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Scientific Reports Jun 2024The application of beneficial microorganisms for corals (BMC) decreases the bleaching susceptibility and mortality rate of corals. BMC selection is typically performed...
The application of beneficial microorganisms for corals (BMC) decreases the bleaching susceptibility and mortality rate of corals. BMC selection is typically performed via molecular and biochemical assays, followed by genomic screening for BMC traits. Herein, we present a comprehensive in silico framework to explore a set of six putative BMC strains. We extracted high-quality DNA from coral samples collected from the Red Sea and performed PacBio sequencing. We identified BMC traits and mechanisms associated with each strain as well as proposed new traits and mechanisms, such as chemotaxis and the presence of phages and bioactive secondary metabolites. The presence of prophages in two of the six studied BMC strains suggests their possible distribution within beneficial bacteria. We also detected various secondary metabolites, such as terpenes, ectoines, lanthipeptides, and lasso peptides. These metabolites possess antimicrobial, antifungal, antiviral, anti-inflammatory, and antioxidant activities and play key roles in coral health by reducing the effects of heat stress, high salinity, reactive oxygen species, and radiation. Corals are currently facing unprecedented challenges, and our revised framework can help select more efficient BMC for use in studies on coral microbiome rehabilitation, coral resilience, and coral restoration.
Topics: Anthozoa; Animals; Indian Ocean; Probiotics; Genomics; Bacteria; Microbiota
PubMed: 38914624
DOI: 10.1038/s41598-024-65152-8 -
Sheng Wu Gong Cheng Xue Bao = Chinese... Jun 2024Excessive accumulation of nitrogen is a major cause of water eutrophication. Developing an inexpensive and efficient nitrogen removal technology is therefore essential... (Review)
Review
Excessive accumulation of nitrogen is a major cause of water eutrophication. Developing an inexpensive and efficient nitrogen removal technology is therefore essential for wastewater purification. The microbial technology for nitrogen removal has been widely used for its low cost, high efficiency, and strong environmental adaptability. Most recently, with the advances in synthetic biotechnology, artificial multicellular systems have been sufficiently developed and exhibited unique definability and controllability. Compared with those in the natural microbial consortia, the nitrogen removal pathways and environmental response mechanisms are easy to be clarified in the artificial multicellular systems, which allow for efficient nitrogen removal under low cellular metabolic loading. Therefore, artificial multicellular systems demonstrate great application potential in the purification of wastewater, including landfill leachate, industrial wastewater, seawater aquaculture wastewater, and domestic sewage. We focused on the design, building, and application of artificial multicellular systems for nitrogen removal from wastewater. Specifically, we summarized the functional microorganisms and their nitrogen removal mechanisms, introduced the design principles and building methods of artificial multicellular systems, illustrated the application of artificial multicellular systems with examples, and prospected the future research trend in nitrogen removal from wastewater. The conclusion is expected to provide new insights and efficient strategies for optimizing the microbial nitrogen removal from wastewater.
Topics: Wastewater; Nitrogen; Waste Disposal, Fluid; Biodegradation, Environmental; Water Purification; Bacteria; Water Pollutants, Chemical
PubMed: 38914493
DOI: 10.13345/j.cjb.230714 -
Sheng Wu Gong Cheng Xue Bao = Chinese... Jun 2024Filamentous fungi are a group of eukaryotic microorganisms widely found in nature. Some filamentous fungi have been developed as "cell factories" and extensively used... (Review)
Review
Filamentous fungi are a group of eukaryotic microorganisms widely found in nature. Some filamentous fungi have been developed as "cell factories" and extensively used for the production of recombinant proteins, organic acids, and secondary metabolites due to their strong protein secretion capabilities or effective synthesis of many natural products. The growth morphology of filamentous fungi significantly influences the quality and quantity of fermented products. Previous research conducted by the authors' group revealed that an increase in hyphal branches leads to enhanced protein secretion during liquid fermentation. With the development of morphological engineering of filamentous fungi, an increasing number of studies have focused on modifying fungal mycelium morphology to improve the yield of target metabolites during fermentation. While there have been a few reviews on the relationship between fungal fermentation morphology and productivity, research in this area is rapidly developing and requires updates. The paper presents a comprehensive review of domestic and international research reports, along with the authors' own research findings, to systematically review the morphological patterns of filamentous fungi, the impact of fungal morphology on industrial fermentation, as well as methods and strategies for regulating mycelial morphology. The aim of this review is to enhance the understanding of relevant domestic scholars regarding the morphological development of filamentous fungi and provide ideas for the rational engineering of fungal strains suitable for industrial fermentation.
Topics: Fermentation; Fungi; Mycelium; Industrial Microbiology; Genetic Engineering; Recombinant Proteins; Hyphae
PubMed: 38914491
DOI: 10.13345/j.cjb.230717 -
Sheng Wu Gong Cheng Xue Bao = Chinese... Jun 2024Thermophilic cyanobacteria are prokaryotic organisms that possess exceptional heat-resistant characteristics. This group serves as an excellent model for investigating... (Review)
Review
Thermophilic cyanobacteria are prokaryotic organisms that possess exceptional heat-resistant characteristics. This group serves as an excellent model for investigating the heat tolerance of higher photosynthetic organisms, including higher plants, some protists (such as algae and euglena), and bacteria. Analyzing the mechanisms of high-temperature adaptation in thermophilic cyanobacteria can enhance our understanding of how photosynthetic organisms and microorganisms tolerate high temperatures at the molecular level. Additionally, these thermotolerant cyanobacteria have the potential to contribute to breeding heat-tolerant plants and developing microbial cell factories. This review summarizes current research on thermophilic cyanobacteria, focusing on their ecology, morphology, omics studies, and mechanisms of high-temperature tolerance. It offers insight into the potential biotechnological applications of thermophilic cyanobacteria and highlights future research opportunities. Specifically, attention is given to the photosynthetic physiology and metabolism of cyanobacteria, and the molecular basis of heat-tolerance mechanisms in thermophilic cyanobacteria is explored.
Topics: Cyanobacteria; Hot Temperature; Biotechnology; Adaptation, Physiological; Photosynthesis; Thermotolerance
PubMed: 38914490
DOI: 10.13345/j.cjb.230645 -
Sheng Wu Gong Cheng Xue Bao = Chinese... Jun 2024Amino acids as the building blocks of proteins are widely applied in food, medicine, feed, and chemical industries. Amino acid production by microbial cell factories... (Review)
Review
Amino acids as the building blocks of proteins are widely applied in food, medicine, feed, and chemical industries. Amino acid production by microbial cell factories from renewable resources is praised for the environmental friendliness, mild reaction conditions, and high product purity, which helps to achieve the goal of carbon neutrality. Researchers have employed the methods of metabolic engineering and synthetic biology to engineer and and optimized the culture conditions to construct the microbial cell factories with high performance for producing branched chain amino acids, amino acids of the aspartic acid and glutamic acid families, and aromatic amino acids. We review the engineering process of microbial cell factories for high production of amino acids, in the hope of providing a reference for the creation of high-performance microbial cell factories.
Topics: Metabolic Engineering; Amino Acids; Corynebacterium glutamicum; Escherichia coli; Synthetic Biology; Industrial Microbiology
PubMed: 38914487
DOI: 10.13345/j.cjb.230825 -
Sheng Wu Gong Cheng Xue Bao = Chinese... Jun 20242-phenylethanol (2-PE), an aromatic alcohol with a rose fragrance, is the second most widely used flavoring substance in the world. It is widely used in the cosmetic,... (Review)
Review
2-phenylethanol (2-PE), an aromatic alcohol with a rose fragrance, is the second most widely used flavoring substance in the world. It is widely used in the cosmetic, food, and pharmaceutical industries. This paper introduces the chemical synthesis methods of 2-PE and the synthetic pathways in plants and microorganisms, summarizes the strategies to improve the microbial synthesis of 2-PE, reviews the research progress in synthesis of 2-PE in microorganisms, and makes an outlook on the research prospects, aiming to provide a theoretical basis for the industrial production of 2-PE.
Topics: Phenylethyl Alcohol; Industrial Microbiology; Flavoring Agents; Bacteria; Plants
PubMed: 38914486
DOI: 10.13345/j.cjb.230762 -
Sheng Wu Gong Cheng Xue Bao = Chinese... Jun 2024Compatible solutes are highly water-soluble organic osmolytes produced by microorganisms to adapt to extreme environments, such as high salinity and osmotic pressure.... (Review)
Review
Compatible solutes are highly water-soluble organic osmolytes produced by microorganisms to adapt to extreme environments, such as high salinity and osmotic pressure. Among these, ectoine plays a crucial role in repairing and protecting nucleic acids, protein, biofilms, and cells. As a result, it has found widespread applications in cosmetics, biological agents, the enzyme industry, medicine, and other fields. Currently, the market value of ectoine is around US$ 1 000/kg, with a global demand reaching 15 000 tons per year. Although halophilic bacteria serve as the natural source of ectoine synthesis, its production in high-salinity media presents challenges such as equipment corrosion and high cost for industrial production. Advancements in functional genomics, systems biology, and synthetic biology have paved the way for the development of high-yielding cell factories through metabolic engineering, leading to significant progress. For example, engineered achieved a maximum ectoine titer of 131.8 g/L, with a productivity of 1.37 g/(L·h). This review aims to explore the biosynthetic pathway, biochemical characteristics of key enzymes, and the biosynthesis of ectoine, shedding light on current research status and offering insights for industrial-scale ectoine production.
Topics: Amino Acids, Diamino; Metabolic Engineering; Escherichia coli; Biosynthetic Pathways; Hydro-Lyases
PubMed: 38914483
DOI: 10.13345/j.cjb.230640 -
Journal of Obstetrics and Gynaecology :... Dec 2024Microbial colonisation in infants is initially dependent on the mother and is affected by the mode of delivery. Understanding these impacts is crucial as the early-life...
BACKGROUND
Microbial colonisation in infants is initially dependent on the mother and is affected by the mode of delivery. Understanding these impacts is crucial as the early-life gut microbiota plays a vital role in immune development, metabolism, and overall health. Early-life infant gut microbiota is diverse among populations and geographic origins. However, in this context, only a few studies have explored the impact of the mode of delivery on the intestinal microbiome in children in Guangzhou, China. Therefore, this study aimed to investigate the influence of birth mode on the intestinal microbiota of healthy infants in Guangzhou, China.
METHODS
Faecal samples were collected once from 20 healthy full-term infants aged 1-6 months, delivered via either caesarean section (CS) or vaginal delivery (VD), post-enrolment. The intestinal microbiota were characterised using full-length 16S rRNA gene sequencing. Bacterial quantity and community composition were compared between the two groups.
RESULTS
No significant differences in gut bacterial diversity and richness were observed between the CS and VD groups. The Pseudomonadota phylum (44.15 ± 33.05% vs 15.62 ± 15.60%, = 0.028) and Enterobacteriaceae family (44.00 ± 33.11% vs 15.31 ± 15.47%, = 0.028) were more abundant in the CS group than in the VD group. The VD group exhibited a higher abundance of the Bacillota phylum (40.51 ± 32.77% vs 75.57 ± 27.83%, = 0.019).
CONCLUSIONS
The early stage of intestinal bacterial colonisation was altered in the CS group as compared with the VD group. Our findings provide evidence that CS has the potential to disrupt the maturation of intestinal microbial communities in infants by influencing the colonisation of specific microorganisms. Further comprehensive studies that consider geographical locations are necessary to elucidate the progression of microbiota in infants born via different delivery modes.
Topics: Humans; Gastrointestinal Microbiome; Pilot Projects; Female; Infant; Cesarean Section; Feces; Delivery, Obstetric; Pregnancy; Male; China; RNA, Ribosomal, 16S; Bacteria
PubMed: 38913773
DOI: 10.1080/01443615.2024.2368829 -
PloS One 2024Exploration of interspecies interactions between microorganisms can have taxonomic, ecological, evolutionary, or medical applications. To better explore interactions...
Exploration of interspecies interactions between microorganisms can have taxonomic, ecological, evolutionary, or medical applications. To better explore interactions between microorganisms it is important to establish the ideal conditions that ensure survival of all species involved. In this study, we sought to identify the ideal biotic and abiotic factors that would result in high co-culture viability of two interkingdom species, Pseudomonas aeruginosa and Acanthamoeba castellanii, two soil dwelling microbes. There have been limited studies showing long-term interactions between these two organisms as co-culture can result in high mortality for one or both organisms suggesting a predator-predator interaction may exist between them. In this study, we identified biotic and abiotic conditions that resulted in a high viability for both organisms in long-term co-culture, including optimizing temperature, nutrient concentration, choice of bacterial strains, and the initial ratio of interacting partners. These two species represent ideal partners for studying microbial interactions because amoebae act similarly to mammalian immune cells in many respects, and this can allow researchers to study host-pathogen interactions in vitro. Therefore, long-term interaction studies between these microbes might reveal the evolutionary steps that occur in bacteria when subjected to intense predation, like what occurs when pathogens enter the human body. The culture conditions characterized here resulted in high viability for both organisms for at least 14-days in co-culture suggesting that long-term experimental studies between these species can be achieved using these culture conditions.
Topics: Acanthamoeba castellanii; Pseudomonas aeruginosa; Coculture Techniques; Microbial Interactions; Temperature; Soil Microbiology
PubMed: 38913685
DOI: 10.1371/journal.pone.0305973 -
The ISME Journal Jun 2024Soil microbial flora constitutes a highly diverse and complex microbiome on Earth, often challenging to cultivation, with unclear metabolic mechanisms in situ. Here, we...
Soil microbial flora constitutes a highly diverse and complex microbiome on Earth, often challenging to cultivation, with unclear metabolic mechanisms in situ. Here, we present a pioneering concept for the in situ construction of functional microbial consortia (FMCs) and introduce an innovative method for creating FMCs by utilising phenanthrene as a model compound to elucidate their in situ biodegradation mechanisms. Our methodology involves single-cell identification, sorting, and culture of functional microorganisms, resulting in the formation of a precise in situ FMC. Through RACS-SIP, we identified and isolated phenanthrene-degrading bacterial cells from Achromobacter sp. and Pseudomonas sp., achieving precise and controllable in situ consortia based on genome-guided cultivation. Our in situ FMC outperformed conventionally designed functional flora when tested in real soil, indicating its superior phenanthrene degradation capacity. We revealed that microorganisms with high degradation efficiency isolated through conventional methods may exhibit pollutant tolerance but lack actual degradation ability in natural environments. This finding highlights the potential to construct FMCs based on thorough elucidation of in situ functional degraders, thereby achieving sustained and efficient pollutant degradation. Single-cell sequencing linked degraders with their genes and metabolic pathways, providing insights regarding the construction of in situ FMCs. The consortium in situ comprising microorganisms with diverse phenanthrene metabolic pathways might offer distinct advantages for enhancing phenanthrene degradation efficiency, such as the division of labour and cooperation or communication among microbial species. Our approach underscores the importance of in situ, single-cell precision identification, isolation, and cultivation for comprehensive bacterial functional analysis and resource exploration, which can extend to investigate MFCs in archaea and fungi, clarifying FMC construction methods for element recycling and pollutant transformation in complex real-world ecosystems.
PubMed: 38913500
DOI: 10.1093/ismejo/wrae115