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International Journal of Systematic and... Feb 2018Two dark pink pigmented bacterial strains (M3 and M11) were isolated from crude oil contaminated desert sand from Kuwait. Both strains were Gram-stain-negative and...
Two dark pink pigmented bacterial strains (M3 and M11) were isolated from crude oil contaminated desert sand from Kuwait. Both strains were Gram-stain-negative and small-rod to oval-shaped bacteria. Strains M3 and M11 grew at 13-42 °C (optimum, 30-35 °C) and pH 6.5-9.0 (optimum, 7.0-7.5). No additional NaCl was required for the growth of both strains. The genomic DNA G+C content of strains M3 and M11 were 69.5 and 69.0 mol%, respectively. Both strains were closely related and the mean DNA-DNA hybridization value was 92±1 %. 16S rRNA gene sequence comparisons of both strains indicated that they belong to the genus Roseomonas. Strains M3 and M11 had a sequence similarity of 97.3 and 97.4 % with Roseomonas oryzae JC288, respectively. Both strains had <97 % 16S rRNA gene sequence similarity with other members of the genus Roseomonas. Strain M3 showed 18±2 and 13±2 % reassociation (based on DNA-DNA hybridization) with R. oryzae KCTC 42542 and Roseomonas cervicalis KACC 11686, respectively. The major cellular fatty acids (>5 %) were identified as C18 : 1ω6c/C18 : 1ω7c, C16 : 1ω6c/C16 : 1ω7c and C16 : 0 in both strains. Both strains showed diphosphatidylglycerol, phosphatidylglycerol, phosphatidyl-ethanolamine, phosphatidylcholine and unidentified glycolipid as major polar lipids. Based on distinct phenotypic, genotypic and phylogenetic differences from the previously described taxa, we propose the classification of strains M3 and M11 as representative of a novel species in the genus Roseomonas, for which the name Roseomonas deserti sp. nov. is suggested. The type strain is M3 (=KEMB 2255-459=JCM 31275).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Desert Climate; Fatty Acids; Glycolipids; Kuwait; Methylobacteriaceae; Nucleic Acid Hybridization; Petroleum; Phospholipids; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Silicon Dioxide
PubMed: 29388546
DOI: 10.1099/ijsem.0.002565 -
International Journal of Systematic and... Nov 2020A Gram-stain-negative, aerobic, non-motile, pink-pigmented, coccus bacterium, designated CPCC 101081, was isolated from a gravel soil sample collected from Badain Jara...
A Gram-stain-negative, aerobic, non-motile, pink-pigmented, coccus bacterium, designated CPCC 101081, was isolated from a gravel soil sample collected from Badain Jara desert, PR China. Growth of the isolate occurred at 10-37 °C and pH 5.0-8.0, with optimal growth at 28-32 °C and pH 7.0, respectively. The major cellular fatty acids were summed feature 8 (Cω7/C ω6), summed feature 3 (C ω6/Cω7) and C2-OH. Q-10 was detected as the main respiratory quinone. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified phospholipid, an amino-containing lipid and an unidentified glycophospholipid were examined in the polar lipids extraction. The 16S rRNA gene sequence comparison of strain CPCC 101081 with the available sequences in the GenBank database showed that the isolate was closely related to members of the genus , with the highest similarity to DSM 14916 (97.4 %). In the phylogenetic trees based on 16S rRNA gene sequences and the core genomes, strain CPCC 101081 was included within the clade of the genus , representing a species level, with the closest neighbor of DSM 14916 . The genomic DNA G+C content was 68.7 mol%. The average nucleotide identity and the digital DNA-DNA hybridization values between strain CPCC 101081 and the related type strains of the genus were all far lower than the cut-off values for definition species. On the basis of above phenotypic and genotypic characteristics, strain CPCC 101081 is proposed to represent a novel species of the genus with the name sp. nov. strain CPCC 101081 (=KCTC 62852=NBRC 113512) is the type strain of the species.
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Desert Climate; Fatty Acids; Methylobacteriaceae; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone
PubMed: 32936752
DOI: 10.1099/ijsem.0.004467 -
Frontiers in Microbiology 2021In a previous study, we found that the growth performance of the new strain of Huanghe carp is related to gene expression and bacterial community in the gut. In order to...
In a previous study, we found that the growth performance of the new strain of Huanghe carp is related to gene expression and bacterial community in the gut. In order to better understand the relationship between the gene expression level and bacterial abundance in the gut, we studied the growth performance, gut bacterial structure, and transcriptome profile in the 4th generation of the new carp strain (selection group) at harvesting time, and compared them with the control line (traditional Huanghe carp). Body weight, depth, width, and length increased 14.58, 7.14, 5.04, and 5.07%, respectively. The gut microbiome of the selection group also exhibited significantly higher species diversity parameters (Shannon, Simpson, and chao1). Both PCA and phylogenetic analyses divided all gut samples into two parts: control and selection group. was the dominant taxon in the control group, followed by and ; in the selection group, was the dominant taxon, followed by and then . Among the 249 significantly differentially expressed genes, 194 were downregulated and 55 were upregulated. Functional GO annotation produced 13 terms in the biological process, 8 in the cellular component, and 7 in the molecular function categories. KEGG annotation indicated that most of these genes were associated with the immune-related pathways. A total of 2,892 pairs of genes (245) and baceterial genera (256) were analyzed using Pearson's correlation analysis. Most of the identified associations were mapped to the immune system, bacterial community, and cell differentiation categories. The top-10 bacterial genera identified by these analyses were , , , , , , , , , and . Genes paired with bacteria flora were divided into four functional categories: immune, growth, adipocyte differentiation, and nerve regulation. These genes may be related to the comparatively fast growth and high muscle polyunsaturated fatty acid content of the Huanghe carp new strain. Meanwhile, nerve regulation-related genes may be a reflection of the microbiota-gut-brain axis. These results illustrate that gut bacterial community structure is associated with the growth performance and gene expression in the Huanghe carp new strain.
PubMed: 34127924
DOI: 10.3389/fmicb.2021.659602 -
Scientific Reports Jan 2020A mud volcano (MV) is a naturally hydrocarbon-spiked environment, as indicated by the presence of various quantities of PAHs and aromatic isotopic shifts in its...
A mud volcano (MV) is a naturally hydrocarbon-spiked environment, as indicated by the presence of various quantities of PAHs and aromatic isotopic shifts in its sediments. Recurrent expulsion of various hydrocarbons consolidates the growth of hydrocarbonoclastic bacterial communities in the areas around MVs. In addition to the widely-known availability of biologically malleable alkanes, MVs can represent hotbeds of polyaromatic hydrocarbons (PAHs), as well - an aspect that has not been previously explored. This study measured the availability of highly recalcitrant PAHs and the isotopic signature of MV sediments both by GC-MS and δC analyses. Subsequently, this study highlighted both the occurrence and distribution of putative PAH-degrading bacterial OTUs using a metabarcoding technique. The putative hydrocarbonoclastic taxa incidence are the following: Enterobacteriaceae (31.5%), Methylobacteriaceae (19.9%), Bradyrhizobiaceae (16.9%), Oxalobacteraceae (10.2%), Comamonadaceae (7.6%) and Sphingomonadaceae (5.5%). Cumulatively, the results of this study indicate that MVs represent polyaromatic hydrocarbonoclastic hotbeds, as defined by both natural PAH input and high incidence of putative PAH-degrading bacterial OTUs.
PubMed: 31988316
DOI: 10.1038/s41598-020-58282-2 -
Cotton and Surgical Face Masks in Community Settings: Bacterial Contamination and Face Mask Hygiene.Frontiers in Medicine 2021During the current COVID-19 pandemic, the use of face masks has become increasingly recommended and even mandatory in community settings. To evaluate the risk of...
During the current COVID-19 pandemic, the use of face masks has become increasingly recommended and even mandatory in community settings. To evaluate the risk of bacterial cross-contamination, this study analyzed the bacterial bioburden of disposable surgical masks and homemade cotton masks, and surveyed the habits and face mask preferences of the Flemish population. Using culture approaches and 16S rRNA gene amplicon sequencing, we analyzed the microbial community on surgical and/or cotton face masks of 13 healthy volunteers after 4 h of wearing. Cotton and surgical masks contained on average 1.46 × 10 CFU/mask and 1.32 × 10 CFU/mask, respectively. , and spp. were mostly cultured from the masks and 43% of these isolates were resistant to ampicillin or erythromycin. Microbial profiling demonstrated a consistent difference between mask types. Cotton masks mainly contained , and taxa and surgical masks and . After 4 h of mask wearing, the microbiome of the anterior nares and the cheek showed a trend toward an altered beta-diversity. According to dedicated questions in the large-scale Corona survey of the University of Antwerp with almost 25,000 participants, only 21% of responders reported to clean their cotton face mask daily. Laboratory results indicated that the best mask cleaning methods were boiling at 100°C, washing at 60°C with detergent or ironing with a steam iron. Taken together, this study suggests that a considerable number of bacteria, including pathobionts and antibiotic resistant bacteria, accumulate on surgical and even more on cotton face masks after use. Based on our results, face masks should be properly disposed of or sterilized after intensive use. Clear guidelines for the general population are crucial to reduce the bacteria-related biosafety risk of face masks, and measures such as physical distancing and increased ventilation should not be neglected when promoting face mask use.
PubMed: 34540873
DOI: 10.3389/fmed.2021.732047 -
Current Issues in Molecular Biology 2019Methanol, commercially generated from methane, is a renewable chemical feedstock that is highly soluble, relatively inexpensive, and easy to handle. The concept of... (Review)
Review
Methanol, commercially generated from methane, is a renewable chemical feedstock that is highly soluble, relatively inexpensive, and easy to handle. The concept of native methylotrophic bacteria serving as whole cell catalysts for production of chemicals and materials using methanol as a feedstock is highly attractive. In recent years, the available omics data for methylotrophic bacteria, especially for , the most well-characterized model methylotroph, have provided a solid platform for rational engineering of methylotrophic bacteria for industrial production. In addition, there is a strong interest in converting the more traditional heterotrophic production platforms toward the use of single carbon substrates, including methanol, through metabolic engineering. In this chapter, we review the recent progress toward achieving the desired growth and production yields from methanol, by genetically engineered native methylotrophic strains and by the engineered synthetic methylotrophs.
Topics: Biological Products; Biotransformation; Metabolic Engineering; Metabolic Networks and Pathways; Methane; Methanol; Methylobacterium extorquens; Organisms, Genetically Modified; Synthetic Biology
PubMed: 31166195
DOI: 10.21775/cimb.033.225 -
Journal of Hazardous Materials Nov 2016The metalloid arsenic predominantly exists in the arsenite [As(III)] and arsenate [As(V)]. These two forms are respectively oxidized and reduced by microbial redox...
The metalloid arsenic predominantly exists in the arsenite [As(III)] and arsenate [As(V)]. These two forms are respectively oxidized and reduced by microbial redox processes. This study was designed to bioprospect arsenic tolerating bacteria from Lonar lake and to characterize their arsenic redoxing ability. Screening of sixty-nine bacterial species isolated from Lonar lake led to identification of three arsenic-oxidizing and seven arsenic-reducing species. Arsenite oxidizing isolate Roseomonas sp. L-159a being closely related to Roseomonas cervicalis ATCC 49957 oxidized 2mM As(III) in 60h. Gene expression of large and small subunits of arsenite oxidase respectively showed 15- and 17-fold higher expression. Another isolate Nocardioides sp. L-37a formed a clade with Nocardioides ghangwensis JC2055, exhibited normal growth with different carbon sources and pH ranges. It reduced 2mM As(V) in 36h and showed constitutive expression of arsenate reductase which increased over 4-fold upon As(V) exposure. Genetic markers related to arsenic transformation were identified and characterized from the two isolates. Moderate resistance against the arsenicals was exhibited by the two isolates in the range of 1-5mM for As(III) and 1-200mM for As(V). Altogether we provide multiple evidences to indicate that Roseomonas sp. and Nocardioides sp. exhibited arsenic transformation ability.
Topics: Actinomycetales; Arsenate Reductases; Arsenic; Arsenites; Drug Resistance, Bacterial; Gene Expression Regulation, Bacterial; Lakes; Methylobacteriaceae; Oxidation-Reduction; Oxidoreductases; Soil Pollutants; Water Pollutants, Chemical
PubMed: 27498193
DOI: 10.1016/j.jhazmat.2016.07.062 -
International Journal of Systematic and... Mar 2016A novel psychrotolerant bacterium, designed strain M6-79, was isolated from an arctic glacial foreland soil sample collected from Ny-Ålesund in the Svalbard...
A novel psychrotolerant bacterium, designed strain M6-79, was isolated from an arctic glacial foreland soil sample collected from Ny-Ålesund in the Svalbard Archipelago, Norway. Cells of strain M6-79 were Gram-stain-negative, rod-shaped and produced a red-pigment. Strain M6-79 was strictly aerobic, non-motile, non-endospore-forming, oxidase-negative and catalase-positive. Based on 16S rRNA gene sequence analysis, strain M6-79 was phylogenetically related to TR53 (95.2 % 16S rRNA gene sequence similarity), TH-G33 (94.3 %), ' FW-3 (94.3 %), DS-48 (94.1 %) and 5N26 (94.1 %). The unique isoprenoid quinone detected in strain M6-79 was Q-9. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unknown aminolipid and one unknown lipid. Strain M6-79 possessed Cω7, C and summed feature 3 (Cω6 and/or Cω7) as the predominant fatty acids, and the DNA G+C content was 71.2 mol%. Combined data from phylogenetic, phenotypic and chemotaxonomic studies revealed that strain M6-79 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is strain M6-79 ( = CCTCC AB 2013101 = LMG 28251).
PubMed: 26702622
DOI: 10.1099/ijsem.0.000857 -
Antonie Van Leeuwenhoek May 2016A Gram-negative, aerobic, short rod-shaped, pink-pigmented, non-motile bacterium, designated BUT-13(T), was isolated from activated sludge of an herbicide-manufacturing...
A Gram-negative, aerobic, short rod-shaped, pink-pigmented, non-motile bacterium, designated BUT-13(T), was isolated from activated sludge of an herbicide-manufacturing wastewater treatment facility in Jiangsu province, China. Growth was observed at 0-5.5 % NaCl, pH 6.0-9.0 and 12-37 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BUT-13(T) is a member of the genus Roseomonas, and shows high sequence similarities to R. pecuniae N75(T) (98.0 %) and R. rosea 173-96(T) (97.5 %), and lower (<97 %) sequence similarities to all other Roseomonas species. Chemotaxonomic analysis revealed that strain BUT-13(T) possesses Q-10 as the predominant ubiquinone; summed feature 8 (C18:1 w7c and/or C18:1 w6c; 38.8 %), C18:0 (16.6 %), C16:0 (15.2 %), summed feature 3 (C16:1 ω6c and/or C16:1 ω7; 7.9 %) and C18:1 w9c (4.7 %) as the major fatty acids. The polar lipids were found to consist of two aminolipids, a glycolipid, a phospholipid, a phosphoglycolipid, phosphatidylcholine, phosphatidylethanolamine and diphosphatidylglycerol. Strain BUT-13(T) showed low DNA-DNA relatedness with R. pecuniae N75(T) (45.2 %) and R. rosea 173-96(T) (51.2 %). The DNA G+C content was determined to be 67.6 mol%. Based on the phylogenetic analysis, DNA-DNA hybridization and chemotaxonomic analysis, as well as biochemical characteristics, strain BUT-13(T) can be clearly distinguished from all currently recognised Roseomonas species and should be classified as a novel species of the genus Roseomonas, for which the name Roseomonas chloroacetimidivorans sp. nov. is proposed. The type strain is BUT-13(T) (CCTCC AB 2015299(T) = JCM 31050(T)).
Topics: Acetamides; Bacterial Typing Techniques; China; DNA, Bacterial; Herbicides; Manufacturing and Industrial Facilities; Methylobacteriaceae; Phylogeny; Sewage; Soil Microbiology; Wastewater
PubMed: 26896239
DOI: 10.1007/s10482-016-0664-y -
BMC Infectious Diseases Feb 2019Roseomonas mucosa, as a Gram-negative coccobacilli, is an opportunistic pathogen that has rarely been reported in human infections. Here we describe a case of bacteremia... (Review)
Review
BACKGROUND
Roseomonas mucosa, as a Gram-negative coccobacilli, is an opportunistic pathogen that has rarely been reported in human infections. Here we describe a case of bacteremia in an infective endocarditis patient with systemic lupus erythematosus (SLE).
CASE PRESENTATIONS
A 44-year-old female patient with SLE suffered bacteremia caused by Roseomonas mucosa complicated with infective endocarditis (IE). The patient started on treatment with piperacillin-tazobactam and levofloxacin against Roseomonas mucosa, which was switched after 4 days to meropenem and amikacin for an additional 2 weeks. She had a favorable outcome with a 6-week course of intravenous antibiotic therapy.
DISCUSSION AND CONCLUSIONS
Roseomonas mucosa is rarely reported in IE patients; therefore, we report the case in order to improve our ability to identify this pathogen and expand the range of known bacterial causes of infective endocarditis.
Topics: Adult; Amikacin; Anti-Bacterial Agents; Bacteremia; Endocarditis; Endocarditis, Bacterial; Female; Gram-Negative Bacterial Infections; Humans; Levofloxacin; Lupus Erythematosus, Systemic; Methylobacteriaceae; Piperacillin, Tazobactam Drug Combination
PubMed: 30755159
DOI: 10.1186/s12879-019-3774-0