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A recent study (Johansen et al., 2023) shows how the ecological composition of the human gut virome changes with age, showing a decline in core taxa and an enrichment of subdominant taxa, similar to what has been observed in the gut bacteriomes of centenarians. [ABSTRACT FROM AUTHOR]

In this work, the electronic, structural, elastic, and thermodynamic properties of Ti2AX MAX phases (A = Al or Ga, X = C or N) were investigated using density functional theory (DFT). It is shown that the calculations of the electronic, structural, and elastic properties of these structures, using local density approximation (LDA) and generalized gradient approximation (GGA) coupled with projected augmented-wave (PAW) pseudopotentials, agree well with experiments. A thermodynamic model, which considers the vibrational and electronic contributions to the total free energy of the system, was used to investigate the finite-temperature thermodynamic properties of Ti2AX. The vibrational contribution was calculated using the supercell method, whereas the electronic contribution resulted from one-dimensional integration of electronic density of states (DOSs). To verify the model, the specific heats of pure elements were calculated and compared to experimental data. The DFT-D2 technique was used to calculate the heat capacity of graphite, taking into account the van der Waals (vdW) effect. Good agreement between the calculations and experiments for the specific heats of graphite and other pure elements lends validity to the approach used. The calculated results for the specific heats of Ti2AlC and Ti2AlN match well with experimental data. These strengthen the results of specific heats of Ti2GaC and Ti2GaN as well as other calculated thermodynamic properties, including the energies of formation and thermal expansion coefficient. [ABSTRACT FROM AUTHOR]

High-throughput data generation platforms, like mass-spectrometry, microarrays, and second-generation sequencing are susceptible to batch effects due to run-to-run variation in reagents, equipment, protocols, or personnel. Currently, batch correction methods are not commonly applied to microbiome sequencing datasets. In this paper, we compare different batch-correction methods applied to microbiome case-control studies. We introduce a model-free normalization procedure where features (i.e. bacterial taxa) in case samples are converted to percentiles of the equivalent features in control samples within a study prior to pooling data across studies. We look at how this percentile-normalization method compares to traditional meta-analysis methods for combining independent p-values and to limma and ComBat, widely used batch-correction models developed for RNA microarray data. Overall, we show that percentile-normalization is a simple, non-parametric approach for correcting batch effects and improving sensitivity in case-control meta-analyses. [ABSTRACT FROM AUTHOR]

Aims: The effects of shrub encroachment on plant and soil properties have been well studied. However, little is known about how shrub encroachment influences soil bacterial communities. We investigated the effects of shrub encroachment on grassland soil bacterial communities along a soil depth gradient in the Inner Mongolian region of China.Methods: The belowground bacterial communities were examined using high-throughput sequencing of the 16S rRNA gene (V4-V5 region, Illumina MiSeq).Results: Bacterial alpha-diversity was higher in shrub-encroached soils than in control grassland soils. Bacterial OTU richness was highest at 0-20 cm soil depths, while phylogenetic diversity was greatest at 10-20 cm soil depths. At each soil depth layer, shrub encroachment was associated with a significant shift in bacterial community composition. Change in soil pH was the factor most strongly related to change in bacterial community composition associated with shrub encroachment at all four depth horizons in the soils. Shrub encroachment appears to alter the distribution of bacterial life history strategies in the surface soil (i.e., showing an enrichment in copiotrophs and a depletion in oligotrophs) and shrubs are associated with an increase in nitrification potential in deeper soil horizons.Conclusions: Our results indicate that the influence of shrub encroachment on bacterial community composition extends deep into the soil. The intensity of shrub encroachment at this study site suggests that this ecosystem is undergoing dramatic succession towards shrub-dominance, which will likely trigger shifts in ecosystem function. [ABSTRACT FROM AUTHOR]

The article presents considerations for effective synbiotics design and opportunities for economic development in probiotics. It mentions that the market for probiotics is probably to increase and marketing of the organisms might extend beyond digestive diseases. It states that next-generation probiotics need to have some demonstrated health impact, based on either animal studies or clinical trials in humans.

The gut microbiome is a dynamic system that changes with host development, health, behavior, diet, and microbe-microbe interactions. Prior work on gut microbial time series has largely focused on autoregressive models (e.g. Lotka-Volterra). However, we show that most of the variance in microbial time series is non-autoregressive. In addition, we show how community state-clustering is flawed when it comes to characterizing within-host dynamics and that more continuous methods are required. Most organisms exhibited stable, mean-reverting behavior suggestive of fixed carrying capacities and abundant taxa were largely shared across individuals. This mean-reverting behavior allowed us to apply sparse vector autoregression (sVAR)—a multivariate method developed for econometrics—to model the autoregressive component of gut community dynamics. We find a strong phylogenetic signal in the non-autoregressive co-variance from our sVAR model residuals, which suggests niche filtering. We show how changes in diet are also non-autoregressive and that Operational Taxonomic Units strongly correlated with dietary variables have much less of an autoregressive component to their variance, which suggests that diet is a major driver of microbial dynamics. Autoregressive variance appears to be driven by multi-day recovery from frequent facultative anaerobe blooms, which may be driven by fluctuations in luminal redox. Overall, we identify two dynamic regimes within the human gut microbiota: one likely driven by external environmental fluctuations, and the other by internal processes. [ABSTRACT FROM AUTHOR]

Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high microbial diversity and large spatial variability of most soil characteristics. We investigated soil bacterial community structure in a switchgrass stand planted on soil with a history of grassland vegetation at high spatial resolution to determine whether biogeographic trends occurred at the centimeter scale. Moreover, we tested whether such heterogeneity, if present, influenced community structure within or among ecosystems. Pronounced heterogeneity was observed at centimeter scales, with abrupt changes in relative abundance of phyla from sample to sample. At the ecosystem scale (> 10 m), however, bacterial community composition and structure were subtly, but significantly, altered by fertilization, with higher alpha diversity in fertilized plots. Moreover, by comparing these data with data from 1772 soils from the Earth Microbiome Project, it was found that 20% of bacterial taxa were shared between their site and diverse globally sourced soil samples, while grassland soils shared approximately 40% of their operational taxonomic units with the current study. By spanning several orders of magnitude, the analysis suggested that extreme patchiness characterized community structure at smaller scales but that coherent patterns emerged at larger length scales. [ABSTRACT FROM AUTHOR]

Microorganisms are the pillars of life on Earth. Over billions of years, they have evolved into every conceivable niche on the planet. Microbes reshaped the oceans and atmosphere and gave rise to conditions conducive to multicellular organisms. Only in the past decade have we started to peer deeply into the microbial cosmos, and what we have found is amazing. Microbial ecosystems behave, in many ways, like large-scale ecosystems, although there are important exceptions. We review recent advances in our understanding of how microbial diversity is distributed across environments, how microbes influence the ecosystems in which they live, and how these nano-machines might be harnessed to advance our understanding of the natural world. [ABSTRACT FROM AUTHOR]

Aims: Wildfires are important disturbances that help to shape the structure and function of forest ecosystems, and arbuscular mycorrhizal fungi (AMF) are key players in the post-fire recovery of soils and understory vegetation. We aimed to investigate the response of AMF communities to wildfire over different timescales. Methods: Primer set AMV4.5NF/AMDGR was used to amplify soil 18S rRNA gene fragments for the 454 GS-FLX pyrosequencing platform to examine belowground AMF communities 1 and 11 years following low- and high-intensity wildfires in the Greater Khingan Mountains of China. Results: The majority of AMF sequences detected were annotated as Glomeraceae, Claroideoglomeraceae, Diversisporaceae and Acaulosporaceae. Both AMF community composition and alpha-diversity were correlated with herbaceous and shrubby biomass, available phosphorus (AP) and NH, which were in turn altered by wildfire. AMF community composition, alpha-diversity, and phylogenetic structure were significantly altered 1-year-post-fire. However, AMF communities were indistinguishable from unburned forest soils 11-year-post-fire. Conclusions: Our results indicated that AMF communities are resilient to wildfire on decadal timescales. This resilience appears to depend on the post-fire regrowth of understory vegetation and the subsequent recovery of soil chemical properties. [ABSTRACT FROM AUTHOR]

Human-associated bacteria dominate the built environment (BE). Following decontamination of floors, toilet seats, and soap dispensers in four public restrooms, in situ bacterial communities were characterized hourly, daily, and weekly to determine their successional ecology. The viability of cultivable bacteria, following the removal of dispersal agents (humans), was also assessed hourly. A late-successional community developed within 5 to 8 h on restroom floors and showed remarkable stability over weeks to months. Despite late-successional dominance by skin- and outdoor-associated bacteria, the most ubiquitous organisms were predominantly gut-associated taxa, which persisted following exclusion of humans. Staphylococcus represented the majority of the cultivable community, even after several hours of human exclusion. Methicillin-resistant Staphylococcus aureus (MRSA)-associated virulence genes were found on floors but were not present in assembled Staphylococcus pan-genomes. Viral abundances, which were predominantly enterophages, human papilloma virus, and herpesviruses, were significantly correlated with bacterial abundances and showed an unexpectedly low virus-to-bacterium ratio in surface-associated samples, suggesting that bacterial hosts are mostly dormant on BE surfaces. [ABSTRACT FROM AUTHOR]

See also the Commentary by Powell and Sikes [ABSTRACT FROM AUTHOR]

Sediment microbial communities are responsible for a majority of the metabolic activity in river and stream ecosystems. Understanding the dynamics in community structure and function across freshwater environments will help us to predict how these ecosystems will change in response to human land-use practices. Here we present a spatiotemporal study of sediments in the Tongue River (Montana, USA), comprising six sites along 134 km of river sampled in both spring and fall for two years. Sequencing of 16S rRNA amplicons and shotgun metagenomes revealed that these sediments are the richest (∼65,000 microbial ‘species’ identified) and most novel (93% of OTUs do not match known microbial diversity) ecosystems analyzed by the Earth Microbiome Project to date, and display more functional diversity than was detected in a recent review of global soil metagenomes. Community structure and functional potential have been significantly altered by anthropogenic drivers, including increased pathogenicity and antibiotic metabolism markers near towns and metabolic signatures of coal and coalbed methane extraction byproducts. The core (OTUs shared across all samples) and the overall microbial community exhibited highly similar structure, and phylogeny was weakly coupled with functional potential. Together, these results suggest that microbial community structure is shaped by environmental drivers and niche filtering, though stochastic assembly processes likely play a role as well. These results indicate that sediment microbial communities are highly complex and sensitive to changes in land use practices. [ABSTRACT FROM AUTHOR]

Background Individuals with chronic low back pain (CLBP) have altered activations patterns of the anterior trunk musculature when performing the abdominal hollowing manoeuvre (attempt to pull umbilicus inward and upward towards the spine). There is a subgroup of individuals with CLBP who have high neurocognitive and sensory motor deficits with associated primitive reflexes (PR). The objective of the study was to determine if orienting the head and extremities to positions, which mimic PR patterns would alter anterior trunk musculature activation during the hollowing manoeuvre. Methods This study compared surface electromyography (EMG) of bilateral rectus abdominis (RA), external oblique (EO), and internal obliques (IO) of 11 individuals with CLBP and evident PR to 9 healthy controls during the hollowing manoeuvre in seven positions of the upper quarter. Results Using magnitude based inferences it was likely (>75%) that controls had a higher ratio of left IO:RA activation with supine (cervical neutral), asymmetrical tonic neck reflex (ATNR) left and right, right cervical rotation and cervical extension positions. A higher ratio of right IO:RA was detected in the cervical neutral and ATNR left position for the control group. The CLBP group were more likely to show higher activation of the left RA in the cervical neutral, ATNR left and right, right cervical rotation and cervical flexion positions as well as in the cervical neutral and cervical flexion position for the right RA. Conclusions Individuals with CLBP and PR manifested altered activation patterns during the hollowing maneuver compared to healthy controls and that altering cervical and upper extremity position can diminish the group differences. Altered cervical and limb positions can change the activation levels of the IO and EO in both groups. [ABSTRACT FROM AUTHOR]

Predation rates were measured for two Acanthamoeba castellanii strains feeding on metal-tolerant and metal-sensitive strains of Pseudomonas putida and compared with cellular thermodynamic data. Predation rates by A. castellanii strain ATCC 30010 correlated with cell volume of the prey. To explore whether this observation could be environmentally relevant, pseudomonad species were isolated from a pristine and a metal-contaminated river and were paired based on phylogenetic and physiological relatedness. Then, cellular thermodynamics and predation rates were measured on the most similar pseudomonad pair. Under cadmium stress, the strain from contaminated river sediments, Pseudomonas sp. CF150, exited metabolic dormancy faster than its pair from pristine sediments, Pseudomonas sp. N9, but consumed available resources less efficiently (more energy was lost as heat). Predation rates by both strains of ameba were greater on Pseudomonas sp. CF150 than on Pseudomonas sp. N9 at the highest cadmium concentration. [ABSTRACT FROM AUTHOR]

Invasions by non-native plants can alter ecosystem functions and reduce native plant diversity, but relatively little is known about their effect on belowground microbial communities. We show that invasions by knapweed (Centaurea stoebe) and leafy spurge (Euphorbia esula, hereafter spurge)-but not cheatgrass (Bromus tectorum)-support a higher abundance and diversity of symbiotic arbuscular mycorrhizal fungi (AMF) than multi-species native plant communities. The higher AMF richness associated with knapweed and spurge is unlikely due to a co-invasion by AMF, because a separate sampling showed that individual native forbs hosted a similar AMF abundance and richness as exotic forbs. Native grasses associated with fewer AMF taxa, which could explain the reduced AMF richness in native, grass-dominated communities. The three invasive plant species harbored distinct AMF communities, and analyses of co-occurring native and invasive plants indicate that differences were partly driven by the invasive plants and were not the result of pre-invasion conditions. Our results suggest that invasions by mycotrophic plants that replace poorer hosts can increase AMF abundance and richness. The high AMF richness in monodominant plant invasions also indicates that the proposed positive relationship between above and belowground diversity is not always strong. Finally, the disparate responses among exotic plants and consistent results between grasses and forbs suggest that AMF respond more to plant functional group than plant provenance. [ABSTRACT FROM AUTHOR]

Do bacterial taxa demonstrate clear endemism, like macroorganisms, or can one site's bacterial community recapture the total phylogenetic diversity of the world's oceans? Here we compare a deep bacterial community characterization from one site in the English Channel (L4-DeepSeq) with 356 datasets from the International Census of Marine Microbes (ICoMM) taken from around the globe (ranging from marine pelagic and sediment samples to sponge-associated environments). At the L4-DeepSeq site, increasing sequencing depth uncovers greater phylogenetic overlap with the global ICoMM data. This site contained 31.7-66.2% of operational taxonomic units identified in a given ICoMM biome. Extrapolation of this overlap suggests that 1.93 × 1011 sequences from the L4 site would capture all ICoMM bacterial phylogenetic diversity. Current technology trends suggest this limit may be attainable within 3 y. These results strongly suggest the marine biosphere maintains a previously undetected, persistent microbial seed bank. [ABSTRACT FROM AUTHOR]

Microbial communities exhibit exquisitely complex structure. Many aspects of this complexity, from the number of species to the total number of interactions, are currently very difficult to examine directly. However, extraordinary efforts are being made to make these systems accessible to scientific investigation. While recent advances in high-throughput sequencing technologies have improved accessibility to the taxonomic and functional diversity of complex communities, monitoring the dynamics of these systems over time and space - using appropriate experimental design - is still expensive. Fortunately, modeling can be used as a lens to focus low-resolution observations of community dynamics to enable mathematical abstractions of functional and taxonomic dynamics across space and time. Here, we review the approaches for modeling bacterial diversity at both the very large and the very small scales at which microbial systems interact with their environments. We show that modeling can help to connect biogeochemical processes to specific microbial metabolic pathways. [ABSTRACT FROM AUTHOR]

Abstract: We used a combination of sampling and statistical approaches to investigate the relative influence of metals, soil acidity, and organic matter on a suite of analogous plant and microbial community parameters in floodplain soils contaminated by mine wastes in the early twentieth century. We compared the sensitivity of plant and microbial communities to environmental variables and to one another using constrained ordination analyses. Environmental factors accounted for a larger percentage of the total variance in microbial communities (56.2%) than plant communities (22.0%). We also investigated biological and geochemical changes that occurred along a short transect (64cm) that spanned a transition from productive grassland to an area of barren wasteland representing a total functional collapse of the grassland/soil ecosystem. Along this small-scale transect we quantified geochemical parameters and biological parameters in two soil layers, an upper layer (0–10cm) and a lower layer (10–20cm). Results from the short transect indicated that soil respiration was not a strong indicator of underlying metal concentrations, but soil acidity was correlated in the upper and lower layers. PLFA profiles changed with distance along the gradient in the upper, but not the lower layer. Implications for remediation of contaminated floodplain soils are discussed. [Copyright &y& Elsevier]

A novel microcalorimetric approach was used to analyze the responses of a metal-tolerant soil bacterium (Pseudomonas putida strain KT2440) to metal resistance gene deletions in cadmium-amended media. As hypothesized, under cadmium stress, the wild-type strain benefited from the resistance genes by entering the exponential growth phase earlier than two knockout strains. In the absence of cadmium, strain KT1, carrying a deletion in the main component (czcA1) of a Cd/Zn chemiosmotic efflux transporter (CzcCBA1), grew more efficiently than the wild type and released ∼700 kJ (per mole of biomass carbon) less heat than the wild-type strain, showing the energetic cost of maintaining CzcCBA1 in the absence of cadmium. A second mutant strain (KT4) carrying a different gene deletion, ΔcadA2, which encodes the main Cd/Pb efflux transporter (a P-type ATPase), did not survive beyond moderate cadmium concentrations and exhibited a decreased growth yield in the absence of cadmium. Therefore, CadA2 plays an essential role in cadmium resistance and perhaps serves an additional function. The results of this study provide direct evidence that heavy metal cation efflux mechanisms facilitate shorter lag phases in the presence of metals and that the maintenance and expression of tolerance genes carry quantifiable energetic costs and benefits. [ABSTRACT FROM AUTHOR]

Helicoidal composites have been found in shrimp club, lobster claw, beetle cuticle, crab shell, scorpion pincer, and fish scale as a natural material. The helicoidal composite possesses excellent impact resistance and extraordinary damage tolerance due to its hierarchical structure and the unique helicoidal arrangement of its reinforcement fibres. Its structure and performance have been studied through various characterisation and mechanical testing methods. Based on the structure-property relationship of the natural helicoidal composite, researchers have been able to mimic the unique fibre arrangement and develop bio-inspired helicoidal composites with enhanced impact performance. Various helicoidal composites comprising of synthetic fibrous materials such as carbon fibre (CF), glass fibre (GF), and aramid fibre, and matrix materials such as thermoset and thermoplastic polymers have been developed through biomimicry. The failure mechanisms of the bio-inspired helicoidal composites have been studied and the advantages of arranging the fibre reinforcement into helicoidal architectures have been elucidated over conventional composite constructions such as quasi-isotropic (QI) and cross-ply layups. This review systematically elaborates the recent progress of the research work on both natural and bio-inspired helicoidal composites. It sheds light on the distinctive construction of the natural helicoidal composites found in different animals such as shrimps, lobsters, crabs, beetles, scorpions, and fish, and their energy absorption mechanisms. Different manufacturing methods for developing bio-inspired helicoidal composites are discussed and various reinforcements and matrix materials used in the composites are described. The processing-structure-property interrelationship of the bio-inspired helicoidal composites is summarised. This review will contribute to the advancement of the knowledge of the natural helicoidal composite and potentially help researchers to develop highly efficient bio-inspired damage tolerant helicoidal composites. [ABSTRACT FROM AUTHOR]

Background: Individuals with chronic low back pain (CLBP) have altered activations patterns of the anterior trunk musculature when performing the abdominal hollowing manœuvre (attempt to pull umbilicus inward and upward towards the spine). There is a subgroup of individuals with CLBP who have high neurocognitive and sensory motor deficits with associated primitive reflexes (PR). The objective of the study was to determine if orienting the head and extremities to positions, which mimic PR patterns would alter anterior trunk musculature activation during the hollowing manoeuvre.Methods: This study compared surface electromyography (EMG) of bilateral rectus abdominis (RA), external oblique (EO), and internal obliques (IO) of 11 individuals with CLBP and evident PR to 9 healthy controls during the hollowing manoeuvre in seven positions of the upper quarter.Results: Using magnitude based inferences it was likely (>75%) that controls had a higher ratio of left IO:RA activation with supine (cervical neutral), asymmetrical tonic neck reflex (ATNR) left and right, right cervical rotation and cervical extension positions. A higher ratio of right IO:RA was detected in the cervical neutral and ATNR left position for the control group. The CLBP group were more likely to show higher activation of the left RA in the cervical neutral, ATNR left and right, right cervical rotation and cervical flexion positions as well as in the cervical neutral and cervical flexion position for the right RA.Conclusions: Individuals with CLBP and PR manifested altered activation patterns during the hollowing maneuver compared to healthy controls and that altering cervical and upper extremity position can diminish the group differences. Altered cervical and limb positions can change the activation levels of the IO and EO in both groups. [ABSTRACT FROM AUTHOR]

Summary: Through complex interspecies interactions, microbial processes drive nutrient cycling and biogeochemistry. However, we still struggle to predict specifically which organisms, communities and biotic and abiotic processes are determining ecosystem function and how environmental changes will alter their roles and stability. While the tools to create such a predictive microbial ecology capability exist, cross‐disciplinary integration of high‐resolution field measurements, detailed laboratory studies and computation is essential. In this perspective, we emphasize the importance of pursuing a multiscale, systems approach to iteratively link ecological processes measured in the field to testable hypotheses that drive high‐throughput laboratory experimentation. Mechanistic understanding of microbial processes gained in controlled lab systems will lead to the development of theory that can be tested back in the field. Using N2O production as an example, we review the current status of field and laboratory research and layout a plausible path to the kind of integration that is needed to enable prediction of how N‐cycling microbial communities will respond to environmental changes. We advocate for the development of realistic and predictive gene regulatory network models for environmental responses that extend from single‐cell resolution to ecosystems, which is essential to understand how microbial communities involved in N2O production and consumption will respond to future environmental conditions. [ABSTRACT FROM AUTHOR]

The photomechanism of extreme ultraviolet (EUV) exposures in chemically amplified photoresists is much different than that of previous lithographic wavelengths. Electrons generated during EUV exposure are demonstrated to be a source of acid production through a process referred to as electron trapping. Density functional theory modeling indicates that it is energetically favorable for the photoacid generator (PAG) molecule to decompose if an electron is trapped. Low-energy electrons (<10 eV) that are unlikely to produce holes and secondary electrons generate acid-indicating electron-PAG interactions that are capable of inducing decomposition. Additionally, solution phase reduction in PAGs via electrolysis is shown to produce acid. Furthermore, a more easily reduced PAG (i.e., higher likelihood of trapping an electron) produces a higher acid yield, further supporting electron trapping as a process of acid production regardless of the polymer matrix. An acid indicator, Coumarin 6, was used to determine the number of acids generated per absorbed EUV photon. The results of these measurements indicate that electron-PAG interactions are a source of acid production through electron trapping; thus, an increase in the number of electron-hole pairs available to induce chemical reactions would improve sensitivity. [ABSTRACT FROM AUTHOR]

The doctor of business administration (DBA) degree is widely considered as a professional doctorate or professional doctoral degree that is designed to prepare business practitioners. The doctor of philosophy (PhD) in business, by contrast, is thought to prepare research scholars and higher education faculty members. Prior research conducted by the authors comparing the curriculum of DBA and PhD programs, analyzing accreditation and regulation of the degree programs and examining the terminal degrees of business faculty, did not support the theoretical difference between the two degrees. This study consisted of an analysis of 147 DBA versus 151 PhD dissertations. The analysis indicated a significant group mean difference in the number of PhD versus DBA dissertations in institutions with an R1 classification by the Carnegie Commission on Higher Education. However, no significant correlations nor group mean differences were found in methodology choice, sample size, or research type (applied vs. basic), based on the degree type (DBA vs. PhD). [ABSTRACT FROM AUTHOR]

Recent advances in DNA sequencing technologies have allowed scientists to probe increasingly complex biological systems, including the diversity of bacteria in the environment. However, despite a multitude of recent studies incorporating these methods, many questions regarding how environmental samples should be collected and stored still persist. Here, we assess the impact of different soil storage conditions on microbial community composition using Illumina-based 16S rRNA V4 amplicon sequencing. Both storage time and temperature affected bacterial community composition and structure. Frozen samples maintained the highest alpha diversity and differed least in beta diversity, suggesting the utility of cold storage for maintaining consistent communities. Samples stored for intermediate times (three and seven days) had both the highest alpha diversity and the largest differences in overall beta diversity, showing the degree of community change after sample collection. These divergences notwithstanding, differences in neither storage time nor storage temperature substantially altered overall communities relative to more than 500 previously examined soil samples. These results systematically support previous studies and stress the importance of methodological consistency for accurate characterization and comparison of soil microbiological assemblages. [ABSTRACT FROM AUTHOR]

Researchers have used the (calculation of phase diagram) CALPHAD method to solve the forward phase stability problem of mapping from specific thermodynamic conditions (material composition, temperature, pressure, etc.) to the associated phase constitution. Recently, optimization has been used to solve the inverse problem: mapping specific phase constitutions to the thermodynamic conditions that give rise to them. These pointwise results, however, are of limited value since they do not provide information about the forces driving the point to equilibrium. In this paper, we investigate the problem of mapping a desirable region in the phase constitution space to corresponding regions in the space of thermodynamic conditions. We term this problem the generalized inverse phase stability problem (GIPSP) and model the problem as a continuous constraint satisfaction problem (CCSP). In this paper, we propose a new CCSP algorithm tailored for the GIPSP. We investigate the performance of the algorithm on Fe-Ti binary alloy system using ThermoCalc with the TCFE7 database against a related algorithm. The algorithm is able to generate solutions for this problem with high performance. [ABSTRACT FROM AUTHOR]

The structure of the human GI microbiota can change during pregnancy, which may influence gestational metabolism; however, a mechanism of action remains unclear. Here we observed that in wildtype (WT) mice the relative abundance of Actinobacteria and Bacteroidetes increased during pregnancy. Along with these changes, short chain fatty acids (SCFAs), which are mainly produced through gut microbiota fermentation, significantly changed in both the cecum and peripheral blood throughout gestation in these mice. SCFAs are recognized by G protein coupled receptors (GPCRs) such as FFA2, and we have previously demonstrated that the Ffar2 expression is higher in pancreatic islets during pregnancy. Using female Ffar2-/- mice, we explored the physiological relevance of signaling through this GPCR and found that Ffar2-deficient female mice developed fasting hyperglycemia and impaired glucose tolerance in the setting of impaired insulin secretion as compared to WT mice during, but not prior to, pregnancy. Insulin tolerance tests were similar in Ffar2-/- and WT mice before and during pregnancy. Next, we examined the role of FFA2 in gestational ß cell mass, observing that Ffar2-/- mice had diminished gestational expansion of ß cells during pregnancy. Interestingly, mouse genotype had no significant impact on the composition of the gut microbiome, but did affect the observed SCFA profiles, suggesting a functional difference in the microbiota. Together, these results suggest a potential link between increased Ffar2 expression in islets and the alteration of circulating SCFA levels, possibly explaining how changes in the gut microbiome contribute to gestational glucose homeostasis. [ABSTRACT FROM AUTHOR]

Accurate natural resource damage assessment necessitates monitoring organisms or communities that respond most sensitively to contaminants. Observational studies have demonstrated a correlation between fluvial heavy metal deposition and hyporheic microbial community structure. To establish a causal relationship between sediment metal content and the structure of colonizing bacterial communities, we performed a controlled field experiment River sediments of 1.75-2.36 mm in diameter with five different contaminant concentrations were collected from an environmental metal contamination gradient Sediments were sterilized and then recolonized by incubation in the hyporheic zone of an uncontaminated river (i.e., a common garden experiment was performed). A significant correlation between hyporheic microbial community structure and heavy metal contamination (R ² = 0.81) was observed. The abundance of two phylogenetic groups was highly correlated with the level of heavy metal contamination (Group I, R ² = 0.96; Group III, R² = 0.96, most closely affiliated with the μ- and γ-proteobacteria, respectively). Microbial community structural responses were detected at metal concentrations an order of magnitude lower than those previously reported to impact benthic macroinvertebrate communities. We conclude that hyporheic microbial communities could offer the most sensitive method for assessing natural resource damage in lotic ecosystems in response to fluvial heavy metal deposition. [ABSTRACT FROM AUTHOR]

Broad spectrum antibiotics cause both transient and lasting damage to the ecology of the gut microbiome. Antibiotic-induced loss of gut bacterial diversity has been linked to susceptibility to enteric infections. Prior work on subtherapeutic antibiotic treatment in humans and non-human animals has suggested that entire gut communities may exhibit tolerance phenotypes. In this study, we validate the existence of these community tolerance phenotypes in the murine gut and explore how antibiotic treatment duration or a diet enriched in antimicrobial phytochemicals might influence the frequency of this phenotype. Almost a third of mice exhibited whole-community tolerance to a high dose of the β-lactam antibiotic cefoperazone, independent of antibiotic treatment duration or dietary phytochemical amendment. We observed few compositional differences between non-responder microbiota during antibiotic treatment and the untreated control microbiota. However, gene expression was vastly different between non-responder microbiota and controls during treatment, with non-responder communities showing an upregulation of antimicrobial tolerance genes, like efflux transporters, and a down-regulation of central metabolism. Future work should focus on what specific host- or microbiome-associated factors are responsible for tipping communities between responder and non-responder phenotypes so that we might learn to harness this phenomenon to protect our microbiota from routine antibiotic treatment. Diener, Hoge et al. show that a third of mice exhibit tolerance to a high dose of the β-lactam antibiotic cefoperazone, independent of antibiotic treatment duration or dietary phytochemical amendment. They find that non-responder microbiota upregulates antimicrobial tolerance genes and downregulates central metabolism without altering community composition or diversity, providing insights into the mechanisms of community-wide antibiotic tolerance. [ABSTRACT FROM AUTHOR]

The demand for food will outpace productivity of conventional agriculture due to projected growth of the human population, concomitant with shrinkage of arable land, increasing scarcity of freshwater, and a rapidly changing climate. While aquaponics has potential to sustainably supplement food production with minimal environmental impact, there is a need to better characterize the complex interplay between the various components (fish, plant, microbiome) of these systems to optimize scale up and productivity. Here, we investigated how the commonly-implemented practice of continued microbial community transfer from pre-existing systems might promote or impede productivity of aquaponics. Specifically, we monitored plant growth phenotypes, water chemistry, and microbiome composition of rhizospheres, biofilters, and fish feces over 61-days of lettuce (Lactuca sativa var. crispa) growth in nitrogen-limited aquaponic systems inoculated with bacteria that were either commercially sourced or originating from a pre-existing aquaponic system. Lettuce above- and below-ground growth were significantly reduced across replicates treated with a pre-existing aquaponic system inoculum when compared to replicates treated with a commercial inoculum. Reduced productivity was associated with enrichment in specific bacterial genera in plant roots, including Pseudomonas, following inoculum transfer from pre-existing systems. Increased productivity was associated with enrichment of nitrogen-fixing Rahnella in roots of plants treated with the commercial inoculum. Thus, we show that inoculation from a pre-existing system, rather than from a commercial inoculum, is associated with lower yields. Further work will be necessary to test the putative mechanisms involved. [ABSTRACT FROM AUTHOR]

The Pioneer 100 Wellness Project involved quantitatively profiling 108 participants' molecular physiology over time, including genomes, gut microbiomes, blood metabolomes, blood proteomes, clinical chemistries, and data from wearable devices. Here, we present a longitudinal analysis focused specifically around the Pioneer 100 gut microbiomes. We distinguished a subpopulation of individuals with reduced gut diversity, elevated relative abundance of the genus Prevotella, and reduced levels of the genus Bacteroides. We found that the relative abundances of Bacteroides and Prevotella were significantly correlated with certain serum metabolites, including omega-6 fatty acids. Primary dimensions in distance-based redundancy analysis of clinical chemistries explained 18.5% of the variance in bacterial community composition, and revealed a Bacteroides/Prevotella dichotomy aligned with inflammation and dietary markers. Finally, longitudinal analysis of gut microbiome dynamics within individuals showed that direct transitions between Bacteroides-dominated and Prevotella-dominated communities were rare, suggesting the presence of a barrier between these states. One implication is that interventions seeking to transition between Bacteroides- and Prevotella-dominated communities will need to identify permissible paths through ecological state-space that circumvent this apparent barrier. [ABSTRACT FROM AUTHOR]

Martensitic steels have gained renewed interest recently for their use in automotive, aerospace, and defense applications due to their ultra-high yield strengths and reasonable ductility. A recently discovered low alloy martensitic steel, AF9628, has been shown to exhibit strengths greater than 1.5 GPa with more than 10% tensile ductility, due to the formation of ε-carbide phase. In an effort to produce high strength parts with a high degree of control over geometry, the work herein presents the effects of selective laser melting (SLM) parameters on the microstructure and mechanical properties of this new steel. An optimization framework to determine the process parameters for building porosity-free parts is introduced. This framework utilizes the computationally inexpensive Eagar-Tsai model, calibrated with single track experiments, to predict the melt pool geometry. A geometric criterion for determining maximum allowable hatch spacing is also developed in order to avoid lack of fusion induced porosity in the as-printed parts. Using this framework, fully dense samples were successfully fabricated over a wide range of process parameters, allowing the construction of an SLM processing map for AF9628. The as-printed samples displayed tensile strengths of up to 1.4 GPa, the highest reported to date for any 3D printed alloy, with up to 11% elongation. The demonstrated flexibility in process parameter selection, while maintaining full density, opens up the possibility of local microstructural refinement and parameter optimization for improved mechanical properties in as-printed parts. The process optimization framework introduced here is expected to allow successful printing of new materials in an accelerated fashion. Image, graphical abstract [ABSTRACT FROM AUTHOR]

Depleted gut microbiome α-diversity is associated with several human diseases, but the extent to which this is reflected in the host molecular phenotype is poorly understood. We attempted to predict gut microbiome α-diversity from ~1,000 blood analytes (laboratory tests, proteomics and metabolomics) in a cohort enrolled in a consumer wellness program (N = 399). Although 77 standard clinical laboratory tests and 263 plasma proteins could not accurately predict gut α-diversity, we found that 45% of the variance in α-diversity was explained by a subset of 40 plasma metabolites (13 of the 40 of microbial origin). The prediction capacity of these 40 metabolites was confirmed in a separate validation cohort (N = 540) and across disease states, showing that our findings are robust. Several of the metabolite biomarkers that are reported here are linked with cardiovascular disease, diabetes and kidney function. Associations between host metabolites and gut microbiome α-diversity were modified in those with extreme obesity (body mass index ≥ 35), suggesting metabolic perturbation. The ability of the blood metabolome to predict gut microbiome α-diversity could pave the way to the development of clinical tests for monitoring gut microbial health. Multiomics reveals that almost half of gut microbiome diversity in humans can be explained by 40 blood metabolites. [ABSTRACT FROM AUTHOR]

Dietary interventions to manipulate the human gut microbiome for improved health have received increasing attention. However, their design has been limited by a lack of understanding of the quantitative impact of diet on a host’s microbiota. We present a highly controlled diet perturbation experiment in a healthy, human cohort in which individual micronutrients are spiked in against a standardized background. We identify strong and predictable responses of specific microbes across participants consuming prebiotic spike-ins, at the level of both strains and functional genes, suggesting fine-scale resource partitioning in the human gut. No predictable responses to non-prebiotic micronutrients were found. Surprisingly, we did not observe decreases in day-to-day variability of the microbiota compared to a complex, varying diet, and instead found evidence of diet-induced stress and an associated loss of biodiversity. Our data offer insights into the effect of a low complexity diet on the gut microbiome, and suggest that effective personalized dietary interventions will rely on functional, strain-level characterization of a patient’s microbiota. [ABSTRACT FROM AUTHOR]

Lightweight Fe–Mn–Al–C steels have become a topic of significant interest for the defense and automotive industries. These alloys can maintain high strength and ductility while also reducing weight in structural applications. Conventionally processed Fe–Mn–Al–C austenitic steels with high Al content (∼9 wt%) demonstrate greater than 1.5 GPa strength with 35% elongation. Several recent studies have demonstrated success in fabricating steel parts using laser powder bed fusion (L-PBF) additive manufacturing (AM), which can generate near-net-shape components with complex geometries and is capable of local microstructural control. However, studies on L-PBF processing of Fe–Mn–Al–C alloys have focused on low Al content (<5 wt%) compositional regimes representing alloys that undergo transformation-induced plasticity (TRIP) and twinning-induced plasticity (TWIP). Here, we present the effects of L-PBF processing on the microstructure and mechanical properties of an Fe–30Mn–9Al–1Si-0.5Mo-0.9C austenitic steel. A process optimization framework is employed to determine an ideal L-PBF processing space that will result in >99% density parts. Implementing this framework resulted in near-fully dense specimens fabricated over a broad range of process parameters. Additionally, two bi-directional scan rotation strategies (90° and 67°) were applied to understand their effects on texture and anisotropy in this material. As-printed specimens displayed considerable work-hardening characteristics with average strengths of up to 1.3 GPa and 36% elongation in the build direction. However, solidification microcracks oriented in the build direction resulted in anisotropy in tensile strength and ductility resulting in average strengths of 1.1 GPa and 20% elongation perpendicular to the build direction. The successful L-PBF fabrication of Fe–30Mn–9Al–1Si-0.5Mo-0.9C presented here is expected to open new avenues for weight reduction in structural applications with a high degree of control over part topology. [ABSTRACT FROM AUTHOR]

Background: Clinical guidelines recommend research on sub-groups of patients with low back pain (LBP) but, to date, only few studies have been published. One sub-group of LBP is movement control impairment (MCI) and clinical tests to identify this sub-group have been developed. Also, exercises appear to be beneficial for the management of chronic LBP (CLBP), but very little is known about the management of sub-acute LBP.Methods: A randomized controlled trial (RCT) was conducted to compare the effects of general exercise versus specific movement control exercise (SMCE) on disability and function in patients with MCI within the recurrent sub-acute LBP group. Participants having a MCI attended five treatment sessions of either specific or general exercises. In both groups a short application of manual therapy was applied. The primary outcome was disability, assessed by the Roland-Morris Disability Questionnaire (RMDQ). The measurements were taken at baseline, immediately after the three months intervention and at twelve-month follow-up.Results: Seventy patients met the inclusion criteria and were eligible for the trial. Measurements of 61 patients (SMCE n = 30 and general exercise n = 31) were completed at twelve months. (Drop-out rate 12.9 %). Patients in both groups reported significantly less disability (RMDQ) at twelve months follow-up. However, the mean change on the RMDQ between baseline and the twelve-month measurement showed statistically significantly superior improvement for the SMCE group -1.9 points (-3.9 to -0.5) 95 % (CI). The result did not reach the clinically significant three point difference. There was no statistical difference between the groups measured with Oswestry Disability Index (ODI).Conclusion: For subjects with non-specific recurrent sub-acute LBP and MCI an intervention consisting of SMCE and manual therapy combined may be superior to general exercise combined with manual therapy.Trial Registration: The study protocol registration number is ISRCTN48684087 . It was registered retrospectively 18th Jan 2012. [ABSTRACT FROM AUTHOR]

In this work, the effects of small ternary additions to B2 NiTi structures was investigated through DFT calculations. The analysis considered deviations from stoichiometry arising from either simple substitution of host atoms in a given sublattice or from the formation of anti-sites. The calculations enabled the determination of the site preference of X ternary additions. Moreover, the results suggest that ternary additions located in the central region of the transition metal group across all periods tend to occupy Ni sites due to favorable X–Ti nearest neighbor (NN) interactions. This occupancy is achieved through substitution or through the generation of anti-site defects. On the other hand, ternary additions at both ends of a given transition metal row tend to occupy Ti sites due to favorable X–Ni NN interactions. Once site preferences are determined, the effect of alloying on the thermodynamic and mechanical properties of B2 NiTi–X structures are presented and trends are discussed. [ABSTRACT FROM AUTHOR]

The bacteria that colonize humans and our built environments have the potential to influence our health. Microbial communities associated with seven families and their homes over 6 weeks were assessed, including three families that moved their home. Microbial communities differed substantially among homes, and the home microbiome was largely sourced from humans. The microbiota in each home were identifiable by family. Network analysis identified humans as the primary bacterial vector, and a Bayesian method significantly matched individuals to their dwellings. Draft genomes of potential human pathogens observed on a kitchen counter could be matched to the hands of occupants. After a house move, the microbial community in the new house rapidly converged on the microbial community of the occupants' former house, suggesting rapid colonization by the family's microbiota. [ABSTRACT FROM AUTHOR]

High altitude alpine meadows are experiencing considerably greater than average increases in soil surface temperature, potentially as a result of ongoing climate change. The effects of warming on plant productivity and soil edaphic variables have been established previously, but the influence of warming on soil microbial community structure has not been well characterized. Here, the impact of 15 months of soil warming (both +1 and +2 °C) on bacterial community structure was examined in a field experiment on a Tibetan plateau alpine meadow using bar-coded pyrosequencing. Warming significantly changed ( P < 0.05) the structure of the soil bacterial community, but the alpha diversity was not dramatically affected. Changes in the abundance of the Actinobacteria and Alphaproteobacteria were found to contribute the most to differences between ambient ( AT) and artificially warmed conditions. A variance partitioning analysis ( VPA) showed that warming directly explained 7.15% variation in bacterial community structure, while warming-induced changes in soil edaphic and plant phenotypic properties indirectly accounted for 28.3% and 20.6% of the community variance, respectively. Interestingly, certain taxa showed an inconsistent response to the two warming treatments, for example Deltaproteobacteria showed a decreased relative abundance at +1 °C, but a return to AT control relative abundance at +2 °C. This suggests complex microbial dynamics that could result from conditional dependencies between bacterial taxa. [ABSTRACT FROM AUTHOR]

Background: The Patient-Specific Functional Scale (PSFS) questionnaire was developed by Stratford and colleagues to provide a method for eliciting, measuring and recording descriptions of patients' disabilities. It can be used to guide treatment and assess patient outcome. The aim of the study was to translate and validate a Finnish version of the internationally used PSFS questionnaire, by testing its content validity and responsiveness, and to conduct a cross-cultural adaptation of the measure. Methods: The final version of the Finnish questionnaire underwent a cross-cultural adaptation before the validation study. The subjects of the study were patients receiving physiotherapy for low back pain ( n = 78). They completed the PSFS questionnaire prior to physiotherapy treatment and after treatment series. Roland-Morris Disability Questionnaire (RMDQ) and the visual analogue scale (VAS) were recorded before and after the treatment series. Results: For content validity, a good correlation of the scores between baseline measures of PSFS and RMDQ were 0.65 (Pearson's rho) ( p < 0.01). For responsiveness, moderate to good correlation among the measures between changes of the PSFS, RMDQ and VAS (0-100 mm) scores were analysed. Conclusions: The Finnish translation of the PSFS questionnaire performs as the original, is proven to have adequate content validity and responsiveness, and could be recommended as an assessment tool for clinical and research use. [ABSTRACT FROM AUTHOR]

Summary 1. Disturbance is assumed to be a major driver of plant community composition, but whether similar processes operate on associated soil microbial communities is less known. Based on the assumed trade-off between disturbance tolerance and competiveness, we hypothesize that a severe disturbance applied within a semi-natural grassland would shift the arbuscular mycorrhizal (AM) fungal community towards disturbance-tolerant fungi that are rare in undisturbed soils. 2. We used 454-sequencing of the large subunit rDNA region to characterize AM fungal communities in Plantago lanceolata roots grown in the field for 4 months and exposed either to no disturbance or to severe disturbance where fungi from undisturbed soil were either permitted or prevented from re-colonizing the disturbed area. This allowed for a distinction between AM fungi that survived the disturbance and those that quickly re-colonized after a disturbance. To identify AM fungi that could potentially colonize the experimental plants, we also analysed roots from adjacent, undisturbed vegetation. 3. We found 32 fungal operational taxonomic units (OTUs) distributed across five known AM fungal families. Contrary to our expectations, disturbance did not significantly alter the community composition and OTU richness. Instead, OTU abundances were positively correlated across treatments; i.e., common OTUs in undisturbed soil were also common after the severe disturbance. However, the distribution of OTUs within and between plots was largely unpredictable, with approximately 40% of all sequences within a sample belonging to a single OTU of varying identity. The distribution of two plant species that are often poorly colonized by AM fungi ( Dianthus deltoides and Carex arenaria) correlated significantly with the OTU composition, which may indicate that host quality could be an additional driver of fungal communities. 4. Synthesis. Our results suggest that factors other than disturbance drive the relative abundance of OTUs in this grassland and question the long-held assumption that communities shift in a predictable manner after a disturbance event. The reassembly of this fungal community indicates a high community resilience, but substantial local stochasticity and dominance by single OTUs, which could be due to priority effects among abundant AM fungi possessing a similar - and high - degree of disturbance tolerance. [ABSTRACT FROM AUTHOR]

Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization. [Display omitted] • Thousands of gut bacterial genomes from worldwide human populations were sequenced • HGT occurs at high frequency in the gut microbiome of individual persons • HGT occurs more frequently in the microbiome of industrialized and urban populations • Transferred gene functions in the microbiome reflect the lifestyle of the host A worldwide microbiome analysis from 15 populations along the industrialization gradient reveals that horizontal gene transfer occurs on short timescales and that microbiomes continuously acquire new functionality based on host lifestyle. [ABSTRACT FROM AUTHOR]