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1.
Front Cell Infect Microbiol ; 11: 641920, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33816347

RESUMEN

Pseudomonas aeruginosa is a biofilm-forming opportunistic pathogen which causes chronic infections in immunocompromised patients and leads to high mortality rate. It is identified as a common coinfecting pathogen in COVID-19 patients causing exacerbation of illness. In our hospital, P. aeruginosa is one of the top coinfecting bacteria identified among COVID-19 patients. We collected a strong biofilm-forming P. aeruginosa strain displaying small colony variant morphology from a severe COVID-19 patient. Genomic and transcriptomic sequencing analyses were performed with phenotypic validation to investigate its adaptation in SARS-CoV-2 infected environment. Genomic characterization predicted specific genomic islands highly associated with virulence, transcriptional regulation, and DNA restriction-modification systems. Epigenetic analysis revealed a specific N6-methyl adenine (m6A) methylating pattern including methylation of alginate, flagellar and quorum sensing associated genes. Differential gene expression analysis indicated that this isolate formed excessive biofilm by reducing flagellar formation (7.4 to 1,624.1 folds) and overproducing extracellular matrix components including CdrA (4.4 folds), alginate (5.2 to 29.1 folds) and Pel (4.8-5.5 folds). In summary, we demonstrated that P. aeuginosa clinical isolates with novel epigenetic markers could form excessive biofilm, which might enhance its antibiotic resistance and in vivo colonization in COVID-19 patients.


Asunto(s)
Adaptación Fisiológica/fisiología , Coinfección/complicaciones , Infecciones por Pseudomonas/complicaciones , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/metabolismo , Adhesinas Bacterianas/genética , Adhesinas Bacterianas/metabolismo , Alginatos , Bacterias , Biopelículas/crecimiento & desarrollo , Metilación de ADN , Epigenómica , Perfilación de la Expresión Génica , Regulación Bacteriana de la Expresión Génica , Genoma Bacteriano , Humanos , Infecciones por Pseudomonas/inmunología , Infecciones por Pseudomonas/microbiología , Pseudomonas aeruginosa/clasificación , Percepción de Quorum/genética , Transcriptoma , Virulencia
2.
Artículo en Inglés | MEDLINE | ID: mdl-33881979

RESUMEN

The genera Catabacter (family 'Catabacteraceae') and Christensenella (family Christensenellaceae) are close relatives within the phylum Firmicutes. Members of these genera are strictly anaerobic, non-spore-forming and short straight rods with diverse phenotypes. Phylogenetic analysis of 16S rRNA genes suggest that Catabacter splits Christensenella into a polyphyletic clade. In an effort to ensure that family/genus names represent monophyletic clades, we performed a whole-genome based analysis of the genomes available for the cultured representatives of these genera: four species of Christensenella and two strains of Catabacter hongkongensis. A concatenated alignment of 135 shared protein sequences of single-copy core genes present in the included strains indicates that C. hongkongensis is indeed nested within the Christensenella clade. Based on their evolutionary relationship, we propose the transfer of Catabacter hongkongensis to the genus Christensenella as Christensenella hongkongensis comb. nov.


Asunto(s)
Clostridiales/clasificación , Genoma Bacteriano , Filogenia , Técnicas de Tipificación Bacteriana , Bacilos Grampositivos/clasificación
3.
Artículo en Inglés | MEDLINE | ID: mdl-33881982

RESUMEN

The draft genome sequences of five species of named phototrophic heliobacteria in the order Clostridiales were determined. Whole genome phylogenetic and average nucleotide identity comparison for the heliobacteria suggests that Heliobacterium chlorum and Heliobacillus mobilis are closely related to one another and belong to the same genus. The three species Heliobacterium modesticaldum, Heliobacterium undosum and Heliobacterium gestii all belong in the same genus, but are more divergent from Hbt. chlorum and belong in a separate genus, which we suggest to be called Heliomicrobium. Heliorestis convoluta is properly recognized to be in the same genus as Heliorestis acidaminivorans. Heliophilum fasciatum is clearly unlike any other and rightfully belongs in a separate genus.


Asunto(s)
Clostridiales/clasificación , Filogenia , Genoma Bacteriano
4.
Proc Natl Acad Sci U S A ; 118(18)2021 05 04.
Artículo en Inglés | MEDLINE | ID: mdl-33858942

RESUMEN

As the coronavirus disease 2019 (COVID-19) pandemic rages on, it is important to explore new evolution-resistant vaccine antigens and new vaccine platforms that can produce readily scalable, inexpensive vaccines with easier storage and transport. We report here a synthetic biology-based vaccine platform that employs an expression vector with an inducible gram-negative autotransporter to express vaccine antigens on the surface of genome-reduced bacteria to enhance interaction of vaccine antigen with the immune system. As a proof-of-principle, we utilized genome-reduced Escherichia coli to express SARS-CoV-2 and porcine epidemic diarrhea virus (PEDV) fusion peptide (FP) on the cell surface, and evaluated their use as killed whole-cell vaccines. The FP sequence is highly conserved across coronaviruses; the six FP core amino acid residues, along with the four adjacent residues upstream and the three residues downstream from the core, are identical between SARS-CoV-2 and PEDV. We tested the efficacy of PEDV FP and SARS-CoV-2 FP vaccines in a PEDV challenge pig model. We demonstrated that both vaccines induced potent anamnestic responses upon virus challenge, potentiated interferon-γ responses, reduced viral RNA loads in jejunum tissue, and provided significant protection against clinical disease. However, neither vaccines elicited sterilizing immunity. Since SARS-CoV-2 FP and PEDV FP vaccines provided similar clinical protection, the coronavirus FP could be a target for a broadly protective vaccine using any platform. Importantly, the genome-reduced bacterial surface-expressed vaccine platform, when using a vaccine-appropriate bacterial vector, has potential utility as an inexpensive, readily manufactured, and rapid vaccine platform for other pathogens.


Asunto(s)
/inmunología , Virus de la Diarrea Epidémica Porcina/inmunología , Proteínas Virales de Fusión/inmunología , Vacunas Virales/inmunología , Animales , Anticuerpos Antivirales/sangre , Modelos Animales de Enfermedad , Escherichia coli/genética , Genoma Bacteriano , Interferón gamma/sangre , ARN Viral/análisis , Porcinos , Vacunas de Productos Inactivados/inmunología , Vacunas Sintéticas/inmunología
5.
Nat Commun ; 12(1): 2009, 2021 03 31.
Artículo en Inglés | MEDLINE | ID: mdl-33790294

RESUMEN

Microorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.


Asunto(s)
Genoma Bacteriano/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Metagenoma/genética , Metagenómica/métodos , ARN Ribosómico 16S/genética , Aguas del Alcantarillado/microbiología , Bacterias/clasificación , Bacterias/genética , Reactores Biológicos/microbiología , Dinamarca , Microbiota/genética , Filogenia , ARN Ribosómico 23S/genética , ARN Ribosómico 5S/genética , Aguas Residuales/microbiología , Purificación del Agua/métodos
6.
Nat Commun ; 12(1): 2085, 2021 04 09.
Artículo en Inglés | MEDLINE | ID: mdl-33837194

RESUMEN

Long-term infection of the stomach with Helicobacter pylori can cause gastric cancer. However, the mechanisms by which the bacteria adapt to the stomach environment are poorly understood. Here, we show that a small non-coding RNA of H. pylori (HPnc4160, also known as IsoB or NikS) regulates the pathogen's adaptation to the host environment as well as bacterial oncoprotein production. In a rodent model of H. pylori infection, the genomes of bacteria isolated from the stomach possess an increased number of T-repeats upstream of the HPnc4160-coding region, and this leads to reduced HPnc4160 expression. We use RNA-seq and iTRAQ analyses to identify eight targets of HPnc4160, including genes encoding outer membrane proteins and oncoprotein CagA. Mutant strains with HPnc4160 deficiency display increased colonization ability of the mouse stomach, in comparison with the wild-type strain. Furthermore, HPnc4160 expression is lower in clinical isolates from gastric cancer patients than in isolates derived from non-cancer patients, while the expression of HPnc4160's targets is higher in the isolates from gastric cancer patients. Therefore, the small RNA HPnc4160 regulates H. pylori adaptation to the host environment and, potentially, gastric carcinogenesis.


Asunto(s)
Adaptación Fisiológica/genética , Infecciones por Helicobacter/patología , Helicobacter pylori/fisiología , ARN Bacteriano/metabolismo , ARN Pequeño no Traducido/metabolismo , Neoplasias Gástricas/microbiología , Animales , Antígenos Bacterianos/genética , Proteínas Bacterianas/genética , Carcinogénesis , Modelos Animales de Enfermedad , Mucosa Gástrica/microbiología , Mucosa Gástrica/patología , Regulación Bacteriana de la Expresión Génica/fisiología , Genoma Bacteriano/genética , Gerbillinae , Infecciones por Helicobacter/microbiología , Helicobacter pylori/aislamiento & purificación , Helicobacter pylori/patogenicidad , Interacciones Microbiota-Huesped , Humanos , Masculino , Mutación , ARN Bacteriano/genética , ARN Pequeño no Traducido/genética , RNA-Seq , Neoplasias Gástricas/patología
7.
Nat Commun ; 12(1): 1523, 2021 03 09.
Artículo en Inglés | MEDLINE | ID: mdl-33750782

RESUMEN

Enterococcus faecalis is a commensal and nosocomial pathogen, which is also ubiquitous in animals and insects, representing a classical generalist microorganism. Here, we study E. faecalis isolates ranging from the pre-antibiotic era in 1936 up to 2018, covering a large set of host species including wild birds, mammals, healthy humans, and hospitalised patients. We sequence the bacterial genomes using short- and long-read techniques, and identify multiple extant hospital-associated lineages, with last common ancestors dating back as far as the 19th century. We find a population cohesively connected through homologous recombination, a metabolic flexibility despite a small genome size, and a stable large core genome. Our findings indicate that the apparent hospital adaptations found in hospital-associated E. faecalis lineages likely predate the "modern hospital" era, suggesting selection in another niche, and underlining the generalist nature of this nosocomial pathogen.


Asunto(s)
Infección Hospitalaria/microbiología , Enterococcus faecalis/genética , Enterococcus faecalis/metabolismo , Prednisolona/metabolismo , Prednisolona/farmacología , Animales , Antibacterianos , Aves , Farmacorresistencia Bacteriana/genética , Enterococcus faecalis/efectos de los fármacos , Enterococcus faecalis/aislamiento & purificación , Genes MDR/genética , Genoma Bacteriano , Infecciones por Bacterias Grampositivas/microbiología , Hospitales , Especificidad del Huésped , Humanos , Filogenia , Factores de Virulencia , Secuenciación Completa del Genoma
8.
Methods Mol Biol ; 2278: 31-44, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33649946

RESUMEN

Genome assembly and annotation are two of the key actions that must be undertaken in order to explore the genomic repertoire of (bifido)bacteria. The gathered information can be employed to genomically characterize a given microorganism, and can also be used to perform comparative genome analysis by including other sequenced (bifido)bacterial strains. Here, we highlight various bioinformatic programs able to manage next generation sequencing data starting from the assembly of a genome to the comparative analyses between strains.


Asunto(s)
Bifidobacterium/genética , Genoma Bacteriano , Genómica/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Anotación de Secuencia Molecular/métodos , Filogenia , Análisis de Secuencia de ADN/métodos , Secuenciación Completa del Genoma/métodos
9.
Methods Mol Biol ; 2278: 183-193, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33649957

RESUMEN

Bifidobacteria represent highly prevalent and abundant members of the gut microbiota during mammalian infancy. In this context, bifidobacterial species have been shown to be correlated with many aspects of host health by means of direct interactions with the host and cohabiting microbes. Metagenomic sequencing of fecal DNA represents a valuable approach for taxonomic and functional profiling of bacterial populations, and has allowed us to appreciate the relevance of bifidobacterial taxa in such complex bacterial communities, especially during the first stages of life.


Asunto(s)
Bifidobacterium/genética , Genoma Bacteriano , Metagenómica/métodos , Animales , Bifidobacterium/clasificación , Microbioma Gastrointestinal , Perfilación de la Expresión Génica/métodos , Humanos , Metagenoma , ARN Bacteriano/genética , ARN Ribosómico 16S/genética , Programas Informáticos
10.
Methods Mol Biol ; 2278: 225-232, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33649960

RESUMEN

In this chapter, we present a generic method to achieve de novo genome assembly and methylome analysis of Bifidobacterium genomes using the Pacbio SMRT sequencing and SMRT Link pipeline. The methods described here cover the de novo Pacbio or hybrid Illumina-Pacbio assembly ideally intended to obtain a complete genome sequence, followed by the detection of base modifications and methylome analysis.The identified DNA motifs obtained by methylome analysis can be used to predict active restriction-modification (RM) systems in Bifidobacterium strains. The presence of active RM systems and knowledge on their target motifs may guide selection of suitable cloning or mutagenesis vectors for bifidobacteria.


Asunto(s)
Bifidobacterium/genética , Genoma Bacteriano , Análisis de Secuencia de ADN/métodos , Metilación de ADN , ADN Bacteriano/genética , Motivos de Nucleótidos , Programas Informáticos
11.
J Med Microbiol ; 70(3)2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33704044

RESUMEN

Tigecycline is a last-resort antimicrobial used to treat multidrug-resistant Gram-negative bacterial infections. One of the common antimicrobial resistance mechanisms is the efflux pump system composed of membrane protein complexes to excrete xenobiotic substrates. Recently, a novel gene cluster, tmexCD1-toprJ1, encoding the resistance-nodulation-cell division (RND) efflux pump was identified on plasmids in Klebsiella pneumoniae isolates in China. TMexCD1-TOprJ1 was found to be capable of excreting multiple antimicrobials, including tigecycline, which contributed to the strain's resistance. In this study, we identified K. pneumoniae isolates harbouring the tmexCD1-toprJ1 genes outside of China for the first time. Two tigecycline-resistant K. pneumoniae isolates belonging to ST273 by multilocus sequence typing were collected from different patients in a medical institution in Hanoi, Vietnam, in 2015. Whole-genome sequence analysis revealed that these isolates harboured a 288.0 kb tmexCD1-toprJ1-carrying plasmid with IncFIB and IncHI1B replicons. The tmexCD1-toprJ1 gene cluster was surrounded by several mobile gene elements, including IS26, and the plasmids had high sequence identity with that of K. pneumoniae isolated in China. Our finding suggests that the horizontal spread of tigecycline resistance mediated by tmexCD1-toprJ1-carrying plasmids has occurred in Vietnam and other countries, and raises concern about the further global dissemination.


Asunto(s)
Antibacterianos/farmacología , Farmacorresistencia Bacteriana/genética , Klebsiella pneumoniae/aislamiento & purificación , Plásmidos/genética , Tigeciclina/farmacología , Genes Bacterianos/genética , Genoma Bacteriano/genética , Humanos , Infecciones por Klebsiella/microbiología , Klebsiella pneumoniae/efectos de los fármacos , Klebsiella pneumoniae/genética , Familia de Multigenes , Tipificación de Secuencias Multilocus , Vietnam
12.
Int J Mol Sci ; 22(4)2021 Feb 20.
Artículo en Inglés | MEDLINE | ID: mdl-33672760

RESUMEN

Escherichia coli Nissle 1917 (EcN) is an intestinal probiotic that is effective for the treatment of intestinal disorders, such as inflammatory bowel disease and ulcerative colitis. EcN is a representative Gram-negative probiotic in biomedical research and is an intensively studied probiotic. However, to date, its genome-wide metabolic network model has not been developed. Here, we developed a comprehensive and highly curated EcN metabolic model, referred to as iDK1463, based on genome comparison and phenome analysis. The model was improved and validated by comparing the simulation results with experimental results from phenotype microarray tests. iDK1463 comprises 1463 genes, 1313 unique metabolites, and 2984 metabolic reactions. Phenome data of EcN were compared with those of Escherichia coli intestinal commensal K-12 MG1655. iDK1463 was simulated to identify the genetic determinants responsible for the observed phenotypic differences between EcN and K-12. Further, the model was simulated for gene essentiality analysis and utilization of nutrient sources under anaerobic growth conditions. These analyses provided insights into the metabolic mechanisms by which EcN colonizes and persists in the gut. iDK1463 will contribute to the system-level understanding of the functional capacity of gut microbes and their interactions with microbiota and human hosts, as well as the development of live microbial therapeutics.


Asunto(s)
Escherichia coli/genética , Escherichia coli/metabolismo , Genoma Bacteriano , Modelos Biológicos , Fenómica , Probióticos/metabolismo , Anaerobiosis , Carbono/farmacología , Simulación por Computador , Escherichia coli/efectos de los fármacos , Escherichia coli/crecimiento & desarrollo , Intestinos/microbiología , Análisis de Flujos Metabólicos , Redes y Vías Metabólicas/efectos de los fármacos , Redes y Vías Metabólicas/genética , Familia de Multigenes , Nitrógeno/farmacología , Fenotipo , Reproducibilidad de los Resultados
13.
Methods Mol Biol ; 2259: 191-201, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33687716

RESUMEN

Recent advances in MS/MS technology have made it possible to use proteomic data to predict protein-coding sequences. This approach is called proteogenomics, and it allows to correctly translate start and stop sites and to reveal new open reading frames. Here, we focus on using proteogenomics to improve the annotation of Mycobacteriumtuberculosis strains. We also describe detail procedures of the extraction of proteins and their further preparation for LC-MS/MS analysis and outline the main steps of data analysis.


Asunto(s)
Proteínas Bacterianas/genética , Mycobacterium tuberculosis/genética , Proteogenómica/métodos , Tuberculosis/microbiología , Proteínas Bacterianas/análisis , Proteínas Bacterianas/aislamiento & purificación , Cromatografía Liquida/métodos , Genoma Bacteriano , Humanos , Anotación de Secuencia Molecular , Mycobacterium tuberculosis/química , Espectrometría de Masas en Tándem/métodos
14.
Science ; 372(6539)2021 04 16.
Artículo en Inglés | MEDLINE | ID: mdl-33766942

RESUMEN

Animals in the wild are able to subsist on pathogen-infected and poisonous food and show immunity to various diseases. These may be due to their microbiota, yet we have a poor understanding of animal microbial diversity and function. We used metagenomics to analyze the gut microbiota of more than 180 species in the wild, covering diverse classes, feeding behaviors, geographies, and traits. Using de novo metagenome assembly, we constructed and functionally annotated a database of more than 5000 genomes, comprising 1209 bacterial species of which 75% are unknown. The microbial composition, diversity, and functional content exhibit associations with animal taxonomy, diet, activity, social structure, and life span. We identify the gut microbiota of wild animals as a largely untapped resource for the discovery of therapeutics and biotechnology applications.


Asunto(s)
Animales Salvajes/microbiología , Bacterias , Microbioma Gastrointestinal , Genoma Bacteriano , Metagenoma , Animales , Animales Salvajes/clasificación , Animales Salvajes/fisiología , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Toxinas Bacterianas/metabolismo , Conducta Animal , Biodiversidad , Bases de Datos de Ácidos Nucleicos , Dieta , Ecosistema , Islas Malvinas , Heces/microbiología , Interacciones Microbiota-Huesped , Israel , Madagascar , Metagenómica , Péptido Hidrolasas/genética , Péptido Hidrolasas/metabolismo , Filogenia , Queensland , Uganda
15.
Nat Commun ; 12(1): 1963, 2021 03 30.
Artículo en Inglés | MEDLINE | ID: mdl-33785756

RESUMEN

The order and variability of bacterial chromosome organization, contained within the distribution of chromosome conformations, are unclear. Here, we develop a fully data-driven maximum entropy approach to extract single-cell 3D chromosome conformations from Hi-C experiments on the model organism Caulobacter crescentus. The predictive power of our model is validated by independent experiments. We find that on large genomic scales, organizational features are predominantly present along the long cell axis: chromosomal loci exhibit striking long-ranged two-point axial correlations, indicating emergent order. This organization is associated with large genomic clusters we term Super Domains (SuDs), whose existence we support with super-resolution microscopy. On smaller genomic scales, our model reveals chromosome extensions that correlate with transcriptional and loop extrusion activity. Finally, we quantify the information contained in chromosome organization that may guide cellular processes. Our approach can be extended to other species, providing a general strategy to resolve variability in single-cell chromosomal organization.


Asunto(s)
Caulobacter crescentus/genética , Cromosomas Bacterianos/genética , Modelos Moleculares , Conformación Molecular , Algoritmos , Sitios de Unión , Caulobacter crescentus/citología , Caulobacter crescentus/metabolismo , Segregación Cromosómica/genética , Cromosomas Bacterianos/metabolismo , Regulación Bacteriana de la Expresión Génica , Genoma Bacteriano/genética , Genómica/métodos , Modelos Genéticos
16.
Gene ; 783: 145577, 2021 May 30.
Artículo en Inglés | MEDLINE | ID: mdl-33737123

RESUMEN

Transcriptional response regulators (TRR) are the most abundant signal transducers in prokaryotic systems that mediate intracellular changes in response to environmental signals. They are involved in a wide range of biological processes that allow bacteria to persist in particular habitats. There is strong evidence that the bacterial habitat and their lifestyle influence the size of their TRR genetic repertoire. Therefore, it would be expected that the evolution of bacterial genomes could be linked to natural selection processes. To test this hypothesis, we explored the evolutionary dynamics of TRR genes of the widely studied Harveyi clade of the genus Vibrio at the molecular and genomic levels. Our results suggest that the TRR genetic repertoire of the species belonging to the Harveyi clade is a product of genomic reduction and expansion. The gene loss and gains that drive their genomic reduction and expansion could be attributed to natural selection and random genetic drift. It seems that natural selection acts to maintain the ancestral state of core TRR genes (shared by all species) by purifying processes and could be driving the loss of some accessory (found in certain species) genes through the diversification of sequences. The neutrality observed in gene gain could be attributed to spontaneous events as horizontal gene transfer driven by stochastic events as occurs in random genetic drift.


Asunto(s)
Evolución Molecular , Genes Bacterianos , Genes Reguladores , Vibrio/genética , Regulación Bacteriana de la Expresión Génica , Transferencia de Gen Horizontal , Genoma Bacteriano
17.
Nat Commun ; 12(1): 1422, 2021 03 03.
Artículo en Inglés | MEDLINE | ID: mdl-33658492

RESUMEN

Trans-acyltransferase polyketide synthases (trans-AT PKSs) are bacterial multimodular enzymes that biosynthesize diverse pharmaceutically and ecologically important polyketides. A notable feature of this natural product class is the existence of chemical hybrids that combine core moieties from different polyketide structures. To understand the prevalence, biosynthetic basis, and evolutionary patterns of this phenomenon, we developed transPACT, a phylogenomic algorithm to automate global classification of trans-AT PKS modules across bacteria and applied it to 1782 trans-AT PKS gene clusters. These analyses reveal widespread exchange patterns suggesting recombination of extended PKS module series as an important mechanism for metabolic diversification in this natural product class. For three plant-associated bacteria, i.e., the root colonizer Gynuella sunshinyii and the pathogens Xanthomonas cannabis and Pseudomonas syringae, we demonstrate the utility of this computational approach for uncovering cryptic relationships between polyketides, accelerating polyketide mining from fragmented genome sequences, and discovering polyketide variants with conserved moieties of interest. As natural combinatorial hybrids are rare among the more commonly studied cis-AT PKSs, this study paves the way towards evolutionarily informed, rational PKS engineering to produce chimeric trans-AT PKS-derived polyketides.


Asunto(s)
Aciltransferasas/genética , Proteínas Bacterianas/genética , Filogenia , Sintasas Poliquetidas/genética , Policétidos/metabolismo , Aciltransferasas/metabolismo , Algoritmos , Arabidopsis/microbiología , Proteínas Bacterianas/metabolismo , Evolución Molecular , Genoma Bacteriano , Células HeLa , Humanos , Lactonas/metabolismo , Macrólidos/metabolismo , Familia de Multigenes , Piperidonas/química , Plantas/microbiología , Sintasas Poliquetidas/metabolismo , Policétidos/química , Pseudomonas syringae/metabolismo , Xanthomonas/metabolismo , Xanthomonas/patogenicidad
18.
Methods Mol Biol ; 2291: 87-97, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33704749

RESUMEN

Today, whole genome sequencing (WGS)-based typing is the gold standard approach to detect outbreaks of Shiga toxin-producing Escherichia coli (STEC) and to differentiate them from sporadic cases. Here, we describe an optimized protocol to efficiently determine the genome sequences of STEC using short read Illumina technology and provide information on helpful tools for the subsequent bioinformatic analysis.


Asunto(s)
Biología Computacional , Brotes de Enfermedades , Infecciones por Escherichia coli , Genoma Bacteriano , Escherichia coli Shiga-Toxigénica/genética , Secuenciación Completa del Genoma , Infecciones por Escherichia coli/epidemiología , Infecciones por Escherichia coli/genética , Humanos
19.
Methods Mol Biol ; 2291: 99-117, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33704750

RESUMEN

Escherichia coli is a species of bacteria that can be present in a wide variety of mammalian hosts and potentially soil environments. E. coli has an open genome and can show considerable diversity in gene content between isolates. It is a reasonable assumption that gene content reflects evolution of strains in particular host environments and therefore can be used to predict the host most likely to be the source of an isolate. An extrapolation of this argument is that strains may also have gene content that favors success in multiple hosts and so the possibility of successful transmission from one host to another, for example, from cattle to human, can also be predicted based on gene content. In this methods chapter, we consider the issue of Shiga toxin (Stx)-producing E. coli (STEC) strains that are present in ruminants as the main host reservoir and for which we know that a subset causes life-threatening infections in humans. We show how the genome sequences of E. coli isolated from both cattle and humans can be used to build a classifier to predict human and cattle host association and how this can be applied to score key STEC serotypes known to be associated with human infection. With the example dataset used, serogroups O157, O26, and O111 show the highest, and O103 and O145 the lowest, predictions for human association. The long-term ambition is to combine such machine learning predictions with phylogeny to predict the zoonotic threat of an isolate based on its whole genome sequence (WGS).


Asunto(s)
Infecciones por Escherichia coli/genética , Genoma Bacteriano , Aprendizaje Automático , Filogenia , Serogrupo , Escherichia coli Shiga-Toxigénica , Secuenciación Completa del Genoma , Animales , Bovinos , Humanos , Escherichia coli Shiga-Toxigénica/clasificación , Escherichia coli Shiga-Toxigénica/genética
20.
Nat Commun ; 12(1): 1500, 2021 03 08.
Artículo en Inglés | MEDLINE | ID: mdl-33686077

RESUMEN

Diphtheria is a respiratory disease caused by the bacterium Corynebacterium diphtheriae. Although the development of a toxin-based vaccine in the 1930s has allowed a high level of control over the disease, cases have increased in recent years. Here, we describe the genomic variation of 502 C. diphtheriae isolates across 16 countries and territories over 122 years. We generate a core gene phylogeny and determine the presence of antimicrobial resistance genes and variation within the tox gene of 291 tox+ isolates. Numerous, highly diverse clusters of C. diphtheriae are observed across the phylogeny, each containing isolates from multiple countries, regions and time of isolation. The number of antimicrobial resistance genes, as well as the breadth of antibiotic resistance, is substantially greater in the last decade than ever before. We identified and analysed 18 tox gene variants, with mutations estimated to be of medium to high structural impact.


Asunto(s)
Corynebacterium diphtheriae/genética , Toxina Diftérica/genética , Difteria/microbiología , Difteria/prevención & control , Antiinfecciosos/farmacología , Corynebacterium diphtheriae/efectos de los fármacos , Toxoide Diftérico , Farmacorresistencia Bacteriana/genética , Variación Genética , Genoma Bacteriano , Genómica , Humanos , India , Pruebas de Sensibilidad Microbiana , Filogenia , Polimorfismo de Nucleótido Simple
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