OTUs significantly (p<0.05) differed between the groups with high sequence alignment identity (>95%) with known pathogenic strains.

<p>Out of 65 OTUs significantly altered between the treatment groups (Fig C in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154061#pone.0154061.s001" target="_blank">S1 File</a>), the majority could not be provisionally assigned to species or genus level using 97% or 95% similarity cut-off. Among the phylotypes with sequence similarity >95%, some candidates showed high sequence alignment (blast against 16S microbial database) to known pathogens. Panel A shows potentially pathogenic OTUs reduced in additives while panel B shows potentially pathogenic OTUs increased in additive groups. Y axes indicate % of abundance in each group. The bars represent standard error for n>12.</p

Bacterial genera significantly (<i>p</i><0.05) differed between birds fed control diet (Ctrl) and groups with feed supplemented with biochar (BC), bentonite (BT) and zeolite (ZT).

<p>Members of order Actinomycetales are marked with “Act” above the bars chart, while other marking indicates genera belonging to Betaproteobacteria (Beta), Epsilonproteobacteria (Eps) or Gammaproteobacteria (Gamma). The bars represent standard error for n>12.</p

Bacterial families significantly (<i>p</i><0.05) differed between birds fed control diet (Ctrl) and groups with feed supplemented with biochar (BC), bentonite (BT) and zeolite (ZT).

<p>The families altered were members of order Actinomycetales (marked with “Act” above the bar chart) or phylum Proteobacteria’s <u>Alpha</u>proteobacteria, <u>Beta</u>proteobacteria, <u>Eps</u>ilonproteobacteria or <u>Gamma</u>proteobacteria (also <u>marked</u> above the bar chart). Families induced in BT Bradyrhizobiaceae, Phyllobacteriaceae, are plant-associated bacteria, Sphingomonadaceae is a candidate for bioremediation and Oxalobacteraceae are known as nitrogen fixing. The bars represent standard error for n>12.</p

Influence of biochar (BC), bentonite (BT) and zeolite (ZT) feed supplementation on abundance of phylum Proteobacteria in chicken cloaca.

<p>Phylum Proteobacteria was significantly different between the three additives and control. The reduction of Proteobacteria in additive groups was due to significant alterations in two of its classes: Epsilonproteobacteria (<i>p</i> = 0.0179) and Gammaproteobacteria (<i>p</i> = 0.0191) (top right panel). The Epsilonproteobacteria was comprised of only two genera—<i>Campylobacter</i> and <i>Helicobacter</i> (bottom row), each represented with only one species. <i>Campylobacter</i> OTU269490 was 100% identical to <i>Campylobacter jejuni</i> subsp. <i>jejuni</i> NCTC 11168 = ATCC 700819 strain, while <i>Helicobacter</i> OTU574168, (not significantly altered, <i>p</i> = 0.4758), was identified as 99% identical <i>H</i>. <i>pullorum</i>. <i>Campylobacter jejuni</i> was reduced from mean of relative abundance 0.0013, equalling 1.3%, in control diet fed birds to mean of 0.02% in BC, completely absent in BT and down to 0.016% in ZT. The bars represent standard error for n>12.</p