Recent studies have shown the importance of the human intestinal microbiome in maintaining a healthy gastrointestinal tract, as well as in the development of pathological processes. The intestinal microbiome manifests itself primarily as fecal metabolites. In the past decade, there has been growing interest in studying its composition, which for the most part had to do with the possibility of using the metabolomic analysis in clinical diagnosis. In contrast to the comprehensive description of blood serum, urine, saliva, and cerebrospinal fluid metabolites, data on fecal metabolites is sparse. Despite the instrumental and methodological achievements in the metabolomic analysis in general, the analysis of fecal metabolome remains less well developed, mainly because of the inhomogeneity of its composition and the lack of standardized methods for collecting, processing, and analyzing fecal samples. This review summarizes data on methods for studying and describing various groups of fecal metabolites. It also assesses their potential as tools in the diagnosis of gastrointestinal diseases.
Recent studies have shown the importance of the human intestinal microbiome in maintaining a healthy gastrointestinal tract, as well as in the development of pathological processes. The intestinal microbiome manifests itself primarily as fecal metabolites. In the past decade, there has been growing interest in studying its composition, which for the most part had to do with the possibility of using the metabolomic analysis in clinical diagnosis. In contrast to the comprehensive description of blood serum, urine, saliva, and cerebrospinal fluid metabolites, data on fecal metabolites is sparse. Despite the instrumental and methodological achievements in the metabolomic analysis in general, the analysis of fecal metabolome remains less well developed, mainly because of the inhomogeneity of its composition and the lack of standardized methods for collecting, processing, and analyzing fecal samples. This review summarizes data on methods for studying and describing various groups of fecal metabolites. It also assesses their potential as tools in the diagnosis of gastrointestinal diseases.
Inflammatory bowel diseases (IBD), which include ulcerative colitis (UC) and Crohn's disease (CD), are chronic intestinal inflammatory disorders with an unknown etiology. They are characterized by chronic recurrent inflammation of the intestinal mucosa and lead to a significant decrease in the quality of life and death of patients. IBD are associated with suppression of normal intestinal microflora, including a decrease in bacteria, producers of short chain fatty acids (SCFAs), exhibiting anti-inflammatory and protective properties. Among the various methods of intestinal microflora correction, fecal microbiota transplantation (FMT), which engrafts the fecal microbiota from a healthy donor into a patient recipient, is of a particular interest. As a result, a positive therapeutic effect is observed, accompanied by the restoration of the normal intestinal microflora of the patient. A significant drawback of the method is the lack of standardization. Metabolites produced by intestinal microflora, namely SCFAs, allow objective assessment of the functional state of the intestinal microbiota and, consequently, the success of the FMT procedure. Using gas chromatography and nuclear magnetic resonance spectroscopy techniques, we have analyzed concentrations and molar ratios of SCFAs in fecal samples of 60 healthy donors. Results were in good accord when comparing two methods as well as with published data. Analysis of SCFAs in feces of patients with UC (19 patients) and CD (17 patients) revealed a general decrease in the concentration of fatty acids in the experimental groups with significant fluctuations in the values in experimental groups compared to control group of healthy donors. On the limited group of IBD patients (6 patients with UC and 5 patients with CD) concentration of SCFAs before and within 30 days of observation after FMT was determined. It was shown that FMT had a significant impact on the SCFAs levels within 1 month term; tendency to reach characteristics of healthy donors is unambiguously traced for both diseases.
Fecal microbiota transplantation (FMT) targeting gut microbiota has recently been applied in treatment of Crohn’s disease (CD) and ulcerative colitis (UC). However, only a fraction of patients respond positively to this therapy. In this regard, it is gaining popularity to study the combinations of approved medications and FMT to increase the effectiveness of therapy. Here we present a pilot longitude project for the study of FMT application combined with the anti-inflammatory therapy in CD (n = 8) and UC (n = 6) patients. Using the shotgun sequencing of stool samples (n = 56) we evaluated the temporal changes in the taxonomic and functional structure of the patients’ metagenomes and donor-derived microbes engraftment due to the FMT procedure. According to our analysis, the gut microbiota was changed both in CD and UC patients whereas reshaping nature in experimental groups was differ. Only in the UC group the shift of gut microbiota composition towards donor and the donor-derived microbes engraftment were more extensive in comparison with the CD group. Moreover, we observed that beneficial and prevailing in human population microbes such as Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Eubacterium rectale, and others are the best colonizers. The difference in the microbial engraftment can be explained by differences in the pathogenesis of CD and UC. On the other hand, mucosal and intestinal lumen conditions in the UC group may have been better corrected due to the proposed treatment which allowed the donor microbes to colonize these patients more successfully. In addition, the evolutionary formed ecological relationship between the gut microbiota and the host can be linked with the FMT therapeutic effect.
1 Медицинская академия АО «ГК «Медси», г. Москва 2 ГБУЗ МО «Московский областной научно-исследовательский клинический институт имени М.Ф. Владимирского» 3 ФГБУ «Федеральный научно-клинический центр физико-химической медицины» ФМБА России, г. Москва 4 ФГАОУ ВО «Российский университет дружбы народов », г. Москва Белова Наталья Дмитриевна -аналитик ФГБУ ФНКЦ ФХМ ФМБА России. 119435, г. Москва, ул. Малая Пироговская, д. 1А. Цель исследования: показать эффективность трансплантации микробиоты кишечника при различных заболеваниях желудочно-кишечного тракта (ЖКТ). Дизайн: открытое несравнительное исследование. Материалы и методы. После первичной идентификации и типирования состава микрофлоры кишечника с использованием микробиологических, генетических и метаболомных методов субстрат микробиоты, предварительно забранной у подготовленных здоровых доноров, вводили 30 больным различными заболеваниями ЖКТ (псевдомембранозным клостридийным колитом, язвенным колитом, болезнью Крона, синдромом раздраженного кишечника, синдромом хронической усталости). Эффективность процедуры определяли по динамике клинической картины, общеклинических лабораторных показателей и путем сравнения состояния микробиоты до пересадки и в минимум трех реперных точках -через 2 недели, 1 и 3 месяца после трансплантации, с использованием микробиологических и метагеномных методов. Результаты. У всех пациентов с антибиотико-ассоциированным Clostridium difficile-колитом после однократной процедуры наступали ремиссия и восстановление нормальной микрофлоры. Больным с воспалительными заболеваниями кишечника на фоне базовой терапии проводилось от 1 до 2 процедур (в зависимости от степени выраженности процесса) с положительным эффектом у всех (наступление ремиссии, возможность снижения доз принимаемых препаратов). Заключение. Опыт проведения трансплантации фекальных масс при различных патологических состояниях пищеварительного тракта показал ее перспективность, огромный терапевтический потенциал в отношении таких заболеваний, как язвенный колит, болезнь Крона, C. difficile-ассоциированный колит, функциональные заболевания ЖКТ, метаболические нарушения. Эффективность эндоскопического перорального метода проведения трансплантации оказалась выше по сравнению с таковой ректального введения или использования лиофилизированного материала в капсулах. Ключевые слова: микробиота, желудочно-кишечный тракт, микрофлора кишечника, трансплантация фекальной микрофлоры, эндоскопия, гастроэнтерология, язвенный колит, болезнь Крона, Clostridium difficile.
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