paltr

• Bødtker, Gunhild; Coutris, Claire; Denison, Eva Marie-Louise; Bukhvalova, Barbara Alexandra; Frostegård, Åsa & Joner, Erik [Show all 11 contributors for this article] (2026). Scoping review of research on environmental effects of biodegradable plastics relevant to Norwegian conditions. VKM Report. 2026(02), p. 1–71. doi: https:/vkm.no/download/18.620c7df519c1e2e820838f8d/1770632458334/Scoping%20review%20of%20research%20on%20%20environmental%20effects%20of%20%20biodegradable%20plastics.pdf. Full text in Research Archive Show summary

  There is an increasing global production and demand for biodegradable plastics. But there are still many uncertainties about how and to what extent these plastics degrade and their environmental impacts. To gain a better understanding of these aspects, the Scientific Committee for Food and Environment (VKM) has conducted a self-initiated scoping review of existing scientific literature on biodegradable plastics and their environmental impacts. VKM has specifically focused on studies that are relevant to Norwegian and Nordic conditions. The first literature search (June 2024) revealed 2428 international research studies, including primary studies and systematic and non-systematic review articles. The primary studies were divided into three categories: materials, microbiology and ecotoxicology, based on the main focus of the studies. From each category, a quarter of the primary studies and non-systematic review articles were randomly selected for full text analysis. A total of 168 articles were included in the final mapping. A new literature search (October 2025), with a focus on Nordic research and particularly Norwegian conditions, revealed 178 articles, of which 19 were subject to further analysis. The most studied types of biodegradable plastics were polylactic acid (PLA), polyhydroxyalkanoate (PHA) and polybutylene adipate terephthalate (PBAT). Many of the studies focused on the degradation process of biodegradable mulch film used in agriculture, and how their use affects the environmental conditions in agricultural soils. Most studies reported incomplete degradation during the trial period, which underlines the concern for accumulation of plastic material with repeated use. Other studies simulated different pollution scenarios, such as lost fishing gear, an area that has received attention in recent Nordic studies. Ecotoxicological effects of biodegradable plastics were often only observed at concentrations far above those expected to occur in natural environments. There were indications that effects observed in soil and aquatic ecosystems could just as well be indirect, resulting from changes in physical and chemical properties of soil and water. In general, the effects of biodegradable plastics are comparable to those of conventional (micro)plastics in both terrestrial and aquatic ecosystems. However, there were studies that suggest that biodegradable plastics are more toxic than conventional plastics under specific conditions, such as after UV exposure, or for certain test organisms. Testing the ecotoxicity of commercial biodegradable plastics was complicated by the lack of transparency about their chemical composition. Only a minority of studies investigated the ecotoxicity of chemical substances leaching from plastic materials, and the results reported were inconsistent. There is a lack of studies that combined degradation studies with toxicological effects. This knowledge gap has also been pointed out in systematic review articles. The review revealed several weaknesses in the existing research, related to study design, analytical methods, definitions and terminology. Current research practice provides many individual studies that are difficult to compare. Thus, they provide limited insight into how degradation and environmental impact occur over time, and in different environments. The review points to the need for strengthened and standardized research, so that the knowledge base becomes more robust and a better understanding of the environmental impact of plastics over time and in different environments can be gained.

• 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.

• 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.

• Nielsen, Kaare Magne; Kausrud, Kyrre Linné; Simonsen, Gunnar Skov; Steinbakk, Martin; Trosvik, Pål & Wester, Astrid Louise [Show all 12 contributors for this article] (2022). Surveillance of antimicrobial resistance in the environment. Scientific Opinion of the Panel on Microbial Ecology of the Norwegian Scientific Committee for Food and Environment. VKM Report. 28. Full text in Research Archive
• 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.

• Rowe, Melissah; Veerus, Liisa; Trosvik, Pål; Buckling, Angus & Pizzari, Tommaso (2020). The reproductive microbiome: An emerging driver of sexual selection, sexual conflict, mating systems, and reproductive isolation. Trends in Ecology & Evolution. ISSN 0169-5347. 35(3), p. 220–234. doi: 10.1016/j.tree.2019.11.004. Full text in Research Archive Show summary

  All multicellular organisms host microbial communities in and on their bodies, and these microbiomes can have major influences on host biology. Most research has focussed on the oral, skin, and gut microbiomes, whereas relatively little is known about the reproductive microbiome. Here, we review empirical evidence to show that reproductive microbiomes can have significant effects on the reproductive function and performance of males and females. We then discuss the likely repercussions of these effects for evolutionary processes related to sexual selection and sexual conflict, as well as mating systems and reproductive isolation. We argue that knowledge of the reproductive microbiome is fundamental to our understanding of the evolutionary ecology of reproductive strategies and sexual dynamics of host organisms.

• Rowe, Melissah; Veerus, Liisa; Trosvik, Pål; Buckling, Angus & Pizzari, Tommaso (2020). Reproductive Microbiomes and the Sexual Transmission of Beneficial Microbes: Reply to Lombardo et al. Trends in Ecology & Evolution. ISSN 0169-5347. 35(11), p. 964–965. doi: 10.1016/j.tree.2020.08.017. Full text in Research Archive
• Wasteson, Yngvild; Blix, Hege Salvesen; Joner, Erik; Madslien, Elisabeth Henie; Ottoson, Jakob & Sørum, Henning [Show all 12 contributors for this article] (2020). Assessment of the impact of wastewater and sewage sludge treatment methods on antimicrobial resistance. Scientific opinion of the Panel on Microbial Ecology of the Norwegian Scientific Committee for Food and Environment. VKM Report. 2020:08. Full text in Research Archive Show summary

  The request from NFSA and NEA:Antimicrobial agents and microorganisms are introduced to sewage systems by differenthuman activities, from private homes, institutions such as schools and hospitals, officebuildings, industrial and commercial activities, i.e., from everywhere where people work andlive.The Norwegian Food Safety Authority (NFSA) and Norwegian Environment Agency (NEA)asked the Norwegian Scientific Committee for Food and Environment (Vitenskapskomiteenfor mat og miljø, VKM) for an extension of the 2009 VKM report “Risk assessment ofcontaminants in sewage sludge applied on Norwegian soils” regarding the impact ofwastewater (WW)- and sewage sludge treatment methods used in Norway, on the fate andsurvival of antimicrobial resistant bacteria, fate of antimicrobial resistance genes, and maindrivers for resistance (e.g. antibiotics, antifungal agents, heavy metals, disinfectants).The request addressed by VKM:VKM appointed a working group, consisting of three members of the Panel on MicrobialEcology, four external members and VKM staff to prepare a draft Opinion document. ThePanel on Microbial Ecology has reviewed and revised the draft prepared by the workinggroup and approved the Opinion document “Assessment of the impact of wastewater andsewage sludge treatment methods on antimicrobial resistance”.The antimicrobial resistance cycle:Exposure to antimicrobial agents is regarded as the most important driver for developmentand dissemination of AMR in microorganisms. Consequently, an important location for thedevelopment of AMR is the gut of humans or animals receiving antimicrobial drug therapy.As ARB, ARG, resistance genes and antimicrobial agents will end up in the WW system, thissystem could be regarded as a potential hot spot for interactions between differentmicroorganisms, between different antimicrobial agents, and between microorganisms andantimicrobial agents. Hospitals and pharmaceutical companies are regarded as being animportant source for antimicrobial drug residues released in WW.At the wastewater treatment plant (WWTP), bacteria and genes end up either in the effluentwastewater fraction or in the sludge fraction. When ARB and ARG are distributed with theWW sludge, they may reach arable land when the sludge is used as soil improver andfertilising product, and thus be recycled into the food-production chain. When following theeffluent WW fraction, ARB and ARB will be released into WW recipients, such as lakes, riversor fjords, and may, from these environments, also be recycled into food production. In eachstep of these cycles, ARB and ARG will be introduced into new environmental compartmentsto which they must adapt, and to microbial communities with which they must compete for survival and growth. Depending on the bacterial species, these new environmentalcompartments will be more or less hostile, but they will also provide opportunities formicrobial interactions, like dissemination of ARG due to horizontal gene transfer (HGT) withinand between bacterial species.Findings:It is challenging to deliver a general assessment of the nature of as well as the probabilityfor direct discharge of ARB and ARG into effluent WW and applied sludge. This is due to thecombined complexity of resistance carriers, traits, various sources of variation, and the WWsystems. Moreover, there is currently a lack of harmonized methods and protocols tocompare studies from different systems. However, there are no strong indications that thereis a significant enrichment of ARB in WWTP operated under European conditions, which, ona general level, also applies to the Norwegian situation. Although some studies indicate aslight increase in the fraction of ARB, the absolute reduction in bacterial load during WWtreatment (WWT) is significant; removal of between 99 % to 99.9 % of faecal indicatorbacteria is generally achieved by secondary treatment, including biological and physicochemical treatment steps.Effluent WW is often released into water recipients, and there are many mechanisms(physical, mechanical, and chemical) that will limit the extent that ARB of faecal origin aretransferred to the food-production chain. However, there are different views on thesignificance of this release for the development of AMR. Results from single studies indicatethat WWTP effluents contribute little to the total AMR exposure of micro – and macroorganisms in aquatic and marine environments. On the other hand, freshwater environmentsin general are regarded as an important reservoir of novel antibiotic resistance determinants,and in some areas, relative abundance of resistance determinants in effluents has beenobserved to be considerably higher than in pristine natural water sources. Some imprint ofAMR in recipient waters, compared to pristine waters, is unavoidable.During WWT, bacteria largely adhere to particles that are aggregated and precipitated toform a solid sludge. The mandatory hygienisation of sludge kills a large proportion of thesebacteria, notably all thermosensitive faecal bacteria. However, the resulting hygienisedsludge is still rich in bacteria, some of which are carriers of ARGs. The current Norwegianregulations on use of sludge on soil contribute to prevent contamination of food withantimicrobial resistant bacteria and antimicrobial resistance genes from sludge. Yet, soils docontain a pool of both natural and sludge-derived antimicrobial resistance. The contributionof sludge to this antimicrobial resistance pool is probably temporally limited to a period aftersoil amendment with sludge. A recent, comprehensive study from Sweden showed that longterm application of sewage sludge on farmland only resulted in minor changes of soilbacterial community composition. No evidence could be found for enrichment ofantimicrobial resistant bacteria or antimicrobial resistance genes in soil amended withdigested and stored sewage. Hospital WW contains more ARB, ARG, and antibiotic residues than municipal sewage, butthe difference is not large for ARB and the impact may be minimal in large WW systems. Insmaller WW infrastructures, a hospital or similar institution may have a higher impact on theeffluent water from the WWTP, and this might suggest that local treatment of the WW at thehospital could be advantageous. A recent Norwegian study monitored bacterial diversity indifferent WW in the Oslo area, and found the highest concentration of AMR (ARB and/orARG) in hospital WW. But surprisingly, high concentrations were also found in the studiedcommunity wastewater. The relative contribution of hospital effluents seemed low in termsof dissemination of antimicrobial resistant bacteria to the wastewater treatment plant.All measures that can be taken at source to avoid dissemination of antimicrobial agents,ARB, and ARG should be evaluated for their contribution towards combatting AMRemergence. Concentrations of antimicrobial agents, ARB, and ARG are highest in the sewagesystem and at the inlet to WWTPs. Separation of the different fractions of antimicrobials,ARB, and ARG for individual treatment may therefore reduce the total load reaching theWWTPs. Due to the high concentrations of ARB and ARG in the sewage system, risks fromsewage pipe leakages are of concern. Intrusion of contaminated water into the drinkingwater distribution system should also raise concern. Rehabilitation of the sewage anddrinking water networks will considerably mitigate risks. The level of sewage treatment inNorway is rather low, and upgrading will decrease the concentration of bacteria discharged.However, WWTPs are generally not designed for removal of AMR. Membrane processesseem to be the most promising option for increasing such removal rates.Future perspectives:The opinion discusses how the “concept of sensitive recipients” for requirements of the levelof WWT could be revisited. This concept is currently based on controlling nutrient loads tothe environment, rather than on trace contaminants or contaminants such as ARB and ARGthat develop in the stressed environment. In the future, it might be of value to definerequirements for WWT based on the relative increase caused by the discharge to thepollution level. Using such a paradigm, a small load with contaminants to a rather unpollutedenvironment would be rated as being highly critical and the discharge would require furthertreatment. In addition to the amount of ARB, the type of resistance and their level ofhorizontal mobility are also important in this aspect.This opinion also proposes the establishment of a new monitoring programme, parallel to theexisting NORM and NORM-VET monitoring programmes; “NORM-ECO”. There is relativelylittle knowledge on AMR in non-clinical compartments, compared with hospital and otherclinical settings, and parameters that would trigger immediate responses from NFAS or NEAare not yet identified. However, establishment of a “NORM-ECO”-system requires clarificationof that needs further definition.

• 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
• 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.

• Rueness, Eli Knispel; Naidenko, Sergei; Trosvik, Pål & Stenseth, Nils Christian (2014). Large-scale genetic structuring of a widely distributed carnivore - The eurasian lynx (Lynx lynx). PLOS ONE. 9(4). doi: 10.1371/journal.pone.0093675. Full text in Research Archive Show summary

  Over the last decades the phylogeography and genetic structure of a multitude of species inhabiting Europe and North America have been described. The flora and fauna of the vast landmasses of north-eastern Eurasia are still largely unexplored in this respect. The Eurasian lynx is a large felid that is relatively abundant over much of the Russian sub-continent and the adjoining countries. Analyzing 148 museum specimens collected throughout its range over the last 150 years we have described the large-scale genetic structuring in this highly mobile species. We have investigated the spatial genetic patterns using mitochondrial DNA sequences (D-loop and cytochrome b) and 11 microsatellite loci, and describe three phylogenetic clades and a clear structuring along an east-west gradient. The most likely scenario is that the contemporary Eurasian lynx populations originated in central Asia and that parts of Europe were inhabited by lynx during the Pleistocene. After the Last Glacial Maximum (LGM) range expansions lead to colonization of north-western Siberia and Scandinavia from the Caucasus and north-eastern Siberia from a refugium further east. No evidence of a Berinigan refugium could be detected in our data. We observed restricted gene flow and suggest that future studies of the Eurasian lynx explore to what extent the contemporary population structure may be explained by ecological variables.

• Skånseng, Beate; Svihus, Birger; Rudi, Knut; Trosvik, Pål & Moen, Birgitte (2013). Effect of Different Feed Structures and Bedding on the Horizontal Spread of Campylobacter jejuni within Broiler Flocks. Agriculture. 3(4), p. 741–760. doi: 10.3390/agriculture3040741. Full text in Research Archive
• 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.

• Trosvik, Pål; Stenseth, Nils Christian & Rudi, Knut (2010). Convergent temporal dynamics of the human infant gut microbiota. The ISME Journal. ISSN 1751-7362. 4(2), p. 151–158. doi: 10.1038/ismej.2009.96. Full text in Research Archive Show summary

  Temporal dynamics of the human gut microbiota is of fundamental importance for the development of proper gut function and maturation of the immune system. Here we present a description of infant gut ecological dynamics using a combination of nonlinear data modeling and simulations of the early infant gut colonization processes. Principal component analysis of infant microbiota 16S rRNA gene microarray data showed that the main directions of variation were defined by three phylum-specific probes targeting Bacteroides, Proteobacteria and Firmicutes. Nonlinear regression analysis identified several dynamic interactions between these three phyla. Simulations of the early phylum-level colonization process showed the relatively rapid establishment of an equilibrium community after an unstable initial phase. In general, varying the initial composition of phyla in the simulations had little bearing on the final equilibrium. The dynamic interaction model was found to maintain its predictive ability for Proteobacteria and Firmicutes well into the simulation, whereas Bacteroides densities tended to be underestimated, possibly due to host top-down selection for Bacteroides. In accordance with our model, initial perturbation of the microbiota by different mode of delivery (vaginal and C-section) did not affect the later phylum composition in the infants investigated. Considering the predictive ability and convergence of our phylum-level model, we now propose that deterministic bacterial-bacterial interactions are more important for shaping the human infant gut microbiota than previously anticipated. The ISME Journal (2010) 4, 151-158; doi:10.1038/ismej.2009.96; published online 27 August 2009

• Trosvik, Pål; Rudi, Knut; Strætkvern, Knut Olav; Jakobsen, Kjetill Sigurd; Næs, Tormod & Stenseth, Nils Christian (2010). Web of ecological interactions in an experimental gut microbiota. Environmental Microbiology. ISSN 1462-2912. 12(10), p. 2677–2687. doi: 10.1111/j.1462-2920.2010.02236.x. Full text in Research Archive
• Skånseng, Beate; Kaldhusdal, Magne; Moen, Birgitte; Gjevre, Anne Gerd; Johannessen, Gro & Sekelja, Monika [Show all 8 contributors for this article] (2010). Prevention of intestinal Campylobacter jejuni colonization in broilers by combinations of in-feed organic acids. Journal of Applied Microbiology. ISSN 1364-5072. 109(4), p. 1265–1273. doi: 10.1111/j.1365-2672.2010.04766.x. Full text in Research Archive
• Zimonja, Monika Sekelja; Rudi, K; Trosvik, Pål & Næs, Tormod (2008). Multivariate curve resolution of mixed bacterial DNA sequence spectra: identification and quantification of bacteria in undefined mixture samples. Journal of Chemometrics. ISSN 0886-9383. 22, p. 309–322. doi: 10.1002/cem.1115. Full text in Research Archive
• Trosvik, Pål; Rudi, Knut; Næs, Tormod; Kohler, Achim; Chan, Kai-Ming & Jakobsen, Kjetill S. [Show all 7 contributors for this article] (2008). Characterizing mixed microbial population dynamics using time-series analysis. The ISME Journal. ISSN 1751-7362. 2(7), p. 707–715. Full text in Research Archive Show summary

  Due to a general shortage of temporal population data, dynamic structures in microbial communities remain largely unexplored. Knowledge of community dynamics is, however, essential for understanding the mechanisms by which microbes interact. Here, we have used a computational approach for quantification of bacteria in multispecies populations, generating data for time-series modeling. Moreover, we have used online FR-IR spectroscopy to monitor the main metabolic processes. The approach enabled us to provide a functional description of the parameters governing the population dynamics in a three-species model bacterial community, demonstrating density-dependent regulation, interspecies competition and even a case of cooperation between two species. Since the field of microbial ecology has yet to embrace many of the concepts and methods developed for the study of ecology of higher plants and animals, the realization that microbial systems can be analyzed within the same conceptual framework as other ecosystems is of fundamental importance.

• Zimonja, Monika; Rudi, Knut; Trosvik, Pål & Næs, Tormod (2008). Multivariate curve resolution of mixed bacterial DNA sequence spectra: identification and quantification of bacteria in undefined mixture samples. Journal of Chemometrics. ISSN 0886-9383. 22(05.jun), p. 309–322. doi: 10.1002/cem.1115. Full text in Research Archive Show summary

  A comprehensive understanding of factors that influence microbial competition and cooperation, their diversity and processes will be greatly beneficial in many research areas. Current tools for microflora determinations are far from suitable for high-throughput monitoring of development in complex microbial communities. Here, we describe the application of a calibration free method, multivariate curve resolution with alternating least squares (MCR-ALS), for identification and quantification of different microbes in mixture samples. The idea is to utilize MCR-ALS to enable close monitoring of ecology in a variety of microbial communities. The data from two designed experiments consisting of DNA sequence spectra measured on mixtures were analysed with MCR-ALS using no prior information on the data except for appropriate constraints, such as non-negativity and closure. The results were compared both to the known true concentrations as well as to the results obtained from the well-established multivariate calibration method partial least squares (PLS) regression. MCR-ALS performed as well as PLS regression, successfully extracting all pure bacterial spectra and quantitative information on these, with 97.81% and 97.91% explained variance for the first and the second data set, respectively. Copyright (C) 2008 John Wiley & Sons, Ltd.

• Trosvik, Pål; Rudi, Knut; Næs, Tormod; Kohler, Achim; Chan, Kung-Sik & Jakobsen, Kjetill Sigurd [Show all 7 contributors for this article] (2008). Characterizing mixed microbial population dynamics using time-series analysis. The ISME Journal. ISSN 1751-7362. 2(7), p. 707–715. doi: 10.1038/ismej.2008.36. Full text in Research Archive
• Skånseng, Beate; Trosvik, Pål; Zimonja, Monika; Johnsen, Gro; Bjerrum, Lotte & Pedersen, Karl [Show all 8 contributors for this article] (2007). Co-Infection Dynamics of a Major Food-borne Zoonotic Pathogen in Chicken. PLoS Pathogens. ISSN 1553-7366. 3(11), p. 1–8. doi: 10.1371/journal.ppat.0030175. Full text in Research Archive
• Rudi, Knut; Zimonja, Monika Sekelja; Trosvik, Pål & Næs, Tormod (2007). Use of multivariate statistics for 16S rRNA gene analysis of microbial communities. International journal of food microbiology. ISSN 0168-1605. 120, p. 95–99. Full text in Research Archive
• Skanseng, B; Trosvik, Pål; Zimonja, Monika Sekelja; Johnsen, G; Bjerrum, L & Pedersen, K [Show all 8 contributors for this article] (2007). Co-infection dynamics of a major food-borne zoonotic pathogen in chicken. PLoS Pathogens. ISSN 1553-7366. 3, p. 1790–1797. doi: 10.1371/journal.ppat.0030175. Full text in Research Archive
• Trosvik, Pål; Skanseng, B; Jakobsen, Kjetill Sigurd; Stenseth, Nils Christian; Næs, Tormod & Rudi, K (2007). Multivariate analysis of complex DNA sequence electropherograms for high-throughput quantitative analysis of mixed microbial populations. Applied and Environmental Microbiology. ISSN 0099-2240. 73, p. 4975–4983. doi: 10.1128/AEM.00128-07. Full text in Research Archive
• Rudi, Knut; Zimonja, Monika; Næs, Tormod & Trosvik, Pål (2007). Use of multivariate statistics for 16S rRNA gene analysis of microbial communities. International journal of food microbiology. ISSN 0168-1605. 120(01.feb), p. 95–99. Full text in Research Archive Show summary

  Understanding dynamic processes and diversity in microbial communities is of key importance for combating pathogens and for stimulating beneficial bacteria. We have addressed these challenges utilising multivariate statistics for analyses of microbial community structures. We based our microbial community analyses on 16S rRNA gene data. This gene is by far the most widely applied genetic marker for phylogenetic and microbial community studies. Both probe and clone library data were analysed. We analysed the clone library data using a newly developed coordinate-based phylogenetic approach. By using coordinates, we avoid both DNA sequence alignments and the need for definition of operational taxonomic units (OTUs). The basic principle is to transform the sequence data to frequencies of multimers (short sequences of n=2 to 6), and then to use principal component analyses (PCA) for data compression into an orthogonal coordinate space. We used our coordinate method for global 16S rRNA gene analyses of prokaryotes. When comparing microbial communities, it is often important to determine the relationship between the microflora and knowledge about the samples analysed. We used partial least square regression (PLSR) to relate physical/chemical properties to microbial community composition. This was done by analysing both probe and clone library data using the effect of modified atmosphere packaging (MAP) on fish microflora as an example. We are currently investigating approaches to describe dynamic microbial community interactions. Our ultimate goal is to understand and model the main dynamic interactions in complete microbial communities. Notes: Journal article

• Trosvik, Pål; Skånseng, Beate; Jakobsen, Kjetill S.; Stenseth, Nils Christian; Næs, Tormod & Rudi, Knut (2007). Multivariate Analysis of Complex DNA Sequence Electropherograms for High-Throughput Quantitative Analysis of Mixed Microbial Populations. Applied and Environmental Microbiology. ISSN 0099-2240. 73(15), p. 4975–4983. doi: 10.1128/AEM.00128-07. Full text in Research Archive Show summary

  High-throughput quantification of genetically coherent units (GCUs) is essential for deciphering population dynamics and species interactions within a community of microbes. Current techniques for microbial community analyses are, however, not suitable for this kind of high-throughput application. Here, we demonstrate the use of multivariate statistical analysis of complex DNA sequence electropherograms for the effective and accurate estimation of relative genotype abundance in cell samples from mixed microbial populations. The procedure is no more labor-intensive than standard automated DNA sequencing and provides a very effective means of quantitative data acquisition from experimental microbial communities. We present results with the Campylobacter jejuni strain-specific marker gene gltA, as well as the 16S rRNA gene, which is a universal marker across bacterial assemblages. The statistical models computed for these genes are applied to genetic data from two different experimental settings, namely, a chicken infection model and a multispecies anaerobic fermentation model, demonstrating collection of time series data from model bacterial communities. The method presented here is, however, applicable to any experimental scenario where the interest is quantification of GCUs in genetically heterogeneous DNA samples.

View all works in NVA

• Bødtker, Gunhild; Coutris, Claire; Denison, Eva Marie-Louise; Frostegård, Åsa; Joner, Erik & Lunestad, Bjørn Tore [Show all 9 contributors for this article] (2025). Protocol for a scoping review of research on environmental effects of biodegradable plastics relevant for Norwegian conditions. Full text in Research Archive Show summary

  In this self-tasking scoping review, VKM will map research about the environmental impacts of biodegradable plastics, including biodegradation rates and material persistence in different environments and geographical regions, the influence on microbial ecology and activity, and ecotoxicological effects of materials and associated chemical substances. Related to this is also research associated with the development of methodology, standards, environmental risk assessment, life cycle impact analyses, material sources and properties of biodegradable plastics and products. The aim is to 1) determine the extent of evidence summarised in reviews and original research papers within this emerging research area and 2) map the evidence according to the materials and chemicals studied, types of environments and geographical regions covered, the hypotheses addressed, the type of endpoints assessed and the reported key findings. Systematic literature searches will be performed to identify the summarised evidence, applying APRIO to develop a tailored search protocol that addresses the multi- and cross-disciplinary nature of the research area. We will select and map the identified publications applying Rayyan and sort them into three categories based on their main scientific focus and aim of study: 1) material properties and application, 2) biodegradation and microbial ecology, and 3) ecotoxicology. There will be no geographical restrictions on the search and study selection, but in the data charting process we will highlight findings relevant to Norway and other Nordic countries. The current project adheres to the “Preferred Reporting Items for Systematic Reviews and MetaAnalyses extension for Scoping Reviews (PRISMA-ScR) Checklist” for protocol development and reporting. We will address uncertainties associated with research studies applying EFSA guidelines and their generic list of common types of uncertainty affecting scientific studies and assessments.

• Schultz, Gry Irene Granli; Parr, Christine Louise; Trosvik, Pål; Yazdankhah, Siamak Pour; Andersen, Lene Frost & Dalen, Knut Tomas [Show all 14 contributors for this article] (2025). Health risk assessment of Bifidobacterium breve M-16V in infant formula. VKM Bulletin. 2025(VKM Bulletin 2025: 09), p. 1–115. Full text in Research Archive Show summary

  VKM has not identified any short-term negative health effects from consuming infant formula with Bifidobacterium breve M-16V. However, there is uncertainty and limited research on possible long-term effects. There is also little research conducted independently of the manufacturers. The Norwegian Food Safety Authority has asked VKM to assess whether there may be health risks associated with giving infants (up to 12 months) infant formula supplemented with a specific probiotic bacterium (Bifidobacterium breve M-16V). "Probiotics" generally refers to health products containing live microorganisms, usually bacteria. Currently, some infant formulas outside Norway are supplemented with freeze-dried probiotic bacteria. The bacterium Bifidobacterium breve M-16V (B. breve M-16V) in given concentrations is considered safe in the USA and EU for use in food, but this status is regularly reviewed in the EU and may change if negative health effects are discovered. In infants, the intestinal microbiota (composition of microorganisms) and immune system are not fully developed, and it is uncertain whether the addition of high doses of probiotic bacteria during infancy may have unintended long-term effects. Background for the risk assessment A company has applied to the Norwegian Food Safety Authority to market two specific infant formulas in Norway: one peptide-based and another amino acid-based. The products are intended for infants having allergies and are regulated as foods for special medical purposes. Both products are supplemented with the probiotic bacterium B. breve M-16V. The Norwegian Food Safety Authority has asked VKM to assess whether there may be health risks associated with giving infants these products specifically, and infant formula supplemented with B. breve M-16V in general. VKM’s methodology A multidisciplinary project group appointed by VKM has reviewed documentation from the company. The group has also conducted a systematic literature review of health effects reported in studies where infants received infant formula supplemented with B. breve M-16V and calculated the possible intake of infant formula and B. breve M-16V among Norwegian infants. VKM has only assessed the risk of negative health effects based on the assignment and according to guidelines for probiotics in food, not as a medicinal product. The assessment has been approved by a multidisciplinary approval group, also appointed by VKM. Findings VKM has not found any unwanted properties of B. breve M-16V based on reported laboratory studies and animal experiments. VKM has also not found negative health effects in 13 clinical studies involving a total of 1580 children, of whom 836 received infant formula supplemented with B. breve M-16V (test) and the rest received infant formula without B. breve M-16V (control). The studies lasted from 6 weeks to 12 months (median 16 weeks). VKM found no consistent differences between test and control groups in reported side effects, children's growth, or symptoms from the gastrointestinal tract, skin, or respiratory system as long as the studies were ongoing (short-term). VKM has found only two studies of long-term effects in children one year (development of asthma symptoms) or 3-5 years (neurocognitive outcomes) after they received infant formula with B. breve M-16V. This is too little to draw conclusions about long-term effects.

• Lind, Vibeke; Trosvik, Pål; Muincke, Eric de; Skjånes, Kari; Jørgensen, Grete Helen Meisfjord & Borgvang, Stig A. (2022). Microalgae (Chlorella vulgaris) in diet to sheep for DNA profile in rumen microbiomes. 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 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
• Nielsen, Kaare Magne; Wasteson, Yngvild; Yazdankhah, Siamak Pour; Bergh, Øivind; Eklo, Ole Martin & Joner, Erik [Show all 9 contributors for this article] (2020). Antimicrobial resistance (AMR) from an environmental perspective. A short summary of assessments prepared by VKM in the period 2015- 2020. VKM Report. 2020:10, p. 1–36. Full text in Research Archive
• Rowe, Melissah; Muinck, Erik de; Fredriksen, Simen; Carneiro, Diana; Star, Bastiaan & Trosvik, Pål (2018). Ejaculate microbiota of birds: inter-specific variation and disease transmission. Full text in Research Archive
• Rueness, Eli Knispel; Trosvik, Pål; Atickem, Anagaw Meshesha; Sillero-Zubiri, Claudio & Trucchi, Emiliano (2015). The African wolf is a missing link in the wolf-like canid phylogeny. BioRxiv. ISSN 0362-4331. doi: 10.1101/017996. Full text in Research Archive
• Stenseth, Nils Christian; Voje, Kjetil L.; Holen, Øistein Haugsten; Liow, Lee Hsiang & Trosvik, Pål (2014). Biotic and abiotic interactions in evolution: the Red Queen perspective on evolution in biotic communities. 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
• Stenseth, Nils Christian; Voje, Kjetil L.; Holen, Øistein Haugsten; Liow, Lee Hsiang & Trosvik, Pål (2014). Coevolution in multispecies communities: the Red Queen Perspective. Full text in Research Archive
• Skånseng, Beate; Trosvik, Pål; Zimonja, Monika; Johnsen, Gro; Bjerrum, Lotte & Pedersen, Karl [Show all 8 contributors for this article] (2008). Co-Infection Dynamics of a Majo food-Borne Zoonotic Pathogen in Chicken. Full text in Research Archive
• Madslien, Elisabeth Henie; Asare, Nana Yaa Ohene; Bergh, Øivind; Joner, Erik; Trosvik, Pål & Yazdankhah, Siamak Pour [Show all 10 contributors for this article] (2019). Current knowledge of the health and environmental risks of microbialbased cleaning products. Scientific opinion of the Panel on Microbial Ecology of the Norwegian Scientific Committee for Food and Environment. Norwegian Scientific Committee for Food and Environment (VKM). ISSN 9788282593250. 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.

• Trosvik, Pål (2008). Ecology of gut bacteria : Microbial community dynamics investigated using an integrated approach. Universitetet i Oslo. Full text in Research Archive Show summary

  I dette arbeidet har vi utviklet molekylære metoder for simultant å måle forekomsten av ulike mikrober i komplekse samfunn. Koblet med økologisk analyse gir dette oss helt nye muligheter til å forstå hvordan bakteriesamfunn fungerer, kunnskap av potensielt stor verdi for eksempel i forebygging og behandling av infeksjoner. <br> I sine naturlige miljøer lever bakteriene gjerne i kompliserte samfunn, det være seg i jord, vann eller i menneskekroppen. For eksempel består den normale humane bakterieflora av så mye som 1014 bakterieceller, ca. 100 ganger så mange som det finnes menneskeceller i kroppen. En voksende mengde litteratur dokumenterer en rekke viktige roller disse mikrobene spiller i helse og sykdom, men allikevel er vår viten om deres økologi fortsatt svært ufullkommen. En mye brukt fremgangsmåte i økologiske studier av planter og dyr er analyse av tidsseriedata, en tilnærming som kan gi informasjon om hvilke forhold som styrer utvikingen av økosystemer, for eksempel mekanismer som ligger bak det at populasjoner kollapser og blomstrer. Denne typen analyse er langt mindre brukt til å studere mikrobenes verden, til dels fordi fagdisiplinene generell økologi og mikrobiologi lenge har utviklet seg som separate enheter, men også fordi populasjonsdata på mikrober i komplekse samfunn er vanskelige å oppdrive. Bakterier er i praksis usynlige (utenom i mikroskop), de er ofte vanskelige å skille fra hverandre ut ifra morfologiske kriterier, og de har ekstremt kort generasjonstid (så lite som 10 min. under gunstige forhold). Metodene vi har utviklet gjør det mulig å følge bakteriesamfunn gjennom tid på en relativt hurtig og enkel måte. De er basert på simultan registrering av DNA-molekyler som kan diskriminere mellom de ulike medlemmene av et samfunn, og påfølgende analyse av DNA-signalene v.h.a. regnemetoder som normalt brukes kjemi. Vi har brukt metodene både i infeksjonssituasjoner og laboratoriekulturer, og analyse av de resulterende tidsseriene har gjort oss i stand til å danne hypoteser om hvordan bakteriesamfunn fungerer. Slik informasjon er relevant bl.a. i forhold til sykdommer som oppstår som følge av endringer i kroppens naturlige bakterieflora.<br> Avhandlingen er et resultat av tverrfaglig samarbeid mellom NOFIMA Mat (tidligere Matforsk AS) og Centre for Ecological and Evolutionary Synthesis (CEES, Senter for Fremragende Forskning ved Biologisk Institutt ved UiO).

View all works in NVA