World Data Centre for Microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide

The World Data Centre for Microorganisms (WDCM) was established 50 years ago as the data center of the World Federation for Culture Collections (WFCC) Microbial Resource Center (MIRCEN). WDCM aims to provide integrated information services using big data technology for microbial resource centers and microbiologists all over the world. Here, we provide an overview of WDCM including all of its integrated services. Culture Collections Information Worldwide (CCINFO) provides metadata information on 708 culture collections from 72 countries and regions. Global Catalogue of Microorganism (GCM) gathers strain catalogue information and provides a data retrieval, analysis, and visualization system of microbial resources. Currently, GCM includes more than 368,000 strains from 103 culture collections in 43 countries and regions. Analyzer of Bioresource Citation (ABC) is a data mining tool extracting strain related publications, patents, nucleotide sequences and genome information from public data sources to form a knowledge base. Reference Strain Catalogue (RSC) maintains a database of strains listed in International Standards Organization (ISO) and other international or regional standards. RSC allocates a unique identifier to strains recommended for use in diagnosis and quality control, and hence serves as a valuable cross-platform reference. WDCM provides free access to all these services at www.wdcm.org.National High Technology Research and Development Program of China [2014AA021501, 2014AA021503, 2015AA020108]; International S&T Cooperation Program of China (ISTCP) [2015DFG32550]; Bureau of Science & Technology for Development of Chinese Academy of Sciences (Strategic bio-resources information center) and Field Cloud Project of Chinese Academy of Sciences [XXH12503-05-01]. Funding for open access charge: National High Technology Research and Development Program of China [2014AA021501, 2014AA021503, 2015AA020108]; International S&T Cooperation Program of China (ISTCP) [2015DFG32550] ; Bureau of Science & Technology for Development of Chinese Academy of Sciences [Strategic bio-resources information center]; Field Cloud Project of Chinese Academy of Sciences [XXH12503-05-01]

MycoBank gearing up for new horizons.

MycoBank, a registration system for fungi established in 2004 to capture all taxonomic novelties, acts as a coordination hub between repositories such as Index Fungorum and Fungal Names. Since January 2013, registration of fungal names is a mandatory requirement for valid publication under the International Code of Nomenclature for algae, fungi and plants (ICN). This review explains the database innovations that have been implemented over the past few years, and discusses new features such as advanced queries, registration of typification events (MBT numbers for lecto, epi- and neotypes), the multi-lingual database interface, the nomenclature discussion forum, annotation system, and web services with links to third parties. MycoBank has also introduced novel identification services, linking DNA sequence data to numerous related databases to enable intelligent search queries. Although MycoBank fills an important void for taxon registration, challenges for the future remain to improve links between taxonomic names and DNA data, and to also introduce a formal system for naming fungi known from DNA sequence data only. To further improve the quality of MycoBank data, remote access will now allow registered mycologists to act as MycoBank curators, using Citrix software

Global catalogue of microorganisms (gcm): a comprehensive database and information retrieval, analysis, and visualization system for microbial resources

Abstract Background Throughout the long history of industrial and academic research, many microbes have been isolated, characterized and preserved (whenever possible) in culture collections. With the steady accumulation in observational data of biodiversity as well as microbial sequencing data, bio-resource centers have to function as data and information repositories to serve academia, industry, and regulators on behalf of and for the general public. Hence, the World Data Centre for Microorganisms (WDCM) started to take its responsibility for constructing an effective information environment that would promote and sustain microbial research data activities, and bridge the gaps currently present within and outside the microbiology communities. Description Strain catalogue information was collected from collections by online submission. We developed tools for automatic extraction of strain numbers and species names from various sources, including Genbank, Pubmed, and SwissProt. These new tools connect strain catalogue information with the corresponding nucleotide and protein sequences, as well as to genome sequence and references citing a particular strain. All information has been processed and compiled in order to create a comprehensive database of microbial resources, and was named Global Catalogue of Microorganisms (GCM). The current version of GCM contains information of over 273,933 strains, which includes 43,436bacterial, fungal and archaea species from 52 collections in 25 countries and regions.A number of online analysis and statistical tools have been integrated, together with advanced search functions, which should greatly facilitate the exploration of the content of GCM. Conclusion A comprehensive dynamic database of microbial resources has been created, which unveils the resources preserved in culture collections especially for those whose informatics infrastructures are still under development, which should foster cumulative research, facilitating the activities of microbiologists world-wide, who work in both public and industrial research centres. This database is available from http://gcm.wfcc.info.Peer Reviewe

The global catalogue of microorganisms 10K type strain sequencing project: closing the genomic gaps for the validly published prokaryotic and fungi species

Genomic information is essential for taxonomic, phylogenetic and functional studies to comprehensively decipher the characteristics of microorganisms, to explore microbiomes through metagenomics, and to answer fundamental questions of nature and human life. However, large gaps remain in the available genomic sequencing information published for bacterial and archaeal species, and the gaps are even larger for fungal type strains. The Global Catalogue of Microorganisms (GCM) leads an internationally coordinated effort to sequence type strains and close gaps in the genomic maps of microbes. Hence, the GCM aims to promote research by deep-mining genomic data.This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (grant XDA19050301), the Bureau of International Cooperation of the Chinese Academy of Sciences (grants 153211KYSB20160029 and 153211KYSB20150010), the National Key Research Program of China (grants 2017YFC1201202, 2016YFC1201303, and 2016YFC0901702), the 13th Five-year Informatization Plan of the Chinese Academy of Sciences (grant XXH13506), and the National Science Foundation for Young Scientists of China (grant 31701157).info:eu-repo/semantics/publishedVersio

Laboratory information management system for biosafety laboratory: Safety and efficiency

Laboratory information management system (LIMS) has been widely used to facilitate laboratory activities. However, the current LIMSs do not contain functions to improve the safety of laboratory work, which is the major concern of biosafety laboratories (BSLs). With tons of biosafety information that need to be managed and an increasing number of biosafety-related research projects under way, it is worthy of expanding the current framework of LIMS and building a system that is more suitable for BSL usage. Such a system should carefully trade off between the safety and efficiency of regular lab activities, allowing the laboratory staff to conduct their research as free as possible while ensuring their and the environment’s safety. In order to achieve this goal, the information on the research contents, laboratory personnel, experimental materials and experimental equipment need to be well collected and fully utilized by a centralized system and its databases

Preeclampsia in twin pregnancies: association with selective intrauterine growth restriction

<p><i>Objective</i>: To identify the association between preeclampsia (PE) and selective intrauterine growth restriction (sIUGR) in twin pregnancies.</p> <p><i>Methods</i>: This was a retrospective cohort study of 1004 twin pregnancies from 2008 to 2014. We specifically compared the incidence, clinical characteristics and outcomes of PE between sIUGR and normal-growth twin pregnancies.</p> <p><i>Results</i>: PE occurred more frequently in sIUGR pregnancies [29.0% (51/176)] than in normal-growth twin pregnancies [13.1% (99/756), <i>p</i> < 0.001, adjusted odds ratio 3.29]. Among sIUGR, the incidence of PE was significantly higher in dichorionic (DC) pregnancies (37.5%, 30/80) than in monochorionic (MC) pregnancies (21.9%, 21/96). The rates of onset at <32 weeks (<i>p</i> = 0.045) and of severe PE (<i>p</i> = 0.025) were higher in sIUGR pregnancies with PE. The systolic blood pressure was also higher in sIUGR pregnancies with PE (152.6 ± 11.8 mmHg) than in normal-growth pregnancies with PE (148.0 ± 8.2 mmHg) (<i>p</i> = 0.042). Additionally, more sIUGR pregnancies were delivered at 32–36 weeks (<i>p</i> = 0.001), and fewer were delivered at ≥36 weeks (<i>p</i> < 0.001). Moreover, the prevalence of severe neonatal asphyxia was higher in sIUGR pregnancies with PE than in normal-growth pregnancies with PE (8.8% versus 2.5%, <i>p</i> = 0.020).</p> <p><i>Conclusions</i>: sIUGR is associated with increased odds of developing severe PE in twin pregnancies, leading to poorer perinatal outcomes.</p

Web Resources for Microbial Data

There are multitudes of web resources that are quite useful for the microbial scientific research community. Here, we provide a brief introduction on some of the most notable microbial web resources and an evaluation of them based upon our own user experience

Optimizing ex vivo culture conditions to study human gut microbiome

Abstract The inter-individual variations of gut microbiome contribute to the different responses toward drug therapy among populations, developing a reliable ex vivo culture method for mixed bacteria is the urgent need for predicting personal reaction to drug therapy. Unfortunately, very few attentions have been paid to the bias that could be introduced during the culture process for mixed bacteria. Here we systemically evaluated the factors that may affect the outcomes of cultured bacteria from human feces. We demonstrated that inter-individual difference of host gut microbiome was the main factor affecting the outcomes of cultured bacteria, followed by the culture medium and time point. We further optimized a new medium termed GB based on our established multi-dimensional evaluation method, which could mimic the status of in situ host gut microbiome to the highest extent. Finally, we assessed the inter-individual metabolism by host gut microbiome from 10 donors on three frequently used clinical drugs (aspirin, levodopa and doxifluridine) based on the optimized GB medium. Our results revealed obvious variation in drug metabolism by microbiome from different donors, especially levodopa and doxifluridine. This work suggested the optimized culture medium had the potential for exploring the inter-individual impacts of host gut microbiome on drug metabolism