Fundamental and applied aspects of microbiology

Whole genome sequencing of a ST2594 MRSA strain causing non-mucosal preoperative colonization and low-grade postoperative infection Abstract We present a post-operative infection caused by a methicillin-resistant Staphylococcus aureus strain, previously isolated in the preoperative screening, in a patient submitted to femoral osteosynthesis, successfully treated with oral ciprofloxacin. The isolate exhibited in vitro resistance to ciprofloxacin, Staphylococcal Cassette Chromosome mec type IV, it was negative for the lukS-PV Panton–Valentine leucocidin gene and belonged to ST2594 in multilocus sequence typing analysis. Whole genome sequencing revealed a genome size of 2,818,289 base pairs. The annotated genomes of ST2594 and N315 strains were compared, looking for genes related to virulence and resistance. The lack of the tst, sec, sel genes, associated with a mutation in the clfA gene, may partially explain the low morbity in this case.

Renaming of ' Candidatus Methylocucumis oryzae' as Methylocucumis oryzae gen. nov., sp. nov., a novel Type I methanotroph isolated from India Abstract Candidatus Methylocucumis (Mcu.) oryzae, strain Sn10-6, a Gram-negative, pale pink pigmented, motile, large Type I methanotroph (3–6 µm × 1.5–2 µm) was recently isolated from an Indian rice field. Due to the difficulties in preservation of the strain it could not be deposited and preserved in two recognised culture collections with public access located in two different countries. Hence, Sn10-6 was described as a member of a Candidatusgenus and species, 'Ca. Mcu. oryzae'. Subsequent to the publication, the strain has been preserved in the Japan Collection of Microorganisms, Japan (JCM 32869T) in addition to its earlier preservation in the Korean collection for type cultures, KCTC, Korea and in National Centre for Microbial Resources, India. Addition of DMSO as a cryopreserving agent proved to be useful in the preservation of the strain. The deposition of the strain in two recognised culture collections in two different countries and additionally in the home country repository makes the strain eligible to be proposed as the type strain of the type species of a new genus and species with the name Methylocucumis oryzae strain Sn10-6T. In this paper we formally propose the name Mcu. oryzae, with Sn10-6T as the type strain, for the earlier described Ca. Mcu. oryzae. Other characteristics including the digital protologue of the culture (CA00040) remain the same as described earlier for Ca. Mcu. oryzae (Pandit et al. in Antonie Van Leeuwenhoek 111:2473–2484, 2018). Mcu. oryzae Sn10-6T (= MCC 3492 = KCTC 15683 = JCM 32869) represents a new genus and species within the family Methylococcaceae of the class Gammaproteobacteria.

Paracoccus indicus sp. nov., isolated from surface seawater in the Indian Ocean Abstract Strain IO390502T, isolated from surface seawater in the Indian Ocean, was characterised using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain IO390502T belongs to the genus Paracoccus and is closely related to Paracoccus seriniphilus DSM 14827T (97.6%), followed by P. zeaxanthinifaciens JCM 21774T (97.5%), P. homiensis DSM 17862T (97.3%), P. marcusiiDSM 11574T (97.2%), P. haeundaensis BC 74171T (97.0%) and P. carotinifaciens E-396T (97.0%). Cells are Gram-negative, aerobic, poly-β-hydroxybutyrate-accumulating, motile, rod-shaped, and forms creamy-white colonies. Optimal growth occurred at 25–30 °C, pH 5–8, and in the presence of 3–8% NaCl. The genome of strain IO390502T has a G+C content of 64.9 mol% and a 3.5 Mb chromosome. The in silico DNA–DNA hybridisation and average nucleotide identity values between strain IO390502T and the three closely related taxa, P. seriniphilus DSM 14827T, P. zeaxanthinifaciens JCM 21774T and P. homiensis DSM 17862T, are 19.6%, 21.9% and 20.6%, and 76.0%, 79.9% and 77.8%, respectively. Phosphatidylglycerol is the major lipid present, ubiquinone-10 (Q-10) is the sole isoprenoid quinone, and the major cellular fatty acid is C18:1ω7c. Based on data from phenotypic tests and genotypic differences between strain IO390502T and its close phylogenetic relatives, strain IO390502T represents a new species belonging to the genus Paracoccus, for which the name Paracoccus indicus sp. nov. is proposed. The type strain is IO390502T (= JCM 32637T = CCTCC AB 2018071T).

Description of Wenzhouxiangella salilacus sp. nov., a moderate halophilic bacterium isolated from a salt lake in Xinjiang Province, China Abstract A Gram-stain negative, non-motile, strictly aerobic and rod-shaped bacterium, designated as 15181T, was isolated from a salt lake in Xinjiang Province, China. Strain 15181T was able to grow at 10–40 °C (optimum 37 °C), pH 6.0–8.5 (optimum 7.0) and with 1–14% NaCl (optimum 4%, w/v). According to phylogenetic analysis based on 16S rRNA gene sequences, strain 15181T was assigned to the genus Wenzhouxiangella with high 16S rRNA gene sequence similarity of 97.4% to Wenzhouxiangella sediminis XDB06T, followed by Wenzhouxiangella marina KCTC 42284T (95.9%). Strain 15181T exhibited ANI values of 80.0% and 72.0% to W. sediminisXDB06T and W. marina KCTC 42284T, respectively. The in silico DDH analysis revealed that strain 15181T shared 19.1% and 18.7% DNA relatedness with W. sediminis XDB06T and W. marina KCTC 42284T, respectively. Chemotaxonomic analysis showed that the sole respiratory quinone was ubiquinone-8, the major fatty acids included iso-C15:0, iso-C16:0 and summed feature 9 (C16:0 10-methyl and/or iso-C17:1ω9c). The major polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified glycolipids, two unidentified phospholipids, two unidentified aminophospholipids and an unidentified lipid. On the basis of phenotypic, genotypic and chemotaxonomic characteristics presented in this study, strain 15181T is concluded to represent a novel species in the genus Wenzhouxiangella, for which the name Wenzhouxiangella salilacussp. nov. is proposed. The type strain is 15181T (=KCTC 62172T=MCCC 1K03442T).

Description and genomic characterization of Massiliimalia massiliensis gen. nov., sp. nov., and Massiliimalia timonensis gen. nov., sp. nov., two new members of the family Ruminococcaceae isolated from the human gut Abstract Using the culturomics approach, we isolated two strains, Marseille-P2963 and Marseille-P3753, from the intestinal microbiota of a 19-year-old healthy Saudi Arabian Bedouin male and from a 32-year-old healthy Senegalese male faecal transplant donor. Here, we studied their phenotypic, phylogenetic and genomic characteristics. Both strains were phylogenetically related, but different from Ruminococcus species. Bacterial cells were anaerobic, rod-shaped, non-spore-forming and not motile, with neither catalase nor oxidase activities. Their growth temperatures ranged from 28 to 45 °C, with an optimal growth at 37 °C. The genomes are 2,842,720 bp- and 2,707,061 bp-long respectively. The G + C contents are 47.18% and 46.90%, respectively. Based on these characteristics, we propose the creation of a new genus within the family Ruminococcaceaenamed Massiliimalia gen. nov., that contains the new species Massiliimalia massiliensis gen. nov., sp. nov., and Massiliimalia timonensis gen. nov., sp. nov. Strains Marseille-P2963T (= CSUR P2963 = DSM 106837) and Marseille-P3753T (= CSUR P3753 = CCUG 71632) are their type strains, respectively.

Ethanol stress responses of Kluyveromyces marxianus CCT 7735 revealed by proteomic and metabolomic analyses Abstract Kluyveromyces marxianus CCT 7735 offers advantages to ethanol production over Saccharomyces cerevisiae, including thermotolerance and the ability to convert lactose to ethanol. However, its growth is impaired at high ethanol concentrations. Herein we report on the protein and intracellular metabolite profiles of K. marxianus at 1 and 4 h under ethanol exposure. The concentration of some amino acids, trehalose and ergosterol were also measured. We observed that proteins and metabolites from carbon pathways and translation were less abundant, mainly at 4 h of ethanol stress. Nevertheless, the concentration of some amino acids and trehalose increased at 8 and 12 h under ethanol stress, indicating an adaptive response. Moreover, our results show that the abundance of proteins and metabolites related to the oxidative stresses responses increased. The results obtained in this study provide insights into understanding the physiological changes in K. marxianus under ethanol stress, indicating possible targets for ethanol tolerant strains construction.

Rhodobacter thermarum sp. nov., a novel phototrophic bacterium isolated from sediment of a hot spring Abstract An ovoid to rod-shaped, phototrophic, purple non-sulfur bacterium was isolated from a sediment sample of a hot spring in Tibet, China. Cells of strain YIM 73036T were Gram-stain negative, non-motile and multiplied by binary fission. Strain YIM 73036T grew optimally at pH 7.0–7.5 at 37–45 °C. Growth occurred in 0.5–3.5% (w/v) NaCl. Vitamins were not required for growth. The presence of photosynthesis genes pufL and pufM were shown and photosynthesis pigments were formed. Bacteriochlorophyll α, the bacteriopheophytin and carotenoids were present as photosynthetic pigments. Internal cytoplasmic membranes were of the lamellar type. The organism YIM 73036T was able to grow chemo-organoheterophically, chemo-lithoautotrophically and photo-organoheterotrophically but photo-lithoautotrophic and fermentative growth were not demonstrated. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain YIM 73036T is closely related to Rhodobacter blasticus ATCC 33485T (96.65% sequence similarity) and clustered with species of the genus Rhodobacter of the family Rhodobacteraceae. Whole-genome sequence analyses based on the average nucleotide BLAST identity (ANI < 82%) indicated that this isolate belongs to a novel species. The genomic DNA G+C content of organism YIM 73036T was determined to be 66.0 mol%. Strain YIM 73036T contained Q-10 as the predominant ubiquinone and C18:1ω7c, C18:1ω7c 11-methyl and C18:0 as the major fatty acids. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and unidentified phospholipid. Differential phenotypic and chemotaxonomic properties, together with the phylogenetic distinctiveness, demonstrated that strain YIM 73036T is distinguishable from other species of the genus Rhodobacter. On the basis of the data presented, strain YIM 73036T is considered to represent a novel species of the genus Rhodobacter, for which the name Rhodobacter thermarum sp. nov. [type strain YIM 73036T (= KCTC 52712T = CCTCC AB 2016298T)] is proposed.

Dysgonomonas massiliensis sp. nov., a new species isolated from the human gut and its taxonogenomic description Abstract Culturomics has allowed the isolation of a significant number of new bacterial species from the human gut microbiota and proved to be a valuable complement to culture-independent techniques. Using this culture-based approach, a new bacterial species has been isolated from a stool sample of a 39-year-old healthy Pygmy male and described using the taxonogenomic strategy. Cells of strain Marseille-P4356T are Gram-stain negative cocci. The strain grows optimally at 37 °C and is catalase positive but oxidase negative. Its 16S rRNA gene sequence exhibited 92.96% sequence similarity with Dysgonomonas gadei strain JCM 16698T (NR_113134.1), currently its phylogenetically closest species that has been validly named. The genome of strain Marseille-P4356T is 3,472,011 bp long with 37.3 mol% G+C content. Phenotypic, biochemical, proteomic, genomic and phylogenetic analyses, clearly demonstrate that strain Marseille-P4356T (= CCUG 71356T = CSUR P4356T) represents a new species within the genus Dysgonomonas, for which we propose the name Dysgonomonas massiliensis sp. nov.

Salipaludibacillus keqinensis sp. nov., a moderately halophilic bacterium isolated from a saline–alkaline lake Abstract A novel Gram-stain positive, short rod, forming sub-terminal endospores of ellipsoidal shape, halophilic, alkaliphilic and aerobic bacterium, designated strain KQ-12T, was isolated from a saline–alkaline lake in China, and characterised by a polyphasic taxonomic approach. The isolate grew at 4–40 °C (optimum, 25 °C), at pH 8.0–10.0 (pH 9.0) and in the presence of 0–16% (w/v) NaCl (8%). 16S rRNA gene sequence similarity of KQ-12T to species in the genera Salipaludibacillus ranged from 96.6 to 98.1%. Phylogenetic trees indicated that the strain should be assigned to the genus Salipaludibacillus. The polar lipids of KQ-12T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified phospholipid and its major cellular fatty acids were anteiso-C15:0, anteiso-C17:0, iso-C15:0, and C16:0. The isoprenoid quinone was MK-7. These key chemotaxonomic properties also confirmed the affiliation of the strain to the genus Salipaludibacillus. However, some physiological, biochemical properties, low average nucleotide identity and low digital DNA–DNA hybridization relatedness values enabled the strain to be differentiated from closely related species of the genus Salipaludibacillus. Thus, KQ-12T can be classified as a novel species in the genus Salipaludibacillus, for which the name Salipaludibacillus keqinensis sp. nov. is proposed. The type strain is KQ-12T ( =  ACCC 60430T   =  KCTC 33935T).

Nocardioides speluncae sp. nov., a novel actinobacterium isolated from a karstic subterranean environment sample Abstract A novel actinobacterial strain, designated YIM ART13T, was isolated from a soil sample collected from a karst cave in Xingyi county, Guizhou province, South western China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were found to aerobic and Gram-stain positive. On the basis of 16S rRNA gene sequence analysis, strain YIM ART13T was found to be closely related to Nocardioides pakistanensis NCCP 1340T (96.1% sequence similarity) and is therefore considered to represent a member of the genus Nocardioides. In addition, ll-diaminopimelic acid was identified as the diagnostic diamino acid in the cell wall peptidoglycan. The whole cell sugars were found to be mannose, galactose, glucose and ribose. The major isoprenoid quinone was identified as MK-8(H4), while the major fatty acids (> 10%) were identified as iso-C16:0, C18:1ω9c and C18:0 10-methyl. The polar lipids were found to contain diphosphatidylglycerol, phosphatidylglycerol phosphatidylinositol and phosphatidylinositol mannoside, an unidentified phospholipid. The genomic DNA G+C content of strain YIM ART13T was determined from the draft genome sequence to be 70.1 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain YIM ART13Trepresents a novel species of the genus Nocardioides, for which the name Nocardioides speluncae sp. nov. is proposed. The type strain is YIM ART13T (= KCTC 39593T = DSM 100493T).