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Du Y, Qian C, Li X, Zheng X, Huang S, Yin Z, Chen T, Pan L. Unveiling intraspecific diversity and evolutionary dynamics of the foodborne pathogen Bacillus paranthracis through high-quality pan-genome analysis. Curr Res Food Sci 2024; 9:100867. [PMID: 39376581 PMCID: PMC11456886 DOI: 10.1016/j.crfs.2024.100867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2024] [Revised: 09/20/2024] [Accepted: 09/20/2024] [Indexed: 10/09/2024] Open
Abstract
Understanding the evolutionary dynamics of foodborne pathogens throughout host-associated habitats is of utmost importance. Bacterial pan-genomes, as dynamic entities, are strongly influenced by ecological lifestyles. As a phenotypically diverse species in the Bacillus cereus group, Bacillus paranthracis is recognized as an emerging foodborne pathogen and a probiotic simultaneously. This poorly understood species is a suitable study model for adaptive pan-genome evolution. In this study, we determined the biogeographic distribution, abundance, genetic diversity, and genotypic profiles of key genetic elements of B. paranthracis. Metagenomic read recruitment analyses demonstrated that B. paranthracis members are globally distributed and abundant in host-associated habitats. A high-quality pan-genome of B. paranthracis was subsequently constructed to analyze the evolutionary dynamics involved in ecological adaptation comprehensively. The open pan-genome indicated a flexible gene repertoire with extensive genetic diversity. Significant divergences in the phylogenetic relationships, functional enrichment, and degree of selective pressure between the different components demonstrated different evolutionary dynamics between the core and accessory genomes driven by ecological forces. Purifying selection and gene loss are the main signatures of evolutionary dynamics in B. paranthracis pan-genome. The plasticity of the accessory genome is characterized by horizontal gene transfer (HGT), massive gene losses, and weak purifying or positive selection, which might contribute to niche-specific adaptation. In contrast, although the core genome dominantly undergoes purifying selection, its association with HGT and positively selected mutations indicates its potential role in ecological diversification. Furthermore, host fitness-related dynamics are characterized by the loss of secondary metabolite biosynthesis gene clusters (BGCs) and CAZyme-encoding genes and the acquisition of antimicrobial resistance (AMR) and virulence genes via HGT. This study offers a case study of pan-genome evolution to investigate the ecological adaptations reflected by biogeographical characteristics, thereby advancing the understanding of intraspecific diversity and evolutionary dynamics of foodborne pathogens.
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Affiliation(s)
- Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological slaEngineering, South China University of Technology, Guangzhou, 510006, Guangdong, PR China
| | - Chengqian Qian
- School of Biology and Biological Engineering, Guangzhou Higher Education Mega Centre, South China University of Technology, Guangzhou, 510006, Guangdong, PR China
- Foshan Branch of Tianyan (Tianjin) High-tech Co., Ltd, Foshan, 528000, Guangdong, PR China
| | - Xianxin Li
- Foshan Branch of Tianyan (Tianjin) High-tech Co., Ltd, Foshan, 528000, Guangdong, PR China
| | - Xinqian Zheng
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological slaEngineering, South China University of Technology, Guangzhou, 510006, Guangdong, PR China
| | - Shoucong Huang
- Foshan Haitian (Gaoming) Flavouring Food Co., Ltd, Foshan, 52a8000, Guangdong, PR China
| | - Zhiqiu Yin
- Department of Clinical Laboratory, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510700, Guangdong, PR China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological slaEngineering, South China University of Technology, Guangzhou, 510006, Guangdong, PR China
| | - Li Pan
- School of Biology and Biological Engineering, Guangzhou Higher Education Mega Centre, South China University of Technology, Guangzhou, 510006, Guangdong, PR China
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Brepoels P, De Wit G, Lories B, Belpaire TER, Steenackers HP. Selective pressures for public antibiotic resistance. Crit Rev Microbiol 2024:1-10. [PMID: 39158370 DOI: 10.1080/1040841x.2024.2367666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 05/25/2024] [Indexed: 08/20/2024]
Abstract
The rapid increase of antibiotic-resistant pathogens is severely limiting our current treatment possibilities. An important subset of the resistance mechanisms conferring antibiotic resistance have public effects, allowing otherwise susceptible bacteria to also survive antibiotic treatment. As susceptible bacteria can survive treatment without bearing the metabolic cost of producing the resistance mechanism, there is potential to increase their relative frequency in the population and, as such, select against resistant bacteria. Multiple studies showed that this altered selection for resistance is dependent on various environmental and treatment parameters. In this review, we provide a comprehensive overview of their most important findings and describe the main factors impacting the selection for resistance. In-depth understanding of the driving forces behind selection can aid in the design and implementation of alternative treatments which limit the risk of resistance development.
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Affiliation(s)
- Pauline Brepoels
- Centre for Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Gitta De Wit
- Centre for Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Bram Lories
- Centre for Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Tom E R Belpaire
- Centre for Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Division of Mechatronics, Biostatistics, and Sensors, KU Leuven, Leuven, Belgium
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Babajanyan SG, Garushyants SK, Wolf YI, Koonin EV. Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model. BMC Biol 2024; 22:148. [PMID: 38965531 PMCID: PMC11225191 DOI: 10.1186/s12915-024-01937-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/13/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Microbiomes are generally characterized by high diversity of coexisting microbial species and strains, and microbiome composition typically remains stable across a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. Therefore, the long-term persistence of microbiome diversity calls for an explanation. RESULTS To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis were obtained, namely, pure competition, host-parasite relationship, and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environment. CONCLUSIONS The results of this modeling study show that basic phenomena that are universal in microbial communities, namely, environmental variation and HGT, provide for stabilization and persistence of microbial diversity, and emergence of ecological complexity.
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Affiliation(s)
- Sanasar G Babajanyan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA.
| | - Sofya K Garushyants
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA.
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Ferrario E, Kallio JP, Emdadi M, Strømland Ø, Rack JGM, Ziegler M. Evolution of fungal tuberculosis necrotizing toxin (TNT) domain-containing enzymes reveals divergent adaptations to enhance NAD cleavage. Protein Sci 2024; 33:e5071. [PMID: 38895984 PMCID: PMC11187862 DOI: 10.1002/pro.5071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/05/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024]
Abstract
Tuberculosis necrotizing toxin (TNT) is a protein domain discovered on the outer membrane of Mycobacterium tuberculosis (Mtb), and the fungal pathogen Aspergillus fumigatus. TNT domains have pure NAD(P) hydrolytic activity, setting them apart from other NAD-cleaving domains such as ADP-ribosyl cyclase and Toll/interleukin-1 receptor homology (TIR) domains which form a wider set of products. Importantly, the Mtb TNT domain has been shown to be involved in immune evasion via depletion of the intracellular NAD pool of macrophages. Therefore, an intriguing hypothesis is that TNT domains act as "NAD killers" in host cells facilitating pathogenesis. Here, we explore the phylogenetic distribution of TNT domains and detect their presence solely in bacteria and fungi. Within fungi, we discerned six TNT clades. In addition, X-ray crystallography and AlphaFold2 modeling unveiled clade-specific strategies to promote homodimer stabilization of the fungal enzymes, namely, Ca2+ binding, disulfide bonds, or hydrogen bonds. We show that dimer stabilization is a requirement for NADase activity and that the group-specific strategies affect the active site conformation, thereby modulating enzyme activity. Together, these findings reveal the evolutionary lineage of fungal TNT enzymes, corroborating the hypothesis of them being pure extracellular NAD (eNAD) cleavers, with possible involvement in microbial warfare and host immune evasion.
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Affiliation(s)
| | | | - Mahdi Emdadi
- Department of BiomedicineUniversity of BergenBergenNorway
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Gong W, Guo L, Huang C, Xie B, Jiang M, Zhao Y, Zhang H, Wu Y, Liang H. A systematic review of antibiotics and antibiotic resistance genes (ARGs) in mariculture wastewater: Antibiotics removal by microalgal-bacterial symbiotic system (MBSS), ARGs characterization on the metagenomic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172601. [PMID: 38657817 DOI: 10.1016/j.scitotenv.2024.172601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/10/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024]
Abstract
Antibiotic residues in mariculture wastewater seriously affect the aquatic environment. Antibiotic Resistance Genes (ARGs) produced under antibiotic stress flow through the environment and eventually enter the human body, seriously affecting human health. Microalgal-bacterial symbiotic system (MBSS) can remove antibiotics from mariculture and reduce the flow of ARGs into the environment. This review encapsulates the present scenario of mariculture wastewater, the removal mechanism of MBSS for antibiotics, and the biomolecular information under metagenomic assay. When confronted with antibiotics, there was a notable augmentation in the extracellular polymeric substances (EPS) content within MBSS, along with a concurrent elevation in the proportion of protein (PN) constituents within the EPS, which limits the entry of antibiotics into the cellular interior. Quorum sensing stimulates the microorganisms to produce biological responses (DNA synthesis - for adhesion) through signaling. Oxidative stress promotes gene expression (coupling, conjugation) to enhance horizontal gene transfer (HGT) in MBSS. The microbial community under metagenomic detection is dominated by aerobic bacteria in the bacterial-microalgal system. Compared to aerobic bacteria, anaerobic bacteria had the significant advantage of decreasing the distribution of ARGs. Overall, MBSS exhibits remarkable efficacy in mitigating the challenges posed by antibiotics and resistant genes from mariculture wastewater.
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Affiliation(s)
- Weijia Gong
- School of Engineering, Northeast Agricultural University, 600 Changjiang Street, Xiangfang District, Harbin 150030, PR China; State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), Harbin Institute of Technology, 73 Huanghe Road, Nangang District, Harbin 150090, PR China.
| | - Lin Guo
- School of Engineering, Northeast Agricultural University, 600 Changjiang Street, Xiangfang District, Harbin 150030, PR China
| | - Chenxin Huang
- School of Engineering, Northeast Agricultural University, 600 Changjiang Street, Xiangfang District, Harbin 150030, PR China
| | - Binghan Xie
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, PR China.
| | - Mengmeng Jiang
- School of Engineering, Northeast Agricultural University, 600 Changjiang Street, Xiangfang District, Harbin 150030, PR China
| | - Yuzhou Zhao
- School of Engineering, Northeast Agricultural University, 600 Changjiang Street, Xiangfang District, Harbin 150030, PR China
| | - Haotian Zhang
- School of Engineering, Northeast Agricultural University, 600 Changjiang Street, Xiangfang District, Harbin 150030, PR China
| | - YuXuan Wu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, PR China
| | - Heng Liang
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), Harbin Institute of Technology, 73 Huanghe Road, Nangang District, Harbin 150090, PR China
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Rivera-Galindo MA, Aguirre-Garrido F, Garza-Ramos U, Villavicencio-Pulido JG, Fernández Perrino FJ, López-Pérez M. Relevance of the Adjuvant Effect between Cellular Homeostasis and Resistance to Antibiotics in Gram-Negative Bacteria with Pathogenic Capacity: A Study of Klebsiella pneumoniae. Antibiotics (Basel) 2024; 13:490. [PMID: 38927157 PMCID: PMC11200652 DOI: 10.3390/antibiotics13060490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Antibiotic resistance has become a global issue. The most significant risk is the acquisition of these mechanisms by pathogenic bacteria, which can have a severe clinical impact and pose a public health risk. This problem assumes that bacterial fitness is a constant phenomenon and should be approached from an evolutionary perspective to develop the most appropriate and effective strategies to contain the emergence of strains with pathogenic potential. Resistance mechanisms can be understood as adaptive processes to stressful conditions. This review examines the relevance of homeostatic regulatory mechanisms in antimicrobial resistance mechanisms. We focus on the interactions in the cellular physiology of pathogenic bacteria, particularly Gram-negative bacteria, and specifically Klebsiella pneumoniae. From a clinical research perspective, understanding these interactions is crucial for comprehensively understanding the phenomenon of resistance and developing more effective drugs and treatments to limit or attenuate bacterial sepsis, since the most conserved adjuvant phenomena in bacterial physiology has turned out to be more optimized and, therefore, more susceptible to alterations due to pharmacological action.
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Affiliation(s)
- Mildred Azucena Rivera-Galindo
- Doctorado en Ciencias Biológicas y de la Salud Universidad Autónoma Metropolitana, Ciudad de México, México Universidad Autónoma Metropolitana-Unidad Xochimilco Calz, del Hueso 1100, Coapa, Villa Quietud, Coyoacán CP 04960, Mexico;
| | - Félix Aguirre-Garrido
- Environmental Sciences Department, Division of Biological and Health Sciences, Autonomous Metropolitan University (Lerma Unit), Av. de las Garzas N◦ 10, Col. El Panteón, Lerma de Villada CP 52005, Mexico; (F.A.-G.); (J.G.V.-P.)
| | - Ulises Garza-Ramos
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca CP 62100, Mexico;
| | - José Geiser Villavicencio-Pulido
- Environmental Sciences Department, Division of Biological and Health Sciences, Autonomous Metropolitan University (Lerma Unit), Av. de las Garzas N◦ 10, Col. El Panteón, Lerma de Villada CP 52005, Mexico; (F.A.-G.); (J.G.V.-P.)
| | - Francisco José Fernández Perrino
- Department of Biotechnology, Division of Biological and Health Sciences, Universidad Autónoma Metropolitana-Unidad Iztapalapa, Av. San Rafael Atlixco 186, Leyes de Reforma, México City CP 09340, Mexico;
| | - Marcos López-Pérez
- Environmental Sciences Department, Division of Biological and Health Sciences, Autonomous Metropolitan University (Lerma Unit), Av. de las Garzas N◦ 10, Col. El Panteón, Lerma de Villada CP 52005, Mexico; (F.A.-G.); (J.G.V.-P.)
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Liu Q, Peng Y, Liao J, Liu X, Peng J, Wang JH, Shao Z. Broad-spectrum hydrocarbon-degrading microbes in the global ocean metagenomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171746. [PMID: 38521276 DOI: 10.1016/j.scitotenv.2024.171746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 03/25/2024]
Abstract
Understanding the diversity and functions of hydrocarbon-degrading microorganisms in marine environments is crucial for both advancing knowledge of biogeochemical processes and improving bioremediation methods. In this study, we leveraged nearly 20,000 metagenome-assembled genomes (MAGs), recovered from a wide array of marine samples across the global oceans, to map the diversity of aerobic hydrocarbon-degrading microorganisms. A broad bacterial diversity was uncovered, with a notable preference for degrading aliphatic hydrocarbons over aromatic ones, primarily within Proteobacteria and Actinobacteriota. Three types of broad-spectrum hydrocarbon-degrading bacteria were identified for their ability to degrade various hydrocarbons and possession of multiple copies of hydrocarbon biodegradation genes. These bacteria demonstrate extensive metabolic versatility, aiding their survival and adaptability in diverse environmental conditions. Evidence of gene duplication and horizontal gene transfer in these microbes suggested a potential enhancement in the diversity of hydrocarbon-degrading bacteria. Positive correlations were observed between the abundances of hydrocarbon-degrading genes and environmental parameters such as temperature (-5 to 35 °C) and salinity (20 to 42 PSU). Overall, our findings offer valuable insights into marine hydrocarbon-degrading microorganisms and suggest considerations for selecting microbial strains for oil pollution remediation.
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Affiliation(s)
- Qing Liu
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Yongyi Peng
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Jing Liao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xinyue Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Jiaxue Peng
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Jiang-Hai Wang
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China.
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519099, China.
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Ma T, Rothschild J, Halabeya F, Zilman A, Milstein JN. Mechanics limits ecological diversity and promotes heterogeneity in confined bacterial communities. Proc Natl Acad Sci U S A 2024; 121:e2322321121. [PMID: 38728226 PMCID: PMC11098131 DOI: 10.1073/pnas.2322321121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 04/06/2024] [Indexed: 05/12/2024] Open
Abstract
Multispecies bacterial populations often inhabit confined and densely packed environments where spatial competition determines the ecological diversity of the community. However, the role of mechanical interactions in shaping the ecology is still poorly understood. Here, we study a model system consisting of two populations of nonmotile Escherichia coli bacteria competing within open, monolayer microchannels. The competitive dynamics is observed to be biphasic: After seeding, either one strain rapidly fixates or both strains orient into spatially stratified, stable communities. We find that mechanical interactions with other cells and local spatial constraints influence the resulting community ecology in unexpected ways, severely limiting the overall diversity of the communities while simultaneously allowing for the establishment of stable, heterogeneous populations of bacteria displaying disparate growth rates. Surprisingly, the populations have a high probability of coexisting even when one strain has a significant growth advantage. A more coccus morphology is shown to provide a selective advantage, but agent-based simulations indicate this is due to hydrodynamic and adhesion effects within the microchannel and not from breaking of the nematic ordering. Our observations are qualitatively reproduced by a simple Pólya urn model, which suggests the generality of our findings for confined population dynamics and highlights the importance of early colonization conditions on the resulting diversity and ecology of bacterial communities. These results provide fundamental insights into the determinants of community diversity in dense confined ecosystems where spatial exclusion is central to competition as in organized biofilms or intestinal crypts.
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Affiliation(s)
- Tianyi Ma
- Department of Physics, University of Toronto, Toronto, ONM5S 3J1, Canada
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, ONL5L 1C6, Canada
| | - Jeremy Rothschild
- Department of Physics, University of Toronto, Toronto, ONM5S 3J1, Canada
| | - Faisal Halabeya
- Department of Physics, University of Toronto, Toronto, ONM5S 3J1, Canada
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, ONL5L 1C6, Canada
| | - Anton Zilman
- Department of Physics, University of Toronto, Toronto, ONM5S 3J1, Canada
| | - Joshua N. Milstein
- Department of Physics, University of Toronto, Toronto, ONM5S 3J1, Canada
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, ONL5L 1C6, Canada
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García-Bayona L, Said N, Coyne MJ, Flores K, Elmekki NM, Sheahan ML, Camacho AG, Hutt K, Yildiz FH, Kovács ÁT, Waldor MK, Comstock LE. A pervasive large conjugative plasmid mediates multispecies biofilm formation in the intestinal microbiota increasing resilience to perturbations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.590671. [PMID: 38746121 PMCID: PMC11092513 DOI: 10.1101/2024.04.29.590671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Although horizontal gene transfer is pervasive in the intestinal microbiota, we understand only superficially the roles of most exchanged genes and how the mobile repertoire affects community dynamics. Similarly, little is known about the mechanisms underlying the ability of a community to recover after a perturbation. Here, we identified and functionally characterized a large conjugative plasmid that is one of the most frequently transferred elements among Bacteroidales species and is ubiquitous in diverse human populations. This plasmid encodes both an extracellular polysaccharide and fimbriae, which promote the formation of multispecies biofilms in the mammalian gut. We use a hybridization-based approach to visualize biofilms in clarified whole colon tissue with unprecedented 3D spatial resolution. These biofilms increase bacterial survival to common stressors encountered in the gut, increasing strain resiliency, and providing a rationale for the plasmid's recent spread and high worldwide prevalence.
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10
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Gordils-Valentin L, Ouyang H, Qian L, Hong J, Zhu X. Conjugative type IV secretion systems enable bacterial antagonism that operates independently of plasmid transfer. Commun Biol 2024; 7:499. [PMID: 38664513 PMCID: PMC11045733 DOI: 10.1038/s42003-024-06192-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Bacterial cooperation and antagonism mediated by secretion systems are among the ways in which bacteria interact with one another. Here we report the discovery of an antagonistic property of a type IV secretion system (T4SS) sourced from a conjugative plasmid, RP4, using engineering approaches. We scrutinized the genetic determinants and suggested that this antagonistic activity is independent of molecular cargos, while we also elucidated the resistance genes. We further showed that a range of Gram-negative bacteria and a mixed bacterial population can be eliminated by this T4SS-dependent antagonism. Finally, we showed that such an antagonistic property is not limited to T4SS sourced from RP4, rather it can also be observed in a T4SS originated from another conjugative plasmid, namely R388. Our results are the first demonstration of conjugative T4SS-dependent antagonism between Gram-negative bacteria on the genetic level and provide the foundation for future mechanistic studies.
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Affiliation(s)
- Lois Gordils-Valentin
- Department of Chemical Engineering, Texas A&M University, College Station, 77843, TX, US
- Interdisciplinary Graduate Program in Genetics & Genomics, Texas A&M University, College Station, 77843, TX, US
| | - Huanrong Ouyang
- Department of Chemical Engineering, Texas A&M University, College Station, 77843, TX, US
| | - Liangyu Qian
- Department of Chemical Engineering, Texas A&M University, College Station, 77843, TX, US
| | - Joshua Hong
- Department of Biology, Texas A&M University, College Station, 77843, TX, US
| | - Xuejun Zhu
- Department of Chemical Engineering, Texas A&M University, College Station, 77843, TX, US.
- Interdisciplinary Graduate Program in Genetics & Genomics, Texas A&M University, College Station, 77843, TX, US.
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11
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Baglivo I, Malgieri G, Roop RM, Barton IS, Wang X, Russo V, Pirone L, Pedone EM, Pedone PV. MucR protein: Three decades of studies have led to the identification of a new H-NS-like protein. Mol Microbiol 2024. [PMID: 38619026 DOI: 10.1111/mmi.15261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/16/2024]
Abstract
MucR belongs to a large protein family whose members regulate the expression of virulence and symbiosis genes in α-proteobacteria species. This protein and its homologs were initially studied as classical transcriptional regulators mostly involved in repression of target genes by binding their promoters. Very recent studies have led to the classification of MucR as a new type of Histone-like Nucleoid Structuring (H-NS) protein. Thus this review is an effort to put together a complete and unifying story demonstrating how genetic and biochemical findings on MucR suggested that this protein is not a classical transcriptional regulator, but functions as a novel type of H-NS-like protein, which binds AT-rich regions of genomic DNA and regulates gene expression.
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Affiliation(s)
- Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Roy Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Ian S Barton
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | | | - Luciano Pirone
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | - Emilia M Pedone
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
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Vega-Heredia S, Giffard-Mena I, Reverter M. Bacterial and viral co-infections in aquaculture under climate warming: co-evolutionary implications, diagnosis, and treatment. DISEASES OF AQUATIC ORGANISMS 2024; 158:1-20. [PMID: 38602294 DOI: 10.3354/dao03778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Climate change and the associated environmental temperature fluctuations are contributing to increases in the frequency and severity of disease outbreaks in both wild and farmed aquatic species. This has a significant impact on biodiversity and also puts global food production systems, such as aquaculture, at risk. Most infections are the result of complex interactions between multiple pathogens, and understanding these interactions and their co-evolutionary mechanisms is crucial for developing effective diagnosis and control strategies. In this review, we discuss current knowledge on bacteria-bacteria, virus-virus, and bacterial and viral co-infections in aquaculture as well as their co-evolution in the context of global warming. We also propose a framework and different novel methods (e.g. advanced molecular tools such as digital PCR and next-generation sequencing) to (1) precisely identify overlooked co-infections, (2) gain an understanding of the co-infection dynamics and mechanisms by knowing species interactions, and (3) facilitate the development multi-pathogen preventive measures such as polyvalent vaccines. As aquaculture disease outbreaks are forecasted to increase both due to the intensification of practices to meet the protein demand of the increasing global population and as a result of global warming, understanding and treating co-infections in aquatic species has important implications for global food security and the economy.
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Affiliation(s)
- Sarahí Vega-Heredia
- Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Ensenada, México, Egresada del Programa de Ecología Molecular y Biotecnología, carretera transpeninsular Ensenada-Tijuana No. 3917, C.P. 22860, México
| | - Ivone Giffard-Mena
- Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Ensenada, México
| | - Miriam Reverter
- School of Biological and Marine Sciences, Plymouth University, Drake Circus, Devon PL4 8AA, UK
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13
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Yescas-Zazueta V, Rocha-Gracia RDC, González-Bonilla CR, Ayala-Zavala JF, Enciso-Martínez Y, Carreón-León EA, González Corona BA, Valencia D, Ballesteros-Monrreal MG, Barrios-Villa E. Resistance phenotype and virulence potential of Leclercia adecarboxylata strains isolated from different sources. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001457. [PMID: 38661713 PMCID: PMC11084626 DOI: 10.1099/mic.0.001457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
Introduction. Leclercia adecarboxylata is a member of Enterobacterales, often considered an opportunistic pathogen. Recent reports have highlighted L. adecarboxylata as an emerging pathogen harbouring virulence and resistance determinants.Gap statement. Little information exists on virulence and resistance determinants in L. adecarboxylata strains isolated from environmental, food, and clinical samples.Aim. To determine the presence of resistance and virulence determinants and plasmid features in L. adecarboxylata strains isolated from environmental, food, and clinical samples, as well as their phylogenetic relationship.Results. All strains tested showed resistance to β-lactams and quinolones but were sensitive to aminoglycosides and nitrofurans. However, even though fosfomycin resistance is considered a characteristic trait of L. adecarboxylata, the resistance phenotype was only observed in 50 % of the strains; bla TEM was the most prevalent BLEE gene (70 %), while the quinolone qnrB gene was observed in 60 % of the strains. Virulence genes were differentially observed in the strains, with adhesion-related genes being the most abundant, followed by toxin genes. Finally, all strains carried one to seven plasmid bands ranging from 7 to 125 kbps and harboured several plasmid addiction systems, such as ParDE, VagCD, and CcdAB in 80 % of the strains.Conclusions. L. adecarboxylata is an important emerging pathogen that may harbour resistance and virulence genes. Additionally, it has mobilizable genetic elements that may contribute to the dissemination of genetic determinants to other bacterial genera.
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Affiliation(s)
- Viviana Yescas-Zazueta
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, campus Caborca, Av. Universidad e Irigoyen S/N, 83621 H. Caborca, Sonora, Mexico
| | - Rosa del Carmen Rocha-Gracia
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, 72570 Puebla, Mexico
| | - Cesar R. González-Bonilla
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, 72570 Puebla, Mexico
| | - J. Fernando Ayala-Zavala
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A.C., 83304 Hermosillo, Mexico
| | - Yessica Enciso-Martínez
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, campus Caborca, Av. Universidad e Irigoyen S/N, 83621 H. Caborca, Sonora, Mexico
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A.C., 83304 Hermosillo, Mexico
| | - Eder A. Carreón-León
- Laboratorio de Análisis Clínicos de la Universidad Autónoma de Chihuahua, Av. Universidad S/N, Circuito Universitario Campus 1, 31310 Chihuahua, Mexico
| | - Brigitte A. González Corona
- Laboratorio de Análisis Clínicos de la Universidad Autónoma de Chihuahua, Av. Universidad S/N, Circuito Universitario Campus 1, 31310 Chihuahua, Mexico
| | - Dora Valencia
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, campus Caborca, Av. Universidad e Irigoyen S/N, 83621 H. Caborca, Sonora, Mexico
| | - Manuel G. Ballesteros-Monrreal
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, campus Caborca, Av. Universidad e Irigoyen S/N, 83621 H. Caborca, Sonora, Mexico
| | - Edwin Barrios-Villa
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, campus Caborca, Av. Universidad e Irigoyen S/N, 83621 H. Caborca, Sonora, Mexico
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, 72570 Puebla, Mexico
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Jeong Y, Ahmad S, Irudayaraj J. Dynamic Effect of β-Lactam Antibiotic Inactivation Due to the Inter- and Intraspecies Interaction of Drug-Resistant Microbes. ACS Biomater Sci Eng 2024; 10:1461-1472. [PMID: 38315631 PMCID: PMC10936524 DOI: 10.1021/acsbiomaterials.3c01678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/07/2024]
Abstract
The presence of β-lactamase positive microorganisms imparts a pharmacological effect on a variety of organisms that can impact drug efficacy by influencing the function or composition of bacteria. Although studies to assess dynamic intra- and interspecies communication with bacterial communities exist, the efficacy of drug treatment and quantitative assessment of multiorganism response is not well understood due to the lack of technological advances that can be used to study coculture interactions in a dynamic format. In this study, we investigate how β-lactamase positive microorganisms can neutralize the effect of β-lactam antibiotics in a dynamic format at the inter- and intraspecies level using microbial bead technology. Three interactive models for the biological compartmentalization of organisms were demonstrated to evaluate the effect of β-lactam antibiotics on coculture systems. Our model at the intraspecies level attempts to mimic the biofilm matrix more closely as a community-level feature of microorganisms, which acknowledges the impact of nondrug-resistant species in shaping the dynamic response. In particular, the results of intraspecies studies are highly supportive of the biofilm mode of bacterial growth, which can provide structural support and protect the bacteria from an assault on host or environmental factors. Our findings also indicate that β-lactamase positive bacteria can neutralize the cytotoxic effect of β-lactam antibiotics at the interspecies level when cocultured with cancer cells. Results were validated using β-lactamase positive bacteria isolated from environmental niches, which can trigger phenotypical alteration of β-lactams when cocultured with other organisms. Our compartmentalization strategy acts as an independent ecosystem and provides a new avenue for multiscale studies to assess intra- and interspecies interactions.
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Affiliation(s)
- Yoon Jeong
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
- Cancer
Center at Illinois, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, Illinois 61801, United States
| | - Saeed Ahmad
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, Illinois 61801, United States
| | - Joseph Irudayaraj
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
- Cancer
Center at Illinois, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, Illinois 61801, United States
- Carle
R. Woese Institute for Genomic Biology, Beckman Institute, Urbana, Illinois 61801, United States
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15
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Gómez-Baltazar A, Godínez-Oviedo A, Segura-García LE, Hernández-Pérez CF, Hernández-Iturriaga M, Cabrera-Díaz E. Genomic diversity of Salmonella enterica isolated from raw chicken at retail establishments in Mexico. Int J Food Microbiol 2024; 411:110526. [PMID: 38154253 DOI: 10.1016/j.ijfoodmicro.2023.110526] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/25/2023] [Accepted: 12/11/2023] [Indexed: 12/30/2023]
Abstract
The genomic diversity of circulating non-typhoidal Salmonella in raw chicken was investigated in three states of central Mexico. A total of 192 S. enterica strains from chicken meat samples collected at supermarkets, fresh markets, and butcher shops were analyzed by whole-genome sequencing. The serovar distribution, occurrence of genes encoding for antimicrobial resistance, metal resistance, biocide resistance, plasmids and virulence factors, and clonal relatedness based on single nucleotide polymorphism (SNP) analysis were investigated. Serovars Infantis, Schwarzengrund and Enteritidis predominated among twenty identified. The distribution of serovars and proportion of AMR genes was different according to the state, year, season, and retail establishment (p < 0.001). Genes encoding metals resistance were identified in all the strains. A total of 145 virulence genes were identified and strains were classified into 32 virulotypes; serovars Infantis, Typhimurium, and Enteritidis showed the highest number of virulence genes. The strains matched 34 SNP clusters in the NCBI Pathogen Detection server and 59 %, which corresponded to Infantis, Schwarzengrund, Saintpaul, and Enteritidis, were associated with five major clusters and matched with chicken, environmental and clinical isolates from at least three countries. These results provide useful information to understand the epidemiology of Salmonella, conduct microbial risk assessment, and design risk-based control measures.
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Affiliation(s)
- Adrián Gómez-Baltazar
- Departamento de Investigación y Posgrado de Alimentos, Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas s/n, Colonia Las Campanas, Querétaro 76010, Qro., Mexico
| | - Angélica Godínez-Oviedo
- Departamento de Investigación y Posgrado de Alimentos, Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas s/n, Colonia Las Campanas, Querétaro 76010, Qro., Mexico
| | - Luis Eduardo Segura-García
- Departamento de Salud Pública, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ramón Padilla Sánchez 2100, Zapopan 45200, Jalisco, Mexico
| | - Cindy Fabiola Hernández-Pérez
- Centro Nacional de Referencia en Inocuidad y Bioseguridad Agroalimentaria del SENASICA, Carretera México Pachuca Km 35.5, Tecámac. CP. 55740, Estado de México, Mexico
| | - Montserrat Hernández-Iturriaga
- Departamento de Investigación y Posgrado de Alimentos, Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas s/n, Colonia Las Campanas, Querétaro 76010, Qro., Mexico.
| | - Elisa Cabrera-Díaz
- Departamento de Salud Pública, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ramón Padilla Sánchez 2100, Zapopan 45200, Jalisco, Mexico.
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16
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Chen Y, Yan Z, Zhou Y, Zhang Y, Jiang R, Wang M, Yuan S, Lu G. Dynamic evolution of antibiotic resistance genes in plastisphere in the vertical profile of urban rivers. WATER RESEARCH 2024; 249:120946. [PMID: 38043355 DOI: 10.1016/j.watres.2023.120946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/05/2023]
Abstract
Microplastics (MPs) can vertically transport in the aquatic environment due to their aging and biofouling, forming distinct plastisphere in different water layers. However, even though MPs have been regarded as hotspots for antibiotic resistance genes (ARGs), little is known about the propagation and transfer of ARGs in plastisphere in waters, especially in the vertical profile. Therefore, this study investigated the dynamic responses and evolution of ARGs in different plastisphere distributed vertically in an urbanized river. The biofilm biomass in the polylactic acid (PLA) plastisphere was relatively higher than that in the polyethylene terephthalate (PET), showing depth-decay variations. The ARGs abundance in plastisphere were much higher than that in the surrounding waters, especially for the PLA. In the vertical profiles, the ARGs abundance in the PET plastisphere increased with water depths, while the highest abundance of ARGs in the PLA mostly appeared at intermediate waters. In the temporal dynamic, the ARGs abundance in plastisphere increased and then decreased, which may be dominated by the MP types at the initial periods. After long-term exposure, the influences of water depths seemed to be strengthened, especially in the PET plastisphere. Compared with surface waters, the microbiota attached in plastisphere in deep waters showed high species richness, strong diversity, and complex interactions, which was basically consistent with the changes of nutrient contents in different water layers. These vertical variations in microbiota and nutrients (e.g., nitrogen) may be responsible for the propagation of ARGs in plastisphere in deep waters. The host bacteria for ARGs in plastisphere was also developed as water depth increased, leading to an enrichment of ARGs in deep waters. In addition, the abundance of ARGs in plastisphere in bottom waters was positively correlated with the mobile genetic elements (MGEs) of intI1 and tnpA05, indicative of a frequent horizontal gene transfer of ARGs. Overall, water depth played a critical role in the propagation of ARGs in plastisphere, which should not be ignored in a long time series. This study provides new insights into the dynamic evolution of ARGs propagation in plastisphere under increasing global MPs pollution, especially in the vertical profile.
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Affiliation(s)
- Yufang Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Zhenhua Yan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China.
| | - Yixin Zhou
- College of Environment, Hohai University, Nanjing 210098, China
| | - Yan Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Runren Jiang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Min Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Saiyu Yuan
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China
| | - Guanghua Lu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
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17
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Babajanyan SG, Garushyants SK, Wolf YI, Koonin EV. Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576128. [PMID: 38313259 PMCID: PMC10836074 DOI: 10.1101/2024.01.17.576128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Microbiomes are generally characterized by high diversity of coexisting microbial species and strains that remains stable within a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis obtained, namely, pure competition, host-parasite relationship and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environments. These findings show that basic phenomena that are universal in microbial communities, environmental variation and HGT, provide for stabilization of microbial diversity and ecological complexity.
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Affiliation(s)
- Sanasar G. Babajanyan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Sofya K. Garushyants
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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18
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Dobrange E, Porras-Domínguez JR, Van den Ende W. The Complex GH32 Enzyme Orchestra from Priestia megaterium Holds the Key to Better Discriminate Sucrose-6-phosphate Hydrolases from Other β-Fructofuranosidases in Bacteria. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:1302-1320. [PMID: 38175162 DOI: 10.1021/acs.jafc.3c06874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Inulin is widely used as a prebiotic and emerging as a priming compound to counteract plant diseases. We isolated inulin-degrading strains from the lettuce phyllosphere, identified as Bacillus subtilis and Priestia megaterium, species hosting well-known biocontrol organisms. To better understand their varying inulin degradation strategies, three intracellular β-fructofuranosidases from P. megaterium NBRC15308 were characterized after expression in Escherichia coli: a predicted sucrose-6-phosphate (Suc6P) hydrolase (SacAP1, supported by molecular docking), an exofructanase (SacAP2), and an invertase (SacAP3). Based on protein multiple sequence and structure alignments of bacterial glycoside hydrolase family 32 enzymes, we identified conserved residues predicted to be involved in binding phosphorylated (Suc6P hydrolases) or nonphosphorylated substrates (invertases and fructanases). Suc6P hydrolases feature positively charged residues near the structural catalytic pocket (histidine, arginine, or lysine), whereas other β-fructofuranosidases contain tryptophans. This correlates with our phylogenetic tree, grouping all predicted Suc6P hydrolases in a clan associated with genomic regions coding for transporters involved in substrate phosphorylation. These results will help to discriminate between Suc6P hydrolases and other β-fructofuranosidases in future studies and to better understand the interaction of B. subtilis and P. megaterium endophytes with sucrose and/or fructans, sugars naturally present in plants or exogenously applied in the context of defense priming.
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Affiliation(s)
- Erin Dobrange
- Laboratory of Molecular Plant Biology, KU Leuven, Kasteelpark Arenberg 31, Leuven 3001, Belgium
| | | | - Wim Van den Ende
- Laboratory of Molecular Plant Biology, KU Leuven, Kasteelpark Arenberg 31, Leuven 3001, Belgium
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Wang S, Mu L, Yu C, He Y, Hu X, Jiao Y, Xu Z, You S, Liu SL, Bao H. Microbial collaborations and conflicts: unraveling interactions in the gut ecosystem. Gut Microbes 2024; 16:2296603. [PMID: 38149632 PMCID: PMC10761165 DOI: 10.1080/19490976.2023.2296603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/14/2023] [Indexed: 12/28/2023] Open
Abstract
The human gut microbiota constitutes a vast and complex community of microorganisms. The myriad of microorganisms present in the intestinal tract exhibits highly intricate interactions, which play a crucial role in maintaining the stability and balance of the gut microbial ecosystem. These interactions, in turn, influence the overall health of the host. The mammalian gut microbes have evolved a wide range of mechanisms to suppress or even eliminate their competitors for nutrients and space. Simultaneously, extensive cooperative interactions exist among different microbes to optimize resource utilization and enhance their own fitness. This review will focus on the competitive mechanisms among members of the gut microorganisms and discuss key modes of actions, including bacterial secretion systems, bacteriocins, membrane vesicles (MVs) etc. Additionally, we will summarize the current knowledge of the often-overlooked positive interactions within the gut microbiota, and showcase representative machineries. This information will serve as a reference for better understanding the complex interactions occurring within the mammalian gut environment. Understanding the interaction dynamics of competition and cooperation within the gut microbiota is crucial to unraveling the ecology of the mammalian gut microbial communities. Targeted interventions aimed at modulating these interactions may offer potential therapeutic strategies for disease conditions.
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Affiliation(s)
- Shuang Wang
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
| | - Lingyi Mu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Chong Yu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yuting He
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Xinliang Hu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yanlei Jiao
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Ziqiong Xu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Shaohui You
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Hongxia Bao
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
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20
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Suyama R, Cetraro N, Yew JY, Kai T. Microbes control Drosophila germline stem cell increase and egg maturation through hormonal pathways. Commun Biol 2023; 6:1287. [PMID: 38123715 PMCID: PMC10733356 DOI: 10.1038/s42003-023-05660-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
Reproduction is highly dependent on environmental and physiological factors including nutrition, mating stimuli and microbes. Among these factors, microbes facilitate vital functions for host animals such as nutritional intake, metabolic regulation, and enhancing fertility under poor nutrition conditions. However, detailed molecular mechanisms by which microbes control germline maturation, leading to reproduction, remain largely unknown. In this study, we show that environmental microbes exert a beneficial effect on Drosophila oogenesis by promoting germline stem cell (GSC) proliferation and subsequent egg maturation via acceleration of ovarian cell division and suppression of apoptosis. Moreover, insulin-related signaling is not required; rather, the ecdysone pathway is necessary for microbe-induced increase of GSCs and promotion of egg maturation, while juvenile hormone contributes only to increasing GSC numbers, suggesting that hormonal pathways are activated at different stages of oogenesis. Our findings reveal that environmental microbes can enhance host reproductivity by modulating host hormone release and promoting oogenesis.
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Affiliation(s)
- Ritsuko Suyama
- Laboratory of Germline Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka Suita, Osaka, 565-0871, Japan.
| | - Nicolas Cetraro
- Pacific Biosciences Research Center, University of Hawai'i at Manoa, 1993 East-West Road, Honolulu, HI, 96822, USA
| | - Joanne Y Yew
- Pacific Biosciences Research Center, University of Hawai'i at Manoa, 1993 East-West Road, Honolulu, HI, 96822, USA.
| | - Toshie Kai
- Laboratory of Germline Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka Suita, Osaka, 565-0871, Japan.
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21
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Ru J, Xue J, Sun J, Cova L, Deng L. Unveiling the hidden role of aquatic viruses in hydrocarbon pollution bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132299. [PMID: 37597386 DOI: 10.1016/j.jhazmat.2023.132299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/28/2023] [Accepted: 08/12/2023] [Indexed: 08/21/2023]
Abstract
Hydrocarbon pollution poses substantial environmental risks to water and soil. Bioremediation, which utilizes microorganisms to manage pollutants, offers a cost-effective solution. However, the role of viruses, particularly bacteriophages (phages), in bioremediation remains unexplored. This study examines the diversity and activity of hydrocarbon-degradation genes encoded by environmental viruses, focusing on phages, within public databases. We identified 57 high-quality phage-encoded auxiliary metabolic genes (AMGs) related to hydrocarbon degradation, which we refer to as virus-encoded hydrocarbon degradation genes (vHYDEGs). These genes are encoded by taxonomically diverse aquatic phages and highlight the under-characterized global virosphere. Six protein families involved in the initial alkane hydroxylation steps were identified. Phylogenetic analyses revealed the diverse evolutionary trajectories of vHYDEGs across habitats, revealing previously unknown biodegraders linked evolutionarily with vHYDEGs. Our findings suggest phage AMGs may contribute to alkane and aromatic hydrocarbon degradation, participating in the initial, rate-limiting hydroxylation steps, thereby aiding hydrocarbon pollution bioremediation and promoting their propagation. To support future research, we developed vHyDeg, a database containing identified vHYDEGs with comprehensive annotations, facilitating the screening of hydrocarbon degradation AMGs and encouraging their bioremediation applications.
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Affiliation(s)
- Jinlong Ru
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg 85764, Germany; Chair of Prevention for Microbial Infectious Disease, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Jinling Xue
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg 85764, Germany; Chair of Prevention for Microbial Infectious Disease, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Jianfeng Sun
- Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Linda Cova
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg 85764, Germany
| | - Li Deng
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg 85764, Germany; Chair of Prevention for Microbial Infectious Disease, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Freising 85354, Germany.
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22
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Lee IPA, Eldakar OT, Gogarten JP, Andam CP. Recombination as an enforcement mechanism of prosocial behavior in cooperating bacteria. iScience 2023; 26:107344. [PMID: 37554437 PMCID: PMC10405257 DOI: 10.1016/j.isci.2023.107344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/11/2023] [Accepted: 07/06/2023] [Indexed: 08/10/2023] Open
Abstract
Prosocial behavior is ubiquitous in nature despite the relative fitness costs carried by cooperative individuals. However, the stability of cooperation in populations is fragile and often maintained through enforcement. We propose that homologous recombination provides such a mechanism in bacteria. Using an agent-based model of recombination in bacteria playing a public goods game, we demonstrate how changes in recombination rates affect the proportion of cooperating cells. In our model, recombination converts cells to a different strategy, either freeloading (cheaters) or cooperation, based on the strategies of neighboring cells and recombination rate. Increasing the recombination rate expands the parameter space in which cooperators outcompete freeloaders. However, increasing the recombination rate alone is neither sufficient nor necessary. Intermediate benefits of cooperation, lower population viscosity, and greater population size can promote the evolution of cooperation from within populations of cheaters. Our findings demonstrate how recombination influences the persistence of cooperative behavior in bacteria.
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Affiliation(s)
- Isaiah Paolo A. Lee
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
- National Institute of Molecular Biology and Biotechnology, University of the Philippines–Diliman, Quezon City 1101, Philippines
| | - Omar Tonsi Eldakar
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
| | - J. Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
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23
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Yuxiang W, Peretolchina TE, Romanova EV, Sherbakov DY. Comparison of the evolutionary patterns of DNA repeats in ancient and young invertebrate species flocks of Lake Baikal. Vavilovskii Zhurnal Genet Selektsii 2023; 27:349-356. [PMID: 37465187 PMCID: PMC10350863 DOI: 10.18699/vjgb-23-42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 07/20/2023] Open
Abstract
DNA repeat composition of low coverage (0.1-0.5) genomic libraries of four amphipods species endemic to Lake Baikal (East Siberia) and four endemic gastropod species of the fam. Baicaliidae have been compared to each other. In order to do so, a neighbor joining tree was inferred for each quartet of species (amphipods and mollusks) based on the ratio of repeat classes shared in each pair of species. The topology of this tree was compared to the phylogenies inferred for the same species from the concatenated protein-coding mitochondrial nucleotide sequences. In all species analyzed, the fraction of DNA repeats involved circa half of the genome. In relatively more ancient amphipods (most recent common ancestor, MRCA, existed approximately sixty millions years ago), the most abundant were species-specific repeats, while in much younger Baicaliidae (MRCA equal to ca. three millions years) most of the DNA repeats were shared among all four species. If the presence/absence of a repeat is regarded as a separate independent trait, and the ratio of shared to total numbers of repeats in a species pair is used as the measure of distance, the topology of the NJ tree is the same as the quartet phylogeny inferred for the mitogenomes protein coding nucleotide sequences. Meanwhile, in each group of species, a substantial number of repeats were detected pointing to the possibility of non-neutral evolution or a horizontal transfer between species occupying the same biotope. These repeats were shared by non-sister groups while being absent in the sister genomes. On the other hand, in such cases some traits of ecological significance were also shared.
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Affiliation(s)
- Wang Yuxiang
- Limnological institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - T E Peretolchina
- Limnological institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - E V Romanova
- Limnological institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - D Y Sherbakov
- Limnological institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia Novosibirsk State University, Novosibirsk, RussiaIrkutsk State University, Irkutsk, Russia
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24
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Makhalanyane TP, Bezuidt OKI, Pierneef RE, Mizrachi E, Zeze A, Fossou RK, Kouadjo CG, Duodu S, Chikere CB, Babalola OO, Klein A, Keyster M, du Plessis M, Yorou NS, Hijri M, Rossouw T, Kamutando CN, Venter S, Moleleki LN, Murrell C. African microbiomes matter. Nat Rev Microbiol 2023:10.1038/s41579-023-00925-y. [PMID: 37328673 DOI: 10.1038/s41579-023-00925-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Affiliation(s)
- Thulani P Makhalanyane
- DSI/NRF SARChI in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| | - Oliver K I Bezuidt
- DSI/NRF SARChI in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Rian E Pierneef
- DSI/NRF SARChI in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Adolphe Zeze
- Laboratoire de Biotechnologies Végétale et Microbienne/UMRI Sciences Agronomiques et Génie Rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Romain K Fossou
- Laboratoire de Biotechnologies Végétale et Microbienne/UMRI Sciences Agronomiques et Génie Rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Claude Ghislaine Kouadjo
- Laboratoire Central de Biotechnologies, Centre National de la Recherche Agronomique, Abidjan, Côte d'Ivoire
| | - Samuel Duodu
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Chioma B Chikere
- Department of Microbiology, University of Port Harcourt, Port Harcourt, Nigeria
| | - Olubukola O Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Science, North-West University, Mmabatho, South Africa
| | - Ashwil Klein
- Plant Omics Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Marshall Keyster
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Mornè du Plessis
- Genetics Department, University of the Free State, Bloemfontein, South Africa
| | - Nourou S Yorou
- Research Unit Tropical Mycology and Plant-Soil Fungi Interactions, Faculty of Agronomy, University of Parakou, Parakou, Benin
| | - Mohamed Hijri
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Theresa Rossouw
- Department of Immunology, University of Pretoria School of Medicine, Pretoria, South Africa
| | - Casper N Kamutando
- Department of Plant Production Sciences and Technologies, University of Zimbabwe, Harare, Zimbabwe
| | - Stephanus Venter
- Forestry and Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Lucy N Moleleki
- Forestry and Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, UK
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25
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Wang Q, Wei S, Silva AF, Madsen JS. Cooperative antibiotic resistance facilitates horizontal gene transfer. THE ISME JOURNAL 2023; 17:846-854. [PMID: 36949153 PMCID: PMC10203111 DOI: 10.1038/s41396-023-01393-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/24/2023]
Abstract
The rise of β-lactam resistance among pathogenic bacteria, due to the horizontal transfer of plasmid-encoded β-lactamases, is a current global health crisis. Importantly, β-lactam hydrolyzation by β-lactamases, not only protects the producing cells but also sensitive neighboring cells cooperatively. Yet, how such cooperative traits affect plasmid transmission and maintenance is currently poorly understood. Here we experimentally show that KPC-2 β-lactamase expression and extracellular activity were higher when encoded on plasmids compared with the chromosome, resulting in the elevated rescue of sensitive non-producers. This facilitated efficient plasmid transfer to the rescued non-producers and expanded the potential plasmid recipient pool and the probability of plasmid transfer to new genotypes. Social conversion of non-producers by conjugation was efficient yet not absolute. Non-cooperative plasmids, not encoding KPC-2, were moderately more competitive than cooperative plasmids when β-lactam antibiotics were absent. However, in the presence of a β-lactam antibiotic, strains with non-cooperative plasmids were efficiently outcompeted. Moreover, plasmid-free non-producers were more competitive than non-producers imposed with the metabolic burden of a plasmid. Our results suggest that cooperative antibiotic resistance especially promotes the fitness of replicons that transfer horizontally such as conjugative plasmids.
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Affiliation(s)
- Qinqin Wang
- Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Shaodong Wei
- National Food Institute, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Ana Filipa Silva
- Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
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26
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Scott TW, West SA, Dewar AE, Wild G. Is cooperation favored by horizontal gene transfer? Evol Lett 2023; 7:113-120. [PMID: 37251586 PMCID: PMC10210433 DOI: 10.1093/evlett/qrad003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/18/2023] [Accepted: 01/31/2023] [Indexed: 05/31/2023] Open
Abstract
It has been hypothesized that horizontal gene transfer on plasmids can facilitate the evolution of cooperation, by allowing genes to jump between bacteria, and hence increase genetic relatedness at the cooperative loci. However, we show theoretically that horizontal gene transfer only appreciably increases relatedness when plasmids are rare, where there are many plasmid-free cells available to infect (many opportunities for horizontal gene transfer). In contrast, when plasmids are common, there are few opportunities for horizontal gene transfer, meaning relatedness is not appreciably increased, and so cooperation is not favored. Plasmids, therefore, evolve to be rare and cooperative, or common and noncooperative, meaning plasmid frequency and cooperativeness are never simultaneously high. The overall level of plasmid-mediated cooperation, given by the product of plasmid frequency and cooperativeness, is therefore consistently negligible or low.
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Affiliation(s)
- Thomas W Scott
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Stuart A West
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Anna E Dewar
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Geoff Wild
- Department of Mathematics, University of Western Ontario, London, Ontario, Canada
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27
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Msaddak A, Mars M, Quiñones MA, Lucas MM, Pueyo JJ. Lupin, a Unique Legume That Is Nodulated by Multiple Microsymbionts: The Role of Horizontal Gene Transfer. Int J Mol Sci 2023; 24:ijms24076496. [PMID: 37047476 PMCID: PMC10094711 DOI: 10.3390/ijms24076496] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Lupin is a high-protein legume crop that grows in a wide range of edaphoclimatic conditions where other crops are not viable. Its unique seed nutrient profile can promote health benefits, and it has been proposed as a phytoremediation plant. Most rhizobia nodulating Lupinus species belong to the genus Bradyrhizobium, comprising strains that are phylogenetically related to B. cytisi, B. hipponenese, B. rifense, B. iriomotense/B. stylosanthis, B. diazoefficiens, B. japonicum, B. canariense/B. lupini, and B. retamae/B. valentinum. Lupins are also nodulated by fast-growing bacteria within the genera Microvirga, Ochrobactrum, Devosia, Phyllobacterium, Agrobacterium, Rhizobium, and Neorhizobium. Phylogenetic analyses of the nod and nif genes, involved in microbial colonization and symbiotic nitrogen fixation, respectively, suggest that fast-growing lupin-nodulating bacteria have acquired their symbiotic genes from rhizobial genera other than Bradyrhizobium. Horizontal transfer represents a key mechanism allowing lupin to form symbioses with bacteria that were previously considered as non-symbiotic or unable to nodulate lupin, which might favor lupin’s adaptation to specific habitats. The characterization of yet-unstudied Lupinus species, including microsymbiont whole genome analyses, will most likely expand and modify the current lupin microsymbiont taxonomy, and provide additional knowledge that might help to further increase lupin’s adaptability to marginal soils and climates.
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Affiliation(s)
- Abdelhakim Msaddak
- Department of Soil. Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources, BVBAA, Faculty of Sciences, University of Gabès, Erriadh, Zrig, Gabès 6072, Tunisia
| | - Mohamed Mars
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources, BVBAA, Faculty of Sciences, University of Gabès, Erriadh, Zrig, Gabès 6072, Tunisia
| | - Miguel A. Quiñones
- Department of Soil. Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain
| | - M. Mercedes Lucas
- Department of Soil. Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain
| | - José J. Pueyo
- Department of Soil. Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain
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28
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Shao M, Liu L, Liu B, Zheng H, Meng W, Liu Y, Zhang X, Ma X, Sun C, Luo X, Li F, Xing B. Hormetic Effect of Pyroligneous Acids on Conjugative Transfer of Plasmid-mediated Multi-antibiotic Resistance Genes within Bacterial Genus. ACS ENVIRONMENTAL AU 2023; 3:105-120. [PMID: 37102089 PMCID: PMC10125354 DOI: 10.1021/acsenvironau.2c00056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 04/28/2023]
Abstract
Spread of antibiotic resistance genes (ARGs) by conjugation poses great challenges to public health. Application of pyroligneous acids (PA) as soil amendments has been evidenced as a practical strategy to remediate pollution of ARGs in soils. However, little is known about PA effects on horizontal gene transfer (HGT) of ARGs by conjugation. This study investigated the effects of a woody waste-derived PA prepared at 450°C and its three distillation components (F1, F2, and F3) at different temperatures (98, 130, and 220°C) on conjugative transfer of plasmid RP4 within Escherichia coli. PA at relatively high amount (40-100 μL) in a 30-mL mating system inhibited conjugation by 74-85%, following an order of PA > F3 ≈ F2 ≈ F1, proving the hypothesis that PA amendments may mitigate soil ARG pollution by inhibiting HGT. The bacteriostasis caused by antibacterial components of PA, including acids, phenols, and alcohols, as well as its acidity (pH 2.81) contributed to the inhibited conjugation. However, a relatively low amount (10-20 μL) of PA in the same mating system enhanced ARG transfer by 26-47%, following an order of PA > F3 ≈ F2 > F1. The opposite effect at low amount is mainly attributed to the increased intracellular reactive oxygen species production, enhanced cell membrane permeability, increased extracellular polymeric substance contents, and reduced cell surface charge. Our findings highlight the hormesis (low-amount promotion and high-amount inhibition) of PA amendments on ARG conjugation and provide evidence for selecting an appropriate amount of PA amendment to control the dissemination of soil ARGs. Moreover, the promoted conjugation also triggers questions regarding the potential risks of soil amendments (e.g., PA) in the spread of ARGs via HGT.
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Affiliation(s)
- Mengying Shao
- Institute
of Coastal Environmental Pollution Control, Ministry of Education
Key Laboratory of Marine Environment and Ecology, College of Environmental
Science and Engineering, Frontiers Science Center for Deep Ocean Multispheres
and Earth System, Ocean University of China, Qingdao 266100, China
- Marine
Ecology and Environmental Science Laboratory, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Liuqingqing Liu
- Institute
of Coastal Environmental Pollution Control, Ministry of Education
Key Laboratory of Marine Environment and Ecology, College of Environmental
Science and Engineering, Frontiers Science Center for Deep Ocean Multispheres
and Earth System, Ocean University of China, Qingdao 266100, China
- Marine
Ecology and Environmental Science Laboratory, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Bingjie Liu
- Institute
of Coastal Environmental Pollution Control, Ministry of Education
Key Laboratory of Marine Environment and Ecology, College of Environmental
Science and Engineering, Frontiers Science Center for Deep Ocean Multispheres
and Earth System, Ocean University of China, Qingdao 266100, China
- Ministry
of Ecology and Environment, South China
Institute of Environmental Sciences, Guangzhou 510535, China
| | - Hao Zheng
- Institute
of Coastal Environmental Pollution Control, Ministry of Education
Key Laboratory of Marine Environment and Ecology, College of Environmental
Science and Engineering, Frontiers Science Center for Deep Ocean Multispheres
and Earth System, Ocean University of China, Qingdao 266100, China
- Marine
Ecology and Environmental Science Laboratory, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Sanya
Oceanographic Institution, Ocean University
of China, Sanya 572000, China
| | - Wei Meng
- Institute
of Coastal Environmental Pollution Control, Ministry of Education
Key Laboratory of Marine Environment and Ecology, College of Environmental
Science and Engineering, Frontiers Science Center for Deep Ocean Multispheres
and Earth System, Ocean University of China, Qingdao 266100, China
| | - Yifan Liu
- Institute
of Coastal Environmental Pollution Control, Ministry of Education
Key Laboratory of Marine Environment and Ecology, College of Environmental
Science and Engineering, Frontiers Science Center for Deep Ocean Multispheres
and Earth System, Ocean University of China, Qingdao 266100, China
| | - Xiao Zhang
- Institute
of Coastal Environmental Pollution Control, Ministry of Education
Key Laboratory of Marine Environment and Ecology, College of Environmental
Science and Engineering, Frontiers Science Center for Deep Ocean Multispheres
and Earth System, Ocean University of China, Qingdao 266100, China
| | - Xiaohan Ma
- Institute
of Coastal Environmental Pollution Control, Ministry of Education
Key Laboratory of Marine Environment and Ecology, College of Environmental
Science and Engineering, Frontiers Science Center for Deep Ocean Multispheres
and Earth System, Ocean University of China, Qingdao 266100, China
- Marine
Ecology and Environmental Science Laboratory, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Cuizhu Sun
- Institute
of Coastal Environmental Pollution Control, Ministry of Education
Key Laboratory of Marine Environment and Ecology, College of Environmental
Science and Engineering, Frontiers Science Center for Deep Ocean Multispheres
and Earth System, Ocean University of China, Qingdao 266100, China
- Marine
Ecology and Environmental Science Laboratory, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Xianxiang Luo
- Institute
of Coastal Environmental Pollution Control, Ministry of Education
Key Laboratory of Marine Environment and Ecology, College of Environmental
Science and Engineering, Frontiers Science Center for Deep Ocean Multispheres
and Earth System, Ocean University of China, Qingdao 266100, China
- Marine
Ecology and Environmental Science Laboratory, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Sanya
Oceanographic Institution, Ocean University
of China, Sanya 572000, China
| | - Fengmin Li
- Institute
of Coastal Environmental Pollution Control, Ministry of Education
Key Laboratory of Marine Environment and Ecology, College of Environmental
Science and Engineering, Frontiers Science Center for Deep Ocean Multispheres
and Earth System, Ocean University of China, Qingdao 266100, China
- Marine
Ecology and Environmental Science Laboratory, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Sanya
Oceanographic Institution, Ocean University
of China, Sanya 572000, China
| | - Baoshan Xing
- Stockbridge
School of Agriculture, University of Massachusetts, Amherst, Massachusetts 01003, United States
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29
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Weltzer ML, Wall D. Social Diversification Driven by Mobile Genetic Elements. Genes (Basel) 2023; 14:648. [PMID: 36980919 PMCID: PMC10047993 DOI: 10.3390/genes14030648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/17/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Social diversification in microbes is an evolutionary process where lineages bifurcate into distinct populations that cooperate with themselves but not with other groups. In bacteria, this is frequently driven by horizontal transfer of mobile genetic elements (MGEs). Here, the resulting acquisition of new genes changes the recipient's social traits and consequently how they interact with kin. These changes include discriminating behaviors mediated by newly acquired effectors. Since the producing cell is protected by cognate immunity factors, these selfish elements benefit from selective discrimination against recent ancestors, thus facilitating their proliferation and benefiting the host. Whether social diversification benefits the population at large is less obvious. The widespread use of next-generation sequencing has recently provided new insights into population dynamics in natural habitats and the roles MGEs play. MGEs belong to accessory genomes, which often constitute the majority of the pangenome of a taxon, and contain most of the kin-discriminating loci that fuel rapid social diversification. We further discuss mechanisms of diversification and its consequences to populations and conclude with a case study involving myxobacteria.
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Affiliation(s)
- Michael L Weltzer
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Daniel Wall
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
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30
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Beltran LC, Cvirkaite-Krupovic V, Miller J, Wang F, Kreutzberger MAB, Patkowski JB, Costa TRD, Schouten S, Levental I, Conticello VP, Egelman EH, Krupovic M. Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery. Nat Commun 2023; 14:666. [PMID: 36750723 PMCID: PMC9905601 DOI: 10.1038/s41467-023-36349-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/27/2023] [Indexed: 02/09/2023] Open
Abstract
Conjugation is a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens. It involves establishing a junction between a donor and a recipient cell via an extracellular appendage known as the mating pilus. In bacteria, the conjugation machinery is encoded by plasmids or transposons and typically mediates the transfer of cognate mobile genetic elements. Much less is known about conjugation in archaea. Here, we determine atomic structures by cryo-electron microscopy of three conjugative pili, two from hyperthermophilic archaea (Aeropyrum pernix and Pyrobaculum calidifontis) and one encoded by the Ti plasmid of the bacterium Agrobacterium tumefaciens, and show that the archaeal pili are homologous to bacterial mating pili. However, the archaeal conjugation machinery, known as Ced, has been 'domesticated', that is, the genes for the conjugation machinery are encoded on the chromosome rather than on mobile genetic elements, and mediates the transfer of cellular DNA.
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Affiliation(s)
- Leticia C Beltran
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22903, USA
| | | | - Jessalyn Miller
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22903, USA
- Department of Biochemistry and Molecular Genetics, University of Alabama Birmingham, Birmingham, AL, 35233, USA
| | - Mark A B Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22903, USA
| | - Jonasz B Patkowski
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Tiago R D Costa
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Stefan Schouten
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
| | - Ilya Levental
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA, 22903, USA
| | | | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22903, USA.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 75015, Paris, France.
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Synergy between microalgae and microbiome in polluted waters. Trends Microbiol 2023; 31:9-21. [PMID: 35985939 DOI: 10.1016/j.tim.2022.06.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 11/22/2022]
Abstract
Microalga-microbiome interactions are central to both health and disease of aquatic environments. Despite impressive advances in deciphering how microorganisms participate in and impact aquatic ecosystems, the evolution and ecological involvement of microalgae and the microbiome in polluted waters are typically studied independently. Here, the phycosphere (i.e., the consortia of microalgae and the related microbiome) is regarded as an independent and integrated life form, and we summarize the survival strategies exhibited by this symbiont when exposed to anthropogenic pollution. We highlight the cellular strategies and discuss the modulation at the transcriptional and population levels, which reciprocally alters community structure or genome composition for medium-term acclimation or long-term adaptation. We propose a 'PollutantBiome' concept to help the understanding of microalga-microbiome interactions and development of beneficial microbial synthetic communities for pollutant remediation.
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32
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Distribution of CRISPR-Cas systems in the Burkholderiaceae family and its biological implications. Arch Microbiol 2022; 204:703. [DOI: 10.1007/s00203-022-03312-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/20/2022] [Accepted: 10/29/2022] [Indexed: 11/14/2022]
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33
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Hao C, Dewar AE, West SA, Ghoul M. Gene transferability and sociality do not correlate with gene connectivity. Proc Biol Sci 2022; 289:20221819. [PMID: 36448285 PMCID: PMC9709509 DOI: 10.1098/rspb.2022.1819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The connectivity of a gene, defined as the number of interactions a gene's product has with other genes' products, is a key characteristic of a gene. In prokaryotes, the complexity hypothesis predicts that genes which undergo more frequent horizontal transfer will be less connected than genes which are only very rarely transferred. We tested the role of horizontal gene transfer, and other potentially important factors, by examining the connectivity of chromosomal and plasmid genes, across 134 diverse prokaryotic species. We found that (i) genes on plasmids were less connected than genes on chromosomes; (ii) connectivity of plasmid genes was not correlated with plasmid mobility; and (iii) the sociality of genes (cooperative or private) was not correlated with gene connectivity.
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Affiliation(s)
- Chunhui Hao
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Anna E. Dewar
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Stuart A. West
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Melanie Ghoul
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
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34
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Surachat K, Kantachote D, Wonglapsuwan M, Chukamnerd A, Deachamag P, Mittraparp-arthorn P, Jeenkeawpiam K. Complete Genome Sequence of Weissella cibaria NH9449 and Comprehensive Comparative-Genomic Analysis: Genomic Diversity and Versatility Trait Revealed. Front Microbiol 2022; 13:826683. [PMID: 35663880 PMCID: PMC9161744 DOI: 10.3389/fmicb.2022.826683] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/12/2022] [Indexed: 11/13/2022] Open
Abstract
Lactic acid bacteria (LAB) in the genus Weissella spp. contain traits in their genome that confer versatility. In particular, Weissella cibaria encodes several beneficial genes that are useful in biotechnological applications. The complete genome of W. cibaria NH9449 was sequenced and an in silico comparative analysis was performed to gain insight into the genomic diversity among members of the genus Weissella. A total of 219 Weissella genomes were used in a bioinformatics analysis of pan-genomes, phylogenetics, self-defense mechanisms, virulence factors, antimicrobial resistance, and carbohydrate-active enzymes. These investigations showed that the strain NH9449 encodes several restriction-modification-related genes and a CRISPR-Cas region in its genome. The identification of carbohydrate-active enzyme-encoding genes indicated that this strain could be beneficial in biotechnological applications. The comparative genomic analysis reveals the very high genomic diversity in this genus, and some marked differences in genetic variation and genes among Weissella species. The calculated average amino acid identity (AAI) and phylogenetic analysis of core and accessory genes shows the possible existence of three new species in this genus. These new genomic insights into Weissella species and their biological functions could be useful in the food industry and other applications.
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Affiliation(s)
- Komwit Surachat
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- *Correspondence: Komwit Surachat,
| | - Duangporn Kantachote
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Monwadee Wonglapsuwan
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Arnon Chukamnerd
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Panchalika Deachamag
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Pimonsri Mittraparp-arthorn
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Kongpop Jeenkeawpiam
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
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