Biology subjects

Torres, R. C.

Publications and source records attributed to Torres, R. C..

4 recordsLinked to original sources

bioRxiv2025

CagY sequence and structural motifs are associated with ancestry and 1 disease in world-wide Helicobacter pylori strains

Helicobacter pylori (Hp) interacts with gastric epithelial cells using a multi-protein type 4 secretion system (T4SS) whose function is regulated by CagY. CagY is the T4SS backbone, connecting the bacterial cytoplasm with the epithelial cytoplasm and interacting with most other T4SS proteins. However, its mechanisms of action are unknown. We aimed to comprehensively analyse cagY in a worldwide collection of strains to unmask any correlation between ancestry and/or disease and sequence diversity, including an analysis of critical domains and associated structural changes. We used 674 cagY sequences derived from1,012 Hp genomes, sequenced with Single Molecule Real-Time from the Hp Genome Project. Phylogenetic and principal component analyses (PCA) revealed a strong population structure among European, Asian, African and American clusters, which interfered with other analyses. To address this heterogeneity, dimensional reduction analysis with PCA and Linear Discriminant Analyses were used to minimize interference before studying possible association of cagY diversity with disease. For this analysis, cagY genes were fragmented using unitig-caller with a designed analytical pipeline that clearly separated the non-atrophic gastritis (NAG), advanced intestinal metaplasia and gastric cancer (GC) groups. Sixty-four unitigs significantly separated GC from NAG based on cagY sequences, and the most GC-associated unitigs were localized in the middle repeat region of the protein (MRR), particularly in the A module, including the cysteine-containing motif YLDCVSQ. Proline was enriched in the MRR and VirB10 regions. The consequences of the diversity on the protein structure were analysed using ChimeraX. The validated and stabilized 14-multimer model showed major structural changes along the multimer-structure, particularly in the cysteine-rich MRR region, that might be one mechanism by which CagY regulates T4SS function.

bioinformatics↗

bioRxiv2025

The oral cavity of chronically homeless adults is home for unusual extremophile environmental bacteria

Chronically homeless adults (CHA) often face limited healthcare access, poor nutrition, frequent substance use, and close contact with stray animals. These factors can significantly alter their oral microenvironment. This study aimed to characterize the oral microbiota of this vulnerable and understudied population. We analyzed saliva samples from 60 chronically homeless men and 40 asymptomatic men with no history of homelessness, all living in Mexico City. DNA was extracted, and the V1-V3 regions of the 16S rRNA gene were sequenced. Taxonomic classification was performed using human and non-human databases. Diversity metrics were calculated using the vegan v2.6-4 package in R, and informative species were identified through machine learning and statistical approaches. Microbial correlation networks were inferred using NetCoMi in RStudio. Bacterial diversity was significantly higher in the CHA group. While both groups shared 369 species, only eight were exclusive to the control group, and 149 were unique to CHA. Several of these taxa had never been reported in humans and are typically found in extreme environments. For example, Megasphaera cerevisiae, adapted to high ethanol and low pH, was the most abundant species. Syntrophocurvum alkaliphilum, from a hypersaline lake in Siberia, and Sinanaerobacter chloroacetimidivorans, from anaerobic bioreactors, were also prevalent. Marked differences in microbial network structure were observed between groups. These findings highlight the adaptability of extremophile bacteria to human environments under chronic stress and poor hygiene. This study provides a first look into the oral microbiota of individuals experiencing chronic homelessness, emphasizing the need for more research into marginalized populations.

bioinformatics↗

bioRxiv2023

Meat without vegetables: An ancient ecotype of Helicobacter pylori found in Indigenous populations and animal adapted lineages.

The colonization of our stomachs by Helicobacter pylori is believed to predate the oldest splits between extant human populations. We identify a "Hardy" ecospecies of H. pylori associated with indigenous groups, isolated from people in Siberia, Canada, USA and Chile. The ecospecies shares the ancestry of "Ubiquitous" H. pylori from the same geographical region in most of the genome but has nearly fixed SNP differences in 100 genes, many of which encode outer membrane proteins and host interaction factors. For these parts of the genome, the ecospecies has a separate, independently evolving gene pool with a distinct evolutionary history. H. acinonychis, found in big cats, and a newly identified primate-associated lineage both belong to the Hardy ecospecies and both represent human to animal host jumps. Most strains from the ecospecies encode an additional iron-dependent urease that is shared by Helicobacter from carnivorous hosts, as well as a tandem duplication of vacA, encoding the vacuolating toxin. We conclude that H. pylori split into two highly distinct ecospecies in Africa and that both dispersed around the globe with humans, but the Hardy ecospecies has gone extinct in most parts of the world. Our analysis also pushes back the likely length of the association between H. pylori and humans.

microbiology↗

bioRxiv2021

Selective pressure on membrane proteins drives the evolution of Helicobacter pylori Colombian subpopulations

Helicobacter pylori have coevolved with mankind since its origins, adapting to different human groups. In America H. pylori has evolved in several subpopulations specific for regions or even countries. In this study we analyzed the genome of 163 Colombian strains along with 1,113 strains that represent worldwide H. pylori populations to better discern the ancestry and adaption to Colombian people. Population structure was inferred with FineStructure and chromosome painting identifying the proportion of ancestries in Colombian isolates. Phylogenetic relationship was analyzed using the SNPs present in the core genome. Also, a Fst analysis was done to identify the gene variants with the strongest fixation in the identified Colombian subpopulations in relation to their parent population hspSWEurope. Worldwide, population structure analysis allowed the identification of two Colombian subpopulations, the previously described hspSWEuropeColombia and a novel subpopulation named hspColombia. In addition, three subgroups of H. pylori were identified within hspColombia that follow their geographic origin. The Colombian H. pylori subpopulations represent an admixture of European, African and Native indigenous ancestry; although some genomes showed a high proportion of self-identity, suggesting a strong adaption to these mestizo Colombian groups. The Fst analysis identified 82 SNPs significantly fixed in 26 genes of the hspColombia subpopulation that encode mainly for outer membrane proteins and proteins involved in central metabolism. The strongest fixation indices were identified in genes encoding the membrane proteins HofC, HopE, FrpB-4 and Sialidase A. These findings demonstrate that H. pylori has evolved in Colombia to give rise to subpopulations following a geographical structure, evolving to an autochthonous genetic pool, drive by a positive selective pressure especially on genes encoding for outer membrane proteins.

genomics↗