The gut microbiome has important effects on human health, yet its importance in human ageing remains unclear. In the present study, we demonstrate that, starting in mid-to-late adulthood, gut microbiomes become increasingly unique to individuals with age. We leverage three independent cohorts comprising over 9,000 individuals and find that compositional uniqueness is strongly associated with microbially produced amino acid derivatives circulating in the bloodstream. In older age (over ~80 years), healthy individuals show continued microbial drift towards a unique compositional state, whereas this drift is absent in less healthy individuals. The identified microbiome pattern of healthy ageing is characterized by a depletion of core genera found across most humans, primarily Bacteroides. Retaining a high Bacteroides dominance into older age, or having a low gut microbiome uniqueness measure, predicts decreased survival in a 4-year follow-up. Our analysis identifies increasing compositional uniqueness of the gut microbiome as a component of healthy ageing, which is characterized by distinct microbial metabolic outputs in the blood.

Defining a 'healthy' gut microbiome has been a challenge in the absence of detailed information on both host health and microbiome composition. Here, we analyzed a multi-omics dataset from hundreds of individuals (discovery n=399, validation n=540) enrolled in a consumer scientific wellness program to identify robust associations between host physiology and gut microbiome structure. We attempted to predict gut microbiome α-diversity from nearly 1000 analytes measured from blood, including clinical laboratory tests, proteomics and metabolomics. While a broad panel of 77 standard clinical laboratory tests and a set of 263 proteins from blood could not accurately predict gut microbial α-diversity, we found that 45% of the variance in microbial community diversity was explained by a subset of 40 blood metabolites, many of microbial origin. This relationship between the host metabolome and gut microbiome α-diversity was very robust, persisting across disease conditions and antibiotics use. Several of these novel metabolic biomarkers of gut microbial diversity were previously associated with host health (e.g. cardiovascular disease risk, diabetes, and kidney function). A subset of 11 metabolites classified participants with potentially problematic low α-diversity (ROC AUC=0.88, Precision-Recall AUC=0.76). Relationships between host metabolites and α-diversity remained consistent across most of the Body Mass Index (BMI) spectrum, but were modified in extreme obesity (class II/III, but not class I), suggesting a significant metabolic shift. Out-of-sample prediction accuracy of αdiversity from the 40 identified blood metabolites in a validation cohort, whose microbiome samples were analyzed by a different vendor, confirmed the robust correspondence between gut microbiome structure and host physiology. Collectively, our results reveal a strong coupling between the human blood metabolome and gut microbial diversity, with implications for human health.

BackgroundOvercoming systemic dormancy and initiating secondary tumor grow under unique microenvironmental conditions is a major rate-limiting step in metastatic progression. Disseminated tumor cells encounter major changes in nutrient supplies and oxidative stresses compared to the primary tumor and must demonstrate significant metabolic plasticity to adapt to specific metastatic sites. Recent studies suggest that differential utilization of pyruvate sits as a critical node in determining the organotropism of metastatic breast cancer. Pyruvate carboxylase (PC) is key enzyme that converts pyruvate into oxaloacetate for utilization in gluconeogenesis and replenishment of the TCA cycle.MethodsPatient survival was analyzed with respect to gene copy number alterations and differential mRNA expression levels of PC. Expression of PC was analyzed in the MCF-10A, D2-HAN and the 4 T1 breast cancer progression series under in vitro and in vivo growth conditions. PC expression was depleted via shRNAs and the impact on in vitro cell growth, mammary fat pad tumor growth, and pulmonary and non-pulmonary metastasis was assessed by bioluminescent imaging. Changes in glycolytic capacity, oxygen consumption, and response to oxidative stress were quantified upon PC depletion.ResultsGenomic copy number increases in PC were observed in 16–30% of metastatic breast cancer patients. High expression of PC mRNA was associated with decreased patient survival in the MCTI and METABRIC patient datasets. Enhanced expression of PC was not recapitulated in breast cancer progression models when analyzed under glucose-rich in vitro culture conditions. In contrast, PC expression was dramatically enhanced upon glucose deprivation and in vivo in pulmonary metastases. Depletion of PC led to a dramatic decrease in 4 T1 pulmonary metastasis, but did not affect orthotopic primary tumor growth. Tail vein inoculations confirmed the role of PC in facilitating pulmonary, but not extrapulmonary tumor initiation. PC-depleted cells demonstrated a decrease in glycolytic capacity and oxygen consumption rates and an enhanced sensitivity to oxidative stress.ConclusionsOur studies indicate that PC is specifically required for the growth of breast cancer that has disseminated to the lungs. Overall, these findings point to the potential of targeting PC for the treatment of pulmonary metastatic breast cancer.Electronic supplementary materialThe online version of this article (10.1186/s13058-018-1008-9) contains supplementary material, which is available to authorized users.