Search Google Scholar | Search PubMed
375.
Xuanyu Tao Megan L. Kempher, Rong Song
Effects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Temperature Journal Article
In: Mbio, vol. 11, no. 4, pp. 2020, 2020.
@article{kempher2020effects,
title = {Effects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Temperature},
author = {Megan L. Kempher, Xuanyu Tao, Rong Song, Bo Wu, David A. Stahl, Judy D. Wall, Adam P. Arkin,
Aifen Zhou, Jizhong Zhou},
year = {2020},
date = {2020-08-18},
journal = {Mbio},
volume = {11},
number = {4},
pages = {2020},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
374.
Kothari, Ankita; Roux, Simon; Zhang, Hanqiao; Prieto, Anatori; Soneja, Drishti; Chandonia, John-Marc; Spencer, Sarah J; Wu, Xiaoqin; Altenburg, Sarah; Fields, Matthew W; Deutschbauer, Adam M; Arkin, Adam P; Alm, Eric J; Chakraborty, Romy; Mukhopadhyay, Aindrila
Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance Journal Article
In: BioRxiv, 2020.
Abstract | Links | BibTeX | Tags: enigma
@article{kothari_2020,
title = {Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance},
author = {Ankita Kothari and Simon Roux and Hanqiao Zhang and Anatori Prieto and Drishti Soneja and John-Marc Chandonia and Sarah J Spencer and Xiaoqin Wu and Sarah Altenburg and Matthew W Fields and Adam M Deutschbauer and Adam P Arkin and Eric J Alm and Romy Chakraborty and Aindrila Mukhopadhyay},
url = {http://biorxiv.org/lookup/doi/10.1101/2020.07.14.203604},
doi = {10.1101/2020.07.14.203604},
year = {2020},
date = {2020-07-15},
urldate = {2021-05-25},
journal = {BioRxiv},
abstract = {Viruses are ubiquitous microbiome components, shaping ecosystems via strain-specific predation, horizontal gene transfer and redistribution of nutrients through host lysis. Viral impacts are important in groundwater ecosystems, where microbes drive many nutrient fluxes and metabolic processes, however little is known about the diversity of viruses in these environments. We analyzed four groundwater plasmidomes and identified 200 viral sequences, which clustered into 41 ~ genus-level viral clusters (equivalent to viral genera) including 9 known and 32 putative new genera. We use publicly available bacterial whole genome sequences (WGS) and WGS from 261 bacterial isolates from this groundwater environment to identify potential viral hosts. We linked 76 of the 200 viral sequences to a range of bacterial phyla, the majority associated with Proteobacteria, followed by Firmicutes, Bacteroidetes and Actinobacteria. The publicly available microbial genome sequences enabled mapping bacterial hosts to a breadth of viral sequences. The WGS of groundwater isolates increased depth of host prediction by allowing identification of hosts at the strain level. The latter included 4 viruses that were almost entirely (textgreater99% query coverage, textgreater99% identity) identified as integrated in the genomes of specific Pseudomonas, Acidovorax and Castellaniella strains, resulting in very high-confidence host assignments. Lastly, 21 of these viruses encoded putative auxiliary metabolite genes for metal and antibiotic resistance, which might drive their infection cycles and/or provide selective advantage to infected hosts. Exploring the groundwater virome provides a necessary foundation for integration of viruses into ecosystem models where they act as key players in microbial adaption to environmental stress.},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
Viruses are ubiquitous microbiome components, shaping ecosystems via strain-specific predation, horizontal gene transfer and redistribution of nutrients through host lysis. Viral impacts are important in groundwater ecosystems, where microbes drive many nutrient fluxes and metabolic processes, however little is known about the diversity of viruses in these environments. We analyzed four groundwater plasmidomes and identified 200 viral sequences, which clustered into 41 ~ genus-level viral clusters (equivalent to viral genera) including 9 known and 32 putative new genera. We use publicly available bacterial whole genome sequences (WGS) and WGS from 261 bacterial isolates from this groundwater environment to identify potential viral hosts. We linked 76 of the 200 viral sequences to a range of bacterial phyla, the majority associated with Proteobacteria, followed by Firmicutes, Bacteroidetes and Actinobacteria. The publicly available microbial genome sequences enabled mapping bacterial hosts to a breadth of viral sequences. The WGS of groundwater isolates increased depth of host prediction by allowing identification of hosts at the strain level. The latter included 4 viruses that were almost entirely (textgreater99% query coverage, textgreater99% identity) identified as integrated in the genomes of specific Pseudomonas, Acidovorax and Castellaniella strains, resulting in very high-confidence host assignments. Lastly, 21 of these viruses encoded putative auxiliary metabolite genes for metal and antibiotic resistance, which might drive their infection cycles and/or provide selective advantage to infected hosts. Exploring the groundwater virome provides a necessary foundation for integration of viruses into ecosystem models where they act as key players in microbial adaption to environmental stress.
373.
Simon Rouxb Ankita Kotharia, Hanqiao Zhanga
Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance Journal Article
In: 2020.
@article{kothari2020ecogenomics,
title = {Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance},
author = {Ankita Kotharia, Simon Rouxb, Hanqiao Zhanga, Anatori Prietoa, Drishti Sonejaa, John-MarcChandoniaa, Sarah Spencer, Xiaoqin Wud, Sara Altenburgl, Matthew W. Fields, Adam M.Deutschbauer, Adam P. Arkinc, Eric J. Almh, Romy Chakrabortyd, Aindrila Mukhopadhyay},
year = {2020},
date = {2020-07-15},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
372.
Meja-Almonte, C; Busby, S J W; Wade, J T; van Helden, J; Arkin, A P; Stormo, G D; Eilbeck, K; Palsson, B O; Galagan, J E; Collado-Vides, J
Redefining fundamental concepts of transcription initiation in bacteria Journal Article
In: Nat. Rev. Genet., 2020.
@article{pmid32665585,
title = {Redefining fundamental concepts of transcription initiation in bacteria},
author = {C Meja-Almonte and S J W Busby and J T Wade and J van Helden and A P Arkin and G D Stormo and K Eilbeck and B O Palsson and J E Galagan and J Collado-Vides},
year = {2020},
date = {2020-07-01},
journal = {Nat. Rev. Genet.},
abstract = {Despite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived from a small number of initial studies, classic definitions for concepts of gene regulation have evolved as the number of characterized promoters has increased. Together with discoveries made using new technologies, this knowledge has led to revised generalizations and principles. In this Expert Recommendation, we suggest precise, updated definitions that support a logical, consistent conceptual framework of bacterial gene regulation, focusing on transcription initiation. The resulting concepts can be formalized by ontologies for computational modelling, laying the foundation for improved bioinformatics tools, knowledge-based resources and scientific communication. Thus, this work will help researchers construct better predictive models, with different formalisms, that will be useful in engineering, synthetic biology, microbiology and genetics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Despite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived from a small number of initial studies, classic definitions for concepts of gene regulation have evolved as the number of characterized promoters has increased. Together with discoveries made using new technologies, this knowledge has led to revised generalizations and principles. In this Expert Recommendation, we suggest precise, updated definitions that support a logical, consistent conceptual framework of bacterial gene regulation, focusing on transcription initiation. The resulting concepts can be formalized by ontologies for computational modelling, laying the foundation for improved bioinformatics tools, knowledge-based resources and scientific communication. Thus, this work will help researchers construct better predictive models, with different formalisms, that will be useful in engineering, synthetic biology, microbiology and genetics.
371.
Price, Morgan N; Deutschbauer, Adam M; Arkin, Adam P
Gapmind: automated annotation of amino acid biosynthesis. Journal Article
In: mSystems, vol. 5, no. 3, 2020.
Abstract | Links | BibTeX | Tags: enigma
@article{price_2020,
title = {Gapmind: automated annotation of amino acid biosynthesis.},
author = {Morgan N Price and Adam M Deutschbauer and Adam P Arkin},
url = {http://dx.doi.org/10.1128/mSystems.00291-20},
doi = {10.1128/mSystems.00291-20},
year = {2020},
date = {2020-06-23},
urldate = {2021-05-25},
journal = {mSystems},
volume = {5},
number = {3},
abstract = {GapMind is a Web-based tool for annotating amino acid biosynthesis in bacteria and archaea (http://papers.genomics.lbl.gov/gaps). GapMind incorporates many variant pathways and 130 different reactions, and it analyzes a genome in just 15 s. To avoid error-prone transitive annotations, GapMind relies primarily on a database of experimentally characterized proteins. GapMind correctly handles fusion proteins and split proteins, which often cause errors for best-hit approaches. To improve GapMind's coverage, we examined genetic data from 35 bacteria that grow in defined media without amino acids, and we filled many gaps in amino acid biosynthesis pathways. For example, we identified additional genes for arginine synthesis with succinylated intermediates in Bacteroides thetaiotaomicron, and we propose that Dyella japonica synthesizes tyrosine from phenylalanine. Nevertheless, for many bacteria and archaea that grow in minimal media, genes for some steps still cannot be identified. To help interpret potential gaps, GapMind checks if they match known gaps in related microbes that can grow in minimal media. GapMind should aid the identification of microbial growth requirements.IMPORTANCE Many microbes can make all of the amino acids (the building blocks of proteins). In principle, we should be able to predict which amino acids a microbe can make, and which it requires as nutrients, by checking its genome sequence for all of the necessary genes. However, in practice, it is difficult to check for all of the alternative pathways. Furthermore, new pathways and enzymes are still being discovered. We built an automated tool, GapMind, to annotate amino acid biosynthesis in bacterial and archaeal genomes. We used GapMind to list gaps: cases where a microbe makes an amino acid but a complete pathway cannot be identified in its genome. We used these gaps, together with data from mutants, to identify new pathways and enzymes. However, for most bacteria and archaea, we still do not know how they can make all of the amino acids. Copyright copyright 2020 Price et al.},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
GapMind is a Web-based tool for annotating amino acid biosynthesis in bacteria and archaea (http://papers.genomics.lbl.gov/gaps). GapMind incorporates many variant pathways and 130 different reactions, and it analyzes a genome in just 15 s. To avoid error-prone transitive annotations, GapMind relies primarily on a database of experimentally characterized proteins. GapMind correctly handles fusion proteins and split proteins, which often cause errors for best-hit approaches. To improve GapMind's coverage, we examined genetic data from 35 bacteria that grow in defined media without amino acids, and we filled many gaps in amino acid biosynthesis pathways. For example, we identified additional genes for arginine synthesis with succinylated intermediates in Bacteroides thetaiotaomicron, and we propose that Dyella japonica synthesizes tyrosine from phenylalanine. Nevertheless, for many bacteria and archaea that grow in minimal media, genes for some steps still cannot be identified. To help interpret potential gaps, GapMind checks if they match known gaps in related microbes that can grow in minimal media. GapMind should aid the identification of microbial growth requirements.IMPORTANCE Many microbes can make all of the amino acids (the building blocks of proteins). In principle, we should be able to predict which amino acids a microbe can make, and which it requires as nutrients, by checking its genome sequence for all of the necessary genes. However, in practice, it is difficult to check for all of the alternative pathways. Furthermore, new pathways and enzymes are still being discovered. We built an automated tool, GapMind, to annotate amino acid biosynthesis in bacterial and archaeal genomes. We used GapMind to list gaps: cases where a microbe makes an amino acid but a complete pathway cannot be identified in its genome. We used these gaps, together with data from mutants, to identify new pathways and enzymes. However, for most bacteria and archaea, we still do not know how they can make all of the amino acids. Copyright copyright 2020 Price et al.
370.
Price, M N; Deutschbauer, A M; Arkin, A P
GapMind: Automated Annotation of Amino Acid Biosynthesis Journal Article
In: mSystems, vol. 5, no. 3, 2020.
Abstract | BibTeX | Tags: arkin lab
@article{pmid32576650,
title = {GapMind: Automated Annotation of Amino Acid Biosynthesis},
author = {M N Price and A M Deutschbauer and A P Arkin},
year = {2020},
date = {2020-06-01},
journal = {mSystems},
volume = {5},
number = {3},
abstract = {GapMind is a Web-based tool for annotating amino acid biosynthesis in bacteria and archaea (http://papers.genomics.lbl.gov/gaps). GapMind incorporates many variant pathways and 130 different reactions, and it analyzes a genome in just 15 s. To avoid error-prone transitive annotations, GapMind relies primarily on a database of experimentally characterized proteins. GapMind correctly handles fusion proteins and split proteins, which often cause errors for best-hit approaches. To improve GapMind's coverage, we examined genetic data from 35 bacteria that grow in defined media without amino acids, and we filled many gaps in amino acid biosynthesis pathways. For example, we identified additional genes for arginine synthesis with succinylated intermediates in Bacteroides thetaiotaomicron, and we propose that Dyella japonica synthesizes tyrosine from phenylalanine. Nevertheless, for many bacteria and archaea that grow in minimal media, genes for some steps still cannot be identified. To help interpret potential gaps, GapMind checks if they match known gaps in related microbes that can grow in minimal media. GapMind should aid the identification of microbial growth requirements.IMPORTANCE Many microbes can make all of the amino acids (the building blocks of proteins). In principle, we should be able to predict which amino acids a microbe can make, and which it requires as nutrients, by checking its genome sequence for all of the necessary genes. However, in practice, it is difficult to check for all of the alternative pathways. Furthermore, new pathways and enzymes are still being discovered. We built an automated tool, GapMind, to annotate amino acid biosynthesis in bacterial and archaeal genomes. We used GapMind to list gaps: cases where a microbe makes an amino acid but a complete pathway cannot be identified in its genome. We used these gaps, together with data from mutants, to identify new pathways and enzymes. However, for most bacteria and archaea, we still do not know how they can make all of the amino acids.},
keywords = {arkin lab},
pubstate = {published},
tppubtype = {article}
}
GapMind is a Web-based tool for annotating amino acid biosynthesis in bacteria and archaea (http://papers.genomics.lbl.gov/gaps). GapMind incorporates many variant pathways and 130 different reactions, and it analyzes a genome in just 15 s. To avoid error-prone transitive annotations, GapMind relies primarily on a database of experimentally characterized proteins. GapMind correctly handles fusion proteins and split proteins, which often cause errors for best-hit approaches. To improve GapMind's coverage, we examined genetic data from 35 bacteria that grow in defined media without amino acids, and we filled many gaps in amino acid biosynthesis pathways. For example, we identified additional genes for arginine synthesis with succinylated intermediates in Bacteroides thetaiotaomicron, and we propose that Dyella japonica synthesizes tyrosine from phenylalanine. Nevertheless, for many bacteria and archaea that grow in minimal media, genes for some steps still cannot be identified. To help interpret potential gaps, GapMind checks if they match known gaps in related microbes that can grow in minimal media. GapMind should aid the identification of microbial growth requirements.IMPORTANCE Many microbes can make all of the amino acids (the building blocks of proteins). In principle, we should be able to predict which amino acids a microbe can make, and which it requires as nutrients, by checking its genome sequence for all of the necessary genes. However, in practice, it is difficult to check for all of the alternative pathways. Furthermore, new pathways and enzymes are still being discovered. We built an automated tool, GapMind, to annotate amino acid biosynthesis in bacterial and archaeal genomes. We used GapMind to list gaps: cases where a microbe makes an amino acid but a complete pathway cannot be identified in its genome. We used these gaps, together with data from mutants, to identify new pathways and enzymes. However, for most bacteria and archaea, we still do not know how they can make all of the amino acids.
369.
Ashley L. Azadeh Sean Carim, Alexey E. Kazakov
Systematic Discovery of Pseudomonad Genetic Factors Involved in Sensitivity to Tailocins Journal Article
In: 2020.
BibTeX | Tags: arkin lab, biodesign
@article{sean,
title = {Systematic Discovery of Pseudomonad Genetic Factors Involved in Sensitivity to Tailocins},
author = {Sean Carim, Ashley L. Azadeh, Alexey E. Kazakov, Morgan N. Price, Peter J. Walian, Romy Chakraborty, Adam M. Deutschbauer, Vivek K. Mutalik, Adam P. Arkin},
year = {2020},
date = {2020-05-27},
keywords = {arkin lab, biodesign},
pubstate = {published},
tppubtype = {article}
}
368.
Filipe Liu Samuel M. D. Seaver, Qizhi Zhang; Henry, Christopher S.
The ModelSEED Database for the integration of metabolic annotations and the reconstruction, comparison, and analysis of metabolic models for plants, fungi, and microbes Journal Article
In: 2020.
@article{seaver2020modelseed,
title = {The ModelSEED Database for the integration of metabolic annotations and the reconstruction, comparison, and analysis of metabolic models for plants, fungi, and microbes},
author = {Samuel M. D. Seaver, Filipe Liu, Qizhi Zhang, James Jeffryes, José P. Faria, Janaka N. Edirisinghe, Michael Mundy, Nicholas Chia, Elad Noor, Moritz E. Beber, Aaron A. Best, Matthew DeJongh, Jeffrey A. Kimbrel, Patrik D'haeseleer, Erik Pearson, Shane Canon, Elisha M. Wood-Charlson, Robert W. Cottingham, Adam P. Arkin and Christopher S. Henry},
year = {2020},
date = {2020-05-12},
keywords = {kbase},
pubstate = {published},
tppubtype = {article}
}
367.
Carlson, Hans K; Lui, Lauren M; Price, Morgan N; Kazakov, Alexey E; Carr, Alex V; Kuehl, Jennifer V; Owens, Trenton K; Nielsen, Torben; Arkin, Adam P; Deutschbauer, Adam M
Selective carbon sources influence the end products of microbial nitrate respiration. Journal Article
In: The ISME Journal, vol. 14, no. 8, pp. 2034-2045, 2020, ISSN: 1751-7362.
Abstract | Links | BibTeX | Tags: enigma
@article{carlson_2020,
title = {Selective carbon sources influence the end products of microbial nitrate respiration.},
author = {Hans K Carlson and Lauren M Lui and Morgan N Price and Alexey E Kazakov and Alex V Carr and Jennifer V Kuehl and Trenton K Owens and Torben Nielsen and Adam P Arkin and Adam M Deutschbauer},
url = {http://www.nature.com/articles/s41396-020-0666-7},
doi = {10.1038/s41396-020-0666-7},
issn = {1751-7362},
year = {2020},
date = {2020-05-05},
urldate = {2021-05-25},
journal = {The ISME Journal},
volume = {14},
number = {8},
pages = {2034-2045},
abstract = {Respiratory and catabolic genes are differentially distributed across microbial genomes. Thus, specific carbon sources may favor different respiratory processes. We profiled the influence of 94 carbon sources on the end products of nitrate respiration in microbial enrichment cultures from diverse terrestrial environments. We found that some carbon sources consistently favor dissimilatory nitrate reduction to ammonium (DNRA/nitrate ammonification) while other carbon sources favor nitrite accumulation or denitrification. For an enrichment culture from aquatic sediment, we sequenced the genomes of the most abundant strains, matched these genomes to 16S rDNA exact sequence variants (ESVs), and used 16S rDNA amplicon sequencing to track the differential enrichment of functionally distinct ESVs on different carbon sources. We found that changes in the abundances of strains with different genetic potentials for nitrite accumulation, DNRA or denitrification were correlated with the nitrite or ammonium concentrations in the enrichment cultures recovered on different carbon sources. Specifically, we found that either L-sorbose or D-cellobiose enriched for a Klebsiella nitrite accumulator, other sugars enriched for an Escherichia nitrate ammonifier, and citrate or formate enriched for a Pseudomonas denitrifier and a Sulfurospirillum nitrate ammonifier. Our results add important nuance to the current paradigm that higher concentrations of carbon will always favor DNRA over denitrification or nitrite accumulation, and we propose that, in some cases, carbon composition can be as important as carbon concentration in determining nitrate respiratory end products. Furthermore, our approach can be extended to other environments and metabolisms to characterize how selective parameters influence microbial community composition, gene content, and function.},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
Respiratory and catabolic genes are differentially distributed across microbial genomes. Thus, specific carbon sources may favor different respiratory processes. We profiled the influence of 94 carbon sources on the end products of nitrate respiration in microbial enrichment cultures from diverse terrestrial environments. We found that some carbon sources consistently favor dissimilatory nitrate reduction to ammonium (DNRA/nitrate ammonification) while other carbon sources favor nitrite accumulation or denitrification. For an enrichment culture from aquatic sediment, we sequenced the genomes of the most abundant strains, matched these genomes to 16S rDNA exact sequence variants (ESVs), and used 16S rDNA amplicon sequencing to track the differential enrichment of functionally distinct ESVs on different carbon sources. We found that changes in the abundances of strains with different genetic potentials for nitrite accumulation, DNRA or denitrification were correlated with the nitrite or ammonium concentrations in the enrichment cultures recovered on different carbon sources. Specifically, we found that either L-sorbose or D-cellobiose enriched for a Klebsiella nitrite accumulator, other sugars enriched for an Escherichia nitrate ammonifier, and citrate or formate enriched for a Pseudomonas denitrifier and a Sulfurospirillum nitrate ammonifier. Our results add important nuance to the current paradigm that higher concentrations of carbon will always favor DNRA over denitrification or nitrite accumulation, and we propose that, in some cases, carbon composition can be as important as carbon concentration in determining nitrate respiratory end products. Furthermore, our approach can be extended to other environments and metabolisms to characterize how selective parameters influence microbial community composition, gene content, and function.
366.
Crystal Zhong Benjamin A. Adler, Hualan Liu
Systematic Discovery of Salmonella Phage-Host Interactions via High-Throughput Genome-Wide Screens Journal Article
In: bioRxiv, 2020.
BibTeX | Tags: arkin lab, biodesign
@article{adler2020systematic,
title = {Systematic Discovery of Salmonella Phage-Host Interactions via High-Throughput Genome-Wide Screens},
author = {Benjamin A. Adler, Crystal Zhong, Hualan Liu, Elizabeth Kutter, Adam M.
Deutschbauer, Vivek K. Mutalik, Adam P. Arkin},
year = {2020},
date = {2020-04-28},
journal = {bioRxiv},
keywords = {arkin lab, biodesign},
pubstate = {published},
tppubtype = {article}
}
365.
Price, Morgan N.; Arkin, Adam P.
Short Methionine Synthases Journal Article
In: 2020.
@article{morgan,
title = {Short Methionine Synthases},
author = {Morgan N. Price and Adam P. Arkin},
year = {2020},
date = {2020-04-23},
keywords = {arkin lab},
pubstate = {published},
tppubtype = {article}
}
364.
Caitlin M. Gionfriddo Regina L. Wilpiszeski, Ann M. Wymore
In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations Journal Article
In: bioRxiv, 2020.
@article{uwu,
title = {In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations},
author = {Regina L. Wilpiszeski, Caitlin M. Gionfriddo, Ann M. Wymore, Ji-Won Moon, Kenneth A. Lowe, Mircea Podar, Sa’ad Rafie, Matthew W. Fields, Terry C. Hazen, Xiaoxuan Ge, Farris Poole, Michael W.W. Adams, Romy Chakraborty, Yupeng Fan, Joy D. Van Nostrand, Jizhong Zhou, Adam P. Arkin, Dwayne A. Elias},
year = {2020},
date = {2020-04-19},
journal = {bioRxiv},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
363.
Tian, Renmao; Ning, Daliang; He, Zhili; Zhang, Ping; Spencer, Sarah J; Gao, Shuhong; Shi, Weiling; Wu, Linwei; Zhang, Ya; Yang, Yunfeng; Adams, Benjamin G; Rocha, Andrea M; Detienne, Brittny L; Lowe, Kenneth A; Joyner, Dominique C; Klingeman, Dawn M; Arkin, Adam P; Fields, Matthew W; Hazen, Terry C; Stahl, David A; Alm, Eric J; Zhou, Jizhong
Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity. Journal Article
In: Microbiome, vol. 8, no. 1, pp. 51, 2020.
Abstract | Links | BibTeX | Tags: enigma
@article{tian_2020,
title = {Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity.},
author = {Renmao Tian and Daliang Ning and Zhili He and Ping Zhang and Sarah J Spencer and Shuhong Gao and Weiling Shi and Linwei Wu and Ya Zhang and Yunfeng Yang and Benjamin G Adams and Andrea M Rocha and Brittny L Detienne and Kenneth A Lowe and Dominique C Joyner and Dawn M Klingeman and Adam P Arkin and Matthew W Fields and Terry C Hazen and David A Stahl and Eric J Alm and Jizhong Zhou},
url = {http://dx.doi.org/10.1186/s40168-020-00825-w},
doi = {10.1186/s40168-020-00825-w},
year = {2020},
date = {2020-04-06},
urldate = {2021-05-25},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {51},
abstract = {BACKGROUND: The newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse superphylum including textgreater 20 candidate phyla (a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known. RESULTS: Here, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of textgreater 600 Gbp sequence data. We observed that, while the members of Patescibacteria have reduced genomes (~ 1 Mbp) exclusively, functions essential to growth and reproduction such as genetic information processing were retained. Surprisingly, they have sharply reduced redundant and nonessential functions, including specific metabolic activities and stress response systems. The Patescibacteria have ultra-small cells and simplified membrane structures, including flagellar assembly, transporters, and two-component systems. Despite the lack of CRISPR viral defense, the bacteria may evade predation through deletion of common membrane phage receptors and other alternative strategies, which may explain the low representation of prophage proteins in their genomes and lack of CRISPR. By establishing the linkages between bacterial features and the groundwater environmental conditions, our results provide important insights into the functions and evolution of this CPR group. CONCLUSIONS: We found that Patescibacteria has streamlined many functions while acquiring advantages such as avoiding phage invasion, to adapt to the groundwater environment. The unique features of small genome size, ultra-small cell size, and lacking CRISPR of this large lineage are bringing new understandings on life of Bacteria. Our results provide important insights into the mechanisms for adaptation of the superphylum in the groundwater environments, and demonstrate a case where less is more, and small is mighty.},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: The newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse superphylum including textgreater 20 candidate phyla (a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known. RESULTS: Here, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of textgreater 600 Gbp sequence data. We observed that, while the members of Patescibacteria have reduced genomes (~ 1 Mbp) exclusively, functions essential to growth and reproduction such as genetic information processing were retained. Surprisingly, they have sharply reduced redundant and nonessential functions, including specific metabolic activities and stress response systems. The Patescibacteria have ultra-small cells and simplified membrane structures, including flagellar assembly, transporters, and two-component systems. Despite the lack of CRISPR viral defense, the bacteria may evade predation through deletion of common membrane phage receptors and other alternative strategies, which may explain the low representation of prophage proteins in their genomes and lack of CRISPR. By establishing the linkages between bacterial features and the groundwater environmental conditions, our results provide important insights into the functions and evolution of this CPR group. CONCLUSIONS: We found that Patescibacteria has streamlined many functions while acquiring advantages such as avoiding phage invasion, to adapt to the groundwater environment. The unique features of small genome size, ultra-small cell size, and lacking CRISPR of this large lineage are bringing new understandings on life of Bacteria. Our results provide important insights into the mechanisms for adaptation of the superphylum in the groundwater environments, and demonstrate a case where less is more, and small is mighty.
362.
Lui, Lauren M; Nielsen, Torben N; Arkin, Adam P
A method for achieving complete microbial genomes and better quality bins from metagenomics data Journal Article
In: BioRxiv, 2020.
Abstract | Links | BibTeX | Tags: enigma
@article{lui_2020,
title = {A method for achieving complete microbial genomes and better quality bins from metagenomics data},
author = {Lauren M Lui and Torben N Nielsen and Adam P Arkin},
url = {http://biorxiv.org/lookup/doi/10.1101/2020.03.05.979740},
doi = {10.1101/2020.03.05.979740},
year = {2020},
date = {2020-03-06},
urldate = {2021-05-25},
journal = {BioRxiv},
abstract = {Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete microbial genomes (i.e., circular with no misassemblies) from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Only 63 circularized bacterial and archaeal genomes have been assembled from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a method to achieve circularized genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one copy of ribosomal RNA genes. We present 34 circular CPR genomes, one circular Margulisbacteria genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA.},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete microbial genomes (i.e., circular with no misassemblies) from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Only 63 circularized bacterial and archaeal genomes have been assembled from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a method to achieve circularized genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one copy of ribosomal RNA genes. We present 34 circular CPR genomes, one circular Margulisbacteria genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA.
361.
Torben N. Nielsen Lauren M. Lui, Adam P. Arkin
A method for achieving complete microbial genomes and better quality bins from metagenomics data Journal Article
In: BioRxiv, 2020.
BibTeX | Tags: arkin lab, enigma
@article{lui2020method,
title = {A method for achieving complete microbial genomes and better quality bins from metagenomics data},
author = {Lauren M. Lui, Torben N. Nielsen, Adam P. Arkin},
year = {2020},
date = {2020-03-06},
journal = {BioRxiv},
keywords = {arkin lab, enigma},
pubstate = {published},
tppubtype = {article}
}
360.
Mengting Yuan Daliang Ning, Linwei Wu
A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming Journal Article
In: 2020.
@article{ning2020quantitativeb,
title = {A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming},
author = {Daliang Ning, Mengting Yuan, Linwei Wu, Ya Zhan, Xue Guo, Xishu Zhou , Yunfeng Yang, Adam P. Arkin, Mary K. Firestone, Jizhong Zhou},
year = {2020},
date = {2020-02-25},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
359.
Benjamin A. Adler Vivek K. Mutalik, Harneet S. Rishi
High-throughput mapping of the phage resistance landscape in E. coli Journal Article
In: 2020.
BibTeX | Tags: arkin lab, biodesign
@article{Mutalik2020,
title = {High-throughput mapping of the phage resistance landscape in E. coli},
author = {Vivek K. Mutalik, Benjamin A. Adler, Harneet S. Rishi, Denish Piya, Crystal Zhong,Britt Koskella, Richard Calendar, Pavel Novichkov, Morgan N. Price, Adam M. Deutschbauer, Adam P. Arkin},
year = {2020},
date = {2020-02-16},
keywords = {arkin lab, biodesign},
pubstate = {published},
tppubtype = {article}
}
358.
Abel, Anthony J; Hilzinger, Jacob M; Arkin, Adam P; Clark, Douglas S
Systems-informed genome mining for electroautotrophic microbial production Journal Article
In: bioRxiv, 2020.
@article{Abel2020,
title = {Systems-informed genome mining for electroautotrophic microbial production},
author = {Anthony J Abel and Jacob M Hilzinger and Adam P Arkin and Douglas S Clark},
year = {2020},
date = {2020-01-01},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
keywords = {cubes},
pubstate = {published},
tppubtype = {article}
}
357.
Berliner, Aaron; Hilzinger, Jacob M; Abel, Anthony J; McNulty, Matthew; Makrygiorgos, George; Averesch, Nils J H; Gupta, Soumyajit Sen; Benvenuti, Alexander; Caddell, Daniel; Cestellos-Blanco, Stefano
Towards a Biomanufactory on Mars Journal Article
In: preprints.org, 2020.
@article{Berliner2020,
title = {Towards a Biomanufactory on Mars},
author = {Aaron Berliner and Jacob M Hilzinger and Anthony J Abel and Matthew McNulty and George Makrygiorgos and Nils J H Averesch and Soumyajit Sen Gupta and Alexander Benvenuti and Daniel Caddell and Stefano Cestellos-Blanco},
doi = {doi: 10.20944/preprints202012.0714.v1},
year = {2020},
date = {2020-01-01},
journal = {preprints.org},
publisher = {Preprints},
keywords = {cubes},
pubstate = {published},
tppubtype = {article}
}
356.
Tian, R; Ning, D; He, Z; Zhang, P; Spencer, S J; Gao, S; Shi, W; Wu, L; Zhang, Y; Yang, Y; Adams, B G; Rocha, A M; Detienne, B L; Lowe, K A; Joyner, D C; Klingeman, D M; Arkin, A P; Fields, M W; Hazen, T C; Stahl, D A; Alm, E J; Zhou, J
Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity Journal Article
In: Microbiome, vol. 8, no. 1, pp. 51, 2020.
Abstract | BibTeX | Tags: enigma
@article{pmid32252814,
title = {Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity},
author = {R Tian and D Ning and Z He and P Zhang and S J Spencer and S Gao and W Shi and L Wu and Y Zhang and Y Yang and B G Adams and A M Rocha and B L Detienne and K A Lowe and D C Joyner and D M Klingeman and A P Arkin and M W Fields and T C Hazen and D A Stahl and E J Alm and J Zhou},
year = {2020},
date = {2020-01-01},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {51},
abstract = {The newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse superphylum including > 20 candidate phyla (a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known. Here, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of > 600 Gbp sequence data. We observed that, while the members of Patescibacteria have reduced genomes (~ 1 Mbp) exclusively, functions essential to growth and reproduction such as genetic information processing were retained. Surprisingly, they have sharply reduced redundant and nonessential functions, including specific metabolic activities and stress response systems. The Patescibacteria have ultra-small cells and simplified membrane structures, including flagellar assembly, transporters, and two-component systems. Despite the lack of CRISPR viral defense, the bacteria may evade predation through deletion of common membrane phage receptors and other alternative strategies, which may explain the low representation of prophage proteins in their genomes and lack of CRISPR. By establishing the linkages between bacterial features and the groundwater environmental conditions, our results provide important insights into the functions and evolution of this CPR group. We found that Patescibacteria has streamlined many functions while acquiring advantages such as avoiding phage invasion, to adapt to the groundwater environment. The unique features of small genome size, ultra-small cell size, and lacking CRISPR of this large lineage are bringing new understandings on life of Bacteria. Our results provide important insights into the mechanisms for adaptation of the superphylum in the groundwater environments, and demonstrate a case where less is more, and small is mighty.},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
The newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse superphylum including > 20 candidate phyla (a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known. Here, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of > 600 Gbp sequence data. We observed that, while the members of Patescibacteria have reduced genomes (~ 1 Mbp) exclusively, functions essential to growth and reproduction such as genetic information processing were retained. Surprisingly, they have sharply reduced redundant and nonessential functions, including specific metabolic activities and stress response systems. The Patescibacteria have ultra-small cells and simplified membrane structures, including flagellar assembly, transporters, and two-component systems. Despite the lack of CRISPR viral defense, the bacteria may evade predation through deletion of common membrane phage receptors and other alternative strategies, which may explain the low representation of prophage proteins in their genomes and lack of CRISPR. By establishing the linkages between bacterial features and the groundwater environmental conditions, our results provide important insights into the functions and evolution of this CPR group. We found that Patescibacteria has streamlined many functions while acquiring advantages such as avoiding phage invasion, to adapt to the groundwater environment. The unique features of small genome size, ultra-small cell size, and lacking CRISPR of this large lineage are bringing new understandings on life of Bacteria. Our results provide important insights into the mechanisms for adaptation of the superphylum in the groundwater environments, and demonstrate a case where less is more, and small is mighty.
