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Page 2 of 20 Puhlmann et al. Microbiome Res Rep 2024;3:28 https://dx.doi.org/10.20517/mrr.2024.04

biopsies to fermentation supernatants in an Ussing chamber model.

Results: The plant cell matrix of dried chicory root cubes remained intact throughout upper gastrointestinal transit.
Dried chicory root fermentation resulted in higher final relative abundances of pectin-degrading Monoglobus and
butyrate-producing Roseburia spp. compared to inulin and a seven-fold increase in Bifidobacterium spp. in donors
where these species were present. Dried chicory root cubes yielded similar total SCFAs but higher final butyrate
levels than chicory root powder or isolated inulin with less gas produced. No uniform but donor-specific effects of
fermentation supernatants on the maintenance of gut barrier integrity were detected.

Conclusion: The intact plant cell matrix of dried chicory root affected its colonic breakdown kinetics and
microbiota, underpinning its beneficial effect in vivo.

Keywords: Plant cell wall, chicory root, intrinsic fiber, gut health, gut microbiota, colonic fermentation, butyrate
production

INTRODUCTION
Dietary fibers are omnipresent in human food products and play a fundamental role in maintaining human
health. The health benefit of fibers was originally attributed to their physicochemical properties, which
[1]
improve satiety by water-binding and regulate lipid homeostasis by binding cholesterol and bile acids .
However, research of the past two decades revealed that a large part of the beneficial effect of fibers is
mediated by the human gastrointestinal tract microbiota. As dietary fibers are, by definition, compounds
[2,3]
that cannot be broken down by human endogenous enzymes, they reach the lower gut undigested . There,
they are used as substrates by the human gut microbiota, a collective of fungi, protozoa, archaea, and
predominantly bacteria that have the enzymatic machinery to break down dietary fibers and thereby
produce a range of microbial metabolites . The interaction between the gut microbiota, its metabolites, and
[4]
the human body mediates the beneficial effect of fibers on human health beyond their physical interaction
with the upper gastrointestinal tract. A major group of fiber-derived bacterial metabolites are short-chain
fatty acids (SCFAs), including acetate, propionate, and butyrate, that signal to GPR receptors and may have
[5]
local or systemic effects . Notably, butyrate has been recognized to be essential for maintaining human gut
health as it serves as fuel for colonocytes, strengthens the gut lining, and improves gut barrier function .
[6]
That has led to increasing efforts to understand how butyrate production in the human colon can be
stimulated using dietary fibers.

Approaches to studying fiber-microbiota relationships have progressively become reductionist with a focus
on single fibers’ molecular breakdown . One particularly studied fiber is inulin, known for its prebiotic
[7]
effect, which means it is selectively used by human gut bacteria - notably bifidobacteria - thereby conferring
[3]
health benefits , contributing to a health claim for stool frequency maintenance . Another well-studied
[8]
group of fibers includes pectins that have been recognized to regulate postprandial glucose response, blood
[9]
cholesterol levels, and satiety , while some of their fragments have immune-modulatory benefits (RG-I ).
[10]
For the purpose of establishing such structure-function relationships and health outcomes, fibers are often
studied in isolation, which means they have been extracted and purified from the original plant food matrix.
It is hypothesized that these isolated fibers are mainly fermented in the proximal colon with subsequently
low levels of SCFAs in the distal colon, which favors fermentation of residual proteins [11,12] . While these
reductionist approaches allow us to understand how specific fibers elicit specific microbial responses, they
ignore how fibers are commonly consumed: intrinsically present in plants foods with each their unique
plant cell matrix [13,14] . Fibers like pectin and inulin in plant foods make up an intrinsic, complex plant cell
network in which pectin is intertwined with hemicellulose and cellulose, forming the structure of the plant