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Journal of Natural Products May 2022Investigation of the marine sponge MeOH fractions using feature-based molecular networking, dereplication, and isolation led to the discovery of new... (Review)
Review
Investigation of the marine sponge MeOH fractions using feature-based molecular networking, dereplication, and isolation led to the discovery of new bromopyrrole-derived metabolites. An in-house library of bromopyrrole alkaloids previously isolated from and sp. was utilized, along with the investigation of an MS/MS fragmentation of these compounds. Our strategy led to the isolation and identification of the disparamides A-C (-), with a novel carbon skeleton. Additionally, new dispyrins B-F (-) and nagelamides H2 and H3 ( and ) and known nagelamide H (), citrinamine B (), ageliferin (), bromoageliferin (), and dibromoageliferin () were also isolated and identified by analysis of spectroscopic data. Analysis of MS/MS fragmentation data and molecular networking analysis indicated the presence of hymenidin (), oroidin (), dispacamide (), monobromodispacamide (), keramadine (), longamide B (), methyl ester of longamide B (), hanishin (), methyl ester of 3-debromolongamide B (), and 3-debromohanishin (). Antibacterial activity of ageliferin (), bromoageliferin (), and dibromoageliferin () was evaluated against susceptible and multi-drug-resistant ESKAPE pathogenic bacteria , , , , , and . Dibromoageliferin () displayed the most potent antimicrobial activity against all tested susceptible and MDR strains. Compounds - presented no significant hemolytic activity up to 100 μM.
Topics: Agelas; Alkaloids; Animals; Anti-Bacterial Agents; Escherichia coli; Esters; Molecular Structure; Porifera; Pyrroles; Tandem Mass Spectrometry
PubMed: 35427139
DOI: 10.1021/acs.jnatprod.2c00094 -
Oncogene Feb 2023Appendectomy impacts the homeostasis of gut microbiome in patients. We aimed to study the role of appendectomy in colorectal cancer (CRC) risk through causing gut...
Appendectomy impacts the homeostasis of gut microbiome in patients. We aimed to study the role of appendectomy in colorectal cancer (CRC) risk through causing gut microbial dysbiosis. Population-based longitudinal study (cohort 1, n = 129,155) showed a 73.0% increase in CRC risk among appendectomy cases throughout 20 years follow-up (Adjusted sub-distribution hazard ratio (SHR) 1.73, 95% CI 1.49-2.01, P < 0.001). Shotgun metagenomic sequencing was performed on fecal samples from cohort 2 (n = 314). Gut microbial dysbiosis in appendectomy subjects was observed with significant enrichment of 7 CRC-promoting bacteria (Bacteroides vulgatus, Bacteroides fragilis, Veillonella dispar, Prevotella ruminicola, Prevotella fucsa, Prevotella dentalis, Prevotella denticola) and depletion of 5 beneficial commensals (Blautia sp YL58, Enterococcus hirae, Lachnospiraceae bacterium Choco86, Collinsella aerofaciens, Blautia sp SC05B48). Microbial network analysis showed increased correlation strengths among enriched bacteria and their enriched oncogenic pathways in appendectomy subjects compared to controls. Of which, B. fragilis was the centrality in the network of the enriched bacteria. We further confirmed that appendectomy promoted colorectal tumorigenesis in mice by causing gut microbial dysbiosis and impaired intestinal barrier function. Collectively, this study revealed appendectomy-induced microbial dysbiosis characterized by enriched CRC-promoting bacteria and depleted beneficial commensals, signifying that the gut microbiome may play a crucial role in CRC development induced by appendectomy.
Topics: Animals; Mice; Gastrointestinal Microbiome; Dysbiosis; Appendectomy; Longitudinal Studies; Colorectal Neoplasms
PubMed: 36539569
DOI: 10.1038/s41388-022-02569-3 -
Journal of Clinical Microbiology Nov 2000Data from four recent studies (S. H. Goh et al., J. Clin. Microbiol. 36:2164-2166, 1998; S. H. Goh et al., J. Clin. Microbiol. 34:818-823, 1996; S. H. Goh et al., J....
Identification of Enterococcus species and phenotypically similar Lactococcus and Vagococcus species by reverse checkerboard hybridization to chaperonin 60 gene sequences.
Data from four recent studies (S. H. Goh et al., J. Clin. Microbiol. 36:2164-2166, 1998; S. H. Goh et al., J. Clin. Microbiol. 34:818-823, 1996; S. H. Goh et al., J. Clin. Microbiol. 35:3116-3121, 1997; A. Y. C. Kwok et al., Int. J. Syst. Bacteriol. 49:1181-1192, 1999) suggest that an approximately 600-bp region of the chaperonin 60 (Cpn60) gene, amplified by PCR with a single pair of degenerate primers, has utility as a potentially universal target for bacterial identification (ID). This Cpn60 gene ID method correctly identified isolates representative of numerous staphylococcal species and Streptococcus iniae, a human and animal pathogen. We report herein that this method enabled us to distinguish clearly between 17 Enterococcus species (Enterococcus asini, Enterococcus rattus, Enterococcus dispar, Enterococcus gallinarum, Enterococcus hirae, Enterococcus durans, Enterococcus cecorum, Enterococcus faecalis, Enterococcus mundtii, Enterococcus casseliflavus, Enterococcus faecium, Enterococcus malodoratus, Enterococcus raffinosus, Enterococcus avium, Enterococcus pseudoavium, Enterococcus new sp. strain Facklam, and Enterococcus saccharolyticus), and Vagococcus fluvialis, Lactococcus lactis, and Lactococcus garvieae. From 123 blind-tested samples, only two discrepancies were observed between the Facklam and Collins phenotyping method (R. R. Facklam and M. D. Collins, J. Clin. Microbiol. 27:731-734, 1989) and the Cpn60 ID method. In each case, the discrepancies were resolved in favor of the Cpn60 ID method. The species distributions of the 123 blind-tested isolates were Enterococcus new sp. strain Facklam (ATCC 700913), 3; E. asini, 1; E. rattus, 4; E. dispar, 2; E. gallinarum, 20; E. hirae, 9; E. durans, 9; E. faecalis, 12; E. mundtii, 3; E. casseliflavus, 8; E. faecium, 25; E. malodoratus, 3; E. raffinosus, 8; E. avium, 4; E. pseudoavium, 1; an unknown Enterococcus clinical isolate, sp. strain R871; Vagococcus fluvialis, 4; Lactococcus garvieae, 3; Lactococcus lactis, 3; Leuconostoc sp., 1; and Pediococcus sp., 1. The Cpn60 gene ID method, coupled with reverse checkerboard hybridization, is an effective method for the identification of Enterococcus and related organisms.
Topics: Bacterial Typing Techniques; Chaperonin 60; Enterococcus; Gram-Positive Bacterial Infections; Gram-Positive Cocci; Humans; Lactococcus; Luminescent Measurements; Molecular Sequence Data; Nucleic Acid Hybridization; Phenotype; Phylogeny; Polymerase Chain Reaction; Sequence Analysis, DNA
PubMed: 11060051
DOI: 10.1128/JCM.38.11.3953-3959.2000 -
Journal of Applied Microbiology Apr 2010The aim of this study was to identify and characterize the population of Enterococcus sp. in domestic wastewater as it flows through a constructed wetland.
AIMS
The aim of this study was to identify and characterize the population of Enterococcus sp. in domestic wastewater as it flows through a constructed wetland.
METHODS AND RESULTS
Four hundred and eighty-four Enterococcus isolates were collected from the inlet, various sites within and from the outlet of a plastic lined constructed wetland in College Station, TX. The wetland treated septic tank effluent that passed sequentially through two 1.89 m(3) septic tanks and a 1.89 m(3) pump tank allowing 48 l doses at a 24 l min(-1) rate. The Enterococcus isolates were identified to species using the commercial Biolog system. The 484 Enterococcus isolates were comprised of ten different species, including Enterococcus faecalis (30.6%), Enterococcus pseudoavium (24.0%), Enterococcus casseliflavus (12.8%), Enterococcus faecium (11.2%), Enterococcus mundtii (7.9%), Enterococcus gallinarum (6.2%), Enterococcus dispar (3.7%), Enterococcus hirae (2.1%), Enterococcus durans and Enterococcus flavescens both 0.8%. Of the 88 isolates collected from the inlet, only 9.1% of the isolates were identified as Ent. faecalis and Ent. pseudoavium (36.4%) was identified as the predominant species. Whereas of the 74 isolates collected from the outlet, the predominant species were identified as Ent. faecalis (29.7%). Species identification varied among sites within the wetland, but often Ent. faecalis was the predominant species.
CONCLUSIONS
Our data suggest that while Ent. faecalis is the predominant species of Enterococcus found in domestic wastewater, the populations may shift during treatment as the wastewater flows through the constructed wetland.
SIGNIFICANCE AND IMPACT OF THE STUDY
We found that shifts in Enterococcus species composition occurred during domestic wastewater treatment. This has implications for the identification of faecal pollution based on the presence of specific bacterial types associated with domestic wastewater.
Topics: Bacterial Load; Enterococcus; Phenotype; Sewage; Waste Disposal, Fluid; Water; Water Microbiology; Wetlands
PubMed: 19778344
DOI: 10.1111/j.1365-2672.2009.04516.x -
Microorganisms May 2020Oral bacteria possess the ability to form biofilms on solid surfaces. After the penetration of oral bacteria into the pulp, the contact between biofilms and pulp tissue...
Oral bacteria possess the ability to form biofilms on solid surfaces. After the penetration of oral bacteria into the pulp, the contact between biofilms and pulp tissue may result in pulpitis, pulp necrosis and/or periapical lesion. Depending on the environmental conditions and the availability of nutrients in the pulp chamber and root canals, mainly Gram-negative anaerobic microorganisms predominate and form the intracanal endodontic biofilm. The objective of the present study was to investigate the role of different substrates on biofilm formation as well as the separate and collective incorporation of six endodontic pathogens, namely and into a nine-species "basic biofilm". This biofilm was formed in vitro as a standard subgingival biofilm, comprising and The resulting endodontic-like biofilms were grown 64 h under the same conditions on hydroxyapatite and dentin discs. After harvesting the endodontic-like biofilms, the bacterial growth was determined using quantitative real-time PCR, were labeled using fluorescence in situ hybridization (FISH) and analyzed by confocal laser scanning microscopy (CLSM). The addition of six endodontic pathogens to the "basic biofilm" induced a decrease in the cell number of the "basic" species. Interestingly, counts increased in biofilms containing and respectively, both on hydroxyapatite and on dentin discs, whereas counts increased only on dentin discs by addition of . The growth of on hydroxyapatite discs and of and on dentin discs were significantly higher in the biofilm containing all species than in the "basic biofilm". Contrarily, the counts of , and on hydroxyapatite discs as well as counts of and on dentin discs decreased in the all-species biofilm. Overall, all bacterial species associated with endodontic infections were successfully incorporated into the standard multispecies biofilm model both on hydroxyapatite and dentin discs. Thus, future investigations on endodontic infections can rely on this newly established endodontic-like multispecies biofilm model.
PubMed: 32384777
DOI: 10.3390/microorganisms8050674 -
Microbiology Resource Announcements Jan 2023Enterococcus dispar was isolated for the first time from synovial fluid and stool cultures and described as a new species in 1991. Here, we report the genome of E....
Enterococcus dispar was isolated for the first time from synovial fluid and stool cultures and described as a new species in 1991. Here, we report the genome of E. dispar CoE-457-22, which was obtained from traditionally produced Montenegrin dry sausage (sudzuk).
PubMed: 36515530
DOI: 10.1128/mra.01038-22 -
Atherosclerosis May 2019Although most risk factors for cardiac valve calcification (VC) are similar to those for coronary artery disease (CAD), they differ regarding lesions and clinical... (Comparative Study)
Comparative Study
BACKGROUND AND AIMS
Although most risk factors for cardiac valve calcification (VC) are similar to those for coronary artery disease (CAD), they differ regarding lesions and clinical symptoms. Recently, increasing evidence suggests that intestinal bacteria play essential roles in cardiovascular disease (CVD). It is plausible that the gut microbiota is linked to the occurrence of different CVDs under similar risk factors. Thus, we aimed to explore the gut microbiomes in patients with VC or CAD and determine their underlying connections.
METHODS
We collected samples from 119 subjects and performed 16S rRNA gene sequencing to analyze the gut microbiomes in VC and CAD patients and in control volunteers.
RESULTS
The gut microbiomes of VC and CAD patients were significantly different in terms of beta-diversity. Bacteria from Veillonella dispar, Bacteroides plebeius and Fusobacterium were enriched in the VC group, while members of Collinsella aerofaciens, Megamonas, Enterococcus, Megasphaera, Dorea and Blautia were decreased. According to the association with dyslipidemia, seven operational taxonomic units (OTUs), including Parabacteroides distasonis, Megamonas, Fusobacterium, Bacteroides sp., Bacteroides plebeius, Lactobacillus and Prevotella copri, were regarded as potential pathogens for CVDs. Additionally, Prevotella copri might be a keystone of CVDs, especially in VC patients, while Collinsella aerofaciens is a possible keystone of CAD, based on the multi-correlations of these bacteria with other OTUs in microbial communities.
CONCLUSIONS
Patients with VC and CAD suffer from different gut microbial dysbiosis. The gut microbiomes are associated with the clinical characteristics in these diseases and might be potential therapeutic targets.
Topics: Adult; Aged; Calcinosis; Coronary Artery Disease; Dysbiosis; Female; Gastrointestinal Microbiome; Heart Valve Diseases; Humans; Male; Middle Aged
PubMed: 30897381
DOI: 10.1016/j.atherosclerosis.2018.11.038 -
Journal of Global Infectious Diseases Sep 2010The objectives of the present study were to identify the species of enterococci isolated from nosocomial infections and to determine the antibiotic susceptibility...
OBJECTIVES
The objectives of the present study were to identify the species of enterococci isolated from nosocomial infections and to determine the antibiotic susceptibility pattern with reference to high-level aminoglycosides and vancomycin.
MATERIALS AND METHODS
Enterococci were isolated from various clinical samples collected from patients after 72 hours of hospitalization. Various species of Enterococcus were identified by standard methods. High-level aminoglycoside resistance and vancomycin susceptibility in enterococci were detected by disk-diffusion and agar-screen methods.
RESULTS
One hundred eighty enterococcal strains were isolated from various clinical samples. Various species of Enterococcus - Enterococcus fecalis 130 (72.22%), Enterococcus casseliflavus 24 (13.33%), Enterococcus fecium 17 (9.44%), Enterococcus durans 7 (3.89%) and Enterococcus dispar 2 (1.11%) - were isolated. The highest resistance to aminoglycoside was observed among E. fecium, followed by E. durans, E. fecalis and E. casseliflavus, both by disk-diffusion and agar-screen methods. The high-level aminoglycoside resistance (HLAR) was significantly (P<0.05) higher in E. fecium by agar-screen method. All enterococci showed minimum inhibitory concentration (MIC) of ≤8 μg/mL to vancomycin. Sixteen (12.31%) E. fecalis and 3 (12.5%) E. fecium strains were intermediately resistant to vancomycin (MIC= 8 μg/mL), whereas other strains were susceptible to vancomycin.
CONCLUSION
The occurrence of high-level aminoglycoside resistance in enterococcal isolates in our setup was high. Even though none of the enterococcal strains showed resistance to vancomycin, yet reduced susceptibility to vancomycin was noticed in our study. This would require routine testing of enterococcal isolates for HLAR and vancomycin susceptibility. Agar-screen method was found to be superior to disk-diffusion method in detecting resistant strains to aminoglycosides and vancomycin.
PubMed: 20927283
DOI: 10.4103/0974-777X.68534 -
World Journal of Gastroenterology Jul 2017To characterize the gut bacterial microbiota of patients with primary sclerosing cholangitis (PSC) and ulcerative colitis (UC). (Comparative Study)
Comparative Study
AIM
To characterize the gut bacterial microbiota of patients with primary sclerosing cholangitis (PSC) and ulcerative colitis (UC).
METHODS
Stool samples were collected and relevant clinical data obtained from 106 study participants, 43 PSC patients with ( = 32) or without ( = 11) concomitant inflammatory bowel disease, 32 UC patients, and 31 healthy controls. The V3 and V4 regions of the 16S ribosomal RNA gene were sequenced on Illumina MiSeq platform to cover low taxonomic levels. Data were further processed in QIIME employing MaAsLin and LEfSe tools for analysis of the output data.
RESULTS
Microbial profiles in both PSC and UC were characterized by low bacterial diversity and significant change in global microbial composition. , , , , and three other genera were markedly overrepresented in PSC regardless of concomitant inflammatory bowel disease (IBD). , and were tracked to the species level to identify , , , and along with and . PSC was further characterized by decreased abundance of and . Decrease in genus was linked to presence of colonic inflammation regardless of IBD phenotype. , and were decreased in UC along with genus . Low levels of serum albumin were significantly correlated with enrichment of order Actinomycetales.
CONCLUSION
PSC is associated with specific gut microbes independently of concomitant IBD and several bacterial taxa clearly distinguish IBD phenotypes (PSC-IBD and UC).
Topics: Adult; Aged; Bacteria; Cholangitis, Sclerosing; Colitis, Ulcerative; Colon; Dysbiosis; Feces; Female; Gastrointestinal Microbiome; Healthy Volunteers; Humans; Intestinal Mucosa; Male; Middle Aged; RNA, Ribosomal, 16S; Sequence Analysis, RNA
PubMed: 28740343
DOI: 10.3748/wjg.v23.i25.4548 -
Journal of Bacteriology Dec 2000The elongation factor Tu, encoded by tuf genes, is a GTP binding protein that plays a central role in protein synthesis. One to three tuf genes per genome are present,...
The elongation factor Tu, encoded by tuf genes, is a GTP binding protein that plays a central role in protein synthesis. One to three tuf genes per genome are present, depending on the bacterial species. Most low-G+C-content gram-positive bacteria carry only one tuf gene. We have designed degenerate PCR primers derived from consensus sequences of the tuf gene to amplify partial tuf sequences from 17 enterococcal species and other phylogenetically related species. The amplified DNA fragments were sequenced either by direct sequencing or by sequencing cloned inserts containing putative amplicons. Two different tuf genes (tufA and tufB) were found in 11 enterococcal species, including Enterococcus avium, Enterococcus casseliflavus, Enterococcus dispar, Enterococcus durans, Enterococcus faecium, Enterococcus gallinarum, Enterococcus hirae, Enterococcus malodoratus, Enterococcus mundtii, Enterococcus pseudoavium, and Enterococcus raffinosus. For the other six enterococcal species (Enterococcus cecorum, Enterococcus columbae, Enterococcus faecalis, Enterococcus sulfureus, Enterococcus saccharolyticus, and Enterococcus solitarius), only the tufA gene was present. Based on 16S rRNA gene sequence analysis, the 11 species having two tuf genes all have a common ancestor, while the six species having only one copy diverged from the enterococcal lineage before that common ancestor. The presence of one or two copies of the tuf gene in enterococci was confirmed by Southern hybridization. Phylogenetic analysis of tuf sequences demonstrated that the enterococcal tufA gene branches with the Bacillus, Listeria, and Staphylococcus genera, while the enterococcal tufB gene clusters with the genera Streptococcus and Lactococcus. Primary structure analysis showed that four amino acid residues encoded within the sequenced regions are conserved and unique to the enterococcal tufB genes and the tuf genes of streptococci and Lactococcus lactis. The data suggest that an ancestral streptococcus or a streptococcus-related species may have horizontally transferred a tuf gene to the common ancestor of the 11 enterococcal species which now carry two tuf genes.
Topics: Amino Acid Sequence; Blotting, Southern; Enterococcus; Evolution, Molecular; Gene Transfer, Horizontal; Genes, Bacterial; Gram-Positive Bacteria; Molecular Sequence Data; Peptide Elongation Factor Tu; Phylogeny; Sequence Alignment; Sequence Analysis, DNA
PubMed: 11092850
DOI: 10.1128/JB.182.24.6913-6920.2000