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Applied and Environmental Microbiology Feb 2022Bacteria were isolated from wastewater and soil containing charred wood remnants based on their ability to use levoglucosan as a sole carbon source and on their...
Bacteria were isolated from wastewater and soil containing charred wood remnants based on their ability to use levoglucosan as a sole carbon source and on their levoglucosan dehydrogenase (LGDH) activity. On the basis of their 16S rRNA gene sequences, these bacteria represented the diverse genera , , , and Klebsiella. Genomic sequencing of the isolates verified that two isolates represented novel species, MEC069 and MEC087, while the remaining isolates were closely related to Microbacterium lacusdiani or Klebsiella pneumoniae. The genetic sequence of LGDH, , was found in the genomes of these four isolates as well as Pseudarthrobacter phenanthrenivorans Sphe3. The identity of the LGDH was experimentally verified following recombinant expression in Escherichia coli. Comparison of the putative genes surrounding in the isolate genomes indicated that several other gene products facilitate the bacterial catabolism of levoglucosan, including a putative sugar isomerase and several transport proteins. Levoglucosan is the most prevalent soluble carbohydrate remaining after high-temperature pyrolysis of lignocellulosic biomass, but it is not fermented by typical production microbes such as Escherichia coli and Saccharomyces cerevisiae. A few fungi metabolize levoglucosan via the enzyme levoglucosan kinase, while several bacteria metabolize levoglucosan via levoglucosan dehydrogenase. This study describes the isolation and characterization of four bacterial species that degrade levoglucosan. Each isolate is shown to contain several genes within an operon involved in levoglucosan degradation, furthering our understanding of bacteria that metabolize levoglucosan.
Topics: Biomass; Glucose; Paenibacillus; RNA, Ribosomal, 16S
PubMed: 34910566
DOI: 10.1128/AEM.01868-21 -
Frontiers in Microbiology 2017Deep sea is a unique and extreme environment. It is a hot spot for hunting marine actinomycetes resources and secondary metabolites. The novel deep sea actinomycete... (Review)
Review
Deep sea is a unique and extreme environment. It is a hot spot for hunting marine actinomycetes resources and secondary metabolites. The novel deep sea actinomycete species reported from 2006 to 2016 including 21 species under 13 genera with the maximum number from , followed by and , and one novel species for the other 9 genera. Eight genera of actinomycetes were reported to produce secondary metabolites, among which is the richest producer. Most of the compounds produced by the deep sea actinomycetes presented antimicrobial and anti-cancer cell activities. Gene clusters related to biosynthesis of desotamide, heronamide, and lobophorin have been identified from the deep sea derived .
PubMed: 28507537
DOI: 10.3389/fmicb.2017.00760 -
Frontiers in Microbiology 2023The taxonomic relationships of 10 strains isolated from seaweeds collected from two beaches in Republic of Korea were studied by sequencing and analyses of 16S rRNA...
The taxonomic relationships of 10 strains isolated from seaweeds collected from two beaches in Republic of Korea were studied by sequencing and analyses of 16S rRNA genes and whole genomes. For the construction of a more reliable and robust 16S rRNA gene phylogeny, the authentic and nearly complete 16S rRNA gene sequences of all the type strains were selected through pairwise comparison of the sequences contained in several public databases including the List of Prokaryotic names with Standing in Nomenclature (LPSN). The clustering of the ten study strains into five distinct groups was apparent in this single gene-based phylogenetic tree. In addition, the 16S rRNA gene sequences of a few type strains were shown to be incorrectly listed in LPSN. An overall phylogenomic clustering of the genus was performed with a total of 113 genomes by core genome analysis. As a result, nine major (≥ three type strains) and eight minor (two type strains) clusters were defined mostly at gene support index of 92 and mean intra-cluster OrthoANIu of >80.00%. All of the study strains were assigned to a clade and distributed further into four subclusters in the core genome-based phylogenetic tree. phenotypic assays for physiological, biochemical, and chemotaxonomic characteristics were also carried out with the ten study strains and seven closely related type strains. Comparison of the overall genomic relatedness indices (OGRI) including OrthoANIu and digital DNA-DNA hybridization supported that the study strains constituted four new species of the genus . In addition, some type strains were reclassified as members of preexisting species. Moreover, some of them were embedded in a new genus of the family based on their distinct separation in the core genome-based phylogenetic tree and amino acid identity matrices. Based on the results here, four new species, namely, sp. nov., sp. nov., sp. nov., and sp. nov., are described, along with the proposal of gen. nov. containing five reclassified species from the " clade", with gen. nov., comb. nov. as the type species.
PubMed: 38164402
DOI: 10.3389/fmicb.2023.1299950 -
Microbiology Resource Announcements Jan 2023spp. are a group of microbes that have been recovered from a wide variety of environments in nature. Here, I report the complete genomic data for Microbacterium oxydans...
spp. are a group of microbes that have been recovered from a wide variety of environments in nature. Here, I report the complete genomic data for Microbacterium oxydans and Microbacterium maritypicum type strains that are already present in public culture repositories. The genome of the M. oxydans strain was 3,894,869 bp long, with a G+C content of 68.26%. The genome of the M. maritypicum strain was 3,668,377 bp long, with a G+C content of 68.44%.
PubMed: 36598287
DOI: 10.1128/mra.01089-22 -
Microorganisms Sep 2021Mastitis is the most common disease for cattle, causing great economic losses for the global dairy industry. Recent studies indicate the multi-agent and microbiome...
Mastitis is the most common disease for cattle, causing great economic losses for the global dairy industry. Recent studies indicate the multi-agent and microbiome diversity of this disease. To understand the nature of mastitis and investigate the role of the microbiome in the development of pathologies in the udder of bovines, we performed NGS sequencing of the 16S rRNA gene of cow's milk with pathologies of the udder. The obtained data show a significant increase in the , , , , and genera for groups of cows with udder pathologies. Increasing relative abundance of the and genera was associated with subclinical mastitis. Our data show that a relative increase in abundance of the and genera may be an early sign of infection. We have shown, for the first time, an increase in the , and genera in groups of cows with mastitis. These results expand our understanding of the role of the microbiome in the development of bovine mastitis.
PubMed: 34576870
DOI: 10.3390/microorganisms9091974 -
Foods (Basel, Switzerland) Mar 2021Biofilm characteristics of D84 () and subsp. () on polytetrafluoroethylene and AISI-304 stainless steel at early- (24, 48 h) and late-stage (144, 192 h) biofilm...
Biofilm characteristics of D84 () and subsp. () on polytetrafluoroethylene and AISI-304 stainless steel at early- (24, 48 h) and late-stage (144, 192 h) biofilm formation were investigated. biofilm structure was more developed compared to , representing vastly mature biofilms with a strongly developed amorphous matrix, possibly extracellular polymeric substances (EPSs), at late-stage biofilm formation. showed faster growth behavior but still resulted in a relatively flat biofilm structure. Strong correlations were found between several roughness parameters and surface coverage (r ≥ 0.98), and between total surface free energy (γs) and surface coverage (r = 0.89), while remained mostly unaffected. The pronounced ubiquitous biofilm characteristics make D84 a suitable model for biofilm research. Studying biofilm formation of these bacteria may help one understand bacterial adhesion on interfaces and hence reduce biofilm formation in the food industry.
PubMed: 33805651
DOI: 10.3390/foods10030611 -
WormBook : the Online Review of C.... Sep 2005A wide variety of bacterial pathogens, as well as several fungi, kill C. elegans or produce non-lethal disease symptoms. This allows the nematode to be used as a simple,... (Review)
Review
A wide variety of bacterial pathogens, as well as several fungi, kill C. elegans or produce non-lethal disease symptoms. This allows the nematode to be used as a simple, tractable model host for infectious disease. Human pathogens that affect C. elegans include gram-negative bacteria of genera Burkholderia, Pseudomonas, Salmonella, Serratia and Yersinia; gram-positive bacteria Enterococcus, Staphylococcus and Streptococcus; and the fungus Cryptococcus neoformans. Microbes that are not pathogenic to mammals, such as the insect pathogen Bacillus thuringiensis and the nematode-specific Microbacterium nematophilum, are also studied with C. elegans. Many of the pathogens investigated colonize the C. elegans intestine, and pathology is usually quantified as decreased lifespan of the nematode. A few microbes adhere to the nematode cuticle, while others produce toxins that kill C. elegans without a requirement for whole, live pathogen cells to contact the worm. The rapid growth and short generation time of C. elegans permit extensive screens for mutant pathogens with diminished killing, and some of the factors identified in these screens have been shown to play roles in mammalian infections. Genetic screens for toxin-resistant C. elegans mutants have identified host pathways exploited by bacterial toxins.
Topics: Animals; Bacterial Physiological Phenomena; Caenorhabditis elegans; Disease Models, Animal; Fungi; Humans; Intestines
PubMed: 18050390
DOI: 10.1895/wormbook.1.21.1 -
Genome Medicine Jan 2022With over 350,000 estimated deaths worldwide in 2018, prostate cancer (PCa) continues to be a major health concern and a significant cause of cancer-associated mortality...
BACKGROUND
With over 350,000 estimated deaths worldwide in 2018, prostate cancer (PCa) continues to be a major health concern and a significant cause of cancer-associated mortality among men. While cancer in general is considered a disease of the human genome, there is a growing body of evidence suggesting that changes to the healthy microbiota could play a vital role in cancer development, progression, and/or treatment outcome.
METHODS
Using a metatranscriptomic approach, we annotated the microbial reads obtained from total RNA sequencing of 106 prostate tissue samples from 94 PCa patients (discovery cohort). We investigated microbial dysbiosis associated with PCa by systematically comparing the microbiomes between benign and malignant tissue samples, between less vs. more-aggressive PCa, and between patients who had biochemical recurrence as opposed to those who did not. We further performed differential gene expression and cell type enrichment analysis to explore the host transcriptomic and cellular responses to selected microbial genera. A public dataset (GSE115414) of total RNA sequencing reads from 24 prostate tissue samples (8 benign and 16 malignant) served as the validation cohort.
RESULTS
We observed decreased species diversity and significant under-representation of Staphylococcus saprophyticus and Vibrio parahaemolyticus, as well as significant over-abundance of Shewanella in malignant as compared to benign prostate tissue samples in both the discovery (p < 0.01) and validation (p < 0.05) cohorts. In addition, we identified Microbacterium species (p < 0.01) to be significantly over-abundant in pathologically advanced T3 tumors compared to T2 in the discovery cohort. Malignant samples having high vs. low Shewanella counts were associated with downregulated Toll-like receptor signaling pathways and decreased enrichment of dendritic cells. Malignant samples having low vs. high V. parahaemolyticus counts were enriched for olfactory transduction and drug metabolism pathways. Finally, malignant samples were enriched for M1 and M2 macrophages as compared to benign tissue samples.
CONCLUSIONS
The results from this exploratory study support the existence of an important biological link between the prostate microbiota and PCa development/progression. Our results highlight Shewanella, V. parahaemolyticus, and Microbacterium sp. as interesting candidates for further investigation of their association with PCa.
Topics: Gene Expression Profiling; Humans; Male; Microbiota; Prostate; Prostatic Neoplasms; Transcriptome
PubMed: 35078527
DOI: 10.1186/s13073-022-01011-3 -
Marine Drugs Oct 2023Dextranase, also known as glucanase, is a hydrolase enzyme that cleaves α-1,6 glycosidic bonds. In this study, a dextranase-producing strain was isolated from water...
Dextranase, also known as glucanase, is a hydrolase enzyme that cleaves α-1,6 glycosidic bonds. In this study, a dextranase-producing strain was isolated from water samples of the Qingdao Sea and identified as sp. This strain was further evaluated for growth conditions, enzyme-producing conditions, enzymatic properties, and hydrolysates. Yeast extract and sodium chloride were found to be the most suitable carbon and nitrogen sources for strain growth, while sucrose and ammonium sodium were found to be suitable carbon and nitrogen sources for fermentation. The optimal pH was 7.5, with a culture temperature of 40 °C and a culture time of 48 h. Dextranase produced by strain XD05 showed good thermal stability at 40 °C by retaining more than 70% relative enzyme activity. The pH stability of the enzyme was better under a weak alkaline condition (pH 6.0-8.0). The addition of NH increased dextranase activity, while Co and Mn had slight inhibitory effects on dextranase activity. In addition, high-performance liquid chromatography showed that dextran is mainly hydrolyzed to maltoheptanose, maltohexanose, maltopentose, and maltootriose. Moreover, it can form corn porous starch. Dextranase can be used in various fields, such as food, medicine, chemical industry, cosmetics, and agriculture.
Topics: Microbacterium; Dextranase; Hydrogen-Ion Concentration; Starch; Carbon; Nitrogen
PubMed: 37888463
DOI: 10.3390/md21100528 -
Frontiers in Fungal Biology 2023Disease outbreaks have been recorded due to exposure to and fumonisin, a mycotoxin produced by this fungus. is a fungal pathogen of maize that causes infections,... (Review)
Review
Disease outbreaks have been recorded due to exposure to and fumonisin, a mycotoxin produced by this fungus. is a fungal pathogen of maize that causes infections, such as wilting and rotting, while contact with its fumonisin derivative manifests in the form of mild to severe illnesses in humans and animals. Maize infection by causes loss or reduction in expected crop yield, thereby influencing households and nations' economies. While several efforts have been made to control the pathogenic fungus and its occurrence in the environment, it remains a challenge in agriculture, particularly in maize production. Several microorganisms which are plant-associated, especially those associated with the rhizosphere niche have been noted to possess antagonistic effects against . They can inhibit the pathogen and tackle its debilitating effects on plants. Hence this study reviews the use of rhizosphere-associated biocontrol agents, such as spp., and which forms part of the phytomicrobiome in other to prevent and control this toxicogenic fungus. These microorganisms were found to not only be effective in controlling its occurrence on maize plants but are environmentally safe and promote crop yield.
PubMed: 37746120
DOI: 10.3389/ffunb.2023.1095765