Functional classification of genes induced in CEFs after infection with wild-type <i>S</i>. Enteritidis.

<p>Genes are ranked in descending order of their expression fold change. Functional annotation of genes was performed with the STRING database v9.1. and is represented by gene ontology (GO) terms for biological process (BP).</p

Interaction analysis of genes inducible in CEFs infected with <i>S</i>. Enteritidis.

<p>Figure presents a confidence view of protein interactions in chicken (<i>Gallus gallus</i>) generated by the STRING Database v9.1 for genes significantly upregulated more than threefold in CEFs in response to both <i>Salmonella</i> strains. Lines represent associations based on experimental data, co-expression, databases and/or homology.</p

List of OTUs and their taxonomic classification found in at least 40 out of 45 samples tested by pyrosequencing 16S rRNA genes.

<p>List of OTUs and their taxonomic classification found in at least 40 out of 45 samples tested by pyrosequencing 16S rRNA genes.</p

List of primers used in this study.

<p>List of primers used in this study.</p

Antibiotic resistance gene prevalence in poultry fecal microbiota.

<p>Antibiotic resistance gene prevalence is presented as the median with 25^th and 75^th percentile (box) and the whiskers indicating minimum and maximum values recorded. Mind the logarithmic scaling of Y axis.</p

Identification of core chicken fecal microbiota.

<p>Cluster I (CI) of positively correlating bacterial families represents families common to established chicken fecal microbiota of adult hens. Interestingly, representatives of <i>Helicobacteraceae</i> and <i>Campylobacteraceae</i> were clustered with these families, although as the most distant members. Cluster II (CII) was formed mainly by the families which are characteristic of aquatic environments. Cluster III (CIII) of positively correlating bacterial families included bacterial families that were mainly characteristic of gut microbiota of young broilers. Families in green belong to the phylum <i>Firmicutes</i>, purple to <i>Bacteroidetes</i>, blue to <i>Proteobacteria</i> and red to <i>Actinobacteria</i>. Shades of brown – positively correlating families; shades of blue – negatively correlating families.</p

List of OTUs present 10 or more times in either hen or broiler fecal microbiota.

<p>* numbers show the number of samples in which particular OTU was recorded, out of 15 hen and 30 broiler fecal microbiota samples.</p><p>List of OTUs present 10 or more times in either hen or broiler fecal microbiota.</p

Microbiota diversity in fecal samples of broilers and hens.

<p>UniFrac analysis followed by PCoA showed that the two main factors explained 69% of the variability observed in the microbiota composition in poultry fecal samples. Slovenian egg layer microbiota were similar to samples originating from broilers and Hungarian samples of broiler origin clustered between broiler samples from Slovenia and Croatia, and egg laying hen samples from Croatia and the Czech Republic. SLO – Slovenia, CRO – Croatia, CZE – Czech Republic, HUN – Hungary, Hen - samples from egg laying hens, Bro – samples from broilers.</p