Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment

Abstract

The interaction between the human microbiome and immune system has an effect on several human metabolic functions and impacts our well-being. Additionally, the interaction between humans and microbes can also play a key role in determining the wellness or disease status of the human body. Dysbiosis is related to a plethora of diseases, including skin, inflammatory, metabolic, and neurological disorders. A better understanding of the host-microbe interaction is essential for determining the diagnosis and appropriate treatment of these ailments. The significance of the microbiome on host health has led to the emergence of new therapeutic approaches focused on the prescribed manipulation of the host microbiome, either by removing harmful taxa or reinstating missing beneficial taxa and the functional roles they perform. Culturing large numbers of microbial taxa in the laboratory is problematic at best, if not impossible. Consequently, this makes it very difficult to comprehensively catalog the individual members comprising a specific microbiome, as well as understanding how microbial communities function and influence host-pathogen interactions. Recent advances in sequencing technologies and computational tools have allowed an increasing number of metagenomic studies to be performed. These studies have provided key insights into the human microbiome and a host of other microbial communities in other environments. In the present review, the role of the microbiome as a therapeutic agent and its significance in human health and disease is discussed. Advances in high-throughput sequencing technologies for surveying host-microbe interactions are also discussed. Additionally, the correlation between the composition of the microbiome and infectious diseases as described in previously reported studies is covered as well. Lastly, recent advances in state-of-the-art bioinformatics software, workflows, and applications for analysing metagenomic data are summarized.

The Role of the Cervicovaginal Microbiome on the Genesis and as a Biomarker of Premalignant Cervical Intraepithelial Neoplasia and Invasive Cervical Cancer

“…Currently, second generation high-throughput sequencing (HTS) technologies, such as those provided by Illumina platforms, are being extensively applied to microbiome studies. More recently, third generation HTS technologies have also reached and contributed to the microbiome research field [24,25].…”

Press disturbance unveils different community structure, function and assembly of bacterial taxa and functional genes in mesocosm-scale bioreactors

“…Not surprisingly, the majority of existing studies on microbial community assembly focused on taxonomic OTU datasets from 16S rRNA gene metabarcoding [17,18,[33][34][35][36][37][38], while a few others evaluated functional data via GeoChip [22,43]. To our knowledge, only one previous study used metagenomics data to interrogate assembly mechanisms in microbial communities [21], despite the fact that the trend in microbial community analysis is moving towards metagenomics with the advent of faster, PCRindependent, long-read sequencing [82].…”

Computational Modeling of the Human Microbiome

“…However, the limit in the read length in these kinds of studies sometimes misses the detection of some bacterial species and strains [8]. Although, this has been a long standing problem for now, people have already started making efforts to address this issue by utilizing recently developed sequencing technologies [74,75]. These are one molecule real time technologies which have been shown to decrease the short read problems and furthermore, a higher data yield at lower cost can be obtained by using this approach [76].…”