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Marine Drugs Jun 2024Three new cyclic lipopeptides, olenamidonins A-C (-), in addition to two previously reported metabolites ( and ), were accumulated in the Δ deletion mutant of...
Three new cyclic lipopeptides, olenamidonins A-C (-), in addition to two previously reported metabolites ( and ), were accumulated in the Δ deletion mutant of deepsea-derived SCSIO 1071. The structures of these cyclic lipopeptides were determined by a combination of spectroscopic methods and circular dichroism (CD) measurement. The antibacterial assay results showed that compounds displayed different degrees of growth inhibition against multidrug-resistant (MDR) bacterial strains CCARM 5172 and CCARM 5203 with minimum inhibitory concentrations (MICs) of 1.56-6.25 μg/mL.
Topics: Streptomyces; Lipopeptides; Microbial Sensitivity Tests; Anti-Bacterial Agents; Enterococcus faecalis; Peptides, Cyclic; Enterococcus faecium; Drug Resistance, Multiple, Bacterial; Bacterial Proteins
PubMed: 38921573
DOI: 10.3390/md22060262 -
Marine Drugs May 2024Antarctica, one of the most extreme environments on Earth, hosts diverse microbial communities. These microbes have evolved and adapted to survive in these hostile...
Antarctica, one of the most extreme environments on Earth, hosts diverse microbial communities. These microbes have evolved and adapted to survive in these hostile conditions, but knowledge on the molecular mechanisms underlying this process remains limited. The Italian Collection of Antarctic Bacteria ( (CIBAN)), managed by the University of Messina, represents a valuable repository of cold-adapted bacterial strains isolated from various Antarctic environments. In this study, we sequenced and analyzed the genomes of 58 marine Gammaproteobacteria strains from the CIBAN collection, which were isolated during Italian expeditions from 1990 to 2005. By employing genome-scale metrics, we taxonomically characterized these strains and assigned them to four distinct genera: , , and . Genome annotation revealed a previously untapped functional potential, including secondary metabolite biosynthetic gene clusters and antibiotic resistance genes. Phylogenomic analyses provided evolutionary insights, while assessment of cold-shock protein presence shed light on adaptation mechanisms. Our study emphasizes the significance of CIBAN as a resource for understanding Antarctic microbial life and its biotechnological potential. The genomic data unveil new horizons for insight into bacterial existence in Antarctica.
Topics: Antarctic Regions; Phylogeny; Genome, Bacterial; Gammaproteobacteria; Genomics; Psychrobacter; Pseudoalteromonas; Multigene Family
PubMed: 38921549
DOI: 10.3390/md22060238 -
Marine Drugs May 2024Clavatols exhibit a wide range of biological activities due to their diverse structures. A genome mining strategy identified an cluster from sp. MYA5, derived from the...
Clavatols exhibit a wide range of biological activities due to their diverse structures. A genome mining strategy identified an cluster from sp. MYA5, derived from the Arctic plant , is responsible for clavatol biosynthesis. Seven clavatols, including one new clavatol derivate named penicophenone F () and six known clavatols (-), were isolated from sp. MYA5 using a transcriptome mining strategy. These structures were elucidated by comprehensive spectroscopic analysis. Antibacterial, aldose reductase inhibition, and siderophore-producing ability assays were conducted on compounds -. Compounds and demonstrated inhibitory effects on the ALR2 enzyme with inhibition rates of 75.3% and 71.6% at a concentration of 10 μM, respectively. Compound exhibited antibacterial activity against and with MIC values of 4.0 μg/mL and 4.0 μg/mL, respectively. Additionally, compounds , , and also showed potential iron-binding ability.
Topics: Penicillium; Anti-Bacterial Agents; Staphylococcus aureus; Genomics; Escherichia coli; Microbial Sensitivity Tests; Transcriptome; Arctic Regions; Siderophores; Aldehyde Reductase
PubMed: 38921547
DOI: 10.3390/md22060236 -
Journal of Fungi (Basel, Switzerland) Jun 2024(formerly ) is a methylotrophic yeast widely used in laboratories around the world to produce recombinant proteins. Given its advantageous features, it has also gained... (Review)
Review
(formerly ) is a methylotrophic yeast widely used in laboratories around the world to produce recombinant proteins. Given its advantageous features, it has also gained much interest in the context of modern biotechnology. In this review, we present the utilization of as a platform to produce several products of economic interest such as biopharmaceuticals, renewable chemicals, fuels, biomaterials, and food/feed products. Finally, we present synthetic biology approaches currently used for strain engineering, aiming at the production of new bioproducts.
PubMed: 38921397
DOI: 10.3390/jof10060411 -
Cells Jun 2024causes 6.4 million cases of tuberculosis and claims 1.6 million lives annually. Mycobacterial adhesion, invasion of host cells, and subsequent intracellular survival...
causes 6.4 million cases of tuberculosis and claims 1.6 million lives annually. Mycobacterial adhesion, invasion of host cells, and subsequent intracellular survival are crucial for the infection and dissemination process, yet the cellular mechanisms underlying these phenomena remain poorly understood. This study created a (BCG) transposon library using a MycomarT7 phage carrying a Himar1 Mariner transposon to identify genes related to mycobacteria adhesion and invasion. Using adhesion and invasion model screening, we found that the mutant strain B2909 lacked adhesion and invasion abilities because of an inactive gene, which encodes a fatty-acyl CoA ligase, although the specific function of this gene remains unclear. To investigate the role of FadD18, we constructed a complementary strain and observed that expression enhanced the colony size and promoted the formation of a stronger cord-like structure; FadD18 expression also inhibited BCG growth and reduced BCG intracellular survival in macrophages. Furthermore, FadD18 expression elevated levels of the proinflammatory cytokines IL-6, IL-1β, and TNF-α in infected macrophages by stimulating the NF-κB and MAPK signaling pathways. Overall, the FadD18 plays a key role in the adhesion and invasion abilities of mycobacteria while modulating the intracellular survival of BCG by influencing the production of proinflammatory cytokines.
Topics: Mycobacterium tuberculosis; Cytokines; Macrophages; Mycobacterium bovis; Mice; Bacterial Proteins; Animals; Humans; NF-kappa B; Microbial Viability; Bacterial Adhesion
PubMed: 38920649
DOI: 10.3390/cells13121019 -
Parasites & Vectors Jun 2024Past findings demonstrate that arthropods can egest midgut microbiota into the host skin leading to dual colonization of the vertebrate host with pathogens and saliva...
BACKGROUND
Past findings demonstrate that arthropods can egest midgut microbiota into the host skin leading to dual colonization of the vertebrate host with pathogens and saliva microbiome. A knowledge gap exists on how the saliva microbiome interacts with the pathogen in the saliva. To fill this gap, we need to first define the microbial composition of mosquito saliva.
METHODS
The current study aimed at analyzing and comparing the microbial profile of Aedes albopictus saliva and midgut as well as assessing the impact of Zika virus (ZIKV) infection on the midgut and saliva microbial composition. Colony-reared Ae. albopictus strains were either exposed to ZIKV infectious or noninfectious bloodmeal. At 14 ays postinfection, the 16S V3-V4 hypervariable rRNA region was amplified from midgut and saliva samples and sequenced on an Illumina MiSeq platform. The relative abundance and diversity of midgut and saliva microbial taxa were assessed.
RESULTS
We observed a richer microbial community in the saliva compared with the midgut, yet some of the microbial taxa were common in the midgut and saliva. ZIKV infection did not impact the microbial diversity of midgut or saliva. Further, we identified Elizabethkingia spp. in the Ae. albopictus saliva.
CONCLUSIONS
This study provides insights into the microbial community of the Ae. albopictus saliva as well as the influence of ZIKV infection on the microbial composition of its midgut and saliva. The identification of Elizabethkingia spp., an emerging pathogen of global health significance, in Ae. albopictus saliva is of medical importance. Future studies to assess the interactions between Ae. albopictus saliva microbiome and ZIKV could lead to novel strategies for developing transmission barrier tools.
Topics: Animals; Saliva; Aedes; Zika Virus; Mosquito Vectors; Microbiota; Gastrointestinal Microbiome; RNA, Ribosomal, 16S; Female; Zika Virus Infection; Gastrointestinal Tract
PubMed: 38918848
DOI: 10.1186/s13071-024-06334-1 -
Microbiome Jun 2024Microbial adaptation to salinity has been a classic inquiry in the field of microbiology. It has been demonstrated that microorganisms can endure salinity stress via...
BACKGROUND
Microbial adaptation to salinity has been a classic inquiry in the field of microbiology. It has been demonstrated that microorganisms can endure salinity stress via either the "salt-in" strategy, involving inorganic ion uptake, or the "salt-out" strategy, relying on compatible solutes. While these insights are mostly based on laboratory-cultured isolates, exploring the adaptive mechanisms of microorganisms within natural salinity gradient is crucial for gaining a deeper understanding of microbial adaptation in the estuarine ecosystem.
RESULTS
Here, we conducted metagenomic analyses on filtered surface water samples collected from a typical subtropical short residence-time estuary and categorized them by salinity into low-, intermediate-, and high-salinity metagenomes. Our findings highlighted salinity-driven variations in microbial community composition and function, as revealed through taxonomic and Clusters of Orthologous Group (COG) functional annotations. Through metagenomic binning, 127 bacterial and archaeal metagenome-assembled genomes (MAGs) were reconstructed. These MAGs were categorized as stenohaline-specific to low-, intermediate-, or high-salinity-based on the average relative abundance in one salinity category significantly exceeding those in the other two categories by an order of magnitude. Those that did not meet this criterion were classified as euryhaline, indicating a broader range of salinity tolerance. Applying the Boruta algorithm, a machine learning-based feature selection method, we discerned important genomic features from the stenohaline bacterial MAGs. Of the total 12,162 COGs obtained, 40 were identified as important features, with the "inorganic ion transport and metabolism" COG category emerging as the most prominent. Furthermore, eight COGs were implicated in microbial osmoregulation, of which four were related to the "salt-in" strategy, three to the "salt-out" strategy, and one to the regulation of water channel activity. COG0168, annotated as the Trk-type K transporter related to the "salt-in" strategy, was ranked as the most important feature. The relative abundance of COG0168 was observed to increase with rising salinity across metagenomes, the stenohaline strains, and the dominant Actinobacteriota and Proteobacteria phyla.
CONCLUSIONS
We demonstrated that salinity exerts influences on both the taxonomic and functional profiles of the microbial communities inhabiting the estuarine ecosystem. Our findings shed light on diverse salinity adaptation strategies employed by the estuarine microbial communities, highlighting the crucial role of the "salt-in" strategy mediated by Trk-type K transporters for microorganisms thriving under osmotic stress in the short residence-time estuary. Video Abstract.
Topics: Estuaries; Salinity; Metagenomics; Bacteria; Archaea; Metagenome; Adaptation, Physiological; Microbiota; Seawater; Water Microbiology
PubMed: 38918820
DOI: 10.1186/s40168-024-01817-w -
BMC Veterinary Research Jun 2024Acinetobacter lwoffii (A. lwoffii) is a Gram-negative bacteria common in the environment, and it is the normal flora in human respiratory and digestive tracts. The...
BACKGROUND
Acinetobacter lwoffii (A. lwoffii) is a Gram-negative bacteria common in the environment, and it is the normal flora in human respiratory and digestive tracts. The bacteria is a zoonotic and opportunistic pathogen that causes various infections, including nosocomial infections. The aim of this study was to identify A. lwoffii strains isolated from bovine milk with subclinical mastitis in China and get a better understanding of its antimicrobial susceptibility and resistance profile. This is the first study to analyze the drug resistance spectrum and corresponding mechanisms of A. lwoffii isolated in raw milk.
RESULTS
Four A. lwoffii strains were isolated by PCR method. Genetic evolution analysis using the neighbor-joining method showed that the four strains had a high homology with Acinetobacter lwoffii. The strains were resistant to several antibiotics and carried 17 drug-resistance genes across them. Specifically, among 23 antibiotics, the strains were completely susceptible to 6 antibiotics, including doxycycline, erythromycin, polymyxin, clindamycin, imipenem, and meropenem. In addition, the strains showed variable resistance patterns. A total of 17 resistance genes, including plasmid-mediated resistance genes, were detected across the four strains. These genes mediated resistance to 5 classes of antimicrobials, including beta-lactam, aminoglycosides, fluoroquinolones, tetracycline, sulfonamides, and chloramphenicol.
CONCLUSION
These findings indicated that multi-drug resistant Acinetobacter lwoffii strains exist in raw milk of bovine with subclinical mastitis. Acinetobacter lwoffii are widespread in natural environmental samples, including water, soil, bathtub, soap box, skin, pharynx, conjunctiva, saliva, gastrointestinal tract, and vaginal secretions. The strains carry resistance genes in mobile genetic elements to enhance the spread of these genes. Therefore, more attention should be paid to epidemiological surveillance and drug resistant A. lwoffii.
Topics: Animals; Cattle; Mastitis, Bovine; Female; Acinetobacter; Milk; China; Anti-Bacterial Agents; Microbial Sensitivity Tests; Acinetobacter Infections; Drug Resistance, Bacterial; Drug Resistance, Multiple, Bacterial
PubMed: 38918815
DOI: 10.1186/s12917-024-04119-3 -
BMC Microbiology Jun 20245-Fluorouracil (5-FU) is used as an antineoplastic agent in distinct cancer types. Increasing evidence suggests that the gut microbiota might modulate 5-FU efficacy and...
Prebiotic fibre mixtures counteract the manifestation of gut microbial dysbiosis induced by the chemotherapeutic 5-Fluorouracil (5-FU) in a validated in vitro model of the colon.
BACKGROUND
5-Fluorouracil (5-FU) is used as an antineoplastic agent in distinct cancer types. Increasing evidence suggests that the gut microbiota might modulate 5-FU efficacy and toxicity, potentially affecting the patient's prognosis. The current experimental study investigated 5-FU-induced microbiota alterations, as well as the potential of prebiotic fibre mixtures (M1-M4) to counteract these shifts.
METHODS
A pooled microbial consortium was derived from ten healthy donors, inoculated in an in vitro model of the colon, and treated with 5-FU, with or without prebiotic fibre mixtures for 72 h. Four different prebiotic fibre mixtures were tested: M1 containing short-chain galacto-oligosaccharides (sc GOS), long-chain fructo-oligosaccharides (lcFOS), and low viscosity pectin (lvPect), M2 consisting of arabinoxylan, beta-glucan, pectin, and resistant starch, M3 which was a mixture of scGOS and lcFOS, and M4 containing arabinoxylan, beta-glucan, pectin, resistant starch, and inulin.
RESULTS
We identified 5-FU-induced changes in gut microbiota composition, but not in microbial diversity. Administration of prebiotic fibre mixtures during 5-FU influenced gut microbiota composition and taxa abundance. Amongst others, prebiotic fibre mixtures successfully stimulated potentially beneficial bacteria (Bifidobacterium, Lactobacillus, Anaerostipes, Weissella, Olsenella, Senegalimassilia) and suppressed the growth of potentially pathogenic bacteria (Klebsiella, Enterobacter) in the presence of 5-FU. The short-chain fatty acid (SCFA) acetate increased slightly during 5-FU, but even more during 5-FU with prebiotic fibre mixtures, while propionate was lower due to 5-FU with or without prebiotic fibre mixtures, compared to control. The SCFA butyrate and valerate did not show differences among all conditions. The branched-chain fatty acids (BCFA) iso-butyrate and iso-valerate were higher in 5-FU, but lower in 5-FU + prebiotics, compared to control.
CONCLUSIONS
These data suggest that prebiotic fibre mixtures represent a promising strategy to modulate 5-FU-induced microbial dysbiosis towards a more favourable microbiota, thereby possibly improving 5-FU efficacy and reducing toxicity, which should be evaluated further in clinical studies.
Topics: Fluorouracil; Prebiotics; Dysbiosis; Gastrointestinal Microbiome; Humans; Dietary Fiber; Colon; Bacteria; Male; Fatty Acids, Volatile; Female; Adult; Pectins
PubMed: 38918717
DOI: 10.1186/s12866-024-03384-4 -
Nature Communications Jun 2024Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene...
Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84-99% and 18-61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.
Topics: Archaea; RNA, Ribosomal, 16S; Anaerobiosis; Bacteria; Microbiota; Biodiversity; Phylogeny; Wastewater; Bioreactors; Methane; Sequence Analysis, DNA
PubMed: 38918384
DOI: 10.1038/s41467-024-49641-y