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Goussarov G, Mysara M, Cleenwerck I, Claesen J, Leys N, Vandamme P, Van Houdt R. Benchmarking short-, long- and hybrid-read assemblers for metagenome sequencing of complex microbial communities. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001469. [PMID: 38916949 PMCID: PMC11261854 DOI: 10.1099/mic.0.001469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/23/2024] [Indexed: 06/26/2024]
Abstract
Metagenome community analyses, driven by the continued development in sequencing technology, is rapidly providing insights in many aspects of microbiology and becoming a cornerstone tool. Illumina, Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) are the leading technologies, each with their own advantages and drawbacks. Illumina provides accurate reads at a low cost, but their length is too short to close bacterial genomes. Long reads overcome this limitation, but these technologies produce reads with lower accuracy (ONT) or with lower throughput (PacBio high-fidelity reads). In a critical first analysis step, reads are assembled to reconstruct genomes or individual genes within the community. However, to date, the performance of existing assemblers has never been challenged with a complex mock metagenome. Here, we evaluate the performance of current assemblers that use short, long or both read types on a complex mock metagenome consisting of 227 bacterial strains with varying degrees of relatedness. We show that many of the current assemblers are not suited to handle such a complex metagenome. In addition, hybrid assemblies do not fulfil their potential. We conclude that ONT reads assembled with CANU and Illumina reads assembled with SPAdes offer the best value for reconstructing genomes and individual genes of complex metagenomes, respectively.
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Affiliation(s)
- Gleb Goussarov
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Mohamed Mysara
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Bioinformatics group, Information Technology & Computer Science, Nile University, Giza, Egypt
| | - Ilse Cleenwerck
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Jürgen Claesen
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Natalie Leys
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
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2
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Alexa EA, Cobo-Díaz JF, Renes E, O Callaghan TF, Kilcawley K, Mannion D, Skibinska I, Ruiz L, Margolles A, Fernández-Gómez P, Alvarez-Molina A, Puente-Gómez P, Crispie F, López M, Prieto M, Cotter PD, Alvarez-Ordóñez A. The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits. MICROBIOME 2024; 12:78. [PMID: 38678226 PMCID: PMC11055350 DOI: 10.1186/s40168-024-01790-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/08/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe a detailed longitudinal study assessing the impact of ripening in three natural caves on the microbiome and resistome succession across three different producers of Cabrales blue-veined cheese. RESULTS Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome. Lactococcus and the former Lactobacillus genus, among other taxa, showed high abundance in cheeses at initial stages of ripening, either coming from the raw material, starter culture used, and/or the environment of processing plants. Along cheese ripening in caves, these taxa were displaced by other bacteria, such as Tetragenococcus, Corynebacterium, Brevibacterium, Yaniella, and Staphylococcus, predominantly originating from cave environments (mainly food contact surfaces), as demonstrated by source-tracking analysis, strain analysis at read level, and the characterization of 613 metagenome-assembled genomes. The high abundance of Tetragenococcus koreensis and Tetragenococcus halophilus detected in cheese has not been found previously in cheese metagenomes. Furthermore, Tetragenococcus showed a high level of horizontal gene transfer with other members of the cheese microbiome, mainly with Lactococcus and Staphylococcus, involving genes related to carbohydrate metabolism functions. The resistome analysis revealed that raw milk and the associated processing environments are a rich reservoir of antimicrobial resistance determinants, mainly associated with resistance to aminoglycosides, tetracyclines, and β-lactam antibiotics and harbored by aerobic gram-negative bacteria of high relevance from a safety point of view, such as Escherichia coli, Salmonella enterica, Acinetobacter, and Klebsiella pneumoniae, and that the displacement of most raw milk-associated taxa by cave-associated taxa during ripening gave rise to a significant decrease in the load of ARGs and, therefore, to a safer end product. CONCLUSION Overall, the cave environments represented an important source of non-starter microorganisms which may play a relevant role in the quality and safety of the end products. Among them, we have identified novel taxa and taxa not previously regarded as being dominant components of the cheese microbiome (Tetragenococcus spp.), providing very valuable information for the authentication of this protected designation of origin artisanal cheese. Video Abstract.
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Affiliation(s)
- Elena A Alexa
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Erica Renes
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Tom F O Callaghan
- School of Food and Nutritional Sciences, University College Cork, Cork, T12 Y337, Ireland
| | | | - David Mannion
- Teagasc Food Research Centre, Fermoy, Co., Cork, Ireland
| | | | - Lorena Ruiz
- Dairy Research Institute, Spanish National Research Council, Instituto de Productos Lácteos de Asturias-CSIC, Villaviciosa, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011, Oviedo, Asturias, Spain
| | - Abelardo Margolles
- Dairy Research Institute, Spanish National Research Council, Instituto de Productos Lácteos de Asturias-CSIC, Villaviciosa, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011, Oviedo, Asturias, Spain
| | | | | | - Paula Puente-Gómez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Fiona Crispie
- Teagasc Food Research Centre, Fermoy, Co., Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Mercedes López
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Miguel Prieto
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Paul D Cotter
- Teagasc Food Research Centre, Fermoy, Co., Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- VistaMilk, Cork, Ireland
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain.
- Institute of Food Science and Technology, Universidad de León, León, Spain.
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3
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Lin A, Torres CM, Hobbs EC, Bardhan J, Aley SB, Spencer CT, Taylor KL, Chiang T. Computational and Systems Biology Advances to Enable Bioagent Agnostic Signatures. Health Secur 2024; 22:130-139. [PMID: 38483337 PMCID: PMC11044874 DOI: 10.1089/hs.2023.0076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Affiliation(s)
- Andy Lin
- Andy Lin, PhD, is a Linus Pauling Distinguished Postdoctoral Fellow; in the National Security Directorate, Pacific Northwest National Laboratory, Seattle, WA
| | - Cameron M. Torres
- Cameron M. Torres is a Graduate Research Assistant and Wieland Fellow, Department of Biological Sciences; at the University of Texas at El Paso, El Paso, TX
| | - Errett C. Hobbs
- Errett C. Hobbs, PhD, is a Data Scientist; in the National Security Directorate, Pacific Northwest National Laboratory, Seattle, WA
| | - Jaydeep Bardhan
- Jaydeep Bardhan, PhD, is a Research Line Manager, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA
| | - Stephen B. Aley
- Stephen B. Aley, PhD, is a Professor, Biological Sciences, and an Associate Vice President for Research, Sponsored Projects; at the University of Texas at El Paso, El Paso, TX
| | - Charles T. Spencer
- Charles T. Spencer, PhD, is an Associate Professor, Biological Sciences, and Edward and Barbara Brown Egbert Endowed Chair of the Department of Biological Sciences; at the University of Texas at El Paso, El Paso, TX
| | - Karen L. Taylor
- Karen L. Taylor, MS, is a Research Line Manager; in the National Security Directorate, Pacific Northwest National Laboratory, Seattle, WA
| | - Tony Chiang
- Tony Chiang, PhD, is a Data Scientist; in the National Security Directorate, Pacific Northwest National Laboratory, Seattle, WA
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4
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Lin A, Torres C, Hobbs EC, Bardhan J, Aley S, Spencer CT, Taylor KL, Chiang T. Computational and Systems Biology Advances to Enable Bioagent Agnostic Signatures. ARXIV 2024:arXiv:2310.13898v3. [PMID: 37961741 PMCID: PMC10635321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Enumerated threat agent lists have long driven biodefense priorities. The global SARS-CoV-2 pandemic demonstrated the limitations of searching for known threat agents as compared to a more agnostic approach. Recent technological advances are enabling agent-agnostic biodefense, especially through the integration of multi-modal observations of host-pathogen interactions directed by a human immunological model. Although well-developed technical assays exist for many aspects of human-pathogen interaction, the analytic methods and pipelines to combine and holistically interpret the results of such assays are immature and require further investments to exploit new technologies. In this manuscript, we discuss potential immunologically based bioagent-agnostic approaches and the computational tool gaps the community should prioritize filling.
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Affiliation(s)
- Andy Lin
- National Security Directorate, Pacific Northwest National Laboratory, Seattle, WA 98109, USA
| | - Cameron Torres
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas 79968 USA
| | - Errett C Hobbs
- National Security Directorate, Pacific Northwest National Laboratory, Seattle, WA 98109, USA
| | - Jaydeep Bardhan
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Seattle, WA 98109, USA
| | - Stephen Aley
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas 79968 USA
| | - Charles T Spencer
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas 79968 USA
| | - Karen L Taylor
- National Security Directorate, Pacific Northwest National Laboratory, Seattle, WA 98109, USA
| | - Tony Chiang
- National Security Directorate, Pacific Northwest National Laboratory, Seattle, WA 98109, USA
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas 79968 USA
- Department of Mathematics, University of Washington, Seattle 98102 USA
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5
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Djordjevic SP, Jarocki VM, Seemann T, Cummins ML, Watt AE, Drigo B, Wyrsch ER, Reid CJ, Donner E, Howden BP. Genomic surveillance for antimicrobial resistance - a One Health perspective. Nat Rev Genet 2024; 25:142-157. [PMID: 37749210 DOI: 10.1038/s41576-023-00649-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2023] [Indexed: 09/27/2023]
Abstract
Antimicrobial resistance (AMR) - the ability of microorganisms to adapt and survive under diverse chemical selection pressures - is influenced by complex interactions between humans, companion and food-producing animals, wildlife, insects and the environment. To understand and manage the threat posed to health (human, animal, plant and environmental) and security (food and water security and biosecurity), a multifaceted 'One Health' approach to AMR surveillance is required. Genomic technologies have enabled monitoring of the mobilization, persistence and abundance of AMR genes and mutations within and between microbial populations. Their adoption has also allowed source-tracing of AMR pathogens and modelling of AMR evolution and transmission. Here, we highlight recent advances in genomic AMR surveillance and the relative strengths of different technologies for AMR surveillance and research. We showcase recent insights derived from One Health genomic surveillance and consider the challenges to broader adoption both in developed and in lower- and middle-income countries.
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Affiliation(s)
- Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia.
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia.
| | - Veronica M Jarocki
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Torsten Seemann
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Max L Cummins
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Anne E Watt
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Barbara Drigo
- UniSA STEM, University of South Australia, Adelaide, South Australia, Australia
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - Ethan R Wyrsch
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Cameron J Reid
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
- Cooperative Research Centre for Solving Antimicrobial Resistance in Agribusiness, Food, and Environments (CRC SAAFE), Adelaide, South Australia, Australia
| | - Benjamin P Howden
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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6
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Cerk K, Ugalde‐Salas P, Nedjad CG, Lecomte M, Muller C, Sherman DJ, Hildebrand F, Labarthe S, Frioux C. Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing. Microb Biotechnol 2024; 17:e14396. [PMID: 38243750 PMCID: PMC10832553 DOI: 10.1111/1751-7915.14396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 11/27/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024] Open
Abstract
Building models is essential for understanding the functions and dynamics of microbial communities. Metabolic models built on genome-scale metabolic network reconstructions (GENREs) are especially relevant as a means to decipher the complex interactions occurring among species. Model reconstruction increasingly relies on metagenomics, which permits direct characterisation of naturally occurring communities that may contain organisms that cannot be isolated or cultured. In this review, we provide an overview of the field of metabolic modelling and its increasing reliance on and synergy with metagenomics and bioinformatics. We survey the means of assigning functions and reconstructing metabolic networks from (meta-)genomes, and present the variety and mathematical fundamentals of metabolic models that foster the understanding of microbial dynamics. We emphasise the characterisation of interactions and the scaling of model construction to large communities, two important bottlenecks in the applicability of these models. We give an overview of the current state of the art in metagenome sequencing and bioinformatics analysis, focusing on the reconstruction of genomes in microbial communities. Metagenomics benefits tremendously from third-generation sequencing, and we discuss the opportunities of long-read sequencing, strain-level characterisation and eukaryotic metagenomics. We aim at providing algorithmic and mathematical support, together with tool and application resources, that permit bridging the gap between metagenomics and metabolic modelling.
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Affiliation(s)
- Klara Cerk
- Quadram Institute BioscienceNorwichUK
- Earlham InstituteNorwichUK
| | | | - Chabname Ghassemi Nedjad
- Inria, University of Bordeaux, INRAETalenceFrance
- University of Bordeaux, CNRS, Bordeaux INP, LaBRI, UMR 5800TalenceFrance
| | - Maxime Lecomte
- Inria, University of Bordeaux, INRAETalenceFrance
- INRAE STLO¸University of RennesRennesFrance
| | | | | | - Falk Hildebrand
- Quadram Institute BioscienceNorwichUK
- Earlham InstituteNorwichUK
| | - Simon Labarthe
- Inria, University of Bordeaux, INRAETalenceFrance
- INRAE, University of Bordeaux, BIOGECO, UMR 1202CestasFrance
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7
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Kharnaior P, Tamang JP. Microbiome and metabolome in home-made fermented soybean foods of India revealed by metagenome-assembled genomes and metabolomics. Int J Food Microbiol 2023; 407:110417. [PMID: 37774634 DOI: 10.1016/j.ijfoodmicro.2023.110417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/10/2023] [Accepted: 09/22/2023] [Indexed: 10/01/2023]
Abstract
Grep-chhurpi, peha, peron namsing and peruñyaan are lesser-known home-made fermented soybean foods prepared by the native people of Arunachal Pradesh in India. Present work aims to study the microbiome, their functional annotations, metabolites and recovery of metagenome-assembled genomes (MAGs) in these four fermented soybean foods. Metagenomes revealed the dominance of bacteria (97.80 %) with minor traces of viruses, eukaryotes and archaea. Bacillota is the most abundant phylum with Bacillus subtilis as the abundant species. Metagenome also revealed the abundance of lactic acid bacteria such as Enterococcus casseliflavus, Enterococcus faecium, Mammaliicoccus sciuri and Staphylococcus saprophyticus in all samples. B. subtilis was the major species found in all products. Predictive metabolic pathways showed the abundance of genes associated with metabolisms. Metabolomics analysis revealed both targeted and untargeted metabolites, which suggested their role in flavour development and therapeutic properties. High-quality MAGs, identified as B. subtilis, Enterococcus faecalis, Pediococcus acidilactici and B. velezensis, showed the presence of several biomarkers corresponding to various bio-functional properties. Gene clusters of secondary metabolites (antimicrobial peptides) and CRISPR-Cas systems were detected in all MAGs. This present work also provides key elements related to the cultivability of identified species of MAGs for future use as starter cultures in fermented soybean food product development. Additionally, comparison of microbiome and metabolites of grep-chhurpi, peron namsing and peruñyaan with that of other fermented soybean foods of Asia revealed a distinct difference.
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Affiliation(s)
- Pynhunlang Kharnaior
- Department of Microbiology, Sikkim University, Science Building, Tadong 737102, Gangtok, Sikkim, India
| | - Jyoti Prakash Tamang
- Department of Microbiology, Sikkim University, Science Building, Tadong 737102, Gangtok, Sikkim, India.
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8
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Kang X, Xu J, Luo X, Schönhuth A. Hybrid-hybrid correction of errors in long reads with HERO. Genome Biol 2023; 24:275. [PMID: 38041098 PMCID: PMC10690975 DOI: 10.1186/s13059-023-03112-7] [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: 04/03/2023] [Accepted: 11/16/2023] [Indexed: 12/03/2023] Open
Abstract
Although generally superior, hybrid approaches for correcting errors in third-generation sequencing (TGS) reads, using next-generation sequencing (NGS) reads, mistake haplotype-specific variants for errors in polyploid and mixed samples. We suggest HERO, as the first "hybrid-hybrid" approach, to make use of both de Bruijn graphs and overlap graphs for optimal catering to the particular strengths of NGS and TGS reads. Extensive benchmarking experiments demonstrate that HERO improves indel and mismatch error rates by on average 65% (27[Formula: see text]95%) and 20% (4[Formula: see text]61%). Using HERO prior to genome assembly significantly improves the assemblies in the majority of the relevant categories.
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Affiliation(s)
- Xiongbin Kang
- College of Biology, Hunan University, Changsha, China
- Genome Data Science, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Jialu Xu
- College of Biology, Hunan University, Changsha, China
| | - Xiao Luo
- College of Biology, Hunan University, Changsha, China.
| | - Alexander Schönhuth
- Genome Data Science, Faculty of Technology, Bielefeld University, Bielefeld, Germany.
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9
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You L, Jin H, Kwok LY, Lv R, Zhao Z, Bilige M, Sun Z, Liu W, Zhang H. Intraspecific microdiversity and ecological drivers of lactic acid bacteria in naturally fermented milk ecosystem. Sci Bull (Beijing) 2023; 68:2405-2417. [PMID: 37718237 DOI: 10.1016/j.scib.2023.09.001] [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: 03/20/2023] [Revised: 05/31/2023] [Accepted: 08/31/2023] [Indexed: 09/19/2023]
Abstract
Traditional fermented milks are produced by inoculating technique, which selects well-adapted microorganisms that have been passed on through generations. Few reports have used naturally fermented milks as model ecosystems to investigate the mechanism of formation of intra-species microbial diversity. Here, we isolated and whole-genome-sequenced a total of 717 lactic acid bacterial isolates obtained from 12 independent naturally fermented milks collect from 12 regions across five countries. We further analyzed the within-sample intra-species phylogenies of 214 Lactobacillus helveticus isolates, 97 Lactococcus lactis subsp. lactis isolates, and 325 Lactobacillus delbrueckii subsp. bulgaricus isolates. We observed a high degree of intra-species genomic and functional gene diversity within-/between-sample(s). Single nucleotide polymorphism-based phylogenetic reconstruction revealed great within-sample intra-species heterogeneity, evolving from multiple lineages. Further phylogenetic reconstruction (presence-absence gene profile) revealed within-sample inter-clade functional diversity (based on carbohydrate-active enzyme- and peptidase-encoding genes) in all three investigated species/subspecies. By identifying and mapping clade-specific genes of intra-sample clades of the three species/subspecies to the respective fermented milk metagenome, we found extensive potential inter-/intra-species horizontal gene transfer events. Finally, the microbial composition of the samples is closely linked to the nucleotide diversity of the respective species/subspecies. Overall, our results contribute to the conservation of lactic acid bacteria resources, providing ecological insights into the microbial ecosystem of naturally fermented dairy products.
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Affiliation(s)
- Lijun You
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Hao Jin
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lai-Yu Kwok
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Ruirui Lv
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Zhixin Zhao
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Menghe Bilige
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Zhihong Sun
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Wenjun Liu
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China.
| | - Heping Zhang
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China.
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10
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Cai H, Zhou Y, Li X, Xu T, Ni Y, Wu S, Yu Y, Wang Y. Genomic Analysis and Taxonomic Characterization of Seven Bacteriophage Genomes Metagenomic-Assembled from the Dishui Lake. Viruses 2023; 15:2038. [PMID: 37896815 PMCID: PMC10611076 DOI: 10.3390/v15102038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Viruses in aquatic ecosystems exhibit remarkable abundance and diversity. However, scattered studies have been conducted to mine uncultured viruses and identify them taxonomically in lake water. Here, whole genomes (29-173 kbp) of seven uncultured dsDNA bacteriophages were discovered in Dishui Lake, the largest artificial lake in Shanghai. We analyzed their genomic signatures and found a series of viral auxiliary metabolic genes closely associated with protein synthesis and host metabolism. Dishui Lake phages shared more genes with uncultivated environmental viruses than with reference viruses based on the gene-sharing network classification. Phylogeny of proteomes and comparative genomics delineated three new genera within two known viral families of Kyanoviridae and Autographiviridae, and four new families in Caudoviricetes for these seven novel phages. Their potential hosts appeared to be from the dominant bacterial phyla in Dishui Lake. Altogether, our study provides initial insights into the composition and diversity of bacteriophage communities in Dishui Lake, contributing valuable knowledge to the ongoing research on the roles played by viruses in freshwater ecosystems.
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Affiliation(s)
- Haoyun Cai
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yifan Zhou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Xiefei Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Tianqi Xu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yimin Ni
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Shuang Wu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yongxin Yu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture and Rural Affairs, Shanghai 201306, China
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11
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Sessitsch A, Wakelin S, Schloter M, Maguin E, Cernava T, Champomier-Verges MC, Charles TC, Cotter PD, Ferrocino I, Kriaa A, Lebre P, Cowan D, Lange L, Kiran S, Markiewicz L, Meisner A, Olivares M, Sarand I, Schelkle B, Selvin J, Smidt H, van Overbeek L, Berg G, Cocolin L, Sanz Y, Fernandes WL, Liu SJ, Ryan M, Singh B, Kostic T. Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet. Microbiol Mol Biol Rev 2023; 87:e0021222. [PMID: 37367231 PMCID: PMC10521359 DOI: 10.1128/mmbr.00212-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.
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Affiliation(s)
| | | | | | - Emmanuelle Maguin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Tomislav Cernava
- University of Southampton, Faculty of Environmental and Life Sciences, Southampton, United Kingdom
| | | | | | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland and VistaMilk, Cork, Ireland
| | | | - Aicha Kriaa
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pedro Lebre
- University of Pretoria, Pretoria, South Africa
| | - Don Cowan
- University of Pretoria, Pretoria, South Africa
| | - Lene Lange
- LL-BioEconomy, Valby, Copenhagen, Denmark
| | | | - Lidia Markiewicz
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Department of Immunology and Food Microbiology, Olsztyn, Poland
| | - Annelein Meisner
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | - Marta Olivares
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Inga Sarand
- Tallinn University of Technology, Department of Chemistry and Biotechnology, Tallinn, Estonia
| | | | | | - Hauke Smidt
- Wageningen University and Research, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Leo van Overbeek
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | | | | | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | | | - S. J. Liu
- Chinese Academy of Sciences, Institute of Microbiology, Beijing, China
| | - Matthew Ryan
- Genetic Resources Collection, CABI, Egham, United Kingdom
| | - Brajesh Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Tanja Kostic
- AIT Austrian Institute of Technology GmbH, Tulln, Austria
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12
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Zhang ZF, Liu LR, Pan YP, Pan J, Li M. Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments. MICROBIOME 2023; 11:188. [PMID: 37612768 PMCID: PMC10464287 DOI: 10.1186/s40168-023-01630-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/21/2023] [Indexed: 08/25/2023]
Abstract
BACKGROUND Mangrove wetlands are coastal ecosystems with important ecological features and provide habitats for diverse microorganisms with key roles in nutrient and biogeochemical cycling. However, the overall metabolic potentials and ecological roles of microbial community in mangrove sediment are remained unanswered. In current study, the microbial and metabolic profiles of prokaryotic and fungal communities in mangrove sediments were investigated using metagenomic analysis based on PacBio single-molecule real time (SMRT) and Illumina sequencing techniques. RESULTS Comparing to Illumina short reads, the incorporation of PacBio long reads significantly contributed to more contiguous assemblies, yielded more than doubled high-quality metagenome-assembled genomes (MAGs), and improved the novelty of the MAGs. Further metabolic reconstruction for recovered MAGs showed that prokaryotes potentially played an essential role in carbon cycling in mangrove sediment, displaying versatile metabolic potential for degrading organic carbons, fermentation, autotrophy, and carbon fixation. Mangrove fungi also functioned as a player in carbon cycling, potentially involved in the degradation of various carbohydrate and peptide substrates. Notably, a new candidate bacterial phylum named as Candidatus Cosmopoliota with a ubiquitous distribution is proposed. Genomic analysis revealed that this new phylum is capable of utilizing various types of organic substrates, anaerobic fermentation, and carbon fixation with the Wood-Ljungdahl (WL) pathway and the reverse tricarboxylic acid (rTCA) cycle. CONCLUSIONS The study not only highlights the advantages of HiSeq-PacBio Hybrid assembly for a more complete profiling of environmental microbiomes but also expands our understanding of the microbial diversity and potential roles of distinct microbial groups in biogeochemical cycling in mangrove sediment. Video Abstract.
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Affiliation(s)
- Zhi-Feng Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Present Address: Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Li-Rui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yue-Ping Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
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13
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Spealman P, De T, Chuong JN, Gresham D. Best Practices in Microbial Experimental Evolution: Using Reporters and Long-Read Sequencing to Identify Copy Number Variation in Experimental Evolution. J Mol Evol 2023; 91:356-368. [PMID: 37012421 PMCID: PMC10275804 DOI: 10.1007/s00239-023-10102-7] [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: 09/28/2022] [Accepted: 02/21/2023] [Indexed: 04/05/2023]
Abstract
Copy number variants (CNVs), comprising gene amplifications and deletions, are a pervasive class of heritable variation. CNVs play a key role in rapid adaptation in both natural, and experimental, evolution. However, despite the advent of new DNA sequencing technologies, detection and quantification of CNVs in heterogeneous populations has remained challenging. Here, we summarize recent advances in the use of CNV reporters that provide a facile means of quantifying de novo CNVs at a specific locus in the genome, and nanopore sequencing, for resolving the often complex structures of CNVs. We provide guidance for the engineering and analysis of CNV reporters and practical guidelines for single-cell analysis of CNVs using flow cytometry. We summarize recent advances in nanopore sequencing, discuss the utility of this technology, and provide guidance for the bioinformatic analysis of these data to define the molecular structure of CNVs. The combination of reporter systems for tracking and isolating CNV lineages and long-read DNA sequencing for characterizing CNV structures enables unprecedented resolution of the mechanisms by which CNVs are generated and their evolutionary dynamics.
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Affiliation(s)
- Pieter Spealman
- Department of Biology, New York University, New York, NY, 10003, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Titir De
- Department of Biology, New York University, New York, NY, 10003, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Julie N Chuong
- Department of Biology, New York University, New York, NY, 10003, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - David Gresham
- Department of Biology, New York University, New York, NY, 10003, USA.
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA.
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14
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Jolicoeur AP, Lemay ML, Beaubien E, Bélanger J, Bergeron C, Bourque-Leblanc F, Doré L, Dupuis MÈ, Fleury A, Garneau JE, Labrie SJ, Labrie S, Lacasse G, Lamontagne-Drolet M, Lessard-Hurtubise R, Martel B, Menasria R, Morin-Pelchat R, Pageau G, Samson JE, Rousseau GM, Tremblay DM, Duquenne M, Lamoureux M, Moineau S. Longitudinal Study of Lactococcus Phages in a Canadian Cheese Factory. Appl Environ Microbiol 2023; 89:e0042123. [PMID: 37074184 PMCID: PMC10231144 DOI: 10.1128/aem.00421-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 04/20/2023] Open
Abstract
The presence of virulent phages is closely monitored during cheese manufacturing, as these bacterial viruses can significantly slow down the milk fermentation process and lead to low-quality cheeses. From 2001 to 2020, whey samples from cheddar cheese production in a Canadian factory were monitored for the presence of virulent phages capable of infecting proprietary strains of Lactococcus cremoris and Lactococcus lactis used in starter cultures. Phages were successfully isolated from 932 whey samples using standard plaque assays and several industrial Lactococcus strains as hosts. A multiplex PCR assay assigned 97% of these phage isolates to the Skunavirus genus, 2% to the P335 group, and 1% to the Ceduovirus genus. DNA restriction profiles and a multilocus sequence typing (MLST) scheme distinguished at least 241 unique lactococcal phages from these isolates. While most phages were isolated only once, 93 of them (out of 241, 39%) were isolated multiple times. Phage GL7 was isolated 132 times from 2006 to 2020, demonstrating that phages can persist in a cheese factory for long periods of time. Phylogenetic analysis of MLST sequences showed that phages could be clustered based on their bacterial hosts rather than their year of isolation. Host range analysis showed that Skunavirus phages exhibited a very narrow host range, whereas some Ceduovirus and P335 phages had a broader host range. Overall, the host range information was useful in improving the starter culture rotation by identifying phage-unrelated strains and helped mitigating the risk of fermentation failure due to virulent phages. IMPORTANCE Although lactococcal phages have been observed in cheese production settings for almost a century, few longitudinal studies have been performed. This 20-year study describes the close monitoring of dairy lactococcal phages in a cheddar cheese factory. Routine monitoring was conducted by factory staff, and when whey samples were found to inhibit industrial starter cultures under laboratory conditions, they were sent to an academic research laboratory for phage isolation and characterization. This led to a collection of at least 241 unique lactococcal phages, which were characterized through PCR typing and MLST profiling. Phages of the Skunavirus genus were by far the most dominant. Most phages lysed a small subset of the Lactococcus strains. These findings guided the industrial partner in adapting the starter culture schedule by using phage-unrelated strains in starter cultures and removing some strains from the starter rotation. This phage control strategy could be adapted for other large-scale bacterial fermentation processes.
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Affiliation(s)
- Alice P. Jolicoeur
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Marie-Laurence Lemay
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
- Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Université de Montréal, Montréal, Québec, Canada
| | - Elyse Beaubien
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Jessy Bélanger
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Claudia Bergeron
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Françoise Bourque-Leblanc
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Laurie Doré
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Marie-Ève Dupuis
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Audrey Fleury
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Josiane E. Garneau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Simon J. Labrie
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Steve Labrie
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Geneviève Lacasse
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Marianne Lamontagne-Drolet
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Roxanne Lessard-Hurtubise
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Bruno Martel
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Rym Menasria
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Rachel Morin-Pelchat
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Gabrielle Pageau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Julie E. Samson
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Geneviève M. Rousseau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Denise M. Tremblay
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
- Félix d’Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Québec, Canada
| | | | | | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
- Félix d’Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Québec, Canada
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15
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Zhao J, Zhang M, Hui W, Zhang Y, Wang J, Wang S, Kwok LY, Kong J, Zhang H, Zhang W. Roles of adenine methylation in the physiology of Lacticaseibacillus paracasei. Nat Commun 2023; 14:2635. [PMID: 37149616 PMCID: PMC10164179 DOI: 10.1038/s41467-023-38291-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 04/21/2023] [Indexed: 05/08/2023] Open
Abstract
Lacticaseibacillus paracasei is an economically important bacterial species, used in the food industry and as a probiotic. Here, we investigate the roles of N6-methyladenine (6mA) modification in L. paracasei using multi-omics and high-throughput chromosome conformation capture (Hi-C) analyses. The distribution of 6mA-modified sites varies across the genomes of 28 strains, and appears to be enriched near genes involved in carbohydrate metabolism. A pglX mutant, defective in 6mA modification, shows transcriptomic alterations but only modest changes in growth and genomic spatial organization.
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Affiliation(s)
- Jie Zhao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Meng Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Wenyan Hui
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yue Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Jing Wang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Shaojing Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Jian Kong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Wenyi Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China.
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China.
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China.
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16
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Chen TH, Cheng CY, Huang CK, Ho YH, Lin JC. Exploring the Relevance between Gut Microbiota-Metabolites Profile and Chronic Kidney Disease with Distinct Pathogenic Factor. Microbiol Spectr 2023; 11:e0280522. [PMID: 36475922 PMCID: PMC9927243 DOI: 10.1128/spectrum.02805-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
The intimate correlation of chronic kidney disease (CKD) with structural alteration in gut microbiota or metabolite profile has been documented in a growing body of studies. Nevertheless, a paucity of demonstrated knowledge regarding the impact and underlying mechanism of gut microbiota or metabolite on occurrence or progression of CKD is unclarified thus far. In this study, a liquid chromatography coupled-mass spectrometry and long-read sequencing were applied to identify gut metabolites and microbiome with statistically-discriminative abundance in diabetic CKD patients (n = 39), hypertensive CKD patients (n = 26), or CKD patients without comorbidity (n = 40) compared to those of healthy participants (n = 60). The association between CKD-related species and metabolite was evaluated by using zero-inflated negative binomial (ZINB) regression. The predictive utility of identified operational taxonomic units (OTUs), metabolite, or species-metabolite association toward the diagnosis of incident chronic kidney disease with distinct pathogenic factor was assessed using the random forest regression model and the receiver operating characteristic (ROC) curve. The results of statistical analyses indicated alterations in the relative abundances of 26 OTUs and 41 metabolites that were specifically relevant to each CKD-patient group. The random forest regression model with only species, metabolites, or its association differentially distinguished the hypertensive, diabetic CKD patients, or enrolled CKD patients without comorbidity from the healthy participants. IMPORTANCE Gut dysbiosis-altered metabolite association exhibits specific and convincing utility to differentiate CKD associated with distinct pathogenic factor. These results present the validity of pathogenesis-associated markers across healthy participants and high-risk population toward the early screening, prevention, diagnosis, or personalized treatment of CKD.
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Affiliation(s)
- Tso-Hsiao Chen
- Division of Nephrology, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
- Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Taipei Medical University-Research Center of Urology and Kidney (RCUK), School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chung-Yi Cheng
- Division of Nephrology, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
- Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Taipei Medical University-Research Center of Urology and Kidney (RCUK), School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chun-Kai Huang
- Department of Laboratory Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Yi-Hsien Ho
- Department of Laboratory Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Jung-Chun Lin
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Pulmonary Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
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17
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Arumugam K, Bessarab I, Haryono MAS, Williams RBH. Recovery and Analysis of Long-Read Metagenome-Assembled Genomes. Methods Mol Biol 2023; 2649:235-259. [PMID: 37258866 DOI: 10.1007/978-1-0716-3072-3_12] [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: 06/02/2023]
Abstract
The development of long-read nucleic acid sequencing is beginning to make very substantive impact on the conduct of metagenome analysis, particularly in relation to the problem of recovering the genomes of member species of complex microbial communities. Here we outline bioinformatics workflows for the recovery and characterization of complete genomes from long-read metagenome data and some complementary procedures for comparison of cognate draft genomes and gene quality obtained from short-read sequencing and long-read sequencing.
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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
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore.
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18
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Long-Read Sequencing Improves Recovery of Picoeukaryotic Genomes and Zooplankton Marker Genes from Marine Metagenomes. mSystems 2022; 7:e0059522. [PMID: 36448813 PMCID: PMC9765425 DOI: 10.1128/msystems.00595-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Long-read sequencing offers the potential to improve metagenome assemblies and provide more robust assessments of microbial community composition and function than short-read sequencing. We applied Pacific Biosciences (PacBio) CCS (circular consensus sequencing) HiFi shotgun sequencing to 14 marine water column samples and compared the results with those for short-read metagenomes from the corresponding environmental DNA samples. We found that long-read metagenomes varied widely in quality and biological information. The community compositions of the corresponding long- and short-read metagenomes were frequently dissimilar, suggesting higher stochasticity and/or bias associated with PacBio sequencing. Long reads provided few improvements to the assembly qualities, gene annotations, and prokaryotic metagenome-assembled genome (MAG) binning results. However, only long reads produced high-quality eukaryotic MAGs and contigs containing complete zooplankton marker gene sequences. These results suggest that high-quality long-read metagenomes can improve marine community composition analyses and provide important insight into eukaryotic phyto- and zooplankton genetics, but the benefits may be outweighed by the inconsistent data quality. IMPORTANCE Ocean microbes provide critical ecosystem services, but most remain uncultivated. Their communities can be studied through shotgun metagenomic sequencing and bioinformatic analyses, including binning draft microbial genomes. However, most sequencing to date has been done using short-read technology, which rarely yields genome sequences of key microbes like SAR11. Long-read sequencing can improve metagenome assemblies but is hampered by technological shortcomings and high costs. In this study, we compared long- and short-read sequencing of marine metagenomes. We found a wide range of long-read metagenome qualities and minimal improvements to microbiome analyses. However, long reads generated draft genomes of eukaryotic algal species and provided full-length marker gene sequences of zooplankton species, including krill and copepods. These results suggest that long-read sequencing can provide greater genetic insight into the wide diversity of eukaryotic phyto- and zooplankton that interact as part of and with the marine microbiome.
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19
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Bassi C, Guerriero P, Pierantoni M, Callegari E, Sabbioni S. Novel Virus Identification through Metagenomics: A Systematic Review. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122048. [PMID: 36556413 PMCID: PMC9784588 DOI: 10.3390/life12122048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.
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Affiliation(s)
- Cristian Bassi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Paola Guerriero
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Marina Pierantoni
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Elisa Callegari
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Silvia Sabbioni
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Correspondence: ; Tel.: +39-053-245-5319
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20
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Cheng H, Sun Y, Yang Q, Deng M, Yu Z, Zhu G, Qu J, Liu L, Yang L, Xia Y. A rapid bacterial pathogen and antimicrobial resistance diagnosis workflow using Oxford nanopore adaptive sequencing method. Brief Bioinform 2022; 23:6762743. [PMID: 36259361 DOI: 10.1093/bib/bbac453] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/16/2022] [Accepted: 09/22/2022] [Indexed: 12/14/2022] Open
Abstract
Metagenomic sequencing analysis (mNGS) has been implemented as an alternative approach for pathogen diagnosis in recent years, which is independent of cultivation and is able to identify all potential antibiotic resistance genes (ARGs). However, current mNGS methods have to deal with low amounts of prokaryotic deoxyribonucleic acid (DNA) and high amounts of host DNA in clinical samples, which significantly decrease the overall microbial detection resolution. The recently released nanopore adaptive sampling (NAS) technology facilitates immediate mapping of individual nucleotides to a given reference as each molecule is sequenced. User-defined thresholds allow for the retention or rejection of specific molecules, informed by the real-time reference mapping results, as they are physically passing through a given sequencing nanopore. We developed a metagenomics workflow for ultra-sensitive diagnosis of bacterial pathogens and ARGs from clinical samples, which is based on the efficient selective 'human host depletion' NAS sequencing, real-time species identification and species-specific resistance gene prediction. Our method increased the microbial sequence yield at least 8-fold in all 21 sequenced clinical Bronchoalveolar Lavage Fluid (BALF) samples (4.5 h from sample to result) and accurately detected the ARGs at species level. The species-level positive percent agreement between metagenomic sequencing and laboratory culturing was 100% (16/16) and negative percent agreement was 100% (5/5) in our approach. Further work is required for a more robust validation of our approach with large sample size to allow its application to other infection types.
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Affiliation(s)
- Hang Cheng
- School of Medicine, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Yuhong Sun
- School of Environmental Science & Engineering, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Qing Yang
- School of Environmental Science & Engineering, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Minggui Deng
- Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518055, China
| | - Zhijian Yu
- Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518055, China
| | - Gang Zhu
- Third People's Hospital of Shenzhen, the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiuxin Qu
- Third People's Hospital of Shenzhen, the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518055, China
| | - Lei Liu
- Third People's Hospital of Shenzhen, the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518055, China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Yu Xia
- School of Environmental Science & Engineering, Southern University of Science and Technology of China, Shenzhen 518055, China
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21
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VeChat: correcting errors in long reads using variation graphs. Nat Commun 2022; 13:6657. [PMID: 36333324 PMCID: PMC9636371 DOI: 10.1038/s41467-022-34381-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Error correction is the canonical first step in long-read sequencing data analysis. Current self-correction methods, however, are affected by consensus sequence induced biases that mask true variants in haplotypes of lower frequency showing in mixed samples. Unlike consensus sequence templates, graph-based reference systems are not affected by such biases, so do not mistakenly mask true variants as errors. We present VeChat, as an approach to implement this idea: VeChat is based on variation graphs, as a popular type of data structure for pangenome reference systems. Extensive benchmarking experiments demonstrate that long reads corrected by VeChat contain 4 to 15 (Pacific Biosciences) and 1 to 10 times (Oxford Nanopore Technologies) less errors than when being corrected by state of the art approaches. Further, using VeChat prior to long-read assembly significantly improves the haplotype awareness of the assemblies. VeChat is an easy-to-use open-source tool and publicly available at https://github.com/HaploKit/vechat .
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22
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Sola L, Quadu E, Bortolazzo E, Bertoldi L, Randazzo CL, Pizzamiglio V, Solieri L. Insights on the bacterial composition of Parmigiano Reggiano Natural Whey Starter by a culture-dependent and 16S rRNA metabarcoding portrait. Sci Rep 2022; 12:17322. [PMID: 36243881 PMCID: PMC9569347 DOI: 10.1038/s41598-022-22207-y] [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: 07/19/2022] [Accepted: 10/11/2022] [Indexed: 01/10/2023] Open
Abstract
Natural whey starters (NWS) are undefined bacterial communities produced daily from whey of the previous cheese-making round, by application of high temperature. As a result, in any dairy plant, NWS are continuously evolving, undefined mixtures of several strains and/or species of lactic acid bacteria, whose composition and performance strongly depend on the selective pressure acting during incubation. While NWS is critical to assure consistency to cheese-making process, little is known about the composition, functional features, and plant-to-plant fluctuations. Here, we integrated 16S rRNA metabarcoding and culture-dependent methods to profile bacterial communities of 10 NWS sampled in the production area of Parmigiano Reggiano cheese. 16S rRNA metabarcoding analysis revealed two main NWS community types, namely NWS type-H and NWS type-D. Lactobacillus helveticus was more abundant in NWS type-H, whilst Lactobacillus delbrueckii/St. thermophilus in NWS type-D, respectively. Based on the prediction of metagenome functions, NWS type-H samples were enriched in functional pathways related to galactose catabolism and purine metabolism, while NWS type-D in pathways related to aromatic and branched chain amino acid biosynthesis, which are flavor compound precursors. Culture-dependent approaches revealed low cultivability of individual colonies as axenic cultures and high genetic diversity in the pool of cultivable survivors. Co-culturing experiments showed that fermentative performance decreases by reducing the bacterial complexity of inoculum, suggesting that biotic interactions and cross-feeding relationships could take place in NWS communities, assuring phenotypic robustness. Even though our data cannot directly predict these ecological interactions, this study provides the basis for experiments targeted at understanding how selective regime affects composition, bacterial interaction, and fermentative performance in NWS.
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Affiliation(s)
- Laura Sola
- grid.7548.e0000000121697570Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy
| | - Emanuele Quadu
- grid.7548.e0000000121697570Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy
| | - Elena Bortolazzo
- grid.423913.eCentro Ricerche Produzioni Animali, 42121 Reggio Emilia, Italy
| | | | - Cinzia L. Randazzo
- grid.8158.40000 0004 1757 1969Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy ,ProBioEtna Srl, 95123 Catania, Italy
| | - Valentina Pizzamiglio
- grid.433295.aConsorzio del Formaggio Parmigiano Reggiano, 42124 Reggio Emilia, Italy
| | - Lisa Solieri
- grid.7548.e0000000121697570Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy ,NBFC, National Biodiversity Future Center, 90133 Palermo, Italy
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23
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Somerville V, Schowing T, Chabas H, Schmidt RS, von Ah U, Bruggmann R, Engel P. Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities. MICROBIOME 2022; 10:137. [PMID: 36028909 PMCID: PMC9419375 DOI: 10.1186/s40168-022-01328-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/17/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2778 bacterial genomes and 188 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments. RESULTS We corroborate previous laboratory findings that in cheese-associated communities nearly identical strains contain diverse and highly variable arsenals of innate and adaptive (i.e., CRISPR-Cas) immunity systems suggesting rapid turnover. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, providing evidence that CRISPR does not enable complete immunity against all phages, and that the innate immune mechanisms may have complementary roles. CONCLUSIONS Our findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships. These findings can have implications for the design of robust synthetic communities used in biotechnology and the food industry. Video Abstract.
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Affiliation(s)
- Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
- Agroscope, Bern, Switzerland.
| | - Thibault Schowing
- Agroscope, Bern, Switzerland
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Hélène Chabas
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
| | | | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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24
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Escudeiro P, Henry CS, Dias RP. Functional characterization of prokaryotic dark matter: the road so far and what lies ahead. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100159. [PMID: 36561390 PMCID: PMC9764257 DOI: 10.1016/j.crmicr.2022.100159] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/18/2022] [Accepted: 08/05/2022] [Indexed: 12/25/2022] Open
Abstract
Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer than two-hundred thousand prokaryotic species have been described. This uncharted fraction of microbial diversity, and its undisclosed coding potential, is known as the "microbial dark matter" (MDM). Next-generation sequencing has allowed to collect a massive amount of genome sequence data, leading to unprecedented advances in the field of genomics. Still, harnessing new functional information from the genomes of uncultured prokaryotes is often limited by standard classification methods. These methods often rely on sequence similarity searches against reference genomes from cultured species. This hinders the discovery of unique genetic elements that are missing from the cultivated realm. It also contributes to the accumulation of prokaryotic gene products of unknown function among public sequence data repositories, highlighting the need for new approaches for sequencing data analysis and classification. Increasing evidence indicates that these proteins of unknown function might be a treasure trove of biotechnological potential. Here, we outline the challenges, opportunities, and the potential hidden within the functional dark matter (FDM) of prokaryotes. We also discuss the pitfalls surrounding molecular and computational approaches currently used to probe these uncharted waters, and discuss future opportunities for research and applications.
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Affiliation(s)
- Pedro Escudeiro
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
| | - Christopher S. Henry
- Argonne National Laboratory, Lemont, Illinois, USA,University of Chicago, Chicago, Illinois, USA
| | - Ricardo P.M. Dias
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal,iXLab - Innovation for National Biological Resilience, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal,Corresponding author.
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25
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Kang X, Luo X, Schönhuth A. StrainXpress: strain aware metagenome assembly from short reads. Nucleic Acids Res 2022; 50:e101. [PMID: 35776122 PMCID: PMC9508831 DOI: 10.1093/nar/gkac543] [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: 09/20/2021] [Revised: 05/27/2022] [Accepted: 06/30/2022] [Indexed: 12/05/2022] Open
Abstract
Next-generation sequencing–based metagenomics has enabled to identify microorganisms in characteristic habitats without the need for lengthy cultivation. Importantly, clinically relevant phenomena such as resistance to medication, virulence or interactions with the environment can vary already within species. Therefore, a major current challenge is to reconstruct individual genomes from the sequencing reads at the level of strains, and not just the level of species. However, strains of one species can differ only by minor amounts of variants, which makes it difficult to distinguish them. Despite considerable recent progress, related approaches have remained fragmentary so far. Here, we present StrainXpress, as a comprehensive solution to the problem of strain aware metagenome assembly from next-generation sequencing reads. In experiments, StrainXpress reconstructs strain-specific genomes from metagenomes that involve up to >1000 strains and proves to successfully deal with poorly covered strains. The amount of reconstructed strain-specific sequence exceeds that of the current state-of-the-art approaches by on average 26.75% across all data sets (first quartile: 18.51%, median: 26.60%, third quartile: 35.05%).
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Affiliation(s)
- Xiongbin Kang
- Genome Data Science, Faculty of Technology, Bielefeld University, Bielefeld, 33615, Germany
| | - Xiao Luo
- Genome Data Science, Faculty of Technology, Bielefeld University, Bielefeld, 33615, Germany
| | - Alexander Schönhuth
- Genome Data Science, Faculty of Technology, Bielefeld University, Bielefeld, 33615, Germany
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26
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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]
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27
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Ferrocino I, Rantsiou K, Cocolin L. Microbiome and -omics application in food industry. Int J Food Microbiol 2022; 377:109781. [DOI: 10.1016/j.ijfoodmicro.2022.109781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 11/30/2022]
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28
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Schultz J, Argentino ICV, Kallies R, Nunes da Rocha U, Rosado AS. Polyphasic Analysis Reveals Potential Petroleum Hydrocarbon Degradation and Biosurfactant Production by Rare Biosphere Thermophilic Bacteria From Deception Island, an Active Antarctic Volcano. Front Microbiol 2022; 13:885557. [PMID: 35602031 PMCID: PMC9114708 DOI: 10.3389/fmicb.2022.885557] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/14/2022] [Indexed: 01/19/2023] Open
Abstract
Extreme temperature gradients in polar volcanoes are capable of selecting different types of extremophiles. Deception Island is a marine stratovolcano located in maritime Antarctica. The volcano has pronounced temperature gradients over very short distances, from as high as 100°C in the fumaroles to subzero next to the glaciers. These characteristics make Deception a promising source of a variety of bioproducts for use in different biotechnological areas. In this study, we isolated thermophilic bacteria from sediments in fumaroles at two geothermal sites on Deception Island with temperatures between 50 and 100°C, to evaluate the potential capacity of these bacteria to degrade petroleum hydrocarbons and produce biosurfactants under thermophilic conditions. We isolated 126 thermophilic bacterial strains and identified them molecularly as members of genera Geobacillus, Anoxybacillus, and Brevibacillus (all in phylum Firmicutes). Seventy-six strains grew in a culture medium supplemented with crude oil as the only carbon source, and 30 of them showed particularly good results for oil degradation. Of 50 strains tested for biosurfactant production, 13 showed good results, with an emulsification index of 50% or higher of a petroleum hydrocarbon source (crude oil and diesel), emulsification stability at 100°C, and positive results in drop-collapse, oil spreading, and hemolytic activity tests. Four of these isolates showed great capability of degrade crude oil: FB2_38 (Geobacillus), FB3_54 (Geobacillus), FB4_88 (Anoxybacillus), and WB1_122 (Geobacillus). Genomic analysis of the oil-degrading and biosurfactant-producer strain FB4_88 identified it as Anoxybacillus flavithermus, with a high genetic and functional diversity potential for biotechnological applications. These initial culturomic and genomic data suggest that thermophilic bacteria from this Antarctic volcano have potential applications in the petroleum industry, for bioremediation in extreme environments and for microbial enhanced oil recovery (MEOR) in reservoirs. In addition, recovery of small-subunit rRNA from metagenomes of Deception Island showed that Firmicutes is not among the dominant phyla, indicating that these low-abundance microorganisms may be important for hydrocarbon degradation and biosurfactant production in the Deception Island volcanic sediments.
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Affiliation(s)
- Júnia Schultz
- Microbial Ecogenomics and Biotechnology Laboratory, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - René Kallies
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Alexandre Soares Rosado
- Microbial Ecogenomics and Biotechnology Laboratory, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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29
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Wang C, Wang L, Ok YS, Tsang DCW, Hou D. Soil plastisphere: Exploration methods, influencing factors, and ecological insights. JOURNAL OF HAZARDOUS MATERIALS 2022; 430:128503. [PMID: 35739682 DOI: 10.1016/j.jhazmat.2022.128503] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/10/2022] [Accepted: 02/13/2022] [Indexed: 06/15/2023]
Abstract
Microplastic (MP), an emerging contaminant, is globally prevalent and poses potential environmental threats and ecological risks to both aquatic and terrestrial ecosystems. When MPs enter into natural environments, they may serve as artificial substrates for microbial colonization and plastisphere formation, providing new ecological niches for microorganisms. Recent studies of the plastisphere have focused on aquatic ecosystems. However, our understanding of the soil plastisphere e.g. its formation process, microbial ecology, co-transport of organic pollutants and heavy metals, and effects on biogeochemical processes is still very limited. This review summarizes latest methods used to explore the soil plastisphere, assesses the factors influencing the microbial ecology of the soil plastisphere, and sheds light on potential ecological risks caused by the soil plastisphere. The formation and succession of soil plastisphere communities can be driven by MP characteristics and soil environmental factors. The soil plastisphere may affect a series of ecological processes, especially the co-transport of environmental contaminants, biodegradation of MPs, and soil carbon cycling. We aim to narrow the knowledge gap between the soil and aquatic plastisphere, and provide valuable guidance for future research on the soil plastisphere in MP-contaminated soils.
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Affiliation(s)
- Chengqian Wang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Liuwei Wang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Yong Sik Ok
- Korea Biochar Research Center, APRU Sustainable Waste Management Program & Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Daniel C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Deyi Hou
- School of Environment, Tsinghua University, Beijing 100084, China.
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30
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Luo X, Kang X, Schönhuth A. Enhancing Long-Read-Based Strain-Aware Metagenome Assembly. Front Genet 2022; 13:868280. [PMID: 35646097 PMCID: PMC9136235 DOI: 10.3389/fgene.2022.868280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/01/2022] [Indexed: 11/18/2022] Open
Abstract
Microbial communities are usually highly diverse and often involve multiple strains from the participating species due to the rapid evolution of microorganisms. In such a complex microecosystem, different strains may show different biological functions. While reconstruction of individual genomes at the strain level is vital for accurately deciphering the composition of microbial communities, the problem has largely remained unresolved so far. Next-generation sequencing has been routinely used in metagenome assembly but there have been struggles to generate strain-specific genome sequences due to the short-read length. This explains why long-read sequencing technologies have recently provided unprecedented opportunities to carry out haplotype- or strain-resolved genome assembly. Here, we propose MetaBooster and MetaBooster-HiFi, as two pipelines for strain-aware metagenome assembly from PacBio CLR and Oxford Nanopore long-read sequencing data. Benchmarking experiments on both simulated and real sequencing data demonstrate that either the MetaBooster or the MetaBooster-HiFi pipeline drastically outperforms the state-of-the-art de novo metagenome assemblers, in terms of all relevant metagenome assembly criteria, involving genome fraction, contig length, and error rates.
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Affiliation(s)
- Xiao Luo
- Genome Data Science, Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Life Science and Health, Centrum Wiskunde and Informatica, Amsterdam, Netherlands
| | - Xiongbin Kang
- Genome Data Science, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Alexander Schönhuth
- Genome Data Science, Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Life Science and Health, Centrum Wiskunde and Informatica, Amsterdam, Netherlands
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31
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A review of methods for the inference and experimental confirmation of microbial association networks in cheese. Int J Food Microbiol 2022; 368:109618. [DOI: 10.1016/j.ijfoodmicro.2022.109618] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/21/2022] [Accepted: 03/06/2022] [Indexed: 12/15/2022]
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32
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Adler A, Poirier S, Pagni M, Maillard J, Holliger C. Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter. Environ Microbiol 2022; 24:2136-2156. [PMID: 35315560 PMCID: PMC9311429 DOI: 10.1111/1462-2920.15947] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 02/19/2022] [Indexed: 11/26/2022]
Abstract
Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragmented and incomplete genomes. Here, the metagenomes of four samples of aerobic granular sludge bioreactors containing Candidatus (Ca.) Accumulibacter, a phosphate-accumulating organism of interest for wastewater treatment, were sequenced with both PacBio and Illumina. Different strategies of genome assembly and binning were investigated, including published protocols and a binning procedure adapted to the binning of long contigs (MuLoBiSC). Multiple criteria were considered to select the best strategy for Ca. Accumulibacter, whose multiple strains in every sample represent a challenging microdiversity. In this case, the best strategy relies on long-read only assembly and a custom binning procedure including MuLoBiSC in metaWRAP. Several high-quality Ca. Accumulibacter MAGs, including a novel species, were obtained independently from different samples. Comparative genomic analysis showed that MAGs retrieved in different samples harbour genomic rearrangements in addition to accumulation of point mutations. The microdiversity of Ca. Accumulibacter, likely driven by mobile genetic elements, causes major difficulties in recovering MAGs, but it is also a hallmark of the panmictic lifestyle of these bacteria.
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Affiliation(s)
- Aline Adler
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Simon Poirier
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marco Pagni
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,IFP Energie nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison Cedex, France
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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Marquet M, Zöllkau J, Pastuschek J, Viehweger A, Schleußner E, Makarewicz O, Pletz MW, Ehricht R, Brandt C. Evaluation of microbiome enrichment and host DNA depletion in human vaginal samples using Oxford Nanopore's adaptive sequencing. Sci Rep 2022; 12:4000. [PMID: 35256725 PMCID: PMC8901746 DOI: 10.1038/s41598-022-08003-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/01/2022] [Indexed: 12/28/2022] Open
Abstract
Metagenomic sequencing is promising for clinical applications to study microbial composition concerning disease or patient outcomes. Alterations of the vaginal microbiome are associated with adverse pregnancy outcomes, like preterm premature rupture of membranes and preterm birth. Methodologically these samples often have to deal with low relative amounts of prokaryotic DNA and high amounts of host DNA (> 90%), decreasing the overall microbial resolution. Nanopore's adaptive sampling method offers selective DNA depletion or target enrichment to directly reject or accept DNA molecules during sequencing without specialized sample preparation. Here, we demonstrate how selective 'human host depletion' resulted in a 1.70 fold (± 0.27 fold) increase in total sequencing depth, providing higher taxonomic profiling sensitivity. At the same time, the microbial composition remains consistent with the control experiments. The complete removal of all human host sequences is not yet possible and should be considered as an ethical approval statement might still be necessary. Adaptive sampling increased microbial sequencing yield in all 15 sequenced clinical routine vaginal samples, making it a valuable tool for clinical surveillance and medical-based research, which can be used in addition to other host depletion methods before sequencing.
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Affiliation(s)
- Mike Marquet
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany.
| | - Janine Zöllkau
- Department of Obstetrics, Jena University Hospital, Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Jana Pastuschek
- Department of Obstetrics, Jena University Hospital, Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Adrian Viehweger
- Department of Medical Microbiology and Virology, University Hospital Leipzig, Leipzig, Germany
| | - Ekkehard Schleußner
- Department of Obstetrics, Jena University Hospital, Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Oliwia Makarewicz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
| | - Mathias W Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
- Institute of Physical Chemistry, Friedrich-Schiller-University Jena, Jena, Germany
| | - Christian Brandt
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
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Hiraoka S, Sumida T, Hirai M, Toyoda A, Kawagucci S, Yokokawa T, Nunoura T. Diverse DNA modification in marine prokaryotic and viral communities. Nucleic Acids Res 2022; 50:1531-1550. [PMID: 35051998 PMCID: PMC8919816 DOI: 10.1093/nar/gkab1292] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/30/2021] [Accepted: 12/17/2021] [Indexed: 11/15/2022] Open
Abstract
DNA chemical modifications, including methylation, are widespread and play important roles in prokaryotes and viruses. However, current knowledge of these modification systems is severely biased towards a limited number of culturable prokaryotes, despite the fact that a vast majority of microorganisms have not yet been cultured. Here, using single-molecule real-time sequencing, we conducted culture-independent 'metaepigenomic' analyses (an integrated analysis of metagenomics and epigenomics) of marine microbial communities. A total of 233 and 163 metagenomic-assembled genomes (MAGs) were constructed from diverse prokaryotes and viruses, respectively, and 220 modified motifs and 276 DNA methyltransferases (MTases) were identified. Most of the MTase genes were not genetically linked with the endonuclease genes predicted to be involved in defense mechanisms against extracellular DNA. The MTase-motif correspondence found in the MAGs revealed 10 novel pairs, 5 of which showed novel specificities and experimentally confirmed the catalytic specificities of the MTases. We revealed novel alternative specificities in MTases that are highly conserved in Alphaproteobacteria, which may enhance our understanding of the co-evolutionary history of the methylation systems and the genomes. Our findings highlight diverse unexplored DNA modifications that potentially affect the ecology and evolution of prokaryotes and viruses in nature.
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Affiliation(s)
- Satoshi Hiraoka
- Research Center for Bioscience and Nanoscience (CeBN),
Research Institute for Marine Resources Utilization, Japan Agency for
Marine-Earth Science and Technology (JAMSTEC),
Yokosuka,
Kanagawa 237–0061,
Japan
| | - Tomomi Sumida
- Research Center for Bioscience and Nanoscience (CeBN),
Research Institute for Marine Resources Utilization, Japan Agency for
Marine-Earth Science and Technology (JAMSTEC),
Yokosuka,
Kanagawa 237–0061,
Japan
| | - Miho Hirai
- Institute for Extra-cutting-edge Science and Technology
Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and
Technology (JAMSTEC), Yokosuka,
Kanagawa 237–0061,
Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of
Genetics, Mishima,
Shizuoka 411-8540,
Japan
| | - Shinsuke Kawagucci
- Institute for Extra-cutting-edge Science and Technology
Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and
Technology (JAMSTEC), Yokosuka,
Kanagawa 237–0061,
Japan
- Marine Biodiversity and Environmental Assessment Research
Center (BioEnv), Research Institute for Global Change (RIGC), Japan
Agency for Marine-Earth Science and Technology (JAMSTEC),
Yokosuka,
Kanagawa 237–0061,
Japan
| | - Taichi Yokokawa
- Institute for Extra-cutting-edge Science and Technology
Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and
Technology (JAMSTEC), Yokosuka,
Kanagawa 237–0061,
Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN),
Research Institute for Marine Resources Utilization, Japan Agency for
Marine-Earth Science and Technology (JAMSTEC),
Yokosuka,
Kanagawa 237–0061,
Japan
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35
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Somerville V, Berthoud H, Schmidt RS, Bachmann HP, Meng YH, Fuchsmann P, von Ah U, Engel P. Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures. THE ISME JOURNAL 2022; 16:388-399. [PMID: 34363005 PMCID: PMC8776748 DOI: 10.1038/s41396-021-01071-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 02/07/2023]
Abstract
Undefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly controlled environments over centuries. This makes them interesting for understanding eco-evolutionary dynamics governing microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to an important Swiss cheese starter culture and analyzed historical and experimental samples reflecting 82 years of starter culture propagation. We found that the bacterial community is highly stable and dominated by only a few coexisting strains of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Genome sequencing, metabolomics analysis, and co-culturing experiments of 43 isolates show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large and diverse repertoire of matching CRISPR spacers. Our findings show that functionally equivalent strains can coexist in domesticated microbial communities and highlight an important role of bacteria-phage interactions that are different from kill-the-winner dynamics.
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Affiliation(s)
- Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
- Agroscope, Bern, Switzerland.
| | | | | | | | | | | | | | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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36
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Somerville V, Berthoud H, Schmidt RS, Bachmann HP, Meng YH, Fuchsmann P, von Ah U, Engel P. Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures. THE ISME JOURNAL 2022; 16:388-399. [PMID: 34363005 DOI: 10.1101/2021.01.14.426499v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 05/27/2023]
Abstract
Undefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly controlled environments over centuries. This makes them interesting for understanding eco-evolutionary dynamics governing microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to an important Swiss cheese starter culture and analyzed historical and experimental samples reflecting 82 years of starter culture propagation. We found that the bacterial community is highly stable and dominated by only a few coexisting strains of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Genome sequencing, metabolomics analysis, and co-culturing experiments of 43 isolates show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large and diverse repertoire of matching CRISPR spacers. Our findings show that functionally equivalent strains can coexist in domesticated microbial communities and highlight an important role of bacteria-phage interactions that are different from kill-the-winner dynamics.
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Affiliation(s)
- Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
- Agroscope, Bern, Switzerland.
| | | | | | | | | | | | | | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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Ben Khedher M, Ghedira K, Rolain JM, Ruimy R, Croce O. Application and Challenge of 3rd Generation Sequencing for Clinical Bacterial Studies. Int J Mol Sci 2022; 23:1395. [PMID: 35163319 PMCID: PMC8835973 DOI: 10.3390/ijms23031395] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
Over the past 25 years, the powerful combination of genome sequencing and bioinformatics analysis has played a crucial role in interpreting information encoded in bacterial genomes. High-throughput sequencing technologies have paved the way towards understanding an increasingly wide range of biological questions. This revolution has enabled advances in areas ranging from genome composition to how proteins interact with nucleic acids. This has created unprecedented opportunities through the integration of genomic data into clinics for the diagnosis of genetic traits associated with disease. Since then, these technologies have continued to evolve, and recently, long-read sequencing has overcome previous limitations in terms of accuracy, thus expanding its applications in genomics, transcriptomics and metagenomics. In this review, we describe a brief history of the bacterial genome sequencing revolution and its application in public health and molecular epidemiology. We present a chronology that encompasses the various technological developments: whole-genome shotgun sequencing, high-throughput sequencing, long-read sequencing. We mainly discuss the application of next-generation sequencing to decipher bacterial genomes. Secondly, we highlight how long-read sequencing technologies go beyond the limitations of traditional short-read sequencing. We intend to provide a description of the guiding principles of the 3rd generation sequencing applications and ongoing improvements in the field of microbial medical research.
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Affiliation(s)
- Mariem Ben Khedher
- Bacteriology Laboratory, Archet 2 Hospital, CHU Nice, 06000 Nice, France
- Institute for Research on Cancer and Aging Nice (IRCAN), CNRS, INSERM, Université Côte d’Azur, 06108 Nice, France
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institute Pasteur of Tunis, Tunis 1002, Tunisia;
| | - Jean-Marc Rolain
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Université, 13005 Marseille, France;
| | - Raymond Ruimy
- Bacteriology Laboratory, Archet 2 Hospital, CHU Nice, 06000 Nice, France
- Centre Méditerranéen de Médecine Moléculaire (C3M), INSERM, Université Côte D’Azur, 06108 Nice, France
| | - Olivier Croce
- Institute for Research on Cancer and Aging Nice (IRCAN), CNRS, INSERM, Université Côte d’Azur, 06108 Nice, France
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Luo X, Kang X, Schönhuth A. Strainline: full-length de novo viral haplotype reconstruction from noisy long reads. Genome Biol 2022; 23:29. [PMID: 35057847 PMCID: PMC8771625 DOI: 10.1186/s13059-021-02587-6] [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: 06/25/2021] [Accepted: 12/17/2021] [Indexed: 12/02/2022] Open
Abstract
Haplotype-resolved de novo assembly of highly diverse virus genomes is critical in prevention, control and treatment of viral diseases. Current methods either can handle only relatively accurate short read data, or collapse haplotype-specific variations into consensus sequence. Here, we present Strainline, a novel approach to assemble viral haplotypes from noisy long reads without a reference genome. Strainline is the first approach to provide strain-resolved, full-length de novo assemblies of viral quasispecies from noisy third-generation sequencing data. Benchmarking on simulated and real datasets of varying complexity and diversity confirm this novelty and demonstrate the superiority of Strainline.
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Galata V, Busi SB, Kunath BJ, de Nies L, Calusinska M, Halder R, May P, Wilmes P, Laczny CC. Functional meta-omics provide critical insights into long- and short-read assemblies. Brief Bioinform 2021; 22:bbab330. [PMID: 34453168 PMCID: PMC8575027 DOI: 10.1093/bib/bbab330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/13/2021] [Accepted: 07/26/2021] [Indexed: 11/12/2022] Open
Abstract
Real-world evaluations of metagenomic reconstructions are challenged by distinguishing reconstruction artifacts from genes and proteins present in situ. Here, we evaluate short-read-only, long-read-only and hybrid assembly approaches on four different metagenomic samples of varying complexity. We demonstrate how different assembly approaches affect gene and protein inference, which is particularly relevant for downstream functional analyses. For a human gut microbiome sample, we use complementary metatranscriptomic and metaproteomic data to assess the metagenomic data-based protein predictions. Our findings pave the way for critical assessments of metagenomic reconstructions. We propose a reference-independent solution, which exploits the synergistic effects of multi-omic data integration for the in situ study of microbiomes using long-read sequencing data.
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Affiliation(s)
- Valentina Galata
- Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg
| | - Susheel Bhanu Busi
- Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg
| | - Benoît Josef Kunath
- Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg
| | - Laura de Nies
- Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg
| | - Magdalena Calusinska
- BioSystems and Bioprocessing Engineering, Luxembourg Institute of Science and Technology, Rue du Brill 41, Belvaux L-4422, Luxembourg
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg
| | - Cédric Christian Laczny
- Luxembourg Centre for Systems Biomedicine, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg
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Maggiori C, Raymond-Bouchard I, Brennan L, Touchette D, Whyte L. MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes. Sci Rep 2021; 11:21041. [PMID: 34702846 PMCID: PMC8548342 DOI: 10.1038/s41598-021-00026-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/30/2021] [Indexed: 01/04/2023] Open
Abstract
Genome reconstruction from metagenomes enables detailed study of individual community members, their metabolisms, and their survival strategies. Obtaining high quality metagenome-assembled genomes (MAGs) is particularly valuable in extreme environments like sea ice cryoconites, where the native consortia are recalcitrant to culture and strong astrobiology analogues. We evaluated three separate approaches for MAG generation from Allen Bay, Nunavut sea ice cryoconites-HiSeq-only, MinION-only, and hybrid (HiSeq + MinION)-where field MinION sequencing yielded a reliable metagenome. The hybrid assembly produced longer contigs, more coding sequences, and more total MAGs, revealing a microbial community dominated by Bacteroidetes. The hybrid MAGs also had the highest completeness, lowest contamination, and highest N50. A putatively novel species of Octadecabacter is among the hybrid MAGs produced, containing the genus's only known instances of genomic potential for nitrate reduction, denitrification, sulfate reduction, and fermentation. This study shows that the inclusion of MinION reads in traditional short read datasets leads to higher quality metagenomes and MAGs for more accurate descriptions of novel microorganisms in this extreme, transient habitat and has produced the first hybrid MAGs from an extreme environment.
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Affiliation(s)
- Catherine Maggiori
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada.
| | - Isabelle Raymond-Bouchard
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Laura Brennan
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - David Touchette
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Lyle Whyte
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada
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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.
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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.
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Varliero G, Rafiq M, Singh S, Summerfield A, Sgouridis F, Cowan DA, Barker G. Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost. FEMS Microbiol Ecol 2021; 97:fiab127. [PMID: 34468725 PMCID: PMC8445667 DOI: 10.1093/femsec/fiab127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022] Open
Abstract
Permafrost represents a reservoir for the biodiscovery of cold-adapted proteins which are advantageous in industrial and medical settings. Comparisons between different thermo-adapted proteins can give important information for cold-adaptation bioengineering. We collected permafrost active layer samples from 34 points along a proglacial transect in southwest Greenland. We obtained a deep read coverage assembly (>164x) from nanopore and Illumina sequences for the purposes of i) analysing metagenomic and metatranscriptomic trends of the microbial community of this area, and ii) creating the Cold-Adapted Predicted Protein (CAPP) database. The community showed a similar taxonomic composition in all samples along the transect, with a solid permafrost-shaped community, rather than microbial trends typical of proglacial systems. We retrieved 69 high- and medium-quality metagenome-assembled clusters, 213 complete biosynthetic gene clusters and more than three million predicted proteins. The latter constitute the CAPP database that can provide cold-adapted protein sequence information for protein- and taxon-focused amino acid sequence modifications for the future bioengineering of cold-adapted enzymes. As an example, we focused on the enzyme polyphenol oxidase, and demonstrated how sequence variation information could inform its protein engineering.
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Affiliation(s)
- Gilda Varliero
- School of Life Sciences, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TQ, United Kingdom
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Natural Sciences 2 Building, Private Bag X20, Hatfield 0028, South Africa
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Airport Road, Baleli, Quetta, Balochistan, Pakistan
- School of Geographical Sciences, University of Bristol, Wills Memorial Building, Bristol BS8 1RL, United Kingdom
| | - Swati Singh
- School of Life Sciences, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TQ, United Kingdom
- School of Chemistry, University of Bristol, Cantock's Cl, Bristol BS8 1TS, United Kingdom
| | - Annabel Summerfield
- School of Life Sciences, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TQ, United Kingdom
| | - Fotis Sgouridis
- School of Geographical Sciences, University of Bristol, Wills Memorial Building, Bristol BS8 1RL, United Kingdom
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Natural Sciences 2 Building, Private Bag X20, Hatfield 0028, South Africa
| | - Gary Barker
- School of Life Sciences, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TQ, United Kingdom
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43
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Garneau JR, Legrand V, Marbouty M, Press MO, Vik DR, Fortier LC, Sullivan MB, Bikard D, Monot M. High-throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome. Sci Rep 2021; 11:18319. [PMID: 34526611 PMCID: PMC8443750 DOI: 10.1038/s41598-021-97867-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 08/27/2021] [Indexed: 11/13/2022] Open
Abstract
Viruses that infect bacteria (phages) are increasingly recognized for their importance in diverse ecosystems but identifying and annotating them in large-scale sequence datasets is still challenging. Although efficient scalable virus identification tools are emerging, defining the exact ends (termini) of phage genomes is still particularly difficult. The proper identification of termini is crucial, as it helps in characterizing the packaging mechanism of bacteriophages and provides information on various aspects of phage biology. Here, we introduce PhageTermVirome (PTV) as a tool for the easy and rapid high-throughput determination of phage termini and packaging mechanisms using modern large-scale metagenomics datasets. We successfully tested the PTV algorithm on a mock virome dataset and then used it on two real virome datasets to achieve the rapid identification of more than 100 phage termini and packaging mechanisms, with just a few hours of computing time. Because PTV allows the identification of free fully formed viral particles (by recognition of termini present only in encapsidated DNA), it can also complement other virus identification softwares to predict the true viral origin of contigs in viral metagenomics datasets. PTV is a novel and unique tool for high-throughput characterization of phage genomes, including phage termini identification and characterization of genome packaging mechanisms. This software should help researchers better visualize, map and study the virosphere. PTV is freely available for downloading and installation at https://gitlab.pasteur.fr/vlegrand/ptv.
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Affiliation(s)
| | - Véronique Legrand
- Infrastructure et Ingénierie Scientifique, Institut Pasteur, 75015, Paris, France
| | - Martial Marbouty
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, 75015, Paris, France
| | | | - Dean R Vik
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - Louis-Charles Fortier
- Faculty of Medicine and Health Sciences, Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - David Bikard
- Département de Microbiologie, Institut Pasteur, Groupe Biologie de Synthèse, 75015, Paris, France
| | - Marc Monot
- Biomics Platform, C2RT, Institut Pasteur, 75015, Paris, France.
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44
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Ferrocino I, Rantsiou K, Cocolin L. Investigating dairy microbiome: an opportunity to ensure quality, safety and typicity. Curr Opin Biotechnol 2021; 73:164-170. [PMID: 34474311 DOI: 10.1016/j.copbio.2021.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/01/2021] [Accepted: 08/06/2021] [Indexed: 11/19/2022]
Abstract
A detailed understanding of the microbiome of cheese and dairy products is key to the optimization of flavour, appearance, overall quality and safety. Microorganisms (including bacteria, yeasts, moulds and viruses, especially bacteriophages) from the environment can enter the dairy supply chain at multiple stages with several implications. The ability to track these microorganisms and to understand their function and interaction can be greatly enhanced by the use of high-throughput sequencing. Depending on the specific production technology, dairy products can harbor several strains and antibiotic-resistance genes that can potentially interact with the gut microbiome, once the product is ingested. Milk-associated or cheese-associated microbial communities with their interaction, function and diversity are a key factor for the dairy industry. Multi-omics approaches have been seldom utilized in literature and they need to be further considered. Studying the role, origin, diversity and function of the microbial species involved in the complex system of dairy production can help improve processes in several fields of application. Integrating an extensive sampling procedure with an extensive culture based methodology is necessary. To this end, local producers, and in general stakeholders, should be guided to discover and maintain their microbial diversity. A better management of microbial resources through precision fermentation processes will in turn reduce overall food losses and increase the possibility to use the microbiome in order to increase the local producers' income.
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Affiliation(s)
- Ilario Ferrocino
- DISAFA-Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | - Kalliopi Rantsiou
- DISAFA-Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | - Luca Cocolin
- DISAFA-Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy.
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45
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Haro-Moreno JM, López-Pérez M, Rodriguez-Valera F. Enhanced Recovery of Microbial Genes and Genomes From a Marine Water Column Using Long-Read Metagenomics. Front Microbiol 2021; 12:708782. [PMID: 34512586 PMCID: PMC8430335 DOI: 10.3389/fmicb.2021.708782] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/30/2021] [Indexed: 12/12/2022] Open
Abstract
Third-generation sequencing has penetrated little in metagenomics due to the high error rate and dependence for assembly on short-read designed bioinformatics. However, second-generation sequencing metagenomics (mostly Illumina) suffers from limitations, particularly in the assembly of microbes with high microdiversity and retrieval of the flexible (adaptive) fraction of prokaryotic genomes. Here, we have used a third-generation technique to study the metagenome of a well-known marine sample from the mixed epipelagic water column of the winter Mediterranean. We have compared PacBio Sequel II with the classical approach using Illumina Nextseq short reads followed by assembly to study the metagenome. Long reads allow for efficient direct retrieval of complete genes avoiding the bias of the assembly step. Besides, the application of long reads on metagenomic assembly allows for the reconstruction of much more complete metagenome-assembled genomes (MAGs), particularly from microbes with high microdiversity such as Pelagibacterales. The flexible genome of reconstructed MAGs was much more complete containing many adaptive genes (some with biotechnological potential). PacBio Sequel II CCS appears particularly suitable for cellular metagenomics due to its low error rate. For most applications of metagenomics, from community structure analysis to ecosystem functioning, long reads should be applied whenever possible. Specifically, for in silico screening of biotechnologically useful genes, or population genomics, long-read metagenomics appears presently as a very fruitful approach and can be analyzed from raw reads before a computationally demanding (and potentially artifactual) assembly step.
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Affiliation(s)
- Jose M. Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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46
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Tedersoo L, Albertsen M, Anslan S, Callahan B. Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology. Appl Environ Microbiol 2021; 87:e0062621. [PMID: 34132589 PMCID: PMC8357291 DOI: 10.1128/aem.00626-21] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Short-read, high-throughput sequencing (HTS) methods have yielded numerous important insights into microbial ecology and function. Yet, in many instances short-read HTS techniques are suboptimal, for example, by providing insufficient phylogenetic resolution or low integrity of assembled genomes. Single-molecule and synthetic long-read (SLR) HTS methods have successfully ameliorated these limitations. In addition, nanopore sequencing has generated a number of unique analysis opportunities, such as rapid molecular diagnostics and direct RNA sequencing, and both Pacific Biosciences (PacBio) and nanopore sequencing support detection of epigenetic modifications. Although initially suffering from relatively low sequence quality, recent advances have greatly improved the accuracy of long-read sequencing technologies. In spite of great technological progress in recent years, the long-read HTS methods (PacBio and nanopore sequencing) are still relatively costly, require large amounts of high-quality starting material, and commonly need specific solutions in various analysis steps. Despite these challenges, long-read sequencing technologies offer high-quality, cutting-edge alternatives for testing hypotheses about microbiome structure and functioning as well as assembly of eukaryote genomes from complex environmental DNA samples.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Sten Anslan
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany
| | - Benjamin Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
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47
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Vicedomini R, Quince C, Darling AE, Chikhi R. Strainberry: automated strain separation in low-complexity metagenomes using long reads. Nat Commun 2021; 12:4485. [PMID: 34301928 PMCID: PMC8302730 DOI: 10.1038/s41467-021-24515-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/18/2021] [Indexed: 02/07/2023] Open
Abstract
High-throughput short-read metagenomics has enabled large-scale species-level analysis and functional characterization of microbial communities. Microbiomes often contain multiple strains of the same species, and different strains have been shown to have important differences in their functional roles. Recent advances on long-read based methods enabled accurate assembly of bacterial genomes from complex microbiomes and an as-yet-unrealized opportunity to resolve strains. Here we present Strainberry, a metagenome assembly pipeline that performs strain separation in single-sample low-complexity metagenomes and that relies uniquely on long-read data. We benchmarked Strainberry on mock communities for which it produces strain-resolved assemblies with near-complete reference coverage and 99.9% base accuracy. We also applied Strainberry on real datasets for which it improved assemblies generating 20-118% additional genomic material than conventional metagenome assemblies on individual strain genomes. We show that Strainberry is also able to refine microbial diversity in a complex microbiome, with complete separation of strain genomes. We anticipate this work to be a starting point for further methodological improvements on strain-resolved metagenome assembly in environments of higher complexities.
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Affiliation(s)
- Riccardo Vicedomini
- Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Paris, France.
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, United Kingdom
- Gut Microbes and Health, Quadram Institute, Norwich, United Kingdom
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Aaron E Darling
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Rayan Chikhi
- Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Paris, France
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48
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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.
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Affiliation(s)
- Ilana Lauren Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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49
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Mancini A, Rodriguez MC, Zago M, Cologna N, Goss A, Carafa I, Tuohy K, Merz A, Franciosi E. Massive Survey on Bacterial-Bacteriophages Biodiversity and Quality of Natural Whey Starter Cultures in Trentingrana Cheese Production. Front Microbiol 2021; 12:678012. [PMID: 34194413 PMCID: PMC8236940 DOI: 10.3389/fmicb.2021.678012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/29/2021] [Indexed: 01/04/2023] Open
Abstract
This study focused on the microbial and bacteriophages identification and characterization in cheese-production facilities that use natural whey starter (NWS) cultures for Trentingrana production. Bacterial and phage screening was carried out on cooked not acidified whey and NWS samples isolated from six dairy factories, for 4 consecutive days in four different months. By means of a combined approach, using plate counts, bacterial isolation, and metataxonomic analysis Lactobacillus helveticus was found occurring as the dominant species in NWS cultures and Levilactobacillus brevis as codominant in the cheese factories where the temperature of NWS production was mainly lower than 40°C, suggesting that the variability in the parameters of the NWS culture preparation could differently modulate the bacterial species in NWS cultures. Using turbidity test approach on 303 bacterial isolates from the NWS cultures, 120 distinct phages were identified. L. helveticus phage contamination of NWS cultures was revealed in most of the analyzed samples, but despite the great recovery of bacteriophage contamination cases, the microbial quality of NWS cultures was high. Our results support the presence of natural bacteriophage resistance mechanisms in L. helveticus. The use of NWS cultures probably creates an ideal environment for the proliferation of different L. helveticus strains balanced with their phages without a clear dominance. It is evident, from this study, that the presence of a high biodiversity of NWS bacterial strains is relevant to avoid phages dominance in NWS cultures and consequently to keep a good acidification ability.
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Affiliation(s)
- Andrea Mancini
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Maria Cid Rodriguez
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Miriam Zago
- Centro di ricerca Zootecnia e Acquacoltura (CREA-ZA), Lodi, Italy
| | - Nicola Cologna
- Trentingrana Consorzio dei Caseifici Sociali Trentini s.c.a., Trento, Italy
| | - Andrea Goss
- Trentingrana Consorzio dei Caseifici Sociali Trentini s.c.a., Trento, Italy
| | - Ilaria Carafa
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Kieran Tuohy
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Andrea Merz
- Trentingrana Consorzio dei Caseifici Sociali Trentini s.c.a., Trento, Italy
| | - Elena Franciosi
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
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50
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Li Y, Jin Y, Zhang J, Pan H, Wu L, Liu D, Liu J, Hu J, Shen J. Recovery of human gut microbiota genomes with third-generation sequencing. Cell Death Dis 2021; 12:569. [PMID: 34078878 PMCID: PMC8172872 DOI: 10.1038/s41419-021-03829-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/26/2022]
Abstract
Human gut microbiota modulates normal physiological functions, such as maintenance of barrier homeostasis and modulation of metabolism, as well as various chronic diseases including type 2 diabetes and gastrointestinal cancer. Despite decades of research, the composition of the gut microbiota remains poorly understood. Here, we established an effective extraction method to obtain high quality gut microbiota genomes, and analyzed them with third-generation sequencing technology. We acquired a large quantity of data from each sample and assembled large numbers of reliable contigs. With this approach, we constructed tens of completed bacterial genomes in which there were several new bacteria species. We also identified a new conditional pathogen, Enterococcus tongjius, which is a member of Enterococci. This work provided a novel and reliable approach to recover gut microbiota genomes, facilitating the discovery of new bacteria species and furthering our understanding of the microbiome that underlies human health and diseases.
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Affiliation(s)
- Yanfei Li
- Shanghai University of Medicine & Health Sciences affiliated Zhoupu Hospital, 201318, Shanghai, China.,School of Basic Medical Sciences and Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, 201318, Shanghai, China
| | - Yueling Jin
- Shanghai University of Medicine & Health Sciences affiliated Zhoupu Hospital, 201318, Shanghai, China
| | | | - Haoying Pan
- Shanghai University of Medicine & Health Sciences affiliated Zhoupu Hospital, 201318, Shanghai, China
| | - Lan Wu
- Shanghai University of Medicine & Health Sciences affiliated Zhoupu Hospital, 201318, Shanghai, China.,School of Basic Medical Sciences and Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, 201318, Shanghai, China
| | - Dingsheng Liu
- Shanghai University of Medicine & Health Sciences affiliated Zhoupu Hospital, 201318, Shanghai, China
| | - Jinlong Liu
- Shanghai University of Medicine & Health Sciences affiliated Zhoupu Hospital, 201318, Shanghai, China
| | - Jing Hu
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, 201204, Shanghai, China.
| | - Junwei Shen
- Shanghai East Hospital, Tongji University School of Medicine, 200120, Shanghai, China.
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