Resident Microbiome Research Articles

Elevated levels of Merkel cell polyoma virus in the anophthalmic conjunctiva

The human ocular surface hosts a paucibacterial resident microbiome and virome. The factors contributing to homeostasis of this mucosal community are presently unknown. To determine the impact of ocular enucleation and prosthesis placement on the ocular surface microbiome, we sampled conjunctival swabs from 20 anophthalmic and 20 fellow-eye intact conjunctiva. DNA was extracted and subjected to quantitative 16S rDNA PCR, biome representational karyotyping (BRiSK), and quantitative PCR (qPCR) confirmation of specific organisms. 16S ribosomal qPCR revealed equivalent bacterial loads between conditions. Biome representational in silico karyotyping (BRiSK) demonstrated comparable bacterial fauna between anophthalmic and intact conjunctiva. Both torque teno virus and Merkel cell polyoma virus (MCPyV) were detected frequently in healthy and anophthalmic conjunctiva. By qPCR, MCPyV was detected in 19/20 anophthalmic samples compared with 5/20 fellow eyes. MCPyV copy number averaged 891 copies/ng in anophthalmic conjunctiva compared with 193 copies/ng in fellow eyes (p < 0.001). These results suggest that enucleation and prosthesis placement affect the ocular surface flora, particularly for the resident virome. As MCPyV has been shown to be the etiologic cause of Merkel cell carcinoma, understanding the mechanisms by which the ocular surface regulates this virus may have clinical importance.

Janthinobacter additions reduce rotifer grazing of microalga Microchloropsis salina in biotically complex communities

Grazing and parasitism in algal production systems are significant causes of crop loss. Biological control of algal ponds, such as application of protective bacteria, represents a promising alternative to current mitigation strategies. The major barriers to probiotic methods are the lack of identified protective bacteria and uncertainty of scale-up effects, including potential negative interactions with the resident algal microbiome. Here, we report that application of Janthinobacter lividum affords robust protection against rotifer (Brachionus plicatilis) grazing on Microchloropsis salina. Protection was observed at laboratory scale from live bacteria and solvent extract additions as well as in biologically complex communities from bacterial additions to outdoor mesocosms. J. lividum persisted in outdoor communities for at least 3 days following addition, and did not lead to selective exclusion of specific taxa in the resident microbiome. These results demonstrate that J. lividum can provide protection against grazers in these diverse communities, without severe effects on the resident microbiome. Our results suggest that J. lividum is a promising treatment to mitigate algal crop losses due to pests. Additionally, the study highlights the importance of an ecologically-informed approach to algal crop management that will aid future applications in the biological control of algal ponds.

In-vivo impact of common cosmetic preservative systems in full formulation on the skin microbiome.

Preservatives play an essentially role in ensuring that cosmetic formulations remain safe for use via control of microbial contamination. Commonly used preservatives include organic acids, alcohols and phenols and these play an essential role in controlling the growth of bacteria, fungi and moulds in substrates that can potentially act as a rich food source for microbial contaminants. Whilst the activity of these compounds is clear, both in vitro and in formulation, little information exists on the potential impact that common preservative systems, in full formulation, have on the skin’s resident microbiome. Dysbiosis of the skin’s microbiome has been associated with a number of cosmetic conditions but there currently are no in vivo studies investigating the potential for preservative ingredients, when included in personal care formulations under normal use conditions, to impact the cutaneous microbiome. Here we present an analysis of four in vivo studies that examine the impact of different preservation systems in full formulation, in different products formats, with varying durations of application. This work demonstrates that despite the antimicrobial efficacy of the preservatives in vitro, the skin microbiome is not impacted by preservative containing products in vivo.

Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome

BackgroundImproving probiotic engraftment in the human gut requires a thorough understanding of the in vivo adaptive strategies of probiotics in diverse contexts. However, for most probiotic strains, these in vivo genetic processes are still poorly characterized. Here, we investigated the effects of gut selection pressures from human, mice, and zebrafish on the genetic stability of a candidate probiotic Lactiplantibacillus plantarum HNU082 (Lp082) as well as its ecological and evolutionary impacts on the indigenous gut microbiota using shotgun metagenomic sequencing in combination with isolate resequencing methods.ResultsWe combined both metagenomics and isolate whole genome sequencing approaches to systematically study the gut-adaptive evolution of probiotic L. plantarum and the ecological and evolutionary changes of resident gut microbiomes in response to probiotic ingestion in multiple host species. Independent of host model, Lp082 colonized and adapted to the gut by acquiring highly consistent single-nucleotide mutations, which primarily modulated carbohydrate utilization and acid tolerance. We cultivated the probiotic mutants and validated that these gut-adapted mutations were genetically stable for at least 3 months and improved their fitness in vitro. In turn, resident gut microbial strains, especially competing strains with Lp082 (e.g., Bacteroides spp. and Bifidobacterium spp.), actively responded to Lp082 engraftment by accumulating 10–70 times more evolutionary changes than usual. Human gut microbiota exhibited a higher ecological and genetic stability than that of mice.ConclusionsCollectively, our results suggest a highly convergent adaptation strategy of Lp082 across three different host environments. In contrast, the evolutionary changes within the resident gut microbes in response to Lp082 were more divergent and host-specific; however, these changes were not associated with any adverse outcomes. This work lays a theoretical foundation for leveraging animal models for ex vivo engineering of probiotics to improve engraftment outcomes in humans.1TYRt-mQpEqyYou2DA7bqRVideo abstract

Escherichia coli Shiga Toxins and Gut Microbiota Interactions.

Escherichia coli (EHEC) and Shigella dysenteriae serotype 1 are enterohemorrhagic bacteria that induce hemorrhagic colitis. This, in turn, may result in potentially lethal complications, such as hemolytic uremic syndrome (HUS), which is characterized by thrombocytopenia, acute renal failure, and neurological abnormalities. Both species of bacteria produce Shiga toxins (Stxs), a phage-encoded exotoxin inhibiting protein synthesis in host cells that are primarily responsible for bacterial virulence. Although most studies have focused on the pathogenic roles of Stxs as harmful substances capable of inducing cell death and as proinflammatory factors that sensitize the host target organs to damage, less is known about the interface between the commensalism of bacterial communities and the pathogenicity of the toxins. The gut contains more species of bacteria than any other organ, providing pathogenic bacteria that colonize the gut with a greater number of opportunities to encounter other bacterial species. Notably, the presence in the intestines of pathogenic EHEC producing Stxs associated with severe illness may have compounding effects on the diversity of the indigenous bacteria and bacterial communities in the gut. The present review focuses on studies describing the roles of Stxs in the complex interactions between pathogenic Shiga toxin-producing E. coli, the resident microbiome, and host tissues. The determination of these interactions may provide insights into the unresolved issues regarding these pathogens.

'GutFeel': an in silico method for predicting gut health status based on the metabolic functional capabilities of the resident microbiome.

Dysbiosis or imbalance in the gut microbiome has been correlated with the etiology of a number of diseases/disorders. Thus, gut microbial communities can potentially be utilized for assessing the health of the human gut. Although the taxonomic composition of the microbiomes is dependent on factors such as diet, lifestyle, and geography, these microbes perform a specific set of common functions in the gut. In this study, metabolic pathway-based markers (agnostic to above-mentioned factors) specific to commensals and those specific to pathogens are utilized as indicators of gut health. Furthermore, this gut health assessment requires only a small set of features rather than complete sequencing of metagenomes. The proposed scheme can also be used to design personalized biotherapeutics, depending on functional aspects observed in an individual.

Microbiome Signature and Diversity Profiling of Normal Skin of Human in Saudi Arabia

Background: Studying human skin-associated bacterial communities is crucial to understanding human diseases, disease progression, and their role in maintaining human health. Objectives: This study aimed to identify normal (healthy) skin microbiome signatures of eight individuals living in Jeddah, Makkah Al-Mukarramah region, Saudi Arabia. Methods: The study involved the analysis of resident skin microbiome in inner elbow of the right arm after ethical approval is issued and an informed consent form is signed by participant individuals. Results: Phylogenetic tree indicated the existence of four phyla, e.g., Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria. Firmicutes were shown to be the highest in abundance, while Bacteroidetes were the lowest. At the genus level, Staphylococcus was the highest in abundance, while Enterococcus was the lowest. At the species level, Bacillus cereus was the highest in abundance, while Roseomonas mucosa was the lowest. The analysis for the highly abundant operational taxonomic units (OTUs) indicated a dramatic difference between sexes referring to either genera or species of which Staphylococcus sp., Erwinia sp., Pseudomonas sp., Sphingomonas sp., Corynebacterium sp., Propionibacterium acnes, Kocuria palustris are higher in males, while Bacillus cereus, Bacillus sp., Erwinia sp., Corynebacterium sp., Micrococcus sp., Pseudomonas sp. are lower in males. Conclusions: The study succeeded in detecting the skin microbiome of individuals in Saudi Arabia.

The Human Microbiome, an Emerging Key-Player in the Sex Gap in Respiratory Diseases.

The sex gap is well-documented in respiratory diseases such as cystic fibrosis and chronic obstructive pulmonary disease. While the differences between males and females in prevalence, severity and prognosis are well-established, the pathophysiology of the sex difference has been poorly characterized to date. Over the past 10 years, metagenomics-based studies have revealed the presence of a resident microbiome in the respiratory tract and its central role in respiratory disease. The lung microbiome is associated with host immune response and health outcomes in both animal models and patient cohorts. The study of the lung microbiome is therefore an interesting new avenue to explore in order to understand the sex gap observed in respiratory diseases. Another important parameter to consider is the gut-lung axis, since the gut microbiome plays a crucial role in distant immune modulation in respiratory diseases, and an intestinal “microgenderome” has been reported: i.e., sexual dimorphism in the gut microbiome. The microgenderome provides new pathophysiological clues, as it defines the interactions between microbiome, sex hormones, immunity and disease susceptibility. As research on the microbiome is increasing in volume and scope, the objective of this review was to describe the state-of-the-art on the sex gap in respiratory medicine (acute pulmonary infection and chronic lung disease) in the light of the microbiome, including evidence of local (lung) or distant (gut) contributions to the pathophysiology of these diseases.

A dysbiotic gut microbiome suppresses antibody-mediated protection against Vibrio cholerae

Abstract Vibrio cholerae is the etiologic agent of cholera, a severe diarrheal disease that represents a significant burden on global health and productivity. Given the need for more effective prophylactics, more research is needed to ascertain the interplay of protective immune responses and the resident gut microbiome, which in cholera-endemic areas is strongly and repeatedly modulated by malnutrition, cholera, and non-cholera infectious diarrhea. Initially, we conducted fecal transplants from healthy human donors into germ-free mice in order to characterize differential immune response activity. As we observed distinctive responses in our initial sampling, we moved to a more tractable antibiotic-treated mouse model where we assemble representative model communities of either human gut microbes resembling those of healthy individuals or those of individuals recovering from diarrhea or malnutrition. We establish these communities in a murine infection model, and show that the dysbiotic gut microbiome, commonly present in areas where malnutrition and diarrhea are common, suppresses the immune response against Vibrio cholerae through the action of CD4+ cells. Our findings suggest that the composition of the gut microbiome at time of infection may be pivotal for providing robust mucosal immunity, suggesting a target for the improvement of responses to oral cholera vaccines.

Differential Impact of Urban vs. Rural Diets on Gut Microbiome Composition and Circulating Endotoxin in Mourning Doves

Human and rodent studies suggest a Western diet (high in refined carbohydrates, saturated fats, and salt) promotes gut dysbiosis that arises from changes in the resident gut microbiome (GM). This dietary pattern has also been associated with increased circulating concentrations of the endotoxin and immunostimulant, lipopolysaccharide (LPS), which is mediated, in part, through alterations in the GM. In relation, urbanization influences food quality and availability for many wild species which may promote a shift in the GM that could ultimately impact host physiology. As a heavily affected class it is currently unknown how the avian GM is affected following consumption of this dietary model. Therefore, we investigated the potential differential effects of an urban vs. rural dietary intervention on the GM and circulating LPS in Mourning doves (Zenaida macroura). Specifically, adult animals were brought into captivity from a wild population on the Arizona State University campus (Tempe, Arizona; 33° 25′ 11.5” N - 111° 55′ 55.6” W; altitude: 365 m.a.s.l.) and fed either a seed-based diet (rural; n = 6) or urbanized diet (urban; n = 7) over 4-weeks. The urban diet consisted of a mixture of seed and French fries (a food source readily available to birds in urban environments). We hypothesized that the urban diet would differently impact the GM community and increase plasma LPS compared to animals fed a rural diet. After the 4-week intervention, there were no differences in alpha diversity (Shannon index, Pielou's e, Faith's PD; P's ≥ 0.33) or beta diversity (Bray-Curtis, weighted and unweighted UniFrac; P's ≥ 0.35) between groups. However, linear discriminant analysis (LDA) of effect sizes revealed significant differences between the two diets, with rural-fed birds showing increased Chloroflexi (Chloroflexi and Anaerolineae) and Cyanobacteria (Phormidiaceae, Oscillatoriales, Oscillatoriophycideae, Phormidium) (LDA scores ~ 6.0). Moreover, and contrary to our hypothesis, plasma LPS concentrations were significantly higher in the rural group (51.01 ± 1.18 ng/L vs. 45.11 ± 1.02 ng/L, P = 0.003). Notably, birds are transporters of Cyanobacteria which often reside in bodies of water. The LPS molecules in Cyanobacteria also seem to provide protection from antimicrobial compounds which could be beneficial for these animals by promoting the proliferation of commensal microbes. Interesting to note that the lipid A portion of Cyanobacterial LPS is structurally similar to a well-known toll-like receptor 4 (TLR4) antagonist called lipid IVa and is less toxic than other gram-negative-derived LPS. It may be that higher LPS in the seed diet animals could be similarly protective against the TLR4 pathway as they had significantly higher abundance of Cyanobacteria. Future work should look at inflammatory markers downstream of LPS activation to confirm if these diets differ in relation to host health. In conclusion, the urban diet did not support the proliferation of several beneficial microbes that release protective endotoxins, which may have important physiological relevance for birds living in urban environments.

Effect of chlorpyrifos on the earthworm Eudrilus euginae and their gut microbiomeby toxicological and metagenomic analysis.

The earthworms are important soil invertebrates and play a crucial role in pedogenesis. The application of pesticides and prolonged exposure to pesticides causes mortality of earthworms apart from profoundly affecting the resident gut microbiome. The microbiome plays a significant effect on the metabolic processes associated with earthworms. The pesticide Chlorpyrifos (CPF) was studied for its toxicity on Eudrilus euginae by toxicity studies. The LC50 value of filter paper contact test and acute toxicity test was 3.8mg/mL and 180mg/kg. The prolonged exposure of earthworms to pesticide on reproductive toxicity resulted in the mortality of earthworms and absence of cocoon formation. Further, the effects of CPF on the whole gut microbiome of E. euginae was analyzed using a long amplicon Nanopore sequencing. Results indicated no fluctuations with Firmicutes and Bacteroidetes, that were found to be dominant at bacterial phyla level while at the genus level, remarkable differences were noticed. Clostridium dominated the earthworm gut prior to CPF exposure while Bacillus dominated after exposure. Similarly, the fungal members such as Ascomycota and Basidiomycota were observed to dominate the gut of earthworm at the phyla level before and after exposure to CPF. In contrast, Clavispora (65%) was the dominant genus before CPF exposure and Taloromyces (42%) dominated after the CPF exposure. Our study demonstrates the effect of CPF on the mortality of E. euginae while the amplicon sequencing established the unique microbiome of the gut in response to the CPF exposure.

Dysbiosis of the Human Oral Microbiome During the Menstrual Cycle and Vulnerability to the External Exposures of Smoking and Dietary Sugar.

Physiological hormonal fluctuations exert endogenous pressures on the structure and function of the human microbiome. As such, the menstrual cycle may selectively disrupt the homeostasis of the resident oral microbiome, thus compromising oral health. Hence, the aim of the present study was to structurally and functionally profile the salivary microbiome of 103 women in reproductive age with regular menstrual cycle, while evaluating the modifying influences of hormonal contraceptives, sex hormones, diet, and smoking. Whole saliva was sampled during the menstrual, follicular, and luteal phases (n = 309) of the cycle, and the participants reported questionnaire-based data concerning their life habits and oral or systemic health. No significant differences in alpha-diversity or phase-specific clustering of the overall microbiome were observed. Nevertheless, the salivary abundances of genera Campylobacter, Haemophilus, Prevotella, and Oribacterium varied throughout the cycle, and a higher species-richness was observed during the luteal phase. While the overall community structure maintained relatively intact, its functional properties were drastically affected. In particular, 11 functional modules were differentially abundant throughout the menstrual cycle, including pentose phosphate metabolism, and biosynthesis of cobalamin and neurotransmitter gamma-aminobutyric acid. The menstrual cycle phase, but not oral contraceptive usage, was accountable for greater variations in the metabolic pathways of the salivary microbiome. Further co-risk factor analysis demonstrated that Prevotella and Veillonella were increased in current smokers, whereas high dietary sugar consumption modified the richness and diversity of the microbiome during the cycle. This is the first large study to systematically address dysbiotic variations of the oral microbiome during the course of menstrual cycle, and document the additive effect of smoking and sugar consumption as environmental risk factors. It reveals the structural resilience and functional adaptability of the oral microbiome to the endogenous hormonal pressures of the menstrual cycle, while revealing its vulnerability to the exogenous exposures of diet and smoking.

Conserved bacterial de novo guanine biosynthesis pathway enables microbial survival and colonization in the environmental niche of the urinary tract.

In bacteria, guaA encodes guanosine monophosphate synthetase that confers an ability to biosynthesize guanine nucleotides de novo. This enables bacterial colonization in different environments and, while guaA is widely distributed among Bacteroidetes and Firmicutes, its contribution to the inhabitation of the human microbiome by commensal bacteria is unclear. We studied Streptococcus as a commensal urogenital tract bacterium and opportunistic pathogen, and explored the role of guaA in bacterial survival and colonization of urine. Analysis of guaA-deficient Streptococcus revealed guanine utilization is essential for bacterial colonization of this niche. The genomic location of guaA in other commensals of the human urogenital tract revealed substantial cross-phyla diversity and organizational structures of guaA that are divergent across phyla. Essentiality of guaA for Streptococcus colonization in the urinary tract establishes that purine biosynthesis is a critical element of the ability of this bacterium to survive and colonize in the host as part of the resident human microbiome.

Probiotic Streptococcus A12 Strain in Caries Prevention: A Systematic Review

Background: Dental Caries is a biofilm-mediated multi factorial disease affecting around 5 billionpeople worldwide. A consensus is now emerging that caries preventive measures should not only correctthe environmental pressures responsible for the plaque biofilm dysbiosis, but also help to maintain ahealthy resident microbiome which plays a crucial role in preventing caries and promoting oral health.This PROSPERO registered review (registration no 166695) aimed to examine the evidence on the role ofprobiotic Streptococcus A12 in caries prevention.Objectives: To know the effectiveness of A12 strain in caries prevention in early stages of disease onset.Intervention: Streptococcus A12 strains.Results: A preliminary search yielded a total of 2630 studies recorded through database searching and 23additional records were identified through manual search. From 2653 articles, 2504 were excluded basedon screening through review of titles. 8 articles were included for qualitative synthesis. Streptococcus A12strains demonstrates antimicrobial efficacy by neutralization of the environment by arginine metabolism.Conclusion: Streptococcus A12 strains demonstrates antimicrobial efficacy by neutralization of theenvironment by arginine metabolism, which leads to the reduction in Streptococcus mutans count and helpsin lowering the acidic nature of saliva is the potential strength of A12 strain. Due to a lack of controlledclinical studies on probiotics for caries prevention, evidence on their caries-preventive potential is weak.Future studies are needed to examine the probiotics as a potential agent against cariogenic pathogens.

1099 LPS, IL-1β or U.parvum-induced chorioamnionitis in primates alters inflammation and the resident microbiome

Historically, chorioamnionitis has been thought to result from ascending microbes driving inflammation of the chorioamnion, and is associated with preterm labor, perinatal morbidity, and adverse fetal outcomes. However, pathophysiology studies in humans suggest that it results from focal membrane colonization, and we and many others have shown that there is a sparse but present resident intrauterine microbiome. Recently, in some situations preterm chorioamnionitis can be “treated” and pregnancies can continue. Here, we aimed to determine if sterile intraamniotic injection (IA) of IL1β, LPS, or Ureaplasma parvum (UP) induced-chorioamnionitis is associated with alterations in the resident metagenomics composition and its function. Under ultrasound guidance, IA of saline, 1mg LPS (E. coli 055:B5), 10μg IL-1β, or 107 CFU UP were given to preterm (126-132 days) Rhesus macaques (n=54). Fetuses were delivered via sterile cesarean one-week post injection. Oral and vaginal swabs, stool, placental tissue, meconium and amniotic fluid were collected for DNA extraction. DNA was subjected to next-generation sequencing using appropriate contamination “kit” controls. 16S sequencing (n=211) was performed on the V1V3 (454) and was analyzed using QIIME2. WGS sequencing (n=196) was performed on Illumina HiSeq platform, and were filtered and analyzed using krakenuniq. IA injection of IL-1β or LPS induces histologic chorioamnionitis, with significant (p<0.01) increases in neutrophils and proinflammatory cytokines in amniotic fluid. Similar changes were not observed in parallel colon samples (Fig.1) indicating absence of systemic inflammation. These changes were accompanied by significant alterations in the beta diversity of the sparse placental and amniotic fluid microbiome, to control but not in the vaginal, oral or stool microbiomes (Fig.2). Chorioamnionitis is a localized phenomenon rather than a systemic infection, and the variations in amniotic and placental microbiome are consistent with localized inflammation and which alters the sparse but present resident microbiome.View Large Image Figure ViewerDownload Hi-res image Download (PPT)

Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture.

Light, water and healthy soil are three essential natural resources required for agricultural productivity. Industrialization of agriculture has resulted in intensification of cropping practices using enormous amounts of chemical pesticides and fertilizers that damage these natural resources. Therefore, there is a need to embrace agriculture practices that do not depend on greater use of fertilizers and water to meet the growing demand of global food requirements. Plants and soil harbor millions of microorganisms, which collectively form a microbial community known as the microbiome. An effective microbiome can offer benefits to its host, including plant growth promotion, nutrient use efficiency, and control of pests and phytopathogens. Therefore, there is an immediate need to bring functional potential of plant-associated microbiome and its innovation into crop production. In addition to that, new scientific methodologies that can track the nutrient flux through the plant, its resident microbiome and surrounding soil, will offer new opportunities for the design of more efficient microbial consortia design. It is now increasingly acknowledged that the diversity of a microbial inoculum is as important as its plant growth promoting ability. Not surprisingly, outcomes from such plant and soil microbiome studies have resulted in a paradigm shift away from single, specific soil microbes to a more holistic microbiome approach for enhancing crop productivity and the restoration of soil health. Herein, we have reviewed this paradigm shift and discussed various aspects of benign microbiome-based approaches for sustainable agriculture.

Alterations in Urobiome in Patients With Bladder Cancer and Implications for Clinical Outcome: A Single-Institution Study.

Numerous studies indicate that resident microbiome exists in urine of healthy individuals and dysbiosis of the urobiome (urinary microbiome) may be associated with pathological conditions. This study was performed to characterize the alterations in urobiome and explore its implications of clinical outcome in male patients with bladder cancer. 62 male patients with bladder cancer and 19 non-neoplastic controls were recruited. The follow-up study cohort included 40 patients who were diagnosed with non-muscle invasive bladder cancer (NMIBC) and underwent transurethral resection of bladder tumor (TURBT). Mid-stream urine samples were collected from all the participants the day before cystoscopy. DNA was extracted from urine pellet samples and processed for high throughput 16S rRNA amplicon sequencing of the V4 region using Illumina MiSeq. Sequencing reads were filtered using QIIME and clustered using UPARSE. We found bacterial richness indices (Observed Species index, Chao1 index, Ace index; all P < 0.01) increased in cancer group when compared with non-neoplastic group, while there were no differences in Shannon and Simpson index between two groups. During a median follow-up time of 12 (5.25–25) months, 5/40 (12.5%)of the patients developed recurrence and no patient suffered from progression to muscle-invasive disease. Species diversity of the microbiome was significantly higher in the recurrence group compared with non-recurrence group in patients with NMIBC after TURBT. The LEfSe analysis demonstrated that 9 genera were increased (e.g., Micrococcus and Brachybacterium) in recurrence group. To our knowledge we report the relative comprehensive study to date of the male bladder cancer urinary microbiome and its relationship to pathogenesis and clinical outcomes. Given our preliminary data, additional studies evaluating the urine microbiome in relation to clinical outcomes are warranted to improve our understanding of tumor recurrence after TURBT.

Defending the Homeland: Microbiome Molecules Provide Protection to Their Vertebrate Hosts

Aim: The resident bacterial microbiome may shape and protect the health of vertebrate host. An array of molecules secreted by microbiome may contribute to the ecological stability of the microbiome itself. Material & methods: ELISA, radioactivity, immunofluorescenceand cytokines measurements were used to observe the bioactivity and stability of colicin Ia level in oviparous and viviparous animal circulation. Results: Colicin Ia, a protein antimicrobial produced by Escherichia coli, is not present in animals at birth, but increases in concentration with the establishment of a stable gut microbiome and drops when the microbiome is experimentally disrupted. Colicin introduced in vivo is transported to tissues at concentrations able to prevent or eliminate bacterial infection. Conclusion: Our findings suggest an unexpected benefit provided by the presence of a resident microbiome in the form of active, circulating, bacterially-synthesized antimicrobial molecules.

Disinfectant, Soap or Probiotic Cleaning? Surface Microbiome Diversity and Biofilm Competitive Exclusion.

This study extends probiotic cleaning research to a built environment. Through an eight-month cleaning trial, we compared the effect of three cleaning products (disinfectant, plain soap, and a probiotic cleaner containing a patented Bacillus spore consortium), and tap water as the control, on the resident microbiome of three common hospital surfaces (linoleum, ceramic, and stainless steel). Pathogens, Escherichia coli and Staphylococcus aureus, were deposited and desiccated, and competitive exclusion was assessed for each microbiome. Cell survival was shown to be an incomplete tool for measuring microbial competitive exclusion. Biofilm competition offered a fuller understanding of competitive dynamics. A test for culturable cell survival showed that both plain soap and probiotic cleaner regimes established a surface microbiome that outcompeted the two pathogens. A different picture emerged when observing biofilms with a deposited and desiccated GFP-labeled pathogen, Pseudomonas aeruginosa. Competitive exclusion was again demonstrated. On surfaces cleaned with disinfectant the pathogen outcompeted the microbiomes. On surfaces cleaned with plain soap, the microbiomes outcompeted the pathogen. However, on surfaces cleaned with probiotic cleaner, despite the exponentially higher surface microbial loads, the microbiome did not completely outcompete the pathogen. Thus, the standard culturable cell test for survival on a surface confirmed the competitive advantage that is typically reported for probiotic cleaners. However, observation of competition in biofilms showed that the more diverse microbiome (according to alpha and beta indices) established on a surface cleaned with plain soap had a better competitive advantage than the monoculture established by the probiotic cleaner. Therefore, microbial diversity appears to be as critical to the competitive exclusion principle as cell numbers. The study showed that both plain soap and probiotic cleaner fostered competitive exclusion far more effectively than disinfectant. Probiotic cleaners with microbial diversity could be worth considering for hospital cleaning.

A novel tick protein supports integrity of gut peritrophic matrix impacting existence of gut microbiome and Lyme disease pathogens.

The peritrophic matrix (PM) is an acellular membrane that covers the gut epithelium in arthropods and physically separates it from the lumen. The structure is thought to play an important role in tick biology. The PM is also known to impact the persistence of tick-borne pathogens like Borrelia burgdorferi, although limited information is available about its molecular constituents or their biological significance. Herein, we characterise a novel PM-associated gut protein in Ixodes scapularis ticks, annotated as Peritrophic Membrane Chitin Binding Protein (PM_CBP), for its role in the integrity and function of the matrix. The PM_CBP displays homology to the chitin deacetylase metalloenzyme, shows upregulation during tick feeding, and is localized at the luminal surface of the gut epithelium. The structural integrity of the PM was impaired both by the knock down of PM_CBP expression via RNA interference and by treatment with anti-PM_CBP antibodies, as revealed by its electron microscopic appearance. Additionally, the duration of tick engorgement on mice and the passage of experimentally-inoculated fluorescent dextran molecules across the PM are affected by the knock down of PM_CBP expression. The transfer of anti-PM_CBP antibodies into the tick gut impacted the overall composition of the resident microbiome, and also influenced B. burgdorferi acquisition in ticks and its transmission to mice. Taken together, these data highlight the biological significance of the Ixodes PM and suggest that the targeting of its molecular constituents may contribute to the development of novel interventions against tick-borne infections.