A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research.

Our understanding of how the gut microbiome interacts with its human host has been restrained by limited access to longitudinal datasets to examine stability and dynamics, and by having only a few isolates to test mechanistic hypotheses. Here, we present the Broad Institute-OpenBiome Microbiome Library (BIO-ML), a comprehensive collection of 7,758 gut bacterial isolates paired with 3,632 genome sequences and longitudinal multi-omics data. We show that microbial species maintain stable population sizes within and across humans and that commonly used 'omics' survey methods are more reliable when using averages over multiple days of sampling. Variation of gut metabolites within people over time is associated with amino acid levels, and differences across people are associated with differences in bile acids. Finally, we show that genomic diversification can be used to infer eco-evolutionary dynamics and in vivo selection pressures for strains within individuals. The BIO-ML is a unique resource designed to enable hypothesis-driven microbiome research.

Metabolomics signatures associated with an oral glucose challenge in pregnant women.

AIM: The oral glucose tolerance test (OGTT), widely used as a gold standard for gestational diabetes mellitus (GDM) diagnosis, provides a broad view of glucose pathophysiology in response to a glucose challenge. We conducted the present study to evaluate metabolite changes before and after an oral glucose challenge in pregnancy; and to examine the extent to which metabolites may serve to predict GDM diagnosis in pregnant women. METHODS: Peruvian pregnant women (n=100) attending prenatal clinics (mean gestation 25 weeks) participated in the study with 23% of them having GDM diagnosis. Serum samples were collected immediately prior to and 2-hours after administration of a 75-g OGTT. Targeted metabolic profiling was performed using a LC-MS based metabolomics platform. Changes in metabolite levels were evaluated using paired Student's t-tests and the change patterns were examined at the level of pathways. Multivariate regression procedures were used to examine metabolite pairwise differences associated with subsequent GDM diagnosis. RESULTS: Of the 306 metabolites detected, the relative concentration of 127 metabolites were statistically significantly increased or decreased 2-hours after the oral glucose load (false discovery rate [FDR] corrected P-value<0.001). We identified relative decreases in metabolites in acylcarnitines, fatty acids, and diacylglycerols while relative increases were noted among bile acids. In addition, we found that C58:10 triacylglycerol (ß=-0.08, SE=0.04), C58:9 triacylglycerol (ß=-0.07, SE=0.03), adenosine (ß=0.70, SE=0.32), methionine sulfoxide (ß=0.36, SE=0.13) were significantly associated with GDM diagnosis even after adjusting for age and body mass index. CONCLUSIONS: We identified alterations in maternal serum metabolites, representing distinct cellular and metabolic pathways including fatty acid metabolism, in response to an oral glucose challenge. These findings offer novel perspectives on the pathophysiological mechanisms underlying GDM.

Role of OATP transporters in steroid uptake by prostate cancer cells in vivo.

BACKGROUND: Epidemiologic and in vitro studies suggest that SLCO-encoded organic anion transporting polypeptide (OATP) transporters influence the response of prostate cancer (PCa) to androgen deprivation by altering intratumor androgens. We have previously shown that castration-resistant metastases express multiple SLCO transporters at significantly higher levels than primary PCa, suggesting that OATP-mediated steroid transport is biologically relevant in advanced disease. However, whether OATP-mediated steroid transport can actually modify prostate tumor androgen levels in vivo has never been demonstrated. METHODS: We sought to determine whether OATP-mediated steroid transport can measurably alter PCa androgen levels in vivo. We evaluated the uptake of dehydroepiandrosterone (DHEAS), E1S and testosterone in LNCaP cells engineered to express OATP1B1, 1B3, 2B1 or 4A1. We measured the uptake via administration of tritiated steroids to castrate mice bearing vector control or OATP1B1-, 2B1- or 4A1-expressing xenografts. We treated tumor-bearing mice with DHEAS and testosterone at physiologically relevant levels and measured intratumor accumulation of administered steroids by mass spectrometry. RESULTS: OATP1B1- and 2B-expressing xenografts each showed a threefold increase in tritiated-DHEAS uptake vs vector controls (P=0.002 and P=0.036, respectively). At circulating DHEAS levels similar to those in abiraterone-treated men (~15 µg dl-1), OATP1B1- and 2B1-expressing xenografts showed a 3.9-fold (P=0.057) and 1.9-fold (P=0.048) increase in tumor accumulation of DHEAS and a 1.6-fold (P=0.057) and 2.7-fold (P=0.095) increase in DHEA, respectively. At the substantial circulating testosterone levels found in eugonadal men, a consistent effect of OATP1B1, 2B1 or 4A1 on testosterone uptake in vivo was not detected. CONCLUSIONS: OATP transporters measurably alter DHEAS uptake and intratumor androgen levels in prostate tumors in vivo, even at circulating androgen levels achieved in abiraterone-treated patients. These novel data emphasize the continued need to inhibit ligand-mediated androgen receptor signaling in PCa tumors, and support prospective evaluation of studies designed to test inhibition of OATP-mediated DHEAS uptake and utilization.

Recurrent Clostridium difficile infection associates with distinct bile acid and microbiome profiles.

BACKGROUND: The healthy microbiome protects against the development of Clostridium difficile infection (CDI), which typically develops following antibiotics. The microbiome metabolises primary to secondary bile acids, a process if disrupted by antibiotics, may be critical for the initiation of CDI. AIM: To assess the levels of primary and secondary bile acids associated with CDI and associated microbial changes. METHODS: Stool and serum were collected from patients with (i) first CDI (fCDI), (ii) recurrent CDI (rCDI) and (iii) healthy controls. 16S rRNA sequencing and bile salt metabolomics were performed. Random forest regression models were constructed to predict disease status. PICRUSt analyses were used to test for associations between predicted bacterial bile salt hydrolase (BSH) gene abundances and bile acid levels. RESULTS: Sixty patients (20 fCDI, 19 rCDI and 21 controls) were enrolled. Secondary bile acids in stool were significantly elevated in controls compared to rCDI and fCDI (P < 0.0001 and P = 0.0007 respectively). Primary bile acids in stool were significantly elevated in rCDI compared to controls (P < 0.0001) and in rCDI compared to fCDI (P = 0.02). Using random forest regression, we distinguished rCDI and fCDI patients 84.2% of the time using bile acid ratios. Stool deoxycholate to glycoursodeoxycholate ratio was the single best predictor. PICRUSt analyses found significant differences in predicted abundances of bacterial BSH genes in stool samples across the groups. CONCLUSIONS: Primary and secondary bile acid composition in stool was different in those with rCDI, fCDI and controls. The ratio of stool deoxycholate to glycoursodeoxycholate was the single best predictor of disease state and may be a potential biomarker for recurrence.

Simultaneous spontaneous bilateral pneumothoraces in an asthmatic / Neumotórax espontáneos bilaterales simultáneos en un asmático

The occurrence of simultaneous spontaneous bilateral pneumothoraces is a very rare event. We present a case of a 14-year old asthmatic female patient who presented to the emergency room for routine treatment. While receiving nebulizations, she suddenly developed supraclavicular fullness with crepitus. Further examination revealed a clinical diagnosis of bilateral pneumothoraces. Although this phenomenon is more commonly associated with patients on mechanical ventilation, this case illustrates that physicians must be cognizant of this unique presentation in order to initiate early and aggressive life- saving therapy. With rapid bilateral needle thoracocentesis followed by placement of bilateral thora-costomy tubes, the patient recovered well. In this report, we also attempt to briefly review the possible pathophysiology of this form of spontaneous pneumothorax.

La incidencia del neumotórax espontáneo bilateral simultáneo en un asmático es un acontecimiento raro. Presentamos un caso de una paciente asmática hembra de 14 años de edad, quien acudió a la sala de emergencia para tratamiento de rutina. Mientras recibía nebulizaciones, desarrolló súbitamente plenitud supraclavicular con crépito. El examen posterior reveló un diagnóstico clínico de pneumotórax bilateral. Aunque este fenómeno se halla más comúnmente asociado con pacientes en ventilación mecánica, este caso ilustra que los médicos tienen que tener conciencia de esta presentación única para iniciar una terapia agresiva y temprana que haga posible la salvación del paciente. Con una rápida toracocentesis bilateral mediante aguja, seguida de colocaciones de tubos de tora-costomía bilateral, la paciente se recuperó bien. En este reporte también intentamos realizar una breve revisión de la posible patofisiología de esta forma de neumotórax espontáneo.

Group therapy for patients with psychogenic nonepileptic seizures: a pilot study.

Great advances have been made in the diagnosis of people with psychogenic nonepileptic seizures (PNES) since the advent of video/EEG monitoring. However, treatment options for this population have lagged significantly. This pilot study was undertaken to evaluate whether group therapy done with a psychodynamic focus would offer a useful intervention. Twelve patients entered the study and seven completed at least 75% of the 32 weekly sessions. The Beck Depression Inventory and the Global Severity Index of the Symptom Checklist-90 showed improvement as well as an overall decrease in PNES frequency. The data suggest that group therapy focusing on interpersonal issues may benefit patients with PNES.

Simultaneous spontaneous bilateral pneumothoraces in an asthmatic.

The occurrence of simultaneous spontaneous bilateral pneumothoraces is a very rare event. We present a case of a 14-year old asthmatic female patient who presented to the emergency room for routine treatment. While receiving nebulizations, she suddenly developed supraclavicular fullness with crepitus. Further examination revealed a clinical diagnosis of bilateral pneumothoraces. Although this phenomenon is more commonly associated with patients on mechanical ventilation, this case illustrates that physicians must be cognizant of this unique presentation in order to initiate early and aggressive lifesaving therapy. With rapid bilateral needle thoracocentesis followed by placement of bilateral thoracostomy tubes, the patient recovered well. In this report, we also attempt to briefly review the possible pathophysiology of this form of spontaneous pneumothorax.

A simple processing method allowing comparison of renal enhancing volumes derived from standard portal venous phase contrast-enhanced multidetector CT images to derive a CT estimate of differential renal function with equivalent results to nuclear medicine quantification.

As iodinated contrast medium is cleared by glomerular filtration, it should be possible to apply the same principles utilized in radionuclide studies to derive differential renal function by comparison of enhancing renal volumes derived from contrast enhanced multidetector CT (CEMDCT). Having established a technique iteratively which appeared successful, a retrospective study was performed using 25 consecutive patients with a wide range of urological conditions who had undergone both CEMDCT, including the renal area in the portal venous phase, and nuclear medicine (NM) assessment of renal function with no urological intervention between the studies. Proprietary volume software was used to quantify the volume and attenuation of each kidney, the products of which (after subtraction of soft tissue attenuation derived from a region of interest over psoas) gave right and left enhancing renal volumes. The contribution by each kidney as a percentage of total renal enhancing tissue was derived. Comparison with NM studies resulted in excellent correlation of relative renal function by CEMDCT and NM assessments having a regression of near unity and a Pearson's correlation coefficient of 0.96. Bland Altman and Passing Bablock tests confirmed good agreement between the two methods with no bias. This is a simple, practicable processing technique using standard portal venous phase CEMDCT images to quantify differential function. This technique may allow a one-stop CT assessment of both anatomy and function.

Descending urethral ultrasound of the native and reconstructed urethra in patients with hypospadias.

A retrospective study, over a 7 year period, examining the use of descending urethral ultrasound in corrected and uncorrected hypospadias was performed. 15 examinations were performed on 14 patients; 12 patients had undergone previous surgery for hypospadias, ranging from urethral reconstruction to stricture dilatation. Eight strictures, four irregular urethras, two normal post-operative urethras and one urethral valve were demonstrated. All the clinically significant abnormalities (those which impaired the flow of urine) demonstrated by ultrasound were confirmed with subsequent urethroscopy or contrast urethrography. This small series illustrates the application of descending urethral ultrasound in patients with hypospadias who are difficult to examine with more conventional radiographic techniques.

Interaction between complement receptor gC1qR and hepatitis C virus core protein inhibits T-lymphocyte proliferation.

Hepatitis C virus (HCV) is an important human pathogen that is remarkably efficient at establishing persistent infection. The HCV core protein is the first protein expressed during the early phase of HCV infection. Our previous work demonstrated that the HCV core protein suppresses host immune responses, including anti-viral cytotoxic T-lymphocyte responses in a murine model. To investigate the mechanism of HCV core-mediated immunosuppression, we searched for host proteins capable of associating with the core protein using a yeast two-hybrid system. Using the core protein as bait, we screened a human T cell-enriched expression library and identified a gene encoding the gC1q receptor (gC1qR). C1q is a ligand of gC1qR and is involved in the early host defense against infection. Like C1q, HCV core can inhibit T-cell proliferative responses in vitro. This core-induced anti-T-cell proliferation is reversed by addition of anti-gC1qR Ab in a T-cell proliferation assay. Furthermore, biochemical analysis of the interaction between core and gC1qR indicates that HCV core binds the region spanning amino acids 188 to 259 of gC1qR, a site distinct from the binding region of C1q. The inhibition of T-cell responsiveness by HCV core may have important implications for HCV persistence in humans.

Relationship between a bull's parental genetic merit difference and subsequent progeny trait variability in Angus, Gelbvieh, and Limousin cattle.

Data from the American Angus Association, American Gelbvieh Association, and the North American Limousin Foundation were analyzed to determine whether parental genetic differences are associated with Mendelian sampling of their bull progeny or with Mendelian sampling variances and weight variances of their bull progeny's offspring. Parental differences were measured as the difference between the parents' EPD for birth weight (DIF(BW)), weaning weight direct (DIF(WW)), and yearling weight (DIF(YW)). A bull's data were used if both parents had calculated EPD and the bull had at least 25 progeny with records for the specific trait. Traits calculated for each bull were his Mendelian sampling (MS(Bull)), progeny Mendelian sampling variance (MSsigma2progeny), progeny weight variance (WTsigma2), and progeny corrected weight variance (CWTsigma2 = adjusted weight minus appropriate dam EPD) for birth, weaning, and yearling weights. Pearson correlations were computed between DIF(BW), DIF(WW), and DIF(YW) and MS(Bull), MSsigma2progeny, WTsigma2, and CWTsigma2 for each trait, within each breed. Across breeds, the correlations ranged from -.07 to .11 for MS(Bull) .01 to .14 for MSsigma2progeny, -.06 to .09 for WTsigma2, and -.06 to .08 for CWTsigma2. Although some of the correlations were significantly different from zero their relatively small magnitude indicates little relationship between parental differences in genetic merit and subsequent offspring variability for each of the three breeds.

Is the conservative management of ureteric calculi of > 4 mm safe?

OBJECTIVE: To determine the safety of the conservative management of ureteric calculi of > 4 mm in diameter, using mercapto-acetyltriglycine (MAG3) radioisotope renography to monitor renal parenchymal function. PATIENTS AND METHODS: Patients with symptomatic unilateral ureteric calculi were recruited prospectively. After confirming the position of the stone using contrast urography, a MAG3 radioisotope renogram was taken within 48 h of admission and again 1 month after the patients became stone-free. The indications for intervention were ipsilateral loss of function (>/= 5% loss), infection, pain or any combination of these factors. The recovery of function was determined by follow-up renography. RESULTS: In all, 54 patients were recruited; 18 were initially allocated to conservative treatment although four later required intervention for pain. The remainder required early intervention for pain (eight), diminished function only (15) or diminished function with infection (13). Of the 54 patients, 28% had 'silent' loss of renal function at presentation. No calculi of > 7 mm diameter passed without intervention. The mode of initial management was determined according to individual clinical need. The upper tracts of all patients were relieved of obstruction and all patients were rendered stone-free. Intervention for reduced function only (at

Dental care of patients with substance abuse.

Patients who abuse alcohol, crack, heroin or prescription drugs, are likely to interact with the dental professional. The dentist should therefore be able to identify problems of abuse and provide informed care and referral. Substance abuse should be a consideration in all patients who present with dental trauma and those who present with frequent vague complaints, multiple pain medication allergies, and regimens with multiple narcotic medications. Polydrug use, either prescription or illicit, is also a possibility, and effective treatment requires prompt recognition. Dentists should be alert to drug-seeking behavior within the context of pain management, and because pain severity is an objective experience, each patient must be treated carefully and sensitively. Unrelieved or unremitting pain can be a relapse trigger and therefore adequate pain control is a necessity in the recovering chemically dependent patient. New modalities, such as coanalgesia with low-dose ketamine in the opioid addicted have been shown to work effectively. In the post-dental surgical patient with chemical dependency, agents with less psychoactive activity than their drugs of abuse, such as extended-release morphine (MS Contin) have been tried with variable success. An informed treatment plan includes recognition of substance abuse, appropriate intervention, and referral. This plan may include universal screening, followed by brief interventional therapy for positive patients and in some cases, pharmacological pain control. On discharge from the office, instructions concerning referral to a substance abuse program or, in the case of the patient who may require more immediate treatment, to the emergency department are important.