Biology subjects

Tyakht, A. V.

Publications and source records attributed to Tyakht, A. V..

9 recordsLinked to original sources

bioRxiv2026

Micro-Cm: restrictase-free microbiome-wide chromosome conformation profiling

Mobile genetic elements like plasmids, viruses and transposons can considerably augment the genomic repertoire of individual bacterial members of a complex multi-species microbiome and influence community dynamics. As linking a mobile element to its bacterial host based on metagenome sequencing alone proves challenging, such assays have been augmented with high-throughput chromosome conformation capture (Hi-C). However, the efficacy of Hi-C metagenomics is constrained by the protocol limitations and a lack of ground-truth reference datasets. In order to overcome these limitations, we present Micro-C metagenomics (Micro-Cm) - an adaptation of a superior, restrictase-free Micro-C technique for processing microbiome samples and mapping plasmid-host associations. We validated the developed experimental protocol and bioinformatic workflow on a simulated, defined consortium of diverse gut bacterial species and applied them to a long-read human gut microbiome sample. The proportion of valid reads in the synthetic community was an order of magnitude higher than that observed in multiple Hi-C metagenomic studies. For both samples, we obtained high-quality contact maps, which in the case of the synthetic community revealed fine-scale chromosome interactions. Moreover, successful recovery of plasmid-host interactions in the simulated community validated the method, which we then applied to the real stool sample. Our plasmid-host association analysis in a complex bacterial community successfully identified bacterial hosts for most of the identified complete plasmids. Our results show that Micro-Cm method improves profiling of complex microbiomes, exploration of mobile genetic element dynamics and community-wide, detailed investigation of chromosomal conformation patterns.

microbiology↗

bioRxiv2026

Co-targeting an AMPK--MAPK axis reprograms CAFs and suppresses PDAC

Pancreatic ductal adenocarcinoma (PDAC) is a fatal cancer characterized by limited therapeutic options and a highly treatment-resistant tumor microenvironment. Beyond tumor-intrinsic genetic alterations, growing evidence indicates that host-microbiome interactions influence cancer progression through microbial metabolites. However, how microbiome-derived metabolites influence oncogenic signaling in PDAC remains unclear. Here, integrated profiling revealed a consistent reduction of the microbial metabolite acetic acid in fecal samples from treatment-naive patients with PDAC and in a genetically defined Drosophila model recapitulating key PDAC driver alterations. Acetic acid activates AMP-activated protein kinase, and pharmacological activation of this pathway together with inhibition of mitogen-activated protein kinase signaling suppressed tumor growth in fly and mouse models. Combined pathway targeting restored AMPK activity and suppressed cancer-associated fibroblast activation. These findings identify a microbiome-associated metabolic vulnerability in PDAC and suggest that coordinated targeting of metabolic and oncogenic signaling may restrain tumor progression and improve therapeutic strategies.

cancer biology↗

bioRxiv2025

D- and L-lactate consumers in the human gut are taxonomically, biochemically, and energetically different

The human gut microbiota routinely produces D- and L-lactate during fermentation; however, the microbial fate of these stereoisomers, particularly the neurotoxic D-lactate, remains poorly understood. Given that D-lactate is an unavoidable byproduct of digestion, understanding its microbial turnover is essential for linking gut metabolism to host health. Here, we used chemostat bioreactors (pH 7.0, 37{degrees}C, and a solids retention time [SRT] of 4 d) to simulate gut-relevant, transient nutrient conditions and to enrich for lactate-consuming communities. DL-lactate-consuming consortia were enriched from a human-derived microbiota and then inoculated into duplicate bioreactors, which were fed exclusively D- or L-lactate. After steady-state was reached, the fed lactate stereoisomers were switched to assess community resilience. Regardless of the fed stereoisomer, the fermentation product spectra were consistent and dominated by acetate, propionate, and CO2. However, microbial communities and biomass yields diverged sharply, with a high relative abundance of Anaerotignum in D-lactate enrichments and Acidipropionibacterium and Propionibacterium in L-lactate enrichments. Notably, the biomass yield for D-lactate feeding was less than half that for L-lactate feeding, suggesting that the two isomers are metabolized through distinct biochemical pathways despite similar product spectra. Metagenomic and metaproteomic analyses confirmed this divergence at the pathway level. Our findings reveal how the stereoisomer identity of microbes shapes their niche specialization in the gut, with implications for understanding the ecology and clinical impact of lactate metabolism.

bioengineering↗

bioRxiv2025

Human gut flagellome profiling using FlaPro reveals TLR5-related phenotype-specific alterations in IBD

BackgroundFlagellin is the protein monomer of the bacterial flagellum, which confers motility, allowing bacteria to reach their favored niches. Flagellin is highly conserved across bacterial species and thus the target of the innate immune receptor Toll-like receptor 5 (TLR5). In the gut, bacterial flagellin agonizes human TLR5, triggering a pro-inflammatory response. However, the ability to bind and activate TLR5 varies considerably between different flagellins, suggesting that the composition of an individuals flagellin repertoire - the flagellome - may mediate the inflammatory response to the microbiome, with relevance to inflammatory bowel diseases. However, to date, methods to assess the inflammatory potential of a flagellome are lacking. MethodsWe constructed a curated database of human gut microbiome-derived flagellins. To predict the inflammatory potential of the flagellome by sorting flagellins into either "stimulatory" (strong TLR5 agonists) or "silent" (weak TLR5 agonists), we trained a machine learning model on experimentally characterized flagellins with known binding and stimulatory activities. The FlaPro pipeline was implemented using the Snakemake workflow engine for high-throughput analysis and is available at https://github.com/leylabmpi/FlaPro. A publicly available multi-omics dataset from an inflammatory bowel disease (IBD) cohort was used to explore associations between flagellome features and clinical status. FindingsFlaPro enables robust profiling of the human gut flagellome from metagenomic and metatranscriptomic data. Analysis of the IBD datasets revealed a depletion of flagellome diversity and a reduced silent-to-stimulatory flagellin abundance ratio in Crohns disease and ulcerative colitis, observed at both the genomic and transcriptional levels. Multiple condition-specific alterations were identified at the level of individual flagellin clusters. InterpretationThese findings indicate that IBD is associated with distinct alterations in the gut flagellome, particularly in relation to TLR5 recognition. Flagellome features represent a functionally interpretable class of microbiome-derived markers with potential utility in microbiome-wide association studies in the context of human health and disease. FundingThis work was supported by the Max Planck Society and the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme Grant agreement ID: 101142834 (ERC Advanced Grant SilentFlame).

bioinformatics↗

bioRxiv2025

Infection with gut parasites correlates with gut microbiome diversity across human populations in Africa

Soil-transmitted helminths (STH) are common in (sub)tropical regions and primarily affect impoverished populations. STHs reside in the gut, interacting both with the gut microbiota and host immunity. Clinical STH detection is laborious and often not performed within the context of gut microbiome studies. Here, we assessed whether fecal metagenome data could be used to assess STH infection, and to relate STH infection to microbiome diversity. We generated 310 gut metagenomes for mother-child pairs from two different locations in Gabon: one rural and one semi-urban. The presence and abundance of four STH parasites (Ascaris lumbricoides, Strongyloides stercoralis, Trichuris trichiura, and Necator americanus) were assessed using both microscopy and qPCR. Sequence data were used to characterize the microbiomes and to detect the presence of these four STH parasites. We found that metagenome data could accurately detect the presence of all four STHs, as reflected by high sensitivity and specificity compared to microscopy or qPCR detection. Furthermore, the number of STH species present in stool was associated with microbiome diversity and with the abundances of specific taxa, most notably in young children. We applied this approach to microbiome data from five other populations in Africa and corroborated our findings. Our results demonstrate that human intestinal parasites can be accurately detected via metagenomic sequencing, and highlight how infection with multiple STH parasites is linked to consistent features in the gut microbiome in populations in Africa.

microbiology↗

bioRxiv2025

Selection and transmission of the gut microbiome alone shifts mammalian behavior

Natural selection acts on phenotypic variation, which is influenced by genetic and environmental factors including the microbiome. Whether microbiome-mediated host phenotypes can be selected and transmitted remains untested in vertebrates. Here, we first identified locomotor activity as a trait transmissible through the gut microbiome in mice. We then performed a selection experiment, where we serially transferred microbiomes from low-activity mice to independently bred germ-free mice. Over four transfer rounds, microbiome transfer significantly reduced locomotor activity. Reduced locomotion was associated with increased Lactobacilli and their metabolite indolelactate. In a test of causality, independent administration to the mouse gut of Lactobacillus johnsonii or indolelactate reduced locomotion. These findings demonstrate that selection and transmission of microbes can modulate host traits independently of selection on the mammalian genome. One Sentence SummarySerial transfer of the gut microbiome of low-activity mice to germfree recipients reproducibly transferred activity levels, revealing the microbiomes potential to impact the hosts response to selection without host genomic changes.

evolutionary biology↗

bioRxiv2023

CDK8/19 Inhibition Attenuates G1 Arrest Induced by BCR-ABL Antagonists and Accelerates Death of Chronic Myelogenous Leukemia Cells

Imatinib mesylate (IM) and other BCR-ABL tyrosine kinase inhibitors (BCR-ABLi) are the mainstay of chronic myelogenous leukemia (CML) treatment. However, activation of circumventing signaling pathways and quiescence may limit BCR-ABLi efficacy. CDK8/19 Mediator kinases have been implicated in the emergence of non-genetic drug resistance. Dissecting the effects of pharmacological CDK8/19 inhibition on CML survival in response to BCR-ABLi, we found that a selective, non-toxic CDK8/19 inhibitor (CDK8/19i) Senexin B (SenB) and other CDK8/19i sensitized K562 cells to different BCR-ABLi via attenuation of cell cycle arrest. In particular, SenB prevented IM-induced upregulation of genes that negatively regulate cell cycle progression. SenB also antagonized IM-activated p27Kip1 elevation thereby diminishing the population of G1-arrested cells. After transient G1 arrest, cells treated with IM+SenB re-entered the S phase, where they were halted and underwent replicative stress. Consequently, the combination of IM and SenB intensified apoptotic cell death, measured by activation of caspase 9 and 3, subsequent cleavage of poly(ADPriboso)polymerase 1, positive Annexin V staining and increase of subG1 fraction. In contrast, IM-treated BCR-ABL-positive KU812 CML cells, which did not induce p27Kip1, readily died regardless of SenB treatment. Thus, CDK8/19i prevent the quiescence-mediated escape from BCR-ABLi-induced apoptosis, suggesting a strategy for avoiding the CML relapse.

cancer biology↗

bioRxiv2020

Suppression of liquid-liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells

Liquid-liquid phase separation (LLPS) contributes to the spatial and functional segregation of molecular processes. However, the role played by LLPS in chromatin folding in living cells remains unclear. Here, using stochastic optical reconstruction microscopy (STORM) and Hi-C techniques, we studied the effects of 1,6-hexanediol (1,6-HD)-mediated LLPS modulation on higher-order chromatin organization in living cells. We found that 1,6-HD treatment caused the enlargement of nucleosome nanodomains and their more uniform distribution in the nuclear space. At a megabase-scale, chromatin underwent moderate but irreversible perturbations that resulted in the partial mixing of A and B compartments. The removal of 1,6-HD from the culture medium did not allow chromatin to acquire initial configurations, but increased further mixing of the chromatin compartments and resulted in more compact repressed chromatin than in untreated cells. 1,6-HD treatment also weakened enhancer-promoter interactions but did not considerably affect CTCF-dependent loops. Our results suggest that 1,6-HD-sensitive LLPS plays a limited role in chromatin spatial organization by constraining its folding patterns and facilitating compartmentalization at different levels.

molecular biology↗

bioRxiv2017

MetaCherchant - an algorithm for analyzing genomicenvironment of antibiotic resistance genein gut microbiota

Antibiotic resistance is an important global public health problem. Human gut human microbiota is an accumulator of resistance genes potentially providing them to pathogens. It is important to develop tools for identifying the mechanisms of how resistance is transmitted between gut microbial species and pathogens. We developed MetaCherchant - an algorithm for extracting the genomic environment of antibiotic resistance genes from metagenomic data in the form of a graph. The algorithm was validated on simulated datasets and applied to new \"shotgun\" metagenomes of gut microbiota from patients with Helicobacter pylori who underwent antibiotic therapy. Genomic context was reconstructed for several dominant resistance genes; taxonomic annotation of the context showed the species carrying the genes. Application of MetaCherchant in differential mode produced specific graph structures suggesting the evidence of possible resistance gene transmission within a mobile element that occurred as a result of the antibiotic therapy. MetaCherchant is a promising tool giving researchers an opportunity to get an insight into dynamics of resistance transmission in vivo based on metagenomic data.

bioinformatics↗