56 research outputs found
Fluorescence <i>in situ</i> hybridization, performed on a human skin wipe-sample for visualization of Archaea.
<p>DNA-containing cell (DAPI stain): blue, Archaea: green, Bacteria: red. I-V: Examples of positive archaeal signals (small cocci, probe ARC915 labeled with rhodamine green) are shown, which give a positive signal with DAPI and no signal with the Bacteria-directed probe (EUB338/I labeled with CY3). VI: Example of a positive bacterial signal. Bar: 2 µm.</p
Abundance of bacterial and archaeal 16 S rRNA gene copies retrieved from front torsos of 13 people.
<p>Values above bar graphs give percent of archaeal gene copies in the entire prokaryotic microbiome detected. Asterisks indicate an archaeal percentage lower than 0.01. X-axis gives human sample number (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065388#pone-0065388-t001" target="_blank">Table 1</a>), Y-axis shows log-transformed abundances of 16 S rRNA genes.</p
Maximum likelihood tree based on archaeal <i>amoA</i> gene sequences.
<p>Sequences recovered in this study are shown in bold. Information in parenthesis gives the number of retrieved sequences. Bar refers to 10% nucleotide substitutions per site.</p
Maximum likelihood tree displaying all detected OTUs from human skin, intensive care unit, and clean room environments.
<p>Symbol “<i>man</i>”: phylotype retrieved from human skin (the number of symbols gives the number of individuals carrying this phylotype; 5 subjects were screened with respect to the archaeal 16 S rRNA gene pool). Symbol “<i>hospital</i>” (square with cross): phylotype detected in intensive care unit (two intensive care units were screened). Symbol “<i>square</i>”: detected in a spacecraft assembly clean room (one facility was analyzed). Symbol “<i>star</i>” highlights phylotypes that were also found in the propidium monoazide (PMA)-treated sample, i.e. from cells with intact membranes. Scale bar refers to 10% nucleotide substitutions. <i>Pyrobaculum arsenaticum</i> and <i>Thermofilum pendens</i> (Crenarchaeota) were used as an outgroup.</p
BiomTable_MiSeq_Pferschy-Wenzig_et_al_2017.xlsx
<p>Text-formatted biom table of MiSeq sequencing data produced in the study published as:</p><p>Pferschy-Wenzig, E-M, Koskinen, K, Moissl-Eichinger, C, Bauer, R.
</p><p><b>A combined LC-MS metabolomics- and 16S rRNA sequencing
platform to assess interactions between herbal medicinal products and human gut
bacteria <i>in vitro</i>: A pilot study on
willow bark extract" </b></p><p><b>in Frontiers in Pharmacology, 2017. doi: 10.3389/fphar.2017.00893</b></p><p><br></p
Core OTU network
<p>(spring embedded eweighted) of CCR (red), CCR+ (orange), UAF (blue) and UAF+ (green) samples. Node size represents OTU abundance and edge width and opacity is weighted. OTUs resolved to genus level are highlighted and font size correlates with OTU abundance. Bacterial genera in red represent potential spore formers. Samples treated with PMA prior to DNA extraction are indicated by a plus symbol. CCR: controlled cleanroom. UAF: uncontrolled adjoining facility.</p
OTU heatmap.
<p>based on taxa, which are part of the respective core microbiome from CCR (controlled cleanroom) and UAF (uncontrolled adjoining facility). Color code from blue via white to red (0–50–100%) gives relative amount [%] of respective taxonomic group. Table was rarefied to 3406 OTUs (CCR samples), and 6665 OTUs (UAF samples). Table was sorted according to resulting P-values (p) of an ANOVA test (significant (p) at an alpha of 0.05 are highlighted in bold). (p) were corrected with false discovery rate (fdr (p)) and bonferroni (bonf. (p)). Samples treated with PMA prior to DNA extraction are indicated by a plus symbol.</p
Summary of the microbial abundance and diversity detected in the spacecraft assembly cleanroom (controlled cleanroom–CCR) at NASA Jet Propulsion Laboratory, Pasadena, CA, USA and its surrounding uncontrolled adjoining facility—UAF.
<p>(Numbers for quantitative measures are given per m<sup>2</sup>).</p
Beta-diversity (unweighted).
<p>(A) NMDS plot based on unweighted (left) unifrac distance matrix of rarefied OTUs to 10,011 sequences. Samples treated with PMA prior to DNA extraction are indicated by a plus symbol. CCR: controlled cleanroom. UAF: uncontrolled adjoining facility. Variances are explained per each axis (NMDS1 and NMDS2, Stress = 0.06). (B) Distance based comparison heatmap combined with a hierarchical cluster analysis based on average neighbor (HCAN) of unweighted unifrac distances. Dissimilarity of samples is indicated by a color gradient from blue (similar) via white to red (dissimilar). Samples treated with PMA prior to DNA extraction are indicated by a plus symbol. CCR: controlled cleanroom. UAF: uncontrolled adjoining facility.</p
Quantitative evaluations.
<p>of controlled cleanroom (CCR) and uncontrolled adjoining facility (UAF) per square meter floor surface. Upper panel shows ATP counts for total (grey bars) and intracellular ATP (black bars) in CCR and UAF (total and intracellular ATP was determined in duplicate). Lower panel shows 16S rRNA gene copies in CCR and UAF with (black bars)–and without (grey bars) PMA (propidium monoazide) treatment in triplicate (error bars represent positive and negative standard deviations).</p
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