Despite recent advances in metagenomic binning, reconstruction of microbial species from metagenomics data remains challenging. Here we develop variational autoencoders for metagenomic binning ...(VAMB), a program that uses deep variational autoencoders to encode sequence coabundance and k-mer distribution information before clustering. We show that a variational autoencoder is able to integrate these two distinct data types without any previous knowledge of the datasets. VAMB outperforms existing state-of-the-art binners, reconstructing 29-98% and 45% more near-complete (NC) genomes on simulated and real data, respectively. Furthermore, VAMB is able to separate closely related strains up to 99.5% average nucleotide identity (ANI), and reconstructed 255 and 91 NC Bacteroides vulgatus and Bacteroides dorei sample-specific genomes as two distinct clusters from a dataset of 1,000 human gut microbiome samples. We use 2,606 NC bins from this dataset to show that species of the human gut microbiome have different geographical distribution patterns. VAMB can be run on standard hardware and is freely available at https://github.com/RasmussenLab/vamb .
Despite the accelerating number of uncultivated virus sequences discovered in metagenomics and their apparent importance for health and disease, the human gut virome and its interactions with ...bacteria in the gastrointestinal tract are not well understood. This is partly due to a paucity of whole-virome datasets and limitations in current approaches for identifying viral sequences in metagenomics data. Here, combining a deep-learning based metagenomics binning algorithm with paired metagenome and metavirome datasets, we develop Phages from Metagenomics Binning (PHAMB), an approach that allows the binning of thousands of viral genomes directly from bulk metagenomics data, while simultaneously enabling clustering of viral genomes into accurate taxonomic viral populations. When applied on the Human Microbiome Project 2 (HMP2) dataset, PHAMB recovered 6,077 high-quality genomes from 1,024 viral populations, and identified viral-microbial host interactions. PHAMB can be advantageously applied to existing and future metagenomes to illuminate viral ecological dynamics with other microbiome constituents.
A mesocosm experiment with intact benthic communities was conducted to evaluate the effects of mine tailings on benthic community structure and biogeochemical processes. Two types of tailings were ...supplied from process plants using flotation and flocculation chemicals, while a third type was absent of added chemicals. All tailings impacted the sediment community at thin layers, and through more mechanisms than merely hypersedimentation. In general, the strongest impact was observed in a very fine-grained tailings containing flotation chemicals. The second strongest occurred in tailings with no process chemicals. The tailings with flocculation chemicals initiated the weakest response. Fluxes of oxygen, nitrate and ammonium provided some indications on biodegradation of organic phases. Release of phosphate and silicate decreased with increasing layer thickness of all three tailings. A threshold level of 2cm was identified both for faunal responses and for fluxes of phosphate and silicate. The particular impact mechanisms should receive more attention in future studies in order to minimize the environmental risk associated with tailings disposal.
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•Dose and response of 3 types of mine tailings studied in a soft-bottom mesocosm•Apparent effect threshold at 2cm layer thickness•All tailings affected the fauna through more factors than hypersedimentation.•Most severe effects of fine grained CaCO3 with remnants of flotation chemicals.•Indications were found on in situ biodegradation of flotation chemicals.
There is scant knowledge of dentists' total prescribing patterns, and little is published on this internationally. The Norwegian Prescription Database (NorPD) includes data on all dispensed ...prescription medication in Norway from 2004 and can be used to investigate how dentists' prescribing has changed over time. There are few Norwegian guidelines supporting dentists' prescribing, and Norwegian legislation on dentists' prescribing rights leaves room for interpretation. The aim of this study was therefore to give an overview of all prescribing from dentists in Norway in the period 2005 to 2015 and to identify trends in their prescribing pattern over this time span. We also give characteristics of the prescribing dentists.
The study had a retrospective pharmacoepidemiologic design. Data on all medication prescribed by dentists and dispensed from Norwegian pharmacies in the time period 2005 to 2015 were extracted from the NorPD. Changes over time in the prescribers, patients, and medications are reported.
There was an increase of 50% in total number of prescriptions from dentists in Norway from 2005 to 2015; adjusted for the growth in population, there was a 33% increase. The majority of prescriptions from dentists were for antibiotics and analgesics; however, the data reveal that the dentists prescribed from all major therapeutic groups. Dentists increased antibiotic prescribing in a period when total antibiotic prescribing in Norway decreased.
Our study finds antibiotics and analgesics dominate prescriptions from Norwegian dentists and shows an increase in use over time. It highlights the need for creating evidence-based prescribing guidelines for dentists and for ensuring that existing guidelines are implemented.
Calcium oxide (CaO) is being considered as a possible treatment for both the control of echinoderm populations and the treatment against sea lice infestation in Norwegian salmon farms. CaO particles ...produce an exothermal reaction when in contact with water, which can cause epidermal burns and lesions to certain target organisms leading to death. The aim of the present study was to determine the effects of fine (<0.8 mm) and coarse (<2.5 mm) CaO particles to a range of marine species from different taxonomic groups: two echinoderms (Asterias ruben and Strongylocentrotus droebachiensis); two crustaceans (Carcinus maenas and Tisbe battagliai); two molluscs (Mytilus edulis and Hinia reticulata); a polychaete (Nereis pelagica); a fish (Cyclopterus sp.); and seaweed germlings (Fucus vesiculosus). Overall, the fine CaO particles were more toxic to the selected marine species than the coarse particles. Coarse CaO particle effects were only observed in four of the nine species tested (A. rubens, S. droebachiensis, N. pelagica, T. battagliai) with similar LC50 values between 207 and 268 g/m2. For the fine CaO particles, the lowest LC50 was for the epibenthic copepod (T. battagliai) at 3.14 g/m2, followed by the sea urchin (20.1 g/m2), starfish (22.2 g/m2), ragworm (29.6 g/m2), and netted dog whelk (41.9 g/m2). Lump sucker fish exhibited significant mortalities only at the highest fine CaO concentration tested (320 g/m2) and recorded an LC50 of 226 g/m2. The toxicity data were used to generate species sensitivity distributions (SSDs) for both fine and coarse CaO particles. The hazard concentrations for 5% of the species (HC5) calculated from the SSDs, based on NOEC values, for the coarse and fine particles were 35.5 and 1.5 g/m2 respectively. Using a recommended assessment factor of 5, the Predicted No Effect Concentration (PNEC) was calculated as 7.1 and 0.3 g/m2 for coarse and fine CaO particles respectively.
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•Coarse CaO particles caused no harm to fish, shore crab, mussel or Fucus germlings.•CaO fine particles (<0.8 mm) were more harmful than coarse (<2.5 mm) particles.•The epibenthic copepod, Tisbe battagliai were most sensitive to fine CaO particles.•PNEC values of 7.1 and 0.3 g/m2 for coarse and fine CaO particles were calculated.
Water browning, due to increased runoff of terrestrial dissolved organic carbon (DOC), has recently gained considerable attention. While it is well settled how browning affects light regime and ...thereby aquatic primary production, other impacts on the aquatic biota is less explored. Water browning shelters against UV radiation, and may thus benefit range expansion of UV sensitive organisms, such as midges. We mapped occurrence of Chaoborids in 148 subalpine and alpine ponds in Norway, and identified an apparent threshold for their presence around 3 mg total organic carbon (TOC) l
−1
. The field study was complemented with laboratory experiments on
Chaoborus nyblaei
(Zetterstedt, 1838), to test if this species is able to identify and select water colour (concentrations of DOC) for oviposition. Number of egg rafts on brown water tanks was significantly higher than in clear water tanks, indicating that
C. nyblaei
performs oviposition habitat selection. Chaoborids are effective predators in planktonic habitats, and our findings support the hypothesis that climate change may cascade through the ecosystem and promote range shifts of species due to alternated habitat frame conditions.
Abstract The many microbial communities around us form interactive and dynamic ecosystems called microbiomes. Though concealed from the naked eye, microbiomes govern and influence macroscopic systems ...including human health, plant resilience, and biogeochemical cycling. Such feats have attracted interest from the scientific community, which has recently turned to machine learning and deep learning methods to interrogate the microbiome and elucidate the relationships between its composition and function. Here, we provide an overview of how the latest microbiome studies harness the inductive prowess of artificial intelligence methods. We start by highlighting that microbiome data – being compositional, sparse, and high-dimensional – necessitates special treatment. We then introduce traditional and novel methods and discuss their strengths and applications. Finally, we discuss the outlook of machine and deep learning pipelines, focusing on bottlenecks and considerations to address them.
This study examines the potential implications of biofouling management on the development of an infectious disease in Norwegian farmed salmon. The hydroid Ectopleura larynx frequently colonises cage ...nets at high densities (thousands of colonies per m2) and is released into the water during regular in-situ net cleaning. Contact with the hydroids' nematocysts has the potential to cause irritation and pathological damage to salmon gills. Amoebic gill disease (AGD), caused by the amoeba Paramoeba perurans, is an increasingly international health challenge in Atlantic salmon farming. AGD often occurs concomitantly with other agents of gill disease. This study used laboratory challenge trials to: (1) characterise the gill pathology resulting from the exposure of salmon to hydroids, and (2) investigate if such exposure can predispose the fish to secondary infections-using P. perurans as an example. Salmon in tanks were exposed either to freshly 'shredded' hydroids resembling waste material from net cleaning, or to authentic concentrations of free-living P. perurans, or first to 'shredded' hydroids and then to P. perurans. Gill health (AGD gill scores, non-specific gill scores, lamellar thrombi, epithelial hyperplasia) was monitored over 5 weeks and compared to an untreated control group. Nematocysts of E. larynx contained in cleaning waste remained active following high-pressure cleaning, resulting in higher non-specific gill scores in salmon up to 1 day after exposure to hydroids. Higher average numbers of gill lamellar thrombi occurred in fish up to 7 days after exposure to hydroids. However, gill lesions caused by hydroids did not affect the infection rates of P. perurans or the disease progression of AGD. This study discusses the negative impacts hydroids and current net cleaning practices can have on gill health and welfare of farmed salmon, highlights existing knowledge gaps and reiterates the need for alternative approaches to net cleaning.
Abstract
Assembly of reads from metagenomic samples is a hard problem, often resulting in highly fragmented genome assemblies. Metagenomic binning allows us to reconstruct genomes by re-grouping the ...sequences by their organism of origin, thus representing a crucial processing step when exploring the biological diversity of metagenomic samples. Here we present Adversarial Autoencoders for Metagenomics Binning (AAMB), an ensemble deep learning approach that integrates sequence co-abundances and tetranucleotide frequencies into a common denoised space that enables precise clustering of sequences into microbial genomes. When benchmarked, AAMB presented similar or better results compared with the state-of-the-art reference-free binner VAMB, reconstructing ~7% more near-complete (NC) genomes across simulated and real data. In addition, genomes reconstructed using AAMB had higher completeness and greater taxonomic diversity compared with VAMB. Finally, we implemented a pipeline Integrating VAMB and AAMB that enabled improved binning, recovering 20% and 29% more simulated and real NC genomes, respectively, compared to VAMB, with moderate additional runtime.
Most investigations of geographical within-species differences are limited to focusing on a single species. Here, we investigate global differences for multiple bacterial species using a dataset of ...757 metagenomics sewage samples from 101 countries worldwide. The within-species variations were determined by performing genome reconstructions, and the analyses were expanded by gene focused approaches. Applying these methods, we recovered 3353 near complete (NC) metagenome assembled genomes (MAGs) encompassing 1439 different MAG species and found that within-species genomic variation was in 36% of the investigated species (12/33) coherent with regional separation. Additionally, we found that variation of organelle genes correlated less with geography compared to metabolic and membrane genes, suggesting that the global differences of these species are caused by regional environmental selection rather than dissemination limitations. From the combination of the large and globally distributed dataset and in-depth analysis, we present a wide investigation of global within-species phylogeny of sewage bacteria. The global differences found here emphasize the need for worldwide data sets when making global conclusions.
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