It takes guts to learn: machine learning techniques for disease detection from the gut microbiome

Associations between the human gut microbiome and expression of host illness have been noted in a variety of conditions ranging from gastrointestinal dysfunctions to neurological deficits. Machine learning (ML) methods have generated promising results for disease prediction from gut metagenomic information for diseases including liver cirrhosis and irritable bowel disease, but have lacked efficacy when predicting other illnesses. Here, we review current ML methods designed for disease classification from microbiome data. We highlight the computational challenges these methods have effectively overcome and discuss the biological components that have been overlooked to offer perspectives on future work in this area.

Quantifying mediation between omics layers and complex traits

Background: High-dimensional omics datasets provide valuable resources to determine the causal role of molecular traits in mediating the path from genotype to phenotype. Making use of quantitative trait loci (QTL) and genome-wide association studies (GWASs) summary statistics, we developed a multivariable Mendelian randomization (MVMR) framework to quantify the connectivity between three omics layers (DNA methylome (DNAm), transcriptome and proteome) and their cascading causal impact on complex traits and diseases. Results: Evaluating 50 complex traits, we found that on average 37.8% (95% CI: [36.0%-39.5%]) of DNAm-to-trait effects were mediated through transcripts in the cis-region, while only 15.8% (95% CI: [11.9%-19.6%]) are mediated through proteins in cis. DNAm sites typically regulate multiple transcripts, and while found to predominantly decrease gene expression, this was only the case for 53.4% across ~47,000 significant DNAm-transcript pairs. The average mediation proportion for transcript-to-trait effects through proteins (encoded for by the assessed transcript or located in trans) was estimated to be 5.27% (95%CI: [4.11%-6.43%]). Notable differences in the transcript and protein QTL architectures were detected with only 22% of protein levels being causally driven by their corresponding transcript levels. Several regulatory mechanisms were hypothesized including an example where cg10385390 (chr1:8,022,505) increases the risk of irritable bowel disease by reducing PARK7 transcript and protein expression. Conclusions: The proposed integrative framework identified putative causal chains through omics layers providing a powerful tool to map GWAS signals. Quantification of causal effects between successive layers indicated that molecular mechanisms can be more complex than what the central dogma of biology would suggest.

Faecal Microbiota Composition Varies between Patients with Breast Cancer and Healthy Women: A Comparative Case-Control Study

The intestinal microbiota plays an essential role in many diseases, such as obesity, irritable bowel disease (IBD), and cancer. This study aimed to characterize the faecal microbiota from early-stage breast cancer (BC) patients and healthy controls. Faeces from newly diagnosed breast cancer patients, mainly for an invasive carcinoma of no specific type (HR+ and HER2−), before any therapeutic treatment and healthy controls were collected for metabarcoding analyses. We show that the Shannon index, used as an index of diversity, was statistically lower in the BC group compared to that of controls. This work highlights a reduction of microbial diversity, a relative enrichment in Firmicutes, as well as a depletion in Bacteroidetes in patients diagnosed with early BC compared to those of healthy women. A tendency towards a decreased relative abundance of Odoribacter sp., Butyricimonas sp., and Coprococcus sp. was observed. This preliminary study suggests that breast cancer patients may differ from healthy subjects in their intestinal bacterial composition.

FUNCTIONAL PROPERTIES OF PLATELET IN CHILDREN WITH IRRITABLE BOWEL DISEASE

The aim of the study was to evaluate platelet activation and aggregation in children with irritable bowel disease (IBD), as well as the effect of hyperbaric oxygenation on these processes. Platelet activation and aggregation in artificial shear flow were studied in 120 patients of both sexes aged 6 to 17 years with IBD. In pediatric patients with CD and UC, a significant increase in the activation and aggregation of platelets was revealed under shear flow conditions. The use of hyperbaric oxygen therapy leads to a decrease in the studied processes. It was found that IBD in children is characterized by significant changes in the functional properties of platelets (activation and aggregation processes).

A CONCEPTUAL STUDY ON EFFECT OF NAGARADYA CHURNA IN GRAHANI ROGA

Grahani Roga is one of the leading disorders of Annavaha Srotasa. It is mentioned in classics that root cause of all the diseases is Mandagni, which occurs due to improper following of dietary regimen and daily routine. The main site of Agni is Grahani the part of intestine between Amashaya & Pakwashaya. Therefore disturbance in function of Agni leads the disorder known as Grahani Roga. The symptoms of Grahani Roga are similar to mal-absorption syndrome, coeliac disease, tropical sprue, and irritable bowel disease as described in modern medical science. Grahani Roga is treated by Shamana and Samsodhana Chikitsa. Deepana Pachana drugs are useful to enhance the potency of Agni. Now the need of Ayurvedic medicine arises to fill this lacuna. there are number of preparation described in Ayurveda text and Nagaradya Churna in one among them and it has wonderful propertiese that helps in curing Grahani Roga . Thus Ayurvedic treatment is more effective in managing the patients of Grahani Roga by breaking the pathogenesis due to Deepana-Pachana, Grahi, and Srotoshodhaka properties.

Functional interplay of melatonin in the bile duct and gastrointestinal tract to mitigate disease development: An overview

Prevalence of bile duct and gastrointestinal (GI) tract associated diseases is increasing globally. Commonly, the bile duct epithelial cell (cholangiocytes) malfunction and its uncontrolled proliferation often cause liver fibrosis and tumorigenesis, particularly the cholangiocarcinoma. Specifically, GI tract is constantly under diverse endogenous and exogenous stressors which interrupt GI physiological functions and promote inflammation, tissue damage, ulceration, gastrointestinal bleeding, gastroesophageal reflux disease (GERD), irritable bowel disease (IBD) and gastritis. On the other hand, melatonin exhibits important functions in both cholangiocyte and GI tract. The abundance of melatonin generated in the GI tract and its widely distributed receptors facilitate its protective effects in GI tissues. In the most of the cases, the disease progression in GI tract, particularly in bile duct, is associated with endogenous melatonergic system suppression. Therefore, to increase the endogenous melatonin production appears a suitable strategy to retard the disease development in these tissues. Melatonin administration or, exposure to prolonged darkness not only reverse the detrimental biochemical alterations, but also inhibit cholangiocyte proliferation as well as ulceration in the GI tract. Thus, use of melatonin as a natural therapeutic agent is beneficial and exhibits advantages over other contemporary drugs in prevention and treatment of bile duct and gastrointestinal tract associated diseases.

Non-Celiac Gluten Sensitivity and Irritable Bowel Disease: looking for the culprits

During the last thirty years, a gluten-free diet (GFD) is classified among the most popular fad diets mainly due to the ambiguous notion that gluten avoidance promotes health. Gluten intolerance has been implicated with non-celiac gluten sensitivity (NCGS) and irritable bowel syndrome (IBS), two disorders with overlapping symptoms and increasing trend. Together with gluten, other wheat components, fermentable oligo-, di-, monosaccharides, and polyols (FODMAPs) and amylase trypsin inhibitors (ATIs), are implicated in the pathogenesis of both disorders. Gut microflora alterations in IBS and NCGS have been described, while microbiota manipulations have been shown promising in some IBS cases. This literature review summarizes our current knowledge on the impact of wheat ingredients (gluten, FODMAPs and ATIs) in IBS and NCGS. In both disorders, FODMAPs and ATIs trigger gut dysbiosis suggesting that gluten may be not the culprit and microbiota manipulations can be applied in diagnostic and intervention approaches.

Enhancement of Biological Properties of Blackcurrants by Lactic Acid Fermentation and Incorporation into Yogurt: A Review

Blackcurrants (BC) and yogurt are known to possess several health benefits. The objective of this review was to compile the latest information on the effect of lactic acid fermentation on BC and their incorporation into yogurt, including the impact of this combination on chemical composition, sensory aspects, and health attributes of the blend. Google Scholar, Scopus, and PubMed were used to research the most recent literature on BC juice, the whole BC berry, and yogurt. Health benefits were assessed from human and animal studies within the last 5 years. The results suggest that BC have several health promoting compounds that ameliorate some neurological disorders and improve exercise recovery. Yogurt contains compounds that can be used to manage diseases such as type 2 diabetes (T2D) and irritable bowel disease (IBD). Fermenting BC with lactic acid bacteria (LAB) and its incorporation into yogurt products increases the polyphenol and antioxidant capacity of BC, creating a blend of prebiotics and probiotics compounds with enhanced benefits. More research is needed in the area of lactic acid fermentation of berries in general, especially BC.

Seorang penderita dengan enteropatik artritis

Abstrak. Enteropatik artritis adalah bentuk artritis yang terkait dengan penyakit peradangan usus kronis /irritable bowel disease (IBD) dengan manifestasi tersering berupa kolitis ulseratif, dan penyakit Crohn. Ini merupakan salah satu manifestasi klinis dari spondiloartritis seronegatif. Diare dan artritis merupakan dua hal yang sering muncul sebagai gejala klinis pada enteropatik artritis. Salah satu alarm symptom pasien enteropatik artritis adalah buang air besar (BAB) cair dan berdarah. Berikut dilaporkan seorang pasien dengan keluhan BAB berdarah yang disebabkan enteropatik artritis yang mendapat terapi non farmakologis dan farmakologis, pasien mengalami perbaikan secara klinis dan dapat menjalani terapi lanjutan secara optimal melalui poli rheumatologi. Kata kunci: Enteropatik artritis, diare berdarah, colitis Abstrak. Enteropathic arthritis is a form of arthritis which associated with chronic inflammatory bowel disease (IBD). The most common manifestations are ulcerative colitis and Crohn's disease. This is one of the clinical spectrum of seronegative spondylarthritis. Diarrhea and arthritis are two symptoms that often appear as clinical manifestation in enteropathic arthritis. One of the alarm symptoms of enteropathic arthritis patients is haematoschezia. In this article, we reported a patient with bloody diarrhea caused by enteropathic arthritis. He received non-pharmacological and pharmacological therapy, and experienced clinical improvement. He then can undergo optimal further therapy through poly rheumatology. Keywords: arthritis enteropathic, bloody diarrhea, colitis