Contextual data collected concurrently with molecular samples are critical to the use of metagenomics in the fields of marine biodiversity, bioinformatics and biotechnology. We present here Marine Microbial Biodiversity, Bioinformatics and Biotechnology (M2B3) standards for "Reporting" and "Serving" data. The M2B3 Reporting Standard (1) describes minimal mandatory and recommended contextual information for a marine microbial sample obtained in the epipelagic zone, (2) includes meaningful information for researchers in the oceanographic, biodiversity and molecular disciplines, and (3) can easily be adopted by any marine laboratory with minimum sampling resources. The M2B3 Service Standard defines a software interface through which these data can be discovered and explored in data repositories. The M2B3 Standards were developed by the European project Micro B3, funded under 7(th) Framework Programme "Ocean of Tomorrow", and were first used with the Ocean Sampling Day initiative. We believe that these standards have value in broader marine science.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4511511 | PMC |
| http://dx.doi.org/10.1186/s40793-015-0001-5 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Interaction with refuse piles is associated with co-occurrence of core gut microbiota in workers of the ant Aphaenogaster picea.
Access Microbiol
January 2025
Department of Biological Sciences, The George Washington University, Washington DC 20052, USA.
Comparing the diversity of gut microbiota between and within social insect colonies can illustrate interactions between bacterial community composition and host behaviour. In many eusocial insect species, different workers exhibit different task behaviours. Evidence of compositional differences between core microbiota in different worker types could suggest a microbial association with the division of labour among workers.
View Article and Find Full Text PDFNon-coding RNAs and regulatory networks involved in the Ameson portunus (Microsporidia)-Portunus trituberculatus interaction.
Fish Shellfish Immunol
January 2025
The Laboratory of Aquatic Parasitology and Microbial Resources, School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266237, China. Electronic address:
Ameson portunus, the causative agent of "toothpaste disease" in Portunus trituberculatus and "slurry-like syndrome" in Scylla paramamosain, has resulted in considerable economic losses in the marine crab aquaculture industry in China. Practical control strategies are yet unavailable. Non-coding RNAs (ncRNAs) are crucial components of gene regulation of intracellular parasites, however, their roles in regulating the microsporidia-host interaction remain limited.
View Article and Find Full Text PDFFlavobacterium plantiphilum sp. nov., Flavobacterium rhizophilum sp. nov., Flavobacterium rhizosphaerae sp. nov., Chryseobacterium terrae sp. nov., and Sphingomonas plantiphila sp. nov. isolated from salty soil showing plant growth promoting potential.
Syst Appl Microbiol
January 2025
Marine Microbiology Group (MMG), Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
Members of the genera Flavobacterium, Chryseobacterium and Sphingomonas constitute a group of microorganisms in the rhizosphere associated with plant growth promoting (PGP) features. A polyphasic approach was employed to ascertain the taxonomic status of five selected strains. Overall genome relatedness indices of digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) between the strains and the other members of the genera Flavobacterium, Chryseobacterium and Sphingomonas were found to be below the established thresholds, respectively.
View Article and Find Full Text PDFConformational dynamics of a multienzyme complex in anaerobic carbon fixation.
Science
January 2025
Redox and Metalloprotein Research Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
In the ancient microbial Wood-Ljungdahl pathway, carbon dioxide (CO) is fixed in a multistep process that ends with acetyl-coenzyme A (acetyl-CoA) synthesis at the bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS). In this work, we present structural snapshots of the CODH/ACS from the gas-converting acetogen , characterizing the molecular choreography of the overall reaction, including electron transfer to the CODH for CO reduction, methyl transfer from the corrinoid iron-sulfur protein (CoFeSP) partner to the ACS active site, and acetyl-CoA production. Unlike CODH, the multidomain ACS undergoes large conformational changes to form an internal connection to the CODH active site, accommodate the CoFeSP for methyl transfer, and protect the reaction intermediates.
View Article and Find Full Text PDFPatterns of microbial contamination on Northumberland Strait shores.
PLoS One
January 2025
Department of Biology, Mount Allison University, Sackville, NB, Canada.
The re-emergence of episodic faecal contamination of Parlee and Murray Corner beaches, on the Northumberland Strait of New Brunswick, Canada, in 2017, raised renewed community concerns on the health, environmental and tourism sustainability of these community resources, and led to creation of an Integrated Watershed Management Plan for the Shediac Bay Watershed (October 2021). In response we have to date compiled, curated and made accessible 205,772 microbial water quality data records spanning over 80 years from Southeastern New Brunswick and the Northumberland Strait. This dataset derives in large part from Shellfish Surveys completed by Environment and Climate Change Canada, along with data generated by multiple government agencies, Non-Governmental Organizations and citizen science sources.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!