Circular genomes of two bacterial strains capable of growing in a CO2-containing atmosphere.

The bacterial strains Brochothrix thermosphacta DH-B18 and Rathayibacter sp. DH-RSZ4 were isolated from raw sausage and escalope samples and grown in a CO2-rich modified atmosphere. Here, we present both circular genomes obtained by nanopore sequencing.

Fungi under Modified Atmosphere-The Effects of CO2 Stress on Cell Membranes and Description of New Yeast Stenotrophomyces fumitolerans gen. nov., sp. nov.

High levels of carbon dioxide are known to inhibit the growth of microorganisms. A total of twenty strains of filamentous fungi and yeasts were isolated from habitats with enriched carbon dioxide concentration. Most strains were derived from modified atmosphere packed (MAP) food products or mofettes and were cultivated under an atmosphere of 20% CO2 and 80% O2. The influence of CO2 on fungal cell membrane fatty acid profiles was examined in this study. Major changes were the increase in linolenic acid (C18:3 cis 9, 12, 15) and, additionally in most strains, linoleic acid (C18:2 cis 9, 12) with a maximum of 24.8%, at the expense of oleic (C18:1 cis 9), palmitic (C16:0), palmitoleic (C16:1 cis 9) and stearic acid (C18:0). The degree of fatty acid unsaturation increased for all of the strains in the study, which consequently led to lower melting temperatures of the cell membranes after incubation with elevated levels of CO2, indicating fluidization of the membrane and a potential membrane malfunction. Growth was reduced in 18 out of 20 strains in laboratory experiments and a change in pigmentation was observed in several strains. Two of the isolated strains, strain WT5 and strain WR1, were found to represent a hitherto undescribed yeast for which the new genus and species Stenotrophomyces fumitolerans (MB# 849906) is proposed.

Phenotypic and genomic assessment of the potential threat of human spaceflight-relevant Staphylococcus capitis isolates under stress conditions.

Previous studies have reported that spaceflight specific conditions such as microgravity lead to changes in bacterial physiology and resistance behavior including increased expression of virulence factors, enhanced biofilm formation and decreased susceptibility to antibiotics. To assess if spaceflight induced physiological changes can manifest in human-associated bacteria, we compared three spaceflight relevant Staphylococcus capitis isolates (DSM 111179, ISS; DSM 31028, clean room; DSM 113836; artificial gravity bedrest study) with the type strain (DSM 20326T). We tested the three strains regarding growth, colony morphology, metabolism, fatty acid and polar lipid pattern, biofilm formation, susceptibility to antibiotics and survival in different stress conditions such as treatment with hydrogen peroxide, exposure to desiccation, and irradiation with X-rays and UV-C. Moreover, we sequenced, assembled, and analyzed the genomes of all four strains. Potential genetic determinants for phenotypic differences were investigated by comparative genomics. We found that all four strains show similar metabolic patterns and the same susceptibility to antibiotics. All four strains were considered resistant to fosfomycin. Physiological differences were mainly observed compared to the type strain and minor differences among the other three strains. The ISS isolate and the bedrest study isolate exhibit a strong delayed yellow pigmentation, which is absent in the other two strains. Pigments were extracted and analyzed by UV/Vis spectroscopy showing characteristic carotenoid spectra. The ISS isolate showed the highest growth rate as well as weighted average melting temperature (WAMT) of fatty acids (41.8°C) of all strains. The clean room isolate showed strongest biofilm formation and a high tolerance to desiccation. In general, all strains survived desiccation better in absence of oxygen. There were no differences among the strains regarding radiation tolerance. Phenotypic and genomic differences among the strains observed in this study are not inevitably indicating an increased virulence of the spaceflight isolate. However, the increased growth rate, higher WAMT and colony pigmentation of the spaceflight isolate are relevant phenotypes that require further research within the human spaceflight context. We conclude that combining genetic analysis with classical microbiological methods allows the detailed assessment of the potential threat of bacteria in highly regulated and extreme environments such as spaceflight environments.

Polar lipid characterization and description of Chryseobacterium capnotolerans sp. nov., isolated from high CO2-containing atmosphere and emended descriptions of the genus Chryseobacterium, and the species C. balustinum, C. daecheongense, C. formosense, C. gleum, C. indologenes, C. joostei, C. scophthalmum and C. ureilyticum.

Modified atmosphere (MA) packaging plays an important role in improving food quality and safety. By using different gas mixtures and packaging materials the shelf life of fresh produce can significantly be increased. A Gram-negative-staining, rod-shaped, orange-pigmented strain DH-B6T, has been isolated from MA packed raw pork sausage (20% CO2, 80% O2). The strain produced biofilms and showed growth at high CO2 levels of up to 40%. Complete 16S rRNA gene and whole-genome sequences revealed that strain DH-B6T belongs to the genus Chryseobacterium, being closely related to strain Chryseobacterium indologenes DSM 16777T (98.4%), followed by Chryseobacterium gleum NCTC11432T (98.3%) and Chryseobacterium lactis KC1864T (98.2%). Average nucleotide identity value between DH-B6T and C. indologenes DSM 16777T was 81.1% and digital DNA-DNA hybridisation was 24.9%, respectively. The DNA G+C content was 35.51 mol%. Chemotaxonomical analysis revealed the presence of the rare glycine lipid cytolipin, the serine-glycine lipid flavolipin and the sulfonolipid sulfobacin A, as well as phosphatidylethanolamine, monohexosyldiacylglycerol and ornithine lipid, including the hydroxylated forms. Major fatty acids were iC15 : 0 (50.7%) and iC17 : 1 cis 9 (28.7%), followed by iC15 : 0 2-OH (7.0%) and iC17 : 0 3-OH (6.2%). The isolated strain contained MK-6 as the only respiratory quinone and flexirubin-like pigments were detected as the major pigments. Based on the phenotypic, chemotaxonomic and phylogenetic characteristics, the strain DH-B6T (=DSM 110542T=LMG 31915T) represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium capnotolerans sp. nov. is proposed. Emended descriptions of the genus Chryseobacterium and eight species of this genus based on polar lipid characterisation are also proposed.

Sphingomonas aliaeris sp. nov., a new species isolated from pork steak packed under modified atmosphere.

Species belonging to the genus Sphingomonas have been isolated from environments such as soil, water and plant tissues. Many strains are known for their capability of degrading aromatic molecules and producing extracellular polymers. A Gram-stain-negative, strictly aerobic, motile, red-pigmented, oxidase-negative, catalase-positive, rod-shaped strain, designated DH-S5T, has been isolated from pork steak packed under CO2-enriched modified atmosphere. Cell diameters were 1.5×0.9 µm. Growth optima were at 30 °C and at pH 6.0. Phylogenetic analyses based on both complete 16S rRNA gene sequence and whole-genome sequence data revealed that strain DH-S5T belongs to the genus Sphingomonas, being closely related to Sphingomonas alpina DSM 22537T (97.4 % gene sequence similarity), followed by Sphingomonas qilianensis X1T (97.4 %) and Sphingomonas hylomeconis GZJT-2T (97.3 %). The DNA G+C content was 64.4 mol%. The digital DNA-DNA hybridization value between the isolate strain and S. alpina DSM 22537T was 21.0 % with an average nucleotide identity value of 77.03 %. Strain DH-S5T contained Q-10 as the ubiquinone and major fatty acids were C18 : 1 cis 11 (39.3 %) and C16 : 1 cis 9 (12.5 %), as well as C16 : 0 (12.1 %) and C14 : 0 2-OH (11.4 %). As for polar lipids, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, dimethylphosphatidylethanolamine and sphingoglycolipid could be detected, alongside traces of monomethylphosphatidylethanolamine. Based on its phenotypic, chemotaxonomic and phylogenetic characteristics, strain DH-S5T (=DSM 110829T=LMG 31606T) is classified as a representative of the genus Sphingomonas, for which the name Sphingomonas aliaeris sp. nov. is proposed.

Arthrobacter bussei sp. nov., a pink-coloured organism isolated from cheese made of cow's milk.

A pink-coloured bacterium (strain KR32T) was isolated from cheese and assigned to the 'Arthrobacter agilis group'. Members of the 'pink Arthrobacter agilis group' form a stable clade (100 % bootstrap value) and contain the species Arthrobacter agilis, Arthrobacter ruber and Arthrobacter echini, which share ≥99.0 % 16S rRNA gene sequence similarity. Isolate KR32T showed highest 16S rRNA gene sequence similarity (99.9 %) to A. agilis DSM 20550T. Additional multilocus sequence comparison confirmed the assignment of strain KR32T to the clade 'pink A. agilis group'. Average nucleotide identity and digital DNA-DNA hybridization values between isolate KR32T and A. agilis DSM 20550T were 82.85 and 26.30 %, respectively. The G+C content of the genomic DNA of isolate KR32T was 69.14 mol%. Chemotaxonomic analysis determined anteiso-C15 : 0 as the predominant fatty acid and MK-9(H2) as the predominant menaquinone. Polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and monoacyldimannosyl-monoacylglycerol. The peptidoglycan type of the isolate was A3α. The carotenoid bacterioruberin was detected as the major pigment. At 10 °C, strain KR32T grew with increased concentrations of bacterioruberin and production of unsaturated fatty acids. Strain KR32T was a Gram-stain-positive, catalase-positive, oxidase-positive and coccus-shaped bacterium with optimal growth at 27-30 °C and pH 8. The results of phylogenetic and phenotypic analyses enabled the differentiation of the isolate from other closely related species of the 'pink A. agilis group'. Therefore, strain KR32T represents a novel species for which the name Arthrobacter bussei sp. nov. is proposed. The type strain is KR32T (=DSM 109896T=LMG 31480T=NCCB 100733T).

Galactobacter caseinivorans gen. nov., sp. nov. and Galactobacter valiniphilus sp. nov., two novel species of the family Micrococcaceae, isolated from high bacterial count raw cow's milk.

Four Gram-stain positive, rod-shaped bacterial isolates, strains JZ R-183T, JZ RK-117, DI-46 and JZ R-35T, were recovered from bulk tank raw cow's milk from three different dairy farms in Germany. Analysis of their 16S rRNA gene sequences indicated that these isolates belonged to the family Micrococcaceae, closely related to the genera Arthrobacter, Neomicrococcus,Glutamicibacter and Citricoccus. The 16S rRNA gene sequence similarity between the isolates and the next related type strains was below 97.3 %. Phylogenetic analysis of 16S rRNA, recA and gyrB genes revealed that these isolates formed two different groups in an independent cluster within the family Micrococcaceae. Chemotaxonomic analyses determined anteiso-C15 : 0 as predominant fatty acid, but also large amounts of iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0 were detected. The menaquinones MK-9(H2) and MK-7(H2) were present in all of the isolates and the polar lipid pattern contained the phospholipids diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol and a glycolipid. The peptidoglycan type of the isolates was A4α, with alanine, lysine and glutamate as dominating cell wall amino acids. The fatty acid and menaquinone profile differentiated the strains from the genera Arthrobacter, Neomicrococcus,Citricoccus and Glutamicibacter. The results of phylogenetic, phenotypic and chemotaxonomic analyses indicated that the isolates belonged to two novel species of a novel genus, for which the names Galactobacter caseinivorans gen. nov., sp. nov. and Galactobacter valiniphilus sp. nov. are proposed. The type strains are JZ R-183T (=DSM 107700T=LMG 30902T) and JZ R-35T (=DSM 107699T=LMG 30901T).