Raval, R. | Search bioRxiv

bioRxiv2021

Synchronous seasonality in the gut microbiota of wild wood mouse populations

O_LIThe gut microbiome performs many important functions in mammalian hosts, with community composition shaping its functional role. However, what factors drive individual microbiota variation in wild animals and to what extent these are predictable or idiosyncratic across populations remains poorly understood. C_LIO_LIHere, we use a multi-population dataset from a common rodent species (the wood mouse, Apodemus sylvaticus), to test whether a consistent set of core gut microbes is identifiable in this species, and to what extent the predictors of microbiota variation are consistent across populations. C_LIO_LIBetween 2014 and 2018 we used capture-mark-recapture and 16S rRNA profiling to intensively monitor two wild UK mouse populations and their gut microbiota, as well as characterising the microbiota from a laboratory-housed colony of the same species. C_LIO_LIAlthough broadly similar at high taxonomic levels and despite being only 50km apart, the two wild populations did not share a single bacterial amplicon sequence variant (ASV). Meanwhile, the laboratory-housed colony shared many ASVs with one of the wild populations from which it is thought to have been founded decades ago. Despite strong taxonomic divergence in the microbiota, the factors predicting compositional variation in each wild population were remarkably similar. We identified a strong and consistent pattern of seasonal microbiota restructuring that occurred at both sites, in all years, and within individual mice. While the microbiota was highly individualised, seasonal convergence in the gut microbiota among individuals occurred in late winter/early spring. C_LIO_LIThese findings reveal highly repeatable seasonal gut microbiota dynamics across distinct populations of this species, despite divergent taxa being involved. Providing a platform for future work to understand the drivers and functional implications of such predictable seasonal microbiome restructuring, including whether it might provide the host with adaptive seasonal phenotypic plasticity. C_LI

ecology↗

bioRxiv2021

Identification and quantification of chimeric sequencing reads in a highly multiplexed RAD-seq protocol

Highly multiplexed approaches have become a common practice in genomic studies. They have improved the cost-effectiveness of genotyping hundreds of individuals by using combinatorially-barcoded adapters. These strategies, however, can potentially misassign reads to incorrect samples. Here we used a modified quaddRAD protocol to analyse the occurrence of index hopping and PCR chimeras in a series of experiments with up to a 100 multiplexed samples per sequencing lane (total n = 639). We created two types of sequencing libraries: four libraries of Type A, where PCR reactions were run on individual samples before multiplexing, and three libraries of Type B, where PCRs were run on pooled samples. We used fixed pairs of inner barcodes to identify chimeric reads. Type B libraries show a higher percentage of misassigned reads (1.15%) compared to Type A libraries (0.65%). We also quantify the commonly undetectable chimeric sequences that occur whenever multiplexed groups of samples with different outer barcodes are sequenced together on a single flow cell. Our results suggest that these types of chimeric sequences represent up to 1.56% and 1.29% of reads in Type A and B libraries, respectively. We review the source of such errors, provide recommendations for developing highly-multiplexed RAD-seq protocols and analysing the resulting data to minimise the generation of chimeric sequences, allow their quantification, and provide finer control over the number of PCR cycles necessary to generate enough input DNA for library preparation.

bioinformatics↗