Zoo animal manure as an overlooked reservoir of antibiotic resistance genes and multidrug-resistant bacteria

Min, Jihyeon; Kim, Pureun; Yun, Sohyeon; Hong, Minyoung; Park, Woojun

doi:10.1007/s11356-022-22279-3

Cited by 12 publications

(10 citation statements)

References 94 publications

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“…The copy number was estimated using a threshold cycle of 25 as described in Min et al. (2023). Specific primer sets were designed (as listed in Table S1) to assess the expression (fold‐change) of photosystem genes ( psa B and psb D) in M. aeruginosa and lasso peptide biosynthesis genes ( plp B and plp C) in P. aquatile B51.…”

Section: Methodsmentioning

confidence: 99%

“…To normalize the DNA amounts, we calculated the relative abundance of genes by dividing the estimated total target gene copies by the estimated copies of the 16S rRNA gene. The copy number was estimated using a threshold cycle of 25 as described in Min et al (2023). Specific primer sets were designed (as listed in Table S1) to assess the expression (fold-change) of photosystem genes (psaB and psbD) in M. aeruginosa and lasso peptide biosynthesis genes (plpB and plpC) in P. aquatile B51.…”

Section: Bacterial Total Rna Extraction and Quantitative Real-time Pc...mentioning

confidence: 99%

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Antagonistic actions of Paucibacter aquatileB51 and its lasso peptide paucinodin toward cyanobacterial bloom‐forming Microcystis aeruginosaPCC7806

Cha,

Kim,

Park

et al. 2023

Journal of Phycology

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Superior antagonistic activity against axenic Microcystis aeruginosa PCC7806 was observed with Paucibacter sp. B51 isolated from cyanobacterial bloom samples among 43 tested freshwater bacterial species. Complete genome sequencing, analyzing average nucleotide identity and digital DNA–DNA hybridization, designated the B51 strain as Paucibacter aquatile. Electron and fluorescence microscopic image analyses revealed the presence of the B51 strain in the vicinity of M. aeruginosa cells, which might provoke direct inhibition of the photosynthetic activity of the PCC7806 cells, leading to perturbation of cellular metabolisms and consequent cell death. Our speculation was supported by the findings that growth failure of the PCC7806 cells led to low pH conditions with fewer chlorophylls and down‐regulation of photosystem genes (e.g., psbD and psaB) during their 48‐h co‐culture condition. Interestingly, the concentrated ethyl acetate extracts obtained from B51‐grown supernatant exhibited a growth‐inhibitory effect on PCC7806. The physical separation of both strains by a filter system led to no inhibitory activity of the B51 cells, suggesting that contact‐mediated anti‐cyanobacterial compounds might also be responsible for hampering the growth of the PCC7806 cells. Bioinformatic tools identified 12 gene clusters that possibly produce secondary metabolites, including a class II lasso peptide in the B51 genome. Further chemical analysis demonstrated anti‐cyanobacterial activity from fractionated samples having a rubrivinodin‐like lasso peptide, named paucinodin. Taken together, both contact‐mediated inhibition of photosynthesis and the lasso peptide secretion of the B51 strain are responsible for the anti‐cyanobacterial activity of P. aquatile B51.

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Section: Methodsmentioning

confidence: 99%

Section: Bacterial Total Rna Extraction and Quantitative Real-time Pc...mentioning

confidence: 99%

Antagonistic actions of Paucibacter aquatileB51 and its lasso peptide paucinodin toward cyanobacterial bloom‐forming Microcystis aeruginosaPCC7806

Cha,

Kim,

Park

et al. 2023

Journal of Phycology

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“…Taken together, the genomic relatedness and whole-genome-based phylogenetic tree analysis strongly suggest that strain Ran72 T represents a novel species within the genus Kaistella, consistent with the findings presented in Table 1. Strain Ran72 T , obtained from a faecal sample of rhinoceros exposed to various antibiotics during captivity, highlights concern about potential antibiotic-resistance genes (ARGs) in animal microbiomes, urging a comprehensive analysis due to the implications for multidrug-resistant bacteria and human health surveillance [16,[24][25][26]. To examine the antibiotic resistance genes present in strain Ran72 T , we utilized the Microbial Genomics modules within CLC Genomics Workbench version 21 (Qiagen).…”

Section: Genomic Relatedness and Phylogenomic Analysismentioning

confidence: 99%

“…Strain Ran72 T was isolated from the faeces of Ceratotherium simum housed at Seoul Grand Park (37° 25′ 39.1″ N 127° 1′ 1.3″ E). The strain was isolated using the same methods as in previous studies [15,16]. In brief, the faeces of rhinoceros were collected to isolate the faecal micro-organisms within 12 h after excretion during the summer month of August 2020.…”

Section: Isolationmentioning

confidence: 99%

Kaistella rhinocerotis sp. nov., isolated from the faeces of rhinoceros and reclassification of Chryseobacterium faecale as Kaistella faecalis comb. nov.

Park,

Min,

Kim

et al. 2024

International Journal of Systematic and Evolutionary Microbiology

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Strain Ran72T, a novel Gram-stain-negative, obligately aerobic, non-motile, and rod-shaped bacterium, was isolated from the faeces of the rhinoceros species Ceratotherium simum. The novel bacterial strain grew optimally in Reasoner's 2A medium under the following conditions: 0 % (w/v) NaCl, pH 7.5, and 30 °C. Based on phylogenetic analysis using 16S rRNA gene sequencing, strain Ran72T was found to be most closely related to Chryseobacterium faecale F4T (98.4 %), Kaistella soli DKR-2T (98.0 %), and Kaistella haifensis H38T (97.4 %). A comprehensive genome-level comparison between strain Ran72T with C. faecale F4T, K. soli DKR-2T, and K. haifensis H38T revealed average nucleotide identity, digital DNA–DNA hybridization, and average amino acid identity values of ≤74.9, ≤19.3, and ≤78.7 %, respectively. The major fatty acids were anteiso-C15 : 0 (22.3 %), with MK-6 being the predominant respiratory quinone. The major polar lipids of strain Ran72T were phosphatidylethanolamine, four unidentified aminolipids, and two unidentified lipids. Based on our chemotaxonomic, genotypic, and phenotype characterizations, strain Ran72T was identified as representing a novel species in the genus Kaistella, for which the name Kaistella rhinocerotis sp. nov. is proposed, with the type strain Ran72T (=KACC 23136T=JCM 36038T). Based on the outcomes of our phylogenomic study, Chryseobacterium faecale should be reclassified under the genus Kaistella as Kaistella faecalis comb. nov.

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“…The 16S rRNA gene sequences of Niabella species were amplified by PCR using the 27F (5′-AGAGTTTGATCMTGGCTCAG-3′) and 1492R (5′-TACG GYTA CCTT GTTA CGACT T-3′) universal bacterial primers [10]. The following mixture was used for the PCR analysis: primer pairs (2 µl of 5 pmol, respectively), 1.6 µl dNTPs (10 mM), 2 µl 10×Taq buffer, and 0.2 µl Han-Taq polymerase (Genenmed) [11].…”

Section: S Rrna Gene and Whole-genome Phylogenymentioning

confidence: 99%

Niabella defluvii sp. nov., isolated from influent water of a wastewater treatment plant

Min,

Son,

Park

et al. 2024

International Journal of Systematic and Evolutionary Microbiology

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Strain I65T (=KACC 22647T=JCM 35315T), a novel Gram-stain-negative, strictly aerobic, non-motile, non-spore-forming, rod-shaped, and orange-pigmented bacterium was isolated from influent water of a wastewater treatment system after treatment with several antibiotics, such as meropenem, gentamicin, and macrolide. The newly identified bacterial strain I65T exhibits significant multi-drug and heavy metal resistance characteristics. Strain I65T was grown in Reasoner's 2A medium [0 %–2 % (w/v) NaCl (optimum, 0 %), pH 5.0–10.0 (optimum, pH 7.0), and 20–45°C (optimum, 30 °C)]. Phylogenetic analysis based on 16S rRNA gene sequencing confirmed that strain I65T was closely related to Niabella yanshanensis CCBAU 05354T (99.56 % sequence similarity), Niabella hibiscisoli THG-DN5.5T (97.51 %), and Niabella ginsengisoli GR10-1T (97.09 %). Further analysis of the whole-genome sequence confirmed that the digital DNA–DNA hybridization, average nucleotide identity, and average amino acid identity values between strain I65T and N. yanshanensis CCBAU 05354T were 23.4, 80.7, and 85.0 %, respectively, suggesting that strain I65T is distinct from N. yanshanensis. The genome size of strain I65T was 6.1 Mbp, as assessed using the Oxford Nanopore platform, and its genomic DNA G+C content was 43.0 mol%. The major fatty acids of strain I65T were iso-C15 : 0 and iso-C15 : 1 G, and the major respiratory quinone was MK-7. Moreover, the major polar lipid of strain I65T was phosphatidylethanolamine. Based on genotypic, chemotaxonomic, and phenotype data, strain I65T represents a novel species belonging to the genus Niabella, for which the name Niabella defluvii sp. nov. is proposed. The type strain is I65T (=KACC 22647T=JCM 35315T).

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Zoo animal manure as an overlooked reservoir of antibiotic resistance genes and multidrug-resistant bacteria

Cited by 12 publications

References 94 publications

Antagonistic actions of Paucibacter aquatileB51 and its lasso peptide paucinodin toward cyanobacterial bloom‐forming Microcystis aeruginosaPCC7806

Antagonistic actions of Paucibacter aquatileB51 and its lasso peptide paucinodin toward cyanobacterial bloom‐forming Microcystis aeruginosaPCC7806

Kaistella rhinocerotis sp. nov., isolated from the faeces of rhinoceros and reclassification of Chryseobacterium faecale as Kaistella faecalis comb. nov.

Niabella defluvii sp. nov., isolated from influent water of a wastewater treatment plant

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