Data from: Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome

The human gut microbiota is an important metabolic organ. However, little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In the current study, gnotobiotic mice colonized with a simplified model microbiota composed of 12 sequenced human gut bacterial species were fed oscillating diets of disparate composition. Rapid, reproducible and reversible changes in community structure were observed. Time series microbial RNA-Seq analyses revealed staggered functional responses to diet shifts throughout the community that were heavily focused on carbohydrate and amino acid metabolism. High-resolution shotgun metaproteomics confirmed many of these responses at a protein level. One member, Bacteroides cellulosilyticus WH2, proved exceptionally fit regardless of diet. Its genome encoded more carbohydrate active enzymes than any known Bacteroidetes. Transcriptional profiling indicated that B. cellulosilyticus WH2 is an adaptive forager that tailors its versatile carbohydrate utilization strategy to available dietary polysaccharides, with a strong emphasis on plant-derived xylans abundant in dietary staples like cereal grains. Two highly expressed, diet-specific polysaccharide utilization loci (PULs) in B. cellulosilyticus WH2 were identified, one with characteristics of xylan utilization systems. Introduction of a B. cellulosilyticus WH2 library comprising 26,750 isogenic transposon mutants into gnotobiotic mice along with other model community members confirmed that these loci represent critical diet-specific fitness determinants. The specific carbohydrates that trigger overexpression of these two loci and many of the organism's 111 other predicted PULs were identified by RNA-Seq during in vitro growth on 31 distinct carbohydrate substrates, allowing us to better interpret in vivo RNA-Seq and proteomics data. These results offer insight into how gut microbes adapt to dietary perturbations, both at a community level and from the perspective of a well-adapted symbiont with exceptional saccharolytic capabilities, and illustrate the value of studying defined models of the human gut microbiota.人体肠道菌群（human gut microbiota）是一类关键的代谢器官。然而，学界对其单个菌种如何相互协作、确立优势定植地位，以及如何响应饮食等环境因子变化的认知仍较为有限。本研究中，研究人员对定植了由12株已测序人体肠道细菌组成的简化模式菌群的悉生小鼠（gnotobiotic mice）喂食成分迥异的周期性变换饮食。实验观察到菌群群落结构发生快速、可重复且可逆的动态变化。时序微生物RNA测序（RNA-Seq）分析显示，整个群落对饮食转变呈现出交错的功能响应，且此类响应高度集中于碳水化合物与氨基酸代谢通路。高分辨率鸟枪法宏蛋白质组学（shotgun metaproteomics）在蛋白质层面验证了诸多此类响应。其中一株菌种——解纤维素拟杆菌WH2（Bacteroides cellulosilyticus WH2）——无论饮食条件如何，均展现出极强的适应性定植能力。该菌的基因组编码的碳水化合物活性酶（carbohydrate-active enzymes, CAZymes）数量超过所有已知拟杆菌门（Bacteroidetes）菌种。转录组分析（transcriptional profiling）显示，解纤维素拟杆菌WH2属于适应性觅食型共生菌，可根据可获取的膳食多糖灵活调整其多功能碳水化合物利用策略，尤其偏好谷物等主食中富含的植物源性木聚糖。研究在解纤维素拟杆菌WH2中鉴定出两个高表达的饮食特异性多糖利用基因座（polysaccharide utilization loci, PULs），其中一个具备木聚糖利用系统的典型特征。将包含26750株同基因转座子突变体（transposon mutants）的解纤维素拟杆菌WH2突变文库，与其他模式群落菌种共同定植于悉生小鼠体内，实验证实这两个基因座是至关重要的饮食适应性定植决定因子。研究通过在31种不同碳水化合物底物上开展体外（in vitro）培养的RNA测序，鉴定出可诱导这两个基因座以及该菌种其余111个预测多糖利用基因座过度表达的特异性碳水化合物，为体内（in vivo）RNA测序与宏蛋白质组学数据的解读提供了更清晰的依据。本研究结果既从群落生态学层面，也从一株具备卓越糖分解能力的适应性共生菌的视角，揭示了肠道微生物如何响应饮食扰动，并彰显了构建并研究人体肠道菌群简化模式模型的重要学术价值。