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Emerging evidence suggests that the nasal microbiome may influence host susceptibility to initial development and severity of respiratory viral infections. While not as extensively studied as the microbiota of the alimentary tract, it is now clearly established that the microbial composition of this niche is influenced by medical, social and pharmacological influences, predisposing some subpopulations to respiratory infections. The resulting specific microbial profiles may explain variance in susceptibility to viral infection. This review summaries the evolution and constituents of the commensal nasal microbiome; the bacterial-virus, bacterial-host and interbacterial interactions which potentiate disease; and considers the effects of interventions such as vaccination and probiotics. [ABSTRACT FROM AUTHOR]

Background: Bacteroidetes are the most common bacterial phylum in the mammalian intestine and the effects of several Bacteroides spp. on multiple facets of host physiology have been previously described. Of the Bacteroides spp., Bacteroides ovatus has recently garnered attention due to its beneficial effects in the context of intestinal inflammation. In this study, we aimed to examine model host intestinal physiological conditions and dietary modifications to characterize their effects on B. ovatus growth.Methods and Results: Using Biolog phenotypic microarrays, we evaluated 62 primary carbon sources and determined that B. ovatus ATCC 8384 can use the following carbohydrates as primary carbon sources: 10 disaccharides, 4 trisaccharides, 4 polysaccharides, 4 polymers, 3 L-linked sugars, 6 D-linked sugars, 5 amino-sugars, 6 alcohol sugars, and 15 organic acids. Proteomic profiling of B. ovatus bacteria revealed that a significant portion of the B. ovatus proteome contains proteins important for metabolism. Among the proteins, we found glycosyl hydrolase (GH) familes GH2, GH5, GH20, GH 43, GH88, GH92, and GH95. We also identified multiple proteins with antioxidant properties and reasoned that these proteins may support B. ovatus growth in the GI tract. Upon further testing, we showed that B. ovatus grew robustly in various pH, osmolarity, bile, ethanol, and H2O2 concentrations; indicating that B. ovatus is a well-adapted gut microbe.Conclusion: Taken together, we have demonstrated that key host and diet-derived changes in the intestinal environment influence B. ovatus growth. These data provide the framework for future work toward understanding how diet and lifestyle interventions may promote a beneficial environment for B. ovatus growth.

Fish are widely exposed to higher microbial loads compared to land and air animals. It is known that the microbiome plays an essential role in the health and development of the host. The oral microbiome is vital in females of different organisms, including the maternal mouthbrooding species such as Nile tilapia (Oreochromis niloticus). The present study reports for the first time the microbial composition in the buccal cavity of female and male Nile tilapia reared in a recirculating aquaculture system. Mucus samples were collected from the buccal cavity of 58 adult fish (∼1 kg), and 16S rRNA gene amplicon sequencing was used to profile the microbial communities in females and males. The analysis revealed that opportunistic pathogens such as Streptococcus sp. were less abundant in the female buccal cavity. The power play of certain bacteria such as Acinetobacter, Acidobacteria (GP4 and GP6), and Saccharibacteria that have known metabolic advantages was evident in females compared to males. Association networks inferred from relative abundances showed few microbe–microbe interactions of opportunistic pathogens in female fish. The findings of opportunistic bacteria and their interactions with other microbes will be valuable for improving Nile tilapia rearing practices. The presence of bacteria with specific functions in the buccal cavity of female fish points to their ability to create a protective microbial ecosystem for the offspring.

Background: Bacteroidetes are the most common bacterial phylum in the mammalian intestine and the effects of several Bacteroides spp. on multiple facets of host physiology have been previously described. Of the Bacteroides spp., Bacteroides ovatus has recently garnered attention due to its beneficial effects in the context of intestinal inflammation. In this study, we aimed to examine model host intestinal physiological conditions and dietary modifications to characterize their effects on B. ovatus growth. Methods and Results: Using Biolog phenotypic microarrays, we evaluated 62 primary carbon sources and determined that B. ovatus ATCC 8384 can use the following carbohydrates as primary carbon sources: 10 disaccharides, 4 trisaccharides, 4 polysaccharides, 4 polymers, 3 L-linked sugars, 6 D-linked sugars, 5 amino-sugars, 6 alcohol sugars, and 15 organic acids. Proteomic profiling of B. ovatus bacteria revealed that a significant portion of the B. ovatus proteome contains proteins important for metabolism. Among the proteins, we found glycosyl hydrolase (GH) familes GH2, GH5, GH20, GH 43, GH88, GH92, and GH95. We also identified multiple proteins with antioxidant properties and reasoned that these proteins may support B. ovatus growth in the GI tract. Upon further testing, we showed that B. ovatus grew robustly in various pH, osmolarity, bile, ethanol, and H2O2 concentrations; indicating that B. ovatus is a well-adapted gut microbe. Conclusion: Taken together, we have demonstrated that key host and diet-derived changes in the intestinal environment influence B. ovatus growth. These data provide the framework for future work toward understanding how diet and lifestyle interventions may promote a beneficial environment for B. ovatus growth. [ABSTRACT FROM AUTHOR]

Fish are widely exposed to higher microbial loads compared to land and air animals. It is known that the microbiome plays an essential role in the health and development of the host. The oral microbiome is vital in females of different organisms, including the maternal mouthbrooding species such as Nile tilapia (Oreochromis niloticus). The present study reports for the first time the microbial composition in the buccal cavity of female and male Nile tilapia reared in a recirculating aquaculture system. Mucus samples were collected from the buccal cavity of 58 adult fish (∼1 kg), and 16S rRNA gene amplicon sequencing was used to profile the microbial communities in females and males. The analysis revealed that opportunistic pathogens such as Streptococcus sp. were less abundant in the female buccal cavity. The power play of certain bacteria such as Acinetobacter , Acidobacteria (GP4 and GP6), and Saccharibacteria that have known metabolic advantages was evident in females compared to males. Association networks inferred from relative abundances showed few microbe–microbe interactions of opportunistic pathogens in female fish. The findings of opportunistic bacteria and their interactions with other microbes will be valuable for improving Nile tilapia rearing practices. The presence of bacteria with specific functions in the buccal cavity of female fish points to their ability to create a protective microbial ecosystem for the offspring. [ABSTRACT FROM AUTHOR]

Urinary tract infection (UTI) has been reported most often in recent days. In a clinical aspect there are various reasons for this cause. Out of 100 samples tested (Clinical samples from Rashi Diagnostic Center-Bangalore NABL laboratory), under the analytical aspect several comparative analysis was done. Urine was tested within half an hour of the collection. Physical characteristics of Urine sample were studied initially. Laura M is the device used to analyses the Uro-dip. Sugar and the presence of albumin was also found. Sediment of the centrifuged sample was subjected to gram staining and direct microscopic analysis. Pus cells, epithelial cells, yeast cells and rod shaped bacteria. It was found that epithelial cells are visualized in female samples and very less or not visualized in male samples. Bilirubin content, Bile salt content and ketone bodies were analyzed and compared in each of the samples. Sample is then subjected to culturing were the T streak is done on the Mac Conkey agar and Blood agar. This will differentiate between the lactose and Non-Lactose fermenting bacteria. Each of the colony is subjected to Gram staining. Yeast cells are also reported often. Though the yeast cells are the commensals they are considered non-pathogenic. But it was found that the yeast with pseudo-hyphae are pathogenic in nature. Both Lactose and Non-Lactose fermenting bacterial colonies from Blood agar is subjected to various biochemical methods to identify the organism. The most commonly noticed non-lactose fermenting organism was Pseudomonas spp. And Lactose fermenting organisms were Escherichia coli, Enterobacteria spp and Klebsiella spp. Each Colony from the culture plate was picked and streaked on the MHA agar and Kirby Bauer method has been performed (Disc diffusion method) under the McFerland standard. Zone of inhibition of each organism towards the antibiotic in the disc was recorded. [ABSTRACT FROM AUTHOR]

Skin is an organ with a dynamic ecosystem that harbours pathogenic and commensal microbes, which constantly communicate amongst each other and with the host immune system. Evolutionarily, skin and its microbiota have evolved to remain in homeostasis. However, frequently this homeostatic relationship is disturbed by a variety of factors such as environmental stress, diet, genetic mutations, and the microbiome itself. Commensal microbes also play a major role in the maintenance of microbial homeostasis. In addition to their ability to limit pathogens, many skin commensals such as Staphylococcus epidermidis and Cutibacterium acnes have recently been implicated in disease pathogenesis either by directly modulating the host immune components or by supporting the expansion of other pathogenic microbes. Likewise, opportunistic skin pathogens such as Staphylococcus aureus and Staphylococcus lugdunensis are able to breach the skin and cause disease. Though much has been established about the microbiota's function in skin immunity, we are in a time where newer mechanistic insights rapidly redefine our understanding of the host/microbial interface in the skin. In this review, we provide a concise summary of recent advances in our understanding of the interplay between host defense strategies and the skin microbiota. [ABSTRACT FROM AUTHOR]

Several species of martens (Martes spp.) are reported to use buildings as resting or den sites. However, such behaviour has not been attributed to American Marten (Martes americana). We report American Marten using occupied buildings and evidence of suspected use of an abandoned cabin, as resting sites in southern Yukon, Canada. These observations further highlight the behavioural flexibility of North American species of Martes with regard to using novel structures as resting sites. [ABSTRACT FROM AUTHOR]

This present study successfully constructed a specific commensal model of two species (Commensal- Host) in a syn eco-system with harvesting in both ways (i.e constant and variable rates). The nine equilibrium points are obtained with the essential conditions for their existence and also categorized under Interdependent and non Interdependent cases. The global stability of this ecological model is examined with Liapunov Technique. [ABSTRACT FROM AUTHOR]

Induction of commensal-specific immunity contributes to tissue homeostasis, yet the mechanisms underlying induction of commensal-specific B cells remain poorly understood in part due to a lack of tools to identify these cells. Using phage display, we identified segmented filamentous bacteria (SFB) antigens targeted by serum and intestinal antibodies and generated B cell tetramers to track SFB-specific B cells in gut-associated lymphoid tissues. We revealed a compartmentalized response in SFB-specific B cell activation, with a gradient of immunoglobulin A (IgA), IgG1, and IgG2b isotype production along Peyer's patches contrasted by selective production of IgG2b within mesenteric lymph nodes. V(D)J sequencing and monoclonal antibody generation identified somatic hypermutation driven affinity maturation to SFB antigens under homeostatic conditions. Combining phage display and B cell tetramers will enable investigation of the ontogeny and function of commensal-specific B cell responses in tissue immunity, inflammation, and repair. [Display omitted] • Phage display screening identifies immunogenic commensal antigens • B cell antigen tetramers enable identification of SFB-specific B cells • SFB-specific B cells display anatomically compartmentalized effector functions • Affinity maturation of SFB-specific B cells occurs under homeostatic conditions Adaptive immunity to commensal microbes promotes tissue homeostasis, immunity, and repair, but approaches to identify commensal-specific B cell responses are lacking. Verma et al. utilize phage display screening and subsequent generation of B cell tetramers to identify anatomical compartmentalization of SFB-specific B cell responses in gut-associated lymphoid tissues. [ABSTRACT FROM AUTHOR]

Recent advances in metagenomic testing opened a new window into the mammalian blood virome. Comprised of well-known viruses like human immunodeficiency virus, hepatitis C virus, and hepatitis B virus, the virome also includes many other eukaryotic viruses and phages whose medical significance, lifecycle, epidemiology, and impact on human health are less well known and thus regarded as commensals. This review synthesizes available information for the so-called commensal virome members that circulate in the blood of humans considering their restriction to and interaction with the human host, their natural history, and their impact on human health and physiology. [Display omitted] • Many healthy humans have viruses circulating in blood. • The viruses that circulate in blood (blood virome) are virologically distinct. • Blood virome acquisition and medical significance represent new frontiers in research. [ABSTRACT FROM AUTHOR]

The human commensal Staphylococcus aureus (SA) is a leading cause of skin/soft tissue and surgical-site infections, and bacteremia. Functional antibodies and T-cell-mediated immunity, particularly Th1/Th17 responses, are thought to mediate protection. Vaccine development may be hindered by modulation of vaccine-induced T cells by pathogen-activated immunoregulatory responses, e.g., via IL-10. We screened SA proteins for CD4+ T-cell-activating and IL-10/IL-17-inducing capacities using healthy donor-derived PBMCs. Responses were characterized (Th1/Th17/Th22/immunosuppressive IL-10-producing cells) using intracellular cytokine staining and flow cytometry. Phenotypic plasticity of Th1/Th17 cells was evaluated under pro- or anti-inflammatory conditions using modulatory cytokines. The impact of vaccination on SA-specific memory responses was assessed using samples from a clinical trial evaluating AS03-adjuvanted and non-adjuvanted multicomponent (CPS5/CPS8/α-toxin/ClfA) vaccines (NCT01160172). The donors exhibited SA-specific memory T-cell responses, indicative of pre-existing immunity to SA. We identified effective activators of Th1 responses (EbhA/IsaA/SdrE/MntC/Aaa/α-toxin), and Th17 and Th1/Th17 responses (EbhA/IsaA/SdrE and, to a lesser extent, α-toxin), but not of Th22 responses or IL-10 production. MRPII, IsdA, and ClfA were inefficient CD4+ T-cell activators in our assays. IL-10, likely produced by innate immune cells, influenced mainly Th1 cells by suppressing IFN-γ production. The memory CD4+ T-cells observed after long-term stimulation with α-toxin and ClfA indicated that vaccination with these proteins had induced expansion of pre-existing Th1 but not Th17 responses, without apparent adjuvant effect, confirming the trial data. The Th1/Th17-driving proteins (EbhA/IsaA/SdrE) shared low IL-10-promoting abilities and restricted phenotypic plasticity under pro- and anti-inflammatory conditions. Given the complex immunopathology and multiple virulence factors, identification of Th1/Th17-driving antigens, adjuvants and administration routes, and delineation of the role of memory responses, may advance vaccine development.

Abstract Background The pathogenic role of mycoplasmas in the lower respiratory tract (LRT) of dogs is debated, because mycoplasmas can be isolated from both healthy and sick dogs. Objectives To critically assess available data from controlled observational studies on the role of 4 mycoplasma species in LRT disease of dogs. Design Systematic review and meta‐analyses. Methods Seven electronic databases were searched for relevant publications. Risk of bias was assessed by the Newcastle‐Ottawa Scale. Meta‐analyses, stratified by mycoplasmal species, were performed using a random effects Bayesian model with noninformative priors to estimate pooled odds ratios (ORs) and 95% confidence intervals (CIs) for the association between Mycoplasma cynos, Mycoplasma canis, Mycoplasma spumans, and Mycoplasma edwardii and LRT disease in dogs. Results Five studies were included from 1201 references identified. All studies dealt with M. cynos, whereas 3 dealt with the other mycoplasma species. A significant association was found between M. cynos and LRT disease (Bayesian OR, 3.60; CI, 1.31‐10.29). Conversely, M. canis, M. spumans, and M. edwardii were not significantly associated with LRT signs (Bayesian OR, 1.06; CI, 0.10‐14.63; Bayesian OR, 3.40; CI, 0.16‐54.27; and Bayesian OR, 1.04; CI, 0.05‐23.54, respectively). Conclusions and Clinical Importance Results support a pathogenic role of M. cynos and a commensal role of M. canis and M. edwardii in LRT in dogs. Although the association was not significant based on the CI, the point estimate of the Bayesian OR was relatively high for M. spumans, making its role less clear. Mycoplasma cynos‐specific polymerase chain reaction should be considered on samples from dogs with LRT.

Abstract Background Antimicrobial resistance (AMR) is an increasing public health problem worldwide. We studied some patient-related factors that might influence the antimicrobial resistance. and whether the volume of antibiotic prescribing of the primary care physicians correlate with the antibiotic resistance rates of commensal nasal Staphylococcus aureus and Streptococcus pneumoniae. Methods The socio-demographic questionnaires, the antibiotic prescription and resistance data of commensal nasal S. aureus and S. pneumoniae were collected in the 20 participating Hungarian practices of the APRES study. Multivariate logistic regression analyses were performed on the patient-related data and the antimicrobial resistance of the S. aureus and S. pneumoniae on individual, patient level. Ecological analyses were performed with Spearman’s rank correlations at practice level, the analyses were performed in the whole sample (all practices) and in the cohorts of primary care practices taking care of adults (adult practices) or children (paediatric practices). Results According to the multivariate model, age of the patients significantly influenced the antimicrobial resistance of the S. aureus (OR = 0.42, p = 0.004) and S. pneumoniae (OR = 0.89, p

Despite its commonly overlooked role as a commensal, Ralstonia mannitolilytica becomes an emerging global opportunistic human pathogen and a causative agent of various infections and diseases. In respiratory illnesses, including cystic fibrosis and chronic obstructive pulmonary disease (COPD), R. mannitolilytica is also identified presumably as colonizer. In this study, one distinctive clone of R. mannitolilytica was firstly identified as colonizer for the first 20 days during hospitalization of a patient. It was then identified as a causative agent for catheter-related bloodstream infection with negative identification after effective treatment, verifying its transition from commensal to pathogen. In conclusion, we provide convincing evidence that during hospitalization of a patient, R. mannitolilytica transitioned from commensal to pathogen in the respiratory tract leading to catheter-related bloodstream infection (CRBSI).

Alien species are among the greatest threats to biodiversity, but the evolutionary origins of invasiveness remain obscure. We conducted the first range-wide sampling of Hemidactylus mabouia from more than 120 localities across Africa, Madagascar and the Neotropics to understand the evolutionary history of one of the most widely distributed, invasive vertebrates in the world. We used a multi-locus phylogeny, species delimitation, fossil-calibrated timetree, ancestral area reconstruction and species distribution models (SDMs) to determine how many putative species-level lineages are contained within H. mabouia, the timing and tempo of diversification, and the origins of commensality—providing insights into the evolutionary origins of invasiveness. Our analyses suggest ‘H. mabouia’ originated in the Miocene in the Zambezian biogeographic region and includes as many as 20 putative species-level lineages, of which only Hemidactylus mabouia sensu stricto is invasive and widely distributed, including all Neotropical records. Zambezia is the hotspot for diversity within the group with 14 species in southeastern Zambezia. SDMs suggest that H. mabouia was able to establish in the Neotropics due to habitat suitability, and globalization and the slave trade probably allowed it to cross the Atlantic. Distribution models for the H. mabouia complex overpredict the range of the invasive H. mabouia sensu stricto—highlighting the importance of taxonomy in invasive species management.

There is a high incidence of upper respiratory viral infections in the human population, with infection severity being unique to each individual. Upper respiratory viruses have been associated previously with secondary bacterial infection, however, several cross-sectional studies analyzed in the literature indicate that an inverse relationship can also occur. Pathobiont abundance and/or bacterial dysbiosis can impair epithelial integrity and predispose an individual to viral infection. In this review we describe common commensal microorganisms that have the capacity to reduce the abundance of pathobionts and maintain bacterial symbiosis in the upper respiratory tract and discuss the potential and limitations of localized probiotic formulations of commensal bacteria to reduce the incidence and severity of viral infections.

Bumblebees are important natural pollinators due to their services to wild and cultivated plants. They commonly nest in cavities in the ground where they are exposed to numerous organisms or interact with them. One Bombus pauloensis nest in the Sabana of Bogotá (Colombia) was transferred to an artificial nest and relocated close to a honeybee apiary after the original nest was threatened by an intentional fire. The objective was to preserve the colony and simultaneously identify arthropods associated with a bumblebee nest as this is poorly studied in Colombia. Samples of the organisms found in the bumblebees’ nest were collected for taxonomic identification. Several commensal, scavenger and parasitic organisms were found, including Antherophagus sp. (Coleoptera: Crytophagidae), wireworm beetles (Coleoptera: Elateride), Fannia canicularis (Diptera: Fanniidae), and mites of genera Parasitellus and Pneumolaelaps. This is the first report of other organisms besides Antherophagus from a B. pauloensis nest in Colombia.

There is a high incidence of upper respiratory viral infections in the human population, with infection severity being unique to each individual. Upper respiratory viruses have been associated previously with secondary bacterial infection, however, several cross-sectional studies analyzed in the literature indicate that an inverse relationship can also occur. Pathobiont abundance and/or bacterial dysbiosis can impair epithelial integrity and predispose an individual to viral infection. In this review we describe common commensal microorganisms that have the capacity to reduce the abundance of pathobionts and maintain bacterial symbiosis in the upper respiratory tract and discuss the potential and limitations of localized probiotic formulations of commensal bacteria to reduce the incidence and severity of viral infections. [ABSTRACT FROM AUTHOR]

Coastal tide pools in southern Japan are inhabited by the rock-boring sea urchin Echinostrephus molaris, which excavate pits in the substrate. These pits are subsequently used by non-boring sea urchins such as Anthocidaris crassispina and Echinometra sp. B, and the recolonized pits are often inhabited by a commensal limpet-like trochid snail species, Broderipia iridescens. We explored the population and community dynamics of these sea urchins and the limpet-like snail by monitoring occupancy of 512 pits in tide pools in Shirahama, Japan from May 2017–May 2019. Initially, nearly all pits were occupied by any one of the three sea urchin species, but an unusual cold event in February 2018 caused a mass die off of these sea urchins. After this event, occupancy decreased from 99% to 15%, and the tropical species Echinometra sp. B disappeared from the study pools. We observed slow population recovery of E. molaris and A. crassispina, provably via migration of sub-adults from the subtidal zone. Turnover rate of the pit-occupying sea urchin species was <1.0% before the cold event, but drastically increased after the cold event. Population size of the commensal snail decreased along with those of their host, but the rate of commensalism was constant at 50–55% throughout the study period, suggesting that these snails followed their host sea urchins repeating inter-pit migration. Despite mass mortality and slow recovery, the sea urchin density remained high enough to maintain persistent sea urchin barrens throughout the study period. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The occurrence of polychaete borers was recorded from the alien clam Anadara kagoshimensis (Tokunaga, 1906) at Chushka Spit near Port Kavkaz in January 2020. On the basis of morphological analysis, the polychaetes were identified as Polydora websteri Hartman in Loosanoff & Engle, 1943, alien to the Azov-Black Sea basin. This species was recorded for the first time from coastal waters of Romania on carbonate rocks in 1997 and, subsequently, coastal areas of Sevastopol and Lake Donuzlav in oysters Crassostrea gigas (Thunberg, 1793) in 2009 and 2019. Polydora websteri was not previously recorded from the Kerch Strait and the Sea of Azov. This is the first report of its occurrence in Anadara kagoshimensis in the Azov-Black Sea region, which is an invasion area for both species. [ABSTRACT FROM AUTHOR]

The gopher frog Lithobates capito is one of the most terrestrial frogs in the southeastern United States and often inhabits gopher tortoise burrows Gopherus polyphemus outside of the breeding season. Gopher frog populations have declined, and the species is under review for listing as threatened or endangered under the U.S. Endangered Species Act. Much of our knowledge on the status of gopher frogs is based on detections of larvae at breeding wetlands, which can be challenging because of environmental variability and provides no information on the terrestrial life stages of the species. Therefore, an alternative method is called for. We recorded observations of gopher frogs during gopher tortoise surveys at four conservation lands in Florida and used line-transect distance sampling to estimate frog abundance. We also recorded burrow size, incidence of frog co-occupancy with tortoises, and distance from frog-occupied burrows to breeding wetlands. We observed 274 gopher frogs in 1,097 tortoise burrows at the four sites. The proportion of burrows occupied by gopher frogs among sites ranged from 0.17 to 0.25. Gopher frog abundance in tortoise burrows was 742 (512–1,076 95% CL) at Etoniah Creek State Forest, 465 (352–615) at Ft. White Wildlife Environmental Area, 411 (283–595) at Mike Roess Gold Head Branch State Park, and 134 (97–186) at Watermelon Pond Wildlife Environmental Area. We observed up to four frogs in a single burrow. The proportion of frogs detected in burrows occupied by a gopher tortoise ranged from 0.46 to 0.79 among sites, and overall, gopher frogs preferred burrows occupied by tortoises over unoccupied burrows (χ2 = 15.875; df = 3; P = 0.001). Gopher frogs used burrows from 7 to 43 cm in width; mean width of frog-occupied burrows did not differ from that of unoccupied burrows (F1,3 = 0.049, P = 0.825). Distance from frog-occupied tortoise burrows to the nearest breeding wetland ranged from 141 to 3,402 m. Our data on gopher frogs collected in conjunction with gopher tortoise monitoring efforts using line-transect distance sampling and burrow cameras provided novel information on frog abundance in their terrestrial habitat and required no additional effort. However, the extent to which frogs use tortoise burrows relative to other available refuges (small mammal burrows, stumps, or other structures) is unknown; thus, our estimates should be considered conservative. We suggest that terrestrial abundance estimates for gopher frogs can complement efforts to monitor breeding activity to provide a more comprehensive means of monitoring population trends in this cryptic species. [ABSTRACT FROM AUTHOR]

Background Effort is invested in maintaining sterility of the operating field, but less attention is paid to potential healthcare associated infection (HAIs) sources through patient contact by non-scrubbed healthcare providers (HCPs). A single microbiological assessment of hands can provide a good assessment of the potential dynamic transmission of microorganisms. The aim of this study was to identify and quantify the microbial growth on the hands of HCPs in the operating theatres of Chris Hani Baragwanath Academic Hospital. Methods A prospective, contextual and descriptive study design was followed. Seventy-five samples were collected using convenience sampling from an equal number of surgeons, anaesthetists and nurses. Specimens were taken using agar platesand underwent semi-quantitative analysis. Results All hands of HCPs displayed growth, of which 82% grew commensals and 80% grew pathogens. Twelve commensal microorganisms and 27 pathological microorganisms were noted. Two or more organisms were cultured on 76% of HCPs’ hands. Comparisons of commensal, pathological and combined levels of contaminationamong the three groups were not statistically significant (p=0.266, p=0.673, p=0.180). There was no significant difference between the growth of combined microorganisms (p=0.927)and pathological microorganisms (p=0.499) among the groups.Surgeons had significantly more commensal growth (p=0.019) than anaesthetists and nurses. There was no statistically significant difference between sexes (p=0.611). Conclusion It was concerning that 100% of the hands of HCPs who were about to commence with the surgical list had microbial growth. These HCPs could have already been in contact with patients and equipment in the theatre environment. Microorganisms cultured on hands are a source of cross-transmission which may result in HAIs. Institutions require the implementation of a multidimensional model to amend guidelines, implement guidelines and increase awareness of hand hygiene.

Jellyfish are known to carry various epibionts, including many of the subphylum Crustacea. However, the associations between gelatinous zooplankton and other invertebrates have been chronically overlooked. Crustacea, a massive clade of economically, ecologically, and culturally important species, includes many taxa that utilize gelatinous zooplankton for food, transport, and protection as both adults and juveniles. Here we compile 211 instances of epifaunal crustaceans recorded on Hydromedusae and Scyphomedusae from a century of literature. These include 78 identified crustacean species in 65 genera across nine orders found upon 37 Hydromedusa species and 48 Scyphomedusae. The crustacean life stage, location, nature of the association with the medusa, years, months, and depths are compiled to form a comprehensive view of the current state of the literature. Additionally, this review highlights areas where the current literature is lacking, particularly noting our poor understanding of the relationships between juvenile crabs of commercially valuable species and medusae.

The significance of microbiology and immunology with regard to caries and periodontal disease gained substantial clinical or research consideration in the mid 1960's. This enhanced emphasis related to several simple but elegant experiments illustrating the relevance of bacteria to oral infections. Since that point, the understanding of oral diseases has become increasingly sophisticated and many of the original hypotheses related to disease causality have either been abandoned or amplified. The COVID pandemic has reminded us of the importance of history relative to infectious diseases and in the words of Churchill “those who fail to learn from history are condemned to repeat it.” This review is designed to present an overview of broad general directions of research over the last 60 years in oral microbiology and immunology, reviewing significant contributions, indicating emerging foci of interest, and proposing future directions based on technical advances and new understandings. Our goal is to review this rich history (standard microbiology and immunology) and point to potential directions in the future (omics) that can lead to a better understanding of disease. Over the years, research scientists have moved from a position of downplaying the role of bacteria in oral disease to one implicating bacteria as true pathogens that cause disease. More recently it has been proposed that bacteria form the ecological first line of defense against “foreign” invaders and also serve to train the immune system as an acquired host defensive stimulus. While early immunological research was focused on immunological exposure as a modulator of disease, the “hygiene hypothesis,” and now the “old friends hypothesis” suggest that the immune response could be trained by bacteria for long-term health. Advanced “omics” technologies are currently being used to address changes that occur in the host and the microbiome in oral disease. The “omics” methodologies have shaped the detection of quantifiable biomarkers to define human physiology and pathologies. In summary, this review will emphasize the role that commensals and pathobionts play in their interaction with the immune status of the host, with a prediction that current “omic” technologies will allow researchers to better understand disease in the future.

Rodent eradications undertaken on tropical islands have had a lower success rate than those attempted in temperate regions. A recent project undertaken to eradicate Rattus tanezumi and R. exulans from the 3 islands comprising Wake Atoll is illustrative. R. tanezumi was successfully removed from all 3 islands. R. exulans was permanently eradicated on Peale Island (95 ha) and temporarily on Wilkes Island (76 ha). R. exulans eradication on Wake Island (525 ha) was unsuccessful and the species has since repopulated Wake Island and recolonized Wilkes Island. We completed a detailed review of the project in an attempt to isolate potential causes of eradication failure. Based on the evidence available, we were not able to positively identify a single factor to explain why R. exulans survived on Wake Island. However, monitoring after the operation points to a sequence of events that comprised delayed mortality amongst a subset of breeding females and the emergence of young rats after bait was no longer readily available. Such an event was likely influenced by an abundance of natural food resources throughout the treatment area, a high density of rats, interspecific competition for toxic bait, and rapid disappearance of bait because of consumption by non-target consumers (land crabs). These factors are common to many tropical islands. We provide recommendations for addressing these factors in a future attempt to remove rats from Wake Atoll.

Background: Bifidobacteria are commensal microbes of the mammalian gastrointestinal tract. In this study, we aimed to identify the intestinal colonization mechanisms and key metabolic pathways implemented by Bifidobacterium dentium. Results: B. dentium displayed acid resistance, with high viability over a pH range from 4 to 7; findings that correlated to the expression of Na+/H+ antiporters within the B. dentium genome. B. dentium was found to adhere to human MUC2+ mucus and harbor mucin-binding proteins. Using microbial phenotyping microarrays and fully-defined media, we demonstrated that in the absence of glucose, B. dentium could metabolize a variety of nutrient sources. Many of these nutrient sources were plant-based, suggesting that B. dentium can consume dietary substances. In contrast to other bifidobacteria, B. dentium was largely unable to grow on compounds found in human mucus; a finding that was supported by its glycosyl hydrolase (GH) profile. Of the proteins identified in B. dentium by proteomic analysis, a large cohort of proteins were associated with diverse metabolic pathways, indicating metabolic plasticity which supports colonization of the dynamic gastrointestinal environment. Conclusions: Taken together, we conclude that B. dentium is well adapted for commensalism in the gastrointestinal tract. [ABSTRACT FROM AUTHOR]

Jellyfish are known to carry various epibionts, including many of the subphylum Crustacea. However, the associations between gelatinous zooplankton and other invertebrates have been chronically overlooked. Crustacea, a massive clade of economically, ecologically, and culturally important species, includes many taxa that utilize gelatinous zooplankton for food, transport, and protection as both adults and juveniles. Here we compile 211 instances of epifaunal crustaceans recorded on Hydromedusae and Scyphomedusae from a century of literature. These include 78 identified crustacean species in 65 genera across nine orders found upon 37 Hydromedusa species and 48 Scyphomedusae. The crustacean life stage, location, nature of the association with the medusa, years, months, and depths are compiled to form a comprehensive view of the current state of the literature. Additionally, this review highlights areas where the current literature is lacking, particularly noting our poor understanding of the relationships between juvenile crabs of commercially valuable species and medusae. [ABSTRACT FROM AUTHOR]

The significance of microbiology and immunology with regard to caries and periodontal disease gained substantial clinical or research consideration in the mid 1960's. This enhanced emphasis related to several simple but elegant experiments illustrating the relevance of bacteria to oral infections. Since that point, the understanding of oral diseases has become increasingly sophisticated and many of the original hypotheses related to disease causality have either been abandoned or amplified. The COVID pandemic has reminded us of the importance of history relative to infectious diseases and in the words of Churchill "those who fail to learn from history are condemned to repeat it." This review is designed to present an overview of broad general directions of research over the last 60 years in oral microbiology and immunology, reviewing significant contributions, indicating emerging foci of interest, and proposing future directions based on technical advances and new understandings. Our goal is to review this rich history (standard microbiology and immunology) and point to potential directions in the future (omics) that can lead to a better understanding of disease. Over the years, research scientists have moved from a position of downplaying the role of bacteria in oral disease to one implicating bacteria as true pathogens that cause disease. More recently it has been proposed that bacteria form the ecological first line of defense against "foreign" invaders and also serve to train the immune system as an acquired host defensive stimulus. While early immunological research was focused on immunological exposure as a modulator of disease, the "hygiene hypothesis," and now the "old friends hypothesis" suggest that the immune response could be trained by bacteria for long-term health. Advanced "omics" technologies are currently being used to address changes that occur in the host and the microbiome in oral disease. The "omics" methodologies have shaped the detection of quantifiable biomarkers to define human physiology and pathologies. In summary, this review will emphasize the role that commensals and pathobionts play in their interaction with the immune status of the host, with a prediction that current "omic" technologies will allow researchers to better understand disease in the future. [ABSTRACT FROM AUTHOR]

Gut microbiota have myriad roles in host physiology, development, and immunity. Though confined to the intestinal lumen by the epithelia, microbes influence distal systems via poorly characterized mechanisms. Recent work has considered the role of extracellular vesicles in interspecies communication, but whether they are involved in systemic microbe-host interaction is unclear. Here, we show that distinctive nanoparticles can be isolated from mouse blood within 2.5 h of consuming Lacticaseibacillus rhamnosus JB-1. In contrast to blood nanoparticles from saline-fed mice, they reproduced lipoteichoic acid-mediated immune functions of the original bacteria, including activation of TLR2 and increased IL-10 expression by dendritic cells. Like the fed bacteria, they also reduced IL-8 induced by TNF in an intestinal epithelial cell line. Though enriched for host neuronal proteins, these isolated nanoparticles also contained proteins and viral (phage) DNA of fed bacterial origin. Our data strongly suggest that oral consumption of live bacteria rapidly leads to circulation of their membrane vesicles and phages and demonstrate a nanoparticulate pathway whereby beneficial bacteria and probiotics may systemically affect their hosts.

The skin microbial community is a multifunctional ecosystem aiding prevention of infections from transient pathogens, maintenance of host immune homeostasis, and skin health. A better understanding of the complex milieu of microbe-microbe and host-microbe interactions will be required to define the ecosystem’s optimal function and enable rational design of microbiome targeted interventions. Malassezia, a fungal genus currently comprising 18 species and numerous functionally distinct strains, are lipid-dependent basidiomycetous yeasts and integral components of the skin microbiome. The high proportion of Malassezia in the skin microbiome makes understanding their role in healthy and diseased skin crucial to development of functional skin health knowledge and understanding of normal, healthy skin homeostasis. Over the last decade, new tools for Malassezia culture, detection, and genetic manipulation have revealed not only the ubiquity of Malassezia on skin but new pathogenic roles in seborrheic dermatitis, psoriasis, Crohn’s disease, and pancreatic ductal carcinoma. Application of these tools continues to peel back the layers of Malassezia/skin interactions, including clear examples of pathogenicity, commensalism, and potential protective or beneficial activities creating mutualism. Our increased understanding of host- and microbe-specific interactions should lead to identification of key factors that maintain skin in a state of healthy mutualism or, in turn, initiate pathogenic changes. These approaches are leading toward development of new therapeutic targets and treatment options. This review discusses recent developments that have expanded our understanding of Malassezia’s role in the skin microbiome, with a focus on its multiple roles in health and disease as commensal, pathogen, and protector.

The health of mammals depends on a complex interplay with their microbial ecosystems. Compartments exposed to external environments such as the mucosal surfaces of the gastrointestinal tract accommodate the gut microbiota, composed by a wide range of bacteria. The gut microbiome confers benefits to the host, including expansion of metabolic potential and the development of an immune system that can robustly protect from external and internal insults. The cooperation between gut microbiome and host is enabled in part by the formation of partitioned niches that harbor diverse bacterial phyla. Bacterial secretion systems are commonly employed to manipulate the composition of these local environments. Here, we explore the roles of the bacterial type VI secretion system (T6SS), present in ~25% of gram-negative bacteria, including many symbionts, in the establishment and perturbation of bacterial commensalism, and symbiosis in host mucosal sites. This versatile apparatus drives bacterial competition, although in some cases can also interfere directly with host cells and facilitate nutrient acquisition. In addition, some bacterial pathogens cause disease when their T6SS leads to dysbiosis and subverts host immune responses in defined animal models. This review explores our knowledge of the T6SS in the context of the “host-microbiota-pathogen” triumvirate and examines contexts in which the importance of this secretion system may be underappreciated.

Whole-genome sequencing has enabled detailed studies on bacterial evolution during infection, but there is limited knowledge on intraclonal variation. In this study, we sought to provide a snapshot of the intraclonal diversity of Escherichia coli as both commensal in the faecal environment and pathogen during urinary tract infection, respectively. This was performed by whole-genome sequencing and analyses of single nucleotide polymorphisms (SNPs) and gene-content variation in ten isolates belonging to the same clone and isolated from rectal swabs or urine samples. We identified only one clone in eight of the nine urines sampled (89 %). In both the commensal and pathogenic state, the within-host diversity was limited with intraclonal SNP diversity of 0–2 non-synonymous SNPs for each clone. The genetic diversity showed variation in gene content in a range of 2–15 genes in total for all clones, including genes positioned on plasmids, and in the K- and O-antigen cluster. The observed SNP- and gene variation shows that sampling of one colony would be enough for surveillance, outbreak investigations and clonal evolution. However, for studies of adaptation during or between colonization and infection, this variation is relevant to consider.

Abstract Acne is one of the most common skin diseases worldwide and results in major health care costs and significant morbidity to severely affected individuals. However, the pathophysiology of this disorder is not well understood. Host-microbiome interactions that affect both innate and adaptive immune homeostasis appear to be a central factor in this disease, with recent observations suggesting that the composition and activities of the microbiota in acne is perturbed. Staphylococcus epidermidis and Cutibacterium acnes (C. acnes; formerly Propionibacterium acnes) are two major inhabitants of the skin that are thought to contribute to the disease but are also known to promote health by inhibiting the growth and invasion of pathogens. Because C. acnes is ubiquitous in sebaceous-rich skin, it is typically labeled as the etiological agent of acne yet it fails to fulfill all of Koch’s postulates. The outdated model of acne progression proposes that increased sebum production promotes over-proliferation of C. acnes in a plugged hair follicle, thereby driving inflammation. In contrast, growing evidence indicates that C. acnes is equally abundant in both unaffected and acne-affected follicles. Moreover, recent advances in metagenomic sequencing of the acne microbiome have revealed a diverse population structure distinct from healthy individuals, uncovering new lineage-specific virulence determinants. In this article, we review recent developments in the interactions of skin microbes with host immunity, discussing the contribution of dysbiosis to the immunobiology of acne and newly emerging skin microbiome-based therapeutics to treat acne.

Abstract Bacterial surface colonization and biofilm formation often rely on the production of an extracellular polymeric matrix that mediates cell-cell and cell-surface contacts. In Escherichia coli and many Betaproteobacteria and Gammaproteobacteria cellulose is often the main component of the extracellular matrix. Here we report the complete genome sequence of the cellulose producing strain E. coli 1094 and compare it with five other closely related genomes within E. coli phylogenetic group A. We present a comparative analysis of the regions encoding genes responsible for cellulose biosynthesis and discuss the changes that could have led to the loss of this important adaptive advantage in several E. coli strains. Data deposition: The annotated genome sequence has been deposited at the European Nucleotide Archive under the accession number PRJEB21000.

Background: Increase in the number of infections caused by Gram-negative bacteria in neutropenic cancer patients has prompted the search for novel therapeutic agents having dual anticancer and antimicrobial properties. Bacteriocins are cationic proteins of prokaryotic origin that have emerged as one of the most promising alternative antimicrobial agents with applications as food preservatives and therapeutic agents. Apart from their antimicrobial activities, bacteriocins are also being explored for their anticancer potential. Results: In this study, a broad-spectrum, cell membrane-permeabilizing enterocin with a molecular weight of 65 kDa was purified and characterized from the culture supernatant of vaginal Enterococcus faecium 12a. Enterocin 12a inhibited multidrug-resistant strains of various Gram-negative pathogens such as Salmonella enterica, Shigella flexneri, Vibrio cholerae, Escherichia coli and Gram-positive, Listeria monocytogenes, but had no activities against different strains of gut lactobacilli. The mass spectrometric analysis showed that the enterocin 12a shared partial homology with 4Fe-4S domain-containing redox protein of E. faecalis R712. Further, enterocin 12a selectively inhibited the proliferation of various human cancer cell lines in a dose-dependent manner but not that of normal human peripheral blood mononuclear cells. Enterocin 12a-treated cancer cells showed apoptosis-like morphological changes. Conclusion: Enterocin 12a is a novel bacteriocin that has anticancer properties against human cell lines and negligible activity towards non-malignant cells. Therefore, it should be further evaluated for its anticancer potential in animal models. [ABSTRACT FROM AUTHOR]

The skin microbial community is a multifunctional ecosystem aiding prevention of infections from transient pathogens, maintenance of host immune homeostasis, and skin health. A better understanding of the complex milieu of microbe-microbe and host-microbe interactions will be required to define the ecosystem's optimal function and enable rational design of microbiome targeted interventions. Malassezia , a fungal genus currently comprising 18 species and numerous functionally distinct strains, are lipid-dependent basidiomycetous yeasts and integral components of the skin microbiome. The high proportion of Malassezia in the skin microbiome makes understanding their role in healthy and diseased skin crucial to development of functional skin health knowledge and understanding of normal, healthy skin homeostasis. Over the last decade, new tools for Malassezia culture, detection, and genetic manipulation have revealed not only the ubiquity of Malassezia on skin but new pathogenic roles in seborrheic dermatitis, psoriasis, Crohn's disease, and pancreatic ductal carcinoma. Application of these tools continues to peel back the layers of Malassezia /skin interactions, including clear examples of pathogenicity, commensalism, and potential protective or beneficial activities creating mutualism. Our increased understanding of host- and microbe-specific interactions should lead to identification of key factors that maintain skin in a state of healthy mutualism or, in turn, initiate pathogenic changes. These approaches are leading toward development of new therapeutic targets and treatment options. This review discusses recent developments that have expanded our understanding of Malassezia 's role in the skin microbiome, with a focus on its multiple roles in health and disease as commensal, pathogen, and protector. [ABSTRACT FROM AUTHOR]

Some native cricetid rodents are well adapted to modified environments; therefore, they could inhabit periurban or even urban environments. The city of Diamante is a small riverside city immersed in a matrix of wetland and croplands which are inhabited by cricetid rodents. This city could offer available habitats to island rodents principally during extreme flood events. The objective of this study was to determine the composition of the rodent assemblage in this small riverside city of Diamante, Entre Ríos, Argentina, not studied so far, after an exceptional magnitude flood mediated by an ENSO-El Niño event. Small rodents were live-trapped in autumn and spring 2016 in 127 sampling units (houses and vacant lots). The relationship among rodent abundance and the minimal distance to the Paraná river and to boundaries of the city, and the presence of dogs, cats, chickens and litter were explored by means of Generalized Linear Models. Mus musculus and Rattus rattus were captured in the 18.7% and 1.9% of the sampling units, respectively, while R. norvegicus and Oxymycterus rufus were found in the 0.9% of these. Mus musculus abundance was not associated with its presence in houses or vacant lots or with any other explanatory variables. This study showed that this riverside city does not harbor populations of native rodents, not even in extreme flooding periods. [ABSTRACT FROM AUTHOR]

Cutibacterium acnes (C acnes) is a mysterious member of the shoulder microbiome and is associated with chronic postoperative complications and low-grade infections. Nevertheless, it is unclear whether it represents a contaminant or whether it accounts for true infections. Because it can persist intracellularly in macrophages at several body sites, it might in fact be an intra-articular commensal of the shoulder joint. In 23 consecutive, otherwise healthy patients (17 male, 6 female; 58 years) who had no previous injections, multiple specimens were taken from the intra-articular tissue during first-time arthroscopic and open shoulder surgery. The samples were investigated by cultivation, genetic phylotyping, and immunohistochemistry using C acnes –specific antibodies and confocal laser scanning microscopy. In 10 patients (43.5%), cultures were C acnes –positive. Phylotype IA1 dominated the subcutaneous samples (71%), whereas type II dominated the deep tissue samples (57%). Sixteen of 23 patients (69.6%) were C acnes –positive by immunohistochemistry; in total, 25 of 40 samples were positive (62.5%). Overall, 56.3% of glenohumeral immunohistochemical samples, 62.5% of subacromial samples, and 75% of acromioclavicular (AC) joint samples were positive. In 62.5% of the tested patients, C acnes was detected immunohistochemically to reside intracellularly within stromal cells and macrophages. These data indicate that C acnes is a commensal of the human shoulder joint, where it persists within macrophages and stromal cells. Compared with culture-based methods, immunohistochemical staining can increase C acnes detection. Phylotype II seems to be most prevalent in the deep shoulder tissue. The high detection rate of C acnes in osteoarthritic AC joints might link its intra-articular presence to the initiation of osteoarthritis. [ABSTRACT FROM AUTHOR]

Effort is invested in maintaining the sterility of the operating field, but less attention is paid to potential healthcare associated infection (HAI) sources through patient contact with non-scrubbed healthcare providers (HCPs). A single microbiological assessment of hands can provide a good assessment of the potential dynamic transmission of microorganisms. The aim of this study was to identify and quantify the microbial growth on the hands of HCPs in the operating theatres of Chris Hani Baragwanath Academic Hospital. A prospective, contextual and descriptive study design was followed. Seventy-five samples were collected using convenience sampling from an equal number of surgeons, anaesthetists and nurses. Specimens were taken using agar plates and underwent semi-quantitative analysis. All the hands of the HCPs displayed growth; 95% grew commensals and 64% grew pathogens. Eighteen commensal microorganisms and 21 pathological microorganisms were noted. Comparisons of commensal, pathological and combined levels of contamination among the three groups were not statistically significant (p = 0.061, p = 0.481, p = 0.236). No significant difference between the growth of combined microorganisms (p = 0.634) and pathological microorganisms (p = 0.499) among the groups. Surgeons had significantly more commensal growth (p = 0.041). There was no statistically significant difference between sexes (p = 0.290). It was concerning that 100% of the hands of HCPs who were about to commence with the surgical list had microbial growth. These HCPs could have already been in contact with patients and equipment in the theatre environment. [ABSTRACT FROM AUTHOR]

We explored the between-group and temporal variations in the intestinal Escherichia coli populations of broilers under experimental conditions, taking both antimicrobial resistance and virulence into consideration. Four replicates of 45 commercial chicks were reared in four animal facilities. On their first day of life (Day 0), they were orally inoculated with two extended-spectrum-cephalosporin-resistant (ESCR) E. coli (2.72 log10 CFU of a blaCMY-2- and 2.55 log10 CFU of a blaCTX-M-carrying E. coli). Faecal samples were then collected weekly and caecal samples were obtained from birds sacrificed on Days 21 or 42. The total, ESC-, ciprofloxacin- and gentamicin-resistant E. coli populations were enumerated on MacConkey (MC) and MC-supplemented media, and eight virulence-associated genes (VAGs) (iroN, iutA, iss, ompT, hlyF, vat, frzorf4, and fyuA) were sought by PCR on isolates obtained on MC agar. The results showed significant between-group differences in the size of the resistant sub-populations and the presence of VAGs. Contrary to blaCTX-M-positive strains, blaCMY-positive strains persisted up to Day 42, but represented only a minor fraction of the total E. coli population. The ESC-, gentamicin- and ciprofloxacin-resistant populations decreased over time. Isolates obtained during the first week contained a mean of 5.1 VAGs. The percentages of some VAG profiles differed between faecal isolates on Day 41 and caecal isolates on Day 42. The fluctuations or differences between E. coli isolates according to group, age, and faecal or caecal origin need to be considered when designing experimental protocols and seeking to improve colibacillosis control. RESEARCH HIGHLIGHTS Temporal variations in the intestinal E. coli populations of broilers was studied. The antibiotic-resistant populations decreased over time. Virulence profiles differed between faecal isolates on Day 41 and caecal isolates on Day 42. Strains with the highest numbers of virulence genes were present during the first days. [ABSTRACT FROM AUTHOR]

The health of mammals depends on a complex interplay with their microbial ecosystems. Compartments exposed to external environments such as the mucosal surfaces of the gastrointestinal tract accommodate the gut microbiota, composed by a wide range of bacteria. The gut microbiome confers benefits to the host, including expansion of metabolic potential and the development of an immune system that can robustly protect from external and internal insults. The cooperation between gut microbiome and host is enabled in part by the formation of partitioned niches that harbor diverse bacterial phyla. Bacterial secretion systems are commonly employed to manipulate the composition of these local environments. Here, we explore the roles of the bacterial type VI secretion system (T6SS), present in ~25% of gram-negative bacteria, including many symbionts, in the establishment and perturbation of bacterial commensalism, and symbiosis in host mucosal sites. This versatile apparatus drives bacterial competition, although in some cases can also interfere directly with host cells and facilitate nutrient acquisition. In addition, some bacterial pathogens cause disease when their T6SS leads to dysbiosis and subverts host immune responses in defined animal models. This review explores our knowledge of the T6SS in the context of the "host-microbiota-pathogen" triumvirate and examines contexts in which the importance of this secretion system may be underappreciated. [ABSTRACT FROM AUTHOR]

The recent explosive increase in the number of works on gut microbiota has been accompanied by the spread of rather vague or improper definitions, chosen more for common use than for experimental evidence. Among them are those defining the human gut microbiota as an organ of our body or as a commensal. But, is the human gut microbiota an organ or a commensal? Here, we address this issue to spearhead a reflection on the real roles of the human gut microbiota in our life. Actually, the misuse of the vocabulary used to describe the properties and functions of the gut microbiota may generate confusion and cause misunderstandings both in the scientific community and among the general public. [ABSTRACT FROM AUTHOR]

Previous studies have shown that skunks present negative interactions with foxes. However, recently published observations have demonstrated that southern spotted skunk (Spilogale angustifrons) individuals follow gray foxes (Urocyon cinereoargenteus) in the Tehuacán-Cuicatlán Biosphere Reserve (TCBR) in Mexico. In this paper, we reported the same interaction in other locations in the TCBR and evaluated whether this interaction is casual or statistically positive. In this analysis, we included data pertaining to three skunk species (S. angustifrons, Conepatus leuconotus, and Mephitis macroura) and U. cinereoargenteus. We sampled 172 sites using camera traps from 2011 to 2018 for a total effort of 49,764 trap-days. The four studied species were nocturnal; the overlap coefficient between foxes and skunks varied from 0.70 to 0.83. Of the 32 consecutive records between S. angustifrons and U. cinereoargenteus, 11 showed that individuals of this skunk species closely followed U. cinereoargenteus and that these encounters were not random (time interval <1 min). We did not find evidence of a behavioral association of U. cinereoargenteus with C. leuconotus and M. macroura. [ABSTRACT FROM AUTHOR]

We aimed to compare the effectiveness of single- vs multiple-strain probiotics in a network meta-analysis of randomized trials. We searched MEDLINE, Embase, Science Citation Index Expanded, CINAHL, Scopus, Cochrane CENTRAL, BIOSIS Previews, and Google Scholar through January 1, 2019, for studies of single-strain and multistrain probiotic formulations on the outcomes of preterm, low-birth-weight neonates. We used a frequentist approach for network meta-analysis and the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach to assess the certainty of evidence. Primary outcomes included all-cause mortality, severe necrotizing enterocolitis (NEC) (Bell stage II or more), and culture-proven sepsis. We analyzed data from 63 trials involving 15,712 preterm infants. Compared with placebo, a combination of 1 or more Lactobacillus species (spp) and 1 or more Bifidobacterium spp was the only intervention with moderate- or high-quality evidence of reduced all-cause mortality (odds ratio [OR], 0.56; 95% confidence interval [CI], 0.39–0.80). Among interventions with moderate- or high-quality evidence for efficacy compared with placebo, combinations of 1 or more Lactobacillus spp and 1 or more Bifidobacterium spp, Bifidobacterium animalis subspecies lactis, Lactobacillus reuteri, or Lactobacillus rhamnosus significantly reduced severe NEC (OR, 0.35 [95% CI, 0.20–0.59]; OR, 0.31 [95% CI, 0.13–0.74]; OR, 0.55 [95% CI, 0.34–0.91]; and OR, 0.44 [95% CI, 0.21–0.90], respectively). There was moderate- or high-quality evidence that combinations of 1 or more Lactobacillus spp and 1 or more Bifidobacterium spp and Saccharomyces boulardii reduced the number of days to reach full feeding (mean reduction of 3.30 days [95% CI, reduction of 5.91–0.69 days]). There was moderate- or high-quality evidence that, compared with placebo, the single-species product B animalis subsp lactis or L reuteri significantly reduced duration of hospitalization (mean reduction of 13.00 days [95% CI, reduction of 22.71–3.29 days] and mean reduction of 7.89 days [95% CI, reduction of 11.60–4.17 days], respectively). In a systematic review and network meta-analysis of studies to determine the effects of single-strain and multistrain probiotic formulations on outcomes of preterm, low-birth-weight neonates, we found moderate to high evidence for the superiority of combinations of 1 or more Lactobacillus spp and 1 or more Bifidobacterium spp vs single- and other multiple-strain probiotic treatments. The combinations of Bacillus spp and Enterococcus spp, and 1 or more Bifidobacterium spp and Streptococcus salivarius subsp thermophilus , might produce the largest reduction in NEC development. Further trials are needed. [ABSTRACT FROM AUTHOR]

Background: Staphylococcus epidermidis is a commensal of human skin flora and a frequent causative microorganism in prosthetic joint infections (PJIs). To date, no single marker has been identified to distinguish infecting strains from commensal S. epidermidis populations.Aim: We aimed to find possible genetic markers to distinguish between the two populations.Methods: We analyzed 50 S. epidermidis strains from patients with PJIs, 50 from skin of healthy individuals (commensal strains) and 17 from the surgical field of patients undergoing primary arthroplasty. In these three groups we studied the antimicrobial susceptibility profile, sequence type, biofilm formation, and virulence factors. Strains from the surgical field have not been compared previously with strains from the other two groups.Findings: S. epidermidis strains from PJI patients were significantly more antibiotic resistant than commensal strains and surgical field strains. A wide variety of sequences types was found in commensal and surgical field strains. The predominant sequence type was ST2 and it was only present in PJI strains (44%). Differences in biofilm production did not differ between populations. Virulence genes sdrF and bhp, the complete ica operon, and the insertion sequence IS256 were significantly predominant in PJI strains. In contrast, embp and hld genes and the mobile element ACME were more prevalent in commensal strains. Surgical field strains could be a valid control group to discriminate between infecting and commensal strains.Conclusion: A combination of characteristic features can differentiate between infecting and commensal S. epidermidis strains in PJI, while a single marker cannot. [ABSTRACT FROM AUTHOR]

Multimammate mice of the genus Mastomys are widespread in sub-Saharan Africa and occur in a wide range of open habitats. Representatives of this genus are the most common African rodents, the main vertebrate agricultural pests and vectors of human pathogens. In Ethiopia, the biogeographically most complex eastern African country, several species have been reported, but their distribution has never been described because of their cryptic morphology. Here we present genetically identified species from 377 Ethiopian Mastomys specimens and analyse their distributional patterns. The genus, represented by four species, inhabits most of the country, with the exception of the highest mountains and dry areas, such as the Afar triangle and the Somali region. For the first time we document M. kollmannspergeri from a single locality in the northernmost part of Ethiopia. Three previously recorded species are more widespread – M. erythroleucus was found at 32 localities, M. natalensis at 13 localities and the Ethiopian endemic species M. awashensis at 18 localities. Phylogenetic analysis of mitochondrial cytochrome b gene sequences indicates that only one of the six phylogroups of M. natalensis and one of the four phylogroups of M. erythroleucus are represented in Ethiopia. Haplotype network analysis indicates two subclades of Ethiopian M. erythroleucus separated by the Ethiopian Rift Valley. Using presence records, we constructed distribution models for the species and analysed the level of overlap. The predicted distribution shows most overlap between M. awashensis and M. natalensis, which is in agreement with empirical data as both species were found in sympatry at four localities. A medium level of overlap was predicted between M. natalensis and M. erythroleucus and both species were found co-existing at two localities. This study not only presents the first detailed distribution of cryptic Mastomys species, but also clearly identifies multimammate mice as model taxa for future evolutionary studies (e.g. the evolution of coexistence or host-parasite interactions) and indicates the regions suitable for such studies. [ABSTRACT FROM AUTHOR]