1
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Rosch MEG, Rehner J, Schmartz GP, Manier SK, Becker U, Müller R, Meyer MR, Keller A, Becker SL, Keller V. Time series of chicken stool metagenomics and egg metabolomics in changing production systems: preliminary insights from a proof-of-concept. One Health Outlook 2024; 6:4. [PMID: 38549118 PMCID: PMC10979557 DOI: 10.1186/s42522-024-00100-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/06/2024] [Indexed: 04/01/2024]
Abstract
BACKGROUND Different production systems of livestock animals influence various factors, including the gut microbiota. METHODS We investigated whether changing the conditions from barns to free-range chicken farming impacts the microbiome over the course of three weeks. We compared the stool microbiota of chicken from industrial barns after introducing them either in community or separately to a free-range environment. RESULTS Over the six time points, 12 taxa-mostly lactobacilli-changed significantly. As expected, the former barn chicken cohort carries more resistances to common antibiotics. These, however, remained positive over the observed period. At the end of the study, we collected eggs and compared metabolomic profiles of the egg white and yolk to profiles of eggs from commercial suppliers. Here, we observed significant differences between commercial and fresh collected eggs as well as differences between the former barn chicken and free-range chicken. CONCLUSION Our data indicate that the gut microbiota can undergo alterations over time in response to changes in production systems. These changes subsequently exert an influence on the metabolites found in the eggs. The preliminary results of our proof-of-concept study motivate larger scale observations with more individual chicken and longer observation periods.
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Affiliation(s)
- Michael E G Rosch
- Medical Doctor program Human Medicine, Saarland University/ Saarland University Medical Center, 66123/66421, Saarbrücken/Homburg, Germany
| | - Jacqueline Rehner
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421, Homburg/Saar, Germany
| | - Georges P Schmartz
- Department of Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Sascha K Manier
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Saarland University, Center for Molecular Signaling (PZMS), 66421, Homburg/Saar, Germany
| | - Uta Becker
- MIP Pharma GmbH, 66386, Sankt Ingbert, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
| | - Markus R Meyer
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Saarland University, Center for Molecular Signaling (PZMS), 66421, Homburg/Saar, Germany
| | - Andreas Keller
- Department of Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421, Homburg/Saar, Germany
| | - Verena Keller
- Department of Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany.
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2
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Hirsch P, Tagirdzhanov A, Kushnareva A, Olkhovskii I, Graf S, Schmartz GP, Hegemann JD, Bozhüyük KAJ, Müller R, Keller A, Gurevich A. ABC-HuMi: the Atlas of Biosynthetic Gene Clusters in the Human Microbiome. Nucleic Acids Res 2024; 52:D579-D585. [PMID: 37994699 PMCID: PMC10767846 DOI: 10.1093/nar/gkad1086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/18/2023] [Accepted: 10/30/2023] [Indexed: 11/24/2023] Open
Abstract
The human microbiome has emerged as a rich source of diverse and bioactive natural products, harboring immense potential for therapeutic applications. To facilitate systematic exploration and analysis of its biosynthetic landscape, we present ABC-HuMi: the Atlas of Biosynthetic Gene Clusters (BGCs) in the Human Microbiome. ABC-HuMi integrates data from major human microbiome sequence databases and provides an expansive repository of BGCs compared to the limited coverage offered by existing resources. Employing state-of-the-art BGC prediction and analysis tools, our database ensures accurate annotation and enhanced prediction capabilities. ABC-HuMi empowers researchers with advanced browsing, filtering, and search functionality, enabling efficient exploration of the resource. At present, ABC-HuMi boasts a catalog of 19 218 representative BGCs derived from the human gut, oral, skin, respiratory and urogenital systems. By capturing the intricate biosynthetic potential across diverse human body sites, our database fosters profound insights into the molecular repertoire encoded within the human microbiome and offers a comprehensive resource for the discovery and characterization of novel bioactive compounds. The database is freely accessible at https://www.ccb.uni-saarland.de/abc_humi/.
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Affiliation(s)
- Pascal Hirsch
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
| | - Azat Tagirdzhanov
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Aleksandra Kushnareva
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Ilia Olkhovskii
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Saarbrücken Graduate School of Computer Science, Saarland University, Saarbrücken 66123, Germany
| | - Simon Graf
- Department of Computer Science, Saarland University, Saarbrücken 66123, Germany
| | - Georges P Schmartz
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Department of Pharmacy, Saarland University, Saarbrücken 66123, Germany
| | - Kenan A J Bozhüyük
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Department of Pharmacy, Saarland University, Saarbrücken 66123, Germany
| | - Andreas Keller
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Alexey Gurevich
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Department of Computer Science, Saarland University, Saarbrücken 66123, Germany
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3
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Müller NJ, Porawski D, Wilde L, Fink D, Trap G, Engel A, Schmartz GP. Neuro-explicit semantic segmentation of the diffusion cloud chamber. Rev Sci Instrum 2023; 94:063304. [PMID: 37862541 DOI: 10.1063/5.0109284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 06/03/2023] [Indexed: 10/22/2023]
Abstract
For decades, in diffusion cloud chambers, different types of subatomic particle tracks from radioactive sources or cosmic radiation had to be identified with the naked eye which limited the amount of data that could be processed. In order to allow these classical particle detectors to enter the digital era, we successfully developed a neuro-explicit artificial intelligence model that, given an image from the cloud chamber, automatically annotates most of the particle tracks visible in the image according to the type of particle or process that created it. To achieve this goal, we combined the attention U-Net neural network architecture with methods that model the shape of the detected particle tracks. Our experiments show that the model effectively detects particle tracks and that the neuro-explicit approach decreases the misclassification rate of rare particles by 73% compared with solely using the attention U-Net.
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Affiliation(s)
- Nicola J Müller
- Bachelor's Program Data Science and Artificial Intelligence, Saarland University, Saarbrücken 66123, Germany
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken 66123, Germany
| | - Daniel Porawski
- Bachelor's Program Data Science and Artificial Intelligence, Saarland University, Saarbrücken 66123, Germany
| | - Lukas Wilde
- Bachelor's Program Data Science and Artificial Intelligence, Saarland University, Saarbrücken 66123, Germany
| | - Dennis Fink
- Luxembourg Science Center, Differdange 4573, Luxembourg
| | - Guillaume Trap
- Luxembourg Science Center, Differdange 4573, Luxembourg
- Foundation Jeunes Scientifiques Luxembourg, 40 Boulevard Pierre Dupong, L-1430 Luxembourg
| | - Annika Engel
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken 66123, Germany
| | - Georges P Schmartz
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken 66123, Germany
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4
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Aparicio-Puerta E, Hirsch P, Schmartz GP, Kern F, Fehlmann T, Keller A. miEAA 2023: updates, new functional microRNA sets and improved enrichment visualizations. Nucleic Acids Res 2023:7161530. [PMID: 37177999 DOI: 10.1093/nar/gkad392] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/21/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play a critical role in regulating diverse biological processes. Extracting functional insights from a list of miRNAs is challenging, as each miRNA can potentially interact with hundreds of genes. To address this challenge, we developed miEAA, a flexible and comprehensive miRNA enrichment analysis tool based on direct and indirect miRNA annotation. The latest release of miEAA includes a data warehouse of 19 miRNA repositories, covering 10 different organisms and 139 399 functional categories. We have added information on the cellular context of miRNAs, isomiRs, and high-confidence miRNAs to improve the accuracy of the results. We have also improved the representation of aggregated results, including interactive Upset plots to aid users in understanding the interaction among enriched terms or categories. Finally, we demonstrate the functionality of miEAA in the context of ageing and highlight the importance of carefully considering the miRNA input list. MiEAA is free to use and publicly available at https://www.ccb.uni-saarland.de/mieaa/.
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Affiliation(s)
| | - Pascal Hirsch
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Georges P Schmartz
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Tobias Fehlmann
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
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5
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Berger FK, Schmartz GP, Fritz T, Veith N, Alhussein F, Roth S, Schneitler S, Gilcher T, Gärtner BC, Pirpilashvili V, Pohlemann T, Keller A, Rehner J, Becker SL. Occurrence, resistance patterns and management of carbapenemase-producing bacteria in war-wounded refugees from Ukraine. Int J Infect Dis 2023; 132:89-92. [PMID: 37072055 DOI: 10.1016/j.ijid.2023.04.394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 02/19/2023] [Accepted: 04/11/2023] [Indexed: 04/20/2023] Open
Abstract
We analysed consecutive clinical cases of infections due to carbapenemase-producing Gram-negative bacteria detected in war-wounded patients from Ukraine who were treated at one University medical centre in southwest Germany between June and December 2022. Isolates of multiresistant Gram-negative bacteria were subjected to a thorough microbiological characterisation and whole-genome sequencing. We identified five war-wounded Ukrainian patients who developed infections with NDM-1-positive Klebsiella pneumoniae. Two isolates also carried OXA-48 carbapenemases. The bacteria were resistant to novel antibiotics such as ceftazidime/avibactam and cefiderocol. Employed treatment strategies included combinations of ceftazidime/avibactam + aztreonam, colistin, or tigecycline. Whole-genome sequencing suggested transmission during primary care in Ukraine. We conclude that there is an urgent need for thorough surveillance of multiresistant pathogens in patients from war zones.
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Affiliation(s)
- Fabian K Berger
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany
| | - Georges P Schmartz
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Tobias Fritz
- Department of Trauma, Hand and Reconstructive Surgery, Saarland University Medical Center, Homburg/Saar, Germany
| | - Nils Veith
- Department of Trauma, Hand and Reconstructive Surgery, Saarland University Medical Center, Homburg/Saar, Germany
| | - Farah Alhussein
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany
| | - Sophie Roth
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany
| | - Sophie Schneitler
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany
| | - Thomas Gilcher
- Hospital Pharmacy, Saarland University, Homburg/Saar, Germany
| | - Barbara C Gärtner
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany
| | - Vakhtang Pirpilashvili
- Department of Trauma, Hand and Reconstructive Surgery, Saarland University Medical Center, Homburg/Saar, Germany
| | - Tim Pohlemann
- Department of Trauma, Hand and Reconstructive Surgery, Saarland University Medical Center, Homburg/Saar, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Jacqueline Rehner
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany.
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6
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Rehner J, Schmartz GP, Kramer T, Keller V, Keller A, Becker SL. The Effect of a Planetary Health Diet on the Human Gut Microbiome: A Descriptive Analysis. Nutrients 2023; 15:nu15081924. [PMID: 37111144 PMCID: PMC10144214 DOI: 10.3390/nu15081924] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 03/13/2023] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
In 2019, researchers from the EAT-Lancet Commission developed the 'Planetary Health (PH) diet'. Specifically, they provided recommendations pertaining to healthy diets derived from sustainable food systems. Thus far, it has not been analysed how such a diet affects the human intestinal microbiome, which is important for health and disease development. Here, we present longitudinal genome-wide metagenomic sequencing and mass spectrometry data on the gut microbiome of healthy volunteers adhering to the PH diet, as opposed to vegetarian or vegan (VV) and omnivorous (OV) diets. We obtained basic epidemiological information from 41 healthy volunteers and collected stool samples at inclusion and after 2, 4, and 12 weeks. Individuals opting to follow the PH diet received detailed instructions and recipes, whereas individuals in the control groups followed their habitual dietary pattern. Whole-genome DNA was extracted from stool specimens and subjected to shotgun metagenomic sequencing (~3 GB per patient). Conventional bacterial stool cultures were performed in parallel and bacterial species were identified with matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. We analysed samples from 16 PH, 16 OV, and 9 VV diet patterns. The α-diversity remained relatively stable for all dietary groups. In the PH group, we observed a constant increase from 3.79% at inclusion to 4.9% after 12 weeks in relative abundance of Bifidobacterium adolescentis. Differential PH abundance analysis highlighted a non-significant increase in possible probiotics such as Paraprevotella xylaniphila and Bacteroides clarus. The highest abundance of these bacteria was observed in the VV group. Dietary modifications are associated with rapid alterations to the human gut microbiome, and the PH diet led to a slight increase in probiotic-associated bacteria at ≥4 weeks. Additional research is required to confirm these findings.
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Affiliation(s)
- Jacqueline Rehner
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421 Homburg, Germany
| | - Georges P Schmartz
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Tabea Kramer
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421 Homburg, Germany
| | - Verena Keller
- Department of Medicine II, Saarland University Medical Center, 66421 Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421 Homburg, Germany
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7
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Aparicio-Puerta E, Hirsch P, Schmartz GP, Fehlmann T, Keller V, Engel A, Kern F, Hackenberg M, Keller A. isomiRdb: microRNA expression at isoform resolution. Nucleic Acids Res 2022; 51:D179-D185. [PMID: 36243964 PMCID: PMC9825445 DOI: 10.1093/nar/gkac884] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/19/2022] [Accepted: 09/30/2022] [Indexed: 01/29/2023] Open
Abstract
A significant fraction of mature miRNA transcripts carries sequence and/or length variations, termed isomiRs. IsomiRs are differentially abundant in cell types, tissues, body fluids or patients' samples. Not surprisingly, multiple studies describe a physiological and pathophysiological role. Despite their importance, systematically collected and annotated isomiR information available in databases remains limited. We thus developed isomiRdb, a comprehensive resource that compiles miRNA expression data at isomiR resolution from various sources. We processed 42 499 human miRNA-seq datasets (5.9 × 1011 sequencing reads) and consistently analyzed them using miRMaster and sRNAbench. Our database provides online access to the 90 483 most abundant isomiRs (>1 RPM in at least 1% of the samples) from 52 tissues and 188 cell types. Additionally, the full set of over 3 million detected isomiRs is available for download. Our resource can be queried at the sample, miRNA or isomiR level so users can quickly answer common questions about the presence/absence of a particular miRNA/isomiR in tissues of interest. Further, the database facilitates to identify whether a potentially interesting new isoform has been detected before and its frequency. In addition to expression tables, isomiRdb can generate multiple interactive visualisations including violin plots and heatmaps. isomiRdb is free to use and publicly available at: https://www.ccb.uni-saarland.de/isomirdb.
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Affiliation(s)
| | | | - Georges P Schmartz
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Tobias Fehlmann
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany,Rejuvenome, Astera Institute, Berkeley, CA 94705, USA
| | - Verena Keller
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany,Department for Internal Medicine II, Saarland University Hospital, 66421 Homburg, Germany
| | - Annika Engel
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany,Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)–Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Michael Hackenberg
- Genetics Department, Faculty of Science, Universidad de Granada, 18071 Granada, Spain
| | - Andreas Keller
- To whom correspondence should be addressed. Tel: +49 681 30268611; Fax: +49 681 30268610;
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8
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Schmartz GP, Hirsch P, Amand J, Dastbaz J, Fehlmann T, Kern F, Müller R, Keller A. OUP accepted manuscript. Nucleic Acids Res 2022; 50:W132-W137. [PMID: 35489067 PMCID: PMC9252796 DOI: 10.1093/nar/gkac298] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/07/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Despite recent methodology and reference database improvements for taxonomic profiling tools, metagenomic assembly and genomic binning remain important pillars of metagenomic analysis workflows. In case reference information is lacking, genomic binning is considered to be a state-of-the-art method in mixed culture metagenomic data analysis. In this light, our previously published tool BusyBee Web implements a composition-based binning method efficient enough to function as a rapid online utility. Handling assembled contigs and long nanopore generated reads alike, the webserver provides a wide range of supplementary annotations and visualizations. Half a decade after the initial publication, we revisited existing functionality, added comprehensive visualizations, and increased the number of data analysis customization options for further experimentation. The webserver now allows for visualization-supported differential analysis of samples, which is computationally expensive and typically only performed in coverage-based binning methods. Further, users may now optionally check their uploaded samples for plasmid sequences using PLSDB as a reference database. Lastly, a new application programming interface with a supporting python package was implemented, to allow power users fully automated access to the resource and integration into existing workflows. The webserver is freely available under: https://www.ccb.uni-saarland.de/busybee.
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Affiliation(s)
- Georges P Schmartz
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Pascal Hirsch
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Clinical Bioinformatics (CLIB), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany
| | - Jérémy Amand
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Clinical Bioinformatics (CLIB), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany
| | - Jan Dastbaz
- Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Clinical Bioinformatics (CLIB), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Andreas Keller
- To whom correspondence should be addressed. Tel: +49 681 30268611; Fax: +49 681 30268610;
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9
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Schmartz GP, Hartung A, Hirsch P, Kern F, Fehlmann T, Müller R, Keller A. PLSDB: advancing a comprehensive database of bacterial plasmids. Nucleic Acids Res 2021; 50:D273-D278. [PMID: 34850116 PMCID: PMC8728149 DOI: 10.1093/nar/gkab1111] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [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: 09/15/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 12/24/2022] Open
Abstract
Plasmids are known to contain genes encoding for virulence factors and antibiotic resistance mechanisms. Their relevance in metagenomic data processing is steadily growing. However, with the increasing popularity and scale of metagenomics experiments, the number of reported plasmids is rapidly growing as well, amassing a considerable number of false positives due to undetected misassembles. Here, our previously published database PLSDB provides a reliable resource for researchers to quickly compare their sequences against selected and annotated previous findings. Within two years, the size of this resource has more than doubled from the initial 13,789 to now 34,513 entries over the course of eight regular data updates. For this update, we aggregated community feedback for major changes to the database featuring new analysis functionality as well as performance, quality, and accessibility improvements. New filtering steps, annotations, and preprocessing of existing records improve the quality of the provided data. Additionally, new features implemented in the web-server ease user interaction and allow for a deeper understanding of custom uploaded sequences, by visualizing similarity information. Lastly, an application programming interface was implemented along with a python library, to allow remote database queries in automated workflows. The latest release of PLSDB is freely accessible under https://www.ccb.uni-saarland.de/plsdb.
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Affiliation(s)
- Georges P Schmartz
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Anna Hartung
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Pascal Hirsch
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8 1, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8 1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8 1, 66123 Saarbrücken, Germany
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Yang AC, Kern F, Losada PM, Agam MR, Maat CA, Schmartz GP, Fehlmann T, Stein JA, Schaum N, Lee DP, Calcuttawala K, Vest RT, Berdnik D, Lu N, Hahn O, Gate D, McNerney MW, Channappa D, Cobos I, Ludwig N, Schulz-Schaeffer WJ, Keller A, Wyss-Coray T. Publisher Correction: Dysregulation of brain and choroid plexus cell types in severe COVID-19. Nature 2021; 598:E4. [PMID: 34625744 PMCID: PMC8500262 DOI: 10.1038/s41586-021-04080-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Andrew C Yang
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA, USA.,ChEM-H, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Patricia M Losada
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Maayan R Agam
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Christina A Maat
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Georges P Schmartz
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Julian A Stein
- Institute for Neuropathology, Saarland University Hospital and Medical Faculty of Saarland University, Homburg, Germany
| | - Nicholas Schaum
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Davis P Lee
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Kruti Calcuttawala
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan T Vest
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniela Berdnik
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Nannan Lu
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver Hahn
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - David Gate
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - M Windy McNerney
- Department of Psychiatry, Stanford University School of Medicine, Stanford, CA, USA
| | - Divya Channappa
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Inma Cobos
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Walter J Schulz-Schaeffer
- Institute for Neuropathology, Saarland University Hospital and Medical Faculty of Saarland University, Homburg, Germany
| | - Andreas Keller
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA. .,Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany.
| | - Tony Wyss-Coray
- ChEM-H, Stanford University, Stanford, CA, USA. .,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA. .,Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA. .,Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.
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Yang AC, Kern F, Losada PM, Agam MR, Maat CA, Schmartz GP, Fehlmann T, Stein JA, Schaum N, Lee DP, Calcuttawala K, Vest RT, Berdnik D, Lu N, Hahn O, Gate D, McNerney MW, Channappa D, Cobos I, Ludwig N, Schulz-Schaeffer WJ, Keller A, Wyss-Coray T. Dysregulation of brain and choroid plexus cell types in severe COVID-19. Nature 2021; 595:565-571. [PMID: 34153974 PMCID: PMC8400927 DOI: 10.1038/s41586-021-03710-0] [Citation(s) in RCA: 340] [Impact Index Per Article: 113.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 06/07/2021] [Indexed: 01/08/2023]
Abstract
Although SARS-CoV-2 primarily targets the respiratory system, patients with and survivors of COVID-19 can suffer neurological symptoms1-3. However, an unbiased understanding of the cellular and molecular processes that are affected in the brains of patients with COVID-19 is missing. Here we profile 65,309 single-nucleus transcriptomes from 30 frontal cortex and choroid plexus samples across 14 control individuals (including 1 patient with terminal influenza) and 8 patients with COVID-19. Although our systematic analysis yields no molecular traces of SARS-CoV-2 in the brain, we observe broad cellular perturbations indicating that barrier cells of the choroid plexus sense and relay peripheral inflammation into the brain and show that peripheral T cells infiltrate the parenchyma. We discover microglia and astrocyte subpopulations associated with COVID-19 that share features with pathological cell states that have previously been reported in human neurodegenerative disease4-6. Synaptic signalling of upper-layer excitatory neurons-which are evolutionarily expanded in humans7 and linked to cognitive function8-is preferentially affected in COVID-19. Across cell types, perturbations associated with COVID-19 overlap with those found in chronic brain disorders and reside in genetic variants associated with cognition, schizophrenia and depression. Our findings and public dataset provide a molecular framework to understand current observations of COVID-19-related neurological disease, and any such disease that may emerge at a later date.
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Affiliation(s)
- Andrew C Yang
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Patricia M Losada
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Maayan R Agam
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Christina A Maat
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Georges P Schmartz
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Julian A Stein
- Institute for Neuropathology, Saarland University Hospital and Medical Faculty of Saarland University, Homburg, Germany
| | - Nicholas Schaum
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Davis P Lee
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Kruti Calcuttawala
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan T Vest
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniela Berdnik
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Nannan Lu
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver Hahn
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - David Gate
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - M Windy McNerney
- Department of Psychiatry, Stanford University School of Medicine, Stanford, CA, USA
| | - Divya Channappa
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Inma Cobos
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Walter J Schulz-Schaeffer
- Institute for Neuropathology, Saarland University Hospital and Medical Faculty of Saarland University, Homburg, Germany
| | - Andreas Keller
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany.
| | - Tony Wyss-Coray
- ChEM-H, Stanford University, Stanford, CA, USA.
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.
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Tranchevent LC, Nazarov PV, Kaoma T, Schmartz GP, Muller A, Kim SY, Rajapakse JC, Azuaje F. Predicting clinical outcome of neuroblastoma patients using an integrative network-based approach. Biol Direct 2018; 13:12. [PMID: 29880025 PMCID: PMC5992838 DOI: 10.1186/s13062-018-0214-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 05/04/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND One of the main current challenges in computational biology is to make sense of the huge amounts of multidimensional experimental data that are being produced. For instance, large cohorts of patients are often screened using different high-throughput technologies, effectively producing multiple patient-specific molecular profiles for hundreds or thousands of patients. RESULTS We propose and implement a network-based method that integrates such patient omics data into Patient Similarity Networks. Topological features derived from these networks were then used to predict relevant clinical features. As part of the 2017 CAMDA challenge, we have successfully applied this strategy to a neuroblastoma dataset, consisting of genomic and transcriptomic data. In particular, we observe that models built on our network-based approach perform at least as well as state of the art models. We furthermore explore the effectiveness of various topological features and observe, for instance, that redundant centrality metrics can be combined to build more powerful models. CONCLUSION We demonstrate that the networks inferred from omics data contain clinically relevant information and that patient clinical outcomes can be predicted using only network topological data. REVIEWERS This article was reviewed by Yang-Yu Liu, Tomislav Smuc and Isabel Nepomuceno.
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Affiliation(s)
- Léon-Charles Tranchevent
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
| | - Petr V. Nazarov
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
| | - Tony Kaoma
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
| | - Georges P. Schmartz
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
- Bioinformatics bachelor program, Universität des Saarlandes, Saarbrücken, Germany
| | - Arnaud Muller
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
| | - Sang-Yoon Kim
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
| | - Jagath C. Rajapakse
- Bioinformatics Research Center, School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Francisco Azuaje
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
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