Thesis (Bachelor of Science in Biotechnology)

Permanent URI for this collectionhttps://hdl.handle.net/10361/28396

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Open Access
Hierarchical evolution of endosomal trafficking proteins reveals conserved catalytic cores and lineage-specific divergent regulatory layers across eukaryotes
(BRAC University, 2026-04) Suhair, Silmi; Ahmad, Marisha; Kabir, Md Raiyan; Rashid, Md Tawsif Ur; Department of Biotechnology
Membrane trafficking proteins are essential for organelle communication. However, whether different functional classes evolve under distinct evolutionary pressures remains unclear. In order to investigate this, eight protein families (ESCRT-0, ESCRT-I, ESCRT-II, ESCRT-III, Rab GTPases, VPS4, SNAREs and tetraspanins) were taken across Saccharomyces cerevisiae, Arabidopsis thaliana and Homo sapiens. Sequence identity, domain architecture, motif conservation, phylogenetic relationship, structural overlays and intrinsic disorder patterns were inspected to find out which features remain conserved and which are not. The investigation showed a clear hierarchy where the catalytic proteins (Rab GTPases, VPS4) showed high sequence identity, near perfect motif conservation along with strong structural similarity. However, structural proteins (ESCRT-I, II, III and SNAREs) showed moderate conservation with preserved folds despite sequence divergence. And finally the regulatory adaptor proteins (ESCRT-0, tetraspanins) showed the greatest divergence, including missing domains, very low sequence identity, and increased disorder. These results from our investigation led us to believe that conservation in the membrane trafficking systems is not uniform. Rather, it follows a hierarchy in which it offers compensation in the structural and adaptor regions while remaining highly conserved for the catalytic roles.
Open Access
A review of isolation and characterization of heavy metal and antibiotic co-resistant bacteria from tannery effluent
(BRAC University, 2020-10) Sarker, Sujoy; Siddique, Romana; Department of Mathematics and Natural Sciences
The use of heavy metals in the tannery industry for leather processing and discharge of untreated effluents from this industry in the environment is a leading challenge to solve. Hence, micro-organism has a great potential to grow in the presence of toxic substances and it is a novel, cost-effective and eco-friendly approach to remove these heavy metals (Cr, Pb, Cu, Zn) from these contaminated sites and safeguard our environment. Toxic substances are hard to degrade, and microbes develop detoxifying mechanisms to counteract these substances' toxic effects. This article reviews the isolation of the heavy metal resistant bacteria and their ability to co-resistant against the antibiotic. Escherichia coli, Staphylococcus sp., Klebsiella sp., Pseudomonas sp. was identified to resist toxic substances to a minimum inhibitory concentration. In some cases, the same isolates showed co-resistance to multiple heavy metals. All the isolates were also resistant to several antibiotics. My study highlights the organisms' physiological color change in response to any stimuli like heavy metals as the media is incorporated with the heavy metals. Besides, interaction with different toxic compounds is still unclear if these patterns of color change are simply the consequences of heavy metals or any underlying factor or enzyme is responsible for the color transformation.
Open Access
Environmental isolation, characterization & antimicrobial resistance profiling of klebsiella pneumoniae & acinetobacter baumannii from community wastewater in Dhaka: a comparative analysis
(BRAC University, 2026-04) Wazid, Meer Zeshanul; Mannan, Athoy; Haque, Fahim Kabir Monjurul; Department of Mathematics and Natural Sciences
Environmental antimicrobial resistance has become a growing global health concern, where community wastewater plays a critical role in the accumulation, persistence, and distribution of the resistant pathogens. This study focuses on investigating the environmental occurrence, phenotypic and molecular characterization, and antimicrobial resistance profiling of Klebsiella pneumoniae and Acinetobacter baumannii isolated from the community wastewater in multiple areas of Dhaka, Bangladesh, along with emphasizing the presence of potential co-existence of these organisms with associated resistance dynamics. The community wastewater samples were collected from different areas of Dhaka city and processed using culture-based isolation. Afterwards, the phenotypic identification and molecular characterization provided a validated species identification. Importantly, Antimicrobial susceptibility testing (AST) was performed to identify the resistance intensity and potential risk across these isolates. Moreover, 45 isolates of Klebsiella pneumoniae and 41 isolates of Acinetobacter baumannii were isolated and characterized from 32 samples of community wastewater, resulting in the highest co-dominance in the Mohammadpur area of Dhaka with 47.6% Klebsiella pneumoniae and 52.4% Acinetobacter baumannii prevalence. Besides, both organisms were frequently isolated with mixed colonies, indicating their co-existence across all sampling sites. Further, AST of mixed colonies exhibited an extreme resistance with 90% isolates with MAR index 1.0, and more the 90% isolates showed MAR index >0.2, indicating high antibiotic selective pressure in comparison to the resistance profile of Klebsiella pneumoniae and Acinetobacter baumannii, respectively. These findings highlight the Dhaka community wastewater as a high-risk AMR contamination site and co-existing pathogens promoting resistance dissemination and amplification via horizontal gene transfer and biofilm-mediated interactions, suggesting a critical need for integrated environmental surveillance and strategies to control the increasing antimicrobial resistance.
Open Access
Multi-drug resistance patterns in water Escherichia coli: prevalence and co-occurrence associations
(BRAC University, 2026-04) Adib, Adhamul Islam; Nadim, Erina Arowa; Nawar, Fairooz; Rashid, Md Tawsif Ur; Department of Mathematics and Natural Sciences
Antimicrobial resistance (AMR) in the environmental water system is an emerging health issue of concern in the general population, especially in densely populated low and middle-income countries with poor wastewater management systems. This paper has explored the prevalence, diversity, and patterns of co-resistance of multidrug-resistant (MDR) Escherichia coli in three ecologically different urban water bodies in Dhaka, Bangladesh-Hatirjheel, Banasree, and the BRAC University water body during a longitudinal surveillance period of April to December 2025. A total of 150 environmental E. coli isolates were confirmed by biochemical IMViC characterization and colony PCR. The Kirby-Bauer disk diffusion technique was used to measure phenotypic susceptibility using eight clinical-relevant agents that represented the six antibiotic classes: fluoroquinolones, phosphonic acids, tetracyclines, beta-lactams, cephalosporins, and macrolides. Breakpoint interpretation was done in accordance with CLSI thresholds. Statistical analyses including- K-means clustering, Principal Component Analysis (PCA), Chi-square testing, Mann-Whitney U testing, and co-occurrence network analysis were conducted in R (version 4.3.1). The overall resistance burden was high: six out of eight antibiotics had resistance rates over 80% in all isolates. PCA indicated a strong spatial variation among sampling locations with the first two principal components having a cumulative (59%) total resistance variance. A statistically significant difference in the prevalence of resistance between broad-spectrum and narrow-spectrum antibiotics was seen at population level but not at isolate level (chi-square = 7.533, p =.006), which agrees with a generalized MDR phenotype. Co-occurrence network analysis revealed that there were two statistically significant pairwise co-resistance relationships; levofloxacin-azithromycin (0.473, p = 0.002), indicating possible cross-class resistance involving efflux pumps, and piperacillin-tazobactam-cefepime (0.452, p< 0.00). Inter-site comparison revealed that MDR was most prevalent in the BRAC University site followed by Banasree and finally, Hatirjheel. These results confirm the hypothesis that urban water bodies in Dhaka support high populations of MDR E. coli that is the result of multi-mechanistic resistance co-selection. The findings highlight the importance of the combination of environmental AMR surveillance, molecular characterization of resistance determinants, and evidence-based wastewater management policy in a One Health framework.
Open Access
A comparative analysis of expanded quantitative urine culture and standard urine culture methods in patients with urinary tract infections
(BRAC University, 2026-01) Srabony, Tajri Hasan; Kunder, Stella Bijoyee; Shafi, K M Abdullah Hel; Deen, Nadia Sultana; Department of Mathematics and Natural Sciences
Urinary tract infections (UTI) are one of the most common bacterial infections of humans. Accurate diagnosis of the cause of UTI is necessary for effective treatment. Even though clinically Standard Urine Culture (SUC) is common for detecting bacterial presence in urine samples, latest reports show that Expanded Quantitative Urine Culture (EQUC) provides better diagnostic sensitivity compared to SUC. To test this, SUC and EQUC methods were compared to analyse bacterial load and diversity using urine samples collected from 20 patients with UTI symptoms and 20 healthy controls in this study. Samples were diluted and inoculated on nutrient agar, HiChrome UTI agar, MacConkey agar and blood agar for SUC method, then incubated at 37°C for 24 hours under aerobic conditions. On the other hand, for EQUC, in addition to all the media, chocolate agar was used with different conditions like carbon-enriched, anaerobic environment with incubation at 37°C for 48 hours. Colony characteristics and polymerase chain reaction (PCR) were performed for bacterial detection. Antibiotic susceptibility test was conducted by the Kirby-Baur method. On nutrient agar medium, EQUC yielded 5-fold higher bacteria than SUC and portrayed higher bacterial diversity. While several bacterial species for example, klebsiella spp., Staphylococcus aureus, and Pseudomonas aeruginosa was detected by SUC and EQUC based on colony characteristics, EQUC exclusively detected the presence of Staphylococcus haemolyticus. Seventy-five percent of presumptive Klebsiella and 73.3% of presumptive E. coli were confirmed by PCR. AST was performed on E. coli and Klebsiella. Notably, bacteria grown via EQUC showed a diverse resistance pattern compared to SUC. Further molecular diagnoses will be performed to validate these findings.
Open Access
Comparative analysis of urinary microbiome diversity in diabetic patients with and without suspected UTI
(BRAC University, 2025-10) Chowdhury, Zannat; Imran, Birdil; Haque, Munima; Tawsif Ur Rashid, Md; Turja, Subarno Hossain; Department of Mathematics and Natural Sciences
Urinary tract infections (UTIs) represent one of the most common bacterial infections worldwide, imposing a considerable global health and economic burden. According to Hu et al. (2025), the incidence of UTIs among older women increased by 132% between 1990 and 2021, rising from 15.87 million to 36.77 million cases. In 2019 alone, UTIs accounted for approximately 404.61 million cases and 236,790 deaths globally. In light of these alarming trends, this study aims to address key gaps in microbial characterization of UTIs among diabetic patients. A cross-sectional survey was conducted involving both inpatient and outpatient participants, categorized into two groups: Group 1 (No UTI; patients with no clinical evidence of infection), and Group 2 (Suspected UTI; patients presenting clinical signs or symptoms suggestive of a UTI but not yet confirmed). The findings of this study provide compelling evidence that the clinical state of a suspected UTI in diabetic patients is defined by a profound ecological shift in the urinary microbiome, underscoring the complex interplay between host metabolic state and microbial community dynamics.
Detection of carbapenemase gene from multidrug-resistant Pseudomonas aeruginosa isolated from hospital sewage waste water and adjacent community tap water
(BRAC University, 2023-01) Islam, Anika Aysha; Jothee, Shagufa Ali; Ahmed, Akash; Department of Mathematics and Natural Sciences
Introduction: Hospital wastewater is a prime breeding ground for antibiotic-resistant pathogenic microorganisms. The goal of our study is to explore the multi drug resistance pattern of Pseudomonas aeruginosa discovered in both hospital and community water to anticipate how our routine commutes are being exposed. Methods: A total of 33 non-duplicate isolates of Pseudomonas aeruginosa were obtained from both the hospital and the surrounding community tap water. Initially, phenotype technique was used to identify multi-drug-resistant isolates. Antimicrobial susceptibility was detected by using the Kirby disk diffusion method. Each isolate was tested resistance to carbapenem, aminoglycosides, fluoroquinolones, lipopeptide, macrolides, beta-lactam combination agents, penicillin, and monobactam. The presence of the Metallo-beta-lactamase (MBLS) and Extended spectrum β-lactamase (ESBL) gene was determined using the traditional PCR method. Result: Out of 33 isolates collected from hospital wastewater and community water show a comparable antimicrobial-susceptibility pattern against the stated antibiotic classes. Only 15 were selected for further antimicrobial-susceptibility test against the stated antibiotic classes. Isolates found resistant to Amikacin (26.6%), Amoxyclav (93.3%), Azithromycin (100%), Aztreonam (66.6%), Cefepime (20%), Ceftazidime (20%), Ceftriaxone (53.3%), Chloramphenicol (55.5%), Ciprofloxacin (33.3%), Colistin (26.6%), Erythromycin (93.3%), Gentamicin (26.6%), Imipenem (20%), Norfloxacin (40%), Piperacillin-tazobactam (26.6%), Polymyxin (13.3%) and Tetracycline (46.6%). On the contrary, 4 isolates obtained from both Hospital waste water and adjacent Community Tap water showed resistance to most of the mentioned antibiotics. Those isolates were tested positive for the presence of bla-NDM, NDM- 1, bla-CTX-M, bla-OXA 48 and bla-TEM by PCR as, confirming the existence of a gene encoding extended spectrum beta-lactamase and MBL. Conclusion: The result of this study provided insights into the high proportion of NDM-1, OXA-48, CTX-M and TEM producers concluding that Hospital wastes have an impact on the emergence of new diseases by transmitting multidrug-resistant microorganisms to nearby areas, exposing the general population to antibiotic resistance at an early stage and making them resistant to any treatments.
Open Access
Comparative analysis of plasmid presence and antibiotic resistance profiles in water samples with a focus on Dhaka City's water bodies (Dhanmondi & Gulshan Lake)
(BRAC University, 12/18/2025) Progga, Addrota Khan; Ahmed, Subhat Sumaila; Rahman, Tazkia; Naser, Iftekhar Bin; Department of Mathematics and Natural Sciences
Antimicrobial resistance (AMR) is a growing global public health concern, with environmental reservoirs contributing significantly to the spread of antibiotic-resistant bacteria. Urban surface water bodies in densely populated cities are recognized as important hotspots due to continuous exposure to domestic, medical, and industrial waste. In Dhaka, Bangladesh, rapid urbanization and inadequate wastewater management have intensified this problem. This study comparatively analyzed the antibiotic resistance profiles and plasmid presence of Escherichia coli, Salmonella spp., and Vibrio cholerae isolated from water samples collected from Dhanmondi Lake and Gulshan Lake. Samples were processed using selective culture methods, followed by molecular confirmation through polymerase chain reaction (PCR). Antibiotic susceptibility testing was conducted using the Kirby–Bauer disk diffusion method, and plasmid DNA isolation was performed to assess the potential role of plasmids in resistance dissemination. Results indicated a high prevalence of antibiotic-resistant isolates in both lakes, with several strains exhibiting multidrug resistance. Differences in resistance patterns between the two sites suggest variation in environmental contamination pressures. A substantial proportion of isolates carried plasmids, highlighting the potential contribution of horizontal gene transfer to environmental AMR spread. These findings underscore the role of urban water bodies as reservoirs of antibiotic-resistant bacteria and resistance-associated plasmids, emphasizing the need for continuous monitoring and improved waste management strategies in rapidly urbanizing regions.
Open Access
Correlation between plasmid presence & antibiotic resistance: in enteric bacteria; isolated from different water bodies inside Dhaka City
(BRAC University, 2/19/2026) Tabassum, Tasnim; Sarker, Aurchi; Asha, Kamrun Nahar; Naser, Iftekhar Bin; Department of Mathematics and Natural Sciences
Antimicrobial resistance (AMR) is an endemic issue of public health in the world, and there is increasing evidence that surface water bodies are significant environmental reservoirs of antibiotic-resistant bacteria. This study has analyzed the relationship between the occurrence of plasmids and antibiotic resistance in the pathogenic enteric bacteria that develop in surface water sources in Dhaka Metropolitan City. To identify the contribution of anthropogenic interference to the waters of three urban water bodies, namely, Hatirjheel, Curzon Hall, and Ramna Lake, water samples were taken from January to June 2025, and with varying degrees of anthropogenic impact. Three clinically and ecologically important bacteria, i. e. Escherichia coli, Salmonella spp., and Vibrio cholerae, were the subject of the investigation. The selective and differential media (EMB, TCBS, and SS agar) were used to perform isolation, and antibiotic susceptibility testing was conducted to identify the profiles of resistance. Molecular validation was done by polymerase chain reaction (PCR) and plasmid isolation done to assess genetic basis of resistance. PCR amplicons and plasmid DNA were analyzed utilizing agarose gel electrophoresis, which allowed performing the correlation analysis between the plasmid carriage and the observed resistance patterns. The results showed that the prevalence of PCR-confirmed antibiotic-resisting isolates and plasmid-bearing isolates were very high in Hatirjheel and then in Ramna Lake, but relatively low in Curzon Hall. There was a close correlation existing between the presence of plasmids and the presence of multidrug resistance thereby highlighting the importance of plasmid-mediated horizontal gene transfer in water.
Open Access
Assessment of sleep quality in women with endometriosis in Bangladesh
(BRAC University, 2026-01) Marzan, Mubashira; Muztoba, Muhammad; Haque, Munima; Department of Mathematics and Natural Sciences
Endometriosis is a chronic gynecological condition affecting approximately 10% of women of reproductive age worldwide. Emerging evidence suggests a strong correlation between endometriosis and poor sleep quality, which can significantly impact a patient’s overall health and well-being. However, no such studies have been conducted in Bangladesh. This research addresses a critical gap by exploring sleep quality in Bangladeshi women diagnosed with endometriosis. A cross-sectional descriptive study was conducted from June 2024 to October 2025 at Kurmitola General Hospital in Dhaka, Bangladesh. A total of 401 reproductive-aged women (15–45 years), among whom 201 were clinically diagnosed with endometriosis and confirmed by ultrasonography or laparoscopy, were recruited based on availability. Data were gathered using a structured questionnaire developed in consultation with three gynecologists, including demographic details, clinical symptoms, and the Pittsburgh Sleep Quality Index (PSQI). Data analysis was performed using SPSS version 27, employing independent t-tests, Chi-square tests, and, with a P-value < .05, considered statistically significant. Based on the data, a significant number of women with endometriosis experience poor sleep quality. The mean global PSQI (Pittsburgh Sleep Quality Index) score indicated an overall poor sleep quality. Specific areas affected include increased sleep latency (mean = 2.06 ± 1.03) and reduced sleep duration and efficiency. Moreover, symptoms such as dyspareunia, dysmenorrhea, excessive bleeding, and pelvic pain were significantly associated with poor sleep quality. These findings suggest a strong link between endometriosis-related symptoms and impaired sleep, highlighting the importance of addressing sleep disturbances in the clinical management of endometriosis.
Open Access
Combined effects of vitamin C & food-derived ingredients against multidrug-resistant Staphylococcus aureus and Pseudomonas aeruginosa
(BRAC University, 2025-12) Homa, Khadiza Tul; Akhtar, Nusrat; Jaba, Jabonnahar; Hossain, Mohammed Mahboob; Department of Mathematics and Natural Sciences
The growing interest in food-derived antimicrobial therapy is driven by the expectation that natural compounds with antibacterial properties might serve as adjunctive strategies against antimicrobial resistance. This study examined whether common food-derived compounds can modify the activity of ciprofloxacin against multidrug-resistant Staphylococcus aureus and Pseudomonas aeruginosa, both listed in the 2024 WHO Bacterial Priority Pathogens List. Vitamin C, turmeric, black seed, garlic, gallic acid and vanillin were prepared as 2 g/10 ml stocks and tested by disc diffusion at 5–15 μl per disc, giving total loads of roughly 300–3000 μg of natural compound. Ciprofloxacin (30 μg per disc) was used as the antibiotic control. On their own, the food-derived agents showed little or no inhibition at doses comparable to normal intake, and clear zones appeared only when vitamin C, gallic acid or vanillin were pushed into the upper hundreds of micrograms per disc. Ciprofloxacin was then combined with vitamin C plus either gallic acid or vanillin at stock ratios of 4:6, 3:7 and 2:0, keeping the ciprofloxacin dose at 30 μg while varying the total phenolic load between about 300 and 3000 μg per disc. In S. aureus, several gallic-acid–vitamin-C mixtures at 4:6 and 3:7 gave zones up to about 40 mm, compared with 37–38 mm for ciprofloxacin alone, indicating a modest synergistic effect. In contrast, vanillin-rich mixtures and many P. aeruginosa combinations produced smaller zones, around 25–30 mm where the ciprofloxacin control was 37–39 mm, consistent with antagonism. Some intermediate ratios were essentially indifferent. Overall, vitamin C and food-derived phenolics showed both synergistic and antagonistic interactions with ciprofloxacin, depending on dose and ratio, highlighting the need for careful optimisation before considering such combinations as antimicrobial adjuvants. Although the study is limited to an in vitro model, the results underscore the importance of further evaluating how antioxidant-rich supplements and dietary phenolics may enhance or complement antibiotic function. These observations support continued investigation in mammalian cell lines and in vivo systems to clarify their safety, pharmacokinetic behavior, and potential clinical benefits when used alongside conventional antibiotic therapy.
Open Access
An integrative analysis of ctDNA fragmentomics and methylation across breast cancer subtypes to identify subtype-specific prognostic biomarkers
(BRAC University, 2025-12) Raida, Ruhin Rahman; Kaniz, Nafisa; Ferdaus, Tarunima; Shishir, Tushar Ahmed; Department of Mathematics and Natural Sciences
In cancer patients, a substantial fraction of cell-free DNA (cfDNA), derived from tumor cells, offers a non-invasive opportunity to interrogate tumor biology. This study aimed to extract, profile and identify unique fragmentation and methylation patterns in four different breast cancer subtypes (HER2+, Luminal B, Triple Negative Breast Cancer, Triple Positive Breast Cancer) compared to healthy controls. Furthermore, it utilizes the fragmentation feature profiles along with epigenetic analysis to evaluate their potential for subtype -specific detection. Public cfDNA sequencing datasets from healthy controls and four types of breast cancer subtypes cases were retrieved from the NCBI SRA repository. Fragmentation features including Fragment Size Distribution (FSD), Fragmentation Size Ratio (FSR), Fragmentation Size Coverage (FSC), BreakPoint Motif (BPM), End Motif (EDM), Copy Number Variation (CNV) and epigenetics profiles like methylation profiles were searched using a python based workflow and downstream analyzed in R. Our findings indicated subtype specific distinctions in TNBC and TPBC, where notable differences in fragmentation and methylation patterns were observed when compared with controls and other subtypes. Among the fragmentomic features evaluated, Fragment Size Ratio showed noticeable difference for TPBC and TNBC but did not demonstrate the same level of distinction for LB or HER2+. In methylation, end motif and breakpoint motif analyses, observable patterns were also more prominent in TNBC and TPBC, while clear differentiation was not consistently evident for LB and HER2+ within this dataset. The integrated analysis of cfDNA hypermethylation and fragmentomic features reveal distinct fragmentation signatures in TPBC and TNBC, emphasizing the potential of cfDNA-based assays for precise, non-invasive molecular subtyping and the development of liquid biopsy strategies for early detection and disease monitoring.
Open Access
CRISPR-Cas systems in antiviral and antimicrobial defence: recent advances, challenges, and biodefense implications
(BRAC University, 2025-10) Tarique, Mubarrat Tazwar Bin; Shishir, Tushar Ahmed; Department of Mathematics and Natural Sciences
CRISPR–Cas systems have evolved from a bacterial immune mechanism into a versatile platform for precision medicine and molecular diagnostics. This review synthesizes design principles and failure modes for three main application areas: (i) antivirals, where conservation-aware, multiplexed guides and delivery methods (AAV, LNP, or RNA RNP) are crucial for sustained suppression; (ii) precision antimicrobials, which allow for strain-specific killing or genetic disarming (chromosomal cuts, plasmid curing, CRISPRi) with minimal impact on commensal microbes; and (iii) Cas12/Cas13 diagnostics, promoting rapid, contamination-controlled, sample-to-answer workflows. In various use cases, we focus on specificity mapping (GUIDE-seq/CIRCLE-seq and related assays), escape management (including multiplexing, ortholog switching, and Acr awareness), and governance practices (such as assay hygiene, data provenance, and biosafety). We also address delivery challenges, matrix effects, and surveillance-driven retargeting as key factors influencing success. The aim is to create a playbook that guides choices of effectors, guide design and validation, delivery routes, and quality control measures, enabling the translation of programs from research to real-world deployment.
Open Access
Isolation and characterization of bacteriophage targeting multidrug-resistant Klebsiella pneumoniae from wastewater
(BRAC University, 2025-10) Nashita, Syeda Nowshin; Mushtari, Tasnia; Hossain, M. Mahboob; Department of Mathematics and Natural Sciences
The emergence of multidrug-resistant Klebsiella pneumoniae has become a major global concern due to its rapid dissemination and limited treatment options. This study aimed to isolate and characterize bacteriophages from wastewater samples targeting MDR K. pneumoniae. Blue colonies on HiCrome KPC agar indicated carbapenemase-producing isolates. Six distinct lytic phages were recovered using the double-layer agar method, and among them, phage 1.3B exhibited the most stable and consistent lytic profile. The phage was tested for stability across various NaCl concentrations (0.5–5%), demonstrating optimal activity at 0.9% salinity. PCR confirmed the presence of resistance-associated genes, including blaNDM, and blaTEM and virulent gene iroB. These findings highlight the potential of naturally occurring phages as alternative biocontrol agents against MDR K. pneumoniae and provide a foundation for further genomic and therapeutic evaluation.
Open Access
Phytochemical profiling, antioxidant potential, and antimicrobial assessment of the essential oil extracted from Moringa oleifera
(BRAC University, 2025-11) Amir, Nafisa; Kabir, Tasnim; Opsory, Munia Haque; Nafisa, Nusrat Jahan; Turna, Noorjahan Islam; Hossain, Mohammed Mahboob; Department of Mathematics and Natural Sciences
Since antibiotic resistance is still on the rise, the search for safe plant-based bioactives keeps growing in importance. The "Miracle Tree," Moringa oleifera, also has immense potential since it contains a vast pool of compounds and is also said to be capable of curing a vast pool of diseases as well. Phytochemical content, antioxidant activity, and antibacterial activity of Moringa oleifera leaf extracts in ethanol, ethyl acetate, and chloroform solvents were investigated comprehensively in this study. Four fractions: crude ethanol, non-partitioned ethyl acetate, organic chloroform, and aqueous chloroform, were subjected to Thin Layer Chromatography (TLC), DPPH antioxidant assay, and Kirby-Bauer antibacterial test. Thin Layer Chromatography (TLC) of Moringa oleifera leaf extracts exhibited solvent-dependent variation in bioactive compound profiles. The most compositionally rich was ethanol extract, with several flavonoid bands (Rf ≈ 0.55–0.93), alkaloid bands (Rf ≈ 0.51–0.88), anthraquinone bands (Rf ≈ 0.57–0.64), phenolics, and proteins, showing efficient extraction of mid-polar and polar compounds. Moderate alkaloids, flavonoids, and anthraquinones bands (Rf ≈ 0.24–0.75) were shown by the organic chloroform fraction, while the ethyl acetate extract showed weak bands of phenolics and alkaloids (Rf ≈ 0.78–0.93). No bands were seen by aqueous chloroform extract, showing low yield of phytochemicals. Overall, ethanol was the most suitable solvent since it had extracted the broadest range of bioactive compounds for the antimicrobial and antioxidant activity of Moringa oleifera leaves. DPPH assay for antioxidant assay showed that extracts had dose-dependent radical scavenging activity. Ethanol extract was superior, with an IC₅₀ value of 56.54 μg/mL. Ethyl acetate, aqueous chloroform, and organic chloroform extracts were inferior with IC₅₀ values 159.40 μg/mL, 300.52 μg/mL, and 580.25 μg/mL, respectively. 5 Compared to the control ascorbic acid (IC₅₀ = 6.1–10.47 μg/mL), the ethanol extract was around 5–9-fold lower. Yet it was greater than 90% scavenging activity at 1000 μg/mL and therefore was highly active against antioxidants owing to the presence of flavonoids and phenolics. No zone of inhibition was found in well diffusion and disk diffusion antibacterial activity against Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Klebsiella pneumoniae, Salmonella typhi, Shigella flexneri, Vibrio cholerae, and Enterococcus faecalis. Inhibition of activity because of small quantity of the extract (30 mg/disc), inability of lipophilic molecules to diffuse via agar, and ultimate break-down of heat labile molecules. Moringa oleifera leaf extracts, particularly the ethanol fraction, were rich in phytochemicals and showed vigorous antioxidant activity with poor antibacterial inhibition under the assay conditions. The research highlights the solvent polarity as a driving force for phytochemical recovery and antioxidant activity and as a foundation for its future optimization and for improved nano-formulation approaches to antimicrobial delivery.
Open Access
Isolation and characterization of Rhizobia isolates from Glycine max
(BRAC University, 2025-10) Rahman, Tahira Sifawa; Noor, Nafisa; Choudhury, Areana Sarwat; Chowdhury, Jebunnesa; Department of Mathematics and Natural Sciences
The soybean plant (Glycine max), gradually gaining popularity as a cash crop in Bangladesh, plays a crucial role in the country's agriculture. However, intensive chemical fertilizers are used in its cultivation each year. The symbiotic relationship of soybean with rhizobia bacteria is vital for biological nitrogen fixation, where rhizobia converts atmospheric nitrogen into a form that plants can absorb and utilize. The identification of beneficial nitrogen-fixing rhizobia specific to the host can allow growers to select the right inoculum, which can increase yield and reduce usage of chemical fertilizers. The objective of this research was to identify and isolate nodule forming rhizobial strains, analyze their diversity, and characteristics. 30 nodule-associated bacteria were isolated from 8 Soybean plants. The isolates were classified based on their nodule formation capacities in the nitrogen free Jensen’s media (Sucrose 20 g/L, Dipotassium phosphate 1g/L, Magnesium sulphate 0.5g/L, Sodium chloride 0.5 g/L, Ferrous sulphate 0.1 g/L, Sodium molybdate 0.005 g/L, Calcium carbonate 2g/L and agar 15 g/L).via an in-vitro infection test. A series of biochemical tests such as Glucose Peptone Agar test, Bromothymol Blue test, Nitrate Reduction, Oxidase, Catalase and Urease tests were performed. Additionally, stress tests were performed by observing growth of the isolates in a range of pH and salt concentrations. Among the isolates some were found to successfully nodulate the soybean plants in-vitro. During the infection test, significant effects of rhizobial strain in the growth of plants’ lateral and tap roots, shoot is observed among the nodulating and non-nodulating plants. The rhizobia spp. was identified as stress-tolerant, slow-growing rhizobia spp. with capacity to withstand extreme low pH and salinity. All isolates were found to be positive for oxidase and nitrate reduction tests, and the majority were positive for urease tests as well. Moreover, the isolates were found to be capable of withstanding up to 6% NaCl. They could also withstand lower pH up to 4, making them ideal for commercial inoculum development in coastal regions and highly acidic soil.
Open Access
Isolation and characterization of heavy metal (lead) resistant bacteria for bioremediation of industrial wastewater
(BRAC University, 2025-09) Muhammad, Nazif; Tabib, Hasan Mostafiz; Saha, Prome; Hossain, Mahboob; Department of Mathematics and Natural Sciences
Lead pollution in industrial wastewater poses an important environmental and health crisis due to its toxicity and persistence. To address this issue, two soil samples were collected from two lead-contaminated industrial zones in Bangladesh, an automobile workshop situated in Mohakhali, Dhaka and an old battery factory area in Comilla. Atomic Absorption Spectroscopy confirmed elevated levels of lead (Pb) (42.6 ppm and 61.5 ppm respectively). Metagenomic analysis of soil samples by bacterial 16s rDNA sequencing revealed diverse microbial populations, dominated by Pseudomonadati and Bacillati phylum, suggesting adaptation to heavy metal stress in natural settings. AAS of the cell free supernatants from isolated bacteria demonstrated remarkable bioremediation efficiency, removing approximately 97% and 95% of lead from 100 ppm lead-supplemented solution. Further analysis by 16S rDNA sequencing of the isolated bacterial strain L1 and L2, revealed morphological adaptations under lead stress and identified both isolates as Priestia spp.
Open Access
The human gut virome at the crossroads of immunity, disease and therapeutics: a comprehensive review
(BRAC University, 2025-08) Zaman, Taasfia Binte; Haque, Munima; Department of Mathematics and Natural Sciences
The human gut virome, a complex and dynamic part of the gut microbiome, is an important but understudied mediator of health and disease. Encompassing bacteriophages, eukaryotic viruses, and endogenous viral elements, the gut virome is intricately linked to bacteriome, immune, and host metabolic systems, which impacts the development of diseases including inflammatory bowel disease (IBD) and metabolic diseases, and even neuropsychiatric and autoimmune diseases. The development of metagenomic sequencing techniques over the past few years has brought to light the high degree of interindividual variability of the virome, as well as its rapid response to environmental factors such as diet and antibiotics, and its age-dependent evolution. Dysbiosis in viral communities—characterized by changes in activity of temperate phages, reductions in viral diversity, or expansion of pathogenic viruses—are associated with mucosal inflammation, microbial dysbiosis, and systemic disease. Novel treatments under development, including fecal virome transplantation (FVT) and targeted phage therapy, demonstrate the potential of the virome in re-establishing microbial balance and combatting antibiotic resistant infections. Yet, obstacles exist in organizing virome characterization, determining causal associations, and guaranteeing safety of viral-based treatment modalities. The focus of this review is to integrate current insights into the diversity and stability, as well as functional attributes of the gut virome, while stressing its reciprocal relationships with host immunity and disease development. It investigates the virome in other settings, such as inflammatory bowel disease (IBD), type 1 and type 2 diabetes, obesity, liver diseases, arthritis and neuropsychiatric conditions, and how diet, stress and geography influence viral ecology. By combining multi-omics strategies with the personalized aspect of the virome, new biomarkers and precision therapies could be discovered in the future. This study highlights the virome as an important frontier in microbiome research with potentially transformative implications for diagnostics, therapeutics, and preventive medicine in the context of personalized health.
Open Access
Cationic thiazine and azo dye along with petroleum hydrocarbon microbial degradation and assessment of physiochemical and radionuclides parameters of targeted point source (water)
(BRAC University, 2025-08) Mahi, Md. Moniruzzaman; Haque, Munima; Department of Mathematics and Natural Sciences
Background: Water pollution remains a critical environmental and public health issue in Bangladesh, particularly in Dhaka and its surrounding areas. The continuous discharge of untreated sewage, industrial effluents, and chemical wastes has led to the deterioration of aquatic ecosystems, contributing to the emergence of fish and human diseases. Regular monitoring is essential to assess the extent of pollution, track microbial adaptation, and detect potential outbreaks of novel pathogens. Method: Water samples were systematically collected from multiple locations and transported at 4°C to preserve microbial integrity. Selective and differential media were employed to isolate bacteria resistant to hydrocarbons (petrol, kerosene) and azo dyes. Enrichment cultures in Bushnell-Haas broth, supplemented with pollutants as carbon sources and ammonium nitrate as a nitrogen source, facilitated the degradation process over seven days. Gas chromatography was utilized to analyze the breakdown of hydrocarbon pollutants. Molecular identification of isolates was performed using 16S rDNA gene sequencing. For heavy metal and radionuclide analysis, samples were acidified and analyzed using Atomic Absorption Spectroscopy (AAS) for metal quantification, while High-Purity Germanium (HPGe) detectors were used for radionuclide profiling. Results: Radionuclide analysis of surface and groundwater samples from Dhaka showed Th- 232, Ra-226, and K-40 levels within safe limits, indicating no significant radiological risk. Molecular characterization identified Pseudomonas aeruginosa with notable hydrocarbondegrading abilities. Gas chromatography confirmed biodegradation of hydrocarbons like toluene, naphthalene, and hexadecane. However, AAS detected Pb toxic heavy metal exceeding permissible limits in Signboard River and Shitalakha River, indicating localized heavy metal pollution. Conclusions: Overall, the combined microbial and chemical analyses underscore the natural bioremediation potential of indigenous microbes in mitigating hydrocarbon and azo dye pollution in the aquatic environment of Dhaka and its surroundings.
Open Access
Prevalence of psoriasis among the patients in Dhaka and Chittagong and comparison of cytokine profiling and association of gut microbiota
(BRAC University, 2025-09) Saha, Ranita; Marjan, Tufatun Nur; Sarwar, Shaneen Nayat; Haque, Munima; Department of Mathematics and Natural Sciences
Psoriasis is a non-contagious skin inflammatory condition characterized by erythematous, silvery scaling and itchy plaques which are seen commonly on regions of elbow and knee with bleeding spots at scraped off parts. The early explanatory models of psoriasis pointed to genetic and environmental factors as being able to explain the pathogenesis of the disease especially in familial predisposition or environmental exposures. This research aims to find a multi-dimensional insight of psoriasis to focus on the interaction between immune-transducing molecules, the dynamics of intestinal microbiome and environmental contextual factors which will further help in enhancing global awareness of the disease and covering information gaps. According to the current evidence, constant inflammation is caused mostly by immunological dysregulation. Interleukin-17 (IL-17) has become the subject of interest to many researchers as it mediates critical immune signaling by influencing the activation process of keratinocytes and recruits immune effectors to the dermal surface to fuel the development of plaque and incite inflammation. IL-6 is locally and systemically active and promotes differentiation of Th17 lineage and upregulation of pathways mediated by IL-17. The gut microbiome further alters cutaneous health through the skin-gut axis. Preliminary findings from our research suggests an association between changes in the gastrointestinal microbial community (both temporary and chronic) and intestinal hyperpermeability, blunted immune stimulation, and systemic inflammatory diseases, which can either aggravate or trigger psoriasis. To detect the mechanism, serum cytokines levels were quantified by ELISA, whereas to detect the presence of Helicobacter pylori PCR was done for genomic DNA after isolating from human stool samples. These insights can be used to raise the awareness of its complexity and provide future approaches towards diagnosis and therapeutic intervention.

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