era7 bioinformatics R&D group

A short report about the Conference Exploring Human Host-Microbiome Interactions in Health and Disease at Wellcome Trust, Hinxton on May 8 - 10, 2012

In my opinion, Curtis Huttenhower presented the newest perspectives for understanding human microbiome. Some ideas from his talk:

  • Not who, but why: the IBD microbiome is defined by adaptation to oxidative stress.
  • Niche specialization is crucial in human microbiome.
  • Human Microbiome Project Unified Metabolic Analysis Network: Who’s there vs what they’re doing.
  • Species-level resolution is critical for understanding microbiome function, strain-level is even better.

Some interesting ideas presented at the conference:

Ian Wilson:

  • Disease and microbiome: causal or casual?
  • Recolonization after Atbs resulted in cage-dependent subgroups with different bacterial populations and metabotypes.

Karen Scott:

  • Anaerobic Roseburia/E. rectale group bacteria constitute 10% of gut microbiota in healthy individuals.
  • The main fermentation product of Roseburia species is butyrate. The genomic analysis of the enzymes involved is complex.
  • Dietary interventions (augmenting the amount of starch consumed) can dramatically affect Roseburia genus presence in gut.

Barbara Pachikian:

  • Fructooligosaccharides (FOS) supplementation reverses hepatic steatosis.

Francisco Guarner:

  • In IBD mucosal lesions are caused by immune response against colonic bacteria.

Paul Cotter:

  • Bacteriocins as tools to alter the composition of gut microbiota.

Ruth Ley:

  • In the third trimester of pregnancy gut bacterial composition shows a dramatic shift.
  • The third trimester microbiota could induce low-grade inflammation, adiposity gain and reduced insulin sensitivity beneficial in pregnancy R.Ley
  • Gut microbiota’s impact on metabolism: highly adaptive in pregnancy and detrimental in obese host.

Fredrik Backhed:

  • Apoe -/- germ-free male mice are resistant to diet-induced atherosclerosis.
  • Gut microbiota modulate bile acid synthesis.

Simon Murch:

  • There are differences between the flora from cesarean infants and from vaginally delivered infants.
  • Different bacteria induce different gene expression in the host
  • Breast milking and reduction of antibiotic exposure are critical for microbial diversity in low birth weight neonates.

A. Walker:

  • CF infants have more pathogenic bacteria in their lower respiratory microbiota (P. aeruginosa, S. maltophilia, B. cepacia)

Elisa Noll:

  • Gut-microbial metabolism can alter host metabolism in the favour of obesity and insulin resistance.

Fergus Shanaham:

  • What is a healthy gut? Low biodiversity implies more pathogens colonization.

Douwe van Sinderen:

  • Bifidobacterial pili and surface polysaccharide allow competitive host colonization and persistence -Perhaps genes involved in colonization are not expressed in vitro.

Catarina Simoes:

  • Diet affects the gut microbiota in twins.

Kathleen Sim:

  • Missing bifidobacteria: undercounting in neonatal gut microbiota using classical universal primers.

Julian Marchesi:

  • Experiments colonizing gut from mices with human microbiota
  • Core functions of gut microbiota need to be useful to the host but at the same time to the bacteria.

Willem de Vos:

  • Gut microbiome with low diversity in colitis
  • Ileum microbiota is shaped by fast sugar uptake
  • Microbiota diversity likely to provide resilience
  • Diversity and stability characterize a healthy microbiome.

Jeremy K. Nicholson:

  • There are many more targets for cancer in human microbiome than in human genome
  • The microbiome as a therapeutic target
  • Influence of maternal genome on early microbiome development.