Cumulative production of SCFA.

<p>A) acetate, B) propionate, C) <i>n</i>-butyrate and D) lactate produced during 72 h fermentation of apple fiber, sugar beet pectin, GOS and lactulose using microbiota from lean or obese subjects.</p

MOESM2 of The fungal composition of natural biofinishes on oil-treated wood

Additional file 2: Table S2. Fungal isolates of each colony type with their culture collection numbers and GenBank accession numbers for the sequenced loci

MOESM4 of The fungal composition of natural biofinishes on oil-treated wood

Additional file 4: Table S4. Illumina amplicon sequences identified by a BLAST search against the database of GenBank, Q-bank and CBS (type strains of the CBS Barcoding database were selected from data generated until September 2015). Sequences were identified to genus level when possible and marked as ‘unidentified genus’ when BLAST resulted in hits with an identity below 97%. The number of reads of each unique sequence is listed for each sample

Energy extraction.

<p>Values obtained after 72 h fermentation of GOS, lactulose, apple fiber and sugar beet using microbiota from lean or obese subjects. Total energy extraction for control-L and -O were 176 and 162 kJ, respectively. The calculation was performed by multiplying the SCFA and lactate produced by their corresponding kJ mol⁻¹ value as explained in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113864#s2" target="_blank">materials and methods</a> section.</p

MOESM3 of The fungal composition of natural biofinishes on oil-treated wood

Additional file 3: Table S3. ITS specific clones inferred from biofinish DNA, their identification and GenBank accession number

Diversity of species and genera found within different honey bee colony environments.

<p>(A) Venn diagram representation of species-level diversity (97% identity) of the active bacterial communities that were found within three bee-associated sampling environments (bee bread, bee guts, and whole bees), pooled across colony type. The total species richness in the dataset was 1,019 OTUs, with the most species-rich environment being bee guts (824 total species). (B) The core microbiota among all three environments included 103 species that spanned 26 genera, with <i>Oenococcus</i> and <i>Succinivibrionaceae</i> comprising the largest fractions.</p

Relative change of bacterial genera after 72 h of fermentation experiments in TIM-2¹.

1<p>The ratio between a sampling time point and t₋₁₆ was calculated (e.g., t₇₂/t₋₁₆). The ratio for this value and the pool was then determined to obtain fold changes. A value equal to 1 indicates no change; a value of >1 indicates an increase; and a value of <1 indicates a decrease of the respective microbial genera. Sequences of the 16S rDNA gene that are not fully available in the database but represent a high similarity in the genus tagged are presented as unclassified groups and are listed in the table as OTU###, with ### being a number.</p><p>Relative change of bacterial genera after 72 h of fermentation experiments in TIM-2^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113864#nt101" target="_blank">1</a>}.</p

Genetically diverse colonies are host to more active, potentially probiotic genera and fewer potentially pathogenic genera.

<p>Number of sequences in bee guts sampled from genetically uniform and genetically diverse colonies, classified into potential pathogenic and probiotic genera. Total number of sequences sampled for each colony type is given in parentheses in the header bar, and fraction of colonies sampled that had these pathogenic or probiotic genera is in parentheses for each genus. The same 7 genetically uniform and 5 genetically diverse colonies had these pathogens present (i.e., a colony either had all three pathogens in it, or none of them).</p

Honey bee colony samples cluster according to environment sampled.

<p>(A) Weighted, species-based (97% identity) Unifrac clustering of sampled environments in each study colony, with clades colored coded by environment. Additionally, branches representing the microbiota found in genetically uniform colonies are colored in red; black branches are genetically diverse colonies. (B) Each column below a Unifrac tree tip is the ranked abundance of bacterial classes found that sample, represented as a heat map; the most active classes were Bacilli and γ-proteobacteria. Bee-gut samples (in lavender) cluster to the exclusion of whole-bee (in green) and bee-bread samples (in pink), largely because of the presence of <i>Succinovibrionaceae</i>.</p

Sequence abundance of the 13 most active taxa from each colony environment that affiliated with distinct phylogenetic groups.

1<p>unclassified (could not classify beyond family for this group).</p><p>Percentage of total sequences (classified into genera) are given, as well as the number of species (based on 97% sequence identity) that was found within each genus in parentheses. See supplementary materials for a complete list of all bacterial sequences from the sampled environments from each study colony (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032962#pone.0032962.s005" target="_blank">Tables S2</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032962#pone.0032962.s006" target="_blank">S3</a>).</p