scholarly journals Nongenetic individuality, changeability, and inheritance in bacterial behavior

2021 ◽  
Vol 118 (13) ◽  
pp. e2023322118
Author(s):  
Maroš Pleška ◽  
David Jordan ◽  
Zak Frentz ◽  
BingKan Xue ◽  
Stanislas Leibler
Keyword(s):  
Phenotypic Diversity ◽  
E Coli ◽  
Behavioral Traits ◽  
Behavioral Diversity ◽  
Two Generations ◽  
Model Independent ◽  
Positive Correlations ◽  
Nongenetic Inheritance ◽  
Low Dimensional ◽  
General Studies

Isogenic populations often display remarkable levels of phenotypic diversity even in constant, homogeneous environments. Such diversity results from differences between individuals (“nongenetic individuality”) as well as changes during individuals’ lifetimes (“changeability”). Yet, studies that capture and quantify both sources of diversity are scarce. Here we measure the swimming behavior of hundreds of Escherichia coli bacteria continuously over two generations and use a model-independent method for quantifying behavior to show that the behavioral space of E. coli is low-dimensional, with variations occurring mainly along two independent and interpretable behavioral traits. By statistically decomposing the diversity in these two traits, we find that individuality is the main source of diversity, while changeability makes a smaller but significant contribution. Finally, we show that even though traits of closely related individuals can be remarkably different, they exhibit positive correlations across generations that imply nongenetic inheritance. The model-independent experimental and theoretical framework developed here paves the way for more general studies of microbial behavioral diversity.

scholarly journals Genus-wide characterization of bumblebee genomes reveals variation associated with key ecological and behavioral traits of pollinators

2020 ◽  
Author(s):  
Cheng Sun ◽  
Jiaxing Huang ◽  
Yun Wang ◽  
Xiaomeng Zhao ◽  
Long Su ◽  
...  
Keyword(s):  
Social Evolution ◽  
De Novo ◽  
Phenotypic Diversity ◽  
Incomplete Lineage Sorting ◽  
Repetitive Sequences ◽  
Gene Tree ◽  
Pathogen Transmission ◽  
Genomic Variation ◽  
Social Parasite ◽  
Behavioral Traits

AbstractBumblebees are a diverse group of globally important pollinators in natural ecosystems and for agricultural food production. With both eusocial and solitary lifecycle phases, and some social parasite species, they are especially interesting models to understand social evolution, behavior, and ecology. Reports of many species in decline point to pathogen transmission, habitat loss, pesticide usage, and global climate change, as interconnected causes. These threats to bumblebee diversity make our reliance on a handful of well-studied species for agricultural pollination particularly precarious. To broadly sample bumblebee genomic and phenotypic diversity, we de novo sequenced and assembled the genomes of 17 species, representing all 15 subgenera, producing the first genus-wide quantification of genetic and genomic variation potentially underlying key ecological and behavioral traits. The species phylogeny resolves subgenera relationships while incomplete lineage sorting likely drives high levels of gene tree discordance. Five chromosome-level assemblies show a stable 18-chromosome karyotype, with major rearrangements creating 25 chromosomes in social parasites. Differential transposable element activity drives changes in genome sizes, with putative domestications of repetitive sequences influencing gene coding and regulatory potential. Dynamically evolving gene families and signatures of positive selection point to genus-wide variation in processes linked to foraging, diet and metabolism, immunity and detoxification, as well as adaptations for life at high altitudes. These high-quality genomic resources capture natural genetic and phenotypic variation across bumblebees, offering new opportunities to advance our understanding of their remarkable ecological success and to identify and manage current and future threats.

scholarly journals Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits

2020 ◽  
Author(s):  
Cheng Sun ◽  
Jiaxing Huang ◽  
Yun Wang ◽  
Xiaomeng Zhao ◽  
Long Su ◽  
...  
Keyword(s):  
Social Evolution ◽  
De Novo ◽  
Phenotypic Diversity ◽  
Incomplete Lineage Sorting ◽  
Repetitive Sequences ◽  
Gene Tree ◽  
Pathogen Transmission ◽  
Genomic Variation ◽  
Social Parasite ◽  
Behavioral Traits

Abstract Bumblebees are a diverse group of globally important pollinators in natural ecosystems and for agricultural food production. With both eusocial and solitary life-cycle phases, and some social parasite species, they are especially interesting models to understand social evolution, behavior, and ecology. Reports of many species in decline point to pathogen transmission, habitat loss, pesticide usage, and global climate change, as interconnected causes. These threats to bumblebee diversity make our reliance on a handful of well-studied species for agricultural pollination particularly precarious. To broadly sample bumblebee genomic and phenotypic diversity, we de novo sequenced and assembled the genomes of 17 species, representing all 15 subgenera, producing the first genus-wide quantification of genetic and genomic variation potentially underlying key ecological and behavioral traits. The species phylogeny resolves subgenera relationships while incomplete lineage sorting likely drives high levels of gene tree discordance. Five chromosome-level assemblies show a stable 18-chromosome karyotype, with major rearrangements creating 25 chromosomes in social parasites. Differential transposable element activity drives changes in genome sizes, with putative domestications of repetitive sequences influencing gene coding and regulatory potential. Dynamically evolving gene families and signatures of positive selection point to genus-wide variation in processes linked to foraging, diet and metabolism, immunity and detoxification, as well as adaptations for life at high altitudes. Our study reveals how bumblebee genes and genomes have evolved across the Bombus phylogeny and identifies variations potentially linked to key ecological and behavioral traits of these important pollinators.

scholarly journals Genomewide Mutational Diversity in Escherichia coli Population Evolving in Prolonged Stationary Phase

mSphere ◽  
2017 ◽  
Vol 2 (3) ◽  
Author(s):  
Savita Chib ◽  
Farhan Ali ◽  
Aswin Sai Narain Seshasayee
Keyword(s):  
Escherichia Coli ◽  
Genetic Diversity ◽  
Stationary Phase ◽  
Phenotypic Diversity ◽  
Model System ◽  
Content Type ◽  
Neutral Drift ◽  
E Coli ◽  
Evolution By Natural Selection ◽  
Over Time

ABSTRACT Prolonged stationary phase in bacteria, contrary to its name, is highly dynamic, with extreme nutrient limitation as a predominant stress. Stationary-phase cultures adapt by rapidly selecting a mutation(s) that confers a growth advantage in stationary phase (GASP). The phenotypic diversity of starving E. coli populations has been studied in detail; however, only a few mutations that accumulate in prolonged stationary phase have been described. This study documented the spectrum of mutations appearing in Escherichia coli during 28 days of prolonged starvation. The genetic diversity of the population increases over time in stationary phase to an extent that cannot be explained by random, neutral drift. This suggests that prolonged stationary phase offers a great model system to study adaptive evolution by natural selection. Prolonged stationary phase is an approximation of natural environments presenting a range of stresses. Survival in prolonged stationary phase requires alternative metabolic pathways for survival. This study describes the repertoire of mutations accumulating in starving Escherichia coli populations in lysogeny broth. A wide range of mutations accumulates over the course of 1 month in stationary phase. Single nucleotide polymorphisms (SNPs) constitute 64% of all mutations. A majority of these mutations are nonsynonymous and are located at conserved loci. There is an increase in genetic diversity in the evolving populations over time. Computer simulations of evolution in stationary phase suggest that the maximum frequency of mutations observed in our experimental populations cannot be explained by neutral drift. Moreover, there is frequent genetic parallelism across populations, suggesting that these mutations are under positive selection. Finally, functional analysis of mutations suggests that regulatory mutations are frequent targets of selection. IMPORTANCE Prolonged stationary phase in bacteria, contrary to its name, is highly dynamic, with extreme nutrient limitation as a predominant stress. Stationary-phase cultures adapt by rapidly selecting a mutation(s) that confers a growth advantage in stationary phase (GASP). The phenotypic diversity of starving E. coli populations has been studied in detail; however, only a few mutations that accumulate in prolonged stationary phase have been described. This study documented the spectrum of mutations appearing in Escherichia coli during 28 days of prolonged starvation. The genetic diversity of the population increases over time in stationary phase to an extent that cannot be explained by random, neutral drift. This suggests that prolonged stationary phase offers a great model system to study adaptive evolution by natural selection.

scholarly journals Acetate and glycerol are not uniquely suited for the evolution of cross-feeding in E. coli

2020 ◽  
Vol 16 (11) ◽  
pp. e1008433
Author(s):  
Magdalena San Roman ◽  
Andreas Wagner
Keyword(s):  
Carbon Source ◽  
Experimental Evolution ◽  
Phenotypic Diversity ◽  
Carbon Sources ◽  
Metabolic Modeling ◽  
Metabolic Changes ◽  
E Coli ◽  
Biochemical Pathways ◽  
Genome Scale ◽  
Feeding Interactions

The evolution of cross-feeding among individuals of the same species can help generate genetic and phenotypic diversity even in completely homogeneous environments. Cross-feeding Escherichia coli strains, where one strain feeds on a carbon source excreted by another strain, rapidly emerge during experimental evolution in a chemically minimal environment containing glucose as the sole carbon source. Genome-scale metabolic modeling predicts that cross-feeding of 58 carbon sources can emerge in the same environment, but only cross-feeding of acetate and glycerol has been experimentally observed. Here we use metabolic modeling to ask whether acetate and glycerol cross-feeding are especially likely to evolve, perhaps because they require less metabolic change, and thus perhaps also less genetic change than other cross-feeding interactions. However, this is not the case. The minimally required metabolic changes required for acetate and glycerol cross feeding affect dozens of chemical reactions, multiple biochemical pathways, as well as multiple operons or regulons. The complexity of these changes is consistent with experimental observations, where cross-feeding strains harbor multiple mutations. The required metabolic changes are also no less complex than those observed for multiple other of the 56 cross feeding interactions we study. We discuss possible reasons why only two cross-feeding interactions have been discovered during experimental evolution and argue that multiple new cross-feeding interactions may await discovery.

scholarly journals Effect of inoculum size and antibiotics on bacterial traveling bands in a thin microchannel defined by optical adhesive

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Yang Liu ◽  
Thomas Lehnert ◽  
Martin A. M. Gijs
Keyword(s):  
Phenotypic Diversity ◽  
Swimming Performance ◽  
Effective Diffusion ◽  
Bacterial Chemotaxis ◽  
Microfluidic Channel ◽  
Adhesive Layer ◽  
Inoculum Size ◽  
E Coli ◽  
Optical Adhesive ◽  
The Impact

AbstractPhenotypic diversity in bacterial flagella-induced motility leads to complex collective swimming patterns, appearing as traveling bands with transient locally enhanced cell densities. Traveling bands are known to be a bacterial chemotactic response to self-generated nutrient gradients during growth in resource-limited microenvironments. In this work, we studied different parameters of Escherichia coli (E. coli) collective migration, in particular the quantity of bacteria introduced initially in a microfluidic chip (inoculum size) and their exposure to antibiotics (ampicillin, ciprofloxacin, and gentamicin). We developed a hybrid polymer-glass chip with an intermediate optical adhesive layer featuring the microfluidic channel, enabling high-content imaging of the migration dynamics in a single bacterial layer, i.e., bacteria are confined in a quasi-2D space that is fully observable with a high-magnification microscope objective. On-chip bacterial motility and traveling band analysis was performed based on individual bacterial trajectories by means of custom-developed algorithms. Quantifications of swimming speed, tumble bias and effective diffusion properties allowed the assessment of phenotypic heterogeneity, resulting in variations in transient cell density distributions and swimming performance. We found that incubation of isogeneic E. coli with different inoculum sizes eventually generated different swimming phenotype distributions. Interestingly, incubation with antimicrobials promoted bacterial chemotaxis in specific cases, despite growth inhibition. Moreover, E. coli filamentation in the presence of antibiotics was assessed, and the impact on motility was evaluated. We propose that the observation of traveling bands can be explored as an alternative for fast antimicrobial susceptibility testing.

POPULATION INCREASES IN OBESITY APPEAR TO BE PARTLY DUE TO GENETICS

2004 ◽  
Vol 36 (5) ◽  
pp. 547-559 ◽  
Author(s):  
LEE ELLIS ◽  
DAN HAMAN
Keyword(s):  
Genetic Factors ◽  
The Body ◽  
Obese Women ◽  
Normal Range ◽  
Adoption Studies ◽  
Medical Treatments ◽  
Overweight Women ◽  
North Americans ◽  
Two Generations ◽  
Positive Correlations

Studies have documented substantial increases in obesity throughout most of the industrialized world in recent decades. The majority of explanations for these increases have centred around environmental factors such as the increasing availability of high-fat, high-carbohydrate foods and sedentary lifestyles. This study sought to determine if genetic factors might be contributing to the increases in the proportions of North Americans who are obese and overweight. The body mass index (BMI) for a large sample of two generations of United States and Canadian subjects was correlated with family fertility indicators. Small but highly significant positive correlations were found between the BMIs of family members and their reproduction rates, especially in the case of women. For instance, mothers in the sample (most of whom were born in the 1940s and 50s) who were in the normal or below normal range had an average of 4·3 siblings and 3·2 children, compared with 4·8 siblings and 3·5 children for mothers who were overweight or obese. When combined with evidence from twin and adoption studies indicating that genes make substantial contributions to obesity, this study suggests that recent increases in obesity are partially the result of overweight and obese women having more children than is true for average and underweight women. It is speculated that improvements in medical treatments for conditions associated with obesity – particularly diabetes and heart disease – are making it possible for overweight women to live longer and to be more fertile than was true historically.

scholarly journals Commercial microbiota test revealed differences in the composition of intestinal microorganisms between children with autism spectrum disorders and neurotypical peers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Magdalena Jendraszak ◽  
Mirosława Gałęcka ◽  
Małgorzata Kotwicka ◽  
Aleksandra Regdos ◽  
Michalina Pazgrat-Patan ◽  
...  
Keyword(s):  
Autism Spectrum Disorders ◽  
Negative Correlation ◽  
Children With Autism ◽  
Autism Spectrum ◽  
Healthy Children ◽  
E Coli ◽  
Intestinal Microorganisms ◽  
Akkermansia Muciniphila ◽  
Spectrum Disorders ◽  
Positive Correlations

AbstractThe early-life modifications of intestinal microbiota may impact children's subsequent emotional and cognitive development. Studies show that some bacteria species in gut microbiota, and the lack of others, may play a key role in autism spectrum disorders (ASD) development. Fecal samples were obtained from three groups of children: 16 healthy, 24 with allergies (ALG), and 33 with ASD (probiotics and non-probiotics users). The analysis was carried out according to the KyberKompakt Pro protocol. We observed a significantly higher level of Klebsiella spp. in the healthy children from the non-probiotics group, considering three groups. In the same group, Bifidobacterium spp. the level was lower in ASD compared to neurotypical individuals. In healthy children who did not use probiotics, strong positive correlations were observed in E. coli and Enterococcus spp. and Bacteroides and Klebsiella spp., and a negative correlation for Akkermansia muciniphila with both Klebsiella spp. and Bacteroides spp. In the ASD group who take probiotics, a strongly negative correlation was observed in Lactobacillus spp., and both Faecalibacterium prausnitzii and Akkermansia muciniphila levels. In the ALG group, the strongest, negative correlation was found between Enterococcus spp. and Lactobacillus spp. as in Akkermansia muciniphila and Bifidobacterium spp. The simple commercial test revealed minor differences in the composition of intestinal microorganisms between children with autism spectrum disorders and neurotypical peers.

scholarly journals Behavioral diversity in microbes and low-dimensional phenotypic spaces

2013 ◽  
Vol 110 (34) ◽  
pp. 14018-14023 ◽  
Author(s):  
David Jordan ◽  
Seppe Kuehn ◽  
Eleni Katifori ◽  
Stanislas Leibler
Keyword(s):  
Behavioral Diversity ◽  
Low Dimensional
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