Applied
Microbiology &
Food Technology
The Department of Applied Microbiology and Food Technology has always been inspired by the incredible diversity of Nepal—its ecosystems, cultures, and food traditions. While our earlier work focused on isolating and studying actinomycetes from higher altitudes and extreme environments, this continues to be a key area of research, complementing our newer initiatives.
Our ongoing projects emphasize food and cultural diversity, particularly the microbial communities in traditional fermented Nepali foods and livestock milk. We are studying lactic acid bacteria (LAB) strains isolated from a variety of fermented foods, such as gundruk, a staple Nepali fermented vegetable product, and from milk samples collected from various altitudes across Nepal. These efforts aim to uncover microbial strains with potential applications in health, nutrition, and sustainable food production. By understanding the microbial composition of these foods and dairy products, we hope to enhance their quality and safety while exploring possibilities for probiotics and functional food development.
Another focus of the department has been water microbiology. Since 2023, we have been collaborating with the University of Illinois at Chicago to study microbial communities in river water samples across Kathmandu. This research specifically evaluates methods for preserving and detecting microbial DNA in surface water samples during international transport without refrigeration and also involves comparing DNA-based results with traditional culture methods. In parallel, we are also collaborating with Phutung Research Institute in their research on developing innovative technology for detecting water contamination in real time.
Isolation and molecular identification of actinomycetes and other virulent strains from higher altitude regions of Nepal are under progress in the department. Characterization of compounds like antibiotics, toxins from these species and identification of pharmaceutically important compounds for drug development are areas of research in the future.
To explore novel soil Streptomyces in Nepal in pursuit of potential antibiotics using Biochemical and Molecular Methods.
The World Academy of Sciences (TWAS), Italy
Link: http://twas.ictp.it/
Numerous microbial natural products have been discovered and used as therapeutics for the treatment of human infections. Nevertheless, due to the growing prevalence of superbugs that have developed resistance to most of the current antibiotics, there is an urgent need for new drugs with new mechanisms of actions to combat these multidrug-resistant superbugs. Streptomyces represent the largest antibiotic-producing strains in the microbial world which produce antibacterial, antifungal, antiviral and antiparasitic drugs, and a wide variety of other therapeutic compounds, such as antitumor, anti-hypertensive and immunosuppressant drugs. Despite extensive screening of secondary metabolites from Streptomyces, only a small fraction of bioactive compounds has been discovered. The urgent demand for new antimicrobial drugs due to the increasing threat of drug resistance, concomitant with decreasing research and development of new antibiotics by pharmaceutical industry have enforced us to investigate the untapped natural product sources such as indigenous Streptomyces from so far unexplored habitats of Nepal. Thus, we undertook the present study with an aim to identify and characterize Streptomyces strains from different parts of Nepal and to evaluate their antibiotic producing potentials.
During primary screening, 61 different soil-dwelling Streptomyces were isolated. Among them, 38 Streptomyces isolates exhibited various degrees of antimicrobial activities against Staphylococcus aureus, Bacillus subtilis, Enterbacter spp. and Klebsiella pneumonia. Microscopic observations of submerged cultures showed that these strains form an extensively branched substrate mycelium. In addition, scanning electron microscopy of some of the isolates (Streptomyces_S1A, Streptomyces_S5A, Streptomyces_1.6_A2, Streptomyces_ILLM2 and Streptomyces_1.2_P3) revealed that mycelia were well-developed without fragmentation and spores were oval, smooth and non-motile. The genus of the isolates was further confirmed at genetic level. A confirmatory identification to some of the Streptomyces isolates (Streptomyces_S1A, Streptomyces_S5A, Streptomyces_1.6_A2, Streptomyces_ILLM2 and Streptomyces_1.2_P3) was done by 16S rDNA gene sequencing followed by phylogenetic tree construction. 16S rDNA gene sequences of selected strains exhibited ~ 99 % similarity with the reported Streptomyces 16S rDNA gene sequences in the gene bank and phylogenetic analysis based on 16S rDNA gene sequences revealed that these strains form distinct, but related, phyletic lines in the Streptomyces 16S rDNA gene tree. The results obtained from our study demonstrated that the soil habitats of Nepal are rich sources of bioactive Streptomyces. We speculate that further comprehensive taxonomic studies would definitely lead to the discovery of novel Streptomyces strains.
Investigation of pathogenic bacteria and their biofilm composition in the oral cavity of Nepalese population from different geographic locations and analysis of its impacts on distribution, genetic variation, and pathogenic potential.
The World Academy of Sciences (TWAS), Italy
Link: http://twas.ictp.it/
Poor oral cavity hygiene is the major cause of many dental related health issues. In order to develop efficient oral cavity cleaning products, there should be enough scientific information about the oral microbial diversity in biofilm and its chemical composition. Such scientific data is not available here for the Nepalese population. Due to various geographic variations and multiple ethnic populations with multiple cultures and living customs, different oral microbial composition must be obtained. A comprehensive study encompassed the collection of 153 samples derived from oral patients across 17 diverse locations throughout Nepal. The assortment of samples included extracted teeth, dental plaque, and dental calculus, procured from dental clinics, dental hospitals, and dental camps. Employing six distinct culture media, namely nutrient agar (NA), Muller Hilton agar (MHA), mannitol salt agar (MSA), blood agar (BA), brain heart infusion agar (BHA), and potato dextrose agar (PDA) for potential fungal strains, plates were meticulously incubated at 37°C for 5-7 days. The ensuing bacterial colonies were judiciously isolated, and their morphological and biochemical traits were scrutinized. The microscopic structures of the bacterial cells were examined, considering shape, size, colour, opacity, and texture. Gram-staining was employed, and each colony’s biochemical attributes were assessed for protease, pectinase, cellulase, and lipase enzymes. From the 1200 colonies isolated from dental samples, 300 diverse colonies, distinguished by morphological and biochemical characteristics, were chosen for further taxonomic identification. Subsequent sequencing revealed the identification of 60 distinct species within 21 genera of bacterial isolates, including Achromobacter, Bacillus, Chryseobacterium, Citrobacter, Curtobacterium, Enterobacter, Enterococcus, Escherichia, Flavobacterium, Klebsiella, Kocuria, Lyinibacillus, Novosphingobium, Ochrobactrum, Proteus, Pseudomonas, Sporosarcina, Staphylococcus, Stenotrophomonas, Serratia and Streptococcus. The research underscored the presence of various pathogenic bacterial species in oral samples.
Investigation of beta-galactosidase and galacto-oligosaccharides production from cheese whey by lactic acid bacteria isolated from different dairy products of Nepal.
The World Academy of Sciences (TWAS), Italy
Link: http://twas.ictp.it/
Lactic acid bacteria (LAB) are the most dominating organisms present in raw milk. This study aims to detect and quantify β-Galactosidase (β-GAL) enzyme produced by isolated LAB from raw milk of livestock (cow, buffalo, goat, and sheep) found at different altitudes of Nepal (80 m to 3360 m). The removal of lactose from milk products for lactose intolerant people and the synthesis of galactosylated products are two industrial applications of the enzyme. A total of 71 MRS grown and 88 M17 grown LAB were isolated from various milk samples. Their ability to hydrolyze 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-GAL) and o-nitrophenyl--D-galactopyranoside (ONPG) was assessed. Among the enzyme-producing isolates, 66 isolates (20 MRS grown LAB and 46 M17 grown LAB) tested positive for β-GAL production. By using the sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE), a protein band of the β-GAL enzyme was also discovered. Protein bands of 110-135 kDa was detected in most of the cell-free extracts of the isolates. The results from a quantitative assay showed the bacterial isolate from cows of Bishnupur-Katti (80 m) and sheep from Khopra (3660 m) have high β-GAL activity. So, these isolates can potentially be used as a catalyst for prebiotic (GOS) production from cheese whey. However, further studies need to be performed to confirm their potential health benefits and applications.
Antibiogram and molecular characterization for carbapenem resistant bacteria isolated from fresh produce collected from local markets in Kathmandu, Nepal.
International Foundation for Science (IFS), Sweden
Link: http://www.ifs.se
The project aims to understand the prevalence of carbapenem resistant microbes, especially those that the World Health Organization (WHO) has listed as “critical”, in fresh fruits and vegetables sold in Kathmandu valley. Furthermore, the project also targets on molecular characterization of the genes responsible for causing the resistance.
Faecal pollution source tracking in the holy Bagmati River by portable 16S rRNA gene sequencing
GCRF and EPSRC
A suitcase laboratory was used for 16S rRNA amplicon sequencing to assess microbial water quality in the holy Bagmati River, Kathmandu, Nepal. SourceTracker analysis and Volcano plots revealed that microbial communities in the downstream part of the river were mainly contributed by untreated sewage. Seasonal variability in the sewage microbiome was reflected in the downstream river water quality. The bacterial genera Acidovorax, Geobacillus and Caulobacter predominated in the upstream sites, while genera containing putative human pathogens and gut bacteria, such as Clostridium, Prevotella, Arcobacter, Lactobacillus, Enterococcus and Streptococcus become prominent in the downstream sites. Marker gene qPCR assays for total bacteria, total coliforms, Human E. coli, Arcobacter butzleri and Vibrio cholerae confirmed the sequencing data trends. Even though basic sanitation provision is nowadays near universal in Nepal, our findings show how inadequate wastewater management may turn an urban river into an open sewer, which poses a public health risk.
Unravelling the Chemical Diversity of Actinobacteria Obtained from Unique Asian Ecological Niches
DAAD, Germany
Actinobacteria play a vital role in pharmaceutical drug discovery therefore they are even considered as nature’s pharmacists. This phylum of bacteria has been very prolific in the production of secondary metabolites and many thereof are used in the form of medicines serving the humankind. Most of the drugs that get prescribed today are mimics of nature that researchers around the globe were capable to understand. However, there is still a lot to discover and learn from nature. In our study, we have relied on the concept that bioprospecting strains from underexplored geographical locations and unique Asian niches which will in return offer the opportunity of finding novel compounds for pharmaceutical purposes.
Following this approach, we designed a work to isolate strains from various ecological niches of Nepal, which is still a virgin land in terms of natural product research. This attempt represents the pioneering work where we used Nepalese isolates to identify novel chemistry. Nepal has a varied climate and a broad bandwidth of altitudes (100 – 8849 meter) within a short distance. These unique features make it one of the most biodiverse countries in all of Asia. Therefore, the first part of the thesis will mainly focus on soil-borne Streptomyces isolated from Nepal and their chemical analysis using a metabolomics-based workflow. Similarly, this study is continued with the investigation of the chemistry of rare actinomycetes isolated this time from mud dauber wasp nests which are used as a traditional medicine in some parts of Nepal. The second part of the thesis describes the isolation and structure elucidation of nucleoside antibiotics from the marine strain, Streptomyces sp. SHP-22-7 isolated from the underexplored Enggano Island, Indonesia. In this study four novel structures belonging to the plicacetin/amicetin family were identified with a combined genomics and metabolomics approach. Upon bioactivity analysis, the isolated pure compounds possessed an anti-mycobacterial activity. Furthermore, we have also probed successfully the concept of precursor directed biosynthesis to generate novel unnatural plicacetin derivatives.
OUR
Responsible Department Members
OUR
Responsible Department Members