Master in GastroenterologiaRoma, 27 novembre 2016
La Gastroenterologia Clinica: from Deskside to Bedside
Microbiota, Antibiotici e Probiotici in Gastroenterologia
Antonio Gasbarrini
Medicina Interna, Gastroenterologia e Malatie del Fegato
Area GastroenterologicaPolo Malattie dell’Apparato Digerente
Fondazione Policlinico Universitario GemelliUniversita’ Cattolica, Roma
Hollister EB et al. Gastroenterology 2014
Gastric acid
Biliary salts
Mucosal IgA
AN ANATOMO-MICROBIOLOGICAL BARRIERBacteria interactions
Mucus
Motility
CuriosityZein.net
Acquiredand
Innate immunity
Vascular and lymphatic systems
Neuroenteric system
Digestive enzymes
MucosalBarrier
Epithelial barrier
Endocrinesystem
Virus/phages BacteriaYeast
Microbiota has many components
Helminth
ParasiteArchea
Protozoa
Micro-eukaryotes
Acquiredand
Innate immunity
Vascular and lymphatic systems
Neuroenteric system
Digestive enzymes
MucosalBarrier
Epithelial barrier
Endocrinesystem
Virus/phages BacteriaYeast
Gut Bacteriome
Helminth
ParasiteArchea
Protozoa
Micro-eukaryotes
Microbial Taxonomic Rank
DOMINIUM
REGNUM
PHYLUM
CLASSE
ORDO
FAMILIA
GENUS
SPECIES
SUBSPECIES
95%
99%
100%
Genes identity
Enterococcus
Dethlefsen et al., Nature, 2007 18;449(7164):811-8 Ley et al., Science, 2008, 20;320(5883):1647-51Tap et al., Environ Microbiol, 2009, 11(10):2574-84
Firmicutes60 to 80 %
Firmicutes60 to 80 %
Clostridium coccoides (cluster
XIVa)
Clostridium coccoides (cluster
XIVa)
Clostridium leptum (cluster
IV)
Clostridium leptum (cluster
IV)
LactobacillalesLactobacillales
Bacteroidetes20 to 40 %
Bacteroidetes20 to 40 %
Faecalibacterium prausnitzii
Lactobacillus
Bacteroides thetaiotaomicron
Streptococcus thermophilus
Bifidobacterium
Escherichia coli
ActinobacteriaActinobacteria
ProteobacteriaProteobacteria
Phylogenetic diversity of human gut Bacteriome
Helicobacter pylori
2 major phyla: Firmicutes and Bacteroidetes (>70%)
Acquiredand
Innate immunity
Vascular and lymphatic systems
Neuroenteric system
Digestive enzymes
MucosalBarrier
Epithelial barrier
Endocrinesystem
Virus/phages BacteriaYeast
Other components of the Microbiota
Helminth
ParasiteArchea
Protozoa
Micro-eukaryotes
The gut is home to >50 genera of fungi with Candida, Saccharomyces and Cladosporium species being particularly common
Commensal fungal populations are more variable than those of bacteria and may be influenced by fungi in the environment (less abundant and less robust?)Diet can affect the fungal microbiota: plant-based diet ↑Candida species, animal-based diet ↑ Penicillium species
Dollive S, et al. Genome Biol 2014 Cui et al. Genome Med 2014
HUMAN GUT MYCOME
Fungal microbiome
Bacterial microbiome
MUCUS
Gut microbiome
Bacteria
Fungi
Huffnagle GB et al. Trends Microbiol 2014
HUMANE GUT VIROME
Berg Miller et al, Environ Microbiol 2011
• In the gut have been isolated >30.000 different viral genotypes. Majority ( 78%) of sequences ∼ did not match any previously described virus
• Some are human, most are bacterial virus or bacteriophages (caudovirales, corticoviridae,
• myoviridae, microviridae, siphoviridae..)
• Metabolic profiling revealed an enrichment of sequences with putative functional roles in DNA, protein and carbohydrate metabolism
• Phage have a main role in bacteriome adaptation to perturbations (diet, antibiotics..)
• Pro phages outnumbered lytic phages: 2:1
Correlation network analysis between relative abundance of bacterial phylotypes, yeast and bacteriophage-matching reads
EU= good BIOS= life
In a healthy Microbiota species are in equilibrium: EUBIOSIS
How to define an EUBIOTIC enterotype?
Kitamoto S et al. J Gastroenterol 2015
Microbiota “sensing”Osmolarity
Bicarbonate
Oxygen pH
Fucose SCFAs
Bile
Viscosity
Attachment shear stress
Cell density
Unknown
Metabolic sensing
Physico-chemical sensing
Mechano sensing
Quorum sensing
Shenderov et al. Anaerobe 2011 Schauder et al. Genes & Development 2001
How Bacteria Talk to Each Other?Highly specific as well as universal QUORUM
SENSING languages exist: METABIOTICS
Regardless of the type of signal used, QS allows coordinated regulation of behavior
QS enables a group of bacteria to act in a concerted manner, and thus acquire some of
the characteristics of multicellular organisms, becoming similar to eukaryotes
Bacterial behaviors are regulated by QUORUM SENSING, including symbiotic features, virulence, biofilm
formation, genes expression and epigenetic regulation, apoptosis
Some of the neurological diseases are associated with an altered microbiota composition, such as autism
In this study 3 chemically diverse quorum sensing peptides were investigated for their brain influx and efflux properties in an in vivo mouse model to determine blood-brain transfer properties
Evelien Wynendaele et al., PLoS One 2015
3 chemically diverse QUOUM SENSING PEPTIDES: BIP-2 (Quorumpeps ID 102, GLWEDLLYNINRYAHYIT)PhrANTH2 (Quorumpeps ID 186, SKDYN)PhrCACET1 (Quorumpeps ID 206, SYPGWSW)
1.BIP-2 (bacteriocin-inducing peptide 2): synthesized by Streptococcus pneumonia (commensal of the human nasopharynx)
2.PhrANTH2: produced by Bacillus anthracis
3.PhrCACET1: formed by Clostridium acetobutylicum Clostridium spp are predominant in the gut of
autistic children
Evelien Wynendaele et al., PLoS One 2015
Wynendaele et al., PLoS One 2015
PhrCACET1 showed the highest brain influx: it very efficiently crossed the BBB with a measured clearance by the brain that was higher than that of dermorphin (positive control), followed by BIP-2
PhrANTH2 shows no significant brain influx, similar to BSA (negative control)
…specific effects in each GI tract!
GUT MICROBIOTA AND HOST HEALTH
Barrier effect Immunocompetence/ToleranceSynthesisMetabolismDrug metabolismBehavior conditioning
Small Bowel
Barrier effect Immunocompetence/ToleranceSynthesisMetabolismDrug metabolismBehavior conditioning
GUT MICROBIOTA AND HOST HEALTH
Innate immune response•Epithelial cells•Myeloid cells•Innate lymphoid cells
Adaptive immune response•IgA•TH17 cells•Treg cells
Microbiota and immune system relationship
Microbiota stimulation of Treg cells
SCFA derived from fementation of complex dietary carbohydrates (high-fiber diet) by colonic microbiota
SCFA downregulate proinflammatory responses at the site of antigenic insult and also influence bone marrow-derived APCs
Honda and Lit tmann Nature 2016
Colon
Barrier effect Immunocompetence/ToleranceSynthesisMetabolismDrug metabolismBehavior conditioning
GUT MICROBIOTA AND HOST HEALTH
Failure of MICROBIOTA equilibrium
Quali-quantitative alterations of oral, esophageal, gastric, small bowel and/or
colonic microbiota
DYSBIOSIS
Digestive and extradigestive diseases
EUBIOSIS
Breastfeeding/formula feeding
Fecal microbiota (mother)
Koenig JE et al, PNAS 2010
During the weaning phase (first 2-3 years of age)
a Native CORE microbiota populates the gut (early programming with life long-effects )
Mode of delivery (vaginal microbiota)
Other (e.g. antibiotcs)
Environment(mother/father/parents/
babysitter/siblings/pets..)
Huffnagle GB et al. Trends Microbiol 2014
EARLY LIFE DYSBIOTIC EVENTS
Fungal microbiome
Bacterial microbiome
• Existence of a critical window in early life, when the gut microbiota can influence the development of persisting metabolic traits
• Recipients of penicillin altered microbiota had decreased expression of intestinal immune-response genes, similar to their donors Immunologic and metabolic changes are not caused by direct effects of antibiotics but rather by derived changes in the gut microbiota
• Currently there is no direct evidence for a causal relationship in humans
Jess T., N Engl J Med. 2014
Cox – Cell 2014
• Mice receiving penicillin during weaning gained total mass and fat mass in adult age
• Mice receiving penicillin-altered microbiota (transfer of the cecal microbiota from 18 w-old penicillin-treated mice to 3 w-old Germ Free mice) gained total mass and fat mass at a significantly faster rate
Antibiotics in early life and obesity
Hollister EB et al. Gastroenterology 2014
Gastric acid
Biliary salts
Mucosal IgA
GUT BARRIER INTEGRITYBacteria interactions
Mucus
Motility
Microbiota new knowledge caused the falling of the Single Germ Theory
• With the Microbiota revolution differences in proportions of various bacteria in different disease state are important rather than the appearance of a single microrganism
• To understand disease pathogenesis the emphasis has to be on the balance of different microbes rather than a single pathological microrganism
All Digestive Diseases have been associated to a LEAKY GUT
• Gastrointestinal infections• Irritable Bowel Syndrome • Small Intestine Bacterial Overgrowth• Diverticulosis• Inflammatory Bowel Diseases• Gastro-intestinal Cancers• Food Intolerance/Allergy• Celiac disease• Liver diseases• Pancreatic diseases• Obesity, Diabetes and Metabolic Syndrome
• Gastrointestinal infections• Irritable Bowel Syndrome • Small Intestine Bacterial Overgrowth• Diverticulosis• Inflammatory Bowel Diseases• Gastro-intestinal Cancers• Food Intolerance/Allergy• Celiac disease• Liver diseases• Pancreatic diseases• Obesity, Diabetes and Metabolic Syndrome
Digestive Diseases associated to DYSBIOSIS/LEAKY GUT
SMALL INTESTINE BACTERIAL OVERGROWTH is associated with IBS symptoms (bloating,
diarrhea/constipation, pain) and food intolerance
Lin, JAMA 2004Fermentation and gas production
SIBO prevalence increases with age
< 50 years
50-74 years
> 75 years
0%
64%
10%
Riordan SM, Am J Gastro 1997
SIBO RISK FACTORS: 2. AGEING
• Gastrointestinal infections• Irritable Bowel Syndrome • Small Intestine Bacterial Overgrowth• Diverticulosis• Inflammatory Bowel Diseases• Gastro-intestinal Cancers• Food Intolerance/Allergy• Celiac disease• Liver diseases• Pancreatic diseases• Obesity, Diabetes and Metabolic Syndrome
Digestive Diseases associated to DYSBIOSIS/LEAKY GUT
IBS pts are DYSBIOTIC1. Reduction of bacterial abundance
Human intestinal tract chip phylogenetic microarray that enables the parallel profiling and semi-quantitative analysis of >1000 representative intestinal phylotypes
Microbiota of IBS and healthy subjects are
significantly different (P =0.0005) with a
reduction of abundance of species
HC
IBS
Rajilic-Stojanovic. Gastroenterology 2011;141(5):1792-801
Rajilic-Stojanovic - Gastroenterology 2011
45 phylogenetic groups differed significantly between IBS and controls
*Especially B gallicum and B pseudocatenulatum
*
IBS pts are DYSBIOTIC2. Different bacterial variety
Digestive diseases associated to DYSBIOSIS/LEAKY GUT
• Gastrointestinal infections• Irritable Bowel Syndrome • Intestinal Bacterial Overgrowth• Diverticulosis• Inflammatory Bowel Diseases• Gastro-intestinal Cancers• Food Intolerance/Allergy• Celiac disease• Liver diseases• Pancreatic diseases• Obesity, Diabetes and Metabolic Syndrome
Junjie Qin et al. Nature 2010;464(7285):59-65
IBD pts are DYSBIOTIC1. Reduction of bacterial abundance
Daniel N. Frank et al., PNAS 2007;104(34):13780-5
IBD pts are DYSBIOTIC2. Different bacterial variety
Norman – Cell 2015
The enteric virome richness increases in CD and UC
Decreases in bacterial diversity and richness in IBD do not explain virome changes
Virome changes in CD and UC are disease-specific
IBD pts are DYSBIOTIC3. Alterations in enteric Virome
Increased abundance of Basidiomycota and an equivalent decrease in Ascomycota in IBD (particularly in flare)
Among decreased Ascomycota in IBD flare, Malassezia sympodialis was identified
In IBD, Saccharomyces genus (particularly S. cerevisiae) exhibited the strongest signals. S. Cerevisiae decreases both in absolute number and regarding the proportion, particularly in flare
IBD pts are DYSBIOTIC4. Alterations in enteric Mycobiome
Sokol H, GUT 2016
Digestive diseases associated to DYSBIOSIS/LEAKY GUT
• Gastrointestinal infections• Irritable Bowel Syndrome • Intestinal Bacterial Overgrowth• Diverticulosis• Inflammatory Bowel Diseases• Gastro-intestinal Cancers• Food Intolerance/Allergy• Celiac disease• Liver diseases• Pancreatic diseases• Obesity, Diabetes and Metabolic Syndrome
Sanchez. Appl Environ Microbiol 2013
Untreated CD VS GFD-CD VS Controls
Proteobacteria (11 vs 2%)
Enterobacteriaceae (15 vs 5%)
Staphylococcaceae (22 vs 10%)
Firmicutes (73 vs 92%)
Bacterial Microbiota dysbiosis in Celiac Disease
Breastfed/vaginally delivered infants with first-degree CD relative HLA-DQ2 VS non-HLA-DQ2/8 carriers 16S rRNA gene Pyrosequencing + qRT PCR
DQ2 vs Non DQ2/8 - Genus level
Bifidobacterium Unclassified Bifidobacteriaceae
Corynebacterium; GemellaClostridium sensu stricto,Unclassified ClostridiaceaeUnclassified Enterobacteriaceae Raoultella
Olivares. Gut 2015;64(3):406-17
De Palma. Br J Nutr 2009;102(8):1154-60
30 days of GFD in healthy people
BifidobacteriumC. lituseburense F. prausnitzii
BifidobacteriumLactobacillus
Enterobacteriaceae E.coli
FISH
qPCR
Gluten Free Diet causes dysbiosis in not Celiacs subjects
Digestive diseases associated to DYSBIOSIS/LEAKY GUT
• Gastrointestinal infections• Irritable Bowel Syndrome • Intestinal Bacterial Overgrowth• Diverticulosis• Inflammatory Bowel Diseases• Gastro-intestinal Cancers• Food Intolerance/Allergy• Celiac disease• Liver diseases• Pancreatic diseases• Obesity, Diabetes and Metabolic Syndrome
GUT MICROBIOTA INFLUENCE ON ENERGY STORAGE
• Wild Type (WT) mice have 42%
more total body fat and 47%
more gonadal fat than germ-
free (GF) mice
• Colonisation of GF mice with
microbiota from WT produces a
60% increase in body fat mass,
associated with increased
insulin resistance
Backhed et al – PNAS 2004
Microbiota transmit adiposity phenotype
Ridaura et al. Science 2013Walker AW et al. Science 2013
TRANSFERRED INTO THE INTESTINESOF GERM-FREE MICE (Ob) twin + mice = adiposity (Ln) twin + mice = adiposity
Fecal microbiota from 4 human female twin pairs discordant for obesity
COHOUSING(Ob) twin transplanted mice + (Ln) twin transplanted mice = (Ob) mice became LEAN(Ln) mice remain LEAN
TRANSMISSIBILITY OF INTESTINAL MICROBES
AND ADIPOSITY PHENOTYPE ARE TIGHTLY LINKED
Acetate promotes metabolic syndrome through activation of the parasympathetic nervous system
Perry – Nature 2016
• Increased production of acetate due to a gut microbiota–nutrient interaction in HFD-fed rodents
• Activation of the parasympathetic nervous system
• Increased glucose-stimulated
insulin secretion
• Increased ghrelin secretion
• Hyperphagia
• Obesity
Bile acids - Microbiota-induced obesity requires farnesoid X receptor
Parseus - Gut 2016
• Farnesoid X receptor (FXR) is a bile acid nuclear receptor
• GF versus wild-type and Fxr−/− mice fed with HFD for 10 weeks
• FXR and gut microbiota regulate development of diet-induced obesity
• Gut microbiota increases hepatic steatosis and expression of genes involved in lipoprotein uptake through FXR
• The obesity phenotype is transferable by transferring the caecal microbiota from HFD-fed Fxr−/− and wild-type mice into GF mice
Bile acids - Microbiota-induced obesity requires farnesoid X receptor
Parseus - Gut 2016
Obesity is associated with:
•Reduced bacterial diversity
•Phylum-level changes
•Altered representation of bacterial genes and metabolic pathways
Turnbaugh – Nature 2009
obesecontrol
Gut microbiota in obese humans
BACTEROIDETES/ FIRMICUTES
Adiposity index
Changes in gut microbial ecology• Low bacterial richness (Low gene count)• Microbiotal phenotype• Higher rate of systemic inflammation
Bacterial alteration Reduction in F. prausnitzii, A. muciniphila, Alistipes… Proinflammatory bacteria dominate (Ruminococcus gnavus.)
Consequences• Reduction in butyrate production and increased mucus degradation• Increased oxidative stress and metainflammation
Tilg and Moschen , Gut 2014
obesecontrol
Gut microbiota in obese humans
Akkermansia muciniphilaMicrobiota fingerprint of obesity?
Everard – PNAS 2013
Akkermansia muciniphila is a mucin-degrading bacteria that resides in the mucus layer
Lower abundance of A. muciniphila in leptin-deficient obese than in lean mice
100-fold decrease of A. muciniphila in high-fat-fed mice
Schneerberg et al - Sci Rep 2015
A. muciniphila inversely correlates with onset of inflammation, altered adipose tissue metabolism and metabolic disorders during obesity in mice exposed to HFD
• A. muciniphila, Bifidobacterium spp. and Lactobacillus spp. were significantly decreased after HFD, although this decrease was transient for Bifidobacteria and Lactobacilli
• Abundance of Akkermansia muciniphila decreased gradually to finally reach a level ~ 10,000 times lower than the initial one
Akkermansia muciniphilaMicrobiota fingerprint of obesity?
Dao et al – Gut 2015
A. muciniphila is associated with a healthier metabolic status and better clinical outcomes after Caloric Restriction in overweight/obese adults
6-w caloric restriction period followed by a 6-w weight stabilisation diet in 49 overweight and obese adults
• Baseline A. muciniphila inversely related to fasting glucose, waist-to-hip ratio and subcutaneous adipocyte diameter.
• Individuals with higher A. muciniphila abundance at baseline displayed greater improvement in insulin sensitivity markers and other clinical parameters after CR
Akkermansia muciniphilaMicrobiota fingerprint of obesity?
Akkermansia muciniphilaMicrobiota fingerprint of obesity?
Metformine and diabetesA microbiota-dependent pathway?
Meta-analysis of metagenomic data from 199 T2D patients, from whom information on antidiabetic treatment was available, and 554 non-diabetic controls, comprising Swedish, Danish and Chinese individuals
Metformin changes gut microbiota in T2D patients
Forslund et al – Nature 2015
Metformin-treated T2D pts
Intestinibacter spp abundance
Escherichia spp abundance
Metformine and diabetesA microbiota-dependent pathway?
Meta-analysis of metagenomic data from 199 T2D patients, from whom information on antidiabetic treatment was available, and 554 non-diabetic controls, comprising Swedish, Danish, and Chinese individuals
• Bacterial gene function modules for butyrate and propionate production increase as metformine serum levels do
• Identification of T2D patients treated with metformin based on their gut microbial composition
Forslund et al – Nature 2015
Metformin changes gut microbiota in T2D patients
Beside diet composition (HFD..) and caloric amount, other Microbiota influencers could have a role in Obesity
and Metabolic disorders
4 groups of C57BL/6 mice:•Low Fat/Sedentary•Low Fat/Exercise•High Fat/Sedentary•Hfigh Fat/Exercise
•HFD resulted in significantly greater body weight and adiposity as well as decreased glucose tolerance that were prevented by Exercise
Evans – Plos One 2014
Microbiota influencers in Met DisordersExercise
Exercise prevents weight gain and alters microbiota in HFD-induced obesity
• At week 12, exercise changed the levels of phyla of bacteria:
Bacteroidetes
Firmicutes
Proteoacteria
Evans – Plos One 2014
Microbiota influencers in Met DisordersExercise
Non caloric artificial sweeteners (NAS: SACHARIN, SUCRALOSE, ASPARTAME) drive development of glucose intolerance through induction of compositional and functional alterations of gut microbiota
NAS-mediated effects can be abrogated by antibiotic treatment
NAS-mediated effects are fully transferrable to germ free mice upon transplantation of microbiota from NAS consuming mice or of microbiota anaerobically incubated in presence of NAS
Suez et al, Nature 2014
CALLING FOR A REASSESSMENT OF MASSIVE SWEETENERS USAGE
Microbiota influencers in Met DisordersNon caloric artificial sweeteners
Poroiko, Sci Rep 2016
Microbiota influencers in Met DisordersChronic sleep disruption
Chronic Sleep Disruption Alters Gut Microbiota, Induces Systemic and Adipose Tissue Inflammation and Insulin Resistance in Mice
Mice were exposed to Sleep Fragmentation (SF) for 4 w and then allowed to recover for 2 w
• Sleep Fragmentation increases food intake, visceral fat and insulin resistance
Poroiko – Sci Rep 2016
Microbiota influencers in Met DisordersChronic sleep disruption
Chronic Sleep Disruption Alters Gut Microbiota
Mice were exposed to Sleep Fragmentation (SF) for 4 w and then allowed to recover for 2 w
Firmicutes Lachnospiraceae Ruminococcaceae
Bacteroidetes Bifidobacteriaceae Lactobacillaceae
Reversible gut microbiota changes after SF
Digestive diseases associated to DYSBIOSIS/LEAKY GUT
• Gastrointestinal infections• Irritable Bowel Syndrome • Intestinal Bacterial Overgrowth• Diverticulosis• Inflammatory Bowel Diseases• Gastro-intestinal Cancers• Food Intolerance/Allergy• Celiac disease• Liver diseases• Pancreatic diseases• Obesity, Diabetes and Metabolic Syndrome
GI Cancers associated to DYSBIOSIS
• Oral cavity• Esophagus• Stomach• Small Bowel• Colon• Liver• Bile trat • Pancreas
H. pylori
Gut microbiota
Microbiota in anticancer immunotherapy
Antibodies targeting CTLA-4 have been successfully used as cancer immunotherapy. Their effect depends on the presence of microbiota.
Vétizou et al. Science 2015
Tumors in antibiotic-treated or germ-free mice did not respond to CTLA blockade.
The antitumor effects of CTLA-4 blockade depend on distinct Bacteroides species.
In mice and patients, T cell responses specific for B. thetaiotaomicron or B. fragilis were associated with the efficacy of CTLA-4 blockade.
Microbiota in anticancer immunotherapy
Vétizou et al. Science 2015
Digestive diseases associated to DYSBIOSIS/LEAKY GUT
• Gastrointestinal infections• Irritable Bowel Syndrome • Intestinal Bacterial Overgrowth• Diverticulosis• Inflammatory Bowel Diseases• Gastro-intestinal Cancers• Food Intolerance/Allergy• Celiac disease• Liver diseases• Pancreatic diseases• Obesity, Diabetes and Metabolic Syndrome
ETOH NAFLDHBV/HCV
HCC
Auto immunity
Encephalopathy
Iron.. Portal hypertension
HRS
Ascites/SBP
DYSBIOSIS+
LEAKY GUT
DISEASE PROGRESSION
DISEASE PROGRESSION
DISEASE PROGRESSION
Ge PS et al. NEJM 2016
TODAY… GUT MICROBIOTA HAS A PROGNOSTIC VALUE
IN LIVER CIRRHOSIS
Gut microbiota Mucosal immune system
Muco-epithelial barrier
Vascular pathway Neuroendocrine/Neuroenteric
Systems
How to mantain an Eubiotic gut barrier?
How to modulate Gut Microbiota?
Diet and Nutritional SupportDiet composition (meat, cheese, fibers, high glicemic index, saturated fatty acids, ethanol, sweeteners…)Caloric amount, minerals, vitamins..
Removal of predisposing conditionsTreat diabetes, endocrine, other motility disorders..Surgery or prokinetics when indicatedStop PPI or other antiacid, NSAIDs, antibiotic, immunosoppressant, antidepressant….
Intervention Fecal Microbial Transplantation
Biotherapy (prebiotics, probiotis, symbiotics, postbiotics)
Antibiotics
How to modulate Gut Microbiota?
Diet and Nutritional SupportDiet composition (meat, cheese, fibers, high glicemic index, saturated fatty acids, ethanol, sweeteners…)Caloric amount, minerals, vitamins..
Removal of predisposing conditionsTreat diabetes, endocrine, other motility disorders..Surgery or prokinetics when indicatedStop PPI or other antiacid, NSAIDs, antibiotic, immunosoppressant, antidepressant….
Intervention Fecal Microbial Transplantation
Biotherapy (prebiotics, probiotis, symbiotics, postbiotics)
Antibiotics
How to modulate Gut Microbiota?
Diet and Nutritional SupportDiet composition (meat, cheese, fibers, high glicemic index, saturated fatty acids, ethanol, sweeteners…)Caloric amount, minerals, vitamins..
Removal of predisposing conditionsTreat diabetes, endocrine, other motility disorders..Surgery or prokinetics when indicatedStop PPI or other antiacid, NSAIDs, antibiotic, immunosoppressant, antidepressant….
Intervention Fecal Microbial Transplantation
Biotherapy (prebiotics, probiotis, symbiotics, postbiotics)
Antibiotics
How to modulate Gut Microbiota?
Diet and Nutritional SupportDiet composition (meat, cheese, fibers, high glicemic index, saturated fatty acids, ethanol, sweeteners…)Caloric amount, minerals, vitamins..
Removal of predisposing conditionsTreat diabetes, endocrine, other motility disorders..Surgery or prokinetics when indicatedStop PPI or other antiacid, NSAIDs, antibiotic, immunosoppressant, antidepressant….
Intervention Fecal Microbial Transplantation
Biotherapy (prebiotics, probiotis, symbiotics, postbiotics)
Antibiotics
FMT: therapeutical applications
• C Difficile* and other antibiotic resistant GI
infection
• IBD and IBS
• Other inflammatory/autoimmune conditions
• NAFLD and other liver diseases
• Diabetes, Metabolic Syndrome, Obesity
• GI cancer
• Oncohematology
• Neurological and psichiatric disorders*Approved
Short vanco+FMT vs Short vanco+bowel prep vs Standard vanco
Study stop after an interim analysis
Resolution of CDAD
Mild diarrhea and abdominal cramping in the FMT group on the infusion day
• FMT group (n=16): 81%1 FMT, 94% >1 FMT• Vancomycin group (n=13): 31%• Bowel prep (n=13): 23%
Van Nood et al – NEJM 2013
RCT: FMT nasoduodenal tube
Short vanco+FMT vs Standard vanco
Study stop after a 1-year interim analysis
Resolution of CDAD
5/7 pts with severe disease (PMC): progressive disappearance of PMC and resolution of CDAD after multiple FMT
No significant adverse events
RCT: FMT colonoscopy
• FMT group (n=20): 90%• Vancomycin group (n=19): 26%
Cammarota et al – APT 2015
FMT for recurrent C. Diff entered in the European Guidelines
FMT is strongly suggested in combination with antibiotics for multiple recurrent CDI
SoR: AQoE: 1
Debast et al – Clin Microbiol Infect 2014
Youngster – JAMA 2014
20 pts with rCDI received 15 FMT capsules by healthy volunteers on 2 consecutive days and were followed up for symptom resolution and adverse events for up to 6 months
Resolution of diarrhea in 14 patients (70%; 95%CI, 47%-85%) after a single capsule-based FMT
All 6 non-responders were re-treated; 4 had resolution of diarrhea, resulting in an overall 90% rate of clinical resolution of diarrhea (18/20)
No serious adverse events attributed to FMT
Moayeddi et al Gastroenterology 2015, 16-5085 (15) 451-5
FMT induces remission of UC
Parallel study of UC patients FMT vs placebo 50 ml via Enema from anonymous donors FMT once weekly for 6 weeks Primary end points: remission (Mayo score <2) and
endoscopic Mayo score of 0 at week 7
Trial stopped for futility 24% of FMT reached remission vs 5% of controls No differences in adverse events 7 out of 9 pts in remission received FMT from a
single donor THE MAGIC POOP!
How to modulate Gut Microbiota?
Diet and Nutritional SupportCaloric amount, minerals, vitamins..Diet composition (fibers/high glicemic index/saturated fatty acids…)
Removal of predisposing conditionsTreat diabetes, endocrine, other motility disorders..Surgery or prokinetics when indicatedStop PPI or other antiacid, NSAIDs, antibiotic, immunosoppressant, antidepressant….
Intervention Antibiotics
Biotherapy (prebiotics, probiotics, symbiotics, postbiotics)
Lactobacillus spp• casei spp (Rhamnosus, DN..)• reuteri• acidophilus• shirota• delbrueckii, sp. Bulgaricus• brevis• plantarum
Bifidobacterium spp• bifidum• infantum• longum• thermophilum• lactis
Which PROBIOTIC?
Cocci gram-positive• Streptococcus thermophilus• Enterococcus faecium• Streptococcus intermedieus• Streptococcus alfa-emoliticus
Bacillus gram-negative• Escherichia coli Nissle (1917)
Guarino A. Bruzzese E. 2001; FAO/WHO, 2001
Bacillus gram-positive• Bacillus clausii
Yeast• Saccharomyces boulardii
Needs for a Subspecie (Strain)-specific Microbial
Therapy
Different action for each Probiotic:Knowledge of micro-organism functions and host genetic modulation by different Species/Strain is
crucial
How to choose the right Probiotic?
Different action for each Probiotic:Knowledge of micro-organism functions and host genetic modulation by different Species/Strain is
crucial
HOW TO CHOOSE A PROBIOTIC?
Single strain Multistrains
Alive Dead
Bacteria Yeasts
Mechanism of action
Needs to know: mechanisms of Probiotic/Host interaction
Immunological benefits:Macrophage activation to increase antigen presentation to B cells and IgA
production
Modulate cytokine profiles
Induce hyporesponsiveness to food antigens
Non-immunological benefits: Digest food and compete for nutrients with pathogens
Alter local pH to create an unfavorable local environment for pathogens
Produce bacteriocins to inhibit pathogens
Scavenge superoxide radicals
Stimulate epithelial mucin production//enhance intestinal barrier function
Compete for adhesion with pathogens
Modify pathogen-derived toxins WGO 2011
LEVEL OF EVIDENCE FOR PROBIOTICS IN GASTROINTESTINAL DISORDERS
Reduction of Antibiotic-associated Diarrhea
Prevention and treatment of Infectious Diarrhea
Adjuvant for H. pylori and C. difficile treatment
Treatment of Necrotizing enterocolitis
Treatment of Sugar Intolerance
Prevention and treatment of Pouchitis
Maintenance of remission of IBD
Treatment of IBS
A
Practice guidelines on Probiotics usageWorld Gastroenterology Organization (2011)
LACTOBACILLUS CASEI sp RHAMNOSUS
Reduction of Antibiotic-associated Diarrhea
Prevention and treatment of Infectious Diarrhea
Adjuvant for H. pylori and C. difficile treatment
Treatment of Necrotizing enterocolitis
Treatment of Sugar Intolerance
Prevention and treatment of Pouchitis
Maintenance of remission in Ulcerative Colitis
Treatment of IBS
Practice guidelines on Probiotics usage World Gastroenterology Organization (2011)
LACTOBACILLUS REUTERII
Reduction of Antibiotic-associated Diarrhea
Prevention and treatment of Infectious Diarrhea
Adjuvant for H. pylori and C. difficile treatment
Treatment of Necrotizing enterocolitis
Treatment of Sugar Intolerance
Prevention and treatment of Pouchitis
Maintenance of remission in Ulcerative Colitis
Treatment of IBS
Practice guidelines on Probiotics usage World Gastroenterology Organization (2011)
ESCHERICHIA COLI sp NISSLE 1917
Reduction of Antibiotic-associated Diarrhea
Prevention and treatment of Infectious Diarrhea
Adjuvant for H. pylori treatment
Treatment of Necrotizing enterocolitis
Treatment of Sugar Intolerance
Prevention and treatment of Pouchitis
Maintenance of remission of Ulcerative Colitis
Treatment of IBS
Practice guidelines on Probiotics usage World Gastroenterology Organization (2011)
BACILLUS COAGULANS GBI-30, 6086
Reduction of Antibiotic-associated Diarrhea
Prevention and treatment of Infectious Diarrhea
Adjuvant for H. pylori treatment
Treatment of Necrotizing enterocolitis
Treatment of Sugar Intolerance
Treatment and maintenance of remission of Ulcerative
Colitis
Treatment of IBS
Practice guidelines on Probiotics usage World Gastroenterology Organization (2011)
Multistrains combination VSL 3
Reduction of Antibiotic-associated Diarrhea
Prevention and treatment of Infectious Diarrhea
Treatment of Necrotizing enterocolitis
Treatment of Sugar Intolerance
Prevention and treatment of Pouchitis
Treatment and maintenance of remission of Ulcerative
Colitis
Treatment of IBS
Practice guidelines on Probiotics usage World Gastroenterology Organization (2011)
SACCHAROMYCES CEREVISAE sp BOULARDII
Reduction of Antibiotic-associated Diarrhea
Prevention and treatment of Infectious Diarrhea
Adjuvant for H. pylori and C. Difficile treatment
Treatment of Traveller’s diarrhea
Treatment of Necrotizing enterocolitis
Prevention and treatment of Pouchitis
Maintenance of remission in IBD
Treatment of IBS
Practice guidelines on Probiotics usage World Gastroenterology Organization (2011)
Mechanisms of action of each strain
Optimal dose
Duration of treatment
Selection of strains and/or strains combinatios
Safety? Stability?
Probiotics: many unsolved questions
..waiting NEXT GENERATION PROBIOTICS
1.Faecalibacterium Prausnitzii2.Akkermansia Muciniphila3.Eubacterium halii4.…
How to modulate Gut Microbiota?
Diet and Nutritional SupportDiet composition (meat, cheese, fibers, high glicemic index, saturated fatty acids, ethanol, sweeteners…)Caloric amount, minerals, vitamins..
Removal of predisposing conditionsTreat diabetes, endocrine, other motility disorders..Surgery or prokinetics when indicatedStop PPI or other antiacid, NSAIDs, antibiotic, immunosoppressant, antidepressant….
Intervention Fecal Microbial Transplantation
Biotherapy (prebiotics, probiotics, symbiotics, postbiotics)
Antibiotics
Targets of antibiotic therapy
1. Eradicate specific pathogenic bacteria • H. Pylori, Yersinia, Shigella, Toxic E. Coli....
2. Modulate mutualistic gut microbiota
• Colonic diverticulosis
• Liver cirrhosis complications (encephalopathy, PBS)
• Intestine Bacterial Overgrowth
• IBS/IBD
•…..
Rifaximin and liver disease
-Rifaximin with or without lactulose is able to reduce the risk of hepatic encephalopathy (HE) recurrence and the rate of HE-related hospitalizations. Rifaximin has also been reported to improve operational abilities and input integration capacity in patients with minimal HE
-Rifaximin reduces the occurrence of spontaneous bacterial peritonitis (SBP) increasing transplant free survival
-Rifaximin reduces endotoxemia and the hepatic venous pressure gradient (HVPG), as well as the incidence of complications related to portal hypertension, such as variceal bleeding and thrombocytopenia
Bass NM et al. N Engl J Med. 2010Neff GW wt al. J Clin Gastroenterol 2012
Sharma BC et al. Am H Gastroenterol 2013Maharshi S et al. Gut 2014
Sharma K et al. Saudi J Gastorenterol 2014Bajaj JS et al Gastroenterology 2011
Hanouneh MA et al. J Clin Gastroenterol 2012
Vlachogiannakos J et al. J Gastroenterol Hepatol 2012Kalambokis GN et al. Hepatology 2012
Kalambokis GN et al. Liv Int 2012Bajaj JS et al. PLoS One 2013
Rifaximin and GI diseases
-Rifaximin is effective in preventing traveler’s dyarrhea, treat Small Intestine Bacterial Overgrowth, obtaining symptoms relief in patients with uncomplicated diverticular disease and in those with irritable bowel syndrome (IBS) without constipation
-Rifaximin induces remission in patients with active Crohn’s disease
-Rifaximin reduces stool frequency, rectal bleeding and sigmoidoscopic score and helps in achieving remission in patients with ulcerative colitis
Guslandi M et al. Inflamm Bowel Dis 2006Gionchetti P et al. Digest Dis Sci 1999
Papi C et al. Aliment Pharmacol Ther 1995Colecchia A et al. World J Gastroenterol 2007
Gasbarrini et al, Alim Pharm Ther 2005 Pimentel M et al. N Engl J Med 2011
Prantera C et al. Aliment Pharmacol Ther 2006Shafran I et al. Curr Med Res Opin 2005Shafran I et al. Am J Gastroenterol 2008
Prantera C. Gastroenterology 2012
•Alteration of virulence
•Inhibition of bacterial adherence to gut mucosa
•Reduced bacteria internalization
•Anti-inflammatory activity
•Gut microbiota modulation
HOW RIFAXIMIN WORKS?A «NON CONVENTIONAL» ANTIBIOTIC
EUBIOTIC EFFECT OF RIFAXIMIN
Design of the study: observational prospective
Population under study:
•Ulcerative Colitis (U), •Crohn’s disease (C)•Irritable bowel syndrome (I)•Diverticular disease (D) •Liver cirrhosis with hepatic encephalopathy (HE)
undergoing 1200 mg/day of Rifaximin x 10 days
Gasbarrini et al, Dig Dis 2016
Time a vs Time b P.Value adj.P.Valf__Rikenellaceae 0,0001 0,002 <f__Streptococcaceae 0,002 0,026 <f__Lactobacillaceae 0,005 0,039 >
Time a vs Time c P.Value adj.P.Valf__Lactobacillaceae 0,000028 0,0006 >f__Rikenellaceae 0,0002 0,002 >f__Enterobacteriaceae 0,007 0,057 >f__Streptococcaceae 0,011 0,06 <
Time b vs Time c P.Value adj.P.Valf__Streptococcaceae 0,0003 0,007 >f__Lactobacillaceae 0,0009 0,010 >f__Rikenellaceae 0,003 0,028 >f__Enterobacteriaceae 0,008 0,048 >
Time a (baseline) vs time b (stop Rifa)
Time a (baseline) vs time c (1 month after Rifa)
Time b (stop Rifa) vs time c (1 month after Rifa)
Gasbarrini et al, Dig Dis 2016
EUBIOTIC EFFECT OF RIFAXIMIN
Soldi, Gasbarrini et al. Clin Exp Gastroenterol 2015
• 15 non-C IBS patients
• Treated with Rifaximin 550 mg t.i.d. for 14 days
Fecal sample collection was performed at baseline (T0), at the end of 14 days of treatment, and at the end of the 6-week follow-up period (T56)
In IBS patients, a general stability of the investigated groups across the different time
points was observed
EUBIOTIC EFFECT OF RIFAXIMIN IN IBS
• Faecalibacterium prausnitzii (from 5.6% at T0 to 8.5% at T14)• Roseburia inulinivorans (from 2.4% at T0 to 1.9% at T56)• Streptococcus salivarius (from 1% at T0 to 0.4% at T14• Blautia luti (from 1.6% at T0 to 0.7% at T14)
Soldi, Gasbarrini et al. Clin Exp Gastroenterol 2015
EUBIOTIC EFFECT OF RIFAXIMIN IN IBS
Loosely adherent
mucus layer
Firmly adherent
mucus layer
Bad bacteria
Bile acids
Lumen
Recettori ionici
Water
Stomach Duodenum and
Jejunum
Ileum Colon
Adhesions molecules
Immune cells
Food antigens
EndotheliumAnd fibroblasts
Nerve and miocytes
Non-Immune cells
Food antigens
Good bacteria
Lumen
Immune cells
EndotheliumAnd fibroblasts
Nerve and miocytes
Non-Immune cells
SEVERE LEAKY GUT AND DYSBIOSIS
GASBARRINI A, UNPUBLISHED
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