Biology subjects

Souza, V.

Publications and source records attributed to Souza, V..

13 recordsLinked to original sources

bioRxiv2026

One placement, many fields: robust voxel-wise mapping with multichannel TMS

Understanding the human brain at the individual level is central to understanding its function and a prerequisite for personalized therapy. Transcranial magnetic stimulation (TMS) can map structure-function relationships at high resolution by regressing trial-wise variation in the TMS-induced electric field (E-field) against a response such as motor evoked potentials (MEPs). This requires distinct E-fields across pulses at different cortical locations, which single-coil TMS (sTMS) achieves by physically repositioning the coil (typically supported by neuronavigation software such as InVesalius Navigator; Souza et al., 2018)--increasingly reliant on robotic guidance and capped by the coil geometry. Multichannel TMS (mTMS) instead steers the E-field electronically via independent currents in several coils, opening a design space of high variability without physical repositioning. We adapt determinant-based sequence optimization from discrete sTMS coil-placement sets to the continuous mTMS current space (D-optimal design), identifying pulse sequences whose induced cortical E-fields are as mutually dissimilar as biophysical constraints allow. We benchmarked optimized mTMS sequences against random baselines and optimized sTMS placements in virtual motor mapping across multiple head models, assessing three mTMS array geometries (5-channel planar, 6- and 12-channel spherical), two figure-of-eight sTMS coils, and varying pulse counts, response noise, and cortical depth. D-optimal mTMS currents substantially outperformed random currents and optimized sTMS at matched pulse counts. The gain was modest without noise but increased significantly with it: at the highest noise level, optimized sTMS failed to converge after 100 pulses (~20-22 mm error), whereas all mTMS arrays reached median errors at or below 6 mm. mTMS also recovered deep targets better than sTMS (up to 35 mm skin-cortex distance, versus 25 mm) and performed uniformly across the region of interest. A coil-space scheme based only on the magnetic vector potential, precomputable once per array without per-subject MRI, captured most of the benefit, matching subject-specific optimization at 100 pulses. mTMS thus makes voxel-wise mapping robust throughout a region of interest without coil repositioning.

neuroscience↗

bioRxiv2023

Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Cienegas Basin, Mexico

The sheer diversity of unculturable viruses has prompted the need to describe new viruses through culture-independent techniques. The associated host is one important phenotypic feature that can be inferred from metagenomic viral contigs -- thanks to the development of various bioinformatic tools. Here we compare the performance of recently developed tools for virus-host prediction on a dataset of 1,046 virus-host pairs and then apply the best-performing tools on a metagenomic dataset derived from a highly diverse transiently hypersaline site known as Archaean Domes within the Cuatro Cienegas Basin, Coahuila, Mexico. We also introduce a virus-host prediction tool called CrisprCustomDB, which uses specific criteria to solve controversial host assignments with custom spacers databases. Host-dependent alignment-based methods showed an average precision of 83% and a sensitivity from 13.7% to 17.7%, whereas host-dependent alignment-free methods achieved an average precision of 75.7% and a sensitivity of 57.5%. RaFAH, a virus-dependent alignment-based tool, had the best performance overall (F1_score = 95.7%). However, when applied to the highly diverse metagenomic dataset, the host-dependent alignment-based (e.g., CrisprCustomDB) and alignment-free (e.g., PHP) methods showed the greatest agreement with each other, even though they are fundamentally different methods. This is because instead of depending on known hosts or viruses-with-known-host databases, they can directly relate metagenomic viral contigs and metagenome-assembled genomes from the same dataset. Such methods also showed the greatest consistency between the source environment and the predicted host taxonomy, habitat, lifestyle, or metabolism, revealing that Archaean Domes viruses likely infect halophilic Archaea as well as a variety of Bacteria which may be halophilic, halotolerant, alkaliphilic, thermophilic, oligotrophic, sulfate-reducing or marine-related. Consequently, using a combination of methods and qualitative validations relating to the source environment and the predicted host biology will increase the number of correct predictions, mainly when dealing with novel viruses.

bioinformatics↗

bioRxiv2023

Unveiling Local Radiation Events through Metagenome Assembled Genomes of Archaea and Bacteria in Hypersaline Microbial Mats from the Archean Domes Site, Cuatro Cienegas, Coahuila, Mexico

A comprehensive study was conducted in the Cuatro Cienegas Basin (CCB) in Coahuila, Mexico, known for its remarkable microbiological diversity and unique physicochemical properties. The ''Archaean Domes '' (DA) in the CCB are hypersaline, non-lithifying microbial mats. This study focused on analyzing the small domes and circular structures formed in DA through metagenome assembly genomes (MAGs) with the aim of finding new microorganisms and providing information on the tree of life in a place as diverse as the CCB. In total, 329 MAGs were identified, including 52 archaea and 277 bacteria. Remarkably, 30 Archaea and 154 Bacteria could not be classified at the genus level, highlighting the remarkable diversity of CCB. The CCBs showed significant diversity at the phylum level, with Proteobacteria being the most abundant, followed by Euryarchaeota, Firmicutes, Bacteroidetes, Actinobacteria, Cyanobacteria, Spirochaetes, Chloroflexi, Planctomycetes, Candidatus Parvarchaeota, Verrucomicrobia, Balneolaeota, Nitrospirae, and Tenericutes. Subsequently, the MAGs were classified into a phylogenetic tree. In Archaea, monophyletic groups MAGs belonged to the phyla Archaeoglobi, Candidatus Aenigmarchaeota, Candidatus Nanoarchaeota, Candidatus Lokiarchaeota, and Halobacteriota. Among the Bacteria, monophyletic groups were identified as well, including Spirochaetes, Proteobacteria, Planctomycetota, Actinobacteria, Verrucomicrobiota, Bacteroidetes, Bipolaricaulota, Desulfobacterota, and Cyanobacteria. These monophyletic clusters may indicate radiation events that are likely influenced by geographical isolation as well as extreme environmental conditions reported in AD pond like phosphorus deficiency (122:42:1 C:N:P), fluctuating pH and a salinity of 5.28%

microbiology↗

bioRxiv2022

Metagenomic insight into taxonomic composition, environmental filtering, and functional redundancy for shaping worldwide modern microbial mats

Although microbial mats are considered relictual communities that are nowadays mostly constrained in their distribution by predation and phosphorus availability, they are still found in a wide range of environmental conditions. Their ancestral history, geographical isolation, stratified community composition and interspecies dynamics make them an interesting model to study community ecological processes and concepts. In this study, we analyzed different metagenomic datasets from worldwide modern microbial mats to compare community structure and functions. We found significant differentiation in both alpha and beta diversity of taxonomic and functional categories without significant correlation with temperature and pH. Differences depended more on the presence of very highly abundant cyanobacteria and some generalist microorganisms. Our results suggest that there is more than just Grinnellian niche dynamics in the determination of microbial mat community assembly, opening the hypothesis of interactions as the driver behind these ancient communities. We also discuss the influence of niche dynamics and environmental filtering in the community assembly of microbial mats.

ecology↗

bioRxiv2022

Taxonomic, genomic, and functional variation in the gut microbiomes of wild spotted hyenas across two decades of study

The gut microbiome provides vital functions for mammalian hosts, yet research on the variability and function of the microbiome across adult lifespans and multiple generations is limited in large mammalian carnivores. Here we use 16S rRNA gene and metagenomic sequencing to profile the taxonomic composition, genomic diversity, and metabolic function of the gut microbiome of 12 wild spotted hyenas (Crocuta crocuta) residing in the Masai Mara National Reserve, Kenya over a 23-year period spanning three generations. We determined the extent to which host factors predict variation in the gut microbiome and identify the core microbes present in the guts of hyenas. We also investigate novel genomic diversity in the mammalian gut by reporting the first metagenome-assembled genomes (MAGs) for hyenas. We found that gut microbiome taxonomic composition was highly variable across the two decades of sampling, but despite this, a core set of 14 bacterial genera and 19 amplicon sequence variants were identified. The strongest predictors of microbiome alpha and beta-diversity were host identity and age, suggesting that hyenas possess individualized microbiomes, and that these may change with age during adulthood. Gut microbiome functional profiles were also individual-specific, and were moderately correlated with antelope prey abundance, indicating that the functions of the gut microbiome vary with host diet. We recovered 149 high-quality MAGs from the hyena gut, spanning 25 bacterial orders and 51 genera. Some MAGs were classified as taxa previously reported for other carnivores, but many were novel and lacked species level matches to genomes in existing reference databases. ImportanceThere is a gap in knowledge regarding the genomic diversity and variation of the gut microbiome across a hosts lifespan and across multiple generations of hosts in wild mammals. Using two types of sequencing approaches, we demonstrate that although gut microbiomes are individualized and temporally variable among hyenas, they correlate similarly to large-scale changes in their hosts ecological environment. We also recovered 149 high-quality MAGs from the hyena gut, greatly expanding the microbial genome repertoire known for hyenas, carnivores and wild mammals in general. Some MAGs came from genera abundant in the gastrointestinal tracts of canid species and other carnivores but over 80% of MAGs were novel and from species previously not represented in genome databases. Collectively, our novel body of work illustrates the importance of surveying the gut microbiome of non-model wild hosts, using multiple sequencing methods and computational approaches, and at distinct scales of analysis.

microbiology↗

bioRxiv2021

Modern microbial mats from the Chihuahuan Desert provide insights into ecological stability throughout Earth's history

Microbial mats are complex ecological assemblages that are found in the Precambrian fossil record and in extant extreme environments. Hence, these structures are regarded as highly stable ecosystems. In this work, we assess the ecological stability in a modern, fluctuating, hypersaline pond from the Cuatro Cienegas Basin. From the 2016 to 2019 metagenomic sampling of this site, we found that this microbial site is sensitive to disturbances, which leads to high taxonomic replacement. Additionally, the mats have shown to be functionally stable throughout time, and could be differentiated between dry and rainy seasonal states. We speculate that this microbial system could represent modern analogs of ancient microbial mats where functions were preserved over time, whereas composition was subject to diversification in the face of local and planetary perturbations.

ecology↗

bioRxiv2021

Ecological relevance of abundant and rare taxa in a high-diverse elastic hypersaline microbial mat, using a small-scale sampling

We evaluated the microbial diversity and metabolome profile of an uncommon hypersaline elastic microbial mat from Cuatro Cienegas Basin (CCB) in the Chihuahuan Desert of Coahuila, Mexico. We collected ten samples on a small scale transect (1.5-meters) and described its microbial diversity through NGS-based ITS and 16S rDNA gene sequencing. A very low number of taxa comprised a considerable proportion of the mat and were shared across all sampling points, whereas the rare biosphere was more phylogenetically diverse (Faiths Phylogenetic Diversity (FPD) index) and phylogenetically disperse (using a null model distribution of Phylogenetic Species Clustering (nmdPSC)) than the abundant (high read count) taxa for both analyzed libraries. We also found a distinctive metabolome profile for each sample and were able to tentatively annotate several classes of compounds with relevant biological properties.

microbiology↗

bioRxiv2019

Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria

Dimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton, is predominantly degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: 1) a recent common ancestor of DmdA and GcvT, 2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and 3) pre-adapted enzymes to DMSP prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to exposition to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur rich atmosphere and anoxic ocean, compared to recent Roseobacter ecoparalogs (copies performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

evolutionary biology↗

bioRxiv2019

Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation.

BackgroundIn bacteria, pan-genomes are the result of the evolutionary \"tug of war\" between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size, resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Cienegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes.\n\nResultsWe obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high effective population size (Ne) estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low Ne, suggesting a recent origin. The recombination and mutation estimators (r/m) ranged from 0.0052 to 2.7249, which are similar to oceanic Vibrionaceae estimations; however, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation purging the genomes and keeping closed pan-genome patterns. Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes under this SNPs were related to sodium transport.\n\nConclusionsDifferent lines of evidence suggest that the sampled Vibrionaceae, are part of the rare biosphere usually living under famine conditions. Two of these lineages were reported by the first time. Most Vibrionaceae lineages of CCB are adapted to their microhabitats rather than to the sampled environments. This pattern of adaptation agrees with the association of closed pan-genomes and local adaptation.

evolutionary biology↗

bioRxiv2019

Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment

Several universal genomic traits affect the capacity, cost, and efficiency of biochemical information processing underpinning metabolism and reproduction. We analyzed their role in mediating planktonic microbial community responses to nutrient enrichment in an oligotrophic, phosphorus-deficient pond in Cuatro Cienegas, Mexico--one of the first whole-ecosystem experiments involving replicated metagenomic assessments. As predicted assuming oligotrophy favors lower information-processing costs whereas copiotrophy favors higher processing rates, mean bacteria genome size was higher in the fertilized treatment, as were GC content, total number of tRNA genes, total number of rRNA genes and codon usage bias in ribosomal protein sequences. However, contrasting changes in trait variances also suggested differences between traits in mediating assembly under oligotrophic versus copiotrophic conditions. Tradeoffs in information-processing traits are apparently sufficiently pronounced to play a role in community assembly and all different components of metabolism-- information, energy, and nutrient requirements--are fine-tuned to an organisms growth and trophic strategy.

ecology↗

bioRxiv2018

The lost world of Cuatro Cienegas Basin, a relictual bacterial niche in a desert oasis.

Barriers to immigration can lead to localized adaptive radiations and increased endemism. We propose that extreme oligotrophy can be a strong barrier to immigration over geological timescales, and facilitate the evolution of diverse and coevolved microbial communities. We show here that the endangered oasis of Cuatro Cienegas Basin can be a model for a lost world, where the ancient niche of extreme oligotrophy favoured survival of ancestral microorganisms that persisted due to environmental stability and low extinction rates, generating a diverse and unique bacteria diversity. Diversification/extinction rates in Bacillus showed several CCB endemic clades that diverged from the rest of Bacillus spp. in different times of the Paleozoic and Mesozoic, in contrast to more recent Bacillus, Clostridium and Bacteroidetes lineages. CCB conservation is vital to the understanding of early evolutionary and ecological processes.

evolutionary biology↗

bioRxiv2017

MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle

BACKGROUNDThe increasing number of metagenomic and genomic sequences has dramatically improved our understanding of microbial diversity, yet our ability to infer metabolic capabilities in such datasets remains challenging.\n\nFINDINGSWe describe the Multigenomic Entropy Based Score pipeline (MEBS), a software platform designed to evaluate, compare and infer complex metabolic pathways in large omic datasets, including entire biogeochemical cycles. MEBS is open source and available through https://github.com/eead-csic-compbio/metagenome_Pfam_score. To demonstrate its use we modeled the sulfur cycle by exhaustively curating the molecular and ecological elements involved (compounds, genes, metabolic pathways and microbial taxa). This information was reduced to a collection of 112 characteristic Pfam protein domains and a list of complete-sequenced sulfur genomes. Using the mathematical framework of relative entropy (H), we quantitatively measured the enrichment of these domains among sulfur genomes. The entropy of each domain was used to both: build up a final score that indicates whether a (meta)genomic sample contains the metabolic machinery of interest and to propose marker domains in metagenomic sequences such as DsrC (PF04358). MEBS was benchmarked with a dataset of 2,107 non-redundant microbial genomes from RefSeq and 935 metagenomes from MG-RAST. Its performance, reproducibility, and robustness were evaluated using several approaches, including random sampling, linear regression models, Receiver Operator Characteristic plots and the Area Under the Curve metric (AUC). Our results support the broad applicability of this algorithm to accurately classify (AUC=0.985) hard to culture genomes (e.g., Candidatus Desulforudis audaxviator), previously characterized ones and metagenomic environments such as hydrothermal vents, or deep-sea sediment.\n\nCONCLUSIONSOur benchmark indicates that an entropy-based score can capture the metabolic machinery of interest and be used to efficiently classify large genomic and metagenomic datasets, including uncultivated/unexplored taxa

bioinformatics↗

bioRxiv2017

A new multi-genomic approach for the study of biogeochemical cycles at global scale: the molecular reconstruction of the sulfur cycle

Despite the great advances in microbial ecology and the explosion of high throughput sequencing, our ability to understand and integrate the global biogeochemical cycles is still limited. Here we propose a novel approach to summarize the complexity of the Sulfur cycle based on the minimum ecosystem concept, the microbial mat model and the relative entropy of protein domains involved in S-metabolism. This methodology produces a single value, called the Sulfur Score (SS), which informs about the specific S-related molecular machinery. After curating an inventory of microorganisms, pathways and genes taking part in this cycle, we benchmark the performance of the SS on a collection of 2,107 non-redundant RefSeq genomes, 900 metagenomes from MG-RAST and 35 metagenomes analyzed for the first time. We find that the SS is able to correctly classify microorganisms known to be involved in the S-cycle, yielding an Area Under the ROC Curve of 0.985. Moreover, when sorting environments the top-scoring metagenomes were hydrothermal vents, microbial mats and deep-sea sediments, among others. This methodology can be generalized to the analysis of other biogeochemical cycles or processes. Provided that an inventory of relevant pathways and microorganisms can be compiled, entropy-based scores could be used to detect environmental patterns and informative samples in multi-genomic scale.

bioinformatics↗