Brevibacterium sandarakinum sp. nov., isolated from a wall of an indoor environment

Kämpfer, Peter; Schafer, James A.; Lodders, Nicole; Busse, Hans‐Jürgen

doi:10.1099/ijs.0.014100-0

Cited by 23 publications

(8 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The description is as before (Kämpfer et al, 2010b ) with the following addition. The G+C content of the type-strain genome is 63.3%, its approximate size 4.44 Mbp, its GenBank deposit SAMN04489751 .…”

Section: Discussionmentioning

confidence: 99%

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

et al. 2018

View full text Add to dashboard Cite

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

show abstract

Section: Discussionmentioning

confidence: 99%

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

et al. 2018

View full text Add to dashboard Cite

show abstract

“…In addition, it was an interesting finding that although most of the isolates could be assigned to already described species, several of them could not be clearly assigned to any known species or even genera, and hence novel species and genera have been proposed, such as for example, Pseudonocardia parietis [45], Citricoccus parietis [46], Prauserella muralis [47], Promicromonospora umidemergens [33], Brevibacterium sandarkinum [23], Microlunatus parietis [25], Kytococcus aerolatus [24], and Murinocardiopsis flavida [27].…”

Section: Discussionmentioning

confidence: 99%

Analysis of Actinobacteria from mould-colonized water damaged building material

Schafer

Jäckel

Kämpfer

2010

Systematic and Applied Microbiology

Self Cite

View full text Add to dashboard Cite

Mould-colonized water damaged building materials are frequently eo-colonized by actinomycetes. Here, we report the results of the analyses of Actinobacteria on different wall materials from water damaged buildings obtained by both cultivation-dependent and cultivation-independent methods. Actinobacteria were detected in all but one of the investigated materials by both methods. The detected concentrations of Actinobacteria ranged between 1.8 x 10 4 and 7.6 x 10 7 CFU g-1 of investigated material. A total of265 isolates from 17 materials could be assigned to 31 different genera of the classActinobacteria on the basis of 165 rRNA gene sequence analyses. On the basis of the cultivation-independent approach, 165 rRNA gene inserts of 800 clones (50%) were assigned to 47 different genera. Representatives of the genera Streptomyces, Amycolatopsis, Nocardiopsis, Saccharopolyspora, Promicromonospora, and Pseudonocardia were found most frequently. The results derived from both methods indicated a high abundance and variety of Actinobacteria in water damaged buildings. Four bioaerosol samples were investigated by the cultivation-based approach in order to compare the communities of Actinobacteria in building material and associated air samples. A comparison of the detected genera of bioaerosol samples with those directly obtained from material samples resulted in a congruent finding of 9 of the overall 35 detected genera (25%), whereas four genera were only detected in bioaerosolsamples.

show abstract

“… 239c Camembert cheese PRJEB19828 FXZH01000001-FXZH01000068 Permanent draft This study B. sp. Mu109 Munster cheese PRJEB19840 FXZF01000001-FXZF01000126 Permanent draft This study B. iodinum ATCC 49514 T Cow milk PRJEB19872 FXYX01000001-FXYX01000065 Permanent draft This study B. jeotgali SJ5-8 T Seafood PRJEB19841 FXZM01000001-FXZM01000047 Permanent draft This study B. aurantiacum ATCC 9174 a Romadur cheese PRJNA405 AAGP01000001-AAGP01000076 Permanent draft DOE JGI, 2005 (direct submission) B. album DSM 18261 T Soil PRJNA195785 AUFJ01000001-AUFJ01000016 Permanent draft Kyrpides et al , 2013 (direct submission) B. sandarakinum DSM 22082 T Wall surface PRJEB16423 LT629739 Complete Varghese, 2016 (direct submission) Kämpfer et al, 2010 [ 91 ] B. linens AE038–8 Fresh water PRJNA268212 JTJZ01000001-JTJZ01000029 Permanent draft Maizel et al , 2015 [ 92 ] B. siliguriense DSM 23676 T Fresh water PRJNA303729 LT629766 Complete Varghese, 2016 (direct submission) B. sp. VCM10 Fresh water PRJNA234061 JAJB01000001-JAJB01000141 Permanent draft Muthukrishnan et al , 2014 (direct submission) B. casei S18 Human...…”

Section: Methodsmentioning

confidence: 99%

Comparative genomic analysis of Brevibacterium strains: insights into key genetic determinants involved in adaptation to the cheese habitat

et al. 2017

View full text Add to dashboard Cite

Background Brevibacterium strains are widely used for the manufacturing of surface-ripened cheeses, contributing to the breakdown of lipids and proteins and producing volatile sulfur compounds and red-orange pigments. The objective of the present study was to perform comparative genomic analyses in order to better understand the mechanisms involved in their ability to grow on the cheese surface and the differences between the strains.ResultsThe genomes of 23 Brevibacterium strains, including twelve strains isolated from cheeses, were compared for their gene repertoire involved in salt tolerance, iron acquisition, bacteriocin production and the ability to use the energy compounds present in cheeses. All or almost all the genomes encode the enzymes involved in ethanol, acetate, lactate, 4-aminobutyrate and glycerol catabolism, and in the synthesis of the osmoprotectants ectoine, glycine-betaine and trehalose. Most of the genomes contain two contiguous genes encoding extracellular proteases, one of which was previously characterized for its activity on caseins. Genes encoding a secreted triacylglycerol lipase or involved in the catabolism of galactose and D-galactonate or in the synthesis of a hydroxamate-type siderophore are present in part of the genomes. Numerous Fe3+/siderophore ABC transport components are present, part of them resulting from horizontal gene transfers. Two cheese-associated strains have also acquired catecholate-type siderophore biosynthesis gene clusters by horizontal gene transfer. Predicted bacteriocin biosynthesis genes are present in most of the strains, and one of the corresponding gene clusters is located in a probable conjugative transposon that was only found in cheese-associated strains.Conclusions Brevibacterium strains show differences in their gene repertoire potentially involved in the ability to grow on the cheese surface. Part of these differences can be explained by different phylogenetic positions or by horizontal gene transfer events. Some of the distinguishing features concern biotic interactions with other strains such as the secretion of proteases and triacylglycerol lipases, and competition for iron or bacteriocin production. In the future, it would be interesting to take the properties deduced from genomic analyses into account in order to improve the screening and selection of Brevibacterium strains, and their association with other ripening culture components.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4322-1) contains supplementary material, which is available to authorized users.

show abstract

Brevibacterium sandarakinum sp. nov., isolated from a wall of an indoor environment

Cited by 23 publications

References 34 publications

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

Analysis of Actinobacteria from mould-colonized water damaged building material

Comparative genomic analysis of Brevibacterium strains: insights into key genetic determinants involved in adaptation to the cheese habitat

Contact Info

Product

Resources

About