Table_1_The interplay between gingival crevicular fluid microbiome and metabolomic profile in intensively treated people with type 1 diabetes - a combined metagenomic/metabolomic approach cross-sectional study.docx

AimsThis study aimed to assess the gingival crevicular fluid (GCF) microbiome and metabolome of adults with type 1 diabetes (T1D) treated with continuous subcutaneous insulin infusion (CSII).MethodsIn this cross-sectional study, the GCF of adults with T1D treated with CSII and non-diabetic controls were sampled, and metagenomic/metabolomic analyses were performed.ResultsIn total, 65 participants with T1D and 45 healthy controls with a mean age of 27.05 ± 5.95 years were investigated. There were 22 cases of mild gingivitis (G) in the T1D group. There were no differences considering the Shannon and Chao indices and β-diversity between people with T1D and G, with T1D without G, and healthy controls. Differential taxa were identified, which were mainly enriched in people with T1D and G. Acetic acid concentration was higher in people with T1D, regardless of the presence of G, than in healthy controls. Propionic acid was higher in people with T1D and G than in healthy controls. Isobutyric and isovaleric acid levels were higher in individuals with T1D and G than in the other two subgroups. The concentration of valeric acid was lower and that of caproic acid was higher in people with T1D (regardless of gingival status) than in healthy controls.ConclusionsThe identification of early changes in periodontal tissues by targeting the microbiome and metabolome could potentially enable effective prevention and initial treatment of periodontal disease in people with T1D.</p

DataSheet_1_The interplay between gingival crevicular fluid microbiome and metabolomic profile in intensively treated people with type 1 diabetes - a combined metagenomic/metabolomic approach cross-sectional study.docx

AimsThis study aimed to assess the gingival crevicular fluid (GCF) microbiome and metabolome of adults with type 1 diabetes (T1D) treated with continuous subcutaneous insulin infusion (CSII).MethodsIn this cross-sectional study, the GCF of adults with T1D treated with CSII and non-diabetic controls were sampled, and metagenomic/metabolomic analyses were performed.ResultsIn total, 65 participants with T1D and 45 healthy controls with a mean age of 27.05 ± 5.95 years were investigated. There were 22 cases of mild gingivitis (G) in the T1D group. There were no differences considering the Shannon and Chao indices and β-diversity between people with T1D and G, with T1D without G, and healthy controls. Differential taxa were identified, which were mainly enriched in people with T1D and G. Acetic acid concentration was higher in people with T1D, regardless of the presence of G, than in healthy controls. Propionic acid was higher in people with T1D and G than in healthy controls. Isobutyric and isovaleric acid levels were higher in individuals with T1D and G than in the other two subgroups. The concentration of valeric acid was lower and that of caproic acid was higher in people with T1D (regardless of gingival status) than in healthy controls.ConclusionsThe identification of early changes in periodontal tissues by targeting the microbiome and metabolome could potentially enable effective prevention and initial treatment of periodontal disease in people with T1D.</p

Results of PCA analysis of infant gut microbiome in infants delivered vaginally compared with those of infants delivered by cesarean section.

<p>Only 10 of the most abundant OTUs are shown. PC, principal component; var., variance; 0, day 0; 2w, 2 weeks; and 6w, 6 weeks after probiotic or placebo supplementation.</p

Image_3_Breast cancer but not the menopausal status is associated with small changes of the gut microbiota.jpeg

BackgroundPossible relationships between gut dysbiosis and breast cancer (BC) development and progression have been previously reported. However, the results of these metagenomics studies are inconsistent. Our study involved 88 patients diagnosed with breast cancer and 86 cancer-free control women. Participants were divided into groups based on their menopausal status. Fecal samples were collected from 47 and 41 pre- and postmenopausal newly diagnosed breast cancer patients and 51 and 35 pre- and postmenopausal controls, respectively. In this study, we performed shotgun metagenomic analyses to compare the gut microbial community between pre- and postmenopausal BC patients and the corresponding controls.ResultsFirstly, we identified 12, 64, 158, and 455 bacterial taxa on the taxonomy level of phyla, families, genera, and species, respectively. Insignificant differences of the Shannon index and β-diversity were found at the genus and species levels between pre- and postmenopausal controls; the differences concerned only the Chao index at the species level. No differences in α-diversity indexes were found between pre- and postmenopausal BC patients, although β-diversity differed these subgroups at the genus and species levels. Consistently, only the abundance of single taxa differed between pre- and postmenopausal controls and cases, while the abundances of 14 and 23 taxa differed or tended to differ between premenopausal cases and controls, and between postmenopausal cases and controls, respectively. There were similar differences in the distribution of enterotypes. Of 460 bacterial MetaCyc pathways discovered, no pathways differentiated pre- and postmenopausal controls or BC patients, while two and one pathways differentiated cases from controls in the pre- and postmenopausal subgroups, respectively.ConclusionWhile our findings did not reveal an association of changes in the overall microbiota composition and selected taxa with the menopausal status in cases and controls, they confirmed differences of the gut microbiota between pre- and postmenopausal BC patients and the corresponding controls. However, these differences were less extensive than those described previously.</p

Additional file 2: Figure S1. of Prolonged transfer of feces from the lean mice modulates gut microbiota in obese mice

Rarefraction curves from all samples on family level drawn with MEGAN5 software. (PDF 4369 kb

Relative levels of bacterial DNA extracted from fecal samples in preterm infants delivered vaginally (VD) or by cesarean section (CS).

<p>0, day 0; 2w, 2 weeks; and 6w, 6 weeks after supplementation.</p

Boxplot of community α diversity, as expressed by the Simpson index, categorized according to the administration of the probiotic <i>Saccharomyces boulardii</i> (<i>S</i>. <i>Boulardii</i>) or placebo at 2 (2w) and 6 (6w) weeks following intervention.

<p>P-values in Mann-Whitney U-test are shown for respective times.</p

Additional file 1: Tables S1–S5. of Prolonged transfer of feces from the lean mice modulates gut microbiota in obese mice

Table S1. Taxonomic Assignments Table. Full taxonomic assignments in SILVA Taxonomy, as classified by Mothur. Taxa are given with bootstrap values for each taxonomic level. Taxa are classified to family, unless there was only one classifiable genus (or lower level) present in the family. Table S2. Serum biochemical parameters at the end of the experiment. Normal diet (ND), high-fat diet (HFD), HFD supplemented with feces of ND-fed mice (HFDS). Table S3. Differential taxa abundances between weeks 0 and 12 and weeks 0 and 28, tested with paired Mann-Whitney U-tests for each experimental group. Taxon = taxon denotation (full taxonomic assignments in SILVA taxonomy are presented in Additional file 1: Table S1); Mann-Whitney U statistic = statistic from paired Mann-Whitney U-tests; pValue = p-value from paired Mann-Whitney U-test; qValue = p-value after FDR correction. Table S4. Results of model comparison for taxa. Taxon = taxon denotation (full taxonomic assignments in SILVA taxonomy are presented in Additional file 1: Table S1); pValue time and pValue diet = p-values for comparisons between null models, models including time and models including time and diet, respectively; qValue time and diet = p-values after FDR correction. Table S5. Differential taxa abundances at 12 and 28 weeks. Taxon = bacteria taxon in SILVA taxonomy, genera (if applicable) are given in parentheses; week = week of experiment; comparison = groups compared; mean 1 group = mean abundance of taxon in first group in comparison field; mean 2 group = mean abundance of taxon in second group; pValue = p-value of Mann-Whitney U-tests; qValue = p-value after FDR correction. Taxa that were differentiated in two groups at both time points are highlighted in bold text. (XLSX 60 kb

Boxplot of community α diversity at day 0 (prior to supplementation) according to the Simpson index and categorized according to gestational age at birth.

<p>Data are shown only for the weeks in which at least five infants were born.</p

Image_2_Breast cancer but not the menopausal status is associated with small changes of the gut microbiota.jpeg

BackgroundPossible relationships between gut dysbiosis and breast cancer (BC) development and progression have been previously reported. However, the results of these metagenomics studies are inconsistent. Our study involved 88 patients diagnosed with breast cancer and 86 cancer-free control women. Participants were divided into groups based on their menopausal status. Fecal samples were collected from 47 and 41 pre- and postmenopausal newly diagnosed breast cancer patients and 51 and 35 pre- and postmenopausal controls, respectively. In this study, we performed shotgun metagenomic analyses to compare the gut microbial community between pre- and postmenopausal BC patients and the corresponding controls.ResultsFirstly, we identified 12, 64, 158, and 455 bacterial taxa on the taxonomy level of phyla, families, genera, and species, respectively. Insignificant differences of the Shannon index and β-diversity were found at the genus and species levels between pre- and postmenopausal controls; the differences concerned only the Chao index at the species level. No differences in α-diversity indexes were found between pre- and postmenopausal BC patients, although β-diversity differed these subgroups at the genus and species levels. Consistently, only the abundance of single taxa differed between pre- and postmenopausal controls and cases, while the abundances of 14 and 23 taxa differed or tended to differ between premenopausal cases and controls, and between postmenopausal cases and controls, respectively. There were similar differences in the distribution of enterotypes. Of 460 bacterial MetaCyc pathways discovered, no pathways differentiated pre- and postmenopausal controls or BC patients, while two and one pathways differentiated cases from controls in the pre- and postmenopausal subgroups, respectively.ConclusionWhile our findings did not reveal an association of changes in the overall microbiota composition and selected taxa with the menopausal status in cases and controls, they confirmed differences of the gut microbiota between pre- and postmenopausal BC patients and the corresponding controls. However, these differences were less extensive than those described previously.</p