Daniel Segrè
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View article: Exploring chemotaxis in spatio-temporal stoichiometric models of metabolism: <i>Pseudomonas simiae</i> as a case study
Exploring chemotaxis in spatio-temporal stoichiometric models of metabolism: <i>Pseudomonas simiae</i> as a case study Open
Summary/Abstract Chemotaxis is the movement of cells or organisms in the direction of an increasing or decreasing gradient of a chemical, i.e. a chemoattractant or chemorepellent, respectively. In bacteria, this movement is typically manif…
View article: Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity
Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity Open
SUMMARY Despite calls for the development of consensus methods, most analyses of shotgun metagenomics data for microbiome studies use a single taxonomic classifier. In this study, we compare inferences from two broadly used classifiers, Me…
View article: MACAW: a method for semi-automatic detection of errors in genome-scale metabolic models
MACAW: a method for semi-automatic detection of errors in genome-scale metabolic models Open
Genome-scale metabolic models (GSMMs) are used to predict metabolic fluxes, with applications ranging from identifying novel drug targets to engineering microbial metabolism. Erroneous or missing reactions, scattered throughout densely int…
View article: Improved detection of fungi and uncultivated microorganisms in soil metagenomes using a comprehensive genome database
Improved detection of fungi and uncultivated microorganisms in soil metagenomes using a comprehensive genome database Open
Soils harbor diverse microbial communities crucial for ecosystem functioning, but poor genomic representation of many uncultured soil microorganisms limits the utility of existing databases to address some of the most pressing questions in…
View article: Wasp intestinal cues drive yeast toward outbreeding strategies
Wasp intestinal cues drive yeast toward outbreeding strategies Open
Saccharomyces cerevisiae relies on social wasps (e.g. Vespa crabro, Polistes spp.) for dispersal and genetic mixing. Unlike most natural environments, wasp intestines provide conditions that support yeast survival, sporulation, spore germi…
View article: Dynamic metabolic modeling of ATP allocation during viral infection
Dynamic metabolic modeling of ATP allocation during viral infection Open
Summary Viral pathogens, like SARS-CoV-2, hijack the host’s macromolecular production machinery, imposing an energetic burden that is distributed across cellular metabolism. To explore the dynamic metabolic tension between the host’s survi…
View article: Reduced methane emissions in transgenic rice genotypes are associated with altered rhizosphere microbial hydrogen cycling
Reduced methane emissions in transgenic rice genotypes are associated with altered rhizosphere microbial hydrogen cycling Open
Rice paddies contribute substantially to atmospheric methane (CH 4 ) and these emissions are expected to increase as the need to feed the human population grows. Here, we show that two independent rice genotypes overexpressing genes for PL…
View article: Metabolic Flux Modeling in Marine Ecosystems
Metabolic Flux Modeling in Marine Ecosystems Open
Ocean metabolism constitutes a complex, multiscale ensemble of biochemical reaction networks harbored within and between the boundaries of a myriad of organisms. Gaining a quantitative understanding of how these networks operate requires m…
View article: Semi-Automatic Detection of Errors in Genome-Scale Metabolic Models
Semi-Automatic Detection of Errors in Genome-Scale Metabolic Models Open
Background Genome-Scale Metabolic Models (GSMMs) are used for numerous tasks requiring computational estimates of metabolic fluxes, from predicting novel drug targets to engineering microbes to produce valuable compounds. A key limiting st…
View article: Diversity in the utilization of different molecular classes of dissolved organic matter by heterotrophic marine bacteria
Diversity in the utilization of different molecular classes of dissolved organic matter by heterotrophic marine bacteria Open
Heterotrophic marine bacteria utilize and recycle dissolved organic matter (DOM), impacting biogeochemical cycles. It is currently unclear to what extent distinct DOM components can be used by different heterotrophic clades. Here, we ask h…
View article: Project Assessment for Biological and Environmental Research: Report from the BER Advisory Committee
Project Assessment for Biological and Environmental Research: Report from the BER Advisory Committee Open
The construction, operation, and stewardship of large-scale scientific user facilities and cutting edge capabilities have been integral to the mission of the U.S. Department of Energy (DOE) Office of Science from its earliest days. To help…
View article: Multi-Attribute Subset Selection enables prediction of representative phenotypes across microbial populations
Multi-Attribute Subset Selection enables prediction of representative phenotypes across microbial populations Open
The interpretation of complex biological datasets requires the identification of representative variables that describe the data without critical information loss. This is particularly important in the analysis of large phenotypic datasets…
View article: A Unified Data Infrastructure for Biological and Environmental Research: A Report from the BER Advisory Committee
A Unified Data Infrastructure for Biological and Environmental Research: A Report from the BER Advisory Committee Open
The Biological and Environmental Research (BER) program within the U.S. Department of Energy (DOE) Office of Science supports large-scale data generation efforts across its two divisions: Biological Systems Science and Earth and Environmen…
View article: Nasopharyngeal Dysbiosis Precedes the Development of Lower Respiratory Tract Infections in Young Infants, a Longitudinal Infant Cohort Study
Nasopharyngeal Dysbiosis Precedes the Development of Lower Respiratory Tract Infections in Young Infants, a Longitudinal Infant Cohort Study Open
Background Infants suffering from lower respiratory tract infections (LRTIs) have distinct nasopharyngeal (NP) microbiome profiles that correlate with severity of disease. Whether these profiles precede the infection or are a consequence o…
View article: Biophysical metabolic modeling of complex bacterial colony morphology
Biophysical metabolic modeling of complex bacterial colony morphology Open
Summary Microbial colony growth is shaped by the physics of biomass propagation and nutrient diffusion, and by the metabolic reactions that organisms activate as a function of the surrounding environment. While microbial colonies have been…
View article: Diversity in the Utilization of Different Molecular Classes of Dissolved Organic Matter by Heterotrophic Marine Bacteria
Diversity in the Utilization of Different Molecular Classes of Dissolved Organic Matter by Heterotrophic Marine Bacteria Open
Heterotrophic marine bacteria utilize and recycle dissolved organic matter (DOM), impacting biogeochemical cycles. It is currently unclear to what extent distinct DOM components can be utilized by different heterotrophic clades. Here, we a…
View article: Metabolic complexity drives divergence in microbial communities
Metabolic complexity drives divergence in microbial communities Open
Microbial communities are shaped by the metabolites available in their environment, but the principles that govern whether different communities will converge or diverge in any given condition remain unknown, posing fundamental questions a…
View article: Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation
Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation Open
Microbes commonly organize into communities consisting of hundreds of species involved in complex interactions with each other. 16S ribosomal RNA (16S rRNA) amplicon profiling provides snapshots that reveal the phylogenies and abundance pr…
View article: Construction and Modeling of a Coculture Microplate for Real-Time Measurement of Microbial Interactions
Construction and Modeling of a Coculture Microplate for Real-Time Measurement of Microbial Interactions Open
Microbial communities participate in many essential processes from biogeochemical cycles to the maintenance of human health. The structure and functions of these communities are dynamic properties that depend on poorly understood interacti…
View article: Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability
Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability Open
Filamentous fungi drive carbon and nutrient cycling across our global ecosystems, through its interactions with growing and decaying flora and their constituent microbiomes. The remarkable metabolic diversity, secretion ability, and fiber-…
View article: Environmental microbiome engineering for the mitigation of climate change
Environmental microbiome engineering for the mitigation of climate change Open
Environmental microbiome engineering is emerging as a potential avenue for climate change mitigation. In this process, microbial inocula are introduced to natural microbial communities to tune activities that regulate the long‐term stabili…
View article: Inferring microbial co-occurrence network from amplicon data: a systematic evaluation
Inferring microbial co-occurrence network from amplicon data: a systematic evaluation Open
Supporting data for the manuscript "Inferring microbial co-occurrence network from amplicon data: a systematic evaluation".
View article: Inferring microbial co-occurrence network from amplicon data: a systematic evaluation
Inferring microbial co-occurrence network from amplicon data: a systematic evaluation Open
Supporting data for the manuscript "Inferring microbial co-occurrence network from amplicon data: a systematic evaluation".
View article: Inferring microbial co-occurrence network from amplicon data: a systematic evaluation
Inferring microbial co-occurrence network from amplicon data: a systematic evaluation Open
Supporting data for the manuscript "Inferring microbial co-occurrence network from amplicon data: a systematic evaluation".
View article: Toward FAIR Representations of Microbial Interactions
Toward FAIR Representations of Microbial Interactions Open
Despite an ever-growing number of data sets that catalog and characterize interactions between microbes in different environments and conditions, many of these data are neither easily accessible nor intercompatible. These limitations prese…
View article: A resource for the comparison and integration of heterogeneous microbiome networks
A resource for the comparison and integration of heterogeneous microbiome networks Open
Naturally occurring microbial communities often comprise thousands of taxa involved in complex networks of interactions. These interactions can be mediated by several mechanisms, including the competition for resources, the exchange of sig…
View article: Growth instabilities shape morphology and genetic diversity of microbial colonies
Growth instabilities shape morphology and genetic diversity of microbial colonies Open
Cellular populations assume an incredible variety of shapes ranging from circular molds to irregular tumors. While we understand many of the mechanisms responsible for these spatial patterns, little is known about how the shape of a popula…
View article: Metabolic Phenotyping of Marine Heterotrophs on Refactored Media Reveals Diverse Metabolic Adaptations and Lifestyle Strategies
Metabolic Phenotyping of Marine Heterotrophs on Refactored Media Reveals Diverse Metabolic Adaptations and Lifestyle Strategies Open
Half of the Earth’s annual primary production is carried out by phytoplankton in the surface ocean. However, this metabolic activity is heavily impacted by heterotrophic bacteria, which dominate the transformation of organic matter release…
View article: Prediction of representative phenotypes using Multi-Attribute Subset Selection
Prediction of representative phenotypes using Multi-Attribute Subset Selection Open
The interpretation of complex biological datasets requires the identification of representative variables that describe the data without critical information loss. This is particularly important in the analysis of large phenotypic datasets…