Microbiota of GIT

PRESENTER: DAWIT WORKNEH (SR I)

MODERATOR: ZELALEM A. (ASSISTANT PROFESSOR OF SURGERY, GENERAL & COLORECTAL

SURGEON)
Outline
Introduction
Symbiosis
Dysbiosis
Clinically important Microbiota
Bowel preparation
Prebiotics, Probiotics, Synbiotics
Fecal Microbiota Transplantation (FMT)
Introduction
 Normal flora (Microbiome) - MO inhabiting muco-cutaneous surface of healthy
individuals
 Core Vs. secondary Microbiome

 Symbiosis – commensalism

 Human Microbiome project

 There are 2 classes of GI Microflora

 Allocthonus (transient)

 Autocthonus (indigenous)
 Prevalence and composition in different parts of the GI
depends on

 Mode of delivery  Nutrient availability

 Age  Redox potential
 Diet  Bacterial antagonism
 Peristalsis  Bacterial adhesion
 PH  Antibiotic use
 Constipation  Personal hygiene
 Exogenous toxins
 Total number of bacterial spp. In individuals is >500
with the colon alone reported to have 500-1000
spp./individual however most of them cant be grown.
 16S ribosomal RNA found universally in all bacteria's.

 number of bacteria and cells ??

 30% of fecal dry weight is composed of bacterias ( 1011-1012/g of
feaces)
 90-99.9% of culturable flora are anaerobes
 Most common anaerobe & aerobe are bacteriodes and

E. coli spp. Respectively

Anaerobes are the most common in a polymicrobial
ecology
Strict (obligate) Vs Moderate (Microaerophilic)
Most clinically important anaerobes are moderate,
however 99.9% are strict (obligate) anaerobs
e.g. Bacteroidetes, Prevotella, Fusobacterium
 Intestinal gas
Composition: N2, O2, H2, CO2, CH3
Sources

1. Swallowed air
2. Diffusion from blood
3. Intraluminal production
100-200ml found within GIT & 400-1200ml/d are released as
flatus depending on the type of food digested
 Composition in different parts of the GI tract
 Oral cavity: Viridian streptocooci, Gram –ve diplococcic, diphteroids,
lactobacillus
 Esophagus: MO arriving with saliva and food
 Stomach: lactobacillus, Gram positive cocci
 Pancreaticobillary tree: normally not colonized
 Proximal Small bowel : lactobacillus, enterococci, coliforms,
bacteriodes
 Distal ileum & Large bowel: bacteriodes, prevotella, clostridium, and
peptostreptococcus
Physiologic functions (Symbiosis)
 Serves as a barrier flora: drastic Vs permissive
 Colonization resistance – selective modulation of fecal flora
 Prevention of CDAD & Osmotic diarrhea
 Stimulation of gut immune system e.g. Ig A, Mucin,
AMPs
 Breakdown of CHO & proteins in the colon
 Production of Vitamin K, folate, & SCFA’s
 Modulates GI motility
 Produce antimicrobial proteins against other MO
 E.g. bacitracin (colicin by E.coli) , H2O2

 Metabolize Xenobiotic e.g. drugs and food toxins

Harmful effects (Dysbiosis)
 Occurs when Translocated from their specific site
accidentally (transcellular or Paracellular) or
damaged by antibiotics.
 Role in as a cause of disease
 IBD & CDAD
 Obesity & metabolic syndrome
 Bladder/colorectal CA
 Celiac sprue
 Chronic wound infection
 Atopic dermatitis
 NEC & EONS
 Vaginitis
 Infective endocarditis (IE)
Clinically important Microbata
INFECTIONS OF ORAL CAVITY
HELICOBACTER PYLORI
CLOSTRIDIOIDES DIFFICLE
ANAEROBIC INTRABDOMINAL INFECTION
Infection of oral cavity
 Infectionof the mouth & respiratory tract are usually
caused by mixed oronasal flora including anaerobes
 Periodontal infection, perioral abscess, sinusitis &
mastoiditis predominantly involve Prevotella spp (P.
melaninogenica), Fusobacterias, and peptostreptococci.
 S. mutans can lead to bacteremia following dental
procedures, colonizing damaged or prosthetic heart valves
(IE)
H. pylori
 Spiral shaped, Microareophilic, Gram negative
 Coccoid form – in less ideal env’t, more resistant
 Media – blood agar, skirrows
 Catalase, oxidase & urase +ve
 2 species of HP: Gastric & Enterohepatic
 Gastric adaptation is possible due to
 Urease activity (15% of total protein weight)

 Motility – spiral, flagella, mucolytic enzymes

 Specific receptor mediated adhesion

 Evasion of immune response

 Epidemiology Pathogenesis

 80% in developing, 10 – 50 % in  Colonizes gastric type but not

developed, prevalence increases
with age
 Transmission
 Oral – Oral, Feco - Oral
 Risk
Factors
 Poor socioeconomic status
 Level of education/income
 Race/ethnicity
 Consumption of salted foods
 Hereditary susceptibility??
intestinal type epithelial cells
 Effector proteins/adhesions
Neutrophil activating protein A, heat
shock protein 60, sialic acid binding
adhesion
 Cytotoxins
 Mucinase, Phospholipase, CagA,
VacA
 80-90% of all gastritis ass. With H.pylori
 In HP infected individuals 90% of gastric bacteria are
HP but in those with negative HP test flora is made of
Firmiucates, Bacteriodets, Fusobacterias, Actinobacter,
Proteobacterium
 Anthrum is most favored site.
 Typically do not invade surface epithelial cells
rather triggers host immune response
 90% of DU & 70% of GU have HP infection
 Reinfection rate( <2%/yr)
 Cag A +ve HP infection is associated with acute gastritis,
GU, precancerous lesions & gastric CA development
H. pylori Diagnostic investigations

Dx test Sensetivity (%) Specificity (%)

Serology 88-99 86-99

Stool antigen 94 97

14C-urea breath test 90-99 89-99

Rapid urea breath test 88-95 95-100

Culture 70-92 100

Histology 95 98
Clinical feature Treatment
 Asymptomatic in most especially
chronic gastritis or mild dyspeptic
symptoms
 Disease association: Gastritis
(Acute/Chronic), PUD, GCA,
MALTOMA
 Look for alarming features
 Extraintestinal manifestation
 Iron deficiency anemia
 ITP
 Vitamin B12 deficiency
 C. difficile
 Gram +ve, spore forming, toxin
producing, motile, anaerobes
 Parts of novel flora where >2oo spp.
Of them are identified with few being
pathogenic.
 C. difficile, c. botulinum, c. tetani, c.
preferinges
 Blood enriched medias or other
anaerobic medias.
 Non toxicogenic C.difficile (10-30%)
clinical isolates make up the normal
flora of GI microbiome
 Pathogenesis
 Disease is mediated by 2 toxins, an
enterotoxin (Toxin A) & a cytotoxin
(Toxin B).
 Toxin A is chemotactic for neutrophils,
so initiates infiltration of PMNC and
cytokine release

 Toxin B causes cytoskeletal destruction

of intestinal epithelial cells
 Hypervirulent strain – NAP1/BI/027
 Transmission : Feco-oral
 Risk factors
 Antibiotic use
 Advanced age (>65yrs)
 Hospitalization,
 severe comorbid illness
 IBD
 GIT surgery
 PPI use,
 Recent Hospitalization
 Spectrum of manifestation ranges from asymptomatic
carrier (20%) to fulminant disease with toxic megacolon.
 Diarrhea with colitis : non severe vs severe
 Antibiotic association (90-95%) – on/following Rx ( <1mnth
usually 2wks)

 Any Abx can predispose to CDI but most frequent ones are
Fluoroquinolones, Clindamycin, Cephalosporin, and Penicillin
 DX
 Unexplained leukocytosis >15000/ul
 Imaging: patchy mild erythema, friability, pseudomembraneus colitis
 Recurrent CDI??
 Rx
 Non severe disease: vancomycin ,Metronidazole, Fidaxomycin
 severe disease with fulminant colitis
 Vancomycin (PO or as Retention enema) + Metronidazole (IV)
 Fecal microbiota transplantation (FMT)
 Surgery : colectomy
Antimicrobial agents that may induce closridioides
difficile diarrhea & colitis
Frequently associated Occaisonally associated Rarely associated

Fluoroquinolones Macrolides Aminoglycosides

Clindamycin CPT Tetracycline

Penicillin (broad spectrum) Sulphonamides Chloramphenicol

cephalosporin Metronidazole

Vancomycin
Anaerobic intrabdominal infection
 Polymicrobial infections resulting when microbiota is
disrupted or displaced to normally sterile body sites.
 Anerobes lack the following metabolic/Biochemical
conditions
 Cythochrome system for the metabolism of O2
 Superoxide dismutase (SOD)
 Catalase

 Are mostly by moderate anerobes

 Bacteroides spp: following intrabdominal infections, PID or ovarian
abscess
 Others: clostridium spp, peptoniphilus, peptostreptococcus
 Clinical clues to anerobic infection
 Putrid drainage ( considered Dx of anaerobic infection)
 Polymicrobial flora on Gram stain exudates
 Involves normal flora of adjacent mucosal surfaces
 Abscess formation
 Negative aerobic culture result
 Gas in tissues (production of CO2 & H2 )
 Perforation of the proximal small bowel as with perforated PUD, leads to
infection reflecting flora of upper GIT
 Aerobic & Anaerobic Gram +ve bacteria's
 Antimicrobial choice
 Empiric antibiotics with coverage of coliforms & anaerobes.

 Mild to moderate CA intraabdominal infection e.g. perforated

PUD/Appendix

1. Single agent: Cefoxitin, Ertapenem, Moxifloxacin, Tigecycline

2. Combination: Ceftazoline, Cefuroxime, Ceftriaxone, Cefotaxime,

Ciprofloxacin or Levofloxacin + Cetronidazole
 Severe CA intraabdominal infection + Immunocompromised, advanced age, DM

1. Single agent: Imipenem-Cilastatin, Meropenem, Doripenem or Piperacilin-

Tazobactam

2. Combination: Cefepime, Ceftazidime, Ciprofloxacin or Levofloxacin +

Metronidazole
Bowel Preparation
 Area of controversy among different surgical societies in regards to colon and
rectal surgeries but accepted in preparation bundle prior to colonoscopy.

 Purpose: facilitate bowel manipulation

: reduce post op SSI & anastomotic leak

: enable passage & firing of surgical staplers/sutures

: increase quality of Visualization during colonoscopy

 Contraindications
 Ileus

 Significant gastric retention

 Suspected or established mechanical bowel obstruction
 Severe inflammatory or infectious colitis
 Neurologic or cognitive impairment preventing safe swallowing
 Methods

1. Mechanical bowel preparation (MBO)

 Osmotic agents: absorbed Vs non absorbed

e.g. PEG, Magnesium citrate

 Stimulant Laxatives: Bisacodyl, castor oil

 combinations
 Antibiotics : PO Vs. IV ??
 Neomycin sulphate 1g + Erythromycin 1g at 2pm, 3pm & 10pm
 Neomycin sulphate 1g + Metronidazole 1g at 2pm, 3pm & 10pm
 Cleansing enema & Fluid diet
 sodium phosphate, glycerin, or saline solutions.
 low-residue liquid supplements/meals
 The American Society of Colon and Rectal Surgeons Clinical Practice
Guidelines for the Use of Bowel Preparation in Elective Colon and Rectal
Surgery, 2019
 MBP combined with preoperative oral antibiotics is typically recommended for
elective colorectal resections - Grade1B.
 Preoperative MBP alone, without oral antibiotics, is generally not recommended –
Grade 1A
 Preoperative
oral antibiotics alone, without mechanical preparation, are generally
not recommended – Grade 2C
 Preoperative
enemas alone, without MBP and oral antibiotics, are generally not
recommended – Grade 2b
 Conclusion

 Clinical evidence supports the use of MBP as an adjunct

to the use of the oral antibiotic bowel preparation But
not alone.
 In our setup bowel preparation involves
1. Clear Fluid diet for 2 days preop
2. Cleansing enema BID for 2 days preop
3. Laxatives
 castor oil 30ml BID or Bisacodyl 10mg po BID for 24hr preop
4. Oral Antibiotics
 Amoxacilin 1g and Metronidazole 500mg at 5pm, 7pm, & 11pm
24hrs preop
Prebiotics, Probiotics, & Synbiotics
 Definition

 Prebiotics

a substrate that is selectively used by host microorganisms conferring health

benefit. They typically contain non digestible CHO but may also be fatty
acids, phenolic & phytochemicals.

e.g. inulin, fructooligosacharides (FOS), galactooligosacharides (GOS)

 Probiotics

 live MO, which when administered in adequate amounts confer

a health benefit on the host.

e.g. lactobacilli and bifidobacterium strains

 Synbiotics

 combination of prebiotics and probiotics

Fecal Microbiota Transplantation (FMT)
 Is defined as the instillation of processed stool collected from a
healthy donor in to the intestinal microbiota of a patient.
 Candidates are patients with third or subsequent non severe
recurrent CDI despite appropriate antibiotic therapy.
 Can be administered through oral capsules, lower GI tract
procedures (retention enema, colonoscopy) or via upper GI tract
procedures (Nasojejunal or Nasoduodenal tube)
References
 Medical Microbiology, 9th ed.
 Basic Medical Microbilogy,
 Jaweth Medical Microbilogy, 28th ed.
 Shackelford’s Surgery of Alimentarytract, 8th ed.
 Schwartz 11th ed.
 2020 Up Todate
 American Society of Colon and Rectal Surgeons Clinical Practice Guidelines
for the Use of Bowel Preparation in Elective Colon and Rectal Surgery, 2019
“ Thank you
”
Q are welcomed !