Extensive description and comparison of human supra-gingival microbiome in root caries and health.

Knowledge of the polymicrobial etiology of root caries is limited. To conduct a comprehensive research study on root caries, we utilized 454-pyrosequencing of 16S rRNA gene libraries and quantitative PCR to compare supra-gingival bacterial communities from healthy sites and carious sites of 21 patients with root caries (Patient-controls and Patient-cases) and the sites of 21 healthy individuals (Healthy-controls) from two nursing homes. Healthy-controls and Patient-cases showed no significant differences in terms of biomass, species richness, and species diversity. However, as for beta diversity based on either community membership metric (unweighted UniFrac) or community structure metric (weighted UniFrac), Healthy-controls and Patient-cases were clearly distinguished from each other, appearing more variable in the community membership and structure in root caries microbiome but relatively conserved in the health microbiome. The Patient-controls group was at an intermediate stage between Healthy-controls and Patient-cases, but was more inclined to the former. Demonstrated in both relative abundance and prevalence of species in health and root caries, Propionibacterium acidifaciens, Streptococcus mutans, Olsenella profusa, Prevotella multisaccharivorax, and Lactobacillus crispatus were found to be most associated with root caries, whereas Delftia acidovorans, Bacteroidetes[G-2] sp., Lachnospiraceae[G-3] sp., and Prevotella intermedia are most associated with health. Our study provides a basis for further elucidating the microbial etiology of root caries in the elderly

Addition of acacia gum to a FOS/inulin blend improves its fermentation profile in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME (R))

The Simulator of the Human Intestinal Microbial Ecosystem (SHIME (R)) was used to assess the impact of the partial substitution of fructooligosaccharides (FOS) and inulin by acacia gum in a fibre blend. Both blends were well fermented and the presence of acacia gum modified the intestinal fermentation of the blend from a boosted fermentation into a gradual one in the complete colon. Confirmation of the gradual fermentation was obtained by analysis of the pH profile, measurement of the residual acacia gum fractions in the colon and by the increased expression of specific catabolic enzymes. Both blends increased the total amount of short chain fatty acids (SCFAs; +42 mmol/L), propionate (+26 mmol/L) and butyrate (+9 mmol/L) and showed bifidogenic properties. Metagenomic Illumina sequencing confirmed that the blends exerted a diverse modulating activity in the different areas of the colon. Long-term repeated administration of the prebiotic blends is needed to reach gradual changes in the gut microbial community structure and activity. The partial substitution of FOS and inulin by acacia gum slowed the speed of the fermentation of the blend. In humans, this may translate into benefits for gut health, allowing for incorporation of higher amounts of fibre into the diet. (C) 2015 Elsevier Ltd. All rights reserved.publisher: Elsevier articletitle: Addition of acacia gum to a FOS/inulin blend improves its fermentation profile in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) journaltitle: Journal of Functional Foods articlelink: http://dx.doi.org/10.1016/j.jff.2015.04.039 content_type: article copyright: Copyright © 2015 Elsevier Ltd. All rights reserved.status: publishe

Addition of acacia gum to a FOS/inulin blend improves its fermentation profile in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®)

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DNA sequencing reveals the midgut microbiota of diamondback moth, Plutella xylostella (L.) and a possible relationship with insecticide resistance.

Insect midgut microbiota is important in host nutrition, development and immune response. Recent studies indicate possible links between insect gut microbiota and resistance to biological and chemical toxins. Studies of this phenomenon and symbionts in general have been hampered by difficulties in culture-based approach. In the present study, DNA sequencing was used to examine the midgut microbiota of diamondback moth (DBM), Plutella xylostella (L.), a destructive pest that attacks cruciferous crops worldwide. Its ability to develop resistance to many types of synthetic insecticide and even Bacillus thuringiensis toxins makes it an important species to study.Bacteria of the DBM larval midgut in a susceptible and two insecticide (chlorpyrifos and fipronil) resistant lines were examined by Illumina sequencing sampled from an insect generation that was not exposed to insecticide. This revealed that more than 97% of the bacteria were from three orders: Enterobacteriales, Vibrionales and Lactobacillales. Both insecticide-resistant lines had more Lactobacillales and the much scarcer taxa Pseudomonadales and Xanthomonadales with fewer Enterobacteriales compared with the susceptible strain. Consistent with this, a second study observed an increase in the proportion of Lactobacillales in the midgut of DBM individuals from a generation treated with insecticides.This is the first report of high-throughput DNA sequencing of the entire microbiota of DBM. It reveals differences related to inter- and intra-generational exposure to insecticides. Differences in the midgut microbiota among susceptible and insecticide-resistant lines are independent of insecticide exposure in the sampled generations. While this is consistent with the hypothesis that Lactobacillales or other scarcer taxa play a role in conferring DBM insecticide resistance, further studies are necessary to rule out other possibilities. Findings constitute the basis for future molecular work on the functions of insect midgut microbiota taxa and their possible role in conferring host resistance to toxins

Alpha diversity and beta diversity.

<p>(a) Boxplots for alpha diversity metrics of Chao1 (species richness) and Shannon Diversity Index (species diversity). (b) Beta diversity metrics of unweighted UniFrac (community membership) and weighted UniFrac (community structure). The color in the heatmaps indicates the UniFrac distance between each pair of samples (see color key at the left). * denotes P < 0.1; ** denotes P < 0.05; *** denotes P < 0.01.</p

Maximum likelihood phylogenetic tree at the species level.

<p>Inner loop displays species with color ranges for the class level (see color key at the bottom left); middle loop indicates mean relative abundance in each group (see color key at the top left); outer loop indicates significantly different species detected between groups (see color key at the top left). An online tool of iTOL was used to construct this tree.</p

Boxplots for comparison of bacterial loads by qPCR and bacterial relative abundances by 454 pyrosequencing.

<p>(a) Boxplot for total bacterial load. (b) Boxplots for the total loads of genera <i>Bifidobacterium</i>, <i>Lactobacillus</i>, and species <i>Streptococcus mutans</i>. (c) Boxplots for the pyrosequencing relative abundances of the same taxa as (b). Gene copy number shown above was transformed by natural logarithm (ln) and relative abundance was transformed by percent (%). * denotes P < 0.1; ** denotes P < 0.05; *** denotes P < 0.01.</p

Samples clustering by PCoA.

<p>All PCoA plots were first constructed on the basis of unweighted UniFrac distance (see the panel at the top left). Then the points in PCoA plots were weighted by the relative abundances of the top 12 root caries-associated species and top 12 health-associated species of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117064#pone.0117064.g005" target="_blank">Fig. 5</a>.</p