Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps

Ailloud, Florent; Didelot, Xavier; Woltemate, Sabrina; Pfaffinger, Gudrun; Overmann, Jörg; Bader, Ruth Christiane; Schulz, Christian; Malfertheiner, Peter; Suerbaum, Sebastian

doi:10.1038/s41467-019-10050-1

Cited by 115 publications

(133 citation statements)

References 88 publications

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“…On the other hand, our formal framework is a first and necessary step to study the effect of restriction enzymes in the DNA composition of bacteria and virus. Consider, for example, the phylogenetic studies in [1], where our H. pylori taboo-set T H.py was taken from. Is the inferred evolutionary time between two H. pylori populations affected by T H.py ?…”

Section: Discussionmentioning

confidence: 99%

“…In H. pylori 21-A-EK1 (studied in [1]), many restriction enzymes have been identified. For the sake of clarity, let us write T H.py = A T G T C T T T, where a T denotes those taboos in T H.py whose first symbol is a ∈ Σ.…”

Section: Helicobacter Pylorimentioning

confidence: 99%

“…Since |T T.pa [1,1]| < m, Corollary 25 implies that every graph Γ s n (T T.pa ) is connected. Therefore the evolution of the DNA sequences can potentially reach any other taboo-free DNA sequence, no matter which suffix was conserved along this process.…”

Section: Turneriella Parvamentioning

confidence: 99%

“…Graph Γn(T) for n ∈[1,5] for binary alphabet Σ = {0, 1} and T = {11, 000}. Set V n+1 (T) is constructed by adding every allowed symbol at the beginning of each string in Vn(T).…”

mentioning

confidence: 99%

“…If Σ = {0, 1} and T = {10, 01}, then T is left proper and |T[1,1]| = |T[2, 2]| = 2 = |Σ|. For n ≥ 2, V n (T) = {0 · · · 0, 1 · · · 1}, what makes Γ n (T) disconnected.The trivial graphs Γ 0 n (T) and Γ 1 n (T) are both connected.…”

mentioning

confidence: 99%

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Structure of the space of taboo-free sequences

Manuel

Haeseler

2019

Preprint

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Models of sequence evolution typically assume that all sequences are possible. However, restriction enzymes that cut DNA at specific recognition sites provide an example where carrying a recognition sequence can be lethal. Motivated by this observation, we studied the set of strings over a finite alphabet with taboos, that is, with prohibited substrings. The taboo-set is referred to as T and any allowed string as a taboo-free string. We consider the graph Γ n (T) whose vertices are taboo-free strings of length n and whose edges connect two taboo-free strings if their Hamming distance equals 1. Any (random) walk on this graph describes the evolution of a DNA sequence that avoids deleterious taboos. We describe the construction of the vertex set of Γ n (T). Then we state conditions under which Γ n (T) and its suffix subgraphs are connected. Moreover, we provide a simple algorithm that can determine, for an arbitrary T, if all these graphs are connected. We concluded that bacterial taboo-free Hamming graphs are nearly always connected, although 4 properly chosen taboos are enough to disconnect one of its suffix subgraphs.

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Section: Discussionmentioning

confidence: 99%

Section: Helicobacter Pylorimentioning

confidence: 99%

Section: Turneriella Parvamentioning

confidence: 99%

“…Graph Γn(T) for n ∈[1,5] for binary alphabet Σ = {0, 1} and T = {11, 000}. Set V n+1 (T) is constructed by adding every allowed symbol at the beginning of each string in Vn(T).…”

mentioning

confidence: 99%

mentioning

confidence: 99%

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Structure of the space of taboo-free sequences

Manuel

Haeseler

2019

Preprint

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Protonated Charge Reversal Nanodrugs for Active Targeting Clearance of Helicobacter Pylori Accompanied by Gut Microbiota Protection

Liu

Chen

Sun

et al. 2023

Adv Funct Materials

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Helicobacter pylori (H. pylori) is listed as a definite carcinogen and clinical triple therapy is less satisfactory because H. pylori colonizes beneath the gastric mucous layer and easily forms biofilm. More importantly, the frequent and excessive use of antibiotics causes a disorder of gut microbiota due to the lack of targeting to H. pylori. Here, a kind of protonated charge reversal metal based nanodrugs (MNDs)—ZnO‐Ag‐mercaptoacetamide@chitosan for H. pylori eradication treatment without affecting beneficial gut microbiota is prepared. In H. pylori infected mouse model, the MNDs actively target submucosa colonized H. pylori owing to mucous penetrability and protonation effect, and further eradicate H. pylori and its biofilm by producing metal ions and reactive oxygen species. Transcriptomic analysis shows that there are no obvious side effects to intestinal microorganisms during the treatment. Besides, it is found that the MNDs are great potential to remove gastric inflammation along with the blocking of inflammatory pathways and the reduction of virulence factors, which is related to the infiltration of CD4+ T cells to clear H. pylori.

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Cancer‐related genetic variants of Helicobacter pylori strains determined using gastric wash‐based whole‐genome analysis with single‐molecule real‐time technology

Watanabe

Oikawa

Kodaka

et al. 2020

Intl Journal of Cancer

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Helicobacter pylori (H. pylori) are a primary factor in the pathogenesis of gastric cancer (GC); GC ranks third among cancer-related mortality. A clear understanding of the H. pylori genome factors underlying GC is necessary to develop more effective methods to prevent GC. A single-molecule real-time DNA sequencing-based H. pylori genomewide association study analysis was performed using the H. pylori genome present in five early-stage GC (EGC) and five non-GC clinical DNA samples recovered from gastric washes. A total of 275 genes with 702 nucleotide variants (NVs) were found to be common to three or more patients with EGC but no non-GC patients (single-NV:

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Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps

Cited by 115 publications

References 88 publications

Structure of the space of taboo-free sequences

Structure of the space of taboo-free sequences

Protonated Charge Reversal Nanodrugs for Active Targeting Clearance of Helicobacter Pylori Accompanied by Gut Microbiota Protection

Cancer‐related genetic variants of Helicobacter pylori strains determined using gastric wash‐based whole‐genome analysis with single‐molecule real‐time technology

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