Journal of Microbiology

Review

Recent advances in targeted mutagenesis to expedite the evolution of biological systems: Seungjin Kim, Seungwon Lee, Hyun Gyu Lim; J. Microbiol. 2025;63(3):e2501008. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501008

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Evolution has been systematically exploited to engineer biological systems to obtain improved or novel functionalities by selecting beneficial mutations. Recent innovations in continuous targeted mutagenesis within living cells have emerged to generate large sequence diversities without requiring multiple steps. This review comprehensively introduces recent advancements in this field, categorizing them into three approaches depending on methods to create mutations: orthogonal error-prone DNA polymerases, site-specific base editors, and homologous recombination of mutagenic DNA fragments. Combined with high-throughput screening methods, these advances expedited evolution processes with significant reduction of labor and time. These approaches promise broader industrial and research applications, including enzyme improvement, metabolic engineering, and drug resistance studies.

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

Journal Articles

Repeated Exposure of Vancomycin to Vancomycin-Susceptible Staphylococcus aureus (VSSA) Parent Emerged VISA and VRSA Strains with Enhanced Virulence Potentials: An Nguyen, J Jean Sophy Roy, Ji-Hoon Kim, Kyung-Hee Yun, Wonsik Lee, Kyeong Kyu Kim, Truc Kim, Akhilesh Kumar Chaurasia; J. Microbiol. 2024;62(7):535-553. Published online May 30, 2024; DOI: https://doi.org/10.1007/s12275-024-00139-8

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Abstract: The emergence of resistance against the last-resort antibiotic vancomycin in staphylococcal infections is a serious concern for human health. Although various drug-resistant pathogens of diverse genetic backgrounds show higher virulence potential, the underlying mechanism behind this is not yet clear due to variability in their genetic dispositions. In this study, we investigated the correlation between resistance and virulence in adaptively evolved isogenic strains. The vancomycin-susceptible Staphylococcus aureus USA300 was exposed to various concentrations of vancomycin repeatedly as a mimic of the clinical regimen to obtain mutation(s)-accrued-clonally-selected (MACS) strains. The phenotypic analyses followed by expression of the representative genes responsible for virulence and resistance of MACS strains were investigated. MACS strains obtained under 2 and 8 µg/ml vancomycin, named Van2 and Van8, respectively; showed enhanced vancomycin minimal inhibitory concentrations (MIC) to 4 and 16 µg/ml, respectively. The cell adhesion and invasion of MACS strains increased in proportion to their MICs. The correlation between resistance and virulence potential was partially explained by the differential expression of genes known to be involved in both virulence and resistance in MACS strains compared to parent S. aureus USA300. Repeated treatment of vancomycin against vancomycin-susceptible S. aureus (VSSA) leads to the emergence of vancomycin-resistant strains with variable levels of enhanced virulence potentials.

In Silico Intensive Analysis for the E4 Gene Evolution of Human Adenovirus Species D: Chanhee Lee, Anyeseu Park, Jeong Yoon Lee; J. Microbiol. 2024;62(5):409-418. Published online April 30, 2024; DOI: https://doi.org/10.1007/s12275-024-00132-1

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Abstract: Adenovirus (Ad) is a ubiquitous pathogen capable of infecting a wide range of animals and humans. Human Adenovirus (HAdV) can cause severe infection, particularly in individuals with compromised immune systems. To date, over 110 types of HAdV have been classified into seven species from A to G, with the majority belonging to the human adenovirus species D (HAdV-D). In the HAdV-D, the most significant factor for the creation of new adenovirus types is homologous recombination between viral genes involved in determining the virus tropism or evading immune system of host cells. The E4 gene, consisting of seven Open Reading Frames (ORFs), plays a role in both the regulation of host cell metabolism and the replication of viral genes. Despite long-term studies, the function of each ORF remains unclear. Based on our updated information, ORF2, ORF3, and ORF4 have been identified as regions with relatively high mutations compared to other ORFs in the E4 gene, through the use of in silico comparative analysis. Additionally, we managed to visualize high mutation sections, previously undetectable at the DNA level, through a powerful amino acid sequence analysis tool known as proteotyping. Our research has revealed the involvement of the E4 gene in the evolution of human adenovirus, and has established accurate sequence information of the E4 gene, laying the groundwork for further research.

Review

Genomic Evolution and Recombination Dynamics of Human Adenovirus D Species: Insights from Comprehensive Bioinformatic Analysis: Anyeseu Park, Chanhee Lee, Jeong Yoon Lee; J. Microbiol. 2024;62(5):393-407. Published online March 7, 2024; DOI: https://doi.org/10.1007/s12275-024-00112-5

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Abstract

Human adenoviruses (HAdVs) can infect various epithelial mucosal cells, ultimately causing different symptoms in infected organ systems. With more than 110 types classified into seven species (A-G), HAdV-D species possess the highest number of viruses and are the fastest proliferating. The emergence of new adenovirus types and increased diversity are driven by homologous recombination (HR) between viral genes, primarily in structural elements such as the penton base, hexon and fiber proteins, and the E1 and E3 regions. A comprehensive analysis of the HAdV genome provides valuable insights into the evolution of human adenoviruses and identifies genes that display high variation across the entire genome to determine recombination patterns. Hypervariable regions within genetic sequences correlate with functional characteristics, thus allowing for adaptation to new environments and hosts. Proteotyping of newly emerging and already established adenoviruses allows for prediction of the characteristics of novel viruses. HAdV-D species evolved in a direction that increased diversity through gene recombination. Bioinformatics analysis across the genome, particularly in highly variable regions, allows for the verification or re-evaluation of recombination patterns in both newly introduced and pre-existing viruses, ultimately aiding in tracing various biological traits such as virus tropism and pathogenesis. Our research does not only assist in predicting the emergence of new adenoviruses but also offers critical guidance in regard to identifying potential regulatory factors of homologous recombination hotspots.

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In Silico Intensive Analysis for the E4 Gene Evolution of Human Adenovirus Species D
Chanhee Lee, Anyeseu Park, Jeong Yoon Lee
Journal of Microbiology.2024; 62(5): 409. CrossRef

Journal Articles

Prevalence of Indigenous Antibiotic‑Resistant Salmonella Isolates and Their Application to Explore a Lytic Phage vB_SalS_KFSSM with an Intra‑Broad Specificity: Jaein Choe , Su-Hyeon Kim , Ji Min Han , Jong-Hoon Kim , Mi-Sun Kwak , Do-Won Jeong , Mi-Kyung Park; J. Microbiol. 2023;61(12):1063-1073. Published online January 2, 2024; DOI: https://doi.org/10.1007/s12275-023-00098-6

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Abstract: The consumption of fresh produce has led to increase in antibiotic-resistant (AR) Salmonella outbreaks. In this study, indigenous Salmonella was isolated from a total of two hundred-two samples including fresh produce and agricultural environmental samples in Korea. After biochemical confirmation using the Indole, Methyl Red, Voges-Proskauer, Citrate tests, presumable Salmonella isolates were identified by 16S rRNA sequencing. Identified Salmonella isolates were evaluated for antibiotic susceptibility against twenty-two antibiotics. The specificity and the efficiency of plating (EOP) of vB_SalS_KFSSM were evaluated against fifty-three bacterial strains. Twenty-five suspected Salmonella were isolated and confirmed by the positive
result
for methyl red and citrate, of which ten were identified as Salmonella spp. through 16S rRNA gene sequencing. Eight Salmonella isolates (4.0%, n = 8/202) were resistant to at least one antibiotic, among which five were multi-drug resistant. As a lytic phage against Salmonella spp. CMGS-1, vB_SalS_KFSSM was isolated from cow manure. The phage was observed as a tailed phage belonging to the class Caudoviricetes. It exhibited an intra-broad specificity against four indigenous AR Salmonella isolates, two indigenous Salmonella isolates, and five other Salmonella serotypes with great efficiencies (EOP ≥ 0.75). Thus, this study suggested the potential of vB_SalS_KFSSM to combat indigenous AR Salmonella.

Heterologous Production and Structure Determination of a New Lanthipeptide Sinosporapeptin Using a Cryptic Gene Cluster in an Actinobacterium Sinosporangium siamense: Keita Saito , Keiichiro Mukai , Issara Kaweewan , Hiroyuki Nakagawa , Takeshi Hosaka , Shinya Kodani; J. Microbiol. 2023;61(6):641-648. Published online June 12, 2023; DOI: https://doi.org/10.1007/s12275-023-00059-z

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Abstract

Lipolanthine is a subclass of lanthipeptide that has the modification of lipid moiety at the N-terminus. A cryptic biosynthetic gene cluster comprising four genes (sinA, sinKC, sinD, and sinE) involved in the biosynthesis of lipolanthine was identified in the genome of an actinobacterium Sinosporangium siamense. Heterologous coexpression of a precursor peptide coding gene sinA and lanthipeptide synthetase coding gene sinKC in the host Escherichia coli strain BL21(DE3) resulted in the synthesis of a new lanthipeptide, sinosporapeptin. It contained unusual amino acids, including one labionin and two dehydrobutyrine residues, as determined using NMR and MS analyses. Another coexpression experiment with two additional genes of decarboxylase (sinD) and N-acetyl transferase (sinE) resulted in the production of a lipolanthine-like modified sinosporapeptin.

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Heterologous biosynthesis of myxobacterial lanthipeptides melittapeptins
Issara Kaweewan, Keiichiro Mukai, Pratchaya Rukthanapitak, Hiroyuki Nakagawa, Takeshi Hosaka, Shinya Kodani
Applied Microbiology and Biotechnology.2024;[Epub] CrossRef
Facile Method for Determining Lanthipeptide Stereochemistry
Youran Luo, Shuyun Xu, Autumn M. Frerk, Wilfred A. van der Donk
Analytical Chemistry.2024; 96(4): 1767. CrossRef
Antimicrobial Peptides Derived from Bacteria: Classification, Sources, and Mechanism of Action against Multidrug-Resistant Bacteria
Raynichka Mihaylova-Garnizova, Slavena Davidova, Yordan Hodzhev, Galina Satchanska
International Journal of Molecular Sciences.2024; 25(19): 10788. CrossRef

Recombinant Protein Mimicking the Antigenic Structure of the Viral Surface Envelope Protein Reinforces Induction of an Antigen‑Specific and Virus‑Neutralizing Immune Response Against Dengue Virus: Ju Kim , Tae Young Lim , Jisang Park , Yong&#; J. Microbiol. 2023;61(1):131-143. Published online February 1, 2023; DOI: https://doi.org/10.1007/s12275-023-00021-z

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Abstract

Dengue virus (DENV), belonging to the family Flaviviridae, is the causative agent of dengue and comprises four serotypes. A second heterologous DENV infection is a critical risk factor for severe dengue, and no effective vaccine is available to prevent infection by all four DENV serotypes. Recombinant DENV vaccines are primarily based on the envelope proteins, prM and E. The E protein and its envelope domain III (EDIII) have been investigated as candidate antigens (Ags) for recombinant subunit vaccines. However, most EDIII-based Ags are monomers that do not display the cognate antigenic structure of E protein, which is essential for induction of virus-neutralizing immunity. Here, we developed recombinant DENV-2 envelope domain (r2ED) protein as an Ag that mimics the quaternary structure of E protein on the DENV surface. We confirmed that r2ED retained the conformational epitope displayed at the E-dimer interface, which reportedly exhibits broad virus-neutralizing capacity, without displaying the fusion loop epitope that causes antibody (Ab)-dependent enhancement. Furthermore, compared with EDIII alone, r2ED elicited stronger Ag-specific and cross-reactive neutralizing Ab and T cell-mediated immune responses in mice. This Ag-specific immunity was maintained at an elevated level 6 months after the last immunization, suggesting sustained Ag-specific immune memory. Taken together, these observations suggest that r2ED could be used to develop an improved subunit vaccine capable of inducing a broadly cross-reactive and long-lasting immune response against DENV infection.

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Peptides of a Feather: How Computation Is Taking Peptide Therapeutics under Its Wing
Thomas David Daniel Kazmirchuk, Calvin Bradbury-Jost, Taylor Ann Withey, Tadesse Gessese, Taha Azad, Bahram Samanfar, Frank Dehne, Ashkan Golshani
Genes.2023; 14(6): 1194. CrossRef

Blue-Red LED wavelength shifting strategy for enhancing beta-carotene production from halotolerant microalga, Dunaliella salina: Sang-Il Han , Sok Kim , Changsu Lee , Yoon-E Choi; J. Microbiol. 2019;57(2):101-106. Published online September 28, 2018; DOI: https://doi.org/10.1007/s12275-019-8420-4

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Abstract

In the present study, to improve the photosynthetic betacarotene productivity of Dunaliella salina, a blue-red LED wavelength-shifting system (B-R system) was investigated. Dunaliella salina under the B-R system showed enhanced density and beta-carotene productivity compared to D. salina cultivated under single light-emitting diode light wavelengths (blue, white, and red light-emitting diode). Additionally, we developed blue light-adapted D. salina (ALE-D. salina) using an adaptive laboratory evolution (ALE) approach. In combination with the B-R system applied to ALE-D. salina (ALE B-R system), the beta-carotene concentration (33.94 ± 0.52 μM) was enhanced by 19.7% compared to that observed for the non-ALE-treated wild-type of D. salina (intact D. salina) under the B-R system (28.34 ± 0.24 μM).

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Melih Onay, Zehra Sapci Ayas
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Jim Junhui Huang, Wenwen Xu, Shaoling Lin, Peter Chi Keung Cheung
Critical Reviews in Biotechnology.2024; : 1. CrossRef
Expanding horizons: Harnessing Dunaliella microalgae for sustainable organic pigment production
Gurunathan Baskar, M. Muthulakshmi, Ravichandran Pravin, Anil Kumar Patel
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Vanessa Campos Guedes, Guilherme Meneghetti Palma, Antonio Carlos Luperni Horta
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Xunqiang Wang, Cece Yang, Xing Zhang, Caiping Ye, Wenping Liu, Chengmin Wang
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Mojgan Mohebi Najafabadi, Fereshteh Naeimpoor
Journal of Applied Phycology.2024; 36(5): 2517. CrossRef
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Vanessa Campos Guedes, Ana Teresa Lombardi, Antonio Carlos Luperni Horta
Brazilian Journal of Chemical Engineering.2023; 40(4): 1089. CrossRef
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Ruyu Zhang, Yangyang Luo, Xiaolin Yu, Menghan Dang, Xuechao Hu, Lujing Ren
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Amirreza Zarekarizi, Linn Hoffmann, David J. Burritt
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Wladimir A. Fae Neto, Joseph L. Tomkins, W. Jason Kennington
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Koray BENAS, İlknur AK
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Wavelength tune of InGaN based blue LEDs by changing indium percentage and operational voltage variables
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Microalgal secondary metabolite productions as a component of biorefinery: A review
Yun Hwan Park, Sang-Il Han, Byeolnim Oh, Hyun Soo Kim, Min Seo Jeon, Sok Kim, Yoon-E Choi
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Ayesha Aslam, Ali Bahadar, Rabia Liaquat, Muhammad Saleem, Adeel Waqas, Mohammed Zwawi
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Adaptive Laboratory Evolution of Microalgae: A Review of the Regulation of Growth, Stress Resistance, Metabolic Processes, and Biodegradation of Pollutants
Bo Zhang, Jiangyue Wu, Fanping Meng
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A common evolutionary pathway for maintaining quorum sensing in Pseudomonas aeruginosa: Bai-min Lai , Hui-cong Yan , Mei-zhen Wang , Na Li , Dong-sheng Shen; J. Microbiol. 2018;56(2):83-89. Published online February 2, 2018; DOI: https://doi.org/10.1007/s12275-018-7286-1

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Abstract

In the bacterium Pseudomonas aeruginosa, the synthesis and secretion of extracellular protease is a typical cooperative behavior regulated by quorum sensing. However, this type of cooperative behavior is easily exploited by other individuals who do not synthesize public goods, which is known as the “tragedy of the commons”. Here P. aeruginosa was inoculated into casein media with different nitrogen salts added. In casein broth, protease (a type of public good) is necessary for bacterial growth. After 30 days of sequential transfer, some groups propagated stably and avoided “tragedy of the commons”. The evolved cooperators who continued to synthesize protease were isolated from these stable groups. By comparing the characteristics of quorum sensing in these cooperators, an identical evolutionary pattern was found. A variety of cooperative behaviors regulated by quorum sensing, such as the synthesis and secretion of protease and signals, were significantly reduced during the process of evolution. Such reductions improved the efficiency of cooperation, helping to prevent cheating. In addition, the production of pyocyanin, which is regulated by the RhlIR system, increased during the process of evolution, possibly due to its role in stabilizing the cooperation. This study contributes towards our understanding of the evolution of quorum sensing of P. aeruginosa.

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Diesel degradation capability and environmental robustness of strain Pseudomonas aeruginosa WS02
Penghong Luo, Yankui Tang, Jiahua Lu, Lu Jiang, Yiting Huang, Qiming Jiang, Xuemin Chen, Tianfu Qin, Holly Alice Shiels
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Biofilm control on metallic materials in medical fields from the viewpoint of materials science – from the fundamental aspects to evaluation
Hideyuki Kanematsu, Dana M. Barry, Hajime Ikegai, Yoshimitsu Mizunoe
International Materials Reviews.2023; 68(3): 247. CrossRef
To cheat or not to cheat: cheatable and non-cheatable virulence factors in Pseudomonas aeruginosa
Katya Dafne Guadarrama-Orozco, Caleb Perez-Gonzalez, Kokila Kota, Miguel Cocotl-Yañez, Jesús Guillermo Jiménez-Cortés, Miguel Díaz-Guerrero, Mariel Hernández-Garnica, Julia Munson, Frederic Cadet, Luis Esaú López-Jácome, Ángel Yahir Estrada-Velasco, Ana M
FEMS Microbiology Ecology.2023;[Epub] CrossRef
Exoprotease exploitation and social cheating in a Pseudomonas aeruginosa environmental lysogenic strain with a noncanonical quorum sensing system
Daniel Huelgas-Méndez, Daniel Cazares, Luis David Alcaraz, Corina Diana Ceapã, Miguel Cocotl-Yañez, Toya Shotaro, Toshinari Maeda, Ana María Fernández-Presas, Oswaldo Tostado-Islas, Ana Lorena González-Vadillo, Aldo Limones-Martínez, Carlos Eduardo Hernan
FEMS Microbiology Ecology.2023;[Epub] CrossRef
3-Phenylpropan-1-Amine Enhanced Susceptibility of Serratia marcescens to Ofloxacin by Occluding Quorum Sensing
Lujun Yin, Ping-Ping Zhang, Wei Wang, Shi Tang, Shi-Ming Deng, Ai-Qun Jia, Gyanu Lamichhane
Microbiology Spectrum.2022;[Epub] CrossRef
A deep insight into the suppression mechanism of Sedum alfredii root exudates on Pseudomonas aeruginosa based on quorum sensing
Min Zhu, Yusheng Yang, Meizhen Wang, Xiaoxiao Li, Ruifang Han, Qianqian Chen, Dongsheng Shen, Jiali Shentu
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Tobramycin Adaptation Enhances Policing of Social Cheaters in Pseudomonas aeruginosa
Rhea G. Abisado, John H. Kimbrough, Brielle M. McKee, Vaughn D. Craddock, Nicole E. Smalley, Ajai A. Dandekar, Josephine R. Chandler, Rebecca E. Parales
Applied and Environmental Microbiology.2021;[Epub] CrossRef
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Reviews

REVIEW] H5 influenza, a global update: Rhodri Harfoot , Richard J. Webby; J. Microbiol. 2017;55(3):196-203. Published online February 28, 2017; DOI: https://doi.org/10.1007/s12275-017-7062-7

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Abstract

H5 influenza viruses have caused much alarm globally due to their high pathogenic potential. As yet we have not seen sustained spread of the virus amongst humans despite a high prevalence of the virus in avian populations. Nevertheless, isolated human cases of infection have demonstrated high mortality and there are substantial efforts being taken to monitor the evolution of the virus and to undertake preparedness activities. Here we review and discuss the evolution of the A/goose/Guangdong/1/96 (H5N1) virus with emphasis on recent events.

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MINIREVIEW] Transcriptional control of sexual development in Cryptococcus neoformans: Matthew E. Mead , Christina M. Hull; J. Microbiol. 2016;54(5):339-346. Published online April 20, 2016; DOI: https://doi.org/10.1007/s12275-016-6080-1

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Abstract

Developmental processes are essential for the normal life cycles of many pathogenic fungi, and they can facilitate survival in challenging environments, including the human host. Sexual development of the human fungal pathogen Cryptococcus neoformans not only produces infectious particles (spores) but has also enabled the evolution of new disease-related traits such as drug resistance. Transcription factor networks are essential to the development and pathogenesis of C. neoformans, and a variety of sequence-specific DNA-binding proteins control both key developmental transitions and virulence by regulating the expression of their target genes. In this review we discuss the roles of known transcription factors that harbor important connections to both development and virulence. Recent studies of these transcription factors have identified a common theme in which metabolic, stress, and other responses that are required for sexual development appear to have been co-opted for survival in the human host, thus facilitating pathogenesis. Future work elucidating the connection between development and pathogenesis will provide vital insights into the evolution of complex traits in eukaryotes as well as mechanisms that may be used to combat fungal pathogens.

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Microbial ecology in Hydra: Why viruses matter: Thomas C.G. Bosch , Juris A. Grasis , Tim Lachnit; J. Microbiol. 2015;53(3):193-200. Published online March 3, 2015; DOI: https://doi.org/10.1007/s12275-015-4695-2

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Abstract

While largely studied because of their harmful effects on human health, there is growing appreciation that viruses are also important members of the animal holobiont. This review highlights recent findings on viruses associated with Hydra and related Cnidaria. These early evolutionary diverging animals not only select their bacterial communities but also select for viral communities in a species-specific manner. The majority of the viruses associating with these animals are bacteriophages. We demonstrate that the animal host and its virome have evolved into a homeostatic, symbiotic relationship and propose that viruses are an important part of the Hydra holobiont by controlling the species-specific microbiome. We conclude that beneficial virus-bacterial-host interactions should be considered as an integral part of animal development and evolution.

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Journal Article

Comparative Study of the marR Genes within the Family Enterobacteriaceae: Dan Wang , Changjiang Guo , Longjiang Gu , Xiaohui Zhang; J. Microbiol. 2014;52(6):452-459. Published online April 11, 2014; DOI: https://doi.org/10.1007/s12275-014-3586-2

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Abstract

marR genes are members of an ancient family originally identified in Escherichia coli. This family is widely distributed in archaea and bacteria. Homologues of this family have a conserved winged helix fold. MarR proteins are involved in non-specific resistance systems conferring resistance to multiple antibiotics. Extensive studies have shown the importance of MarR proteins in physiology and pathogenicity in Enterobacteria, but little is known about their origin or evolution. In this study, all the marR genes in 43 enterobacterial genomes representing 14 genera were identified, and the phylogenetic relationships and genetic parameters were analyzed. Several major findings were made. Three conserved marR genes originated earlier than Enterobacteriaceae and a geneloss event was found to have taken place in Yersinia pestis Antiqua. Three functional genes, rovA, hor, and slyA, were found to be clear orthologs among Enterobacteriaceae. The copy number of marR genes in Enterobacteriaceae was found to vary from 2 to 11. These marR genes exhibited a faster rate of nucleotide substitution than housekeeping genes did. Specifically, the regions of marR domain were found to be subject to strong purifying selection. The phylogenetic relationship and genetic parameter analyses were consistent with conservation and specificity of marR genes. These dual characters helped MarR to maintain a conserved binding motif and variable C-terminus, which are important to adaptive responses to a number of external stimuli in Enterobacteriaceae.

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Comparative Phylogenetic Relationships and Genetic Structure of the Caterpillar Fungus Ophiocordyceps sinensis and Its Host Insects Inferred from Multiple Gene Sequences: Qing-Mei Quan , Qing-Xia Wang , Xue-Li Zhou , Shan Li , Xiao-Ling Yang , Yun-Guo Zhu , Zhou Cheng; J. Microbiol. 2014;52(2):99-105. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3391-y

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Abstract

Ophiocordyceps sinensis (Ascomycota: Ophiocordycipitaceae) is a native fungal parasite of Hepialidae caterpillars and one of the most economically important medicinal caterpillar fungi in China. However, little is known about the phylogenetic and evolutionary relationships between O. sinensis and its host insects. In this study, nuclear ITS and β-tubulin sequences from O. sinensis and mitochondrial COI, COII, and Cytb sequences from its hosts were analyzed across 33 populations sampled from five regions in China. Phylogenetically, both O. sinensis and its hosts were divided into three geographically correlated clades, and their phylogenies were congruent. Analysis of molecular variance and calculated coefficients of genetic differentiation revealed significant genetic divergence among the clades within both O. sinensis (FST=0.878, NST=0.842) and its hosts (FST=0.861, NST=0.816). Estimated gene flow was very low for O. sinensis (Nm=0.04) and the host insects (Nm=0.04) among these three clades. Mantel tests demonstrated a significant correlation (P<0.01) between the genetic distances for O. sinensis and its hosts, as well as a significant association (P<0.05) between geographic and genetic distances in both. The similar phylogenetic relationships, geographic distributions, and genetic structure and differentiation between O. sinensis and its hosts imply that they have coevolved.

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A Genome-Wide Identification of Genes Potentially Associated with Host Specificity of Brucella Species: Kyung Mo Kim , Kyu-Won Kim , Samsun Sung , Heebal Kim; J. Microbiol. 2011;49(5):768-775. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1084-3

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Abstract

Brucella species are facultative intracellular pathogenic α-Proteobacteria that can cause brucellosis in humans and domestic animals. The clinical and veterinary importance of the bacteria has led to well established studies on the molecular mechanisms of Brucella infection of host organisms. However, to date, no genome-wide study has scanned for genes related to the host specificity of Brucella spp. The majority of bacterial genes related to specific environmental adaptations such as host specificity are well-known to have evolved under positive selection pressure. We thus detected signals of positive selection for individual orthologous genes among Brucella genomes and identified genes related to host specificity. We first determined orthologous sets from seven completely sequenced Brucella genomes using the Reciprocal Best Hits (RBH). A maximum likelihood analysis based on the branch-site test was accomplished to examine the presence of positive selection signals, which was subsequently confirmed by phylogenetic analysis. Consequently, 12 out of 2,033 orthologous genes were positively selected by specific Brucella lineages, each of which belongs to a particular animal host. Extensive literature reviews revealed that half of these computationally identified genes are indeed involved in Brucella host specificity. We expect that this genome-wide approach based on positive selection may be reliably used to screen for genes related to environmental adaptation of a particular species and that it will provide a set of appropriate candidate genes.

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