Ostaizka Aizpurua, Robert R Dunn, Lars H Hansen, M T P Gilbert, Antton Alberdi
{"title":"Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data.","authors":"Ostaizka Aizpurua, Robert R Dunn, Lars H Hansen, M T P Gilbert, Antton Alberdi","doi":"10.1080/07388551.2023.2254933","DOIUrl":"10.1080/07388551.2023.2254933","url":null,"abstract":"<p><p>Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":null,"pages":null},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41113414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Biomaterials with antifungal strategies to fight oral infections.","authors":"Jontana Allkja, Maryam Roudbary, Anelise Maria Vasconcelos Alves, Lucia Černáková, Célia Fortuna Rodrigues","doi":"10.1080/07388551.2023.2236784","DOIUrl":"10.1080/07388551.2023.2236784","url":null,"abstract":"<p><p>Oral fungal infections pose a threat to human health and increase the economic burden of oral diseases by prolonging and complicating treatment. A cost-effective strategy is to try to prevent these infections from happening in the first place. With this purpose, biomaterials with antifungal properties are a crucial element to overcome fungal infections in the oral cavity. In this review, we go through different kinds of biomaterials and coatings that can be used to functionalize them. We also review their potential as a therapeutic approach in addition to prophylaxis, by going through traditional and alternative antifungal compounds, e.g., essential oils, that could be incorporated in them, to enhance their efficacy against fungal pathogens. We aim to highlight the potential of these technologies and propose questions that need to be addressed in prospective research. Finally, we intend to concatenate the key aspects and technologies on the use of biomaterials in oral health, to create an easy to find summary of the current state-of-the-art for researchers in the field.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":null,"pages":null},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10013794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pooja Sharma, Sheetal Kishor Parakh, To Hung Tsui, Ambreen Bano, Surendra Pratap Singh, Vijay Pratap Singh, Su Shiung Lam, Ashok Kumar Nadda, Yen Wah Tong
{"title":"Synergetic anaerobic digestion of food waste for enhanced production of biogas and value-added products: strategies, challenges, and techno-economic analysis.","authors":"Pooja Sharma, Sheetal Kishor Parakh, To Hung Tsui, Ambreen Bano, Surendra Pratap Singh, Vijay Pratap Singh, Su Shiung Lam, Ashok Kumar Nadda, Yen Wah Tong","doi":"10.1080/07388551.2023.2241112","DOIUrl":"10.1080/07388551.2023.2241112","url":null,"abstract":"<p><p>The generation of food waste (FW) is increasing at an alarming rate, contributing to a total of 32% of all the waste produced globally. Anaerobic digestion (AD) is an effective method for dealing with organic wastes of various compositions, like FW. Waste valorization into value-added products has increased due to the conversion of FW into biogas using AD technology. A variety of pathways are adopted by microbes to avoid unfavorable conditions in AD, including competition between sulfate-reducing bacteria and methane (CH<sub>4</sub>)-forming bacteria. Anaerobic bacteria decompose organic matter to produce biogas, a digester gas. The composition depends on the type of raw material and the method by which the digestion process is conducted. Studies have shown that the biogas produced by AD contains 65-75% CH<sub>4</sub> and 35-45% carbon dioxide (CO<sub>2</sub>). <i>Methanothrix soehngenii</i> and <i>Methanosaeta concilii</i> are examples of species that convert acetate to CH<sub>4</sub> and CO<sub>2</sub>. <i>Methanobacterium bryantii</i>, <i>Methanobacterium thermoautotrophicum</i>, and <i>Methanobrevibacter arboriphilus</i> are examples of species that produce CH<sub>4</sub> from hydrogen and CO<sub>2</sub>. <i>Methanobacterium formicicum</i>, <i>Methanobrevibacter smithii</i>, and <i>Methanococcus voltae</i> are examples of species that consume formate, hydrogen, and CO<sub>2</sub> and produce CH<sub>4</sub>. The popularity of AD has increased for the development of biorefinery because it is seen as a more environmentally acceptable alternative in comparison to physico-chemical techniques for resource and energy recovery. The review examines the possibility of using accessible FW to produce important value-added products such as organic acids (acetate/butyrate), biopolymers, and other essential value-added products.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":null,"pages":null},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10112464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Biodegradable acids for pyrite depression and green flotation separation - an overview.","authors":"Ali Asimi Neisiani, Saeed Chehreh Chelgani","doi":"10.1080/07388551.2023.2238885","DOIUrl":"10.1080/07388551.2023.2238885","url":null,"abstract":"<p><p>Exponential increasing demands for base metals have made meaningful processing of their quite low-grade (>1%) resources. Froth flotation is the most important physicochemical pretreatment technique for processing low-grade sulfide ores. In other words, flotation separation can effectively upgrade finely liberated base metal sulfides based on their surface properties. Various sulfide surface characters can be modified by flotation surfactants (collectors, activators, depressants, pH regulators, frothers, etc.). However, these reagents are mostly toxic. Therefore, using biodegradable flotation reagents would be essential for a green transition of ore treatment plants, while flotation circuits deal with massive volumes of water and materials. Pyrite, the most abundant sulfide mineral, is frequently associated with valuable minerals as a troublesome gangue. It causes severe technical and environmental difficulties. Thus, pyrite should be removed early in the beneficiation process to minimize its problematic issues. Recently, conventional inorganic pyrite depressants (such as cyanide, lime, and sulfur-oxy compounds) have been successfully assisted or even replaced with eco-friendly and green reagents (including polysaccharide-based substances and biodegradable acids). Yet, no comprehensive review is specified on the biodegradable acid depression reagents (such as tannic, lactic, humic acids, etc.) for pyrite removal through flotation separation. This study has comprehensively reviewed the previously conducted investigations in this area and provides suggestions for future assessments and developments. This robust review has systematically explored depression performance, various adsorption mechanisms, and aspects of these reagents on pyrite surfaces. Furthermore, factors affecting their efficiency were analyzed, and gaps within each area were highlighted.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":null,"pages":null},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10031955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Microbial enhanced oil recovery (MEOR): recent development and future perspectives.","authors":"Cong-Yu Ke, Rui Sun, Ming-Xia Wei, Xiu-Ni Yuan, Wu-Juan Sun, Si-Chang Wang, Qun-Zheng Zhang, Xun-Li Zhang","doi":"10.1080/07388551.2023.2270578","DOIUrl":"10.1080/07388551.2023.2270578","url":null,"abstract":"<p><p>After conventional oil recovery operations, more than half of the crude oil still remains in a form, which is difficult to extract. Therefore, exploring and developing new enhanced oil recovery (EOR) technologies have always been priority research in oilfield development. Microbial enhanced oil recovery (MEOR) is a promising tertiary oil recovery technology that has received widespread attention from the global oil industry in recent years due to its environmental friendliness, simplicity of operation, and cost-effectiveness. This review presents the: principle, characteristics, classification, recent development, and applications of MEOR technology. Based on hundreds of field trials conducted worldwide, the microbial strains, nutrient systems, and actual effects used in these technologies are summarized, with an emphasis on the achievements made in the development and application of MEOR in China in recent years. These technical classifications involve: microbial huff and puff recovery (MHPR), microbial flooding recovery (MFR), microbial selective plugging recovery (MSPR), and microbial wax removal and control (MWRC). Most of them have achieved good results, with a success rate of approximately 80%. These successful cases have accumulated into rich experiential indications for the popularization and application of MEOR technology, but there are still important yet uncertain factors that hinder the industrialization of this technology. Finally, based on the extensive research and development of MEOR by the authors, especially in both laboratory and industrial large scales, the main challenges and future perspectives of the industrial application for MEOR are presented.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":null,"pages":null},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138498014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Vinoj Chamilka Liyanaarachchi, Gannoru Kankanamalage Sanuji Hasara Nishshanka, P H Viraj Nimarshana, Jo-Shu Chang, Thilini U Ariyadasa, Dillirani Nagarajan
{"title":"Modeling of astaxanthin biosynthesis via machine learning, mathematical and metabolic network modeling.","authors":"Vinoj Chamilka Liyanaarachchi, Gannoru Kankanamalage Sanuji Hasara Nishshanka, P H Viraj Nimarshana, Jo-Shu Chang, Thilini U Ariyadasa, Dillirani Nagarajan","doi":"10.1080/07388551.2023.2237183","DOIUrl":"10.1080/07388551.2023.2237183","url":null,"abstract":"<p><p>Natural astaxanthin is synthesized by diverse organisms including: bacteria, fungi, microalgae, and plants involving complex cellular processes, which depend on numerous interrelated parameters. Nonetheless, existing knowledge regarding astaxanthin biosynthesis and the conditions influencing astaxanthin accumulation is fairly limited. Thus, manipulation of the growth conditions to achieve desired biomass and astaxanthin yields can be a complicated process requiring cost-intensive and time-consuming experiment-based research. As a potential solution, modeling and simulation of biological systems have recently emerged, allowing researchers to predict/estimate astaxanthin production dynamics in selected organisms. Moreover, mathematical modeling techniques would enable further optimization of astaxanthin synthesis in a shorter period of time, ultimately contributing to a notable reduction in production costs. Thus, the present review comprehensively discusses existing mathematical modeling techniques which simulate the bioaccumulation of astaxanthin in diverse organisms. Associated challenges, solutions, and future perspectives are critically analyzed and presented.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":null,"pages":null},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10013792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Adolf Acheampong, Lamei Li, Shereen M Elsherbiny, Yahui Wu, Mohammed Sharif Swallah, Precious Bondzie-Quaye, Qing Huang
{"title":"A crosswalk on the genetic and conventional strategies for enhancing astaxanthin production in <i>Haematococcus pluvialis</i>.","authors":"Adolf Acheampong, Lamei Li, Shereen M Elsherbiny, Yahui Wu, Mohammed Sharif Swallah, Precious Bondzie-Quaye, Qing Huang","doi":"10.1080/07388551.2023.2240009","DOIUrl":"10.1080/07388551.2023.2240009","url":null,"abstract":"<p><p>Astaxanthin is a naturally occurring xanthophyll with powerful: antioxidant, antitumor, and antibacterial properties that are widely employed in food, feed, medicinal and nutraceutical industries. Currently, chemical synthesis dominates the world's astaxanthin market, but the increasing demand for natural products is shifting the market for natural astaxanthin. <i>Haematococcus pluvialis (H. pluvialis)</i> is the factory source of natural astaxanthin when grown in optimal conditions. Currently, various strategies for the production of astaxanthin have been proposed or are being developed in order to meet its market demand. This up-to-date review scrutinized the current approaches or strategies that aim to increase astaxanthin yield from <i>H. pluvialis</i>. We have emphasized the genetic and environmental parameters that increase astaxanthin yield. We also looked at the transcriptomic dynamics caused by environmental factors (phytohormones induction, light, salt, temperature, and nutrient starvation) on astaxanthin synthesizing genes and other metabolic changes. Genetic engineering and culture optimization (environmental factors) are effective approaches to producing more astaxanthin for commercial purposes. Genetic engineering, in particular, is accurate, specific, potent, and safer than conventional random mutagenesis approaches. New technologies, such as CRISPR-Cas9 coupled with omics and emerging computational tools, may be the principal strategies in the future to attain strains that can produce more astaxanthin. This review provides accessible data on the strategies to increase astaxanthin accumulation natively. Also, this review can be a starting point for new scholars interested in <i>H. pluvialis</i> research.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":null,"pages":null},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41113432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lucrezia Caselli, Gisele R Rodrigues, Octavio L Franco, Martin Malmsten
{"title":"Pulmonary delivery systems for antimicrobial peptides.","authors":"Lucrezia Caselli, Gisele R Rodrigues, Octavio L Franco, Martin Malmsten","doi":"10.1080/07388551.2023.2254932","DOIUrl":"10.1080/07388551.2023.2254932","url":null,"abstract":"<p><p>Bacterial infections of the respiratory tract cause millions of deaths annually. Several diseases exist wherein (1) bacterial infection is the main cause of disease (e.g., tuberculosis and bacterial pneumonia), (2) bacterial infection is a consequence of disease and worsens the disease prognosis (e.g., cystic fibrosis), and (3) bacteria-triggered inflammation propagates the disease (e.g., chronic obstructive pulmonary disease). Current approaches to combat infections generally include long and aggressive antibiotic treatments, which challenge patient compliance, thereby making relapses common and contributing to the development of antibiotic resistance. Consequently, the proportion of infections that cannot be treated with conventional antibiotics is rapidly increasing, and novel therapies are urgently needed. In this context, antimicrobial peptides (AMPs) have received considerable attention as they may exhibit potent antimicrobial effects against antibiotic-resistant bacterial strains but with modest toxicity. In addition, some AMPs suppress inflammation and provide other host defense functions (motivating the alternative term host defense peptides (HDPs)). However, the delivery of AMPs is complicated because they are large, positively charged, and amphiphilic. As a result of this, AMP delivery systems have recently attracted attention. For airway infections, the currently investigated delivery approaches range from aerosols and dry powders to various self-assembly and nanoparticle carrier systems, as well as their combinations. In this paper, we discuss recent developments in the field, ranging from mechanistic mode-of-action studies to the application of these systems for combating bacterial infections in the airways.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":null,"pages":null},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41113322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Extension characteristics of TdT and its application in biosensors.","authors":"He Yang, Longjiao Zhu, Xinxin Wang, Yuhan Song, Yulan Dong, Wentao Xu","doi":"10.1080/07388551.2023.2270772","DOIUrl":"10.1080/07388551.2023.2270772","url":null,"abstract":"<p><p>The advantages of rapid amplification of nucleic acid without a template based on terminal deoxyribonucleotidyl transferase (TdT) have been widely used in the field of biosensors. However, the catalytic efficiency of TdT is affected by extension conditions. The sensitivity of TdT- mediated biosensors can be improved only under appropriate conditions. Therefore, in this review, we provide a comprehensive overview of TdT extension characteristics and its applications in biosensors. We focus on the relationship between TdT extension conditions and extension efficiency. Furthermore, the construction strategy of TdT-mediated biosensors according to five different recognition types and their applications in targets are discussed and, finally, several current challenges and prospects in the field are taken into consideration.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":null,"pages":null},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50161024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Huanyu Zhang, Lanping Guo, Yaowu Su, Rubing Wang, Wenqi Yang, Wenrong Mu, Liangshuang Xuan, Luqi Huang, Juan Wang, Wenyuan Gao
{"title":"Hosts engineering and <i>in vitro</i> enzymatic synthesis for the discovery of novel natural products and their derivatives.","authors":"Huanyu Zhang, Lanping Guo, Yaowu Su, Rubing Wang, Wenqi Yang, Wenrong Mu, Liangshuang Xuan, Luqi Huang, Juan Wang, Wenyuan Gao","doi":"10.1080/07388551.2023.2236787","DOIUrl":"10.1080/07388551.2023.2236787","url":null,"abstract":"<p><p>Novel natural products (NPs) and their derivatives are important sources for drug discovery, which have been broadly applied in the fields of agriculture, livestock, and medicine, making the synthesis of NPs and their derivatives necessarily important. In recent years, biosynthesis technology has received increasing attention due to its high efficiency in the synthesis of high value-added novel products and its advantages of green, environmental protection, and controllability. In this review, the technological advances of biosynthesis strategies in the discovery of novel NPs and their derivatives are outlined, with an emphasis on two areas of host engineering and <i>in vitro</i> enzymatic synthesis. In terms of hosts engineering, multiple microorganisms, including <i>Streptomyces</i>, <i>Aspergillus</i>, and <i>Penicillium</i>, have been used as the biosynthetic gene clusters (BGCs) provider and host strain for the expression of BGCs to discover new compounds over the past years. In addition, the use of <i>in vitro</i> enzymatic synthesis strategy to generate novel compounds such as triterpenoid saponins and flavonoids is also hereby described.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":null,"pages":null},"PeriodicalIF":8.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9990382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}