The data include: SEM and TEM micrographs of four types of NHs before and after their exposure to E. coli for 6 h; Raman and TGA analyses of four types of NHs; Antibacterial effect of four different types of NHs on E. coli growth curve and growth inhibition at 6 h; The amount of ROS release from E. coli exposed to four different types of NHs over time; The FT-IR analysis of four different types of NHs with and without E. coli cells. This dataset is associated with the following publication: Baek, S., S.H. Joo, C. Su, and M. Toborek. Antibacterial effects of graphene- and carbon-nanotube-based nanohybrids on Escherichia coli: implications for treating multidrug-resistant bacteria. JOURNAL OF ENVIRONMENTAL MANAGEMENT. Elsevier Science Ltd, New York, NY, USA, 247: 214-223, (2019).

The file contains the raw data that was used to generate Figure 2 and 4 from the manuscript Surwade, P., Luxton, T., Clar, J., Xin, F. and Shah, V.H. (2020) Impact of the changes in bacterial outer membrane structure on the anti-bacterial activity of zinc oxide nanoparticles. J. Nanopart. Res. 22, 8. This dataset is associated with the following publication: Surwade, P., T. Luxton, J. Clar, F. Xin, and V. Shah. Impact of the changes in bacterial outer membrane structure on the anti-bacterial activity of zinc oxide nanoparticles. Journal of Nanoparticle Research. Springer SBM, New York, NY, USA, 22: 43, (2020).

Lanthanide binding tags (LBTs) have been engineered onto native Escherichia coli (E. coli) bacterial surfaces to enhance extraction and recovery of rare earth elements (REEs). Three strains of E. coli were studied: (1) the native E. coli surface, (2) a mutant E. coli surface with hindered, non-binding lanthanide binding tags, and (3) an LBT E. coli surface with fully functioning lanthanide binding tags. A three discrete site, constant capacitance surface complexation modeling approach was taken in studying these strains with an ultimate goal of comparing site type affinities to the model rare earth, Terbium. Our results show a possible increase in native carboxyl functional groups when the LBTs are overexpressed on the cell surface. LBTs are confirmed to have a higher stability constant with Terbium than that of the native functional groups. Incorporation of LBTs into the E. coli cell wall poses two major benefits: (1) the presence of a high-affinity, low-capacity LBT site for selective Terbium binding at low metal loading regions, and (2) a lower-affinity carboxyl site that increases the sorption capacity of the native bacterial surface during sorption at higher metal loading regions.

,Using the SHIME (an in vitro simulator of the human gut microbiome) we studied changes in the gut metabolome that occurred in response to the administration of the Laticaseibacillus rhamnosus strain GG (LGG). Using fecal inoculum from three healthy human donors, reactors were established representing three colonic regions and both the luminal and mucosal microbiome in those regions. Samples were collected before, during, and after inoculation of the reactors with LGG.,This dataset includes untargeted metabolomics data. Shallow shotgun metagenomic sequencing data can be found in the NCBI Sequence Read Archive associated with BioProject PRJNA893635 : https://www.ncbi.nlm.nih.gov/bioproject/PRJNA893635.,Resources in this dataset:,

Background Experimental populations of Escherichia coli have evolved for 20,000 generations in a uniform environment. Their rate of improvement, as measured in competitions with the ancestor in that environment, has declined substantially over this period. This deceleration has been interpreted as the bacteria approaching a peak or plateau in a fitness landscape. Alternatively, this deceleration might be caused by non-transitive competitive interactions, in particular such that the measured advantage of later genotypes relative to earlier ones would be greater if they competed directly. Results To distinguish these two hypotheses, we performed a large set of competitions using one of the evolved lines. Twenty-one samples obtained at 1,000-generation intervals each competed against five genetically marked clones isolated at 5,000-generation intervals, with three-fold replication. The pattern of relative fitness values for these 315 pairwise competitions was compared with expectations under transitive and non-transitive models, the latter structured to produce the observed deceleration in fitness relative to the ancestor. In general, the relative fitness of later and earlier generations measured by direct competition agrees well with the fitness inferred from separately competing each against the ancestor. These data thus support the transitive model. Conclusion Non-transitive competitive interactions were not a major feature of evolution in this population. Instead, the pronounced deceleration in its rate of fitness improvement indicates that the population early on incorporated most of those mutations that provided the greatest gains, and subsequently relied on beneficial mutations that were fewer in number, smaller in effect, or both.

This repository includes the raw data, analysis code, and results of a systematic analysis of natural transformation (i.e., horizontal gene transfer; HGT) of bacteria in a naturally occurring microbiome (human stool) following exposure to free extracellular DNA (eDNA) that coded for antibiotic resistance. A full description of this effort is available in the associated publication.

This study demonstrates simulated microgravity effects on E. coli K 12 MG1655 when grown on LB medium supplemented with glycerol. The results imply that E. coli readily reprograms itself to combat the multiple stresses imposed due to microgravity. Under these conditions it survives by upregulating oxidative stress protecting genes and simultaneously down regulating the membrane transporters and synthases to maintain cell homeostasis. In this study a clinostat that mimics microgravity conditions was used to investigate the effects of microgravity on E. coli grown in LB medium supplemented with glycerol to monitor the effects on growth and global gene expression using Affymetrix DNA microarrays.

,The data presents the antimicrobial susceptibility testing results in three separate files: 1) third generation cephalosporin resistant E. coli isolates obtained on cefotaxime supplemented media; 2) extended spectrum beta-lactamase (ESBL) producing E. coli, and 3) ESBL-producing Klebsiella, Enterobacter and Citrobacter species obtained on chromogenic media. The data was generated as part of a research project that evaluated the impact of tylosin supplementation of feedlot cattle on the dynamics of antimicrobial resistant fecal bacteria. The study was a longitudinal design with periodic sampling of fecal samples from individual animals over the entire feeding period. Two publications from the project, one describing the study design in detail, and the other specifically reporting on these data, are linked to the database.,Resources in this dataset:,

Selected bacterial, and antibiotic resistance genes sul and INTI1 concentrations by qPCR assays, and ASV tables of bacterial communities growing in biofilms incubated in river -and wastewater treatment plant effluent amended -river water. This dataset is associated with the following publication: Eytcheson, S., S. Brown, H. Wu, C. Nietch, P. Weaver, J. Darling, E. Pilgrim, T. Purucker, and M. Molina. Assessment of Emerging Pathogens and Antibiotic Resistance Genes in the Biofilm of Microplastics Incubated Under a Wastewater Discharge Simulation. Environmental Microbiology. Wiley-Blackwell Publishing, Hoboken, NJ, USA, 27(5): e70103, (2025).

,Using the SHIME (an in vitro simulator of the human gut microbiome) we tracked the fate of the probiotic Lacticaseibacillus rhamnosus GG (LGG) over time and across colonic regions. Using fecal inoculum from three healthy human donors, reactors were established representing three colonic regions and both the luminal and mucosal microbiome in those regions. Community composition before, during, and after inoculation of the reactors with LGG as well as short chain fatty acid concentrations representing microbiome metabolic outputs. This dataset includes short-chain fatty acid concentrations and qPCR-based cell concentrations. Raw 16S rRNA amplicon sequencing of the V1-V2 regions can be found in the NCBI Sequence Read Archive associated with BioProject PRJNA893635: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA893635.,Resources in this dataset:,