The α diversity of ileal samples.

<p>The α diversity of ileal samples.</p

The α diversity of cecal samples.

<p>The α diversity of cecal samples.</p

A comparison of diversity and composition between ileal and cecal microbiotas.

<p>The PCA plot (A) shows that the bacterial profile differed strongly by sampling site (<i>R</i> = 0.9138, <i>P</i> = 0.001). Taxa significantly associated with communities of ileum <i>versus</i> cecum were identified by the LEfSe algorithm (B) and are shown in the circular cladogram (C).</p

Effects of <i>Lactobacillus acidophilus</i> on gut microbiota composition in broilers challenged with <i>Clostridium perfringens</i>

<div><p>This study shows the effects of dietary supplementation with <i>Lactobacillus acidophilus</i> on the gut microbiota of broiler chickens challenged with <i>Clostridium perfringens</i> infection during a 21-day period according to pyrosequencing of the 16S ribosomal RNA gene. In a 2 × 2 factorial arrangement of treatments, 308 1-day-old male Arbor Acres broiler chicks were analyzed for the effects of the probiotic (groups without or with <i>L</i>. <i>acidophilus</i> supplementation), pathogen challenge (groups without or with <i>C</i>. <i>perfringens</i>), and the effects of interaction. The infection decreased the number of Observed species, Chao1, and ACE of ileal microbiota and increased Chao1 of cecal microbiota of broilers, whereas <i>L</i>. <i>acidophilus</i> supplementation decreased the Shannon index of the ileal microbiota. Shannon index and Simpson indices were lower in the ileal microbiota than in the cecal microbiota. In the ileal microbiota, the control group had higher relative abundance of <i>Lachnospiraceae</i> and <i>Ruminococcaceae</i> in comparison with the other groups; however, the relative abundance of <i>Gammaproteobacteria</i> was significantly higher in the challenge group than in the other groups. <i>C</i>. <i>perfringens</i> infection tended to increase lactate concentration and decreasedconcentrations of formate, acetate and propionate in the ileum; decreased isobutyrate concentration; and tended to decrease isovalerate concentration in the cecum. Besides, <i>L</i>. <i>acidophilus</i> supplementation increased the concentration of lactate and butyrate and decreased concentrations of formate and propionate in the ileum, and increased concentrations of lactate and valerate in the cecum. In conclusion, <i>C</i>. <i>perfringens</i> infection and/or dietary supplementation with <i>L</i>. <i>acidophilus</i> modulated the relative abundance of some bacteria taxa, and the <i>L</i>. <i>acidophilus</i> supplementation helped to restore the microbial community disrupted by <i>C</i>. <i>perfringens</i> infection.</p></div

Diversity and composition of ileal microbiota.

<p>Rarefaction curves of the observed OTUs (<b>A</b>) for ileal samples. The community structure among the treatment groups did not differ according to the Principle component analysis (PCA) of 20 ileal samples (<b>B</b>). Linear discriminant analysis (LDA) effect size (LEfSe) showed the phylotypes that differ among treatment groups with statistical and biological significance (<b>C</b>). Histograms indicate the highest relative abundance of the families <i>Lachnospiraceae</i> (<b>D</b>) and <i>Ruminococcaceae</i> (<b>E</b>) in the ileal microbiota of the CTL group, and of the class <i>Gammaproteobacteria</i> (<b>F</b>) in the ileal microbiota of the CLG group. CTL: control group; LA: <i>L</i>. <i>acidophilus</i> supplementation group; CLG: Challenge group; LACLG: challenge group supplemented with <i>L</i>. <i>acidophilus</i>.</p

Diversity and composition of cecal microbiota.

<p>There were significant interaction effects of <i>L</i>. <i>acidophilus</i> and the infectious challenge on the number of observed OTUs (<b>A</b>). The PCA plot shows separation of bacterial communities between the CTL group and LA group (<i>R</i> = 0.42, <i>P</i> = 0.024), between the CTL group and CLG group (<i>R</i> = 0.404, <i>P</i> = 0.027), and between the CTL group and LACLG group (<i>R</i> = 0.50, <i>P</i> = 0.012) (<b>B</b>). Key phylotypes in the cecum responding to treatments were identified by the LEfSe algorithm (<b>C</b>). The circular cladogram (<b>D</b>) shows the taxa that are significantly associated with treatments.</p

Effects of <i>Kluyveromyces marxianus</i> on growth performance¹ of broilers.

<p>Effects of <i>Kluyveromyces marxianus</i> on growth performance<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0180884#t003fn002" target="_blank">¹</a> of broilers.</p

Data_Sheet_1_Dietary l-arginine Supplementation Alleviates the Intestinal Injury and Modulates the Gut Microbiota in Broiler Chickens Challenged by Clostridium perfringens.docx

<p>Our previous reports suggested that Dietary l-arginine supplementation attenuated gut injury of broiler chickens infected with Clostridium perfringens by enhancing intestinal immune responses, absorption and barrier function, but its effect on the gut microbiome of broiler chickens remains unclear. This experiment aimed at evaluating the effects of Dietary l-arginine supplementation on the gut bacterial community composition and function of broiler chickens challenged with C. perfringens. In total, 105 1-day-old male Arbor Acres broiler chickens were assigned to three groups: Control (CTL), C. perfringens-challenged (CP), and C. perfringens-challenged and fed diet supplemented with 0.3% l-arginine (ARGCP) groups. The challenge led to macroscopic and histomorphological gut lesions, decreased villus height and increased the number of Observed species, Shannon, Chao1 and ACE indices of ileal microbiota, whereas l-arginine addition reversed these changes. Moreover, the three treatments harbored distinct microbial communities (ANOSIM, P < 0.05). At the genus level, 24 taxa (e.g., Nitrosomonas spp., Coxiella spp., Ruegeria spp., and Thauera spp.) were significantly more abundant in CP group than in CTL group (P < 0.05), whereas the levels of 23 genera of them were significantly decreased by l-arginine supplementation (P < 0.05). The abundances of only 3 genera were different between CTL and ARGCP groups (P < 0.05). At the species level, the challenge promoted the relative abundance of Nitrospira sp. enrichment culture clone M1-9, Bradyrhizobium elkanii, Nitrospira bacterium SG8-3, and Pseudomonas veronii, which was reversed by l-arginine supplementation (P < 0.05). Furthermore, the challenge decreased the levels of Lactobacillus gasseri (P < 0.05). Predictive functional profiling of microbial communities by PICRUSt showed that compared with CP group, ARGCP group had enriched pathways relating to membrane transport, replication and repair, translation and nucleotide metabolism and suppressed functions corresponding to amino acid and lipid metabolisms (P < 0.05). The relative abundances of KEGG pathways in l-arginine-fed broilers were almost equal to those of the controls. In conclusion, l-arginine alleviated the gut injury and normalized the ileal microbiota of C. perfringens-challenged chickens to resemble that of unchallenged controls in terms of microbial composition and functionality.</p