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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 -
Archives of Microbiology Feb 2024Three Gram-reaction-positive bacterial strains, designated KSW-18, KSW2-22, and KSW4-11, were isolated from seawater, and two dried seaweed samples collected at Gwakji...
Three Gram-reaction-positive bacterial strains, designated KSW-18, KSW2-22, and KSW4-11, were isolated from seawater, and two dried seaweed samples collected at Gwakji Beach in Jeju, Republic of Korea, respectively, and their taxonomic positions were examined by a polyphasic approach. The 16S rRNA gene phylogeny showed that strain KSW4-11 was tightly associated with Microbacterium oleivorans NBRC 103075, while strains KSW-18 and KSW2-22 formed a distinctive subline at the base of a clade including the above two strains. The three isolates showed high sequence similarity with one another (99.7-99.9%; 1-4 nt differences) and Microbacterium oleivorans (99.8-99.9%; 1-3 nt differences). The chemotaxonomic features were typical for the genus Microbacterium; Lysine as the diagnostic diamino acid and N-glycolylated muramic acid of the peptidoglycans, the predominant menaquinones of MK-11, MK-10 and MK-12, the major fatty acids of anteiso-C and anteiso-C, and the major polar lipids including diphosphatidylglycerol, phosphatidylglycerol, and two or three unidentified glycolipids. In core genome-based phylogenetic tree, strains KSW-18 and KSW2-22 were closely associated with Microbacterium oleivorans NBRC 103075, while strain KSW4-11 formed a distinctive subline at the base of a clade including the above three strains, in contrast to the 16S rRNA gene tree. Strains KSW-18 and KSW2-22 shared an OrthoANIu of 98.6% and a digital DNA-DNA hybridization of 87.6% with each other, representing that they were strains of a species, while the OrthoANIu and digital DNA-DNA hybridization values between strains KSW-18 and KSW4-11, and between both of these isolates and all members of the genus Microbacterium were ≤86.5% and ≤30.7%, respectively. The analyses of overall genomic relatedness indices and phenotypic distinctness support that the three isolates represent two new species of the genus Microbacterium. Based on the results obtained here, Microbacterium aquilitoris sp. nov. (type strain KSW-18 = KCTC 49623 = NBRC 115222) and Microbacterium gwkjiense sp. nov. (type strain KSW4-11 = KACC 23321 = DSM 116380) are proposed.
Topics: Microbacterium; Phylogeny; RNA, Ribosomal, 16S; Actinomycetales; DNA
PubMed: 38353773
DOI: 10.1007/s00203-023-03804-5 -
International Journal of Systematic and... Mar 2023Two Gram-positive bacterial strains, designated as YMB-B2 and BWT-G7, were isolated from larvae of L. and , respectively, and their taxonomic positions examined by a...
Two Gram-positive bacterial strains, designated as YMB-B2 and BWT-G7, were isolated from larvae of L. and , respectively, and their taxonomic positions examined by a polyphasic approach. Both of the isolates contained ornithine as the cell-wall diamino acid. The acyl type of murein was -glycolyl. The predominant menaquinones were MK-11 and MK-12. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. Both of the isolates contained C anteiso and C anteiso as the major fatty acids. Strain YMB-B2 also had C iso as an additional major fatty acid. The 16S rRNA gene phylogeny showed that the novel strains formed two distinct sublines within the genus . Strain YMB-B2 was most closely related to the type strains of (99.1 % sequence similarity) and (99.0 %) whereas strain BWT-G7 formed a tight cluster with the type strain of (98.9 %). The phylogenomic analysis based on 92 core genes supported their relationships in 16S rRNA gene phylogeny. Overall genomic relatedness indices warranted that the isolates represent two new species of the genus . Based on the results obtained here, sp. nov. (type strain YMB-B2=KCTC 49593=CCM 9151) and sp. nov. (type strain BWT-G7=KACC 22262=NBRC 115127) are proposed.
Topics: Animals; Fatty Acids; Larva; Tenebrio; Microbacterium; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Phylogeny; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Actinomycetales; Coleoptera; Vitamin K 2
PubMed: 36896792
DOI: 10.1099/ijsem.0.005729 -
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 -
International Journal of Systematic and... Nov 2023Two novel plant growth-promoting, rod-shaped, Gram-positive and non-motile rhizobacteria, W1N and W2R, were isolated from wetland plants and respectively, in China....
Two novel plant growth-promoting, rod-shaped, Gram-positive and non-motile rhizobacteria, W1N and W2R, were isolated from wetland plants and respectively, in China. The results of the 16S rRNA sequence alignment analysis showed that they were related to , with the highest similarity to (98.7 %) and (98.5 %) for strain W1N, and to (98.1 %) and (98.0 %) for strain W2R. Phylogenetic analyses based on 16S rRNA gene sequences and 92 conserved concatenated proteins suggested that the two strains belong to the genus and were placed in two separate novel phylogenetic clades. The genome sizes of the two strains were 3.2 and 3.7 Mb, and the G+C contents were 71.7 and 68.5 mol%, respectively. The comparative genome results showed that the average nucleotide identity values between W1N and W2R and other species ranged from 73.5 to 83.6 %, and the digital DNA-DNA hybridization values ranged from 19.7 to 26.8 %. These two strains show physiological and biochemical features that differ from those of closely related species. Rhamnose, galactose and glucose were present in the characteristic sugar fractions of strains W1N and W2R. The peptidoglycan of strains W1N and W2R contained the amino acids ornithine, alanine and aspartic acid. C anteiso, C anteiso and C iso were the predominant cellular fatty acids in W1N and W2R. Phosphatidylglycerol and diphosphatidylglycerol are major polar lipid components. Strain W1N not only formed bacterial biofilms but also had the ability to solubilize phosphorus and produce indole-3-acetic acid. Strain W2R had siderophore-producing and lignin-degrading properties. Based on their genetic and phenotypic characteristics, strains W1N and W2R were classified as novel bacteria in the genus and designated as sp. nov. (type strain W1N=ACCC 61807=GDMCC 1.2966=JCM 35339) and sp. nov. (type strain W2R=ACCC 61808=GDMCC 1.2967=JCM 35340).
Topics: Base Composition; Fatty Acids; Microbacterium; Phylogeny; RNA, Ribosomal, 16S; Wetlands; Sequence Analysis, DNA; DNA, Bacterial; Bacterial Typing Techniques; China; Actinomycetales
PubMed: 37917000
DOI: 10.1099/ijsem.0.006121 -
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 -
International Journal of Systematic and... Jul 2021Four aerobic, Gram-stain-positive, rod-shaped bacteria (HY60, HY54, HY82 and HY89) were isolated from bat faeces of and species collected in PR China. Phylogenetic...
Four aerobic, Gram-stain-positive, rod-shaped bacteria (HY60, HY54, HY82 and HY89) were isolated from bat faeces of and species collected in PR China. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the four novel strains formed two separate but adjacent subclades close to CGMCC 1.12260 (97.6-97.7 % similarity), JCM 18706 (97.3-97.5 %) and JCM 30493 (97.3-97.4 %). The 16S rRNA gene sequence similarity was 98.3 % between strains HY60 and HY82, and identical within strain pairs HY60/HY54 and HY82/HY89. The DNA G+C contents of strains HY60 and HY82 were 61.9 and 63.3 mol%, respectively. The digital DNA-DNA hybridization and average nucleotide identity values between each novel strain and their closest relatives were all below the 70 % and 95-96 % thresholds for species delimitation, respectively. All four novel strains contained -C, -C, -C and -C as the main fatty acids, MK-11 and MK-12 as the major respiratory quinones, and diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid as the predominant polar lipids. The cell-wall peptidoglycan was of B type and contained alanine, glutamate, glycine and ornithine. The acyl type of the muramic acid was glycolyl. The whole-cell sugars were rhamnose and ribose. Based on the foregoing polyphasic analyses, it was concluded that the four uncharacterized strains represented two novel species of the genus , for which the names sp. nov. [type strain HY60 (=CGMCC 1.17468=GDMCC 1.1951=KACC 22102)] and sp. nov. [type strain HY82 (=CGMCC 1.17469=GDMCC 1.1949=KACC 22101)] are proposed, respectively.
Topics: Animals; Bacterial Typing Techniques; Base Composition; China; Chiroptera; DNA, Bacterial; Fatty Acids; Feces; Microbacterium; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Vitamin K 2
PubMed: 34232856
DOI: 10.1099/ijsem.0.004858 -
International Journal of Systematic and... Feb 2021Four novel bacterial strains (ST-M6, L-033, L-031 and Z-333) were isolated from the intestinal contents of plateau pikas () collected on the QinghaiTibet Plateau, PR...
Four novel bacterial strains (ST-M6, L-033, L-031 and Z-333) were isolated from the intestinal contents of plateau pikas () collected on the QinghaiTibet Plateau, PR China. Cells were aerobic, non-motile, Gram-stain-positive, catalase-positive, oxidase-negative, capsuled and short-rod-shaped. Phylogenetic analyses based on the 16S rRNA gene sequences and 387 core genes indicated that the four isolates belong in the genus and clearly separate from recognized species. The two type strains (ST-M6 and L-031) shared low 16S rRNA similarity, average nucleotide identity values and digital DNA-DNA hybridization relatedness with their phylogenetic neighbours ( DSM 18659, DSM 19179, JCM 30598, CCTCC M208212, DSM 16091 and DSM 20754). The genomic DNA G+C contents of strains ST-M6 and L-031 were 70.4 and 70.7 mol%, respectively. The major cellular fatty acids of strain ST-M6 were anteiso-C, anteiso-C and iso-C, in contrast to anteiso-C, anteiso-C and anteiso-C 9 of strain L-031. Both type strains (ST-M6 and L-031) were glycolate test positive and shared the following common features: MK-11 and MK-12 as major menaquinones; rhamnose, ribose, mannose and galactose as major cell-wall sugars; diphosphatidylglycerol, phosphatidylglycerol and two glycolipids as polar lipids; and ornithine, alanine, glycine and glutamic acid as cell-wall amino acids. Comparing the phenotypic, phylogenetic and chemotaxonomic features of the four strains and their related taxa, strains ST-M6 and L-031 represent two novel species of the genus , for which the names sp. nov. (type strain ST-M6=CGMCC 1.16364=DSM 104058) and sp. nov. (type strain L-031 =CGMCC 1.16363=DSM 106170) are proposed.
Topics: Animals; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Gastrointestinal Contents; Lagomorpha; Microbacterium; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Tibet; Vitamin K 2
PubMed: 33502309
DOI: 10.1099/ijsem.0.004662 -
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