Evidence of horizontal gene transfer by transposase gene analyses in Fervidobacterium species

Cuecas, Alba; Kanoksilapatham, Wirojne; Gonzalez, Juan M.

doi:10.1371/journal.pone.0173961

Cited by 30 publications

(25 citation statements)

References 30 publications

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“…However, a transposase virulence factor coding for Klebsiella pneumoniae, a total coliform bacterium, was detected in municipal tap and drinking fountain water samples ( Table 3). Transposases have potential to promote horizontal gene transfer across bacteria [94,95], and because Klebsiella pneumoniae was not detected in these samples, these genes might be indicative of horizontal gene transfer.…”

Section: Plos Onementioning

confidence: 99%

A comparative analysis of drinking water employing metagenomics

et al. 2020

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The microbiological content of drinking water traditionally is determined by employing culture-dependent methods that are unable to detect all microorganisms, especially those that are not culturable. High-throughput sequencing now makes it possible to determine the microbiome of drinking water. Thus, the natural microbiota of water and water distribution systems can now be determined more accurately and analyzed in significantly greater detail, providing comprehensive understanding of the microbial community of drinking water applicable to public health. In this study, shotgun metagenomic analysis was performed to determine the microbiological content of drinking water and to provide a preliminary assessment of tap, drinking fountain, sparkling natural mineral, and non-mineral bottled water. Predominant bacterial species detected were members of the phyla Actinobacteria and Proteobacteria, notably the genera Alishewanella, Salmonella, and Propionibacterium in non-carbonated non-mineral bottled water, Methyloversatilis and Methylibium in sparkling natural mineral water, and Mycobacterium and Afipia in tap and drinking fountain water. Fecal indicator bacteria, i.e., Escherichia coli or enterococci, were not detected in any samples examined in this study. Bacteriophages and DNA encoding a few virulence-associated factors were detected but determined to be present only at low abundance. Antibiotic resistance markers were detected only at abundance values below our threshold of confidence. DNA of opportunistic plant and animal pathogens was identified in some samples and these included bacteria (Mycobacterium spp.), protozoa (Acanthamoeba mauritaniensis and Acanthamoeba palestinensis), and fungi (Melampsora pinitorqua and Chryosporium queenslandicum). Archaeal DNA (Candidatus Nitrosoarchaeum) was detected only in sparkling natural mineral water. This preliminary study reports the complete microbiome (bacteria, viruses, fungi, and protists) of selected types of drinking water employing whole-genome high-throughput sequencing and bioinformatics. Investigation into activity and function of the organisms detected is in progress.

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Section: Plos Onementioning

confidence: 99%

A comparative analysis of drinking water employing metagenomics

et al. 2020

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“…Targeted metagenomics indicated that the gene clusters involved in denitrification were also probably subject to shuffling by HGT between bacteria ( Demanèche et al, 2009 ). The puzzled presence of the denitrification genes in different related strains is an example of the known plasticity of bacterial genomes ( Cuecas et al, 2017 ). An example is the presence of a denitrification genomic island which can be spread by HGT among T. thermophilus strains ( Alvarez et al, 2011 ; Bricio et al, 2011 ).…”

Section: Horizontal Gene Transfer and The Colonization Of Low-temperamentioning

confidence: 99%

Nitric Oxide Accumulation: The Evolutionary Trigger for Phytopathogenesis

2017

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Many publications highlight the importance of nitric oxide (NO) in plant–bacteria interactions, either in the promotion of health and plant growth or in pathogenesis. However, the role of NO in the signaling between bacteria and plants and in the fate of their interaction, as well as the reconstruction of their interactive evolution, remains largely unknown. Despite the complexity of the evolution of life on Earth, we explore the hypothesis that denitrification and aerobic respiration were responsible for local NO accumulation, which triggered primordial antagonistic biotic interactions, namely the first phytopathogenic interactions. N-oxides, including NO, could globally accumulate via lightning synthesis in the early anoxic ocean and constitute pools for the evolution of denitrification, considered an early step of the biological nitrogen cycle. Interestingly, a common evolution may be proposed for components of denitrification and aerobic respiration pathways, namely for NO and oxygen reductases, a theory compatible with the presence of low amounts of oxygen before the great oxygenation event (GOE), which was generated by Cyanobacteria. During GOE, the increase in oxygen caused the decrease of Earth’s temperature and the consequent increase of oxygen dissolution and availability, making aerobic respiration an increasingly dominant trait of the expanding mesophilic lifestyle. Horizontal gene transfer was certainly important in the joint expansion of mesophily and aerobic respiration. First denitrification steps lead to NO formation through nitrite reductase activity, and NO may further accumulate when oxygen binds NO reductase, resulting in denitrification blockage. The consequent transient NO surplus in an oxic niche could have been a key factor for a successful outcome of an early denitrifying prokaryote able to scavenge oxygen by NO/oxygen reductase or by an independent heterotrophic aerobic respiration pathway. In fact, NO surplus could result in toxicity causing “the first disease” in oxygen-producing Cyanobacteria. We inspected in bacteria the presence of sequences similar to the NO-producing nitrite reductase nirS gene of Thermus thermophilus, an extreme thermophilic aerobe of the Thermus/Deinococcus group, which constitutes an ancient lineage related to Cyanobacteria. In silico analysis revealed the relationship between the presence of nirS genes and phytopathogenicity in Gram-negative bacteria.

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“…We detected 2186 gene fusion events, which involve 1280 genes and 800 different gene functions. Gene fusion events containing genes associated with the mechanism of HGT include recombinase family protein (51/2186) [ 56 ], plasmid mobilization relaxosome protein Mob (39/2186) [ 57 ], IS110 family transposase (23/2186) [ 58 ], site-specific integras (23/2186) [ 59 ], conjugal transfer protein Tra (20/2186) [ 60 ] and transposase (2/2186) [ 58 ]. Specifically, as shown in Table 1 in Appendix section, we detected 7 and 1 fusions of multidrug transporter genes in IBD and Non-IBD samples, respectively.…”

Section: Resultsmentioning

confidence: 99%

Understanding Horizontal Gene Transfer network in human gut microbiota

Chen

2020

Gut Pathog

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Background Horizontal Gene Transfer (HGT) is the process of transferring genetic materials between species. Through sharing genetic materials, microorganisms in the human microbiota form a network. The network can provide insights into understanding the microbiota. Here, we constructed the HGT networks from the gut microbiota sequencing data and performed network analysis to characterize the HGT networks of gut microbiota. Results We constructed the HGT network and perform the network analysis to two typical gut microbiota datasets, a 283-sample dataset of Mother-to-Child and a 148-sample dataset of longitudinal inflammatory bowel disease (IBD) metagenome. The results indicated that (1) the HGT networks are scale-free. (2) The networks expand their complexities, sizes, and edge numbers, accompanying the early stage of lives; and microbiota established in children shared high similarity as their mother (p-value = 0.0138), supporting the transmission of microbiota from mother to child. (3) Groups harbor group-specific network edges, and network communities, which can potentially serve as biomarkers. For instances, IBD patient group harbors highly abundant communities of Proteobacteria (p-value = 0.0194) and Actinobacteria (p-value = 0.0316); children host highly abundant communities of Proteobacteria (p-value = 2.8785 ) and Actinobacteria (p-value = 0.0015), and the mothers host highly abundant communities of Firmicutes (p-value = 8.0091 ). IBD patient networks contain more HGT edges in pathogenic genus, including Mycobacterium , Sutterella , and Pseudomonas . Children’s networks contain more edges from Bifidobacterium and Escherichia . Conclusion Hence, we proposed the HGT network constructions from the gut microbiota sequencing data. The HGT networks capture the host state and the response of microbiota to the environmental and host changes, and they are essential to understand the human microbiota.

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Evidence of horizontal gene transfer by transposase gene analyses in Fervidobacterium species

Cited by 30 publications

References 30 publications

A comparative analysis of drinking water employing metagenomics

A comparative analysis of drinking water employing metagenomics

Nitric Oxide Accumulation: The Evolutionary Trigger for Phytopathogenesis

Understanding Horizontal Gene Transfer network in human gut microbiota

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