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A globally applicable code of conduct specifically dedicated to biosecurity has been developed together with guidance for its procedural implementation. This is to address the regulations governing potential dual-use of biological materials, associated information and technologies, and reduce the potential for their malicious use. Scientists researching and exchanging micro-organisms have a responsibility to prevent misuse of the inherently dangerous ones, that is, those possessing characters such as pathogenicity or toxin production. The code of conduct presented here is based on best practice principles for scientists and their institutions working with biological resources with a specific focus on micro-organisms. It aims to raise awareness of regulatory needs and to protect researchers, their facilities and stakeholders. It reflects global activities in this area in response to legislation such as that in the USA, the PATRIOT Act of 2001, Uniting and Strengthening America by Providing Appropriate Tools Required to Intercept and Obstruct Terrorism Act of 2001; the Anti-Terrorism Crime and Security Act 2001 and subsequent amendments in the UK; the EU Dual-Use Regulation; and the recommendations of the Organization for Economic Co-operation and Development (OECD), under their Biological Resource Centre (BRC) Initiative at the beginning of the millennium (OECD, 2001). Two project consortia with international partners came together with experts in the field to draw up a Code of Conduct on Biosecurity for BRCs to ensure that culture collections and microbiologists in general worked in a way that met the requirements of such legislation. A BRC is the modern day culture collection that adds value to its holdings and implements common best practice in the collection and supply of strains for research and development. This code of conduct specifically addresses the work of public service culture collections and describes the issues of importance and the controls or practices that should be in place. However, these best practices are equally applicable to all other microbiology laboratories holding, using and sharing microbial resources. The code was introduced to the Seventh Review Conference to the Biological and Toxin Weapons Convention (BTWC), United Nations, Geneva, 2011; the delegates to the States’ parties recommended that this code of conduct be broadly applied in the life sciences and disseminated amongst microbiologists, hence the publishing of it here along with practical implementation guidance. This paper considers the regulatory and working environment for microbiology, defines responsibilities and provides practical advice on the implementation of best practice in handling the organism itself, associated data and technical know-how.

A Gram-positive, moderately halophilic, alkalitolerant, strictly aerobic, oxidase- and catalase-positive, rod-shaped bacterium, strain YIM kkny3T, was isolated from a sediment sample collected from a salt lake in the Qaidam Basin of north-west China. Cells were motile by means of peritrichous flagella and formed ellipsoidal endospores lying in subterminal swollen sporangia. Growth occurred with 1-20% (w/v) total salts (optimum, 5-10%) and at pH 6.0-10.5 (optimum, pH 7.5-8.0) and 10-55 degrees C (optimum, 35-40 degrees C). It was unable to grow with NaCl as the only salt. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The strain contained menaquinone 7 (MK-7) as the predominant respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as polar lipids. The major cellular fatty acids were anteiso-C15:0 and anteiso-C17:0. The DNA G+C content was 40.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM kkny3T belonged to the genus Virgibacillus, and was most closely related to the type strains of Virgibacillus olivae (97.1% similarity), Virgibacillus marismortui (97.0%) and Virgibacillus kekensis (96.8%). Levels of DNA-DNA relatedness between strain YIM kkny3T and the type strains of V. olivae, V. marismortui and V. kekensis were 12.4, 10.6 and 15.7%, respectively. The combination of phylogenetic analysis, genotypic data, phenotypic characteristics and chemotaxonomic differences indicated that strain YIM kkny3T represents a novel species of the genus Virgibacillus, for which the name Virgibacillus sediminis sp. nov. is proposed. The type strain is YIM kkny3T (=CCTCC AA 207023T=DSM 19797T=KCTC 13193T).

A Gram-positive, moderately halophilic, motile, strictly aerobic, endospore-forming, oxidase- and catalase-positive, rod-shaped bacterium, strain YIM kkny16(T), was isolated from a saline mud sample collected from the Keke salt lake in the Qaidam Basin, north-west China. This isolate grew in the presence of 0-25 % (w/v) NaCl and at pH 6.0-10.0 and 10-50 degrees C; optimum growth was observed with 10 % (w/v) NaCl and at pH 7.0 and 37 degrees C. Strain YIM kkny16(T) had meso-diaminopimelic acid as the diagnostic diamino acid, MK-7 as the predominant respiratory quinone, with a significant amount of MK-6, and anteiso-C(15 : 0), iso-C(14 : 0) and C(16 : 1)omega7c alcohol as major fatty acids. Major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C content was 41.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain YIM kkny16(T) was a member of the genus Virgibacillus, exhibiting sequence similarities of 94.9-97.3 % to the type strains of recognized Virgibacillus species. Strain YIM kkny16(T) could be differentiated from recognized Virgibacillus species based on phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and DNA-DNA hybridization data. On the basis of evidence from this polyphasic study, strain YIM kkny16(T) is considered to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus kekensis sp. nov. is proposed. The type strain is YIM kkny16(T) (=DSM 17056(T)=CGMCC 1.6298(T)).

The term 'biological resources' is applied to the living biological material collected, held and catalogued in culture collections: bacterial and fungal cultures; animal, human and plant cells; viruses; and isolated genetic material. A wealth of information on these materials has been accumulated in culture collections, and most of this information is accessible. Digitalisation of data has reached a high level; however, information is still dispersed. Individual and coordinated approaches have been initiated to improve accessibility of biological resource centres, their holdings and related information through the Internet. These approaches cover subjects such as standardisation of data handling and data accessibility, and standardisation and quality control of laboratory procedures. This article reviews some of the most important initiatives implemented so far, as well as the most recent achievements. It also discusses the possible improvements that could be achieved by adopting new communication standards and technologies, such as web services, in view of a deeper and more fruitful integration of biological resources information in the bioinformatics network environment.

The conspicuous morphological feature of endospore formation has lent itself from early on as an easily recognized property for taxonomic differentiation. Prior to 1980, the year of the compilation of the Approved Lists of Bacterial Names, four genera of aerobic endospore-forming bacteria had been established, with the genus Bacillus being the largest and most prominent. However, modern developments in taxonomic methodology have helped to reveal an enormous breadth in physiological and genetical diversity within the groups of aerobic bacteria that have endospore formation as a common trait. To better reflect this existing diversity and to provide more appropriate taxonomic arrangements, numerous valid descriptions of new genera and new species have been realized as well as many reclassifications that became necessary. Today, the group of aerobic endospore-forming bacteria embraces more than 25 genera and over 200 species.

The systematic position of the alkaliphilic and halotolerant strain Bacillus sp. FTU was refined in view of the comprehensive taxonomic revision of the group of alkaliphilic and alkalitolerant Bacillus strains. Sequence analysis of almost the entire 16S rRNA gene of Bacillus sp. FTU revealed 99.8% homology with two Bacillus pseudofirmus strains. Subsequent DNA-DNA hybridization analysis confirmed the close relationship of Bacillus sp. FTU with the type strain of B. pseudofirmus (the level of homology reached 86%). Results of physiological and biochemical characterizations relevant for the group clearly underlined the positioning of strain FTU within this species. It is therefore concluded that Bacillus sp. FTU represents a strain of the alkaliphilic species B. pseudofirmus and is to be renamed as B. pseudofirmus FTU. The phylogeny of different Bacillus species is discussed using N-terminal sequence homologies of some caa (3)-type oxidase subunits.

Ten obligately alkaliphilic, extremely halotolerant Bacillus isolates were studied and compared with strain WN13T (T = type strain), an earlier isolate provided by H. G. Truper. All of these strains produced round, terminally located spores in swollen sporangia. DNA-DNA hybridization values (78 to 91%) and phenotypic similarity analyses revealed that 10 of the 11 strains formed a relatively homogeneous group, and although one strain (strain AH/6/1) could not be distinguished phenotypically, it exhibited hybridization values of only 46 to 47%. This group of strains is sufficiently different from all previously validly described Bacillus species in its morphological, physiological, and biochemical properties that a separate species is considered appropriate, for which the name Bacillus haloalkaliphilus sp. nov. is proposed.

Summary: One hundred and nineteen strains of alkaliphilic and alkalitolerant, aerobic endospore-forming bacteria were examined for 47 physiological and biochemical characters, and DNA base composition. Numerical analysis (S J and S SM/UPGMA clustering) revealed 11 clusters that comprised three or more strains. Most of the phena were further characterized by analysis of carbohydrate utilization profiles using the API 50CH system, but strains of two taxa could not be cultured by this method. DNA reassociation studies showed that nine of the phena were homogeneous, but strains of phenon 4 and phenon 8 were each subdivided into two DNA hydridization groups. The strains could therefore be classified into 13 taxa plus a number of unassigned single-membered clusters. Two taxa were equated with Bacillus cohnii and B. alcalophilus and nine of the remainder are proposed as new species with the following names: B. agaradhaerens sp. nov., B. clarkii sp. nov., B. clausii sp. nov., B. gibsonii sp. nov., B. halmapalus sp. nov., B. halodurans comb, nov., B. horikoshii sp. nov., B. pseudalcalophilus sp. nov. and B. pseudofirmus sp. nov. Two taxa were insufficiently distinct to allow confident identification and these have therefore not been proposed as new species.

Comparative sequence analysis of the 16S rDNA of 14 alkaliphilic or alkalitolerant, Gram-positive, aerobic, endo-spore forming bacterial strains was performed. Bacillus alcalophilus DSM 485T and Bacillus cohnii DSM 6307T were included to represent the two validly described alkaliphiles assigned to the genus Bacillus. The majority of isolates (8 strains) clustered with B. alcalophilus DSM 485T forming a distinct phylogenetic group (rRNA group 6) within the radiation of the genus Bacillus and related taxa. Bacillus cohnii DSM 6307T and two of the isolates, DSM 8719 and DSM 8723, grouped with B. fastidiosus and B. megaterium and are allocated to rRNA group 1. The remaining two strains DSM 8720 and DSM 8721 show an equidistant relationship to both groups.

Bacillus and related genera are characterised by the ability to form vegetative cells and spores. Endospore-forming catalase-positive bacteria have been traditionally allocated to the genus Bacillus. These organisms are widespread within environmental niches and habitats. Their spores are resistant to heat and other means of sterilization, so spore-forming bacteria are a major concern to food microbiologists. Virtually any food can be colonized by these organisms due to their ubiquitous distribution, their physiological diversity and thus in their growth requirements. With respect to diagnostics, it is therefore not possible to design a single medium which allows growth of all or most species within this group. Numerous media have been described for the cultivation of individual species; however, most of these are not selective and only some of them are elective. Bacillus strains do not form endospores under all cultural conditions. Sporulation is inducible; e.g. by limitation of nutrient factors, including carbon or nitrogen. Further, most Bacillus strains form endospores in media supplemented with manganese salts. The only selective media for aerobic spore-forming bacteria in the mesophilic/neutrophilic range have been those developed for the so-called Bacillus cereus group. This group consists of genetically closely related species, B. anthracis, B. cereus, B. thuringiensis, B. weihenstephanensis, B. mycoides and B. pseudomycoides. Despite the variations in potential virulence, the differentiation of the B. cereus group members remains a difficult important task. The most widely used plating media for detection of B. cereus are mannitol egg-yolk polymyxin agar (MEYP or MYP) and polymyxin egg-yolk mannitol bromothymol blue agar (PEMBA). Procedures for reliable enumeration and identification of Bacillus cereus are included in international standards, e.g. EN ISO 7932:2004 and EN ISO 21871:2006. Recently, two new chromogenic media have been developed for the Bacillus cereus group, supplemented with 5-bromo-4-chloro-3-indoxyl myo-inositol-1-phosphate. Other simple methods of selection are to adjust media to certain pH values or to incubate at certain temperatures. This physiological approach has been successful e.g. with Alicyclobacillus spp., emerging food spoilage organisms in the fruit juice and fruit juice products industry. In general it should be noted that aerobic spore-forming organisms are no longer just the traditional genus Bacillus, but fall into an increasing number of additional genera. Recent reports have described toxin-producing B. subtilis group members and the analysis of plasmids, which are very common in the B. cereus group, became a focal point of interest. As it cannot be assumed that novel species are of no relevance to food, it is sometimes advisable to perform a more thorough taxonomic identification to complement the diagnostic approach. Genomic studies and the development of more and better diagnostic media would probably aid the detection of aerobic spore forming bacteria in foods.

International audience; Minimal standards for describing new taxa within the aerobic endospore-forming bacteria are proposed, following Recommendation 30b of the Bacteriological Code (1990 Revision). These minimal standards are recommended as guidelines to assist authors in the preparation of descriptions for novel taxa. They encourage broad polyphasic characterization and the construction of descriptions that are practically useful in routine diagnostic laboratories. The proposals have been endorsed by the Subcommittee on the Taxonomy of the Genus Bacillus and Related Organisms of the International Committee on Systematics of Prokaryotes.

The DNA base compositions of 78 alkaliphilic Bacillus strains were determined. These strains were grouped as follows: DNA group A, guanine-plus-cytosine (G+C) content of 34.0 to 37.5 mol% (17 strains); DNA group B, G+C content of 38.2 to 40.8 mol% (33 strains); and DNA group C, G+C content of 42.1 to 43.9 mol% (28 strains). DNA group A includes the type strain of Bacillus alcalophilus Vedder 1934. DNA-DNA hybridization studies with DNA group A strains revealed that only one strain, strain DSM 2526, exhibited a high level of DNA homology with B. alcalophilus DSM 485T (T = type strain). Neither strain DSM 485T nor any other DNA group A strain is homologous to any of the Bacillus type strains with comparable base compositions. Six strains formed a distinct group containing three highly homologous strains and three strains exhibiting greater than 50% DNA homology.

Two Gram-positive, aerobic, spore-forming rods, F73T and I80T, were isolated from upland soil. A phylogenetic analysis of 16S rRNA gene sequences placed both isolates within the genus Sporosarcina, and showed a sequence similarity of 98.9 % between the two strains and a similarity of approximately 94.6–97.3 % with respect to Sporosarcina species with validly published names. The values for DNA–DNA relatedness between the two isolates and related type strains of the genus Sporosarcina were below 28.0 %. For both strains, the major cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0. In both cases, the cell-wall peptidoglycan was of the A4α type (l-Lys–d-Glu) and the major menaquinone was MK-7. Diaminopimelic acid was absent from both strains. The genomic DNA G+C contents of strains F73T and I80T were 46.5 and 44.5 mol%, respectively. On the basis of the phylogenetic analysis and physiological and chemotaxonomic data, the isolates represent two novel species of the genus Sporosarcina, for which the names Sporosarcina koreensis sp. nov. (type strain F73T =KACC 11299T =DSM 16921T) and Sporosarcina soli sp. nov. (type strain I80T =KACC 11300T =DSM 16920T) are proposed.

The taxonomic position of two spore-forming strains 6T19Tand 6T29, isolated from cotton composts for the cultivation of oyster mushroom (Pleurotus ostreatus), was investigated by a polyphasic approach. Cells of strains 6T19Tand 6T29 were rod-shaped, Gram-negative and strictly aerobic. Sequencing and comparative analyses for the 16S rRNA genes of these strains clearly showed their phylogenetic affiliation to the genusUreibacillus. Their closest relativesUreibacillus thermosphaericusandUreibacillus terrenushave sequence similarity of 96·9 and 97·5 %, respectively. The isoprenoid quinones of isolate 6T19Twere MK-9, MK-8, MK-7, MK-10 and MK-6 (45 : 27 : 18 : 5 : 4 %), the peptidoglycan type wasl-lys←d-Asp and the main cellular fatty acid was i-C16 : 0. DNA–DNA hybridization experiments resulted in relatedness values of 37 % between 6T19TandU. thermosphaericusDSM 10633Tand 41 % between 6T19TandU. terrenusDSM 12654T. Based on the polyphasic data, strains 6T19Tand 6T29 can be described as members of a novel species of the genusUreibacillus, for which the nameUreibacillus suwonenesissp. nov. is proposed. The type strain is 6T19T(=KACC 11287T=DSM 16752T).

A Gram-positive, endospore-forming, xylanase-producing bacterium isolated from a rice field was studied taxonomically. The strain grows at 10–40 °C and in the presence of lysozyme or 5 % (w/v) NaCl. Chemotaxonomic analysis revealed that MK-7 was the predominant menaquinone of the isolated strain, while the major fatty acid was anteiso-C15 : 0. Comparison of 16S rRNA gene sequences showed that strain BP-23T fell within the radiation of the cluster comprising Paenibacillus species. The highest 16S rRNA gene sequence similarities were found with Paenibacillus illinoisensis (97·4 %), Paenibacillus pabuli (97·1 %) and Paenibacillus amylolyticus (96·9 %). The DNA–DNA relatedness of strain BP-23T with respect to these three species was very low (32·7, 31·6 and 23·0 %, respectively). On the basis of phenotypic and genotypic data, strain BP-23T should be placed in the genus Paenibacillus and designated a novel species, for which the name Paenibacillus barcinonensis sp. nov. is proposed. The type strain is BP-23T (=CECT 7022T=DSM 15478T).

Twenty-two agarolytic, aerobic, spore-forming strains were characterized taxonomically by DNA-DNA reassociation experiments, riboprint analyses, 16S rDNA sequencing and phenetic similarity analyses. Based on riboprint analyses, the strains formed eight ribogroups, six of which contained 2-6 strains and two encompassed single strains. Within the multi-strain ribogroups, similarities ranged from 91-99%. Phylogenetic analyses of representatives of the eight groups by 16S rDNA sequence analysis showed that the strains were affiliated to the genus Paenibacillus, but relatedness to described Paenibacillus species was only moderate (

Eleven psychrotolerant Bacillus strains with ornithine as diamino acid in position 3 of the peptide side chain of the cell wall and a G+C range of 35.7-38.4 mol% were characterized taxonomically. DNA-DNA hybridization studies confirmed previously physiologically established groups. High DNA-binding values (> 70%) were found within groups I A (consisting of the type strain of Bacillus insolitus DSM 5(T) and Bacillus insolitus DSM 2272), I B (consisting of isolates 3H1(T0, 71H1, 84E1, 87H2 and 4H2) and I C (consisting of isolates 68E39T), 61E1, 4E3 and 67E1). Low DNA-binding values (< 60%) were revealed between the three groups. Consequently, strains of groups I B and I C were considered as being representatives of new psychrotolerant species. For group I B strains the name Bacillus psychrotolerans sp. nov. is proposed with the type strain 3H1(T) (= DSM 11706(T) = NCIMB 13838(T)) and for group I C strains the name Bacillus psychrodurans sp. nov. is proposed with the type strain 68E3(T) (= DSM 11713(T) = NCIMB 13837(T)).

Spores are resistant to heat and other means of sterilization, so sporeforming bacteria are of major concern to food microbiologists. Virtually any food can be colonized by these organisms due to their ubiquitous distribution, their diversity in physiological properties and thus in growth requirements. With respect to diagnostics, it is therefore not possible to design a single medium which allows growth of all or most species of this group. Numerous media have been described for the cultivation of individual species of aerobic spore forming organisms, however, most of these are not selective and only some are elective. The only largely selective media in the area of aerobic spore forming bacteria acting in the mesophilic/neutrophilic range have been developed for Bacillus cereus and related species. The most widely used among those are MEYP (Mannitol Egg Yolk Polymyxin agar) and PEMBA (Polymyxin Egg yolk Mannitol Bromothymol blue Agar)). Another suitable form of selectivity that is easily achieved, is to adjust media (even standard media) to certain pH values or to incubate at certain temperatures. This physiological approach has been successful e.g with Alicyclobacillus. In most cases, however, even under those conditions, groups of species rather than individual species can be expected. For up-to-date results in food microbiology, it should be understood that the aerobic spore forming organisms are no longer just the traditional genus Bacillus but fall into a number of genera. In addition, several of the traditionally well known species such as B. subtilis, B. circulans or B. sterarothermophilus have been divided up into newly established species to form more consistent taxa. As it cannot be assumed that the newly described species are of no relevance to food, it is advisable to perform under certain circumstances a more thorough taxonomic identification to complete the diagnostic approach. Further research into the development of more and better diagnostic media would be worthwhile to ease the detection of members of the large group of aerobic spore forming bacteria in foods. This review aims to describe the physiological peculiarities and relationships within the group in order to support and encourage the development of additional selective or elective media for other aerobic spore forming organisms of relevance to food.

On the basis of high DNA-DNA reassociation values and confirmatory automated RiboPrint analysis, two aerobic spore-forming strains hitherto allocated to Bacillus subtilis and used as bioindicators (DSM 675, hot-air sterilization control; DSM 2277, ethylene oxide sterilization control) are reclassified as Bacillus atrophaeus.

A group of 20 alkaliphilic Bacillus strains in which all strains revealed the same unique comination of properties--obligate alkaliphily, oval spores distending the sporangium, and ornithine and aspartic acid instead of diaminopimelic acid in the cell wall--was examined. Most of the strains had been isolated by a five-step enrichment and isolation procedure. The G+C content was determined to span a range from 33.5 to 35.0 mol%. Unsaturated fatty acids amounted to 17 to 28% of the total cellular fatty acids. Through DNA-DNA hybridization experiments 11 strains could be grouped in one species. Low homology values with the type strains of validly published Bacillus species with similar G+C contents suggest that these strains belong to a hitherto undescribed species for which the name Bacillus cohnii is proposed. The type strain of the new species is strain RSH (= DSM 6307).

Worldwide development of biotechnology results increasingly in the recognition of the importance of microbial culture collections and their holdings. In particular, it is recognised that the knowledge on these holdings accumulated in culture collections should be put more easily at the use of researchers. Far sighted scientists, under the leadership of the late VBD Skerman, had set up, already from the mid 1960s on, activities to catalogue culture collections and their holdings.

A century ago, when a young scientist detected that a bacterium which Pasteur had thought to be a coccus was in fact a short rod, Pasteur’s comment was, “I wish I could convey to you how little that information excites me” (Duclaux, 1896). Obviously, Pasteur was interested in microorganisms mainly for what they do rather than what they are. Whereas this remains a legitimate interest today, early bacteriologists felt that, with the increasing diversity of organisms isolated, there was a need to arrange bacteria distinctly. The easiest way to do this was to put them into groups with common properties, to study the relationships of such groups and their role in nature, and to develop methods that would enable scientists to identify new isolates with already known groups.