Eric Jacques de Muinck

• Hofsvang, Aurora; Hanssen, Eirik Natås; Muinck, Eric de; Trosvik, Pål & Fonneløp, Ane Elida (2025). Forensic geolocation of Norwegian soil samples using random forest analysis of microbiomes. Forensic Science International: Genetics. ISSN 1872-4973. 82. doi: 10.1016/j.fsigen.2025.103408. Full text in Research Archive Show summary

  Soil is a substrate easily picked up during everyday activities due to its ubiquity and adhesiveness. A method to determine the origin of soil precisely would therefore be useful in forensic casework as it can provide insight into a person`s or object`s previous whereabouts. To evaluate the potential of microbiomes for soil provenance determination, we collected soil samples from 15 locations in and around Oslo, Norway. Samples were collected multiple times from the same locations to assess changes in the microbiome over time. Additionally, a mock soil stain on clothing sample was collected at each site to validate this sample type. The microbial composition of samples was determined via amplicon sequencing of the V4 region of the 16S rRNA bacterial gene. Our results showed that the microbiomes were significantly impacted by location, with both soil and soil stain samples from the same site mainly exhibiting greater similarity than those from different sites. Notably, seasonal variations affected microbiome composition, leading to significant changes in some locations. Machine learning was employed to associate samples with their geographic origins, achieving classification accuracies above 85 % for both soil stain samples and soil samples collected within one week of each other. However, accuracies were lower for samples collected across different seasons, between 55 % and 64 %, indicating that temporal variation can limit the reliability of soil microbiome analysis when there is a delay between sample collection times.

• Noordzij, Hanna Theodora; Wortel, Meike Tessa; Heintz-Buschart, Anna; Petrikonyte, Patricija; Muinck, Eric de & Trosvik, Pål (2025). Assembly-based analysis of the infant gut microbiome reveals novel ubiquitous plasmids. Plasmid. ISSN 0147-619X. 134, p. 1–15. doi: 10.1016/j.plasmid.2025.102761. Full text in Research Archive Show summary

  Little is known about the role of mobile genetic elements in natural ecosystems such as the infant gut microbiome. Here, we conduct the most comprehensive longitudinal study of the infant plasmidome to date by analyzing monthly fecal samples from 12 infants from birth to one year of age. We employ an assembly-based bioinformatic pipeline for the reconstruction and identification of full-length plasmids, including a novel approach for assigning putative plasmid hosts. We then investigated plasmid content and dynamics in the infant gut microbiome. After assembly and identification, we identified 620 unique circular plasmids in the infant cohort, including a number of novel sequences. Independent assembly of the same plasmids in several samples and infants helped corroborate the authenticity of the plasmids. Among the observed plasmids was the recently described ubiquitous and abundant Bacteroides plasmid pBI143. Overall, the genus Bacteroides had the highest plasmid carriage, while the highest plasmid diversity was observed in Clostridium, including 5 previously unknown widespread plasmids. Lastly, we leveraged the longitudinal nature of our dataset to investigate contemporaneous correlations between temporal variations in plasmid abundances and species dynamics. This enabled us to link co-residing plasmids and tightly linked plasmid-taxon pairs within each infant. These insights into plasmid ecology help us understand determinants driving plasmid distribution in complex microbial communities.

• Kamenova, Stefaniya Kamenova; Albon, Steve D.; Loe, Leif Egil; Irvine, R. Justin; Langvatn, Rolf & Gusarova, Galina [Show all 8 contributors for this article] (2025). Arctic Greening Drives Changes in the Diet and Gut Microbiome of a Large Herbivore With Consequences for Body Mass. Ecology and Evolution. 15(7). doi: 10.1002/ece3.71731. Full text in Research Archive Show summary

  Rapid climate warming is ‘greening’ the tundra, reflecting a higher plant biomass, particularly of deciduous shrubs and grasses. However, the consequences of these changes for herbivore nutrition are unclear. Although, the gut microbiome mediates nutrient metabolism, and hence herbivores' capacity to adapt to dietary change, few studies have investigated the effect of annual changes in the diet-gut microbiome nexus on fitness-related traits. In a model system, the Svalbard reindeer, a species experiencing the greatest rate of climate warming on Earth, we investigate how changes in diet and the gut microbiome impact reindeer body mass. Using high-resolution DNA metabarcoding, we assessed diet and gut microbiome bacterial composition in rumen samples from animals culled in October from 1998 to 2004 in four different valleys. Overall diet diversity and grass relative reads abundance (RRA) were significantly higher following warmer summers, while the RRA of the dwarf shrub Salix polaris increased with the maximum normalised difference vegetation index (NDVI), our measure of annual biomass. Autumn body mass, a strong proxy of fitness in Svalbard reindeer, was significantly, positively correlated with Salix RRA, most pronounced in females that had reproduced, and by that depleted body reserves. Multivariate analyses revealed a highly significant relationship between diet and microbiome composition at the individual level. This included a significant positive correlation between Salix and bacterial diversity. However, a structural equation model revealed that the direct path effect of Salix on reindeer body mass was stronger than the indirect path effect, mediated through the gut microbiome. Our results suggest that climate-driven Arctic greening may have implications for herbivore body mass, operating through a change in diet composition. These findings reveal some of the mechanistic underpinnings of Arctic warming on herbivore populations and highlight the importance of the diet−gut microbiome nexus in facilitating species resilience to rapid climate change.

• Drevland, Ole Martin; Muinck, Eric de; Trosvik, Pål; Hammerstad, Marta; Kvitne, Kine Eide & Midtvedt, Karsten [Show all 8 contributors for this article] (2025). Microbiome-derived reactivation of mycophenolate explains variations in enterohepatic recirculation in kidney transplant recipients. Microbiome. 13(1). doi: 10.1186/s40168-025-02142-6. Full text in Research Archive Show summary

  Background The pivotal role of microbes in drug metabolism is increasingly recognized, as variation in the gut microbiome composition between individuals has been shown to impact systemic drug exposure, efficacy and toxicity. Mycophenolate mofetil (MMF) is a cornerstone in immunosuppressive therapy following solid organ transplantation. However, dosing and tolerance are challenged by significant pharmacokinetic variability among patients, largely due to variable degrees of enterohepatic recirculation of mycophenolic acid (MPA), the active moiety of MMF. It is hypothesized that the variability in MPA recirculation is driven by gut microbiome-derived β-glucuronidase (β-GUS) mediated cleavage of MPA-glucuronide (MPAG) excreted in the bile. Here, we investigated the bidirectional interaction between MPA and the gut microbiome in kidney transplant recipients, using a combination of in vivo and in vitro data. Results We compared the fecal microbiomes of kidney transplant recipients (n = 21) both pre- and post-transplantation to healthy individuals (n = 15) using shotgun metagenomic sequencing. We also determined the individual microbiome-derived reactivation rate of MPAG to MPA and show a strong positive correlation between this reactivation rate and the degree of MPA enterohepatic recirculation in vivo. Through metagenomic analysis, the reactivation rate of MPA was linked to specific gut microbial species. In particular, specific β-GUS gene variants associated with Faecalibacterium prausnitzii showed a strong impact on the conversion of MPAG to MPA. Furthermore, our study confirmed a significant shift in microbial composition post-transplantation and revealed notable fluctuations in species such as F. prausnitzii and Akkermansia muciniphila across different time points after transplantation. Lastly, we provide evidence that the microbiome-derived reactivation rate of MPA is linked to specific beta-glucuronidase alleles. Conclusions We highlight for the first time that the ex vivo determined reactivation rate of MPA explains the variation of enterohepatic recirculation, emphasizing the important role of F. prausnitzii in this process. More broadly, our findings suggest that the gut microbiome significantly influences the degree of enterohepatic recirculation of MPA, providing valuable insights that could be relevant for optimizing individualized immunosuppressive drug dosing in transplant patients.

• Nguyen, Nga; Fashing, Peter; Trosvik, Pål; Stenseth, Nils Christian & Muinck, Eric de (2024). A Quantitative Comparison of Patterns of Play and Conflict in Nature Preschool and Traditional Preschool Children in Norway. International Journal of Early Childhood. ISSN 0020-7187. doi: 10.1007/s13158-024-00394-1. Full text in Research Archive Show summary

  Early childhood experiences have lifelong physical, social, emotional, and cognitive impacts. High quality early childhood education and care (ECEC) can put children on the path to personal development, lifelong learning, and future employability. Among the fastest growing ECEC options are nature-based preschools, where children spend most or all of each day outdoors in natural environments, but comparative studies of children’s behavior in nature-based versus traditional preschools are needed. We conducted an observational study comparing conflict, activity patterns, and play behavior among children at a nature preschool and a traditional preschool, both in Norway, where access to high quality ECEC is a universal right. We found that preschool children’s behavior varied with time spent outdoors in natural environments: (1) play was more physically active, less gendered, and less often incorporated human-made items at the nature preschool, (2) conflict was almost twice as common at the traditional preschool, and (3) daily group activities at the traditional preschool like sitting down to a cooked meal and gathering up and putting away toys were absent from the nature preschool. While both the traditional and nature preschools offered children equal amounts of play time and a variety of physically and socially stimulating play activities, our results suggest that access to natural environments impacts preschool children’s behavior and interactions in meaningful ways.

• Trosvik, Pål; Noordzij, Hanna Theodora & Muinck, Eric Jacques de (2024). Antibiotic resistance gene dynamics in the commensal infant gut microbiome over the first year of life. Scientific Reports. 14(1). doi: 10.1038/s41598-024-69275-w. Full text in Research Archive Show summary

  Colonization of the infant gut is an important developmental process characterized by high carriage of antimicrobial resistance genes (ARGs) and high abundances of pathobionts. The horizontal transfer of ARGs to pathogenic bacteria represents a major public health concern. However, there is still a paucity of longitudinal studies surveilling ARGs in healthy infant guts at high temporal resolution. Furthermore, we do not yet have a clear view of how temporal variation in ARG carriage relates to the dynamics of specific bacterial populations, as well as community virulence potential. Here, we performed deep shotgun metagenomic sequencing of monthly fecal samples from a cohort of 12 infants, covering the first year of life to interrogate the infant gut microbiome for ARG content. We further relate ARG dynamics to the dynamics of taxa, virulence potential, as well as the potential for ARG mobilization. We identify a core resistome dominated by efflux systems typically associated with Enterobacteriaceae. Overall ARG carriage declined over the first year of life and showed strong contemporaneous correlation with the population dynamics of Proteobacteria. Furthermore, the majority of ARGs could be further mapped to metagenome-assembled genomes (MAGs) classified to this phylum. We were able to assign a large number of ARGs to E. coli by correlating the temporal dynamics of individual genes with species dynamics, and we show that the temporal dynamics of ARGs and virulence factors are highly correlated, suggesting close taxonomic associations between these two gene classes. Finally, we identify ARGs linked with various categories of mobile genetic elements, demonstrating preferential linkage among mobility categories and resistance to different drug classes. While individual variation in ARG carriage is substantial during infancy there is a clear reduction over the first year of life. With few exceptions, ARG abundances closely track the dynamics of pathobionts and community virulence potential. These findings emphasize the potential for development of resistant pathogens in the developing infant gut, and the importance of effective surveillance in order to detect such events.

• Cobb, Lauren Louise; Muinck, Eric de; Kollias, Spyridon; Skage, Morten; Gilfillan, Gregor & Sydenham, Markus A. K. [Show all 8 contributors for this article] (2024). High-throughput sequencing of insect specimens with sub-optimal DNA preservation using a practical, plate-based Illumina-compatible Tn5 transposase library preparation method. PLOS ONE. 19(3). doi: 10.1371/journal.pone.0300865. Full text in Research Archive Show summary

  Entomological sampling and storage conditions often prioritise efficiency, practicality and conservation of morphological characteristics, and may therefore be suboptimal for DNA preservation. This practice can impact downstream molecular applications, such as the generation of high-throughput genomic libraries, which often requires substantial DNA input amounts. Here, we use a practical Tn5 transposase tagmentation-based library preparation method optimised for 96-well plates and low yield DNA extracts from insect legs that were stored under sub-optimal conditions for DNA preservation. The samples were kept in field vehicles for extended periods of time, before long-term storage in ethanol in the freezer, or dry at room temperature. By reducing DNA input to 6ng, more samples with sub-optimal DNA yields could be processed. We matched this low DNA input with a 6-fold dilution of a commercially available tagmentation enzyme, significantly reducing library preparation costs. Costs and workload were further suppressed by direct post-amplification pooling of individual libraries. We generated medium coverage (>3-fold) genomes for 88 out of 90 specimens, with an average of approximately 10-fold coverage. While samples stored in ethanol yielded significantly less DNA compared to those which were stored dry, these samples had superior sequencing statistics, with longer sequencing reads and higher rates of endogenous DNA. Furthermore, we find that the efficiency of tagmentation-based library preparation can be improved by a thorough post-amplification bead clean-up which selects against both short and large DNA fragments. By opening opportunities for the use of sub-optimally preserved, low yield DNA extracts, we broaden the scope of whole genome studies of insect specimens. We therefore expect these results and this protocol to be valuable for a range of applications in the field of entomology.

• Muinck, Eric de; Trosvik, Pål; Nguyen, Nga; Fashing, Peter J.; Stigum, Vetle Malmer & Robinson, Nina [Show all 9 contributors for this article] (2023). Reduced abundance of Faecalibacterium prausnitzii in the gut microbiota of children diagnosed with cancer, a pilot study. Frontiers in Mircobiomes. ISSN 2813-4338. 2. doi: 10.3389/frmbi.2023.1151889. Full text in Research Archive Show summary

  Background There is an increasing awareness of the importance of the gut microbiome in disease progression and the maintenance of human health. However, links between the microbiome and cancer onset remain relatively unexplored. This is especially the case for childhood cancers, which although rare, are the predominant cause of death among children in Western countries. Methods Fecal samples were collected from patients, before the onset of treatment, by the Norwegian Childhood Cancer Biobank in Oslo and from children attending kindergartens in Oslo, Norway. Using 16S rRNA gene amplicon sequencing, we compared the gut microbiome compositions of the children diagnosed with cancer with children attending kindergarten. Results We observed significant differences in the relative abundances of several taxa, including a striking depletion of Faecalibacterium prausnitzii , an important taxa linked to gut health maintenance. Conclusions Our observations provide evidence that the gut microbiome may play an important role in physiological changes associated with the onset of childhood cancer. However, further studies should be designed in order to validate our findings. Furthermore, these results suggest that variations in the microbial community could potentially be used as an early indicator of childhood cancer.

• Evangelista, Charlotte; Kamenova, Stefaniya; Pauli, Beatriz Diaz; Sandkjenn, Joakim; Vøllestad, Leif Asbjørn & Edeline, Eric [Show all 8 contributors for this article] (2023). Within-species variation in the gut microbiome of medaka (Oryzias latipes) is driven by the interaction of light intensity and genetic background. Peer Community Journal. 3. doi: 10.24072/pcjournal.306. Full text in Research Archive Show summary

  Unravelling evolution-by-environment interactions on the gut microbiome is particularly relevant considering the unprecedented level of human-driven disruption of the ecological and evolutionary trajectories of species. Here, we aimed to evaluate whether an evolutionary response to size-selective mortality influences the gut microbiome of medaka (Oryzias latipes), how environmental conditions interact with the genetic background of medaka on their microbiota, and the association between microbiome diversity and medaka growth-related traits. To do so, we studied two lineages of medaka with known divergence in foraging efficiency and life history raised under antagonistic size-selective regimes for 10 generations (i.e. the largest or the smallest breeders were removed to mimic fishing-like or natural mortality). In pond mesocosms, the two lineages were subjected to contrasting population density and light intensity (used as proxies of resource availability). We observed significant differences in the gut microbiome composition and richness between the two lines, and this effect was mediated by light intensity. The bacterial richness of fishing-like medaka (small-breeder line) was reduced by 34% under low-light conditions compared to high-light conditions, while it remained unchanged in natural mortality-selected medaka (large-breeder line). However, the observed changes in bacterial richness did not correlate with changes in adult growth-related traits. Given the growing evidence about the gut microbiomes importance to host health, more in-depth studies are required to fully understand the role of the microbiome in size-selected organisms and the possible ecosystem-level consequences.

• Kamenova, Stefaniya; Muinck, Eric de; Veiberg, Vebjørn; Utsi, Tove Hilde Ågnes; Steyaert, Sam & Albon, Steve [Show all 8 contributors for this article] (2023). Gut microbiome biogeography in reindeer supersedes millennia of ecological and evolutionary separation. FEMS Microbiology Ecology. ISSN 0168-6496. 99(12). doi: 10.1093/femsec/fiad157. Full text in Research Archive Show summary

  Ruminants are dependent on their gut microbiomes for nutrient extraction from plant diets. However, knowledge about the composition, diversity, function, and spatial structure of gut microbiomes, especially in wild ruminants, is limited, largely because analysis has been restricted to faeces or the rumen. In two geographically separated reindeer subspecies, 16S rRNA gene amplicon sequencing revealed strong spatial structuring, and pronounced differences in microbial diversity of at least 33 phyla across the stomach, small intestine, and large intestine (including faeces). The main structural feature was the Bacteroidota to Firmicutes ratio, which declined from the stomach to the large intestine, likely reflecting functional adaptation. Metagenome shotgun sequencing also revealed highly significant structuring in the relative occurrence of carbohydrate-active enzymes (CAZymes). CAZymes were enriched in the rumen relative to the small and large intestines. Interestingly, taxonomic diversity was highest in the large intestine, suggesting an important and understudied role for this organ. Despite the two study populations being separated by an ocean and six millennia of evolutionary history, gut microbiome structuring was remarkably consistent. Our study suggests a strong selection for gut microbiome biogeography along the gastrointestinal tract in reindeer subspecies.

• Herstad, Kristin Marie Valand; Trosvik, Pål; Haaland, Anita Haug; Haverkamp, Thomas Hendricus Augustus; Muinck, Eric de & Skancke, Ellen (2021). Changes in the fecal microbiota in dogs with acute hemorrhagic diarrhea during an outbreak in Norway. Journal of Veterinary Internal Medicine (JVIM). ISSN 0891-6640. 35(5), p. 2177–2186. doi: 10.1111/jvim.16201. Full text in Research Archive Show summary

  Background A severe form of acute hemorrhagic diarrhea syndrome (AHDS) occurred in dogs in the Oslo region of Norway during autumn 2019. Objectives To characterize the fecal microbiota of dogs with AHDS during the outbreak and compare it to that of healthy dogs from the same period and before the outbreak. Animals Dogs with AHDS (n = 50), dogs with nonhemorrhagic diarrhea (n = 3), and healthy dogs (n = 11) were sampled during the outbreak. In addition, 78 healthy dogs from the same region were sampled before the outbreak between 2017 and 2018. Methods Retrospective case-control study. The fecal microbiotas were characterized using 16S rRNA gene amplicon sequencing. Results Dogs with AHDS had significantly different microbiota composition (R2 = .07, P < .001) and decreased intestinal diversity relative to healthy dogs from the outbreak period (median, 2.7; range, 0.9-3.5 vs median, 3.2; range, 2.6-4.0; P < .001). The microbiota in dogs with AHDS was characterized by a decrease of Firmicutes and an outgrowth of Proteobacteria, with increased numbers of Clostridium perfringens and Providencia spp. Among the Providencia spp., 1 showed 100% sequence identity with a Providencia alcalifaciens strain that was cultivated and isolated from the same outbreak. No Providencia spp. was found in healthy dogs sampled before the outbreak. Conclusions and Clinical Importance Dogs with AHDS had marked changes in fecal microbiota including increased numbers of Providencia spp. and C. perfringens, which may have contributed to the severity of this illness.

• Muinck, Eric de & Trosvik, Pål (2018). Individuality and convergence of the infant gut microbiota during the first year of life. Nature Communications. 9(1), p. 1–8. doi: 10.1038/s41467-018-04641-7. Full text in Research Archive Show summary

  The human gut microbiota plays a vital role in health and disease, and microbial colonization is a key process in infant development. Here, we analyze 2684 fecal specimens from 12 infants during their first year of life, providing detailed insights into the human gut colonization process. Maturation of the gut microbial community shows strong temporal structure and specific developmental stages. At 2–4 months of age, there is a period of accelerated convergence concurrent with a bloom of Bifidobacterium, a genus associated with metabolism of oligosaccharides found in breast milk. The end of this period coincides with the introduction of solid food, a reduction in the relative abundance of Bifidobacterium, and an increase in several groups of Firmicutes. Our findings highlight the dynamic nature and individuality of the gut colonization process, and the need for high-frequency sampling over an extended period when designing and interpreting infant microbiome studies.

• Trosvik, Pål; Rueness, Eli Knispel; Muinck, Eric de; Moges, Amera & Mekonnen, Addisu (2018). Ecological plasticity in the gastrointestinal microbiomes of Ethiopian Chlorocebus monkeys. Scientific Reports. 8(1), p. 1–10. doi: 10.1038/s41598-017-18435-2. Full text in Research Archive Show summary

  Human activities can cause habitat degradation that may alter the types and quality of available food resources and thus influence the microbiomes of wild animal populations. Furthermore, seasonal shifts in food availability may cause adaptive responses in the gut microbiome to meet the need for different metabolic capabilities. Here, we demonstrate local-scale population structure in the gastrointestinal microbiotas of Chlorocebus monkeys, in southern Ethiopia, in response to varying degrees of human encroachment. We further provide evidence of adaptation to ecological conditions associated with the dry and wet seasons, and show seasonal effects to be more pronounced in areas with limited human activity. Finally, we report species-level microbiota differences between the endemic Ethiopian Bale monkey, an ecological specialist, and generalist Chlorocebus species from the same geographical region.

• Trosvik, Pål; Muinck, Eric de; Rueness, Eli Knispel; Fashing, Peter; Beierschmitt, Evan C. & Callingham, Kadie R. [Show all 12 contributors for this article] (2018). Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate. Microbiome. 6(84), p. 1–18. doi: 10.1186/s40168-018-0468-6. Full text in Research Archive Show summary

  Background The gelada monkey (Theropithecus gelada), endemic to the Ethiopian highlands, is the only graminivorous primate, i.e., it feeds mainly on grasses and sedges. In spite of known dental, manual, and locomotor adaptations, the intestinal anatomy of geladas is similar to that of other primates. We currently lack a clear understanding of the adaptations in digestive physiology necessary for this species to subsist on a graminoid-based diet, but digestion in other graminivores, such as ruminants, relies heavily on the microbial community residing in the gastrointestinal (GI) system. Furthermore, geladas form complex, multilevel societies, making them a suitable system for investigating links between sociality and the GI microbiota. Results Here, we explore the gastrointestinal microbiota of gelada monkeys inhabiting an intact ecosystem and document how factors like multilevel social structure and seasonal changes in diet shape the GI microbiota. We compare the gelada GI microbiota to those of other primate species, reporting a gradient from geladas to herbivorous specialist monkeys to dietary generalist monkeys and lastly humans, the ultimate ecological generalists. We also compare the microbiotas of the gelada GI tract and the sheep rumen, finding that geladas are highly enriched for cellulolytic bacteria associated with ruminant digestion, relative to other primates. Conclusions This study represents the first analysis of the gelada GI microbiota, providing insights into the adaptations underlying graminivory in a primate. Our results also highlight the role of social organization in structuring the GI microbiota within a society of wild animals.

• Muinck, Eric de; Trosvik, Pål; Gilfillan, Gregor Duncan; Hov, Johannes Espolin Roksund & Sundaram, Arvind (2017). A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform. Microbiome. doi: 10.1186/s40168-017-0279-1. Full text in Research Archive Show summary

  Background Advances in sequencing technologies and bioinformatics have made the analysis of microbial communities almost routine. Nonetheless, the need remains to improve on the techniques used for gathering such data, including increasing throughput while lowering cost and benchmarking the techniques so that potential sources of bias can be better characterized. Methods We present a triple-index amplicon sequencing strategy to sequence large numbers of samples at significantly lower c ost and in a shorter timeframe compared to existing methods. The design employs a two-stage PCR protocol, incorpo rating three barcodes to each sample, with the possibility to add a fourth-index. It also includes heterogeneity spacers to overcome low complexity issues faced when sequencing amplicons on Illumina platforms. Results The library preparation method was extensively benchmarked through analysis of a mock community in order to assess biases introduced by sample indexing, number of PCR cycles, and template concentration. We further evaluated the method through re-sequencing of a standardized environmental sample. Finally, we evaluated our protocol on a set of fecal samples from a small cohort of healthy adults, demonstrating good performance in a realistic experimental setting. Between-sample variation was mainly related to batch effects, such as DNA extraction, while sample indexing was also a significant source of bias. PCR cycle number strongly influenced chimera formation and affected relative abundance estimates of species with high GC content. Libraries were sequenced using the Illumina HiSeq and MiSeq platforms to demonstrate that this protocol is highly scalable to sequence thousands of samples at a very low cost. Conclusions Here, we provide the most comprehensive study of performance and bias inherent to a 16S rRNA gene amplicon sequencing method to date. Triple-indexing greatly reduces the number of long custom DNA oligos required for library preparation, while the inclusion of variable length heterogeneity spacers minimizes the need for PhiX spike-in. This design results in a significant cost reduction of highly multiplexed amplicon sequencing. The biases we characterize highlight the need for highly standardized protocols. Reassuringly, we find that the biological signal is a far stronger structuring factor than the various sources of bias.

• Muinck, Eric de; Lundin, Knut Erik Aslaksen & Trosvik, Pål (2017). Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota. mSystems. 2(5). doi: 10.1128/mSystems.00086-17. Full text in Research Archive Show summary

  The gastrointestinal (GI) microbiome is a densely populated ecosystem where dynamics are determined by interactions between microbial community members, as well as host factors. The spatial organization of this system is thought to be important in human health, yet this aspect of our resident microbiome is still poorly understood. In this study, we report significant spatial structure of the GI microbiota, and we identify general categories of spatial patterning in the distribution of microbial taxa along a healthy human GI tract. We further estimate the biotic interaction structure in the GI microbiota, both through time series and cooccurrence modeling of microbial community data derived from a large number of sequentially collected fecal samples. Comparison of these two approaches showed that species pairs involved in significant negative interactions had strong positive contemporaneous correlations and vice versa, while for species pairs without significant interactions, contemporaneous correlations were distributed around zero. We observed similar patterns when comparing these models to the spatial correlations between taxa identified in the adherent microbiota. This suggests that colocalization of microbial taxon pairs, and thus the spatial organization of the GI microbiota, is driven, at least in part, by direct or indirect biotic interactions. Thus, our study can provide a basis for an ecological interpretation of the biogeography of the human gut.

• Liljegren, Mikkel Meyn; Muinck, Eric De & Trosvik, Pål (2016). Microsatellite length scoring by single molecule real time sequencing - Effects of sequence structure and PCR regime. PLOS ONE. 11(7), p. 1–17. doi: 10.1371/journal.pone.0159232. Full text in Research Archive
• Trosvik, Pål; Muinck, Eric De & Stenseth, Nils Christian (2015). Biotic interactions and temporal dynamics of the human gastrointestinal microbiota. The ISME Journal. ISSN 1751-7362. 9(3), p. 533–541. doi: 10.1038/ismej.2014.147. Full text in Research Archive
• Tapia, German; Bøås, Håkon; Muinck, Eric De; Cinek, Ondrej; Stene, Lars Christian & Torjesen, Peter A [Show all 8 contributors for this article] (2015). Saffold Virus, a Human Cardiovirus, and Risk of Persistent Islet Autoantibodies in the Longitudinal Birth Cohort Study MIDIA. PLOS ONE. 10(8). doi: 10.1371/journal.pone.0136849. Full text in Research Archive Show summary

  The aim of this study was to describe the frequency and distribution of Saffold virus in longitudinal stool samples from children, and test for association with development of persistent autoantibodies predictive of type 1 diabetes. A cohort of Norwegian children carrying the HLA genotype associated with highest risk of type 1 diabetes (“DR4-DQ8/DR3-DQ2”) was followed with monthly stool samples from 3 to 35 months of age. Blood samples were tested for autoantibodies to insulin, glutamic acid decarboxylase65 and Islet Antigen-2. 2077 stool samples from 27 children with ≥2 repeatedly positive islet autoantibodies (cases), and 53 matched controls were analysed for Saffold virus genomic RNA by semi-quantitative real-time reverse transcriptase PCR. Saffold virus was found in 53 of 2077 (2.6%) samples, with similar proportions between cases (2.5%) and controls (2.6%). The probability of being infected by 3 years of age was 28% (95% CI 0.18–0.40). Viral quantities ranged from <1 to almost 105 copies/μl. Estimated odds ratio between islet autoimmunity and infection episodes prior to seroconversion was 1.98 (95% CI: 0.57–6.91, p = 0.29). Saffold virus had no statistically significant association with islet autoimmunity.

• Trosvik, Pål & Muinck, Eric De (2015). Ecology of bacteria in the human gastrointestinal tract — identification of keystone and foundation taxa. Microbiome. 3(44), p. 1–12. doi: 10.1186/s40168-015-0107-4. Full text in Research Archive Show summary

  Background Determining ecological roles of community members and the impact of specific taxa on overall biodiversity in the gastrointestinal (GI) microbiota is of fundamental importance. A step towards a systems-level understanding of the GI microbiota is characterization of biotic interactions. Community time series analysis, an approach based on statistical analysis of changing population abundances within a single system over time, is needed in order to say with confidence that one population is affecting the dynamics of another. Results Here, we characterize biotic interaction structures and define ecological roles of major bacterial groups in four healthy individuals by analysing high-resolution, long-term (>180 days) GI bacterial community time series. Actinobacteria fit the description of a keystone taxon since they are relatively rare, but have a high degree of ecological connectedness, and are positively correlated with diversity both within and between individuals. Bacteriodetes were found to be a foundation taxon in that they are numerically dominant and interact extensively, in particular through positive interactions, with other taxa. Although community structure, diversity and biotic interaction patterns were specific to each individual, we observed a strong tendency towards more intense competition within than between phyla. This is in agreement with Darwin’s limiting similarity hypothesis as well as a published biotic interaction model of the GI microbiota based on reverse ecology. Finally, we link temporal enterotype switching to a reciprocal positive interaction between two key genera. Conclusions In this study, we identified ecological roles of key taxa in the human GI microbiota and compared our time series analysis results with those obtained through a reverse ecology approach, providing further evidence in favour of the limiting similarity hypothesis first put forth by Darwin. Larger longitudinal studies are warranted in order to evaluate the generality of basic ecological concepts as applied to the GI microbiota, but our results provide a starting point for achieving a more profound understanding of the GI microbiota as an ecological system.

• Muinck, Eric De; Stenseth, Nils Christian; Sachse, Daniel; Roost, Jan Pieter Vander; Rønningen, Kjersti Skjold & Rudi, Knut [Show all 7 contributors for this article] (2013). Context-Dependent Competition in a Model Gut Bacterial Community. PLOS ONE. 8(6). doi: 10.1371/journal.pone.0067210. Full text in Research Archive
• Muinck, Eric De; Lagesen, Karin; Afset, Jan Egil; Didelot, Xavier; Rønningen, Kjersti Skjold & Rudi, Knut [Show all 8 contributors for this article] (2013). Comparisons of infant Escherichia coli isolates link genomic profiles with adaptation to the ecological niche. BMC Genomics. 14. doi: 10.1186/1471-2164-14-81. Full text in Research Archive Show summary

  Despite being one of the most intensely studied model organisms, many questions still remain about the evolutionary biology and ecology of Escherichia coli. An important step toward achieving a more complete understanding of E.coli biology entails elucidating relationships between gene content and adaptation to the ecological niche. Here, we present genome comparisons of 16 E.coli strains that represent commensals and pathogens isolated from infants during a specific time period in Trondheim, Norway. Using differential gene content, we characterized enrichment profiles of the collection of strains relating to phylogeny, early vs. late colonization, pathogenicity and growth rate. We found clear gene content distinctions relating to the various grouping criteria. We also found that different categories of strains use different genetic elements for similar biological processes. The sequenced genomes included two pairs of strains where each pair was isolated from the same infant at different time points. One pair, in which the strains were isolated four months apart, showed maintenance of an early colonizer genome profile but also gene content and codon usage changes toward the late colonizer profile. Lastly, we placed our sequenced isolates into a broader genomic context by comparing them with 25 published E.coli genomes that represent a variety of pathotypes and commensal strains. This analysis demonstrated the importance of geography in shaping strain level gene content profiles. Our results indicate a general pattern where alternative genetic pathways lead toward a consistent ecological role for E.coli as a species. Within this framework however, we saw selection shaping the coding repertoire of E.coli strains toward distinct ecotypes with different phenotypic properties.

• Muinck, Eric de; Øien, Torbjørn; Storrø, Ola; Johnsen, Roar; Stenseth, Nils Christian & Rønningen, Kjersti Skjold [Show all 7 contributors for this article] (2011). Diversity, transmission and persistence of Escherichia coli in a cohort of mothers and their infants. Environmental Microbiology Reports. 3(3), p. 352–359. doi: 10.1111/j.1758-2229.2010.00231.x. Full text in Research Archive

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• Lind, Vibeke; Muinck, Eric de; Jørgensen, Grete Helen Meisfjord & Trosvik, Pål (2022). Micro- and macroalgae additives to mitigate enteric methane emisisons from Norwegian sheep. 8th International Greenhouse Gas & Animal Agriculture Conference. 8, p. 140–140. Full text in Research Archive
• Lind, Vibeke; Muinck, Eric de; Jørgensen, Grete Helen Meisfjord & Trosvik, Pål (2022). Micro- and macroalgae additives to mitigate enteric methane emissions from Norwegian sheep. Full text in Research Archive
• Easterday, William Ryan; Muinck, Eric de & Stigum, Vetle Malmer (2021). the not so straight-forward way of generating long reads on the PacBio. Full text in Research Archive
• Roell, Marc-Sven; Noordzij, Hanna Theodora; Mjønes, Caroline Skar; Boye, Ole; Levchenko, Vladimir & Kimara, Chiharu [Show all 12 contributors for this article] (2015). Methane Incorporated. Full text in Research Archive
• Roell, Marc-Sven; Noordzij, Hanna Theodora; Mjønes, Caroline Skar; Boye, Ole; Levchenko, Vladimir & Kimara, Chiharu [Show all 12 contributors for this article] (2015). Methane Incorporated - iGEM Lecture. Full text in Research Archive
• Trosvik, Pål & Muinck, Eric De (2014). Biotic interactions and temporal dynamics of the human GI microbiota. Full text in Research Archive
• Muinck, Eric de (2012). Genome comparisons of infant Escherichia coli isolates. Full text in Research Archive
• Muinck, Eric de; Stenseth, Nils Christian; Rønningen, Kjersti Skjold; Rudi, Knut & Trosvik, Pål (2013). Deep characterization of Escherichia coli in a cohort of mothers and their infants. Universitetet i Oslo. Full text in Research Archive Show summary

  This work is a deep characterization of Escherichia coli (E.coli) colonization of a cohort of infants and their mothers in Trondheim, Norway. E.coli cause ~2 million deaths due to infant diarrhea and ~150 million cases of uncomplicated cystitis. However, even given this potentially severe impact on human health, almost every one of us carries about a billion E.coli cells with no problems. Furthermore, there is often almost little or no difference between a disease causing strain and one that lives commensally with the host. Our parent study examined the impact of whole gut microbial colonization on the development of atopic disease and found that early E.coli colonization of the infant was linked to protection from atopy and that the mother was found to be a likely source of infant colonization. In this thesis we first developed a simple and novel technique that allowed us to uncover limits on the diversity of colonizing E.coli strains and confirmed evidence of transmission from the mothers to the infants. We then placed these colonizing strains into a phylogenetic context and thus into the overall diversity of E. coli. This allowed us to understand and compare strains colonizing infants in a defined geographic area with the wider population structure of this species. We then investigated differences in growth characteristics of isolated E. coli strains from this cohort that were either early or late colonizers of the infant gut. In vitro competition studies revealed potential mechanisms that modulate strain competitive dynamics. Finally, through genome sequencing, we compared several phenotypic characteristics using differential gene content in order to determine enrichment profiles that may explain these traits. Enrichment comparisons included: phylogenetic, pathogenic vs. commensal, growth rate, and early or late colonization. The signatures we found can be used for further investigations into genotype-phenotype connections within E. coli strain ecology.

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