Biology subjects

Kevorkian, R.

Publications and source records attributed to Kevorkian, R..

3 recordsLinked to original sources

bioRxiv2024

Time resolved multi-omics reveals diverse metabolic strategies of Salmonella during diet-induced inflammation

With a rise in antibiotic resistance and chronic infection, the metabolic response of Salmonella enterica serovar Typhimurium to various dietary conditions over time remains an understudied avenue for novel, targeted therapeutics. Elucidating how enteric pathogens respond to dietary variation not only helps us decipher the metabolic strategies leveraged for expansion but also assists in proposing targets for therapeutic interventions. Here, we use a multi-omics approach to identify the metabolic response of Salmonella enterica serovar Typhimurium in mice on both a fibrous diet and high-fat diet over time. When comparing Salmonella gene expression between diets, we found a preferential use of respiratory electron acceptors consistent with increased inflammation of the high-fat diet mice. Looking at the high-fat diet over the course of infection, we noticed heterogeneity of samples based on Salmonella ribosomal activity, which separated into three infection phases: early, peak, and late. We identified key respiratory, carbon, and pathogenesis gene expression descriptive of each phase. Surprisingly, we identified genes associated with host-cell entry expressed throughout infection, suggesting sub-populations of Salmonella or stress-induced dysregulation. Collectively, these results highlight not only the sensitivity of Salmonella to its environment but also identify phase-specific genes that may be used as therapeutic targets to reduce infection. ImportanceIdentifying novel therapeutic strategies for Salmonella infection that occur in relevant diets and over time is needed with the rise of antibiotic resistance and global shifts towards Western diets that are high in fat and low in fiber. Mice on a high-fat diet are more inflamed compared to those on a fibrous diet, creating an environment that results in more favorable energy generation for Salmonella. Over time on a high-fat diet, we observed differential gene expression across infection phases. Together, these findings reveal the metabolic tuning of Salmonella to dietary and temporal perturbations. Research like this, exploring the dimensions of pathogen metabolic plasticity, can pave the way for rationally designed strategies to control disease.

microbiology↗

bioRxiv2020

Evidence for a growth zone for deep subsurface microbial clades in near-surface anoxic sediments

Global marine sediments harbor a large and highly diverse microbial biosphere, but the mechanism by which this biosphere is established during sediment burial is largely unknown. During burial in marine sediments, concentrations of easily-metabolized organic compounds and total microbial cell abundance decrease steadily. However, it is unknown whether some microbial clades increase with depth, despite the overall trend of abundance decrease. We show total population increases in 38 microbial families over 3 cm of sediment depth in the upper 7.5 cm of White Oak River (WOR) estuary sediments. Clades that increased with depth were more often anaerobic, uncultured, or common in deep marine sediments relative to those that decreased. Minimum turnover times (which are minimum in situ doubling times of growth rates) were estimated to be 2-25 years by combining sedimentation rate with either quantitative PCR (qPCR) or the product of the Fraction Read Abundance of 16S rRNA genes and total Cell counts (FRAxC). Turnover times were within an order of magnitude of each other in two adjacent cores, as well as in two laboratory enrichments of Cape Lookout Bight (CLB), NC, sediments (average difference of 28 {+/-} 19%). qPCR and FRAxC in WOR cores and FRAxC in CLB incubations produced similar turnover times for key deep subsurface uncultured clades Bathyarchaeota (8.7 {+/-} 1.9 years) and Thermoprofundales/MBG-D (4.1 {+/-} 0.7 years). We conclude that common deep subsurface microbial clades experience a narrow zone of growth in shallow sediments, offering an opportunity for natural selection of traits for long-term subsistence after resuspension events. Significance statementThe current dogma is that the deeply-branching uncultured microbes that dominate global marine sediments do not actually increase in population size as they are buried in marine sediments - rather they exist in a sort of prolonged torpor for thousands of years. This is because no evidence has ever been found that these clades actually increase population sizes, or grow, as they are gradually buried. We discovered that they actually do increase population sizes during burial, but only in the upper few centimeters. This changes our dogma about marine sediments as a vast repository of non-growing microbes, to a vast repository of non-growing microbes with a thin and relatively rapid area of growth in the upper 10 centimeters.

microbiology↗

bioRxiv2020

ANME-1 archaea drive methane accumulation and removal in estuarine sediments

Uncultured members of the Methanomicrobia called ANME-1 perform the anaerobic oxidation of methane (AOM) through a process that uses much of the methanogenic pathway. It is unknown whether ANME-1 obligately perform AOM, or whether some of them can perform methanogenesis when methanogenesis is exergonic. Most marine sediments lack advective transport of methane, so AOM occurs in the sulfate methane transition zone (SMTZ) where sulfate-reducing bacteria consume hydrogen produced by fermenters, making hydrogenotrophic methanogenesis exergonic in the reverse direction. When sulfate is depleted deeper in the sediments, hydrogen accumulates making hydrogenotrophic methanogenesis exergonic, and methane accumulates in the methane zone (MZ). In White Oak River estuarine sediments, we found that ANME-1 comprised 99.5% of 16S rRNA genes from amplicons and 100% of 16S rRNA genes from metagenomes of the Methanomicrobia in the SMTZ and 99.9% and 98.3%, respectively, in the MZ. Each of the 16 ANME-1 OTUs (97% similarity) had peaks in the SMTZ that coincided with peaks of putative sulfate-reducing bacteria Desulfatiglans sp. and SEEP-SRB1. In the MZ, ANME-1, but no putative sulfate-reducing bacteria or cultured methanogens, increased with depth. Using publicly available data, we found that ANME-1 was the only group expressing methanogenic genes during both net AOM and net methanogenesis in an enrichment. The commonly-held belief that ANME-1 perform AOM is based on the fact that they dominate natural settings and enrichments where net AOM is measured. We found that ANME-1 also dominate natural settings and enrichment where net methanogenesis is measured, so we conclude that ANME-1 perform methane production. Alternating between AOM and methanogenesis, either in a single ANME-1 cell or between different subclades with similar 16S rRNA sequences of ANME-1, may confer a competitive advantage, explaining the predominance of low-energy adapted ANME-1 in methanogenic sediments worldwide. Abstract ImportanceLife may operate differently at very low energy levels. Natural populations of microbes that make methane survive on some of the lowest energy yields of all life. From all available data, we infer that these microbes alternate between methane production and oxidation, depending on which process is energy-yielding in the environment. This means that much of the methane produced naturally in marine sediments occurs through an organism that is also capable of destroying it under different circumstances.

microbiology↗