Near-complete whole-genome sequence of Paenibacillus sp. nov. Strain J5C2022, a sucretolerant and endospore-forming bacterium isolated from highly concentrated sugar brine

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

ITS1 amplicon sequencing of feline gut mycobiome of Malaysian local breeds using Nanopore Flongle

The gut mycobiome exhibits major influence on the gastrointestinal health and disease but received less attention due to low abundance. This study characterizes the fungal community and compares the microbial diversity between indoor and outdoor cats. Genomic DNA was extracted and sequenced by targeting the Internal Transcribed Spacer 1 (ITS1) region using Flongle flow cell on MinION™ sequencing platform. Results show the phylum Ascomycota and genus Peniophorella were numerous in indoor cats, whereas the Basidiomycota and Pichia were abundant in outdoor cats. Peniophorella formed the core mycobiome in both feline populations. Furthermore, alpha (p value = 0.0207) and beta diversities (p value = 0.009) results showed significant differences between the two groups. Overall, indoor cats have greater amounts of Peniophorella, whereas outdoor cats have higher Trichosporon and unclassified Sordariaceae. The study also suggests that keeping a cat indoors or left as a stray will affect their respective gut mycobiome

Evaluation of pre-treated healthcare wastes during COVID-19 pandemic reveals pathogenic microbiota, antibiotics residues, and antibiotic resistance genes against beta-lactams

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 < 0.002), respectively. FC samples were found to acquire more pathogenic microorganisms than FA and FV samples. Paenibacillus and unclassified Bacilli genera were shared among three groups of samples, meanwhile, antibiotic-resistant bacteria Proteus mirabilis, Enterococcus faecium, and Enterococcus faecalis were found in modest quantities. A total of 19 antibiotic compounds were discovered and linked with the microbial abundance detected in the healthcare waste samples. The principal component analysis demonstrated a positive antibiotic-bacteria correlation for genera Pseudomonas, Aerococcus, Comamonas, and Vagococcus, while the other bacteria were negatively linked with antibiotics. Nevertheless, deep bioinformatic analysis confirmed the presence of blaTEM-1 and penP which are associated with the production of class A beta-lactamase and beta-lactam resistance pathways. Microorganisms and contaminants, which serve as putative indicators in healthcare waste treatment evaluation revealed the ineffectiveness of microbial inactivation using the microwave sterilization method. Our findings suggested that the occurrence of clinically relevant microorganisms, antibiotic contaminants, and associated antibiotic resistance genes (ARGs) represent environmental and human health hazards when released into landfills via ARGs transmission

Whole-genome sequence of a stenotrophomonas maltophilia isolate from tap water in an intensive care unit

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

Complete whole genome sequencing of Vibrio parahaemolyticus strain UMP001VA, isolated from sea cucumber Holothuria leucospilota from Malaysia harbouring blaCARB-33 gene

Pathogenic strain of Vibrio parahaemolyticus found in marine and coastal ecosystems can cause infections in marine animals. Increasing antibiotic resistance reported in Vibrio species may be linked to environmental contamination. Here, we present a 4.99-Mbp complete genome sequence of V. parahaemolyticus strain UMP001VA, a Gram-negative bacterium that was isolated from the gut content of a sea cucumber Holothuria leucospilota collected from Pulau Rhu, Terengganu, Malaysia. The whole genome sequencing was performed using hybrid de novo assembly using Illumina and the Oxford Nanopore Technology platforms. The genome analysis reported a total length of 4,991,208 bp of V. parahaemolyticus genome sequences with 45.3 % GC content. The functional annotation of the genome showcased that 56 genes of V. parahaemolyticus were associated with virulence, disease, and defence function. Virulence factors found in H. leucospilota were related to T3SS1, together with the presence of blaCARB-33 antibiotic resistance gene conferring ampicillin, piperacillin, and amoxicillin drug resistance were reported. The presence of virulence factors and antibiotic resistance genes reveals the considerable pathogenic potential of V. parahaemolyticus in sea cucumbers. Therefore, the whole genome sequencing presented here provides a fundamental genome insight for future assessment of V. parahaemolyticus in marine organisms

Characterization of bacterial communities in prebiotics and probiotics treated shrimp farms from Kuantan

Aims: Prebiotics and probiotics profoundly enhance water quality and shrimp development to tackle infectious disease in shrimp farming. This study evaluated the impact of prebiotics and probiotics treatments in water by assessing the physicochemical properties and bacterial communities in local shrimp ponds. Methodology and results: Water was collected from shrimp pond 1 (SP1), treated with prebiotics and probiotics, and shrimp pond 2 (SP2), treated with only prebiotics. The physicochemical parameters of water from two shrimp ponds were measured, including pH, dissolved oxygen (DO), ammonia concentration and temperature. The total environmental DNA (eDNA) was extracted from the water samples and sequenced using amplicon sequencing targeting the full length of the 16S rRNA gene region via the Oxford Nanopore Technology Flongle. The water quality analysis indicated that SP1 had better water quality than SP2 for shrimp aquaculture. The dominant phyla in both shrimp ponds were Proteobacteria and Bacteroidota. SP1 samples had unique microbiota at the phylum level, including Bdellovibrionota, Firmicutes A, Patescibacteria and unclassified Rhizobiales, Saprospiraceae, Vulcanococcus and HIMB114 at the genus level. The alpha- and beta-diversity showed insignificant differences in microbiota composition between SP1 and SP2 (p-value>0.05). Conclusion, significance and impact of study: Research findings demonstrated that the probiotic-treated shrimp pond (SP1) had better water quality and more diverse microbial communities than the shrimp pond that was not treated with probiotics (SP2)

Characterization of bacterial communities in prebiotics and probiotics treated shrimp farms from Kuantan

Aims: Prebiotics and probiotics profoundly enhance water quality and shrimp development to tackle infectious disease in shrimp farming. This study evaluated the impact of prebiotics and probiotics treatments in water by assessing the physicochemical properties and bacterial communities in local shrimp ponds. Methodology and results: Water was collected from shrimp pond 1 (SP1), treated with prebiotics and probiotics, and shrimp pond 2 (SP2), treated with only prebiotics. The physicochemical parameters of water from two shrimp ponds were measured, including pH, dissolved oxygen (DO), ammonia concentration and temperature. The total environmental DNA (eDNA) was extracted from the water samples and sequenced using amplicon sequencing targeting the full length of the 16S rRNA gene region via the Oxford Nanopore Technology Flongle. The water quality analysis indicated that SP1 had better water quality than SP2 for shrimp aquaculture. The dominant phyla in both shrimp ponds were Proteobacteria and Bacteroidota. SP1 samples had unique microbiota at the phylum level, including Bdellovibrionota, Firmicutes A, Patescibacteria and unclassified Rhizobiales, Saprospiraceae, Vulcanococcus and HIMB114 at the genus level. The alpha- and beta-diversity showed insignificant differences in microbiota composition between SP1 and SP2 (p-value>0.05). Conclusion, significance and impact of study: Research findings demonstrated that the probiotic-treated shrimp pond (SP1) had better water quality and more diverse microbial communities than the shrimp pond that was not treated with probiotics (SP2)

Gut microbiome and metabolome of sea cucumber (Stichopus ocellatus) as putative markers for monitoring the marine sediment pollution in Pahang, Malaysia

Antibiotic contamination in the marine environment forms an emerging threat to marine ecosystems. This study aimed to compare the gut and coelomic microbiota of Stichopus ocellatus with sediments between two coastal districts of Pahang, which potentially conferring as putative biomarkers for sediment pollution monitoring. The composition of the bacteria communities was determined using 16S rRNA V3-region gene amplicon sequencing, while hybrid whole-genome sequencing was employed to analyze the genome of Vibrio parahaemolyticus. The trace elements and antibiotic compositions were access using high-throughput spectrometry. The alpha- and beta-diversity of bacteria in gut and sediment samples from Kuantan differed substantially within (p-value = 0.017604) and between samples (p-value <0.007), respectively. Vibrio genera predominated in Kuantan samples, while Flavobacterium and Synechococcus_E genera predominated in Pekan samples. Vibrio parahaemolyticus revealed the presence of tet(35) and blaCARB-33 genes that conceived resistance towards tetracycline and betalactam antibiotics, respectively, which were detected in sediment and gut samples

Gut microbiome and metabolome of sea cucumber (Stichopus ocellatus) as putative markers for monitoring the marine sediment pollution in Pahang, Malaysia

Antibiotic contamination in the marine environment forms an emerging threat to marine ecosystems. This study aimed to compare the gut and coelomic microbiota of Stichopus ocellatus with sediments between two coastal districts of Pahang, which potentially conferring as putative biomarkers for sediment pollution monitoring. The composition of the bacteria communities was determined using 16S rRNA V3-region gene amplicon sequencing, while hybrid whole-genome sequencing was employed to analyze the genome of Vibrio parahaemolyticus. The trace elements and antibiotic compositions were access using high throughput spectrometry. The alpha- and beta-diversity of bacteria in gut and sediment samples from Kuantan differed substantially within (p-value = 0.017604) and between samples (p-value <0.007), respectively. Vibrio genera predominated in Kuantan samples, while Flavobacterium and Synechococcus_E genera predominated in Pekan samples. Vibrio parahaemolyticus revealed the presence of tet (35) and blaCARB-33 genes that conceived resistance towards tetracycline and beta-lactam antibiotics, respectively, which were detected in sediment and gut samples

Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia

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