Additional file 4: Figure S3. of Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns

Correlation between Prevotella (A) and Bacteroides (B) oligotypes and metabolome. Heatplot showing Spearman’s correlations between oligotypes, urinary TMAO and faecal SCFA levels. Rows and columns are clustered by Euclidean distance and Ward linkage hierarchical clustering. The intensity of the colours represents the degree of association between oligotypes and metabolites as measured by Spearman’s correlations. Asterisks denote significant correlations after P value corrections (P < 0.05). (TIF 8860 kb

Additional file 2: Table S1A. of Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns

Prevotella oligotypes representative sequences and BLASTn top hit. Table S1B. Bacteroides oligotypes representative sequences and BLASTn top hit. (DOCX 129 kb

Score plot and loading plot of the first and secondary principal components based on area and number peaks obtained from reverse phase high pressure liquid chromatography (RP-HPLC).

<p>Score plot and loading plot (panels 1, 3, 5) of the first and secondary principal components (PC) (panels 2, 4, 6) after PC analysis based on area and number peaks obtained from reversed-phase high-protein liquid chromatograms of the pH 4.6-soluble fractions of Fiore Sardo (A), Pecorino Siciliano (B) and Pecorino Toscano (C). Nine sub-blocks are identified by the letters A—I. Sub-blocks A, D, and G, and sub-blocks C, F and I were collected from top and bottom surface region, respectively, whereas sub-blocks B and H from inner side region, and sub-block E from the core. The whole slice was the control Control. Further details were reported in the Material and Methods and in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0153213#pone.0153213.g001" target="_blank">Fig 1</a>.</p

Concentrations of total free amino acids (FAA) (mg/kg) identified in Fiore Sardo, Pecorino Siciliano and Pecorino Toscano cheeses.

<p>Nine sub-blocks are identified by the letters A—I. Sub-blocks A, D, and G, and sub-blocks C, F and I were collected from top and bottom surface region, respectively, whereas sub-blocks B and H from inner side region, and sub-block E from the core. The whole slice was the control Control. Further details were reported in the Material and Methods and in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0153213#pone.0153213.g001" target="_blank">Fig 1</a>.</p

Operational taxonomic unit (OTUs) occurring at 0.1% abundance in at least one sample and related number, assigned to the species level when such assignment was possible of Fiore Sardo, Pecorino Siciliano and Pecorino Toscano cheeses.

<p>Operational taxonomic unit (OTUs) occurring at 0.1% abundance in at least one sample and related number, assigned to the species level when such assignment was possible of Fiore Sardo, Pecorino Siciliano and Pecorino Toscano cheeses.</p

Correlations between the abundance of operational taxonomic units (OTUs) and proteolysis and synthesis of volatile components.

<p>Correlations between the abundance of OTUs and total free amino acid (FFA), concentration of Ser, Glu, Asp, and Arg, number of hydrophilic peaks of the pH 4.6-soluble nitrogen fractions, and volatile components (arbitrary units of area) identified from Fiore Sardo, Pecorino Siciliano, and Pecorino Toscano cheeses. Euclidean distance and McQuitty’s criterion (weighted pair group method with averages) were used for clustering. The colors correspond to normalized mean data levels from low (grey) to high (yellow). The color scale, in terms of units of standard deviation, is shown at the top. Only the positive correlations with a P<0.05, FDR<0.05 and r>0.7 are reported. <i>Lactococcus lactis</i>, Lc. lactis; <i>Streptococcus thermophilus</i>, Sc. thermophilus; <i>Staphylococcus equorum</i>, St. equorum; <i>Lactobacillus plantarum</i>, Lb. plantarum; <i>Lactobacillus brevis</i>, Lb. brevis; <i>Lactobacillus coryniformis</i>, Lb. coryniformis; <i>Lactobacillus helveticus</i>, Lb. helveticus; <i>Lactobacillus delbrueckii</i>, Lb. delbruekii; <i>Lactobacillus</i> sp., Lb. sp; <i>Lactobacillus crustorum</i>, Lb. crustorum; <i>Lactobacillus buchneri</i>, Lb. buchneri; <i>Lactobacillus parabuchneri</i>, Lb. parabuchneri; <i>Brevibacterium</i> sp., B; <i>Brachybacterium</i> sp., Br; <i>Halomonas variabilis</i>, H. variabilis; Art, <i>Arthrobacter</i>.</p

Cell numbers (log CFU/g)^* of various microbial groups in Fiore Sardo, Pecorino Siciliano and Pecorino Toscano cheeses.

<p>Cell numbers (log CFU/g)<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0153213#t001fn002" target="_blank">^*</a> of various microbial groups in Fiore Sardo, Pecorino Siciliano and Pecorino Toscano cheeses.</p

Abundance and number of operational taxonomic units (OTUs) assigned at genus level occurring in Fiore Sardo, Pecorino Siciliano, and Pecorino Toscano cheeses.

<p>Distribution of the OTUs assigned at genus level occurring in Fiore Sardo (A), Pecorino Siciliano (B), and Pecorino Toscano (C) cheese. Nine sub-blocks are identified by the letters A—I. Sub-blocks A, D, and G, and sub-blocks C, F and I were collected from top and bottom surface region, respectively, whereas sub-blocks B and H from inner side region, and sub-block E from the core. The whole slice was the control. Further details were reported in the Material and Methods and in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0153213#pone.0153213.g001" target="_blank">Fig 1</a>.</p

Image_1_Dynamic and Assembly of Epiphyte and Endophyte Lactic Acid Bacteria During the Life Cycle of Origanum vulgare L..pdf

<p>Origanum vulgare L. (oregano) was chosen as suitable model to investigate the ability of the endophyte-microbiome, especially that of lactic acid bacteria, to develop specific interactions with the plant, mediated by the essential oils (EOs). Combined culture-dependent and -independent approaches analyzed the bacterial dynamic and assembly of Origanum vulgare L. throughout the life cycle. Epiphyte bacteria were more abundant than the endophyte ones. The number of presumptive lactic acid bacteria increased throughout oregano life cycle, according to the plant organ. Diverse species of lactic acid bacteria populated the plant, but Lactobacillus plantarum stably dominated both epiphyte and endophyte populations. High-throughput DNA sequencing showed highest epiphyte bacterial diversity at early vegetative and full-flowering stages, with blooming signing the main microbial differentiation among plant organs. Proteobacteria, Actinobacteria and Bacteroidetes, and Firmicutes and Cyanobacteria at lower abundance were the main phyla. Various genera were detectable, but oregano harbored mainly Methylobacterium, Sphingomonas, Rhizobium and Aurantimonas throughout phenological stages. Firmicutes epiphyte and endophyte microbiotas were different, with a core microbiota consisting of Bacillus, Exiguobacterium, Streptococcus, Staphylococcus and Lactobacillus genera. Bacillus dominated throughout phenological stages. High-throughput DNA sequencing confirmed the dominance of L. plantarum within the epiphyte and endophyte populations of lactic acid bacteria. Yields of EOs varied among plant organs and throughout plant life cycle. L. plantarum strains were the most resistant to the total EOs (mainly thymol and carvacrol) as extracted from the plant. The positive correlation among endophyte lactic acid bacteria and the EOs content seems confirm the hypothesis that the colonization within plant niches may be regulated by mechanisms linked to the synthesis of the secondary metabolites.</p

Table_1_Dynamic and Assembly of Epiphyte and Endophyte Lactic Acid Bacteria During the Life Cycle of Origanum vulgare L..pdf

<p>Origanum vulgare L. (oregano) was chosen as suitable model to investigate the ability of the endophyte-microbiome, especially that of lactic acid bacteria, to develop specific interactions with the plant, mediated by the essential oils (EOs). Combined culture-dependent and -independent approaches analyzed the bacterial dynamic and assembly of Origanum vulgare L. throughout the life cycle. Epiphyte bacteria were more abundant than the endophyte ones. The number of presumptive lactic acid bacteria increased throughout oregano life cycle, according to the plant organ. Diverse species of lactic acid bacteria populated the plant, but Lactobacillus plantarum stably dominated both epiphyte and endophyte populations. High-throughput DNA sequencing showed highest epiphyte bacterial diversity at early vegetative and full-flowering stages, with blooming signing the main microbial differentiation among plant organs. Proteobacteria, Actinobacteria and Bacteroidetes, and Firmicutes and Cyanobacteria at lower abundance were the main phyla. Various genera were detectable, but oregano harbored mainly Methylobacterium, Sphingomonas, Rhizobium and Aurantimonas throughout phenological stages. Firmicutes epiphyte and endophyte microbiotas were different, with a core microbiota consisting of Bacillus, Exiguobacterium, Streptococcus, Staphylococcus and Lactobacillus genera. Bacillus dominated throughout phenological stages. High-throughput DNA sequencing confirmed the dominance of L. plantarum within the epiphyte and endophyte populations of lactic acid bacteria. Yields of EOs varied among plant organs and throughout plant life cycle. L. plantarum strains were the most resistant to the total EOs (mainly thymol and carvacrol) as extracted from the plant. The positive correlation among endophyte lactic acid bacteria and the EOs content seems confirm the hypothesis that the colonization within plant niches may be regulated by mechanisms linked to the synthesis of the secondary metabolites.</p