The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies DOI Creative Commons
Ryan Cook, Nathan Brown, Branko Rihtman

et al.

Microbial Genomics, Journal Year: 2024, Volume and Issue: 10(2)

Published: Feb. 20, 2024

Viral metagenomics has fuelled a rapid change in our understanding of global viral diversity and ecology. Long-read sequencing hybrid assembly approaches that combine long- short-read technologies are now being widely implemented bacterial genomics metagenomics. However, the use long-read to investigate communities is still its infancy. While Nanopore PacBio have been applied metagenomics, it not known what extent different will impact reconstruction community. Thus, we constructed mock bacteriophage community previously sequenced phage genomes them using Illumina, tested number approaches. When single technology, Illumina assemblies were best at recovering genomes. Nanopore- PacBio-only performed poorly comparison both genome recovery error rates, which varied with assembler used. The had errors manifested as SNPs INDELs frequencies 41 157 % higher than found only assemblies, respectively. 12 78 Illumina-only Despite high-read coverage, long-read-only recovered maximum one complete from any assembly, unless reads down-sampled prior assembly. Overall approach was by combination reads, reduced rates levels comparable short-read-only assemblies. approach. differences between technology downstream impacts on gene prediction, subsequent estimates within sample. These findings provide starting point for others choice algorithms analysis viromes.

Language: Английский

PhaTYP: predicting the lifestyle for bacteriophages using BERT DOI Creative Commons
Jiayu Shang, Xubo Tang, Yanni Sun

et al.

Briefings in Bioinformatics, Journal Year: 2022, Volume and Issue: 24(1)

Published: Oct. 17, 2022

Bacteriophages (or phages), which infect bacteria, have two distinct lifestyles: virulent and temperate. Predicting the lifestyle of phages helps decipher their interactions with bacterial hosts, aiding phages' applications in fields such as phage therapy. Because experimental methods for annotating cannot keep pace fast accumulation sequenced phages, computational method predicting lifestyles has become an attractive alternative. Despite some promising results, prediction remains difficult because limited known annotations sheer amount contigs assembled from metagenomic data. In particular, most existing tools precisely predict short contigs. this work, we develop PhaTYP (Phage TYPe tool) to improve accuracy on We design different training tasks, self-supervised fine-tuning overcome difficulties. rigorously tested compared four state-of-the-art methods: DeePhage, PHACTS, PhagePred BACPHLIP. The results show that outperforms all these achieves more stable performance addition, demonstrated utility analyzing human neonates' gut This application shows is a useful means studying data extend our understanding microbial communities.

Language: Английский

Citations

104
Unraveling the functional dark matter through global metagenomics DOI Creative Commons
Georgios A. Pavlopoulos, Fotis A. Baltoumas, Sirui Liu

et al.

Nature, Journal Year: 2023, Volume and Issue: 622(7983), P. 594 - 602

Published: Oct. 11, 2023

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity functions and activities

Language: Английский

Citations

85
Genome binning of viral entities from bulk metagenomics data DOI Creative Commons
Joachim Johansen, Damian R. Plichta, Jakob Nybo Nissen

et al.

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

Published: Feb. 18, 2022

Abstract Despite the accelerating number of uncultivated virus sequences discovered in metagenomics and their apparent importance for health disease, human gut virome its interactions with bacteria gastrointestinal tract are not well understood. This is partly due to a paucity whole-virome datasets limitations current approaches identifying viral data. Here, combining deep-learning based binning algorithm paired metagenome metavirome datasets, we develop Phages from Metagenomics Binning (PHAMB), an approach that allows thousands genomes directly bulk data, while simultaneously enabling clustering into accurate taxonomic populations. When applied on Human Microbiome Project 2 (HMP2) dataset, PHAMB recovered 6,077 high-quality 1,024 populations, identified viral-microbial host interactions. can be advantageously existing future metagenomes illuminate ecological dynamics other microbiome constituents.

Language: Английский

Citations

77
Promises of microbiome-based therapies DOI Creative Commons
Jasmohan S. Bajaj, Siew C. Ng, Bernd Schnabl

et al.

Journal of Hepatology, Journal Year: 2022, Volume and Issue: 76(6), P. 1379 - 1391

Published: May 16, 2022

Language: Английский

Citations

73
Diversity in the soil virosphere: to infinity and beyond? DOI Creative Commons
Simon Roux, Joanne Emerson

Trends in Microbiology, Journal Year: 2022, Volume and Issue: 30(11), P. 1025 - 1035

Published: May 26, 2022

Viruses are key members of Earth's microbiomes, shaping microbial community composition and metabolism. Here, we describe recent advances in 'soil viromics', that is, virus-focused metagenome metatranscriptome analyses offer unprecedented windows into the soil virosphere. Given emerging picture high viral activity, diversity, dynamics over short spatiotemporal scales, then outline eco-evolutionary processes hypothesize major diversity drivers for viruses. We argue a effort is needed to establish 'global virosphere atlas' can be used address roles viruses microbiomes terrestrial biogeochemical cycles across scales.

Language: Английский

Citations

71
Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting DOI Creative Commons
Hanpeng Liao, Chen Liu,

Chaofan Ai

et al.

The ISME Journal, Journal Year: 2023, Volume and Issue: 17(6), P. 916 - 930

Published: April 8, 2023

Abstract While decomposition of organic matter by bacteria plays a major role in nutrient cycling terrestrial ecosystems, the significance viruses remains poorly understood. Here we combined metagenomics and metatranscriptomics with temporal sampling to study mesophilic thermophilic their on during industrial-scale hyperthermophilic composting (HTC). Our results show that virus-bacteria density dynamics activity are tightly coupled, where specific track host densities, triggering microbial community succession via top-down control HTC. Moreover, encoded expressed several auxiliary metabolic genes (AMGs) linked carbon cycling, impacting turnover alongside bacteria. Nutrient correlated positively virus–host ratio, indicative positive relationship between ecosystem functioning, viral abundances, activity. These effects were predominantly driven DNA as most detected RNA associated eukaryotes not phase composting. findings suggest could drive HTC recycling bacterial biomass through cell lysis expressing key AMGs. Viruses hence potentially be used indicators functioning optimize productivity biotechnological agricultural systems.

Language: Английский

Citations

57
Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats DOI Creative Commons
Yunha Hwang,

Simon Roux,

Clément Coclet

et al.

Nature Microbiology, Journal Year: 2023, Volume and Issue: 8(5), P. 946 - 957

Published: April 6, 2023

Abstract Many microbes in nature reside dense, metabolically interdependent communities. We investigated the and extent of microbe-virus interactions relation to microbial density syntrophy by examining a biomass deep-sea hydrothermal mat. Using metagenomic sequencing, we find numerous instances where phylogenetically distant (up domain level) encode CRISPR-based immunity against same viruses Evidence viral with hosts cross-cutting domains is particularly striking between known syntrophic partners, for example those engaged anaerobic methanotrophy. These patterns are corroborated proximity-ligation-based (Hi-C) inference. Surveys public datasets reveal additional interacting across diverse ecosystems harbour biofilms. propose that entry particles and/or DNA non-primary host cells may be common phenomenon densely populated ecosystems, eco-evolutionary implications CRISPR-mediated inter-population augmentation resilience viruses.

Language: Английский

Citations

51
Interrogating the viral dark matter of the rumen ecosystem with a global virome database DOI Creative Commons
Ming Yan, Akbar Adjie Pratama, Sripoorna Somasundaram

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Aug. 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.

Language: Английский

Citations

49
You can move, but you can't hide: identification of mobile genetic elements with geNomad DOI Creative Commons
Antônio Pedro Camargo, Simon Roux, Frederik Schulz

et al.

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

Published: March 6, 2023

Identifying and characterizing mobile genetic elements (MGEs) in sequencing data is essential for understanding their diversity, ecology, biotechnological applications, impact on public health. Here, we introduce geNomad, a classification annotation framework that combines information from gene content deep neural network to identify sequences of plasmids viruses. geNomad uses large dataset marker proteins provide functional taxonomic assignment viral genomes. Using conditional random field model, also detects proviruses integrated into host genomes with high precision. In benchmarks included diverse MGE chromosome sequences, significantly outperformed other tools all evaluated clades Leveraging geNomad's speed scalability, were able process metagenomes metatranscriptomes, leading the discovery millions new viruses are available through IMG/VR IMG/PR databases. We anticipate will enable further advancements research, it at https://portal.nersc.gov/genomad.

Language: Английский

Citations

44
The gut virome is associated with stress-induced changes in behaviour and immune responses in mice DOI Creative Commons
Nathaniel L. Ritz, Lorraine A. Draper, Thomaz F. S. Bastiaanssen

et al.

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(2), P. 359 - 376

Published: Feb. 5, 2024

The microbiota-gut-brain axis has been shown to play an important role in the stress response, but previous work focused primarily on of bacteriome. gut virome constitutes a major portion microbiome, with bacteriophages having potential remodel bacteriome structure and activity. Here we use mouse model chronic social stress, employ 16S rRNA whole metagenomic sequencing faecal pellets determine how is modulated by contributes effects stress. We found that led behavioural, immune alterations mice were associated changes bacteriophage class Caudoviricetes unassigned viral taxa. To whether these causally related stress-associated behavioural or physiological outcomes, conducted transplant from before autochthonously transferred it undergoing transfer protected against behaviour sequelae restored stress-induced select circulating cell populations, cytokine release, gene expression amygdala. These data provide evidence plays modulation during indicating populations should be considered when designing future microbiome-directed therapies.

Language: Английский

Citations

34