With reference to the first Principle of the International Code of Nomenclature of Bacteria, which emphasizes stability of names, it is proposed that the original names Streptococcus sanguis, Streptococcus rattus, Streptococcus cricetus, Erwinia ananas, Eubacterium tarantellus, Lactobacillus sake, Nitrosococcus oceanus, Pseudomonas betle, Rickettsia canada and Streptomyces rangoon, all included in the Approved Lists of Bacterial Names, be conserved. Request for an Opinion.

An extensive phenotypic description and an improved classification and nomenclature of the genus Xanthomonas are presented. A total of 266 strains obtained from different geographical areas, including representative strains of all species of the genus Xanthomonas and most pathovars of Xanthomonas campestris, as well as strains which might be genetically related to the genus Xanthomonas, were examined for 295 morphological, biochemical, and physiological features. Similarities among the strains were expressed numerically by using the coefficient of Sokal and Michener. Clustering was performed by using the unweighted average pair group method. The conclusions described below were reached. (i) The genus Xanthomonas comprises at least the following eight phena: X. campestris, Xanthomonas albilineans, Xanthomonas axonopodis, Xanthomonas fragariae, Xanthomonas populi, Xanthomonas maltophilia, Xanthomonas oryzae Swings et al. 1990, and X. campestris pv. graminis Egli and Schmidt 1982 [not X. campestris pv. graminis (Egli et al. 1975) ISPP List 1980]. (ii) X. populi (Rid? 1958) Rid? and Rid? 1978 is a separate species. (iii) X. maltophilia Swings et al. 1983 forms a separate species. (iv) X. campestris pv. oryzae ISPP List 1980 can no longer be regarded as pathovar of X. campestris, and its recent reclassification as a new species, X. oryzae (Swings et al., Int. J. Syst. Bacteriol. 40:309-311, 1990), is supported. (v) X. campestris pv. graminis Egli and Schmidt 1982 [not X. campestris pv. graminis (Egli et al. 1975) ISPP List 1980] seems to form a separate complex of highly related pathovars obtained from members of the Poaceae; the taxonomic implications of this are discussed. (vi) Strains of nearly all X. campestris pathovars cluster together in the X. campestris phenon. Within this species we were able to differentiate some entities on phenotypic grounds; these groups sometimes corresponded to named pathovars (e.g., X. campestris pv. manihotis, X. campestris pv. cassavae, X. campestris pv. phlei). In several other cases, pathovars were found to be heterogeneous. (vii) A number of dubious Pseudomonas species were identified as members of or as being close to Xanthomonas species. Both Pseudomonas betle and Pseudomonas hibiscicola are synonyms of X. maltophilia. We also confirmed that Pseudomonas mangiferaeindicae, Pseudomonas vitiswoodrowii, and Pseudomonas gardneri belong to X. campestris. (viii) Forty phenotypic features allow the differentiation of the eight Xanthomonas phena. (ix) A number of additional features of the genera Xanthomonas and Xylophilus are described.

A gram-negative bacterium was isolated from a cerebrospinal fluid sample from an HIV-seropositive Rwandan refugee with primary meningoencephalitis. This Marseille-Goma sample B isolate, strain MGBT (T = type strain), was found to exhibit evolutionary homology with Stenotrophomonas maltophilia, as determined by a 16S rRNA gene sequence analysis, and this finding was reflected by similar phenotypic traits. MGBT could, however, be distinguished from the S. maltophilia type strain by using a number of biochemical and physiological tests, and a genotypic analysis of the two strains in which DNA homology was used revealed only 35% homology between them. Furthermore, the antibiotic susceptibility of MGBT was restricted to netilmicin, ciprofloxacin, trimethoprim-sulfamethoxazole, and colimycin. On the basis of these results we propose that MGBT is a representative of a new species in the genus Stenotrophomonas, Stenotrophomonas africana.

The inclusion of "Pseudomonas maltophilia" Hugh 1981 in the genus Xanthomonas as Xanthomonas maltophilia (Hugh 1981) Swings et al. 1983 is questioned in view of the significant differences between these two taxa. This reclassification is not acceptable if practical means of differentiation in this genus are considered. The proposed alteration of the description of the genus Xanthomonas is also questionable because of the implications for everyday phytobacteriology. In view of the natural similarities, as well as the profound differences, between X. maltophilia and the genus Xanthomonas, we propose that a new genus should be created for X. maltophilia, which could be placed together with the genus Xanthomonas in a separate natural group.

The broad and vague phenotypic definition allowed the genus Pseudomonas to become a dumping ground for incompletely characterized polarly flagellated, gram-negative, rod-shaped, aerobic bacteria, and a large number of species have been accommodated in the genus Pseudomonas. The 16S rRNA sequences of 128 valid and invalid Pseudomonas species, which included almost valid species of the genus Pseudomonas listed in the Approved Lists of Bacterial Names, were obtained: sequences of 59 species were determined and those of 69 species were obtained from the GenBank/EMBL/DDBJ databases. These sequences were compared with the sequences of other species of the Proteobacteria. Fifty-seven valid or invalid species including Pseudomonas aeruginosa (type species of the genus Pseudomonas Migula 1894) belonged to the genus Pseudomonas (sensu stricto). Seven subclusters were formed in the cluster of the genus Pseudomonas (sensu stricto), and the resulting clusters conformed well to the rRNA-DNA hybridization study by Palleroni (1984). The other species did not belong to the genus Pseudomonas (sensu stricto) and were related to other genera, which were placed in four subclasses of the Proteobacteria (alpha, beta, gamma and gamma-beta subclasses). Twenty-six examined species, which were not included in the cluster of the Pseudomonas (sensu stricto) and have not been transferred to other genera as yet, are listed alphabetically: 'Pseudomonas abikonensis', Pseudomonas antimicrobica, Pseudomonas beijerinckii, Pseudomonas beteli, Pseudomonas boreopolis, 'Pseudomonas butanovora', Pseudomonas carboxydohydrogena, Pseudomonas cissicola, Pseudomonas doudoroffii, Pseudomonas echinoides, Pseudomonas elongata, Pseudomonas flectens, Pseudomonas geniculata, Pseudomonas halophila, Pseudomonas hibiscicola, Pseudomonas huttiensis, Pseudomonas iners, Pseudomonas lanceolata, Pseudomonas lemoignei, Pseudomonas mephitica, Pseudomonas pictorum, Pseudomonas saccharophila, Pseudomonas spinosa, Pseudomonas stanier, Pseudomonas syzygii and Pseudomonas woodsii. The phylogenetic affiliations of these 26 pseudomonads species are shown.

Together with 31 other incorrectly formed (i.e. as nominative nouns in apposition) specific epithets, the epithet of Streptomyces scabies was corrected to Streptomyces scabiei in Taxonomic Notes published in 1997 and 1998. A subsequent Request for an Opinion, published in 2001, to reinstate the incorrect epithets for ten of these species was denied by the Judicial Commission in 2002. In 2007, a further Request for an Opinion was submitted to the Judicial Commission which proposed the conservation of the incorrect epithet of Streptomyces 'scabies' over the corrected one, scabiei. After having stated once that the corrections made to the epithets were performed according to the correct application of the International Code of Nomenclature of Bacteria (now 'of Prokaryotes', ICNP), the Judicial Commission would lose authority and credibility if it were to follow a request to abandon even one of the now correct 32 epithets in favour of its incorrectly formed predecessor. Microbiologists who accept changes in names of genera should also accept the correction of grammatical or orthographical changes in specific epithets.

In consideration of the criticisms of the transfer of Pseudomonas maltophilia to the genus Xanthomonas proposed by J. Swings, P. De Vos, M. Van den Mooter, and J. De Ley (Int. J. Syst. Bacteriol. 33:409-413, 1983), a new generic name is created for this taxon. The name Stenotrophomonas is here proposed for the new genus, which includes a single species, Stenotrophomonas maltophilia. This proposal restores the genus Xanthomonas to its former definition (J. Bradbury, p. 199-210, in N. R. Krieg and J. G. Holt, ed., Bergey's Manual of Systematic Bacteriology, 1984) The arguments on which this proposal is based are presented.

Genomic resource of type strains and historically important strains of genus Stenotrophomonas allowed us to reveal the existence of 18 distinct species by applying modern phylogenomic criterions. Apart from Stenotrophomonas maltophilia, S. africana represents another species of clinical importance. Interestingly, Pseudomonas hibsicola, P. beteli, and S. pavani that are of plant origin are closer to S. maltophilia than the majority of the environmental isolates. The genus has an open pan-genome. By providing the case study on genes encoding metallo-�]-lactamase and Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) regions, we have tried to show the importance of this genomic dataset in understanding its ecology.

Type and reference strains of Stenotrophomonas maltophilia and Stenotrophomonas africana were compared with each other and with the type strains of other Stenotrophomonas species, using SDS-PAGE of whole-cell proteins, DNA-DNA hybridization and extensive biochemical characterization. S. maltophilia LMG 958T and S. africana LMG 22072T had very similar whole-cell-protein patterns and were also biochemically very similar. A DNA-DNA binding level of 70% between both type strains confirmed that S. africana and S. maltophilia represent the same taxon. It is concluded that S. africana is a later synonym of S. maltophilia.