Biology subjects

Sandoval-Motta, S.

Publications and source records attributed to Sandoval-Motta, S..

5 recordsLinked to original sources

bioRxiv2025

Global diversity of integrating conjugative elements (ICEs) in Helicobacter pylori and their influence on genome architecture

Integrating conjugative elements (ICEs) are mobile genetic elements conferring a wide range of beneficial functions upon their bacterial hosts. Generally, they can be activated from their integrated states to undergo horizontal gene transfer via conjugation. In the case of the human gastric pathogen Helicobacter pylori, a paradigm for extensive genetic diversity, highly efficient natural transformation and recombination processes may superimpose canonical transfer of its two ICEs termed ICEHptfs3 and ICEHptfs4, and thus shape their composition substantially. Here, as a part of the Helicobacter pylori Genome Project (HpGP) initiative, we have analyzed high-quality genome sequences from 1011 clinical strains with respect to their ICE content and variability. We show that both elements are highly prevalent in all H. pylori populations, but have a strong tendency for gene erosion. ICE sequence variations reflect the population structure and show a clear signature of increased horizontal transfer. A detailed map of ICE integration sites revealed local preferences, but also how recombination processes result in hybrid elements or genome rearrangements. Population-specific differences in ICE cargo genes might reflect distinct requirements in the biological functions provided by these mobile elements.

microbiology↗

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

A single-cell transposable element atlas of human cell identity

Single cell RNA sequencing (scRNA-seq) is revolutionizing the study of complex biological systems. However, most sequencing studies overlook the contribution of transposable element (TE) expression to the transcriptome. In both scRNA-seq and bulk tissue RNA sequencing (RNA-seq), quantification of TE expression is challenging due to repetitive sequence content and poorly characterized TE gene models. Here, we developed a tool and analysis pipeline for Single cell Transposable Element Locus Level Analysis of scRNA Sequencing (Stellarscope) that reassigns multi-mapped reads to specific genomic loci using an expectation-maximization algorithm. Using Stellarscope, we built an atlas of TE expression in human PBMCs. We found that locus-specific TEs delineate cell types and define new cell subsets not identified by standard mRNA expression profiles. Altogether, this study provides comprehensive insights into the influence of transposable elements in human biology.

genomics↗

bioRxiv2021

Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter

Horizontal gene transfer (HGT) can allow traits that have evolved in one bacterial species to transfer to another. This has potential to rapidly promote new adaptive trajectories such as zoonotic transfer or antimicrobial resistance. However, for this to occur requires gaps to align in barriers to recombination within a given time frame. Chief among these barriers is the physical separation of species with distinct ecologies in separate niches. Within the genus Campylobacter there are species with divergent ecologies, from rarely isolated single host specialists to multi-host generalist species that are among the most common global causes of human bacterial gastroenteritis. Here, by characterising these contrasting ecologies, we can quantify HGT among sympatric and allopatric species in natural populations. Analysing recipient and donor population ancestry among genomes from 30 Campylobacter species we show that cohabitation in the same host can lead to a 6-fold increase in HGT between species. This accounts for up to 30% of all SNPs within a given species and identifies highly recombinogenic genes with functions including host adaptation and antimicrobial resistance. As described in some animal and plant species, ecological factors are a major evolutionary force for speciation in bacteria and changes to the host landscape can promote partial convergence of distinct species through HGT.

microbiology↗

bioRxiv2020

Phenotype Heritability in holobionts: An Evolutionary Model

Many complex diseases are expressed with high incidence only in certain populations. Genealogy studies determine that these diseases are inherited with a high probability. However, genetic studies have been unable to identify the genomic signatures responsible for such heritability, as identifying the genetic variants that make a population prone to a given disease is not enough to explain its high occurrence within the population. This gap is known as the missing heritability problem. We know that the microbiota plays a very important role in determining many important phenotypic characteristics of its host, in particular, the complex diseases for which the missing heritability occurs. Therefore, when computing the heritability of a phenotype it is important to consider not only the genetic variation in the host but also in its microbiota. Here we test this hypothesis by studying an evolutionary model based on gene regulatory networks. Our results show that the holobiont (the host plus its microbiota) is capable of generating a much larger variability than the host alone, greatly reducing the missing heritability of the phenotype. This result strongly suggests that a considerably large part of the missing heritability can be attributed to the microbiome.

systems biology↗