Biology subjects

Durand, H. K.

Publications and source records attributed to Durand, H. K..

2 recordsLinked to original sources

bioRxiv2019

High-throughput isolation and culture of human gut bacteria with droplet microfluidics

Isolation and culture of gut bacteria enable testing for microbial roles in disease and may also lead to novel therapeutics. However, the diversity of human gut microbial communities (microbiota) impedes comprehensive experimental studies of individual bacterial taxa. Here, we combine advances in droplet microfluidics and high-throughput DNA sequencing to develop a platform for isolating and assaying microbiota members in picoliter droplets (MicDrop). MicDrop can be used to create millions of distinct bacterial colonies in a single experiment while using off-the-shelf parts compact enough to fit in an anaerobic chamber. In proof-of-concept experiments, we used the platform to characterize inter-individual metabolic variation among hundreds of polysaccharide-degrading gut bacteria from nine stool donors. We also used MicDrop to test the hypothesis that growth kinetics of individual gut bacterial taxa are associated with longterm community dynamics in an artificial gut. These demonstrations suggest the MicDrop platform could support future diagnostic efforts to personalize microbiota-directed therapies, as well as to provide comprehensive new insights into the ecology of human gut microbiota.

microbiology↗

bioRxiv2019

Measuring and Mitigating PCR Bias in Microbiome Data

PCR amplification plays a central role in the measurement of mixed microbial communities via high-throughput sequencing. Yet PCR is also known to be a common source of bias in microbiome data. Here we present a paired modeling and experimental approach to characterize and mitigate PCR bias in microbiome studies. We use experimental data from mock bacterial communities to validate our approach and human gut microbiota samples to characterize PCR bias under real-world conditions. Our results suggest that PCR can bias estimates of microbial relative abundances by a factor of 2-4 but that this bias can be mitigated using simple Bayesian multinomial logistic-normal linear models.\n\nAuthor summaryHigh-throughput sequencing is often used to profile host-associated microbial communities. Many processing steps are required to transform a community of bacteria into a pool of DNA suitable for sequencing. One important step is amplification where, to create enough DNA for sequencing, DNA from many different bacteria are repeatedly copied using a technique called Polymerase Chain Reaction (PCR). However, PCR is known to introduce bias as DNA from some bacteria are more efficiently copied than others. Here we introduce an experimental procedure that allows this bias to be measured and computational techniques that allow this bias to be mitigated in sequencing data.

genomics↗