Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale

Rustam Aminov; Alan W. Walker; Sylvia H. Duncan; Hermie J. M. Harmsen; Gjalt W. Welling; Harry J. Flint

doi:10.1128/AEM.00701-06

Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale

Rustam Aminov, Alan W. Walker, Sylvia H. Duncan, Hermie J. M. Harmsen, Gjalt W. Welling, Harry J. Flint

Research output: Contribution to journal › Journal article › Research › peer-review

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Abstract

Phylogenetic analysis was used to compare 16S rRNA sequences from 19 cultured human gut strains of Roseburia and Eabacterium rectale with 356 related sequences derived from clone libraries. The cultured strains were found to represent five of the six phylotypes identified. A new oligonucleotide probe, Rrec584, and the previous group probe Rint623, when used in conjunction with a new helper oligonucleotide, each recognized an average of 7% of bacteria detected by the eubacterial probe Eub338 in feces from 10 healthy volunteers. Most of the diversity within this important group of butyrate-producing gut bacteria can apparently be retrieved through cultivation.

Original language	English
Journal	Applied and Environmental Microbiology
Volume	72
Issue number	9
Pages (from-to)	6371-6376
Number of pages	6
ISSN	0099-2240
DOIs	https://doi.org/10.1128/AEM.00701-06
Publication status	Published - 2006
Externally published	Yes

Keywords

Bacteria, Anaerobic
Base Sequence
Colony Count, Microbial
Digestive System
Eubacterium
Feces
Genes, Bacterial
Genetic Variation
Humans
In Situ Hybridization, Fluorescence
Molecular Sequence Data
Oligonucleotide Probes
Phylogeny
RNA, Bacterial
RNA, Ribosomal, 16S
Fluorescence
Genetic engineering
Molecular structure
Probes
Bacteria
oligonucleotide
bacterium
hybridization
in situ test
molecular analysis
phylogenetics
probe
RNA
species diversity
article
bacterial strain
bacterium culture
bacterium detection
eubacterium rectale
fluorescence in situ hybridization
genetic variability
intestine flora
molecular recognition
nonhuman
nucleotide sequence
oligonucleotide probe
phylogeny
RNA sequence
Roseburia
Variation (Genetics)
Bacteria (microorganisms)
Eubacterium rectale
Clone libraries
Molecular diversity
Oligonucleotide probe
Phylogenetic analysis
X
BIOTECHNOLOGY
MICROBIOLOGY
16S RIBOSOMAL-RNA
BUTYRATE-PRODUCING BACTERIA
HUMAN FECAL SAMPLES
HUMAN FECES
OLIGONUCLEOTIDE PROBES
HUMAN COLON
PHYLOGENETIC-RELATIONSHIPS
GEN-NOV
COMMUNITIES
ACCESSIBILITY
amino acid sequence
molecular diversity
phylotype
sequence numbers
Actinomycetes and Related Organisms Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Irregular Nonsporing Gram-Positive Rods [08890] Eubacterium ramulus species Eubacterium rectale species strain-A1-86, strain-ATCC 33656, strain-L2-21, strain-M104/1, strain-S2As2/7, strain-S2Ss2/2, strain-T1-815 Butyrivibrio fibrisolvens species strain-AR27 Bifidobacterium adolescentis species strain-L2-32 Bifidobacterium longum species strain-NCIMB 8809 Bifidobacterium infantis species strain-DSM 20088 Bifidobacterium breve species strain-MMB 3035
Anaerobic Gram-Negative Rods Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Bacteroidaceae [06901] Roseburia intestinalis species strain-L1-81, strain-L1-8151, strain-L1-82, strain-L1-93, strain-L1-952, strain-M50/1 Roseburia hominis species strain-A2-183, strain-A2-181 Roseburia faecis species strain-M6/1, strain-M72/1, strain-M88/1 Roseburia inulinivorans species strain-A2-194, strain-L1-83
Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Gram-Positive Cocci [07700] Enterococcus faecium species strain-DSM 20477 Enterococcus faecalis species strain-JH2-2 Streptococcus gordonii species strain-DL-1 Streptococcus bovis species strain-26-R Streptococcus mutans species strain-DSM 20523 Ruminococcus albus species strain-SY3-R Ruminococcus bromii species strain-L2-63
Facultatively Anaerobic Gram-Negative Rods Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Enterobacteriaceae [06702] Escherichia coli species strain-JM109, strain-L01859, strain-ATCC 25922
Primates Mammalia Vertebrata Chordata Animalia (Animals, Chordates, Humans, Mammals, Primates, Vertebrates) - Hominidae [86215] human common adult, middle age female, male
Eub338
gene expression
ribosomal RNA rRNA expression
Rint623
Rrec584
03502, Genetics - General
03508, Genetics - Human
10062, Biochemistry studies - Nucleic acids, purines and pyrimidines
14004, Digestive system - Physiology and biochemistry
31000, Physiology and biochemistry of bacteria
31500, Genetics of bacteria and viruses
Biochemistry and Molecular Biophysics
Ingestion and Assimilation
feces digestive system
gut digestive system
fluorescence in-situ hybridization FISH laboratory techniques, genetic techniques
Methods and Techniques
Molecular Genetics
FLUORESCENCE in situ hybridization

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1128/AEM.00701-06

Roseburia diversityFinal published version, 194 KB

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Cite this

Aminov, R., Walker, A. W., Duncan, S. H., Harmsen, H. J. M., Welling, G. W., & Flint, H. J. (2006). Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale. Applied and Environmental Microbiology, 72(9), 6371-6376. https://doi.org/10.1128/AEM.00701-06

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author = "Rustam Aminov and Walker, {Alan W.} and Duncan, {Sylvia H.} and Harmsen, {Hermie J. M.} and Welling, {Gjalt W.} and Flint, {Harry J.}",

year = "2006",

doi = "10.1128/AEM.00701-06",

language = "English",

volume = "72",

pages = "6371--6376",

journal = "Applied and Environmental Microbiology",

issn = "0099-2240",

publisher = "American Society for Microbiology",

number = "9",

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Aminov, R, Walker, AW, Duncan, SH, Harmsen, HJM, Welling, GW & Flint, HJ 2006, 'Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale', Applied and Environmental Microbiology, vol. 72, no. 9, pp. 6371-6376. https://doi.org/10.1128/AEM.00701-06

Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale. / Aminov, Rustam; Walker, Alan W.; Duncan, Sylvia H. et al.
In: Applied and Environmental Microbiology, Vol. 72, No. 9, 2006, p. 6371-6376.

Research output: Contribution to journal › Journal article › Research › peer-review

TY - JOUR

T1 - Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale

AU - Aminov, Rustam

AU - Walker, Alan W.

AU - Duncan, Sylvia H.

AU - Harmsen, Hermie J. M.

AU - Welling, Gjalt W.

AU - Flint, Harry J.

PY - 2006

Y1 - 2006

N2 - Phylogenetic analysis was used to compare 16S rRNA sequences from 19 cultured human gut strains of Roseburia and Eabacterium rectale with 356 related sequences derived from clone libraries. The cultured strains were found to represent five of the six phylotypes identified. A new oligonucleotide probe, Rrec584, and the previous group probe Rint623, when used in conjunction with a new helper oligonucleotide, each recognized an average of 7% of bacteria detected by the eubacterial probe Eub338 in feces from 10 healthy volunteers. Most of the diversity within this important group of butyrate-producing gut bacteria can apparently be retrieved through cultivation.

AB - Phylogenetic analysis was used to compare 16S rRNA sequences from 19 cultured human gut strains of Roseburia and Eabacterium rectale with 356 related sequences derived from clone libraries. The cultured strains were found to represent five of the six phylotypes identified. A new oligonucleotide probe, Rrec584, and the previous group probe Rint623, when used in conjunction with a new helper oligonucleotide, each recognized an average of 7% of bacteria detected by the eubacterial probe Eub338 in feces from 10 healthy volunteers. Most of the diversity within this important group of butyrate-producing gut bacteria can apparently be retrieved through cultivation.

KW - Bacteria, Anaerobic

KW - Base Sequence

KW - Colony Count, Microbial

KW - Digestive System

KW - Eubacterium

KW - Feces

KW - Genes, Bacterial

KW - Genetic Variation

KW - Humans

KW - In Situ Hybridization, Fluorescence

KW - Molecular Sequence Data

KW - Oligonucleotide Probes

KW - Phylogeny

KW - RNA, Bacterial

KW - RNA, Ribosomal, 16S

KW - Fluorescence

KW - Genetic engineering

KW - Molecular structure

KW - Probes

KW - Bacteria

KW - oligonucleotide

KW - bacterium

KW - hybridization

KW - in situ test

KW - molecular analysis

KW - phylogenetics

KW - probe

KW - RNA

KW - species diversity

KW - article

KW - bacterial strain

KW - bacterium culture

KW - bacterium detection

KW - eubacterium rectale

KW - fluorescence in situ hybridization

KW - genetic variability

KW - intestine flora

KW - molecular recognition

KW - nonhuman

KW - nucleotide sequence

KW - oligonucleotide probe

KW - phylogeny

KW - RNA sequence

KW - Roseburia

KW - Variation (Genetics)

KW - Bacteria (microorganisms)

KW - Eubacterium rectale

KW - Clone libraries

KW - Molecular diversity

KW - Oligonucleotide probe

KW - Phylogenetic analysis

KW - X

KW - BIOTECHNOLOGY

KW - MICROBIOLOGY

KW - 16S RIBOSOMAL-RNA

KW - BUTYRATE-PRODUCING BACTERIA

KW - HUMAN FECAL SAMPLES

KW - HUMAN FECES

KW - OLIGONUCLEOTIDE PROBES

KW - HUMAN COLON

KW - PHYLOGENETIC-RELATIONSHIPS

KW - GEN-NOV

KW - COMMUNITIES

KW - ACCESSIBILITY

KW - amino acid sequence

KW - molecular diversity

KW - phylotype

KW - sequence numbers

KW - Actinomycetes and Related Organisms Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Irregular Nonsporing Gram-Positive Rods [08890] Eubacterium ramulus species Eubacterium rectale species strain-A1-86, strain-ATCC 33656, strain

KW - Anaerobic Gram-Negative Rods Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Bacteroidaceae [06901] Roseburia intestinalis species strain-L1-81, strain-L1-8151, strain-L1-82, strain-L1-93, strain-L1-952, strain-M50/1 Roseburia

KW - Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Gram-Positive Cocci [07700] Enterococcus faecium species strain-DSM 20477 Enterococcus faecalis species strain-JH2-2 Streptococcus gordonii species strain-DL-1 Streptococcus bovis

KW - Facultatively Anaerobic Gram-Negative Rods Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Enterobacteriaceae [06702] Escherichia coli species strain-JM109, strain-L01859, strain-ATCC 25922

KW - Primates Mammalia Vertebrata Chordata Animalia (Animals, Chordates, Humans, Mammals, Primates, Vertebrates) - Hominidae [86215] human common adult, middle age female, male

KW - Eub338

KW - gene expression

KW - ribosomal RNA rRNA expression

KW - Rint623

KW - Rrec584

KW - 03502, Genetics - General

KW - 03508, Genetics - Human

KW - 10062, Biochemistry studies - Nucleic acids, purines and pyrimidines

KW - 14004, Digestive system - Physiology and biochemistry

KW - 31000, Physiology and biochemistry of bacteria

KW - 31500, Genetics of bacteria and viruses

KW - Biochemistry and Molecular Biophysics

KW - Ingestion and Assimilation

KW - feces digestive system

KW - gut digestive system

KW - fluorescence in-situ hybridization FISH laboratory techniques, genetic techniques

KW - Methods and Techniques

KW - Molecular Genetics

KW - FLUORESCENCE in situ hybridization

U2 - 10.1128/AEM.00701-06

DO - 10.1128/AEM.00701-06

M3 - Journal article

C2 - 16957265

SN - 0099-2240

VL - 72

SP - 6371

EP - 6376

JO - Applied and Environmental Microbiology

JF - Applied and Environmental Microbiology

IS - 9

ER -

Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale

Abstract

Keywords

UN SDGs

Access to Document

OpenUrl availability

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Cite this