Text-Mining to Identify Gene Sets Involved in Biocorrosion by Sulfate-Reducing Bacteria: A Semi-Automated Workflow DOI Creative Commons

Payal Thakur,

Mathew O. Alaba,

Shailabh Rauniyar

et al.

Microorganisms, Journal Year: 2023, Volume and Issue: 11(1), P. 119 - 119

Published: Jan. 3, 2023

A significant amount of literature is available on biocorrosion, which makes manual extraction crucial information such as genes and proteins a laborious task. Despite the fast growth biology related corrosion studies, there limited number gene collections relating to process (biocorrosion). Text mining offers potential solution by automatically extracting essential from unstructured text. We present text workflow that extracts biocorrosion associated genes/proteins in sulfate-reducing bacteria (SRB) databases (e.g., PubMed PMC). This semi-automatic built with Named Entity Recognition (NER) method Convolutional Neural Network (CNN) model. With PMCID inputs, identified 227 belonging several Desulfovibrio species. To validate their functions, Gene Ontology (GO) enrichment biological network analysis was performed using UniprotKB STRING-DB, respectively. The GO showed metal ion binding, sulfur electron transport were among principal molecular functions. Furthermore, generated three interlinked clusters containing involved cellular respiration, transfer, suggests involvement extracted set biocorrosion. Finally, dataset validated through curation, yielding similar our workflow; these, hysB hydA, sat dsrB binding metabolism genes, mapped pangenome 63 SRB genomes yielded distribution these across based amino acid sequence similarity further categorized core accessory families. SRB’s role involves transfer electrons surface via hydrogen medium sulfate reduction pathway. Therefore, encoding hydrogenases cytochromes might be participating removing metals transfer. Moreover, production corrosive sulfide indirectly contributes localized pitting metals. After corroboration results mechanisms, we suggest framework could utilized for significantly reduce curation time.

Language: Английский

Microbially mediated metal corrosion DOI
Dake Xu, Tingyue Gu, Derek R. Lovley

et al.

Nature Reviews Microbiology, Journal Year: 2023, Volume and Issue: 21(11), P. 705 - 718

Published: June 21, 2023

Language: Английский

Citations

213
Biofilms: Formation, drug resistance and alternatives to conventional approaches DOI Creative Commons

Ruba Mirghani,

Tania Saba,

Hebba Khaliq

et al.

AIMS Microbiology, Journal Year: 2022, Volume and Issue: 8(3), P. 239 - 277

Published: Jan. 1, 2022

<abstract> <p>Biofilms are aggregates of bacteria, in most cases, which resistant usually to broad-spectrum antibiotics their typical concentrations or even higher doses. A trend increasing multi-drug resistance biofilms, responsible for emerging life-threatening nosocomial infections, is becoming a serious problem. Biofilms, however, at various sensitivity levels environmental factors and versatile infectivity depending on virulence factors. This review presents the fundamental information about biofilms: formation, antibiotic resistance, impacts public health alternatives conventional approaches. Novel developments micro-biosystems that help reveal new treatment tools by sensing characterization biofilms will also be discussed. Understanding structure, physiology properties better helps eliminate them usage appropriate control novel therapy approaches, such as anti-biofilm molecules, effective gene editing, drug-delivery systems probiotics.</p> </abstract>

Language: Английский

Citations

146
Microbiologically influenced corrosion—more than just microorganisms DOI Creative Commons
Judit Knisz, Richard B. Eckert, Lisa M. Gieg

et al.

FEMS Microbiology Reviews, Journal Year: 2023, Volume and Issue: 47(5)

Published: July 11, 2023

Abstract Microbiologically influenced corrosion (MIC) is a phenomenon of increasing concern that affects various materials and sectors society. MIC describes the effects, often negative, material can experience due to presence microorganisms. Unfortunately, although several research groups industrial actors worldwide have already addressed MIC, discussions are fragmented, while information sharing willingness reach out other disciplines limited. A truly interdisciplinary approach, which would be logical for this material/biology/chemistry-related challenge, rarely taken. In review, we highlight critical non-biological aspects sometimes overlooked by microbiologists working on but highly relevant an overall understanding phenomenon. Here, identify gaps, methods, approaches help solve MIC-related challenges, with emphasis metals. We also discuss application existing tools managing propose ideas promote improved MIC. Furthermore, areas where insights expertise needed progress field.

Language: Английский

Citations

77
Quorum Sensing, Biofilm, and Intestinal Mucosal Barrier: Involvement the Role of Probiotic DOI Creative Commons
Zhaoxi Deng, Xin Luo, Jianxin Liu

et al.

Frontiers in Cellular and Infection Microbiology, Journal Year: 2020, Volume and Issue: 10

Published: Sept. 25, 2020

The intestine is a particularly dynamic environment in which the host constantly interacts with trillions of symbiotic bacteria called microbiota. Using quorum sensing (QS) communication, can coordinate their social behavior and influence cell activities noninvasive manner. Nowadays, large amount research has greatly spurred understanding how bacterial QS communication regulates cooperative behaviors due to coexistence host-microbe interactions. In this review, we discuss gut its role biofilm formation. As biological barrier, mucosal immune system effectively prevent pathogenic microorganisms other immunogenic components from entering internal host. We focus on relationship between intestinal immunity, probiotic may regulate them. This review provide theoretical basis for development new techniques including probiotics targeting barrier function, thereby improving health.

Language: Английский

Citations

107
Microbial corrosion of metals: The corrosion microbiome DOI
Yassir Lekbach, Tao Liu, Yingchao Li

et al.

Advances in microbial physiology/Advances in Microbial Physiology, Journal Year: 2021, Volume and Issue: unknown, P. 317 - 390

Published: Jan. 1, 2021

Language: Английский

Citations

93
Community-wide changes reflecting bacterial interspecific interactions in multispecies biofilms DOI
Faizan Ahmed Sadiq, Mette Burmølle, Marc Heyndrickx

et al.

Critical Reviews in Microbiology, Journal Year: 2021, Volume and Issue: 47(3), P. 338 - 358

Published: March 2, 2021

Existence of most bacterial species, in natural, industrial, and clinical settings the form surface-adhered communities or biofilms has been well acknowledged for decades. Research predominantly focusses on single-species as these are relatively easy to study. However, microbiologists now interested studying multispecies revealing interspecific interactions because existence a plethora different species together almost all natural settings. Multispecies biofilms-led emergent properties triggered by social which have huge implication research practical knowledge useful control manipulation microbial communities. Here, we discuss some important that take place biofilm provide insights into community-wide changes indicate elucidate underlying mechanisms.

Language: Английский

Citations

64
Antimicrobial Activity of Non-steroidal Anti-inflammatory Drugs on Biofilm: Current Evidence and Potential for Drug Repurposing DOI Creative Commons
Rodrigo Cuiabano Paes Leme,

Raquel Bandeira da Silva

Frontiers in Microbiology, Journal Year: 2021, Volume and Issue: 12

Published: July 27, 2021

It has been demonstrated that some non-steroidal anti-inflammatory drugs (NSAIDs), like acetylsalicylic acid, diclofenac, and ibuprofen, have anti-biofilm activity in concentrations found human pharmacokinetic studies, which could fuel an interest repurposing these well tolerated as adjunctive therapies for biofilm-related infections. Here we sought to review the currently available data on of NSAIDs its relevance a clinical context. We performed systematic literature identify most commonly tested last 5 years, bacterial species be responsive their actions, emergence resistance molecules. studies investigating NSAIDs’ against biofilms were vitro , frequently non-clinical isolates, may not adequately represent populations cause clinically-relevant Furthermore, concerning antibiotic are scarce, with divergent outcomes. Although potential use control infections seems exciting avenue, there is paucity using appropriate vivo models biofilm or controlled trials support agents.

Language: Английский

Citations

56
A review of risk-based decision-making models for microbiologically influenced corrosion (MIC) in offshore pipelines DOI
Mohammad Yazdi, Faisal Khan, Rouzbeh Abbassi

et al.

Reliability Engineering & System Safety, Journal Year: 2022, Volume and Issue: 223, P. 108474 - 108474

Published: March 16, 2022

Language: Английский

Citations

56
Incubation habitats and aging treatments affect the formation of biofilms on polypropylene microplastics DOI

Encui Shan,

Xiaoli Zhang,

Jiasen Li

et al.

The Science of The Total Environment, Journal Year: 2022, Volume and Issue: 831, P. 154769 - 154769

Published: March 23, 2022

Language: Английский

Citations

52
Investigating Biofilms: Advanced Methods for Comprehending Microbial Behavior and Antibiotic Resistance DOI Creative Commons
Ahmad Almatroudi

Frontiers in Bioscience-Landmark, Journal Year: 2024, Volume and Issue: 29(4), P. 133 - 133

Published: March 29, 2024

Biofilms, which consist of microorganisms enclosed in an extracellular polymeric material (EPS), hold immense importance the fields environmental research, industry, and medicine. They play a significant role ecosystem dynamics stability, but they also pose issues such as biofouling, corrosion, pollution. Biofilms medical environments are linked to persistent infections elevated healthcare expenses. The EPS matrix plays crucial maintaining structural integrity antibiotic resistance these structures. research primarily investigates facilitating horizontal gene transfer among biofilm communities, with particular emphasis on its impact this process. process is recognized pivotal mechanism emergence resistance, underscoring function biofilms. analysis highlights financial constraints caused by biofilms several industries. Biofilm-associated sector result escalated treatment expenses extended hospitalization periods. In industrial context, have increasing maintenance product contamination, emphasizing need for efficient management solutions. This review presents most recent progress utilization sophisticated imaging tools molecular methodologies. addition conventional techniques, explores tools, DNA RNA sequencing, conjunction proteomics. These approaches essential assessing genetic metabolic mechanisms that regulate development resistance. underscores significance employing interdisciplinary methodology study By incorporating range approaches, analysis, comprehensive understanding may be achieved. approach opens up possibilities developing novel solutions address negative impacts health, environment.

Language: Английский

Citations

14