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See detailIsolation of nucleic acids from low biomass samples: detection and removal of sRNA contaminants
Heintz-Buschart, Anna; Yusuf, Dilmurat; Kaysen, Anne UL et al

E-print/Working paper (2017)

Sequencing-based analyses of low-biomass samples are known to be prone to misinterpretation due to the potential presence of contaminating molecules derived from laboratory reagents and environments. Due ... [more ▼]

Sequencing-based analyses of low-biomass samples are known to be prone to misinterpretation due to the potential presence of contaminating molecules derived from laboratory reagents and environments. Due to its inherent instability, contamination with RNA is usually considered to be unlikely. Here we report the presence of small RNA (sRNA) contaminants in widely used microRNA extraction kits and means for their depletion. Sequencing of sRNAs extracted from human plasma samples was performed and significant levels of non-human (exogenous) sequences were detected. The source of the most abundant of these sequences could be traced to the microRNA extraction columns by qPCR-based analysis of laboratory reagents. The presence of artefactual sequences originating from the confirmed contaminants were furthermore replicated in a range of published datasets. To avoid artefacts in future experiments, several protocols for the removal of the contaminants were elaborated, minimal amounts of starting material for artefact-free analyses were defined, and the reduction of contaminant levels for identification of bona fide sequences using 'ultra-clean' extraction kits was confirmed. In conclusion, this is the first report of the presence of RNA molecules as contaminants in laboratory reagents. The described protocols should be applied in the future to avoid confounding sRNA studies. [less ▲]

Detailed reference viewed: 171 (2 UL)
See detailFunction First: Systems Ecology of the Human Gut Microbiome
Wilmes, Paul UL

Presentation (2017, November)

Detailed reference viewed: 35 (0 UL)
See detailMetaproteomics and integrated multi-omics: highlighting unknowns
Wilmes, Paul UL

Presentation (2017, November)

Detailed reference viewed: 34 (2 UL)
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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 ▲]

Detailed reference viewed: 197 (12 UL)
See detailIntegrated multi-omics for enhanced metaproteomics
Wilmes, Paul UL

Scientific Conference (2017, October)

Detailed reference viewed: 37 (0 UL)
See detailLe microbiome humain et son impact sur la santé
Wilmes, Paul UL

Scientific Conference (2017, October)

Detailed reference viewed: 37 (0 UL)
See detailForm follows function: systems ecology of the human gut microbiome
Wilmes, Paul UL

Presentation (2017, October)

Detailed reference viewed: 36 (2 UL)
See detailSystems ecology of microbial pioneers in the gut
Wilmes, Paul UL

Presentation (2017, October)

Detailed reference viewed: 38 (3 UL)
See detailForm follows function: integrated multi-omics of the human gut microbiome
Wilmes, Paul UL

Scientific Conference (2017, September)

Detailed reference viewed: 34 (0 UL)
See detailSystems ecology of microbiomes: a new frontier of discovery in microbiology
Wilmes, Paul UL

Scientific Conference (2017, September)

Detailed reference viewed: 41 (1 UL)
See detailFrom integrated multi-omics to microbial systems ecology: quo vadis?
Wilmes, Paul UL

Scientific Conference (2017, August)

Detailed reference viewed: 34 (1 UL)
See detailSystems ecology of microbiomes: a new frontier of discovery in microbiology
Wilmes, Paul UL

Presentation (2017, August)

Detailed reference viewed: 35 (0 UL)
See detailSystems ecology of microbiomes: a new frontier of discovery in microbiology
Wilmes, Paul UL

Presentation (2017, August)

Detailed reference viewed: 30 (0 UL)
See detailIntegrated multi-omics for identifying discriminant features in the human microbiome
Wilmes, Paul UL

Scientific Conference (2017, June)

Detailed reference viewed: 34 (3 UL)
See detailUntangling the microbial ecology of anaerobic digestion through integrated multi-omics
Wilmes, Paul UL

Scientific Conference (2017, May)

Detailed reference viewed: 47 (0 UL)
See detailSystems Ecology of Microbiomes: A New Frontier of Discovery in Microbiology
Wilmes, Paul UL

Scientific Conference (2017, May)

Detailed reference viewed: 40 (0 UL)
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Peer Reviewed
See detailColonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life
Wampach, Linda UL; Heintz, Anna UL; Hogan, Angela et al

in Frontiers in Microbiology (2017)

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 ... [more ▼]

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. [less ▲]

Detailed reference viewed: 457 (22 UL)