Microbial Communities in the Human Small Intestine: Coupling Diversity to Metagenomics

Booijink, Carien C G M; Zoetendal, Erwin G.; Kleerebezem, Michiel; Vos, Willem M. de

doi:10.2217/17460913.2.3.285

Cited by 138 publications

(110 citation statements)

References 83 publications

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“…Consequently, lactobacilli gained a reputation as numerically dominant intestinal inhabitants, and even the advent of anaerobic culture techniques did little to correct this situation. Lactobacilli are still listed as numerically dominant organisms of the human gut in current microbiology text books (52,70,76), and even researchers working on functional and applied aspects of intestinal lactobacilli have continued to adhere to this dogma (11,42,57,69,71,97).…”

Section: The Good the Bad And The Uglymentioning

confidence: 99%

Ecological Role of Lactobacilli in the Gastrointestinal Tract: Implications for Fundamental and Biomedical Research

Walter

2008

Appl Environ Microbiol

631

460

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Section: The Good the Bad And The Uglymentioning

confidence: 99%

Ecological Role of Lactobacilli in the Gastrointestinal Tract: Implications for Fundamental and Biomedical Research

Walter

2008

Appl Environ Microbiol

631

460

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“…Fecal microbial diversity and composition was studied in detail using the Human Intestinal Tract chip (HITChip) as described previously (Rajilic-Stojanovic et al, 2009) (for further details see SI Materials and methods). This phylogenetic microarray has been shown to be a powerful tool for deep GI tract microbiota composition analysis and has been benchmarked against several classical 16S rRNA gene-based methodologies, such as qPCR, fluorescence in situ hybridization and 454 pyrosequencing (Booijink et al, 2007;Claesson et al, 2009;Rajilic-Stojanovic et al, 2009;van den Bogert et al, 2011) as well as metagenomics (Arumugam et al, 2011). HITChip probes are assigned to three phylogenetic levels: level 1, defined as order-like 16S rRNA gene sequence groups; level 2, defined as genus-like 16S rRNA gene sequence groups (sequence similarity 490%); and level 3, phylotype-like 16S rRNA gene sequence groups (sequence similarity 498%) (Rajilic-Stojanovic et al, 2009).…”

Section: Twin Pair Classification Into Bmi Phenotypesmentioning

confidence: 99%

Microbiota conservation and BMI signatures in adult monozygotic twins

et al. 2012

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The human gastrointestinal (GI) tract microbiota acts like a virtual organ and is suggested to be of great importance in human energy balance and weight control. This study included 40 monozygotic (MZ) twin pairs to investigate the influence of the human genotype on GI microbiota structure as well as microbial signatures for differences in body mass index (BMI). Phylogenetic microarraying based on 16S rRNA genes demonstrated that MZ twins have more similar microbiotas compared with unrelated subjects (Po0.001), which allowed the identification of 35 genus-like microbial groups that are more conserved between MZ twins. Half of the twin pairs were selected on discordance in terms of BMI, which revealed an inverse correlation between Clostridium cluster IV diversity and BMI. Furthermore, relatives of Eubacterium ventriosum and Roseburia intestinalis were positively correlated to BMI differences, and relatives of Oscillospira guillermondii were negatively correlated to BMI differences. Lower BMI was associated with a more abundant network of primary fiber degraders, while a network of butyrate producers was more prominent in subjects with higher BMI. Combined with higher butyrate and valerate contents in the fecal matter of higher BMI subjects, the difference in microbial networks suggests a shift in fermentation patterns at the end of the colon, which could affect human energy homeostasis.

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“…However, in contrast to other ecological niches, the biodiversity found in the human gut microbiota is relatively low (46). In fact, this ecosystem appears to be dominated by a relatively small number of bacterial taxa, in particular by representatives of Bacteroidetes and Firmicutes (4,6,8,37,60). The structure and composition of the human GIT microbiota reflect natural selection at both the microbial and host levels through complex competitive and symbiotic interactions.…”

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confidence: 99%

Exploring the Diversity of the Bifidobacterial Population in the Human Intestinal Tract

Turroni

Foroni

Pizzetti

et al. 2009

Appl Environ Microbiol

284

215

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Although the health-promoting roles of bifidobacteria are widely accepted, the diversity of bifidobacteria among the human intestinal microbiota is still poorly understood. We performed a census of bifidobacterial populations from human intestinal mucosal and fecal samples by plating them on selective medium, coupled with molecular analysis of selected rRNA gene sequences (16S rRNA gene and internally transcribed spacer [ITS] 16S-23S spacer sequences) of isolated colonies. A total of 900 isolates were collected, of which 704 were shown to belong to bifidobacteria. Analyses showed that the culturable bifidobacterial population from intestinal and fecal samples include six main phylogenetic taxa, i.e., Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bifidobacterium adolescentis, Bifidobacterium pseudolongum, Bifidobacterium breve, and Bifidobacterium bifidum, and two species mostly detected in fecal samples, i.e., Bifidobacterium dentium and Bifidobacterium animalis subp. lactis. Analysis of bifidobacterial distribution based on age of the subject revealed that certain identified bifidobacterial species were exclusively present in the adult human gut microbiota whereas others were found to be widely distributed. We encountered significant intersubject variability and composition differences between fecal and mucosa-adherent bifidobacterial communities. In contrast, a modest diversification of bifidobacterial populations was noticed between different intestinal regions within the same individual (intrasubject variability). Notably, a small number of bifidobacterial isolates were shown to display a wide ecological distribution, thus suggesting that they possess a broad colonization capacity.

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Microbial Communities in the Human Small Intestine: Coupling Diversity to Metagenomics

Cited by 138 publications

References 83 publications

Ecological Role of Lactobacilli in the Gastrointestinal Tract: Implications for Fundamental and Biomedical Research

Ecological Role of Lactobacilli in the Gastrointestinal Tract: Implications for Fundamental and Biomedical Research

Microbiota conservation and BMI signatures in adult monozygotic twins

Exploring the Diversity of the Bifidobacterial Population in the Human Intestinal Tract

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