Browsing by Subject "Intestinal microbiota"

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  • Pesonen, Noora (Helsingin yliopisto, 2020)
    Objectives. Recent results of both animal and human studies suggest that intestinal microbiota, i.e. microorganisms inhabiting the gastrointestinal system, may be connected to their host’s cognition. However, the diverse effects of intestinal microbiota are still poorly understood and especially knowledge of its associations with normative childhood cognitive development is very scarce. The purpose of the current study was to examine the possible associations between infant intestinal microbial composition, richness and diversity and cognitive performance in early childhood. Methods. The current study sample consisted of the children taking part in Finnish Health and Early Life Microbiota (HELMi) longitudinal birth cohort study. The cognitive abilities of 424 children were assessed at 2 years of age with Bayley Scales of Infant and Toddler Development, using cognitive, receptive language and expressive language subscales. Of 424 tested children, those from whom microbiota analysis for at least one fecal sample was available at the time of the start of this study, were included. Fecal samples were collected when infants were 3, 6 and 12 weeks old and 6, 9 and 12 months old, and the bacterial composition, richness and diversity were analyzed with 16S rRNA- amplicon sequencing method. Results and conclusions. Intestinal microbial composition in infancy was found to be related to cognitive abilities of the children, more specifically, receptive language skills and expressive language skills. A higher abundance of the genus Finegoldia at 12 weeks of age and the genus Serratia at 6 months of age were related to worse receptive language performance at 2 years of age. A higher abundance of the family Enterococcaceae at 12 weeks of age and the genus Alistipes at 6 months of age, were associated with worse expressive language skills. In addition, the children who scored in lowest 20th percentile in the receptive language tasks, had richer intestinal microbiota at 3 weeks and 6 months of age. Conclusions cannot yet be drawn based on these preliminary findings, but the results suggest that infant intestinal microbiota may be one of the factors influencing cognitive, especially verbal, development in early childhood.
  • Jouhten, Hanne (Helsingfors universitet, 2015)
    Clostridium difficile infection (CDI) is a microbiota-related disease. Typically, antibiotic-induced perturbation of gut microbiota precedes the infection, while a healthy gut microbiota provides protection, i.e. colonization resistance, against it. Furthermore, in the case of recurrent CDI that is not resolved by antibiotics, restoring the gut microbiota with a fecal microbiota transplantation (FMT) is among the few treatment options that really work. Although FMT is effective in the treatment of CDI, the factors behind treatment success remain unclear. Both, the key species and the functions that are necessary to restore the healthy microbiota and eradicate C. difficile, are a matter of speculation. This study was based on the hypothesis that the adherence of some commensal bacteria to the gut epithelial cells could play a role in eradicating C. difficile by competing for epithelial binding with it. Furthermore, the isolation of those bacteria from the donor feces would enable more detailed mechanistic studies and development of a bacterial product for the treatment of CDI in the future. As a pre-selection step, bacterial adhesion to Caco-2 cells was utilized to isolate and cultivate epithelium-adherent bacteria from the donor feces. Microbiota composition of fecal sample, and the adhered and cultured sub-populations thereof, was determined by partial 16S rDNA amplicon sequencing using MiSeq method. The pre-selection approach was successful, since the obtained populations were different, both after the adhesion and cultivation, as compared to the original fecal sample. In addition, most obtained pure isolates adhered well to enterocytes. The ability of fecal bacteria to compete with C. difficile for binding to gut epithelial cells in vitro was also studied. Isolated bacteria from Caco-2-adhered populations were applied in competition and exclusion assays with C. difficile as purified or multi-species cultures, and reduction in C. difficile binding was observed due to the certain bacteria or bacterial populations. These assays still need developing and the results must be confirmed with more repetitions. However, the results are promising and a useful ground for future work in developing bacteriotherapeutic formulations for the treatment of CDI.
  • Jian, Ching; Luukkonen, Panu; Sädevirta, Sanja; Yki-Järvinen, Hannele; Salonen, Anne (2021)
    Backgrounds & aims: Intestinal microbiota may be causally involved in the pathogenesis of non-alcoholic fatty liver disease (NAFLD). We aimed to study the effect of short-term overfeeding on human gut microbiota in relation to baseline and overfeeding-induced liver steatosis. We also asked whether the baseline microbiota composition is associated to the overfeeding-induced increase in liver fat. Methods: In a randomized trial, 38 overweight and obese subjects were assigned to consume an excess of 1000 kcal/day of diets rich in either saturated fat, unsaturated fat, or simple sugars for 3 weeks. Fasting blood samples and H-1-MR spectroscopy were used for extensive clinical phenotyping as previously reported (PMID: 29844096). Fecal samples were collected for the analysis of the gut microbiota using 16S rRNA amplicon sequencing, imputed metagenomics and qPCR. Microbiota results were correlated with dietary intakes and clinical measurements before and during overfeeding. Results: The overall community structure of the microbiota remained highly stable and personalized during overfeeding based on between-sample Bray-Curtis dissimilarity, but the relative abundances of individual taxa were altered in a diet-specific manner: overfeeding saturated fat increased Proteobacteria, while unsaturated fat increased butyrate producers. Sugar overfeeding increased Lactococcus and Escherichia coli. Imputed functions of the gut microbiota were not affected by overfeeding. Several taxa affected by overfeeding significantly correlated with the changes in host metabolic markers. The baseline levels of proteobacterial family Desulfovibrionaceae, and especially genus Bilophila, were significantly associated to overfeeding-induced liver fat increase independently of the diet arm. In general, limited overlap was observed between the overfeeding-induced microbiota changes and the liver fat-associated microbiota features at baseline. Conclusions: Our work indicates that the human gut microbiota is resilient to short-term overfeeding on community level, but specific taxa are altered on diet composition-dependent manner. Generalizable microbiota signatures directly associated with liver steatosis could not be identified. Instead, the carriage of Bilophila was identified as a potential novel risk factor for diet-induced liver steatosis in humans. (C) 2020 Published by Elsevier Ltd.
  • Nylund, Lotta; Satokari, Reetta; Nikkila, Janne; Rajilic-Stojanovic, Mirjana; Kalliomaki, Marko; Isolauri, Erika; Salminen, Seppo; de Vos, Willem M. (2013)
  • Hynönen, Ulla; Zoetendal, Erwin G.; Virtala, Anna-Maija K.; Shetty, Sudarshan; Hasan, Shah; Jakava-Viljanen, Miia; de Vos, Willem M.; Palva, Airi (2020)
    In our previous studies on irritable bowel syndrome (IBS) –associated microbiota by molecular methods, we demonstrated that a particular 16S rRNA gene amplicon was more abundant in the feces of healthy subjects or mixed type IBS (IBS-M) –sufferers than in the feces of individuals with diarrhea-type IBS (IBS-D). In the current study, we demonstrated that this, so called Ct85-amplicon, consists of a cluster of very heterogeneous 16S rRNA gene sequences, and defined six 16S rRNA gene types, a to f, within this cluster, each representing a novel species-, genus- or family level taxon. We then designed specific PCR primers for these sequence types, mapped the distribution of the Ct85-cluster sequences and that of the newly defined sequence types in several animal species and compared the sequence types present in the feces of healthy individuals and IBS sufferers using two IBS study cohorts, Finnish and Dutch. Various Ct85-cluster sequence types were detected in the fecal samples of several companion and production animal species with remarkably differing prevalences and abundances. The Ct85 sequence type composition of swine closely resembled that of humans. One of the five types (d) shared between humans and swine was not present in any other animals tested, while one sequence type (b) was found only in human samples. In both IBS study cohorts, one type (e) was more prevalent in healthy individuals than in the IBS-M group. By revealing various sequence types in the widespread Ct85-cluster and their distribution, the results improve our understanding of these uncultured bacteria, which is essential for future efforts to cultivate representatives of the Ct85-cluster and reveal their roles in IBS.
  • Laatikainen, Reijo; Jalanka, Jonna; Loponen, Jussi; Hongisto, Sanna-Maria; Hillilä, Markku; Koskenpato, Jari; Korpela, Riitta; Salonen, Anne (BioMed Central, 2019)
    Abstract Background A low intake of Fermentable, Oligo-, Di-, Mono-saccharides and Polyols (FODMAPs) is effective in the symptom control of irritable bowel syndrome (IBS) patients but may exert negative effects on the intestinal microbiota. The microbial effects of increasing regular or non-FODMAP fibre sources are largely unknown. Furthermore, it is not known if the baseline microbiota composition is associated with individual symptom control during the consumption of different rye products in IBS patients. Our objective was to evaluate whether increased consumption of low-FODMAP rye bread or regular rye bread for 4 weeks would alter the intestinal microbiota composition of IBS patients following their habitual diet, and whether these changes associate to symptoms and/or the baseline microbiota. Methods The study was conducted as a randomized double blind controlled cross-over study (n = 50). Microbiota was analysed by 16S rRNA gene sequencing and associated with gastrointestinal symptoms. Both microbial changes and their associations to symptoms were secondary outcomes. Results The consumption of the test breads did not alter microbiota diversity. Compared to baseline, consumption of the low FODMAP rye bread decreased the abundance of Bacteroides, Flavonifractor, Holdemania, Parasutterella and Klebsiella and showed a trend towards increased bifidobacteria, whereas the regular rye bread decreased the abundance of Flavonifractor. When comparing between the two test breads, Klebsiella was decreased after low-FODMAP rye bread intake. Patients whose symptoms decreased during the low-FODMAP rye bread displayed more Blautia and less Barnesiella at baseline. Conclusions Consumption of low-FODMAP rye bread had modest, potentially beneficial effects on patients’ microbiota while increasing their intake of fibre substantially. The baseline microbiota composition was associated with the variable degrees of symptom relief experienced by the patients. Consumption of a low-FODMAP rye bread might be one way to increase dietary fibre intake and improve the mild dysbiosis often observed among patients with IBS. Trial registration ClinicalTrials.gov: NCT02161120 . Retrospectively registered 11 June 2014.