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Dueholm MKD, Andersen KS, Korntved AKC, Rudkjøbing V, Alves M, Bajón-Fernández Y, Batstone D, Butler C, Cruz MC, Davidsson Å, Erijman L, Holliger C, Koch K, Kreuzinger N, Lee C, Lyberatos G, Mutnuri S, O'Flaherty V, Oleskowicz-Popiel P, Pokorna D, Rajal V, Recktenwald M, Rodríguez J, Saikaly PE, Tooker N, Vierheilig J, De Vrieze J, Wurzbacher C, Nielsen PH. MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters. Nat Commun 2024; 15:5361. [PMID: 38918384 PMCID: PMC11199495 DOI: 10.1038/s41467-024-49641-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84-99% and 18-61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.
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Affiliation(s)
- Morten Kam Dahl Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
| | - Kasper Skytte Andersen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Anne-Kirstine C Korntved
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Vibeke Rudkjøbing
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Madalena Alves
- Centre of Biological Engineering, University of Minho, Minho, Portugal
| | | | - Damien Batstone
- Australian Centre for Water and Environmental Biotechnology (ACWEB), The University of Queensland, Brisbane, Australia
| | - Caitlyn Butler
- Department of Civil and Environmental Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | - Mercedes Cecilia Cruz
- Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Salta, Argentina
| | - Åsa Davidsson
- Department of Chemical Engineering, Lund University, Lund, Sweden
| | - Leonardo Erijman
- INGEBI-CONICET, University of Buenos Aires, Buenos Aires, Argentina
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Konrad Koch
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), Garching, Germany
| | - Norbert Kreuzinger
- Institute of Water Quality and Resource Management, TU Wien, Vienna, Austria
| | - Changsoo Lee
- Department of Civil, Urban, Earth, and Environmental Engineering & Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Gerasimos Lyberatos
- School of Chemical Engineering, National Technical University of Athens, Zografou, Greece
| | - Srikanth Mutnuri
- Applied Environmental Biotechnology Laboratory, Birla Institute of Technology and Science (BITS-Pilani), Pilani, Goa campus, Goa, India
| | - Vincent O'Flaherty
- School of Biological and Chemical Sciences and Ryan Institute, University of Galway, Galway, Ireland
| | - Piotr Oleskowicz-Popiel
- Water Supply and Bioeconomy Division, Faculty of Environmental Engineering and Energy, Poznan University of Technology, Poznan, Poland
| | - Dana Pokorna
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Veronica Rajal
- Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Salta, Argentina
| | | | - Jorge Rodríguez
- Chemical Engineering Department, Khalifa University, Khalifa, UAE
| | - Pascal E Saikaly
- Environmental Science and Engineering Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Nick Tooker
- Department of Civil and Environmental Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | - Julia Vierheilig
- Institute of Water Quality and Resource Management, TU Wien, Vienna, Austria
| | - Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), Garching, Germany
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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Eisenhofer R, Nesme J, Santos-Bay L, Koziol A, Sørensen SJ, Alberdi A, Aizpurua O. A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics. Microbiol Spectr 2024; 12:e0359023. [PMID: 38451230 PMCID: PMC10986573 DOI: 10.1128/spectrum.03590-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/11/2024] [Indexed: 03/08/2024] Open
Abstract
Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level of detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well as a combination of both. To assess the pros and cons of these different approaches, we used 22 fecal DNA extracts collected weekly for 11 weeks from two respective lab mice to study seven performance metrics over four combinations of sequencing depth and technology: (i) 20 Gbp of Illumina short-read data, (ii) 40 Gbp of short-read data, (iii) 20 Gbp of PacBio HiFi long-read data, and (iv) 40 Gbp of hybrid (20 Gbp of short-read +20 Gbp of long-read) data. No strategy was best for all metrics; instead, each one excelled across different metrics. The long-read approach yielded the best assembly statistics, with the highest N50 and lowest number of contigs. The 40 Gbp short-read approach yielded the highest number of refined bins. Finally, the hybrid approach yielded the longest assemblies and the highest mapping rate to the bacterial genomes. Our results suggest that while long-read sequencing significantly improves the quality of reconstructed bacterial genomes, it is more expensive and requires deeper sequencing than short-read approaches to recover a comparable amount of reconstructed genomes. The most optimal strategy is study-specific and depends on how researchers assess the trade-off between the quantity and quality of recovered genomes.IMPORTANCEMice are an important model organism for understanding the gut microbiome. When studying these gut microbiomes using DNA techniques, researchers can choose from technologies that use short or long DNA reads. In this study, we perform an extensive benchmark between short- and long-read DNA sequencing for studying mice gut microbiomes. We find that no one approach was best for all metrics and provide information that can help guide researchers in planning their experiments.
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Affiliation(s)
- Raphael Eisenhofer
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Luisa Santos-Bay
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Adam Koziol
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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Chen P, Wang S, Li H, Qi X, Hou Y, Ma T. Comparative genomic analyses of Cutibacterium granulosum provide insights into genomic diversity. Front Microbiol 2024; 15:1343227. [PMID: 38304712 PMCID: PMC10832045 DOI: 10.3389/fmicb.2024.1343227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
Cutibacterium granulosum, a commensal bacterium found on human skin, formerly known as Propionibacterium granulosum, rarely causes infections and is generally considered non-pathogenic. Recent research has revealed the transferability of the multidrug-resistant plasmid pTZC1 between C. granulosum and Cutibacterium acnes, the latter being an opportunistic pathogen in surgical site infections. However, there is a noticeable lack of research on the genome of C. granulosum, and the genetic landscape of this species remains largely uncharted. We investigated the genomic features and evolutionary structure of C. granulosum by analyzing a total of 30 Metagenome-Assembled Genomes (MAGs) and isolate genomes retrieved from public databases, as well as those generated in this study. A pan-genome of 6,077 genes was identified for C. granulosum. Remarkably, the 'cloud genes' constituted 62.38% of the pan-genome. Genes associated with mobilome: prophages, transposons [X], defense mechanisms [V] and replication, recombination and repair [L] were enriched in the cloud genome. Phylogenomic analysis revealed two distinct mono-clades, highlighting the genomic diversity of C. granulosum. The genomic diversity was further confirmed by the distribution of Average Nucleotide Identity (ANI) values. The functional profiles analysis of C. granulosum unveiled a wide range of potential Antibiotic Resistance Genes (ARGs) and virulence factors, suggesting its potential tolerance to various environmental challenges. Subtype I-E of the CRISPR-Cas system was the most abundant in these genomes, a feature also detected in C. acnes genomes. Given the widespread distribution of C. granulosum strains within skin microbiome, our findings make a substantial contribution to our broader understanding of the genetic diversity, which may open new avenues for investigating the mechanisms and treatment of conditions such as acne vulgaris.
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Affiliation(s)
- Peishan Chen
- Institute of Integrative Medicine for Acute Abdominal Diseases, Tianjin Nankai Hospital, Tianjin, China
| | - Shaojing Wang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Hongyan Li
- College of Bioengineering, Tianjin University of Science and Technology, Tianjin, China
- Tianjin JOYSTAR Technology Co., Ltd, Tianjin, China
| | - Xiaoye Qi
- College of Bioengineering, Tianjin University of Science and Technology, Tianjin, China
- Tianjin JOYSTAR Technology Co., Ltd, Tianjin, China
| | - Yuanyuan Hou
- College of Pharmacy, Nankai University, Tianjin, China
| | - Ting Ma
- College of Life Sciences, Nankai University, Tianjin, China
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