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1.
Environ Sci Pollut Res Int ; 28(1): 1224-1234, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-32839909

RESUMO

Overuse of heavy metal and antibiotics in livestock husbandry has led to the accumulation of heavy metal resistance genes (HMRGs) and antibiotic resistance genes (ARGs) in environment. This research aims to reveal the variation of heavy metal speciation and potential horizontal gene transfer (HGT) of HMRGs and ARGs in manure composting under different initial chlortetracycline (CTC) concentrations. Treatments spiked with 20 mg/kg CTC (treatment P1), 100 mg/kg CTC (treatment P2), and the control (treatment CK) were operated. Results showed that CTC could be completely removed in the thermophilic phase of all the treatments despite of the initial concentrations. Bioavailable Cu in treatments CK, P1, and P2 declined by 14.5%, 27.1%, and 26.7% and bioavailable Zn declined by 15.3%, 29.5%, and 12.1%, respectively, after the composting, respectively. Relative abundance of HMRGs decreased by 6.49 log, 8.88 log, and 5.77 log, respectively, in treatments CK, P1, and P2. Relative abundance of ARGs decreased by 3.37 log, 4.86 log, and 3.32 log, respectively, in treatments CK, P1, and P2. Composting could effectively reduce genes pcoD, pcoA, zntA, tetQ, and tetA, which might locate on the same plasmid. CTC of 100 mg/kg promoted the co-selection of ARGs and HMRGs and increased the potential HGT of gene cusA.


Assuntos
Clortetraciclina , Compostagem , Metais Pesados , Animais , Antibacterianos , Transferência Genética Horizontal , Genes Bacterianos , Esterco , Suínos
2.
Environ Pollut ; 268(Pt B): 115903, 2021 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-33120155

RESUMO

Co-selection of antibiotic resistance genes (ARGs) by heavy metals might facilitate the spread of ARGs in the environments. Cadmium contamination is ubiquitous, while, it remains unknown the extent to which cadmium (Cd2+) impact plasmid-mediated transfer of ARGs in aquatic bacterial communities. In the present study, we found that Cd2+ amendment at sub-inhibitory concentration significantly increased conjugation frequency of RP4 plasmid from Pseudomonas putida KT2442 to a fresh water microbial community by liquid mating method. Cd2+ treatment (1-100 mg/L) significantly increased the cell membrane permeability and antioxidant activities of conjugation mixtures. Amendments of 10 and 100 mg/L Cd2+ significantly enhanced the mRNA expression levels of mating pair formation gene (trbBp) and the DNA transfer and replication gene (trfAp) due to the repression of regulatory genes (korA, korB and trbA). Phylogenetic analysis of transconjugants indicated that Proteobacteria was the dominant recipients and high concentration of Cd2+ treatment resulted in expanded recipient taxa. This study suggested that sub-inhibitory Cd2+ contamination would facilitate plasmid conjugation and contributed to the maintenance and spread of plasmid associated ARGs, and highlighted the urgent need for effective remediation of Cd2+ in aquatic environments.


Assuntos
Conjugação Genética , Microbiota , Cádmio , Água Doce , Transferência Genética Horizontal , Genes Bacterianos , Filogenia , Plasmídeos/genética
3.
Elife ; 92020 12 08.
Artigo em Inglês | MEDLINE | ID: mdl-33289629

RESUMO

Analysis of the smallest known arthropod genome reveals a mechanism for genome reduction that appears to be driven by a specialized ecological interaction with plants.


Assuntos
Evolução Molecular , Transferência Genética Horizontal , Animais , Genoma , Herbivoria , Filogenia
4.
Nat Commun ; 11(1): 6217, 2020 12 04.
Artigo em Inglês | MEDLINE | ID: mdl-33277504

RESUMO

Although the taxonomic composition of the human microbiome varies tremendously across individuals, its gene composition or functional capacity is highly conserved - implying an ecological property known as functional redundancy. Such functional redundancy has been hypothesized to underlie the stability and resilience of the human microbiome, but this hypothesis has never been quantitatively tested. The origin of functional redundancy is still elusive. Here, we investigate the basis for functional redundancy in the human microbiome by analyzing its genomic content network - a bipartite graph that links microbes to the genes in their genomes. We find that this network exhibits several topological features that favor high functional redundancy. Furthermore, we develop a simple genome evolution model to generate genomic content network, finding that moderate selection pressure and high horizontal gene transfer rate are necessary to generate genomic content networks with key topological features that favor high functional redundancy. Finally, we analyze data from two published studies of fecal microbiota transplantation (FMT), finding that high functional redundancy of the recipient's pre-FMT microbiota raises barriers to donor microbiota engraftment. This work elucidates the potential ecological and evolutionary processes that create and maintain functional redundancy in the human microbiome and contribute to its resilience.


Assuntos
Fezes/microbiologia , Microbioma Gastrointestinal/genética , Trato Gastrointestinal/microbiologia , Metagenoma/genética , Metagenômica/métodos , Microbiota/genética , Algoritmos , Bactérias/classificação , Bactérias/genética , Redes Reguladoras de Genes , Transferência Genética Horizontal , Humanos , Modelos Genéticos
5.
PLoS Genet ; 16(11): e1009200, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-33137105

RESUMO

Lateral gene transfer (LGT) has impacted prokaryotic genome evolution, yet the extent to which LGT compromises vertical evolution across individual genes and individual phyla is unknown, as are the factors that govern LGT frequency across genes. Estimating LGT frequency from tree comparisons is problematic when thousands of genomes are compared, because LGT becomes difficult to distinguish from phylogenetic artefacts. Here we report quantitative estimates for verticality across all genes and genomes, leveraging a well-known property of phylogenetic inference: phylogeny works best at the tips of trees. From terminal (tip) phylum level relationships, we calculate the verticality for 19,050,992 genes from 101,422 clusters in 5,655 prokaryotic genomes and rank them by their verticality. Among functional classes, translation, followed by nucleotide and cofactor biosynthesis, and DNA replication and repair are the most vertical. The most vertically evolving lineages are those rich in ecological specialists such as Acidithiobacilli, Chlamydiae, Chlorobi and Methanococcales. Lineages most affected by LGT are the α-, ß-, γ-, and δ- classes of Proteobacteria and the Firmicutes. The 2,587 eukaryotic clusters in our sample having prokaryotic homologues fail to reject eukaryotic monophyly using the likelihood ratio test. The low verticality of α-proteobacterial and cyanobacterial genomes requires only three partners-an archaeal host, a mitochondrial symbiont, and a plastid ancestor-each with mosaic chromosomes, to directly account for the prokaryotic origin of eukaryotic genes. In terms of phylogeny, the 100 most vertically evolving prokaryotic genes are neither representative nor predictive for the remaining 97% of an average genome. In search of factors that govern LGT frequency, we find a simple but natural principle: Verticality correlates strongly with gene distribution density, LGT being least likely for intruding genes that must replace a preexisting homologue in recipient chromosomes. LGT is most likely for novel genetic material, intruding genes that encounter no competing copy.


Assuntos
Archaea/genética , Bactérias/genética , Evolução Molecular , Transferência Genética Horizontal , Genoma Arqueal/genética , Genoma Bacteriano/genética , Filogenia
6.
Nat Commun ; 11(1): 5968, 2020 11 24.
Artigo em Inglês | MEDLINE | ID: mdl-33235212

RESUMO

Escherichia coli is the leading cause of urinary tract infection, one of the most common bacterial infections in humans. Despite this, a genomic perspective is lacking regarding the phylogenetic distribution of isolates associated with different clinical syndromes. Here, we present a large-scale phylogenomic analysis of a spatiotemporally and clinically diverse set of 907 E. coli isolates, including 722 uropathogenic E. coli (UPEC) isolates. A genome-wide association approach identifies the (P-fimbriae-encoding) papGII locus as the key feature distinguishing invasive UPEC, defined as isolates associated with severe UTI, i.e., kidney infection (pyelonephritis) or urinary-source bacteremia, from non-invasive UPEC, defined as isolates associated with asymptomatic bacteriuria or bladder infection (cystitis). Within the E. coli population, distinct invasive UPEC lineages emerged through repeated horizontal acquisition of diverse papGII-containing pathogenicity islands. Our findings elucidate the molecular determinants of severe UTI and have implications for the early detection of this pathogen.


Assuntos
Adesinas de Escherichia coli/genética , Transferência Genética Horizontal/genética , Ilhas Genômicas/genética , Escherichia coli Uropatogênica , DNA Bacteriano/genética , Infecções por Escherichia coli/microbiologia , Fímbrias Bacterianas/genética , Genoma Bacteriano , Estudo de Associação Genômica Ampla , Humanos , Filogenia , Sistema Urinário/microbiologia , Infecções Urinárias/microbiologia , Escherichia coli Uropatogênica/genética , Escherichia coli Uropatogênica/patogenicidade , Fatores de Virulência/genética
7.
Nat Commun ; 11(1): 6064, 2020 11 27.
Artigo em Inglês | MEDLINE | ID: mdl-33247110

RESUMO

By providing broad resistance to environmental biocides, transporters from the small multidrug resistance (SMR) family drive the spread of multidrug resistance cassettes among bacterial populations. A fundamental understanding of substrate selectivity by SMR transporters is needed to identify the types of selective pressures that contribute to this process. Using solid-supported membrane electrophysiology, we find that promiscuous transport of hydrophobic substituted cations is a general feature of SMR transporters. To understand the molecular basis for promiscuity, we solved X-ray crystal structures of a SMR transporter Gdx-Clo in complex with substrates to a maximum resolution of 2.3 Å. These structures confirm the family's extremely rare dual topology architecture and reveal a cleft between two helices that provides accommodation in the membrane for the hydrophobic substituents of transported drug-like cations.


Assuntos
Proteínas de Bactérias/química , Farmacorresistência Bacteriana Múltipla , Proteínas de Membrana Transportadoras/química , Sequência de Aminoácidos , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Transporte Biológico , Cristalografia por Raios X , Escherichia coli/metabolismo , Transferência Genética Horizontal , Guanina/metabolismo , Interações Hidrofóbicas e Hidrofílicas , Proteínas de Membrana Transportadoras/metabolismo , Modelos Moleculares , Riboswitch , Especificidade por Substrato
8.
Proc Natl Acad Sci U S A ; 117(45): 27777-27785, 2020 11 10.
Artigo em Inglês | MEDLINE | ID: mdl-33122438

RESUMO

Articles on CRISPR commonly open with some variant of the phrase "these short palindromic repeats and their associated endonucleases (Cas) are an adaptive immune system that exists to protect bacteria and archaea from viruses and infections with other mobile genetic elements." There is an abundance of genomic data consistent with the hypothesis that CRISPR plays this role in natural populations of bacteria and archaea, and experimental demonstrations with a few species of bacteria and their phage and plasmids show that CRISPR-Cas systems can play this role in vitro. Not at all clear are the ubiquity, magnitude, and nature of the contribution of CRISPR-Cas systems to the ecology and evolution of natural populations of microbes and the strength of selection mediated by different types of phage and plasmids to the evolution and maintenance of CRISPR-Cas systems. In this perspective, with the aid of heuristic mathematical-computer simulation models, we explore the a priori conditions under which exposure to lytic and temperate phage and conjugative plasmids will select for and maintain CRISPR-Cas systems in populations of bacteria and archaea. We review the existing literature addressing these ecological and evolutionary questions and highlight the experimental and other evidence needed to fully understand the conditions responsible for the evolution and maintenance of CRISPR-Cas systems and the contribution of these systems to the ecology and evolution of bacteria, archaea, and the mobile genetic elements that infect them.


Assuntos
Bactérias/genética , Sistemas CRISPR-Cas/fisiologia , Plasmídeos/genética , Archaea/genética , Bacteriófagos/genética , Simulação por Computador , Evolução Molecular , Transferência Genética Horizontal , Sequências Repetitivas Dispersas , Modelos Teóricos , Vírus/genética
9.
C R Biol ; 343(2): 155-176, 2020 Oct 09.
Artigo em Francês | MEDLINE | ID: mdl-33108120

RESUMO

Domestication is the process of organism evolution under selection by humans, and as such has been a model for studying adaptation since Charles Darwin. Here we review recent studies on the genomics of adaptation and domestication syndrome in two cheese-making fungal lineages, Penicillium roqueforti used for maturing blue cheeses, and the Penicillium camemberti species complex used for making soft cheeses such as Camembert and Brie. Comparative genomics have revealed horizontal gene transfers involved in convergent adaptation to cheese. Population genomics have identified differentiated populations with contrasted traits, several populations having independently been domesticated for cheese making in both P. roqueforti and the Penicillium camemberti species complex, and having undergone bottlenecks. The different cheese populations have acquired traits beneficial for cheese making in comparison to non-cheese populations, regarding color, spore production, growth rates on cheese, salt tolerance, lipolysis, proteolysis, volatile compound or toxin production and/or competitive ability. The cheese populations also show degeneration for some unused functions such as decreased ability of sexual reproduction or of growth under harsh conditions. These recent findings have fundamental importance for our understanding of adaptation and have applied interest for strain improvement.


Assuntos
Queijo/microbiologia , Penicillium/genética , Domesticação , Transferência Genética Horizontal , Humanos
10.
Nucleic Acids Res ; 48(19): 10832-10847, 2020 11 04.
Artigo em Inglês | MEDLINE | ID: mdl-33045730

RESUMO

Horizontally acquired genes are typically regulated by ancestral regulators. This regulation enables expression of horizontally acquired genes to be coordinated with that of preexisting genes. Here, we report a singular example of the opposite regulation: a horizontally acquired gene that controls an ancestral regulator, thereby promoting bacterial virulence. We establish that the horizontally acquired regulatory gene ssrB is necessary to activate the ancestral regulatory system PhoP/PhoQ of Salmonella enterica serovar Typhimurium (S. Typhimurium) in mildly acidic pH, which S. Typhimurium experiences inside macrophages. SsrB promotes phoP transcription by binding upstream of the phoP promoter. SsrB also increases ugtL transcription by binding to the ugtL promoter region, where it overcomes gene silencing by the heat-stable nucleoid structuring protein H-NS, enhancing virulence. The largely non-pathogenic species S. bongori failed to activate PhoP/PhoQ in mildly acidic pH because it lacks both the ssrB gene and the SsrB binding site in the target promoter. Low Mg2+ activated PhoP/PhoQ in both S. bongori and ssrB-lacking S. Typhimurium, indicating that the SsrB requirement for PhoP/PhoQ activation is signal-dependent. By controlling the ancestral genome, horizontally acquired genes are responsible for more crucial abilities, including virulence, than currently thought.


Assuntos
Proteínas de Bactérias/genética , Transferência Genética Horizontal , Proteínas de Membrana/genética , Salmonella typhimurium/genética , Fatores de Transcrição/genética , Animais , Proteínas de Bactérias/metabolismo , Linhagem Celular , Evolução Molecular , Feminino , Regulação Bacteriana da Expressão Gênica , Proteínas de Membrana/metabolismo , Camundongos , Camundongos Endogâmicos BALB C , Regiões Promotoras Genéticas , Salmonella typhimurium/patogenicidade , Fatores de Transcrição/metabolismo , Ativação Transcricional , Virulência/genética
11.
Nat Commun ; 11(1): 5235, 2020 10 16.
Artigo em Inglês | MEDLINE | ID: mdl-33067437

RESUMO

Wolbachia is an iconic example of a successful intracellular bacterium. Despite its importance as a manipulator of invertebrate biology, its evolutionary dynamics have been poorly studied from a genomic viewpoint. To expand the number of Wolbachia genomes, we screen over 30,000 publicly available shotgun DNA sequencing samples from 500 hosts. By assembling over 1000 Wolbachia genomes, we provide a substantial increase in host representation. Our phylogenies based on both core-genome and gene content provide a robust reference for future studies, support new strains in model organisms, and reveal recent horizontal transfers amongst distantly related hosts. We find various instances of gene function gains and losses in different super-groups and in cytoplasmic incompatibility inducing strains. Our Wolbachia-host co-phylogenies indicate that horizontal transmission is widespread at the host intraspecific level and that there is no support for a general Wolbachia-mitochondrial synchronous divergence.


Assuntos
Genoma Bacteriano , Wolbachia/genética , Evolução Molecular , Transferência Genética Horizontal , Especificidade de Hospedeiro , Filogenia , Wolbachia/classificação , Wolbachia/fisiologia
12.
Nat Commun ; 11(1): 5494, 2020 10 30.
Artigo em Inglês | MEDLINE | ID: mdl-33127895

RESUMO

Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organisms in the nitrogen cycle, but the mechanisms driving their radiation into diverse ecosystems remain underexplored. Here, existing thaumarchaeotal genomes are complemented with 12 genomes belonging to the previously under-sampled Nitrososphaerales to investigate the impact of lateral gene transfer (LGT), gene duplication and loss across thaumarchaeotal evolution. We reveal a major role for gene duplication in driving genome expansion subsequent to early LGT. In particular, two large LGT events are identified into Nitrososphaerales and the fate of these gene families is highly lineage-specific, being lost in some descendant lineages, but undergoing extensive duplication in others, suggesting niche-specific roles. Notably, some genes involved in carbohydrate transport or coenzyme metabolism were duplicated, likely facilitating niche specialisation in soils and sediments. Overall, our results suggest that LGT followed by gene duplication drives Nitrososphaerales evolution, highlighting a previously under-appreciated mechanism of genome expansion in archaea.


Assuntos
Archaea/classificação , Archaea/genética , Duplicação Gênica , Genoma Arqueal , Filogenia , Archaea/metabolismo , Ecossistema , Evolução Molecular , Transferência Genética Horizontal , Metagenômica , Proteoma
13.
Nat Commun ; 11(1): 5490, 2020 10 30.
Artigo em Inglês | MEDLINE | ID: mdl-33127909

RESUMO

Halobacteria (henceforth: Haloarchaea) are predominantly aerobic halophiles that are thought to have evolved from anaerobic methanogens. This remarkable transformation most likely involved an extensive influx of bacterial genes. Whether it entailed a single massive transfer event or a gradual stream of transfers remains a matter of debate. To address this, genomes that descend from methanogen-to-halophile intermediates are necessary. Here, we present five such near-complete genomes of Marine Group IV archaea (Hikarchaeia), the closest known relatives of Haloarchaea. Their inclusion in gene tree-aware ancestral reconstructions reveals an intermediate stage that had already lost a large number of genes, including nearly all of those involved in methanogenesis and the Wood-Ljungdahl pathway. In contrast, the last Haloarchaea common ancestor gained a large number of genes and expanded its aerobic respiration and salt/UV resistance gene repertoire. Our results suggest that complex and gradual patterns of gain and loss shaped the methanogen-to-halophile transition.


Assuntos
Archaea/classificação , Archaea/genética , Euryarchaeota/genética , Genoma Arqueal , Filogenia , Archaea/metabolismo , Proteínas Arqueais/metabolismo , Euryarchaeota/classificação , Euryarchaeota/metabolismo , Evolução Molecular , Transferência Genética Horizontal , Genes Bacterianos , Metagenômica , Metano/metabolismo , Família Multigênica , RNA Ribossômico 16S/genética
14.
PLoS One ; 15(10): e0241058, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33104745

RESUMO

Many epidemiological studies provide us with the evidence of horizontal gene transfer (HGT) contributing to the bacterial genomic diversity that benefits the bacterial populations with increased ability to adapt to the dynamic environments. Campylobacter jejuni, a major cause of acute enteritis in the U.S., often linked with severe post-infection neuropathies, has been reported to exhibit a non-clonal population structure and comparatively higher strain-level genetic variation. In this study, we provide evidence of the HGT of chromosomally encoded genetic markers between C. jejuni cells in the biphasic MH medium. We used two C. jejuni NCTC-11168 mutants harbouring distinct antibiotic-resistance genes [chloramphenicol (Cm) and kanamycin (Km)] present at two different neutral genomic loci. Cultures of both marker strains were mixed together and incubated for 5 hrs, then plated on MH agar plates supplemented with both antibiotics. The recombinant cells with double antibiotic markers were generated at the frequency of 0.02811 ± 0.0035% of the parental strains. PCR assays using locus-specific primers confirmed that transfer of the antibiotic-resistance genes was through homologous recombination. Also, the addition of chicken cecal content increased the recombination efficiency approximately up to 10-fold as compared to the biphasic MH medium (control) at P < 0.05. Furthermore, treating the co-culture with DNase I decreased the available DNA, which in turn significantly reduced recombination efficiency by 99.92% (P < 0.05). We used the cell-free supernatant of 16 hrs-culture of Wild-type C. jejuni as a template for PCR and found DNA sequences from six different genomic regions were easily amplified, indicating the presence of released chromosomal DNA in the culture supernatant. Our findings suggest that HGT in C. jejuni is facilitated in the chicken gut environment contributing to in vivo genomic diversity. Additionally, C. jejuni might have an active mechanism to release its chromosomal DNA into the extracellular environment, further expediting HGT in C. jejuni populations.


Assuntos
Campylobacter jejuni/genética , Resistência ao Cloranfenicol/genética , Transferência Genética Horizontal , Resistência a Canamicina/genética , Animais , Infecções por Campylobacter/microbiologia , Galinhas , DNA Bacteriano , Marcadores Genéticos , Genoma Bacteriano , Recombinação Homóloga
15.
Proc Natl Acad Sci U S A ; 117(43): 26868-26875, 2020 10 27.
Artigo em Inglês | MEDLINE | ID: mdl-33055207

RESUMO

Horizontal gene transfer (HGT) confers the rapid acquisition of novel traits and is pervasive throughout microbial evolution. Despite the central role of HGT, the evolutionary forces that drive the dynamics of HGT alleles in evolving populations are poorly understood. Here, we show that HGT alters the evolutionary dynamics of genetic variation, so that deleterious genetic variants, including antibiotic resistance genes, can establish in populations without selection. We evolve antibiotic-sensitive populations of the human pathogen Helicobacter pylori in an environment without antibiotic but with HGT from an antibiotic-resistant isolate of H. pylori We find that HGT increases the rate of adaptation, with most horizontally transferred genetic variants establishing at a low frequency in the population. When challenged with antibiotic, this low-level variation potentiates adaptation, with HGT populations flourishing in conditions where nonpotentiated populations go extinct. By extending previous models of evolution under HGT, we evaluated the conditions for the establishment and spread of HGT-acquired alleles into recipient populations. We then used our model to estimate parameters of HGT and selection from our experimental evolution data. Together, our findings show how HGT can act as an evolutionary force that facilitates the spread of nonselected genetic variation and expands the adaptive potential of microbial populations.


Assuntos
Adaptação Fisiológica/genética , Evolução Biológica , Farmacorresistência Bacteriana/genética , Transferência Genética Horizontal , Helicobacter pylori/genética , Antibacterianos , Fluxo Gênico , Aptidão Genética , Variação Genética , Metronidazol , Seleção Genética
16.
Huan Jing Ke Xue ; 41(8): 3748-3757, 2020 Aug 08.
Artigo em Chinês | MEDLINE | ID: mdl-33124350

RESUMO

In order to explore the conjugation of genes encoding extended-spectrum ß-lactamase (ESBL), ESBL-expressing P. aeruginosa and E.coli strains isolated from the wastewater of major hospitals in Singapore were used as donors. gfp-tagged E.coli SCC1 strains resistant to chloramphenicol (CHL) were chosen as recipients. Using response surface analysis, we detected and analyzed the induction of conjugal transfer under single-exposure and co-exposure of tetracycline (TC), sulfamethoxazole (SMZ), and ceftazidime (CAZ) at sublethal concentrations. It was found that the ESBL plasmid could be conjugal transferred from P. aeruginosa and E.coli strains to the recipient E.coli SCC1 strains at an average frequency of 0.0015 and 0.0042, respectively, without stress from inducing antibiotics, thus showing a low fitness cost and higher conjugal frequency between E.coli strains under the exposure of sub-MIC antibiotics. A significant conjugation between E.coli strains occurred under the single-exposure or co-exposure of a TC concentration of <0.03 mg·L-1 and a CAZ concentration of <0.002 mg·L-1, as inhibited by a sub-MIC level of TC. The conjugation between P. aeruginosa and E.coli strains was stimulated under the exposure of TC and CAZ with concentrations 5-times larger than the MIC, while no significant induction was detected from the sub-MIC antibiotics.


Assuntos
Antibacterianos , Transferência Genética Horizontal , Antibacterianos/toxicidade , Ceftazidima , Escherichia coli/genética , Plasmídeos/genética , beta-Lactamases/genética
18.
Nat Commun ; 11(1): 4506, 2020 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-32908149

RESUMO

Bacteriophages play critical roles in the biosphere, but their vast genomic diversity has obscured their evolutionary origins, and phylogenetic analyses have traditionally been hindered by their lack of universal phylogenetic marker genes. In this study we mine metagenomic data and identify a clade of Caudovirales that encodes the ß and ß' subunits of multi-subunit RNA polymerase (RNAP), a high-resolution phylogenetic marker which enables detailed evolutionary analyses. Our RNAP phylogeny revealed that the Caudovirales RNAP forms a clade distinct from cellular homologs, suggesting an ancient acquisition of this enzyme. Within these multimeric RNAP-encoding Caudovirales (mReC), we find that the similarity of major capsid proteins and terminase large subunits further suggests they form a distinct clade with common evolutionary origin. Our study characterizes a clade of RNAP-encoding Caudovirales and suggests the ancient origin of this enzyme in this group, underscoring the important role of viruses in the early evolution of life on Earth.


Assuntos
Evolução Biológica , Caudovirales/genética , RNA Polimerases Dirigidas por DNA/genética , Subunidades Proteicas/genética , Proteínas Virais/genética , DNA Viral/genética , Conjuntos de Dados como Assunto , Transferência Genética Horizontal , Metagenômica , Filogenia , Análise de Sequência de DNA
19.
Nat Commun ; 11(1): 4379, 2020 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-32873785

RESUMO

The gut microbiome harbors a 'silent reservoir' of antibiotic resistance (AR) genes that is thought to contribute to the emergence of multidrug-resistant pathogens through horizontal gene transfer (HGT). To counteract the spread of AR, it is paramount to know which organisms harbor mobile AR genes and which organisms engage in HGT. Despite methods that characterize the overall abundance of AR genes in the gut, technological limitations of short-read sequencing have precluded linking bacterial taxa to specific mobile genetic elements (MGEs) encoding AR genes. Here, we apply Hi-C, a high-throughput, culture-independent method, to surveil the bacterial carriage of MGEs. We compare two healthy individuals with seven neutropenic patients undergoing hematopoietic stem cell transplantation, who receive multiple courses of antibiotics, and are acutely vulnerable to the threat of multidrug-resistant infections. We find distinct networks of HGT across individuals, though AR and mobile genes are associated with more diverse taxa within the neutropenic patients than the healthy subjects. Our data further suggest that HGT occurs frequently over a several-week period in both cohorts. Whereas most efforts to understand the spread of AR genes have focused on pathogenic species, our findings shed light on the role of the human gut microbiome in this process.


Assuntos
Antibacterianos/farmacologia , Farmacorresistência Bacteriana/genética , Microbioma Gastrointestinal/genética , Transferência Genética Horizontal , Genes Bacterianos/efeitos dos fármacos , Adulto , Idoso , Antibacterianos/uso terapêutico , DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , Microbioma Gastrointestinal/efeitos dos fármacos , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Sequências Repetitivas Dispersas/efeitos dos fármacos , Pessoa de Meia-Idade
20.
Nat Commun ; 11(1): 4403, 2020 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-32879312

RESUMO

Bacteriophage genomes rapidly evolve via mutation and horizontal gene transfer to counter evolving bacterial host defenses; such arms race dynamics should lead to divergence between phages from similar, geographically isolated ecosystems. However, near-identical phage genomes can reoccur over large geographical distances and several years apart, conversely suggesting many are stably maintained. Here, we show that phages with near-identical core genomes in distant, discrete aquatic ecosystems maintain diversity by possession of numerous flexible gene modules, where homologous genes present in the pan-genome interchange to create new phage variants. By repeatedly reconstructing the core and flexible regions of phage genomes from different metagenomes, we show a pool of homologous gene variants co-exist for each module in each location, however, the dominant variant shuffles independently in each module. These results suggest that in a natural community, recombination is the largest contributor to phage diversity, allowing a variety of host recognition receptors and genes to counter bacterial defenses to co-exist for each phage.


Assuntos
Bacteriófagos/genética , Camada de Gelo/virologia , Metagenoma , Cianobactérias/virologia , Ecossistema , Transferência Genética Horizontal , Genes Virais , Genoma Viral , Interações entre Hospedeiro e Microrganismos/genética , Camada de Gelo/microbiologia , Metagenômica , Filogenia
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