Quantifying the impact of workshops promoting microbiome data standards and data stewardship

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: March 22, 2025

The field of microbiome research continues to grow at a rapid pace, with multi-omics approaches becoming widely used interrogate diverse samples. However, due lagging awareness and implementation standards data stewardship, many datasets are produced that not comparable, reproducible, or reusable. In 2021, the National Microbiome Data Collaborative launched its Ambassador Program, which utilizes community-learning model annually train cohort early-career researchers in stewardship best practices. These Ambassadors then host workshops other events communicate these themes their respective communities. To quantify impact this learning for promoting experience data, we conducted survey workshop participants from hosted by 2023 cohort. 13 collectively 21 events, reaching over 550 researchers. distributed an anonymous post-workshop event effectiveness training materials, format, thematic content. From results were successfully collected 15 those total 122 Overall, working range types variety institutions responded reported overwhelmingly positive experiences content 98% respondents reporting they gained knowledge event. Participants across also increase understanding metadata standards, principles management reporting, importance standardization processing. expressed willingness apply what learned about own research. study demonstrate hands-on communicating practices lessons details cohort-based contained herein intended assist groups efforts create improve similar strategies.

Language: Английский

---

Genomic insights into host–Endozoicomonadaceae cophylogeny

Microbial Genomics, Journal Year: 2025, Volume and Issue: 11(4)

Published: April 3, 2025

The congruence between host and symbiont phylogenies reflects the evolutionary links among ecologically important interactions. As potential key symbionts, members affiliated to family Endozoicomonadaceae have previously been investigated for cophylogenetic relationship with their hosts using 16S rRNA gene sequences. However, this approach neglects genomic features of symbionts that may influence long-term associations hosts. Here, we collected available high-quality genomes from diverse features, including genome size, phages, insertion elements composition functional genes. We also tested –Endozoicomonadaceae cophylogeny examined correlation squared residuals members. Our results revealed a pattern various Moreover, found were differentially eroded by phages elements. Additionally, smaller, more tended exhibit lower Gene function analysis further closer carried specific genes related infection processes host–symbiont This study suggests intimate associations.

Language: Английский

---

Unveiling plasmid diversity and functionality in pristine groundwater

Environmental Microbiome, Journal Year: 2025, Volume and Issue: 20(1)

Published: April 24, 2025

Language: Английский

---

High-quality metagenome assembly from nanopore reads with nanoMDBG

Published: April 24, 2025

Abstract Third-generation long-read sequencing technologies, have been shown to significantly enhance the quality of metagenome assemblies. The results obtained using highly accurate reads generated by PacBio HiFi particularly notable yielding hundreds circularized, complete genomes as metagenome-assembled (MAGs) without manual intervention. Oxford Nanopore Technologies (ONT) has recently improved accuracy its reads, achieving a per-base error rate approximately 1-2%. Given high-throughput, convenience and low-cost ONT this could accelerate uptake long read metagenomics. However, current assemblers are optimized for data underperform on latest do not scale large sets that it enables. We present nanoMDBG, an evolution metaMDBG assembler, designed support newer through novel pre-processing step performs fast correction in minimizer-space. Across range datasets, including 400 Gbp soil sample sequenced specifically study, nanoMDBG reconstructs up twice many high-quality MAGs next best metaFlye, while requiring third CPU time memory. As result these advances, we show technology can now produce comparable those at same depth.

Language: Английский

---

Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome

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

Published: Sept. 27, 2024

The human gut contains diverse communities of bacteriophage, whose interactions with the broader microbiome and potential roles in health are only beginning to be uncovered. Here, we combine multiple types data quantitatively estimate phage population dynamics lifestyle characteristics subjects. Unifying results from previous studies, show that an average a low ratio particles bacterial cells (~1:100), but much larger genomes (~4:1), implying most effectively temperate (e.g., integrated prophage, phage-plasmids, etc.). By integrating imaging sequencing generalized model dynamics, induction lysis occurs at rate (~0.001-0.01 per bacterium day), imposing modest fitness burden on their hosts. Consistent these estimates, find composition synthetic community gnotobiotic mice can predicted abundances alone, while still exhibiting diversity comparable native microbiomes. These provide foundation for interpreting existing future studies links between virome health.

Language: Английский

---

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

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

Published: Aug. 1, 2023

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 OmcZ nanowire-like electron-exporting 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

---

An extended catalog of integrated prophages in the infant and adult fecal microbiome shows high prevalence of lysogeny

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: Sept. 5, 2023

The acquisition and gradual maturation of gut microbial communities during early childhood is central to an individual's healthy development. Bacteriophages have the potential shape bacterial communities. However, complex ecological interactions between phages their host are still poorly characterized. In this study, we investigated abundance diversity integrated prophages in infant adult bacteria by detecting metagenome assembled genomes (MAGs) commensal bacteria.

Language: Английский

---

Large language models improve annotation of viral proteins

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: May 2, 2023

Abstract Viral sequences are poorly annotated in environmental samples, a major roadblock to understanding how viruses influence microbial community structure. Current annotation approaches rely on alignment-based sequence homology methods, which limited by available viral and divergence proteins. Here, we show that protein language model representations capture function beyond the limits of remote targeting two axes annotation: systematic labeling families identification for biologic discovery. Protein functional properties specific expand fraction ocean virome 37%. Among unannotated families, identify novel DNA editing family defines new mobile element marine picocyanobacteria. models thus significantly enhance detection proteins can be utilized enable biological discovery across diverse categories.

Language: Английский

---

Revisiting evolutionary trajectories and the organization of the Pleolipoviridae family

PLoS Genetics, Journal Year: 2023, Volume and Issue: 19(10), P. e1010998 - e1010998

Published: Oct. 13, 2023

Archaeal pleomorphic viruses belonging to the Pleolipoviridae family represent an enigmatic group as they exhibit unique genomic features and are thought have evolved through recombination with different archaeal plasmids. However, most of our understanding diversity evolutionary trajectories this clade comes from a handful isolated representatives. Here we present 164 new genomes pleolipoviruses obtained metagenomic data Australian hypersaline lakes publicly available data. We perform comprehensive analysis on relationships newly discovered previously described pleolipoviruses. propose classify into five genera within family, one genus represented only by virus retrieved in study. Our support current hypothesis that reshaped their recombining multiple groups plasmids, which is reflected predicted replication strategies. show proposed Epsilonpleolipovirus has ties pRN1-like plasmids Sulfolobus, suggesting could be infecting other phyla. Interestingly, observed genome size correlated presence or absence integrase. Analyses host range revealed all but extremely narrow range, tertiary structure spike protein strongly associated specific adaptation S-layer glycoprotein organization.

Language: Английский

---

Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression

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

Published: Dec. 12, 2023

There are an estimated 300,000 mammalian viruses from which infectious diseases in humans may arise. They inhabit human tissues such as the lungs, blood, and brain often remain undetected. Efficient accurate detection of viral infection is vital to understanding its impact on health make predictions limit adverse effects, future epidemics. The increasing use high-throughput sequencing methods research, agriculture, healthcare provides opportunity for cost-effective surveillance diversity investigation virus-disease correlation. However, existing identifying data rely limited reference genomes or cannot retain single-cell resolution through cell barcode tracking. We introduce a method that accurately rapidly detects sequences bulk transcriptomics based highly conserved amino acid domains, enables RNA covering up 10

Language: Английский

---