Table_5_Characterization and Comparison of Microbiota in the Gastrointestinal Tracts of the Goat (Capra hircus) During Preweaning Development.XLSX

Bacterial communities in gastrointestinal tracts (GIT) play an important role in animal health and performance. Despite its importance, little information is available on the establishment of microbial populations in the goat GIT or on changes occurring during early development. Therefore, this study investigated the bacterial community dynamics of the rumen, duodenum, jejunum, ileum, cecum, and colon in 15 goats at five developmental stages (0, 14, 28, 42, and 56 days old) by using 16S rDNA sequencing and quantitative real-time PCR technology. 940 genera were found to belong to 44 phyla distributed along the GIT. As a whole, the microbial richness and diversity showed a clear increasing trend as the kids aged and alpha diversity differed significantly among GIT compartments mainly occurring at middle day ages (14 and 28 days). Principal coordinate analysis indicated that the bacterial community displayed distinct temporal and spatial specificity along the GIT in preweaning goats. As kids aged, the phylum Firmicutes was replaced by Bacteroidetes in rumen, whereas Proteobacteria in the large intestine was displaced by Firmicutes. The phylum Proteobacteria was mainly present in the small intestine in older animals. In the rumen, taxa, such as Bacillus and Lactococcus decreased and Prevotella, Treponema, Ruminococcus, and unclassified Prevotellaceae increased with the age of kids. Furthermore, a lower proportion of taxa, such as Lactobacillus and Bacteroides was observed with higher abundances of both Christensenellaceae_R_7 and Ruminococcus in duodenum and jejunum in older animals. In the large intestine, the microbiota displayed taxonomic dynamics with increases of Ruminococcaceae UCG 005, unclassified Lachnospiraceae, Barnesiella, and Blautia as kids aged. Predicted pathway analysis suggested that genes involved in amino acid metabolism, and translation were abundant in both rumen and duodenum, while genes involved in membrane transport and carbohydrate metabolism were enriched in the large intestine. These results indicate that both the microbial colonization process and potential function exert a temporal-spatial specificity throughout the GIT of goats. This study provides new insight into the temporal dynamics of GIT microbiota development during preweaning and will aid to develop strategies for improving animal health and downstream production.

胃肠道（gastrointestinal tracts, GIT）内的细菌群落对动物健康与生产性能具有关键作用。尽管其重要性已得到广泛认可，但目前关于山羊胃肠道微生物菌群的定植过程，以及早期发育阶段菌群的动态变化，相关研究仍较为匮乏。因此，本研究采用16S rDNA测序与实时定量PCR（quantitative real-time PCR）技术，对15只山羊在5个发育阶段（0、14、28、42及56日龄）的瘤胃、十二指肠、空肠、回肠、盲肠与结肠内的细菌群落动态展开了探究。本研究共鉴定出隶属于44个门的940个菌属，这些菌群广泛分布于胃肠道各分段。总体而言，随着羔羊日龄增长，微生物丰富度与多样性呈现显著上升趋势；而α多样性在胃肠道各分段间存在显著差异，该差异主要集中在中期日龄阶段（14日龄与28日龄）。主坐标分析结果显示，断奶前山羊的细菌群落沿胃肠道呈现出鲜明的时空特异性。随着羔羊日龄增加，瘤胃内的厚壁菌门（Firmicutes）逐渐被拟杆菌门（Bacteroidetes）取代；而大肠内的变形菌门（Proteobacteria）则被厚壁菌门所替代。在日龄较大的山羊体内，变形菌门主要定植于小肠段。在瘤胃中，芽孢杆菌属（Bacillus）、乳球菌属（Lactococcus）等菌属的相对丰度随日龄增长而降低，而普雷沃氏菌属（Prevotella）、密螺旋体属（Treponema）、瘤胃球菌属（Ruminococcus）以及未分类普雷沃氏菌科（unclassified Prevotellaceae）的丰度则显著升高。此外，在十二指肠与空肠中，日龄较大的羔羊乳杆菌属（Lactobacillus）、拟杆菌属（Bacteroides）的占比较低，而克里斯滕森菌科R_7（Christensenellaceae_R_7）与瘤胃球菌属（Ruminococcus）的丰度更高。在大肠内，菌群的分类学动态表现为随着日龄增长，瘤胃菌科UCG 005（Ruminococcaceae UCG 005）、未分类毛螺菌科（unclassified Lachnospiraceae）、巴恩斯氏菌属（Barnesiella）以及布劳特氏菌属（Blautia）的丰度显著上升。功能预测分析结果表明，参与氨基酸代谢与翻译过程的基因在瘤胃与十二指肠中富集度较高；而参与膜转运与碳水化合物代谢的基因则在大肠中更为丰富。上述结果表明，山羊胃肠道内的微生物定植过程与潜在功能均呈现出鲜明的时空特异性。本研究为阐明断奶前山羊胃肠道菌群发育的时间动态提供了新的视角，同时可为改善动物健康与下游生产的相关策略研发提供理论支撑。