Patterns and determinants of the global herbivorous mycobiome.

Despite their role in host nutrition, the anaerobic gut fungal (AGF) component of the herbivorous gut microbiome remains poorly characterized. Here, to examine global patterns and determinants of AGF diversity, we generate and analyze an amplicon dataset from 661 fecal samples from 34 mammalian species, 9 families, and 6 continents. We identify 56 novel genera, greatly expanding AGF diversity beyond current estimates (31 genera and candidate genera). Community structure analysis indicates that host phylogenetic affiliation, not domestication status and biogeography, shapes the community rather than. Fungal-host associations are stronger and more specific in hindgut fermenters than in foregut fermenters. Transcriptomics-enabled phylogenomic and molecular clock analyses of 52 strains from 14 genera indicate that most genera with preferences for hindgut hosts evolved earlier (44-58 Mya) than those with preferences for foregut hosts (22-32 Mya). Our results greatly expand the documented scope of AGF diversity and provide an ecologically and evolutionary-grounded model to explain the observed patterns of AGF diversity in extant animal hosts.

The Effect of a High-Grain Diet on the Rumen Microbiome of Goats with a Special Focus on Anaerobic Fungi.

This work investigated the changes of the rumen microbiome of goats switched from a forage to a concentrate diet with special attention to anaerobic fungi (AF). Female goats were fed an alfalfa hay (AH) diet (0% grain; n = 4) for 20 days and were then abruptly shifted to a high-grain (HG) diet (40% corn grain, 60% AH; n = 4) and treated for another 10 days. Rumen content samples were collected from the cannulated animals at the end of each diet period (day 20 and 30). The microbiome structure was studied using high-throughput sequencing for bacteria, archaea (16S rRNA gene) and fungi (ITS2), accompanied by qPCR for each group. To further elucidate unclassified AF, clone library analyses were performed on the ITS1 spacer region. Rumen pH was significantly lower in HG diet fed goats, but did not induce subacute ruminal acidosis. HG diet altered prokaryotic communities, with a significant increase of Bacteroidetes and a decrease of Firmicutes. On the genus level Prevotella 1 was significantly boosted. Methanobrevibacter and Methanosphaera were the most abundant archaea regardless of the diet and HG induced a significant augmentation of unclassified Thermoplasmatales. For anaerobic fungi, HG triggered a considerable rise in Feramyces observed with both ITS markers, while a decline of Tahromyces was detected by ITS2 and decrease of Joblinomyces by ITS1 only. The uncultured BlackRhino group revealed by ITS1 and further elucidated in one sample by LSU analysis, formed a considerable part of the AF community of goats fed both diets. Results strongly indicate that the rumen ecosystem still acts as a source for novel microorganisms and unexplored microbial interactions and that initial rumen microbiota of the host animal considerably influences the reaction pattern upon diet change.

Pseudobutyrivibrio xylanivorans adhesion to epithelial cells.

The ruminal bacteria Pseudobutyrivibrio xylanivorans strain 2 (P. xylanivorans 2), that mediates the digestion of plant fiber, is considered an attractive candidate for probiotics. Adherence to the epithelium of the digestive tract of the host is one of the major requirements for probiotics. In this study, we assessed the adhesion of P. xylanivorans 2 to SW480 cells and characterized this process utilizing multiple microscopy approaches. Our results indicate that a multiplicity of infection of 200 CFU/cell allows the highest bacteria to cell binding ratio, with a lower percentage of auto-agglutination events. The comparison of the adherence capacity subjected heat-shock treatment (100 °C, 1 min), which produces the denaturalization of proteins at the bacterial surface, as opposed untreated P. xylanivorans, suggested that this bacteria may attach to SW480 cells utilizing a proteinaceous structure. Confocal microscopy analyses indicate that P. xylanivorans 2 attachment induces the formation of F-actin-enriched areas on the surface of SW480 cells. Transmission electron microscopy (TEM) revealed the formation of a structure similar to a pedestal in the area of the epithelial cell surface, where the bacterium rests. Finally, a casual finding of TEM analysis of transverse and longitudinal thin-sections of P. xylanivorans 2, revealed irregular intra-cytoplasmic structures compatibles with the so-called bacterial microcompartments. This is the first ultrastructural description of bacterial microcompartments-like structures in the genus Pseudobutyrivibrio.

Analysis of the rumen bacterial diversity of goats during shift from forage to concentrate diet.

High-grain feeding used in the animal production is known to affect the host rumen bacterial community, but our understanding of consequent changes in goats is limited. This study was therefore aimed to evaluate bacterial population dynamics during 20 days adaptation of 4 ruminally cannulated goats to the high-grain diet (grain: hay - ratio of 40:60). The dietary transition of goats from the forage to the high-grain-diet resulted in the significant decrease of rumen fluid pH, which was however still higher than value established for acute or subacute ruminal acidosis was not diagnosed in studied animals. DGGE analysis demonstrated distinct ruminal microbial populations in hay-fed and grain-fed animals, but the substantial animal-to-animal variation were detected. Quantitative PCR showed for grain-fed animals significantly higher number of bacteria belonging to Clostridium leptum group at 10 days after the incorporation of corn into the diet and significantly lower concentration of bacteria belonging to Actinobacteria phylum at the day 20 after dietary change. Taxonomic distribution analysed by NGS at day 20 revealed the similar prevalence of the phyla Firmicutes and Bacteroidetes in all goats, significantly higher presence of the unclassified genus of groups of Bacteroidales and Ruminococcaceae in grain-fed animals and significantly higher presence the genus Prevotella and Butyrivibrio in the forage-fed animals. The three different culture-independent methods used in this study show that high proportion of concentrate in goat diet does not induce any serious disturbance of their rumen ecosystem and indicate the good adaptive response of caprine ruminal bacteria to incorporation of corn into the diet.

Identification of GH10 xylanases in strains 2 and Mz5 of Pseudobutyrivibrio xylanivorans.

Genes encoding glycosyl hydrolase family 11 (GH11) xylanases and xylanases have been identified from Pseudobutyrivibrio xylanivorans. In contrast, little is known about the diversity and distribution of the GH10 xylanase in strains of P. xylanivorans. Xylanase and associated activities of P. xylanivorans have been characterized in detail in the type strain, Mz5. The aim of the present study was to identify GH10 xylanase genes in strains 2 and Mz5 of P. xylanivorans. In addition, we evaluated degradation and utilization of xylan by P. xylanivorans 2 isolated from rumen of Creole goats. After a 12-h culture, P. xylanivorans 2 was able to utilize up to 53% of the total pentose content present in birchwood xylan (BWX) and to utilize up to 62% of a ethanol-acetic acid-soluble fraction prepared from BWX. This is the first report describing the presence of GH10 xylanase-encoding genes in P. xylanivorans. Strain 2 and Mz5 contained xylanases which were related to GH10 xylanase of Butyrivibrio sp. Identifying xylanase-encoding genes and activity of these enzymes are a step toward understanding possible functional role of P. xylanivorans in the rumen ecosystem and contribute to providing an improved choice of enzymes for improving fiber digestion in ruminant animals, agricultural biomass utilization for biofuel production, and other industries.

Frecuencia de dermatofitos en una muestra de felinos del área urbana del Gran Mendoza, Argentina / Frequency of dermatophytes in a sample of cats in the urban area of Gran Mendoza, Argentina

Antecedentes. El gato, considerado el principal reservorio de Microsporum canis, cumple un rol importante en la aparición de las dermatomicosis cuando es habitante de zonas urbanas. Objetivos. Conocer y analizar la frecuencia de aislamiento de dermatofitos zoonóticos en una muestra de felinos del área urbana del Gran Mendoza. Métodos. Se seleccionaron animales de compañía y menores de un año que estuvieran transitoriamente en refugios y criaderos de zonas urbanas del Gran Mendoza. Se analizaron 45 muestras de gatos con y sin lesiones dermatológicas, recogidas mediante raspados de piel y depilación, o cepillado de Mackenzie, respectivamente. Las muestras se procesaron con KOH y glicerol tras exposición al calor. El cultivo se realizó durante 30 días en agar inclinado de Sabouraud glucosado y Lactrimel con cloranfenicol y cicloheximida. Resultados. La frecuencia de aislamiento de dermatofitos en este estudio preliminar fue de 13,3%. No se encontraron diferencias estadísticamente significativas en la procedencia, edad, sexo, raza ni estado dermatológico. Se hallaron dermatofitos zoonóticos en 2 animales de compañía de 21 que tenían contacto directo con niños o ancianos. M. canis tuvo una frecuencia de aislamiento de 83,3%. Conclusiones. La frecuencia de aislamiento de dermatofitos zoonóticos en la muestra de felinos del área urbana del Gran Mendoza fue del 13,3%, mayor a la esperada. M. canis fue el dermatofito más frecuentemente aislado(AU)

Background. The cat, considered the main reservoir of Microsporum canis, lives in urban areas, and also plays an important role in the emergence of dermatomycoses. Aims. To determine and analyse the frequency of zoonotic dermatophytes in a sample of cats in an urban area of the Gran Mendoza region. Methods. The animals selected were household cats and cats less than one year old that came from shelters and kennels from urban areas in the Gran Mendoza region. A total of 45 samples from cats with and without dermatological lesions were analysed. These samples were collected through skin scraping, hair removal and Mackenzie brush, respectively. Direct observation was made with KOH and glycerol after heat exposure. Samples were cultured on Sabouraud and Lactrimel agar slants with chloramphenicol and cycloheximide for 30 days. Results. The frequency of dermatophytes isolated in this preliminary study was 13.3%. There were not statistically significant differences by source, age, sex, race or dermatological condition. Zoonotic dermatophytes were found in 2 household cats out of the 21 that had direct contact with children or the elderly. M. canis was isolated in 83.3% cases. Conclusions. The frequency of isolation of zoonotic dermatophytes in the sample of cats in an urban area of the Gran Mendoza region was 13.3%, a value higher than expected. M. canis was the most isolated species(AU)

[Frequency of dermatophytes in a sample of cats in the urban area of Gran Mendoza, Argentina]. / Frecuencia de dermatofitos en una muestra de felinos del área urbana del Gran Mendoza, Argentina.

BACKGROUND: The cat, considered the main reservoir of Microsporum canis, lives in urban areas, and also plays an important role in the emergence of dermatomycoses. AIMS: To determine and analyse the frequency of zoonotic dermatophytes in a sample of cats in an urban area of the Gran Mendoza region. METHODS: The animals selected were household cats and cats less than one year old that came from shelters and kennels from urban areas in the Gran Mendoza region. A total of 45 samples from cats with and without dermatological lesions were analysed. These samples were collected through skin scraping, hair removal and Mackenzie brush, respectively. Direct observation was made with KOH and glycerol after heat exposure. Samples were cultured on Sabouraud and Lactrimel agar slants with chloramphenicol and cycloheximide for 30 days. RESULTS: The frequency of dermatophytes isolated in this preliminary study was 13.3%. There were not statistically significant differences by source, age, sex, race or dermatological condition. Zoonotic dermatophytes were found in 2 household cats out of the 21 that had direct contact with children or the elderly. M. canis was isolated in 83.3% cases. CONCLUSIONS: The frequency of isolation of zoonotic dermatophytes in the sample of cats in an urban area of the Gran Mendoza region was 13.3%, a value higher than expected. M. canis was the most isolated species.

Brucella alters endocytic pathway in J774 macrophages.

Brucella is a facultative intracellular bacterium which causes chronic infections in mammals by surviving and replicating within host cells. The putative role of the endoplasmic reticulum (ER) in the formation of the phagosome in non-professional phagocytes is supported by several research groups, but still leaves open the question of the fate of Brucella inside professional phagocytes and its resistance mechanisms therein. Macrophages are particularly important for the survival and spreading of Brucella during infection. The intracellular transport of Brucella in these cells has not been thoroughly characterized. To study the maturation process of Brucella-containing phagosomes in phagocytes, we comparatively monitored the intracellular transport of a virulent strain (2308) with two vaccine strains (S19 and RB51) in J 774 macrophages. Then, we compared the behavior of all three strains studied through transmission electron microscopy. The results indicate that the virulent strain not only occupies two different kinds of compartments but also alters the endocytic pathway of the cell it parasitizes, unlike what has been reported for non-professional phagocytes, like HeLa cell. Besides, differences are observed in the behavior of both Brucella abortus vaccine strains.

Meta-analysis: can Helicobacter pylori eradication treatment reduce the risk for gastric cancer?

BACKGROUND: Helicobacter pylori infection is associated with gastric cancer, but the effect of eradication treatment on gastric cancer risk is not well defined. PURPOSE: To determine whether H. pylori eradication treatment can reduce the risk for gastric cancer. DATA SOURCES: PubMed, EMBASE, Cochrane Library, Google Scholar, and online clinical trial registers through 31 January 2009, without language restrictions. STUDY SELECTION: Randomized trials that compared eradication treatment with no treatment in H. pylori-positive patients and that assessed gastric cancer or progression of preneoplastic lesions during follow-up. DATA EXTRACTION: Two authors independently reviewed articles and extracted data. DATA SYNTHESIS: Seven studies met inclusion criteria, 1 of which was excluded from pooled analysis because of clinical and methodological heterogeneity. All studies were performed in areas with high incidence of gastric cancer, mostly in Asia. Overall, 37 of 3388 (1.1%) treated patients developed gastric cancer compared with 56 of 3307 (1.7%) untreated (control) participants. In a pooled analysis of 6 studies with a total of 6695 participants followed from 4 to 10 years, the relative risk for gastric cancer was 0.65 (95% CI, 0.43 to 0.98). LIMITATIONS: All studies but 1 were performed in Asia. Only 2 assessed gastric cancer incidence, and only 2 were double-blinded. CONCLUSION: Helicobacter pylori eradication treatment seems to reduce gastric cancer risk.

Effects of probiotics for the prevention and treatment of radiation-induced diarrhea.

BACKGROUND AND AIMS: Probiotic supplementation seems to provide beneficial effects in the prevention and treatment of radiation-induced diarrhea. We performed a systematic review and meta-analysis to estimate the efficacy of probiotic supplementation for prevention and treatment of radiation-induced diarrhea. METHODS: Two reviewers independently searched PubMed, EMBASE, Cochrane Library, Google Scholar and on-line clinical trials registers (up to January 2009) for randomized controlled trials that evaluated the efficacy of probiotic supplementation for the prevention and treatment of radiation-induced diarrhea. Each clinical trial was separately evaluated for study characteristics, methodologic quality and outcomes. Results of the randomized controlled trials were pooled in a meta-analysis. RESULTS: Four randomized controlled trials were included. Three clinical trials, with a total of 632 subjects, evaluated the preventive effects of probiotic supplementation and 1 study evaluated the therapeutic role. Random effects meta-analysis of the preventive trials did not show significant differences between probiotic supplementation and control groups (odds ratio 0.47; 95% confidence interval: 0.13-1.67). However, the few available trials and the presence of significant clinical and statistical heterogeneity limited the analysis. Similarly, the therapeutic clinical trial did not show significant differences between active and placebo groups. No major adverse events owing to probiotic supplementation were reported in any study. CONCLUSIONS: Probiotic supplementation showed beneficial effect in the prevention and treatment of radiation-induced diarrhea in experimental animal studies. Encouraging results have been observed in humans; however, the few available clinical studies do not allow firm conclusions. More well-performed, randomized placebo-controlled studies are needed.

Timing of precut procedure does not influence success rate and complications of ERCP procedure: a prospective randomized comparative study.

BACKGROUND: There is scarce information on whether performing the precut procedure early rather than after several cannulation attempts is associated with different success and complication rates. OBJECTIVE: To compare the success and complication rates of precutting implemented either early or after prolonged attempts by the standard approach. DESIGN: Single-center prospective randomized study. SETTING: Tertiary care center. PATIENTS: Over the 2-year study period, 1078 therapeutic ERCP procedures were performed. One hundred forty-six patients (mean age 68.5 years [range: 34-88 years], 67 men and 79 women) met the selection criteria and were randomized into 2 groups (on a 1:3 basis): group A underwent precut immediately after randomization (36 patients) and group B underwent standard cannulation attempts for a further 20 minutes followed by needle-knife precut in case of failure (110 patients). MAIN OUTCOME MEASUREMENTS: Deep biliary cannulation and the incidence of post-ERCP complications. RESULTS: The precut procedure performed in group A allowed deep cannulation of the common bile duct in 33 of 36 patients (92%). In group B, cannulation was successfully achieved in 104 of 110 patients (95%). Among group B patients, biliary cannulation was achieved with the standard approach in 78 patients, whereas precutting was performed in 32 patients, and deep cannulation was achieved in 26 of them. The overall complication rate was 8% (3/36) in group A and 6% (7/110) in group B. LIMITATIONS: Small sample size. CONCLUSIONS: Timing of pre-cutting does not appear to influence success and complication rates of ERCP procedures.

Meta-analysis: duration of first-line proton-pump inhibitor based triple therapy for Helicobacter pylori eradication.

BACKGROUND: Proton-pump inhibitor (PPI)-based triple therapy is the recommended first-line treatment for Helicobacter pylori infection. A consensus on treatment duration is lacking. PURPOSE: To summarize the benefits and harms of different durations of PPI-based triple therapy. DATA SOURCES: PubMed, EMBASE, the Cochrane Library, and proceedings of major meetings through May 2007. STUDY SELECTION: English-language reports of randomized, controlled trials that compared duration (7, 10, or 14 days) of triple therapy and in which adequate testing confirmed the initial H. pylori infection and its eradication. DATA EXTRACTION: Two authors independently extracted data on study design, treatment, number of patients enrolled and number of patients with successful eradication, disease at enrollment, testing, adverse effects, year of publication, publication format, and country. DATA SYNTHESIS: Of 21 included studies, 11 compared 7-day therapy with 10-day therapy, and 13 compared 7-day therapy with 14-day therapy. Meta-analysis yielded relative risks (RRs) for eradication of 1.05 (95% CI, 1.01 to 1.10) for 7-day compared with 10-day amoxicillin-containing triple therapy (10 studies) and 1.07 (CI, 1.02 to 1.12) for 7-day compared with 14-day therapy (11 studies). Meta-analysis of the 3 studies that compared 7-day with 14-day metronidazole-containing therapy yielded an RR of 1.08 (CI, 0.96 to 1.22). The 7-day versus 10-day comparisons yielded RRs of 1.03 (CI, 0.97 to 1.10) for peptic ulcer disease and 1.10 (CI, 1.02 to 1.20) for nonulcer dyspepsia. For the 7-day versus 14-day comparisons, the RRs were 1.04 (CI, 0.99 to 1.09) and 1.03 (CI, 0.88 to 1.20), respectively. The RRs for frequency of adverse events were 0.98 (CI, 0.85 to 1.14) and 1.08 (CI, 0.84 to 1.40) for 7-day therapy compared with 10- and 14-day therapy, respectively. Diarrhea and taste disturbance were the most frequently reported adverse events (5%). LIMITATIONS: Subgroup analyses were limited by the few studies evaluating different drug regimens and disease at enrollment. Seventeen of the included studies had poor methodological quality or inadequate reporting. CONCLUSION: Available data suggest that extending triple therapy beyond 7 days is unlikely to be a clinically useful strategy.