1
|
Yang W, Luyten Y, Reister E, Mangelson H, Sisson Z, Auch B, Liachko I, Roberts RJ, Ettwiller L. Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5 C methyltransferase specificities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.15.603628. [PMID: 39071437 PMCID: PMC11275837 DOI: 10.1101/2024.07.15.603628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Methylation patterns in bacteria can be used to study Restriction-Modification (RM) or other defense systems with novel properties. While m4 C and m6 A methylation is well characterized mainly through PacBio sequencing, the landscape of m5 C methylation is under-characterized. To bridge this gap, we performed RIMS-seq2 on microbiomes composed of resolved assemblies of distinct genomes through proximity ligation. This high-throughput approach enables the identification of m5 C methylated motifs and links them to cognate methyltransferases directly on native microbiomes without the need to isolate bacterial strains. Methylation patterns can also be identified on viral DNA and compared to host DNA, strengthening evidence for virus-host interaction. Applied to three different microbiomes, the method unveils over 1900 motifs that were deposited in REBASE. The motifs include a novel 8-base recognition site (CAT m5 CGATG) that was experimentally validated by characterizing its cognate methyltransferase. Our findings suggest that microbiomes harbor arrays of untapped m5 C methyltransferase specificities, providing insights to bacterial biology and biotechnological applications.
Collapse
|
2
|
Gan M, Zhang Y, Yan G, Wang Y, Lu G, Wu B, Chen W, Zhou W. Antimicrobial resistance prediction by clinical metagenomics in pediatric severe pneumonia patients. Ann Clin Microbiol Antimicrob 2024; 23:33. [PMID: 38622723 PMCID: PMC11020437 DOI: 10.1186/s12941-024-00690-7] [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: 11/08/2023] [Accepted: 03/26/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is a major threat to children's health, particularly in respiratory infections. Accurate identification of pathogens and AMR is crucial for targeted antibiotic treatment. Metagenomic next-generation sequencing (mNGS) shows promise in directly detecting microorganisms and resistance genes in clinical samples. However, the accuracy of AMR prediction through mNGS testing needs further investigation for practical clinical decision-making. METHODS We aimed to evaluate the performance of mNGS in predicting AMR for severe pneumonia in pediatric patients. We conducted a retrospective analysis at a tertiary hospital from May 2022 to May 2023. Simultaneous mNGS and culture were performed on bronchoalveolar lavage fluid samples obtained from pediatric patients with severe pneumonia. By comparing the results of mNGS detection of microorganisms and antibiotic resistance genes with those of culture, sensitivity, specificity, positive predictive value, and negative predictive value were calculated. RESULTS mNGS detected bacterial in 71.7% cases (86/120), significantly higher than culture (58/120, 48.3%). Compared to culture, mNGS demonstrated a sensitivity of 96.6% and a specificity of 51.6% in detecting pathogenic microorganisms. Phenotypic susceptibility testing (PST) of 19 antibiotics revealed significant variations in antibiotics resistance rates among different bacteria. Sensitivity prediction of mNGS for carbapenem resistance was higher than penicillins and cephalosporin (67.74% vs. 28.57%, 46.15%), while specificity showed no significant difference (85.71%, 75.00%, 75.00%). mNGS also showed a high sensitivity of 94.74% in predicting carbapenem resistance in Acinetobacter baumannii. CONCLUSIONS mNGS exhibits variable predictive performance among different pathogens and antibiotics, indicating its potential as a supplementary tool to conventional PST. However, mNGS currently cannot replace conventional PST.
Collapse
Affiliation(s)
- Mingyu Gan
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, People's Republic of China
| | - Yanyan Zhang
- Department of Neonatology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Gangfeng Yan
- Department of Critical Care Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, People's Republic of China
| | - Yixue Wang
- Department of Critical Care Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, People's Republic of China
| | - Guoping Lu
- Department of Critical Care Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, People's Republic of China
| | - Bingbing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, People's Republic of China
| | - Weiming Chen
- Department of Critical Care Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, People's Republic of China.
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, People's Republic of China.
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510005, China.
| |
Collapse
|
3
|
da Roza PA, Muller H, Sullivan GJ, Walker RSK, Goold HD, Willows RD, Palenik B, Paulsen IT. Chromosome-scale assembly of the streamlined picoeukaryote Picochlorum sp. SENEW3 genome reveals Rabl-like chromatin structure and potential for C 4 photosynthesis. Microb Genom 2024; 10. [PMID: 38625719 DOI: 10.1099/mgen.0.001223] [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: 04/17/2024] Open
Abstract
Genome sequencing and assembly of the photosynthetic picoeukaryotic Picochlorum sp. SENEW3 revealed a compact genome with a reduced gene set, few repetitive sequences, and an organized Rabl-like chromatin structure. Hi-C chromosome conformation capture revealed evidence of possible chromosomal translocations, as well as putative centromere locations. Maintenance of a relatively few selenoproteins, as compared to similarly sized marine picoprasinophytes Mamiellales, and broad halotolerance compared to others in Trebouxiophyceae, suggests evolutionary adaptation to variable salinity environments. Such adaptation may have driven size and genome minimization and have been enabled by the retention of a high number of membrane transporters. Identification of required pathway genes for both CAM and C4 photosynthetic carbon fixation, known to exist in the marine mamiellale pico-prasinophytes and seaweed Ulva, but few other chlorophyte species, further highlights the unique adaptations of this robust alga. This high-quality assembly provides a significant advance in the resources available for genomic investigations of this and other photosynthetic picoeukaryotes.
Collapse
Affiliation(s)
- Patrick A da Roza
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Héloïse Muller
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
| | - Geraldine J Sullivan
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Roy S K Walker
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Hugh D Goold
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- New South Wales Department of Primary Industries, Orange, NSW 2800, Australia
| | - Robert D Willows
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Brian Palenik
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202, USA
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, Australia
| |
Collapse
|
4
|
Meyer S, Laval L, Pimenta M, González-Flores Y, Gaschet M, Couvé-Deacon E, Barraud O, Dagot C, Ploy MC. [Tracking transfers of resistance-carrying bacteria between animals, humans and the environment]. C R Biol 2024; 346:13-15. [PMID: 37655941 DOI: 10.5802/crbiol.114] [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: 01/24/2023] [Revised: 02/06/2023] [Accepted: 03/09/2023] [Indexed: 09/02/2023]
Abstract
The fight against antibiotic resistance must incorporate the "One Health" concept to be effective. This means having a holistic approach embracing the different ecosystems, human, animal, and environment. Transfers of resistance genes may exist between these three domains and different stresses related to the exposome may influence these transfers. Various targeted or pan-genomic molecular biology techniques can be used to better characterise the dissemination of bacterial clones and to identify exchanges of genes and mobile genetic elements between ecosystems.
Collapse
|
5
|
Serizay J, Matthey-Doret C, Bignaud A, Baudry L, Koszul R. Orchestrating chromosome conformation capture analysis with Bioconductor. Nat Commun 2024; 15:1072. [PMID: 38316789 PMCID: PMC10844600 DOI: 10.1038/s41467-024-44761-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: 09/02/2023] [Accepted: 12/28/2023] [Indexed: 02/07/2024] Open
Abstract
Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data structures, computational methods and visualization tools available in Bioconductor to investigate Hi-C, micro-C and other 3C-related data, in R. An online book ( https://bioconductor.org/books/OHCA/ ) further provides prospective end users with a number of workflows to process, import, analyze and visualize any type of chromosome conformation capture data.
Collapse
Affiliation(s)
- Jacques Serizay
- Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France.
| | - Cyril Matthey-Doret
- Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
- Swiss Data Science Center, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Amaury Bignaud
- Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Lyam Baudry
- Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
- Université de Lausanne, Center for Integrative Genomics, Quartier Sorge, 1015, Lausanne, Switzerland
| | - Romain Koszul
- Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
| |
Collapse
|
6
|
Chaudhuri D, Mulder BM. Molecular Dynamics Simulation of a Feather-Boa Model of a Bacterial Chromosome. Methods Mol Biol 2024; 2819:611-623. [PMID: 39028526 DOI: 10.1007/978-1-0716-3930-6_28] [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: 07/20/2024]
Abstract
The chromosome of a bacterium consists of a mega-base pair-long circular DNA, which self-organizes within the micron-sized bacterial cell volume, compacting itself by three orders of magnitude. Unlike eukaryotic chromosomes, it lacks a nuclear membrane and freely floats in the cytosol confined by the cell membrane. It is believed that strong confinement, cross-linking by associated proteins, and molecular crowding all contribute to determine chromosome size and morphology. Modelling the chromosome simply as a circular polymer decorated with closed side loops in a cylindrical confining volume has been shown to already recapture some of the salient properties observed experimentally. Here we describe how a computer simulation can be set up to study structure and dynamics of bacterial chromosomes using this model.
Collapse
Affiliation(s)
- Debasish Chaudhuri
- Institute of Physics, Bhubaneswar, India.
- Homi Bhaba National Institute, Mumbai, India.
| | | |
Collapse
|
7
|
Hoareau M, Gerges E, Crémazy FGE. Shedding Light on Bacterial Chromosome Structure: Exploring the Significance of 3C-Based Approaches. Methods Mol Biol 2024; 2819:3-26. [PMID: 39028499 DOI: 10.1007/978-1-0716-3930-6_1] [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: 07/20/2024]
Abstract
The complex architecture of DNA within living organisms is essential for maintaining the genetic information that dictates their functions and characteristics. Among the many complexities of genetic material organization, the folding and arrangement of DNA into chromosomes play a critical role in regulating gene expression, replication, and other essential cellular processes. Bacteria, despite their apparently simple cellular structure, exhibit a remarkable level of chromosomal organization that influences their adaptability and survival in diverse environments. Understanding the three-dimensional arrangement of bacterial chromosomes has long been a challenge due to technical limitations, but the development of Chromosome Conformation Capture (3C) methods revolutionized our ability to explore the hierarchical structure and the dynamics of bacterial genomes. Here, we review the major advances in the field of bacterial chromosome structure using 3C technology over the past decade.
Collapse
Affiliation(s)
- Marion Hoareau
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, Montigny-Le-Bretonneux, France
| | - Elias Gerges
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, Montigny-Le-Bretonneux, France
| | - Frédéric G E Crémazy
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, Montigny-Le-Bretonneux, France.
| |
Collapse
|
8
|
Marinov GK, Doughty B, Kundaje A, Greenleaf WJ. The landscape of the histone-organized chromatin of Bdellovibrionota bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564843. [PMID: 37961278 PMCID: PMC10634947 DOI: 10.1101/2023.10.30.564843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Histone proteins have traditionally been thought to be restricted to eukaryotes and most archaea, with eukaryotic nucleosomal histones deriving from their archaeal ancestors. In contrast, bacteria lack histones as a rule. However, histone proteins have recently been identified in a few bacterial clades, most notably the phylum Bdellovibrionota, and these histones have been proposed to exhibit a range of divergent features compared to histones in archaea and eukaryotes. However, no functional genomic studies of the properties of Bdellovibrionota chromatin have been carried out. In this work, we map the landscape of chromatin accessibility, active transcription and three-dimensional genome organization in a member of Bdellovibrionota (a Bacteriovorax strain). We find that, similar to what is observed in some archaea and in eukaryotes with compact genomes such as yeast, Bacteriovorax chromatin is characterized by preferential accessibility around promoter regions. Similar to eukaryotes, chromatin accessibility in Bacteriovorax positively correlates with gene expression. Mapping active transcription through single-strand DNA (ssDNA) profiling revealed that unlike in yeast, but similar to the state of mammalian and fly promoters, Bacteriovorax promoters exhibit very strong polymerase pausing. Finally, similar to that of other bacteria without histones, the Bacteriovorax genome exists in a three-dimensional (3D) configuration organized by the parABS system along the axis defined by replication origin and termination regions. These results provide a foundation for understanding the chromatin biology of the unique Bdellovibrionota bacteria and the functional diversity in chromatin organization across the tree of life.
Collapse
Affiliation(s)
- Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Benjamin Doughty
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
- Arc Institute, Palo Alto, California, USA
| |
Collapse
|
9
|
Yáñez-Cuna FO, Koszul R. Insights in bacterial genome folding. Curr Opin Struct Biol 2023; 82:102679. [PMID: 37604045 DOI: 10.1016/j.sbi.2023.102679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 08/23/2023]
Abstract
Chromosomes in all domains of life are well-defined structural entities with complex hierarchical organization. The regulation of this hierarchical organization and its functional interplay with gene expression or other chromosome metabolic processes such as repair, replication, or segregation is actively investigated in a variety of species, including prokaryotes. Bacterial chromosomes are typically gene-dense with few non-coding sequences and are organized into the nucleoid, a membrane-less compartment composed of DNA, RNA, and proteins (nucleoid-associated proteins or NAPs). The continuous improvement of imaging and genomic methods has put the organization of these Mb-long molecules at reach, allowing to disambiguate some of their highly dynamic properties and intertwined structural features. Here we review and discuss some of the recent advances in the field of bacterial chromosome organization.
Collapse
Affiliation(s)
- Fares Osam Yáñez-Cuna
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015, Paris, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015, Paris, France.
| |
Collapse
|
10
|
Mathers TC, Wouters RHM, Mugford ST, Biello R, van Oosterhout C, Hogenhout SA. Hybridisation has shaped a recent radiation of grass-feeding aphids. BMC Biol 2023; 21:157. [PMID: 37443008 PMCID: PMC10347838 DOI: 10.1186/s12915-023-01649-4] [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: 12/19/2022] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Aphids are common crop pests. These insects reproduce by facultative parthenogenesis involving several rounds of clonal reproduction interspersed with an occasional sexual cycle. Furthermore, clonal aphids give birth to live young that are already pregnant. These qualities enable rapid population growth and have facilitated the colonisation of crops globally. In several cases, so-called "super clones" have come to dominate agricultural systems. However, the extent to which the sexual stage of the aphid life cycle has shaped global pest populations has remained unclear, as have the origins of successful lineages. Here, we used chromosome-scale genome assemblies to disentangle the evolution of two global pests of cereals-the English (Sitobion avenae) and Indian (Sitobion miscanthi) grain aphids. RESULTS Genome-wide divergence between S. avenae and S. miscanthi is low. Moreover, comparison of haplotype-resolved assemblies revealed that the S. miscanthi isolate used for genome sequencing is likely a hybrid, with one of its diploid genome copies closely related to S. avenae (~ 0.5% divergence) and the other substantially more divergent (> 1%). Population genomics analyses of UK and China grain aphids showed that S. avenae and S. miscanthi are part of a cryptic species complex with many highly differentiated lineages that predate the origins of agriculture. The complex consists of hybrid lineages that display a tangled history of hybridisation and genetic introgression. CONCLUSIONS Our analyses reveal that hybridisation has substantially contributed to grain aphid diversity, and hence, to the evolutionary potential of this important pest species. Furthermore, we propose that aphids are particularly well placed to exploit hybridisation events via the rapid propagation of live-born "frozen hybrids" via asexual reproduction, increasing the likelihood of hybrid lineage formation.
Collapse
Affiliation(s)
- Thomas C Mathers
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK.
- Tree of Life, Welcome Sanger Institute, Hinxton, Cambridge, UK.
| | - Roland H M Wouters
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Sam T Mugford
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Roberto Biello
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK.
| |
Collapse
|
11
|
McCallum GE, Rossiter AE, Quraishi MN, Iqbal TH, Kuehne SA, van Schaik W. Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts. Microb Genom 2023; 9:mgen001030. [PMID: 37272920 PMCID: PMC10327510 DOI: 10.1099/mgen.0.001030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 04/11/2023] [Indexed: 06/06/2023] Open
Abstract
The gut microbiota is a reservoir for antimicrobial resistance genes (ARGs). With current sequencing methods, it is difficult to assign ARGs to their microbial hosts, particularly if these ARGs are located on plasmids. Metagenomic chromosome conformation capture approaches (meta3C and Hi-C) have recently been developed to link bacterial genes to phylogenetic markers, thus potentially allowing the assignment of ARGs to their hosts on a microbiome-wide scale. Here, we generated a meta3C dataset of a human stool sample and used previously published meta3C and Hi-C datasets to investigate bacterial hosts of ARGs in the human gut microbiome. Sequence reads mapping to repetitive elements were found to cause problematic noise in, and may importantly skew interpretation of, meta3C and Hi-C data. We provide a strategy to improve the signal-to-noise ratio by discarding reads that map to insertion sequence elements and to the end of contigs. We also show the importance of using spike-in controls to quantify whether the cross-linking step in meta3C and Hi-C protocols has been successful. After filtering to remove artefactual links, 87 ARGs were assigned to their bacterial hosts across all datasets, including 27 ARGs in the meta3C dataset we generated. We show that commensal gut bacteria are an important reservoir for ARGs, with genes coding for aminoglycoside and tetracycline resistance being widespread in anaerobic commensals of the human gut.
Collapse
Affiliation(s)
- Gregory E. McCallum
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Amanda E. Rossiter
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | | | - Tariq H. Iqbal
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Sarah A. Kuehne
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- School of Dentistry, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| |
Collapse
|
12
|
Lamy-Besnier Q, Bignaud A, Garneau JR, Titecat M, Conti DE, Von Strempel A, Monot M, Stecher B, Koszul R, Debarbieux L, Marbouty M. Chromosome folding and prophage activation reveal specific genomic architecture for intestinal bacteria. MICROBIOME 2023; 11:111. [PMID: 37208714 DOI: 10.1186/s40168-023-01541-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/04/2023] [Indexed: 05/21/2023]
Abstract
BACKGROUND Bacteria and their viruses, bacteriophages, are the most abundant entities of the gut microbiota, a complex community of microorganisms associated with human health and disease. In this ecosystem, the interactions between these two key components are still largely unknown. In particular, the impact of the gut environment on bacteria and their associated prophages is yet to be deciphered. RESULTS To gain insight into the activity of lysogenic bacteriophages within the context of their host genomes, we performed proximity ligation-based sequencing (Hi-C) in both in vitro and in vivo conditions on the 12 bacterial strains of the OMM12 synthetic bacterial community stably associated within mice gut (gnotobiotic mouse line OMM12). High-resolution contact maps of the chromosome 3D organization of the bacterial genomes revealed a wide diversity of architectures, differences between environments, and an overall stability over time in the gut of mice. The DNA contacts pointed at 3D signatures of prophages leading to 16 of them being predicted as functional. We also identified circularization signals and observed different 3D patterns between in vitro and in vivo conditions. Concurrent virome analysis showed that 11 of these prophages produced viral particles and that OMM12 mice do not carry other intestinal viruses. CONCLUSIONS The precise identification by Hi-C of functional and active prophages within bacterial communities will unlock the study of interactions between bacteriophages and bacteria across conditions (healthy vs disease). Video Abstract.
Collapse
Affiliation(s)
- Quentin Lamy-Besnier
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 25-28 Rue du Dr Roux, 75015, Paris, France
- Institut Pasteur, Université Paris Cité, Spatial Regulation of Genomes Group, CNRS UMR 3525, 25-28 Rue du Dr Roux, 75015, Paris, France
| | - Amaury Bignaud
- Institut Pasteur, Université Paris Cité, Spatial Regulation of Genomes Group, CNRS UMR 3525, 25-28 Rue du Dr Roux, 75015, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Julian R Garneau
- Institut Pasteur, Université Paris Cité, Plate-Forme Technologique Biomics, 75015, Paris, France
| | - Marie Titecat
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 25-28 Rue du Dr Roux, 75015, Paris, France
- Université de Lille, INSERM, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, Lille, 59000, France
| | - Devon E Conti
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 25-28 Rue du Dr Roux, 75015, Paris, France
- Institut Pasteur, Université Paris Cité, Spatial Regulation of Genomes Group, CNRS UMR 3525, 25-28 Rue du Dr Roux, 75015, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Alexandra Von Strempel
- Max Von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Marc Monot
- Institut Pasteur, Université Paris Cité, Plate-Forme Technologique Biomics, 75015, Paris, France
| | - Bärbel Stecher
- Max Von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site LMU Munich, Munich, Germany
| | - Romain Koszul
- Institut Pasteur, Université Paris Cité, Spatial Regulation of Genomes Group, CNRS UMR 3525, 25-28 Rue du Dr Roux, 75015, Paris, France
| | - Laurent Debarbieux
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 25-28 Rue du Dr Roux, 75015, Paris, France.
| | - Martial Marbouty
- Institut Pasteur, Université Paris Cité, Spatial Regulation of Genomes Group, CNRS UMR 3525, 25-28 Rue du Dr Roux, 75015, Paris, France.
| |
Collapse
|
13
|
Smith L, Goldobina E, Govi B, Shkoporov AN. Bacteriophages of the Order Crassvirales: What Do We Currently Know about This Keystone Component of the Human Gut Virome? Biomolecules 2023; 13:584. [PMID: 37189332 PMCID: PMC10136315 DOI: 10.3390/biom13040584] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 05/17/2023] Open
Abstract
The order Crassvirales comprises dsDNA bacteriophages infecting bacteria in the phylum Bacteroidetes that are found in a variety of environments but are especially prevalent in the mammalian gut. This review summarises available information on the genomics, diversity, taxonomy, and ecology of this largely uncultured viral taxon. With experimental data available from a handful of cultured representatives, the review highlights key properties of virion morphology, infection, gene expression and replication processes, and phage-host dynamics.
Collapse
|
14
|
Theelen MJP, Luiken REC, Wagenaar JA, Sloet van Oldruitenborgh-Oosterbaan MM, Rossen JWA, Schaafstra FJWC, van Doorn DA, Zomer AL. Longitudinal study of the short- and long-term effects of hospitalisation and oral trimethoprim-sulfadiazine administration on the equine faecal microbiome and resistome. MICROBIOME 2023; 11:33. [PMID: 36850017 PMCID: PMC9969626 DOI: 10.1186/s40168-023-01465-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Hospitalisation and antimicrobial treatment are common in horses and significantly impact the intestinal microbiota. Antimicrobial treatment might also increase levels of resistant bacteria in faeces, which could spread to other ecological compartments, such as the environment, other animals and humans. In this study, we aimed to characterise the short- and long-term effects of transportation, hospitalisation and trimethoprim-sulfadiazine (TMS) administration on the faecal microbiota and resistome of healthy equids. METHODS In a longitudinal experimental study design, in which the ponies served as their own control, faecal samples were collected from six healthy Welsh ponies at the farm (D0-D13-1), immediately following transportation to the hospital (D13-2), during 7 days of hospitalisation without treatment (D14-D21), during 5 days of oral TMS treatment (D22-D26) and after discharge from the hospital up to 6 months later (D27-D211). After DNA extraction, 16S rRNA gene sequencing was performed on all samples. For resistome analysis, shotgun metagenomic sequencing was performed on selected samples. RESULTS Hospitalisation without antimicrobial treatment did not significantly affect microbiota composition. Oral TMS treatment reduced alpha-diversity significantly. Kiritimatiellaeota, Fibrobacteres and Verrucomicrobia significantly decreased in relative abundance, whereas Firmicutes increased. The faecal microbiota composition gradually recovered after discontinuation of TMS treatment and discharge from the hospital and, after 2 weeks, was more similar to pre-treatment composition than to composition during TMS treatment. Six months later, however, microbiota composition still differed significantly from that at the start of the study and Spirochaetes and Verrucomicrobia were less abundant. TMS administration led to a significant (up to 32-fold) and rapid increase in the relative abundance of resistance genes sul2, tetQ, ant6-1a, and aph(3")-lb. lnuC significantly decreased directly after treatment. Resistance genes sul2 (15-fold) and tetQ (six-fold) remained significantly increased 6 months later. CONCLUSIONS Oral treatment with TMS has a rapid and long-lasting effect on faecal microbiota composition and resistome, making the equine hindgut a reservoir and potential source of resistant bacteria posing a risk to animal and human health through transmission. These findings support the judicious use of antimicrobials to minimise long-term faecal presence, excretion and the spread of antimicrobial resistance in the environment. Video Abstract.
Collapse
Affiliation(s)
- Mathijs J. P. Theelen
- Department of Clinical Sciences (Equine Sciences), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 112, 3584 CM Utrecht, the Netherlands
- Department of Biomolecular Health Sciences (Infectious Diseases and Immunology), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - Roosmarijn E. C. Luiken
- Department of Biomolecular Health Sciences (Infectious Diseases and Immunology), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - Jaap A. Wagenaar
- Department of Biomolecular Health Sciences (Infectious Diseases and Immunology), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/OIE Reference Laboratory for Campylobacteriosis, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | | | - John W. A. Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
- Department of Pathology, University of Utah School of Medicine, 15 North Medical Drive East, Ste #1100, Salt Lake City, Utah 84112 USA
| | - Femke J. W. C. Schaafstra
- HAS University of Applied Sciences, Onderwijsboulevard 221, 5223 DE ‘s-Hertogenbosch, the Netherlands
- Department of Population Health Sciences (Farm Animal Health), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, 3584 CL Utrecht, the Netherlands
| | - David A. van Doorn
- Department of Clinical Sciences (Equine Sciences), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 112, 3584 CM Utrecht, the Netherlands
- Department of Population Health Sciences (Farm Animal Health), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, 3584 CL Utrecht, the Netherlands
| | - Aldert L. Zomer
- Department of Biomolecular Health Sciences (Infectious Diseases and Immunology), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/OIE Reference Laboratory for Campylobacteriosis, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| |
Collapse
|
15
|
Du Y, Fuhrman JA, Sun F. ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data. Nat Commun 2023; 14:502. [PMID: 36720887 PMCID: PMC9889337 DOI: 10.1038/s41467-023-35945-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/09/2023] [Indexed: 02/01/2023] Open
Abstract
The introduction of high-throughput chromosome conformation capture (Hi-C) into metagenomics enables reconstructing high-quality metagenome-assembled genomes (MAGs) from microbial communities. Despite recent advances in recovering eukaryotic, bacterial, and archaeal genomes using Hi-C contact maps, few of Hi-C-based methods are designed to retrieve viral genomes. Here we introduce ViralCC, a publicly available tool to recover complete viral genomes and detect virus-host pairs using Hi-C data. Compared to other Hi-C-based methods, ViralCC leverages the virus-host proximity structure as a complementary information source for the Hi-C interactions. Using mock and real metagenomic Hi-C datasets from several different microbial ecosystems, including the human gut, cow fecal, and wastewater, we demonstrate that ViralCC outperforms existing Hi-C-based binning methods as well as state-of-the-art tools specifically dedicated to metagenomic viral binning. ViralCC can also reveal the taxonomic structure of viruses and virus-host pairs in microbial communities. When applied to a real wastewater metagenomic Hi-C dataset, ViralCC constructs a phage-host network, which is further validated using CRISPR spacer analyses. ViralCC is an open-source pipeline available at https://github.com/dyxstat/ViralCC .
Collapse
Affiliation(s)
- Yuxuan Du
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Fengzhu Sun
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
| |
Collapse
|
16
|
Kariti H, Feld T, Kaplan N. Hypothesis-driven probabilistic modelling enables a principled perspective of genomic compartments. Nucleic Acids Res 2023; 51:1103-1119. [PMID: 36629266 PMCID: PMC9943678 DOI: 10.1093/nar/gkac1258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/30/2022] [Accepted: 01/10/2023] [Indexed: 01/12/2023] Open
Abstract
The Hi-C method has revolutionized the study of genome organization, yet interpretation of Hi-C interaction frequency maps remains a major challenge. Genomic compartments are a checkered Hi-C interaction pattern suggested to represent the partitioning of the genome into two self-interacting states associated with active and inactive chromatin. Based on a few elementary mechanistic assumptions, we derive a generative probabilistic model of genomic compartments, called deGeco. Testing our model, we find it can explain observed Hi-C interaction maps in a highly robust manner, allowing accurate inference of interaction probability maps from extremely sparse data without any training of parameters. Taking advantage of the interpretability of the model parameters, we then test hypotheses regarding the nature of genomic compartments. We find clear evidence of multiple states, and that these states self-interact with different affinities. We also find that the interaction rules of chromatin states differ considerably within and between chromosomes. Inspecting the molecular underpinnings of a four-state model, we show that a simple classifier can use histone marks to predict the underlying states with 87% accuracy. Finally, we observe instances of mixed-state loci and analyze these loci in single-cell Hi-C maps, finding that mixing of states occurs mainly at the cell level.
Collapse
Affiliation(s)
- Hagai Kariti
- Department of Physiology, Biophysics & Systems Biology, Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Haifa, Israel
| | - Tal Feld
- Department of Physiology, Biophysics & Systems Biology, Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Haifa, Israel,Viterbi Faculty of Electrical & Computer Engineering, Technion – Israel Institute of Technology, Haifa, Israel
| | - Noam Kaplan
- To whom correspondence should be addressed. Tel: +972 4 8295293;
| |
Collapse
|
17
|
Ngo VQH, Enault F, Midoux C, Mariadassou M, Chapleur O, Mazéas L, Loux V, Bouchez T, Krupovic M, Bize A. Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics. Environ Microbiol 2022; 24:4853-4868. [PMID: 35848130 PMCID: PMC9796341 DOI: 10.1111/1462-2920.16120] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/01/2022] [Accepted: 06/29/2022] [Indexed: 01/01/2023]
Abstract
Diversity of viruses infecting non-extremophilic archaea has been grossly understudied. This is particularly the case for viruses infecting methanogenic archaea, key players in the global carbon biogeochemical cycle. Only a dozen of methanogenic archaeal viruses have been isolated so far. In the present study, we implemented an original coupling between stable isotope probing and complementary shotgun metagenomic analyses to identify viruses of methanogens involved in the bioconversion of formate, which was used as the sole carbon source in batch anaerobic digestion microcosms. Under our experimental conditions, the microcosms were dominated by methanogens belonging to the order Methanobacteriales (Methanobacterium and Methanobrevibacter genera). Metagenomic analyses yielded several previously uncharacterized viral genomes, including a complete genome of a head-tailed virus (class Caudoviricetes, proposed family Speroviridae, Methanobacterium host) and several near-complete genomes of spindle-shaped viruses. The two groups of viruses are predicted to infect methanogens of the Methanobacterium and Methanosarcina genera and represent two new virus families. The metagenomics results are in good agreement with the electron microscopy observations, which revealed the dominance of head-tailed virus-like particles and the presence of spindle-shaped particles. The present study significantly expands the knowledge on the viral diversity of viruses of methanogens.
Collapse
Affiliation(s)
- Vuong Quoc Hoang Ngo
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - François Enault
- Université Clermont Auvergne, CNRS, LMGEClermont‐FerrandFrance
| | - Cédric Midoux
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance,Université Paris‐Saclay, INRAE, MaIAGEJouy‐en‐JosasFrance,Université Paris‐Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics FacilityJouy‐en‐JosasFrance
| | - Mahendra Mariadassou
- Université Paris‐Saclay, INRAE, MaIAGEJouy‐en‐JosasFrance,Université Paris‐Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics FacilityJouy‐en‐JosasFrance
| | - Olivier Chapleur
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - Laurent Mazéas
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - Valentin Loux
- Université Paris‐Saclay, INRAE, MaIAGEJouy‐en‐JosasFrance,Université Paris‐Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics FacilityJouy‐en‐JosasFrance
| | - Théodore Bouchez
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - Mart Krupovic
- Institut Pasteur, Université de Paris, CNRS UMR6047, Archaeal Virology UnitParisFrance
| | - Ariane Bize
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| |
Collapse
|
18
|
Smith SE, Huang W, Tiamani K, Unterer M, Khan Mirzaei M, Deng L. Emerging technologies in the study of the virome. Curr Opin Virol 2022; 54:101231. [DOI: 10.1016/j.coviro.2022.101231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 11/03/2022]
|
19
|
Ruppé E, d'Humières C, Armand-Lefèvre L. Inferring antibiotic susceptibility from metagenomic data: dream or reality? Clin Microbiol Infect 2022; 28:1225-1229. [PMID: 35551982 DOI: 10.1016/j.cmi.2022.04.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND The diagnosis of bacterial infections continues to rely on culture, a slow process in which antibiotic susceptibility profiles of potential pathogens are made available to clinicians 48h after sampling, at best. Recently, clinical metagenomics (CMg), the metagenomic sequencing of samples with the purpose of identifying microorganisms and determining their susceptibility to antimicrobials, has emerged as a potential diagnostic tool that could prove faster than culture. CMg indeed has the potential to detect antibiotic resistance genes (ARGs) and mutations associated with resistance. Nevertheless, many challenges have yet to be overcome in order to make rapid phenotypic inference of antibiotic susceptibility from metagenomic data a reality. OBJECTIVES The objective of this narrative review is to discuss the challenges underlying the phenotypic inference of antibiotic susceptibility from metagenomic data. SOURCES We conducted a narrative review using published articles available in the NCBI Pubmed database. CONTENT We review the current ARG databases with a specific emphasis on those which now provide associations with phenotypic data. Next, we discuss the bioinformatic tools designed to identify ARGs in metagenomes. We then report on the performance of phenotypic inference from genomic data and the issue predicting the expression of ARGs. Finally, we address the challenge of linking an ARG to this host. IMPLICATIONS Significant improvements have recently been made in associating ARG and phenotype, and the inference of susceptibility from genomic data has been demonstrated in pathogenic bacteria such as Staphylococci and Enterobacterales. Resistance involving gene expression is more challenging however, and inferring susceptibility from species such as Pseudomonas aeruginosa remains difficult. Future research directions include the consideration of gene expression via RNA sequencing and machine learning.
Collapse
Affiliation(s)
- Etienne Ruppé
- Université de Paris Cité, INSERM UMR1137 IAME, F-75018 Paris, France; AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, F-75018 Paris, France.
| | - Camille d'Humières
- Université de Paris Cité, INSERM UMR1137 IAME, F-75018 Paris, France; AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, F-75018 Paris, France
| | - Laurence Armand-Lefèvre
- Université de Paris Cité, INSERM UMR1137 IAME, F-75018 Paris, France; AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, F-75018 Paris, France
| |
Collapse
|
20
|
HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities. PLoS Genet 2022; 18:e1009776. [PMID: 35286304 PMCID: PMC8947609 DOI: 10.1371/journal.pgen.1009776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 03/24/2022] [Accepted: 02/07/2022] [Indexed: 11/19/2022] Open
Abstract
Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a comprehensive laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli. The bioinformatics pipeline code is available at https://github.com/lkalmar/HAM-ART.
Collapse
|
21
|
Du Y, Sun F. HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps. Genome Biol 2022; 23:63. [PMID: 35227283 PMCID: PMC8883645 DOI: 10.1186/s13059-022-02626-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 02/06/2022] [Indexed: 01/20/2023] Open
Abstract
AbstractRecovering high-quality metagenome-assembled genomes (MAGs) from complex microbial ecosystems remains challenging. Recently, high-throughput chromosome conformation capture (Hi-C) has been applied to simultaneously study multiple genomes in natural microbial communities. We develop HiCBin, a novel open-source pipeline, to resolve high-quality MAGs utilizing Hi-C contact maps. HiCBin employs the HiCzin normalization method and the Leiden clustering algorithm and includes the spurious contact detection into binning pipelines for the first time. HiCBin is validated on one synthetic and two real metagenomic samples and is shown to outperform the existing Hi-C-based binning methods. HiCBin is available at https://github.com/dyxstat/HiCBin.
Collapse
|
22
|
Diversity and Evolution of Mamiellophyceae: Early-Diverging Phytoplanktonic Green Algae Containing Many Cosmopolitan Species. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10020240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The genomic revolution has bridged a gap in our knowledge about the diversity, biology and evolution of unicellular photosynthetic eukaryotes, which bear very few discriminating morphological features among species from the same genus. The high-quality genome resources available in the class Mamiellophyceae (Chlorophyta) have been paramount to estimate species diversity and screen available metagenomic data to assess the biogeography and ecological niches of different species on a global scale. Here we review the current knowledge about the diversity, ecology and evolution of the Mamiellophyceae and the large double-stranded DNA prasinoviruses infecting them, brought by the combination of genomic and metagenomic analyses, including 26 metabarcoding environmental studies, as well as the pan-oceanic GOS and the Tara Oceans expeditions.
Collapse
|
23
|
Abstract
Naturally occurring plasmids come in different sizes. The smallest are less than a kilobase of DNA, while the largest can be over three orders of magnitude larger. Historically, research has tended to focus on smaller plasmids that are usually easier to isolate, manipulate and sequence, but with improved genome assemblies made possible by long-read sequencing, there is increased appreciation that very large plasmids—known as megaplasmids—are widespread, diverse, complex, and often encode key traits in the biology of their host microorganisms. Why are megaplasmids so big? What other features come with large plasmid size that could affect bacterial ecology and evolution? Are megaplasmids 'just' big plasmids, or do they have distinct characteristics? In this perspective, we reflect on the distribution, diversity, biology, and gene content of megaplasmids, providing an overview to these large, yet often overlooked, mobile genetic elements. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
Collapse
Affiliation(s)
- James P J Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - João Botelho
- Antibiotic Resistance Evolution Group, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian Albrechts University, Kiel, Germany
| | - Adrian Cazares
- EMBL's European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - David A Baltrus
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| |
Collapse
|
24
|
Carron L, Morlot JB, Lesne A, Mozziconacci J. The 3D Organization of Chromatin Colors in Mammalian Nuclei. Methods Mol Biol 2022; 2301:317-336. [PMID: 34415544 DOI: 10.1007/978-1-0716-1390-0_17] [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: 06/13/2023]
Abstract
While many computational methods have been proposed for 3D chromosome reconstruction from chromosomal contact maps, these methods are rarely used for the interpretation of such experimental data, in particular Hi-C data. We posit that this is due to the lack of an easy-to-use implementation of the proposed algorithms, as well as to the important computational cost of most methods. We here give a detailed implementation of the fast ShRec3D algorithm. We provide a tutorial that will enable the reader to reconstruct 3D consensus structures for human chromosomes and to decorate these structures with chromatin epigenetic states. We use this methodology to show that the bivalent chromatin, including Polycomb-rich domains, is spatially segregated and located in between the active and the quiescent chromatin compartments.
Collapse
Affiliation(s)
- Leopold Carron
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, Paris, France
- Sorbonne Université, CNRS, Laboratory of Computational and Quantitative Biology, Paris, France
| | - Jean-Baptiste Morlot
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, Paris, France
| | - Annick Lesne
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, Paris, France.
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France.
| | - Julien Mozziconacci
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, Paris, France.
- Muséum National d'Histoire Naturelle, Structure et Instabilité des Genomes, Paris, France.
- Institut Universitaire de France (IUF), Paris, France.
| |
Collapse
|
25
|
Abstract
Microbial communities are key components of all ecosystems, but characterization of their complete genomic structure remains challenging. Typical analysis tends to elude the complexity of the mixes in terms of species, strains, as well as extrachromosomal DNA molecules. Recently, approaches have been developed that bins DNA contigs into individual genomes and episomes according to their 3D contact frequencies. Those contacts are quantified by chromosome conformation capture experiments (3C, Hi-C), also known as proximity-ligation approaches, applied to metagenomics samples. Here, we present a simple computational pipeline that allows to recover high-quality Metagenomics Assemble Genomes (MAGs) starting from metagenomic 3C or Hi-C datasets and a metagenome assembly.
Collapse
|
26
|
Matthey-Doret C, Baudry L, Mortaza S, Moreau P, Koszul R, Cournac A. Normalization of Chromosome Contact Maps: Matrix Balancing and Visualization. Methods Mol Biol 2022; 2301:1-15. [PMID: 34415528 DOI: 10.1007/978-1-0716-1390-0_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Over the last decade, genomic proximity ligation approaches have reshaped our vision of chromosomes 3D organizations, from bacteria nucleoids to larger eukaryotic genomes. The different protocols (3Cseq, Hi-C, TCC, MicroC [XL], Hi-CO, etc.) rely on common steps (chemical fixation digestion, ligation…) to detect pairs of genomic positions in close proximity. The most common way to represent these data is a matrix, or contact map, which allows visualizing the different chromatin structures (compartments, loops, etc.) that can be associated to other signals such as transcription, protein occupancy, etc. as well as, in some instances, to biological functions.In this chapter we present and discuss the filtering of the events recovered in proximity ligation experiments as well as the application of the balancing normalization procedure on the resulting contact map. We also describe a computational tool for visualizing normalized contact data dubbed Scalogram.The different processes described here are illustrated and supported by the laboratory custom-made scripts pooled into "hicstuff," an open-access python package accessible on github ( https://github.com/koszullab/hicstuff ).
Collapse
Affiliation(s)
- Cyril Matthey-Doret
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Lyam Baudry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Shogofa Mortaza
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
| | - Pierrick Moreau
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
| | - Axel Cournac
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France.
| |
Collapse
|
27
|
Hill BM, Bisht K, Atkins GR, Gomez AA, Rumbaugh KP, Wakeman CA, Brown AMV. Lysis-Hi-C as a method to study polymicrobial communities and eDNA. Mol Ecol Resour 2021; 22:1029-1042. [PMID: 34669257 PMCID: PMC9215119 DOI: 10.1111/1755-0998.13535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 11/30/2022]
Abstract
Microbes interact in natural communities in a spatially structured manner, particularly in biofilms and polymicrobial infections. While next generation sequencing approaches provide powerful insights into diversity, metabolic capacity, and mutational profiles of these communities, they generally fail to recover in situ spatial proximity between distinct genotypes in the interactome. Hi‐C is a promising method that has assisted in analysing complex microbiomes, by creating chromatin cross‐links in cells, that aid in identifying adjacent DNA, to improve de novo assembly. This study explored a modified Hi‐C approach involving an initial lysis phase prior to DNA cross‐linking, to test whether adjacent cell chromatin can be cross‐linked, anticipating that this could provide a new avenue for study of spatial‐mutational dynamics in structured microbial communities. An artificial polymicrobial mixture of Pseudomonas aeruginosa, Staphylococcus aureus, and Escherichia coli was lysed for 1–18 h, then prepared for Hi‐C. A murine biofilm infection model was treated with sonication, mechanical lysis, or chemical lysis before Hi‐C. Bioinformatic analyses of resulting Hi‐C interspecies chromatin links showed that while microbial species differed from one another, generally lysis significantly increased links between species and increased the distance of Hi‐C links within species, while also increasing novel plasmid‐chromosome links. The success of this modified lysis‐Hi‐C protocol in creating extracellular DNA links is a promising first step toward a new lysis‐Hi‐C based method to recover genotypic microgeography in polymicrobial communities, with potential future applications in diseases with localized resistance, such as cystic fibrosis lung infections and chronic diabetic ulcers.
Collapse
Affiliation(s)
- Bravada M Hill
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Karishma Bisht
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Georgia Rae Atkins
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Amy A Gomez
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Kendra P Rumbaugh
- Department of Surgery, School of Medicine, Texas Tech Health Sciences Center, Lubbock, Texas, USA
| | - Catherine A Wakeman
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Amanda M V Brown
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| |
Collapse
|
28
|
McDaniel EA, Wahl SA, Ishii S, Pinto A, Ziels R, Nielsen PH, McMahon KD, Williams RBH. Prospects for multi-omics in the microbial ecology of water engineering. WATER RESEARCH 2021; 205:117608. [PMID: 34555741 DOI: 10.1016/j.watres.2021.117608] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions - including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful functional predictions to specific taxonomical groups with increasing fidelity. Additionally, related developments in both whole community gene expression surveys and metabolite profiling have permitted for direct surveys of community-scale functions in specific environmental settings. These advances have allowed for a shift in microbiome science away from descriptive studies and towards mechanistic and predictive frameworks for designing and harnessing microbial communities for desired beneficial outcomes. Water engineers, microbiologists, and microbial ecologists studying activated sludge, anaerobic digestion, and drinking water distribution systems have applied various (meta)omics techniques for connecting microbial community dynamics and physiologies to overall process parameters and system performance. However, the rapid pace at which new omics-based approaches are developed can appear daunting to those looking to apply these state-of-the-art practices for the first time. Here, we review how modern genome-resolved metagenomic approaches have been applied to a variety of water engineering applications from lab-scale bioreactors to full-scale systems. We describe integrated omics analysis across engineered water systems and the foundations for pairing these insights with modeling approaches. Lastly, we summarize emerging omics-based technologies that we believe will be powerful tools for water engineering applications. Overall, we provide a framework for microbial ecologists specializing in water engineering to apply cutting-edge omics approaches to their research questions to achieve novel functional insights. Successful adoption of predictive frameworks in engineered water systems could enable more economically and environmentally sustainable bioprocesses as demand for water and energy resources increases.
Collapse
Affiliation(s)
- Elizabeth A McDaniel
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA.
| | | | - Shun'ichi Ishii
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Yokosuka 237-0061, Japan
| | - Ameet Pinto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, USA
| | - Ryan Ziels
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | | | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA; Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Republic of Singapore.
| |
Collapse
|
29
|
Abstract
During the past decade, Chromosome Conformation Capture (3C/Hi-C)-based methods have been used to probe the 3D structure and organization of bacterial genomes, revealing fundamental aspects of chromosome dynamics. However, the current protocols are expensive, inefficient, and limited in their resolution. Here we present a simple, cost-effective Hi-C approach that is readily applicable to a range of Gram-positive and Gram-negative bacteria.
Collapse
|
30
|
Xu Z, Dixon JR. Genome reconstruction and haplotype phasing using chromosome conformation capture methodologies. Brief Funct Genomics 2021; 19:139-150. [PMID: 31875884 DOI: 10.1093/bfgp/elz026] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/06/2019] [Accepted: 09/15/2019] [Indexed: 12/22/2022] Open
Abstract
Genomic analysis of individuals or organisms is predicated on the availability of high-quality reference and genotype information. With the rapidly dropping costs of high-throughput DNA sequencing, this is becoming readily available for diverse organisms and for increasingly large populations of individuals. Despite these advances, there are still aspects of genome sequencing that remain challenging for existing sequencing methods. This includes the generation of long-range contiguity during genome assembly, identification of structural variants in both germline and somatic tissues, the phasing of haplotypes in diploid organisms and the resolution of genome sequence for organisms derived from complex samples. These types of information are valuable for understanding the role of genome sequence and genetic variation on genome function, and numerous approaches have been developed to address them. Recently, chromosome conformation capture (3C) experiments, such as the Hi-C assay, have emerged as powerful tools to aid in these challenges for genome reconstruction. We will review the current use of Hi-C as a tool for aiding in genome sequencing, addressing the applications, strengths, limitations and potential future directions for the use of 3C data in genome analysis. We argue that unique features of Hi-C experiments make this data type a powerful tool to address challenges in genome sequencing, and that future integration of Hi-C data with alternative sequencing assays will facilitate the continuing revolution in genomic analysis and genome sequencing.
Collapse
|
31
|
Abstract
Bacteria acquire novel DNA through horizontal gene transfer (HGT), a process that enables an organism to rapidly adapt to changing environmental conditions, provides a competitive edge and potentially alters its relationship with its host. Although the HGT process is routinely exploited in laboratories, there is a surprising disconnect between what we know from laboratory experiments and what we know from natural environments, such as the human gut microbiome. Owing to a suite of newly available computational algorithms and experimental approaches, we have a broader understanding of the genes that are being transferred and are starting to understand the ecology of HGT in natural microbial communities. This Review focuses on these new technologies, the questions they can address and their limitations. As these methods are applied more broadly, we are beginning to recognize the full extent of HGT possible within a microbiome and the punctuated dynamics of HGT, specifically in response to external stimuli. Furthermore, we are better characterizing the complex selective pressures on mobile genetic elements and the mechanisms by which they interact with the bacterial host genome.
Collapse
Affiliation(s)
- Ilana Lauren Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
32
|
Xiang Y, Surovtsev IV, Chang Y, Govers SK, Parry BR, Liu J, Jacobs-Wagner C. Interconnecting solvent quality, transcription, and chromosome folding in Escherichia coli. Cell 2021; 184:3626-3642.e14. [PMID: 34186018 DOI: 10.1016/j.cell.2021.05.037] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/09/2020] [Accepted: 05/25/2021] [Indexed: 12/12/2022]
Abstract
All cells fold their genomes, including bacterial cells, where the chromosome is compacted into a domain-organized meshwork called the nucleoid. How compaction and domain organization arise is not fully understood. Here, we describe a method to estimate the average mesh size of the nucleoid in Escherichia coli. Using nucleoid mesh size and DNA concentration estimates, we find that the cytoplasm behaves as a poor solvent for the chromosome when the cell is considered as a simple semidilute polymer solution. Monte Carlo simulations suggest that a poor solvent leads to chromosome compaction and DNA density heterogeneity (i.e., domain formation) at physiological DNA concentration. Fluorescence microscopy reveals that the heterogeneous DNA density negatively correlates with ribosome density within the nucleoid, consistent with cryoelectron tomography data. Drug experiments, together with past observations, suggest the hypothesis that RNAs contribute to the poor solvent effects, connecting chromosome compaction and domain formation to transcription and intracellular organization.
Collapse
Affiliation(s)
- Yingjie Xiang
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, CT 06520, USA; Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
| | - Ivan V Surovtsev
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Yunjie Chang
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sander K Govers
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA; Department of Biology and Institute of Chemistry, Engineering and Medicine for Human Health, Stanford University, Palo Alto, CA 94305, USA
| | - Bradley R Parry
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Jun Liu
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA; Department of Biology and Institute of Chemistry, Engineering and Medicine for Human Health, Stanford University, Palo Alto, CA 94305, USA.
| |
Collapse
|
33
|
Cockram C, Thierry A, Koszul R. Generation of gene-level resolution chromosome contact maps in bacteria and archaea. STAR Protoc 2021; 2:100512. [PMID: 34027477 PMCID: PMC8121701 DOI: 10.1016/j.xpro.2021.100512] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Chromosome conformation capture (Hi-C) has become a routine method for probing the 3D organization of genomes. However, when applied to bacteria and archaea, current protocols are expensive and limited in their resolution. By dissecting the different steps of published eukaryotic and prokaryotic Hi-C protocols, we have developed a cost- and time-effective approach to generate high-resolution (down to 500 bp – 1 kb) contact matrices of both bacteria and archaea genomes. For complete details on the use and execution of this protocol, please refer to Cockram et al. (2020). Optimized Hi-C protocol for archaeal and bacterial genomes Generation of genome-wide contact maps up to 1 kb resolution Detailed description of steps from cell fixation to sequencing library preparation A cost- and time-effective approach offering gene-level resolution contact maps
Collapse
Affiliation(s)
- Charlotte Cockram
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, 5015 Paris, France
| | - Agnès Thierry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, 5015 Paris, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, 5015 Paris, France
| |
Collapse
|
34
|
Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing. Nat Methods 2021; 18:491-498. [PMID: 33820988 PMCID: PMC8107137 DOI: 10.1038/s41592-021-01109-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 03/03/2021] [Indexed: 01/09/2023]
Abstract
Bacterial DNA methylation occurs at diverse sequence contexts and plays important functional roles in cellular defense and gene regulation. Existing methods for detecting DNA modification from nanopore sequencing data do not effectively support de novo study of unknown bacterial methylomes. In this work, we observed that a nanopore sequencing signal displays complex heterogeneity across methylation events of the same type. To enable nanopore sequencing for broadly applicable methylation discovery, we generated a training dataset from an assortment of bacterial species and developed a method, named nanodisco ( https://github.com/fanglab/nanodisco ), that couples the identification and fine mapping of the three forms of methylation into a multi-label classification framework. We applied it to individual bacteria and the mouse gut microbiome for reliable methylation discovery. In addition, we demonstrated the use of DNA methylation for binning metagenomic contigs, associating mobile genetic elements with their host genomes and identifying misassembled metagenomic contigs.
Collapse
|
35
|
Arumugam K, Bessarab I, Haryono MAS, Liu X, Zuniga-Montanez RE, Roy S, Qiu G, Drautz-Moses DI, Law YY, Wuertz S, Lauro FM, Huson DH, Williams RBH. Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing. NPJ Biofilms Microbiomes 2021; 7:23. [PMID: 33727564 PMCID: PMC7966762 DOI: 10.1038/s41522-021-00196-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 02/12/2021] [Indexed: 01/31/2023] Open
Abstract
New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes from complex microbial communities. Using long read data (ONT MinION) obtained from an ensemble of activated sludge enrichment bioreactors we recover 22 closed or complete genomes of community members, including several species known to play key functional roles in wastewater bioprocesses, specifically microbes known to exhibit the polyphosphate- and glycogen-accumulating organism phenotypes (namely Candidatus Accumulibacter and Dechloromonas, and Micropruina, Defluviicoccus and Candidatus Contendobacter, respectively), and filamentous bacteria (Thiothrix) associated with the formation and stability of activated sludge flocs. Additionally we demonstrate the recovery of close to 100 circularised plasmids, phages and small microbial genomes from these microbial communities using long read assembled sequence. We describe methods for validating long read assembled genomes using their counterpart short read metagenome-assembled genomes, and assess the influence of different correction procedures on genome quality and predicted gene quality. Our findings establish the feasibility of performing long read metagenome-assembled genome recovery for both chromosomal and non-chromosomal replicons, and demonstrate the value of parallel sampling of moderately complex enrichment communities to obtaining high quality reference genomes of key functional species relevant for wastewater bioprocesses.
Collapse
Affiliation(s)
- Krithika Arumugam
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Irina Bessarab
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Mindia A S Haryono
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Rogelio E Zuniga-Montanez
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Department of Civil and Environmental Engineering, One Shields Avenue, University of California, Davis, CA, USA
| | - Samarpita Roy
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Guanglei Qiu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Environment and Energy, South China University of Technology, Guangzhou, China
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ying Yu Law
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
| | - Federico M Lauro
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | - Daniel H Huson
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore.
| |
Collapse
|
36
|
Blake KS, Choi J, Dantas G. Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria. Cell Mol Life Sci 2021; 78:2585-2606. [PMID: 33582841 PMCID: PMC8005480 DOI: 10.1007/s00018-020-03717-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/26/2020] [Accepted: 11/17/2020] [Indexed: 12/24/2022]
Abstract
Hospital-associated infections are a major concern for global public health. Infections with antibiotic-resistant pathogens can cause empiric treatment failure, and for infections with multidrug-resistant bacteria which can overcome antibiotics of "last resort" there exists no alternative treatments. Despite extensive sanitization protocols, the hospital environment is a potent reservoir and vector of antibiotic-resistant organisms. Pathogens can persist on hospital surfaces and plumbing for months to years, acquire new antibiotic resistance genes by horizontal gene transfer, and initiate outbreaks of hospital-associated infections by spreading to patients via healthcare workers and visitors. Advancements in next-generation sequencing of bacterial genomes and metagenomes have expanded our ability to (1) identify species and track distinct strains, (2) comprehensively profile antibiotic resistance genes, and (3) resolve the mobile elements that facilitate intra- and intercellular gene transfer. This information can, in turn, be used to characterize the population dynamics of hospital-associated microbiota, track outbreaks to their environmental reservoirs, and inform future interventions. This review provides a detailed overview of the approaches and bioinformatic tools available to study isolates and metagenomes of hospital-associated bacteria, and their multi-layered networks of transmission.
Collapse
Affiliation(s)
- Kevin S Blake
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - JooHee Choi
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.
| |
Collapse
|
37
|
Marbouty M, Thierry A, Millot GA, Koszul R. MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut. eLife 2021; 10:60608. [PMID: 33634788 PMCID: PMC7963479 DOI: 10.7554/elife.60608] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 02/20/2021] [Indexed: 12/15/2022] Open
Abstract
Bacteriophages play important roles in regulating the intestinal human microbiota composition, dynamics, and homeostasis, and characterizing their bacterial hosts is needed to understand their impact. We applied a metagenomic Hi-C approach on 10 healthy human gut samples to unveil a large infection network encompassing more than 6000 interactions bridging a metagenomic assembled genomes (MAGs) and a phage sequence, allowing to study in situ phage-host ratio. Whereas three-quarters of these sequences likely correspond to dormant prophages, 5% exhibit a much higher coverage than their associated MAG, representing potentially actively replicating phages. We detected 17 sequences of members of the crAss-like phage family, whose hosts diversity remained until recently relatively elusive. For each of them, a unique bacterial host was identified, all belonging to different genus of Bacteroidetes. Therefore, metaHiC deciphers infection network of microbial population with a high specificity paving the way to dynamic analysis of mobile genetic elements in complex ecosystems.
Collapse
Affiliation(s)
- Martial Marbouty
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, Paris, France
| | - Agnès Thierry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, Paris, France
| | - Gaël A Millot
- Institut Pasteur, Bioinformatics and Biostatistics Hub, CNRS, USR 3756, Paris, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, Paris, France
| |
Collapse
|
38
|
Myers KN, Conn D, Brown AMV. Essential Amino Acid Enrichment and Positive Selection Highlight Endosymbiont's Role in a Global Virus-Vectoring Pest. mSystems 2021; 6:e01048-20. [PMID: 33531407 PMCID: PMC7857533 DOI: 10.1128/msystems.01048-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/05/2021] [Indexed: 12/20/2022] Open
Abstract
Host-associated microbes display remarkable convergence in genome repertoire resulting from selection to supplement missing host functions. Nutritional supplementation has been proposed in the verrucomicrobial endosymbiont Xiphinematobacter sp., which lives within a globally widespread group of plant-parasitic nematodes that vector damaging nepoviruses to plants. Only one genome sequence has been published from this symbiont, leaving unanswered questions about its diversity, host range, role, and selective pressures within its hosts. Because its hosts are exceptionally resistant to culturing, this symbiont is best studied through advanced genomic approaches. To analyze the role of Xiphinematobacter sp. in its host, sequencing was performed on nematode communities, and then genomes were extracted for comparative genomics, gene ontology enrichment tests, polymorphism analysis, de Bruijn-based genome-wide association studies, and tests of pathway- and site-specific selection on genes predicted play a role in the symbiosis. Results showed a closely clustered set of Xiphinematobacter isolates with reduced genomes of ∼917 kbp, for which a new species was proposed. Symbionts shared only 2.3% of genes with outgroup Verrucomicrobia, but comparative analyses showed high conservation of all 10 essential amino acid (EAA) biosynthesis pathways plus several vitamin pathways. These findings were supported by gene ontology enrichment tests and high polymorphisms in these pathways compared with background. Genome-wide association analysis confirmed high between-species fixation of alleles with significant functional enrichment for EAA and thiamine synthesis. Strong positive selection was detected on sites within these pathways, despite several being under increased purifying selection. Together, these results suggest that supplementation of EAAs missing in the host diet may drive this widespread symbiosis.IMPORTANCE Xiphinematobacter spp. are distinctly evolved intracellular symbionts in the phylum Verrucomicrobia, which includes the important human gut-associated microbe Akkermansia muciniphila and many highly abundant free-living soil microbes. Like Akkermansia sp., Xiphinematobacter sp. is obligately associated with the gut of its hosts, which in this case consists of a group of plant-parasitic nematodes that are among the top 10 most destructive species to global agriculture, by vectoring plant viruses. This study examined the hypothesis that the key to this symbiont's stable evolutionary association with its host is through provisioning nutrients that its host cannot make that may be lacking in the nematode's plant phloem diet, such as essential amino acids and several vitamins. The significance of our research is in demonstrating, using population genomics, the signatures of selective pressure on these hypothesized roles to ultimately learn how this independently evolved symbiont functionally mirrors symbionts of phloem-feeding insects.
Collapse
Affiliation(s)
- Kaitlyn N Myers
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Daniel Conn
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Amanda M V Brown
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| |
Collapse
|
39
|
Gauthier J, Boulain H, van Vugt JJFA, Baudry L, Persyn E, Aury JM, Noel B, Bretaudeau A, Legeai F, Warris S, Chebbi MA, Dubreuil G, Duvic B, Kremer N, Gayral P, Musset K, Josse T, Bigot D, Bressac C, Moreau S, Periquet G, Harry M, Montagné N, Boulogne I, Sabeti-Azad M, Maïbèche M, Chertemps T, Hilliou F, Siaussat D, Amselem J, Luyten I, Capdevielle-Dulac C, Labadie K, Merlin BL, Barbe V, de Boer JG, Marbouty M, Cônsoli FL, Dupas S, Hua-Van A, Le Goff G, Bézier A, Jacquin-Joly E, Whitfield JB, Vet LEM, Smid HM, Kaiser L, Koszul R, Huguet E, Herniou EA, Drezen JM. Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization. Commun Biol 2021; 4:104. [PMID: 33483589 PMCID: PMC7822920 DOI: 10.1038/s42003-020-01623-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Endogenous viruses form an important proportion of eukaryote genomes and a source of novel functions. How large DNA viruses integrated into a genome evolve when they confer a benefit to their host, however, remains unknown. Bracoviruses are essential for the parasitism success of parasitoid wasps, into whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome at a chromosomal scale, that bracovirus genes colonized all ten chromosomes of Cotesia congregata. Most form clusters of genes involved in particle production or parasitism success. Genomic comparison with another wasp, Microplitis demolitor, revealed that these clusters were already established ~53 mya and thus belong to remarkably stable genomic structures, the architectures of which are evolutionary constrained. Transcriptomic analyses highlight temporal synchronization of viral gene expression without resulting in immune gene induction, suggesting that no conflicts remain between ancient symbiotic partners when benefits to them converge.
Collapse
Affiliation(s)
- Jérémy Gauthier
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France ,grid.466902.f0000 0001 2248 6951Geneva Natural History Museum, 1208 Geneva, Switzerland
| | - Hélène Boulain
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France ,grid.418656.80000 0001 1551 0562EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Joke J. F. A. van Vugt
- grid.418375.c0000 0001 1013 0288Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Lyam Baudry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris, 75015 France ,grid.462844.80000 0001 2308 1657Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Emma Persyn
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Jean-Marc Aury
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Benjamin Noel
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Anthony Bretaudeau
- grid.410368.80000 0001 2191 9284IGEPP, INRAE, Institut Agro, Univ Rennes, 35000 Rennes, France ,grid.420225.30000 0001 2298 7270Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France
| | - Fabrice Legeai
- grid.410368.80000 0001 2191 9284IGEPP, INRAE, Institut Agro, Univ Rennes, 35000 Rennes, France ,grid.420225.30000 0001 2298 7270Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France
| | - Sven Warris
- grid.4818.50000 0001 0791 5666Applied Bioinformatics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mohamed A. Chebbi
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Géraldine Dubreuil
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Bernard Duvic
- grid.503158.aUniversité Montpellier, INRAE, DGIMI, 34095 Montpellier, France
| | - Natacha Kremer
- grid.462854.90000 0004 0386 3493Laboratoire de Biométrie et Biologie Evolutive Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5558, 43 bd du 11 novembre 1918, bat. G. Mendel, 69622 Villeurbanne Cedex, France
| | - Philippe Gayral
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Karine Musset
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Thibaut Josse
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Diane Bigot
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Christophe Bressac
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Sébastien Moreau
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Georges Periquet
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Myriam Harry
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Nicolas Montagné
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Isabelle Boulogne
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Mahnaz Sabeti-Azad
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Martine Maïbèche
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Thomas Chertemps
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Frédérique Hilliou
- grid.435437.20000 0004 0385 8766Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia-Antipolis, France
| | - David Siaussat
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Joëlle Amselem
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Isabelle Luyten
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Claire Capdevielle-Dulac
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Karine Labadie
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Bruna Laís Merlin
- grid.11899.380000 0004 1937 0722Insect Interactions Laboratory, Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo 13418-900 Brazil
| | - Valérie Barbe
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Jetske G. de Boer
- grid.418375.c0000 0001 1013 0288Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Laboratory of Entomology, Wageningen University, P.O. Box 16, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands ,grid.4830.f0000 0004 0407 1981Evolutionary Genetics, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Martial Marbouty
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris, 75015 France
| | - Fernando Luis Cônsoli
- grid.11899.380000 0004 1937 0722Insect Interactions Laboratory, Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo 13418-900 Brazil
| | - Stéphane Dupas
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Aurélie Hua-Van
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Gaelle Le Goff
- grid.435437.20000 0004 0385 8766Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia-Antipolis, France
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Emmanuelle Jacquin-Joly
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - James B. Whitfield
- Department of Entomology, 320 Morrill Hall, 505 South Goodwin Avenue, University of Illinois, Urbana, IL 61801 USA
| | - Louise E. M. Vet
- grid.418375.c0000 0001 1013 0288Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Laboratory of Entomology, Wageningen University, P.O. Box 16, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Hans M. Smid
- grid.4818.50000 0001 0791 5666Laboratory of Entomology, Wageningen University, P.O. Box 16, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Laure Kaiser
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris, 75015 France
| | - Elisabeth Huguet
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Elisabeth A. Herniou
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| |
Collapse
|
40
|
A Brief Review of Current 3D Genomics Research. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11594-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
41
|
Cockram C, Thierry A, Gorlas A, Lestini R, Koszul R. Euryarchaeal genomes are folded into SMC-dependent loops and domains, but lack transcription-mediated compartmentalization. Mol Cell 2020; 81:459-472.e10. [PMID: 33382984 DOI: 10.1016/j.molcel.2020.12.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 10/01/2020] [Accepted: 12/07/2020] [Indexed: 12/26/2022]
Abstract
Hi-C has become a routine method for probing the 3D organization of genomes. However, when applied to prokaryotes and archaea, the current protocols are expensive and limited in their resolution. We develop a cost-effective Hi-C protocol to explore chromosome conformations of these two kingdoms at the gene or operon level. We first validate it on E. coli and V. cholera, generating sub-kilobase-resolution contact maps, and then apply it to the euryarchaeota H. volcanii, Hbt. salinarum, and T. kodakaraensis. With a resolution of up to 1 kb, we explore the diversity of chromosome folding in this phylum. In contrast to crenarchaeota, these euryarchaeota lack (active/inactive) compartment-like structures. Instead, their genomes are composed of self-interacting domains and chromatin loops. In H. volcanii, these structures are regulated by transcription and the archaeal structural maintenance of chromosomes (SMC) protein, further supporting the ubiquitous role of these processes in shaping the higher-order organization of genomes.
Collapse
Affiliation(s)
- Charlotte Cockram
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, 75015 Paris, France
| | - Agnès Thierry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, 75015 Paris, France
| | - Aurore Gorlas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Roxane Lestini
- Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS UMR7645 - INSERM U1182, IP Paris, 91128 Palaiseau Cedex, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, 75015 Paris, France.
| |
Collapse
|
42
|
Matthey-Doret C, Baudry L, Breuer A, Montagne R, Guiglielmoni N, Scolari V, Jean E, Campeas A, Chanut PH, Oriol E, Méot A, Politis L, Vigouroux A, Moreau P, Koszul R, Cournac A. Computer vision for pattern detection in chromosome contact maps. Nat Commun 2020; 11:5795. [PMID: 33199682 PMCID: PMC7670471 DOI: 10.1038/s41467-020-19562-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/16/2020] [Indexed: 02/08/2023] Open
Abstract
Chromosomes of all species studied so far display a variety of higher-order organisational features, such as self-interacting domains or loops. These structures, which are often associated to biological functions, form distinct, visible patterns on genome-wide contact maps generated by chromosome conformation capture approaches such as Hi-C. Here we present Chromosight, an algorithm inspired from computer vision that can detect patterns in contact maps. Chromosight has greater sensitivity than existing methods on synthetic simulated data, while being faster and applicable to any type of genomes, including bacteria, viruses, yeasts and mammals. Our method does not require any prior training dataset and works well with default parameters on data generated with various protocols. Chromatin loops bridging distant loci within chromosomes can be detected by a variety of techniques such as Hi-C. Here the authors present Chromosight, an algorithm applied on mammalian, bacterial, viral and yeast genomes, able to detect various types of pattern in chromosome contact maps, including chromosomal loops.
Collapse
Affiliation(s)
- Cyril Matthey-Doret
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756, Paris, France.,Sorbonne Université, Collège Doctoral, F-75005, Paris, France
| | - Lyam Baudry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756, Paris, France.,Sorbonne Université, Collège Doctoral, F-75005, Paris, France
| | - Axel Breuer
- ENGIE, Global Energy Management, Paris, France
| | - Rémi Montagne
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756, Paris, France
| | - Nadège Guiglielmoni
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756, Paris, France
| | - Vittore Scolari
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756, Paris, France
| | - Etienne Jean
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756, Paris, France
| | | | | | - Edgar Oriol
- ENGIE, Global Energy Management, Paris, France
| | - Adrien Méot
- ENGIE, Global Energy Management, Paris, France
| | | | | | - Pierrick Moreau
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756, Paris, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756, Paris, France.
| | - Axel Cournac
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756, Paris, France.
| |
Collapse
|
43
|
A Chromosome-Scale Genome Assembly for the Fusarium oxysporum Strain Fo5176 To Establish a Model Arabidopsis-Fungal Pathosystem. G3-GENES GENOMES GENETICS 2020; 10:3549-3555. [PMID: 32843521 PMCID: PMC7534451 DOI: 10.1534/g3.120.401375] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Plant pathogens cause widespread yield losses in agriculture. Understanding the drivers of plant-pathogen interactions requires decoding the molecular dialog leading to either resistance or disease. However, progress in deciphering pathogenicity genes has been severely hampered by suitable model systems and incomplete fungal genome assemblies. Here, we report a significant improvement of the assembly and annotation of the genome of the Fusarium oxysporum (Fo) strain Fo5176. Fo comprises a large number of serious plant pathogens on dozens of plant species with largely unresolved pathogenicity factors. The strain Fo5176 infects Arabidopsis thaliana and, hence, constitutes a highly promising model system. We use high-coverage Pacific Biosciences Sequel long-read and Hi-C sequencing data to assemble the genome into 19 chromosomes and a total genome size of 67.98 Mb. The genome has a N50 of 4 Mb and a 99.1% complete BUSCO score. Phylogenomic analyses based on single-copy orthologs clearly place the Fo5176 strain in the Fo f sp. conglutinans clade as expected. We generated RNAseq data from culture medium and plant infections to train gene predictions and identified ∼18,000 genes including ten effector genes known from other Fo clades. We show that Fo5176 is able to infect cabbage and Brussel sprouts of the Brassica oleracea, expanding the usefulness of the Fo5176 model pathosystem. Finally, we performed large-scale comparative genomics analyses comparing the Fo5176 to 103 additional Fo genomes to define core and accessory genomic regions. In conjunction with the molecular tool sets available for A. thaliana, the Fo5176 genome and annotation provides a crucial step toward the establishment of a highly promising pathosystem.
Collapse
|
44
|
Willis KA, Stewart JD, Ambalavanan N. Recent advances in understanding the ecology of the lung microbiota and deciphering the gut-lung axis. Am J Physiol Lung Cell Mol Physiol 2020. [PMID: 32877224 PMCID: PMC7642895 DOI: 10.1152/ajplung.00360.2020 10.1152/ajplung.00360.2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A rapidly expanding new field of lung research has been produced by the emergence of culture-independent next-generation sequencing technologies. While pulmonary microbiome research lags behind the exploration of the microbiome in other organ systems, the field is maturing and has recently produced multiple exciting discoveries. In this mini-review, we will explore recent advances in our understanding of the lung microbiome and the gut-lung axis from an ecological perspective.
Collapse
Affiliation(s)
- Kent A. Willis
- 1Division of Neonatology, Department of Pediatrics, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Justin D. Stewart
- 2Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Namasivayam Ambalavanan
- 1Division of Neonatology, Department of Pediatrics, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama,3Department of Pathology, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama,4Department of Cell, Developmental and Integrative Biology, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| |
Collapse
|
45
|
Willis KA, Stewart JD, Ambalavanan N. Recent advances in understanding the ecology of the lung microbiota and deciphering the gut-lung axis. Am J Physiol Lung Cell Mol Physiol 2020; 319:L710-L716. [PMID: 32877224 DOI: 10.1152/ajplung.00360.2020] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A rapidly expanding new field of lung research has been produced by the emergence of culture-independent next-generation sequencing technologies. While pulmonary microbiome research lags behind the exploration of the microbiome in other organ systems, the field is maturing and has recently produced multiple exciting discoveries. In this mini-review, we will explore recent advances in our understanding of the lung microbiome and the gut-lung axis from an ecological perspective.
Collapse
Affiliation(s)
- Kent A Willis
- Division of Neonatology, Department of Pediatrics, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Justin D Stewart
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Namasivayam Ambalavanan
- Division of Neonatology, Department of Pediatrics, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama.,Department of Pathology, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama.,Department of Cell, Developmental and Integrative Biology, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| |
Collapse
|
46
|
Wang B, Yu H, Jia Y, Dong Q, Steinberg C, Alabouvette C, Edel-Hermann V, Kistler HC, Ye K, Ma LJ, Guo L. Chromosome-Scale Genome Assembly of Fusarium oxysporum Strain Fo47, a Fungal Endophyte and Biocontrol Agent. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1108-1111. [PMID: 32552518 DOI: 10.1094/mpmi-05-20-0116-a] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Here, we report a chromosome-level genome assembly of Fusarium oxysporum Fo47 (12 pseudomolecules; contig N50: 4.52 Mb), generated using a combination of PacBio long-read, Illumina paired end, and high-throughput chromosome conformation capture sequencing data. Although F. oxysporum causes vascular wilt to over 100 plant species, the strain Fo47 is classified as an endophyte and is widely used as a biocontrol agent for plant disease control. The Fo47 genome carries a single accessory chromosome of 4.23 Mb, compared with the reference genome of F. oxysporum f. sp. lycopersici Fol4287. The high-quality assembly and annotation of the Fo47 genome will be a valuable resource for studying the mechanisms underlying the endophytic interactions between F. oxysporum and plants as well as for deciphering the genome evolution of the F. oxysporum species complex.
Collapse
Affiliation(s)
- Bo Wang
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Houlin Yu
- Graduate Program of Plant Biology, University of Massachusetts Amherst, Amherst, MA 01003, U.S.A
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, U.S.A
| | - Yanyan Jia
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Quanbin Dong
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049 China
| | - Christian Steinberg
- Agroécologie, AgroSup Dijon, INRA, University of Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Claude Alabouvette
- Agroécologie, AgroSup Dijon, INRA, University of Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Veronique Edel-Hermann
- Agroécologie, AgroSup Dijon, INRA, University of Bourgogne Franche-Comté, F-21000 Dijon, France
| | - H Corby Kistler
- USDA ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Kai Ye
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049 China
| | - Li-Jun Ma
- Graduate Program of Plant Biology, University of Massachusetts Amherst, Amherst, MA 01003, U.S.A
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, U.S.A
| | - Li Guo
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049 China
| |
Collapse
|
47
|
Saak CC, Dinh CB, Dutton RJ. Experimental approaches to tracking mobile genetic elements in microbial communities. FEMS Microbiol Rev 2020; 44:606-630. [PMID: 32672812 PMCID: PMC7476777 DOI: 10.1093/femsre/fuaa025] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
Horizontal gene transfer is an important mechanism of microbial evolution and is often driven by the movement of mobile genetic elements between cells. Due to the fact that microbes live within communities, various mechanisms of horizontal gene transfer and types of mobile elements can co-occur. However, the ways in which horizontal gene transfer impacts and is impacted by communities containing diverse mobile elements has been challenging to address. Thus, the field would benefit from incorporating community-level information and novel approaches alongside existing methods. Emerging technologies for tracking mobile elements and assigning them to host organisms provide promise for understanding the web of potential DNA transfers in diverse microbial communities more comprehensively. Compared to existing experimental approaches, chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts. We also briefly discuss how fermented food microbiomes, given their experimental tractability and moderate species complexity, make ideal models to which to apply the techniques discussed herein and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities.
Collapse
Affiliation(s)
- Christina C Saak
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Cong B Dinh
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Rachel J Dutton
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| |
Collapse
|
48
|
Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C. Nat Commun 2020; 11:4379. [PMID: 32873785 PMCID: PMC7463002 DOI: 10.1038/s41467-020-18164-7] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/06/2020] [Indexed: 01/13/2023] Open
Abstract
The gut microbiome harbors a ‘silent reservoir’ of antibiotic resistance (AR) genes that is thought to contribute to the emergence of multidrug-resistant pathogens through horizontal gene transfer (HGT). To counteract the spread of AR, it is paramount to know which organisms harbor mobile AR genes and which organisms engage in HGT. Despite methods that characterize the overall abundance of AR genes in the gut, technological limitations of short-read sequencing have precluded linking bacterial taxa to specific mobile genetic elements (MGEs) encoding AR genes. Here, we apply Hi-C, a high-throughput, culture-independent method, to surveil the bacterial carriage of MGEs. We compare two healthy individuals with seven neutropenic patients undergoing hematopoietic stem cell transplantation, who receive multiple courses of antibiotics, and are acutely vulnerable to the threat of multidrug-resistant infections. We find distinct networks of HGT across individuals, though AR and mobile genes are associated with more diverse taxa within the neutropenic patients than the healthy subjects. Our data further suggest that HGT occurs frequently over a several-week period in both cohorts. Whereas most efforts to understand the spread of AR genes have focused on pathogenic species, our findings shed light on the role of the human gut microbiome in this process. Linking antibiotic resistance (AR) in the gut microbiome with their bacterial hosts remains challenging. Here, the authors apply bacterial Hi-C to map mobile genetic elements in metagenomes, and illustrate that genes are present in more diverse taxa in neutropenic patients than healthy subjects.
Collapse
|
49
|
Brown CT, Moritz D, O'Brien MP, Reidl F, Reiter T, Sullivan BD. Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity. Genome Biol 2020; 21:164. [PMID: 32631445 PMCID: PMC7336657 DOI: 10.1186/s13059-020-02066-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 05/29/2020] [Indexed: 11/10/2022] Open
Abstract
Genomes computationally inferred from large metagenomic data sets are often incomplete and may be missing functionally important content and strain variation. We introduce an information retrieval system for large metagenomic data sets that exploits the sparsity of DNA assembly graphs to efficiently extract subgraphs surrounding an inferred genome. We apply this system to recover missing content from genome bins and show that substantial genomic sequence variation is present in a real metagenome. Our software implementation is available at https://github.com/spacegraphcats/spacegraphcats under the 3-Clause BSD License.
Collapse
Affiliation(s)
- C Titus Brown
- Department of Population Health and Reproduction, University of California Davis, Davis, USA.
| | - Dominik Moritz
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, USA
| | | | - Felix Reidl
- Department of Computer Science, NC State University, Raleigh, USA
| | - Taylor Reiter
- Department of Population Health and Reproduction, University of California Davis, Davis, USA
| | - Blair D Sullivan
- Department of Computer Science, NC State University, Raleigh, USA.
| |
Collapse
|
50
|
instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder. Genome Biol 2020; 21:148. [PMID: 32552806 PMCID: PMC7386250 DOI: 10.1186/s13059-020-02041-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 05/11/2020] [Indexed: 02/06/2023] Open
Abstract
Hi-C exploits contact frequencies between pairs of loci to bridge and order contigs during genome assembly, resulting in chromosome-level assemblies. Because few robust programs are available for this type of data, we developed instaGRAAL, a complete overhaul of the GRAAL program, which has adapted the latter to allow efficient assembly of large genomes. instaGRAAL features a number of improvements over GRAAL, including a modular correction approach that optionally integrates independent data. We validate the program using data for two brown algae, and human, to generate near-complete assemblies with minimal human intervention.
Collapse
|