Fungal microbiome. Gwen Falony BVMDM symposium 19 th of November 2015
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1 Fungal microbiome Gwen Falony BVMDM symposium 19 th of November 2015
2 How human are you? There are times more bacteria on your body than there are humans on earth. You have 10 times more bacterial cells than human ones. You have 100 times more bacterial genes than human ones.
3 The human gut microbiota expands our digestive capacity, produces essential nutrients increases colonization resistance against pathogenic intruders assists in the detoxification of xenobiotics
4 Metagenomics Access to the uncultivable fraction of microbial life Traditional Microbial Genomics Environmental Genomics isolate individuals cultivation prepare DNA, sequence randomly prepare DNA, sequence randomly assemble genome assemble (partial) genomes
5 Metagenomics teach you who lives where and what they can do The Huttenhower Lab
6 Towards health monitoring through gut microbiota screening
7 Flemish Gut Flora Project
8 The flora is seeded at birth
9 Inoculation at birth: unstable microbiota development of until weaning Infant guts Palmer et al., PLOS Biology 2007
10 Gut microbiota distribution <10³ bacteria/g 10 4 bacteria/g 10 7 bacteria/g bacteria/g
11 Colon microbiota fermentation processes A trophic chain in a microbial ecosystem polysaccharide degradation carbohydrate metabolism protein degradation amino acid metabolism gas production
12 Substantial overlap in gut microbiota between individuals 1/3 rd of species present in almost all individuals 1500 species in total 160 species/individual =
13 Enterotypes - microbiota configurations in gut microbiome space Microbiota constellations independent from gender, age, and nationality Arumugam*, Raes* et al., Nature 2011
14 Enterotype configurations in the Flemish population Prevalent microbiome constellations differ in relative abundances of enterotype identifiers
15 Long term dietary patterns might determine enterotype No effect shown by short term interventions Wu et al., Science 2011
16 Enterotype stratification is linked to microbial substrate preference
17 Stool consistency is associated with microbiota richness and enterotypes diet stool consistency microbiome composition Vandeputte et al., Gut 2015
18 Recurring theme: a healthy microbiota is a diverse microbiota Claesson et al., Nature 2012 Microbiota diversity thought to reflect colon ecosystem stability and resilience
19 More and more diseases linked to disturbed gut microbiota
20 Association Causality Confounder analyses are required
21 Obesity is associated with microbiota dysbiosis 292 individuals Le Chatelier et al., Nature 2013
22 Microbiota modulation as therapy - Fecal Microbiota Transplantation Vrieze et al., Gastroenterology 2012 Transfer of intestinal microbiota from lean donors increases Insulin Sensitivity in individuals with Metabolic Syndrome
23 Gut microbiota: more than bacteria (A) (B) (C) (D) (E) (F) (G) (H) (I) (J) (K) (L) stramenopile Blastocystis hominis diplomonadid Enteromonas hominis retortamonadid Retortamonas intestinalis trichomonadid Pentratrichomonas hominis tritrichomonadid Dientamoeba fragilis retortamonadid Chilomastix mesnili amoebozoan Entamoeba hartmani amoebozoan Endolimax nana amoebozoan Entamoeba coli amoebozoan Entamoeba dispar coccidian Isospora belli amoebozoan Iodamoeba buetschli (M) microsporidian Encephalitozoon cuniculi (N) ascomycete Candida albicans Lukes et al., PLOS Pathogens 2015
24 The human mycobiota Underhill et al., Nature Reviews Immunology 2014 Parfrey et al., Frontiers in Microbiology 2014
25 The rare biosphere Less abundant (<0.1%), but more diverse, component of the microbiome Amplicon-based markers for mycobiome studies: Nuclear ribosomal internal transcribed spacer (ITS) region Cui et al., Genome Medicine 2013; Huffnagle et al., Trends in Microbiology 2013
26 Correlations with diet and bacterial residents 98 healthy volunteers, US Saccharomyces present in 89% of fecal samples, Candida in 57% Candida: positive correlation with carbohydrates and negative with total saturated fatty acids consumption Aspergillus: negative correlation with SCFA consumption Saccharomyces: not associated to defined dietary pattern Hoffmann et al., PLoS ONE 2013
27 Mycobiome research focusses on disease 19 Crohn s disease patients versus 7 healthy controls Perturbation of fungal fecal community in CD fungal dysbiosis? Increased diversity Increase prevalence of Candida albicans Fungal diversity correlates with CRP levels and CD activity index Li et al., Journal of Clinical Gastroenterology
28 Candida albicans is not always the preferential yeast colonizing the human intestine Wayampi people, an indigenous tribe from French Guiana 151 individuals, fecal samples collected in 2006 and 2010 Rectal swabs of 213 wild and domestic animals Culture/isolation/identification approach Candida krusei and Saccharomyces cerevisiae identified as most abundant gut fungal species Carriage of foodborne origin, associated with a common environmental source, such as plants or water Specific risk factors associated with Candida albicans carriage are gender (female) and living in a crowded household Angebault et al., Journal of Infectious Diseases 2013
29 Thanks for your attention
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