Ecological niches and assembly dynamics of diverse microbial consortia in the gastrointestine of goat kids
Ecological niches and assembly dynamics of diverse microbial consortia in the gastrointestine of goat kids
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DOI：
10.1093/ismejo/wrae002
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发表时间：
2024-01-08
期刊：
影响因子：
11
通讯作者：
Wang，Min
中科院分区：
文献类型：
--
作者：
Jiao，Jinzhen;Wu，Jian;Wang，Min
山羊是平衡粮食安全和环境影响的全球宝贵反刍动物，其胃肠道（GIT）中的肠道微生物组与动物健康和生产力相关。然而，山羊GIT微生物的参考基因组和功能库尚未完全阐明。在此，我们使用宏基因组测序和分箱对山羊的GIT微生物组进行了全面的景观调查，跨越了空间上覆盖三个胃肠道隔室和时间上覆盖五个发育年龄的密集采样制度。我们回收了1002个高质量的宏基因组组装基因组（称为山羊KIT微生物目录[GKGMC]），其中618个是新的。它们编码超过230万个非冗余蛋白质，并代表各种碳水化合物降解酶和代谢基因簇。GKGMC富集的微生物类群，特别是嗜钠菌，扩大了山羊幼崽的微生物生命树。使用这种GKGMC，我们首先破译了瘤胃和结肠中碳水化合物分解的纤维降解细菌的流行，而回肠微生物群专门吸收和转化单糖。此外，GIT微生物出生后迅速组装，其碳水化合物代谢适应发生在三个阶段的进展。最后，植物生素改变了回肠微生物组的代谢级联，以Sharpea azabuensis和Olsenellaspp的富集为基础。涉及乳酸盐的形成和利用。这GKGMC参考提供了新的见解早期生活微生物发育动力学在不同的隔间，并提供了扩大资源GIT微生物相关的研究在山羊孩子。
Goats are globally invaluable ruminants that balance food security and environmental impacts, and their commensal microbiome residing in the gastrointestinal tract (GIT) is associated with animal health and productivity. However, the reference genomes and functional repertoires of GIT microbes in goat kids have not been fully elucidated. Herein, we performed a comprehensive landscape survey of the GIT microbiome of goat kids using metagenomic sequencing and binning, spanning a dense sampling regime covering three gastrointestinal compartments spatially and five developmental ages temporally. We recovered 1002 high-quality metagenome-assembled genomes (termed the goat kid GIT microbial catalog [GKGMC]), 618 of which were novel. They encode more than 2.3 million nonredundant proteins, and represent a variety of carbohydrate-degrading enzymes and metabolic gene clusters. The GKGMC-enriched microbial taxa, particularlySodaliphilus, expanded the microbial tree of life in goat kids. Using this GKGMC, we first deciphered the prevalence of fiber-degrading bacteria for carbohydrate decomposition in the rumen and colon, while the ileal microbiota specialized in the uptake and conversion of simple sugars. Moreover, GIT microorganisms were rapidly assembled after birth, and their carbohydrate metabolic adaptation occurred in three phases of progression. Finally, phytobiotics modified the metabolic cascades of the ileal microbiome, underpinned by the enrichment ofSharpea azabuensisandOlsenellaspp. implicated in lactate formation and utilization. This GKGMC reference provides novel insights into the early-life microbial developmental dynamics in distinct compartments, and offers expanded resources for GIT microbiota-related research in goat kids.