Population Dynamics Of Bacteria Research Articles

Deterministic Modeling of the Issue of Dental Caries and Oral Bacterial Growth: A Brief Review

Dental caries is a chronic disease that mostly interferes with oral health worldwide. It is caused by acidic bacteria on the enamel surface, mainly Streptococcus mutans, forming an oral biofilm that can be transmitted among people. The spread behavior and population dynamics of bacteria must be studied to control this disease, which can be approached through mathematical modeling. In this review, we aimed to identify the utilization of compartmental models in studying bacterial behavior. The aim was to explore compartmental model utilization and reveal the research gaps. This study was conducted with the PRISMA guidelines for scoping reviews to identify an existing mathematical model to study the phenomenon. Four databases, Scopus, ScienceDirect, PubMed, and Dimensions, were used to search for related studies. Our results showed that compartmental model utilization for studying bacteria’s role in dental caries is sparse and poorly explained. Moreover, the constructed models have not yet considered more intervention efforts. A study is needed to explore this phenomenon by developing a mathematical model considering some situations. When conducted, it will result in more insights into controlling the spread of bacteria to prevent dental caries.

Feasibility of engineered Bacillus subtilis for use as a microbiome-based topical drug delivery platform.

Non-adherence to medication is a major challenge in healthcare that results in worsened treatment outcomes for patients. Reducing the frequency of required administrations could improve adherence but is challenging for topical drug delivery due to the generally short residence time of topical formulations on the skin. In this study, we sought to determine the feasibility of developing a microbiome-based, long-acting, topical delivery platform using Bacillus subtilis for drug production and delivery on the skin, which was assessed using green fluorescent protein as a model heterologous protein for delivery. We developed a computational model of bacteria population dynamics on the skin and used its qualitative predictions to guide experimental design choices. Using an ex vivo pig skin model and a human skin tissue culture model, we saw persistence of delivered bacteria for multiple days and observed little evidence of cytotoxicity to human keratinocyte cells in vitro. Finally, using an in vivo mouse model, we found that the delivered bacteria persisted on the skin for at least 1 day during every-other-day application and did not appear to present safety concerns. Taken together, our results support the feasibility of using engineered B. subtilis for topical drug delivery.

Charge transport, information scrambling and quantum operator-coherence in a many-body system with U(1) symmetry

In this work, we derive an exact hydrodynamical description for the coupled, charge and operator dynamics, in a quantum many-body system with U(1) symmetry. Using an emergent symmetry in the complex Brownian SYK model with charge conservation, we map the operator dynamics in the model to the imaginary-time dynamics of an SU(4) spin-chain. We utilize the emergent SU(4) description to demonstrate that the U(1) symmetry causes quantum-coherence to persist even after disorder-averaging, in sharp contrast to models without symmetries. In line with this property, we write down a ‘restricted’ Fokker-Planck equation for the out-of-time ordered correlator (OTOC) in the large-N limit, which permits a classical probability description strictly in the incoherent sector of the global operator-space. We then exploit this feature to describe the OTOC in terms of a Fisher-Kolmogorov-Petrovsky-Piskun (FKPP)-equation which couples the operator with the charge and is valid at all time-scales and for arbitrary charge-density profiles. The coupled equations obtained belong to a class of models also used to describe the population dynamics of bacteria embedded in a diffusive media. We simulate them to explore operator-dynamics in a background of non-uniform charge configuration, which reveals that the charge transport can strongly affect dynamics of operators, including those that have no overlap with the charge.

Nonlinear Diffusion for Bacterial Traveling Wave Phenomenon.

The bacterial traveling waves observed in experiments are of pulse type which is different from the monotone traveling waves of the Fisher-KPP equation. For this reason, the Keller-Segel equations are widely used for bacterial waves. Note that the Keller-Segel equations do not contain the population dynamics of bacteria, but the population of bacteria multiplies and plays a crucial role in wave propagation. In this paper, we consider the singular limits of a linear system with active and inactive cells together with bacterial population dynamics. Eventually, we see that if there are no chemotactic dynamics in the system, we only obtain a monotone traveling wave. This is evidence that chemotaxis dynamics are needed even if population growth is included in the system.

Information geometry in the population dynamics of bacteria

In recent years, researchers have delved into the relationship between information and stochastic thermodynamics. In this paper, we apply the information geometry to discover the physical limitation in bacterial growth. By mapping the evolution of distribution to the motion on the hypersphere, we discover a relationship between evolutionary time and cost in the bacterial growth process. Through the change in fitness, we can understand how natural selection affects this relationship. From the expression of geodesic in the maximum entropy (MaxEnt) model, we find that the statistical distance between two steady distributions of bacterial growth rate is positively correlated to the number of independent fluxes.

Synchronizing use of sophisticated wet-laboratory and in-field handheld technologies for real-time monitoring of key microalgae, bacteria and physicochemical parameters influencing efficacy of water quality in a freshwater aquaculture recirculation system: A case study from the Republic of Ireland

There has been growing interest in exploiting microalgae as a natural process for low cost wastewater treatment and for water quality control and remediation in aquaculture. This constitutes the first study to report on a strong relationship between use of sophisticated wet-laboratory flow cytometry equipment and in-field AlgaeTorch® technologies for determining microalgae and bacteria population dynamics in a freshwater pill-pond aquaculture farm over a 10-month monitoring period producing Eurasian Perch, Perca fluviatilis, in the Republic of Ireland. Nitrate levels and temperature were the most significant factors influencing microalgae numbers in rearing and treatment ponds as determined by Principle Component Analysis. Variance in climate, namely drought conditions that occurred during monitoring period, did not affect microalgae or microbial numbers. Chlorophyta, Bacillariophyta and Cryptophyta were the most dominant algal divisions observed in this recirculating aquaculture system, many of these are recognized as a natural source of beneficial prebiotics for fish. Determining baseline microalgal profiles in rearing water, followed by elucidating physicochemical parameters governing wastewater treatment performance, can inform future intensification and diversification of freshwater aquaculture by exploiting and replicating knowledge of favourable algal-microbial ecosystems. Furthermore, holistic datasets can be utilised for smart agriculture by way of informing management tools for future remote monitoring and decision-making by producers.

Effect of inoculated azotobacteria and Phanerochaete chrysosporium on the composting of olive pomace: Microbial community dynamics and phenols evolution

The effect of inoculated azotobacteria and basidiomycetes white-rot fungi on the population dynamics of bacteria and eumycetes during the co-composting of olive mill pomace and wheat straw was evaluated by Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) analysis combined with sequencing of rRNA gene amplicons from selected DGGE bands. The evolution of pH, temperature, phytotoxicity and water-soluble phenol content during co-composting was also monitored. In general, a similar evolution of microbial biodiversity was seen in both the inoculated and uninoculated (control) piles, which was in keeping with a similar evolution of phytotoxicity and water-soluble phenol content. Overall, under the conditions applied, data suggest a marginal influence of the inoculated starters on the physical, chemical and microbiological properties of compost piles, with the resident microbiota playing a major role.

Nonlocal singular elliptic system arising from the amoeba–bacteria population dynamics

In this paper, we prove the existence of coexistence states for a nonlocal singular elliptic system that arises from the interaction between amoeba and bacteria populations. Our study is based on fixed point arguments using a version of the Bolzano’s theorem, for which we will first analyze a local system by bifurcation theory. Moreover, we study the behavior of the coexistence region obtained and we interpret our results according to the growth rate of both species.

Viable and Total Bacterial Populations Undergo Equipment- and Time-Dependent Shifts during Milk Processing.

We set out to identify the viable and total bacterial content in milk as it passes through a large-scale, dairy product manufacturing plant for pasteurization, concentration, separation, blending, and storage prior to cheese manufacture. A total of 142 milk samples were collected from up to 10 pieces of equipment for a period spanning 21 h on two collection dates in the spring and late summer of 2014. Bacterial composition in the milk was determined by 16S rRNA marker gene, high-throughput DNA sequencing. Milk samples from the late summer were paired such that half were treated with propidium monoazide (PMA) to enrich for viable cells prior to quantification by PCR and identification by DNA sequence analysis. Streptococcus had the highest median relative abundance across all sampling sites within the facility on both sampling dates. The proportions of Anoxybacillus, Thermus, Lactococcus, Lactobacillus, Micrococcaceae, and Pseudomonas were also elevated in some samples. Viable cells detected by PMA treatment showed that Turicibacter was enriched after high-temperature short-time pasteurization, whereas proportions of Staphylococcus were significantly reduced. Using clean-in-place (CIP) times as a reference point, Bacillus, Pseudomonas, and Anoxybacillus were found in high relative proportions in several recently cleaned silos (<19 h since CIP). At later times (>19 h after CIP), 10 of 11 silos containing elevated viable cell numbers were enriched in Acinetobacter and/or Lactococcus These results show the tremendous point-to-point and sample-dependent variations in bacterial composition in milk during processing.IMPORTANCE Milk undergoes sustained contact with the built environment during processing into finished dairy products. This contact has the potential to influence the introduction, viability, and growth of microorganisms within the milk. Currently, the population dynamics of bacteria in milk undergoing processing are not well understood. Therefore, we measured for total and viable bacterial composition and cell numbers in milk over time and at different processing points in a cheese manufacturing facility in California. Our results provide new perspectives on the dramatic variations in microbial populations in milk during processing even over short amounts of time. Although some of the changes in the milk microbiota were predictable (e.g., reduced viable cell numbers after pasteurization), other findings could not be easily foreseen based on knowledge of bacteria contained in raw milk or when the equipment was last cleaned. This information is important for predicting and controlling microbial spoilage contaminants in dairy products.

Linking microbial diversity and population dynamics to the removal efficiency of pharmaceutically active compounds (PhACs) in an anaerobic/anoxic/aerobic (A2O) system

The removal efficiencies (REs) of nineteen pharmaceutically active compounds (PhACs) (six antibiotics-clarithromycin, ofloxacin, sulfadiazine, sulfamethazine, sulfamethoxazole and trimethoprim -, four β-blockers -atenolol, metoprolol, propranolol and sotalol-, two antihypertensives/diuretics -furosemide and hydrochlorothiazide-, three lipid regulators -bezafibrate, fenofibrate and gemfibrozil-, and four psychiatric medications -carbamazepine, diazepam, lorazepam and paroxetine) were ascertained in a pilot-scale anaerobic/anoxic/aerobic (A2O) system treating urban wastewater, long term operated during two experimental phases using different sets of environmental conditions and operating parameters. Illumina MiSeq sequencing was used to investigate the structure, diversity and population dynamics of bacteria, archaea and fungi communities in the activated sludge. The results showed that mixed liquor suspended solids (MLSS) and food-to-microorganisms ratio (F/M) were operational parameters significantly influencing the REs of five of the analyzed PhACs in the A2O system. Biota-environment (BIO-ENV) analysis revealed strong correlations between population shifts of the activated sludge community and the REs of PhACs of the different pharmaceutical families. Increased REs of clarithromycin, furosemide, bezafibrate and gemfibrozil were concomitant to higher relative abundances of bacterial phylotypes classified within the Rhodobacteraceae and Sphingomonadaceae (Alphaproteobacteria), while those of Betaproteobacteria, Chloroflexi and Methanomethylovorans (Euryarchaea) correlated positively with the REs of up to seven PhACs belonging to different therapeutic groups.

Predictive modelling of a novel anti-adhesion therapy to combat bacterial colonisation of burn wounds.

As the development of new classes of antibiotics slows, bacterial resistance to existing antibiotics is becoming an increasing problem. A potential solution is to develop treatment strategies with an alternative mode of action. We consider one such strategy: anti-adhesion therapy. Whereas antibiotics act directly upon bacteria, either killing them or inhibiting their growth, anti-adhesion therapy impedes the binding of bacteria to host cells. This prevents bacteria from deploying their arsenal of virulence mechanisms, while simultaneously rendering them more susceptible to natural and artificial clearance. In this paper, we consider a particular form of anti-adhesion therapy, involving biomimetic multivalent adhesion molecule 7 coupled polystyrene microbeads, which competitively inhibit the binding of bacteria to host cells. We develop a mathematical model, formulated as a system of ordinary differential equations, to describe inhibitor treatment of a Pseudomonas aeruginosa burn wound infection in the rat. Benchmarking our model against in vivo data from an ongoing experimental programme, we use the model to explain bacteria population dynamics and to predict the efficacy of a range of treatment strategies, with the aim of improving treatment outcome. The model consists of two physical compartments: the host cells and the exudate. It is found that, when effective in reducing the bacterial burden, inhibitor treatment operates both by preventing bacteria from binding to the host cells and by reducing the flux of daughter cells from the host cells into the exudate. Our model predicts that inhibitor treatment cannot eliminate the bacterial burden when used in isolation; however, when combined with regular or continuous debridement of the exudate, elimination is theoretically possible. Lastly, we present ways to improve therapeutic efficacy, as predicted by our mathematical model.

Effect of Seasonal Variation on Anaerobic Treatment of Organic Municipal Solid Waste-II: Population Dynamics of Bacteria and Archaea Communities

This study was designed to investigate the effect of seasonal variation on population dynamics of bacteria and archaea communities during anaerobic treatment of organic municipal solid waste. The waste was subjected to anaerobic treatment inside one-stage 250 L-capacity batch-type mesophilic poly-tank reactors with used volume of 230 L, substrate concentration of 5.53% total solids, rumen juice as the source of microbial inoculum and a retention time of 84 days. The first Anaerobic Digestion (ADH) treatment was conducted during the dry season (between February and April, 2016) while the second Anaerobic Digestion (ADC) treatment, a repeat of the first process, was conducted during the rainy season (between July and October, 2016). To monitor performance of the anaerobic treatment process, populations of selected bacteria and archaea groups and biodegradation of the feed where estimated with time using standard methods. Inside the ADH system, the population of Acetoclastic Methanogens (AMA), Hydrogenotrophic Methanogens (HMA), Strict Anaerobic Bacteria (SAB) and Facultative Anaerobic Bacteria (FAB) ranged from not-detected to 8.76 × 106 CFU/ml, not-detected to 7.93 × 106 CFU/ml, 1.45 × 106 CFU/ml to 4.18 × 107 CFU/ml and 1.2 × 106 MPN/ml to 7.5 × 107 MPN/ml respectively with time. Inside the ADC system, the population of AMA, HMA, SAB and FAB ranged from not-detected to 1.46 × 106 CFU/ml, not-detected to 1.05 × 106 CFU/ml, 9.2 × 105 CFU/ml to 1.85 × 107 CFU/ml and 2.4 × 106 MPN/ml to 1.2 × 108 MPN/ml respectively with time. Biodegradation of the feed inside the ADH system and the ADC system, increased to 97.21% and 75.86% respectively after 84 days. Microbial populations inside the ADH-system increased significantly more than the microbial populations inside the ADC-systems with time, leading to a significantly (p<0.05) better performance of the ADH-system than the ADC-system with respect to biodegradation of the feed. Therefore, seasonal variation appears to have influenced the population dynamics of microbial communities during anaerobic degradation of the waste.

Lactic acid bacteria population dynamics during spontaneous fermentation of radish (Raphanus sativus L.) roots in brine.

The aim of the present study was to assess the microecosystem development and the dynamics of the lactic acid bacteria population during spontaneous fermentation of radish (Raphanus sativus L.) roots in brine at 20 and 30 °C. In both temperatures, lactic acid bacteria prevailed the fermentation; as a result, the pH value was reduced to ca. 3.6 and total titrable acidity increased to ca. 0.4% lactic acid. Enterococci population increased and formed a secondary microbiota while pseudomonads, Enterobacteriaceae and yeasts/molds populations were below enumeration limit already before the middle of fermentation. Pediococcus pentosaceus dominated during the first days, followed by Lactobacillus plantarum that prevailed the fermentation until the end. Lactobacillus brevis was also detected during the final days of fermentation. A succession at sub-species level was revealed by the combination of RAPD-PCR and rep-PCR analyses. Glucose and fructose were the main carbohydrates detected in brine and were metabolized into lactic acid, acetic acid and ethanol.

Prevalence of Proteobacteria and Armatimonadetes phyla in a Photobioreactor under Carbon- and Nitrogen-Free Production Process

In prokaryotes, the autotrophic population within the bacteria kingdom presents great biotechnological potential. For taxonomic analysis of species, the sequence encoding the small subunit ribosomal RNA gene (16S rRNA) is currently the most reliable technique for phylogenetic bacterial classification. Sequencing can define the population diversity and ecological importance within a habitat. The study of autotrophic bacteria population dynamics in a photobioreactor using a carbon and nitrogen free culture medium could provide information about succession dynamics under controlled conditions. The aim of this study was to identify the bacterial populations present in a photobioreactor by 16S rRNA amplicon sequence comparison from samples taken at 0, 7, and 14 fermentation days. Most of the identified clones were described to the level of genera from the following phyla: Proteobacteria (40%), Armatimonadetes (35%), Firmicutes (17.5%), Actinobacteria (2.5%), and Cyanobacteria/Chloroplast (2.5%). Bacterial strains from those phyla have been reported in aquatic environments and were considered uncultivable; however, sequences indicated the presence of the clones A-123 (ID: HQ860522.1) from time 0, and YHS25 (GU305825.1) after 7 days of culture. Our findings demonstrated the major presence of autotrophic bacterial populations of the Proteobacteria and Armatimonadetes phyla, which grew under artificial culture conditions in a photobioreactor.

Community and functional diversity of bacteria associated with propagative and dispersal forms of Bursaphelenchus xylophilus

The pine wood nematode (PWN),Bursaphelenchus xylophilus, the pathogen of pine wilt disease, has propagative and dispersal forms in its life cycle, which is associated with the insect vectorMonochamus alternatus. Pine wood nematode-associated bacteria could play important roles in pine wilt disease. In this study, the diversity and population dynamics of bacteria in propagative and dispersal stages of PWN were analysed using cultural and Biolog Eco™ methods coupled with high-throughput sequencing. The results revealed that culturableStenotrophomonasin PWN from diseased pine was not found fromM. alternatus. Bacteria in dispersal PWN carried byM. alternatusshowed the highest total carbon utilisation. The high-throughput analysis showed thatStenotrophomonas,AchromobacterandSphingobacteriumwere more abundant in propagative PWN than in dispersal PWN, whereasCitrobacter,Vibrioand Enterobacteriaceae were more abundant in dispersal PWN. The results showed that bacteria of PWN in different developmental forms differed. This change of bacteria might help PWN to adapt to the changing environment.

Velocity Vector Field Optimization in Bioventing

AbstractBioventing is a technology used to remove some kinds of pollutants from the subsoil and it is based on the capability of some bacteria species to biodegrade contaminants. The biochemical reaction requires, among other things, oxygen and, therefore, oxygen is inflated into the subsoil by wells. The mathematical model describes the movement of the different fluids which are present in the subsoil – air, water, pollutants, oxygen and so on – and the bacteria population dynamics. The presence of source reactive terms in the continuity equations allows the contaminant biodegradation to be described.The design of a subsoil decontamination intervention concerns bioavailability problems and, in particular, the oxygen concentration. Therefore, in order to enhance the biodegradation phenomenon, the optimization of the subsoil oxygen velocity field in the polluted area is required, by an appropriate choice of the well positions and of the well air inflating rates. In mathematical terms, the goal is to obtain the decontamination of the subsoil with an optimal value of an objective function by acting on some control variables which, in this case, are the well positions and the inflating rates. In this paper several kind of objective function are proposed. (© 2015 Wiley‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)

The dynamics of bacteria population on the skin, throat, and gastrointestinal tract of HIV-seropositive patients

Background: The study determined bacteria population on the skin, throat, and gastrointestinal tract of human immunodeficiency virus (HIV)-seropositive patients and HIV seronegative controls at the baseline, 3 months, and 6 months, respectively, at Obafemi Awolowo University Teaching Hospitals Complex (OAUTHC), Ile-Ife, Osun State, Nigeria and State Specialist Hospital, Akure, Ondo State, Nigeria between May and November, 2012. Materials and Methods: Seventy HIV-seropositive subjects and 51 HIV seronegative controls who attended the HIV clinics were recruited. Skin, throat, and rectal swabs were obtained from the participants using sterile cotton-tipped applicators introduced into thioglycollate broth and incubated at 37°C overnight. When growth was noticed, the broth culture was streaked on different bacteriologic media and the isolates were characterized by the standard methods and disc diffusion for antibiotic sensitivity. Results: The number of isolates cultured from the HIV-seropositive subjects was 934, with the distribution being 397, 326, and 211 at the baseline, 3 months, and 6 months, respectively. The distribution of 1,138 isolates cultured from 51 HIV-seronegative controls was 433, 354, and 351 at the baseline, 3 months, and 6 months, respectively. At the baseline among HIV-seropositive patients, the predominant isolates were Arcanobacterium haemolyticum, Pseudomonas aeruginosa (P. aeruginosa), and Bacillus cereus (B. cereus). However, Corynebacterium haemolyticum, Enterococcus faecalis, and Escherichia coli (E. coli) were predominant at 3 months while at 6 months, Corynebacterium haemolyticum and Corynebacterium diphtheriae had the highest frequency followed by Pseudomonas fluorescens (P. fluorescens). In the controls, Corynebacterium diphtheriae, Listeria monocytogenes, and Staphylococcus xylosus (S. xylosus) predominated at the baseline and at 3 months while at 6 months, B. cereus, S. xylosus, and Staphylococcus aureus (S. aureus) were prevalent. Multiple resistances were widespread among the isolates. Conclusion: A preponderance of opportunists was observed in the HIV-seronegatives but higher multiresistant strains in the HIV-seropositives, suggesting both groups live in an antibiotic pressurized environment.

Growth and death of bacteria and fungi underlie rainfall-induced carbon dioxide pulses from seasonally dried soil.

The rapid increase in microbial activity that occurs when a dry soil is rewetted has been well documented and is of great interest due to implications of changing precipitation patterns on soil C dynamics. Several studies have shown minor net changes in microbial population diversity or abundance following wet-up, but the gross population dynamics of bacteria and fungi resulting from soil wet-up are virtually unknown. Here we applied DNA stable isotope probing with H218O coupled with quantitative PCR to characterize new growth, survival, and mortality of bacteria and fungi following the rewetting of a seasonally dried California annual grassland soil. Microbial activity, as determined by CO2 production, increased significantly within three hours of wet-up, yet new growth was not detected until after three hours, suggesting a pulse of nongrowth activity immediately following wet-up, likely due to osmo-regulation and resuscitation from dormancy in response to the rapid change in water potential. Total microbial abundance revealed little change throughout the seven-day post-wet incubation, but there was substantial turnover of both bacterial and fungal populations (49% and 52%, respectively). New growth was linear between 24 and 168 hours for both bacteria and fungi, with average growth rates of 2.3 x 10(8) bacterial 16S rRNA gene copies x [g dry mass](-1) x h(-1) and 4.3 x 10(7) fungal ITS copies x [g dry mass](-1) x h(-1). While bacteria and fungi differed in their mortality and survival characteristics during the seven-day incubation, mortality that occurred within the first three hours was similar, with 25% and 27% of bacterial and fungal gene copies disappearing from the pre-wet community, respectively. The rapid disappearance of gene copies indicates that cell death, occurring either during the extreme dry down period (preceding five months) or during the rapid change in water potential due to wet-up, generates a significant pool of available C that likely contributes to the large pulse in CO2 associated with wet-up. A dynamic assemblage of growing and dying organisms controlled the CO2 pulse, but the balance between death and growth resulted in relatively stable total population abundances, even after a profound and sudden change in environment.

Mathematical modeling on bacterial resistance to multiple antibiotics caused by spontaneous mutations

We formulate a mathematical model that describes the population dynamics of bacteria exposed to multiple antibiotics simultaneously, assuming that acquisition of resistance is through mutations due to antibiotic exposure. Qualitative analysis reveals the existence of a free-bacteria equilibrium, resistant-bacteria equilibrium and an endemic equilibrium where both bacteria coexist.

Opening the Black Box: Understanding the Influence of Cropping Systems and Plant Communities on Bacterial and Fungal Population Dynamics

Since the development of agriculture 10,000 years ago, crops and the soil they grow in have interacted and affected each other‟s existence. Soil microbial communities exert an important role in maintaining the health of soil and productivity of crops, and in turn, their population dynamics are influenced by agricultural systems. Researchers have attempted to assess community structure, as well as abundance, distribution, and function of species under different agricultural management systems. The effect of plants, soil, and agricultural management practices on the population dynamics of bacteria and fungi is reviewed, and methods to describe microbial communities are discussed.Ceylon Journal of Science (Bio. Sci.) 41 (2): 89-110, 2012 DOI: http://dx.doi.org/10.4038/cjsbs.v41i2.5380