Nikitina, Darja

Pratarmė. Mieli studentai, Gastroenterologija yra viena įdomiausių ir greičiausiai besiplėtojančių medicinos sričių. Dėl mokslo ir technologijų pažangos XXI a. gastroenterologija apima vis platesnį kepenų ir virškinamojo kanalo ligų, gydymo metodų spektrą. Tai neabejotinai viena įvairiapusiškiausių specialybių, kur akivaizdi klinikinių įgūdžių, molekulinių ir ultragarsinių tyrimų bei sudėtingų endoskopinių intervencijų sąsaja. Uždegiminės žarnyno ligos, retos virškinamojo kanalo ligos, mikrobiotos ir kepenų transplantacija yra tik nedidelė dalis sričių, kurios yra patikėtos gydytojams gastroenterologams. Šis Lietuvos sveikatos mokslų universiteto Medicinos akademijos Medicinos fakulteto Gastroenterologijos klinikos (toliau - Gastroenterologijos klinika) kolektyvo parengtas vadovėlis yra skirtas studentams, siekiantiems susipažinti su gastroenterologijos pagrindais. Jau beveik 30 metų Gastroenterologijos klinika aktyviai dalyvauja rengiant tarptautines diagnostikos ir gydymo gaires, yra prestižinių tarptautinių mokslo projektų ir konsorciumų dalyvė, o 2020 m. klinika tapo ir asocijuota Europos retų kepenų ligų tinklo nare. Mūsų klinikos mokslinių tyrimų rezultatai yra publikuojami prestižiniuose mokslo leidiniuose: Nature, Lancet, New England Journal of Medicine, Nature Genetics ir kituose. Rengdami šį vadovėlį stengėmės perteikti visą klinikos sukauptą ilgametę pedagoginę ir klinikinę patirtį bei naujausius mokslo pasiekimus. Tikimės, kad šis vadovėlis ne tik suteiks Jums pagrindinių žinių apie gastroenterologiją, bet ir paskatins rinktis šią specialybę rezidentūros studijose. Autorių vardu prof. Juozas Kupčinskas

Introduction: Over recent decades, the study of the bacterial microbiome has gained increasing attention due to its vital role in human health. The development of the gut microbiome is especially critical during infancy, as it supports nutrient absorption, metabolic regulation, and immune system maturation. Several perinatal factors, including delivery mode, gestational age, and health status, have been shown to influence micro -biome establishment. Preterm and low-birth-weight infants, in particular, face heightened vulnerability to disruptions in microbiome development, which may contribute to adverse health outcomes. Aims & Methods: This study aimed to analyze the longitudinal development of the gut microbiome in preterm, low-birth-weight neonates over the first two months of life and to identify microbial patterns and alterations associated with delivery mode, gestational age, and clinical conditions. The study cohort included 115 low-birth-weight preterm infants and 99full-term, normal-weight controls. Stool samples from preterm infants were collected at multiple time points between day 1 and day 61 of life and grouped into six age categories for analysis. In total, 819 stool samples were examined. DNA was extracted and amplified targeting the V3–V4 region of the 16S rRNA gene, followed by sequencing on the Illumina MiSeq platform. Microbiome data were analyzed using bioinformatic and statistical tools to assess taxonomic composition, alpha diversity, and beta diversity. Results: Significant differences in microbiome profiles were associated with gestational age, mode of delivery, postnatal age, maternal medication, and the presence of necrotizing enterocolitis (NEC). Bacterial com-munities began to stabilize between days 26 and 35. A total of 56 bacterial genera — including Bifidobacterium, Clostridium, Escherichia-Shigella, Gemella, Klebsiella, Lactobacillus, and Streptococcus — showed a positive correlation with infants’ age in days, while 31 genera — including Bacillus, Cutibacterium, Flavobacterium, Macrococcus, Pseudomonas, and Staphylococcus — were negatively correlated. Eighteen bacterial genera were associated with the mode of delivery at various time points. Genera such as Fusobacterium, Bacteroides, Entero-coccus, Streptococcus, Gemella, and Corynebacterium were more commonly associated with vaginal birth, while Staphylococcus, Rahnella, Yokenella, Millisia, Negativicoccus, Finegoldia, Haemophilus, Acinetobacter, Conservatibacter, Serratia, Stenotrophomonas, and Peptoniphilus were associated with Caesarean section delivery. Moderate differences in early-life microbiome composition were also ob -served between low-birth-weight preterm and full-term infants. Conclusion: Gut microbiome development in preterm, low-birth-weight newborns is strongly influenced by clinical and perinatal factors, particularly during the first month of life. Mode of delivery, gestational maturity, and disease presence such as NEC contribute to microbial variability and delayed community stabilization. These findings highlight the importance of early-life monitoring and tailored interventions to support healthy microbiome development in vulnerable neonates.

Background: Cirrhosis is increasing in prevalence but is hard to diagnose in the compensated stage. Gut microbiota are altered in cirrhosis, but studies find greatest differences centered on the easily diagnosable decompensated cirrhosis. Also there are major countrylevel variations. Aim: determine a gut metagenomic signature separating compensated cirrhosis from healthy controls across a global cohort. Methods: Compensated cirrhosis (comp) patients & healthy controls were recruited from seven countries. Clinical data, including demographics, cirrhosis severity (MELD, complications, medications), & dietary were collected. Stool samples underwent deep metagenomic sequencing & analysis using MetaPhlAn & MaAsLin2. Model evaluation was performed using repeated stratified 3-fold cross-validation with SMOTE applied within each training fold to address class imbalance. Models were trained on 70% of the full dataset & internally validated on the remaining 30%. Random forest (RF) model performance was assessed on the held-out test folds only. The final model was also tested separately in each country cohort. Results: We enrolled 618 participants (Comp =299; controls = 319) from 7 countries (USA n = 109, Türkiye n =95, South Korea n = 99, Denmark n= 66, Lithuania n =72, Brazil n =101, & Mexico n= 85) . Comp pts were older (59 ± 9 vs 50 ± 16, p <0.001) & more likely to be men (57 vs 42%, p< 0.001) consistently across countries. Major etiologies were alcohol 25%, HCV 24%, MASH 21% & HBV 16%. Microbiome analysis: Shannon diversity & richness (FigA) were lower in comp in all countries except Türkiye & Denmark (where only richness showed a significant decrease). β-diversity adjusting for demographics showed significant differences in microbial community structure between comp & controls. Microbial differences: In the entire cohort, 381 species were significantly different between controls and comp. 6 species were significantly different in five of seven countries. A set of 182 bacteria, significantly different in ≥2 countries, was selected as input features for RF model development. The final RF model, consisting of 40 species (Erysipelatoclostridium ramosum, Streptococcus anginosus, Veillonella parvula, Rothia mucilaginosa, Eubacterium rectale, Coprococcus catus, Bifidobacterium dentium, & Parabacteroides goldsteinii among others), achieved an AUC of 80.6% with an NPV of 83.2% (Fig B). Country-specific testing of the globally trained model demonstrated consistently strong within-cohort performance across all seven countries (Fig C). Conclusion: Gut metagenomic profiles effectively distinguish compensated cirrhosis from healthy controls across diverse geographic populations with granular metadata. Despite inter-country variability, a shared subset of bacterial features enabled robust and consistent model performance. These findings support the potential of microbiome-based tools for early detection of cirrhosis.

Over the past decades, bacterial microbiome studies have become increasingly important. The development of the gut microbiome has been shown to play an essential role in human health, and to be especially decisive in infants [1]. It influences nutrient absorption, metabolism regulation, and immune system development. Various factors have been proposed to modulate the development of the microbiome and therefore shape the growth and health of newborns [2]. Premature babies are often lowweight and even more sensitive to health issues. This study aims to analyse the development of the microbiome in preterm neonates over the first two months of life and look for patterns and alterations associated with several factors, like delivery mode, gestation time and necrotizing enterocolitis (NEC). A total of 78 preterm newborns were included in the study, with stool samples being taken at several timepoints from each baby. In total 515 samples were collected. The timepoints varied between ages of one and 61 days and were grouped in six age groups during the analysis. Genomic DNA was extracted from stool samples, and the bacterial V3–V4 hypervariable region of the 16S rRNA gene was amplified and sequenced on the Illumina MiSeq platform. The data were processed using bioinformatical tools and analysed bioinformatically and statistically to access microbiome composition, abundancies, alpha- and beta-diversities. The analysis revealed significant differences in the bacterial profiles across different timepoints, gestational ages, delivery modes, and in relation to the development of NEC. Alpha diversity indices increased over time; however, fewer or no significant differences were observed between the later timepoints. Consistent patterns emerged from both PCoA and PERMANOVA analyses. Notably, NEC was associated with distinct bacterial. Additionally, the abundance of several bacterial taxa correlated with gestational age. The bacterial profile of premature, low-birth-weight newborns varies according to factors such as age, delivery mode, gestational age, and the presence of disease. Comparing these microbiome dynamics in low-birth-weight infants with those in full-term newborns could provide valuable insights into the development of neonatal diseases such as necrotizing enterocolitis.

Background and aims: Recent studies have highlighted the significant role of gut microbiota in the pathogenesis of liver diseases. While research on bacterial changes in the gut has grown, the role of gut fungi (mycobiota) in LC has only recently begun to gain attention. However, further studies are essential to fully understand the impact of mycobiota alterations in LC. The aim of this study was to examine changes in the mycobiota profile by comparing stool samples from LC patients to those of a control group, and to explore the relationship between mycobiota alterations and clinical characteristics of the patients. Method: The study analyzed stool samples from 83 LC patients and 48 control participants. LC group included Child-Turcotte-Pugh (CTP) A – 38%, CTP B – 38%, CTP C – 24%; MELD score ≥15–49%, MELD score <15–51%; Compensated LC – 24%, Decompensated LC – 60%, Recompensated LC – 16%. Additionally, 42% of patients were on lactulose, 29% on proton pump inhibitors, and 32% on carvedilol. Only DNA samples meeting the quality criteria were used for PCR amplification of the fungi-specific ITS2 region. Sequencing was performed using the NanoKit Illumina kit and the MiSeq Illumina platform.

Background and aims: Prediction of outcomes such as hospitalizations is critical in cirrhosis to ensure timely prevention. Microbial composition is altered in cirrhosis but can show wide variation between countries. Aim: define microbial features that associate with 90-day hospitalization in a multi-national cirrhosis cohort. Method: Cirrhosis outpatients were recruited from 7 countries (USA, Türkiye, Korea, Denmark, Lithuania, Brazil & Mexico). Demographics, cirrhosis severity (MELD, complications, labs, medications), diet history, were recorded, stool collected & pts followed for 90 days for hospitalizations. Shotgun metagenomics for NGS was performed on stool. Regression analysis was performed using Maaslin2 for 90-day hospitalizations prediction. Covariates were chosen after PERMANOVA analysis & microbial species were added. Variables with p < 0.05 & q < 0.05 were considered significant. Results: 679 cirrhosis pts (170 US, 90 Brazil, 53 Denmark, 93 each Lithuania & Mexico, 99 Korea & 84 Türkiye) were enrolled. 60% were men, MELD 12 ± 5, albumin3.5 ± 0.70, Na 138 ± 7. Most common etiology was alcohol (35%) then viral (31%) & MASLD (17%). 56% were decompensated (35% on lactulose, 19% on rifaximin, 44% prior ascites, 19% prior variceal bleed, 31% on NS βblockers). Diet varied esp with yogurt & coffee intake. 90-day Hospitalizations: Seen in 169 (25%), most of which 133 (79%) were liver-related. Country-wise rate differed with lowest in Brazil & Türkiye and highest in Lithuania & Korea). PERMANOVA showed that MELD, decomp status, yogurt intake, country of origin & HE-medications were significant covariates. Maaslin2: 15 species associated with hospitalizations after controlling for country, decomp status, MELD score, yogurt, HE medications & alcohol etiology. Linked with ↓ hospitalizations: All had p < 0.01, Ruthenibacterium lactatiformans (coeff = 2.9, q < 0.001), Bacteroides uniformis (−2.3, p & q < 0.001), Flavonifactor plautii (−2.2, q < 0.001), Faecalibacterium prausnitzii (−1.9, q = 0.02), Clostridium fessum (−1.7, p & q < 0.001), Eggerthella lenta (−1.7, q = 0.01), Clostridiales bacterium (−1.7, q = 0.01), Bifidobacterium pseudocatenulatum (−1.7, q = 0.05), Anaerobutyricum hallii (−1.6, q = 0.02), Eubacterium ramulus (−1.4, q = 0.02), Clostridium leptum (−1.4, q = 0.04), Intestinimonas butyriciproducens (−1.3, q = 0.04), GGB9614_SGB15049 (−1.2 q = 0.04) & GGB2653_SGB3574 (−1.2, q = 0.03). These are short-chain fatty acid or lactate producers, or those involved in beneficial immune function. Linked with ↑ hospitalizations: Enterococcus faecium (Coeff 2.0, p < 0.001, q = 0.003), which is a pathobiont. Conclusion: In a prospective cohort of outpatients with cirrhosis from 7 countries, microbial profiles could predict 90-day hospitalizations despite controlling for diet, cirrhosis details, country of origin, and demographics. Microbial profiling could improve risk prediction in cirrhosis beyond single center studies.

The rapid emergence of multidrug-resistant bacterial species poses a critical threat by reducing the efficacy of antibiotics and complicating infection treatment. Bacteriocins, such as klebicin KvarM, have emerged as promising alternatives to traditional antibiotics due to their targeted antimicrobial activity. In this study, we evaluated the therapeutic potential of Eudragit-coated klebicin KvarM in a mouse model of Klebsiella pneumoniae intestinal colonization, assessing both its antimicrobial effectiveness and impact on commensal gut microbiota.

Išradime aprašytas storosios žarnos vėžio (SŽV) nustatymo būdas. Šis būdas apima biologinio mėginio paėmimą, laisvai cirkuliuojančios DNR išskyrimą iš biologinio mėginio (kraujo plazmos), Staphylococcaceae ir Staphylococcus hominis bakterijų sekų nustatymą laisvai cirkuliuojančioje DNR naudojant naujos kartos sekoskaitą, Staphylococcaceae ir Staphylococcus hominis bakterijų sekų santykinio skaičiaus biologiniame mėginyje paliginimo su referentinėmis reikšmėmis (atitinkamai 9,0 proc. ir 0.3 proc.), jei Staphylococcaceae ir Staphylococcus hominis bakterijų sekų santykinis skaičius paciento biologiniame mėginyje viršija referentinę reikšmę, pacientui nustatomas SŽV. Būdas pasižymi aukštu jautrumu ir specifiškumu, todėl jis yra perspektyvi alternatyva ankstyvajai SŽV diagnostikai.

Išradime aprašytas storosios žarnos vėžio (SŽV) nustatymo būdas. Šis būdas apima biologinio mėginio paėmimą, laisvai cirkuliuojančios DNR išskyrimą iš biologinio mėginio (kraujo plazmos), Staphylococcaceae ir Staphylococcus hominis bakterijų sekų nustatymą laisvai cirkuliuojančioje DNR naudojant naujos kartos sekoskaitą, Staphylococcaceae ir Staphylococcus hominis bakterijų sekų santykinio skaičiaus biologiniame mėginyje paliginimo su referentinėmis reikšmėmis (atitinkamai 9,0 proc. ir 0.3 proc.), jei Staphylococcaceae ir Staphylococcus hominis bakterijų sekų santykinis skaičius paciento biologiniame mėginyje viršija referentinę reikšmę, pacientui nustatomas SŽV. Būdas pasižymi aukštu jautrumu ir specifiškumu, todėl jis yra perspektyvi alternatyva ankstyvajai SŽV diagnostikai.

Įvadas: Kepenų cirozė (KC) - tai vėlyva kepenų fibrozės stadija, kuriai būdingas progresuojantis kepenų funkcijos blogėjimas, kas veda prie gyvybei pavojingų komplikacijų. Naujausi tyrimai, analizuojantys žarnyno bakterijų pokyčius parodė bakterijų ryšį su kepenų ligos patogeneze, dekompensacija ir hospitalizacijos rodikliais. Pastaruoju metu vis daugiau dėmesio skiriama žarnyno grybelių (mikobiotos) pokyčių vaidmeniui KC, tačiau šioje srityje reikalingi tolimesni tyrimai. Tikslas: Nustatyti mikobiotos profilio pokyčius lyginant KC sergančių pacientų išmatų mėginius su kontroline grupe bei ištirti mikobiotos profilio sąsają su pacientų klinikiniais požymiais. Metodai: Tyrimui buvo naudoti 83 KC pacientų ir 48 kontrolinės grupės dalyvių išmatų mėginiai. Iš ėminių buvo išskirtos DNR molekulės, atliktas nukleorūgščių kiekio ir kokybės įvertinimas. Kokybės įverčius atitinkantys mėginiai buvo naudoti siekiant PGR metodu amplifikuoti grybams specifinį ITS2 regioną, pagausinti fragmentai buvo išvalyti, kiekvieno mėginio ekvivalentai tūriai buvo naudoti siekiant paruošti sekoskaitos biblioteką. Sekoskaita atlikta naudojant NanoKit Illumina rinkinį ir MiSeq Illumina sekoskaitos aparatą. Bioinformatinė ir statistinė analizė buvo atlikta R Studio programinėje įrangoje naudojant dada2, phyloseq, vegan, deseq2 ir kt. programinius įrankius. Rezultatai: KC sergančiųjų pacientų mikobiotos profilis statistiškai reikšmingai skyrėsi nuo kontrolinės grupės. Kai kurie aptikti grybai skyrėsi ne tik lyginant KC ir kontrolinę grupes, bet ir pagal klinikinius duomenis. Tyrimas parodė, kad Candida gentis statistiškai buvo gausesnė ne tik tarp KC sergančių pacientų, bet ir tarp pačių pacientų, sergančių sunkesne kepenų cirozės forma. Saccharomyces rūšys ir Kazachstania gentis buvo sumažėjusios KC grupėje ir labiau siejamos su lengvesne KC forma. Išvados: KC sergančių pacientų mikobiomo profilis reikšmingai skiriasi nuo kontrolinės grupės. Candida genties gausumas yra susijęs su sunkesnėmis KC stadijomis, tuo tarpu kiti grybai, tokie kaip Saccharomyces ir Kazachstania, labiau siejami su lengvesnėmis ligos formomis arba kontrolinės grupės mėginiais. Tai rodo, kad mikobiotos pokyčių analizė potencialiai galėtų prisidėti prie kepenų cirozės diagnozavimo ir progresavimo stebėsenos.