Biology subjects

Ozkurt, E.

Publications and source records attributed to Ozkurt, E..

5 recordsLinked to original sources

bioRxiv2026

Enriching the Human Stool Microeukaryotes for Shotgun Sequencing

The human gut microbiome harbours a diverse community of microeukaryotes, predominantly fungi, which may potentially play important roles in gut ecology and homeostasis. Despite their potential, the study of gut microeukaryotes has been hampered by the limited sensitivity of standard sequencing approaches, which struggle to capture DNA from low-abundance microorganisms against the overwhelming background of bacterial biomass. To address this, we developed a method to selectively enrich for microeukaryotic cells in human faecal samples by depleting bacterial cells prior to metagenomic sequencing. Through systematic comparison and optimisation at each processing step, we established a robust standard operating procedure (SOP) for microeukaryotic cell enrichment. By benchmarking this SOP across eight human faecal samples with three technical replicates each, we showed that it consistently increased microeukaryote representation in metagenomic libraries, greater microeukaryotic taxonomic diversity, and a reduced proportion of unclassified taxa. Together, these improvements enabled substantially deeper characterisation of the microeukaryotic fraction of the human gut microbiome.

microbiology↗

bioRxiv2024

Ecological assembly dynamics of the seed-borne microbiome in cultivated and wild wheat

BackgroundPlants host diverse microbial communities that can significantly impact plant health. A portion of these communities is vertically transmitted to the next generation through seeds, influencing early plant development. While seed microbiota composition is known to be shaped by environmental, genetic, and stochastic factors, detailed insights into the factors that govern variation within and between plants of the same species remain limited. Furthermore, the dynamic of the vertically-transmitted microbes and their mode of host colonization are poorly understood. ResultsIn this study, we characterized the bacterial communities of multiple seeds originating from the same spike of adult wheat plants and demonstrated a high extent of homogeneity in the composition of microorganisms. We propagated wheat seedlings under controlled conditions to monitor host colonization by these microorganisms. Intriguingly, in spite of a relatively homogeneous composition of bacteria in individual seeds, the microbes colonizing early-stage seedlings, particularly during their initial leaf development, vary extensively, even among seedlings of seeds from the same spike. Applying a neutral assembly model, we show that the transmission of microbiomes from seeds to seedlings is primarily governed by selective processes, whereas post-transmission microbial assembly in seedlings is governed by stochastic events. ConclusionsOverall, this study introduces a novel experimental approach for investigating microbiome inheritance in plants. By leveraging high replication of seeds from the same wheat plant and field, we provide new insights into the stochastic nature of seed-associated microbiome composition and transmission in wheat.

microbiology↗

bioRxiv2023

A single dietary factor, daily consumption of a fermented beverage, can modulate the gut microbiome within the same ethnic community

In this study, the impact of traditional rice-based fermented alcoholic beverages (Apong) on the gut microbiome and health of the Mishing community in India was examined. Two groups that consumed one of these beverages were compared to a control group that did not consume either beverage. Gut microbial composition was analyzed by sequencing 16S rRNA of fecal metagenomes and analyzing untargeted fecal metabolites, and short-chain fatty acids (SCFAs). We also collected data on anthropometric measures and serum biochemical markers. Our results showed that Apong drinkers had higher blood pressure, but lower blood glucose and total protein levels than other non-drinkers. Also, gut microbiome composition was found to be affected by the choice of Apong, with Apong drinkers having a more diverse and distinct microbiome compared to non-drinkers. Apong drink type or being a non-drinker explained even a higher variation of fecal metabolome composition than microbiome composition and Apong drinkers had lower levels of the SCFA isovaleric acid than non-drinkers. Overall, this study shows that a single dietary factor can significantly impact the gut microbiome of a community and highlights the potential role of traditional fermented beverages in maintaining gut health.

microbiology↗

bioRxiv2021

LotuS2: An ultrafast and highly accurate tool for amplicon sequencing analysis

BackgroundAmplicon sequencing is an established and cost-efficient method for profiling microbiomes. However, many available tools to process this data require both bioinformatics skills and high computational power to process big datasets. Furthermore, there are only few tools that allow for long read amplicon data analysis. To bridge this gap, we developed the LotuS2 (Less OTU Scripts 2) pipeline, enabling user-friendly, resource friendly, and versatile analysis of raw amplicon sequences. ResultsIn LotuS2, six different sequence clustering algorithms as well as extensive pre- and post-processing options allow for flexible data analysis by both experts, where parameters can be fully adjusted, and novices, where defaults are provided for different scenarios. We benchmarked three independent gut and soil datasets, where LotuS2 was on average 29 times faster compared to other pipelines - yet could better reproduce the alpha- and beta-diversity of technical replicate samples. Further benchmarking a mock community with known taxa composition showed that, compared to the other pipelines, LotuS2 recovered a higher fraction of correctly identified genera and species (98% and 57%, respectively). At ASV/OTU level, precision and F-score were highest for LotuS2, as was the fraction of correctly reconstructed 16S sequences. ConclusionLotuS2 is a lightweight and user-friendly pipeline that is fast, precise and streamlined. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. AvailabilityLotuS2 is available from GitHub, conda or via a Galaxy web interface, documented at http://lotus2.earlham.ac.uk/.

bioinformatics↗

bioRxiv2019

Higher stochasticity of microbiota composition in seedlings of domesticated wheat compared to wild wheat

Plants constitute an ecological niche for microbial communities that colonize different plant tissues and explore the plant habitat for reproduction and dispersal. The association of microbiota and plant may be altered by ecological and evolutionary changes in the host population. Seedborne microbiota, expected to be largely vertically-transferred, have the potential to co-adapt with their host over generations. Reduced host diversity because of strong directional selection and polyploidization during plant domestication and cultivation may have impacted the assembly and transmission of seed-associated microbiota. Nonetheless, the effect of plant domestication on the diversity of their associated microbes is poorly understood. Here we show that microbial communities in domesticated wheat, Triticum aestivum, are less diverse but more inconsistent among individual plants compared to the wild wheat species, T. dicoccoides. We found that diversity of microbes in seeds overall is low, but comparable in different wheat species, independent of their genetic and geographic origin. However, the diversity of seedborne microbiota that colonize the roots and leaves of the young seedling is significantly reduced in domesticated wheat genotypes. Moreover, we observe a higher variability between replicates of T. aestivum suggesting a stronger effect of chance events in microbial colonization and assembly. We also propagated wild and domesticated wheat in two different soils and found that different factors govern the assembly of soil-derived and seedborne microbial communities. Overall, our results demonstrate that the role of stochastic processes in seedborne microbial community assembly is larger in domesticated wheat compared to the wild wheat. We suggest that the directional selection on the plant host and polyploidization events during domestication may have decreased the degree of wheat-microbiota interactions and consequently led to a decreased stable core microbiota.

microbiology↗