Advances in applied microbiology最新文献

{"title":"Degradation strategies and associated regulatory mechanisms/features for aromatic compound metabolism in bacteria.","authors":"Prashant S Phale,&nbsp;Harshit Malhotra,&nbsp;Bhavik A Shah","doi":"10.1016/bs.aambs.2020.02.002","DOIUrl":"https://doi.org/10.1016/bs.aambs.2020.02.002","url":null,"abstract":"<p><p>As a result of anthropogenic activity, large number of recalcitrant aromatic compounds have been released into the environment. Consequently, microbial communities have adapted and evolved to utilize these compounds as sole carbon source, under both aerobic and anaerobic conditions. The constitutive expression of enzymes necessary for metabolism imposes a heavy energy load on the microbe which is overcome by arrangement of degradative genes as operons which are induced by specific inducers. The segmentation of pathways into upper, middle and/or lower operons has allowed microbes to funnel multiple compounds into common key aromatic intermediates which are further metabolized through central carbon pathway. Various proteins belonging to diverse families have evolved to regulate the transcription of individual operons participating in aromatic catabolism. These proteins, complemented with global regulatory mechanisms, carry out the regulation of aromatic compound metabolic pathways in a concerted manner. Additionally, characteristics like chemotaxis, preferential utilization, pathway compartmentalization and biosurfactant production confer an advantage to the microbe, thus making bioremediation of the aromatic pollutants more efficient and effective.</p>","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"112 ","pages":"1-65"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.aambs.2020.02.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38246549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antimicrobial resistance genes in bacteria from animal-based foods.","authors":"Isadora de Alcântara Rodrigues,&nbsp;Rafaela Gomes Ferrari,&nbsp;Pedro Henrique Nunes Panzenhagen,&nbsp;Sergio Borges Mano,&nbsp;Carlos Adam Conte-Junior","doi":"10.1016/bs.aambs.2020.03.001","DOIUrl":"https://doi.org/10.1016/bs.aambs.2020.03.001","url":null,"abstract":"<p><p>Antimicrobial resistance is a worldwide public health threat. Farm animals are important sources of bacteria containing antimicrobial resistance genes (ARGs). Although the use of antimicrobials in aquaculture and livestock has been reduced in several countries, these compounds are still routinely applied in animal production, and contribute to ARGs emergence and spread among bacteria. ARGs are transmitted to humans mainly through the consumption of products of animal origin (PAO). Bacteria can present intrinsic resistance, and once antimicrobials are administered, this resistance may be selected and multiply. The exchange of genetic material is another mechanism used by bacteria to acquire resistance. Some of the main ARGs found in bacteria present in PAO are the bla, mcr-1, cfr and tet genes, which are directly associated to antibiotic resistance in the human clinic.</p>","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"112 ","pages":"143-183"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.aambs.2020.03.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38246551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clostridium thermocellum: A microbial platform for high-value chemical production from lignocellulose.","authors":"R Mazzoli,&nbsp;D G Olson","doi":"10.1016/bs.aambs.2020.07.004","DOIUrl":"https://doi.org/10.1016/bs.aambs.2020.07.004","url":null,"abstract":"<p><p>Second generation biorefining, namely fermentation processes based on lignocellulosic feedstocks, has attracted tremendous interest (owing to the large availability and low cost of this biomass) as a strategy to produce biofuels and commodity chemicals that is an alternative to oil refining. However, the innate recalcitrance of lignocellulose has slowed progress toward economically viable processes. Consolidated bioprocessing (CBP), i.e., single-step fermentation of lignocellulose may dramatically reduce the current costs of 2nd generation biorefining. Metabolic engineering has been used as a tool to develop improved microbial strains supporting CBP. Clostridium thermocellum is among the most efficient cellulose degraders isolated so far and one of the most promising host organisms for application of CBP. The development of efficient and reliable genetic tools has allowed significant progress in metabolic engineering of this strain aimed at expanding the panel of growth substrates and improving the production of a number of commodity chemicals of industrial interest such as ethanol, butanol, isobutanol, isobutyl acetate and lactic acid. The present review aims to summarize recent developments in metabolic engineering of this organism which currently represents a reference model for the development of biocatalysts for 2nd generation biorefining.</p>","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"113 ","pages":"111-161"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.aambs.2020.07.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38395050","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Detection of the 'Big Five' mold killers of humans: Aspergillus, Fusarium, Lomentospora, Scedosporium and Mucormycetes.","authors":"Christopher R Thornton","doi":"10.1016/bs.aambs.2019.10.003","DOIUrl":"https://doi.org/10.1016/bs.aambs.2019.10.003","url":null,"abstract":"<p><p>Fungi are an important but frequently overlooked cause of morbidity and mortality in humans. Life-threatening fungal infections mainly occur in immunocompromised patients, and are typically caused by environmental opportunists that take advantage of a weakened immune system. The filamentous fungus Aspergillus fumigatus is the most important and well-documented mold pathogen of humans, causing a number of complex respiratory diseases, including invasive pulmonary aspergillosis, an often fatal disease in patients with acute leukemia or in immunosuppressed bone marrow or solid organ transplant recipients. However, non-Aspergillus molds are increasingly reported as agents of disseminated diseases, with Fusarium, Scedosporium, Lomentospora and mucormycete species now firmly established as pathogens of immunosuppressed and immunocompetent individuals. Despite well-documented risk factors for invasive fungal diseases, and increased awareness of the risk factors for life-threatening infections, the number of deaths attributable to molds is likely to be severely underestimated driven, to a large extent, by the lack of readily accessible, cheap, and accurate tests that allow detection and differentiation of infecting species. Early diagnosis is critical to patient survival but, unlike Aspergillus diseases, where a number of CE-marked or FDA-approved biomarker tests are now available for clinical diagnosis, similar tests for fusariosis, scedosporiosis and mucormycosis remain experimental, with detection reliant on insensitive and slow culture of pathogens from invasive bronchoalveolar lavage fluid, tissue biopsy, or from blood. This review examines the ecology, epidemiology, and contemporary methods of detection of these mold pathogens, and the obstacles to diagnostic test development and translation of novel biomarkers to the clinical setting.</p>","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"110 ","pages":"1-61"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.aambs.2019.10.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37917894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Engineering transport systems for microbial production.","authors":"Moses Onyeabor,&nbsp;Rodrigo Martinez,&nbsp;Gavin Kurgan,&nbsp;Xuan Wang","doi":"10.1016/bs.aambs.2020.01.002","DOIUrl":"https://doi.org/10.1016/bs.aambs.2020.01.002","url":null,"abstract":"<p><p>The rapid development in the field of metabolic engineering has enabled complex modifications of metabolic pathways to generate a diverse product portfolio. Manipulating substrate uptake and product export is an important research area in metabolic engineering. Optimization of transport systems has the potential to enhance microbial production of renewable fuels and chemicals. This chapter comprehensively reviews the transport systems critical for microbial production as well as current genetic engineering strategies to improve transport functions and thus production metrics. In addition, this chapter highlights recent advancements in engineering microbial efflux systems to enhance cellular tolerance to industrially relevant chemical stress. Lastly, future directions to address current technological gaps are discussed.</p>","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"111 ","pages":"33-87"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.aambs.2020.01.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37969661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Contributors","authors":"","doi":"10.1016/s0065-2164(20)30035-6","DOIUrl":"https://doi.org/10.1016/s0065-2164(20)30035-6","url":null,"abstract":"","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/s0065-2164(20)30035-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"55849369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gaps in the assortment of rapid assays for microorganisms of interest to the dairy industry.","authors":"John O'Grady, Ultan Cronin, Joseph Tierney, Anna V Piterina, Elaine O'Meara, Martin G Wilkinson","doi":"10.1016/bs.aambs.2020.07.001","DOIUrl":"10.1016/bs.aambs.2020.07.001","url":null,"abstract":"<p><p>This review presents the results of a study into the offering of rapid microbial detection assays to the Irish dairy industry. At the outset, a consultation process was undertaken whereby key stakeholders were asked to compile a list of the key microorganisms of interest to the sector. The resultant list comprises 19 organisms/groups of organisms divided into five categories: single pathogenic species (Cronobacter sakazakii, Escherichia coli and Listeria monocytogenes); genera containing pathogenic species (Bacillus, Clostridium, Listeria, Salmonella; Staphylococcus); broad taxonomic groupings (Coliforms, Enterobacteriaceae, fecal Streptococci, sulfite reducing bacteria/sulfite reducing Clostridia [SRBs/SRCs], yeasts and molds); organisms displaying certain growth preferences or resistance as regards temperature (endospores, psychrotrophs, thermodurics, thermophiles); indicators of quality (total plate count, Pseudomonas spp.). A survey of the rapid assays commercially available for the 19 organisms/groups of organisms was conducted. A wide disparity between the number of rapid tests available was found. Four categories were used to summarize the availability of rapid assays per organism/group of organisms: high coverage (>15 assays available); medium coverage (5-15 assays available); low coverage (<5 assays available); no coverage (0 assays available). Generally, species or genera containing pathogens, whose presence is regulated-for, tend to have a good selection of commercially available rapid assays for their detection, whereas groups composed of heterogenous or even undefined genera of mainly spoilage organisms tend to be \"low coverage\" or \"no coverage.\" Organisms/groups of organisms with \"low coverage\" by rapid assays include: Clostridium spp.; fecal Streptococci; and Pseudomonas spp. Those with \"no coverage\" by rapid assays include: endospores; psychrotrophs; SRB/SRCs; thermodurics; and thermophiles. An important question is: why have manufacturers of rapid microbiological assays failed to respond to the necessity for rapid methods for these organisms/groups of organisms? The review offers explanations, ranging from the technical difficulty involved in detecting as broad a group as the thermodurics, which covers the spores of multiple sporeforming genera as well at least six genera of mesophilic nonsporeformers, to the taxonomically controversial issue as to what constitutes a fecal Streptococcus or SRBs/SRCs. We review two problematic areas for assay developers: validation/certification and the nature of dairy food matrices. Development and implementation of rapid alternative test methods for the dairy industry is influenced by regulations relating to both the microbiological quality standards and the criteria alternative methods must meet to qualify as acceptable test methods. However, the gap between the certification of developer's test systems as valid alternative methods in only a handful of representative matrices, and the req","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"113 ","pages":"1-56"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7426214/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38395051","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":"Microalgae for biofuel production.","authors":"D James Gilmour","doi":"10.1016/bs.aambs.2019.10.001","DOIUrl":"https://doi.org/10.1016/bs.aambs.2019.10.001","url":null,"abstract":"<p>Microalgae have been used commercially since the 1950s and 1960s, particularly in the Far East for human health foods and in the United States for wastewater treatment. Initial attempts to produce bulk chemicals such as biofuels from microalgae were not successful, despite commercially favorable conditions during the 1970s oil crisis. However, research initiatives at this time, many using extremophilic microalgae and cyanobacteria (e.g., <em>Dunaliella</em> and <em>Spirulina</em>), did solve many problems and clearly identified biomass productivity and harvesting as the two main constraints stopping microalgae producing bulk chemicals, such as biofuels, on a large scale. In response to the growing unease around global warming, induced by anthropogenic CO₂ emissions, microalgae were again suggested as a carbon neutral process to produce biofuels. This recent phase of microalgae biofuels research can be thought to have started around 2007, when a very highly cited review by Chisti was published. Since 2007, a large body of scientific publications have appeared on all aspects of microalgae biotechnology, but with a clear emphasis on neutral lipid (triacylglycerol) synthesis and the use of neutral lipids as precursors for biodiesel production. In this review, the key research on microalgal biotechnology that took place prior to 2007 will be summarized and then the research trends post 2007 will be examined emphasizing the research into producing biodiesel from microalgae.</p>","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"4 7","pages":"1-30"},"PeriodicalIF":0.0,"publicationDate":"2019-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138508742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advances in yeast alcoholic fermentations for the production of bioethanol, beer and wine.","authors":"Kevy Pontes Eliodório,Gabriel Caetano de Gois E Cunha,Caroline Müller,Ana Carolina Lucaroni,Reinaldo Giudici,Graeme Maxwell Walker,Sérgio Luiz Alves,Thiago Olitta Basso","doi":"10.1016/bs.aambs.2019.10.002","DOIUrl":"https://doi.org/10.1016/bs.aambs.2019.10.002","url":null,"abstract":"<p>Yeasts have a long-standing relationship with humankind that has widened in recent years to encompass production of diverse foods, beverages, fuels and medicines. Here, key advances in the field of yeast fermentation applied to alcohol production, which represents the predominant product of industrial biotechnology, will be presented. More specifically, we have selected industries focused in producing bioethanol, beer and wine. In these bioprocesses, yeasts from the genus <em>Saccharomyces</em> are still the main players, with <em>Saccharomyces cerevisiae</em> recognized as the preeminent industrial ethanologen. However, the growing demand for new products has opened the door to diverse yeasts, including non-<em>Saccharomyces</em> strains. Furthermore, the development of synthetic media that successfully simulate industrial fermentation medium will be discussed along with a general overview of yeast fermentation modeling.</p>","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"8 12","pages":"61-119"},"PeriodicalIF":0.0,"publicationDate":"2019-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138508754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Research progress on the basic helix-loop-helix transcription factors of Aspergillus species.","authors":"Bao-Teng Wang,Xing-Ye Yu,Yun-Jia Zhu,Miao Zhuang,Zhi-Min Zhang,Long Jin,Feng-Jie Jin","doi":"10.1016/bs.aambs.2019.09.001","DOIUrl":"https://doi.org/10.1016/bs.aambs.2019.09.001","url":null,"abstract":"<p>Basic helix-loop-helix (bHLH) proteins belong to a superfamily of transcription factors, and they are widely distributed in eukaryotic organisms. Members of the bHLH protein family can form homodimers or heterodimers with themselves or other family members, and they often play bifunctional roles as activators and repressors to uniquely regulate the transcription of downstream target genes. The bHLH transcription factors are usually involved in developmental processes, including cellular proliferation and differentiation. Therefore, these transcription factors often play crucial roles in regulating growth, development, and differentiation in eukaryotes. <em>Aspergillus</em> species fungi are widely distributed in the environment, and they play important roles not only in the decomposition of organic matter as an important environmental microorganism but also in the fermentation and the food processing industry. Furthermore, some pathogenic fungi, such as <em>Aspergillus flavus</em> and <em>Aspergillus fumigatus</em>, affect the environment and human health in important ways. Recent research has shown that some <em>Aspergillus</em> bHLH proteins are significantly involved in the regulation of asexual and sexual reproduction, secondary metabolite production, carbohydrate metabolism, conidial and sclerotial production, among other processes. Here, we review the regulatory mechanisms and biological functions of the bHLH transcription factors of the <em>Aspergillus</em> genus to provide a theoretical reference for further study on the growth and development of <em>Aspergillus</em> and the functions of bHLHs.</p>","PeriodicalId":7298,"journal":{"name":"Advances in applied microbiology","volume":"8 8","pages":"31-59"},"PeriodicalIF":0.0,"publicationDate":"2019-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138508755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}