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Whole genome sequencing analysis of Komagataeibacter nataicola reveals its potential in food waste valorisation for cellulose production

Nasharudin MIH, Siew SW, Ahmad HF, Mahmud N

Mol Biol Rep, 2024 Apr 11;51(1):503.
PMID: 38600404 DOI: 10.1007/s11033-024-09492-8

BACKGROUND: Komagataeibacter nataicola (K. nataicola) is a gram-negative acetic acid bacterium that produces natural bacterial cellulose (BC) as a fermentation product under acidic conditions. The goal of this work was to study the complete genome of K. nataicola and gain insight into the functional genes in K. nataicola that are responsible for BC synthesis in acidic environments.
METHODS AND RESULT: The pure culture of K. nataicola was obtained from yeast-glucose-calcium carbonate (YGC) agar, followed by genomic DNA extraction, and subjected to whole genome sequencing on a Nanopore flongle flow cell. The genome of K. nataicola consists of a 3,767,936 bp chromosome with six contigs and 4,557 protein coding sequences. The maximum likelihood phylogenetic tree and average nucleotide identity analysis confirmed that the bacterial isolate was K. nataicola. The gene annotation via RAST server discovered the presence of cellulose synthase, along with three genes associated with lactate utilization and eight genes involved in lactate fermentation that could potentially contribute to the increase in acid concentration during BC synthesis.
CONCLUSION: A more comprehensive genome study of K. nataicola may shed light into biological pathway in BC productivity as well as benefit the analysis of metabolites generated and understanding of biological and chemical interactions in BC production later.
Fulltext Near-Complete Whole-Genome Sequence of Paenibacillus sp. nov. Strain J5C2022, a Sucretolerant and Endospore-Forming Bacterium Isolated from Highly Concentrated Sugar Brine

Musa SM, Siew SW, Tay DD, Ahmad HF

Microbiol Resour Announc, 2023 Apr 18;12(4):e0105522.
PMID: 36877039 DOI: 10.1128/mra.01055-22

Here, we present a 7.62-Mbp genome sequence of Paenibacillus sp. nov. strain J5C2022, a Gram-positive facultatively anaerobic bacterium that was isolated from 4-month-old fruit pickle brine and sequenced using the Illumina platform.
Fulltext Whole-Genome Sequence of a Stenotrophomonas maltophilia Isolate from Tap Water in an Intensive Care Unit

Zainulabid UA, Siew SW, Musa SM, Soffian SN, Periyasamy P, Ahmad HF

Microbiol Resour Announc, 2023 Feb 16;12(2):e0099522.
PMID: 36633414 DOI: 10.1128/mra.00995-22

Here, we present a 4,508,936-bp complete genome sequence of Stenotrophomonas maltophilia strain HW002Y, which was isolated from the tap water in an intensive care unit at Sultan Ahmad Shah Medical Centre at the International Islamic University of Malaysia (Kuantan, Pahang, Malaysia). Sequencing was performed using a Nanopore Flongle flow cell.
Fulltext Evaluation of pre-treated healthcare wastes during COVID-19 pandemic reveals pathogenic microbiota, antibiotics residues, and antibiotic resistance genes against beta-lactams

Siew SW, Musa SM, Sabri N', Farida Asras MF, Ahmad HF

Environ Res, 2023 Feb 15;219:115139.
PMID: 36565841 DOI: 10.1016/j.envres.2022.115139

The disposal of healthcare waste without prior elimination of pathogens and hazardous contaminants has negative effects on the environment and public health. This study aimed to profile the complete microbial community and correlate it with the antibiotic compounds identified in microwave pre-treated healthcare wastes collected from three different waste operators in Peninsular Malaysia. The bacterial and fungal compositions were determined via amplicon sequencing by targeting the full-length 16S rRNA gene and partial 18S with full-length ITS1-ITS2 regions, respectively. The antibiotic compounds were characterized using high-throughput spectrometry. There was significant variation in bacterial and fungal composition in three groups of samples, with alpha- (p-value = 0.04) and beta-diversity (p-values <0.006 and
Fulltext Method for detection of pathogenic bacteria from indoor air microbiome samples using high-throughput amplicon sequencing

Mat-Hussin NH, Siew SW, Maghpor MN, Gan HM, Ahmad HF

MethodsX, 2024 Jun;12:102636.
PMID: 38439930 DOI: 10.1016/j.mex.2024.102636

The exposure of the air microbiome in indoor air posed a detrimental health effect to the building occupants compared to the outdoor air. Indoor air in hospitals has been identified as a reservoir for various pathogenic microbes. The conventional culture-dependent method has been widely used to access the microbial community in the air. However, it has limited capability in enumerating the complex air microbiome communities, as some of the air microbiomes are uncultivable, slow-growers, and require specific media for cultivation. Here, we utilized a culture-independent method via amplicon sequencing to target the V3 region of 16S rRNA from the pool of total genomic DNA extracted from the dust samples taken from hospital interiors. This method will help occupational health practitioners, researchers, and health authorities to efficiently and comprehensively monitor the presence of harmful air microbiome thus take appropriate action in controlling and minimizing the health risks to the hospital occupants. Key features;•Culture-independent methods offer fast, comprehensive, and unbias profiles of pathogenic and non-pathogenic bacteria from the air microbiomes.•Unlike the culture-dependent method, amplicon sequencing allows bacteria identification to the lowest taxonomy levels.
Shallow shotgun sequencing of healthcare waste reveals plastic-eating bacteria with broad-spectrum antibiotic resistance genes

Siew SW, Khairi MHF, Hamid NA, Asras MFF, Ahmad HF

Environ Pollut, 2025 Jan 01;364(Pt 1):125330.
PMID: 39551377 DOI: 10.1016/j.envpol.2024.125330

The burgeoning crises of antimicrobial resistance and plastic pollution are converging in healthcare settings, presenting a complex challenge to global health. This study investigates the microbial populations in healthcare waste to understand the extent of antimicrobial resistance and the potential for plastic degradation by bacteria. Our metagenomic analysis, using both amplicon and shallow shotgun sequencing, provided a comprehensive view of the taxonomic diversity and functional capacity of the microbial consortia. The viable bacteria in healthcare waste samples were analyzed employing full-length 16S rRNA sequencing, revealing a diverse bacterial community dominated by Firmicutes and Proteobacteria phyla. Notably, Proteus mirabilis VFC3/3 and Pseudomonas sp. VFA2/3 were detected, while Stenotrophomonas maltophilia VFV3/2 surfaced as the predominant species, holding implications for the spread of hospital-acquired infections and antimicrobial resistance. Antibiotic susceptibility testing identified multidrug-resistant strains conferring antimicrobial genes, including the broad-spectrum antibiotic carbapenem, underscoring the critical need for improved waste management and infection control measures. Remarkably, we found genes linked to the breakdown of plastic that encoded for enzymes of the esterase, depolymerase, and oxidoreductase classes. This suggests that specific bacteria found in medical waste may be able to reduce the amount of plastic pollution that comes from biological and medical waste. The information is helpful in formulating strategies to counter the combined problems of environmental pollution and antibiotic resistance. This study emphasises the importance of monitoring microbial communities in hospital waste in order to influence waste management procedures and public health policy. The findings highlight the need for a multidisciplinary approach to mitigate the risks associated with antimicrobial resistance and plastic waste, especially in hospital settings where they intersect most acutely.
Fulltext Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia

Zainulabid UA, Kamarudin N, Zulkifly AH, Gan HM, Tay DD, Siew SW, et al.

Microbiol Resour Announc, 2021 Aug 05;10(31):e0065721.
PMID: 34351228 DOI: 10.1128/MRA.00657-21

Here, we report the nearly complete genome sequences of nine severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with the D614G mutation. These viruses were detected from various infected individuals with different levels of severity from Pahang, Malaysia. In addition, this study described the presence of lineage B.1.351 as a type of variant of concern (VOC) and lineages B.1.466.2 and B.1.524 as local variants.