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proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes
2016
Nucleic Acids Research
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It is nevertheless difficult to obtain consistent taxonomic and integrated functional annotations for defined prokaryotic clades. ...
Thus, we developed proGenomes, a resource that provides user-friendly access to currently 25 038 high-quality genomes whose sequences and consistent annotations can be retrieved individually or by taxonomic ...
D.R.M. would further like to thank Sebastian Schmidt and Frank Aylward for helpful discussions. ...
doi:10.1093/nar/gkw989
pmid:28053165
pmcid:PMC5210662
fatcat:xg2rdi5xpvdzzipjnyuhulrdry
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes
2019
Nucleic Acids Research
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Comparative genomics approaches have been a major advance, but consistent and accurate annotations of genomes can be hard to obtain. ...
Microbiology depends on the availability of annotated microbial genomes for many applications. ...
ACKNOWLEDGEMENTS The authors would like to thank the members of the Bork group, in particular Yan-Ping Yuan for technical support. ...
doi:10.1093/nar/gkz1002
pmid:31647096
pmcid:PMC7145564
fatcat:hqvc3agp5rarlcwm62ekvrkzta
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
2018
Nucleic Acids Research
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eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations. ...
Finally, we improved eggNOG online services for fast functional annotation and orthology prediction of custom genomics or metagenomics datasets. ...
Version 5 of eggNOG should thus be a useful resource for ecological, evolutionary or medical -omics analysis, also serving as an entry point for fast functional annotation of newly sequenced genes, genomes ...
doi:10.1093/nar/gky1085
pmid:30418610
fatcat:7gq2yqm3hjgspetm2c36xd3c3u
GUNC: detection of chimerism and contamination in prokaryotic genomes
2021
Genome Biology
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GUNC provides a fast and robust tool to substantially improve prokaryotic genome quality. ...
We present GUNC (the Genome UNClutterer), a tool that accurately detects and quantifies genome chimerism based on the lineage homogeneity of individual contigs using a genome's full complement of genes ...
We thank Oleksandr M Maistrenko and Donovan Parks for comments and feedback on the manuscript, as well as all members of the Bork lab for insightful discussions. ...
doi:10.1186/s13059-021-02393-0
pmid:34120611
pmcid:PMC8201837
fatcat:j4iim444rbal3iwbvevbol4gyi
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity
[article]
2019
bioRxiv
pre-print
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Hence, pan-genomes are increasingly used to characterize the strain diversity of prokaryotic species. ...
We show that many pan-genome features such as functional diversity and core genome nucleotide diversity are correlated to each other. ...
Mende DR, Letunic I, Huerta-Cepas J, Li SS, Forslund K, Sunagawa S, et al. proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. ...
doi:10.1101/735696
fatcat:454jtye3nneojd65wccn7dk6fq
MVP: a microbe–phage interaction database
2017
Nucleic Acids Research
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from published datasets, public databases and re-analysis of genomic and metagenomic sequences. ...
The main purpose of MVP (Microbe Versus Phage) is to provide a comprehensive catalog of phage-microbe interactions and assist users to select phage(s) that can target (and potentially to manipulate) specific ...
Second, we identified putative prophage sequences from complete bacterial and archaeal genomes downloaded from the NCBI prokaryotic reference genome database (40) and EMBL proGenomes database (41) . ...
doi:10.1093/nar/gkx1124
pmid:29177508
pmcid:PMC5753265
fatcat:jhblq52svjbjngnmapzsuhlpfy
Metagenomics: a path to understanding the gut microbiome
2021
Mammalian Genome
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AbstractThe gut microbiome is a major determinant of host health, yet it is only in the last 2 decades that the advent of next-generation sequencing has enabled it to be studied at a genomic level. ...
Shotgun sequencing is beginning to provide insight into the prokaryotic as well as eukaryotic and viral components of the gut community, revealing not just their taxonomy, but also the functions encoded ...
One of the largest resources for metagenome annotation and functional interpretation is the Kyoto Encyclopaedia of Genes and Genomes (KEGG), which curates functional information at both a genomic and systems ...
doi:10.1007/s00335-021-09889-x
pmid:34259891
pmcid:PMC8295064
fatcat:a7pfj4ugfzfh5nzyybpzko25eu
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives
2019
Marine Drugs
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As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies ...
It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment ...
The proGenomes initiative represents an attempt to provide a highly accurate prokaryotic genome database with curated taxonomic affiliations and functional annotations based on different collections, including ...
doi:10.3390/md17100576
pmid:31614509
pmcid:PMC6835618
fatcat:jch7dwrhgrhipihvf42zr6bljm
GUNC: Detection of Chimerism and Contamination in Prokaryotic Genomes
[article]
2020
biorxiv/medrxiv
pre-print
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We present GUNC (the Genome UNClutterer), a tool that accurately detects and quantifies genome chimerism based on the lineage homogeneity of individual contigs using a genome's full complement of genes ...
GUNC provides a fast and robust tool to substantially improve prokaryotic genome quality. Source code (GPLv3+): https://github.com/grp-bork/gunc ...
We thank Oleksandr M Maistrenko for comments and feedback on the manuscript, as well as all members of the Bork lab for insightful discussions.
Author Contributions ...
doi:10.1101/2020.12.16.422776
fatcat:wgkb3bprvja65mkhoasodpdyjm
Nitrogen availability drives gene length of dominant prokaryotes and diversity of genes acquiring Nitrogen-species in oceanic systems
[article]
2021
bioRxiv
pre-print
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Our findings introduce a novel and most effective mode of evolutionary adaptation of prokaryotes to save resources including N and energy. ...
Nitrogen (N) is a key element for prokaryotes in the oceans and often limits phytoplankton primary production. ...
In total 38% percent of nr genes were functionally annotated by homology to 92 a KEGG ortholog (KO) . ...
doi:10.1101/2021.01.10.426031
fatcat:zxckag3bancfvlah5virwemsma
Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile
2021
PLoS ONE
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Regardless of the differences at the taxonomic level, functionally the two mats were similar. Thus, similar roles could be fulfilled by different organisms. ...
In spite of presenting less taxonomic diversity, Tebenquiche mats showed increased abundance and variety of rhodopsin genes. ...
Acknowledgments The authors thank Marco Contreras for his support during the sampling campaign and Geol. ...
doi:10.1371/journal.pone.0246656
pmid:33561170
fatcat:ijd2d2bpgff7tbdqatdir6visa
Dispersal strategies shape persistence and evolution of human gut bacteria
2021
Cell Host and Microbe
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Our analyses revealed that a subset of gut species is extremely persistent in individuals, families, and geographic regions, represented often by locally successful strains of the phylum Bacteroidota. ...
Human gut bacterial strains can co-exist with their hosts for decades, but little is known about how these microbes persist and disperse, and evolve thereby. ...
., and Bork, P. (2017). proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. Nucleic Acids Res 45, D529-D534. ...
doi:10.1016/j.chom.2021.05.008
pmid:34111423
pmcid:PMC8288446
fatcat:4h5p2eyjpjditbrtoowjv2toly
Structure and function of the global topsoil microbiome
2018
Nature
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Dutch law entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of ...
You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work. ...
Liiv for technical and laboratory assistance; S. Waszak for comments on the manuscript; Y. P. Yuan and A. Glazek for bioinformatics support and A. ...
doi:10.1038/s41586-018-0386-6
pmid:30069051
fatcat:t4c25q37wnhs5owamf4deytm3i
Discovery, diversity and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts
[article]
2021
bioRxiv
pre-print
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Analysis of their genomic features revealed that closely related crAss-like phages can possess strikingly divergent regions responsible for transcription, presumably acquired through recombination. ...
Finally, we explored the temporal stability of crAss-like phages over a 4-year period and identified associations between the abundance of crAss-like phages and several human phenotypes, including depletion ...
We would like to thank Lianmin Chen and Sergio Andreu-Sánchez for technical support, Kate Mc Intyre for editing the manuscript, the Center for Information Technology of the University of Groningen for ...
doi:10.1101/2021.06.01.446427
fatcat:hbcajzqwynadllkzsv5jcmilby
Co-culture and biogeography of Prochlorococcus and SAR11
[article]
2018
bioRxiv
pre-print
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To place our results in context, we assessed the relative contribution of Prochlorococcus and SAR11 genome equivalents to those of identifiable bacteria and archaea in over 800 marine metagenomes. ...
With a combined global population of about 2.7 x 1028 cells, they numerically dominate bacterioplankton communities in oligotrophic ocean gyres and yet they have never been grown together in vitro. ...
Mende DR, Letunic I, Huerta-Cepas J, Li SS, Forslund K, Sunagawa S, et al. 563 proGenomes: a resource for consistent functional and taxonomic annotations of 564 prokaryotic genomes. ...
doi:10.1101/460428
fatcat:lsiw44qxqbaltko4or6tincxsu
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