The changes of gut microbiota induced by treating with APEC and/or baicalin in chicken
The composition of gut microbiota in control (CON), baicalin-treated (BAI), APEC-treated (APEC), baicalin+APEC treatment (BAI+APEC) group chickens were differed in high-confidence OTUs, with lower diversity and richness in BAI group compared to CON group (Fig. 4A). In addition, infection of APEC significantly increased the microbiota diversity and richness compared to the CON group chickens (Fig. 4B-C). However, pre-treatment with BAI before APEC infection (BAI+APEC) reduced the higher levels of microbiota diversity and richness induced by APEC (Fig. 4B-C).
Furthermore, the changes of bacterial phyla in different treatment group chickens were showed that though gut microbiota in different treatment groups chicken were dominated by Firmicutes(means=87.32%-96.70%), Proteobacteria (means=0.62%-11.6%),Tenericutes (means=1.0%-2.16%), and Actinobacteria(means=0.20%-0.79%) (Fig. 5A and Table S3). Infection of APEC reduced the relative abundance of Proteobacteria , and increased the relative abundance of Actinobacteria compared to the CON group chickens, while BAI treatment (BAI+APEC) group reversed those changes induced by APEC (Fig. 5B). In addition, the relative abundance ofProteobacteria in BAI group was higher than those in CON group chickens, while Actinobacteria was lower than those in CON group chickens (Fig. 5B).
Moreover, the characteristics of microbiota composition at the genus level were detected at the top 20 most abundant taxa indicated that the gut bacterial was dominated by Lachnospiraceae_unclassified ,Ruminococcaceae_UCG-014 , Ruminococcaceae_unclassified ,Intestinimonas , Blautia , Escherichia-Shigella ,Erysipelatoclostridium , Ruminococcus_torques_group ,Clostridiales_vadin BB60-group_unclassified , andFournierella (Fig. 5C and supplementary Table S4). Furthermore, t-test analysis revealed infection of APEC increased the abundance ofRuminococcaceae_UCG-014 , Ruminococcaceae_unclassified ,Clostridiales_vadinBB60_group_unclassified , andRuminiclostridium_5 , while reduced the abundance ofLachnospiraceae_unclssified , Blautia ,Escherichia-Shigella , and Pygmaiobacter . However, those changes were reversed in BAI+APEC group (Fig. 5D).
In addition, the proportion of shared bacterial genera among CON, BAI, APEC, and BAI+APEC group chickens were 25.72%, 23,63%, 19.03%, and 22.01% (Fig. S3). Furthermore, to evaluated whether a unique bacterial was associated with the protective role of BAI during APEC-induced chicken colibacillosis, we conducted a biomarker analysis by linear discriminant analysis (LDA = 4.0) effect size (LEfSe) and a cladogram generated from LEfSe analysis on the microbiota on the different treatment group chickens. At both genus and species levels,Clostridiales_vadinBB60_group_unclassified ,Ruminococcaceae_UCG_014 , andRuminococcaceae_unclassified were enriched in the chicken of infected with APEC compared to the CON group chickens (Fig. 6A-B). While pretreatment of BAI partly inhibited these bacteria induced by APEC (Fig. 6C-D). In addition, compared to the CON group chickens,Intestinimonas genera was enriched in the chicken of treated with BAI (Fig. 6E-F). These results suggested that baicalin may protect against chicken colibacillosis partly by reversing the changes of gut microbiota induced by APEC.