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See detailIntegration of omics data for biotechnology-relevant microbial communities
Herold, Malte UL

Doctoral thesis (2018)

Naturally occurring and artificial bacterial communities play an import role in many biotechnological processes. To elucidate bacterial interactions that are important for potential optimized ... [more ▼]

Naturally occurring and artificial bacterial communities play an import role in many biotechnological processes. To elucidate bacterial interactions that are important for potential optimized biotechnological applications, high-throughput measurements of biomolecules, metagenomics, metratranscriptomics,metaproteomics, and meta-metabolomics provide a detailed snapshot of mixed microbial consortia. Integration of multiple layers of omics data allows to reconstruct structure and function of complex microbial communities and is demonstrated for two different model systems. The first chapter focuses on synthetic communities consisting of strains representing key species found in biomining operations and acid mine drainage and that are of economical interest for copper production. A high-quality closed reference genome for L. ferriphilum was obtained by DNA sequencing and was subsequently used to integrate functional omics data, i.e. transcriptomic and proteomic profiling. The combination of genomics, genome annotation, and functional omics data allowed an in-depth characterization of L. ferriphilum in culture medium and in the presence of the iron sulfide mineral chalcopyrite, an economically relevant copper ore. Subsequently, analyses were performed for co-cultures of up to three organisms highlighting specific interaction mechanisms. The cultures without L. ferriphilum showed higher copper solubilisation rates, as the highly efficient iron oxidiser might raise the redox potential above the optimal range. For in situ studies, reference-based analyses are of limited use, e.g. due to a lack in reference genomes of culturable isolates. Hence, the second chapter focuses on an approach to study mixed microbial communities independent of prior knowledge and available reference genomes. A timeseries of oleaginous floating sludge samples that spans over one and a half years was analysed by integrating metagenomic, metatranscriptomic, metaproteomic, and meta-metabolomic data. This allowed the reconstruction of population level genomes and the characterization of the niches of the respective populations. The functional potential was assessed, as well as expression profiles over time, yielding a detailed view on lifestyle strategies and the potential impact of abiotic factors. Understanding the niche ecology of the predominant lipid accumulators in the system could lead towards optimized biofuel production. [less ▲]

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See detailFirst draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ
Muller, Emilie UL; Narayanasamy, Shaman UL; Zeimes, Myriam et al

in Standards in Genomic Sciences (2017), 12(64),

The Gram-negative beta-proteobacterium Zoogloea sp. LCSB751 (LMG 29444) was newly isolated from foaming activated sludge of a municipal wastewater treatment plant. Here, we describe its draft genome ... [more ▼]

The Gram-negative beta-proteobacterium Zoogloea sp. LCSB751 (LMG 29444) was newly isolated from foaming activated sludge of a municipal wastewater treatment plant. Here, we describe its draft genome sequence and annotation together with a general physiological and genomic analysis, as the first sequenced representative of the Zoogloea genus. Moreover, Zoogloea sp. gene expression in its environment is described using metatranscriptomic data obtained from the same treatment plant. The presented genomic and transcriptomic information demonstrate a pronounced capacity of this genus to synthesize poly-β-hydroxyalkanoate within wastewater. [less ▲]

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See detailIMP: a pipeline for reproducible referenceindependent integrated metagenomic and metatranscriptomic analyses
Narayanasamy, Shaman UL; Jarosz, Yohan UL; Muller, Emilie UL et al

in Genome Biology (2016), 17

Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the ... [more ▼]

Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data. IMP incorporates robust read preprocessing, iterative co-assembly, analyses of microbial community structure and function, automated binning, as well as genomic signature-based visualizations. The IMP-based data integration strategy enhances data usage, output volume, and output quality as demonstrated using relevant use-cases. Finally, IMP is encapsulated within a user-friendly implementation using Python and Docker. IMP is available at http://r3lab.uni.lu/web/imp/ (MIT license). [less ▲]

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See detailIdentification, recovery, and refinement of hitherto undescribed population-level genomes from the human gastrointestinal tract
Laczny, Cedric C.; Muller, Emilie UL; Heintz-Buschart, Anna UL et al

in Frontiers in Microbiology (2016), 7(884),

Linking taxonomic identity and functional potential at the population-level is important for the study of mixed microbial communities and is greatly facilitated by the availability of microbial reference ... [more ▼]

Linking taxonomic identity and functional potential at the population-level is important for the study of mixed microbial communities and is greatly facilitated by the availability of microbial reference genomes. While the culture-independent recovery of population-level genomes from environmental samples using the binning of metagenomic data has expanded available reference genome catalogs, several microbial lineages remain underrepresented. Here, we present two reference-independent approaches for the identification, recovery, and refinement of hitherto undescribed population-level genomes. The first approach is aimed at genome recovery of varied taxa and involves multi-sample automated binning using CANOPY CLUSTERING complemented by visualization and human-augmented binning using VIZBINpost hoc. The second approach is particularly well-suited for the study of specific taxa and employs VIZBINde novo. Using these approaches, we reconstructed a total of six population-level genomes of distinct and divergent representatives of the Alphaproteobacteria class, the Mollicutes class, the Clostridiales order, and the Melainabacteria class from human gastrointestinal tract-derived metagenomic data. Our results demonstrate that, while automated binning approaches provide great potential for large-scale studies of mixed microbial communities, these approaches should be complemented with informative visualizations because expert-driven inspection and refinements are critical for the recovery of high-quality population-level genomes. [less ▲]

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