Journal of Microbiology

Volume 60(10); October 2022

Review

[Minireview]Biodegradation of plastics: mining of plastic-degrading microorganisms and enzymes using metagenomics approaches: Dae-Wi Kim , Jae-Hyung Ahn , Chang-Jun Cha; J. Microbiol. 2022;60(10):969-976. Published online September 27, 2022; DOI: https://doi.org/10.1007/s12275-022-2313-7

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Plastic pollution exacerbated by the excessive use of synthetic plastics and its recalcitrance has been recognized among the most pressing global threats. Microbial degradation of plastics has gained attention as a possible eco-friendly countermeasure, as several studies have shown microbial metabolic capabilities as potential degraders of various synthetic plastics. However, still defined biochemical mechanisms of biodegradation for the most plastics remain elusive, because the widely used culture-dependent approach can access only a very limited amount of the metabolic potential in each microbiome. A culture-independent approach, including metagenomics, is becoming increasingly important in the mining of novel plastic-degrading enzymes, considering its more expanded coverage on the microbial metabolism in microbiomes. Here, we described the advantages and drawbacks associated with four different metagenomics approaches (microbial community analysis, functional metagenomics, targeted gene sequencing, and whole metagenome sequencing) for the mining of plastic-degrading microorganisms and enzymes from the plastisphere. Among these approaches, whole metagenome sequencing has been recognized among the most powerful tools that allow researchers access to the entire metabolic potential of a microbiome. Accordingly, we suggest strategies that will help to identify plastisphere-enriched sequences as de novo plastic-degrading enzymes using the whole metagenome sequencing approach. We anticipate that new strategies for metagenomics approaches will continue to be developed and facilitate to identify novel plastic-degrading microorganisms and enzymes from microbiomes.

Citations

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Molecular docking and metagenomics assisted mitigation of microplastic pollution
Dinesh Parida, Konica Katare, Atmaadeep Ganguly, Disha Chakraborty, Oisi Konar, Regina Nogueira, Kiran Bala
Chemosphere.2024; 351: 141271. CrossRef
Recent advances in screening and identification of PET-degrading enzymes
Shengwei Sun
Environmental Reviews.2024; 32(3): 294. CrossRef
Metagenomic analysis of soil from landfill site reveals a diverse microbial community involved in plastic degradation
Akhilesh Kumar, Sudarshan Singh Lakhawat, Kashmir Singh, Vikram Kumar, Kumar Sambhav Verma, Umesh Kumar Dwivedi, S.L. Kothari, Naveen Malik, Pushpender Kumar Sharma
Journal of Hazardous Materials.2024; 480: 135804. CrossRef
PEZy-miner: An artificial intelligence driven approach for the discovery of plastic-degrading enzyme candidates
Renjing Jiang, Zhenrui Yue, Lanyu Shang, Dong Wang, Na Wei
Metabolic Engineering Communications.2024; 19: e00248. CrossRef
Mining strategies for isolating plastic-degrading microorganisms
Ziyao Zhang, Qi Zhang, Huihui Yang, Li Cui, Haifeng Qian
Environmental Pollution.2024; 346: 123572. CrossRef
Microenvironment of Landfill-Mined Soil-Like Fractions (LMSF): Evaluating the Polymer Composting Potential Using Metagenomics and Geoenvironmental Characterization
Arnab Banerjee, Charakho N. Chah, Manoj Kumar Dhal, Kshitij Madhu, Kiran Vilas Dhobale, Bharat Rattan, Vimal Katiyar, Sreedeep Sekharan
International Journal of Environmental Research.2024;[Epub] CrossRef
Progress in polystyrene biodegradation by insect gut microbiota
Luhui Xu, Zelin Li, Liuwei Wang, Zihang Xu, Shulin Zhang, Qinghua Zhang
World Journal of Microbiology and Biotechnology.2024;[Epub] CrossRef
Recent trends in microbial and enzymatic plastic degradation: a solution for plastic pollution predicaments
Swagata Lakshmi Dhali, Dinesh Parida, Bikash Kumar, Kiran Bala
Biotechnology for Sustainable Materials.2024;[Epub] CrossRef
Deconstructing PET: Advances in enzyme engineering for sustainable plastic degradation
Jiaxin Yao, Yao Liu, Zhenghua Gu, Liang Zhang, Zhongpeng Guo
Chemical Engineering Journal.2024; 497: 154183. CrossRef
Mechanistic Insights into Cellular and Molecular Basis of Protein‐Nanoplastic Interactions
Goutami Naidu, Nupur Nagar, Krishna Mohan Poluri
Small.2024;[Epub] CrossRef
Searching for new plastic-degrading enzymes from the plastisphere of alpine soils using a metagenomic mining approach
Beat Frey, Margherita Aiesi, Basil M. Rast, Joel Rüthi, Jérôme Julmi, Beat Stierli, Weihong Qi, Ivano Brunner, Sinosh Skarlyachan
PLOS ONE.2024; 19(4): e0300503. CrossRef
Discovery and characterization of two novel polyethylene terephthalate hydrolases: One from a bacterium identified in human feces and one from the Streptomyces genus
Zhengyang Han, Mario Roque Huanca Nina, Xiaoyan Zhang, Hanyao Huang, Daidi Fan, Yunpeng Bai
Journal of Hazardous Materials.2024; 472: 134532. CrossRef
Synthesis of Renewable and Cost-Effective Bioplastic from Apple Waste: Physicochemical and Biodegradability Studies
Nicholas Yung Li Loh, Hui Ying Pang, Wan Ting Tee, Billie Yan Zhang Hiew, Svenja Hanson, Siewhui Chong, Suchithra Thangalazhy-Gopakumar, Suyin Gan, Lai Yee Lee
Waste and Biomass Valorization.2023; 14(10): 3235. CrossRef
Validated High-Throughput Screening System for Directed Evolution of Nylon-Depolymerizing Enzymes
Hendrik Puetz, Christoph Janknecht, Francisca Contreras, Mariia Vorobii, Tetiana Kurkina, Ulrich Schwaneberg
ACS Sustainable Chemistry & Engineering.2023; 11(43): 15513. CrossRef
Perspectives on biorefineries in microbial production of fuels and chemicals
Stephen R. Decker, Roman Brunecky, John M. Yarbrough, Venkataramanan Subramanian
Frontiers in Industrial Microbiology.2023;[Epub] CrossRef
Microbial Enzyme Biotechnology to Reach Plastic Waste Circularity: Current Status, Problems and Perspectives
Marco Orlando, Gianluca Molla, Pietro Castellani, Valentina Pirillo, Vincenzo Torretta, Navarro Ferronato
International Journal of Molecular Sciences.2023; 24(4): 3877. CrossRef
Trends in in-silico guided engineering of efficient polyethylene terephthalate (PET) hydrolyzing enzymes to enable bio-recycling and upcycling of PET
Sandhya K. Jayasekara, Hriday Dhar Joni, Bhagya Jayantha, Lakshika Dissanayake, Christopher Mandrell, Manuka M.S. Sinharage, Ryan Molitor, Thushari Jayasekara, Poopalasingam Sivakumar, Lahiru N. Jayakody
Computational and Structural Biotechnology Journal.2023; 21: 3513. CrossRef
From waste to resource: Metagenomics uncovers the molecular ecological resources for plastic degradation in estuaries of South China
Lei Zhou, Shilei Sang, Jiajie Li, Yusen Li, Dapeng Wang, Lihong Gan, Zelong Zhao, Jun Wang
Water Research.2023; 242: 120270. CrossRef
Biodegradation of Different Types of Bioplastics through Composting—A Recent Trend in Green Recycling
Wazir Aitizaz Ahsan, Adnan Hussain, Chitsan Lin, Minh Ky Nguyen
Catalysts.2023; 13(2): 294. CrossRef
Biodegradation of Poly(ethylene terephthalate) by Bacillus safensis YX8
Caiting Zeng, Fanghui Ding, Jie Zhou, Weiliang Dong, Zhongli Cui, Xin Yan
International Journal of Molecular Sciences.2023; 24(22): 16434. CrossRef

Journal Articles

Phenotypic and genomic characteristics of Brevibacterium zhoupengii sp. nov., a novel halotolerant actinomycete isolated from bat feces: Yuyuan Huang , Lingzhi Dong , Jian Gong , Jing Yang , Shan Lu , Xin-He Lai , Dong Jin , Qianni Huang , Ji Pu , Liyun Liu , Jianguo Xu; J. Microbiol. 2022;60(10):977-985. Published online August 19, 2022; DOI: https://doi.org/10.1007/s12275-022-2134-8

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Abstract

Two strictly aerobic, Gram-staining-positive, non-spore-forming, regular rod-shaped (approximately 0.7 × 1.9 mm) bacteria (HY170T and HY001) were isolated from bat feces collected from Chongzuo city, Guangxi province (22°20􍿁54􍿂N, 106°49􍿁20􍿂E, July 2011) and Chuxiong Yi Autonomous Prefecture, Yunnan province (25°09􍿁10􍿂N, 102°04􍿁39􍿂E, October 2013) of South China, respectively. Optimal growth is obtained at 25–28°C (range, 4–32°C) on BHI-5% sheep blood plate with pH 7.5 (range, 5.0–10.0) in the presence of 0.5– 1.0% NaCl (w/v) (range, 0–15% NaCl [w/v]). The phylogenetic and phylogenomic trees based respectively on the 16S rRNA gene and 845 core gene sequences revealed that the two strains formed a distinct lineage within the genus Brevibacterium, most closely related to B. aurantiacum NCDO 739T (16S rRNA similarity, both 98.5%; dDDH, 46.7–46.8%; ANI, 91.9–92.1%). Strain HY170T contained MK-8(H2), diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG), galactose and ribose as the predominant menaquinone, major polar lipids, and main sugars in the cell wall teichoic acids, respectively. The meso-diaminopimelic acid (meso-DAP) was the diagnostic diamino acid of the peptidoglycan found in strain HY170T. Anteiso-C15:0 and anteiso-C17:0 were the major fatty acids (> 10%) of strains HY170T and HY001, with anteiso-C17:1A predominant in strain HY170T but absent in strain HY001. Mining the genomes revealed the presence of secondary metabolite biosynthesis gene clusters encoding for non-alpha poly-amino acids (NAPAA), ectoine, siderophore, and terpene. Based on results from the phylogenetic, chemotaxonomic and phenotypic analyses, the two strains could be classified as a novel species of the genus Brevibacterium, for which the name Brevibacterium zhoupengii sp. nov. is proposed (type strain HY170T = CGMCC 1.18600T = JCM 34230T).

Citations

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Antagonistic Behavior of Streptomyces chartreuse against Pathogenic Bacteria in Ricinus communis L.
Bhoomi N. Patel, Priti Patel, Gayatri Patel
Biosciences Biotechnology Research Asia.2024; 21(1): 185. CrossRef
Functional genomics and taxonomic insights into heavy metal tolerant novel bacterium Brevibacterium metallidurans sp. nov. NCCP-602T isolated from tannery effluent in Pakistan
Sadia Manzoor, Saira Abbas, Sobia Zulfiqar, Hong-Chuan Wang, Min Xiao, Wen-Jun Li, Muhammad Arshad, Iftikhar Ahmed
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Description of Ornithinimicrobium cryptoxanthini sp. nov., a Novel Actinomycete Producing β-cryptoxanthin Isolated from the Tongtian River Sediments
Yuyuan Huang, Yifan Jiao, Sihui Zhang, Yuanmeihui Tao, Suping Zhang, Dong Jin, Ji Pu, Liyun Liu, Jing Yang, Shan Lu
Journal of Microbiology.2023; 61(4): 379. CrossRef
Morphological and genomic characteristics of two novel actinomycetes, Ornithinimicrobium sufpigmenti sp. nov. and Ornithinimicrobium faecis sp. nov. isolated from bat faeces (Rousettus leschenaultia and Taphozous perforates)
Yuyuan Huang, Suping Zhang, Yuanmeihui Tao, Jing Yang, Shan Lu, Dong Jin, Ji Pu, Wenbo Luo, Han Zheng, Liyun Liu, Jia-fu Jiang, Jianguo Xu
Frontiers in Cellular and Infection Microbiology.2023;[Epub] CrossRef

Microbial co-occurrence network in the rhizosphere microbiome: its association with physicochemical properties and soybean yield at a regional scale: Sarbjeet Niraula , Meaghan Rose , Woo-Suk Chang; J. Microbiol. 2022;60(10):986-997. Published online September 27, 2022; DOI: https://doi.org/10.1007/s12275-022-2363-x

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Abstract

Microbial communities in the rhizosphere play a crucial role in determining plant growth and crop yield. A few studies have been performed to evaluate the diversity and co-occurrence patterns of rhizosphere microbiomes in soybean (Glycine max) at a regional scale. Here, we used a culture-independent
method
to compare the bacterial communities of the soybean rhizosphere between Nebraska (NE), a high-yield state, and Oklahoma (OK), a low-yield state. It is well known that the rhizosphere microbiome is a subset of microbes that ultimately get colonized by microbial communities from the surrounding bulk soil. Therefore, we hypothesized that differences in the soybean yield are attributed to the variations in the rhizosphere microbes at taxonomic, functional, and community levels. In addition, soil physicochemical properties were also evaluated from each sampling site for comparative study. Our result showed that distinct clusters were formed between NE and OK in terms of their soil physicochemical property. Among 3 primary nutrients (i.e., nitrogen, phosphorus, and potassium), potassium is more positively correlated with the high-yield state NE samples. We also attempted to identify keystone communities that significantly affected the soybean yield using co-occurrence network patterns. Network analysis revealed that communities formed distinct clusters in which members of modules having significantly positive correlations with the soybean yield were more abundant in NE than OK. In addition, we identified the most influential bacteria for the soybean yield in the identified modules. For instance, included are class Anaerolineae, family Micromonosporaceae, genus Plantomyces, and genus Nitrospira in the most complex module (ME9) and genus Rhizobium in ME23. This research would help to further identify a way to increase soybean yield in low-yield states in the U.S. as well as worldwide by reconstructing the microbial communities in the rhizosphere.

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The rhizosphere microbiome of 51 potato cultivars with diverse plant growth characteristics
Benoit Renaud Martins, Viviane Radl, Krzysztof Treder, Dorota Michałowska, Karin Pritsch, Michael Schloter
FEMS Microbiology Ecology.2024;[Epub] CrossRef
Response of Soil Microorganisms and Phenolic to Pseudostelariae heterophylla Cultivation in Different Soil Types
Yingying Liu, Dan Wu, Yongjun Kan, Li Zhao, Chang Jiang, Wensheng Pang, Juan Hu, Meilan Zhou
Eurasian Soil Science.2024; 57(3): 446. CrossRef
Analysis of the rhizosphere bacterial diversity of Angelica dahurica var. formosana from different experimental sites and varieties (strains)
Meiyan Jiang, Fei Yao, Yunshu Yang, Yang Zhou, Kai Hou, Yinyin Chen, Dongju Feng, Wei Wu
PeerJ.2023; 11: e15997. CrossRef
Long-term fertilization coupled with rhizobium inoculation promotes soybean yield and alters soil bacterial community composition
Wanling Wei, Dawei Guan, Mingchao Ma, Xin Jiang, Fenliang Fan, Fangang Meng, Li Li, Baisuo Zhao, Yubin Zhao, Fengming Cao, Huijun Chen, Jun Li
Frontiers in Microbiology.2023;[Epub] CrossRef

Enzyme activity of Aspergillus section Nigri strains isolated from the Korean fermentation starter, nuruk: Eunji Jeong , Jeong-Ah Seo; J. Microbiol. 2022;60(10):998-1006. Published online August 19, 2022; DOI: https://doi.org/10.1007/s12275-022-2071-6

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Abstract

Aspergillus section Nigri is a fungus used industrially because of its ability to produce enzymes such as cellulolytic, amylolytic and proteolytic enzymes. In this study, we obtained twentyeight strains of Aspergillus section Nigri from the traditional Korean fermentation starter, nuruk, which is known as a mixed culture of enzymatic filamentous fungi and yeasts. All strains were identified as Aspergillus section Nigri through combined phylogenetic analysis using partial β-tubulin and calmodulin gene sequences. The cellulase, amylase and protease activities of Korean strains were measured and compared with ten reference strains of Aspergillus niger. Most Korean strains showed higher cellulolytic activity than reference strains, and Aspergillus neoniger KCN5 showed the highest β-glucosidase activity. Two-thirds of the Korean strains showed similar levels of α- and glucoamylase activity as the reference strains. The protease activity of Aspergillus section Nigri strains was the highest at pH 3.0, and A. niger KSJ2 showed the highest acidic protease activity. By comparing ten reference strains and twenty-eight Korean strains, our results suggested useful Aspergillus section Nigri strains from nuruk with high enzyme activity, such as KCN5 and KSJ2, and their potential for industrial applications as enzyme producers.

Citations

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Effect of Aspergillus niger Fermentation on the Metabolites in Corn Stalks
Zhen Fan, Tianming Chen, Guolin Cai, Xiaoyu Huang, Suchuan Zhong, Xiaoming Li, Enping Zhang
Fermentation.2023; 9(1): 50. CrossRef

Genomic and physiological analysis of C50 carotenoid-producing novel Halorubrum ruber sp. nov.: Chi Young Hwang , Eui-Sang Cho , Won Jong Rhee , Eunjung Kim , Myung-Ji Seo; J. Microbiol. 2022;60(10):1007-1020. Published online August 26, 2022; DOI: https://doi.org/10.1007/s12275-022-2173-1

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Abstract

A novel haloarchaeal species designated as MBLA0099T was isolated from seawater near Yeongheung Island. Cells were Gram-negative, non-motile, red-pigmented, and rod-shaped. They grew at 10–45°C, within pH 5.5–9.0, and between 7.5% and 30% NaCl concentrations. Cells were able to grow without Mg2+ and were lysed in distilled water. The size of the whole-genome and G + C content of DNA was 3.02 Mb and 68.9 mol%, respectively. Phylogenetic analysis shows that the strain MBLA0099T belongs to the genus Halorubrum. The average nucleotide and amino acid identity, and in silico DNA-DNA hybridization values were below the species delineation threshold. Pan-genomic analysis revealed that 3.2% of all genes present in strain MBLA0099T were unique to the strain. The red carotenoid produced by strain MBLA0099T was subjected to spectrometric and chromatographic analyses and confirmed to be bacterioruberin as C50 carotenoid. Mevalonic acid, terpenoid backbone, and carotenoid biosynthesis pathway were annotated for strain MBLA0099T. The C50 carotenoid production by strain MBLA0099T was also enhanced under various stress conditions including relatively netural pH, high oxidative and salinity conditions. Additionally, the strain MBLA0099T-derived bacterioruberin showed the antioxidant activity with EC50 value of 12.29 μg/ml, based on the evaluation of DPPH free radical scavenging activity. The present study would be the first report on the identification of C50 carotenoid from the strain MBLA0099T representing a novel species of the genus Halorubrum, for which the name Halorubrum ruber sp. nov. is proposed. The typestrain used was MBLA0099T (= KCTC 4296T = JCM 34701T).

Citations

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Optimization of bacterioruberin production from Halorubrum ruber and assessment of its antioxidant potential
Chi Young Hwang, Eui-Sang Cho, Sungjun Kim, Kyobum Kim, Myung-Ji Seo
Microbial Cell Factories.2024;[Epub] CrossRef
Microbial Bacterioruberin: A Comprehensive Review
Mouliraj Palanisamy, Sathishkumar Ramalingam
Indian Journal of Microbiology.2024; 64(4): 1477. CrossRef
Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef
Genomic insights on carotenoid synthesis by extremely halophilic archaea Haloarcula rubripromontorii BS2, Haloferax lucentense BBK2 and Halogeometricum borinquense E3 isolated from the solar salterns of India
Devika. N. Nagar, Kabilan Mani, Judith M. Braganca
Scientific Reports.2024;[Epub] CrossRef
Microbial bacterioruberin: The new C50 carotenoid player in food industries
Cassamo U. Mussagy, Angie V. Caicedo-Paz, Fabiane O. Farias, Leonardo M. de Souza Mesquita, Daniele Giuffrida, Laurent Dufossé
Food Microbiology.2024; 124: 104623. CrossRef
Evaluation of Various Escherichia coli Strains for Enhanced Lycopene Production
Jun Ren, Junhao Shen, Thi Duc Thai, Min-gyun Kim, Seung Ho Lee, Wonseop Lim, Dokyun Na
Journal of Microbiology and Biotechnology.2023; 33(7): 973. CrossRef
Bioactive molecules from haloarchaea: Scope and prospects for industrial and therapeutic applications
Jamseel Moopantakath, Madangchanok Imchen, V. T. Anju, Siddhardha Busi, Madhu Dyavaiah, Rosa María Martínez-Espinosa, Ranjith Kumavath
Frontiers in Microbiology.2023;[Epub] CrossRef

Observational Study

Early gut microbiota in very low and extremely low birth weight preterm infants with feeding intolerance: a prospective case-control study: Ling Liu , Dang Ao , Xiangsheng Cai , Peiyi Huang , Nali Cai , Shaozhu Lin , Benqing Wu; J. Microbiol. 2022;60(10):1021-1031. Published online August 19, 2022; DOI: https://doi.org/10.1007/s12275-022-2180-2

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Abstract

The potential role of the gut microbiota in the pathogenesis of feeding intolerance (FI) remains unclear. Understanding the role of the gut microbiota could provide a new avenue for microbiota-targeted therapeutics. This study aimed to explore the associations between aberrant gut microbiota and FI in very low or extremely low birth weight (VLBW/ELBW) preterm infants. In this observational case-control study, VLBW/ ELBW infants were divided into two groups: FI group and feeding tolerance (FT) group. 16S rRNA gene sequencing was performed to analyze the gut microbial diversity and composition of the infants. The differences in the gut microbiota of the two groups were compared. In total, 165 stool samples were obtained from 44 infants, among which, 31 developed FI and 13 served as controls. Alpha diversity was the highest in the meconium samples of the two groups. LEfSe analysis revealed that the abundances of Peptostreptococcaceae, Clostridiales and Clostridia in the FT group were significantly higher than in the FI group. At the phylum level, the FI group was dominated by Proteobacteria, and the FT group was dominated by Firmicutes. The meconium samples of the FI group had higher proportions of γ-proteobacteria and Escherichia-Shigella and a lower proportion of Bacteroides compared with the FT group. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that aberrant gut bacteria in the FI group were strongly associated with dysregulation of C5-Brancheddibasic- acid-metabolism, protein kinases, and sporulation. These findings reveal candidate microbial markers to prevent FI. Increased relative abundances of γ-proteobacteria and Escherichia-Shigella and decreased abundance of Bacteroides in meconium were associated with an increased risk of FI, while Peptostreptococcaceae, Clostridiales and Clostridia reduced the risk of FI in VLBW/ELBW infants.

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Reduced Gut Bacterial Diversity in Early Life Predicts Feeding Intolerance in Preterm Neonates
Maria Di Chiara, Alessandro Lazzaro, Daniela Scribano, Maria Trancassini, Valeria Pietropaolo, Michele Sonnessa, Chiara De Luca, Rita Prota, Elisa Onestà, Gianluigi Laccetta, Gianluca Terrin
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Calorie restriction during gestation impacts maternal and offspring fecal microbiome in mice
Stephanie P. Gilley, Meghan L. Ruebel, Sree V. Chintapalli, Clyde J. Wright, Paul J. Rozance, Kartik Shankar
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Dynamics alteration of the gut microbiota and faecal metabolomes in very low or extremely low birth weight infants: a Chinese single-center, prospective cohort study
Ling Liu, Chaohong Chen, YeShan Li, Dang Ao, Jiayuan Wu, Nali Cai, Wen Li, Min Xiang
Frontiers in Microbiology.2024;[Epub] CrossRef
Metabolic and fecal microbial changes in adult fetal growth restricted mice
Stephanie P. Gilley, Miguel A. Zarate, Lijun Zheng, Purevsuren Jambal, Deaunabah N. Yazza, Sree V. Chintapalli, Paul S. MacLean, Clyde J. Wright, Paul J. Rozance, Kartik Shankar
Pediatric Research.2024; 95(3): 647. CrossRef
A digital twin of the infant microbiome to predict neurodevelopmental deficits
Nicholas Sizemore, Kaitlyn Oliphant, Ruolin Zheng, Camilia R. Martin, Erika C. Claud, Ishanu Chattopadhyay
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Investigating prenatal and perinatal factors on meconium microbiota: a systematic review and cohort study
Jenni Turunen, Mysore V. Tejesvi, Niko Paalanne, Tytti Pokka, Sajeen Bahadur Amatya, Surbhi Mishra, Anna Kaisanlahti, Justus Reunanen, Terhi Tapiainen
Pediatric Research.2024; 95(1): 135. CrossRef
Novel scoring system for early diagnosis of necrotizing enterocolitis: integrating clinical and laboratory data with urinary caveolin-1 levels
Brigitta I.R.V. Corebima, Rinawati Rohsiswatmo, Dewi Santosaningsih, Wisnu Barlianto, Kusworini Handono
Archives of Medical Science.2023; 20(2): 444. CrossRef
Dynamics and Crosstalk between Gut Microbiota, Metabolome, and Fecal Calprotectin in Very Preterm Infants: Insights into Feeding Intolerance
Luyang Hong, Yihuang Huang, Junyan Han, Shujuan Li, Lan Zhang, Siyuan Jiang, Qi Zhou, Xincheng Cao, Weiyin Yu, Yi Yang, Shangyu Hong, Yufeng Zhou, Weili Yan, Yun Cao
Nutrients.2023; 15(22): 4849. CrossRef
Characteristics of Gut Microbiota in Small for Gestational Age Infants with Very Low Birth Weight
Hung-Yang Chang, Jen-Shiu Chiang Chiau, Jui-Hsing Chang, Chyong-Hsin Hsu, Chia-Ying Lin, Mary Hsin-Ju Ko, Hung-Chang Lee
Nutrients.2022; 14(23): 5158. CrossRef
Compositional Differences of Meconium Microbiomes of Preterm and Term Infants, and Infants That Developed Necrotizing Enterocolitis or Feeding Intolerance
Hyun Mi Kang, Sol Kim, Seok Hwang-Bo, In Hyuk Yoo, Yu-Mi Seo, Moon Yeon Oh, Soo-Ah Im, Young-Ah Youn
Pathogens.2022; 12(1): 55. CrossRef

Journal Articles

DNA vaccine dual-expressing viral hemorrhagic septicemia virus glycoprotein and C-C motif chemokine ligand 19 induces the expression of immune-related genes in zebrafish (Danio rerio): Jin-Young Kim , Hyoung Jun Kim , Jeong Su Park , Se Ryun Kwon; J. Microbiol. 2022;60(10):1032-1038. Published online August 1, 2022; DOI: https://doi.org/10.1007/s12275-022-2231-8

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Abstract

Glycoprotein (G protein)-based DNA vaccines are effective in protecting aquaculture fish from rhabdoviruses but the degree of immune response they elicit depends on plasmid concentration and antigen cassette. Here, we developed a DNA vaccine using the viral hemorrhagic septicemia virus G (VG) gene and chemokine (C-C motif) ligand 19 (CCL19)a.2 regulated by the CMV promoter as the molecular adjuvant. After transfection of the prepared plasmid (pVG + CCL19) into epithelioma papulosum cyprini cells, mRNA expression was confirmed through quantitative real-time polymerase chain reaction. The vaccine was intramuscularly injected into zebrafish (Danio rerio), and 28 days after immunization, viral hemorrhagic septicemia virus (105 TCID50/10 μl/fish) was intraperitoneally injected. A survival rate of 68% was observed in the pVG + CCL19 group but this was not significantly different from the survival rate of fish treated with pVG alone, that is, without the adjuvant. However, the expression of interferonand cytokine-related genes in the spleen and kidney tissues of zebrafish was significantly increased (p < 0.05) on days 1, 3, 7, and 14 after immunization. Thus, CCL19a.2 induced an initial immune response as a molecular adjuvant, which may provide initial protection against virus infection before vaccination- induced antibody formation. This study provides insights on the functions of CCL19a.2 adjuvant in DNA vaccines.

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LncRNA activates immune response against Vibrio anguillarum in the intestine-liver axis of turbot (Scophthalmus maximus L.) by sponging miRNA in a ceRNA regulatory network
Xin Cai, Chengbin Gao, Alan J. Lymbery, Le Ma, Qiang Fu, Ranran Huang, Chao Li
Aquaculture.2023; 576: 739882. CrossRef
Determining transcriptomic response of kidneys of olive flounder to viral hemorrhagic septicemia virus infection using next-generation sequencing
Hyoung Jun Kim, Jeong Su Park, Se Ryun Kwon, Youngjin Park
Aquaculture.2023; 562: 738886. CrossRef
Integrative transcriptomic profiling reveals the key pathways in the regulation mechanism of fish intestine-spleen immunity during the bacterial challenges
Chengbin Gao, Xin Cai, Alan J. Lymbery, Le Ma, Min Cao, Chao Li
Aquaculture.2023; 568: 739320. CrossRef

Core promoter mutation of nucleotides A1762T and G1764A of hepatitis B virus increases core promoter transactivation by hepatocyte nuclear factor 1: Mi So Seong , Hyeon Jeong Hwang , Eun Ah Jang , Jeong Ah Jang , Wah Wah Aung , Yi Yi Kyaw , JaeHun Cheong; J. Microbiol. 2022;60(10):1039-1047. Published online September 27, 2022; DOI: https://doi.org/10.1007/s12275-022-1675-1

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Abstract

Hepatitis B virus (HBV) infection highly increases the risk for liver cirrhosis and hepatocellular carcinoma (HCC). The clinical manifestation of HBV infection is determined by the mutual interplay of the viral genotype, host genetic factors, mode of transmission, adaptive mutations, and environmental factors. Core promoter activation plays a critical role in the pre-genomic RNA transcription of HBV for HBV replication. The mutations of core promoter have been implicated in HCC development. We had obtained HBV genes from Myanmar HBV infectants and identified gene variations at the core promoter region. For measuring the relative transactivation activity on core promoter, we prepared the core-promoter reporter construct. Both of A1762T and G1764A mutation were consistently found in the HBV genes with hepatocellular carcinoma. The A1762T/G1764A mutation was corresponding to K130M/V131I of HBx protein. We prepared the core promoter- luciferase reporter construct containing the double A1762T/G1764A mutation and the K130M/V131I HBx protein expression construct. The A1762T/G1764A mutation highly was responsive to core promoter transactivation by HBx, regardless of HBx mutation. The A1762T/G1764A mutation newly created hepatocyte nuclear factor 1 (HNF1) responsive element. Ectopic expression of HNF1 largely increased the HBV core promoter containing A1762T/G1764A mutation. In addition, hepatic rich fatty acid, palmitic acid and oleic acid, increased K130M/V131I HBx level by core promoter activation. These results provide biological properties and clinical significance of specific HBV core promoter mutants related with HCC development.

Citations

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A Survey of HBV Core/Pre-Core Mutations in Iraqi Patients with Chronic Hepatitis
Abdulhussain Kadhim Jwaziri, Maryam Esghaei, Mohammad Hadi Karbalaie Niya, Hadi Sayah, Mohammad Hossein Razizadeh, Ali Gholami, Leila Mousavizadeh, Hossein Keyvani
Hepatitis Monthly.2023;[Epub] CrossRef
The A1762T/G1764A mutations enhance HBV replication by alternating viral transcriptome
Danli Yang, Jun Zou, Guiwen Guan, Xiaoyu Feng, Ting Zhang, Guixin Li, Hui Liu, Huiling Zheng, Jingyuan Xi, Guangxin Yu, Lizhong Dai, Fengmin Lu, Xiangmei Chen
Journal of Medical Virology.2023;[Epub] CrossRef
Clinical application value of hepatitis B virus basal core promoter 1762/1764 and GGTII and GGT in patients with HBV-DNA-positive primary liver cancer
Shunhua Qiu, Lifen Jin, Dan Yang, Dewen Zhang
Medicine.2023; 102(43): e35699. CrossRef

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