Journal: bioRxiv

Article Title: Leveraging CryoEM and AI-Driven Morphological Feature Analysis for Insights on Bacterial Structures

doi: 10.64898/2025.12.06.692658

Figure Lengend Snippet:

Article Snippet: Single colonies were used to inoculate liquid cultures in either rich R2A broth (R2A Broth Premix, TEKnova, Inc.), minimal MOPS medium supplemented with 0.4% glucose (MOPS + glucose) or minimal MOPS medium supplemented with 0.4 succinate (MOPS + succinate).

Techniques:

Journal: bioRxiv

Article Title: Leveraging CryoEM and AI-Driven Morphological Feature Analysis for Insights on Bacterial Structures

doi: 10.64898/2025.12.06.692658

Figure Lengend Snippet: Quantitative analysis using the bacterial cell envelope thickness tool. ( a ) Radial plots of Pantoea sp. YR343 envelope thickness in R2A, MOPS + glucose, and MOPS + succinate media. The 0° position marks pole 1, followed counterclockwise by side 1 (90°), pole 2 (180°), and side 2 (270°). ( b ) Violin plots showing global thickness distributions across media types. ( c ) Correlation between AI- and manual-based thickness measurements (n=50).

Article Snippet: Single colonies were used to inoculate liquid cultures in either rich R2A broth (R2A Broth Premix, TEKnova, Inc.), minimal MOPS medium supplemented with 0.4% glucose (MOPS + glucose) or minimal MOPS medium supplemented with 0.4 succinate (MOPS + succinate).

Techniques:

Journal: bioRxiv

Article Title: Leveraging CryoEM and AI-Driven Morphological Feature Analysis for Insights on Bacterial Structures

doi: 10.64898/2025.12.06.692658

Figure Lengend Snippet: Quantitative analysis using the FOV tool. ( a ) Low-magnification grid-square cryoEM image of Pantoea sp. YR343 in R2A at 260 × showing bacteria (green circles/arrows) and ice crystals (yellow arrows) in vitreous ice. Scale bar: 10 µm. ( b ) Search-map montage at 3.8 k× showing higher-resolution views of bacteria and cubic/hexagonal ice. ( c ) AI-derived bacterial counts per grid square across media. ( d ) Correlation between AI- and manual-based counts across grid squares (R²=0.97).

Article Snippet: Single colonies were used to inoculate liquid cultures in either rich R2A broth (R2A Broth Premix, TEKnova, Inc.), minimal MOPS medium supplemented with 0.4% glucose (MOPS + glucose) or minimal MOPS medium supplemented with 0.4 succinate (MOPS + succinate).

Techniques: Bacteria, Derivative Assay

Journal: bioRxiv

Article Title: Ecological tristability driven by total carbon availability over resource complexity in a synthetic microbial community

doi: 10.64898/2026.02.26.708221

Figure Lengend Snippet: A | After pre-culturing each of the 16 species of the community for one growth cycle, we adjusted optical density of each culture, pooled them at equal volume and inoculated 96 resource environments, with each condition replicated 8 times. Each culture was serially transferred for 16 days, with 1% of the culture transferred every 48 h. B | At each transfer, we measured OD 600 of each community. In addition, we conducted 16S rRNA sequencing of all communities at the end-point and measured growth traits of each of the dominant species ( A. caviae, P. chlororaphis, C. koseri ) in monoculture in all carbon levels in the absence of R2A. Alt text. Two-panel schematic representing the study set-up. Panel A describes parameters of the serial passaging experiment. Panel B explains analytical procedures of the community and single-species experiments.

Article Snippet: R2A medium was prepared by dissolving R2A Broth powder (Neogen, UK) in M9 minimal medium.

Techniques: Sequencing, Passaging

Journal: bioRxiv

Article Title: Ecological tristability driven by total carbon availability over resource complexity in a synthetic microbial community

doi: 10.64898/2026.02.26.708221

Figure Lengend Snippet: A | Shannon diversity shown separately for each resource environment. The x- axis shows the total carbon level (doubling concentrations spaced evenly) and point color indicates resource complexity level. The figure contains 768 data points (8 replicates in 96 resources). B | Hump metric for total carbon gradient ( y -axis) at each level of resource complexity ( x -axis). Points show the estimated peak height (hump statistic); error bars show 95 % bootstrap confidence intervals. C | Variance partitioning of Shannon diversity using nested linear models. Bars show unique R 2 contributions of total carbon level, resource complexity (% R2A carbon contribution), and their interaction. Alt text. Three-panel figure representing diversity measures, with panel A containing data on Shannon diversity, resolved for each resource environment, panel showing a hump metric for total carbon gradient ( y -axis) at each level of resource complexity ( x -axis), and panel C showing variance partitioning of Shannon diversity using nested linear models.

Article Snippet: R2A medium was prepared by dissolving R2A Broth powder (Neogen, UK) in M9 minimal medium.

Techniques: