PBG 270
Co-Evolution of Microbiomes and Hosts
Mondays 12:10-1:00 PM

Storer 2342

The communities of microbes that live in and on various multicellular organisms (so called microbiomes) are of growing interest. This PBG270 journal club will focus on papers on the co-evolution of microbiomes and their hosts - over long, medium and short evolutionary time scales.  Possible topics include GWAS and QTL studies of host-microbiome interactions, theoretical modelling of microbiome evolution, convergence of microbiomes between distantly related hosts, and inferring ancestral microbiomes for various phylogenetic groups.

Winter Quarter Schedule in progress

Fall Quarter Schedule

9/28: General overview

10/5: Sonia Ghose and Jonathan Eisen

• Subsistence strategies in traditional societies distinguish gut microbiomes
• Gut microbiome of the Hadza hunter-gatherers

10/12: Jennifer Schmidt and Melissa Kardish

• Host-specificity among abundant and rare taxa in the sponge microbiome
• Root microbiome relates to plant host evolution in maize and other Poaceae

10/19 : Camille Scott and Megan Morris

• The Gut Microbial Community of Midas Cichlid Fish in Repeatedly Evolved Limnetic-Benthic Species Pairs
• Removing environmental sources of variation to gain insight on symbionts vs. transient microbes in high and low microbial abundance sponges

10/26: Brendan Cornwell and Anna O'Brien

• The relative importance of rapid evolution for plant-microbe interactions depends on ecological context
• Symbiote transmission and maintenance of extra-genomic associations

11/2: Nicole Kollars and Victoria Morgan

• Bacteria associated with Artemia spp. along the salinity gradient of the solar salterns at Eilat (Israel)
• Niche Limits of Symbiotic Gut Microbiota Constrain the Salinity Tolerance of Brine Shrimp
• Ed Yong Blog: Why Sea Monkeys Love Salt: A Fable on the Cost of Symbiosis 

11/9: Katrina Brock

• The Evolution of Mutualism in Gut Microbiota Via Host Epithelial Selection
• Neutral Models of Microbiome Evolution

11/16: Erin Calfee and Amanda Everitt

• Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes" 
• "Host sanctions and the legume-rhizobium mutualism" 

11/23: Lisa Cohen

• A BAYESIAN FRAMEWORK FOR THE ANALYSIS OF COSPECIATION
• Disparate rates of molecular evolution in cospeciating hosts and parasites

11/30: Liz Henry and Betsy Alford

• Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley
• Human Genetics Shape the Gut Microbiome

Co-evolution of hosts and microbiomes papers of possible interest

• Methods

• Phylogenetic framework for coevolutionary studies: a compass for exploring jungles of tangled trees

• Primates

• Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities (2010)
• Rapid changes in the gut microbiome during human evolution (2015)
• Subsistence strategies in traditional societies distinguish gut microbiomes (2015)
• Gut microbiome of the Hadza hunter-gatherers
• Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance (2014)
• Incorporating the gut microbiota into models of human and non-human primate ecology and evolution. (2015). Suggested by Jack Gilbert.

• Mammals

• Worlds within worlds: evolution of the vertebrate gut microbiota (2008)
• Evolution of mammals and their gut microbes (2008)
• Status of the phylogenetic diversity census of ruminal microbiomes (2011)
• Microbiome analysis among bats describes influences of host phylogeny, life history, physiology and geography.
• Phylogenetics and the Human Microbiome

• Many Animals

• Unique and shared responses of the gut microbiota to prolonged fasting: a comparative study across five classes of vertebrate hosts (2014). Suggested by Uri on my blog.
• Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes

• Birds

• From the wild red jungle fowl to domesticated chickens: modification of eimerian-microbiome-host interactions

• Fish

• The Gut Microbial Community of Midas Cichlid Fish in Repeatedly Evolved Limnetic-Benthic Species Pairs
• Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies.

• Sponges

• Phylogenetic signal in the community structure of host-specific microbiomes of tropical marine sponges
• Phylogenetic diversity, host-specificity and community profiling of sponge-associated bacteria in the northern Gulf of Mexico.
• Relationships between host phylogeny, host type and bacterial community diversity in cold-water coral reef sponges.

• Shrimp

• Effects of Host Phylogeny and Habitats on Gut Microbiomes of Oriental River Prawn (Macrobrachium nipponense).

• Plants

• Root microbiome relates to plant host evolution in maize and other Poaceae (2014)
• Impact of plant domestication on rhizosphere microbiome assembly and functions (2015)
• Conservation and diversity of seed associated endophytes in Zea across boundaries of evolution, ethnography and ecology (2011)
• Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley
• Rapid responses of soil microorganisms improve plant fitness in novel environments (2012) - Experimental evolution in hosts

Microbiome QTL and GWAS

• Reviews

• Unravelling the effects of the environment and host genotype on the gut microbiome

• Mouse QTL studies

• Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors
• Genome-wide mapping of gene–microbiota interactions in susceptibility to autoimmune skin blistering
• 2012 Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits

• Human GWAS studies

• 2015 Human paper: Host genetic variation impacts microbiome composition across human body sites
• 2014 mtDNA haplogroup and single nucleotide polymorphisms structure human microbiome communities.
  2012 A metagenome-wide association study of gut microbiota in type 2 diabetes

• Poplar

• Host genotype shapes the foliar fungal microbiome of balsam poplar (Populus balsamifera).

Convergence or not of Communities

• Convergence of gut microbiomes in myrmecophagous mammals

• Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans
• Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies
• Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores (2015)

Heritability

• Maize

• Diversity and heritability of the maize rhizosphere microbiome under field conditions

• Humans

• Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood
• Human Genetics Shape the Gut Microbiome

General theory

• Neutral Models of Microbiome Evolution
• The Evolution of Mutualism in Gut Microbiota Via Host Epithelial Selection

Host specialization evolution

• Evolution of host specialization in gut microbes: the bee gut as a model
• Microbiome analysis among bats describes influences of host phylogeny, life history, physiology and geography
• The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome
• The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome

Microbiomes as drivers of evolution

• The Hologenomic Basis of Speciation: Gut Bacteria Cause Hybrid Lethality in the Genus Nasonia

• with Response: Comment on “The hologenomic basis of speciation: Gut bacteria cause hybrid lethality in the genus Nasonia

• Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution
• Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes
• Research highlights for issue 5: the role of the microbiome in shaping evolution
• Patterns, causes and consequences of defensive microbiome dynamics across multiple scales

Experimental studies of host-microbe interactions / co-evolution

• Experimental replacement of an obligate insect symbiont

Reviews

• Microbiomes: unifying animal and plant systems through the lens of community ecology theory

• The Human Gut Microbiome: Ecology and Recent Evolutionary Changes
• Ecological and Evolutionary Forces Shaping Microbial Diversity in the Human Intestine
• Towards an Evolutionary Model of Animal-Associated Microbiomes
• Co-evolution in context: The importance of studying gut microbiomes in wild animals
• Engineering Microbiomes to Improve Plant and Animal Health 
• Microbiome: Ecology of stable gut communities