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Machine learning in wastewater: opportunities and challenges — “not everything is a nail!”
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2025-02-24 DOI: 10.1016/j.copbio.2025.103271
Peter A Vanrolleghem , Mostafa Khalil , Marcello Serrao , Jeff Sparks , Jean-David Therrien
{"title":"Machine learning in wastewater: opportunities and challenges — “not everything is a nail!”","authors":"Peter A Vanrolleghem ,&nbsp;Mostafa Khalil ,&nbsp;Marcello Serrao ,&nbsp;Jeff Sparks ,&nbsp;Jean-David Therrien","doi":"10.1016/j.copbio.2025.103271","DOIUrl":"10.1016/j.copbio.2025.103271","url":null,"abstract":"<div><div>This paper highlights the potential of machine learning (ML) for wastewater applications, with a focus on key applications and considerations. It underscores the need for simplicity in ML models to ensure their interpretability and trustworthiness, cautioning against the use of overly complex ‘black box’ models unless absolutely necessary, especially with limited data. Not all modelling problems should be considered nails for which the ML hammer is the best-available tool. We emphasise the critical role of thorough data collection, including metadata, given its scarcity in some areas. Future research is encouraged to develop benchmark hybrid models to bridge the educational gap for environmental engineers and to establish best practices for managing data and model metadata, thereby improving ML’s accessibility and utility in wastewater applications.</div></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"93 ","pages":"Article 103271"},"PeriodicalIF":7.1,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143479946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bacterial microcompartment architectures as biomaterials for conversion of gaseous substrates
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2025-02-19 DOI: 10.1016/j.copbio.2025.103268
Samuel N Snyder , Yali Wang , Matthew E Dwyer , Daipayan Sarkar , Cheryl A Kerfeld
{"title":"Bacterial microcompartment architectures as biomaterials for conversion of gaseous substrates","authors":"Samuel N Snyder ,&nbsp;Yali Wang ,&nbsp;Matthew E Dwyer ,&nbsp;Daipayan Sarkar ,&nbsp;Cheryl A Kerfeld","doi":"10.1016/j.copbio.2025.103268","DOIUrl":"10.1016/j.copbio.2025.103268","url":null,"abstract":"<div><div>Bacterial microcompartments (BMCs) are protein shells encapsulating multiple enzymes of a metabolic pathway. Interpretations of early experiments on carboxysomes led to the narrative that transport of small gases (CO<sub>2</sub>, O<sub>2</sub>) across the shell membrane is restricted. Since then, this notion has been largely contradicted by studies of engineered shells, although these shell constructs lack important proteins present in the native BMCs, altering the synthetic shells’ topology, surface and mechanical properties. We discuss here an updated model of gas permeability that informs the design of engineered shells for catalysis on gas substrates and outline how nonshell suprastructures of BMC shell proteins could be used in formulating sustainable biomaterials for hydrogen generation via methane pyrolysis and for other greenhouse gas mitigations.</div></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"92 ","pages":"Article 103268"},"PeriodicalIF":7.1,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143445935","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}
引用次数: 0
Advances in engineering substrate scope of Pseudomonas cell factories
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2025-02-19 DOI: 10.1016/j.copbio.2025.103270
Miguel Silva , Stefano Donati , Pavel Dvořák
{"title":"Advances in engineering substrate scope of Pseudomonas cell factories","authors":"Miguel Silva ,&nbsp;Stefano Donati ,&nbsp;Pavel Dvořák","doi":"10.1016/j.copbio.2025.103270","DOIUrl":"10.1016/j.copbio.2025.103270","url":null,"abstract":"<div><div>Most current industrial bioprocesses use well-established model microorganisms and simple sugar substrates from edible starch or molasses. To broaden and sustain bioprocesses, we need to explore new robust microbial hosts with desirable traits and ideally exploit diverse waste-derived substrates. <em>Pseudomonas</em> species are prime candidates for new generation of industrial biotechnology due to their resilient physiology and adaptable metabolism. However, natural isolates are not always suitable for demanding biotechnological applications. Despite pseudomonads’ typically broad substrate range, their catabolism can be further enhanced through metabolic engineering, synthetic biology, and/or laboratory evolution to efficiently degrade, utilize, and valorize alternative waste substrates derived from lignocellulosic residues, synthetic plastics, C1 compounds, or their mixtures.</div></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"92 ","pages":"Article 103270"},"PeriodicalIF":7.1,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143445938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The tier system: a host development framework for bioengineering
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2025-02-10 DOI: 10.1016/j.copbio.2025.103260
Chris M Yeager , Nathan J Hillson , Katherine L Wozniak , Vivek K Mutalik , Christopher W Johnson , Kyle Pomraning , Philip Laible , Taraka Dale , Adam M Guss
{"title":"The tier system: a host development framework for bioengineering","authors":"Chris M Yeager ,&nbsp;Nathan J Hillson ,&nbsp;Katherine L Wozniak ,&nbsp;Vivek K Mutalik ,&nbsp;Christopher W Johnson ,&nbsp;Kyle Pomraning ,&nbsp;Philip Laible ,&nbsp;Taraka Dale ,&nbsp;Adam M Guss","doi":"10.1016/j.copbio.2025.103260","DOIUrl":"10.1016/j.copbio.2025.103260","url":null,"abstract":"<div><div>Development of microorganisms into mature bioproduction host strains has typically been a slow and circuitous process, wherein multiple groups apply disparate approaches with minimal coordination over decades. To help organize and streamline host development efforts, we introduce the <em>Tier System for Host Development</em>, a conceptual model and guide for developing microbial hosts that can ultimately lead to a systematic, standardized, less expensive, and more rapid workflow. The <em>Tier System</em> is made up of three Tiers, each consisting of a unique set of strain development Targets, including experimental tools, strain properties, experimental information, and process models. By introducing the <em>Tier System</em>, we hope to improve host development activities through standardization and systematization pertaining to nontraditional chassis organisms.</div></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"92 ","pages":"Article 103260"},"PeriodicalIF":7.1,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143377730","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}
引用次数: 0
Wastewater biorefineries: exploring biological phosphorus removal and integrated recovery solutions
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2025-02-10 DOI: 10.1016/j.copbio.2025.103266
Samarpita Roy , Jette F Petersen , Sarah Müller , Zivile Kondrotaite , Mark van Loosdrecht , Thomas Wintgens , Per H Nielsen
{"title":"Wastewater biorefineries: exploring biological phosphorus removal and integrated recovery solutions","authors":"Samarpita Roy ,&nbsp;Jette F Petersen ,&nbsp;Sarah Müller ,&nbsp;Zivile Kondrotaite ,&nbsp;Mark van Loosdrecht ,&nbsp;Thomas Wintgens ,&nbsp;Per H Nielsen","doi":"10.1016/j.copbio.2025.103266","DOIUrl":"10.1016/j.copbio.2025.103266","url":null,"abstract":"<div><div>The emphasis on phosphorus removal and recovery from wastewater treatment plants has intensified in recent years due to the urgent need to reduce dependency on nonrenewable phosphorus reserves. Enhanced biological phosphorus removal (EBPR), driven by a diverse community of polyphosphate-accumulating organisms with distinct metabolic capabilities, offers several advantages over chemical precipitation methods. These benefits include reduced chemical use, lower sludge volumes, decreased reliance on costly chemical precipitants, and improved phosphorus recovery quality. Recent advancements in recovery technologies now enable efficient phosphorus extraction from digester supernatant, dewatered digested sewage sludge, and sewage sludge ash, each yielding different recovery efficiencies. Despite these advances, a comprehensive assessment of the phosphorus recovery potential from these target streams in conjunction with EBPR remains crucial and has yet to be fully explored.</div></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"92 ","pages":"Article 103266"},"PeriodicalIF":7.1,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143377729","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}
引用次数: 0
Harnessing photosynthesis for materials, devices, and environmental technologies
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2025-02-06 DOI: 10.1016/j.copbio.2025.103265
Fan Jiang , Friedrich H Kleiner , Marie-Eve Aubin-Tam
{"title":"Harnessing photosynthesis for materials, devices, and environmental technologies","authors":"Fan Jiang ,&nbsp;Friedrich H Kleiner ,&nbsp;Marie-Eve Aubin-Tam","doi":"10.1016/j.copbio.2025.103265","DOIUrl":"10.1016/j.copbio.2025.103265","url":null,"abstract":"<div><div>Photosynthetic organisms convert solar light into chemical energy through the process of photosynthesis. The employment of photosynthetic organisms in novel materials and devices provides them with a solar-powered and sustainable functionality. In general, photosynthesis utilizes light, water, and CO<sub>2</sub> to generate various organic compounds while releasing secondary valuable products such as O<sub>2</sub>, extracellular electrons, carbohydrates, or H<sub>2</sub>. The light-dependent inputs and outputs are harnessed for environmental purification, biomedical applications, and production of biofuel, electricity, nanomaterials, or bioplastics. In this review, we summarize photosynthesis-assisted materials and engineering applications based on the products and substrates of photosynthetic processes, and we highlight key challenges that remain to be addressed.</div></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"92 ","pages":""},"PeriodicalIF":7.1,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143183672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Engineered microbial living matter for diagnostics, prevention, and therapy
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2025-02-06 DOI: 10.1016/j.copbio.2025.103269
Ali Khazem , Rosanne Schmachtenberg , Anke Weiand , Shrikrishnan Sankaran , Wilfried Weber
{"title":"Engineered microbial living matter for diagnostics, prevention, and therapy","authors":"Ali Khazem ,&nbsp;Rosanne Schmachtenberg ,&nbsp;Anke Weiand ,&nbsp;Shrikrishnan Sankaran ,&nbsp;Wilfried Weber","doi":"10.1016/j.copbio.2025.103269","DOIUrl":"10.1016/j.copbio.2025.103269","url":null,"abstract":"<div><div>Living therapeutic and diagnostic materials based on engineered microorganisms are emerging as a novel approach with the perspective of providing patient-tailored, sustainable, and cost-effective healthcare solutions. In this review, we focus on recent advances in using genetically or chemically engineered microorganisms as living diagnostics, therapeutics, and as a means of prevention for various diseases. We also highlight the applications of living therapeutics for acute and chronic diseases, and the role of micro/macro-encapsulation of the engineered microorganisms. We further showcase the current success of engineered living therapeutics in clinical trials and discuss challenges and future trends in the field.</div></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"92 ","pages":"Article 103269"},"PeriodicalIF":7.1,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143208025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Matchmaking at the cell surface using bispecifics to put cells on their best behavior
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2025-02-05 DOI: 10.1016/j.copbio.2025.103267
Claudia L Driscoll , Mark R Howarth
{"title":"Matchmaking at the cell surface using bispecifics to put cells on their best behavior","authors":"Claudia L Driscoll ,&nbsp;Mark R Howarth","doi":"10.1016/j.copbio.2025.103267","DOIUrl":"10.1016/j.copbio.2025.103267","url":null,"abstract":"<div><div>Intermolecular relationships at the cell surface dictate the behavior and regulatory network of cells. Such interactions often require precise spatial control for optimal response. By binding simultaneously to two different target sites, bispecific binders can bridge molecules of interest. Despite decades of bispecific development, only recently have bispecifics been engineered with programmable, tuneable geometries to replicate natural interaction geometries or achieve new responses from unnatural arrangements. This review highlights emerging methods of protein engineering and modular bioconjugation to control pairing and orientation of binders in bispecific scaffolds. We also describe novel biophysical and phenotypic assays, which reveal how bispecific geometries change cell fate. These approaches are informing design of next-generation precision therapeutics, as well as uncovering fundamental features of signal integration.</div></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"92 ","pages":"Article 103267"},"PeriodicalIF":7.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143183673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Engineering plant biosensors: recent advances in design and applications 工程植物生物传感器：设计与应用的最新进展。
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2025-02-01 DOI: 10.1016/j.copbio.2024.103240
Oscar Castaneda-Méndez , Shammi Akter , Jesús Beltrán
{"title":"Engineering plant biosensors: recent advances in design and applications","authors":"Oscar Castaneda-Méndez ,&nbsp;Shammi Akter ,&nbsp;Jesús Beltrán","doi":"10.1016/j.copbio.2024.103240","DOIUrl":"10.1016/j.copbio.2024.103240","url":null,"abstract":"<div><div>Plants have evolved sophisticated molecular switches to perceive and respond to both endogenous and exogenous signals, enabling changes in form and function in response to environmental and developmental cues. As autotrophic, multicellular organisms, plants represent promising platforms for designing and engineering sense-and-report modules. Advances in protein engineering and functional screening have facilitated the reprogramming of native switches into biosensors capable of detecting novel small molecules. These sensors can be incorporated into plants to activate signaling cascades or to control new biological functions. This review highlights recent advancements in plant biosensor engineering for small molecules, discusses emerging applications, and provides insights into biotechnological uses. Additionally, it explores the challenges and opportunities of using plant-based biosensors in agriculture and environmental contexts.</div></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"91 ","pages":"Article 103240"},"PeriodicalIF":7.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142853175","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}
引用次数: 0
Phage biocontrol in water treatment and reuse systems: a nascent field with significant innovation opportunities 水处理和回用系统中的噬菌体生物防治：一个具有重大创新机会的新兴领域。
IF 7.1 2区 工程技术
Current opinion in biotechnology Pub Date : 2025-02-01 DOI: 10.1016/j.copbio.2024.103242
Pei-Ying Hong , Jacques Mathieu , Hong Cheng , Shaman Narayanasamy , Darwin A Castillo , Ramesh Goel , Pedro JJ Alvarez
{"title":"Phage biocontrol in water treatment and reuse systems: a nascent field with significant innovation opportunities","authors":"Pei-Ying Hong ,&nbsp;Jacques Mathieu ,&nbsp;Hong Cheng ,&nbsp;Shaman Narayanasamy ,&nbsp;Darwin A Castillo ,&nbsp;Ramesh Goel ,&nbsp;Pedro JJ Alvarez","doi":"10.1016/j.copbio.2024.103242","DOIUrl":"10.1016/j.copbio.2024.103242","url":null,"abstract":"<div><div>While the use of phages in the food and biomedical sectors occurs commercially, their application in the water sector is less common and is typically demonstrated at a lower technological readiness level. This is so despite the potential that phages have to enhance the control of problematic bacteria (including pathogens) and protect infrastructure within the water sector. Fulfilling the great potential of this nascent field requires more research and development. Here, we highlight innovation opportunities and discern critical knowledge gaps and research needs to facilitate the use of phages as precise biocontrol agents in the water sector. First, while the advent of sequencing technologies made it easier to identify bacterial communities and understand their functional roles, identifying and cultivating the appropriate phages that can be effective against the bacterial target requires more research. The large volumes of water to be spiked with phages also require optimizing the phage biocontrol strategy, minimizing the associated costs and enhancing scaling up. In addition, bacterial hosts may gain phage resistance after long-term exposure, which is common in most water-engineered systems, and strategies to minimize or delay resistance must be considered. In this opinion, we provide an overview of pertinent literature and bioinformatic tools that help identify appropriate bacterial hosts and phages for water systems applications. We then discuss strategies that can aid in prolonging the efficacy and enhancing the feasibility of phage biocontrol approaches.</div></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"91 ","pages":"Article 103242"},"PeriodicalIF":7.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142876520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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