Category Archives: Microbial Ecology

Host lifestyle affects human microbiota on daily timescales

Fascinating! Abstract: Disturbance to human microbiota may underlie several pathologies. Yet, we lack a comprehensive understanding of how lifestyle affects the dynamics of human-associated microbial communities. Here, we link over 10,000 longitudinal measurements of human wellness and action to the … Continue reading

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Eco-evolutionary feedbacks drive species interactions

This. Is. Awesome. Link Abstract: In the biosphere, many species live in close proximity and can thus interact in many different ways. Such interactions are dynamic and fall along a continuum between antagonism and cooperation. Because interspecies interactions are the … Continue reading

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High-Throughput Characterization and Comparison of Microbial Communities

Halwachs et al. 2012 Computational Medicine The human microbiome plays an important role in health and disease, but the structure of the bacterial communities and their interaction with the human body are still poorly understood. The recent introduction of next-generation … Continue reading

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Diversity, stability and resilience of the human gut microbiota

Lozupone et al. Nature 2012 Trillions of microbes inhabit the human intestine, forming a complex ecological community that influences normal physiology and susceptibility to disease through its collective metabolic activities and host interactions. Understanding the factors that underlie changes in … Continue reading

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Determination of Whether Quorum Quenching Is a Common Activity in Marine Bacteria by Analysis of Cultivable Bacteria and Metagenomic Sequences

I thought that some of you might be interested in this article. It’s interesting and there are a lot of seemingly good references and technical information. Abstract: The abundance of quorum quenching (QQ) activity was evaluated in cultivable bacteria obtained … Continue reading

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Microdroplet-enabled highly parallel co-cultivation of microbial communities

by Park et al. 2011 PLoS One



Microbial interactions in natural microbiota are, in many cases, crucial for the sustenance of the communities, but the precise nature of these interactions remain largely unknown because of the inherent complexity and difficulties in laboratory cultivation. Conventional pure culture-oriented cultivation does not account for these interactions mediated by small molecules, which severely limits its utility in cultivating and studying “unculturable” microorganisms from synergistic communities. In this study, we developed a simple microfluidic device for highly parallel co-cultivation of symbiotic microbial communities and demonstrated its effectiveness in discovering synergistic interactions among microbes. Using aqueous micro-droplets dispersed in a continuous oil phase, the device could readily encapsulate and co-cultivate subsets of a community. A large number of droplets, up to ~1,400 in a 10 mm×5 mm chamber, were generated with a frequency of 500 droplets/sec. A synthetic model system consisting of cross-feeding E. coli mutants was used to mimic compositions of symbionts and other microbes in natural microbial communities. Our device was able to detect a pair-wise symbiotic relationship when one partner accounted for as low as 1% of the total population or each symbiont was about 3% of the artificial community.


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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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