A genomic catalog of Earth’s microbiomes

Nature Biotechnology, Journal Year: 2020, Volume and Issue: 39(4), P. 499 - 509

Published: Nov. 9, 2020

Abstract The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology evolution environmental host-associated microbiomes. Here we applied this approach to >10,000 collected diverse habitats covering all Earth’s continents oceans, including human animal hosts, engineered environments, natural agricultural soils, capture extant microbial, metabolic functional potential. This comprehensive catalog includes 52,515 metagenome-assembled representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. expands known phylogenetic diversity bacteria archaea by 44% is broadly available for streamlined comparative analyses, interactive exploration, modeling bulk download. We demonstrate utility collection understanding secondary-metabolite biosynthetic potential resolving thousands new host linkages uncultivated viruses. resource underscores value genome-centric approaches revealing genomic properties microorganisms that affect ecosystem processes.

Language: Английский

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Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin

Nature Ecology & Evolution, Journal Year: 2018, Volume and Issue: 2(10), P. 1556 - 1562

Published: Aug. 16, 2018

Language: Английский

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Tara Oceans: towards global ocean ecosystems biology

Nature Reviews Microbiology, Journal Year: 2020, Volume and Issue: 18(8), P. 428 - 445

Published: May 12, 2020

Language: Английский

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phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes

mSystems, Journal Year: 2020, Volume and Issue: 5(5)

Published: Oct. 27, 2020

The small-subunit rRNA (SSU rRNA) gene is the key marker in molecular ecology for all domains of life, but it largely absent from metagenome-assembled genomes that often are only resource available environmental microbes. Here, we present phyloFlash, a pipeline to overcome this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based binning full metagenomic assemblies. We show cleanup artifacts pivotal even curated reference database. With such filtered database, general-purpose mapper BBmap extracts reads five times faster than rRNA-specialized tool SortMeRNA similar sensitivity higher selectivity on simulated metagenomes. Reference-based assemblers yielded either highly fragmented assemblies or high levels chimerism, so employ genomic assembler SPAdes. Our optimized implementation independent database composition has satisfactory chimera formation. phyloFlash quickly processes Illumina (meta)genomic data, straightforward use, as part high-throughput quality control, user-friendly output reports. software at https://github.com/HRGV/phyloFlash (GPL3 license) documented an online manual.IMPORTANCE To track organisms across gold standard. Many microbes known sequence gene, visualization by probes link existing literature, missing (MAGs). easy-to-use suite tackles linking MAGs. Starting cleaned profiles diversity assembles sorted reads. design domain agnostic covers eukaryotes, archaea, bacteria alike. also provides utilities visualize multisample comparisons integrate recovered rRNAs metagenomics workflow them MAGs using assembly graph parsing.

Language: Английский

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Mitochondrial dysfunction: mechanisms and advances in therapy

Signal Transduction and Targeted Therapy, Journal Year: 2024, Volume and Issue: 9(1)

Published: May 15, 2024

Abstract Mitochondria, with their intricate networks of functions and information processing, are pivotal in both health regulation disease progression. Particularly, mitochondrial dysfunctions identified many common pathologies, including cardiovascular diseases, neurodegeneration, metabolic syndrome, cancer. However, the multifaceted nature elusive phenotypic threshold dysfunction complicate our understanding contributions to diseases. Nonetheless, these complexities do not prevent mitochondria from being among most important therapeutic targets. In recent years, strategies targeting have continuously emerged transitioned clinical trials. Advanced intervention such as using healthy replenish or replace damaged mitochondria, has shown promise preclinical trials various Mitochondrial components, mtDNA, mitochondria-located microRNA, associated proteins can be potential agents augment function immunometabolic diseases tissue injuries. Here, we review current knowledge pathophysiology concrete examples We also summarize treat perspective dietary supplements targeted therapies, well translational situation related pharmacology agents. Finally, this discusses innovations applications transplantation an advanced promising treatment.

Language: Английский

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Mechanisms and regulation of protein synthesis in mitochondria

Nature Reviews Molecular Cell Biology, Journal Year: 2021, Volume and Issue: 22(5), P. 307 - 325

Published: Feb. 16, 2021

Language: Английский

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Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes

Frontiers in Genetics, Journal Year: 2020, Volume and Issue: 11

Published: Sept. 25, 2020

Understanding the complexity of genomic structures and their unique architecture is linked with power visualization tools used to represent these features. Such should be able provide a realistic scalable version content. Here we present an online organelle plotting tool focused on chloroplasts, which was developed visualize exclusive structure genomes. The distinguished features this program include its ability Single Short Copy (SSC) regions in reverse complement, allows depiction codon usage bias index for each gene, along possibility minor mismatches between Inverted Repeat (IR) regions, user-specified layers. versatile color schemes diverse functionalities are specifically designed reflect accurate representation plastid We introduce Shiny app website easy use program; more advanced application possible by further development modification downloadable source codes provided online. software libraries completely coded R, available at https://irscope.shinyapps.io/chloroplot/.

Language: Английский

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Extreme heterogeneity of human mitochondrial DNA from organelles to populations

Nature Reviews Genetics, Journal Year: 2020, Volume and Issue: 22(2), P. 106 - 118

Published: Sept. 28, 2020

Language: Английский

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MIROs and DRP1 drive mitochondrial-derived vesicle biogenesis and promote quality control

Nature Cell Biology, Journal Year: 2021, Volume and Issue: 23(12), P. 1271 - 1286

Published: Dec. 1, 2021

Language: Английский

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Shaping Neuronal Fate: Functional Heterogeneity of Direct Microglia-Neuron Interactions

Neuron, Journal Year: 2020, Volume and Issue: 109(2), P. 222 - 240

Published: Dec. 2, 2020

Language: Английский

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