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What is the difference between species abundance and density?



Tips: "Density Abundance Species":
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Density abundance species discussion

Joel Dore: #UEGW2011 Dusko Ehrlich, France @ UEGW - Bacteria, friends or foes? their role in health and chronic diseases.
Comment: Quantitative metagenomics is completely novel tool to explore metagenome of human intestinal microbiota
high density short sequencing + mapping of short sequence on reference gene catalog allows to generate gene abundance profiles
first reference gene catalog published 2011 Qui et al Nature. 3.3 Million genes, 160 fold the human genome. covers 85% of abudant gut genes. 80-85% of USA and Japan metagenomic data
enterotypes : 3 different clusters of individuals appear in human cohorts, driven by specific netweorks of microbial populations. clustering seen with bacterial species are also seen when using functional genetic information
can we identify specific microbial populations in metagenome of obese patients? MetaHIT programme works on Inter99 DAnish cohort.
Quantitative metagenomics allows to present data as MetaHIT barcode, showing species associated with low gene count versus high gene count. example Metnobrevibacter smithii is associated with hi gene counts
=> massive changes in microbiota is associated with inflammation and insulin sensitivity ; see following session in A6/7 lecture hall at 11:00 by C Clément and O Pedrsen.
applying ROC curves, models with 6 species explain very well the patients versus healthy controls in test and validation cohorts. AUC is 0.89
Also possible to identify relapse rate associated species, most yet unknown. comparing rare versus frequent relapse, do see species associated with physiopathology evolution
SDEhrlich invites to attend tuesday presentation on modulation of microbiota by transplantation of microbiota
Discussion : work is observational. transplantation of gut microbiota - is it small number of species or global associations with the host? microbiome is individual but numerous associations might be beneficial. Challenge is to modulate be it global or targeted.
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