Topic 158

microbial coli nutrient microbes communities metabolic escherichia growth bacteria microbiology community bacterial systems metabolism microbiome gut nutrients environments conditions carbon under composition nutritional glucose health interactions antibiotic environment strain changes how metabolite microbiota predict competition understanding fitness commensal such competitive system scale colonization host perturbations mathematical response can microbe flux some strategies dietary even stress strains synthetic experimental understand physiology laboratory media utilization adapt availability complex resources model pathways bacterium feeding consortia source dependent environmental iterative dynamics resistance determine acid competitors acids condition shifts constraints physiological our rate especially fed it mg1655 starvation dynamic survival coculture cellular microorganisms modeling amino

75 items. Top items listed below.

Predicting global dynamics of spatial microbial communities from local interaction rules 158 99 38 17 5

Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence 158 99 38 29 17 5 4

Resident microbial communities inhibit growth and antibiotic resistance evolution of Escherichia coli in human gut microbiome samples 158 143 29 12 5

Raman spectroscopy-based measurements of single-cell phenotypic diversity in microbial communities 158 38 18 17 5

Microbial community composition interacts with local abiotic conditions to drive colonization resistance in human gut microbiome samples 158 29 17 12 5

Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments 158 112 4

Predicting trajectories and mechanisms of antibiotic resistance evolution 158 21 5

Glucose promotes resistance of human commensal Escherichia coli against contact-killing by pandemic Vibrio cholerae 158 79 12 3

Transcriptome signature in E. coli under a prolonged starvation environment 158 79 12 9 5

Metabolite sequestration enables rapid recovery from fatty acid depletion in Escherichia coli 158 67 38 12

Proteome constraints reveal targets for improving microbial fitness in nutrient-rich environments 158 67 38 12

Understanding the host-microbe interactions using metabolic modeling 158 101 29 12 4

Exposure to lysed bacteria can promote or inhibit growth of neighbouring live bacteria depending on local abiotic conditions 158 79 12 5

Phage cocktail strategies for the suppression of a pathogen in a cross-feeding coculture 158 143 12 5

Bacterial evolution in high osmolarity environments 158 21 5

Escherichia coli has a Unique Transcriptional Program in Long-Term Stationary Phase 158 79 21 5

Genome-wide analysis of Escherichia coli fitness determinants in a cross-feeding mutualism with Rhodopseudomonas palustris 158 29 12 5

The adaptive response to long term nitrogen starvation in Escherichia coli requires the breakdown of allantoin 158 79 67 12

Metabolic multi-stability and hysteresis in a model aerobe-anaerobe microbiome community 158 99 29 17 5

Effects of substrate availability on growth and metabolism in soil microbes: Insights from theoretical modeling of studies of the Warburg effect and substrate-induced respiration 158 67 29 17 12

Iron Supplementation Eliminates Antagonistic Interactions Between Root Associated Bacteria 158 29 12 5

Nutrient-dependent trade-offs between ribosomes and division protein synthesis control bacterial cell size and growth 158 127 38 12 8

Colonization with heterologous bacteria reprograms a Caenorhabditis elegans nutritional phenotype 158 29 12 5

Polarization of microbial communities between competitive and cooperative metabolism 158 29 17 5

Crucial role of ppGpp in the resilience of Escherichia coli to growth disruption 158 79 67 12

Environmental and physiological factors affecting high-throughput measurements of bacterial growth 158 67 12

Cell-to-cell heterogeneity in Escherichia coli stress response originates from pulsatile expression and growth 158 127 38 18

Computational study on ratio-sensing in yeast galactose utilization pathway 158 38

Competition sensing alters antibiotic production in Streptomyces 158 79 12 5

Gut bacteria mediate nutrient availability in Drosophila diets 158 143 29 5

Decomposition of transcriptional responses provides insights into differential antibiotic susceptibility 158 52 12

Exometabolite dynamics over stationary phase reveal strain-specific responses to nutrient limitation 158 67 12 5

Optogenetic control of gut bacterial metabolism to promote longevity 158 90 67 12

Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism 158 67 38 18

Elucidation of regulatory modes for five two-component systems in Escherichia coli reveals novel relationships 158 79 9

Protein allocation and enzymatic constraints explain Escherichia coli wildtype and mutant phenotypes 158 67 38

Carbohydrate complexity structures stable diversity in gut-derived microbial consortia under high dilution pressure 158 29 12 5

Human-associated microbiota suppress invadingbacteria even under disruption by antibiotics 158 29 12 5

Cell growth model with stochastic gene expression helps understand the growth advantage of metabolic exchange and auxotrophy 158 38 5

Pathway-based and phylogenetically adjusted quantification of metabolic interaction between microbial species 143 29 4

Mechanisms underlying proximity between oral commensal bacteria 158 29 12 5

A distinct growth physiology enhances bacterial growth under rapid nutrient fluctuations 158 79 12 5

Metabolic profiling reveals nutrient preferences during carbon utilization in Bacillus species 158 114 79 12 5

Investigation of microbial community interactions between lake Washington methanotrophs using genome-scale metabolic modeling 158 67 29 17 5

Donor-recipient interactions drive dynamics of horizontal gene transfer via natural competence 158 99 29 12

Continuous variable response, kinetic gating and connectivity that determine topology of insulin signaling are perturbed in hyper-insulinemic states 158 38

Soil microbial diversity impacts plant microbiomes more than herbivory 17 5

Single strain control of microbial consortia 158 99 29 18 12 5

Predicting experimental designs leading to rewiring of transcription program and evolution of anticipatory regulation in E. coli. 158 79 21 12 5

A cross-species interaction with a symbiotic commensal enables cell-density-dependent growth and in vivo virulence of an oral pathogen 158 114 29 12

Limitation by a shared mutualist promotes coexistence of multiple competing partners 99 17 5

Microbial competition reduces interaction distances to the low {micro}m-range 158 127 38 18 5

Diagnosing and predicting mixed culture fermentations with unicellular and guild-based metabolic models 158 29 12

Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria 143 29 5

Phenotypic changes of bacteria through opportunity and global methylation leads to antibiotic resistance 158 79 52 12

Continuous variable response, kinetic gating and connectivity that govern IS topology are perturbed in hyperinsulinemia 158 38

Constrained proteome allocation affects coexistence inmodels of competitive microbial communities 99 38 17 5

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth 158 67 38

Design of synthetic human gut microbiome assembly and function 158 29 4

Bacterial processing of glucose modulates C. elegans lifespan and healthspan 158 90 79 12 10 3

Targeted manipulation of abundant and rare taxa in the Daphnia magna microbiota with antibiotics impacts host fitness differentially 99 29 17 5

Non-lethal exposure to H2O2 boosts bacterial survival and evolvability against oxidative stress 128 79 21 12 5

Overlaid positive and negative feedback loops shape dynamical properties of PhoPQ two-component system 38

Clostridioides difficile exploits toxin-mediated inflammation to alter the host nutritional landscape and exclude competitors from the gut microbiota 158 114 79 12 10 3

An enhanced characterization of the human skin microbiome: a new biodiversity of microbial interactions 29 12 5

Microbial species coexistence depends on the host environment 99 29 17 5

Dynamic Regulation of Growth and Physiology of Microbes under Complex Changing Conditions 158 18

The assembly of Hfq into foci-like structures in response to long-term nitrogen starvation in Escherichia coli 79 12 8 3

High-throughput mapping of the phage resistance landscape in E. coli 143 12 5

Bacterial diets differentially alter lifespan and healthspan trajectories in C. elegans 158 29 12 5

Novel two-stage processes for optimal chemical production in microbes 7

Integrated metabolic modeling, culturing and transcriptomics explains enhanced virulence of V. cholerae during co-infection with ETEC 114 12

Strain background, species frequency and environmental conditions are important in determining population dynamics and species co-existence between Pseudomonas aeruginosa and Staphylococcus aureus 99 5

Ecology-guided prediction of cross-feeding interactions in the human gut microbiome 105 26 4

Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria 158 67 12 5

Exploring the niche concept in a simple metaorganism 7 5

Impact of Rap-Phr system abundance on adaptation of Bacillus subtilis 79 12 5

Escherichia coli metabolism under short-term repetitive substrate dynamics: Adaptation and trade-offs 67 12 5

Adaptation is influenced by the complexity of environmental change during evolution in a dynamic environment 21 5

Investigating the dynamics of microbial consortia in spatially structured environments 158 99 38 29 17

Aerobic metabolism in Vibrio cholerae is required for population expansion during infection 114 79 67 12

Systematic variation in the temperature dependence of bacterial carbon use efficiency 86 17 5

From iron to antibiotics: Identification of conserved bacterial-fungal interactions across diverse partners 143 29 12 5

Antibiotics shift the temperature response curve of Escherichia coli growth 86 17 5

Pseudomonas aeruginosa reverse diauxie is an optimized, resource utilization strategy 158 67 12 5

Host immunity alters successional ecology and stability of the microbiome in a C. elegans model 90 29 17 5

Cooperation increases robustness to ecological disturbance in microbial cross-feeding networks 99 21 5

Gene expression noise can promote the fixation of beneficial mutations in fluctuating environments 21 5

Social environment drives sex and age-specific variation in Drosophila melanogaster microbiome composition and predicted function. 56 29 5

Phenotypic delay in the evolution of bacterial antibiotic resistance: mechanistic models and their implications 185 21 5

FITNESS BENEFITS TO BACTERIA OF CARRYING PROPHAGES AND PROPHAGE-ENCODED ANTIBIOTIC-RESISTANCE GENES PEAK IN DIFFERENT ENVIRONMENTS 143 52 21 12 5

Trait-based approach to bacterial growth efficiency 29 5

Commensal bacteria differentially shape the nutritional requirements of Drosophila during juvenile growth 158 29 12

Collateral fitness effects of mutations 21 5 3

Strain-dependent inhibition of Clostridioides difficile by commensal Clostridia encoding the bile acid inducible (bai) operon 158 12 10

Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments 29 17 5

Nutrient supplementation experiments on saltern microbial communities support utilization of DNA as a source of phosphorus 29 12 5

Analysis of Metabolic Network Disruption in Engineered Microbial Hosts due to Enzyme Promiscuity 67 38 33 12

Identification of simplified microbial communities that inhibit Clostridioides difficile infection through dilution/extinction 101 29 12 10

When the microbiome defines the host phenotype: selection on vertical transmission in varying environments 132 21 5