Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals.

Although strain tolerance to high product concentrations is a barrier to the economically viable biomanufacturing of industrial chemicals, chemical tolerance mechanisms are often unknown. To reveal tolerance mechanisms, an automated platform was utilized to evolve Escherichia coli to grow optimally in the presence of 11 industrial chemicals (1,2-propanediol, 2,3-butanediol, glutarate, adipate, putrescine, hexamethylenediamine, butanol, isobutyrate, coumarate, octanoate, hexanoate), reaching tolerance at concentrations 60%-400% higher than initial toxic levels. Sequencing genomes of 223 isolates from 89 populations, reverse engineering, and cross-compound tolerance profiling were employed to uncover tolerance mechanisms.

Ethanol-lactate transition of Lachancea thermotolerans is linked to nitrogen metabolism.

Climate change increases sugar content in grapes, resulting in unwanted increase in ethanol content of wine. Lachancea thermotolerans ferments glucose and fructose into both ethanol and lactate, decreasing final ethanol content and positively affecting wine acidity. Reported Lachancea thermotolerans strains show big variation in lactate production during fermentation.

Rational and evolutionary engineering of Saccharomyces cerevisiae for production of dicarboxylic acids from lignocellulosic biomass and exploring genetic mechanisms of the yeast tolerance to the biomass hydrolysate.

Background: Lignosulfonates are significant wood chemicals with a $700 million market, produced by sulfite pulping of wood. During the pulping process, spent sulfite liquor (SSL) is generated, which in addition to lignosulfonates contains hemicellulose-derived sugars-in case of hardwoods primarily the pentose sugar xylose. The pentoses are currently underutilized.

A dual-reporter system for investigating and optimizing protein translation and folding in E. coli.

Strategies for investigating and optimizing the expression and folding of proteins for biotechnological and pharmaceutical purposes are in high demand. Here, we describe a dual-reporter biosensor system that simultaneously assesses in vivo protein translation and protein folding, thereby enabling rapid screening of mutant libraries. We have validated the dual-reporter system on five different proteins and find an excellent correlation between reporter signals and the levels of protein expression and solubility of the proteins.

Updated Genome Sequence for the Probiotic Bacterium Bifidobacterium animalis subsp. BB-12.

The genome of Bifidobacterium animalis subsp. BB-12 was sequenced using Oxford Nanopore Technologies long-read and Illumina short-read sequencing platforms. A hybrid genome assembly approach was used to construct an updated complete genome sequence for BB-12 containing 1,944,152 bp, with a G+C content of 60.

Screening for texturing Leuconostoc and genomics behind polysaccharide production.

Synthesis of polysaccharides by Leuconostoc can result in improved texture of fermented products. A total of 249 Leuconostoc strains were screened for homo-polysaccharide production and for texturing capabilities in milk. A total of six Ln.

Three biofilm types produced by a model pseudomonad are differentiated by structural characteristics and fitness advantage.

Model bacterial biofilm systems suggest that bacteria produce one type of biofilm, which is then modified by environmental and physiological factors, although the diversification of developing populations might result in the appearance of adaptive mutants producing altered structures with improved fitness advantage. Here we compare the air-liquid (A-L) interface viscous mass (VM) biofilm produced by SBW25 and the wrinkly spreader (WS) and complementary biofilm-forming strain (CBFS) biofilm types produced by adaptive SBW25 mutants in order to better understand the link between these physical structures and the fitness advantage they provide in experimental microcosms. WS, CBFS and VM biofilms can be differentiated by strength, attachment levels and rheology, as well as by strain characteristics associated with biofilm formation.

Adaptive radiation of Pseudomonas fluorescens SBW25 in experimental microcosms provides an understanding of the evolutionary ecology and molecular biology of A-L interface biofilm formation.

Combined experimental evolutionary and molecular biology approaches have been used to investigate the adaptive radiation of Pseudomonas fluorescens SBW25 in static microcosms leading to the colonisation of the air-liquid interface by biofilm-forming mutants such as the Wrinkly Spreader (WS). In these microcosms, the ecosystem engineering of the early wild-type colonists establishes the niche space for subsequent WS evolution and colonisation. Random WS mutations occurring in the developing population that deregulate diguanylate cyclases and c-di-GMP homeostasis result in cellulose-based biofilms at the air-liquid interface.

Biofilm formation and cellulose expression by Bordetella avium 197N, the causative agent of bordetellosis in birds and an opportunistic respiratory pathogen in humans.

Although bacterial cellulose synthase (bcs) operons are widespread within the Proteobacteria phylum, subunits required for the partial-acetylation of the polymer appear to be restricted to a few γ-group soil, plant-associated and phytopathogenic pseudomonads, including Pseudomonas fluorescens SBW25 and several Pseudomonas syringae pathovars. However, a bcs operon with acetylation subunits has also been annotated in the unrelated β-group respiratory pathogen, Bordetella avium 197N. Our comparison of subunit protein sequences and GC content analyses confirms the close similarity between the B.

Rapid resistome mapping using nanopore sequencing.

The emergence of antibiotic resistance in human pathogens has become a major threat to modern medicine. The outcome of antibiotic treatment can be affected by the composition of the gut. Accordingly, knowledge of the gut resistome composition could enable more effective and individualized treatment of bacterial infections.

Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution.

L-serine is a promising building block biochemical with a high theoretical production yield from glucose. Toxicity of L-serine is however prohibitive for high-titer production in E. coli.

Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes.

Escherichia coli strains are widely used in academic research and biotechnology. New technologies for quantifying strain-specific differences and their underlying contributing factors promise greater understanding of how these differences significantly impact physiology, synthetic biology, metabolic engineering, and process design. Here, we quantified strain-specific differences in seven widely used strains of E.

Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?

Background: The primary cause of morbidity and mortality in cystic fibrosis (CF) patients is lung infection by Pseudomonas aeruginosa. Therefore much work has been done to understand the adaptation and evolution of P. aeruginosa in the CF lung.

EasyCloneMulti: A Set of Vectors for Simultaneous and Multiple Genomic Integrations in Saccharomyces cerevisiae.

Saccharomyces cerevisiae is widely used in the biotechnology industry for production of ethanol, recombinant proteins, food ingredients and other chemicals. In order to generate highly producing and stable strains, genome integration of genes encoding metabolic pathway enzymes is the preferred option. However, integration of pathway genes in single or few copies, especially those encoding rate-controlling steps, is often not sufficient to sustain high metabolic fluxes.

Adaptation of the autotrophic acetogen Sporomusa ovata to methanol accelerates the conversion of CO2 to organic products.

Acetogens are efficient microbial catalysts for bioprocesses converting C1 compounds into organic products. Here, an adaptive laboratory evolution approach was implemented to adapt Sporomusa ovata for faster autotrophic metabolism and CO2 conversion to organic chemicals. S.

The presence of anti-LPS antibodies and human serum activity against Proteus mirabilis S/R forms in correlation with TLR4 (Thr399Ile) gene polymorphism in rheumatoid arthritis.

Objectives: Proteus mirabilis strains are human pathogens responsible for urinary tract infections, which may also be involved in rheumatoid arthritis (RA).

Design And Methods: We determined whether the binding site of anti-LPS antibodies on the O-polysaccharide part of P. mirabilis LPS correlates with the level of TLR4 (Thr399Ile) gene polymorphism in the sera of RA patients.

Surfactants expressed by soil pseudomonads alter local soil-water distribution, suggesting a hydrological role for these compounds.

Several biological roles have been demonstrated for surfactants expressed by soil and rhizosphere Pseudomonas spp., but the impact of these powerful surface-active agents on the local soil-water distribution within the partially saturated soil pore network has not been examined. To investigate this potential hydrological role, the liquid surface tension (γ)-reducing activities (LSTRA) of 72 pseudomonads isolated from a sandy loam soil by tensiometry of culture supernatants were characterized.

Environmental modification and niche construction: developing O2 gradients drive the evolution of the Wrinkly Spreader.

The evolutionary success of the novel Wrinkly Spreader (WS) genotypes in diversifying Pseudomonas fluorescens SBW25 populations in static liquid microcosms has been attributed to the greater availability of O(2) at the air-liquid (A-L) interface where the WS produces a physically cohesive-class biofilm. However, the importance of O(2) gradients in SBW25 adaptation has never been examined. We have explicitly tested the role of O(2) in evolving populations using microsensor profiling and experiments conducted under high and low O(2) conditions.

Characterization of a novel air-liquid interface biofilm of Pseudomonas fluorescens SBW25.

Pseudomonads are able to form a variety of biofilms that colonize the air-liquid (A-L) interface of static liquid microcosms, and differ in matrix composition, strength, resilience and degrees of attachment to the microcosm walls. From Pseudomonas fluorescens SBW25, mutants have evolved during prolonged adaptation-evolution experiments which produce robust biofilms of the physically cohesive class at the A-L interface, and which have been well characterized. In this study we describe a novel A-L interface biofilm produced by SBW25 that is categorized as a viscous mass (VM)-class biofilm.

[The chemical structure of Helicobacter pylori lipopolysaccharide and innate immune response].

H. pylori is a causative agent of chronic gastritis. Gastrointestinal disorders are associated with a bacterial mechanism of adaptation to the stomach's environment and the immune responses of gastric epithelial cells.

Embryogenesis of the serotonergic system in the earthworm Eisenia fetida (Annelida, Oligochaeta): immunohistochemical and biochemical studies.

Organization of the serotonergic system and changes of the serotonin (5-HT) content were studied during the embryogenesis of the earthworm Eisenia fetida, using immunocytochemistry and HPLC. A gradual emergence of 5-HT immunoreactive (IR) cells and their axon projections in the several ganglia of the central (CNS) and peripheral nervous system are described in the context of a staged time-scale of development. The first 5-HT-IR neurons appear in the subesophageal ganglion at an early embryonic stage (E2), followed by neurons in some rostrally located ventral ganglia.

Evidence for the presence of thyroid stimulating hormone, thyroglobulin and their receptors in Eisenia fetida: a multilevel hormonal interface between the nervous system and the peripheral tissues.

The present study describes the localization and distribution of thyroid-stimulating hormone (TSH), thyroglobulin (TGB) and their receptors in Eisenia fetida (Annelida, Oligochaeta) as revealed by immunohistological methods. Immunopositive neuronal and non-neuronal cells are present in both the central nervous system and some peripheral organs (e.g.

Neurochemical characterization of nervous elements innervating the body wall of earthworms (Lumbricus, Eisenia): immunohistochemical and pharmacological studies.

The distribution and chemical neuroanatomy of nervous elements and certain pharmacological-physiological characteristics of the innervation of the body wall in earthworms are described. Solitary sensory bipolar cells can be found among the epithelial cells. These bipolar cells contain serotonin, tyrosine hydroxylase, histamine, gamma-amino-butyric acid (GABA), Eisenia tetradecapeptide, proctolin or rhodopsin in various combinations.

Embryogenesis of GABAergic elements in the nervous system of Eisenia fetida (Annelida, Oligochaeta).

The appearance and development of the GABA-immunoreactive nervous elements in the central nervous system of Eisenia fetida were studied by immunocytochemistry. The nervous system originates from the neuroectoderm situated on the ventral side of the embryo. The organization of the circumpharyngeal ring starts earlier than that of the ventral cord.