Endre søk
Begrens søket
12 51 - 76 of 76
RefereraExporteraLink til resultatlisten
Permanent link
Referera
Referensformat
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annet format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annet språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf
Treff pr side
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sortering
  • Standard (Relevans)
  • Forfatter A-Ø
  • Forfatter Ø-A
  • Tittel A-Ø
  • Tittel Ø-A
  • Type publikasjon A-Ø
  • Type publikasjon Ø-A
  • Eldste først
  • Nyeste først
  • Skapad (Eldste først)
  • Skapad (Nyeste først)
  • Senast uppdaterad (Eldste først)
  • Senast uppdaterad (Nyeste først)
  • Disputationsdatum (tidligste først)
  • Disputationsdatum (siste først)
  • Standard (Relevans)
  • Forfatter A-Ø
  • Forfatter Ø-A
  • Tittel A-Ø
  • Tittel Ø-A
  • Type publikasjon A-Ø
  • Type publikasjon Ø-A
  • Eldste først
  • Nyeste først
  • Skapad (Eldste først)
  • Skapad (Nyeste først)
  • Senast uppdaterad (Eldste først)
  • Senast uppdaterad (Nyeste først)
  • Disputationsdatum (tidligste først)
  • Disputationsdatum (siste først)
Merk
Maxantalet träffar du kan exportera från sökgränssnittet är 250. Vid större uttag använd dig av utsökningar.
  • 51. Lindh, Markus V.
    et al.
    Sjostedt, Johanna
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Baltar, Federico
    Hugerth, Luisa W.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Lundin, Daniel
    Muthusamy, Saraladevi
    Legrand, Catherine
    Pinhassi, Jarone
    Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling2015Inngår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 17, nr 7, s. 2459-2476Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Multiyear comparisons of bacterioplankton succession reveal that environmental conditions drive community shifts with repeatable patterns between years. However, corresponding insight into bacterioplankton dynamics at a temporal resolution relevant for detailed examination of variation and characteristics of specific populations within years is essentially lacking. During 1 year, we collected 46 samples in the Baltic Sea for assessing bacterial community composition by 16S rRNA gene pyrosequencing (nearly twice weekly during productive season). Beta-diversity analysis showed distinct clustering of samples, attributable to seemingly synchronous temporal transitions among populations (populations defined by 97% 16S rRNA gene sequence identity). A wide spectrum of bacterioplankton dynamics was evident, where divergent temporal patterns resulted both from pronounced differences in relative abundance and presence/absence of populations. Rates of change in relative abundance calculated for individual populations ranged from 0.23 to 1.79 day(-1). Populations that were persistently dominant, transiently abundant or generally rare were found in several major bacterial groups, implying evolution has favoured a similar variety of life strategies within these groups. These findings suggest that high temporal resolution sampling allows constraining the timescales and frequencies at which distinct populations transition between being abundant or rare, thus potentially providing clues about physical, chemical or biological forcing on bacterioplankton community structure.

  • 52. Lindh, Markus V.
    et al.
    Sjostedt, Johanna
    Ekstam, Borje
    Casini, Michele
    Lundin, Daniel
    Hugerth, Luisa W.
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för bioteknologi (BIO).
    Hu, Yue O. O.
    KTH, Skolan för bioteknologi (BIO). KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO). KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Andersson, Agneta
    Legrand, Catherine
    Pinhassi, Jarone
    Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers2017Inngår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, nr 3, s. 1222-1236Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations. Notably, the occupancy-frequency distributions were significantly bimodal with a satellite mode of rare endemic populations and a core mode of abundant cosmopolitan populations (e.g. Synechococcus, SAR11 and SAR86 clade members). Temporal changes in population distributions supported several theoretical frameworks. Still, bimodality was found among bacterioplankton communities across the entire Baltic Sea, and was also frequent in globally distributed datasets. Datasets spanning waters with widely different physicochemical characteristics or environmental gradients typically lacked significant bimodal patterns. When such datasets were divided into subsets with coherent environmental conditions, bimodal patterns emerged, highlighting the importance of positive feedbacks between local abundance and occupancy within specific biomes. Thus, metapopulation theory applied to microbial biogeography can provide novel insights into the mechanisms governing shifts in biodiversity resulting from natural or anthropogenically induced changes in the environment.

  • 53. Logue, Jurg B.
    et al.
    Stedmon, Colin A.
    Kellerman, Anne M.
    Nielsen, Nikoline J.
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Laudon, Hjalmar
    Lindstrom, Eva S.
    Kritzberg, Emma S.
    Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter2016Inngår i: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, nr 3, s. 533-545Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Bacteria play a central role in the cycling of carbon, yet our understanding of the relationship between the taxonomic composition and the degradation of dissolved organic matter (DOM) is still poor. In this experimental study, we were able to demonstrate a direct link between community composition and ecosystem functioning in that differently structured aquatic bacterial communities differed in their degradation of terrestrially derived DOM. Although the same amount of carbon was processed, both the temporal pattern of degradation and the compounds degraded differed among communities. We, moreover, uncovered that low-molecular-weight carbon was available to all communities for utilisation, whereas the ability to degrade carbon of greater molecular weight was a trait less widely distributed. Finally, whereas the degradation of either low-or high-molecular-weight carbon was not restricted to a single phylogenetic clade, our results illustrate that bacterial taxa of similar phylogenetic classification differed substantially in their association with the degradation of DOM compounds. Applying techniques that capture the diversity and complexity of both bacterial communities and DOM, our study provides new insight into how the structure of bacterial communities may affect processes of biogeochemical significance.

  • 54. Logue, Jürg Brendan
    et al.
    Langenheder, Silke
    Andersson, Anders F.
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Bertilsson, Stefan
    Drakare, Stina
    Lanzén, Anders
    Lindström, Eva S.
    Freshwater bacterioplankton richness in oligotrophic lakes depends on nutrient availability rather than on species-area relationships2012Inngår i: The ISME Journal, ISSN 1751-7362, Vol. 6, nr 6, s. 1127-1136Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A central goal in ecology is to grasp the mechanisms that underlie and maintain biodiversity and patterns in its spatial distribution can provide clues about those mechanisms. Here, we investigated what might determine the bacterioplankton richness (BR) in lakes by means of 454 pyrosequencing of the 16S rRNA gene. We further provide a BR estimate based upon a sampling depth and accuracy, which, to our knowledge, are unsurpassed for freshwater bacterioplankton communities. Our examination of 22 669 sequences per lake showed that freshwater BR in fourteen nutrient-poor lakes was positively influenced by nutrient availability. Our study is, thus, consistent with the finding that the supply of available nutrients is a major driver of species richness; a pattern that may well be universally valid to the world of both micro- and macro-organisms. We, furthermore, observed that BR increased with elevated landscape position, most likely as a consequence of differences in nutrient availability. Finally, BR decreased with increasing lake and catchment area that is negative species-area relationships (SARs) were recorded; a finding that re-opens the debate about whether positive SARs can indeed be found in the microbial world and whether positive SARs can in fact be pronounced as one of the few 'laws' in ecology.

  • 55.
    Lundgren, M.
    et al.
    Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University.
    Andersson, Anders
    KTH, Tidigare Institutioner, Bioteknologi.
    Chen, L. M.
    Danish Archaea Center, Institute of Molecular Biology, University of Copenhagen.
    Nilsson, Peter
    KTH, Tidigare Institutioner, Bioteknologi.
    Bernander, R.
    Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University.
    Three replication origins in Sulfolobus species: synchronous initiation of chromosome replication and asynchronous termination2004Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 101, nr 18, s. 7046-7051Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Chromosome replication origins were mapped in vivo in the two hyperthermophilic archaea, Sulfolobus acidocaidarius and Sulfolobus solfataricus, by using microarray-based marker frequency analysis. Bidirectional replication was found to be initiated in near synchrony from three separate sites in both organisms. Two of the three replication origins in each species were located in the vicinity of a cdc6/orc1 replication initiation gene, whereas no known replication-associated gene could be identified near the third origin in either organism. In contrast to initiation, replication termination occurred asynchronously, such that certain replication forks continued to progress for >40 min after the others had terminated. In each species, all replication forks advanced at similar DNA polymerization rates; this was found to be an order of magnitude below that displayed by Escherichia coli and thus closer to eukaryotic elongation rates. In S. acidocaidarius, a region containing short regularly spaced repeats was found to hybridize aberrantly, as compared to the rest of the chromosome, raising the possibility of a centromere-like function.

  • 56.
    Lundin, Daniel
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Severin, I.
    Logue, J. B.
    Östman, O.
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Lindström, E. S.
    Which sequencing depth is sufficient to describe patterns in bacterial alpha- and beta-diversity?2012Inngår i: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 4, nr 3, s. 367-372Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The vastness of microbial diversity implies that an almost infinite number of individuals needs to be identified to accurately describe such communities. Practical and economical constraints may therefore prevent appropriate study designs. However, for many questions in ecology it is not essential to know the actual diversity but rather the trends among samples thereof. It is, hence, important to know to what depth microbial communities need to be sampled to accurately measure trends in diversity. We used three data sets of freshwater and sediment bacteria, where diversity was explored using 454 pyrosequencing. Each data set contained 615 communities from which 15 00020 000 16S rRNA gene sequences each were obtained. These data sets were subsampled repeatedly to 10 different depths down to 200 sequences per community. Diversity estimates varied with sequencing depth, yet, trends in diversity among samples were less sensitive. We found that 1000 denoised sequences per sample explained to 90% the trends in beta-diversity (Bray-Curtis index) among samples observed for 15 00020 000 sequences. Similarly, 5000 denoised sequences were sufficient to describe trends in a-diversity (Shannon index) with the same accuracy. Further, 5000 denoised sequences captured to more than 80% the trends in Chao1 richness and Pielou's evenness.

  • 57.
    Lundmark, Anna
    et al.
    Karolinska Inst, Dept Dent Med, Div Periodontol, Huddinge, Sweden..
    Hu, Yue O. O.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab. Karolinska Inst, CTMR, Dept Microbiol Tumor & Cell Biol, Stockholm, Sweden..
    Huss, Mikael
    Stockholm Univ, Natl Bioinformat Infrastruct Sweden, Dept Biochem & Biophys, Sci Life Lab, Solna, Sweden..
    Johannsen, Gunnar
    Karolinska Inst, Dept Dent Med, Div Periodontol, Huddinge, Sweden..
    Andersson, Anders F.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Yucel-Lindberg, Tulay
    Karolinska Inst, Dept Dent Med, Div Periodontol, Huddinge, Sweden..
    Identification of Salivary Microbiota and Its Association With Host Inflammatory Mediators in Periodontitis2019Inngår i: Frontiers in Cellular and Infection Microbiology, E-ISSN 2235-2988, Vol. 9, artikkel-id 216Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Periodontitis is a microbial-induced chronic inflammatory disease, which may not only result in tooth loss, but can also contribute to the development of various systemic diseases. The transition from healthy to diseased periodontium depends on microbial dysbiosis and impaired host immune response. Although periodontitis is a common disease as well as associated with various systemic inflammatory conditions, the taxonomic profiling of the salivary microbiota in periodontitis and its association with host immune and inflammatory mediators has not been reported. Therefore, the aim of this study was to identify key pathogens and their potential interaction with the host's inflammatory mediators in saliva samples for periodontitis risk assessment. The microbial 16S rRNA gene sequencing and the levels of inflammatory mediators were performed in saliva samples from patients with chronic periodontitis and periodontally healthy control subjects. The salivary microbial community composition differed significantly between patients with chronic periodontitis and healthy controls. Our analyses identified a number of microbes, including bacteria assigned to Eubacterium saphenum, Tannerella forsythia, Filifactor alocis, Streptococcus mitis/parasanguinis, Parvimonas micra, Prevotella sp., Phocaeicola sp., and Fretibacterium sp. as more abundant in periodontitis, compared to healthy controls. In samples from healthy individuals, we identified Campylobacter concisus, and Veillonella sp. as more abundant. Integrative analysis of the microbiota and inflammatory mediators/cytokines revealed associations that included positive correlations between the pathogens Treponema sp. and Selenomas sp. and the cytokines chitinase 3-like 1, sIL-6R alpha, sTNF-R1, and gp 130/sIL-6R beta. In addition, a negative correlation was identified between IL-10 and Filifactor alocis. Our results reveal distinct and disease-specific patterns of salivary microbial composition between patients with periodontitis and healthy controls, as well as significant correlations between microbiota and host-mediated inflammatory cytokines. The positive correlations between the pathogens Treponema sp. and Selenomas sp. and the cytokines chitinase 3-like 1, sIL-6R alpha, sTNF-R1, and gp 130/sIL-6R beta might have the future potential to serve as a combined bacteria-host salivary biomarker panel for diagnosis of the chronic infectious disease periodontitis. However, further studies are required to determine the capacity of these microbes and inflammatory mediators as a salivary biomarker panel for periodontitis.

  • 58.
    Marin-Beltran, Isabel
    et al.
    CSIC, Inst Ciencies Mar, Barcelona, Spain.;Univ Algarve, Ctr Ciencias Mar Algarve CCMAR, Faro, Portugal..
    Logue, Jurg B.
    Lund Univ, Dept Biol Aquat Ecol, Lund, Sweden.;Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden..
    Andersson, Anders F.
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi.
    Peters, Francesc
    CSIC, Inst Ciencies Mar, Barcelona, Spain..
    Atmospheric Deposition Impact on Bacterial Community Composition in the NW Mediterranean2019Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 10, artikkel-id 858Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Atmospheric deposition is a source of inorganic nutrients and organic matter to the ocean, and can favor the growth of some planktonic species over others according to their nutrient requirements. Atmospheric inputs from natural and anthropogenic sources are nowadays increasing due to desertification and industrialization, respectively. While the impact of mineral dust (mainly from the Saharan desert) on phytoplankton and bacterial community composition has been previously assessed, the effect of anthropogenic aerosols on marine bacterial assemblages remains poorly studied. Since marine bacteria play a range of roles in the biogeochemical cycles of inorganic nutrients and organic carbon, it is important to determine which taxa of marine bacteria may benefit from aerosol fertilization and which not. Here, we experimentally assessed the effect of Saharan dust and anthropogenic aerosols on marine bacterioplankton community composition across a spatial and temporal range of trophic conditions in the northwestern Mediterranean Sea. Results from 16S rDNA sequencing showed that bacterial diversity varied significantly with seasonality and geographical location. While atmospheric deposition did not yield significant changes in community composition when all the experiments where considered together, it did produce changes at certain places and during certain times of the year. These effects accounted for shifts in the bacterial community's relative abundance of up to 28%. The effect of aerosols was overall greatest in summer, both types of atmospheric particles stimulating the groups Alphaproteobacteria, Betaproteobacteria, and Cyanobacteria in the location with the highest anthropogenic footprint. Other bacterial groups benefited from one or the other aerosol depending on the season and location. Anthropogenic aerosols increased the relative abundance of groups belonging to the phylum Bacteriodetes (Cytophagia, Flavobacteriia, and Sphingobacteriia), while Saharan dust stimulated most the phytoplanktonic group of Cyanobacteria and, more specifically, Synechococcus.

  • 59.
    Markussen, Trine
    et al.
    Univ Copenhagen, Dept Biol, Marine Biol Sect, Helsingor, Denmark..
    Happel, Elisabeth M.
    Univ Copenhagen, Dept Biol, Marine Biol Sect, Helsingor, Denmark..
    Teikari, Jonna E.
    Univ Helsinki, Dept Microbiol, Helsinki, Finland..
    Huchaiah, Vimala
    Univ Tartu, Inst Technol, Tartu, Estonia..
    Alneberg, Johannes
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Andersson, Anders F.
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Sivonen, Kaarina
    Univ Helsinki, Dept Microbiol, Helsinki, Finland..
    Riemann, Lasse
    Univ Copenhagen, Dept Biol, Marine Biol Sect, Helsingor, Denmark..
    Middelboe, Mathias
    Univ Copenhagen, Dept Biol, Marine Biol Sect, Helsingor, Denmark..
    Kisand, Veljo
    Univ Tartu, Inst Technol, Tartu, Estonia..
    Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change2018Inngår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 20, nr 8, s. 3083-3099Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Bacteria are major drivers of biogeochemical nutrient cycles and energy fluxes in marine environments, yet how bacterial communities respond to environmental change is not well known. Metagenomes allow examination of genetic responses of the entire microbial community to environmental change. However, it is challenging to link metagenomes directly to biogeochemical process rates. Here, we investigate metagenomic responses in natural bacterioplankton communities to simulated environmental stressors in the Baltic Sea, including increased river water input, increased nutrient concentration, and reduced oxygen level. This allowed us to identify informative prokaryotic gene markers, responding to environmental perturbation. Our results demonstrate that metagenomic and metabolic changes in bacterial communities in response to environmental stressors are influenced both by the initial community composition and by the biogeochemical factors shaping the functional response. Furthermore, the different sources of dissolved organic matter (DOM) had the largest impact on metagenomic blueprint. Most prominently, changes in DOM loads influenced specific transporter types reflecting the substrate availability and DOC assimilation and consumption pathways. The results provide new knowledge for developing models of ecosystem structure and biogeochemical cycling in future climate change scenarios and advance our exploration of the potential use of marine microorganisms as markers for environmental conditions.

  • 60.
    Marquina, Daniel
    et al.
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden.;Stockholm Univ, Dept Zool, Stockholm, Sweden..
    Andersson, Anders F.
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Ronquist, Fredrik
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden..
    New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods2019Inngår i: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 19, nr 1, s. 90-104Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Insect metabarcoding has been mainly based on PCR amplification of short fragments within the "barcoding region" of the gene cytochrome oxidase I (COI). However, because of the variability of this gene, it has been difficult to design good universal PCR primers. Most primers used today are associated with gaps in the taxonomic coverage or amplification biases that make the results less reliable and impede the detection of species that are present in the sample. We identify new primers for insect metabarcoding using computational approaches (ecoprimers and degeprime) applied to the most comprehensive reference databases of mitochondrial genomes of Hexapoda assembled to date. New primers are evaluated in silico against previously published primers in terms of taxonomic coverage and resolution of the corresponding amplicons. For the latter criterion, we propose a new index, exclusive taxonomic resolution, which is a more biologically meaningful measure than the standard index used today. Our results show that the best markers are found in the ribosomal RNA genes (12S and 16S); they resolve about 90% of the genetically distinct species in the reference database. Some markers in protein-coding genes provide similar performance but only at much higher levels of primer degeneracy. Combining two of the best individual markers improves the effective taxonomic resolution with up to 10%. The resolution is strongly dependent on insect taxon: COI primers detect 40% of Hymenoptera, while 12S primers detect 12% of Collembola. Our results indicate that amplicon-based metabarcoding of insect samples can be improved by choosing other primers than those commonly used today.

  • 61.
    Paerl, Ryan W.
    et al.
    Univ Copenhagen, Dept Biol, Marine Biol Sect, DK-3000 Helsingor, Denmark.;North Carolina State Univ, Dept Marine Earth & Atmospher Sci, Raleigh, NC 27695 USA..
    Sundh, John
    Stockholm Univ, Natl Bioinformat Infrastruct Sweden, Sci Life Lab, Dept Biochem & Biophys, S-17121 Solna, Sweden.;KTH Royal Inst Technol, Sci Life Lab, Dept Gene Technol, S-17121 Solna, Sweden..
    Tan, Demeng
    Univ Copenhagen, Dept Biol, Marine Biol Sect, DK-3000 Helsingor, Denmark..
    Svenningsen, Sine L.
    Univ Copenhagen, Dept Biol, Biomol Sci Sect, DK-2200 Copenhagen, Denmark..
    Hylander, Samuel
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, SE-39182 Kalmar, Sweden..
    Pinhassi, Jarone
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, SE-39182 Kalmar, Sweden..
    Andersson, Anders F.
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi.
    Riemann, Lasse
    Univ Copenhagen, Dept Biol, Marine Biol Sect, DK-3000 Helsingor, Denmark..
    Prevalent reliance of bacterioplankton on exogenous vitamin B1 and precursor availability2018Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, nr 44, s. E10447-E10456Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Vitamin B1 (B1 herein) is a vital enzyme cofactor required by virtually all cells, including bacterioplankton, which strongly influence aquatic biogeochemistry and productivity and modulate climate on Earth. Intriguingly, bacterioplankton can be de novo B1 synthesizers or B1 auxotrophs, which cannot synthesize B1 de novo and require exogenous B1 or B1 precursors to survive. Recent isolate-based work suggests select abundant bacterioplankton are B1 auxotrophs, but direct evidence of B1 auxotrophy among natural communities is scant. In addition, it is entirely unknown if bulk bacterioplankton growth is ever B1-limited. We show by surveying for B1-related genes in estuarine, marine, and freshwater metagenomes and metagenome-assembled genomes (MAGs) that most naturally occurring bacterioplankton are B1 auxotrophs. Pyrimidine B1-auxotrophic bacterioplankton numerically dominated metagenomes, but multiple other B1-auxotrophic types and distinct uptake and B1-salvaging strategies were also identified, including dual (pyrimidine and thiazole) and intact B1 auxotrophs that have received little prior consideration. Time-series metagenomes from the Baltic Sea revealed pronounced shifts in the prevalence of multiple B1-auxotrophic types and in the B1-uptake and B1salvaging strategies over time. Complementarily, we documented B1/precursor limitation of bacterioplankton production in three of five nutrient-amendment experiments at the same time-series station, specifically when intact B1 concentrations were <= 3.7 pM, based on bioassays with a genetically engineered Vibrio anguillarum B1-auxotrophic strain. Collectively, the data presented highlight the prevalent reliance of bacterioplankton on exogenous B1/precursors and on the bioavailability of the micronutrients as an overlooked factor that could influence bacterioplankton growth and succession and thereby the cycling of nutrients and energy in aquatic systems.

  • 62. Quince, Christopher
    et al.
    Lundin, Elin E.
    Andreasson, Anna N.
    Greco, Dario
    Rafter, Joseph
    Talley, Nicholas J.
    Agreus, Lars
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Engstrand, Lars
    D'Amato, Mauro
    The impact of Crohn's disease genes on healthy human gut microbiota: a pilot study2013Inngår i: Gut, ISSN 0017-5749, E-ISSN 1468-3288, Vol. 62, nr 6, s. 952-954Artikkel i tidsskrift (Fagfellevurdert)
  • 63. Rodin, S.
    et al.
    Andersson, Anders F.
    Swedish Institute for Infectious Disease Control, SE-17182 Solna, Sweden. Limnology/Department of Ecology and Evolution, Uppsala University .
    Wirta, V.
    Eriksson, L.
    Ljungström, M.
    Björkholm, B.
    Lindmark, H.
    Engstrand, L.
    Performance of a 70-mer oligonucleotide microarray for genotyping of Campylobacter jejuni2008Inngår i: BMC Microbiology, ISSN 1471-2180, E-ISSN 1471-2180, Vol. 8Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    BACKGROUND: Campylobacter jejuni is widespread in the environment and is the major cause of bacterial gastroenteritis in humans. In the present study we use microarray-based comparative genomic hybridizations (CGH), pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) to analyze closely related C. jejuni isolates from chicken and human infection. RESULTS: With the exception of one isolate, the microarray data clusters the isolates according to the five groups determined by PFGE. In contrast, MLST defines only three genotypes among the isolates, indicating a lower resolution. All methods show that there is no inherit difference between isolates infecting humans and chicken, suggesting a common underlying population of C. jejuni. We further identify regions that frequently differ between isolates, including both previously described and novel regions. Finally, we show that genes that belong to certain functional groups differ between isolates more often than expected by chance. CONCLUSION: In this study we demonstrated the utility of 70-mer oligonucleotide microarrays for genotyping of Campylobacter jejuni isolates, with resolution outperforming MLST.

  • 64. Skoglund, A.
    et al.
    Bjorkholm, B.
    Nilsson, C.
    Andersson, Anders F.
    Swedish Institute of Infectious Disease Control, Solna, Sweden.
    Jernberg, C.
    Schirwitz, K.
    Enroth, C.
    Krabbe, M.
    Engstrand, L.
    Functional analysis of the M.HpyAIV DNA methyltransferase of Helicobacter pylori2007Inngår i: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 189, nr 24, s. 8914-8921Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A large number of genes encoding restriction-modification (R-M) systems are found in the genome of the human pathogen Helicobacter pylori. R-M genes comprise approximately 10% of the strain-specific genes, but the relevance of having such an abundance of these genes is not clear. The type II methyltransferase (MTase) M.HpyAIV, which recognizes GANTC sites, was present in 60% of the H. pylori strains analyzed, whereof 69% were resistant to restriction enzyme digestion, which indicated the presence of an active MTase. H. pylori strains with an inactive M.HpyAIV phenotype contained deletions in regions of homopolymers within the gene, which resulted in premature translational stops, suggesting that M.HpyAIV may be subjected to phase variation by a slipped-strand mechanism. An M.HpyAIV gene mutant was constructed by insertional mutagenesis, and this mutant showed the same viability and ability to induce interleukin-8 in epithelial cells as the wild type in vitro but had, as expected, lost the ability to protect its self-DNA from digestion by a cognate restriction enzyme. The M.HpyAIV from H. pylori strain 26695 was overexpressed in Escherichia coli, and the protein was purified and was able to bind to DNA and protect GANTC sites from digestion in vitro. A bioinformatic analysis of the number of GANTC sites located in predicted regulatory regions of H. pylori strains 26695 and J99 resulted in a number of candidate genes. katA, a selected candidate gene, was further analyzed by quantitative real-time reverse transcription-PCR and shown to be significantly down-regulated in the M.HpyAIV gene mutant compared to the wild-type strain. This demonstrates the influence of M.HpyAIV methylation in gene expression.

  • 65.
    Svartström, Olov
    et al.
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    Alneberg, Johannes
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Terrapon, Nicolas
    Lombard, Vincent
    de Bruijn, Ino
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Malmsten, Jonas
    Dalin, Ann-Marie
    El Muller, Emilie
    Shah, Pranjul
    Wilmes, Paul
    Henrissat, Bernard
    Aspeborg, Henrik
    KTH, Skolan för bioteknologi (BIO), Industriell bioteknologi.
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation2017Inngår i: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 11, nr 11, s. 2538-2551Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes and were overall overrepresented in the moose microbiome compared with other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a large numbers of dockerins, a module usually associated with cellulosomes. The Bacteroidetes dockerins were often linked to CAZymes and sometimes encoded inside polysaccharide utilization loci, which has never been reported before. The almost 100 CAZyme-annotated genomes reconstructed in this study provide an in-depth view of an efficient lignocellulose-degrading microbiome and prospects for developing enzyme technology for biorefineries.

  • 66. van der Oost, John
    et al.
    Walther, Jasper
    Brouns, Stan J. J.
    van de Verken, Harmen J. G.
    Snijders, Ambrosius P. L.
    Wright, Phillip C.
    Andersson, Anders
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Bernander, Rolf
    de Vos, Willem M.
    Functional genomics of the thermo-acidophilic archaeon Sulfolobus solfataricus2006Inngår i: EXTREMOPHILES / [ed] Rainey, FA; Oren, A, LONDON: ACADEMIC PRESS LTD-ELSEVIER SCIENCE LTD , 2006, Vol. 35, s. 201-231Kapittel i bok, del av antologi (Annet vitenskapelig)
  • 67. Wampach, L.
    et al.
    Heintz-Buschart, A.
    Fritz, J. V.
    Ramiro-Garcia, J.
    Habier, J.
    Herold, M.
    Narayanasamy, S.
    Kaysen, A.
    Hogan, A. H.
    Bindl, L.
    Bottu, J.
    Halder, R.
    Sjöqvist, Conny
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    May, P.
    Andersson, Anders F.
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    de Beaufort, C.
    Wilmes, P.
    Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential2018Inngår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, nr 1, artikkel-id 5091Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The rate of caesarean section delivery (CSD) is increasing worldwide. It remains unclear whether disruption of mother-to-neonate transmission of microbiota through CSD occurs and whether it affects human physiology. Here we perform metagenomic analysis of earliest gut microbial community structures and functions. We identify differences in encoded functions between microbiomes of vaginally delivered (VD) and CSD neonates. Several functional pathways are over-represented in VD neonates, including lipopolysaccharide (LPS) biosynthesis. We link these enriched functions to individual-specific strains, which are transmitted from mothers to neonates in case of VD. The stimulation of primary human immune cells with LPS isolated from early stool samples of VD neonates results in higher levels of tumour necrosis factor (TNF-α) and interleukin 18 (IL-18). Accordingly, the observed levels of TNF-α and IL-18 in neonatal blood plasma are higher after VD. Taken together, our results support that CSD disrupts mother-to-neonate transmission of specific microbial strains, linked functional repertoires and immune-stimulatory potential during a critical window for neonatal immune system priming.

  • 68. Wampach, Linda
    et al.
    Heintz-Buschart, Anna
    Hogan, Angela
    Muller, Emilie E. L.
    Narayanasamy, Shaman
    Laczny, Cedric C.
    Hugerth, Luisa
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Bindl, Lutz
    Bottu, Jean
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    de Beaufort, Carine
    Wilmes, Paul
    Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life2017Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, artikkel-id 738Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Perturbations to the colonization process of the human gastrointestinal tract have been suggested to result in adverse health effects later in life. Although much research has been performed on bacterial colonization and succession, much less is known about the other two domains of life, archaea, and eukaryotes. Here we describe colonization and succession by bacteria, archaea and microeukaryotes during the first year of life (samples collected around days 1, 3, 5, 28, 150, and 365) within the gastrointestinal tract of infants delivered either vaginally or by cesarean section and using a combination of quantitative real-time PCR as well as 16S and 18S rRNA gene amplicon sequencing. Sequences from organisms belonging to all three domains of life were detectable in all of the collected meconium samples. The microeukaryotic community composition fluctuated strongly over time and early diversification was delayed in infants receiving formula milk. Cesarean section-delivered (CSD) infants experienced a delay in colonization and succession, which was observed for all three domains of life. Shifts in prokaryotic succession in CSD infants compared to vaginally delivered (VD) infants were apparent as early as days 3 and 5, which were characterized by increased relative abundances of the genera Streptococcus and Staphylococcus, and a decrease in relative abundance for the genera Bifidobacterium and Bacteroides. Generally, a depletion in Bacteroidetes was detected as early as day 5 postpartum in CSD infants, causing a significantly increased Firmicutes/Bacteroidetes ratio between days 5 and 150 when compared to VD infants. Although the delivery mode appeared to have the strongest influence on differences between the infants, other factors such as a younger gestational age or maternal antibiotics intake likely contributed to the observed patterns as well. Our findings complement previous observations of a delay in colonization and succession of CSD infants, which affects not only bacteria but also archaea and microeukaryotes. This further highlights the need for resolving bacterial, archaeal, and microeukaryotic dynamics in future longitudinal studies of microbial colonization and succession within the neonatal gastrointestinal tract.

  • 69. Willing, Ben P.
    et al.
    Dicksved, Johan
    Halfvarson, Jonas
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Lucio, Marianna
    Zheng, Zongli
    Jarnerot, Gunnar
    Tysk, Curt
    Jansson, Janet K.
    Engstrand, Lars
    A Pyrosequencing Study in Twins Shows That Gastrointestinal Microbial Profiles Vary With Inflammatory Bowel Disease Phenotypes2010Inngår i: Gastroenterology, ISSN 0016-5085, E-ISSN 1528-0012, Vol. 139, nr 6, s. 1844-U105Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    BACKGROUND & AIMS: The composition of the gastrointestinal microbiota is thought to have an important role in the etiology of inflammatory bowel diseases (IBDs) such as Crohn's disease (CD) and ulcerative colitis (UC). Interindividual variation and an inability to detect less abundant bacteria have made it difficult to correlate specific bacteria with disease. METHODS: We used 454 pyrotag sequencing to determine the compositions of microbial communities in feces samples collected from a cohort of 40 twin pairs who were concordant or discordant for CD or UC, and in mucosal samples from a subset of the cohort. The cohort primarily comprised patients who were in remission, but also some with active disease. RESULTS: The profiles of the microbial community differed with disease phenotypes; relative amounts of bacterial populations correlated with IBD phenotypes. The microbial compositions of individuals with CD differed from those of healthy individuals, but were similar between healthy individuals and individuals with UC. Profiles from individuals with CD that predominantly involved the ileum differed from those with CD that predominantly involved the colon; several bacterial populations increased or decreased with disease type. Changes specific to patients with ileal CD included the disappearance of core bacteria, such as Faecalibacterium and Roseburia, and increased amounts of Enterobacteriaceae and Ruminococcus gnavus. CONCLUSIONS: Bacterial populations differ in abundance among individuals with different phenotypes of CD. Specific species of bacteria are associated with ileal CD; further studies should investigate their role in pathogenesis.

  • 70. Wilmes, P.
    et al.
    Andersson, Anders F.
    Department of Earth and Planetary Sciences, University of California at Berkeley.
    Lefsrud, M. G.
    Wexler, M.
    Shah, M.
    Zhang, B.
    Hettich, R. L.
    Bond, P. L.
    VerBerkmoes, N. C.
    Banfield, J. F.
    Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal2008Inngår i: ISME JOURNAL, ISSN 1751-7362, Vol. 2, nr 8, s. 853-864Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Enhanced biological phosphorus removal (EBPR) selects for polyphosphate accumulating microorganisms to achieve phosphate removal from wastewater. We used high-resolution community proteomics to identify key metabolic pathways in 'Candidatus Accumulibacter phosphatis' (A. phosphatis)-mediated EBPR and to evaluate the contributions of co-existing strains within the dominant population. Overall, 702 proteins from the A. phosphatis population were identified. Results highlight the importance of denitrification, fatty acid cycling and the glyoxylate bypass in EBPR. Strong similarity in protein profiles under anaerobic and aerobic conditions was uncovered (only 3% of A. phosphatis-associated proteins exhibited statistically significant abundance differences). By comprehensive genome-wide alignment of 13,930 orthologous proteins, we uncovered substantial differences in protein abundance for enzyme variants involved in both core-metabolism and EBPR-specific pathways among the A. phosphatis population. These findings suggest an essential role for genetic diversity in maintaining the stable performance of EBPR systems and, hence, demonstrate the power of integrated cultivation-independent genomics and proteomics for the analysis of complex biotechnological systems.

  • 71. Wu, Xiaofen
    et al.
    Pedersen, Karsten
    Edlund, Johanna
    Eriksson, Lena
    Astrom, Mats
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Bertilsson, Stefan
    Dopson, Mark
    Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters2017Inngår i: Microbiome, ISSN 0026-2633, E-ISSN 2049-2618, Vol. 5, artikkel-id 37Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Deep terrestrial biosphere waters are separated from the light-driven surface by the time required to percolate to the subsurface. Despite biofilms being the dominant form of microbial life in many natural environments, they have received little attention in the oligotrophic and anaerobic waters found in deep bedrock fractures. This study is the first to use community DNA sequencing to describe biofilm formation under in situ conditions in the deep terrestrial biosphere. Results: In this study, flow cells were attached to boreholes containing either "modern marine" or "old saline" waters of different origin and degree of isolation from the light-driven surface of the earth. Using 16S rRNA gene sequencing, we showed that planktonic and attached populations were dissimilar while gene frequencies in the metagenomes suggested that hydrogen-fed, carbon dioxide-and nitrogen-fixing populations were responsible for biofilm formation across the two aquifers. Metagenome analyses further suggested that only a subset of the populations were able to attach and produce an extracellular polysaccharide matrix. Initial biofilm formation is thus likely to be mediated by a few bacterial populations which were similar to Epsilonproteobacteria, Deltaproteobacteria, Betaproteobacteria, Verrucomicrobia, and unclassified bacteria. Conclusions: Populations potentially capable of attaching to a surface and to produce extracellular polysaccharide matrix for attachment were identified in the terrestrial deep biosphere. Our results suggest that the biofilm populations were taxonomically distinct from the planktonic community and were enriched in populations with a chemolithoautotrophic and diazotrophic metabolism coupling hydrogen oxidation to energy conservation under oligotrophic conditions.

  • 72. Zangenah, S.
    et al.
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Ozenci, V.
    Bergman, P.
    Genomic analysis reveals the presence of a class D beta-lactamase with broad substrate specificity in animal bite associated Capnocytophaga species2017Inngår i: European Journal of Clinical Microbiology and Infectious Diseases, ISSN 0934-9723, E-ISSN 1435-4373, Vol. 36, nr 4, s. 657-662Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Capnocytophga canimorsus and Capnocytophga cynodegmi can be transmitted from cats and dogs to humans, and can cause a wide range of infections including wound infections, sepsis, or endocarditis. We and others recently discovered two new Capnocytophaga species, C. canis and C. stomatis, mainly associated with wound infections. The first-line treatment of animal bite related infections is penicillin, and in case of allergy, doxycycline and trimethoprim/sulfamethoxazole. However, there is a lack of antibiotic susceptibility patterns for animal bite associated Capnocytophaga species. Thus, we i >> inverted question markset out to study the antibiotic profiles against animal bite associated Capnocytophaga species isolated from wound and blood cultures after cat and dog bites and coupled the findings to whole genome sequencing data. A total of 24 strains were included in the study. Phenotypic analysis of antibiotic resistance was performed with E-tests. The web-based tool 'Resfinder' was used to identify resistance genes in the whole genome dataset. Two strains of C. cynodegmi and two strains of the recently discovered C. stomatis were resistant to penicillin (MIC 24 mgi >> inverted question mark/L) and cephalosporins (MIC 24 mg/i >> inverted question markL), and three out of these strains also exhibited resistance to imipenem (MIC = 32 mg/i >> inverted question markL). Genomic analysis revealed that these strains carried a class D beta-lactamase gene, which has not previously been found in Capnocytophaga spp. A class D beta lactamase with broad substrate specificity was found in animal bite associated Capnocytophaga species, which could have important implications when treating wound infections after cat and dog bites. It also suggests that pet animal bacteria can harbour resistance genes with relevance for human infections.

  • 73. Zangenah, Salah
    et al.
    Abbasi, Nasir
    Univ Miguel Hernandez,Spain.
    Andersson, Anders F.
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Bergman, Peter
    Whole genome sequencing identifies a novel species of the genus Capnocytophaga isolated from dog and cat bite wounds in humans2016Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, artikkel-id 22919Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    C. canimorsus and C. cynodegmi are dog and cat commensals which can be transmitted to humans via bites or scratches and can cause sepsis, meningitis, endocarditis, and eye- or wound infections. Recently an additional Capnocytophaga species was identified as part of the oral flora of healthy dogs and was given the name "C. canis". We previously identified a Capnocytophaga isolate that could not be typed with available diagnostic tests including MALDI-TOF, 16S rRNA sequencing or species-specific PCR. This strain and 21 other Capnocytophaga spp isolated in Sweden from clinical blood- or wound-cultures were subjected to whole genome sequencing using the Illumina platform. Phylogenetic analysis revealed that the previously non-typable isolate belongs to the putative new species "C. canis". Since this strain was isolated from a wound it also shows that members of "C. canis" have the potential to be pathogenic. In addition, our phylogenetic analysis uncovered an additional species of Capnocytophaga, which can be transmitted from dogs and cats to humans, suggesting a speciation within the Capnocytophaga family that has not been observed before. We propose the name of "C. stomatis" for this putative novel species.

  • 74. Zheng, Z.
    et al.
    Advani, A.
    Melefors, O.
    Glavas, S.
    Nordström, H.
    Ye, W.
    Engstrand, L.
    Andersson, Anders
    Swedish Institute for Infectious Disease Control, Solna, Sweden. Limnology/Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University .
    Titration-free massively parallel pyrosequencing using trace amounts of starting material2010Inngår i: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 38, nr 13Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Continuous efforts have been made to improve next-generation sequencing methods for increased robustness and for applications on low amounts of starting material. We applied double-stranded library protocols for the Roche 454 platform to avoid the yield-reducing steps associated with single-stranded library preparation, and applied a highly sensitive Taqman MGB-probe-based quantitative polymerase chain reaction (qPCR) method. The MGB-probe qPCR, which can detect as low as 100 copies, was used to quantify the amount of effective library, i.e. molecules that form functional clones in emulsion PCR. We also demonstrate that the distribution of library molecules on capture beads follows a Poisson distribution. Combining the qPCR and Poisson statistics, the labour-intensive and costly titration can be eliminated and trace amounts of starting material such as precious clinical samples, transcriptomes of small tissue samples and metagenomics on low biomass environments is applicable.

  • 75. Zheng, Zongli
    et al.
    Advani, Abdolreza
    Melefors, Öjar
    Glavas, Steve
    Nordström, Henrik
    Ye, Weimin
    Engstrand, Lars
    Andersson, Anders F.
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Titration-free 454 sequencing using Y adapters2011Inngår i: Nature Protocols, ISSN 1754-2189, E-ISSN 1750-2799, Vol. 6, nr 9, s. 1367-1376Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We describe a protocol for construction and quantification of libraries for emulsion PCR (emPCR)-based sequencing platforms such as Roche 454 or Ion Torrent PGM. The protocol involves library construction using customized Y adapters, quantification using TaqMan-MGB (minor groove binder) probe-based quantitative PCR (qPCR) and calculation of an optimal template-to-bead ratio based on Poisson statistics, thereby avoiding the need for a laborious titration assay. Unlike other qPCR methods, the TaqMan-MGB probe specifically quantifies effective libraries in molar concentration and does not require specialized equipment. A single quality control step prior to emulsion PCR ensures that libraries contain no adapter dimers and have an optimal length distribution. The presented protocol takes similar to 7 h to prepare eight barcoded libraries from genomic DNA into libraries that are ready to use for full-scale emPCR. It will be useful, for example, to allow analyses of precious clinical samples and amplification-free metatranscriptomics.

  • 76. Zheng, Zongli
    et al.
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Ye, Weimin
    Nyrén, Olof
    Normark, Staffan
    Engstrand, Lars
    A Method for Metagenomics of Helicobacter pylori from Archived Formalin-Fixed Gastric Biopsies Permitting Longitudinal Studies of Carcinogenic Risk2011Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, nr 10, s. e26442-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The human microbiota has come into focus in the search for component causes of chronic diseases, such as gastrointestinal cancers. Presumably long induction periods and altered local environments after disease onset call for the development of methods for characterization of microorganisms colonizing the host decades before disease onset. Sequencing of microbial genomes in old formalin-fixed and paraffin-embedded (FFPE) gastrointestinal biopsies provides a means for such studies but is still challenging. Here we report a method based on laser capture micro-dissection and modified Roche 454 high-throughput pyrosequencing to obtain metagenomic profiles of Helicobacter pylori. We applied this method to two 15 year old FFPE biopsies from two patients. Frozen homogenized biopsies from the same gastroscopy sessions were also available for comparison after re-culture of H. pylori. For both patients, H. pylori DNA dissected from FFPE sections had similar to 96.4% identity with culture DNA from the same patients, while only similar to 92.5% identity with GenBank reference genomes, and with culture DNA from the other patient. About 82% and 60% of the predicted genes in the two genomes were captured by at least a single sequencing read. Along with sequences displaying high similarity to known H. pylori genes, novel and highly variant H. pylori sequences were identified in the FFPE sections by our physical enrichment approach, which would likely not have been detected by a sequence capture approach. The study demonstrates the feasibility of longitudinal metagenomic studies of H. pylori using decade-preserved FFPE biopsies.

12 51 - 76 of 76
RefereraExporteraLink til resultatlisten
Permanent link
Referera
Referensformat
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annet format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annet språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf