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1. A genomic catalog of Earth’s microbiomes

Author

Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N., Schulz, F., Wu, D., Paez-Espino, D., Chen, I., Huntemann, M., Palaniappan, K., Ladau, J., Mukherjee, S., Reddy, T., Nielsen, T., Kirton, E., Faria, J., Edirisinghe, J., Henry, C., Jungbluth, S., Chivian, D., Dehal, P., Wood-Charlson, E., Arkin, A., Tringe, S., Visel, A., Abreu, H., Acinas, S., Allen, E., Allen, M., Alteio, L., Andersen, G., Anesio, A., Attwood, G., Avila-Magaña, V., Badis, Y., Bailey, J., Baker, B., Baldrian, P., Barton, H., Beck, D., Becraft, E., Beller, H., Beman, J., Bernier-Latmani, R., Berry, T., Bertagnolli, A., Bertilsson, S., Bhatnagar, J., Bird, J., Blanchard, J., Blumer-Schuette, S., Bohannan, B., Borton, M., Brady, A., Brawley, S., Brodie, J., Brown, S., Brum, J., Brune, A., Bryant, D., Buchan, A., Buckley, D., Buongiorno, J., Cadillo-Quiroz, H., Caffrey, S., Campbell, A., Campbell, B., Carr, S., Carroll, J., Cary, S., Cates, A., Cattolico, R., Cavicchioli, R., Chistoserdova, L., Coleman, M., Constant, P., Conway, J., Mac Cormack, W., Crowe, S., Crump, B., Currie, C., Daly, R., DeAngelis, K., Denef, V., Denman, S., Desta, A., Dionisi, H., Dodsworth, J., Dombrowski, N., Donohue, T., Dopson, M., Driscoll, T., Dunfield, P., Dupont, C., Dynarski, K., Edgcomb, V., Edwards, E., Elshahed, M., Figueroa, I., Flood, B., Fortney, N., Fortunato, C., Francis, C., Gachon, C., Garcia, S., Gazitua, M., Gentry, T., Gerwick, L., Gharechahi, J., Girguis, P., Gladden, J., Gradoville, M., Grasby, S., Gravuer, K., Grettenberger, C., Gruninger, R., Guo, J., Habteselassie, M., Hallam, S., Hatzenpichler, R., Hausmann, B., Hazen, T., Hedlund, B., Henny, C., Herfort, L., Hernandez, M., Hershey, O., Hess, M., Hollister, E., Hug, L., Hunt, D., Jansson, J., Jarett, J., Kadnikov, V., Kelly, C., Kelly, R., Kelly, W., Kerfeld, C., Kimbrel, J., Klassen, J., Konstantinidis, K., Lee, L., Li, W., Loder, A., Loy, A., Lozada, M., MacGregor, B., Magnabosco, C., Maria da Silva, A., McKay, R., McMahon, K., McSweeney, C., Medina, M., Meredith, L., Mizzi, J., Mock, T., Momper, L., Moran, M., Morgan-Lang, C., Moser, D., Muyzer, G., Myrold, D., Nash, M., Nesbø, C., Neumann, A., Neumann, R., Noguera, D., Northen, T., Norton, J., Nowinski, B., Nüsslein, K., O’Malley, M., Oliveira, R., Maia de Oliveira, V., Onstott, T., Osvatic, J., Ouyang, Y., Pachiadaki, M., Parnell, J., Partida-Martinez, L., Peay, K., Pelletier, D., Peng, X., Pester, M., Pett-Ridge, J., Peura, S., Pjevac, P., Plominsky, A., Poehlein, A., Pope, P., Ravin, N., Redmond, M., Reiss, R., Rich, V., Rinke, C., Rodrigues, J., Rodriguez-Reillo, W., Rossmassler, K., Sackett, J., Salekdeh, G., Saleska, S., Scarborough, M., Schachtman, D., Schadt, C., Schrenk, M., Sczyrba, A., Sengupta, A., Setubal, J., Shade, A., Sharp, C., Sherman, D., Shubenkova, O., Sierra-Garcia, I., Simister, R., Simon, H., Sjöling, S., Slonczewski, J., Correa de Souza, R., Spear, J., Stegen, J., Stepanauskas, R., Stewart, F., Suen, G., Sullivan, M., Sumner, D., Swan, B., Swingley, W., Tarn, J., Taylor, G., Teeling, H., Tekere, M., Teske, A., Thomas, T., Thrash, C., Tiedje, J., Ting, C., Tully, B., Tyson, G., Ulloa, O., Valentine, D., Van Goethem, M., VanderGheynst, J., Verbeke, T., Vollmers, J., Vuillemin, A., Waldo, N., Walsh, D., Weimer, B., Whitman, T., van der Wielen, P., Wilkins, M., Williams, T., Woodcroft, B., Woolet, J., Wrighton, K., Ye, J., Young, E., Youssef, N., Yu, F., Zemskaya, T., Ziels, R., Woyke, T., Mouncey, N., Ivanova, N., Kyrpides, N., Eloe-Fadrosh, E., Consortium, I., and Agencia Estatal de Investigación (España)

Subjects
Resource, Life sciences, biology, Biomedical Engineering, FILOGENIA, Bioengineering, Genomics, Biology, Microbiology, Applied Microbiology and Biotechnology, Genome, purl.org/becyt/ford/1 [https], 03 medical and health sciences, ddc:570, EARTH MICROBIOME PROJECT, Microbiome, purl.org/becyt/ford/1.6 [https], 030304 developmental biology, 2. Zero hunger, 0303 health sciences, 030306 microbiology, Phylum, 15. Life on land, biology.organism_classification, Computational biology and bioinformatics, Phylogenetic diversity, Evolutionary biology, Earth Microbiome Project, Molecular Medicine, Evolutionary ecology, MAGS, GENOMICS, Biotechnology, Archaea, MICROBIAL DIVERSITY
Abstract

13 pages, 5 figures, supplementary information https://doi.org/10.1038/s41587-020-0718-6.-- Data availability: All available metagenomic data, bins and annotations are available through the IMG/M portal (https://img.jgi.doe.gov/). Bulk download for the 52,515 MAGs is available at https://genome.jgi.doe.gov/GEMs and https://portal.nersc.gov/GEM. Genome-scale metabolic models for the nonredundant, high-quality GEMs are summarized at https://doi.org/10.25982/53247.64/1670777 and available in KBase (https://narrative.kbase.us/#org/jgimags). IMG/M identifiers of all metagenomes binned, including detailed information for each metagenome, are available in Supplementary Table 1.-- The pipeline used to generate the metagenome bins is available at https://bitbucket.org/berkeleylab/metabat/src/master/, Publisher Correction: A genomic catalog of Earth’s microbiomes; Nature Biotechnology 39: 520 (2021); https://doi.org/10.1038/s41587-020-00769-4, The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes, This work was conducted by the US DOE Joint Genome Institute, a DOE Office of Science User Facility (contract no. DE-AC02–05CH11231), and used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the US DOE (contract no. DE-AC02–05CH11231). This work was also supported as part of the Genomic Sciences Program DOE Systems Biology KBase (award nos. DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886).-- With the funding support of the ‘Severo Ochoa Centre of Excelle

Published
2020

2. A genomic catalog of Earth’s microbiomes

Author

Nayfach, S, Roux, S, Seshadri, R, Udwary, D, Varghese, N, Schulz, F, Wu, D, Paez-Espino, D, Chen, IM, Huntemann, M, Palaniappan, K, Ladau, J, Mukherjee, S, Reddy, TBK, Nielsen, T, Kirton, E, Faria, JP, Edirisinghe, JN, Henry, CS, Jungbluth, SP, Chivian, D, Dehal, P, Wood-Charlson, EM, Arkin, AP, Tringe, SG, Visel, A, Abreu, H, Acinas, SG, Allen, E, Allen, MA ; https://orcid.org/0000-0002-8852-1454, Alteio, LV, Andersen, G, Anesio, AM, Attwood, G, Avila-Magaña, V, Badis, Y, Bailey, J, Baker, B, Baldrian, P, Barton, HA, Beck, DAC, Becraft, ED, Beller, HR, Beman, JM, Bernier-Latmani, R, Berry, TD, Bertagnolli, A, Bertilsson, S, Bhatnagar, JM, Bird, JT, Blanchard, JL, Blumer-Schuette, SE, Bohannan, B, Borton, MA, Brady, A, Brawley, SH, Brodie, J, Brown, S, Brum, JR, Brune, A, Bryant, DA, Buchan, A, Buckley, DH, Buongiorno, J, Cadillo-Quiroz, H, Caffrey, SM, Campbell, AN, Campbell, B, Carr, S, Carroll, JL, Cary, SC, Cates, AM, Cattolico, RA, Cavicchioli, R ; https://orcid.org/0000-0001-8989-6402, Chistoserdova, L, Coleman, ML, Constant, P, Conway, JM, Mac Cormack, WP, Crowe, S, Crump, B, Currie, C, Daly, R, DeAngelis, KM, Denef, V, Denman, SE, Desta, A, Dionisi, H, Dodsworth, J, Dombrowski, N, Donohue, T, Dopson, M, Driscoll, T, Dunfield, P, Dupont, CL, Dynarski, KA, Edgcomb, V, Edwards, EA, Elshahed, MS, Figueroa, I, Williams, Timothy, Thomas, Torsten ; https://orcid.org/0000-0001-9557-3001, Nayfach, S, Roux, S, Seshadri, R, Udwary, D, Varghese, N, Schulz, F, Wu, D, Paez-Espino, D, Chen, IM, Huntemann, M, Palaniappan, K, Ladau, J, Mukherjee, S, Reddy, TBK, Nielsen, T, Kirton, E, Faria, JP, Edirisinghe, JN, Henry, CS, Jungbluth, SP, Chivian, D, Dehal, P, Wood-Charlson, EM, Arkin, AP, Tringe, SG, Visel, A, Abreu, H, Acinas, SG, Allen, E, Allen, MA ; https://orcid.org/0000-0002-8852-1454, Alteio, LV, Andersen, G, Anesio, AM, Attwood, G, Avila-Magaña, V, Badis, Y, Bailey, J, Baker, B, Baldrian, P, Barton, HA, Beck, DAC, Becraft, ED, Beller, HR, Beman, JM, Bernier-Latmani, R, Berry, TD, Bertagnolli, A, Bertilsson, S, Bhatnagar, JM, Bird, JT, Blanchard, JL, Blumer-Schuette, SE, Bohannan, B, Borton, MA, Brady, A, Brawley, SH, Brodie, J, Brown, S, Brum, JR, Brune, A, Bryant, DA, Buchan, A, Buckley, DH, Buongiorno, J, Cadillo-Quiroz, H, Caffrey, SM, Campbell, AN, Campbell, B, Carr, S, Carroll, JL, Cary, SC, Cates, AM, Cattolico, RA, Cavicchioli, R ; https://orcid.org/0000-0001-8989-6402, Chistoserdova, L, Coleman, ML, Constant, P, Conway, JM, Mac Cormack, WP, Crowe, S, Crump, B, Currie, C, Daly, R, DeAngelis, KM, Denef, V, Denman, SE, Desta, A, Dionisi, H, Dodsworth, J, Dombrowski, N, Donohue, T, Dopson, M, Driscoll, T, Dunfield, P, Dupont, CL, Dynarski, KA, Edgcomb, V, Edwards, EA, Elshahed, MS, Figueroa, I, Williams, Timothy, and Thomas, Torsten ; https://orcid.org/0000-0001-9557-3001

Abstract

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

Published
2021

3. Author Correction: A genomic catalog of Earth’s microbiomes (Nature Biotechnology, (2021), 39, 4, (499-509), 10.1038/s41587-020-0718-6)

Author

Nayfach, S, Roux, S, Seshadri, R, Udwary, D, Varghese, N, Schulz, F, Wu, D, Paez-Espino, D, Chen, IM, Huntemann, M, Palaniappan, K, Ladau, J, Mukherjee, S, Reddy, TBK, Nielsen, T, Kirton, E, Faria, JP, Edirisinghe, JN, Henry, CS, Jungbluth, SP, Chivian, D, Dehal, P, Wood-Charlson, EM, Arkin, AP, Tringe, SG, Visel, A, Abreu, H, Acinas, SG, Allen, E, Allen, MA ; https://orcid.org/0000-0002-8852-1454, Alteio, LV, Andersen, G, Anesio, AM, Attwood, G, Avila-Magaña, V, Badis, Y, Bailey, J, Baker, B, Baldrian, P, Barton, HA, Beck, DAC, Becraft, ED, Beller, HR, Beman, JM, Bernier-Latmani, R, Berry, TD, Bertagnolli, A, Bertilsson, S, Bhatnagar, JM, Bird, JT, Blanchard, JL, Blumer-Schuette, SE, Bohannan, B, Borton, MA, Brady, A, Brawley, SH, Brodie, J, Brown, S, Brum, JR, Brune, A, Bryant, DA, Buchan, A, Buckley, DH, Buongiorno, J, Cadillo-Quiroz, H, Caffrey, SM, Campbell, AN, Campbell, B, Carr, S, Carroll, JL, Cary, SC, Cates, AM, Cattolico, RA, Cavicchioli, R, Chistoserdova, L, Coleman, ML, Constant, P, Conway, JM, Mac Cormack, WP, Crowe, S, Crump, B, Currie, C, Daly, R, DeAngelis, KM, Denef, V, Denman, SE, Desta, A, Dionisi, H, Dodsworth, J, Dombrowski, N, Donohue, T, Dopson, M, Driscoll, T, Dunfield, P, Dupont, CL, Dynarski, KA, Edgcomb, V, Edwards, EA, Elshahed, MS, Figueroa, I, Thomas, Torsten ; https://orcid.org/0000-0001-9557-3001, Williams, Timothy, Nayfach, S, Roux, S, Seshadri, R, Udwary, D, Varghese, N, Schulz, F, Wu, D, Paez-Espino, D, Chen, IM, Huntemann, M, Palaniappan, K, Ladau, J, Mukherjee, S, Reddy, TBK, Nielsen, T, Kirton, E, Faria, JP, Edirisinghe, JN, Henry, CS, Jungbluth, SP, Chivian, D, Dehal, P, Wood-Charlson, EM, Arkin, AP, Tringe, SG, Visel, A, Abreu, H, Acinas, SG, Allen, E, Allen, MA ; https://orcid.org/0000-0002-8852-1454, Alteio, LV, Andersen, G, Anesio, AM, Attwood, G, Avila-Magaña, V, Badis, Y, Bailey, J, Baker, B, Baldrian, P, Barton, HA, Beck, DAC, Becraft, ED, Beller, HR, Beman, JM, Bernier-Latmani, R, Berry, TD, Bertagnolli, A, Bertilsson, S, Bhatnagar, JM, Bird, JT, Blanchard, JL, Blumer-Schuette, SE, Bohannan, B, Borton, MA, Brady, A, Brawley, SH, Brodie, J, Brown, S, Brum, JR, Brune, A, Bryant, DA, Buchan, A, Buckley, DH, Buongiorno, J, Cadillo-Quiroz, H, Caffrey, SM, Campbell, AN, Campbell, B, Carr, S, Carroll, JL, Cary, SC, Cates, AM, Cattolico, RA, Cavicchioli, R, Chistoserdova, L, Coleman, ML, Constant, P, Conway, JM, Mac Cormack, WP, Crowe, S, Crump, B, Currie, C, Daly, R, DeAngelis, KM, Denef, V, Denman, SE, Desta, A, Dionisi, H, Dodsworth, J, Dombrowski, N, Donohue, T, Dopson, M, Driscoll, T, Dunfield, P, Dupont, CL, Dynarski, KA, Edgcomb, V, Edwards, EA, Elshahed, MS, Figueroa, I, Thomas, Torsten ; https://orcid.org/0000-0001-9557-3001, and Williams, Timothy

Abstract

In the version of this article initially published, four people were missing from the alphabetical list of IMG/M Data Consortium members: Lauren V. Alteio of the Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria; Jeffrey L. Blanchard of the Biology Department, University of Massachusetts Amherst, Amherst, MA, USA; Kristen M. DeAngelis of the Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA; and William Rodriguez-Reillo of the Research Computing Division, Harvard Medical School, Boston, MA, USA. The error has been corrected in the PDF and HTML versions of the article.

Published
2021

4. Publisher Correction: A genomic catalog of Earth’s microbiomes (Nature Biotechnology, (2021), 39, 4, (499-509), 10.1038/s41587-020-0718-6)

Author

Nayfach, S, Roux, S, Seshadri, R, Udwary, D, Varghese, N, Schulz, F, Wu, D, Paez-Espino, D, Chen, IM, Huntemann, M, Palaniappan, K, Ladau, J, Mukherjee, S, Reddy, TBK, Nielsen, T, Kirton, E, Faria, JP, Edirisinghe, JN, Henry, CS, Jungbluth, SP, Chivian, D, Dehal, P, Wood-Charlson, EM, Arkin, AP, Tringe, SG, Visel, A, Abreu, H, Acinas, SG, Allen, E, Allen, MA ; https://orcid.org/0000-0002-8852-1454, Andersen, G, Anesio, AM, Attwood, G, Avila-Magaña, V, Badis, Y, Bailey, J, Baker, B, Baldrian, P, Barton, HA, Beck, DAC, Becraft, ED, Beller, HR, Beman, JM, Bernier-Latmani, R, Berry, TD, Bertagnolli, A, Bertilsson, S, Bhatnagar, JM, Bird, JT, Blumer-Schuette, SE, Bohannan, B, Borton, MA, Brady, A, Brawley, SH, Brodie, J, Brown, S, Brum, JR, Brune, A, Bryant, DA, Buchan, A, Buckley, DH, Buongiorno, J, Cadillo-Quiroz, H, Caffrey, SM, Campbell, AN, Campbell, B, Carr, S, Carroll, JL, Cary, SC, Cates, AM, Cattolico, RA, Cavicchioli, R, Chistoserdova, L, Coleman, ML, Constant, P, Conway, JM, Mac Cormack, WP, Crowe, S, Crump, B, Currie, C, Daly, R, Denef, V, Denman, SE, Desta, A, Dionisi, H, Dodsworth, J, Dombrowski, N, Donohue, T, Dopson, M, Driscoll, T, Dunfield, P, Dupont, CL, Dynarski, KA, Edgcomb, V, Edwards, EA, Elshahed, MS, Figueroa, I, Flood, B, Fortney, N, Fortunato, CS, Williams, Timothy, Thomas, Torsten ; https://orcid.org/0000-0001-9557-3001, Nayfach, S, Roux, S, Seshadri, R, Udwary, D, Varghese, N, Schulz, F, Wu, D, Paez-Espino, D, Chen, IM, Huntemann, M, Palaniappan, K, Ladau, J, Mukherjee, S, Reddy, TBK, Nielsen, T, Kirton, E, Faria, JP, Edirisinghe, JN, Henry, CS, Jungbluth, SP, Chivian, D, Dehal, P, Wood-Charlson, EM, Arkin, AP, Tringe, SG, Visel, A, Abreu, H, Acinas, SG, Allen, E, Allen, MA ; https://orcid.org/0000-0002-8852-1454, Andersen, G, Anesio, AM, Attwood, G, Avila-Magaña, V, Badis, Y, Bailey, J, Baker, B, Baldrian, P, Barton, HA, Beck, DAC, Becraft, ED, Beller, HR, Beman, JM, Bernier-Latmani, R, Berry, TD, Bertagnolli, A, Bertilsson, S, Bhatnagar, JM, Bird, JT, Blumer-Schuette, SE, Bohannan, B, Borton, MA, Brady, A, Brawley, SH, Brodie, J, Brown, S, Brum, JR, Brune, A, Bryant, DA, Buchan, A, Buckley, DH, Buongiorno, J, Cadillo-Quiroz, H, Caffrey, SM, Campbell, AN, Campbell, B, Carr, S, Carroll, JL, Cary, SC, Cates, AM, Cattolico, RA, Cavicchioli, R, Chistoserdova, L, Coleman, ML, Constant, P, Conway, JM, Mac Cormack, WP, Crowe, S, Crump, B, Currie, C, Daly, R, Denef, V, Denman, SE, Desta, A, Dionisi, H, Dodsworth, J, Dombrowski, N, Donohue, T, Dopson, M, Driscoll, T, Dunfield, P, Dupont, CL, Dynarski, KA, Edgcomb, V, Edwards, EA, Elshahed, MS, Figueroa, I, Flood, B, Fortney, N, Fortunato, CS, Williams, Timothy, and Thomas, Torsten ; https://orcid.org/0000-0001-9557-3001

Abstract

This paper was originally published under standard Springer Nature copyright (© The Author(s), under exclusive licence to Springer Nature America, Inc.). It is now available as an open-access paper under a Creative Commons Attribution 4.0 International license. The error has been corrected in the print, HTML and PDF versions of the article.

Published
2021

5. IMG/VR: A database of cultured and uncultured DNA viruses and retroviruses

Author

Paez-Espino, D, Chen, IMA, Palaniappan, K, Ratner, A, Chu, K, Szeto, E, Pillay, M, Huang, J, Markowitz, VM, Nielsen, T, Huntemann, M, Reddy, TBK, Pavlopoulos, GA, Sullivan, MB, Campbell, BJ, Chen, F, McMahon, K, Hallam, SJ, Denef, V, Cavicchioli, R ; https://orcid.org/0000-0001-8989-6402, Caffrey, SM, Streit, WR, Webster, J, Handley, KM, Salekdeh, GH, Tsesmetzis, N, Setubal, JC, Pope, PB, Liu, WT, Rivers, AR, Ivanova, NN, Kyrpides, NC, Paez-Espino, D, Chen, IMA, Palaniappan, K, Ratner, A, Chu, K, Szeto, E, Pillay, M, Huang, J, Markowitz, VM, Nielsen, T, Huntemann, M, Reddy, TBK, Pavlopoulos, GA, Sullivan, MB, Campbell, BJ, Chen, F, McMahon, K, Hallam, SJ, Denef, V, Cavicchioli, R ; https://orcid.org/0000-0001-8989-6402, Caffrey, SM, Streit, WR, Webster, J, Handley, KM, Salekdeh, GH, Tsesmetzis, N, Setubal, JC, Pope, PB, Liu, WT, Rivers, AR, Ivanova, NN, and Kyrpides, NC

Abstract

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparingwith external sequences, thus serving as an essential resource in the viral genomics community.

Published
2017

9. Growth Substrate- and Phase-Specific Expression of Biphenyl, Benzoate, and C1 Metabolic Pathways in Burkholderia xenovorans LB400.

Author

Denef, V. J., Patrauchan, M. A., Florizone, C., Park, J., Tsoi, T. V., Verstraete, W., Tiedje, J. M., and Eltis, L. D.

Subjects
*POLYCHLORINATED biphenyls, *BENZOATES, *PROTEINS, *PROTEIN microarrays, *ELECTROPHORESIS, *PROTEOMICS
Abstract

Recent microarray experiments suggested that Burkholderia xenovorans LB400, a potent polychlorinated biphenyl (PCB)-degrading bacterium, utilizes up to three apparently redundant benzoate pathways and a C1 metabolic pathway during biphenyl and benzoate metabolism. To better characterize the roles of these pathways, we performed quantitative proteome profiling of cells grown on succinate, benzoate, or biphenyl and harvested during either mid-logarithmic growth or the transition between the logarithmic and stationary growth phases. The Bph enzymes, catabolizing biphenyl, were 16-fold more abundant in biphenyl-versus succinate-grown cells. Moreover, the upper and lower bph pathways were independently regulated. Expression of each benzoate pathway depended on growth substrate and phase. Proteins specifying catabolism via benzoate dihydroxylation and catechol ortho-cleavage (ben-cat pathway) were approximately an order of magnitude more abundant in benzoate-versus biphenyl-grown cells at the same growth phase. The chromosomal copy of the benzoyl-coenzyme A (CoA) (boxC) pathway was also expressed during growth on biphenyl: BoxC proteins were approximately twice as abundant as Ben and Cat proteins under these conditions. By contrast, proteins of the megaplasmid copy of the benzoyl-CoA (boxM) pathway were only detected in transition-phase benzoate-grown cells. Other proteins detected at increased levels in benzoate- and biphenyl-grown cells included general stress response proteins potentially induced by reactive oxygen species formed during aerobic aromatic catabolism. Finally, C1 metabolic enzymes were present in biphenyl-grown cells during transition phase. This study provides insights into the physiological roles and integration of apparently redundant catabolic pathways in large-genome bacteria and establishes a basis for investigating the PCB-degrading abilities of this strain. [ABSTRACT FROM AUTHOR]

Published
2005
Full Text
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11. IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

Author

Paez-Espino D, Chen IA, Palaniappan K, Ratner A, Chu K, Szeto E, Pillay M, Huang J, Markowitz VM, Nielsen T, Huntemann M, K Reddy TB, Pavlopoulos GA, Sullivan MB, Campbell BJ, Chen F, McMahon K, Hallam SJ, Denef V, Cavicchioli R, Caffrey SM, Streit WR, Webster J, Handley KM, Salekdeh GH, Tsesmetzis N, Setubal JC, Pope PB, Liu WT, Rivers AR, Ivanova NN, and Kyrpides NC

Subjects
Environmental Microbiology, Host-Pathogen Interactions, Metagenome, Sequence Analysis, DNA, DNA Viruses genetics, Databases, Genetic, Genome, Viral, Genomics methods, Metagenomics methods, Retroviridae genetics, Software
Abstract

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community., (© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2017
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12. Coping with polychlorinated biphenyl (PCB) toxicity: Physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB-mediated stress.

Author

Parnell JJ, Park J, Denef V, Tsoi T, Hashsham S, Quensen J 3rd, and Tiedje JM

Subjects
Aroclors pharmacology, Biodegradation, Environmental, Burkholderia cytology, Burkholderia physiology, Environmental Pollutants metabolism, Gene Expression drug effects, Polychlorinated Biphenyls metabolism, Burkholderia drug effects, Environmental Pollutants pharmacology, Genome, Bacterial physiology, Polychlorinated Biphenyls pharmacology
Abstract

The biodegradation of polychlorinated biphenyls (PCBs) relies on the ability of aerobic microorganisms such as Burkholderia xenovorans sp. LB400 to tolerate two potential modes of toxicity presented by PCB degradation: passive toxicity, as hydrophobic PCBs potentially disrupt membrane and protein function, and degradation-dependent toxicity from intermediates of incomplete degradation. We monitored the physiological characteristics and genome-wide expression patterns of LB400 in response to the presence of Aroclor 1242 (500 ppm) under low expression of the structural biphenyl pathway (succinate and benzoate growth) and under induction by biphenyl. We found no inhibition of growth or change in fatty acid profile due to PCBs under nondegrading conditions. Moreover, we observed no differential gene expression due to PCBs themselves. However, PCBs did have a slight effect on the biosurface area of LB400 cells and caused slight membrane separation. Upon activation of the biphenyl pathway, we found growth inhibition from PCBs beginning after exponential-phase growth suggestive of the accumulation of toxic compounds. Genome-wide expression profiling revealed 47 differentially expressed genes (0.56% of all genes) under these conditions. The biphenyl and catechol pathways were induced as expected, but the quinoprotein methanol metabolic pathway and a putative chloroacetaldehyde dehydrogenase were also highly expressed. As the latter protein is essential to conversion of toxic metabolites in dichloroethane degradation, it may play a similar role in the degradation of chlorinated aliphatic compounds resulting from PCB degradation.

Published
2006
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