Helicobacter pylori

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A Microbial Biorealm page on the genus Helicobacter pylori



Higher order taxa

Bacteria (Domain); Proteobacteria (Phylum); Epsilon Proteobacteria (Class); Campylobacterales (Order); Helicobacteraceae (Family); Helicobacter (Genus)


NCBI: Taxonomy

Helicobacter pylori

Description and significance

Helicobacter pylori is a Gram-negative organism that has a helical or spiral shape and has 6-8 flagella at one end. The size of the organism measures about 2-4 um x 0.5-1.0 um. H. pylori are found in a very acidic environments, at a pH of 2.0 or less. The bacterium has been cultured in microaerobic (low oxygen conditions) but it adapts to high oxygen at high culture densities. It is commonly found inside the lining of the stomach and the duodenum. H. pylori are a slow growing organisms that can cause peptic ulcers and gastritis that can lead to gastric cancer and gastric MALT (mucosa-associated lymphoid tissue) lymphoma.

It was first observed in 19th century that curved bacteria were living in the lining of the stomach, but growing and isolating the bacteria was neglected. H. pylori was later isolated in Perth, Western Australia by Barry Marshall and Robin Warren in 1983. They discovered that H. pylori were related to peptic ulcers. To prove this hypothesis, the organism was cultured from the stomach, and through conclusive studies was determined that H. pylori was the bacteria that caused peptic ulcers and gastritis [Tomb] In 2005, Marshall and Warren received the Nobel Prize in physiology or medicine for their discovery of the Helicobacter pylori.

Helicobacter pylori was initially named Campylobacter pylordis because it appeared that the organism was similar to other Campylobacters. It shared a similar appearance with Campylobacter jejuni. [Megraud] Using rRNA hybridation and sequencing, H. pylori was shown to be different from the Campylobacter genus. H. pylori was separated into its own genus Helicobacter in 1989. The Helicobacter name reflects the appearances of the organism. However, the bacteria are helical in vivo, but often rod like in vitro. [Marshall]

Genome structure

The genomes of two strains have been completely sequenced: H. pylori 26695 and J99. Both were sequenced using a random shotgun approach from libraries of cloned chromosomal fragments of ~2.5kb. The 26695 genome was 24kb larger than the J99, but both of the genomes had GC% of 39%. Both genomes had similar average lengths of coding sequences, coding density and the bias of initiation codons. The origin of replication of the genome J99 was not clearly identifiable. [Mobley]

The genome of Helicobacter pylori strain "26695" is circular and contains 1,667,867 base pairs, and strain "J99" contains 1,643,831 base pairs. The chromosome of the organism contains genes that encode the urease gene cluster, cytotoxins in the membrane, and the cag pathogenicity island. In 1989, CagA gene was found and identified as the marker strain of the risk of peptic ulcers and gastric cancer. The CagA pathogenicity island recognizes the type IV secretion system, which CagA proteins are moved to the host cells. [Blaser] The DNA content of H. pylori has GC range of 35-38% which categorized itself to the Campylobacter species. However, the comparisons of the 16S ribosomal RNA showed that H. pylori were different from Campylobacter but similar to Wolinella succinogenes which its GC range was 42-49%. H. pylori were placed into its own genus, Helicobacter after the analysis of the ultra structure, fatty acid composition and biochemical tests which proved different for H. pylori and W. succinogenes. [Marshall]

The analysis of H. pylori sequences specifies the diversity and the development of the organism. The genome contains sequences that encode for the membrane proteins. For example, the F1F0 ATP synthase complex, various oxidoreductases such as cytochrome o, and some transporters. [Modlin] Sequences show that H. pylori contians a “well developed systems for motility, for scavenging iron, and for DNA restriction and modification.” [Tomb] Helicobacter pylori are capable to uptake DNA from other H. pylori. Due to the uncertainty of the strain linkages, recombination occurs because of the repetitive DNA sequences, which allows high frequency deletion and duplication and mismatch in-between the strands. Lack of mismatch repairing can increase in frequency of random variation but it can also convert the gene which can bring down the diversity of the organism. [Blaser]

Cell structure and metabolism

The motility of H. pylori depends on the flagella which is driven by the proton motive force. The motility and the shape of the bacteria is specifically adapted to the gastric mucus. The flagella have a molecular weight of 50,000-62,000. The shape helps the bacteria to move easily in viscous environments. They do not only provide motility but they have bulbs on the ends of the flagella which favors the adhesion. The flagella are 4um in length (average), and the diameter of each flagella is 30nm. [Mobley]

The genome of H. pylori has homologs for all the enzymes required for the assembly of peptidoglycan by the use of precursors of the cytoplasmic synthesis. After the transport through the cytoplasmic membrane, the precursors are imbedded into the peptidoglycan layer by penicillin-binding proteins. The peptidoglycan of H. pylori differs from that of E. coli. H. pylori peptidoglycan has muropeptides with pentapeptide side chains that ends with glycine. Through the genome, F0 proton-channeling complex (a,b,c subunits) and catalytic, peripheral headpiece of the F1 have all been identified.[Mobley] Through the analysis of the genomes of 26695 and J99, H. pylori do not use complex carbohydrates as energy sources. The only carbohydrate used by H. pylori is glucose. It is metabolized via the Entner Douderoff pathway (reaction that catabolize glucose to pyruvate using glycolysis or pentose phosphate pathway). But it is likely used for anabolic biosynthesis rather than catabolic production. The primary sources of pyruvate in H. pylori are lactate, L-alanine, L-serine, D-Amino acids rather than glucose or malate. It has been reported that fermentation of pyruvate produces acetate. J99 contains homologs to the pta (phosphate acetyl transferase) and ackA (acetate kinase) genes. The 26695 pta has a frameshift mutation which inactivates the gene product. [Mobley]

The urease is a potent virulence factor for H. pylori. Urease is central to H. pylori's metabolism and virulence and helps the microorganism colonize the gastric mucosa. Urease: NH2C=ONH2 + H2O ---> NH3 + NH2-COOH and NH2COOH + 2H2O ---> NH3 + H2CO3. This reaction increases in pH. H. pylori synthesize a huge amount of urease. They use it to convert urea into ammonia and bicarbonate to counteract the low acidity of the stomach. With high urease activity, H. pylori can protect the bacterium from acid damage by buffering the cell and the environment. The hydrolysis of urea molecules in the gastric juices creates ammmonia which acts as an acceptor for the H+ ions to increase the local pH. H. pylori demonstrate the highest activity of acidity. The enzyme must be consistently available for the organism to survive in the acidic environment. The defense of the body cannot fight H .pylori because killer T cells and white cells cannot easily get through the lining of the stomach. As the defense cells die, the H. pylori feed off the superoxide radicals on the stomach lining of the cells. [Mobley]


Helicobacter pylori is found commonly in the lining of the stomach and the duodenum because they adapt well to the acidic, low pH environment. Urease is the central metabolism of H. pylori. In order to survive, the organism uses urea to produce ammonia and bicarbonate to neutralize the acid in the stomach. The metabolic products from H. pylorican alter the host, and change the acidity of the environment and increase the supplements of nutrients to colonize the stomach. [Blaser]


Helicobacter pylori are known for peptic ulcers and gastritis. The organism weakens the mucous lining of the stomach and allows acid to enter to the sensitive coating of the stomach. The acid and the bacteria irritate the lining and cause an ulcer. It is very common to humans, and animals. Half of the population is infected by H. pylori. Since it is a slow growing bacterium, many people have the organism but are asymptomatic, that is they don't get ulcers or gastritis. H. pylori are able to adapt and survive in the acidic environment of the stomach because the conversion of urea to bicarbonate and ammonia neutralizes the gastric acid. The motility of the bacteria, the flagella and the shape favors colonization which allows spiral shape to excavate through the lining. [Modlin]

The protein cagA has an increasing host response. The function is unknown but it is part of the pathogenicity island which has a region that contains 40 genes, and appears to affect virulence. This island contains DNA with different bases compared to the rest of the genome. [Modlin] CagA is coexpressed with VacA. VacA is known as a gene that is mosaic. It shows a clear pathway for the secreted toxins that contribute to the virulence and the colonization in many ways. [Cover] Another gene that is mostly identified with virulence is iceA. iceA shows a clear relationship between expression and clinical outcome of the genes. There are number of membrane inserted proteins involved with the export of proteins within the pathogenicity island. It is sometimes difficult to detect the infection of H. pylori by using its genomic base. In Asia, CagA is not the marker for pathogenesis in contrast to Western countries. [Modlin]

Several spiral shaped bacteria looking like H. pylori have been found in the gastric mucosa in animals like cats, dogs, baboons and ferrets. They are often called gastric Campylobacter like organisms, but they do not cause gastritis or ulcer. Macaca mulatta, M. nemestrina and baboons seem to be the only animals that naturally harbor H. pylori. Using ELISA and immunoperoxidase staining, the antibodies of the H. pylori was found in serum. [Marshall] Most people with H. pylori do not show symptoms, usually they are asymptomatic. But people with the infection are likely to develop peptic ulcers. Symptoms in patients can be pain in the upper abdomen, nausea, vomiting, loss of appetite, and indigestion. [Modlin]

Application to Biotechnology

It is found that H. pylori, has a Lys gene that is an autolytic (break down of tissue) enzyme that degrades the walls of Gram-positive and Gram-negative bacteria. It was found in the unrelated clinical strain. The gene is expressed in vitro, and lytic activity is on both Gram-positive and negative cell walls. The hydrolytic action of the protein was confirmed by the clone and the expression of the gene. [Marsich]

Current Research

Helicobacter pylori flagella: antigenic profile and protective immunity.

Recent research of the vaccine for H. pylori has been tested on mice. The colonization of the organism is hard to express because H. pylori has a “reproducible induction of sterilizing immunity.’’ Since motility is crucial for this organism by using its flagella, researchers hypothesized that the vaccine which targeted the flagella would improve the protection and reduce the colonization of this organism. To prove this hypothesis, the vaccine was tested on mice and it was observed that immunized mice with whole cell lysate cultivated for the flagella sheath proteins had reduced the colonization of the organism. However, it is indicated that the proteins of the flagella are not evident in “whole cell lysate and shows the differences in antigenicity of the whole cell lysate antisera.” [Skene]

Primary antibiotic resistance in Helicobacter pylori strains isolated in northern and central Italy.

To determine the antibiotic resistance in the strains of H. pylori, researchers used the two strains that were isolated in Italy. The two strains were isolated in two locations, Bologna, Northern Italy and Rome, Central Italy. The strain was isolated from patients who never got treated for the infection. The antibiotic resistance that was tested on the isolated strain was clarithromycin, metronidazole and levofloxacin, and the purpose was to break the inhibitory concentration point of the strain. [Zullo] The 255 strain had a resistance rate of 16.9%, 29.4%, and 19.1% for clarithromycin, metronidazole and levofloxacin. The patients who had non ulcer dyspepsia had a higher resistance rate in clarithomycin. Italian patients had higher resistance in metronidazole and old patients had higher resistance in levofoxacin. The levofoxacin resistance was more likely to appear in a strains with either clarithomycin or metronidazole resistance. The study of the three antibiotic resistances that were tested was in a very high rate. [Zullo]

Targeting Helicobacter pylori in gastric carcinogenesis.

Genes associated with virulence located in the pathogenicity island has been identified with being related to the risk of gastric cancer. Recent studies show that H. pylori was recognized with “both bacterial and host factors.” The host’s gastric inflammatory is affected by the virulence and the cytotoxin associated genes which mediate the cytokine receptors that trigger the risk of having gastric cancer. They targeted the organism with antibiotics and indicated that it may prevent the gastric cancer, but only to patients who have not yet developed “preneoplastic lesions”. The best way of preventing gastric cancer is to target the organism with vaccination. [Lee]


1. Blaser Martin J. "Ecology of Helicobacter pylori in the Human Stomach" J. Clin. Invest.Volume 100, Number 4, August 1997, 759-762

2. Blaser, Martin J and Atherton, John C."Helicobacter pylori persistence: biology and disease". J Clin Invest. 2004 February 1; 113(3): 321–333.

3. Cover, TL, Blanke SR. "Helicobacter pylori VacA, a paradigm for toxin multifunctionality." 2005 Apr;3(4):320-32.

4. Lee DS, Moss Sf. “Targeting Helicobacter pylori in gastric carcinogenesis.” 2007 Jun;11(6):757-69.

5. Marshall Barry J, McCallum Richard W and Guerrant Richard L. "Helicobacter pylori in peptic ulceration and gastritis." Blackwell Scientific Publications 1991; 24-25, 58

6. Marsich, Eleonora, Zuccato, Pierfrancesco, Rizzie, Sonia, Vetere, Amedeo, Tonin, Enrico, and Paoletti, Sergio. "Helicobacter pylori Expresses an Autolytic Enzyme: Gene Identification, Cloning, and Theoretical Protein Structure" J Bacteriol. 2002 November; 184(22): 6270–6279.

7. Megraud, F. "Taxonomy and Biology of Helicobacter pylori- a comment". "Helicobacter pylori, Gastritis and Peptic Ulcer". Springer-Verlag Berlin Heidelberg 1990; 59

8. Mobley Harry L.T, Mendz George L. and Hazell Stuart L. "Helicobacter pylori physiology and genetics". ASM Press 2001; 69-71, 75-76, 300

9. Modlin Irvin M. and Sachs George. "Acid Related Diseases, Biology and treatment" Lippincott Williams and Wilkins 2004; 461-462, 479-481.

10. Skene C, Young A, Every A, Sutton P. “Helicobacter pylori flagella: antigenic profile and protective immunity.” 2007 May 23

11. Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA, Nelson K, Quackenbush J, Zhou L, Kirkness EF, Peterson S, Loftus B, Richardson D, Dodson R, Khalak HG, Glodek A, McKenney K, Fitzegerald LM, Lee N, Adams MD, Hickey EK, Berg DE, Gocayne JD, Utterback TR, Peterson JD, Kelley JM, Cotton MD, Weidman JM, Fujii C, Bowman C, Watthey L, Wallin E, Hayes WS, Borodovsky M, Karp PD, Smith HO, Fraser CM, Venter JC. "The complete genome sequence of the gastric pathogen Helicobacter pylori." Nature 1997. 388(6642): 515-6

12. Zullo A, Perna F, Hassan C, Ricci C, Saracino I, Morini S, Vaira D. “Primary antibiotic resistance in Helicobacter pylori strains isolated in northern and central Italy.” 2007 Jun;25(12):1429-1434.

Edited by Katherine Park student of Rachel Larsen and Kit Pogliano

Edited KMG

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