Gnanasekaran Thiyagarajan, Assis Geraldo Juliana, Ahrenkiel David Wilczek, Alvarez-Silva Camila, Saenz Carmen, Khan Adnan, Hanteer Obaida, Gunalan Vithiagaran, Trost Kajetan, Moritz Thomas, Arumugam Manimozhiyan
Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagengrid.5254.6, Copenhagen, Denmark.
mSystems. 2021 Aug 31;6(4):e0023221. doi: 10.1128/mSystems.00232-21. Epub 2021 Jul 27.
Longitudinal studies of gut microbiota following specific interventions are vital for understanding how they influence host health. However, robust longitudinal sampling of gut microbiota is a major challenge, which can be addressed using fermentors hosting complex microbial communities. Here, by employing 16S rRNA gene amplicon sequencing, we investigated the adaptation and succession of human fecal microbial communities in an automated multistage fermentor. We performed two independent experiments using different human donor fecal samples, one configured with two units of three colon compartments each studied for 22 days and another with one unit of two colon compartments studied for 31 days. The fermentor maintained a trend of increasing microbial alpha diversity along colon compartments. Within each experiment, microbial compositions followed compartment-specific trajectories and reached independent stable configurations. While compositions were highly similar between replicate units, they were clearly separated between different experiments, showing that they maintained the individuality of fecal inoculum rather than converging on a fermentor-specific composition. While some fecal amplicon sequence variants (ASVs) were undetected in the fermentor, many ASVs undetected in the fecal samples flourished . These bloomer ASVs accounted for significant proportions of the population and included prominent health-associated microbes such as Bacteroides fragilis and Akkermansia muciniphila. Turnover in community compositions is likely explained by feed composition and pH, suggesting that these communities can be easily modulated. Our results suggest that fermentors are promising tools to study complex microbial communities harboring important members of human gut microbiota. fermentors that can host complex gut microbial communities are promising tools to investigate the dynamics of human gut microbiota. In this work, using an automated gut fermentor consisting of different colon compartments, we investigated the adaptation dynamics of two different human fecal microbial communities over 22 and 31 days. By observing the temporal trends of different community members, we found that many dominant members of the fecal microbiota failed to maintain their dominance , and some of the low-abundance microbes undetected in the fecal microbiota successfully grew in the communities. Microbiome compositional changes and blooming could largely be explained by feed composition and pH, suggesting that these communities can be modulated to desired compositions via optimizing culture conditions. Thus, our results open up the possibility of modulating microbial communities to predefined compositions by optimizing feed composition and culture conditions.
对特定干预措施后的肠道微生物群进行纵向研究，对于理解它们如何影响宿主健康至关重要。然而，对肠道微生物群进行可靠的纵向采样是一项重大挑战，使用承载复杂微生物群落的发酵罐可以解决这一问题。在这里，通过采用16S rRNA基因扩增子测序，我们研究了人类粪便微生物群落在自动多级发酵罐中的适应和演替。我们使用不同人类供体的粪便样本进行了两项独立实验，一个实验配置了两个单元，每个单元有三个结肠隔室，研究22天，另一个实验有一个单元，包含两个结肠隔室，研究31天。发酵罐维持了微生物α多样性沿结肠隔室增加的趋势。在每个实验中，微生物组成遵循特定隔室的轨迹，并达到独立的稳定构型。虽然重复单元之间的组成高度相似，但不同实验之间明显分开，表明它们保持了粪便接种物的个体性，而不是趋向于发酵罐特有的组成。虽然一些粪便扩增子序列变体（ASV）在发酵罐中未被检测到，但许多在粪便样本中未被检测到的ASV却大量繁殖。这些大量繁殖的ASV在菌群中占相当大的比例，包括与健康相关的重要微生物，如脆弱拟杆菌和嗜黏蛋白阿克曼氏菌。群落组成的变化可能是由饲料组成和pH值解释的，这表明这些群落可以很容易地被调节。我们的结果表明，发酵罐是研究包含人类肠道微生物群重要成员的复杂微生物群落的有前途的工具。能够承载复杂肠道微生物群落的发酵罐是研究人类肠道微生物群动态的有前途的工具。在这项工作中，我们使用一个由不同结肠隔室组成的自动肠道发酵罐，研究了两种不同人类粪便微生物群落在22天和31天内的适应动态。通过观察不同群落成员的时间趋势，我们发现粪便微生物群的许多优势成员未能保持其优势地位，并且一些在粪便微生物群中未被检测到的低丰度微生物在群落中成功生长。微生物组组成的变化和大量繁殖在很大程度上可以由饲料组成和pH值解释，这表明可以通过优化培养条件将这些群落调节到所需的组成。因此,我们的结果开启了通过优化饲料组成和培养条件将微生物群落调节到预定义组成的可能性。
