Identification Of Ileal Microbiota And Gene Expression Profile Of Ileal Mucosa In Male Geese Between Cage And Floor Rearing Systems

Breeding parent lineages is one of the main methods in meat goose breeding.However,the current establishment of single paternal lineages is based on floor-rearing population breeding,which cannot achieve the needs of individualized and precision breeding.Cage breeding can achieve precision breeding through pedigree records and optimized matching and is often used in conjunction with artificial insemination technology.In recent years,research on the intestinal microbiota and intestinal functional aspects of meat geese have primarily focused on floor rearing and net online rearing systems.Breeding male geese under cage rearing conditions is still in the exploratory stage,and the research on the composition of intestinal microbiota and intestinal mucosal gene expression profiles of breeding male geese under cage rearing conditions is relatively limited.Therefore,the purpose of this study is to compare and analyze the differences in the ileal microbiota and mucosal functional gene expression of breeding male geese raised under cage rearing and floor rearing conditions using 16 S r RNA microbiome and intestinal transcriptome analysis,to deepen our understanding of the relationship between the composition of ileal microbiota and ileal mucosal gene expression,as well as their effects on abdominal fat deposition in geese.The main results are as follows:(1)Comparative analysis of the slaughter traits of two groups of geese revealed that the relative weight of leg muscles in cage-reared geese was higher than that of the floor-reared group,but the absolute and relative weight of abdominal fat was lower than that of the floorreared group.In addition,the ratio of ileal villus height to crypt depth,the number of ileal GC cells and IEL cells in cage-reared geese were significantly higher than those in the floorreared group(P<0.05).(2)The ileal microbiota analysis results showed that the dominant bacterial phyla in both cage-reared and floor-reared geese were Firmicutes,Proteobacteria,Fusobacteriota and Bacteroidota;and the dominant bacterial genera were Romboutsia,Fusobacterium,Clostridium＿sensu＿stricto＿1,and Lactobacillus.In addition,comparative analysis revealed that the abundance of Stenotrophomonas and Anaerobiospirillum genera in cage-reared geese was significantly higher than that in floor-reared geese(P<0.05),while the relative abundance of Proteiniphilum,Proteiniclasticum,Syner-01,Paraclostridium,Petrimonas,OPB41,Campylobacter,and Subdoligranulum genera was significantly lower than that in floor-reared geese(P<0.05).(3)The correlation analysis indicated that the abundance of Stenotrophomonas,which significantly increased in cage-reared geese,was negatively correlated with the absolute and relative weight of abdominal fat(P<0.01),whereas the abundance of OPB41,Proteiniphilum,Proteiniclasticum,Syner-01,and Paraclostridium,which significantly increased in the floorreared group,were positively correlated with the absolute and relative weight of abdominal fat(P<0.05).(4)The expression profile analysis of the ileal mucosa revealed that compared with floor-reared geese,cage-reared geese had 502 upregulated genes and 135 downregulated genes.In cage-reared geese,the genes related to energy metabolism(ALDOC,KHK,TKFC),DNA repair(HES1,RMI2,OGG1),and antioxidant defense(GSTM2,PAOX,GPX)were significantly upregulated(P<0.01).(5)The Spearman correlation results showed that the abundance of Stenotrophomonas and Anaerobiospirillum,which significantly increased in the cage-reared group,were positively correlated with the expression of OGG1,DGKA,RMI2,and HES1 genes(P<0.05).In the floor-reared group,the abundance of OPB41,Campylobacter,Proteiniclasticum,Subdoligranulum,Syner-01,and Thermovirga were positively correlated with the expression of DGKA,RMI2,PARP3,BRCA2,OGG1,HMGCL,and KHK genes(P<0.05).However,the abundance of Paraclostridium in the floor-reared group was negatively correlated with the expression of ALDOC and GMPPB genes(P<0.05).In summary,the lower abdominal fat content in cage-reared geese than in floor-reared geese may be associated with a reduction in the abundance of ileal microbiota related to abdominal fat deposition,which may involve changes in the expression of genes related to energy metabolism,DNA repair,and antioxidant defense in the ileal mucosa.