从出生到市场对猪肠道微生物组进行纵向研究，揭示了与阶段和生长性能相关的细菌。

Longitudinal investigation of the swine gut microbiome from birth to market reveals stage and growth performance associated bacteria.

机构信息

Department of Animal Science, University of Arkansas, Fayetteville, AR, USA.

Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China.

出版信息

Microbiome. 2019 Jul 30;7(1):109. doi: 10.1186/s40168-019-0721-7.

DOI:10.1186/s40168-019-0721-7

PMID:31362781

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6664762/

Abstract

BACKGROUND

Despite recent advances in the understanding of the swine gut microbiome at different growth stages, a comprehensive longitudinal study of the lifetime (birth to market) dynamics of the swine gut microbiome is lacking.

RESULTS

To fill in this gap of knowledge, we repeatedly collected a total of 273 rectal swabs from 18 pigs during lactation (day (d) 0, 11, 20), nursery (d 27, 33, 41, 50, 61), growing (d 76, 90, 104, 116), and finishing (d 130, 146, 159, 174) stages. DNA was extracted and subjected to sequencing with an Illumina Miseq sequencer targeting the V4 region of the 16S rRNA gene. Sequences were analyzed with the Deblur algorithm in the QIIME2 package. A total of 19 phyla were detected in the lifetime pig gut microbiome with Firmicutes and Bacteroidetes being the most abundant. Alpha diversity including community richness (e.g., number of observed features) and diversity (e.g., Shannon index) showed an overall increasing trend. Distinct shifts in microbiome structure along different growth stages were observed. LEfSe analysis revealed 91 bacterial features that are stage-specific. To validate these discoveries, we performed fecal microbiota transplantation (FMT) by inoculating weanling pigs with mature fecal microbiota from a growing stage pig. Similar stage-specific patterns in microbiome diversity and structures were also observed in both the FMT pigs and their littermates. Although FMT remarkably increased growth performance, it did not change the overall swine gut microbiome. Only a few taxa including those associated with Streptococcus and Clostridiaceae were enriched in the FMT pigs. These data, together with several other lines of evidence, indicate potential roles these taxa play in promoting animal growth performance. Diet, especially crude fiber from corn, was a major factor shaping the swine gut microbiome. The priority effect, i.e., the order and timing of species arrival, was more evident in the solid feed stages.

CONCLUSIONS

The distinct stage-associated swine gut microbiome may be determined by the differences in diet and/or gut physiology at different growth stages. Our study provides insight into mechanisms governing gut microbiome succession and also underscores the importance of optimizing stage-specific probiotics aimed at improving animal health and production.

摘要

背景

尽管近年来人们对不同生长阶段猪肠道微生物组有了更深入的了解，但对于猪肠道微生物组一生（从出生到上市）的动态变化，仍缺乏全面的纵向研究。

结果

为了填补这一知识空白，我们在哺乳期（第 0、11、20 天）、保育期（第 27、33、41、50、61 天）、生长期（第 76、90、104、116 天）和育肥期（第 130、146、159、174 天），从 18 头猪中反复采集了总共 273 份直肠拭子。提取 DNA 后，用 Illumina Miseq 测序仪对 16S rRNA 基因的 V4 区进行测序。使用 QIIME2 软件包中的 Deblur 算法对序列进行分析。在猪肠道微生物组的一生中共检测到 19 个门，其中厚壁菌门和拟杆菌门最为丰富。包括群落丰富度（例如，观察到的特征数量）和多样性（例如，香农指数）在内的α多样性呈总体上升趋势。不同生长阶段的微生物组结构发生了明显变化。LEfSe 分析显示有 91 种细菌特征具有特定的阶段特异性。为了验证这些发现，我们通过向断奶仔猪接种生长阶段猪的成熟粪便微生物群进行粪便微生物群移植（FMT）。在 FMT 猪及其同窝仔猪中也观察到了类似的阶段特异性微生物组多样性和结构模式。尽管 FMT 显著提高了生长性能，但它并没有改变整个猪肠道微生物组。只有少数分类群，包括与链球菌和梭菌科相关的分类群，在 FMT 猪中富集。这些数据以及其他几条证据表明，这些分类群在促进动物生长性能方面可能发挥了作用。饮食，尤其是来自玉米的粗饲料，是塑造猪肠道微生物组的主要因素。优先效应，即物种到达的顺序和时间，在固体饲料阶段更为明显。