Displaying publications 1 - 20 of 447 in total

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  1. Microcystin production by oscillatorialean cyanobacteria isolated from cryopreserved Antarctic mats
    Usman AS, Merican F, Zaki S, Broady P, Convey P, Muangmai N
    Harmful Algae, 2022 Dec;120:102336.
    PMID: 36470600 DOI: 10.1016/j.hal.2022.102336
    Twenty cyanobacterial strains of eight morphospecies isolated from deep-frozen (-15 °C) mat samples originally collected on Ross Island, in Victoria Land, and on the McMurdo Ice Shelf were screened for the presence of genes encoding for production of anatoxins, cylindrospermopsin, microcystin/nodularin and saxitoxin. One strain of each of Microcoleus autumnalis and Phormidesmis priestleyi and two strains of Wilmottia murrayi were found to produce microcystin. No toxin production was detected in the other 16 strains representing five species. The four toxin-producing strains were characterised using both morphological and molecular approaches. Phylogenetic analyses using partial 16S rRNA sequences were consistent with the morphological identification of all four strains. They were all found to contain a fragment of the mcyE gene, which is involved in microcystin biosynthesis. ELISA analysis of extracts from cultures of these strains confirmed the presence of low concentrations of microcystin: 0.35 μg/L in M. autumnalis, <0.15 μg/L in P. priestleyi, 1.60 μg/L in W. murrayi strain 1 and 0.9 μg/L in W. murrayi strain 2. This study includes the first report of microcystin synthesis by W. murrayi.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  2. Rapid shifts in methanotrophic bacterial communities mitigate methane emissions from a tropical hydropower reservoir and its downstream river
    Reis PCJ, Ruiz-González C, Crevecoeur S, Soued C, Prairie YT
    Sci Total Environ, 2020 Dec 15;748:141374.
    PMID: 32823225 DOI: 10.1016/j.scitotenv.2020.141374
    Methane-oxidizing bacteria (MOB) present in the water column mitigate methane (CH4) emissions from hydropower complexes to the atmosphere. By creating a discontinuity in rivers, dams cause large environmental variations, including in CH4 and oxygen concentrations, between upstream, reservoir, and downstream segments. Although highest freshwater methanotrophic activity is often detected at low oxygen concentrations, CH4 oxidation in well-oxygenated downstream rivers below dams has also been reported. Here we combined DNA and RNA high-throughput sequencing with microscopic enumeration (by CARD-FISH) and biogeochemical data to investigate the abundance, composition, and potential activity of MOB taxa from upstream to downstream waters in the tropical hydropower complex Batang Ai (Malaysia). High relative abundance of MOB (up to 61% in 16S rRNA sequences and 19% in cell counts) and enrichment of stable isotopic signatures of CH4 (up to 0‰) were detected in the hypoxic hypolimnion of the reservoir and in the outflowing downstream river. MOB community shifts along the river-reservoir system reflected environmental sorting of taxa and an interrupted hydrologic connectivity in which downstream MOB communities resembled reservoir's hypolimnetic communities but differed from upstream and surface reservoir communities. In downstream waters, CH4 oxidation was accompanied by fast cell growth of particular MOB taxa. Our results suggest that rapid shifts in active MOB communities allow the mitigation of CH4 emissions from different zones of hydropower complexes, including in quickly re-oxygenated rivers downstream of dams.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  3. Characterization, molecular identification, and antimicrobial activity of lactic acid bacteria isolated from selected fermented foods and beverages in Malaysia
    Haryani Y, Halid NA, Guat GS, Nor-Khaizura MAR, Hatta A, Sabri S, et al.
    FEMS Microbiol Lett, 2023 Jan 17;370.
    PMID: 37002414 DOI: 10.1093/femsle/fnad023
    The present work investigated the profile and biodiversity of lactic acid bacteria (LAB) isolated from selected manufactured and homemade fermented foods in Malaysia. A total of 55 LAB were isolated from 20 samples, and identified based on the sequencing of 16S rRNA gene. The LAB isolates were identified as Lacticaseibacillus rhamnosus (34.5%), Lactiplantibacillus plantarum (20%), Limosilactobacillus fermentum (20%), Lacticaseibacillus paracasei (12.7%), Lacticaseibacillus casei (3.6%), Lactobacillus sp. (1.8%), Enterococcus faecalis (3.6%), Enterococcus faecium (1.8%), and Enterococcus durans (1.8%). Majority (94%) of the LAB isolates exhibited broad-spectrum antimicrobial activity against selected foodborne pathogens, and four isolates (L. fermentum SC1001, L. paracasei K2003, and L. rhamnosus KF1002 and MK2003) could produce bacteriocin-like inhibitory substance (BLIS). Lacticaseibacillus paracasei M1001 (homemade mozzarella) exhibited high-temperature tolerance and acid resistance, was homofermentative, and generated good antimicrobial activity, which strongly implied its potential for industrial applications. The present work results would potentially widen our knowledge of LAB diversity in Malaysian fermented foods and provide a potential for their applications in the food industry or other purposes.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  4. Plankton assemblages from microplastics of tropical coastal environments reveal high diversity and evidence of toxic species
    Curren E, Leong SCY
    Mar Environ Res, 2024 Jan;193:106251.
    PMID: 37952304 DOI: 10.1016/j.marenvres.2023.106251
    Microplastics are a major constituent of plastic waste and are of an increasing global concern. Although microplastics are prevalent in marine ecosystems, the characterisation of plankton communities has been largely neglected in this aspect, especially in tropical ecosystems. To better understand the role of microplastics as a carrier of harmful plankton in marine ecosystems, epiplastic plankton communities in tropical marine ecosystems were studied from beach sediments along the Johor and Singapore Straits. Complementary analysis of microscopy and high throughput sequencing of the 16S rRNA (V3-V4) and 18S (V4) rRNA regions provided evidence that the plastisphere provided an appropriate environment to host a wide range of planktonic organisms. An average of 781 OTUs were identified across the three sampling sites. The structures of plankton communities were distinct across the sampling sites and were generally dominated by dinoflagellates, fungi and chlorophytes. We demonstrate that marine microplastics serve as microhabitats that are a host to harmful phytoplankton species, including viable resting cysts of dinoflagellates. Furthermore, plastics isolated from the location with the greatest anthropogenic influence demonstrated the greatest plankton diversity. This study presents evidence of diverse toxic plankton species present on the plastisphere and highlights its importance as a vector of the transport of harmful opportunistic species in relation to anthropogenic influence, in the marine environment.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  5. Habitat shapes the gut microbiome diversity of Malayan tigers (Panthera tigris jacksoni) as revealed through metabarcoding 16S rRNA profiling
    Gani M, Mohd-Ridwan AR, Sitam FT, Kamarudin Z, Selamat SS, Awang NMZ, et al.
    World J Microbiol Biotechnol, 2024 Feb 28;40(4):111.
    PMID: 38416247 DOI: 10.1007/s11274-023-03868-x
    The gut microbiome refers to the microorganism community living within the digestive tract. The environment plays a crucial role in shaping the gut microbiome composition of animals. The gut microbiome influences the health and behavior of animals, including the critically endangered Malayan tiger (Panthera tigris jacksoni). However, the gut microbiome composition of Malayan tigers, especially those living in their natural habitats, remains poorly understood. To address this knowledge gap, we used next-generation sequencing DNA metabarcoding techniques to analyze the gut microbiome of wild Malayan tigers using fecal samples collected from their natural habitats and in captivity. Our aim was to determine the gut microbiota composition of the Malayan tiger, considering the different types of habitat environments. The results revealed a diverse microbial community within the gut microbiome of Malayan tigers. The prominent phyla that were observed included Firmicutes, Proteobacteria, Actinobacteriota, Fusobacteriota and Bacteroidota. Beta diversity analysis revealed significant differences in gut microbiome composition of Malayan tigers that inhabited oil palm plantations, in villages and protected areas. Diversity analysis also revealed significant difference in the gut microbiome between wild and captive Malayan tigers. However, the distinctions of gut microbiome between wild and captive alpha diversity did not yield significant differences. The differences in microbiome diversity resulted from the interplay of dietary intake and environmental factors. This information will facilitate the establishment of focused conservation approaches and enhance our understanding of the effect of microbiome composition on Malayan tiger health.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  6. Whole genome sequence of moderate halophilic marine bacterium Marinobacter litoralis SW-45: Abundance of non-coding RNAs
    Musa H, Kasim FH, Gunny AAN, Gopinath SCB, Chinni SV, Ahmad MA
    Int J Biol Macromol, 2019 Jul 15;133:1288-1298.
    PMID: 31055112 DOI: 10.1016/j.ijbiomac.2019.05.003
    A report on the de novo Whole Genome Sequence (WGS) of Marinobacter litoralis SW-45, a moderately salt-tolerant bacterium isolated from the seawater in Malaysia is presented. The strain has a genome size of 3.45 Mb and is capable of producing halophilic lipase, protease and esterase enzymes. Computational prediction of non-coding RNA (ncRNA) genes in M. litoralis SW-45 was performed using standalone software known as the non-coding RNA characterization (nocoRNAc). In addition, a phylogenetic tree showing the evolutionary relationship between the strain and other members of the genus Marinobacter was constructed using 16SrRNA sequence information. A total of 385 ncRNA transcripts, 1124 terminator region, and 2350 Stress Induced Duplex Destabilization sites were predicted. The current WGS shotgun project has provided the relevant genetic information that may be useful for the strain's improvement studies. This manuscript gives the first description of M. litoralis with a complete genome.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  7. Fulltext Unexpectedly high levels of lineage diversity in Sundaland puddle frogs (Dicroglossidae: Occidozyga Kuhl and van Hasselt, 1822)
    Flury JM, Haas A, Brown RM, Das I, Pui YM, Boon-Hee K, et al.
    Mol Phylogenet Evol, 2021 10;163:107210.
    PMID: 34029720 DOI: 10.1016/j.ympev.2021.107210
    One of the most urgent contemporary tasks for taxonomists and evolutionary biologists is to estimate the number of species on earth. Recording alpha diversity is crucial for protecting biodiversity, especially in areas of elevated species richness, which coincide geographically with increased anthropogenic environmental pressures - the world's so-called biodiversity hotspots. Although the distribution of Puddle frogs of the genus Occidozyga in South and Southeast Asia includes five biodiversity hotspots, the available data on phylogeny, species diversity, and biogeography are surprisingly patchy. Samples analyzed in this study were collected throughout Southeast Asia, with a primary focus on Sundaland and the Philippines. A mitochondrial gene region comprising ~ 2000 bp of 12S and 16S rRNA with intervening tRNA Valine and three nuclear loci (BDNF, NTF3, POMC) were analyzed to obtain a robust, time-calibrated phylogenetic hypothesis. We found a surprisingly high level of genetic diversity within Occidozyga, based on uncorrected p-distance values corroborated by species delimitation analyses. This extensive genetic diversity revealed 29 evolutionary lineages, defined by the > 5% uncorrected p-distance criterion for the 16S rRNA gene, suggesting that species diversity in this clade of phenotypically homogeneous forms probably has been underestimated. The comparison with results of other anuran groups leads to the assumption that anuran species diversity could still be substantially underestimated in Southeast Asia in general. Many genetically divergent lineages of frogs are phenotypically similar, indicating a tendency towards extensive morphological conservatism. We present a biogeographic reconstruction of the colonization of Sundaland and nearby islands which, together with our temporal framework, suggests that lineage diversification centered on the landmasses of the northern Sunda Shelf. This remarkably genetically structured group of amphibians could represent an exceptional case for future studies of geographical structure and diversification in a widespread anuran clade spanning some of the most pronounced geographical barriers on the planet (e.g., Wallace's Line). Studies considering gene flow, morphology, ecological and bioacoustic data are needed to answer these questions and to test whether observed diversity of Puddle frog lineages warrants taxonomic recognition.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  8. Molecular identification and biofilm-forming ability of Elizabethkingia species
    Puah SM, Fong SP, Kee BP, Puthucheary SD, Chua KH
    Microb Pathog, 2022 Jan;162:105345.
    PMID: 34896547 DOI: 10.1016/j.micpath.2021.105345
    Recently, Elizabethkingia species have gained attention as a cause of life-threatening infections. The identification via phenotypic methods of three important species- Elizabethkingia meningoseptica, E. anophelis and E. miricola is difficult. Our objectives were to re-assess 30 archived Flavobacterium meningosepticum isolates using 16S rRNA gene sequencing, ERIC-PCR, and biofilm formation assay. Twenty-four isolates were re-identified as E. anophelis and 6 as E. miricola. All of them had the ability to form biofilm as shown in microtiter plate assay based on crystal violet staining. Overall, E. anophelis had a higher specific biofilm formation index compared to E. miricola. A total of 42% (10 out of 24) of E. anophelis were classified as strong, 29% (7 out of 24) as moderate and 29% (7 out of 24) as weak biofilm producers. E. miricola, 17% (1 out of 6) isolates were strong biofilm producers, 50% (3 out of 6) moderate and 33% (2 out of 6) were weak producers. E. anophelis from tracheal secretions were significantly associated with (p = 0.0361) strong biofilm formation. In summary, this study showed that the isolates originally identified as F. meningosepticum were re-classified using the 16S rRNA gene as one of two Elizabethkingia species. The ability of E. anophelis to form strong biofilm in endotracheal tubes indicates their probable role in the pathogenesis of Elizabethkingia infections.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  9. Fulltext Aerobic Methanotrophy and Co-occurrence Networks of a Tropical Rainforest and Oil Palm Plantations in Malaysia
    Ho A, Zuan ATK, Mendes LW, Lee HJ, Zulkeflee Z, van Dijk H, et al.
    Microb Ecol, 2022 Nov;84(4):1154-1165.
    PMID: 34716776 DOI: 10.1007/s00248-021-01908-3
    Oil palm (OP) plantations are gradually replacing tropical rainforest in Malaysia, one of the largest palm oil producers globally. Conversion of lands to OP plantations has been associated with compositional shifts of the microbial community, with consequences on the greenhouse gas (GHG) emissions. While the impact of the change in land use has recently been investigated for microorganisms involved in N2O emission, the response of the aerobic methanotrophs to OP agriculture remains to be determined. Here, we monitored the bacterial community composition, focusing on the aerobic methanotrophs, in OP agricultural soils since 2012, 2006, and 1993, as well as in a tropical rainforest, in 2019 and 2020. High-affinity methane uptake was confirmed, showing significantly lower rates in the OP plantations than in the tropical rainforest, but values increased with continuous OP agriculture. The bacterial, including the methanotrophic community composition, was modified with ongoing OP agriculture. The methanotrophic community composition was predominantly composed of unclassified methanotrophs, with the canonical (Methylocystis) and putative methanotrophs thought to catalyze high-affinity methane oxidation present at higher relative abundance in the oldest OP plantation. Results suggest that the methanotrophic community was relatively more stable within each site, exhibiting less temporal variations than the total bacterial community. Uncharacteristically, a 16S rRNA gene-based co-occurrence network analysis revealed a more complex and connected community in the OP agricultural soil, which may influence the resilience of the bacterial community to disturbances. Overall, we provide a first insight into the ecology and role of the aerobic methanotrophs as a methane sink in OP agricultural soils.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  10. Diversity and Distribution of Microbial Communities Associated with Reef Corals of the Malay Peninsula
    Kanisan DP, Quek ZBR, Oh RM, Afiq-Rosli L, Lee JN, Huang D, et al.
    Microb Ecol, 2023 Jan;85(1):37-48.
    PMID: 35043221 DOI: 10.1007/s00248-022-01958-1
    Coral-associated bacteria play critical roles in the regulation of coral health and function. Environmental perturbations that alter the bacterial community structure can render the coral holobiont more susceptible and less resilient to disease. Understanding the natural variation of the coral microbiome across space and host species provides a baseline that can be used to distinguish shifts in community structure. Using a 16S rRNA gene metabarcoding approach, this study examines bacterial community structure across three scleractinian coral hosts. Our results show that corals of three regions-eastern and western Peninsular Malaysia and Singapore-host distinct bacterial communities; despite these differences, we were able to identify a core microbiome shared across all three species. This core microbiome was also present in samples previously collected in Thailand, suggesting that these core microbes play an important role in promoting and maintaining host health. For example, several have been identified as dimethylsulfoniopropionate (DMSP) metabolizers that have roles in sulfur cycling and the suppression of bacterial pathogens. Pachyseris speciosa has the most variable microbiome, followed by Porites lutea, with the composition of the Diploastrea heliopora microbiome the least variable throughout all locations. Microbial taxa associated with each region or site are likely shaped by local environmental conditions. Taken together, host identity is a major driver of differences in microbial community structure, while environmental heterogeneity shapes communities at finer scales.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  11. Biodegradation of monocrotophos by Brucella intermedia Msd2 isolated from cotton plant
    Shazmin, Ahmad SA, Naqvi TA, Munis MFH, Javed MT, Chaudhary HJ
    World J Microbiol Biotechnol, 2023 Mar 31;39(6):141.
    PMID: 37000294 DOI: 10.1007/s11274-023-03575-7
    Widespread and inadequate use of Monocrotophos has led to several environmental issues. Biodegradation is an ecofriendly method used for detoxification of toxic monocrotophos. In the present study, Msd2 bacterial strain was isolated from the cotton plant growing in contaminated sites of Sahiwal, Pakistan. Msd2 is capable of utilizing the monocrotophos (MCP) organophosphate pesticide as its sole carbon source for growth. Msd2 was identified as Brucella intermedia on the basis of morphology, biochemical characterization and 16S rRNA sequencing. B. intermedia showed tolerance of MCP up to 100 ppm. The presence of opd candidate gene for pesticide degradation, gives credence to B. intermedia as an effective bacterium to degrade MCP. Screening of the B. intermedia strain Msd2 for plant growth promoting activities revealed its ability to produce ammonia, exopolysaccharides, catalase, amylase and ACC-deaminase, and phosphorus, zinc and potassium solubilization. The optimization of the growth parameters (temperatures, shaking rpm, and pH level) of the MCP-degrading isolate was carried out in minimal salt broth supplemented with MCP. The optimal pH, temperature, and rpm for Msd2 growth were observed as pH 6, 35 °C, and 120 rpm, respectively. Based on optimization results, batch degradation experiment was performed. Biodegradation of MCP by B. intermedia was monitored using HPLC and recorded 78% degradation of MCP at 100 ppm concentration within 7 days of incubation. Degradation of MCP by Msd2 followed the first order reaction kinetics. Plant growth promoting and multi-stress tolerance ability of Msd2 was confirmed by molecular analysis. It is concluded that Brucella intermedia strain Msd2 could be beneficial as potential biological agent for an effective bioremediation for polluted environments.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  12. First Report on Novel Psychrotrophic Phosphorus-Solubilizing Ochrobactrum thiophenivorans EU-KL94 from Keylong Region in Great Himalayas and Their Role in Plant Growth Promotion of Oats (Avena sativa L.)
    Kour D, Yadav AN
    Curr Microbiol, 2023 May 30;80(7):227.
    PMID: 37249717 DOI: 10.1007/s00284-023-03308-x
    Cold stress leads to the disruption of the cellular homeostasis in plants and generation of reactive oxygen species (ROS) and productivity losses. In the present study, 94 psychrotrophic phosphorus-solubilizing bacteria with multiple plant growth-promoting (PGP) capabilities were isolated from rhizosphere of wheat. The most efficient strain EU-KL94 showing highest amount of solubilized phosphorus and maximum number of PGP attributes was identified using 16S rRNA sequencing as Ochrobactrum thiophenivorans. Ochrobactrum thiophenivorans EU-KL94 along with recommended doses of the chemical fertilizers as controls were used for alleviation of cold stress in oats. The strain improved the root and shoot length, dry and fresh weight, proline, glycine betaine, chlorophyll content as well as the superoxide dismutase (SOD) and glutathione reductase (GR) activities of oats under cold stress conditions. Ochrobactrum thiophenivorans with all promising plant growth activities under cold stress could be used as an environmental friendly strategy for mitigation of low temperature stress. To the best of our knowledge, Ochrobactrum thiophenivorans has been reported for the first time as P-solubilizer and as bioinoculants in oats for cold stress mitigation.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  13. Application of High-Throughput Sequencing (HTS) to Enhance the Well-Being of an Endangered Species (Malayan Tapir): Characterization of Gut Microbiome Using MG-RAST
    Arumugam R, Ravichandran P, Yeap SK, Sharma RSK, Zulkifly SB, Yawah D, et al.
    Methods Mol Biol, 2023;2649:175-194.
    PMID: 37258862 DOI: 10.1007/978-1-0716-3072-3_8
    The Tapirus indicus, also known as Malayan tapir, has been listed as a rapidly declining animal species in the past decades, along with being declared and categorized as an endangered species by the International Union for Conservation of Nature (IUCN) 2016. This tapir species is geographically distributed across several countries in Southeast Asia such as Peninsular Malaysia, Indonesia (Sumatra), South Thailand, and Myanmar. Amongst these countries, the Peninsula Malaysia forest is recorded to contain the highest number of Malayan tapir population. Unfortunately, in the past decades, the population of Malayan tapirs has declined swiftly due to serious deforestation, habitat fragmentation, and heavy vehicle accidents during road crossings at forest routes. Concerned by this predicament, the Department of Wildlife and National Parks (DWNP) Peninsular Malaysia collaborated with a few local universities to conduct various studies aimed at increasing the population number of tapirs in Malaysia. Several studies were conducted with the aim of enhancing the well-being of tapirs in captivity. Veterinarians face problems when it comes to selecting healthy and suitable tapirs for breeding programs at conservation centers. Conventional molecular methods using high-throughput sequencing provides a solution in determining the health condition of Malayan tapirs using the Next-Generation Sequencing (NGS) technology. Unaware by most, gut microbiome plays an important role in determining the health condition of an organism by various aspects: (1) digestion control; (2) benefiting the immune system; and (3) playing a role as a "second brain." Commensal gut bacterial communities (microbiomes) are predicted to influence organism health and disease. Imbalance of unhealthy and healthy microbes in the gut may contribute to weight gain, high blood sugar, high cholesterol, and other disorders. In infancy, neonatal gut microbiomes are colonized with maternal and environmental flora, and mature toward a stable composition in two to three years. Interactions between the microorganism communities and the host allow for the establishment of microbiological roles. Identifying the core microbiome(s) are essential in the prediction of diseases and changes in environmental behavior of microorganisms. The dataset of 16S rRNA amplicon sequencing of Malayan tapir was deposited in the MG-RAST portal. Parameters such as quality control, taxonomic prediction (unknown and predicted), diversity (rarefaction), and diversity (alpha) were analyzed using sequencing approaches (Amplicon sequencing). Comparisons of parameters, according to the type of sequencing, showed significant differences, except for the prediction variable. In the Amplicon sequencing datasets, the parameters Rarefaction and Unknown had the highest correlation, while Alpha and Predicted had the lowest. Firmicutes, Bacteroidetes, Proteobacteria, Bacilli, and Bacteroidia were the most representative genera in Malayan tapir amplicon sequences, which indicated that most of the tapirs were healthy. However, continuous assessment to maintain the well-being of tapir for long term is still required. This chapter focuses on the introduction of 16S rRNA amplicon metagenomics in analyzing Malayan tapir gut microbiome dataset.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  14. Fulltext Bacterial flora varies throughout the saltwater crocodile (Crocodylus porosus) gastrointestinal tract
    Siddiqui R, Maciver SK, Anuar TS, Khan NA
    Am J Vet Res, 2023 Aug 01;84(8).
    PMID: 37353216 DOI: 10.2460/ajvr.23.03.0061
    OBJECTIVE: The objective of this study was to determine bacterial flora throughout the gastrointestinal tract of a saltwater crocodile (Crocodylus porosus) using 16S rRNA gene analysis.

    ANIMALS: A convention on international trade in endangered species (CITES) of wild fauna and flora registered crocodile farm, provided a healthy male saltwater crocodile, Crocodylus porosus for this study.

    PROCEDURES: Three samples were taken from the oral cavity, 3 samples from the proximal region of the small intestine (jejunum), and 3 samples from the distal part of the large intestine of the gastrointestinal tract of C. porosus were obtained using sterile cotton swabs. Next, swabs were placed in 15 mL sterile centrifuge tubes, individually, and kept on ice for immediate transportation to the laboratory. This was followed by 16S rRNA gene analysis using specific primers (341F-CCTAYGGGRBGCASCAG, and 806R-GGACTACNNGGGTATCTAAT). Amplicons were sequenced on Illumina paired-end platform, and bacterial gastrointestinal communities, the relative abundance of taxa, and principal component and coordinate analysis were performed.

    RESULTS: The findings revealed that bacterial community structures from differing regions exhibited several differences. The number of observed bacterial operational taxonomic units (OTUs) was 153 in the oral cavity, 239 in the small intestine, and 119 in the large intestine of C. porosus. The small intestine reflects the highest richness. In contrast, the large intestine exhibited the least richness of microbial communities. Relative abundance of taxa showed that Proteobacteria, Bacteroidetes, and Firmicutes were dominant in all 3 sample sites. Pseudomonas differed in the oral cavity and the large intestine, with the latter exhibiting less distribution of Pseudomonas. Stenotrophomonas and Castellaniella were higher in the oral cavity, while the relative abundance of Comamonas and Salmonella was higher in the small intestine. Conversely, the relative abundance of Salmonella and Pannonibacter was augmented in the large intestine.

    CLINICAL RELEVANCE: For the first time, this study demonstrates the bacterial diversity along the segments of the gastrointestinal tract of C. porosus. Bacterial flora varies throughout the gastrointestinal tract. Although further studies using large cohorts are warranted; however, our findings suggest that microbiome composition may have the potential as a biomarker in determining the overall health and well-being of C. porosus.

    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  15. Fulltext Isolation of Spirosoma foliorum sp. nov. from the fallen leaf of Acer palmatum by a novel cultivation technique
    Han HL, Nurcahyanto DA, Muhammad N, Lee YJ, Nguyen TTH, Kim SG, et al.
    Sci Rep, 2023 Sep 06;13(1):14684.
    PMID: 37673882 DOI: 10.1038/s41598-023-35108-5
    In the effort of isolating novel microbial species, the strain PL0132T was isolated from a fallen leaf under fresh water at a stream, which glided when grown on a tap water medium (without nutrients). The strain was determined to be Gram-negative, strictly aerobic, and rod-shaped, which grew optimally at 25 °C, pH 6-7, and the strain tolerates 1% (w/v) NaCl concentration. The complete genome of strain PL0132T comprises one contig with a sequencing depth of 76×, consisting of 8,853,064 base pairs and the genomic DNA G + C content was 46.7% (genome). 16S rRNA gene sequence analysis revealed that strain PL0132T represents a member of the phylum Bacteroidetes and is affiliated with the genus Spirosoma. Based on genomic, phenotypic, and chemotaxonomic characteristics, the strain PL0132T represents a novel species of the genus Spirosoma, for which the name Spirosoma foliorum sp. nov. is proposed (= KCTC 72228 T = InaCC B1447T).
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  16. Fulltext Isolation of Streptococcus cuniculi from corneal lesion in laboratory-raised mice
    Tiong V, Loong SK, Mohamad Wali HA, Tan KK, Jee PF, Lim FS, et al.
    J Vet Med Sci, 2021 Mar 05;83(2):280-284.
    PMID: 33441499 DOI: 10.1292/jvms.20-0070
    Corneal lesions appearing as white mass beneath intact epithelium, with ocular discharge in one mouse, was observed in a batch of laboratory-raised BALB/c mice (n=9 of 56). The affected mice remained active, well-groomed and had normal appetite. Isolates recovered from swab cultures of the external and internal contents of the eye had partial 16S rRNA gene sequence of 99.1% similarity to Streptococcus cuniculi. No previous report of S. cuniculi infection in laboratory rodents has been presented. The isolate was susceptible to all antibiotics tested. We suggest S. cuniculi is an opportunistic bacteria in laboratory mice but are uncertain of its source. Our findings revealed that S. cuniculi is able to colonize laboratory mice and should be considered when mice present with eye lesion or ocular discharge.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  17. Fulltext Diet, lifestyle and gut microbiota composition among Malaysian women with gestational diabetes mellitus: a prospective cohort study
    Kunasegaran T, Balasubramaniam VRMT, Thirunavuk Arasoo VJ, Palanisamy UD, Tan YK, Ramadas A
    Sci Rep, 2024 Mar 22;14(1):6891.
    PMID: 38519592 DOI: 10.1038/s41598-024-57627-5
    The study addressed a significant gap in the profiling and understanding of the gut microbiota's influence on Malaysian Malay women with gestational diabetes mellitus (GDM). This prospective cohort study aimed to explore the intricate relationship between gut microbiota, dietary choices, and lifestyle factors among Malay women, both with and without GDM. The research specifically focused on participants during the second (T0) and third (T1) trimesters of pregnancy in Johor Bahru, Malaysia. In Part 1 of the study, a diverse pool of pregnant women at T0 was categorized into two groups: those diagnosed with GDM and those without GDM, with a total sample size of 105 individuals. The assessments encompassed demographic, clinical, lifestyle, and dietary factors at the T0 and T1 trimesters. Part 2 of the study delved into microbiome analysis, targeting a better understanding of the gut microbiota among the participants. Stool samples were randomly collected from 50% of the individuals in each group (GDM and non-GDM) at T0 and T1. The collected samples underwent processing, and 16s rRNA metagenomic analysis was employed to study the microbial composition. The results suggested an association between elevated body weight and glucose levels, poor sleep quality, lack of physical activity, greater intake of iron and meat, and reduced fruit consumption among women with GDM compared to non-GDM groups. The microbiome analysis revealed changes in microbial composition over time, with reduced diversity observed in the GDM group during the third trimester. The genera Lactiplantibacillus, Parvibacter, Prevotellaceae UCG001, and Vagococcus positively correlated with physical activity levels in GDM women in the second trimester. Similarly, the genus Victivallis exhibited a strong positive correlation with gravida and parity. On the contrary, the genus Bacteroides and Roseburia showed a negative correlation with omega-3 polyunsaturated fatty acids (PUFAs) in women without GDM in the third trimester. The study highlighted the multifaceted nature of GDM, involving a combination of lifestyle factors, dietary choices, and changes in gut microbiota composition. The findings emphasized the importance of considering these interconnected elements in understanding and managing gestational diabetes among Malaysian Malay women. Further exploration is essential to comprehend the mechanisms underlying this relationship and develop targeted interventions for effective GDM management.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  18. Fulltext Endometrial microbiota composition is associated with reproductive outcome in infertile patients
    Moreno I, Garcia-Grau I, Perez-Villaroya D, Gonzalez-Monfort M, Bahçeci M, Barrionuevo MJ, et al.
    Microbiome, 2022 Jan 04;10(1):1.
    PMID: 34980280 DOI: 10.1186/s40168-021-01184-w
    BACKGROUND: Previous evidence indicates associations between the female reproductive tract microbiome composition and reproductive outcome in infertile patients undergoing assisted reproduction. We aimed to determine whether the endometrial microbiota composition is associated with reproductive outcomes of live birth, biochemical pregnancy, clinical miscarriage or no pregnancy.

    METHODS: Here, we present a multicentre prospective observational study using 16S rRNA gene sequencing to analyse endometrial fluid and biopsy samples before embryo transfer in a cohort of 342 infertile patients asymptomatic for infection undergoing assisted reproductive treatments.

    RESULTS: A dysbiotic endometrial microbiota profile composed of Atopobium, Bifidobacterium, Chryseobacterium, Gardnerella, Haemophilus, Klebsiella, Neisseria, Staphylococcus and Streptococcus was associated with unsuccessful outcomes. In contrast, Lactobacillus was consistently enriched in patients with live birth outcomes.

    CONCLUSIONS: Our findings indicate that endometrial microbiota composition before embryo transfer is a useful biomarker to predict reproductive outcome, offering an opportunity to further improve diagnosis and treatment strategies. Video Abstract.

    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  19. Purification and Characterization of Desferrioxamine B of Pseudomonas fluorescens and Its Application to Improve Oil Content, Nutrient Uptake, and Plant Growth in Peanuts
    Nithyapriya S, Sundaram L, Eswaran SUD, Perveen K, Alshaikh NA, Sayyed RZ, et al.
    Microb Ecol, 2024 Apr 17;87(1):60.
    PMID: 38630182 DOI: 10.1007/s00248-024-02377-0
    Microorganisms produce siderophores, which are low-molecular-weight iron chelators when iron availability is limited. The present analyzed the role of LNPF1 as multifarious PGPR for improving growth parameters and nutrient content in peanut and soil nutrients. Such multifarious PGPR strains can be used as effective bioinoculants for peanut farming. In this work, rhizosphere bacteria from Zea mays and Arachis hypogaea plants in the Salem area of Tamil Nadu, India, were isolated and tested for biochemical attributes and characteristics that stimulate plant growth, such as the production of hydrogen cyanide, ammonia (6 µg/mL), indole acetic acid (76.35 µg/mL), and solubilizing phosphate (520 µg/mL). The 16S rRNA gene sequences identified the isolate LNPF1 as Pseudomonas fluorescens with a similarity percentage of 99% with Pseudomonas sp. Isolate LNPF1 was evaluated for the production of siderophore. Siderophore-rich supernatant using a Sep Pack C18 column and Amberlite-400 Resin Column (λmax 264) produced 298 mg/L and 50 mg/L of siderophore, respectively. The characterization of purified siderophore by TLC, HPLC, FTIR, and 2D-NMR analysis identified the compound as desferrioxamine, a hydroxamate siderophore. A pot culture experiment determined the potential of LNPF1 to improve iron and oil content and photosynthetic pigments in Arachis hypogaea L. and improve soil nutrient content. Inoculation of A. hypogea seeds with LNPF1 improved plant growth parameters such as leaf length (60%), shoot length (22%), root length (54.68%), fresh weight (47.28%), dry weight (37%), and number of nuts (66.66) compared to the control (untreated seeds). This inoculation also improved leaf iron content (43.42), short iron content (38.38%), seed iron (46.72%), seed oil (31.68%), carotenoid (64.40%), and total chlorophyll content (98.%) compared to control (untreated seeds). Bacterized seeds showed a substantial increase in nodulation (61.65%) and weight of individual nodules (95.97) vis-à-vis control. The results of the present study indicated that P. fluorescens might be utilized as a potential bioinoculant to improve growth, iron content, oil content, number of nuts and nodules of Arachishypogaea L., and enrich soil nutrients.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  20. Fulltext Molecular identification and phylogenetic analysis of GABA-producing lactic acid bacteria isolated from indigenous dadih of West Sumatera, Indonesia
    Anggraini L, Marlida Y, Wizna W, Jamsari J, Mirzah M, Adzitey F, et al.
    F1000Res, 2018 10 19;7:1663.
    PMID: 32201563 DOI: 10.12688/f1000research.16224.3
    Background: Dadih (fermented buffalo milk) is a traditional Indonesian food originating from West Sumatra province. The fermentation process is carried out by lactic acid bacteria (LAB), which are naturally present in buffalo milk.  Lactic acid bacteria have been reported as one of potential producers of γ-aminobutyric acid (GABA). GABA acts as a neurotransmitter inhibitor of the central nervous system. Methods: In this study, molecular identification and phylogenetic analysis of GABA producing LAB isolated from indigenous dadih of West Sumatera were determined. Identification of the GABA-producing LAB DS15 was based on conventional polymerase chain reaction. 16S rRNA gene sequence analysis was used to identify LAB DS15. Results: PCR of the 16S rRNA gene sequence of LAB DS15 gave an approximately 1400 bp amplicon.  Phylogenetic analysis showed that LAB DS15 was Pediococcusacidilactici, with high similarity of 99% at 100% query coverage to Pediococcusacidilactici strain DSM 20284. Conclusions: It can be concluded that GABA producing LAB isolated from indigenous dadih was Pediococcus acidilactici.
    Matched MeSH terms: RNA, Ribosomal, 16S
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