Metatranscriptome Analysis of the Human Fecal Microbiota Reveals Subject-Specific Expression Profiles, with Genes Encoding Proteins Involved in Carbohydrate Metabolism Being Dominantly Expressed

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Published inApplied and Environmental Microbiology Vol. 76; no. 16; pp. 5533 - 5540
Main Authors Booijink, Carien C. G. M., Boekhorst, Jos, Zoetendal, Erwin G., Smidt, Hauke, Kleerebezem, Michiel, de Vos, Willem M.
Format Journal Article
LanguageEnglish
Published Washington, DC American Society for Microbiology 01.08.2010
American Society for Microbiology (ASM)
Subjects
16s ribosomal-rna
Amplified fragment length polymorphism
bacteria
Biological and medical sciences
carbohydrate metabolism
Carbohydrate Metabolism - genetics
Carbohydrates
cdna-aflp
Cluster Analysis
communities
complementary DNA
distal gut microbiome
diversity
DNA Fingerprinting - methods
dna-microarrays
Feces
Feces - microbiology
Fundamental and applied biological sciences. Psychology
gastrointestinal-tract
Gene expression
Gene Expression Profiling - methods
Human Experimentation
Humans
messenger RNA
Metabolism
Metagenome - genetics
microarray analysis
Microbial activity
microbial communities
Microbial Ecology
Microbiology
Molecular Sequence Data
multigene family
Proteins
Ribonucleic acid
ribosomal RNA
RNA
samples
sequence analysis
Sequence Analysis, DNA
Time Factors
Human
Gene
Microflora
Carbohydrate
Feces
Metabolism
Protein
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Abstract Classifications Services AEM Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit StumbleUpon Twitter current issue Spotlights in the Current Issue AEM About AEM Subscribers Authors Reviewers Advertisers Inquiries from the Press Permissions & Commercial Reprints ASM Journals Public Access Policy AEM RSS Feeds 1752 N Street N.W. • Washington DC 20036 202.737.3600 • 202.942.9355 fax • journals@asmusa.org Print ISSN: 0099-2240 Online ISSN: 1098-5336 Copyright © 2014 by the American Society for Microbiology.   For an alternate route to AEM .asm.org, visit: AEM       
AbstractList The human gastrointestinal (GI) tract provides home to a complex microbial community, collectively termed microbiota. Although major efforts have been made to describe the diversity and stability of the microbiota, functional studies have been largely restricted to intestinal isolates and include few community studies. The aim of this study was to explore the in situ gene expression of the fecal microbiota and to evaluate the RNA fingerprinting method cDNA-AFLP (cDNA amplified fragment length polymorphism) for this purpose. To this end, cDNA-AFLP analysis of enriched mRNA revealed that two healthy subjects showed highly divergent expression profiles with considerable fluctuations in time. Subsequent excision and sequence determination of bands from the mRNA-enriched profiles resulted in 122 identifiable sequences (transcripts and rRNAs). The classification of retrieved transcripts into functional clusters based on COG (cluster of orthologous genes) annotation showed that most assigned transcripts belonged to the metabolism cluster (26% of all sequences), underlining that even at the very end of the intestinal tract the microbiota is still very active. This study furthermore revealed that cDNA-AFLP is a useful tool to compare gene expression profiles in time in complex microbial communities
The human gastrointestinal (GI) tract provides home to a complex microbial community, collectively termed microbiota. Although major efforts have been made to describe the diversity and stability of the microbiota, functional studies have been largely restricted to intestinal isolates and include few community studies. The aim of this study was to explore the in situ gene expression of the fecal microbiota and to evaluate the RNA fingerprinting method cDNA-AFLP (cDNA amplified fragment length polymorphism) for this purpose. To this end, cDNA-AFLP analysis of enriched mRNA revealed that two healthy subjects showed highly divergent expression profiles with considerable fluctuations in time. Subsequent excision and sequence determination of bands from the mRNA-enriched profiles resulted in 122 identifiable sequences (transcripts and rRNAs). The classification of retrieved transcripts into functional clusters based on COG (cluster of orthologous genes) annotation showed that most assigned transcripts belonged to the metabolism cluster (26% of all sequences), underlining that even at the very end of the intestinal tract the microbiota is still very active. This study furthermore revealed that cDNA-AFLP is a useful tool to compare gene expression profiles in time in complex microbial communities.
The human gastrointestinal (GI) tract provides home to a complex microbial community, collectively termed microbiota. Although major efforts have been made to describe the diversity and stability of the microbiota, functional studies have been largely restricted to intestinal isolates and include few community studies. The aim of this study was to explore the in situ gene expression of the fecal microbiota and to evaluate the RNA fingerprinting method cDNA-AFLP (cDNA amplified fragment length polymorphism) for this purpose. To this end, cDNA-AFLP analysis of enriched mRNA revealed that two healthy subjects showed highly divergent expression profiles with considerable fluctuations in time. Subsequent excision and sequence determination of bands from the mRNA-enriched profiles resulted in 122 identifiable sequences (transcripts and rRNAs). The classification of retrieved transcripts into functional clusters based on COG (cluster of orthologous genes) annotation showed that most assigned transcripts belonged to the metabolism cluster (26% of all sequences), underlining that even at the very end of the intestinal tract the microbiota is still very active. This study furthermore revealed that cDNA-AFLP is a useful tool to compare gene expression profiles in time in complex microbial communities. [PUBLICATION ABSTRACT]
The human gastrointestinal (GI) tract provides home to a complex microbial community, collectively termed microbiota. Although major efforts have been made to describe the diversity and stability of the microbiota, functional studies have been largely restricted to intestinal isolates and include few community studies. The aim of this study was to explore the in situ gene expression of the fecal microbiota and to evaluate the RNA fingerprinting method cDNA-AFLP (cDNA amplified fragment length polymorphism) for this purpose. To this end, cDNA-AFLP analysis of enriched mRNA revealed that two healthy subjects showed highly divergent expression profiles with considerable fluctuations in time. Subsequent excision and sequence determination of bands from the mRNA-enriched profiles resulted in 122 identifiable sequences (transcripts and rRNAs). The classification of retrieved transcripts into functional clusters based on COG (cluster of orthologous genes) annotation showed that most assigned transcripts belonged to the metabolism cluster (26% of all sequences), underlining that even at the very end of the intestinal tract the microbiota is still very active. This study furthermore revealed that cDNA-AFLP is a useful tool to compare gene expression profiles in time in complex microbial communities.
The human gastrointestinal (GI) tract provides home to a complex microbial community, collectively termed microbiota. Although major efforts have been made to describe the diversity and stability of the microbiota, functional studies have been largely restricted to intestinal isolates and include few community studies. The aim of this study was to explore the in situ gene expression of the fecal microbiota and to evaluate the RNA fingerprinting method cDNA-AFLP (cDNA amplified fragment length polymorphism) for this purpose. To this end, cDNA-AFLP analysis of enriched mRNA revealed that two healthy subjects showed highly divergent expression profiles with considerable fluctuations in time. Subsequent excision and sequence determination of bands from the mRNA-enriched profiles resulted in 122 identifiable sequences (transcripts and rRNAs). The classification of retrieved transcripts into functional clusters based on COG (cluster of orthologous genes) annotation showed that most assigned transcripts belonged to the metabolism cluster (26% of all sequences), underlining that even at the very end of the intestinal tract the microbiota is still very active. This study furthermore revealed that cDNA-AFLP is a useful tool to compare gene expression profiles in time in complex microbial communities.The human gastrointestinal (GI) tract provides home to a complex microbial community, collectively termed microbiota. Although major efforts have been made to describe the diversity and stability of the microbiota, functional studies have been largely restricted to intestinal isolates and include few community studies. The aim of this study was to explore the in situ gene expression of the fecal microbiota and to evaluate the RNA fingerprinting method cDNA-AFLP (cDNA amplified fragment length polymorphism) for this purpose. To this end, cDNA-AFLP analysis of enriched mRNA revealed that two healthy subjects showed highly divergent expression profiles with considerable fluctuations in time. Subsequent excision and sequence determination of bands from the mRNA-enriched profiles resulted in 122 identifiable sequences (transcripts and rRNAs). The classification of retrieved transcripts into functional clusters based on COG (cluster of orthologous genes) annotation showed that most assigned transcripts belonged to the metabolism cluster (26% of all sequences), underlining that even at the very end of the intestinal tract the microbiota is still very active. This study furthermore revealed that cDNA-AFLP is a useful tool to compare gene expression profiles in time in complex microbial communities.
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Author Hauke Smidt
Michiel Kleerebezem
Erwin G. Zoetendal
Jos Boekhorst
Carien C. G. M. Booijink
Willem M. de Vos
AuthorAffiliation TI Food and Nutrition, and Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, Netherlands, 1 CMBI 260, NCMLS, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, Netherlands, 2 NIZO Food Research, Health and Safety Department, P.O. Box 20, 6710 BA Ede, Netherlands 3
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  surname: Boekhorst
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  organization: CMBI 260, NCMLS, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
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  givenname: Erwin G.
  surname: Zoetendal
  fullname: Zoetendal, Erwin G.
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  organization: TI Food and Nutrition, and Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, Netherlands
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  givenname: Michiel
  surname: Kleerebezem
  fullname: Kleerebezem, Michiel
  organization: TI Food and Nutrition, and Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, Netherlands, NIZO Food Research, Health and Safety Department, P.O. Box 20, 6710 BA Ede, Netherlands
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  surname: de Vos
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  organization: TI Food and Nutrition, and Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, Netherlands
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Issue 16
Keywords Human
Gene
Microflora
Carbohydrate
Feces
Metabolism
Protein
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Present address: Bioinformatics, Department of Biology, Utrecht University, P.O. Box 80.056, 3508 TB Utrecht, Netherlands.
Present address: University of Applied Sciences, Institute for Life Sciences and Chemistry, F.C. Dondersstraat 65, 3572 JE Utrecht, Netherlands.
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Snippet Classifications Services AEM Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit...
The human gastrointestinal (GI) tract provides home to a complex microbial community, collectively termed microbiota. Although major efforts have been made to...
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SubjectTerms 16s ribosomal-rna
Amplified fragment length polymorphism
bacteria
Biological and medical sciences
carbohydrate metabolism
Carbohydrate Metabolism - genetics
Carbohydrates
cdna-aflp
Cluster Analysis
communities
complementary DNA
distal gut microbiome
diversity
DNA Fingerprinting - methods
dna-microarrays
Feces
Feces - microbiology
Fundamental and applied biological sciences. Psychology
gastrointestinal-tract
Gene expression
Gene Expression Profiling - methods
Human Experimentation
Humans
messenger RNA
Metabolism
Metagenome - genetics
microarray analysis
Microbial activity
microbial communities
Microbial Ecology
Microbiology
Molecular Sequence Data
multigene family
Proteins
Ribonucleic acid
ribosomal RNA
RNA
samples
sequence analysis
Sequence Analysis, DNA
Time Factors
Title Metatranscriptome Analysis of the Human Fecal Microbiota Reveals Subject-Specific Expression Profiles, with Genes Encoding Proteins Involved in Carbohydrate Metabolism Being Dominantly Expressed
URI http://aem.asm.org/content/76/16/5533.abstract
https://www.ncbi.nlm.nih.gov/pubmed/20562280
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Volume 76
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