Journal of Microbiology

Journal Articles

Mammaliicoccus sciuri's Pan-Immune System and the Dynamics of Horizontal Gene Transfer Among Staphylococcaceae: a One-Health CRISPR Tale.: Allan de Carvalho, Marcia Giambiagi-deMarval, Ciro César Rossi; J. Microbiol. 2024;62(9):775-784. Published online July 22, 2024; DOI: https://doi.org/10.1007/s12275-024-00156-7

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Abstract: Recently emancipated from the Staphylococcus genus due to genomic differences, Mammaliicoccus sciuri, previously classified as an occasional pathogen, emerges as a significant player in the landscape of resistance gene dissemination among Staphylococcaceae. Despite its classification, its role remained enigmatic. In this study, we delved into the genomic repertoire of M. sciuri to unravel its contribution to resistance and virulence gene transfer in the context of One Health. Through comprehensive analysis of publicly available genomes, we unveiled a diverse pan-immune system adept at defending against exogenous genetic elements, yet concurrently fostering horizontal gene transfer (HGT). Specifically, exploration of CRISPR-Cas systems, with spacer sequences as molecular signatures, elucidated a global dissemination pattern spanning environmental, animal, and human hosts. Notably, we identified the integration of CRISPR-Cas systems within SCCmecs (Staphylococcal Cassette Chromosome mec), harboring key genes associated with pathogenicity and resistance, especially the methicillin resistance gene mecA, suggesting a strategic adaptation to outcompete other mobile genetic elements. Our findings underscored M. sciuri's active engagement in HGT dynamics and evolutionary trajectories within Staphylococcaceae, emphasizing its central role in shaping microbial communities and highlighting the significance of understanding its implications in the One Health framework, an interdisciplinary approach that recognizes the interconnectedness of human, animal, and environmental health to address global health challenges.

Delineating the Acquired Genetic Diversity and Multidrug Resistance in Alcaligenes from Poultry Farms and Nearby Soil.: Abhilash Bhattacharjee, Anil Kumar Singh; J. Microbiol. 2024;62(7):511-523. Published online June 21, 2024; DOI: https://doi.org/10.1007/s12275-024-00129-w

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Abstract: Alcaligenes faecalis is one of the most important and clinically significant environmental pathogens, increasing in importance due to its isolation from soil and nosocomial environments. The Gram-negative soil bacterium is associated with skin endocarditis, bacteremia, dysentery, meningitis, endophthalmitis, urinary tract infections, and pneumonia in patients. With emerging antibiotic resistance in A. faecalis, it has become crucial to understand the origin of such resistance genes within this clinically significant environmental and gut bacterium. In this research, we studied the impact of antibiotic overuse in poultry and its effect on developing resistance in A. faecalis. We sampled soil and faecal materials from five poultry farms, performed whole genome sequencing & analysis and identified four strains of A. faecalis. Furthermore, we characterized the genes in the genomic islands of A. faecalis isolates. We found four multidrug-resistant A. faecalis strains that showed resistance against vancomycin (MIC >1000 μg/ml), ceftazidime (50 μg/ml), colistin (50 μg/ml) and ciprofloxacin (50 μg/ml). From whole genome comparative analysis, we found more than 180 resistance genes compared to the reference sequence. Parts of our assembled contigs were found to be similar to different bacteria which included pbp1A and pbp2 imparting resistance to amoxicillin originally a part of Helicobacter and Bordetella pertussis. We also found the Mycobacterial insertion element IS6110 in the genomic islands of all four genomes. This prominent insertion element can be transferred and induce resistance to other bacterial genomes. The results thus are crucial in understanding the transfer of resistance genes in the environment and can help in developing regimes for antibiotic use in the food and poultry industry.

Letter

Proposal of Flavihumibacter fluvii sp. nov. as a replacement name for the effectively published but invalidated epithet Flavihumibacter fluminis Park et al. 2022: Miri S. Park , Hyeonuk Sa , Ilnam Kang , Jang-Cheon Cho; J. Microbiol. 2023;61(6):649-651. Published online June 12, 2023; DOI: https://doi.org/10.1007/s12275-023-00057-1

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Abstract: The name Flavihumibacter fluminis Park et al. 2022, which was effectively published but invalidated, is an illegitimate homonymic epithet of Flavihumibacter fluminis Guo et al. 2023. The low 16S rRNA gene sequence similarity and genomic relatedness between the type strains IMCC34837T and RY-1T of the two homonymic species indicated that they are different species. To avoid further confusion, we propose a new name Flavihumibacter fluvii sp. nov. to replace the effectively published but invalidated homonymic epithet Flavihumibacter fluminis Park et al. 2022.

Journal Articles

The Revision of Lichen Flora Around Maxwell Bay, King George Island, Maritime Antarctic: Jae Eun So , Josef P. Halda , Soon Gyu Hong , Jae&# , Ji Hee Kim; J. Microbiol. 2023;61(2):159-173. Published online February 27, 2023; DOI: https://doi.org/10.1007/s12275-023-00015-x

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1 Citations

Abstract: Since the floristic study of lichens at the Barton and Weaver Peninsulas of King George Island in 2006, there have been intense investigations of the lichen flora of the two peninsulas as well as that of Fildes Peninsula and Ardley Island in Maxwell Bay, King George Island, South Shetland Islands, maritime Antarctic. In this study, a total of 104 species belonging to 53 genera, are identified from investigations of lichens that were collected in austral summer seasons from 2008 to 2016. Phenotypic and molecular analyses were incorporated for taxonomic identification. In particular, 31 species are found to be endemic to the Antarctic and 22 species are newly recorded to the Maxwell Bay region. Lepra dactylina, Stereocaulon caespitosum, and Wahlenbergiella striatula are newly recorded in the Antarctic, and the previously reported taxon Cladonia furcata is excluded from the formerly recorded list due to misidentification. We also provide ecological and geographical information about lichen associations and habitat preferences.

Varicella‑Zoster Virus ORF39 Transmembrane Protein Suppresses Interferon‑Beta Promoter Activation by Interacting with STING: Gwang Myeong Lee , Shuang Gong , Seong&# , Hyemin Ko , Woo&# , Jihyun Lee , Ok Sarah Shin , Jin&#; J. Microbiol. 2023;61(2):259-270. Published online February 20, 2023; DOI: https://doi.org/10.1007/s12275-023-00019-7

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Abstract: Varicella-Zoster virus (VZV) causes varicella in primary infection of children and zoster during reactivation in adults. Type I interferon (IFN) signaling suppresses VZV growth, and stimulator of interferon genes (STING) plays an important role in anti-VZV responses by regulating type I IFN signaling. VZV-encoded proteins are shown to inhibit STING-mediated activation of the IFN-β promoter. However, the mechanisms by which VZV regulates STING-mediated signaling pathways are largely unknown. In this study, we demonstrate that the transmembrane protein encoded by VZV open reading frame (ORF) 39 suppresses STING-mediated IFN-β production by interacting with STING. In IFN-β promoter reporter assays, ORF39 protein (ORF39p) inhibited STING-mediated activation of the IFN-β promoter. ORF39p interacted with STING in co-transfection assays, and this interaction was comparable to that of STING dimerization. The cytoplasmic N-terminal 73 amino acids region of ORF39P was not necessary for ORF39 binding and suppression of STING-mediated IFN-β activation. ORF39p also formed a complex containing both STING and TBK1. A recombinant VZV expressing HA-tagged ORF39 was produced using bacmid mutagenesis and showed similar growth to its parent virus. During HA-ORF39 virus infection, the expression level of STING was markedly reduced, and HA-ORF39 interacted with STING. Moreover, HA-ORF39 also colocalized with glycoprotein K (encoded by ORF5) and STING at the Golgi during virus infection. Our results demonstrate that the transmembrane protein ORF39p of VZV plays a role in evading the type I IFN responses by suppressing STINGmediated activation of the IFN-β promoter.

Functional analysis of ascP in Aeromonas veronii TH0426 reveals a key role in the regulation of virulence: Yongchao Guan , Meng Zhang , Yingda Wang , Zhongzhuo Liu , Zelin Zhao , Hong Wang , Dingjie An , Aidong Qian , Yuanhuan Kang , Wuwen Sun , Xiaofeng Shan; J. Microbiol. 2022;60(12):1153-1161. Published online November 10, 2022; DOI: https://doi.org/10.1007/s12275-022-2373-8

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Abstract: Aeromonas veronii is a pathogen which can induce diseases in humans, animals and aquatic organisms, but its pathogenic mechanism and virulence factors are still elusive. In this study, we successfully constructed a mutant strain (ΔascP) by homologous recombination. The results showed that the deletion of the ascP gene significantly down-regulated the expression of associated effector proteins in A. veronii compared to its wild type. The adhesive and invasive abilities of ΔascP to EPC cells were 0.82-fold lower in contrast to the wild strain. The toxicity of ΔascP to cells was decreased by about 2.91-fold (1 h) and 1.74-fold (2 h). Furthermore, the LD50 of the mutant strain of crucian carp was reduced by 19.94-fold, and the virulence was considerably attenuated. In contrast to the wild strain, the ΔascP content in the liver and spleen was considerably lower. The titers of serum cytokines (IL-8, TNF-α, and IL-1β) in crucian carp after the infection of the ΔascP strain were considerably lower in contrast to the wild strain. Hence, the ascP gene is essential for the etiopathogenesis of A. veronii TH0426.

Differences in the methanogen community between the nearshore and offshore sediments of the South Yellow Sea: Ye Chen , Yu Zhen , Jili Wan , Siqi Li , Jiayin Liu , Guodong Zhang , Tiezhu Mi; J. Microbiol. 2022;60(8):814-822. Published online July 14, 2022; DOI: https://doi.org/10.1007/s12275-022-2022-2

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Abstract: The differences in methanogen abundance and community composition were investigated between nearshore and offshore sediments in the South Yellow Sea (SYS). Shannon, Simpson, and Chao1 indices revealed a higher diversity of methanogens in the nearshore sediments than in the offshore sediments. The Mann–Whitney U test demonstrated that the relative abundance of Methanococcoides was significantly higher in the offshore sediments, while the relative abundances of Methanogenium, Methanosarcina, Methanosaeta, Methanolinea, and Methanomassiliicoccus were significantly higher in the nearshore sediments (P < 0.05). The abundance of the mcrA gene in the nearshore sediments was significantly higher than that in the offshore sediments. Furthermore, a similar vertical distribution of the methanogen and sulfatereducing bacteria (SRB) abundances was observed in the SYS sediments, implying there is potential cooperation between these two functional microbes in this environment. Finally, total organic carbon (TOC) was significantly correlated with methanogen community composition.

Description of Flavobacterium cyclinae sp. nov. and Flavobacterium channae sp. nov., isolated from the intestines of Cyclina sinensis (Corb shell) and Channa argus (Northern snakehead): Seomin Kang , Jae-Yun Lee , Jeong Eun Han , Yun-Seok Jeong , Do-Hun Gim , Jin-Woo Bae; J. Microbiol. 2022;60(9):890-898. Published online June 22, 2022; DOI: https://doi.org/10.1007/s12275-022-2075-2

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6 Citations

Abstract: Two novel bacterial strains, KSM-R2A25T and KSM-R2A30T, were isolated from intestines of Cyclina sinensis (corb shell) and Channa argus (northern snakehead), respectively. Both specimens were collected in Korea. The strains were Gramstain- negative, non-motile, and strictly aerobic. According to phylogenetic analyses based on 16S rRNA gene sequences, strains belonged to the genus Flavobacterium within the family Flavobacteriaceae. 16S rRNA gene sequences of strains KSMR2A25T and KSM-R2A30T were closely related to Flavobacterium cucumis DSM 18830T and Flavobacterium aquaticum JC164T with sequence similarities of 97.77% and 98.54%, respectively. Further genomic analyses including reconstruction of the UBCG tree and overall genome-related indices suggested them as novel species of the genus Flavobacterium. Both strains contained menaquinone with six isoprene units (MK-6) as a major isoprenoid quinone and iso-C15:1 G, iso- C15:0, and iso-C16:0 as major cellular fatty acids. The major polar lipid in both strains was phosphatidylethanolamine. The genomic G + C contents of strains KSM-R2A25T and KSMR2A30T were 31.7 and 31.9%, respectively. Based on the polyphasic taxonomic study presented here, strains KSM-R2A25T and KSM-R2A30T represent novel species of the genus Flavobacterium, for which the names Flavobacterium cyclinae sp. nov and Flavobacterium channae sp. nov are proposed. The type strains of F. cyclinae sp. nov and F. channae sp. nov are KSM-R2A25T (= KCTC 82978T = JCM 34997T) and KSMR2A30T (= KCTC 82979T = JCM 34998T), respectively.

Effects of tryptophan and phenylalanine on tryptophol production in Saccharomyces cerevisiae revealed by transcriptomic and metabolomic analyses: Xiaowei Gong , Huajun Luo , Liu Hong , Jun Wu , Heng Wu , Chunxia Song , Wei Zhao , Yi Han , Ya Dao , Xia Zhang , Donglai Zhu , Yiyong Luo; J. Microbiol. 2022;60(8):832-842. Published online May 27, 2022; DOI: https://doi.org/10.1007/s12275-022-2059-2

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Abstract: Tryptophol (TOL) is a metabolic derivative of tryptophan (Trp) and shows pleiotropic effects in humans, plants and microbes. In this study, the effect of Trp and phenylalanine (Phe) on TOL production in Saccharomyces cerevisiae was determined, and a systematic interpretation of TOL accumulation was offered by transcriptomic and metabolomic analyses. Trp significantly promoted TOL production, but the output plateaued (231.02−266.31 mg/L) at Trp concentrations ≥ 0.6 g/L. In contrast, Phe reduced the stimulatory effect of Trp, which was strongly dependent on the Phe concentration. An integrated genomic, transcriptomic, and metabolomic analysis revealed that the effect of Trp and Phe on TOL production was mainly related to the transamination and decarboxylation of the Ehrlich pathway. Additionally, other genes, including thiamine regulon genes (this), the allantoin catabolic genes dal1, dal2, dal4, and the transcriptional activator gene aro80, may play important roles. These findings were partly supported by the fact that the thi4 gene was involved in TOL production, as shown by heterologous expression analysis. To the best of our knowledge, this novel biological function of thi4 in S. cerevisiae is reported here for the first time. Overall, our findings provide insights into the mechanism of TOL production, which will contribute to TOL production using metabolic engineering strategies.

Characterization of a cold-adapted debranching enzyme and its role in glycogen metabolism and virulence of Vibrio vulnificus MO6-24/O: Ah-Reum Han , Haeyoung Kim , Jong-Tae Park , Jung-Wan Kim; J. Microbiol. 2022;60(4):375-386. Published online February 14, 2022; DOI: https://doi.org/10.1007/s12275-022-1507-3

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4 Citations

Abstract: Vibrio vulnificus MO6-24/O has three genes annotated as debranching enzymes or pullulanase genes. Among them, the gene encoded by VVMO6_03032 (vvde1) shares a higher similarity at the amino acid sequence level to the glycogen debranching enzymes, AmyX of Bacillus subtilis (40.5%) and GlgX of Escherichia coli (55.5%), than those encoded by the other two genes. The vvde1 gene encoded a protein with a molecular mass of 75.56 kDa and purified Vvde1 efficiently hydrolyzed glycogen and pullulan to shorter chains of maltodextrin and maltotriose (G3), respectively. However, it hydrolyzed amylopectin and soluble starch far less efficiently, and β-cyclodextrin (β-CD) only rarely. The optimal pH and temperature of Vvde1 was 6.5 and 25°C, respectively. Vvde1 was a cold-adapted debranching enzyme with more than 60% residual activity at 5°C. It could maintain stability for 2 days at 25°C and 1 day at 35°C, but it destabilized drastically at 40°C. The Vvde1 activity was inhibited considerably by Cu2+, Hg2+, and Zn2+, while it was slightly enhanced by Co2+, Ca2+, Ni2+, and Fe2+. The vvde1 knock-out mutant accumulated more glycogen than the wild-type in media supplemented with 1.0% maltodextrin; however, the side chain length distribution of glycogen was similar to that of the wild-type except G3, which was much more abundant in the mutant. Therefore, Vvde1 seemed to debranch glycogen with the degree of polymerization 3 (DP3) as the specific target branch length. Virulence of the pathogen against Caenorhabditis elegans was attenuated significantly by the vvde1 mutation. These results suggest that Vvde1 might be a unique glycogen debranching enzyme that is involved in both glycogen utilization and shaping of glycogen molecules, and contributes toward virulence of the pathogen.

Review

Coordinated regulation of interferon and inflammasome signaling pathways by SARS-CoV-2 proteins: Na-Eun Kim , Yoon-Jae Song; J. Microbiol. 2022;60(3):300-307. Published online January 28, 2022; DOI: https://doi.org/10.1007/s12275-022-1502-8

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5 Citations

Abstract: Type I and III interferons (IFNs) and the nucleotide-binding domain (NBD) leucine-rich repeat (LRR)-containing receptor (NLR) family pyrin domain containing 3 (NLRP3) inflammasome play pivotal roles in the pathogenesis of SARS-CoV-2. While optimal IFN and inflammasome responses are essential for limiting SARS-CoV-2 infection, aberrant activation of these innate immune responses is associated with COVID-19 pathogenesis. In this review, we focus our discussion on recent findings on SARS-CoV-2-induced type I and III IFNs and NLRP3 inflammasome responses and the viral proteins regulating these mechanisms.

Journal Articles

Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity: Dongwook Kim , Sein Park , Jongsik Chun; J. Microbiol. 2021;59(5):476-480. Published online April 28, 2021; DOI: https://doi.org/10.1007/s12275-021-1154-0

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170 Citations

Abstract: The average amino acid identity (AAI) is an index of pairwise genomic relatedness, and multiple studies have proposed its application in prokaryotic taxonomy and related disciplines. AAI demonstrates better resolution in elucidating taxonomic structure beyond the species rank when compared with average nucleotide identity (ANI), which is a standard criterion in species delineation. However, an efficient and easy-to-use computational tool for AAI calculation in large-scale taxonomic studies is not yet available. Here, we introduce a bioinformatic pipeline, named EzAAI, which allows for rapid and accurate AAI calculation in prokaryote sequences. The EzAAI tool is based on the MMSeqs2 program and computes AAI values almost identical to those generated by the standard BLAST algorithm with significant improvements in the speed of these evaluations. Our pipeline also provides a function for hierarchical clustering to create dendrograms, which is an essential part of any taxonomic study. EzAAI is available for download as a standalone JAVA program at http:// leb.snu.ac.kr/ezaai.

The synergy effect of arbuscular mycorrhizal fungi symbiosis and exogenous calcium on bacterial community composition and growth performance of peanut (Arachis hypogaea L.) in saline alkali soil: Dunwei Ci , Zhaohui Tang , Hong Ding , Li Cui , Guanchu Zhang , Shangxia Li , Liangxiang Dai , Feifei Qin , Zhimeng Zhang , Jishun Yang , Yang Xu; J. Microbiol. 2021;59(1):51-63. Published online November 17, 2020; DOI: https://doi.org/10.1007/s12275-021-0317-3

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18 Citations

Abstract: Peanut (Arachis hypogaea. L) is an important oil seed crop. Both arbuscular mycorrhizal fungi (AMF) symbiosis and calcium (Ca2+) application can ameliorate the impact of saline soil on peanut production, and the rhizosphere bacterial communities are also closely correlated with peanut salt tolerance; however, whether AMF and Ca2+ can withstand high-salinity through or partially through modulating rhizosphere bacterial communities is unclear. Here, we used the rhizosphere bacterial DNA from saline alkali soil treated with AMF and Ca2+ alone or together to perform high-throughput sequencing of 16S rRNA genes. Taxonomic analysis revealed that AMF and Ca2+ treatment increased the abundance of Proteobacteria and Firmicutes at the phylum level. The nitrogenfixing bacterium Sphingomonas was the dominant genus in these soils at the genus level, and the soil invertase and urease activities were also increased after AMF and Ca2+ treatment, implying that AMF and Ca2+ effectively improved the living environment of plants under salt stress. Moreover, AMF combined with Ca2+ was better than AMF or Ca2+ alone at altering the bacterial structure and improving peanut growth in saline alkali soil. Together, AMF and Ca2+ applications are conducive to peanut salt adaption by regulating the bacterial community in saline alkali soil.

Oecophyllibacter saccharovorans gen. nov. sp. nov., a bacterial symbiont of the weaver ant Oecophylla smaragdina: Kah-Ooi Chua , Wah-Seng See-Too , Jia-Yi Tan , Sze-Looi Song , Hoi-Sen Yong , Wai-Fong Yin , Kok-Gan Chan; J. Microbiol. 2020;58(12):988-997. Published online October 23, 2020; DOI: https://doi.org/10.1007/s12275-020-0325-8

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7 Citations

Abstract: In this study, bacterial strains Ha5T, Ta1, and Jb2 were isolated from different colonies of weaver ant Oecophylla smaragdina. They were identified as bacterial symbionts of the ant belonging to family Acetobacteraceae and were distinguished as different strains based on distinctive random-amplified polymorphic DNA (RAPD) fingerprints. Cells of these bacterial strains were Gram-negative, rod-shaped, aerobic, non-motile, catalase-positive and oxidase-negative. They were able to grow at 15–37°C (optimum, 28–30°C) and in the presence of 0–1.5% (w/v) NaCl (optimum 0%). Their predominant cellular fatty acids were C18:1 ω7c, C16:0, C19:0 ω8c cyclo, C14:0, and C16:0 2-OH. Strains Ha5T, Ta1, and Jb2 shared highest 16S rRNA gene sequence similarity (94.56–94.63%) with Neokomagataea tanensis NBRC106556T of family Acetobacteraceae. Both 16S rRNA gene sequence-based phylogenetic analysis and core gene-based phylogenomic analysis placed them in a distinct lineage in family Acetobacteraceae. These bacterial strains shared higher than species level thresholds in multiple overall genome-relatedness indices which indicated that they belonged to the same species. In addition, they did not belong to any of the current taxa of Acetobacteraceae as they had low pairwise average nucleotide identity (< 71%), in silico DNA-DNA hybridization (< 38%) and average amino acid identity (< 67%) values with all the type members of the family. Based on these results, bacterial strains Ha5T, Ta1, and Jb2 represent a novel species of a novel genus in family Acetobacteraceae, for which we propose the name Oecophyllibacter saccharovorans gen. nov. sp. nov., and strain Ha5T as the type strain.

In vitro disinfection efficacy and clinical protective effects of common disinfectants against acute hepatopancreatic necrosis disease (AHPND)-causing Vibrio isolates in Pacific white shrimp Penaeus vannamei: Peizhuo Zou , Qian Yang , Hailiang Wang , Guosi Xie , Zhi Cao , Xing Chen , Wen Gao , Jie Huang; J. Microbiol. 2020;58(8):675-686. Published online July 27, 2020; DOI: https://doi.org/10.1007/s12275-020-9537-1

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Abstract: Acute hepatopancreatic necrosis disease (AHPND) is one of the most significant bacterial diseases in global shrimp culture, causing severe economic losses. In the present study, we carried out in vitro antimicrobial tests to investigate the disinfection efficacy of 14 common disinfectants toward different AHPND-causing Vibrio spp., including eight isolates of V. parahaemolyticus, four isolates of V. campbellii, and one isolate of V. owensii. Polyhexamethylene biguanidine hydrochloride (PHMB) was revealed to possess the strongest inhibitory activity. Through analyzing and evaluating the results of antimicrobial tests and acute toxicity test, we selected PHMB and hydrogen peroxide (H2O2) for further clinical protection test. Clinical manifestations indicated that both PHMB (2 mg/L and 4 mg/L) and H2O2 (12 mg/L) could effectively protect juvenile Penaeus vannamei from the infection of V. parahaemolyticus isolate Vp362 at 106 CFU/ml, and the survival rate was over 80%. When the bacterial concentration was reduced to 105 CFU/ml, 104 CFU/ml, and 103 CFU/ml, the survival rate after treated by 1 mg/L PHMB was 64.44%, 93.33%, and 100%, respectively. According to the results, PHMB and H2O2 showed a lower toxicity while a better protection activity, particularly against a lower concentration of the pathogens. Therefore, these two disinfectants are proved to be promising disinfectants that can be applied to prevent and control AHPND in shrimp culture. Moreover, the methods of this study also provided valuable information for the prevention of other important bacterial diseases and suggested a reliable means for screening potential drugs in aquaculture.

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