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1. Towards the biogeography of prokaryotic genes

Author

Coelho, Luis Pedro, Alves, Renato, del Río, Álvaro Rodríguez, Myers, Pernille Neve, Cantalapiedra, Carlos P., Giner-Lamia, Joaquín, Schmidt, Thomas Sebastian, Mende, Daniel R., Orakov, Askarbek, Letunic, Ivica, Hildebrand, Falk, Van Rossum, Thea, Forslund, Sofia K., Khedkar, Supriya, Maistrenko, Oleksandr M., Pan, Shaojun, Jia, Longhao, Ferretti, Pamela, Sunagawa, Shinichi, Zhao, Xing-Ming, Nielsen, Henrik Bjørn, Huerta-Cepas, Jaime, and Bork, Peer

Published
2022
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3. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes

Author

European Molecular Biology Laboratory, Swiss National Science Foundation, German Research Foundation, European Commission, Agencia Estatal de Investigación (España), Ministerio de Universidades (España), Fullam, Anthony [0000-0002-0884-8124], Letunic, Ivica [0000-0003-3560-4288], Schmidt, Thomas Sebastian [B0000-0001-8587-4177], Ducarmon, Quinten R. [0000-0001-7077-2127], Karcher, Nicolai [0000-0001-7894-8182], Khedkar, Supriya [0000-0001-6606-2202], Kuhn, Michael [0000-0002-2841-872X], Larralde, Martin [0000-0002-3947-4444], Maistrenko, Oleksandr M. [0000-0003-1961-7548], Malfertheiner, Lukas [0000-0002-5697-2007], Milanese, Alessio [0000-0002-7050-2239], Rodrigues, Joao Frederico Matias [0000-0001-8413-9920], Sanchis-López, Claudia [0000-0002-8206-1565], Schudoma, Christian [0000-0003-1157-1354], Szklarczyk, Damian [0000-0002-4052-5069], Sunagawa, Shinichi [0000-0003-3065-0314], Zeller, Georg [0000-0003-1429-7485], Huerta-Cepas, Jaime [0000-0003-4195-5025], von Mering, Christian [0000-0001-7734-9102], Bork, Peer [0000-0002-2627-833X], Mende, Daniel R. [0000-0001-6831-4557], Fullam, Anthony, Letunic, Ivica, Schmidt, Thomas Sebastian, Ducarmon, Quinten R., Karcher, Nicolai, Khedkar, Supriya, Kuhn, Michael, Larralde, Martin, Maistrenko, Oleksandr M., Malfertheiner, Lukas, Milanese, Alessio, Rodrigues, Joao Frederico Matias, Sanchis-López, Claudia, Schudoma, Christian, Szklarczyk, Damian, Sunagawa, Shinichi, Zeller, Georg, Huerta-Cepas, Jaime, von Mering, Christian, Bork, Peer, Mende, Daniel R., European Molecular Biology Laboratory, Swiss National Science Foundation, German Research Foundation, European Commission, Agencia Estatal de Investigación (España), Ministerio de Universidades (España), Fullam, Anthony [0000-0002-0884-8124], Letunic, Ivica [0000-0003-3560-4288], Schmidt, Thomas Sebastian [B0000-0001-8587-4177], Ducarmon, Quinten R. [0000-0001-7077-2127], Karcher, Nicolai [0000-0001-7894-8182], Khedkar, Supriya [0000-0001-6606-2202], Kuhn, Michael [0000-0002-2841-872X], Larralde, Martin [0000-0002-3947-4444], Maistrenko, Oleksandr M. [0000-0003-1961-7548], Malfertheiner, Lukas [0000-0002-5697-2007], Milanese, Alessio [0000-0002-7050-2239], Rodrigues, Joao Frederico Matias [0000-0001-8413-9920], Sanchis-López, Claudia [0000-0002-8206-1565], Schudoma, Christian [0000-0003-1157-1354], Szklarczyk, Damian [0000-0002-4052-5069], Sunagawa, Shinichi [0000-0003-3065-0314], Zeller, Georg [0000-0003-1429-7485], Huerta-Cepas, Jaime [0000-0003-4195-5025], von Mering, Christian [0000-0001-7734-9102], Bork, Peer [0000-0002-2627-833X], Mende, Daniel R. [0000-0001-6831-4557], Fullam, Anthony, Letunic, Ivica, Schmidt, Thomas Sebastian, Ducarmon, Quinten R., Karcher, Nicolai, Khedkar, Supriya, Kuhn, Michael, Larralde, Martin, Maistrenko, Oleksandr M., Malfertheiner, Lukas, Milanese, Alessio, Rodrigues, Joao Frederico Matias, Sanchis-López, Claudia, Schudoma, Christian, Szklarczyk, Damian, Sunagawa, Shinichi, Zeller, Georg, Huerta-Cepas, Jaime, von Mering, Christian, Bork, Peer, and Mende, Daniel R.

Abstract

The interpretation of genomic, transcriptomic and other microbial 'omics data is highly dependent on the availability of well-annotated genomes. As the number of publicly available microbial genomes continues to increase exponentially, the need for quality control and consistent annotation is becoming critical. We present proGenomes3, a database of 907 388 high-quality genomes containing 4 billion genes that passed stringent criteria and have been consistently annotated using multiple functional and taxonomic databases including mobile genetic elements and biosynthetic gene clusters. proGenomes3 encompasses 41 171 species-level clusters, defined based on universal single copy marker genes, for which pan-genomes and contextual habitat annotations are provided. The database is available at http://progenomes.embl.de/.

Published
2023

4. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes

Author

Fullam, Anthony; https://orcid.org/0000-0002-0884-8124, Letunic, Ivica; https://orcid.org/0000-0003-3560-4288, Schmidt, Thomas S B; https://orcid.org/0000-0001-8587-4177, Ducarmon, Quinten R; https://orcid.org/0000-0001-7077-2127, Karcher, Nicolai; https://orcid.org/0000-0001-7894-8182, Khedkar, Supriya; https://orcid.org/0000-0001-6606-2202, Kuhn, Michael; https://orcid.org/0000-0002-2841-872X, Larralde, Martin; https://orcid.org/0000-0002-3947-4444, Maistrenko, Oleksandr M; https://orcid.org/0000-0003-1961-7548, Malfertheiner, Lukas; https://orcid.org/0000-0002-5697-2007, Milanese, Alessio; https://orcid.org/0000-0002-7050-2239, Rodrigues, Joao Frederico Matias; https://orcid.org/0000-0001-8413-9920, Sanchis-López, Claudia; https://orcid.org/0000-0002-8206-1565, Schudoma, Christian; https://orcid.org/0000-0003-1157-1354, Szklarczyk, Damian; https://orcid.org/0000-0002-4052-5069, Sunagawa, Shinichi; https://orcid.org/0000-0003-3065-0314, Zeller, Georg; https://orcid.org/0000-0003-1429-7485, Huerta-Cepas, Jaime; https://orcid.org/0000-0003-4195-5025, von Mering, Christian; https://orcid.org/0000-0001-7734-9102, Bork, Peer; https://orcid.org/0000-0002-2627-833X, Mende, Daniel R; https://orcid.org/0000-0001-6831-4557, Fullam, Anthony; https://orcid.org/0000-0002-0884-8124, Letunic, Ivica; https://orcid.org/0000-0003-3560-4288, Schmidt, Thomas S B; https://orcid.org/0000-0001-8587-4177, Ducarmon, Quinten R; https://orcid.org/0000-0001-7077-2127, Karcher, Nicolai; https://orcid.org/0000-0001-7894-8182, Khedkar, Supriya; https://orcid.org/0000-0001-6606-2202, Kuhn, Michael; https://orcid.org/0000-0002-2841-872X, Larralde, Martin; https://orcid.org/0000-0002-3947-4444, Maistrenko, Oleksandr M; https://orcid.org/0000-0003-1961-7548, Malfertheiner, Lukas; https://orcid.org/0000-0002-5697-2007, Milanese, Alessio; https://orcid.org/0000-0002-7050-2239, Rodrigues, Joao Frederico Matias; https://orcid.org/0000-0001-8413-9920, Sanchis-López, Claudia; https://orcid.org/0000-0002-8206-1565, Schudoma, Christian; https://orcid.org/0000-0003-1157-1354, Szklarczyk, Damian; https://orcid.org/0000-0002-4052-5069, Sunagawa, Shinichi; https://orcid.org/0000-0003-3065-0314, Zeller, Georg; https://orcid.org/0000-0003-1429-7485, Huerta-Cepas, Jaime; https://orcid.org/0000-0003-4195-5025, von Mering, Christian; https://orcid.org/0000-0001-7734-9102, Bork, Peer; https://orcid.org/0000-0002-2627-833X, and Mende, Daniel R; https://orcid.org/0000-0001-6831-4557

Abstract

The interpretation of genomic, transcriptomic and other microbial 'omics data is highly dependent on the availability of well-annotated genomes. As the number of publicly available microbial genomes continues to increase exponentially, the need for quality control and consistent annotation is becoming critical. We present proGenomes3, a database of 907 388 high-quality genomes containing 4 billion genes that passed stringent criteria and have been consistently annotated using multiple functional and taxonomic databases including mobile genetic elements and biosynthetic gene clusters. proGenomes3 encompasses 41 171 species-level clusters, defined based on universal single copy marker genes, for which pan-genomes and contextual habitat annotations are provided. The database is available at http://progenomes.embl.de/.

Published
2023

5. Towards the biogeography of prokaryotic genes

Author

European Commission, European Research Council, Helmut Horten Foundation, National Key Research and Development Program (China), Shanghai Municipal Education Commission, International Development Research Centre (Canada), Fundación la Caixa, Agencia Estatal de Investigación (España), Innovation Fund Denmark, Coelho, Luis Pedro [0000-0002-9280-7885], Alves, Renato [0000-0002-7212-0234], Del Río, Álvaro Rodríguez [0000-0003-3907-3904], Myers, Pernille Neve [0000-0002-1824-3305], Cantalapiedra, Carlos P [0000-0001-5263-533X], Giner-Lamia, Joaquín [0000-0003-1553-8295], Mende, Daniel R. [0000-0001-6831-4557], Orakov, Askarbek [0000-0001-6823-5269], Letunic, Ivica [0000-0003-3560-4288], Hildebrand, Falk [0000-0002-0078-8948], Van Rossum, Thea [0000-0002-3598-5001], Forslund, Sofia K [0000-0003-4285-6993], Khedkar, Supriya [0000-0001-6606-2202], Maistrenko, Oleksandr M [0000-0003-1961-7548], Pan, Shaojun [0000-0002-5270-5614], Jia, Longhao [0000-0002-3490-840X], Ferretti, Pamela [0000-0002-1707-9013], Sunagawa, Shinichi [0000-0003-3065-0314], Nielsen, Henrik Bjørn [0000-0003-2281-5713], Huerta-Cepas, Jaime [0000-0003-4195-5025], Bork, Peer [0000-0002-2627-833X], Coelho, Luis Pedro, Alves, Renato, Del Río, Álvaro Rodríguez, Myers, Pernille Neve, Cantalapiedra, Carlos P, Giner-Lamia, Joaquín, Schmidt, Thomas Sebastian, Mende, Daniel R., Orakov, Askarbek, Letunic, Ivica, Hildebrand, Falk, Van Rossum, Thea, Forslund, Sofía K., Khedkar, Supriya, Maistrenko, Oleksandr M., Pan, Shaojun, Jia, Longhao, Ferretti, Pamela, Sunagawa, Shinichi, Zhao, Xing-Ming, Nielsen, Henrik Bjørn, Huerta-Cepas, Jaime, Bork, Peer, European Commission, European Research Council, Helmut Horten Foundation, National Key Research and Development Program (China), Shanghai Municipal Education Commission, International Development Research Centre (Canada), Fundación la Caixa, Agencia Estatal de Investigación (España), Innovation Fund Denmark, Coelho, Luis Pedro [0000-0002-9280-7885], Alves, Renato [0000-0002-7212-0234], Del Río, Álvaro Rodríguez [0000-0003-3907-3904], Myers, Pernille Neve [0000-0002-1824-3305], Cantalapiedra, Carlos P [0000-0001-5263-533X], Giner-Lamia, Joaquín [0000-0003-1553-8295], Mende, Daniel R. [0000-0001-6831-4557], Orakov, Askarbek [0000-0001-6823-5269], Letunic, Ivica [0000-0003-3560-4288], Hildebrand, Falk [0000-0002-0078-8948], Van Rossum, Thea [0000-0002-3598-5001], Forslund, Sofia K [0000-0003-4285-6993], Khedkar, Supriya [0000-0001-6606-2202], Maistrenko, Oleksandr M [0000-0003-1961-7548], Pan, Shaojun [0000-0002-5270-5614], Jia, Longhao [0000-0002-3490-840X], Ferretti, Pamela [0000-0002-1707-9013], Sunagawa, Shinichi [0000-0003-3065-0314], Nielsen, Henrik Bjørn [0000-0003-2281-5713], Huerta-Cepas, Jaime [0000-0003-4195-5025], Bork, Peer [0000-0002-2627-833X], Coelho, Luis Pedro, Alves, Renato, Del Río, Álvaro Rodríguez, Myers, Pernille Neve, Cantalapiedra, Carlos P, Giner-Lamia, Joaquín, Schmidt, Thomas Sebastian, Mende, Daniel R., Orakov, Askarbek, Letunic, Ivica, Hildebrand, Falk, Van Rossum, Thea, Forslund, Sofía K., Khedkar, Supriya, Maistrenko, Oleksandr M., Pan, Shaojun, Jia, Longhao, Ferretti, Pamela, Sunagawa, Shinichi, Zhao, Xing-Ming, Nielsen, Henrik Bjørn, Huerta-Cepas, Jaime, and Bork, Peer

Abstract

Microbial genes encode the majority of the functional repertoire of life on earth. However, despite increasing efforts in metagenomic sequencing of various habitats1,2,3, little is known about the distribution of genes across the global biosphere, with implications for human and planetary health. Here we constructed a non-redundant gene catalogue of 303 million species-level genes (clustered at 95% nucleotide identity) from 13,174 publicly available metagenomes across 14 major habitats and use it to show that most genes are specific to a single habitat. The small fraction of genes found in multiple habitats is enriched in antibiotic-resistance genes and markers for mobile genetic elements. By further clustering these species-level genes into 32 million protein families, we observed that a small fraction of these families contain the majority of the genes (0.6% of families account for 50% of the genes). The majority of species-level genes and protein families are rare. Furthermore, species-level genes, and in particular the rare ones, show low rates of positive (adaptive) selection, supporting a model in which most genetic variability observed within each protein family is neutral or nearly neutral.

Published
2021

6. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes

Author

Fullam, Anthony, primary, Letunic, Ivica, additional, Schmidt, Thomas S B, additional, Ducarmon, Quinten R, additional, Karcher, Nicolai, additional, Khedkar, Supriya, additional, Kuhn, Michael, additional, Larralde, Martin, additional, Maistrenko, Oleksandr M, additional, Malfertheiner, Lukas, additional, Milanese, Alessio, additional, Rodrigues, Joao Frederico Matias, additional, Sanchis-López, Claudia, additional, Schudoma, Christian, additional, Szklarczyk, Damian, additional, Sunagawa, Shinichi, additional, Zeller, Georg, additional, Huerta-Cepas, Jaime, additional, von Mering, Christian, additional, Bork, Peer, additional, and Mende, Daniel R, additional

Published
2022
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8. Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes

Author

Khedkar, Supriya, primary, Smyshlyaev, Georgy, additional, Letunic, Ivica, additional, Maistrenko, Oleksandr M, additional, Coelho, Luis Pedro, additional, Orakov, Askarbek, additional, Forslund, Sofia K, additional, Hildebrand, Falk, additional, Luetge, Mechthild, additional, Schmidt, Thomas S B, additional, Barabas, Orsolya, additional, and Bork, Peer, additional

Published
2022
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9. GUNC Poster at ISME 2022

Author

Orakov, Askarbek, Fullam, Anthony, Coelho, Luis Pedro, Khedkar, Supriya, Szklarczyk, Damian, Mende, Daniel R., Sebastian Benedikt Schmidt, Thomas, and Bork, Peer

Abstract

It's a poster to present the GUNC tool at ISME 2022 Conference. GUNC (the Genome UNClutterer) is a tool that accurately detects and quantifies prokaryotic genome chimerism based on the lineage homogeneity of individual contigs using a genome’s full complement of genes.

Published
2022
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11. Towards the biogeography of prokaryotic genes

Author

Coelho, Luis Pedro, primary, Alves, Renato, additional, del Río, Álvaro Rodríguez, additional, Myers, Pernille Neve, additional, Cantalapiedra, Carlos P., additional, Giner-Lamia, Joaquín, additional, Schmidt, Thomas Sebastian, additional, Mende, Daniel R., additional, Orakov, Askarbek, additional, Letunic, Ivica, additional, Hildebrand, Falk, additional, Van Rossum, Thea, additional, Forslund, Sofia K., additional, Khedkar, Supriya, additional, Maistrenko, Oleksandr M., additional, Pan, Shaojun, additional, Jia, Longhao, additional, Ferretti, Pamela, additional, Sunagawa, Shinichi, additional, Zhao, Xing-Ming, additional, Nielsen, Henrik Bjørn, additional, Huerta-Cepas, Jaime, additional, and Bork, Peer, additional

Published
2021
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12. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes.

Author

Fullam, Anthony, Letunic, Ivica, Schmidt, Thomas S B, Ducarmon, Quinten R, Karcher, Nicolai, Khedkar, Supriya, Kuhn, Michael, Larralde, Martin, Maistrenko, Oleksandr M, Malfertheiner, Lukas, Milanese, Alessio, Rodrigues, Joao Frederico Matias, Sanchis-López, Claudia, Schudoma, Christian, Szklarczyk, Damian, Sunagawa, Shinichi, Zeller, Georg, Huerta-Cepas, Jaime, von Mering, Christian, and Bork, Peer

Published
2023
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14. Additional file 1 of GUNC: detection of chimerism and contamination in prokaryotic genomes

Author

Orakov, Askarbek, Fullam, Anthony, Coelho, Luis Pedro, Khedkar, Supriya, Szklarczyk, Damian, Mende, Daniel R., Schmidt, Thomas S. B., and Bork, Peer

Abstract

Additional file 1: Figure S1. a Percent stacked bar chart of CheckM inferred marker lineage levels (colors) for type 3a simulated chimeric genomes (see Methods & Fig. 2a) across different: 1) divergence levels of source genomes (x-axis); 2) simulated portions of contamination (columns); and 3) scenarios of contamination (‘added’ vs ‘replaced’, rows; see Methods). In a and b, the first column (“0”) are clean (non-chimeric) genomes shown for comparison. b Average inferred CheckM marker lineage depth (y-axis) of simulated chimeric genomes under different contamination scenarios (‘added’ in dark blue; ‘replaced’ in light blue). The true taxonomic depth of divergence between source genomes are indicated in green. c Equivalent to a, but using chimeric genomes simulated from multiple sources (type 3b in Fig. 2a). Columns indicate the number of equally contributing source genomes (n_sources); rows indicate simulation setups (‘0.5’ if 50% of each source genome was used; ‘1/n_sources’ for equal source parts; see Methods). In c & d, the first column (“1”) are clean (non-chimeric) genomes, the second column (“2”) are type 3a genomes as in a & b, shown for comparison. d Average inferred CheckM marker lineage depths (y-axis) with different portions of contamination, equivalent to panel b. Figure S2. Comparison of median scores from GUNC and CheckM of simulations of genomes type 3a and 3b where source genomes make equal contributions summing 1 in total (e.g. 0.2 from each of 5 sources or 0.25 from each of 4 sources). This shows that the trend from Fig. 2b persists when multiple source genomes are mixed in a simulated chimeric genome. Figure S3. F-scores of distinction between clean and chimeric genomes across all divergence levels of source genomes for different simulation scenarios. MIMAG medium is CheckM contamination < 10% and CheckM completeness ≥50%. MIMAG high is CheckM contamination 90% and due to irrelevance to our simulations we decided that additional criteria of presence of rRNAs and tRNAs can be ignored here. “Cont” stands for CheckM contamination and GUNC means GUNC CSS of 0.45 & contamination >2%). The stacked bar plot on the right indicates the numbers of genomes from the overlap in each category. These categories do have overlaps and therefore genomes in them were counted and removed from the set used to count remaining categories in the following order of their genome counts: 71 > 34 > 86 > 187 & 29. Figure S8. a Cumulative plot summarizing genome qualities of various sets of genomes represented by lines of different colors. Any point in a plot indicates a portion of genomes retained in a set (y-axis) after filtering out genomes with GUNC CSS higher than the cutoff (x-axis) & GUNC contamination >5% (ignoring species-level scores). b Cumulative plot illustrating the number of species-level genome bins (SGBs) (from Pasolli et al. 2019). Lines indicate the portion of unique SGBs retained (y-axis) after filtering out SGBs where either “all” or “at least one” genome has GUNC CSS score higher than the cutoff (x-axis) & GUNC contamination >5%. Figure S9. Cumulative plots summarizing genome quality for various genome reference and MAG datasets. This plot is equivalent to main Fig. 3a, but using a reference set based on GTDB v95 instead of GUNC’s default based on proGenomes 2.1 (see Methods for details). Note that the Almeida, Pasolli and Nayfach sets were pre-filtered using variations of the MIMAG medium criterion based on CheckM estimates. GTDB, Genome Taxonomy Database; GMGC, Global Microbial Gene Catalogue. Figure S10. Alluvial illustration of the fate of genomes in GMGC based on filters by GUNC and CheckM. Three filters are: 1) CheckM contamination

Published
2021
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26. Genome Sequencing Unveils a Novel Sea Enterotoxin-Carrying PVL Phage in Staphylococcus aureus ST772 from India.

Author

Prabhakara, Sushma, Khedkar, Supriya, Shambat, Srikanth Mairpady, Srinivasan, Rajalakshmi, Basu, Atanu, Norrby-Teglund, Anna, Seshasayee, Aswin Sai Narain, and Arakere, Gayathri

Subjects
*STAPHYLOCOCCUS aureus, *GENOMES, *ENTEROTOXINS, *CELL proliferation, *CELL-mediated cytotoxicity, *SEQUENCE analysis, *MICROBIAL virulence, *IMMUNE system
Abstract

Staphylococcus aureus is a major human pathogen, first recognized as a leading cause of hospital-acquired infections. Community-associated S. aureus (CA-SA) pose a greater threat due to increase in severity of infection and disease among children and healthy adults. CA-SA strains in India are genetically diverse, among which is the sequence type (ST) 772, which has now spread to Australia, Europe and Japan. Towards understanding the genetic characteristics of ST772, we obtained draft genome sequences of five relevant clinical isolates and studied the properties of their PVL-carrying prophages, whose presence is a defining hallmark of CA-SA. We show that this is a novel prophage, which carries the structural genes of the hlb-carrying prophage and includes the sea enterotoxin. This architecture probably emerged early within the ST772 lineage, at least in India. The sea gene, unique to ST772 PVL, despite having promoter sequence characteristics typical of low expression, appears to be highly expressed during early phase of growth in laboratory conditions. We speculate that this might be a consequence of its novel sequence context. The crippled nature of the hlb-converting prophage in ST772 suggests that widespread mobility of the sea enterotoxin might be a selective force behind its ‘transfer’ to the PVL prophage. Wild type ST772 strains induced strong proliferative responses as well as high cytotoxic activity against neutrophils, likely mediated by superantigen SEA and the PVL toxin respectively. Both proliferation and cytotoxicity were markedly reduced in a cured ST772 strain indicating the impact of the phage on virulence. The presence of SEA alongside the genes for the immune system-modulating PVL toxin may contribute to the success and virulence of ST772. [ABSTRACT FROM AUTHOR]

Published
2013
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27. A novel form of gene regulation in bacteria.

Author

Khedkar, Supriya and Perinchery, Aathfra

Subjects
GENETIC regulation, ESCHERICHIA coli, METHYLATION, DNA
Abstract

The article presents a study that investigates the gene regulation of the bacteria Escherichia coli in India. Researchers studied the DNA of Escherichia coli by isolating its genomics at its different stages of growth after they treated it with the reagent bisulfite to know its methylation status. They discovered that a particular protein known as rpoS, that regulates genes in stationary growth, is present in higher levels.

Published
2012

28. Towards the biogeography of prokaryotic genes

Author

Luis Pedro Coelho, Renato Alves, Álvaro Rodríguez del Río, Pernille Neve Myers, Carlos P. Cantalapiedra, Joaquín Giner-Lamia, Thomas Sebastian Schmidt, Daniel R. Mende, Askarbek Orakov, Ivica Letunic, Falk Hildebrand, Thea Van Rossum, Sofia K. Forslund, Supriya Khedkar, Oleksandr M. Maistrenko, Shaojun Pan, Longhao Jia, Pamela Ferretti, Shinichi Sunagawa, Xing-Ming Zhao, Henrik Bjørn Nielsen, Jaime Huerta-Cepas, Peer Bork, European Commission, European Research Council, Helmut Horten Foundation, National Key Research and Development Program (China), Shanghai Municipal Education Commission, International Development Research Centre (Canada), Fundación 'la Caixa', Agencia Estatal de Investigación (España), Innovation Fund Denmark, Coelho, Luis Pedro, Alves, Renato, Del Río, Álvaro Rodríguez, Myers, Pernille Neve, Cantalapiedra, Carlos P, Giner-Lamia, Joaquín, Mende, Daniel R, Orakov, Askarbek, Letunic, Ivica, Hildebrand, Falk, Van Rossum, Thea, Forslund, Sofia K, Khedkar, Supriya, Maistrenko, Oleksandr M, Pan, Shaojun, Jia, Longhao, Ferretti, Pamela, Sunagawa, Shinichi, Nielsen, Henrik Bjørn, Huerta-Cepas, Jaime, Bork, Peer, Coelho, Luis Pedro [0000-0002-9280-7885], Alves, Renato [0000-0002-7212-0234], Del Río, Álvaro Rodríguez [0000-0003-3907-3904], Myers, Pernille Neve [0000-0002-1824-3305], Cantalapiedra, Carlos P [0000-0001-5263-533X], Giner-Lamia, Joaquín [0000-0003-1553-8295], Mende, Daniel R [0000-0001-6831-4557], Orakov, Askarbek [0000-0001-6823-5269], Letunic, Ivica [0000-0003-3560-4288], Hildebrand, Falk [0000-0002-0078-8948], Van Rossum, Thea [0000-0002-3598-5001], Forslund, Sofia K [0000-0003-4285-6993], Khedkar, Supriya [0000-0001-6606-2202], Maistrenko, Oleksandr M [0000-0003-1961-7548], Pan, Shaojun [0000-0002-5270-5614], Jia, Longhao [0000-0002-3490-840X], Ferretti, Pamela [0000-0002-1707-9013], Sunagawa, Shinichi [0000-0003-3065-0314], Nielsen, Henrik Bjørn [0000-0003-2281-5713], Huerta-Cepas, Jaime [0000-0003-4195-5025], and Bork, Peer [0000-0002-2627-833X]

Subjects
Multidisciplinary, Humans, Metagenome, Drug Resistance, Microbial, Metagenomics, Ecosystem, Article, Anti-Bacterial Agents
Abstract

Funding was provided by the European Union’s Horizon 2020 Research and Innovation Programme (grant 686070: DD-DeCaF to P.B.) and Marie Skłodowska-Curie Actions (grant 713673 to A.R.d.R.), the European Research Council (ERC) MicrobioS (ERC-AdG-669830 to P.B.), JTC project jumpAR (01KI1706 to P.B.), a BMBF Grant (grant 031L0181A: LAMarCK to P.B.), the European Molecular Biology Laboratory (P.B.), the ETH and Helmut Horten Foundation (S.S.), the National Key R&D Program of China (grant 2020YFA0712403 to X.-M.Z.), (grant 61932008 to X.-M.Z.; grant 61772368 to X.-M.Z.; grant 31950410544 to L.P.C.), the Shanghai Municipal Science and Technology Major Project (grant 2018SHZDZX01 to X.-M.Z. and L.P.C.) and Zhangjiang Lab (X.-M.Z. and L.P.C.), the International Development Research Centre (grant 109304, EMBARK under the JPI AMR framework; to L.P.C.), la Caixa Foundation (grant 100010434, fellowship code LCF/BQ/DI18/11660009 to A.R.d.R.), the Severo Ochoa Program for Centres of Excellence in R&D from the Agencia Estatal de Investigación of Spain (grant SEV-2016-0672 (2017–2021) to C.P.C.), the Ministerio de Ciencia, Innovación y Universidades (grant PGC2018-098073-A-I00 MCIU/AEI/FEDER to J.H.-C. and J.G.-L.), the Innovation Fund Denmark (grant 4203-00005B, PNM), the Biotechnology and Biological Sciences research Council (BBSrC) Gut MicroInstitute Strategic Programmebes and Health BB/r012490/1 and its constituent project BBS/e/F/000Pr10355 (F.H.). R.A. is a member of the Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences.

Published
2021

29. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes

Author

Anthony Fullam, Ivica Letunic, Thomas S B Schmidt, Quinten R Ducarmon, Nicolai Karcher, Supriya Khedkar, Michael Kuhn, Martin Larralde, Oleksandr M Maistrenko, Lukas Malfertheiner, Alessio Milanese, Joao Frederico Matias Rodrigues, Claudia Sanchis-López, Christian Schudoma, Damian Szklarczyk, Shinichi Sunagawa, Georg Zeller, Jaime Huerta-Cepas, Christian von Mering, Peer Bork, Daniel R Mende, Medical Microbiology and Infection Prevention, AII - Infectious diseases, University of Zurich, European Molecular Biology Laboratory, Swiss National Science Foundation, German Research Foundation, European Commission, Agencia Estatal de Investigación (España), Ministerio de Universidades (España), Fullam, Anthony, Letunic, Ivica, Schmidt, Thomas Sebastian, Ducarmon, Quinten R., Karcher, Nicolai, Khedkar, Supriya, Kuhn, Michael, Larralde, Martin, Maistrenko, Oleksandr M., Malfertheiner, Lukas, Milanese, Alessio, Rodrigues, Joao Frederico Matias, Sanchis-López, Claudia, Schudoma, Christian, Szklarczyk, Damian, Sunagawa, Shinichi, Zeller, Georg, Huerta-Cepas, Jaime, von Mering, Christian, Bork, Peer, and Mende, Daniel R.

Subjects
UFSP13-7 Evolution in Action: From Genomes to Ecosystems, Cardiovascular and Metabolic Diseases, Genetics, 570 Life sciences, biology, 10124 Institute of Molecular Life Sciences
Abstract

7 Pág., The interpretation of genomic, transcriptomic and other microbial 'omics data is highly dependent on the availability of well-annotated genomes. As the number of publicly available microbial genomes continues to increase exponentially, the need for quality control and consistent annotation is becoming critical. We present proGenomes3, a database of 907 388 high-quality genomes containing 4 billion genes that passed stringent criteria and have been consistently annotated using multiple functional and taxonomic databases including mobile genetic elements and biosynthetic gene clusters. proGenomes3 encompasses 41 171 species-level clusters, defined based on universal single copy marker genes, for which pan-genomes and contextual habitat annotations are provided. The database is available at http://progenomes.embl.de/., Amsterdam UMC; European Molecular Biology Laboratory (EMBL); Swiss National Science Foundation (SNSF) [205321_184955 to S.S.]; NCCR Microbiomes [51NF40_180575 to S.S. and C.v.M.]; German Federal Ministry of Education and Research (BMBF); de.NBI network [031A537B to P.B., 031L0181A to G.Z.]; German Research Foundation (DFG) [395357507 – SFB 1371 to G.Z., ‘NFDI4Microbiota’ to P.B.]; European Grant with code [PGC2018-098073-A-I00MCIU/AEI/FEDER to J.H.-C.]; Spanish Ministry of Universities [FPU-19/06635 to C.S.-L.]. Funding for open access charge: EMBL.

Published
2022

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