Dancing the Nanopore limbo – Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction DOI Creative Commons
Sophie A. Simon, Katharina Schmidt,

Lea Griesdorn

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Feb. 16, 2023

Abstract Background While genome-resolved metagenomics has revolutionized our understanding of microbial and genetic diversity in environmental samples, assemblies short-reads often result incomplete and/or highly fragmented metagenome-assembled genomes (MAGs), hampering in-depth genomics. Although Nanopore sequencing increasingly been used as long reads greatly improve the assembly quality MAGs, recommended DNA quantity usually exceeds recoverable amount samples. Here, we evaluated lower-than-recommended quantities for library preparation by determining quality, community composition, recovery MAGs. Results We generated 27 metagenomes using commercially available ZYMO mock varied input from 1000 ng (the minimum) down to 1 eight steps. The remained stable across all levels. read mapping accuracy, which reflects how well match a known reference genome, was consistently high libraries. relative abundance species levels 50 ng. High-quality MAGs (> 95% completeness, ≤ 5% contamination) could be recovered 35 material. When combined with publicly Illumina community, low improved hybrid assemblies. Conclusion Our results show that can substantially reduced without any adverse effects genome still bolster when short-read data. posit presented herein will enable studies low-biomass environments, enhancing microbiome understanding.

Language: Английский

Asgard archaea shed light on the evolutionary origins of the eukaryotic ubiquitin-ESCRT machinery DOI Creative Commons
Tomoyuki Hatano, Saravanan Palani, Dimitra Papatziamou

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: June 13, 2022

Abstract The ESCRT machinery, comprising of multiple proteins and subcomplexes, is crucial for membrane remodelling in eukaryotic cells, processes that include ubiquitin-mediated multivesicular body formation, repair, cytokinetic abscission, virus exit from host cells. This system appears to have simpler, ancient origins, since many archaeal species possess homologues ESCRT-III Vps4, the components execute final scission reaction, where they been shown play roles cytokinesis, extracellular vesicle formation viral egress. Remarkably, metagenome assemblies Asgard archaea, closest known living relatives eukaryotes, were recently encode entire cascade involved remodelling, including ubiquitin itself, ESCRT-I ESCRT-II Vps4. Here, we explore phylogeny, structure, biochemistry machinery associated ubiquitylation system. We provide evidence subcomplexes being ubiquitin-directed recruitment ESCRT-III, as it eukaryotes. Taken together, our analyses suggest a pre-eukaryotic origin ubiquitin-coupled likely path evolution via series gene duplication diversification events.

Language: Английский

Citations

76
Megataxonomy and global ecology of the virosphere DOI Creative Commons
Eugene V. Koonin, Jens H. Kuhn, Valerian V. Dolja

et al.

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Nearly all organisms are hosts to multiple viruses that collectively appear be the most abundant biological entities in biosphere. With recent advances metagenomics and metatranscriptomics, known diversity of substantially expanded. Comparative analysis these using advanced computational methods culminated reconstruction evolution major groups enabled construction a virus megataxonomy, which has been formally adopted by International Committee on Taxonomy Viruses. This comprehensive taxonomy consists six realms, aspired monophyletic assembled based conservation hallmark proteins involved capsid structure formation or genome replication. The different taxa differ host range accordingly ecological niches. In this review article, we outline latest developments megataxonomy discoveries will likely lead reassessment some taxa, particular, split three current realms into two more independent realms. We then discuss correspondence between distribution among niches, as well abundance versus cells habitats. across environments appears primarily determined ranges, i.e. virome is shaped composition biome given habitat, itself affected abiotic factors.

Language: Английский

Citations

25
Three families of Asgard archaeal viruses identified in metagenome-assembled genomes DOI
Sofia Medvedeva, Jiarui Sun, Natalya Yutin

et al.

Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(7), P. 962 - 973

Published: June 27, 2022

Language: Английский

Citations

38
The virome of the last eukaryotic common ancestor and eukaryogenesis DOI
Mart Krupovìč, Valerian V. Dolja, Eugene V. Koonin

et al.

Nature Microbiology, Journal Year: 2023, Volume and Issue: 8(6), P. 1008 - 1017

Published: May 1, 2023

Language: Английский

Citations

35
Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome DOI Creative Commons
Rafael Laso-Pérez, Fabai Wu, Antoine Crémière

et al.

Nature Microbiology, Journal Year: 2023, Volume and Issue: 8(2), P. 231 - 245

Published: Jan. 19, 2023

Abstract ‘ Candidatus Methanophagales’ (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution ANME-1 remain poorly understood. In this study, we use metagenomics on hydrothermal samples to expand diversity uncover the effect virus–host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, Methanospirareceae’, closely related short-chain alkane oxidizers. Global phylogeny near-complete genomes show that hydrogen metabolism within ancient trait was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting archaea, showing unique structural replicative signatures. expansive virome contains metabolic gene repertoire can influence host through virus-mediated displacement. Our results suggest evolutionary continuum between oxidizers underscore effects viruses dynamics methane-driven ecosystems.

Language: Английский

Citations

34
Cellular homologs of the double jelly-roll major capsid proteins clarify the origins of an ancient virus kingdom DOI Creative Commons
Mart Krupovìč, Kira S. Makarova, Eugene V. Koonin

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(5)

Published: Jan. 25, 2022

Viruses are a distinct type of replicators that encode structural proteins encasing virus genomes in virions. For some the widespread capsid and other major components virions, likely ancestors encoded by cellular life forms identifiable. In particular, one most common proteins, with single jelly-roll (SJR) fold, appears to have evolved from particular family carbohydrate-binding proteins. However, double protein (DJR-MCP), hallmark enormously diverse viruses kingdom

Language: Английский

Citations

38
A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses DOI Creative Commons
Daniel Tamarit, Eva Caceres, Mart Krupovìč

et al.

Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(7), P. 948 - 952

Published: June 27, 2022

Asgard archaea have recently been identified as the closest archaeal relatives of eukaryotes. Their ecology, and particularly their virome, remain enigmatic. We reassembled closed chromosome Candidatus Odinarchaeum yellowstonii LCB_4, through long-range PCR, revealing CRISPR spacers targeting viral contigs. found related viruses in genomes diverse prokaryotes from geothermal environments, including other archaea. These open research avenues into ecology evolution

Language: Английский

Citations

37
Genomes of six viruses that infect Asgard archaea from deep-sea sediments DOI Open Access
Ian M. Rambo, Marguerite V. Langwig, Pedro Leão

et al.

Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(7), P. 953 - 961

Published: June 27, 2022

Language: Английский

Citations

31
Candidatus List. Lists of names of prokaryotic Candidatus phyla DOI Open Access
Aharon Oren, Markus Göker

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Journal Year: 2023, Volume and Issue: 73(5)

Published: May 9, 2023

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher we support invest in the microbiology community, to benefit of everyone. This supports our principal goal develop, expand strengthen networks available members so that they can generate new knowledge about microbes ensure it is shared with other communities.

Language: Английский

Citations

17
Description of Asgardarchaeum abyssi gen. nov. spec. nov., a novel species within the class Asgardarchaeia and phylum Asgardarchaeota in accordance with the SeqCode DOI Creative Commons
Daniel Tamarit, Stephan Köstlbacher, Kathryn E. Appler

et al.

Systematic and Applied Microbiology, Journal Year: 2024, Volume and Issue: 47(4), P. 126525 - 126525

Published: June 15, 2024

Asgardarchaeota, commonly referred to as Asgard archaea, is a candidatus phylum-rank archaeal clade that includes the closest relatives of eukaryotes. Despite their prevalence in scientific literature, name Asgardarchaeota lacks nomenclatural validation. Here, we describe novel high-quality metagenome-assembled genome (MAG), AB3033_2

Language: Английский

Citations

7