Systematic review: The gut microbiome and its potential clinical application in inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic relapsing-remitting systemic disease of the gastrointestinal tract. It is well established that the gut microbiome has a profound impact on IBD pathogenesis. Our aim was to systematically review the literature on the IBD gut microbiome and its usefulness to provide microbiome-based biomarkers. A systematic search of the online bibliographic database PubMed from inception to August 2020 with screening in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines was conducted. One-hundred and forty-four papers were eligible for inclusion. There was a wide heterogeneity in microbiome analysis methods or experimental design. The IBD intestinal microbiome was generally characterized by reduced species richness and diversity, and lower temporal stability, while changes in the gut microbiome seemed to play a pivotal role in determining the onset of IBD. Multiple studies have identified certain microbial taxa that are enriched or depleted in IBD, including bacteria, fungi, viruses, and archaea. The two main features in this sense are the decrease in beneficial bacteria and the increase in pathogenic bacteria. Significant differences were also present between remission and relapse IBD status. Shifts in gut microbial community composition and abundance have proven to be valuable as diagnostic biomarkers. The gut microbiome plays a major role in IBD, yet studies need to go from casualty to causality. Longitudinal designs including newly diagnosed treatment-naïve patients are needed to provide insights into the role of microbes in the onset of intestinal inflammation. A better understanding of the human gut microbiome could provide innovative targets for diagnosis, prognosis, treatment and even cure of this relevant disease.This work is supported by Sara Borrell contract CD19/00247 from the Instituto de Salud Carlos III (ISCIII) to L.A.-G

Assessment of intraspecies variability in fungal growth initiation of Aspergillus flavus and aflatoxin B1 production under static and changing temperature levels using different initial conidial inoculum levels

Intraspecies variability in fungal growth and mycotoxin production has important implications for food safety. Using the Bioscreen C we have examined spectrophotometrically intraspecies variability of A. flavus using 10 isolates under different environments, including temperature shifts, in terms of growth and aflatoxin B1 (AFB1) production. Five high and five low AFB1 producers were examined. The study was conducted at 5 isothermal conditions (from 15 to 37 °C) and 4 dynamic scenarios (between 15 and 30 °C). The experiments were carried out in a semisolid YES medium at 0.92 aw and two inoculum levels, 102 and 103 spores/mL. The Time to Detection (TTD) of growth initiation was determined and modelled as a function of temperature through a polynomial equation and the model was used to predict TTD under temperature upshifts conditions using a novel approach. The results obtained in this study have shown that a model can be developed to describe the effect of temperature upshifts on the TTD for all the studied isolates and inoculum levels. Isolate variability increased as the growth conditions became more stressful and with a lower inoculum level. Inoculum level affected the intraspecies variability but not the repeatability of the experiments. In dynamic conditions, isolate responses depended both on the temperature shift and, predominantly, the final temperature level. AFB1 production was highly variable among the isolates and greatly depended on temperature (optimum temperature at 30–35 °C) and inoculum levels, with often higher production with lower inoculum. This suggests that, from an ecological point of view, the potential isolate variability and interaction with dynamic conditions should be taken into account in developing strategies to control growth and predicting mycotoxin risks by mycotoxigenic fungi

The interplay between immune system and microbiota in inflammatory bowel disease: A narrative review

The importance of the gut microbiota in human health is currently well established. It contributes to many vital functions such as development of the host immune system, digestion and metabolism, barrier against pathogens or brain–gut communication. Microbial colonization occurs during infancy in parallel with maturation of the host immune system; therefore, an adequate cross‐talk between these processes is essential to generating tolerance to gut microbiota early in life, which is crucial to prevent allergic and immune‐mediated diseases. Inflammatory bowel disease (IBD) is characterized by an exacerbated immune reaction against intestinal microbiota. Changes in abundance in the gut of certain microorganisms such as bacteria, fungi, viruses, and archaea have been associated with IBD. Microbes that are commonly found in high abundance in healthy gut microbiomes, such as F. prausnitzii or R. hominis, are reduced in IBD patients. E. coli, which is usually present in a healthy gut in very low concentrations, is increased in the gut of IBD patients. Microbial taxa influence the immune system, hence affecting the inflammatory status of the host. This review examines the IBD microbiome profile and presents IBD as a model of dysbiosis.This study was supported by Instituto de Salud Carlos III (ISCIII), Spain (grant numbers PI16/01296 and PI19/01034), by Sara Borrell contract CD19/00247 to L.A.-G. and by CIBEReh

Modelling the Probability of Growth and Aflatoxin B1 Production of Aspergillus Flavus under Changing Temperature Conditions in Pistachio Nuts

Proceedings of the 9th International Conference on Predictive Modelling in FoodThe aim of this work was to use probability models for the prediction of growth and aflatoxin production by Aspergillus flavus as a strategy to mitigate the aflatoxin presence in pistachio nuts during postharvest. Logistic models, with temperature and time as explanatory variables, were fitted to the probability of growth and aflatoxin B1 (AFB1) production under constant temperature levels, afterwards they were used to predict probabilities under non-isothermal scenarios. The models obtained showed levels of concordance from 80 to 100% in most of the cases. Moreover, the presence of AFB1 in pistachio nuts could be correctly predicted through AFB1 models developed in agar medium or through growth models in pistachio nuts. These findings can support decision making, at transport and storage level, and could be used by producers and processors to predict the time for AFB1 production by A. flavus in pistachio nuts in postharvest

Antiviral activities of Boletus edulis, Pleurotus ostreatus and Lentinus edodes extracts and polysaccharide fractions against Herpes simplex virus type 1

Deposited with permissionAntiviral properties of water and methanol extracts from Lentinus edodes, Boletus edulis and Pleurotus ostreatus were evaluated against herpes simplex virus type 1 (HSV-1). Pre-treatment of Vero cells with 75 mg·ml-1 water extracts before virus addition, inhibited 60% of the virus infection and its addition during the virus adsorption period inhibited it up to 80%. Moreover, the mushrooms water extracts were able to significantly inhibit the in vitro virus replication, showing the concentration of a substance required to reduce plaque number in Vero cells by 50% (IC50) values from 26.69 mg·ml-1 to 35.12 mg·ml-1. Methanol extracts exhibited a lower antiviral activity in all cases. In order to identify the type of compounds responsible for the antiviral activity, the low molecular weight (LMW) and high molecular weight (HMW) fractions were evaluated. The activity was found to correlate with the β-glucans present in the polysaccharide fractions, which showed higher antiviral activity than the complete water extracts except for B. edulis where other compounds (probably chitin-binding lectins) might have contributed to the observed activity.This work was also supported by the ALIBIRD-CM S2009/AGR-1469 regional program from the Comunidad de Madrid (Spain

Pressurized water extraction of β-glucan enriched fractions with bile acids-binding capacities obtained from edible mushrooms

This is the peer reviewed version of the following article: Biotechnology Progress 30.2 (2014): 391-400, which has been published in final form at http://dx.doi.org/10.1002/btpr.1865.  This article may be used for non-commercial purposes in accordance With Wiley Terms and Conditions for self-archivingA pressurized water extraction (PWE) method was developed in order to extract β-glucans with bile acids-binding capacities from cultivated mushrooms (Agaricus bisporus, Lentinula edodes and Pleurotus ostreatus) to be used as supplements to design novel foods with hypocholesterolemic properties. Extraction yields were higher in individual than sequential extractions being the optimal extraction parameters: 200ºC, 5 cycles of 5 min each at 10.3 MPa. The crude polysaccharide (PSC) fractions, isolated from the PWE extracts contained mainly β-glucans (including chitooligosaccharides deriving from chitin hydrolysis), -glucans and other PSCs (hetero-/proteo-glucans) depending on the extraction temperature and mushroom strain considered. The observed bile acids-binding capacities of some extracts were similar to a β-glucan enriched fraction obtained from cereals.The research was supported by the European Union within the 7th framework programme (7FM-PEOPLE-2009-IIF project 251285), ALIBIRD-CM S2009/AGR-1469 regional program from the Community of Madrid (Spain) and AGL2010-21537 national R+D program from the Spanish Ministry of Science and Innovation. CTICH is also acknowledged for the cultivation and supplying of the mushrooms fruiting bodie