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1. Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium

Author

Džunková, Mária, La Clair, James J, Tyml, Tomáš, Doud, Devin, Schulz, Frederik, Piquer-Esteban, Samuel, Porcel Sanchis, Dafne, Osborn, Andrew, Robinson, David, Louie, Katherine B, Bowen, Ben P, Bowers, Robert M, Lee, Janey, Arnau, Vicente, Díaz-Villanueva, Wladimiro, Stepanauskas, Ramunas, Gosliner, Terrence, Date, Shailesh V, Northen, Trent R, Cheng, Jan-Fang, Burkart, Michael D, and Woyke, Tanja

Subjects
Microbiology, Biological Sciences, Infectious Diseases, Genetics, Cancer, Human Genome, Biotechnology, Animals, Bacteria, Biological Products, Fluorescent Dyes, Gastropoda, Lactones, Pharmaceutical Preparations, Microbial single-cell genomics, Nudibranchs, Tethybacterales, Beta-lactone, Biosynthetic gene clusters, Ecology, Medical Microbiology, Evolutionary biology
Abstract

BackgroundNudibranchs comprise a group of > 6000 marine soft-bodied mollusk species known to use secondary metabolites (natural products) for chemical defense. The full diversity of these metabolites and whether symbiotic microbes are responsible for their synthesis remains unexplored. Another issue in searching for undiscovered natural products is that computational analysis of genomes of uncultured microbes can result in detection of novel biosynthetic gene clusters; however, their in vivo functionality is not guaranteed which limits further exploration of their pharmaceutical or industrial potential. To overcome these challenges, we used a fluorescent pantetheine probe, which produces a fluorescent CoA-analog employed in biosynthesis of secondary metabolites, to label and capture bacterial symbionts actively producing these compounds in the mantle of the nudibranch Doriopsilla fulva.ResultsWe recovered the genome of Candidatus Doriopsillibacter californiensis from the Ca. Tethybacterales order, an uncultured lineage of sponge symbionts not found in nudibranchs previously. It forms part of the core skin microbiome of D. fulva and is nearly absent in its internal organs. We showed that crude extracts of D. fulva contained secondary metabolites that were consistent with the presence of a beta-lactone encoded in Ca. D. californiensis genome. Beta-lactones represent an underexplored group of secondary metabolites with pharmaceutical potential that have not been reported in nudibranchs previously.ConclusionsAltogether, this study shows how probe-based, targeted sorting approaches can capture bacterial symbionts producing secondary metabolites in vivo. Video Abstract.

Published
2023

2. Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere

Author

Doud, Devin FR, Bowers, Robert M, Schulz, Frederik, De Raad, Markus, Deng, Kai, Tarver, Angela, Glasgow, Evan, Vander Meulen, Kirk, Fox, Brian, Deutsch, Sam, Yoshikuni, Yasuo, Northen, Trent, Hedlund, Brian P, Singer, Steven W, Ivanova, Natalia, and Woyke, Tanja

Subjects
Microbiology, Biological Sciences, Genetics, Biodefense, Infectious Diseases, Human Genome, Biotechnology, Clinical Research, Emerging Infectious Diseases, 1.1 Normal biological development and functioning, Bacteria, Bacterial Proteins, Cellulase, Cellulose, Environmental Microbiology, Genome, Bacterial, Genomics, Metagenomics, Phylogeny, RNA, Ribosomal, 16S, Environmental Sciences, Technology, Biological sciences, Environmental sciences
Abstract

Assigning a functional role to a microorganism has historically relied on cultivation of isolates or detection of environmental genome-based biomarkers using a posteriori knowledge of function. However, the emerging field of function-driven single-cell genomics aims to expand this paradigm by identifying and capturing individual microbes based on their in situ functions or traits. To identify and characterize yet uncultivated microbial taxa involved in cellulose degradation, we developed and benchmarked a function-driven single-cell screen, which we applied to a microbial community inhabiting the Great Boiling Spring (GBS) Geothermal Field, northwest Nevada. Our approach involved recruiting microbes to fluorescently labeled cellulose particles, and then isolating single microbe-bound particles via fluorescence-activated cell sorting. The microbial community profiles prior to sorting were determined via bulk sample 16S rRNA gene amplicon sequencing. The flow-sorted cellulose-bound microbes were subjected to whole genome amplification and shotgun sequencing, followed by phylogenetic placement. Next, putative cellulase genes were identified, expressed and tested for activity against derivatives of cellulose and xylose. Alongside typical cellulose degraders, including members of the Actinobacteria, Bacteroidetes, and Chloroflexi, we found divergent cellulases encoded in the genome of a recently described candidate phylum from the rare biosphere, Goldbacteria, and validated their cellulase activity. As this genome represents a species-level organism with novel and phylogenetically distinct cellulolytic activity, we propose the name Candidatus 'Cellulosimonas argentiregionis'. We expect that this function-driven single-cell approach can be extended to a broad range of substrates, linking microbial taxonomy directly to in situ function.

Published
2020

3. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Author

Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Genome Standards Consortium, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, AM, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, and Woyke, Tanja

Subjects
Genome Standards Consortium
Abstract

In the version of this article initially published, the author A. Murat Eren was listed as A.M. Eren. The corresponding affiliation was given as the Knapp Center for Biomedical Discovery, rather than Department of Medicine, University of Chicago, Chicago, Illinois, USA, and Marine Biological Laboratory, Woods Hole, Massachusetts, USA. The errors have been corrected in the HTML and PDF versions of the article as of 29 November 2017. In the version of this article initially published, the following acknowledgment was omitted: A.L. was supported by the Russian Science Foundation (grant number 14-50-00069). The error has been corrected in the HTML and PDF versions of the article as of 7 December 2017.

Published
2018

4. Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Author

Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, A Murat, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, and Woyke, Tanja

Subjects
Biological Sciences, Genetics, Genome Standards Consortium
Published
2018

5. Analysis of single-cell genome sequences of bacteria and archaea.

Author

Bowers, Robert, Doud, Devin, and Woyke, Tanja

Subjects
assembly, genome sequence, quality control, single cell
Abstract

Single-cell genome sequencing of individual archaeal and bacterial cells is a vital approach to decipher the genetic makeup of uncultured microorganisms. With this review, we describe single-cell genome analysis with a focus on the unique properties of single-cell sequence data and with emphasis on quality assessment and assurance.

Published
2017

6. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Author

Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Murat Eren, A, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, and Woyke, Tanja

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Cancer, Cancer Genomics, Biotechnology, Human Genome, Genome, Archaeal, Genome, Bacterial, Genomics, Metagenomics, Sequence Analysis, DNA, Genome Standards Consortium
Abstract

We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.

Published
2017

7. Novel approaches in function-driven single-cell genomics

Author

Doud, Devin FR and Woyke, Tanja

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Cancer, Human Genome, Cancer Genomics, Biotechnology, 1.1 Normal biological development and functioning, Genomics, Microbiological Techniques, Single-Cell Analysis, function-driven sequencing, single-cell genomics, microbial dark matter, single-cell activity, Medical Microbiology
Abstract

Deeper sequencing and improved bioinformatics in conjunction with single-cell and metagenomic approaches continue to illuminate undercharacterized environmental microbial communities. This has propelled the 'who is there, and what might they be doing' paradigm to the uncultivated and has already radically changed the topology of the tree of life and provided key insights into the microbial contribution to biogeochemistry. While characterization of 'who' based on marker genes can describe a large fraction of the community, answering 'what are they doing' remains the elusive pinnacle for microbiology. Function-driven single-cell genomics provides a solution by using a function-based screen to subsample complex microbial communities in a targeted manner for the isolation and genome sequencing of single cells. This enables single-cell sequencing to be focused on cells with specific phenotypic or metabolic characteristics of interest. Recovered genomes are conclusively implicated for both encoding and exhibiting the feature of interest, improving downstream annotation and revealing activity levels within that environment. This emerging approach has already improved our understanding of microbial community functioning and facilitated the experimental analysis of uncharacterized gene product space. Here we provide a comprehensive review of strategies that have been applied for function-driven single-cell genomics and the future directions we envision.

Published
2017

9. Supplementary Information Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium

Author

Džunková, Mária, La Clair, James J., Tyml, Tomáš, Doud, Devin, Schulz, Frederik, Piquer-Esteban, Samuel, Porcel Sanchis, Dafne, Osborn, Andrew, Robinson, David, Louie, Katherine B., Bowen, Benjamin P., Bowers, Robert M., Lee, Janey, Arnau, Vicente, Díaz-Villanueva, Wladimiro, Stepanauskas, Ramunas, Gosliner, Terrence, Date, Shailesh V., Northen, Trent R., Cheng, Jan-Fang, Burkart, Michael D., Woyke, Tanja, Džunková, Mária, La Clair, James J., Tyml, Tomáš, Doud, Devin, Schulz, Frederik, Piquer-Esteban, Samuel, Porcel Sanchis, Dafne, Osborn, Andrew, Robinson, David, Louie, Katherine B., Bowen, Benjamin P., Bowers, Robert M., Lee, Janey, Arnau, Vicente, Díaz-Villanueva, Wladimiro, Stepanauskas, Ramunas, Gosliner, Terrence, Date, Shailesh V., Northen, Trent R., Cheng, Jan-Fang, Burkart, Michael D., and Woyke, Tanja

Abstract

Supplementary Information: Additional file 1: Supplementary Figure S1. Photorhabdus luminescens incubated with the KC-12 probe during 70 h. Supplementary Note 1. Taxonomic Appendix. Supplementary Figure S2. Hybridization of cells from nudibranch skin, gut, gills and gonads. Supplementary Figure S3. KEGG modules of Ca. D. californiensis and medium quality Ca. Tethybacterales MAGs from sponges. Supplementary Figure S4. Sulfur and nitrogen metabolism of Ca. D. californiensis and medium quality Ca. Tethybacterales MAGs from sponges. Supplementary Figure S5. ABC transporters of Ca. D. californiensis and medium quality Ca. Tethybacterales MAGs from sponges. Supplementary Figure S6. Phylogenetic tree of 16S rDNA gene sequences from public datasets. Supplementary Figure S7. Proportion of reads with >92% sequence similarity to Ca. D. californiensis in other nudibranchs. Supplementary Figure S8. Heatmap showing relative abundances of top ASVs across all 16S rDNA amplicon samples. Supplementary Figure S9. Core microbiome of D. fulva mantle. Supplementary Figure S10. ASVs determining the ordination of samples in the PCA anlaysis of nudibranch microbiome samples. Supplementary Figure S11. Phylogenetic tree of full length 16S rDNA gene sequences from nudibranch skin and mucus obtained by Sanger sequencing. Supplementary Figure S12. Ca. D. californiensis betalactone gene cluster compared to the best antiSMASH matches. Supplementary Figure S13. Similarity of the genes in the Ca. D. californiensis betalactone gene cluster with the 'nr' database of NCBI. Supplementary Figure S14. Similarity of the genes in the Ca. D. californiensis betalactone gene cluster with other members of the Ca. Tethybacterales order. Supplementary Figure S15. Biosynthetic pathway comparison to known betalactone natural product pathways. Supplementary Figure S16. NMR analysis of extracts from D. fulva nudibranchs. Supplementary Figure S17. Quantification of the dcbD expression in the CRAGE strains and nudibran

Published
2023

10. Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium

Author

Department of Energy (US), Joint Genome Institute (US), John Templeton Foundation, Gordon and Betty Moore Foundation, Generalitat Valenciana, Ministerio de Universidades (España), Džunková, Mária, La Clair, James J., Tyml, Tomáš, Doud, Devin, Schulz, Frederik, Piquer-Esteban, Samuel, Porcel Sanchis, Dafne, Osborn, Andrew, Robinson, David, Louie, Katherine B., Bowen, Benjamin P., Bowers, Robert M., Lee, Janey, Arnau, Vicente, Díaz-Villanueva, Wladimiro, Stepanauskas, Ramunas, Gosliner, Terrence, Date, Shailesh V., Northen, Trent R., Cheng, Jan-Fang, Burkart, Michael D., Woyke, Tanja, Department of Energy (US), Joint Genome Institute (US), John Templeton Foundation, Gordon and Betty Moore Foundation, Generalitat Valenciana, Ministerio de Universidades (España), Džunková, Mária, La Clair, James J., Tyml, Tomáš, Doud, Devin, Schulz, Frederik, Piquer-Esteban, Samuel, Porcel Sanchis, Dafne, Osborn, Andrew, Robinson, David, Louie, Katherine B., Bowen, Benjamin P., Bowers, Robert M., Lee, Janey, Arnau, Vicente, Díaz-Villanueva, Wladimiro, Stepanauskas, Ramunas, Gosliner, Terrence, Date, Shailesh V., Northen, Trent R., Cheng, Jan-Fang, Burkart, Michael D., and Woyke, Tanja

Abstract

[Background] Nudibranchs comprise a group of > 6000 marine soft-bodied mollusk species known to use secondary metabolites (natural products) for chemical defense. The full diversity of these metabolites and whether symbiotic microbes are responsible for their synthesis remains unexplored. Another issue in searching for undiscovered natural products is that computational analysis of genomes of uncultured microbes can result in detection of novel biosynthetic gene clusters; however, their in vivo functionality is not guaranteed which limits further exploration of their pharmaceutical or industrial potential. To overcome these challenges, we used a fluorescent pantetheine probe, which produces a fluorescent CoA-analog employed in biosynthesis of secondary metabolites, to label and capture bacterial symbionts actively producing these compounds in the mantle of the nudibranch Doriopsilla fulva., [Results] We recovered the genome of Candidatus Doriopsillibacter californiensis from the Ca. Tethybacterales order, an uncultured lineage of sponge symbionts not found in nudibranchs previously. It forms part of the core skin microbiome of D. fulva and is nearly absent in its internal organs. We showed that crude extracts of D. fulva contained secondary metabolites that were consistent with the presence of a beta-lactone encoded in Ca. D. californiensis genome. Beta-lactones represent an underexplored group of secondary metabolites with pharmaceutical potential that have not been reported in nudibranchs previously., [Conclusions] Altogether, this study shows how probe-based, targeted sorting approaches can capture bacterial symbionts producing secondary metabolites in vivo.

Published
2023

13. Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere.

Author

Deng, Kai, Deng, Kai, Tarver, Angela, Glasgow, Evan, Vander Meulen, Kirk, Fox, Brian, Deutsch, Sam, Doud, Devin, Bowers, Robert, Hedlund, Brian, Singer, Steven, Ivanova, Natalia, Woyke, Tanja, Yoshikuni, Yasuo, Northen, Trent, de Raad, Markus, Schulz, Frederik, Deng, Kai, Deng, Kai, Tarver, Angela, Glasgow, Evan, Vander Meulen, Kirk, Fox, Brian, Deutsch, Sam, Doud, Devin, Bowers, Robert, Hedlund, Brian, Singer, Steven, Ivanova, Natalia, Woyke, Tanja, Yoshikuni, Yasuo, Northen, Trent, de Raad, Markus, and Schulz, Frederik

Abstract

Assigning a functional role to a microorganism has historically relied on cultivation of isolates or detection of environmental genome-based biomarkers using a posteriori knowledge of function. However, the emerging field of function-driven single-cell genomics aims to expand this paradigm by identifying and capturing individual microbes based on their in situ functions or traits. To identify and characterize yet uncultivated microbial taxa involved in cellulose degradation, we developed and benchmarked a function-driven single-cell screen, which we applied to a microbial community inhabiting the Great Boiling Spring (GBS) Geothermal Field, northwest Nevada. Our approach involved recruiting microbes to fluorescently labeled cellulose particles, and then isolating single microbe-bound particles via fluorescence-activated cell sorting. The microbial community profiles prior to sorting were determined via bulk sample 16S rRNA gene amplicon sequencing. The flow-sorted cellulose-bound microbes were subjected to whole genome amplification and shotgun sequencing, followed by phylogenetic placement. Next, putative cellulase genes were identified, expressed and tested for activity against derivatives of cellulose and xylose. Alongside typical cellulose degraders, including members of the Actinobacteria, Bacteroidetes, and Chloroflexi, we found divergent cellulases encoded in the genome of a recently described candidate phylum from the rare biosphere, Goldbacteria, and validated their cellulase activity. As this genome represents a species-level organism with novel and phylogenetically distinct cellulolytic activity, we propose the name Candidatus Cellulosimonas argentiregionis. We expect that this function-driven single-cell approach can be extended to a broad range of substrates, linking microbial taxonomy directly to in situ function.

Published
2020

14. Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere

Author

Doud, Devin F. R., primary, Bowers, Robert M., additional, Schulz, Frederik, additional, De Raad, Markus, additional, Deng, Kai, additional, Tarver, Angela, additional, Glasgow, Evan, additional, Vander Meulen, Kirk, additional, Fox, Brian, additional, Deutsch, Sam, additional, Yoshikuni, Yasuo, additional, Northen, Trent, additional, Hedlund, Brian P., additional, Singer, Steven W., additional, Ivanova, Natalia, additional, and Woyke, Tanja, additional

Published
2019
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16. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Nature Biotechnology (2017) 35 (725-731) DOI: 10.1038/nbt.3893)

Author

Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B.K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J.G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, Woyke, Tanja, other, and, Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B.K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J.G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, Woyke, Tanja, and other, and

Abstract

In the version of this article initially published, the author A. Murat Eren was listed as A.M. Eren. The corresponding affiliation was given as the Knapp Center for Biomedical Discovery, rather than Department of Medicine, University of Chicago, Chicago, Illinois, USA, and Marine Biological Laboratory, Woods Hole, Massachusetts, USA. The errors have been corrected in the HTML and PDF versions of the article as of 29 November 2017. In the version of this article initially published, the following acknowledgment was omitted: A.L. was supported by the Russian Science Foundation (grant number 14-50-00069). The error has been corrected in the HTML and PDF versions of the article as of 7 December 2017.

Published
2018

17. Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Author

Woyke, Tanja, Hugenholtz, Philip, Banfield, Jillian F., Schriml, Lynn, Eren, A. M., Parks, Donovan H., Yilmaz, Pelin, Meyer, Folker, Lapidus, Alla, Rinke, Christian, Tyson, Gene W., Karsch-Mizrachi, Ilene, Cochrane, Guy, Finn, Rob, Knight, Rob, Fierer, Noah, McMahon, Katherine D., Hedlund, Brian, Eisen, Jonathan A., Rattei, Thomas, Baker, Brett J., Liu, Wen-Tso, Konstantinidis, Konstantinos T., Tighe, Scott, Ettema, Thijs J. G., Jungbluth, Sean P., Hallam, Steven J., Nelson, William C., Gilbert, Jack A., Glockner, Frank O., Sutton, Granger, Yooseph, Shibu, Dodsworth, Jeremy A., Garrity, George M., Weinstock, George M., Bork, Peer, Podar, Mircea, Birren, Bruce, Malmstrom, Rex R., Becraft, Eric D., Clum, Alicia, Copeland, Alex, Ivanova, Natalia N., Tringe, Susannah G., Eloe-Fadrosh, Emiley A., Rivers, Adam R., Jarett, Jessica, Schulz, Frederik, Reddy, T. B. K., Doud, Devin, Harmon-Smith, Miranda, Stepanauskas, Ramunas, Kyrpides, Nikos C., Bowers, Robert M., Woyke, Tanja, Hugenholtz, Philip, Banfield, Jillian F., Schriml, Lynn, Eren, A. M., Parks, Donovan H., Yilmaz, Pelin, Meyer, Folker, Lapidus, Alla, Rinke, Christian, Tyson, Gene W., Karsch-Mizrachi, Ilene, Cochrane, Guy, Finn, Rob, Knight, Rob, Fierer, Noah, McMahon, Katherine D., Hedlund, Brian, Eisen, Jonathan A., Rattei, Thomas, Baker, Brett J., Liu, Wen-Tso, Konstantinidis, Konstantinos T., Tighe, Scott, Ettema, Thijs J. G., Jungbluth, Sean P., Hallam, Steven J., Nelson, William C., Gilbert, Jack A., Glockner, Frank O., Sutton, Granger, Yooseph, Shibu, Dodsworth, Jeremy A., Garrity, George M., Weinstock, George M., Bork, Peer, Podar, Mircea, Birren, Bruce, Malmstrom, Rex R., Becraft, Eric D., Clum, Alicia, Copeland, Alex, Ivanova, Natalia N., Tringe, Susannah G., Eloe-Fadrosh, Emiley A., Rivers, Adam R., Jarett, Jessica, Schulz, Frederik, Reddy, T. B. K., Doud, Devin, Harmon-Smith, Miranda, Stepanauskas, Ramunas, Kyrpides, Nikos C., and Bowers, Robert M.

Abstract

Nat. Biotechnol. 35, 725–731 (2017); published online 8 August 2017; corrected after print 29 November 2017; corrected after print 7 December 2017 In the version of this article initially published, the author A. Murat Eren was listed as A.M. Eren. The corresponding affiliation was given as the Knapp Center for Biomedical Discovery, rather than Department of Medicine, University of Chicago, Chicago, Illinois, USA, and Marine Biological Laboratory, Woods Hole, Massachusetts, USA. The errors have been corrected in the HTML and PDF versions of the article as of 29 November 2017. In the version of this article initially published, the following acknowledgment was omitted: A.L. was supported by the Russian Science Foundation (grant number 14-50-00069). The error has been corrected in the HTML and PDF versions of the article as of 7 December 2017.

Published
2018

18. Erratum: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Author

Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, AM, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, Woyke, Tanja, Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, AM, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, and Woyke, Tanja

Published
2018

21. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Author

Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, Woyke, Tanja, Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, and Woyke, Tanja

Abstract

We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.

Published
2017
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36. Novel approach in algae biofuel production using advanced photonics.

Author

Jung, Erica E., Kalontarov, Michael, Doud, Devin, Angenent, Largus T., Sinton, David, and Erickson, David

Abstract

Utilization of evanescent fields for photosynthetic bacteria to produce biofuel can lead to thousandfold decrease in the volume of photobioreactors. We demonstrate the growth of bacteria enabled by the evanescent excitation using planar waveguides. [ABSTRACT FROM PUBLISHER]

Published
2012

37. Engineering Applications Using The Innate Redox Environment Of Rhodopseudomonas Palustris

Author

Doud, Devin

Subjects
Rhodopseudomonas palustris, Microbial Electrochemistry, Metabolic Engineering
Abstract

Rhodopseudomonas palustris is currently the most metabolically versatile organism known. Because of this, it has become a model organism not only for it's many forms of metabolism, but also for the complex coordination required to regulate them. Under anaerobic conditions, R. palustris has received considerable attention regarding how it handles excess reducing equivalents. Herein, I investigated alternate routes for either pushing or pulling reducing equivalents into the metabolism of R. palustris for applications relating to bioenergy. Of particular interest to my research are the anaerobic metabolic processes of: i. anoxygenic photosynthesis; ii. metabolism of the molecules n-butyrate and p-coumarate; iii. photoautotrophic growth with iron(II) as a sole electron donor; iv. nitrogenase based production of H2; and v. fixation of CO2. In my first study, I focused on the lethal redox imbalance that R. palustris encounters when growing on n-butyrate with no viable electron sinks. Excess reducing equivalents were harnessed to drive the metabolically engineered production of the biofuel nbutanol. Because the reduction of n-butyrate to n-butanol became the only route of maintaining redox balance, this metabolically engineered activity became obligate for growth. In the second study, I co-cultured R. palustris and the model exoelectrogen Geobacter sulfurreducens together in a bioelectrochemical system to investigate metabolite sharing of the lignin monomer pcoumarate by R. palustris. The electrochemical system functioned as a tool for measuring the effect of G. sulfurreducens aiding R. palustris in maintaining redox balance. The third study characterized the ability of R. palustris to take up electrons from a negatively poised electrode through mediated iron cycling as a sole source of electrons for growth. It was observed that volumetric rates of electron uptake were very low, so to improve these rates and demonstrate that this mechanism could be the foundation of a future microbial electrosynthesis technology, improvements in reactor design were made. The electrode was removed from the growth reactor, which allowed optimization of both the photosynthetic bioreactor and the abiotic electrochemical reactor. These two components were then connected through a closed recirculation loop to recycle and regenerate the iron substrate. This resulted in increased volumetric iron consumption 56 times higher in the illuminated reactor compared to previously measured in conventional bioelectrochemical reactors.

Published
2014

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