Genetic variation and function: revealing potential factors associated with microbial phenotypes

Abstract

Innovations in sequencing technology have generated voluminous microbial and host genomic data, making it possible to detect these genetic variations and analyze the function influenced by them. Recently, many studies have linked such genetic variations to phenotypes through association or comparative analysis, which have further advanced our understanding of multiple microbial functions. In this review, we summarized the application of association analysis in microbes like Mycobacterium tuberculosis , focusing on screening of microbial genetic variants potentially associated with phenotypes such as drug resistance, pathogenesis and novel drug targets etc .; reviewed the application of additional comparative genomic or transcriptomic methods to identify genetic factors associated with functions in microbes; expanded the scope of our study to focus on host genetic factors associated with certain microbes or microbiome and summarized the recent host genetic variations associated with microbial phenotypes, including susceptibility and load after infection of HIV, presence/absence of different taxa, and quantitative traits of microbiome, and lastly, discussed the challenges that may be encountered and the apparent or potential viable solutions. Gene-function analysis of microbe and microbiome is still in its infancy, and in order to unleash its full potential, it is necessary to understand its history, current status, and the challenges hindering its development.

Identifying Host and Bacterial Biomarkers to Predict Sepsis

“…Combined with classical gene knockout studies they can be a powerful tool which give greater understanding to disease progression and may serve as potential markers of infection in addition, identifying genes and mechanisms associated with infection may lead to a greater diversity of therapeutic options for many infectious diseases [451]. Several different tools have become available for identifying genetic associations between bacterial traits all of which have advantages and disadvantages [439,452].…”