Vertical pelvic movement asymmetry and lameness location in ipsilateral combined forelimb and hindlimb lameness cases.

BACKGROUND: Compensatory vertical head and pelvis movement asymmetry may occur in trotting horses with a primary cause of lameness in one end of the body due to the weight shifting between limbs, leading to apparent combined forelimb and hindlimb lameness (CFHL). Little is known about CFHL patterns observed with body-mounted inertial sensors (BMIS) and regardless of their underlying mechanisms, compensatory and secondary lameness may complicate the definitive identification of the primary causes of lameness. OBJECTIVE: Determine associations between vertical pelvic movement asymmetry and location of primary lameness in ipsilateral CFHL cases where hindlimb lameness is solely impact or push-off type. STUDY DESIGN: Retrospective cohort. METHODS: From a body-mounted inertial sensor (BMIS) evaluated equine lameness database, we identified cases with a consistent, low-variability ipsilateral impact (IpI) or ipsilateral pushoff (IpP) hindlimb lameness in a straight-line trot and that had definitive diagnoses. Cases were categorised by lameness location to the limb(s), diagnosis, and ratio of the amplitude of forelimb to hindlimb lameness (Forea/Hinda). Differences in the numbers of IpI and IpP cases in these categories were analysed with chi-square tests, effect sizes, and odds ratios. RESULTS: Among the 2375 total lameness cases screened, 49 IpI and 36 IpP cases met the criteria for consistency, low variability, and definitive diagnosis. IpI cases were more likely than IpP cases to have forelimb-only lameness causes when Forea/Hinda >1 (OR = 43, 95% CI = 2.3-798). IpP cases were more likely than IpI cases to have hindlimb-only causes at both Forea/Hinda >1.0 (OR = 20, 95% CI = 2.2-200) and <1.0 (OR = 14, 95% CI = 2.9-66.7). Compared with IpI, IpP cases were more frequently diagnosed with tendon, suspensory ligament, or high-motion joint disorders in hindlimbs (OR = 3.6, 95% CI = 1.1-12.3) and less with unknown causes (OR = 13.2, 95% CI = 3.2-75.2). In IpI cases, positive forelimb regional anaesthesia often reduced hindlimb lameness, whereas in IpP cases, positive hindlimb regional anaesthesia typically lessened forelimb lameness. MAIN LIMITATIONS: Most cases were Quarter Horses. The likelihood of location and cause of lameness may be different for other breeds. CONCLUSIONS: The type of pelvic movement asymmetry observed in IpI and IpP cases is linked to the location and underlying cause of the primary lameness.

Large-scale genomic data reveal the phylogeny and evolution of owlet moths (Noctuoidea).

The owlet moths (Noctuoidea; ~43-45K described species) are one of the most ecologically diverse and speciose superfamilies of animals. Moreover, they comprise some of the world's most notorious pests of agriculture and forestry. Despite their contributions to terrestrial biodiversity and impacts on ecosystems and economies, the evolutionary history of Noctuoidea remains unclear because the superfamily lacks a statistically robust phylogenetic and temporal framework. We reconstructed the phylogeny of Noctuoidea using data from 1234 genes (946.4 kb nucleotides) obtained from the genome and transcriptome sequences of 76 species. The relationships among the six families of Noctuoidea were well resolved and consistently recovered based on both concatenation and gene coalescence approaches, supporting the following relationships: Oenosandridae + (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))). A Yule tree prior with three unlinked molecular clocks was identified as the preferred BEAST analysis using marginal-likelihood estimations. The crown age of Noctuoidea was estimated at 74.5 Ma, with most families originating before the end of the Paleogene (23 Ma). Our study provides the first statistically robust phylogenetic and temporal framework for Noctuoidea, including all families of owlet moths, based on large-scale genomic data.

Reconstituted Extracellular Vesicles from Human Platelets Decrease Viral Myocarditis in Mice.

Patients with viral myocarditis are at risk of sudden death and may progress to dilated cardiomyopathy (DCM). Currently, no disease-specific therapies exist to treat viral myocarditis. Here it is examined whether reconstituted, lyophilized extracellular vesicles (EVs) from platelets from healthy men and women reduce acute or chronic myocarditis in male mice. Human-platelet-derived EVs (PEV) do not cause toxicity, damage, or inflammation in naïve mice. PEV administered during the innate immune response significantly reduces myocarditis with fewer epidermal growth factor (EGF)-like module-containing mucin-like hormone receptor-like 1 (F4/80) macrophages, T cells (cluster of differentiation molecules 4 and 8, CD4 and CD8), and mast cells, and improved cardiac function. Innate immune mediators known to increase myocarditis are decreased by innate PEV treatment including Toll-like receptor (TLR)4 and complement. PEV also significantly reduces perivascular fibrosis and remodeling including interleukin 1 beta (IL-1ß), transforming growth factor-beta 1, matrix metalloproteinase, collagen genes, and mast cell degranulation. PEV given at days 7-9 after infection reduces myocarditis and improves cardiac function. MicroRNA (miR) sequencing reveals that PEV contains miRs that decrease viral replication, TLR4 signaling, and T-cell activation. These data show that EVs from the platelets of healthy individuals can significantly reduce myocarditis and improve cardiac function.

Phase I evaluation of CycloSam® (Sm-153-DOTMP) bone seeking radiopharmaceutical in dogs with spontaneous appendicular osteosarcoma.

153 Sm-DOTMP (CycloSam® ) is a newly-patented radiopharmaceutical for bone tumor treatment. DOTMP (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetramethylene-phosphonate) is a macrocyclic chelating agent with superior binding properties to 153 Sm when compared with EDTMP (Quadramet™, used for palliative treatment of bone cancer). CycloSam® was administered at 1 mCi/kg (37 MBq/kg) in a prospective pilot study to seven dogs with bone cancer resulting in no myelosuppression. Then, 13 dogs were enrolled in a prospective clinical trial study using traditional 3+3 dose escalation and starting at 1.5 mCi/kg. Baseline evaluation included hematologic and biochemical testing, diagnosis confirmation, thoracic and limb radiographs, technetium-99 m-HDP bone scintigraphy, and 18 F-FDG PET scan (SUVmax). Toxicity (primary endpoint) was assessed through weekly blood counts and adverse events. Dogs received 1.5 mCi/kg (n = 4), 1.75 mCi/kg (n = 6), and 2 mCi/kg (n = 3) of 153 Sm-DOTMP. Dose-limiting neutropenia and thrombocytopenia were seen at 2 mCi/kg. No dose-limiting nonhematologic toxicities occurred. Efficacy (secondary endpoint) was assessed by objective lameness measurement (body-mounted inertial sensors), owner quality-of-life (QoL) questionnaire, and repeat PET scan. Objective lameness measurement improved in four dogs (53%-60% decrease) was equivocal in three dogs, and worsened in four dogs (66%-115% increase); two dogs were not evaluable. Repeat 18 F-FDG PET scan results varied and change in lameness did not consistently correlate with SUVmax changes. QoL score worsened (n = 5) or was improved/stable (n = 7). Carboplatin chemotherapy (300 mg/m2 IV every 3 weeks ×4) started 4 weeks after 153 Sm-DOTMP injection. No dog died of chemotherapy-related complications. All dogs completed study monitoring. The recommended dose for CycloSam® in dogs is 1.75 mCi/kg, which resulted in some pain control with minimal toxicity and was safely combined with chemotherapy.

Prevalence and clinical significance of increasing head height asymmetry as a measure of forelimb lameness in horses when trotting in a straight line after palmar digital nerve block.

BACKGROUND: Some horses increase in forelimb lameness, measured as vertical head height asymmetry, or differences in maximums and minimums of head heights (HDmax, HDmin), after a palmar digital nerve (PDN) block. The prevalence of this finding, or what it means clinically, has not been reported in peer-reviewed literature. OBJECTIVES: To estimate the prevalence of increasing head height asymmetry after a PDN block and determine if this is associated with cause of forelimb lameness. STUDY DESIGN: Retrospective case series. METHODS: Head height asymmetry, normalised to expected vertical head displacement, from inertial-sensor data collections of all horses evaluated for forelimb lameness while trotting in a straight line at two different clinics were screened for cases that had an initial PDN block and then another more proximal block in the same limb during the same lameness evaluation. Medical records of the screened cases (n = 213) were evaluated to determine the cause of lameness. Prevalence of increasing head height asymmetry was calculated. Differences in lameness amplitude between groups of cases that remained unchanged (Group 1), that increased (Group 2), and that decreased (Group 3) in head height asymmetry before and after the initial PDN block were compared (Kruskal-Wallis). Determination of the location of the cause of lameness and final diagnoses of cases were compared between Group 1 and Group 2 (chi-squared tests of independence). RESULTS: The PDN block increased head height asymmetry at a prevalence of 32.5% (95% CI = 24.5%-41.5%) and 13.8% (95% CI = 7.3%-22.9%), in clinic 1 and 2, respectively. Increasing head height asymmetry after an initial PDN block did not predict localization of the cause of forelimb lameness or specific diagnosis (p = 0.1), other than indicating that it is unlikely to be in the foot (p = 0.02). MAIN LIMITATIONS: Study samples consisted primarily of Warmbloods (clinic 1) and Quarter Horses (clinic 2). Analysis of blocking induced changes was limited to straight line trot only. CONCLUSIONS: Increasing head height asymmetry after PDN block is common during forelimb lameness evaluations. Other than indicating that the cause of lameness is more proximal in the blocked forelimb, this does not help determine the final diagnosis.

Anti-nociceptive efficacy of the soluble epoxide hydrolase inhibitor t-TUCB in horses with mechanically induced lameness.

INTRODUCTION: Soluble epoxide hydrolase (sEH) inhibitors are novel anti-inflammatory and analgesic agents that could improve pain management in horses. The objective of the present study was to evaluate the anti-nociceptive effect of a single-dose intravenous administration of the sEH inhibitor trans-4-{4-[3-(4-trifluro-methoxy-phenyl)-ureido]-cyclohexyloxy}-benzoic acid (t-TUCB) using an adjustable heart bar shoe (a-HBS) model of lameness. We hypothesized that t-TUCB would improve objective and subjective lameness measures compared to the control. MATERIALS AND METHODS: Reversible lameness was induced in 8 horses for 24 h using an a-HBS in a randomized, crossover design. A vehicle-control placebo (DMSO) or t-TUCB (1 mg/kg) was intravenously administered at time 0 following a baseline induced lameness evaluation. Blood was collected and lameness was objectively measured with an inertial sensor system at 0-, 1-, 3-, 6-, 12-, and 24-h time points. Front-facing videos were obtained at each time point for subjective evaluation by three blinded evaluators using a visual analog scale (VAS). RESULTS: Treatment with t-TUCB significantly decreased (i.e. improved) lameness compared to placebo at 1-h and compared to baseline at 1-, 3-, and 6-h following administration. Lameness significantly increased (i.e. worsened) from baseline in placebo-treated horses 12 h after administration. All horses returned to baseline soundness within 24 h of reversing lameness. CONCLUSION: Treatment with single-dose IV administration of t-TUCB improved lameness induced by the a-HSB, suggesting that t-TUCB has anti-nociceptive effects in horses. CLINICAL RELEVANCE: The soluble epoxide hydrolase inhibitor, t-TUCB, is a promising novel analgesic for horses.

The Scope and Impact of the COVID-19 Pandemic on Neuroemergent Patient Transfers, Clinical Care and Patient Outcomes.

Introduction: The SARS-CoV-2 (COVID-19) pandemic continues to substantially alter previously established clinical practice patterns and has transformed patient care in American healthcare. However, studies to evaluate the impact of COVID-19 on neuroemergent patient care and associated clinical outcomes are limited. Herein, we describe the impact of COVID-19 on the Neuroemergency Transfer Program (NTP) - a novel, urban, high volume interhospital patient transfer program. Objective: To evaluate and describe the clinical impact of the COVID-19 pandemic on the NTP. Study Design: A single-center retrospective study of prospectively collected consecutive neuroemergent patient transfer data between 2018-2021 was analyzed. Adult patients were divided based upon transfer date into a Pre-COVID (PCOV) or COVID cohort. Patient demographics, transfer characteristics and clinical data and outcomes were analyzed. Results: 3,096 patients were included for analysis. Mean age at transfer in the PCOV and COVID cohorts were 62.4 ± 0.36 and 61.1 ± 0.6 years. A significant decrease in mean transfers per month was observed between cohorts (PCOV = 97.8 vs. COV = 68.2 transfers/month, p < 0.01). Total transfer time in the PCOV cohort was 155.1 ± 3.4 min which increased to 169.3 ± 12.8 min in the COVID cohort (p = 0.13). Overall mean transfer distance was significantly longer in the PCOV cohort at 22.0 ± 0.4 miles vs. 20.3 ± 0.67 miles in the COV cohort (p = 0.03). The relative frequency of transfer diagnoses was unchanged between cohorts. A significant increase in mean inpatient length of stay was noted, 7.9 ± 0.15 days to 9.6 ± 0.33 days in the PCOV vs. COVID cohorts (p < 0.01). Ultimately, no difference in the frequency of good vs. poor clinical outcome were noted between the PCOV (79.8% and 19.4%) vs. COV (78.8% and 20.4%) cohorts. Conclusion: The impact of COVID-19 on current healthcare dynamics are far reaching. Here, we show a significant decrease in interhospital patient transfers and increased length of stay between a Pre-COVID and COVID cohort. Further work to better elucidate the specific interplay of clinical contributors to account for these changes is indicated.

A retrospective comparison of radiographic and clinical outcomes in single-level degenerative lumbar disease undergoing anterior versus transforaminal lumbar interbody fusion.

BACKGROUND: Single-level lumbar degenerative disc disease (DDD) remains a significant cause of morbidity in adulthood. Anterior lumbar interbody fusion (ALIF) and Transforaminal lumbar interbody fusion (TLIF) are surgical techniques developed to treat this condition. With limited studies on intermediate term outcomes in a single cohort, we compare radiographic and clinical outcomes in patients undergoing ALIF and TLIF. METHODS: A retrospective chart review was performed on 164 patients (111 TLIF; 53 ALIF) over a 60-month period. X-ray radiographs obtained pre-operatively, prior to discharge, and at one year were utilized for radiographic assessment. Segmental lordosis, lumbar lordosis and HRQOL scores were measured preoperatively and at one-year timepoints. RESULTS: Changes in lumbar lordosis and segmental lordosis were significantly greater after ALIF (4.6° vs. -0.6°, P=0.05; 4.7° vs. -0.7°, P<0.05) at one year (mean time, 366±20 days). At one year or greater, there was a greater reduction in mean VAS-leg score in TLIF patients (3.4 vs. 0.6, P<0.05) and ODI score (16.2 vs. 5.4, P<0.05). Similar outcomes were seen for VAS-back, SF-12 Physical Health, and SRS-30 Function/Activity. SF-12 Mental Health scores were found to be lower in patients undergoing TLIF (-3.5 vs. 2.7, P<0.05). CONCLUSIONS: ALIF demonstrated a superior method of increasing lumbar and segmental lordosis. TLIF was utilized more in patients with higher pre-operative VAS-leg pain scores and therefore, showed a greater magnitude of VAS-leg pain improvement. TLIF also demonstrated a greater improvement in ODI scores despite similar baseline scores, suggesting a possible enhanced functional outcome.

Transforaminal lumbar interbody fusion using a novel minimally invasive expandable interbody cage: patient-reported outcomes and radiographic parameters.

OBJECTIVE: The goal of this study was to evaluate the clinical and radiographic outcomes of a novel multidirectional in situ expandable minimally invasive surgery (MIS) transforaminal lumbar interbody fusion (TLIF) cage. METHODS: A retrospective analysis of 69 consecutive patients undergoing a 1- or 2-level MIS TLIF using an expandable cage was performed over a 2-year period. Standard MIS techniques with pedicle screw fixation were used in all cases. Upright lateral dynamic flexion/extension radiographs were reviewed prior to and at 1 year after surgery. Clinical metrics included numeric rating scale for back and leg pain, Oswestry Disability Index, and the SF-12 and VR-12 physical and mental health surveys. Radiographic parameters included anterior and posterior disc height, neuroforaminal height, spondylolisthesis, segmental lordosis, lumbar lordosis, and fusion rate. RESULTS: A total of 69 patients representing 75 operative levels met study inclusion criteria. The mean patient age at surgery was 63.4 ± 1.2 years, with a female predominance of 51%. The average radiographic and clinical follow-ups were 372 and 368 days, respectively. A total of 63 patients (91%) underwent 1-level surgery and 6 patients (9%) underwent 2-level surgery. Significant reductions of numeric rating scale scores for back and leg pain were observed-from 6.1 ± 0.7 to 2.5 ± 0.3 (p < 0.0001) and 4.9 ± 0.6 to 1.9 ± 0.2 (p < 0.0001), respectively. A similar reduction in Oswestry Disability Index from 38.0 ± 4.6 to 20.0 ± 2.3 (p < 0.0001) was noted. Likewise, SF-12 and VR-12 scores all showed statistically significant improvement from baseline (p < 0.001). The mean anterior and posterior disc heights improved from 8.7 ± 1.0 mm to 13.4 ± 1.5 mm (p = 0.0001) and 6.5 ± 0.8 mm to 9.6 ± 1.1 mm (p = 0.0001), respectively. Neuroforaminal height improved from 17.6 ± 2.0 mm to 21.9 ± 2.5 mm (p = 0.0001). When present, spondylolisthesis was, on average, reduced from 4.3 ± 0.5 mm to 1.9 ± 0.2 mm (p = 0.0001). Lumbar lordosis improved from 47.8° ± 5.5° to 58.5° ± 6.8° (p = 0.2687), and no significant change in segmental lordosis was observed. The overall rate of radiographic fusion was 93.3% at 1 year. No perioperative complications requiring operative revision were encountered. CONCLUSIONS: In this series of MIS TLIFs, use of this novel interbody cage was shown to be safe and effective. Significant improvements in pain and disability were observed. Effective and durable restoration of disc height and neuroforaminal height and reduction of spondylolisthesis were obtained, with concurrent gains in lumbar lordosis. Taken together, this device offers excellent clinical and radiographic outcomes via an MIS approach.

Comparison of results for body-mounted inertial sensor assessment with final lameness determination in 1,224 equids.

OBJECTIVE: To compare results for initial body-mounted inertial sensor (BMIS) measurement of lameness in equids trotting in a straight line with definitive findings after full lameness evaluation. ANIMALS: 1,224 equids. PROCEDURES: Lameness measured with BMIS equipment while trotting in a straight line was classified into categories of none, forelimb only, hind limb only, and 8 patterns of combined forelimb and hind limb lameness (CFHL). Definitive findings after full lameness evaluation were established in most horses and classified into types (no lameness, forelimb- or hind limb-only lameness, CFHL, or lameness not localized to the limbs). Observed proportions of lameness type in equids with definitive findings for each initial BMIS-assessed category were compared with hypothetical expected proportions through χ2 goodness-of-fit analysis. RESULTS: The most common initial BMIS-assessed lameness category was CFHL (693/1,224 [56.6%]), but this was the least common definitive finding (94/ 862 [10.9%]). The observed frequency of no lameness after full lameness evaluation was greater than expected only when initial BMIS measurements indicated no lameness. The observed frequency of forelimb-only lameness was greater than expected when initially measured as forelimb-only lameness and for CFHL categories consistent with the diagonal movement principle of compensatory lameness. Observed frequency of hind limb-only lameness was greater than expected when initially measured as hind limb-only lameness and for CFHL categories consistent with the sagittal movement principle of compensatory lameness. Equids initially assessed as having no lameness had the highest (103/112 [92%]) and those assessed as CFHL pattern 7 (forelimb with contralateral hind limb impact-only lameness) had the lowest (36/66 [55%]) rates of definitive findings. CONCLUSIONS AND CLINICAL RELEVANCE: In equids, results of initial straight-line trotting evaluations with a BMIS system did not necessarily match definitive findings but may be useful in planning the remaining lameness evaluation.

Effect of induced hindlimb length difference on body-mounted inertial sensor measures used to evaluate hindlimb lameness in horses.

This study has investigated the immediate effect of induced hindlimb length difference on hindlimb lameness measured as differences in minimum (Pmin) and maximum (Pmax) pelvic heights in 16 horses trotting in a straight line and lungeing on both hard and soft surfaces with body-mounted inertial sensors. Hindlimb length differences were induced by applying an Easyboot Glue-on shoe to one hindlimb. Changes in Pmin and Pmax with induced hindlimb length difference were assessed with a two-way repeated-measures ANOVA with trial (straight, lunge with inside limb elevation, lunge with outside limb elevation) and surface (hard, soft) as within-subject factors. Change in Pmin, indicating an impact-type lameness, in the hind limb with the elevation, was significant in both the straight line and while lunging on both hard and soft surfaces. Change in Pmax, indicating pushoff-type lameness, in the opposite, non-elevated hind limb, was significant when trotting in a straight line but not while lunging.

An attempt to detect lameness in galloping horses by use of body-mounted inertial sensors.

OBJECTIVE To evaluate head, pelvic, and limb movement to detect lameness in galloping horses. ANIMALS 12 Thoroughbreds. PROCEDURES Movement data were collected with inertial sensors mounted on the head, pelvis, and limbs of horses trotting and galloping in a straight line before and after induction of forelimb and hind limb lameness by use of sole pressure. Successful induction of lameness was determined by measurement of asymmetric vertical head and pelvic movement during trotting. Differences in gallop strides before and after induction of lameness were evaluated with paired-sample statistical analysis and neural network training and testing. Variables included maximum, minimum, range, and time indices of vertical head and pelvic acceleration, head rotation in the sagittal plane, pelvic rotation in the frontal plane, limb contact intervals, stride durations, and limb lead preference. Difference between median standardized gallop strides for each limb lead before and after induction of lameness was calculated as the sum of squared differences at each time index and assessed with a 2-way ANOVA. RESULTS Head and pelvic acceleration and rotation, limb timing, stride duration measurements, and limb lead preference during galloping were not significantly different before and after induction of lameness in the forelimb or hind limb. Differences between limb leads before induction of lameness were similar to or greater than differences within limb leads before and after lameness induction. CONCLUSIONS AND CLINICAL RELEVANCE Galloping horses maintained asymmetry of head, pelvic, and limb motion between limb leads that was unrelated to lameness.

Associations of force plate and body-mounted inertial sensor measurements for identification of hind limb lameness in horses.

OBJECTIVE: To investigate associations between inertial sensor and stationary force plate measurements of hind limb lameness in horses. ANIMALS: 21 adult horses with no lameness or with mild hind limb lameness. PROCEDURES: Horses were instrumented with inertial sensors and evaluated for lameness with a stationary force plate while trotting in a straight line. Inertial sensor-derived measurements of maximum and minimum pelvic height differences between right and left halves of the stride were compared with vertical and horizontal ground reaction forces (GRFs). Stepwise linear regression was performed to investigate the strength of association between inertial sensor measurements of hind limb lameness and amplitude, impulse, and time indices of important events in the vertical and horizontal GRF patterns. RESULTS: Difference in minimum pelvic position was moderately (Ra(2) = 0.60) associated with the difference in peak vertical GRF but had little association with any horizontal GRF measurements. Difference in maximum pelvic position was strongly (Ra(2) = 0.77) associated with a transfer of vertical to horizontal ground reaction impulse in the second half of the stance but was not associated with difference in peak vertical GRF. CONCLUSIONS AND CLINICAL RELEVANCE: Inertial sensor-derived measurements of asymmetric pelvic fall (difference in minimum pelvic position) indicated a decrease in vertical GRF, but similar measurements of asymmetric pelvis rise (difference in maximum pelvic position) indicated a transfer of vertical to horizontal force impulse in the second half of the stance. Evaluation of both pelvic rise and fall may be important when assessing hind limb lameness in horses.

MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function.

Approaches in molecular biology, particularly those that deal with high-throughput sequencing of entire microbial communities (the field of metagenomics), are rapidly advancing our understanding of the composition and functional content of microbial communities involved in climate change, environmental pollution, human health, biotechnology, etc. Metagenomics provides researchers with the most complete picture of the taxonomic (i.e., what organisms are there) and functional (i.e., what are those organisms doing) composition of natively sampled microbial communities, making it possible to perform investigations that include organisms that were previously intractable to laboratory-controlled culturing; currently, these constitute the vast majority of all microbes on the planet. All organisms contained in environmental samples are sequenced in a culture-independent manner, most often with 16S ribosomal amplicon methods to investigate the taxonomic or whole-genome shotgun-based methods to investigate the functional content of sampled communities. Metagenomics allows researchers to characterize the community composition and functional content of microbial communities, but it cannot show which functional processes are active; however, near parallel developments in transcriptomics promise a dramatic increase in our knowledge in this area as well. Since 2008, MG-RAST (Meyer et al., BMC Bioinformatics 9:386, 2008) has served as a public resource for annotation and analysis of metagenomic sequence data, providing a repository that currently houses more than 150,000 data sets (containing 60+ tera-base-pairs) with more than 23,000 publically available. MG-RAST, or the metagenomics RAST (rapid annotation using subsystems technology) server makes it possible for users to upload raw metagenomic sequence data in (preferably) fastq or fasta format. Assessments of sequence quality, annotation with respect to multiple reference databases, are performed automatically with minimal input from the user (see Subheading 4 at the end of this chapter for more details). Post-annotation analysis and visualization are also possible, directly through the web interface, or with tools like matR (metagenomic analysis tools for R, covered later in this chapter) that utilize the MG-RAST API ( http://api.metagenomics.anl.gov/api.html ) to easily download data from any stage in the MG-RAST processing pipeline. Over the years, MG-RAST has undergone substantial revisions to keep pace with the dramatic growth in the number, size, and types of sequence data that accompany constantly evolving developments in metagenomics and related -omic sciences (e.g., metatranscriptomics).

The MG-RAST metagenomics database and portal in 2015.

MG-RAST (http://metagenomics.anl.gov) is an open-submission data portal for processing, analyzing, sharing and disseminating metagenomic datasets. The system currently hosts over 200,000 datasets and is continuously updated. The volume of submissions has increased 4-fold over the past 24 months, now averaging 4 terabasepairs per month. In addition to several new features, we report changes to the analysis workflow and the technologies used to scale the pipeline up to the required throughput levels. To show possible uses for the data from MG-RAST, we present several examples integrating data and analyses from MG-RAST into popular third-party analysis tools or sequence alignment tools.

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River.

Knowledge of the diversity and ecological function of the microbial consortia of James River in Virginia, USA, is essential to developing a more complete understanding of the ecology of this model river system. Metagenomic analysis of James River's planktonic microbial community was performed for the first time using an unamplified genomic library and a 16S rDNA amplicon library prepared and sequenced by Ion PGM and MiSeq, respectively. From the 0.46-Gb WGS library (GenBank:SRR1146621; MG-RAST:4532156.3), 4 × 10(6) reads revealed >3 × 10(6) genes, 240 families of prokaryotes, and 155 families of eukaryotes. From the 0.68-Gb 16S library (GenBank:SRR2124995; MG-RAST:4631271.3; EMB:2184), 4 × 10(6) reads revealed 259 families of eubacteria. Results of the WGS and 16S analyses were highly consistent and indicated that more than half of the bacterial sequences were Proteobacteria, predominantly Comamonadaceae. The most numerous genera in this group were Acidovorax (including iron oxidizers, nitrotolulene degraders, and plant pathogens), which accounted for 10 % of assigned bacterial reads. Polaromonas were another 6 % of all bacterial reads, with many assignments to groups capable of degrading polycyclic aromatic hydrocarbons. Albidiferax (iron reducers) and Variovorax (biodegraders of a variety of natural biogenic compounds as well as anthropogenic contaminants such as polycyclic aromatic hydrocarbons and endocrine disruptors) each accounted for an additional 3 % of bacterial reads. Comparison of these data to other publically-available aquatic metagenomes revealed that this stretch of James River is highly similar to the upper Mississippi River, and that these river systems are more similar to aquaculture and sludge ecosystems than they are to lakes or to a pristine section of the upper Amazon River. Taken together, these analyses exposed previously unknown aspects of microbial biodiversity, documented the ecological responses of microbes to urban effects, and revealed the noteworthy presence of 22 human-pathogenic bacterial genera (e.g., Enterobacteriaceae, pathogenic Pseudomonadaceae, and 'Vibrionales') and 6 pathogenic eukaryotic genera (e.g., Trypanosomatidae and Vahlkampfiidae). This information about pathogen diversity may be used to promote human epidemiological studies, enhance existing water quality monitoring efforts, and increase awareness of the possible health risks associated with recreational use of James River.

Microbial Metabolism Shifts Towards an Adverse Profile with Supplementary Iron in the TIM-2 In vitro Model of the Human Colon.

Oral iron administration in African children can increase the risk for infections. However, it remains unclear to what extent supplementary iron affects the intestinal microbiome. We here explored the impact of iron preparations on microbial growth and metabolism in the well-controlled TNO's in vitro model of the large intestine (TIM-2). The model was inoculated with a human microbiota, without supplementary iron, or with 50 or 250 µmol/L ferrous sulfate, 50 or 250 µmol/L ferric citrate, or 50 µmol/L hemin. High resolution responses of the microbiota were examined by 16S rDNA pyrosequencing, microarray analysis, and metagenomic sequencing. The metabolome was assessed by fatty acid quantification, gas chromatography-mass spectrometry (GC-MS), and (1)H-NMR spectroscopy. Cultured intestinal epithelial Caco-2 cells were used to assess fecal water toxicity. Microbiome analysis showed, among others, that supplementary iron induced decreased levels of Bifidobacteriaceae and Lactobacillaceae, while it caused higher levels of Roseburia and Prevotella. Metagenomic analyses showed an enrichment of microbial motility-chemotaxis systems, while the metabolome markedly changed from a saccharolytic to a proteolytic profile in response to iron. Branched chain fatty acids and ammonia levels increased significantly, in particular with ferrous sulfate. Importantly, the metabolite-containing effluent from iron-rich conditions showed increased cytotoxicity to Caco-2 cells. Our explorations indicate that in the absence of host influences, iron induces a more hostile environment characterized by a reduction of microbes that are generally beneficial, and increased levels of bacterial metabolites that can impair the barrier function of a cultured intestinal epithelial monolayer.

A metagenomics portal for a democratized sequencing world.

The democratized world of sequencing is leading to numerous data analysis challenges; MG-RAST addresses many of these challenges for diverse datasets, including amplicon datasets, shotgun metagenomes, and metatranscriptomes. The changes from version 2 to version 3 include the addition of a dedicated gene calling stage using FragGenescan, clustering of predicted proteins at 90% identity, and the use of BLAT for the computation of similarities. Together with changes in the underlying software infrastructure, this has enabled the dramatic scaling up of pipeline throughput while remaining on a limited hardware budget. The Web-based service allows upload, fully automated analysis, and visualization of results. As a result of the plummeting cost of sequencing and the readily available analytical power of MG-RAST, over 78,000 metagenomic datasets have been analyzed, with over 12,000 of them publicly available in MG-RAST.

The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012.

This report details the outcome of the 1st Hospital Microbiome Project workshop held on June 7th-8th, 2012 at the University of Chicago, USA. The workshop was arranged to determine the most appropriate sampling strategy and approach to building science measurement to characterize the development of a microbial community within a new hospital pavilion being built at the University of Chicago Medical Center. The workshop made several recommendations and led to the development of a full proposal to the Alfred P. Sloan Foundation as well as to the creation of the Hospital Microbiome Consortium.