Journal of Microbiology

Review

Advancements in the production of value-added products via methane biotransformation by methanotrophs: Current status and future perspectives: Ok Kyung Lee, Jong Seok Lee, Yoonyong Yang, Moonsuk Hur, Kyung Jin Lee, Eun Yeol Lee; J. Microbiol. 2025;63(3):e2412024. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2412024

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Methane gas is recognized as a promising carbon substrate for the biosynthesis of value-added products due to its abundance and low price. Methanotrophs utilized methane as their sole source of carbon and energy, thus they can serve as efficient biocatalysts for methane bioconversion. Methanotrophs-catalyzed microbial bioconversion offer numerous advantages, compared to chemical processes. Current indirect chemical conversions of methane suffer from their energy-intensive processes and high capital expenditure. Methanotrophs can be cell factories capable of synthesizing various value-added products from methane such as methanol, organic acids, ectoine, polyhydroxyalkanoates, etc. However, the large-scale commercial implementation using methanotrophs remains a formidable challenge, primarily due to limitations in gas-liquid mass transfer and low metabolic capacity. This review explores recent advancements in methanotroph research, providing insights into their potential for enabling methane bioconversion.

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Advancing microbial engineering through synthetic biology
Ki Jun Jeong
Journal of Microbiology.2025; 63(3): e2503100. CrossRef

Journal Article

Intervention with kimchi microbial community ameliorates obesity by regulating gut microbiota: Seong-Eun Park , Sun Jae Kwon , Kwang-Moon Cho , Seung-Ho Seo , Eun-Ju Kim , Tatsuya Unno , So-Hyeon Bok , Dae-Hun Park , Hong-Seok Son; J. Microbiol. 2020;58(10):859-867. Published online September 2, 2020; DOI: https://doi.org/10.1007/s12275-020-0266-2

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Abstract

The objective of this study was to evaluate anti-obesity effects of kimchi microbial community (KMC) on obesity and gut microbiota using a high fat diet-induced mouse model compared to effects of a single strain. Administration of KMC decreased body weight, adipose tissue, and liver weight gains. Relative content of Muribaculaceae in the gut of the KMCtreated group was higher than that in the high-fat diet (HFD) group whereas relative contents of Akkermansiaceae, Coriobacteriaceae, and Erysipelotrichaceae were lower in KMCtreated group. Metabolic profile of blood was found to change differently according to the administration of KMC and a single strain of Lactobacillus plantarum. Serum metabolites significantly increased in the HFD group but decreased in the KMC-treated group included arachidic acid, stearic acid, fumaric acid, and glucose, suggesting that the administration of KMC could influence energy metabolism. The main genus in KMC was not detected in guts of mice in KMC-treated group. Since the use of KMC has advantages in terms of safety, it has potential to improve gut microbial community for obese people.

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Anti-obesity activity of lactic acid bacteria-starter-based kimchi in high-fat diet-induced obese mice
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Review

[Minireivew]Microbial consortia including methanotrophs: some benefits of living together: Rajendra Singh , Jaewon Ryu , Si Wouk Kim; J. Microbiol. 2019;57(11):939-952. Published online October 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9328-8

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Abstract

With the progress of biotechnological research and improvements made in bioprocessing with pure cultures, microbial consortia have gained recognition for accomplishing biological processes with improved effectiveness. Microbes are indispensable tool in developing bioprocesses for the production of bioenergy and biochemicals while utilizing renewable resources due to technical, economic and environmental advantages. They communicate with specific cohorts in close proximity to promote metabolic cooperation. Use of positive microbial associations has been recognized widely, especially in food industries and bioremediation of toxic compounds and waste materials. Role of microbial associations in developing sustainable energy sources and substitutes for conventional fuels is highly promising with many commercial prospects. Detoxification of chemical contaminants sourced from domestic, agricultural and industrial wastes has also been achieved through microbial catalysis in pure and co-culture systems. Methanotrophs, the sole biological sink of greenhouse gas methane, catalyze the methane monooxygenasemediated oxidation of methane to methanol, a high energy density liquid and key platform chemical to produce commodity chemical compounds and their derivatives. Constructed microbial consortia have positive effects, such as improved biomass, biocatalytic potential, stability etc. In a methanotroph- heterotroph consortium, non-methanotrophs provide key nutrient factors and alleviate the toxicity from the culture. Non-methanotrophic organisms biologically stimulate the growth and activity of methanotrophs via production of growth stimulators. However, methanotrophs in association with cocultured microorganisms are in need of further exploration and thorough investigation to study their interaction mode and application with improved effectiveness.

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Journal Articles

Magnetite production and transformation in the methanogenic consortia from coastal riverine sediments: Shiling Zheng , Bingchen Wang , Fanghua Liu , Oumei Wang; J. Microbiol. 2017;55(11):862-870. Published online October 27, 2017; DOI: https://doi.org/10.1007/s12275-017-7104-1

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Abstract

Minerals that contain ferric iron, such as amorphous Fe(III) oxides (A), can inhibit methanogenesis by competitively accepting electrons. In contrast, ferric iron reduced products, such as magnetite (M), can function as electrical conductors to stimulate methanogenesis, however, the processes and effects of magnetite production and transformation in the methanogenic consortia are not yet known. Here we compare the effects on methanogenesis of amorphous Fe (III) oxides (A) and magnetite (M) with ethanol as the electron donor. RNAbased terminal restriction fragment length polymorphism with a clone library was used to analyse both bacterial and archaeal communities. Iron (III)-reducing bacteria including Geobacteraceae and methanogens such as Methanosarcina were enriched in iron oxide-supplemented enrichment cultures for two generations with ethanol as the electron donor. The enrichment cultures with A and non-Fe (N) dominated by the active bacteria belong to Veillonellaceae, and archaea belong to Methanoregulaceae and Methanobacteriaceae, Methanosarcinaceae (Methanosarcina mazei), respectively. While the enrichment cultures with M, dominated by the archaea belong to Methanosarcinaceae (Methanosarcina barkeri). The
results
also showed that methanogenesis was accelerated in the transferred cultures with ethanol as the electron donor during magnetite production from A reduction. Powder X-ray diffraction analysis indicated that magnetite was generated from microbial reduction of A and M was transformed into siderite and vivianite with ethanol as the electron donor. Our data showed the processes and effects of magnetite production and transformation in the methanogenic consortia, suggesting that significantly different effects of iron minerals on microbial methanogenesis in the iron-rich coastal riverine environment were present.

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A novel methanotroph in the genus Methylomonas that contains a distinct clade of soluble methane monooxygenase: Ngoc-Loi Nguyen , Woon-Jong Yu , Hye-Young Yang , Jong-Geol Kim , Man-Young Jung , Soo-Je Park , Seong-Woon Roh , Sung-Keun Rhee; J. Microbiol. 2017;55(10):775-782. Published online September 28, 2017; DOI: https://doi.org/10.1007/s12275-017-7317-3

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Abstract

Aerobic methane oxidation is a key process in the global carbon cycle that acts as a major sink of methane. In this study, we describe a novel methanotroph designated EMGL16-1 that was isolated from a freshwater lake using the floating filter culture technique. Based on a phylogenetic analysis of 16S rRNA gene sequences, the isolate was found to be closely related to the genus Methylomonas in the family Methylococcaceae of the class Gammaproteobacteria with 94.2–97.4% 16S rRNA gene similarity to Methylomonas type strains. Comparison of chemotaxonomic and physiological properties further suggested that strain EMGL16-1 was taxonomically distinct from other species in the genus Methylomonas. The isolate was versatile in utilizing nitrogen sources such as molecular nitrogen, nitrate, nitrite, urea, and ammonium. The genes coding for subunit of the particulate form methane monooxygenase (pmoA), soluble methane monooxygenase (mmoX), and methanol dehydrogenase (mxaF) were detected in strain EMGL16-1. Phylogenetic analysis of mmoX indicated that mmoX of strain EMGL16-1 is distinct from those of other strains in the genus Methylomonas. This isolate probably represents a novel species in the genus. Our study provides new insights into the diversity of species in the genus Methylomonas and their environmental adaptations.

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Environmental Science & Technology.2018; 52(11): 6084. CrossRef
Factors affecting the selection of PHB accumulating methanotrophs from waste activated sludge while utilizing ammonium as their nitrogen source
Ahmed Fergala, Ahmed AlSayed, Ahmed Eldyasti
Journal of Chemical Technology & Biotechnology.2018; 93(5): 1359. CrossRef

Metagenomic analysis reveals the contribution of anaerobic methanotroph-1b in the oxidation of methane at the Ulleung Basin, East Sea of Korea: Jin-Woo Lee , Kae Kyoung Kwon , Jang-Jun Bahk , Dong-Hun Lee , Hyun Sook Lee , Sung Gyun Kang , Jung-Hyun Lee; J. Microbiol. 2016;54(12):814-822. Published online November 26, 2016; DOI: https://doi.org/10.1007/s12275-016-6379-y

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Abstract

We have previously identified a sulfate methane transition zone (SMTZ) within the methane hydrate-bearing sediment in the Ulleung Basin, East Sea of Korea, and the presence of ANME-1b group in the sediment has been shown by phylogenetic analysis of a 16S rRNA gene. Herein, we describe taxonomic and functional profiling in the SMTZ sample by metagenomic analysis, comparing with that of surface sediment. Metagenomic sequences of 115 Mbp and 252 Mbp were obtained from SMTZ and surface sediments, respectively. The taxonomic profiling using BLASTX against the SEED within MG-RAST showed the prevalence of methanogens (19.1%), such as Methanosarcinales (12.0%) and Methanomicrobiales (4.1%) predominated within the SMTZ metagenome. A number of 185,200 SMTZ reads (38.9%) and 438,484 surface reads (62.5%) were assigned to functional categories, and methanogenesis-related reads were statistically significantly overrepresented in the SMTZ metagenome. However, the mapping analysis of metagenome reads to the reference genomes, most of the sequences of the SMTZ metagenome were mapped to ANME-1 draft genomes, rather than those of methanogens. Furthermore, the two copies of the methyl-coenzyme M reductase gene (mcrA) segments of the SMTZ metagenome were clustered with ANME-1b in the phylogenetic cluster. These results indicate that ANME- 1b reads were miss-annotated to methanogens due to limitation of database. Many of key genes necessary for reverse methanogenesis were present in the SMTZ metagenome, except for N5,N10-methenyl-H4MPT reductase (mer) and CoBCoM heterodisulfide reductase subunits D and E (hdrDE). These data suggest that the ANME-1b represents the primary player the anaerobic methane oxidation in the SMTZ, of the methane hydrate-bearing sediment at the Ulleung Basin, East Sea of Korea.

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Methane seepage intensity distinguish microbial communities in sediments at the Mid-Okinawa Trough
Youzhi Xin, Nengyou Wu, Zhilei Sun, Hongmei Wang, Ye Chen, Cuiling Xu, Wei Geng, Hong Cao, Xilin Zhang, Bin Zhai, Dawei Yan
Science of The Total Environment.2022; 851: 158213. CrossRef
Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments
Anna J. Wallenius, Paula Dalcin Martins, Caroline P. Slomp, Mike S. M. Jetten
Frontiers in Microbiology.2021;[Epub] CrossRef
Roles of Organohalide-Respiring Dehalococcoidia in Carbon Cycling
Yi Yang, Robert Sanford, Jun Yan, Gao Chen, Natalie L. Cápiro, Xiuying Li, Frank E. Löffler, Nick Bouskill
mSystems.2020;[Epub] CrossRef
Community structure and distribution of benthic Bacteria and Archaea in a stratified coastal lagoon in the Southern Gulf of Mexico
Santiago Cadena, M. Leopoldina Aguirre-Macedo, Daniel Cerqueda-García, Francisco J. Cervantes, Jorge A. Herrera-Silveira, José Q. García-Maldonado
Estuarine, Coastal and Shelf Science.2019; 230: 106433. CrossRef

Review

MINIREVIEW] Hydroxylation of methane through component interactions in soluble methane monooxygenases: Seung Jae Lee; J. Microbiol. 2016;54(4):277-282. Published online April 1, 2016; DOI: https://doi.org/10.1007/s12275-016-5642-6

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Abstract

Methane hydroxylation through methane monooxygenases (MMOs) is a key aspect due to their control of the carbon cycle in the ecology system and recent applications of methane gas in the field of bioenergy and bioremediation. Methanotropic bacteria perform a specific microbial conversion from methane, one of the most stable carbon compounds, to methanol through elaborate mechanisms. MMOs express particulate methane monooxygenase (pMMO) in most strains and soluble methane monooxygenase (sMMO) under copper-limited conditions. The mechanisms of MMO have been widely studied from sMMO belonging to the bacterial multicomponent monooxygenase (BMM) superfamily. This enzyme has diiron active sites where different types of hydrocarbons are oxidized through orchestrated hydroxylase, regulatory and reductase components for precise control of hydrocarbons, oxygen, protons, and electrons. Recent advances in biophysical studies, including structural and enzymatic achievements for sMMO, have explained component interactions, substrate pathways, and intermediates of sMMO. In this account, oxidation of methane in sMMO is discussed with recent progress that is critical for understanding the microbial applications of C-H activation in one-carbon substrates.

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Complete genome sequences of Methylococcus capsulatus (Norfolk) and Methylocaldum szegediense (Norfolk) isolated from a landfill methane biofilter
David Pearce, Elliot Brooks, Charles Wright, Daniel Rankin, Andrew T. Crombie, J. Colin Murrell, Elinne Becket
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Patrik Török, Dóra Lakk-Bogáth, Duenpen Unjaroen, Wesley R. Browne, József Kaizer
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Crucial Role of the Chaperonin GroES/EL for Heterologous Production of the Soluble Methane Monooxygenase from Methylomonas methanica MC09
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A. A. Shteinman
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Research Support, U.S. Gov't, Non-P.H.S.

Salinity as a Regulator of DMSP Degradation in Ruegeria pomeroyi DSS-3: Paula Salgado , Ronald Kiene , William Wiebe , Catarina Magalhães; J. Microbiol. 2014;52(11):948-954. Published online October 3, 2014; DOI: https://doi.org/10.1007/s12275-014-4409-1

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Abstract

Dimethylsulfoniopropionate (DMSP) is an important carbon and sulfur source to marine bacterial communities and the main precursor of dimethylsulfide (DMS), a gas that influences atmospheric chemistry and potentially the global climate. In nature, bacterial DMSP catabolism can yield different proportions of DMS and methanethiol (MeSH), but relatively little is known about the factors controlling the pathways of bacterial degradation that select between their formation (cleavage vs. demethiolation). In this study, we carried out experiments to evaluate the influence of salinity on the routes of DMSP catabolism in Ruegeria pomeroyi DSS-3. We monitored DMS and MeSH accumulation in cell suspensions grown in a range of salinities (10, 20, 30 ppt) and with different DMSP amendments (0, 50, 500 μM). Significantly higher concentrations of DMS accumulated in low salinity treatments (10 ppt; P < 0.001), in both Marine Basal Medium (MBM) and half-strength Yeast Tryptone Sea Salts (½ YTSS) media. Results showed a 47.1% and 87.5% decrease of DMS accumulation, from salinity 10 to 20 ppt, in MBM and ½ YTSS media, respectively. On the other hand, MeSH showed enhanced accumulations at higher salinities (20, 30 ppt), with a 90.6% increase of MeSH accumulation from the 20 ppt to the 30 ppt salinity treatments. Our results with R. pomeroyi DSS-3 in culture are in agreement with previous results from estuarine sediments and demonstrate that salinity can modulate selection of the DMSP enzymatic degradation routes, with a consequent potential impact on DMS and MeSH liberation into the atmosphere.

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SAR92 clade bacteria are potentially important DMSP degraders and sources of climate-active gases in marine environments
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DMSP Production by Coral-Associated Bacteria
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Stressed out: Bacterial response to high salinity using compatible solute biosynthesis and uptake systems, lessons from Vibrionaceae
Gwendolyn J. Gregory, E. Fidelma Boyd
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Laura Hernández, Alberto Vicens, Luis E. Eguiarte, Valeria Souza, Valerie De Anda, José M. González
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J. Yu, J.‐Y. Tian, Z.‐Y. Zhang, G.‐P. Yang, H.‐J. Chen, R. Xu, R. Chen
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Phylogenetic diversity of dimethylsulfoniopropionatedependent demethylase gene dmdA in distantly related bacteria isolated from Arctic and Antarctic marine environments
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Shuanghu Fan, Junhuan Wang, Yanchun Yan, Jiayi Wang, Yang Jia
International Journal of Molecular Sciences.2018; 19(9): 2803. CrossRef
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Cheng‐Xuan Li, Bao‐Dong Wang, Gui‐Peng Yang, Zi‐Cheng Wang, Jian‐Fang Chen, Yang Lyu
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Hannah A. Bullock, Haiwei Luo, William B. Whitman
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J Motard-Côté, RP Kiene
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Impact of river discharge on distribution of dimethyl sulfide (DMS) and its fluxes in the coastal Bay of Bengal
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Distribution and activity of sulfate-reducing bacteria in lake soyang sediments: Jin, Ho Yong , Lee, Dong Hun , Zo, Young Gun , Kang Chan Su , Kim Sang Jong; J. Microbiol. 1996;34(2):131-136.

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Abstract: In order to known the extend of contribution to the degradation of organic materials and nutrient recycling by sulfate-reducing bacteria (SRB) and methane-producing bacteria (MPB) in sediment, the distribution and activity of these two groups of microorganisms were studied montly in 1994 at two sites, one littoral (Sanggulri) and the other profundal (DAM), in Lake Soyang. In the seasonal distribution of two microorganisms, SRB were 1.07 × 10^3 - 2.42 × 10^5 cells/g-dry weight at Sanggulri, 2.40 × 10^5 - 1.29 × 10^6 at Dam and MPB were 0.52 × 10^3 cells/g-dry weight at Sangguri and 1.44 × 10^3 - 6.89 × 10^3 at Dam. In these results, the density of SRB in Lake Soyang is much higher than other lakes. These high values might be due to higher sulfate concentration, 0.69-4.05 mM, than normal freshwater, 0.01-1.2 mM. And a good correlation of SRB and chlorophyll a concentration implied that the important environmental factor on distribution of SRB might be the concentration of available organic matter. In a comparison of sulfate-reducing rate and methane producing rate in 1995, the activity of SRB for the degradation of organic matter was higher than MPB by factor of 359. Conclusively SRB superior to MPB in the distribution and activity are more important anaerobic bacteria in Lake Soyang sediments.

Inhibitory Effects of Lactic Acid Bacteria (LAB) on the Azoxymethane-induced Colonic Preneoplastic Lesions: Sang-Myeong Lee , Wan-Kyu Lee; J. Microbiol. 2000;38(3):169-175.

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Abstract: Epidemiological and experimental studies provide evidences that diet and intestinal microflora play an important role in colon carcinogenesis. In recent years, it has been suggested that lactic acid bacteria (LAB) used to ferment dairy products have an inhibitory effect on the colon cancer. This study was designed to determine the effect of Bifidobacterium longum HY8001 (Bif) and Lactobacillus acidophilus HY2104 (Lac) of Korean origin on azoxymethane (AOM)-induced colonic preneoplastic lesions such as aberrant crypt foci (ACF) formation and cecal pH. At five weeks of age, Spraque-Dawley rats were divided at random into four (AOM alone, Bif, Lac, and Bif+Lac) groups. Animals were weighed weekly and oral administration of LAB cultures were performed daily until the termination of the study. Two weeks later, all animals were given a subcutaneous injection of AOM dissolved in normal saline at a dose of 15 mg/kg of body weight once per week for 2 weeks. All rats were necropsied 7 weeks after the last AOM injection, and the ACF were visualized under light microscopy in the formalin-fixed, unsectioned methylene blue-stained colons. The total number of aberrant crypt in Bif, Lac, and Bif+Lac groups were significantly lower than that of the AOM alone group and the percentage of inhibitions weas 35.0, 45.4 and 45.0%, respectively. Significant inhibition (p<0.001) in the total number of ACF was also observed in LAB treated groups (Bif, Lac, and Bif+Lac group by 30.3, 38.6, and 41.2%, respec-tively). Furthermore, cecal pH appeared to significantly decrease by LAB administration. The results of present study provide some evidences for potential colon tumor-inhibitory properties of lactic cultures and fermented dairy products.

Effects of Lactic Acid Bacteria on Intestinal Microbial Enzyme Activity and Composition in Rats Treated with Azoxymethane: Sang-Myeong Lee , Wan-Kyu Lee; J. Microbiol. 2001;39(3):154-161.

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Abstract: In recent years, colon cancer has been reported to be one of the most important causes of cancer morbidity and mortality in Korea. Epidemiological and experimental studies suggest that lactic acid bacteria (LAB) used to ferment dairy products inhibits colon carcinogenesis. The present study was designed to determine whether the colon cancer inhibitory effect of LAB (Bifidobacterium longum HY8001; Bif and Lactobacillus acidophilus HY2104; Lac) of Korean origin, is associated with intestinal microflora composition and certain enzyme activity in rats treated with azoxymethane (AOM). At five weeks of age, SD rats were divided at random into four (AOM alone, Bif, Lac, and Bif+Lac) groups. Oral administration of lactic acid bacteria cultures were performed daily until the termination of the study. Two weeks later, all animals were given a subcutaneous injection of AOM dissolved in normal saline at a dose of 15 mg/kg of body weight once weekly for 2 weeks. Every two weeks for 10 weeks, five of the rats in each group were randomly chosen for fecal specimen collection. The fecal specimens were used for assay of [beta]-glucuronidase and nitroreductase, and analysis of intestinal microflora composition. The activity of [beta]-glucuronidase which plays an important role in the production of the carcinogenic metabolite of azoxymethane was remarkably increased in the AOM alone group after AOM injection and maintained the high level during the experiment. However, LAB inhibited the AOM-induced increase in [beta]-glucuronidase activity. Nitroreductase activity decreased by 30-40% in LAB treated groups in comparison with that of the AOM alone group. The results of the present study suggest that LAB inhibits colon carcinogenesis by modulating the metabolic activity of intestinal microflora and improving the composition of intestinal microflora.

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