Abstract：Antimicrobial peptide(AMP), a burgeoning feed additive, is rarely reported when it apllies to the ruminant. The aim of this study was to evaluate the effects of antibacterial peptide (AMP) on rumen ciliate community structure by MiSeq high throughput sequencing technology. Twelve male Chuanzhong black goats(4-month-old) were randomly divided into 4 groups according to the similar weight. Four groups were normal concentrate group (A 300g /d), normal concentrate+AMP group (C 300g /d+3 g/kg), double concentrate group (D 600 g/d) and double concentrate+AMP group (E 600 g/d+3 g/kg), The rumen fluid samples were collected after 20 d, and then the total DNA were extraced for amplification 18S rRNA(547F-V4R), sequencing by MiSeq Illumina250. The results showed that: 1)A total of 471 580 valid 18S rDNA sequences and 1 398 operational taxonomic unit (OTU) across 12 samples were obtained. 2) The 99.17% of all OTUs belonged to eukaryotes, At phylum level, Ciliophora was the most abundant phyla in A and C groups(A: 46.0%; C: 48.2%), followed by incertae sedis (A: 35.5%; C: 42.83%); On the contrary, incertae sedis was the most abundant phyla in D and E groups (D: 49.93%; E: 60.27%), followed by Ciliophora (D: 45.33%; E: 35.23%), and no significant difference between the groups. 3) At family level, only two families (Ophryoscolecidae, Isotrichidae) were found belong to ciliates. And the differences between the groups were not obvious. 4) At genus level, a total of nine different ciliates genera were detected in every last sample. And the content of Ophryoscolex in C group were significantly higher than A group (P＜0.05), but no significant difference between D and E (P＞0.05); the content of Entodinium in C group are significant lower than A group (P＜0.05), but there have not significant difference between D and E (P＞0.05); The content of Polyplastron in E group are significant higher than C group(P＜0.05), and the content of Ophryoscolex were significantly lower than C group (P＜0.05). 5) There were no significantly difference between groups on alpha diversity index (Chao, ACE, Shannon and Simpson). In conclusion, Polyplastron was the most abundant genus in the rumen ciliate communities of young Chuanzhong black goats; there were still a lot of valuable information about eukaryotic microorganisms need to study in rumen. The contents of Ophryoscolex were significantly higher by the supplementation of 3 g/kg complex antibacterial peptide (P＜0.05), and the content of Entodinium were significantly lower by the supplementation of 3 g/kg complex antibacterial peptide (P＜0.05), but there were no significantly difference with feeding 600 g/d concentrate. The ciliate community structure was not affected when the amount of concentrate changed from 300 to 600. Moreover, alpha diversity index also was not affected by supplementation of 3 g/kg complex antibacterial peptide or the amount of concentrate changed from 300 to 600. The result of this study provides a theoretical basis for the application of complex antimicrobial peptide in ruminant.
