Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults.
Mirjana Rajilić-Stojanović,Hans G.H.J. Heilig,Douwe Molenaar,Kajsa Kajander,Anu Surakka,Hauke Smidt,Willem M. de Vos,Willem M. de Vos +7 more
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TLDR
An in silico assessment of the diversity of variable regions of the small subunit ribosomal RNA (SSU rRNA) gene based on an ecosystem-specific curated database and a probe design procedure based on two hypervariable regions with minimal redundancy are presented.Abstract:
In this paper we present the in silico assessment of the diversity of variable regions of the small subunit ribosomal RNA (SSU rRNA) gene based on an ecosystem-specific curated database, describe a probe design procedure based on two hypervariable regions with minimal redundancy and test the potential of such probe design strategy for the design of a flexible microarray platform. This resulted in the development and application of a phylogenetic microarray for studying the human gastrointestinal microbiota--referred as the human intestinal tract chip (HITChip). Over 4800 dedicated tiling oligonucleotide probes were designed based on two hypervariable regions of the SSU rRNA gene of 1140 unique microbial phylotypes (< 98% identity) following analysis of over 16,000 human intestinal SSU rRNA sequences. These HITChip probes were hybridized to a diverse set of human intestinal samples and SSU rRNA clones to validate its fingerprinting and quantification potential. Excellent reproducibility (median Pearson's correlation of 0.99) was obtained following hybridization with T7 polymerase transcripts generated in vitro from SSU rRNA gene amplicons. A linear dose-response was observed with artificial mixtures of 40 different representative amplicons with relative abundances as low as 0.1% of total microbiota. Analysis of three consecutively collected faecal samples from ten individuals (five young and five elderly adults) revealed temporal dynamics and confirmed that the adult intestinal microbiota is an individual-specific and relatively stable ecosystem. Further analysis of the stable part allowed for the identification of a universal microbiota core at the approximate genus level (90% sequence similarity). This core consists of members of Actinobacteria, Bacteroidetes and Firmicutes. Used as a phylogenetic fingerprinting tool with the possibility for relative quantification, the HITChip has the potential to bridge the gaps in our knowledge in the quantitative and qualitative description of the human gastrointestinal microbiota composition.read more
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Enterotypes of the human gut microbiome
Manimozhiyan Arumugam,Jeroen Raes,Eric Pelletier,Denis Le Paslier,Takuji Yamada,Daniel R. Mende,Gabriel Fernandes,Julien Tap,Thomas Brüls,Jean-Michel Batto,Marcelo Bertalan,Natalia Borruel,Francesc Casellas,Leyden Fernández,Laurent Gautier,Torben Hansen,Masahira Hattori,Tetsuya Hayashi,Michiel Kleerebezem,Ken Kurokawa,Marion Leclerc,Florence Levenez,Chaysavanh Manichanh,H. Bjørn Nielsen,Trine Nielsen,Nicolas Pons,Julie Poulain,Junjie Qin,Thomas Sicheritz-Pontén,Sebastian Tims,David Torrents,Edgardo Ugarte,Erwin G. Zoetendal,Jun Wang,Francisco Guarner,Oluf Pedersen,Willem M. de Vos,Søren Brunak,Joël Doré,Jean Weissenbach,S. Dusko Ehrlich,Peer Bork +41 more
TL;DR: Three robust clusters (referred to as enterotypes hereafter) are identified that are not nation or continent specific and confirmed in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous.
Journal ArticleDOI
Richness of human gut microbiome correlates with metabolic markers
Trine Nielsen,Junjie Qin,Edi Prifti,Falk Hildebrand,Gwen Falony,Mathieu Almeida,Manimozhiyan Arumugam,Jean-Michel Batto,Sean Kennedy,Pierre Leonard,Junhua Li,Kristoffer Sølvsten Burgdorf,Niels Grarup,Torben Jørgensen,Torben Jørgensen,Torben Jørgensen,Ivan Brandslund,Henrik Nielsen,Agnieszka S. Juncker,Marcelo Bertalan,Florence Levenez,Nicolas Pons,Simon Rasmussen,Shinichi Sunagawa,Julien Tap,Sebastian Tims,Erwin G. Zoetendal,Søren Brunak,Karine Clément,Karine Clément,Joël Doré,Michiel Kleerebezem,Karsten Kristiansen,Pierre Renault,Thomas Sicheritz-Pontén,Willem M. de Vos,Willem M. de Vos,Jean-Daniel Zucker,Jean-Daniel Zucker,Jean-Daniel Zucker,Jeroen Raes,Torben Hansen,Torben Hansen,Peer Bork,Jun Wang,S. Dusko Ehrlich,Oluf Pedersen +46 more
TL;DR: The authors' classifications based on variation in the gut microbiome identify subsets of individuals in the general white adult population who may be at increased risk of progressing to adiposity-associated co-morbidities.
Journal ArticleDOI
Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile
Els van Nood,A. Vrieze,Max Nieuwdorp,Susana Fuentes,Erwin G. Zoetendal,Willem M. de Vos,Caroline E. Visser,Ed J. Kuijper,Peter Speelman,Josbert J. Keller +9 more
TL;DR: The infusion of donor feces was significantly more effective for the treatment of recurrent C. difficile infection than the use of vancomycin and patients showed increased fecal bacterial diversity, similar to that in healthy donors, with an increase in Bacteroidetes species and clostridium clusters IV and XIVa and a decrease in Proteobacteria species.
Journal ArticleDOI
Gut microbiota composition correlates with diet and health in the elderly
Marcus J. Claesson,Ian B. Jeffery,Susana Conde,Susan E. Power,Eibhlís M. O'Connor,Siobhán Cusack,Hugh M. B. Harris,M. Coakley,Bhuvaneswari Lakshminarayanan,Orla O'Sullivan,Gerald F. Fitzgerald,Jennifer Deane,Michael O'Connor,Norma Harnedy,Kieran O'Connor,Denis O'Mahony,Denis O'Mahony,Douwe van Sinderen,Martina Wallace,Lorraine Brennan,Catherine Stanton,Catherine Stanton,Julian R. Marchesi,Anthony P. Fitzgerald,Fergus Shanahan,Colin Hill,R. Paul Ross,R. Paul Ross,Paul W. O'Toole +28 more
TL;DR: The data support a relationship between diet, microbiota and health status, and indicate a role for diet-driven microbiota alterations in varying rates of health decline upon ageing.
Journal ArticleDOI
Transfer of Intestinal Microbiota From Lean Donors Increases Insulin Sensitivity in Individuals With Metabolic Syndrome
A. Vrieze,Els van Nood,Frits Holleman,Jarkko Salojärvi,Ruud S. Kootte,Joep F. Bartelsman,Geesje M. Dallinga-Thie,Mariëtte T. Ackermans,Mireille J. Serlie,Raish Oozeer,Muriel Derrien,Anne Druesne,Johan E. T. van Hylckama Vlieg,Vincent W. Bloks,Albert K. Groen,Hans G.H.J. Heilig,Erwin G. Zoetendal,Erik S.G. Stroes,Willem M. de Vos,Willem M. de Vos,Joost B. L. Hoekstra,Max Nieuwdorp +21 more
TL;DR: Six weeks after infusion of microbiota from lean donors, insulin sensitivity of recipients increased along with levels of butyrate-producing intestinal microbiota, and intestinal microbiota might be developed as therapeutic agents to increase insulin sensitivity in humans.
References
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TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
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