| 1. |
- Kurilshikov, Alexander, et al.
(författare)
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Large-scale association analyses identify host factors influencing human gut microbiome composition
- 2021
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 53:2, s. 156-165
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Tidskriftsartikel (refereegranskat)abstract
- To study the effect of host genetics on gut microbiome composition, the MiBioGen consortium curated and analyzed genome-wide genotypes and 16S fecal microbiome data from 18,340 individuals (24 cohorts). Microbial composition showed high variability across cohorts: only 9 of 410 genera were detected in more than 95% of samples. A genome-wide association study of host genetic variation regarding microbial taxa identified 31 loci affecting the microbiome at a genome-wide significant (P < 5 x 10(-8)) threshold. One locus, the lactase (LCT) gene locus, reached study-wide significance (genome-wide association study signal: P = 1.28 x 10(-20)), and it showed an age-dependent association with Bifidobacterium abundance. Other associations were suggestive (1.95 x 10(-10) < P < 5 x 10(-8)) but enriched for taxa showing high heritability and for genes expressed in the intestine and brain. A phenome-wide association study and Mendelian randomization identified enrichment of microbiome trait loci in the metabolic, nutrition and environment domains and suggested the microbiome might have causal effects in ulcerative colitis and rheumatoid arthritis.
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| 2. |
- Carlquist, Magnus, et al.
(författare)
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Physiological heterogeneities in microbial populations and implications for physical stress tolerance
- 2012
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Ingår i: Microbial Cell Factories. - : Springer Science and Business Media LLC. - 1475-2859. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Background: Traditionally average values of the whole population are considered when analysing microbial cell cultivations. However, a typical microbial population in a bioreactor is heterogeneous in most phenotypes measurable at a single-cell level. There are indications that such heterogeneity may be unfavourable on the one hand (reduces yields and productivities), but also beneficial on the other hand (facilitates quick adaptation to new conditions - i.e. increases the robustness of the fermentation process). Understanding and control of microbial population heterogeneity is thus of major importance for improving microbial cell factory processes. Results: In this work, a dual reporter system was developed and applied to map growth and cell fitness heterogeneities within budding yeast populations during aerobic cultivation in well-mixed bioreactors. The reporter strain, which was based on the expression of green fluorescent protein (GFP) under the control of the ribosomal protein RPL22a promoter, made it possible to distinguish cell growth phases by the level of fluorescence intensity. Furthermore, by exploiting the strong correlation of intracellular GFP level and cell membrane integrity it was possible to distinguish subpopulations with high and low cell membrane robustness and hence ability to withstand freeze-thaw stress. A strong inverse correlation between growth and cell membrane robustness was observed, which further supports the hypothesis that cellular resources are limited and need to be distributed as a trade-off between two functions: growth and robustness. In addition, the trade-off was shown to vary within the population, and the occurrence of two distinct subpopulations shifting between these two antagonistic modes of cell operation could be distinguished. Conclusions: The reporter strain enabled mapping of population heterogeneities in growth and cell membrane robustness towards freeze-thaw stress at different phases of cell cultivation. The described reporter system is a valuable tool for understanding the effect of environmental conditions on population heterogeneity of microbial cells and thereby to understand cell responses during industrial process-like conditions. It may be applied to identify more robust subpopulations, and for developing novel strategies for strain improvement and process design for more effective bioprocessing.
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| 3. |
- Lekberg, Ylva, et al.
(författare)
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454-sequencing reveals stochastic local reassembly and high disturbance tolerance within arbuscular mycorrhizal fungal communities
- 2012
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Ingår i: Journal of Ecology. - : Wiley. - 1365-2745 .- 0022-0477. ; 100:1, s. 151-160
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Tidskriftsartikel (refereegranskat)abstract
- 1. Disturbance is assumed to be a major driver of plant community composition, but whether similar processes operate on associated soil microbial communities is less known. Based on the assumed trade-off between disturbance tolerance and competiveness, we hypothesize that a severe disturbance applied within a semi-natural grassland would shift the arbuscular mycorrhizal (AM) fungal community towards disturbance-tolerant fungi that are rare in undisturbed soils.
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| 4. |
- Fernandes, Rita Lencastre, et al.
(författare)
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Cell mass and cell cycle dynamics of an asynchronous budding yeast population: Experimental observations, flow cytometry data analysis, and multi-scale modeling
- 2013
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Ingår i: Biotechnology and Bioengineering. - : Wiley. - 1097-0290 .- 0006-3592. ; 110:3, s. 812-826
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Tidskriftsartikel (refereegranskat)abstract
- Despite traditionally regarded as identical, cells in a microbial cultivation present a distribution of phenotypic traits, forming a heterogeneous cell population. Moreover, the degree of heterogeneity is notably enhanced by changes in micro-environmental conditions. A major development in experimental single-cell studies has taken place in the last decades. It has however not been fully accompanied by similar contributions within data analysis and mathematical modeling. Indeed, literature reporting, for example, quantitative analyses of experimental single-cell observations and validation of model predictions for cell property distributions against experimental data is scarce. This study focuses on the experimental and mathematical description of the dynamics of cell size and cell cycle position distributions, of a population of Saccharomyces cerevisiae, in response to the substrate consumption observed during batch cultivation. The good agreement between the proposed multi-scale model (a population balance model [PBM] coupled to an unstructured model) and experimental data (both the overall physiology and cell size and cell cycle distributions) indicates that a mechanistic model is a suitable tool for describing the microbial population dynamics in a bioreactor. This study therefore contributes towards the understanding of the development of heterogeneous populations during microbial cultivations. More generally, it consists of a step towards a paradigm change in the study and description of cell cultivations, where average cell behaviors observed experimentally now are interpreted as a potential joint result of various co-existing single-cell behaviors, rather than a unique response common to all cells in the cultivation. Biotechnol. Bioeng. 2013; 110: 812826. (c) 2012 Wiley Periodicals, Inc.
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| 5. |
- Kang, Dingrong, et al.
(författare)
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Comparative Genomics Analysis of Keratin-Degrading Chryseobacterium Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production
- 2021
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Ingår i: Microorganisms. - : MDPI AG. - 2076-2607. ; 9:5
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Tidskriftsartikel (refereegranskat)abstract
- A promising keratin-degrading strain from the genus Chryseobacterium (Chryseobacterium sp. KMC2) was investigated using comparative genomic tools against three publicly available reference genomes to reveal the keratinolytic potential for biosynthesis of valuable secondary metabolites. Genomic features and metabolic potential of four species were compared, showing genomic differences but similar functional categories. Eleven different secondary metabolite gene clusters of interest were mined from the four genomes successfully, including five common ones shared across all genomes. Among the common metabolites, we identified gene clusters involved in biosynthesis of flexirubin-type pigment, microviridin, and siderophore, showing remarkable conservation across the four genomes. Unique secondary metabolite gene clusters were also discovered, for example, ladderane from Chryseobacterium sp. KMC2. Additionally, this study provides a more comprehensive understanding of the potential metabolic pathways of keratin utilization in Chryseobacterium sp. KMC2, with the involvement of amino acid metabolism, TCA cycle, glycolysis/gluconeogenesis, propanoate metabolism, and sulfate reduction. This work uncovers the biosynthesis of secondary metabolite gene clusters from four keratinolytic Chryseobacterium species and shades lights on the keratinolytic potential of Chryseobacterium sp. KMC2 from a genome-mining perspective, can provide alternatives to valorize keratinous materials into high-value bioactive natural products.
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| 6. |
- Maraha, Ninwe
(författare)
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Physiological status of bacteria used for environmental applications
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Several bacteria have properties of interest for biotechnological applications, such as bioremediation of pollutants and biocontrol of plant pathogens. In order to perform their intended tasks in the environment the cells need to remain viable and active. Therefore, the aim of this thesis was to use a combination of molecular approaches to determine the physiological status of specific bacterial populations in soil. Complementary experiments were done in pure cultures to gain a better understanding of specific physiological states, such as bacterial dormancy. In some studies, the bacteria were tagged with the following marker genes to enable them to be specifically detected in soil: gfp (encoding the green fluorescent protein, GFP), luxAB (encoding bacterial luciferase) or luc (encoding eukaryotic luciferase). Viability stains, 5-cyano-2,3-ditolyl-tetrazolium chloride (CTC) and propidium iodide (PI), were used to stain active and dead cells, respectively. The marker-gene tagged cells were incubated in soil under different conditions and the number of GFP fluorescent and stained cells was enumerated by flow cytometry at specified sampling periods. Luciferase activity was used to monitor metabolic activity of the population. In addition, the number of culturable cells was determined by selective plate counting and compared to the results obtained by flow cytometry. Finally, in one study, proteomics was used to elucidate which proteins were expressed under different nutrient conditions. The physiological status of Arthrobacter chlorophenolicus A6 (a chlorophenol degrading bacterium) was investigated after introduction into soil incubated at different temperatures, 5 and 28 °C. The majority of the A6 population remained metabolically active after 20 days of incubation in soil at 5 °C. However, there was a fraction of the GFP-fluorescent A6 population that was not stained with CTC or PI, presumably indicating a subfraction of dormant cells that were alive but inactive. By contrast, after the same period of incubation at 28 °C, the majority of the cells died. The ability of A. chlorophenolicus A6 to enter a state of dormancy during incubation at cold temperatures, makes this strain a good candidate for treating chlorophenol contaminated soil in temperate climates. Two Pseudomonas fluorescens strains, proposed for improving crop yields, were also studied. Pseudomonas fluoresens A506 is used to reduce frost damage to plants and Pseudomonas fluorescens SBW25 is a plant growth promoting bacterium. First, a GFPtagged variant of the A506 strain was studied to determine whether GFP could be used to detect the cells when they were viable but non-culturable (VBNC). The results showed that GFP tagged cells could be detected even in a V13NC state as long as the cell membrane was intact. The SBW25 strain was studied in pure cultures and in soil to determine the physiological status of the cells under different nutritional conditions, using many of the approaches described above for A6. Most of the cells died after incubation for nine days in nutrient rich medium. By contrast when incubated under starvation conditions, most of the population was not stained with CTC or PI, indicating that most of the cells were presumably dormant. In soil, a subpopulation of the SBW25 cell population died. However, approximately 60% of the population in soil apparently entered a state of dormancy, similar to that observed under starvation conditions in pure cultures. Several differences were found in the proteins that were expressed when SBW25 was incubated under nutrient rich conditions compared to starvation conditions. These differences provide a clue as to what proteins enable SBW25 to survive starvation and dormant states.
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| 7. |
- Sorensen, Jens N., et al.
(författare)
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Simulation of wind turbine wakes using the actuator line technique
- 2015
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Ingår i: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. - : The Royal Society. - 1364-503X .- 1471-2962. ; 373, s. 2035-
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Tidskriftsartikel (refereegranskat)abstract
- The actuator line technique was introduced as a numerical tool to be employed in combination with large eddy simulations to enable the study of wakes and wake interaction in wind farms. The technique is today largely used for studying basic features of wakes as well as for making performance predictions of wind farms. In this paper, we give a short introduction to the wake problem and the actuator line methodology and present a study in which the technique is employed to determine the near-wake properties of wind turbines. The presented results include a comparison of experimental results of the wake characteristics of the flow around a three-bladed model wind turbine, the development of a simple analytical formula for determining the near-wake length behind a wind turbine and a detailed investigation of wake structures based on proper orthogonal decomposition analysis of numerically generated snapshots of the wake.
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| 8. |
- Sundberg, Carina, et al.
(författare)
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454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters
- 2013
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Ingår i: FEMS Microbiology Ecology. - : Wiley-Blackwell. - 0168-6496 .- 1574-6941. ; 85:3, s. 612-626
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Tidskriftsartikel (refereegranskat)abstract
- The microbial community of 21 full-scale biogas reactors was examined using 454 pyrosequencing of 16S rRNA gene sequences. These reactors included seven (six mesophilic and one thermophilic) digesting sewage sludge (SS) and 14 (ten mesophilic and four thermophilic) codigesting (CD) various combinations of wastes from slaughterhouses, restaurants, households, etc. The pyrosequencing generated more than 160 000 sequences representing 11 phyla, 23 classes, and 95 genera of Bacteria and Archaea. The bacterial community was always both more abundant and more diverse than the archaeal community. At the phylum level, the foremost populations in the SS reactors included Actinobacteria, Proteobacteria, Chloroflexi, Spirochetes, and Euryarchaeota, while Firmicutes was the most prevalent in the CD reactors. The main bacterial class in all reactors was Clostridia. Acetoclastic methanogens were detected in the SS, but not in the CD reactors. Their absence suggests that methane formation from acetate takes place mainly via syntrophic acetate oxidation in the CD reactors. A principal component analysis of the communities at genus level revealed three clusters: SS reactors, mesophilic CD reactors (including one thermophilic CD and one SS), and thermophilic CD reactors. Thus, the microbial composition was mainly governed by the substrate differences and the process temperature.
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