Gene expression profiling gut microbiota in different races of humans

• Published in: Scientific reports 2016-03, Vol.6 (1), p.23075-23075, Article 23075
• Main Authors: Chen, Lei, Zhang, Yu-Hang, Huang, Tao, Cai, Yu-Dong
• Format: Article
• Language: English
• Subjects: 45/43; 631/208/199; 639/705/1042; Algorithms; Asian Continental Ancestry Group; China; Cluster Analysis; Digestive system; Eating behavior; Europe; European Continental Ancestry Group; Feeding Behavior - ethnology; Gastrointestinal Microbiome - genetics; Gastrointestinal tract; Gene expression; Gene Expression Profiling - methods; Humanities and Social Sciences; Humans; Intestinal microflora; Intestine; Learning algorithms; Machine Learning; Metagenome - genetics; Metagenomics - methods; Microorganisms; multidisciplinary; Oligonucleotide Array Sequence Analysis - methods; Races; Science; United States
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/srep23075

The gut microbiome is shaped and modified by the polymorphisms of microorganisms in the intestinal tract. Its composition shows strong individual specificity and may play a crucial role in the human digestive system and metabolism. Several factors can affect the composition of the gut microbiome, such as eating habits, living environment and antibiotic usage. Thus, various races are characterized by different gut microbiome characteristics. In this present study, we studied the gut microbiomes of three different races, including individuals of Asian, European and American races. The gut microbiome and the expression levels of gut microbiome genes were analyzed in these individuals. Advanced feature selection methods (minimum redundancy maximum relevance and incremental feature selection) and four machine-learning algorithms (random forest, nearest neighbor algorithm, sequential minimal optimization, Dagging) were employed to capture key differentially expressed genes. As a result, sequential minimal optimization was found to yield the best performance using the 454 genes, which could effectively distinguish the gut microbiomes of different races. Our analyses of extracted genes support the widely accepted hypotheses that eating habits, living environments and metabolic levels in different races can influence the characteristics of the gut microbiome.