Advanced Gut & Microbiome Research

Background. Ulcerative colitis (UC) is a type of inflammatory bowel disease (IBD) delineated by inflammation or ulcers in the colon that may cause diarrhea, abdominal pain, blood in the stool, tenesmus, etc. Objective. To determine therapeutic effectiveness and explore the mechanism of MeEt extract against DSS (3%)-induced UC in Swiss albino mice. Methods. Six mice were allocated into five groups at random: group1: vehicle control; group 2: DSS control; group 3: DSS+mesalazine (MSZ, 100 mg/kg BW); group 4: DSS+MeEt (200 mg/kg BW); and group 5: DSS+MeEt (400 mg/kg BW). Except for group 1, DSS (3%) in drinking water was given to all other groups to induce UC. %BW, average food intake, and mean stool consistency were determined for obtaining DAI scores. Mice were euthanized on the 8^th day, and colonic tissues were taken to measure the colon length. Serum and tissue levels of the cytokines were also determined using ELISA kits, followed by histopathological analysis of colon tissue. In addition, hematological and serum biochemical parameters were also determined to assess the treatment effectiveness. Result. During the induction, DAI scores, colon length, and cytokines levels were significantly increased. MSZ at 100 mg/kg BW and MeEt at 400 mg/kg BW doses via oral route significantly reversed the DAI scores and colon length. Further, MeEt 400 also downregulated the expression of IL-6, IL-8, TNF-α, IFN-γ, and IL-1 and upregulated the production of IL-1β and IL-10. Also, improvements in hematological and serum biochemical parameters were reported. Histopathological analysis revealed a decrease in inflammation and damage to colon tissue with the administration of MeEt extract. Conclusion. MeEt at a 400 mg/kg BW dose may be used as an alternate treatment for the management of UC, which is comparable with that of MSZ.

The search for potential probiotic bacteria of value to medicine, food industry, agriculture, and aquaculture has been extended in this study where bacterial isolates from the intestines of talakitok (Alectis sp.), a Philippine marine fish cultured and grown using de Man-Rogosa-Sharpe agar, were used to isolate Gram-positive rods that are catalyse negative. Its identity of 93-95% with Lactobacillus plantarum strains was confirmed by NCBI BLAST of the 16S rRNA forward and reverse sequences.

Objectives. To compare four DNA extraction methods for recovering bacterial DNA from mammalian faecal samples. Methods and Results. Three commercial kits from QIAamp, TIANamp, and MAGEN, together with the classic cetyltrimethylammonium bromide (CTAB) method, were evaluated for their performance in extracting bacterial DNA from the gut microbiota of five mammals, including humans (Homo sapiens), macaques (Macaca mulatta), dogs (Canis lupus familiaris), golden hamsters (Mesocricetus auratus), and mice (Mus musculus). First, we assessed the efficiency of the four methods based on DNA yield, purity, and integrity. Then, we investigated the impact of these methods on microbial composition and diversity and examined the relative abundance of dominant phyla bacteria based on 16S rRNA gene sequencing and real-time quantitative PCR. Our results showed that the CTAB method yielded relatively larger amounts of DNA, while the MAGEN kit yielded more Firmicutes DNA and reflected the true status of the microbiota more accurately. Conclusions. Of the four methods tested, the traditional CTAB method and commercial MAGEN kit accomplished the best performance in terms of DNA concentration and Firmicutes abundance across most of the tested species. As the CTAB method and MAGEN kit exhibited different advantages, we further tested and compared their DNA extraction performance on a defined microbiota comprising six strains from four dominant phyla to see which one better reflected the true status of the microbiota. In conclusion, the MAGEN kit was found to be superior to the CTAB method, as the testing results were closer to that of the defined microbiota.

Background. Helicobacter pylori (H. pylori) eradication regimens have been a concern, all along. Our study is aimed at assessing the effect of para- and probiotics plus minerals (Pyloshot) on H. pylori eradication rate. Methods. In this open-label randomized trial, 69 eligible adult patients with naïve H. pylori infection-related dyspepsia were randomly assigned into the group A, who received esomeprazole 40 mg BID, amoxicillin 1000 mg BID, and clarithromycin 500 mg BID, and group B with the same regimen plus one Pyloshot capsule BID for 10 days. Demographics and dyspepsia symptom severity scores (SSS), number needed to treat (NNT), dyspepsia SSS, and drug adverse effects were recorded at baseline and the end of treatment. H. pylori eradication was confirmed via ¹⁴C UBT eight weeks later. Results. Sixty-six patients completed the study. The intention-to-treat (ITT) and per-protocol (PP) eradication rates were slightly better in group B (85.2% vs. 80%, , and 87.8% vs. 84.8%, , respectively). Adverse effects were significantly lower in group B (20.6% vs. 54.3%; ). No significant differences in dyspepsia symptom improvement rates () and mean difference of SSS () were found between treatment groups. NNT for overall dyspepsia and epigastric pain syndrome (EPS) was 11 and 5 at the end of treatment, respectively. Conclusion. Adding Pyloshot to the H. pylori regimen could slightly improve the eradication rate and SSS of dyspepsia. NNT was considerably better among EPS patients. Adverse effects were significantly decreased by this regimen. Further trials with larger sample sizes should be thought out. This trial is registered with IRCT20141201020178N10.

The composition and diversity of gut microbiome are in crosstalk with the genetic makeup and diet of an individual. Under normal health conditions, the gut commensals are in homeostasis with the host; while they inhabit the gut for their normal growth, they protect against invading pathogens through anticolonization mechanisms and contribute largely to the metabolism of several macromolecules in the gut. Specific genetic variants in genes that are responsible for maintaining the composition of the gut commensal, such as genes of the immune system, are described to result in gut dysbiosis that can lead to the development of several autoimmune diseases such as inflammatory bowel disease and type-1 diabetes. Similarly, the diet of an individual shapes the gut microbiota by allowing the predominance of microbes that metabolize an abundant macromolecule in the diet. Epigenetically, the microbial metabolites produced by these microbes can be beneficial in the treatment of cancer or deteriorating by serving as carcinogens. Therefore, the complex association of the gut microbiome with the genetic makeup and diet of an individual plays a significant role in the development of several diseases and health conditions. Recently, the association between the human genome and the gut microbiome has been analyzed and considered a multiomic approach, and extensive genome-wide association studies were conducted to further understand the complex relationship.

Background. Alkylresorcinols (ARs) are polyphenolic compounds of microbial origin with a wide spectrum of biological activities and are potentially involved in host immune functioning. The present study is aimed at evaluating alterations in AR content in blood serum and faeces from healthy donors and patients with lung cancer in connection with response to immune checkpoint inhibitor (ICI) therapy to estimate the regulatory potential of AR. Methods. Quantitative analysis of AR levels, as well as other microbial metabolites in blood serum and faeces, was performed using gas chromatography with mass spectrometric detection; estimation of lymphocyte subsets was performed by flow cytometry; faecal microbiota transplantation (FMT) from lung cancer patients after ICI therapy to germ-free mice was performed to explore whether the intestinal microbiota could produce AR molecules. Results. AR concentrations in both faeces and serum differ dramatically between healthy and lung cancer donors. The significant increase in AR concentrations in mouse faeces after FMT points to the microbial origin of ARs. For several ARs, there were strong positive and negative correlations in both faeces and serum with immune cells and these interrelationships differed between the therapy-responsive and nonresponsive groups. Conclusions. The content of ARs may influence the response to ICI therapy in lung cancer patients. ARs may be considered regulatory molecules that determine the functioning of antitumor immunity.