Systematically assessing microbiome-disease associations identifies drivers of inconsistency in metagenomic research.

Evaluating the relationship between the human gut microbiome and disease requires computing reliable statistical associations. Here, using millions of different association modeling strategies, we evaluated the consistency-or robustness-of microbiome-based disease indicators for 6 prevalent and well-studied phenotypes (across 15 public cohorts and 2,343 individuals). We were able to discriminate between analytically robust versus nonrobust results. In many cases, different models yielded contradictory associations for the same taxon-disease pairing, some showing positive correlations and others negative. When querying a subset of 581 microbe-disease associations that have been previously reported in the literature, 1 out of 3 taxa demonstrated substantial inconsistency in association sign. Notably, >90% of published findings for type 1 diabetes (T1D) and type 2 diabetes (T2D) were particularly nonrobust in this regard. We additionally quantified how potential confounders-sequencing depth, glucose levels, cholesterol, and body mass index, for example-influenced associations, analyzing how these variables affect the ostensible correlation between Faecalibacterium prausnitzii abundance and a healthy gut. Overall, we propose our approach as a method to maximize confidence when prioritizing findings that emerge from microbiome association studies.

Modeling the Effect of TNF-α upon Drug-Induced Toxicity in Human, Tissue-Engineered Myobundles.

A number of significant muscle diseases, such as cachexia, sarcopenia, systemic chronic inflammation, along with inflammatory myopathies share TNF-α-dominated inflammation in their pathogenesis. In addition, inflammatory episodes may increase susceptibility to drug toxicity. To assess the effect of TNF-α-induced inflammation on drug responses, we engineered 3D, human skeletal myobundles, chronically exposed them to TNF-α during maturation, and measured the combined response of TNF-α and the chemotherapeutic doxorubicin on muscle function. First, the myobundle inflammatory environment was characterized by assessing the effects of TNF-α on 2D human skeletal muscle cultures and 3D human myobundles. High doses of TNF-α inhibited maturation in human 2D cultures and maturation and function in 3D myobundles. Then, a tetanus force dose-response curve was constructed to characterize doxorubicin's effects on function alone. The combination of TNF-α and 10 nM doxorubicin exhibited a synergistic effect on both twitch and tetanus force production. Overall, the results demonstrated that inflammation of a 3D, human skeletal muscle inflammatory system alters the response to doxorubicin.

Human, Tissue-Engineered, Skeletal Muscle Myobundles to Measure Oxygen Uptake and Assess Mitochondrial Toxicity.

Mitochondrial dysfunction is responsible for the toxicity of a number of drugs. Current isolated mitochondria or cellular monoculture mitochondrial respiration measurement systems lack physiological relevance. Using a tissue engineering rather than cell- or mitochondria-based approach enables a more physiologically relevant detection of drug-induced mitochondrial impairment. To probe oxygen consumption and mitochondrial health, we assayed the bioenergetic profile of engineered three-dimensional human skeletal muscle myobundles derived from primary myoblasts. Through experimental and computational techniques, we did not find external or internal oxygen transport limiting the engineered myobundles in the commercial O2k system to measure oxygen consumption. In response to the complex I inhibitor rotenone, myobundle basal respiration decreased dose dependently with an IC50 of 9.24 ± 0.03 nM. At a 20 nM concentration of rotenone, myobundle maximal respiration decreased by 44.4% ± 9.8%. Respiratory depression by rotenone suggests that cultured myobundles rely heavily on the complex I pathway for ATP synthesis during times of both basal and increased energy demand. To address whether these decrements in mitochondrial function corresponded to alterations in physiological muscle function, we determined fatigue susceptibility that revealed a 46.0% ± 7.4% depression at 20 nM rotenone. The bioenergetic health index, which is a measure of normal oxidative mitochondrial function, was inversely correlated with the extent of fatigue. The human myobundles reproduce normal muscle metabolism under both basal and maximal energy demand conditions enabling the detection of drug-induced mitochondrial toxicity.

The effect of obesity on 12-month survival following admission to intensive care: a prospective study.

OBJECTIVE: Evaluate the effect of intensive care (ICU) admission body mass index (BMI) on 30-day and 12-month survival in critically ill patients and determine the impact of obesity on outcome. DESIGN: Prospective, observational cohort study. SETTING: Fourteen-bed medical and surgical ICU of a university-affiliated hospital. PATIENTS: Four hundred and ninety-three adult patients. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: BMI (kg/m) was calculated from height (m) and measured weight (kg) within 4 hrs of ICU admission, using the PROMED weighing device, or premorbid weight (documented in the previous month) (BMImeasured). Follow-up was for >/=12 months post-ICU admission. Time to mortality outcome, censored at 30 and 365 days (12-months), was analyzed using a log-normal accelerated failure time regression model. Predictor variables were parameterized as time ratios (TR), where TR <1 is associated with decreased survival time and TR >1 is associated with prolonged survival time. Mean (sd) age and Acute Physiology and Chronic Health Evaluation II score were 62.3 (17.5) years and 20.7(8.4), respectively; 56.0% (285 of 493) of patients were male and 60.6% (299 of 493) medical. ICU admission weight and BMImeasured (available in 433 patients) were 79.1 (22.1) kg and 27.8 (7.0) kg/m, respectively. In 16.9% (73 of 433) of patients, weight was >/=100 kg, and in 29.8% (129 of 433), BMImeasured was >/=30 kg/m. Raw intensive care, 30-day, and 12-month mortality rates were 15.2% (66 of 433), 22.3% (95 of 433), and 37.3% (159 of 433), respectively. BMImeasured was a significant determinant of mortality at 30 days (TR 1.853, 95% confidence interval 1.053-3.260, p = .032) and 12 months (TR 1.034, 95% confidence interval 1.005-1.063, p = .019). The effect of BMI on 12-month mortality was linear, such that increasing BMI was associated with decreasing mortality. CONCLUSIONS: ICU admission BMI was a determinant of short- to medium-term survival. Obesity was not associated with adverse outcomes and may be protective.