@article{Cestellos-Blanco2021,

title = {Production of PHB From CO2-Derived Acetate With Minimal Processing Assessed for Space Biomanufacturing},

author = {Stefano Cestellos-Blanco and Skyler Friedline and Kyle B. Sander and Anthony J. Abel and Ji Min Kim and Douglas S. Clark and Adam P. Arkin and Peidong Yang},

doi = {10.3389/fmicb.2021.700010},

issn = {1664-302X},

year  = {2021},

date = {2021-07-28},

journal = {Front. Microbiol.},

volume = {12},

publisher = {Frontiers Media SA},

abstract = {Providing life-support materials to crewed space exploration missions is pivotal for mission success. However, as missions become more distant and extensive, obtaining these materials from in situ resource utilization is paramount. The combination of microorganisms with electrochemical technologies offers a platform for the production of critical chemicals and materials from CO2 and H2O, two compounds accessible on a target destination like Mars. One such potential commodity is poly(3-hydroxybutyrate) (PHB), a common biopolyester targeted for additive manufacturing of durable goods. Here, we present an integrated two-module process for the production of PHB from CO2. An autotrophic Sporomusa ovata (S. ovata) process converts CO2 to acetate which is then directly used as the primary carbon source for aerobic PHB production by Cupriavidus basilensis (C. basilensis). The S. ovata uses H2 as a reducing equivalent to be generated through electrocatalytic solar-driven H2O reduction. Conserving and recycling media components is critical, therefore we have designed and optimized our process to require no purification or filtering of the cell culture media between microbial production steps which could result in up to 98% weight savings. By inspecting cell population dynamics during culturing we determined that C. basilensis suitably proliferates in the presence of inactive S. ovata. During the bioprocess 10.4 mmol acetate L –1 day–1 were generated from CO2 by S. ovata in the optimized media. Subsequently, 12.54 mg PHB L–1 hour–1 were produced by C. basilensis in the unprocessed media with an overall carbon yield of 11.06% from acetate. In order to illustrate a pathway to increase overall productivity and enable scaling of our bench-top process, we developed a model indicating key process parameters to optimize.},

keywords = {Microbiology, Microbiology (medical)},

pubstate = {published},

tppubtype = {article}

}

@article{Kothari2021,

title = {Ecogenomics of Groundwater Phages 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 Spencer and Xiaoqin Wu and Sara Altenburg and Matthew W. Fields and Adam M. Deutschbauer and Adam P. Arkin and Eric J. Alm and Romy Chakraborty and Aindrila Mukhopadhyay},

editor = {Ileana M. Cristea},

doi = {10.1128/msystems.00537-21},

issn = {2379-5077},

year  = {2021},

date = {2021-06-29},

urldate = {2021-06-29},

journal = {mSystems},

volume = {6},

number = {3},

publisher = {American Society for Microbiology},

abstract = {<jats:p>To our knowledge, this is the first study to identify the bacteriophage distribution in a groundwater ecosystem shedding light on their prevalence and distribution across metal-contaminated and background sites. Our study is uniquely based on selective sequencing of solely the extrachromosomal elements of a microbiome followed by analysis for viral signatures, thus establishing a more focused approach for phage identifications.</jats:p>},

keywords = {Behavior and Systematics, Biochemistry, biodesign, Computer Science Applications, Ecology, Evolution, Genetics, Microbiology, Modeling and Simulation, Molecular Biology, Physiology},

pubstate = {published},

tppubtype = {article}

}

@article{paradis_2021,

title = {Sustained ability of a natural microbial community to remove nitrate from groundwater},

author = {Charles J Paradis and John I Miller and Ji-Won Moon and Sarah J Spencer and Lauren M Lui and Joy D Van Nostrand and Daliang Ning and Andrew D Steen and Larry D {McKay} and Adam P Arkin and Jizhong Zhou and Eric J Alm and Terry C Hazen},

url = {http://biorxiv.org/lookup/doi/10.1101/2021.05.27.446013},

doi = {10.1101/2021.05.27.446013},

year  = {2021},

date = {2021-05-28},

urldate = {2021-06-04},

journal = {BioRxiv},

abstract = {Microbial-mediated nitrate removal from groundwater is widely recognized as the predominant mechanism for nitrate attenuation in contaminated aquifers and is largely dependent on the presence of a carbon-bearing electron donor. The repeated exposure of a natural microbial community to an electron donor can result in the sustained ability of the community to remove nitrate; this phenomenon has been clearly demonstrated at the laboratory scale. However, in situ demonstrations of this ability are lacking. For this study, ethanol (electron donor) was repeatedly injected into a groundwater well (treatment) for six consecutive weeks to establish the sustained ability of a microbial community to remove nitrate. A second well (control) located up-gradient was not injected with ethanol during this time. The treatment well demonstrated strong evidence of sustained ability as evident by concomitant ethanol and nitrate removal and subsequent sulfate removal upon consecutive exposures. Both wells were then monitored for six additional weeks under natural (no injection) conditions. During the final week, ethanol was injected into both treatment and control wells. The treatment well demonstrated sustained ability as evident by concomitant ethanol and nitrate removal whereas the control did not. Surprisingly, the treatment well did not indicate a sustained and selective enrichment of a microbial community. These results suggested that the predominant mechanism(s) of sustained ability likely exist at the enzymatic- and/or genetic-levels. The results of this study demonstrated that the in situ ability of a microbial community to remove nitrate can be sustained in the prolonged absence of an electron donor. Moreover, these results implied that the electron-donor exposure history of nitrate-contaminated groundwater can play an important role nitrate attenuation. ARTICLE IMPACT STATEMENT: Groundwater microbes sustain ability to remove nitrate in absence of carbon and energy source.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{lui_2021,

title = {A method for achieving complete microbial genomes and improving bins from metagenomics data.},

author = {Lauren M Lui and Torben N Nielsen and Adam P Arkin},

url = {http://dx.doi.org/10.1371/journal.pcbi.1008972},

doi = {10.1371/journal.pcbi.1008972},

year  = {2021},

date = {2021-05-07},

urldate = {2021-05-26},

journal = {PLoS Computational Biology},

volume = {17},

number = {5},

pages = {e1008972},

abstract = {Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Some studies have attempted to extract complete bacterial, archaeal, and viral genomes and often focus on species with circular genomes so they can help confirm completeness with circularity. However, less than 100 circularized bacterial and archaeal genomes have been assembled and published 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 semi-automated method called Jorg to help circularize small bacterial, archaeal, and viral 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 ribosomal RNA operon. In addition to 34 circular CPR genomes, we present one circular Margulisbacteria genome, one circular Chloroflexi 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. Code and a tutorial for this method is available at https://github.com/lmlui/Jorg and is available on the DOE Systems Biology KnowledgeBase as a beta app.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{nayfach_2021,

title = {A genomic catalog of Earth's microbiomes.},

author = {Stephen Nayfach and Simon Roux and Rekha Seshadri and Daniel Udwary and Neha Varghese and Frederik Schulz and Dongying Wu and David Paez-Espino and I-Min Chen and Marcel Huntemann and Krishna Palaniappan and Joshua Ladau and Supratim Mukherjee and T B K Reddy and Torben Nielsen and Edward Kirton and José P Faria and Janaka N Edirisinghe and Christopher S Henry and Sean P Jungbluth and Dylan Chivian and Paramvir Dehal and Elisha M Wood-Charlson and Adam P Arkin and Susannah G Tringe and Axel Visel and IMG and Tanja Woyke and Nigel J Mouncey and Natalia N Ivanova and Nikos C Kyrpides and Emiley A Eloe-Fadrosh},

url = {http://www.nature.com/articles/s41587-020-0718-6},

doi = {10.1038/s41587-020-0718-6},

issn = {1087-0156},

year  = {2021},

date = {2021-04-01},

urldate = {2021-06-04},

journal = {Nature Biotechnology},

volume = {39},

number = {4},

pages = {499-509},

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 textgreater10,000 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.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{Lui2021,

title = {Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology},

author = {Lauren M. Lui and Erica L.-W. Majumder and Heidi J. Smith and Hans K. Carlson and Frederick von Netzer and Matthew W. Fields and David A. Stahl and Jizhong Zhou and Terry C. Hazen and Nitin S. Baliga and Paul D. Adams and Adam P. Arkin},

doi = {10.3389/fmicb.2021.642422},

issn = {1664-302X},

year  = {2021},

date = {2021-03-24},

journal = {Front. Microbiol.},

volume = {12},

publisher = {Frontiers Media SA},

abstract = {Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.},

keywords = {Microbiology, Microbiology (medical)},

pubstate = {published},

tppubtype = {article}

}

@article{lui_2021a,

title = {Mechanism across scales: A holistic modeling framework integrating laboratory and field studies for microbial ecology.},

author = {Lauren M Lui and Erica L-W Majumder and Heidi J Smith and Hans K Carlson and Frederick von Netzer and Matthew W Fields and David A Stahl and Jizhong Zhou and Terry C Hazen and Nitin S Baliga and Paul D Adams and Adam P Arkin},

url = {https://www.frontiersin.org/articles/10.3389/fmicb.2021.642422/full},

doi = {10.3389/fmicb.2021.642422},

issn = {1664-302X},

year  = {2021},

date = {2021-03-24},

urldate = {2021-05-25},

journal = {Frontiers in microbiology},

volume = {12},

pages = {642422},

abstract = {Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments. Copyright copyright 2021 Lui, Majumder, Smith, Carlson, von Netzer, Fields, Stahl, Zhou, Hazen, Baliga, Adams and Arkin.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{wall_2021,

title = {Deletion Mutants, Archived Transposon Library, and Tagged Protein Constructs of the Model Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough.},

author = {Judy D Wall and Grant M Zane and Thomas R Juba and Jennifer V Kuehl and Jayashree Ray and Swapnil R Chhabra and Valentine V Trotter and Maxim Shatsky and Kara B De León and Kimberly L Keller and Kelly S Bender and Gareth Butland and Adam P Arkin and Adam M Deutschbauer},

url = {http://dx.doi.org/10.1128/MRA.00072-21},

doi = {10.1128/MRA.00072-21},

year  = {2021},

date = {2021-03-18},

urldate = {2021-05-25},

journal = {Microbiology Resource Announcements},

volume = {10},

number = {11},

abstract = {The dissimilatory sulfate-reducing deltaproteobacterium Desulfovibrio vulgaris Hildenborough (ATCC 29579) was chosen by the research collaboration ENIGMA to explore tools and protocols for bringing this anaerobe to model status. Here, we describe a collection of genetic constructs generated by ENIGMA that are available to the research community. Copyright copyright 2021 Wall et al.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{song_2021,

title = {A simple, cost-effective and automation-friendly direct PCR approach for bacterial community analysis},

author = {Fangchao Song and Jennifer V Kuehl and Arjun Chandran and Adam P Arkin},

url = {http://biorxiv.org/lookup/doi/10.1101/2021.03.01.433496},

doi = {10.1101/2021.03.01.433496},

year  = {2021},

date = {2021-03-02},

urldate = {2021-06-04},

journal = {BioRxiv},

abstract = {Bacterial communities in water, soil, and humans play an essential role in environmental ecology and human health. PCR-based amplicon analysis, such as 16s ribosomal RNA sequencing, is a fundamental tool for quantifying and studying microbial composition, dynamics, and interactions. However, given the complexity of microbial communities, a substantial amount of samples becomes necessary to analyses that parse the factors that determine microbial composition. A common bottleneck in performing these kinds of experiments is genomic DNA (gDNA) extraction, which can be biased on the types of species, time-consuming and expensive. Direct PCR methods are a potentially simpler and more accurate alternative to gDNA extraction methods that do not require the intervening purification step. In this study, we evaluated three variations of direct PCR methods using diverse heterogeneous bacterial cultures, ZymoBIOMICS Microbial Community Standards, and groundwater. By comparing direct PCR methods with DNeasy blood and tissue kits and DNeasy Powersoil kits, we found a specific variant of the direct PCR method exhibits a comparable overall accuracy to the conventional DNeasy Powersoil protocol. We also found the method showed higher efficiency for extracting gDNA from the gram negative strains compared to DNeasy blood and tissue protocol. This direct PCR method is 1600 times cheaper ($0.34 for 96 samples), 10 times simpler (15 min hands-on time for 96 samples) than DNeasy Powersoil protocol. The direct PCR method can also be fully automated, and is compatible with small volume samples, thereby permitting scaling of samples and replicates needed to support high-throughput large-scale bacterial community analysis.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{carim_2021,

title = {Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins.},

author = {Sean Carim and Ashley L Azadeh and Alexey E Kazakov and Morgan N Price and Peter J Walian and Lauren M Lui and Torben N Nielsen and Romy Chakraborty and Adam M Deutschbauer and Vivek K Mutalik and Adam P Arkin},

url = {http://www.nature.com/articles/s41396-021-00921-1},

doi = {10.1038/s41396-021-00921-1},

issn = {1751-7362},

year  = {2021},

date = {2021-03-01},

urldate = {2021-05-25},

journal = {The ISME Journal},

abstract = {Tailocins are bactericidal protein complexes produced by a wide variety of bacteria that kill closely related strains and may play a role in microbial community structure. Thanks to their high specificity, tailocins have been proposed as precision antibacterial agents for therapeutic applications. Compared to tailed phages, with whom they share an evolutionary and morphological relationship, bacterially produced tailocins kill their host upon production but producing strains display resistance to self-intoxication. Though lipopolysaccharide (LPS) has been shown to act as a receptor for tailocins, the breadth of factors involved in tailocin sensitivity, and the mechanisms behind resistance to self-intoxication, remain unclear. Here, we employed genome-wide screens in four non-model pseudomonads to identify mutants with altered fitness in the presence of tailocins produced by closely related pseudomonads. Our mutant screens identified O-antigen composition and display as most important in defining sensitivity to our tailocins. In addition, the screens suggest LPS thinning as a mechanism by which resistant strains can become more sensitive to tailocins. We validate many of these novel findings, and extend these observations of tailocin sensitivity to 130 genome-sequenced pseudomonads. This work offers insights into tailocin-bacteria interactions, informing the potential use of tailocins in microbiome manipulation and antibacterial therapy.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{Liu2021,

title = {Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments},

author = {Hualan Liu and Anthony L. Shiver and Morgan N. Price and Hans K. Carlson and Valentine V. Trotter and Yan Chen and Veronica Escalante and Jayashree Ray and Kelsey E. Hern and Christopher J. Petzold and Peter J. Turnbaugh and Kerwyn Casey Huang and Adam P. Arkin and Adam M. Deutschbauer},

doi = {10.1016/j.celrep.2021.108789},

issn = {2211-1247},

year  = {2021},

date = {2021-03-00},

journal = {Cell Reports},

volume = {34},

number = {9},

publisher = {Elsevier BV},

keywords = {General Biochemistry, Genetics and Molecular Biology},

pubstate = {published},

tppubtype = {article}

}

@article{price_2021,

title = {Four families of folate-independent methionine synthases.},

author = {Morgan N Price and Adam M Deutschbauer and Adam P Arkin},

url = {http://dx.doi.org/10.1371/journal.pgen.1009342},

doi = {10.1371/journal.pgen.1009342},

year  = {2021},

date = {2021-02-03},

urldate = {2021-05-25},

journal = {PLoS Genetics},

volume = {17},

number = {2},

pages = {e1009342},

abstract = {Although most organisms synthesize methionine from homocysteine and methyl folates, some have "core" methionine synthases that lack folate-binding domains and use other methyl donors. In vitro, the characterized core synthases use methylcobalamin as a methyl donor, but in vivo, they probably rely on corrinoid (vitamin B12-binding) proteins. We identified four families of core methionine synthases that are distantly related to each other (under 30% pairwise amino acid identity). From the characterized enzymes, we identified the families MesA, which is found in methanogens, and MesB, which is found in anaerobic bacteria and archaea with the Wood-Ljungdahl pathway. A third uncharacterized family, MesC, is found in anaerobic archaea that have the Wood-Ljungdahl pathway and lack known forms of methionine synthase. We predict that most members of the MesB and MesC families accept methyl groups from the iron-sulfur corrinoid protein of that pathway. The fourth family, MesD, is found only in aerobic bacteria. Using transposon mutants and complementation, we show that MesD does not require 5-methyltetrahydrofolate or cobalamin. Instead, MesD requires an uncharacterized protein family (DUF1852) and oxygen for activity.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{Qi2021,

title = {Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression},

author = {Lei S. Qi and Matthew H. Larson and Luke A. Gilbert and Jennifer A. Doudna and Jonathan S. Weissman and Adam P. Arkin and Wendell A. Lim},

doi = {10.1016/j.cell.2021.01.019},

issn = {0092-8674},

year  = {2021},

date = {2021-02-00},

journal = {Cell},

volume = {184},

number = {3},

publisher = {Elsevier BV},

keywords = {General Biochemistry, Genetics and Molecular Biology},

pubstate = {published},

tppubtype = {article}

}

@article{trotter_2021,

title = {Large-scale Genetic Characterization of a Model Sulfate Reducing Bacterium},

author = {Valentine V Trotter and Maxim Shatsky and Morgan N Price and Thomas R Juba and Grant M Zane and Kara P De Leon and Erica L Majumder and Qin Gui and Rida Ali and Kelly M Wetmore and Jennifer V Kuehl and Adam P Arkin and Judy D Wall and Adam M Deutschbauer and John-Marc Chandonia and Gareth P Butland},

url = {http://biorxiv.org/lookup/doi/10.1101/2021.01.13.426591},

doi = {10.1101/2021.01.13.426591},

year  = {2021},

date = {2021-01-13},

urldate = {2021-05-25},

journal = {BioRxiv},

abstract = {Sulfate-reducing bacteria (SRB) are obligate anaerobes that can couple their growth to the reduction of sulfate. Despite the importance of SRB to global nutrient cycles and their damage to the petroleum industry, our molecular understanding of their physiology remains limited. To systematically provide new insights into SRB biology, we generated a randomly barcoded transposon mutant library in the model SRB Desulfovibrio vulgaris Hildenborough (DvH) and used this genome-wide resource to assay the importance of its genes under a range of metabolic and stress conditions. In addition to defining the essential gene set of DvH, we identified a conditional phenotype for 1,137 non-essential genes. Through examination of these conditional phenotypes, we were able to make a number of novel insights into our molecular understanding of DvH, including how this bacterium synthesizes vitamins. For example, we identified DVU0867 as an atypical L-aspartate decarboxylase required for the synthesis of pantothenic acid, provided the first experimental evidence that biotin synthesis in DvH occurs via a specialized acyl carrier protein and without methyl esters, and demonstrated that the uncharacterized dehydrogenase DVU0826:DVU0827 is necessary for the synthesis of pyridoxal phosphate. In addition, we used the mutant fitness data to identify genes involved in the assimilation of diverse nitrogen sources, and gained insights into the mechanism of inhibition of chlorate and molybdate. Our large-scale fitness dataset and RB-TnSeq mutant library are community-wide resources that can be used to generate further testable hypotheses into the gene functions of this environmentally and industrially important group of bacteria.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{Seaver2020,

title = {The ModelSEED Biochemistry 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 and Filipe Liu and Qizhi Zhang and James Jeffryes and José P Faria and Janaka N Edirisinghe and Michael Mundy and Nicholas Chia and Elad Noor and Moritz E Beber and Aaron A Best and Matthew DeJongh and Jeffrey A Kimbrel and Patrik D’haeseleer and Sean R McCorkle and Jay R Bolton and Erik Pearson and Shane Canon and Elisha M Wood-Charlson and Robert W Cottingham and Adam P Arkin and Christopher S Henry},

doi = {10.1093/nar/gkaa746},

issn = {1362-4962},

year  = {2021},

date = {2021-01-08},

volume = {49},

number = {D1},

pages = {D575--D588},

publisher = {Oxford University Press (OUP)},

abstract = {AbstractFor over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical ‘Rosetta Stone’ to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org/biochem and KBase.},

keywords = {Genetics},

pubstate = {published},

tppubtype = {article}

}

@article{Berliner2021,

title = {Extension of Equivalent System Mass for Human Exploration Missions on Mars},

author = {Aaron Berliner and George Makrygiorgos and Avery Hill},

doi = {doi: 10.20944/preprints202101.0363.v1},

year  = {2021},

date = {2021-01-01},

journal = {preprints.org},

publisher = {Preprints},

keywords = {cubes},

pubstate = {published},

tppubtype = {article}

}

@article{ge_2020a,

title = {Draft Genome Sequence of Bacillus sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated Sediment.},

author = {Xiaoxuan Ge and Michael P Thorgersen and Farris L Poole and Adam M Deutschbauer and John-Marc Chandonia and Pavel S Novichkov and Paul D Adams and Adam P Arkin and Terry C Hazen and Michael W W Adams},

url = {http://dx.doi.org/10.1128/MRA.01149-20},

doi = {10.1128/MRA.01149-20},

year  = {2020},

date = {2020-10-29},

urldate = {2021-05-25},

journal = {Microbiology Resource Announcements},

volume = {9},

number = {44},

abstract = {Bacillus sp. strain EB106-08-02-XG196 was isolated from a high-nitrate- and heavy metal-contaminated site at the Oak Ridge Reservation in Tennessee. We report the draft genome sequence of this strain to provide insights into the genomic basis for surviving in this unique environment. Copyright copyright 2020 Ge et al.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{ge_2020,

title = {Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation},

author = {Xiaoxuan Ge and Michael P Thorgersen and Farris L Poole and Adam M Deutschbauer and John-Marc Chandonia and Pavel S Novichkov and Sara Gushgari-Doyle and Lauren M Lui and Torben Nielsen and Romy Chakraborty and Paul D Adams and Adam P Arkin and Terry C Hazen and Michael W W Adams},

url = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.587127/full},

doi = {10.3389/fmicb.2020.587127},

issn = {1664-302X},

year  = {2020},

date = {2020-10-19},

urldate = {2021-05-25},

journal = {Frontiers in microbiology},

volume = {11},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{10.3389/fmicb.2020.587127,

title = {Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation},

author = {Xiaoxuan Ge, Michael P. Thorgersen, Farris L. Poole II, Adam M. Deutschbauer, John-Marc Chandonia, Pavel S. Novichkov, Sara Gushgari-Doyle, Lauren M. Lui, Torben Nielsen, Romy Chakraborty, Paul D. Adams, Adam P. Arkin, Terry C. Hazen and Michael W. W. Adams},

url = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.587127/full},

doi = {https://doi.org/10.3389/fmicb.2020.587127},

year  = {2020},

date = {2020-10-19},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{mutalik_2020,

title = {High-throughput mapping of the phage resistance landscape in E. coli.},

author = {Vivek K Mutalik and Benjamin A Adler and Harneet S Rishi and Denish Piya and Crystal Zhong and Britt Koskella and Elizabeth M Kutter and Richard Calendar and Pavel S Novichkov and Morgan N Price and Adam M Deutschbauer and Adam P Arkin},

url = {https://dx.plos.org/10.1371/journal.pbio.3000877},

doi = {10.1371/journal.pbio.3000877},

issn = {1545-7885},

year  = {2020},

date = {2020-10-13},

urldate = {2021-05-25},

journal = {PLoS Biology},

volume = {18},

number = {10},

pages = {e3000877},

abstract = {Bacteriophages (phages) are critical players in the dynamics and function of microbial communities and drive processes as diverse as global biogeochemical cycles and human health. Phages tend to be predators finely tuned to attack specific hosts, even down to the strain level, which in turn defend themselves using an array of mechanisms. However, to date, efforts to rapidly and comprehensively identify bacterial host factors important in phage infection and resistance have yet to be fully realized. Here, we globally map the host genetic determinants involved in resistance to 14 phylogenetically diverse double-stranded DNA phages using two model Escherichia coli strains (K-12 and BL21) with known sequence divergence to demonstrate strain-specific differences. Using genome-wide loss-of-function and gain-of-function genetic technologies, we are able to confirm previously described phage receptors as well as uncover a number of previously unknown host factors that confer resistance to one or more of these phages. We uncover differences in resistance factors that strongly align with the susceptibility of K-12 and BL21 to specific phage. We also identify both phage-specific mechanisms, such as the unexpected role of cyclic-di-GMP in host sensitivity to phage N4, and more generic defenses, such as the overproduction of colanic acid capsular polysaccharide that defends against a wide array of phages. Our results indicate that host responses to phages can occur via diverse cellular mechanisms. Our systematic and high-throughput genetic workflow to characterize phage-host interaction determinants can be extended to diverse bacteria to generate datasets that allow predictive models of how phage-mediated selection will shape bacterial phenotype and evolution. The results of this study and future efforts to map the phage resistance landscape will lead to new insights into the coevolution of hosts and their phage, which can ultimately be used to design better phage therapeutic treatments and tools for precision microbiome engineering.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}