Biology subjects

Md Zoqratt, M. Z. H.

Publications and source records attributed to Md Zoqratt, M. Z. H..

4 recordsLinked to original sources

bioRxiv2026

Microbial Taxonomy and Function Linked to Carbon Cycling in Mangrove Sediments

Microbial communities are central to the biogeochemical cycling of nutrients, critically shaping ecosystem functioning and influencing climate change mitigation. Mangrove ecosystems are among the most important global carbon sinks that enable large amounts of carbon to be sequestered and stored. However, gaps persist in understanding the fundamental aspects of microbial-driven carbon cycling in these environments. This research explores the microbial taxonomic and functional diversity related to carbon cycling in selected tropical mangrove sediments across various locations and depths. Sequencing data analyses based on the 16S rRNA gene revealed distinct microbial community composition but conserved predicted functions across the different mangrove locations. Depth was a strong influence on the functional composition, with carbon-related pathways and metabolic strategies differing between top and bottom sediments. Putative functional gene abundance analyses revealed that carbon fixation processes were among the top carbon-related pathways, suggesting the key role of mangrove microbial communities in sustaining long-term carbon storage. Within these communities, Desulfobacterota appeared as a primary contributor to carbon fixation, while Chloroflexota played a significant role in carbon metabolism and methane cycling. Co-occurrence network analyses also revealed that these microbial groups were among the keystone taxa in mangrove sediments. Our study adds on to the body of knowledge on the mangrove microbiome and their carbon metabolic processes, which helps to improve strategies for managing and leveraging these vital carbon sinks.

microbiology↗

bioRxiv2024

Identification of novel prophages and variants of Integrative and Conjugative Elements in Elizabethkingia anophelis clinical isolates from Seremban, Malaysia

Elizabethkingia anophelis is an emerging multidrug-resistant pathogen that has been identified globally, including in Malaysia. In this study, we used the Oxford Nanopore Technologies (ONT) long-read platform to generate the complete genome sequences of seven clinical isolates of E. anophelis from a tertiary hospital in the city of Seremban, located in the state of Negeri Sembilan in Peninsular Malaysia. These sequences were analysed alongside over 400 publicly available E. anophelis genomes from other countries. Three of the seven E. anophelis isolates, Eli4, Eli5, and Eli6, were almost identical and their isolation over a period of six weeks from the same hospital was suggestive of nosocomial transmission. Besides these three isolates, the other E. anophelis isolates were genetically diverse and related to distinct isolates from other countries. No plasmids were identified in the genomes of all seven E. anophelis isolates. A novel 39,686 bp prophage was identified in the genome of E. anophelis Eli4 while a presumptive incomplete prophage was found in the genomes of Eli2, Eli4, Eli5 and Eli6. E. anophelis genomes are notable for possessing integrative and conjugative elements (ICEs), which enable the bacterium to acquire new genes, including those encoding antimicrobial resistance or virulence. Several novel ICE sequences were discovered in the Seremban E. anophelis genomes, and this includes an ICE found in Eli8, designated Eli8_ICE1, which encodes phage defence genes such as type I restriction-modification systems, a bacterial cyclic oligonucleotide-based anti-phage signalling system (CBASS) and prokaryotic argonaute systems. The latter two phage defence genes have so far not been reported in the E. anophelis genome. This study demonstrates the utility of long-read sequencing in assessing the diversity and plasticity of E. anophelis genomes and emphasises further research into the role of ICEs in phage defence systems and their potential impact on antimicrobial treatment and phage therapy. RepositoriesThe Elizabethkingia anophelis genomes in this study have been deposited in the NCBI database under BioProject PRJNA1175025.

microbiology↗

bioRxiv2020

A fluoroquinolone-sensitive Shigella sonnei UKMCC1015 downregulates the expression of ribosomal proteins in response to sub-lethal concentration of norfloxacin

1.Shigella causes shigellosis that requires antibiotic treatment in severe cases. Sub-lethal antibiotic concentrations can promote resistance, but their effect on antibiotic-sensitive bacteria before resistance development is unknown. This study investigated the effects of sublethal norfloxacin (NOR) challenges on a norfloxacin-sensitive strain, Shigella sonnei UKMCC1015. Firstly, the whole genome of S. sonnei UKMCC1015 was assembled, and 45 antimicrobial resistance (AMR) genes were identified. However, transcriptomic analysis showed that low NOR levels do not change the expression of AMR genes and norfloxacin targets. Instead, multiple ribosomal protein genes were downregulated, which could be attributed to decreased ribosomal protein promoter activity, modulated by elevated ppGpp levels. This alarmone is involved in the bacterial stringent response during environmental stress, and it is mainly produced from the ppGpp synthetase (relA). However, high levels of ppGpp (due to relA overexpression) are detrimental to the continued survival of S. sonnei during prolonged exposure to NOR. This study revealed that a norfloxacin-sensitive strain responds differently to sub-lethal NOR than commonly reported in resistant strains. Overexpression of relA (high ppGpp levels) may reduce the mutability of S. sonnei UKMCC1015 in response to NOR exposure and affect NOR tolerance.

microbiology↗

bioRxiv2020

The microbiota of Malaysian fermented fish sauce

Budu is a Malaysian fermented anchovy sauce produced by immersing small fishes into a brine solution for 6 to 18 months. Fermentation of the anchovy sauce is contributed partly by microbial enzymes, but little is known about the microbial community in Budu. Therefore, a better understanding of the Budu microbiome is necessary to better control the quality, consistency and safety of the product. In this study, we collected 60 samples from twenty bottles of Budu produced by seven different manufacturers. We analyzed their microbiota based on V3-V4 16S rRNA amplicon sequencing at the time of opening the bottle as well as 3- and 7-months post-opening. Tetragenococcus was the dominant genus in many samples, reaching a maximum proportion of 98.62%, but was found in low abundance, or absent, in other samples. When Budu samples were not dominated by a dominant taxa, we observed a wider genera diversity such as Staphylococcus, Acinetobacter, Halanaerobium and Bacillus. While the taxonomic composition was relatively stable across sampling periods, samples from two brands showed a sudden increase in relative abundance of the genus Chromobacterium in the 7th month. Based on prediction of metagenome functions, non-Tetragenococcus-dominated samples were predicted to have enriched functional pathways related to amino acid metabolism and purine metabolism compared to Tetragenococcus-dominated microbiome; these two pathways are fundamental fermented quality and health attributes of fish sauce. Within the non-Tetragenococcus-dominated group, contributions towards amino acid metabolism and purine metabolism were biased towards the dominant taxa when species evenness is low, while in samples with higher species evenness, the contributions towards the two pathways were predicted to be evenly distributed between taxa.

molecular biology↗