Edited by: Nicole Marie Koropatkin, University of Michigan, United States
Reviewed by: Mirjam Czjzek, UMR 8227 Laboratoire de Biologie Intégrative des Modèles Marins, France; Elisabeth Lowe, Newcastle University, United Kingdom
This article was submitted to Microbial Physiology and Metabolism, a section of the journal Frontiers in Microbiology
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The human diet is temporally and spatially dynamic, and influenced by culture, regional food systems, socioeconomics, and consumer preference. Such factors result in enormous structural diversity of ingested glycans that are refractory to digestion by human enzymes. To convert these glycans into metabolizable nutrients and energy, humans rely upon the catalytic potential encoded within the gut microbiome, a rich collective of microorganisms residing in the gastrointestinal tract. The development of high-throughput sequencing methods has enabled microbial communities to be studied with more coverage and depth, and as a result, cataloging the taxonomic structure of the gut microbiome has become routine. Efforts to unravel the microbial processes governing glycan digestion by the gut microbiome, however, are still in their infancy and will benefit by retooling our approaches to study glycan structure at high resolution and adopting next-generation functional methods. Also, new bioinformatic tools specialized for annotating carbohydrate-active enzymes and predicting their functions with high accuracy will be required for deciphering the catalytic potential of sequence datasets. Furthermore, physiological approaches to enable genotype-phenotype assignments within the gut microbiome, such as fluorescent polysaccharides, has enabled rapid identification of carbohydrate interactions at the single cell level. In this review, we summarize the current state-of-knowledge of these methods and discuss how their continued development will advance our understanding of gut microbiome function.
Human diets contain a vast diversity of complex carbohydrates; yet the human genome encodes only 17 known digestive enzymes to digest lactose, starch, and sucrose (
Human diets contain structurally diverse carbohydrates that vary between food groups (
Examples of carbohydrates in human foods grouped by source.
It is common knowledge that dietary fiber is good for digestive health and the abundance of available supplements, such as Metamucil® derived from the
Among the currently accepted sources of prebiotics, inulin-type fructans and fructooligosaccharides (
Different glycomic methods are required to study unique structural features of carbohydrates, such as linkage, monosaccharide content, or dp, and selecting the appropriate preparative and analytical method needs to be carefully considered (
Several methods exist to provide a more detailed understanding of carbohydrate structures. For example, GC-MS/FID is a preeminent tool for linkage analysis (methylation analysis) of food carbohydrates (
The human gut microbiome encodes a wealth of carbohydrate-active enzymes (CAZymes) designed for the biosynthesis and modification of glycans and their derivatives, as well as the saccharification of dietary glycans to promote the growth of metabolically capable microbes. CAZymes have evolved to accommodate the diversity of monosaccharide composition, stereochemical linkage, and branching of dietary glycans (
The CAZy database, established in 1999, is responsible for the curation of CAZyme classes and families (
Current
Not all polyspecific families have been divided into subfamilies. This is the case for GH92s, which have been shown to be tailored for saccharification of α-mannans in fungal polysaccharides and human glycans, with members tailored for α-1,2, α-1,3, α-1,4, α-1,6 linked and α-1-mannosyl-phosphate substrates (
Although the accuracy and ease of functional gene prediction is rapidly improving, advances in functional assignment of microbial-glycan interactions have been limited. This is because cultivation can be difficult and low throughput (
Most carbohydrate probes are produced by isotope or chemical labeling. Historically, radioactive and stable isotope probes have been used to characterize cellular function, most commonly with isotopic monosaccharide and oligosaccharides that are commercially prepared (
Relative to isotopic labels, chemical labels are often less expensive, more easily detected, and include a wider variety of adducts that can be used simultaneously to create multi-colored images. Several strategies exist to conjugate a carbohydrate to a chemical adduct. One example is click chemistry, which is a unique approach to study biomolecules in living systems (
Another commonly used chemical labeling method to study carbohydrates in biological systems is fluorescence-based labeling (
Although FLA-PS have been used to study glycan metabolism in marine systems since the 1990s (
Moving forward, FLA-PS has great potential to streamline the identification and isolation of metabolically active microorganisms in microbiome research. FLA-PS could be used to visualize spatial distribution and mobility of fluorescent carbohydrates in the gastrointestinal tract of animals using whole-body imaging systems or as a means to sort metabolically active cells by fluorescence-activated cell sorting (FACS) (
Dietary glycans shape the structure, function, and diversity of the gut microbiome. New methods have provided a welcomed refresh to the toolkit researchers have to study glycan structure and determine how they interact with members of the gut microbiome. These recent technical advances will provide unprecedented insight into processes by which glycans are selectively consumed by bacterial populations within complex microbial communities. Combined use of glycomics, CAZyme bioinformatic tools, and chemical probes to study next-generation physiology approaches will be pivotal for deciphering sequence datasets and open a new frontier for prescribed use of glycans as drivers of microbiome function and human health.
LK wrote main section of the manuscript and prepared figures. XX wrote glycomics section and verified carbohydrate structures in
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
The Supplementary Material for this article can be found online at: