N0909OPBG Metagenome. human gut metagenome

Cystic fibrosis (CF), is a lethal hereditary disorder leading to respiratory infections, chronic inflammation, repeated antibiotic treatments, all of them have a known or suspected link to the gut microbiota. The aim of this work was to investigate the gut microbiota composition and modulation of CF patients by metagenomic and metabolomic combined analyses in relation with healthy children. Thirty faecal samples from either CF patients and healthy children (HC) (age range 1-6 years), were collected. After the filtering protocols, a total of 316,006 sequence reads of 16S rRNA gene amplicons were obtained with an average of 5,356 reads/sample and an average length of 487 bp calculated after primer removal. The results of alpha-diversity analysis indicated a satisfactory coverage of the microbial diversity as shown by the Good’s estimated sample coverage (ESC) that was in all cases above 97%. The sample type (CF vs HC) significantly influenced the composition of the microbiota as measured using ADONIS and ANOSIM methods (p<0.001). Accordingly, beta-diversity analyses performed by unweighted uniFrac showed a clear differentiation between CF and HC individuals suggesting that different taxa characterized the fecal microbiota of the two types of subjects. In fact, Clostridiaceae were more abundant in CF (avg. 20%) compared to HC (avg. 3%) samples (p<0.005) while Ruminococcaceae and Erysipelotrichaceae were more abundant in HC samples (p<0.005). At deeper taxonomic assignment, Clostridium sp. (avg. 9.8% in CF vs 2.2 in HC) and Clostridium difficile (avg. 2.9% in CF vs 0.0 in HC) were more abundant in CF patients (p=0.04 and p=0.01, respectively). By contrast, Eggerthella sp., Eggerthella lenta, Ruminococcus sp., Ruminococcus bromii, Dialister sp. and Dialister invisus were more abundant in HC feces (p<0.05).

囊性纤维化（Cystic fibrosis, CF）是一种致死性遗传性疾病，可引发呼吸道感染、慢性炎症，且患者需反复接受抗生素治疗；上述表型均与肠道菌群存在已知或疑似关联。本研究旨在通过宏基因组学与代谢组学联合分析，探究囊性纤维化患者的肠道菌群组成及变化特征，并与健康儿童（healthy children, HC）进行对照。本研究共收集30份粪便样本，受试者年龄区间为1~6岁，分别来自囊性纤维化患者与健康儿童。经过滤流程处理后，共获得316,006条16S rRNA基因扩增子序列读段，平均每样本包含5,356条读段；去除引物序列后，序列平均长度为487 bp。α多样性分析结果显示，所有样本的Good’s估计样本覆盖率（Good’s estimated sample coverage, ESC）均高于97%，表明本次测序对微生物多样性的覆盖度良好。采用ADONIS与ANOSIM方法分析表明，样本类型（囊性纤维化患者vs健康儿童）对菌群组成具有显著影响（p<0.001）。相应地，通过未加权UniFrac法开展的β多样性分析显示，囊性纤维化患者与健康儿童的菌群群落呈现明显分化，提示两类受试者的粪便菌群具有特征性的类群差异。具体而言，梭菌科（Clostridiaceae）在囊性纤维化患者样本中的平均丰度为20%，显著高于健康儿童样本的3%（p<0.005）；而瘤胃球菌科（Ruminococcaceae）与埃里希氏菌科（Erysipelotrichaceae）在健康儿童样本中的丰度更高（p<0.005）。在更精细的分类学水平上，梭菌属（Clostridium sp.）的平均丰度在囊性纤维化患者中为9.8%，健康儿童中为2.2%（p=0.04）；艰难梭菌（Clostridium difficile）的平均丰度在囊性纤维化患者中为2.9%，健康儿童中未检出（p=0.01）。与之相反，艾克曼菌属（Eggerthella sp.）、迟缓艾克曼菌（Eggerthella lenta）、瘤胃球菌属（Ruminococcus sp.）、布氏瘤胃球菌（Ruminococcus bromii）、嗜胆菌属（Dialister sp.）以及隐匿嗜胆菌（Dialister invisus）在健康儿童粪便样本中的丰度更高（p<0.05）。