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Even in the absence of antibiotic exposure, the gut microbiome of infants has been shown to contain numerous antibiotic resistance genes (ARGs), but the mechanism for this remains unclear. In environmental bacteria, the selective advantage of ARGs can be increased through co-localization with genes such as other ARGs, biocide resistance genes, metal resistance genes, and virulence genes. However, this phenomenon is unknown from the human gut microbiome during early life despite frequent exposures to biocides and metals from an early age. Here, we conducted a comprehensive analysis of genetic co-localization of resistance genes in a cohort of 662 Danish children and examined the association between such co-localization and environmental factors as well as gut microbial maturation. Our study showed that co-localization of ARGs with other resistance and virulence genes is common in the early gut microbiome and is associated with gut bacteria that are indicative of low maturity, especiallyE. coli. The most common forms of co-localization involved tetracycline and fluoroquinolone resistance genes located near other ARGs, and, on plasmids, co-localization predominantly occurred in the form of class 1 integrons. Antibiotic use caused a short-term increase in mobile ARGs, while non-mobile ARGs showed no significant change. Finally, we found that a high abundance of virulence genes was associated with low gut microbial maturity and that virulence genes showed even higher potential for mobility than ARGs. Our study highlights important constraints that need to be considered when developing strategies to combat ARG dissemination.

Type 2 diabetes (T2D) management is based on combined pharmacological and lifestyle intervention approaches. While their clinical benefits are well studied, less is known about their effects on the gut microbiota. We aimed to investigate if an intensive lifestyle intervention combined with conventional standard care leads to a different gut microbiota composition compared to standard care alone treatment in individuals with T2D, and if gut microbiota is associated with the clinical benefits of the treatments. Ninety-eight individuals with T2D were randomized to either an intensive lifestyle intervention combined with standard care group (N = 64), or standard care alone group (N = 34) for 12 months. All individuals received standardized, blinded, target-driven medical therapy, and individual counseling. The lifestyle intervention group moreover received intensified physical training and dietary plans. Clinical characteristics and fecal samples were collected at baseline, 3-, 6-, 9-, and 12-month follow-up. The gut microbiota was profiled with 16S rRNA gene amplicon sequencing. There were no statistical differences in the change of gut microbiota composition between treatments after 12 months, except minor and transient differences at month 3. The shift in gut microbiota alpha diversity at all time windows did not correlate with the change in clinical characteristics, and the gut microbiota did not mediate the treatment effect on clinical characteristics. The clinical benefits of intensive lifestyle and/or pharmacological interventions in T2D are unlikely to be explained by, or causally related to, changes in the gut microbiota composition.

The redundant kinematic structure of the human upper body provides sufficient dexterity in performing daily living activities, such as drinking, eating, and other manipulation tasks. Most of these Activities of Daily Living (ADL) tasks can be performed using various trajectories; however, healthy humans employ some possible trajectories to accomplish these tasks. Assistive robots can explore these Cartesian trajectories and joint angles’ trajectories from human demonstrations and utilize artificial intelligence techniques to recognize, learn, and perform ADLs using robotic arms. This paper aims to develop a platform for Assistive Robots to identify and perform ADLs through human demonstration. In this paper, two Mask Regional Convolutional Neural Networks (Mask R-CNN) were developed to predict human intention for a given task, and the Reinforcement Learning approach was implemented for optimum trajectory planning. The First Mask R-CNN network, which was used for the detection of an object, was trained on a novel dataset. This dataset comprises images captured by the research team as well as gathered images from the internet. The first Mask R-CNN is expected to achieve two main objectives. The first objective is related to structure learning, which detects an object in a cluttered environment. The second objective is to estimate parameters that maximize the weight and detection rate of diverse types of similar objects. The first Mask R-CNN tries to detect the object with its location in the image and provides a soft mask on it. The second Mask R-CNN, which tries to detect human posture, was trained on a pre-existing dataset comprising human posture images. The output of these two Mask R-CNN’s then feed-forward to recognize human intensions that can be achieved through human-pose key points. Prediction of human intention was performed if the detected object and human pose match a range of pre-stored values specific to ADLs. Once the human intention has been identified via Mask R-CNN networks, the system starts planning for an optimal trajectory. For the trajectory planning, the Q-learning approach was implemented, which uses the concept of reward and penalty while exploring the unstructured environment in order to find an optimal trajectory. Experiments were conducted to determine the level of accuracy and reliability provided by our assistive platform in predicting human actions and performing trajectory planning. Results show that our assistive platform successfully recognized human actions such as water pouring, cereal making, and opening the door, as well as finding optimized trajectories to perform those actions.

Persons with disabilities who use power wheelchairs often have difficulty finding accessible routes to their destination from their outdoor location into the desired building or from their indoor location into another destination. This challenge can be alleviated through sensory information and preloaded map of the building and its surrounding outdoor areas. In this work, a power wheelchair system is integrated with a sensory suite and an autonomous control module to navigate the wheelchair in autonomous mode. A landmark-based autonomous navigation system using Quick Response (QR) code and Global Positioning System (GPS) technology is used for automatic communication between the power wheelchair and various locations in a designated building. For the outdoor navigation system, Autonomous Wheelchair Indoor-Outdoor Navigation System (AWI-ONS) relies on GPS signals and Google Maps. For indoor navigation, QR codes are placed in several key locations inside and outside the building, such as parking lots and garages, doorways, offices, bathrooms, stores, elevators, accessible entrances, and passageways. When scanned by the onboard camera, the AWI-ONS downloads the building floorplan from the Firebase server for indoor navigation. The floor plan with QR code information generates a topological map that is made available to the user through a touch screen user interface (UI). The user can select the destination, and AWI-ONS will generate the most viable and accessible path to the desired location using modified Breadth-First Search (BFS) algorithm. The AWI-ONS is fitted with Ultrasound-based obstacle avoidance system that is designed to avoid a possible collision while navigating towards the destination.

The arms race between (bacterio)phages and their hosts is a recognised hot spot for genome evolution. Indeed, phages and their components have historically paved the way for many molecular biology techniques and biotech applications. Further exploration into their complex lifestyles has revealed that phages are often parasitised by distinct types of hyperparasitic mobile genetic elements. These so-called phage satellites exploit phages to ensure their own propagation and horizontal transfer into new bacterial hosts, and their prevalence and peculiar lifestyle has caught the attention of many researchers. Here, we review the parasite–host dynamics of the known phage satellites, their genomic organisation and their hijacking mechanisms. Finally, we discuss how these elements can be repurposed for diverse biotech applications, kindling a new catalogue of exciting tools for microbiology and synthetic biology.

Antimicrobial resistance (AMR) is an accelerating global threat to modern medicine, yet the nature of AMR in the gut microbiome and how AMR is acquired during early life remain largely unknown. In a cohort of 662 Danish children, we characterized the antibiotic resistance genes (ARGs) acquired during the first year of life and assessed the impacts of diverse environmental exposures on ARG load. Our study reveals a clear bimodal distribution of ARG abundance that is driven by the composition of the gut microbiome, especially E. coli. ARG profiles were significantly affected by various environmental factors. Among these factors, the importance of antibiotics diminished with time since treatment. Finally, ARG load and ARG clusters were also associated with the maturity of the gut microbiome and an asthma-associated bacterial composition. These findings broaden our understanding of AMR in the early life, and have critical implications for efforts to mitigate its spread.

Today, all the newspapers and online news content are flooded with the news of coronavirus (i.e., COVID-19). The virus has spread across the globe at an alarming rate. Thus, people need to remain updated about news regarding the ongoing pandemic which has taken whole world by storm. Therefore, named entity recognition (NER) is applied to extract important information from these news headlines and articles and further used for more applications related to COVID-19 in India. This chapter uses the SpaCy module to categorize the tokens extracted from the news headlines database into various pre-defined tags. Further, four different machine learning models, namely CRF Model, LSTM Model, LightGBM Model, and AdaBoost Model, are applied for performing tagging. After that, these tags are used to predict different information regarding COVID-19. Some of these applications include finding nearby hospitals and pharmacies, predicting future potential hotspots in India, worst affected states of India, gender-based comparisons, age group-based comparisons, and area-based spreading of the virus.

Opportunistic pathogens are associated with several widespread, recalcitrant chronic infections in humans. As the pipeline for new antibiotics thins, virulence management presents an alternative solution to the rising antimicrobial resistance crisis in treating chronic infections. However, the nature of virulence in opportunists is not fully understood. The trade-off hypothesis has been a popular rationalization for the evolution of parasitic virulence since it was first proposed in the early 1980s, but whether it accurately models the evolutionary trajectories of opportunistic pathogens is still uncertain. Here, we tested the evolution of virulence in the human opportunist Pseudomonas aeruginosa PA14 in a murine chronic wound model. We found that in a serial passage experiment where transmission potential is no longer an epidemiological restriction, virulence does not necessarily increase as is predicted by the trade-off hypothesis, and in fact may evolve in different directions. We also assessed P. aeruginosa adaptations to a chronic wound after ten rounds of selection, and found that phenotypic heterogeneity in P. aeruginosa is limited in chronic wounds compared to heterogeneity seen in cystic fibrosis (CF) infections. Using whole genome sequencing, we found that genes coding for virulence factors thought to be crucial in P. aeruginosa pathogenesis acquired mutations during adaptation in chronic wounds. Our findings highlight that (i) current virulence models do not adequately explain the diverging evolutionary trajectories observed during P. aeruginosa chronic wound infection, (ii) P. aeruginosa phenotypic heterogeneity is less extensive in chronic wounds than in CF lungs, (iii) genes involved in P. aeruginosa virulence acquire mutations in chronic wounds, and (iv) similar adaptations are employed by P. aeruginosa both in a chronic wound and CF lung.

Background Urbanization is linked with an increased burden of asthma and atopic traits. A putative mechanism is insufficient exposure to beneficial microbes early in life, leading to immune dysregulation, as was previously shown for indoor microbial exposures. Objective Our aim was to investigate whether urbanization is associated with the microbiota composition in the infants’ body and early immune function, and whether these contribute to the later risk of asthma and atopic traits. Methods We studied the prospective Copenhagen Prospective Studies on Asthma in Childhood 20102010 mother-child cohort of 700 children growing up in areas with different degrees of urbanization. During their first year of life, airway and gut microbiotas, as well as immune marker concentrations, were defined. When the children were 6 years of age, asthma and atopic traits were diagnosed by pediatricians. Results In adjusted analyses, the risk of asthma and aeroallergen sensitization were increased in urban infants. The composition of especially airway but also gut microbiotas differed between urban and rural infants. The living environment–related structure of the airway microbiota was already associated with immune mediator concentrations at 1 month of age. An urbanized structure of the airway and gut microbiotas was associated with an increased risk of asthma coherently during multiple time points and also with the risks of eczema and sensitization. Conclusion Our findings suggest that urbanization-related changes in the infant microbiota may elevate the risk of asthma and atopic traits, probably via cross talk with the developing immune system. The airways may facilitate this effect, as they are open for colonization by environmental airborne microbes and serve as an immune interface.

Background The hamadryas baboon (Papio hamadryas) is a highly social primate that lives in complex multilevel societies exhibiting a wide range of group behaviors akin to humans. In contrast to the widely studied human microbiome, there is a paucity of information on the host-associated microbiomes of nonhuman primates (NHPs). Here, our goal was to understand the microbial composition throughout different body sites of cohabiting baboons. Results We analyzed 170 oral, oropharyngeal, cervical, uterine, vaginal, nasal and rectal samples from 16 hamadryas baboons via 16S rRNA gene sequencing. Additionally, raw Miseq sequencing data from 1041 comparable publicly available samples from the human oral cavity, gut and vagina were reanalyzed using the same pipeline. We compared the baboon and human microbiome of the oral cavity, gut and vagina, showing that the baboon microbiome is distinct from the human. Baboon cohabitants share similar microbial profiles in their cervix, uterus, vagina, and gut. The oral cavity, gut and vagina shared more bacterial amplicon sequence variants (ASVs) in group living baboons than in humans. The shared ASVs had significantly positive correlations between most body sites, suggesting a potential bacterial exchange throughout the body. No significant differences in gut microbiome composition were detected within the maternity line and between maternity lines, suggesting that the offspring gut microbiota is shaped primarily through bacterial exchange among cohabitants. Finally, Lactobacillus was not so predominant in baboon vagina as in the human vagina but was the most abundant genus in the baboon gut. Conclusions This study is the first to provide comprehensive analyses of the baboon microbiota across different body sites. We contrast this to human body sites and find substantially different microbiomes. This group of cohabitating baboons generally showed higher microbial diversity and remarkable similarities between body sites than were observed in humans. These data and findings from one group of baboons can form the basis of future microbiome studies in baboons and be used as a reference in research where the microbiome is expected to impact human modeling with baboons.

Microbes are faced with environmental fluctuations and it is therefore important to understand how change affects bacterial evolution and population dynamics. Here, we evolved a model bacterium, Pseudomonas aeruginosa PA14, under both constant and changing conditions where settlement by biofilm formation or migration by swimming motility was induced. In changing environments, a heterogeneous population evolved with both specialists and generalists. Interestingly, over time, generalists were outcompeted despite being better at both phenotypes compared to the ancestor. However, generalists became dominant when faced with local competition after resettlement. Reintroduction into a burn wound model, the environment PA14 originally was isolated from, further suggested a tradeoff between niche breadth and peak fitness in agreement with the evolution experiments. Mutations in the c-di-GMP system were key for adaptation of the phenotypes. No mutants lost their ability to regulate c-di-GMP, but generalists acquired mutations that optimized their phenotypic response by efficiently adjusting c-di-GMP levels.

Plasmids facilitate rapid bacterial adaptation by shuttling a wide variety of beneficial traits across microbial communities. However, under non-selective conditions, maintaining a plasmid can be costly to the host cell. Nonetheless, plasmids are ubiquitous in nature where bacteria adopt their dominant mode of life - biofilms. Here, we demonstrate that biofilms can act as spatiotemporal reserves for plasmids, allowing them to persist even under non-selective conditions. However, under these conditions, spatial stratification of plasmid-carrying cells may promote the dispersal of cells without plasmids, and biofilms may thus act as plasmid sinks.

Background From early life, children are exposed to a multitude of environmental exposures, which may be of crucial importance for healthy development. Here, the environmental microbiota may be of particular interest as it represents the interface between environmental factors and the child. As infants in modern societies spend a considerable amount of time indoors, we hypothesize that the indoor bed dust microbiota might be an important factor for the child and for the early colonization of the airway microbiome. To explore this hypothesis, we analyzed the influence of environmental exposures on 577 dust samples from the beds of infants together with 542 airway samples from the Copenhagen Prospective Studies on Asthma in Childhood2010 cohort. Results Both bacterial and fungal community was profiled from the bed dust. Bacterial and fungal diversity in the bed dust was positively correlated with each other. Bacterial bed dust microbiota was influenced by multiple environmental factors, such as type of home (house or apartment), living environment (rural or urban), sex of siblings, and presence of pets (cat and/or dog), whereas fungal bed dust microbiota was majorly influenced by the type of home (house or apartment) and sampling season. We further observed minor correlation between bed dust and airway microbiota compositions among infants. We also analyzed the transfer of microbiota from bed dust to the airway, but we did not find evidence of transfer of individual taxa. Conclusions Current study explores the influence of environmental factors on bed dust microbiota (both bacterial and fungal) and its correlation with airway microbiota (bacterial) in early life using high-throughput sequencing. Our findings demonstrate that bed dust microbiota is influenced by multiple environmental exposures and could represent an interface between environment and child.

Additional file1: Fig. S1. Rarefaction curves of the (a) Bacteria (16S rRNA gene), and (b) Fungi (ITS) samples. Fig. S2. Influence of potential contaminant ASVs. Fig. S3. Bacterial microbiome by 16S rRNA gene (panels a–d) at four taxonomic levels (a) phylum (b) class (c) family, and (d) genus. Fig. S4. Fungal microbiome by ITS (panels a–d) at four taxonomic levels (a) phylum (b) class (c) family, and (d) genus. Fig. S5. Spearman correlation between fungi in bed dust. Fig. S6. Spearman correlation between bacteria in bed dust. Fig. S7. Box plots of the bacterial richness according to home type and living environment. Fig. S8. Box plots of the fungal richness according to home type and living environment. Fig. S9. Box plots of fungal alpha-diversity according to pet ownership. Fig. S10. PCoA plot of (a) bacterial and (b) fungal community composition based on weighted Unifrac distance. Fig. S11. Differentially abundant analysis between rural and urban living environment. Fig. S12. The odds for transfer of taxa (at genus level) from dust to airway microbiota of children. Table S1. Characteristics of the study population. Table S2.Bacterial abundance in bed dust samples at phylum level. Table S3. Bacterial abundance in bed dust samples at genus level. Table S4. Fungal abundance in bed dust samples at phylum level. Table S5. Fungal abundance in bed dust samples at class level. Table S6. Fungal abundance in bed dust samples at genus level. Table S7. Differentially abundant bacterial taxa in bed dust samples for homes with dog and cat both. Table S8. Differentially abundant bacterial taxa in bed dust samples for homes with dog. Table S9. Differentially abundant bacterial taxa in bed dust samples for homes with cat. Table S10. Differentially abundant fungal taxa in bed dust samples for homes with dog and cat both. Table S11. Differentially abundant fungal taxa in bed dust samples for homes with dog. Table S12. Differentially abundant fungal taxa in bed dust samples for homes with cat. Table S13. Bacteria present in rural and urban environment at genus level. Table S14. The effects of season and environmental factors on bed dust alpha and beta-diversity. Table S15. The adjusted (marginal) effects of environmental factors on bed dust alpha and beta-diversity.

Additional file 3.

Staphylococcus aureus is a prominent etiological agent of suppurative abscesses. In principle, abscess formation and purulent exudate are classical physiological features of healing and tissue repair. However, S. aureus deploys two coagulases that can usurp this classical host response and form distinct abscess lesions. Here, we establish that during coinfection with coagulase producers and non-producers, coagulases are shared public goods that contribute to staphylococcal persistence, abscess formation, and disease progression. Coagulase-negative mutants that do not produce the public goods themselves are able to exploit those cooperatively secreted by producers and thereby thrive during coinfection at the expense of others. This study shows the importance of social interactions among pathogens concerning clinical outcomes.

The mother’s vaginal microbiota represents the first microbes to which a child is exposed when delivered vaginally. However, little is known about the composition and development of the vaginal microbiota during pregnancy and birth. Here, we analyzed the vaginal microbiota of 57 women in pregnancy week 24, 36 and at birth after rupture of membranes but before delivery, and further compared the composition with that of the gut and airways of the 1-week-old child. The vaginal community structure had dramatic changes in bacterial diversity and taxonomic distribution, yet carried an individual-specific signature. The relative abundance of most bacterial taxa increased stepwise from week 24 of pregnancy until birth, with a gradual decline of Lactobacillus. Mother-to-child vertical transfer, as suggested by sharing, was modest, with the strongest transfer being for Clostridiales followed by Lactobacillales and Enterobacteriales. In conclusion, late gestation is associated with an increase in maternal vaginal microbiota diversity, and vaginal bacteria at birth only modestly predict the composition of the neonatal microbiota.

Additional file 2. Supplementary material: controls manage risk of contamination during wet-lab processing and sterile surgical procedure manage risk of contamination at sampling.

Summary Antimicrobial resistance (AMR) is an accelerating global threat, yet the nature of AMR in the gut microbiome and how AMR is acquired during early life remain largely unknown. In a cohort of 662 Danish children, we characterized the antibiotic resistance genes (ARGs) acquired during the first year of life and assessed the impacts of diverse environmental exposures on ARG load. Our study reveals a clear bimodal distribution of ARG richness that is driven by the composition of the gut microbiome, especially E. coli. ARG profiles were significantly affected by various environmental factors. Among these factors, the importance of antibiotics diminished with time since treatment. Finally, ARG load and ARG clusters were also associated with the maturity of the gut microbiome and a bacterial composition associated with increased risk of asthma. These findings broaden our understanding of AMR in early life and have critical implications for efforts to mitigate its spread.

Next-Generation Sequencing (NGS) of 16S rRNA gene is now one of the most widely used application to investigate the microbiota at any given body site in research. Since NGS is more sensitive than traditional culture methods (TCMs), many studies have argued for them to replace TCMs. However, are we really ready for this transition? Here we compare the diagnostic efficiency of the two methods using a large number of samples (n = 1,748 fecal and n = 1,790 hypopharyngeal), among healthy children at different time points. Here we show that bacteria identified by NGS represented 75.70% of the unique bacterial species cultured in each sample, while TCM only identified 23.86% of the bacterial species found by amplicon sequencing. We discuss the pros and cons of both methods and provide perspective on how NGS can be implemented effectively in clinical settings., Shashank Gupta, Martin Mortensen et al. compare the diagnostic efficiency of culturing and amplicon sequencing for studying the human microbiome. They show that amplicon sequencing identifies a greater number of species per sample, and can be implemented in clinical settings.

There have been reports of associations between cesarean section delivery and the risk of childhood asthma, potentially mediated through changes in the gut microbiota. We followed 700 children in the Copenhagen Prospective Studies on Asthma in Childhood2010 (COPSAC2010) cohort prospectively from birth. We examined the effects of cesarean section delivery on gut microbial composition by 16S rRNA gene amplicon sequencing during the first year of life. We then explored whether gut microbial perturbations due to delivery mode were associated with a risk of developing asthma in the first 6 years of life. Delivery by cesarean section was accompanied by marked changes in gut microbiota composition at one week and one month of age, but by one year of age only minor differences persisted compared to vaginal delivery. Increased asthma risk was found in children born by cesarean section only if their gut microbiota composition at 1 year of age still retained a cesarean section microbial signature, suggesting that appropriate maturation of the gut microbiota could mitigate against the increased asthma risk associated with gut microbial changes due to cesarean section delivery.

Coagulation is an innate defense mechanism intended to limit blood loss and trap invading pathogens during infection. However, Staphylococcus aureus has the ability to hijack the coagulation cascade and generate clots via secretion of coagulases. Although many S. aureus have this characteristic, some do not. The population dynamics regarding this defining trait have yet to be explored. We report here that coagulases are public goods that confer protection against antimicrobials and immune factors within a local population or community, thus promoting growth and virulence. By utilizing variants of a methicillin-resistant S. aureus we infer that the secretion of coagulases is a cooperative trait, which is subject to exploitation by invading mutants that do not produce the public goods themselves. However, overexploitation, "tragedy of the commons," does not occur at clinically relevant conditions. Our micrographs indicate this is due to spatial segregation and population viscosity. These findings emphasize the critical role of coagulases in a social evolution context and provide a possible explanation as to why the secretion of these public goods is maintained in mixed S. aureus communities.

The increase in antibiotic drug resistance and the low number of new antibacterial drugs approved in the last few decades requires the development of new antimicrobial strategies. Antimicrobial peptides (AMPs) are very promising molecules to fight microbial infection since they kill quickly bacteria and, in some cases, target bacterial membrane. Although some AMPs may be stable against proteolytic degradation by chemical modification, in general, low AMP activity and stability in the presence of serum and proteolytic enzymes as well as their cytotoxicity have impaired their clinical translation. Here, we describe a one-step methodology to generate AMP-conjugated gold nanoparticles (Au NPs), with a high concentration of AMPs (CM-SH) (≈240 AMPs per NP), controlled size (14 nm) and low polydispersity. AMP-conjugated Au NPs demonstrated higher antimicrobial activity and stability in serum and in the presence of non-physiological concentrations of proteolytic enzymes than soluble AMP, as well as low cytotoxicity against human cells. Moreover, the NPs demonstrated high antimicrobial activity after in vivo administration in a chronic wound and in an animal model of systemic infection.

Background Macrolides are commonly prescribed for respiratory infections and asthma-like episodes in children. While their clinical benefits have been proved, concerns regarding the side-effects of their therapeutic use have been raised. Here we assess the short- and long-term impacts of azithromycin on the gut microbiota of young children. Methods We performed a randomized, double-blind, placebo-controlled trial in a group of children aged 12–36 months, diagnosed with recurrent asthma-like symptoms from the COPSAC2010 cohort. Each acute asthma-like episode was randomized to a 3-day course of azithromycin oral solution of 10 mg/kg per day or placebo. Azithromycin reduced episode duration by half, which was the primary end-point and reported previously. The assessment of gut microbiota after treatment was the secondary end-point and reported in this study. Fecal samples were collected 14 days after randomization (N = 59, short-term) and again at age 4 years (N = 49, long-term, of whom N = 18 were placebo treated) and investigated by 16S rRNA gene amplicon sequencing. Findings Short-term, azithromycin caused a 23% reduction in observed richness and 13% reduction in Shannon diversity. Microbiota composition was shifted primarily in the Actinobacteria phylum, especially a reduction of abundance in the genus Bifidobacterium. Long-term (13–39 months after treatment), we did not observe any differences between the azithromycin and placebo recipients in their gut microbiota composition. Interpretation Azithromycin treatment induced a perturbation in the gut microbiota 14 days after randomization but did not have long-lasting effects on the gut microbiota composition. However, it should be noted that our analyses included a limited number of fecal samples for the placebo treated group at age 4 years. Fund Lundbeck Foundation, Danish Ministry of Health, Danish Council for Strategic Research, Capital Region Research Foundation, China Scholarship Council.

Detecting humans and objects during walking has been a very difficult problem for people with visual impairment. To safely avoid collision with any object or human and to navigate from one location to another, it is significant to know how far and what kind of obstacle the user is facing. In recent years, many researches have shown that providing different vibration stimulation can be very useful to convey important information to the user. In this paper, we present our stereovision system with high definition camera to detect and identify humans and obstacles in real time and compare it with a modified version of existing wearable haptic belt that uses high-performance Ultrasonic sensors. The aim of this paper is to present the practicability of stereovision system over cane and assistive technology such as vibrotactile belt. The study is based on two assistive technologies. The first one consists of the vibrotactile belt connected to ultrasonic sensors and an accelerometer which returns user movement & speed information to the microcontroller. The microcontroller initiates expressive vibrotactile stimulation based on sensor data. Data gathered from this technology will be used as the baseline data for comparison with our stereovision system. Second, we present a novel approach to detect the type of obstacle using object recognition algorithm and the best approach to avoid it using the stereovision feedback. Data gathered from this technology with be comparted against the baseline data from the vibrotactile belt. In addition, we present the results of the comparative study which shows that stereovision system has plethora of advantages over vibrotactile belt.

The oral pathogen Aggregatibacter actinomycetemcomitans (Aa) resides in infection sites with many microbes, including commensal streptococci such as Streptococcus gordonii (Sg). During infection, Sg promotes the virulence of Aa by producing its preferred carbon source, l-lactate, a phenomenon referred to as cross-feeding. However, as with many streptococci, Sg also produces high levels of the antimicrobial hydrogen peroxide (H2O2), leading to the question of how Aa deals with this potent antimicrobial during coinfection. Here, we show that Aa possesses two complementary responses to H2O2: a detoxification or fight response mediated by catalase (KatA) and a dispersion or flight response mediated by Dispersin B (DspB), an enzyme that dissolves Aa biofilms. Using a murine abscess infection model, we show that both of these responses are required for Sg to promote Aa virulence. Although the role of KatA is to detoxify H2O2 during coinfection, 3D spatial analysis of mixed infections revealed that DspB is required for Aa to spatially organize itself at an optimal distance (>4 µm) from Sg, which we propose allows cross-feeding but reduces exposure to inhibitory levels of H2O2. In addition, these behaviors benefit not only Aa but also Sg, suggesting that fight and flight stimulate the fitness of the community. These results reveal that an antimicrobial produced by a human commensal bacterium enhances the virulence of a pathogenic bacterium by modulating its spatial location in the infection site.

A fundamental aspect of most infectious diseases is the need for the invading microbe to proliferate in the host. However, little is known about the metabolic pathways required for pathogenic microbes to colonize and persist in their hosts. In this study, we used RNA sequencing (RNA-seq) to generate a high-resolution transcriptome of the opportunistic pathogen Aggregatibacter actinomycetemcomitans in vivo . We identified 691 A. actinomycetemcomitans transcriptional start sites and 210 noncoding RNAs during growth in vivo and as a biofilm in vitro . Compared to in vitro biofilm growth on a defined medium, ∼14% of the A. actinomycetemcomitans genes were differentially regulated in vivo . A disproportionate number of genes coding for proteins involved in metabolic pathways were differentially regulated in vivo , suggesting that A. actinomycetemcomitans in vivo metabolism is distinct from in vitro growth. Mutational analyses of differentially regulated genes revealed that formate dehydrogenase H and fumarate reductase are important A. actinomycetemcomitans fitness determinants in vivo . These results not only provide a high-resolution genomic analysis of a bacterial pathogen during in vivo growth but also provide new insight into metabolic pathways required for A. actinomycetemcomitans in vivo fitness.

Opportunistic infections caused by Pseudomonas aeruginosa can be acute or chronic. While acute infections often spread rapidly and can cause tissue damage and sepsis with high mortality rates, chronic infections can persist for weeks, months, or years in the face of intensive clinical intervention. Remarkably, this diverse infectious capability is not accompanied by extensive variation in genomic content, suggesting that the genetic capacity to be an acute or a chronic pathogen is present in most P. aeruginosa strains. To investigate the genetic requirements for acute and chronic pathogenesis in P. aeruginosa infections, we combined high-throughput sequencing-mediated transcriptome profiling (RNA-seq) and genome-wide insertion mutant fitness profiling (Tn-seq) to characterize gene expression and fitness determinants in murine models of burn and non-diabetic chronic wound infection. Generally we discovered that expression of a gene in vivo is not correlated with its importance for fitness, with the exception of metabolic genes. By combining metabolic models generated from in vivo gene expression data with mutant fitness profiles, we determined the nutritional requirements for colonization and persistence in these infections. Specifically, we found that long-chain fatty acids represent a major carbon source in both chronic and acute wounds, and P. aeruginosa must biosynthesize purines, several amino acids, and most cofactors during infection. In addition, we determined that P. aeruginosa requires chemotactic flagellar motility for fitness and virulence in acute burn wound infections, but not in non-diabetic chronic wound infections. Our results provide novel insight into the genetic requirements for acute and chronic P. aeruginosa wound infections and demonstrate the power of using both gene expression and fitness profiling for probing bacterial virulence., Author Summary Soft tissue infections, such as those in burns, bed sores, and diabetic ulcers, are a significant healthcare and economic burden in the developed and developing world. The opportunistic pathogen P. aeruginosa can cause both acute and chronic infections, and the trajectory of these two types of infections is vastly different. We used high-throughput sequencing to profile P. aeruginosa genome-wide gene expression and mutant fitness during mouse model acute and non-diabetic chronic wound infections. Using these data, we show that wounds are nutrient-rich growth environments in which long-chain fatty acids are a primary source of carbon and energy. We also show that the ability to travel along spatio-chemical gradients by chemotaxis is critical for bacterial fitness and virulence in acute but not chronic infections. Our results demonstrate the utility of simultaneous mutant fitness and gene expression profiling to discover critical functions in complex growth environments.

Diabetes mellitus (DM) affects 23.6 million people in the USA and approximately 20–25% of diabetic patients will develop foot ulceration during the course of their disease. Up to a quarter of these patients will develop infections that will necessitate amputation. Although many studies report that the rates of antibiotic resistant infections have increased dramatically in the DM population over the last decade, to our knowledge there have been no reports directly comparing the rates of antibiotic resistant infections in DM versus non-DM wounds. We performed a retrospective study comparing the wound infections of 41 DM patients to those of 74 non-DM patients to test the hypothesis that infections with multidrug resistant organisms (MDRO) were more prevalent in the DM population. We found that 63.4% of DM and 50% of non-DM patients had MDRO infections, which was not statistically different. However, 61% of the DM patients hadPseudomonasinfections compared to only 18.9% of non-DM patients. Furthermore, DM patients had significantly more coinfections with bothPseudomonasandStaphylococcus aureus. Though our initial hypothesis was incorrect, we demonstrated a significant correlation betweenPseudomonasandPseudomonas/S. aureuscoinfections within DM wounds.

Most infections result from colonization by more than one microbe. Within such polymicrobial infections, microbes often display synergistic interactions that result in increased disease severity. Although many clinical studies have documented the occurrence of synergy in polymicrobial infections, little is known about the underlying molecular mechanisms. A prominent pathogen in many polymicrobial infections is Pseudomonas aeruginosa , a Gram-negative bacterium that displays enhanced virulence during coculture with Gram-positive bacteria. In this study we discovered that during coinfection, P. aeruginosa uses peptidoglycan shed by Gram-positive bacteria as a cue to stimulate production of multiple extracellular factors that possess lytic activity against prokaryotic and eukaryotic cells. Consequently, P. aeruginosa displays enhanced virulence in a Drosophila model of infection when cocultured with Gram-positive bacteria. Inactivation of a gene ( PA0601 ) required for peptidoglycan sensing mitigated this phenotype. Using Drosophila and murine models of infection, we also show that peptidoglycan sensing results in P. aeruginosa -mediated reduction in the Gram-positive flora in the infection site. Our data suggest that P. aeruginosa has evolved a mechanism to survey the microbial community and respond to Gram-positive produced peptidoglycan through production of antimicrobials and toxins that not only modify the composition of the community but also enhance host killing. Additionally, our results suggest that therapeutic strategies targeting Gram-positive bacteria might be a viable approach for reducing the severity of P. aeruginosa polymicrobial infections.

Bacterial growth and virulence often depends upon the cooperative release of extracellular factors excreted in response to quorum sensing (QS). We carried out an in vivo selection experiment in mice to examine how QS evolves in response to variation in relatedness (strain diversity), and the consequences for virulence. We started our experiment with two bacterial strains: a wild-type that both produces and responds to QS signal molecules, and a lasR (signal-blind) mutant that does not release extracellular factors in response to signal. We found that: (i) QS leads to greater growth within hosts; (ii) high relatedness favours the QS wild-type; and (iii) low relatedness favours the lasR mutant. Relatedness matters in our experiment because, at relatively low relatedness, the lasR mutant is able to exploit the extracellular factors produced by the cells that respond to QS, and hence increase in frequency. Furthermore, our results suggest that because a higher relatedness favours cooperative QS, and hence leads to higher growth, this will also lead to a higher virulence, giving a relationship between relatedness and virulence that is in the opposite direction to that usually predicted by virulence theory.

Diabetic patients are more susceptible to the development of chronic wounds than non-diabetics. The impaired healing properties of these wounds, which often develop debilitating bacterial infections, significantly increase the rate of lower extremity amputation in diabetic patients. We hypothesize that bacterial biofilms, or sessile communities of bacteria that reside in a complex matrix of exopolymeric material, contribute to the severity of diabetic wounds. To test this hypothesis, we developed an in vivo chronic wound, diabetic mouse model to determine the ability of the opportunistic pathogen, Pseudomonas aeruginosa, to cause biofilm-associated infections. Utilizing this model, we observed that diabetic mice with P. aeruginosa-infected chronic wounds displayed impaired bacterial clearing and wound closure in comparison with their non-diabetic littermates. While treating diabetic mice with insulin improved their overall health, it did not restore their ability to resolve P. aeruginosa wound infections or speed healing. In fact, the prevalence of biofilms and the tolerance of P. aeruginosa to gentamicin treatment increased when diabetic mice were treated with insulin. Insulin treatment was observed to directly affect the ability of P. aeruginosa to form biofilms in vitro. These data demonstrate that the chronically wounded diabetic mouse appears to be a useful model to study wound healing and biofilm infection dynamics, and suggest that the diabetic wound environment may promote the formation of biofilms. Further, this model provides for the elucidation of mechanistic factors, such as the ability of insulin to influence antimicrobial effectiveness, which may be relevant to the formation of biofilms in diabetic wounds.