scholarly journals HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4015 ◽  
Author(s):  
Weizhi Song ◽  
Kerrin Steensen ◽  
Torsten Thomas
Keyword(s):  
Microbial Community ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Microbial Communities ◽  
Metagenomic Data ◽  
Community Members ◽  
Data Simulation ◽  
Simulation Tools ◽  
Link Type

The development and application of metagenomic approaches have provided an opportunity to study and define horizontal gene transfer (HGT) on the level of microbial communities. However, no current metagenomic data simulation tools offers the option to introduce defined HGT within a microbial community. Here, we present HgtSIM, a pipeline to simulate HGT event among microbial community members with user-defined mutation levels. It was developed for testing and benchmarking pipelines for recovering HGTs from complex microbial datasets. HgtSIM is implemented in Python3 and is freely available at: https://github.com/songweizhi/HgtSIM.

Microbial communities and their interactions in biofilm systems: an overview

2004 ◽  
Vol 49 (11-12) ◽  
pp. 327-336 ◽  
Author(s):  
S. Wuertz ◽  
S. Okabe ◽  
M. Hausner
Keyword(s):  
Microbial Community ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Microbial Communities ◽  
Enrichment Culture ◽  
Community Analysis ◽  
Microbial Populations ◽  
Community Members ◽  
Biofilm Architecture

Several important advances have been made in the study of biofilm microbial populations relating to their spatial structure (or architecture), their community structure, and their dependence on physicochemical parameters. With the knowledge that hydrodynamic forces influence biofilm architecture came the realization that metabolic processes may be enhanced if certain spatial structures can be forced. An example is the extent of plasmid-mediated horizontal gene transfer in biofilms. Recent in situ work in defined model systems has shown that the biofilm architecture plays a role for genetic transfer by bacterial conjugation in determining how far the donor cells can penetrate the biofilm. Open channels and pores allow for more efficient donor transport and hence more frequent cell collisions leading to rapid spread of the genes by horizontal gene transfer. Such insight into the physical environment of biofilms can be utilized for bioenhancement of catabolic processes by introduction of mobile genetic elements into an existing microbial community. If the donor organisms themselves persist, bioaugmentation can lead to successful establishment of newly introduced species and may be a more successful strategy than biostimulation (the addition of nutrients or specific carbon sources to stimulate the authochthonous population) as shown for an enrichment culture of nitrifying bacteria added to rotating disk biofilm reactors using fluorescent in situ hybridization (FISH) and microelectrode measurements of NH4+, NO2-, NO3-, and O2. However, few studies have been carried out on full-scale systems. Bioaugmentation and bioenhancement are most successful if a constant selective pressure can be maintained favoring the promulgation of the added enrichment culture. Overall, knowledge gain about microbial community interactions in biofilms continues to be driven by the availability of methods for the rapid analysis of microbial communities and their activities. Molecular tools can be grouped into those suitable for ex situ and in situ community analysis. Non-spatial community analysis, in the sense of assessing changes in microbial populations as a function of time or environmental conditions, relies on general fingerprinting methods, like DGGE and T-RFLP, performed on nucleic acids extracted from biofilm. These approaches have been most useful when combined with gene amplification, cloning and sequencing to assemble a phylogenetic inventory of microbial species. It is expected that the use of oligonucleotide microarrays will greatly facilitate the analysis of microbial communities and their activities in biofilms. Structure-activity relationships can be explored using incorporation of 13C-labeled substrates into microbial DNA and RNA to identify metabolically active community members. Finally, based on the DNA sequences in a biofilm, FISH probes can be designed to verify the abundance and spatial location of microbial community members. This in turn allows for in situ structure/function analysis when FISH is combined with microsensors, microautoradiography, and confocal laser scanning microscopy with advanced image analysis.

scholarly journals Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Vanessa L. Brisson ◽  
Jennifer E. Schmidt ◽  
Trent R. Northen ◽  
John P. Vogel ◽  
Amélie C. M. Gaudin
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Microbial Community Analysis ◽  
Agricultural System ◽  
Community Members ◽  
Genetic Groups ◽  
Maize Domestication ◽  
Rhizosphere Microbial Community

Abstract Maize domestication and breeding have resulted in drastic and well documented changes in aboveground traits, but belowground effects on root system functioning and rhizosphere microbial communities remain poorly understood, despite their critical importance for nutrient and water acquisition. We investigated the rhizosphere microbial community composition and structure of ten Zea mays accessions along an evolutionary transect (two teosinte, three inbred maize lines, and five modern maize hybrids) grown in nutrient depleted soil from a low input agricultural system. Microbial community analysis revealed significant differences in community composition between soil compartments (proximal vs. distal rhizosphere) and between plant genetic groups (teosinte, inbred, and modern hybrid). Only a small portion of the microbial community was differentially selected across plant genetic groups: 3.7% of prokaryotic community members and 4.9% of fungal community members were significantly associated with a specific plant genetic group. Indicator species analysis showed the greatest differentiation between modern hybrids and the other two plant genetic groups. Co-occurrence network analysis revealed that microbial co-occurrence patterns of the inbred maize lines’ rhizosphere were significantly more similar to those of the teosintes than to the modern hybrids. Our results suggest that advances in hybrid development significantly impacted rhizosphere microbial communities and network assembly.

scholarly journals Variability in Assembly of Degradation Operons for Naphthalene and its derivative, Carbaryl, Suggests Mobilization through Horizontal Gene Transfer

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 569 ◽  
Author(s):  
Phale ◽  
Shah ◽  
Malhotra
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Food Web ◽  
Microbial Communities ◽  
Metabolic Pathways ◽  
Anthropogenic Activities ◽  
Genetic Material ◽  
Genomic Islands ◽  
Biochemical Pathways ◽  
Integrative Conjugative Elements

In the biosphere, the largest biological laboratory, increased anthropogenic activities have led microbes to evolve and adapt to the changes occurring in the environment. Compounds, specifically xenobiotics, released due to such activities persist in nature and undergo bio-magnification in the food web. Some of these compounds act as potent endocrine disrupters, mutagens or carcinogens, and therefore their removal from the environment is essential. Due to their persistence, microbial communities have evolved to metabolize them partially or completely. Diverse biochemical pathways have evolved or been assembled by exchange of genetic material (horizontal gene transfer) through various mobile genetic elements like conjugative and non-conjugative plasmids, transposons, phages and prophages, genomic islands and integrative conjugative elements. These elements provide an unlimited opportunity for genetic material to be exchanged across various genera, thus accelerating the evolution of a new xenobiotic degrading phenotype. In this article, we illustrate examples of the assembly of metabolic pathways involved in the degradation of naphthalene and its derivative, Carbaryl, which are speculated to have evolved or adapted through the above-mentioned processes.

scholarly journals Horizontal Gene Transfer Can Help Maintain the Equilibrium of Microbial Communities

2017 ◽  
Author(s):  
Yuhang Fan ◽  
Yandong Xiao ◽  
Babak Momeni ◽  
Yang-Yu Liu
Keyword(s):  
Population Dynamics ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Microbial Communities ◽  
Transfer Rate ◽  
Species Coexistence ◽  
Focal Points ◽  
Dynamics Model ◽  
Population Dynamics Model ◽  
Evolutionary Advantage

Horizontal gene transfer and species coexistence are two focal points in the study of microbial communities. The evolutionary advantage of horizontal gene transfer has not been well-understood and is constantly being debated. Here we propose a simple population dynamics model based on the frequency-dependent interactions between different genotypes to evaluate the influence of horizontal gene transfer on microbial communities. We find that both structural stability and robustness of the microbial community are strongly affected by the gene transfer rate and direction. An optimal gene flux can stablize the ecosystem, helping it recover from disturbance and maintain the species coexistence.

scholarly journals Diverse Viruses in Deep-Sea Hydrothermal Vent Fluids Have Restricted Dispersal across Ocean Basins

mSystems ◽  
2021 ◽  
Author(s):  
Elaina Thomas ◽  
Rika E. Anderson ◽  
Viola Li ◽  
L. Jenni Rogan ◽  
Julie A. Huber
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Microbial Communities ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Viral Ecology ◽  
Unique Nature

Viruses play important roles in manipulating microbial communities and their evolution in the ocean, yet not much is known about viruses in deep-sea hydrothermal vents. However, viral ecology and evolution are of particular interest in hydrothermal vent habitats because of their unique nature: previous studies have indicated that most viruses in hydrothermal vents are temperate rather than lytic, and it has been established that rates of horizontal gene transfer (HGT) are particularly high among thermophilic vent microbes, and viruses are common vectors for HGT.

scholarly journals Cohesiveness in microbial community coalescence

2018 ◽  
Author(s):  
Nanxi Lu ◽  
Alicia Sanchez-Gorostiaga ◽  
Mikhail Tikhonov ◽  
Alvaro Sanchez
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Empirical Work ◽  
Invasion Success ◽  
Community Members ◽  
Interacting Species ◽  
Resource Interactions ◽  
Different Origins ◽  
Microbial Community Assembly ◽  
Selection Of

AbstractMicrobial invasions exhibit many unique properties; notably, entire microbial communities often invade one another, a phenomenon known as community coalescence. In spite of the potential importance of this process for the dynamics and stability of microbiome assembly, our understanding of it is still very limited. Recent theoretical and empirical work has proposed that large microbial communities may exhibit an emergent cohesiveness, as a result of collective consumer-resource interactions and metabolic feedbacks between microbial growth and the environment. A fundamental prediction of this proposal is the presence of ecological co-selection during community coalescence, where the invasion success of a given taxon is determined by its community members. To establish the generality of this prediction in experimental microbiomes, we have performed over one hundred invasion and coalescence experiments with environmental communities of different origins that had spontaneously and stably assembled in two different synthetic aerobic environments. We show that the dominant species of the coalesced communities can both recruit their community members (top-down co-selection) and be recruited by them (bottom-up co-selection) into the coalesced communities. Our results provide direct evidence that collective invasions generically produce ecological co-selection of interacting species, emphasizing the importance of community-level interactions during microbial community assembly.

scholarly journals Horizontal Gene Transfer of Antibiotic Resistance from Acinetobacter baylyi to Escherichia coli on Lettuce and Subsequent Antibiotic Resistance Transmission to the Gut Microbiome

mSphere ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Marlène Maeusli ◽  
Bosul Lee ◽  
Sarah Miller ◽  
Zeferino Reyna ◽  
Peggy Lu ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Resistance Genes ◽  
Gut Microbiome ◽  
Acinetobacter Baylyi ◽  
Antibiotic Resistant ◽  
Content Type ◽  
Plant Foods ◽  
Link Type

ABSTRACT Agricultural use of antibiotics is recognized by the U.S. Centers for Disease Control and Prevention as a major contributor to antibiotic-resistant infections. While most One Health attention has been on the potential for antibiotic resistance transmission from livestock and contaminated meat products to people, plant foods are fundamental to the food chain for meat eaters and vegetarians alike. We hypothesized that environmental bacteria that colonize plant foods may serve as platforms for the persistence of antibiotic-resistant bacteria and for horizontal gene transfer of antibiotic-resistant genes. Donor Acinetobacter baylyi and recipient Escherichia coli were cocultured in vitro, in planta on lettuce, and in vivo in BALB/c mice. We showed that nonpathogenic, environmental A. baylyi is capable of transferring plasmids conferring antibiotic resistance to E. coli clinical isolates on lettuce leaf discs. Furthermore, transformant E. coli from the in planta assay could then colonize the mouse gut microbiome. The target antibiotic resistance plasmid was identified in mouse feces up to 5 days postinfection. We specifically identified in vivo transfer of the plasmid to resident Klebsiella pneumoniae in the mouse gut. Our findings highlight the potential for environmental bacteria exposed to antibiotics to transmit resistance genes to mammalian pathogens during ingestion of leafy greens. IMPORTANCE Previous efforts have correlated antibiotic-fed livestock and meat products with respective antibiotic resistance genes, but virtually no research has been conducted on the transmission of antibiotic resistance from plant foods to the mammalian gut (C. S. Hölzel, J. L. Tetens, and K. Schwaiger, Pathog Dis 15:671–688, 2018, https://doi.org/10.1089/fpd.2018.2501; C. M. Liu et al., mBio 9:e00470-19, 2018, https://doi.org/10.1128/mBio.00470-18; B. Spellberg et al., NAM Perspectives, 2016, https://doi.org/10.31478/201606d; J. O’Neill, Antimicrobials in agriculture and the environment, 2015; Centers for Disease Control and Prevention, Antibiotic resistance threats in the United States, 2019). Here, we sought to determine if horizontal transmission of antibiotic resistance genes can occur between lettuce and the mammalian gut microbiome, using a mouse model. Furthermore, we have created a new model to study horizontal gene transfer on lettuce leaves using an antibiotic-resistant transformant of A. baylyi (AbzeoR).

Genetic relatedness of Streptococcus dysgalactiae isolates causing recurrent bacteraemia

2021 ◽  
Author(s):  
Erik Senneby ◽  
Björn Hallström ◽  
Magnus Rasmussen
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Trees ◽  
Genetic Relatedness ◽  
Sequence Similarity ◽  
Streptococcus Dysgalactiae ◽  
High Sequence Similarity ◽  
Content Type ◽  
Link Type ◽  
Clonal Origin

Introduction. Streptococcus dysgalactiae subspecies equisimilis (SDSE) is becoming increasingly recognized as an important human pathogen. Recurrent bacteremia with SDSE has been described previously. Aim. The aims of the study were to establish the genetic relatedness of SDSE isolates with emm-type stG643 that had caused recurrent bacteraemia in three patients and to search for signs of horizontal gene transfer of the emm gene in a collection of SDSE stG643 genomes. Hypothesis. Recurring SDSE bacteremia is caused by the same clone in one patient. Methodology. Whole genome sequencing of 22 clinical SDSE stG643 isolates was performed, including three paired blood culture isolates and sixteen isolates from various sites. All assemblies were aligned to a reference assembly and SNPs were extracted. A total of 53 SDSE genomes were downloaded from GenBank. Two phylogenetic trees, including all 75 SDSE isolates, were created. One tree was based on the emm gene only and one tree was based on all variable positions in the genomes. Results. The genomes from the three pairs of SDSE isolates showed high sequence similarity (1–17 SNPs difference between the pairs), whereas the median SNP difference between the 22 isolates in our collection was 1694 (range 1–11257). The paired isolates were retrieved with 7–53 months between episodes. The 22 SDSE isolates from our collection formed a cluster in the phylogenetic tree based on the emm gene, while they were more scattered in the tree based on all variable positions. Conclusions. Our results show that the paired isolates were of the same clonal origin, which in turn supports carriage between bacteraemia episodes. The phylogenetic analysis indicates that horizontal gene transfer of the emm-gene between some of the SDSE isolates has occurred.

scholarly journals Quantitative Metagenomic Analyses Based on Average Genome Size Normalization

2011 ◽  
Vol 77 (7) ◽  
pp. 2513-2521 ◽  
Author(s):  
Jeremy A. Frank ◽  
Søren J. Sørensen
Keyword(s):  
Microbial Communities ◽  
Genome Size ◽  
Metagenomic Data ◽  
Gene Copy ◽  
Rrna Gene ◽  
Sequence Information ◽  
Ssu Rrna ◽  
Community Members ◽  
Ssu Rrna Gene ◽  
Photosynthetic Carbon

ABSTRACTOver the past quarter-century, microbiologists have used DNA sequence information to aid in the characterization of microbial communities. During the last decade, this has expanded from single genes to microbial community genomics, or metagenomics, in which the gene content of an environment can provide not just a census of the community members but direct information on metabolic capabilities and potential interactions among community members. Here we introduce a method for the quantitative characterization and comparison of microbial communities based on the normalization of metagenomic data by estimating average genome sizes. This normalization can relieve comparative biases introduced by differences in community structure, number of sequencing reads, and sequencing read lengths between different metagenomes. We demonstrate the utility of this approach by comparing metagenomes from two different marine sources using both conventional small-subunit (SSU) rRNA gene analyses and our quantitative method to calculate the proportion of genomes in each sample that are capable of a particular metabolic trait. With both environments, to determine what proportion of each community they make up and how differences in environment affect their abundances, we characterize three different types of autotrophic organisms: aerobic, photosynthetic carbon fixers (theCyanobacteria); anaerobic, photosynthetic carbon fixers (theChlorobi); and anaerobic, nonphotosynthetic carbon fixers (theDesulfobacteraceae). These analyses demonstrate how genome proportionality compares to SSU rRNA gene relative abundance and how factors such as average genome size and SSU rRNA gene copy number affect sampling probability and therefore both types of community analysis.

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