Report 9th edition - 2020 Moving gut microbiome science from the bench to actionable advice: Gut Microbiota for Health
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Report
9th edition - 2020
Moving gut microbiome science
from the bench to actionable advice:
major learnings and paths to explore
Madrid (SPAIN)
Gut microbiome science has exponentially increased over the last two decades,
as has the general population’s interest in harnessing this knowledge for
better health. When it comes to science-backed tools for improving our gut
microbiome, according to experts’ conclusions from the GMFH World Summit
2020, diet diversity, prebiotics and probiotics are all worth considering.
Sponsoring societies Endorsing societies The 2020 summit has been made
possible by our major supporters:
Biocodex, Danone (the Founding
Supporter) and Sanofi.
ADVANCING GUT MICROBIOME SCIENCE
FOR BETTER HEALTH IS NOT STRAIGHTFORWARD:
THE MAJOR CHALLENGES
AND HOW TO OVERCOME THEM
Gut microbiome publications have •T
aking into account individuality
exponentially increased over the when interpreting microbiome
last decade, with the subsequent studies;
impact on both basic science re
•A
voiding defining a gut micro
search and clinical practice. While
biome as ‘healthy’ or ‘unhealthy’
it is clear that the roadmap to cli
(any effect of the gut microbiota
nical translation consists of deve
on host health is likely to depend “The microbiome
loping gut microbiome-related so
also on individual host genetics, will prove to be
lutions for better health, Colin Hill
diet and environment); a rich source of
from University College Cork (Cork,
Ireland) acknowledged during his • Considering all factors that can sha therapies and
keynote lecture that higher stan pe gut microbiota composition;
smart food, feed
dards must be rigorously applied to •C
hoosing the right methodology
overcome roadblocks when moving ingredients and diets
for studying the gut microbiome;
from bench to bedside. and that will improve the
•H
aving long-term data regarding
human condition.”
To deliver precision gut microbiome- the safety of gut microbiota-tar Colin Hill
based science, accuracy (and a geted interventions n
healthy dose of common sense) is
necessary in all steps: from micro-
biome sampling to specific lan
guage used when explaining the
benefits of taking care of the gut
microbiota. Hill explained that ma
jor challenges to be addressed to
get the right microbiome science
include:
•U
sing precise language when
communicating gut microbiome
science;
•
Adopting consensus definitions
(see the ISAPP consensus docu
ments of probiotics and prebio
tics);
•R
elying more on actual numbers
rather than percentages when
clarifying to what extent two or
©D.R.
more microbiomes are identical
or different;
Report 2019
WHICH HOST AND DIET FACTORS
SHAPE THE GUT MICROBIOME?
Each person has the gut of a C-section on the infant’s gut Rectal mother-to-
microbiome is barely noticeable du
microbiome they deserve ring the first weeks of life and when child transmission,
and this is how it changes the procedure is performed (that rather than vaginal
throughout life is, before or during labor) affects bacteria, appears
children’s gut microbiome in the
same way. In this regard, the high
to affect newborn
The first three years of life represent number of shared strains between gut colonization
the most critical period for dietary C-sections and vaginal deliveries efficiency.
interventions aimed at gut micro suggests that rectal mother-to-
biota modulation to improve child child transmission, rather than va-
growth and development and posi ginal bacteria, appear to be what
tively affect health. Moran Yassour affects newborn gut colonization
from the Hebrew University of Jeru efficiency.
salem (Israel) focused on the origin
and extent of microbe transmission
from mother to infant. A longitudi
nal sampling of gut bacterial trans
mission in 44 mother-infant pairs
enabled Yassour and colleagues to
find that two patterns of mother-
to-child bacterial transmission exist
in the first 3 months of a child’s
life. While often the mother’s do-
minant strain (Bacteroides vulga-
tus and Bifidobacterium adoles-
centis) is transmitted to the child,
sometimes her secondary strains
(often Bacteroides dorei) can pre-
ferentially colonize the infant gut.
Interestingly, in families where the
secondary strain of Bacteroides uni-
formis is inherited, a starch utiliza
tion gene that is missing in the mo
ther is available in the newborn for
facilitating the metabolism of the
mother’s milk, explained Yassour.
Diet keeps the gut
Likewise, the transmission of some Paul O’Toole from University Colle
antibiotic resistance genes may also ge Cork (Ireland) covered diet-mi microbiome fit in the
be inherited. crobiota health interactions in el elderly: it is not the
derly people (aged >65 years). In quantity of calories
Regarding the impact of delivery this population, lifestyle and habi
mode on the child gut microbiome, tual diet can outweigh age-related per se that matters,
Yassour explained that, contra gut microbiota changes. Specifi but the quality
ry to common belief, the impact cally, elderly people living in their of the diet.
Report 2020 - 3
homes and looked after by care correlated with inflammation, in a
givers show the highest diversity manner independent of body mass
in their gut microbiota, with sub index and age. It was also possible
jects residing in long-term care to identify 44 Operational Taxono
facilities (consuming a diet with a mic Units (OTUs) that were more
low diversity of food components) abundant when the MedDiet was “Our findings
showing the least diverse microbio strictly observed (named “diet posi show the benefits
ta. Furthermore, these microbiota tive”), whereas 45 OTUs were nega
changes correlated with increased tively associated with adherence to
of following a
frailty and increased values of mar the diet (named “diet negative”). In Mediterranean diet
kers of inflammation, explained conclusion, the study supports the to modulate the gut
O’Toole. fact that diet quality matters more microbiota, which,
than the quantity of calories per se,
in turn, has the
The gut microbiota composition even in subjects of advanced age,
profile groups change according to and gut microbiota can explain the potential to promote
the duration of stays in long-term benefits of a highly diverse and ba healthier aging.”
residential care and O’Toole’s re lanced diet. Paul O’Toole
search group was interested in ex
ploring whether modulation of the
gut microbiota through diet could
lead to healthier aging. A dietary
intervention in elderly subjects and
young healthy controls showed
how an intake of prebiotics with a
high content of resistant starch for
6 months can modulate specific
gut microbiota taxa (such as Ru-
minococcaceae, Parabacteroides,
and Phascolarctobacterium) and
reduce inflammation in the elder
ly. In the light of these findings, it
might be possible to improve the
loss of certain taxa in the gut mi-
crobiota of frail long-stay older
people through prebiotic supple-
mentation.
In another study presented, O’Toole
and colleagues showed that adhe- Your allies for looking
rence to the Mediterranean diet
(MedDiet) for 1 year in 612 elder- after your gut microbiota: Not all fermented foods are
ly non-frail and pre-frail European fermented foods, a source of probiotics. Learn
subjects led to a higher abun- probiotics and prebiotics more about the impact of
dance of different taxa that are kefir and major non-dairy
positively associated with markers fermented foods on the gut
of lower frailty and better cogni- Different dietary strategies are cur microbiota and gastrointesti-
nal health here.
tive function but also negatively rently undergoing a surge in po
Report 2020 - 4
“The most widely
investigated
fermented foods are
fermented milks
and kefir, with
human evidence
suggesting beneficial
effects on lactose
malabsorption
for yogurt and
functional
constipation, lactose
pularity, as a means of improving bacteria and yeast within the gas
gastrointestinal health by shaping trointestinal tract. However, Whelan malabsorption and
the gut microbiota. Kevin Whelan acknowledged that not all probio Helicobacter pylori
from King’s College London (United tics work in the same way and ca eradication for kefir”
Kingdom) summarized human in reless use of this word as a generic Kevin Whelan
tervention studies investigating the descriptor without specifying the
impact of fermented foods, probio content (genus, species and strain)
tics and prebiotics on gastrointesti or clinical indication often makes for
nal health and disease. The most wi- a superficial imprecise term. In addi
dely investigated fermented foods tion, humans’ response to probiotics
are fermented milks and kefir, with is highly individualized and clini-
human evidence suggesting be- cians should focus on health outco-
neficial effects on lactose malab- mes rather than whether a probiotic
sorption for yogurt and functional colonizes or has detectable effects
constipation, lactose malabsorp- on the indigenous microbiota. Pro
tion and Helicobacter pylori era- biotics have been shown to be bene
dication for kefir. There is limited ficial in constipation, irritable bowel
clinical evidence for the effective syndrome (IBS) and ulcerative coli
ness of kombucha, sauerkraut, soya tis, whereas their role in Crohn’s di
fermented foods (miso, natto and sease is controversial.
tempeh), kimchi and sourdough in
gastrointestinal health and disease, Prebiotics, meanwhile, act by se
explained by a variable microbial lectively stimulating the growth
composition in fermented foods of some gut bacteria. The most
and the lack of human studies. studied prebiotics are inulin-type
fructans (inulin, oligofructose) and
Beyond fermented foods, probiotics galactooligosacharides, while resis
are also a way to deliver beneficial tant starch and pectins are conside
Report 2020 - 5
Physicians Committee for Res
ponsible Medicine (USA) presented
the results of a randomized clinical
trial looking at changes in gut mi
crobiota in response to a low-fat
vegan diet. In 147 participants who “Our study
were overweight and insulin resis highlights the
tant but who had not yet been dia importance of fiber
gnosed with diabetes, Kahleova and
colleagues looked at their fecal mi intake for diabetes
crobiota, body composition and in prevention because
sulin sensitivity at baseline and after Faecalibacterium
randomizing them to follow a vegan
diet or to stay on their usual diet for
prausnitzii feed on
16 weeks. fiber and produce
short-chain fatty
The vegan diet led to a 5.8kg re
acids with positive
Adobe Stock
duction in body weight, which was
mainly due to a reduction in fat mass metabolic benefits.”
The vegan diet. analyzed using dual energy X-ray Hana Kahleova
absorptiometry. More interestingly,
red candidate prebiotics. Similar to metabolic outcome improvements
what happens with probiotics, Whe were also related to changes in the
lan explained that the response to a gut microbiome. Specifically, an in
prebiotic is largely affected by the crease in the butyrate-producing
background gut microbiota profile bacterium Faecalibacterium praus-
and habitual dietary fiber intake. nitzii – which has been found to be
Science-backed indications for pre depleted in patients with type 2 dia
biotics include constipation and IBS. betes and has also been linked to in
creased inflammation and increased
insulin resistance – in response to
A 16-week plant-based the vegan diet was associated with
changes in body weight, fat mass
diet can boost the gut and visceral fat. In addition, the ve
microbiome, helping with gan diet led to less of a drop in Bac
weight loss and overall teroides fragilis compared with the
Western diet, and that too was re
health lated to changes in weight loss, fat
mass and insulin sensitivity n
A wealth of data has shown the be
nefits of plant-based diets for pre
venting and managing diabetes,
with gut microbiome research
connecting the dots between in
flammation, insulin resistance and
diabetes. Hana Kahleova from the
Report 2020 - 6
THE GUT MICROBIOME-IMMUNE SYSTEM BALANCE:
WHY DOES IT MATTER?
The neonatal period
integrity, and even tryptophan and
spanning birth to nucleotide metabolism in offspring.
weaning represents the “As the early-life microbiota is see-
most critical period for ded by vertical transmission, the
education of immunity in offspring “As the early-
dietary interventions is critically dependent on mater- life microbiota is
aimed at microbiota nal commensals,” acknowledged
seeded by vertical
modulation. McCoy. In addition, the maternal
microbiome can also have an im transmission,
pact on disease development la the education
Kathy McCoy from the University of ter in life. It seems that an altered of immunity
Calgary (Canada) covered the in microbiota can increase intestinal
fluence of maternal gut microbiome permeability and thus promote the in offspring is
on the training and maturation of development of a pro-inflammatory critically dependent
the neonatal immune system, even milieu that stimulates beta-cell au on maternal
before birth. McCoy started by pro toimmunity in the predisposed host.
viding evidence supporting the For example, differences in human
commensals”
Kathy McCoy
theory that seeding of early-life milk oligosaccharide-utilizing bac
microbiota with maternal microbes teria provide a route to differences
leaves a lasting imprint on the offs in immune education that may pre
pring. Studies in mice have covered dispose the body to immune and
the critical role of colonization by metabolic-related conditions such
maternal microbes in early life for as diabetes.
normal immune development, inclu
ding innate immune cell production, Gérard Eberl from Institut Pasteur
antibody production, immune regu (Paris, France) presented findings
latory functions, epithelial barrier in mice showing how important an
Effects of the maternal microbiota on early life immune development Time windows for immune development by microbiota.
Source: McDonald B & McCoy KD, Science. 2019; 365(6457):984-5. Source: Al Nabhani Z et al., Immunity. 2019; 50(5):1276-88.
Report 2020 - 7
adequate response by the immune in terms of host genetic susceptibi
system to the expanding gut micro lity is unknown. Sokol shared obser
biota during the gradual switch from vational data showing associations
a diet composed exclusively of milk between four major genetic va
to a diet that includes other foods riants linked to an increased risk of
is for health later in life. However, an IBD and gut bacterial populations. “In order to develop
altered gut microbiota during the Within them, a link between NOD2 a balanced immune
weaning period (e.g., secondary to genes and a reduction in both the
antibiotics or due to a high fat diet) Roseburia and Faecalibacterium
system, mice and
may hinder adequate development prausnitzii genera was replicated in humans need to
of host immune responses, which three independent cohorts. Overall, be exposed to
leads to increased susceptibility to these findings show that the gut
immune-related diseases such as microbiota might be a potential
microbiota during
allergy later in life. The right food in mechanism underlying the asso- the neonatal period
take during this weaning period also ciation between IBD and genetic spanning birth
matters for a balanced activation of variants. In addition, gut microbio
to weaning”
the immune system. For example, ta-derived metabolites are gaining
Gérard Eberl
compounds of dietary origin such interest as potential targets for
as retinoic acid, whose metabolism precision therapeutic modulation
is affected by the gut microbiota, in IBD. Increased tryptophan me
appear to shape the developing im tabolism has been associated with
mune system. By contrast, microbial the activity of IBDs, generating aryl
exposure after weaning does not hydrocarbon receptor agonists that
alter the development of immune have a wealth of effects on mucosal
responses, highlighting the critical immunity and homeostasis.
window of weaning for preventing
immunopathologies in adult life. Finally, Sokol shared the findings
of a recent randomized controlled
trial as the first to evaluate the use
of fecal microbiota transplantation
The gut microbiome in maintaining remission in Crohn’s
and the immune system patients. The authors found a hi
in inflammatory bowel gher rate of steroid-free remission
in Crohn’s patients treated with FMT
disease: what is the as well as improved lesions and in
chicken and what flammatory markers. Although fur
is the egg? ther studies on larger patient po
pulations are needed, the results
Learn more about the contri-
of this pilot trial are promising for bution of gut microbiota-de-
Harry Sokol from Saint Antoine Hos the many patients suffering from rived metabolites in IBD here.
pital (Paris, France) updated major Crohn’s disease. n
learnings on using gut microbiota
as a therapeutic tool in inflammato
ry bowel diseases (IBDs). Although
specific gut microbiome signatures
have been defined in IBDs, the role
of the microbiota in the onset of IBD
Report 2020 - 8
FOOD INTOLERANCES AND FUNCTIONAL
GUT DISORDERS ARE CLOSELY CONNECTED:
WHY IT IS TIME TO FOCUS
ON THE SMALL INTESTINE?
Although the small intestine is a rier dysfunction in the absence of
harsh environment for microorga mucosal damage. Interestingly, Lac
nisms to thrive, its involvement in tobacillus can degrade ATIs, leading
driving immune responses and di to a reduction in its pro-inflammato
gesting macronutrients makes it ry effects. These findings open the “Understanding the
worthwhile to explore in the context potential of gut microbiome-modu basics of bacterial-
of food sensitivities and entero lating strategies through gluten and diet interactions will
pathies. Alberto Caminero from ATI-degrading bacteria in patients
McMaster University (Hamilton, with wheat-related disorders.
help us better treat
Canada) presented findings sug patients with food
gesting the gut microbiota’s invol Purna Kashyap from Mayo Cli sensitivities and
vement in the processes underlying nic (Rochester, USA) focused on
gluten or wheat sensitivity. Certain the small intestinal microbiome in
enteropathies, such
small-intestinal bacteria, such as functional gastrointestinal disor as celiac disease”
Pseudomonas, produce elastases ders. Small intestinal bacterial over Alberto Caminero
that contribute to gluten degrada growth (SIBO) has been suggested
tion. However, in mice expressing as a culprit of common functional
genes associated with coeliac di gastrointestinal symptoms, inclu
sease (HLA-DQ8), bacterial elas ding IBS and intestinal bloating.
tase can synergize with gluten to However, there is no gold standard
induce severe inflammation. Simi for diagnosing SIBO and Kashyap
Learn more about current re-
larly, non-gluten proteins present showed that high-throughput se-
search on how changes in the
in wheat, such as α-amylase trypsin quencing analysis of the duode-
gut microbiota play a role in
inhibitors (ATIs), can induce an in nal microbiome, rather than dia- food sensitivities: here.
nate immune response, causing bar gnosing SIBO using the traditional
Wheat components involved in
increased intestinal inflammation in
patients with celiac disease or other
wheat-related disorders
(e.g., non-celiac wheat sensitivity and
irritable bowel syndrome).
Report 2020 - 9
“Small intestinal
bacterial overgrowth
(SIBO) has been
suggested as a
culprit of common
functional
gastrointestinal
symptoms, including
IBS and intestinal
bloating.”
aspiration and culture of small in- that resolved on resumption of the
testinal contents, correlates with subjects’ habitual high-fiber diet.
functional symptoms in 126 indivi- This means diet affects the small
duals who had various gastrointes- intestinal microbiome and may be a
tinal symptoms. Indeed, asympto factor determining SIBO.
matic individuals commonly met
criteria for SIBO. In addition, meta Beyond dietary fiber, Kashyap
bolic pathways involved in metabo acknowledged that other dietary
lizing simple sugars were enriched components and drugs may modu
in symptomatic individuals, whe late the small intestinal microbiome.
reas complex carbohydrate degra For example, consumption of a high
“It is time to move
dation pathways were decreased. fat diet can profoundly alter the away from SIBO for
These findings led the investigators microbiota in the small intestine, predicting functional
to hypothesize that dietary factors which increases fat absorption in
gastrointestinal
might be relevant to alterations mice. Although the long-term im
of the duodenal microbiome and pact of these results in the clinical symptoms and
prompted them to examine the ef setting remains to be seen, it turns to focus on the
fect of fiber content in the diet on out that it is time to move away from
small intestinal
gastrointestinal symptoms and the SIBO for predicting functional gas
small intestinal microbiome in 16 trointestinal symptoms and to focus microbiome as a
healthy individuals. Switching to on the small intestinal microbiome key protagonist
a low-fiber and high simple sugar as a key protagonist in functional in functional
diet for 7 days increased small in- gastrointestinal symptoms n
testinal permeability and induced gastrointestinal
IBS-type symptoms (such as bloa- symptoms.”
ting and abdominal discomfort)
Report 2020 - 10THE MICROBIOME CANNOT BE IGNORED
WHEN LOOKING AT HOW DRUGS
ACT IN THE BODY
It is not only antibiotics of enteric infections caused by a de
that can have an impact creased colonization resistance for
Clostridioides difficile infection due
on our gut bacteria; a to a reduction of stomach barrier “Microbiome studies
quarter of drugs designed function; and altering gut microbio should be corrected
to act on human cells ta functions (e.g., increased purine
deoxyribonucleoside degradation
for medications use,
do too. as a source of carbon in PPI users). including proton
Notably, long-term effects tied to pump inhibitors,
Medication, together with diet, chronic PPI consumption include an
stands out as a major environmental altered response to immune check
metformin, laxatives,
factor that influences gut microbio point inhibitors in cancer and the selective serotonin
ta composition. Rinse K. Weersma development of childhood obesity. reuptake inhibitors
from the University of Groningen
and antibiotics.”
(Netherlands) highlighted that the Meanwhile, Athanasios Typas from
Rinse K. Weersma
identification of a causal impact of the European Molecular Biology La
proton pump inhibitors (PPIs) and boratory (Heidelberg, Germany) fo
the anti-diabetic drug metformin cused on the impact of non-antibio
on the gut microbiome provides tic drugs on gut microbes. Typas’s
firm evidence of gut microbiome group found that nearly one quar-
perturbation by drugs other than ter of more than 1,000 commonly
antibiotics. PPIs have the potential used drugs had antibiotic effects,
to alter the gut microbiota by redu which are reflected in side effects
cing acidity in the stomach that leads in humans. Drugs that have the
to an overrepresentation of oral mi most profound effect include anti
crobes in the gut; increasing the risk cancer drugs, antipsychotics and
Different scenarios in which drug-gut microbiome interactions can occur:
Source: Doestzada M et al., Protein Cell. 2018; 9(5):432-45. doi: 10.1007/s13238-018-0547-2.
Report 2020 - 11antihypertensive drugs. As specific and respond to in vivo signals, such “Selective antidotes
therapeutic classes target not only as in the healthy or diseased gut. are being developed
human cells but also gut microbes, The unique abilities of living or- as a means of
this might imply the role of poly ganisms with the potential to im-
pharmacy as a strong driver of an prove how we care for patients in-
stopping the impact
timicrobial resistance. Typas also clude being able to integrate and of antibiotics and
showed that the detrimental effects respond to new signals; accessing human-targeted
of antibiotics on the gut microbio parts of the body inaccessible to
ta are not limited to their ability to standard technology; producing
drugs on gut
stop the growth of gut microbes and delivering biological thera- commensals,
and include collateral damage such peutics directly to the site of di- while not affecting
as the lysis of gut commensals. In sease; and showing a durable per-
antibiotic effects on
this regard, experimental research formance (lasting even longer than
has started exploring selective an 6 months) within the gut. pathogens.”
tidotes for avoiding the side ef Athanasios Typas
fects of wide-spectrum antibiotics On the whole, the use of live, en-
on Gram-negative gut commen gineered probiotics represents a
sals, while retaining activity for pa new frontier in managing gut di-
thogens. seases and as a novel mechanism
for drug delivery. Major challenges
include the availability of libraries
The next frontier in and conditions to be tested in or
der to better understand bacteria
medicine: harnessing behavior within the complex gut
living bacteria in our environment n
body as a non-invasive
way to detect and treat
disease
David Riglar from Imperial Colle
ge London presented the poten
tial of engineering living bacteria
in our body as non-invasive tools
for detecting and treating disease.
The Riglar lab uses a combination
of synthetic biology, imaging and
sequencing-based approaches to
better understand the function of
the gut and its microbiota during
health and disease. Riglar explored
the potential of living engineered
probiotics for probing and control
ling the gut environment. For exa
©iStock
mple, studies have shown engi
neered gut bacteria can survive in
The use of live, engineered probiotics represents a new frontier in managing gut
the mouse gut and sense, record diseases and as a novel mechanism for drug delivery.
Report 2020 - 12GUT MICROBES SHOW THE WAY
TOWARDS BETTER
MENTAL HEALTH
John F. Cryan from University Colle have an impact on the intestinal
ge Cork gave an overall glimpse of microbiota and subsequent men
the role of intestinal microbiota in tal illnesses in the developing teen.
regulating the gut-brain axis across In addition, as we age, changes in
lifespan. The role of the gut micro the gut microbiota and associated
biota in brain and behavior is sup increases in gut permeability, in
ported by initial findings in which flammation and arterial dysfunction
“Gut bacteria are
germ-free mice showed alterations may be important mediators of im directly linked to
in neuron myelination and activity, pairments in the behavioral, affec our mental health.
dendritic growth and even blood- tive and cognitive functions seen in
brain-barrier permeability. In other aging.
We have coined the
words, the brain does not develop term psychobiotic for
appropriately without microbes. Due to the close interaction means of influencing
Mode of delivery is among the most between gut microbiota and the
the microbiome
studied factor playing a pivotal role brain, scientists have started ex
in regulating early brain develop ploring means of influencing the for mental health
ment, with enduring neurobeha gut microbiome for the benefit of benefits, including
vioral effects. More interestingly, mental health. While the term psy probiotics,
C-section-induced effects on beha chobiotic was introduced by Iri
vior can be reversed by targeting sh scientists in 2013 and originally prebiotics, synbiotics
microbiota with probiotics, at least referred to a subset of probiotics and postbiotics.”
in animal models. As for later in that could produce a health bene John Cryan
life, Cryan explored the gut micro fit in those with psychiatric illness,
biota’s influence on brain develop more recently, the definition of psy
ment through adolescence, which chobiotics has expanded to include
is a time of enormous developmen other means of influencing the
tal change. Cryan explained that microbiome for mental health be
gut microbiota undergoes a shift nefits. Psychobiotics, therefore, can
in structure and balance during include a range of substances that “Psychobiotics,
adolescence and external sources affect microbiota-gut-brain axis si
therefore, can
of stress during this period may gnaling, including probiotics, pre
include a range
of substances that
affect microbiota-
gut-brain axis
signaling, including
probiotics,
prebiotics, synbiotics
and postbiotics.”
Report 2020 - 13“Serotonin of
microbial origin
can have an
impact on host
functions, including
gastrointestinal
motility and platelet
function.”
Ways of targeting the gut microbiome for mental health benefits.
Source: Long-Smith et al., Annu Rev Pharmacol Toxicol. 2020; 60:477-502.
biotics, synbiotics and postbiotics. more than 90% of the body’s se
These substances can be delivered rotonin is synthesized in the gut,
through supplements, functional Lynch showed the important contri
foods, and improvements to die bution of indigenous spore-forming
tary intake. For instance, targeting bacteria dominated by Clostridia
the gut microbiome by using dieta ceae and Turicibacteraceae from
ry prebiotics can reverse neuroim the mouse and human microbiota in
mune alterations in middle-aged promoting serotonin synthesis. This
mice. In addition, the consump implies that serotonin of microbial
tion of probiotic Bifidobacterium origin can have an impact on host
longum 1714 has been associated functions, including gastrointesti
with reduced stress and improved nal motility and platelet function.
memory in healthy adults. Current In the opposite way, specific domi
unknowns include dose responses nant members of the gut microbio
and the long-term effects of psy ta are well equipped to respond to
chobiotics’ anxiolytic and antide intestinal serotonin, with an impact
pressant effects. on host lipid metabolism that is not
completely understood. These re
Serotonin acts as a node sults reveal that certain gut bacteria
modulate host physiology and its
for gut microbiota-brain regulation could have therapeutic
interactions implications n
When going deeper into the com
munication across the micro
biome-gut-brain axis, there is also
evidence to suggest that seroto
nin may be an important mediator.
Jonathan B. Lynch from the Uni
versity of California, Los Angeles
updated how the gut microbiota
influences body functions by mo
dulating serotonin levels. Although
Report 2020 - 14GUT MICROBIOME DATA WILL HELP CLINICIANS MOVE
TOWARDS CUSTOMIZED PATIENT
HEALTH MANAGEMENT
Joël Doré from the French National riencing complications associated
Research Institute for Agriculture, with liver cirrhosis. This means that
Food and Environment discussed nutritionists or clinicians can have
the progress toward clinical insights an idea of healthy individuals or pa
from gut microbiome data. Al tients’ lower or higher risk of me
though it is known that a disrupted tabolic conditions or response to
host-microbe symbiosis is a com certain treatments based on their “Gut microbiota
mon thread in chronic conditions, gut microbiota richness assessed richness might help
Doré acknowledged that harnes using full shotgun metagenomic
clinicians make
sing available gut microbiome da sequencing.
tasets to develop diagnostic, pre better decisions in
ventive and therapeutic tools is For gut microbiome data to be terms of clinically
not straightforward. In this regard, come useful in the clinical setting, managing
a good starting point is grouping however, it is important to stan
people according to low or high dardize sample collection and ana the patient.”
richness enterotypes depending lysis. Only with well documented Joël Doré
on species diversity/gene count in microbiome standards that allow
their gut microbiota. While a gut for robust and reproducible ana
microbiota showing high richness lysis will reliable data that provide
is considered a marker of health, a clear picture of the microbiome
people with low gut microbiota help guide clinical decisions. In
richness appear to be at higher risk this regard, the International Hu
of metabolic conditions such as dia man Microbiome Standards project
betes and obesity, may show a re has developed standard operating
duced response to treatment (e.g., procedures to optimize data qua
dietary intervention in obesity), and lity and comparability in the human “A gut microbiota
may even be more prone to expe microbiome n
showing high
richness is
considered a marker
of health, people with
low gut microbiota
richness appear
to be at higher risk
of metabolic
conditions such
as diabetes
and obesity.”
Report 2020 - 15Conclusion
9th edition - 2020
W While initial studies in the human microbiome field fo-
cused on describing alterations in gut microbial commu-
nities in disease states compared with healthy individuals, du-
ring the last decade we have gained insights regarding how the
microbiome shapes health and disease across lifespan. This has
led to the development of gut microbiome-targeted strategies
that will allow clinicians to make better decisions in terms of
clinically managing the patient. Scientists agree that the recipe
for achieving a healthier gut microbiome that can aid gut-re-
lated conditions and systemic indications include nutrition,
prebiotics, probiotics and fermented foods.
Plenary sessions replay available here.
Tweet Activity of #GMFH2020
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Gut Summit 2020
was accompanied by 750
interactive conversations
500
on Twitter. We thank the
580 participants 250
who played an active role
0
in the 4 5 6 7 8 8 10
March 2020
#GMFH2020
conversation.
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Report 2020 - 16KEY DEFINITIONS
Amylase trypsin inhibitors (ATIs): non-gluten proteins pre in the blood, it is a sign of gut barrier impairment, with
sent in wheat that may promote intestinal inflammation, subsequent long-lasting effects that go beyond the gut
increased intestinal permeability and gut dysmotility. (e.g., obesity has been linked to an increased intestinal
Research in mice has shown Lactobacillus can degrade permeability, favoring the shift of LPS from the gut lu
wheat ATIs to reduce intestinal dysfunction induced by men to the bloodstream).
immunogenic wheat proteins.
Microbiome: this term is used for two concepts. One to
Dysbiosis: an imprecise term used for defining a perturbed refer to the collective genomes harbored by microbes,
microbial ecosystem compared with the healthy state and another for referring to the entire habitat, including
or homeostasis. Instead of being measured by species the microorganisms and their genomes. Nowadays, this
richness or diversity, scientists highlight that functional term is commonly used to refer to the microorganisms
diversity, stability and resilience also matter when asses themselves.
sing the health of the microbiota and the host. Instead of
dysbiosis, scientists acknowledge that the terms “diffe Microbiota: the community of micro-organisms living in a
rent”, “altered” or “adapted” are more accurate when re specific environment. For example, ‘the gut microbiota’
ferring to a dysbiotic gut microbiota composition and/ refers to all microbial communities within the intestinal
or function. tract.
Enterotype: name for a type of microbiome classification Microbiota-gut-brain axis: a network comprising the gas
described in 2012 based on the proportions of certain trointestinal tract, the gut microbiota, the enteric ner
microbes, in particular Bacteroides, Prevotella, and Ru vous system and the brain. Bidirectional communications
minococcus. As communities of gut bacteria may form a between the gut and the brain regulate important func
spectrum rather than falling into distinct groups, a new tions, including immunity, digestion, metabolism, satiety
definition classifies gut microbiota enterotypes into two and stress reactions.
entities based on species diversity/gene count. One of
the enterotypes is low richness (more prevalent in pa Operational taxonomic units (OTUs) or phylotypes: similar
tients with more severe conditions) and the other is high bacterial individuals based on a predetermined similarity
richness (considered a marker of health). threshold (e.g., 97% similarity).
Fermented foods: foods or beverages whose production Postbiotics: bacterial metabolites with a direct effect on
involves extensive microbial growth. The fermented host nutrition, metabolism and immunity (e.g., short-
foods containing live organisms that have been charac chain fatty acids).
terized and have clinical evidence of a health benefit are
considered probiotics. For example, many fermented Prebiotics: these are substrates that are selectively utilized
milks have probiotic activity for conditions relating to the by host microorganisms conferring health benefits. Not
digestive tract and the immune system. all food fibers are considered prebiotics as selective uti
lization by gut bacteria is a requirement for a prebiotic.
Full shotgun metagenomic sequencing: a bioinformatics
technique that identifies which microbes are present in Probiotics: live microorganisms that, when administered in
a sample and their functional potential. It gives more adequate amounts, confer a health benefit to the host.
reliable functional predictions compared with 16S rRNA
sequencing. Psychobiotics: targeted interventions of the microbiome
for mental health benefits. It refers to probiotics, prebio
Germ-free: a host without a microbiome. Generally refers tics and other means of influencing the microbiome for
to mice and rats that were born and reared in a sterile the benefit of mental health.
environment for research purposes.
Short-chain fatty acids: fatty acids with two to six carbon
Inflammatory bowel disease (IBD): an umbrella term used atoms that are produced by bacterial fermentation of
to describe disorders characterized by an excessive dietary fibers (e.g., acetate, propionate and butyrate).
swelling of the wall of one section of the digestive tract.
Types of IBD include Crohn’s disease, ulcerative colitis Small intestinal bacterial overgrowth (SIBO): a poorly un
and pouchitis. Both genetic and environmental factors derstood entity characterized by an excessive growth of
potentially affect microbiota composition, which plays a bacteria within the small intestine. These excessive bac
role in IBD pathogenesis. teria have been linked to functional gut disorders such
as IBS.
Irritable bowel syndrome (IBS): a common functional di
sorder affecting up to 20% of people worldwide, with a Synbiotics: synergistic combination of prebiotics and pro
higher prevalence in women. It is indeed the main moti biotics.
vation behind gastroenterology conditions. Researchers
believe it may originate from an unbalanced gut micro Taxa: a scientifically classified group. Ways of classifying
biota. the members of a defined microbiome, in decreasing
order: Phylum -> Class -> Order -> Family -> Genus ->
Lipopolysaccharide (LPS): the major component of the ou Species -> Strain.
ter membrane of Gram-negative bacteria. When found
Report 2020 - 17You can also read
