scholarly journals Host life-history traits influence the distribution of prophages and the genes they carry

2021 ◽  
Vol 377 (1842) ◽  
Author(s):  
Tyler Pattenden ◽  
Christine Eagles ◽  
Lindi M. Wahl
Keyword(s):  
Life History Traits ◽  
Bacterial Species ◽  
Gene Content ◽  
Bacterial Strains ◽  
Theme Issue ◽  
Bioinformatics Pipeline ◽  
Fast Growing ◽  
Evolutionary Forces ◽  
Host Life ◽  
Slow Growing

Bacterial strains with a short minimal doubling time—‘fast-growing’ hosts—are more likely to contain prophages than their slow-growing counterparts. Pathogenic bacterial species are likewise more likely to carry prophages. We develop a bioinformatics pipeline to examine the distribution of prophages in fast- and slow-growing lysogens, and pathogenic and non-pathogenic lysogens, analysing both prophage length and gene content for each class. By fitting these results to a mathematical model of the evolutionary forces acting on prophages, we predict whether the observed differences can be attributed to different rates of lysogeny among the host classes, or other evolutionary pressures. We also test for significant differences in gene content among prophages, identifying genes that are preferentially lost or maintained in each class. We find that fast-growing hosts and pathogens have a greater fraction of full-length prophages, and our analysis predicts that induction rates are significantly reduced in slow-growing hosts and non-pathogenic hosts. Consistent with previous results, we find that several proteins involved in the packaging of new phage particles and lysis are preferentially lost in cryptic prophages. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

Effect of protozoan predation on relative abundance of fast- and slow-growing bacteria

1989 ◽  
Vol 35 (5) ◽  
pp. 578-582 ◽  
Author(s):  
James L. Sinclair ◽  
Martin Alexander
Keyword(s):  
Growth Rate ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Growth Rates ◽  
Bacterial Species ◽  
Test Species ◽  
Fast Growing ◽  
Population Sizes ◽  
Slow Growing ◽  
Fast Growing Species

The survival of six bacterial species that had different growth rates was tested in raw sewage and sewage that was rendered free of protozoa. When test bacteria were added to protozoa-free sewage at densities of approximately 105 to 106 cells/mL, five of the six species did not decline below 105 cells/mL. If protozoa were present, the population sizes of all test species were markedly reduced, but bacterial species able to grow faster in artificial media had the larger number of survivors. When the same bacteria were inoculated into protozoa-free sewage at densities of less than 103 cells/mL, only the three species able to grow quickly in artificial media increased in abundance. When the six species were inoculated at the same densities into sewage containing protozoa, the three slow-growing species were rapidly eliminated, and two of the three fast-growing species survived in detectable numbers. We suggest that in environments with intense protozoan predation, protozoa may alter the composition of the bacterial community by eliminating slow-growing bacteria.Key words: growth rate, predation, protozoa, sewage.

scholarly journals Regime shifts in a phage-bacterial ecosystem and strategies for its control

2019 ◽  
Author(s):  
Sergei Maslov ◽  
Kim Sneppen
Keyword(s):  
Control Strategy ◽  
Partial Resistance ◽  
Bacterial Species ◽  
Alternative Stable States ◽  
Regime Shifts ◽  
Individual Species ◽  
Abortive Infection ◽  
Susceptible Host ◽  
Fast Growing ◽  
Slow Growing

ABSTRACTThe competition between bacteria often involves both nutrients and phage predators and may give rise to abrupt regime shifts between the alternative stable states characterized by different species compositions. While such transitions have been previously studied in the context of competition for nutrients, the case of phage-induced bistability between competing bacterial species has not been considered yet. Here we demonstrate a possibility of regime shifts in well-mixed phage-bacterial ecosystems. In one of the bistable states the fast-growing bacteria competitively exclude the slow-growing ones by depleting their common nutrient. Conversely, in the second state the slow-growing bacteria with a large burst size generate such a large phage population that the other species cannot survive. This type of bistability can be realized as the competition between a strain of bacteria protected from phage by abortive infection and another strain with partial resistance to phage. It is often desirable to reliably control the state of microbial ecosystems, yet bistability significantly complicates this task. We discuss successes and limitations of one control strategy in which one adds short pulses to populations of individual species. Our study proposes a new type of phage therapy, where introduction of the phage is supplemented by addition of a partially resistant host bacteria.IMPORTANCEPhage-microbial communities play an important role in human health as well as natural and industrial environments. Here we show that these communities can assume several alternative species compositions separated by abrupt regime shifts. Our model predicts these regime shifts in the competition between bacterial strains protected by two different phage defense mechanisms: abortive infection/CRISPR and partial resistance. The history dependence caused by regime shifts greatly complicates the task of manipulation and control of a community. We propose and study a successful control strategy via short population pulses aimed at inducing the desired regime shifts. In particular, we predict that a fast-growing pathogen could be eliminated by a combination of its phage and a slower-growing susceptible host.

Alistipes inops sp. nov. and Coprobacter secundus sp. nov., isolated from human faeces

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4580-4588 ◽  
Author(s):  
Andrei N. Shkoporov ◽  
Andrei V. Chaplin ◽  
Ekaterina V. Khokhlova ◽  
Victoria A. Shcherbakova ◽  
Oksana V. Motuzova ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Bacterial Species ◽  
Phylogenomic Analysis ◽  
Bacterial Strains ◽  
Positive Bacterium ◽  
Human Faeces ◽  
Cellular Fatty Acids ◽  
Faecal Microbiome ◽  
Slow Growing

Culture-based study of the faecal microbiome in two adult female subjects revealed the presence of two obligately anaerobic, non-spore-forming, rod-shaped, non-motile, Gram-negative bacterial strains that represent novel species. The first strain, designated 627T, was a fastidious, slow-growing, indole-positive bacterium with a non-fermentative type of metabolism. The strain was characterized by the production of acetic and succinic acids as metabolic end products, the prevalence of iso-C15 : 0 fatty acid and the presence of menaquinones MK-10 and MK-11. The DNA G+C content was found to be 56.6 mol%. The second strain, designated 177T, was capable of fermenting a rich collection of carbohydrate substrates, producing acetic acid as a terminal product. The strain was indole-negative and resistant to bile. The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0 (in a 1 : 1 ratio) and the predominant menaquinone was MK-11. The DNA G+C content was 37.8 mol%. A phylogenomic analysis of the draft genomes of strains 627T and 177T placed these bacteria in the genera Alistipes (family Rikenellaceae) and Coprobacter (family Porphyromonadaceae), respectively. On the basis of the phenotypic and genotypic properties of strains 627T and 177T, we conclude that these strains from human faeces represent two novel bacterial species, for which the names Alistipes inops sp. nov. (type strain 627T = DSM 28863T = VKM B-2859T) and Coprobacter secundus sp. nov. (type strain 177T = DSM 28864T = VKM B-2857T) are proposed.

scholarly journals Regime Shifts in a Phage-Bacterium Ecosystem and Strategies for Its Control

mSystems ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Sergei Maslov ◽  
Kim Sneppen
Keyword(s):  
Control Strategy ◽  
Partial Resistance ◽  
Bacterial Species ◽  
Alternative Stable States ◽  
Regime Shifts ◽  
Individual Species ◽  
Abortive Infection ◽  
Susceptible Host ◽  
Fast Growing ◽  
Slow Growing

ABSTRACT The competition between bacteria often involves both nutrients and phage predators and may give rise to abrupt regime shifts between the alternative stable states characterized by different species compositions. While such transitions have been previously studied in the context of competition for nutrients, the case of phage-induced bistability between competing bacterial species has not been considered yet. Here we demonstrate a possibility of regime shifts in well-mixed phage-bacterium ecosystems. In one of the bistable states, the fast-growing bacteria competitively exclude the slow-growing ones by depleting their common nutrient. Conversely, in the second state, the slow-growing bacteria with a large burst size generate such a large phage population that the other species cannot survive. This type of bistability can be realized as the competition between a strain of bacteria protected from phage by abortive infection and another strain with partial resistance to phage. It is often desirable to reliably control the state of microbial ecosystems, yet bistability significantly complicates this task. We discuss successes and limitations of one control strategy in which one adds short pulses to populations of individual species. Our study proposes a new type of phage therapy, where introduction of the phage is supplemented by the addition of a partially resistant host bacteria. IMPORTANCE Phage-microbe communities play an important role in human health as well as natural and industrial environments. Here we show that these communities can assume several alternative species compositions separated by abrupt regime shifts. Our model predicts these regime shifts in the competition between bacterial strains protected by two different phage defense mechanisms: abortive infection/CRISPR and partial resistance. The history dependence caused by regime shifts greatly complicates the task of manipulation and control of a community. We propose and study a successful control strategy via short population pulses aimed at inducing the desired regime shifts. In particular, we predict that a fast-growing pathogen could be eliminated by a combination of its phage and a slower-growing susceptible host.

scholarly journals The Conservation of Low Complexity Regions in Bacterial Proteins Depends on the Pathogenicity of the Strain and Subcellular Location of the Protein

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 451
Author(s):  
Pablo Mier ◽  
Miguel A. Andrade-Navarro
Keyword(s):  
Membrane Proteins ◽  
Outer Membrane ◽  
Bacterial Species ◽  
Outer Membrane Proteins ◽  
Subcellular Location ◽  
Low Complexity ◽  
Extracellular Proteins ◽  
Bacterial Strains ◽  
Bacterial Proteins ◽  
Protein Subcellular Location

Low complexity regions (LCRs) in proteins are characterized by amino acid frequencies that differ from the average. These regions evolve faster and tend to be less conserved between homologs than globular domains. They are not common in bacteria, as compared to their prevalence in eukaryotes. Studying their conservation could help provide hypotheses about their function. To obtain the appropriate evolutionary focus for this rapidly evolving feature, here we study the conservation of LCRs in bacterial strains and compare their high variability to the closeness of the strains. For this, we selected 20 taxonomically diverse bacterial species and obtained the completely sequenced proteomes of two strains per species. We calculated all orthologous pairs for each of the 20 strain pairs. Per orthologous pair, we computed the conservation of two types of LCRs: compositionally biased regions (CBRs) and homorepeats (polyX). Our results show that, in bacteria, Q-rich CBRs are the most conserved, while A-rich CBRs and polyA are the most variable. LCRs have generally higher conservation when comparing pathogenic strains. However, this result depends on protein subcellular location: LCRs accumulate in extracellular and outer membrane proteins, with conservation increased in the extracellular proteins of pathogens, and decreased for polyX in the outer membrane proteins of pathogens. We conclude that these dependencies support the functional importance of LCRs in host–pathogen interactions.

scholarly journals Isolation and efficacy of two bacterial strains antagonists of Erwinia amylovora and Pectobacterium carotovorum

2021 ◽  
Vol 31 (1) ◽  
Author(s):  
M’hamed BENADA ◽  
Boualem BOUMAAZA ◽  
Sofiane BOUDALIA ◽  
Omar KHALADI
Keyword(s):  
Fire Blight ◽  
Erwinia Amylovora ◽  
Bacterial Species ◽  
Crop Protection ◽  
Soft Rot ◽  
Causal Agent ◽  
Plant Diseases ◽  
Ecological Niches ◽  
Pectobacterium Carotovorum ◽  
Bacterial Strains

Abstract Background The development of ecofriendly tools against plant diseases is an important issue in crop protection. Screening and selection process of bacterial strains antagonists of 2 pathogenic bacterial species that limit very important crops, Erwinia amylovora, the causal agent of the fire blight disease, and Pectobacterium carotovorum, the causal agent of bacterial potato soft rot, were reported. Bacterial colonies were isolated from different ecological niches, where both pathogens were found: rhizosphere of potato tubers and fruits and leaves of pear trees from the northwest region of Algeria. Direct and indirect confrontation tests against strains of E. amylovora and P. carotovorum were performed. Results Results showed a significant antagonistic activity against both phytopathogenic species, using direct confrontation method and supernatants of cultures (p<0.005). In vitro assays showed growth inhibitions of both phytopathogenic species. Furthermore, results revealed that the strains of S. plymuthica had a better inhibitory effect than the strains of P. fluorescens against both pathogens. In vivo results on immature pear fruits showed a significant decrease in the progression of the fire blight symptoms, with a variation in the infection index from one antagonistic strain to another between 31.3 and 50%, and slice of potato showed total inhibition of the pathogen (P. carotovorum) by the antagonistic strains of Serratia plymuthica (p<0.005). Conclusion This study highlighted that the effective bacteria did not show any infection signs towards plant tissue, and considered as a potential strategy to limit the fire blight and soft rot diseases.

scholarly journals Genotypic traits and tradeoffs of fast growth in silver birch, a pioneer tree

Oecologia ◽  
2021 ◽  
Author(s):  
Juha Mikola ◽  
Katariina Koikkalainen ◽  
Mira Rasehorn ◽  
Tarja Silfver ◽  
Ulla Paaso ◽  
...  
Keyword(s):  
Resource Competition ◽  
Leaf Growth ◽  
N Uptake ◽  
Insect Herbivory ◽  
Fast Growth ◽  
Grass Cover ◽  
Soil N ◽  
Fast Growing ◽  
Slow Growing ◽  
Leaf N

AbstractFast-growing and slow-growing plant species are suggested to show integrated economics spectrums and the tradeoffs of fast growth are predicted to emerge as susceptibility to herbivory and resource competition. We tested if these predictions also hold for fast-growing and slow-growing genotypes within a silver birch, Betula pendula population. We exposed cloned saplings of 17 genotypes with slow, medium or fast height growth to reduced insect herbivory, using an insecticide, and to increasing resource competition, using naturally varying field plot grass cover. We measured shoot and root growth, ectomycorrhizal (EM) fungal production using ergosterol analysis and soil N transfer to leaves using 15N-labelled pulse of NH4+. We found that fast-growing genotypes grew on average 78% faster, produced 56% and 16% more leaf mass and ergosterol, and showed 78% higher leaf N uptake than slow-growing genotypes. The insecticide decreased leaf damage by 83% and increased shoot growth, leaf growth and leaf N uptake by 38%, 52% and 76%, without differences between the responses of fast-growing and slow-growing genotypes, whereas root mass decreased with increasing grass cover. Shoot and leaf growth of fast-growing genotypes decreased and EM fungal production of slow-growing genotypes increased with increasing grass cover. Our results suggest that fast growth is genotypically associated with higher allocation to EM fungi, better soil N capture and greater leaf production, and that the tradeoff of fast growth is sensitivity to competition, but not to insect herbivory. EM fungi may have a dual role: to support growth of fast-growing genotypes under low grass competition and to maintain growth of slow-growing genotypes under intensifying competition.

scholarly journals Studies on the Regulation of Algal Growth by Gibberellin

1971 ◽  
Vol 24 (4) ◽  
pp. 1115 ◽  
Author(s):  
RC Jennings
Keyword(s):  
Red Algae ◽  
Algal Growth ◽  
Red Alga ◽  
General Phenomenon ◽  
Hypnea Musciformis ◽  
Fast Growing ◽  
High Concentrations ◽  
Amo 1618 ◽  
Slow Growing

CCC and Amo.1618, at relatively high concentrations only, inhibited the growth of excised branch apices of the red alga Hypnea musciformis. Neither GA3 nor GA7 stimulated growth of the alga in the presence or absence of these compounds, and gibberellin-like material extracted from H. musciformis also failed to stimulate growth. However, both gibberellins stimulated the growth of slow-growing, but not fast-growing, branch apices of the related red alga Gracilaria verucosa. It is concluded that endogenous gibberellins may not regulate the growth of H. musciformis, but this is likely to be a peculiarity of this species and not a general phenomenon in red algae.

In vitro evaluation of the effect of nicotine, cotinine, and caffeine on oral microorganisms

2008 ◽  
Vol 54 (6) ◽  
pp. 501-508 ◽  
Author(s):  
Karina Cogo ◽  
Michelle Franz Montan ◽  
Cristiane de Cássia Bergamaschi ◽  
Eduardo D. Andrade ◽  
Pedro Luiz Rosalen ◽  
...  
Keyword(s):  
High Performance Liquid Chromatography ◽  
Liquid Chromatography ◽  
High Performance ◽  
Culture Media ◽  
Bacterial Species ◽  
In Vitro Study ◽  
Bacterial Strains ◽  
Planktonic Cells ◽  
Susceptibility Tests

The aim of this in vitro study was to evaluate the effects of nicotine, cotinine, and caffeine on the viability of some oral bacterial species. It also evaluated the ability of these bacteria to metabolize those substances. Single-species biofilms of Streptococcus gordonii , Porphyromonas gingivalis , or Fusobacterium nucleatum and dual-species biofilms of S. gordonii – F. nucleatum and F. nucleatum – P. gingivalis were grown on hydroxyapatite discs. Seven species were studied as planktonic cells, including Streptococcus oralis , Streptococcus mitis , Propionibacterium acnes , Actinomyces naeslundii , and the species mentioned above. The viability of planktonic cells and biofilms was analyzed by susceptibility tests and time-kill assays, respectively, against different concentrations of nicotine, cotinine, and caffeine. High-performance liquid chromatography was performed to quantify nicotine, cotinine, and caffeine concentrations in the culture media after the assays. Susceptibility tests and viability assays showed that nicotine, cotinine, and caffeine cannot reduce or stimulate bacterial growth. High-performance liquid chromatography results showed that nicotine, cotinine, and caffeine concentrations were not altered after bacteria exposure. These findings indicate that nicotine, cotinine, and caffeine, in the concentrations used, cannot affect significantly the growth of these oral bacterial strains. Moreover, these species do not seem to metabolize these substances.

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