Biology subjects

Schramm, A.

Publications and source records attributed to Schramm, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Artesunate Exploits Glutathione-Dependent Redox Vulnerability in Metastatic Lung Adenocarcinoma

Metastatic dissemination remains the principal cause of mortality in lung adenocarcinoma. To identify metabolic vulnerabilities associated with metastasis, we used cell lines with distinct metastatic abilities derived from the KrasG12D;p53KO mouse model. Building on evidence of mitochondrial dysfunction in metastasis-derived cells, we performed an in vivo screen of a focused metabolic drug library using a multiplexed DNA-barcoding platform. This approach identified artesunate as a selective inhibitor of metastatic seeding, which was validated in vivo to reduce metastatic burden while leaving primary tumor growth unaffected. Mechanistically, artesunate induced oxidative stress, characterized by reactive oxygen species and lipid peroxidation. Transcriptomic and mechanistic profiling revealed altered redox homeostasis in metastasis-derived cells. Inhibition of glutathione synthesis specifically sensitized these cells to artesunate, resulting in extensive cell death, whereas primary tumor-derived cells remained resistant. These findings identify glutathione-dependent redox homeostasis as a metabolic vulnerability in metastatic cells that can be specifically targeted using artesunate.

cancer biology↗

bioRxiv2026

Loss of the Y chromosome drives basal identity and metastatic potential via epigenetic reprogramming in pancreatic cancer

Loss of the Y chromosome (LOY) has been largely unexplored in pancreatic ductal adenocarcinoma (PDAC), and no mechanistic framework previously explained its role in tumor biology. We identify LOY as a recurrent, functionally consequential alteration affecting ~50% of male PDAC patients across two independent cohorts, with strong enrichment in advanced disease and, critically, in the basal subtype, establishing LOY as a clinically actionable biomarker. Comprehensive genomic profiling positions LOY as a distinct genetic event associated with TP53 mutations, implicating it in aggressive tumor evolution. Integrative analyses across bulk tumors, single-cell datasets and CRISPR-engineered PDAC models converge on epithelial-to-mesenchymal transition (EMT) as the dominant LOY-driven program. Y-chromosome deletion alone induces EMT transcriptional states, mesenchymal morphology and enhanced metastatic ability. Mechanistically, LOY disrupts epigenetic regulation through loss of Y-linked chromatin modifiers, reshaping DNA methylation at EMT- and basal-defining loci and reducing chemotherapy sensitivity. These findings establish LOY as a causal genetic driver of PDAC progression and a clinically accessible biomarker with direct therapeutic relevance.

cancer biology↗

bioRxiv2026

SigA forms amyloid fibrils and supports the competition of Shigella with the microbiota

Shigella sonnei is an enteropathogen that causes bacillary dysentery. During the first step of its virulence cycle, it must outcompete the resident microbiota to establish its own niche. Here we report that SigA, the sole SPATE (Serine Protease Autotransporter of Enterobacteriaceae) family member in S. sonnei, plays an indirect but central role in this process. A genome-wide analysis showed that the SPATE family includes SigA, Pic, SepA, and Sat. We demonstrated that SigA self-assembles into amyloid fibrils (F-SigA) independently of its protease activity. F-SigA remains associated with the S. sonnei surface in vitro and in vivo. Purified F-SigA fibrils have a diameter of 17.7 {+/-} 3.2 nm, and their amyloid organization was confirmed using specific markers and biochemical methods. F-SigA is secreted into the lumen in vivo and localizes to the surface of the colonic epithelium. We found that colicin E1 (ColE1) interacts with F-SigA amyloid fibrils, and that F-SigA-ColE1 complexes display antimicrobial activity that promotes S. sonnei competition with other bacteria. Because Pic, another Shigella SPATE, also forms amyloid fibrils, we anticipate that this virulence mechanism may be relevant across a wide range of Shigella strains and enterobacteria and may serve additional roles during the Shigella virulence cycle.

microbiology↗

bioRxiv2026

Loss of the Y chromosome drives epigenetic and transcriptomic plasticity in lung adenocarcinoma

Loss of the Y chromosome (LOY) is associated with poor survival across multiple solid tumors, yet the underlying molecular mechanisms remain poorly understood. Here, we identify LOY as a central driver of lineage plasticity and epigenetic heterogeneity in lung adenocarcinoma. Integrating multi-omic profiling of primary samples with isogenic cellular models, we show that LOY triggers epithelial-to-mesenchymal transition (EMT). Mechanistically, LOY causes haploinsufficiency of dosage-sensitive regulators, leading to widespread DNA hypomethylation at EMT gene promoters, including THY1 and LOX. Single-cell multi-omic analyses demonstrate that LOY induces epigenetic heterogeneity, destabilizes the chromatin landscape, and increases lineage plasticity, enabling rapid cellular adaptation to metabolic and genotoxic stress. Moreover, LOY-induced plasticity facilitates tumor engraftment and metastatic dissemination in vivo. These findings establish Y-linked gene dosage as a critical guardian of epigenetic stability, providing a mechanistic rationale for how its loss amplifies phenotypic diversity and lineage plasticity, ultimately driving adverse clinical outcomes in LOY patients.

cancer biology↗

bioRxiv2026

Artificial sediments enable reproducible cultivation and recapitulate ecological interactions of cable bacteria

Cable bacteria are filamentous microbes that couple sulfide oxidation to oxygen reduction over centimeter distances via long-distance electron transport. While their activity creates characteristic biogeochemical gradients that shape sediment ecology, the study of cable bacteria has been constrained by the chemical and physical heterogeneity of the natural sediments they inhabit. To date, laboratory cultivation efforts have relied on these undefined environmental matrices. Here, we established a reproducible enrichment and cultivation platform using an artificial sediment matrix coupled with chemically defined media. This matrix successfully supported the growth of both freshwater and marine cable bacteria and enabled serial propagation over multiple transfers. Microsensor profiling confirmed that the incubations recapitulated hallmark geochemical signatures, including the sulfide, oxygen and pH gradients associated with electrogenic sulfur oxidation. Scanning electron microscopy confirmed the presence of cable bacteria, while 16S rRNA sequencing confirmed enrichment of the cable bacteria together with a stable co-enriched community that included taxa associated with sulfur and iron cycling as well as cellulose decomposition. This defined cultivation system eliminates the variability inherent to natural samples, providing a controlled platform for dissecting the physiology, genetics, and microbial interactions of cable bacteria.

microbiology↗

bioRxiv2026

Quantifying Treatment Resistance in Mixtures of Gastrointestinal Stromal Tumor Cells with BARMIX

Targeted therapies in gastrointestinal stromal tumors (GIST) often fail due to heterogeneous resistance mutations arising across metastatic sites. Efficient, rational design of mutation-specific therapies requires the ability to quantify treatment resistance across many genotypes in parallel. Here, we present BARcode MIXture analysis (BARMIX), a platform combining multiplexed experiments with DNA-barcoded cancer cell mixtures in vitro and in vivo, and a probabilistic framework for quantitative assessment of genotype-specific treatment resistance. BARMIX efficiently and accurately recapitulated known clinical resistance patterns in GIST and matched resistance measurements from individual cell lines in vitro and in vivo. This experimental-computational approach provides a scalable and broadly applicable strategy for quantifying treatment responses in complex cell populations, enabling systematic preclinical testing of new drugs and combinations to identify mutation-specific therapeutic options for precision oncology in GIST and beyond.

systems biology↗

bioRxiv2025

Extracellular electron transfer in cable bacteria enables growth rates comparable to aerobic respiration

Cable bacteria are filamentous sulphide-oxidisers performing long-distance electron transfer in redox-stratified sediments by transporting electrons over centimetre-scale distances to reduce oxygen. Here, we show that the freshwater cable bacterium Electronema aureum GS can respire insoluble electron acceptors under anoxic conditions via a versatile extracellular electron transfer (EET) system, supporting growth rates comparable to those under aerobic conditions. Using electrochemical and molecular biology analyses, we demonstrate that E. aureum GS engages in both direct and mediated electron transfer to electrodes, including at +600 mV vs. Ag/AgCl--an unusually high redox potential typically not accessed by electroactive bacteria. Two distinct cell-surface redox components were identified, which are metal-dependent, pH-sensitive, and heat-labile, consistent with outer-membrane-localised cytochromes. Moreover, the redox shuttle riboflavin accumulated extracellularly and enhanced current production in bioelectrochemical systems, indicating a role for soluble mediators in cable bacteria. Together, these findings reveal a previously unrecognised respiratory flexibility in E. aureum GS and highlight EET as a key alternative strategy for energy conservation in fluctuating redox environments.

microbiology↗

bioRxiv2025

Datavzrd: Rapid programming- and maintenance-free interactive visualization and communication of tabular data

Tabular data, often scattered across multiple tables, is the primary output of data analyses in virtually all scientific fields. Exchange and communication of tabular data is therefore a central challenge. We present Datavzrd, a tool for creating portable, visually rich, interactive reports from tabular data in any kind of scientific discipline. Datavzrd unifies the strengths of currently common generic approaches for interactive visualization like R Shiny with the portability, ease of use and sustainability of plain spreadsheets. The generated reports do not require the maintenance of a web server nor the installation of specialized software for viewing and can simply be attached to emails, shared via cloud services, or serve as manuscript supplements. They can be specified without requiring imperative programming, thereby enabling rapid development and offering accessibility for non-computational scientists, unlocking the look and feel of dedicated manually crafted web applications without the maintenance and development burden. Datavzrd reports scale from small tables to thousands or millions of rows and offer the ability to link multiple related tables, allowing to jump between corresponding rows or hierarchically explore growing levels of detail.

bioinformatics↗

bioRxiv2025

A computational model elucidates the effect of oncogene induced expression alterations on the energy metabolism of neuroblastoma

An altered energy metabolism is recognized as a hallmark of cancer. Experimental evidence shows that oncogenes play a key role in the reprogramming of metabolism. In neuroblastoma the oncogene MYCN, a main risk factor of poor prognosis, has been demonstrated to lead to expression changes in numerous glycolytic enzymes. Since it is not clear whether all these targets are required and how the overall metabolic response is shaped, we here dissect the effect of MYCN targets on the pathway individually and in combination using a computational modeling approach. We develop a first mathematical model of the energy metabolism in neuroblastoma cells based on our published experimental data. The analysis shows that MYCN overexpression overall leads to Warburg-like flux alterations with characteristic changes for the individual MYCN targets highlighting that MYCN targets can have opposing and sometimes unexpected effects. Interestingly, not all described MYCN targets contribute to notable flux alterations, at least in glycolysis. Our model moreover predicts a potential bistability of the cellular metabolism with an occurrence of a low-flux state likely representing quiescence. Overall, our study highlights the importance of analysing perturbations such as expression changes in the context of realistic pathways capturing their specific interactions and complex regulations.

systems biology↗

bioRxiv2024

Extracellular electron transfer genes expressed by candidate flocking bacteria in cable bacteria sediment

Cable bacteria, filamentous sulfide oxidizers that live in sediments, are at times associated with large flocks of swimming bacteria. It has been proposed that these flocks of bacteria transport electrons extracellularly to cable bacteria via an electron shuttle intermediate, but the identity and activity of these bacteria in freshwater sediment remains mostly uninvestigated. We coupled metagenomics and metatranscriptomics to 16S rRNA amplicon-based correlations with cable bacteria from two time series experiments up to 155 days. We identified bacteria expressing genes for extracellular electron transfer and motility, including synthesis genes for potential extracellular electron shuttles: phenazines and flavins. Of the 85 high quality MAGs (Metagenome Assembled Genomes >90% complete and <5% contaminated), 56 had genes encoding flagellar proteins, and of these 22 had genes encoding extracellular electron transport proteins. The candidate flockers constituted 21.4% of all MAGs and 42.1% of the proposed flocking bacteria expressed extracellular electron transfer genes. The proposed flockers belonged to a large variety of taxonomic groups: 18 genera spread across 9 phyla. Our data suggest that electric relationships in freshwater sediments between cable bacteria and other microbes likely help to generate and/or sustain cryptic element cycling and deep oxygen breathing, affecting more element cycles than sulfur, like metal- and in particular iron- and carbon cycles.

microbiology↗

bioRxiv2023

Comparative electric and ultrastructural studies of cable bacteria reveal new components of conduction machinery

Cable bacteria encompass at least two genera, and they are known to vary greatly in habitat preferences and filament thickness. We systematically investigated variations and similarities in cellular structures and electrical properties of different cable bacteria strains. Using SEM, TEM, STEM-EDX and ToF-SIMS, we characterized shared features of cable bacteria, such as inner and outer membranes, surface layer and cell junction architecture, as well as strain specific features, like the number and size of periplasmic conductive fibers (PCFs). Our data indicates that the PCFs are organized as loose stranded rope-like structures. With spatially resolved elemental analysis we detected nickel-containing co-factors within the PCF of cable bacteria strains in both genera suggesting a conserved conduction mechanism. Electrical conductivity of different cable bacteria strains showed a range of values covering three orders of magnitude indicating an unknown metabolic adaptation. Using cryogenic electron tomography we discovered multiple polar chemosensory arrays, abundant cytoplasmic inner membrane-attached vesicles (IMVs), polysomes and inner membrane invaginations that shed light on cable bacteria metabolism including complex motility control mechanisms, localized protein synthesis, and membrane remodeling. We propose that the IMVs discovered in this work are novel metabolic hubs closely connected to the unique conductive fiber structure of cable bacteria.

microbiology↗

bioRxiv2023

Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

In the ongoing debates about eukaryogenesis, the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors, members of the Asgard archaea play a key role as the closest archaeal relatives of eukaryotes. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved. Here, we analyze distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea, as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree/species tree reconciliation approaches, we show that, in analogy to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared to other archaea. Finally, we infer that the last common ancestor of Asgard archaea likely was a thermophilic chemolithotroph, and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and the platform for the emergence of cellular complexity in eukaryotic cells.

evolutionary biology↗

bioRxiv2022

Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria

Cable bacteria of the Desulfobulbaceae family are centimeter-long filamentous bacteria, which are capable of conducting long-distance electron transfer. Currently, all cable bacteria are classified into two candidate genera: Candidatus Electronema, typically found in freshwater environments, and Candidatus Electrothrix, typically found in saltwater environments. This taxonomic framework is based on both 16S rRNA gene sequences and metagenome-assembled genome (MAG) phylogenies. However, most of the currently available MAGs are highly fragmented, incomplete, and thus likely miss key genes essential for deciphering the physiology of cable bacteria. To address this, we performed Nanopore long read (total 162.4 Gbp) and Illumina short read (total 148.3 Gbp) shotgun sequencing of selected environmental samples and a single-strain enrichment of Ca. Electronema aureum. We recovered multiple cable bacteria MAGs, including two circular and one single-contig. Phylogenomic analysis, also confirmed by 16S rRNA gene-based phylogeny, classified one circular MAG and the single-contig MAG as novel species of cable bacteria, which we propose to name Ca. Electronema halotolerans and Ca. Electrothrix laxa, respectively. The Ca. Electronema halotolerans, despite belonging to the previously recognized freshwater genus of cable bacteria, was retrieved from brackish-water sediment. Metabolic predictions showed several adaptations to a high salinity environment, similar to the "saltwater" Ca. Electrothrix species, indicating how Ca. Electronema halotolerans may be the evolutionary link between marine and freshwater cable bacteria lineages.

microbiology↗

bioRxiv2022

Effects of microplastic ingestion on hydrogen production and microbiomes in the gut of the terrestrial isopod Porcellio scaber

Microplastic (MP) pollution is an environmental burden. MP enters food webs via ingestion by macrofauna, including isopods (Porcellio scaber) in terrestrial ecosystems. However, MP-effects on the host and its gut microbiome are largely unknown. We tested the hypothesis that biodegradable (polylactic acid, PLA) and non-biodegradable (polyethylene terephthalate, PET; polystyrene, PS) MP have contrasting effects on P. scaber mediated by changes of the associated gut microbiome. Although the isopods avoided food containing PS, isopod fitness after eight-week MP-exposure was unaffected. Qualitative and quantitative 16S rRNA gene and 16S rRNA analyses of gut microbiomes indicated general MP effects, MP-type specific indicator taxa, and stimulation by PLA compared to MP-free controls. Isopods emitted hydrogen, and its production increased and decreased after PLA-food and PET- or PS-food ingestion, respectively, relative to controls as indicated by microsensor measurements. Gut pH was unaffected by MP. We identified the gut of P. scaber as significant mobile source of reductant for soil microbiomes likely due to Enterobacteriaceae related fermentation activities that were stimulated by lactate generated during PLA-degradation. The findings suggest negative effects of PET and PS on gut fermentation, modulation of isopod hydrogen emissions by MP pollution, and the potential of MP to affect terrestrial food webs.

microbiology↗

bioRxiv2021

EIF4EBP1 is transcriptionally upregulated by MYCN and associates with poor prognosis in neuroblastoma

BackgroundNeuroblastoma (NB) accounts for 15% of cancer-related deaths in childhood despite considerable therapeutic improvements. While several risk factors, including MYCN amplification and alterations in RAS and p53 pathway genes, have been defined in NB, the clinical outcome is very variable and difficult to predict. Since genes of the mTOR pathway are up-regulated in MYCN-amplified NB, we aimed to define the predictive value of the mTOR substrate-encoding gene eukaryotic translation initiation factor 4E-binding protein 1 (EIF4EBP1) expression in NB patients. MethodsSeveral independent NB patient cohorts with corresponding mRNA expression data were analyzed for EIF4EBP1 expression. An institutional NB cohort consisting of 69 prospectively collected tumors was employed to immunohistochemically analyze expression of EIF4EBP1-encoded protein (4EBP1). In addition, we performed an in vitro luciferase reporter gene assay with an episomal EIF4EBP1 promoter and genetically modulated MYCN expression in NB cells. FindingsEIF4EBP1 mRNA expression was positively correlated with MYCN expression and elevated in stage 4 and high-risk NB patients. High EIF4EBP1 mRNA expression was associated with reduced overall and event-free survival in the entire group of NB patients in three cohorts, as well as in stage 4 and high-risk patients. High levels of 4EBP1 were significantly associated with prognostically unfavorable NB histology. Functional analyses in vitro revealed that EIF4EBP1 expression is transcriptionally controlled by MYCN binding to the EIF4EBP1 promoter. InterpretationHigh EIF4EBP1 expression is associated with poor prognosis in NB patients and may serve to stratify patients with high-risk NB. FundingG.L. was supported by funding from the Elterninitiative Dusseldorf e.V., the Research Commission of the Medical Faculty of Heinrich Heine University, the Deutsche Forschungsgemeinschaft (Grant LE 3751/2-1), and the German Cancer Aid (Grant 70112624). The laboratory of T.G.P.G. is supported by the Barbara und Wilfried Mohr Foundation. BR is supported by the Israel Science Foundation (grant No. 1436/19). RESEARCH IN CONTEXT Evidence before this studyNB represents a particularly heterogeneous cancer entity, with 5-year event-free survival rate ranging from 50% to 98% depending on the patients risk group. While genes of the nutrient-sensing mTOR pathway were found to be up-regulated in MYCN-amplified NB tumors, their clinical relevance and prognostic value in NB patients remain unclear. In particular, the mTOR substrate-encoding gene EIF4EBP1 was studied in NB by three different groups and high EIF4EBP1 mRNA expression was observed in MYCN-amplified or contradictorily in more favorable stages 1 and 2 patients. Also, EIF4EBP1 was included in a prognostic gene signature for poor overall survival in NB. However, the prognostic value of EIF4EBP1 alone was not determined in NB and the expression of EIF4EBP1 encoded protein, 4EBP1, was not analyzed in NB tumor tissues and not correlated with clinicopathological features such as histological subtypes. Additionally, the transcriptional regulation of the EIF4EBP1 promoter by MYCN was not characterized. Added value of this studyThis study uncovers the prognostic potential of EIF4EBP1 at the mRNA and protein levels in NB patients. We report that high EIF4EBP1 expression is correlated with poor survival in three independent cohorts and that high 4EBP1 levels is associated with a prognostically unfavorable histological subtype. High EIF4EBP1 expression is also a factor of poor prognosis in stage 4 and high-risk patient groups. Finally, we found that MYCN activates the human EIF4EBP1 promoter through binding at three binding motifs. Implications of all the available evidenceEIF4EBP1 mRNA and 4EBP1 protein expression have prognostic value in NB, especially to stratify patients with advanced and more aggressive NB, such as patients with stage 4 disease and high-risk patients including those with unfavorable histological subtype NB. Enhanced EIF4EBP1 mRNA and 4EBP1 protein expression in NB are driven by direct transcriptional activation of EIF4EBP1 by MYCN.

cancer biology↗

bioRxiv2021

Microphaser - a small-scale phasing approach for improved personalized neopeptidome creation

MotivationHaplotype phasing approaches have been shown to improve accuracy of the search space of neoantigen prediction by determining if adjacent variants are located on the same chromosomal copy. However, the aneuploid nature of cancer cells as well as the admixture of different clones in tumor bulk sequencing data are challenging the current diploid based phasing algorithms. We present microphaser, a small-scale phasing approach to improve haplotyping variants in cancer samples. Microphaser aims to create a more accurate neopeptidome for downstream neoantigen prediction. ResultsMicrophaser achieves large concordance with state-of-the-art phasing-aware neoantigen prediction pipeline neoepiscope, with differences in edge cases and an improved filtering step. AvailabilityMicrophaser is written in the Rust programming language. It is made available via Github (https://github.com/koesterlab/microphaser)and Bioconda. The corresponding prediction pipeline (https://github.com/snakemake-workflows/dna-seq-neoantigen-prediction) has been written within the Snakemake workflow management system and can be deployed as part of the snakemake-workflows project.

bioinformatics↗

bioRxiv2020

Dissimilatory Nitrate Reduction To Ammonium In The Cable Bacterium Ca. Electronema Sp. GS

Cable bacteria are filamentous Desulfobulbaceae that split the energy-conserving reaction of sulphide oxidation into two half reactions occurring in distinct cells. Cable bacteria can use nitrate, but the reduction pathway is unknown, making it difficult to assess their direct impact on the N-cycle. Here we show that the freshwater cable bacterium Ca. Electronema sp. GS performs dissimilatory nitrate reduction to ammonium (DNRA). 15NO3--amended sediment with Ca. Electronema sp. GS showed higher rates of DNRA and nitrite production than sediment without Ca. Electronema sp. GS. Electron flux from sulphide oxidation, inferred from electric potential measurements, matched the electron flux needed to drive cable bacteria-mediated nitrate reduction. Ca. Electronema sp. GS expressed a complete nap operon for periplasmic nitrate reduction to nitrite, and genes encoding a periplasmic multiheme cytochrome (pMHC), homolog to a pMHC that can catalyse nitrite reduction to ammonium in Ca. Maribeggiatoa. Phylogenetic analysis suggests that the capacity for DNRA was acquired in multiple events through horizontal gene transfer from different organisms, before cable bacteria split into different salinity niches. The architecture of the nitrate reduction system suggests absence of energy conservation through oxidative phosphorylation, indicating that cable bacteria primarily conserve energy through the half reaction of sulfide oxidation.

microbiology↗

bioRxiv2019

Near-complete Lokiarchaeota genomes from complex environmental samples using long and short read metagenomic analyses

Asgard archaea is a recently proposed superphylum currently comprised of five recognised phyla: Lokiarchaeota, Thorarchaeota, Odinarchaeota, Heimdallarchaeota and Helarchaeota. Members of this group have been identified based on culture-independent approaches with several metagenome-assembled genomes (MAGs) reconstructed to date. However, most of these genomes consist of several relatively small contigs, and, until recently, no complete Asgard archaea genome is yet available. Large scale phylogenetic analyses suggest that Asgard archaea represent the closest archaeal relatives of eukaryotes. In addition, members of this superphylum encode proteins that were originally thought to be specific to eukaryotes, including components of the trafficking machinery, cytoskeleton and endosomal sorting complexes required for transport (ESCRT). Yet, these findings have been questioned on the basis that the genome sequences that underpin them were assembled from metagenomic data, and could have been subjected to contamination and other assembly artefacts. Even though several lines of evidence indicate that the previously reported findings were not affected by these issues, having access to high-quality and preferentially fully closed Asgard archaea genomes is needed to definitively close this debate. Current long-read sequencing technologies such as Oxford Nanopore allow the generation of long reads in a high-throughput manner making them suitable for their use in metagenomics. Although the use of long reads is still limited in this field, recent analyses have shown that it is feasible to obtain complete or near-complete genomes of abundant members of mock communities and metagenomes of various level of complexity. Here, we show that long read metagenomics can be successfully applied to obtain near-complete genomes of low-abundant members of complex communities from sediment samples. We were able to reconstruct six MAGs from different Lokiarchaeota lineages that show high completeness and low fragmentation, with one of them being a near-complete genome only consisting of three contigs. Our analyses confirm that the eukaryote-like features previously associated with Lokiarchaeota are not the result of contamination or assembly artefacts, and can indeed be found in the newly reconstructed genomes.

microbiology↗