Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice.

Autism spectrum disorder (ASD) manifests as alterations in complex human behaviors including social communication and stereotypies. In addition to genetic risks, the gut microbiome differs between typically developing (TD) and ASD individuals, though it remains unclear whether the microbiome contributes to symptoms. We transplanted gut microbiota from human donors with ASD or TD controls into germ-free mice and reveal that colonization with ASD microbiota is sufficient to induce hallmark autistic behaviors. The brains of mice colonized with ASD microbiota display alternative splicing of ASD-relevant genes. Microbiome and metabolome profiles of mice harboring human microbiota predict that specific bacterial taxa and their metabolites modulate ASD behaviors. Indeed, treatment of an ASD mouse model with candidate microbial metabolites improves behavioral abnormalities and modulates neuronal excitability in the brain. We propose that the gut microbiota regulates behaviors in mice via production of neuroactive metabolites, suggesting that gut-brain connections contribute to the pathophysiology of ASD.

Survival of patients with basal cell carcinoma, squamous cell carcinoma, and squamous cell carcinoma in situ: A whole population study.

BACKGROUND: Keratinocyte carcinoma (KC) is the commonest type of malignancy in humans; however, the impact of KC on survival is poorly understood. OBJECTIVES: This study characterizes the impact of basal cell carcinoma (BCC), squamous cell carcinoma (SCC), and squamous cell carcinoma in situ (SCCis) on the survival of Icelanders. METHODS: This whole population study evaluated relative survival of KC in Iceland by using a cancer registry containing records of all BCC, SCCis, and SCC cases recorded in Iceland between 1981 and 2015. RESULTS: Between 1981 and 2015, 8767 Icelanders were diagnosed with their first localized KC. A total of 6473 individuals with BCC, 1194 with SCCis, and 1100 with invasive SCC, respectively. BCC was not associated with decreased survival except for men diagnosed with BCC between 1981 and 1995 for whom decreased 10-year relative survival was observed (85.3, 95% CI [77.9-92.7]). SCC and SCCis were both associated with a decrease in relative survival for certain population subgroups such as individuals <50 years of age at time of diagnosis. CONCLUSION: Our whole population cohort survival study examining the Icelandic Cancer Registry supports prior studies demonstrating that BCC is not associated with a reduction in relative survival and that SCC and SCCis are associated with comparatively poor relative survival in certain population subgroups.

Intracellular pathways for lignin catabolism in white-rot fungi.

Lignin is a biopolymer found in plant cell walls that accounts for 30% of the organic carbon in the biosphere. White-rot fungi (WRF) are considered the most efficient organisms at degrading lignin in nature. While lignin depolymerization by WRF has been extensively studied, the possibility that WRF are able to utilize lignin as a carbon source is still a matter of controversy. Here, we employ 13C-isotope labeling, systems biology approaches, and in vitro enzyme assays to demonstrate that two WRF, Trametes versicolor and Gelatoporia subvermispora, funnel carbon from lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways. These results provide insights into global carbon cycling in soil ecosystems and furthermore establish a foundation for employing WRF in simultaneous lignin depolymerization and bioconversion to bioproducts-a key step toward enabling a sustainable bioeconomy.

Soil metabolome response to whole-ecosystem warming at the Spruce and Peatland Responses under Changing Environments experiment.

In this study, a suite of complementary environmental geochemical analyses, including NMR and gas chromatography-mass spectrometry (GC-MS) analyses of central metabolites, Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) of secondary metabolites, and lipidomics, was used to investigate the influence of organic matter (OM) quality on the heterotrophic microbial mechanisms controlling peatland CO2, CH4, and CO2:CH4 porewater production ratios in response to climate warming. Our investigations leverage the Spruce and Peatland Responses under Changing Environments (SPRUCE) experiment, where air and peat warming were combined in a whole-ecosystem warming treatment. We hypothesized that warming would enhance the production of plant-derived metabolites, resulting in increased labile OM inputs to the surface peat, thereby enhancing microbial activity and greenhouse gas production. Because shallow peat is most susceptible to enhanced warming, increases in labile OM inputs to the surface, in particular, are likely to result in significant changes to CO2 and CH4 dynamics and methanogenic pathways. In support of this hypothesis, significant correlations were observed between metabolites and temperature consistent with increased availability of labile substrates, which may stimulate more rapid turnover of microbial proteins. An increase in the abundance of methanogenic genes in response to the increase in the abundance of labile substrates was accompanied by a shift toward acetoclastic and methylotrophic methanogenesis. Our results suggest that as peatland vegetation trends toward increasing vascular plant cover with warming, we can expect a concomitant shift toward increasingly methanogenic conditions and amplified climate-peatland feedbacks.

ORT: a workflow linking genome-scale metabolic models with reactive transport codes.

MOTIVATION: Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As 'omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed. RESULTS: We propose a workflow ('Omics to Reactive Transport-ORT) for utilizing metagenomic and environmental data to describe the effect of microbiological processes in macroscopic reactive transport models. This workflow utilizes and couples two open-source software packages: KBase (a software platform for systems biology) and PFLOTRAN (a reactive transport modeling code). We describe the architecture of ORT and demonstrate an implementation using metagenomic and geochemical data from a river system. Our demonstration uses microbiological drivers of nitrification and denitrification to predict nitrogen cycling patterns which agree with those provided with generalized stoichiometries. While our example uses data from a single measurement, our workflow can be applied to spatiotemporal metagenomic datasets to allow for iterative coupling between KBase and PFLOTRAN. AVAILABILITY AND IMPLEMENTATION: Interactive models available at https://pflotranmodeling.paf.subsurfaceinsights.com/pflotran-simple-model/. Microbiological data available at NCBI via BioProject ID PRJNA576070. ORT Python code available at https://github.com/subsurfaceinsights/ort-kbase-to-pflotran. KBase narrative available at https://narrative.kbase.us/narrative/71260 or static narrative (no login required) at https://kbase.us/n/71260/258. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Microbial sensitivity to temperature and sulfate deposition modulates greenhouse gas emissions from peat soils.

Peatlands are among the largest natural sources of atmospheric methane (CH4 ) worldwide. Microbial processes play a key role in regulating CH4 emissions from peatland ecosystems, yet the complex interplay between soil substrates and microbial communities in controlling CH4 emissions as a function of global change remains unclear. Herein, we performed an integrated analysis of multi-omics data sets to provide a comprehensive understanding of the molecular processes driving changes in greenhouse gas (GHG) emissions in peatland ecosystems with increasing temperature and sulfate deposition in a laboratory incubation study. We sought to first investigate how increasing temperatures (4, 21, and 35°C) impact soil microbiome-metabolome interactions; then explore the competition between methanogens and sulfate-reducing bacteria (SRBs) with increasing sulfate concentrations at the optimum temperature for methanogenesis. Our results revealed that peat soil organic matter degradation, mediated by biotic and potentially abiotic processes, is the main driver of the increase in CO2 production with temperature. In contrast, the decrease in CH4 production at 35°C was linked to the absence of syntrophic communities and the potential inhibitory effect of phenols on methanogens. Elevated temperatures further induced the microbial communities to develop high growth yield and stress tolerator trait-based strategies leading to a shift in their composition and function. On the other hand, SRBs were able to outcompete methanogens in the presence of non-limiting sulfate concentrations at 21°C, thereby reducing CH4 emissions. At higher sulfate concentrations, however, the prevalence of communities capable of producing sufficient low-molecular-weight carbon substrates for the coexistence of SRBs and methanogens was translated into elevated CH4 emissions. The use of omics in this study enhanced our understanding of the structure and interactions among microbes with the abiotic components of the system that can be useful for mitigating GHG emissions from peatland ecosystems in the face of global change.

Multi-institutional assessment of the prevalence of neuroendocrine tumors in children undergoing laparoscopic appendectomy for acute appendicitis in the United States.

As non-operative management of acute appendicitis in children has become more common, missed incidental appendiceal pathology can be an unintended consequence. We assessed the prevalence of neuroendocrine tumors in appendectomy specimens from eight US children's hospitals from 2012 to 2021. The prevalence of neuroendocrine tumors (NET) was found to be 1:271, with a median age of 14 years and 62% female. Most tumors were small (median 6 mm; interquartile range [IQR]: 3-10), and no recurrence was noted during the follow-up period (median 22.5 months; IQR: 3-53). The possibility of delayed diagnosis of these tumors should be part of the discussion for non-operative management of pediatric acute appendicitis.

Discrimination, Abuse, Harassment, and Burnout in Surgical Residency Training.

BACKGROUND: Physicians, particularly trainees and those in surgical subspecialties, are at risk for burnout. Mistreatment (i.e., discrimination, verbal or physical abuse, and sexual harassment) may contribute to burnout and suicidal thoughts. METHODS: A cross-sectional national survey of general surgery residents administered with the 2018 American Board of Surgery In-Training Examination assessed mistreatment, burnout (evaluated with the use of the modified Maslach Burnout Inventory), and suicidal thoughts during the past year. We used multivariable logistic-regression models to assess the association of mistreatment with burnout and suicidal thoughts. The survey asked residents to report their gender. RESULTS: Among 7409 residents (99.3% of the eligible residents) from all 262 surgical residency programs, 31.9% reported discrimination based on their self-identified gender, 16.6% reported racial discrimination, 30.3% reported verbal or physical abuse (or both), and 10.3% reported sexual harassment. Rates of all mistreatment measures were higher among women; 65.1% of the women reported gender discrimination and 19.9% reported sexual harassment. Patients and patients' families were the most frequent sources of gender discrimination (as reported by 43.6% of residents) and racial discrimination (47.4%), whereas attending surgeons were the most frequent sources of sexual harassment (27.2%) and abuse (51.9%). Proportion of residents reporting mistreatment varied considerably among residency programs (e.g., ranging from 0 to 66.7% for verbal abuse). Weekly burnout symptoms were reported by 38.5% of residents, and 4.5% reported having had suicidal thoughts during the past year. Residents who reported exposure to discrimination, abuse, or harassment at least a few times per month were more likely than residents with no reported mistreatment exposures to have symptoms of burnout (odds ratio, 2.94; 95% confidence interval [CI], 2.58 to 3.36) and suicidal thoughts (odds ratio, 3.07; 95% CI, 2.25 to 4.19). Although models that were not adjusted for mistreatment showed that women were more likely than men to report burnout symptoms (42.4% vs. 35.9%; odds ratio, 1.33; 95% CI, 1.20 to 1.48), the difference was no longer evident after the models were adjusted for mistreatment (odds ratio, 0.90; 95% CI, 0.80 to 1.00). CONCLUSIONS: Mistreatment occurs frequently among general surgery residents, especially women, and is associated with burnout and suicidal thoughts.

Interlayer Cation Polarizability Affects Supercritical Carbon Dioxide Adsorption by Swelling Clays.

Several strategies for mitigating the build-up of atmospheric carbon dioxide (CO2) bring wet supercritical CO2 (scCO2) in contact with phyllosilicates such as illites and smectites. While some work has examined the role of the charge-balancing cation and smectite framework features on CO2/smectite interactions, to our knowledge no one has examined how the polarizability of the charge-balancing cation influences these behaviors. In this paper, the scCO2 adsorption properties of Pb2+, Rb+, and NH4+ saturated smectite clays at variable relative humidity are studied by integrating in situ high-pressure X-ray diffraction (XRD), infrared spectroscopic titrations, and magic angle spinning nuclear magnetic resonance (MAS NMR) methods. The results are combined with previously published data for Na+, Cs+, and Ca2+ saturated versions of the same smectites to isolate the roles of the charge-balancing cations and perform two independent tests of the role of charge-balancing cation polarizability in determining the interlayer fluid properties and smectite expansion. Independent correlations developed for (i) San Bernardino hectorite (SHCa-1) and (ii) Wyoming montmorillonite (SWy-2) both show that cation polarizability is important in predicting the interlayer composition (mol% CO2 in the interlayer fluid and CO2/cation ratio in interlayer) and the expansion behavior for smectites in contact with wet and dry scCO2. In particular, this study shows that the charge-balancing cation polarizability is the most important cation-associated parameter in determining the expansion of the trioctahedral smectite, hectorite, when in contact with dry scCO2. While both independent tests show that cation polarizability is an important factor in smectite-scCO2 systems, the correlations for hectorite are different from those determined for montmorillonite. The root of these differences is likely associated with the roles of the smectite framework on adsorption, warranting follow-up studies with a larger number of unique smectite frameworks. Overall, the results show that the polarizability of the charge-balancing cation should be considered when preparing smectite clays (or industrial processes involving smectites) to capture CO2 and in predicting the behavior of caprocks over time.

Elucidating Drought-Tolerance Mechanisms in Plant Roots through 1H NMR Metabolomics in Parallel with MALDI-MS, and NanoSIMS Imaging Techniques.

As direct mediators between plants and soil, roots play an important role in metabolic responses to environmental stresses such as drought, yet these responses are vastly uncharacterized on a plant-specific level, especially for co-occurring species. Here, we aim to examine the effects of drought on root metabolic profiles and carbon allocation pathways of three tropical rainforest species by combining cutting-edge metabolomic and imaging technologies in an in situ position-specific 13C-pyruvate root-labeling experiment. Further, washed (rhizosphere-depleted) and unwashed roots were examined to test the impact of microbial presence on root metabolic pathways. Drought had a species-specific impact on the metabolic profiles and spatial distribution in Piper sp. and Hibiscus rosa sinensis roots, signifying different defense mechanisms; Piper sp. enhanced root structural defense via recalcitrant compounds including lignin, while H. rosa sinensis enhanced biochemical defense via secretion of antioxidants and fatty acids. In contrast, Clitoria fairchildiana, a legume tree, was not influenced as much by drought but rather by rhizosphere presence where carbohydrate storage was enhanced, indicating a close association with symbiotic microbes. This study demonstrates how multiple techniques can be combined to identify how plants cope with drought through different drought-tolerance strategies and the consequences of such changes on below-ground organic matter composition.

Association of Surgical Resident Wellness With Medical Errors and Patient Outcomes.

OBJECTIVES: The aims of this study were to: (1) measure the prevalence of self-reported medical error among general surgery trainees, (2) assess the association between general surgery resident wellness (ie, burnout and poor psychiatric well-being) and self-reported medical error, and (3) examine the association between program-level wellness and objectively measured patient outcomes. SUMMARY OF BACKGROUND DATA: Poor wellness is prevalent among surgical trainees but the impact on medical error and objective patient outcomes (eg, morbidity or mortality) is unclear as existing studies are limited to physician and patient self-report of events and errors, small cohorts, or examine few outcomes. METHODS: A cross-sectional survey was administered immediately following the January 2017 American Board of Surgery In-training Examination to clinically active general surgery residents to assess resident wellness and self-reported error. Postoperative patient outcomes were ascertained using a validated national clinical data registry. Associations were examined using multivariable logistic regression models. RESULTS: Over a 6-month period, 22.5% of residents reported committing a near miss medical error, and 6.9% reported committing a harmful medical error. Residents were more likely to report a harmful medical error if they reported frequent burnout symptoms [odds ratio 2.71 (95% confidence interval 2.16-3.41)] or poor psychiatric well-being [odds ratio 2.36 (95% confidence interval 1.92-2.90)]. However, there were no significant associations between program-level resident wellness and any of the independently, objectively measured postoperative American College of Surgeons National Surgical Quality improvement Program outcomes examined. CONCLUSIONS: Although surgical residents with poor wellness were more likely to self-report a harmful medical error, there was not a higher rate of objectively reported outcomes for surgical patients treated at hospitals with higher rates of burnout or poor psychiatric well-being.

Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales.

Hydraulic fracturing is one of the industrial processes behind the surging natural gas output in the United States. This technology inadvertently creates an engineered microbial ecosystem thousands of meters below Earth's surface. Here, we used laboratory reactors to perform manipulations of persisting shale microbial communities that are currently not feasible in field scenarios. Metaproteomic and metabolite findings from the laboratory were then corroborated using regression-based modeling performed on metagenomic and metabolite data from more than 40 produced fluids from five hydraulically fractured shale wells. Collectively, our findings show that Halanaerobium, Geotoga, and Methanohalophilus strain abundances predict a significant fraction of nitrogen and carbon metabolites in the field. Our laboratory findings also exposed cryptic predatory, cooperative, and competitive interactions that impact microorganisms across fractured shales. Scaling these results from the laboratory to the field identified mechanisms underpinning biogeochemical reactions, yielding knowledge that can be harnessed to potentially increase energy yields and inform management practices in hydraulically fractured shales.

Post Hepatectomy Liver Failure Risk Calculator for Preoperative and Early Postoperative Period Following Major Hepatectomy.

BACKGROUND: Post hepatectomy liver failure (PHLF) is associated with significant perioperative morbidity and mortality. A tool to identify patients at risk for PHLF may allow for earlier intervention to mitigate its severity and help clinicians when counseling patients. Our objective was to develop a PHLF risk calculator. STUDY DESIGN: Patients who underwent hepatectomy for any indication from 2014 to 2017 were identified from ACS NSQIP. A multivariable logistic regression model was developed that included preoperative and intraoperative variables. Model fit was assessed for discrimination using the C-statistic, and calibration using Hosmer and Lemeshow (HL) Chi square. Validation of the calculator was performed utilizing tenfold cross validation. RESULTS: Among 15,636 hepatectomy patients analyzed, the overall incidence of clinically significant PHLF was 2.8%. Preoperative patient factors associated with increased PHLF were male gender, preoperative ascites within 30 days of surgery, higher ASA class, preoperative total bilirubin greater than 1.2 mg/dl, and AST greater than 40 units/l. Disease related factors associated with PHLF included histology, and use of neoadjuvant therapy. Intraoperative factors associated with PHLF were extent of resection, open surgical approach, abnormal liver texture, and biliary reconstruction. The calculator's C-statistic was 0.83 and the HL Chi square was 10.9 (p = 0.21) demonstrating excellent discrimination and calibration. On tenfold cross validation, the mean test group C-statistic was 0.82 and the HL p value was 0.26. CONCLUSION: We present a multi-institutional preoperative and early postoperative PHLF risk calculator, which demonstrated excellent discrimination and calibration. This tool can be used to help identify high-risk patients to facilitate earlier interventions.

Unraveling the Dynamic Network in the Reactions of an Alkyl Aryl Ether Catalyzed by Ni/γ-Al2O3 in 2-Propanol.

The reductive cleavage of aryl ether linkages is a key step in the disassembly of lignin to its monolignol components, where selectivity is determined by the kinetics of multiple parallel and consecutive liquid-phase reactions. Triphasic hydrogenolysis of 13C-labeled benzyl phenyl ether (BPE, a model compound for the major ß-O-4 linkage in lignin), catalyzed by Ni/γ-Al2O3, was observed directly at elevated temperatures (150-175 °C) and pressures (79-89 bar) using operando magic-angle spinning NMR spectroscopy. Liquid-vapor partitioning in the NMR rotor was quantified using the 13C NMR resonances for the 2-propanol solvent, whose chemical shifts report on the internal reactor temperature. At 170 °C, BPE is converted to toluene and phenol with k1 = 0.17 s-1 gcat-1 and an apparent activation barrier of (80 ± 8) kJ mol-1. Subsequent phenol hydrogenation occurs much more slowly (k2 = 0.0052 s-1 gcat-1 at 170-175 °C), such that cyclohexanol formation is significant only at higher temperatures. Toluene is stable under these reaction conditions, but its methyl group undergoes facile H/D exchange (k3 = 0.046 s-1 gcat-1 at 175 °C). While the source of the reducing equivalents for both hydrogenolysis and hydrogenation is exclusively H2/D2(g) rather than the alcohol solvent at these temperatures, the initial isotopic composition of adsorbed H/D on the catalyst surface is principally determined by the solvent isotopic composition (2-PrOH/D). All reactions are preceded by a pronounced induction period associated with catalyst activation. In air, Ni nanoparticles are passivated by a surface oxide monolayer, whose removal under H2 proceeds with an apparent activation barrier of (72 ± 13) kJ mol-1. The operando NMR spectra provide molecularly specific, time-resolved information about the multiple simultaneous and sequential processes as they occur at the solid-liquid interface.

An Empirical National Assessment of the Learning Environment and Factors Associated With Program Culture.

OBJECTIVES: To empirically describe surgical residency program culture and assess program characteristics associated with program culture. SUMMARY BACKGROUND DATA: Despite concerns about the impact of the learning environment on trainees, empirical data have not been available to examine and compare program-level differences in residency culture. METHODS: Following the 2018 American Board of Surgery In-Training Examination, a cross-sectional survey was administered to all US general surgery residents. Survey items were analyzed using principal component analysis to derive composite measures of program culture. Associations between program characteristics and composite measures of culture were assessed. RESULTS: Analysis included 7387 residents at 260 training programs (99.3% response rate). Principal component analysis suggested that program culture may be described by 2 components: Wellness and Negative Exposures. Twenty-six programs (10.0%) were in the worst quartile for both Wellness and Negative Exposure components. These programs had significantly higher rates of duty hour violations (23.3% vs 11.1%), verbal/physical abuse (41.6% vs 28.6%), gender discrimination (78.7% vs 64.5%), sexual harassment (30.8% vs 16.7%), burnout (54.9% vs 35.0%), and thoughts of attrition (21.6% vs 10.8%; all P < 0.001). Being in the worst quartile of both components was associated with percentage of female residents in the program (P = 0.011), but not program location, academic affiliation, size, or faculty demographics. CONCLUSIONS: Residency culture was characterized by poor resident wellness and frequent negative exposures and was generally not associated with structural program characteristics. Additional qualitative and quantitative studies are needed to explore unmeasured local social dynamics that may underlie measured differences in program culture.

National Cluster-Randomized Trial of Duty-Hour Flexibility in Surgical Training.

BACKGROUND: Concerns persist regarding the effect of current surgical resident duty-hour policies on patient outcomes, resident education, and resident well-being. METHODS: We conducted a national, cluster-randomized, pragmatic, noninferiority trial involving 117 general surgery residency programs in the United States (2014-2015 academic year). Programs were randomly assigned to current Accreditation Council for Graduate Medical Education (ACGME) duty-hour policies (standard-policy group) or more flexible policies that waived rules on maximum shift lengths and time off between shifts (flexible-policy group). Outcomes included the 30-day rate of postoperative death or serious complications (primary outcome), other postoperative complications, and resident perceptions and satisfaction regarding their well-being, education, and patient care. RESULTS: In an analysis of data from 138,691 patients, flexible, less-restrictive duty-hour policies were not associated with an increased rate of death or serious complications (9.1% in the flexible-policy group and 9.0% in the standard-policy group, P=0.92; unadjusted odds ratio for the flexible-policy group, 0.96; 92% confidence interval, 0.87 to 1.06; P=0.44; noninferiority criteria satisfied) or of any secondary postoperative outcomes studied. Among 4330 residents, those in programs assigned to flexible policies did not report significantly greater dissatisfaction with overall education quality (11.0% in the flexible-policy group and 10.7% in the standard-policy group, P=0.86) or well-being (14.9% and 12.0%, respectively; P=0.10). Residents under flexible policies were less likely than those under standard policies to perceive negative effects of duty-hour policies on multiple aspects of patient safety, continuity of care, professionalism, and resident education but were more likely to perceive negative effects on personal activities. There were no significant differences between study groups in resident-reported perception of the effect of fatigue on personal or patient safety. Residents in the flexible-policy group were less likely than those in the standard-policy group to report leaving during an operation (7.0% vs. 13.2%, P<0.001) or handing off active patient issues (32.0% vs. 46.3%, P<0.001). CONCLUSIONS: As compared with standard duty-hour policies, flexible, less-restrictive duty-hour policies for surgical residents were associated with noninferior patient outcomes and no significant difference in residents' satisfaction with overall well-being and education quality. (FIRST ClinicalTrials.gov number, NCT02050789.).

Deep-Subsurface Pressure Stimulates Metabolic Plasticity in Shale-Colonizing Halanaerobium spp.

Bacterial Halanaerobium strains become the dominant persisting microbial community member in produced fluids across geographically distinct hydraulically fractured shales. Halanaerobium is believed to be inadvertently introduced into this environment during the drilling and fracturing process and must therefore tolerate large changes in pressure, temperature, and salinity. Here, we used a Halanaerobium strain isolated from a natural gas well in the Utica Point Pleasant formation to investigate metabolic and physiological responses to growth under high-pressure subsurface conditions. Laboratory incubations confirmed the ability of Halanaerobium congolense strain WG8 to grow under pressures representative of deep shale formations (21 to 48 MPa). Under these conditions, broad metabolic and physiological shifts were identified, including higher abundances of proteins associated with the production of extracellular polymeric substances. Confocal laser scanning microscopy indicated that extracellular polymeric substance (EPS) production was associated with greater cell aggregation when biomass was cultured at high pressure. Changes in Halanaerobium central carbon metabolism under the same conditions were inferred from nuclear magnetic resonance (NMR) and gas chromatography measurements, revealing large per-cell increases in production of ethanol, acetate, and propanol and cessation of hydrogen production. These metabolic shifts were associated with carbon flux through 1,2-propanediol in response to slower fluxes of carbon through stage 3 of glycolysis. Together, these results reveal the potential for bioclogging and corrosion (via organic acid fermentation products) associated with persistent Halanaerobium growth in deep, hydraulically fractured shale ecosystems, and offer new insights into cellular mechanisms that enable these strains to dominate deep-shale microbiomes.IMPORTANCE The hydraulic fracturing of deep-shale formations for hydrocarbon recovery accounts for approximately 60% of U.S. natural gas production. Microbial activity associated with this process is generally considered deleterious due to issues associated with sulfide production, microbially induced corrosion, and bioclogging in the subsurface. Here we demonstrate that a representative Halanaerobium species, frequently the dominant microbial taxon in hydraulically fractured shales, responds to pressures characteristic of the deep subsurface by shifting its metabolism to generate more corrosive organic acids and produce more polymeric substances that cause "clumping" of biomass. While the potential for increased corrosion of steel infrastructure and clogging of pores and fractures in the subsurface may significantly impact hydrocarbon recovery, these data also offer new insights for microbial control in these ecosystems.

A novel high-temperature MAS probe with optimized temperature gradient across sample rotor for in-situ monitoring of high-temperature high-pressure chemical reactions.

We present a novel nuclear magnetic resonance (NMR) probe design focused on optimizing the temperature gradient across the sample for high temperature magic angle spinning (MAS) experiments using standard rotors. Computational flow dynamics (CFD) simulations were used to assess and optimize the temperature gradient across the sample under MAS conditions. The chemical shift and linewidth of 207Pb direct polarization in lead nitrate were used to calibrate the sample temperature and temperature gradient, respectively. A temperature gradient of less than 3 °C across the sample was obtained by heating bearing gas flows and adjusting its temperature and flow rate during variable temperature (VT) experiments. A maximum temperature of 350 °C was achieved in this probe using a Varian 5 mm MAS rotor with standard Vespel drive tips and end caps. Time-resolved 13C and 1H MAS NMR experiments were performed at 325 °C and 60 bar to monitor an in-situ mixed phase reverse water gas shift reaction, industrial synthesis of CH3OH from a mixture of CO2 and H2 with a Cu/ZnO/Al2O3 catalyst, demonstrating the first in-situ NMR monitoring of a chemical system at temperatures higher than 250 °C in a pressurized environment. The combination of this high-temperature probe and high-pressure rotors will allow for in-situ NMR studies of a great variety of chemical reactions that are inaccessible to conventional NMR setup.

Comparative genomics and physiology of the genus Methanohalophilus, a prevalent methanogen in hydraulically fractured shale.

About 60% of natural gas production in the United States comes from hydraulic fracturing of unconventional reservoirs, such as shales or organic-rich micrites. This process inoculates and enriches for halotolerant microorganisms in these reservoirs over time, resulting in a saline ecosystem that includes methane producing archaea. Here, we survey the biogeography of methanogens across unconventional reservoirs, and report that members of genus Methanohalophilus are recovered from every hydraulically fractured unconventional reservoir sampled by metagenomics. We provide the first genomic sequencing of three isolate genomes, as well as two metagenome assembled genomes (MAGs). Utilizing six other previously sequenced isolate genomes and MAGs, we perform comparative analysis of the 11 genomes representing this genus. This genomic investigation revealed distinctions between surface and subsurface derived genomes that are consistent with constraints encountered in each environment. Genotypic differences were also uncovered between isolate genomes recovered from the same well, suggesting niche partitioning among closely related strains. These genomic substrate utilization predictions were then confirmed by physiological investigation. Fine-scale microdiversity was observed in CRISPR-Cas systems of Methanohalophilus, with genomes from geographically distinct unconventional reservoirs sharing spacers targeting the same viral population. These findings have implications for augmentation strategies resulting in enhanced biogenic methane production in hydraulically fractured unconventional reservoirs.

Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders.

Evidence supporting that gut problems are linked to ASD symptoms has been accumulating both in humans and animal models of ASD. Gut microbes and their metabolites may be linked not only to GI problems but also to ASD behavior symptoms. Despite this high interest, most previous studies have looked mainly at microbial structure, and studies on fecal metabolites are rare in the context of ASD. Thus, we aimed to detect fecal metabolites that may be present at significantly different concentrations between 21 children with ASD and 23 neurotypical children and to investigate its possible link to human gut microbiome. Using 1H-NMR spectroscopy and 16S rRNA gene amplicon sequencing, we examined metabolite profiles and microbial compositions in fecal samples, respectively. Of the 59 metabolites detected, isopropanol concentrations were significantly higher in feces of children with ASD after multiple testing corrections. We also observed similar trends of fecal metabolites to previous studies; children with ASD have higher fecal p-cresol and possibly lower GABA concentrations. In addition, Fisher Discriminant Analysis (FDA) with leave-out-validation suggested that a group of metabolites-caprate, nicotinate, glutamine, thymine, and aspartate-may potentially function as a modest biomarker to separate ASD participants from the neurotypical group (78% sensitivity and 81% specificity). Consistent with our previous Arizona cohort study, we also confirmed lower gut microbial diversity and reduced relative abundances of phylotypes most closely related to Prevotella copri in children with ASD. After multiple testing corrections, we also learned that relative abundances of Feacalibacterium prausnitzii and Haemophilus parainfluenzae were lower in feces of children with ASD. Despite a relatively short list of fecal metabolites, the data in this study support that children with ASD have altered metabolite profiles in feces when compared with neurotypical children and warrant further investigation of metabolites in larger cohorts.