Health-related quality of life is linked to the gut microbiome in kidney transplant recipients.

Kidney transplant recipients (KTR) have impaired health-related quality of life (HRQoL) and suffer from intestinal dysbiosis. Increasing evidence shows that gut health and HRQoL are tightly related in the general population. Here, we investigate the association between the gut microbiome and HRQoL in KTR, using metagenomic sequencing data from fecal samples collected from 507 KTR.

Association of a Mediterranean Diet With Outcomes for Patients Treated With Immune Checkpoint Blockade for Advanced Melanoma.

Importance: Immune checkpoint blockade (ICB) has improved the survival of patients with advanced melanoma. Durable responses are observed for 40% to 60% of patients, depending on treatment regimens. However, there is still large variability in the response to treatment with ICB, and patients experience a range of immune-related adverse events of differing severity.

Quantum dynamics of the Br (B-excited state) photodissociation in superfluid helium nanodroplets: importance of the recombination process.

We have studied the Br photodissociation dynamics (B ← X electronic transition) of Br( = 0, X)@(He) doped nanodroplets ( = 0.37 K) at zero angular momentum, with in the 100-1000 interval. To do this, we have used a quantum mechanical hybrid strategy proposed by us and, as far as we know, this is the second quantum dynamics study available on the photodissociation of molecules in superfluid helium nanodroplets.

Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project.

Host genetics are known to influence the gut microbiome, yet their role remains poorly understood. To robustly characterize these effects, we performed a genome-wide association study of 207 taxa and 205 pathways representing microbial composition and function in 7,738 participants of the Dutch Microbiome Project. Two robust, study-wide significant (P < 1.

Discovery, diversity, and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts.

The crAss-like phages are a diverse group of related viruses that includes some of the most abundant viruses of the human gut. To explore their diversity and functional role in human population and clinical cohorts, we analyze gut metagenomic data collected from 1,950 individuals from the Netherlands. We identify 1,556 crAss-like phage genomes, including 125 species-level and 32 genus-level clusters absent from the reference databases used.

Gut microbiota in inflammatory bowel diseases: moving from basic science to clinical applications.

In recent years, large efforts have been made to unravel the role of the gut microbiota in inflammatory bowel disease (IBD), which is a chronic inflammatory disorder of the gastro-intestinal tract. Considering the heterogeneity patients with IBD display in their disease course and response to treatment, there is a big need in translating these findings towards clinical practise. In this perspective article, we discuss strategies to facilitate the transition from basic science on gut microbiota in IBD to clinical applications.

Quantum-classical approach to the reaction dynamics in a superfluid helium nanodroplet. The Ne dimer and Ne-Ne adduct formation reaction Ne + Ne-doped nanodroplet.

The dynamics of the Ne dimer and Ne-Ne adduct formation in a superfluid helium nanodroplet [(He); T = 0.37 K], Ne + Ne@(He)→ Ne@(He)/Ne-Ne@(He) + (N-N')He with N = 500, has been investigated using a hybrid approach (quantum and classical mechanics (QM-CM) descriptions for helium and the Ne atoms, respectively) and taking into account the angular momentum of the attacking Ne atom, Ne. Comparison with zero angular momentum QM results of our own shows that the present results are similar to the quantum ones for the initial Ne velocities (v) of 500 and 800 m s (the former one being the most probable velocity of Ne at 300 K), in all cases leading to the Ne dimer (r = 3.

Rotational energy relaxation quantum dynamics of a diatomic molecule in a superfluid helium nanodroplet and study of the hydrogen isotopes case.

The rotational energy relaxation (RER) of a molecule X2(j,mj) in a 4He superfluid nanodroplet [HeND or (4He)N; T = 0.37 K] has been investigated using a hybrid quantum dynamics approach recently proposed by us. As far as we know, this is the first theoretical study about rotational relaxation inside HeNDs, and here several (real and hypothetical) isotopes of H2 have been examined, in order to analyze the influence of the rotational constant Be of these fast rotors on the dynamics.

Quantum-classical dynamics of the capture of neon atoms by superfluid helium nanodroplets.

The capture of a Ne atom by a superfluid helium nanodroplet, Ne + (4He)N → Ne@(4He)N' + (N - N') 4He, was studied using a hybrid quantum (helium)-classical (Ne) approach and taking into account the angular momentum. The atom is captured by (4He)N and follows elliptical rotating trajectories, and large energy and angular momentum transfer from the atom to the nanodroplet occur. Evaporation of helium atoms from (4He)N allows removal of the excess energy and angular momentum of the doped nanodroplet.

Shared gut, but distinct oral microbiota composition in primary Sjögren's syndrome and systemic lupus erythematosus.

Objective: Alterations in the microbiota composition of the gastro-intestinal tract are suspected to be involved in the etiopathogenesis of two closely related systemic inflammatory autoimmune diseases: primary Sjögren's syndrome (pSS) and systemic lupus erythematosus (SLE). Our objective was to assess whether alterations in gut and oral microbiota compositions are specific for pSS and SLE.

Methods: 16S ribosomal RNA gene sequencing was performed on fecal samples from 39 pSS patients, 30 SLE patients and 965 individuals from the general population, as well as on buccal swab and oral washing samples from the same pSS and SLE patients.

Pharmacomicrobiomics: a novel route towards personalized medicine?

Inter-individual heterogeneity in drug response is a serious problem that affects the patient's wellbeing and poses enormous clinical and financial burdens on a societal level. Pharmacogenomics has been at the forefront of research into the impact of individual genetic background on drug response variability or drug toxicity, and recently the gut microbiome, which has also been called the second genome, has been recognized as an important player in this respect. Moreover, the microbiome is a very attractive target for improving drug efficacy and safety due to the opportunities to manipulate its composition.

Environment dominates over host genetics in shaping human gut microbiota.

Human gut microbiome composition is shaped by multiple factors but the relative contribution of host genetics remains elusive. Here we examine genotype and microbiome data from 1,046 healthy individuals with several distinct ancestral origins who share a relatively common environment, and demonstrate that the gut microbiome is not significantly associated with genetic ancestry, and that host genetics have a minor role in determining microbiome composition. We show that, by contrast, there are significant similarities in the compositions of the microbiomes of genetically unrelated individuals who share a household, and that over 20% of the inter-person microbiome variability is associated with factors related to diet, drugs and anthropometric measurements.

Vibrational energy relaxation dynamics of diatomic molecules inside superfluid helium nanodroplets. The case of the I molecule.

The vibrational energy relaxation (VER) of a homonuclear diatomic molecule (X) in a He superfluid nanodroplet (HeND; T = 0.37 K) was studied adapting appropriately a hybrid theoretical quantum approach recently proposed by us. In the first application the interesting case of the I(X) molecule was examined and, as far as we know, this corresponds to the first theoretical investigation on the VER of molecules embedded in HeND.

Reaction dynamics inside superfluid helium nanodroplets: the formation of the Ne molecule from Ne + Ne@(He).

A hybrid time dependent quantum dynamics approach [DFT (helium) + quantum wave packet (dopant)] proposed by us (J. Chem. Theory Comput.

The effect of host genetics on the gut microbiome.

The gut microbiome is affected by multiple factors, including genetics. In this study, we assessed the influence of host genetics on microbial species, pathways and gene ontology categories, on the basis of metagenomic sequencing in 1,514 subjects. In a genome-wide analysis, we identified associations of 9 loci with microbial taxonomies and 33 loci with microbial pathways and gene ontology terms at P < 5 × 10.

Mass effects in the photodissociation of homonuclear diatomic molecules in helium nanodroplets: inelastic collision and viscous flow energy exchange regimes.

The influence of the mass in the photodissociation dynamics of a homonuclear diatomic molecule (X), embedded in a superfluid helium nanodroplet (T = 0.37 K) of 300 atoms, has been investigated using a hybrid quantum dynamics method recently proposed by us. Several hypothetical isotopic variants of Cl have been examined in order to make possible the analysis of a wide diversity of masses (m: 0.

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.

Deep sequencing of the gut microbiomes of 1135 participants from a Dutch population-based cohort shows relations between the microbiome and 126 exogenous and intrinsic host factors, including 31 intrinsic factors, 12 diseases, 19 drug groups, 4 smoking categories, and 60 dietary factors. These factors collectively explain 18.7% of the variation seen in the interindividual distance of microbial composition.

Relaxation dynamics of helium nanodroplets after photodissociation of a dopant homonuclear diatomic molecule. The case of Cl2@((4)He)(N).

To investigate the quantum dynamics of the relaxation process of excited helium nanodroplets, (4)HeN, arising from the photodissociation of Cl2 embedded molecules (B ← X electronic transition), here we have performed a time dependent density functional theory (TDDFT) study considering nanodroplets of different sizes (N = 50, 100, 200, 300 and 500), extending a previous study which was centered on the photodissociation step. The relaxation process takes place in the timescale of several hundred picoseconds and a simple dependence of this process on time has been found. The results have been satisfactorily analyzed in terms of a phenomenological model proposed here and also by applying the Rice-Ramsperger-Kassel (RRK) statistical chemical kinetic model for unimolecular reactions.

Quantum dynamics of the pick up process of atoms by superfluid helium nanodroplets: the Ne + ((4)He)1000 system.

The capture dynamics of a Ne atom by a superfluid helium nanodroplet (((4)He)N=1000; T = 0.37 K), Ne + ((4)He)N→ Ne@((4)He)N', was investigated using a quantum approach (TDDFT (helium) + quantum wave packet (Ne)) at zero angular momentum and a rather wide range of Ne atom initial mean velocities (〈v0〉: 90-1300 m s(-1)). This is probably the first quantum dynamics study focusing on the pick up process and the evolution of the dopant inside the nanodroplet and the second more detailed investigation on this topic.

Quantum interferences in the photodissociation of Cl2(B) in superfluid helium nanodroplets ((4)He)N.

Quantum interferences are probably one of the most fascinating phenomena in chemical physics and, particularly, in reaction dynamics, where they are often very elusive from an experimental perspective. Here, we have theoretically investigated, using a hybrid method recently proposed by us, the dynamics of the formation of confinement quantum interferences in the photodissociation of a Cl2 molecule (B ← X electronic excitation) embedded in a superfluid helium nanodroplet of different sizes (50-500 (4)He atoms), which is to the best of our knowledge the first time that this type of interference is described in reaction dynamics. Thus, we have widely extended a recent contribution of our group, where interferences were not the main target, identifying the way they are formed and lead to the production of strongly oscillating velocity distributions in the Cl dissociating atoms, and also paying attention to the energy transfer processes involved.

Photodissociation Dynamics of Homonuclear Diatomic Molecules in Helium Nanodroplets. The Case of Cl₂@(⁴He)N.

To investigate the photodissociation dynamics of diatomic homonuclear molecules in helium nanodroplets, a hybrid quantum mechanical theoretical method that combines time dependent density functional theory (helium) and quantum dynamics (molecule) has been developed. This method has been applied to investigate the Cl2 photodissociation arising from the B ← X electronic transition, considering Cl2(v = 0,X)@((4)He)N nanodroplets with N = 50, 100, 200, 300, and 500 (initial configuration for the dynamics). A time scale of a few picoseconds has been determined, and the time required for the dissociating atoms to reach the nanodroplet surface increases with N.

Identification of Clinical and Genetic Parameters Associated with Hidradenitis Suppurativa in Inflammatory Bowel Disease.

Background: Hidradenitis suppurativa (HS) has recently been associated with inflammatory bowel disease (IBD). The objective of this study is to investigate the prevalence of HS in IBD and to identify clinical and genetic parameters associated with HS in IBD.

Methods: A questionnaire, validated for HS, was sent to 1969 patients suffering from IBD.