Fecal microbiota transplantation (FMT) is a promising strategy in the management of inflammatory bowel disease (IBD). The clinical effects of this practice are still largely unknown and ...unpredictable. In this study, two children affected by mild and moderate ulcerative colitis (UC), were pre- and post-FMT monitored for clinical conditions and gut bacterial ecology. Microbiota profiling relied on receipts’ time-point profiles, donors and control cohorts’ baseline descriptions. After FMT, the improvement of clinical conditions was recorded for both patients. After 12 months, the mild UC patient was in clinical remission, while the moderate UC patient, after 12 weeks, had a clinical worsening. Ecological analyses highlighted an increase in microbiota richness and phylogenetic distance after FMT. This increase was mainly due to Collinsella aerofaciens and Eubacterium biforme, inherited by respective donors. Moreover, a decrease of Proteus and Blautia producta, and the increment of Parabacteroides, Mogibacteriaceae, Bacteroides eggerthi, Bacteroides plebeius, Ruminococcus bromii, and BBacteroidesovatus were associated with remission of the patient’s condition. FMT results in a long-term response in mild UC, while in the moderate form there is probably need for multiple FMT administrations. FMT leads to a decrease in potential pathogens and an increase in microorganisms correlated to remission status.
Commensal bacteria are known to promote host growth. Such effect partly relies on the capacity of microbes to regulate the host’s transcriptional response. However, these evidences mainly come from ...comparing the transcriptional response caused by commensal bacteria with that of axenic animals, making it difficult to identify the animal genes that are specifically regulated by beneficial microbes. Here, we employ Drosophila melanogaster associated with Lactiplantibacillus plantarum to understand the host genetic pathways regulated by beneficial bacteria and leading to improved host growth. We show that microbial benefit to the host relies on the downregulation of peptidoglycan-recognition proteins. Specifically, we report that bacterial proliferation triggers the lower expression of PGRP-SC1 in larval midgut, which ultimately leads to improved host growth and development. Our study helps elucidate the mechanisms underlying the beneficial effect exerted by commensal bacteria, defining the role of immune effectors in the relationship between Drosophila and its gut microbes.
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•Beneficial L. plantarum strains downregulate the expression of Drosophila PGRP-SC1•L. plantarum proliferation triggers the lower expression of Drosophila PGRP-SC1•Downregulation of PGRP-SC1 relies on the loss of function of L. plantarum ackA gene•PGRP-SCs downregulation is sufficient to improve L. plantarum beneficial effect
Immunology; Microbiology; Microbiome
Background:
Faecal microbiota transplantation (FMT) is a reasonable therapeutic option for the treatment of Clostridioides difficile infection (CDI) recurrent and refractory (RCDI) to therapy, but ...little evidence on the long-term impact of this therapy is currently available in the literature. The aim of this study was to evaluate the efficacy and safety of FMT in recurrent and refractory CDI and the modifications of the recipient’s gut microbiota in the medium–long term.
Methods:
This prospective study collects the clinical and laboratory data of RCDI patients treated with FMT by colonoscopy from February 2016 to October 2019. Stool samples for metagenomic analysis were collected pre-FMT at 1 week and at 6 and 12–24 months post-FMT.
Results:
In the study period, 20 FMT procedures were performed on 19 patients. Overall, FMT was effective in 85% of treated patients. No serious adverse event was recorded. In the medium- to long-term follow up, a newly diagnosed case of collagenous colitis was observed. Post-FMT, significant changes in microbiota were observed, characterised by the transition from a low- to a greater-diversity profile. Therefore, FMT restores eubiosis and maintains it over time.
Conclusion:
FMT is a safe and effective treatment option in RCDI patients. This procedure induces profound microbiota changes that explain its high clinical efficacy.
The role of animal hosts in shaping gut microbiome variation Maritan, Elisa; Quagliariello, Andrea; Frago, Enric ...
Philosophical transactions of the Royal Society of London. Series B. Biological sciences,
05/2024, Letnik:
379, Številka:
1901
Journal Article
Recenzirano
Odprti dostop
Millions of years of co-evolution between animals and their associated microbial communities have shaped and diversified the nature of their relationship. Studies continue to reveal new layers of ...complexity in host-microbe interactions, the fate of which depends on a variety of different factors, ranging from neutral processes and environmental factors to local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics and mathematical modelling to disentangle the individual contribution of ecological factors to microbiome evolution. Within this framework, host factors are known to be among the dominant drivers of microbiome composition in different animal species. However, the extent to which they shape microbiome assembly and evolution remains unclear. In this review, we summarize our understanding of how host factors drive microbial communities and how these dynamics are conserved and vary across taxa. We conclude by outlining key avenues for research and highlight the need for implementation of and key modifications to existing theory to fully capture the dynamics of host-associated microbiomes. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
Different factors are known to influence the early gut colonization in newborns, among them the perinatal use of antibiotics. On the other hand, the effect on the baby of the administration of ...antibiotics to the mother during labor, referred to as intrapartum antibiotic prophylaxis (IAP), has received less attention, although routinely used in group B
Streptococcus
positive women to prevent the infection in newborns. In this work, the fecal microbiota of neonates born to mothers receiving IAP and of control subjects were compared taking advantage for the first time of high-throughput DNA sequencing technology. Seven different 16S rDNA hypervariable regions (V2, V3, V4, V6 + V7, V8, and V9) were amplified and sequenced using the Ion Torrent Personal Genome Machine. The results obtained showed significant differences in the microbial composition of newborns born to mothers who had received IAP, with a lower abundance of
Actinobacteria
and
Bacteroidetes
as well as an overrepresentation of
Proteobacteria
. Considering that the seven hypervariable regions showed different discriminant ability in the taxonomic identification, further analyses were performed on the V4 region evidencing in IAP infants a reduced microbial richness and biodiversity, as well as a lower number of bacterial families with a predominance of
Enterobacteriaceae
members. In addition, this analysis pointed out a significant reduction in
Bifidobacterium
spp. strains. The reduced abundance of these beneficial microorganisms, together with the increased amount of potentially pathogenic bacteria, may suggest that IAP infants are more exposed to gastrointestinal or generally health disorders later in age.
Celiac disease (CD) is an immune-mediated systemic disease, caused by ingestion of gluten in genetically predisposed individuals. Gut microbiota dysbiosis might play a significant role in ...pathogenesis of chronic enteropathies and its modulation can be used as an intervention strategy in CD as well. In this study, we aimed to identify correlations between fecal microbiota, serum tumor necrosis factor alpha (TNF-α) and fecal short-chain fatty acids (SCFAs) in healthy children and children with CD after administration of probiotic Bifidobacterium breve BR03 and B632.
A double-blind placebo-controlled study enrolled 40 children with CD (CD) and 16 healthy children (HC). CD children were randomly allocated into two groups, of which 20 belonged to the placebo (PL) group and 20 to the Probiotic (PR) group. The PR group received a probiotic formulation containing a mixture of 2 strains, B. breve BR03 (DSM 16604) and B. breve B632 (DSM 24706) in 1:1 ratio for 3 months. Subsequently, for statistical analysis, blood and fecal samples from CD children (on enrolment - T0 and after 3 months, at the end of intervention with probiotic/placebo - T1) and HC children were used. The HC group was sampled only once (T0).
Verrucomicrobia, Parcubacteria and some yet unknown phyla of Bacteria and Archaea may be involved in the disease, indicated by a strong correlation to TNF-α. Likewise, Proteobacteria strongly correlated with fecal SCFAs concentration. The effect of probiotic administration has disclosed a negative correlation between Verrucomicrobia, some unknown phyla of Bacteria, Synergistetes, Euryarchaeota and some SCFAs, turning them into an important target in microbiome restoration process. Synergistetes and Euryarchaeota may have a role in the anti-inflammatory process in healthy human gut.
Our results highlight new phyla, which may have an important relation to disease-related parameters, CD itself and health.
Background
Dental calculus is the result of dental plaque mineralization, originating from the tooth‐associated bacterial biofilm. Recent evidence revealed that the dental calculus microbiome has a ...more complex composition than previously considered, including an unstructured mix of both aerobes and anaerobes bacteria. Actually, we lack information about the influence of host lifestyle factors, such as diet and health on this highly biodiverse ecosystem. Here, we provide a pilot study investigating dental calculus microbial biodiversity and its relation with the host diet.
Methods
We collected 40 dental calculus samples during routine dental inspection; deoxyribonucleic acid was extracted and analyzed through 16S amplicon sequencing, while dietary information was retrieved through a questionnaire. Associations between diet and oral bacteria taxonomy and functional pathways were statistically tested.
Results
Overall, microbiome composition was dominated by 10 phyla and 39 bacterial genera, which were differently distributed among samples. Cluster analysis revealed four main groups based on the taxonomic profile and two groups based on functional pathways. Each taxonomic cluster was dominated by different microbial biomarkers: Streptococcus, Rothia, Tannerella, Lautropia, and Fusobacterium. Bacteria genera and pathways were also associated with specific dietary elements, especially vegetable and fruit intake suggesting an overall effect of diet on dental calculus microbiome.
Conclusions
The present study demonstrates that there exists an inter‐variability in the microbial composition of dental calculus among individuals of a rather homogeneous population. Furthermore, the observed biodiversity and microbial functions can find an association with specific dietary habits, such as a high‐fiber diet or a protein‐rich diet.
Aims
To identify fecal microbiota profiles associated with metabolic abnormalities belonging to the metabolic syndrome (MS), high count of white blood cells (WBCs) and insulin resistance (IR).
...Methods
Sixty-eight young patients with obesity were stratified for percentile distribution of MS abnormalities. A MS risk score was defined as low, medium, and high MS risk. High WBCs were defined as a count ≥ 7.0 10
3
/µL; severe obesity as body mass index Z-score ≥ 2 standard deviations; IR as homeostatic assessment model algorithm of IR (HOMA) ≥ 3.7. Stool samples were analyzed by 16S rRNA-based metagenomics.
Results
We found reduced bacterial richness of fecal microbiota in patients with IR and high diastolic blood pressure (BP). Distinct microbial markers were associated to high BP (
Clostridium
and Clostridiaceae), low high-density lipoprotein cholesterol (Lachnospiraceae, Gemellaceae,
Turicibacter
), and high MS risk (Coriobacteriaceae), WBCs (
Bacteroides caccae
, Gemellaceae), severe obesity (Lachnospiraceae), and impaired glucose tolerance (
Bacteroides ovatus
and Enterobacteriaceae). Conversely, taxa such as
Faecalibacterium prausnitzii
,
Parabacterodes
,
Bacteroides caccae
,
Oscillospira
,
Parabacterodes distasonis
,
Coprococcus
, and
Haemophilus parainfluenzae
were associated to low MS risk score, triglycerides, fasting glucose and HOMA-IR, respectively. Supervised multilevel analysis grouped clearly “variable” patients based on the MS risk.
Conclusions
This was a proof-of-concept study opening the way at the identification of fecal microbiota signatures, precisely associated with cardiometabolic risk factors in young patients with obesity. These evidences led us to infer, while some gut bacteria have a detrimental role in exacerbating metabolic risk factors some others are beneficial ameliorating cardiovascular host health.
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