A diversified dataset is crucial for training a well-generalized supervised computer vision algorithm. However, in the field of microbiology, generation and annotation of a diverse dataset including field-taken images are time consuming, costly, and in some cases impossible. Image to image translation frameworks allow us to diversify the dataset by transferring images from one domain to another. However, most existing image translation techniques require a paired dataset (original image and its corresponding image in the target domain), which poses a significant challenge in collecting such datasets. In addition, the application of these image translation frameworks in microbiology is rarely discussed. In this study, we aim to develop an unpaired GAN-based (Generative Adversarial Network) image to image translation model for microbiological images, and study how it can improve generalization ability of object detection models. In this paper, we present an unpaired and unsupervised image translation model to translate laboratory-taken microbiological images to field images, building upon the recent advances in GAN networks and Perceptual loss function. We propose a novel design for
The statistical properties of the density map (DM) approach to counting microbiological objects on images are studied in detail. The DM is given by U$^2$-Net. Two statistical methods for deep neural networks are utilized: the bootstrap and the Monte Carlo (MC) dropout. The detailed analysis of the uncertainties for the DM predictions leads to a deeper understanding of the DM model's deficiencies. Based on our investigation, we propose a self-normalization module in the network. The improved network model, called \textit{Self-Normalized Density Map} (SNDM), can correct its output density map by itself to accurately predict the total number of objects in the image. The SNDM architecture outperforms the original model. Moreover, both statistical frameworks -- bootstrap and MC dropout -- have consistent statistical results for SNDM, which were not observed in the original model. The SNDM efficiency is comparable with the detector-base models, such as Faster and Cascade R-CNN detectors.
Shifting from traditional hazard-based food safety management toward risk-based management requires statistical methods for evaluating intermediate targets in food production, such as microbiological criteria (MC), in terms of their effects on human risk of illness. A fully risk-based evaluation of MC involves several uncertainties that are related to both the underlying Quantitative Microbiological Risk Assessment (QMRA) model and the production-specific sample data on the prevalence and concentrations of microbes in production batches. We used Bayesian modeling for statistical inference and evidence synthesis of two sample data sets. Thus, parameter uncertainty was represented by a joint posterior distribution, which we then used to predict the risk and to evaluate the criteria for acceptance of production batches. We also applied the Bayesian model to compare alternative criteria, accounting for the statistical uncertainty of parameters, conditional on the data sets. Comparison of the posterior mean relative risk, $E(\mathit{RR}|\mathrm{data})=E(P(\mathrm{illness}|\mathrm{criterion is met})/P(\mathrm{illness})|\mathrm{data})$, and relative posterior risk, $\mathit{RPR}=P(\mathrm
In this paper, an in-depth analysis of Escherichia coli seawater measurements during the bathing season in the city of Rijeka, Croatia was conducted. Submerged sources of groundwater were observed at several measurement locations which could be the cause for increased E. coli values. This specificity of karst terrain is usually not considered during the monitoring process, thus a novel measurement methodology is proposed. A cascade machine learning model is used to predict coastal water quality based on meteorological data, which improves the level of accuracy due to data imbalance resulting from rare occurrences of measurements with reduced water quality. Currently, the cascade model is employed as a filter method, where measurements not classified as excellent quality need to be further analyzed. However, with improvements proposed in the paper, the cascade model could be ultimately used as a standalone method.
Mathematical models are increasingly a part of microbiological research. Here, we share our perspective on how modeling advances the discipline by: (i) enforcing logical consistency, (ii) enabling quantitative prediction, (iii) extracting hidden parameters from data, and (iv) generating intuitive understanding. We map a spectrum of modeling frameworks, from whole-cell simulations to minimal logistic growth equations, and provide interactive examples for some common frameworks. Building on this overview, we outline pragmatic criteria for choosing an appropriate level of description to capture phenomena of interest. Finally, we present a case study in modeling of microbial ecosystems from our own work to illustrate how mechanistic modeling can yield generalizable intuition. This perspective aims to be an introductory roadmap for integrating mathematical modeling into experimental microbiology.
The detection and classification of bacterial colonies in images of agar-plates is important in microbiology, but is hindered by the lack of labeled datasets. Therefore, we propose Colony Grounded SAM2, a zero-shot inference pipeline to detect and segment bacterial colonies in multiple settings without any further training. By utilizing the pre-trained foundation models Grounding DINO and Segment Anything Model 2, fine-tuned to the microbiological domain, we developed a model that is robust to data changes. Results showed a mean Average Precision of 93.1\% and a $Dice@detection$ score of 0.85, showing excellent detection and segmentation capabilities on out-of-distribution datasets. The entire pipeline with model weights are shared open access to aid with annotation- and classification purposes in microbiology.
Unsafe drinking water remains a major public health concern globally, particularly in low-resource regions where routine microbiological surveillance is limited. Although Escherichia coli is the internationally recognized indicator of fecal contamination, laboratory-based testing is often inaccessible at scale. In this study, we developed and evaluated a two-stage machine-learning framework for predicting E. coli presence in decentralized household point-of-use drinking water in Chennai, India using low-cost physicochemical and contextual indicators. The dataset comprised 3,023 samples collected under the Peoples Water Data initiative; after harmonization, technical cleaning, and outlier screening, 2,207 valid samples were retained. This framework provides a scalable decision-support tool for prioritizing microbiological testing in resource-constrained environments and addresses an important gap in point-of-use contamination risk assessment. Beyond predictive modeling, the present study was conducted within an AI-supported field implementation framework that combined student-facing guidance and real-time QC to improve protocol adherence, traceability, and data reliability in decent
Biofilms in human tonsillar crypts show long term persistence with episodic dispersal that current biochemical and microbiological descriptions do not fully explain, particularly with respect to spatial localization. We introduce a biophysical framework in which tonsillar biofilm dynamics arise from the interaction between two mechanical phenomena: a Kosterlitz Thouless type defect nucleation process and a Kelvin Helmholtz type shear driven interfacial instability. Crypt geometry is modeled as a confined, heterogeneous environment that promotes mechanically persistent surface defects generated by growth induced compression. Tangential shear associated with breathing and swallowing selectively amplifies these defects, producing organized surface deformations. Numerical simulations show that only the coexistence of both mechanisms yields localized, propagating, and persistent interface structures, whereas their absence leads to diffuse, unstructured dynamics.
Ribosomal protein S30 (RS30) exhibits potent antimicrobial activity against a broad spectrum of bacteria. Despite its efficacy, the underlying action mechanism remained elusive. In this study, we unravel the fundamental mechanism by which RS30 exerts its bactericidal effects, using a combination of microbiological assays and advanced biophysical techniques. Microbiological analyses reveal that RS30 kills bacteria primarily through membrane depolarization, despite limited membrane permeabilization, indicating an unconventional mode of action involving no or partial lysis of the membrane. Importantly, RS30 demonstrates time-dependent bactericidal activity with no detectable cytotoxicity toward mammalian cells, underscoring its high selectivity. This selective action was further confirmed using biophysical experiments on model membrane systems composed of anionic (bacterial mimic) and zwitterionic (mammalian mimic) phospholipids. Our measurements suggested that RS30 preferentially binds to anionic membranes via electrostatic interactions, undergoes a conformational transition from a random coil to an α-helix upon binding, and induces vesicle aggregation. Quasielastic neutron scatterin
The Antibiotic Resistance Microbiology Dataset (ARMD) is a de-identified resource derived from electronic health records (EHR) that facilitates research in antimicrobial resistance (AMR). ARMD encompasses big data from adult patients collected from over 15 years at two academic-affiliated hospitals, focusing on microbiological cultures, antibiotic susceptibilities, and associated clinical and demographic features. Key attributes include organism identification, susceptibility patterns for 55 antibiotics, implied susceptibility rules, and de-identified patient information. This dataset supports studies on antimicrobial stewardship, causal inference, and clinical decision-making. ARMD is designed to be reusable and interoperable, promoting collaboration and innovation in combating AMR. This paper describes the dataset's acquisition, structure, and utility while detailing its de-identification process.
The Earth possesses many environmental extremes that mimic conditions on extraterrestrial worlds. The stratosphere at 30-40 km altitude closely resembles the surface of Mars in terms of pressure, temperature, and radiation levels (UV, proton, and Galactic cosmic rays). While microbial life in the troposphere is well documented, the true upper limit of Earth's biosphere remains unclear. The stratosphere offers a promising environment to explore microbial survival in such extreme conditions. Despite its significance to astrobiology, this region remains largely unexplored due to difficulties in access and avoiding contamination. To address this, we have developed SAMPLE (Stratospheric Altitude Microbiology Probe for Life Existence), a balloon-borne payload designed to collect dust samples from the stratosphere and return them in conditions suitable for lab analysis. The entire system is novel and designed in-house, with weight- and stress-optimized components. The main payload includes three pre-sterilized sampling trays and a controller that determines altitude and governs tray operation. One tray will remain closed during flight (airborne control) and another on the ground (cleanroo
The process of quantifying mold colonies on Petri dish samples is of critical importance for the assessment of indoor air quality, as high colony counts can indicate potential health risks and deficiencies in ventilation systems. Conventionally the automation of such a labor-intensive process, as well as other tasks in microbiology, relies on the manual annotation of large datasets and the subsequent extensive training of models like YoloV9. To demonstrate that exhaustive annotation is not a prerequisite anymore when tackling a new vision task, we compile a representative dataset of 5000 Petri dish images annotated with bounding boxes, simulating both a traditional data collection approach as well as few-shot and low-shot scenarios with well curated subsets with instance level masks. We benchmark three vision foundation models against traditional baselines on task specific metrics, reflecting realistic real-world requirements. Notably, MaskDINO attains near-parity with an extensively trained YoloV9 model while finetuned only on 150 images, retaining competitive performance with as few as 25 images, still being reliable on $\approx$ 70% of the samples. Our results show that data-eff
The study of microorganisms, or microbiology, has demonstrated significant development since its inception and is currently a key field of biological sciences that has a huge impact on modern society and scientific research. Over the centuries, this discipline has undergone significant changes, shaping our understanding of infectious diseases and food safety. Starting from the simplest observations of microscopic organisms such as bacteria, viruses, fungi and protozoa, and ending with modern molecular and genomic research methods. This article describes a brief historical path of microbiology development. The heuristic, morphological, physiological, immunological, and molecular genetic stages are the main periods into which the development of this science is traditionally divided, despite the lack of full-fledged and precise boundaries between them.
This study addresses from the Optimal Experimental Design perspective the use of the isothermal experimentation procedure to precisely estimate the parameters defining models used in predictive microbiology. Starting from a case study set out in the literature, and taking the Baranyi model as the primary model, and the Ratkowsky square-root model as the secondary, D- and c-optimal designs are provided for isothermal experiments, taking the temperature both as a value fixed by the experimenter and as a variable to be designed. The designs calculated show that those commonly used in practice are not efficient enough to estimate the parameters of the secondary model, leading to greater uncertainty in the predictions made via these models. Finally, an analysis is carried out to determine the effect on the efficiency of the possible reduction in the final experimental time.
Microorganisms are ubiquitous in nature, and microbial activities are closely intertwined with the entire life cycle system and human life. Developing novel technologies for the detection, characterization and manipulation of microorganisms promotes their applications in clinical, environmental and industrial areas. Over the last two decades, terahertz (THz) technology has emerged as a new optical tool for microbiology. The great potential originates from the unique advantages of THz waves including the high sensitivity to water and inter-/intra-molecular motions, the non-invasive and label-free detecting scheme, and their low photon energy. THz waves have been utilized as a stimulus to alter microbial functions, or as a sensing approach for quantitative measurement and qualitative differentiation. This review specifically focuses on recent research progress of THz technology applied in the field of microbiology, including two major parts of THz biological effects and the microbial detection applications. In the end of this paper, we summarize the research progress and discuss the challenges currently faced by THz technology in microbiology, along with potential solutions. We also
Confined motions in complex environments are ubiquitous in microbiology. These situations invariably involve the intricate coupling between fluid flow, soft boundaries, surface forces and fluctuations. In the present study, such a coupling is investigated using a novel method combining holographic microscopy and advanced statistical inference. Specifically, the Brownian motion of softmicrometric oil droplets near rigid walls is quantitatively analyzed. All the key statistical observables are reconstructed with high precision, allowing for nanoscale resolution of local mobilities and femtonewton inference of conservative or non-conservative forces. Strikingly, the analysis reveals the existence of a novel, transient, but large, soft Brownian force. The latter might be of crucial importance for microbiological and nanophysical transport, target finding or chemical reactions in crowded environments, and hence the whole life machinery.
Models of soil organic carbon (SOC) frequently overlook the effects of spatial dimensions and microbiological activities. In this paper, we focus on two reaction-diffusion chemotaxis models for SOC dynamics, both supporting chemotaxis-driven instability and exhibiting a variety of spatial patterns as stripes, spots and hexagons when the microbial chemotactic sensitivity is above a critical threshold. We use symplectic techniques to numerically approximate chemotaxis-driven spatial patterns and explore the effectiveness of the piecewice dynamic mode decomposition (pDMD) to reconstruct them. Our findings show that pDMD is effective at precisely recreating chemotaxis-driven spatial patterns, therefore broadening the range of application of the method to classes of solutions different than Turing patterns. By validating its efficacy across a wider range of models, this research lays the groundwork for applying pDMD to experimental spatiotemporal data, advancing predictions crucial for soil microbial ecology and agricultural sustainability.
Exoplanet habitability remains a challenging field due to the large distances separating Earth from other stars. Using insights from biology and astrophysics, we studied the habitability of M-dwarf exoplanets by modeling their surface temperature and flare UV and X-ray doses using the Martian atmosphere as a shielding model. Analyzing the Proxima Centauri and TRAPPIST-1 systems, our models suggest that Proxima b and TRAPPIST-1 e are likeliest to have temperatures compatible with surface liquid water, as well as tolerable radiation environments. Results of the modeling were used as a basis for microbiology experiments to assess spore survival of the melanin-rich fungus Aspergillus niger to exoplanet-like radiation (UV-C and X-rays). Results showed that A. niger spores can endure superflare events on M-dwarf planets when shielded by a Mars-like atmosphere or by a thin layer of soil or water. Melanin-deficient spores suspended in a melanin-rich solution showed higher survival rates and germination efficiency when compared to melanin-free solutions. Overall, the models developed in this work establish a framework for microbiological research in habitability studies. Finally, we showed
Variability of motility behavior in populations of microbiological agents is a ubiquitous phenomenon even in the case of genetically identical cells. Accordingly, passive objects introduced into such biological systems and driven by them will also exhibit heterogeneous motion patterns. Here, we study a biohybrid system of passive beads driven by active ameboid cells and use a likelihood approach to estimate the heterogeneity of the bead dynamics from their discretely sampled trajectories. We showcase how this approach can deal with information-scarce situations and provides natural uncertainty bounds for heterogeneity estimates. Using these advantages we particularly uncover that the heterogeneity in the system is time-dependent.
The SSPACE Astrobiology Payload (SAP) series, starting with the SAP-1 project is designed to conduct in-situ microbiology experiments in low earth orbit. This payload series aims to understand the behaviour of microbial organisms in space, particularly those critical for human health, and the corresponding effects due to microgravity and solar/galactic radiation. SAP-1 focuses on studying Bacillus clausii and Bacillus coagulans, bacteria beneficial to humans. It aims to provide a space laboratory for astrobiology experiments under microgravity conditions. The hardware developed for these experiments is indigenous and tailored to meet the unique requirements of autonomous microbiology experiments by controlling pressure, temperature, and nutrition flow to bacteria. A rotating platform, which forms the core design, is innovatively utilised to regulate the flow and mixing of nutrients with dormant bacteria. The technology demonstration models developed at SSPACE have yielded promising results, with ongoing efforts to refine, adapt for space conditions, and prepare for integration with nanosatellites or space modules. The anticipated payload will be compact, approximately 1U in size (1