Estimating the overall fraction of phenotypic variance attributed to high-dimensional predictors measured with error.

In prospective genomic studies (e.g., DNA methylation, metagenomics, and transcriptomics), it is crucial to estimate the overall fraction of phenotypic variance (OFPV) attributed to the high-dimensional genomic variables, a concept similar to heritability analyses in genome-wide association studies (GWAS). Unlike genetic variants in GWAS, these genomic variables are typically measured with error due to technical limitation and temporal instability. While the existing methods developed for GWAS can be used, ignoring measurement error may severely underestimate OFPV and mislead the design of future studies. Assuming that measurement error variances are distributed similarly between causal and noncausal variables, we show that the asymptotic attenuation factor equals to the average intraclass correlation coefficients of all genomic variables, which can be estimated based on a pilot study with repeated measurements. We illustrate the method by estimating the contribution of microbiome taxa to body mass index and multiple allergy traits in the American Gut Project. Finally, we show that measurement error does not cause meaningful bias when estimating the correlation of effect sizes for two traits.

A multi-bin rarefying method for evaluating alpha diversities in TCR sequencing data.

MOTIVATION: T cell receptors (TCRs) constitute a major component of our adaptive immune system, governing the recognition and response to internal and external antigens. Studying the TCR diversity via sequencing technology is critical for a deeper understanding of immune dynamics. However, library sizes differ substantially across samples, hindering the accurate estimation/comparisons of alpha diversities. To address this, researchers frequently use an overall rarefying approach in which all samples are sub-sampled to an even depth. Despite its pervasive application, its efficacy has never been rigorously assessed. RESULTS: In this paper, we develop an innovative "multi-bin" rarefying approach that partitions samples into multiple bins according to their library sizes, conducts rarefying within each bin for alpha diversity calculations, and performs meta-analysis across bins. Extensive simulations using real-world data highlight the inadequacy of the overall rarefying approach in controlling the confounding effect of library size. Our method proves robust in addressing library size confounding, outperforming competing normalization strategies by achieving better-controlled type-I error rates and enhanced statistical power in association tests. AVAILABILITY AND IMPLEMENTATION: The code is available at https://github.com/mli171/MultibinAlpha. The datasets are freely available at https://doi.org/10.21417/B7001Z and https://doi.org/10.21417/AR2019NC. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Admix-kit: an integrated toolkit and pipeline for genetic analyses of admixed populations.

SUMMARY: Admixed populations, with their unique and diverse genetic backgrounds, are often underrepresented in genetic studies. This oversight not only limits our understanding but also exacerbates existing health disparities. One major barrier has been the lack of efficient tools tailored for the special challenges of genetic studies of admixed populations. Here, we present admix-kit, an integrated toolkit and pipeline for genetic analyses of admixed populations. Admix-kit implements a suite of methods to facilitate genotype and phenotype simulation, association testing, genetic architecture inference, and polygenic scoring in admixed populations. AVAILABILITY AND IMPLEMENTATION: Admix-kit package is open-source and available at https://github.com/KangchengHou/admix-kit. Additionally, users can use the pipeline designed for admixed genotype simulation available at https://github.com/UW-GAC/admix-kit_workflow.

In vivo evidence for GDP-fucose transport in the absence of transporter SLC35C1 and putative transporter SLC35C2.

Slc35c1 encodes an antiporter that transports GDP-fucose into the Golgi and returns GMP to the cytoplasm. The closely related gene Slc35c2 encodes a putative GDP-fucose transporter and promotes Notch fucosylation and Notch signaling in cultured cells. Here, we show that HEK293T cells lacking SLC35C1 transferred reduced amounts of O-fucose to secreted epidermal growth factor-like repeats from NOTCH1 or secreted thrombospondin type I repeats from thrombospondin 1. However, cells lacking SLC35C2 did not exhibit reduced fucosylation of these epidermal growth factor-like repeats or thrombospondin type I repeats. To investigate SLC35C2 functions in vivo, WW6 embryonic stem cells were targeted for Slc35c2. Slc35c2[-/-] mice were viable and fertile and exhibited no evidence of defective Notch signaling during skeletal or T cell development. By contrast, mice with inactivated Slc35c1 exhibited perinatal lethality and marked skeletal defects in late embryogenesis, typical of defective Notch signaling. Compound Slc35c1[-/-]Slc35c2[-/-] mutants were indistinguishable in skeletal phenotype from Slc35c1[-/-] embryos and neonates. Double mutants did not exhibit the exacerbated skeletal defects predicted if SLC35C2 was functionally important for Notch signaling in vivo. In addition, NOTCH1 immunoprecipitated from Slc35c1[-/-]Slc35c2[-/-] neonatal lung carried fucose detected by binding of Aleuria aurantia lectin. Given that the absence of both SLC35C1, a known GDP-fucose transporter, and SLC35C2, a putative GDP-fucose transporter, did not lead to afucosylated NOTCH1 nor to the severe Notch signaling defects and embryonic lethality expected if all GDP-fucose transport were abrogated, at least one more mechanism of GDP-fucose transport into the secretory pathway must exist in mammals.

Pharmacological inhibition of RUNX1 reduces infarct size after acute myocardial infarction in rats and underlying mechanism revealed by proteomics implicates repressed cathepsin levels.

Myocardial infarction (MI) results in prolonged ischemia and the subsequent cell death leads to heart failure which is linked to increased deaths or hospitalizations. New therapeutic targets are urgently needed to prevent cell death and reduce infarct size among patients with MI. Runt-related transcription factor-1 (RUNX1) is a master-regulator transcription factor intensively studied in the hematopoietic field. Recent evidence showed that RUNX1 has a critical role in cardiomyocytes post-MI. The increased RUNX1 expression in the border zone of the infarct heart contributes to decreased cardiac contractile function and can be therapeutically targeted to protect against adverse cardiac remodelling. This study sought to investigate whether pharmacological inhibition of RUNX1 function has an impact on infarct size following MI. In this work we demonstrate that inhibiting RUNX1 with a small molecule inhibitor (Ro5-3335) reduces infarct size in an in vivo rat model of acute MI. Proteomics study using data-independent acquisition method identified increased cathepsin levels in the border zone myocardium following MI, whereas heart samples treated by RUNX1 inhibitor present decreased cathepsin levels. Cathepsins are lysosomal proteases which have been shown to orchestrate multiple cell death pathways. Our data illustrate that inhibition of RUNX1 leads to reduced infarct size which is associated with the suppression of cathepsin expression. This study demonstrates that pharmacologically antagonizing RUNX1 reduces infarct size in a rat model of acute MI and unveils a link between RUNX1 and cathepsin-mediated cell death, suggesting that RUNX1 is a novel therapeutic target that could be exploited clinically to limit infarct size after an acute MI.

C-176 reduces inflammation-induced pain by blocking the cGAS-STING pathway in microglia.

OBJECTIVE: Inflammatory pain, is caused by lesions or diseases of the somatosensory tissue, is a prevalent chronic condition that profoundly impacts the quality of life. However, clinical treatment for this type of pain remains limited. Traditionally, the stimulation of microglia and subsequent inflammatory reactions are considered crucial elements to promote the worsening of inflammatory pain. Recent research has shown the crucial importance of the cGAS-STING pathway in promoting inflammation. It is still uncertain if the cGAS-STING pathway plays the role in the fundamental cause of inflammatory pain. We aim to explore the treatment of inflammatory pain by interfering with cGAS-STING signaling pathway. METHODS: In this study, we established an inflammatory pain model by CFA into the plantar of mice. Activation of microglia, various inflammatory factors and cGAS-STING protein in the spinal dorsal horn were evaluated. Immunofluorescence staining was used to observe the cellular localization of cGAS and STING. The cGAS-STING pathway proteins expression and mRNA expression of indicated microglial M1/M2 phenotypic markers in the BV2 microglia were detected. STING inhibitor C-176 was intrathecal injected into mice with inflammatory pain, and the pain behavior and microglia were observed. RESULTS: This research showed that injecting CFA into the left hind paw of mice caused mechanical allodynia and increased inflammation in the spine. Our research results suggested that the cGAS-STING pathway had a function in the inflammation mediated by microglia in the spinal cord dorsal horn. Blocking the cGAS-STING pathway using STING antagonists (C-176) led to reduced release of inflammatory factors and prevented M1 polarization of BV2 microglia in a laboratory setting. Additionally, intrathecal administration of C-176 reduced the allodynia in CFA treated mice. CONCLUSION: Our results suggest that inhibiting microglial polarization through the cGAS-STING pathway represents a potential novel therapeutic strategy for inflammatory pain.

Nucleon Energy Correlators.

We introduce the concept of the nucleon energy correlators, a set of novel objects that encode the microscopic details of a nucleon, such as the parton angular distribution in a nucleon, the collinear splitting to all orders, as well as the internal transverse dynamics of the nucleon. The nucleon energy correlators complement the conventional nucleon or nucleus tomography, but without introducing the nonperturbative fragmentation functions or the jet clustering algorithms. We demonstrate how the nucleon energy correlators can be measured in the lepton-nucleon deep inelastic scattering. The predicted distributions display a fascinating phase transition between the perturbative and nonperturbative regime. In the perturbative phase, a polar angle version of the Bjorken scaling behavior is predicted. We discuss its possible applications and expect it to aggrandize the physics content at the electron ion colliders with a far-forward detector.

Analyzing N-Point Energy Correlators inside Jets with CMS Open Data.

Jets of hadrons produced at high-energy colliders provide experimental access to the dynamics of asymptotically free quarks and gluons and their confinement into hadrons. In this Letter, we show that the high energies of the Large Hadron Collider (LHC), together with the exceptional resolution of its detectors, allow multipoint correlation functions of energy flow operators to be directly measured within jets for the first time. Using Open Data from the CMS experiment, we show that reformulating jet substructure in terms of these correlators provides new ways of probing the dynamics of QCD jets, which enables direct imaging of the confining transition to free hadrons as well as precision measurements of the scaling properties and interactions of quarks and gluons. This opens a new era in our understanding of jet substructure and illustrates the immense unexploited potential of high-quality LHC data sets for elucidating the dynamics of QCD.

Nucleon Energy Correlators for the Color Glass Condensate.

We demonstrate the recently proposed nucleon energy-energy correlator (NEEC) f_{EEC}(x,θ) can unveil the gluon saturation in the small-x regime in eA collisions. The novelty of this probe is that it is fully inclusive just like the deep-inelastic scattering (DIS), with no requirements of jets or hadrons but still provides an evident portal to the small-x dynamics through the shape of the θ distribution. We find that the saturation prediction is significantly different from the expectation of the collinear factorization.

Pd-catalysed cross-coupling of allenylic carbonates with gem-diborylalkanes: efficient synthesis of isoprenylboronates.

A simple and novel Pd-catalysed cross-coupling reaction of allenylic carbonates with different gem-diborylalkanes was developed. Under mild reaction conditions, synthetically useful and versatile isoprenylboronates could be obtained selectively in moderate to high yields. Furthermore, the utility of the novel isoprenylboronate is demonstrated through isoprenylboration and homologation.

Age-related promoter-switch regulates Runx1 expression in adult rat hearts.

BACKGROUND: Runt-related transcription factor-1 (RUNX1), a key member of the core-binding factor family of transcription factors, has emerged as a novel therapeutic target for cardiovascular disease. There is an urgent need to fully understand the expression pattern of Runx1 in the heart and the mechanisms by which it is controlled under normal conditions and in response to disease. The expression of Runx1 is regulated at the transcriptional level by two promoters designated P1 and P2. Alternative usage of these two promoters creates differential mRNA transcripts diversified in distribution and translational potential. While the significance of P1/P2 promoter-switch in the transcriptional control of Runx1 has been highlighted in the embryogenic process, very little is known about the level of P1- and P2-specific transcripts in adult hearts, and the underlying mechanisms controlling the promoter-switch. METHODS: To amplify P1/P2 specific sequences in the heart, we used two different sense primers complementary to either P1 or P2 5'-regions to monitor the expression of P1/P2 transcripts. DNA methylation levels were assessed at the Runx1 promoter regions. Rats were grouped by age. RESULTS: The expression levels of both P1- and P2-derived Runx1 transcripts were decreased in older rats when compared with that in young adults, paralleled with an age-dependent decline in Runx1 protein level. Furthermore, older rats demonstrated a higher degree of DNA methylation at Runx1 promoter regions. Alternative promoter usage was observed in hearts with increased age, as reflected by altered P1:P2 mRNA ratio. CONCLUSION: Our data demonstrate that the expression of Runx1 in the heart is age-dependent and underscore the importance of gene methylation in the promoter-mediated transcriptional control of Runx1, thereby providing new insights to the role of epigenetic regulation in the heart.

Downregulation of a mitochondrial micropeptide, MPM, promotes hepatoma metastasis by enhancing mitochondrial complex I activity.

We and others have shown that MPM (micropeptide in mitochondria) regulates myogenic differentiation and muscle development. However, the roles of MPM in cancer development remain unknown. Here we revealed that MPM was downregulated significantly in human hepatocellular carcinoma (HCC) tissues and its decrease was associated with increased metastasis potential and HCC recurrence. Gain- and loss-of-function investigations disclosed that in vitro migration/invasion and in vivo liver/lung metastasis of hepatoma cells were repressed by restoring MPM expression and increased by silencing MPM. Mechanism investigations revealed that MPM interacted with NDUFA7. Mitochondrial complex I activity was inhibited by overexpressing MPM and enhanced by siMPM, and this effect of siMPM was attenuated by knocking down NDUFA7. The NAD+/NADH ratio, which was regulated by complex I, was reduced by MPM but increased by siMPM. Treatment with the NAD+ precursor nicotinamide abrogated the inhibitory effect of MPM on hepatoma cell migration. Further investigations showed that miR-17-5p bound to MPM and inhibited MPM expression. miR-17-5p upregulation was associated with MPM downregulation in HCC tissues. These findings indicate that a decrease in MPM expression may promote hepatoma metastasis by increasing mitochondrial complex I activity and the NAD+/NADH ratio.

Prognostic value of day-of-event serum calcium and magnesium for predicting 1-year prognosis after intracerebral hemorrhage.

AIM: To investigate whether serum calcium and magnesium on the day of symptom onset contribute to prognosis at 1 year after intracerebral hemorrhage (ICH). METHODS: We prospectively enrolled patients admitted < 24 h after symptom onset of primary ICH to West China Hospital between January 2012 and October 2014. Blood samples were collected at admission to determine the concentration of serum calcium and magnesium. We analyzed associations of the serum concentration of calcium and magnesium with unfavorable outcome (defined as modified Rankin scale, mRS ≥ 3) at 1 year. RESULTS: We included 874 patients (mean age 59.1 ± 13.5 years, 67.6% males), of whom 470 patients had mRS ≥ 3 and 284 patients died at 1 year. Compared to patients with the highest tertile level of calcium concentration (≥ 2.29 mmol/L), patients in the lowest tertile (≤ 2.15 mmol/L) had higher odds of unfavorable outcome (odds ratio, OR 1.61, 95% confidence interval [CI] 1.04-2.50, P = 0.034). The Kaplan-Meier survival curve revealed a significant difference of cumulative survival rate across calcium tertiles (log-rank P value = 0.038). There was no significant association between serum concentration of magnesium and functional outcome at 1 year. CONCLUSION: A reduced serum concentration of calcium on the day-of-event was associated with unfavorable outcome at 1 year after ICH. Future studies are needed to illustrate the pathophysiological mechanism of calcium and whether calcium could be a treatment target for improving outcomes after ICH.

Effects of overexpression of histone H3K9me3 demethylase on development of porcine cloned embryos.

The abnormal modification of histone is an important factor restricting development of porcine cloned embryos. Overexpression of histone H3K9me3 demethylase KDM4 family can effectively improve the developmental efficiency of cloned embryos. In order to explore the effects of overexpression of H3K9me3 demethylase on the development of porcine cloned embryos, KDM4A mRNA and KDM4D mRNA were injected respectively into porcine cloned embryos at the 1-cell stage and 2-cell stage to detect the blastocyst rate; 2-cell stage cloned embryos injected with KDM4A mRNA and embryo injection water (the control group) at the 1-cell stage were collected to detect the expression level of H3K9me3, and 4-cell stage cloned embryos were collected for single cell transcriptome sequencing, then the sequencing data was analyzed with KEGG and GO. The results showed that the blastocyst rate of porcine cloned embryos injected with KDM4A mRNA at 1-cell stage was significantly higher than that of the control group (25.32 ± 0.74% vs 14.78 ± 0.87%), while cloned embryos injected with KDM4D mRNA had a similar blastocyst rate with cloned embryos in control group (16.27 ± 0.77% vs 14.78 ± 0.87%). Porcine cloned embryos injected with KDM4A mRNA and KDM4D mRNA at 2-cell stage had a similar blastocyst rate with cloned embryos in control group (32.18 ± 1.67%, 30.04 ± 0.91% vs 31.22 ± 1.40%). The expression level of H3K9me3 in cloned embryos injected with KDM4A mRNA at 1-cell stage was lower than that in control group. There were 133 differentially expressed genes detected by transcriptome sequencing, including 52 up-regulated genes and 81 down-regulated genes. Pathways enriched by GO analyses were mainly related to protein localization. Pathways enriched by KEGG analyses were related to cellular senescence and acute myeloid leukemia. These results suggest that overexpression of histone H3K9me3 demethylase KDM4A can significantly improve the developmental efficiency of porcine cloned embryos.

An updated review of the new hadron states.

The past decades witnessed the golden era of hadron physics. Many excited open heavy flavor mesons and baryons have been observed since 2017. We shall provide an updated review of the recent experimental and theoretical progresses in this active field. Besides the conventional heavy hadrons, we shall also review the recently observed open heavy flavor tetraquark statesX(2900) andTcc+(3875)as well as the hidden heavy flavor multiquark statesX(6900),Pcs(4459)0,Zcs(3985)-,Zcs(4000)+, andZcs(4220)+. We will also cover the recent progresses on the glueballs and light hybrid mesons, which are the direct manifestations of the non-AbelianSU(3) gauge interaction of the Quantum Chromodynamics in the low-energy region.

Extending Precision Perturbative QCD with Track Functions.

Collider experiments often exploit information about the quantum numbers of final state hadrons to maximize their sensitivity, with applications ranging from the use of tracking information (electric charge) for precision jet substructure measurements, to flavor tagging for nucleon structure studies. For such measurements, perturbative calculations in terms of quarks and gluons are insufficient, and nonperturbative track functions describing the energy fraction of a quark or gluon converted into a subset of hadrons (e.g., charged hadrons) must be incorporated. Unlike fragmentation functions, track functions describe correlations between hadrons and therefore satisfy complicated nonlinear evolution equations whose structure has so far eluded calculation beyond the leading order. In this Letter, we develop an understanding of track functions and their interplay with energy flow observables beyond the leading order, allowing them to be used in state-of-the-art perturbative calculations for the first time. We identify a shift symmetry in the evolution of their moments that fixes their structure, and we explicitly compute the evolution of the first three moments at next-to-leading order, allowing for the description of up to three-point energy correlations. We then calculate the two-point energy correlator on charged particles at O(α_{s}^{2}), illustrating explicitly that infrared singularities in perturbation theory are absorbed by moments of the track functions and also highlighting how these moments seamlessly interplay with modern techniques for perturbative calculations. Our results extend the boundaries of traditional perturbative QCD, enabling precision perturbative predictions for energy flow observables sensitive to the quantum numbers of hadronic states.

Dilepton Rapidity Distribution in Drell-Yan Production to Third Order in QCD.

We compute for the first time the lepton-pair rapidity distribution in the photon-mediated Drell-Yan process to next-to-next-to-next-to-leading order in QCD. The calculation is based on the q_{T}-subtraction method, suitably extended to this order for quark-antiquark initiated Born processes. Our results display sizeable QCD corrections at next-to-next-to-next-to-leading order over the full rapidity region and provide a fully independent confirmation of the recent results for the total Drell-Yan cross section at this order.

The pathophysiologic significance of lymphocyte subset determination in children with infectious mononucleosis, mycoplasma pneumonia and Henoch-Schönlein purpura.

OBJECTIVE: This study aimed to explore lymphocyte subset determinations as an aid to understanding the pathophysiology of infectious mononucleosis (IM), pneumonia due to mycoplasma infection (P-MI) and Henoch-Schönlein purpura in children. METHODS: The peripheral blood lymphocyte subsets of 45 children with IM, 20 children with P-MI, and 31 children with Henoch-Schönlein purpura (HSP), who were treated in the pediatrics department of our hospital from April 2019 to February 2020, were determined by flow cytometry, and the number and percentage of lymphocyte subsets with CD3+, CD3 + CD4+, CD3 + CD8+, CD3 + CD4+/CD3 + CD8+, CD3-CD16 + CD56+, and CD3-CD19 + cells were observed, and the results were compared and analyzed. RESULTS: (1) The percentages of CD3+, CD3 + CD8 + lymphocyte subsets in children in IM group were significantly higher than those in children with P-MI and HSP, and the percentages of CD3-CD19 + lymphocyte subsets in children in IM group were significantly lower than those in children with P-MI and HSP. The percentages of CD3 + CD4 + lymphocyte subsets in children in the three groups were the lowest in children with IM, and the highest in children with P-MI.The differences in the percentages of CD3+, CD3 + CD4+, CD + CD8+, and CD3-CD19 + lymphocyte subsets among the IM, P-MI, and HSP groups were statistically significant (P < 0.01). (2) The results of CD3 + CD4+/CD3 + CD8 + in the three groups were the lowest in children with IM and the highest in children with P-MI. There was a significant difference among the three groups (P < 0.01); The ages of the children with IM and P-MI were lower than that of the children with HSP (p < 0.01), while there was no difference in the ages of the children with IM and P-MI (p > 0.05). (3) The difference in the percentage of CD3-CD16 + CD56 + lymphocyte subsets among the three groups was not statistically significant (P > 0.05). CONCLUSION: The determination of peripheral blood lymphocyte subsets is of significance for understanding the pathophysiology of IM, mycoplasma pneumonia, and HSP in children.

Associations of fecal microbial profiles with breast cancer and nonmalignant breast disease in the Ghana Breast Health Study.

The gut microbiota may play a role in breast cancer etiology by regulating hormonal, metabolic and immunologic pathways. We investigated associations of fecal bacteria with breast cancer and nonmalignant breast disease in a case-control study conducted in Ghana, a country with rising breast cancer incidence and mortality. To do this, we sequenced the V4 region of the 16S rRNA gene to characterize bacteria in fecal samples collected at the time of breast biopsy (N = 379 breast cancer cases, N = 102 nonmalignant breast disease cases, N = 414 population-based controls). We estimated associations of alpha diversity (observed amplicon sequence variants [ASVs], Shannon index, and Faith's phylogenetic diversity), beta diversity (Bray-Curtis and unweighted/weighted UniFrac distance), and the presence and relative abundance of select taxa with breast cancer and nonmalignant breast disease using multivariable unconditional polytomous logistic regression. All alpha diversity metrics were strongly, inversely associated with odds of breast cancer and for those in the highest relative to lowest tertile of observed ASVs, the odds ratio (95% confidence interval) was 0.21 (0.13-0.36; Ptrend < .001). Alpha diversity associations were similar for nonmalignant breast disease and breast cancer grade/molecular subtype. All beta diversity distance matrices and multiple taxa with possible estrogen-conjugating and immune-related functions were strongly associated with breast cancer (all Ps < .001). There were no statistically significant differences between breast cancer and nonmalignant breast disease cases in any microbiota metric. In conclusion, fecal bacterial characteristics were strongly and similarly associated with breast cancer and nonmalignant breast disease. Our findings provide novel insight into potential microbially-mediated mechanisms of breast disease.

Variation in oral microbiome is associated with future risk of lung cancer among never-smokers.

OBJECTIVE: To prospectively investigate whether diversity in oral microbiota is associated with risk of lung cancer among never-smokers. DESIGN AND SETTING: A nested case-control study within two prospective cohort studies, the Shanghai Women's Health Study (n=74 941) and the Shanghai Men's Health Study (n=61 480). PARTICIPANTS: Lifetime never-smokers who had no cancer at baseline. Cases were subjects who were diagnosed with incident lung cancer (n=114) and were matched 1:1 with controls on sex, age (≤2 years), date (≤30 days) and time (morning/afternoon) of sample collection, antibiotic use during the week before sample collection (yes/no) and menopausal status (for women). MAIN OUTCOMES AND MEASURES: Metagenomic shotgun sequencing was used to measure the community structure and abundance of the oral microbiome in pre-diagnostic oral rinse samples of each case and control. Multivariable logistic regression models were used to estimate the association of lung cancer risk with alpha diversity metrics and relative abundance of taxa. The Microbiome Regression-Based Kernel Association Test (MiRKAT) evaluated the association between risk and the microbiome beta diversity. RESULTS: Subjects with lower microbiota alpha diversity had an increased risk of lung cancer compared with those with higher microbial alpha diversity (Shannon: ptrend=0.05; Simpson: ptrend=0.04; Observed Species: ptrend=0.64). No case-control differences were apparent for beta diversity (pMiRKAT=0.30). After accounting for multiple comparisons, a greater abundance of Spirochaetia (ORlow 1.00 (reference), ORmedium 0.61 (95% CI 0.32 to 1.18), ORhigh 0.42 (95% CI 0.21 to 0.85)) and Bacteroidetes (ORlow 1.00 (reference), ORmedium 0.66 (95% CI 0.35 to 1.25), ORhigh 0.31 (95% CI 0.15 to 0.64)) was associated with a decreased risk of lung cancer, while a greater abundance of the Bacilli class (ORlow 1.00 (reference), ORmedium 1.49 (95% CI 0.73 to 3.08), ORhigh 2.40 (95% CI 1.18 to 4.87)) and Lactobacillales order (ORlow 1.00 (reference), ORmedium 2.15 (95% CI 1.03 to 4.47), ORhigh 3.26 (95% CI 1.58 to 6.70)) was associated with an increased risk of lung cancer. CONCLUSIONS: Our prospective study of never-smokers suggests that lower alpha diversity was associated with a greater risk of lung cancer and the abundance of certain specific taxa was associated with altered risk, providing further insight into the aetiology of lung cancer in the absence of active tobacco smoking.