Predicted functional profiles of the cecal microbiota of control chickens and those with <i>C</i>. <i>perfringens</i>, <i>Eimeria</i> challenge and fishmeal supplementation, in the presence and absence of <i>Bacillus licheniformis</i>.

<p>Differences between groups were assessed using a bootstrap Mann–Whitney U-test with cutoffs of <i>P</i> < 0.01, false discovery rate < 0.1, and mean counts >10. NC, negative control; PC, treated with <i>C</i>. <i>perfringens</i>, coccidia, and fishmeal; BL, pre-treated with <i>B</i>. <i>licheniformis</i> then treated with <i>C</i>. <i>perfringens</i>, coccidia, and fishmeal.</p

Taxa that were significantly differentially represented in the control group compared with the groups that had <i>C</i>. <i>perfringens</i>, <i>Eimeria</i> challenge and fishmeal supplementation, with and without <i>Bacillus licheniformis</i> treatment.

<p><b>(</b>A) Differentially overrepresented taxa in group NC versus group BL. (B) Differentially overrepresented taxa in group NC versus group PC. Phylum and genus level names are shown. Sequences that could not be classified at the genus level were named according to the next highest level. NC, negative control; PC, treated with <i>C</i>. <i>perfringens</i>, coccidia, and fishmeal; BL, pre-treated with <i>B</i>. <i>licheniformis</i> then treated with <i>C</i>. <i>perfringens</i>, coccidia, and fishmeal.</p

Predicted functional profiles of the cecal microbiota of control chickens and those with <i>C</i>. <i>perfringens</i>, <i>Eimeria</i> challenge and fishmeal supplementation, in the presence and absence of <i>Bacillus licheniformis</i>.

<p>Differences between groups were assessed using a bootstrap Mann–Whitney U-test with cutoffs of <i>P</i> < 0.01, false discovery rate < 0.1, and mean counts >10. NC, negative control; PC, treated with <i>C</i>. <i>perfringens</i>, coccidia, and fishmeal; BL, pre-treated with <i>B</i>. <i>licheniformis</i> then treated with <i>C</i>. <i>perfringens</i>, coccidia, and fishmeal.</p

Taxa that were significantly differentially represented in the ceca of chickens with <i>C</i>. <i>perfringens</i>, <i>Eimeria</i> challenge and fishmeal supplementation compared with the negative control and <i>Bacillus licheniformis</i> treatment groups.

<p><b>(</b>A) Differentially overrepresented taxa in group PC versus group BL. (B) Differentially overrepresented taxa in group PC versus group NC. Phylum and genus level names are shown. Sequences that could not be classified at the genus level were named according to the next highest level. NC, negative control; PC, treated with <i>C</i>. <i>perfringens</i>, coccidia, and fishmeal; BL, pre-treated with <i>B</i>. <i>licheniformis</i> then treated with <i>C</i>. <i>perfringens</i>, coccidia, and fishmeal.</p

Effects of <i>Bacillus licheniformis</i> on the growth performance of broilers from day 1 to 22.

<p>Effects of <i>Bacillus licheniformis</i> on the growth performance of broilers from day 1 to 22.</p

Principal coordinate analysis of the bacterial community structures in the cecal microbiota of chickens with <i>C</i>. <i>perfringens</i> in the presence and absence of <i>Bacillus licheniformis</i> treatment.

<p>NC, negative control; PC, treated with <i>C</i>. <i>perfringens</i>, coccidia, and fishmeal; BL, pre-treated with <i>B</i>. <i>licheniformis</i> then treated with <i>C</i>. <i>perfringens</i>, coccidia, and fishmeal.</p

Image_5_Microbial Biogeography Along the Gastrointestinal Tract of a Red Panda.TIF

<p>The red panda (Ailurus fulgens) is a herbivorous carnivore that is protected worldwide. The gastrointestinal tract (GIT) microbial community has widely acknowledged its vital role in host health, especially in diet digestion; However, no study to date has revealed the GIT microbiota in the red panda. Here, we characterized the microbial biogeographical characteristics in the GIT of a red panda using high-throughput sequencing technology. Significant differences were observed among GIT segments by beta diversity of microbiota, which were divided into four distinct groups: the stomach, small intestine, large intestine, and feces. The stomach and duodenum showed less bacterial diversity, but contained higher bacterial abundance and the most unclassified tags. The number of species in the stomach and small intestine samples was higher than that of the large intestine and fecal samples. A total of 133 core operational taxonomic units were obtained from the GIT samples with 97% sequence identity. Proteobacteria (52.16%), Firmicutes (10.09%), and Bacteroidetes (7.90%) were the predominant phyla in the GIT of the red panda. Interestingly, Escherichia–Shigella were largely abundant in the stomach, small intestine, and feces whereas the abundance of Bacteroides in the large intestine was high. Overall, our study provides a deeper understanding of the gut biogeography of the red panda microbial population. Future research will be important to investigate the microbial culture, metagenomics and metabolism of red panda GIT, especially in Escherichia–Shigella.</p

Image_4_Microbial Biogeography Along the Gastrointestinal Tract of a Red Panda.TIF

<p>The red panda (Ailurus fulgens) is a herbivorous carnivore that is protected worldwide. The gastrointestinal tract (GIT) microbial community has widely acknowledged its vital role in host health, especially in diet digestion; However, no study to date has revealed the GIT microbiota in the red panda. Here, we characterized the microbial biogeographical characteristics in the GIT of a red panda using high-throughput sequencing technology. Significant differences were observed among GIT segments by beta diversity of microbiota, which were divided into four distinct groups: the stomach, small intestine, large intestine, and feces. The stomach and duodenum showed less bacterial diversity, but contained higher bacterial abundance and the most unclassified tags. The number of species in the stomach and small intestine samples was higher than that of the large intestine and fecal samples. A total of 133 core operational taxonomic units were obtained from the GIT samples with 97% sequence identity. Proteobacteria (52.16%), Firmicutes (10.09%), and Bacteroidetes (7.90%) were the predominant phyla in the GIT of the red panda. Interestingly, Escherichia–Shigella were largely abundant in the stomach, small intestine, and feces whereas the abundance of Bacteroides in the large intestine was high. Overall, our study provides a deeper understanding of the gut biogeography of the red panda microbial population. Future research will be important to investigate the microbial culture, metagenomics and metabolism of red panda GIT, especially in Escherichia–Shigella.</p

Table_4_Microbial Biogeography Along the Gastrointestinal Tract of a Red Panda.DOC

<p>The red panda (Ailurus fulgens) is a herbivorous carnivore that is protected worldwide. The gastrointestinal tract (GIT) microbial community has widely acknowledged its vital role in host health, especially in diet digestion; However, no study to date has revealed the GIT microbiota in the red panda. Here, we characterized the microbial biogeographical characteristics in the GIT of a red panda using high-throughput sequencing technology. Significant differences were observed among GIT segments by beta diversity of microbiota, which were divided into four distinct groups: the stomach, small intestine, large intestine, and feces. The stomach and duodenum showed less bacterial diversity, but contained higher bacterial abundance and the most unclassified tags. The number of species in the stomach and small intestine samples was higher than that of the large intestine and fecal samples. A total of 133 core operational taxonomic units were obtained from the GIT samples with 97% sequence identity. Proteobacteria (52.16%), Firmicutes (10.09%), and Bacteroidetes (7.90%) were the predominant phyla in the GIT of the red panda. Interestingly, Escherichia–Shigella were largely abundant in the stomach, small intestine, and feces whereas the abundance of Bacteroides in the large intestine was high. Overall, our study provides a deeper understanding of the gut biogeography of the red panda microbial population. Future research will be important to investigate the microbial culture, metagenomics and metabolism of red panda GIT, especially in Escherichia–Shigella.</p

Table_1_Microbial Biogeography Along the Gastrointestinal Tract of a Red Panda.DOC

<p>The red panda (Ailurus fulgens) is a herbivorous carnivore that is protected worldwide. The gastrointestinal tract (GIT) microbial community has widely acknowledged its vital role in host health, especially in diet digestion; However, no study to date has revealed the GIT microbiota in the red panda. Here, we characterized the microbial biogeographical characteristics in the GIT of a red panda using high-throughput sequencing technology. Significant differences were observed among GIT segments by beta diversity of microbiota, which were divided into four distinct groups: the stomach, small intestine, large intestine, and feces. The stomach and duodenum showed less bacterial diversity, but contained higher bacterial abundance and the most unclassified tags. The number of species in the stomach and small intestine samples was higher than that of the large intestine and fecal samples. A total of 133 core operational taxonomic units were obtained from the GIT samples with 97% sequence identity. Proteobacteria (52.16%), Firmicutes (10.09%), and Bacteroidetes (7.90%) were the predominant phyla in the GIT of the red panda. Interestingly, Escherichia–Shigella were largely abundant in the stomach, small intestine, and feces whereas the abundance of Bacteroides in the large intestine was high. Overall, our study provides a deeper understanding of the gut biogeography of the red panda microbial population. Future research will be important to investigate the microbial culture, metagenomics and metabolism of red panda GIT, especially in Escherichia–Shigella.</p