| The sika deer(Cervus nippon)is a Class I key protected animal in China,Alaska horse deer(Cervus elaphus alashanicus)is a Class II key protected wild animals in China,the fallow deer is an introduced species in Europe.In this experiment,the diversity and structure of intestinal flora of three captive deer species were analyzed under captive conditions by controlling food,individual,sex and season,using 16 S rRNA high-throughput sequencing technology to provide a theoretical basis for the ex situ conservation of the three target animals,and also to build a basis for improving the captive system of deer species.The three species were classified into seasonal groups,sex groups,and species groups for taxonomic comparison,and the results of the study were as follows:(1)All samples were annotated to 25 phyla,51 classes,79 orders,163 families and 330 genera.There were a total of 1978 OTUs(Operational Taxonomic Units)for captive plum deer,fallow deer and Alaska horse deer,361 OTUs unique to plum deer,220 OTUs unique to fallow deer and 222 OTUs unique to Alaska horse deer.(2)In the seasonal groups,the mycobiota of males and females of the three deer species in different seasons showed that the top five in abundance at the phylum taxonomic level contained Firmicutes,Bacteroidetes,and the top five in abundance at the phylum taxonomic level in the winter group contained Proteobaoteria,Proteobaoteria,and Bacteroidetes;the summer group had a higher percentage of Firmicutes The summer group had a higher proportion of Proteobaoteria and Proteobacteria,and the winter group had a higher proportion of Proteobacteria.When comparing the diversity of intestinal flora,we found that the species richness was greater in summer than in winter;and there were significant differences between winter and summer.In the STAMP analysis,in the summer group,the sika deer males in the phyla Nitrospirae,Planctomycetes,Acidobacteria,Candidatus＿Saccharibacteria,unclassified＿Bacteria,Cyanobacteria＿Chloroplast,and Thick-walled Phylum were significantly different(P<0.05);among females,unclassified＿Bacteria,Warty Microflora,Synergistetes,Acidobacteria,Actinobacteroa,Thick-walled(P < 0.05),and Cyanobacteria＿Chloroplast(P < 0.05);in the winter group,there were significant differences(P<0.05)in the phylum Methylobacteria in males;and in females,there were significant differences(P < 0.05)in the phylum Fibrobacteres,Tenericutes,Spirochaetes,and Mucor.Spirochaetes,and Lentisphaerae were significantly different in females(P < 0.05).In the summer group,there were significant differences(P < 0.05)in the fallow deer males in the phylum Phyllobacterium,Phylum Nitrospirochaetes,Phylum Acidobacter,Candidatus＿Saccharibacteria,Phylum Mutualist,Phylum Thick-walled,and unclassified＿Bacteria;and in the females in the phylum Phyllobacterium,Phylum Spirochaetes,Candidatus＿Saccharibacteria,Nitrospirochaetes,Verrucaria,Actinomycetes,unclassified＿Bacteria,Anaplasma,Acidobacteria,and Thickwalled＿Bacteria in females(P<0.05);in the winter group,significant differences were found in Anaplasma in fallow deer males(P<0.05);and in Anaplasma in females(P<0.05).In the summer group,there were significant differences(P<0.05)in the warty microflora,spirochete phylum,anthropoid phylum,acidophilus phylum,thick-walled phylum,and soft-walled phylum in red deer males;significant differences(P < 0.05)in the thick-walled phylum,nitrospirochete phylum,and mutualistic phylum in females;and significant differences(P<0.05)in the anamorphic phylum in red deer males in the winter group.(3)In the sex group,the mycobiota of males and females of the three deer species showed that: in summer,the two most abundant phyla in male and female samples were Clostridiales and Pseudomonadales,accounting for more than 80% of the total,and the most abundant orders were Clostridiales and Bacteroidales under the phylum Clostridiales;in winter,the two most abundant phyla in male and female samples were Clostridiales and Pseudomonadales,with the exception of M.melanogaster.The two most abundant phyla were Clostridiales and Pseudomonadales,and the two most abundant orders were Clostridiales and Pseudomonadales in the phylum Clostridiales.Comparison of the intestinal flora diversity between sex groups revealed that only the winter sika deer had statistically significant differences between male and female individuals.In STAMP analysis,there were significant differences(P < 0.05)among winter females of plum deer in the phylum Thick-walled,Pseudomonadales,Phylum Anaplasma,Phylum Spirochaetes,and Phylum Mucilaginous Spheroid;among summer males of red deer in the phylum Warty Microbacteria and Phytoplasma(P < 0.05);and among summer females of fallow deer in the phylum Nitrospirillum(P<0.05).(4)Among the species groups,comparing different species in the same season and same sex,the results showed that the highest abundance proportion in the summer group was Phylum Thick-walled Bacteroides,followed by Phylum Bacteroides,with a combined proportion of more than 80%;in the winter group,except for female Muihua deer,the highest abundance proportion was Phylum Anaplasma,followed by Phylum Thick-walled Bacteroides and Phylum Bacteroides.Comparison of intestinal flora diversity between species groups revealed that the community richness of sika deer was greater than that of red deer,and there were significant differences in indices between winter sika deer and red horse deer.In STAMP analysis,there were significant differences(P < 0.05)in soft-walled phylum,thick-walled phylum,and unclassified＿Bacteria in summer males in the plum deer,and thick-walled phylum,mucilaginous spherical phylum,Candidatus＿Saccharibacteria,and unclassified＿Bacteria in the fallow deer group.Bacteria were significantly different(P<0.05),and in red deer,there were significant differences(P < 0.05)in the phylum Warty Microbacteria,Soft Wall Bacteria,Helicobacteria,Floating Mycobacteria,Thick Wall Bacteria,and Fibrobacteria.In winter males,there were significant differences(P<0.05)in sika deer,Candidatus＿Saccharibacteria,Phylum Warty Microflora in fallow deer,and Phylum Warty Microflora,Phylum Chloroflexi in red deer(P<0.05).In summer females,there were significant differences(P<0.05)in the phylum Warty Microflora in sika deer,and in the phylum Spirochetes,Candidatus＿Saccharibacteria in fallow deer(P<0.05).In winter females,there were significant differences(P<0.05)in the phylum Thick-walled＿Bacteria,unclassified＿Bacteria,Phylum Methanobacterium,Phylum Aspergillus,Phylum Fibrobacter,Phylum Soft-walled＿Bacteria,and Phylum Spirochaetes in sika deer,Candidatus＿Saccharibacteria and Phylum Aspergillus in fallow deer(P<0.05),and in horse deer There were significant differences in Cyanobacteria＿Chloroplast in fallow deer(P<0.05)and in red deer(P<0.05). 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