This is an update, on a rainy March 31, 2015, live from the 5th Congress of the International Human Microbiome Consortium, held in LuxExpo, Luxembourg.
Here we are again, after the Hangzhou meeting 18 months ago, in Europe this time. We are all expecting another nice meeting and indeed the plenary sessions of the afternoon did set the pace nicely.
Joe Alcock, from University of New Mexico, started with a talk on ‘evolution and the origin of the microbiome’. Joe Alcock set the stage and illustrated how, in spite of a long co-evolution, fitness interest of the host and its microbes may well most often not be aligned. He then stressed how the host promotes cooperation, via adaptive and innate immunity, via provision of nutrients, via vertical transmission, domestication… And now “what do humans do?” asks Joe Alcock. They over-use broad spectrum antibiotics with which unexpected consequences? Missing microbes!! We are likely causing a loss of species (as much as forest fires). And the more we look, the more we find coevolution altering features implemented by human decision/choice.
Frederic Dixon Bushman continued with a talk on ‘viral impact on the evolution of the microbiome’. With an estimated 10^11 bacteriophages per gram of stool, somewhat more than bacteria, Frederic Dixon Bushman indicated that the diversity of viral sequences to be found is massive. Frederic then asked whether there could be “viral transfer during fecal microbial transplantation”. Studying 3 kids treated for ulcerative colitis, receiving the same donor stool and sample pre-, early-post and late-post fecal microbiota transplant, Chehoud et al. indicated that not all viruses transferred, and conversely, some transfered irrespective of the recipient microbiome (qPCR confirmed). Frederic speculated that Siphoviridae, enriched among transferred phages, could be transferred as prophages and induced for lysis after transplantation. He concluded by citing an estimate that 7.5% of bacteria are killed by phage ‘predation’ per day.
Andrew Benson followed with a rather energetic account of ‘host genetic control of the microbiome’, with fascinating work on crossed mice attempting to decipher the respective impacts of host genotype, long term diet, short term diet and niche construction on selection, diversification and dispersal, leading in the end to resistant and resilient microbiomes. Andrew raised questions such as “Does the core microbiome act as a complex phylogenetic trait?” and “Which of genetic versus environment (diet) factors control the microbiome?”. He concluded that the genetic effect is measurable, but the effect-size for QTL is not large. Conversely, diet can interact with genetic effect and even override it, which makes diet usable to modulate the microbiome. Finally, the host can enrich for functions irrespective of taxa, likely via metabolic functions.
Kjersti Aagaard of BCM gave a lecture on ‘maternal diet during pregnancy and lactation driving microbiome’. Kjersti presented work done on macaque monkeys and showed how the maternal intestinal microbiome is structured by diet and not obesity. She then illustrated that maternal diet during pregnancy alters juvenile microbiome. “Microbial metabolic pathways are altered by virtue of gestational diet!” she said. Moreover, the gestational effect of maternal diet is not fully correctable, and the post-weaning diet did not correct dysbiosis. Microbiome alpha diversity is affected from birth on, and possibly all the way to 3 years of age. Addressing the relevance of these observations for humans, Kjersti looked for the impact of excess gestational weight gain. Prepregnancy obesity had no impact on the ‘newborn’ microbiome and most alterations were in preterm infants from excess gestational weight-gain mothers compared to preterm without excess gestational weight-gain mothers. Kjersti Aagaard suggested a possible link between the reported loss of H. pylori from ancient to premodern to postmodern hominids (Blaser, 2013) with the loss of Campylobacter she reported.
Lanjuan Li, from Hangzhou, China, gave a presentation on ‘human gut microecology and infectious disease’. Professor Li is president of CDIC, the Collaborative Innovation Centre for diagnosis and treatment of infectious diseases, supported by a 200 million Yuan investment. She discussed a potential vicious circle whereby dysbiosis affects microbiota structure, function, and translocation impacting risk of infection, while infection yields alteration of host inflammatory signals promoting dysbiosis. She presented a new strategy for the treatment of H7N9 infection including balance of microecology as one of the key elements in treatment. In liver transplantation, professor Li suggested pre-operative dysbiosis could be associated with a higher risk of post operative infection.
Maria Gloria Dominguez Bello gave a presentation on ‘the Amerindian microbiome’.
Maria Gloria stressed the fact that, as trans-culturation is happening at a fast pace, we are still mainly characterizing microbiomes of urban populations, so we are far from representing ancestral populations. “We are putting effort in studying microbiota that has already been affected” she says. Studying remote Yanomami Indians of Venezuela, in comparison with Guahibo and others, she observed unprecedented high diversity. Abundance-prevalence curves showed more abundance and more shared taxa in Yanomami compared to Guahibo or Malawi or USA. Maria Gloria Dominguez Bello developed an account of her work on c-section versus vaginal delivery. C-section delivery has increased quite dramatically worldwide; in the USA it is associated with administration of 1g penicillin. In the city of Rio today 9 out of 10 births are by c-section, when the WHO estimates today that 15% of c-sections are clinically justified. In poor countries though, <15% still comes with infant mortality. C-section is also associated with more bottle feeding. Antibiotherapy at birth is also higher; each US kid has >3 antibiotic treatments over its first 4 years of life.
Maria Gloria concluded :
– Modern lifestyle changes early microbial exposure,
– Modern lifestyle is associated with reduced microbiome diversity,
– Modern lifestyle is associated with increased risk of immune diseases.
She suggests there might still be time to revise our attitudes through transculturation and management of the birth process.
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