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Microbiome Research Is Becoming the Key to Better Understanding Health and Nutrition.

ABSTRACT: The human microbiome has emerged as the crucial moderator in the interactions between food and our body. It is increasingly recognised that the microbiome can change our mind and health status, or switch on a wide range of diseases including cancer, cardio-metabolic diseases, allergies, and obesity. The causes of diseases are often only partially understood. However, nutrients, metabolites, and microbes are increasingly regarded as key players, even where the complete disease mechanisms remain unclear. The key to progress in the future will be to use and exploit additional, newly emerging disciplines such as metagenomics to complement patient information and to bring our understanding of diseases and the interrelation and effects of nutritional molecules to the next level. The EU has already funded 216 projects under the 7th Framework Programme and Horizon 2020 programmes to promote metagenomics and to advance our knowledge of microbes. This support started with the catalysing MetaHIT project that has produced a catalogue of gut microbes, and has arrived now at the very multi-disciplinary SYSCID action looking at how the microbiome is driving its resilience potential and our health. Together, these projects involve an investment of more than €498 M. However, in Horizon 2020, the new EU Health and Food Work Programmes for 2018-2020 go even further by setting new goals to find applications and to generate more knowledge on the microbiome, nutrition, various hosts of microbes, and their relation to health and disease. The big vision is to modulate health and diseases via the microbiome and nutrition, while at the same time other factors such as omics, molecular signatures, and lifestyle are constant. In this way, microbiome and nutrition research is moving from an isolated and despised offside position to a beacon of hope with a lot of potential and possibilities.

SUBMITTER: Hadrich D

PROVIDER: S-EPMC6009232 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Microbiome Research Is Becoming the Key to Better Understanding Health and Nutrition.

Hadrich Dirk D

Frontiers in genetics 20180613

The human microbiome has emerged as the crucial moderator in the interactions between food and our body. It is increasingly recognised that the microbiome can change our mind and health status, or switch on a wide range of diseases including cancer, cardio-metabolic diseases, allergies, and obesity. The causes of diseases are often only partially understood. However, nutrients, metabolites, and microbes are increasingly regarded as key players, even where the complete disease mechanisms remain u ...[more]

PMID: 29951086

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Project description:Microbial sequences inferred as belonging to one sample may not have originated from that sample. Such contamination may arise from laboratory or reagent sources or from physical exchange between samples. This study seeks to rigorously assess the behavior of this often-neglected between-sample contamination. Using unique bacteria, each assigned a particular well in a plate, we assess the frequency at which sequences from each source appear in other wells. We evaluate the effects of different DNA extraction methods performed in two laboratories using a consistent plate layout, including blanks and low-biomass and high-biomass samples. Well-to-well contamination occurred primarily during DNA extraction and, to a lesser extent, in library preparation, while barcode leakage was negligible. Laboratories differed in the levels of contamination. Extraction methods differed in their occurrences and levels of well-to-well contamination, with plate methods having more well-to-well contamination and single-tube methods having higher levels of background contaminants. Well-to-well contamination occurred primarily in neighboring samples, with rare events up to 10 wells apart. This effect was greatest in samples with lower biomass and negatively impacted metrics of alpha and beta diversity. Our work emphasizes that sample contamination is a combination of cross talk from nearby wells and background contaminants. To reduce well-to-well effects, samples should be randomized across plates, samples of similar biomasses should be processed together, and manual single-tube extractions or hybrid plate-based cleanups should be employed. Researchers should avoid simplistic removals of taxa or operational taxonomic units (OTUs) appearing in negative controls, as many will be microbes from other samples rather than reagent contaminants.IMPORTANCE Microbiome research has uncovered magnificent biological and chemical stories across nearly all areas of life science, at times creating controversy when findings reveal fantastic descriptions of microbes living and even thriving in what were once thought to be sterile environments. Scientists have refuted many of these claims because of contamination, which has led to robust requirements, including the use of controls, for validating accurate portrayals of microbial communities. In this study, we describe a previously undocumented form of contamination, well-to-well contamination, and show that this sort of contamination primarily occurs during DNA extraction rather than PCR, is highest with plate-based methods compared to single-tube extraction, and occurs at a higher frequency in low-biomass samples. This finding has profound importance in the field, as many current techniques to "decontaminate" a data set simply rely on an assumption that microbial reads found in blanks are contaminants from "outside," namely, the reagents or consumables.

Dataset Information

Microbiome Research Is Becoming the Key to Better Understanding Health and Nutrition.

Publications

Microbiome Research Is Becoming the Key to Better Understanding Health and Nutrition.

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