Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory condition that has a rapidly changing global epidemiology. IBD has been traditionally viewed as a primary immune system dysfunction, but emerging evidence more accurately describes IBD as a perturbance of the intricate balance between host immunity, the intestinal microbiome, and intestinal metabolism. Although genetic and environmental components have long been recognized as contributors, accumulating evidence increasingly highlights the pivotal role of microbial dysbiosis in the pathogenesis of IBD. In patients with IBD, intestinal dysbiosis, which is often characterized by reduced Firmicutes and increased pro-inflammatory bacteria, triggers a cascade of pathogenic events. These pathogenic events include impaired epithelial barrier function, dysregulated immune activation against luminal antigens, and immune reprogramming. Central to these processes are functional changes in microbial metabolism, particularly in pathways involving short-chain fatty acids (SCFAs), bile acids, and redox homeostasis, which critically contribute to the development of chronic mucosal inflammation. The current therapeutic backbone of IBD—including aminosalicylates, biologics, and immunomodulators—largely targets the inflammatory response. However, the challenges such as primary non-response, secondary loss of response, and systemic side effects are often problematic. Consequently, there is an urgent need to develop novel therapeutic and preventive strategies that target the underlying microbial and metabolic causes of the disease rather than modulating immune responses. This review integrates the pathomechanistic implications of the microbiome-metabolic axis in the maintenance of gut homeostasis and its disruption in IBD, with particular emphasis on the global epidemiology of the disease. We further evaluate emerging therapeutic and preventive strategies aimed at restoring the microbiome-metabolic axis, including fecal microbiota transplantation (FMT), probiotic therapy, bacteriophage therapy, and helminth-based therapies. In addition, we explore the potential of advanced approaches such as microbiome engineering and precision genome editing to enable highly personalized therapeutic paradigms. By bridging microbial ecology with clinical pathology, this review highlights the transformative potential of targeting the host-microbiota interface to achieve improved long-term outcomes in IBD.

Staphylococcus saprophyticus is a gram-positive commensal characteristically resistant to novobiocin. Clinically, it is associated with urinary tract and other opportunistic infections. But reports on phages against them are scanty, which underlines the importance of the study. We isolated a Staphylococcus saprophyticus strain from soiled socks. The strain was characterised through biochemical tests and 16S rDNA ribotyping. Furthermore, the antibiogram revealed that the strain is resistant to penicillinase-resistant beta-lactam antibiotics. A double-stranded DNA temperate phage, ØPh_SS01, was isolated against S. saprophyticus from a mixed sewage sample. The phage is stable over a wide range of temperatures, including pH and salt, with 67.08 ± 25 virions/cell following adsorption within 14 min. The potential of ØPh_SS01 was established in Mannitol Salt broth with a 7-log reduction of S. saprophyticus over a period of 24 h. Moreover, it inhibited and disrupted biofilm at efficiencies of 77% and 69%, respectively, at an MOI of 100. Studies on adherent immortalised human keratinocytes and urethral cell lines did not result in any significant change in viability. Sequence analysis of ØPh_SS01 depicted a genome size of 47 Kb with 37.36% GC content. A similarity of 91.5% to related entries indicated its novelty. The textile matrices immobilised with phages could reduce the bacterial load by about 7-log, which shows the potential of the phage in infection control.

Postbiotics are increasingly recognized as a predominant group of biotherapeutic agents sourced from the microbial secretome, offering functional benefits, while circumventing the safety concerns associated with the application of live microbial consortia. These microbial derivatives are emerging as promising approaches for tackling complex diseases, encompassing cancer, autoimmune diseases, and metabolic disorders, through modulation of host cell signalling pathways, including G protein-coupled receptors (GPCRs), the NF-κB (Nuclear Factor Kappa B) pathway, and epigenetic regulatory pathways. Besides systemic effects, postbiotics may also have localized effects, such as epithelial regeneration, modulation of fibroblast functions, and control of collagen remodelling. Eventually, the scale-up in the production of postbiotics has initiated new avenues in improving sustainable agriculture and environmental biotechnology. This comprehensive review attempts to integrate mechanistic insights and translational applications, highlighting the therapeutic potential of postbiotics across biomedical and ecological domains. These observations could pave the way to bridge the gap between microbiome regulation, precision medicine, and sustainable biotechnology, thereby positioning postbiotics as a versatile tool addressing some of the most pressing health and sustainability challenges of the 21st century.

The synergistic effects of accelerated climate change and anthropogenic land-use shifts increasingly compromise the functional integrity of terrestrial ecosystems. To preserve soil health and ensure global food security, a transition toward biointensive, climate-smart agriculture is imperative. This review provides a comprehensive synthesis of the multifaceted role of plant growth-promoting rhizobacteria (PGPR) as “rhizosphere architects,” bridging global biogeochemical cycles with intricate molecular and digital interventions. Microbe mediated mitigation of atmospheric stressors is evaluated by monitoring increases in soil carbon sequestration and concomitant reductions in greenhouse gas (GHG) emissions. Central to ecosystem recovery is the physiochemical regeneration of marginal and polluted soils, where PGPR facilitate the detoxification of xenobiotics, including heavy metals, microplastics, and organic contaminants, while promoting the structural restoration of degraded edaphic environments. At the tripartite plant-microbe-soil interface, the synergistic regulation of root system architecture (RSA) is investigated alongside the emerging role of epigenetic modifications, such as DNA methylation and histone acetylation, as critical drivers of transgenerational stress memory against extreme climatic conditions. These molecular and structural shifts are functionally correlated with rhizosphere enzymatic activity, including specific enzyme fluxes (e.g., urease, phosphatase, and dehydrogenase), which serve as biochemical proxies for soil health restoration. To address the historical inconsistency of field inoculants, a translational framework is proposed that integrates Industry 4.0 technologies, such as AI-assisted bioformulation design and IoT-based precision monitoring, for real-time microbiome management. By discussing the translational hurdles of microbial competition and regulatory frameworks, this synthesis underscores how the fusion of microbial ecology and digital agriculture provides a robust pathway toward resilient terrestrial ecosystems and sustained agricultural productivity in the Anthropocene.

Ginger (Zingiber officinale) is an economically important spice crop widely cultivated for its culinary and medicinal values. However, its productivity is severely constrained by soft rot disease, causing substantial yield losses, quality, and persistent challenges in ginger cultivation. In this study, the major pathogenic fungus GI-FS1 was isolated from Z. officinale with typical symptoms and was identified as Fusarium species through morphological and molecular identification. The antifungal potential of plumbagin, a plant-derived naphthoquinone from Plumbago rosea, noted for antibacterial, antioxidant, and anticancer properties, was evaluated against GI-FS1. Plumbagin treatment significantly inhibited conidial germination and mycelial growth with Minimum Inhibitory Concentration (MIC) and Minimum Fungicidal Concentration (MFC) values of 10 & micro;g/mL and 15 & micro;g/mL, respectively. Conidial germination assays, microscopy, onion peel epidermis penetration confirmed inhibition, as plumbagin-treated spores failed to germinate and penetrate epidermis. 4',6-Diamidino-2-phenylindole (DAPI) staining showed chromatin condensation and Acridine orange/ethidium bromide (AO/EB) revealed membrane disruption, coupled with 2,7-dichlorodihydrofluorescein diacetate (DCFH-DA) detected Reactive oxygen species (ROS) accumulation, signifying oxidative stress-induced cell death by plumbagin. Elevated electrolyte leakage and DNA fragmentation supported apoptosis-like mechanisms underlying fungal growth inhibition; however, further studies on apoptotic factor gene expression are required to confirm this mechanism. Scanning Electron Microscopy (SEM) analysis revealed spore shrinkage and thinner, collapsed, rough mycelia, indicating loss of cell integrity on treatment with plumbagin. Overall, these findings provide the first report on the targeted mechanisms of plumbagin in inhibiting Fusarium conidial germination and inducing apoptotic-like cell death. By disrupting fungal viability through oxidative stress and apoptosis-related pathways, the study highlights plumbagin's potential as a natural antifungal agent for the sustainable management of soft rot disease in ginger.

Acinetobacter junii is an emerging opportunistic human and animal pathogen, fast gaining antimicrobial resistance. As conventional treatment becomes ineffective, alternatives are needed to address this challenge. Bacteriophages offer a promising yet underexplored solution in combating A. junii infections. Here, we report the isolation and characterisation of a temperate phage, ɸPh_AJ01, effective against a carbapenem-resistant A. junii. Moreover, the study adopts a technique for biasing the temperate phage to the lytic life cycle to address the issues of lysogeny. The efficacy of the phage in rescuing A. junii-infected Caenorhabditis elegans is also demonstrated. Phage ɸPh_AJ01 was isolated and purified from the Cooum River in Chennai, India. Host range analysis, adsorption assay, growth curve, and in vitro bacteriolytic test were performed. Transmission electron microscopy and whole-genome sequencing were carried out to understand its morphological and genetic features. Phage stability was tested in different temperatures and pH conditions. Antibiofilm activity of the phage was studied using inhibition and disruption assays. Bacteriophage-insensitive mutation frequency of A. junii was evaluated by the patch screen test. Experiment to bias the temperate phage towards lytic life cycle and, survival assay with A. junii-infected C. elegans were also performed. ɸPh_AJ01 is a temperate, narrow-spectrum, icosahedral, tailed phage that efficiently infected A. junii, yielding a burst size of 74 ± 8 virions per cell with good temperature and pH stability. ɸPh_AJ01 inhibited biofilm formation by 92

Approximately 40-50% of municipal solid waste is organic and causing biogenic malodor and infections, due to inefficient treatment methods. Biorefinery-based bioremediation and valorization is in vogue against these conventional strategies since it combines unit operations for better efficiency and productivity. Deriving inspiration, the proposed strategy puts together a unique and compatible combination of processes. This novel two-step valorization workflow involves the extraction of small molecules using organic solvents, and fermentation of resulting denatured residues (increased biodegradability or decreased recalcitrance) of reduced microbial load. The extraction step also doubles up as a sterilization event, with different solvents (petroleum ether, chloroform, ethyl methyl ketone and methanol) exhibiting varied efficiency, methanol and ethyl methyl ketone being the most effective. Different recalcitrant plant organic wastes resulting from four plants (Cocos nucifera, Allium cepa, Artocarpus hirsutus and Swietenia mahagoni) were used as feedstocks in the preliminary exploratory study using chosen pathogenic bacteria. Onion peel (Allium cepa) ethyl methyl ketone extract was chosen for further studies, as it inhibits Salmonella enterica, which is associated with infection and malodour (due to biogenic H2S) in wastewater. Further, fractionation of the extract yielded quercetin and its glycoside. The onion peel residue, after solvent extraction was fortified with peptone and essential minerals to promote the growth of Bacillus clausii. Fortified post-extraction residue supported the growth better than the pre-extraction residue. The residue resultant after solvent extraction was fermented with Bacillus clausii and with release of bioactive supernatants. The concentrated supernatant showed significant inhibition of Salmonella enterica and Shigella dysenteriae. Additionally, all the exudates showed considerable inhibition in H2S production, respectively.

Arsenic contamination of soil and water is a major environmental issue. Bioremediation through plant growth-promoting bacteria is viable, cost-effective, and sustainable. Along with arsenic removal, it also improves plant productivity under stressful conditions. A crucial aspect of such a strategy is the selection of bacterial inoculum. The described study demonstrates that the indigenous wastewater isolate, ASBT-KP1, could be a promising candidate. Identified as Klebsiella pneumoniae, ASBT-KP1 harbors genes associated with heavy metal and oxidative stress resistance, production of antimicrobial compounds and growth-promotion activity. The isolate efficiently accumulated 30 μg/g bacterial dry mass of arsenic. Tolerance toward arsenate and arsenite was 120 mM and 70 mM, respectively. Plant biomass content of Vigna radiata improved by 13% when grown in arsenic-free soil under laboratory conditions in the presence of the isolate. The increase became even more significant under the same conditions in the presence of arsenic, recording a 37% increase. The phylogenetic analysis assigned ASBT-KP1 to the clade of Klebsiella strains that promote plant growth. Similar results were also observed in Oryza sativa, employed to assess the ability of the strain to promote growth, in plants other than V. radiata. This study identifies a prospective candidate in ASBT-KP1 that could be employed as a plant growth-promoting rhizoinoculant in agricultural practices.

[This corrects the article DOI: 10.3389/fphar.2023.1159409.].

Wastewater malodour is the proverbial ‘elephant in the room’ notwithstanding its severe implications on sanitation, health, and hygiene. The predominant malodorous compounds associated with wastewater treatment plants and toilets are volatile organic compounds, such as hydrogen sulphide, ammonia, methanethiol, and organic acids. Among them, methanethiol warrants more attention owing to its relatively low olfactory threshold and associated cytotoxicity. This requires an efficient odour-abatement method since conventional techniques are either cost-prohibitive or leave recalcitrant byproducts. Bacteriophage-based methodology holds promise, and the described work explores the potential. In this study, a non-lysogenous Pseudomonas putida strain is used as a model organism that produces methanethiol in the presence of methionine. Two double-stranded DNA phages of genome sizes > 10 Kb were isolated from sewage. ɸPh_PP01 and ɸPh_PP02 were stable at suboptimal pH, temperature, and at 10% chloroform. Moreover, they showed adsorption efficiencies of 53% and 89% in 12 min and burst sizes of 507 ± 187 and 105 ± 7 virions per cell, respectively. In augmented synthetic wastewater, ɸPh_PP01 and ɸPh_PP02 reduced methanethiol production by 52% and 47%, respectively, with the concomitant reduction in P. putida by 3 logs in 6 h. On extension of the study in P. putida spiked-sewage sample, maximum reduction in methanethiol production was achieved in 3 h, with 49% and 48% for ɸPh_PP01 and ɸPh_PP02, respectively. But at 6 h, efficiency reduced to 36% with both the phages. The study clearly demonstrates the potential of phages as biocontrol agents in the reduction of malodour in wastewater.

IntroductionEnvironmental enteropathy (EE), a chronic small intestine disease characterized by gut inflammation, is widely prevalent in low-income countries and is hypothesized to be caused by continuous exposure to fecal contamination. Targeted nutritional interventions using potential probiotic strains from fermented foods can be an effective strategy to inhibit enteric pathogens and prevent chronic gut inflammation.MethodsWe isolated potential strains from fermented rice water and lemon pickle and investigated their cell surface properties, antagonistic properties, adhesion to HT-29 cells, and inhibition of pathogen adherence to HT-29 cells. Bacteriocin-like inhibitory substances (BLIS) were purified, and in vivo, survival studies in Caenorhabditis elegans infected with Salmonella enterica MW116733 were performed. We further checked the expression pattern of pro and anti-inflammatory cytokines (IL-6, IL8, and IL-10) in HT-29 cells supplemented with strains.ResultsThe strains isolated from rice water (RS) and lemon pickle (T1) were identified as Limosilactobacillus fermentum MN410703 and MN410702, respectively. Strains showed probiotic properties like tolerance to low pH (pH 3.0), bile salts up to 0.5%, simulated gastric juice at low pH, and binding to extracellular matrix molecules. Auto-aggregation of T1 was in the range of 85% and significantly co-aggregated with Klebsiella pneumoniae, S. enterica, and Escherichia coli at 48, 79, and 65%, respectively. Both strains had a higher binding affinity to gelatin and heparin compared to Bacillus clausii. Susceptibility to most aminoglycoside, cephalosporin, and macrolide classes of antibiotics was also observed. RS showed BLIS activity against K. pneumoniae, S. aureus, and S. enterica at 60, 48, and 30%, respectively, and the protective effects of BLIS from RS in the C. elegans infection model demonstrated a 70% survival rate of the worms infected with S. enterica. RS and T1 demonstrated binding efficiency to HT-29 cell lines in the 38–46% range, and both strains inhibited the adhesion of E. coli MDR and S. enterica. Upregulation of IL-6 and IL-10 and the downregulation of IL-8 were observed when HT-29 cells were treated with RS, indicating the immunomodulatory effects of the strain.DiscussionThe potential strains identified could effectively inhibit enteric pathogens and prevent environmental enteropathy.

The current COVID-19 pandemic situation has posed a significant threat to human health. This calls for versatile facemask filters with high filtration efficiency and biocidal activity. Herein, we have rationally designed a three-layered nanofilter mask consisting of electrospun polycaprolactone (PCL) and curcumin as a nanocoating on a polypropylene spunbond membrane. The nanomask thus developed had a particulate filtration efficiency of 96.8 +/- 0.1%, with good breathability (64 +/- 2 Pa) and a high quality factor (0.052 +/- 0.0005 Pa-1) for a coating thickness of similar to 20 mu m. An aerosol filtration efficiency of >99.99% was achieved for both bacteria and bacteriophages (a virus surrogate). Curcumin loading into the nanocoating induced significant contact-killing efficiency against bacteria and bacteriophages, implying the high biocidal activity presented by the nanomask. Furthermore, this mask could be reused up to 30 times after successive washing and drying, without alterations in its particle-filtration efficiency or fibrous morphology. Thus, by adopting a simple, scalable technique, a nanomask with manifold features was developed that satisfies the essential demands of air filtration in the current pandemic era.

Robust control of pathogens in sewage facilitates safe reuse of wastewater rich in valuable nutrients for potential valorization through biological means. Aspergillus niger is widely reported in bioremediation of wastewater but studies on control of enteric pathogens in sewage are very sparse. So, this study aimed at exploring the antibacterial and nematicidal activity of A. niger culture filtrate (ACF). Antibacterial activity of ACF on enteric pathogens (Klebsiella pneumoniae, Pseudomonas aeruginosa, Vibrio cholerae, Salmonella enterica, Shigella dysenteriae, Escherichia coli, Staphylococcus aureus, Klebsiella variicola) was determined by spectrophotometric growth analysis, resazurin based viability assay and biofilm formation assay. ACF showed inhibition against all enteric pathogens except Pseudomonas aeruginosa. Nematicidal studies on Caenorhabditis elegans showed 85% egg hatch inhibition and 52% mortality of L1 larvae. Sewage treatment with ACF at 1:1 (v/v) showed 2–3 log reduction in coliforms, Klebsiella, Shigella, Salmonella, S. aureus and Vibrio except Pseudomonas, indicating significant alteration of complex microbial dynamics in wastewater. Application of ACF can potentially be used as a robust biocontrol strategy against infectious microbes in wastewater and subsequent valorization by cultivating beneficial Pseudomonas.

Owing to their selective nature, bacteriophages are prospective in targeted wastewater disinfection. Other potential applications include the removal of biogenic malodour and the mitigation of corrosion in sewerage pipelines. Nevertheless, its applications are ridden with challenges, the most prominent of which is scaling up. Towards that end, effective methodologies are required for dispersing phages into wastewater. The study describes a device arbitrarily named Lytics Broadcasting System. In principle, the device contains phages that can be continuously dispersed into wastewater. The modified version is called Bacteriophage Amplification Reactor, which operates with both phages and their respective hosts, ensuring continual production and dissemination of phages. Both prototypes utilize 0.22 mu m cellulose membranes as an interface through which phage diffuse passively and selectively owing to its smaller size and established through membrane-overlay method. In the study, previously reported bacteriophage phi Ph Se01 and Salmonella enterica were used. A reduction of 3-4 log was achieved with both the prototypes after 48 h of operation in 1 L of augmented synthetic sewage. Subsequently, the biogenic H2S produced by Salmonella enterica was reduced by 64-74% indicating its utility for targeted disinfection and malodour mitigation of wastewater. This study aims to provide a framework for the development of scalable prototypes of Lytic Broadcasting Systems for real-world wastewater applications.

Bacterial pathogens are fostered in and transmitted through wastewater. Hence, monitoring their impact on sanitation and hygiene is imperative. As part of the monitoring process, culture-based methodologies are primarily used, which centre on the use of selective and differential media. Media available today are, at best, difficult to formulate and, at worst, prohibitively expensive. To address this lacuna, the study proposes a selective and differential medium for Klebsiella spp. Klebsiella blue agar (KBA) is completely selective against selected gram-positive bacteria ( Bacillus spp., Staphylococcus aureus ) and a few gram-negative bacteria ( Acinetobacter baumanii , Serratia marcescens ) . On the other hand, it supports the growth of the chosen members of the Klebsiella pneumoniae species-complex with a characteristic green colouration. Methylene blue, tryptophan, and bile salt make up the selective components of KBA. Moreover, methylene blue, 0.6% NaCl, and glycerol render it differential. KBA was more selective than HiCrome™ Klebsiella Selective Agar Base (KSA) in replica plating experiments. KBA promoted only 157 CFUs against 209 CFUs in KSA when stamped with 253 CFUs grown on LB. The colonies so isolated were predominantly Klebsiella spp., on identification through colony polymerase chain reaction. Moreover, the differential nature of KBA distinguished Klebsiella aerogenes from other species. On the contrary, KSA lodged colonies indistinguishable from each other and Klebsiella spp. Due to its ease of formulation, high selectivity, differential nature, and cost-effective composition, KBA is a viable option for the routine culture of Klebsiella spp. in environmental and clinical settings. Key points • Formulated a novel selective and differential media for Klebsiella spp., named Klebsiella Blue agar • Facile formulation methodology • Can be employed to isolate Klebsiella spp. from complex sources such as wastewater

Bacteriophages are generally specific, and a cocktail of phages is needed to combat different bacterial targets. Their production usually requires pathogenic isolation hosts. We identified a novel strain, Escherichia coli ST155, that could serve as a production host for three different polyvalent phages (ϕPh_SE03, ϕPh_SD01, and ϕPh_EC01), thus superseding the use of individual isolation hosts. Upon propagation in E. coli ST155, the phages demonstrated differential intergeneric infectivity against Salmonella enterica, E. coli OP50, Shigella dysenteriae, E. coli MDR, and Acinetobacter baumannii. Phages were characterised based on morphology, latent period, burst size, the efficiency of plating, and restriction enzyme profile. Survival assay on Caenorhabditis elegans, the absence of Shiga toxin, and enterotoxigenic E. coli virulence genes indicated that E. coli ST155 could be non-pathogenic. Lack of antibiotic resistance and absence of functional prophages rendered the host suitable for environmental applications. As a proof-of-concept, phage ϕPh_SE03 was produced in ST155 by employing a unique Bacteriophage Amplification Reactor-Lytics Broadcasting System and was simultaneously disseminated into S. enterica augmented wastewater, which resulted in a 3-log reduction in 24 h. The study establishes the potential of E. coli ST155 as a phage production host thereby minimising the possibility of accidental release of pathogenic hosts into wastewater.

Value-added phytochemicals from food by-products and waste materials have gained much interest and among them, dietary polyphenolic compounds with potential biological properties extend a promising sustainable approach. Oxyresveratrol (Oxy), a stilbenoid polyphenol, possesses great therapeutic potential, though its pharmacokinetic issues need attention. A good source of oxyresveratrol was found in underutilized coconut shells and the synbiotic applications of the compound in combination with a potential probiotic isolate Limosilactobacillus fermentum ASBT-2 was investigated. The compound showed lower inhibitory effects on the strain with minimum inhibitory concentration (MIC) of 1000 µg/mL. Oxyresveratrol at sub-MIC concentrations (500 µg/mL and 250 µg/mL) enhanced the probiotic properties without exerting any inhibitory effects on the strain. The combination at sub- MIC concentration of the compound inhibited Salmonella enterica and in silico approaches were employed to elucidate the possible mode of action of oxy on the pathogen. Thus, the combination could target pathogens in the gut without exerting negative impacts on growth of beneficial strains. This approach could be a novel perspective to address the poor pharmacokinetic properties of the compound.

Pathogenic microorganisms are always a challenge when they form biofilms on submerged surfaces such as pipes, drains, or sewers, which are difficult to remove using normal chemical or biological treatments. Developing a fundamental understanding of the biodiversity of sewage microbiome or finding out the key species that can be targeted to significantly reduce the pathogenic population within can be critical in advancing and optimizing the technology for maintaining environmental health. Hence to find articles with relevant information about this microbiome and the interactions within is like finding a needle from the haystack. There comes the need for data mining tools, a key part of such a tool would be named entity recognition. To train a NER model, a relevant dataset with the required entities tagged is required and no such were to be found in the biomedical domain. So, in our study, we intended to develop a microbiome dataset with all the relevant concepts tagged for training a NER model which is to be a part of a semantic information retrieval tool. For this, we engineered a dataset specifically focusing on keywords related to the characteristics of the wastewater microbiome that could cluster out the relevant information from the bulk data of PubMed literature. The new engineered data was then used for fine-tuning NER models with different variants of BERT models for analyzing which had the most efficiency with our dataset. We implemented NER models capable of accurately predicting the concepts tagged in the microbiome dataset and designed experiments to validate the efficiency of the different models on our dataset and also other open-source biomedical datasets like JNLPA and BC5CDR. The results show that out of the three BERT variants, BioBERT was the most performant model, and also even with a fairly limited size compared to other biomedical NER datasets, we were able to achieve similar scores. The NER model fine-tuned using the microbiome dataset was able to successfully predict the tagged concepts/named entities in the datasets.

Sulphate-reducing bacteria (SRB) is widespread in sewers and wastewater treatment plants. They generate hydrogen sulphide (H2S) through anaerobic respiration using sulphur compounds as a terminal electron acceptor. H2S apart from causing undesired odour, is also responsible for corrosion in sewerage systems. Approaches in controlling odour and corrosion essentially involve the prevention of sulphide generation by SRBs. With that objective, bacteriophages were investigated for their potential in reducing H2S, using a multidrug resistant (MDR) Salmonella enterica clinical strain as a model SRB in simulated synthetic sewage settings. Two lytic phages specific to S. enterica were isolated from wastewater collected from the effluent treatment plant. The phages phi Ph_Se01 and phi Ph_Se02 possessed different plaque morphology and exhibited a distinct host range. Burst sizes of phi Ph_Se01 and phi Ph_Se02 were estimated to be 42 and 27 phages per infected cell respectively, with a latent period of 10 +/- 5 min. Furthermore, nucleic acid analysis and melt curve profiles confirmed the diversity of these phages. Additionally, quantitative characterisation with regards to their stability in 10% (v/v) chloroform was used to comprehend their tolerance in large scale production. The study successfully demonstrated the application of phi Ph_Se01 and phi Ph_Se02 in the reduction of H2S by 62% and 70% respectively, within 6 h in synthetic sewage compared with the non-phage control. We also investigated the bacteriolytic ability of phi Ph_Se01 and phi Ph_Se02 in reducing the S. enterica by 4-log. This study demonstrates the potential of phage-mediated reduction of H2S and infection in wastewater.

Enteric infection by faecal contamination of drinking water is a major concern in developing nations contributing to the huge burden of malnutrition and infant mortality. We have developed a holistic approach, named as gut to gutter approach, to treat wastewater treatment, by screening potential probiotic strains from staple food sources. The strains could be potentially used for competing out the enteric pathogens in different applications such as food and wastewater treatment. We focused on two strains isolated from rice water (RS) and lemon pickle (T1), identified as Lactobacillus fermentum and characterized for their probiotic and wastewater treatment capabilities. The strains showed many probiotic properties (tolerance to low pH (pH 3), bile salts up to 0.5% and simulated gastric juice at low pH and binding to extracellular matrix molecules, heparin and gelatin. Auto-aggregation of T1 was in the range of 85% and the strain exhibited significant co-aggregating ability with enteric pathogens, Klebsiella pneumoniae, Salmonella enterica and E. coli (MDR) with 48%, 79% and 65% respectively. Both strains had a higher binding affinity to gelatin and heparin, compared to widely claimed “probiotic” Bacillus clausii and the pathogenic E. coli ET. The strains had high galactosidase activities. Further, the cell free supernatant from RS showed BLIS (bacteriocin like inhibitory substance) activity against Klebsiella pneumoniae , Staphylococcus aureus and Salmonella enterica at 60%, 48% and 30% respectively. T1 strains and B. clausii effectively reduced the coliform count by by 90% (1-log) when immobilized in a biofilter to treat wastewater.