-
Scientific Reports Mar 2021In the present study, we characterized the distinctive signatures of the gut microbiota (GM) from overweight/obese patients (OB), and normal-weight controls (NW), both...
In the present study, we characterized the distinctive signatures of the gut microbiota (GM) from overweight/obese patients (OB), and normal-weight controls (NW), both of Sardinian origin. Fecal bacterial composition of 46 OB patients (BMI = 36.6 ± 6.0; F/M = 40/6) was analyzed and compared to that of 46 NW subjects (BMI = 21.6 ± 2.1; F/M = 41/5), matched for sex, age and smoking status, by using 16S rRNA gene sequencing on MiSeq Illumina platform. The gut microbial community of OB patients exhibited a significant decrease in the relative abundance of several Bacteroidetes taxa (i.e. Flavobacteriaceae, Porphyromonadaceae, Sphingobacteriaceae, Flavobacterium, Rikenella spp., Pedobacter spp., Parabacteroides spp., Bacteroides spp.) when compared to NW; instead, several Firmicutes taxa were significantly increased in the same subjects (Lachnospiraceae, Gemellaceae, Paenibacillaceae, Streptococcaceae, Thermicanaceae, Gemella, Mitsuokella, Streptococcus, Acidaminococcus spp., Eubacterium spp., Ruminococcus spp., Megamonas spp., Streptococcus, Thermicanus, Megasphaera spp. and Veillonella spp.). Correlation analysis indicated that body fatness and waist circumference negatively correlated with Bacteroidetes taxa, while Firmicutes taxa positively correlated with body fat and negatively with muscle mass and/or physical activity level. Furthermore, the relative abundance of several bacterial taxa belonging to Enterobacteriaceae family, known to exhibit endotoxic activity, was increased in the OB group compared to NW. The results extend our knowledge on the GM profiles in Italian OB, identifying novel taxa linking obesity and intestine.
Topics: Adult; Bacteria; Female; Gastrointestinal Microbiome; Humans; Italy; Male; Middle Aged; Obesity; RNA, Bacterial; RNA, Ribosomal, 16S
PubMed: 33750881
DOI: 10.1038/s41598-021-84928-w -
Genome Medicine Mar 2021Recent studies have indicated an association of gut microbiota and microbial metabolites with type 2 diabetes mellitus (T2D). However, large-scale investigation of the...
BACKGROUND
Recent studies have indicated an association of gut microbiota and microbial metabolites with type 2 diabetes mellitus (T2D). However, large-scale investigation of the gut microbiota of "prediabetic" (PD) subjects has not been reported. Identifying robust gut microbiome signatures of prediabetes and characterizing early prediabetic stages is important for the understanding of disease development and could be crucial in early diagnosis and prevention.
METHODS
The current study performed amplification and sequencing on the variable regions (V1-V5) of the 16S rRNA genes to profile and compare gut microbiota of prediabetic individuals (N = 262) with normoglycemic individuals (N = 275) from two cohorts in India and Denmark. Similarly, fasting serum inflammatory biomarkers were profiled from the study participants.
RESULTS
After correcting for strong country-specific cohort effect, 16 operational taxonomic units (OTUs) including members from the genera Prevotella9, Phascolarctobacterium, Barnesiella, Flavonifractor, Tyzzerella_4, Bacteroides, Faecalibacterium, and Agathobacter were identified as enriched in normoglycaemic subjects with respect to the subjects with prediabetes using a negative binomial Wald test. We also identified 144 OTUs enriched in the prediabetic subjects, which included members from the genera Megasphaera, Streptococcus, Prevotella9, Alistipes, Mitsuokella, Escherichia/Shigella, Prevotella2, Vibrio, Lactobacillus, Alloprevotella, Rhodococcus, and Klebsiella. Comparative analyses of relative abundance of bacterial taxa revealed that the Streptococcus, Escherichia/Shigella, Prevotella2, Vibrio, and Alloprevotella OTUs exhibited more than fourfold enrichment in the gut microbiota of prediabetic subjects. When considering subjects from the two geographies separately, we were able to identify additional gut microbiome signatures of prediabetes. The study reports a probable association of Megasphaera OTU(s) with impaired glucose tolerance, which is significantly pronounced in Indian subjects. While the overall results confirm a state of proinflammation as early as in prediabetes, the Indian cohort exhibited a characteristic pattern of abundance of inflammatory markers indicating low-grade intestinal inflammation at an overall population level, irrespective of glycemic status.
CONCLUSIONS
The results present trans-ethnic gut microbiome and inflammation signatures associated with prediabetes, in Indian and Danish populations. The identified associations may be explored further as potential early indicators for individuals at risk of dysglycemia.
Topics: Adult; Aged; Algorithms; Biomarkers; Cohort Studies; Denmark; Ethnicity; Female; Gastrointestinal Microbiome; Genetic Predisposition to Disease; Humans; India; Inflammation; Male; Middle Aged; Phenotype; Phylogeny; Prediabetic State
PubMed: 33658065
DOI: 10.1186/s13073-021-00851-9 -
Animal Microbiome Sep 2020Little is known about maturation of calves' gut microbiome in veal farms, in which animals are confined under intensive-farming conditions and the administration of...
BACKGROUND
Little is known about maturation of calves' gut microbiome in veal farms, in which animals are confined under intensive-farming conditions and the administration of collective antibiotic treatment in feed is common. We conducted a field study on 45 calves starting seven days after their arrival in three veal farms. We collected monthly fecal samples over six months and performed 16S rRNA gene sequencing and quantitative PCR of Escherichia coli to follow the dynamics of their microbiota, including that of their commensal E. coli populations. We used mixed-effect models to characterize the dynamics of α-diversity indices and numbers of E. coli, and searched for an effect of collective antibiotic treatments on the estimated parameters. On two farms, we also searched for associations between recommended daily doses of milk powder and bacterial abundance.
RESULTS
There was high heterogeneity between calves' microbiota upon their arrival at the farms, followed by an increase in similarity, starting at the first month. From the second month, 16 genera were detected at each sampling in all calves, representing 67.5% (± 9.9) of their microbiota. Shannon diversity index showed a two-phase increase, an inflection occurring at the end of the first month. Calves receiving antibiotics had a lower intercept estimate for Shannon index (- 0.17 CI[-0.27; - -0.06], p = 0.003) and a smaller number of E. coli/ gram of feces during the treatment and in the 15 days following it (- 0.37 log (E. coli/g) CI[- 0.66; - 0.08], p = 0.01) than unexposed calves. There were moderate to strong positive associations between the dose of milk powder and the relative abundances of the genera Megasphaera, Enterococcus, Dialister and Mitsuokella, and the number of E. coli (r ≥ 0.40; Bonferroni corrected p < 0.05).
CONCLUSIONS
This observational study shows early convergence of the developing microbiota between veal calves and associations between the dose of milk powder and members of their microbiota. It suggests that administration of collective antibiotic treatment results in a reduction of microbial diversity and size of the E. coli population and highlights the need for additional work to fully understand the impact of antibiotic treatment in the veal industry.
PubMed: 33499974
DOI: 10.1186/s42523-020-00052-6 -
Animal Microbiome May 2020Dietary yeast inclusions in a pig diet may drive changes both in gut bacterial composition and bacterial functional profile. This study investigated the effect of...
BACKGROUND
Dietary yeast inclusions in a pig diet may drive changes both in gut bacterial composition and bacterial functional profile. This study investigated the effect of Cyberlindnera jadinii as a protein to replace 40% of the conventional proteins in a diet for weanling pigs on the microbiota in the small and large intestine, colonic short-chain fatty acid concentration, and colonic histopathology parameters. Seventy-two pigs weaned at 28 days of age were randomly assigned to either a control or a C. jadinii-based diet and followed for 2 weeks.
RESULTS
Compared with the controls, higher numbers of cultivable lactic acid-producing bacteria in the small and large intestine were registered in the yeast group. Alpha and beta bacterial diversity were different between the diet groups with lower alpha-diversity and distinct bacterial composition in the large intestine in the yeast group compared with those of the controls. The large intestine microbiota in the yeast group had higher numbers of Prevotella, Mitsuokella and Selenomonas compared with those of the controls. The concentrations of colonic acetate and butyrate were higher in the controls compared with that of the yeast group. The colonic crypt depth was deeper in the control group. The gut histopathology of colonic tissues revealed no differences between the diets. The colonic crypt depth tended to be deeper with higher relative abundance of an unclassified Spirochetes, higher colonic butyrate concentration, and higher bacterial richness. The concentration of colonic butyrate was positively associated with the relative abundance of the Faecalibacterium prausnitzii, Dialister, and an unclassified amplicon of the Spirochaetaceae family in the colon.
CONCLUSIONS
The replacement of the conventional proteins by proteins from Cyberlindnera jadinii in a weanling pig diet reshaped the large intestine microbiota structure. The novel yeast diet appeared to be selective for Lactobacillus spp., which may represent an added value resulting from using the sustainably produced yeast protein ingredient as an alternative to conventional protein ingredients in animal diets. The large intestine bacterial composition and their metabolites may be involved in an adaptive alteration of the colonic crypts without pathological consequences.
PubMed: 33499966
DOI: 10.1186/s42523-020-00031-x -
Gut Microbes 2021The fermentation of dietary fibre (DF) leads to the production of bioactive metabolites, the most volatile ones being excreted in the breath. The aim of this study was...
The fermentation of dietary fibre (DF) leads to the production of bioactive metabolites, the most volatile ones being excreted in the breath. The aim of this study was to analyze the profile of exhaled breath volatile metabolites (BVM) and gastrointestinal symptoms in healthy volunteers after a single ingestion of maltodextrin (placebo) versus chitin-glucan (CG), an insoluble DF previously shown to be fermented into short-chain fatty acids (SCFA) by the human microbiota in vitro. Maltodextrin (4.5 g at day 0) or CG (4.5 g at day 2) were added to a standardized breakfast in fasting healthy volunteers (n = 15). BVM were measured using selected ion flow tube mass spectrometry (SIFT-MS) throughout the day. A single ingestion of 4.5 g CG did not induce significant gastrointestinal discomfort. Untargeted metabolomics analysis of breath highlighted that 13 MS-fragments (among 408 obtained from ionizations of breath) discriminated CG versus maltodextrin acute intake in the posprandial state. The targeted analysis revealed that CG increased exhaled butyrate and 5 other BVM - including the microbial metabolites 2,3-butanedione and 3-hydroxybutanone - with a peak observed 6 h after CG intake. Correlation analyses with fecal microbiota (Illumina 16S rRNA sequencing) spotlighted as a potential genus responsible for the presence of butyric acid, triethylamine and 3-hydroxybutanone in the breath. In conclusion, measuring BMV in the breath reveals the microbial signature of the fermentation of DF after a single ingestion. This protocol allows to analyze the time-course of released bioactive metabolites that could be proposed as new biomarkers of DF fermentation, potentially linked to their biological properties. Trial registration: Clinical Trials NCT03494491. Registered 11 April 2018 - Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT03494491.
Topics: Breath Tests; Chitin; Dietary Fiber; Fatty Acids, Volatile; Feces; Fermentation; Gastrointestinal Microbiome; Glucans; Healthy Volunteers; Humans; Polysaccharides; RNA, Ribosomal, 16S; Respiratory Aerosols and Droplets; Young Adult
PubMed: 33461385
DOI: 10.1080/19490976.2020.1862028 -
Scientific Reports Nov 2020Medicated feed is a common strategy to control the occurrence of Streptococcus suis disease in swine production, but feed additives may constitute an alternative to...
Medicated feed is a common strategy to control the occurrence of Streptococcus suis disease in swine production, but feed additives may constitute an alternative to metaphylaxis. In a farm with post-weaning S. suis disease, the following additives were tested: lysozyme (Lys), medium chain fatty acids plus lysozyme (FA + Lys), FA plus a natural anti-inflammatory (FA + antiinf) and amoxicillin (Amox). During the course of the study, FA + antiinf and Amox groups showed lower prevalence of clinical signs compatible with S. suis disease than the rest of the groups. Piglets from the FA + antiinf group showed high diversity and richness in their nasal and faecal microbiota. Diet supplements did not have major effects on the faecal microbiota, where the genus Mitsuokella was the only differentially present in the FA + Lys group. In the nasal microbiota, piglets from FA + antiinf presented higher differential abundance of a sequence variant from Ruminococcaceae and lower abundance of an unclassified genus from Weeksellaceae. In general, we detected more significant changes in the nasal than in the feacal microbiota, and found that parity of the dams affected the microbiota composition of their offspring, with piglets born to gilts exhibiting lower richness and diversity. Our results suggest that additives could be useful to control post-weaning disease when removing antimicrobials in farms.
Topics: Agriculture; Amoxicillin; Animal Feed; Animals; Anti-Infective Agents; DNA, Bacterial; Dietary Supplements; Fatty Acids; Feces; Female; Food Additives; Microbiota; Muramidase; Nasal Mucosa; Parity; Polymerase Chain Reaction; Pregnancy; Streptococcal Infections; Streptococcus suis; Swine; Treatment Outcome; Weaning
PubMed: 33230191
DOI: 10.1038/s41598-020-77313-6 -
Journal of Oral Microbiology Oct 2020A once-annual caries preventive (Intervention) treatment was offered to Aboriginal and Torres Strait Islander schoolchildren-a population with disproportionately poorer...
A once-annual caries preventive (Intervention) treatment was offered to Aboriginal and Torres Strait Islander schoolchildren-a population with disproportionately poorer oral health than non-Indigenous Australian children-in the Northern Peninsula Area (NPA) of Far North Queensland (FNQ), which significantly improved their oral health. Here, we examine the salivary microbiota of these children (mean age = 10 ± 2.96 years; n = 103), reconstructing the bacterial community composition with high-throughput sequencing of the V4 region of bacterial gene. Microbial communities of children who received the Intervention had lower taxonomic diversity than those who did not receive treatment (Shannon, p < 0.05). Moreover, the Intervention resulted in further decreased microbial diversity in children with active carious lesions existing at the time of saliva collection. Microbial species associated with caries were detected; , and HMT 131 were significantly increased (p < 0.05) in children with severe caries, especially in children who did not receive the Intervention. These insights into microbial associations and community differences prompt future considerations to the mechanisms behind caries-preventive therapy induced change; important for understanding the long-term implications of like treatment to improve oral health disparities within Australia. , .
PubMed: 33149844
DOI: 10.1080/20002297.2020.1830623 -
Infectious Diseases and Therapy Mar 2021This study aimed to analyze the diversity of intestinal flora in patients with chronic hepatitis B (CHB) and investigate the effect of entecavir on the intestinal flora...
INTRODUCTION
This study aimed to analyze the diversity of intestinal flora in patients with chronic hepatitis B (CHB) and investigate the effect of entecavir on the intestinal flora in these patients.
METHODS
Thirty patients with CHB and 30 healthy controls were recruited from the Department of Infectious Diseases and Department of Gastroenterology of Shanghai Tongji Hospital between January 2017 and December 2018. Stool samples were collected for the detection of intestinal flora by high-throughput sequencing. Patients with CHB received antivirus therapy with entecavir for 8 weeks. The biochemical and virological responses were assessed and the intestinal flora were compared.
RESULTS
After entecavir treatment, the blood levels of alanine aminotransferase (ALT), interleukin-6 (IL-6), IL-8, tumor necrosis factor (TNF), and hepatitis B virus (HBV) DNA reduced significantly in patients with CHB and the species abundance of intestinal flora increased markedly. In patients with CHB, the unique genera included Butyrivibrio, Phaseolus acutifolius, and Prevotellaceae NK3B31 group before treatment and Howardella, Candidatus Stoquefichus, Citrobacter, Dysgonomonas, Faecalicoccus, Methanobrevibacter, Mitsuokella, Mobilitalea, Succinivibrio, Gluconobacter, and Plesiomonas after treatment. The abundance of the following genera increased significantly after entecavir treatment in patients with CHB: Clostridium sensu stricto 1, Erysipelotrichaceae UCG-007, and Intestinibacter. The abundance of Streptococcus, Atopobium, and Murdochiella reduced markedly after entecavir treatment in patients with CHB.
CONCLUSION
After 8-week entecavir treatment, the blood biochemical, immunological, and virological responses improved significantly, the species abundance of intestinal flora increased markedly, and there were unique genera in patients with CHB before and after treatment.
PubMed: 33111216
DOI: 10.1007/s40121-020-00355-w -
Microbiome Oct 2020Interest in the interplay between host genetics and the gut microbiome in complex human diseases is increasing, with prior evidence mainly being derived from animal...
BACKGROUND
Interest in the interplay between host genetics and the gut microbiome in complex human diseases is increasing, with prior evidence mainly being derived from animal models. In addition, the shared and distinct microbiome features among complex human diseases remain largely unclear.
RESULTS
This analysis was based on a Chinese population with 1475 participants. We estimated the SNP-based heritability, which suggested that Desulfovibrionaceae and Odoribacter had significant heritability estimates (0.456 and 0.476, respectively). We performed a microbiome genome-wide association study to identify host genetic variants associated with the gut microbiome. We then conducted bidirectional Mendelian randomization analyses to examine the potential causal associations between the gut microbiome and complex human diseases. We found that Saccharibacteria could potentially decrease the concentration of serum creatinine and increase the estimated glomerular filtration rate. On the other hand, atrial fibrillation, chronic kidney disease and prostate cancer, as predicted by host genetics, had potential causal effects on the abundance of some specific gut microbiota. For example, atrial fibrillation increased the abundance of Burkholderiales and Alcaligenaceae and decreased the abundance of Lachnobacterium, Bacteroides coprophilus, Barnesiellaceae, an undefined genus in the family Veillonellaceae and Mitsuokella. Further disease-microbiome feature analysis suggested that systemic lupus erythematosus and chronic myeloid leukaemia shared common gut microbiome features.
CONCLUSIONS
These results suggest that different complex human diseases share common and distinct gut microbiome features, which may help reshape our understanding of disease aetiology in humans. Video Abstract.
Topics: Adult; Aged; Animals; Case-Control Studies; Disease; Female; Gastrointestinal Microbiome; Genome-Wide Association Study; Humans; Leukemia, Myelogenous, Chronic, BCR-ABL Positive; Lupus Erythematosus, Systemic; Male; Middle Aged
PubMed: 33032658
DOI: 10.1186/s40168-020-00923-9 -
Animals : An Open Access Journal From... Sep 2020Coconut oil has a high content of lauric acid, which has selective antibacterial activity. This study aimed to explore the effect of coconut oil ingestion on the...
Coconut oil has a high content of lauric acid, which has selective antibacterial activity. This study aimed to explore the effect of coconut oil ingestion on the gastrointestinal microbiomes of pigs. A 14-day-long feeding experiment included 19 pigs in two groups (9 on a normal diet and 10 on a diet supplemented with coconut oil). At the start and end of the experiment, a rectal swab sample was taken from each pig in both groups, and total bacterial DNA was extracted. We used 16S RNA high-throughput amplicon sequencing to evaluate the microbiome changes during the feeding experiment. A total of 446 operational taxonomic units (OTUs) were detected in the whole sample set. Shannon's indices of bacterial diversity did not change significantly during the experiment. Changes in the bacterial community during the study period and in response to the coconut oil treatment were highly significant ( < 0.001). During the study, an increase in the abundance of was detected in the group treated with coconut oil. An increase in , and and a decrease in , , and were attributed to the coconut oil treatment. Although the addition of coconut oil to pig feed did not affect Shannon's index of diversity, it had a positive effect on the abundance of bacterial groups that are considered to be commensal and/or probiotic.
PubMed: 33003372
DOI: 10.3390/ani10101764