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Verhoeven MD, Nielsen PH, Dueholm MKD. Amplicon-guided isolation and cultivation of previously uncultured microbial species from activated sludge. Appl Environ Microbiol 2023; 89:e0115123. [PMID: 38051071 PMCID: PMC10734543 DOI: 10.1128/aem.01151-23] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/23/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Biological wastewater treatment relies on complex microbial communities that assimilate nutrients and break down pollutants in the wastewater. Knowledge about the physiology and metabolism of bacteria in wastewater treatment plants (WWTPs) may therefore be used to improve the efficacy and economy of wastewater treatment. Our current knowledge is largely based on 16S rRNA gene amplicon profiling, fluorescence in situ hybridization studies, and predictions based on metagenome-assembled genomes. Bacterial isolates are often required to validate genome-based predictions as they allow researchers to analyze a specific species without interference from other bacteria and with simple bulk measurements. Unfortunately, there are currently very few pure cultures representing the microbes commonly found in WWTPs. To address this, we introduce an isolation strategy that takes advantage of state-of-the-art microbial profiling techniques to uncover suitable growth conditions for key WWTP microbes. We furthermore demonstrate that this information can be used to isolate key organisms representing global WWTPs.
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Affiliation(s)
- Maarten D. Verhoeven
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Per H. Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Morten K. D. Dueholm
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
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Petriglieri F, Kondrotaite Z, Singleton C, Nierychlo M, Dueholm MKD, Nielsen PH. A comprehensive overview of the Chloroflexota community in wastewater treatment plants worldwide. mSystems 2023; 8:e0066723. [PMID: 37992299 PMCID: PMC10746286 DOI: 10.1128/msystems.00667-23] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/09/2023] [Indexed: 11/24/2023] Open
Abstract
IMPORTANCE Chloroflexota are often abundant members of the biomass in wastewater treatment plants (WWTPs) worldwide, typically with a filamentous morphology, forming the backbones of the activated sludge floc. However, their overgrowth can often cause operational issues connected to poor settling or foaming, impairing effluent quality and increasing operational costs. Despite their importance, few Chloroflexota genera have been characterized so far. Here, we present a comprehensive overview of Chloroflexota abundant in WWTPs worldwide and an in-depth characterization of their morphology, phylogeny, and ecophysiology, obtaining a broad understanding of their ecological role in activated sludge.
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Affiliation(s)
- Francesca Petriglieri
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Zivile Kondrotaite
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Caitlin Singleton
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Marta Nierychlo
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten K. D. Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per H. Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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Singh Y, Trautwein C, Romani J, Salker MS, Neckel PH, Fraccaroli I, Abeditashi M, Woerner N, Admard J, Dhariwal A, Dueholm MKD, Schäfer KH, Lang F, Otzen DE, Lashuel HA, Riess O, Casadei N. Overexpression of human alpha-Synuclein leads to dysregulated microbiome/metabolites with ageing in a rat model of Parkinson disease. Mol Neurodegener 2023; 18:44. [PMID: 37403161 DOI: 10.1186/s13024-023-00628-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 05/24/2023] [Indexed: 07/06/2023] Open
Abstract
BACKGROUND Braak's hypothesis states that sporadic Parkinson's disease (PD) follows a specific progression of pathology from the peripheral to the central nervous system, and this progression can be monitored by detecting the accumulation of alpha-Synuclein (α-Syn) protein. Consequently, there is growing interest in understanding how the gut (commensal) microbiome can regulate α-Syn accumulation, as this could potentially lead to PD. METHODS We used 16S rRNA and shotgun sequencing to characterise microbial diversity. 1H-NMR was employed to understand the metabolite production and intestinal inflammation estimated using ELISA and RNA-sequencing from feces and the intestinal epithelial layer respectively. The Na+ channel current and gut permeability were measured using an Ussing chamber. Immunohistochemistry and immunofluorescence imaging were applied to detect the α-Syn protein. LC-MS/MS was used for characterization of proteins from metabolite treated neuronal cells. Finally, Metascape and Ingenuity Pathway Analysis (IPA) bioinformatics tools were used for identification of dysregulated pathways. RESULTS We studied a transgenic (TG) rat model overexpressing the human SNCA gene and found that a progressive gut microbial composition alteration characterized by the reduction of Firmicutes to Bacteroidetes ratio could be detected in the young TG rats. Interestingly, this ratio then increased with ageing. The dynamics of Lactobacillus and Alistipes were monitored and reduced Lactobacillus and increased Alistipes abundance was discerned in ageing TG rats. Additionally, the SNCA gene overexpression resulted in gut α-Syn protein expression and increased with advanced age. Further, older TG animals had increased intestinal inflammation, decreased Na+ current and a robust alteration in metabolite production characterized by the increase of succinate levels in feces and serum. Manipulation of the gut bacteria by short-term antibiotic cocktail treatment revealed a complete loss of short-chain fatty acids and a reduction in succinate levels. Although antibiotic cocktail treatment did not change α-Syn expression in the enteric nervous system of the colon, however, reduced α-Syn expression was detected in the olfactory bulbs (forebrain) of the TG rats. CONCLUSION Our data emphasize that the gut microbiome dysbiosis synchronous with ageing leads to a specific alteration of gut metabolites and can be modulated by antibiotics which may affect PD pathology.
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Affiliation(s)
- Yogesh Singh
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstaße 7, 72076, Tübingen, Germany.
- NGS Competence Centre Tübingen (NCCT), University of Tübingen, Calwerstaße 7, 72076, Tübingen, Germany.
- Research Institute of Women's Health, University of Tübingen, Calwerstaße 7/6, 72076, Tübingen, Germany.
| | - Christoph Trautwein
- Werner Siemens Imaging Centre (WSIC), Department of Preclinical Imaging and Radiopharmacy, University of Tübingen, Röntgenweg 13, 72076, Tübingen, Germany
| | - Joan Romani
- School of Life Sciences, Institute of Bioengineering, Laboratory of Molecular and Chemical Biology of Neurodegeneration, École Polytechnique Fédérale de Lausanne (EPFL), SV LMNN Station 19, 1015 CH, Lausanne, Switzerland
| | - Madhuri S Salker
- Research Institute of Women's Health, University of Tübingen, Calwerstaße 7/6, 72076, Tübingen, Germany
| | - Peter H Neckel
- Institute of Clinical Anatomy and Cell Analysis, University of Tübingen, Österbergstraße 3, 72074, Tübingen, Germany
| | - Isabel Fraccaroli
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstaße 7, 72076, Tübingen, Germany
| | - Mahkameh Abeditashi
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstaße 7, 72076, Tübingen, Germany
| | - Nils Woerner
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstaße 7, 72076, Tübingen, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstaße 7, 72076, Tübingen, Germany
| | - Achal Dhariwal
- Institute of Oral Biology, University of Oslo, Sognsvannsveien 10, 0316, Oslo, Norway
| | - Morten K D Dueholm
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Karl-Herbert Schäfer
- Enteric Nervous System Working Group, University of Applied Sciences Kaiserslautern, Zweibrücken Campus, Amerikastrasse 1, 66482, Zweibrücken, Germany
| | - Florian Lang
- Institute of Vegetative Physiology, University of Tübingen, Wilhelmstaße 56, 72074, Tübingen, Germany
| | - Daniel E Otzen
- Interdisciplinary Naonscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Hilal A Lashuel
- School of Life Sciences, Institute of Bioengineering, Laboratory of Molecular and Chemical Biology of Neurodegeneration, École Polytechnique Fédérale de Lausanne (EPFL), SV LMNN Station 19, 1015 CH, Lausanne, Switzerland
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstaße 7, 72076, Tübingen, Germany.
- NGS Competence Centre Tübingen (NCCT), University of Tübingen, Calwerstaße 7, 72076, Tübingen, Germany.
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstaße 7, 72076, Tübingen, Germany.
- NGS Competence Centre Tübingen (NCCT), University of Tübingen, Calwerstaße 7, 72076, Tübingen, Germany.
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Kondrotaite Z, Valk LC, Petriglieri F, Singleton C, Nierychlo M, Dueholm MKD, Nielsen PH. Diversity and Ecophysiology of the Genus OLB8 and Other Abundant Uncultured Saprospiraceae Genera in Global Wastewater Treatment Systems. Front Microbiol 2022; 13:917553. [PMID: 35875537 PMCID: PMC9304909 DOI: 10.3389/fmicb.2022.917553] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/30/2022] [Indexed: 11/30/2022] Open
Abstract
The Saprospiraceae family within the phylum Bacteroidota is commonly present and highly abundant in wastewater treatment plants (WWTPs) worldwide, but little is known about its role. In this study, we used MiDAS 4 global survey with samples from 30 countries to analyze the abundance and distribution of members of Saprospiraceae. Phylogenomics were used to delineate five new genera from a set of 31 high-quality metagenome-assembled genomes from Danish WWTPs. Newly designed probes for fluorescence in situ hybridization (FISH) revealed rod-shaped morphologies for all genera analyzed, including OLB8, present mostly inside the activated sludge flocs. The genomes revealed potential metabolic capabilities for the degradation of polysaccharides, proteins, and other complex molecules; partial denitrification; and storage of intracellular polymers (glycogen, polyphosphate, and polyhydroxyalkanoates). FISH in combination with Raman microspectroscopy confirmed the presence of intracellular glycogen in Candidatus Brachybacter, Candidatus Parvibacillus calidus (both from the former genus OLB8), and Candidatus Opimibacter, and the presence of polyhydroxyalkanoates in Candidatus Defluviibacterium haderslevense and Candidatus Vicinibacter. These results provide the first overview of the most abundant novel Saprospiraceae genera present in WWTPs across the world and their potential involvement in nutrient removal and the degradation of macromolecules.
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Affiliation(s)
| | | | | | | | | | | | - Per H. Nielsen
- Department of Chemistry and Bioscience, Center of Microbial Communities, Aalborg University, Aalborg, Denmark
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