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  • 1.
    Alneberg, Johannes
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Bjarnason, Brynjar Smári
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    de Bruijn, Ino
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab. Bioinformatics Infrastructure for Life Sciences (BILS), Sweden.
    Schirmer, Melanie
    Quick, Joshua
    Ijaz, Umer Z.
    Lahti, Leo
    Loman, Nicholas J.
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Quince, Christopher
    Binning metagenomic contigs by coverage and composition2014Inngår i: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 11, nr 11, s. 1144-1146Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Shotgun sequencing enables the reconstruction of genomes from complex microbial communities, but because assembly does not reconstruct entire genomes, it is necessary to bin genome fragments. Here we present CONCOCT, a new algorithm that combines sequence composition and coverage across multiple samples, to automatically cluster contigs into genomes. We demonstrate high recall and precision on artificial as well as real human gut metagenome data sets.

  • 2. Bagnoud, Alexandre
    et al.
    Chourey, Karuna
    Hettich, Robert L.
    de Bruijn, Ino
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Andersson, Anders F.
    Leupin, Olivier X.
    Schwyn, Bernhard
    Bernier-Latmani, Rizlan
    Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock2016Inngår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, artikkel-id 12770Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present.

  • 3.
    Herlemann, D. P. R.
    et al.
    Leibniz Inst Baltic Sea Res Warnemunde, Rostock, Germany.;Estonian Univ Life Sci, Ctr Limnol, Elva Parish, Tartu County, Estonia..
    Markert, S.
    Ernst Moritz Arndt Univ Greifswald, Inst Pharm, Dept Pharmaceut Biotechnol, Greifswald, Germany.;Inst Marine Biotechnol eV, Greifswald, Germany..
    Meeske, C.
    Leibniz Inst Baltic Sea Res Warnemunde, Rostock, Germany..
    Andersson, Anders F.
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    de Bruijn, Ino
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Hentschker, C.
    Ernst Moritz Arndt Univ Greifswald, Dept Microbial Prote, Inst Microbiol, Greifswald, Germany..
    Unfried, F.
    Ernst Moritz Arndt Univ Greifswald, Inst Pharm, Dept Pharmaceut Biotechnol, Greifswald, Germany.;Inst Marine Biotechnol eV, Greifswald, Germany..
    Becher, D.
    Ernst Moritz Arndt Univ Greifswald, Dept Microbial Prote, Inst Microbiol, Greifswald, Germany..
    Juergens, K.
    Leibniz Inst Baltic Sea Res Warnemunde, Rostock, Germany..
    Schweder, T.
    Ernst Moritz Arndt Univ Greifswald, Inst Pharm, Dept Pharmaceut Biotechnol, Greifswald, Germany.;Inst Marine Biotechnol eV, Greifswald, Germany..
    Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations2019Inngår i: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 85, nr 15, artikkel-id UNSP e00825-19Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Enclosure experiments are frequently used to investigate the impact of changing environmental conditions on microbial assemblages. Yet, how the incubation itself challenges complex bacterial communities is thus far unknown. In this study, metaproteomic profiling, 16S rRNA gene analyses, and cell counts were combined to evaluate bacterial communities derived from marine, mesohaline, and oligohaline conditions after long-term batch incubations. Early in the experiment, the three bacterial communities were highly diverse and differed significantly in their compositions. Manipulation of the enclosures with terrigenous dissolved organic carbon resulted in notable differences compared to the control enclosures at this early phase of the experiment. However, after 55 days, bacterial communities in the manipulated and the control enclosures under marine and mesohaline conditions were all dominated by gammaproteobacterium Spongiibacter. In the oligohaline enclosures, actinobacterial cluster I of the hgc group (hgc-I) remained abundant in the late phase of the incubation. Metaproteome analyses suggested that the ability to use outer membrane-based internal energy stores, in addition to the previously described grazing resistance, may enable the gammaproteobacterium Spongiibacter to prevail in long-time incubations. Under oligohaline conditions, the utilization of external recalcitrant carbon appeared to be more important (hgc-I). Enclosure experiments with complex natural microbial communities are important tools to investigate the effects of manipulations. However, species-specific properties, such as individual carbon storage strategies, can cause manipulation-independent effects and need to be considered when interpreting results from enclosures. IMPORTANCE In microbial ecology, enclosure studies are often used to investigate the effect of single environmental factors on complex bacterial communities. However, in addition to the manipulation, unintended effects ("bottle effect") may occur due to the enclosure itself. In this study, we analyzed the bacterial communities that originated from three different salinities of the Baltic Sea, comparing their compositions and physiological activities both at the early stage and after 55 days of incubation. Our results suggested that internal carbon storage strategies impact the success of certain bacterial species, independent of the experimental manipulation. Thus, while enclosure experiments remain valid tools in environmental research, microbial community composition shifts must be critically followed. This investigation of the metaproteome during long-term batch enclosures expanded our current understanding of the so-called "bottle effect," which is well known to occur during enclosure experiments.

  • 4.
    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.

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