Browsing by Autor "Alejandro Reyes"

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A Latin American perspective on microbiome research
(Nature Portfolio, 2025) Alejandro Reyes; Claudio Durán; Silvia Rodríguez-Otálora; Deborah Delgado Pugley; Gregorio Iraola; Maria Gloria Domínguez-Bello; Trevor D. Lawley; Pablo Tsukayama
Changing a Generation’s Way of Thinking: Teaching Computational Thinking Through Programming
(SAGE Publishing, 2017) Francisco Buitrago Flórez; Rubby Casallas; Marcela Hernández; Alejandro Reyes; Silvia Restrepo; Giovanna Danies
Computational thinking (CT) uses concepts that are essential to computing and information science to solve problems, design and evaluate complex systems, and understand human reasoning and behavior. This way of thinking has important implications in computer sciences as well as in almost every other field. Therefore, we contend that CT should be taught in elementary schools and included in every university’s educational curriculum. Several studies that measure the impact of teaching programming, analytical thinking, and CT have been conducted. In this review, we analyze and discuss findings from these studies and highlight the importance of learning programming with a focus on the development of CT skills at a young age. We also describe the tools that are available to improve the teaching of CT and provide a state-of-the-art overview of how programming is being taught at schools and universities in Colombia and around the world.
Entrevista de Polaf Safi a Georg Iggers en Kilavuz 52 Traducción Red Distrital de Estudiantes de Historia
(2016) Alejandro Reyes; César Duque; Liliana Calderón; Luisa Guevara; Andrés Lindermann; Cristian Parra; Miguel Ángel Niño; Jenny Julio; Daniela Prada
Harmony in diversity: exploring the rich microbiomes of South American wildlife
(2024) Alejandro Reyes
Harmony in diversity: exploring the rich microbiomes of South American wildlife
(2024) Alejandro Reyes
Metagenomic, metabolomic and sensorial characteristics of fermented <i>Coffea arabica</i> L. var. Castillo beans inoculated with microbial starter cultures
(2025) Maria Antonia Madrid-Restrepo; Ana M. León-Inga; Aida Esther Penuela; Mónica P. Cala; Alejandro Reyes
ABSTRACT Coffee is one of the most important and widely consumed drinks around the world, and fermentation plays a pivotal role in shaping its quality. This research explores the impact of co-fermentation with “starter cultures” on the sensory and metabolic profiles, as well as in the microbial communities involved in coffee processing. Freshly harvested Arabica coffee beans were subjected to two wet-fermentation processes, where one was inoculated with a microbial starter culture and the other, spontaneous fermentation was allowed to occur. Quantitative descriptive analysis revealed that the inoculated coffee outperformed the spontaneous fermentation in all sensory attributes, boasting a higher sweetness, reduced acidity and bitterness, and presence of consumer-preferred notes. Untargeted metabolomic analysis identified over a hundred differential metabolites distinguishing both fermentation processes in green and roasted coffee beans. Inoculated coffee displayed elevated levels of compounds such as sucrose, mannitol, methyl phenylacetate, and organic acids like malic, citric, and quinic acid, compounds likely associated with a better sensory perception. The inoculated process featured abundant lactic acid bacteria and Kazachstania yeasts, which are linked to desirable metabolites like lactic, acetic, isobutyric, and hexanoic acids. Our results strongly suggest that the use of starter cultures can enhance coffee beverage quality as determined by standardized cupping and reflected by changes in the metabolic profile and microbial community structures. Future studies should focus on microbial identification and the association between species and resulting metabolic compounds, where specific bacterial and fungal groups could be isolated to be used as commercially available starter cultures for coffee fermentation. IMPORTANCE Our study demonstrates that inoculating coffee fermentation alters the sensory qualities of coffee and affects the dynamics of bacterial and fungal communities during this process. We identified specific changes in microbial diversity and associated metabolite profiles resulting from inoculation. Notably, we found that inoculation influences the metabolite composition of coffee beans and identified key compounds, such as aminophenol and phenol, which are likely linked to phenolic defects. This suggests that inoculation could serve as a tool to control cup defects by modifying the fermentation microbiota. Our findings advance the understanding of coffee fermentation and open opportunities for developing techniques to produce coffee with unique and desirable qualities.
Metagenomic, Metabolomic and Sensorial Characteristics of Fermented Coffea Arabica L. VAR. Castillo Beans Inoculated with Microbial Starter Cultures
(RELX Group (Netherlands), 2024) Maria Antonia Madrid-Restrepo; Ana M. León-Inga; Aída Esther Peñuela-Martínez; Mónica P. Cala; Alejandro Reyes
Metagenomic, metabolomic, and sensorial characteristics of fermented <i>Coffea arabica</i> L. var. Castillo beans inoculated with microbial starter cultures
(American Society for Microbiology, 2025) Maria Antonia Madrid-Restrepo; Ana M. León-Inga; Aída Esther Peñuela-Martínez; Mónica P. Cala; Alejandro Reyes
Our study demonstrates that inoculating coffee fermentation alters the sensory qualities of coffee and reshapes the dynamics of bacterial and fungal communities during this process. We identified distinct changes in microbial diversity and metabolite composition associated with inoculation, which correlated with improved sensory attributes. In addition, we detected aminophenol and phenol at higher levels in spontaneously fermented coffees, compounds that are likely responsible for phenolic defects. To our knowledge, this is the first report directly linking these compounds to defective flavor notes in coffee. Together, these findings show that inoculation not only enhances desirable flavor profiles but may also serve as a strategy to reduce the risk of cup defects by modulating the fermentation microbiota. Our work advances the understanding of community-level microbial processes in coffee fermentation and opens opportunities for developing techniques to produce coffee with unique, high-quality, and reproducible sensory characteristics.
Salmonella Phage cocktail, its effects and benefits on the gut of chickens in a commercial farm.
(2020) Viviana Clavijo; Laura Tatiana Morales; Martha Josefina Vives Flores; Alejandro Reyes
<title>Abstract</title> BackgroundThe microbiota of broiler chicken gut affects positively or negatively the health, metabolism and immunity of chickens thus it has a significant impact on the animal productivity. Phages, host-specific parasites of bacterial cells, are a promising antimicrobial alternative that selectively target pathogens without disturbing the microbiota. The aim of the study is further characterizing the behaviour of phages and its effect on the commensal microbial community.MethodsWe used <italic>16S rRNA</italic> gene amplicon sequencing to evaluate the effect of SalmoFree® (a phage cocktail against <italic>Salmonella</italic>) on the microbiota of the cecum of broilers reared in a commercial farming system. Two field trials were carried out including 2 control and 2 experimental houses. Phages were incorporated in the broilers’ drinking water using three doses at the grower stage. The core microbiome, differentially abundant taxa between treatments as well as taxa associated with age were identified using Qiime2 and the R-Project for statistics.ResultsAnalyses of similarities among communities over time allowed us to identify two stages of microbiota development at the last stage of the production cycle. The core microbiome identified some key species in the adaptation of the microbiota at the last stage of the cycle. Among these there are important degraders of complex polysaccharides and producers of short chain fatty acids such as <italic>Eisenbergiella</italic> and <italic>Lachnoclostridium</italic>. Additionally, the phage cocktail did not affect the normal development of the microbiota structure while its application contributes to reduce the presence of pathogenic Enterobacteria including <italic>Salmonella</italic>. The addition of the phage cocktail led to a significant reduction in the abundance of <italic>Campylobacter</italic> and <italic>Helicobacter</italic> and increase in <italic>Butyricimonas</italic> and <italic>Rikenellaceae</italic> abundance which are common inhabitants of the chicken gut with known negative and positive effects in the health, respectively.ConclusionsOur results suggest that phages can contribute to improve the chicken health and reduce pathogens burden at the end of the production cycle of broilers. Furthermore, it presents for the first time a detailed look of the microbiota composition and changes in broilers in a commercial scenario, information that will valuable towards the implementation of phage therapy technologies in the field.
Taxonomical evaluation of plant genetic markers by Bayesian Classifier
(2020) Luisa Matiz-Céron; Alejandro Reyes; Juan Manuel Anzola
DNA barcodes are standardized sequences that range between 400-800 bp, vary at different taxonomic levels, and make it possible to identify individuals of species that have been previously assigned taxonomically. Several barcodes have been identified in different groups in the tree of life. However, there are groups that lack an accurate DNA marker, and even more so, accurate strategies that enable verification of their taxonomic affiliation. Several DNA barcodes have been postulated for plants, nonetheless, their classification potential has not been evaluated for metabarcoding, and as a result, it would appear as no one of them excels above the others in this area. One tool that has recently gained traction is Naïve Bayesian Classifiers; this type of classifier is based on the independence of attributes and the allocation of categories in each context. The present study aims at evaluating the classification power of several plant genetic markers that have been proposed as barcodes ( trnL, rpoB, rbcL, matK, psbA-trnH and psbK ) using a Naïve Bayesian Classifier, in order to determine the markers with higher performance at different taxonomic levels for metabarcoding analysis and to identify problematic genera at the time of species assignment. We propose matK and trnL as potential candidates up to the genus assignment. Some problematic genera ( Aegilops, Gueldenstaedtia, Helianthus, Oryza, Shorea, Thysananthus and Triticum ) within certain families in a sample could lead to misclassification no matter which marker is used. Finally, we propose recommendations when performing taxonomic identification analysis of plants in samples with multiple individuals.
Viral and bacterial dynamics in response to drastic and short dietary shifts in creole Colombian cattle
(2025) Ruth Hernández; Laura Milena Forero‐Junco; Yesid Avellaneda Avellaneda; Diego Velasco; Gerson-Dirceu López; Cesar A. Vargas-García; Chiara Carazzone; Hugo Jiménez; Alejandro Caro‐Quintero; Alejandro Reyes
<title>Abstract</title> The inclusion of grains in cattle diets aims to boost milk and meat production but can reduce ruminal pH and disrupt normal rumen function, mainly affecting fiber-degrading microbes. While bacterial responses to pH shifts are well documented, the effects on rumen bacteriophage (phage) communities remain unclear. This study aimed at characterizing the viral and bacterial dynamics upon a short-term acidotic challenge induced by adding corn to the diets of three Colombian BON (Blanco Orejinegro) cows, ( <italic>Bos Taurus</italic> ), usually fed on pasture. Ruminal fluid samples were analyzed to monitor viral and bacterial diversity, pH, and short-chain fatty acids (SCFAs). Viral alpha diversity indices declined significantly with pH reduction, possibly due to lysogeny or phages with broad host ranges. In contrast, bacterial diversity stayed relatively stable, suggesting higher resilience to short-term pH shifts. Beta diversity analysis indicated that individual animal variation, rather than diet, was the main driver shaping both viral and bacterial communities. Moreover, distinct viral abundance patterns were strongly associated with pH fluctuations, highlighting the potential of phages as sensitive early indicators of ruminal acidification. These findings emphasize the important ecological role of the rumen virome and suggest that monitoring phage dynamics could improve understanding of ruminal pH-related disturbances in cattle.