Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels

Abstract

The study of the biological response of microbial cells interacting with natural and synthetic interfaces has acquired a new dimension with the development and constant progress of advanced omics technologies. New methods allow the isolation and analysis of nucleic acids, proteins and metabolites from complex samples, of interest in diverse research areas, such as materials sciences, biomedical sciences, forensic sciences, biotechnology and archeology, among others. The study of the bacterial recognition and response to surface contact or the diagnosis and evolution of ancient pathogens contained in archeological tissues require, in many cases, the availability of specialized methods and tools. The current review describes advances in in vitro and in silico approaches to tackle existing challenges (e.g., low-quality sample, low amount, presence of inhibitors, chelators, etc.) in the isolation of high-quality samples and in the analysis of microbial cells at genomic, transcriptomic, proteomic and metabolomic levels, when present in complex interfaces. From the experimental point of view, tailored manual and automatized methodologies, commercial and in-house developed protocols, are described. The computational level focuses on the discussion of novel tools and approaches designed to solve associated issues, such as sample contamination, low quality reads, low coverage, etc. Finally, approaches to obtain a systems level understanding of these complex interactions by integrating multi omics datasets are presented.

Revisiting the current and emerging concepts of postharvest fresh fruit and vegetable pathology for next‐generation antifungal technologies

“…Developing more comprehensible strategies that can reduce postharvest spoilage of FFVs is essential. Recently, significant progress has been made in metagenomics, artificial intelligence, chemistry, biological processes, high‐throughput sequencing techniques, multi‐omics technology, software development, and data connectivity (González‐Plaza et al., 2022). The infectious context can now be assessed in greater detail and accuracy.…”

Special Issue “Deployment of Proteomics Approaches in Biomedical Research”

“…During recent years, an additional expansion of biomedical proteomics has been the study of protein inventories derived from microbial communities, as well as their functional activity and dynamic composition [31][32][33]. In this field, the continuous evaluation and testing of bioinformatic pipelines for mining the acquired datasets is pivotal to obtain confident data, as well as to potentially improve LC-MS/MS strategies.…”