Novel resistance functions uncovered using functional metagenomic investigations of resistance reservoirs

Pehrsson, Erica C.; Forsberg, Kevin J.; Gibson, Molly K.; Ahmadi, Sara; Dantas, Gautam

doi:10.3389/fmicb.2013.00145

Cited by 89 publications

(94 citation statements)

References 98 publications

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“…1). In total, 1,932 metagenomic fragments were assembled (N 50 of Ͼ1.35 kb) containing 2,283 ORFs which generally appeared unlike sequences deposited in public repositories, consistent with past observations from soil metagenomes (28,(46)(47)(48)(49)(50)(51). The average amino acid identity of all 2,283 ORFs to their closest homolog in the NCBI database was 52.7% Ϯ 19.0% (mean Ϯ standard deviation) (Fig.…”

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Identification of Genes Conferring Tolerance to Lignocellulose-Derived Inhibitors by Functional Selections in Soil Metagenomes

Forsberg

Patel

Witt

et al. 2016

Appl Environ Microbiol

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The production of fuels or chemicals from lignocellulose currently requires thermochemical pretreatment to release fermentable sugars. These harsh conditions also generate numerous small-molecule inhibitors of microbial growth and fermentation, limiting production. We applied small-insert functional metagenomic selections to discover genes that confer microbial tolerance to these inhibitors, identifying both individual genes and general biological processes associated with tolerance to multiple inhibitory compounds. Having screened over 248 Gb of DNA cloned from 16 diverse soil metagenomes, we describe gain-of-function tolerance against acid, alcohol, and aldehyde inhibitors derived from hemicellulose and lignin, demonstrating that uncultured soil microbial communities hold tremendous genetic potential to address the toxicity of pretreated lignocellulose. We recovered genes previously known to confer tolerance to lignocellulosic inhibitors as well as novel genes that confer tolerance via unknown functions. For instance, we implicated galactose metabolism in overcoming the toxicity of lignin monomers and identified a decarboxylase that confers tolerance to ferulic acid; this enzyme has been shown to catalyze the production of 4-vinyl guaiacol, a valuable precursor to vanillin production. These metagenomic tolerance genes can enable the flexible design of hardy microbial catalysts, customized to withstand inhibitors abundant in specific bioprocessing applications. Many lignocellulosic feedstocks (e.g., switchgrass) are preferred to maize, sugarcane, and other traditional food crops for the production of fuels and chemicals because they are able to grow on marginal land, often require little attention or energy input, and do not compete directly with the food supply (1-6). However, lignocellulose requires harsh thermochemical pretreatment methods to liberate fermentable monosaccharides (7-9), producing an additional compendium of compounds inhibitory to microbial growth that ultimately reduce production efficiencies (10-12). These small-molecule inhibitors derived from lignocellulose pretreatment (here called lignocellulosic inhibitors) are typically aldehydes, organic acids, furans, or phenolics and can originate from the cellulosic, hemicellulosic, and lignified fractions of the feedstock (11-15).Engineering hardier microbial production hosts with elevated tolerance to these inhibitors offers potential to ameliorate the toxic effects of these compounds without incurring the high process costs associated with detoxifying the lignocellulosic hydrolysate (16, 17). Unfortunately, the modes of toxicity of many of these toxins are poorly described, and genes conferring tolerance to many of these compounds have not been identified (18,19). An expanded catalog of tolerance-conferring genotypes may shed light on mechanisms of toxicity and enable synthetic biology approaches for the design of diverse production hosts with broadspectrum tolerance.Soil microorganisms, including white-rot fungi (20) and many bacteria (21), ar...

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“…Our discoveries highlight the potential for the soil metagenome to enable process improvements in industrial biotechnology. The tremendous genetic diversity in soil (28,(46)(47)(48)(49)(50)(51) (Fig. 2), however, remains mostly unexplored, and this potential is largely waiting to be realized.…”

Section: Discussionmentioning

confidence: 99%

Identification of Genes Conferring Tolerance to Lignocellulose-Derived Inhibitors by Functional Selections in Soil Metagenomes

Forsberg

Patel

Witt

et al. 2016

Appl Environ Microbiol

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“…2A-C). 35,42 These libraries, representing a total of 107 Gb of bacterial DNA, were screened against 16 antibiotics, including those routinely used in NICUs. Of the 794 functionally identified antibiotic resistance genes, 42% were encoded by E. coli, Enterobacter cloacae, and K. pneumoniae, taxa which include many pathogenic strains implicated in nosocomial infections in preterm infants.…”

Section: Antibiotics Disrupt the Preterm Gut Microbiota Richness And mentioning

confidence: 99%

“…In contrast, deep sequencing of microbiomes paired with functional metagenomics offers an unbiased method to identify functional resistance determinants in stool, and can provide quantitative information on microbiome and resistome architecture. 35,36 Gibson et al recently used this suite of techniques to develop a sequence-unbiased account of the effects of antibiotic therapy on the preterm infant microbiota with respect to phylogeny and antibiotic resistance gene distribution. 37 A longitudinal, sequencing based interrogation of the preterm infant gut microbiota…”

Section: Introductionmentioning

confidence: 99%

Antibiotic perturbation of the preterm infant gut microbiome and resistome

Gasparrini¹,

Crofts²,

Gibson³

et al. 2016

Gut Microbes

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The gut microbiota plays important roles in nutrient absorption, immune system development, and pathogen colonization resistance. Perturbations early in life may be detrimental to host health in the short and the long-term. Antibiotics are among the many factors that influence the development of the microbiota. Because antibiotics are heavily administered during the first critical years of gut microbiota development, it is important to understand the effects of these interventions. Infants, particularly those born prematurely, represent an interesting population because they receive early and often extensive antibiotic therapy in the first months after birth.Gibson et al. recently demonstrated that antibiotic therapy in preterm infants can dramatically affect the gut microbiome. While meropenem, ticarcillin-clavulanate, and cefotaxime treatments were associated with decreased species richness, gentamicin and vancomycin had variable effects on species richness. Interestingly, the direction of species richness response could be predicted based on the abundance of 2 species and 2 genes in the microbiome prior to gentamicin or vancomycin treatment. Nonetheless, all antibiotic treatments enriched the presence of resistance genes and multidrug resistant organisms. Treatment with different antibiotics further resulted in unique population shifts of abundant organisms and selection for different sets of resistance genes. In this addendum, we provide an extended discussion of these recent findings, and outline important future directions for elucidating the interplay between antibiotics and preterm infant gut microbiota development.

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“…The diverse range of novel antibiotic resistance genes could be accessible to clinically relevant bacteria and play a critical role in the emergence of antibiotic resistance among pathogens. Pehrsson et al (2013) provided an insightful review for the novel resistance functions uncovered using the functional metagenomic examination of various resistance reservoirs. Municipal biosolids that are produced during the activated sludge treatment are also a significant reservoir of antibiotic resistance as assessed by Kaplan et al (2013).…”

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confidence: 99%

Mechanisms of antibiotic resistance

Cattoir

2015

Frontiers Research Topics

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Novel resistance functions uncovered using functional metagenomic investigations of resistance reservoirs

Cited by 89 publications

References 98 publications

Identification of Genes Conferring Tolerance to Lignocellulose-Derived Inhibitors by Functional Selections in Soil Metagenomes

Identification of Genes Conferring Tolerance to Lignocellulose-Derived Inhibitors by Functional Selections in Soil Metagenomes

Antibiotic perturbation of the preterm infant gut microbiome and resistome

Mechanisms of antibiotic resistance

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