Abstract
To understand the activities of complex microbial communities in various natural environments and living organisms, we need to capture the compositional changes in their taxonomic abundance. Here, we propose a new computational framework to detect compositional changes in microorganisms, including minor bacteria. This framework is designed to statistically assess relative variations in taxonomic abundance. By using this approach, we detected compositional changes in the human gut microbiome that might be associated with short-term human dietary changes. Our approach can shed light on the compositional changes of minor microorganisms that are easily overlooked.
Highlights
A vast variety of microbial communities exist in various environments, such as the ocean, soil, and parts of living organisms [1,2,3,4]
We described microorganisms whose composition significantly changed after the diet intervention as outliers
To detect the diet-induced taxonomic abundance changes across the study period, the authors performed high-throughput amplicon sequencing for the 16S ribosomal RNA gene and the internal transcribed spacer region for several bacteria (Lactococcus lactis, Pediococcus acidilactici, Staphylococcus, Streptococcus thermophilus) and fungi (Candida sp., Debaryomyces, Penicillium, Scopulariopsis), which may be associated with the animal-based diet
Summary
A vast variety of microbial communities exist in various environments, such as the ocean, soil, and parts of living organisms [1,2,3,4]. The majority of the microorganisms in these environments remain uncultured. Next-generation sequencing (NGS) technologies have opened the possibility of performing genetic analyses of these culture-independent microorganisms [5]. Bioinformatics approaches for NGS technologies can promote the understanding of complex microbial communities [6], but the roles of many microorganisms remain to be clarified. The knowledge of bacterial taxonomic composition changes in various environments is essential to understand the roles of their complex communities [7,8]. Further investigations of taxonomic compositional variation in microbial communities may highlight the potential roles of several microorganisms
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