An overview of gut microbiota

An overview of gut microbiota

Nadine MoubayedMedical Research Center

King Saud University

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Introduction

• Humans evolved in the presence of numerous microbial communities forming the normal flora on different body sites: on the skin, oral cavity, and the gastrointestinal cavity.

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•The role of these microbial communities is a matter of considerable interest.•The microbial populations that reside in and on the host cells are commonly referred to as “microbiota”.•The gastro-intestinal (upper and lower tract) (GIT) or gut microbiota is a complex community of microorganisms that live in the digestive tracts of humans and other animals, including insects.•The intestinal microbiota has been extensively studied compared to any other sites of the body.

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• Over 400 bacterial species colonize the human gut and co-evolved with the host in a symbiotic relationship:

Bacteroides Clostridium Faecalibacterium Eubacterium Ruminococcus Peptococcus Peptostreptococcus Bifidobacterium Escherichia and Lactobacillus• Over 99% of bacteria in the gut are anaerobes.

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• The normal intestinal bacteria perform a host useful functions:

Providing the host cells with essential nutrients.Fermenting unused energy substrates. Producing vitamins (vitamin K, folate, short chain fatty

acids) Training the immune system ( production of cytokines)Regulating the peristaltic movement.

Preventing the invasion of pathogenic bacteria as well as the overgrowth of the existing opportunistic pathogens.

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Main Function of The GI Microbiota

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Human acquisition of the normal flora

• In humans the gut flora is established at 1 or 2 years after birth.

• During birth and thereafter, bacteria from the mother and the surrounding environment colonize the infant’s gut. Where the composition of the gut flora is simple first and changes a great deal with time.

• Breast fed babies become dominated with Bifidobacteria (B. breve, B. bifidum, B. infantis).

• Formula fed infants intestinal microbiota is more diverse and contains high numbers of Enterobacteriaceae, Enterococci, Bifidobacteria, Bacteroides and Clostridia.

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GI Tract Composition and Bacterial Distribution

It differs along the GI tract and among humans depending on the: Age DietCultural conditions Use of antibiotics, which in its turn greatly disturbs the composition of the normal flora

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Upper gastrointestinal tract: stomach and the small intestine (duodenum,

jejunum, and upper ileum)

Large intestine

Few species are present The bacterial content increases distally :108 bacteria per g (dry weight) of ileal

content up to 1012 bacteria per g (dry weight) of colonic content(60% of the fecal mass).

Gram positive cocci mainly Streptococci (Enterococcus feacalis)

Peptostreptococcus.

Obligate anaerobes mainly of the genus Bacteroides

Staphylococcus Anaerobic gram positive cocci such as Peptostreptococcus sp., Eubacteria sp.,

Enterococci

Acid- tolerant lactobacilli Lactobacillus sp. and Bifidobacterium sp.,

Helicobacter pylori (opportunistic pathogen)

Clostridium sp.

Types of yeast facultative anaerobes such as E.coli

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pH 2Streptococcus Lactobacillus, Enterococcus,

Helicobacter pylori

pH 5-7Bacteroides, Colistridium,

Streptococcus, Lactobacillus,

Proteobacteria, Enterococcus

pH 5-7Bcateroides, Colstridium,Prevotella,

Porphyromonas, Eubacterium, Ruminococcus, streptococcus,

Enterobacterium, Enterococcus, Lactobacillus, Peptostreptococcus,

Fusobacteria

GI Bacterial Distribution

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Bacteria commonly found in the human colon

Bacterium Incidence (%)

Bacteroides fragilis 100

Bacteroides melaninogenicus 100

Bacteroides oralis 100

Enterococcus faecalis 100

Escherichia coli 100

Enterobacter sp. 40–80

Klebsiella sp. 40–80

Bifidobacterium bifidum 30–70

Staphylococcus aureus 30–50

Lactobacillus 20–60

Clostridium perfringens 25–35

Proteus mirabilis 5–55

Clostridium tetani 1–35

Clostridium septicum 5–25

Pseudomonas aeruginosa 3–11

Salmonella enteritidis 3–7

Commensal vs Pathogens

• The flora includes low populations of potentially pathogenic organisms (opportunistic pathogens) such as enterotoxigenic E.coli and Clostridium difficile

• Once the host’s immune system is weakened, the balance of the normal flora will be upset and consequently favors both infection by exogenous and overgrowth of endogenous pathogens causing harm to the host cells.

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(Gibson & Roberfroid, J. Nutr. 125, 1995)

Ps. aeruginosa

Proteus

Staphylococci

Clostridia

Veillonellae

Enterococci

E. coli

Lactobacilli

Streptococci

Eubacteria

Bifidobacteria

Bacteroides

Pathogenic, including

production of toxins

Production of carcinogens

Intestinal putrefaction

Inhibition of growth of harmful bacteria

Stimulation of immune functions

Aid in digestion or

absorption of nutrients

Synthesis of vitamins

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No/

g Fe

ces (

log 10

)

Harmful/pathogenic effects Health promoting functions / effects

Disturbance of the GI Tract

Bacterial Diarrhea

•Enterotoxigenic E. coli strains and Vibrio cholera attach to the small intestine cause watery diarrhea by producing an enterotoxin that stimulates mucosal cells to secrete fluid. •On the other hand, invasive bacteria such as, Shigella, Salmonella sp. and Campylobacter (contaminated water and food), penetrate the intestinal epithelium and cause bloody, mucoid diarrheal stool with inflammatory exudate.

Antibiotic Associated Diarrhea (AAD)•Antibiotic intake (AAD) or failure to eat, allow pathogenic bacteria to grow such as C. difficile a gram postivie anaerobic spore forming rod shape organism causing severe inflammation of the colon (pseudomembranous colitis) with diarrhea. •Taking priobiotics with Lactobacillus sp. or Bifidobacterium sp. prevent C. difficile infection following antibiotic treatment.

•Another harmful effect of antibiotics is the increase in numbers of antibiotic-resistant bacteria.

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• Thus, a reduction in levels of native bacterial species disrupts their ability to inhibit the growth of harmful species such as C. difficile, Enterotoxigenic E. coli, Salmonella sp., Campylobacter sp. and Shigella sp.

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Conclusion• Knowledge on the composition and diversity of a

healthy microbiota and on how changes in the intestinal microbiota lead to or are associated with disease is far from complete.

• More research is needed to examine the species and strain diversity in the GI tract

• Understanding the molecular mechanisms of action attributed to commensal and pathogenic bacteria will contribute to better-designed probiotic products.

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