Comparative genomic analysis of the Dietzia genus: an insight into genomic diversity, and adaptation

Dietzia strains are widely distributed in the environment, presenting an opportunistic role, and some species have undetermined taxonomic characteristics. Here, we propose the existence of errors in the classification of species in this genus using comparative genomics. We performed ANI, dDDH, pangenome and genomic plasticity analyses better to elucidate the phylogenomic relationships between Dietzia strains. For this, we used 55 genomes of Dietzia downloaded from public databases that were combined with a newly sequenced. Sequence analysis of a phylogenetic tree based on genome similarity comparisons and dDDH, ANI analyses supported grouping different Dietzia species into four distinct groups. The pangenome analysis corroborated the classification of these groups, supporting the idea that some species of Dietzia could be reassigned in a possible classification into three distinct species, each containing less variability than that found within the global pangenome of all strains. Additionally, analysis of genomic plasticity based on groups containing Dietzia strains found differences in the presence and absence of symbiotic Islands and pathogenic islands related to their isolation site. We propose that the comparison of pangenome subsets together with phylogenomic approaches can be used as an alternative for the classification and differentiation of new species of the genus Dietzia.

Succession, Replacement, and Modification of Chicken Litter Microbiota

Chickens are in constant interaction with their environment, e.g., bedding and litter, and their microbiota. However, how litter microbiota develops over time and whether bedding and litter microbiota may affect the cecal microbiota is not clear. We addressed these questions using sequencing of V3/V4 variable region of 16S rRNA genes of cecal, bedding, and litter samples from broiler breeder chicken flocks for 4 months of production. Cecal, bedding, and litter samples were populated by microbiota of distinct composition. The microbiota in the bedding material did not expand in the litter. Similarly, major species from litter microbiota did not expand in the cecum. Only cecal microbiota was found in the litter forming approximately 20% of total litter microbiota. A time-dependent development of litter microbiota was observed. Escherichia coli, Staphylococcus saprophyticus, and Weissella jogaejeotgali were characteristic of fresh litter during the first month of production. Corynebacterium casei, Lactobacillus gasseri, and Lactobacillus salivarius dominated in a 2-month-old litter, Brevibacterium, Brachybacterium, and Sphingobacterium were characteristic for 3-month-old litter, and Salinococcus, Dietzia, Yaniella, and Staphylococcus lentus were common in a 4-month-old litter. Although the development was likely determined by physicochemical conditions in the litter, it might be interesting to test some of these species for active modification of litter to improve the chicken environment and welfare. IMPORTANCE Despite intimate contact, the composition of bedding, litter, and cecal microbiota differs considerably. Species characteristic for litter microbiota at different time points of chicken production were identified thus opening the possibility for active manipulation of litter microbiota.

Pan-genomic analysis reveals that the evolution of Dietzia species depends on their living habitats

The bacterial genus Dietzia is widely distributed in various environments. The genomes of 26 diverse strains of Dietzia, including almost all the type strains, were analysed in this study. This analysis revealed a lipid metabolism gene richness, which could explain the ability of Dietzia to live in oil related environments. The pan-genome consists of 83,976 genes assigned into 10,327 gene families, 792 of which are shared by all the genomes of Dietzia. Mathematical extrapolation of the data suggests that the Dietzia pan-genome is open. Both gene duplication and gene loss contributed to the open pan-genome, while horizontal gene transfer was limited. Dietzia strains primarily gained their diverse metabolic capacity through more ancient gene duplications. Phylogenetic analysis of Dietzia isolated from aquatic and terrestrial environments showed two distinct clades from the same ancestor. The genome sizes of Dietzia strains from aquatic environments were significantly larger than those from terrestrial environments, which was mainly due to the occurrence of more gene loss events during the evolutionary progress of the strains from terrestrial environments. The evolutionary history of Dietzia was tightly coupled to environmental conditions, and iron concentrations should be one of the key factors shaping the genomes of the Dietzia lineages.

Fatty acids in bacterium Dietzia sp. grown on simple and complex hydrocarbons determined as FAME by GC-MS

The influence of growth substrates on the fatty acids produced by Dietzia sp. A14101 has been studied to investigate how qualitative and semi-quantitative information on fatty acids correlates with the ability of this strain to access and utilize a wide range of water-immiscible HC-substrates by modifying the FA content and thus also the properties of the cellular membrane. After incubation on different substrates and media, the profiles of fatty acids (FA) were analyzed by gas chromatography and mass spectrometry (GC-MS). The equivalent chain length (ECL) index calibration system was employed to identify FA. The effect of each substrate on the cell surface charge and on the hydrophobicity of the cellular membrane was also investigated. The results indicate that the variation of the content of saturated fatty acids (SAT-FA) versus mono-unsaturated fatty acids (MUFA) was found to be the most pronounced while branched FA exhibited much less variation in spite of different substrate regimes. The regulation of the ratio of SAT-FA and MUFA seems to be coupled with the regulation of the charge and hydrophobicity of the outer cellular surface. The exposure to a water immiscible substrate led to the development of the negative cellular surface charge, production of carotenoid-type pigments and increased hydrophobicity of the cellular surface. The specific aspects of the adaptation mechanism could have implications for bioremediation and/or (M)EOR applications.

Dietzia aurantiaca sp. nov., isolated from a human clinical specimen

A Gram-positive, coccoid, non-endospore-forming actinobacterium (strain CCUG 35676T) was isolated from cerebrospinal fluid from a 24-year-old woman in Gothenborg, Sweden. Based on pairwise 16S rRNA gene sequence similarity studies, strain CCUG 35676T was shown to belong to the genus Dietzia and was most closely related to the type strains of Dietzia aerolata (99.3 %), Dietzia lutea (98.8 %), Dietzia schimae (98.5 %), Dietzia maris (98.5 %), Dietzia alimentaria (98.3 %) and Dietzia cercidiphylli (98.0 %). The major menaquinone was MK-8(H2). Major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, an unidentified aminophospholipid (APL1), an unidentified phospholipid (PL1) and unidentified glycolipids (GL1 and GL3). Numerous other lipids were also detected. The fatty acid profile, comprising C16 : 0, C17 : 0, C18 : 1ω9c and 10-methyl-C18 : 0 as major fatty acids, supported the affiliation of strain CCUG 35676T to the genus Dietzia. On the basis of the results of physiological and biochemical tests and DNA–DNA hybridizations, a clear phenotypic and genotypic differentiation of strain CCUG 35676T from the most closely related Dietzia species is possible. Strain CCUG 35676T represents a novel species, for which the name Dietzia aurantiaca sp. nov. is proposed, with CCUG 35676T ( = JCM 17645T) as the type strain.

Draft genome sequence of Dietzia alimentaria 72T, belonging to the family Dietziaceae, isolated from a traditional Korean food

Actinobacterial strain 72(T), named Dietzia alimentaria, which belongs to the family Dietziaceae, was isolated from a traditional Korean food made from clams. The draft genome sequence of D. alimentaria 72(T) contains 3,352,817 bp, with a G+C content of 67.34%.

Dietzia alimentaria sp. nov., isolated from a traditional Korean food

An actinobacterial strain, designated 72T, was isolated from a traditional salt-fermented seafood in Korea. Colonies were coral red and cells were Gram-reaction-positive, non-motile rods. Strain 72T grew with 0–10 % (w/v) NaCl, at pH 7–10 and at 15–37 °C. Optimum growth conditions were 2 % NaCl, pH 7.0 and 30 °C. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain 72T belonged to the genus Dietzia. The major cellular fatty acids (>5 %) were C16 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), 10-methyl C18 : 0, C17 : 0, C19 : 0 and C18 : 1ω9c. 16S rRNA gene sequence analysis and DNA–DNA hybridization, coupled with physiological and biochemical tests, revealed genotypic and phenotypic differences between strain 72T and other members of the genus Dietzia. Based on these data, strain 72T represents a novel species, for which the name Dietzia alimentaria sp. nov. is proposed. The type strain is 72T ( = JCM 16360T  = KACC 21126T).