Bacteroides thetaiotaomicron in the gut: Molecular aspects of their interaction

Zocco, Maria Assunta; Ainora, Maria Elena; Gasbarrini, Giovanni; Gasbarrini, Antonio

doi:10.1016/j.dld.2007.04.003

Cited by 105 publications

(74 citation statements)

References 46 publications

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“…Using the 1%-to-1.3% threshold for operational identification of species based on 16S rRNA genes (45), 24 species were found to have intragenomic diversity equal to or higher than the operational threshold ( borderline (between 1% and 1.3%) in 10 species and Ն1.3% in 14 species. In particular, this phenomenon was seen in 7 bacterial species associated with the human microbiome or diseases (Table 2), including Escherichia coli (1.10%), Bacillus subtilis (1.16%), Pseudomonas stutzeri (1.23%), Bacteroides thetaiotaomicron (1.30%), Bifidobacterium adolescentis (1.30%), "Candidatus Protochlamydia amoebophila" (1.34%), and Borrelia afzelii (20.38%) (15,19,20,22,39,46,55). The sequence diversity observed in these species appears to follow five patterns: intervening sequences, regional diversity, random diversity, pseudogene, and gene truncation/partial rRNA operon.…”

Section: Smentioning

confidence: 99%

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

Pei

Oberdorf²,

Nossa³

et al. 2010

Appl Environ Microbiol

238

181

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Analysis of intragenomic variation of 16S rRNA genes is a unique approach to examining the concept of ribosomal constraints on rRNA genes; the degree of variation is an important parameter to consider for estimation of the diversity of a complex microbiome in the recently initiated Human Microbiome Project (http://nihroadmap.nih.gov/hmp). The current GenBank database has a collection of 883 prokaryotic genomes representing 568 unique species, of which 425 species contained 2 to 15 copies of 16S rRNA genes per genome (2.22 ؎ 0.81). Sequence diversity among the 16S rRNA genes in a genome was found in 235 species (from 0.06% to 20.38%; 0.55% ؎ 1.46%). Compared with the 16S rRNA-based threshold for operational definition of species (1 to 1.3% diversity), the diversity was borderline (between 1% and 1.3%) in 10 species and >1.3% in 14 species. The diversified 16S rRNA genes in Haloarcula marismortui (diversity, 5.63%) and Thermoanaerobacter tengcongensis (6.70%) were highly conserved at the 2°structure level, while the diversified gene in B. afzelii (20.38%) appears to be a pseudogene. The diversified genes in the remaining 21 species were also conserved, except for a truncated 16S rRNA gene in "Candidatus Protochlamydia amoebophila." Thus, this survey of intragenomic diversity of 16S rRNA genes provides strong evidence supporting the theory of ribosomal constraint. Taxonomic classification using the 16S rRNA-based operational threshold could misclassify a number of species into more than one species, leading to an overestimation of the diversity of a complex microbiome. This phenomenon is especially seen in 7 bacterial species associated with the human microbiome or diseases.

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Section: Smentioning

confidence: 99%

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

Pei

Oberdorf²,

Nossa³

et al. 2010

Appl Environ Microbiol

238

181

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“…Next, we examined their influence on the activity of human DPP III and bacterial DPP III. The enzyme from the Bacteroides thetaiotaomicron was chosen, because this bacterium is a prominent member of the human intestinal microflora and contributes to the host physiology 25,26 .…”

Section: Introductionmentioning

confidence: 99%

Novel dipeptidyl hydroxamic acids that inhibit human and bacterial dipeptidyl peptidase III

Cvitešić¹,

Sabljić

Makarević³

et al. 2016

Journal of Enzyme Inhibition and Medicinal Chemistry

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Human dipeptidyl peptidase III (hDPP III), a zinc-metallopeptidase of the family M49, is an activator of the Keap1-Nrf2 cytoprotective pathway involved in defense against oxidative stress. Pathophysiological roles of DPP III have not been elucidated yet, partly due to the lack of specific inhibitors. We showed that substrate analog H-Tyr-Phe-NHOH is a strong competitive inhibitor of hDPP III, while H-Tyr-Gly-NHOH expresses much weaker inhibition. To investigate the effects of amino acid substitutions in inhibitor P1 position, we synthesized three new dipeptidyl hydroxamates and examined their influence on the activity of hDPP III and DPP III from the human gut symbiont Bacteroides thetaiotaomicron. The extent of inhibition of hDPP III, but not of bacterial enzyme, was dependent on the amino acid in P1. H-Phe-Phe-NHOH is recognized as one of the strongest inhibitors of hDPP III (K i ¼ 0.028 mM), and H-Phe-Leu-NHOH discriminated between human and bacterial ortholog of the M49 family.

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“…The vast complexity of the human colon microbiota, the key element of the large-intestinal ecosystem, has inspired researchers to describe it as a postnatally acquired microbial organ located inside a host organ (1,46). The microbial colon community is estimated to be composed of up to 100 trillion microorganisms, a number exceeding 10 times the total number of somatic and germ cells of a human adult (18,38).…”

mentioning

confidence: 99%

Coculture Fermentations ofBifidobacteriumSpecies andBacteroides thetaiotaomicronReveal a Mechanistic Insight into the Prebiotic Effect of Inulin-Type Fructans

Falony

Calmeyn

Leroy

et al. 2009

Appl Environ Microbiol

107

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Four bifidobacteria, each representing a cluster of strains with specific inulin-type-fructan degradation capacities, were grown in coculture fermentations with Bacteroides thetaiotaomicron LMG 11262, a strain able to metabolize both oligofructose and inulin. In a medium for colon bacteria with inulin as the sole added energy source, the ability of the bifidobacteria to compete for this substrate reflected phenotypical variation. Bifidobacterium breve Yakult, a strain that was not able to degrade oligofructose or inulin, was outcompeted by B. thetaiotaomicron LMG 11262. Bifidobacterium adolescentis LMG 10734, a strain that could degrade oligofructose (displaying a preferential breakdown mechanism) but that did not grow on inulin, managed to become competitive when oligofructose and short fractions of inulin started to accumulate in the fermentation medium. Bifidobacterium angulatum LMG 11039T , a strain that was previously shown to degrade all oligofructose fractions simultaneously and to be able to partially break down inulin, was competitive from the beginning of the fermentation, consuming short fractions of inulin from the moment they appeared. Bifidobacterium longum LMG 11047, representing a cluster of bifidobacteria that shared both high fructose consumption and oligofructose degradation rates and were able to perform partial breakdown of inulin, was the dominating strain in a coculture with B. thetaiotaomicron LMG 11262. These observations indicate that distinct subgroups within the large-intestinal Bifidobacterium population will be stimulated by different groups of prebiotic inulin-type fructans, a variation that could be reflected in differences concerning their health-promoting effects.

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Bacteroides thetaiotaomicron in the gut: Molecular aspects of their interaction

Cited by 105 publications

References 46 publications

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

Novel dipeptidyl hydroxamic acids that inhibit human and bacterial dipeptidyl peptidase III

Coculture Fermentations ofBifidobacteriumSpecies andBacteroides thetaiotaomicronReveal a Mechanistic Insight into the Prebiotic Effect of Inulin-Type Fructans

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