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2,286 results for “Microbiome”
Inventory of soil prokaryotic microbiome (via 16S based on rRNA gene amplicons) in freshwater and brackish water marshes following saltwater intrusion along Shark River Slough boundary, Everglades National Park (FCE LTER), Florida, USA, September 2018
Global sea-level rise is transforming coastal ecosystems, especially freshwater wetlands, in part due to increased episodic or chronic saltwater exposure, leading to shifts in microbial communities and related ecological services. Soil prokaryotes play a fundamental role in regulating important biogeochemical processes in coastal wetland ecosystem. Yet, it is still difficult to predict how soil prokaryotic communities respond to the saltwater exposure because of poorly understood prokaryotic sensitivity within complex wetland soil microbial communities, as well as the high heterogeneity of wetland soils and saltwater exposure. To address this, a four-year experimental simulation of saltwater intrusion in a pristine freshwater site and a previously saltwater-impacted site was conducted. The saltwater addition started in October 2014 on a monthly basis and continued through October 2018. The dataset contains amplicon sequencing date of 16S rRNA gene obtained from saltwater-exposed soils and unmanipulated native soils in both sites (collected in September 2018). The 2018 data are published in Zhao et al. 2023. A detailed list of sequence data and their accession numbers in GenBank is provided, and data collection is complete. This data package is an inventory of sequence read archive (SRA) entries available through GenBank BioProject PRJNA804545 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA804545). This data package is associated with the following publication: Zhao, J., Chakrabarti, S., Chambers, R., Weisenhorn, P., Travieso, R., Stumpf, S., Standen, E., Briceno, H., Troxler, T., Gaiser, E., Kominoski, J., Dhillon, B., & Martens-Habbena, W. (2023). Year-around survey and manipulation experiments reveal differential sensitivities of soil prokaryotic and fungal communities to saltwater intrusion in Florida Everglades wetlands. Science of The Total Environment, 858, 159865. https://doi.org/10.1016/j.scitotenv.2022.159865 Instead of citing this package, which is an
Inventory of soil prokaryotic and fungal microbiome (via 16S rRNA gene amplicons and ITS sequencing) from Shark River Slough and Taylor Slough, Everglades National Park (FCE LTER), Florida, USA, February 2019 - October 2020
Global sea-level rise is transforming coastal ecosystems, especially freshwater wetlands, in part due to increased saltwater exposure, leading to change in soil microbial communities and many important biogeochemical processes. Given the high spatial and temporal heterogeneity in coastal wetlands, especially in tropical or subtropical climates characterized by seasonal temperature, precipitation, and tidal fluctuations, it remains unclear which environmental factors influence the compositions of soil microbial communities in wetlands affected by varying degrees of sea-water intrusion. To address this, a two-year survey was conducted on microbial community structure in submerged surface soils from 14 wetland sites across the Florida Everglades, representing three major ecosystem types, i.e. freshwater marshes, mangrove forests, and seagrass meadows. Bulk surface soil samples of each site were collected from February 2019 to October 2020 to cover dry and wet seasons. In addition to bulk soil samples, soil cores were collected from each site in August 2020 to assess vertical gradients of microbial communities. The dataset contains amplicon sequencing data of 16S rRNA gene (both bulk soil and soil cores) and ITS gene (only the bulk soil). The 2019 to 2020 data are published in Zhao et al. 2023. A detailed list of sequence data and their accession numbers in GenBank is provided, and data collection is complete. This data package is an inventory of sequence read archive (SRA) entries available through GenBank BioProject PRJNA804243 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA804243), PRJNA804246 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA804246), and PRJNA804228 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA804228). This data package is associated with the following publication: Zhao, J., Chakrabarti, S., Chambers, R., Weisenhorn, P., Travieso, R., Stumpf, S., Standen, E., Briceno, H., Troxler, T., Gaiser, E., Kominoski, J., Dhillon, B., & Martens-H
Alpine plant seed microbiomes, germination, and plant-soil feedbacks, Niwot Ridge and Green Lakes Valley, 2018.
Seed and soil microbiomes strongly affect plant performance, and these effects can scale-up to influence plant community structure. However, seed and soil microbial community composition are variable across landscapes, and different microbial communities can differentially influence multiple plant metrics (biomass, germination rate), and community stabilizing mechanisms. We measured how microbiomes inside seeds and in soils varied among alpine plant species and communities that differed in plant species richness and density. Across 10 common alpine plant species, we found a total of 318 bacterial and 128 fungal operational taxonomic units (OTUs) associated with seeds, with fungal richness affected by plant species identity more than sampling location. However, seed microbes had only marginally significant effects on plant germination success and timing. In contrast, soil microbes associated with two different plant species had significant effects on plant biomass, and their effect depended both on the plant species and the location the soils were sampled from.
Metagenomic assembly and bin3C clustering result for a healthy human faecal microbiome transplant donor
<p>Metagenomic WGS assembly and Hi-C deconvolution of a healthy human faecal microbiome transplant donor.</p> <p>Metagenomic assembly was produced using Spades (v3.13.1).</p> <p>Extracted MAGs were produced using bin3C (v0.3.3) and QC'd using CheckM (v1.0.18).</p>
Reproductive hormones mediate changes in the gut microbiome during pregnancy and lactation in Phayre's leaf monkeys
Studies in multiple host species have shown that gut microbial diversity and composition change during pregnancy and lactation. However, the specific mechanisms underlying these shifts are not well understood. Here, we use longitudinal data from wild Phayre's leaf monkeys to test the hypothesis that fluctuations in reproductive hormone concentrations contribute to gut microbial shifts during pregnancy. We described the microbial taxonomic composition of 91 fecal samples from 15 females (n=16 cycling, n=36 pregnant, n=39 lactating) using 16S rRNA gene amplicon sequencing and assessed whether the resulting data were better explained by overall reproductive stage or by fecal estrogen (fE) and progesterone (fP) concentrations. Our results indicate that while overall reproductive stage affected gut microbiome composition, the observed patterns were driven by reproductive hormones. Females had lower gut microbial diversity during pregnancy and fP concentration was negatively correlated with diversity. Additionally, fP concentration predicted both unweighted and weighted UniFrac distances, while reproductive state only predicted unweighted UniFrac distances. Seasonality (rainfall and periods of phytoprogestin consumption) additionally influenced gut microbial diversity and composition. Our results indicate that reproductive hormones, specifically progestagens, contribute to the shifts in the gut microbiome during pregnancy and lactation.
MMGC: custom Kraken2/Bracken database for analysing the mouse gut microbiome
<p>Custom Kraken2/Bracken database built using the representative genomes for 1,021 microbial species from the mouse gut microbiota. Genomes include isolates and MAGs, but all are near-complete (>90% completeness; <5% contamination; maximum genome size ≤ 8 Mb; maximum contig count ≤ 500; N50 ≥ 10 kb; mean contig length ≥ 5 kb). This database achieved a mean read classification rate of 87.7% when benchmarked on 1,785 independent (i.e. non-contributory) mouse gut shotgun metagenome samples. An equivalent human database (UHGG) only attained classification rates of 36.6%.</p> <p>This database is a publicly available resource to facilitate more efficient/deeper analyses of mouse gut shotgun metagenomes.</p> <p>Find out more about the Mouse Microbial Genome Collection at our <a href="https://github.com/BenBeresfordJones/MMGC">GitHub repository</a>.</p>
The impact of Opisthorchis felineus infection and praziquantel treatment on the intestinal microbiome in children
<p>The presence of some species of helminths is associated with changes in host microbiota composition and diversity, which varies widely depending on the infecting helminth species and other factors. We conducted a prospective case-control study to evaluate the gut microbiota in children with Opisthorchis felineus infection (n=50) before and after anthelmintic treatment and in uninfected children (n=49) in the endemic region. A total of 99 children and adolescents aged between 7 and 18 years were enrolled to the study. Helminth infection was assessed before and at 3 months after treatment with praziquantel. A complex examination for each participant was performed in the study, including an assessment of the clinical symptoms and an intestinal microbiota survey by 16S rRNA gene sequencing of stool samples. There was no change in alpha diversity between O. felineus-infected and control groups. We found significant changes in the abundances of bacterial taxa at different taxonomic levels between the infected and uninfected individuals. Enterobacteriaceae family was more abundant in infected participants compared to uninfected children. On the genus level, O. felineus-infected participants’ microbiomes showed higher levels of Lachnospira, Escherichia-Shigella, Bacteroides, Eubacterium eligens group, Ruminiclostridium 6, Barnesiella, Oscillibacter, Faecalitalea and Anaerosporobacter and reduction of Blautia, Lachnospiraceae FCS020 and Eubacterium hallii group in comparison with the uninfected individuals. Following praziquantel therapy, there were significant differences in abundances of some microorganisms, including an increase of Faecalibacterium and decrease of Megasphaera, Roseburia. Enterobacteriaceae and Escherichia abundances were decreased up to the control group values. Our results highlight the importance of the host-parasite-microbiota interactions for the community health in the endemic regions.</p>
Putative mobilized colistin resistance (mcr) genes co-occurring with other antibiotic resistance genes are widespread in the human gut microbiome
<p><strong>The dataset from the article </strong><strong>Putative mobilized colistin resistance (mcr) genes co-occurring with other antibiotic resistance genes are widespread in the human gut microbiome</strong></p>
Assembly-based analysis of the infant gut microbiome reveals novel ubiquitous plasmids
<p>Assembly-based plasmids found in the gut microbiome of 12 infants born in Norway (BabyBiome project).</p>
Unraveling community adaption and survival strategy of soil microbiome under vanadium stress in nationwide mining environments
<p class="Abstract"><span><span>The vanadium (V) smelters soil harbor wide ranges of microorganisms, whose survival relies on their metabolic activities under stress.</span><span> Nonetheless, the characteristics and functions of soil microbiome in V mining environments have not been recognized at a continental scale. This study investigates microbial diversity, community assembly and metabolic traits of soil microbiome across 90 V smelters in China. A decrease in alpha diversity is observed, along with community variation, which is also jointly explained by other environmental, climatic and geographic factors. Null model shows that V promotes homogeneous selection. V also mediates co-occurrence patterns, with increased positive interspecific associations under higher V concentrations (</span><span>></span><span>559.6 mg/kg)</span><span>, e.g., <em>f_Gemmatimonadaceae</em>, <em>Nocardioides</em>, <em>Micromonospora</em>, <em>Rubrobacter</em>.</span><span> In addition, 67 metagenome assembled genomes are retrieved via metagenomic analysis. The metabolic pathways of keystone taxa are disentangled to reveal their putative involvement in the V(V) reduction process. Nitrate and nitrite reductase (<em>nirK</em>, <em>narG</em>), and <em>mtrABC</em> are found to be taxonomically affiliated with <em>Micromonospora</em>. sp, <em>FEN-1250</em>. sp, <em>Nocardioides</em>. sp, etc. Additionally, reverse citric acid cycle (rTCA) serves the main carbon fixation pathway, synthetizing alternative energy for putative V reducers, highlighting a synergistic relationship between autotrophic and heterotrophic processes to support the microbial survival. Our findings comprehensively reveal the driving forces for soil community variation under V stress, suggesting the robust strategies adopted by indigenous microorganisms to alleviate V impact, which can be exploited for bioremediation application.</span></span></p>
Growth of Thalassiosira gravida and Thalassiosira rotula across different levels of temperature, photoperiod, and microbiome presence
<p>The provided data represent maximum growth rates of the temperate diatom <em>Thalassiosira</em> <em>rotula</em> obtained from<span> the Harder Lab (University of Bremen; strain <em>T. rotula</em>_S16)</span> and the polar diatom <em>Thalassiosira</em> <em>gravida</em> was obtained <span>from the Norwegian culture collection of algae (NORCCA strain number UIO 478). Data were </span>assessed in a nanocosm (microtiter-plate) 7-day multi-stressor laboratory experiment conducted in November 2022. The experimental design includes different combinations of temperature (4°C; 9°C; 13.5°C), photoperiod (4:20; 16:8; 24:0) and microbiome presence (xenic; axenic) at which growth was assessed to evaluate interactive effects of abiotic factors (temperature & photoperiod) and biotic facors (interactions with microbiome bacteria). Moreover, the code to process the data for statistical analysis is provided.</p>
Microbiome depletion and recovery in the sea anemone, Aiptasia, following antibiotic exposure
<p>This provides data for the manuscript Microbiome depletion and recovery in the sea anemone, Aiptasia, following antibiotic exposure; 16smetadata.xlsx file used for in the DADA2 pipeline is provided, and the CFU count data is provided in cfu-counts-2022-01-20-modified.csv. The data for total protein content, pedal lacerate counts and algal abundance can all be found in the physio-2022-01-20.csv with the associated dataset (i.e. protein, algae, pedal lacerates) specified in the variable column.</p>
Maternal body condition affects the response of the gut microbiome to a widespread contaminant in larval spined toads
<p>Datasets (metadata and phyloseq object) </p> <p>Scripts used for the statistical analyses</p>
Effects of environmental translocation and host characteristics on skin microbiomes of sun-basking fish
<p>Variation in the composition of skin-associated microbiomes has been attributed to host species, geographic location, and habitat, but the role of intraspecific phenotypic variation among host individuals remains elusive. We explored if and how host environment and different phenotypic traits were associated with microbiome composition. We conducted repeated sampling of dorsal and ventral skin microbiomes of carp individuals (<em>Cyprinus</em> <em>carpio</em>) before and after translocation from laboratory conditions to a semi-natural environment. Both alpha and beta diversity of skin-associated microbiomes increased substantially within and among individuals following translocation, particularly on dorsal body sites. The variation in microbiome composition among hosts was significantly associated with body site, sun-basking, habitat switch, and growth, but not temperature gain while basking, sex, personality, or colour morph. We suggest that the overall increase in the alpha and beta diversity estimates among hosts were induced by individuals expressing greater variation in behaviours and thus exposure to potential colonizers in the pond environment compared to the laboratory. Our results exemplify how biological diversity at one level of organization (phenotypic variation among and within fish host individuals) together with the external environment impacts biological diversity at a higher hierarchical level of organisation (richness and composition of fish-associated microbial communities).</p>
Decoding host-microbiome interactions through co-expression network analysis within the non-human primate intestine
<p>Supplementary Table Captions:</p> <p>Supplementary Table S9. Evaluation and parameter determination of host and microbiome RNA read classification using simulation datasets</p> <p>Supplementary Table S10. 40 pathways significantly upregulated in the cecum as compared to the transverse colon</p> <p>Supplementary Table S11. Host-microbiome gene co-expression network edges</p> <p>Supplementary Table S12. Host-host gene co-expression network edges</p> <p>Supplementary Table S13. Microbiome-microbiome gene co-expression network edges</p> <p>Supplementary Table S14. List of genes included in each gene module identified from the gene co-expression network</p> <p>Supplementary Table S15. Results of enrichment analysis for each gene module identified from the gene co-expression network</p> <p>Supplementary Table S16. The top 32 bacterial species in terms of expression abundance based on metatranscriptome profiles</p> <p>Supplementary Table S17. Number of microbiome RNA reads annotated by the KEGG database</p> <p>Supplementary Table S18. Results of enrichment analysis of gene modules for each parameter</p> <p>Supplementary Table S19. Evaluation of modules in each parameter of Newman algorithm</p> <p>Supplementary Table S20. Evaluation of modules in each parameter of Louvain algorithm</p> <p>Supplementary Table S21. Evaluation of modules in each parameter of Leiden algorithm</p> <p>Supplementary Table S22. Evaluation of modules in each parameter of WGCNA</p>
Ant handling changes myrmecochore seed coat microbiomes and alters diversity of seed-borne plant pathogenic fungi
<p>The putative benefits to seeds in myrmecochory (ant-mediated seed dispersal) are often cast in a reward context. However, microbes have been mostly overlooked as seed mortality agents in myrmecochory, as have potential treatments provided by ant-handling. We investigated the effects of ant handling on the diversity of seed coat fungal communities of three myrmecochorous plant species. Ant-handling altered measures of both alpha and beta diversity of fungal communities. Ant-handled seeds harbored different overall fungal communities and plant pathogen communities than non-ant-handled seeds. The myrmecochore pathogenic fungal community showed high dissimilarity (high pairwise community turnover) between ant-handled and control seeds, while beta diversity measures for ant-handled seeds and seeds with manually-removed elaiosomes were less dissimilar. Ant handling may offer an additional benefit to myrmecochorous seeds via the reduction of the seed coat pathogenic community, which may be driven by elaiosome removal or as a byproduct of ant cleaning behaviors and chemical secretions. </p>
The reproductive microbiome and maternal transmission via eggs in Sceloporus virgatus
<p>Maternal transmission of microbes occurs across the animal kingdom and is vital for the development and long-term health of offspring. The mechanisms of this transfer are most well studied in humans and other mammals, but are less well understood in egg-laying animals, especially in those with no parental care. Here we investigate the transfer of maternal microbes in <em>Sceloporus virgatus</em>, an oviparous spiny lizard. We compared three maternal tissue microbiomes – oviduct, cloaca, and intestine – to three offspring sample types: egg contents and eggshells on the day of oviposition, and hatchling intestinal tissue on the day of hatching. We found that dam ID is an important factor in hatchling microbiome composition, indicating that maternal transmission is occurring. The maternal cloacal and oviductal communities contribute to offspring microbiomes in all three sample types, but there was minimal influence of maternal intestinal microbes. This indicates that the maternal reproductive microbiome is more important for microbial inheritance than the gut microbiome, and that the tissue-level variation of the adult <em>S. virgatus</em> microbiome must develop as the hatchling matures. Despite differences between adult and hatchling communities, the offspring microbiome was still dominated by Enterobacteriaceae and Yersiniaceae, consistent with past studies of adult <em>S. virgatus</em> microbiomes.</p>
Determinants of microbiome composition: Insights from free-ranging hybrid zebras (Equus quagga × grevyi)
<p>The composition of mammalian gut microbiomes is highly conserved within species, yet the mechanisms by which microbiome composition is transmitted and maintained within lineages of wild animals remain unclear. Mutually compatible hypotheses exist, including that microbiome fidelity results from inherited dietary habits, shared environmental exposure, morphophysiological filtering, and/or maternal effects. Interspecific hybrids are a promising system in which to interrogate the determinants of microbiome composition because hybrids can decouple traits and processes that are otherwise co-inherited in their parent species. We used a population of free-living hybrid zebras (<em>Equus quagga</em> × <em>grevyi</em>) in Kenya to evaluate the roles of these four mechanisms in regulating microbiome composition. We analyzed fecal DNA for both the <em>trn</em>L-P6 and the 16S rRNA V4 region to characterize the diets and microbiomes of the hybrid zebra and of their parent species, plains zebra (<em>E. quagga</em>) and Grevy's zebra (<em>E. grevyi</em>). We found that both diet and microbiome composition clustered by species, and that hybrid diets and microbiomes were largely nested within those of the maternal species, plains zebra. Hybrid microbiomes were less variable than those of either parent species where they co-occurred. Diet and microbiome composition were strongly correlated, although the strength of this correlation varied between species. These patterns are most consistent with the maternal-effects hypothesis, somewhat consistent with the diet hypothesis, and largely inconsistent with the environmental-sourcing and morphophysiological-filtering hypotheses. Maternal transmittance likely operates in conjunction with inherited feeding habits to conserve microbiome composition within species.</p>
Oak seedling microbiome assembly under climate warming and drought
<p><span lang="EN-US">Despite that climate change is currently one of the most pervasive challenges, its effects on the plant-associated microbiome is still poorly studied. The aim of this study was to evaluate the impact of the independent and combinatory effect of climate warming and drought on the microbiome assembly of oak from seed to seedling. In a multifactorial experimental set up, acorns were subjected to different temperatures (15 °C, 20 °C, and 25 °C) and soil moisture levels (drought (15 %) and control (60 %)) from germination until the seedling stage, after which the bacterial and fungal communities associated to the rhizosphere and phyllosphere were characterized by amplicon sequencing and qPCR. The results showed a stronger effect of temperature on fungal than on bacterial diversity and the effect was more pronounced in the phyllosphere. Under drought condition, temperature had a significantly negative effect on phyllosphere fungal diversity. In the rhizosphere, temperature had a significant effect on the fungal community composition which was primarily caused by species turnover</span><span>.</span> <span lang="EN-US">Regardless of temperature, <em>Actinobacteriota</em> was significantly enriched in drought, a group of bacteria known to increase plant drought tolerance. This study provides new insights into the effect of climate change on the plant microbiome in natural ecosystems.</span></p>
Alpha-synuclein overexpression can drive microbiome dysbiosis in mice
<p>Growing evidence indicates that persons living with Parkinson disease (PD), have a unique composition of indigenous gut microbes. Given the long prodromal or pre-diagnosed period, longitudinal studies of the human and rodent gut microbiome prior to symptomatic onset and for the duration of the disease period are currently lacking. PD is characterized in part by accumulation of the protein α-synuclein (α-syn) into insoluble aggregates, in both the central and enteric nervous systems. As such, a number of experimental rodent and non-human primate models of α-syn overexpression recapitulate some of hallmark pathophysiologies of PD. These animal models provide an opportunity to assess how the gut microbiome changes with age under disease relevant conditions. Here, we used a transgenic mouse strain, the Thy1-hSYN “line 61” mice which over express wild-type human α-syn to test how the gut microbiome composition responds in this model of PD pathology during aging. Using shotgun metagenomics, we find significant, age and genotype dependent bacterial taxa that become altered over age. We reveal that α-syn overexpression can drive alterations to the gut microbiome composition and suggest that it limits the expansion of diversity through age. Given emerging data on potential contributions of the gut microbiome to PD pathologies, our data provide an experimental foundation to understand how the PD-associated microbiome may arise as a trigger or co-pathology to disease.</p>
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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.