An integrated strategy for functional analysis of microbial communities based on gene ontology and 16S rRNA gene

In order to analyse the similarity among microbial communities on functional state after assigning 16S rRNA sequences from all microbial communities to species. It's an important addition to the species-level relationship between two compared communities and can quantify their differences in function. We downloaded all functional annotation data of several microbiotas. It's developed to identify the functional distribution and the significantly enriched functional categories of microbial communities. We analysed the similarity between two microbial communities on functional state. In the experimental results, it shows that the semantic similarity can quantify the difference between two compared species on function level. It can analyse the function of microbial communities by gene ontology based on 16S rRNA gene. Exploration of the function relationship between two sets of species assemblages will be a key result of microbiome studies and may provide new insights into assembly of a wide range of ecosystems.

[1]  Hai Hu,et al.  Assessing semantic similarity measures for the characterization of human regulatory pathways , 2006, Bioinform..

[2]  Carole A. Goble,et al.  Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation , 2003, Bioinform..

[3]  F. Bäckhed,et al.  Obesity alters gut microbial ecology. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[4]  V. Mai,et al.  Colonic bacterial flora: changing understandings in the molecular age. , 2004, The Journal of nutrition.

[5]  Vipin Kumar,et al.  Incorporating functional inter-relationships into protein function prediction algorithms , 2009, BMC Bioinformatics.

[6]  Satoshi Koike,et al.  Molecular ecological analysis of the gastrointestinal microbiota: a review. , 2004, The Journal of nutrition.

[7]  Rolf Apweiler,et al.  CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins , 2001, Nucleic Acids Res..

[8]  Gregor Reid,et al.  Probiotics to prevent urinary tract infections: the rationale and evidence , 2006, World Journal of Urology.

[9]  Dekang Lin,et al.  An Information-Theoretic Definition of Similarity , 1998, ICML.

[10]  P. Hylemon,et al.  Diet, anaerobic bacterial metabolism, and colon cancer: a review of the literature. , 2005, Journal of clinical gastroenterology.

[11]  Thomas Lengauer,et al.  A new measure for functional similarity of gene products based on Gene Ontology , 2006, BMC Bioinformatics.

[12]  Pedro M. Coutinho,et al.  Implementation of a Functional Semantic Similarity Measure between Gene-Products , 2003 .

[13]  R. Ley,et al.  Ecological and Evolutionary Forces Shaping Microbial Diversity in the Human Intestine , 2006, Cell.

[14]  Thomas Lengauer,et al.  Improved scoring of functional groups from gene expression data by decorrelating GO graph structure , 2006, Bioinform..

[15]  Philip S. Yu,et al.  A new method to measure the semantic similarity of GO terms , 2007, Bioinform..

[16]  Philip Hugenholtz,et al.  A renaissance for the pioneering 16S rRNA gene. , 2008, Current opinion in microbiology.

[17]  Angel Rubio,et al.  Correlation between Gene Expression and GO Semantic Similarity , 2005, TCBB.

[18]  Philip Resnik,et al.  Semantic Similarity in a Taxonomy: An Information-Based Measure and its Application to Problems of Ambiguity in Natural Language , 1999, J. Artif. Intell. Res..

[19]  Ruslan Medzhitov,et al.  Recognition of Commensal Microflora by Toll-Like Receptors Is Required for Intestinal Homeostasis , 2004, Cell.

[20]  I. Wilson,et al.  Gut microorganisms, mammalian metabolism and personalized health care , 2005, Nature Reviews Microbiology.

[21]  Olivier Bodenreider,et al.  Gene expression correlation and gene ontology-based similarity: an assessment of quantitative relationships , 2004, 2004 Symposium on Computational Intelligence in Bioinformatics and Computational Biology.

[22]  Rick L. Stevens,et al.  Functional metagenomic profiling of nine biomes , 2008, Nature.

[23]  N. Pace.  A molecular view of microbial diversity and the biosphere. , 1997, Science.

[24]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[25]  A. Servin,et al.  Antagonistic activities of lactobacilli and bifidobacteria against microbial pathogens. , 2004, FEMS microbiology reviews.

[26]  Haifeng Lu,et al.  Symbiotic gut microbes modulate human metabolic phenotypes , 2008, Proceedings of the National Academy of Sciences.

[27]  L. Hooper,et al.  Bacterial contributions to mammalian gut development. , 2004, Trends in microbiology.

[28]  Olivier Bodenreider,et al.  An ontology-driven clustering method for supporting gene expression analysis , 2005, 18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05).

[29]  Itzhak Brook,et al.  The Role of Bacterial Interference in Otitis, Sinusitis and Tonsillitis , 2005, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[30]  Simon Kasif,et al.  Seeing the forest for the trees: using the Gene Ontology to restructure hierarchical clustering , 2009, Bioinform..

[31]  D. Relman,et al.  An ecological and evolutionary perspective on human–microbe mutualism and disease , 2007, Nature.

[32]  Francisco Guarner,et al.  Enteric Flora in Health and Disease , 2006, Digestion.

[33]  David W. Conrath,et al.  Semantic Similarity Based on Corpus Statistics and Lexical Taxonomy , 1997, ROCLING/IJCLCLP.

[34]  Junguk Hur,et al.  A graph-theoretic modeling on GO space for biological interpretation of gene clusters , 2004, Bioinform..

[35]  S. Duncan,et al.  Oxalobacter formigenes and its role in oxalate metabolism in the human gut. , 2004, FEMS microbiology letters.

[36]  S. Mazmanian,et al.  An Immunomodulatory Molecule of Symbiotic Bacteria Directs Maturation of the Host Immune System , 2005, Cell.

[37]  A. Sepulveda,et al.  Why do African Americans get more colon cancer than Native Africans? , 2007, The Journal of nutrition.

[38]  Ting Wang,et al.  The gut microbiota as an environmental factor that regulates fat storage. , 2004, Proceedings of the National Academy of Sciences of the United States of America.