Additional file 2: of Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut

Summary of DNA concentrations obtained from the PPs extracted with optimized and adapted methods. The concentrations of DNA were determined by fluorometry. Values shown represent the measurements of three fecal samples using two biological replicates. (1.08 MB

Additional file 1: of Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut

Description of samples (per subject) used for evaluation of the optimized routes for pre-processing and purification of fecal bacteriophages for virome characterization. The first biological replicates/extractions are represented by X1, Y1 and Z1, while the second one by X2, Y2 and Z2 (each of them were extracted with LIT, PEG and TFF for a total of 18 extractions). All samples and replicates were used for analysis of spiked phage recovery (c2, ϕ29 and T4 phages) and quantification of PPs/DNA. TEM analyses were only carried out with replicates obtained from extractions X1 and Y1 (carried out with LIT, PEG and TFF). The construction of metaviromes was performed using the bacteriophages obtained from Subject X and extracted with LIT, PEG and TFF. (874 KB

Additional file 7: of A prebiotic intervention study in children with autism spectrum disorders (ASDs)

Figure S6. OPLS-DA obtained comparing the metabolic profile in faecal samples of ASD children in unrestricted diet taking B-GOS to those taking placebo. Compounds identified: dimethylglycine (DMG); glutamate; butyrate; valerate; ethanol; alanine; lactate; isoleucine; leucine; valine; uracil; phenylalanine; tyrosine. (PNG 100 kb

Additional file 2: of A prebiotic intervention study in children with autism spectrum disorders (ASDs)

Table S1. Bacterial groups (Log10) significantly associated with separation in RDA model (P < 0.004). (DOCX 15 kb

Additional file 4: of A prebiotic intervention study in children with autism spectrum disorders (ASDs)

Figure S3. (A) RDA model showing the separation between samples from ASD children following exclusion diet after the intervention (placebo vs B-GOS®). Blue dots: samples from children taking placebo; Pink dots: samples from children taking B-GOS®. (B) Bar chart of the most abundant bacteria in ASD children following exclusion diet after intervention (placebo vs B-GOS®; bacterial abundances above 1%). (JPG 174 kb

Additional file 6: of A prebiotic intervention study in children with autism spectrum disorders (ASDs)

Figure S5. OPLS-DA obtained comparing the metabolic profile in urine samples of ASD children in unrestricted diet taking B-GOSÂŽ to those taking placebo. Compounds identified: dimethylglycine (DMG); dimenthylalanine (DMA); creatinine; creatine; PAG (Phenylacetilglycine); cartine; malonate; TMAO (trimethylamine-N-oxide); citrate; adipate; beta-hydroxybutyrate; phenylalanine. (JPG 79 kb

Additional file 5: of A prebiotic intervention study in children with autism spectrum disorders (ASDs)

Figure S4. Analysis of the most abundant Bifidobacterium spp. using 16S rRNA sequencing. (1) before B-GOS®; (2) after B-GOS®; (3) before placebo; (4) after placebo; (5) unrestricted diet before B-GOS®; (6) unrestricted diet after B-GOS®; (7) unrestricted diet before placebo; (8) unrestricted diet after placebo; (9) exclusion diet before B-GOS®; (10) exclusion diet after B-GOS®; (11) exclusion diet before placebo; (12) exclusion diet after placebo. *P < 0.05. (JPG 65 kb

Additional file 1: of A prebiotic intervention study in children with autism spectrum disorders (ASDs)

Figure S1. Comparison of the gut microbiota composition between ASD children following exclusion diet and ASD children following unrestricted diet. (A) Sørensen-Dice distance based PCoA; (B) Bray-Curtis distance based PCoA. Red dots: exclusion diet; green dots: unrestricted diet. (JPG 51 kb

Additional file 3: of A prebiotic intervention study in children with autism spectrum disorders (ASDs)

Figure S2. Comparison of bacterial richness and diversity before and after B-GOS treatment in ASD children following unrestricted diet. Rarefaction curves and box plots showed that B-GOS supplementation increased the diversity in gut microbial composition of ASD children in unrestricted diet. (JPG 83 kb