Academic literature on the topic 'Commensal digestive flora'

Dendritic cells present in the digestive tract are constantly exposed to environmental antigens, commensal flora, and invading pathogens. Under steady-state conditions, these cells have high tolerogenic potential, triggering differentiation of regulatory T cells to protect the host from unwanted proinflammatory immune responses to innocuous antigens or commensals. On the other hand, these cells must discriminate between commensal flora and invading pathogens and mount powerful immune response against pathogens. A potential result of unbalanced tolerogenic versus proinflammatory responses mediated by dendritic cells is associated with chronic inflammatory conditions, such as Crohn’s disease, ulcerative colitis, food allergies, and celiac disease. Herein, we review the dendritic cell population involved in mediating tolerance and immunity in mucosal surfaces, the progress in unveiling their development in vivo, and factors that can influence their functions.

Enterococcus spp. are Gram-positive, facultative, anaerobic cocci, which are found in the intestinal flora and, less frequently, in the vagina or mouth. Enterococcus faecalis and Enterococcus faecium are the most common species found in humans. As commensals, enterococci colonize the digestive system and participate in the modulation of the immune system in humans and animals. For many years reference enterococcal strains have been used as probiotic food additives or have been recommended as supplements for the treatment of intestinal dysbiosis and other conditions. The use of Enterococcus strains as probiotics has recently become controversial due to the ease of acquiring different virulence factors and resistance to various classes of antibiotics. Enterococci are also seen as opportunistic pathogens. This problem is especially relevant in hospital environments, where enterococcal outbreaks often occur. Their ability to translocate from the gastro-intestinal tract to various tissues and organs as well as their virulence and antibiotic resistance are risk factors that hinder eradication. Due to numerous reports on the plasticity of the enterococcal genome and the acquisition of pathogenic microbial features, we ask ourselves, how far is this commensal genus from acquiring pathogenicity? This paper discusses both the beneficial properties of these microorganisms and the risk factors related to their evolution towards pathogenicity.

Candida albicans species is located in the oral cavity, digestive tract and genital region as the commensal flora in more than half of the healthy population. Infection with species of Candida genus is the most common cause of vaginal infections, second only to bacterial vaginitis. Candida albicans species is ubuquitous commensal yeast that develops in the mucous membranes. Under normal conditions of host health, this microorganism is in balance with the microbiota of these areas but also with the host�s immune system. The aim of this study was to determine and compare the sensibility and the resistance of some Candida albicans strains isolated from oro-pharyngeal and vaginal secretions to different azole compunds. In the case of oro-pharyngeal infections, most of the Candida isolated species were resistant to ketoconazole, itraconazole and fluconazole and in the case of isolated species in vaginal infections the resistance was increased in the case of fluconazole, itraconazole and ketoconazole, in different percentages compared to oro-pharyngeal site.

Summary We report a case of lactobacillus gasseri peritonitis in a patient treated by peritoneal dialysis. Streptococcus anginus and lactobacillus gasseri bacteria are commensal organisms of human oral, small intestinal, colic and vaginal mucous membranes. An infection with streptococcus anginosus during peritoneal dialysis, one responsible for an intra-abdominal abscess, has already been described, this type of streptococcus being widely associated with abscess formation. In contrast, no case of peritoneal infection with lactobacillus gasseri has ever been described. This bacterium is native to the mucous membranes, and colonizes the digestive tract of infants during childbirth, as they pass through the vaginal canal. It has local adaptation capacities, namely tolerance to acid pH, adhesion to the mucous membrane and resistance to bile salts. It is recognized as having an antimicrobial and probiotic function due to its production of bacteriocin, its local immunomodulatory role, its attenuation of the development of helicobacter pylori, its positive effect on the balance of the vaginal flora and its improvement of infectious diarrhea. This usually makes it an ally that contributes to our systemic balance but its irruption in the peritoneum has made it a pathogenic bacterium. The treatment of this peritoneal infection required a classic duration of treatment of organisms of digestive origin, i.e. 3 weeks

Abstract Introduction: The impact of commensal bacteria harbored in the gastrointestinal tract known as the microbiota has long been recognized as a pivotal factor in allogeneic hematopoietic stem cell transplantation (aHSCT). The microbiota is at the origin of acute graft-versus-host disease (aGVHD) and infections, two important lethal complications in aHSCT. High-dose conditioning chemotherapy prior aHSCT disrupts the gut epithelial barrier allowing bacterial by-products to translocate into the peripheral blood and modulates T cell response and pro-inflammatory cytokines. Such observation led to an effort by certain transplant centers to eliminate bacterial colonization prior to aHSCT to decrease the risk of gram-negative bacterial translocation. In this study, we assessed whether patients' gut decontamination prior to allogeneic stem cell infusion influenced the frequency of aGVHD, pneumomatosis coli (PC) a significant complication of gastrointestinal (GI) GVHD and overall survival. Methods: We retrospectively reviewed the charts of 543 patients who had undergone a single myeloablative or nonmyeloabaltive aHSCT for hematological malignancies from two academic hospitals in the province of Quebec, Canada between January 2005 and December 2012. Exclusion criteria included prior aHSCT, syngeneic and haploidentical aHSCT. Each university hospital has implemented a different pre-transplant antibioprophylaxis guideline. At HMR hospital, ciprofloxacin or moxifloxacine were started at initiation of the conditioning regimen for gut decontamination, but were omitted in patients with fluoroquinolone or penicillin allergy and during nosocomial infections outbreak. On the other hand, in the CHU de Quebec patients were not prescribed prophylactic antibiotics (ATB). In addition, ATB used to treat infections before the stem cells infusion were considered. To determine the impact of ATB, we performed multivariable analyses adjusting for the following confounding factors: age, gender, stem cell origin (source), donor type/match, and conditioning regimens to compare the frequency of aGVHD, PC, leucocytes recovery at day+14 and overall survival (OS) in patients receiving or not ATB. Results: 500 patients were included and a total of 240 (48%) patients received ATB at the time of conditioning regimen. Demographics were similar in both groups with mean age of 48 years. Frequency of grade II-IV aGVHD was more elevated in patients receiving ATB compared to the no ATB group (42% vs 28% respectively with adjusted OR (aOR)=1.53 (p<0.05). The severity of the aGVHD in the ATB group was driven by the GI-GVHD with a higher level of grade II-IV (20.7%) compared to no ATB group (10.8%) with aOR=2.00 (p<0.01). Severity of skin and liver GVHD were similar in both groups. Among the 12 patients that developed PC diagnosed on CT-scan, all received ciprofloxacin during conditioning and PC was associated with 80% mortality. The difference of aGVH frequency may have translated into survival as the ATB group was associated to lower 1 year survival compared to no ATB group (74% vs 88%, OR=0.36 and aOR=0.38 (p<0.05). This significant survival difference at 1 year persisted over time and median OS was 4 and 5 years respectively (p<0.05). Taking into consideration the entire follow-up period of 10 years, the hazard rates associated with ATB were estimated at 1.61(p<0.06) and 1.43 (p<0.05) after adjusting for clinical parameters. Interestingly, post-hoc analysis revealed independent impact of the ATB on D+14 neutrophils. This was reflected by a lower neutrophil count in patients on ATB that received stem cells from a match-related donor compared to no ATB counterpart with a ratio of 0.38 (p<0.05). Discussion: This retrospective study indicated that ATB were associated to a more severe aGVHD driven by digestive manifestations of the GVHD and higher incidence of PC even after multivariable analysis. These life-threatening complications may impact on the 1-year and OS that were lower in the ATB group. Without undermining the role of ATB prophylaxis to prevent infection in aHSCT setting, treatment with ATB impact on the commensal microbiota and diminishes its diversity. This imbalance created by the ATB may have contributed to the pathophysiology of GI-GVHD. This ultimately highlights the importance to reconsider antibioprophylaxis to preserve an intact flora and its benefits in aHSCT. Disclosures No relevant conflicts of interest to declare.

Staphylococcus epidermidis is part of the normal bacterial flora on the ocular surface. The chromosomal DNA of bacterial isolates obtained from the conjunctival sac, upper and lower lid margins, and upper and lower Meibomian glands of healthy volunteers was subjected to SmaI digestion and PFGE to study the genetic diversity of the organisms. Multiple colonies were also examined of S. epidermidis derived from the conjunctival sac of the same subjects. Lastly, commensal bacteria were harvested from the ocular surfaces of four healthy subjects once a month for 6 months, and the genetic background of the S. epidermidis isolates was analysed. It was found that bacterial strains not only from different subjects but also from multiple ocular surface sites of the same subject exhibited different PFGE patterns. In five of 42 subjects multiple colonies of S. epidermidis were isolated from the conjunctival sac; three harboured multiple colonies with different PFGE patterns, and two manifested multiple colonies with identical PFGE patterns. S. epidermidis isolated from the conjunctival sac of the same subjects over a 6-month period exhibited varying PFGE patterns. The data demonstrate the polyclonality of S. epidermidis on the healthy ocular surface.

Apart from its main functions of digestion, absorption and faecal processing, the human gastrointestinal tract has a complex pattern of muscular activity regulated by a largely autonomous nervous system, and its various organs contain large concentrations of immune and endocrine tissues. Any failure of these closely-integrated systems can lead to diseases ranging from the mildly irritating to the life threatening. Food contains a huge variety of chemical species, many of which are biologically active, and the distal regions of the gut are colonised by a rich and metabolically-active commensal flora that depend on nutrients derived ultimately from the host’s dietary residues. The present paper explores the evidence for significant effects of food ingredients on functional bowel disorders, intestinal infections, and aspects of epithelial cell physiology involved in the development of colo-rectal neoplasia. Various strategies, including the manipulation of the colo-rectal microflora with pre- and probiotics, and the development of new products and plant varieties containing biologically-active constituents, have the potential to underpin the development of novel functional food products. However, these products will need to be based on proven biological principles, and fully tested for efficacy and safety. The rapidly-developing fields of functional genomics and cell biology will open up new experimental strategies to explore these possibilities, and emerging processing technologies seem likely to provide novel methods for their exploitation.

AbstractThe human oral and gut commensal microbes play vital roles in the development and maintenance of immune homeostasis, while its association with susceptibility and severity of SARS-CoV-2 infection is barely understood. In this study, we investigated the dynamics of the oral and intestinal flora before and after the clearance of SARS-CoV-2 in 53 COVID-19 patients, and then examined their microbiome alterations in comparison to 76 healthy individuals. A total of 140 throat swab samples and 81 fecal samples from these COVID-19 patients during hospitalization, and 44 throat swab samples and 32 fecal samples from sex and age-matched healthy individuals were collected and then subjected to 16S rRNA sequencing and viral load inspection. We found that SARS-CoV-2 infection was associated with alterations of the microbiome community in patients as indicated by both alpha and beta diversity indexes. Several bacterial taxa were identified related to SARS-CoV-2 infection, wherein elevated Granulicatella and Rothia mucilaginosa were found in both oral and gut microbiome. The SARS-CoV-2 viral load in those samples was also calculated to identify potential dynamics between COVID-19 and the microbiome. These findings provide a meaningful baseline for microbes in the digestive tract of COVID-19 patients and will shed light on new dimensions for disease pathophysiology, potential microbial biomarkers, and treatment strategies for COVID-19.

Background: Yeasts naturally colonize the mammalian digestive tract and play an important role in health and disease. This community is composed of commensal yeasts, mostly Candida and Saccharomyces described as a part of the intestinal mycobiome and could be associated with resident or transient flora. Objectives: The aim of our study was to perform the phenotypic and genotypic characterization of culturable Candida isolates present in stool specimens of healthy Tunisian individuals and to evaluate their antifungal susceptibility. Methods: Yeasts were recovered from 46 stool samples cultured on Sabouraud dextrose agar at 37°C. Species were identified using conventional methods and ITS-PCR sequencing. Candida isolates were tested by exploring their tolerance to oxidative stress and extreme acidic conditions. In addition, their biofilm formation ability and in vitro resistance to antifungals was determined by the VITEK 2 system. Results: The identification by sequencing the ITS1-5.8S-ITS2 region of the 56 yeast strains isolated from 37 stool samples revealed that Candida was the dominant genus and was represented by Candida albicans (n = 21), C. parapsilosis (n = 10), C. glabrata (n = 9), and C. krusei (n = 9). In contrast, the other genera, including Trichosporon, Geotrichum, and Rhodotorula, were sporadically occurring. We found that most Candida isolates were able to form biofilms under oxidative stress and extreme pH conditions. Regarding antifungal susceptibility, a higher resistance rate to fluconazole was revealed in comparison to caspofungin and micafungin. However, no resistance was revealed against voriconazole, amphotericin B, and 5-flucytosine. Conclusions: This is the first work-generated data on cultivable yeasts from stool specimens of healthy individuals in Tunisia. Further metagenomic studies with a larger sample size are needed to better characterize the intestinal mycobiota.

Abstract A description is provided for Candida albicans. Information is included on the disease caused by the organism, its transmission, geographical distribution, and hosts. DISEASE: Candida albicans is the commonest cause of candidosis in humans and is also implicated in diseases, notably of the respiratory tract, in birds and other warm-blooded animals. The literature relating to candidosis goes back to approximately 400 BC when Hippocrates described two cases of thrush in his Epidemics book 3 (translated by F. Adams, Baltimore: Williams + Wilkins, 1939). Infections in humans may be superficial (oral thrush, vaginitis, paronychia and cutaneous candidosis) or deep-seated as a result of dissemination via the blood-stream (e.g. endocarditis, endophthalmitis). Single organs may be involved as a result of direct invasion (e.g. pulmonary candidosis). Candidosis may occur in almost any part of the body but rarely occurs in the absence of one or more predisposing factors. Candida albicans occurs commonly as a commensal of mucous membranes and the digestive tract and infection generally results from an overgrowth of the patient's indigenous flora. Predisposing factors involve those associated with hospitalization and serious underlying disease e.g. broad-spectrum antibacterial chemotherapy (see Odds, 1979), use of intravenous catheters and surgical procedures as well as malignant and immunological disorders and intravenous drug abuse. Certain groups within the healthy population are also at risk including neonates (oral thrush), pregnant women (vaginitis) and kitchen workers (paronychia). Chronic mucocutaneous candidosis is a severe superficial disease, usually in children, thought to be linked with cellular immune deficiencies and endocrinopathy syndromes. The pathogenicity of Candida albicans has been established by careful clinical studies of patients with candidosis and by laboratory experiments with animals including mice, guineapigs and rabbits. Disseminated candidosis has been produced by intravenous and intra-peritoneal inoculation of unmodified laboratory animals and may affect visceral organs with the kidney generally the focus of infection. Pretreatment with corticosteroids, irradiation etc. generally enhances the susceptibility of the animal to candidosis (see Odds, 1979 for a review of the literature). GEOGRAPHICAL DISTRIBUTION: Probably worldwide. Reported from Africa, Asia, Australasia, Europe, North and South America.

L'antibiothérapie chez les animaux contribue à la sélection de résistances bactériennes au niveau du tube digestif, potentiellement transmissibles à l'homme. La caractérisation phénotypique et génotypique de l'émergence d'entérobactéries digestives résistantes, lors de pression de sélection par une bêta-lactamine, a été réalisée chez le porc. Des souches d'E. Coli majoritairement multirésistantes ont été sélectionnées et l'analyse des pulsotypes des ces souches suggère une sélection de clones déjà présents mais minoritaires dans le tube digestif. Une stratégie thérapeutique visant à prévenir l'émergence de bactéries digestives résistantes lors d'administration orale de bêta-lactamines chez le porc a été proposée. Elle consiste en l'association d'un ester de bêta-lactamine avec des billes à vectorisation iléocolique contenant des bêta-lactamases. Les caractéristiques d'absorption de l'ester et de libération par l'enrobage sélectionné encouragent à poursuivre l'exploration de cette stratégie
Antibiotic administration in animals is involved in the selection of antibiotic resistant bacteria in the digestive tract, potentially transferable to humans. Phenotypic and genotypic characterization of the emergence of resistant digestive enterobacteria, under selective pressure by a beta-lactam antibiotic, was performed in pig. Multiresistant E. Coli isolates were mainly selected and the analysis of the relatedness of these isolate suggested the selection of clones, which were already present at low level in the digestive tract before any treatment. A therapeutic strategy aiming at preventing the emergence of digestive resistant bacteria, during beta-lactam antibiotic administration by the oral route in pigs, was proposed. It consists of the association of an ester of beta-lactam antibiotic with coated beads which release beta-lactamase at the ileocaecal junction. The characteristics of the absorption of the ester and the characteristics of the delivery of the selected coating encourage us to follow the exploration of this strategy

L’épithélium digestif est recouvert par une épaisse couche de mucus majoritairement composé de mucines qui joue un rôle essentiel dans le maintien de l’homéostasie avec la microflore résidente et dans la protection de l’épithélium digestif contre la colonisation par des organismes pathogènes. Au cours de ma thèse, je me suis intéressée à l’étude des interactions hôtes / bactéries dans le tractus gastro-intestinal. En utilisant différents modèles in vivo ou in vitro, nous avons plus particulièrement étudié l’influence de bactéries commensales et pathogènes sur la glycosylation des mucines du tractus digestif. Nous avons tout d’abord caractérisé le profil de glycosylation des mucines gastriques humaines d’individus sains, de patients asymptomatiques infectés par Helicobacter pylori et de patients atteints de métaplasie intestinale incomplète. Afin de mieux décrypter le dialogue qui s’établit entre les mucines et les bactéries, nous avons également caractérisé les modifications de glycosylation des mucines intestinales à partir de modèles animaux et cellulaires d’infections bactériennes. Nous avons étudié l’effet de deux bactéries commensales : Bacteroides thetaiotaomicron et Faecalibacterium prausnitzii et d’une bactérie pathogène : Shigella flexneri. Les mucines apparaissent comme un élément incontournable dans l’interaction hôte/bactéries. Nos travaux indiquent que la barrière mucosale, même si elle exerce un rôle de défense indéniable pour l’épithélium digestif, n’est pas infaillible vis-à-vis des pathogènes. Ils soulignent l’importance du dialogue tripartite entre les mucines, le microbiote et le système immunitaire dans la lutte contre les infections
The gut epithelium is covered by a thick layer of mucus mainly composed of mucins which plays an essential role in maintaining homeostasis with the resident microflora but it also protects the digestive epithelium against colonization by pathogens. During my PhD work, I focused my interest in the study of host / bacteria interactions in the gastrointestinal tract. Using different in vivo or in vitro models, we specifically investigated the influence of commensal and pathogenic bacteria on the glycosylation of mucins of the digestive tract. We first characterized the glycosylation profile of human gastric mucins from healthy, from asymptomatic patients infected with Helicobacter pylori and from patients with incomplete intestinal metaplasia. To better understand the cross-talk between mucins and bacteria, we also studied changes in the glycosylation of intestinal mucins from animal and cellular models of bacterial infections. We analyzed the effect of two commensal bacteria: Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii, and one pathogenic bacteria: Shigella flexneri. Mucins appear as a key element in the host / bacteria interactions. Our work indicates that the mucosal barrier, even though it plays a major role in the defense of gastrointestinal epithelium, is not infallible regarding pathogens. Our work emphasizes the importance of the tripartite dialogue between mucins, the microbiota and the immune system in the fight against infections