Biology subjects

Victor, M.

Publications and source records attributed to Victor, M..

4 recordsLinked to original sources

bioRxiv2025

From Diversity to Dominance: How Salt and CO2 Shape LAB-dominated Ecosystems in Vegetable Fermentations

Research on microbial ecosystems is often challenging due to high diversity of microbial taxa present and the complexity of controlling environmental variables. To address these challenges, fermented foods are simpler and more reproducible model ecosystems, where both community composition and environmental factors can be more precisely controlled and manipulated. In this study, we focused on fermented vegetables which are typically dominated by lactic acid bacteria (LAB). It is not completely understood why lactic acid bacteria (LAB) consistently drive the spontaneous fermentation of vegetables such as cabbage and carrots and how variables such as vegetable substrates, salt addition, and carbon dioxide levels can impact microbial community dynamics. Here, we explored the temporal microbial dynamics in standardized fermentations of 11 different vegetables (including beetroot, bell pepper, cabbage, carrot, cucumber, fennel, green asparagus, leek, parsnip, sunroot, and tomato), revealing a consistent dominance of Leuconostoc and other LAB. Additionally, we investigated the impact of varying salt concentrations, demonstrating that lower salt levels resulted in a delayed appearance of the typically dominant LAB community, while simultaneously revealing a higher abundance of Weissella and various Enterobacterales taxa. These effects imposed by reduced salt concentrations were mitigated by CO2 injection, which reverted the enhanced Enterobacterales levels and increased the overall abundance of Lactobacillales. This study demonstrates how targeted manipulation of environmental parameters, such as salinity and gas composition, can be used to uncover ecological principles governing microbial succession and community assembly in reproducible fermentation-based model ecosystems. ImportanceUnderstanding the ecological principles that shape microbial community assembly is essential for advancing our knowledge of microbial ecosystems. Fermented vegetables, increasingly popular among the general population, provide tractable and reproducible model systems to study microbial succession under controlled environmental conditions. By systematically manipulating variables such as vegetable type, salinity and gas composition, we uncovered the effect of these factors on the microbial dynamics throughout the fermentation. These insights not only contribute to a better understanding of the microbial ecology of these man-made food systems but also suggest directions for novel strategies to optimize fermentation processes for producing faster, safer, and more flavorful foods.

microbiology↗

bioRxiv2024

Identification of clinical carbapenemases, 478 novel β-lactamases and putative seven new bacterial phyla from wastewater contaminated high arctic fjord sediments.

Arctic microbiota is enigmatic and highly underexplored. With the aim of understanding the resistome and microbiota of high-Arctic fjord sediments and the effect of wastewater discharge on sediment microbiota, we analysed sediments using metagenomics. We show presence of 888 clinically relevant antibiotic resistance genes including genes coding resistance against last-resort antibiotics such as carbapenems, colistin, vancomycin, linezolid and tigecycline in sediment microbiota. Using computational models, 478 novel {beta}-lactamases belonging to 217 novel {beta}-lactamases families were revealed in sediment microbiota from Adventfjorden in Svalbard. We identified hosts for 69 novel gene families and showed that these genes are widespread in the Arctic environment. Further, in 644 metagenome-assembled genomes (MAGs) from sediment metagenomes >97% belong to novel taxa, representing seven putative novel phyla. These MAGs encoded important functions like nutrient cycling and methane metabolism etc. Our study demonstrated mixing of human associated bacteria and Arctic sediment microbiota. It provides the first comprehensive dataset of the distribution and diversity of novel microbes and {beta}-lactamases in the high Arctic sediments.

microbiology↗

bioRxiv2022

Parabolic avalanche scaling in the synchronization of cortical cell assemblies

Neurons in cortex synchronize their spiking in response to local and distant inputs. These synchronized assemblies are fundamental to cortex function, yet basic dynamical aspects about their size and duration are largely unknown. Using 2-photon imaging of neurons in superficial cortex of awake mice, we show that synchronized assemblies organize as scale-invariant avalanches that quadratically grow with duration. This quadratic expansion was found only for correlated neurons and required temporal coarse graining to compensate for spatial subsampling when network dynamics are critical, as demonstrated in simulations. The corresponding time course of an inverted parabola with exponent of {chi} = 2 described avalanches of up to 5 s duration and maximized temporal complexity in the ongoing activity of prefrontal and somatosensory cortex and in visual responses of primary visual cortex. Our results identify a scale-invariant order in the synchronization of highly diverse cortical cell assemblies in the form of parabolic avalanches. Significance StatementThe synchronization of cell assemblies is fundamental to many brain theories. Here we show such synchronization to grow according to an inverted parabola that maximizes temporal complexity. This quadratic scaling found for cell assemblies of highly diverse size and duration is in line with prediction for neuronal avalanches and the cortex being in a critical state.

neuroscience↗

bioRxiv2020

An in-silico study on SARS-CoV-2: Its compatibility with human tRNA pool, and the polymorphism arising in a single lineage over a month

SARS-CoV-2 has caused a global pandemic that has costed enormous human lives in the recent past. The present study is an investigation of the viral codon adaptation, ORFs stability and tRNA co-adaptation with humans. We observed that for the codon usage bias in viral ssRNA, ORFs have near values of folding free energies and codon adaptation index with mRNAs of the human housekeeping CDS. However, the correlation between the stability of the ORFs in ssRNA and CAI is stronger than the mRNA stability and CAI of HKG, suggesting a greater expression capacity of SARS-CoV-2. Mutational analysis reflects polymorphism in the virus for ORF1ab, surface glycoprotein and nucleocapsid phosphoprotein ORFs. Non-synonymous mutations have shown non-polar substitutions. Out of the twelve mutations nine are for a higher t-RNA copy number. Viruses in general have high mutation rates. To understand the chances of survival for the mutated SARS-CoV-2 we did simulation for synonymous mutations. It resulted in 50% ORFs with higher stability than their native equivalents. Thus, considering only the synonymous mutations the virus can exhibit a lot of polymorphism. Collectively our data provides new insights for SARS-CoV-2 mutations and the human t-RNA compatibility. SignificanceSurvivability of SARS-CoV-2 in humans is essential for its spread. It has overlapping genes exhibiting a high codon optimization with humans even after a higher codon usage bias. They seem to possess cognizance for high copy number t-RNA (cognate or near-cognate) in humans, while mutating. Even though, it has been well established that native transcripts posses the highest stability, our in-silico studies show that SARS-CoV-2 under mutations give rise to ORFs with higher stability. These results significantly present the viruss ability and the credibility of survival for the mutants. Despite its focus on a geographical location it explains the ongoing behavior of SARS-CoV-2 for a steady existence in humans as all the different lineages have a common origin. Wuhan, China.

bioinformatics↗