Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research
نویسندگان
چکیده
Sequence-based approaches to study microbiomes, such as 16S rRNA gene sequencing and metagenomics, are uncovering associations between microbial taxa and a myriad of factors. A drawback of these approaches is that the necessary sequencing library preparation and bioinformatic analyses are complicated and continuously changing, which can be a barrier for researchers new to the field. We present three essential components to conducting a microbiome experiment from start to finish: first, a simplified and step-by-step custom gene sequencing protocol that requires limited lab equipment, is cost-effective, and has been thoroughly tested and utilized on various sample types; second, a series of scripts to integrate various commonly used bioinformatic tools that is available as a standalone installation or as a single downloadable virtual image; and third, a set of bioinformatic workflows and tutorials to provide step-by-step guidance and education for those new to the microbiome field. This resource will provide the foundations for those newly entering the microbiome field and will provide much-needed guidance and best practices to ensure that quality microbiome research is undertaken. All protocols, scripts, workflows, tutorials, and virtual images are freely available through the Microbiome Helper website (https://github.com/mlangill/microbiome_helper/wiki). IMPORTANCE As the microbiome field continues to grow, a multitude of researchers are learning how to conduct proper microbiome experiments. We outline here a streamlined and custom approach to processing samples from detailed sequencing library construction to step-by-step bioinformatic standard operating procedures. This allows for rapid and reliable microbiome analysis, allowing researchers to focus more on their experiment design and results. Our sequencing protocols, bioinformatic tutorials, and bundled software are freely available through Microbiome Helper. As the microbiome research field continues to evolve, Microbiome Helper will be updated with new protocols, scripts, and training materials.
منابع مشابه
A Metagenomic Analysis of Lung Microbiome in Chemically Injured and Healthy Individuals
Background and Aim: The role of the lung microbiome in respiratory complications associated with chemicals such as sulfur mustard or chlorine gas has yet to be determined. The aim of this study was to compare the structure and composition of the lung microbiome in chemically injured and healthy individuals in order to understand the relation between the population of the lung microbiota and res...
متن کاملHuman Microbiome
Humans are almost identical in their genetic pattern, but the slight differences in our DNA lead to remarkable phenotypic variation among the human population. There are a variety of microbial communities and their genes (microbiomes) in the human body that play an essential role in human health and disease. The microbes inhabiting our bodies is quite a bit more variable, with only a third of i...
متن کاملNext Generation Sequencing and its Application in the Study of Microbiome in Plant Diseases Suppressive Soils
Progress in next-generation sequencing has played a significant role in ecological studies of microbial populations. These advances have led to a rapid evaluation in metagenomics studies (analysis of DNA of microbial communities without the need to culture). Many statistical and computational tools and metagenomics databases have led to the discovery of huge amounts of data. In this research, i...
متن کاملA Review of The Role of The Microbiome on Immune Responses and Its Association With Cystic Fibrosis
In recent years, the microbiome has been recognized as a key regulator of immune responses. Evidence suggests that changes in the microbiome can lead to chronic disease and even exacerbation of the disease. Impairment of innate immunity resulting from microbial incompatibility may worsen host susceptibility to infection and exacerbate chronic lung diseases. Specific microbes play a key role in ...
متن کاملRole of Gut Microbiome in Polycystic Ovary Syndrome
Polycystic ovary syndrome (PCOS) is a complex endocrine disorder that affects 8-13% of women at reproductive age worldwide. This disorder is usually associated with menstrual disorders, infertility, obesity, and insulin resistance. The underlying cause of this syndrome is unknown, however in recent years, researchers have shown an association between intestinal microbiota alterations )dysbiosi...
متن کامل