BackgroundThe composition of bacteria in and on the human body varies widely across human individuals, and has been associated with multiple health conditions. While microbial communities are influenced by environmental factors, some degree of genetic influence of the host on the microbiome is also expected. This study is part of an expanding effort to comprehensively profile the interactions between human genetic variation and the composition of this microbial ecosystem on a genome- and microbiome-wide scale.ResultsHere, we jointly analyze the composition of the human microbiome and host genetic variation. By mining the shotgun metagenomic data from the Human Microbiome Project for host DNA reads, we gathered information on host genetic variation for 93 individuals for whom bacterial abundance data are also available. Using this dataset, we identify significant associations between host genetic variation and microbiome composition in 10 of the 15 body sites tested. These associations are driven by host genetic variation in immunity-related pathways, and are especially enriched in host genes that have been previously associated with microbiome-related complex diseases, such as inflammatory bowel disease and obesity-related disorders. Lastly, we show that host genomic regions associated with the microbiome have high levels of genetic differentiation among human populations, possibly indicating host genomic adaptation to environment-specific microbiomes.ConclusionsOur results highlight the role of host genetic variation in shaping the composition of the human microbiome, and provide a starting point toward understanding the complex interaction between human genetics and the microbiome in the context of human evolution and disease.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0759-1) contains supplementary material, which is available to authorized users.

We present a complete 6-dimensional potential energy surface for the benzene dimer obtained using symmetry-adapted perturbation theory (SAPT) of intermolecular interactions based on Kohn-Sham's description of monomers. Ab initio calculations were performed for 491 dimer geometries in a triple-zeta-quality basis set supplemented by bond functions. An accurate analytic fit to the ab initio results has been developed and low-energy stationary points on the potential energy surface have been found. We have determined that there are three minima on the surface. Two of them, the tilted T-shape and the parallel-displaced, are nearly isoenergetic with interaction energies of -2.77 and -2.74 kcal/mol, respectively. The third minimum, a twisted edge-to-edge conformation, is significantly less attractive, with the interaction energy equal to -1.82 kcal/mol. Both the T-shape and sandwich geometries, sometimes assumed to be minima, are shown to be only saddle points. The potential energy surface is extremely flat between the two lowest minima, the barrier being only 0.10 kcal/mol above the global minimum. The second-virial coefficient obtained with the new potential agrees well with experimental results over a wide range of temperatures. The SAPT approach rigorously decomposes the interaction energy into physical components. The relative importance of these components has been analyzed.

A force field for water has been developed entirely from first principles, without any fitting to experimental data. It contains both pairwise and many-body interactions. This force field predicts the properties of the water dimer and of liquid water in excellent agreement with experiments, a previously elusive objective. Precise knowledge of the intermolecular interactions in water will facilitate a better understanding of this ubiquitous substance.

The symmetry-adapted perturbation theory (SAPT) has been employed to calculate an accurate potential energy curve for the helium dimer. For major components of the interaction energy, saturated values have been obtained using extended Gaussian-type geminal bases. Some other, less significant components were computed using a large orbital basis and the standard set of SAPT codes. The remaining small fraction of the interaction energy has been obtained using a nonstandard SAPT program specific for two-electron monomers and the supermolecular full configuration interaction (FCI) calculations in a moderately large orbital basis. Accuracy of the interaction energy components has been carefully examined. The most accurate to date values of the electrostatic, exchange, induction, and dispersion energies are reported for distances from 3.0 to 7.0 bohr. After adding the retardation correction predicted by the Casimir theory, our new potential has been shown [A. R. Janzen and R. A. Aziz (submitted)] to recover the known bulk and scattering data for helium more accurately than other existing ab initio and empirical potentials. However, the calculated dissociation energy of 1.713 mK and the bond length of 45.8 Å differ somewhat from the values inferred recently from a transmission experiment using nanoscale sieves.

A four-dimensional intermolecular potential energy surface for the carbon dioxide dimer has been computed using the many-body symmetry-adapted perturbation theory (SAPT) and a large 5s3p2d1f basis set including bond functions. The SAPT level applied is approximately equivalent to the supermolecular many-body perturbation theory at the second-order level. An accurate fit to the computed data has been obtained in a form of an angular expansion incorporating the asymptotic coefficients computed ab initio at the level consistent with the applied SAPT theory. A simpler site-site fit has also been developed to facilitate the use of the potential in molecular dynamics and Monte Carlo simulations. The quality of the new potential has been tested by computing the values of the second virial coefficient which agree very well with the experimental data over a wide range of temperatures. Our potential energy surface turns out to be substantially deeper than previous ab initio potentials. The minimum of −484 cm−1 has been found for the slipped parallel geometry at the intermolecular separation R=3.54 Å and a saddle point at −412 cm−1 for the T-shaped configuration and R=4.14 Å. Three minima and two first-order saddle points have been located on the pairwise-additive potential energy surface of the CO2 trimer. The nonplanar structure of C2 symmetry has been found to be 48.8 cm−1 more stable than the cyclic planar form of C3h symmetry, in disagreement with experimental observation. It is suggested that the relative stability of the two isomers cannot be reliably determined by pairwise-additive potential and inclusion of three-body forces is necessary for this purpose.

BackgroundCharacterization of genetic variations in maize has been challenging, mainly due to deterioration of collinearity between individual genomes in the species. An international consortium of maize research groups combined resources to develop the maize haplotype version 3 (HapMap 3), built from whole-genome sequencing data from 1218 maize lines, covering predomestication and domesticated Zea mays varieties across the world.ResultsA new computational pipeline was set up to process more than 12 trillion bp of sequencing data, and a set of population genetics filters was applied to identify more than 83 million variant sites.ConclusionsWe identified polymorphisms in regions where collinearity is largely preserved in the maize species. However, the fact that the B73 genome used as the reference only represents a fraction of all haplotypes is still an important limiting factor.

Background: Despite increasing popularity and improvements in terminal restriction fragment length polymorphism (T-RFLP) and other microbial community fingerprinting techniques, there are still numerous obstacles that hamper the analysis of these datasets. Many steps are required to process raw data into a format ready for analysis and interpretation. These steps can be timeintensive, error-prone, and can introduce unwanted variability into the analysis. Accordingly, we developed T-REX, free, online software for the processing and analysis of T-RFLP data.

The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a W22 reference genome using short-read sequencing technologies. We show that significant structural heterogeneity exists in comparison to the B73 reference genome at multiple scales, from transposon composition and copy number variation to single-nucleotide polymorphisms. The generation of this reference genome enables accurate placement of thousands of Mutator (Mu) and Dissociation (Ds) transposable element insertions for reverse and forward genetics studies. Annotation of the genome has been achieved using RNA-seq analysis, differential nuclease sensitivity profiling and bisulfite sequencing to map open reading frames, open chromatin sites and DNA methylation profiles, respectively. Collectively, the resources developed here integrate W22 as a community reference genome for functional genomics and provide a foundation for the maize pan-genome.