Scanning electron micrographs of <i>F. prausnitzii</i>-containing formulations.

<p>All formulations shown contained cysteine and riboflavin supplemented either with corn starch (A), inulin (B), or wheat bran, corn starch and inulin (C and D). Corn starch has a discrete bead-like appearence (A). In contrast, inulin forms a flake-like matrix (B), that can form a coating around corn starch and/or wheat bran, thereby entrapping the bacterial cells (C and D). Images A, B and C were recorded at 500× magnification, and image D was recorded at 1500× magnification. The arrows indicate entrapped <i>F. prausnitzii</i> cells.</p

Tentative schematic representation of a formulation in which <i>F. prausnitzii</i> cells were adhered on cornstarch or wheat bran, and entrapped by an inulin matrix containing riboflavin and cysteine as antioxidants and redox mediators.

<p>Tentative schematic representation of a formulation in which <i>F. prausnitzii</i> cells were adhered on cornstarch or wheat bran, and entrapped by an inulin matrix containing riboflavin and cysteine as antioxidants and redox mediators.</p

Physical appearance of freeze-dried granules containing <i>F. praunitzii</i>.

<p>A, Formulation with cysteine and riboflavin results in compact and pellet-like granules. B, Formulation with inulin, riboflavin and cysteine results in a foam-like matrix with a high bulk volume. C, Formulation with wheat bran, inulin, corn starch, cysteine and riboflavin results in hard and compact granules with considerable bulk volume.</p

Schematic representation of the methodology employed to investigate the survival of <i>F. prausnitzii</i> in different formulations upon exposure to air.

<p>Steps 1–4 were conducted in an anaerobic chamber, and steps 5–7 were conducted aerobically in ambient air. The final step 8, involving rehydration and viability assays, was conducted in an anaerobic chamber.</p

Survival of <i>F. prausnitzii</i> in different formulations.

<p>Inu, Inulin; Rb, Riboflavin; Cys, Cysteine; Cs, Corn starch; Wb, Wheat bran; nd, not determined.</p><p>Please note that the data shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096097#pone-0096097-t001" target="_blank">Table 1</a> result from a single experiment. In this experiment we focused predominantly on 24 h survival at ambient air, because this period of time is probably needed for future formulation processes.</p

Overview of isolate characteristics using several methodologies.

<p>Abbreviations: +, positive; v, variable; (+) or (−), weak reaction; −, negative; S, susceptible; R, resistant; ND, not determined. Symbols for colony morphology indicate similarity and differences. All data were obtained in this study, except data for <i>B. cereus</i>, <i>B. anthracis</i>, <i>B. thuringiensis</i> and <i>B. mycoides</i> that were compiled <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098871#pone.0098871-Logan1" target="_blank">[21]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098871#pone.0098871-Logan2" target="_blank">[22]</a>.</p><p>*Gamma phage susceptibility is not truly specific for <i>B. anthracis</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098871#pone.0098871-Turnbull1" target="_blank">[32]</a>.</p

PCR oligonucleotide primers used in this study.

<p>Bold: T7 and UP extension, respectively.</p><p>Abbreviations: FAM, carboxyfluorescein; CY, cyanine; BHQ, Black Hole Quencher.</p

16S rDNA sequence signature comparison of isolates according to the Sacchi et[31] type scheme.

<p>Abbreviations: R, A or G nucleotide; Y, C or T nucleotide; M, A or C nucleotide; W, A or T nucleotide. Nucleotides between brackets indicate a weak double signal of that nucleotide at that position.</p

The epithelial barrier is comprised of a single layer of epithelial cells intertwined by tight junctions.

<p>The mechanical barrier is increased further by a mucus layer. Binding of bacteria to TLRs present on epithelial cells results in the activation of NFκB, ultimately resulting in the release of pro-inflammatory and anti-inflammatory cytokines. After phagocytosis, bacterial products are internalized and then are recognized by receptors of the NOD family (NLRs), resulting in the modulation of the inflammatory response. Dendritic cells are capable of internalizing bacteria sampled from the lumen, after which bacteria are presented to immune effector cells. HSPs, heat shock proteins; NLR, NOD-like receptor; sIgA, secretory immunoglobulin A; TLR, Toll-like receptor.</p

The resident microbiota interferes in the process of mucositis.

<p>Depicted are five possible ways in which intestinal bacteria can attenuate or aggrevate mucositis: 1) influencing the inflammatory process, 2) influencing intestinal permeability, 3) influencing the composition of the mucus layer, 4) influencing resistance to harmful stimuli and enhancing epithelial repair, and finally, 5) the activation and release of immune effector molecules.</p