Comparison of sequence libraries generated by cloning and by barcoded pyrosequencing of ITS1 genes.

<p>Cluster analysis of clone libraries (prefixed CL) and pyrosequencing libraries (prefixed PL) constructed from 6 different rumen samples based on anaerobic fungal ITS1 gene sequences using the Bray-Curtis distance metric and UPGMA treeing. DNA was extracted twice from the rumen sample of sheep S4 on summer pasture, and two independent pyrosequencing libraries (suffixed 1 and 2) were constructed for this sample. Abbreviations are used as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036866#pone-0036866-g001" target="_blank">Figure 1</a>. The length of the scale bar represents anaerobic fungal community dissimilarity of 10%.</p

Clone library prefixes, numbers of clones sequenced from each library, and corresponding GenBank accession numbers.

<p>Clone library prefixes, numbers of clones sequenced from each library, and corresponding GenBank accession numbers.</p

Spearman's rank correlation matrix of the dominant microbial populations across domains in analyzed rumen samples.

<p>Microbial populations listed represent at least 1% of the bacterial, archaeal, ciliate, or fungal communities in at least one sample and were detected in at least 50% of the rumen samples analyzed. Strong correlations are indicated by large squares, whereas weak correlations are indicated by small squares. The colours of the scale bar denote the nature of the correlation with 1 indicating perfect positive correlation (dark blue) and -1 indicating perfect negative correlation (dark red) between two microbial populations. Correlations marked with circles are discussed in the text.</p

Macronutrient profile of a commercially available Association of American Feed Control Officials (AAFCO) feed tested maintenance diets fed to domestic short hair kittens (<i>Felis catus</i>).

1<p>Ingredient list of Diet A (from pack): Corn, chicken and chicken meal, chicken digest, maize gluten, chicken tallow, tuna meal, poultry and poultry meal, iodinised salt, vegetable oil.</p>2<p>Ingredient list of Diet B (from pack): Meat by-products and meat derived from chicken, lamb, beef, and mutton; gelling agent; minerals; vegetable oil, emulsifier; colouring; vitamins, chelating agents.</p>3<p>Nitrogen free extractables calculated by difference (100 - crude protein - crude fat - crude fibre - ash).</p>4<p>Determined using modified Atwater factors of: crude protein (3·5 kcal ME/g DM), crude fat (8·5 kcal ME/g DM), NFE (3·5 kcal ME/g DM).</p

Overview of rumen samples analyzed in this study.

a<p>animals were grazing freely, ^b diets were administered to the animals, ^c DNA extracted twice from two subsamples and labelled S4SG1PN and S4SG2PN.</p><p>The rumen samples analyzed in this study were obtained from sheep, cattle, and red deer feeding on different diets. Samples were taken via a rumen fistula, via stomach tubing, or at slaughter. Animals with the same herd/flock number were co-housed at the location indicated.</p

Principal Coordinate Analysis plot of weighted Unifrac phylogenetic distances showing the similarities between bacterial communities of queens fed Diet A or Diet B and their offspring fed Diet A (B-A or A-A) or Diet B (B-B or A-B) post-weaning.

<p>Percentage of variation captured by each component indicated on axes.</p

Distribution of barcode mappable and quality-filtered sequencing reads across domains for each mixing ratio tested.

<p>The mixing ratios represent bacteria:archaea:ciliate protozoa (1∶1∶1), and bacteria:archaea:ciliate protozoa:fungi (5∶1∶1∶1 and 5∶1∶1∶0.2).</p

Faecal Microbiota of Forage-Fed Horses in New Zealand and the Population Dynamics of Microbial Communities following Dietary Change

<div><p>The effects of abrupt dietary transition on the faecal microbiota of forage-fed horses over a 3-week period were investigated. Yearling Thoroughbred fillies reared as a cohort were exclusively fed on either an ensiled conserved forage-grain diet (“Group A”; n = 6) or pasture (“Group B”; n = 6) for three weeks prior to the study. After the Day 0 faecal samples were collected, horses of Group A were abruptly transitioned to pasture. Both groups continued to graze similar pasture for three weeks, with faecal samples collected at 4-day intervals. DNA was isolated from the faeces and microbial 16S and 18S rRNA gene amplicons were generated and analysed by pyrosequencing. The faecal bacterial communities of both groups of horses were highly diverse (Simpson’s index of diversity >0.8), with differences between the two groups on Day 0 (<i>P</i><0.017 adjusted for multiple comparisons). There were differences between Groups A and B in the relative abundances of four genera, BF311 (family Bacteroidaceae; <i>P</i> = 0.003), CF231 (family Paraprevotellaceae; <i>P</i> = 0.004), and currently unclassified members within the order Clostridiales (<i>P</i> = 0.003) and within the family Lachnospiraceae (<i>P</i> = 0.006). The bacterial community of Group A horses became similar to Group B within four days of feeding on pasture, whereas the structure of the archaeal community remained constant pre- and post-dietary change. The community structure of the faecal microbiota (bacteria, archaea and ciliate protozoa) of pasture-fed horses was also identified. The initial differences observed appeared to be linked to recent dietary history, with the bacterial community of the forage-fed horses responding rapidly to abrupt dietary change.</p></div

Correlations between selected groups of microorganisms.

<p>Correlation between relative abundances of (A) <i>Bacteroidales</i>- and <i>Clostridiales</i>-related sequencing reads, and (B) methanogens of the <i>Methanobrevibacter ruminantium</i> and <i>M. gottschalkii</i> clades in pyrosequencing libraries of the 12 analyzed DNA samples.</p

The effects of pre-weaning (gestation and lactation) or post-weaning (Diet A or Diet B) diets on the different bacterial genera (proportion of total sequences) present in at least 5 faecal samples from the domestic kitten (<i>Felis catus</i>; n = 5 per treatment) at a level of 0.5% or higher.

<p>Diet A- Diet B (A-B) n = 3 females, n = 2 males.</p><p>Diet B- Diet A (B-A) n = 3 females, n = 2 males.</p><p>Diet B- Diet B (B-B) n = 4 females, n = 1 male.</p>1<p>Comparisons between Diets A-A and A-B vs B-A and B-B.</p>2<p>Comparison between Diets A-A and B-A and B-B and A-B.</p><p>Results represent an average of samples taken at week 8 and 17. <i>P value</i> indicates ANOVA significance of rank transformed data and False discovery Rate (<i>FDR)</i> indicates multiple testing adjusted <i>P</i> value. Diet A-Diet A (A-A) n = 3 females, n = 2 males.</p