Next-generation physiology approaches to study microbiome function at single cell level

Abstract

The function of cells in their native habitat often cannot be reliably predicted from genomic data or from physiology studies of isolates. Traditional experimental approaches to study the function of taxonomically and metabolically diverse microbiomes are limited by their destructive nature, low spatial resolution, or low throughput. Recently developed technologies can offer new insights into cellular function in natural and human-made systems and how microorganisms interact with and shape the environments that they inhabit. In this Review, we provide an overview of these next-generation physiology approaches and discuss how the non-destructive analysis of cellular phenotypes, in combination with the separation of the target cells for downstream analyses, provide powerful new, complementary ways to study microbiome function. We anticipate that the widespread application of next-generation physiology approaches will transform the field of microbial ecology and dramatically improve our understanding of how microorganisms function in their native environment. ToC blurbIn this Review, Hatzenpichler et al. introduce next-generation physiology, which is a suite of new techniques that enable to investigate the phenotypes of individual cells in a non-destructive manner. Next-generation physiology complements genomics and culturing and provides new insights into microbiome function.

Metabolic Implications of Using BioOrthogonal Non-Canonical Amino Acid Tagging (BONCAT) for Tracking Protein Synthesis

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Brockarchaeota, a novel archaeal lineage capable of methylotrophy

“…Given their broad distribution, and versatile carbon metabolism, they are likely key players in global carbon cycling. However, this first description is limited to genomic characterization, thus culturing or in activity measurements are needed to confirm their physiological activities 47 . Overall, the description of this new phylum enhances our understanding of biodiversity of archaea and suggests they are mediating unique roles in anoxic carbon cycling.…”

Response of gut microbiota to feed-borne bacteria depends on fish growth rate: a snapshot survey of farmed juvenileTakifugu obscurus

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