论文题目:Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet
scholar 引用:2
页数:13
发表时间:2019.08
发表刊物:Cell Host & Microbe
作者:Jordan E. Bisanz, Vaibhav Upadhyay,...Peter J. Turnbaugh
摘要:
Multiple research groups have shown that diet impacts the gut microbiome; however, variability in experimental design and quantitative assessment have made it challenging to assess the degree to which similar diets have reproducible effects across studies. Through an unbiased subject-level meta-analysis framework, we re-analyzed 27 dietary studies including 1,101 samples from rodents and humans. We demonstrate that a high-fat diet (HFD) reproducibly changes gut microbial community structure. Finer taxonomic analysis revealed that the most reproducible signals of a HFD are Lactococcus species, which we experimentally demonstrate to be common dietary contaminants. Additionally, a machine-learning approach defined a signature that predicts the dietary intake of mice and demonstrated that phylogenetic and gene-centric transformations of this model can be translated to humans. Together, these results demonstrate the utility of microbiome meta-analyses in identifying robust and reproducible features for mechanistic studies in preclinical models.
Highlights:
- A generalizable approach is presented for meta-analysis of microbiome datasets
- High-fat diets induce reproducible shifts in the mouse gut microbiome
- Nonviable Lactococcus(乳球菌) contamination is widespread in experimental diets
- Phylogenetic and gene signatures translate to human microbiomes
正文组织架构:
1. Introduction
2. Results
2.1 Study Selection and Characteristics
2.2 Effect of HFD on Microbial Diversity
2.3 HFD Reproducibly Alters Community Composition
2.4 Predictive Microbial Responses to HFD
3. Discussion
正文部分内容摘录:
1. Biological Problem: What biological problems have been solved in this paper?
- meta-analysis
- investigating the effect of HFD on the gut microbiome in murine models.
2. Main discoveries: What is the main discoveries in this paper?
- Through an unbiased subject-level meta-analysis framework, we re-analyzed 27 dietary studies including 1,101 samples from rodents and humans. 明明说筛出来了25个研究做荟萃分析,但是为什么这里就变成了27个呢。。。 Two additional human studies were identified to examine translatability of mouse studies to humans 原来如此
- We demonstrate that a high-fat diet (HFD) reproducibly changes gut microbial community structure.
- Finer taxonomic analysis revealed that the most reproducible signals of a HFD are Lactococcus species, which we experimentally demonstrate to be common dietary contaminants.
- a machine-learning approach defined a signature that predicts the dietary intake of mice and demonstrated that phylogenetic and gene-centric transformations of this model can be translated to humans.
- Despite major differences in experimental design, we are able to identify microbial signatures that are consistent and predictive of HFD intake.
3. ML(Machine Learning) Methods: What are the ML methods applied in this paper?
- A total of 427 unique studies were retrieved by our search methodology, this left 25 murine studies for inclusion in our meta-analysis. 从427个研究中筛选25个合格的。。。这工作量,好吧。服。。。
- We used a random forest classifier to define reliable biomarkers of the gut microbial response to HFD. As a first pass, we conducted a leave-one-dataset-out analysis in which each study using conventionally colonized mice was systematically excluded from training and then subsequently predicted using the model, demonstrating excellent reproducibility with a median area under the receiver curve (AUROC) of 0.93 (interquartile range = 0.22) using OTU abundances.
4. ML Advantages: Why are these ML methods better than the traditional methods in these biological problems?
5. Biological Significance: What is the biological significance of these ML methods’ results?
6. Prospect: What are the potential applications of these machine learning methods in biological science?
- these results demonstrate the utility of microbiome meta-analyses in identifying robust and reproducible features for mechanistic studies in preclinical models.
- The statistical power of our meta-analysis is also reduced by the large extent of missing data for published studies.
7. Mine Question(Optional)