Biology subjects

Kurt, Z.

Publications and source records attributed to Kurt, Z..

3 recordsLinked to original sources

bioRxiv2018

Host Genetic Background and Gut Microbiota Contribute to Differential Metabolic Responses to High Fructose Consumption in Mice

BackgroundIt is unclear how high fructose consumption induces disparate metabolic responses in genetically diverse mouse strains. ObjectiveWe aim to investigate whether the gut microbiota contributes to differential metabolic responses to fructose. MethodsEight-week-old male C57BL/6J (B6), DBA/2J (DBA), and FVB/NJ (FVB) mice were given 8% fructose solution or regular water (control) for 12 weeks. The gut microbiota composition in cecum and feces was analyzed using 16S rDNA sequencing, and PERMANOVA was used to compare community across mouse strains, treatments, and time points. Microbiota abundance was correlated with metabolic phenotypes and host gene expression in hypothalamus, liver and adipose tissues using Biweight midcorrelation. To test the causal role of the gut microbiota in determining fructose response, we conducted fecal transplants from B6 to DBA mice and vice versa for 4 weeks, as well as gavaged antibiotic-treated DBA mice with Akkermansia for 9 weeks, accompanied with or without fructose treatment. ResultsCompared to B6 and FVB, DBA mice had significantly higher Firmicutes/Bacteroidetes ratio and lower baseline levels of Akkermansia and S24-7 (P < 0.05), accompanied by metabolic dysregulation after fructose consumption. Fructose altered specific microbial taxa in individual mouse strains, such as a 7.27-fold increase in Akkermansia in B6 and 0.374-fold change in Rikenellaceae in DBA (FDR < 5%), which demonstrated strain-specific correlations with host metabolic and transcriptomic phenotypes. Fecal transplant experiments indicated that B6 microbes conferred resistance to fructose-induced weight gain in DBA mice (F = 43.1, P < 0.001), and Akkermansia colonization abrogated the fructose-induced weight gain (F = 17.8, P <0.001) and glycemic dysfunctions (F = 11.8, P = 0.004) in DBA mice. ConclusionsOur findings support that differential microbiota composition between mouse strains is partially responsible for host metabolic sensitivity to fructose, and that Akkermansia is a key bacterium that confers resistance to fructose-induced metabolic dysregulation.

systems biology↗

bioRxiv2018

Microbial Diversity in a Military Impacted Lagoon (Vieques, Puerto Rico) as Revealed by Metagenomics

The Anones Lagoon, located in the island municipality of Vieques, Puerto Rico (PR), received extensive bombing during military practices by the US Navy for decades. After military activities ceased in 2003, the bombing range was designated as part of a larger Superfund site by US EPA. Here, we employed shotgun metagenomic sequencing to investigate how microbial communities responded to pollution by heavy metals and explosives at this lagoon. Sediment samples (0-5 cm) from Anones were collected in 2005 and 2014 and compared to samples from two reference lagoons, i.e., Guaniquilla, Cabo Rojo (a natural reserve) and Condado, San Juan (PRs capital city). Consistent with selection under low anthropogenic impacts, Guaniquilla exhibited the highest degree of diversity with lower frequency of genes related to xenobiotics metabolism among the three lagoons. Notably, a clear shift was observed in Anones, with Euryarchaeota becoming enriched (9% of total) and a concomitant increase in community diversity, by about one order of magnitude, after almost 10 years without bombing activities. In contrast, genes associated with explosives biodegradation and heavy metal transformation significantly decreased in abundance in Anones 2014 (by 91.5%). Five unique population genomes were recovered from the Anones 2005 sample that encoded genetic determinants implicated in biodegradation of contaminants. Collectively, these results provided new insights into the natural attenuation of explosive contaminants by the benthic microbial communities of the Anones lagoon and could serve as reference points to enhance bioremediation actions at this site and for assessing other similarly impacted sites.\n\nImportanceThis study represents the first assessment of the benthic microbial community in the Anones Lagoon in Vieques, Puerto Rico after the impact of intense pollution by bombs and unconventional weapons during military training exercises. Evaluating the microbial diversity of Anones, represents an opportunity to assess the microbial succession patterns during the active process of natural attenuation of pollutants. The culture-independent techniques employed to study these environmental samples allowed the recovery of almost complete genomes of several abundant species that were likely involved in the biodegradation of pollutants and thus, represented species responding to the strong selection pressure posed by military activities. Further, our results showed that natural attenuation has proceeded to a great extend ten years after the cease of military activities.

microbiology↗

bioRxiv2017

DepEst: an R package of important dependency estimators for gene network inference algorithms

Gene network inference algorithms (GNI) are popular in bioinformatics area. In almost all GNI algorithms, the main process is to estimate the dependency (association) scores among the genes of the dataset.\n\nWe present a bioinformatics tool, DepEst (Dependency Estimators), which is a powerful and flexible R package that includes 11 important dependency score estimators that can be used in almost all GNI Algorithms. DepEst is the first bioinformatics package that includes such a large number of estimators that runs both in parallel and serial.\n\nDepEst is currently available at https://github.com/altayg/Depest. Package access link, instructions, various workflows and example data sets are provided in the supplementary file.

bioinformatics↗