Cold adaptation and replicable microbial community development during long-term low temperature anaerobic digestion treatment of synthetic sewage

The development and, activity of a cold-adapting microbial community was monitored during low temperature anaerobic digestion (LtAD) treatment of wastewater. Two replicate hybrid anaerobic sludge bed-fixed-film reactors treated a synthetic sewage wastewater at 12°C, at organic loading rates of 0.25–1.0 kg Chemical Oxygen Demand (COD) m−3 d−1, over 889 days. The inoculum was obtained from a full-scale AD reactor, which was operated at 37˚C. Both LtAD reactors readily degraded the influent with COD removal efficiencies regularly exceeding 78% for both the total and soluble COD fractions. The biomass from both reactors was sampled temporally and tested for activity against hydrolytic and methanogenic substrates at 12˚C and 37˚C. Data indicated that significantly enhanced low-temperature hydrolytic and methanogenic activity developed in both systems. For example, the hydrolysis rate constant (K) at 12°C had increased 20–30-fold by comparison to the inoculum by day 500. Substrate affinity also increased for hydrolytic substrates at low temperature. Next generation sequencing demonstrated that a shift in community structure occurred over the trial, involving a 1-log-fold change in 25 SEQS (OTU-free approach) from the inoculum. Microbial community structure changes and process performance were replicable in the LtAD reactors

Letter: reproducible evidence shows that exclusive enteral nutrition significantly reduces faecal calprotectin concentrations in children with active Crohn's Disease

No abstract available

Neutral processes dominate microbial community assembly in Atlantic salmon, Salmo salar

In recent years a wealth of studies have examined the relationships between a host and its microbiome across diverse taxa. Many studies characterise the host microbiome without considering the ecological processes that underpin microbiome assembly. In this study, the intestinal microbiota of Atlantic salmon, Salmo salar, sampled from farmed and wild environments was first characterised using 16s rDNA MiSeq sequencing analysis. We used neutral community models to determine the balance of stochastic and deterministic processes that underpin microbial community assembly and transfer across lifecycle stage and between gut compartments. Across gut compartments in farmed fish, neutral models suggest that most microbes are transient with no evidence of adaptation to their environment. In wild fish, we find declining taxonomic and functional microbial community richness as fish mature through different lifecycle stages. Alongside neutral community models applied to wild fish, we suggest declining richness demonstrates an increasing role for the host in filtering microbial communities that is correlated with age. We find a limited subset of gut microflora adapted to the farmed and wild host environment among which Mycoplasma sp. are prominent. Our study reveals the ecological drivers underpinning community assembly in both farmed and wild Atlantic salmon and underlines the importance of understanding the role of stochastic processes such as random drift and small migration rates in microbial community assembly, before considering any functional role of the gut microbes encountered

Alopecia areata is characterized by dysregulation in systemic type 17 and type 2 cytokines, which may contribute to disease‐associated psychological morbidity

Background: Alopecia areata (AA) is a common autoimmune disease, causing patchy hair loss that can progress to involve the entire scalp (totalis) or body (universalis). CD8+NKG2D+ T cells dominate hair follicle pathogenesis, but the specific mechanisms driving hair loss are not fully understood. Objectives To provide a detailed insight into the systemic cytokine signature associated with AA, and assess the association between cytokines and depression. Methods: Multiplex analysis of plasma cytokines from AA patients, psoriatic arthritis (PsA) patients and healthy controls. We also assessed incidence of depression and anxiety using the Hospital Anxiety and Depression Scale. Results: Our analysis identified a systemic inflammatory signature associated with AA, characterised by elevated levels of IL-17A, IL-17F, IL-21 and IL-23 indicative of a type 17 immune response. Circulating levels of the type 2 cytokines IL-33, IL-31 and IL-17E/25 are also significantly increased in AA. In comparison to PsA, AA was associated with higher levels of IL-17F, IL-17E and IL-23. We hypothesised that circulating inflammatory cytokines may contribute to wider comorbidities associated with AA. We assessed psychiatric comorbidity in AA using the Hospital Anxiety and Depression Scale and found that 18% and 51% of people with AA experienced symptoms of depression and anxiety, respectively. Using linear regression modelling, we identified that levels of IL-22 and IL-17E are positively and significantly associated with depression. Conclusion: Our data highlight changes in both type 17 and 2 cytokines, suggesting that complex systemic cytokine profiles may contribute both to the pathogenesis of AA and to the associated depression

Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae

Background: Aquaculture successfully meets global food demands for many fish species. However, aquaculture production of Atlantic cod (Gadus morhua) is just 2.5% of total market production. For cod farming to be a viable economic venture specific challenges on how to increase growth, health and farming productivity need to be addressed. Feed ingredients play a key role here. Macroalgae (seaweeds) have been suggested as a functional feed supplement with both health and economic benefits for terrestrial farmed animals and fish. The impact of such dietary supplements to cod gut integrity and microbiota, which contribute to overall fish robustness is unknown. The objective of this study was to supplement the diet of juvenile Atlantic cod with macroalgae and determine the impacts on fish condition and growth, gut morphology and hindgut microbiota composition (16S rRNA amplicon sequencing). Fish were fed one of three diets: control (no macroalgal inclusion), 10% inclusion of either egg wrack (Ascophyllum nodosum) or sea lettuce (Ulva rigida) macroalgae in a 12-week trial. Results: The results demonstrated there was no significant difference in fish condition, gut morphology or hindgut microbiota between the U. rigida supplemented fish group and the control group at any time-point. This trend was not observed with the A. nodosum treatment. Fish within this group were further categorised as either ‘Normal’ or ‘Lower Growth’. ‘Lower Growth’ individuals found the diet unpalatable resulting in reduced weight and condition factor combined with an altered gut morphology and microbiome relative to the other treatments. Excluding this group, our results show that the hindgut microbiota was largely driven by temporal pressures with the microbial communities becoming more similar over time irrespective of dietary treatment. The core microbiome at the final time-point consisted of the orders Vibrionales (Vibrio and Photobacterium), Bacteroidales (Bacteroidetes and Macellibacteroides) and Clostridiales (Lachnoclostridium). Conclusions: Our study indicates that U. rigida macroalgae can be supplemented at 10% inclusion levels in the diet of juvenile farmed Atlantic cod without any impact on fish condition or hindgut microbial community structure. We also conclude that 10% dietary inclusion of A. nodosum is not a suitable feed supplement in a farmed cod diet

Genome erosion and evidence for an intracellular niche – exploring the biology of mycoplasmas in Atlantic salmon

Mycoplasmas are the smallest autonomously self-replicating life form on the planet. Members of this bacterial genus are known to parasitise a wide array of metazoans including vertebrates. Whilst much research has been significant targeted at parasitic mammalian mycoplasmas, very little is known about their role in other vertebrates. In the current study, we aim to explore the biology of mycoplasmas in Atlantic Salmon, a species of major significance for aquaculture, including cellular niche, genome size structure and gene content. Using fluorescent in-situ hybridisation (FISH), mycoplasmas were targeted in epithelial tissues across the digestive tract (stomach, pyloric caecum and midgut) from different development stages (eggs, parr, subadult) of farmed Atlantic salmon (Salmo salar), and we present evidence for an intracellular niche for some of the microbes visualised. Via shotgun metagenomic sequencing, a nearly complete, albeit small, genome (~0.57 MB) as assembled from a farmed Atlantic salmon subadult. Phylogenetic analysis of the recovered genome revealed taxonomic proximity to other salmon derived mycoplasmas, as well as to the human pathogen Mycoplasma penetrans (~1.36 Mb). We annotated coding sequences and identified riboflavin pathway encoding genes and sugar transporters, the former potentially consistent with micronutrient provisioning in salmonid development. Our study provides insights into mucosal adherence, the cellular niche and gene catalog of Mycoplasma in the gut ecosystem of the Atlantic salmon, suggesting a high dependency of this minimalist bacterium on its host. Further study is required to explore and functional role of Mycoplasma in the nutrition and development of its salmonid host

MdaB and NfrA, Two novel reductases important in the survival and persistence of the major enteropathogen Campylobacter jejuni

The paralogues RrpA and RrpB, which are members of the MarR family of DNA binding proteins, are important for the survival of the global bacterial foodborne pathogen Campylobacter jejuni under redox stress. We report that RrpA is a positive regulator of mdaB, encoding a flavin-dependent quinone reductase that contributes to the protection from redox stress mediated by structurally diverse quinones, while RrpB negatively regulates the expression of cj1555c (renamed nfrA for NADPH-flavin reductase A), encoding a flavin reductase. NfrA reduces riboflavin at a greater rate than its derivatives, suggesting that exogenous free flavins are the natural substrate. MdaB and NfrA both prefer NADPH as an electron donor. Cysteine substitution and posttranslational modification analyses indicated that RrpA and RrpB employ a cysteine-based redox switch. Complete genome sequence analyses revealed that mdaB is frequently found in Campylobacter and related Helicobacter spp., while nfrA is predominant in C. jejuni strains. Quinones and flavins are redox cycling agents secreted by a wide range of cell types that can form damaging superoxide by one-electron reactions. We propose a model for stress adaptation where MdaB and NfrA facilitate a two-electron reduction mechanism to the less toxic hydroquinones, thus aiding survival and persistence of this major pathogen. IMPORTANCE Changes in cellular redox potential result in alteration in the oxidation state of intracellular metabolites and enzymes; consequently, cells make adjustments that favor growth and survival. The work we present here answers some of the many questions that have remained elusive over the years of investigation into the enigmatic microaerophile bacterium Campylobacter jejuni. We employed molecular approaches to understand the regulation mechanisms and functional analyses to reveal the roles of two novel quinone and flavin reductases; both serve as major pools of cellular redox-active molecules. This work extends our knowledge on bacterial redox sensing mechanisms and the significance of hemostasis

Three-dimensional ultrasound imaging

This review is about the development of three-dimensional (3D) ultrasonic medical imaging, how it works, and where its future lies. It assumes knowledge of two-dimensional (2D) ultrasound, which is covered elsewhere in this issue. The three main ways in which 3D ultrasound may be acquired are described: the mechanically swept 3D probe, the 2D transducer array that can acquire intrinsically 3D data, and the freehand 3D ultrasound. This provides an appreciation of the constraints implicit in each of these approaches together with their strengths and weaknesses. Then some of the techniques that are used for processing the 3D data and the way this can lead to information of clinical value are discussed. A table is provided to show the range of clinical applications reported in the literature. Finally, the discussion relating to the technology and its clinical applications to explain why 3D ultrasound has been relatively slow to be adopted in routine clinics is drawn together and the issues that will govern its development in the future explored

A study of similarity measures for in vivo 3D ultrasound volume registration

Most of the conventional ultrasound machines in hospitals work in two dimensions. However, there are some applications where doctors would like to be able to gather ultrasound data as a three-dimensional (3D) block rather than a two-dimensional (2D) slice. Two different types of 3D ultrasound have been developed to meet this requirement. One type involves a special probe that can record a fixed block of data, either by having an internal sweeping mechanism or by using electronic steering. The other type of 3D ultrasound uses a conventional 2D ultrasound probe together with a position sensor and is called freehand 3D ultrasound. A natural progression of the mechanically-swept 3D ultrasound system is to combine it with the free hand sensor. This results in an extended field of view. There are two major problems with using a position sensor. Firstly, line-of-sight needs to be maintained between the sensor and the reference point. Secondly, the multiple volumes rarely register because of tissue displacement and deformation. Therefore, the objective of this paper is to get rid of the inconvenient position sensor and to use an automatic image-based registration technique. We provide an experimental study of several intensity-based similarity measures for the registration of 3D ultrasound volumes. Rather than choosing a conventional voxel array to represent the 3D blocks, we use corresponding vertical and horizontal image slices from the blocks to be matched. This limits the amount of data thus making the calculation of the similarity measure less computationally expensive

Particle swarm optimization for in vivo 3D ultrasound volume registration

As three-dimensional (3D) ultrasound is becoming more and more popular, there has been increased interest in using a position sensor to track the trajectory of the 3D ultrasound probe during the scan. One application is the improvement of image quality by fusion of multiple scans from different orientations. With a position sensor mounted on the probe, the clinicians face additional difficulties, for example, maintaining a line-of-sight between the sensor and the reference point. Therefore, the objective of this paper is to register the volumes using an automatic image-based registration technique. In this paper, we employ the particle swarm optimization (PSO) technique to calculate the six rigid-body transformation parameters (three for translation and three for rotation) between successive volumes of 3D ultrasound data. We obtain vertical and horizontal slices through the acquired volumes and then use an intensity-based similarity measure as a fitness function for each particle. We considered various settings in the PSO to find a set of parameters to give the best convergence. We found the visually acceptable registration when the initial orientations of the particles were confined to within a few degrees of the orientations obtained from position sensor