Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies

Abstract

The study of the human microbiome has become a very popular topic. Our microbial counterpart, in fact, appears to play an important role in human physiology and health maintenance. Accordingly, microbiome alterations have been reported in an increasing number of human diseases. Despite the huge amount of data produced to date, less is known on how a microbial dysbiosis effectively contributes to a specific pathology. To fill in this gap, other approaches for microbiome study, more comprehensive than 16S rRNA gene sequencing, i.e., shotgun metagenomics and metatranscriptomics, are becoming more widely used. Methods standardization and the development of specific pipelines for data analysis are required to contribute to and increase our understanding of the human microbiome relationship with health and disease status.

Microbiota and Human Reproduction: The Case of Female Infertility

“…The availability of highly sensitive technologies, i.e., next-generation sequencing, for the in-depth study of microbial communities’ composition and richness, has prompted the interest into metagenomics. As a consequence, novel insights regarding the role of the microbiota in human physiology and pathology are gathering [ 1 , 2 , 3 ].…”

Microbiota and Human Reproduction: The Case of Male Infertility

“…Owing to the availability of high-resolution molecular methods that are able to investigate microbial communities’ richness and biodiversity, metagenomic studies have been prompted and microbes have been described in almost all body tissues and niches [ 1 , 2 , 3 ]. With regard to the male reproductive system, the semen microbiota has been described in humans and seems to play a role in healthy status maintenance [ 8 , 9 , 12 ].…”

“…Almost all human tissues host microbes that have been widely recognized as important players for human health and disease status [ 1 , 2 ]. Indeed, microbes have also been found in several body niches previously considered to be sterile, and may influence humans’ physiology and/or pathology already before birth [ 3 ].…”

“…Indeed, microbes have also been found in several body niches previously considered to be sterile, and may influence humans’ physiology and/or pathology already before birth [ 3 ]. As a consequence, the study of microbial genomes, i.e., the microbiome, has gathered increasing interest, with the aim to better understand and define the microbial contribution to human diseases, thus opening novel opportunities for diagnosis and therapy [ 1 , 2 , 3 ].…”

The High-Throughput Analyses Era: Are We Ready for the Data Struggle?

“…Today, NGS methods offer a plethora of applications investigating different biological systems, both in a deeper focused and/or genome-wide manner [ 2 , 5 , 6 , 7 , 8 , 9 , 10 , 62 ]. Each of these procedures requires specific validated pipelines to address a specific biological question, i.e., identify disease-related mutations, obtain a differential expression analysis, or define the microbiome composition [ 2 , 5 , 6 , 7 , 8 , 9 , 10 , 62 , 63 ]. These operations not only need highly qualified, specific expertise to develop highly sensitive (and preferably easy-to-use) tools for data management and analysis, but also need cooperative efforts to establish quality guidelines ensuring data comparison among different datasets and different laboratories worldwide [ 9 , 64 ].…”