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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 -
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 -
Nature Communications Sep 2023The cell walls of pathogenic and acidophilic bacteria, such as Mycobacterium tuberculosis and Mycobacterium leprae, contain lipoarabinomannan and arabinogalactan. These...
The cell walls of pathogenic and acidophilic bacteria, such as Mycobacterium tuberculosis and Mycobacterium leprae, contain lipoarabinomannan and arabinogalactan. These components are composed of D-arabinose, the enantiomer of the typical L-arabinose found in plants. The unique glycan structures of mycobacteria contribute to their ability to evade mammalian immune responses. In this study, we identified four enzymes (two GH183 endo-D-arabinanases, GH172 exo-α-D-arabinofuranosidase, and GH116 exo-β-D-arabinofuranosidase) from Microbacterium arabinogalactanolyticum. These enzymes completely degraded the complex D-arabinan core structure of lipoarabinomannan and arabinogalactan in a concerted manner. Furthermore, through biochemical characterization using synthetic substrates and X-ray crystallography, we elucidated the mechanisms of substrate recognition and anomer-retaining hydrolysis for the α- and β-D-arabinofuranosidic bonds in both endo- and exo-mode reactions. The discovery of these D-arabinan-degrading enzymes, along with the understanding of their structural basis for substrate specificity, provides valuable resources for investigating the intricate glycan architecture of mycobacterial cell wall polysaccharides and their contribution to pathogenicity.
Topics: Animals; Female; Humans; Galactans; Lipopolysaccharides; Mycobacterium tuberculosis; Endometriosis; Mammals
PubMed: 37726269
DOI: 10.1038/s41467-023-41431-2 -
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 -
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 -
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 -
International Journal of Environmental... Mar 2022Lake Vostok is the deepest lake of Antarctica but has poor accessibility for study due to a thick glacial cover, however, water samples of this lake have become...
Lake Vostok is the deepest lake of Antarctica but has poor accessibility for study due to a thick glacial cover, however, water samples of this lake have become available for study just recently. Previously, only the microbiome of the ice cover samples was characterized. Here we report results of bacteriological seeding with subsequent identification of the heterotrophic microorganisms (bacteria and micellar fungi) present by 16S rDNA sequencing as well as results of a direct molecular study of the water microbiome. Surprisingly, the data obtained gave evidence of a predominant occurrence of common chemoorganotrophs that were rather psychrotolerant than psychrophilic. We isolated and described strains belonging to eight heterotrophic microbial species able to grow in a rich medium: six bacterial strains belonging to the species and , , , sp. and ; and two fungal strains belonging to sp. and . Direct study of 16S rDNA purified water samples confirmed the predominance of the , , and () .
Topics: Antarctic Regions; DNA, Ribosomal; Lakes; Microbiota; Sphingomonadaceae; Water; Water Microbiology
PubMed: 35409708
DOI: 10.3390/ijerph19074025 -
3 Biotech Jun 2021Banana ( spp.), a major cash and staple fruit crop in many parts of the world, is infected by wilt, which contributes up to 100% yield loss and causes social... (Review)
Review
UNLABELLED
Banana ( spp.), a major cash and staple fruit crop in many parts of the world, is infected by wilt, which contributes up to 100% yield loss and causes social consequences. Race 1 and race 2 of Panama wilt caused by f. sp. () are prevalent worldwide and seriously affect many traditional varieties. The threat of tropical race 4 ( TR4) is looming large in African counties. However, its incidence in India has been confined to Bihar (Katihar and Purnea), Uttar Pradesh (Faizabad), Madhya Pradesh (Burhanpur) and Gujarat (Surat). Management of races by employing fungicides is often not a sustainable option as the disease spread is rapid and they negatively alter the biodiversity of beneficial ectophytes and endophytes. Besides, soil drenching with carbendazim/trifloxystrobin + tebuconazole is also not effective in suppressing the wilt of banana. Improvement of resistance to wilt in susceptible cultivars is being addressed through both conventional and advanced breeding approaches. However, engineering of banana endosphere with bacterial endophytes from resistant genotypes like Pisang lilly and YKM5 will induce the immune response against , irrespective of races. The composition of the bacterial endomicrobiome in different banana cultivars is dominated by the phyla Proteobacteria, Bacteroidetes and Actinobacteria. The major bacterial endophytic genera antagonistic to are , , , , , , , , spp., sp., spp. , , , , , , , , , , , , , , , , , , , , , , , , and . These bacterial endophytes promote the growth of banana plantlets by solubilising phosphate, producing indole acetic acid and siderophores. Application of banana endophytes during the hardening phase of tissue-cultured clones serves as a shield against . Hitherto, MAMP molecules of endophytes including flagellin, liposaccharides, peptidoglycans, elongation factor, cold shock proteins and hairpins induce microbe-associated molecular pattern (MAMP)-triggered immunity to suppress plant pathogens. The cascade of events associated with ISR and SAR is induced through MAPK and transcription factors including WRKY and MYC. Studies are underway to exploit the potential of antagonistic bacterial endophytes against isolates and to develop an understanding of the MAMP-triggered immunity and metabolomics cross talk modulating resistance. This review explores the possibility of harnessing the potential bacterial endomicrobiome against and developing nanoformulations with bacterial endophytes for increased efficacy against lethal pathogenic races of infecting banana.
SUPPLEMENTARY INFORMATION
The online version contains supplementary material available at 10.1007/s13205-021-02833-5.
PubMed: 34017673
DOI: 10.1007/s13205-021-02833-5 -
Journal of Reproductive Immunology Jun 2023There have been few studies concerning an association between unexplained recurrent pregnancy loss (RPL) and the microbiome. A recent study including 67 patients...
There have been few studies concerning an association between unexplained recurrent pregnancy loss (RPL) and the microbiome. A recent study including 67 patients demonstrated that an increase in Ureaplasma species in the endometrium raised the risk of miscarriage with an euploid karyotype. While endometrial sampling is invasive, cervicovaginal sampling is not. We compared vaginal and cervical microbiomes with a 16 S ribosomal RNA sequence between 88 patients with unexplained RPL and 17 healthy women with no history of miscarriage. We prospectively assessed risk factors for maternal colonization at a subsequent miscarriage without an aneuploid karyotype in patients. Cervicovaginal bacteria were dominated by Lactobacillus iners, Gardnerella vaginalis, Atopobium vaginae and Bifidobacterium breve in Japanese population. The proportions of Delftia and unknown bacteria in the cervix were significantly higher in patients with RPL than in controls. Streptococcus, Microbacterium, Delftia, Anaerobacillus and Chloroplast in the cervix were significantly higher in patients with a history of chorioamnionitis compared to the controls. The abundance of Cutibacterium and Anaerobacillus in the cervix was significantly higher in patients who had subsequently miscarried compared to those who gave birth. The miscarriage rate in patients with higher proportions of both Cutibacterium and Anaerobacillus (66.7%, 2/3) was significantly greater than that of patients who lacked these bacteria (9.2%, 6/65, adjusted odds ratio 16.90, 95% confidence interval 1.27-225.47, p = 0.032). The presence of certain bacteria could be a predictor of subsequent miscarriage without an aneuploid karyotype. The cervicovaginal microbiome might be useful for investigating a possible cause of RPL.
Topics: Pregnancy; Humans; Female; Vagina; Cervix Uteri; Abortion, Habitual; Aneuploidy; Microbiota
PubMed: 37060795
DOI: 10.1016/j.jri.2023.103944