Gene expression profiling gut microbiota in different races of humans

Abstract

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.

RIFS: a randomly restarted incremental feature selection algorithm

“…This study proposes two hypothetical modifications of the Incremental Feature Selection (IFS) strategy 13,20,48 based on the experiment data, as shown in Fig. 2.…”

The interaction between invariant Natural Killer T cells and the mucosal microbiota

“…Host-derived variables, like gender and genetics, are known to impact the microbiota. 102,103 The list is longer for environmental variables, inducing the diet (e.g. fibre content, antibiotics/probiotics), housing (e.g.…”

Intestinal Microbiota: Facts and Fiction

“…But when comparing 2 groups, healthy and diseased, the quality of both is equally important. Environmental factors, such as eating habits, medication, age and place of residence [40,41] , or other diseases and conditions [42] may independently influence both control and IBD groups, thus causing noise in the data. In reality, it is almost impossible to control all these factors in other ways than with large numbers of samples.…”

“…In fact, microbiota of healthy resident of industrialized country may be considered dysbiotic, when compared with microbiota of primitive hunter-gatherers [43] . While not the major factor, human genetics could shape the gut microbiome [44] ; yet the analyses of microbiota across all races are rare [41] . Taken together, the definitions of 'healthy gut microbiota' and dysbiosis are far from being perfect and may be unique for particular study.…”