Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
287
datasets available to search
ShareScore release 0.9.0
Dataset results
287 results for “Bacterial communities”
Correlations between dominant vegetation type and composition and diversity of soil bacterial communities in a subtropical forest
Open the record for dataset details and reuse information.
Effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on associated soil bacterial communities: a field-based experiment
<p>Loss of plant biodiversity can result in reduced abundance and diversity of associated species with implications for ecosystem functioning. In ecosystems low in plant species diversity, such as Neotropical mangrove forests, it is thought that genetic diversity within the dominant plant species could play an important role in shaping associated communities. Here, we used a manipulative field experiment to study the effects of maternal genotypic identity and genetic diversity of the red mangrove <i>Rhizophora mangle</i> on the composition and richness of associated soil bacterial communities. Using terminal restriction fragment length polymorphism (T-RFLP) community fingerprinting, we found that bacterial community composition differed among <i>R. mangle</i> maternal genotypes but not with genetic diversity. Bacterial taxa richness, total soil nitrogen, and total soil carbon were not significantly affected by maternal genotypic identity or genetic diversity of <i>R. mangle</i>. Our findings show that genotype selection in reforestation projects could influence soil bacterial community composition. Further research is needed to determine what impact these bacterial community differences might have on ecosystem processes, such as carbon and nitrogen cycling.</p>
Data from: Bacterial epibiont communities of panmictic Antarctic krill are spatially structured
<p>Antarctic krill (<i>Euphausia superba</i>) are amongst the most abundant animals on Earth, with a circumpolar distribution in the Southern Ocean. Genetic and genomic studies have failed to detect any population structure for the species, suggesting a single panmictic population. However, the hyper-abundance of krill slows the rate of genetic differentiation, masking potential underlying structure. Here we use high-throughput sequencing of bacterial 16S rRNA genes to show that krill bacterial epibiont communities exhibit spatial structuring, driven mainly by distance rather than environmental factors, especially for strongly krill-associated bacteria. Estimating the ecological processes driving bacterial community turnover indicated this was driven by bacterial dispersal limitation increasing with geographic distance. Furthermore, divergent epibiont communities generated from a single krill swarm split between aquarium tanks under near identical conditions suggests physical isolation in itself can cause krill-associated bacterial communities to diverge. Our findings show that Antarctic krill-associated bacterial communities are geographically structured, in direct contrast with the lack of structure observed for krill genetic and genomic data.</p>
Data from: Bacterial communities within Phengaris (Maculinea) alcon caterpillars are shifted following transition from solitary living to social parasitism of Myrmica ant colonies
Bacterial symbionts are known to facilitate a wide range of physiological processes and ecological interactions for their hosts. In spite of this, caterpillars with highly diverse life histories appear to lack resident microbiota. Gut physiology, endogenous digestive enzymes, and limited social interactions may contribute to this pattern, but the consequences of shifts in social activity and diet on caterpillar microbiota are largely unknown. Phengaris alcon caterpillars undergo particularly dramatic social and dietary shifts when they parasitize Myrmica ant colonies, rapidly transitioning from solitary herbivory to ant tending (i.e., receiving protein‐rich regurgitations through trophallaxis). This unique life history provides a model for studying interactions between social living, diet, and caterpillar microbiota. Here, we characterized and compared bacterial communities within P. alcon caterpillars before and after their association with ants, using 16S rRNA amplicon sequencing and quantitative PCR. After being adopted by ants, bacterial communities within P. alcon caterpillars shifted substantially, with a significant increase in alpha diversity and greater consistency in bacterial community composition in terms of beta dissimilarity. We also characterized the bacterial communities within their host ants (Myrmica schencki), food plant (Gentiana cruciata), and soil from ant nest chambers. These data indicated that the aforementioned patterns were influenced by bacteria derived from caterpillars' surrounding environments, rather than through transfers from ants. Thus, while bacterial communities are substantially reorganized over the life cycle of P. alcon caterpillars, it appears that they do not rely on transfers of bacteria from host ants to complete their development.
Data from: Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome
Although common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non-photoautotrophic bacteria found in lichen microbiomes are increasingly regarded as integral components of lichen thalli. For this study, comparative analyses were conducted on lichen-associated bacterial communities to test for effects of photobiont-types (i.e., green algal vs. cyanobacterial), mycobiont-types, and large-scale spatial distances (from tropical to arctic latitudes). Amplicons of the 16S (SSU) rRNA gene were examined using both Sanger sequencing of cloned fragments and barcoded pyrosequencing. Rhizobiales is typically the most abundant and taxonomically diverse order in lichen microbiomes; however, overall bacterial diversity in lichens is shown to be much higher than previously reported. Members of Acidobacteriaceae, Acetobacteraceae, Brucellaceae, and sequence group LAR1 are the most commonly found groups across the phylogenetically and geographically broad array of lichens examined here. Major bacterial community trends are significantly correlated with differences in large-scale geography, photobiont-type, and mycobiont-type. The lichen as a microcosm represents a structured, unique microbial habitat with greater ecological complexity and bacterial diversity than previously appreciated and can serve as a model system for studying larger ecological and evolutionary principles.
Data from: The bacterial community structure and functional profile in the heavy metal contaminated paddy soils,surrounding a nonferrous smelter in South Korea
The pollution of agricultural soils by the heavy metals affects the productivity of the land and has an impact on the quality of the surrounding ecosystems. The present study investigated the bacterial community structure in the heavy metal contaminated sites along a smelter and a distantly located paddy field to elucidate the factors that are related to the alterations of the bacterial communities under the conditions of heavy metal pollution. Among the study sites, the bacterial communities in the soil did not show any significant differences in their richness and diversity. The soil bacterial communities at the three study sites were distinct from one another at each site, possessing a distinct set of bacterial phylotypes. Among the study sites, significant changes were observed in the abundances of the bacterial phyla and genera. The variations in the bacterial community structure were mostly related to the general soil properties at the phylum level, while at the finer taxonomic levels, the concentrations of arsenic (As) and lead (Pb) were the significant factors, affecting the community structure. The relative abundances of the genera Desulfatibacillum and Desulfovirga were negatively correlated to the concentrations of As, Pb, and cadmium (Cd) in the soil, while the genus Bacillus was positively correlated to the concentrations of As and Cd. According to the results of the prediction of bacterial community functions, the soil bacterial communities of the heavy metal polluted sites were characterized by the more abundant enzymes, involved in DNA replication and repair, translation, transcription, and the nucleotide metabolism pathways, while the amino acid and lipid metabolism, as well as the biodegradation potential of xenobiotics, were reduced. Our results showed that the adaptation of the bacterial communities to the heavy metal contamination was predominantly attributed to the replacement process, while the changes in community richness were linked to the variations in the soil pH values.
Data from: Unearthing carrion beetles' microbiome: characterization of bacterial and fungal hindgut communities across the Silphidae
Carrion beetles (Coleoptera, Silphidae) are well known for their behaviour of exploiting vertebrate carcasses for nutrition. While species in the subfamily Silphinae feed on large carcasses and on larvae of competing scavengers, the Nicrophorinae are unique in monopolizing, burying and defending small carrion, and providing extensive biparental care. As a first step towards investigating whether microbial symbionts may aid in carcass utilization or defence, we characterized the microbial hindgut communities of six Nicrophorinae (Nicrophorus spp.) and two Silphinae species (Oiceoptoma noveboracense and Necrophila americana) by deep ribosomal RNA amplicon sequencing. Across all species, bacteria in the family Xanthomonadaceae, related to Ignatzschineriao larvae, were consistently common, and several other taxa were present in lower abundance (Enterobacteriales, Burkholderiales, Bacilli, Clostridiales and Bacteroidales). Additionally, the Nicrophorinae showed high numbers of unusual Clostridiales, while the Silphinae were characterized by Flavobacteriales and Rhizobiales (Bartonella sp.). In addition to the complex community of bacterial symbionts, each species of carrion beetle harboured a diversity of ascomycetous yeasts closely related to Yarrowia lipolytica. Despite the high degree of consistency in microbial communities across the Silphidae—specifically within the Nicrophorinae—both the fungal symbiont phylogeny and distance-based bacterial community clustering showed higher congruence with sampling locality than host phylogeny. Thus, despite the possibility for vertical transmission via anal secretions, the distinct hindgut microbiota of the Silphidae appears to be shaped by frequent horizontal exchange or environmental uptake of symbionts. The microbial community profiles, together with information on host ecology and the metabolic potential of related microorganisms, allow us to propose hypotheses on putative roles of the symbionts in carcass degradation, detoxification and defence.
Data from: Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities
Environmental degradation may have strong effects on community assembly processes. We examined the assembly of bacterial and fungal communities in anthropogenically altered and near-pristine streams. Using pyrosequencing of bacterial and fungal DNA from decomposed alder Alnus incana leaves, we specifically examined if environmental degradation deterministically decreases or increases the compositional turnover of bacterial and fungal communities. Our results showed that near-pristine streams and anthropogenically altered streams supported distinct fungal and bacterial communities. The mechanisms assembling these communities were different in near-pristine and altered environments. Environmental disturbance homogenized bacterial communities, whereas fungal communities were more dissimilar in disturbed sites than in near-pristine sites. Compositional variation of both bacteria and fungi was related to water chemistry variables in disturbed sites, further implying the influence of environmental degradation on community assembly. Bacterial and fungal communities in near-pristine streams were weakly controlled by environmental factors, suggesting that the relative importance of niche-based versus neutral processes in assembling microbial communities may strongly depend on the spatial scale and local environmental context. Our results thus suggest that environmental degradation may strongly affect the composition and β-diversity of stream microbial communities colonizing leaf litter, and that the direction of the change can be different between bacteria and fungi. A better understanding of the environmental tolerances of microbes and the mechanisms assembling microbial communities in natural environmental settings is needed to predict how environmental alteration is likely to affect microbial communities.
Data from: Smooth brome invasion increases rare soil bacterial species prevalence and alters soil bacterial community composition
Plant and soil communities are tightly linked, but the mechanisms by which the invasion of an exotic plant and the resulting shifts in plant diversity and productivity influence soil bacterial community structure remain poorly understood. We investigated the effects of invasive smooth brome (Bromus inermis) on grassland soil bacterial community structure using massively-parallel sequencing of the 16S rRNA gene to determine bacterial community richness, evenness, composition, and beta diversity (UniFrac indices) of soils collected along a gradient of smooth brome abundance. We evaluated several hypotheses including: a) that the declines in native plant diversity associated with smooth brome invasion would cause declines in bacterial community diversity, and b) that mechanisms driving smooth brome effects on bacterial community structure involved altered soil edaphic properties rather than preferential invasion in areas of high soil nitrogen and distinct soil microbial communities. Smooth brome invasion led to increased soil nitrogen, soil carbon and root biomass. Bacterial evenness and bacterial richness increased with increasing smooth brome cover, while bacterial beta diversity declined. We found no evidence of a dominant direct link between the alteration of soil edaphic properties by brome and the changes in the soil bacterial community. Rather, the main controls on the soil bacterial community were direct effects of pH and smooth brome that could not be linked to the edaphic changes. The most important effect of brome on the bacterial community was the selective suppression of dominant bacterial species, which allowed rarer bacteria to increase in relative abundance. Synthesis: Here we show that plant community composition influences bacterial community structure at a very fine scale, but that these changes are not due to altered soil total nitrogen or carbon content. The dominant direct effect of smooth brome invasion on soil communities suggests non-edaphic, i.e. inter and intra-trophic, interactions among smooth brome and non-bacterial components of the soil ecosystem are key drivers of soil community structure. Some of the data in this repository were also reported in the following paper: Piper, C.L., Lamb, E.G. & Siciliano, S.D. (In Press) Smooth brome changes gross soil nitrogen cycling processes during invasion of a rough fescue grassland. Plant Ecology. doi:10.1007/s11258-014-0431-y
Data from: Postoperative changes in fecal bacterial communities and fermentation products in obese patients undergoing bilio-intestinal bypass
We assessed the gut microbial ecology of 11 severely obese patients before and after bilio-intestinal bypass (BIB). Fecal samples were evaluated for microbial communities using 16S rDNA Illumina sequencing, real-time PCR targeting functional genes, and gas chromatography of short chain fatty acids (SCFAs). At 6 months after surgery, subjects exhibited significant improvements in metabolic markers (body weight, glucose, and lipid metabolism) compared with baseline. The fecal microbiota of post-surgery individuals was characterized by an overall decrease of bacterial diversity, with a significant reduction in Lachnospiraceae, Clostridiaceae, Ruminococcaceae, Eubacteriaceae, and Coriobacteriaceae. On the contrary, there were significant increases of genera Lactobacillus, Megasphaera, and Acidaminococcus and the family Enterobacteriaceae. The pH was decreased in fecal samples from patients after BIB and SCFA profiles were altered, with lower percentages of acetate and propionate and higher levels of valerate and hexanoate. Some changes in the bacterial populations were associated with variations in the patients' metabolic health parameters, namely Gemmiger and glucose, Lactobacillus and glucose, and Faecalibacterium and triglycerides. The results from this study of BIB patients furthers our understanding of the composition of gut microbiota and the functional changes that may be involved in improving obesity-related conditions following weight-loss surgery.
Data from: Experimental exposure to trace metals affects plumage bacterial community in the feral pigeon
Bacteria are fundamental associates of animals, and recent studies have highlighted their major role in host behaviour, immunity or reproductive investment. Thus, any environmental factor modifying bacterial community may affect host fitness. In birds, trace metals emitted by anthropogenic activities accumulate onto the plumage where they may alter bacterial community and ultimately affect bird fitness. Although trace metals are current major environmental issues in urban habitats, their effects on feather bacterial community have never been investigated. Here, we supplemented feral pigeons Columba livia, an emblematic urban species, with zinc and/or lead in drinking and bath water. As expected, lead and zinc supplementations modified plumage bacterial community composition. Zinc decreased bacterial load, while lead decreased bacterial richness and the frequency of preening behaviour in birds, known to regulate feather bacteria. Our results demonstrate for the first time the effects of common urban trace metals on plumage bacterial community and shed light on one of the mechanisms by which trace metals can affect bird fitness. Further studies are now needed to investigate how this effect modulates avian life history traits known to depend on plumage bacterial community.
Bacterial community richness shifts the balance between volatile organic compound-mediated microbe-pathogen and microbe-plant interactions
Even though bacteria are important in determining plant growth and health via volatile organic compounds (VOCs), it is unclear how these beneficial effects emerge in multi-species microbiomes. Here we studied this using a model plant-bacteria system, where we manipulated bacterial community richness and composition and determined the subsequent effects on VOC production and VOC-mediated pathogen suppression and plant growth-promotion. We assembled VOC-producing bacterial communities in different richness levels ranging from one to twelve strains using three soil-dwelling bacterial genera (Bacillus, Paenibacillus and Pseudomonas) and investigated how the composition and richness of bacterial community affect the production and functioning of VOCs. We found that VOC production correlated positively with pathogen suppression and plant growth-promotion and that all bacteria produced a diverse set of VOCs. However, while pathogen suppression was maximized at intermediate community richness levels when the relative amount and the number of VOCs were the highest, plant growth-promotion was maximized at low richness levels and was only affected by the relative amount of plant growth-promoting VOCs. The contrasting effects of richness could be explained by differences in the amount and number of produced VOCs and by opposing effects of community productivity and evenness on pathogen suppression and plant-growth promotion along the richness gradient. Together, these results suggest that the number of interacting bacterial species and the structure of the rhizosphere microbiome drive the balance between VOC-mediated microbe-pathogen and microbe-plant interactions potentially affecting plant disease outcomes in natural and agricultural ecosystems.
Data from: Bacterial community dynamics during embryonic and larval development of three confamilial echinoids
Development of some animals is influenced by and, in some cases, dependent on the associated microbiota. The timing of when associated bacterial communities are established during the development of marine invertebrates and their subsequent dynamics across stages are known for only a few species. Here, we compared the bacterial communities of 3 confamilial echinoids from egg to juvenile using sequence-based approaches. Bacterial communities are established on unfertilized eggs and change gradually during embryonic and larval development. Despite the differences amongst these pre-metamorphic stages, approximately 30% of operational taxonomic units (OTUs) identified in association with unfertilized eggs were present in the juveniles. During embryonic development, host-associated communities diverged from the environmental microbiota but later converged following the onset of larval feeding. Taken together, the data presented here support the hypothesis that bacterial communities are established prior to fertilization and community composition shifts gradually thereafter, all the while remaining distinct from the environment. Future work will need to determine the relative influence of the host and bacteria–bacteria interactions in shaping the associated bacterial community to more broadly determine the potential functional importance of bacteria during the development of larval sea urchins and benthic marine invertebrates.
Large-scale homogenization of soil bacterial communities in response to agricultural practices in paddy fields, China
<div>This dataset contains data from 257 sites in four typical rice-growing regions across a 4,000-km transect in China, including geographic location data and environment factors data.</div> <div> <br> The study was conducted across a 4,000-km transect of China's rice-growing areas, from Heilong Jiang province to Yunnan province (100°55′ E to 134°08′° E, 22°46′ N to 48°02′ N, Table S1). Four typical rice-growing regions were selected along this transect: Sanjiang Plain (modern mechanical farming), Taihu Plain (mechanical plus minor manual farming), Lianghu Plain (manual plus minor mechanical farming), and Hani Terrace (traditional manual farming).</div> <div> <br> Field sampling was conducted during July and August in 2014 and 2015. Soil samples were collected from 178 flooded paddy fields and 79 surrounding non-paddy areas across four typical rice-growing regions of China. At each site, one homogenized sample was obtained, which was then separated into two parts. One part, which was obtained for DNA extraction, was placed into a sterile plastic tube then immediately placed in liquid nitrogen for short-term transportation. After shipping to the laboratory, these tubes were stored at −80 °C. The second part of the soil sample was placed into a plastic bag and stored at 4.0 °C for determining the soil physicochemical properties.</div> <div> <br> Main results of the experiments are that: (1) Distance–decay patterns of bacterial communities in paddy fields revealed reduced β-diversity compared to surrounding natural habitats. (2) Modern rice farming practices (plowing with machines) caused stronger homogenization of soil bacterial communities than traditional farming (plowing by hand). Among the four paddy regions, plowing by hand retained the highest soil bacterial β-diversity. (3) Moreover, a significant inverse correlation was observed between bacterial β-diversity and the agricultural mechanization level. (4) Among multiple environmental factors, dramatic spatial homogenization of soil physicochemical properties, particularly soil nutrient contents, and reduced dispersal limitation caused by modern farming activities both strongly predict a reduction of bacterial β-diversity in modern paddy fields.</div>
Taxonomic abundance of bacterial community of Bactrocera dorsalis as affected by antibiotics treatments and eggs disinfection
<p><span>In order to understand the role of symbionts for their insect hosts, it is customary to treat them with antibiotics or to sterilize eggs (treatments), resulting in aposymbiotic and axenic insects, respectively. Such axenic insects can then be compared to untreated controls. Fruit flies often bear complex communities which are greatly reduced by such treatments. However, the bacterial community is not completely eliminated. Here, we examine the effect of these procedures on the structure of the remaining bacterial communities of <i>Bactrocera dorsalis</i> (Diptera: Tephritidae) and on the insect longevity. The antibiotics (Norfloxacin and Ceftazedime) were administered to 1 day old adult flies through sugar meal for seven days, and eggs were surface sterilized and dechorionated to produce axenic lines. The flies were starved from protein before they were offered full diets or diets containing non-essential amino acids only. Antibiotic and egg disinfection treatments resulted in significant reduction of the vast majority of gut bacterial populations, especially Proteobacteria, Firmicutes and Bacteroidetes. On the other hand, it allowed the persistence of Actinobacteria, Cyanobacteria and Acidobacteria populations. In untreated control flies, longevity was extended irrespective of diet quality in comparison to treated flies. Conversely, when gut bacteria were largely reduced (aposymbiotic and axenic flies), longevity was reduced in the non-essential amino acids diet treatment versus slightly improved in the presence of a protein diet. We discuss these results in an ecological–life history perspective.</span></p>
Gut bacterial community structure shifts in successive generations of Spodoptera exigua under short-term thermal stress
<p class="MsoNormal"><span>Long-term studies that advance our mechanistic understanding of gut bacterial symbionts of insect hosts in response to the successive generations of short-term thermal stress are lacking. The beet armyworm, <em>Spodoptera exigua</em> </span><span>is a notorious agricultural pest worldwide</span><span> and has often experienced stressful temperature fluctuations in field environments. In this study, 1,795,224 reads and 2,565 operational taxonomic units (OTUs) were detected in 23 gut samples of<em> S. exigua</em> fed for five successive generations<em> </em>using 16S rRNA high-throughput sequencing technology. Overall, we identified 618 bacterial genera from 30 phyla, and Proteobacteria and Firmicutes were the most dominant phyla. <a name="_Hlk98529962"></a><a name="_Hlk98688137"></a><span>Alpha-diversity </span><span>of gut microbiome revealed significant differences among these generation </span>treatment groups<em>.</em> We detected the highest bacterial richness and alpha diversity in the fifth generation and the lowest in the first generation under short-term thermal stress.<a name="_Hlk98529975"></a> Beta diversity indicated that the gut microbial community structure of <em>S. exigua</em> in the first generation was significantly different from that of other generations. Finally,<a name="_Hlk98576503"></a> </span><span><span>PICRUSt </span></span><span><span>analysis showed that </span></span><span>most functional prediction categories</span><span> were </span><span>related to</span><span> RNA processing and modification</span><span>.</span><span> Our findings represent the first investigation of the successive generations of short-term thermal stress that can affect the microbial communities associated with lepidopteran insects and broaden our understanding of the ecological adaptation of this species.</span></p>
Data from: Atmospheric N deposition alters co-occurrence, but not functional potential among saprotrophic bacterial communities
The use of co-occurrence patterns to investigate interactions between micro-organisms has provided novel insight into organismal interactions within microbial communities. However, anthropogenic impacts on microbial co-occurrence patterns and ecosystem function remain an important gap in our ecological knowledge. In a northern hardwood forest ecosystem located in Michigan, USA, 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. This ecosystem-level response occurred concomitantly with compositional changes in saprophytic fungi and bacteria. Here, we investigated the influence of experimental N deposition on biotic interactions among forest floor bacterial assemblages by employing phylogenetic and molecular ecological network analysis. When compared to the ambient treatment, the forest floor bacterial community under experimental N deposition was less rich, more phylogenetically dispersed and exhibited a more clustered co-occurrence network topology. Together, our observations reveal the presence of increased biotic interactions among saprotrophic bacterial assemblages under future rates of N deposition. Moreover, they support the hypothesis that nearly two decades of experimental N deposition can modify the organization of microbial communities and provide further insight into why anthropogenic N deposition has reduced decomposition, increased soil C storage and accelerated phenolic DOC production in our field experiment.
Bacterial community of the Lambro river (Italy)
<p><span>Characterization of the microbial community of a river can provide various indications, such as its general state of health or the presence of contamination. Furthermore, the study of <em>Bacteroidetes</em>, which have a high degree of host specificity, can provide information on the species involved in any fecal contamination. We report the characterization of the bacterial community of the Lambro river (Italy) through the analysis of the 16S rRNA gene </span>from 15 sampling points.</p>
Supplementary Information: CHAPTER 2 - Unveiling genomic features linked to traits of plant-growth-promoting bacterial communities from sugarcane
<p>Appendix A. Summary of counts of subreads and circular consensus sequencing (CCS) sequences obtained for PacBio sequencing of SMRT libraries. (EMS_1.xlsx)</p> <p>Appendix B. Taxonomy assignment of MAGs at the higher taxonomic rank obtained from GTDB-tk and Kraken tools. (EMS_2.xlsx)</p> <p>Appendix C. Report of the classification workflow using GTDB-tk. (EMS_3.xlsx)</p> <p>Appendix D. Matrix of the KEGG Orthology (KOs) frequencies annotated by the EnrichM tool. (EMS_4.xlsx)</p> <p>Appendix E. Reconstruction and completeness of KEGG modules annotated by EnrichM. The asterisks (*) in the header represent additional values obtained by the script ‘classKEGGModules.pl’ (https://github.com/dgpinheiro/bioinfoutilities) to estimate PGPTs in KEGG modules. (EMS_5.xlsx)</p> <p>Appendix F. The secondary metabolite biosynthesis gene clusters (BGCs) identified with AntiSMASH. (EMS_6.xlsx)</p> <p>Appendix G. The raw count of plant growth-promoting traits (PGPTs) annotations, according to KEGG Orthology (KO) predictions for MAGs. (EMS_7.xlsx)</p> <p>Appendix H. The raw count of plant growth-promoting traits (PGPTs) that comprises the 39 classes (level 5 hierarchy) identified as enriched according to the results of Pearson's Chi-square test (qvalue ≤ 0.1). (EMS_8.xlsx)</p>
Differences in the genomic potential of soil bacterial and phage communities between urban greenspaces and natural arid soils.
<p>This repository holds the final data products from metagenomics processing of bacteria and viruses from the article : "Differences in the genomic potential of soil bacterial and phage communities between urban greenspaces and natural arid soils"</p> <p>Contents: </p> <ul> <li>LU_metadata.csv: information on the samples</li> <li>soil_chemistry.txt: physicochemical information on samples</li> <li>*_len.csv: tables containing the length information for annotated genes, divided by database. These are used to calculate RPKM abundances from count tables. </li> <li>BACTERIA</li> <li>ko_table, ko_unknown, ko2level, ko_description: count table of KEGG annotations, total counts for unnanotated genes, match of ko number to level and description</li> <li>all_bracken.csv: count table of taxonomic bacterial annotations using kraken2 and bracken</li> <li>mags_tax.csv: taxonomy assignments to MAGs (metagenome assembled genomes)</li> <li>mags_count_table.csv: abundante table of MAGs in counts</li> <li>ags_result, gc_mean, gc_variance: functional traits results, average genome size, and gc content</li> <li>lu_c_count, lu_n_count, card_d0, metals_count_table: abundance tables of genes annotated with Cazy (carbon), Ncydb (nitrogen), CARD (antibiotic resistance genes), and Bacmet (heavy metal resistance genes)</li> <li>VIRUS</li> <li>amg_summary.csv: results from AMG annotation with DRAM-V, filtered to keep genes of interest</li> <li>genomad_virus_summary.tsv: viral taxonomy annotations with geNomad</li> <li>virus_len.txt: length of inferred viruses (used for calculation of RPKM from count tables)</li> <li>all_host_prediction_to_genus.csv: virus host annotation with IPhop</li> <li>final_checkv.tsv: table of final viral inferences with quality estimates</li> <li>viral_species_count_table.txt: abundance table of infered viral contigs in counts</li> </ul>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.