Biology subjects

Gaya-Vidal, M.

Publications and source records attributed to Gaya-Vidal, M..

6 recordsLinked to original sources

bioRxiv2020

Characterization of the oral microbiome of medically controlled type-2 diabetes patients

Type 2 diabetes mellitus (T2DM) is a chronic metabolic disease that is becoming a significant global health care problem. Several studies have shown that people with diabetes are more susceptible to oral problems, such as periodontitis and, although the causes are still inconclusive, the oral microbiota seems to be an important factor in this interaction. This study aimed to characterize the oral microbiome of a sample representing T2DM patients from Portugal and exploit potential associations between some microorganisms and variables like teeth brushing, smoking habits, and nutrient intake. By sequencing the hypervariable regions V3-V4 of the 16S rRNA gene in 50 individuals belonging to a group of diabetes patients and a control group, we found a total of 233 taxa, from which only 65% were shared between both groups. No differences were found in terms of alpha and beta diversity between groups or habits categories. Also, there were no significant differences in the oral microbiome profiles of control and diabetes patients. Only the class Synergistia and the genus TG5, which are related to periodontitis, were statistically more frequent in the control group. This finding can be justified by the fact that these diabetic patients usually have their oral health under close medical control than an average healthy person, which in this study was represented by the control group. IMPORTANCEDiabetes has become a significant global health care issue as its incidence continues to increase exponentially, with type 2 diabetes being responsible for more than 90% of these cases. Portugal is one of the countries with a higher prevalence of diabetes in Europe. It has been reported that diabetic people have an increased risk of developing several health problems such as oral infections mostly caused by opportunistic pathogens. Some studies have pointed out a relationship between diabetes and oral microbiome. Therefore, the characterization of the microbial ecosystem of the mouth in reference groups is crucial to provide information to tackle oral health pathogen-borne conditions. In this study, we provide the first characterization of the oral microbiome of type 2 diabetes mellitus patients from Portugal, and therefore, contributing new data and knowledge to elucidate the relationship between diabetes and the oral microbiome.

microbiology↗

bioRxiv2019

Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR

Despite the interest in characterizing all genomic variation, the presence of large repeats at the breakpoints of many structural variants hinders their analysis. This is especially problematic in the case of inversions, since they are balanced changes without gain or loss of DNA. Here we tested novel linkage-based droplet digital PCR (ddPCR) assays on 20 inversions ranging from 3.1 to 742 kb and flanked by long inverted repeats (IRs) of up to 134 kb. Among these, we validated 13 inversions predicted by different genome-wide techniques. In addition, we have generated new experimental human population information across 95 African, European and East-Asian individuals for 16 of them, including four already known inversions for which there were no high-throughput methods to determine directly the orientation, like the well-characterized 17q21 inversion. Through comparison with previous data, independent replicates and both inversion breakpoints, we have demonstrated that the technique is highly accurate and reproducible. Most of the studied inversions are frequent and widespread across continents, showing a negative correlation with genetic length. Moreover, all except two show clear signs of being recurrent, and the new data allowed us to define more clearly the factors affecting recurrence levels and estimate the inversion rate across the genome. Finally, thanks to the generated genotypes, we have been able to check inversion functional effects in multiple tissues, validating gene expression differences reported before for two inversions and finding new candidate associations. Our work therefore provides a tool to screen these and other complex genomic variants quickly in a large number of samples for the first time, highlighting the importance of direct genotyping to assess their potential consequences and clinical implications.

genomics↗

bioRxiv2019

Mozambican genetic variation provides new insights into the Bantu expansion

The Bantu expansion, which started in West Central Africa around 5,000 BP, constitutes a major migratory movement involving the joint spread of peoples and languages across sub-Saharan Africa. Despite the rich linguistic and archaeological evidence available, the genetic relationships between different Bantu-speaking populations and the migratory routes they followed during various phases of the expansion remain poorly understood. Here, we analyze the genetic profiles of southwestern and southeastern Bantu-speaking peoples located at the edges of the Bantu expansion by generating genome-wide data for 200 individuals from 12 Mozambican and 3 Angolan populations using [~]1.9 million autosomal single nucleotide polymorphisms. Incorporating a wide range of available genetic data, our analyses confirm previous results favoring a \"late split\" between West and East Bantu speakers, following a joint passage through the rainforest. In addition, we find that Bantu speakers from eastern Africa display genetic substructure, with Mozambican populations forming a gradient of relatedness along a North-South cline stretching from the coastal border between Kenya and Tanzania to South Africa. This gradient is further associated with a southward increase in genetic homogeneity, and involved minimum admixture with resident populations. Together, our results provide the first genetic evidence in support of a rapid North-South dispersal of Bantu peoples along the Indian Ocean Coast, as inferred from the distribution and antiquity of Early Iron Age assemblages associated with the Kwale archaeological tradition.

genetics↗

bioRxiv2018

Functional and evolutionary impact of polymorphic inversions in the human genome

Inversions are one type of structural variants linked to phenotypic differences and adaptation in multiple organisms. However, there is still very little information about inversions in the human genome due to the difficulty of their detection. Here, thanks to the development of a new high-throughput genotyping method, we have performed a complete study of a representative set of 45 common human polymorphic inversions. Most inversions promoted by homologous recombination occur recurrently both in humans and great apes and, since they are not tagged by SNPs, they are missed by genome-wide association studies. Furthermore, there is an enrichment of inversions showing signatures of positive or balancing selection, diverse functional effects, such as gene disruption and gene-expression changes, or association with phenotypic traits. Therefore, our results indicate that the genome is more dynamic than previously thought and that human inversions have important functional and evolutionary consequences, making possible to determine for the first time their contribution to complex traits.

genomics↗

bioRxiv2018

Genetic analysis of Sephardic ancestry in the Iberian Peninsula

The Sephardim are a major Jewish ethnic division whose origins can be traced back to the Iberian Peninsula. We used genome-wide SNP data to investigate the degree of Sephardic admixture in seven populations from the Iberian Peninsula and surrounding regions in the aftermath of their religious persecution starting in the late 14th century. To this end, we used Eastern Mediterranean (from South Italy, Greece and Israel) and North African (Tunisian and Moroccan) populations as proxies for the major ancestral components found in the target populations and carried out unlinked- and linked-marker analyses on the available genetic data. We report evidence of Sephardic ancestry in some of our Iberian samples, as well as in North Italy and Tunisia. We find the Sephardic admixture to be more recent relative to the Berber admixture following an out-of-Iberia geographic dispersal, suggesting Sephardic gene flow from Spain outwards. We also report some of the challenges in assigning Sephardic ancestry to potentially admixed individuals due to the lack of a clear genetic signature.

genomics↗

bioRxiv2017

The maternal genetic history of the Angolan Namib Desert: a key region for understanding the peopling of southern Africa

Southern Angola is a poorly studied region, inhabited by populations that have been associated with different migratory movements into southern Africa. Besides the long-standing presence of indigenous Kxa-speaking foragers and the more recent arrival of Bantu-speaking pastoralists, ethnographic and linguistic studies have suggested that other pre-Bantu communities were also present in the Namib desert, including peripatetic groups like the Kwepe (formerly Kwadi speakers), Twa and Kwisi. Here we evaluate previous peopling hypotheses by analyzing the relationships between seven groups from the Namib desert (Kuvale, Himba, Tjimba, Kwisi, Twa, Kwepe) and Kunene Province (!Xun), based on newly collected linguistic data and 295 complete mtDNA genomes. We found that: i) all groups from the Namib desert have genealogically-consistent matriclanic systems that had a strong impact on their maternal genetic structure by enhancing genetic drift and population differentiation; ii) the dominant pastoral groups represented by the Kuvale and Himba were part of a Bantu proto-population that also included the ancestors of present-day Damara and Herero peoples from Namibia; iii) Tjimba are closely related to the Himba; iv) the Kwepe, Twa and Kwisi have a divergent Bantu-related mtDNA profile and probably stem from a single population that does not show clear signs of being a pre-Bantu indigenous group. Taken together, our results suggest that the maternal genetic structure of the different groups from the Namib desert is largely derived from endogamous Bantu peoples, and that their social stratification and different subsistence patterns are not indicative of remnant groups, but reflect Bantu-internal variation and ethnogenesis.

genetics↗