Ekaterina Avershina

• Avershina, Ekaterina; Birkeland, Einar Elvbakken; Johannessen, Cecilie Bucher - & Rounge, Trine Ballestad (2026). CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut. Gut microbes. ISSN 1949-0976. 18(1). doi: 10.1080/19490976.2026.2734649. Full text in Research Archive
• Birkeland, Einar Elvbakken; Kværner, Ane Sørlie; Avershina, Ekaterina; Johannessen, Cecilie Bucher -; Bemanian, Vahid & Blix, Hege Salvesen [Show all 14 contributors for this article] (2026). Microbiome signatures for detection of colorectal lesions in population-based FIT screening. Nature Communications. 17. doi: 10.1038/s41467-026-75962-1. Full text in Research Archive Show summary

  The gut microbiome has been linked to colorectal cancer (CRC) development, with microbe-based classifiers distinguishing between CRC patients and healthy controls. However, there is a lack of studies addressing the utility of the microbiome in screening-relevant settings, including both precancers and CRC. In this Norwegian population-based study, we used fecal immunochemical test (FIT) leftovers from 1034 FIT-positive (i.e. positive for occult blood) screening participants for gut metagenome profiling using shotgun sequencing. Using comprehensive clinical, demographic, and lifestyle data, we modeled gut microbiome associations with CRC screening outcomes. Combining microbial profiles with quantitative FIT values improved detection of premalignant lesions beyond optimizing the FIT value alone, even after incorporating established CRC risk factors. Still, the FIT value maintained superior discriminative ability for CRC. We confirmed enrichment of bacteria such as Fusobacterium nucleatum and Peptostreptococcus stomatis in CRC. In contrast, other bacteria previously associated with the presence of CRC, including Hungatella hathewayi and Clostridium symbiosum, as well as pks-negative Escherichia coli, were enriched in those with no neoplastic findings, suggesting that in a FIT-positive population their presence may reflect other conditions causing intestinal bleeding rather than underlying neoplasia. Microbial profiles were predominantly associated with distal rather than proximal lesions. Together, our findings highlight the potential for microbial markers to improve FIT-based CRC screening, especially by differentiating those with premalignant lesions from those who test FIT-positive for other reasons.

• Kværner, Ane Sørlie; Birkeland, Einar Elvbakken; Avershina, Ekaterina; Botteri, Edoardo; Bucher-Johannessen, Cecilie & Knudsen, Markus Dines [Show all 14 contributors for this article] (2026). Alcohol consumption and colorectal carcinogenesis: an exploration of the gut microbial pathway as a potential mediator. European Journal of Nutrition. ISSN 1436-6207. 65(4), p. 1–18. doi: 10.1007/s00394-026-03960-6. Full text in Research Archive Show summary

  Background Alcohol consumption is one of the major risk factors of colorectal cancer (CRC), yet the mechanisms underlying this relationship, particularly the role of gut microbes, are not fully understood. Objective To study associations of alcohol intake with the gut microbiome and colorectal lesions among CRC screening participants. Of particular interest was the potential role of gut microbes in mediating the association between alcohol intake and colorectal lesions. Methods Screening participants with a positive faecal immunochemical test at ages 55–77 were eligible for the CRCbiome study. Alcohol intake was assessed using a validated, semi-quantitative food frequency questionnaire and linked with shotgun metagenome based gut microbial profiles to study associations with screen-detected colorectal lesions. The potential role of alcohol-associated gut microbes in mediating the association between alcohol intake and colorectal lesions was examined using causal mediation analysis. Results Of 1468 participants with dietary data, 414 were diagnosed with advanced lesions. Alcohol intake was positively associated with advanced lesions in a dose-dependent manner (ptrend = 0.008), with odds ratio of 1.09 (95% confidence interval, 1.00, 1.19) per 10 g/day increase. Compared to non-consumers, those consuming alcohol were characterized by a distinct microbial profile, manifested as modest, but consistent, shifts in α- and β-diversity, and differentially abundant bacteria. A causal mediation analysis showed that 12% of the association between alcohol intake and advanced lesions was mediated by alcohol-associated gut bacteria. Conclusion Alcohol consumption was associated with a distinct microbial profile, which partly explained the association between alcohol intake and advanced colorectal lesions.

• Zakhartseva, Ekaterina Avershina; Qureshi, Arfa Irej; Winther-Larsen, Hanne Cecilie & Rounge, Trine Ballestad (2025). Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases. Microbiome. 13(1). doi: 10.1186/s40168-025-02048-3. Full text in Research Archive Show summary

  Background The mycobiome, representing the fungal component of microbial communities, is increasingly acknowledged as an integral part of the gut microbiome. However, research in this area remains relatively limited. The characterization of mycobiome taxa from metagenomic data is heavily reliant on the quality of the software and databases. In this study, we evaluated the feasibility of mycobiome profiling using existing bioinformatics tools on simulated fungal metagenomic data. Results We identified seven tools claiming to perform taxonomic assignment of fungal shotgun metagenomic sequences. One of these was outdated and required substantial modifications of the code to be functional and was thus excluded. To evaluate the accuracy of identification and relative abundance of the remaining tools (Kraken2, MetaPhlAn4, EukDetect, FunOMIC, MiCoP, and HumanMycobiomeScan), we constructed 18 mock communities of varying species richness and abundance levels. The mock communities comprised up to 165 fungal species belonging to the phyla Ascomycota and Basidiomycota, commonly found in gut microbiomes. Of the tools, FunOMIC and HumanMycobiomeScan needed source code modifications to run. Notably, only one species, Candida orthopsilosis, was consistently identified by all tools across all communities where it was included. Increasing community richness improved precision of Kraken2 and the relative abundance accuracy of all tools on species, genus, and family levels. MetaPhlAn4 accurately identified all genera present in the communities and FunOMIC identified most species. The top three tools for overall accuracy in both identification and relative abundance estimation were EukDetect, MiCoP, and FunOMIC, respectively. Adding 90% and 99% bacterial background did not significantly impact these tools’ performance. Among the whole genome reference tools (Kraken2, HMS, and MiCoP), MiCoP exhibited the highest accuracy when the same reference database was used. Conclusion Our survey of mycobiome-specific software revealed a very limited selection of such tools and their poor robustness due to error-prone software, along with a significant lack of comprehensive databases enabling characterization of the mycobiome. None of the implemented tools fully agreed on the mock community profiles. FunOMIC recognized most of the species, but EukDetect and MiCoP provided predictions that were closest to the correct compositions. The bacterial background did not impact these tools’ performance. Video Abstract

• Bucher-Johannessen, Cecilie; Senthakumaran, Thulasika; Avershina, Ekaterina; Birkeland, Einar Elvbakken; Hoff, Geir Svein & Bemanian, Vahid [Show all 8 contributors for this article] (2024). Species-level verification of Phascolarctobacterium association with colorectal cancer. mSystems. 9(10). doi: 10.1128/msystems.00734-24. Full text in Research Archive Show summary

  We have previously demonstrated an association between increased abundance of Phascolarctobacterium and colorectal cancer (CRC) and adenomas in two independent Norwegian cohorts. Here we seek to verify our previous findings using new cohorts and methods. In addition, we characterize lifestyle and sex specificity, the functional potential of the Phascolarctobacterium species, and their interaction with other microbial species. We analyze Phascolarctobacterium with 16S rRNA sequencing, shotgun metagenome sequencing, and species-specific qPCR, using 2350 samples from three Norwegian cohorts-CRCAhus, NORCCAP, and CRCbiome-and a large publicly available data set, curatedMetagenomicData. Using metagenome-assembled genomes from the CRCbiome study, we explore the genomic characteristics and functional potential of the Phascolarctobacterium pangenome. Three species of Phascolarctobacterium associated with adenoma/CRC were consistently detected by qPCR and sequencing. Positive associations with adenomas/CRC were verifi

• Istvan, Paula; Birkeland, Einar Elvbakken; Avershina, Ekaterina; Kværner, Ane Sørlie; Bemanian, Vahid & Pardini, Barbara [Show all 11 contributors for this article] (2024). Exploring the gut DNA virome in fecal immunochemical test stool samples reveals associations with lifestyle in a large population-based study. Nature Communications. 15. doi: 10.1038/s41467-024-46033-0. Full text in Research Archive Show summary

  Abstract Stool samples for fecal immunochemical tests (FIT) are collected in large numbers worldwide as part of colorectal cancer screening programs. Employing FIT samples from 1034 CRCbiome participants, recruited from a Norwegian colorectal cancer screening study, we identify, annotate and characterize more than 18000 DNA viruses, using shotgun metagenome sequencing. Only six percent of them are assigned to a known taxonomic family, with Microviridae being the most prevalent viral family. Linking individual profiles to comprehensive lifestyle and demographic data shows 17/25 of the variables to be associated with the gut virome. Physical activity, smoking, and dietary fiber consumption exhibit strong and consistent associations with both diversity and relative abundance of individual viruses, as well as with enrichment for auxiliary metabolic genes. We demonstrate the suitability of FIT samples for virome analysis, opening an opportunity for large-scale studies of this enigmatic part of the gut microbiome. The diverse viral populations and their connections to the individual lifestyle uncovered herein paves the way for further exploration of the role of the gut virome in health and disease.

• Avershina, Ekaterina; Khezri, Abdolrahman & Ahmad, Rafi (2023). Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics—Current State and Whole Genome Sequencing Implementation Perspectives. Antibiotics. 12(4). doi: 10.3390/antibiotics12040781. Full text in Research Archive Show summary

  Antimicrobial resistance (AMR), defined as the ability of microorganisms to withstand antimicrobial treatment, is responsible for millions of deaths annually. The rapid spread of AMR across continents warrants systematic changes in healthcare routines and protocols. One of the fundamental issues with AMR spread is the lack of rapid diagnostic tools for pathogen identification and AMR detection. Resistance profile identification often depends on pathogen culturing and thus may last up to several days. This contributes to the misuse of antibiotics for viral infection, the use of inappropriate antibiotics, the overuse of broad-spectrum antibiotics, or delayed infection treatment. Current DNA sequencing technologies offer the potential to develop rapid infection and AMR diagnostic tools that can provide information in a few hours rather than days. However, these techniques commonly require advanced bioinformatics knowledge and, at present, are not suited for routine lab use. In this review, we give an overview of the AMR burden on healthcare, describe current pathogen identification and AMR screening methods, and provide perspectives on how DNA sequencing may be used for rapid diagnostics. Additionally, we discuss the common steps used for DNA data analysis, currently available pipelines, and tools for analysis. Direct, culture-independent sequencing has the potential to complement current culture-based methods in routine clinical settings. However, there is a need for a minimum set of standards in terms of evaluating the results generated. Additionally, we discuss the use of machine learning algorithms regarding pathogen phenotype detection (resistance/susceptibility to an antibiotic).

• Avershina, Ekaterina; Frye, Stephan Alfons; ali, jawad; Taxt, Arne Michael & Ahmad, Rafi (2022). Ultrafast and Cost-Effective Pathogen Identification and Resistance Gene Detection in a Clinical Setting Using Nanopore Flongle Sequencing. Frontiers in Microbiology. 13. doi: 10.3389/fmicb.2022.822402. Full text in Research Archive Show summary

  Rapid bacterial identification and antimicrobial resistance gene (ARG) detection are crucial for fast optimization of antibiotic treatment, especially for septic patients where each hour of delayed antibiotic prescription might have lethal consequences. This work investigates whether the Oxford Nanopore Technology’s (ONT) Flongle sequencing platform is suitable for real-time sequencing directly from blood cultures to identify bacteria and detect resistance-encoding genes. For the analysis, we used pure bacterial cultures of four clinical isolates of Escherichia coli and Klebsiella pneumoniae and two blood samples spiked with either E. coli or K. pneumoniae that had been cultured overnight. We sequenced both the whole genome and plasmids isolated from these bacteria using two different sequencing kits. Generally, Flongle data allow rapid bacterial ID and resistome detection based on the first 1,000–3,000 generated sequences (10 min to 3 h from the sequencing start), albeit ARG variant identification did not always correspond to ONT MinION and Illumina sequencing-based data. Flongle data are sufficient for 99.9% genome coverage within at most 20,000 (clinical isolates) or 50,000 (positive blood cultures) sequences generated. The SQK-LSK110 Ligation kit resulted in higher genome coverage and more accurate bacterial identification than the SQK-RBK004 Rapid Barcode kit.

• Hanrahan, Niall; Lister, Adam; Highmore, Callum; Rajith, Leena; Avershina, Ekaterina & Ali, Jawad [Show all 9 contributors for this article] (2022). Enhanced Raman techniques for infection diagnostics. Proceedings of SPIE, the International Society for Optical Engineering. ISSN 0277-786X. 12203, p. 6–17. doi: 10.1117/12.2635324. Full text in Research Archive Show summary

  In this paper we describe our recent work in multi-excitation surface enhanced Raman spectroscopy (MX-SERS), and its application for robust strain-level bacteria identification. The development of MX-SERS follows directly from our previous work in rapid bacterial identification using multiexcitation Raman spectroscopy (MX-Raman), which enabled highly accurate (up to 99.75%) strainlevel distinction of bacteria, including antibiotic resistant strains of bacteria and from within complex media. In this work we use the strong wavelength dependence of both the Raman scattering crosssection and the surface plasmon to demonstrate a novel capability in bacteria identification. Compared to MX-Raman, MX-SERS has up to 8x faster data acquisition speed as well as up to 4000x lower laser power incident on the sample. Furthermore, we fabricate SERS-active substrates with a simple and low-cost fabrication method that can be adapted to fit a chosen wavelength regime. This combination of strain-level sensitivity and high-speed detection, combined with a low-cost SERS substrate, has strong potential applications in clinical diagnostics, and could be integrated within a real-world pathogen detection workflow. This presents new capabilities in label-free bacterial detection including novel culture-free investigation capabilities, and an improved methodology for sample handling with minimal preparation and processing.

View all works in NVA

• Birkeland, Einar Elvbakken; Kværner, Ane Sørlie; Istvan, Paula; Bermanian, Vahid; Bucher-Johannessen, Cecilie & Avershina, Ekaterina [Show all 9 contributors for this article] (2022). The microbiome in fecal immunochemical tests from colorectal cancer screening participants – can it be used as a screening biomarker? Full text in Research Archive

View all works in NVA