scholarly journals Exopolysaccharide anchoring creates an extreme resistance to sedimentation

2021 ◽  
Author(s):  
Nickolas G. Kessler ◽  
David M. Caraballo Delgado ◽  
Neel K. Shah ◽  
Jeff A. Dickinson ◽  
Sean D. Moore
Keyword(s):  
Single Species ◽  
Adaptive Strategy ◽  
Genetic Screens ◽  
E Coli ◽  
Aqueous Environments ◽  
Sedimentation Resistance ◽  
Surface Dwelling ◽  
Stress Sensing ◽  
Response To Temperature ◽  
Unusual Phenotype

By evolving strains of E. coli that hyper-resist sedimentation, we discovered an uncharacterized mechanism that bacteria can use to remain in suspension indefinitely without expending energy. This unusual phenotype was traced to the anchoring of long colanic acid polymers (CAP) that project from the cell surface. Although each characterized mutant activated this same mechanism, the genes responsible and the strengths of the phenotypes varied. Mutations in rcsC, lpp, igaA, or the yjbEFGH operon were sufficient to stimulate sedimentation resistance, while mutations altering the cps promoter, cdgI, or yjbF provided phenotypic enhancements. The sedimentation resistances changed in response to temperature, growth phase, and carbon source and each mutant exhibited significantly reduced biofilm formation. We discovered that the degree of colony mucoidy exhibited by these mutants was not related to the degree of Rcs pathways activation or to the amount of CAP that was produced; rather, it was related to the fraction of CAP that was shed as a true exopolysaccharide. Therefore, these and other mutations that activate this phenotype are likely to be absent from genetic screens that relied on centrifugation to harvest bacteria. We also found that this anchored CAP form is not linked to LPS cores and may not be attached to the outer membrane. IMPORTANCE Bacteria can partition in aqueous environments between surface-dwelling, planktonic, sedimentary, and biofilm forms. Residence in each location provides an advantage depending on nutritional and environmental stresses and a community of a single species is often observed to be distributed throughout two or more of these niches. Another adaptive strategy is to produce an extracellular capsule, which provides an environmental shield for the microbe and can allow escape from predators and immune systems. We discovered that bacteria can either shed or stably anchor capsules to dramatically alter their propensity to sediment. The degree to which the bacteria anchor their capsule is controlled by a stress sensing system, suggesting that anchoring may be used as an adaptive response to severe environmental challenges.

scholarly journals Antifreeze protein from Ammopiptanthus nanus functions in temperature-stress through domain A

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
HaoQiang Yu ◽  
HongYing Zheng ◽  
Yuan Liu ◽  
QingQing Yang ◽  
WanChen Li ◽  
...  
Keyword(s):  
Temperature Stress ◽  
Heat Tolerance ◽  
Antifreeze Protein ◽  
Functional Domain ◽  
E Coli ◽  
Ammopiptanthus Nanus ◽  
Cold Sensitive ◽  
Crystal Binding ◽  
Function Expression ◽  
Response To Temperature

AbstractTemperature stress restricts plant growth and development. Antifreeze protein (AFP) can improve plants antifreeze ability. In our previous study, the AnAFP gene cloned from Ammopiptanthus nanus was confirmed to be an excellent candidate enhancing plant cold resistance. But, AnAFP protein shared similar structures with KnS type dehydrins including K, N and S domains except ice crystal binding domain A. Here, we generated AnAFPΔA, AnAFPΔK, AnAFPΔN and AnAFPΔS, and transformed them into ordinary and cold sensitive strains of E. coli, and Arabidopsis KS type dehydrin mutant to evaluate their function. Expression of AnAFPΔA decreases cold and heat tolerance in E. coli, meanwhile, AnAFP enhances heat tolerance in Arabidopsis, suggesting that domain A is a thermal stable functional domain. AnAFP, AnAFPΔA and AnAFPΔS localize in whole cell, but AnAFPΔK and AnAFPΔN only localizes in nucleus and cytoplasm, respectively, exhibiting that K and N domains control localization of AnAFP. Likewise, K domain blocks interaction between AnAFP and AnICE1. The result of RT-qPCR showed that expression of AnAFP, AnICE1 and AnCBF genes was significantly induced by high-temperature, indicating that the AnAFP is likely regulated by ICE1-CBF-COR signal pathway. Taken together, the study provides insights into understanding the mechanism of AnAFP in response to temperature stress and gene resource to improve heat or cold tolerance of plants in transgenic engineering.

scholarly journals Reclassification of Shigella species as later heterotypic synonyms of Escherichia coli in the Genome Taxonomy Database

2021 ◽  
Author(s):  
Donovan H Parks ◽  
Maria Chuvochina ◽  
Peter R Reeves ◽  
Scott A Beatson ◽  
Philip Hugenholtz
Keyword(s):  
Escherichia Coli ◽  
Type Strain ◽  
Shigella Flexneri ◽  
Laboratory Strain ◽  
Single Species ◽  
Species Definition ◽  
E Coli ◽  
Shigella Species ◽  
K 12 ◽  
Common Laboratory

Members of the genus Shigella have high genomic similarity to Escherichia coli and are often considered to be atypical members of this species. In an attempt to retain Shigella species as recognizable entities, they were reclassified as Escherichia species in the Genome Taxonomy Database (GTDB) using an operational average nucleotide identity (ANI)-based approach nucleated around type strains. This resulted in nearly 80% of E. coli genomes being reclassified to new species including the common laboratory strain E. coli K-12 (to 'E. flexneri') because it is more closely related to the type strain of Shigella flexneri than it is to the type strain of E. coli. Here we resolve this conundrum by treating Shigella species as later heterotypic synonyms of E. coli, present evidence supporting this reclassification, and show that assigning E. coli/Shigella strains to a single species is congruent with the GTDB-adopted genomic species definition.

Long-term fasting and realimentation in hypogean and epigean isopods: a proposed adaptive strategy for groundwater organisms

2002 ◽  
Vol 205 (14) ◽  
pp. 2079-2087 ◽  
Author(s):  
Frédéric Hervant ◽  
David Renault
Keyword(s):  
Metabolic Response ◽  
Large Body ◽  
Adaptive Strategy ◽  
Energy System ◽  
Adaptive Responses ◽  
Rapid Restoration ◽  
Surface Dwelling ◽  
Unpredictable Environment ◽  
Lipid Stores

SUMMARYThe effects of long-term fasting and subsequent refeeding on digestive physiology and energy metabolism were investigated in a subterranean aquatic crustacean, Stenasellus virei, and in a morphologically similar surface-dwelling species, Asellus aquaticus. Metabolic response to food deprivation was monophasic in A. aquaticus, with an immediate,large decrease in all energy reserves. In contrast, S. vireidisplayed three successive periods of phosphageno-glucidic, lipidic and,finally, proteo-lipidic-dominant catabolism over the course of the nutritional stress. To represent the responses of subterranean crustaceans to food stress and renutrition, a sequential energy strategy was hypothesized, suggesting that four successive phases (called stress, transition, adaptation and recovery) can be distinguished. Based on these results, a general adaptive strategy for groundwater organisms was proposed. Their remarkable resistance to long-term fasting may be partly explained by (1) a depressed metabolism,during which they mainly subsist on lipid stores, (2) a prolonged state of glycogen- and protein-sparing, (3) low energetic requirements and (4) large body stores. In addition, these groundwater species displayed high recovery abilities during refeeding, showing an optimal utilization of available food and a rapid restoration of their body reserves. These adaptive responses might be considered for numerous subterranean organisms as an efficient energy-saving strategy in a harsh and unpredictable environment where fasting(and/or hypoxic) periods of variable duration alternate with sporadic feeding events (and/or normoxic periods). Therefore, food-limited and/or hypoxia-tolerant groundwater species appear to be good examples of animals representing a low-energy system.

scholarly journals Common adaptive strategies underlie within-host evolution of bacterial pathogens

2020 ◽  
Author(s):  
Yair E Gatt ◽  
Hanah Margalit
Keyword(s):  
Bacterial Infections ◽  
Large Scale ◽  
Bacterial Species ◽  
Adaptive Strategies ◽  
Single Species ◽  
Adaptive Strategy ◽  
Host Immune System ◽  
Glycerol Phosphate ◽  
Genomic Changes ◽  
Virulence Attenuation

Abstract Within-host adaptation is a hallmark of chronic bacterial infections, involving substantial genomic changes. Recent large-scale genomic data from prolonged infections allow the examination of adaptive strategies employed by different pathogens and open the door to investigate whether they converge towards similar strategies. Here, we compiled extensive data of whole-genome sequences of bacterial isolates belonging to miscellaneous species sampled at sequential time points during clinical infections. Analysis of these data revealed that different species share some common adaptive strategies, achieved by mutating various genes. While the same genes were often mutated in several strains within a species, different genes related to the same pathway, structure or function were changed in other species utilizing the same adaptive strategy (e.g. mutating flagellar genes). Strategies exploited by various bacterial species were often predicted to be driven by the host immune system, a powerful selective pressure that is not species-specific. Remarkably, we find adaptive strategies identified previously within single species to be ubiquitous. Two striking examples are shifts from siderophore-based to heme-based iron scavenging (previously shown for Pseudomonas aeruginosa), and changes in glycerol-phosphate metabolism (previously shown to decrease sensitivity to antibiotics in Mycobacterium tuberculosis). Virulence factors were often adaptively affected in different species, indicating shifts from acute to chronic virulence and virulence attenuation during infection. Our study presents a global view on common within-host adaptive strategies employed by different bacterial species and provides a rich resource for further studying these processes.

scholarly journals Facultative Anaerobes Shape Multispecies Biofilms Composed of Meat Processing Surface Bacteria and Escherichia coli O157:H7 or Salmonella enterica Serovar Typhimurium

2019 ◽  
Vol 85 (17) ◽  
Author(s):  
Jeyachchandran Visvalingam ◽  
Hui Wang ◽  
Tim C. Ells ◽  
Xianqin Yang
Keyword(s):  
Food Processing ◽  
Salmonella Enterica ◽  
Biofilm Formation ◽  
Single Species ◽  
Meat Processing ◽  
Content Type ◽  
E Coli ◽  
Facultative Anaerobes ◽  
Serovar Typhimurium ◽  
Multispecies Biofilms

ABSTRACT This study investigated the microbial dynamics in multispecies biofilms of Escherichia coli O157:H7 strain 1934 (O157) or Salmonella enterica serovar Typhimurium ATCC 14028 (ST) and 40 strains of meat processing surface bacteria (MPB). Biofilms of O157 or ST with/without MPB were developed on stainless steel coupons at 15°C for up to 6 days. Bacteria in suspensions (inoculum, days 2 and 6) and biofilms (days 2 and 6) were enumerated by plating. The composition of multispecies cultures was determined by 16S rRNA gene sequencing. In suspensions, levels of O157 and ST were ∼2 log higher in single-species than in multispecies cultures on both sampling days. ST was 3 log higher in single-species than in multispecies biofilms. A similar trend, though to a lesser extent, was observed for O157 in biofilms on day 2 but not on day 6. No difference (P > 0.05) in bacterial counts was noted for the two MPB-pathogen cocultures at any time during incubation. Bacterial diversity in multispecies cultures decreased with incubation time, irrespective of the pathogen or culture type. The changes in the relative abundance of MPB were similar for the two MPB-pathogen cocultures, though different interbacterial interactions were noted. Respective fractions of ST and O157 were 2.1% and 0.97% initially and then 0.10% and 0.07% on day 2, and 0.60% and 0.04% on day 6. The relative proportions of facultative anaerobes in both multispecies cultures were greater in both suspensions and biofilms than in the inoculum. Citrobacter, Hafnia, Aeromonas, and Carnobacterium predominated in biofilms but not always in the planktonic cultures. IMPORTANCE Results of this study demonstrate that Salmonella enterica serovar Typhimurium and E. coli O157:H7 can integrate into biofilms when cocultured with bacteria from meat plant processing surfaces. However, the degree of biofilm formation for both pathogens was substantially reduced in the presence of the competing microbiota, with S. Typhimurium more greatly affected than E. coli O157:H7. The expression of extracellular determinants such as curli and cellulose appears to be less important for biofilm formation of the pathogens in multispecies cultures than in monoculture. In contrast to previous reports regarding food processing surface bacteria, data collected here also demonstrate that facultative anaerobes may have a competitive edge over strict aerobes in establishing multispecies biofilms. It would be important to take into account the presence of background bacteria when evaluating the potential persistence of a pathogen in food processing facilities.

Anaerobic bacteria as indicators of faecal pollution

1980 ◽  
Vol 78 (3-4) ◽  
pp. s161-s169 ◽  
Author(s):  
D. W. F. Wheater ◽  
D. Mara ◽  
A. Opara ◽  
P. Singleton
Keyword(s):  
Intestinal Tract ◽  
Anaerobic Bacteria ◽  
Anaerobic Growth ◽  
Strictly Anaerobic ◽  
Gram Positive ◽  
E Coli ◽  
Faecal Pollution ◽  
Aqueous Environments ◽  
Intestinal Pathogens ◽  
Special Circumstances

SynopsisIn several well-authenticated instances intestinal pathogens, includingSalmonellaspecies, have been isolated from water in the absence of bacteria, such asEscherichia coli,commonly used to detect faecal pollution. The present study examines certain anaerobic, non-sporing commensals of the intestinal tract as alternative ‘indicator’ bacteria. The numbers of bifidobacteria andBacteroides fragilisrecovered from faecal specimens were between 109 and 1010 per gram while the Gram-positive, anaerobic cocci numbered only about 106per gram. In sewage, this numerical difference was eliminated by a rapid loss of viability of bifidobacteria andB. fragilisso that the counts of all three types of bacteria approximated to those ofE. coli.Storage tests with aerated and non-aerated sewage established that further loss of viability of bifidobacteria andB. fragilisoccurred only fairly slowly. In samples of water from the Dighty Water and River Tay Estuary, shown to be faecally polluted, the three anaerobic types of bacteria were recovered in numbers roughly equal to those ofE. coliand their persistence in the surface of the bed of the Dighty Water was also at least equal to that ofE. coli.These results demonstrated that, in spite of their strictly anaerobic growth requirements, Bifidobacteria,B. fragilisand the Gram-positive, anaerobic cocci persist in aerobic, aqueous environments. If their habitat can be shown to be reasonably restricted to the intestinal tract they are likely, under special circumstances, to be useful indicators of faecal pollution.

scholarly journals Antithetic population response to antibiotics in a polybacterial community

2020 ◽  
Vol 6 (10) ◽  
pp. eaaz5108 ◽  
Author(s):  
L. Galera-Laporta ◽  
J. Garcia-Ojalvo
Keyword(s):  
Escherichia Coli ◽  
Mathematical Model ◽  
Bacillus Subtilis ◽  
Bacterial Species ◽  
Single Species ◽  
Population Response ◽  
E Coli ◽  
Collective Response ◽  
Lactam Antibiotic ◽  
Mixed Community

Much is known about the effects of antibiotics on isolated bacterial species, but their influence on polybacterial communities is less understood. Here, we study the joint response of a mixed community of nonresistant Bacillus subtilis and Escherichia coli bacteria to moderate concentrations of the β-lactam antibiotic ampicillin. We show that when the two organisms coexist, their population response to the antibiotic is opposite to that in isolation: Whereas in monoculture B. subtilis is tolerant and E. coli is sensitive to ampicillin, in coculture it is E. coli who can proliferate in the presence of the antibiotic, while B. subtilis cannot. This antithetic behavior is predicted by a mathematical model constrained only by the responses of the two species in isolation. Our results thus show that the collective response of mixed bacterial ecosystems to antibiotics can run counter to what single-species potency studies tell us about their efficacy.

Interactions of Pseudomonas aeruginosa in predominant biofilm or planktonic forms of existence in mixed culture with Escherichia coli in vitro

2013 ◽  
Vol 59 (9) ◽  
pp. 604-610 ◽  
Author(s):  
Marina V. Kuznetsova ◽  
Irina L. Maslennikova ◽  
Tamara I. Karpunina ◽  
Larisa Yu. Nesterova ◽  
Vitaly A. Demakov
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Total Concentration ◽  
Single Species ◽  
Mixed Cultures ◽  
Interspecies Interactions ◽  
E Coli ◽  
Predominant Form ◽  
The One

Pseudomonas aeruginosa and Escherichia coli are known to be involved in mixed communities in diverse niches. In this study we examined the influence of the predominant form of cell existence of and the exometabolite production by P. aeruginosa strains on interspecies interactions, in vitro. Bacterial numbers of P. aeruginosa and E. coli in mixed plankton cultures and biofilms compared with their numbers in single plankton cultures and biofilms changed in a different way, but were in accordance with the form of P. aeruginosa cell existence. The mass of a mixed-species biofilm was greater than the mass of a single-species biofilm. Among the mixed biofilms, the one with the “planktonic” P. aeruginosa strain had the least biomass. The total pyocyanin and pyoverdin levels were found to be lower in all mixed plankton cultures. Despite this, clinical P. aeruginosa strains irrespective of the predominant form of existence (“biofilm” or “planktonic”) had a higher total concentration of exometabolites than did the reference strain in 12–24 h mixed cultures. The metabolism of E. coli, according to its bioluminescence, was reduced in mixed cultures, and the decrease was by 20- to 100-fold greater with the clinical Pseudomonas strains than the reference Pseudomonas strain. Thus, both the predominant form of existence of and the exometabolite production by distinct P. aeruginosa strains should be considered to fully understand the interspecies relationship and bacteria survival in natural communities.

scholarly journals Nucleotide-resolution bacterial pan-genomics with reference graphs

2020 ◽  
Author(s):  
Rachel M Colquhoun ◽  
Michael B Hall ◽  
Leandro Lima ◽  
Leah W Roberts ◽  
Kerri M Malone ◽  
...  
Keyword(s):  
Reference Genome ◽  
Cohort Analysis ◽  
Single Species ◽  
Epidemiological Studies ◽  
Error Rates ◽  
Genomic Variation ◽  
Nucleotide Polymorphisms ◽  
E Coli ◽  
Pan Genome ◽  
Nucleotide Resolution

AbstractBackgroundBacterial genomes follow a U-shaped frequency distribution whereby most genomic loci are either rare (accessory) or common (core); the union of these is the pan-genome. The alignable fraction of two genomes from a single species can be low (e.g. 50-70%), such that no single reference genome can access all single nucleotide polymorphisms (SNPs). The pragmatic solution is to choose a close reference, and analyse SNPs only in the core genome. Given much bacterial adaptability hinges on the accessory genome, this is an unsatisfactory limitation.ResultsWe present a novel pan-genome graph structure and algorithms implemented in the software pandora, which approximates a sequenced genome as a recombinant of reference genomes, detects novel variation and then pan-genotypes multiple samples. The method takes fastq as input and outputs a multi-sample VCF with respect to an inferred data-dependent reference genome, and is available at https://github.com/rmcolq/pandora.Constructing a reference graph from 578 E. coli genomes, we analyse a diverse set of 20 E. coli isolates. We show pandora recovers at least 13k more rare SNPs than single-reference based tools, achieves equal or better error rates with Nanopore as with Illumina data, 6-24x lower Nanopore error rates than other tools, and provides a stable framework for analysing diverse samples without reference bias. We also show that our inferred recombinant VCF reference genome is significantly better than simply picking the closest RefSeq reference.ConclusionsThis is a step towards comprehensive cohort analysis of bacterial pan-genomic variation, with potential impacts on genotype/phenotype and epidemiological studies.

scholarly journals Antibacterial Activity of Chlorhexidine Bigluconate in Relation to Biofilm Monocultures

2021 ◽  
Vol 6 (1) ◽  
pp. 184-193
Author(s):  
G. G. Chistyakova ◽  
◽  
G. A. Skorokhod ◽  
I. O. Pohodenko-Chudakova
Keyword(s):  
Antimicrobial Activity ◽  
Antibacterial Activity ◽  
Statistical Processing ◽  
Single Species ◽  
Modern Medicine ◽  
Reduction Factor ◽  
The Body ◽  
Contact Method ◽  
E Coli ◽  
High Level

On the background of a high percentage of caries incidence, the prevalence of its complications is increasing – pulpitis, apical periodontitis. Teeth with complicated caries can cause odontogenic inflammatory processes in the maxillofacial region. Being foci of chronic infection and intoxication, they have an adverse effect on the body as a whole. In connection with the above, it is obvious that determining the optimal concentration of chlorhexidine bigluconate and exposure to the dentin of the crown part of the tooth in case of carious lesion of the latter is currently very important. The purpose of the study was to evaluate the antimicrobial activity of chlorhexidine (by suspension and contact method) in various concentrations in relation to monocultures of biofilm formed on tooth sections and in U-shaped 96-well plastic plates. Material and methods. In this work, one of the most relevant pathogens for modern medicine was Staphylococcus aureus, which was one of the most powerful pathogens that form biofilms, was used as a model. The antimicrobial activity of chlorhexidine bigluconate was evaluated on S. aureus and E. coli biofilm cultures formed on dental samples and in polystyrene plastic tablets. Antimicrobial activity was evaluated by the reduction factor was determined by the difference in the number of decimal logarithms of CFU/ml in the experiment compared to the control. The obtained data was subjected to statistical processing. Results and discussion. The study revealed that 2.0 % solution of chlorhexidine bigluconate had a high level of antibacterial activity against tablet biofilm cultures of S. aureus and E. coli. When it was exposed to S. aureus and E. coli tablet biofilm cultures with exposures of 30 and 60 seconds, statistically significant differences were found (p=0.02). Secondly, statistically significant differences in the effect of sensitivity of single-species biofilm cultures of dental samples to the effect of antiseptic at the specified concentration were determined (p=0.007). At the same time, the level of antibacterial activity of 2.0 % chlorhexidine bigluconate solution in respect of tablet biofilm cultures of S. aureus and E. coli was significantly higher than in biofilm cultures of S. aureus and E. coli of dental samples (p<0.05). Conclusion. The obtained results give grounds for using them in clinical practice in order to improve the effectiveness of caries treatment which will help reduce the number of complications and on the one hand, corresponds to the main direction of medicine ‒ prevention and on the other hand, increases the level of specialized medical care provided to the population as a whole

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