Microbiota composition
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Každý jedinec žije v úzkém společenství s mikroorganizmy, které osidlují všechny epitelové povrchy sliznic a kůže. Stále rostoucí množství nových poznatků o významu komenzálních mikrobů pro zdraví vyvolává velký zájem o mikrobiotu napříč lékařskými obory. Mikrobiota, zejména střevní, hraje klíčovou roli ve vývoji a fungování řady fyziologických mechanizmů, zejména imunitních. Mikrobiota vytváří s hostitelem symbiotický vztah: podmiňuje imunologickou rovnováhu, umožňuje efektivní imunitní reakce a brání kolonizaci patogenními mikroorganizmy. Alterace vzájemného vztahu mikrobioty a hostitele (dysbióza) vede k vývoji zánětlivých, autoimunitních i nádorových chorob. Pro medicínu budoucnosti se nyní otevírají nové možnosti: ovlivnit složení a funkci mikrobioty i její interakce nejen změnou životního stylu a způsobu stravování, ale i přímo, probiotiky nebo přenosem fekální mikrobioty.
Each individual is colonized by broad spectrum of microbes. Recent surge of interest in microbiota across all fields of medicine was motivated by an increasing body of knowledge on how commensals influence human health. This is most notable in the gut, where most microbes reside, but microbes colonizing other niches, such as oral cavity or skin, may influence health as well. Microbiota fundamentally influences the immune system development and its perturbation, i.e. dysbiosis, is associated with many inflammatory, autoimmune and neoplastic diseases. Microbiota forms a symbiotic relationship with the host - maintaining balanced and efficient immune response and protects from colonization by pathogens. Modern medicine may benefit greatly by adopting these ideas for therapeutic or prophylactic purposes. These may include manipulation with microbiota by diet, changes in lifestyle or directly by probiotics or fecal microbiota transfer.
- MeSH
- lidé MeSH
- mikrobiota * imunologie MeSH
- probiotika terapeutické užití MeSH
- slizniční imunita * MeSH
- střevní mikroflóra imunologie MeSH
- zánět imunologie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- přehledy MeSH
Different housing systems can be used in pig production and little is known about their effect on gut microbiota composition. In this study we characterized fecal microbiota by sequencing the rRNA genes in sows kept during gestation in conventional pens with a slatted floor and in enriched pens with a floor covered with deep straw. After farrowing, microbiota of 1- and 4-day-old piglets were also monitored. Microbiota of sows from the enriched system contained significantly more Prevotella, Parabacteroides, CF231, Phascolarctobacterium, Fibrobacter, Anaerovibrio and YRC22 and significantly less Lactobacillus, Bulleidia, Lachnospira, Dorea, Ruminococcus and Oscillospira than microbiota of sows from the conventional system. The Firmicutes to Bacteroidetes ratio was 0.96 in the microbiota of sows kept in the enriched pens and this increased to 1.66 in the microbiota of sows kept in the conventional system. The production system therefore influenced microbiota composition, most likely due the ingestion of the straw. The microbiota of 1- and 4-day-old piglets differed from the microbiota of sows and sows therefore did not represent the most important source for their colonization in early days of life.
- MeSH
- bydlení zvířat * MeSH
- chov zvířat * MeSH
- chování zvířat * MeSH
- feces mikrobiologie MeSH
- mikrobiota fyziologie MeSH
- novorozená zvířata MeSH
- prasata MeSH
- střevní mikroflóra * MeSH
- zvířata MeSH
- Check Tag
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- srovnávací studie MeSH
Gut microbiota is of considerable importance for each host. Despite this, germ-free animals can be obtained and raised to sexual maturity and consequences of the presence or absence of gut microbiota on gene expression of the host remain uncharacterised. In this study, we performed an unbiased study of protein expression in the caecum of germ-free and colonised chickens. The major difference between these two groups was in the expression of immunoglobulins which were essentially absent in the germ-free chickens. Microbiota also caused a minor decrease in the expression of focal adhesion and extracellular matrix proteins and an increase in the expression of argininosuccinate synthase ASS1, redox potential sensing, fermentative metabolic processes and detoxification systems represented by sulfotransferases SULT1C3 or SULT1E1. Since we also analysed expression in the caecum of E. coli Nissle and E. faecium DSM7134 mono-associated chickens, we concluded that at least immunoglobulin expression and expression of cystathionine synthase (CBS) was dependent on microbiota composition with E. coli Nissle stimulating more immunoglobulin and PIGR expression and E. faecium DSM7134 stimulating more CBS expression. Gut microbiota and its composition therefore affected protein expression in the chicken caecum though except for immunoglobulin production, the remaining differences were unexpectedly low.
- MeSH
- cékum metabolismus mikrobiologie MeSH
- Enterococcus faecium fyziologie MeSH
- Escherichia coli fyziologie MeSH
- exprese genu * MeSH
- gnotobiologické modely MeSH
- kur domácí genetika mikrobiologie MeSH
- ptačí proteiny metabolismus MeSH
- střevní mikroflóra fyziologie MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Fecal microbiota transfer may serve as a therapeutic tool for treating obesity and related disorders but currently, there is no consensus regarding the optimal donor characteristics. We studied how microbiota from vegan donors, who exhibit a low incidence of non-communicable diseases, impact on metabolic effects of an obesogenic diet and the potential role of dietary inulin in mediating these effects. Ex-germ-free animals were colonized with human vegan microbiota and fed a standard or Western-type diet (WD) with or without inulin supplementation. Despite the colonization with vegan microbiota, WD induced excessive weight gain, impaired glucose metabolism, insulin resistance, and liver steatosis. However, supplementation with inulin reversed steatosis and improved glucose homeostasis. In contrast, inulin did not affect WD-induced metabolic changes in non-humanized conventional mice. In vegan microbiota-colonized mice, inulin supplementation resulted in a significant change in gut microbiota composition and its metabolic performance, inducing the shift from proteolytic towards saccharolytic fermentation (decrease of sulfur-containing compounds, increase of SCFA). We found that (i) vegan microbiota alone does not protect against adverse effects of WD; and (ii) supplementation with inulin reversed steatosis and normalized glucose metabolism. This phenomenon is associated with the shift in microbiota composition and accentuation of saccharolytic fermentation at the expense of proteolytic fermentation.
- MeSH
- fekální transplantace MeSH
- glukosa farmakologie MeSH
- inulin farmakologie MeSH
- lidé MeSH
- myši MeSH
- potravní vláknina farmakologie MeSH
- střevní mikroflóra * MeSH
- vegani MeSH
- západní dieta MeSH
- ztučnělá játra * prevence a kontrola farmakoterapie MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
The Campylobacter jejuni-host interaction may be affected by the host's gut microbiota through competitive exclusion, metabolites, or modification of the immune response. To understand this interaction, C. jejuni colonization and local immune responses were compared in chickens with different gut microbiota compositions. Birds were treated with an antibiotic cocktail (AT) (experiments 1 and 2) or raised under germfree (GF) conditions (experiment 3). At 18 days posthatch (dph), they were orally inoculated either with 104 CFU of C. jejuni or with diluent. Cecal as well as systemic C. jejuni colonization, T- and B-cell numbers in the gut, and gut-associated tissue were compared between the different groups. Significantly higher numbers of CFU of C. jejuni were detected in the cecal contents of AT and GF birds, with higher colonization rates in spleen, liver, and ileum, than in birds with a conventional gut microbiota (P < 0.05). Significant upregulation of T and B lymphocyte numbers was detected in cecum, cecal tonsils, and bursa of Fabricius of AT or GF birds after C. jejuni inoculation compared to the respective controls (P < 0.05). This difference was less clear in birds with a conventional gut microbiota. Histopathological gut lesions were observed only in C. jejuni-inoculated AT and GF birds but not in microbiota-colonized C. jejuni-inoculated hatchmates. These results demonstrate that the gut microbiota may contribute to the control of C. jejuni colonization and prevent lesion development. Further studies are needed to identify key players of the gut microbiota and the mechanisms behind their protective role.
- MeSH
- antibakteriální látky farmakologie MeSH
- B-lymfocyty imunologie mikrobiologie MeSH
- bursa Fabricii účinky léků imunologie mikrobiologie MeSH
- Campylobacter jejuni účinky léků imunologie patogenita MeSH
- cékum účinky léků imunologie mikrobiologie MeSH
- gnotobiologické modely imunologie MeSH
- ileum účinky léků imunologie mikrobiologie MeSH
- interakce hostitele a patogenu imunologie MeSH
- játra účinky léků imunologie mikrobiologie MeSH
- kampylobakterové infekce imunologie mikrobiologie veterinární MeSH
- kur domácí MeSH
- mikrobiální interakce imunologie MeSH
- nemoci drůbeže imunologie mikrobiologie MeSH
- počet mikrobiálních kolonií MeSH
- slezina účinky léků imunologie mikrobiologie MeSH
- střevní mikroflóra imunologie MeSH
- T-lymfocyty imunologie mikrobiologie MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Since microbiota may influence the physiology of its host including body weight increase, growth rate or feed intake, in this study we determined the microbiota composition in high or low residual feed intake (HRFI and LRFI) pig lines, of different age and/or subjected to sanitary stress by sequencing the V3/V4 variable region of 16S rRNA genes. Allisonella, Megasphaera, Mitsuokella, Acidaminococcus (all belonging to Firmicutes/class Negativicutes), Lactobacillus, Faecalibacterium, Catenibacterium, Butyrivibrio, Erysipelotrichaceae, Holdemania, Olsenella and Collinsella were more abundant in HRFI pigs. On the other hand, 26 genera including Bacteroides, Clostridium sensu stricto, Oscillibacter, Paludibacter, Elusimicrobium, Bilophila, Pyramidobacter and TM7 genera, and Clostridium XI and Clostridium XIVa clusters were more abundant in LRFI than HRFI pigs. Adaptation of microbiota to new diet after weaning was slower in LRFI than in HRFI pigs. Sanitary stress was of relatively minor influence on pig microbiota composition in both tested lines although abundance of Helicobacter increased in LRFI pigs subjected to stress. Selection for residual feed intake thus resulted in a selection of fecal microbiota of different composition. However, we cannot conclude whether residual feed intake was directly affected by different microbiota composition or whether the residual feed intake and microbiota composition are two independent consequences of yet unknown genetic traits differentially selected in the pigs of the two lines.
- MeSH
- bakteriální RNA MeSH
- dieta * MeSH
- druhová specificita * MeSH
- feces mikrobiologie MeSH
- fyziologický stres fyziologie MeSH
- odstavení MeSH
- přijímání potravy MeSH
- RNA ribozomální 16S MeSH
- střevní mikroflóra genetika fyziologie MeSH
- Sus scrofa MeSH
- věkové faktory MeSH
- životní prostředí * MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
BACKGROUND: Infection of newly hatched chicks with Salmonella enterica serovar Enteritidis (S. Enteritidis) results in an inflammatory response in the intestinal tract which may influence the composition of gut microbiota. In this study we were therefore interested whether S. Enteritidis induced inflammation results in changes in the cecal microbiota. To reach this aim, we compared the cecal microbiota of non-infected chickens and those infected by S. Enteritidis by pyrosequencing the V3/V4 variable regions of genes coding for 16S rRNA. RESULTS: Cecal microbiota of chickens up to 19 days of life was dominated by representatives of Enterobacteriaceae, Lachnospiraceae and Ruminococcaceae, followed by Lactobacillaceae. The presence of Lachnospiraceae did not change after S. Enteritidis infection. Enterobacteriaceae increased and Ruminococcaceae decreased after S. Enteritidis infection in two independent experiments although these results were not significant. A significant increase in both experiments was observed only for the representatives of Lactobacillaceae which may correlate with their microaerophilic growth characteristic compared to the obligate anaerobes from the families Lachnospiraceae and Ruminococcaceae. CONCLUSIONS: We conclude that S. Enteritidis infection influences the composition of the cecal microbiota in chickens but these changes are minor in nature and should be understood more as an indirect consequence of infection and inflammation rather than a positively selected evolutionary trait.
- MeSH
- cékum mikrobiologie MeSH
- kur domácí mikrobiologie MeSH
- kvantitativní polymerázová řetězová reakce veterinární MeSH
- Lactobacillus MeSH
- mikrobiota * genetika MeSH
- nemoci drůbeže mikrobiologie MeSH
- RNA ribozomální 16S genetika MeSH
- Salmonella enteritidis fyziologie MeSH
- salmonelová infekce u zvířat mikrobiologie MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Recurrent acute otitis media (rAOM) poses a significant challenge in children aged 1 to 6 years, characterized by frequent and treatment-resistant ear infections. While existing studies predominantly focus on alterations in the nasopharyngeal microbiome associated with rAOM, our research explores the understudied association with the gut microbiome. In this cross-sectional observational prospective study, we enrolled 35 children aged 1 to 6 years during the 2021/2022 cold season. The test group comprised children with rAOM (n = 16), and the control group consisted of generally healthy children (n = 19). Samples (stool and nasopharyngeal swabs) were collected in late spring to ensure an antibiotic-free period. Detailed metadata was gathered through a questionnaire examining factors potentially influencing microbiota. Microbiota composition was assessed through amplicon sequencing of the V3-V4 region of the 16S rRNA gene. Our findings revealed limited alterations in gut microbiota composition among children with rAOM compared to healthy controls. Six bacterial taxa (Veillonella, Lachnospiraceae, Ruminococcaceae, Lachnospiraceae, Bacteroides and Blautia) were differentially represented with weak statistical significance. However, several bacterial taxa displayed correlations with multiple consecutive infections, with Turicibacter showing the most significant association. Additionally, day care centre attendance emerged as a potent gut microbiota modifier, independent of rAOM. Although our study identified limited differences in gut microbiota composition between children with rAOM and healthy controls, the observed correlations between the number of infections and specific bacterial taxa suggest a potential link between rAOM and the gut microbiota, warranting further investigation.
- MeSH
- akutní nemoc MeSH
- Bacteria * klasifikace genetika izolace a purifikace MeSH
- dítě MeSH
- feces mikrobiologie MeSH
- kojenec MeSH
- lidé MeSH
- nazofarynx mikrobiologie MeSH
- otitis media * mikrobiologie MeSH
- předškolní dítě MeSH
- prospektivní studie MeSH
- průřezové studie MeSH
- recidiva MeSH
- RNA ribozomální 16S * genetika MeSH
- střevní mikroflóra * MeSH
- Check Tag
- dítě MeSH
- kojenec MeSH
- lidé MeSH
- mužské pohlaví MeSH
- předškolní dítě MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- pozorovací studie MeSH
Infectious bursal disease (IBD) is an acute, highly contagious and immunosuppressive poultry disease. IBD virus (IBDV) is the causative agent, which may lead to high morbidity and mortality rates in susceptible birds. IBDV-pathogenesis studies have focused mainly on primary lymphoid organs. It is not known if IBDV infection may modify the development of the gut associated lymphoid tissues (GALT) as well as the microbiota composition. The aim of the present study was to investigate the effects of IBDV-infection on the bursa of Fabricius (BF), caecal tonsils (CT) and caecum, and to determine the effects on the gut microbiota composition in the caecum. Commercial broiler chickens were inoculated with a very virulent (vv) strain of IBDV at 14 (Experiment 2) or 15 (Experiment 1) days post hatch (dph). Virus replication, lesion development, immune parameters including numbers of T and B lymphocytes, macrophages, as well as the gut microbiota composition were compared between groups. Rapid IBDV-replication was detected in the BF, CT and caecum. It was accompanied by histological lesions including an infiltration of heterophils. In addition a significant reduction in the total mucosal thickness of the caecum was observed in vvIBDV-infected birds compared to virus-free controls (P < 0.05). vvIBDV infection also led to an increase in T lymphocyte numbers and macrophages, as well as a decrease in the number of B lymphocytes in the lamina propria of the caecum, and in the caecal tonsils. Illumina sequencing analysis indicated that vvIBDV infection also induced changes in the abundance of Clostridium XIVa and Faecalibacterium over time. Overall, our results suggested that vvIBDV infection had a significant impact on the GALT and led to a modulation of gut microbiota composition, which may lead to a higher susceptibility of affected birds for pathogens invading through the gut.
- MeSH
- cékum mikrobiologie MeSH
- infekce viry z čeledi Birnaviridae patologie veterinární virologie MeSH
- kur domácí MeSH
- lymfoidní tkáň mikrobiologie patologie MeSH
- mikrobiota * MeSH
- nemoci drůbeže patologie virologie MeSH
- virus infekční bursitidy drůbeže patogenita MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
INTRODUCTION: Human urine microbiota (UM) research has uncovered associations between composition of microbial communities of the lower urinary tract and various disease states including several reports on the putative link between UM and bladder cancer (BC). The aim of this study was to investigate male UM in patients with BC and controls using catheterised urine specimens unlike in previous studies. METHODS: Urine samples were obtained in theatre after surgical prepping and draping using aseptic catheterisation. DNA was extracted and hypervariable region V4 of the 16S rRNA gene was amplified using 515F and 806R primers. Sequencing was performed on Illumina MiSeq platform. Sequencing data were processed using appropriate software tools. Alpha diversity measures were calculated and compared between groups. Prevalence Interval for Microbiome Evaluation was used to test differences in beta diversity. RESULTS: A total of 63 samples were included in the analysis. Mean age of study subjects was 65.1 years (SD 12.5). Thirty-four men had bladder cancer and 29 participants were undergoing interventions for benign conditions (benign prostate hyperplasia or upper urinary tract stone disease). BC patients had lower UM richness and diversity than controls (83 vs. 139 operational taxonomic units, P = 0.015; Shannon index: 2.46 vs. 2.94, P = 0.049). There were specific taxa enriched in cancer (Veillonella, Varibaculum, Methylobacterium-Methylorubrum) and control groups (Pasteurella, Corynebacterium, Acinetobacter), respectively. CONCLUSION: BC patients had lower bladder microbiota richness and diversity than controls. Specific genera were enriched in cancer and control groups, respectively. These results corroborate some of previous reports while contradicting others. Future microbiota research would benefit from parallel transcriptomic/metabolomic analysis.
