Species-specific surface dwell times and accumulation of microbes investigated by holographic microscopy
Bibliographic record
Abstract
Microscopic swimmers, such as bacteria and archaea, are paradigmatic examples of active matter systems. The study of these systems has given rise to novel concepts such as rectification of bacterial swimmers, in which microstructures can passively separate swimmers from non-swimming, inert particles. Many bacteria and archaea swim using rotary molecular motors to drive helical propellers called flagella or archaella. The arrangement of these filaments around the cell body varies between species, yielding a range of swimming patterns. Solid boundaries might affect these swimming patterns in different ways, limiting the generality of artificial rectification devices. We performed three-dimensional cell tracking on four species of bacteria with different flagellation patterns ( Escherichia coli , Salmonella enterica , Campylobacter jejuni and Shewanella putrefaciens ), and compared these to two environmental isolates of archaea, previously identified with the genera Haloarcula and Haloferax . Despite differences in the cells’ flagellation patterns, swimming speeds and swimming patterns, we find that the shapes of cell tracks as individuals leave surfaces are surprisingly consistent. This information reduces the potential parameter space for the design of artificial rectification devices, and increases the possibility of constructing a multi-species bacterial rectifier. This article is part of the theme issue ‘Biological fluid dynamics: emerging directions’.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".