International Union Of Microbiological Societies Research Articles

A scientist and a world-class personality: Nikolai Petrovich Elinov (1928–2017)

The essay is dedicated to Nikolai Petrovich Elinov, an eminent scientist with a global reputation, who has made a substantial contribution to the development of medical microbiology, mycology, and biotechnology in the Russian Federation. N. P. Elinov is a professor, Doctor of Biological Sciences, Honored Scientist of the RSFSR, and rector of the Leningrad Chemical-Pharmaceutical Institute. He is an active member of the St. Petersburg Engineering Academy and the New York Academy of Sciences, author of 10 textbooks, 8 handbooks, 10 monographs, over 400 articles in domestic and foreign journals, and holds 70 patents for inventions. Professor N. P. Elinov is widely recognized in the scientific community for his work in areas such as biology of aposporous yeast, chemistry and biotechnology of microbial polysaccharides, and others. He has established a school of students and followers, including 50 candidates and 9 Doctors of Science. Under his guidance, the microbiology department laid the foundations for engineering and microbiological training of specialists. As the rector of LCFI, Nikolai Petrovich contributed to the organization of the country’s only faculty for training biotechnology engineers, leading the university to top positions in preparing specialists for the pharmaceutical industry. In 1968, Nikolai Petrovich became a member of the International Commission on Yeast Organisms of the International Union of Microbiological Societies. His name was included in the book “2000 Outstanding Scientists of the Late 20th Century” (1998) by the Cambridge International Biographical Center (UK), where he was recognized as a specialist in microbiology and biotechnology. This essay, based on archival materials, publications, articles, and colleagues’ memories, reveals the key milestones in the life and scientific achievements of Nikolai Petrovich Elinov.

Recent trend, biases and limitations of cultivation-based diversity studies of microbes.

The current study attempts to analyze recent trends, biases and limitations of cultivation-based microbial diversity studies based on published, novel species in the past 6 years in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), an official publication of the International Committee on Systematics of Prokaryotes (ICSP) and the Bacteriology and Applied Microbiology (BAM) Division of the International Union of Microbiological Societies (IUMS). IJSEM deals with taxa that have validly published names under the International Code of Nomenclature of Prokaryotes (ICNP). All the relevant publications from the last 6 years were retrieved, sorted and analyzed to get the answers to What is the current rate of novel species description? Which country has contributed substantially and which phyla represented better in culturable diversity studies? What are the current limitations? Published data for the past 6 years indicate that 500-900 novel species are reported annually. China, Korea, Germany, UK, India and the USA are at the forefront while contributions from other nations are meager. Despite the recent development in culturomics tools the dominance of Proteobacteria, Bacteroidetes and Actinobacteria are still prevalent in cultivation, while the representation of archaea, obligate anaerobes, microaerophiles, synergistic symbionts, aerotolerant and other fastidious microbes is poor. Single strain-based taxonomic descriptions prevail and emphasis on objective-based cultivation for biotechnological and environmental significance is not yet conspicuous.

Microbial Taxonomy Run Amok.

DNA sequencing has led to an explosion in discovery of microbial phylogenetic novelty, especially that represented by uncultivated taxa, to which the traditional system of prokaryotic taxonomy has not adapted. A lack of expansion of the International Code of Nomenclature of Prokaryotes (ICNP, 'the Code') to effectively capture this information has created a 'wild west' situation where names are published or appear in popular reference databases without further verification or validation. The rapid propagation of variant and questionable naming methods has led to widespread confusion and undermines prior accomplishments. We exemplify inconsistencies that have arisen from this practice and endanger the interoperability of scientific findings. The immediate solution to this problem is to develop and adopt universal best practices that are accepted by expert researchers, major publishers, the International Committee on Systematics of Prokaryotes (ICSP), and international microbiological societies.

A machine-compiled microbial supertree from figure-mining thousands of papers

Background There is a huge diversity of microbial taxa, the majority of which have yet to be fully characterized or described. Plant, animal and fungal taxa are formally named and described in numerous vehicles. For prokaryotes, by constrast, all new validly described taxa appear in just one repository: the International Journal of Systematics and Evolutionary Microbiology (IJSEM). This is the official journal of record for bacterial names of the International Committee on Systematics of Prokaryotes (ICSP) of the International Union of Microbiological Societies (IUMS). It also covers the systematics of yeasts. This makes IJSEM an excellent candidate against which to test systems for the automated and semi-automated synthesis of published phylogenies. New information In this paper we apply computer vision techniques to automatically convert phylogenetic tree figure images from IJSEM back into re-usable, computable, phylogenetic data in the form of Newick strings and NEXML. Furthermore, we go on to use the extracted phylogenetic data to compute a formal phylogenetic MRP supertree synthesis, and we compare this to previous hypotheses of taxon relationships given by NCBI’s standard taxonomy tree. This is the world’s first attempt at automated supertree construction using data exclusively extracted by machines from published figure images. Additionally we reflect on how recent changes to UK copyright law have enabled this project to go ahead without requiring permission from copyright holders, and the related challenges and limitations of doing research on copyright-restricted material.

Strained fermented milks – A review of existing legislative provisions, survey of nutritional labelling of commercial products in selected markets and terminology of products in some selected countries

A survey of the information contained in the labels of 109 commercial concentrated fermented milks from the Eastern Mediterranean, Australasia, the United Kingdom, Ireland, the United States of America and Canada plus Skyr (from Iceland), Ymer (from Denmark) and Chakka (from India) was carried out in late 2012 and early 2013. There were substantial differences in composition. The carbohydrate, fat and protein contents ranged between 1–12, 0–20 and 3.3–11 g/100 g, respectively. Considering the compositional data of the product and existing legislative provisions, a typical strained product should have a protein content of ≥8 g/100 and ~5 g/100 g of carbohydrates, and it would be appropriate to name such products as ‘strained yoghurt’, ‘Greek strained yoghurt’ and/or ‘Labneh’. A higher content of carbohydrate would suggest that the product was made using the product formulation method (i.e. without straining the fermentate), or the milk base had been fortified with skimmed milk before straining the fermentate to enhance the yield of the product, and such products should be known, for example, as ‘Greek‐style yoghurt’. It was also observed in some of the samples that the nomenclature of the starter cultures did not conform to recommendations of the International Union of Microbiological Societies (IUMS). Manufacturers could address such issues to minimise consumer confusion.

Recently agreed changes to the International Code of Virus Classification and Nomenclature

The International Committee on Taxonomy of Viruses (ICTV; http://www.ictvonline.org/) is a committee of Virology Division of the International Union of Microbiological Societies, and its operation is governed by Statutes agreed with Virology Division. The classification and nomenclature of viruses is then subject to rules formalized into a Code (required by Statute 8.1). The need for a review of the Statutes and Code became clear during editorial work involved in production of the Ninth ICTV Report [1]. Changes to these documents require the approval of the ICTV Executive Committee (EC) and the full ICTV membership. Changes to the Statutes also require the agreement of Virology Division. The changes described in this article were discussed and agreed by the ICTV EC over a period of more than two years. Notification of a ballot was sent via email on 14 January 2013 to the 165 members of ICTV, namely the ICTV EC Members, Life Members, ICTV Subcommittee Members and ICTV National Representatives. Members were then requested to vote on whether or not to ratify the proposals (voting closed on 14 February 2013). The return rate of votes was approximately 41%, and all proposed changes were accepted, mostly unanimously. The only significant exception was the proposed change to the species definition in Rule 3.21 (Rule 3.20 in the latest version of the code) which was approved by 45:21 with two abstentions. In this article, we present the new version of the Code, highlighted in bold to show those parts that have recently been changed. Those changes are then explained in the sections that follow. It should be noted that some rules were deleted and that some renumbering of sections has therefore taken place. In recent years, the Code has been published with some explanatory Comments from the EC, and the opportunity has been taken to revise and update these where necessary. The changes to the Statutes are the subject of a separate article [2].

Recently agreed changes to the Statutes of the International Committee on Taxonomy of Viruses

The International Committee on Taxonomy of Viruses (ICTV; http://www.ictvonline.org/) is a committee of Virology Division of the International Union of Microbiological Societies, and its operation is governed by Statutes agreed with Virology Division. The classification and nomenclature of viruses is then subject to rules formalized into a Code (required by Statute 8.1). The need for a review of the Statutes and Code became clear during editorial work involved in production of the Ninth ICTV Report [1]. Changes to these documents require the approval of the ICTV Executive Committee (EC) and the full ICTV membership. Changes to the Statutes also require the agreement of Virology Division. The changes to the Statutes described in this article were discussed and agreed by the ICTV EC over a period of more than two years. Many of these changes are relatively minor adaptations and clarifications. Notification of a ballot was sent via email on 14 January 2013 to the 165 members of ICTV, namely the ICTV EC Members, Life Members, ICTV Subcommittee Members and ICTV National Representatives. Members were then requested to vote on whether or not to ratify the proposals (voting closed on 14 February 2013). The return rate of votes was approximately 41 %, and all proposed changes were accepted unanimously. The proposed changes to the Statutes were then submitted to Virology Division and were approved unanimously by the Advisory Board and Executive Committee on 19 April 2013. In this article, we present the new version of the Statutes, highlighted in bold to show those parts that have recently been changed. Those changes are then explained in the sections that follow. The changes to the Code are the subject of a separate article [2].

アメリカのバイオテクノロジーの父は日本人だった

アメリカのバイオテクノロジーの父は日本人だった

World Federation for Culture Collections: professionals underpinning microbial systematics

The World Federation for Culture Collections (WFCC) is a multidisciplinary commission of the International Union of Biological Sciences (IUBS) and a Federation within the International Union of Microbiological Societies (IUMS). The WFCC is concerned with the collection, authentication, maintenance and distribution of cultures of microorganisms and cultured cells. Its aim is to promote and support the establishment of culture collections and related services, to provide liaison and networking between the collections and their users, to organise workshops and conferences, publications and newsletters and work to ensure the long-term perpetuation of important collections.

Report from the 40th meeting of the Executive Committee of the International Committee of Taxonomy of Viruses

The Executive Committee (EC) of the International Committee on Taxonomy of Viruses (ICTV) held its 40th meeting at the Istanbul Convention and Exhibition Centre in Istanbul, Turkey, from August 7 to 9, 2008. This was just prior to the XIV International Congress of Virology (ICV), part of the joint meeting organized by the International Union of Microbiological Societies (IUMS), also in Istanbul, Turkey, from August 11 to 15, 2008. Most of the EC meeting was concerned with the discussion of taxonomic proposals. This communication reports the principal items of business discussed at the meeting.

Modulation of the Structure, Catalytic Activity, and Fidelity of African Swine Fever Virus DNA Polymerase X by a Reversible Disulfide Switch

African swine fever virus polymerase X (pol X) is the smallest DNA polymerase known (174 amino acids), and its tertiary structure resembles the C-terminal half of prototypical X-family pol beta, which includes a catalytic dNTP-binding site (palm domain) and a finger domain. This structural similarity and the presence of viral genes coding for other base excision repair proteins suggest that pol X functions in a manner similar to pol beta, but inconsistencies concerning pol X catalysis have been reported. We examined the structural and functional properties of two forms of pol X using spectroscopic and kinetic analysis. Using (1)H-(15)N correlated NMR, we unambiguously demonstrated the slow interconversion of pol X between a reduced (pol X(red)) and an oxidized form (pol X(ox)), confirmed by mass spectrometry. Steady-state kinetic analysis revealed that pol X(ox), with a disulfide bond between Cys-81 and Cys-86, has approximately 10-fold lower fidelity than pol X(red) during dNTP insertion opposite a template G. The disulfide linkage is located between two beta-strands in the palm domain, near the putative dNTP-binding site. Structural alignment of pol X with a pol beta ternary structure suggests that the disulfide switch may modulate fidelity by altering the ability of the palm domain to align and stabilize the primer terminus and catalytic metal ion for deprotonation of the 3'-OH group and subsequent phosphoryl transfer. Thus, DNA polymerase fidelity is altered by the redox state of the enzyme and its related conformational changes.

Alcoholic fermentation: beverages to biofuel

The history of yeast association with human society is synonymous with the production of alcoholic beverages such as wine and beer, and the scientific discovery by Louis Pasteur, some 150 years ago, that yeasts such as Saccharomyces cerevisiae metabolize sugars into ethanol. Today, the production of alcoholic beverages is a massive, globalized industry that exploits ongoing advances in knowledge about the ecology, biochemistry, physiology and molecular biology of yeasts. Recent concerns about the sustainability of world energy derived from fossil fuels and the associated impacts of climate change have focused attention on ethanol as an alternative or additional energy source, and its production by yeasts as a biofuel. With this background, the International Commission on Yeasts hosted the 26th International Specialized Symposium on Yeasts (ISSY26) with the theme –‘From alcoholic beverages to bioethanol for transportation: a new challenge for fermenting yeast.’ The International Commission on Yeasts is a commission within the Mycology Division of the International Union of Microbiological Societies (IUMS, http://www.iums.org) that hosts general congresses on yeasts every four years and specialized symposia on yeasts every other year. ISSY26 was held at Sorrento, Italy, June 3–7, 2007. This thematic edition of FEMS Yeast Research brings together a selection of 20 articles comprising MiniReviews and research papers that …

The Eleventh International Congress of Mycology of the International Union of Microbiological Societies, San Francisco, California, 23–28 July 2005

The International Union of Microbiological Societies has three divisions – Bacteriology and Applied Microbiology, Mycology and Virology – which come together every 3 years for the organization of their international congresses. In 2005, the American Society for Microbiology hosted these congresses in San Francisco. Yeasts fall within the Division of Mycology and this report covers the numerous contributions on yeasts to the Mycology Congress. Overall, about 3000 registrants attended the combined Congresses, with about 275 delegates focussing on Mycology. The Mycology program was organized into plenary, symposium and poster sessions under the themes of Development, Evolution, Ecology, Medical Mycology and Industrial Mycology. Contributions on yeasts were represented throughout these themes. The application of genomics was prominent in most presentations and has emerged as a fundamental tool to study and understand yeast evolution, phylogeny, ecological adaptation, physiology, structural development, mechanisms of pathogenesis and epidemiology. Under the impact of genomic analyses, the traditional research boundaries between yeasts and filamentous fungi are beginning to blur, and an increasing number of fungal biologists are now working in …

Biological Information Standards

Biological Information Standards

Viruses in and out

A report on the twelfth Congress of Virology, part of 'The world of microbes', the joint meeting of the three divisions of the International Union of Microbiological Societies, Paris, France, 27 July to 1 August 2002

Nomenclature of major antimicrobial-resistant clones of Streptococcus pneumoniae defined by the pneumococcal molecular epidemiology network.

The emergence of disease caused by penicillin-resistant and multidrug-resistant pneumococci has become a global concern, necessitating the identification of the epidemiological spread of such strains. The Pneumococcal Molecular Epidemiology Network was established in 1997 under the auspices of the International Union of Microbiological Societies with the aim of characterizing, standardizing, naming, and classifying antimicrobial agent-resistant pneumococcal clones. Here we describe the nomenclature for 16 pneumococcal clones that have contributed to the increase in antimicrobial resistance worldwide. Guidelines for the recognition of these clones using molecular typing procedures (pulsed-field gel electrophoresis, BOX-PCR, and multilocus sequence typing) are presented, as are the penicillin-binding profiles and macrolide resistance determinants for the 16 clones. This network can serve as a prototype for the collaboration of scientists in identifying clones of important human pathogens and as a model for the development of other networks.

The Tenth International Symposium on Yeasts (ISY 2000). "The rising power of yeasts in science and industry".

The Tenth International Symposium on Yeasts was held at Papendal, Arnhem, The Netherlands, during 27 August–1 September 2000. It was organized by Hans van Dijken (chair), Lex Scheffers (secretary), Pieter de Geus, Wendell Iverson and Ria Komen-Zimmerman under the auspices of The Netherlands Foundation for Biotechnology and the Delft University of Technology, on behalf of the International Commission for Yeasts (ICY). The ICY is affiliated with the International Union of Microbiological Societies (IUMS) through its Mycology Division, and was established in 1966. Its mission is to promote international interest and collaboration on yeasts through the organisation of two series of symposia. The first of the series are the International Symposia on Yeasts (ISY) which are held every four years and focus on all aspects of yeast biology and technology (e. g. ISY 2000). The second series, the International Specialized Symposia on Yeasts (ISSY) are held every year between the ISY and focus on more specific topics. So far, the ICY has commissioned the organization of 10 ISY and 20 ISSY, which have been held in a range of countries. This Tenth International Symposium on Yeasts attracted some 400 registrants from 40 countries. The scientific program was introduced by 12 plenary lectures that provided the foundations for several thematic sessions, and covered the broad spectrum of interest in yeast research. In all, 107 oral presentations and 165 poster displays were delivered during the 41/2 days of meeting. Some highlights of the program are presented in the following sections. Functional genomic analysis . Stephen Oliver started the scientific program with a plenary paper that described a systematic analytical approach, through EUROFAN, to determine the function of the 6000 open reading frames in Saccharomyces cerevisiae . This was followed by presentations that described the genomics of regulatory networks, transporters, cell wall chitin production, …

The current state of plant virus taxonomy

The current state of plant virus taxonomy

Address by the representative of the “International Union of Microbiological Societies”, IUMS, and the “International Committee on Food Microbiology”, ICFMH, to the “World Conference on Science” (WCS), Budapest, Hungary, 26 June–1 July 1999.

Address by the representative of the “International Union of Microbiological Societies”, IUMS, and the “International Committee on Food Microbiology”, ICFMH, to the “World Conference on Science” (WCS), Budapest, Hungary, 26 June–1 July 1999.

Quality control of culture media — perspectives and problems

The Working Party on Culture Media (WPCM) of the International Union of Microbiological Societies (IUMS) has promoted and facilitated the development of methods for quality control of culture media used for the detection and enumeration of food-borne microorganisms since the early 1980s. While progress has been made in establishing protocols to test for productivity and selectivity of media, problems associated with the influence of food constituents and background microflora, as well as the presence of sublethally injured cells in test foods, are yet to be fully addressed before optimum methods for assessing the quality of media can be defined. However, for various reasons, the development of standardised procedures which account for the influence of food constituents or state of debilitation of target microorganisms may not be practical or even desirable.