Gut microbiome in Hadza huntergatherers, adaptation to a Paleolithic lifestyle

Transcription

1 Gut microbiome in Hadza huntergatherers, adaptation to a Paleolithic lifestyle Patrizia Brigidi Dept. Pharmacy and Biotechnology University of Bologna patrizia.brigidi@unibo.it THE HUMAN MICROBIOTA: PHYLOGENETIC DIVERSITY we are 90% bacteria, colonize our body and the great majority of these microorganisms is hidden in the GI tract > 1000 species 5 (out of 100) bacterial phyla Firmicutes (65%), Bacteroidetes (25%) Actinobacteria (5%), Proteobacteria (<8%), Fusobacteria (1%) and Verrucomicrobia (1%) 1

2 FUNCTIONAL DIVERSITY MICROBIOME Collective genome of the microbiota 10 6 GENES 58% KNOWN 42% UNKNOWN carbohydrate metabolism (CAZymes) energy metabolism amino acid metabolism biosynthesis of secondary metabolites metabolism of cofactors and vitamins MICROBIOTA-HOST MUTUALISM HUMAN INTESTINAL MICROBIOTA ECOLOGICAL SERVICES our bacterial counterpart provides essential physiological features we have not evolved enhancement of the digestive efficiency and modulation of energetic homeostasis competitive barrier against colonization/invasion development, education and function of the immune system strengthening of the GIT epithelium impermeability vitamin synthesis detoxification of xenobiotics central nervous system modulation endocrine system modulation 2

3 SELECTION TOWARDS A CHANGEABLE INDIVIDUAL MICROBIOME PROFILE GM responds very quickly to environmental and dietary changes host adaptation ECOSYSTEM PLASTICITY UNIQUENESS OF OUR HISTORY; ADAPTATION TO OUR PECULIAR PHYSIOLOGY, AND LIFESTYLE peculiar structure and temporal dynamics of the individual intestinal microbiota provide microbiota ecosystem services in the face of personalized physiology, immune system, environmental or dietary exposure and lifestyle EFFECT OF LIFESTYLE ON THE GUT MICROBIOME to explore the extent to which GM-host coevolution is responsible for our physiological flexibility and environmental adaptation Western lifestyle Industrial food Antibiotics, sterile cleaners High-fat and high-protein diet Hunter- gatherer lifestyle Immediately processed available food Low-fat and plant polysaccharide-rich diet Contaminated food The intestinal microbiome of the Hadza hunter-gatherers Schnorr et al., Nat. Commun

4 THE HADZA: ONE OF THE LAST HUNTING AND GATHERING COMMUNITIES East Africa along the Rift Valley, around the shore of Lake Eyasi (where early hominins lived) Small mobile camps (core group of 30 people; movement resource driven, depending on dry or wet season) Foraging population (no cultivation or domestication of plants and animals, minimal agricultural products from external sources, < 5% calories) Hazda lifestyle closely resembles that of Paleolithic humans THE HADZA DIET The wild foods consumed by the Hadza fall into 5 main categories: meat, honey, baobab, berries, and tubers (available and exploited year round) Fibres are not swallowed by the Hazda but chewed for few min, kept against cheek and teeth and then expectorated Pre-chewed Post-chewing MAK ALITAKO tuber (Emminia entennulifa) The digestible fraction is very variable but composed of largely water, simple sugars, starch and soluble fibre 4

5 THE HADZA DIET Annual Hazda diet: 70% of kcal from plant foods; 30% from bird and animal meat (dry season) diet rich in simple sugars, starch and protein while lean in fat STUDY DESIGN (I) 27 Hadza, (aged 8-70y, mean 32y, 9F, 18M) from 2 separate camps, Dedauko and Sengele, situated in the Rift valley ecosystem 16 Italians (aged 20-40y, mean age 32y, 11F, 5 M) Collection of Hazda fecal samples: over 2 weeks in January (between 2 rainy periods variety of plant food available) Handling and storage of samples: ethanol and silica two-step procedure (Hadza stool samples could not remain frozen during their removal from Tanzania due to unreliable sourcing of dry ice shipping materials) 5

6 STUDY DESIGN (II) DNA extraction Pyrosequenced in the V4 gene region (454-Roche) Resulting in 309,952 high-quality reads Average of 7208 ± 2650 reads per subject Reads were clustered into OTUs at 97% identity Italian subjects No antibiotics, probiotics or prebiotics for at least 3 months before sampling Dietary habit (24 h dietary recall for 3 days, 2 week days and 1 weekend day) DIET OF THE ITALIAN COHORT Mediterranean diet abundant plant food, fresh fruit, pasta, bread and olive-oil; low to moderate amounts of dairy, poultry, fish and read meat 6

7 BIODIVERSITY OF THE HADZA MICROBIOTA α- diversity at 97% and 95% similarity Hadza have a more diverse gut microbe ecosystem compared to the Italian cohort. P h y l u m BACTERIAL RELATIVE ABUNDANCE OF HADZA AND ITALIAN SUBJECTS HAZDA Firmicutes 72% Bacteriodetes 17% Proteobacteria 6% Spirochaetes 3% 2% of OTU remaining unclassified at phylum level F a m i l y Ruminococcaceae 34% Lachnospiraceae 10% Prevotellaceae 6% Clostridiales Incertae Sedis XIV (3%) Succinivibrionaceae 3% Spirochetaceae 2% Eubacteriaceae 2% 7

8 THE HADZA GUT MICROBIOTA: SIGNIFICANT SEPARATION BY SEX Sex-based labor divisions within the Hadza community Cellulose and xylan hydrolizers adaptation to higher amounts of plant fiber in diet Buffering women from resource gaps Provision for pregnancy and lactation Female Gathering tubers twice a day Treponema Male Hunting wild animals and searching honey Eubacterium Blautia COMPARISON TO ITALIAN CONTROLS Remarkable differences in subdominant phyla (< 10% relative abundance) Hadza Italians depletion of Bifidobacterium, Bacteroides and butyrate producers of the Clostridium clusters IV and XIVa (Faecalibacterium, Roseburia, Ruminococcus) enriched in Prevotella, unclassified Clostridiales and unclassified Ruminococcaceae enriched in what are generally considered opportunistic microorganisms, such as members of Proteobacteria, Succinivibrio, and Treponema 8

9 ABSENCE OF BIFIDOBACTERIUM IN HAZDA Never reported for any other human group (confirmed by qpcr) Hypothesis consequence of the post-weaning GM composition in the absence of agro-pastoralderived foods (consumption of dairy into adulthood could be one reason most Western populations maintain a relatively large bifidobacteria presence) Hadza neither domesticate nor have direct contact with livestock animals (swine, cattle and rabbit) conditions for interspecies transfer and colonization of bifidobacteria do not occur for the Hadza Absence of bifidobacteria combined with the enrichment in opportunistic bacteria (Proteobacteria and Spirochaetes) Hadza GM likely represents a new equilibrium that is beneficial and symbiotic to their living environment SCFA: MICROBIAL METABOLITES WITH A KEY MULTIFACTORIAL ROLE IN HOST NUTRITION SCFA dominant metabolites resulting from bacterial fermentation of plant derived substrates SCFA: butyrate - acetate - propionate energy source for the colonic epithelium lipid synthesis in the liver gluconeogenesis insulin secretion 1 2 energy extraction 5-15% of the total energy required 2 energy storage 9

10 SHORT-CHAIN FATTY ACID PROFILE OF HADZA AND ITALIANS Hadza propionate role in human physiology and energy contribution directly to the host Italians butyrate associates with local health of the colon Bifidobacterium, Bacteroides, Blautia, Faecalibacterium and Ruminococcus are positively correlated with butyrate Bifidobacterium, Blautia and Lachnospiraceae show a significant negative correlation with propionate, while Prevotella demonstrates a positive correlation Hazda GM: absence of Bifidobacterium, lower relative abundance of Blautia, Ruminococcus and Faecalibacterium and greater relative abundance of Prevotella These differences may reflect dietary variation in both amount and type of fiber and carbohydrates consumed by Hadza and Italians COMPARISON OF GM RELATIVE ABUNDANCE AMONG POPULATIONS REFLECTS SUBSISTENCE PATTERNS GM of 2 rural African groups and their respective western controls were compared with Hazda 11 children from Burkina Faso aged 5-6 y and 12 Italian children aged 3-6 y; 22 rural young adults from Malawi (southeast Africa) aged y and 17 US adults aged y Clustering analysis: clear separation between western controls and Africans (30% variability) separation between H, BF and M (19% variability) Less separation and large interspersion between western controls 10

11 DISTINCT BACTERIAL CO-ABUNDANCE GROUPS (CAGs) DEFINE EACH POPULATION Co-abundance associations between genera to identify patterns of microbial community variation among African and Western populations Network plots indicate pattern of variation of the 6 identified CAGs in Hadza, Malawi, BF and western controls Africans are characterized by Prevotella CAG; Western controls by Faecalibacterium CAG Hazda, respect to Malawi e BF, are enriched in Ruminococcaceae and Treponema COMPARISON TO AFRICAN AGRICULTURAL SOCIETIES Co-abundance groups distribution allowed to distinguish 3 different modes of subsistence: foraging, rural farming, and industrial agriculture 11

12 The Hadza microbiota CONCLUSIONS > biodiversity compared to western populations evidence of a sex-related divergence in microbial structure enriched in previously unknown fiber-degrading microorganisms, and rare opportunistic bacteria, while depleted in health-promoting microbial groups, such as the well-known probiotic genus Bifidobacterium unique configuration that redefines our notions of healthy and unhealthy, demonstrating that these distinctions are context dependent improved understanding of how gut microbiota may have helped our ancestors adapting and surviving during the Paleolithic FUTURE PERSPECTIVE Functional metagenomic analysis Testing GM activity using in vivo techniques (gnotobiotic mice) or in vitro techniques (simulation of the large intestine) Thanks for your attention Marco Candela Manuela Centanni Elena Biagi Silvia Turroni Sara Quercia Simone Rampelli Amanda Henry, Stephanie Schnorr (Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany) Alyssia Crittenden (Dept. of Anthropology, University of Nevada, Las Vegas, USA) Audax Mabulla (College of Art and Social Sciences, University of Dar en Salaam, Tanzania) 12

13 DRIED VS FROZEN STORAGE PROTOCOLS Reliability of the drying method for use in stool storage Samples from 2 western individuals were collected and splitted into 2 samples each: One fraction -80 Second fraction dried following a 2 steps EtOH submersion and silica storage procedure Comparable DNA yield, GM and SCFA profiles from frozen and dry aliquots of the same stool GM profiles were shown to cluster by subject independent of the storage method 13