Validation of a batch cultivation protocol for fecal microbiota of Kenyan infants.
Validation of a batch cultivation protocol for fecal microbiota of Kenyan infants.
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DOI：
10.1186/s12866-023-02915-9
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发表时间：
2023-07-04
期刊：
影响因子：
4.2
通讯作者：
Geirnaert, Annelies
中科院分区：
文献类型：
--
作者：
Rachmuhl, Carole;Lacroix, Christophe;Giorgetti, Ambra;Stoffel, Nicole U. U.;Zimmermann, Michael B. B.;Brittenham, Gary M. M.;Geirnaert, Annelies
将培养研究与分子分析方法相结合，可以深入表征复杂的人类肠道微生物群。生活在撒哈拉以南非洲农村的婴儿的体外培养研究很少。在这项研究中，对肯尼亚婴儿粪便微生物群的批量培养方案进行了验证。从肯尼亚农村地区的10名婴儿中收集新鲜粪便样本。样品在保护条件下运输，随后在不到30 h内制备接种，用于分批培养。使用了一种适应饮食的培养基，模仿断奶期间肯尼亚婴儿每天摄入的母乳和玉米粥。进行16 S rRNA基因扩增子测序和HPLC分析，以分别评估分批培养24 h后粪便微生物群的组成和代谢活性。在肯尼亚婴儿粪便微生物群中检测到高丰度的双歧杆菌（53.4 ± 11.1%）和高比例的乙酸盐（占总代谢物的56 ± 11%）和乳酸盐（占总代谢物的24 ± 22%）。在初始pH 7.6下开始培养后，发酵和粪便样品之间共享的顶级细菌属（丰度≥ 1%）的分数高达97 ± 5%。然而，随着双歧杆菌丰度的下降，志贺氏菌、狭义梭菌1、拟杆菌和肠球菌富集。将初始pH降低至6.9导致孵育后双歧杆菌的丰度更高，并且增加了发酵和粪便样品的组成相似性。尽管培养后所有粪便微生物群的总代谢产物产量相似，但代谢产物谱的个体间差异是明显的。在宿主和饮食适应条件下的保护性运输和分批培养允许顶级丰富属的再生长和新鲜肯尼亚婴儿粪便微生物群的代谢活性的再现。经验证的分批培养方案可用于体外研究肯尼亚婴儿粪便微生物群的组成和功能潜力。在线版本包含补充材料，可通过10.1186/s12866-023-02915-9获得。
The combination of cultivation studies with molecular analysis approaches allows characterization of the complex human gut microbiota in depth. In vitro cultivation studies of infants living in rural sub-Saharan Africa are scarce. In this study, a batch cultivation protocol for Kenyan infant fecal microbiota was validated. Fresh fecal samples were collected from 10 infants living in a rural area of Kenya. Samples were transported under protective conditions and subsequently prepared for inoculation within less than 30 h for batch cultivation. A diet-adapted cultivation medium was used that mimicked the daily intake of human milk and maize porridge in Kenyan infants during weaning. 16 S rRNA gene amplicon sequencing and HPLC analyses were performed to assess the composition and metabolic activity, respectively, of the fecal microbiota after 24 h of batch cultivation. High abundance of Bifidobacterium (53.4 ± 11.1%) and high proportions of acetate (56 ± 11% of total metabolites) and lactate (24 ± 22% of total metabolites) were detected in the Kenyan infant fecal microbiota. After cultivation started at an initial pH 7.6, the fraction of top bacterial genera (≥ 1% abundant) shared between fermentation and fecal samples was high at 97 ± 5%. However, Escherichia-Shigella, Clostridium sensu stricto 1, Bacteroides and Enterococcus were enriched concomitant with decreased Bifidobacterium abundance. Decreasing the initial pH to 6.9 lead to higher abundance of Bifidobacterium after incubation and increased the compositional similarity of fermentation and fecal samples. Despite similar total metabolite production of all fecal microbiota after cultivation, inter-individual differences in metabolite profiles were apparent. Protected transport and batch cultivation in host and diet adapted conditions allowed regrowth of the top abundant genera and reproduction of the metabolic activity of fresh Kenyan infant fecal microbiota. The validated batch cultivation protocol can be used to study the composition and functional potential of Kenyan infant fecal microbiota in vitro. The online version contains supplementary material available at 10.1186/s12866-023-02915-9.
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