From our recent survey of non-pigmented rapidly growing mycobacteria in the Parisian water system, three groups of isolates (taxons 1-3) corresponding to possible novel species were selected for taxonomic study. The three taxa each formed creamy white, rough colonies, had an optimal growth temperature of 30 °C, hydrolyzed Tween 80, were catalase-positive at 22 °C and expressed arylsulfatase activity. All three were susceptible to amikacin, ciprofloxacin and tigecycline. The three taxa produced specific sets of mycolic acids, including one family that has never previously been described, as determined by thin layer chromatography and nuclear magnetic resonance. The partial rpoB sequences (723 bp) showed 4-6 % divergence from each other and more than 5 % differences from the most similar species. Partial 16S rRNA gene sequences showed 99 % identity within each species. The most similar sequences for 16S rRNA genes (98-99 % identity over 1444-1461 bp) were found in the Mycobacterium fortuitum group, Mycobacterium septicum and Mycobacterium farcinogenes. The three taxa formed a new clade (bootstrap value, 99 %) on trees reconstructed from concatenated partial 16S rRNA, hsp65 and rpoB sequences. The above results led us to propose three novel species for the three groups of isolates, namely Mycobacterium lutetiense sp. nov. [type strain 071T=ParisRGMnew_1T (CIP 110656T=DSM 46713T)], Mycobacterium montmartrense sp. nov. [type strain 196T=ParisRGMnew_2T (CIP 110655T=DSM 46714T)] and Mycobacteriu marcueilense sp. nov. [type strain of 269T=ParisRGMnew_3T (CIP 110654T=DSM 46715T)].

Bac.te.ro.i.de'tes. N.L. fem. pl. n. Bacteroidales type order of the phylum; N.L. fem. pl. n. Bacteroidetes the phylum of Bacteroidales . Bacteroidetes

The arrangement of content follows a phylogenetic framework or road map based largely on analyses of nucleotide sequences of the ribosomal small subunit RNA rather than on phenotypic data. Implicit in the use of the road map are the convictions that prokaryotes have a phylogeny and that phylogeny matters. However, phylogenies, like other experimentally derived hypotheses, are not static but may change whenever new data and/or improved methods of analysis become available. Thus, the large increases in data have led to a re‐evaluation of the road map. Not surprisingly, the taxonomic hierarchy has been modified or newly interpreted for a number of taxonomic units.

Publicly available sequence databases of the small subunit ribosomal RNA gene, also known as 16S rRNA in bacteria and archaea, are growing rapidly, and the number of entries currently exceeds 4 million. However, a unified classification and nomenclature framework for all bacteria and archaea does not yet exist. In this Analysis article, we propose rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggest a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and archaea. Our analyses show that only nearly complete 16S rRNA sequences give accurate measures of taxonomic diversity. In addition, our analyses suggest that most of the 16S rRNA sequences of the high taxa will be discovered in environmental surveys by the end of the current decade.

High quality 16S ribosomal RNA (rRNA) gene sequences from the type strains of all species with validly published names, as defined by the International Code of Nomenclature of Bacteria, are a prerequisite for their accurate affiliations within the global genealogical classification and for the recognition of potential new taxa. During the last few years, the Living Tree Project (LTP) has taken care to create a high quality, aligned 16S and 23S rRNA gene sequence database of all type strains. However, the manual curation of the sequence dataset and type strain information revealed that a total of 552 "orphan" species (about 5.7% of the currently classified species) had to be excluded from the reference trees. Among them, 322 type strains were not represented by an SSU entry in the public sequence repositories. The remaining 230 type strains had to be discarded due to bad sequence quality. Since 2010, the LTP team has coordinated a network of researchers and culture collections in order to improve the situation by (re)-sequencing the type strains of these "orphan" species. As a result, we can now report 351 16S rRNA gene sequences of type strains. Nevertheless, 201 species could not be sequenced because cultivable type strains were not available (121), the cultures had either been lost or were never deposited in the first place (66), or it was not possible due to other constraints (14). The International Code of Nomenclature of Bacteria provides a number of mechanisms to deal with the problem of missing type strains and we recommend that due consideration be given to the appropriate mechanisms in order to help solve some of these issues.

The identification of a diverse microbiome in otic secretions from healthy young adults challenged the entrenched dogma of middle ear sterility and underscored previously unknown roles for oral commensals in the seeding of otic biofilms. We gained insights into the selective forces that enrich for specific groups of oral migrants in the middle ear mucosa by investigating the phylogeny and physiology of 19 strains isolated previously from otic secretions and representing otic commensals (Streptococcus) or transient migrants (Staphylococcus, Neisseria and actinobacterial Micrococcus and Corynebacterium). Phylogenetic analyses of full length 16S rRNA sequences recovered from partially sequenced genomes resolved close relationships between the isolates and (peri)oral commensals. Physiological functions that facilitate mucosal colonization (swarming motility, surfactant production) and nutrition (mucin and protein degradation) were also widespread among the cultivars, as was their ability to grow in the presence or absence of oxygen. Yet, streptococci stood out for their enhanced biofilm-forming abilities under oxic and anoxic conditions and ability to ferment host-derived mucosal substrates into lactate, a key metabolic intermediate in the otic trophic webs. Additionally, the otic streptococci inhibited the growth of common otopathogens, an antagonistic interaction that could exclude competitors and protect the middle ear mucosa from infections. These adaptive traits allow streptococcal migrants to colonize the otic mucosa and grow microcolonies with syntrophic anaerobic partners, establishing trophic interactions with other commensals that mirror those formed by the oral ancestors in buccal biofilms.

The names 'Mycobacterium abscessus subsp. abscessus' and 'Mycobacterium abscessus subsp. massiliense', proposed by Leao et al. (2009, J Clin Microbiol 47, 2691-2698), cannot be validly published. The purpose of this report is to provide a description in accordance with the Rules of the Bacteriological Code (1990 Revision). Moreover, the proposal of the name 'Mycobacterium abscessus subsp. massiliense' is contrary to Rule 38 and the correct name of this taxon, at the rank of subspecies, is Mycobacterium abscessus subsp. bolletii comb. nov. A description of Mycobacterium abscessus subsp. abscessus subsp. nov. and an emended description of Mycobacterium abscessus are also given.

The taxonomic road map proposed was derived from phylogenetic and principal‐component analyses of comprehensive datasets of small‐subunit rRNA gene sequences. Since the introduction of comparative rRNA sequencing there has been a continuous debate concerning the justification and power of a single marker molecule for elucidating phylogeny and establishing taxonomy of organisms. Although generally well established in taxonomy, the polyphasic approach cannot currently be applied for sequence‐based analyses due to the lack of adequate comprehensive datasets for alternative marker molecules. Even in the age of genomics, the datasets for non‐rRNA markers are poor in comparison to more than 400,000 rRNA primary structures available in general and special databases. Nevertheless, the data provided by the full genome‐sequencing projects allow the definiton of a small set of genes representing the conserved core of prokaryotic genomes. Furthermore, comparative analyses of the core gene sequences globally support the small subunit rRNA derived view of prokaryotic evolution. Although the tree topologies reconstructed from alternative markers differ in detail, the major groups (and taxa) are verified or at least not disproved. Consequently, the structuring of this volume is based on updated and curated databases of processed small‐subunit rRNA primary structures.

The phylum Bacteroidetes is a phenotypically diverse group of Gram-stain-negative rods that do not form endospores. They are circumscribed for this volume on the basis of phylogenetic analysis of 16S rRNA gene sequences.

The "All-Species Living Tree Project" (LTP) provides the scientific community with a useful taxonomic tool consisting of a curated database of type strain sequences, a universal and optimized alignment and a single phylogenetic tree harboring all the type strains of the hitherto classified species [33]. On the website http://www.arb-silva.de/projects/living-tree an update has been regularly maintained by including the 1301 new descriptions that have appeared in the validation and notification lists of the IJSEM journal. The topology of the 16S rRNA-based tree was validated with a detailed comparison against a collection of taxa-specific and broad-range trees made using different approaches, subsets of sequences and alignments. Seven percent of the classified species is still missing, as their type strains do not have a good quality SSU sequence. In addition, a new database of type strains for which adequate 235 rRNA entries existed in public repositories was built. Among the 8602 species with validly published names until February 2010, we were able to find good quality LSU representatives for 792 type strains, whereas around 91% of the complete catalogue still remains unsequenced. Despite the scarce representation of some groups in LSU databases, we have devised a highly optimized alignment and a reliable LSU tree in order to set up a stable phylogenetic starting point for taxonomic purposes. The current release corresponds to the fourth update of the project (LTP5102), and contains additional features which increase usability and compatibility. Use the contact address living-tree@arb-silva.de to provide additional input for the development of this taxonomic tool. (C) 2010 Elsevier GmbH. All rights reserved.

The family name Heliobacteriaceae is not validly published. The purpose of this note is to provide a description of this family in accordance with the Rules of the Bacteriological Code (1990 Revision).

Phylogenetic analyses of the SSU rRNA sequences of representatives of the phylum Actinobacteria were performed to identify the major taxonomic groups. The current release of the integrated small subunit rRNA database of the SILVA project [1] provided the sequences. The tools of the ARB software package [2] were used for data evaluation, optimization and phylogenetic inference. The alignment of sequences comprising at least 1000 monomers was manually evaluated and optimized for all representatives of the phylum. Phylogenetic treeing was performed with all sequences which contain at least 1400 nucleotides and an additional 1000 sequences from representatives of the other phyla and domains. For recognizing and avoiding the influences of chimeric sequences, all calculations were performed twice, once including and once excluding environmental clone data. The data sets also varied with respect to the inclusion of highly variable sequence positions, which were eliminated in some analyses [3]. The consensus tree used for evaluating or modifying the taxonomic outline was based on maximum likelihood analyses (RAXML, implemented in the ARB package; [4]) and further evaluated by maximum parsimony and distance matrix analyses with the respective ARB tools [2]. In the case that type strains were only represented by partial sequences (less than 1400 nucleotides), the respective data were inserted by a special ARB-tool allowing the optimally positioning of branches to the reference tree without admitting topology changes.

The prokaryotic generic name Frondicola Zhang et al. 2007 is illegitimate because it is a later homonym of a fungal genus name Frondicola Hyde, 1992 (Fungi, Ascomycota, Sordariomycetes, Xylariomycetidae, Xylariales, Hyponectriaceae) [Principle 2 and Rule 51b(4) of the Bacteriological Code (1990 Revision)]. It is also questionable whether the genus name can be validly published. Therefore, a new genus name, Frondihabitans gen. nov., is proposed for this taxon. As a result, a new name is proposed for the type species, Frondihabitans australicus sp. nov., to replace the illegitimate combination Frondicola australicus Zhang et al. 2007. The type strain of Frondihabitans australicus is E1HC-02(T) (=JCM 13598(T) =DSM 17894(T)).

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The prokaryotic generic names Yania Li et al. 2004 and Sinococcus Li et al. 2006 are illegitimate because they are later homonyms of the names Yania Roewer 1919 (Opiliones, Arachnida, Arthropoda, Animalia), Yania Huang 1997 (Lepidoptera: Hesperiidae) and Sinococcus Wu and Zheng 2000 (Homoptera: Coccomorpha) [Principle 2 of the Bacteriological Code (1990 Revision)]. Therefore, new generic names, Yaniella gen. nov. and Sinobaca gen. nov., are proposed for these taxa. In addition, a new family name, Yaniellaceae fam. nov., is proposed to accommodate Yaniella gen. nov. As a result, new combinations are required for the species to replace the illegitimate species names.