Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine.
Marcus J. Claesson,Orla O'Sullivan,Qiong Wang,Janne Nikkilä,Julian R. Marchesi,Hauke Smidt,Willem M. de Vos,Willem M. de Vos,R. Paul Ross,R. Paul Ross,Paul W. O'Toole +10 more
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TLDR
This is the deepest sequencing of single gastrointestinal samples reported to date, but microbial richness levels have still not leveled out, and correlations of sequence abundance and hybridization signal intensities were very high for lower-order ranks, but lower at family-level, which was probably due to ambiguous taxonomic groupings.Abstract:
Background: Variations in the composition of the human intestinal microbiota are linked to diverse health conditions. Highthroughput molecular technologies have recently elucidated microbial community structure at much higher resolution than was previously possible. Here we compare two such methods, pyrosequencing and a phylogenetic array, and evaluate classifications based on two variable 16S rRNA gene regions. Methods and Findings: Over 1.75 million amplicon sequences were generated from the V4 and V6 regions of 16S rRNA genes in bacterial DNA extracted from four fecal samples of elderly individuals. The phylotype richness, for individual samples, was 1,400–1,800 for V4 reads and 12,500 for V6 reads, and 5,200 unique phylotypes when combining V4 reads from all samples. The RDP-classifier was more efficient for the V4 than for the far less conserved and shorter V6 region, but differences in community structure also affected efficiency. Even when analyzing only 20% of the reads, the majority of the microbial diversity was captured in two samples tested. DNA from the four samples was hybridized against the Human Intestinal Tract (HIT) Chip, a phylogenetic microarray for community profiling. Comparison of clustering of genus counts from pyrosequencing and HITChip data revealed highly similar profiles. Furthermore, correlations of sequence abundance and hybridization signal intensities were very high for lower-order ranks, but lower at family-level, which was probably due to ambiguous taxonomic groupings. Conclusions: The RDP-classifier consistently assigned most V4 sequences from human intestinal samples down to genuslevel with good accuracy and speed. This is the deepest sequencing of single gastrointestinal samples reported to date, but microbial richness levels have still not leveled out. A majority of these diversities can also be captured with five times lower sampling-depth. HITChip hybridizations and resulting community profiles correlate well with pyrosequencing-based compositions, especially for lower-order ranks, indicating high robustness of both approaches. However, incompatible grouping schemes make exact comparison difficult.read more
Citations
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Journal ArticleDOI
Diversity, stability and resilience of the human gut microbiota
Catherine A. Lozupone,Jesse Stombaugh,Jeffrey I. Gordon,Janet K. Jansson,Rob Knight,Rob Knight +5 more
TL;DR: Viewing the microbiota from an ecological perspective could provide insight into how to promote health by targeting this microbial community in clinical treatments.
Journal ArticleDOI
Ribosomal Database Project: data and tools for high throughput rRNA analysis
James R. Cole,Qiong Wang,Jordan A. Fish,Benli Chai,Donna M. McGarrell,Yanni Sun,C. Titus Brown,Andrea Porras-Alfaro,Cheryl R. Kuske,James M. Tiedje +9 more
TL;DR: RDP now includes a collection of fungal large subunit rRNA genes, and most tools are now available as open source packages for download and local use by researchers with high-volume needs or who would like to develop custom analysis pipelines.
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
Composition, variability, and temporal stability of the intestinal microbiota of the elderly
Marcus J. Claesson,Siobhán Cusack,Orla O'Sullivan,Rachel Greene-Diniz,Heleen de Weerd,E. Flannery,Julian R. Marchesi,Julian R. Marchesi,Daniel Falush,Timothy G. Dinan,Gerald F. Fitzgerald,Catherine Stanton,Catherine Stanton,Douwe van Sinderen,Michael O'Connor,Norma Harnedy,Kieran O'Connor,Colm Henry,Denis O'Mahony,Denis O'Mahony,Anthony P. Fitzgerald,Fergus Shanahan,C. Twomey,C. Twomey,Colin Hill,R. Paul Ross,R. Paul Ross,Paul W. O'Toole +27 more
TL;DR: It is concluded that the fecal microbiota of the elderly shows temporal stability over limited time in the majority of subjects but is characterized by unusual phylum proportions and extreme variability.
Journal ArticleDOI
Through Ageing, and Beyond: Gut Microbiota and Inflammatory Status in Seniors and Centenarians
Elena Biagi,Lotta Nylund,Lotta Nylund,Marco Candela,Rita Ostan,Laura Bucci,Elisa Pini,Janne Nikkilä,Daniela Monti,Reetta Satokari,Claudio Franceschi,Patrizia Brigidi,Willem M. de Vos,Willem M. de Vos +13 more
TL;DR: Evidence is provided for the fact that the ageing process deeply affects the structure of the human gut microbiota, as well as its homeostasis with the host's immune system, because of its crucial role in the host physiology and health status.
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