Revealing the Genetic Basis of Natural Bacterial Phenotypic Divergence

Freddolino, Peter L.; Goodarzi, Hani; Tavazoie, Saeed

doi:10.1128/jb.01039-13

Cited by 7 publications

(6 citation statements)

References 38 publications

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“…The value of this genetic transfer mechanism to researchers was seen as early as 1944 by Avery et al ., when naturally competent Streptococcus pneumoniae were used to show that DNA is the genetic material, or “the transforming principle” [ 5 ]. But only recently has exploiting natural competence (and other gene transfer mechanisms) become a practical means to investigate the genetic basis for natural phenotypic variation, as massively parallel sequencing technologies have become cost effective [ 6 – 9 ].…”

Section: Introductionmentioning

confidence: 99%

Transformed Recombinant Enrichment Profiling Rapidly Identifies HMW1 as an Intracellular Invasion Locus in Haemophilus influenzae

et al. 2016

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Many bacterial species actively take up and recombine homologous DNA into their genomes, called natural competence, a trait that offers a means to identify the genetic basis of naturally occurring phenotypic variation. Here, we describe “transformed recombinant enrichment profiling” (TREP), in which natural transformation is used to generate complex pools of recombinants, phenotypic selection is used to enrich for specific recombinants, and deep sequencing is used to survey for the genetic variation responsible. We applied TREP to investigate the genetic architecture of intracellular invasion by the human pathogen Haemophilus influenzae, a trait implicated in persistence during chronic infection. TREP identified the HMW1 adhesin as a crucial factor. Natural transformation of the hmw1 operon from a clinical isolate (86-028NP) into a laboratory isolate that lacks it (Rd KW20) resulted in ~1,000-fold increased invasion into airway epithelial cells. When a distinct recipient (Hi375, already possessing hmw1 and its paralog hmw2) was transformed by the same donor, allelic replacement of hmw2A Hi375 by hmw1A 86-028NP resulted in a ~100-fold increased intracellular invasion rate. The specific role of hmw1A 86-028NP was confirmed by mutant and western blot analyses. Bacterial self-aggregation and adherence to airway cells were also increased in recombinants, suggesting that the high invasiveness induced by hmw1A 86-028NP might be a consequence of these phenotypes. However, immunofluorescence results found that intracellular hmw1A 86-028NP bacteria likely invaded as groups, instead of as individual bacterial cells, indicating an emergent invasion-specific consequence of hmw1A-mediated self-aggregation.

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Section: Introductionmentioning

confidence: 99%

Transformed Recombinant Enrichment Profiling Rapidly Identifies HMW1 as an Intracellular Invasion Locus in Haemophilus influenzae

et al. 2016

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“…Differences in E. coli strains of Nissle and K-12 in the utilization of diverse nutrient substrates were identified ( Figure 2 ) and could, in many cases, be correlated with genotypic differences ( Figure 3 ). In general, genome sequence data alone do not allow the identification of the genetic determinants of a given phenotypic variation, and the number of genetic differences even between closely related strains is often too large to be evaluated by gene deletion and complementation tests [ 59 ]. The metabolic simulations for nutrient utilization described in this study outline a general strategy for identifying the genetic basis of phenotypic divergence based on clues from comparative genome and phenome analyses.…”

Section: Discussionmentioning

confidence: 99%

Development of a Genome-Scale Metabolic Model and Phenome Analysis of the Probiotic Escherichia coli Strain Nissle 1917

Kim

Yoon

2021

IJMS

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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.

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“…Indeed, these emerging technologies unlocked the potential for microbial genome-wide association studies (GWAS), aiming at dissecting the genetic basis of known phenotypic traits (e.g., carbohydrate metabolism) (Dutilh et al 2013 ). Understanding certain genotype-phenotype associations brings unprecedented opportunities for better utilization/exploration of technologically useful microorganisms, such as starter cultures in food technology (Wu et al 2017 ), but also for the engineering of novel microbial organisms and consortia in synthetic biology applications (Freddolino et al 2014 ). Bacterial evolution, epidemiology, pathogens’ traceability during disease outbreaks, pathogenesis, antibiotic resistance, rapid detection, and food safety (Chen and Shapiro 2015 ; Brbić et al 2016 ; Klemm and Dougan 2016 ; Deurenberg et al 2017 ; Ruppé et al 2017 ), exemplify areas where sequencing and GWAS revolutionized modern microbiology.…”

Section: Introductionmentioning

confidence: 99%

Uncovering carbohydrate metabolism through a genotype-phenotype association study of 56 lactic acid bacteria genomes

Buron-Moles

Chailyan

Dolejš

et al. 2019

Appl Microbiol Biotechnol

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Owing to their unique potential to ferment carbohydrates, both homo- and heterofermentative lactic acid bacteria (LAB) are widely used in the food industry. Deciphering the genetic basis that determine the LAB fermentation type, and hence carbohydrate utilization, is paramount to optimize LAB industrial processes. Deep sequencing of 24 LAB species and comparison with 32 publicly available genome sequences provided a comparative data set including five major LAB genera for further analysis. Phylogenomic reconstruction confirmed Leuconostoc and Pediococcus species as independently emerging from the Lactobacillus genus, within one of the three phylogenetic clades identified. These clades partially grouped LABs according to their fermentation types, suggesting that some metabolic capabilities were independently acquired during LAB evolution. In order to apply a genome-wide association study (GWAS) at the multigene family level, utilization of 49 carbohydrates was also profiled for these 56 LAB species. GWAS results indicated that obligately heterofermentative species lack 1-phosphofructokinase, required for d -mannose degradation in the homofermentative pathway. Heterofermentative species were found to often contain the araBAD operon, involved in l -arabinose degradation, which is important for heterofermentation. Taken together, our results provide helpful insights into the genetic determinants of LAB carbohydrate metabolism, and opens for further experimental research, aiming at validating the role of these candidate genes for industrial applications. Electronic supplementary material The online version of this article (10.1007/s00253-019-09701-6) contains supplementary material, which is available to authorized users.

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Revealing the Genetic Basis of Natural Bacterial Phenotypic Divergence

Cited by 7 publications

References 38 publications

Transformed Recombinant Enrichment Profiling Rapidly Identifies HMW1 as an Intracellular Invasion Locus in Haemophilus influenzae

Transformed Recombinant Enrichment Profiling Rapidly Identifies HMW1 as an Intracellular Invasion Locus in Haemophilus influenzae

Development of a Genome-Scale Metabolic Model and Phenome Analysis of the Probiotic Escherichia coli Strain Nissle 1917

Uncovering carbohydrate metabolism through a genotype-phenotype association study of 56 lactic acid bacteria genomes

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