Browsing by Subject "HOST"

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  • van der Lugt, Benthe; van Beek, Adriaan A.; Aalvink, Steven; Meijer, Ben; Sovran, Bruno; Vermeij, Wilbert P.; Brandt, Renata M. C.; de Vos, Willem M.; Savelkoul, Huub F. J.; Steegenga, Wilma T.; Belzer, Clara (2019)
    BackgroundThe use of Akkermansia muciniphila as potential therapeutic intervention is receiving increasing attention. Health benefits attributed to this bacterium include an improvement of metabolic disorders and exerting anti-inflammatory effects. The abundance of A. muciniphila is associated with a healthy gut in early mid- and later life. However, the effects of A. muciniphila on a decline in intestinal health during the aging process are not investigated yet. We supplemented accelerated aging Ercc1(-/7) mice with A. muciniphila for 10weeks and investigated histological, transcriptional and immunological aspects of intestinal health.ResultsThe thickness of the colonic mucus layer increased about 3-fold after long-term A. muciniphila supplementation and was even significantly thicker compared to mice supplemented with Lactobacillus plantarum WCFS1. Colonic gene expression profiles pointed towards a decreased expression of genes and pathways related to inflammation and immune function, and suggested a decreased presence of B cells in colon. Total B cell frequencies in spleen and mesenteric lymph nodes were not altered after A. muciniphila supplementation. Mature and immature B cell frequencies in bone marrow were increased, whereas B cell precursors were unaffected. These findings implicate that B cell migration rather than production was affected by A. muciniphila supplementation. Gene expression profiles in ileum pointed toward a decrease in metabolic- and immune-related processes and antimicrobial peptide production after A. muciniphila supplementation. Besides, A. muciniphila decreased the frequency of activated CD80(+)CD273(-) B cells in Peyer's patches. Additionally, the increased numbers of peritoneal resident macrophages and a decrease in Ly6C(int) monocyte frequencies in spleen and mesenteric lymph nodes add evidence for the potentially anti-inflammatory properties of A. muciniphila.ConclusionsAltogether, we show that supplementation with A. muciniphila prevented the age-related decline in thickness of the colonic mucus layer and attenuated inflammation and immune-related processes at old age. This study implies that A. muciniphila supplementation can contribute to a promotion of healthy aging.
  • Seppala, Otto; Karvonen, Anssi; Kuosa, Marja; Haataja, Maarit; Jokela, Jukka (2013)
  • Mäntynen, Sari; Laanto, Elina; Oksanen, Hanna M.; Poranen, Minna M.; Diaz-Munoz, Samuel L. (2021)
    The canonical lytic-lysogenic binary has been challenged in recent years, as more evidence has emerged on alternative bacteriophage infection strategies. These infection modes are little studied, and yet they appear to be more abundant and ubiquitous in nature than previously recognized, and can play a significant role in the ecology and evolution of their bacterial hosts. In this review, we discuss the extent, causes and consequences of alternative phage lifestyles, and clarify conceptual and terminological confusion to facilitate research progress. We propose distinct definitions for the terms 'pseudolysogeny' and 'productive or non-productive chronic infection', and distinguish them from the carrier state life cycle, which describes a population-level phenomenon. Our review also finds that phages may change their infection modes in response to environmental conditions or the physiological state of the host cell. We outline known molecular mechanisms underlying the alternative phage-host interactions, including specific genetic pathways and their considerable biotechnological potential. Moreover, we discuss potential implications of the alternative phage lifestyles for microbial biology and ecosystem functioning, as well as applied topics such as phage therapy.
  • Pakarinen, Aku; Fritze, Hannu; Timonen, Sari; Kivijarvi, Pirjo; Velmala, Sannakajsa (2021)
    Arbuscular mycorrhizal fungi (AMF) enhance plant phosphorus uptake, increase soil water holding abilities, reduce soil erosion and can protect their hosts from soil-borne pathogens. Hence, AMF play an important part in improving sustainable agricultural practices, and information about the effects of different preceding crop species on the following crop's AMF well-being is crucial for designing crop rotations. We studied onion root and soil microbial diversity and onion root AMF colonization rates after being preceded by three AMF hosting and one non-hosting green manure crop species in a boreal climate organic field. One-season cultivation of different preceding green manure crops did not have a strong effect on AMF colonization or microbial diversity in onion roots nor in the surrounding soil. Onions had high AMF colonization and microbial diversity after all four preceding crops. The overall fungal and bacterial populations of the soil reacted more strongly to seasonal variations than preceding crops. The study suggests that one season is a too short time to influence the AMF community in boreal climate organic fields with conventional tillage. Thus, non-host preceding crops can also be used in rotations, especially together with AMF host crops.
  • Wirta, Helena K.; Hebert, Paul D. N.; Kaartinen, Riikka; Prosser, Sean W.; Varkonyi, Gergely; Roslin, Tomas (2014)
  • Kun, Roland S.; Meng, Jiali; Salazar-Cerezo, Sonia; Makela, Miia R.; de Vries, Ronald P.; Garrigues, Sandra (2020)
    The CRISPR/Cas9 system has been successfully applied for gene editing in filamentous fungi. Previous studies reported that single stranded oligonucleotides can be used as repair templates to induce point mutations in some filamentous fungi belonging to genus Aspergillus. In Aspergillus niger, extensive research has been performed on regulation of plant biomass degradation, addressing transcription factors such as XlnR or GaaR, involved in (hemi-)cellulose and pectin utilization, respectively. Single nucleotide mutations leading to constitutively active forms of XlnR and GaaR have been previously reported. However, the mutations were performed by the introduction of versions obtained through site-directed or UV-mutagenesis into the genome. Here we report a more time- and cost-efficient approach to obtaining constitutively active versions by application of the CRISPR/Cas9 system to generate the desired mutation on-site in the A. niger genome. This was also achieved using only 60-mer single stranded oligonucleotides, shorter than the previously reported 90-mer strands. In this study, we show that CRISPR/Cas9 can also be used to efficiently change functional properties of the proteins encoded by the target gene by on-site genomic mutations in A. niger. The obtained strains with constitutively active XlnR and GaaR versions resulted in increased production of plant biomass degrading enzymes and improved release of D-xylose and L-arabinose from wheat bran, and D-galacturonic acid from sugar beet pulp.
  • Gursoy, Ulvi Kahraman; Pussinen, Pirkko J.; Salomaa, Veikko; Syrjalainen, Sanna; Kononen, Eija (2018)
    Objective: Aim was to analyze the diagnostic ability of cumulative risk score (CRS), which uses salivary levels of Porphyromonas gingivalis, interleukin (IL)-1 beta, and matrix metalloproteinase (MMP)-8 in an adaptive design, compared to previously reported thresholds of each marker alone. Materials and Methods: Oral and general health information of 463 participants were included in the analysis. Having the percentage of bleeding on probing (BOP) > 25%, having at least two sites with probing pocket depth (PPD) of 4-5 mm or having at least one tooth with alveolar bone loss (ABL) of at least 1/3 of the root length were accepted as outcome variables. Being above the salivary threshold concentrations of P. gingivalis, IL-1 beta, and MMP-8 and CRS values were used as explanatory variables. Receiver operating characteristics (ROC) producing an area under the curve (AUC) and multinomial regression analysis were used in statistical analysis. Results: CRS provided AUCs larger than any other tested biomarker threshold. Sensitivity and specificity of CRS for detecting clinical markers of periodontitis were acceptable, and a strong association was observed between the highest CRS score and having at least two sites with PPD of 4-5 mm. Conclusion: CRS brings additional power over fixed thresholds of single biomarkers in detecting periodontitis.
  • Kettunen, Elina Johanna; Schmidt, Alexander; Diederich, Paul; Grabenhorst, Heinrich; Rikkinen, Jouko (2018)
    A diversity of filamentous microfungi was discovered from thallus surfaces of epiphytic lichens preserved in Bitterfeld and Baltic amber. We report seven distinct morphologies of dematiaceous hyphomycetes, some of which closely resemble species of the extant genera Sporidesmium, Taeniolella s. lat. and Taeniolina. Both the placement of the fungi on their substrates and the exquisite preservation of delicate structures indicate that the fungi were fully developed before they were engulfed by fresh resin. The lichens probably grew on the trunks of resin producing trees and became embedded in resin flows together with their fungal associates. The findings demonstrate that a wide range of presumably specialised fungi have lived on living and decomposing lichen thalli at least since the Paleogene. The findings add an interesting new component to the as yet poorly known mycota of the ancient European amber forests.
  • Boldin, Barbara; Kisdi, Eva (2016)
    Evolutionary suicide is a riveting phenomenon in which adaptive evolution drives a viable population to extinction. Gyllenberg and Parvinen (Bull Math Biol 63(5):981-993, 2001) showed that, in a wide class of deterministic population models, a discontinuous transition to extinction is a necessary condition for evolutionary suicide. An implicit assumption of their proof is that the invasion fitness of a rare strategy is well-defined also in the extinction state of the population. Epidemic models with frequency-dependent incidence, which are often used to model the spread of sexually transmitted infections or the dynamics of infectious diseases within herds, violate this assumption. In these models, evolutionary suicide can occur through a non-catastrophic bifurcation whereby pathogen adaptation leads to a continuous decline of host (and consequently pathogen) population size to zero. Evolutionary suicide of pathogens with frequency-dependent transmission can occur in two ways, with pathogen strains evolving either higher or lower virulence.
  • Kolmeder, Carolin A.; Salojarvi, Jarkko; Ritari, Jarmo; de Been, Mark; Raes, Jeroen; Falony, Gwen; Vieira-Silva, Sara; Kekkonen, Riina A.; Corthals, Garry L.; Palva, Airi; Salonen, Anne; de Vos, Willem M. (2016)
    Recent metagenomic studies have demonstrated that the overall functional potential of the intestinal microbiome is rather conserved between healthy individuals. Here we assessed the biological processes undertaken in-vivo by microbes and the host in the intestinal tract by conducting a metaproteome analysis from a total of 48 faecal samples of 16 healthy adults participating in a placebo-controlled probiotic intervention trial. Half of the subjects received placebo and the other half consumed Lactobacillus rhamnosus GG for three weeks (10(10) cfu per day). Faecal samples were collected just before and at the end of the consumption phase as well as after a three-week follow-up period, and were processed for microbial composition and metaproteome analysis. A common core of shared microbial protein functions could be identified in all subjects. Furthermore, we observed marked differences in expressed proteins between subjects that resulted in the definition of a stable and personalized microbiome both at the mass-spectrometry-based proteome level and the functional level based on the KEGG pathway analysis. No significant changes in the metaproteome were attributable to the probiotic intervention. A detailed taxonomic assignment of peptides and comparison to phylogenetic microarray data made it possible to evaluate the activity of the main phyla as well as key species, including Faecalibacterium prausnitzii. Several correlations were identified between human and bacterial proteins. Proteins of the human host accounted for approximately 14% of the identified metaproteome and displayed variations both between and within individuals. The individually different human intestinal proteomes point to personalized host-microbiota interactions. Our findings indicate that analysis of the intestinal metaproteome can complement gene-based analysis and contributes to a thorough understanding of the activities of the microbiome and the relevant pathways in health and disease.
  • Pino-Bodas, Raquel; Laakso, Into; Stenroos, Soili (2017)
    Heterocephalacria bachmannii is a lichenicolous fungus that takes as hosts numerous lichen species of the genus Cladonia. In the present study we analyze whether the geographical distance, the host species or the host secondary metabolites determine the genetic structure of this parasite. To address the question, populations mainly from the Southern Europe, Southern Finland and the Azores were sampled. The specimens were collected from 20 different host species representing ten chemotypes. Three loci, ITS rDNA, LSU rDNA and mtSSU, were sequenced. The genetic structure was assessed by AMOVA, redundance analyses and Bayesian clustering methods. The results indicated that the host species and the host secondary metabolites are the most influential factors over the genetic structure of this lichenicolous fungus. In addition, the genetic structure of H. bachmannii was compared with that of one of its hosts, Cladonia rangiformis. The population structure of parasite and host were discordant. The contents in phenolic compounds and fatty acids of C. rangiformis were quantified in order to test whether it had some influence on the genetic structure of the species. But no correlation was found with the genetic clusters of H. bachmannii.
  • Schneider, Julia; Hoffmann, Bernd; Fevola, Cristina; Schmidt, Marie Luisa; Imholt, Christian; Fischer, Stefan; Ecke, Frauke; Hoernfeldt, Birger; Magnusson, Magnus; Olsson, Gert E.; Rizzoli, Annapaola; Tagliapietra, Valentina; Chiari, Mario; Reusken, Chantal; Buzan, Elena; Kazimirova, Maria; Stanko, Michal; White, Thomas A.; Reil, Daniela; Obiegala, Anna; Meredith, Anna; Drexler, Jan Felix; Essbauer, Sandra; Henttonen, Heikki; Jacob, Jens; Hauffe, Heidi C.; Beer, Martin; Heckel, Gerald; Ulrich, Rainer G. (2021)
    The development of new diagnostic methods resulted in the discovery of novel hepaciviruses in wild populations of the bank vole (Myodes glareolus, syn. Clethrionomys glareolus). The naturally infected voles demonstrate signs of hepatitis similar to those induced by hepatitis C virus (HCV) in humans. The aim of the present research was to investigate the geographical distribution of bank vole-associated hepaciviruses (BvHVs) and their genetic diversity in Europe. Real-time reverse transcription polymerase chain reaction (RT-qPCR) screening revealed BvHV RNA in 442 out of 1838 (24.0%) bank voles from nine European countries and in one of seven northern red-backed voles (Myodes rutilus, syn. Clethrionomys rutilus). BvHV RNA was not found in any other small mammal species (n = 23) tested here. Phylogenetic and isolation-by-distance analyses confirmed the occurrence of both BvHV species (Hepacivirus F and Hepacivirus J) and their sympatric occurrence at several trapping sites in two countries. The broad geographical distribution of BvHVs across Europe was associated with their presence in bank voles of different evolutionary lineages. The extensive geographical distribution and high levels of genetic diversity of BvHVs, as well as the high population fluctuations of bank voles and occasional commensalism in some parts of Europe warrant future studies on the zoonotic potential of BvHVs.
  • Parratt, Steven R.; Barres, Benoit; Penczykowski, Rachel M.; Laine, Anna-Liisa (2017)
    Predicting and controlling infectious disease epidemics is a major challenge facing the management of agriculture, human and wildlife health. Co-evolutionarily derived patterns of local adaptation among pathogen populations have the potential to generate variation in disease epidemiology; however, studies of local adaptation in disease systems have mostly focused on interactions between competing pathogens or pathogens and their hosts. In nature, parasites and pathogens are also subject to attack by hyperparasitic natural enemies that can severely impact upon their infection dynamics. However, few studies have investigated whether this interaction varies across combinations of pathogen-hyperparasite strains, and whether this influences hyperparasite incidence in natural pathogen populations. Here, we test whether the association between a hyperparasitic fungus, Ampelomyces, and a single powdery mildew host, Podosphaera plantaginis, varies among genotype combinations, and whether this drives hyperparasite incidence in nature. Laboratory inoculation studies reveal that genotype, genotypexgenotype interactions and local adaptation affect hyperparasite infection. However, observations of a natural pathogen metapopulation reveal that spatial rather than genetic factors predict the risk of hyperparasite presence. Our results highlight how sensitive the outcome of biocontrol using hyperparasites is to selection of hyperparasite strains.
  • Bozcal, Elif; Dagdeviren, Melih; Uzel, Atac; Skurnik, Mikael (2017)
    It is crucial to understand the in vitro and in vivo regulation of the virulence factor genes of bacterial pathogens. In this study, we describe the construction of a versatile reporter system for Yersinia enterocolitica serotype O:3 (YeO3) based on the luxCDABE operon. In strain YeO3-luxCDE we integrated the luciferase substrate biosynthetic genes, luxCDE, into the genome of the bacterium so that the substrate is constitutively produced. The luxAB genes that encode the luciferase enzyme were cloned into a suicide vector to allow cloning of any promoter-containing fragment upstream the genes. When the obtained suicide-construct is mobilized into YeO3-luxCDE bacteria, it integrates into the recipient genome via homologous recombination between the cloned promoter fragment and the genomic promoter sequence and thereby generates a single-copy and stable promoter reporter. Lipopolysaccharide (LPS) O-antigen (O-ag) and outer core hexasaccharide (OC) of YeO3 are virulence factors necessary to colonization of the intestine and establishment of infection. To monitor the activities of the OC and O-ag gene cluster promoters we constructed the reporter strains YeO3-P-oc::luxAB and YeO3-P-op1::luxAB, respectively. In vitro, at 37 degrees C both promoter activities were highest during logarithmic growth and decreased when the bacteria entered stationary growth phase. At 22 degrees C the OC gene cluster promoter activity increased during the late logarithmic phase. Both promoters were more active in late stationary phase. To monitor the promoter activities in vivo, mice were infected intragastrically and the reporter activities monitored by the IVIS technology. The mouse experiments revealed that both LPS promoters were well expressed in vivo and could be detected by IVIS, mainly from the intestinal region of orally infected mice.
  • de Haan, Caroline P A; Kivistö, Rauni I; Hakkinen, Marjaana; Corander, Jukka; Hänninen, Marja-Liisa (2010)
  • Culebro, Alejandra; Machado, Miguel P.; Carrico, Joao Andre; Rossi, Mirko (2018)
    Campylobacter jejuni and Campylobacter coli are the most common cause of bacterial gastroenteritis worldwide. Additionally, C. jejuni is the most common bacterial etiological agent in the autoimmune Guillain-Barre syndrome (GBS). Ganglioside mimicry by C. jejuni lipooligosaccharide (LOS) is the triggering factor of the disease. LOS-associated genes involved in the synthesis and transfer of sialic acid (glycosyltranferases belonging to family GT-42) are essential in C. jejuni to synthesize ganglioside-like LOS. Despite being isolated from GBS patients, scarce genetic evidence supports C. coli role in the disease. In this study, through data mining and bioinformatics analysis, C. coli is shown to possess a larger GT-42 glycosyltransferase repertoire than C. jejuni. Although GT-42 glycosyltransferases are widely distributed in C. coli population, only a fraction of C. coli strains (1%) are very likely able to express ganglioside mimics. Even though the activity of C. coli specific GT-42 enzymes and their role in shaping the bacterial population are yet to be explored, evidence presented herein suggest that loss of function of some LOS-associated genes occurred during agriculture niche adaptation.
  • Lohr, Jennifer N.; Haag, Christoph R. (2020)
    Asexual species are thought to suffer more from coevolving parasites than related sexuals. Yet a variety of studies do not find the patterns predicted by theory. Here, to shine light on this conundrum, we investigate one such case of an asexual advantage in the presence of parasites. We follow the frequency dynamics of sexual and asexualDaphnia pulexin a natural pond that was initially dominated by sexuals. Coinciding with an epidemic of a microsporidian parasite infecting both sexuals and asexuals, the pond was rapidly taken over by the initially rare asexuals. With experiments comparing multiple sexual and asexual clones from across the local metapopulation, we confirm that asexuals are less susceptible and also suffer less from the parasite once infected. These results are consistent with the parasite-driven, ecological replacement of dominant sexuals by closely related, but more resistant asexuals, ultimately leading to the extinction of the formerly superior sexual competitor. Our study is one of the clearest examples from nature, backed up by experimental verification, showing a parasite-mediated reversal of competition dynamics. The experiments show that, across the metapopulation, asexuals have an advantage in the presence of parasites. In this metapopulation, asexuals are relatively rare, likely due to their recent invasion. While we cannot rule out other reasons for the observed patterns, the results are consistent with a temporary parasite-mediated advantage of asexuals due to the fact that they are rare, which is an underappreciated aspect of the Red Queen Hypothesis.
  • Aivelo, Tuomas Juho Eero; Norberg, Anna Marja Ilona (2018)
    1. Detecting interaction between species is notoriously difficult, and disentangling species associations in host-related gut communities is especially challenging. Nevertheless, due to contemporary methods, including metabarcoding and 16S sequencing, collecting observational data on community composition has become easier and much more common. 2. We studied the previously collected datasets of intestinal bacterial microbiota and parasite compositions within longitudinally followed mouse lemurs by analysing the potential interactions with diversity metrics and novel joint species distribution modelling. 3. Both methods showed statistical association between certain parasite species and bacterial microbiota composition. Unicellular Eimeria sp. had an effect on diversity of gut microbiota. The cestode Hymenolepis diminuta had negative associations with several bacterial orders, whereas closely related species Hymenolepis nana had positive associations with several bacterial orders. 4. Our results reveal potential interactions between some, but not all, intestinal parasites and gut bacterial microbiota. Host variables contributed over half of the total variation explained with the model, and sex was the most important single host variable; especially with microbiota, there were sex-related differences in the community composition. 5. This study shows how joint species distribution modelling can incorporate both within-host dynamics of several taxa and host characteristics to model potential interactions in intestinal community. These results provide new hypothesis for interactions between and among parasites and bacterial microbiota to be tested further with experimental studies.
  • Kankaanpaa, Tuomas; Vesterinen, Eero; Hardwick, Bess; Schmidt, Niels M.; Andersson, Tommi; Aspholm, Paul E.; Barrio, Isabel C.; Beckers, Niklas; Bety, Joel; Birkemoe, Tone; DeSiervo, Melissa; Drotos, Katherine H.; Ehrich, Dorothee; Gilg, Olivier; Gilg, Vladimir; Hein, Nils; Hoye, Toke T.; Jakobsen, Kristian M.; Jodouin, Camille; Jorna, Jesse; Kozlov, Mikhail; Kresse, Jean-Claude; Leandri-Breton, Don-Jean; Lecomte, Nicolas; Loonen, Maarten; Marr, Philipp; Monckton, Spencer K.; Olsen, Maia; Otis, Josee-Anne; Pyle, Michelle; Roos, Ruben E.; Raundrup, Katrine; Rozhkova, Daria; Sabard, Brigitte; Sokolov, Aleksandr; Sokolova, Natalia; Solecki, Anna M.; Urbanowicz, Christine; Villeneuve, Catherine; Vyguzova, Evgenya; Zverev, Vitali; Roslin, Tomas (2020)
    Climatic impacts are especially pronounced in the Arctic, which as a region is warming twice as fast as the rest of the globe. Here, we investigate how mean climatic conditions and rates of climatic change impact parasitoid insect communities in 16 localities across the Arctic. We focus on parasitoids in a widespread habitat,Dryasheathlands, and describe parasitoid community composition in terms of larval host use (i.e., parasitoid use of herbivorous Lepidoptera vs. pollinating Diptera) and functional groups differing in their closeness of host associations (koinobionts vs. idiobionts). Of the latter, we expect idiobionts-as being less fine-tuned to host development-to be generally less tolerant to cold temperatures, since they are confined to attacking hosts pupating and overwintering in relatively exposed locations. To further test our findings, we assess whether similar climatic variables are associated with host abundances in a 22 year time series from Northeast Greenland. We find sites which have experienced a temperature rise in summer while retaining cold winters to be dominated by parasitoids of Lepidoptera, with the reverse being true for the parasitoids of Diptera. The rate of summer temperature rise is further associated with higher levels of herbivory, suggesting higher availability of lepidopteran hosts and changes in ecosystem functioning. We also detect a matching signal over time, as higher summer temperatures, coupled with cold early winter soils, are related to high herbivory by lepidopteran larvae, and to declines in the abundance of dipteran pollinators. Collectively, our results suggest that in parts of the warming Arctic,Dryasis being simultaneously exposed to increased herbivory and reduced pollination. Our findings point to potential drastic and rapid consequences of climate change on multitrophic-level community structure and on ecosystem functioning and highlight the value of collaborative, systematic sampling effort.