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Publications (10 of 28) Show all publications
Eriksson, K. I., Ahlinder, J., Ramasamy, K. P., Andersson, A., Sundell, D., Karlsson, L., . . . Thelaus, J. (2023). Association between Legionella species and humic substances during early summer in the northern Baltic Sea. Frontiers in Marine Science, 9, Article ID 1070341.
Open this publication in new window or tab >>Association between Legionella species and humic substances during early summer in the northern Baltic Sea
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2023 (English)In: Frontiers in Marine Science, E-ISSN 2296-7745, Vol. 9, article id 1070341Article in journal (Refereed) Published
Abstract [en]

Climate change is projected to cause alterations in northern coastal systems, including humification and intensified nutrient loads, which can lead to ecosystem imbalances and establishment of new bacterial species. Several potential pathogens, such as different species of Legionella, hide in the environment between infections, some by living inside protozoan host cells. Knowledge about the occurrence of Legionella in natural waters is missing, which disable risk assessments of exposure. We performed a study of the species diversity of Legionella in the northern Baltic Sea (Gulf of Bothnia) during early summer to map their occurrence and to identify possible environmental drivers. We detected Legionella and potential protozoan hosts along gradients of the Gulf of Bothnia. We also for the first time present third generation full-length 16S rRNA amplicon sequencing (Nanopore) to resolve environmental species classification of Legionella, with a method suitable to study all bacteria. Our data show that full length 16S rRNA sequences is sufficient to resolve Legionella while the standard short Illumina sequences did not capture the entire diversity. For accurate species classification of Legionella, harmonization between the Nanopore classification methods is still needed and the bias toward the well-studied Legionella pneumophila need to be resolved. Different Legionella species occurred both in the Bothnian Sea and in the Bothnian Bay and their abundance were linked to humic substances and low salinity. The relative abundance of Legionella was higher in the humic-rich northern waters of the Bothnian Bay. The link between Legionella species and humic substances may be indirect via promotion of the heterotrophic microbial food web, allowing Legionella species and similar bacteria to establish. Humic substances are rich in iron, which has been shown crucial for growth of Legionella species and other pathogens. Considering climate change projections in this regional area, with increased humification and freshwater inflow, this bacterial niche containing potential pathogens might become more widespread in the future Baltic Sea. This study demonstrates the significance of DNA sequencing to monitor public health relevant bacteria like Legionella species in the environment. Including sequencing of bacteria and protozoa in the environmental monitoring programs could be used to identify ecosystem imbalances, which enable appropriate responses to emerging diseases.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2023
Keywords
Legionella, protozoa, predation resistance, aquatic microbiology, climate change, ecology change, marginal seas, humification
National Category
Ecology
Identifiers
urn:nbn:se:umu:diva-203899 (URN)10.3389/fmars.2022.1070341 (DOI)000924634400001 ()2-s2.0-85147432283 (Scopus ID)
Funder
Ecosystem dynamics in the Baltic Sea in a changing climate perspective - ECOCHANGESwedish Research Council FormasSwedish Armed Forces
Available from: 2023-01-23 Created: 2023-01-23 Last updated: 2024-07-02Bibliographically approved
Sjödin, K. S., Sjödin, A., Ruszczyński, M., Kristensen, M. B., Hernell, O., Szajewska, H. & West, C. E. (2023). Targeting the gut-lung axis by synbiotic feeding to infants in a randomized controlled trial. BMC Biology, 21(1), Article ID 38.
Open this publication in new window or tab >>Targeting the gut-lung axis by synbiotic feeding to infants in a randomized controlled trial
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2023 (English)In: BMC Biology, E-ISSN 1741-7007, Vol. 21, no 1, article id 38Article in journal (Refereed) Published
Abstract [en]

BACKGROUND: Formula-fed infants are at increased risk of infections. Due to the cross-talk between the mucosal systems of the gastrointestinal and respiratory tracts, adding synbiotics (prebiotics and probiotics) to infant formula may prevent infections even at distant sites. Infants that were born full term and weaned from breast milk were randomized to prebiotic formula (fructo- and galactooligosaccharides) or the same prebiotic formula with Lactobacillus paracasei ssp. paracasei F19 (synbiotics) from 1 to 6 months of age. The objective was to examine the synbiotic effects on gut microbiota development. RESULTS: Fecal samples collected at ages 1, 4, 6, and 12 months were analyzed using 16S rRNA gene sequencing and a combination of untargeted gas chromatography-mass spectrometry/liquid chromatography-mass spectrometry. These analyses revealed that the synbiotic group had a lower abundance of Klebsiella, a higher abundance of Bifidobacterium breve compared to the prebiotic group, and increases in the anti-microbial metabolite d-3-phenyllactic acid. We also analyzed the fecal metagenome and antibiotic resistome in the 11 infants that had been diagnosed with lower respiratory tract infection (cases) and 11 matched controls using deep metagenomic sequencing. Cases with lower respiratory tract infection had a higher abundance of Klebsiella species and antimicrobial resistance genes related to Klebsiella pneumoniae, compared to controls. The results obtained using 16S rRNA gene amplicon and metagenomic sequencing were confirmed in silico by successful recovery of the metagenome-assembled genomes of the bacteria of interest. CONCLUSIONS: This study demonstrates the additional benefit of feeding specific synbiotics to formula-fed infants over prebiotics only. Synbiotic feeding led to the underrepresentation of Klebsiella, enrichment of bifidobacteria, and increases in microbial degradation metabolites implicated in immune signaling and in the gut-lung and gut-skin axes. Our findings support future clinical evaluation of synbiotic formula in the prevention of infections and associated antibiotic treatment as a primary outcome when breastfeeding is not feasible. TRIAL REGISTRATION: ClinicalTrials.gov NCT01625273. Retrospectively registered on 21 June 2012.

Place, publisher, year, edition, pages
BioMed Central (BMC), 2023
Keywords
Antibiotics, Bifidobacteria, Infant gut microbiota, Klebsiella, Lower respiratory tract infection, Prebiotics, Probiotics
National Category
Nutrition and Dietetics Pediatrics
Identifiers
urn:nbn:se:umu:diva-205355 (URN)10.1186/s12915-023-01531-3 (DOI)000936843800002 ()36803508 (PubMedID)2-s2.0-85148399778 (Scopus ID)
Funder
Umeå UniversityRegion VästerbottenMagnus Bergvall FoundationKnut and Alice Wallenberg FoundationSwedish Research Council
Available from: 2023-04-03 Created: 2023-04-03 Last updated: 2025-02-11Bibliographically approved
Svensson, D., Rentoft, M., Dahlin, A. M., Lundholm, E., Olason, P. I., Sjödin, A., . . . Johansson, E. (2020). A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences. PLOS ONE, 15(9), Article ID e0237721.
Open this publication in new window or tab >>A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences
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2020 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 15, no 9, article id e0237721Article in journal (Refereed) Published
Abstract [en]

The number of national reference populations that are whole-genome sequenced are rapidly increasing. Partly driving this development is the fact that genetic disease studies benefit from knowing the genetic variation typical for the geographical area of interest. A whole-genome sequenced Swedish national reference population (n = 1000) has been recently published but with few samples from northern Sweden. In the present study we have whole-genome sequenced a control population (n = 300) (ACpop) from Västerbotten County, a sparsely populated region in northern Sweden previously shown to be genetically different from southern Sweden. The aggregated variant frequencies within ACpop are publicly available (DOI 10.17044/NBIS/G000005) to function as a basic resource in clinical genetics and for genetic studies. Our analysis of ACpop, representing approximately 0.11% of the population in Västerbotten, indicates the presence of a genetic substructure within the county. Furthermore, a demographic analysis showed that the population from which samples were drawn was to a large extent geographically stationary, a finding that was corroborated in the genetic analysis down to the level of municipalities. Including ACpop in the reference population when imputing unknown variants in a Västerbotten cohort resulted in a strong increase in the number of high-confidence imputed variants (up to 81% for variants with minor allele frequency < 5%). ACpop was initially designed for cancer disease studies, but the genetic structure within the cohort will be of general interest for all genetic disease studies in northern Sweden.

Place, publisher, year, edition, pages
Public Library Science, 2020
National Category
Medical Genetics and Genomics
Identifiers
urn:nbn:se:umu:diva-175837 (URN)10.1371/journal.pone.0237721 (DOI)000571887500123 ()32915809 (PubMedID)2-s2.0-85090917774 (Scopus ID)
Available from: 2020-10-16 Created: 2020-10-16 Last updated: 2025-02-10Bibliographically approved
Rentoft, M., Svensson, D., Sjödin, A., Olason, P. I., Sjöström, O., Nylander, C., . . . Johansson, E. (2019). A geographically matched control population efficiently limits the number of candidate disease-causing variants in an unbiased whole-genome analysis. PLOS ONE, 14(3), Article ID e0213350.
Open this publication in new window or tab >>A geographically matched control population efficiently limits the number of candidate disease-causing variants in an unbiased whole-genome analysis
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2019 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 14, no 3, article id e0213350Article in journal (Refereed) Published
Abstract [en]

Whole-genome sequencing is a promising approach for human autosomal dominant disease studies. However, the vast number of genetic variants observed by this method constitutes a challenge when trying to identify the causal variants. This is often handled by restricting disease studies to the most damaging variants, e.g. those found in coding regions, and overlooking the remaining genetic variation. Such a biased approach explains in part why the genetic causes of many families with dominantly inherited diseases, in spite of being included in whole-genome sequencing studies, are left unsolved today. Here we explore the use of a geographically matched control population to minimize the number of candidate disease-causing variants without excluding variants based on assumptions on genomic position or functional predictions. To exemplify the benefit of the geographically matched control population we apply a typical disease variant filtering strategy in a family with an autosomal dominant form of colorectal cancer. With the use of the geographically matched control population we end up with 26 candidate variants genome wide. This is in contrast to the tens of thousands of candidates left when only making use of available public variant datasets. The effect of the local control population is dual, it (1) reduces the total number of candidate variants shared between affected individuals, and more importantly (2) increases the rate by which the number of candidate variants are reduced as additional affected family members are included in the filtering strategy. We demonstrate that the application of a geographically matched control population effectively limits the number of candidate disease-causing variants and may provide the means by which variants suitable for functional studies are identified genome wide.

Place, publisher, year, edition, pages
Public Library of Science, 2019
National Category
Medical Genetics and Genomics
Identifiers
urn:nbn:se:umu:diva-158021 (URN)10.1371/journal.pone.0213350 (DOI)000462465800028 ()30917156 (PubMedID)2-s2.0-85063572524 (Scopus ID)
Funder
Knut and Alice Wallenberg Foundation, 2011.0042
Available from: 2019-04-10 Created: 2019-04-10 Last updated: 2025-02-10Bibliographically approved
Vallesi, A., Sjödin, A., Petrelli, D., Luporini, P., Taddei, A. R., Thelaus, J., . . . Villalobo, E. (2019). A New Species of the gamma-Proteobacterium Francisella, F. adeliensis Sp. Nov., Endocytobiont in an Antarctic Marine Ciliate and Potential Evolutionary Forerunner of Pathogenic Species. Microbial Ecology, 77(3), 587-596
Open this publication in new window or tab >>A New Species of the gamma-Proteobacterium Francisella, F. adeliensis Sp. Nov., Endocytobiont in an Antarctic Marine Ciliate and Potential Evolutionary Forerunner of Pathogenic Species
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2019 (English)In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, Vol. 77, no 3, p. 587-596Article in journal (Refereed) Published
Abstract [en]

The study of the draft genome of an Antarctic marine ciliate, Euplotes petzi, revealed foreign sequences of bacterial origin belonging to the gamma-proteobacterium Francisella that includes pathogenic and environmental species. TEM and FISH analyses confirmed the presence of a Francisella endocytobiont in E. petzi. This endocytobiont was isolated and found to be a new species, named F. adeliensis sp. nov.. F. adeliensis grows well at wide ranges of temperature, salinity, and carbon dioxide concentrations implying that it may colonize new organisms living in deeply diversified habitats. The F. adeliensis genome includes the igl and pdp gene sets (pdpC and pdpE excepted) of the Francisella pathogenicity island needed for intracellular growth. Consistently with an F. adeliensis ancient symbiotic lifestyle, it also contains a single insertion-sequence element. Instead, it lacks genes for the biosynthesis of essential amino acids such as cysteine, lysine, methionine, and tyrosine. In a genome-based phylogenetic tree, F. adeliensis forms a new early branching clade, basal to the evolution of pathogenic species. The correlations of this clade with the other clades raise doubts about a genuine free-living nature of the environmental Francisella species isolated from natural and man-made environments, and suggest to look at F. adeliensis asa pioneer in the Francisella colonization of eukaryotic organisms.

Place, publisher, year, edition, pages
Springer, 2019
Keywords
Endosymbiosis, Microbial associations, Polar microbiology, Environmental Francisella, Francisella phylogeny, Euplotes
National Category
Microbiology
Identifiers
urn:nbn:se:umu:diva-158588 (URN)10.1007/s00248-018-1256-3 (DOI)000464747100003 ()30187088 (PubMedID)2-s2.0-85053440128 (Scopus ID)
Available from: 2019-05-27 Created: 2019-05-27 Last updated: 2023-03-23Bibliographically approved
Hägglund, M., Bäckman, S., Macellaro, A., Lindgren, F., Borgmästars, E., Jacobsson, K., . . . Ahlinder, J. (2018). Accounting for bacterial overlap between raw water communities and contaminating sources improves the accuracy of signature-based microbial source tracking. Frontiers in Microbiology, 9, Article ID 2364.
Open this publication in new window or tab >>Accounting for bacterial overlap between raw water communities and contaminating sources improves the accuracy of signature-based microbial source tracking
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2018 (English)In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 9, article id 2364Article in journal (Refereed) Published
Abstract [en]

Microbial source tracking (MST) analysis is essential to identifying and mitigating the fecal pollution of water resources. The signature-based MST method uses a library of sequences to identify contaminants based on operational taxonomic units (OTUs) that are unique to a certain source. However, no clear guidelines for how to incorporate OTU overlap or natural variation in the raw water bacterial community into MST analyses exist. We investigated how the inclusion of bacterial overlap between sources in the library affects source prediction accuracy. To achieve this, large-scale sampling-including feces from seven species, raw sewage, and raw water samples from water treatment plants - was followed by 16S rRNA amplicon sequencing. The MST library was defined using three settings: (i) no raw water communities represented; (ii) raw water communities selected through clustering analysis; and (iii) local water communities collected across consecutive years. The results suggest that incorporating either the local background or representative bacterial composition improves MST analyses, as the results were positively correlated to measured levels of fecal indicator bacteria and the accuracy at which OTUs were assigned to the correct contamination source increased fourfold. Using the proportion of OTUs with high source origin probability, underpinning a contaminating signal, is a solid foundation in a framework for further deciphering and comparing contaminating signals derived in signature-based MST approaches. In conclusion, incorporating background bacterial composition of water in MST can improve mitigation efforts for minimizing the spread of pathogenic and antibiotic resistant bacteria into essential freshwater resources.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2018
Keywords
microbial source tracking, fecal contamination, bacterial community analysis, microbial community profiling, 16S rRNA amplicon
National Category
Microbiology
Identifiers
urn:nbn:se:umu:diva-152872 (URN)10.3389/fmicb.2018.02364 (DOI)000446079800001 ()2-s2.0-85055200038 (Scopus ID)
Funder
Swedish Civil Contingencies Agency, SOFA-2013-02Swedish Civil Contingencies Agency, SOFA-2013-03
Available from: 2018-10-31 Created: 2018-10-31 Last updated: 2024-01-17Bibliographically approved
Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., . . . Köster, J. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences [Letter to the editor]. Nature Methods, 15(7), 475-476
Open this publication in new window or tab >>Bioconda: sustainable and comprehensive software distribution for the life sciences
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2018 (English)In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 15, no 7, p. 475-476Article in journal, Letter (Refereed) Published
Place, publisher, year, edition, pages
Nature Publishing Group, 2018
National Category
Bioinformatics and Computational Biology
Identifiers
urn:nbn:se:umu:diva-150740 (URN)10.1038/s41592-018-0046-7 (DOI)000437934800003 ()29967506 (PubMedID)2-s2.0-85049501214 (Scopus ID)
Note

Also credited: The Bioconda Team

Available from: 2018-08-27 Created: 2018-08-27 Last updated: 2025-02-07Bibliographically approved
Haas, J. C., Street, N. R., Sjödin, A., Lee, N. M., Högberg, M. N., Näsholm, T. & Hurry, V. (2018). Microbial community response to growing season and plant nutrient optimisation in a boreal Norway spruce forest. Soil Biology and Biochemistry, 125, 197-209
Open this publication in new window or tab >>Microbial community response to growing season and plant nutrient optimisation in a boreal Norway spruce forest
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2018 (English)In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 125, p. 197-209Article in journal (Refereed) Published
Abstract [en]

Interactions between Norway spruce trees and bacteria and fungi in nutrient limited boreal forests can be beneficial for tree growth and fitness. Tree-level effects of anthropogenic nutrient addition have been well studied, however understanding of the long-term effects on the associated microbiota is limited. Here, we report on the sensitivity of microbial community composition to the growing season and nutrient additions. Highthroughput sequencing of the bacterial 16S rRNA gene and fungal ITS1 region was used to characterise changes in the microbial community after application of a complete mineral nutrient mixture for five and 25 years. The experiment was conducted using the Flakaliden forest research site in northern boreal Sweden and included naturally low nutrient control plots. Needle and fine root samples of Norway spruce were sampled in addition to bulk soil during one growing season to provide comprehensive insight into phyllosphere and belowground microbiota community changes. The phyllosphere microbiota was compositionally distinct from the belowground communities and phyllosphere diversity increased significantly over the growing season but was not influenced by the improved nutrient status of the trees. In both root and soil samples, alpha diversity of fungal, in particular ectomycorrhizal fungi (EMF), and bacterial communities increased after long-term nutrient optimisation, and with increasing years of treatment the composition of the fungal and bacterial communities changed toward a community with a higher relative abundance of nitrophilic EMF and bacterial species but did not cause complete loss of nitrophobic species from the ecosystem. From this, we conclude that 25 years of continuous nutrient addition to a boreal spruce stand increased phylotype richness and diversity of the microbiota in the soil, and at the root-soil interface, suggesting that long-term anthropogenic nutrient inputs can have positive effects on belowground biodiversity that may enhance ecosystem robustness. Future studies are needed to assess the impact of these changes to the microbiota on ecosystem carbon storage and nitrogen cycling in boreal forests.

Place, publisher, year, edition, pages
Elsevier, 2018
Keywords
Boreal forest, Ectomycorrhiza, Microbial community composition, Norway spruce, Balanced nutrient addition, Illumina MiSeq
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-151103 (URN)10.1016/j.soilbio.2018.07.005 (DOI)000444660400020 ()2-s2.0-85050000360 (Scopus ID)
Projects
Bio4Energy
Funder
Bio4Energy
Available from: 2018-08-28 Created: 2018-08-28 Last updated: 2024-07-02Bibliographically approved
Goormaghtigh, F., Fraikin, N., Putrins, M., Hallaert, T., Hauryliuk, V., Garcia-Pino, A., . . . Van Melderen, L. (2018). Reassessing the Role of Type II Toxin-Antitoxin Systems in Formation of Escherichia coli Type II Persister Cells. mBio, 9(3), Article ID e00640-18.
Open this publication in new window or tab >>Reassessing the Role of Type II Toxin-Antitoxin Systems in Formation of Escherichia coli Type II Persister Cells
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2018 (English)In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 9, no 3, article id e00640-18Article in journal (Refereed) Published
Abstract [en]

Persistence is a reversible and low-frequency phenomenon allowing a subpopulation of a clonal bacterial population to survive antibiotic treatments. Upon removal of the antibiotic, persister cells resume growth and give rise to viable progeny. Type II toxin-antitoxin (TA) systems were assumed to play a key role in the formation of persister cells in Escherichia coli based on the observation that successive deletions of TA systems decreased persistence frequency. In addition, the model proposed that stochastic fluctuations of (p)ppGpp levels are the basis for triggering activation of TA systems. Cells in which TA systems are activated are thought to enter a dormancy state and therefore survive the antibiotic treatment. Using independently constructed strains and newly designed fluorescent reporters, we reassessed the roles of TA modules in persistence both at the population and single-cell levels. Our data confirm that the deletion of 10 TA systems does not affect persistence to ofloxacin or ampicillin. Moreover, microfluidic experiments performed with a strain reporting the induction of the yefM-yoeB TA system allowed the observation of a small number of type II persister cells that resume growth after removal of ampicillin. However, we were unable to establish a correlation between high fluorescence and persistence, since the fluorescence of persister cells was comparable to that of the bulk of the population and none of the cells showing high fluorescence were able to resume growth upon removal of the antibiotic. Altogether, these data show that there is no direct link between induction of TA systems and persistence to antibiotics. IMPORTANCE Within a growing bacterial population, a small subpopulation of cells is able to survive antibiotic treatment by entering a transient state of dormancy referred to as persistence. Persistence is thought to be the cause of relapsing bacterial infections and is a major public health concern. Type II toxin-antitoxin systems are small modules composed of a toxic protein and an antitoxin protein counteracting the toxin activity. These systems were thought to be pivotal players in persistence until recent developments in the field. Our results demonstrate that previous influential reports had technical flaws and that there is no direct link between induction of TA systems and persistence to antibiotics.

Place, publisher, year, edition, pages
American Society for Microbiology, 2018
Keywords
RelE, YoeB, ampicillin, single cell
National Category
Biological Sciences
Identifiers
urn:nbn:se:umu:diva-155657 (URN)10.1128/mBio.00640-18 (DOI)000454748900022 ()29895634 (PubMedID)2-s2.0-85048558212 (Scopus ID)
Available from: 2019-01-25 Created: 2019-01-25 Last updated: 2023-03-24Bibliographically approved
Svensson, D., Öhrman, C., Bäckman, S., Karlsson, E., Nilsson, E., Byström, M., . . . Sjödin, A. (2015). Complete Genome Sequence of Francisella guangzhouensis Strain 08HL01032(T), Isolated from Air-Conditioning Systems in China. Microbiology Resource Announcements, 3(2), Article ID e00024-15.
Open this publication in new window or tab >>Complete Genome Sequence of Francisella guangzhouensis Strain 08HL01032(T), Isolated from Air-Conditioning Systems in China
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2015 (English)In: Microbiology Resource Announcements, E-ISSN 2576-098X, Vol. 3, no 2, article id e00024-15Article in journal (Refereed) Published
Abstract [en]

We present the complete genome sequence of Francisella guangzhouensis strain 08HL01032(T), which consists of one chromosome (1,658,482 bp) and one plasmid ( 3,045 bp) with G+C contents of 32.0% and 28.7%, respectively.

Place, publisher, year, edition, pages
Washington: American Society for Microbiology, 2015
National Category
Microbiology
Identifiers
urn:nbn:se:umu:diva-163259 (URN)10.1128/genomeA.00024-15 (DOI)000460623100009 ()25792039 (PubMedID)2-s2.0-85007481402 (Scopus ID)
Available from: 2019-09-19 Created: 2019-09-19 Last updated: 2023-03-23Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-5350-4219

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