178
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Faculty of Medicine, 
University of Maribor, 
Maribor, Slovenia
Correspondence/
Korespondenca:
Maja Šikić Pogačar, e: 
maja_sikic@yahoo.com.au
Key words:
diet; gut microbiota; 
polyphenols; probiotics; 
prebiotics
Ključne besede:
prehrana; črevesna 
mikrobiota; polifenoli; 
probiotiki; prebiotiki
Prispelo: 12. 11. 2019
Sprejeto: 27. 9. 2020
eng slo element
en article-lang
10.6016/ZdravVestn.3005 doi
12.11.2019 date-received
27.9.2020 date-accepted
Gastro-enterology Gastroenterologija discipline
Professional article Strokovni članek article-type
The influence of dietary compounds on gut 
microbiota Vpliv prehrane na črevesno mikrobioto article-title
The influence of dietary compounds on gut 
microbiota Vpliv prehrane na črevesno mikrobioto alt-title
diet, gut microbiota, polyphenols, probiotics, 
prebiotics
prehrana, črevesna mikrobiota, polifenoli, probio-
tiki, prebiotiki kwd-group
The authors declare that there are no conflicts 
of interest present.
Avtorji so izjavili, da ne obstajajo nobeni 
konkurenčni interesi. conflict
year volume first month last month first page last page
2021 90 3 4 178 192
name surname aff email
Maja Šikić Pogačar 1 maja_sikic@yahoo.com.au
name surname aff
Dušanka Mičetić Turk 1
eng slo aff-id
Faculty of Medicine, University 
of Maribor, Maribor, Slovenia
Medicinska fakulteta, Univerza v 
Mariboru, Maribor, Slovenija 1
The influence of dietary compounds on gut 
microbiota
Vpliv prehrane na črevesno mikrobioto
Maja Šikić Pogačar, Dušanka Mičetić Turk
Abstract
The gut microbiota is a complex community composed of trillions of microbes that adapts to its 
host over the lifetime. Recently, the advances of the methods of high-throughput sequencing 
have allowed the identification of microbial species in a stool sample, and mass spectrometry 
identification of their metabolites, both of which together have enabled much of the relevant 
research in the field. It has became evident that gut microbiota plays an important role in human 
health and influences the risk of developing many chronic diseases, including obesity, inflam-
matory bowel disease, type 2 diabetes, cardiovascular disease, and cancer. The diverse ecosys-
tem of the gut includes bacteria, viruses, phages, yeasts, archaea, fungi and protozoa. They are 
responsible for the production of bioactive metabolites, regulation of immune function, energy 
homeostasis and protection against pathogens. The mentioned functions are dependent on the 
diversity and abundance of the microbiota which is the reflection of the dietary habits and ge-
netics of the host among other factors. As such, gut microbiota has significant interindividual 
variations. Diet and lifestyle changes present important determinants in microbiota shaping. The 
use of antibiotics, different sanitation measures, consumption of processed food and different 
diets are also reflected in the shifts of gut microbiota composition. Some of the dramatic dietary 
alterations can cause changes in gut microbiota composition already within 24 h and some of 
these changes may be difficult to reverse. Through modulation of gut microbiota composition, 
diet could offer a potential to manage the risk of developing disease and at the same time im-
proving the quality of life and longevity. In this review we look at the role of diet, and specific 
dietary components, namely carbohydrates, proteins, fats and polyphenols on gut microbiota 
composition.
Izvleček
Črevesna mikrobiota je kompleksna skupnost, sestavljena iz milijarde mikroorganizmov, ki živijo 
z gostiteljem in se mu vse življenje prilagajajo. V zadnjem času je napredek metod sekvencioni-
ranja DNK visoke zmogljivosti omogočil identificiranje posameznih vrst bakterij v vzorcu blata, 
metoda masne spektrometrije identifikacijo njihovih presnovkov, oboje pa veliko raziskav na 
tem področju. Postalo je očitno, da igra črevesna mikrobiota pomembno vlogo pri zdravju ljudi 
in vpliva na tveganje za razvoj številnih kroničnih bolezni, vključno z debelostjo, vnetno črevesno 
boleznijo, diabetesom tipa 2, srčno-žilnimi boleznimi in rakom. Raznolik ekosistem v črevesju 
zajema bakterije, viruse, fage, kvasovke, arheje, glive in protozoje. Odgovorni so za tvorbo bio-
aktivnih presnovkov, uravnavanje imunskega delovanja, energijsko homeostazo in zaščito pred 
patogenimi mikroorganizmi. Te funkcije so odvisne od raznolikosti in številčnosti mikrobiote, ki 
pa je med drugim tudi odraz prehranjevalnih navad in genetike gostitelja. Črevesna mikrobio-
ta tako kaže pomembne razlike med posamezniki. Prehrana in življenjski slog sta pomembna 
dejavnika pri oblikovanju mikrobiote. Uporaba antibiotikov, različni sanitarni ukrepi, uživanje 
predelane hrane in različne diete se kažejo tudi v spremembah sestave mikrobiote črevesja. Ne-
katere dramatične prehranske spremembe lahko povzročijo hitre spremembe v sestavi črevesne 
Slovenian
Medical
Journal
179
PROFESSIONAL ARTICLE
The influence of dietary compounds on gut microbiota
1 Introduction
Scientists have been interested in 
gut microbiota for years but the inabil-
ity to isolate and culture anaerobic mi-
croorganisms in vitro was holding back 
much of the relevant research in that 
field. With advances in the methods 
of high-throughput sequencing and 
mass-spectrometry in the last 15 years, 
it has finally become possible to identi-
fy microbial species and their function 
in a stool sample bypassing the tradi-
tional culture-dependent techniques for 
the isolation, identification and char-
acterization of microorganisms (1,2). 
Nowadays, sequencing platforms allow 
analysis of all the genomes within an 
ecosystem (i.e. shotgun metagenomics), 
or a description of the taxa within a giv-
en community by sequencing conserved 
marker genes (i.e. 16S rRNA gene). On 
the other hand, mass spectrometry al-
lowed detection of microbial derived 
products, including metabolites and 
proteins, which regulate numerous bio-
logical pathways and also facilitate inter-
species interactions within the human 
host (1,3,4).
Gut microbiota consists of a diverse 
microbial community that encompasses 
1014 microorganisms, including bacteria, 
mikrobiote, in sicer že v 24 urah, nekatere od teh sprememb pa je težko povrniti v prvotno sesta-
vo. Z moduliranjem sestave črevesne mikrobiote ponuja prehrana orodje za zmanjšanje tveganja 
za razvoj bolezni, hkrati pa izboljša kakovost življenja in vpliva na podaljšanje življenjske dobe. 
Namen preglednega članka je predstaviti dosedanje znanje o vplivu prehrane in posameznih se-
stavin hrane, in sicer ogljikovih hidratov, beljakovin, maščob in polifenolov na sestavo črevesne 
mikrobiote.
Cite as/Citirajte kot: Šikić Pogačar M, Mičetić Turk D. The influence of dietary compounds on gut microbiota. 
Zdrav Vestn. 2021;90(3–4):178–92.
DOI: https://doi.org/10.6016/ZdravVestn.3005
Copyright (c) 2021 Slovenian Medical Journal. This work is licensed under a
Creative Commons Attribution-NonCommercial 4.0 International License.
viruses, phages, yeasts, archaea, fungi 
and protozoa, all of which are commen-
sal and play a role in the complex interac-
tions within the human gastrointestinal 
(GIT) tract (2,5). Within the host, it also 
varies taxonomically and functionally 
according to the intestine anatomical re-
gions (3). The mutual synergy between 
the gut microbiota and its host is often 
being referred to as a »superorganism« 
or a host extra organ (6).
Merely in the colon, the density of 
bacterial cells has been estimated to be 
1012 colony forming units (CFU) per 
gram content (5). The dominant phy-
la in GIT are Firmicutes, Bacteroidetes, 
Actinobacteria, Proteobacteria, Fuso-
bacteria, and Verrucomicrobia. Howev-
er, gram positive Firmicutes and gram 
negative Bacteroidetes represent 90% 
of gut microbiota (3,5). A useful meth-
od to stratify human gut microbiota is 
by separation of major taxa into clusters 
termed enterotypes. Three predominant 
variants (enterotypes) were identified by 
their enrichment in Bacteroides spp. (en-
terotype 1), Prevotella spp. (enterotype 
2) and Ruminococcus spp. (enterotype 
3). Taken into account that enterotypes 
are defined depending on gut microbiota 
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and gut microbiota changes rapidly in 
response to interventions, it would be 
easy to conclude that enterotypes are not 
a constant but rather a dynamic feature 
of individuals. However, even though 
enterotype is influenced by various fac-
tors, the alternations of microbiota com-
position during short intervals of time 
is insufficient to change the enterotype 
patterns due to the reversibility and rel-
ative stability of gut microbiota. Conse-
quently, enterotypes are associated with 
long-term dietary habits and remain 
rather stable throughout the adulthood 
while at the same time are unrelated to 
nationality or host characteristics such 
as body mass index, age or gender (7). 
The gut microbiota is important for the 
health of its host by performing many 
immune and metabolic functions (3). It 
is involved in the extraction, synthesis, 
and absorption of many nutrients and 
metabolites (including bile acids, vita-
mins, amino acids) and it has a crucial 
role in preventing the colonization/in-
vasion of pathogenic bacteria through 
the consumption of available nutrients, 
pH modification, competition for ad-
hesion molecules and receptors, and/
or producing antimicrobial substances 
such as acids, bacteriocins, and others 
(3,5). The most important metabolic ac-
tivity of gut microbiota in the large in-
testine is the production of short chain 
fatty acids (SCFA) (acetate, propionate, 
and butyrate), mainly through fermen-
tation of complex carbohydrates, such 
as oligosaccharides and resistant starch 
(6,8,9). Undigested proteins are also a 
substrate for SCFA production (9). Ab-
sorbable SCFAs are considered anti-in-
flammatory, an important modulators 
of gut health and immune function, in-
testinal hormone production, and lipo-
genesis (5,8,9). Furthermore, gut micro-
biota has a critical role in regulating the 
development, homeostasis and function 
of innate and adaptive immune cells (3).
The gut microbiota composition is 
formed in infancy, when individual is 
colonized by microorganisms from care-
givers and the surrounding environment 
(10). The infant’s microbiota is rather 
instable with low diversity of bacteria 
and is strongly influenced by the mode 
of delivery, birth gestational age, type of 
feeding and the introduction of comple-
mentary feeding. It changes through the 
exposure to a variety of environmental 
factors and eventually evolves toward a 
more stable adult-like composition by 
the age of 4 years (10-15). Furthermore, 
host genetics and dietary habits are re-
sponsible for the huge variability in mi-
crobiota composition and functionality 
among individuals. Likewise, body mass 
index, antibiotics, lifestyle, exercise fre-
quency and ethnicity also influence the 
individual gut microbiota composition. 
Still, there is a similarity in microbiota 
composition among family members 
(3,11,16).
Diet is an important determinant of 
microbiota composition by modulating 
the abundance of specific species and 
their functions. These could in turn in-
duce changes in host physiology, includ-
ing disease development and progres-
sion (10-15). This review aims to provide 
the current knowledge of the role of diet 
(especially macronutrients) on gut mi-
crobiota composition but also presents 
in short other factors.
2 Influence of diet on the gut 
microbiota
In humans diet plays an important 
role in shaping the gut microbiota (17). 
It is the result of nutrient-induced selec-
tive pressures placed on the gut microbi-
ota, favouring bacterial species enriched 
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The influence of dietary compounds on gut microbiota
in the genes required for specific sub-
strate metabolism (18).
There were several fundamen-
tal changes in the lifestyle of humans 
throughout the history, which had an 
impact on the co-evolution of microbi-
al species associated with the host. The 
last radical change of dietary habits oc-
curred less than 200 years ago with the 
Industrial Revolution and the shift away 
from local and seasonal foods. Gut mi-
crobiota had to adapt to these profound 
changes in human diet. The modern diet 
is characterized by a high intake of ani-
mal products and sugars, low intake of 
plant-based foods (fruits, vegetables and 
wholegrain cereals) and the use of addi-
tives and preservatives (5).
Even though the gut microbiota of 
a healthy adult is relatively stable, the 
changes in gut microbiota composition 
and/or abundance occur frequently 
due to dietary choices. Fruits and nuts, 
whole grain products, vegetables and le-
gumes, meat and diary products, as well 
as food constituents, such as fat, protein, 
phytochemicals and fibres, impact gut 
microbiota composition in humans (17). 
In general, plant-based diets increase lu-
minal fibre and complex carbohydrate 
content selecting for species enriched 
in carbohydrate-active enzymes. On the 
other hand, animal-based diets that are 
rich in fats and proteins and low in fi-
bre increase luminal bile acid content, 
favouring bile acid-resistant microbes 
enriched with genes for bile acid metab-
olism, such as bile salt hydrolases and 
sulfite reductase (18).
Particularly significant changes in di-
et (i.e. shifting from meat-based diets to 
strictly plant based) alter the composi-
tion and function of gut microbiota fast, 
already within 24 h (5,19). Furthermore, 
if the diet becomes less diverse or defi-
cient in some nutrients, some species of 
the gut microbiota are cut off causing the 
disruption between the host and its in-
testinal microbiota. On contrary, a var-
ied diet provides nutrients for a plethora 
of species of gut microbiota, which helps 
maintain homeostasis in the gut (11).
3 Carbohydrates and fibres
It has been estimated that the quanti-
ty of dietary carbohydrates that enter the 
colon each day is approximately 40 g and 
they belong to different categories such 
as: resistant starch, non-starch polysac-
charides, oligosaccharides, as well as 
some di- and monosaccharides (4). The 
composition of gut microbiota is suscep-
tible to both quality and quantity of in-
gested carbohydrates, which serve as the 
main carbon and energy source for the 
gut microbiota (11).
Upon degradation in the small intes-
tine, starches and sugars (i.e. glucose, 
fructose, sucrose, and lactose) release 
glucose in the bloodstream and stimu-
late insulin response (5). Fibres may be 
of particular importance as a non-di-
gestible carbohydrates, representing a 
primary energy source for many gut 
microorganisms and stimulating the 
growth and activity of beneficial gut mi-
croorganisms (17).
Excess intake of carbohydrates as part 
of a Western diet high in refined grains, 
starch, and added sugar and low intake of 
dietary fibres (only 15 g/day) negatively 
impacts gut microbiota and is associat-
ed with reduced diversity of gut micro-
biota (i.e. bifidobacteria increased while 
Lactobacillus spp., Streptococcus spp., 
and Roseburia spp. decreased) (20). In 
addition, lower amounts of SCFAs were 
found in individuals consuming a West-
ern diet (20). On the contrary, people 
in traditional societies, with a high fibre 
intake (50–120 g/day) harbour a much 
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more diverse gut microbiota that is char-
acterized by increasing good bacteria 
such as Bifidobacteria spp. and lactic ac-
id bacteria and decreasing the counts of 
Bacteroides spp. (Figure 1). In addition, 
resistant starch and whole grain barley 
increased the abundance of Ruminococ-
cus spp., E. rectale, and Roseburia spp. 
(4). Furthermore, as described in the 
study of Mills et al., people consuming 
high levels of simple sugars (glucose, 
fructose, and sucrose) in the form of date 
fruits had an increased abundance of bi-
fidobacteria, with reduced Bacteroides 
spp. The addition of lactose to such di-
et caused the same bacterial shifts while 
also decreasing Clostridia spp. Also, lac-
tose supplementation increased the fecal 
concentration of SCFAs (4).
Diet high in both sugar and fats result-
ed in gut microbiota dysbiosis character-
ised by a decrease in microbial diversity, 
an increase in clostridia and bacilli and 
a decrease in Lactobacillus spp. A noted 
increase in the Firmicutes:Bacteriodetes 
ratio was observed. Next, high sugar low 
fat diets caused an increase in two Pro-
teobacteria members, namely Sutterella 
spp. and Bilophila spp. (4).
Artificial sweeteners (saccharin, su-
cralose, and aspartame) were originally 
Figure 1: Impact of carbohydrates and fiber on gut microbiota (According to Singh et al., 2017) (22).
marketed as a health-conscious, no-cal-
orie alternative to natural sugar. Howev-
er, recent work by Suez et al. showed that 
artificial sweeteners can lead to glucose 
intolerance faster than glucose or su-
crose. The effects produced by artificial 
sweeteners were thought to be mediated 
through alteration of gut microbiota (i.e. 
increased abundance of Bacteroides spp. 
and decreased Lactobacillus reuteri (21).
4 Dietary protein
Dietary proteins have been reported 
to influence the composition of gut mi-
crobiota since 1977 (6) and the advances 
of 16S rRNA sequencing enabled the as-
sessment of the impact of dietary protein 
on the composition of gut microbiota in 
much more detail. 
Protein serves as an important nitro-
gen source for the gut microbiota (22). 
The undigested nitrogenous compounds 
that are not absorbed in the small intes-
tine are transferred to the large intestine 
where they are metabolized by the resi-
dent gut microbiota. About 25 g of pro-
tein, peptides and free amino acids enter 
the colon on daily basis (4). The initial 
step of bacterial protein catabolism in-
cludes the extracellular hydrolysis of 
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The influence of dietary compounds on gut microbiota
proteins with hundreds of different bac-
terial proteases. Both the amount and 
kind of metabolites are directly influ-
enced by the intake amount and source 
of dietary protein (8).
Bacteria involved in the protein me-
tabolism in the small intestine include 
E.coli, Streptococcus spp., Succinivibrio 
dextrinosolvens, Mitsuokella spp., etc. 
(5,8). In the large intestine, the concen-
tration of bacteria is much higher and 
the transit time longer than in the small 
intestine. Proteolytic activity in the large 
intestine has been associated with the 
genera Bacteroides, Propionibacterium, 
Streptococcus, Fusobacterium, Clostridi-
um, and Lactobacillus (8,23). Gut micro-
biota and residual pancreatic proteases 
digest proteins and peptides that escape 
digestion in the small intestine, resulting 
in the production of numerous micro-
bial metabolites (i.e. SCFAs, ammonia, 
polyamines, hydrogen sulfide, phenolic, 
indolic compounds, etc.). Some of these 
microbial metabolites (i.e. hydrogen sul-
fide, ammonia, and indolic compounds) 
have potentially negative effects on the 
host health. Others are bioactive mole-
cules involved in various physiological 
processes in the host (8).
Factors, such as protein source, con-
centration and amino acid composition, 
can all affect gut microbiota and changes 
of gut microbiota composition can affect 
protein metabolism as well as the con-
tent of microbial metabolites produced. 
Both of the latter are closely associated 
with the health of the host (8).
The protein sources are mainly clas-
sified as of animal or plant origin. Con-
sumption of plant protein positively cor-
relates with overall microbial diversity 
due to its lower digestibility when com-
pared to animal protein (4,5,8).
Consumption of soybean and pea-
nut proteins positively modulates the 
beneficial bacterial composition in the 
GIT. A diet enriched with peanut pro-
tein or whey altered gut microbiota di-
versity with an increase of commensal 
Bifidobacterium spp. and Lactobacillus 
spp., and a reduction of Enterobacteria 
spp., Bacteroides fragilis and Clostridi-
um perfringens (5,8). Increased num-
bers of Bifidobacterium spp. contribute 
to generation of more microbial metab-
olites, including SCFAs and lactic acid, 
resulting in a lower pH in GIT that in-
hibits toxic metabolites, such as amine 
and benzpyrole. Intake of soybean can 
alter gut microbiota composition with 
increased communities of genera Esche-
richia and Propionibacterium (8).
Compared to plant proteins, animal 
proteins are highly digestible, however, 
animal-based diets are often also high in 
fat in addition to protein (5). Increased 
numbers of bile-tolerant anaerobes 
(genera Bacteroides, Alistipes and Bilo-
phila) were found in the microbiota of 
individuals consuming animal-based 
proteins (5). Casein has been shown to 
increase the counts of lactobacilli and 
bifidobacteria, while on the other hand 
decreasing the counts of Staphylococcus 
spp., coliforms, and Streptococcus spp. 
in GIT (8). Moreover, animal protein is 
characterized by a reduction of SCFA 
and an increase of both gut pH and am-
monia concentration (8).
The individuals consuming a diet 
rich in beef had high levels of Bacteroi-
des spp. and Clostridium spp. and at the 
same time low levels in Bifidobacterium 
adolescentis when compared to their 
vegetarian counterparts (5).
When protein intake is increased, 
the amount of undigested protein in the 
large intestine increases. Consequent-
ly, more substrate for gut microbiota is 
available. High concentration of protein 
increased the abundance of bile-tolerant 
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microorganisms (genera Alistipes, Bilo-
phila and Bacteroides) while decreasing 
the levels of Firmicutes that metabolize 
plant polysaccharides (genera Roseburia, 
Eubacterium rectale and Ruminococcus) 
(24). In addition, high-protein diet led 
to a decrease in abundance of genera Ru-
minococcus and Akkermansia (4). High 
concentrations of protein intake can 
result in increases in counts of poten-
tial pathogens due to disruption in the 
homeostasis of the gut micro-ecosystem 
with reductions of beneficial microbes 
(8). Similarly, when the concentration 
of protein in the diet is too low to meet 
the basic requirement of the host, it can 
increase the abundance of potential 
pathogens (i.e. coliforms) and decrease 
the population of beneficial bacteria in 
the gut (i.e. lactobacilli). Furthermore, 
lower concentrations of dietary protein 
decreased butyrate-producing bacteria 
including lactobacilli and bifidobacteria, 
which have a protective, anti-inflamma-
tory activity against carcinogenesis and 
intestinal disorders (25,26).
5 Fats
Dietary fat vary greatly with respect to 
its structure and composition of fatty ac-
ids. The latter can be short (i.e. 6 carbon 
atoms) or long (up to 24 carbon atoms), 
and can also contain double bonds (4). 
Besides the amount, fatty acid composi-
tion of the fat source is important when 
analyzing its impact on gut microbiota 
composition and function. The typical 
Western diet is both high in saturated 
and trans fats while low in mono- and 
polyunsaturated fats (5).
Animal studies have shown that a high 
fat diet leads to the establishment of mi-
crobiota low in Lactobacillus intestinalis 
and high in Clostridiales, Bacteroidales, 
and Enterobacteriales (27). In addition, 
lard-fed mice showed increased num-
bers of Bacteroides spp. and Bilophila 
spp. and reduced levels of Desulfovibrio 
spp., while those fed with fish oil had in-
creased lactic acid bacteria (Lactobacil-
lus spp. and Streptococcus spp.), genera 
Verrucomicrobia (A. muciniphila), and 
Actinobacteria (Bifidobacterium spp. and 
Adlercreutzia spp.) and mice fed with a 
diet rich in milk fat showed increased 
levels of Bilophila wadsworthia (27).
In humans, rapid and profound 
changes of gut microbiota composition 
caused by consumption of high-fat diets 
consisting solely of animal-based foods 
(i.e. meat and cheese) were observed in 
the study of David et al. The particu-
lar study showed that humans given an 
animal-based diet, consisting of 69.5% 
kcal from fat, 30.1% kcal from protein 
and nearly 0 g of fiber, altered the com-
position of gut microbiota within 48 
hours of diet initiation (28). The growth 
of bile-tolerant and pathogenic hydro-
gen-sulfide producing bacteria such as 
Bilophila wadsworthia was observed in 
the same study (28). A recent interven-
tional study has shown that a high-fat 
diet in healthy adults is associated with 
increased levels of Alistipes spp. and 
Bacteroides spp. and a decrease in Fae-
calibacterium spp. (29). Consumption 
of a low fat diet leads to the over-abun-
dance of bifidobacteria and a reduction 
of fasting glucose and total cholesterol, 
while a high saturated fat diet increased 
the relative proportion of Faecalibacteri-
um prausnitzii (30). High-fat diets also 
enrich the abundance of Bacteroides spp. 
as well as of total anaerobic microorgan-
isms (Figure 2) (30,31).
When monounsaturated fat intake 
was high, no shifts in relative abun-
dance of any bacterial genera were ob-
served. However, such diet resulted in a 
reduced total bacterial load and plasma 
Figure 2: Impact of protein and fat on gut microbiota (According to Singh et al., 2017) (22).
185
PROFESSIONAL ARTICLE
The influence of dietary compounds on gut microbiota
lard-fed mice showed increased num-
bers of Bacteroides spp. and Bilophila 
spp. and reduced levels of Desulfovibrio 
spp., while those fed with fish oil had in-
creased lactic acid bacteria (Lactobacil-
lus spp. and Streptococcus spp.), genera 
Verrucomicrobia (A. muciniphila), and 
Actinobacteria (Bifidobacterium spp. and 
Adlercreutzia spp.) and mice fed with a 
diet rich in milk fat showed increased 
levels of Bilophila wadsworthia (27).
In humans, rapid and profound 
changes of gut microbiota composition 
caused by consumption of high-fat diets 
consisting solely of animal-based foods 
(i.e. meat and cheese) were observed in 
the study of David et al. The particu-
lar study showed that humans given an 
animal-based diet, consisting of 69.5% 
kcal from fat, 30.1% kcal from protein 
and nearly 0 g of fiber, altered the com-
position of gut microbiota within 48 
hours of diet initiation (28). The growth 
of bile-tolerant and pathogenic hydro-
gen-sulfide producing bacteria such as 
Bilophila wadsworthia was observed in 
the same study (28). A recent interven-
tional study has shown that a high-fat 
diet in healthy adults is associated with 
increased levels of Alistipes spp. and 
Bacteroides spp. and a decrease in Fae-
calibacterium spp. (29). Consumption 
of a low fat diet leads to the over-abun-
dance of bifidobacteria and a reduction 
of fasting glucose and total cholesterol, 
while a high saturated fat diet increased 
the relative proportion of Faecalibacteri-
um prausnitzii (30). High-fat diets also 
enrich the abundance of Bacteroides spp. 
as well as of total anaerobic microorgan-
isms (Figure 2) (30,31).
When monounsaturated fat intake 
was high, no shifts in relative abun-
dance of any bacterial genera were ob-
served. However, such diet resulted in a 
reduced total bacterial load and plasma 
Figure 2: Impact of protein and fat on gut microbiota (According to Singh et al., 2017) (22).
total- and LDL-cholesterol (30). Like-
wise, consumption of salmon (that is 
high in mono- and polyunsaturated fats) 
was not noted to alter faecal microbi-
ota composition in the study of Urwin 
et al. (32). A study comparing saturated 
fat (lard) to long-chain polyunsaturated 
fatty acids (PUFA, from fish oil) detect-
ed significant differences in the gut mi-
crobiota composition and host adiposity 
(33). High-saturated fat, such as palm 
oil, reduced microbial diversity and in-
creased Firmicutes:Bacteroidetes ratio 
(4). In the study of Martinez et al., diet 
rich in fish oil prevented against nega-
tive shifts in gut microbes and resulted 
in a decrease in host obesity-associated 
inflammation (33). Next, Huang et al. 
showed that a diet rich in omega-6 PUFA 
(from safflower oil) resulted in altered 
gut microbiota composition compared 
with diets rich in saturated milk fat or 
lard (34). Prieto et al. found that a diet 
enriched with extra virgin olive oil had 
a different effect on the gut microbiota 
in comparison with an enriched butter 
diet (35). In people taking omega-3 PU-
FA supplementation a decrease in Fae-
calibacterium spp., often associated with 
an increase in the Bacteroidetes spp. and 
butyrate-producing bacteria belonging 
to the Lachnospiraceae family, has been 
observed (36).
6 Gut microbiota and 
polyphenols
Dietary polyphenols include flavo-
nols, flavones, anthocyanins, proantho-
cyanidins, phenolic acids, catechins, etc. 
Most of them were studied for their an-
tioxidant properties and as inhibitors of 
pathogenic microorganism growth (5). 
Polyphenol intake is affected by several 
factors including geographical area, the 
population characteristics (i.e. age, gen-
der and socio-cultural factors) and most 
importantly their dietary habits. The 
intake of total polyphenols is compa-
rable in European countries and North 
and South America (about 900 mg/day 
and 800 mg/day respectively). Howev-
er, within Europe, the intake of poly-
phenols varies greatly (i.e. Poland and 
France have both intake of above 1000 
mg/day, while Italy has around 650 mg/
day and Spain about 300 mg/day) (37). 
A majority of polyphenols enter the 
large intestine without being absorbed 
in the small intestine (38,49). There the 
polyphenols are degraded by the resi-
dent microbiota, including Bacteroides 
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diastasonis, Bacteroides ovatus, Bacteroi-
des uniformis, Enterococcus casseliflavus, 
Eubacterium cellulosolvens, Eubacterium 
ramulus and Lachnospiraceae CG191 
(11,38). After the initial hydrolysis, the 
resultant monomers and the aglycones 
are metabolized via decarboxylation 
and ring-cleavage to form simpler forms 
such as hydroxyphenyl propionic acid 
and hydroxyphenyl acetic acids (39).
Polyphenols can stimulate the growth 
of commensal and beneficial microbi-
ota while inhibiting pathogenic bac-
teria. Coffee, tea and red wine are all 
rich sources of polyphenols associated 
with prebiotic and bifidogenic activity. 
For example, the growth of Clostridium 
perfringens, C. difficile and Bacteroides 
spp. was significantly inhibited by tea 
phenolics and their derivatives, while 
Bifidobacterium spp. and Lactobacillus 
spp. were less affected (40). Moreover, 
reductions in pathogenic C. perfringens 
and C. histolyticum spp. have been ob-
served after consumption of fruit, seed, 
wine and tea polyphenols (40-44). Next, 
the study of Queipo-Ortuno et al. (45) 
showed that daily consumption of red 
wine polyphenols increased abundance 
of Bifidobacterium spp., Prevotella spp., 
Bacteroides spp., Enterococcus spp., 
Bacteroides uniformis, and Blautia coc-
coides-Eubacterium rectale.
7 Different diets
There are many popular diets includ-
ing Western, gluten-free, vegan or vege-
tarian, Mediterranean, etc. Most of these 
diets due to different composition affect 
selective growth of different bacteria in 
the gut and have been linked to different 
microbiome profiles. For instance, West-
ern diet can cause dysbiosis by increas-
ing the counts of Clostridium innocuum, 
Eubacterium dolichum, Catenibacterium 
mitsuokai and Enterococcus spp. and at 
the same time decreasing Bifidobacteria 
spp., Eubacteria spp. and Bacteroidetes 
spp. (11).
Wu et al. (46) showed that the Bacte-
roides enterotype were highly associated 
with a diet rich in animal protein, partic-
ular types of amino acids and saturated 
fats (as in Western diet) (Figure 3). On 
the contrary, the Prevotella enterotype 
Figure 3: Impact of different diets on gut microbiota (According to Singh et al., 2017) (22).
187
PROFESSIONAL ARTICLE
The influence of dietary compounds on gut microbiota
was associated with high intake of car-
bohydrates and simple sugars (46,47). 
Furthermore, SCFAs are found in low-
er amounts in individuals consuming 
a Western diet due to lower intake of 
dietary fibre. Consumption of Western 
diet has also been linked to production 
of cancer-promoting nitrosamines (5). 
Scott et al. demonstrated that aerobic 
genera, such as Escherichia, Pseudomo-
nas, Proteus, and Klebsiella, were able to 
produce nitrosamines (48).
A gluten free diet (GFD) is a diet 
used for the treatment of celiac disease. 
However, it has also become very pop-
ular among healthy individuals. It has 
been shown that a GFD could lead to 
modifications of the composition of gut 
microbiota and consequently immune 
properties (4). In studies of the intestinal 
microbiota in humans with celiac dis-
ease, the counts of aerobic Staphylococ-
cus spp., as well as anaerobic Clostridium 
and Bacteroides spp., were higher when 
compared with healthy adults. Further-
more, the gut microbiota of individuals 
adhering to GFD is characterized by 
low Bifidobacterium spp. and Lactoba-
cillus spp., whereas potentially patho-
genic bacteria, such as E. coli and total 
Enterobacteriaceae family, increased 
proportionally with the reduction in 
polysaccharide/fibres intake after the in-
troduction of GFD (5,11). Even a short-
term GFD leads to reduced levels of Ru-
minococcus bromii and Roseburia faecis 
and increased Victivallaceae and Clostri-
diaceae spp. (5,11). It is therfore import-
ant to include prebiotic-rich foods in the 
GFD diet, such as fructan type resistant 
starches (i.e. oligofructose and inulin), to 
avoid adverse effects of GFD on the gut 
microbiota and to promote the growth 
of beneficial species in the GIT (11).
Vegan and vegetarian diets are rich in 
fermentable plant-based foods. The high 
amounts of fibre consumed can modu-
late the composition of gut microbio-
ta, and those individuals that adhere to 
vegan or vegetarian diet were reported 
to have a microbiota characterized by a 
lower abundance of Bacteroides spp. and 
Bifidobacterium spp. (5). High amounts 
of fibre intake can result in increased 
SCFA production, which can decrease 
intestinal pH. Individuals consuming a 
vegan or vegetarian diet showed lower 
intestinal and stool pH, which prevent-
ed the growth of potentially pathogenic 
bacteria such as E. coli and other mem-
bers of the Enterobacteriaceae family 
(47). Also, enrichment of genus Prevotel-
la versus Bacteroides was shown for veg-
etarians and individuals who consume a 
high proportion of fruit and vegetables 
and a low proportion of meat (11).
The Mediterranean diet is often re-
garded as a healthy balanced diet. It is 
characterized by high intake of vegeta-
bles, moderate consumption of poultry, 
olive oil, cereals, legumes, wine, nuts, 
fish and a low amount of red meat, dairy 
products, and refined sugars. It is bene-
ficial due to higher content of mono-un-
saturated and poly-unsaturated fatty ac-
ids, as well as high levels of antioxidants, 
fibres and vegetable protein content (5). 
The gut microbiota in individuals con-
suming Mediterranean diet showed in-
creased levels of Lactobacillus spp., Bi-
fidobacterium spp., and Prevotella spp., 
and low levels of Clostridium spp. (5,11). 
The positive effect of Mediterranean diet 
is associated with weight loss, improve-
ment of the lipid profile and decreased 
inflammation, which might be the result 
of diet-derived changes in the composi-
tion of gut microbiota (5).
The dietary protein intake in humans 
differs greatly according to the food 
availability and cultural dietary habits 
(46). While the daily protein intake in 
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developing countries presents a per-
sistent problem, the avarage protein in-
take in developed countries is usually 
higher than the recommended dietary 
intake of 0.83 g of protein/kg/day (49). 
High protein diets are mainly character-
ized by a higher proportion of protein 
(25 – 30% of total energy intake) when 
compared to the usual macronutrient 
proportion (24). Such diets with caloric 
restriction may facilitate body weight re-
duction while increasing satiety but are 
also associated with potentially deleteri-
ous health effects in the long-term (23). 
The ratio of available carbohydrates to 
protein determines substrate utilization 
by the gut microbiota, and the availabil-
ity of complex carbohydrates generally 
lowers protein fermentation (23). 
In individuals consuming a high-pro-
tein diet counts of Bifidobacterium spp. 
and the butyrate producing bacteria 
Roseburia/Eubacterium rectale were re-
duced (23,24).
The ingestion of resistant starch has 
been positively associated with both 
Bifidobacterium and Eubacterium spp., 
and reduced intake of carbohydrates led 
do a decline of both genera (24).
8 Prebiotics and probiotics
Prebiotics are foods or dietary sup-
plements that encourage the growth of 
saccharolytic bacteria that metabolize 
non-digestible carbohydrates such as in-
ulin and fructose-rich oligosaccharides 
(FOS). In order to be considered a pre-
biotic, the product must be resistant to 
gastric acidity, non-digestible by the host 
in the small intestine, fermentable by 
bacteria, and promote the abundance of 
beneficial bacteria (49). Mechanisms be-
hind the beneficial effects of dietary fibre 
include SCFA production, stimulation 
of intestinal gluconeogenesis, increased 
epithelial integrity, release of peptide YY 
(PYY) and of glucagon-like neuropep-
tide-1 (GLP-1) to promote satiety and 
insulin sensitivity, increased expression 
of antimicrobial peptides, and alteration 
of gut microbiota composition (35). In-
clusion of 10% (w/w) short chain FOS in 
high-fat diets (60% kcal from fat) altered 
gut microbiota composition and func-
tion as measured by changes in meta-
bolic by-products of the gut microbiota 
(50). Also, inclusion of fibres improved 
insulin sensitivity in humans (50). Con-
sumption of galacto- oligosaccharides 
(GOS) and FOS has shown to improve 
gut microbiota composition by increas-
ing bifidobacteria and decreasing E. coli 
(50).
Nowadays, probiotics are high-
ly investigated for their effects on host 
health. They also represent one of the 
most widely consumed dietary supple-
ments (10). Lactic acid bacteria can be 
found in fermented food such as yogurt 
and represent microorganisms that may 
beneficially regulate intestinal health 
through their effect on the gut microbi-
ota composition and production of an-
ti-inflammatory cytokine IL-10 (5).
Probiotics are thought to have an-
ti-inflammatory, hypoglycaemic, insuli-
notropic, antioxidative, and satietogenic 
properties (10). However, studies inves-
tigating the effects of probiotics on the 
human gut microbiota have inconclusive 
results which might be a consequence 
of variations in individual responses to 
probiotics and probiotic colonization 
(51-55).
A clinical study of Ferrario et al. that 
included healthy adults who were given 
the probiotic strain L. paracasei DG re-
vealed that the changes observed in the 
gut microbiota composition depend-
ed on an individual’s starting microbial 
profile (53).
189
PROFESSIONAL ARTICLE
The influence of dietary compounds on gut microbiota
Mixed strain probiotics or synbiot-
ics (combination of prebiotics and pro-
biotics) seem to be more efficient than 
single microbial isolate alone (35). A 
randomized placebo-controlled trial of 
Rajkumar et al. included 60 overweight 
healthy adults who were given probiot-
ic mixture containing three strains of 
Bifidobacterium, four strains of Lacto-
bacillus, and one strain of Streptococcus 
(VSL #3) genera. Significant increases 
in the concentration of Lactobacillus 
spp., Bifidobacteria spp., and Strepto-
coccus spp. were found when compared 
to placebo (56). The adults from the 
study also had fewer total coliforms and 
E. coli, as well as reduced triglycerides, 
total cholesterol, LDL-cholesterol, 
VLDL-cholesterol, and high-sensitiv-
ity C-reactive protein. Probiotic-con-
taining yogurt has also been shown to 
significantly reduce counts of the en-
teropathogens E. coli and Helicobacter 
pylori (57).
Even though probiotics present a 
promising therapy, more evidence is 
needed. The assessment of probiot-
ic colonization ability, including their 
load in the lumen or mucosa, position 
throughout the GIT and how long they 
remain in GIT after supplementation 
ceases needs further research. Also, the 
efficacy of probiotics in the modulation 
of gut microbiota composition needs 
further investigation, given the great 
inter- individual variation in microbi-
ota composition (10,35).
9 Conclusion
The gut microbiota is a complex eco-
system that undergoes variations and 
adapts to its host over lifetime due to 
many factors. Increasingly recognized is 
the influence of diet on gut microbiota 
composition. Digestible and non-digest-
ible carbohydrates, protein, fats, poly-
phenols, pre-and probiotics, as well as 
different dietary regimes all induce shifts 
in the gut microbiota with consequent 
modulation of the host immunologic 
and metabolic markers. Gut microbiota 
has been associated with the occurrence 
of diseases such as chronic gastrointes-
tinal diseases, obesity, autism, diabetes, 
chronic inflammation, etc. Considering 
this close relationship between the diet, 
gut microbiota and health, it might be 
possible to improve our health through 
diet modulation. Changing the gut mi-
crobiota through diet, probiotics, pre-
biotics, and even antibiotics might offer 
a powerful route to preventing many of 
‘Western-associated’ diseases. 
Long-term dietary habits have the 
most profound impact on the gut mi-
crobiota. For that reason, healthy eating 
patterns with adequate intake of fruits 
and vegetables, ensuring a rich source of 
dietary fibre, together with healthy fats 
(mono- and poly-unsaturated fatty ac-
ids) and a trend towards more plant-de-
rived proteins could help promote gut 
microbiota diversity and functionality 
enabling it to benefit its host.
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