Translating Microbiome Research From and To the Clinic.

Extensive research has elucidated the influence of the gut microbiota on human health and disease susceptibility and resistance. We review recent clinical and laboratory-based experimental studies associating the gut microbiota with certain human diseases. We also highlight ongoing translational advances that manipulate the gut microbiota to treat human diseases and discuss opportunities and challenges in translating microbiome research from and to the bedside.

Community-acquired Coinfection in Coronavirus Disease 2019: A Retrospective Observational Experience.

Community-acquired coinfection in coronavirus disease 2019 (COVID-19) is not well defined. Current literature describes coinfection in 0-40% of COVID-19 patients. In this retrospective report, coinfection was identified in 3.7% of patients and 41% of patients admitted to intensive care (P < .005). Despite infrequent coinfection, antibiotics were used in 69% of patients.

Increasing importance of deposition of reduced nitrogen in the United States.

Rapid development of agriculture and fossil fuel combustion greatly increased US reactive nitrogen emissions to the atmosphere in the second half of the 20th century, resulting in excess nitrogen deposition to natural ecosystems. Recent efforts to lower nitrogen oxides emissions have substantially decreased nitrate wet deposition. Levels of wet ammonium deposition, by contrast, have increased in many regions. Together these changes have altered the balance between oxidized and reduced nitrogen deposition. Across most of the United States, wet deposition has transitioned from being nitrate-dominated in the 1980s to ammonium-dominated in recent years. Ammonia has historically not been routinely measured because there are no specific regulatory requirements for its measurement. Recent expansion in ammonia observations, however, along with ongoing measurements of nitric acid and fine particle ammonium and nitrate, permit new insight into the balance of oxidized and reduced nitrogen in the total (wet + dry) US nitrogen deposition budget. Observations from 37 sites reveal that reduced nitrogen contributes, on average, ∼65% of the total inorganic nitrogen deposition budget. Dry deposition of ammonia plays an especially key role in nitrogen deposition, contributing from 19% to 65% in different regions. Future progress toward reducing US nitrogen deposition will be increasingly difficult without a reduction in ammonia emissions.

Evaluation of the Impact of National HIV Testing Day - United States, 2011-2014.

Human immunodeficiency virus (HIV) testing is the first step in the continuum of HIV prevention, care, and treatment services, without which, gaps in HIV diagnosis cannot be addressed. National HIV testing campaigns are useful for promoting HIV testing among large numbers of persons. However, the impact of such campaigns on identification of new HIV-positive diagnoses is unclear. To assess whether National HIV Testing Day (NHTD, June 27) was effective in identifying new HIV-positive diagnoses, National HIV Prevention Program Monitoring and Evaluation (NHM&E) data for CDC-funded testing events conducted during 2011-2014 were analyzed. The number of HIV testing events and new HIV-positive diagnoses during June of each year were compared with those in other months by demographics and target populations. The number of HIV testing events and new HIV-positive diagnoses were also compared for each day leading up to and after NHTD in June and July of each year. New HIV-positive diagnoses peaked in June relative to other months and specifically on NHTD. During 2011-2014, NHTD had a substantial impact on increasing the number of persons who knew their HIV status and in diagnosing new HIV infections. NHTD also proved effective in reaching persons at high risk disproportionately affected by HIV, including African American (black) men, men who have sex with men (MSM), and transgender persons. Promoting NHTD can successfully increase the number of new HIV-positive diagnoses, including HIV infections among target populations at high risk for HIV infection.

Fecal metabolite profiling identifies liver transplant recipients at risk for postoperative infection.

Metabolites produced by the intestinal microbiome modulate mucosal immune defenses and optimize epithelial barrier function. Intestinal dysbiosis, including loss of intestinal microbiome diversity and expansion of antibiotic-resistant pathobionts, is accompanied by changes in fecal metabolite concentrations and increased incidence of systemic infection. Laboratory tests that quantify intestinal dysbiosis, however, have yet to be incorporated into clinical practice. We quantified fecal metabolites in 107 patients undergoing liver transplantation (LT) and correlated these with fecal microbiome compositions, pathobiont expansion, and postoperative infections. Consistent with experimental studies implicating microbiome-derived metabolites with host-mediated antimicrobial defenses, reduced fecal concentrations of short- and branched-chain fatty acids, secondary bile acids, and tryptophan metabolites correlate with compositional microbiome dysbiosis in LT patients and the relative risk of postoperative infection. Our findings demonstrate that fecal metabolite profiling can identify LT patients at increased risk of postoperative infection and may provide guideposts for microbiome-targeted therapies.

Effects of mercury deposition and coniferous forests on the mercury contamination of fish in the South Central United States.

Mercury (Hg) is a toxic metal that is found in aquatic food webs and is hazardous to human and wildlife health. We examined the relationship between Hg deposition, land coverage by coniferous and deciduous forests, and average Hg concentrations in largemouth bass (Micropterus salmoides)-equivalent fish (LMBE) in 14 ecoregions located within all or part of six states in the South Central U.S. In 11 ecoregions, the average Hg concentrations in 35.6-cm total length LMBE were above 300 ng/g, the threshold concentration of Hg recommended by the U.S. Environmental Protection Agency for the issuance of fish consumption advisories. Percent land coverage by coniferous forests within ecoregions had a significant linear relationship with average Hg concentrations in LMBE while percent land coverage by deciduous forests did not. Eighty percent of the variance in average Hg concentrations in LMBE between ecoregions could be accounted for by estimated Hg deposition after adjusting for the effects of coniferous forests. Here we show for the first time that fish from ecoregions with high atmospheric Hg pollution and coniferous forest coverage pose a significant hazard to human health. Our study suggests that models that use Hg deposition to predict Hg concentrations in fish could be improved by including the effects of coniferous forests on Hg deposition.

Reduced immunomodulatory metabolite concentrations in peri-transplant fecal samples from heart allograft recipients.

Background: Emerging evidence is revealing the impact of the gut microbiome on hematopoietic and solid organ transplantation. Prior studies postulate that this influence is mediated by bioactive metabolites produced by gut-dwelling commensal bacteria. However, gut microbial metabolite production has not previously been measured among heart transplant (HT) recipients. Methods: In order to investigate the potential influence of the gut microbiome and its metabolites on HT, we analyzed the composition and metabolite production of the fecal microbiome among 48 HT recipients at the time of HT. Results: Compared to 20 healthy donors, HT recipients have significantly reduced alpha, i.e. within-sample, microbiota diversity, with significantly lower abundances of key anaerobic commensal bacteria and higher abundances of potentially pathogenic taxa that have been correlated with adverse outcomes in other forms of transplantation. HT recipients have a wide range of microbiota-derived fecal metabolite concentrations, with significantly reduced levels of immune modulatory metabolites such as short chain fatty acids and secondary bile acids compared to healthy donors. These differences were likely due to disease severity and prior antibiotic exposures but were not explained by other demographic or clinical factors. Conclusions: Key potentially immune modulatory gut microbial metabolites are quantifiable and significantly reduced among HT recipients compared to healthy donors. Further study is needed to understand whether this wide range of gut microbial dysbiosis and metabolite alterations impact clinical outcomes and if they can be used as predictive biomarkers or manipulated to improve transplant outcomes.

Bifidobacteria metabolize lactulose to optimize gut metabolites and prevent systemic infection in patients with liver disease.

Progression of chronic liver disease is precipitated by hepatocyte loss, inflammation and fibrosis. This process results in the loss of critical hepatic functions, increasing morbidity and the risk of infection. Medical interventions that treat complications of hepatic failure, including antibiotic administration for systemic infections and lactulose treatment for hepatic encephalopathy, can impact gut microbiome composition and metabolite production. Here, using shotgun metagenomic sequencing and targeted metabolomic analyses on 847 faecal samples from 262 patients with acute or chronic liver disease, we demonstrate that patients hospitalized for liver disease have reduced microbiome diversity and a paucity of bioactive metabolites, including short-chain fatty acids and bile acid derivatives, that impact immune defences and epithelial barrier integrity. We find that patients treated with the orally administered but non-absorbable disaccharide lactulose have increased densities of intestinal bifidobacteria and reduced incidence of systemic infections and mortality. Bifidobacteria metabolize lactulose, produce high concentrations of acetate and acidify the gut lumen in humans and mice, which, in combination, can reduce the growth of antibiotic-resistant bacteria such as vancomycin-resistant Enterococcus faecium in vitro. Our studies suggest that lactulose and bifidobacteria serve as a synbiotic to reduce rates of infection in patients with severe liver disease.

Wet deposition of fission-product isotopes to North America from the Fukushima Dai-ichi incident, March 2011.

Using the infrastructure of the National Atmospheric Deposition Program (NADP), numerous measurements of radionuclide wet deposition over North America were made for 167 NADP sites before and after the Fukushima Dai-ichi Nuclear Power Station incident of March 12, 2011. For the period from March 8 through April 5, 2011, wet-only precipitation samples were collected by NADP and analyzed for fission-product isotopes within whole-water and filterable solid samples by the United States Geological Survey using gamma spectrometry. Variable amounts of (131)I, (134)Cs, or (137)Cs were measured at approximately 21% of sampled NADP sites distributed widely across the contiguous United States and Alaska. Calculated 1- to 2-week individual radionuclide deposition fluxes ranged from 0.47 to 5100 Becquerels per square meter during the sampling period. Wet deposition activity was small compared to measured activity already present in U.S. soil. NADP networks responded to this complex disaster, and provided scientifically valid measurements that are comparable and complementary to other networks in North America and Europe.

Immunomodulatory fecal metabolites are associated with mortality in COVID-19 patients with respiratory failure.

Respiratory failure and mortality from COVID-19 result from virus- and inflammation-induced lung tissue damage. The intestinal microbiome and associated metabolites are implicated in immune responses to respiratory viral infections, however their impact on progression of severe COVID-19 remains unclear. We prospectively enrolled 71 patients with COVID-19 associated critical illness, collected fecal specimens within 3 days of medical intensive care unit admission, defined microbiome compositions by shotgun metagenomic sequencing, and quantified microbiota-derived metabolites (NCT #04552834). Of the 71 patients, 39 survived and 32 died. Mortality was associated with increased representation of Proteobacteria in the fecal microbiota and decreased concentrations of fecal secondary bile acids and desaminotyrosine (DAT). A microbiome metabolic profile (MMP) that accounts for fecal secondary bile acids and desaminotyrosine concentrations was independently associated with progression of respiratory failure leading to mechanical ventilation. Our findings demonstrate that fecal microbiota composition and microbiota-derived metabolite concentrations can predict the trajectory of respiratory function and death in patients with severe SARS-Cov-2 infection and suggest that the gut-lung axis plays an important role in the recovery from COVID-19.

Passive ammonia monitoring in the United States: comparing three different sampling devices.

The need for ambient gaseous ammonia (NH(3)) measurements has increased in the last decade as reactive NH(3) concentrations and deposition fluxes show little change even with tightening standards on nitrogen oxides (NO(x)) emissions. Currently, there are several networks developing methods for adding NH(3) measurements in the U.S. Gaseous NH(3) measurements will provide scientists and policymakers data which can be used to estimate ecosystem inputs, validate air quality models including trends and regional variability, and evaluate changes to the environment based on additional emission reduction requirements and estimates of critical nitrogen load exceedances. The passive samplers described in this paper were deployed in duplicate or triplicate and collocated with annular denuders or continuous instruments to determine their accuracy. The samplers assessed included the Adapted Low-Cost Passive High Absorption (ALPHA), Radiello(®), and Ogawa passive samplers. The median relative percent differences (MRPD) between the reference method and passive samplers for the ALPHA, Radiello(®) and Ogawa were -2.4%, -37% and -44%, respectively. The precision between duplicate samplers for the ALPHA and Ogawa samplers, was 7% and 6%, respectively. Triplicate Radiello(®) precision was assessed using the coefficient of variation (CV). The CV for the Radiello(®) samplers was 10%. This article discusses the statistical results from these studies.

Cancer, transplant, and immunocompromising conditions were not significantly associated with severe illness or death in hospitalized COVID-19 patients.

OBJECTIVE: Patients with cancer, transplant, and other immunocompromising conditions are at uncertain risk of severe COVID-19 illness. This study aimed to clarify whether patients with immunocompromising conditions were more likely to develop severe COVID-19 illness in a single urban academic medical center. METHODS: A retrospective chart review and electronic data extraction of the first 401 patients at the University of Chicago Hospitals with SARS-CoV-2 infection was performed. Patients met criteria for severe COVID-19 illness if they required ICU level care, high flow oxygen, positive pressure support, helmet non-invasive ventilation, mechanical ventilation, or ECMO, developed ARDS, or died. RESULTS: The mean age was 60 years, 52% were women, 90% were African American, and mortality at 30 days post discharge was 13%. Severe COVID-19 illness was found in 168 (40%) patients. Of the 56 patients with past or current cancer, 25 (45%) had severe illness (p=0.76). Of the 55 patients with other immunocompromised conditions, 24 (44%) had severe illness (p=0.89) After controlling for age, sex, and race, neither cancer (p=0.73) nor immunocompromised conditions (p=0.64) were associated with severe illness. CONCLUSION: No association was found between severe COVID-19 illness and cancer, transplant, and other immunocompromising conditions in a cohort of mostly African American patients.

Comparison of precipitation chemistry measurements obtained by the Canadian Air and Precipitation Monitoring Network and National Atmospheric Deposition Program for the period 1995-2004.

Precipitation chemistry and depth measurements obtained by the Canadian Air and Precipitation Monitoring Network (CAPMoN) and the US National Atmospheric Deposition Program/National Trends Network (NADP/NTN) were compared for the 10-year period 1995-2004. Colocated sets of CAPMoN and NADP instrumentation, consisting of precipitation collectors and rain gages, were operated simultaneously per standard protocols for each network at Sutton, Ontario and Frelighsburg, Ontario, Canada and at State College, PA, USA. CAPMoN samples were collected daily, and NADP samples were collected weekly, and samples were analyzed exclusively by each network's laboratory for pH, H(+), Ca(2+), Mg(2+), Na(+), K(+), NH4(+), Cl(-), NO3(-), and SO4(2-). Weekly and annual precipitation-weighted mean concentrations for each network were compared. This study is a follow-up to an earlier internetwork comparison for the period 1986-1993, published by Alain Sirois, Robert Vet, and Dennis Lamb in 2000. Median weekly internetwork differences for 1995-2004 data were the same to slightly lower than for data for the previous study period (1986-1993) for all analytes except NO3(-), SO4(2-), and sample depth. A 1994 NADP sampling protocol change and a 1998 change in the types of filters used to process NADP samples reversed the previously identified negative bias in NADP data for hydrogen-ion and sodium concentrations. Statistically significant biases (alpha = 0.10) for sodium and hydrogen-ion concentrations observed in the 1986-1993 data were not significant for 1995-2004. Weekly CAPMoN measurements generally are higher than weekly NADP measurements due to differences in sample filtration and field instrumentation, not sample evaporation, contamination, or analytical laboratory differences.

Author Correction: Global and regional trends of atmospheric sulfur.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Global and regional trends of atmospheric sulfur.

The profound changes in global SO2 emissions over the last decades have affected atmospheric composition on a regional and global scale with large impact on air quality, atmospheric deposition and the radiative forcing of sulfate aerosols. Reproduction of historical atmospheric pollution levels based on global aerosol models and emission changes is crucial to prove that such models are able to predict future scenarios. Here, we analyze consistency of trends in observations of sulfur components in air and precipitation from major regional networks and estimates from six different global aerosol models from 1990 until 2015. There are large interregional differences in the sulfur trends consistently captured by the models and observations, especially for North America and Europe. Europe had the largest reductions in sulfur emissions in the first part of the period while the highest reduction came later in North America and East Asia. The uncertainties in both the emissions and the representativity of the observations are larger in Asia. However, emissions from East Asia clearly increased from 2000 to 2005 followed by a decrease, while in India a steady increase over the whole period has been observed and modelled. The agreement between a bottom-up approach, which uses emissions and process-based chemical transport models, with independent observations gives an improved confidence in the understanding of the atmospheric sulfur budget.

Uncertainties in the current knowledge of some atmospheric trace gases associated with U.S. agriculture: a review.

Approximately 80 different crop species are grown in the United States in widely differing geographic areas, climatic and edaphic conditions, and management practices. Although the majority of cultivated acreage in the United States is planted with only about 10 primary crops, uncertainties associated with trace gas emissions arise from: (1) limited data availability, (2) inaccurate estimates because of large temporal and spatial variability in trace gas composition and magnitude of trace gas emissions from agricultural activities, (3) differing characteristics of pollutant emissions from highly dispersed animal feed-lots, and (4) limited understanding of the emissions of semi-volatile organic compounds (SVOCs) associated with agriculture. Although emission issues are of concern, so also is atmospheric deposition to cropping systems, including wet and dry nitrogen, minerals, and organic compounds. These can have feedback effects on trace gas emissions. Overall, the many gaps in our understanding of these aspects of agricultural systems deserve serious attention.