Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods

mSystems, Journal Year: 2024, Volume and Issue: 9(3)

Published: Feb. 20, 2024

ABSTRACT Understanding the ecological impacts of viruses on natural and engineered ecosystems relies accurate identification viral sequences from community sequencing data. To maximize recovery metagenomes, researchers frequently combine tools. However, effectiveness this strategy is unknown. Here, we benchmarked combinations six widely used informatics tools for analysis (VirSorter, VirSorter2, VIBRANT, DeepVirFinder, CheckV, Kaiju), called “rulesets.” Rulesets were tested against mock metagenomes composed taxonomically diverse sequence types aquatic to assess effects degree enrichment habitat tool performance. We found that rulesets achieved equivalent accuracy [Matthews Correlation Coefficient (MCC) = 0.77, P adj ≥ 0.05]. Each contained five our “tuning removal” rule designed remove non-viral contamination. While VirSorter each once in these high-accuracy rulesets, they not combination with other: combining does lead optimal Our validation suggests MCC plateau at 0.77 partly caused by inaccurate labeling within reference databases. In highest ruleset identified more virus-enriched (44%–46%) than cellular (7%–19%). improved algorithms may tools, should be done tandem careful curation recommend using VirSorter2 empirically derived tuning removal rule. provides insight into methods silico will enable robust metagenomic data sets. IMPORTANCE The environmental has offered critical insights microbial ecology. it remains difficult know which optimize their specific study. an attempt recover viruses, studies are increasingly outputs multiple without validating approach. After benchmarking samples, only combined cautiously. Two four maximized minimized contamination compared either single-tool or five- six-tool ones. By providing a rigorous overview behavior strategies pipeline replicate process, findings guide use existing offer blueprint feature engineering new higher-confidence discovery microbiome studies.

Language: Английский

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Hiding in plain sight: The discovery of complete genomes of 11 hypothetical spindle‐shaped viruses that putatively infect mesophilic ammonia‐oxidizing archaea

Environmental Microbiology Reports, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 23, 2024

Abstract The genome of a putative Nitrosopumilaceae virus with hypothetical spindle‐shaped particle morphology was identified in the Yangshan Harbour metavirome from East China Sea through protein similarity comparison and structure analysis. This discovery accompanied by set 10 geographically dispersed close relatives found environmental datasets typical locations ammonia‐oxidizing archaeon distribution. Its host prediction supported iPHoP sequence similarity. predicted major capsid protein, together overall N ‐glycosylation site, transmembrane helices prediction, hydrophilicity profile, docking simulation proteins, indicate that these viruses resemble viruses. It suggests similarly assembled and, consequently, possibly newly discovered archaeal

Language: Английский

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Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: June 26, 2024

Abstract Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming “ Candidatus Methanoperedens” archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and reconstruct new genomes. 13 four near-complete linear share 40 genes that define a largely syntenous genome backbone. We use these conserved identify peatland soil delineate Borg phylogeny, revealing two major clades. Remarkably, encoding nanowire-like electron-transferring cytochromes cell surface proteins more highly expressed than those host Methanoperedens , indicating augment the activity in situ. reconstructed first 4.00 Mbp for is inferred be predicted its methylation motifs, which differ pervasive TC CC motifs Borgs. Thus, may enable distinguish their Very high ratios structural predictions suggest capable encapsulation. The findings clearly as distinct class ECE with shared genomic signatures, establish diversification common ancestor genetic inheritance, raise possibility periodic existence outside cells.

Language: Английский

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Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes

Genome biology, Journal Year: 2024, Volume and Issue: 25(1)

Published: Aug. 19, 2024

Long-read sequencing holds great potential for characterizing complex microbial communities, yet taxonomic profiling tools designed specifically long reads remain lacking. We introduce Melon, a novel marker-based profiler that capitalizes on the unique attributes of reads. Melon employs two-stage classification scheme to reduce computational time and is equipped with an expectation-maximization-based post-correction module handle ambiguous achieves superior performance compared existing in both mock simulated samples. Using wastewater metagenomic samples, we demonstrate applicability by showing it provides reliable estimates overall genome copies, species-level profiles.

Language: Английский

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Terabase-Scale Coassembly of a Tropical Soil Microbiome

Microbiology Spectrum, Journal Year: 2023, Volume and Issue: 11(4)

Published: June 13, 2023

Petabases of reads are being produced by environmental metagenome sequencing. An essential step in analyzing these data is assembly, the computational reconstruction genome sequences from microbial communities. “Coassembly” metagenomic sequence data, which multiple samples assembled together, enables more complete detection genomes an environment than “multiassembly,” individually.

Language: Английский

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Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

Microbiome, Journal Year: 2023, Volume and Issue: 11(1)

Published: July 25, 2023

Porphyromonas gingivalis (hereafter "Pg") is an oral pathogen that has been hypothesized to act as a keystone driver of inflammation and periodontal disease. Although Pg most readily recovered from individuals with actively progressing disease, healthy those stable non-progressing disease are also colonized by Pg. Insights into the factors shaping striking strain-level variation in Pg, its variable associations needed achieve more mechanistic understanding progression. One key forces often diversity microbial communities infection bacteria their viral (phage) predators symbionts. Surprisingly, although subject study for over 40 years, essentially nothing known phages, prevailing paradigm phages not important ecology

Language: Английский

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Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 10, 2024

Abstract Metagenomics has greatly expanded our understanding of the human gut microbiome by revealing a vast diversity bacterial species within and across individuals. Even single species, different strains can have highly divergent gene content, affecting traits such as antibiotic resistance, metabolism, virulence. Methods that harness metagenomic data to resolve strain-level differences in functional potential are crucial for causes consequences this intraspecific diversity. The enormous size pangenome references, strain mixing samples, inconsistent sequencing depth present challenges existing tools analyze samples one at time. To address gap, we updated MIDAS profiler, now released version 3, developed StrainPGC, an approach strain-specific content estimation combines tracking correlations multiple samples. We validate integrated analysis using complex synthetic community from find StrainPGC outperforms approaches. Analyzing large, publicly available metagenome collection inflammatory bowel disease patients healthy controls, catalog repertoires thousands hundreds capturing extensive missing reference databases. Finally, apply metagenomes clinical trial fecal microbiota transplantation treatment ulcerative colitis. identify two Escherichia coli donors both frequently transmitted patients, but notable potential. v3 together enable precise, pangenomic investigations large collections without microbial isolation or de novo assembly.

Language: Английский

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Exploring the roles of ribosomal peptides in prokaryote-phage interactions through deep learning-enabled metagenome mining

Microbiome, Journal Year: 2024, Volume and Issue: 12(1)

Published: May 24, 2024

Abstract Background Microbial secondary metabolites play a crucial role in the intricate interactions within natural environment. Among these metabolites, ribosomally synthesized and post-translationally modified peptides (RiPPs) are becoming promising source of therapeutic agents due to their structural diversity functional versatility. However, biosynthetic capacity ecological functions remain largely underexplored. Results Here, we aim explore profile RiPPs potential roles between microbes viruses ocean, which encompasses vast unique biomes that rich remains chemically We first developed TrRiPP identify from ocean metagenomes, deep learning method detects RiPP precursors hallmark gene-independent manner overcome limitations classic methods processing highly fragmented metagenomic data. Applying this metagenomes global microbiome, uncover diverse array previously uncharacterized putative families with great novelty diversity. Through correlation analysis based on metatranscriptomic data, observed high prevalence antiphage defense-related phage-related protein were co-expressed families. Based association phage infection, constructed an Ocean Virus Database (OVD) established RiPP-involving host-phage interaction network through host prediction co-expression analysis, revealing complex connectivities linking RiPP-encoding prokaryotes, families, viral phages. These findings highlight involved prokaryote-phage coevolution, providing insights into microbiome. Conclusions This study provides systematic investigation microbiome at scale, shedding light essential integration approaches, connectivity. serves as valuable example exploring bacterial particularly associations unexplored microbial interactions.

Language: Английский

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Potential Viral Influence on Sulfur Metabolism in Acid Sulfate Soils

Soil Biology and Biochemistry, Journal Year: 2025, Volume and Issue: 205, P. 109773 - 109773

Published: March 5, 2025

Language: Английский

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Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils

Microbiome, Journal Year: 2025, Volume and Issue: 13(1)

Published: March 20, 2025

Abstract Background Arctic soils are climate-critical areas, where microorganisms play crucial roles in nutrient cycling processes. Acidobacteriota phylogenetically and physiologically diverse bacteria that abundant active tundra soils. Still, surprisingly little is known about acidobacterial viruses general those residing the particular. Here, we applied both culture-dependent -independent methods to study virome of Results Five virus isolates, Tunturi 1–5, were obtained from soils, Kilpisjärvi, Finland (69°N), using Tunturiibacter spp. strains originating same area as hosts. The new isolates have tailed particles with podo- (Tunturi 1, 2, 3), sipho- 4), or myovirus-like 5) morphologies. dsDNA genomes viral 63–98 kbp long, except 5, which a jumbo phage 309-kbp genome. 1 2 share 88% overall nucleotide identity, while other three not related one another. For over half open reading frames genomes, no functions could be predicted. To further assess -associated diversity Kilpisjärvi bulk metagenomes explored total 1881 operational taxonomic units (vOTUs) bioinformatically Almost all vOTUs (98%) assigned class Caudoviricetes . 125 vOTUs, including five (near-)complete ones, hosts -linked across sites, especially fens. Terriglobia proviruses observed being distant biomes. Approximately genus- higher-level similarities found between viruses, soil suggesting some shared groups Conclusions This provides laboratory models for future research adds insights into communities associated Predicted virus-host links gene suggest various interactions their host microorganisms. Largely unknown sequences metagenome-assembled highlight need more extensive sampling better understand contributions ecosystem-wide processes Arctic.

Language: Английский

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