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Tamilarasan, G., M. Arumugam Pillai, and R. Kannan S. Merina Prem Kumari. "Genetic Diversity Studies in Rice for Bacterial Leaf Blight Resistance." International Journal of Trend in Scientific Research and Development Volume-2, Issue-5 (2018): 797–806. http://dx.doi.org/10.31142/ijtsrd15915.
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Draghi, Jeremy A., and Paul E. Turner. "DNA secretion and gene-level selection in bacteria." Microbiology 152, no. 9 (2006): 2683–88. http://dx.doi.org/10.1099/mic.0.29013-0.
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Natural genetic transformation can facilitate gene transfer in many genera of bacteria and requires the presence of extracellular DNA. Although cell lysis can contribute to this extracellular DNA pool, several studies have suggested that the secretion of DNA from living bacteria may also provide genetic material for transformation. This paper reviews the evidence for specific secretion of DNA from intact bacteria into the extracellular environment and examines this behaviour from a population-genetics perspective. A mathematical model demonstrates that the joint action of DNA secretion and transformation creates a novel type of gene-level natural selection. This model demonstrates that gene-level selection could explain the existence of DNA secretion mechanisms that provide no benefit to individual cells or populations of bacteria. Additionally, the model predicts that any trait affecting DNA secretion will experience selection at the gene level in a transforming population. This analysis confirms that the secretion of DNA from intact bacterial cells is fully explicable with evolutionary theory, and reveals a novel mechanism for bacterial evolution.
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He, Yuanhao, Xiaojun Deng, and Feng Che. "Genetic diversity and community structure of soil bacteria in Chinese fir plantations." Soil and Water Research 14, No. 1 (2019): 22–31. http://dx.doi.org/10.17221/10/2018-swr.
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To explore the diversity of soil bacteria and changes in the bacterial community structure of Chinese fir plantations of different generations and developmental stages, the genetic diversity of soil bacteria was studied using the 454 sequencing technology. The results showed that the bacterial genetic diversity and community structure of Chinese fir plantation plots under monoculture planting and rotation planting practices were as follows: the Shannon diversity indices of first-generation young plantation of Chinese fir plantations (FYC), second-generation young plantation (SYC), and third-generation young plantation (TYC) initially decreased and then increased to 8.45, 8.1, and 8.43, respectively. Due to different management and tending measures, the phyla showing considerable differences in relative abundance were Cyanobacteria, Nitrospirae, Fibrobacteres, Thermotogae, and Planctomycetes. The bacterial genetic diversity and community structure of Chinese fir plantations at different developmental stages were as follows: the bacterial diversity and the number of operational taxonomic units (OTUs) decreased with increasing forest age; with the increasing forest age of Chinese fir, the bacteria with considerable differences in the relative abundance were Burkholderiales, Xanthomonadales, Ktedonobacteria, Nitrosomonadales, Anaerolineae, and Holophagae. The predominant bacteria of the Chinese fir plantations were Acidothermus, Bradyrhizobium, Lactococcus, Planctomyces, Sorangium, and Bryobacter.
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Wang, Xindan, Rodrigo Reyes-Lamothe, and David J. Sherratt. "Visualizing genetic loci and molecular machines in living bacteria." Biochemical Society Transactions 36, no. 4 (2008): 749–53. http://dx.doi.org/10.1042/bst0360749.
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An ongoing mission for biologists is to probe the molecular nature of cellular processes within live cells. Although much of what we have discovered during the molecular biology revolution of the last 50 years has been achieved by exploiting bacteria as ‘bags of DNA and proteins’, relatively little has been learnt about how they organize their life processes within cells. The mistaken perception of bacteria cells as unstructured systems arose partly because of the difficulty of performing studies by light microscopy due to their small size (many of them having cell lengths a few times bigger than the wavelength of visible light). With the opportunities provided by a range of new fluorophores and by new microscopic techniques, a revolution in bacterial cell biology is revealing unimagined organization in the bacterial cell. We review the development and exploitation of new visualization methods and reagents and show how they are contributing to the understanding of bacterial structure, chromosome organization, DNA metabolism and their relationship to the cell cycle.
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Nibali, Luigi, Nikos Donos, and Brian Henderson. "Periodontal infectogenomics." Journal of Medical Microbiology 58, no. 10 (2009): 1269–74. http://dx.doi.org/10.1099/jmm.0.012021-0.
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Multicellular creatures consist of a symbiosis between the host and its colonizing bacteria. The oral cavity may contain as many as 19 000 bacterial phylotypes, while each individual presents a proportion of these microbes. Infectogenomics studies the interaction between host genetic variations and composition of the microbiota. This review introduces the concept of periodontal infectogenomics, defined as the relationship between host genetic factors and the composition of the subgingival microbiota. In particular, the evidence for the effect of genetic variants in neutrophil and cytokine genes and the presence of periodontopathogenic bacteria will be discussed. The influence of genetic factors may affect clearance or persistence of pathogenic bacteria subgingivally, therefore increasing the risk for the development of common pathogenic conditions such as gingivitis and periodontitis, leading to early tooth loss. Mechanisms of interaction between genetic and microbiological factors and prospects for future studies will be discussed.
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Yaghoubi, Atieh, Majid Khazaei, Seyed Mahdi Hasanian, Amir Avan, William C. Cho, and Saman Soleimanpour. "Bacteriotherapy in Breast Cancer." International Journal of Molecular Sciences 20, no. 23 (2019): 5880. http://dx.doi.org/10.3390/ijms20235880.
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Breast cancer is the second most common cause of cancer-related mortality among women around the world. Conventional treatments in the fight against breast cancer, such as chemotherapy, are being challenged regarding their effectiveness. Thus, strategies for the treatment of breast cancer need to be continuously refined to achieve a better patient outcome. We know that a number of bacteria are pathogenic and some are even associated with tumor development, however, recent studies have demonstrated interesting results suggesting some bacteria may have potential for cancer therapy. Therefore, the therapeutic role of bacteria has aroused attention in medical and pharmaceutical studies. Furthermore, genetic engineering has been used in bacterial therapy and may led to greater efficacy with few side effects. Some genetically modified non-pathogenic bacterial species are more successful due to their selectivity for cancer cells but with low toxicity for normal cells. Some live, attenuated, or genetically modified bacterias are capable to multiply in tumors and inhibit their growth. This article aims to review the role of bacteria and their products including bacterial peptides, bacteriocins, and toxins for the treatment of breast cancer.
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Oliveira, Pedro H., Marie Touchon, and Eduardo P. C. Rocha. "Regulation of genetic flux between bacteria by restriction–modification systems." Proceedings of the National Academy of Sciences 113, no. 20 (2016): 5658–63. http://dx.doi.org/10.1073/pnas.1603257113.
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Restriction–modification (R-M) systems are often regarded as bacteria's innate immune systems, protecting cells from infection by mobile genetic elements (MGEs). Their diversification has been recently associated with the emergence of particularly virulent lineages. However, we have previously found more R-M systems in genomes carrying more MGEs. Furthermore, it has been suggested that R-M systems might favor genetic transfer by producing recombinogenic double-stranded DNA ends. To test whether R-M systems favor or disfavor genetic exchanges, we analyzed their frequency with respect to the inferred events of homologous recombination and horizontal gene transfer within 79 bacterial species. Genetic exchanges were more frequent in bacteria with larger genomes and in those encoding more R-M systems. We created a recognition target motif predictor for Type II R-M systems that identifies genomes encoding systems with similar restriction sites. We found more genetic exchanges between these genomes, independently of their evolutionary distance. Our results reconcile previous studies by showing that R-M systems are more abundant in promiscuous species, wherein they establish preferential paths of genetic exchange within and between lineages with cognate R-M systems. Because the repertoire and/or specificity of R-M systems in bacterial lineages vary quickly, the preferential fluxes of genetic transfer within species are expected to constantly change, producing time-dependent networks of gene transfer.
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Pinski, Artur, Alexander Betekhtin, Katarzyna Hupert-Kocurek, Luis A. J. Mur, and Robert Hasterok. "Defining the Genetic Basis of Plant–Endophytic Bacteria Interactions." International Journal of Molecular Sciences 20, no. 8 (2019): 1947. http://dx.doi.org/10.3390/ijms20081947.
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Endophytic bacteria, which interact closely with their host, are an essential part of the plant microbiome. These interactions enhance plant tolerance to environmental changes as well as promote plant growth, thus they have become attractive targets for increasing crop production. Numerous studies have aimed to characterise how endophytic bacteria infect and colonise their hosts as well as conferring important traits to the plant. In this review, we summarise the current knowledge regarding endophytic colonisation and focus on the insights that have been obtained from the mutants of bacteria and plants as well as ‘omic analyses. These show how endophytic bacteria produce various molecules and have a range of activities related to chemotaxis, motility, adhesion, bacterial cell wall properties, secretion, regulating transcription and utilising a substrate in order to establish a successful interaction. Colonisation is mediated by plant receptors and is regulated by the signalling that is connected with phytohormones such as auxin and jasmonic (JA) and salicylic acids (SA). We also highlight changes in the expression of small RNAs and modifications of the cell wall properties. Moreover, in order to exploit the beneficial plant-endophytic bacteria interactions in agriculture successfully, we show that the key aspects that govern successful interactions remain to be defined.
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Ramasamy, Rajeswari, Subha Ashley Thanga Subramanian, R. Abinaya Rajagopal, Karthikadevi Muthusamy, Jesteena Johney, and R. Ragunathan. "Molecular Identification and Analysis of Multi-Drug Resistant Klebsiella pneumonia." International Journal of Applied Sciences and Biotechnology 6, no. 3 (2018): 279–84. http://dx.doi.org/10.3126/ijasbt.v6i3.21185.
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Multidrug resistant Klebsiella pneumoniae was resistant to various antibiotics which are commonly used to treat against the bacterial infections, and is now emerged as a great risk. Antibiotic susceptibility tests were performed to determine the scope of drug resistance of the bacteria. Further studies regarding the responsible genetic material were performed by Polymerase Chain Reaction and RFLP techniques. The remedial measures for treating these bacteria were studied with the help of metabolites obtained from various strains.Int. J. Appl. Sci. Biotechnol. Vol 6(3): 279-284
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Hooppaw, Anna J., and Derek J. Fisher. "A Coming of Age Story: Chlamydia in the Post-Genetic Era." Infection and Immunity 84, no. 3 (2015): 612–21. http://dx.doi.org/10.1128/iai.01186-15.
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Chlamydiaspp. are ubiquitous, obligate, intracellular Gram-negative bacterial pathogens that undergo a unique biphasic developmental cycle transitioning between the infectious, extracellular elementary body and the replicative, intracellular reticulate body. The primaryChlamydiaspecies associated with human disease areC. trachomatis, which is the leading cause of both reportable bacterial sexually transmitted infections and preventable blindness, andC. pneumoniae, which infects the respiratory tract and is associated with cardiovascular disease. Collectively, these pathogens are a significant source of morbidity and pose a substantial financial burden on the global economy. Past efforts to elucidate virulence mechanisms of these unique and important pathogens were largely hindered by an absence of genetic methods. Watershed studies in 2011 and 2012 demonstrated that forward and reverse genetic approaches were feasible withChlamydiaand that shuttle vectors could be selected and maintained within the bacterium. While these breakthroughs have led to a steady expansion of the chlamydial genetic tool kit, there are still roads left to be traveled. This minireview provides a synopsis of the currently available genetic methods forChlamydiaalong with a comparison to the methods used in other obligate intracellular bacteria. Limitations and advantages of these techniques will be discussed with an eye toward the methods still needed, and how the current state of the art for genetics in obligate intracellular bacteria could direct future technological advances forChlamydia.
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Zakharova, Yulia, Artem Marchenkov, Nadezhda Volokitina, Aleksey Morozov, Yelena Likhoshway, and Mikhail Grachev. "Strategy for the Removal of Satellite Bacteria from the Cultivated Diatom." Diversity 12, no. 10 (2020): 382. http://dx.doi.org/10.3390/d12100382.
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Multiple ecological and genetic studies of diatom algae require an axenic culture. However, algae-associated bacterial biofilms often form in diatom-produced mucus, both during creation of monoclonal cultures from single cells and during biomass growth, and they may be difficult to remove. In this work, we describe a protocol for removing associated bacteria from a monoclonal culture of Ulnaria danica isolated from Lake Baikal. The axenization strategy involves selecting the latent phase of diatom growth, multiple washes to remove extracellular polymeric substances and bacterial cells, filter deposition, and treatment with antibiotics that are not toxic for diatoms. The absence of bacteria during these stages was controlled by light microscopy with Alcian blue staining for mucus, epifluorescent microscopy with DAPI (4′,6-diamino-2-phenylindole) staining for bacterial DNA, and scanning electron microscopy of the diatom cell surface. High-throughput sequencing of a 16S rRNA fragment, amplified with universal bacterial primers, from total DNA of a final culture failed to detect any bacterial contamination, confirming successful axenization. A detailed comparative description of all stages of our protocol may prove useful in developing axenic cultures of other diatoms for various ecological and genetic studies.
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Casas, Veronica, Joseph Magbanua, Gerico Sobrepeña, Scott T. Kelley, and Stanley R. Maloy. "Reservoir of Bacterial Exotoxin Genes in the Environment." International Journal of Microbiology 2010 (2010): 1–10. http://dx.doi.org/10.1155/2010/754368.
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Many bacteria produce secreted virulence factors called exotoxins. Exotoxins are often encoded by mobile genetic elements, including bacteriophage (phage). Phage can transfer genetic information to the bacteria they infect. When a phage transfers virulence genes to an avirulent bacterium, the bacterium can acquire the ability to cause disease. It is important to understand the role played by the phage that carry these genes in the evolution of pathogens. This is the first report of an environmental reservoir of a bacterial exotoxin gene in an atypical host. Screening bacterial isolates from the environment via PCR identified an isolate with a DNA sequence >95% identical to theStaphylococcus aureusenterotoxin A gene (sea). 16S DNA sequence comparisons and growth studies identified the environmental isolate as a psychrophilicPseudomonasspp. The results indicate that theseagene is present in an alternative bacterial host, providing the first evidence for an environmental pool of exotoxin genes in bacteria.
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Chuo, Sing Chuong, Sarajul Fikri Mohamed, Siti Hamidah Mohd Setapar, et al. "Insights into the Current Trends in the Utilization of Bacteria for Microbially Induced Calcium Carbonate Precipitation." Materials 13, no. 21 (2020): 4993. http://dx.doi.org/10.3390/ma13214993.
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Nowadays, microbially induced calcium carbonate precipitation (MICP) has received great attention for its potential in construction and geotechnical applications. This technique has been used in biocementation of sand, consolidation of soil, production of self-healing concrete or mortar, and removal of heavy metal ions from water. The products of MICP often have enhanced strength, durability, and self-healing ability. Utilization of the MICP technique can also increase sustainability, especially in the construction industry where a huge portion of the materials used is not sustainable. The presence of bacteria is essential for MICP to occur. Bacteria promote the conversion of suitable compounds into carbonate ions, change the microenvironment to favor precipitation of calcium carbonate, and act as precipitation sites for calcium carbonate crystals. Many bacteria have been discovered and tested for MICP potential. This paper reviews the bacteria used for MICP in some of the most recent studies. Bacteria that can cause MICP include ureolytic bacteria, non-ureolytic bacteria, cyanobacteria, nitrate reducing bacteria, and sulfate reducing bacteria. The most studied bacterium for MICP over the years is Sporosarcina pasteurii. Other bacteria from Bacillus species are also frequently investigated. Several factors that affect MICP performance are bacterial strain, bacterial concentration, nutrient concentration, calcium source concentration, addition of other substances, and methods to distribute bacteria. Several suggestions for future studies such as CO2 sequestration through MICP, cost reduction by using plant or animal wastes as media, and genetic modification of bacteria to enhance MICP have been put forward.
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Pinhassi, Jarone, Edward F. DeLong, Oded Béjà, José M. González, and Carlos Pedrós-Alió. "Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology." Microbiology and Molecular Biology Reviews 80, no. 4 (2016): 929–54. http://dx.doi.org/10.1128/mmbr.00003-16.
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SUMMARYThe recognition of a new family of rhodopsins in marine planktonic bacteria, proton-pumping proteorhodopsin, expanded the known phylogenetic range, environmental distribution, and sequence diversity of retinylidene photoproteins. At the time of this discovery, microbial ion-pumping rhodopsins were known solely in haloarchaea inhabiting extreme hypersaline environments. Shortly thereafter, proteorhodopsins and other light-activated energy-generating rhodopsins were recognized to be widespread among marine bacteria. The ubiquity of marine rhodopsin photosystems now challenges prior understanding of the nature and contributions of “heterotrophic” bacteria to biogeochemical carbon cycling and energy fluxes. Subsequent investigations have focused on the biophysics and biochemistry of these novel microbial rhodopsins, their distribution across the tree of life, evolutionary trajectories, and functional expression in nature. Later discoveries included the identification of proteorhodopsin genes in all three domains of life, the spectral tuning of rhodopsin variants to wavelengths prevailing in the sea, variable light-activated ion-pumping specificities among bacterial rhodopsin variants, and the widespread lateral gene transfer of biosynthetic genes for bacterial rhodopsins and their associated photopigments. Heterologous expression experiments with marine rhodopsin genes (and associated retinal chromophore genes) provided early evidence that light energy harvested by rhodopsins could be harnessed to provide biochemical energy. Importantly, some studies with native marine bacteria show that rhodopsin-containing bacteria use light to enhance growth or promote survival during starvation. We infer from the distribution of rhodopsin genes in diverse genomic contexts that different marine bacteria probably use rhodopsins to support light-dependent fitness strategies somewhere between these two extremes.
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Prüβ, Birgit M., Jun Liu, Penelope I. Higgs, and Lynmarie K. Thompson. "Lessons in Fundamental Mechanisms and Diverse Adaptations from the 2015 Bacterial Locomotion and Signal Transduction Meeting." Journal of Bacteriology 197, no. 19 (2015): 3028–40. http://dx.doi.org/10.1128/jb.00384-15.
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In response to rapid changes in their environment, bacteria control a number of processes, including motility, cell division, biofilm formation, and virulence. Research presented in January 2015 at the biennial Bacterial Locomotion and Signal Transduction (BLAST) meeting in Tucson, AZ, illustrates the elegant complexity of the nanoarrays, nanomachines, and networks of interacting proteins that mediate such processes. Studies employing an array of biophysical, genetic, cell biology, and mathematical methods are providing an increasingly detailed understanding of the mechanisms of these systems within well-studied bacteria. Furthermore, comparisons of these processes in diverse bacterial species are providing insight into novel regulatory and functional mechanisms. This review summarizes research presented at the BLAST meeting on these fundamental mechanisms and diverse adaptations, including findings of importance for applications involving bacteria of medical or agricultural relevance.
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Kessler, Peter S., and John A. Leigh. "Genetics of Nitrogen Regulation in Methanococcus maripaludis." Genetics 152, no. 4 (1999): 1343–51. http://dx.doi.org/10.1093/genetics/152.4.1343.
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Abstract We have used genetic methods in Methanococcus maripaludis to study nitrogen metabolism and its regulation. We present evidence for a “nitrogen regulon” in Methanococcus and Methanobacterium species containing genes of nitrogen metabolism that are regulated coordinately at the transcriptional level via a common repressor binding site sequence, or operator. The implied mechanism for regulation resembles the general bacterial paradigm for repression, but contrasts with well-known mechanisms of nitrogen regulation in bacteria, which occur by activation. Genes in the nitrogen regulons include those for nitrogen fixation, glutamine synthetase, (methyl)ammonia transport, the regulatory protein GlnB, and ammonia-dependent NAD synthetase, as well as a gene of unknown function. We also studied the function of two novel GlnB homologues that are encoded within the nif gene cluster of diazotrophic methanogens. The phenotype resulting from a glnB null mutation in M. maripaludis provides direct evidence that glnB-like genes are involved in “ammonia switch-off,” the post-transcriptional inhibition of nitrogen fixation upon addition of ammonia. Finally, we show that the gene nifX is not required for nitrogen fixation, in agreement with findings in several bacteria. These studies illustrate the utility of genetic methods in M. maripaludis and show the enhanced perspective that studies in the Archaea can bring to known biological systems.
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Torres, Von, Jessica Wisniewski, Julian Rood, James Whisstock, and Daouda Traore. "Structural studies on the Clostridium perfringens conjugation system." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C581. http://dx.doi.org/10.1107/s2053273314094182.
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Conjugation is the mechanism by which two bacteria share genetic information. This process relies on the direct transfer of mobile genetic element via a trans-membrane channel between the donor and the recipient. Although this mechanism has been extensively studied in gram-negative organism, very little in known on how this process takes place in their gram-positive counterpart. To address this important question in bacterial evolution, we use the tetracycline resistance plasmid pCW3 from Clostridium perfringens as study model. The pCW3 plasmid encodes 11 proteins necessary for the assembly the C. perfingens conjugation system. Here, I will focus on the relaxosome complex, which is the starting point of DNA transfer. We identified two protein (IntP and TcpK) involved in the processing of the DNA. Sequence analysis revealed that IntP was a potential Tyrosine recombinase and TcpK, directly upstream of IntP was identified a potential accessory protein of the relaxosome. We cloned, expressed and purified IntP and TcpK. These proteins were then subject to biochemical and biophysical characterizations. I will first present why these two proteins are required for efficient conjugative transfer and how they contribute to DNA processing. Then I will present the crystal structure of TcpK and discuss its interaction with IntP and other components of pCW3 apparatus. This study brings a further insight into this important mechanism of DNA transfer in Gram-positive bacteria.
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Davey, Mary Ellen, and George A. O'toole. "Microbial Biofilms: from Ecology to Molecular Genetics." Microbiology and Molecular Biology Reviews 64, no. 4 (2000): 847–67. http://dx.doi.org/10.1128/mmbr.64.4.847-867.2000.
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SUMMARY Biofilms are complex communities of microorganisms attached to surfaces or associated with interfaces. Despite the focus of modern microbiology research on pure culture, planktonic (free-swimming) bacteria, it is now widely recognized that most bacteria found in natural, clinical, and industrial settings persist in association with surfaces. Furthermore, these microbial communities are often composed of multiple species that interact with each other and their environment. The determination of biofilm architecture, particularly the spatial arrangement of microcolonies (clusters of cells) relative to one another, has profound implications for the function of these complex communities. Numerous new experimental approaches and methodologies have been developed in order to explore metabolic interactions, phylogenetic groupings, and competition among members of the biofilm. To complement this broad view of biofilm ecology, individual organisms have been studied using molecular genetics in order to identify the genes required for biofilm development and to dissect the regulatory pathways that control the plankton-to-biofilm transition. These molecular genetic studies have led to the emergence of the concept of biofilm formation as a novel system for the study of bacterial development. The recent explosion in the field of biofilm research has led to exciting progress in the development of new technologies for studying these communities, advanced our understanding of the ecological significance of surface-attached bacteria, and provided new insights into the molecular genetic basis of biofilm development.
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Mutaz Al-Ajlani, Muaz, and Shahida Hasnain. "Bacteria Exhibiting Antimicrobial Activities; Screening for Antibiotics and the Associated Genetic Studies." Open Conference Proceedings Journal 1, no. 1 (2010): 230–38. http://dx.doi.org/10.2174/2210289201001010230.
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Bellete, B., L. E. Cuevas, P. Kazembe, G. Mughogho, D. Sunderland, and C. A. Hart. "Meningococcal disease in Malawi: studies on the genetic relatedness of the bacteria." Annals of Tropical Medicine & Parasitology 88, no. 1 (1994): 59–64. http://dx.doi.org/10.1080/00034983.1994.11812836.
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ANDERSTAM, B., Y. HAMNERIUS, S. HUSSAIN, and L. EHRENBERG. "Studies of possible genetic effects in bacteria of high frequency electromagnetic fields." Hereditas 98, no. 1 (2008): 11–32. http://dx.doi.org/10.1111/j.1601-5223.1983.tb00575.x.
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Audette, Gerald. "Structural, Functional and Dynamic Studies of F Plasmid T4SS Proteins." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1285. http://dx.doi.org/10.1107/s2053273314087142.
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The transfer of genetic material within a bacterial population through the process of conjugation distributes novel genetic elements for survival in unique environments. Bacterial conjugation is important to public health as the spread antibiotic resistance genes among bacteria results in multi-drug resistance. Indeed, approximately 70% of bacteria that cause hospital-acquired infections are resistant to at least one antibiotic. Conjugative systems, such as the F plasmid of Escherichia coli, consist of proteins that share similarities to type IV secretion systems (T4SS). T4SS proteins of the F plasmid form a membrane spanning protein complex and surface exposed pilus. The periplasmic T4SS proteins TraF, TraW and TrbC play important roles during the F pilus assembly and DNA transfer. Functional analysis of a series of TraF mutants has shown that modification to TraF abolishes pilus synthesis and in turn F plasmid conjugation. In addition, dynamic analysis of TraF using time-resolved hydrogen-deuterium exchange mass spectrometry has revealed a well structured C-terminal thioredoxin-like domain and a more dynamic N-terminal domain that is predicted to interact with companion T4SS protein TraH. In addition, interaction analysis of the putative pore forming proteins TraW and TrbC indicate that the C-terminal domain of TrbC is not required for interaction with TraW, unlike previous models of F T4SS assembly. Rather the C-terminal domain of TraW preferentially interacts with the N-terminal domain of TrbC. These studies are providing a clearer picture of the structures and interactions that occur within the F T4SS assembly during the conjugative process.
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Townsend, Jeffrey P., Kaare M. Nielsen, Daniel S. Fisher, and Daniel L. Hartl. "Horizontal Acquisition of Divergent Chromosomal DNA in Bacteria: Effects of Mutator Phenotypes." Genetics 164, no. 1 (2003): 13–21. http://dx.doi.org/10.1093/genetics/164.1.13.
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Abstract We examine the potential beneficial effects of the expanded access to environmental DNA offered by mutators on the adaptive potential of bacterial populations. Using parameters from published studies of recombination in E. coli, we find that the presence of mutators has the potential to greatly enhance bacterial population adaptation when compared to populations without mutators. In one specific example, for which three specific amino acid substitutions are required for adaptation to occur in a 300-amino-acid protein, we found a 3500-fold increase in the rate of adaptation. The probability of a beneficial acquisition decreased if more amino acid changes, or integration of longer DNA fragments, were required for adaptation. The model also predicts that mutators are more likely than nonmutator phenotypes to acquire genetic variability from a more diverged set of donor bacteria. Bacterial populations harboring mutators in a sequence heterogeneous environment are predicted to acquire most of their DNA conferring adaptation in the range of 13–30% divergence, whereas nonmutator phenotypes become adapted after recombining with more homogeneous sequences of 7–21% divergence. We conclude that mutators can accelerate bacterial adaptation when desired genetic variability is present within DNA fragments of up to ∼30% divergence.
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Brazda, Vaclav, Miroslav Fojta, and Richard P. Bowater. "Structures and stability of simple DNA repeats from bacteria." Biochemical Journal 477, no. 2 (2020): 325–39. http://dx.doi.org/10.1042/bcj20190703.
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DNA is a fundamentally important molecule for all cellular organisms due to its biological role as the store of hereditary, genetic information. On the one hand, genomic DNA is very stable, both in chemical and biological contexts, and this assists its genetic functions. On the other hand, it is also a dynamic molecule, and constant changes in its structure and sequence drive many biological processes, including adaptation and evolution of organisms. DNA genomes contain significant amounts of repetitive sequences, which have divergent functions in the complex processes that involve DNA, including replication, recombination, repair, and transcription. Through their involvement in these processes, repetitive DNA sequences influence the genetic instability and evolution of DNA molecules and they are located non-randomly in all genomes. Mechanisms that influence such genetic instability have been studied in many organisms, including within human genomes where they are linked to various human diseases. Here, we review our understanding of short, simple DNA repeats across a diverse range of bacteria, comparing the prevalence of repetitive DNA sequences in different genomes. We describe the range of DNA structures that have been observed in such repeats, focusing on their propensity to form local, non-B-DNA structures. Finally, we discuss the biological significance of such unusual DNA structures and relate this to studies where the impacts of DNA metabolism on genetic stability are linked to human diseases. Overall, we show that simple DNA repeats in bacteria serve as excellent and tractable experimental models for biochemical studies of their cellular functions and influences.
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Kirtikliene, Tatjana, Aistė Mierauskaitė, Ilona Razmienė, and Nomeda Kuisiene. "Multidrug-Resistant Acinetobacter baumannii Genetic Characterization and Spread in Lithuania in 2014, 2016, and 2018." Life 11, no. 2 (2021): 151. http://dx.doi.org/10.3390/life11020151.
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Bacterial resistance to antimicrobial agents plays an important role in the treatment of bacterial infections in healthcare institutions. The spread of multidrug-resistant bacteria can occur during inter- and intra-hospital transmissions among patients and hospital personnel. For this reason, more studies must be conducted to understand how resistance occurs in bacteria and how it moves between hospitals by comparing data from different years and looking out for any patterns that might emerge. Multidrug-resistant (MDR) Acinetobacter spp. was studied at 14 healthcare institutions in Lithuania during 2014, 2016, and 2018 using samples from human bloodstream infections. In total, 194 isolates were collected and identified using MALDI-TOF and VITEK2 analyzers as Acinetobacter baumannii group bacteria. After that, the isolates were analyzed for the presence of different resistance genes (20 genes were analyzed) and characterized by using the Rep-PCR and MLVA (multiple-locus variable-number tandem repeat analysis) genotyping methods. The results of the study showed the relatedness of the different Acinetobacter spp. isolates and a possible circulation of resistance genes or profiles during the different years of the study. This study provides essential information, such as variability and diversity of resistance genes, genetic profiling, and clustering of isolates, to better understand the antimicrobial resistance patterns of Acinetobacter spp. These results can be used to strengthen the control of multidrug-resistant infections in healthcare institutions and to prevent potential outbreaks of this pathogen in the future.
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Vester, Jan Kjølhede, Mikkel Andreas Glaring, and Peter Stougaard. "Improving diversity in cultures of bacteria from an extreme environment." Canadian Journal of Microbiology 59, no. 8 (2013): 581–86. http://dx.doi.org/10.1139/cjm-2013-0087.
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The ikaite columns in the Ikka Fjord in Greenland represent one of the few permanently cold and alkaline environments on Earth, and the interior of the columns is home to a bacterial community adapted to these extreme conditions. The community is characterized by low cell numbers imbedded in a calcium carbonate matrix, making extraction of bacterial cells and DNA a challenge and limiting molecular and genomic studies of this environment. To utilize this genetic resource, cultivation at high pH and low temperature was studied as a method for obtaining biomass and DNA from the fraction of this community that would not otherwise be amenable to genetic analyses. The diversity and community dynamics in mixed cultures of bacteria from ikaite columns was investigated using denaturing gradient gel electrophoresis and pyrosequencing of 16S rDNA. Both medium composition and incubation time influenced the diversity of the culture and many hitherto uncharacterized genera could be brought into culture by extended incubation time. Extended incubation time also gave rise to a more diverse community with a significant number of rare species not detected in the initial community.
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Araújo, Welington L., Walter Maccheroni Jr., Carlos I. Aguilar-Vildoso, Paulo AV Barroso, Halha O. Saridakis, and João Lúcio Azevedo. "Variability and interactions between endophytic bacteria and fungi isolated from leaf tissues of citrus rootstocks." Canadian Journal of Microbiology 47, no. 3 (2001): 229–36. http://dx.doi.org/10.1139/w00-146.
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Fungi and bacteria were isolated from surface disinfected leaf tissues of several citrus rootstocks. The principal bacterial species isolated were Alcaligenes sp., Bacillus spp. (including B. cereus, B. lentus, B. megaterium, B. pumilus, and B. subtilis), Burkholderia cepacia, Curtobacterium flaccumfaciens, Enterobacter cloacae, Methylobacterium extorquens, and Pantoea agglomerans, with P. agglomerans and B. pumilus being the most frequently isolated species. The most abundant fungal species were Colletotrichum gloeosporioides, Guignardia citricarpa, and Cladosporium sp. Genetic variability between 36 endophytic bacterial isolates was analysed by the random amplified polymorphic DNA (RAPD) technique, which indicated that B. pumilus isolates were more diverse than P. agglomerans isolates, although genetic diversity was not related to the host plants. In vitro interaction studies between G. citricarpa isolates and the most frequently isolated endophytic bacteria showed that metabolites secreted by G. citricarpa have an inhibitory growth effect on some Bacillus species, and a stimulatory growth effect on P. agglomerans.Key words: endophytes, citrus, fungal-bacterial interaction, RAPD, diversity, Pantoea agglomerans, Bacillus pumilus, Guignardia citricarpa.
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Bergstrom, Carl T., Marc Lipsitch, and Bruce R. Levin. "Natural Selection, Infectious Transfer and the Existence Conditions for Bacterial Plasmids." Genetics 155, no. 4 (2000): 1505–19. http://dx.doi.org/10.1093/genetics/155.4.1505.
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Abstract Despite the near-ubiquity of plasmids in bacterial populations and the profound contribution of infectious gene transfer to the adaptation and evolution of bacteria, the mechanisms responsible for the maintenance of plasmids in bacterial populations are poorly understood. In this article, we address the question of how plasmids manage to persist over evolutionary time. Empirical studies suggest that plasmids are not infectiously transmitted at a rate high enough to be maintained as genetic parasites. In part i, we present a general mathematical proof that if this is the case, then plasmids will not be able to persist indefinitely solely by carrying genes that are beneficial or sometimes beneficial to their host bacteria. Instead, such genes should, in the long run, be incorporated into the bacterial chromosome. If the mobility of host-adaptive genes imposes a cost, that mobility will eventually be lost. In part ii, we illustrate a pair of mechanisms by which plasmids can be maintained indefinitely even when their rates of transmission are too low for them to be genetic parasites. First, plasmids may persist because they can transfer locally adapted genes to newly arriving strains bearing evolutionary innovations, and thereby preserve the local adaptations in the face of background selective sweeps. Second, plasmids may persist because of their ability to shuttle intermittently favored genes back and forth between various (noncompeting) bacterial strains, ecotypes, or even species.
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Bohannan, B. J. M., and R. E. Lenski. "Linking genetic change to community evolution: insights from studies of bacteria and bacteriophage." Ecology Letters 3, no. 4 (2000): 362–77. http://dx.doi.org/10.1046/j.1461-0248.2000.00161.x.
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Woods, David, and Douglas Rawlings. "Molecular genetic studies on the thiobacilli and the development of improved biomining bacteria." BioEssays 2, no. 1 (1985): 8–10. http://dx.doi.org/10.1002/bies.950020104.
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Kolenbrander, Paul E., Roxanna N. Andersen, David S. Blehert, Paul G. Egland, Jamie S. Foster, and Robert J. Palmer. "Communication among Oral Bacteria." Microbiology and Molecular Biology Reviews 66, no. 3 (2002): 486–505. http://dx.doi.org/10.1128/mmbr.66.3.486-505.2002.
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SUMMARY Human oral bacteria interact with their environment by attaching to surfaces and establishing mixed-species communities. As each bacterial cell attaches, it forms a new surface to which other cells can adhere. Adherence and community development are spatiotemporal; such order requires communication. The discovery of soluble signals, such as autoinducer-2, that may be exchanged within multispecies communities to convey information between organisms has emerged as a new research direction. Direct-contact signals, such as adhesins and receptors, that elicit changes in gene expression after cell-cell contact and biofilm growth are also an active research area. Considering that the majority of oral bacteria are organized in dense three-dimensional biofilms on teeth, confocal microscopy and fluorescently labeled probes provide valuable approaches for investigating the architecture of these organized communities in situ. Oral biofilms are readily accessible to microbiologists and are excellent model systems for studies of microbial communication. One attractive model system is a saliva-coated flowcell with oral bacterial biofilms growing on saliva as the sole nutrient source; an intergeneric mutualism is discussed. Several oral bacterial species are amenable to genetic manipulation for molecular characterization of communication both among bacteria and between bacteria and the host. A successful search for genes critical for mixed-species community organization will be accomplished only when it is conducted with mixed-species communities.
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Banta, Amy B., Jeremy H. Wei, and Paula V. Welander. "A distinct pathway for tetrahymanol synthesis in bacteria." Proceedings of the National Academy of Sciences 112, no. 44 (2015): 13478–83. http://dx.doi.org/10.1073/pnas.1511482112.
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Tetrahymanol is a polycyclic triterpenoid lipid first discovered in the ciliate Tetrahymena pyriformis whose potential diagenetic product, gammacerane, is often used as a biomarker for water column stratification in ancient ecosystems. Bacteria are also a potential source of tetrahymanol, but neither the distribution of this lipid in extant bacteria nor the significance of bacterial tetrahymanol synthesis for interpreting gammacerane biosignatures is known. Here we couple comparative genomics with genetic and lipid analyses to link a protein of unknown function to tetrahymanol synthesis in bacteria. This tetrahymanol synthase (Ths) is found in a variety of bacterial genomes, including aerobic methanotrophs, nitrite-oxidizers, and sulfate-reducers, and in a subset of aquatic and terrestrial metagenomes. Thus, the potential to produce tetrahymanol is more widespread in the bacterial domain than previously thought. However, Ths is not encoded in any eukaryotic genomes, nor is it homologous to eukaryotic squalene-tetrahymanol cyclase, which catalyzes the cyclization of squalene directly to tetrahymanol. Rather, heterologous expression studies suggest that bacteria couple the cyclization of squalene to a hopene molecule by squalene-hopene cyclase with a subsequent Ths-dependent ring expansion to form tetrahymanol. Thus, bacteria and eukaryotes have evolved distinct biochemical mechanisms for producing tetrahymanol.
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Cvitkovitch, D. G. "Genetic Competence and Transformation in Oral Streptococci." Critical Reviews in Oral Biology & Medicine 12, no. 3 (2001): 217–43. http://dx.doi.org/10.1177/10454411010120030201.
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The oral streptococci are normally non-pathogenic residents of the human microflora. There is substantial evidence that these bacteria can, however, act as "genetic reservoirs" and transfer genetic information to transient bacteria as they make their way through the mouth, the principal entry point for a wide variety of bacteria. Examples that are of particular concern include the transfer of antibiotic resistance from oral streptococci to Streptococcus pneumoniae. The mechanisms that are used by oral streptococci to exchange genetic information are not well-understood, although several species are known to enter a physiological state of genetic competence. This state permits them to become capable of natural genetic transformation, facilitating the acquisition of foreign DNA from the external environment. The oral streptococci share many similarities with two closely related Gram-positive bacteria. S. pneumoniae and Bacillus subtilis. In these bacteria, the mechanisms of quorum-sensing, the development of competence, and DNA uptake and integration are well-charaterized. Using this knowledge and the data available in genome databases allowed us to identify putative genes involved in these processes in the oral organism Streptococcus mutans. Models of competence development and genetic transformation in the oral streptococci and strategies to confirm these models are discussed. Future studies of competence in oral biofilms, the natural environment of oral streptococci, will be discussed.
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Roy, Paul H. "Transposons and Integrons: Natural Genetic Engineering of Bacterial Resistance." Canadian Journal of Infectious Diseases 10, suppl c (1999): 5C—8C. http://dx.doi.org/10.1155/1999/619276.
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The advent of antibiotics in clinical medicine has resulted in the emergence of multiresistant strains of bacteria. Bacteria possess sophisticated mechanisms of genetic exchange that have driven their recent evolution. Among these are transposons and integrons, the latter having interesting parallels with genetic engineering techniques used in the laboratory. An understanding of these mechanisms through studies of the molecular basis of the dissemination of resistance genes will aid rational choices in antibiotic therapy.
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Fierer, Noah, Mya Breitbart, James Nulton, et al. "Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil." Applied and Environmental Microbiology 73, no. 21 (2007): 7059–66. http://dx.doi.org/10.1128/aem.00358-07.
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ABSTRACT Recent studies have highlighted the surprising richness of soil bacterial communities; however, bacteria are not the only microorganisms found in soil. To our knowledge, no study has compared the diversities of the four major microbial taxa, i.e., bacteria, archaea, fungi, and viruses, from an individual soil sample. We used metagenomic and small-subunit RNA-based sequence analysis techniques to compare the estimated richness and evenness of these groups in prairie, desert, and rainforest soils. By grouping sequences at the 97% sequence similarity level (an operational taxonomic unit [OTU]), we found that the archaeal and fungal communities were consistently less even than the bacterial communities. Although total richness levels are difficult to estimate with a high degree of certainty, the estimated number of unique archaeal or fungal OTUs appears to rival or exceed the number of unique bacterial OTUs in each of the collected soils. In this first study to comprehensively survey viral communities using a metagenomic approach, we found that soil viruses are taxonomically diverse and distinct from the communities of viruses found in other environments that have been surveyed using a similar approach. Within each of the four microbial groups, we observed minimal taxonomic overlap between sites, suggesting that soil archaea, bacteria, fungi, and viruses are globally as well as locally diverse.
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Dahlberg, Cecilia, and Lin Chao. "Amelioration of the Cost of Conjugative Plasmid Carriage in Eschericha coli K12." Genetics 165, no. 4 (2003): 1641–49. http://dx.doi.org/10.1093/genetics/165.4.1641.
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Abstract Although plasmids can provide beneficial functions to their host bacteria, they might confer a physiological or energetic cost. This study examines how natural selection may reduce the cost of carrying conjugative plasmids with drug-resistance markers in the absence of antibiotic selection. We studied two plasmids, R1 and RP4, both of which carry multiple drug resistance genes and were shown to impose an initial fitness cost on Escherichia coli. To determine if and how the cost could be reduced, we subjected plasmid-containing bacteria to 1100 generations of evolution in batch cultures. Analysis of the evolved populations revealed that plasmid loss never occurred, but that the cost was reduced through genetic changes in both the plasmids and the bacteria. Changes in the plasmids were inferred by the demonstration that evolved plasmids no longer imposed a cost on their hosts when transferred to a plasmid-free clone of the ancestral E. coli. Changes in the bacteria were shown by the lowered cost when the ancestral plasmids were introduced into evolved bacteria that had been cured of their (evolved) plasmids. Additionally, changes in the bacteria were inferred because conjugative transfer rates of evolved R1 plasmids were lower in the evolved host than in the ancestral host. Our results suggest that once a conjugative bacterial plasmid has invaded a bacterial population it will remain even if the original selection is discontinued.
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Thies, J. E., E. M. Holmes, and A. Vachot. "Application of molecular techniques to studies in Rhizobium ecology: a review." Australian Journal of Experimental Agriculture 41, no. 3 (2001): 299. http://dx.doi.org/10.1071/ea99171.
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The symbiosis between legumes and their specific root-nodule bacteria, rhizobia, has been employed to improve agricultural productivity for most of the 20th century. During this time, great advances have been made in our knowledge of both plant and bacterial genomes, the biochemistry of the symbiosis, plant and bacterial signaling and the measurement of nitrogen fixation. However, knowledge of the ecology of the bacterial symbiont has lagged behind, largely due to a lack of practical techniques that can be used to monitor and assess the performance of these bacteria in the field. Most techniques developed in the last few decades have relied on somehow ‘marking’ individual strains to allow us to follow their fate in the field environment. Such techniques, while providing knowledge of the success or failure of specific strains in a range of environments, have not allowed insight into the nature of the pre-existing rhizobial populations in these sites, nor the interaction between marked strains and the background population. The advent of molecular techniques has revolutionised the study of Rhizobium ecology by allowing us to follow the flux of a variety of ecotypes within a particular site and to examine how introduced rhizobia interact with a genetically diverse background. In addition, molecular techniques have increased our understanding of how individual strains and populations of root-nodule bacteria respond to changes in the environment and how genetic diversity evolves in field sites over time. This review focuses on recently developed molecular techniques that hold promise for continuing to develop our understanding of Rhizobium ecology and how these can be used to address a range of applied problems to yield new insights into rhizobial life in soil and as legume symbionts.
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Baymiev, An, O. Lastochkina, I. Koryakov, E. Akimova, A. Vladimirova, and Al Baymiev. "Regularities of the genotype’s distribution of phylogenetically homogenous bacteria Rhizobium leguminosarum in the nodules of separate populations of Lathyrus vernus (spring pea) plants." Biomics 13, no. 1 (2021): 100–105. http://dx.doi.org/10.31301/2221-6197.bmcs.2021-8.
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The genotypes of phylogenetically homogeneous Rhizobium leguminosarum bacterial strains in nodules of Lathyrus vernus plants were studied. The degree of genetic variation between bacteria within nodules of one L. vernus population correlated with the distance between host plants: the greater the distance, the greater the genetic differences between their microsymbionts. This may be due to the ongoing process of exchanging genetic information between Rhizobium strains, with the depends on the distance between them. But in some cases, this pattern was not observed, and there were significant differences between the microsymbionts of neighboring plants. Most likely, with the exception of spatial limitations, there are some other barriers that exist to the free exchange of genetic information between nodule bacteria.
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Huang, Yuqing, and Jan E. Kammenga. "Genetic Variation in Caenorhabditis elegans Responses to Pathogenic Microbiota." Microorganisms 8, no. 4 (2020): 618. http://dx.doi.org/10.3390/microorganisms8040618.
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The bacterivorous nematode Caenorhabditis elegans is an important model species for understanding genetic variation of complex traits. So far, most studies involve axenic laboratory settings using Escherichia coli as the sole bacterial species. Over the past decade, however, investigations into the genetic variation of responses to pathogenic microbiota have increasingly received attention. Quantitative genetic analyses have revealed detailed insight into loci, genetic variants, and pathways in C. elegans underlying interactions with bacteria, microsporidia, and viruses. As various quantitative genetic platforms and resources like C. elegans Natural Diversity Resource (CeNDR) and Worm Quantitative Trait Loci (WormQTL) have been developed, we anticipate that expanding C. elegans research along the lines of genetic variation will be a treasure trove for opening up new insights into genetic pathways and gene functionality of microbiota interactions.
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Kashinskaya, Elena Nikolaevna, Evgeniy Petrovich Simonov, and Mikhail Maryanovich Solovyev. "The current state of molecular genetic research on the taxonomic diversity of the enteric microbiota of Siberian fish." Rybovodstvo i rybnoe hozjajstvo (Fish Breeding and Fisheries), no. 12 (December 1, 2020): 60–74. http://dx.doi.org/10.33920/sel-12-2010-06.
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This paper presents the current state of research on the intestinal microbiota of fish of different ecological groups from water bodies of West and East Siberia. The present study focused on the gut bacterial diversity of 16 species/forms of fish (due to intricate taxonomical position of whitefish from Teletskoye Lake) inhabiting Chany Lake (Novosibirsk oblast), Teletskoye Lake (Altai Republic), Baikal Lake and other water bodies of East Siberia using molecular genetic methods. The analysis of the conducted studies shows the main features of gut bacterial communities in the digestive tract of fish and to better understand the features of the functioning of aquatic ecosystems in Siberia. In all studied fish (except for Lena grayling and Baikal omul), regardless of their habitat, taxonomy, digestive system structure (presence or absence of stomach and pyloric caeca) and feeding habits, bacteria of all four phyla (Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria) were found among the dominants. Such differences can also be explained by sample preparation techniques before sequencing that researchers may apply. Also, the uncultivated microbiota such as Pseudoalteromonadaceae (Lake Chany), Comamonadaceae and Bacillaceae (whitefish from Lake Teletskoye) and Rhodobacteraceae (Baikal omul and whitefish) were often found among the dominant bacterial taxa in the digestive tract of the most studied fish. Moreover, the data focused on the structure of gut bacterial community of fish will be useful for the development of aquaculture industry in the region, since the information makes it possible to identify pathogenic, opportunistic, and probiotic bacteria in aquatic ecosystems.
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Vilas-Bôas, G. T., A. P. S. Peruca, and O. M. N. Arantes. "Biology and taxonomy ofBacillus cereus,Bacillus anthracis, andBacillus thuringiensis." Canadian Journal of Microbiology 53, no. 6 (2007): 673–87. http://dx.doi.org/10.1139/w07-029.
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Three species of the Bacillus cereus group (Bacillus cereus, Bacillus anthracis , and Bacillus thuringiensis ) have a marked impact on human activity. Bacillus cereus and B. anthracis are important pathogens of mammals, including humans, and B. thuringiensis is extensively used in the biological control of insects. The microbiological, biochemical, and genetic characteristics of these three species are reviewed, together with a discussion of several genomic studies conducted on strains of B. cereus group. Using bacterial systematic concepts, we speculate that to understand the taxonomic relationship within this group of bacteria, special attention should be devoted also to the ecology and the population genetics of these species.
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Wang, Meng. "Microbiome-Mitochondria Communication in the Regulation of Host Longevity." Innovation in Aging 4, Supplement_1 (2020): 739. http://dx.doi.org/10.1093/geroni/igaa057.2637.
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Abstract Mitochondria are ancient relatives of bacteria in eukaryotic cells and dynamically interconnected through organelle fusion and fission. Given the close relationship between bacteria and eukaryotic mitochondria during evolution, my group is interested in understanding the critical role of their communication in regulating host’s longevity. We have conducted genome-scale screens to decipher how bacterial genetic composition impacts host longevity, leading to the discovery of specific bacteria-secreted metabolites that fine-tune the mitochondrial fusion-fission balance and consequently promotes longevity across different host species. We have further developed optogenetic approaches to manipulate bacterial gene expression and metabolite production inside the gut of live organisms, in order to investigate the microbiome-mitochondria communication in time and space. Our studies demonstrate a novel mode of signaling communication between bacteria and mitochondria, reveal its vital impacts on host healthy aging, and provide new methods to decipher the spatiotemporal relationship between the microbiome and the host.
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Ramasamy, Dhamodharan, Ajay Kumar Mishra, Jean-Christophe Lagier, et al. "A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species." International Journal of Systematic and Evolutionary Microbiology 64, Pt_2 (2014): 384–91. http://dx.doi.org/10.1099/ijs.0.057091-0.
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Currently, bacterial taxonomy relies on a polyphasic approach based on the combination of phenotypic and genotypic characteristics. However, the current situation is paradoxical in that the genetic criteria that are used, including DNA–DNA hybridization, 16S rRNA gene sequence nucleotide similarity and phylogeny, and DNA G+C content, have significant limitations, but genome sequences that contain the whole genetic information of bacterial strains are not used for taxonomic purposes, despite the decreasing costs of sequencing and the increasing number of available genomes. Recently, we diversified bacterial culture conditions with the aim of isolating uncultivated bacteria. To classify the putative novel species that we cultivated, we used a polyphasic strategy that included phenotypic as well as genomic criteria (genome characteristics as well as genomic sequence similarity). Herein, we review the pros and cons of genome sequencing for taxonomy and propose that the incorporation of genome sequences in taxonomic studies has the advantage of using reliable and reproducible data. This strategy, which we name taxono-genomics, may contribute to the taxonomic classification of bacteria.
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Fomenko, Oleg, Evgeny Mikhailov, Nadezhda Pasko, Svetlana Grin, Andrey Koshchaev, and Mikhail Syromiatnikov. "Studies on genes expression pattern of antioxidant enzymes and enzymes involved into the genetic information implementation in E.coli cells due to the antibiotic resistance against apramycin and cefatoxime." BIO Web of Conferences 17 (2020): 00103. http://dx.doi.org/10.1051/bioconf/20201700103.
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The emergence of antibiotic-resistant bacteria is considered a serious problem. The resistance of bacteria against antimicrobial substances becomes important in the repair systems for damage to DNA and RNA molecules. The role of the antioxidant system in the development of bacterial resistance against antibiotics is not yet practically studied. The article studied the expression regulation of the genes of antioxidant enzymes and enzymes involved in the genetic information in E. coli cells with the antibiotic resistance against apramycin and cefatoxime. The study was conducted on bacterial cells resistant against these two antibiotics. The genes blaOXA-1, blaSHV, blaTEM, mdtK, aadA1, aadA2, sat, strA, blaCTX, blaPER-2, tnpA, tnpR, intC1 and intC1c were identified in bacterial cell case. This indicates the presence of plasmids in bacteria with these genes, which provide bacterial resistance to apramycin and cefatoxime. It was established that during the formation of cefotaxime resistance, there was a sharp increase in the expression of the Cu, Zn superoxide dismutase gene: in comparison with the control group, the representation of its transcripts increased 141.04 times for cefotoxime and 155.42 times for apramycin. It has been established that during the formation of resistance to the studied antibiotics in E. coli, an increase in the expression of the end4 and end3 genes is observed. There is tendency toward an increase in the number of transcripts of the pol3E gene observed in the formation of resistance against cefotaxime and apromycin.
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Stevenson, Brian, James L. Bono, Abdallah Elias, Kit Tilly, and Patricia Rosa. "Transformation of the Lyme Disease Spirochete Borrelia burgdorferi with Heterologous DNA." Journal of Bacteriology 180, no. 18 (1998): 4850–55. http://dx.doi.org/10.1128/jb.180.18.4850-4855.1998.
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ABSTRACT Studies of the spirochete Borrelia burgdorferi have been hindered by the scarcity of genetic tools that can be used in these bacteria. For the first time, a method has been developed by which heterologous DNA (DNA without a naturally occurring B. burgdorferi homolog) can be introduced into and persistently maintained by B. burgdorferi. This technique uses integration of circular DNA into the bacterial genome via a single-crossover event. The ability to transform B. burgdorferi with heterologous DNA will now permit a wide range of experiments on the biology of these bacteria and their involvement in the many facets of Lyme disease.
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Yeung, M. K. "Molecular and Genetic Analyses of Actinomyces SPP." Critical Reviews in Oral Biology & Medicine 10, no. 2 (1999): 120–38. http://dx.doi.org/10.1177/10454411990100020101.
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Members of the genus Actinomyces are predominant primary colonizers of the oral cavity and play an important role in initiating plaque development. These bacteria have evolved unique mechanisms that favor colonization and persistence in this micro-environment. The expression of cell-surface fimbriae is correlated with the ability of these bacteria to adhere to specific receptors on the tooth and mucosal surfaces, and to interact with other plaque bacteria. The elaboration of sialidase is thought to enhance fimbriae-mediated adherence by unmasking the fimbrial receptors on mammalian cells. The presence of certain cell-associated or extracellular enzymes, including those involved in sucrose or urea metabolism, may provide the means for these bacteria to thrive under conditions when other growth nutrients are not available. Moreover, these enzyme activities may influence the distribution of other plaque bacteria and promote selection for Actinomyces spp. in certain ecological niches. The recent development of a genetic transfer system for Actinomyces spp. has allowed for studies the results of which demonstrate the existence of multiple genes involved in fimbriae synthesis and function, and facilitated the construction of allelic replacement mutants at each gene locus. Analyses of these mutants have revealed a direct correlation between the synthesis of assembled fimbriae and the observed adherence properties. Further genetic analysis of the various enzyme activities detected from strains of Actinomyces should allow for an assessment of the role of these components in microbial ecology, and their contribution to the overall success of Actinomyces spp. as a primary colonizer and a key player in oral health and disease.
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Farmehr, P. "Phage therapy is an important replacement for the antibiotic resistance." Pakistan Journal of Medical and Health Sciences 15, no. 5 (2021): 1236–40. http://dx.doi.org/10.53350/pjmhs211551236.
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Antibiotic resistance has become a significant and growing threat to public and environmental health. The emergence of multiple drug-resistant bacteria has prompted interest in alternatives to conventional antimicrobial. One of the possible replacement options for antibiotics is the use of bacteriophages as antimicrobial. We were forced to look for a new approach in treatment. Phage therapy is an important alternative antibiotic in the current of drug-resistance pathogens. In this way, poisoning bacteria bacteriophage bacteria infect and replicate in bacteria, in this therapy, identify the type of virus per person and can be targeted manipulation of harmful bacteria and then returned the person and invented phage therapy. We discuss the advantages and disadvantages of bacteriophages as therapeutic agents in this regard. And so describe a brief history of bacteriophages and clinical studies on their use in bacterial disease. Much hope is placed in genetic modifications of bacteriophages prevents the development of phage-resistant bacteria. Keywords: antibiotic resistance‚ bacteriophage, phage therapy
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Richardson, Alexandra, and Costa Georgopoulos. "Genetic Analysis of the Bacteriophage T4-Encoded Cochaperonin Gp31." Genetics 152, no. 4 (1999): 1449–57. http://dx.doi.org/10.1093/genetics/152.4.1449.
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Abstract Previous genetic and biochemical analyses have established that the bacteriophage T4-encoded Gp31 is a cochaperonin that interacts with Escherichia coli’s GroEL to ensure the timely and accurate folding of Gp23, the bacteriophage-encoded major capsid protein. The heptameric Gp31 cochaperonin, like the E. coli GroES cochaperonin, interacts with GroEL primarily through its unstructured mobile loop segment. Upon binding to GroEL, the mobile loop adopts a structured, β-hairpin turn. In this article, we present extensive genetic data that strongly substantiate and extend these biochemical studies. These studies begin with the isolation of mutations in gene 31 based on the ability to plaque on groEL44 mutant bacteria, whose mutant product interacts weakly with Gp31. Our genetic system is unique because it also allows for the direct selection of revertants of such gene 31 mutations, based on their ability to plaque on groEL515 mutant bacteria. Interestingly, all of these revertants are pseudorevertants because the original 31 mutation is maintained. In addition, we show that the classical tsA70 mutation in gene 31 changes a conserved hydrophobic residue in the mobile loop to a hydrophilic one. Pseudorevertants of tsA70, which enable growth at the restrictive temperatures, acquire the same mutation previously shown to allow plaque formation on groEL44 mutant bacteria. Our genetic analyses highlight the crucial importance of all three highly conserved hydrophobic residues of the mobile loop of Gp31 in the productive interaction with GroEL.
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Buhnik-Rosenblau, Keren, Yael Danin-Poleg, and Yechezkel Kashi. "Predominant Effect of Host Genetics on Levels of Lactobacillus johnsonii Bacteria in the Mouse Gut." Applied and Environmental Microbiology 77, no. 18 (2011): 6531–38. http://dx.doi.org/10.1128/aem.00324-11.
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ABSTRACTThe gut microbiota is strongly associated with the well-being of the host. Its composition is affected by environmental factors, such as food and maternal inoculation, while the relative impact of the host's genetics have been recently uncovered. Here, we studied the effect of the host genetic background on the composition of intestinal bacteria in a murine model, focusing on lactic acid bacteria (LAB) as an important group that includes many probiotic strains. Based on 16S rRNA gene genotyping, variation was observed in fecal LAB populations of BALB/c and C57BL/6J mouse lines.Lactobacillus johnsonii, a potentially probiotic bacterium, appeared at significantly higher levels in C57BL/6J versus BALB/c mouse feces. In the BALB/c gut, theL. johnsoniilevel decreased rapidly after oral administration, suggesting that some selective force does not allow its persistence at higher levels. The genetic inheritance ofL. johnsoniilevels was further tested in reciprocal crosses between the two mouse lines. The resultant F1 offspring presented similarL. johnsoniilevels, confirming that mouse genetics plays a major role in determining these levels compared to the smaller maternal effect. Our findings suggest that mouse genetics has a major effect on the composition of the LAB population in general and on the persistence ofL. johnsoniiin the gut in particular. Concentrating on a narrow spectrum of culturable LAB enables the isolation and characterization of such potentially probiotic bacterial strains, which might be specifically oriented to the genetic background of the host as part of a personalized-medicine approach.
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Waters, B., and J. Davies. "Amino acid variation in the GyrA subunit of bacteria potentially associated with natural resistance to fluoroquinolone antibiotics." Antimicrobial Agents and Chemotherapy 41, no. 12 (1997): 2766–69. http://dx.doi.org/10.1128/aac.41.12.2766.
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In studies of genetic diversity in natural microbial populations, we have analyzed nucleotide sequences in the quinolone resistance-determining region of the bacterial gyrA gene in ciprofloxacin-resistant and nonselected soil bacteria obtained from the environment. It is apparent that this sequence is highly variable, and resistance to fluoroquinolone antibiotics occurring in environmental populations of bacteria is due at least in part to natural sequence variation in this domain. We suggest that the development of new antimicrobial agents, including completely synthetic antimicrobials such as the fluoroquinolones, should incorporate the analysis of resistance mechanisms among microbes in natural environments; these studies could predict potential mechanisms of resistance to be encountered in subsequent clinical use of the agents and would guide chemical modification designed to evade resistance development.