-
Open Forum Infectious Diseases Nov 2019Oral daily tenofovir (TFV) disoproxil fumarate/emtricitabine (TDF/FTC) for human immunodeficiency virus (HIV) pre-exposure prophylaxis (PrEP) is highly effective for...
BACKGROUND
Oral daily tenofovir (TFV) disoproxil fumarate/emtricitabine (TDF/FTC) for human immunodeficiency virus (HIV) pre-exposure prophylaxis (PrEP) is highly effective for HIVprevention, yet long-term effects are not fully understood. We investigated the effects of PrEP on the rectal microbiome in a cohort of men who have sex with men (MSM).
METHODS
This cross-sectional analysis included HIV-negative MSM either on PrEP (n = 37) or not (n = 37) selected from an ongoing cohort using propensity score matching. Rectal swabs were used to examine microbiome composition using 16S ribosomal ribonucleic acid gene sequencing, and associations between PrEP use and microbiota abundance were examined. Hair specimens were used to quantify TFV and FTC exposure over the past 6 weeks on a subset of participants (n = 15).
RESULTS
Pre-exposure prophylaxis use was associated with a significant increase in abundance (adjusted = .015). Similar associations were identified using least absolute shrinkage and selection operator (LASSO) regression, confirming the increase in and also showing increased , , and decreased . Increased was significantly associated with increasing TFV exposure.
CONCLUSIONS
Oral TDF/FTC for PrEP is associated with rectal microbiome changes compared to well matched controls, specifically increased and abundance. This study highlights the need for future investigations of the role of microbiome changes on HIV susceptibility and effectiveness of PrEP.
PubMed: 32258202
DOI: 10.1093/ofid/ofz463 -
Journal of Microbiological Methods Dec 2019The study aimed to adapt the SHIME® model, developed to simulate human digestion and fermentation, to a baby-SPIME (baby Simulator of Pig Intestinal Microbial...
The study aimed to adapt the SHIME® model, developed to simulate human digestion and fermentation, to a baby-SPIME (baby Simulator of Pig Intestinal Microbial Ecosystem). What constitutes a unique feature of this model is its twofold objective of introducing an ileal microbial community and mimicking a dietary weaning transition. This model should then be ideally suited to test the dietary weaning strategies of piglets in vitro. Regarding the microbiota, the main phyla making up the model were Firmicutes, Bacteroidetes and Proteobacteria although Bacteroidetes decreased after inoculation (p = 0.043 in ileum, p = 0.021 in colon) and Delta-Proteobacteria were favoured (p = 0.083 in ileum, p = 0.043 in colon) compared to Gamma-Proteobacteria. The designed model led to a low representation of Bacilli - especially Lactobacillus sp. in the ileum and a weak representation of Bacteroidia in the proximal colon. However, Mitsuokella and Prevotella were part of the major genera of the model along with Bifidobacterium, Fusobacterium, Megasphaera and Bacteroides. As a result of weaning, two major changes - normally occurring in vivo - were detected in the system: firstly, Firmicutes diminished when Bacteroidetes increased particularly in the proximal colon; secondly, Bacteroides decreased and Prevotella increased (mean value for four runs). In terms of metabolite production, while a ratio acetate: propionate: butyrate of 60:26:14 was obtained in post-weaned colon, the expected inversion of the ratio propionate: butyrate in the post-weaned ileum was unfortunately not observed. To conclude, the so-called baby-SPIME model meets expectations regarding the resident microbiota of the proximal colon bioreactor and the metabolites produced thereof. In terms of the evolution of major groups of bacteria, the in vitro weaning process appeared to be successful. However, higher concentration of butyric acid would have been expected in ileum part of newly weaned piglets, as observed in vivo. The microbiota in the ileum bioreactor seemed in fact to act like a pre-colon. This suggests that microbial profile in ileum bioreactor had to be improved.
Topics: Animals; Bacteria; Bioreactors; Colon; Culture Media; Fermentation; Gastrointestinal Microbiome; Genetic Variation; Ileum; In Vitro Techniques; Propionates; Swine; Weaning
PubMed: 31669849
DOI: 10.1016/j.mimet.2019.105735 -
Animal Bioscience Feb 2022The aim of this study was to investigate the effects of dietary supplementation with a multi-strain probiotic (MSP) product containing of Bifidobacterium animalis,...
OBJECTIVE
The aim of this study was to investigate the effects of dietary supplementation with a multi-strain probiotic (MSP) product containing of Bifidobacterium animalis, Lactobacillus casei, Streptococcus faecalis, and Bacillus cerevisiae on growth, health, and fecal bacterial composition of dairy calves during the first month of life.
METHODS
Forty Holstein calves (24 female and 16 male) at 2 d of age were grouped by sex and date of birth then randomly assigned to 1 of 4 treatments: milk replacer supplementation with 0 g (0MSP), 2 g (2MSP), 4 g (4MSP), and 6 g (6MSP) MSP per calf per day.
RESULTS
Supplementation of MSP did not result in any significant differences in parameters of body measurements of calves during the 30 d period. As the dosage of MSP increased, the average daily gain (p = 0.025) and total dry matter intake (p = 0.020) of calves showed a linear increase. The fecal consistency index of the 2MSP, 4MSP, and 6MSP group calves were lower than that of the 0MSP group calves (p = 0.003). As the dosage of MSP increased, the concentrations of lactate dehydrogenase (p = 0.068) and aspartate aminotransferase (p = 0.081) in serum tended to decrease, whereas the concentration of total cholesterol increased quadratically (p = 0.021). The relative abundance of Dorea in feces was lower (p = 0.011) in the 2MSP, 4MSP, and 6MSP group calves than that in the 0MSP group calves. The relative abundance of Dorea (p = 0.001), Faecalibacterium (p = 0.050), and Mitsuokella (p = 0.030) decreased linearly, whereas the relative abundance of Prevotella tended to increase linearly as the dosage of MSP increased (p = 0.058).
CONCLUSION
The MSP product can be used to reduce the diarrhea, improve the performance, and alter the composition of the fecal bacteria in neonatal dairy calves under the commercial conditions.
PubMed: 34445849
DOI: 10.5713/ab.21.0084 -
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 Jun 2019The development of the rumen is an important physiological challenge for young ruminants. Previous studies have shown that starter feeding can effectively facilitate the...
BACKGROUND
The development of the rumen is an important physiological challenge for young ruminants. Previous studies have shown that starter feeding can effectively facilitate the growth and development of the rumen in ruminants. However, the mechanism through which starter feeding stimulates the development of the rumen is not clear. Here, we performed an integrated analysis in ruminal microbiota and a host transcriptomic profile in a lamb model with the intervention of starter feed to understand the ruminal microbiome-host crosstalk in stimulating the development of the ruminal epithelium.
RESULTS
Decreased ruminal pH and increased acetate and butyrate concentrations in the rumen, followed by increasing rumen organ index, were observed in lambs supplemented with starter. Using metagenome sequencing in combination with 16S rRNA and 18S rRNA gene amplicon sequencing, the results showed the abundance of acetate-producing Mitsuokella spp., lactate-producing Sharpea spp., lactate-utilizing Megasphaera spp., and Entodinium spp. was enriched in rumen microbial communities in the starter-feed group. The abundances of genes involved in sugar degradation were decreased in starter-feed lambs, but the GH13 encoding α-amylase was obviously increased. Rumen epithelial transcriptome analysis revealed that seven differentially expressed genes, including MAPK1, PIK3CB, TNFSF10, ITGA6, SNAI2, SAV1, and DLG, related to the cell growth module were upregulated, and BAD's promotion of cell death was downregulated. Correlation analysis revealed that the increase in the concentrations of acetate and butyrate significantly correlated with the expression of these genes, which indicates acetate and butyrate likely acted as important drivers in the ruminal microbiome-host crosstalk.
CONCLUSIONS
The present study comprehensively describes the symbiotic relationship between the rumen microbiota and the host in lambs after starter feeding. Our data demonstrates that the microbiome-driven generation of acetate and butyrate mediated the growth-related genes' regulation of the growth-associated signalling pathway in the ruminal epithelium. These co-development networks regulated many physiological processes in the epithelium, including papillae morphology and rumen epithelial growth.
Topics: Acetates; Animal Feed; Animals; Bacteria; Butyrates; Epithelium; Host Microbial Interactions; Hydrogen-Ion Concentration; Metagenome; Microbiota; RNA, Ribosomal, 16S; Rumen; Sheep; Signal Transduction; Transcriptome
PubMed: 31159860
DOI: 10.1186/s40168-019-0701-y -
Frontiers in Microbiology 2015Lactobacillus reuteri is used as probiotic culture in food and feed applications; however, strain specific properties of L. reuteri that mediate probiotic activity...
Lactobacillus reuteri is used as probiotic culture in food and feed applications; however, strain specific properties of L. reuteri that mediate probiotic activity remain unknown. This study aimed to determine effects of feed fermentation with exopolysaccharide and reutericyclin producing L. reuteri on the transition of the gut microbiome of piglets after weaning. The reutericyclin and reuteran producing L. reuteri TMW1.656 was compared to the reutericyclin negative and levan producing L. reuteri LTH5794 and unfermented controls. Both strains were fermented at conditions supporting exopolysaccharide formation, or at conditions not supporting exopolysaccharide formation. Fecal microbiota were characterized by partial sequencing of 16S rRNA genes, and by quantitative PCR targeting clostridial toxins. The transition to solid food resulted in a transient increase of Proteobacteria to 12% of total bacteria, and increased bacterial diversity by increasing the abundance of anaerobic fiber fermenting Firmicutes. Three weeks after weaning, Prevotella and Lactobacillus were among the dominant bacterial genera. Feed fermentation with L. reuteri affected the abundance of few bacterial taxa and particularly reduced the abundance of Enterobacteriaceae (P < 0.05) when compared to unfermented controls. Reutericyclin producing L. reuteri increased the abundance of Dialister spp. and Mitsuokella spp. (P < 0.05) but did not influence the abundance of clostridial toxins in the feces. In conclusion, data on the contribution of specific metabolic activities of L. reuteri to probiotic activity will facilitate the strain selection for probiotic applications in food and feed.
PubMed: 26284047
DOI: 10.3389/fmicb.2015.00762 -
PloS One 2018Since microbiota may influence the physiology of its host including body weight increase, growth rate or feed intake, in this study we determined the microbiota... (Comparative Study)
Comparative Study
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.
Topics: Age Factors; Animals; Diet; Eating; Environment; Feces; Gastrointestinal Microbiome; RNA, Bacterial; RNA, Ribosomal, 16S; Species Specificity; Stress, Physiological; Sus scrofa; Weaning
PubMed: 30086169
DOI: 10.1371/journal.pone.0201901 -
Antonie Van Leeuwenhoek Sep 2018The goal of this study was to evaluate the microbial communities in the gut and feces from female finishing Landrace pigs with high and low feed conversion ratio (FCR)... (Comparative Study)
Comparative Study
The goal of this study was to evaluate the microbial communities in the gut and feces from female finishing Landrace pigs with high and low feed conversion ratio (FCR) by 16S rRNA gene amplicon sequencing. Many potential biomarkers can distinguish between high and low FCR groups in the duodenum, ileum, cecum, colon, and rectum, according to linear discriminant analysis effect sizes. The relative abundance of microbes were tested by Mann-Whitney test between the high and low FCR groups in different organs: Campylobacter, Prevotella and Sphaerochaeta were different in the duodenum (P < 0.05); Sanguibacter, Kingella and Anaeroplasma in jejunum; Anaeroplasma, Arthrobacter, Kingella, Megasphaera and SMB53 in the ileum; Butyricicoccus, Campylobacter, Mitsuokella, and Coprobacillus in the cecum; Lactococcus and Peptococcus in the colon; Staphylococcus in the rectum; and Rothia in feces. The prevalence of microbial genera in certain locations could potentially be used as biomarkers to distinguish between high and low FCR. Functional prediction clustering analysis suggested that bacteria in the hindgut mainly participated in carbohydrate metabolism and amino acid metabolism, and different in the relative abundance of metabolic pathways, as predicted from the microbial taxa present, were identified by comparing the high and low groups of each location. The results may provide insights for the alteration of the intestinal microbial communities to improve the growth rate of pigs.
Topics: Amino Acids; Animal Feed; Animals; Bacteria; Biodiversity; Carbohydrate Metabolism; Cecum; Colon; DNA, Bacterial; Discriminant Analysis; Feces; Female; Gastrointestinal Microbiome; Intestine, Small; Metabolic Networks and Pathways; Metagenomics; RNA, Ribosomal, 16S; Swine
PubMed: 29497869
DOI: 10.1007/s10482-018-1057-1 -
Current Research in Microbial Sciences 2024Spontaneous fermentation of flour enhances the nutritional potential of this hybrid cereal. However, the effect of consumption of sourdough bread (SDB) on gut health...
Spontaneous fermentation of flour enhances the nutritional potential of this hybrid cereal. However, the effect of consumption of sourdough bread (SDB) on gut health remains to be elucidated. This study investigated the effect of digestion and faecal fermentation of SDB compared to that of traditional baker's yeast (BYB) bread. After 24-h anaerobic faecal fermentation, both SDB and BYB (1% w/v) induced an increase in the relative abundances of , and genera compared to baseline, while concentrations of acetate and butyrate were significantly higher at 24 h for SDB compared to those for BYB. Integrity of intestinal epithelium, as assessed through trans-epithelial electrical resistance (TEER) assay, was slightly increased after incubation with SDB fermentation supernatants, but not after incubation with BYB fermentation supernatants. The SDB stimulated mucosal immune response by inducing early secretion of inflammatory cytokines, IL-6 and TNF-α, followed by downregulation of the inflammatory trigger through induction of anti-inflammatory IL-10 expression. Overall, our findings suggest that sourdough can modulate gut microbiota fermentation activity and positively impact the gut health.
PubMed: 38116184
DOI: 10.1016/j.crmicr.2023.100214 -
Food Research International (Ottawa,... Nov 2023Beer is a source of bioactive compounds, mainly polyphenols, which can reach the large intestine and interact with colonic microbiota. However, the effects of beer...
Beer is a source of bioactive compounds, mainly polyphenols, which can reach the large intestine and interact with colonic microbiota. However, the effects of beer consumption in the gastrointestinal function have scarcely been studied. This paper reports, for the first time, the in vitro digestion of beer and its impact on intestinal microbiota metabolism. Three commercial beers of different styles were subjected to gastrointestinal digestion using the simgi® model, and the digested fluids were further fermented in triplicate with faecal microbiota from a healthy volunteer. The effect of digested beer on human gut microbiota was evaluated in terms of microbial metabolism (short-chain fatty acids (SCFAs) and ammonium ion), microbial diversity and bacterial populations (plate counting and 16S rRNA gene sequencing). Monitoring beer polyphenols through the different digestion phases showed their extensive metabolism, mainly at the colonic stage. In addition, a higher abundance of taxa related to gut health, especially Bacteroides, Bifidobacterium, Mitsuokella and Succinilasticum at the genus level, and the Ruminococcaceae and Prevotellaceae families were found in the presence of beers. Regarding microbial metabolism, beer feeding significantly increased microbial SCFA production (mainly butyric acid) and decreased ammonium content. Overall, these results evidence the positive actions of moderate beer consumption on the metabolic activity of colonic microbiota, suggesting that the raw materials and brewing methods used may affect the beer gut effects.
Topics: Humans; Gastrointestinal Microbiome; Beer; RNA, Ribosomal, 16S; Digestion; Polyphenols; Ammonium Compounds
PubMed: 37803545
DOI: 10.1016/j.foodres.2023.113228