Generalized procrustes analysis (GPA) as a tool to discriminate among sheep breeds

Forty male lambs of five Southern Spanish breeds were used to study the effects of the breed in their sensorial characteristics. The used breeds were: Segureña, Spanish Merino, Grazalema Merino, Churra Lebrijana and Montesina breeds. Milk lambs were slaughtered at 12 kg of live weight. A descriptive sensory evaluation was developed using the longissimus lumborum from each animal by a panel of 12 experts and a Generalized Procrustes Analysis (GPA) was used to discriminate among them. Generalized Procrustes Analysis clearly differentiated Churra Lebrijana of out the rest breeds. Churra Lebrijana was defined as more tender, juicier and with less lamb odour than the rest of the Southern Spanish lamb breeds. Thus, GPA is able to discriminate among breed

Red wine polyphenols modulate fecal microbiota and reduce markers of the metabolic syndrome in obese patients.

This study evaluated the possible prebiotic effect of a moderate intake of red wine polyphenols on the modulation of the gut microbiota composition and the improvement in the risk factors for the metabolic syndrome in obese patients. Ten metabolic syndrome patients and ten healthy subjects were included in a randomized, crossover, controlled intervention study. After a washout period, the subjects consumed red wine and de-alcoholized red wine over a 30 day period for each. The dominant bacterial composition did not differ significantly between the study groups after the two red wine intake periods. In the metabolic syndrome patients, red wine polyphenols significantly increased the number of fecal bifidobacteria and Lactobacillus (intestinal barrier protectors) and butyrate-producing bacteria (Faecalibacterium prausnitzii and Roseburia) at the expense of less desirable groups of bacteria such as LPS producers (Escherichia coli and Enterobacter cloacae). The changes in gut microbiota in these patients could be responsible for the improvement in the metabolic syndrome markers. Modulation of the gut microbiota by using red wine could be an effective strategy for managing metabolic diseases associated with obesity

Host-Feeding Pattern of Culex theileri (Diptera: Culicidae), Potential Vector of Dirofilaria immitis in the Canary Islands, Spain

To identify the host range of potential vectors of Dirofilaria immitis Leidy, the causal agent of canine diroÞlariasis, we studied the bloodmeal origin of mosquitoes trapped on two of the Canary Islands, Gran Canaria and Tenerife, where this disease is considered hyperendemic. On Gran Canaria, mosquitoes were captured using Centers for Disease Control and Prevention (CDC) traps (outdoors) and resting in a bathroom (indoors). Only CDC traps were used to capture mosquitoes in Tenerife. The species captured in decreasing order of abundance were Culex theileri Theobald, Culex pipiens L., Culiseta longiareolata Macquart, Anopheles atroparvus van Thiel, and Anopheles cinereus Theobald. The origins of bloodmeals were identiÞed for 121 Cx. theileri and 4 Cx. pipiens after ampliÞcation and sequencing of a fragment of the vertebrate cytochrome oxidase I (COI) gene. Cx. theileri fed on goats, sheep, dogs, cattle, cats, humans, and chickens, and Cx. pipiens fed on goats and chickens. A lower success of bloodmeal identiÞcation was obtained in mosquitoes captured resting indoors than outdoors in CDC traps, probably because of a longer time period between feeding and capture. Although most Cx. theileri fed on ruminants, this species also fed on different mammal species susceptible to diroÞliarasis, including humans, suggesting it could play a role on parasite transmissionPeer reviewe

Effect of Moderate Consumption of Different Phenolic-Content Beers on the Human Gut Microbiota Composition: A Randomized Crossover Trial

The moderate consumption of beer has been associated with positive effects on health, and these benefits are driven, in part, by the antioxidant properties of phenolic compounds found in this beverage. However, the potential impact of beer polyphenols on the human gut microbiome and their consequences are yet to be elucidated. In this study, our aim was to evaluate the effect of three different phenolic-content beers on the gut microbiome and the potential role of the induced shifts in the antioxidant capacity of beer polyphenols. In total, 20 subjects (10 healthy volunteers and 10 individuals with metabolic syndrome) were randomly assigned in a crossover design to consume each of the different beers (alcohol-free, lager or dark beer) during a 2-week intervention. Significant changes in the relative abundance of Streptococcaceae and Streptococcus were found after beer consumption. An increased abundance of Streptococcaceae and Streptococcus was observed after the consumption of dark beer, with no detected differences between baseline and alcohol-free/lager beer intervention. Moreover, some of the detected differences appeared to be related to the metabolic status. Finally, a decrease in porphyrin metabolism and heme biosynthesis was found after the intervention, especially after the consumption of dark beer. These results show that the antioxidant capacity of beer polyphenols may induce positive shifts in gut microbiota composition, and some of the observed changes may also boost the antioxidant capacity of these compoundsM.Q.-M. was supported by a Manuel de Oya Research fellowship from Foro para la Investigación de la Cerveza y Estilos de Vida (FICYE). I.M.-I. and C.G.-R. were supported by the Miguel Servet Type I program and P.R.-L. by the Sara Borrell program both of the Carlos III Health Institute (co-founded by the European Regional Development Fund-ERDF-) (CP16/00163, CP20/00066 and CD19/00216, respectively). In addition, this study was supported by the “Network of Centers for Biomedical Research” (CIBER) of the Carlos III Health Institute (ISCIII) (CB06/03/0018), research grants from the ISCIII (PI18/01160, PI21/01677) and co-financed by the Regional Development Fund (ERDF). Partial funding for open access charge: Universidad de Málag

A Humanized Diet Profile May Facilitate Colonization and Immune Stimulation in Human Microbiota-Colonized Mice

Background: In spite of the importance of the use of gnotobiotic mice for human fecal transfer, colonization efficiency and immune stimulation after human microbiota inoculation in mice are poorly studied compared to mouse microbiota inoculation. We tested the colonization efficiency and immune responses in mice bred for one additional generation after inoculating the parent generation with either a human (HM) or a mouse microbiota (MM). Furthermore, we tested if colonization efficiency and immune stimulation could be improved in HM-colonized mice by dietary approaches: if these were fed a diet closer to the human diet either in its sources of animal fat and protein [the “animal source” (AS) diet] or in its proportions of macronutrients from the normal sources of a mouse diet [the “human profile” (HP) diet]. Results: Although significantly lower in mice with a human microbiota (30–40% vs. 61– 70%) the colonization efficiency was significantly higher in HM mice fed the HP diet (40%), and in MM mice fed AS (70%). The microbiota of mice fed HP was comparable to the microbiota of mice fed a standard rodent chow, while the microbiota of mice fed the animal source diet (AS) clustered separately. Mice inoculated with mouse fecal matter had significantly more CD4+ T cells and Cd4 expression and significantly fewer regulatory T cells (Tregs) and FoxP3 expression than human microbiota inoculated mice, but cell proportions differences were mostly apparent between mice fed the AS diet. Mice fed the HP diet had significantly higher expression of Cd8a. Conclusion: It is concluded that a diet with a humanized profile could support the establishment of a human microbiota in mice, which will, however, still elicit a lower colonization efficiency compared to mice inoculated with a mouse microbiota.The work was funded by the Innovation Fund Denmark (Grant No. 1355-00004B) and Taconic Biosciences. IM-I was funded during the experimental work by a fellowship associated to her Sara Borrell postdoctoral contract (CD12/00530), and nowadays is supported by a Miguel Servet contract (CP16/00163) both from Instituto de Salud Carlos III co-founded by Fondo Europeo de Desarrollo Regional – FEDER.Ye

Role of Gut Microbiota on Cardio-Metabolic Parameters and Immunity in Coronary Artery Disease Patients with and without Type-2 Diabetes Mellitus

Gut microbiota composition has been reported as a factor linking host metabolism with the development of cardiovascular diseases (CVD) and intestinal immunity. Such gut microbiota has been shown to aggravate CVD by contributing to the production of trimethylamine N-oxide (TMAO), which is a pro-atherogenic compound. Treg cells expressing the transcription factor Forkhead box protein P3 (FoxP3) play an essential role in the regulation of immune responses to commensal microbiota and have an atheroprotective role. However, the aim of this study was to analyze the role of gut microbiota on cardio-metabolic parameters and immunity in coronary artery disease (CAD) patients with and without type-2 diabetes mellitus (DM2). The study included 16 coronary CAD-DM2 patients, and 16 age, sex, and BMI matched CAD patients without DM2 (CAD-NDM2). Fecal bacterial DNA was extracted and analyzed by sequencing in a GS Junior 454 platform followed by a bioinformatic analysis (QIIME and PICRUSt). The present study indicated that the diversity and composition of gut microbiota were different between the CAD-DM2 and CAD-NDM2 patients. The abundance of phylum Bacteroidetes was lower, whereas the phyla Firmicutes and Proteobacteria were higher in CAD-DM2 patients than those in the CAD-NDM2 group. CAD-DM2 patients had significantly less beneficial or commensal bacteria (such as Faecalibacterium prausnitzii and Bacteroides fragilis) and more opportunistic pathogens (such as Enterobacteriaceae, Streptococcus, and Desulfovibrio). Additionally, CAD-DM2 patients had significantly higher levels of plasma zonulin, TMAO, and IL-1B and significantly lower levels of IL-10 and FOXP3 mRNA expression than CAD-NDM2. Moreover, in the CAD-MD2 group, the increase in Enterobacteriaceae and the decrease in Faecalibacterium prausnitzii were significantly associated with the increase in serum TMAO levels, while the decrease in the abundance of Bacteroides fragilis was associated with the reduction in the FOXP3 mRNA expression, implicated in the development and function of Treg cells. These results suggest that the presence of DM2 is related to an impaired regulation of the immune system in CAD patients, mediated in part by the gut microbiota composition and functionality and the production and effects of their gut microbiota derived molecules

Expansion of Rare and Harmful Lineages is Associated with Established Rheumatoid Arthritis

Objectives: To characterize the gut microbiota profile in rheumatoid arthritis (RA) patients and investigate its association with certain characteristics of RA. Patients and methods: A nested case–control cohort of 40 patients with RA and 40 sex-age matched controls was studied. Subjects with diabetes, with any other inflammatory disease, practicing extreme diets, taking antibiotics, probiotics or under any new treatment for at least three months prior to sampling were excluded. The microbiota composition was determined by 16S rRNA pyrosequencing and bioinformatics analysis by Quantitative Insights Into Microbial Ecology (QIIME). Other variables included clinical-laboratory variables and average Disease Activity Score 28 points during the follow-up period. Multiple linear regression models were constructed to investigate the possible risk factors for the microbiota. Results: β-diversity data showed that patients tend to differ from healthy subjects according to their microbiota (p = 0.07). The analysis showed an increase in Collinsella aerofaciens, Sedimentibacter and Enterococcus genera in patients compared to controls, as well as a decrease in Dorea formicigenerans. Likewise, an increase in the activity of arginine deiminase was observed, which was found in approximately 90% of the RA genes of the genus Collinsela. The sequence number of Collinsella aerofaciens was independently associated with age (B (95%CI), −0.347 (−21.6, −2.1)), high ACPA (0.323 (27.4–390.0)) and smoking (0.300 (8.8–256.4)) in RA patients. In addition, we observed decreases in Sarcina, 02d06 and Porphyromonas bacterial lineages. Conclusion: Patients with RA present dysbiosis, resulting from an abundance of certain bacterial lineages and a decrease in others. These alterations could influence the maintenance of autoimmunity to this disease.This work was supported by FIS Grant PI18/00824 (Instituto Carlos III, Fondos FEDER) and “Fundación Andaluza de Reumatología” Grant PI17/00016. Grant for medical researchers of the “Fundación Española de Reumatología”. The research groups belong to the “Centros de Investigación en Red” [CIBERobn, “Instituto de Salud Carlos III”], and thanks for its support to the CIBER-Metagenomics platform, especially to Isaac Plaza and Pablo Rodríguez. P-RL was supported by the “Sara Borrell” program (CD19/00216) from Instituto de Salud Carlos III. IM-I was supported by the “MS type I” program (CP16/00163) from the Instituto de Salud Carlos III cofounded by Fondo Europeo de Desarrollo Regional–FEDER.Ye

Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment

The number of microbiome-related studies has notably increased the availability of data on human microbiome composition and function. These studies provide the essential material to deeply explore host-microbiome associations and their relation to the development and progression of various complex diseases. Improved data-analytical tools are needed to exploit all information from these biological datasets, taking into account the peculiarities of microbiome data, i.e., compositional, heterogeneous and sparse nature of these datasets. The possibility of predicting host-phenotypes based on taxonomy-informed feature selection to establish an association between microbiome and predict disease states is beneficial for personalized medicine. In this regard, machine learning (ML) provides new insights into the development of models that can be used to predict outputs, such as classification and prediction in microbiology, infer host phenotypes to predict diseases and use microbial communities to stratify patients by their characterization of state-specific microbial signatures. Here we review the state-of-the-art ML methods and respective software applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on the application of ML in microbiome studies related to association and clinical use for diagnostics, prognostics, and therapeutics. Although the data presented here is more related to the bacterial community, many algorithms could be applied in general, regardless of the feature type. This literature and software review covering this broad topic is aligned with the scoping review methodology. The manual identification of data sources has been complemented with: (1) automated publication search through digital libraries of the three major publishers using natural language processing (NLP) Toolkit, and (2) an automated identification of relevant software repositories on GitHub and ranking of the related research papers relying on learning to rank approach