Biology subjects

Kalmar, L.

Publications and source records attributed to Kalmar, L..

3 recordsLinked to original sources

bioRxiv2023

Gut microbiome remains stable following COVID-19 vaccination in healthy and immuno-compromised individuals

The bidirectional interaction between the immune system and the gut microbiota is a key contributor to various host physiological functions. Immune-associated diseases such as cancer and autoimmunity, as well as the efficacy of immunomodulatory therapies, have been linked to microbiome variation. While COVID-19 infection has been shown to cause microbial dysbiosis, it remains understudied whether the inflammatory response associated with vaccination also impacts the microbiota. Here, we investigate the temporal impact of COVID-19 vaccination on the gut microbiome in healthy and immuno-compromised individuals; the latter included patients with primary immunodeficiency and cancer patients on immunomodulating therapies. We find that the gut microbiome remained remarkably stable post-vaccination irrespective of diverse immune status, vaccine response, and microbial composition spanned by the cohort. The stability is evident at all evaluated levels including diversity, phylum, species, and functional capacity. Our results indicate the resilience of the gut microbiome to host immune changes triggered by COVID-19 vaccination and suggest minimal, if any, impact on microbiome-mediated processes. These findings encourage vaccine acceptance, particularly when contrasted with the significant microbiome shifts observed during COVID-19 infection.

microbiology↗

bioRxiv2021

HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities.

Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli. Author SummaryAntimicrobial resistance (AMR) is one of the biggest global health threats humanity is facing. Understanding the emergence and spread of AMR between different bacterial species is crucial for the development of effective countermeasures. In this paper we describe a user-friendly, affordable and comprehensive (laboratory and bioinformatics) workflow that is able to identify, associate and track AMR genes in bacteria. We demonstrate the efficiency and reliability of the method by comparing 50 faecal microbiomes from pig farms with high-antibiotic use (conventional farms), and 50 faecal microbiomes from pig farms with low-antibiotic use (organic farms). Our method provides a novel approach to resistance gene tracking, that also leads to the generation of high quality metagenomic assembled genomes that includes genes on mobile genetic elements, such as plasmids, that would not otherwise be included in these assembled genomes.

bioinformatics↗

bioRxiv2021

Fluctuating environment can negate cheater success due to speed-agility trade-off

Stability of microbial cooperation through common goods is susceptible to cheating. Evidence suggests that cheating plays a less prominent role in many natural systems than hitherto predicted by models of eco-evolutionary dynamics and evolutionary game theory. While several cheater negating factors such as spatial segregation have been identified, most consider single-nutrient regimes. Here we propose a cheater-suppressing mechanism based on previous experimental observations regarding the biochemical trade-off between growth speed and delay in switching to alternative nutrients. As changing the nutrient source requires redistribution of enzymatic resources to different metabolic pathways, the advantage in speed is offset by lower agility due to longer time required for resource re-allocation. Using an in silico model system of sucrose utilisation by Saccharomyces cerevisiae, we find that a tradeoff between growth rate and diauxic lag duration can supress cheaters under fluctuating nutrient availability and thereby stabilise cooperation. The resulting temporal dynamics constrain cheaters despite their competitive benefit for the growth on the primary nutrient via avoided public goods synthesis costs. We further show that this speed-agility trade-off can function in synergy with spatial segregation to avoid the collapse of the community due to the cheaters. Taken together, the growth-agility trade-off may contribute to cheater suppression in microbial ecosystems experiencing fluctuating environments, such as plant root microbiota and gut microbiota.

ecology↗