MGnify: the microbiome sequence data analysis resource in 2023.

The MGnify platform (https://www.ebi.ac.uk/metagenomics) facilitates the assembly, analysis and archiving of microbiome-derived nucleic acid sequences. The platform provides access to taxonomic assignments and functional annotations for nearly half a million analyses covering metabarcoding, metatranscriptomic, and metagenomic datasets, which are derived from a wide range of different environments. Over the past 3 years, MGnify has not only grown in terms of the number of datasets contained but also increased the breadth of analyses provided, such as the analysis of long-read sequences. The MGnify protein database now exceeds 2.4 billion non-redundant sequences predicted from metagenomic assemblies. This collection is now organised into a relational database making it possible to understand the genomic context of the protein through navigation back to the source assembly and sample metadata, marking a major improvement. To extend beyond the functional annotations already provided in MGnify, we have applied deep learning-based annotation methods. The technology underlying MGnify's Application Programming Interface (API) and website has been upgraded, and we have enabled the ability to perform downstream analysis of the MGnify data through the introduction of a coupled Jupyter Lab environment.

Discectomy for Lumbar Disc Herniation in Pediatric and Adolescent Populations: A Systematic Review and Meta-Analysis.

Corroborative evidence for discectomy in pediatric or adolescent patients remains scarce, with this single-arm meta-analysis investigating discectomy for lumbar disc herniation (LDH) within this population. PubMed, Embase (Elsevier), CiNAHL, Cochrane Library, Scopus, and Web of Science were searched. Eligible studies reported pediatric patients under 21 years of age with a diagnosis of LDH that was treated surgically with discectomy. This review was registered in PROSPERO (ID: CRD42023463358). Twenty-two studies met the eligibility criteria (n=1182). Visual analog scale (VAS) scores for back pain at baseline were 5.34 (95% CI: 4.48, 6.20, I2=98.9%). Postoperative VAS back pain scores after 12 months were 0.88 (95% CI: 0.57, 1.19, I2=95.6%). VAS scores for leg pain at baseline were 7.03 (95% CI: 6.63, 7.43, I2=93.5%). Postoperative VAS leg pain scores after 12 months were 1.02 (95% CI: 0.68, 1.36, I2=97.0%). Oswestry disability index (ODI) scores at baseline were 55.46 (95% CI: 43.69, 67.24, I2=99.9%). Postoperative ODI scores after 12 months were 7.82 (95% CI: 4.95, 10.69, I2=99.4%). VAS back, VAS leg and ODI scores demonstrated a minimum clinically important difference (MCID) at all postoperative points. Perioperative outcomes demonstrated operative time as 85.71 mins (95% CI: 73.96, 97.46, I2=99.4%) and hospital length of stay as 3.81 days (95% CI: 3.20, 4.41, I2=98.5%). The postoperative reoperation rate at the same level was 0.01 (95% CI: <0.00, 0.02, I2=0%). Discectomy appears safe and effective in pediatric and adolescent patients suffering from LDH. The findings here provide groundwork for future randomized control trials against conservative measures to elaborate on optimal management and elucidate long-term outcomes.

Quantifying temporal change in biodiversity: challenges and opportunities.

Growing concern about biodiversity loss underscores the need to quantify and understand temporal change. Here, we review the opportunities presented by biodiversity time series, and address three related issues: (i) recognizing the characteristics of temporal data; (ii) selecting appropriate statistical procedures for analysing temporal data; and (iii) inferring and forecasting biodiversity change. With regard to the first issue, we draw attention to defining characteristics of biodiversity time series--lack of physical boundaries, uni-dimensionality, autocorrelation and directionality--that inform the choice of analytic methods. Second, we explore methods of quantifying change in biodiversity at different timescales, noting that autocorrelation can be viewed as a feature that sheds light on the underlying structure of temporal change. Finally, we address the transition from inferring to forecasting biodiversity change, highlighting potential pitfalls associated with phase-shifts and novel conditions.

Does pre-enrichment of anodes with acetate to select for Geobacter spp. enhance performance of microbial fuel cells when switched to more complex substrates?

Many factors affect the performance of microbial fuel cells (MFCs). Considerable attention has been given to the impact of cell configuration and materials on MFC performance. Much less work has been done on the impact of the anode microbiota, particularly in the context of using complex substrates as fuel. One strategy to improve MFC performance on complex substrates such as wastewater, is to pre-enrich the anode with known, efficient electrogens, such as Geobacter spp. The implication of this strategy is that the electrogens are the limiting factor in MFCs fed complex substrates and the organisms feeding the electrogens through hydrolysis and fermentation are not limiting. We conducted a systematic test of this strategy and the assumptions associated with it. Microbial fuel cells were enriched using three different substrates (acetate, synthetic wastewater and real domestic wastewater) and three different inocula (Activated Sludge, Tyne River sediment, effluent from an MFC). Reactors were either enriched on complex substrates from the start or were initially fed acetate to enrich for Geobacter spp. before switching to synthetic or real wastewater. Pre-enrichment on acetate increased the relative abundance of Geobacter spp. in MFCs that were switched to complex substrates compared to MFCs that had been fed the complex substrates from the beginning of the experiment (wastewater-fed MFCs - 21.9 ± 1.7% Geobacter spp.; acetate-enriched MFCs, fed wastewater - 34.9 ± 6.7% Geobacter spp.; Synthetic wastewater fed MFCs - 42.5 ± 3.7% Geobacter spp.; acetate-enriched synthetic wastewater-fed MFCs - 47.3 ± 3.9% Geobacter spp.). However, acetate pre-enrichment did not translate into significant improvements in cell voltage, maximum current density, maximum power density or substrate removal efficiency. Nevertheless, coulombic efficiency (CE) was higher in MFCs pre-enriched on acetate when complex substrates were fed following acetate enrichment (wastewater-fed MFCs - CE = 22.0 ± 6.2%; acetate-enriched MFCs, fed wastewater - CE =58.5 ± 3.5%; Synthetic wastewater fed MFCs - CE = 22.0 ± 3.2%; acetate-enriched synthetic wastewater-fed MFCs - 28.7 ± 4.2%.) The relative abundance of Geobacter ssp. and CE represents the average of the nine replicate reactors inoculated with three different inocula for each substrate. Efforts to improve the performance of anodic microbial communities in MFCs utilizing complex organic substrates should therefore focus on enhancing the activity of organisms driving hydrolysis and fermentation rather the terminal-oxidizing electrogens.

The effect of exercise post vertebral augmentation in osteoporotic patients: A systematic review and meta-analysis.

This meta-analysis investigated the effects of exercise on Visual Analog Scale (VAS) and Oswestry Disability Index (ODI) scores following vertebroplasty or kyphoplasty in osteoporotic fractures. A literature search of PubMed, EMBASE (Elsevier), CiNAHL, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, Scopus, and Web of Science was conducted from database inception to October 6, 2022. Eligible studies reported osteoporosis patients over 18 years of age with a diagnosis of at least one vertebral fracture via radiography or clinical assessment. This review was registered in PROSPERO (ID: CRD42022340791). Ten studies met the eligibility criteria (n = 889). VAS scores at baseline were 7.75 (95% CI: 7.54, 7.97, I2 = 76.11%). Following initiation of exercise, VAS scores at the endpoint of 12 months were 1.91 (95% CI: 1.53, 2.29, I2 = 92.69%). ODI scores at baseline were 68.66 (95% CI: 56.19, 81.13, I2 = 85%). Following initiation of exercise, ODI scores at the endpoint of 12 months were 21.20 (95% CI: 14.52, 27.87, I2 = 99.30). A two-arm analysis demonstrated improved VAS and ODI for the exercise group compared to non-exercise control at 6 months (MD = -0.70, 95% CI: -1.08, -0.32, I2 = 87% and MD = -6.48, 95% CI: -7.52, -5.44, I2 = 46%, respectively) and 12 months (MD = -0.88, 95% CI: -1.27, -0.49, I2 = 85% and MD = -9.62, 95% CI: -13.24, -5.99, I2 = 93%). Refracture was the only adverse event reported and occurred almost twice as frequently in the non-exercise group than in the exercise group. Exercise rehabilitation post vertebral augmentation is associated with improved pain and functionality, particularly after 6 months of exposure, and may reduce refracture rate.

Integrating ecosystem markets to co-ordinate landscape-scale public benefits from nature.

Ecosystem markets are proliferating around the world in response to increasing demand for climate change mitigation and provision of other public goods. However, this may lead to perverse outcomes, for example where public funding crowds out private investment or different schemes create trade-offs between the ecosystem services they each target. The integration of ecosystem markets could address some of these issues but to date there have been few attempts to do this, and there is limited understanding of either the opportunities or barriers to such integration. This paper reports on a comparative analysis of eleven ecosystem markets in operation or close to market in Europe, based on qualitative analysis of 25 interviews, scheme documentation and two focus groups. Our results indicate three distinct types of markets operating from the regional to national scale, with different modes of operation, funding and outcomes: regional ecosystem markets, national carbon markets and green finance. The typology provides new insights into the operation of ecosystem markets in practice, which may challenge traditionally held notions of Payment for Ecosystem Services. Regional ecosystem markets, in particular, represent a departure from traditional models, by using a risk-based funding model and aggregating both supply and demand to overcome issues of free-riding, ecosystem service trade-offs and land manager engagement. Central to all types of market were trusted intermediaries, brokers and platforms to aggregate supply and demand, build trust and lower transaction costs. The paper outlines six options for blending public and private funding for the provision of ecosystem services and proposes a framework for integrating national carbon markets and green finance with regional ecosystem markets. Such integration may significantly increase funding for regenerative agriculture and conservation across multiple habitats and services, whilst addressing issues of additionality and ecosystem service trade-offs between multiple schemes.

Evaluation of hydrolysis and fermentation rates in microbial fuel cells.

This study determined the influence of substrate degradation on power generation in microbial fuel cells (MFCs) and microbial community selection on the anode. Air cathode MFCs were fed synthetic medium containing different substrates (acetate, glucose and starch) using primary clarifier sewage as source of electroactive bacteria. The complexity of the substrate affected the MFC performance both for power generation and COD removal. Power output decreased with an increase in substrate complexity from 99±2 mWm(-2) for acetate to 4±2 mWm(-2) for starch. The organic matter removal and coulombic efficiency (CE) of MFCs with acetate and glucose (82% of COD removal and 26% CE) were greater than MFCs using starch (60% of COD removal and 19% of CE). The combined hydrolysis-fermentation rate obtained (0.0024 h(-1)) was considerably lower than the fermentation rate (0.018 h(-1)), indicating that hydrolysis of complex compounds limits current output over fermentation. Statistical analysis of microbial community fingerprints, developed on the anode, showed that microbial communities were enriched according to the type of substrate used. Microbial communities producing high power outputs (fed acetate) clustered separately from bacterial communities producing low power outputs (fed complex compounds).

Energy from algae using microbial fuel cells.

Bioelectricity production from a phytoplankton, Chlorella vulgaris, and a macrophyte, Ulva lactuca was examined in single chamber microbial fuel cells (MFCs). MFCs were fed with the two algae (as powders), obtaining differences in energy recovery, degradation efficiency, and power densities. C. vulgaris produced more energy generation per substrate mass (2.5 kWh/kg), but U. lactuca was degraded more completely over a batch cycle (73 +/- 1% COD). Maximum power densities obtained using either single cycle or multiple cycle methods were 0.98 W/m(2) (277 W/m(3)) using C. vulgaris, and 0.76 W/m(2) (215 W/m(3)) using U. lactuca. Polarization curves obtained using a common method of linear sweep voltammetry (LSV) overestimated maximum power densities at a scan rate of 1 mV/s. At 0.1 mV/s, however, the LSV polarization data was in better agreement with single- and multiple-cycle polarization curves. The fingerprints of microbial communities developed in reactors had only 11% similarity to inocula and clustered according to the type of bioprocess used. These results demonstrate that algae can in principle, be used as a renewable source of electricity production in MFCs.

A single chamber packed bed microbial fuel cell biosensor for measuring organic content of wastewater.

This study reports an investigation of the effect of the anode surface area on the performance of a single chamber microbial fuel cell (SCMFC) based biosensor for measuring the organic content of wastewater. A packed bed of graphite granules was used as the anode. The surface area of the anode was changed by altering the granule bed thickness (0.3 cm and 1 cm). The anode surface area was found to play a role in the dynamic response of the system. For a granule bed thickness of 1 cm and with an external resistance of 500 Omega, the response time (defined as the time required to achieve 95% of the steady-state current) was reduced by approximately 65% in comparison to a SCMFC biosensor with a carbon cloth anode.

Modelling bacterial twitching in fluid flows: a CFD-DEM approach.

Bacterial habitats are often associated with fluid flow environments. Bacterial twitching is important for initial bacterial colonization and biofilm formation. The existing research about bacteria twitching is largely experimental orientated. There is a lack of models of twitching motility of bacteria in shear flows, which could provide fundamental understanding about how bacterial twitching would be affected by bacteria associated properties such as number of pili and their distribution on the cell body and environmental factors such as flow and surface patterns. In this work, a three-dimensional modelling approach of Computational Fluid Dynamics (CFD) coupled with the Discrete Element Method (DEM) proposed to study bacterial twitching on flat and groove surfaces under shear flow conditions. Rod-shaped bacteria are modelled as groups of spherical particles and Type IV pili attached to bacteria are modelled as dynamic springs which can elongate, retract, attach and detach. The CFD-DEM model of rod-shape bacteria is validated against orbiting of immotile bacteria in shear flows. The effects of fluid flow rate and surface topography on twitching motility are studied. The model can successfully predict upstream twitching motility of rod-shaped bacteria in shear flows. Our model can predict that there would be an optimal range of wall shear stress in which bacterial upstream twitching is most efficient. The results also indicate that when bacteria twitch on groove surfaces, they are likely to accumulate around the downstream side of the groove walls.

Operationalizing a Data to Care Strategy in Michigan Through Cross-Agency Collaborations.

BACKGROUND: For persons with HIV infection (PWH), viral load suppression is essential to maintaining health and reducing the likelihood of HIV transmission. Data to Care (D2C) is an important strategy for improving HIV outcomes but may be resource-intensive to execute. SETTING: In 2016, Michigan joined the HIV Health Improvement Affinity Group to strengthen D2C partnerships between its Medicaid and HIV program. Goals included establishing routine data sharing, matching data sources to understand health outcomes, and collaborating to turn data into action. METHODS: Michigan established data use agreements to assess gaps in care for PWH enrolled in Medicaid. The HIV Surveillance Program used Link Plus to match surveillance records on PWH to Medicaid's active beneficiary file to identify PWH who were beneficiaries as of December 31, 2015. RESULTS: Matching the 2,300,877 Michigan Medicaid beneficiaries with the 15,845 PWH in HIV surveillance yielded 4822 matched PWH enrolled in Medicaid in 2015. Of Medicaid beneficiaries with HIV, 597 had no evidence of receiving HIV care, representing 20% of all Michigan residents with HIV and not in care in 2015. CONCLUSION: D2C is an effective strategy for improving HIV care continuum outcomes but can be relatively inefficient if implementation models rely solely on public health infrastructure. Through the HIV Health Improvement Affinity Group, Michigan's Medicaid and HIV programs leveraged their combined data assets to evaluate and improve care quality and outcomes for PWH on Medicaid. Partnerships between Medicaid and public health offer attractive mechanisms for potentially increasing efficiency and effectiveness of D2C investments.

Extracellular Polymeric Substance Production and Aggregated Bacteria Colonization Influence the Competition of Microbes in Biofilms.

The production of extracellular polymeric substance (EPS) is important for the survival of biofilms. However, EPS production is costly for bacteria and the bacterial strains that produce EPS (EPS+) grow in the same environment as non-producers (EPS-) leading to competition between these strains for nutrients and space. The outcome of this competition is likely to be dependent on factors such as initial attachment, EPS production rate, ambient nutrient levels and quorum sensing. We use an Individual-based Model (IbM) to study the competition between EPS+ and EPS- strains by varying the nature of initial colonizers which can either be in the form of single cells or multicellular aggregates. The microbes with EPS+ characteristics obtain a competitive advantage if they initially colonize the surface as smaller aggregates and are widely spread-out between the cells of EPS-, when both are deposited on the substratum. Furthermore, the results show that quorum sensing-regulated EPS production may significantly reduce the fitness of EPS producers when they initially deposit as aggregates. The results provide insights into how the distribution of bacterial aggregates during initial colonization could be a deciding factor in the competition among different strains in biofilms.

A mechanistic Individual-based Model of microbial communities.

Accurate predictive modelling of the growth of microbial communities requires the credible representation of the interactions of biological, chemical and mechanical processes. However, although biological and chemical processes are represented in a number of Individual-based Models (IbMs) the interaction of growth and mechanics is limited. Conversely, there are mechanically sophisticated IbMs with only elementary biology and chemistry. This study focuses on addressing these limitations by developing a flexible IbM that can robustly combine the biological, chemical and physical processes that dictate the emergent properties of a wide range of bacterial communities. This IbM is developed by creating a microbiological adaptation of the open source Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). This innovation should provide the basis for "bottom up" prediction of the emergent behaviour of entire microbial systems. In the model presented here, bacterial growth, division, decay, mechanical contact among bacterial cells, and adhesion between the bacteria and extracellular polymeric substances are incorporated. In addition, fluid-bacteria interaction is implemented to simulate biofilm deformation and erosion. The model predicts that the surface morphology of biofilms becomes smoother with increased nutrient concentration, which agrees well with previous literature. In addition, the results show that increased shear rate results in smoother and more compact biofilms. The model can also predict shear rate dependent biofilm deformation, erosion, streamer formation and breakup.

Microbial fuel cells meet with external resistance.

The influence of external load on the composition of the anodic biofilm microbial community and biomass yield was investigated in a microbial fuel cell fed with glucose and domestic wastewater was used as source of electrogens. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR) amplified 16S rRNA gene fragments revealed distinct differences in anodic bacterial communities formed at the anode of each MFC operated under a different external load. These results implied that in an MFC, electrogenic bacteria were enriched under higher current densities, i.e., low external load, and were able to sustain better current and effluent quality. The influence of the external resistance applied to the MFCs during formation of the bacterial communities from sewage wastewater was shown to have no significant effect on power performance of the MFCs nor to have a significant influence on their anodic activity with both glucose and brewery wastewater as fuel. As expected, current generation, COD removal and the biomass yield were all directly influenced by the external load. Significantly, when operated under lower external load, the biomass yield in the MFC was less than that in conventional anaerobic digestion (i.e., control).

A single-chamber microbial fuel cell as a biosensor for wastewaters.

The traditional 5-day test of the biochemical oxygen demand (BOD(5) test) has many disadvantages, and principally it is unsuitable for process control and real-time monitoring. As an alternative, a single-chamber microbial fuel cell (SCMFC) with an air cathode was tested as a biosensor and the performance analysed in terms of its measurement range, its response time, its reproducibility and its operational stability. When artificial wastewater was used as fuel, the biosensor output had a linear relationship with the BOD concentration up to 350 mg BOD cm(-3); very high reproducibility; and stability over 7 months of operation. The system was further improved by reducing by 75% the total anolyte volume. In this way a response time close to the hydraulic retention time (HRT) of the biosensor (i.e. 40 min) was reached. When the small volume SCMFC biosensor was fed with real wastewater a good correlation between COD concentration and current output was obtained, demonstrating the applicability of this system to real effluents. The measurements obtained with the biosensor were also in accordance with values obtained with standard measurement methods.

Influence of sustainability and immigration in assembling bacterial populations of known size and function.

The rational assembly of microbial communities to perform desired functions would be of great practical benefit to society. Broadly speaking, there are two major theoretical foundations for microbial community assembly: one based on island biogeography theory and another based on niche theory. In this study, we compared a parameter from each theory (immigration rate and sustainability, respectively) to ascertain which was more influential in establishing a functional bacterial population in phenol degrading activated sludge over a 30-day period. Two bacterial strains originally isolated from activated sludge, but differing in their ability to sustain a population in this environment, were repeatedly added to activated sludge reactors at different doses. The resulting size of each population was monitored by competitive polymerase chain reaction. Large, unexpected, yet reproducible fluctuations in population sizes were observed. Irrespective of this, difference in the ability to sustain a population in this environment, overshadowed the influence of 100-fold differences in immigration rate.

Microbial landscapes: new paths to biofilm research.

It is the best of times for biofilm research. Systems biology approaches are providing new insights into the genetic regulation of microbial functions, and sophisticated modelling techniques are enabling the prediction of microbial community structures. Yet it is also clear that there is a need for ecological theory to contribute to our understanding of biofilms. Here, we suggest a concept for biofilm research that is spatially explicit and solidly rooted in ecological theory, which might serve as a universal approach to the study of the numerous facets of biofilms.

The role of ecological theory in microbial ecology.

Microbial ecology is currently undergoing a revolution, with repercussions spreading throughout microbiology, ecology and ecosystem science. The rapid accumulation of molecular data is uncovering vast diversity, abundant uncultivated microbial groups and novel microbial functions. This accumulation of data requires the application of theory to provide organization, structure, mechanistic insight and, ultimately, predictive power that is of practical value, but the application of theory in microbial ecology is currently very limited. Here we argue that the full potential of the ongoing revolution will not be realized if research is not directed and driven by theory, and that the generality of established ecological theory must be tested using microbial systems.