It is becoming increasingly clear that maintaining the equilibrium of gut microbiota homeostasis during viral infections, such as Hantaan virus (HTNV), is of paramount importance. In order to gain insight into the role of NOD-like receptors in the immune system, we conducted a comparative study between C57BL/6 and Nlrx1-/- mouse models to analyze changes in the gut microbiota after HTNV infection. Our findings revealed an increase in the ratio of Firmicutes to Bacteroides in Nlrx1-/- mice, suggesting a potential link to inflammation. In addition, a comprehensive analysis of serum metabolomics revealed that differential metabolites were mainly concentrated in amino acid metabolism and lipid metabolism. Amino acid metabolism mainly involves arginine, lysine, and histidine metabolism, while lipid metabolism is mainly related to glycerophospholipid metabolism and fatty acid synthesis. Analysis of the correlation between microbiota and metabolites revealed an inverse relationship between Bacteroidetes and metabolites related to glutamine metabolism, while Firmicutes were directly associated with these metabolites. Furthermore, we observed a negative correlation between the presence of Actinobacteria, Proteobacteria, and Patescibacteria and the metabolites related to polyunsaturated fatty acids (PUFAs). Our results demonstrate that HTNV infection causes changes in the composition of gut microbiota in both Nlrx1-/- and wild-type (WT) mice. Moreover, the fecal microbiota and serum metabolites of Nlrx1-/- mice display notable differences at various developmental stages. Investigating this further may help to improve our understanding of the pathogenesis of HTNV and provide potential therapeutic options.

Wenjie Sun

Yaxin Ding

Ziyu Liu

Shiyuan Hou

Danni Sun

Ruixue Ma

Huarui Kang

Xiaohan Ma

Jiayu Wang

Hongrui Mu

Yunhua Lv

Tianle Gu

Qikang Ying

Fang Wang

Xingan Wu

Rongrong Liu

Investigating the Impact of HTNV Infection on the Gut Microbiota of Wild-Type and NLRX1 Knockout Mice

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 8th 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.

Monika Joshi

Manju Pandey

Akash Ved

Assessment of Ameliorative Effect of Myrica esculenta in a DSS-Induced Murine Model against Ulcerative Colitis

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.

Nieves L. Capili

Jose Mallari

Lactobacillus plantarum in the Gut of a Marine Fish from a Caloocan Local Market

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.

Yameng Liu

Xianchun Zhong

Yibin Wang

Kanglong Wang

Cuina Li

Xinyu Liang

Suqin Lin

Ru Zhou

Cen Xie

Variations in Gut Microbiome Profiles Based on Different DNA Extraction Methods: A Comparative Study

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%, <svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="18.973pt" style="vertical-align:-3.42938pt" id="M1" height="11.7782pt" version="1.1" viewBox="-0.0498162 -8.34882 18.973 11.7782"><g transform="matrix(.013,0,0,-0.013,0,0)"><path id="g113-113" d="M570 304C570 398 525 448 414 448C385 448 343 445 312 434L329 511L321 518C297 504 262 482 244 460L233 411C195 397 159 381 128 358L135 332C160 347 189 360 224 373L111 -147C97 -210 84 -218 17 -231L13 -257L254 -247L259 -218L233 -216C183 -212 177 -202 189 -142L218 -1C238 -10 266 -12 283 -12C351 3 429 48 483 105C543 168 570 242 570 304ZM482 289C482 161 380 33 304 33C278 33 248 51 233 69L303 396C326 400 352 403 369 403C428 403 482 380 482 289Z"/></g><g transform="matrix(.013,0,0,-0.013,11.342,0)"><path id="g117-34" d="M535 323V373H52V323H535ZM535 138V188H52V138H535Z"/></g></svg><svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="28.184pt" style="vertical-align:-3.42938pt" height="11.7782pt" version="1.1" viewBox="22.555183800000002 -8.34882 28.184 11.7782"><g transform="matrix(.013,0,0,-0.013,22.605,0)"><path id="g113-49" d="M241 635C89 635 35 457 35 312C35 153 89 -12 240 -12C390 -12 443 166 443 312C443 466 390 635 241 635ZM238 602C329 602 354 454 354 312C354 172 330 22 240 22C152 22 124 173 124 313S148 602 238 602Z"/></g><g transform="matrix(.013,0,0,-0.013,28.845,0)"><path id="g113-47" d="M113 -12C146 -12 170 11 170 46C170 78 146 103 114 103S58 78 58 46C58 11 82 -12 113 -12Z"/></g><g transform="matrix(.013,0,0,-0.013,31.809,0)"><path id="g113-54" d="M153 550H386L412 615L406 623H120L82 318C104 327 142 338 184 338C294 338 347 275 347 187C347 112 305 39 221 39C160 39 119 71 97 89C88 97 80 96 71 90C59 80 50 67 49 57C48 45 52 36 66 23C80 9 123 -12 169 -12C221 -11 288 15 342 59C403 109 431 165 431 225C431 308 366 395 238 395C212 395 165 379 127 364L153 550Z"/></g><g transform="matrix(.013,0,0,-0.013,38.049,0)"><path id="g113-55" d="M137 343C167 482 260 545 321 574C357 591 397 603 429 609L423 641C382 634 335 622 295 608C189 570 37 457 37 238C37 84 125 -12 242 -12C362 -12 447 89 447 209C447 311 374 393 267 393C247 393 226 386 204 376L137 343ZM227 337C318 337 361 256 361 173C361 105 336 22 258 22C176 22 126 120 126 240C126 266 127 291 132 310C155 323 189 337 227 337Z"/></g><g transform="matrix(.013,0,0,-0.013,44.289,0)"><path id="g113-51" d="M412 140C382 77 369 73 315 73H129L270 222C362 320 402 379 402 466C402 571 322 635 234 635C177 635 130 609 99 576L42 495L64 475C90 514 133 568 201 568C274 568 318 519 318 435C318 349 255 267 193 193C144 135 87 78 32 23V0H405C417 45 427 89 440 131L412 140Z"/></g></svg>, and 87.8% vs. 84.8%, <svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="18.973pt" style="vertical-align:-3.42938pt" id="M2" height="11.7782pt" version="1.1" viewBox="-0.0498162 -8.34882 18.973 11.7782"><g transform="matrix(.013,0,0,-0.013,0,0)"><use xlink:href="#g113-113"/></g><g transform="matrix(.013,0,0,-0.013,11.342,0)"><use xlink:href="#g117-34"/></g></svg><svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="28.184pt" style="vertical-align:-3.42938pt" height="11.7782pt" version="1.1" viewBox="22.555183800000002 -8.34882 28.184 11.7782"><g transform="matrix(.013,0,0,-0.013,22.605,0)"><use xlink:href="#g113-49"/></g><g transform="matrix(.013,0,0,-0.013,28.845,0)"><use xlink:href="#g113-47"/></g><g transform="matrix(.013,0,0,-0.013,31.809,0)"><path id="g113-56" d="M447 623H65C61 580 56 530 47 475H76C100 541 106 550 172 550H388C308 376 196 170 91 -1L98 -12L172 -2C268 204 360 408 455 611L447 623Z"/></g><g transform="matrix(.013,0,0,-0.013,38.051,0)"><use xlink:href="#g113-51"/></g><g transform="matrix(.013,0,0,-0.013,44.291,0)"><use xlink:href="#g113-49"/></g></svg>, respectively). Adverse effects were significantly lower in group B (20.6% vs. 54.3%; <svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="18.973pt" style="vertical-align:-3.42938pt" id="M3" height="11.7782pt" version="1.1" viewBox="-0.0498162 -8.34882 18.973 11.7782"><g transform="matrix(.013,0,0,-0.013,0,0)"><use xlink:href="#g113-113"/></g><g transform="matrix(.013,0,0,-0.013,11.342,0)"><use xlink:href="#g117-34"/></g></svg><svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="28.184pt" style="vertical-align:-3.42938pt" height="11.7782pt" version="1.1" viewBox="22.555183800000002 -8.34882 28.184 11.7782"><g transform="matrix(.013,0,0,-0.013,22.605,0)"><use xlink:href="#g113-49"/></g><g transform="matrix(.013,0,0,-0.013,28.845,0)"><use xlink:href="#g113-47"/></g><g transform="matrix(.013,0,0,-0.013,31.809,0)"><use xlink:href="#g113-49"/></g><g transform="matrix(.013,0,0,-0.013,38.049,0)"><use xlink:href="#g113-49"/></g><g transform="matrix(.013,0,0,-0.013,44.289,0)"><path id="g113-53" d="M456 178V225H360V632H320C217 496 115 347 20 206V178H280V106C280 40 276 34 189 27V0H445V27C364 34 360 39 360 106V178H456ZM280 225H82C149 335 214 431 278 520H280V225Z"/></g></svg>). No significant differences in dyspepsia symptom improvement rates (<svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="18.973pt" style="vertical-align:-3.42938pt" id="M4" height="11.7782pt" version="1.1" viewBox="-0.0498162 -8.34882 18.973 11.7782"><g transform="matrix(.013,0,0,-0.013,0,0)"><use xlink:href="#g113-113"/></g><g transform="matrix(.013,0,0,-0.013,11.342,0)"><use xlink:href="#g117-34"/></g></svg><svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="28.184pt" style="vertical-align:-3.42938pt" height="11.7782pt" version="1.1" viewBox="22.555183800000002 -8.34882 28.184 11.7782"><g transform="matrix(.013,0,0,-0.013,22.605,0)"><use xlink:href="#g113-49"/></g><g transform="matrix(.013,0,0,-0.013,28.845,0)"><use xlink:href="#g113-47"/></g><g transform="matrix(.013,0,0,-0.013,31.809,0)"><use xlink:href="#g113-51"/></g><g transform="matrix(.013,0,0,-0.013,38.049,0)"><use xlink:href="#g113-54"/></g><g transform="matrix(.013,0,0,-0.013,44.289,0)"><use xlink:href="#g113-54"/></g></svg>) and mean difference of SSS (<svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="18.973pt" style="vertical-align:-3.42938pt" id="M5" height="11.7782pt" version="1.1" viewBox="-0.0498162 -8.34882 18.973 11.7782"><g transform="matrix(.013,0,0,-0.013,0,0)"><use xlink:href="#g113-113"/></g><g transform="matrix(.013,0,0,-0.013,11.342,0)"><use xlink:href="#g117-34"/></g></svg><svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="28.184pt" style="vertical-align:-3.42938pt" height="11.7782pt" version="1.1" viewBox="22.555183800000002 -8.34882 28.184 11.7782"><g transform="matrix(.013,0,0,-0.013,22.605,0)"><use xlink:href="#g113-49"/></g><g transform="matrix(.013,0,0,-0.013,28.845,0)"><use xlink:href="#g113-47"/></g><g transform="matrix(.013,0,0,-0.013,31.809,0)"><use xlink:href="#g113-51"/></g><g transform="matrix(.013,0,0,-0.013,38.049,0)"><path id="g113-52" d="M285 378C315 398 338 416 353 432C373 451 384 474 384 503C384 579 325 635 236 635H235C182 635 136 610 108 579L65 516L85 496C110 533 150 575 205 575C258 575 300 543 300 481C300 407 232 369 141 339L147 310C163 315 188 321 211 321C268 321 338 284 338 192C338 94 288 40 217 40C160 40 119 68 93 91C85 98 77 97 69 91C60 84 47 71 46 58C44 46 48 35 62 22C75 10 116 -12 162 -12C234 -12 424 62 424 224C424 297 373 359 285 376V378Z"/></g><g transform="matrix(.013,0,0,-0.013,44.289,0)"><path id="g113-50" d="M384 0V27C293 34 287 42 287 114V635C232 613 172 594 109 583V559L157 557C201 555 205 550 205 499V114C205 42 199 34 109 27V0H384Z"/></g></svg>) 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 <a target="_blank" href="https://clinicaltrials.gov/ct2/show/IRCT20141201020178N10">IRCT20141201020178N10</a>.

Marjan Mokhtare

Mohammad Ebrahimian

Abolfazl Namazi

Amir M. Sadeghian

Hani Talaee

Mohsen Masoodi

The Efficacy of Paraprobiotic, Probiotic, and Mineral Supplementation on the Eradication Rate of Helicobacter pylori in Patients with Dyspepsia: A Randomized Clinical Trial

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.

Abdullahi Y. Muhammad

Malik Amonov

Atif A. Baig

Farrukh J. Alvi

Gut Microbiome: An Intersection between Human Genome, Diet, and Epigenetics

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Advanced Gut &amp; Microbiome Research is an open access, peer-reviewed journal that publishes original research and review articles related to all aspects of fundamental and applied research on gastroenterology, microbiology and their interactions.

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Chief Editor, Prof Zongxin Ling, is the Principal Investigator of the Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases at Zhejiang University. Dr Ling's research focuses on the&nbsp;cross-talk between host and microbiota in human diseases.

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Advanced Gut & Microbiome Research - Table of contents 2024

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Advanced Gut & Microbiome Research is an open access, peer-reviewed journal that publishes original research and review articles related to all aspects of fundamental and applied research on gastroenterology, microbiology and their interactions.

Advanced Gut & Microbiome Research