IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata

Nucleic Acids Research, Год журнала: 2022, Номер 51(D1), С. D733 - D743

Опубликована: Ноя. 18, 2022

Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration the global virosphere, progressively revealing extensive genomic diversity viruses on Earth and highlighting myriad ways by which impact biological processes. IMG/VR provides access to largest collection viral sequences obtained from (meta)genomes, along with functional annotation rich metadata. A web interface users efficiently browse search based genome features and/or sequence similarity. Here, we present fourth version IMG/VR, composed >15 million virus genomes fragments, a ≈6-fold increase in size compared previous version. These clustered into 8.7 operational taxonomic units, including 231 408 at least one high-quality representative. Viral now systematically identified genomes, metagenomes, metatranscriptomes using new detection approach (geNomad), IMG standard complemented quality estimation CheckV, classification reflecting latest standards, microbial host taxonomy prediction. v4 is available https://img.jgi.doe.gov/vr, underlying data download https://genome.jgi.doe.gov/portal/IMG_VR.

Язык: Английский

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The oral microbiome: diversity, biogeography and human health

Nature Reviews Microbiology, Год журнала: 2023, Номер 22(2), С. 89 - 104

Опубликована: Сен. 12, 2023

Язык: Английский

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PhageScope: a well-annotated bacteriophage database with automatic analyses and visualizations

Nucleic Acids Research, Год журнала: 2023, Номер 52(D1), С. D756 - D761

Опубликована: Окт. 30, 2023

Abstract Bacteriophages are viruses that infect bacteria or archaea. Understanding the diverse and intricate genomic architectures of phages is essential to study microbial ecosystems develop phage therapy strategies. However, existing databases short meticulous annotations. To this end, we propose PhageScope (https://phagescope.deepomics.org), an online database with comprehensive harbors a collection 873 718 sequences from various sources. Applying fifteen state-of-the-art tools perform systematic annotations analyses, provides on genome completeness, host range, lifestyle information, taxonomy classification, nine types structural functional genetic elements, three comparative studies for curated phages. Additionally, incorporates automatic analyses visualizations customized phages, serving as efficient platform study.

Язык: Английский

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Interrogating the viral dark matter of the rumen ecosystem with a global virome database

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Авг. 29, 2023

Abstract The diverse rumen virome can modulate the microbiome, but it remains largely unexplored. Here, we mine 975 published metagenomes for viral sequences, create a global database (RVD), and analyze diversity, virus-host linkages, potential roles in affecting functions. Containing 397,180 species-level operational taxonomic units (vOTUs), RVD substantially increases detection rate of viruses from compared with IMG/VR V3. Most classified vOTUs belong to Caudovirales , differing those found human gut. is predicted infect core including fiber degraders methanogens, carries auxiliary metabolic genes, thus likely impacts ecosystem both top-down bottom-up manner. findings provide useful resources baseline framework future research investigate how may impact digestive physiology.

Язык: Английский

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Immunogenicity of bacteriophages

Trends in Microbiology, Год журнала: 2023, Номер 31(10), С. 1058 - 1071

Опубликована: Май 15, 2023

Язык: Английский

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Viroid-like colonists of human microbiomes

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Янв. 21, 2024

Here, we describe the "Obelisks," a previously unrecognised class of viroid-like elements that first identified in human gut metatranscriptomic data. "Obelisks" share several properties: (i) apparently circular RNA ~1kb genome assemblies, (ii) predicted rod-like secondary structures encompassing entire genome, and (iii) open reading frames coding for novel protein superfamily, which call "Oblins". We find Obelisks form their own distinct phylogenetic group with no detectable sequence or structural similarity to known biological agents. Further, are prevalent tested microbiome metatranscriptomes representatives detected ~7% analysed stool (29/440) ~50% oral (17/32). Obelisk compositions appear differ between anatomic sites capable persisting individuals, continued presence over >300 days observed one case. Large scale searches 29,959 (clustered at 90% nucleotide identity), examples from all seven continents diverse ecological niches. From this search, subset code Obelisk-specific variants hammerhead type-III self-cleaving ribozyme. Lastly, case bacterial species (Streptococcus sanguinis) defined laboratory strains harboured specific population. As such, comprise RNAs have colonised, gone unnoticed in, human, global microbiomes.

Язык: Английский

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A metagenomic catalog of the early-life human gut virome

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Фев. 29, 2024

Early-life human gut microbiome is a pivotal driver of homeostasis and infant health. However, the viral component (known as "virome") remains mostly unexplored. Here, we establish Early-Life Gut Virome (ELGV), catalog 160,478 non-redundant DNA RNA sequences from 8130 virus-like particles (VLPs) enriched or bulk metagenomes in first three years life. By clustering, 82,141 species are identified, 68.3% which absent existing databases built mainly adults, 64 8 based on VLPs-enriched metagenomes, respectively, exhibit potentials biomarkers to distinguish infants adults. With largest longitudinal population profiled by either metagenomic sequencing, track inherent instability temporal development early-life virome, identify differential viruses associated with multiple clinical factors. The mother-infant shared virome interactions between bacteriome early life further expanded. Together, ELGV provides most comprehensive complete blueprint facilitating discovery pediatric disease-virome associations future.

Язык: Английский

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Longitudinal phage–bacteria dynamics in the early life gut microbiome

Nature Microbiology, Год журнала: 2025, Номер unknown

Опубликована: Янв. 24, 2025

Язык: Английский

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Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Июнь 23, 2022

Abstract There is significant interest in altering the course of cardiometabolic disease development via gut microbiomes. Nevertheless, highly abundant phage members complex ecosystem -which impact bacteria- remain understudied. Here, we show virome changes associated with metabolic syndrome (MetS), a prevalent clinical condition preceding disease, 196 participants by combined sequencing bulk whole genome and virus like particle communities. MetS viromes exhibit decreased richness diversity. They are enriched phages infecting Streptococcaceae Bacteroidaceae depleted those Bifidobacteriaceae . Differential abundance analysis identifies eighteen viral clusters (VCs) as significantly either or healthy viromes. Among these MetS-associated Roseburia VC that related to control-associated Faecalibacterium Oscillibacter VCs. Further VCs revealed Candidatus Heliusviridae , widespread lineage found 90+% participants. The identification temperate Ca. provides starting point studies effects on bacteria role this plays MetS.

Язык: Английский

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vRhyme enables binning of viral genomes from metagenomes

Nucleic Acids Research, Год журнала: 2022, Номер 50(14), С. e83 - e83

Опубликована: Апрель 22, 2022

Genome binning has been essential for characterization of bacteria, archaea, and even eukaryotes from metagenomes. Yet, few approaches exist viruses. We developed vRhyme, a fast precise software construction viral metagenome-assembled genomes (vMAGs). vRhyme utilizes single- or multi-sample coverage effect size comparisons between scaffolds employs supervised machine learning to identify nucleotide feature similarities, which are compiled into iterations weighted networks refined bins. To refine bins, unique features genomes, namely protein redundancy scoring mechanism based on the observation that viruses seldom encode redundant genes. Using simulated viromes, we displayed superior performance compared available tools in constructing more complete uncontaminated vMAGs. When applied 10,601 human skin, advanced our understanding resident viruses, highlighted by identification Herelleviridae vMAG comprised 22 scaffolds, another encoding nitrate reductase metabolic gene, representing near-complete post-binning. will enable convention uncultivated potential transform metagenome-based ecology.

Язык: Английский

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