Factors impacting bacterial gut microbiome community composition in wild non-human primates in Taï National Park, Côte d Ivoire
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1 Department of Biology, McGill University, Canada; Robert Koch Institut, Berlin, Germany and the Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany Factors impacting bacterial gut microbiome community composition in wild non-human primates in Taï National Park, Côte d Ivoire Jan F. Gogarten M.C. Nelson, J. Graf, J.P. Gogarten, R. Wittig, S. Calvignac-Spencer, F.H. Leendertz
2
3 Human microbiome 1,000,000+genes Human genome ~23,000 genes
4 Microbiomes + Host = Holobiont Human microbiome outnumbers human cells 10 to 1 Human microbiome 1,000,000+genes Human genome ~23,000 genes Tremaroli and Bäckhed 2012; Collins et al. 2012; Ezenwa and Williams 2014
5 Microbiomes + Host = Holobiont Human microbiome outnumbers human cells 10 to 1 Process of community assembly poorly understood Human microbiome 1,000,000+genes Human genome ~23,000 genes Tremaroli and Bäckhed 2012; Collins et al. 2012; Ezenwa and Williams 2014
6 Microbiomes + Host = Holobiont Human microbiome outnumbers human cells 10 to 1 Process of community assembly poorly understood Human microbiome 1,000,000+genes Human genome ~23,000 genes Human microbiome species depauperate Tremaroli and Bäckhed 2012; Collins et al. 2012; Ezenwa and Williams 2014
7 Microbiomes + Host = Holobiont Human microbiome outnumbers human cells 10 to 1 Process of community assembly poorly understood Human microbiome 1,000,000+genes Human genome ~23,000 genes Human microbiome species depauperate How holobionts evolve largely unknown Tremaroli and Bäckhed 2012; Collins et al. 2012; Ezenwa and Williams 2014
8 Methods Fecal samples from 8 wild diurnal primate species in Taï National Park, Côte d Ivoire Pan troglodytes verus Procolobus verus Piliocolobus badius Colobus polykomos Cercocebus torquatus atys Cercopithecus diana Cercopithecus campbelli 5 5 my Cercopithecus petaurista
9 Methods Pan troglodytes verus Procolobus verus Fecal samples from 8 wild diurnal primate species in Taï National Park, Côte d Ivoire Extracted DNA -> generated amplicons covering 16S V4 hypervariable region -> sequenced using Illumina MiSeq 5 5 my Piliocolobus badius Colobus polykomos Cercocebus torquatus atys Cercopithecus diana Cercopithecus campbelli Cercopithecus petaurista R Core Team 2015; Oksanen et al., 2015
10 Methods Pan troglodytes verus Procolobus verus Fecal samples from 8 wild diurnal primate species in Taï National Park, Côte d Ivoire Extracted DNA -> generated amplicons covering 16S V4 hypervariable region -> sequenced using Illumina MiSeq 5 5 my Piliocolobus badius Colobus polykomos Cercocebus torquatus atys Cercopithecus diana Cercopithecus campbelli Cercopithecus petaurista nmds approach with ENVFIT to examine impact of species, social group, familial relationships + disease R Core Team 2015; Oksanen et al., 2015
11 Pan troglodytes verus Phylogeny Primate of bacterial primate community gut bacteria Procolobus verus Piliocolobus badius Colobus polykomos Cercocebus torquatus atys Cercopithecus diana Cercopithecus campbelli 5 Cercopithecus petaurista
12 April 28th 2014 April 28 th 2014
13 May 5th 2014 May 5 th 2014
14 May 19th 2014 May 19 th 2014
15 May 26th 2014 May 26 th 2014
16 May 13th May
17 Procolobus verus Piliocolobus badius Colobus polykomos 0.8 NMDS With Species As Grouping Factor R 2 = 0.881*** Cercocebus torquatus atys Colobus.polykomos Cercopithecus diana Cercopithecus campbelli 5 Cercopithecus petaurista 0.4 Cercopithecus Cercopithecus.diana petaurista Procolobus.verus Primate bacterial community Procolobus.badius Cercopithecus.campbelli NMDS2 y 0.0 Cercocebus.atys x NMDS1
18 R 2 = 0.088*** Primate bacterial community NMDS2 NMDS1
19 NMDS For Individuals With Multiple Samples With Individual As Grouping Factor R 2 = 0.738*** Individual AMBOSELI ASSINIK BAIHUKU BAKO BALANCAN BAOBENG BARO BOTSIMA BUDONGO BWINDI BZA CAYO CORRIENTES 0.4 CURU DJOUROUTOO DOUALA FANTOM FONGOLI GOMBE GUNUNG HATO Primate bacterial community NMDS2 y 0.0 NGOGO BALANCAN NDOKI IGUACU GOMBE PANTANAL LOPE CAYO NYUNGWE KAKAMEGA RANOMAFANA YAKUSHIMA PHU DJOUROUTOO DOUALA ODZALA LASELVA TIWAI TAIAMBOSELI TINIGUA KAHUZI LANGTANG SANTA GUNUNG BAIHUKU LOMASSONSO FONGOLI MAHALE MGAHINGA MOREMI BUDONGO RAMNAGAR LUIKATAI PRETO BAOBENG BOTSIMA CURU ASSINIK BAKO BZA FANTOM PALO OKAVANGO ZANZIBAR BARO KALABWINDI CORRIENTES HATO TANJUNG IGUACU KAHUZI KAKAMEGA KALA KIBALE LANGTANG LASELVA LOMAS LOPE LUIKATAI MAHALE MGAHINGA MOREMI NDOKI NGOGO NYUNGWE ODZALA OKAVANGO PALO PANTANAL PHU PRETO RAMNAGAR RANOMAFANA KIBALE SANTA SONSO TAI TANJUNG TINIGUA 0.4 TIWAI YAKUSHIMA ZANZIBAR Sex.variable Adult female Adult male Juvenile female Juvenile male Subadult female Subadult male x NMDS1
20 0.4 NMDS with Mother Offspring Pair As Grouping Factor R 2 = 0.441*** 0.2 BAL NDO Mother.offspring Mother Offspring Primate bacterial community FAN GOM Mother.offspring.pair AMB BAL BUD NMDS2 y 0.0 NGO LOM RAN SON PAL FON AMB CUR BUD MAH CUR FAN FON GOM LOM MAH NDO NGO PAL RAN 0.2 TAN SON TAN 0.4 NMDS x
21 R 2 = ns Primate bacterial community NMDS2 NMDS1
22 Non-invasive samples Different scales host social groups ecosystems evolutionary Eco-Evo Facilitation Exclusion Competition 5 Procolobus verus Piliocolobus badius Colobus polykomos Cercocebus torquatus atys Cercopithecus diana Cercopithecus campbelli Cercopithecus petaurista
23 Future directions Examining the virome (particullry phages) More flexible modeling approaches like PGLMMs
24 Acknowledgments Advisors: Colin Chapman, Fabian Leendertz, Roman Wittig, Jonathan Davies Committee: Charles Nunn, Louis Lefebvre, David Marcogliese. Field, research and laboratory assistants at Taï National Park and the Robert Koch Institute. Leendertz Lab, particularly Sébastien Calvignac-Spencer for support and suggestions throughout
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