Commensal Population Research Articles

Modeling and Simulation Study of the Population Dynamics of Commensal-Host-Parasite System

This paper deals with the modeling and simulation study of Commensal-host species system together with the inclusion of parasite population. The model comprises of three populations viz. Host, Commensal and Parasite. The Commensal population gets benefit from Host population but the former do not do any harm to the latter. The parasite population gets benefit and also do harm to Host population. However, the Commensal population only harms the parasites. The mathematical model is comprised of a system of three first order non-linear ordinary differential equations. Mathematical analysis of the model is conducted. Positivity and boundedness of the solution have been verified and thus shown that the model is physically meaningful and biologically acceptable. Scaled model is constructed so as to reduce the number of model parameters. Equilibrium points of the model are identified and stability analysis is conducted. Simulation study is conducted in order to support the mathematical analysis. In the present model the Commensal population lies higher and the parasite population lies below respectively the host population. This fact is well supported by the mathematical analysis as well as simulation study. The results of analysis and simulation are presented and discussed lucidly in the text of the paper.

Specific changes of enteric mycobiota and virome in inflammatory bowel disease.

One of the important features of inflammatory bowel disease (IBD) is dysbiosis of the gut microbiota. It has been well documented that changes in the commensal bacterial population are involved in IBD development. However, the function of the fungal and viral communities in IBD remains unclear. Moreover, the optimal treatment for IBD patients with opportunistic infections is still undecided. This review focused on how the enteric mycobiota and virome changes during the pathogenesis of IBD and discussed potential treatment strategies that open new insights into the managements of IBD.

Dietary and Microbial Metabolites in the Regulation of Host Immunity.

Mucosal surfaces in the body, especially the intestine, are constantly exposed to trillions of microbiomes. Accumulating evidence has revealed that changes in the composition of the gut microbiome, especially that of the commensal bacteria population, are frequently associated with immunologic disorders. These changes coincide with changes in the production of certain dietary metabolites. Recent studies have uncovered the molecular and cellular mechanisms underlying the relationships among diet, commensal bacteria, and the host immune system. In this review, we describe how dietary and microbial metabolites modulate host immunity.

Salmonella enterica Serovar Typhimurium Strategies for Host Adaptation.

Bacterial pathogens must sense and respond to newly encountered host environments to regulate the expression of critical virulence factors that allow for niche adaptation and successful colonization. Among bacterial pathogens, non-typhoidal serovars of Salmonella enterica, such as serovar Typhimurium (S. Tm), are a primary cause of foodborne illnesses that lead to hospitalizations and deaths worldwide. S. Tm causes acute inflammatory diarrhea that can progress to invasive systemic disease in susceptible patients. The gastrointestinal tract and intramacrophage environments are two critically important niches during S. Tm infection, and each presents unique challenges to limit S. Tm growth. The intestinal tract is home to billions of commensal microbes, termed the microbiota, which limits the amount of available nutrients for invading pathogens such as S. Tm. Therefore, S. Tm encodes strategies to manipulate the commensal population and side-step this nutritional competition. During subsequent stages of disease, S. Tm resists host immune cell mechanisms of killing. Host cells use antimicrobial peptides, acidification of vacuoles, and nutrient limitation to kill phagocytosed microbes, and yet S. Tm is able to subvert these defense systems. In this review, we discuss recently described molecular mechanisms that S. Tm uses to outcompete the resident microbiota within the gastrointestinal tract. S. Tm directly eliminates close competitors via bacterial cell-to-cell contact as well as by stimulating a host immune response to eliminate specific members of the microbiota. Additionally, S. Tm tightly regulates the expression of key virulence factors that enable S. Tm to withstand host immune defenses within macrophages. Additionally, we highlight the chemical and physical signals that S. Tm senses as cues to adapt to each of these environments. These strategies ultimately allow S. Tm to successfully adapt to these two disparate host environments. It is critical to better understand bacterial adaptation strategies because disruption of these pathways and mechanisms, especially those shared by multiple pathogens, may provide novel therapeutic intervention strategies.

Morphometric variations at an ecological scale: Seasonal and local variations in feral and commensal house mice

The time scales of evolutionary and ecological studies tend to converge, as shown by evidences that contemporary evolution can occur as fast as ecological processes. This opens new questions regarding variation of characters usually considered to change mostly along an evolutionary time scale, such as morphometric traits, including osteological and dental features such as mandibles and teeth of mammals. Using two-dimensional geometric morphometric approach, we questioned whether such features can change on a seasonal and local basis, in relation to the ecological dynamics of the populations. Our model comprised populations of house mice (Mus musculus domesticus) in two contrasted situations in mainland Western Europe: a feral population vs. two close commensal populations. Mitochondrial DNA (D-loop) provided insight into the diversity and dynamics of the populations.The feral population appeared as genetically highly diversified, suggesting a possible functioning as a sink in relation to the surrounding commensal populations. In contrast, commensal populations were highly homogeneous from a genetic point of view, suggesting each population to be isolated. This triggered morphological differentiation between neighboring farms. Seasonal differences in morphometric traits (mandible size and shape and molar size and shape) were significant in both settings, although seasonal variations were greater in the feral than in the commensal population. Seasonal variations in molar size and shape could be attributed to differential wear in young or overwintered populations. Differences in mandible shape could be related to aging in overwintered animals, but also possibly to differing growth conditions depending on the season. The impact of these ecological processes on morphometric traits is moderate compared to divergence over a large biogeographic scale, but their significance nevertheless underlines that even morphological characters may trace populations dynamics at small scale in time and space.

The Gut-Brain Axis, Including the Microbiome, Leaky Gut and Bacterial Translocation: Mechanisms and Pathophysiological Role in Alzheimer's Disease.

Alzheimer's disease (AD), the most common form of dementia, is a progressive disorder manifested by gradual memory loss and subsequent impairment in mental and behavioral functions. Though the primary risk factor for AD is advancing age, other factors such as diabetes mellitus, hyperlipidemia, obesity, vascular factors and depression play a role in its pathogenesis. The human gastrointestinal tract has a diverse commensal microbial population, which has bidirectional interactions with the human host that are symbiotic in health, and in addition to nutrition, digestion, plays major roles in inflammation and immunity. The most prevalent hypothesis for AD is the amyloid hypothesis, which states that changes in the proteolytic processing of the amyloid precursor protein leads to the accumulation of the amyloid beta (Aβ) peptide. Aβ then triggers an immune response that drives neuroinflammation and neurodegeneration in AD. The specific role of gut microbiota in modulating neuro-immune functions well beyond the gastrointestinal tract may constitute an important influence on the process of neurodegeneration. We first review the main mechanisms involved in AD physiopathology. Then, we review the alterations in gut microbiota and gut-brain axis that might be relevant to mediate or otherwise affect AD pathogenesis, especially those associated with aging. We finally summarize possible mechanisms that could mediate the involvement of gut-brain axis in AD physiopathology, and propose an integrative model.

Changes in the intestinal bacterial community, short-chain fatty acid profile, and intestinal development of preweaned Holstein calves. 1. Effects of prebiotic supplementation depend on site and age.

Digestive disorders are common during the first few weeks of life of newborn calves. Prebiotics are nondigestible but fermentable oligosaccharides that modulate growth and activity of beneficial microbial populations, which can result in enhanced gut health and function. Galactooligosaccharides (GOS) have demonstrated such prebiotic potential. In this study, the effect of GOS supplementation on intestinal bacterial community composition and fermentation profiles; intestinal health, development, and function; and growth was evaluated in dairy calves fed for high rates of growth. Eighty male Holstein calves were assigned either to a control treatment consisting of commercial milk replacer or to a GOS-rich (i.e., 3.4% of dry matter) milk replacer treatment. After 2 and 4wk, 8 calves per treatment were slaughtered at each age. Samples of intestinal digesta and tissue were collected for assessment of bacterial communities, short-chain fatty acid concentrations, in vitro measurement of nutrient transport and permeability, histomorphology, and gastrointestinal organ size. The remaining 48 calves continued to wk 8 to measure body growth, nutrient intake, and fecal and respiratory scores. Calves fed GOS displayed greater Lactobacillus and Bifidobacterium relative abundance and more developed intestinal epithelial structures, but also had greater fecal scores presumably related to greater colonic water secretion. Control calves showed slightly better growth and milk dry matter intake. Size of intestinal organs, intestinal nutrient transport, and epithelium paracellular resistance were not affected by treatment. Excessive GOS supplementation had both prebiotic and laxative effects, which led to slightly lower growth performance while promoting commensal bacteria population and greater intestinal epithelium growth.

The dissemination of multidrug-resistant Enterobacter cloacae throughout the UK and Ireland.

Enterobacter cloacae is a clinically important Gram-negative member of the Enterobacteriaceae, which has increasingly been recognized as a major pathogen in nosocomial infections. Despite this, knowledge about the population structure and the distribution of virulence factors and antibiotic-resistance determinants of this species is scarce. In this study, we analysed a systematic collection of multidrug-resistant E. cloacae isolated between 2001 and 2011 from bloodstream infections across hospitals in the UK and Ireland. We found that the population is characterized by the presence of multiple clones formed at widely different time periods in the past. The clones exhibit a high degree of geographical heterogeneity, which indicates extensive dissemination of these E. cloacae clones across the UK and Ireland. These findings suggest that a diverse, community-based, commensal population underlies multidrug-resistant E. cloacae infections within hospitals.

Use of bacteriophage to target bacterial surface structures required for virulence: a systematic search for antibiotic alternatives.

Bacteriophages (phage) that infect pathogenic bacteria often attach to surface receptors that are coincidentally required for virulence. Receptor loss or modification through mutation renders mutants both attenuated and phage resistant. Such attenuated mutants frequently have no apparent laboratory growth defects, but in the host, they fail to exhibit properties needed to produce disease such as mucosal colonization or survival within professional phagocytic cells. The connection between attenuation and phage resistance has been exploited in experimental demonstrations of phage therapy. In such experiments, phage resistant mutants that arise naturally during therapy are inconsequential because of their attenuated status. A more contemporary approach to exploiting this connection involves identifying small effector molecules, identified in high-throughput screens, that inhibit one or more of the steps needed to produce a functioning phage receptor. Since such biosynthetic steps are unique to bacteria, inhibitors can be utilized therapeutically, in lieu of antibiotics. Also, since the inhibitor is specific to a particular bacterium or group of bacteria, no off-target resistance is generated in the host's commensal bacterial population. This brief review covers examples of how mutations that confer phage resistance produce attenuation, and how this coincidental relationship can be exploited in the search for the next generation of therapeutic agents for bacterial diseases.

Defensins Potentiate a Neutralizing Antibody Response to Enteric Viral Infection.

α-defensins are abundant antimicrobial peptides with broad, potent antibacterial, antifungal, and antiviral activities in vitro. Although their contribution to host defense against bacteria in vivo has been demonstrated, comparable studies of their antiviral activity in vivo are lacking. Using a mouse model deficient in activated α-defensins in the small intestine, we show that Paneth cell α-defensins protect mice from oral infection by a pathogenic virus, mouse adenovirus 1 (MAdV-1). Survival differences between mouse genotypes are lost upon parenteral MAdV-1 infection, strongly implicating a role for intestinal defenses in attenuating pathogenesis. Although differences in α-defensin expression impact the composition of the ileal commensal bacterial population, depletion studies using broad-spectrum antibiotics revealed no effect of the microbiota on α-defensin-dependent viral pathogenesis. Moreover, despite the sensitivity of MAdV-1 infection to α-defensin neutralization in cell culture, we observed no barrier effect due to Paneth cell α-defensin activation on the kinetics and magnitude of MAdV-1 dissemination to the brain. Rather, a protective neutralizing antibody response was delayed in the absence of α-defensins. This effect was specific to oral viral infection, because antibody responses to parenteral or mucosal ovalbumin exposure were not affected by α-defensin deficiency. Thus, α-defensins play an important role as adjuvants in antiviral immunity in vivo that is distinct from their direct antiviral activity observed in cell culture.

A multiple endpoint analysis of the effects of chronic exposure to sediment contaminated with Deepwater Horizon oil on juvenile Southern flounder and their associated microbiomes

Exposure to oiled sediments can negatively impact the health of fish species. Here, we examine the effects of chronic exposure of juvenile southern flounder, Paralichthys lethostigma, to a sediment-oil mixture. Oil:sediment mixtures are persistent over time and can become bioavailable following sediment perturbation or resuspension. Juvenile flounder were exposed for 32 days under controlled laboratory conditions to five concentrations of naturally weathered Macondo MC252 oil mixed into uncontaminated, field-collected sediments. The percent composition of individual polycyclic aromatic hydrocarbons (PAHs) of the weathered oil did not change after mixing with the sediment. Spiked exposure sediments contained 0.04–395mg/kg tPAH50 (sum of 50 individual PAH concentration measurements). Mortality increased with both exposure duration and concentration of sediment-associated PAHs, and flounder exposed to concentrations above 8mg/kg tPAH50 showed significantly reduced growth over the course of the experiment. Evident histopathologic changes were observed in liver and gill tissues of fish exposed to more than 8mg/kg tPAH50. All fish at these concentrations showed hepatic intravascular congestion, macrovesicular hepatic vacoulation, telangiectasia of secondary lamellae, and lamellar epithelial proliferation in gill tissues. Dose-dependent upregulation of Cyp1a expression in liver tissues was observed. Taxonomic analysis of gill and intestinal commensal bacterial assemblages showed that exposure to oiled sediments led to distinct shifts in commensal bacterial population structures. These data show that chronic exposure to environmentally-relevant concentrations of oiled sediments produces adverse effects in flounder at multiple biological levels.

Changes in Activity Patterns and Intergroup Relationships After a Significant Mortality Event in Commensal Long-Tailed Macaques (Macaca Fascicularis) in Bali, Indonesia

Little is known regarding behavioral and social responses of free-ranging primates to demographic changes emerging from significant mortality events. Here, we report on the activity patterns and intergroup sociospatial relationships in a commensal population of long-tailed macaques (Macaca fascicularis) in Bali, Indonesia, that underwent a significant mortality event in summer 2012. During the period of interest, we noted heightened mortality in three of the five social groups present in this population, with adult females and juveniles experiencing higher mortality rates than adult and subadult males. Limited diagnostic data regarding pathogen identification and a lack of any conclusive etiology of the deaths prevent our ascertainment of the agent(s) responsible for the observed mortality, but given the characteristics of the event we assume it was caused by a transmissible disease outbreak. Comparing the pre- and post-mortality event periods, we found significant differences in activity patterns, including a decreased proportion of affiliation in adult females. This result is likely indicative of enhanced social instability induced by the high mortality of adult females that constitute the stable core of macaque social structure. A higher social tension between groups after the mortality event was indicated by more frequent and intense agonistic intergroup encounters. Intergroup conflict success was inversely proportional to the rate of mortality a group suffered. Our results illustrate how changes in demographic structure caused by significant mortality events may have substantial consequences on behavior and social dynamics in primate groups and at the level of a population.

Host microbe interactions: a licence to interfere?

Through many millennia of continuous evolution hosts and microorganisms have developed sophisticated and sometimes extremely complex mechanisms of coexisting through symbiosis and mutualism. It is now known that in humans, the population of commensal bacteria on or inside the body significantly outnumbers the host cells. Despite their numerical superiority, microorganisms have adjusted their physiological clocks to benefit themselves and at the same time their host through the maintenance of a healthy state. This very fine and multifaceted balance can be disrupted occasionally through the introduction of pathogens in the commensal bacterial population. The equilibrium is then perturbed to promote dysbiosis and the onset of disease. Through myriads of interactions within their host milieu, bacterial pathogens have developed mechanisms to sense bacterial or host-derived signalling molecules and adjust their physiology accordingly to favour their survival and propagation within their host. At the same time, the host has evolved systems to interfere with bacterial signalling in such a way as to support pathogen clearing and re-establishment of the balance. An example of a captivating interaction is the one involving the catecholamine hormones adrenaline and noradrenaline. This article will summarise the major findings involving host pathogen communication through bacterial or host-derived molecules and discuss ways to take advantage of our potential to interfere with this intricate signalling to profit the host and prolong a healthy life.

Prebiotic potential of oligosaccharides: A focus on xylan derived oligosaccharides

Abstract Xylan is available abundantly in nature as a major constituent of hemicellulose, a component of lignocellulosic biomass. Agricultural wastes such as straw, stalk, cob, hull, husk, bagasse and pulp of hardwood represent a major source of xylan. Xylooligosaccharides (XOS), the hydrolysis product of xylan is substrate for colonic commensal bacterial population, acting as potential prebiotic. Its fermentation produces short chain fatty acids, improves gut epithelial health and regulates metabolic process. These oligosaccharides possess bound phenolics including ferulic acid, coumaric acid, thus imparting additional antioxidant effect and immunomodulatory activity. This paper deals with xylan based oligosaccharides with an emphasis placed on the need of oligosaccharides and discusses in detail the health benefits of xylooligosaccharides.

Unexplained Benefits of Antibiotics in Childhood: Empiricism in Need of Enlightenment

Infections remain relentless causes of morbidity and mortality, particularly in the developing world. Pneumonia, diarrhea, and malaria kill 3.5 million, 2.5 million, and 655 000 people annually, respectively, and disproportionately injure children less than 5 years of age [1]. Any reduction in thisburdentochildrenshouldbewelcomed. In this issue of The Journal of Infectious Diseases, Gilliams et al [2] report that by adding azithromycin to chloroquine to treat childhood malaria, the incidences of subsequent respiratory and gastrointestinal infections are lowered, and times to next pulmonary and diarrheal illness are prolonged. For every 7 children treated with chloroquine-azithromycin for malaria, 1 case of respiratory-tract infection and 1 case of gastrointestinal-tract infection were apparently averted. This work extends prior efforts in Ethiopia, demonstrating that mass azithromycin treatment for trachoma reduced all-cause and infectious childhood mortality [3] and that azithromycin was associated with reduced mortality in a cluster-randomized trial for trachoma control [4]. The data of Gilliams et al also complement those of Trehan et al, who demonstrated a 40% reduction in mortality in Malawian children by adding amoxicillin or cefdinir to readyto-use therapeutic food regimens for the outpatient treatment of acute severe malnutrition [5]. Why might the addition of azithromycin to chloroquine reduce gut and respiratory infections? It is possible that the illnesses averted in the azithromycin antibiotic group were, in reality, unusual presentations of malaria [6, 7]. However, these children had no smear evidence of malaria when they had these gut and lung infections, making this explanation less likely. Alternatively, the azithromycin could have fortuitously inhibited growth of a specific pathogen acquired by a susceptible child before or during the course of the antibiotic treatment, thereby prohibiting pathogen population expansion or preventing colonization. The nonplasmodial, nonchlamydial target(s) of azithromycin in this cohort might have been Streptococcus pneumoniae, Haemophilus influenzae, Salmonella typhi, nontyphoidal salmonella, other gramnegative bacilli, group B streptococcus, and even mycobacteria, based on studies of childhood sepsis in Africa [8–13]. Another potential explanation for the success of azithromycin is that it altered the host’s commensal microbial population such that a yet to be encountered pulmonary or intestinal pathogen did not take hold. Finally, azithromycin might have had a nonspecific antiinflammatory effect that ameliorated the manifestations of illnesses that resemble lower-respiratory-tract infections or gastroenteritis [14]. There are precedents for antibiotics conferring unintended benefits. For example, 4 decades ago, Steigman et al, at Mount Sinai Hospital in New York, reported the complete absence of earlyonset group B Streptococcus (GBS) infections in their newborns, which they associated with universal use of intramuscular penicillin to prevent opthalmia neonatorum [15].They stated “ . . . we believe there is an urgent need to encourage appropriate, carefully designed prospective alternate case studies in order to determine whether a serendipitous observation can or cannot prevent deaths due to early-onset invasive GBS disease. . . . ” Intrapartum antibiotic prophylaxis of women, prompted by controlled studies and guided by diagnostic microbiology [16], is now established as an intervention to reduce the morbidity and mortality of early-onset GBS infections [17]. Sometimes the benefit of antibiotics is demonstrated before the etiology of a disease is Received 28 February 2014; accepted 13 March 2014; electronically published 20 March 2014. Correspondence: Lori R. Holtz, MD, Department of Pediatrics, Washington University School of Medicine, 660 S. Euclid Ave, Campus Box 8208, St. Louis, MO 63110 (holtz_l@kids.wustl.edu). The Journal of Infectious Diseases 2014;210:514–6 © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals. permissions@oup.com. DOI: 10.1093/infdis/jiu172

PGRP-SC2 Promotes Gut Immune Homeostasis to Limit Commensal Dysbiosis and Extend Lifespan

Interactions between commensals and the host impact the metabolic and immune status of metazoans. Their deregulation is associated with age-related pathologies like chronic inflammation and cancer, especially in barrier epithelia. Maintaining a healthy commensal population by preserving innate immune homeostasis in such epithelia thus promises to promote health and longevity. Here, we show that, in the aging intestine of Drosophila, chronic activation of the transcription factor Foxo reduces expression of peptidoglycan recognition protein SC2 (PGRP-SC2), a negative regulator of IMD/Relish innate immune signaling, and homolog of the anti-inflammatory molecules PGLYRP1-4. This repression causes deregulation of Rel/NFkB activity, resulting in commensal dysbiosis, stem cell hyperproliferation, and epithelial dysplasia. Restoring PGRP-SC2 expression in enterocytes of the intestinal epithelium, in turn, prevents dysbiosis, promotes tissue homeostasis, and extends lifespan. Our results highlight the importance of commensal control for lifespan of metazoans and identify SC-class PGRPs as longevity-promoting factors.

Commensal E. coli as an Important Reservoir of Resistance Encoding Genetic Elements

Background: Diarrheagenic E. coli is the most important cause of diarrhea in children and is a public health concern in developing countries. A major public problem is acquisition and transmission of antimicrobial resistance via mobile genetic elements including plasmids, conjugative transposons, and integrons which may occur through horizontal gene transfer. Objectives: The aim of this study was to investigate the distribution of class 1 and 2 integrons among commensal and enteropathogenic E. coli isolates and assess the role of commensal E. coli population as a reservoir in the acquisition and transmission of antimicrobial resistance. Materials and Methods: Swabs were collected directly from stool samples of the children with diarrhea admitted to three hospitals in Tehran, Iran during July 2012 through October 2012. Antimicrobial susceptibility testing and PCR analysis were performed for analysis of the resistance pattern and integron content of isolates. Results: A total of 20 enteropathogenic E.coli (identified as eae+stx1-stx2-) and 20 commensal E.coli were selected for analysis. The resistance pattern in commensal and pathogenic E.coli was very similar. In both groups a high rate of resistance was seen to tetracycline, streptomycin, cotrimoxazole, nalidixic acid, and minocycline. Of 20 EPEC strains, 3 strains (15 %) and 1 strain (5%) had positive results for int and hep genes, respectively. Among 20 commensal, 65% (13 strains) and 10% (2 strains) had positive results for int and hep genes, respectively. Conclusions: The higher rate of class 1 integron occurrence among commensal population proposes the commensal intestinal organisms as a potential reservoir of mobile resistance gene elements which could transfer the resistance gene cassettes to other pathogenic and/or nonpathogenic organisms in the intestinal lumen at different occasions.

Effect of 3′,5′-cyclic diguanylic acid in a broiler Clostridium perfringens infection model

In an effort to explore strategies to control Clostridium perfringens, we investigated the synergistic effect of a ubiquitous bacterial second messenger 3',5'-cyclic diguanylic acid (c-di-GMP) with penicillin G in a broiler challenge model. All chicks were inoculated in the crop by gavage on d 14, 15, and 16 with a mixture of 4 C. perfringens strains. Birds were treated with saline (control group) or 20 nmol of c-di-GMP by gavage or intramuscularly (IM) on d 24, all in conjunction with penicillin G in water for 5 d. Weekly samplings of ceca and ileum were performed on d 21 to 35 for C. perfringens and Lactobacillus enumeration. On d 35 of age, the IM treatment significantly (P < 0.05) reduced C. perfringens in the ceca, suggesting possible synergistic activity between penicillin G and c-di-GMP against C. perfringens in broiler ceca. Moreover, analysis of ceca DNA for the presence of a series of C. perfringens virulence genes showed a prevalence of 30% for the Clostridium perfringens alpha-toxin gene (cpa) from d 21 to 35 in the IM-treated group, whereas the occurrence of the cpa gene increased from 10 to 60% in the other 2 groups (control and gavage) from d 21 to 35. Detection of β-lactamase genes (blaCMY-2, blaSHV, and blaTEM) indicative of gram-negative bacteria in the same samples from d 21 to 35 did not show significant treatment effects. Amplified fragment-length polymorphism showed a predominant 92% similarity between the ceca of 21-d-old control birds and the 35-d-old IM-treated c-di-GMP group. This suggests that c-di-GMP IM treatment might be effective at restoring the normal microflora of the host on d 35 after being challenged by C. perfringens. Our results suggest that c-di-GMP can reduce the colonization of C. perfringens in the gut without increasing the selection pressure for some β-lactamase genes or altering the commensal bacterial population.

A Commensal Consumer-Induced Mediation Effects on Resource–Consumer Interactions

A general view of resource–consumer interactions is that resource intake by the consumers reduces the growth rate of resource population but it leads to an increase of consumer population. This view is proficiently interpreted with the classic Lotka–Volterra model that successfully describes the effects of changes in consumption rates due to changes in resource and consumer population densities. These effects are resulted in perpetual oscillatory dynamics of both the population densities, and the extent of the effects for given initial densities is measured by the oscillating frequency determined by the model parameters. But in many ecosystems, it has often observed a steep decline and delayed recovery in resource population that cannot be explained by the traditional Lotka–Volterra model. Foraging habits and behaviors of a consumer population may facilitate others, those usually do not affect them directly, to feed on the same resource and then to reproduce successfully. Such commensal consumers (facilitated population) can heavily influence the rate of resource exploitation and thereby affect the usual resource–consumer cycles. While involving such commensal consumer-induced effects, called here commensal mediation, into the Lotka–Volterra type models, it shows that the commensal mediation can have stabilizing or destabilizing effects on resource dynamics depending on the strength of interactions and the conditions in which the interactions occur. In the natural ecosystems where the growth rate of resource population depends on its own density even in absence of consumers, the commensal mediation provides a destabilizing effect on resource dynamics; increasing commensal population density increases the amplitude of resource fluctuations and the time laps from one peak to the next. On the other hand, in the managed ecosystems where the growth rate of resource population is expected to be maintained at a constant level in absence of consumers, the commensal mediation provides stabilizing effect at a certain condition; with a given restriction on the consumer population, decreasing mortality of the commensal population can stabilize the resource population dynamics at a stable, steady-state. Moreover, while the resource population experiences saturation effect, resource–consumer interactions with the commensal mediation exhibit a range of dynamical behaviours starting from stable equilibrium, then damped oscillation, to limit cycles as the resource carrying capacity increases from a critical level. In addition, commensal mediations with both controlling facilitator consumer population and resource harvesting are analyzed separately and the results are discussed for some exemplified managed and natural ecosystems.

Genetic Context and Structural Diversity of Class 1 Integrons from Human Commensal Bacteria in a Hospital Intensive Care Unit

Most surveys for class 1 integrons are at least partly predicated on PCR screening that targets integron conserved regions. However, class 1 integrons are structurally diverse, so dependence on conserved regions may lead to missing clinically relevant examples of class 1 integrons. Here, we surveyed a commensal population of bacteria from patients in an intensive care unit to identify class 1 integrons irrespective of their structure or genetic context. We identified several examples of class 1 integrons linked to complete Tn402-like or Tn402 hybrid transposition modules and diverse insertion points with respect to the inverted repeat IRi boundary. The diversity and abundance of class 1 integrons identified are such that many novel elements seen here would not have been identified by commonly used methods, and they revealed an additional level of complexity.