Displaying publications 1 - 20 of 630 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. VapC toxin switches M. smegmatis cells into dormancy through 23S rRNA cleavage
    Zamakhaev M, Grigorov A, Bespyatykh J, Azhikina T, Goncharenko A, Shumkov M
    Arch Microbiol, 2022 Dec 15;205(1):28.
    PMID: 36520276 DOI: 10.1007/s00203-022-03363-1
    Mycobacterium tuberculosis is an extremely successful pathogen known for its ability to cause latent infection. The latter is connected with the bacterium resting state development and is considered to be based on the activity of toxin-antitoxin (TA) systems at least in part. Here we studied the physiological and proteomic consequences of VapC toxin overexpression together with the features of the protein synthesis apparatus and compared them with the characteristics of dormant mycobacterial cells in an M. smegmatis model. The findings allow suggesting the mechanism mycobacteria enter dormancy, which is realized through VapC-caused cleavage of the 23S rRNA Sarcin-Ricin loop followed by conservation of stalled ribosomes in a membrane-associated manner. The found features of resting mycobacteria protein synthesis apparatus hypothesize the mechanisms of resuscitation from dormancy through the ribosomes de-association off the membrane accompanied by the 23S rRNA break curing, and could be of value for the development of principally new antituberculosis agents.
    Matched MeSH terms: RNA, Ribosomal, 23S/genetics; RNA, Ribosomal, 23S/metabolism
  3. Fulltext Prevalence, complete genome, and metabolic potentials of a phylogenetically novel cyanobacterial symbiont in the coral-killing sponge, Terpios hoshinota
    Chen YH, Chen HJ, Yang CY, Shiu JH, Hoh DZ, Chiang PW, et al.
    Environ Microbiol, 2022 Mar;24(3):1308-1325.
    PMID: 34708512 DOI: 10.1111/1462-2920.15824
    Terpios hoshinota is an aggressive, space-competing sponge that kills various stony corals. Outbreaks of this species have led to intense damage to coral reefs in many locations. Here, the first large-scale 16S rRNA gene survey across three oceans revealed that bacteria related to the taxa Prochloron, Endozoicomonas, SAR116, Ruegeria, and unclassified Proteobacteria were prevalent in T. hoshinota. A Prochloron-related bacterium was the most dominant and prevalent cyanobacterium in T. hoshinota. The complete genome of this uncultivated cyanobacterium and pigment analysis demonstrated that it has phycobiliproteins and lacks chlorophyll b, which is inconsistent with the definition of Prochloron. Furthermore, the cyanobacterium was phylogenetically distinct from Prochloron, strongly suggesting that it should be a sister taxon to Prochloron. Therefore, we proposed this symbiotic cyanobacterium as a novel species under the new genus Candidatus Paraprochloron terpiosi. Comparative genomic analyses revealed that 'Paraprochloron' and Prochloron exhibit distinct genomic features and DNA replication machinery. We also characterized the metabolic potentials of 'Paraprochloron terpiosi' in carbon and nitrogen cycling and propose a model for interactions between it and T. hoshinota. This study builds a foundation for the study of the T. hoshinota microbiome and paves the way for better understanding of ecosystems involving this coral-killing sponge.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics; RNA, Ribosomal, 16S/metabolism
  4. Fulltext Correction to: Absence of Plasmodium inui and Plasmodium cynomolgi, but detection of Plasmodium knowlesi and Plasmodium vivax infections in asymptomatic humans in the Betong division of Sarawak, Malaysian Borneo
    Siner A, Liew ST, Kadir KA, Mohamad DSA, Thomas FK, Zulkarnaen M, et al.
    Malar J, 2017 11 06;16(1):445.
    PMID: 29110664 DOI: 10.1186/s12936-017-2093-4
    After publication of the article [1], it has been brought to our attention that two of the labels on Figure 4 have transposed. The labels "S-type SSU rRNA" and "A-type SSU rRNA" should be in opposite places.
    Matched MeSH terms: RNA, Ribosomal
  5. A cyst-forming coccidian with large geographical range infecting forest and commensal rodents: Sarcocystis muricoelognathis sp. nov
    Qin T, Ortega-Perez P, Wibbelt G, Lakim MB, Ginting S, Khoprasert Y, et al.
    Parasit Vectors, 2024 Mar 15;17(1):135.
    PMID: 38491403 DOI: 10.1186/s13071-024-06230-8
    BACKGROUND: The geographic distribution and host-parasite interaction networks of Sarcocystis spp. in small mammals in eastern Asia remain incompletely known.

    METHODS: Experimental infections, morphological and molecular characterizations were used for discrimination of a new Sarcocystis species isolated from colubrid snakes and small mammals collected in Thailand, Borneo and China.

    RESULTS: We identified a new species, Sarcocystis muricoelognathis sp. nov., that features a relatively wide geographic distribution and infects both commensal and forest-inhabiting intermediate hosts. Sarcocystis sporocysts collected from rat snakes (Coelognathus radiatus, C. flavolineatus) in Thailand induced development of sarcocysts in experimental SD rats showing a type 10a cyst wall ultrastructure that was identical with those found in Rattus norvegicus from China and the forest rat Maxomys whiteheadi in Borneo. Its cystozoites had equal sizes in all intermediate hosts and locations, while sporocysts and cystozoites were distinct from other Sarcocystis species. Partial 28S rRNA sequences of S. muricoelognathis from M. whiteheadi were largely identical to those from R. norvegicus in China but distinct from newly sequenced Sarcocystis zuoi. The phylogeny of the nuclear 18S rRNA gene placed S. muricoelognathis within the so-called S. zuoi complex, including Sarcocystis attenuati, S. kani, S. scandentiborneensis and S. zuoi, while the latter clustered with the new species. However, the phylogeny of the ITS1-region confirmed the distinction between S. muricoelognathis and S. zuoi. Moreover, all three gene trees suggested that an isolate previously addressed as S. zuoi from Thailand (KU341120) is conspecific with S. muricoelognathis. Partial mitochondrial cox1 sequences of S. muricoelognathis were almost identical with those from other members of the group suggesting a shared, recent ancestry. Additionally, we isolated two partial 28S rRNA Sarcocystis sequences from Low's squirrel Sundasciurus lowii that clustered with those of S. scandentiborneensis from treeshews.

    CONCLUSIONS: Our results provide strong evidence of broad geographic distributions of rodent-associated Sarcocystis and host shifts between commensal and forest small mammal species, even if the known host associations remain likely only snapshots of the true associations.

    Matched MeSH terms: RNA, Ribosomal, 18S/genetics; RNA, Ribosomal, 28S/genetics
  6. 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
  7. Acanthamoeba species isolated from marine water in Malaysia exhibit distinct genotypes and variable physiological properties
    Mohd Hussain RH, Abdul Ghani MK, Khan NA, Siddiqui R, Anuar TS
    J Water Health, 2022 Jan;20(1):54-67.
    PMID: 35100154 DOI: 10.2166/wh.2021.128
    The present study identifies the Acanthamoeba genotypes and their pathogenic potential in five marine waters in Malaysia. Fifty water samples were collected between January and May 2019. Physical parameters of water quality were measured in situ, whereas chemical and microbiological analyses were conducted in the laboratory. All samples had undergone filtration using nitrocellulose membrane and were tested for Acanthamoeba using cultivation and polymerase chain reaction by targeting the 18S ribosomal RNA gene. The pathogenic potential of all positive isolates was identified using physiological tolerance tests. Thirty-six (72.0%) samples were positive for Acanthamoeba. Total coliforms (p = 0.013) and pH level (p = 0.023) displayed significant correlation with Acanthamoeba presence. Phylogenetic analysis showed that 27 samples belonged to genotype T4, four (T11), two (T18) and one from each genotype T5, T15 and T20. Thermo- and osmo-tolerance tests signified that three (8.3%) Acanthamoeba strains displayed highly pathogenic attributes. This study is the first investigation in Malaysia describing Acanthamoeba detection in marine water with molecular techniques and genotyping. The study outcomes revealed that the marine water in Malaysia could be an integral source of Acanthamoeba strains potentially pathogenic in humans. Thus, the potential risk of this water should be monitored routinely in each region.
    Matched MeSH terms: RNA, Ribosomal, 18S/genetics
  8. 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
  9. 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
  10. 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
  11. 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
  12. Finding Sarcocystis spp. on the Tioman Island: 28S rRNA gene next-generation sequencing reveals nine new Sarcocystis species
    Lee FCH
    J Water Health, 2019 Jun;17(3):416-427.
    PMID: 31095517 DOI: 10.2166/wh.2019.124
    The Tioman Island of Malaysia experienced acute muscular sarcocystosis outbreaks from 2011 to 2014. So far, a previous study based on the 18S rRNA gene sequencing has reported S. singaporensis, S. nesbitti and Sarcocystis sp. YLL-2013 in water samples acquired from the island, thus confirming the waterborne nature of this emerging parasitic disease. This study aimed to improve the detection methods for Sarcocystis, in order to have a clearer picture of the true diversity of Sarcocystis species in Tioman. A new primer set (28S R7F-28S R8 Deg R) was designed to amplify the 28S rRNA gene of Sarcocystis. Subsequently, Sarcocystidae was detected in 65.6% (21/32) of water samples and 28% (7/25) of soil samples acquired between 2014 and 2015 from Tioman. Next-generation sequencing (NGS) on 18 of the positive samples was then performed using amplicons generated from the same primer set. This yielded 53 potentially unique Sarcocystidae sequences (290 bp), of which nine of the most abundant, prevalent and unique sequences were named herein. In contrast, NGS of the 18S rRNA gene V9 hypervariable region of 10 selected samples detected only two Sarcocystis species (160 bp). S. mantioni was the most ubiquitous sequence found in this study.
    Matched MeSH terms: RNA, Ribosomal, 18S; RNA, Ribosomal, 28S
  13. 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
  14. 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
  15. 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
  16. Fulltext Detection of a Babesia sp. genotype closely related to marsupial-associated Babesia spp. in male Haemaphysalis shimoga from Sarawak, Malaysian Borneo
    Lau AC, Qiu Y, Moustafa MAM, Nakao R, Shimozuru M, Onuma M, et al.
    J Vet Med Sci, 2022 Nov 01;84(11):1469-1473.
    PMID: 36123016 DOI: 10.1292/jvms.22-0304
    In this study, Babesia screening was conducted in 55 rodents and 160 tick samples collected from primary forests and an oil palm plantation in Sarawak, Malaysian Borneo. PCR targeting the 18S ribosomal DNA revealed the presence of Babesia spp. DNA detected in two questing male Haemaphysalis shimoga ticks collected from the oil palm plantation. Sequence analysis revealed that both sequences were identical and had 98.6% identity to a Babesia macropus sequence obtained from Eastern grey kangaroos (Macropus giganteus) in Australia. Phylogenetic tree revealed clustering with marsupial-associated Babesia spp. in the Babesia sensu stricto clade. Whether or not H. shimoga is the competent vector and the importance of the Babesia sp. detected in this study warrants more investigation.
    Matched MeSH terms: RNA, Ribosomal, 18S/genetics
  17. 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
  18. 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
  19. 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
  20. 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
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