Controllable Andreev Bound States in Bilayer Graphene Josephson Junctions from Short to Long Junction Limits.

We demonstrate that the mode number of Andreev bound states in bilayer graphene Josephson junctions can be modulated by controlling the superconducting coherence length in situ. By exploiting the quadratic band dispersion of bilayer graphene, we control the Fermi velocity and thus the coherence length via the application of electrostatic gating. Tunneling spectroscopy of the Andreev bound states reveals a crossover from short to long Josephson junction regimes as we approach the charge neutral point of the bilayer graphene. Furthermore, analysis of different mode numbers of the Andreev energy spectrum allows us to estimate the phase-dependent Josephson current quantitatively. Our Letter provides a new way for studying multimode Andreev levels by tuning the Fermi velocity.

EzBioCloud: a genome-driven database and platform for microbiome identification and discovery.

With the continued evolution of DNA sequencing technologies, the role of genome sequence data has become more integral in the classification and identification of Bacteria and Archaea. Six years after introducing EzBioCloud, an integrated platform representing the taxonomic hierarchy of Bacteria and Archaea through quality-controlled 16S rRNA gene and genome sequences, we present an updated version, that further refines and expands its capabilities. The current update recognizes the growing need for accurate taxonomic information as defining a species increasingly relies on genome sequence comparisons. We also incorporated an advanced strategy for addressing underrepresented or less studied lineages, bolstering the comprehensiveness and accuracy of our database. Our rigorous quality control protocols remain, where whole-genome assemblies from the NCBI Assembly Database undergo stringent screening to remove low-quality sequence data. These are then passed through our enhanced identification bioinformatics pipeline which initiates a 16S rRNA gene similarity search and then calculates the average nucleotide identity (ANI). For genome sequences lacking a 16S rRNA sequence and without a closely related genomic representative for ANI calculation, we apply a different ANI approach using bacterial core genes for improved taxonomic placement (core gene ANI, cgANI). Because of the increase in genome sequences available in NCBI and our newly introduced cgANI method, EzBioCloud now encompasses a total of 109 835 species, of which 21 964 have validly published names. 47 896 are candidate species identified either through 16S rRNA sequence similarity (phylotypes) or through whole genome ANI (genomospecies), and the remaining 39 975 were positioned in the taxonomic tree by cgANI (species clusters). Our EzBioCloud database is accessible at www.ezbiocloud.net/db.

Compositional Changes in the Gut Microbiota of Responders and Non-responders to Probiotic Treatment Among Patients With Diarrhea-predominant Irritable Bowel Syndrome: A Post Hoc Analysis of a Randomized Clinical Trial.

Background/Aims: We aim to evaluate the differences in the microbiome of responders and non-responders, as well as predict the response to probiotic therapy, based on fecal microbiome data in patients with diarrhea-predominant irritable bowel syndrome (IBS-D). Methods: A multi-strain probiotics that contains Lactobacillus acidophilus (KCTC 11906BP), Lactobacillus plantarum (KCTC11867BP), Lactobacillus rhamnosus (KCTC 11868BP), Bifidobacterium breve (KCTC 11858BP), Bifidobacterium lactis (KCTC 11903BP), Bifidobacterium longum (KCTC 11860BP), and Streptococcus thermophilus (KCTC 11870BP) were used. Patients were categorized into probiotic and placebo groups, and fecal samples were collected from all patients before and at the end of 8 weeks of treatment. The probiotic group was further divided into responders and non-responders. Responders were defined as patients who experienced adequate relief of overall irritable bowel syndrome symptoms after probiotic therapy. Fecal microbiota were investigated using Illumina MiSeq and analyzed using the EzBioCloud 16S database and microbiome pipeline (https://www.EZbiocloud.net). Results: There was no significant difference in the alpha and beta diversity between the responder and non-responder groups. The abundances of the phylum Proteobacteria and genus Bacteroides significantly decreased after probiotic treatment. Bifidobacterium bifidum, Pediococcus acidilactici, and Enterococcus faecium showed a significantly higher abundance in the probiotic group after treatment compared to the placebo group. Enterococcus faecalis and Lactococcus lactis were identified as biomarkers of non-response to probiotics. The abundance of Fusicatenibacter saccharivorans significantly increased in the responders after treatment. Conclusions: Probiotic treatment changes some composition of fecal bacteria in patients with IBS-D. E. faecalis and L. lactis may be prediction biomarkers for non-response to probiotics. Increased abundance of F. sccharivorans is correlated to symptom improvement by probiotics in patients with IBS-D.

Steady Floquet-Andreev states in graphene Josephson junctions.

Engineering quantum states through light-matter interaction has created a paradigm in condensed-matter physics. A representative example is the Floquet-Bloch state, which is generated by time-periodically driving the Bloch wavefunctions in crystals. Previous attempts to realize such states in condensed-matter systems have been limited by the transient nature of the Floquet states produced by optical pulses1-3, which masks the universal properties of non-equilibrium physics. Here we report the generation of steady Floquet-Andreev states in graphene Josephson junctions by continuous microwave application and direct measurement of their spectra by superconducting tunnelling spectroscopy. We present quantitative analysis of the spectral characteristics of the Floquet-Andreev states while varying the phase difference of the superconductors, the temperature, the microwave frequency and the power. The oscillations of the Floquet-Andreev-state spectrum with phase difference agreed with our theoretical calculations. Moreover, we confirmed the steady nature of the Floquet-Andreev states by establishing a sum rule of tunnelling conductance4, and analysed the spectral density of Floquet states depending on Floquet interaction strength. This study provides a basis for understanding and engineering non-equilibrium quantum states in nanodevices.

Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity.

The average amino acid identity (AAI) is an index of pairwise genomic relatedness, and multiple studies have proposed its application in prokaryotic taxonomy and related disciplines. AAI demonstrates better resolution in elucidating taxonomic structure beyond the species rank when compared with average nucleotide identity (ANI), which is a standard criterion in species delineation. However, an efficient and easy-to-use computational tool for AAI calculation in large-scale taxonomic studies is not yet available. Here, we introduce a bioinformatic pipeline, named EzAAI, which allows for rapid and accurate AAI calculation in prokaryote sequences. The EzAAI tool is based on the MMSeqs2 program and computes AAI values almost identical to those generated by the standard BLAST algorithm with significant improvements in the speed of these evaluations. Our pipeline also provides a function for hierarchical clustering to create dendrograms, which is an essential part of any taxonomic study. EzAAI is available for download as a standalone JAVA program at http://leb.snu.ac.kr/ezaai .

Rice straw cover decreases soil erosion and sediment-bound C, N, and P losses but increases dissolved organic C export from upland maize fields as evidenced by δ13C.

Soil surface with crop residue is effective in reducing soil erosion and carbon (C), nitrogen (N), and phosphorus (P) losses from sloping fields. However, there is a high possibility that surface cover increases export of dissolved organic C (DOC) though relevant field studies under natural rainfall are lacking. In this study, the effects of surface cover with rice (Oryza sativa L.) straw on soil and CNP losses in both dissolved and sediment-bound forms from maize (Zea mays L.) fields were investigated under two fertilization levels (standard and double) × two types of runoff experiments (natural rainfall and artificial irrigation). Changes in soil properties including moisture, temperature, nutrients, and C concentration as well as maize yield were also examined. Surface cover decreased soil and total CNP losses by up to 82% across the experimental plots with some exceptions. However, surface cover increased DOC export in both natural (by 68-82% in total across all events) and artificial (by 3-4 fold) runoff, suggesting that crop residue cover may act as a DOC pollution source of water bodies. The contribution of rice straw to DOC, which was calculated using the δ13C of DOC from covered plots (-24.1 to -28.0‰) and control plots (-19.6 to -25.1‰), was 52.5-95.8%. The concentrations of K2SO4-extractable and microbial biomass C of the soils did not differ between covered and control plots, suggesting that DOC produced from rice straw was not incorporated into the soils, but rather, was washed out with surface runoff in this study. Surface cover increased maize growth and yield, particularly in double fertilization plots, through improved soil moisture, temperature, and nutrient conditions. To take full advantage of surface cover with crop residue, a further study on reducing DOC loss from crop residue needs to be conducted.

Metagenomic Association Analysis of Gut Symbiont Limosilactobacillus reuteri Without Host-Specific Genome Isolation.

Limosilactobacillus reuteri is a model symbiont that colonizes the guts of vertebrates in studies on host adaptation of the gut symbiont. Previous studies have investigated host-specific phylogenetic and functional properties by isolating the genomic sequence. This dependency on genome isolation is a significant bottleneck. Here, we propose a method to study the association between L. reuteri and its hosts directly from metagenomic reads without strain isolation using pan-genomes. We characterized the host-specificity of L. reuteri in metagenomic samples, not only in previously studied organisms (mice and pigs) but also in dogs. For each sample, two types of profiles were generated: (1) genome-based strain type abundance profiles and (2) gene composition profiles. Our profiles showed host-association of L. reuteri in both phylogenetic and functional aspects without depending on host-specific genome isolation. We observed not only the presence of host-specific lineages, but also the dominant lineages associated with the different hosts. Furthermore, we showed that metagenome-assembled genomes provide detailed insights into the host-specificity of L. reuteri. We inferred evolutionary trajectories of host-associative L. reuteri strains in the metagenomic samples by placing the metagenome-assembled genomes into a phylogenetic tree and identified novel host-specific genes that were unannotated in existing pan-genome databases. Our pan-genomic approach reduces the need for time-consuming and expensive host-specific genome isolation, while producing consistent results with previous host-association findings in mice and pigs. Additionally, we predicted associations that have not yet been studied in dogs.

Introducing Murine Microbiome Database (MMDB): A Curated Database with Taxonomic Profiling of the Healthy Mouse Gastrointestinal Microbiome.

The gut microbiota modulates overall metabolism, the immune system and brain development of the host. The majority of mammalian gut microbiota consists of bacteria. Among various model animals, the mouse has been most widely used in pre-clinical biological experiments. The significant compositional differences in taxonomic profiles among different mouse strains due to gastrointestinal locations, genotypes and vendors have been well documented. However, details of such variations are yet to be elucidated. This study compiled and analyzed 16S rRNA gene-based taxonomic profiles of 554 healthy mouse samples from 14 different projects to construct a comprehensive database of the microbiome of a healthy mouse gastrointestinal tract. The database, named Murine Microbiome Database, should provide researchers with useful taxonomic information and better biological insight about how each taxon, such as genus and species, is associated with locations in the gastrointestinal tract, genotypes and vendors. The database is freely accessible over the Internet at http://leb.snu.ac.kr/mmdb/.

Fly ash and zeolite decrease metal uptake but do not improve rice growth in paddy soils contaminated with Cu and Zn.

Fly ash (FA) and zeolite (Z) are known to reduce bioavailability of metals in soils via immobilization; however, these amendments may not only immobilize metals such as copper (Cu) and zinc (Zn), but also reduce nitrogen (N) and phosphorus (P) availability in the soils via sorption (for N by Z) and precipitation (for P by FA). This study was conducted to evaluate the effects of application of FA and Z (0, 5, and 10% rate) on the availability of nutrients as well as metals in the metal-contaminated soils cultivated with paddy rice (Oryza sativa L.). Both FA and Z reduced Cu and Zn uptake by rice while increasing metal retention in the soils regardless of the application rates. However, reduced uptake of metals did not translate into increase in rice growth, especially at the 10% of amendment rates, due to decreased nutrient uptake as indicated by higher NH4+ and available P concentration in the soils amended with Z and FA, respectively, which inhibited tillering in the early rice growth period and thus reduced biomass accumulation at maturity. Our results suggest that FA and Z may reduce Cu and Zn uptake by rice in the soils contaminated with the metals; however, the availability of N and P is likely to be co-decreased. We suggest that the capacities of FA and Z to immobilize nutrients as well as metals need to be considered prior to using the amendments in metal-contaminated rice paddies.