Abstract
Gut microbiomes are integral microflora located in the human intestine with particular symbiosis. Among all microorganisms in the human intestine, bacteria are the most significant subgroup that contains many unique and functional species. The distribution patterns of bacteria in the human intestine not only reflect the different microenvironments in different sections of the intestine but also indicate that bacteria may have unique biological functions corresponding to their proper regions of the intestine. However, describing the functional differences between the bacterial subgroups and their distributions in different individuals is difficult using traditional computational approaches. Here, we first attempted to introduce four effective sets of bacterial features from independent databases. We then presented a novel computational approach to identify potential distinctive features among bacterial subgroups based on a systematic dataset on the gut microbiome from approximately 1,500 human gut bacterial strains. We also established a group of quantitative rules for explaining such distinctions. Results may reveal the microstructural characteristics of the intestinal flora and deepen our understanding on the regulatory role of bacterial subgroups in the human intestine.
Highlights
Gut microbiome refers to the integral microflora that is located in the human intestine and has symbiosis with human beings (Arumugam et al, 2011;Yatsunenko et al, 2012)
In the present study, using the dataset established by a systematic analysis on the gut microbiome from approximately 1500 human gut bacteria phyla (Zou et al, 2019), we presented a novel computational approach to identify the potential distinctive features among bacterial subgroups and established a group of quantitative rules for explaining such distinctions
We extracted 993 features to represent each sample. These features consist of 342 Antibiotic Resistance Genes Database (ARDB) features, 259 Comprehensive Antibiotic Resistance Database (CARD) features, 243 Kyoto Encyclopedia of Genes and Genomes (KEGG) features, and 149 Virulence Factor Database (VFDB) features, wherein the names and values are given in Supplementary Table S1
Summary
Gut microbiome refers to the integral microflora that is located in the human intestine and has symbiosis with human beings (Arumugam et al, 2011;Yatsunenko et al, 2012). In different sections of the human intestine, the species distributions of bacteria are quite different (Reichardt et al, 2014). In the gut, almost all the identified bacteria are anaerobes; in the cecum, aerobic bacteria, another subgroup of bacteria, are predominant (Wells et al, 1987; Kelly et al, 2004). Such distribution patterns of bacteria in the human intestine reflect the different microenvironments in different sections of the intestine and indicate that bacteria may have their unique biological
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