Metagenomic Surveys of Gut Microbiota

Abstract

Gut microbiota of higher vertebrates is host-specific. The number and diversity of the organisms residing within the gut ecosystem are defined by physiological and environmental factors, such as host genotype, habitat, and diet. Recently, culture-independent sequencing techniques have added a new dimension to the study of gut microbiota and the challenge to analyze the large volume of sequencing data is increasingly addressed by the development of novel computational tools and methods. Interestingly, gut microbiota maintains a constant relative abundance at operational taxonomic unit (OTU) levels and altered bacterial abundance has been associated with complex diseases such as symptomatic atherosclerosis, type 2 diabetes, obesity, and colorectal cancer. Therefore, the study of gut microbial population has emerged as an important field of research in order to ultimately achieve better health. In addition, there is a spontaneous, non-linear, and dynamic interaction among different bacterial species residing in the gut. Thus, predicting the influence of perturbed microbe–microbe interaction network on health can aid in developing novel therapeutics. Here, we summarize the population abundance of gut microbiota and its variation in different clinical states, computational tools available to analyze the pyrosequencing data, and gut microbe–microbe interaction networks.

Factoring the intestinal microbiome into the pathogenesis of autoimmune hepatitis

“…Traditional stool culture techniques are limited in assessing the intestinal microbiome mainly because anaerobic organisms are difficult to culture[235] and some microbial species may elude detection by conventional protocols[235,236]. A common method for studying the diversity of the intestinal microflora has been to sequence the 16S ribosomal ribonucleic acid (rRNA) gene[235,237].…”

“…The 16S rRNA gene is present in all prokaryotic cells; it has highly variable regions interspersed with highly conserved regions; and its sequences are unique to the major groups of prokaryotic organisms[237]. These signature sequences can be used to reconstruct the phylogeny of the intestinal microbiome[236]. …”

“…Databases are available and they continue to evolve for analyses of 16S rRNA gene sequences[236,239]. Quantitative Insights Into Microbial Ecology (QIIME)[240] and Mothur, a comprehensive software package that integrates several algorithms from pre-existing software[241], are open-source tools that can be used to describe and compare microbial communities.…”

“…Short 16S rRNA sequences can be organized into OTUs, and a motif-based hierarchical method can analyze massive metagenomic datasets with high accuracy[242]. The Human Microbiome Project provides a catalogue of bacterial species, and it will help define the nature of the intestinal microbiome, the factors that affect its composition, distribution and evolution, and the relationship of the intestinal microflora to human health and disease[236,243,244]. …”

An Improved Methodology to Overcome Key Issues in Human Fecal Metagenomic DNA Extraction

“…The total number of microbes residing in the human body, especially in the gut, outnumbers that of human cells [3]. A vast array of recent studies has identified many microbial enterotypes in the human gut [4], [5], [6], [7], [8], [9], [10] and their potential roles in immunity [5], [7], [8], development [8], digestion [9], and other functions [10].…”