Einsele
- University Hospital Würzburg, Medical Hospital II, WÜ4i, Würzburg, Germany
| | - Jörg Linde
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany.,Friedrich Löffler Institute, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Jürgen Löffler
- University Hospital Würzburg, Medical Hospital II, WÜ4i, Würzburg, Germany.
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9
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Lison H, Happel MFK, Schneider F, Baldauf K, Kerbstat S, Seelbinder B, Schneeberg J, Zappe M, Goldschmidt J, Budinger E, Schröder UH, Ohl FW, Schilling S, Demuth HU, Scheich H, Reymann KG, Rönicke R. Disrupted cross-laminar cortical processing in β amyloid pathology precedes cell death. Neurobiol Dis 2013; 63:62-73. [PMID: 24291517 DOI: 10.1016/j.nbd.2013.11.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 10/04/2013] [Accepted: 11/19/2013] [Indexed: 02/06/2023] Open
Abstract
Disruption of neuronal networks in the Alzheimer-afflicted brain is increasingly recognized as a key correlate of cognitive and memory decline in Alzheimer patients. We hypothesized that functional synaptic disconnections within cortical columnar microcircuits by pathological β-amyloid accumulation, rather than cell death, initially causes the cognitive impairments. During development of cortical β-amyloidosis with still few plaques in the transgenic 5xFAD mouse model single cell resolution mapping of neuronal thallium uptake revealed that electrical activity of pyramidal cells breaks down throughout infragranular cortical layer V long before cell death occurs. Treatment of 5xFAD mice with the glutaminyl cyclase inhibitor, PQ 529, partially prevented the decline of pyramidal cell activity, indicating pyroglutamate-modified forms, potentially mixed oligomers of Aβ are contributing to neuronal impairment. Laminar investigation of cortical circuit dysfunction with current source density analysis identified an early loss of excitatory synaptic input in infragranular layers, linked to pathological recurrent activations in supragranular layers. This specific disruption of normal cross-laminar cortical processing coincided with a decline of contextual fear learning.
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Affiliation(s)
- H Lison
- Leibniz-Institute for Neurobiology, Brenneckestr. 6, 39118 Magdeburg, Germany
| | - M F K Happel
- Leibniz-Institute for Neurobiology, Brenneckestr. 6, 39118 Magdeburg, Germany
| | - F Schneider
- Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), c/o Universitätsklinikum Magdeburg, Leipziger Strasse 44/Haus 64, 39120 Magdeburg, Germany
| | - K Baldauf
- Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), c/o Universitätsklinikum Magdeburg, Leipziger Strasse 44/Haus 64, 39120 Magdeburg, Germany
| | - S Kerbstat
- Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), c/o Universitätsklinikum Magdeburg, Leipziger Strasse 44/Haus 64, 39120 Magdeburg, Germany
| | - B Seelbinder
- Leibniz-Institute for Neurobiology, Brenneckestr. 6, 39118 Magdeburg, Germany
| | - J Schneeberg
- Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), c/o Universitätsklinikum Magdeburg, Leipziger Strasse 44/Haus 64, 39120 Magdeburg, Germany
| | - M Zappe
- Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), c/o Universitätsklinikum Magdeburg, Leipziger Strasse 44/Haus 64, 39120 Magdeburg, Germany
| | - J Goldschmidt
- Leibniz-Institute for Neurobiology, Brenneckestr. 6, 39118 Magdeburg, Germany
| | - E Budinger
- Leibniz-Institute for Neurobiology, Brenneckestr. 6, 39118 Magdeburg, Germany
| | - U H Schröder
- Leibniz-Institute for Neurobiology, Brenneckestr. 6, 39118 Magdeburg, Germany
| | - F W Ohl
- Leibniz-Institute for Neurobiology, Brenneckestr. 6, 39118 Magdeburg, Germany
| | - S Schilling
- Probiodrug AG, Weinbergweg 22, 06120 Halle (Saale), Germany
| | - H-U Demuth
- Probiodrug AG, Weinbergweg 22, 06120 Halle (Saale), Germany
| | - H Scheich
- Leibniz-Institute for Neurobiology, Brenneckestr. 6, 39118 Magdeburg, Germany
| | - K G Reymann
- Leibniz-Institute for Neurobiology, Brenneckestr. 6, 39118 Magdeburg, Germany; Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), c/o Universitätsklinikum Magdeburg, Leipziger Strasse 44/Haus 64, 39120 Magdeburg, Germany
| | - R Rönicke
- Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), c/o Universitätsklinikum Magdeburg, Leipziger Strasse 44/Haus 64, 39120 Magdeburg, Germany; Department of Clinical Chemistry and Pathobiochemistry, Otto-von-Guericke-University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany.
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