Shotgun metagenomics is an approach increasingly applied to investigate microbial succession and functional potential in complex fermented food systems, including cocoa bean fermentation. In this study, we used Illumina-based shotgun metagenomic sequencing to characterize microbial community dynamics and metabolic potential across two post-harvest cocoa processing routes (R1 and R2) in Boyacá, Colombia, encompassing both fermentation and drying stages. Cocoa beans were sampled at defined time points during fermentation and subsequent natural drying, and non-host metagenomic reads were subjected to taxonomic classification and functional annotation to assess fungi, bacteria, and viruses. A clear multi-ecological succession was observed throughout post-harvest processing. Fungal communities shifted from a yeast-dominated profile, mainly Saccharomyces and Pichia during fermentation, to the emergence of the filamentous fungus Aspergillus during drying. Bacterial populations transitioned from diverse Enterobacteriaceae in early fermentation to a near-complete dominance of Acetobacter , which persisted throughout the drying phase. Viral communities also displayed structured successional patterns, with Lambdavirus and Punavirus prevalent in early fermentation, followed by Spbetavirus , Lafunavirus , and Pemunavirus during later stages and drying. Functional analyses revealed high metabolic potential for carbohydrate, energy, and amino acid metabolism during early fermentation, followed by a marked reduction in later stages, indicating a metabolic slowdown. Core metabolic functions were retained during drying at substantially lower activity levels. This integrated metagenomic analysis links microbial structure to functional potential and provides a scientific basis for optimizing starter cultures and post-harvest processing strategies to enhance cocoa quality and safety.

A fundamental procedure for achieving the highest quality of cocoa is the fermentation of the bean carried out by microorganisms, a process in which the flavor and aroma of chocolate are developed. The objective of this research was to develop a mathematical model of microbial sugar consumption during the cocoa fermentation process. In this way, it is possible to obtain a mathematical tool that allows the representation of sugar consumption during the fermentation process. Initially, the need to construct a mathematical model was proposed due to its economic importance for small-scale producers in the national and international industries. In addition to the lack of control over the fermentation process, the complexity in terms of the microbial communities involved yeast (Y), lactic acid bacteria (LAB), and acetic acid bacteria (AAB). The methodological approach included (i) bibliographic review; (ii) specification of the parameters of the model, state, initial values, and equations; (iii) implementation of the mathematical model with the parameters, state, and initial values defined for each investigation; and (iv) validation of the model by comparing it with the experimental data from each publication. As a result, the model presented here for microbial sugar consumption during cocoa fermentation has the ability to represent each of the selected data points with significantly high precision. Furthermore, the proposed model aims to enhance the quality, efficiency, and sustainability of cocoa production, as well as contribute to scientific research related to this process. However, it is necessarily a simplification of the various biological processes that occur during cocoa bean fermentation. IMPORTANCE: Creating a mathematical model based on ordinary differential equations for glucose and fructose consumption by Y and LAB during cocoa fermentation is vital for advancing scientific and industrial practices. Cocoa fermentation is a complex, multi-step process involving microbial communities that play a key role in developing the flavor and aroma of chocolate. A robust mathematical model helps to understand the interactions between these microorganisms and sugar dynamics, providing a clearer understanding of the fermentation process.

Los macroinvertebrados son organismos utilizados en el monitoreo de la calidad del agua. Se evaluó la calidad ecológica del río La Vega a su paso por la Universidad Pedagógica y Tecnológica de Colombia (UPTC) a través del análisis de la colonización de sustratos artificiales por macroinvertebrados acuáticos. Se seleccionaron cinco puntos de muestreo, en donde se ubicaron dos ladrillos, uno de arcilla y uno madera, para permitir la colonización por estos organismos. En cada punto se realizó la recolección de macroinvertebrados, junto con la medición de variables fisicoquímicas y ambientales. Se destacan familias como Physidae, Polycentropodidae y Chironomidae, con una colonización notable en el ladrillo de madera debido a la mayor capacidad de adherencia proporcionada. Además, se encontró una fuerte correlación entre los macroinvertebrados y variables como intensidad lumínica, oxígeno disuelto, conductividad y profundidad del río. Finalmente se evidenció una mala calidad del agua en el río según el Índice Biótico Andino (ABI), posiblemente por la influencia de actividades antrópicas.

In arid environments, microorganisms face abiotic stressors like temperature extremes, low humidity, nutrient scarcity, and intense solar radiation. This study offers a preliminary characterization of two culturable UV-tolerant bacterial isolates in the Candelaria Desert (Villa de Leyva, Boyacá, Colombia). A 500 g soil sample was collected and processed using a randomized block design with three replicates. Serial dilutions (10^–1 to 10^–3) were plated and exposed to UV light for 72 h. UV-tolerant colonies were subcultured for biochemical characterization, and genomic DNA was extracted from two isolates. 16S rRNA sequencing identified Sinomonas sp. (98.96%) and Leifsonia soli (99.68%). Morphological and biochemical traits matched molecular findings. In silico analysis suggested the presence of UV-resistance mechanisms, including nucleotide excision repair (NER). These results offer initial insight into the adaptive strategies of microorganisms in this desert environment and underscore the importance of further exploring microbial diversity in the Candelaria Desert.