Application of Whole Genome Sequencing and Pan-Family Multi-Locus Sequence Analysis to Characterize Relationships Within the Family Brucellaceae

The bacterial family Brucellaceae is currently composed of seven genera, including species of the genus Brucella, a number of which are significant veterinary and zoonotic pathogens. The bacteriological identification of pathogenic Brucella spp. may be hindered by their close phenotypic similarity to other members of the Brucellaceae, particularly of the genus Ochrobactrum. Additionally, a number of novel atypical Brucella taxa have recently been identified, which exhibit greater genetic diversity than observed within the previously described species, and which share genomic features with organisms outside of the genus. Furthermore, previous work has indicated that the genus Ochrobactrum is polyphyletic, raising further questions regarding the relationship between the genus Brucella and wider Brucellaceae. We have applied whole genome sequencing (WGS) and pan-family multi-locus sequence analysis (MLSA) approaches to a comprehensive panel of Brucellaceae type strains, in order to characterize relationships within the family. Phylogenies based on WGS core genome alignments were able to resolve phylogenetic relationships of 31 non-Brucella spp. type strains from within the family, alongside type strains of twelve Brucella species. A phylogeny based on concatenated pan-family MLSA data was largely consistent with WGS based analyses. Notably, recently described atypical Brucella isolates were consistently placed in a single clade with existing species, clearly distinct from all members of the genus Ochrobactrum and wider family. Both WGS and MLSA methods closely grouped Brucella spp. with a sub-set of Ochrobactrum species. However, results also confirmed that the genus Ochrobactrum is polyphyletic, with seven species forming a separate grouping. The pan-family MLSA scheme was subsequently applied to a panel of 50 field strains of the family Brucellaceae, isolated from a wide variety of sources. This analysis confirmed the utility of the pan-Brucellaceae MLSA scheme in placing field isolates in relation to recognized type strains. However, a significant number of these isolates did not cluster with currently identified type strains, suggesting the existence of additional taxonomic diversity within some members of the Brucellaceae. The WGS and pan-family MLSA approaches applied here provide valuable tools for resolving the identity and phylogenetic relationships of isolates from an expanding bacterial family containing a number of important pathogens.

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

Bacterial Communities of Novaya Zemlya Archipelago Ice and Permafrost

The study of bacterial communities associated with extreme ecosystems is one of the most important tasks in modern microbial ecology. Despite a large number of studies being performed, the ecosystems that have not been sufficiently explored from the microbiological point of view still exist. Such research is needed for improving the understanding of the limits and mechanisms of bacterial survival under extreme conditions, and for revealing previously undescribed species and their role in global biospheric processes and their functional specifics. The results of the complex microbiological characteristics of permafrost and ice—collected on the Severniy Island in the northern part of the Novaya Zemlya archipelago—which have not previously been described from microbiological point of view, are presented in this article. The analysis included both culture-independent and culture-dependent methods, in particular, the spectra of metabolic activity range analysis in vitro under different temperature, pH and salinity conditions. High values for the total number of prokaryotes in situ (1.9 × 108–3.5 × 108 cells/g), a significant part of which was able to return to a metabolically active state after thawing, and moderate numbers of culturable bacteria (3.3 × 106–7.8 × 107 CFU/g) were revealed. Representatives of Proteobacteria, Actinobacteria, and Bacteroidetes were dominant in situ; Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes were the most abundant phyla in vitro. Physiological assays revealed the mesophilic and neutrophilic optima of temperature and pH of culturing conditions, respectively, and wide temperature and pH ranges of culturable communities’ reproduction activity. Isolated strains were characterized by moderate halotolerant properties and antibiotic resistance, including multiple antibiotic resistance. It was found that almost all cultured bacterial diversity revealed (not just a few resistant species) had extremotolerant properties regarding a number of stress factors. This indicates the high adaptive potential of the studied microbial communities and their high sustainability and capability to retain functional activity under changing environmental (including climatic) conditions in wide ranges.

Paenochrobactrum pullorum sp. nov. isolated from a chicken

A Gram-stain-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (strain 280(T)) isolated from a chicken was studied for its taxonomic allocation. 16S rRNA gene sequence analyses clearly allocated the isolate in the genus Paenochrobactrum group with a 16S rRNA gene sequence similarity of 98.8% to the currently recognized species, Paenochrobactrum gallinarii and Paenochrobactrum glaciei. This allocation was confirmed by the fatty acid data (major fatty acids: C18:1ω7c and C19:0 cyclo ω8c) and a polyamine pattern with the major compound putrescine and relatively high amounts of spermidine. Also, the polar lipid profile with phosphatidylethanolamine, phosphatiylmonomethylethanolamine, phosphatidylglycerol, phosphatidylcholine and the genus-specific 'stretched aminolipid' was well in line with the description of the genus Paenochrobactrum. The quinone system consisted predominantly of ubiquinone Q-10 with traces of Q-9 and Q-11. DNA-DNA hybridization of strain 280T with Paenochrobactrum gallinarii Sa25T and Paenochrobactrum glaciei KMM 3858T showed relatedness values of 38.8% (reciprocal 20.2%) and 30.2% (reciprocal 29.8%), respectively. These results in combination with differentiating physiological and biochemical data clearly showed that strain 280T merits species status. We propose the name Paenochrobactrum pullorum sp. nov. to accommodate this strain with the type strain 280T (=LMG 28095T=CIP 110700T).

Falsochrobactrum ovis gen. nov., sp. nov., isolated from a sheep

A Gram-stain-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (B1315(T)) was isolated from the placenta of a sheep with abortion. On the basis of 16S rRNA gene sequence analyses the strain was assigned to the Brucella-Ochrobactrum-Paenochrobactrum-Pseudochrobactrum group with 94.5-94.8 %, 94.3-96.1 %, 95.0-95.1 %, and 95.9-96.1 % sequence similarities to type strains of species of the four genera, respectively. Phylogenetic trees indicated a close relationship to the type strains of Ochrobactrum gallinifaecis and Ochrobactrum oryzae (95.9 and 96.1 % sequence similarity, respectively). Chemotaxonomic data confirmed the allocation of strain B1315(T) to the family Brucellaceae (quinone system: ubiquinone Q-10 and major fatty acids: C18 : 1ω7c and C19 : 0 cyclo ω8c). The polar lipid profile contained the major lipids diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and the unidentified but unique phospholipid PL7. The polyamine pattern of strain B1315(T) contained the major polyamines spermidine and putrescine. On the basis of the 16S rRNA gene and recA sequence phylogeny and chemotaxonomic data strain B1315(T) was clearly different from the genera Brucella, Ochrobactrum, Paenochrobactrum and Pseudochrobactrum. On the basis of these data we propose the novel genus Falsochrobactrum gen. nov. with the type species Falsochrobactrum ovis sp. nov. with the type strain B1315(T) ( = CCM 8460(T) = LMG 27356(T.)) The taxonomic allocation of O. gallinifaecis, which grouped inconsistently together with strain B1315(T) on the basis of 16S rRNA gene sequence data, but shows the chemotaxonomic features of the genus Ochrobactrum, remains to be clarified.

Paenochrobactrum gallinarii gen. nov., sp. nov., isolated from air of a duck barn, and reclassification of Pseudochrobactrum glaciei as Paenochrobactrum glaciei comb. nov

A Gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (Sa25(T)) was isolated from air of a duck barn. 16S rRNA gene and recA sequence analyses clearly placed the isolate in the vicinity of the Brucella-Ochrobactrum-Pseudochrobactrum group, with the closest relative being Pseudochrobactrum glaciei KMM 3858(T). This allocation was confirmed by analyses of the quinone system (ubiquinone Q-10), fatty acid data (major fatty acids C(18 : 1)omega7c and C(19 : 0) cyclo omega8c) and polar lipid profile (major components diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and unknown aminolipid AL1; moderate amounts of three unknown polar lipids, L1-L3, an unknown aminolipid and an unknown aminophospholipid APL2). The polyamine pattern of Sa25(T) exhibited the major compound putrescine and moderate amounts of spermidine; a similar polyamine pattern with the major compound putrescine was also detected in Pseudochrobactrum glaciei KMM 3858(T). DNA-DNA hybridization of strain Sa25(T) with Pseudochrobactrum glaciei KMM 3858(T) and the type strains of the other Pseudochrobactrum species showed values ranging from 50.3 to 24.8 %, and physiological and biochemical data clearly differentiated this isolate from the described Pseudochrobactrum species. Since Sa25(T) and Pseudochrobactrum glaciei KMM 3858(T) form a distinct lineage in the 16S rRNA gene sequence-based phylogenetic tree, and this separate position is supported by unique characteristics of their polyamine patterns and polar lipid profiles, we propose the novel genus Paenochrobactrum gen. nov., with the type species Paenochrobactrum gallinarii sp. nov. (type strain Sa25(T) =CCUG 57736(T) =CCM 7656(T)) and the reclassification of Pseudochrobactrum glaciei as Paenochrobactrum glaciei comb. nov. (type strain Pi26(T) =KMM 3858(T) =NRIC 0733(T) =JCM 15115(T)).

Pseudochrobactrum lubricantis sp. nov., isolated from a metal-working fluid

A Gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (KSS 7.8(T)) was isolated from a water-mixed metal-working fluid. On the basis of 16S rRNA gene and recA sequence similarities, the isolate was clearly grouped in the genus Pseudochrobactrum. This allocation was confirmed by fatty acid data (major fatty acids: C(18 : 2)omega7c and C(19 : 0) cyclo omega8c), polar lipid profile (major components: phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine, plus moderate amounts of phosphatidylmonomethylethanolamine and unknown aminolipid AL1), quinone system (ubiquinone Q-10) and polyamine pattern (spermidine and putrescine predominant). DNA-DNA pairing with the most closely related Pseudochrobactrum species showed values ranging from 24.2 to 45.7 %, and physiological and biochemical data clearly differentiated this isolate from described Pseudochrobactrum species. This organism represents a novel species of the genus Pseudochrobactrum, for which the name Pseudochrobactrum lubricantis sp. nov. is proposed, with the type strain KSS 7.8(T) (=CCUG 56963(T)=CCM 7581(T)).