Microbiomic analysis of the bifidobacterial population in the human distal gut

Turroni, Francesca; Marchesi, Julian R.; Foroni, Elena; Gueimonde, Miguel; Shanahan, Fergus; Margollés, Abelardo; Sinderen, Douwe van; Ventura, Marco

doi:10.1038/ismej.2009.19

Cited by 125 publications

(89 citation statements)

References 35 publications

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“…The role of bifidobacteria in gut ecology illustrates the importance of Actinomyces and other Actinobacteria (491). The phyla Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria constitute more than 99% of all gut microbiota in dogs and cats.…”

Section: Interactions Between Actinobacteria and Vertebratesmentioning

confidence: 99%

Taxonomy, Physiology, and Natural Products of Actinobacteria

Barka

Vatsa

Sanchez

et al. 2016

Microbiol Mol Biol Rev

1,442

1,006

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SUMMARYActinobacteriaare Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. ManyActinobacteriahave a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture.Actinobacteriaplay diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species ofCorynebacterium,Mycobacterium,Nocardia,Propionibacterium, andTropheryma), soil inhabitants (e.g.,MicromonosporaandStreptomycesspecies), plant commensals (e.g.,Frankiaspp.), and gastrointestinal commensals (Bifidobacteriumspp.).Actinobacteriaalso play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum.

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Section: Interactions Between Actinobacteria and Vertebratesmentioning

confidence: 99%

Taxonomy, Physiology, and Natural Products of Actinobacteria

Barka

Vatsa

Sanchez

et al. 2016

Microbiol Mol Biol Rev

1,442

1,006

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show abstract

“…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

231

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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“…Several ecological studies have shown that bifidobacteria are a dominant bacterial group of the infant microbiota as well as a key component of the adult-type intestinal microbiota (8,43). It is believed that bifidobacteria are well adapted to maximize metabolic access to a wide variety of diet-derived and/or hostderived sugars (15)(16)(17).…”

Section: Discussionmentioning

confidence: 99%

Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging

Turroni

Bottacini²,

Foroni³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

323

378

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The human intestine is densely populated by a microbial consortium whose metabolic activities are influenced by, among others, bifidobacteria. However, the genetic basis of adaptation of bifidobacteria to the human gut is poorly understood. Analysis of the 2,214,650-bp genome of Bifidobacterium bifidum PRL2010, a strain isolated from infant stool, revealed a nutrient-acquisition strategy that targets host-derived glycans, such as those present in mucin. Proteome and transcriptome profiling revealed a set of chromosomal loci responsible for mucin metabolism that appear to be under common transcriptional control and with predicted functions that allow degradation of various O-linked glycans in mucin. Conservation of the latter gene clusters in various B. bifidum strains supports the notion that host-derived glycan catabolism is an important colonization factor for B. bifidum with concomitant impact on intestinal microbiota ecology.coevolution | genomics | host-glycans metabolism | human gut intestinal bacteria | mucin

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Microbiomic analysis of the bifidobacterial population in the human distal gut

Cited by 125 publications

References 35 publications

Taxonomy, Physiology, and Natural Products of Actinobacteria

Taxonomy, Physiology, and Natural Products of Actinobacteria

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging

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