Microbial communities perform emergent activities that are essentially different from those carried by their individual members. The gut microbiome and its metabolites have a significant impact on the host, contributing to homeostasis or disease. Food molecules shape this community, being fermented through cross-feeding interactions of metabolites such as lactate, acetate, and amino acids, or products derived from macromolecule degradation. Mathematical and experimental approaches have been applied to understand and predict the interactions between microorganisms in complex communities such as the gut microbiota. Rational and mechanistic understanding of microbial interactions is essential to exploit their metabolic activities and identify keystone taxa and metabolites. The latter could be used in turn to modulate or replicate the metabolic behavior of the community in different contexts. This review aims to highlight recent experimental and modeling approaches for studying cross-feeding interactions within the gut microbiome. We focus on short-chain fatty acid production and fiber fermentation, which are fundamental processes in human health and disease. Special attention is paid to modeling approaches, particularly kinetic and genome-scale stoichiometric models of metabolism, to integrate experimental data under different diet and health conditions. Finally, we discuss limitations and challenges for the broad application of these modeling approaches and their experimental verification for improving our understanding of the mechanisms of microbial interactions.

Consumption of fresh fruit is known to protect against non-communicable diseases due to the fruit's content in compounds with an antioxidant capacity, among them is polyphenols. Asian plums (Prunus salicina L.) accumulate more than 40 phenolic compounds, with a remarkable diversity in their profiles, depending on the variety and environmental conditions. Although candidate genes have been indicated to control this trait, the loci controlling its phenotypic variation have not yet been defined in this species. The aim of this work was to identify the quantitative trait Loci (QTL) controlling the phenolic compounds content in the Asian plum skin and flesh. Using UHPLC-DAD-Orbitrap-MS, we determined that cyanidin-3-glucoside and cyanidin-3-rutinoside are the main anthocyanins in Asian plums. Other anthocyanins found to a lesser extent were tentatively identified as cyanidin bound to different sugar and procyanidin moieties. Then we phenotyped fruits of 92 and 80 F1 seedlings from the cross < “98.99” × “Angeleno”> (98 Ang) for two harvest seasons. We used HPLC-DAD to quantify single anthocyanin and spectrophotometric techniques to determine the total content of phenols, flavonoids, procyanidins, and antioxidant activity (DPPH and FRAP). To determine the phenotype-genotype association of phenolic compounds content, phenotypic values (adjusted by linear mixed-effects models), genotypic data and linkage maps were analyzed with the multiple QTL model (MQM) approach. We found a total of 21 significant trait-marker associations: 13 QTLs segregating from “98.99” and 8 QTLs from “Angeleno.” From these associations, 8 corresponded to phenolic compound content in the flesh and 13 in the skin. Phenotype variance was explained by the detected loci, ranging from 12.4 to 27.1%. The identified loci are related to the content of cyanidin-3-glucoside (LG4), cyanidin-3-rutinoside (LG4), total flavonoids and procyanidins (LG5 and LG8), and minor anthocyanin compounds (LG3 and LG4). These results will help improve the efficiency of breeding programs for the generation of Asian plum varieties with high phenolic compound content.

Since 2014, the ISCB Latin American Student Council Symposium (LA-SCS) serves as the main biannual activity where students from all levels, postdocs and early researchers from the entire Latin American region can gather to discuss recent advances in the fields of bioinformatics and computational biology. This time we faced a major unexpected obstacle, a worldwide pandemic that has completely disrupted human activities at a planetary scale. Countless conferences have been either canceled, reprogrammed for the next year or moved to a virtual format. However, thanks to an important strengthening of the Latin American student network and the creation of several new RSGs in the continent, we were able to get together a fearless team that aimed to overcome the pandemic obstacles and still organise the 4th LA-SCS. Here we summarize our experiences in our first virtual symposium.

Clostridium baratii strains are rare opportunistic pathogens associated with botulism intoxication. They have been isolated from foods, soil and be carried asymptomatically or cause botulism outbreaks. Is not taxonomically related to Clostridium botulinum, but some strains are equipped with BoNT/F7 cluster. Despite their relationship with diseases, our knowledge regarding the genomic features and phylogenetic characteristics is limited. We analyzed the pangenome of C. baratii to understand the diversity and genomic features of this species. We compared existing genomes in public databases, metagenomes, and one newly sequenced strain isolated from an asymptomatic subject. The pangenome was open, indicating it comprises genetically diverse organisms. The core genome contained 28.49% of the total genes of the pangenome. Profiling virulence factors confirmed the presence of phospholipase C in some strains, a toxin capable of disrupting eukaryotic cell membranes. Furthermore, the genomic analysis indicated significant horizontal gene transfer (HGT) events as defined by the presence of prophage genomes. Seven strains were equipped with BoNT/F7 cluster. The active site was conserved in all strains, identifying a missing 7-aa region upstream of the active site in C. baratii genomes. This analysis could be important to advance our knowledge regarding opportunistic clostridia and better understand their contribution to disease.