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.
31
datasets available to search
ShareScore release 0.9.0
Dataset results
31 results for “bacterial abundance”
June 2001 surface water bacterial abundance at ten Georgia Coastal Ecosystems LTER sampling sites
Surface water samples were collected during low tide surveys near ten Georgia Coastal Ecosystem LTER sampling sites in June, 2001. Unfiltered subsamples were immediately preserved with buffered formalin and refrigerated for transport to the laboratory. The abundance of bacteria in each sample was determined using an epifluorescence microscope by counting DAPI-stained cells retained on a 0.2µm polycarbonate filter. This study was part of the GCE-LTER hydrographic monitoring program, and will be repeated quarterly.
October 2001 surface water bacterial abundance at ten Georgia Coastal Ecosystems LTER sampling sites
Surface water samples were collected during low tide surveys near ten Georgia Coastal Ecosystem LTER sampling sites in October, 2001. Unfiltered subsamples were immediately preserved with buffered formalin and refrigerated for transport to the laboratory. The abundance of bacteria in each sample was determined using an epifluorescence microscope by counting DAPI-stained cells retained on a 0.2µm polycarbonate filter. This study was part of the GCE-LTER hydrographic monitoring program, and will be repeated quarterly.
November 2001 surface water bacterial abundance at ten Georgia Coastal Ecosystems LTER sampling sites
Surface water samples were collected during low tide surveys near ten Georgia Coastal Ecosystem LTER sampling sites in November, 2001. Unfiltered subsamples were immediately preserved with buffered formalin and refrigerated for transport to the laboratory. The abundance of bacteria in each sample was determined using an epifluorescence microscope by counting DAPI-stained cells retained on a 0.2µm polycarbonate filter. This study was part of the GCE-LTER hydrographic monitoring program, and will be repeated quarterly.
March 2002 surface water bacterial abundance at ten Georgia Coastal Ecosystems LTER sampling sites
Surface water samples were collected during low tide surveys near ten Georgia Coastal Ecosystem LTER sampling sites in March, 2002. Unfiltered subsamples were immediately preserved with buffered formalin and refrigerated for transport to the laboratory. The abundance of bacteria in each sample was determined using an epifluorescence microscope by counting DAPI-stained cells retained on a 0.2µm polycarbonate filter. This study was part of the GCE-LTER hydrographic monitoring program, and will be repeated quarterly.
September 2002 surface water bacterial abundance at ten Georgia Coastal Ecosystems LTER sampling sites
Surface water samples were collected during low tide surveys near ten Georgia Coastal Ecosystem LTER sampling sites in September, 2002. Unfiltered subsamples were immediately preserved with buffered formalin and refrigerated for transport to the laboratory. The abundance of bacteria in each sample was determined using an epifluorescence microscope by counting DAPI-stained cells retained on a 0.2µm polycarbonate filter. This study was part of the GCE-LTER hydrographic monitoring program, and will be repeated quarterly.
December 2002 surface water bacterial abundance at ten Georgia Coastal Ecosystems LTER sampling sites
Surface water samples were collected during low tide surveys near ten Georgia Coastal Ecosystem LTER sampling sites in December, 2002. Unfiltered subsamples were immediately preserved with buffered formalin and refrigerated for transport to the laboratory. The abundance of bacteria in each sample was determined using an epifluorescence microscope by counting DAPI-stained cells retained on a 0.2µm polycarbonate filter. This study was part of the GCE-LTER hydrographic monitoring program, and will be repeated quarterly.
March 2003 surface water bacterial abundance at ten Georgia Coastal Ecosystems LTER sampling sites
Surface water samples were collected during low tide surveys near ten Georgia Coastal Ecosystem LTER sampling sites in March, 2003. Unfiltered subsamples were immediately preserved with buffered formalin and refrigerated for transport to the laboratory. The abundance of bacteria in each sample was determined using an epifluorescence microscope by counting DAPI-stained cells retained on a 0.2µm polycarbonate filter. This study was part of the GCE-LTER hydrographic monitoring program, and will be repeated quarterly.
June 2003 surface water bacterial abundance at ten Georgia Coastal Ecosystems LTER sampling sites
Surface water samples were collected during low tide surveys near ten Georgia Coastal Ecosystem LTER sampling sites in June, 2003. Unfiltered subsamples were immediately preserved with buffered formalin and refrigerated for transport to the laboratory. The abundance of bacteria in each sample was determined using an epifluorescence microscope by counting DAPI-stained cells retained on a 0.2µm polycarbonate filter. This study was part of the GCE-LTER hydrographic monitoring program, and will be repeated quarterly.
September 2003 surface water bacterial abundance at ten Georgia Coastal Ecosystems LTER sampling sites
Surface water samples were collected during low tide surveys near ten Georgia Coastal Ecosystem LTER sampling sites in September, 2003. Unfiltered subsamples were immediately preserved with buffered formalin and refrigerated for transport to the laboratory. The abundance of bacteria in each sample was determined using an epifluorescence microscope by counting DAPI-stained cells retained on a 0.2µm polycarbonate filter. This study was part of the GCE-LTER hydrographic monitoring program, and will be repeated quarterly.
December 2003 surface water bacterial abundance at ten Georgia Coastal Ecosystems LTER sampling sites
Surface water samples were collected during low tide surveys near ten Georgia Coastal Ecosystem LTER sampling sites in December, 2003. Unfiltered subsamples were immediately preserved with buffered formalin and refrigerated for transport to the laboratory. The abundance of bacteria in each sample was determined using an epifluorescence microscope by counting DAPI-stained cells retained on a 0.2µm polycarbonate filter. This study was part of the GCE-LTER hydrographic monitoring program, and will be repeated quarterly.
March 2004 surface water bacterial abundance at ten Georgia Coastal Ecosystems LTER sampling sites
Surface water samples were collected during low tide surveys near ten Georgia Coastal Ecosystem LTER sampling sites in March, 2004. Unfiltered subsamples were immediately preserved with buffered formalin and refrigerated for transport to the laboratory. The abundance of bacteria in each sample was determined using an epifluorescence microscope by counting DAPI-stained cells retained on a 0.2µm polycarbonate filter. This study was part of the GCE-LTER hydrographic monitoring program, and will be repeated quarterly.
May 2004 surface water bacterial abundance at ten Georgia Coastal Ecosystems LTER sampling sites
Surface water samples were collected during low tide surveys near ten Georgia Coastal Ecosystem LTER sampling sites in May, 2004. Unfiltered subsamples were immediately preserved with buffered formalin and refrigerated for transport to the laboratory. The abundance of bacteria in each sample was determined using an epifluorescence microscope by counting DAPI-stained cells retained on a 0.2µm polycarbonate filter. This study was part of the GCE-LTER hydrographic monitoring program, and will be repeated quarterly.
qPCR raw datasets on the assessments of cover crop monocultures and mixtures improving the rhizosphere bacterial abundance and functionality through rerooting
<p>Quantitative PCR (qPCR) raw data includes the source data that corresponds to the the counts of 16S rRNA gene copies per gram of soil for different variations, as discussed in the research article - "Cover crop monocultures and mixtures improve the rhizosphere bacterial abundance and functionality through rerooting". The copy number of the 16S rRNA gene per gram of soil was quantified by SYBR® Green-based qPCR using a 7500 Fast Real-Time PCR System (Applied Biosystems™, Thermo Fisher Scientific, Waltham, MA, USA). Aliquots of the same DNA extract utilized in amplicon sequencing were used in qPCR. Dilutions of template DNA were used to compensate for the effect of PCR inhibitors in the samples. Each sample was analyzed in triplicate. A PCR amplicon of the <i>Escherichia coli</i> V3 region was used as standard. Each reaction of 20 µL contained 1 µL of template DNA, the forward primer 341F (Muyzer et al., 1993), the reverse primer 518R (Muyzer et al., 1993), and Luna® Universal qPCR Master Mix (NEB). Reaction conditions were an initial denaturation for 1 min at 95 °C, followed by 40 cycles of denaturation at 95 °C for 15 s and extension at 60 °C for 30 s. The melting curve was recorded in the temperature range of 60 °C to 95 °C. The 16S rRNA gene copy numbers per gram of soil were calculated using the standard curve method and then normalized against the standard (Adelowo et al., 2018). The average efficiency value was 100.77 ± 3.15 %. The absolute copy numbers for each bacterial phylum were calculated by multiplying the qPCR values by the relative abundance values in percent obtained from the 16S rRNA gene sequencing analyses.</p>
Degenerative Cervical Myelopathy (DCM) induces sex-specific dysbiosis in the mouse gut bacterial microbiome, altering abundance and function
<p><strong>Background:</strong> Degenerative cervical myelopathy (DCM) represents the commonest cause of spinal cord impairment induced by non-traumatic events in the elderly population. It describes a spectrum of disorders that cause progressive spinal cord compression, neurological impairment, loss of bladder and bowel functions, as well as gastrointestinal dysfunction. The gut microbiota has been increasingly recognized as an environmental factor that can modulate both the central nervous system and immune response through the microbiota-gut-brain axis. Changes in gut microbiota composition or in the microbiota producing factors have been linked in the progression and development of several different pathologies such as traumatic spinal cord injury (SCI). Little is known about the molecular mechanisms that trigger DCM manifestation, and the potential role of the gut microbiota.</p> <p><strong>Results: </strong>Herein DCM was induced in female and male C57BL/6 mice by implanting an aromatic polyether material underneath the C5-6 laminae. The extent of DCM-induced changes in microbiota composition, also known as dysbiosis, was assessed by 16S rRNA sequencing from fecal samples at 3 different time points (6, 9 and 12 weeks after DCM induction). Several bacterial members were identified based on BLAST against the largest collection of metagenome-derived genomes from the mouse gut up to date. In both, female and males DCM caused gut dysbiosis compared with the sham group. However, dysbiosis was more pronounced in males than females, where several bacterial members of the families <em>Lachnospiraceae</em> and <em>Muribaculaceae</em> were significantly altered in the DCM group. These changes were also associated with altered immune cell composition in gut-associated lymphoid tissue, blood, and microbe-derived metabolic changes in propionate, butyrate, and lactate-producing bacterial members.</p> <p><strong>Conclusions: </strong>Our results demonstrate for the first time that DCM causes dynamic changes over time in the gut microbiota. Furthermore, we identify specie-specific abundance changes during DCM progression. DCM strongly reduces the abundance of butyrate-producing bacteria, and lactate-producing bacteria in much less extent. Sequence-based pangenomics cores were not resolved between the latter bacteria, but the gap-filling reactions and metabolic modelling successfully identified pyruvate-to-butanoate and pyruvate-to-propionate genes such as Buk and ACH1, respectively. These results aid to better understand markers and the molecular mechanisms that over time trigger DCM manifestation in females and males.</p>
Absolute abundances of probiotic bacterial species in synthesised vs commercial yogurts local to Qatar.
<p>Absolute abundances of probiotic bacterial species in yogurts local to Qatar and lab synthesised yogurts. (16sRNA sequencing)</p>
Mean relative abundance of fungal and bacterial ASV identified in vegetables and fruits.
<p>Supplementary table S1. Mean relative abundance of fungal and bacterial ASV identified in vegetables and fruits.</p>
Bacterial and phytoplankton abundances by flow cytometry - collected from the Southern Ocean in the austral summer of 2016/2017, during the Antarctic Circumnavigation Expedition.
<p>Seawater surface samples (5 m) were collected every 6 hours from the ship’s underway pump. In addition, vertical profiles (6 depths, generally from 5 to 100-150 m) were sampled from CTD casts using a SBE 911 Plus attached to a rosette of 24 12-L PVC Niskin bottles. This dataset presents the abundances of high-DNA containing and low-DNA containing bacteria, pico and nanophytoplankton from seawater samples collected from the ship’s underway pump and CTDs. Samples were fixed with paraformaldehyde and glutaraldehyde and stored at -80ºC. In the lab, they were thawed, and one replicate, for bacteria, was stained with SYBR-Green and counted in a Cube 8 flow cytometer (SYSMEX PARTEC) based on green fluorescence. Another replicate was analyzed without staining for phytoplankton, and counted based on the red and orange autofluorescences. Samples were collected around the Southern Ocean on the R/V Akademik Tryoshnikov in the austral summer of 2016/2017, as part of the Antarctic Circumnavigation Expedition (ACE).</p>
Data from: Livestock abundance predicts vampire bat demography, immune profiles, and bacterial infection risk
Open the record for dataset details and reuse information.
Data from: Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments
In marine environments, macrofauna living in or on the sediment surface may alter the structure, diversity and function of benthic microbial communities. In particular, microbial nitrogen (N)-cycling processes may be enhanced by the activity of large bioturbating organisms. Here, we study the effect of the burrowing mud shrimp Upogebia deltaura upon temporal variation in the abundance of genes representing key N-cycling functional guilds. The abundance of bacterial genes representing different N-cycling guilds displayed different temporal patterns in burrow sediments in comparison with surface sediments, suggesting that the burrow provides a unique environment where bacterial gene abundances are influenced directly by macrofaunal activity. In contrast, the abundances of archaeal ammonia oxidizers varied temporally but were not affected by bioturbation, indicating differential responses between bacterial and archaeal ammonia oxidizers to environmental physicochemical controls. This study highlights the importance of bioturbation as a control over temporal variation in nitrogen-cycling microbial community dynamics within coastal sediments.
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>
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.