Interplay between inflammatory bowel disease therapeutics and the gut microbiome reveals opportunities for novel treatment approaches.

Inflammatory bowel disease (IBD) is a complex heterogeneous disorder defined by recurring chronic inflammation of the gastrointestinal tract, attributed to a combination of factors including genetic susceptibility, altered immune response, a shift in microbial composition/microbial insults (infection/exposure), and environmental influences. Therapeutics generally used to treat IBD mainly focus on the immune response and include non-specific anti-inflammatory and immunosuppressive therapeutics and targeted therapeutics aimed at specific components of the immune system. Other therapies include exclusive enteral nutrition and emerging stem cell therapies. However, in recent years, scientists have begun to examine the interplay between these therapeutics and the gut microbiome, and we present this information here. Many of these therapeutics are associated with alterations to gut microbiome composition and functionality, often driving it toward a "healthier profile" and preclinical studies have revealed that such alterations can play an important role in therapeutic efficacy. The gut microbiome can also improve or hinder IBD therapeutic efficacy or generate undesirable metabolites. For certain IBD therapeutics, the microbiome composition, particularly before treatment, may serve as a biomarker of therapeutic efficacy. Utilising this information and manipulating the interactions between the gut microbiome and IBD therapeutics may enhance treatment outcomes in the future and bring about new opportunities for personalised, precision medicine.

Modulation of the gut microbiome with nisin.

Nisin is a broad spectrum bacteriocin used extensively as a food preservative that was identified in Lactococcus lactis nearly a century ago. We show that orally-ingested nisin survives transit through the porcine gastrointestinal tract intact (as evidenced by activity and molecular weight determination) where it impacts both the composition and functioning of the microbiota. Specifically, nisin treatment caused a reversible decrease in Gram positive bacteria, resulting in a reshaping of the Firmicutes and a corresponding relative increase in Gram negative Proteobacteria. These changes were mirrored by the modification in relative abundance of pathways involved in acetate, butyrate (decreased) and propionate (increased) synthesis which correlated with overall reductions in short chain fatty acid levels in stool. These reversible changes that occur as a result of nisin ingestion demonstrate the potential of bacteriocins like nisin to shape mammalian microbiomes and impact on the functionality of the community.

Sustainable Management of the African Great Lake Coastal Areas: Motivations and Perspectives of Community Citizen Scientists.

The long-term sustainability of the African Great Lakes is strongly connected to the management and monitoring of their coastal areas. Yet, the communities that live in these areas are rarely involved in monitoring and have limited influence on key management issues. Furthermore, regulatory activities and knowledge sharing in these transnational ecosystems are strongly limited by funding and infrastructure limitations. Citizen science has great potential to advance both scientific and public understanding of the state of the environment. However, there remains a limited understanding of participants' motivations and expectations, especially in developing countries, where citizen science has great potential to complement regulatory monitoring. The present study explores the motivations of citizen scientists in villages along Lake Tanganyika's northern coast and their potential to take a more active role in lake management. Motivations were examined through qualitative interviews, focus groups, and quantitative surveys with 110 citizen scientists and 110 non-citizen scientists from participating villages. Key motivational factors identified were the desire to contribute to scientific research and local knowledge, as well as aspects of financial compensation. The results confirm that participation in citizen science provides many benefits to participants beyond their role as data aggregators and final knowledge users. However, the incentives to participation varied to those typically considered in citizen science programs conducted in developed countries. To create sustainable long-term community based environmental monitoring, these motivations should be incorporated in the program design and participant recruitment.

Pedagogy of teaching with large datasets: Designing and implementing effective data-based activities.

Integrating the use of large datasets into our teaching provides critical and unique opportunities to build students' skills and conceptual knowledge. Here, we discuss the core components needed to develop effective activities based on large datasets, which align with the 5E learning cycle. Data-based activities should be structured around a relevant question, use authentic publicly accessible data, be scaffolded to include choice, and involve discussion of the results. It is important that the software that is used to manipulate, analyze and/or visualize the data is accessible for students. There are a range of strategies to reduce the barriers of working with large datasets through pre-organizing and pre-scripting code for analyses, using online cloud-based versions of software, and reducing opportunities for error in syntax. Resources exist for learning open-source software (e.g., Data Carpentry) as well as for support and professional development in teaching with large datasets (Project EDDIE).

Citizen scientist monitoring accurately reveals nutrient pollution dynamics in Lake Tanganyika coastal waters.

Several studies in Lake Tanganyika have effectively employed traditional methods to explore changes in water quality in open waters; however, coastal monitoring has been restricted and sporadic, relying on costly sample and analytical methods that require skilled technical staff. This study aims in validating citizen science water quality collected data (nitrate, phosphate and turbidity) with those collected and measured by professional scientists in the laboratory. A second objective of the study is to use citizen scientist data to identify the patterns of seasonal and spatial variations in nutrient conditions and forecast potential changes based on expected changes in population and climate (to 2050). The results showed that the concentrations of nitrate and phosphate measured by citizen scientists nearly matched those established by professional scientists, with overall accuracy of 91% and 74%, respectively. For total suspended solids measured by professional and turbidity measured by citizen scientists, results show that, using 14 NTU as a cut-off, citizen scientist measurements of Secchi tube depth to identify lake TSS below 7.0 mg/L showed an accuracy of 88%. In both laboratory and citizen scientist-based studies, all measured water quality variables were significantly higher during the wet season compared to the dry season. Climate factors were discovered to have a major impact on the likelihood of exceeding water quality restrictions in the next decades (2050), which could deteriorate lake conditions. Upscaling citizen science to more communities on the lake and other African Great Lakes would raise environmental awareness, inform management and mitigation activities, and aid long-term decision-making.

Community monitoring of coliform pollution in Lake Tanganyika.

Conventional water quality monitoring has been done for decades in Lake Tanganyika, under different national and international programs. However, these projects utilized monitoring approaches, which were temporally limited, labour intensive and costly. This study examines the use of citizen science to monitor the dynamics of coliform concentrations in Lake Tanganyika as a complementary method to statutory and project-focused measurements. Persons in five coastal communities (Kibirizi, Ilagala, Karago, Ujiji and Gombe) were trained and monitored total coliforms, faecal coliforms and turbidity for one year on a monthly basis, in parallel with professional scientists. A standardized and calibrated Secchi tube was used at the same time to determine turbidity. Results indicate that total and faecal coliform concentrations determined by citizen scientists correlated well to those determined by professional scientists. Furthermore, citizen scientist-based turbidity values were shown to provide a potential indicator for high FC and TC concentrations. As a simple tiered approach to identify increased coliform loads, trained local citizen scientists could use low-cost turbidity measurements with follow up sampling and analysis for coliforms, to inform their communities and regulatory bodies of high risk conditions, as well as to validate local mitigation actions. By comparing the spatial and temporal dynamics of coliform concentrations to local conditions of infrastructure, population, precipitation and hydrology in the 15 sites (3 sites per community) over 12 months, potential drivers of coliform pollution in these communities were identified, largely related to precipitation dynamics and the land use.

Impact of nisin on Clostridioides difficile and microbiota composition in a faecal fermentation model of the human colon.

AIMS: Nisin is a bacteriocin with a broad spectrum of activity against Gram-positive bacteria. The aims were to assess nisin activity against Clostridioides difficile in a complex microbial environment and determine the minimum inhibitory concentration at which C. difficile growth is suppressed whilst having minimal impact on the faecal microbiota. METHODS AND RESULTS: Faecal slurries were prepared from fresh faecal samples and spiked with C. difficile (106  CFU per ml). Nisin was added to each fermentation at a range of concentrations from 0 to 500 µM. Following 24 h, 16S rRNA gene sequencing was performed, and the presence of viable C. difficile was assessed. There was no viable C. difficile detected in the presence of 50-500 µM nisin. There was a decrease in the diversity of the microbiota in a nisin dose-dependent manner. Nisin predominantly depleted the relative abundance of the Gram-positive bacteria whilst the relative abundance of Gram-negative bacteria such as Escherichia Shigella and Bacteroides increased. CONCLUSIONS: Using an ex vivo model of the colon, this study demonstrates the ability of purified nisin to selectively deplete C. difficile in a faecal microbial environment and establishes the minimum concentration at which this occurs whilst having a minimal impact on the composition of the microbiota. SIGNIFICANCE AND IMPACT OF THE STUDY: This study opens up the potential to use nisin as a therapeutic for clostridial gut infections.

Increased winter drownings in ice-covered regions with warmer winters.

Winter activities on ice are culturally important for many countries, yet they constitute a high safety risk depending upon the stability of the ice. Because consistently cold periods are required to form stable and thick ice, warmer winters could degrade ice conditions and increase the likelihood of falling through the ice. This study provides the first large-scale assessment of winter drowning from 10 Northern Hemisphere countries. We documented over 4000 winter drowning events. Winter drownings increased exponentially in regions with warmer winters when air temperatures neared 0°C. The largest number of drownings occurred when winter air temperatures were between -5°C and 0°C, when ice is less stable, and also in regions where indigenous traditions and livelihood require extended time on ice. Rates of drowning were greatest late in the winter season when ice stability declines. Children and adults up to the age of 39 were at the highest risk of winter drownings. Beyond temperature, differences in cultures, regulations, and human behaviours can be important additional risk factors. Our findings indicate the potential for increased human mortality with warmer winter air temperatures. Incorporating drowning prevention plans would improve adaptation strategies to a changing climate.

A database of chlorophyll and water chemistry in freshwater lakes.

Measures of chlorophyll represent the algal biomass in freshwater lakes that is often used by managers as a proxy for water quality and lake productivity. However, chlorophyll concentrations in lakes are dependent on many interacting factors, including nutrient inputs, mixing regime, lake depth, climate, and anthropogenic activities within the watershed. Therefore, integrating a broad scale dataset of lake physical, chemical, and biological characteristics can help elucidate the response of freshwater ecosystems to global change. We synthesized a database of measured chlorophyll a (chla) values, associated water chemistry variables, and lake morphometric characteristics for 11,959 freshwater lakes distributed across 72 countries. Data were collected based on a systematic review examining 3322 published manuscripts that measured lake chla, and we supplemented these data with online repositories such as The Knowledge Network for Biocomplexity, Dryad, and Pangaea. This publicly available database can be used to improve our understanding of how chlorophyll levels respond to global environmental change and provide baseline comparisons for environmental managers responsible for maintaining water quality in lakes.

Fusions involving BCOR and CREBBP are rare events in infiltrating glioma.

BCOR has been recognized as a recurrently altered gene in a subset of pediatric tumors of the central nervous system (CNS). Here, we describe a novel BCOR-CREBBP fusion event in a case of pediatric infiltrating astrocytoma and further probe the frequency of related fusion events in CNS tumors. We analyzed biopsy samples taken from a 15-year-old male with an aggressive, unresectable and multifocal infiltrating astrocytoma. We performed RNA sequencing (RNA-seq) and targeted DNA sequencing. In the index case, the fused BCOR-CREBBP transcript comprises exons 1-4 of BCOR and exon 31 of CREBBP. The fused gene thus retains the Bcl6 interaction domain of BCOR while eliminating the domain that has been shown to interact with the polycomb group protein PCGF1. The fusion event was validated by FISH and reverse transcriptase PCR. An additional set of 177 pediatric and adult primary CNS tumors were assessed via FISH for BCOR break apart events, all of which were negative. An additional 509 adult lower grade infiltrating gliomas from the publicly available TCGA dataset were screened for BCOR or CREBBP fusions. In this set, one case was found to harbor a CREBBP-GOLGA6L2 fusion and one case a CREBBP-SRRM2 fusion. In a third patient, both BCOR-L3MBTL2 and EP300-BCOR fusions were seen. Of particular interest to this study, EP300 is a paralog of CREBBP and the breakpoint seen involves a similar region of the gene to that of the index case; however, the resultant transcript is predicted to be completely distinct. While this gene fusion may play an oncogenic role through the loss of tumor suppressor functions of BCOR and CREBBP, further screening over larger cohorts and functional validation is needed to determine the degree to which this or similar fusions are recurrent and to elucidate their oncogenic potential.

Process Optimisation Studies and Aminonitrile Substrate Evaluation of Rhodococcus erythropolis SET1, A Nitrile Hydrolyzing Bacterium.

A comprehensive series of optimization studies including pH, solvent and temperature were completed on the nitrile hydrolyzing Rhodococcus erythropolis bacterium SET1 with the substrate 3-hydroxybutyronitrile. These identified temperature of 25 °C and pH of 7 as the best conditions to retain enantioselectivity and activity. The effect of the addition of organic solvents to the biotransformation mixture was also determined. The results of the study suggested that SET1 is suitable for use in selected organo-aqueous media at specific ratios only. The functional group tolerance of the isolate with unprotected and protected ß-aminonitriles, structural analogues of ß-hydroxynitriles was also investigated with disappointingly poor isolated yields and selectivity obtained. The isolate was further evaluated with the α- aminonitrile phenylglycinonitrile generating acid in excellent yield and ee (>99 % (S) - isomer and 50 % yield). A series of pH studies with this substrate indicated pH 7 to be the optimum pH to avoid product and substrate degradation.

Encapsulated cyclosporine does not change the composition of the human microbiota when assessed ex vivo and in vivo.

Introduction. Management of steroid-refractory ulcerative colitis has predominantly involved treatment with systemic cyclosporine A (CyA) and infliximab.Aim. The purpose of this study was to assess the effect of using a colon-targeted delivery system CyA formulation on the composition and functionality of the gut microbiota.Methodology. Ex vivo faecal fermentations from six healthy control subjects were treated with coated minispheres (SmPill) with (+) or without (-) CyA and compared with a non-treated control in a model colon system. In addition, the in vivo effect of the SmPill+CyA formulation was investigated by analysing the gut microbiota in faecal samples collected before the administration of SmPill+CyA and after 7 consecutive days of administration from eight healthy subjects who participated in a pilot study.Results. Analysis of faecal samples by 16S rRNA gene sequencing indicated little variation in the diversity or relative abundance of the microbiota composition before or after treatment with SmPill minispheres with or without CyA ex vivo or with CyA in vivo. Short-chain fatty acid profiles were evaluated using gas chromatography, showing an increase in the concentration of n-butyrate (P=0.02) and acetate (P=0.32) in the faecal fermented samples incubated in the presence of SmPill minispheres with or without CyA. This indicated that increased acetate and butyrate production was attributed to a component of the coated minispheres rather than an effect of CyA on the microbiota. Butyrate and acetate levels also increased significantly (P=0.05 for both) in the faecal samples of healthy individuals following 7 days' treatment with SmPill+CyA in the pilot study.Conclusion. SmPill minispheres with or without CyA at the clinically relevant doses tested here have negligible direct effects on the gut microbiota composition. Butyrate and acetate production increased, however, in the presence of the beads in an ex vivo model system as well as in vivo in healthy subjects. Importantly, this study also demonstrates the relevance and value of using ex vivo colon models to predict the in vivo impact of colon-targeted drugs directly on the gut microbiota.

Adoption and consequences of new light-fishing technology (LEDs) on Lake Tanganyika, East Africa.

Maintaining sustainable fisheries requires understanding the influence of technological advances on catch efficiency, as technological creep can ultimately contribute to increased efficiency. Fisheries using light sources for attraction could be widely impacted by the shift to light emitting diode (LED) light systems. We studied the transition from kerosene lanterns to LED lamps in Lake Tanganyika, East Africa, examining factors that led to adoption as well as the impact of the new light sources on fish catch and composition. We used a combination of field experiments with catch assessments, fisher surveys, underwater light spectra measurements, and cost assessments to evaluate the impact of switching from kerosene to LED lamps. Overall, we found a very rapid rate of adoption of homemade outdoor LED light systems in Lake Tanganyika. Most of the batteries used to power these lamps were charged from the city power grid, rather than photovoltaic cells, although the potential exists for a reduction in greenhouse gas emissions. The LED light spectra was distinct from the kerosene light and penetrated much deeper into the water column. Regardless of light type, most of the fish caught within the two dominant species were below maturity. Although the LED lamps were associated with a slight increase in catch, environmental factors, particularly distance offshore, were generally more important in determining fish catch size and composition. The main advantages of the LED lamps were the lower operating costs and their robustness in bad weather. Thus, the primary effect of the use of battery-powered LED lighting systems to attract fish in Lake Tanganyika appears to reduce economic costs and increasing efficiency. However, overall the lake's fishery remains vulnerable to overfishing.

The use of clade-specific PCR assays to identify novel nitrilase genes from environmental isolates.

Nitrilase enzymes (EC 3.5.5.1) are responsible for the direct hydration of nitriles to their corresponding carboxylic acids and ammonia. The utilization of nitrilase enzymes in biocatalysis toward bio-pharmaceuticals and industrial applications facilitates the move towards green chemistry. The body of research presented describes a novel clade-specific touchdown PCR protocol for the detection of novel nitrilase genes. The presented study identified partial sequences of 15 novel nitrilase genes across 7 genera, with partial DNA sequence homology (%) displayed across an additional 16 genera. This research will prove valuable in the screening of microorganisms for the identification of novel clade-specific nitrilase genes, with predicted enantioselective profiles as determined by their clade characterizations.

The enemy of my enemy is my friend: native pine marten recovery reverses the decline of the red squirrel by suppressing grey squirrel populations.

Shared enemies may instigate or modify competitive interactions between species. The dis-equilibrium caused by non-native species introductions has revealed that the outcome of such indirect interactions can often be dramatic. However, studies of enemy-mediated competition mostly consider the impact of a single enemy, despite species being embedded in complex networks of interactions. Here, we demonstrate that native red and invasive grey squirrels in Britain, two terrestrial species linked by resource and disease-mediated apparent competition, are also now linked by a second enemy-mediated relationship involving a shared native predator recovering from historical persecution, the European pine marten. Through combining spatial capture-recapture techniques to estimate pine marten density, and squirrel site-occupancy data, we find that the impact of exposure to predation is highly asymmetrical, with non-native grey squirrel occupancy strongly negatively affected by exposure to pine martens. By contrast, exposure to pine marten predation has an indirect positive effect on red squirrel populations. Pine marten predation thus reverses the well-documented outcome of resource and apparent competition between red and grey squirrels.

Real-time PCR detection of aldoxime dehydratase genes in nitrile-degrading microorganisms.

Aldoxime dehydratase catalyses the conversion of aldoximes to their corresponding nitriles. Utilization of the aldoxime-nitrile metabolising enzyme pathway can facilitate the move towards a greener chemistry. In this work, a real-time PCR assay was developed for the detection of aldoxime dehydratase genes in aldoxime/nitrile metabolising microorganisms which have been purified from environmental sources. A conventional PCR assay was also designed allowing gene confirmation via sequencing. Aldoxime dehydratase genes were identified in 30 microorganisms across 11 genera including some not previously shown to harbour the gene. The assay displayed a limit of detection of 1 pg/µL DNA or 7 CFU/reaction. This real-time PCR assay should prove valuable in the high-throughput screening of micro-organisms for novel aldoxime dehydratase genes towards pharmaceutical and industrial applications.

Ecology under lake ice.

Winter conditions are rapidly changing in temperate ecosystems, particularly for those that experience periods of snow and ice cover. Relatively little is known of winter ecology in these systems, due to a historical research focus on summer 'growing seasons'. We executed the first global quantitative synthesis on under-ice lake ecology, including 36 abiotic and biotic variables from 42 research groups and 101 lakes, examining seasonal differences and connections as well as how seasonal differences vary with geophysical factors. Plankton were more abundant under ice than expected; mean winter values were 43.2% of summer values for chlorophyll a, 15.8% of summer phytoplankton biovolume and 25.3% of summer zooplankton density. Dissolved nitrogen concentrations were typically higher during winter, and these differences were exaggerated in smaller lakes. Lake size also influenced winter-summer patterns for dissolved organic carbon (DOC), with higher winter DOC in smaller lakes. At coarse levels of taxonomic aggregation, phytoplankton and zooplankton community composition showed few systematic differences between seasons, although literature suggests that seasonal differences are frequently lake-specific, species-specific, or occur at the level of functional group. Within the subset of lakes that had longer time series, winter influenced the subsequent summer for some nutrient variables and zooplankton biomass.

Century-Long Warming Trends in the Upper Water Column of Lake Tanganyika.

Lake Tanganyika, the deepest and most voluminous lake in Africa, has warmed over the last century in response to climate change. Separate analyses of surface warming rates estimated from in situ instruments, satellites, and a paleolimnological temperature proxy (TEX86) disagree, leaving uncertainty about the thermal sensitivity of Lake Tanganyika to climate change. Here, we use a comprehensive database of in situ temperature data from the top 100 meters of the water column that span the lake's seasonal range and lateral extent to demonstrate that long-term temperature trends in Lake Tanganyika depend strongly on depth, season, and latitude. The observed spatiotemporal variation in surface warming rates accounts for small differences between warming rate estimates from in situ instruments and satellite data. However, after accounting for spatiotemporal variation in temperature and warming rates, the TEX86 paleolimnological proxy yields lower surface temperatures (1.46 °C lower on average) and faster warming rates (by a factor of three) than in situ measurements. Based on the ecology of Thaumarchaeota (the microbes whose biomolecules are involved with generating the TEX86 proxy), we offer a reinterpretation of the TEX86 data from Lake Tanganyika as the temperature of the low-oxygen zone, rather than of the lake surface temperature as has been suggested previously. Our analyses provide a thorough accounting of spatiotemporal variation in warming rates, offering strong evidence that thermal and ecological shifts observed in this massive tropical lake over the last century are robust and in step with global climate change.

A global database of lake surface temperatures collected by in situ and satellite methods from 1985-2009.

Global environmental change has influenced lake surface temperatures, a key driver of ecosystem structure and function. Recent studies have suggested significant warming of water temperatures in individual lakes across many different regions around the world. However, the spatial and temporal coherence associated with the magnitude of these trends remains unclear. Thus, a global data set of water temperature is required to understand and synthesize global, long-term trends in surface water temperatures of inland bodies of water. We assembled a database of summer lake surface temperatures for 291 lakes collected in situ and/or by satellites for the period 1985-2009. In addition, corresponding climatic drivers (air temperatures, solar radiation, and cloud cover) and geomorphometric characteristics (latitude, longitude, elevation, lake surface area, maximum depth, mean depth, and volume) that influence lake surface temperatures were compiled for each lake. This unique dataset offers an invaluable baseline perspective on global-scale lake thermal conditions as environmental change continues.