TaqMan qPCR quantification of bacterial 16S rRNA coding regions showing lower abundance in patients undergoing chemotherapy and antibiotic treatment (P) than healthy controls (C).

<p>T₀, samples taken before a single shot of chemotherapy; T₁, 1–2 days after chemotherapy; T₂, 5–9 days after chemotherapy; Asterisk indicates a significant difference at p<0.05.</p

Number of bands observed in PCR-DGGE fingerprinting in oncology patients before chemotherapy (T₀), immediately after chemotherapy (T₁) and 5–9 days after chemotherapy (T₂) and healthy controls averaged over all time points.

<p>Number of bands observed in PCR-DGGE fingerprinting in oncology patients before chemotherapy (T₀), immediately after chemotherapy (T₁) and 5–9 days after chemotherapy (T₂) and healthy controls averaged over all time points.</p

Heatmap showing abundances within the 454 sequencing dataset on the genus level.

<p>High throughput sequencing of samples P09 and P11 before (T₀) and after therapy (T₁) further helped to characterize the influence of a single chemotherapeutic cycle on the GI-microbiota. P11 was treated with chemotherapy alone and P09 also received antibiotic treatment.</p

Abundances of bacterial 16S rRNA coding regions over time in oncology patients (P) and healthy controls (C).

<p>The declined abundances of bacteria, <i>Bacteroides</i>, <i>Clostridium</i> cluster <i>XIVa</i>, <i>Clostridium</i> cluster <i>IV</i> and bifidobacteria immediately after chemotherapy (T₁) were observed to recover several days after treatment (T₂). Patients P04, P08 and P13 had never received chemotherapy before; P04, P05, P07, P08, P09 and P10 took antibiotics. Values were z-scored for presentation in this heatmap showing changes over time rather than absolute abundances. T₀, before chemotherapy; T₁, 1–2 days after chemotherapy; T₂, 5–9 days after chemotherapy; F, fever; S, blood stem cell transplantation.</p

16S rRNA gene primers used for PCR-DGGE fingerprinting.

<p>16S rRNA gene primers used for PCR-DGGE fingerprinting.</p

A PCR-DGGE fingerprinting of 16S rRNA coding regions of dominant bacteria over time.

<p>Bands that become stronger or nearly disappear following a single chemotherapeutic treatment are indicated with arrows. B Principal components analysis (PCA) based on dominant bacteria PCR-DGGE fingerprinting. The two outliers in the lower right corner of the plot are two samples of P07 following blood stem cell transplantation. C PCA illustrating the development of <i>Clostridium</i> cluster <i>IV</i> diversity in the course of chemotherapy and antibiotic treatment. Cluster <i>IV</i> diversity drops right after chemotherapy, causing a grouping of samples. Samples under antibiotic treatment (indicated as grey dots) group even closer, indicating a strong influence of antibiotics on <i>Clostridium</i> cluster <i>IV</i> diversity. A, sample of P01 before chemotherapy B, C and D, samples of P01 after chemotherapy; E, healthy control; SL, unrelated standard lane; black symbols… patients under chemotherapy and antibiotic treatment.</p

Phylogenetic tree showing the <i>Peptostreptococcaceae</i> found in samples from two oncology patients before and after chemotherapy.

<p>Identical sequences were grouped; the table on the right hand side shows their abundances in the 454 sequencing dataset. Sequences with >98.9% similarity to <i>Clostridium difficile</i> appeared only in samples taken immediately after chemotherapeutic cycles. Numbers indicate bootstrap values after 100 resamplings.</p

Primers and probes used for TaqMan qPCR quantification of 16S rRNA genes.

<p>Primers and probes used for TaqMan qPCR quantification of 16S rRNA genes.</p

Relevant clinical data of study participants undergoing immunesuppressive chemotherapy.

<p>PBSCT… peripheral blood stem cell transplant.</p