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Jansson, Janet K.
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Publications (10 of 24) Show all publications
Espínola, F., Dionisi, H. M., Borglin, S., Brislawn, C. J., Jansson, J. K., Mac Cormack, W. P., . . . Lozada, M. (2018). Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes. Microbial Ecology (1), 123-139
Open this publication in new window or tab >>Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes
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2018 (English)In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, no 1, p. 123-139Article in journal (Refereed) Published
Abstract [en]

In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.

Place, publisher, year, edition, pages
Springer, 2018
Keywords
Anaerobic biodegradation, Biomarker genes, Cold environments, Community structure, Hydrocarbons, Metagenomics, Subtidal sediments
National Category
Environmental Sciences
Research subject
Environmental Studies
Identifiers
urn:nbn:se:sh:diva-33067 (URN)10.1007/s00248-017-1028-5 (DOI)000418740100012 ()28702706 (PubMedID)2-s2.0-85023166954 (Scopus ID)
Available from: 2017-07-20 Created: 2017-07-20 Last updated: 2020-03-27Bibliographically approved
Musumeci, M. A., Lozada, M., Rial, D. V., Mac Cormack, W. P., Jansson, J. K., Sjöling, S., . . . Dionisi, H. M. (2017). Prospecting Biotechnologically-Relevant Monooxygenases from Cold Sediment Metagenomes: An In Silico Approach. Marine Drugs, 15(4), Article ID 114.
Open this publication in new window or tab >>Prospecting Biotechnologically-Relevant Monooxygenases from Cold Sediment Metagenomes: An In Silico Approach
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2017 (English)In: Marine Drugs, ISSN 1660-3397, E-ISSN 1660-3397, Vol. 15, no 4, article id 114Article in journal (Refereed) Published
Abstract [en]

The goal of this work was to identify sequences encoding monooxygenase biocatalysts with novel features by in silico mining an assembled metagenomic dataset of polar and subpolar marine sediments. The targeted enzyme sequences were Baeyer-Villiger and bacterial cytochrome P450 monooxygenases (CYP153). These enzymes have wide-ranging applications, from the synthesis of steroids, antibiotics, mycotoxins and pheromones to the synthesis of monomers for polymerization and anticancer precursors, due to their extraordinary enantio-, regio-, and chemo- selectivity that are valuable features for organic synthesis. Phylogenetic analyses were used to select the most divergent sequences affiliated to these enzyme families among the 264 putative monooxygenases recovered from the ~14 million protein-coding sequences in the assembled metagenome dataset. Three-dimensional structure modeling and docking analysis suggested features useful in biotechnological applications in five metagenomic sequences, such as wide substrate range, novel substrate specificity or regioselectivity. Further analysis revealed structural features associated with psychrophilic enzymes, such as broader substrate accessibility, larger catalytic pockets or low domain interactions, suggesting that they could be applied in biooxidations at room or low temperatures, saving costs inherent to energy consumption. This work allowed the identification of putative enzyme candidates with promising features from metagenomes, providing a suitable starting point for further developments.

Place, publisher, year, edition, pages
MDPI, 2017
Keywords
Baeyer–Villiger monooxygenases, bacterial cytochrome P450, bioprospecting biocatalysts, molecular modeling, phylogenetic analysis
National Category
Environmental Sciences
Research subject
Environmental Studies
Identifiers
urn:nbn:se:sh:diva-32413 (URN)10.3390/md15040114 (DOI)000404228300030 ()28397770 (PubMedID)2-s2.0-85018661660 (Scopus ID)
Available from: 2017-04-18 Created: 2017-04-18 Last updated: 2020-04-02Bibliographically approved
Matos, M. N., Lozada, M., Anselmino, L. E., Musumeci, M. A., Henrissat, B., Jansson, J. K., . . . Dionisi, H. M. (2016). Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments. Environmental Microbiology, 18(12), 4471-4484
Open this publication in new window or tab >>Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments
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2016 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 18, no 12, p. 4471-4484Article in journal (Refereed) Published
Abstract [en]

Alginates are abundant polysaccharides in brown algae that constitute an important energy source for marine heterotrophic bacteria. Despite the key role of alginate degradation processes in the marine carbon cycle, little information is available on the bacterial populations involved in these processes. The aim of this work was to gain a better understanding of alginate utilization capabilities in cold coastal environments. Sediment metagenomes from four high-latitude regions of both Hemispheres were interrogated for alginate lyase gene homologue sequences and their genomic context. Sediments contained highly abundant and diverse bacterial assemblages with alginolytic potential, including members of Bacteroidetes and Proteobacteria, as well as several poorly characterized taxa. The microbial communities in Arctic and Antarctic sediments exhibited the most similar alginolytic profiles, whereas brackish sediments showed distinct structures with a higher proportion of novel genes. Examination of the gene neighbourhood of the alginate lyase homologues revealed distinct patterns depending on the potential lineage of the scaffolds, with evidence of evolutionary relationships among alginolytic gene clusters from Bacteroidetes and Proteobacteria. This information is relevant for understanding carbon fluxes in cold coastal environments and provides valuable information for the development of biotechnological applications from brown algae biomass.

National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-30655 (URN)10.1111/1462-2920.13433 (DOI)000392946900014 ()27348213 (PubMedID)2-s2.0-84994121145 (Scopus ID)
Available from: 2016-07-20 Created: 2016-07-20 Last updated: 2018-07-05Bibliographically approved
Hjort, K., Bergström, M., Adesina, M. F., Jansson, J. K., Smalla, K. & Sjöling, S. (2010). Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen-suppressive soil. FEMS Microbiology Ecology, 71(2), 197-207
Open this publication in new window or tab >>Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen-suppressive soil
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2010 (English)In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 71, no 2, p. 197-207Article in journal (Refereed) Published
Abstract [en]

Soil that is suppressive to disease caused by fungal pathogens is an interesting source to target for novel chitinases that might be contributing towards disease suppression. In this study, we screened for chitinase genes, in a phytopathogen-suppressive soil in three ways: (1) from a metagenomic library constructed from microbial cells extracted from soil, (2) from directly extracted DNA and (3) from bacterial isolates with antifungal and chitinase activities. Terminal restriction fragment length polymorphism (T-RFLP) of chitinase genes revealed differences in amplified chitinase genes from the metagenomic library and the directly extracted DNA, but approximately 40% of the identified chitinase terminal restriction fragments (TRFs) were found in both sources. All of the chitinase TRFs from the isolates were matched to TRFs in the directly extracted DNA and the metagenomic library. The most abundant chitinase TRF in the soil DNA and the metagenomic library corresponded to the TRF103 of the isolate Streptomyces mutomycini and/or Streptomyces clavifer. There were good matches between T-RFLP profiles of chitinase gene fragments obtained from different sources of DNA. However, there were also differences in both the chitinase and the 16S rRNA gene T-RFLP patterns depending on the source of DNA, emphasizing the lack of complete coverage of the gene diversity by any of the approaches used.

Place, publisher, year, edition, pages
United Kingdom: Wiley-Blackwell Publishing Ltd., 2010
Keywords
metagenomic library, chitinase, terminal restriction fragment length polymorphism (T-RFLP), Streptomycetes, suppressive soil
National Category
Biological Sciences
Research subject
Environmental Studies
Identifiers
urn:nbn:se:sh:diva-6179 (URN)10.1111/j.1574-6941.2009.00801.x (DOI)000273065000003 ()2-s2.0-72949101011 (Scopus ID)
Available from: 2011-02-11 Created: 2011-02-11 Last updated: 2017-12-11Bibliographically approved
Edlund, A., Hårdeman, F., Jansson, J. K. & Sjöling, S. (2008). Active bacterial community structure along vertical redox gradients in Baltic Sea sediment. Environmental Microbiology, 10(8), 2051-2063
Open this publication in new window or tab >>Active bacterial community structure along vertical redox gradients in Baltic Sea sediment
2008 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 10, no 8, p. 2051-2063Article in journal (Refereed) Published
Abstract [en]

Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179, -64 and -337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labelled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities were most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labelled DNA and DNA from reverse transcription polymerase chain reaction showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences, indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths.

Place, publisher, year, edition, pages
United Kingdom: Wiley-Blackwell Publishing Ltd., 2008
Keywords
LENGTH-POLYMORPHISM ANALYSIS; SULFATE-REDUCING BACTERIA; COASTAL MARINE-SEDIMENTS; TIDAL-FLAT SEDIMENTS; MICROBIAL COMMUNITIES; DNA-SEQUENCES; DIVERSITY; DATABASE; DENMARK; CARBON
National Category
Natural Sciences
Research subject
Environmental Studies
Identifiers
urn:nbn:se:sh:diva-6181 (URN)10.1111/j.1462-2920.2008.01624.x (DOI)000257715500012 ()18452546 (PubMedID)2-s2.0-49249138150 (Scopus ID)
Note

Som manuskript i avhandling. As manuscript in dissertation.

Available from: 2011-02-11 Created: 2011-02-11 Last updated: 2017-12-11Bibliographically approved
van Elsas, J. D., Costal, R., Jansson, J., Sjöling, S., Bailey, M., Nalin, R., . . . van Overbeek, L. (2008). The metagenomics of disease-suppressive soils - experiences from the METACONTROL project. Trends in Biotechnology, 26(11), 591-601
Open this publication in new window or tab >>The metagenomics of disease-suppressive soils - experiences from the METACONTROL project
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2008 (English)In: Trends in Biotechnology, ISSN 0167-7799, E-ISSN 1879-3096, Vol. 26, no 11, p. 591-601Article, review/survey (Refereed) Published
Abstract [en]

Soil teems with microbial genetic information that can be exploited for biotechnological innovation. Because only a fraction of the soil microbiota is cultivable, our ability to unlock this genetic complement has been hampered. Recently developed molecular tools, which make it possible to utilize genomic DNA from soil, can bypass cultivation and provide information on the collective soil metagenome with the aim to explore genes that encode functions of key interest to biotechnology. The metagenome of disease-suppressive soils is of particular interest given the expected prevalence of antibiotic biosynthetic clusters. However, owing to the complexity of soil microbial communities, deciphering this key genetic information is challenging. Here, we examine crucial issues and challenges that so far have hindered the metagenomic exploration of soil by drawing on experience from a trans-European project on disease-suppressive soils denoted METACONTROL.

Keywords
Wide Host-Range; Community Structure; Uncultured Microorganisms; Functional Diversity; Escherichia-Coli; Environmental Libraries; Microbial Communities; Natural-Products; Gene-Expression; DNA
National Category
Biological Sciences
Research subject
Environmental Studies
Identifiers
urn:nbn:se:sh:diva-6180 (URN)10.1016/j.tibtech.2008.07.004 (DOI)000260802600003 ()18774191 (PubMedID)2-s2.0-53949095625 (Scopus ID)
Available from: 2011-02-11 Created: 2011-02-11 Last updated: 2017-12-11Bibliographically approved
Jernberg, C., Löfmark, S., Edlund, C. & Jansson, J. K. (2007). Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. The ISME Journal, 1(1), 56-66
Open this publication in new window or tab >>Long-term ecological impacts of antibiotic administration on the human intestinal microbiota
2007 (English)In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 1, no 1, p. 56-66Article in journal (Refereed) Published
Abstract [en]

Antibiotic administration is known to cause short-term disturbances in the microbiota of the human gastrointestinal tract, but the potential long-term consequences have not been well studied. The aims of this study were to analyse the long-term impact of a 7-day clindamycin treatment on the faecal microbiota and to simultaneously monitor the ecological stability of the microbiota in a control group as a baseline for reference. Faecal samples from four clindamycin-exposed and four control subjects were collected at nine different time points over 2 years. Using a polyphasic approach, we observed highly significant disturbances in the bacterial community that persisted throughout the sampling period. In particular, a sharp decline in the clonal diversity of Bacteroides isolates, as assessed by repetitive sequence-based PCR (rep-PCR) and long-term persistence of highly resistant clones were found as a direct response to the antibiotic exposure. The Bacteroides community never returned to its original composition during the study period as assessed using the molecular fingerprinting technique, terminal restriction fragment length polymorphism (T-RFLP). Furthermore, using real-time PCR we found a dramatic and persistent increase in levels of specific resistance genes in DNA extracted from the faeces after clindamycin administration. The temporal variations in the microbiota of the control group were minor compared to the large and persistent shift seen in the exposed group. These results demonstrate that long after the selection pressure from a short antibiotic exposure has been removed, there are still persistent long term impacts on the human intestinal microbiota that remain for up to 2 years post-treatment.

Keywords
Bacteroides, clindamycin, rep-PCR, faeces, T-RFLP
National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-31968 (URN)10.1038/ismej.2007.3 (DOI)000249215800009 ()18043614 (PubMedID)2-s2.0-34248152283 (Scopus ID)
Note

Som manuskript i avhandling. As manuscript in dissertation.

Erratum: Jernberg, C., Löfmark, S., Edlund, C., & Jansson, J. K. (2013). Erratum: Long-term ecological impacts of antibiotic administration on the human intestinal microbiota (ISME journal (2007) 1 (56-66) DOI: 10.1038/ismej.2007.3). ISME Journal, 7(2), 456. doi:10.1038/ismej.2012.91

Available from: 2017-02-07 Created: 2017-02-06 Last updated: 2017-11-29Bibliographically approved
Löfmark, S., Jernberg, C., Jansson, J. K. & Edlund, C. (2006). Clindamycin-induced enrichment and long-term persistence of resistant Bacteroides spp. and resistance genes. Journal of Antimicrobial Chemotherapy, 58(6), 1160-1167
Open this publication in new window or tab >>Clindamycin-induced enrichment and long-term persistence of resistant Bacteroides spp. and resistance genes
2006 (English)In: Journal of Antimicrobial Chemotherapy, ISSN 0305-7453, E-ISSN 1460-2091, Vol. 58, no 6, p. 1160-1167Article in journal (Refereed) Published
Abstract [en]

Objectives: The aim was to study the long-term consequences of 1 week clindamycin administration regarding selection and persistence of resistance, resistance determinants and diversity of the Bacteroides spp. in the intestinal microflora. Methods: A total of 1306 Bacteroides isolates were collected from constitutively cultured faecal samples during a 2 year period from eight healthy volunteers. The strains were identified by biochemical and genotyping methods. MIC values were determined by the agar dilution method and presence of resistance genes was screened by real-time PCR. Results: Ecological changes in the intestinal microflora persisting up to 24 months were recorded after a 7 day clindamycin administration to four healthy volunteers. Compared to a control group, not exposed to clindamycin, an enrichment and stabilization of resistant Bacteroides strains and resistance determinants were discovered up to 2 years after clindamycin exposure. Conclusions: The results indicate that even a short-term antibiotic administration can cause long-term alterations in the commensal microbiota of individual subjects, detectable 2 years after dosing. The recorded selection and persistence of resistant strains and resistance genes, illustrates the importance of increasing our knowledge of the role of the abundant intestinal microbial community as a reservoir for spread of resistance.

National Category
Microbiology Pharmacology and Toxicology Pharmaceutical Sciences
Identifiers
urn:nbn:se:sh:diva-14266 (URN)10.1093/jac/dkl420 (DOI)000242716600009 ()17046967 (PubMedID)2-s2.0-33845349674 (Scopus ID)
Note

Som manuskript i avhandling. As manuscript in dissertation.

Available from: 2011-12-21 Created: 2011-12-20 Last updated: 2018-01-12Bibliographically approved
von der Weid, I., Artursson, V., Seldin, L. & Jansson, J. K. (2005). Antifungal and root surface colonization properties of GFP-tagged Paenibacillus brasilensis PB177. World Journal of Microbiology & Biotechnology, 21(8-9), 1591-1597
Open this publication in new window or tab >>Antifungal and root surface colonization properties of GFP-tagged Paenibacillus brasilensis PB177
2005 (English)In: World Journal of Microbiology & Biotechnology, ISSN 0959-3993, E-ISSN 1573-0972, Vol. 21, no 8-9, p. 1591-1597Article in journal (Refereed) Published
Abstract [en]

This study evaluates the potential of Paenibacillus brasilensis strain PB177 to inhibit phytopathogenic fungi commonly causing maize diseases and to colonize maize plants. In vitro assays demonstrated antagonistic activity against the fungal pathogens, Fusarium moniliforme and Diplodia macrospora. The PB177 strain was tagged with the gfp gene, encoding the green fluorescent protein (GFP) and GFP-tagged bacteria were detected attached to maize roots by stereo- and confocal microscopy. The GFP-tagged bacteria were also used to treat maize seeds before challenging the seeds with two phytopathogenic fungi. The results demonstrated that the bacterial cells are mobilized to the maize roots in the presence of the fungal pathogens. The ability of P. brasilensis PB177 to inhibit fungal growth in vitro and its capability of colonization of maize roots in vivo suggest a potential application of this strain as a biological control agent. This is the first report on the successful introduction of the GFP marker gene into a P. brasilensis strain, enabling the direct observation of these promising plant growth promoting bacteria on maize roots in situ.

National Category
Microbiology
Identifiers
urn:nbn:se:sh:diva-14433 (URN)10.1007/s11274-005-8123-3 (DOI)000234411400040 ()2-s2.0-30044438906 (Scopus ID)
Available from: 2012-01-31 Created: 2011-12-23 Last updated: 2017-12-08Bibliographically approved
Jernberg, C., Sullivan, A., Edlund, C. & Jansson, J. K. (2005). Monitoring of antibiotic-induced alterations in the human intestinal microflora and detection of probiotic strains by use of terminal restriction fragment length polymorphism. Applied and Environmental Microbiology, 71(1), 501-506
Open this publication in new window or tab >>Monitoring of antibiotic-induced alterations in the human intestinal microflora and detection of probiotic strains by use of terminal restriction fragment length polymorphism
2005 (English)In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 71, no 1, p. 501-506Article in journal (Refereed) Published
Abstract [en]

Terminal restriction fragment length polymorphism (T-RFLP) was investigated as a tool for monitoring the human intestinal microflora during antibiotic treatment and during ingestion of a probiotic product. Fecal samples from eight healthy volunteers were taken before, during, and after administration of clindamycin. During treatment, four subjects were given a probiotic, and four subjects were given a placebo. Changes in the microbial intestinal community composition and relative abundance of specific microbial populations in each subject were monitored by using viable counts and T-RFLP fingerprints. T-RFLP was also used to monitor specific bacterial populations that were either positively or negatively affected by clindamycin. Some dominant bacterial groups, such as Eubacterium spp., were easily monitored by T-RFLP, while they were hard to recover by cultivation. Furthermore, the two probiotic Lactobacillus strains were easily tracked by T-RFLP and were shown to be the dominant Lactobacillus community members in the intestinal microflora of subjects who received the probiotic.

National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-17365 (URN)10.1128/AEM.71.1.501-506.2005 (DOI)000226458800062 ()15640226 (PubMedID)2-s2.0-12244292700 (Scopus ID)
Available from: 2012-11-22 Created: 2012-11-19 Last updated: 2017-07-19Bibliographically approved
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