Journal of Microbiology

Review

[MINIREVIEW]Gain and loss of antibiotic resistant genes in multidrug resistant bacteria: One Health perspective: Misung Kim , Jaeeun Park , Mingyeong Kang , Jihye Yang , Woojun Park; J. Microbiol. 2021;59(6):535-545. Published online April 20, 2021; DOI: https://doi.org/10.1007/s12275-021-1085-9

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The emergence of multidrug resistance (MDR) has become a global health threat due to the increasing unnecessary use of antibiotics. Multidrug resistant bacteria occur mainly by accumulating resistance genes on mobile genetic elements (MGEs), made possible by horizontal gene transfer (HGT). Humans and animal guts along with natural and engineered environments such as wastewater treatment plants and manured soils have proven to be the major reservoirs and hotspots of spreading antibiotic resistance genes (ARGs). As those environments support the dissemination of MGEs through the complex interactions that take place at the human-animalenvironment interfaces, a growing One Health challenge is for multiple sectors to communicate and work together to prevent the emergence and spread of MDR bacteria. However, maintenance of ARGs in a bacterial chromosome and/or plasmids in the environments might place energy burdens on bacterial fitness in the absence of antibiotics, and those unnecessary ARGs could eventually be lost. This review highlights and summarizes the current investigations into the gain and loss of ARG genes in MDR bacteria among human-animal- environment interfaces. We also suggest alternative treatments such as combinatory therapies or sequential use of different classes of antibiotics/adjuvants, treatment with enzymeinhibitors, and phage therapy with antibiotics to solve the MDR problem from the perspective of One Health issues.

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Journal Articles

Antarctic tundra soil metagenome as useful natural resources of cold-active lignocelluolytic enzymes: Han Na Oh , Doyoung Park , Hoon Je Seong , Dockyu Kim , Woo Jun Sul; J. Microbiol. 2019;57(10):865-873. Published online September 30, 2019; DOI: https://doi.org/10.1007/s12275-019-9217-1

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Abstract

Lignocellulose composed of complex carbohydrates and aromatic heteropolymers is one of the principal materials for the production of renewable biofuels. Lignocellulose-degrading genes from cold-adapted bacteria have a potential to increase the productivity of biological treatment of lignocellulose biomass by providing a broad range of treatment temperatures. Antarctic soil metagenomes allow to access novel genes encoding for the cold-active lignocellulose-degrading enzymes, for biotechnological and industrial applications. Here, we investigated the metagenome targeting cold-adapted microbes in Antarctic organic matter-rich soil (KS 2-1) to mine lignolytic and celluloytic enzymes by performing single molecule, real-time metagenomic (SMRT) sequencing. In the assembled Antarctic metagenomic contigs with relative long reads, we found that 162 (1.42%) of total 11,436 genes were annotated as carbohydrate-active enzymes (CAZy). Actinobacteria, the dominant phylum in this soil’s metagenome, possessed most of candidates of lignocellulose catabolic genes like glycoside hydrolase families (GH13, GH26, and GH5) and auxiliary activity families (AA7 and AA3). The predicted lignocellulose degradation pathways in Antarctic soil metagenome showed synergistic role of various CAZyme harboring bacterial genera including Streptomyces, Streptosporangium, and Amycolatopsis. From phylogenetic relationships with cellular and environmental enzymes, several genes having potential for participating in overall lignocellulose degradation were also found. The results indicated the presence of lignocellulose-degrading bacteria in Antarctic tundra soil and the potential benefits of the lignocelluolytic enzymes as candidates for cold-active enzymes which will be used for the future biofuel-production industry.

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Khadijah Nabilah Mohd Zahri, Azham Zulkharnain, Claudio Gomez-Fuentes, Suriana Sabri, Khalilah Abdul Khalil, Peter Convey, Siti Aqlima Ahmad
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Jéssica P. Silva, Alonso R. P. Ticona, Pedro R. V. Hamann, Betania F. Quirino, Eliane F. Noronha
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Cr(VI) removal from aqueous solution by thermophilic denitrifying bacterium Chelatococcus daeguensis TAD1 in the presence of single and multiple heavy metals: Han Li , Shaobin Huang , Yongqing Zhang; J. Microbiol. 2016;54(9):602-610. Published online August 31, 2016; DOI: https://doi.org/10.1007/s12275-016-5295-5

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Abstract

Cr(VI) pollution is increasing continuously as a result of ongoing industrialization. In this study, we investigated the thermophilic denitrifying bacterium Chelatococcus daeguensis TAD1, isolated from the biofilm of a biotrickling filter used in nitrogen oxides (NOX) removal, with respect to its ability to remove Cr(VI) from an aqueous solution. TAD1 was capable of reducing Cr(VI) from an initial concentration of 10 mg/L to non-detectable levels over a pH range of 7–9 and at a temperature range of 30–50°C. TAD1 simultaneously removed both Cr(VI) and NO3 −-N at 50°C, when the pH was 7 and the initial Cr(VI) concentration was 15 mg/L. The reduction of Cr(VI) to Cr(III) correlated with the growth metabolic activity of TAD1. The presence of other heavy metals (Cu, Zn, and Ni) inhibited the ability of TAD1 to remove Cr(VI). The metals each individually inhibited Cr(VI) removal, and the extent of inhibition increased in a cooperative manner in the presence of a combination of the metals. The addition of biodegradable cellulose acetate microspheres (an adsorption material) weakened the toxicity of the heavy metals; in their presence, the Cr(VI) removal efficiency returned to a high level. The feasibility and applicability of simultaneous nitrate removal and Cr(VI) reduction by strain TAD1 is promising, and may be an effective biological method for the clean-up of wastewater.

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Research Support, U.S. Gov't, Non-P.H.S.

Synergistic growth in bacteria depends on substrate complexity: Yi-Jie Deng , Shiao Y. Wang; J. Microbiol. 2016;54(1):23-30. Published online January 5, 2016; DOI: https://doi.org/10.1007/s12275-016-5461-9

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Abstract

bacterial synergism, lignocellulose degradation, bacterial activity, enzyme production, microbial interaction

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Research Support, Non-U.S. Gov'ts

Cloning and Functional Characterization of Endo-β-1,4-Glucanase Gene from Metagenomic Library of Vermicompost: Muhammad Yasir , Haji Khan , Syed Sikander Azam , Amar Telke , Seon Won Kim , Young Ryun Chung; J. Microbiol. 2013;51(3):329-335. Published online June 28, 2013; DOI: https://doi.org/10.1007/s12275-013-2697-5

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Abstract: In the vermicomposting of paper mill sludge, the activity of earthworms is very dependent on dietetic polysaccharides including cellulose as energy sources. Most of these polymers are degraded by the host microbiota and considered potentially important source for cellulolytic enzymes. In the present study, a metagenomic library was constructed from vermicompost (VC) prepared with paper mill sludge and dairy sludge (fresh sludge, FS) and functionally screened for cellulolytic activities. Eighteen cellulase expressing clones were isolated from about 89,000 fosmid clones libraries. A short fragment library was constructed from the most active positive clone (cMGL504) and one open reading frame (ORF) of 1,092 bp encoding an endo-β-1,4-glucanase was indentified which showed 88% similarity with Cellvibrio mixtus cellulase A gene. The endo-β-1,4-glucanase cmgl504 gene was overexpressed in Escherichia coli. The purified recombinant cmgl504 cellulase displayed activities at a broad range of temperature (25–55°C) and pH (5.5–8.5). The enzyme degraded carboxymethyl cellulose (CMC) with 15.4 U, while having low activity against avicel. No detectable activity was found for xylan and laminarin. The enzyme activity was stimulated by potassium chloride. The deduced protein and three-dimensional structure of metagenomederived cellulase cmgl504 possessed all features, including general architecture, signature motifs, and N-terminal signal peptide, followed by the catalytic domain of cellulase belonging to glycosyl hydrolase family 5 (GHF5). The cellulases cloned in this work may play important roles in the degradation of celluloses in vermicomposting process and could be exploited for industrial application in future.

The Role of Carbohydrate-Binding Module (CBM) Repeat of a Multimodular Xylanase (XynX) from Clostridium thermocellum in Cellulose and Xylan Binding: Thangaswamy Selvaraj , Sung Kyum Kim , Yong Ho Kim , Yu Seok Jeong , Yu-Jeong Kim , Nguyen Dinh Phuong , Kyung Hwa Jung , Jungho Kim , Han Dae Yun , Hoon Kim; J. Microbiol. 2010;48(6):856-861. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0285-5

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Abstract: A non-cellulosomal xylanase from Clostridium thermocellum, XynX, consists of a family-22 carbohydratebinding module (CBM22), a family-10 glycoside hydrolase (GH10) catalytic module, two family-9 carbohydrate-binding modules (CBM9-I and CBM9-II), and an S-layer homology (SLH) module. E. coli BL21(DE3) (pKM29), a transformant carrying xynX', produced several truncated forms of the enzyme. Among them, three major active species were purified by SDS-PAGE, activity staining, gel-slicing, and diffusion from the gel. The truncated xylanases were different from each other only in their C-terminal regions. In addition to the CBM22 and GH10 catalytic modules, XynX1 had the CBM9-I and most of the CBM9-II, XynX2 had the CBM9-I and about 40% of the CBM9-II, and XynX3 had about 75% of the CBM9-I. The truncated xylanases showed higher binding capacities toward Avicel than those toward insoluble xylan. XynX1 showed a higher affinity toward Avicel (70.5%) than XynX2 (46.0%) and XynX3 (42.1%); however, there were no significant differences in the affinities toward insoluble xylan. It is suggested that the CBM9 repeat, especially CBM9-II, of XynX plays a role in xylan degradation in nature by strengthening cellulose binding rather than by enhancing xylan binding.

Paenibacillus pini sp. nov., a Cellulolytic Bacterium Isolated from the Rhizosphere of Pine Tree: Byung-Chun Kim , Kang Hyun Lee , Mi Na Kim , Eun-Mi Kim , Sung Ran Min , Hyun Soon Kim , Kee-Sun Shin; J. Microbiol. 2009;47(6):699-704. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-009-0343-z

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Abstract: Strain S22T, a novel cellulolytic bacterium was isolated from the rhizosphere of pine trees. This isolate was Gram-reaction positive, motile and rods, and formed terminal or subterminal ellipsoidal spores. S22T represented positive activity for catalase, oxidase, esterase (C4), esterase lipase (C8), β-galactosidase, leucine arylamidase, and hydrolysis of esculin. It contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall. The predominant isoprenoid quinone was menaquinone 7 (MK-7), and the major cellular fatty acids were anteiso-C15:0 (52.9%), iso-C16:0 (11.3%), and iso-C15:0 (10.0%). The DNA G+C content was 43.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that this isolate belonged to the family Paenibacillaceae. S22T exhibited less than 97.0% 16S rRNA gene similarity with all relative type strains in the genus Paenibacillus, and the most closely related strains were Paenibacillus anaericanus MH21T and Paenibacillus ginsengisoli Gsoil 1638T, with equal similarities of 95.8%. This polyphasic evidence suggested that strain S22T should be considered a novel species in the genus Paenibacillus, for which the name, Paenibacillus pini sp. nov., is proposed. The type strain is S22T (=KCTC 13694T =KACC 14198T =JCM 16418T)

Paenibacillus pinihumi sp. nov., a Cellulolytic Bacterium Isolated from the Rhizosphere of Pinus densiflora: Byung-Chun Kim , Kang Hyun Lee , Mi Na Kim , Eun-Mi Kim , Moon-Soo Rhee , O-Yu Kwon , Kee-Sun Shin; J. Microbiol. 2009;47(5):530-535. Published online October 24, 2009; DOI: https://doi.org/10.1007/s12275-009-0270-z

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22 Scopus

Abstract: A novel cellulolytic bacterium, strain S23T, was isolated from the rhizosphere of the pine trees in Daejeon, Republic of Korea. This isolate was Gram-positive, strictly aerobic, rod-shaped, catalase-negative, oxidase- positive, motile by means of peritrichous flagella, and tested positive for alkaline phosphatase, esterase lipase, leucine arylamidase, α-galactosidase, and β-galactosidase activities. The DNA G+C content was 49.5mol%. The main cellular fatty acids were anteiso-C15:0 (51.9%), iso-C16:0 (14.7%), and iso-C15:0 (13.2%). The major isoprenoid quinone was menaquinone 7 (MK-7). Diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. Comparative 16S rRNA gene sequence analysis showed that this strain clustered with Paenibacillus species. The 16S rRNA gene sequence similarity values between S23T and other Paenibacillus species were between 89.9% and 95.9%, and S23T was most closely related to Paenibacillus tarimensis SA-7-6T. On the basis of phylogenetic and phenotypic properties of strain S23T, the isolate is considered as a novel species belonging to the genus Paenibacillus. Therefore, the name, Paenibacillus pinihumi sp. nov., is proposed for the rhizosphere isolate; the type strain is S23T (=KCTC 13695T =KACC 14199T =JCM 16419T)

Degradation of Crystalline Cellulose by the Brown-rot Basidiomycete Fomitopsis palustris: Jeong-Jun Yoon , Young-Kyoon Kim; J. Microbiol. 2005;43(6):487-492.; DOI: https://doi.org/2301 [pii]

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Abstract: This study demonstrated that the brown rot basidiomycete Fomitopsis palustris was able to degrade crystalline cellulose (Avicel). This fungus could also produce the three major cellulases (exoglucanases, endoglucanases, and -glucosidase) when the cells were grown on 2.0% Avicel. Avicel degraded by F. palustris showed a decrease in relative crystallinity from 83% to 78.5% after 14 days of incubation. The characterization study indicated that optimum pH was 4.5 and optimum temperature was 70oC for exoglucanase (cellobiohydrolase) activity. Hydrolysis of Avicel by the crude enzyme from F. palustris yielded 1.6 mg/ml of glucose after 43 h, which corresponded to a cellulose conversion degree of 3.2%. Therefore, this study revealed for the first time that the brown rot basidiomycete F. palustris produces cellulases capable of yielding soluble sugars from crystalline cellulose.

Purification and Characterization of Thermostable β-Glucosidase from the Brown-Rot Basidiomycete Fomitopsis palustris Grown on Microcrystalline Cellulose: Jeong-Jun Yoon , Ki-Yeon Kim , Chang-Jun Cha; J. Microbiol. 2008;46(1):51-55.; DOI: https://doi.org/10.1007/s12275-007-0230-4

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Abstract: An extracellular β-glucosidase was purified 154-fold to electrophoretic homogeneity from the brown-rot basidiomycete Fomitopsis palustris grown on 2.0% microcrystalline cellulose. SDS-polyacrylamide gel electrophoresis gel gave a single protein band and the molecular mass of purified enzyme was estimated to be approximately 138 kDa. The amino acid sequences of the proteolytic fragments determined by nano-LC- MS/MS suggested that the protein has high homology with fungal β-glucosidases that belong to glycosyl hydrolase family 3. The Kms for p-nitorophenyl-β-D-glucoside (p-NPG) and cellobiose hydrolyses were 0.117 and 4.81 mM, and the Kcat values were 721 and 101.8 per sec, respectively. The enzyme was competitively inhibited by both glucose (Ki= 0.35 mM) and gluconolactone (Ki= 0.008 mM), when p-NPG was used as substrate. The optimal activity of the purified β-glucosidase was observed at pH 4.5 and 70°C. The F. palustris protein exhibited half-lives of 97 h at 55°C and 15 h at 65°C, indicating some degree of thermostability. The enzyme has high activity against p-NPG and cellobiose but has very little or no activity against p-nitrophenyl-β-lactoside, p-nitrophenyl-β-xyloside, p-nitrophenyl-α-arabinofuranoside, xylan, and carboxymethyl cellulose. Thus, our results revealed that the β-glucosidase from F. palustris can be classified as an aryl-β-glucosidase with cellobiase activity.

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