Metagenome level metabolic network reconstruction analysis reveals the microbiome in the Bogotá River is functionally close to the microbiome in produced water
Ecological Modelling 2019 2.5
Universidad de los Andes
https://www.sciencedirect.com/science/article/pii/S0304380019300560?via%3Dihub
Points:
物种构成的差异并不等于功能的差异，为了了解波哥大河流的污染情况，作者重构了波哥大河流和网上下载的污染水域微生物群落的curated metagenome level network，发现波哥大河流微生物群落在功能上和污水微生物群落接近
物种构成
MG-RAST
堆积条形图
表格
代谢网络重构
gapfill 找到通路中存在gap的位置，根据数据库添加
为什么可以人为添加路径：The percentage of added reactions in the final model are re- latively small and do not significantly dilute data encoded in the me- tagenome. Other studies using gap filling curation strategy have ob- tained between 10 to 25% of participation of reactions added from an external database in the final model.
几个样本中人为添加的反应路径比例相似，不影响样本间的可比性
表格
拓扑学分析
评判样本间代谢网络是否相似：拓扑参数
表格
结构是否相似：网络图
关键代谢物筛选：The eigencentrality parameter
表格
功能注释
条形图
潜在代谢相似性
The Spearman dissimilarity on the abundance of reaction modules
树，热图
Flux balance analysis
使用反应
The Spearman dissimilarity
热图
分析流程
fastq --> FASTQC+Trimmomatic -->MG-RAST–>Enzyme Commission (EC) numbers -->KEGG–>Reaction data–>MetaNetX standard–>remove unbalanced reactions–>MetaCyc–>GapFind and GapFill algorithms–>Gephi 0.9.2 -->GAMS 23.7.1 CPLEX solver