Monthly Archives: July 2012

Network Analyses in Organic Chemistry What?

These two papers are part of a three paper series in Angewandte Chemie on chemical networks. I know this will not be of broad interest, but that’s the cool thing about this blog. I think its really nifty. They are … Continue reading

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Getting started with networks analyses

Here are a few links to help you get started in thinking about networks! Two types of networks analyses: 1.  Local similarity analysis – includes a time lag, popular for microbial communities The original LSA – Ruan et al. 2006 … Continue reading

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Imaging Mass Spectrometry in Microbiology

A review of IMS according to different ionization sources and by levels of analysis in microbiology (from single cells to microbial communities) Nat Rev Micro 2011 Watrous

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A primer on agar-based microbial imaging mass spectrometry

A how to guide on imaging mass spectrometry (5 steps), along with challenges. J. Bacteriol. 2012 Yang

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Journal: Nat Rev Micro

Metagenomics and 16S pyrosequencing have enabled the study of ecosystem structure and dynamics to great depth and accuracy. Co-occurrence and correlation patterns found in these data sets are increasingly used for the prediction of species interactions in environments ranging from the oceans to the human microbiome. In addition, parallelized co-culture assays and combinatorial labelling experiments allow high-throughput discovery of cooperative and competitive relationships between species. In this Review, we describe how these techniques are opening the way towards global ecosystem network prediction and the development of ecosystem-wide dynamic models.




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Gut microbiota instead of host genotype drive the specificity in the interaction of a natural host-parasite system


  • 16S rRNA;
  • bacterial communities;
  • coevolution;
  • microbiome;
  • parasitology;
  • pathogen;
  • resistance;
  • TRFLP;
  • Trypanosomatidae


Specific interactions between parasite genotypes and host genotypes (Gp × Gh) are commonly found in invertebrate systems, but are largely lacking a mechanistic explanation. The genotype of invertebrate hosts can be complemented by the genomes of microorganisms living on or within the host (‘microbiota’). We investigated whether the bacterial gut microbiota of bumble bees (Bombus terrestris) can account for the specificity of interactions between individuals from different colonies (previously taken as host genotype proxy) and genotypes of the parasite Crithidia bombi. For this, we transplanted the microbiota between individuals of six colonies. Both the general infection load and the specific success of different C. bombi genotypes were mostly driven by the microbiota, rather than by worker genotype. Variation in gut microbiota can therefore be responsible for specific immune phenotypes and the evolution of gut parasites may be driven by interactions with ‘microbiota types’ as well as with host genotypes.

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Speciation by symbiosis

In the Origin of Species, Darwin struggled with how continuous changes within a species lead to the emergence of discrete species. Molecular analyses have since identified nuclear genes and organelles that underpin speciation. In this review, we explore the microbiota as a third genetic component that spurs species formation. We first recall Ivan Wallin’s original conception from the early 20th century on the role that bacteria play in speciation. We then describe three fundamental observations that justify a prominent role for microbes in eukaryotic speciation, consolidate exemplar studies of microbe-assisted speciation and incorporate the microbiota into classic models of speciation.

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