scholarly journals Human Gut Microbiome Response Induced by Fermented Dairy Product Intake in Healthy Volunteers

Nutrients ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 547 ◽  
Author(s):  
Olesya Volokh ◽  
Natalia Klimenko ◽  
Yulia Berezhnaya ◽  
Alexander Tyakht ◽  
Polina Nesterova ◽  
...  

Accumulated data suggests that the gut microbiome can rapidly respond to changes in diet. Consumption of fermented dairy products (FDP) fortified with probiotic microbes may be associated with positive impact on human health. However, the extent and details of the possible impact of FDP consumption on gut community structure tends to vary across individuals. We used microbiome analysis to characterize changes in gut microbiota composition after 30 days of oral intake of a yoghurt fortified with Bifidobacterium animalis subsp. lactis BB-12. 16S rRNA gene sequencing was used to assess the gut microbial composition before and after FDP consumption in healthy adults (n = 150). Paired comparison of gut microbial content demonstrated an increase in presence of potentially beneficial bacteria, particularly, Bifidobacterium genus, as well as Adlercreutzia equolifaciens and Slackia isoflavoniconvertens. At a functional level, an increased capacity to metabolize lactose and synthesize amino acids was observed accompanied by a lowered potential for synthesis of lipopolysaccharides. Cluster analysis revealed that study volunteers segregated into two groups with post-intervention microbiota response that was dependent on the baseline microbial community structure.

2015 ◽  
Vol 35 (suppl_1) ◽  
Author(s):  
Karen J Ho ◽  
Liqun Xiong ◽  
Nathaniel Hubert ◽  
Anuradha Nadimpalli ◽  
Eugene B Chang ◽  
...  

Introduction: There is increasing evidence that the gut microbiome regulates susceptibility to certain diseases through systemic effects of microbe-derived metabolites. Sodium butyrate is a short chain fatty acid that is produced by microbial fermentation of dietary fiber and has known anti-proliferative and anti-migratory effects on vascular smooth muscle cells (VSMC). We hypothesized that perturbation of the gut microbiome with antibiotics would alter systemic serum butyrate concentration and impact neointimal hyperplasia after vascular injury. Methods: 10-wk-old male Lewis Inbred rats were treated with vancomycin (“vanco”) in the drinking water (0.5mg/mL) ± sodium butyrate (“buty”, 0.5mg/mL) for 4 wks prior to undergoing left carotid angioplasty. Serum butyrate concentration was assessed by gas chromatography. Gut microbial composition was assessed by 16S rRNA gene surveys of fecal samples. VSMC were treated with butyrate (0-5mM) and assessed for cell proliferation using cell counting, cell migration using a transwell assay, and cell cycle progression using FACS. Results: Post-angioplasty carotid arteries from vanco-treated rats developed 38% more neointima than controls (0.032±0.004mm2 vs. 0.044±0.003 mm2, P=0.02), but vanco+buty treatment prevented this increase in intimal area (0.035±0.004 mm2, P=.62 vs. control). Analysis of gut microbial communities revealed unique shifts in bacterial clustering by treatment group, which correlated with changes in serum butyrate levels, with the lowest butyrate level detected in vanco-treated rats (0.54±0.1 μmol/mL control, 0.017±0.1 μmol/mL vanco, 0.45±0.1 μmol/mL vanco+buty, P=.008). In vitro, butyrate treatment inhibited VSMC proliferation at 24-48 hrs in a dose-dependent manner, which correlated with induction of G0/G1 cell cycle arrest (P=.001) and a reduction in chemotaxis (P=.03). Conclusions: Oral vancomycin treatment induced a shift in the gut microbial community that was associated with decreased serum butyrate levels and increased neointimal hyperplasia, both of which were reversed by oral butyrate supplementation. These data demonstrate proof-of-concept that there is a correlation between gut microbial dysbiosis and susceptibility to neointimal hyperplasia.


Gut ◽  
2019 ◽  
Vol 69 (3) ◽  
pp. 569-577 ◽  
Author(s):  
Yiran Wei ◽  
Yanmei Li ◽  
Li Yan ◽  
Chunyan Sun ◽  
Qi Miao ◽  
...  

ObjectiveThe 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.DesignWe 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.ResultsThe 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 Veillonella were associated with disease status. Of note, Veillonella dispar, 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.ConclusionOur 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.


2021 ◽  
Vol 5 (Supplement_2) ◽  
pp. 1188-1188
Author(s):  
Sina Ullrich ◽  
Kerstin Thriene ◽  
Nadine Binder ◽  
Lena Amend ◽  
Till Strowig ◽  
...  

Abstract Objectives The effects of fermented foods on the gut microbiome are of great interest, yet evidence regarding its potential to increase gut microbial diversity, a measure likely associated with health, is lacking. Therefore, we analyzed the microbial composition (bacteria and yeasts) of commercially available fermented vegetables. Furthermore, we conducted a pilot study to assess the feasibility of studying effects of regular consumption of fermented vegetables on the gut microbiome. Methods Six healthy male volunteers (age: 25.5 ± 2.9yrs, BMI: 24.3 ± 1.2kg/m2) participated in a randomized crossover trial, with two 2-week intervention phases each of which was preceded by a 2-week washout phase. Participants consumed 150g/d of either sauerkraut (intervention 1) or a variety of six different fermented vegetables (intervention 2). We used 16S rRNA sequencing to assess the effects of each dietary regime on the composition, diversity and dynamics of the gut microbiome, as well as the composition and diversity of the fermented vegetable microbiome. Results Lactobacillus was the dominant genus in all fermented vegetables; still, the alpha diversity, richness and evenness of the microbiota differed substantially among the different products. Among our study participants, we observed an increase in alpha diversity (Shannon index) after both, consumption of sauerkraut (pre intervention: 3.31 ± 0.74, post intervention: 3.58 ± 0.68) and the selection of fermented vegetables (pre: 3.60 ± 0.93, post: 3.84 ± 0.81). However, the results did not reach statistical significance, due to the high inter- and intra-individual variability as evaluated by beta diversity of the gut microbial communities. Conclusions A longer-term intervention study with fermented vegetables and/or sauerkraut seems feasible. Consumption of fermented vegetables appears to increase the diversity of the gut microbiome, even after a relatively short period of time. However, further studies with a larger sample size are warranted to verify our observations. Funding Sources Institutional budget.


2020 ◽  
Vol 4 (Supplement_1) ◽  
Author(s):  
Elizabeth Ann Jensen ◽  
Zachary Jackson ◽  
Jonathan Alan Young ◽  
Jaycie Kuhn ◽  
Maria Onusko ◽  
...  

Abstract Emerging evidence proposes that the gut microbiome has an vital role in host growth, metabolism and endocrinology. That is, gut microbes impact growth by potentially altering the growth hormone (GH)/insulin-like growth factor-1 axis. Our previous research has also shown that GH - in states of absence and excess - is associated with altered gut microbial composition, maturity and predictive metabolic function in mice. Moreover, both GH and the gut microbiome are implicated in development and aging. Yet, it is unknown how GH impacts the longitudinal microbiome. This study thus aimed to characterize the longitudinal changes in the gut microbial profile of bovine GH transgenic mice (a model of chronic, excess GH action and accelerated aging). Microbial composition was quantified from fecal pellets of the same bGH and control mice at 3, 6 and 12 months of age through 16S rRNA gene sequencing and QIIME 2. Additional bioinformatic analyses assessed the unique signature and predictive metabolic function of the microbiome. The bGH mice had a distinct microbial profile compared to controls longitudinally. At 3 months, bGH mice had increased Firmicutes and Actinobacteria, decreased Bacteroidetes, Proteobacteria and Campylobacterota, and a significant reduction in microbial richness and evenness. By 6 months, all of the aforesaid phyla were increased with the exception of Firmicutes. By 12 months, bGH mice exhibited dysbiosis with increased Firmicutes and Proteobacteria and reduced Bacteroidetes, microbial richness and evenness. Moreover, abundance in Firmicutes, Bacteroidetes and Campylobacterota were significantly explained by the combined effect of genotype and age (p = 0.006, 0.005 and 0.02, respectively). Across all timepoints, bGH mice had a significantly different microbiome compared to controls (p = 0.002), and the development of microbial richness and evenness were also significantly different in bGH mice (p = 0.034 and 0.023). Bacterial genera Lactobacillus, Ruminococcaceae and Lachnospiraceae were identified as a unique candidates in bGH mice across all timepoints. Likewise, metabolic pathways involved in biosynthesis of heme b, menaquinol, acetate and butyrate differentiated the longitudinal bGH microbiome. Collectively, these results show that chronic, excess GH impacts the development and aging of the gut microbiome. Notably, several of the stated bacterial genera and metabolic pathways were associated with GH in our previous study, suggesting that GH may influence the longitudinal presence of certain gut microbes and metabolic functions. Additional studies will be performed to further explore the GH-associated gut microbiome and its impact on host health. Research was partially funded by the John J. Kopchick MCB/TBS Fellowship, a fellowship from the Osteopathic Heritage Foundation and the MMPC at UC, Davis (NIH grant U240DK092993).


2021 ◽  
Author(s):  
Artur Trzebny ◽  
Anna Slodkowicz-Kowalska ◽  
Johanna Björkroth ◽  
Miroslawa Dabert

AbstractThe animal gut microbiota consist of many different microorganisms, mainly bacteria, but archaea, fungi, protozoans, and viruses may also be present. This complex and dynamic community of microorganisms may change during parasitic infection. In the present study, we investigated the effect of the presence of microsporidians on the composition of the mosquito gut microbiota and linked some microbiome taxa and functionalities to infections caused by these parasites. We characterised bacterial communities of 188 mosquito females, of which 108 were positive for microsporidian DNA. To assess how bacterial communities change during microsporidian infection, microbiome structures were identified using 16S rRNA microbial profiling. In total, we identified 46 families and four higher taxa, of which Comamonadaceae, Enterobacteriaceae, Flavobacteriaceae and Pseudomonadaceae were the most abundant mosquito-associated bacterial families. Our data suggest that the mosquito gut microbial composition varies among host species. In addition, we found a correlation between the microbiome composition and the presence of microsporidians. The prediction of metagenome functional content from the 16S rRNA gene sequencing suggests that microsporidian infection is characterised by some bacterial species capable of specific metabolic functions, especially the biosynthesis of ansamycins and vancomycin antibiotics and the pentose phosphate pathway. Moreover, we detected a positive correlation between the presence of microsporidian DNA and bacteria belonging to Spiroplasmataceae and Leuconostocaceae, each represented by a single species, Spiroplasma sp. PL03 and Weissella cf. viridescens, respectively. Additionally, W. cf. viridescens was observed only in microsporidian-infected mosquitoes. More extensive research, including intensive and varied host sampling, as well as determination of metabolic activities based on quantitative methods, should be carried out to confirm our results.


2021 ◽  
Vol 15 ◽  
Author(s):  
Jade E. Kenna ◽  
Eng Guan Chua ◽  
Megan Bakeberg ◽  
Alfred Tay ◽  
Sarah McGregor ◽  
...  

Background: There has been increasing recognition of the importance of the gut microbiome in Parkinson’s disease (PD), but the influence of geographic location has received little attention. The present study characterized the gut microbiota and associated changes in host metabolic pathways in an Australian cohort of people with PD (PwP).Methods: The study involved recruitment and assessment of 87 PwP from multiple Movement Disorders Clinics in Australia and 47 healthy controls. Illumina sequencing of the V3 and V4 regions of the 16S rRNA gene was used to distinguish inter-cohort differences in gut microbiota; KEGG analysis was subsequently performed to predict functional changes in host metabolic pathways.Results: The current findings identified significant differences in relative abundance and diversity of microbial operational taxonomic units (OTUs), and specific bacterial taxa between PwP and control groups. Alpha diversity was significantly reduced in PwP when compared to controls. Differences were found in two phyla (Synergistetes and Proteobacteria; both increased in PwP), and five genera (Colidextribacter, Intestinibacter, Kineothrix, Agathobaculum, and Roseburia; all decreased in PwP). Within the PD cohort, there was no association identified between microbial composition and gender, constipation or use of gastrointestinal medication. Furthermore, KEGG analysis identified 15 upregulated and 11 downregulated metabolic pathways which were predicted to be significantly altered in PwP.Conclusion: This study provides the first comprehensive characterization of the gut microbiome and predicted functional metabolic effects in a southern hemisphere PD population, further exploring the possible mechanisms whereby the gut microbiota may exert their influence on this disease, and providing evidence for the incorporation of such data in future individualized therapeutic strategies.


2020 ◽  
Vol 4 (Supplement_2) ◽  
pp. 1450-1450
Author(s):  
Gertraud Maskarinec ◽  
Phyllis Raquinio ◽  
Bruce Kristal ◽  
Lynne Wilkens ◽  
Adrian Franke ◽  
...  

Abstract Objectives As features of the gut microbiome may promote the development of type 2 diabetes (T2D), we examined the hypothesis that gut microbiome composition differs by glycemic/diabetes status within a subset of the Multiethnic Cohort. We also estimated the association of lipopolysaccharide-binding protein (LBP) as a measure of circulating bacterial endotoxin with T2D. This outer membrane component of gram-negative bacteria may affect glucose metabolism. Methods In 2013–16, cohort members from 5 ethnic groups completed clinic visits, questionnaires, and stool collections. Participants with self-reported T2D and/or taking medication were considered T2D cases. Those with fasting glucose &gt;125 and 100–125 mg/dL were classified as undiagnosed (UT2D) and prediabetes (PT2D). We characterized the gut microbiome through 16S rRNA gene sequencing (V1-V3). Plasma LBP was measured by ELISA. Linear regression was applied to estimate associations of gut microbiome community structure and LBP with T2D status adjusting for relevant confounders. Results Among 1756 participants (59.9–77.4 years), 315 (18%) were T2D, 158 (9%) UT2D, 518 (29%) PT2D, and 765 (44%) normoglycemic (NG). The Shannon diversity index was lower (6.30, 6.25, 6.28, 6.18; P = 0.02) and LBP was higher (26.0, 26.6, 28.6, 28.2 µg/mL; P = 0.0009) in T2D than NG participants. Of 10 phyla, Actinobacteria and Firmicutes were inversely associated with T2D status (P = 0.004). Six of 161 genera were significantly related to T2D status after Bonferroni adjustment: the abundance of Clostridium sensu stricto 1, Lachnospira, Lachnospiraceae NC2004, and Peptostreptococcaceae was lower, while Lachnospiraceae uncultured and Escherichia-Shigella were more abundant among T2D than NG participants. In general, those with PT2D and UT2D had values closer to NG than T2D individuals. Conclusions Participants with T2D showed a lower abundance of bacteria capable of fermenting plant polysaccharides and higher levels of gram-negative endotoxin-producing bacteria indicating that a less favorable pattern of gut microbiome community structure may contribute to T2D through endotoxin binding to toll-like receptors via LBP and activation of the NFkB pathway associated with chronic systemic inflammation. Funding Sources NIH grants P01CA169530, U01CA164973, P30CA071789, #UL1TR000130, R01HL140335.


Nutrients ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 467 ◽  
Author(s):  
Yanbei Wu ◽  
Robert Li ◽  
Haiqiu Huang ◽  
Arnetta Fletcher ◽  
Lu Yu ◽  
...  

Accumulated evidence suggests that the cruciferous vegetables-derived compound indole-3-carbinol (I3C) may protect against prostate cancer, but the precise mechanisms underlying its action remain unclear. This study aimed to verify the hypothesis that the beneficial effect of dietary I3C may be due to its modulatory effect on the gut microbiome of mice. Athymic nude mice (5–7 weeks old, male, Balb c/c nu/nu) with established tumor xenografts were fed a basal diet (AIN-93) with or without 1 µmoles I3C/g for 9 weeks. The effects of dietary I3C on gut microbial composition and microbial species interactions were then examined by 16s rRNA gene-based sequencing and co-occurrence network analysis. I3C supplementation significantly inhibited tumor growth (p < 0.0001) and altered the structure of gut microbiome. The abundance of the phylum Deferribacteres, more specifically, Mucispirillum schaedleri, was significantly increased by dietary I3C. Additionally, I3C consumption also changed gut microbial co-occurrence patterns. One of the network modules in the control group, consisting of seven bacteria in family S-27, was positively correlated with tumor size (p < 0.009). Moreover, dietary I3C disrupted microbial interactions and altered this association between specific microbial network and tumor development. Our results unraveled complex relationships among I3C ingestion, gut microbiota, and prostate tumor development and may provide a novel insight into the mechanism for the chemopreventive effect of dietary I3C on prostate cancer.


2019 ◽  
Vol 7 (9) ◽  
pp. 357 ◽  
Author(s):  
Moonsuk Hur ◽  
Soo-Je Park

Heavy metal pollution is a serious environmental problem as it adversely affects crop production and human activity. In addition, the microbial community structure and composition are altered in heavy-metal-contaminated soils. In this study, using full-length 16S rRNA gene sequences obtained by a PacBio RS II system, we determined the microbial diversity and community structure in heavy-metal-contaminated soil. Furthermore, we investigated the microbial distribution, inferred their putative functional traits, and analyzed the environmental effects on the microbial compositions. The soil samples selected in this study were heavily and continuously contaminated with various heavy metals due to closed mines. We found that certain microorganisms (e.g., sulfur or iron oxidizers) play an important role in the biogeochemical cycle. Using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis, we predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories from abundances of microbial communities and revealed a high proportion belonging to transport, energy metabolism, and xenobiotic degradation in the studied sites. In addition, through full-length analysis, Conexibacter-like sequences, commonly identified by environmental metagenomics among the rare biosphere, were detected. In addition to microbial composition, we confirmed that environmental factors, including heavy metals, affect the microbial communities. Unexpectedly, among these environmental parameters, electrical conductivity (EC) might have more importance than other factors in a community description analysis.


Sports ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 14
Author(s):  
Dierdra Bycura ◽  
Anthony C. Santos ◽  
Arron Shiffer ◽  
Shari Kyman ◽  
Kyle Winfree ◽  
...  

In this study we examined changes to the human gut microbiome resulting from an eight-week intervention of either cardiorespiratory exercise (CRE) or resistance training exercise (RTE). Twenty-eight subjects (21 F; aged 18–26) were recruited for our CRE study and 28 subjects (17 F; aged 18–33) were recruited for our RTE study. Fecal samples for gut microbiome profiling were collected twice weekly during the pre-intervention phase (three weeks), intervention phase (eight weeks), and post-intervention phase (three weeks). Pre/post VO2max, three repetition maximum (3RM), and body composition measurements were conducted. Heart rate ranges for CRE were determined by subjects’ initial VO2max test. RTE weight ranges were established by subjects’ initial 3RM testing for squat, bench press, and bent-over row. Gut microbiota were profiled using 16S rRNA gene sequencing. Microbiome sequence data were analyzed with QIIME 2. CRE resulted in initial changes to the gut microbiome which were not sustained through or after the intervention period, while RTE resulted in no detectable changes to the gut microbiota. For both CRE and RTE, we observe some evidence that the baseline microbiome composition may be predictive of exercise gains. This work suggests that the human gut microbiome can change in response to a new exercise program, but the type of exercise likely impacts whether a change occurs. The changes observed in our CRE intervention resemble a disturbance to the microbiome, where an initial shift is observed followed by a return to the baseline state. More work is needed to understand how sustained changes to the microbiome occur, resulting in differences that have been reported in cross sectional studies of athletes and non-athletes.


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