Dataset Information

Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing.

ABSTRACT:

Background

Most studies on the human microbiota have analyzed stool samples, although a large proportion of the absorption of nutrients takes place in upper gut tract. We collected samples from different locations along the entire gastrointestinal tract from six patients who had simultaneously undergone upper endoscopy and colonoscopy, to perform a comprehensive analysis using culturomics with matrix assisted laser desorption ionisation - time of flight (MALDI-TOF) identification and by metagenomics targeting the 16S ribosomal ribonucleic acid (rRNA) gene.

Results

Using culturomics, we isolated 368 different bacterial species, including 37 new species. Fewer species were isolated in the upper gut: 110 in the stomach and 106 in the duodenum, while 235 were isolated from the left colon (p?ConclusionSignificant modifications in bacterial composition and diversity exist throughout the gastrointestinal tract. We suggest that the upper gut may be key to understanding the relationship between the gut microbiota and health.

SUBMITTER: Mailhe M

PROVIDER: S-EPMC6201554 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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Publications

Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing.

Mailhe Morgane M Ricaboni Davide D Vitton Véronique V Gonzalez Jean-Michel JM Bachar Dipankar D Dubourg Grégory G Cadoret Frédéric F Robert Catherine C Delerce Jérémy J Levasseur Anthony A Fournier Pierre-Edouard PE Angelakis Emmanouil E Lagier Jean-Christophe JC Raoult Didier D

BMC microbiology 20181024 1

<h4>Background</h4>Most studies on the human microbiota have analyzed stool samples, although a large proportion of the absorption of nutrients takes place in upper gut tract. We collected samples from different locations along the entire gastrointestinal tract from six patients who had simultaneously undergone upper endoscopy and colonoscopy, to perform a comprehensive analysis using culturomics with matrix assisted laser desorption ionisation - time of flight (MALDI-TOF) identification and by ...[more]

PMID: 30355340

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Dataset Information

Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing.

Background

Results

Publications

Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing.

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