1
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Liu M, Xu N, Chen B, Zhang Z, Chen X, Zhu Y, Hong W, Wang T, Zhang Q, Ye Y, Lu T, Qian H. Effects of different assembly strategies on gene annotation in activated sludge. ENVIRONMENTAL RESEARCH 2024; 252:119116. [PMID: 38734289 DOI: 10.1016/j.envres.2024.119116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/27/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
Activated sludge comprises diverse bacteria, fungi, and other microorganisms, featuring a rich repertoire of genes involved in antibiotic resistance, pollutant degradation, and elemental cycling. In this regard, hybrid assembly technology can revolutionize metagenomics by detecting greater gene diversity in environmental samples. Nonetheless, the optimal utilization and comparability of genomic information between hybrid assembly and short- or long-read technology remain unclear. To address this gap, we compared the performance of the hybrid assembly, short- and long-read technologies, abundance and diversity of annotated genes, and taxonomic diversity by analysing 46, 161, and 45 activated sludge metagenomic datasets, respectively. The results revealed that hybrid assembly technology exhibited the best performance, generating the most contiguous and longest contigs but with a lower proportion of high-quality metagenome-assembled genomes than short-read technology. Compared with short- or long-read technologies, hybrid assembly technology can detect a greater diversity of microbiota and antibiotic resistance genes, as well as a wider range of potential hosts. However, this approach may yield lower gene abundance and pathogen detection. Our study revealed the specific advantages and disadvantages of hybrid assembly and short- and long-read applications in wastewater treatment plants, and our approach could serve as a blueprint to be extended to terrestrial environments.
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Affiliation(s)
- Meng Liu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Bingfeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Xinyu Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Yuke Zhu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Wenjie Hong
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310012, PR China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310012, PR China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Yangqing Ye
- College of Mechanical Engineering, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China.
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2
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Pan C, Reinert K. Leaf: an ultrafast filter for population-scale long-read SV detection. Genome Biol 2024; 25:155. [PMID: 38872200 DOI: 10.1186/s13059-024-03297-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 06/04/2024] [Indexed: 06/15/2024] Open
Abstract
Advances in sequencing technology have facilitated population-scale long-read structural variant (SV) detection. Arguably, one of the main challenges in population-scale analysis is developing effective computational pipelines. Here, we present a new filter-based pipeline for population-scale long-read SV detection. It better captures SV signals at an early stage than conventional assembly-based or alignment-based pipelines. Assessments in this work suggest that the filter-based pipeline helps better resolve intra-read rearrangements. Moreover, it is also more computationally efficient than conventional pipelines and thus may facilitate population-scale long-read applications.
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Affiliation(s)
- Chenxu Pan
- Department of Mathematics and Computer Science, Freie Universität Berlin, Takustr. 9, 14195, Berlin, Germany.
| | - Knut Reinert
- Department of Mathematics and Computer Science, Freie Universität Berlin, Takustr. 9, 14195, Berlin, Germany
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
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3
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Manning VA, Moore PA, Trippe KM. Metagenome-assembled genomes of an acid-tolerant nitrifying bacterial community isolated from a bioreactor used in ammonium scrubbers at animal-rearing facilities. Microbiol Resour Announc 2024:e0038624. [PMID: 38864651 DOI: 10.1128/mra.00386-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024] Open
Abstract
We report 12 metagenome-assembled genomes (MAGS) of a bioreactor community of acid-tolerant nitrifying bacteria. The MAGS include autotrophs in the Nitrospira genus and heterotrophs in the Xanthomonadales, Ktedonobacterales, Cytophagales, Burkholderiales, and Hyphomicrobiales. These taxonomic and genomic data provide insights into the core community members required for nitrification at low pH.
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Affiliation(s)
- Viola A Manning
- USDA-Agricultural Research Service, National Forage Seed Production Research Center, Corvallis, Oregon, USA
| | - Phillip A Moore
- USDA-Agricultural Research Service, Poultry Production and Product Safety Research Center, Fayetteville, Arkansas, USA
| | - Kristin M Trippe
- USDA-Agricultural Research Service, National Forage Seed Production Research Center, Corvallis, Oregon, USA
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, USA
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4
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Tang T, Leisner JJ. Complete genome sequence of Listeria seeligeri strain 43-1 isolated from a Danish forest freshwater swamp. Microbiol Resour Announc 2024:e0031124. [PMID: 38864652 DOI: 10.1128/mra.00311-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/17/2024] [Indexed: 06/13/2024] Open
Abstract
Here, we report the genome sequence of Listeria seeligeri 43-1 isolated from a Danish freshwater swamp using Oxford Nanopore sequencing. The isolate shared a high genomic similarity to two other L. seeligeri isolates from soil and water.
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Affiliation(s)
- Taya Tang
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jørgen J Leisner
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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5
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Medina JE, Castañeda S, Camargo M, Garcia-Corredor DJ, Muñoz M, Ramírez JD. Exploring viral diversity and metagenomics in livestock: insights into disease emergence and spillover risks in cattle. Vet Res Commun 2024:10.1007/s11259-024-10403-2. [PMID: 38865041 DOI: 10.1007/s11259-024-10403-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 05/01/2024] [Indexed: 06/13/2024]
Abstract
Cattle have a significant impact on human societies in terms of both economics and health. Viral infections pose a relevant problem as they directly or indirectly disrupt the balance within cattle populations. This has negative consequences at the economic level for producers and territories, and also jeopardizes human health through the transmission of zoonotic diseases that can escalate into outbreaks or pandemics. To establish prevention strategies and control measures at various levels (animal, farm, region, or global), it is crucial to identify the viral agents present in animals. Various techniques, including virus isolation, serological tests, and molecular techniques like PCR, are typically employed for this purpose. However, these techniques have two major drawbacks: they are ineffective for non-culturable viruses, and they only detect a small fraction of the viruses present. In contrast, metagenomics offers a promising approach by providing a comprehensive and unbiased analysis for detecting all viruses in a given sample. It has the potential to identify rare or novel infectious agents promptly and establish a baseline of healthy animals. Nevertheless, the routine application of viral metagenomics for epidemiological surveillance and diagnostics faces challenges related to socioeconomic variables, such as resource availability and space dedicated to metagenomics, as well as the lack of standardized protocols and resulting heterogeneity in presenting results. This review aims to provide an overview of the current knowledge and prospects for using viral metagenomics to detect and identify viruses in cattle raised for livestock, while discussing the epidemiological and clinical implications.
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Affiliation(s)
- Julián Esteban Medina
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Milena Camargo
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Centro de Tecnología en Salud (CETESA), Innovaseq SAS, Mosquera, Cundinamarca, Colombia
| | - Diego J Garcia-Corredor
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Grupo de Investigación en Medicina Veterinaria y Zootecnia, Facultad de Ciencias Agropecuarias, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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6
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Young R, Ahmed KA, Court L, Castro-Vargas C, Marcora A, Boctor J, Paull C, Wijffels G, Rane R, Edwards O, Walsh T, Pandey G. Improved reference quality genome sequence of the plastic-degrading greater wax moth, Galleria mellonella. G3 (BETHESDA, MD.) 2024; 14:jkae070. [PMID: 38564250 DOI: 10.1093/g3journal/jkae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 12/19/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024]
Abstract
Galleria mellonella is a pest of honeybees in many countries because its larvae feed on beeswax. However, G. mellonella larvae can also eat various plastics, including polyethylene, polystyrene, and polypropylene, and therefore, the species is garnering increasing interest as a tool for plastic biodegradation research. This paper presents an improved genome (99.3% completed lepidoptera_odb10 BUSCO; genome mode) for G. mellonella. This 472 Mb genome is in 221 contigs with an N50 of 6.4 Mb and contains 13,604 protein-coding genes. Genes that code for known and putative polyethylene-degrading enzymes and their similarity to proteins found in other Lepidoptera are highlighted. An analysis of secretory proteins more likely to be involved in the plastic catabolic process has also been carried out.
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Affiliation(s)
| | | | - Leon Court
- CSIRO Environment, Acton, ACT 2601, Australia
| | | | - Anna Marcora
- CSIRO Agriculture and Food, Dutton Park, QLD 4102, Australia
| | - Joseph Boctor
- Bioplastics Innovation Hub, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Cate Paull
- CSIRO Agriculture and Food, Dutton Park, QLD 4102, Australia
| | - Gene Wijffels
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
| | - Rahul Rane
- CSIRO Health and Biosecurity, Parkville, VIC 3052, Australia
| | | | - Tom Walsh
- CSIRO Environment, Acton, ACT 2601, Australia
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7
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Chen Z, Grim CJ, Ramachandran P, Meng J. Advancing metagenome-assembled genome-based pathogen identification: unraveling the power of long-read assembly algorithms in Oxford Nanopore sequencing. Microbiol Spectr 2024; 12:e0011724. [PMID: 38687063 DOI: 10.1128/spectrum.00117-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024] Open
Abstract
Oxford Nanopore sequencing is one of the high-throughput sequencing technologies that facilitates the reconstruction of metagenome-assembled genomes (MAGs). This study aimed to assess the potential of long-read assembly algorithms in Oxford Nanopore sequencing to enhance the MAG-based identification of bacterial pathogens using both simulated and mock communities. Simulated communities were generated to mimic those on fresh spinach and in surface water. Long reads were produced using R9.4.1+SQK-LSK109 and R10.4 + SQK-LSK112, with 0.5, 1, and 2 million reads. The simulated bacterial communities included multidrug-resistant Salmonella enterica serotypes Heidelberg, Montevideo, and Typhimurium in the fresh spinach community individually or in combination, as well as multidrug-resistant Pseudomonas aeruginosa in the surface water community. Real data sets of the ZymoBIOMICS HMW DNA Standard were also studied. A bioinformatic pipeline (MAGenie, freely available at https://github.com/jackchen129/MAGenie) that combines metagenome assembly, taxonomic classification, and sequence extraction was developed to reconstruct draft MAGs from metagenome assemblies. Five assemblers were evaluated based on a series of genomic analyses. Overall, Flye outperformed the other assemblers, followed by Shasta, Raven, and Unicycler, while Canu performed least effectively. In some instances, the extracted sequences resulted in draft MAGs and provided the locations and structures of antimicrobial resistance genes and mobile genetic elements. Our study showcases the viability of utilizing the extracted sequences for precise phylogenetic inference, as demonstrated by the consistent alignment of phylogenetic topology between the reference genome and the extracted sequences. R9.4.1+SQK-LSK109 was more effective in most cases than R10.4+SQK-LSK112, and greater sequencing depths generally led to more accurate results.IMPORTANCEBy examining diverse bacterial communities, particularly those housing multiple Salmonella enterica serotypes, this study holds significance in uncovering the potential of long-read assembly algorithms to improve metagenome-assembled genome (MAG)-based pathogen identification through Oxford Nanopore sequencing. Our research demonstrates that long-read assembly stands out as a promising avenue for boosting precision in MAG-based pathogen identification, thus advancing the development of more robust surveillance measures. The findings also support ongoing endeavors to fine-tune a bioinformatic pipeline for accurate pathogen identification within complex metagenomic samples.
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Affiliation(s)
- Zhao Chen
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
| | - Christopher J Grim
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Padmini Ramachandran
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
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8
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Agustinho DP, Fu Y, Menon VK, Metcalf GA, Treangen TJ, Sedlazeck FJ. Unveiling microbial diversity: harnessing long-read sequencing technology. Nat Methods 2024; 21:954-966. [PMID: 38689099 DOI: 10.1038/s41592-024-02262-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 03/29/2024] [Indexed: 05/02/2024]
Abstract
Long-read sequencing has recently transformed metagenomics, enhancing strain-level pathogen characterization, enabling accurate and complete metagenome-assembled genomes, and improving microbiome taxonomic classification and profiling. These advancements are not only due to improvements in sequencing accuracy, but also happening across rapidly changing analysis methods. In this Review, we explore long-read sequencing's profound impact on metagenomics, focusing on computational pipelines for genome assembly, taxonomic characterization and variant detection, to summarize recent advancements in the field and provide an overview of available analytical methods to fully leverage long reads. We provide insights into the advantages and disadvantages of long reads over short reads and their evolution from the early days of long-read sequencing to their recent impact on metagenomics and clinical diagnostics. We further point out remaining challenges for the field such as the integration of methylation signals in sub-strain analysis and the lack of benchmarks.
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Affiliation(s)
- Daniel P Agustinho
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA
| | - Yilei Fu
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Vipin K Menon
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA
- Senior research project manager, Human Genetics, Genentech, South San Francisco, CA, USA
| | - Ginger A Metcalf
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA
| | - Todd J Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
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9
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Mo C, Wang H, Wei M, Zeng Q, Zhang X, Fei Z, Zhang Y, Kong Q. Complete genome assembly provides a high-quality skeleton for pan-NLRome construction in melon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2249-2268. [PMID: 38430487 DOI: 10.1111/tpj.16705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
Melon (Cucumis melo L.), being under intensive domestication and selective breeding, displays an abundant phenotypic diversity. Wild germplasm with tolerance to stress represents an untapped genetic resource for discovery of disease-resistance genes. To comprehensively characterize resistance genes in melon, we generate a telomere-to-telomere (T2T) and gap-free genome of wild melon accession PI511890 (C. melo var. chito) with a total length of 375.0 Mb and a contig N50 of 31.24 Mb. The complete genome allows us to dissect genome architecture and identify resistance gene analogs. We construct a pan-NLRome using seven melon genomes, which include 208 variable and 18 core nucleotide-binding leucine-rich repeat receptors (NLRs). Multiple disease-related transcriptome analyses indicate that most up-regulated NLRs induced by pathogens are shell or cloud NLRs. The T2T gap-free assembly and the pan-NLRome not only serve as essential resources for genomic studies and molecular breeding of melon but also provide insights into the genome architecture and NLR diversity.
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Affiliation(s)
- Changjuan Mo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haiyan Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Minghua Wei
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingguo Zeng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuejun Zhang
- Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | | | - Yongbing Zhang
- Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Qiusheng Kong
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
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10
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Zhang Z, Xiao J, Wang H, Yang C, Huang Y, Yue Z, Chen Y, Han L, Yin K, Lyu A, Fang X, Zhang L. Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity. Nat Commun 2024; 15:4631. [PMID: 38821971 PMCID: PMC11143213 DOI: 10.1038/s41467-024-49060-z] [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: 08/20/2023] [Accepted: 05/17/2024] [Indexed: 06/02/2024] Open
Abstract
Although long-read sequencing enables the generation of complete genomes for unculturable microbes, its high cost limits the widespread adoption of long-read sequencing in large-scale metagenomic studies. An alternative method is to assemble short-reads with long-range connectivity, which can be a cost-effective way to generate high-quality microbial genomes. Here, we develop Pangaea, a bioinformatic approach designed to enhance metagenome assembly using short-reads with long-range connectivity. Pangaea leverages connectivity derived from physical barcodes of linked-reads or virtual barcodes by aligning short-reads to long-reads. Pangaea utilizes a deep learning-based read binning algorithm to assemble co-barcoded reads exhibiting similar sequence contexts and abundances, thereby improving the assembly of high- and medium-abundance microbial genomes. Pangaea also leverages a multi-thresholding algorithm strategy to refine assembly for low-abundance microbes. We benchmark Pangaea on linked-reads and a combination of short- and long-reads from simulation data, mock communities and human gut metagenomes. Pangaea achieves significantly higher contig continuity as well as more near-complete metagenome-assembled genomes (NCMAGs) than the existing assemblers. Pangaea also generates three complete and circular NCMAGs on the human gut microbiomes.
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Grants
- This research was partially supported by the Young Collaborative Research Grant (C2004-23Y, L.Z.), HMRF (11221026, L.Z.), the open project of BGI-Shenzhen, Shenzhen 518000, China (BGIRSZ20220012, L.Z.), the Hong Kong Research Grant Council Early Career Scheme (HKBU 22201419, L.Z.), HKBU Start-up Grant Tier 2 (RC-SGT2/19-20/SCI/007, L.Z.), HKBU IRCMS (No. IRCMS/19-20/D02, L.Z.).
- This research was partially supported by the open project of BGI-Shenzhen, Shenzhen 518000, China (BGIRSZ20220014, KJ.Y.).
- The study were partially supported by the Science Technology and Innovation Committee of Shenzhen Municipality, China (SGDX20190919142801722, XD.F.),
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Affiliation(s)
- Zhenmiao Zhang
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China
| | - Jin Xiao
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China
| | - Hongbo Wang
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China
| | - Chao Yang
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China
| | | | - Zhen Yue
- BGI Research, Sanya, 572025, China
| | - Yang Chen
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese, Guangzhou, China
| | - Lijuan Han
- Department of Scientific Research, Kangmeihuada GeneTech Co., Ltd (KMHD), Shenzhen, China
| | - Kejing Yin
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | - Aiping Lyu
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Xiaodong Fang
- BGI Research, Shenzhen, 518083, China
- BGI Research, Sanya, 572025, China
- Department of Scientific Research, Kangmeihuada GeneTech Co., Ltd (KMHD), Shenzhen, China
| | - Lu Zhang
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China.
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China.
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11
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Chen X, Li H, Dong Y, Xu Y, Xu K, Zhang Q, Yao Z, Yu Q, Zhang H, Zhang Z. A wild melon reference genome provides novel insights into the domestication of a key gene responsible for melon fruit acidity. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:144. [PMID: 38809285 DOI: 10.1007/s00122-024-04647-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024]
Abstract
KEY MESSAGE A wild melon reference genome elucidates the genomic basis of fruit acidity domestication. Structural variants (SVs) have been reported to impose major effects on agronomic traits, representing a significant contributor to crop domestication. However, the landscape of SVs between wild and cultivated melons is elusive and how SVs have contributed to melon domestication remains largely unexplored. Here, we report a 379-Mb chromosome-scale genome of a wild progenitor melon accession "P84", with a contig N50 of 14.9 Mb. Genome comparison identifies 10,589 SVs between P84 and four cultivated melons with 6937 not characterized in previously analysis of 25 melon genome sequences. Furthermore, the population-scale genotyping of these SVs was determined in 1175 accessions, and 18 GWAS signals including fruit acidity, fruit length, fruit weight, fruit color and sex determination were detected. Based on these genotyped SVs, we identified 3317 highly diverged SVs between wild and cultivated melons, which could be the potential SVs associated with domestication-related traits. Furthermore, we identify novel SVs affecting fruit acidity and proposed the diverged evolutionary trajectories of CmPH, a key regulator of melon fruit acidity, during domestication and selection of different populations. These results will offer valuable resources for genomic studies and genetic improvement in melon.
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Affiliation(s)
- Xinxiu Chen
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hongbo Li
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Shenzhen Branch, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, Guangdong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Yuanhua Dong
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Yuanchao Xu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Shenzhen Branch, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, Guangdong, China
| | - Kuipeng Xu
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qiqi Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Zhiwang Yao
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qing Yu
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Huimin Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Zhonghua Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
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12
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Makri N, Ring N, Shaw DJ, Athinodorou A, Robinson V, Paterson GK, Richardson J, Gow D, Nuttall T. Cytological evaluation, culture and genomics to evaluate the microbiome in healthy rabbit external ear canals. Vet Dermatol 2024. [PMID: 38742484 DOI: 10.1111/vde.13256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/27/2024] [Accepted: 04/18/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND Lop-eared rabbits may be predisposed to otitis externa (OE) as a consequence of their ear conformation. Although otoscopy, otic cytological evaluation and culture are valuable tools in dogs and cats, published data on rabbits remain lacking. HYPOTHESIS/OBJECTIVES This study aimed to assess the utility of otoscopy and cytological results in evaluating healthy rabbit external ear canals (EECs) and to characterise ear cytological and microbiological findings through culture techniques and metagenomic sequencing. ANIMALS Sixty-three otitis-free client-owned rabbits. MATERIALS AND METHODS All rabbits underwent otoscopy and ear cytological evaluation. In a subset of 12 rabbits, further bacterial and fungal culture, fungal DNA assessment and metagenomic sequencing were performed. RESULTS Otic cytological results revealed yeast in 73%, cocci in 42.9% and rods in 28.6% of healthy rabbit EECs. Compared to upright-eared rabbits, lop-eared rabbits had more discharge and more bacteria per oil immersion field. Culture isolated eight different species yet metagenomic sequencing identified 36, belonging to the Bacillota (Firmicutes), Pseudomonadota and Actinomycetota phyla. Staphylococcus were the most commonly observed species with both methods. Ten of 12 rabbits were yeast-positive on cytological evaluation with only three yielding fungal growth identified as Yarrowia (Candida) lipolytica, Eurotium echinulatum and Cystofilobasidium infirmominiatum. CONCLUSIONS AND CLINICAL RELEVANCE Healthy rabbit EECs lack inflammatory cells yet can host yeast and bacteria, emphasising the need to evaluate cytological results alongside the clinical signs. Lop-ear anatomy may predispose to bacterial overgrowth and OE. Notably, yeasts may be present despite a negative culture.
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Affiliation(s)
- Nikoleta Makri
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Midlothian, UK
| | - Natalie Ring
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Midlothian, UK
| | - Darren J Shaw
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Midlothian, UK
| | - Athinodoros Athinodorou
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Midlothian, UK
| | - Victoria Robinson
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Midlothian, UK
| | - Gavin K Paterson
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Midlothian, UK
| | - Jenna Richardson
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Midlothian, UK
| | - Debbie Gow
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Midlothian, UK
| | - Tim Nuttall
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Midlothian, UK
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13
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Warwick-Dugdale J, Tian F, Michelsen ML, Cronin DR, Moore K, Farbos A, Chittick L, Bell A, Zayed AA, Buchholz HH, Bolanos LM, Parsons RJ, Allen MJ, Sullivan MB, Temperton B. Long-read powered viral metagenomics in the oligotrophic Sargasso Sea. Nat Commun 2024; 15:4089. [PMID: 38744831 PMCID: PMC11094077 DOI: 10.1038/s41467-024-48300-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 04/24/2024] [Indexed: 05/16/2024] Open
Abstract
Dominant microorganisms of the Sargasso Sea are key drivers of the global carbon cycle. However, associated viruses that shape microbial community structure and function are not well characterised. Here, we combined short and long read sequencing to survey Sargasso Sea phage communities in virus- and cellular fractions at viral maximum (80 m) and mesopelagic (200 m) depths. We identified 2,301 Sargasso Sea phage populations from 186 genera. Over half of the phage populations identified here lacked representation in global ocean viral metagenomes, whilst 177 of the 186 identified genera lacked representation in genomic databases of phage isolates. Viral fraction and cell-associated viral communities were decoupled, indicating viral turnover occurred across periods longer than the sampling period of three days. Inclusion of long-read data was critical for capturing the breadth of viral diversity. Phage isolates that infect the dominant bacterial taxa Prochlorococcus and Pelagibacter, usually regarded as cosmopolitan and abundant, were poorly represented.
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Affiliation(s)
- Joanna Warwick-Dugdale
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK.
- Plymouth Marine Laboratory, Plymouth, Devon, PL1 3DH, UK.
| | - Funing Tian
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | | | - Dylan R Cronin
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA
| | - Karen Moore
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Audrey Farbos
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Lauren Chittick
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - Ashley Bell
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Ahmed A Zayed
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA
| | - Holger H Buchholz
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA
| | - Luis M Bolanos
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Rachel J Parsons
- Bermuda Institute of Ocean Sciences, St.George's, GE, 01, Bermuda
- School of Ocean Futures, Arizona State University, Tempe, AZ, US
| | - Michael J Allen
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Matthew B Sullivan
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH, 43210, USA
| | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK.
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14
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Buysse M, Koual R, Binetruy F, de Thoisy B, Baudrimont X, Garnier S, Douine M, Chevillon C, Delsuc F, Catzeflis F, Bouchon D, Duron O. Detection of Anaplasma and Ehrlichia bacteria in humans, wildlife, and ticks in the Amazon rainforest. Nat Commun 2024; 15:3988. [PMID: 38734682 PMCID: PMC11088697 DOI: 10.1038/s41467-024-48459-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: 08/30/2023] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Tick-borne bacteria of the genera Ehrlichia and Anaplasma cause several emerging human infectious diseases worldwide. In this study, we conduct an extensive survey for Ehrlichia and Anaplasma infections in the rainforests of the Amazon biome of French Guiana. Through molecular genetics and metagenomics reconstruction, we observe a high indigenous biodiversity of infections circulating among humans, wildlife, and ticks inhabiting these ecosystems. Molecular typing identifies these infections as highly endemic, with a majority of new strains and putative species specific to French Guiana. They are detected in unusual rainforest wild animals, suggesting they have distinctive sylvatic transmission cycles. They also present potential health hazards, as revealed by the detection of Candidatus Anaplasma sparouinense in human red blood cells and that of a new close relative of the human pathogen Ehrlichia ewingii, Candidatus Ehrlichia cajennense, in the tick species that most frequently bite humans in South America. The genome assembly of three new putative species obtained from human, sloth, and tick metagenomes further reveals the presence of major homologs of Ehrlichia and Anaplasma virulence factors. These observations converge to classify health hazards associated with Ehrlichia and Anaplasma infections in the Amazon biome as distinct from those in the Northern Hemisphere.
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Affiliation(s)
- Marie Buysse
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Rachid Koual
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Florian Binetruy
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Benoit de Thoisy
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de Guyane, Cayenne, France
- Association Kwata 'Study and Conservation of Guianan Wildlife', Cayenne, France
| | - Xavier Baudrimont
- Direction Générale des Territoires et de la Mer (DGTM) - Direction de l'environnement, de l'agriculture, de l'alimentation et de la forêt (DEAAF), Cayenne, France
| | - Stéphane Garnier
- Biogéosciences, UMR 6282 uB/CNRS/EPHE, Université Bourgogne Franche-Comté, Dijon, France
| | - Maylis Douine
- Centre d'Investigation Clinique Antilles-Guyane, INSERM 1424, Centre Hospitalier de Cayenne, Cayenne, France
| | | | - Frédéric Delsuc
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - François Catzeflis
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Didier Bouchon
- EBI, University of Poitiers, UMR CNRS 7267, Poitiers, France
| | - Olivier Duron
- MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France.
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15
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Wang YC, Mao Y, Fu HM, Wang J, Weng X, Liu ZH, Xu XW, Yan P, Fang F, Guo JS, Shen Y, Chen YP. New insights into functional divergence and adaptive evolution of uncultured bacteria in anammox community by complete genome-centric analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171530. [PMID: 38453092 DOI: 10.1016/j.scitotenv.2024.171530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/13/2023] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Anaerobic ammonium-oxidation (anammox) bacteria play a crucial role in global nitrogen cycling and wastewater nitrogen removal, but they share symbiotic relationships with various other microorganisms. Functional divergence and adaptive evolution of uncultured bacteria in anammox community remain underexplored. Although shotgun metagenomics based on short reads has been widely used in anammox research, metagenome-assembled genomes (MAGs) are often discontinuous and highly contaminated, which limits in-depth analyses of anammox communities. Here, for the first time, we performed Pacific Biosciences high-fidelity (HiFi) long-read sequencing on the anammox granule sludge sample from a lab-scale bioreactor, and obtained 30 accurate and complete metagenome-assembled genomes (cMAGs). These cMAGs were obtained by selecting high-quality circular contigs from initial assemblies of long reads generated by HiFi sequencing, eliminating the need for Illumina short reads, binning, and reassembly. One new anammox species affiliated with Candidatus Jettenia and three species affiliated with novel families were found in this anammox community. cMAG-centric analysis revealed functional divergence in general and nitrogen metabolism among the anammox community members, and they might adopt a cross-feeding strategy in organic matter, cofactors, and vitamins. Furthermore, we identified 63 mobile genetic elements (MGEs) and 50 putative horizontal gene transfer (HGT) events within these cMAGs. The results suggest that HGT events and MGEs related to phage and integration or excision, particularly transposons containing tnpA in anammox bacteria, might play important roles in the adaptive evolution of this anammox community. The cMAGs generated in the present study could be used to establish of a comprehensive database for anammox bacteria and associated microorganisms. These findings highlight the advantages of HiFi sequencing for the studies of complex mixed cultures and advance the understanding of anammox communities.
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Affiliation(s)
- Yi-Cheng Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518071, Guangdong, China
| | - Hui-Min Fu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China; National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Jin Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Xun Weng
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Zi-Hao Liu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Xiao-Wei Xu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Peng Yan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Fang Fang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Jin-Song Guo
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Yu Shen
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China.
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16
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Greenman N, Hassouneh SAD, Abdelli LS, Johnston C, Azarian T. Improving Bacterial Metagenomic Research through Long-Read Sequencing. Microorganisms 2024; 12:935. [PMID: 38792764 PMCID: PMC11124196 DOI: 10.3390/microorganisms12050935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 04/22/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Metagenomic sequencing analysis is central to investigating microbial communities in clinical and environmental studies. Short-read sequencing remains the primary approach for metagenomic research; however, long-read sequencing may offer advantages of improved metagenomic assembly and resolved taxonomic identification. To compare the relative performance for metagenomic studies, we simulated short- and long-read datasets using increasingly complex metagenomes comprising 10, 20, and 50 microbial taxa. Additionally, we used an empirical dataset of paired short- and long-read data generated from mouse fecal pellets to assess real-world performance. We compared metagenomic assembly quality, taxonomic classification, and metagenome-assembled genome (MAG) recovery rates. We show that long-read sequencing data significantly improve taxonomic classification and assembly quality. Metagenomic assemblies using simulated long reads were more complete and more contiguous with higher rates of MAG recovery. This resulted in more precise taxonomic classifications. Principal component analysis of empirical data demonstrated that sequencing technology affects compositional results as samples clustered by sequence type, not sample type. Overall, we highlight strengths of long-read metagenomic sequencing for microbiome studies, including improving the accuracy of classification and relative abundance estimates. These results will aid researchers when considering which sequencing approaches to use for metagenomic projects.
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Affiliation(s)
- Noah Greenman
- College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (N.G.); (S.A.-D.H.); (C.J.)
| | - Sayf Al-Deen Hassouneh
- College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (N.G.); (S.A.-D.H.); (C.J.)
| | - Latifa S. Abdelli
- Department of Health Science, College of Health Professions and Sciences, University of Central Florida, Orlando, FL 32816, USA;
| | - Catherine Johnston
- College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (N.G.); (S.A.-D.H.); (C.J.)
| | - Taj Azarian
- College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (N.G.); (S.A.-D.H.); (C.J.)
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17
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Bouras G, Houtak G, Wick RR, Mallawaarachchi V, Roach MJ, Papudeshi B, Judd LM, Sheppard AE, Edwards RA, Vreugde S. Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies. Microb Genom 2024; 10:001244. [PMID: 38717808 PMCID: PMC11165638 DOI: 10.1099/mgen.0.001244] [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: 01/08/2024] [Accepted: 04/16/2024] [Indexed: 05/21/2024] Open
Abstract
Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- and long-reads) assembly approaches. Complete genomes allow a deeper understanding of bacterial evolution and genomic variation beyond single nucleotide variants. They are also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance genes. However, small plasmids are often missed or misassembled by long-read assembly algorithms. Here, we present Hybracter which allows for the fast, automatic and scalable recovery of near-perfect complete bacterial genomes using a long-read first assembly approach. Hybracter can be run either as a hybrid assembler or as a long-read only assembler. We compared Hybracter to existing automated hybrid and long-read only assembly tools using a diverse panel of samples of varying levels of long-read accuracy with manually curated ground truth reference genomes. We demonstrate that Hybracter as a hybrid assembler is more accurate and faster than the existing gold standard automated hybrid assembler Unicycler. We also show that Hybracter with long-reads only is the most accurate long-read only assembler and is comparable to hybrid methods in accurately recovering small plasmids.
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Affiliation(s)
- George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery – Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Ghais Houtak
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery – Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Ryan R. Wick
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Michael J. Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
- Adelaide Centre for Epigenetics and South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, Australia
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Lousie M. Judd
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Anna E. Sheppard
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Sarah Vreugde
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery – Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
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18
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Li H, Durbin R. Genome assembly in the telomere-to-telomere era. Nat Rev Genet 2024:10.1038/s41576-024-00718-w. [PMID: 38649458 DOI: 10.1038/s41576-024-00718-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 04/25/2024]
Abstract
Genome sequences largely determine the biology and encode the history of an organism, and de novo assembly - the process of reconstructing the genome sequence of an organism from sequencing reads - has been a central problem in bioinformatics for four decades. Until recently, genomes were typically assembled into fragments of a few megabases at best, but now technological advances in long-read sequencing enable the near-complete assembly of each chromosome - also known as telomere-to-telomere assembly - for many organisms. Here, we review recent progress on assembly algorithms and protocols, with a focus on how to derive near-telomere-to-telomere assemblies. We also discuss the additional developments that will be required to resolve remaining assembly gaps and to assemble non-diploid genomes.
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Affiliation(s)
- Heng Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Richard Durbin
- Department of Genetics, Cambridge University, Cambridge, UK.
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19
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Peres da Silva R, Suphavilai C, Nagarajan N. MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes. BMC Bioinformatics 2024; 25:153. [PMID: 38627615 PMCID: PMC11022314 DOI: 10.1186/s12859-024-05760-3] [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: 09/26/2022] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND With the rapid increase in throughput of long-read sequencing technologies, recent studies have explored their potential for taxonomic classification by using alignment-based approaches to reduce the impact of higher sequencing error rates. While alignment-based methods are generally slower, k-mer-based taxonomic classifiers can overcome this limitation, potentially at the expense of lower sensitivity for strains and species that are not in the database. RESULTS We present MetageNN, a memory-efficient long-read taxonomic classifier that is robust to sequencing errors and missing genomes. MetageNN is a neural network model that uses short k-mer profiles of sequences to reduce the impact of distribution shifts on error-prone long reads. Benchmarking MetageNN against other machine learning approaches for taxonomic classification (GeNet) showed substantial improvements with long-read data (20% improvement in F1 score). By utilizing nanopore sequencing data, MetageNN exhibits improved sensitivity in situations where the reference database is incomplete. It surpasses the alignment-based MetaMaps and MEGAN-LR, as well as the k-mer-based Kraken2 tools, with improvements of 100%, 36%, and 23% respectively at the read-level analysis. Notably, at the community level, MetageNN consistently demonstrated higher sensitivities than the previously mentioned tools. Furthermore, MetageNN requires < 1/4th of the database storage used by Kraken2, MEGAN-LR and MMseqs2 and is > 7× faster than MetaMaps and GeNet and > 2× faster than MEGAN-LR and MMseqs2. CONCLUSION This proof of concept work demonstrates the utility of machine-learning-based methods for taxonomic classification using long reads. MetageNN can be used on sequences not classified by conventional methods and offers an alternative approach for memory-efficient classifiers that can be optimized further.
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Affiliation(s)
- Rafael Peres da Silva
- School of Computing, National University of Singapore, Singapore, 117417, Republic of Singapore.
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), Singapore, 138672, Republic of Singapore.
| | - Chayaporn Suphavilai
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), Singapore, 138672, Republic of Singapore
| | - Niranjan Nagarajan
- School of Computing, National University of Singapore, Singapore, 117417, Republic of Singapore.
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), Singapore, 138672, Republic of Singapore.
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Republic of Singapore.
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20
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Ridley RS, Conrad RE, Lindner BG, Woo S, Konstantinidis KT. Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes. Sci Rep 2024; 14:8798. [PMID: 38627476 PMCID: PMC11021508 DOI: 10.1038/s41598-024-59279-x] [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: 11/17/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
Despite increasing efforts across various disciplines, the fate, transport, and impact of synthetic plastics on the environment and public health remain poorly understood. To better elucidate the microbial ecology of plastic waste and its potential for biotransformation, we conducted a large-scale analysis of all publicly available meta-omic studies investigating plastics (n = 27) in the environment. Notably, we observed low prevalence of known plastic degraders throughout most environments, except for substantial enrichment in riverine systems. This indicates rivers may be a highly promising environment for discovery of novel plastic bioremediation products. Ocean samples associated with degrading plastics showed clear differentiation from non-degrading polymers, showing enrichment of novel putative biodegrading taxa in the degraded samples. Regarding plastisphere pathogenicity, we observed significant enrichment of antimicrobial resistance genes on plastics but not of virulence factors. Additionally, we report a co-occurrence network analysis of 10 + million proteins associated with the plastisphere. This analysis revealed a localized sub-region enriched with known and putative plastizymes-these may be useful for deeper investigation of nature's ability to biodegrade man-made plastics. Finally, the combined data from our meta-analysis was used to construct a publicly available database, the Plastics Meta-omic Database (PMDB)-accessible at plasticmdb.org. These data should aid in the integrated exploration of the microbial plastisphere and facilitate research efforts investigating the fate and bioremediation potential of environmental plastic waste.
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Affiliation(s)
- Rodney S Ridley
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| | - Roth E Conrad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Blake G Lindner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Seongwook Woo
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Konstantinos T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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21
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Bouras G, Houtak G, Wick RR, Mallawaarachchi V, Roach MJ, Papudeshi B, Judd LM, Sheppard AE, Edwards RA, Vreugde S. Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.12.571215. [PMID: 38168369 PMCID: PMC10760025 DOI: 10.1101/2023.12.12.571215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- and long-reads) assembly approaches. Complete genomes allow a deeper understanding of bacterial evolution and genomic variation beyond single nucleotide variants (SNVs). They are also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance (AMR) genes. However, small plasmids are often missed or misassembled by long-read assembly algorithms. Here, we present Hybracter which allows for the fast, automatic, and scalable recovery of near-perfect complete bacterial genomes using a long-read first assembly approach. Hybracter can be run either as a hybrid assembler or as a long-read only assembler. We compared Hybracter to existing automated hybrid and long-read only assembly tools using a diverse panel of samples of varying levels of long-read accuracy with manually curated ground truth reference genomes. We demonstrate that Hybracter as a hybrid assembler is more accurate and faster than the existing gold standard automated hybrid assembler Unicycler. We also show that Hybracter with long-reads only is the most accurate long-read only assembler and is comparable to hybrid methods in accurately recovering small plasmids.
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Affiliation(s)
- George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, South Australia, Australia
| | - Ghais Houtak
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, South Australia, Australia
| | - Ryan R. Wick
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Michael J. Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
- Adelaide Centre for Epigenetics and South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, Australia
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Lousie M. Judd
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Anna E. Sheppard
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Sarah Vreugde
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, South Australia, Australia
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22
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Feng X, Li H. Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies. Genome Biol 2024; 25:92. [PMID: 38605401 PMCID: PMC11007910 DOI: 10.1186/s13059-024-03234-6] [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: 11/21/2022] [Accepted: 03/29/2024] [Indexed: 04/13/2024] Open
Abstract
BACKGROUND In the metagenomic assembly of a microbial community, abundant species are often thought to assemble well given their deeper sequencing coverage. This conjuncture is rarely tested or evaluated in practice. We often do not know how many abundant species are missing and do not have an approach to recover them. RESULTS Here, we propose k-mer based and 16S RNA based methods to measure the completeness of metagenome assembly. We show that even with PacBio high-fidelity (HiFi) reads, abundant species are often not assembled, as high strain diversity may lead to fragmented contigs. We develop a novel reference-free algorithm to recover abundant metagenome-assembled genomes (MAGs) by identifying circular assembly subgraphs. Complemented with a reference-free genome binning heuristics based on dimension reduction, the proposed method rescues many abundant species that would be missing with existing methods and produces competitive results compared to those state-of-the-art binners in terms of total number of near-complete genome bins. CONCLUSIONS Our work emphasizes the importance of metagenome completeness, which has often been overlooked. Our algorithm generates more circular MAGs and moves a step closer to the complete representation of microbial communities.
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Affiliation(s)
- Xiaowen Feng
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA.
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23
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Narsing Rao MP, Singh RN, Sani RK, Banerjee A. Genome-based approach to evaluate the metabolic potentials and exopolysaccharides production of Bacillus paralicheniformis CamBx3 isolated from a Chilean hot spring. Front Microbiol 2024; 15:1377965. [PMID: 38628868 PMCID: PMC11018918 DOI: 10.3389/fmicb.2024.1377965] [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: 01/28/2024] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
In the present study, a thermophilic strain designated CamBx3 was isolated from the Campanario hot spring, Chile. Based on 16S rRNA gene sequence, phylogenomic, and average nucleotide identity analysis the strain CamBx3 was identified as Bacillus paralicheniformis. Genome analysis of B. paralicheniformis CamBx3 revealed the presence of genes related to heat tolerance, exopolysaccharides (EPS), dissimilatory nitrate reduction, and assimilatory sulfate reduction. The pangenome analysis of strain CamBx3 with eight Bacillus spp. resulted in 26,562 gene clusters, 7,002 shell genes, and 19,484 cloud genes. The EPS produced by B. paralicheniformis CamBx3 was extracted, partially purified, and evaluated for its functional activities. B. paralicheniformis CamBx3 EPS with concentration 5 mg mL-1 showed an optimum 92 mM ferrous equivalent FRAP activity, while the same concentration showed a maximum 91% of Fe2+ chelating activity. B. paralicheniformis CamBx3 EPS (0.2 mg mL-1) demonstrated β-glucosidase inhibition. The EPS formed a viscoelastic gel at 45°C with a maximum instantaneous viscosity of 315 Pa.s at acidic pH 5. The present study suggests that B. paralicheniformis CamBx3 could be a valuable resource for biopolymers and bioactive molecules for industrial applications.
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Affiliation(s)
- Manik Prabhu Narsing Rao
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, Talca, Chile
| | - Ram Nageena Singh
- Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD, United States
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota Mines, Rapid City, SD, United States
| | - Rajesh K. Sani
- Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD, United States
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota Mines, Rapid City, SD, United States
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota Mines, Rapid City, SD, United States
- BioWRAP (Bioplastics With Regenerative Agricultural Properties), Rapid City, SD, United States
| | - Aparna Banerjee
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, Talca, Chile
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24
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Ding Y, Er S, Tan A, Gounot JS, Saw WY, Tan LWL, Teo YY, Nagarajan N, Seedorf H. Comparison of tet(X4)-containing contigs assembled from metagenomic sequencing data with plasmid sequences of isolates from a cohort of healthy subjects. Microbiol Spectr 2024; 12:e0396923. [PMID: 38441466 PMCID: PMC10986321 DOI: 10.1128/spectrum.03969-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/12/2024] [Indexed: 04/06/2024] Open
Abstract
Recently discovered tet(X) gene variants have provided new insights into microbial antibiotic resistance mechanisms and their potential consequences for public health. This study focused on detection, analysis, and characterization of Tet(X4)-positive Enterobacterales from the gut microbiota of a healthy cohort of individuals in Singapore using cultivation-dependent and cultivation-independent approaches. Twelve Tet(X4)-positive Enterobacterales strains that were previously obtained from the cohort were fully genome-sequenced and comparatively analyzed. A metagenomic sequencing (MS) data set of the same samples was mined for contigs that harbored the tet(X4) resistance gene. The sequences of tet(X4)-containing contigs and plasmids sequences were compared. The presence of the resistance genes floR and estT (previously annotated as catD) was detected in the same cassette in 10 and 12 out of the 12 tet(X4)-carrying plasmids, respectively. MS detected tet(X4)-containing contigs in 2 out of the 109 subjects, while cultivation-dependent analysis previously reported a prevalence of 10.1%. The tet(X4)-containing sequences assembled from MS data are relatively short (~14 to 33 kb) but show high similarity to the respective plasmid sequences of the isolates. Our findings show that MS can complement efforts in the surveillance of antibiotic resistance genes for clinical samples, while it has a lower sensitivity than a cultivation-based method when the target organism has a low abundance. Further optimization is required if MS is to be utilized in antibiotic resistance surveillance.IMPORTANCEThe global rise in antibiotic resistance makes it necessary to develop and apply new approaches to detect and monitor the prevalence of antibiotic resistance genes in human populations. In this regard, of particular interest are resistances against last-resort antibiotics, such as tigecycline. In this study, we show that metagenomic sequencing can help to detect high abundance of the tigecycline resistance gene tet(X4) in fecal samples from a cohort of healthy human subjects. However, cultivation-based approaches currently remain the most reliable and cost-effective method for detection of antibiotic-resistant bacteria.
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Affiliation(s)
- Yichen Ding
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, Singapore
| | - Shuan Er
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, Singapore
| | - Abel Tan
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, Singapore
| | - Jean-Sebastien Gounot
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Woei-Yuh Saw
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Singapore
| | - Linda Wei Lin Tan
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Yik Ying Teo
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Niranjan Nagarajan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore
| | - Henning Seedorf
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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25
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Cook R, Telatin A, Hsieh SY, Newberry F, Tariq MA, Baker DJ, Carding SR, Adriaenssens EM. Nanopore and Illumina sequencing reveal different viral populations from human gut samples. Microb Genom 2024; 10. [PMID: 38683195 DOI: 10.1099/mgen.0.001236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024] Open
Abstract
The advent of viral metagenomics, or viromics, has improved our knowledge and understanding of global viral diversity. High-throughput sequencing technologies enable explorations of the ecological roles, contributions to host metabolism, and the influence of viruses in various environments, including the human intestinal microbiome. However, bacterial metagenomic studies frequently have the advantage. The adoption of advanced technologies like long-read sequencing has the potential to be transformative in refining viromics and metagenomics. Here, we examined the effectiveness of long-read and hybrid sequencing by comparing Illumina short-read and Oxford Nanopore Technology (ONT) long-read sequencing technologies and different assembly strategies on recovering viral genomes from human faecal samples. Our findings showed that if a single sequencing technology is to be chosen for virome analysis, Illumina is preferable due to its superior ability to recover fully resolved viral genomes and minimise erroneous genomes. While ONT assemblies were effective in recovering viral diversity, the challenges related to input requirements and the necessity for amplification made it less ideal as a standalone solution. However, using a combined, hybrid approach enabled a more authentic representation of viral diversity to be obtained within samples.
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Affiliation(s)
- Ryan Cook
- Quadram Institute Bioscience, Norwich, NR4 7UQ, UK
| | | | | | - Fiona Newberry
- Department of Biosciences, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Mohammad A Tariq
- Faculty of Health and Life Sciences, University of Northumbria, Newcastle upon Tyne, NE1 8ST, UK
| | - Dave J Baker
- Quadram Institute Bioscience, Norwich, NR4 7UQ, UK
| | - Simon R Carding
- Quadram Institute Bioscience, Norwich, NR4 7UQ, UK
- Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ, UK
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26
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Roncero-Ramos B, Savaglia V, Durieu B, Van de Vreken I, Richel A, Wilmotte A. Ecophysiological and genomic approaches to cyanobacterial hardening for restoration. JOURNAL OF PHYCOLOGY 2024; 60:465-482. [PMID: 38373045 DOI: 10.1111/jpy.13436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 02/20/2024]
Abstract
Cyanobacteria inhabit extreme environments, including drylands, providing multiple benefits to the ecosystem. Soil degradation in warm drylands is increasing due to land use intensification. Restoration methods adapted to the extreme stress in drylands are being developed, such as cyanobacteria inoculation to recover biocrusts. For this type of restoration method to be a success, it is crucial to optimize the survival of inoculated cyanobacteria in the field. One strategy is to harden them to be acclimated to stressful conditions after laboratory culturing. Here, we analyzed the genome and ecophysiological response to osmotic desiccation and UVR stresses of an Antarctic cyanobacterium, Stenomitos frigidus ULC029, which is closely related to other cyanobacteria from warm and cold dryland soils. Chlorophyll a concentrations showed that preculturing ULC029 under moderate osmotic stress improved its survival during an assay of desiccation plus rehydration under UVR. Additionally, its sequential exposure to these stress factors increased the production of exopolysaccharides, carotenoids, and scytonemin. Desiccation, but not osmotic stress, increased the concentrations of the osmoprotectants trehalose and sucrose. However, osmotic stress might induce the production of other osmoprotectants, for which the complete pathways were observed in the ULC029 genome. In total, 140 genes known to be involved in stress resistance were annotated. Here, we confirm that the sequential application of moderate osmotic stress and dehydration could improve cyanobacterial hardening for soil restoration by inducing several resistance mechanisms. We provide a high-quality genome of ULC029 and a description of the main resistance mechanisms (i.e., production of exopolysaccharides, osmoprotectants, chlorophyll, and carotenoids; DNA repair; and oxidative stress protection).
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Affiliation(s)
- Beatriz Roncero-Ramos
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - Valentina Savaglia
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Benoit Durieu
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
| | | | - Aurore Richel
- TERRA-Biomass and Green Technologies, University of Liège, Gembloux, Belgium
| | - Annick Wilmotte
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
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27
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Yu W, Luo H, Yang J, Zhang S, Jiang H, Zhao X, Hui X, Sun D, Li L, Wei XQ, Lonardi S, Pan W. Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes. Genome Res 2024; 34:326-340. [PMID: 38428994 PMCID: PMC10984382 DOI: 10.1101/gr.278232.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/23/2024] [Indexed: 03/03/2024]
Abstract
Pacific Biosciences (PacBio) HiFi sequencing technology generates long reads (>10 kbp) with very high accuracy (<0.01% sequencing error). Although several de novo assembly tools are available for HiFi reads, there are no comprehensive studies on the evaluation of these assemblers. We evaluated the performance of 11 de novo HiFi assemblers on (1) real data for three eukaryotic genomes; (2) 34 synthetic data sets with different ploidy, sequencing coverage levels, heterozygosity rates, and sequencing error rates; (3) one real metagenomic data set; and (4) five synthetic metagenomic data sets with different composition abundance and heterozygosity rates. The 11 assemblers were evaluated using quality assessment tool (QUAST) and benchmarking universal single-copy ortholog (BUSCO). We also used several additional criteria, namely, completion rate, single-copy completion rate, duplicated completion rate, average proportion of largest category, average distance difference, quality value, run-time, and memory utilization. Results show that hifiasm and hifiasm-meta should be the first choice for assembling eukaryotic genomes and metagenomes with HiFi data. We performed a comprehensive benchmarking study of commonly used assemblers on complex eukaryotic genomes and metagenomes. Our study will help the research community to choose the most appropriate assembler for their data and identify possible improvements in assembly algorithms.
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Affiliation(s)
- Wenjuan Yu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Haohui Luo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jinbao Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Shengchen Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Heling Jiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xianjia Zhao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Xingqi Hui
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Da Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Liang Li
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350002, China
| | - Xiu-Qing Wei
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350002, China;
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, California 92521, USA;
| | - Weihua Pan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China;
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28
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Ulrich JU, Epping L, Pilz T, Walther B, Stingl K, Semmler T, Renard BY. Nanopore adaptive sampling effectively enriches bacterial plasmids. mSystems 2024; 9:e0094523. [PMID: 38376263 PMCID: PMC10949517 DOI: 10.1128/msystems.00945-23] [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: 09/04/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Bacterial plasmids play a major role in the spread of antibiotic resistance genes. However, their characterization via DNA sequencing suffers from the low abundance of plasmid DNA in those samples. Although sample preparation methods can enrich the proportion of plasmid DNA before sequencing, these methods are expensive and laborious, and they might introduce a bias by enriching only for specific plasmid DNA sequences. Nanopore adaptive sampling could overcome these issues by rejecting uninteresting DNA molecules during the sequencing process. In this study, we assess the application of adaptive sampling for the enrichment of low-abundant plasmids in known bacterial isolates using two different adaptive sampling tools. We show that a significant enrichment can be achieved even on expired flow cells. By applying adaptive sampling, we also improve the quality of de novo plasmid assemblies and reduce the sequencing time. However, our experiments also highlight issues with adaptive sampling if target and non-target sequences span similar regions. IMPORTANCE Antimicrobial resistance causes millions of deaths every year. Mobile genetic elements like bacterial plasmids are key drivers for the dissemination of antimicrobial resistance genes. This makes the characterization of plasmids via DNA sequencing an important tool for clinical microbiologists. Since plasmids are often underrepresented in bacterial samples, plasmid sequencing can be challenging and laborious. To accelerate the sequencing process, we evaluate nanopore adaptive sampling as an in silico method for the enrichment of low-abundant plasmids. Our results show the potential of this cost-efficient method for future plasmid research but also indicate issues that arise from using reference sequences.
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Affiliation(s)
- Jens-Uwe Ulrich
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
- Department of Mathematics and Computer Science, Free University of Berlin, Berlin, Germany
- Phylogenomics Unit, Center for Artificial Intelligence in Public Health Research, Robert Koch Institute, Wildau, Germany
| | - Lennard Epping
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Tanja Pilz
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Birgit Walther
- Advanced Light and Electron Microscopy, Robert Koch Institute, Berlin, Germany
| | - Kerstin Stingl
- National Reference Laboratory for Campylobacter, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Torsten Semmler
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Bernhard Y. Renard
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
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29
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Stewart RD, Myers KS, Amstadt C, Seib M, McMahon KD, Noguera DR. Refinement of the " Candidatus Accumulibacter" genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration. mSystems 2024; 9:e0118823. [PMID: 38415636 PMCID: PMC10949500 DOI: 10.1128/msystems.01188-23] [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: 11/18/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024] Open
Abstract
Members of the "Candidatus Accumulibacter" genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced biological phosphorus removal (EBPR). This diverse lineage includes 18 "Ca. Accumulibacter" species, which have been proposed based on the phylogenetic divergence of the polyphosphate kinase 1 (ppk1) gene and genome-scale comparisons of metagenome-assembled genomes (MAGs). Phylogenetic classification based on the 16S rRNA genetic marker has been difficult to attain because most "Ca. Accumulibacter" MAGs are incomplete and often do not include the rRNA operon. Here, we investigate the "Ca. Accumulibacter" diversity in pilot-scale treatment trains performing BNR under low dissolved oxygen (DO) conditions using genome-resolved metagenomics. Using long-read sequencing, we recovered medium- and high-quality MAGs for 5 of the 18 "Ca. Accumulibacter" species, all with rRNA operons assembled, which allowed a reassessment of the 16S rRNA-based phylogeny of this genus and an analysis of phylogeny based on the 23S rRNA gene. In addition, we recovered a cluster of MAGs that based on 16S rRNA, 23S rRNA, ppk1, and genome-scale phylogenetic analyses do not belong to any of the currently recognized "Ca. Accumulibacter" species for which we propose the new species designation "Ca. Accumulibacter jenkinsii" sp. nov. Relative abundance evaluations of the genus across all pilot plant operations revealed that regardless of the operational mode, "Ca. A. necessarius" and "Ca. A. propinquus" accounted for more than 40% of the "Ca. Accumulibacter" community, whereas the newly proposed "Ca. A. jenkinsii" accounted for about 5% of the "Ca. Accumulibacter" community.IMPORTANCEOne of the main drivers of energy use and operational costs in activated sludge processes is the amount of oxygen provided to enable biological phosphorus and nitrogen removal. Wastewater treatment facilities are increasingly considering reduced aeration to decrease energy consumption, and whereas successful BNR has been demonstrated in systems with minimal aeration, an adequate understanding of the microbial communities that facilitate nutrient removal under these conditions is still lacking. In this study, we used genome-resolved metagenomics to evaluate the diversity of the "Candidatus Accumulibacter" genus in pilot-scale plants operating with minimal aeration. We identified the "Ca. Accumulibacter" species enriched under these conditions, including one novel species for which we propose "Ca. Accumulibacter jenkinsii" sp. nov. as its designation. Furthermore, the MAGs obtained for five additional "Ca. Accumulibacter" species further refine the phylogeny of the "Ca. Accumulibacter" genus and provide new insight into its diversity within unconventional biological nutrient removal systems.
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Affiliation(s)
- Rachel D. Stewart
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin S. Myers
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Carly Amstadt
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Matt Seib
- Madison Metropolitan Sewerage District, Madison, Wisconsin, USA
| | - Katherine D. McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
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30
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Lin Z, Agarwal V, Cong Y, Pomponi SA, Schmidt EW. Short macrocyclic peptides in sponge genomes. Proc Natl Acad Sci U S A 2024; 121:e2314383121. [PMID: 38442178 PMCID: PMC10945851 DOI: 10.1073/pnas.2314383121] [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: 08/22/2023] [Accepted: 01/19/2024] [Indexed: 03/07/2024] Open
Abstract
Sponges (Porifera) contain many peptide-specialized metabolites with potent biological activities and significant roles in shaping marine ecology. It is well established that symbiotic bacteria produce bioactive "sponge" peptides, both on the ribosome (RiPPs) and nonribosomally. Here, we demonstrate that sponges themselves also produce many bioactive macrocyclic peptides, such as phakellistatins and related proline-rich macrocyclic peptides (PRMPs). Using the Stylissa carteri sponge transcriptome, methods were developed to find sequences encoding 46 distinct RiPP-type core peptides, of which ten encoded previously identified PRMP sequences. With this basis set, the genome and transcriptome of the sponge Axinella corrugata was interrogated to find 35 PRMP precursor peptides encoding 31 unique core peptide sequences. At least 11 of these produced cyclic peptides that were present in the sponge and could be characterized by mass spectrometry, including stylissamides A-D and seven previously undescribed compounds. Precursor peptides were encoded in the A. corrugata genome, confirming their animal origin. The peptides contained signal peptide sequences and highly repetitive recognition sequence-core peptide elements with up to 25 PRMP copies in a single precursor. In comparison to sponges without PRMPs, PRMP sponges are incredibly enriched in potentially secreted polypeptides, with >23,000 individual signal peptide encoding genes found in a single transcriptome. The similarities between PRMP biosynthetic genes and neuropeptides in terms of their biosynthetic logic suggest a fundamental biology linked to circular peptides, possibly indicating a widespread and underappreciated diversity of signaling peptide post-translational modifications across the animal kingdom.
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Affiliation(s)
- Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT84112
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA30332
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30332
| | - Ying Cong
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT84112
| | - Shirley A. Pomponi
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL34946
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT84112
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Espinoza JL, Phillips A, Prentice MB, Tan GS, Kamath PL, Lloyd KG, Dupont CL. Unveiling the Microbial Realm with VEBA 2.0: A modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic, and viral multi-omics from either short- or long-read sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.583560. [PMID: 38559265 PMCID: PMC10979853 DOI: 10.1101/2024.03.08.583560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA's versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible platform that bridges the gap between genomics and biotechnological solutions.
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Affiliation(s)
- Josh L. Espinoza
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Allan Phillips
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Gene S. Tan
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Pauline L. Kamath
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Karen G. Lloyd
- Microbiology Department, University of Tennessee, Knoxville, TN 37917, USA
| | - Chris L. Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
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Hui X, Yang J, Sun J, Liu F, Pan W. MCSS: microbial community simulator based on structure. Front Microbiol 2024; 15:1358257. [PMID: 38516019 PMCID: PMC10956353 DOI: 10.3389/fmicb.2024.1358257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/20/2024] [Indexed: 03/23/2024] Open
Abstract
De novo assembly plays a pivotal role in metagenomic analysis, and the incorporation of third-generation sequencing technology can significantly improve the integrity and accuracy of assembly results. Recently, with advancements in sequencing technology (Hi-Fi, ultra-long), several long-read-based bioinformatic tools have been developed. However, the validation of the performance and reliability of these tools is a crucial concern. To address this gap, we present MCSS (microbial community simulator based on structure), which has the capability to generate simulated microbial community and sequencing datasets based on the structure attributes of real microbiome communities. The evaluation results indicate that it can generate simulated communities that exhibit both diversity and similarity to actual community structures. Additionally, MCSS generates synthetic PacBio Hi-Fi and Oxford Nanopore Technologies (ONT) long reads for the species within the simulated community. This innovative tool provides a valuable resource for benchmarking and refining metagenomic analysis methods. Code available at: https://github.com/panlab-bio/mcss.
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Affiliation(s)
- Xingqi Hui
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (ICR, CAAS), Shenzhen, China
| | - Jinbao Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (ICR, CAAS), Shenzhen, China
- College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Jinhuan Sun
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Fang Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Weihua Pan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (ICR, CAAS), Shenzhen, China
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Yang HT, Huang YH, Ho YN. Oceanimonas pelagia sp. nov., a novel biosurfactant-producing and plastic-degrading potential bacterium isolated from marine coastal sediment. Antonie Van Leeuwenhoek 2024; 117:49. [PMID: 38448684 DOI: 10.1007/s10482-024-01948-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: 11/14/2023] [Accepted: 02/08/2024] [Indexed: 03/08/2024]
Abstract
A marine bacterial strain, named NTOU-MSR1T, was isolated from marine sediment of northern coast of Taiwan. This bacterium was Gram-stain-negative, aerobic, and motile, with a single flagellum. Its rod-shaped cells measured approximately 0.5-0.6 µm in width and 1.8-2.0 μm in length. NTOU-MSR1T grew at temperatures ranging from 10 to 45 °C, optimally at 30 °C. The pH range for growth was 7.0-10.0, with optimal growth at pH 7.0-8.0. It tolerated NaCl concentrations up to 12%. The cell membrane predominantly contained fatty acids such C16:1ω7c, C18:1ω7c, and C16:0. The overall genome relatedness indices indicated that strain NTOU-MSR1T had an average nucleotide identity (ANI) of 87.88% and a digital DNA-DNA hybridization (dDDH) value of 35.40% compared to its closest related species, O. marisflavi 102-Na3T. These values fell below the 95% and 70% threshold for species delineation, respectively. These findings suggested that the strain NTOU-MSR1T was a new member of the Oceanimonas genus. Its genomic DNA had a G + C content of 61.0 mol%. Genomic analysis revealed genes associated with the catechol branch of β- ketoadipate pathway for degrading polycyclic aromatic hydrocarbons, resistance to heavy metal, biosynthesis of polyhydroxybutyrate and the production of glycoside hydrolases (GH19, GH23, and GH103) for chitin and glycan digestion. Additionally, NTOU-MSR1T was capable of synthesizing biosurfactants and potentially degrading plastic. The proposed name for this new species is Oceanimonas pelagia, with the type strain designated as NTOU-MSR1T (= BCRC 81403T = JCM 36023T).
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Affiliation(s)
- Hsiao-Tsu Yang
- Institute of Marine Biology, College of Life Science, National Taiwan Ocean University, Keelung, Taiwan
| | - Yi-Hsuan Huang
- Institute of Marine Biology, College of Life Science, National Taiwan Ocean University, Keelung, Taiwan
| | - Ying-Ning Ho
- Institute of Marine Biology, College of Life Science, National Taiwan Ocean University, Keelung, Taiwan.
- Centre of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan.
- Taiwan Ocean Genome Center, National Taiwan Ocean University, Keelung, Taiwan.
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Ament-Velásquez SL, Vogan AA, Wallerman O, Hartmann FE, Gautier V, Silar P, Giraud T, Johannesson H. High-Quality Genome Assemblies of 4 Members of the Podospora anserina Species Complex. Genome Biol Evol 2024; 16:evae034. [PMID: 38386982 PMCID: PMC10936905 DOI: 10.1093/gbe/evae034] [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: 10/31/2023] [Revised: 12/29/2023] [Accepted: 02/17/2024] [Indexed: 02/24/2024] Open
Abstract
The filamentous fungus Podospora anserina is a model organism used extensively in the study of molecular biology, senescence, prion biology, meiotic drive, mating-type chromosome evolution, and plant biomass degradation. It has recently been established that P. anserina is a member of a complex of 7 closely related species. In addition to P. anserina, high-quality genomic resources are available for 2 of these taxa. Here, we provide chromosome-level annotated assemblies of the 4 remaining species of the complex, as well as a comprehensive data set of annotated assemblies from a total of 28 Podospora genomes. We find that all 7 species have genomes of around 35 Mb arranged in 7 chromosomes that are mostly collinear and less than 2% divergent from each other at genic regions. We further attempt to resolve their phylogenetic relationships, finding significant levels of phylogenetic conflict as expected from a rapid and recent diversification.
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Affiliation(s)
- S Lorena Ament-Velásquez
- Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Aaron A Vogan
- Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Comparative Genetics and Functional Genomics, Uppsala University, 752 37 Uppsala, Sweden
| | - Fanny E Hartmann
- Ecologie Systematique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91198 Gif-sur-Yvette, France
| | - Valérie Gautier
- Laboratoire Interdisciplinaire des Energies de Demain (LIED), Université de Paris Cité, F-75013 Paris, France
| | - Philippe Silar
- Laboratoire Interdisciplinaire des Energies de Demain (LIED), Université de Paris Cité, F-75013 Paris, France
| | - Tatiana Giraud
- Ecologie Systematique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91198 Gif-sur-Yvette, France
| | - Hanna Johannesson
- Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
- The Royal Swedish Academy of Sciences, 114 18 Stockholm, Sweden
- Department of Ecology, Environmental and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
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Kostova V, Hanke D, Kaspar H, Fiedler S, Schwarz S, Krüger-Haker H. Macrolide resistance in Mannheimia haemolytica isolates associated with bovine respiratory disease from the German national resistance monitoring program GE RM-Vet 2009 to 2020. Front Microbiol 2024; 15:1356208. [PMID: 38495516 PMCID: PMC10940430 DOI: 10.3389/fmicb.2024.1356208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/13/2024] [Indexed: 03/19/2024] Open
Abstract
Data collected from the German national resistance monitoring program GERM-Vet showed slowly increasing prevalence of macrolide resistance among bovine respiratory disease (BRD)-associated Pasteurellacae from cattle over the last decade. The focus of this study was to analyze the genetic basis of antimicrobial resistance (AMR) and the prevalence of multidrug-resistance (MDR)-mediating integrative and conjugative elements (ICEs) in 13 German BRD-associated Mannheimia haemolytica isolates collected between 2009 and 2020 via whole-genome sequencing. Antimicrobial susceptibility testing (AST) was performed via broth microdilution according to the recommendations of the Clinical and Laboratory Standards Institute for the macrolides erythromycin, tilmicosin, tulathromycin, gamithromycin, tildipirosin, and tylosin as well as 25 other antimicrobial agents. All isolates either had elevated MICs or were resistant to at least one of the macrolides tested. Analysis of whole-genome sequences obtained by hybrid assembly of Illumina MiSeq and Oxford Nanopore MinION reads revealed the presence of seven novel Tn7406-like ICEs, designated Tn7694, and Tn7724- Tn7729. These ICEs harbored the antimicrobial resistance genes erm(T), mef (C), mph(G), floR, catA3, aad(3")(9), aph(3')-Ia, aac(3)-IIa, strA, strB, tet(Y), and sul2 in different combinations. In addition, mutational changes conferring resistance to macrolides, nalidixic acid or streptomycin, respectively, were detected among the M. haemolytica isolates. In addition, four isolates carried a 4,613-bp plasmid with the β-lactamase gene blaROB - 1. The detection of the macrolide resistance genes erm(T), mef (C), and mph(G) together with other resistance genes on MDR-mediating ICEs in bovine M. haemolytica may explain the occurrence of therapeutic failure when treating BRD with regularly used antimicrobial agents, such as phenicols, penicillins, tetracyclines, or macrolides. Finally, pathogen identification and subsequent AST is essential to ensure the efficacy of the antimicrobial agents applied to control BRD in cattle.
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Affiliation(s)
- Valeria Kostova
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Dennis Hanke
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Heike Kaspar
- Federal Office of Consumer Protection and Food Safety (BVL), Berlin, Germany
| | - Stefan Fiedler
- Federal Office of Consumer Protection and Food Safety (BVL), Berlin, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Henrike Krüger-Haker
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
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McKnight DJE, Wong-Bajracharya J, Okoh EB, Snijders F, Lidbetter F, Webster J, Haughton M, Darling AE, Djordjevic SP, Bogema DR, Chapman TA. Xanthomonas rydalmerensis sp. nov., a non-pathogenic member of Group 1 Xanthomonas. Int J Syst Evol Microbiol 2024; 74:006294. [PMID: 38536071 PMCID: PMC10995728 DOI: 10.1099/ijsem.0.006294] [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: 11/06/2023] [Accepted: 03/04/2024] [Indexed: 04/07/2024] Open
Abstract
Five bacterial isolates were isolated from Fragaria × ananassa in 1976 in Rydalmere, Australia, during routine biosecurity surveillance. Initially, the results of biochemical characterisation indicated that these isolates represented members of the genus Xanthomonas. To determine their species, further analysis was conducted using both phenotypic and genotypic approaches. Phenotypic analysis involved using MALDI-TOF MS and BIOLOG GEN III microplates, which confirmed that the isolates represented members of the genus Xanthomonas but did not allow them to be classified with respect to species. Genome relatedness indices and the results of extensive phylogenetic analysis confirmed that the isolates were members of the genus Xanthomonas and represented a novel species. On the basis the minimal presence of virulence-associated factors typically found in genomes of members of the genus Xanthomonas, we suggest that these isolates are non-pathogenic. This conclusion was supported by the results of a pathogenicity assay. On the basis of these findings, we propose the name Xanthomonas rydalmerensis, with DAR 34855T = ICMP 24941 as the type strain.
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Affiliation(s)
- Daniel J. E. McKnight
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
- University of Technology Sydney, 15 Broadway, Ultimo NSW 2007, Australia
| | - Johanna Wong-Bajracharya
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
| | - Efenaide B. Okoh
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
- Western Sydney University, Penrith, NSW, Australia
| | - Fridtjof Snijders
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
| | - Fiona Lidbetter
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
| | - John Webster
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
| | - Mathew Haughton
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
| | - Aaron E. Darling
- University of Technology Sydney, 15 Broadway, Ultimo NSW 2007, Australia
| | | | - Daniel R. Bogema
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
- University of Technology Sydney, 15 Broadway, Ultimo NSW 2007, Australia
| | - Toni A. Chapman
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
- University of Technology Sydney, 15 Broadway, Ultimo NSW 2007, Australia
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Messer LF, Lee CE, Wattiez R, Matallana-Surget S. Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics. MICROBIOME 2024; 12:36. [PMID: 38389111 PMCID: PMC10882806 DOI: 10.1186/s40168-024-01751-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 01/03/2024] [Indexed: 02/24/2024]
Abstract
BACKGROUND Microbial functioning on marine plastic surfaces has been poorly documented, especially within cold climates where temperature likely impacts microbial activity and the presence of hydrocarbonoclastic microorganisms. To date, only two studies have used metaproteomics to unravel microbial genotype-phenotype linkages in the marine 'plastisphere', and these have revealed the dominance of photosynthetic microorganisms within warm climates. Advancing the functional representation of the marine plastisphere is vital for the development of specific databases cataloging the functional diversity of the associated microorganisms and their peptide and protein sequences, to fuel biotechnological discoveries. Here, we provide a comprehensive assessment for plastisphere metaproteomics, using multi-omics and data mining on thin plastic biofilms to provide unique insights into plastisphere metabolism. Our robust experimental design assessed DNA/protein co-extraction and cell lysis strategies, proteomics workflows, and diverse protein search databases, to resolve the active plastisphere taxa and their expressed functions from an understudied cold environment. RESULTS For the first time, we demonstrate the predominance and activity of hydrocarbonoclastic genera (Psychrobacter, Flavobacterium, Pseudomonas) within a primarily heterotrophic plastisphere. Correspondingly, oxidative phosphorylation, the citrate cycle, and carbohydrate metabolism were the dominant pathways expressed. Quorum sensing and toxin-associated proteins of Streptomyces were indicative of inter-community interactions. Stress response proteins expressed by Psychrobacter, Planococcus, and Pseudoalteromonas and proteins mediating xenobiotics degradation in Psychrobacter and Pseudoalteromonas suggested phenotypic adaptations to the toxic chemical microenvironment of the plastisphere. Interestingly, a targeted search strategy identified plastic biodegradation enzymes, including polyamidase, hydrolase, and depolymerase, expressed by rare taxa. The expression of virulence factors and mechanisms of antimicrobial resistance suggested pathogenic genera were active, despite representing a minor component of the plastisphere community. CONCLUSION Our study addresses a critical gap in understanding the functioning of the marine plastisphere, contributing new insights into the function and ecology of an emerging and important microbial niche. Our comprehensive multi-omics and comparative metaproteomics experimental design enhances biological interpretations to provide new perspectives on microorganisms of potential biotechnological significance beyond biodegradation and to improve the assessment of the risks associated with microorganisms colonizing marine plastic pollution. Video Abstract.
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Affiliation(s)
- Lauren F Messer
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland
| | - Charlotte E Lee
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, University of Mons, Mons, 7000, Belgium
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland.
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Tobin LA, Jarocki VM, Kenyon J, Drigo B, Donner E, Djordjevic SP, Hamidian M. Genomic analysis of diverse environmental Acinetobacter isolates identifies plasmids, antibiotic resistance genes, and capsular polysaccharides shared with clinical strains. Appl Environ Microbiol 2024; 90:e0165423. [PMID: 38206028 PMCID: PMC10885009 DOI: 10.1128/aem.01654-23] [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: 10/18/2023] [Accepted: 11/30/2023] [Indexed: 01/12/2024] Open
Abstract
Acinetobacter baumannii, an important pathogen known for its widespread antibiotic resistance, has been the focus of extensive research within its genus, primarily involving clinical isolates. Consequently, data on environmental A. baumannii and other Acinetobacter species remain limited. Here, we utilized Illumina and Nanopore sequencing to analyze the genomes of 10 Acinetobacter isolates representing 6 different species sourced from aquatic environments in South Australia. All 10 isolates were phylogenetically distinct compared to clinical and other non-clinical Acinetobacter strains, often tens of thousands of single-nucleotide polymorphisms from their nearest neighbors. Despite the genetic divergence, we identified pdif modules (sections of mobilized DNA) carrying clinically important antimicrobial resistance genes in species other than A. baumannii, including carbapenemase oxa58, tetracycline resistance gene tet(39), and macrolide resistance genes msr(E)-mph(E). These pdif modules were located on plasmids with high sequence identity to those circulating in globally distributed A. baumannii ST1 and ST2 clones. The environmental A. baumannii isolate characterized here (SAAb472; ST350) did not possess any native plasmids; however, it could capture two clinically important plasmids (pRAY and pACICU2) with high transfer frequencies. Furthermore, A. baumannii SAAb472 possessed virulence genes and a capsular polysaccharide type analogous to clinical strains. Our findings highlight the potential for environmental Acinetobacter species to acquire and disseminate clinically important antimicrobial resistance genes, underscoring the need for further research into the ecology and evolution of this important genus.IMPORTANCEAntimicrobial resistance (AMR) is a global threat to human, animal, and environmental health. Studying AMR in environmental bacteria is crucial to understand the emergence and dissemination of resistance genes and pathogens, and to identify potential reservoirs and transmission routes. This study provides novel insights into the genomic diversity and AMR potential of environmental Acinetobacter species. By comparing the genomes of aquatic Acinetobacter isolates with clinical and non-clinical strains, we revealed that they are highly divergent yet carry pdif modules that encode resistance to antibiotics commonly used in clinical settings. We also demonstrated that an environmental A. baumannii isolate can acquire clinically relevant plasmids and carries virulence factors similar to those of hospital-associated strains. These findings suggest that environmental Acinetobacter species may serve as reservoirs and vectors of clinically important genes. Consequently, further research is warranted to comprehensively understand the ecology and evolution of this genus.
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Affiliation(s)
- Liam A. Tobin
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Veronica M. Jarocki
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
- The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia
| | - Johanna Kenyon
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, Australia
- UniSA STEM, University of South Australia, Mawson Lakes, SA, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, Australia
- Cooperative Research Centre for Solving Antimicrobial Resistance in Agribusiness, Food, and Environments (CRC SAAFE), Adelaide, SA, Australia
| | - Steven P. Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
- The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia
| | - Mehrad Hamidian
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
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Wang FQ, Bartosik D, Sidhu C, Siebers R, Lu DC, Trautwein-Schult A, Becher D, Huettel B, Rick J, Kirstein IV, Wiltshire KH, Schweder T, Fuchs BM, Bengtsson MM, Teeling H, Amann RI. Particle-attached bacteria act as gatekeepers in the decomposition of complex phytoplankton polysaccharides. MICROBIOME 2024; 12:32. [PMID: 38374154 PMCID: PMC10877868 DOI: 10.1186/s40168-024-01757-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/04/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND Marine microalgae (phytoplankton) mediate almost half of the worldwide photosynthetic carbon dioxide fixation and therefore play a pivotal role in global carbon cycling, most prominently during massive phytoplankton blooms. Phytoplankton biomass consists of considerable proportions of polysaccharides, substantial parts of which are rapidly remineralized by heterotrophic bacteria. We analyzed the diversity, activity, and functional potential of such polysaccharide-degrading bacteria in different size fractions during a diverse spring phytoplankton bloom at Helgoland Roads (southern North Sea) at high temporal resolution using microscopic, physicochemical, biodiversity, metagenome, and metaproteome analyses. RESULTS Prominent active 0.2-3 µm free-living clades comprised Aurantivirga, "Formosa", Cd. Prosiliicoccus, NS4, NS5, Amylibacter, Planktomarina, SAR11 Ia, SAR92, and SAR86, whereas BD1-7, Stappiaceae, Nitrincolaceae, Methylophagaceae, Sulfitobacter, NS9, Polaribacter, Lentimonas, CL500-3, Algibacter, and Glaciecola dominated 3-10 µm and > 10 µm particles. Particle-attached bacteria were more diverse and exhibited more dynamic adaptive shifts over time in terms of taxonomic composition and repertoires of encoded polysaccharide-targeting enzymes. In total, 305 species-level metagenome-assembled genomes were obtained, including 152 particle-attached bacteria, 100 of which were novel for the sampling site with 76 representing new species. Compared to free-living bacteria, they featured on average larger metagenome-assembled genomes with higher proportions of polysaccharide utilization loci. The latter were predicted to target a broader spectrum of polysaccharide substrates, ranging from readily soluble, simple structured storage polysaccharides (e.g., laminarin, α-glucans) to less soluble, complex structural, or secreted polysaccharides (e.g., xylans, cellulose, pectins). In particular, the potential to target poorly soluble or complex polysaccharides was more widespread among abundant and active particle-attached bacteria. CONCLUSIONS Particle-attached bacteria represented only 1% of all bloom-associated bacteria, yet our data suggest that many abundant active clades played a pivotal gatekeeping role in the solubilization and subsequent degradation of numerous important classes of algal glycans. The high diversity of polysaccharide niches among the most active particle-attached clades therefore is a determining factor for the proportion of algal polysaccharides that can be rapidly remineralized during generally short-lived phytoplankton bloom events. Video Abstract.
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Grants
- AM 73/9-3 Deutsche Forschungsgemeinschaft,Germany
- SCHW 595/10-3 Deutsche Forschungsgemeinschaft,Germany
- TE 813/2-3 Deutsche Forschungsgemeinschaft,Germany
- RI 969/9-2 Deutsche Forschungsgemeinschaft,Germany
- BE 3869/4-3 Deutsche Forschungsgemeinschaft,Germany
- SCHW 595/11-3 Deutsche Forschungsgemeinschaft,Germany
- FU 627/2-3 Deutsche Forschungsgemeinschaft,Germany
- RI 969/9-2 Deutsche Forschungsgemeinschaft,Germany
- TE 813/2-3 Deutsche Forschungsgemeinschaft,Germany
- AM 73/9-3 Deutsche Forschungsgemeinschaft,Germany
- AWI_BAH_o 1 Biological Station Helgoland, Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research
- AWI_BAH_o 1 Biological Station Helgoland, Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research
- Max Planck Institute for Marine Microbiology (2)
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Affiliation(s)
- Feng-Qing Wang
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Daniel Bartosik
- Institute of Pharmacy, University of Greifswald, Felix-Hausdorff-Straße 3, 17489, Greifswald, Germany
- Institute of Marine Biotechnology, Walther-Rathenau-Straße 49a, 17489, Greifswald, Germany
| | - Chandni Sidhu
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Robin Siebers
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany
| | - De-Chen Lu
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
- Marine College, Shandong University, Weihai, 264209, China
| | - Anke Trautwein-Schult
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Carl von Linné-Weg 10, 50829, Cologne, Germany
| | - Johannes Rick
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, 27483, Germany
| | - Inga V Kirstein
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, 27483, Germany
| | - Karen H Wiltshire
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, 27483, Germany
| | - Thomas Schweder
- Institute of Pharmacy, University of Greifswald, Felix-Hausdorff-Straße 3, 17489, Greifswald, Germany
- Institute of Marine Biotechnology, Walther-Rathenau-Straße 49a, 17489, Greifswald, Germany
| | - Bernhard M Fuchs
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Mia M Bengtsson
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany.
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
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40
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Acheampong SA, Polat MF, Kwong WK. Complete genome sequences of 12 bacterial strains from the honey bee gut, resolved with long-read nanopore sequencing. Microbiol Resour Announc 2024; 13:e0077523. [PMID: 38193702 PMCID: PMC10868161 DOI: 10.1128/mra.00775-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/30/2023] [Indexed: 01/10/2024] Open
Abstract
We report the de novo sequencing of six bacterial strains isolated from the Western honey bee, as well as the resequencing of six strains that have existing draft genomes, to obtain complete, chromosomal-level assemblies. These strains include the bee gut symbiont genera Bartonella, Bifidobacterium, Snodgrassella, Gilliamella, Lactobacillus, and the opportunistic pathogen Serratia marcescens KZ11.
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Affiliation(s)
| | | | - Waldan K. Kwong
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, Oeiras, Portugal
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41
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Vancaester E, Blaxter ML. MarkerScan: Separation and assembly of cobionts sequenced alongside target species in biodiversity genomics projects. Wellcome Open Res 2024; 9:33. [PMID: 38617467 PMCID: PMC11016177 DOI: 10.12688/wellcomeopenres.20730.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2023] [Indexed: 04/16/2024] Open
Abstract
Contamination of public databases by mislabelled sequences has been highlighted for many years and the avalanche of novel sequencing data now being deposited has the potential to make databases difficult to use effectively. It is therefore crucial that sequencing projects and database curators perform pre-submission checks to remove obvious contamination and avoid propagating erroneous taxonomic relationships. However, it is important also to recognise that biological contamination of a target sample with unexpected species' DNA can also lead to the discovery of fascinating biological phenomena through the identification of environmental organisms or endosymbionts. Here, we present a novel, integrated method for detection and generation of high-quality genomes of all non-target genomes co-sequenced in eukaryotic genome sequencing projects. After performing taxonomic profiling of an assembly from the raw data, and leveraging the identity of small rRNA sequences discovered therein as markers, a targeted classification approach retrieves and assembles high-quality genomes. The genomes of these cobionts are then not only removed from the target species' genome but also available for further interrogation. Source code is available from https://github.com/CobiontID/MarkerScan. MarkerScan is written in Python and is deployed as a Docker container.
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Affiliation(s)
| | - Mark L. Blaxter
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
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42
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Orel N, Fadeev E, Herndl GJ, Turk V, Tinta T. Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii. BMC Genomics 2024; 25:146. [PMID: 38321410 PMCID: PMC10845552 DOI: 10.1186/s12864-024-10062-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Environmental monitoring of bacterial pathogens is critical for disease control in coastal marine ecosystems to maintain animal welfare and ecosystem function and to prevent significant economic losses. This requires accurate taxonomic identification of environmental bacterial pathogens, which often cannot be achieved by commonly used genetic markers (e.g., 16S rRNA gene), and an understanding of their pathogenic potential based on the information encoded in their genomes. The decreasing costs of whole genome sequencing (WGS), combined with newly developed bioinformatics tools, now make it possible to unravel the full potential of environmental pathogens, beyond traditional microbiological approaches. However, obtaining a high-quality bacterial genome, requires initial cultivation in an axenic culture, which is a bottleneck in environmental microbiology due to cross-contamination in the laboratory or isolation of non-axenic strains. RESULTS We applied WGS to determine the pathogenic potential of two Vibrio isolates from coastal seawater. During the analysis, we identified cross-contamination of one of the isolates and decided to use this dataset to evaluate the possibility of bioinformatic contaminant removal and recovery of bacterial genomes from a contaminated culture. Despite the contamination, using an appropriate bioinformatics workflow, we were able to obtain high quality and highly identical genomes (Average Nucleotide Identity value 99.98%) of one of the Vibrio isolates from both the axenic and the contaminated culture. Using the assembled genome, we were able to determine that this isolate belongs to a sub-lineage of Vibrio campbellii associated with several diseases in marine organisms. We also found that the genome of the isolate contains a novel Vibrio plasmid associated with bacterial defense mechanisms and horizontal gene transfer, which may offer a competitive advantage to this putative pathogen. CONCLUSIONS Our study shows that, using state-of-the-art bioinformatics tools and a sufficient sequencing effort, it is possible to obtain high quality genomes of the bacteria of interest and perform in-depth genomic analyses even in the case of a contaminated culture. With the new isolate and its complete genome, we are providing new insights into the genomic characteristics and functional potential of this sub-lineage of V. campbellii. The approach described here also highlights the possibility of recovering complete bacterial genomes in the case of non-axenic cultures or obligatory co-cultures.
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Affiliation(s)
- Neža Orel
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia.
| | - Eduard Fadeev
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
| | - Valentina Turk
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Tinkara Tinta
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia.
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43
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Bumunang EW, Castro VS, Alexander T, Zaheer R, McAllister TA, Guan LL, Stanford K. In Silico Analysis of Shiga Toxin-Producing Escherichia coli O157:H7 Strains from Presumptive Super- and Low-Shedder Cattle. Toxins (Basel) 2024; 16:86. [PMID: 38393164 PMCID: PMC10893428 DOI: 10.3390/toxins16020086] [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: 12/01/2023] [Revised: 01/19/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Cattle are the primary reservoir for STEC O157, with some shedding >104 CFU/g in feces, a phenomenon known as super-shedding (SS). The mechanism(s) responsible for SS are not understood but have been attributed to the environment, host, and pathogen. This study aimed to compare genetic characteristics of STEC O157 strains from cattle in the same commercial feedlot pens with SS or low-shedding (LS) status. Strains from SS (n = 35) and LS (n = 28) collected from 11 pens in three feedlots were analyzed for virulence genes, Shiga toxin-carrying bacteriophage insertion sites, and phylogenetic relationships. In silico analysis showed limited variation regarding virulence gene profiles. Stx-encoding prophage insertion sites mrlA and wrbA for stx1a and stx2a, respectively, were all occupied, but two isolates had fragments of the stx-carrying phage in mrlA and wrbA loci without stx1a and stx2a. All strains screened for lineage-specific polymorphism assay (LSPA-6) were 111111, lineage I. Of the isolates, 61 and 2 were clades 1 and 8, respectively. Phylogenetic analysis revealed that pens with more than one SS had multiple distantly related clusters of SS and LS isolates. Although virulence genes and lineage were largely similar within and across feedlots, multiple genetic origins of strains within a single feedlot pen illustrate challenges for on-farm control of STEC.
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Affiliation(s)
- Emmanuel W. Bumunang
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada; (E.W.B.); (T.A.); (R.Z.); (T.A.M.)
| | - Vinicius S. Castro
- Faculty of Agronomy and Zootechnics, Federal University of Mato Grosso (UFMT), Cuiabá 78010-715, Brazil;
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 1M4, Canada
| | - Trevor Alexander
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada; (E.W.B.); (T.A.); (R.Z.); (T.A.M.)
| | - Rahat Zaheer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada; (E.W.B.); (T.A.); (R.Z.); (T.A.M.)
| | - Tim A. McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada; (E.W.B.); (T.A.); (R.Z.); (T.A.M.)
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P9, Canada;
| | - Kim Stanford
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 1M4, Canada
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44
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Hiralal A, Geelhoed JS, Hidalgo-Martinez S, Smets B, van Dijk JR, Meysman FJR. Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads. Microb Genom 2024; 10:001197. [PMID: 38376381 PMCID: PMC10926707 DOI: 10.1099/mgen.0.001197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Many environmentally relevant micro-organisms cannot be cultured, and even with the latest metagenomic approaches, achieving complete genomes for specific target organisms of interest remains a challenge. Cable bacteria provide a prominent example of a microbial ecosystem engineer that is currently unculturable. They occur in low abundance in natural sediments, but due to their capability for long-distance electron transport, they exert a disproportionately large impact on the biogeochemistry of their environment. Current available genomes of marine cable bacteria are highly fragmented and incomplete, hampering the elucidation of their unique electrogenic physiology. Here, we present a metagenomic pipeline that combines Nanopore long-read and Illumina short-read shotgun sequencing. Starting from a clonal enrichment of a cable bacterium, we recovered a circular metagenome-assembled genome (5.09 Mbp in size), which represents a novel cable bacterium species with the proposed name Candidatus Electrothrix scaldis. The closed genome contains 1109 novel identified genes, including key metabolic enzymes not previously described in incomplete genomes of cable bacteria. We examined in detail the factors leading to genome closure. Foremost, native, non-amplified long reads are crucial to resolve the many repetitive regions within the genome of cable bacteria, and by analysing the whole metagenomic assembly, we found that low strain diversity is key for achieving genome closure. The insights and approaches presented here could help achieve genome closure for other keystone micro-organisms present in complex environmental samples at low abundance.
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Affiliation(s)
- Anwar Hiralal
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
| | | | | | - Bent Smets
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
| | | | - Filip J. R. Meysman
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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45
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Cao L, Kong Y, Fan Y, Ni M, Tourancheau A, Ksiezarek M, Mead EA, Koo T, Gitman M, Zhang XS, Fang G. mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome. Nat Methods 2024; 21:236-246. [PMID: 38177508 DOI: 10.1038/s41592-023-02125-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 11/08/2023] [Indexed: 01/06/2024]
Abstract
Metagenomics has enabled the comprehensive study of microbiomes. However, many applications would benefit from a method that sequences specific bacterial taxa of interest, but not most background taxa. We developed mEnrich-seq (in which 'm' stands for methylation and seq for sequencing) for enriching taxa of interest from metagenomic DNA before sequencing. The core idea is to exploit the self versus nonself differentiation by natural bacterial DNA methylation and rationally choose methylation-sensitive restriction enzymes, individually or in combination, to deplete host and background taxa while enriching targeted taxa. This idea is integrated with library preparation procedures and applied in several applications to enrich (up to 117-fold) pathogenic or beneficial bacteria from human urine and fecal samples, including species that are hard to culture or of low abundance. We assessed 4,601 bacterial strains with mapped methylomes so far and showed broad applicability of mEnrich-seq. mEnrich-seq provides microbiome researchers with a versatile and cost-effective approach for selective sequencing of diverse taxa of interest.
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Affiliation(s)
- Lei Cao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yimeng Kong
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yu Fan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mi Ni
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alan Tourancheau
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Magdalena Ksiezarek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edward A Mead
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tonny Koo
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa Gitman
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xue-Song Zhang
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, NJ, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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46
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Djordjevic SP, Jarocki VM, Seemann T, Cummins ML, Watt AE, Drigo B, Wyrsch ER, Reid CJ, Donner E, Howden BP. Genomic surveillance for antimicrobial resistance - a One Health perspective. Nat Rev Genet 2024; 25:142-157. [PMID: 37749210 DOI: 10.1038/s41576-023-00649-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2023] [Indexed: 09/27/2023]
Abstract
Antimicrobial resistance (AMR) - the ability of microorganisms to adapt and survive under diverse chemical selection pressures - is influenced by complex interactions between humans, companion and food-producing animals, wildlife, insects and the environment. To understand and manage the threat posed to health (human, animal, plant and environmental) and security (food and water security and biosecurity), a multifaceted 'One Health' approach to AMR surveillance is required. Genomic technologies have enabled monitoring of the mobilization, persistence and abundance of AMR genes and mutations within and between microbial populations. Their adoption has also allowed source-tracing of AMR pathogens and modelling of AMR evolution and transmission. Here, we highlight recent advances in genomic AMR surveillance and the relative strengths of different technologies for AMR surveillance and research. We showcase recent insights derived from One Health genomic surveillance and consider the challenges to broader adoption both in developed and in lower- and middle-income countries.
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Affiliation(s)
- Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia.
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia.
| | - Veronica M Jarocki
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Torsten Seemann
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Max L Cummins
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Anne E Watt
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Barbara Drigo
- UniSA STEM, University of South Australia, Adelaide, South Australia, Australia
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - Ethan R Wyrsch
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Cameron J Reid
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
- Cooperative Research Centre for Solving Antimicrobial Resistance in Agribusiness, Food, and Environments (CRC SAAFE), Adelaide, South Australia, Australia
| | - Benjamin P Howden
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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47
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Badger JH, Giordano R, Zimin A, Wappel R, Eskipehlivan SM, Muller S, Donthu R, Soto-Adames F, Vieira P, Zasada I, Goodwin S. Direct sequencing of insect symbionts via nanopore adaptive sampling. CURRENT OPINION IN INSECT SCIENCE 2024; 61:101135. [PMID: 37926187 DOI: 10.1016/j.cois.2023.101135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/07/2023]
Abstract
Insect symbionts can alter their host phenotype and their effects can range from beneficial to pathogenic. Moreover, many insects exhibit co-infections, making their study more challenging. Less than 1% of insect species have high-quality referenced genomes available and fewer still also have their symbionts sequenced. Two methods are commonly used to sequence symbionts: whole-genome sequencing to concomitantly capture the host and bacterial genomes, or isolation of the symbiont's genome before sequencing. These methods are limited when dealing with rare or poorly characterized symbionts. Long-read technology is an important tool to generate high-quality genomes as they can overcome high levels of heterozygosity, repeat content, and transposable elements that confound short-read methods. Oxford Nanopore (ONT) adaptive sampling allows a sequencing instrument to select or reject sequences in real time. We describe a method based on ONT adaptive sampling (subtractive) approach that readily permitted the sequencing of the complete genomes of mitochondria, Buchnera and its plasmids (pLeu, pTrp), and Wolbachia genomes in two aphid species, Aphis glycines and Pentalonia nigronervosa. Adaptive sampling is able to retrieve organelles such as mitochondria and symbionts that have high representation in their hosts such as Buchnera and Wolbachia, but is less successful at retrieving symbionts in low concentrations.
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Affiliation(s)
- Jonathan H Badger
- Genetics and Microbiome Core, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Rosanna Giordano
- Institute of Environment, Florida International University, Miami, FL, USA
| | - Aleksey Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Robert Wappel
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | - Ravikiran Donthu
- Centre for Life Sciences, Mahindra University, Bahadurpally, Hyderabad 500043, India
| | - Felipe Soto-Adames
- Florida Department of Agriculture and Consumer Services, Department of Plant Industry, Gainesville, FL 32614, USA
| | - Paulo Vieira
- USDA-ARS Agricultural Research Center, Mycology & Nematology Genetic Diversity & Biology Laboratory, Beltsville, MD, USA
| | - Inga Zasada
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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48
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Duarte VDS, Porcellato D. Host DNA depletion methods and genome-centric metagenomics of bovine hindmilk microbiome. mSphere 2024; 9:e0047023. [PMID: 38054728 PMCID: PMC10826364 DOI: 10.1128/msphere.00470-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/20/2023] [Indexed: 12/07/2023] Open
Abstract
Bovine mastitis is a multi-etiological and complex disease, resulting in serious economic consequences for dairy farmers and industry. In recent years, the microbiological evaluation of raw milk has been investigated in-depth using next-generation sequencing approaches such as metataxonomic analysis. Despite this, host DNA is a major concern in the shotgun metagenomic sequencing of microbial communities in milk samples, and it represents a big challenge. In this study, we aimed to evaluate different methods for host DNA depletion and/or microbial DNA enrichment and assess the use of PCR-based whole genome amplification in milk samples with high somatic cell count (SCC) by using short- and long-read sequencing technologies. Our results evidenced that DNA extraction performed differently in terms of host DNA removal, impacting metagenome composition and functional profiles.. Moreover, the ratio of SCC/bacteria ultimately impacts microbial DNA yield, and samples with low SCC (SCC below 100,000 cells/mL) are the most problematic. When milk samples with high SCC (SCC above 200,000 cells/mL) underwent multiple-displacement amplification (MDA), we successfully recovered high-quality metagenome-assembled genomes (MAGs), and long-read sequencing was feasible even for samples with low DNA concentration. By associating MDA and short-read sequencing, we recovered two times more MAGs than in untreated samples, and an ongoing co-infection not reported by traditional methods was detected for mastitis pathogen. Overall, this new approach will improve the detection of mastitis-associated microorganisms and make it possible to examine host-microbiome interactions in bovine mastitis.IMPORTANCENext-generation sequencing technologies have been widely used to gain new insights into the diversity of the microbial community of milk samples and dairy products for different purposes such as microbial safety, profiling of starter cultures, and host-microbiome interactions. Milk is a complex food matrix, and additionally, the presence of host nucleic acid sequences is considered a contaminant in untargeted high-throughput sequencing studies. Therefore, genomic-centric metagenomic studies of milk samples focusing on the health-disease status in dairy cattle are still scarce, which makes it difficult to evaluate the microbial ecophysiology of bovine hindmilk. This study provides an alternative method for genome-centric metagenome studies applied to hindmilk samples with high somatic cell content, which is indispensable to examining host-microbiome interactions in bovine mastitis.
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Affiliation(s)
- Vinícius da Silva Duarte
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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Curry KD, Yu FB, Vance SE, Segarra S, Bhaya D, Chikhi R, Rocha EP, Treangen TJ. Reference-free Structural Variant Detection in Microbiomes via Long-read Coassembly Graphs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577285. [PMID: 38352454 PMCID: PMC10862772 DOI: 10.1101/2024.01.25.577285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Bacterial genome dynamics are vital for understanding the mechanisms underlying microbial adaptation, growth, and their broader impact on host phenotype. Structural variants (SVs), genomic alterations of 10 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to absence of clear reference genomes and presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing a single metagenome coassembly graph constructed from all samples in a series. The log fold change in graph coverage between subsequent samples is then calculated to call SVs that are thriving or declining throughout the series. We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, which is particularly noticeable as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between subsequent time and temperature samples, suggesting host advantage. Our innovative approach leverages raw read patterns rather than references or MAGs to include all sequencing reads in analysis, and thus provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial genome dynamics.
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Affiliation(s)
- Kristen D. Curry
- Rice University, Department of Computer Science, Houston, TX 77005, United States
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
| | | | - Summer E. Vance
- University of California, Berkeley, Department of Environmental Science, Policy, and Management, Berkeley, CA 94720, United States
| | - Santiago Segarra
- Rice University, Department of Electrical and Computer Engineering, Houston, TX 77005, United States
| | - Devaki Bhaya
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, United States
| | - Rayan Chikhi
- Institut Pasteur, Université Paris Cité, Sequence Bioinformatics unit, 75015 Paris, France
| | - Eduardo P.C. Rocha
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
| | - Todd J. Treangen
- Rice University, Department of Computer Science, Houston, TX 77005, United States
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Kim C, Pongpanich M, Porntaveetus T. Unraveling metagenomics through long-read sequencing: a comprehensive review. J Transl Med 2024; 22:111. [PMID: 38282030 PMCID: PMC10823668 DOI: 10.1186/s12967-024-04917-1] [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: 10/15/2023] [Accepted: 01/21/2024] [Indexed: 01/30/2024] Open
Abstract
The study of microbial communities has undergone significant advancements, starting from the initial use of 16S rRNA sequencing to the adoption of shotgun metagenomics. However, a new era has emerged with the advent of long-read sequencing (LRS), which offers substantial improvements over its predecessor, short-read sequencing (SRS). LRS produces reads that are several kilobases long, enabling researchers to obtain more complete and contiguous genomic information, characterize structural variations, and study epigenetic modifications. The current leaders in LRS technologies are Pacific Biotechnologies (PacBio) and Oxford Nanopore Technologies (ONT), each offering a distinct set of advantages. This review covers the workflow of long-read metagenomics sequencing, including sample preparation (sample collection, sample extraction, and library preparation), sequencing, processing (quality control, assembly, and binning), and analysis (taxonomic annotation and functional annotation). Each section provides a concise outline of the key concept of the methodology, presenting the original concept as well as how it is challenged or modified in the context of LRS. Additionally, the section introduces a range of tools that are compatible with LRS and can be utilized to execute the LRS process. This review aims to present the workflow of metagenomics, highlight the transformative impact of LRS, and provide researchers with a selection of tools suitable for this task.
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Affiliation(s)
- Chankyung Kim
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
- Graduate Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence for Cancer and Inflammation, Chulalongkorn University, Bangkok, Thailand
| | - Thantrira Porntaveetus
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
- Graduate Program in Geriatric and Special Patients Care, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
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