Choice of DNA extraction method affects stool microbiome recovery and subsequent phenotypic association analyses

The lack of standardization in the methods of DNA extraction from fecal samples represents the major source of experimental variation in the microbiome research field. In this study, we aimed to compare the metagenomic profiles and microbiome-phenotype associations obtained by applying two commercially available DNA extraction kits: the AllPrep DNA/RNA Mini Kit (APK) and the QIAamp Fast DNA Stool Mini Kit (FSK). Using metagenomic sequencing data available from 745 paired fecal samples from two independent population cohorts, Lifelines-DEEP (LLD, n = 292) and the 500 Functional Genomics project (500FG, n = 453), we confirmed significant differences in DNA yield and the recovered microbial communities between protocols, with the APK method resulting in a higher DNA concentration and microbial diversity. Further, we observed a massive difference in bacterial relative abundances at species-level between the APK and the FSK protocols, with > 75% of species differentially abundant between protocols in both cohorts. Specifically, comparison with a standard mock community revealed that the APK method provided higher accuracy in the recovery of microbial relative abundances, with the absence of a bead-beating step in the FSK protocol causing an underrepresentation of gram-positive bacteria. This heterogeneity in the recovered microbial composition led to remarkable differences in the association with anthropometric and lifestyle phenotypes. The results of this study further reinforce that the choice of DNA extraction method impacts the metagenomic profile of human gut microbiota and highlight the importance of harmonizing protocols in microbiome studies.

Deeply nonlinear excitation of self-normalized short spin waves

Spin waves are ideal candidates for wave-based computing, but the construction of magnetic circuits is blocked by a lack of an efficient mechanism to excite long-running exchange spin waves with normalized amplitudes. Here, we solve the challenge by exploiting a deeply nonlinear phenomenon for forward volume spin waves in 200-nm-wide nanoscale waveguides and validate our concept using microfocused Brillouin light scattering spectroscopy. An unprecedented nonlinear frequency shift of more than 2 GHz is achieved, corresponding to a magnetization precession angle of 55° and enabling the excitation of spin waves with wavelengths down to 200 nm. The amplitude of the excited spin waves is constant and independent of the input microwave power due to the self-locking nonlinear shift, enabling robust adjustment of the spin-wave amplitudes in future on-chip magnonic integrated circuits.