Biology subjects

Prieto, M. A.

Publications and source records attributed to Prieto, M. A..

5 recordsLinked to original sources

bioRxiv2026

Unlocking Bacterial Cellulose Functionalisation: Comparative Genetic and Co-Culture Strategies in Komagataeibacter

Bacterial cellulose (BC) is produced by diverse bacterial species, including members of the genus Komagataeibacter, and has emerged as a potential sustainable alternative to conventional materials such as plastics and leather. Its production by bacteria is rapid and easily scalable, and via genetic modifications or culturing the bacteria with other microbes, it is possible to rationally enhance the BC that is produced, for example by adding functional components. Here, we systematically evaluated BC functionalization strategies, including genetic engineering and co-culturing with other engineered microbes across the most widely used Komagataeibacter species: K. rhaeticus, K. xylinus, K. medellinensis and K. sucrofermentans. We established that all tested strains are amenable to DNA transformation and capable of expressing heterologous genes from identical genetic constructs. However, we identified species-specific differences in heterologous gene expression, cellulose production in varying environmental conditions and in the abilities of the strains to co-culture with Escherichia coli. Additionally, we demonstrated that all these cellulose-producing bacteria can establish functional symbiotic co-cultures with yeast. While inter-species variations in heterologous gene expression and co-culture dynamics are evident, BC modification through genetic engineering and co-culturing strategies remains achievable across all tested Komagataeibacter species. Our work provides a comparative framework to guide researchers in selecting optimal species based on their specific application requirements.

synthetic biology↗

bioRxiv2023

Bdellovibrio's Prey-Independent Growth is Fuelled by Amino Acids as a Carbon Source

Identifying the nutritional requirements and growth conditions of microorganisms is crucial for determining their applicability in industry and understanding their role in clinical ecology. Predatory bacteria such as Bdellovibrio bacteriovorus have emerged as promising tools for combating infections by human bacterial pathogens due to their natural killing features. Bdellovibrios lifecycle occurs inside prey cells, using the cytoplasm as a source of nutrients and energy. However, this lifecycle supposes a challenge when determining the specific uptake of metabolites from the prey to complete the growth inside cells, a process that has not been completely elucidated. Here, following a model-based approach we illuminate the ability of Bdellovibrio bacteriovorus to replicate DNA, increase biomass, and generate adenosine triphosphate (ATP) in an amino acid-based rich media in the absence of prey, keeping intact its predatory capacity. In this culture, we determined the main carbon sources used and their preference, being glutamate, serine, aspartate, isoleucine, and threonine. This study offers new insights into the role of predatory bacteria in natural environments and establishes the basis for developing new Bdellovibrio applications using appropriate metabolic and physiological methodologies.

microbiology↗

bioRxiv2022

Golden Standard: A complete standard, portable, and interoperative MoClo tool for model and non-model bacterial hosts.

Modular cloning assembly has become a benchmark technology in synthetic biology. However, there is a mismatch between its impressive development and the standardization required to promote interoperability between the different systems available. The full development of the field is thus hampered by a surge of oftentimes incompatible organism-specific systems. To overcome these issues, we present Golden Standard (GS), a Type IIS assembly method underpinned by the Standard European Vector Architecture (SEVA). GS unlocks modular cloning applications with any type of microorganism and delivers consistent combinatorial multi-part assembly of standardized genetic elements to create genetic circuits of up to twenty transcription units. Reliance on the Golden Gate syntax renders GS fully compatible with many existing tools and it sets the path towards efficient reusability of available part libraries and assembled TUs. GS was fully validated in terms of DNA assembly performance, portability and phenotype engineering in model and non-model bacteria. In order to facilitate the widespread adoption and future community-driven development of GS, we provide a web-portal featuring: i) a repository of parts and vectors, ii) a SBOLHub for exchange and analysis of constructs and iii) Wizard and Setup tools to guide the design of constructs using stored and user-specific parts.

synthetic biology↗

bioRxiv2020

A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs.

Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The rapid, sensitive and specific diagnosis of SARS-CoV-2 by fast and unambiguous testing is widely recognized to be critical in responding to the ongoing outbreak. Since the current testing capacity of RT-PCR-based methods is being challenged due to the extraordinary demand of supplies, such as RNA extraction kits and PCR reagents worldwide, alternative and/or complementary testing assays should be developed. Here, we exploit the potential of mass spectrometry technology combined with machine learning algorithms as an alternative fast tool for SARS-CoV-2 detection from nasopharyngeal swabs samples. According to our preliminary results, mass spectrometry-based methods combined with multivariate analysis showed an interesting potential as a complementary diagnostic tool and further steps should be focused on sample preparation protocols and the improvement of the technology applied.

microbiology↗

bioRxiv2020

Providing new insights on the byphasic lifestyle of the predatory bacterium Bdellovibrio bacteriovorus through genome-scale metabolic modeling.

In this study we analyze the growth-phase dependent metabolic states of Bdellovibrio bacteriovorus by constructing a fully compartmented, mass and charge-balanced genome-scale metabolic model of this predatory bacterium (iCH457). Considering the differences between life cycle phases driving the growth of this predator, growth-phase condition-specific models have been generated allowing the systematic study of its metabolic capabilities. Using these unprecedented computational tools, we have been able to analyze, from a system level, the dynamic metabolism of the predatory bacteria as the life cycle progresses. We provide solid computational evidences supporting potential axenic growth of B. bacteriovoruss in a rich medium based its encoded metabolic capabilities. Our systems-level analysis confirms the presence of "energy-saving" mechanisms in this predator as well as an abrupt metabolic shift between the attack and intraperiplasmic growth phases. Our results strongly suggest that predatory bacterias metabolic networks have low robustness, likely hampering their ability to tackle drastic environmental fluctuations, thus being confined to stable and predictable habitats. Overall, we present here a valuable computational testbed based on predatory bacteria activity for rational design of novel and controlled biocatalysts in biotechnological/clinical applications. AUTHOR SUMMARYBacterial predation is an interspecific relationship widely extended in nature. Among other predators, Bdellovibrio and like organism (BALOs) have received recently a great attention due to the high potential applications such as biocontrol agent in medicine, agriculture, aquaculture and water treatment. Despite the increasing interest in of this predatory bacterium its complex lifestyle and growth conditions hamper the full exploitation of their biotechnological properties. In order to overcome these important shortcomings, we provide here the first genome-scale model of a predator bacterium constructed so far. By using the model as a computational testbed, we provide solid evidences of the metabolic autonomy of this interesting bacterium in term of growth, as well as its dynamic metabolism powering the biphasic life style of this predator. We found a low metabolic robustness thus suggesting that Bdellovibrio is more niche-specific than previously thought and that the environmental conditions governing predation may be relatively uniform. Overall, we provide here a valuable computational tool largely facilitating rational design of novel and controlled predator-based biocatalysts in biotechnological/clinical applications.

systems biology↗