Interspecies microbial interactions in bioelectrochemical system and biodegradation: A state of the art review

Microbial mutualistic interaction or synthetic microbiology evolves closely from the concept of cell-cell relations in a complex microbial community, which plays a crucial role in waste degradation, bioremediation, and bioenergy generation. Recently, the application of synthetic microbial consortia has renewed attention in the field of bioelectrochemistry. In the past few years, the influence of microbial mutualistic interaction has been extensively studied in bioelectrochemical systems (BES), especially in microbial fuel cells (MFCs). Nevertheless, synthetic microbial consortia were found to exhibit superior bioremediation performance compared to single strains of microbes for polycyclic aromatic hydrocarbons, synthetic dyes, polychlorinated biphenyls, and other organic pollutants compared to the respective single microbial species. However, a comprehensive understanding of intermicrobial interactions, specifically the metabolic pathways in a mixed-cultured microbial community system, is still lacking. In this study, we have comprehensively reviewed the possible pathways for executing intermicrobial communication within a complex microbial community consortium with various underlying pathways. The influence of mutualistic interactions on the power generation of MFCs and wastewater biodegradation has been widely reviewed. We argue that this study would motivate the design and construction of potential synthetic microbial consortia to stimulate the extraction of bioelectricity and the biodegradation of contaminants.

Antimicrobial peptides: Promising alternatives over conventional capture ligands for biosensor-based detection of pathogenic bacteria

The detection of pathogenic bacteria using biosensing techniques could be a potential alternative to traditional culture based methods. However, the low specificity and sensitivity of conventional biosensors, critically related to the choice of bio-recognition elements, limit their practical applicability. Mammalian antibodies have been widely investigated as biorecognition ligands due to high specificity and technological advancement in antibody production. However, antibody-based biosensors are not considered as an efficient approach due to the batch-to-batch inconsistencies as well as low stability. In recent years, antimicrobial peptides (AMPs) have been increasingly investigated as ligands as they have demonstrated high stability and possessed multiple sites for capturing bacteria. The conjugation of chemo-selective groups with AMPs has allowed effective immobilization of peptides on biosensor surface. However, the specificity of AMPs is a major concern for consideration as an efficient ligand. In this article, we have reviewed the advances and concerns, particularly the selectivity of AMPs for specific detection of pathogenic bacteria. This review also focuses the state-of-the-art mechanisms, challenges and prospects for designing potential AMP conjugated biosensors. The application of AMP in different biosensing transducers such as electrochemical, optical and piezoelectric varieties has been widely discussed. We argue that this review would provide insights to design and construct AMP conjugated biosensors for the pathogenic bacteria detection.

Photocatalytic performance, anti-bacterial activities and 3-chlorophenol sensor fabrication using MnAl2O4·ZnAl2O4 nanomaterials

A MnAl₂O₄·ZnAl₂O₄ nanomaterial was synthesized by co-precipitation and characterized by XRD, SEM, EDS, TEM, AFM, FTIR, PL, CV and EIS. The photocatalytic activity of the nanocomposite against MV dye and its MDR anti-bacterial functions were studied. The nanocomposite shows excellent photocatalytic as well as anti-bacterial activity. A MnAl₂O₄·ZnAl₂O₄ nanomaterial/Nafion/GCE electrode was fabricated and implemented as the working electrode of a 3-CP sensor. The sensor exhibited good sensitivity, with the lowest detection limit, fast response time, large linear dynamic range (LDR), and long-term stability in the chemical environment. The estimated sensitivity is 70.07 μA mM^-1 cm^-2. The LDR, limit of detection (LOD), and limit of quantification (LOQ) are 0.1 nM to 0.01 M, 0.0014 ± 0.0001 nM, and 0.004 nM, respectively. The MnAl₂O₄·ZnAl₂O₄ nanomaterial/Nafion/GCE is a promising fabricated sensor probe for the selective detection of 3-CP for the environmental safety and healthcare fields on a large scale.

Genome-wide Characterization Deciphers Distinct Properties of Aquaporins in Six Phytophthora Species

Background:

Aquaporins, also known as major intrinsic proteins (MIPs), facilitate the membrane diffusion of water and some other small solutes. The roles of MIPs in plant physiological processes are established and now their roles in plant-pathogen interactions are getting more attention.

Objective:

To investigate the evolution, diversity, and structural insights of Phytophthora MIPs (PhyMIPs) and to compare them to those in other domains of life.

Methods:

Bioinformatics approaches were used to identify and characterize the PhyMIPs. The phylogenetic analysis was done with MEGA7.0 using maximum likelihood method. The prediction of transmembrane α-helices was done by using SOSUI and TMpred servers, and that of subcellular localization was performed with WoLF PSORT and Cello prediction system. The structure of PhyMIP genes was predicted by GeneMark.hmm ES-3.0 program. The 3D homology models were generated using the Molecular Operating Environment software and the stereochemical quality of the templates and models was assessed by PROCHECK. The PoreWalker server was used to detect and characterize PhyMIP channels from their 3D structural models.

Results:

Herein, we identified 17, 24, 27, 19, 19, and 22 full-length MIPs, respectively, in the genomes of six Phytophthora species, P. infestans, P. parasitica, P. sojae, P. ramorum, P. capsici, and P. cinnamomi. Phylogenetic analysis showed that the PhyMIPs formed a completely distinct clade from their counterparts in other taxa and were clustered into nine subgroups. Sequence and structural properties indicated that the primary selectivity-related constrictions, including aromatic arginine (ar/R) selectivity filter and Froger's positions in PhyMIPs were distinct from those in other taxa. The substitutions in the conserved Asn-Pro-Ala motifs in loops B and E of many PhyMIPs were also divergent from those in other taxonomic domains. The group-specific consensus sequences/ motifs deciphered in different loops and transmembrane α-helices of PhyMIPs were distinct from those in plants, animals, and other microbes.

Conclusion:

This study represents PhyMIPs with distinct evolutionary and structural properties, and the data collectively indicates that PhyMIPs might have novel functions.

Microbial Metabolites: The Emerging Hotspot of Antiviral Compounds as Potential Candidates to Avert Viral Pandemic Alike COVID-19

The present global COVID-19 pandemic caused by the noble pleomorphic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a vulnerable situation in the global healthcare and economy. In this pandemic situation, researchers all around the world are trying their level best to find suitable therapeutics from various sources to combat against the SARS-CoV-2. To date, numerous bioactive compounds from different sources have been tested to control many viral diseases. However, microbial metabolites are advantageous for drug development over metabolites from other sources. We herein retrieved and reviewed literatures from PubMed, Scopus and Google relevant to antiviral microbial metabolites by searching with the keywords "antiviral microbial metabolites," "microbial metabolite against virus," "microorganism with antiviral activity," "antiviral medicine from microbial metabolite," "antiviral bacterial metabolites," "antiviral fungal metabolites," "antiviral metabolites from microscopic algae' and so on. For the same purpose, the keywords "microbial metabolites against COVID-19 and SARS-CoV-2" and "plant metabolites against COVID-19 and SARS-CoV-2" were used. Only the full text literatures available in English and pertinent to the topic have been included and those which are not available as full text in English and pertinent to antiviral or anti-SARS-CoV-2 activity were excluded. In this review, we have accumulated microbial metabolites that can be used as antiviral agents against a broad range of viruses including SARS-CoV-2. Based on this concept, we have included 330 antiviral microbial metabolites so far available to date in the data bases and were previously isolated from fungi, bacteria and microalgae. The microbial source, chemical nature, targeted viruses, mechanism of actions and IC50/EC50 values of these metabolites are discussed although mechanisms of actions of many of them are not yet elucidated. Among these antiviral microbial metabolites, some compounds might be very potential against many other viruses including coronaviruses. However, these potential microbial metabolites need further research to be developed as effective antiviral drugs. This paper may provide the scientific community with the possible secret of microbial metabolites that could be an effective source of novel antiviral drugs to fight against many viruses including SARS-CoV-2 as well as the future viral pandemics.

Major Insights in Dynamics of Host Response to SARS-CoV-2: Impacts and Challenges

The coronavirus disease 2019 (COVID-19), a pandemic declared by the World Health Organization on March 11, 2020, is caused by the infection of highly transmissible species of a novel coronavirus called severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). As of July 25, 2021, there are 194,372,584 cases and 4,167,937 deaths with high variability in clinical manifestations, disease burden, and post-disease complications among different people around the globe. Overall, COVID-19 is manifested as mild to moderate in almost 90% of the cases and only the rest 10% of the cases need hospitalization. However, patients with older age and those having different comorbidities have made worst the pandemic scenario. The variability of pathological consequences and clinical manifestations of COVID-19 is associated with differential host-SARS-CoV-2 interactions, which are influenced by the factors that originated from the SARS-CoV-2 and the host. These factors usually include the genomic attributes and virulent factors of the SARS-CoV-2, the burden of coinfection with other viruses and bacteria, age and gender of the individuals, different comorbidities, immune suppressions/deficiency, genotypes of major histocompatibility complex, and blood group antigens and antibodies. We herein retrieved and reviewed literatures from PubMed, Scopus, and Google relevant to clinical complications and pathogenesis of COVID-19 among people of different age, sex, and geographical locations; genomic characteristics of SARS-CoV-2 including its variants, host response under different variables, and comorbidities to summarize the dynamics of the host response to SARS-CoV-2 infection; and host response toward approved vaccines and treatment strategies against COVID-19. After reviewing a large number of published articles covering different aspects of host response to SARS-CoV-2, it is clear that one aspect from one region is not working with the scenario same to others, as studies have been done separately with a very small number of cases from a particular area/region of a country. Importantly, to combat such a pandemic as COVID-19, a conclusive understanding of the disease dynamics is required. This review emphasizes on the identification of the factors influencing the dynamics of host responses to SARS-CoV-2 and offers a future perspective to explore the molecular insights of COVID-19.

Main protease inhibitors and drug surface hotspots for the treatment of COVID-19: A drug repurposing and molecular docking approach

Here, drug repurposing and molecular docking were employed to screen approved MPP inhibitors and their derivatives to suggest a specific therapeutic agent for the treatment of COVID-19. The approved MPP inhibitors against HIV and HCV were prioritized, while RNA dependent RNA Polymerase (RdRp) inhibitor remdesivir including Favipiravir, alpha-ketoamide were studied as control groups. The target drug surface hotspot was also investigated through the molecular docking technique. Molecular dynamics was performed to determine the binding stability of docked complexes. Absorption, distribution, metabolism, and excretion analysis was conducted to understand the pharmacokinetics and drug-likeness of the screened MPP inhibitors. The results of the study revealed that Paritaprevir (-10.9 kcal/mol) and its analog (CID 131982844) (-16.3 kcal/mol) showed better binding affinity than the approved MPP inhibitors compared in this study, including remdesivir, Favipiravir, and alpha-ketoamide. A comparative study among the screened putative MPP inhibitors revealed that the amino acids T25, T26, H41, M49, L141, N142, G143, C145, H164, M165, E166, D187, R188, and Q189 are at potentially critical positions for being surface hotspots in the MPP of SARS-CoV-2. The top 5 predicted drugs (Paritaprevir, Glecaprevir, Nelfinavir, and Lopinavir) and the topmost analog showed conformational stability in the active site of the SARS-CoV-2 MP protein. The study also suggested that Paritaprevir and its analog (CID 131982844) might be effective against SARS-CoV-2. The current findings are limited to in silico analysis and lack in vivo efficacy testing; thus, we strongly recommend a quick assessment of Paritaprevir and its analog (CID 131982844) in a clinical trial.

Extracellular metabolites of endophytic fungi from Azadirachta indica inhibit multidrug-resistant bacteria and phytopathogens

Aim: To evaluate antimicrobial activity of extracellular metabolites (EMs) of endophytic fungal isolates (EFIs) from Azadirachta indica. Materials & methods: EFIs were identified by internal transcribed spacer (ITS) sequencing. Antimicrobial activity, and minimum inhibitor concentration (MIC) and minimum bactericidal concentration (MBC) were determined using agar diffusion and microdilution method, respectively. Results: Seventeen EFIs were isolated from different organs of A. indica. Eight of them were identified based on ITS sequencing. The EMs of EFIs inhibited the growth of six multidrug-resistant (MDR) bacterial superbugs and three phytopathogenic fungi. The MDR bacterial superbugs are resistant to six commercial antibiotics of different generations but susceptible to EMs of EFIs. The MIC (0.125-1.0 μg/μl), MBC (0.5-4.0 μg/μl) and minimum fungicidal concentration (1.0-4.0 μg/μl) of the EMs from EFIs are lower enough. Conclusion: The EMs of the EFIs have promising antimicrobial activity against MDR bacteria and phytopathogenic fungi.

Amplicon sequencing reveals significantly increased Vibrio abundance and associated gene functions in vibriosis-infected black tiger shrimp (Penaeus monodon)

Vibriosis caused by luminous Vibrio species is one of the biggest challenges to shrimp industry in Bangladesh. This study aimed to characterize whole microbial communities from Vibrio-infected black tiger shrimp (Penaeus monodon) using 16S rRNA-based amplicon sequencing. A total of 36 disease-free and infected shrimp were collected from six different hatcheries in Bagerhat, Bangladesh. A final pool of 12 samples (n = 6) was created by homogenization of the hepatopancreas samples from three shrimps collected from each hatchery for the same group. The amplicon sequencing data revealed significant (p < .05) decrease of alpha diversity measurements and subsequent effects (p < .05) on the hepatopancreas microbiota in the infected group, compared to control shrimp. Proteobateria and Aeromonas were the most dominant bacteria at phylum and genus level in both groups and identified as core microbiota in the community. Two bacterial groups at phyla level and eight at genus level were found associated with the alteration of hepatopancreas microbial communities and associated gene functions in vibriosis-infected shrimp, revealed by differential abundance and KEGG pathway analysis. The overwhelming abundance of Citroibacter, Shewanella and Candidatus lineages in vibriosis-infected shrimp needs further investigations.

Human Aquaporins: Functional Diversity and Potential Roles in Infectious and Non-infectious Diseases

Aquaporins (AQPs) are integral membrane proteins and found in all living organisms from bacteria to human. AQPs mainly involved in the transmembrane diffusion of water as well as various small solutes in a bidirectional manner are widely distributed in various human tissues. Human contains 13 AQPs (AQP0-AQP12) which are divided into three sub-classes namely orthodox aquaporin (AQP0, 1, 2, 4, 5, 6, and 8), aquaglyceroporin (AQP3, 7, 9, and 10) and super or unorthodox aquaporin (AQP11 and 12) based on their pore selectivity. Human AQPs are functionally diverse, which are involved in wide variety of non-infectious diseases including cancer, renal dysfunction, neurological disorder, epilepsy, skin disease, metabolic syndrome, and even cardiac diseases. However, the association of AQPs with infectious diseases has not been fully evaluated. Several studies have unveiled that AQPs can be regulated by microbial and parasitic infections that suggest their involvement in microbial pathogenesis, inflammation-associated responses and AQP-mediated cell water homeostasis. This review mainly aims to shed light on the involvement of AQPs in infectious and non-infectious diseases and potential AQPs-target modulators. Furthermore, AQP structures, tissue-specific distributions and their physiological relevance, functional diversity and regulations have been discussed. Altogether, this review would be useful for further investigation of AQPs as a potential therapeutic target for treatment of infectious as well as non-infectious diseases.

Photocatalytic, anti-bacterial performance and development of 2,4-diaminophenylhydrazine chemical sensor probe based on ternary doped Ag·SrSnO3 nanorods

Ag·SrSnO₃ NRs is an excellent photocatalyst, kills both Gram positive and Gram negative bacteria. The 2,4-DAPHyd sensor fabricated by layered Ag·SrSnO₃ NRs onto GCE shows high sensitivity (7.5854 μA μM⁻¹ cm⁻²); LDR, 0.1 nM~0.01 mM & LOD, 96.13 ± 4.81 pM.

Photocatalysis, photoinduced enhanced anti-bacterial functions and development of a selective m-tolyl hydrazine sensor based on mixed Ag·NiMn2O4 nanomaterials

In this work, a tri-metal based nanocomposite was synthesized and characterized. A detailed investigation of the photocatalytic dye degradation efficiency of the nanocomposite under visible light showed promising results in a wide pH range, both acidic and basic medium. Studies on anti-bacterial activity against seven pathogenic bacteria, including both Gram positive and Gram negative species, were conducted in the presence and absence of light and compared with the standard antibiotic gentamicin. The minimum inhibitory concentration (MIC) values of Ag·NiMn₂O₄ against multidrug-resistant (MDR) pathogens ranged from 0.008 to 0.65 μg μL^-1, while the minimum bactericidal concentration (MBC) was found to be 0.0016 μg μL^-1. The nanomaterial, Ag·NiMn₂O₄ was deposited onto the surface of a glassy carbon electrode (GCE; 0.0316 cm²) as a thin film to fabricate the chemical sensor probe. The proposed sensor showed linear current (vs. concentration) response to m-THyd (m-tolyl hydrazine) from 1.0 pM to 0.01 mM, which is denoted as the linear dynamic range (LDR). The estimated sensitivity and detection limit of the m-THyd sensor were found to be 47.275 μA μM^-1 cm^-2 and 0.97 ± 0.05 pM, respectively. As a potential sensor, it is reliable due to its good reproducibility, rapid response, higher sensitivity, working stability for long duration and efficiency in the analysis of real environmental samples.

Plants Metabolites: Possibility of Natural Therapeutics Against the COVID-19 Pandemic

COVID-19, a disease induced by SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2), has been the cause of a worldwide pandemic. Though extensive research works have been reported in recent days on the development of effective therapeutics against this global health crisis, there is still no approved therapy against SARS-CoV-2. In the present study, plant-synthesized secondary metabolites (PSMs) have been prioritized to make a review focusing on the efficacy of plant-originated therapeutics for the treatment of COVID-19. Plant metabolites are a source of countless medicinal compounds, while the diversity of multidimensional chemical structures has made them superior to treat serious diseases. Some have already been reported as promising alternative medicines and lead compounds for drug repurposing and discovery. The versatility of secondary metabolites may provide novel antibiotics to tackle MDR (Multi-Drug Resistant) microbes too. This review attempted to find out plant metabolites that have the therapeutic potential to treat a wide range of viral pathogens. The study includes the search of remedies belonging to plant families, susceptible viral candidates, antiviral assays, and the mode of therapeutic action; this attempt resulted in the collection of an enormous number of natural therapeutics that might be suggested for the treatment of COVID-19. About 219 plants from 83 families were found to have antiviral activity. Among them, 149 plants from 71 families were screened for the identification of the major plant secondary metabolites (PSMs) that might be effective for this pandemic. Our investigation revealed that the proposed plant metabolites can serve as potential anti- SARS-CoV-2 lead molecules for further optimization and drug development processes to combat COVID-19 and future pandemics caused by viruses. This review will stimulate further analysis by the scientific community and boost antiviral plant-based research followed by novel drug designing.

Antibacterial activity of graphene oxide nanosheet against multidrug resistant superbugs isolated from infected patients

Graphene oxide (GO) is a derivative of graphene nanosheet which is the most promising material of the decade in biomedical research. In particular, it has been known as an antimicrobial nanomaterial with good biocompatibility. In this study, we have synthesized and characterize GO and checked its antimicrobial property against different Gram-negative and Gram-positive multidrug drug resistant (MDR) hospital superbugs grown in solid agar-based nutrient plates with and without human serum through the utilization of agar well diffusion method, live/dead fluorescent staining and genotoxicity analysis. No significant changes in antibacterial activity were found in these two different conditions. We also compare the bactericidal capability of GO with some commonly administered antibiotics and in all cases the degree of inhibition is found to be higher. The data presented here are novel and show that GO is an effective bactericidal agent against different superbugs and can be used as a future antibacterial agent.

Enhanced visible light-mediated photocatalysis, antibacterial functions and fabrication of a 3-chlorophenol sensor based on ternary Ag2O·SrO·CaO

A novel multi-metal oxide nanocomposite, Ag₂O·SrO·CaO, was synthesized by a facile co-precipitation method followed by calcinations. The synthesized nanocomposite was characterized by XRD, FESEM, EDS, TEM, FTIR spectroscopy and photoluminescence (PL) spectroscopy. The composite showed enhanced photocatalytic activity under visible light irradiation and excellent anti-bacterial performance against both Gram-positive and Gram-negative bacteria. Here, the synthesized Ag₂O·SrO·CaO nanomaterials were deposited on a glassy carbon electrode (GCE) in the form of a thin film to fabricate the desired electrochemical sensor and subjected to I–V analysis of 3-chlorophenol (3-CP) in a phosphate buffer solution (PBS). A calibration curve was plotted from the linear relation of current versus concentration and used to calculate the sensitivity (8.9684 μA μM⁻¹ cm⁻²), linear dynamic range (LDR, 0.1 nM to 0.01 mM) and lower limit of detection (DL, 97.12 ± 4.86 pM). The analytical parameters of the sensor such as response time, reproducibility and long-term stability in the detection of 3-CP were reliable. Finally, it was used to analyze real samples collected from various environmental sources and found to be acceptable.

The electrochemical detection mechanism of 3-CP in PBS buffer using the heterostructure nanocomposite Ag₂O·SrO·CaO. The proposed electrochemical reaction is supposed as C₆OH₅Cl + 11H₂O → 6CO₂ + 27H⁺ + Cl⁻ + 26e⁻.

Identification of AcrAB-TolC Efflux Pump Genes and Detection of Mutation in Efflux Repressor AcrR from Omeprazole Responsive Multidrug-Resistant Escherichia coli Isolates Causing Urinary Tract Infections

Antimicrobial resistance poses a threat in the treatment of infectious diseases in Bangladesh as well as in the world. Multidrug-resistant (MDR) Enterobacteriaceae, the most common cause of one such infectious disease, urinary tract infection (UTI), has contributed to the escalating problem of selecting empiric antibiotics against UTIs. The aim of this study was to investigate the presence of the efflux pump in MDR Escherichia coli isolates from UTI in the North-East region of Bangladesh, to isolate and characterize the AcrAB-TolC efflux pump genes of these locally isolated strains and to do mutation analysis of the efflux pump repressor AcrR gene to understand the AcrAB-TolC efflux pump mechanism. In the presence of omeprazole, an efflux pump inhibitor, every MDR E. coli isolate showed increased susceptibility to at least 1 of the 7 antibiotics investigated, indicating that efflux pump might be involved in their antibiotic resistance. Omeprazole decreased the minimum inhibitory concentration of every antibiotics being investigated by 2- to 8-fold. DNA and the deduced amino acid sequences of the polymerase chain reaction (PCR) products analyzed by bioinformatics tools revealed that the chromosomal AcrAB-TolC and AcrR genes were present in all MDR and antibiotic-susceptible E. coli isolates. However, the deduced amino acid sequences of the amplification refractory mutation system (ARMS) PCR product of the AcrR gene revealed that the substitution of arginine to cysteine at position 45 of AcrR was observed only in the MDR E. coli whose antibiotic susceptibility increased in the presence of omeprazole. Data reported herein support the notion that the increased antibiotic susceptibility of the MDR E. coli isolates in the presence of omeprazole might be due to efflux pump(s) inhibition and the AcrAB-TolC efflux pump might be a contributor to antibiotic resistance when the mutation of arginine to cysteine occurs at position 45 of AcrR.