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Gut Mar 2020The significance of the liver-microbiome axis has been increasingly recognised as a major modulator of autoimmunity. The aim of this study was to take advantage of a...
OBJECTIVE
The significance of the liver-microbiome axis has been increasingly recognised as a major modulator of autoimmunity. The aim of this study was to take advantage of a large well-defined corticosteroids treatment-naïve group of patients with autoimmune hepatitis (AIH) to rigorously characterise gut dysbiosis compared with healthy controls.
DESIGN
We performed a cross-sectional study of individuals with AIH (n=91) and matched healthy controls (n=98) by 16S rRNA gene sequencing. An independent cohort of 28 patients and 34 controls was analysed to validate the results. All the patients were collected before corticosteroids therapy.
RESULTS
The gut microbiome of steroid treatment-naïve AIH was characterised with lower alpha-diversity (Shannon and observed operational taxonomic units, both p<0.01) and distinct overall microbial composition compared with healthy controls (p=0.002). Depletion of obligate anaerobes and expansion of potential pathobionts including were associated with disease status. Of note, , the most strongly disease-associated taxa (p=8.85E-8), positively correlated with serum level of aspartate aminotransferase and liver inflammation. Furthermore, the combination of four patients with AIH-associated genera distinguished AIH from controls with an area under curves of approximately 0.8 in both exploration and validation cohorts. In addition, multiple predicted functional modules were altered in the AIH gut microbiome, including lipopolysaccharide biosynthesis as well as metabolism of amino acids that can be processed by bacteria to produce immunomodulatory metabolites.
CONCLUSION
Our study establishes compositional and functional alterations of gut microbiome in AIH and suggests the potential for using gut microbiota as non-invasive biomarkers to assess disease activity.
Topics: Adolescent; Adult; Aged; Aspartate Aminotransferases; Case-Control Studies; Clostridiales; Cross-Sectional Studies; Dysbiosis; Female; Gastrointestinal Microbiome; Hepatitis, Autoimmune; Humans; Lactobacillus; Male; Middle Aged; Severity of Illness Index; Veillonella; Young Adult
PubMed: 31201284
DOI: 10.1136/gutjnl-2018-317836 -
ACS Applied Materials & Interfaces Jul 2019To combat implant-associated infections, there is a need for novel materials which effectively inhibit bacterial biofilm formation. In the present study, the...
To combat implant-associated infections, there is a need for novel materials which effectively inhibit bacterial biofilm formation. In the present study, the antiadhesive properties of titanium surface functionalization based on the "slippery liquid-infused porous surfaces" (SLIPS) principle were demonstrated and the underlying mechanism was analyzed. The immobilized liquid layer was stable over 13 days of continuous flow in an oral flow chamber system. With increasing flow rates, the surface exhibited a significant reduction in attached biofilm of both the oral initial colonizer Streptococcus oralis and an oral multispecies biofilm composed of S. oralis, Actinomyces naeslundii, Veillonella dispar, and Porphyromonas gingivalis. Using single cell force spectroscopy, reduced S. oralis adhesion forces on the lubricant layer could be measured. Gene expression patterns in biofilms on SLIPS, on control surfaces, and expression patterns of planktonic cultures were also compared. For this purpose, the genome of S. oralis strain ATCC 9811 was sequenced using PacBio Sequel technology. Even though biofilm cells showed clear changes in gene expression compared to planktonic cells, no differences could be detected between bacteria on SLIPS and on control surfaces. Therefore, it can be concluded that the ability of liquid-infused titanium to repel S. oralis biofilms is mainly due to weakened bacterial adhesion to the underlying liquid interface.
Topics: Actinomyces; Bacterial Adhesion; Biofilms; Gene Expression Regulation, Bacterial; Humans; Porphyromonas gingivalis; Single-Cell Analysis; Spectrum Analysis; Streptococcus oralis; Surface Properties; Titanium; Veillonella
PubMed: 31173692
DOI: 10.1021/acsami.9b06817 -
Journal of Clinical Medicine May 2019Cystic fibrosis (CF) is a systemic genetic disease that leads to pulmonary and digestive disorders. In the majority of CF patients, the intestine is the site of chronic...
Cystic fibrosis (CF) is a systemic genetic disease that leads to pulmonary and digestive disorders. In the majority of CF patients, the intestine is the site of chronic inflammation and microbiota disturbances. The link between gut inflammation and microbiota dysbiosis is still poorly understood. The main objective of this study was to assess gut microbiota composition in CF children depending on their intestinal inflammation. We collected fecal samples from 20 children with CF. Fecal calprotectin levels were measured and fecal microbiota was analyzed by 16S rRNA sequencing. We observed intestinal inflammation was associated with microbiota disturbances characterized mainly by increased abundances of , and , along with decreased abundances of , , and . Those changes exhibited similarities with that of Crohn's disease (CD), as evidenced by the elevated CD Microbial-Dysbiosis index that we applied for the first time in CF. Furthermore, the significant over-representation of in children with intestinal inflammation appears to be specific to CF and raises the issue of gut-lung axis involvement. Taken together, our results provide new arguments to link gut microbiota and intestinal inflammation in CF and suggest the key role of the gut-lung axis in the CF evolution.
PubMed: 31083321
DOI: 10.3390/jcm8050645 -
BJOG : An International Journal of... Jan 2020To evaluate the potential impact of intrapartum antibiotics, and their specific classes, on the infant gut microbiota in the first year of life.
OBJECTIVE
To evaluate the potential impact of intrapartum antibiotics, and their specific classes, on the infant gut microbiota in the first year of life.
DESIGN
Prospective study of infants in the New Hampshire Birth Cohort Study (NHBCS).
SETTINGS
Rural New Hampshire, USA.
POPULATION OR SAMPLE
Two hundred and sixty-six full-term infants from the NHBCS.
METHODS
Intrapartum antibiotic use during labour and delivery was abstracted from medical records. Faecal samples collected at 6 weeks and 1 year of age were characterised by 16S rRNA sequencing, and metagenomics analysis in a subset of samples.
EXPOSURES
Maternal exposure to antibiotics during labour and delivery.
MAIN OUTCOME MEASURE
Taxonomic and functional profiles of faecal samples.
RESULTS
Infant exposure to intrapartum antibiotics, particularly to two or more antibiotic classes, was independently associated with lower microbial diversity scores as well as a unique bacterial community at 6 weeks (GUnifrac, P = 0.02). At 1 year, infants in the penicillin-only group had significantly lower α diversity scores than infants not exposed to intrapartum antibiotics. Within the first year of life, intrapartum exposure to penicillins was related to a significantly lower increase in several taxa including Bacteroides, use of cephalosporins was associated with a significantly lower rise over time in Bifidobacterium and infants in the multi-class group experienced a significantly higher increase in Veillonella dispar.
CONCLUSIONS
Our findings suggest that intrapartum antibiotics alter the developmental trajectory of the infant gut microbiome, and specific antibiotic types may impact community composition, diversity and keystone immune training taxa.
TWEETABLE ABSTRACT
Class of intrapartum antibiotics administered during delivery relates to maturation of infant gut microbiota.
Topics: Antibiotic Prophylaxis; Bacteroides; Bacteroidetes; Bifidobacterium; Feces; Female; Gastrointestinal Microbiome; Humans; Infant, Newborn; Lactobacillus; Maternal Exposure; Mothers; Pregnancy; Prospective Studies; RNA, Ribosomal, 16S; Sequence Analysis, RNA; Term Birth; Vagina; beta-Lactamases
PubMed: 31006170
DOI: 10.1111/1471-0528.15799 -
Clinical Oral Investigations Nov 2019To identify the microbiome in sockets with alveolar osteitis and compare it with a control group using metagenomic techniques.
OBJECTIVE
To identify the microbiome in sockets with alveolar osteitis and compare it with a control group using metagenomic techniques.
MATERIALS AND METHODS
A case-control study was conducted in subjects that had undergone a tooth extraction. Microbiological samples were taken from the sockets of 10 patients with dry socket after tooth extraction (AO group) and 10 patients in whom exodontia resulted in no postoperative complications (control group). Bacterial DNA was isolated, and the 16S rRNA gene was amplified and sequenced. Multiplexed tag-encoded sequencing of DNA from the samples was performed, and the reads were processed by Metagenomic Rapid Annotation.
RESULTS
A total of 151 different species were found: 55 bacteria were only found in the AO group, 51 were specific to the control group, and 45 were common to both groups. The most frequently found genera in both groups were Prevotella. Prevotella nanceiensis, Actinomyces odontolyticus, Treponema maltophilum, Veillonella dispar, Tannerella forsythia, and Leuconostoc mesenteroides were found in several patients with alveolar osteitis, with an abundance greater than 0.5%, and were absent in all the control group samples.
CONCLUSIONS
Patients who develop alveolar osteitis after dental extractions might have a different microbiota from that of patients without postoperative complications. Since this is a preliminary report, further research is needed to assess whether bacteria play an important role in the etiology of dry socket.
CLINICAL RELEVANCE
This study seems to indicate that bacteria may play an important role in the alveolar osteitis etiology. Thus, new prevention and treatment strategies should be considered.
Topics: Bacteria; Case-Control Studies; Dry Socket; Female; Humans; Male; Metagenome; RNA, Ribosomal, 16S; Tooth Extraction
PubMed: 30937543
DOI: 10.1007/s00784-019-02855-7 -
Atherosclerosis May 2019Although most risk factors for cardiac valve calcification (VC) are similar to those for coronary artery disease (CAD), they differ regarding lesions and clinical... (Comparative Study)
Comparative Study
BACKGROUND AND AIMS
Although most risk factors for cardiac valve calcification (VC) are similar to those for coronary artery disease (CAD), they differ regarding lesions and clinical symptoms. Recently, increasing evidence suggests that intestinal bacteria play essential roles in cardiovascular disease (CVD). It is plausible that the gut microbiota is linked to the occurrence of different CVDs under similar risk factors. Thus, we aimed to explore the gut microbiomes in patients with VC or CAD and determine their underlying connections.
METHODS
We collected samples from 119 subjects and performed 16S rRNA gene sequencing to analyze the gut microbiomes in VC and CAD patients and in control volunteers.
RESULTS
The gut microbiomes of VC and CAD patients were significantly different in terms of beta-diversity. Bacteria from Veillonella dispar, Bacteroides plebeius and Fusobacterium were enriched in the VC group, while members of Collinsella aerofaciens, Megamonas, Enterococcus, Megasphaera, Dorea and Blautia were decreased. According to the association with dyslipidemia, seven operational taxonomic units (OTUs), including Parabacteroides distasonis, Megamonas, Fusobacterium, Bacteroides sp., Bacteroides plebeius, Lactobacillus and Prevotella copri, were regarded as potential pathogens for CVDs. Additionally, Prevotella copri might be a keystone of CVDs, especially in VC patients, while Collinsella aerofaciens is a possible keystone of CAD, based on the multi-correlations of these bacteria with other OTUs in microbial communities.
CONCLUSIONS
Patients with VC and CAD suffer from different gut microbial dysbiosis. The gut microbiomes are associated with the clinical characteristics in these diseases and might be potential therapeutic targets.
Topics: Adult; Aged; Calcinosis; Coronary Artery Disease; Dysbiosis; Female; Gastrointestinal Microbiome; Heart Valve Diseases; Humans; Male; Middle Aged
PubMed: 30897381
DOI: 10.1016/j.atherosclerosis.2018.11.038 -
International Journal of Obesity (2005) Jan 2020Mother-to-newborn transmission of obesity-associated microbiota may be modified by birth mode (vaginal vs. Cesarean delivery). Prospective data to test this hypothesis...
BACKGROUND
Mother-to-newborn transmission of obesity-associated microbiota may be modified by birth mode (vaginal vs. Cesarean delivery). Prospective data to test this hypothesis are still sparse.
OBJECTIVE
To examine prospective associations of maternal pre-pregnancy BMI and gestational weight gain with the infant gut microbiome by birth-mode strata.
SUBJECTS/METHODS
In 335 mother-infant pairs in the New Hampshire Birth Cohort, we ascertained data from questionnaires and medical records, and generated microbiome data from 6-week-old infants' stool using Illumina 16s rRNA gene sequencing (V4-V5 region). Analyses were stratified by birth mode and conducted before and after adjusting for potential confounders, which included maternal age, education, parity, and Mediterranean diet score.
RESULTS
Among 335 mothers, 56% had normal pre-pregnancy BMI ( < 25, referent), 27% were overweight (BMI 25-30), and 18% obese (BMI > 30). Among the 312 mothers with weight gain data, 10% had inadequate weight gain, 30% adequate (referent), and 60% excess. Birth mode modified associations of pre-pregnancy BMI with several genera, including the most abundant genus, Bacteroides (P for interaction = 0.05). In the vaginal-delivery group, maternal overweight or obesity was associated with higher infant gut microbiome diversity and higher relative abundance of 15 operational taxonomic units (OTUs), including overrepresentation of Bacteroides fragilis, Escherichia coli, Veillonella dispar, and OTUs in the genera Staphylococcus and Enterococcus. In the Cesarean-delivered group, there were no significant associations of pre-pregnancy BMI with infant microbiome (alpha) diversity or OTUs. Gestational weight gain was not associated with differential relative abundance of infant gut microbial OTUs or with measures of microbial diversity in infants delivered vaginally or by Cesarean section.
CONCLUSIONS
Among vaginally-delivered infants, maternal overweight and obesity was associated with altered infant gut microbiome composition and higher diversity. These associations were not observed in Cesarean-delivered infants, whose microbiome development differs from vaginally-delivered infants. Our study provides additional evidence of birth-mode dependent associations of maternal body weight status with the infant gut microbiota. The role of these associations in mediating the intergenerational cycle of obesity warrants further examination.
Topics: Adult; Bacteria; Body Mass Index; Body Weight; Delivery, Obstetric; Feces; Female; Gastrointestinal Microbiome; Gestational Weight Gain; Humans; Infant; Male; Pregnancy; Prospective Studies
PubMed: 30765892
DOI: 10.1038/s41366-018-0273-0 -
Digestive and Liver Disease : Official... May 2019Growing evidence supports the potential role of intestinal microbiota in the pathophysiology of inflammatory bowel diseases (IBD) even if the literature does not reveal...
BACKGROUND
Growing evidence supports the potential role of intestinal microbiota in the pathophysiology of inflammatory bowel diseases (IBD) even if the literature does not reveal uniform alterations. The aim of the study was to evaluate the mucosal (MM) and faecal microbiota (FM) composition in a cohort of IBD patients compared to healthy controls (CTRLs).
METHODS
Faecal and mucosal samples were collected from 14 IBD patients and 11 CTRLs. The V1-V3 region of 16S rRNA locus was amplified on a 454-Junior Genome Sequencer. Reads were grouped into operational taxonomic units (OTUs) at a sequence similarity level of 97% for taxonomic assignment, and aligned for OTUs matching against Greengenes database.
RESULTS
Irrespective of disease localization and activity, in the MM of IBD patients a statistically significant increase of Proteobacteria (especially Enterobacteriaceae, Acidaminococcus, Veillonella dispar) and decrease of Firmicutes (especially Roseburia and Faecalibacterium prausnitzii) and Actinobacteria was found compared to CTRLs. In the colon district some specific bacterial biomarkers were identified: Enterobacteriaceae for IBD stools, Bacteroides for IBD biopsies, Mogibacteriaceae, Ruminococcaceae and Prevotella for CTRL stools, Ruminococcaceae for CTRL biopsies.
CONCLUSIONS
The profiles of FM were more similar to CTRLs, suggesting that microbiota adhering to the gut mucosa better discriminates patients from controls, with the identification of some interesting biomarkers.
Topics: Bacteria; Case-Control Studies; Colon; Feces; Female; Gastrointestinal Microbiome; Humans; Inflammatory Bowel Diseases; Intestinal Mucosa; Male; Middle Aged; RNA, Ribosomal, 16S
PubMed: 30573380
DOI: 10.1016/j.dld.2018.11.021 -
Nitric Oxide : Biology and Chemistry Feb 2019There is conflicting evidence on whether dietary nitrate supplementation can improve exercise performance. This may arise from the complex nature of nitric oxide (NO)...
Variability in nitrate-reducing oral bacteria and nitric oxide metabolites in biological fluids following dietary nitrate administration: An assessment of the critical difference.
There is conflicting evidence on whether dietary nitrate supplementation can improve exercise performance. This may arise from the complex nature of nitric oxide (NO) metabolism which causes substantial inter-individual variability, within-person biological variation (CV), and analytical imprecision (CV) in experimental endpoints. However, no study has quantified the CV and CV of NO metabolites or the factors that influence their production. These data are important to calculate the critical difference (CD), defined as the smallest difference between sequential measurements required to signify a true change. The main aim of the study was to evaluate the CV, CV and CD for markers of NO availability (nitrate and nitrite) in plasma and saliva before and after the ingestion of nitrate-rich beetroot juice (BR). We also assessed the CV of nitrate-reducing bacteria from the dorsal surface of the tongue. It was hypothesised that there would be substantial CV in markers of NO availability and the abundance of nitrate-reducing bacteria. Ten healthy male participants (age 25 ± 5 years) completed three identical trials at least 6 days apart. Blood and saliva were collected before and after (2, 2.5 and 3 h) ingestion of 140 ml of BR (∼12.4 mmol nitrate) and analysed for [nitrate] and [nitrite]. The tongue was scraped and the abundance of nitrate-reducing bacterial species were analysed using 16S rRNA next generation sequencing. There was substantial CV for baseline concentrations of plasma (nitrate 11.9%, nitrite 9.0%) and salivary (nitrate 15.3%, nitrite 32.5%) NO markers. Following BR ingestion, the CV for nitrate (plasma 3.8%, saliva 12.0%) and salivary nitrite (24.5%) were lower than baseline, but higher for plasma nitrite (18.6%). The CD thresholds that need to be exceeded to ensure a meaningful change from baseline are 25, 19, 37, and 87% for plasma nitrate, plasma nitrite, salivary nitrate, and salivary nitrite, respectively. The CV for selected nitrate-reducing bacteria detected were: Prevotella melaninogenica (37%), Veillonella dispar (35%), Haemophilus parainfluenzae (79%), Neisseria subflava (70%), Veillonella parvula (43%), Rothia mucilaginosa (60%), and Rothia dentocariosa (132%). There is profound CV in the abundance of nitrate-reducing bacteria on the tongue and the concentration of NO markers in human saliva and plasma. Where these parameters are of interest following experimental intervention, the CD values presented in this study will allow researchers to interpret the meaningfulness of the magnitude of the change from baseline.
Topics: Administration, Oral; Adult; Anti-Bacterial Agents; Biomarkers; Fruit and Vegetable Juices; Haemophilus parainfluenzae; Healthy Volunteers; Humans; Male; Microbial Sensitivity Tests; Micrococcaceae; Neisseria; Nitrates; Nitric Oxide; Prevotella melaninogenica; Veillonella
PubMed: 30528912
DOI: 10.1016/j.niox.2018.12.003 -
Singapore Medical Journal Oct 2019The objectives of this study were to examine the effects of ethnicity, gender and a proton pump inhibitor (PPI), omeprazole, on the human gut microbiome. PPIs are... (Comparative Study)
Comparative Study
INTRODUCTION
The objectives of this study were to examine the effects of ethnicity, gender and a proton pump inhibitor (PPI), omeprazole, on the human gut microbiome. PPIs are commonly used for the treatment of acid-related disorders. We hypothesised that PPI therapy might perturb microbial communities and alter the gut microbiome.
METHODS
Healthy subjects of Chinese (n = 12), Malay (n = 12) and Indian (n = 10) ancestry, aged 21-37 years, were enrolled. They provided a baseline stool sample (Day 1) and were then given a course of omeprazole at therapeutic dose (20 mg daily) for seven days. Stool samples were collected again on Day 7 and 14 (one week after stopping omeprazole). Microbial DNA was extracted from the stool samples, followed by polymerase chain reaction, library construction, 16S rRNA sequencing using Illumina MiSeq, and statistical and bioinformatics analyses.
RESULTS
The findings showed an increase in species richness (p = 0.018) after omeprazole consumption on Day 7, which reverted to baseline on Day 14. There were significant increases in the relative abundance of Streptococcus vestibularis (p = 0.0001) and Veillonella dispar (p = 0.0001) on Day 7, which diminished on Day 14. Faecalibacterium prausnitzii, Sutterella stercoricanis and Bacteroides denticanum were characteristic of Chinese, Malays and Indians, respectively. Lactobacillaceae and Bacteroides xylanisolvens were the signature taxa of male and female subjects, respectively.
CONCLUSION
The study demonstrated alterations in the gut microbiome following omeprazole treatment. This may explain the underlying pathology of increased risk of Clostridium difficile infections associated with omeprazole therapy.
Topics: Adult; Bacillus; China; Ethnicity; Feces; Female; Gastrointestinal Microbiome; Humans; India; Malaysia; Male; Omeprazole; Proton Pump Inhibitors; Singapore; Young Adult
PubMed: 30488079
DOI: 10.11622/smedj.2018152