Biology subjects

Lopez-Beltran, A.

Publications and source records attributed to Lopez-Beltran, A..

3 recordsLinked to original sources

bioRxiv2025

Microbiota and Small Cell Lung Cancer.A casual bystander or a hidden culprit?

The tumor-associated microbiome is a key player in cancer development, progression, prognosis, and therapeutic response. Notably, distinct microbial signatures have been identified across cancer types. Small cell lung carcinoma (SCLC) accounts for approximately 15% of all lung cancer, yet its microbiome remains unclear. Analyzing the bacteriome composition in tissue from ten SCLC cases and in 10 cases of a heterogenous lung pathology group, we found a distinct microbial signature associated with SCLC with significantly lower diversity and higher dissimilarity, characterized by a higher relative abundance of Firmicutes and Bacteroidota, and a markedly different set of dominant genera (Pseudomonas, Streptococcus and Haemophilus) resulting in an increased Proteobacteria-to-Actinobacteria ratio. Unexpectedly, mycobiome analysis comparing pooled samples of these SCLC cases with ten pooled lung adenocarcinoma (LUAD) cases revealed that the fungal genus Taphrina was uniquely represented in SCLC. Strikingly, mycobiome individual analysis of twenty-one additional SCLC cases compared with 10 LUAD cases showed an increased prevalence of Taphrina sp. in SLCL tissue. Overall, the results suggest that SCLC microbiome is distinct from other lung pathologies and uncovers a novel link between the biotrophic plant pathogenic Taphrina and human cancer.

cancer biology↗

bioRxiv2024

Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome

Arms races between mobile genetic elements and prokaryotic hosts are major drivers of ecological and evolutionary change in microbial communities. Prokaryotic defense systems such as CRISPR-Cas have the potential to regulate microbiome composition by modifying the interactions among bacteria, plasmids, and phages. Here, we used longitudinal metagenomic data from 130 healthy and diseased individuals to study how the interplay of genetic parasites and CRISPR-Cas immunity reflects on the dynamics and composition of the human gut microbiome. Based on the coordinated study of 80,000 CRISPR-Cas loci and their targets, we show that CRISPR-Cas immunity effectively modulates bacteriophage abundances in the gut. Acquisition of CRISPR-Cas immunity typically leads to a decrease in the abundance of lytic phages, but does not necessarily cause their complete disappearance. Much smaller effects are observed for lysogenic phages and plasmids. Conversely, phage-CRISPR interactions shape bacterial microdiversity by producing weak selective sweeps that benefit immune host lineages. Interestingly, distal (and chronologically older) regions of CRISPR arrays are enriched in spacers that are potentially functional and target crass-like phages and local prophages. This suggests that exposure to reactivated prophages and other endemic viruses is a major selective pressure in the gut microbiome that drives the maintenance of long-lasting immune memory.

microbiology↗

bioRxiv2021

UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions

Reverse transcriptases (RTs) are enzymes capable of synthesizing DNA using RNA as a template. Within the last few years, a burst of research has led to the discovery of novel prokaryotic RTs with diverse antiviral properties, such as DRTs (Defense-associated RTs), which belong to the so-called group of unknown RTs (UG) and are closely related to the Abortive Infection system (Abi) RTs. In this work, we performed a systematic analysis of UG and Abi RTs, increasing the number of UG/Abi members up to 42 highly diverse groups, most of which are predicted to be functionally associated with other gene(s) or domain(s). Based on this information, we classified these systems into three major classes. In addition, we reveal that most of these groups are associated with defense functions and/or mobile genetic elements, and demonstrate the antiphage role of four novel groups. Besides, we highlight the presence of one of these systems in novel families of human gut viruses infecting members of the Bacteroidetes and Firmicutes phyla. This work lays the foundation for a comprehensive and unified understanding of these highly diverse RTs with enormous biotechnological potential.

evolutionary biology↗