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. Fulltekst i vitenarkiv
• Birkeland, Einar Elvbakken; Kværner, Ane Sørlie; Avershina, Ekaterina; Johannessen, Cecilie Bucher -; Bemanian, Vahid & Blix, Hege Salvesen [Vis alle 14 forfattere av denne artikkelen] (2026). Microbiome signatures for detection of colorectal lesions in population-based FIT screening. Nature Communications. 17. doi: 10.1038/s41467-026-75962-1. Fulltekst i vitenarkiv Vis sammendrag

  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 [Vis alle 14 forfattere av denne artikkelen] (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), s. 1–18. doi: 10.1007/s00394-026-03960-6. Fulltekst i vitenarkiv Vis sammendrag

  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. Fulltekst i vitenarkiv Vis sammendrag

  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 [Vis alle 8 forfattere av denne artikkelen] (2024). Species-level verification of Phascolarctobacterium association with colorectal cancer. mSystems. 9(10). doi: 10.1128/msystems.00734-24. Fulltekst i vitenarkiv Vis sammendrag

  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 [Vis alle 11 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv Vis sammendrag

  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. Fulltekst i vitenarkiv Vis sammendrag

  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. Fulltekst i vitenarkiv Vis sammendrag

  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 [Vis alle 9 forfattere av denne artikkelen] (2022). Enhanced Raman techniques for infection diagnostics. Proceedings of SPIE, the International Society for Optical Engineering. ISSN 0277-786X. 12203, s. 6–17. doi: 10.1117/12.2635324. Fulltekst i vitenarkiv Vis sammendrag

  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.

• Avershina, Ekaterina; Shapovalova, Valeria & Shipulin, German (2021). Fighting Antibiotic Resistance in Hospital-Acquired Infections: Current State and Emerging Technologies in Disease Prevention, Diagnostics and Therapy. Frontiers in Microbiology. 12. doi: 10.3389/fmicb.2021.707330. Fulltekst i vitenarkiv Vis sammendrag

  Rising antibiotic resistance is a global threat that is projected to cause more deaths than all cancers combined by 2050. In this review, we set to summarize the current state of antibiotic resistance, and to give an overview of the emerging technologies aimed to escape the pre-antibiotic era recurrence. We conducted a comprehensive literature survey of >150 original research and review articles indexed in the Web of Science using “antimicrobial resistance,” “diagnostics,” “therapeutics,” “disinfection,” “nosocomial infections,” “ESKAPE pathogens” as key words. We discuss the impact of nosocomial infections on the spread of multi-drug resistant bacteria, give an overview over existing and developing strategies for faster diagnostics of infectious diseases, review current and novel approaches in therapy of infectious diseases, and finally discuss strategies for hospital disinfection to prevent MDR bacteria spread.

• Khezri, Abdolrahman; Avershina, Ekaterina & Ahmad, Rafi (2021). Hybrid Assembly Provides Improved Resolution of Plasmids, Antimicrobial Resistance Genes, and Virulence Factors in Escherichia coli and Klebsiella pneumoniae Clinical Isolates. Microorganisms. 9(12), s. 1–18. doi: 10.3390/microorganisms9122560. Fulltekst i vitenarkiv Vis sammendrag

  Emerging new sequencing technologies have provided researchers with a unique opportunity to study factors related to microbial pathogenicity, such as antimicrobial resistance (AMR) genes and virulence factors. However, the use of whole-genome sequence (WGS) data requires good knowledge of the bioinformatics involved, as well as the necessary techniques. In this study, a total of nine Escherichia coli and Klebsiella pneumoniae isolates from Norwegian clinical samples were sequenced using both MinION and Illumina platforms. Three out of nine samples were sequenced directly from blood culture, and one sample was sequenced from a mixed-blood culture. For genome assembly, several long-read, (Canu, Flye, Unicycler, and Miniasm), short-read (ABySS, Unicycler and SPAdes) and hybrid assemblers (Unicycler, hybridSPAdes, and MaSurCa) were tested. Assembled genomes from the best-performing assemblers (according to quality checks using QUAST and BUSCO) were subjected to downstream analyses. Flye and Unicycler assemblers performed best for the assembly of long and short reads, respectively. For hybrid assembly, Unicycler was the top-performing assembler and produced more circularized and complete genome assemblies. Hybrid assembled genomes performed substantially better in downstream analyses to predict putative plasmids, AMR genes and β-lactamase gene variants, compared to MinION and Illumina assemblies. Thus, hybrid assembly has the potential to reveal factors related to microbial pathogenicity in clinical and mixed samples.

• Avershina, Ekaterina; Sharma, Priyanka; Taxt, Arne Michael; Singh, Harpreet; Frye, Stephan Alfons & Paul, Kolin [Vis alle 10 forfattere av denne artikkelen] (2021). AMR-Diag: Neural network based genotype-to-phenotype prediction of resistance towards β-lactams in Escherichia coli and Klebsiella pneumoniae. Computational and Structural Biotechnology Journal. 19, s. 1896–1906. doi: 10.1016/j.csbj.2021.03.027. Fulltekst i vitenarkiv Vis sammendrag

  Antibiotic resistance poses a major threat to public health. More effective ways of the antibiotic prescription are needed to delay the spread of antibiotic resistance. Employment of sequencing technologies coupled with the use of trained neural network algorithms for genotype-to-phenotype prediction will reduce the time needed for antibiotic susceptibility profile identification from days to hours.<p> <p>In this work, we have sequenced and phenotypically characterized 171 clinical isolates of Escherichia coli and Klebsiella pneumoniae from Norway and India. Based on the data, we have created neural networks to predict susceptibility for ampicillin, 3rd generation cephalosporins and carbapenems. All networks were trained on unassembled data, enabling prediction within minutes after the sequencing information becomes available. Moreover, they can be used both on Illumina and MinION generated data and do not require high genome coverage for phenotype prediction. We cross-checked our networks with previously published algorithms for genotype-to-phenotype prediction and their corresponding datasets. Besides, we also created an ensemble of networks trained on different datasets, which improved the cross-dataset prediction compared to a single network.<p> <p>Additionally, we have used data from direct sequencing of spiked blood cultures and found that AMR-Diag networks, coupled with MinION sequencing, can predict bacterial species, resistome, and phenotype as fast as 1–8 h from the sequencing start. To our knowledge, this is the first study for genotype-to-phenotype prediction: (1) employing a neural network method; (2) using data from more than one sequencing platform; and (3) utilizing sequence data from spiked blood cultures.

• Avershina, Ekaterina; Larsen, Marte Gro; Aspholm, Marina Elisabeth; Lindbäck, Toril; Storrø, Ola & Øien, Torbjørn [Vis alle 8 forfattere av denne artikkelen] (2020). Culture dependent and independent analyses suggest a low level of sharing of endospore-forming species between mothers and their children. Scientific Reports. doi: 10.1038/s41598-020-58858-y. Fulltekst i vitenarkiv
• Schei, Kasper; Simpson, Melanie Rae; Avershina, Ekaterina; Rudi, Knut; Øien, Torbjørn & Juliusson, Petur Benedikt [Vis alle 9 forfattere av denne artikkelen] (2020). Early gut fungal and bacterial microbiota and childhood growth. Frontiers in Pediatrics. 8, s. 1–11. doi: 10.3389/fped.2020.572538. Fulltekst i vitenarkiv Vis sammendrag

  Introduction: Childhood growth is a sensitive marker of health. Animal studies show increased height and weight velocity in the presence of fungal as well as antibiotic supplement in feed. Human studies on early gut microbiota and anthropometrics have mainly focused on bacteria only and overweight, with diverging results. We thus aimed to investigate the associations between childhood growth [height and body mass index (BMI)] and early fungal and bacterial gut microbiota. Methods: In a population-based cohort, a subset of 278 pregnant mothers was randomized to drink milk with or without probiotic bacteria during and after pregnancy. We obtained fecal samples in offspring at four time points between 0 and 2 years and anthropometric measurements 0 and 9 years. By quantitative PCR and 16S/ITS rRNA gene sequencing, children's gut microbiota abundance and diversity were analyzed against height standard deviation score (SDS) and BMI-SDS and presented as effect estimate (β) of linear mixed models. Results: From 278 included children (149 girls), 1,015 fecal samples were collected. Maternal probiotic administration did not affect childhood growth, and the groups were pooled. Fungal abundance at 2 years was positively associated with height-SDS at 2–9 years (β = 0.11 height-SDS; 95% CI, 0.00, 0.22) but not with BMI-SDS. Also, higher fungal abundance at 1 year was associated with a lower BMI-SDS at 0–1 year (β = −0.09 BMI-SDS; 95% CI, −0.18, −0.00), and both bacterial abundance and bacterial alpha diversity at 1 year were associated with lower BMI-SDS at 0–1 year (β = −0.13 BMI-SDS; 95% CI, −0.22, −0.04; and β = −0.19 BMI-SDS; 95% CI, −0.39, −0.00, respectively). Conclusions: In this prospective cohort following 0–9-year-old children, we observed that higher gut fungal abundances at 2 years were associated with taller children between 2 and 9 years. Also, higher gut fungal and bacterial abundances and higher gut bacterial diversity at 1 year were associated with lower BMI in the first year of life. The results may indicate interactions between early gut fungal microbiota and the human growth-regulating physiology, previously not reported. Clinical Trial Registration: Clinicaltrials.gov, NCT00159523.

• Taxt, Arne Michael; Avershina, Ekaterina; Frye, Stephan Alfons; Naseer, Mohammed Umaer & Ahmad, Rafi (2020). Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing. Scientific Reports. 10(1). doi: 10.1038/s41598-020-64616-x. Fulltekst i vitenarkiv Vis sammendrag

  Bloodstream infections (BSI) and sepsis are major causes of morbidity and mortality worldwide. Blood culture-based diagnostics usually requires 1–2 days for identification of bacterial agent and an additional 2–3 days for phenotypic determination of antibiotic susceptibility pattern. With the escalating burden of antimicrobial resistance (AMR) rapid diagnostics becomes increasingly important to secure adequate antibiotic therapy. Real-time whole genome sequencing represents a genotypic diagnostic approach with the ability to rapidly identify pathogens and AMR-encoding genes. Here we have used nanopore sequencing of bacterial DNA extracted from positive blood cultures for identification of pathogens, detection of plasmids and AMR-encoding genes. To our knowledge, this is the first study to gather the above-mentioned information from nanopore sequencing and conduct a comprehensive analysis for diagnostic purposes in real-time. Identification of pathogens was possible after 10 minutes of sequencing and all predefined AMR-encoding genes and plasmids from monoculture experiments were detected within one hour using raw nanopore sequencing data. Furthermore, we demonstrate the correct identification of plasmids and blaCTX-M subtypes using de novo assembled nanopore contigs. Results from this study hold great promise for future applications in clinical microbiology and for health care surveillance purposes.

• Avershina, Ekaterina; Larsen, Marte Gro; Aspholm, Marina Elisabeth; Lindbäck, Toril; Storrø, Ola & Øien, Torbjørn [Vis alle 8 forfattere av denne artikkelen] (2020). Culture dependent and independent analyses suggest a low level of sharing of endospore-forming species between mothers and their children. Scientific Reports. 10. doi: 10.1038/s41598-020-58858-y. Fulltekst i vitenarkiv Vis sammendrag

  Spore forming bacteria comprise a large part of the human gut microbiota. However, study of the endospores in gut microbiota is limited due to difficulties of culturing and numerous unknown germination factors. In this study we propose a new method for culture-independent characterization of endospores in stool samples. We have enriched DNA of spore-forming bacterial species from stool samples of 40 mother-child pairs from a previously described mother-child cohort. The samples were exposed to a two-step purification process comprising ethanol and ethidium monoazide (EMA) treatment to first kill vegetative cells and to subsequently eliminate their DNA from the samples. The composition of the ethanol-EMA resistant DNA was characterized by 16S rRNA marker gene sequencing. Operational taxonomic units (OTUs) belonging to the Clostridia class (OTU1: Romboutsia, OTU5: Peptostreptococcaceae and OTU14: Clostridium senso stricto) and one belonging to the Bacillus class (OTU20: Turicibacter) were significantly more abundant in the samples from mothers and children after ethanol-EMA treatment than in those treated with ethanol only. No correlation was observed between ethanol-EMA resistant OTUs detected in children and in their mothers, which indicates that a low level of spore-forming species are shared between mothers and their children. Anaerobic ethanol-resistant bacteria were isolated from all mothers and all children over 1 year of age. Generally, in 70% of the ethanol-treated samples used for anaerobic culturing, 16S rRNA gene sequences of bacterial isolates corresponded to OTUs detected in these samples after EMA treatment. We report a new DNA-based method for the characterization of endospores in gut microbiota. Our method has high degree of correspondence to the culture-based method, although it requires further optimization. Our results also indicate a high turnover of endospores in the gut during the first two years of life, perhaps with a high environmental impact.

• Khezri, Abdolrahman; Avershina, Ekaterina & Ahmad, Rafi (2020). Plasmid Identification and Plasmid-Mediated Antimicrobial Gene Detection in Norwegian Isolates. Microorganisms. 9(52). doi: 10.3390/microorganisms9010052. Fulltekst i vitenarkiv Vis sammendrag

  Norway is known for being one of the countries with the lowest levels of antimicrobial resistance (AMR). AMR, through acquired genes located on transposons or conjugative plasmids, is the horizontal transmission of genes required for a given bacteria to withstand antibiotics. In this work, bioinformatic analysis of whole-genome sequences and hybrid assembled data from Escherichia coli, and Klebsiella pneumoniae isolates from Norwegian patients was performed. For detection of putative plasmids in isolates, the plasmid assembly mode in SPAdes was used, followed by annotation of resulting contigs using PlasmidFinder and two curated plasmid databases (Brooks and PLSDB). Furthermore, ResFinder and Comprehensive Antibiotic Resistance Database (CARD) were used for the identification of antibiotic resistance genes (ARGs). The IncFIB plasmid was detected as the most prevalent plasmid in both E. coli, and K. pneumoniae isolates. Furthermore, ARGs such as aph(3″)-Ib, aph(6)-Id, sul1, sul2, tet(D), and qnrS1 were identified as the most abundant plasmid-mediated ARGs in Norwegian E. coli and K. pneumoniae isolates, respectively. Using hybrid assembly, we were able to locate plasmids and predict ARGs more confidently. In conclusion, plasmid identification and ARG detection using whole-genome sequencing data are heavily dependent on the database of choice; therefore, it is best to use several tools and/or hybrid assembly for obtaining reliable identification results. View Full-Text Keywords: Escherichia coli; Klebsiella pneumoniae; antimicrobial resistance; plasmid; plasmid-mediated genes; horizontal gene transfer

• Bjerke, Guro Alette; Rudi, Knut; Avershina, Ekaterina; Moen, Birgitte; Blom, Hans & Axelsson, Lars (2019). Exploring the brine microbiota of a traditional Norwegian fermented fish product (Rakfisk) from six different producers during two consecutive seasonal productions. Foods. 8(72). doi: 10.3390/foods8020072. Fulltekst i vitenarkiv Vis sammendrag

  The purpose of this study was to explore the microbiota of Norwegian fermented fish (rakfisk), a traditional product popular in the Norwegian market. Brine samples, collected from six producers during two subsequent years, were used. The producers applied different salt concentrations (between 3.8% and 7.2% NaCl), ripening temperatures (between 3.5 and 7.5 °C), fish species (trout or char), and fish upbringing (wild trout, on-shore farmed trout or char, and off-shore farmed char). The microbiota in the brine during the ripening process was mainly characterized by DNA-based, culture-independent methods. In total, 1710 samples were processed and of these 1342 were used for the final analysis. The microbiota was dominated by Gammaproteobacteria and Bacilli with the largest variance between samples associated with the genera Psychrobacter and Lactobacillus. The variance in the material was mainly determined by the origin of the samples, i.e., the different producers. The microbiota from the individual producers was to a large extent reproducible from one year to the next and appeared to be determined by the relatively small differences in the salinity and the ripening temperature. This is the first study exploring the microbiota in rakfisk brine and it provides insights into environmental factors affecting the rakfisk ecosystems.

• Ravi, Anuradha; Avershina, Ekaterina; Angell, Inga Leena; Ludvigsen, Jane; Manohar, Prasanth & Padmanaban, Sumathi [Vis alle 9 forfattere av denne artikkelen] (2018). Comparison of reduced metagenome and 16S rRNA gene sequencing for determination of genetic diversity and mother-child overlap of the gut associated microbiota. Journal of Microbiological Methods. ISSN 0167-7012. 149, s. 44–52. doi: 10.1016/j.mimet.2018.02.016. Fulltekst i vitenarkiv
• Avershina, Ekaterina; Angell, Inga Leena; Simpson, Melanie Rae; Storrø, Ola; Øien, Torbjørn & Johnsen, Roar [Vis alle 7 forfattere av denne artikkelen] (2018). Low maternal microbiota sharing across gut, breast milk and vagina, as revealed by 16s rRNA gene and reduced metagenomic sequencing. Genes. 9:231(5), s. 1–12. doi: 10.3390/genes9050231. Fulltekst i vitenarkiv Vis sammendrag

  The maternal microbiota plays an important role in infant gut colonization. In this work we have investigated which bacterial species are shared across the breast milk, vaginal and stool microbiotas of 109 women shortly before and after giving birth using 16S rRNA gene sequencing and a novel reduced metagenomic sequencing (RMS) approach in a subgroup of 16 women. All the species predicted by the 16S rRNA gene sequencing were also detected by RMS analysis and there was good correspondence between their relative abundances estimated by both approaches. Both approaches also demonstrate a low level of maternal microbiota sharing across the population and RMS analysis identified only two species common to most women and in all sample types (Bifidobacterium longum and Enterococcus faecalis). Breast milk was the only sample type that had significantly higher intra- than inter- individual similarity towards both vaginal and stool samples. We also searched our RMS dataset against an in silico generated reference database derived from bacterial isolates in the Human Microbiome Project. The use of this reference-based search enabled further separation of Bifidobacterium longum into Bifidobacterium longum ssp. longum and Bifidobacterium longum ssp. infantis. We also detected the Lactobacillus rhamnosus GG strain, which was used as a probiotic supplement by some women, demonstrating the potential of RMS approach for deeper taxonomic delineation and estimation.

• Avershina, Ekaterina; Slangsvold, Silje; Simpson, Melanie Rae; Storrø, Ola; Johnsen, Roar & Øien, Torbjørn [Vis alle 7 forfattere av denne artikkelen] (2017). Diversity of vaginal microbiota increases by the time of labor onset. Scientific Reports. 7(1), s. 17558–17558. doi: 10.1038/s41598-017-17972-0. Fulltekst i vitenarkiv Vis sammendrag

  Vaginal microbiota is an important early source of bacterial colonization for newborns. However, only a few small studies have investigated the composition of vaginal microbiota during labor. In this work, we analyzed vaginal swabs collected at 36 weeks gestation and at the onset of labor from 256 women participating in a randomized placebo-controlled study of probiotic supplementation for the prevention of atopic dermatitis in offspring. Although individuals’ vaginal microbiota was stable over time, several bacterial families, which are characteristic of mixed community state type (CST) IV, were overrepresented in vaginal swabs sampled at labor. Alpha-diversity also tended to increase by between 36 weeks gestation and the onset of birth. In the majority of women, CST remained the same throughout the study. Among the women who switched their vaginal microbiota from one CST to another, approximately half shifted towards CST IV. Although CST IV is often associated with bacterial vaginosis, which in turn may lead to preterm birth, in our cohort this shift was not associated with self-reported vaginosis, preterm delivery or birthweight. Probiotic consumption did not alter vaginal microbiota.

• Simpson, Melanie Rae; Avershina, Ekaterina; Storrø, Ola; Johnsen, Roar; Rudi, Knut & Øien, Torbjørn (2017). Breastfeeding associated microbiota in human milk following supplementation with Lactobacillus rhamnosus GG, Lactobacillus acidophilus La-5 and Bifidobacterium animalis subspecies lactis Bb-12. Journal of Dairy Science (JDS). ISSN 0022-0302. 101(2), s. 889–899. doi: 10.3168/jds.2017-13411. Fulltekst i vitenarkiv Vis sammendrag

  Breastfeeding is one of the major factors affecting the early development of the infant gut microbiota, and weaning is associated with a shift in the gut microbiota toward a more adult composition. Through breastfeeding, infants receive bioactive components that shape their microbiota while also being exposed to the breast milk and breast surface microbial communities. Recent studies have suggested the possibility of an entero-mammary route of microbial transfer, opening the possibility of infant gut microbiota modulation through maternal probiotic supplementation. In this study, we have analyzed breast milk samples collected at 10 d and 3 mo postpartum from women participating in the Probiotics in the Prevention of Allergy among Children in Trondheim placebo controlled trial. Women who were randomized to the probiotic arm of the Probiotics in the Prevention of Allergy among Children in Trondheim trial received a fermented milk supplemented with Lactobacillus rhamnosus GG, Lactobacillus acidophilus La-5, and Bifidobacterium animalis ssp. lactis Bb-12, consuming this daily from 4 wk before their expected due date until 3 mo after birth. In total, 472 breast milk samples were assessed for the administered bacteria using quantitative real-time PCR and the microbiota transferred during breastfeeding was analyzed using 16S ribosomal RNA gene sequencing of 142 samples. We found that breastfeeding is unlikely to be a significant source of L. rhamnosus GG, L. acidophilus La-5, and B. animalis ssp. lactis Bb-12 for infants in the probiotic arm of the trial. Furthermore, maternal supplementation did not significantly affect the overall composition of the breast milk microbiota transferred during breastfeeding. We also present a descriptive analysis of this microbiota, which was largely dominated by Streptococcus and Staphylococcus genera at both 10 d and 3 mo postpartum. Samples collected at 3 mo postpartum had a statistically significant lower presence and relative abundance of the Staphylococcus genus. These samples also had a greater number of observed species and diversity, including more operational taxonomic units from the Rothia, Veillonella, Granulicatella, and Methylbacterium genera.

• Avershina, Ekaterina; Cabrera, Rubio Raul; Lundgård, Krister; Martines, Gaspar Perez; Collado, Maria Carmen & Storrø, Ola [Vis alle 10 forfattere av denne artikkelen] (2017). Effect of probiotics in prevention of atopic dermatitis is dependent on the intrinsic microbiota at early infancy. Journal of Allergy and Clinical Immunology. ISSN 0091-6749. 139(4), s. 1399–1402.e8. doi: 10.1016/j.jaci.2016.09.056. Fulltekst i vitenarkiv
• Hanssen, Eirik Natås; Avershina, Ekaterina; Rudi, Knut; Gill, Peter & Snipen, Lars-Gustav (2017). Body Fluid Prediction from Microbial Patterns for Forensic Application. Forensic Science International: Genetics. ISSN 1872-4973. 30, s. 10–17. doi: 10.1016/j.fsigen.2017.05.009. Fulltekst i vitenarkiv
• Schei, Kasper; Avershina, Ekaterina; Øien, Torbjørn; Rudi, Knut; Follestad, Turid & Salamati, Saideh [Vis alle 7 forfattere av denne artikkelen] (2017). Early gut mycobiota and mother-offspring transfer. Microbiome. 5(1). doi: 10.1186/s40168-017-0319-x. Fulltekst i vitenarkiv
• Vebø, Heidi; Karlsson, Magdalena Kauczynska; Avershina, Ekaterina; Finnby, Lene & Rudi, Knut (2016). Bead-beating artefacts in the Bacteroidetes to Firmicutes ratio of the human stool metagenome. Journal of Microbiological Methods. ISSN 0167-7012. 129, s. 78–80. doi: 10.1016/j.mimet.2016.08.005. Fulltekst i vitenarkiv
• Kristoffersen, Camilla Thollefsen; Jensen, Rasmus Bovbjerg; Avershina, Ekaterina; Austbø, Dag; Tauson, Anne Helene & Rudi, Knut (2016). Diet-Dependent Modular Dynamic Interactions of the Equine Cecal Microbiota. Microbes and Environments. ISSN 1342-6311. 31(4), s. 378–386. doi: 10.1264/jsme2.ME16061. Fulltekst i vitenarkiv
• Avershina, Ekaterina; Lundgård, Krister; Sekelja, Monika; Dotterud, Christian; Storrø, Ola & Øien, Torbjørn [Vis alle 8 forfattere av denne artikkelen] (2016). Transition from infant- to adult-like gut microbiota. Environmental Microbiology. ISSN 1462-2912. 18(7), s. 2226–2236. doi: 10.1111/1462-2920.13248. Fulltekst i vitenarkiv
• Hansen, Naja C Kærsgaard; Avershina, Ekaterina; Mydland, Liv Torunn; Næsset, Jon Anders; Austbø, Dag & Moen, Birgitte [Vis alle 8 forfattere av denne artikkelen] (2015). High nutrient availability reduces the diversity and stability of the equine caecal microbiota. Microbial Ecology in Health and Disease. ISSN 0891-060X. 26. doi: 10.3402/mehd.v26.27216. Fulltekst i vitenarkiv Vis sammendrag

  For mammals, the function and stability of the gastrointestinal (GI) microbiota are important for health and survival. The GI microbiota supplies the host with volatile fatty acids (VFAs) (1, 2), modulates the host GI immune responses, and forms a barrier against invasion of pathogens (3). It is well established that diet modulates the GI microbiota (2), while our knowledge is limited with respect to how diet affects the functionality, stability, and diversity of the gut microbiota. A particularly intriguing unresolved question is how these factors are affected by postprandial nutrient availability. The GI microbiota is crucial for efficient nutrient utilisation in equines, since up to 60% of the forage is digested by microbial fermentation – mostly occurring in the hindgut (4, 5). The equine caecum is an enlargement of the hindgut, containing a highly complex microbial ecosystem mainly dominated by members of the bacterial phyla Firmicutes and Bacteroides (6, 7). The effects of a single meal on the hindgut microbiota and fermentation pattern will be most significant in the caecum (8). Horse forage is commonly supplemented with whole oats to increase the energy intake. Whole oats consists of a core of easily fermentable starch that can partly be defined as resistant starch (9–11), since the starch-rich endosperm is encapsulated in a hull delaying the access of digestive enzymes to the starch (12). Thus, if not entirely chewed, a part of the starch given in the oat diet will escape small intestinal digestion, being a source for rapid hindgut fermentation. The aim of our work was to evaluate the effect of high and low available nutrient diets on the equine caecal microbiota function and stability. We did this in an in vivo experiment with horses fed hay (low and slower nutrient availability) or a hay/whole oats diet (high and more rapid nutrient availability). We used 16S rRNA gene deep sequencing and direct mixed sequencing for determining the microbiota composition in combination with measurements of VFA, NH3N, and pH for functional analyses of the caecum. We present results showing that the high available nutrient diet reduces both the diversity and the temporal stability of the caecal microbiota. These results are discussed in the light of general ecological theories and potential health consequences.

• Ravi, Anuradha; Avershina, Ekaterina; Foley, Steven L.; Ludvigsen, Jane; Storrø, Ola & Øien, Torbjørn [Vis alle 10 forfattere av denne artikkelen] (2015). The commensal infant gut meta-mobilome as a potential reservoir for persistent multidrug resistance integrons. Scientific Reports. 5:15317. doi: 10.1038/srep15317. Fulltekst i vitenarkiv Vis sammendrag

  Despite the accumulating knowledge on the development and establishment of the gut microbiota, its role as a reservoir for multidrug resistance is not well understood. This study investigated the prevalence and persistence patterns of an integrase gene (int1), used as a proxy for integrons (which often carry multiple antimicrobial resistance genes), in the fecal microbiota of 147 mothers and their children sampled longitudinally from birth to 2 years. The study showed the int1 gene was detected in 15% of the study population and apparently more persistent than the microbial community structure itself. We found int1 to be persistent throughout the first two years of life, as well as between mothers and their 2-year-old children. Metagenome sequencing revealed integrons in the gut meta-mobilome that were associated with plasmids and multidrug resistance. In conclusion, the persistent nature of integrons in the infant gut microbiota makes it a potential reservoir of mobile multidrug resistance.

• Nowak, Piotr; Trøseid, Marius; Avershina, Ekaterina; Barqasho, Babilonia; Neogi, Ujjwal & Holm, Kristian [Vis alle 12 forfattere av denne artikkelen] (2015). Gut microbiota diversity predicts immune status in HIV-1 infection. AIDS (London). ISSN 0269-9370. 29(18), s. 2409–2418. doi: 10.1097/QAD.0000000000000869. Fulltekst i vitenarkiv
• Rodriguez, Juan Miguel; Murphy, Kiera; Stanton, Catherine; Ross, R. Paul; Kober, Olivia I. & Juge, Nathalie [Vis alle 12 forfattere av denne artikkelen] (2015). The composition of the gut microbiota throughout life, with an emphasis on early life. Microbial Ecology in Health and Disease. ISSN 0891-060X. 26. doi: 10.3402/mehd.v26.26050. Fulltekst i vitenarkiv
• Avershina, Ekaterina & Rudi, Knut (2015). Dominant short repeated sequences in bacterial genomes. Genomics. ISSN 0888-7543. 105(3), s. 175–181. doi: 10.1016/j.ygeno.2014.12.009. Fulltekst i vitenarkiv
• Dotterud, Christian; Avershina, Ekaterina; Sekelja, Monika; Simpson, Melanie Rae; Rudi, Knut & Storrø, Ola [Vis alle 8 forfattere av denne artikkelen] (2015). Does maternal perinatal probiotic supplementation alter the intestinal microbiota of mother and child? Journal of Pediatric Gastroenterology and Nutrition - JPGN. ISSN 0277-2116. 61(2), s. 200–207. doi: 10.1097/MPG.0000000000000781. Fulltekst i vitenarkiv
• Avershina, Ekaterina & Rudi, Knut (2015). Confusion about the species richness of human gut microbiota. Beneficial Microbes. ISSN 1876-2883. 6(5), s. 657–659. doi: 10.3920/BM2015.0007. Fulltekst i vitenarkiv
• Avershina, Ekaterina; Ravi, Anuradha; Storrø, Ola; Øien, Torbjørn; Johnsen, Roar & Rudi, Knut (2015). Potential association of vacuum cleaning frequency with an altered gut microbiota in pregnant women and their 2-year-old children. Microbiome. 3(65). doi: 10.1186/s40168-015-0125-2. Fulltekst i vitenarkiv Vis sammendrag

  Background: Westernized lifestyle and hygienic behavior have contributed to dramatic changes in the human-associated microbiota. This particularly relates to indoor activities such as house cleaning. We therefore investigated the associations between washing and vacuum cleaning frequency and the gut microbiota composition in a large longitudinal cohort of mothers and their children. The gut microbiota composition was determined using 16S ribosomal RNA (rRNA) gene Illumina deep sequencing. Results: We found that high vacuum cleaning frequency about twice or more a week was associated with an altered gut microbiota composition both during pregnancy and for 2-year-old children, while there were no associations with house washing frequency. In total, six Operational Taxonomic Units (OTUs) showed significant False Discovery Rate (FDR) corrected associations with vacuum cleaning frequency for mothers (two positive and four negative) and five for 2-year-old children (four positive and one negative). For mothers and the 2-year-old children, OTUs among the dominant microbiota (average >5 %) showed correlation to vacuum cleaning frequency, with an increase in Faecalibacterium prausnitzii for mothers (p = 0.013, FDR corrected), and Blautia sp. for 2-year children (p = 0.012, FDR corrected). Conclusions: Bacteria showing significant associations are among the dominant gut microbiota, which may indicate indirect immunomodulation of the gut microbiota possibly through increased allergen (dust mites) exposure as a potential mechanism. However, further exploration is needed to unveil mechanistic details.

• Avershina, Ekaterina & Rudi, Knut (2015). Over-represented pairwise 16S rRNA gene sequence distance levels among prokaryotes. Annals of Microbiology. ISSN 1590-4261. doi: 10.1007/s13213-015-1107-0. Fulltekst i vitenarkiv
• Schanche, Melissa; Avershina, Ekaterina; Dotterud, Christian Kvikne; Øien, Torbjørn; Storrø, Ola & Johnsen, Roar [Vis alle 7 forfattere av denne artikkelen] (2015). High-Resolution Analyses of Overlap in the Microbiota Between Mothers and Their Children. Current Microbiology. ISSN 0343-8651. 71(2), s. 283–290. doi: 10.1007/s00284-015-0843-5. Fulltekst i vitenarkiv
• Ludvigsen, Jane; Rangberg, Anbjørg; Avershina, Ekaterina; Sekelja, Monika; Kreibich, Claus D & Amdam, Gro Vang [Vis alle 7 forfattere av denne artikkelen] (2015). Shifts in the midgut/pyloric microbiota composition within a honey bee apiary throughout a season. Microbes and Environments. ISSN 1342-6311. 30(3), s. 235–244. doi: 10.1264/jsme2.ME15019. Fulltekst i vitenarkiv
• Nwosu, Felix; Avershina, Ekaterina; Wilson, Robert Charles & Rudi, Knut (2014). Gut microbiota in HIV infection: Implication for disease progression and management. Gastroenterology Research and Practice. ISSN 1687-6121. 2014. doi: 10.1155/2014/803185. Fulltekst i vitenarkiv Vis sammendrag

  Survival rates among HIV patients have significantly improved since the introduction of antiretroviral therapy (ART) in HIV management. However, persistent disease progression and clinical complications in virally suppressed individuals point to additional contributing factors other than HIV replication; microbial translocation is one such factor. The role of underlying commensal microbes and microbial products that traverse the intestinal lumen into systemic circulation in the absence of overt bacteraemia is under current investigation. This review focuses on current knowledge of the complex microbial communities and microbial markers involved in the disruption of mucosal immune T-cells in the promotion of inflammatory processes in HIV infections. Unanswered questions and aims for future studies are addressed. We provide perspective for discussing potential future therapeutic strategies focused on modulating the gut microbiota to abate HIV disease progression.

• Ravi, Anuradha; Avershina, Ekaterina; Rudi, Knut; Ludvigsen, Jane & L'Abée-Lund, Trine (2014). Integrons in the Intestinal Microbiota as Reservoirs for Transmission of Antibiotic Resistance Genes. Pathogens. ISSN 2076-0817. 3, s. 238–248. Fulltekst i vitenarkiv
• Naseribafrouei, Ali; Hestad, Knut; Avershina, Ekaterina; Sekelja, Monika; Linløkken, Arne & Wilson, Robert Charles [Vis alle 7 forfattere av denne artikkelen] (2014). Correlation between the human fecal microbiota and depression. Neurogastroenterology and Motility. ISSN 1350-1925. 26(8), s. 1155–1162. doi: 10.1111/nmo.12378. Fulltekst i vitenarkiv Vis sammendrag

  Background: Depression is a chronic syndrome with a pathogenesis linked to various genetic, biological, and environmental factors. Several links between gut microbiota and depression have been established in animal models. In humans, however, few correlations have yet been demonstrated. The aim of our work was therefore to identify potential correlations between human fecal microbiota (as a proxy for gut microbiota) and depression. Methods: We analyzed fecal samples from 55 people, 37 patients, and 18 non-depressed controls. Our analyses were based on data generated by Illumina deep sequencing of 16S rRNA gene amplicons. Key Results: We found several correlations between depression and fecal microbiota. The correlations, however, showed opposite directions even for closely related Operational Taxonomic Units (OTU's), but were still associated with certain higher order phylogroups. The order Bacteroidales showed an overrepresentation (p = 0.05), while the family Lachnospiraceae showed an underrepresentation (p = 0.02) of OTU's associated with depression. At low taxonomic levels, there was one clade consisting of five OTU's within the genus Oscillibacter, and one clade within Alistipes (consisting of four OTU's) that showed a significant association with depression (p = 0.03 and 0.01, respectively). Conclusions & Inferences: The Oscillibacter type strain has valeric acid as its main metabolic end product, a homolog of neurotransmitter GABA, while Alistipes has previously been shown to be associated with induced stress in mice. In conclusion, the taxonomic correlations detected here may therefore correspond to mechanistic models.

• Avershina, Ekaterina; Storrø, Ola; Øien, Torbjørn; Johnsen, Roar; Pope, Phil & Rudi, Knut (2014). Major faecal microbiota shifts in composition and diversity with age in a geographically restricted cohort of mothers and their children. FEMS Microbiology Ecology. ISSN 0168-6496. 87(1), s. 280–290. doi: 10.1111/1574-6941.12223. Fulltekst i vitenarkiv Vis sammendrag

  Despite the importance, the diversity of the human infant gut microbiota still remains poorly characterized at the regional scale. Here, we investigated the faecal microbiota diversity in a large 16S rRNA gene data set from a healthy cohort of 86 mothers and their children from the Trondheim region in Norway. Samples were collected from mothers during early and late pregnancy, as well as from their children at 3 days, 10 days, 4 months, 1 year and 2 years of age. Using a combination of Sanger sequencing of amplicon mixtures (without cloning), real-time quantitative PCR and deep pyrosequencing, we observed a clear age-related colonization pattern in children that was surprisingly evident between 3- and 10-day samples. In contrast, we did not observe any shifts in microbial composition during pregnancy. We found that alpha-diversity was highest at 2 years and lowest at 4 months, whereas beta-diversity estimates indicated highest interindividual variation in newborns. Variation significantly decreased by the age of 10 days and was observed to be convergent over time; however, there were still major differences between 2 years and adults whom exhibited the lowest interindividual diversity. Taken together, the major age-affiliated population shift within gut microbiota suggests that there are important mechanisms for transmission and persistence of gut bacteria that remain unknown.

• Thorkildsen, Lill-Therese; Nwosu, Felix; Avershina, Ekaterina; Ricanek, Petr; Perminow, Gøri Margrete & Brackmann, Stephan [Vis alle 8 forfattere av denne artikkelen] (2013). Dominant Fecal Microbiota in Newly Diagnosed Untreated Inflammatory Bowel Disease Patients. Gastroenterology Research and Practice. ISSN 1687-6121. doi: 10.1155/2013/636785. Fulltekst i vitenarkiv
• Avershina, Ekaterina; Storrø, Ola; Øien, Torbjørn; Johnsen, Roar; Wilson, Robert & Egeland, Thore [Vis alle 7 forfattere av denne artikkelen] (2013). Bifidobacterial Succession and Correlation Networks in a Large Unselected Cohort of Mothers and Their Children. Applied and Environmental Microbiology. ISSN 0099-2240. 79(2), s. 497–507. doi: 10.1128/AEM.02359-12. Fulltekst i vitenarkiv Vis sammendrag

  Bifidobacteria are a major microbial component of infant gut microbiota, which is believed to promote health benefits for the host and stimulate maturation of the immune system. Despite their perceived importance, very little is known about the natural development of and possible correlations between bifidobacteria in human populations. To address this knowledge gap, we analyzed stool samples from a randomly selected healthy cohort of 87 infants and their mothers with>90% of vaginal delivery and nearly 100% breast-feeding at 4 months. Fecal material was sampled during pregnancy, at 3 and 10 days, at 4 months, and at 1 and 2 years after birth. Stool samples were predicted to be rich in the species Bifidobacterium adolescentis, B. bifidum, B. den- tium, B. breve, and B. longum. Due to high variation, we did not identify a clear age-related structure at the individual level. Within the population as a whole, however, there were clear age-related successions. Negative correlations between the B. longum group and B. adolescentis were detected in adults and in 1- and 2-year-old children, whereas negative correlations between B. longum and B. breve were characteristic for newborns and 4-month-old infants. The highly structured age-related development of and correlation networks between bifidobacterial species during the first 2 years of life mirrors their different or competing nutritional requirements, which in turn may be associated with specific biological functions in the development of healthy gut.

• Nwosu, Felix; Thorkildsen, Lill-Therese; Avershina, Ekaterina; Ricanek, Petr; Perminow, Gøri Margrete & Brackmann, Stephan [Vis alle 8 forfattere av denne artikkelen] (2013). Age-Dependent Fecal Bacterial Correlation to Inflammatory Bowel Disease for Newly Diagnosed Untreated Children. Gastroenterology Research and Practice. ISSN 1687-6121. doi: 10.1155/2013/302398. Fulltekst i vitenarkiv Vis sammendrag

  The knowledge about correlation patterns between the fecal microbiota and inflammatory bowel diseases (IBD)—comprising the two subforms Crohn’s disease (CD) and ulcerative colitis (UC)—for newly diagnosed untreated children is limited. To address this knowledge gap, a selection of faecal specimens (CD, n = 27 and UC, n = 16) and non-IBD controls (n = 30) children (age < 18 years) was analysed utilising bacterial small subunit (SSU) rRNA. We found, surprising age dependence for the fecal microbiota correlating to IBD.The most pronounced patternswere that E. coli was positively (R 2= 0.16, P = 0.05) and Bacteroidetes, negatively (R 2 = 0.15, P = 0.05) correlated to age for CD patients. For UC, we found an apparent opposite age-related disease correlation for both Bacteroides and Escherichia. In addition, there was an overrepresentation of Haemophilus for the UC children. From our results we propose a model where the aetiology of IBD is related to an on-going immunological development in children requiring different age-dependent bacterial stimuli. The impact of our findings could be a better age stratification for understanding and treating IBD in children.

• Storrø, Ola; Avershina, Ekaterina & Rudi, Knut (2013). Diversity of intestinal microbiota in infancy and the risk of allergic disease in childhood. Current Opinion in Allergy and Clinical Immunology. ISSN 1528-4050. 13(3), s. 257–262. doi: 10.1097/ACI.0b013e328360968b. Fulltekst i vitenarkiv Vis sammendrag

  Purpose of review Numerous studies have attempted to describe specific microbiota deviations that may precede atopic sensitization and atopic disease in childhood. This has given rise to a hypothesis suggesting that a reduced intestinal microbial diversity in infancy increases the risk of allergic manifestations. This review intends to sum up the main findings and discuss relevant exposures that regulate intestinal microbial diversity. Recent findings Taken together the three studies in this review lend support to the diversity hypothesis, but reported differences related to atopic sensitization and clinical expression are discussed. A summary on analytic methods and functional aspect of the microbiota in allergic disease is presented to ameliorate a presentation of recent articles on environmental and host-factors regulating microbiota composition and diversity. Summary The current evidence indicates that intestinal microbiota diversity can be associated with allergic diseases, but the exact mechanisms and interactions contributing to this effect are far from understood and need further investigation. Keywords childhood, diversity, environment, host-factors

• Avershina, Ekaterina; Frisli, Trine & Rudi, Knut (2013). De novo Semi-alignment of 16S rRNA Gene Sequences for Deep Phylogenetic Characterization of Next Generation Sequencing Data. Microbes and Environments. ISSN 1342-6311. 28(2), s. 211–216. doi: 10.1264/jsme2.ME12157. Fulltekst i vitenarkiv
• Avershina, Ekaterina & Rudi, Knut (2013). Is it who you are or what you do that is important in the human gut? Beneficial Microbes. ISSN 1876-2883. 4(3), s. 219–222. doi: 10.3920/BM2013.0016. Fulltekst i vitenarkiv

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• Birkeland, Einar Elvbakken; Kværner, Ane Sørlie; Istvan, Paula; Bermanian, Vahid; Bucher-Johannessen, Cecilie & Avershina, Ekaterina [Vis alle 9 forfattere av denne artikkelen] (2022). The microbiome in fecal immunochemical tests from colorectal cancer screening participants – can it be used as a screening biomarker? Fulltekst i vitenarkiv
• Avershina, Ekaterina; Birkeland, Einar Elvbakken; Berstad, Paula; Hoff, Geir Svein & Rounge, Trine Ballestad (2022). Total neoplastic polyp volume is correlated to several bacterial taxa in faecal immunochemical test-positive CRC-screening participants. Fulltekst i vitenarkiv
• Avershina, Ekaterina; Birkeland, Einar Elvbakken; Berstad, Paula; Hoff, Geir Svein & Rounge, Trine Ballestad (2022). Total neoplastic polyp volume is correlated to several bacterial taxa in faecal immunochemical test-positive CRC-screening participants. Fulltekst i vitenarkiv
• Schei, Kasper; Avershina, Ekaterina; Øien, Torbjørn; Rudi, Knut; Follestad, Turid & Salamati, Saideh [Vis alle 7 forfattere av denne artikkelen] (2021). Correction to: Early gut mycobiota and mother-offspring transfer. Microbiome. 9. doi: 10.1186/s40168-021-01094-x. Fulltekst i vitenarkiv
• Ahmad, Rafi; Taxt, Arne Michael; Avershina, Ekaterina; Frye, Stephan Alfons & Naseer, Mohammed Umaer (2020). Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing. Fulltekst i vitenarkiv
• Ahmad, Rafi; Taxt, Arne Michael; Avershina, Ekaterina; Frye, Stephan Alfons & Naseer, Mohammed Umaer (2020). Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing. Fulltekst i vitenarkiv
• Avershina, Ekaterina & Rudi, Knut (2017). Tarmflora ved tidlig alder påvirker effekt av probiotika i forebygging av atopisk dermatitt. BestPractice Dermatologi. 8(26). Fulltekst i vitenarkiv
• Avershina, Ekaterina; Larsen, MarteGro & Rudi, Knut (2017). Culture-independent characterization of spores in stool samples. Fulltekst i vitenarkiv
• Avershina, Ekaterina (2017). Microbial adaptations to human gut. Fulltekst i vitenarkiv
• Avershina, Ekaterina (2017). Impact of gut microbiota development on human health. Methods for culture-independent analysis of complex microbial communities. Fulltekst i vitenarkiv
• Simpson, Melanie Rae; Dotterud, Christian; Avershina, Ekaterina; Sekelja, Monika; Rudi, Knut & Storrø, Ola [Vis alle 8 forfattere av denne artikkelen] (2015). Probiotics to mothers - impact on diversity in offspring (oral presentation). Fulltekst i vitenarkiv
• Avershina, Ekaterina (2013). De novo semi-alignment of 16S rRNA gene sequences for deep phylogenetic characterization of next generation sequencing data. Fulltekst i vitenarkiv
• Hestad, Knut; Linløkken, Arne; Wilson, Robert Charles; Avershina, Ekaterina & Rudi, Knut (2013). Correlation between the human fecal microbiota and depression. Fulltekst i vitenarkiv
• Avershina, Ekaterina & Rudi, Knut (2013). Is it who you are or what you do that is important in the human gut? Fulltekst i vitenarkiv
• Avershina, Ekaterina; Long, Wen-Min; McCartney, Anne & Rudi, Knut (2013). Effects of Carbohydrate source and oxygen on bifidobacteria correlation patterns. The Intestinal Microbiota and Gut Health: Contribution of the Diet, Bacterial Metabolites, Host Interactions and Impact on Health and Disease. Fulltekst i vitenarkiv
• Avershina, Ekaterina; Long, Wen-Min; McCartney, Anne & Rudi, Knut (2013). Effects of Carbohydrate source and oxygen on bifidobacteria correlation patterns. Fulltekst i vitenarkiv
• Ravi, Anuradha; Avershina, Ekaterina & Rudi, Knut (2013). Integrons in the microbiota as a reservoir for transmission of antibiotic resistant genes to pathogens. Fulltekst i vitenarkiv
• Avershina, Ekaterina & Rudi, Knut (2013). De novo semi-alignment of 16S rRNA gene sequences for deep phylogenetic characterization of next generation sequencing data. Fulltekst i vitenarkiv
• Avershina, Ekaterina; Pope, Phil; Storrø, Ola; Øien, Torbjørn; Johnsen, Roar & Rudi, Knut (2012). Human infant gut microbiota shifts in metapopulation composition and ecology with age. Fulltekst i vitenarkiv
• Avershina, Ekaterina; Storrø, Ola; Øyen, T; Johnsen, R; Egeland, Thore & Rudi, Knut (2012). Natural development of Bifidobacteria in a large unselected cohort of mothers and their children. Fulltekst i vitenarkiv
• Avershina, Ekaterina; Storrø, Ola; Øien, Torbjørn; Johnsen, Roar; Wilson, Robert C. & Egeland, Thore [Vis alle 7 forfattere av denne artikkelen] (2012). Natural development of Bifidobacterium spp. in a large unselected cohort of mothers and their infants. Fulltekst i vitenarkiv
• Avershina, Ekaterina; Storrø, Ola; Øien, Torbjørn; Johnsen, Roar; Wilson, Robert C. & Egeland, Thore [Vis alle 7 forfattere av denne artikkelen] (2012). Natural development of Bifidobacterium spp. in a large unselected cohort of mothers and their infants. Fulltekst i vitenarkiv
• Avershina, Ekaterina; Storrø, Ola; Øyen, Tove; Johnsen, R & Rudi, Knut (2011). Development of Bifidobacterium spp. in infants as revealed by mixed sequence analysis. Fulltekst i vitenarkiv

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