Browse
Submit Data
Databases
API
Help

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

More support for Earth's massive microbiome.

ABSTRACT: Until recently, our planet was thought to be home to ~?107 species, largely belonging to plants and animals. Despite being the most abundant organisms on Earth, the contribution of microbial life to global biodiversity has been greatly underestimated and, in some cases, completely overlooked. Using a compilation of data known as the Global Prokaryotic Census (GPC), it was recently claimed that there are ~?106 extant bacterial and archaeal taxa [1], an estimate that is orders of magnitude lower than predictions for global microbial biodiversity based on the lognormal model of biodiversity and diversity-abundance scaling laws [2]. Here, we resolve this discrepancy by 1) identifying violations of sampling theory, 2) correcting for the misuse of biodiversity theory, and 3) conducting a reanalysis of the GPC. By doing so, we uncovered greater support for diversity-abundance scaling laws and the lognormal model of biodiversity, which together predict that Earth is home to 1012 or more microbial taxa. REVIEWERS: This article was reviewed by Alvaro Sanchez and Sean M. Gibbons.

SUBMITTER: Lennon JT

PROVIDER: S-EPMC7055056 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

More support for Earth's massive microbiome.

Lennon Jay T JT Locey Kenneth J KJ

Biology direct 20200304 1

Until recently, our planet was thought to be home to ~ 10<sup>7</sup> species, largely belonging to plants and animals. Despite being the most abundant organisms on Earth, the contribution of microbial life to global biodiversity has been greatly underestimated and, in some cases, completely overlooked. Using a compilation of data known as the Global Prokaryotic Census (GPC), it was recently claimed that there are ~ 10<sup>6</sup> extant bacterial and archaeal taxa [1], an estimate that is order ...[more]

PMID: 32131875

Similar Datasets

Achieving data privacy for decision support systems in times of massive data sharing.

Project description:The world is suffering from a new pandemic of Covid-19 that is affecting human lives. The collection of records for Covid-19 patients is necessary to tackle that situation. The decision support systems (DSS) are used to gather that records. The researchers access the patient's data through DSS and perform predictions on the severity and effect of the Covid-19 disease; in contrast, unauthorized users can also access the data for malicious purposes. For that reason, it is a challenging task to protect Covid-19 patient data. In this paper, we proposed a new technique for protecting Covid-19 patients' data. The proposed model consists of two folds. Firstly, Blowfish encryption uses to encrypt the identity attributes. Secondly, it uses Pseudonymization to mask identity and quasi-attributes, then all the data links with one another, such as the encrypted, masked, sensitive, and non-sensitive attributes. In this way, the data becomes more secure from unauthorized access.

| S-EPMC8743442 | biostudies-literature

Nutritional support in sepsis: when less may be more.

Project description:Despite sound basis to suspect that aggressive and early administration of nutritional support may hold therapeutic benefits during sepsis, recommendations for nutritional support have been somewhat underwhelming. Current guidelines (ESPEN and ASPEN) recognise a lack of clear evidence demonstrating the beneficial effect of nutritional support during sepsis, raising the question: why, given the perceived low efficacy of nutritionals support, are there no high-quality clinical trials on the efficacy of permissive underfeeding in sepsis? Here, we review clinically relevant beneficial effects of permissive underfeeding, motivating the urgent need to investigate the clinical benefits of delaying nutritional support during sepsis.

| S-EPMC7023788 | biostudies-literature

Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing.

Project description:Infections by HIV increase the risk of acquiring secondary viral and bacterial infections and methods are needed to determine the spectrum of co-infections for proper treatment. We used rolling circle amplification (RCA) and Ion Proton sequencing to investigate the vaginal microbiome of 20 HIV positive women from South Africa. A total of 46 different human papillomavirus (HPV) types were found, many of which are not detected by existing genotyping assays. Moreover, the complete genomes of two novel HPV types were determined. Abundance of HPV infections was highly correlated with real-time PCR estimates, indicating that the RCA-Proton method can be used for quantification of individual pathogens. We also identified a large number of other viral, bacterial and parasitic co-infections and the spectrum of these co-infections varied widely between individuals. Our method provides rapid detection of a broad range of pathogens and the ability to reconstruct complete genomes of novel infectious agents.

| S-EPMC3957130 | biostudies-literature

Host Factors Affect the Gut Microbiome More Significantly than Diet Shift.

Project description:The determining factors of the composition of the gut microbiome are one of the main interests in current science. In this work, we compared the effect of diet shift (DS) from heavily relying on meatatarian diets to vegetarian diets and physical exercise (EX) on the composition of the gut microbiome after 3 months. Although both DS and EX affected the composition of the gut microbiome, the patterns of alteration were different. The α-diversity analyzed by InvSimpson, Shannon, Simpson, and Evenness showed that both EX and DS affected the microbiome, causing it to become more diverse, but EX affected the gut microbiome more significantly than DS. The β-diversity analyses indicated that EX and DS modified the gut microbiome in two different directions. Co-occurrence network analysis confirmed that both EX and DS modified the gut microbiome in different directions, although EX modified the gut microbiome more significantly. Most notably, the abundance of Dialister succinatiphilus was upregulated by EX, and the abundances of Bacteroides fragilis, Phascolarctobacterium faecium, and Megasphaera elsdenii were downregulated by both EX and DS. Overall, EX modulated the composition of the gut microbiome more significantly than DS, meaning that host factors are more important in determining the gut microbiome than diets. This work also provides a new theoretical basis for why physical exercise is more health-beneficial than vegetarian diets.

| S-EPMC8707884 | biostudies-literature

The microbiota and microbiome in pancreatic cancer: more influential than expected.

Project description:Microbiota is just beginning to be recognized as an important player in carcinogenesis and the interplay among microbes is greater than expected. Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal disease for which mortality closely parallels incidence. Early detection would provide the best opportunity to increase survival rates. Specific well-studied oral, gastrointestinal, and intrapancreatic microbes and some kinds of hepatotropic viruses and bactibilia may have potential etiological roles in pancreatic carcinogenesis, or modulating individual responses to oncotherapy. Concrete mechanisms mainly involve perpetuating inflammation, regulating the immune system-microbe-tumor axis, affecting metabolism, and altering the tumor microenvironment. The revolutionary technology of omics has generated insight into cancer microbiomes. A better understanding of the microbiota in PDAC might lead to the establishment of screening or early-stage diagnosis methods, implementation of cancer bacteriotherapy, adjustment of therapeutic efficacy even alleviating the adverse effects, creating new opportunities and fostering hope for desperate PDAC patients.

| S-EPMC6526613 | biostudies-literature

Use of SERI Surgical Scaffold for Soft-tissue Support in a Massive Weight Loss Patient.

Project description:SUMMARY:Patients with a history of massive weight loss have compromised and poor-quality skin and fascia. Various body contouring surgeries aim to improve appearance and shape of the trunk and restore fascial integrity. These patients may be at increased risk of recurrent fascial laxity or bulges after conventional techniques. Here, the author presents a case where a silk-based bioresorbable scaffold was used prophylactically in a massive weight loss patient undergoing a circumferential body lift.

| S-EPMC4174106 | biostudies-literature

Restrictive Transfusion Strategy Is More Effective in Massive Burns: Results of the TRIBE Multicenter Prospective Randomized Trial.

Project description:ObjectivesStudies suggest that a restrictive transfusion strategy is safe in burns, yet the efficacy of a restrictive transfusion policy in massive burn injury is uncertain. Our objective: compare outcomes between massive burn (≥60% total body surface area (TBSA) burn) and major (20-59% TBSA) burn using a restrictive or a liberal blood transfusion strategy.MethodsPatients with burns ≥20% were block randomized by age and TBSA to a restrictive (transfuse hemoglobin <7 g/dL) or liberal (transfuse hemoglobin <10 g/dL) strategy throughout hospitalization. Data collected included demographics, infections, transfusions, and outcomes.ResultsThree hundred and forty-five patients received 7,054 units blood, 2,886 in massive and 4,168 in restrictive. Patients were similar in age, TBSA, and inhalation injury. The restrictive group received less blood (45.57 ± 47.63 vs. 77.16 ± 55.0, p < 0.03 massive; 11.0 ± 16.70 vs. 16.78 ± 17.39, p < 0.001) major). In massive burn, the restrictive group had fewer ventilator days (p < 0.05). Median ICU days and LOS were lower in the restrictive group; wound healing, mortality, and infection did not differ. No significant outcome differences occurred in the major (20-59%) group (p > 0.05).ConclusionsA restrictive transfusion strategy may be beneficial in massive burns in reducing ventilator days, ICU days and blood utilization, but does not decrease infection, mortality, hospital LOS or wound healing.

| S-EPMC6430679 | biostudies-literature

Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System.

Project description:Organic farming system and sustainable management of soil pathogens aim at reducing the use of agricultural chemicals in order to improve ecosystem health. Despite the essential role of microbial communities in agro-ecosystems, we still have limited understanding of the complex response of microbial diversity and composition to organic and conventional farming systems and to alternative methods for controlling plant pathogens. In this study we assessed the microbial community structure, diversity and richness using 16S rRNA gene next generation sequences and report that conventional and organic farming systems had major influence on soil microbial diversity and community composition while the effects of the soil health treatments (sustainable alternatives for chemical control) in both farming systems were of smaller magnitude. Organically managed system increased taxonomic and phylogenetic richness, diversity and heterogeneity of the soil microbiota when compared with conventional farming system. The composition of microbial communities, but not the diversity nor heterogeneity, were altered by soil health treatments. Soil health treatments exhibited an overrepresentation of specific microbial taxa which are known to be involved in soil suppressiveness to pathogens (plant-parasitic nematodes and soil-borne fungi). Our results provide a comprehensive survey on the response of microbial communities to different agricultural systems and to soil treatments for controlling plant pathogens and give novel insights to improve the sustainability of agro-ecosystems by means of beneficial microorganisms.

| S-EPMC5209367 | biostudies-literature

T Cell Activation in Microgravity Compared to 1g (Earth's) Gravity

Project description:This study tested the hypothesis that transcription of immediate early genes is inhibited in T cells activated in microgravity (mg). Immunosuppression during spaceflight is a major barrier to safe long-term human space habitation and travel. The goals of these experiments were to prove that mg was the cause of impaired T cell activation during spaceflight as well as understand the mechanisms controlling early T cell activation. T cells from 4 human donors were stimulated with concanavalin A (ConA) and anti-CD28 onboard the International Space Station (ISS). An onboard centrifuge was used to generate a 1g simultaneous control to isolate the effects of mg from other variables of spaceflight. Microarray expression analysis after 1.5 hours of activation demonstrated that mg- and 1g-activated T cells had distinct patterns of global gene expression and identified 47 genes that were significantly differentially down-regulated in mg. Importantly, several key immediate early genes were inhibited in mg.

2012-06-21 | GSE38836 | GEO

Microbiome analysis and confocal microscopy of used kitchen sponges reveal massive colonization by Acinetobacter, Moraxella and Chryseobacterium species.

Project description:The built environment (BE) and in particular kitchen environments harbor a remarkable microbial diversity, including pathogens. We analyzed the bacterial microbiome of used kitchen sponges by 454-pyrosequencing of 16S rRNA genes and fluorescence in situ hybridization coupled with confocal laser scanning microscopy (FISH-CLSM). Pyrosequencing showed a relative dominance of Gammaproteobacteria within the sponge microbiota. Five of the ten most abundant OTUs were closely related to risk group 2 (RG2) species, previously detected in the BE and kitchen microbiome. Regular cleaning of sponges, indicated by their users, significantly affected the microbiome structure. Two of the ten dominant OTUs, closely related to the RG2-species Chryseobacterium hominis and Moraxella osloensis, showed significantly greater proportions in regularly sanitized sponges, thereby questioning such sanitation methods in a long term perspective. FISH-CLSM showed an ubiquitous distribution of bacteria within the sponge tissue, concentrating in internal cavities and on sponge surfaces, where biofilm-like structures occurred. Image analysis showed local densities of up to 5.4 * 1010 cells per cm3, and confirmed the dominance of Gammaproteobacteria. Our study stresses and visualizes the role of kitchen sponges as microbiological hot spots in the BE, with the capability to collect and spread bacteria with a probable pathogenic potential.

| S-EPMC5517580 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data