The content of The Bulletin of BISMiS is restricted to mini-review articles, opinion articles, reports, biographies, autobiographies (by invitation), educational articles, obituaries and letters to the editor that pertain to the subject of microbial systematics and items of interest to members of BISMiS. The Bulletin of BISMiS does not publish original research articles.

• Editor: Paul A. Lawson, e-mail: paul.lawson at ou.edu
• Director of the Editorial Office: William B. Whitman
• Editorial Board Members: Hans-Jurgen Busse, Jongsik Chun, Paul De Vos, Brian P. Hedlund, Peter Kampfer, Wen-Jun Li, Wolfgang Ludwig, Bruce J. Paster, Fred A. Rainey, Ken-ichiro Suzuki, Martha E. Tujillo, William G. Wade, Naomi L. Ward and William B. Whitman, Li-Xin Zhang
• Managing Editor: Aidan C. Parte

Click here for Tables of Contents and abstracts, and for complete issues after the 6-month member-only embargo.

The format of articles and style of references to be submitted to the The Bulletin of BISMiS is the same as that for Bergey's Manual publications - see the Instructions for Authors. All articles must include a list of key words or phrases. Specific information for each of the types of articles is provided below. Articles should be submitted by email to the Editor, James T. Staley, or Associate Editor Paul Lawson.

Figures, which may be in color, and tables are welcome and should follow guidelines for Bergey's Manual Instructions for Authors.

Mini-reviews Mini-reviews may be submitted on any subject that pertains to microbial systematics. They are limited to 5000 words including references. Figures and tables are welcome and should follow guidelines for Bergey's Manual Instructions for Authors.

Opinion articles Opinion articles will be considered on any topic that is of relevance to microbial systematics. These are limited to 5000 words including references. Figures and tables are welcome and should follow guidelines for Bergey's Manual Instructions for Authors.

Reports Reports of microbial taxonomic committees and subcommittees can be published. These should be limited to no more than 5000 words plus references.

Resources for Microbial Systematics This section provides information on culture collections, databases and other non-commercial resources that are of interest to the field. Before submitting an article for this section, please contact the Editor. Figures and tables are welcome and should follow guidelines for the instructions for Bergey's Manual. Length should be less than 5,000 words.

Biographies Biographies may be submitted that describe the life of a scientist who has made significant contributions to the systematics of Bacteria and Archaea or to someone for whom a species or other taxon has been named. Biographies are limited to 3000 words or less and ideally should include at least one photograph of the individual.

Autobiographies (by invitation only) Autobiographies of noted microbial taxonomists or of scientists who have made major contributions in an allied field such as a curator of a culture collection or a contributor to microbial bioinformatics will be invited. These articles should include a summary of the scientist's personal background (birth date, location, nationality, etc), motivation for becoming a scientist, education, positions of employment and contributions to the field of microbial systematics. These articles should be accompanied by at least two photographs of the individual and are limited to 15,000 words plus references. One photograph may be an informal pose perhaps showing the subject while involved in a scientific activity. Another could be a more recent or more formal photograph of the individual. Other photographs showing colleagues, mentors, students or family members are also welcome.

Obituaries Obituaries are welcome for those who have made significant contributions to microbial systematics or an allied field that has a direct impact on microbial systematics. At least one photograph of the scientist should be included. Articles are limited to 3000 words or less.

Abstracts, where published, are given below. Full content will be freely available to non-members of BISMiS 6 months after publication.

Volume 1, issue 1 - December 2010 - download here

Preface

Comprehending microbial diversity: the fourth goal of microbial taxonomy
James T. Staley

The primary goals of microbial taxonomy are Nomenclature, Classification and Identification. This paper proposes that a fourth goal, Comprehending Microbial Diversity, be included along with these three traditional objectives of bacterial and archaeal taxonomy. There are two major reasons for this. First, microbiologists have only recently begun to recognize that a vast, unknown diversity of microbial life exists on Earth. Therefore, there are many thousands or perhaps millions of species of Bacteria and Archaea that have not yet been discovered, cultivated and named. The second reason is that microbiologists are still debating the meaning of what comprises a bacterial species. Evidence from molecular analyses indicates that the current bacterial species is much broader than that of plants and animals therefore suggesting that many more microbial species, at levels below that of the current species, are not yet recognized. For this reason, microbiologists are encouraged to work with botanists and zoologists to develop a universal species concept that would unify biology and make the species taxon more uniform. This paper discusses these areas, the study of which will lead to a fuller and better comprehension of the true diversity of microbial life. Bergey's International Society for Microbial Systematics is an organization that will enhance the ability of the global community of microbiologists to work together to more fully comprehend the full extent of Earth's microbial diversity. Join BISMiS for full access all issues of The Bulletin. Please Log-in

Opinion

The importance of phenotype for bacterial systematics
Peter Kampfer

Over the last 30 years, the characterization and identification of prokaryotes has undergone a dramatic change. Nowadays, the first step in characterization is often the determination of the 16S rRNA gene sequence. Based on a computer-generated comparison of the 16S rRNA gene sequence with sequences from reference strains, it is possible to allocate an unknown to a taxonomic group, often to a genus, rarely to a species. Isolates, which may represent novel taxa (genera or species) are then further characterized in order to find additional markers which are different from those reported for already established taxa. In several cases, only a very restricted set of phenotypic differences is reported and hence the classification of novel taxa is based largely on the 16S rRNA gene sequence differences. Sometimes additional (housekeeping) gene sequence differences are also reported, which may be regarded as sufficient for the delineation of novel species or even genera. There is a current trend to delineate bacterial taxa more and more on the basis of the genotype. But only the phenotype shows what genetic information is expressed and hence the phenotype represents an additional important level of information. In the case of a strain or set of strains which may represent novel taxa, it is therefore still essential that they are characterized both genotypically and phenotypically as comprehensively as possible. Only the interplay between genetic and phenotypic data sets may provide a basis for an in-depth taxonomy of the prokaryotes. Join BISMiS for full access all issues of The Bulletin. Please Log-in

Review

Description of new yeast species - is one strain enough?
Cletus P. Kurtzman

The issue of description of new yeast species on the basis of a single strain is discussed. Single gene sequences, such as those from D1/D2 LSU rRNA, or sequences from ITS1/ITS2 are commonly used as the basis for recognizing new yeast species. Evidence is presented that hybrids and species with polymorphic gene sequences may not be recognized from a single gene analysis, but with multigene sequence comparisons, single-strain species can be accurately determined. Further, description of single-strain species will add to an understanding of yeast phylogeny and species diversity, which would be unknown if new species descriptions were limited to those taxa for which multiple strains were available. Join BISMiS for full access all issues of The Bulletin. Please Log-in

Report

Nomenclature of the Cyanobacteria/Cyanophyta - current problems and proposed solutions
Aharon Oren and Jiri Komarek

This paper presents a report on the roundtable discussion on nomenclature of Cyanobacteria/Cyanophyta that took place on 16 August 2010 during the 18th Symposium of the IAC in Ceske Budejovice, Czech Republic. It highlights the current problems with the dual nomenclature system that have emerged as new taxa of Cyanobacteria/Cyanophyta can be named under the rules of the International Code of Botanical Nomenclature or the International Code of Nomenclature of Prokaryotes. The report presents updates about the current attempts to harmonize the nomenclature of the Cyanobacteria/Cyanophyta under the two Codes. Join BISMiS for full access all issues of The Bulletin. Please Log-in

Autobiographies

Reminiscences and reflections
Don J. Brenner

Bergey's and me
John G. Holt

A life with some strange twists (mostly helical)
Noel R. Krieg

Reflections on microbial systematics
Peter H.A. Sneath



Volume 2, issue 1 - July 2011 - download here

Opinion

Recommendations for a new bacterial species description based on analyses of the unrelated genera Aeromonas and Arcobacter
María José Figueras, Roxana Beaz-Hidalgo, Luis Collado and Antonio Martínez-Murcia

Assigning a strain or a group of strains to a new bacterial species and describing it formally requires at least its phenotypic characterization in order to establish its distinctiveness from existing species and 16S rRNA gene sequences and DNA�NA reassociation results with closely related species (classically those with 16S rRNA similarities >97%). More recently Multilocus Sequence Analysis (MLSA) has been proposed as a potential alternative for DNA hybridization. These are common requirements for species in all genera, irrespective of how different they are. In the present study, the advantages and disadvantages of each of these requirements is reviewed and analyzed using two unrelated bacterial genera Aeromonas (Gammaproteobacteria) and Arcobacter (Epsilonproteobacteria) as models with some additional examples from their close neighbors Vibrio and Campylobacter. The genus Aeromonas, defined in 1943, is considered to have a complex taxonomy because it includes a tight group of species (and several subspecies) with 16S rRNA gene similarities ranging from 96.9 to 100%, some of which have required reclassification. In contrast, the genus Arcobacter, was defined 20 years ago (1991) from members of the genus Campylobacter, and the presently known species show 16S rRNA gene similarities ranging from 92.1 to 98.9%, and none of the species have required reclassification. Therefore, while the similarity of the 16S rRNA gene cannot be used to delineate closely related species of Aeromonas, this is still an excellent tool for Arcobacter, something that may change in the near future with the addition of new species. Several specific topics are discussed, such as the number of isolates needed to define a new bacterial species, the molecular approaches used for recognizing new species and the procedure for validly publishing a new species name. In addition, the need for developing genus-specific guidelines for describing new bacterial species, recommendations for avoiding common errors in the laboratory, and a species definition for prokaryotes in the 21st century are pre- sented. Emphasis is placed on the two factors that govern the proper description of new bacterial spe- cies, the precision of the performance of experimental work and the correct interpretation of results. Join BISMiS for full access all issues of The Bulletin. Please Log-in

What is a bacterial species? I will know it when I see it
Micah I. Krichevsky

An objective definition of bacterial species does not exist. Starting from operational descriptions of the concepts of isolate, strain, and species, the process of building a species description depends on three subjective decisions: (1) the spectrum of individual isolates to be used to construct the species description, (2) the methods used to characterize the isolates, and (3) the computational (or subjective) method(s) used to build the species description. The discussion that follows describes the subjective aspects of the three decision components. The resulting species description has a component of uncertainty. By analogy with quantum mechanics, the methods used to describe and define a species affect the perceived position of the species in the biological universe. Biologists have evolved ad hoc strategies to cope with this uncertainty. Foremost among the strategies is the allowance of competing taxonomies in the rules of nomenclature (except in virology). No judicial mechanisms exist for deciding on the scientific merits of the use of a taxon name other than the opinion of the user. The user must choose a taxonomic framework to organize thought and communicate. As a practical matter, communication does not require the use of species designations. Communication of specific attributes of isolates or strains are necessary and sufficient. In other cases, the communication is at a higher taxonomic level. Join BISMiS for full access all issues of The Bulletin. Please Log-in

Report

Report of the Inaugural Meeting of Bergey's International Society for Microbial
Systematics in Beijing, China, 19-23 May 2011

The meeting was held at the Friendship Hotel in Beijing. The Opening Ceremony began in Ju Ying Hall of the Friendship Palace of the hotel in the afternoon and evening of May 19. Several of the brief welcoming talks and the closing talk are provided verbatim to provide a written record of this historical meeting. Join BISMiS for full access all issues of The Bulletin. Please Log-in

Autobiographies

Microbial systematics, “weaving threads into cloth”
Kazuo Komagata

My career as a curator of microbial cultures
Tian-shen Tao



Volume 2, issue 2 - December 2011 - download here

Review

A century of systematics of the genus Bacteroides: from a single genus up to the 1980s to an explosion of assemblages and the dawn of MALDI-TOF-Mass Spectrometry
Haroun N. Shah and Saheer E. Gharbia

The genus “Bacteroides” comprises the predominant group of micro-organism of the alimentary tract where they coexist to the mutual benefit of the host. Recent studies of the human gut microbiome is revealing the emergence of universal dominant clusters (or enterotypes) of which Bacteroides, Prevotella and Ruminococus are the dominant enterotypes (Arumugam et al., 2011). Perturbations in the local habitat are believed to trigger their translocation to new sites from where they cause numerous infections. The original “Bacteroides”* species were studied extensively in the rumen for nearly half a century and much of the fundamental science including anaerobic techniques were emulated to study infections in man (see e.g. Hungate, 1966). Today their physiological functions and significance are intensively studied in parallel with their phylogenetic relationships (see e.g. Karlsson et al., 2011) but this would not have been possible without painstaking work on their systematics from the mid-1970s. Once their heterogeneity had been ordered into coherent groups of species, more focused studies became possible and with the current interest in the human microbiome, their functional roles in vivo are becoming clearer. However, many taxa are non-fermentative and poorly circumscribed and new techniques are being explored to elucidate differential characters. This latter group has been one of the driving forces for the development of MALDI-TOF and LC-tandem mass spectrometry. This review charts the history of these taxonomic changes against the intransigence of established microbiologists and, the opposing views of newcomers to the field who systematically persevered to overturn the dogma of many decades into an accepted classification that today concurs with their phylogeny. Join BISMiS for full access all issues of The Bulletin. Please Log-in

Opinion

Functional gene sequence studies of pure cultures are the basis of systematic studies of environmental communities of phototrophic bacteria and their species-specific analyses
Johannes F. Imhoff

From the establishment of proper cultivation conditions of phototrophic sulfur bacteria 50 years ago up to today significant improvements have been made to systematically treat the phototrophic green and purple sulfur bacteria and identify them in environmental communities. Important steps for these improvements were first of all the description of a large number of pure cultures representing a proper fraction of environmental diversity, their correct taxonomic treatment and the clear definition of the taxa. Further important steps were the establishment of a phylogenetics-based taxonomy supported by 16S rRNA gene sequences and the demonstration of congruence between phylogenies based on 16S rRNA genes and functional genes. The formation of a large database of fmoA genes of green sulfur bacteria and of pufLM genes of purple sulfur bacteria and their obvious phylogenetic congruence with the 16S rRNA gene enabled detailed studies of environmental communities of these bacteria and the recognition of species and genera in natural habitats. The comprehensive studies of selected habitats yielded promising results and demonstrated the potential of this approach for the systematic characterization of environmental communities. Join BISMiS for full access all issues of The Bulletin. Please Log-in

The importance of cultured representatives of the human intestinal microbiota in the metagenomic era
Harry J. Flint and Sylvia H. Duncan

There has been remarkable progress in the application of molecular approaches, mainly based on analysis of the 16S rRNA gene, to characterize complex microbial ecosystems including that of the human colon. This has been augmented recently by high throughput metagenomic approaches. Although there is an obvious need to link sequence information to functionality, much less emphasis has been given to the isolation and culturing of the gut anaerobes from the colon. Lack of research effort in this area may be due to the fact that the majority of these bacteria are anaerobes that have rather exacting growth requirements. Nevertheless, it is becoming evident that the most dominant bacterial species that are likely to play a significant role in the formation of short-chain fatty acids, including butyrate and propionate, and in the degradation of recalcitrant substrates such a resistant starch and dietary fiber can be isolated and cultured. Many of the bacterial strains representing the dominant species have also recently been genome-sequenced. Moreover, these genome sequences are publicly available and mining this information will provide researchers with the most tremendous insight into the genetic make-up of the inhabitants of our gut. It is important however to continue to culture anaerobic micro-organisms as well as applying molecular methods, as it is only then that we can truly assess the role of these fascinating micro-organisms in the colon. Some novel bacterial isolates may prove to have potential for biotechnological applications or as probiotics. Join BISMiS for full access all issues of The Bulletin. Please Log-in

Working towards a Molecular Systematics Library for Prokaryotes: a perspective
Xiao-Yang Zhi, Wei Zhao, Wen-Jun Li and Guo-Ping Zhao

With the breakthrough of high-throughput DNA sequencing technologies and development of bioinformatics tools, the dramatically increasing availability of genomic data has provided an opportunity and challenge for systematists to renovate the taxonomic system of prokaryotes especially for the classification of species and their related genera and subspecies. With a better understanding of the genetic and ecological diversity of prokaryotes based on meta- and pan-genomic analyses, comprehensive insights into prokaryotic speciation will revitalize the taxonomic system for prokaryotes in the near future. By integrating more comprehensive genotypic information with corresponding phenotypes of the subject taxa at the genomics level, and relying on related physiological and ecological knowledge, we may upgrade our classical taxonomic treatment in encyclopedia-style books to a “Molecular Systematics Library for Prokaryotes” indexed by phylogenomic information and integrated with ever increasing knowledge of biological diversity, which may eventually lead us to a comprehensive understanding of prokaryotic speciation. Join BISMiS for full access all issues of The Bulletin. Please Log-in

Intent of the nomenclatural Code and recommendations about naming new species based on genomic sequences
William B. Whitman

The International Code of Nomenclature of Prokaryotes was a major achievement of the last century. By establishing a clear set of rules, it allowed biologists with many different interests and backgrounds to communicate effectively. Furthermore, it made prokaryotic systematics straightforward and accessible. While the Code itself only governs nomenclature and not systematics or taxonomy, many of the minimal standards for descriptions of taxonomic groups proposed by the Ad Hoc Subcommittees far exceed the requirements of the Code and are contrary to both its explicit intent and spirit. They are exclusionary and prevent biologists with serious interests in prokaryotes from describing novel species. The likely consequences of the widespread implementation of these standards are that many biologists will no longer validate the names of newly described prokaryotes and the literature will once again be full of names of uncertain meaning. Within this context, the application of minimal standards for the evaluation of taxonomic descriptions by journals is an editorial decision and not authorized by the Code. With the availability of inexpensive DNA sequencing, prokaryotic species could be routinely described based upon their genomic sequences. These descriptions would fulfil all the requirements of the Code and provide a wealth of insight into the nature of prokaryotes. For these reasons, the genomic sequence should be included in the initial description of novel species whenever practical. Join BISMiS for full access all issues of The Bulletin. Please Log-in

Biography

Professor Dr Dr h.c. mult. Otto Kandler: distinguished botanist and microbiologist
Karl-Heinz Schleifer

Autobiographies

My life as a microbiologist and naturalist
Richard W. Castenholz

A little kid from Far Rockaway grows up
Sydney M. Finegold

Papers from the Inaugural Meeting of BISMiS, Beijing, May 2011

Isolation of novel natural products from un- or underexplored marine actinomycetes
Na Yang, Biao Ren, Jian Wang and Li-Xin Zhang

Microbial systematics is pivotal to meeting some of the major challenges facing humankind, as exemplified by the need for novel natural product medicines. A systematics-guided bioprospecting investigation of bioactive compounds from unique, untapped, ecological niches, including the construction of high-quality libraries of marine microbes and their crude extracts, has become an efficient approach to drive drug discovery. The criteria for strain selection include: the uniqueness and richness of biodiversity of the ecolological niches from which the strains are isolated (Hayakawa et al., 2004), symbiosis with medicinal plants (i.e. endophytes), morphological and taxonomical distinctiveness, and a bias towards the study of actinomycetes for their proven track record as prolific sources of natural products. We optimize natural product production for the selected strains, prepare extracts and subject them to high-throughput (HTP) screening (both cell-based and target-based), followed up by LC-MS dereplication, and prioritize the strains for fermentation scale-up, isolate and determine the structures of the novel natural products, and produce and assemble the library for screening. Our ecology- and taxonomy-based approach to strain selection for novel natural product discovery contrasts with traditional natural product discovery programs, most of which rely heavily on the designs of the HTP assays to screen often randomly collected micro-organisms. Join BISMiS for full access all issues of The Bulletin. Please Log-in

CVTrees support the Bergey's Systematics and provide high resolution at species levels and below
Bailin Hao

CV stands for Composition Vector. CVTree is an alignment-free method for inferring phylogenetic trees from prokaryote whole genomes by using CVs after a subtraction procedure. CVTree is the name of a public domain Web Server that implements the method. The results obtained by this method or by the Web Server are also sometimes called CVTrees. The branchings in CVTrees are verified by direct comparison with the Bergey� Systematics and agree well with the latter at all taxonomic ranks from phylum down to species with a few exceptions, which in most cases correspond to long-debated problems and may hint on possible taxonomic revisions. Moreover, CVTrees provide higher strain resolution at species level and below. In this mini-review the CVTree method will be described and some of its results will be shown. Join BISMiS for full access all issues of The Bulletin. Please Log-in



Volume 3, issue 1 - July 2012 - contents and abstracts - full issue freely available January 2013

Review

Evolution and diversification of oxygen metabolisms of aerotolerant anaerobes in the order Bacillales and other bacterial taxonomic groups
Daichi Mochizuki, Naoto Tanaka, Morio Ishikawa, Akihito Endo, Yuh Shiwa, Nobuyuki Fujita, Junichi Sato and Youichi Niimura

The relationship between the distribution of bacterial oxygen-protective/oxygen-utilizing enzymes, their phylogeny and implications on taxonomy are described in this review. The NADH oxidase (Nox) or AhpF–AhpC (Prx) systems, which function in both hydrogen peroxide-scavenging or oxygen metabolism are widely distributed in bacterial obligate aerobes, facultative aerobes, aerotolerant anaerobes and obligate anaerobes. Although biologists regard the advent of oxygen production as a major transformational period of Earth’s early biosphere about 2.5 Ga bp, if and how this change has influenced the evolution of bacteria is not well understood. However, the high correlation we report between the bacterial phylogenetic tree based on 16S rRNA gene sequences and the evolutionary trees derived from the amino acid sequences of the Nox and AhpF provide support for the view that bacteria evolved and diversified to produce disparate taxa from the Bacillales to various Gram-stain-negative bacteria that include a variety of species with enzyme systems to cope with oxygen toxicity and utilization. Among the Gram-stain-negative bacteria included in this study were Escherichia coli, Pseudomonas aeruginosa, and Bacteroides fragilis. Additional studies of the evolution of these systems may aid in furthering our understanding of bacterial evolution in response to the production of oxygen and its increase in concentration in the biosphere. Join BISMiS for full access all issues of The Bulletin. Please Log-in

Autobiographies

The topsy-turvy world of a microbial systematist
Kazuo Komagata

Sailing through the scientific ocean – my research on the systematics of actinomycetes
Ji-Sheng Ruan