Phenotypic and genotypic characteristics of O157:non-H7 and O157:H7 strains used in this study.

a<p>Sor, Sorbitol fermentation.</p>b<p>GUD, β-glucuronidase activity.</p>c<p>O-serogroup detected by the <i>E. coli</i> O157-specific antibody.</p>d<p>H-serogroup detected by the <i>E. coli</i> H-specific antibodies. NM; non-motile, UT; untypeable.</p>e<p>genotype detected by the PCR-RFLP assay of the <i>fliC</i> gene. UT; untypeable.</p>f<p>genotype detected by the PCR assay of the <i>eae</i> gene.</p

Schematic drawing of REP sequence-containing regions of O157-antigen biosynthesis gene cluster flanking regions.

<p>(A) Sequence alignment of the REP sequences located in the O157-antigen gene cluster flanking regions. The consensus sequence is derived from previously published data <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023250#pone.0023250-Stern2" target="_blank">[40]</a>. The palindromic motif is underlined. The non-consensus sequences were highlighted. (B) Four regions showing insertion and/or deletion of fragments including REP sequence(s); <i>yeeZ-hisG</i>, <i>hisI-wzz wcaK-wzxC</i> and <i>cpsG-cpsB</i> are compared between strains. REP sequences are indicated by arrowheads and gray boxes indicate missing regions on each of the compared strains. (C) The nucleotide sequences from <i>wcaK</i> to <i>wzxC</i> and from <i>wcaA</i> to <i>wzc</i> on EC95-42 are compared with those of PV57, and the sequences from <i>hisI</i> to <i>wzz</i> on PV01-185 are compared with those of Sakai. Locations of SNPs by pairwise sequence comparison are indicated by vertical lines (lower panel).</p

Comparisons of the O157-antigen biosynthesis gene clusters and their flanking regions in six O157 strains.

<p>(A) Genetic organization of the O157-antigen gene clusters and their flanking regions. Red arrows indicate orthologs associated with the O157-antigen biosynthesis, and white arrows indicate ORFs that are not conserved in all six strains. Arrowheads indicate insertion sites of REP sequences. (B–D) Pairwise sequence comparisons. (B) Comparisons between O157 strains carrying “Sakai-type <i>rfbE</i>”. (C) Comparisons between O157 strains carrying “PV01-185-type <i>rfbE</i>”. (D) Comparisons between “Sakai-type <i>rfbE</i>” and “PV01-185-type <i>rfbE</i>” strains. Sakai is compared with PV01-185, and EC95-42 is compared with PV276. The genetic organization of the O157-antigen gene clusters and their flanking regions are shown in upper panels, and levels of % DNA sequence identity calculated with a 100 bp sliding window and a 10 bp step size are shown in lower panels. The vertical lines indicate regions showing insertion and/or deletion of fragments, and of them, lines with circular heads indi cate indels containing REP sequences.</p

A Single-Batch Fermentation System to Simulate Human Colonic Microbiota for High-Throughput Evaluation of Prebiotics

<div><p>We devised a single-batch fermentation system to simulate human colonic microbiota from fecal samples, enabling the complex mixture of microorganisms to achieve densities of up to 10¹¹ cells/mL in 24 h. 16S rRNA gene sequence analysis of bacteria grown in the system revealed that representatives of the major phyla, including Bacteroidetes, Firmicutes, and Actinobacteria, as well as overall species diversity, were consistent with those of the original feces. On the earlier stages of fermentation (up to 9 h), trace mixtures of acetate, lactate, and succinate were detectable; on the later stages (after 24 h), larger amounts of acetate accumulated along with some of propionate and butyrate. These patterns were similar to those observed in the original feces. Thus, this system could serve as a simple model to simulate the diversity as well as the metabolism of human colonic microbiota. Supplementation of the system with several prebiotic oligosaccharides (including fructo-, galacto-, isomalto-, and xylo-oligosaccharides; lactulose; and lactosucrose) resulted in an increased population in genus <i>Bifidobacterium</i>, concomitant with significant increases in acetate production. The results suggested that this fermentation system may be useful for <i>in vitro</i>, pre-clinical evaluation of the effects of prebiotics prior to testing in humans.</p></div

Changes in production of acetate, propionate, and butyrate after 24 h of fermentation in the single-batch systems using medium supplemented with the prebiotics (FOS, GOS, IMO, XOS, raffinose, lactulose, or lactosucrose).

<p>Samples of human feces (designated F37, F23, M38, F35, M24, or M43) were used to inoculate each system. Changes are presented as the ratio of concentration in the experimental system normalized to that in the control system (without added prebiotics). The control system generated acetate, propionate, and butyrate at concentrations (mean±SD, n = 6) of 104.0±16.3, 28.4±10.1, and 14.8±5.3 mM, respectively.</p

Additional file 14: of Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study

Relative abundance of predicted D-Xylose transporter (KEGG module: M00215). The KEGG module M00215 consists of three KO entries, K10543, K10544 and K10545. Each number indicates a group as shown in Table 1. Box-plots show the interquartile range (IQR) of the relative abundance of the predicted D-Xylose transporter. Open circles indicate outliers from 1.5- to 3.0-fold IQR. (PDF 96 kb

Additional file 13: of Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study

Hierarchical Ward’s linkage clustering based on the proportion of transporter genes predicted by PICRUSt. Age-related groups (adult-enriched and infant/elderly-enriched clusters) were revealed by Ward’s linkage clustering using the squared Euclidean distance. The population densities (z-score) of the transporters scaled by color are displayed together with a dendrogram of the transporters in a heat map. The colors within the horizontal clustering represent the age-segmented groups as shown in Fig. 1 The color code for the vertical clustering indicates KEGG Orthology (KO) as follows: white, ABC Transporters, Eukaryotic Type; yellow, ABC Transporters, Prokaryotic Type; blue, Solute Carrier Family (SLC); orange, Major Facilitator Superfamily (MFS); red, Phosphotransferase System (PTS); and green, Other Transporters. (PDF 209 kb

Bacterial diversity measures by observed species and Shannon-Wiener index in three human volunteers’ feces (F37-1: female, age 37; F37-2: female, age 37; and M54: male, age 54) and corresponding cultures at 6, 9, and 24 h after the initiation of fermentation.

<p>The Shannon-Wiener diversity index characterizes the diversity in a community, i.e., species abundance and evenness.</p

Additional file 10: of Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study

Taxa that are found in more than 50 % of the subjects in any cluster (shown in Additional file 8) with significantly difference between adult 1 and adult 2 clusters. (XLSX 857 kb

Principal component analysis (PCA) of 16S metagenomic data of bacterial species in three human volunteers’ feces (–) (F37-1: female, age 37; F37-2: female, age 37; and M54: male, age 54) and corresponding cultures at 6, 9, and 24 h after the initiation of fermentation.

<p>F37-1, F37-2, and M54 are indicated in blue, orange, and green, respectively. The numbers indicate the sampling time points.</p