Background COVID-19 vaccines show excellent efficacy in clinical trials and effectiveness in real-world data, but some people still become infected with SARS-CoV-2 after vaccination. This study aimed to identify risk factors for post-vaccination SARS-CoV-2 infection and describe the characteristics of post-vaccination illness. Methods This prospective, community-based, nested, case-control study used self-reported data (eg, on demographics, geographical location, health risk factors, and COVID-19 test results, symptoms, and vaccinations) from UK-based, adult (≥18 years) users of the COVID Symptom Study mobile phone app. For the risk factor analysis, cases had received a first or second dose of a COVID-19 vaccine between Dec 8, 2020, and July 4, 2021; had either a positive COVID-19 test at least 14 days after their first vaccination (but before their second; cases 1) or a positive test at least 7 days after their second vaccination (cases 2); and had no positive test before vaccination. Two control groups were selected (who also had not tested positive for SARS-CoV-2 before vaccination): users reporting a negative test at least 14 days after their first vaccination but before their second (controls 1) and users reporting a negative test at least 7 days after their second vaccination (controls 2). Controls 1 and controls 2 were matched (1:1) with cases 1 and cases 2, respectively, by the date of the post-vaccination test, health-care worker status, and sex. In the disease profile analysis, we sub-selected participants from cases 1 and cases 2 who had used the app for at least 14 consecutive days after testing positive for SARS-CoV-2 (cases 3 and cases 4, respectively). Controls 3 and controls 4 were unvaccinated participants reporting a positive SARS-CoV-2 test who had used the app for at least 14 consecutive days after the test, and were matched (1:1) with cases 3 and 4, respectively, by the date of the positive test, health-care worker status, sex, body-mass index (BMI), and age. We used univariate logistic regression models (adjusted for age, BMI, and sex) to analyse the associations between risk factors and post-vaccination infection, and the associations of individual symptoms, overall disease duration, and disease severity with vaccination status. Findings Between Dec 8, 2020, and July 4, 2021, 1 240 009 COVID Symptom Study app users reported a first vaccine dose, of whom 6030 (0·5%) subsequently tested positive for SARS-CoV-2 (cases 1), and 971 504 reported a second dose, of whom 2370 (0·2%) subsequently tested positive for SARS-CoV-2 (cases 2). In the risk factor analysis, frailty was associated with post-vaccination infection in older adults (≥60 years) after their first vaccine dose (odds ratio [OR] 1·93, 95% CI 1·50–2·48; p<0·0001), and individuals living in highly deprived areas had increased odds of post-vaccination infection following their first vaccine dose (OR 1·11, 95% CI 1·01–1·23; p=0·039). Individuals without obesity (...

The gut microbiome is shaped by diet and influences host metabolism, but these links are complex and can be unique to each individual. We performed deep metagenomic sequencing of >1,100 gut microbiomes from individuals with detailed long-term diet information, as well as hundreds of fasting and same-meal postprandial cardiometabolic blood marker measurements. We found strong associations between microbes and specific nutrients, foods, food groups, and general dietary indices, driven especially by the presence and diversity of healthy and plant-based foods. Microbial biomarkers of obesity were reproducible across cohorts, and blood markers of cardiovascular disease and impaired glucose tolerance were more strongly associated with microbiome structure. While some microbes such as Prevotella copri and Blastocystis spp., were indicators of reduced postprandial glucose metabolism, several species were more directly predictive for postprandial triglycerides and C-peptide. The panel of intestinal species associated with healthy dietary habits overlapped with those associated with favourable cardiometabolic and postprandial markers, indicating our large-scale resource can potentially stratify the gut microbiome into generalizable health levels among individuals without clinically manifest disease. Fig. 1: The PREDICT 1 study associates gut microbiome structure with habitual diet and blood cardiometabolic markers. (A)The PREDICT 1 study assessed the gut microbiome of 1,098 volunteers from the UK and US via metagenomic sequencing of stool samples. Phenotypic data obtained through in-person assessment, blood/biospecimen collection, and the return of validated study questionnaires queried a range of relevant host/environmental factors including (1) personal characteristics, such as age, BMI, and estimated visceral fat; (2) habitual dietary intake using semi-quantitative food frequency questionnaires (FFQs);(3) fasting; and (4) postprandial cardiometabolic blood and inflammatory markers, total lipid and lipoprotein concentrations, lipoprotein particle sizes, apolipoproteins, derived metabolic risk scores, glycaemic-mediated metabolites, and metabolites related to fatty acid metabolism. (B) Overall microbiome alpha diversity, estimated as the total number of confidently identified microbial species in a given sample (richness), was correlated with HDL-D (positive) and estimated hepatic steatosis (negative). Up to ten strongest absolute Spearman correlations are reported for each category with q<0.05. Top species based on Shannon diversity are reported in Supplementary Fig. 1A and all correlations are in Supplementary Table 1. Microbial diversity and composition are linked with diet and fasting and postprandial biomarkersWe first leveraged a unique subpopulation of our study comprised of 480 twins to disentangle the confounding effects of shared genetics from other factors on microbiome composition. Our data confirmed that host genetics influences microbiome composition only to a small extent 18 , as intra-twin pair microbiome ...

(Figure 2c), and less than 1% of variation for postprandial triglyceride and postprandial C-peptide (Figure 2b and 2d). Gut microbiome (16S rRNA). We estimated the contribution of gut microbiome composition using relative bacterial taxonomic abundances and measures of community diversity and richness, derived from 16S rRNA high-throughput sequencing of baseline stool specimens (Supplemental Table 4). We found that without adjusting for any other individual characteristics the gut microbiome composition explained 7.5% of postprandial triglyceride6h-rise, 6.4% of postprandial glucoseiAUC0-2h and 5.8% of postprandial C-peptide1h-rise. Meal composition, habitual diet and meal context. To determine the impact of the macronutrient composition of meals, we measured triglyceride6h-rise and C-peptide1h-rise for two standardized home phase meals of contrasting macronutrient compositions (for triglyceride, comparison of meals 1 and 7: 85 vs 28g of carbohydrate and 50 vs 40 g of fat at breakfast, both followed by a lunch of 71g carbohydrate and 22g fat; for C-peptide, comparison of meal 2 and 3: 71 vs 41 g of carbohydrate and 22 vs 35 g of fat; Supplement Table 2) in subsets of participants (n=712 and n=186, respectively). GlucoseiAUC0-2h was measured for seven standardized meals (comparison of meals 1, 2, 4, 5, 6, 7 and 8: 28 -95 g carbohydrate; 0 -53 g fat) totalling 9,102 meals in 920 individuals. The proportions of variance explained by meal composition, habitual diet, and by meal context are shown for triglyceride6h-risein Figure 2b, for glucoseiAUC0-2hin Figure 2c, and for C-peptide1h-risein Figure 2d. A multivariate regression model (meals 1, 2, 4, 5, 6, 7 and 8) revealed that the Glucosei AUC0-2h (mmol/L*s) was significantly (P<0.001) reduced by 79, 142 and 185 for every 1g fat, fiber and protein respectively, after adjustment for carbohydrate consumption. Machine learning model. To estimate the unbiased predictive utility of the factors analysed, we used a machine learning approach robust to overfitting 22 . Random Forest regression models 23 were fitted using all the informative features (meal composition, habitual diet, meal context, anthropometry, genetics, microbiome, clinical and biochemical parameters) to predict triglyceride6h10 described in the Methods, we considered not only the effect of the meal macronutrient and energy content in the response (meal composition), but also considered how each individual responded on average to all their set meals relative to the population (individual glucose scaling), as well as the effect of the individual's meal-specific response, the error attributable to the glucose measurement and other sources of variation (including modifiable sources of variation such as sleep, circadian rhythm and exercise). We found that, consistent with the linear models described earlier, the ANOVA models show that there are three meal-related factors explaining individual glycemic responses. Meal macronutrient composition alters iAUC by 16.73% (95%CI 15.37 -18.92%), but the individual glucose...

Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms from most metagenomes. Here we present MetaPhlAn 4, which integrates information from metagenome assemblies and microbial isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference and metagenome-assembled genomes, we define unique marker genes for 26,970 species-level genome bins, 4,992 of them taxonomically unidentified at the species level. MetaPhlAn 4 explains ~20% more reads in most international human gut microbiomes and >40% in less-characterized environments such as the rumen microbiome and proves more accurate than available alternatives on synthetic evaluations while also reliably quantifying organisms with no cultured isolates. Application of the method to >24,500 metagenomes highlights previously undetected species to be strong biomarkers for host conditions and lifestyles in human and mouse microbiomes and shows that even previously uncharacterized species can be genetically profiled at the resolution of single microbial strains.

The position of fatty acids in the TAG molecule (sn-1, sn-2 and sn-3) determines the physical properties of the fat, which affects its absorption, metabolism and distribution into tissues, which may have implications for the risk of CHD. The TAG structure of fats can be manipulated by the process of interesterification, which is of increasing commercial importance, as it can be used to change the physical characteristics of a fat without the generation of trans-fatty acids. Interesterified fats rich in long-chain SFA are commercially important, but few studies have investigated their health effects. Evidence from animal and human infant studies suggests that TAG structure and interesterification affect digestibility, atherogenicity and fasting lipid levels, with fats containing palmitic and stearic acid in the sn-2 position being better digested and considered to be more atherogenic. However, chronic studies in human adults suggest that TAG structure has no effect on digestibility or fasting lipids. The postprandial effects of fats with differing TAG structure are better characterised but the evidence is inconclusive; it is probable that differences in the physical characteristics of fats resulting from interesterification and changes in TAG structure are key determinants of the level of postprandial lipaemia, rather than the position of fatty acids in the TAG. The present review gives an overview of TAG structure and interesterified palmitic and stearic acid-rich fats, their physical properties and their acute and chronic effects in human adults in relation to CHD.