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This research proposes a first approximation of Inequality of Opportunity (IOp) in Mexico based on a concept of ex-post compensation, fully consistent with Roemer s approach of In-equality of Opportunity. This framework considers the advantage reached by an individual to be determined by the circumstances at origin and by the effort exerted. Following Brunori and Neidhofer (2020), we construct a data-driven procedure using regression trees to identify types based on circumstances. To identify degrees of effort, an algorithm estimates the distribution of outcome in each type based on coefficients of Bernstein polynomials. Our results underline the differences, in terms of opportunities, faced by individuals, based on the territory in which they grew up, the household context, and their sex. We find that the education and the wealth of parents are the principal circumstances that shape their trajectories. Importantly, territorial variables are significant determinants of IOp among the most disadvantaged at origin, but they hold less importance for the most advantaged. IOp is lower in urban areas, in the Northern region and in Mexico City compared to other regions. The Southern region and rural territories are the most unequal. We also estimate that the weight of IOp in terms of total inequality varies according if we adopt an ex-post or an ex-ante approach, which can lead to different conclusions.

Scientometrics and bibliometrics, the subfields of library and information science, deal with the quantity and quality of research outputs. Currently, various scientometric indices are being used to quantify and compare research outputs. The most widely known is the h-index. However, this index and its derivatives suffer from dependence on the mere count of a scholar's highly cited publications. To remedy this deficiency, we developed a novel index, the Universal Research Index (UR-Index) (https://usern2021.github.io/UR-Index/) by which every single publication has its own impact on the total score. We developed this index by surveying international top 1 % cited scientists in various disciplines and included additional component variables such as publication type, leading role of a scholar, co-author count, and source metrics to this scientometric index. We acknowledge that unconscious biases built into the component variables included in the UR-Index might put research from specific groups at a disadvantage, thus continued efforts to improve equitable scholarly impact in science and academia are encouraged.

We consider the motion of a charged particle under the electromagnetic field generated by an electrically neutral infinite straight wire with a time-periodic oscillating (AC-DC) current. By using global continuation and topological degree, we identify a bi-parametric family of radially periodic motions. The proofs involve some delicate estimations of the induced electromagnetic field, which can be of independent interest.

It is proved that if the damped periodically forced Newtonian pendulum does not have periodic solutions, the same happens for the relativistic version of the problem for high values of the parameter c representing the speed of light in the vacuum.

To prevent and treat chronic diseases, including cancer, a global application of systems biology is needed. We report here a whole blood transcriptome test that needs only 50 μl of capillary (fingerprick) blood. This test is suitable for global applications because the samples are preserved at ambient temperature for up to 4 weeks and the RNA preservative inactivates all pathogens, enabling safe transportation. Both the laboratory and bioinformatic steps are automated and performed in a clinical lab, which minimizes batch effects and creates unbiased datasets. Given its clinical testing performance and accessibility to traditionally underrepresented and diverse populations, this test offers a unique ability to reveal molecular mechanisms of disease and enable longitudinal, population-scale studies.

Global climate change predictions include decreased precipitation and more frequent droughts in many world regions. In the aseasonal wet tropics, predicting potential impacts is particularl...

We are grateful to Rafael Ortega for bringing to our attention the position-energy system that has been crucial for the regularization of collisions. We also thank the anonymous referees for their valuable comments and suggestions that contributed to improve the initial version of the paper. This work has been realized thanks to the Agencia Estatal de Investigaci´on, Spain and Ministerio de Ciencia, Innovaci´on y Universidades, Spain grants MTM2017-82348-C2-1-P and MTM2017-86795-C3-1-P., We prove the existence and multiplicity of periodic solutions of bouncing type for a second-order differential equation with a weak repulsive singularity. Such solutions can be cataloged according to the minimal period and the number of elastic collisions with the singularity in each period. The proof relies on the Poincaré–Birkhoff Theorem., Agencia Estatal de Investigación, Spain and Ministerio de Ciencia, Innovación y Universidades, Spain grants MTM2017-82348-C2-1-P and MTM2017-86795-C3-1-P

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome. ispartof: NATURE MICROBIOLOGY vol:4 issue:10 pages:1727-1736 ispartof: location:England status: published

We consider the problem of the existence and multiplicity of periodic solutions associated to a class of scalar equations of the form x ″ + f ( t , x ) = 0 . The class considered is such that the behaviour of its solutions near zero and infinity can be compared two suitable piecewise linear systems. We show how a rotation number approach, together with the Poincare–Birkhoff theorem and the phase-plane analysis of the spiral properties, allows to obtain multiplicity results in terms of the gap between the rotation numbers of the referred piecewise linear systems at zero and at infinity. These systems may also be resonant. In particular, our approach can be used to deal with the problems without both global existence of the Cauchy problems associated to the equation and the sign assumption on f. The typical example is a partially superlinear second order equation. Our main result generalizes some classical results of Jacobowitz and Hartman, among others.

Recognizing and treating the early stages of type 2 diabetes (T2D) is the most cost effective way to decrease prevalence, before heart disease, renal disease, blindness, and limb amputation become inevitable. In this study, we employ high resolution gut microbiome metatranscriptomic analysis of stool samples from 53,970 individuals to identify predictive biomarkers of type 2 diabetes progression and potential for diagnosis and treatment response. The richness of the metatranscriptomic data enabled us to develop a T2D risk model to delineate individuals with glycemic dysregulation from those within normal glucose levels, with ROC-AUC of 0.83+/-0.04. This risk score can predict the probability of having insulin dysregulation before detecting high glycated hemoglobin (HbA1c), the standard-of-care marker for prediabetes and diabetes. Additionally, a machine learning model was able to distinguish novel metatranscriptomic features that segregate patients who receive metformin and are able to control their HbA1c from those who do not. These discoveries set the stage for developing multiple therapeutic avenues for prevention and treatment of T2D.

México es un país altamente desigual y el origen étnico-racial es una de las dimensiones que contribuyen a esta desigualdad. Estudios anteriores han analizado las diferencias salariales por origen-étnico racial y rasgos lingüísticos, pero hasta ahora ninguno ha reconocido que la autoidentificación indígena puede llevar a sesgos de selección en el análisis. En este artículo resolvemos este problema mediante la estimación de un modelo con cambio de régimen, el cual estima, en una primera etapa, la selección en la autoidentificación y, en una segunda, dos ecuaciones de los salarios según cómo se autoidentificó el trabajador. El modelo revela que la mayor parte del diferencial en el promedio de los salarios entre aquellos que se identifican como indígenas y aquellos que no se debe al sesgo de selección. A pesar de esto persiste un diferencial que no se explica por las características observadas ni la autoselección de estas subpoblaciones, el cual se podría deber a discriminación. Estos resultados contrastan con descomposiciones de Oaxaca tradicionales en que no se considera el sesgo de selección y apuntan a que la educación es el factor que más contribuye a la desigualdad salarial étnico-racial.

Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. Fund ing was provided by Ministry of Science and Technology (MTM2017-364758), In this paper, we analyze the influence of the usual movement variables on the spread of an epidemic. Specifically, given two spatial topologies, we can deduce which topology produces less infected individuals. In particular, we determine the topology that minimizes the overall number of infected individuals. It is worth noting that we do not assume any of the common simplifying assumptions in network theory such as all the links have the same diffusion rate or the movement of the individuals is symmetric. Our main conclusion is that the degree of mobility of the population plays a critical role in the spread of a disease. Finally, we derive theoretical insights to management of epidemics., Ministry of Science and Technology MTM2017-364758, CRUE-CSIC agreement, Springer Nature

Made available in DSpace on 2018-11-26T16:32:48Z (GMT). No. of bitstreams: 0 Previous issue date: 2016-07-15 MINECO Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) MINECO/FEDER Generalitat de Catalunya European Community The Lienard equation x + f (x)x' + g(x) = 0 appears as a model in many problems of science and engineering. Since the first half of the 20th century, many papers have appeared providing existence and uniqueness conditions for limit cycles of Lienard equations. In this paper we extend some of these results for the case of the generalized phi-Laplacian Lienard equation, (phi(x'))' f(x)psi(x') + g(x) = 0. This generalization appears when derivations of the equation different from the classical one are considered. In particular, the relativistic van der Pol equation, (x'/root 1 - (x'/c)(2))' + mu(x(2) - 1)x' + x = 0, has a unique periodic orbit when mu = 0. (C) 2016 Elsevier Inc. All rights reserved. Univ Estadual Paulista, Dept Matemat, Rua Cristovao Colombo 2265, BR-15054000 Sao Jose Do Rio Preto, SP, Brazil Univ Autonoma Barcelona, Dept Matemat, Edifici C, E-08193 Barcelona, Spain Univ Granada, Dept Matemat Aplicada, E-18071 Granada, Spain Univ Estadual Paulista, Dept Matemat, Rua Cristovao Colombo 2265, BR-15054000 Sao Jose Do Rio Preto, SP, Brazil MINECO: MTM2013-40998-P CAPES: 1271113 MINECO/FEDER: UNAB13-4E-1604 MINECO/FEDER: MTM2014-52232-P MINECO/FEDER: FQM-1861 Generalitat de Catalunya: 2014SGR568 European Community: FP7-PEOPLE-2012-IRSES-318999 European Community: FP7-PEOPLE-2012-IRSES-316338

We provide sufficient conditions for the existence of periodic solutions of the Lorentz force equation, which models the motion of a charged particle under the action of an electromagnetic fields. The basic assumptions cover relevant models with singularities like Coulomb-like electric potentials or the magnetic dipole.

Polycystic ovary syndrome (PCOS) impacts ∼10% of reproductive-aged women worldwide. In addition to infertility, women with PCOS suffer from metabolic dysregulation which increases their risk of developing type 2 diabetes, cardiovascular disease and non-alcoholic fatty liver disease. Studies have shown differences in the gut microbiome of women with PCOS compared to controls, a pattern replicated in mouse models. Recently, using a letrozole-induced mouse model of PCOS, we demonstrated that cohousing was protective against development of metabolic and reproductive phenotypes and showed via 16S amplicon sequencing that this protection correlated with time-dependent shifts in gut bacteria. Here, we applied untargeted metabolomics and shotgun metagenomics approaches to further analyze the longitudinal samples from the cohousing experiment. Analysis of beta diversity found that untargeted metabolites had the strongest correlation to both disease and cohoused states and that shifts in metabolite diversity were detected prior to shifts in bacterial diversity. In addition, log2-fold analyses found numerous metabolite features, particularly bile acids (BA), to be highly differentiated between placebo (P) and letrozole (LET), as well as cohoused LET versus LET. Our results indicate that changes in gut metabolites, particularly BAs, are associated with a PCOS-like phenotype in the LET mouse model as well as the protective effect of cohousing. Our results also suggest that transfer of metabolites via coprophagy occurs rapidly and may precipitate changes in bacterial diversity. This study joins a growing body of research highlighting changes in primary and secondary bile acids that may provide a link between host metabolism and gut microbes relevant to the pathology of PCOS.IMPORTANCEUsing a combination of untargeted metabolomics and metagenomics, we performed a comparative longitudinal analysis of the feces collected in a cohousing study with a PCOS mouse model. Our results showed that gut metabolite composition experienced earlier and more pronounced differentiation in both the disease model and cohoused mice compared with the microbial composition. Notably, statistical and machine learning approaches identified shifts in the relative abundance of primary and secondary BA, which have been implicated as modifiers of gut microbial growth and diversity. Network correlation analysis showed strong associations between particular BA and bacterial species, particularly members of Lactobacillus, and that these correlations were time and treatment dependent. Our results provide novel insights into host/microbe relationships related to hyperandrogenism in females and indicate that focused research into small molecule control of gut microbial diversity and host physiology may provide new therapeutic options for the treatment of PCOS.

Accurate measurement of the biological markers of the aging process could provide an “aging clock” measuring predicted longevity and allow for the quantification of the effects of specific lifestyle choices on healthy aging. Using modern machine learning techniques, we demonstrate that chronological age can be predicted accurately from (a) the expression level of human genes in capillary blood, and (b) the expression level of microbial genes in stool samples. The latter uses the largest existing metatranscriptomic dataset, stool samples from 90,303 individuals, and is the highest-performing gut microbiome-based aging model reported to date. Our analysis suggests associations between biological age and lifestyle/health factors, e.g., people on a paleo diet or with IBS tend to be biologically older, and people on a vegetarian diet tend to be biologically younger. We delineate the key pathways of systems-level biological decline based on the age-specific features of our model; targeting these mechanisms can aid in development of new anti-aging therapeutic strategies.

The Basener–Ross system is a known model in Population dynamics for the interaction of consumers and resources in an isolated habitat. For an extended version with time-dependent coefficients as a model of possible variations of the environmental conditions, some relations among the coefficients are provided leading to the integrability of the system.

In this paper, we study, using critical point theory for strongly indefinite functionals, the Neumann problem associated to some prescribed mean curvature problems in a FLRW spacetime with one spatial dimension. We assume that the warping function is even and positive and the prescribed mean curvature function is odd and sublinear. Then, we show that our problem has infinitely many solutions. The keypoint is that our problem has a Hamiltonian formulation. The main tool is an abstract result of Clark type for strongly indefinite functionals.

We study the existence of spacelike graphs for the prescribed mean curvature equation in the Friedmann–Lemaitre–Robertson–Walker (FLRW) spacetime. By using a conformal change of variable, this problem is translated into an equivalent problem in the Lorentz–Minkowski spacetime. Then, by using Rabinowitz's global bifurcation method, we obtain the existence and multiplicity of positive solutions for this equation with 0-Dirichlet boundary condition on a ball. Moreover, the global structure of the positive solution set is studied.

Many alcohol-induced health complications are directly attributable to the toxicity of alcohol or its metabolites, but another potential health impact of alcohol may be on the microbial communities of the human gut. Clear distinctions between healthy and diseased-state gut microbiota have been observed in subjects with metabolic diseases, and recent studies suggest that chronic alcoholism is linked to gut microbiome dysbiosis. Here, we investigated the effects of moderate levels of alcohol consumption on the gut microbiome in both rats and humans. The gut microbiota of rats voluntarily consuming a 20 percent ethanol solution, on alternate days, were compared with a non-exposed control group to identify differential taxonomic and functional profiles. Gut microbial diversity profiles were determined using culture-independent amplification, next-generation sequencing and bioinformatic analysis of bacterial 16S ribosomal RNA gene sequence libraries. Our results showed that, compared with controls, ethanol-consuming rats experienced a significant decline in the biodiversity of their gut microbiomes, a state generally associated with dysbiosis. We also observed significant shifts in the overall diversity of the gut microbial communities and a dramatic change in the relative abundance of particular microbes, such as the Lactobacilli. We also compared our results to human fecal microbiome data collected as part of the citizen science American Gut Project. In contrast to the rat data, human drinkers had significantly higher gut microbial biodiversity than non-drinkers. However, we also observed that microbes that differed among the human subjects displayed similar trends in the rat model, including bacteria implicated in metabolic disease.

In this paper, we shall give new insights on dynamics of contact Hamiltonian flows, which are gaining importance in several branches of physics as they model a dissipative behaviour. We divide the contact phase space into three parts, which are corresponding to three differential invariant sets \begin{document}$ \Omega_\pm, \Omega_0 $\end{document}. On the invariant sets \begin{document}$ \Omega_\pm $\end{document}, under some geometric conditions, the contact Hamiltonian system is equivalent to a Hamiltonian system via the Hölder transformation. The invariant set \begin{document}$ \Omega_0 $\end{document} may be composed of several equilibrium points and heteroclinic orbits connecting them, on which contact Hamiltonian system is conservative. Moreover, we have shown that, under general conditions, the zero energy level domain is a domain of attraction. In some cases, such a domain of attraction does not have nontrivial periodic orbits. Some interesting examples are presented.

We would like to thank Prof. Raif Geha, the James L. Gamble Professor of Pediatrics at the Harvard Medical School and Chief of the Division of Immunol‑ ogy, Allergy, and Rheumatology at Boston Children’s Hospital, for his critical comments on this paper., The COVID-19 pandemic has become the leading societal concern. The pandemic has shown that the public health concern is not only a medical problem, but also afects society as a whole; so, it has also become the leading scientifc concern. We discuss in this treatise the importance of bringing the world’s scientists together to fnd efective solu‑ tions for controlling the pandemic. By applying novel research frameworks, interdisciplinary collaboration promises to manage the pandemic’s consequences and prevent recurrences of similar pandemics.

We study the passive particle transport generated by a circular vortex path in a 2D ideal ow con ned in a circular domain. Taking the strength and angular velocity of the vortex path as main parameters, the bi- furcation scheme of relative equilibria is identi ed. For a perturbed path, an in nite number of orbits around the centers are persistent, giving rise to peri- odic solutions with zero winding number.

We study the existence/nonexistence and multiplicity of spacelike graphs for the following mean curvature equation in a standard static spacetime div (a del u/root 1-a(2)vertical bar del u vertical bar(2)) + g (del u, del a)/root 1-a(2)vertical bar del u vertical bar(2) = lambda NH with 0-Dirichlet boundary condition on the unit ball. According to the behavior of H near 0, we obtain the global structure of one-sign radial spacelike graphs for this problem. Moreover, we also obtain the existence and multiplicity of entire spacelike graphs., National Natural Science Foundation of China (NSFC) 11871129, Xinghai Youqing funds from Dalian University of Technology, Spanish MINECO, European Union (EU) MTM2016-78807-C2-1-P MTM2017-82348-C2-1-P

Background Viruses play an important role in ecosystems, including the built environment (BE). While numerous studies have characterized bacterial and fungal microbiomes in the BE, few have focused on the viral microbiome (virome). Longitudinal microbiome studies provide insight into the stability and dynamics of microbial communities; however, few such studies exist for the microbiome of the BE, and most have focused on bacteria. Here, we present a longitudinal, metagenomic-based analysis of the airborne DNA and RNA virome of a children’s daycare center. Specifically, we investigate how the airborne virome varies as a function of season and human occupancy, and we identify possible sources of the viruses and their hosts, mainly humans, animals, plants, and insects. Results Season strongly influenced the airborne viral community composition, and a single sample collected when the daycare center was unoccupied suggested that occupancy also influenced the community. The pattern of influence differed between DNA and RNA viromes. Human-associated viruses were much more diverse and dominant in the winter, while the summertime virome contained a high relative proportion and diversity of plant-associated viruses. Conclusions This airborne microbiome in this building exhibited seasonality in its viral community but not its bacterial community. Human occupancy influenced both types of communities. By adding new data about the viral microbiome to complement burgeoning information about the bacterial and fungal microbiomes, this study contributes to a more complete understanding of the airborne microbiome. Electronic supplementary material The online version of this article (10.1186/s40168-019-0672-z) contains supplementary material, which is available to authorized users.

Approximately 10% of reproductive-aged women worldwide are affected by polycystic ovary syndrome (PCOS). In addition to infertility, many women with PCOS have an increased risk of developing type 2 diabetes, cardiovascular disease, and non-alcoholic fatty liver disease. Studies have shown that the human gut microbiome is altered in humans with metabolic disorders such as obesity and type 2 diabetes and these changes may contribute to metabolic dysfunction. Additionally, studies have reported that changes in the gut microbiome are associated with PCOS in women and in rodent models. These changes include lower alpha diversity (species richness) and changes in specific Bacteroidetes and Firmicutes many of which are also altered in other metabolic diseases. In previous work, we investigated whether the gut microbiome was altered in a PCOS mouse model using letrozole, a nonsteroidal aromatase inhibitor, to increase endogenous testosterone levels and decrease estrogen levels. Letrozole treatment of pubertal female mice results in hallmarks of PCOS including elevated testosterone and LH, acyclicity, polycystic ovaries, and a metabolic phenotype. In the current study, we tested whether manipulation of the gut microbiome in the PCOS mouse model via co-housing improved reproductive and metabolic phenotypes and whether these changes correlated with gut microbial composition. Pubertal female mice were implanted with a placebo or letrozole pellet and divided into 3 groups with two mice per cage: co-housed placebo mice, letrozole mice or placebo and letrozole mice. Our results demonstrated that co-housing letrozole-treated mice with placebo mice resulted in substantial improvement of PCOS reproductive and metabolic phenotypes. Testosterone and LH levels, estrous cycling and ovulation were normalized in letrozole-treated mice co-housed with placebo mice compared to letrozole-treated mice housed together. In addition, weight, fasting blood glucose and insulin levels, and insulin resistance were decreased in letrozole-treated mice co-housed with placebo mice compared to letrozole-treated mice housed together. Using 16S rRNA sequencing, we observed that co-housing letrozole-treated mice with placebo mice did not result in substantial changes in alpha diversity but were associated with changes in specific bacterial genera that may be candidates for pre- or probiotic therapies. Our results suggest that manipulation of the gut microbiome may be a potential treatment option for PCOS.

In this paper we investigate the existence of rotationally symmetric entire graphs (resp. entire spacelike graphs) with prescribed k-th mean curvature function in Euclidean space R n + 1 (resp. Minkowski spacetime L n + 1 ). As a previous step, we analyze the associated homogeneous Dirichlet problem on a ball, which is not elliptic for k > 1 , and then we prove that it is possible to extend the solutions. Moreover, a sufficient condition for uniqueness is given in both cases.

We study the existence and stability of periodic solutions of a differential equation that models the planar oscillations of a satellite in an elliptic orbit around its center of mass. The proof is based on a suitable version of Poincare-Birkhoff theorem and the third order approximation method.

We identify a family of Friedmann–Lemaitre–Robertson–Walker (FLRW) spacetimes such that the radially symmetric prescribed curvature problem with Neumann boundary condition is solvable on a ball of small radius. Such family contains some examples of interest in Cosmology.

We study the existence of twist periodic solutions of second order differential equations with an attractive–repulsive singularity. Such twist periodic solutions are stable in the sense of Lyapunov. The proof is based on the third order approximation method in combination with some location information obtained by the averaging method and the method of upper and lower solutions on the reversed order.

We prove the presence of chaotic dynamics for the classical two-body Kepler problem with a time-periodic gravitational coefficient oscillating between two fixed values. The set of chaotic solutions we detect is coded by the number of revolutions in each period. The chaotic dynamics is obtained for large period T as well as for small angular momentum μ. In particular, we provide an explicit lower bound on T and explicit upper bound on μ which guarantee the existence of complex dynamics. We get our results by applying a simple and well-known topological method, the stretching along the path technique. Our results are robust with respect to small perturbations of the gravitational coefficient and to the addition of a small friction term.

Motivation: The Sequence Read Archive (SRA) contains raw data from many different types of sequence projects. As of 2017, the SRA contained approximately ten petabases of DNA sequence (1016 bp). Annotations of the data are provided by the submitter, and mining the data in the SRA is complicated by both the amount of data and the detail within those annotations. Here, we introduce PARTIE, a partition engine optimized to differentiate sequence read data into metagenomic (random) and amplicon (targeted) sequence data sets. Results: PARTIE subsamples reads from the sequencing file and calculates four different statistics: k-mer frequency, 16S abundance, prokaryotic- and viral-read abundance. These metrics are used to create a RandomForest decision tree to classify the sequencing data, and PARTIE provides mechanisms for both supervised and unsupervised classification. We demonstrate the accuracy of PARTIE for classifying SRA data, discuss the probable error rates in the SRA annotations and introduce a resource assessing SRA data. Availability and Implementation: PARTIE and reclassified metagenome SRA entries are available from https://github.com/linsalrob/partie Contact: redwards@mail.sdsu.edu Supplementary information: Supplementary data are available at Bioinformatics online.

QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. Partial support was also provided by the following: grants NIH U54CA143925 (J.G.C. and T.P.) and U54MD012388 (J.G.C. and T.P.); grants from the Alfred P. Sloan Foundation (J.G.C. and R.K.); ERCSTG project MetaPG (N.S.); the Strategic Priority Research Program of the Chinese Academy of Sciences QYZDB-SSW-SMC021 (Y.B.); the Australian National Health and Medical Research Council APP1085372 (G.A.H., J.G.C., Von Bing Yap and R.K.); the Natural Sciences and Engineering Research Council (NSERC) to D.L.G.; and the State of Arizona Technology and Research Initiative Fund (TRIF), administered by the Arizona Board of Regents, through Northern Arizona University. All NCI coauthors were supported by the Intramural Research Program of the National Cancer Institute. S.M.G. and C. Diener were supported by the Washington Research Foundation Distinguished Investigator Award.

Polycystic ovary syndrome (PCOS) is a common endocrine disorder affecting approximately 10% of reproductive-aged women worldwide. Diagnosis requires two of the following: hyperandrogenism, oligo/anovulation and polycystic ovaries. In addition to reproductive dysfunction, many women with PCOS display metabolic abnormalities associated with hyperandrogenism. Recent studies have reported that the gut microbiome is altered in women with PCOS and rodent models of the disorder. However, it is unknown whether the gut microbiome plays a causal role in the development and pathology of PCOS. Given its potential role, we hypothesized that exposure to a healthy gut microbiome would protect against development of PCOS. A co-housing study was performed using a letrozole-induced PCOS mouse model that recapitulates many reproductive and metabolic characteristics of PCOS. Since mice are coprophagic, co-housing results in repeated, non-invasive inoculation of gut microbes in co-housed mice via the fecal-oral route. In contrast to letrozole-treated mice housed together, letrozole-treated mice co-housed with placebo mice showed significant improvement in both reproductive and metabolic PCOS phenotypes. Using 16S rRNA gene sequencing, we observed that the gut microbial composition of letrozole-treated mice co-housed with placebo mice differed from letrozole mice housed together. In addition, our analyses identified several bacterial taxa including Coprobacillus, Dorea and Adlercreutzia associated with the improved PCOS phenotype in letrozole-treated mice co-housed with placebo mice. These results indicate that disruption of the gut microbiome may play a causal role in PCOS and that manipulation of the gut microbiome may be a potential treatment option for PCOS.SignificancePCOS is a common cause of female infertility and ~80% of women with PCOS have metabolic dysregulation that predisposes them to type 2 diabetes and cardiovascular disease. Since treatment options for the metabolic symptoms of PCOS are limited, there is a need to develop novel therapeutic options. The gut microbiome has emerged as an important player in human health and has been shown to play a causal role in obesity. In this study, we found that exposure to a healthy gut microbiome through co-housing protected against the development of reproductive and metabolic dysregulation in a PCOS mouse model. These results suggest that manipulation of the gut microbiome may be a potential treatment option for women with PCOS.

We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science.

One of the world’s most common infectious disease, periodontitis (PD), derives from largely uncharacterized communities of oral bacteria growing as biofilms (a.k.a. plaque) on teeth and gum surfaces in periodontal pockets. Bacteria associated with periodontal disease trigger inflammatory responses in immune cells, which in later stages of the disease cause loss of both soft and hard tissue structures supporting teeth. Thus far, only a handful of bacteria have been characterized as infectious agents of PD. Although deep sequencing technologies, such as whole community shotgun sequencing have the potential to capture a detailed picture of highly complex bacterial communities in any given environment, we still lack major reference genomes for the oral microbiome associated with PD and other diseases. In recent work, by using a combination of supervised machine learning and genome assembly, we identified a genome from a novel member of the Bacteroidetes phylum in periodontal samples. Here, by applying a comparative metagenomics read-classification approach, including 272 metagenomes from various human body sites, and our previously assembled draft genome of the uncultivated Candidatus Bacteroides periocalifornicus (CBP) bacterium, we show CBP’s ubiquitous distribution in dental plaque, as well as its strong association with the well-known pathogenic “red complex” that resides in deep periodontal pockets. Electronic supplementary material The online version of this article (10.1007/s00248-018-1200-6) contains supplementary material, which is available to authorized users.