Microbial Biotechnology最新文献

{"title":"The hydrocarbon pollution crisis: Harnessing the earth hydrocarbon-degrading microbiome","authors":"Robert Duran,&nbsp;Cristiana Cravo-Laureau","doi":"10.1111/1751-7915.14526","DOIUrl":"10.1111/1751-7915.14526","url":null,"abstract":"<p>As part of the battle against climate change, the decarbonization of human activities has been acted in many countries worldwide. Thus, in order to limit the planet warming, it is expected to reduce the combustion of fossil fuels for decreasing drastically the production of greenhouse gas emissions. Although beneficial for reducing carbon dioxide (CO₂) production to fight against climate change, this countermeasure unfortunately does not mean that hydrocarbon pollution is behind us because hydrocarbon pollution has many sources (Duran &amp; Cravo-Laureau, <span>2016</span>) that will remain. It is estimated that the industrial and petroleum activities, which have already left behind a multitude of hydrocarbon-contaminated sites that still need to be restored, release accidentally between 1.7 and 8.8 million tonnes of oil into the environment each year (Ambaye et al., <span>2022</span>). The decarbonization is also expected to have a beneficial impact on decreasing the industrial release of hydrocarbons into the environment by reducing oil spill frequency and consequences (Little et al., <span>2021</span>). In addition to the direct contribution of hydrocarbons resulting from the continued use of fossil fuels, the human activities also generate indirect inputs such as wildfires introducing polycyclic aromatic hydrocarbon (PAH) into the environment (Campos et al., <span>2019</span>; Paul et al., <span>2023</span>). Particularly “mega fires,” which burn large forest areas, are becoming more frequent as a consequence of climate change (Bracewell et al., <span>2023</span>; van Oldenborgh et al., <span>2021</span>). Of course, the natural sources of hydrocarbon contamination, such as volcanic activities and marine oil seeps, as well as biogenic sources (Duran &amp; Cravo-Laureau, <span>2016</span>), continuously emit hydrocarbons into the environment. Thus, hydrocarbons last to be of concern for the environment in the future. In order to mitigate the impact of hydrocarbons on the environment, exploiting the hydrocarbon degradation potential that microorganisms have is a challenge to meet for scientists and engineers concerned about hydrocarbon pollution.</p><p>Important key knowledge has been gained on microbial hydrocarbon degradation as well as on the ecology of microbial communities inhabiting hydrocarbon-contaminated sites. The hydrocarbon degradation capacity has been described for a large number of microorganisms from diverse terrestrial and aquatic environments. Several specialist hydrocarbon-degrading microbial taxa have been described and isolated, as for example, the marine obligate hydrocarbonoclastic bacteria (OHCB) observed to bloom during marine oil spills (Yakimov et al., <span>2007</span>), hydrocarbon-tolerant fungi found in petroleum-contaminated sediment (Álvarez-Barragán et al., <span>2021</span>), and alkane-degrading specialist populations in soil (Hamamura et al., <span>2013</span>). The characterization of speciali","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 7","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11246598/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141602983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A nuclease domain fused to the Snf2 helicase confers antiphage defence in coral-associated Halomonas meridiana","authors":"Tianlang Liu,&nbsp;Xinyu Gao,&nbsp;Ran Chen,&nbsp;Kaihao Tang,&nbsp;Ziyao Liu,&nbsp;Pengxia Wang,&nbsp;Xiaoxue Wang","doi":"10.1111/1751-7915.14524","DOIUrl":"10.1111/1751-7915.14524","url":null,"abstract":"<p>The coral reef microbiome plays a vital role in the health and resilience of reefs. Previous studies have examined phage therapy for coral pathogens and for modifying the coral reef microbiome, but defence systems against coral-associated bacteria have received limited attention. Phage defence systems play a crucial role in helping bacteria fight phage infections. In this study, we characterized a new defence system, Hma (HmaA-HmaB-HmaC), in the coral-associated <i>Halomonas meridiana</i> derived from the scleractinian coral <i>Galaxea fascicularis</i>. The Swi2/Snf2 helicase HmaA with a C-terminal nuclease domain exhibits antiviral activity against <i>Escherichia</i> phage T4. Mutation analysis revealed the nickase activity of the nuclease domain (belonging to PDD/EXK superfamily) of HmaA is essential in phage defence. Additionally, HmaA homologues are present in ~1000 bacterial and archaeal genomes. The high frequency of HmaA helicase in <i>Halomonas</i> strains indicates the widespread presence of these phage defence systems, while the insertion of defence genes in the <i>hma</i> region confirms the existence of a defence gene insertion hotspot. These findings offer insights into the diversity of phage defence systems in coral-associated bacteria and these diverse defence systems can be further applied into designing probiotics with high-phage resistance.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 7","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11232893/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141562213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The antibiotic resistance crisis and the development of new antibiotics","authors":"Harald Brüssow","doi":"10.1111/1751-7915.14510","DOIUrl":"10.1111/1751-7915.14510","url":null,"abstract":"<p>The Global Burden of Disease report of 2019 estimated 14 million infection-related deaths, making it the second leading cause of death after ischaemic heart disease. Bacterial pathogens accounted for 7.7 million deaths and deaths attributable to bacterial antibiotic resistance amounted to 1.3 million, describing a clear demand for novel antibiotics. Antibiotic development had its golden age in 1930–1960. Following failures in the screening of chemical libraries for novel antibiotics at the beginning of this century, the high cost of launching new antibiotics (estimated at US$ 1.4 billion per registered drug) and difficulties in achieving a return of investment for novel antibiotics, pharmaceutical industry has mostly left the field. The current Lilliput review analyses the question whether scientific or economic hurdles prevented the registration of new antibiotics. Scientifically, substantial progress has been achieved over recent years to define the chemical properties needed to overcome the permeation barrier in Gram-negative pathogens; in extending the chemical space of antibiotic candidates by full modular synthesis of suitable molecules; by extending bioprospecting to previously ‘unculturable’ bacteria or unusual bacteria; by attacking bacterial targets on the outer bacterial membrane; and by looking for support from structural biology, genomics, molecular genetics, phylogenetic analyses and deep machine learning approaches. However, these research activities were mostly conducted by academic researchers and biotech companies with limited financial resources. It thus seems that the development of new antibiotics, frequently described as the drying of the pipeline, is less limited by lack of scientific insight than by lack of the mobilization of the monetary resources needed to bring these discoveries to the market despite recent financial push and pull efforts of the public sector.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 7","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11226406/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141544216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"You get what you test for: The killing effect of phage lysins is highly dependent on buffer tonicity and ionic strength","authors":"Roberto Vázquez,&nbsp;Diana Gutiérrez,&nbsp;Zoë Dezutter,&nbsp;Bjorn Criel,&nbsp;Philippe de Groote,&nbsp;Yves Briers","doi":"10.1111/1751-7915.14513","DOIUrl":"10.1111/1751-7915.14513","url":null,"abstract":"<p>The phage lysin field has done nothing but grow in the last decades. As a result, many different research groups around the world are contributing to the field, often with certain methodological differences that pose a challenge to the interpretation and comparison of results. In this work, we present the case study of three <i>Acinetobacter baumannii</i>-targeting phage lysins (wild-type endolysin LysMK34 plus engineered lysins eLysMK34 and 1D10) plus one lysin with broad activity against Gram-positive bacteria (PlySs2) to provide exemplary evidence on the risks of generalization when using one of the most common lysin evaluation assays: the killing assay with resting cells. To that end, we performed killing assays with the aforementioned lysins using hypo-, iso- and hypertonic buffers plus human serum either as the reaction or the dilution medium in a systematic manner. Our findings stress the perils of creating hypotonic conditions or a hypotonic shock during a killing assay, suggesting that hypotonic buffers should be avoided as a test environment or as diluents before plating to avoid overestimation of the killing effect in the assayed conditions. As a conclusion, we suggest that the nature of both the incubation and the dilution buffers should be always clearly identified when reporting killing activity data, and that for experimental consistency the same incubation buffer should be used as a diluent for posterior serial dilution and plating unless explicitly required by the experimental design. In addition, the most appropriate buffer mimicking the final application must be chosen to obtain relevant results.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 7","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.14513","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141496520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Surface display of the COE antigen of porcine epidemic diarrhoea virus on Bacillus subtilis spores","authors":"Yanhong Tian,&nbsp;Zhichao Wang,&nbsp;Ju Sun,&nbsp;Jiayun Gu,&nbsp;Xiaojuan Xu,&nbsp;Xuwang Cai","doi":"10.1111/1751-7915.14518","DOIUrl":"10.1111/1751-7915.14518","url":null,"abstract":"<p>Porcine epidemic diarrhoea virus (PEDV) infects pigs of all ages by invading small intestine, causing acute diarrhoea, vomiting, and dehydration with high morbidity and mortality among newborn piglets. However, current PEDV vaccines are not effective to protect the pigs from field epidemic strains because of poor mucosal immune response and strain variation. Therefore, it is indispensable to develop a novel oral vaccine based on epidemic strains. <i>Bacillus subtilis</i> spores are attractive delivery vehicles for oral vaccination on account of the safety, high stability, and low cost. In this study, a chimeric gene CotC-Linker-COE (<i>CLE</i>), comprising of the <i>B</i>. <i>subtilis</i> spore coat gene <i>cotC</i> fused to the core neutralizing epitope CO-26 K equivalent (<i>COE</i>) of the epidemic strain PEDV-AJ1102 spike protein gene, was constructed. Then recombinant <i>B</i>. <i>subtilis</i> displaying the CLE on the spore surface was developed by homologous recombination. Mice were immunized by oral route with <i>B</i>. <i>subtilis</i> 168-CLE, <i>B</i>. <i>subtilis</i> 168, or phosphate-buffered saline (PBS) as control. Results showed that the IgG antibodies and cytokine (IL-4, IFN-γ) levels in the <i>B</i>. <i>subtilis</i> 168-CLE group were significantly higher than the control groups. This study demonstrates that <i>B</i>. <i>subtilis</i> 168-CLE can generate specific systemic immune and mucosal immune responses and is a potential vaccine candidate against PEDV infection.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 7","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11218686/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rhodopsin-based light-harvesting system for sustainable synthetic biology","authors":"Weiming Tu,&nbsp;Haris Saeed,&nbsp;Wei E. Huang","doi":"10.1111/1751-7915.14521","DOIUrl":"10.1111/1751-7915.14521","url":null,"abstract":"<p>Rhodopsins, a diverse class of light-sensitive proteins found in various life domains, have attracted considerable interest for their potential applications in sustainable synthetic biology. These proteins exhibit remarkable photochemical properties, undergoing conformational changes upon light absorption that drive a variety of biological processes. Exploiting rhodopsin's natural properties could pave the way for creating sustainable and energy-efficient technologies. Rhodopsin-based light-harvesting systems offer innovative solutions to a few key challenges in sustainable engineering, from bioproduction to renewable energy conversion. In this opinion article, we explore the recent advancements and future possibilities of employing rhodopsins for sustainable engineering, underscoring the transformative potential of these biomolecules.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 7","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.14521","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141464636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of breastfeeding in disease prevention","authors":"Andrea C. Masi,&nbsp;Christopher J. Stewart","doi":"10.1111/1751-7915.14520","DOIUrl":"10.1111/1751-7915.14520","url":null,"abstract":"<p>Human milk provides the infant with many bioactive factors, including immunomodulating components, antimicrobials and prebiotics, which modulate the infant microbiome and immune system maturation. As a result, breastfeeding can impact infant health from infancy, through adolescence, and into adulthood. From protecting the infant from infections, to reducing the risk of obesity, type 1 diabetes and childhood leukaemia, many positive health outcomes are observed in infants receiving breastmilk. For the mother, breastfeeding protects against postpartum bleeding and depression, increases weight loss, and long-term lowers the risk of type 2 diabetes, breast and ovarian cancer, and cardiovascular diseases. Beyond infants and mothers, the wider society is also impacted because of avoidable costs relating to morbidity and mortality derived from a lack of human milk exposure. In this review, Medline was used to search for relevant articles to discuss the health benefits of breastfeeding and its societal impact before exploring future recommendations to enhance our understanding of the mechanisms behind breastfeeding's positive effects and promote breastfeeding on a global scale.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 7","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.14520","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141464637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Controlling the expression of heterologous genes in Bdellovibrio bacteriovorus using synthetic biology strategies","authors":"Sergio Salgado,&nbsp;Natalia Hernández-Herreros,&nbsp;M. Auxiliadora Prieto","doi":"10.1111/1751-7915.14517","DOIUrl":"10.1111/1751-7915.14517","url":null,"abstract":"<p><i>Bdellovibrio bacteriovoru</i>s HD100 is an obligate predatory bacterium that preys upon Gram-negative bacteria. It has been proposed to be applied as a “living antibiotic” in several fields such as agriculture or even medicine, since it is able to prey upon bacterial pathogens. Its interesting lifestyle makes this bacterium very attractive as a microbial chassis for co-culture systems including two partners. A limitation to this goal is the scarcity of suitable synthetic biology tools for predator domestication. To fill this gap, we have firstly adapted the hierarchical assembly cloning technique Golden Standard (GS) to make it compatible with <i>B. bacteriovorus</i> HD100. The chromosomal integration of the Tn<i>7</i> transposon's mobile element, in conjunction with the application of the GS technique, has allowed the systematic characterization of a repertoire of constitutive and inducible promoters, facilitating the control of the expression of heterologous genes in this bacterium. PJ_ExD/EliR proved to be an exceptional promoter/regulator system in <i>B. bacteriovorus</i> HD100 when precise regulation is essential, while the synthetic promoter P_BG37 showed a constitutive high expression. These genetic tools represent a step forward in the conversion of <i>B. bacteriovorus</i> into an amenable strain for microbial biotechnology approaches.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 6","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11209729/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141454240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ecological, beneficial, and pathogenic functions of the Type 9 Secretion System","authors":"Sofia T. Rocha,&nbsp;Dhara D. Shah,&nbsp;Abhishek Shrivastava","doi":"10.1111/1751-7915.14516","DOIUrl":"10.1111/1751-7915.14516","url":null,"abstract":"<p>The recently discovered Type 9 Secretion System (T9SS) is present in bacteria of the Fibrobacteres–Bacteroidetes–Chlorobi superphylum, which are key constituents of diverse microbiomes. T9SS is instrumental in the extracellular secretion of over 270,000 proteins, including peptidases, sugar hydrolases, metal ion-binding proteins, and metalloenzymes. These proteins are essential for the interaction of bacteria with their environment. This mini-review explores the extensive array of proteins secreted by the T9SS. It highlights the diverse functions of these proteins, emphasizing their roles in pathogenesis, bacterial interactions, host colonization, and the overall health of the ecosystems inhabited by T9SS-containing bacteria.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 6","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11205867/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141454242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An efficient visual screening of gene knockout mutants in the insect pathogenic fungus Beauveria bassiana","authors":"Ajing Mao,&nbsp;Junyao Wang,&nbsp;Shengan Zhu,&nbsp;Dan Jin,&nbsp;Yanhua Fan","doi":"10.1111/1751-7915.14512","DOIUrl":"10.1111/1751-7915.14512","url":null,"abstract":"<p><i>Beauveria bassiana</i> is an entomopathognic fungus, which is widely employed in the biological control of pests. Gene disruption is a common method for studying the functions of genes involved in fungal development or its interactions with hosts. However, generating gene deletion mutants was a time-consuming work. The transcriptional factor <i>OpS3</i> has been identified as a positive regulator of a red secondary metabolite oosporein in <i>B. bassiana</i>. In this study, we have designed a new screening system by integrating a constitutive <i>OpS3</i> expression cassette outside one of the homologous arms of target gene. Ectopic transformants predominantly exhibit a red colour with oosporein production, while knockout mutants appear as white colonies due to the loss of the <i>OpS3</i> expression cassette caused by recombinant events. This screening strategy was used to obtain the deletion mutants of both <i>tenS</i> and <i>NRPS</i> genes. Correct mutants were obtained by screening fewer than 10 mutants with a positive efficiency ranging from 50% to 75%. This system significantly reduces the workload associated with DNA extraction and PCR amplification, thereby enhancing the efficiency of obtaining correct transformants in <i>B. bassiana</i>.</p>","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"17 6","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11201804/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141454239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}