scholarly journals Effect of High versus Low Dairy Consumption on the Gut Microbiome: Results of a Randomized, Cross-Over Study

Nutrients ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 2129 ◽  
Author(s):  
J. Casper Swarte ◽  
Coby Eelderink ◽  
Rianne M. Douwes ◽  
M. Yusof Said ◽  
Shixian Hu ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Metabolic Pathways ◽  
Leuconostoc Mesenteroides ◽  
Streptococcus Thermophilus ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Dairy Consumption ◽  
Lower Abundance ◽  
Rrna Gene Sequencing ◽  
Overweight Subjects

The influence of dairy on the gut microbiome has not been studied extensively. We performed a randomized cross-over study to analyze the effect of high dairy intake on the gut microbiome. Subjects were randomly assigned to a high-dairy diet (HDD) (5–6 dairy portions per day) and a low-dairy diet (LDD) (≤1 dairy portion per day) for 6 weeks with a washout period of 4 weeks in between both diets. The gut microbiome was assessed using 16S rRNA gene sequencing. Compositionality and functionality of the gut microbiome was assessed using Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Stool consistency was evaluated using the Bristol stool chart. In total, 46 healthy overweight subjects (BMI range 25–30 kg/m2) completed both intervention periods. During the HDD, there was a significantly higher abundance of the genera Streptococcus, Leuconostoc, and Lactococcus, and the species Streptococcus thermophilus, Erysipelatoclostridium ramosum and Leuconostoc mesenteroides (pFDR < 0.10). Furthermore, during the HDD, there was a significantly lower abundance of the genera Faecalibacterium and Bilophila, and the species Faecalibacterium prausnitzii, Clostridium aldenense, Acetivibrio ethanolgignens, Bilophila wadsworthia and Lactococcus lactis (pFDR < 0.10). There were eight subjects who became constipated during the HDD and these subjects all had a lower abundance of F. prausnitzii. This is the first cross-over study in which the effect of an HDD compared to an LDD on the gut microbiome has been studied. An HDD led to a significantly different composition of the gut microbiome, with a particularly lower abundance of F. prausnitzii and a higher abundance of S. thermophilus. Constipation was observed in several subjects during the HDD. Predicted metabolic pathways were not significantly altered due to an HDD.

scholarly journals Gut microbiome is affected by inter-sexual and inter-seasonal variation in diet for thick-billed murres (Uria lomvia)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Esteban Góngora ◽  
Kyle H. Elliott ◽  
Lyle Whyte
Keyword(s):  
Gut Microbiome ◽  
Sulfur Isotopes ◽  
Trophic Position ◽  
Isotope Analysis ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Uria Lomvia ◽  
Fecal Microbiome ◽  
Prey Specialization ◽  
Rrna Gene Sequencing

AbstractThe role of the gut microbiome is increasingly being recognized by health scientists and veterinarians, yet its role in wild animals remains understudied. Variations in the gut microbiome could be the result of differential diets among individuals, such as variation between sexes, across seasons, or across reproductive stages. We evaluated the hypothesis that diet alters the avian gut microbiome using stable isotope analysis (SIA) and 16S rRNA gene sequencing. We present the first description of the thick-billed murre (Uria lomvia) fecal microbiome. The murre microbiome was dominated by bacteria from the genus Catellicoccus, ubiquitous in the guts of many seabirds. Microbiome variation was explained by murre diet in terms of proportion of littoral carbon, trophic position, and sulfur isotopes, especially for the classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Alphaproteobacteria, and Gammaproteobacteria. We also observed differences in the abundance of bacterial genera such as Catellicoccus and Cetobacterium between sexes and reproductive stages. These results are in accordance with behavioural observations of changes in diet between sexes and across the reproductive season. We concluded that the observed variation in the gut microbiome may be caused by individual prey specialization and may also be reinforced by sexual and reproductive stage differences in diet.

Effect of bamboo vinegar powder as an antibiotic alternative on the digesta bacteria communities of finishing pigs

2018 ◽  
Vol 64 (10) ◽  
pp. 732-743
Author(s):  
Huan Qu ◽  
Yanjie Huang ◽  
Yinghao Shi ◽  
Ying Liu ◽  
Shenglong Wu ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Metabolic Pathways ◽  
Growth And Development ◽  
Intestinal Microflora ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Finishing Pigs ◽  
Rrna Gene Sequencing ◽  
Bacteria Communities

This study investigated the use for bamboo vinegar powder as an antibiotic alternative in the diet of growing–finishing pigs by examining their digestive bacterial communities. Forty-five Duroc × Landrace × Yorkshire growing–finishing pigs were randomly allocated to five diet groups: 0%, 0.5%, 1.0%, or 1.5% bamboo vinegar levels and antibiotics. After 37 days, the digesta in duodenum of four pigs from each treatment were analyzed for their bacterial community compositions using 16S rRNA gene sequencing. The addition of 1.5% bamboo vinegar powder had an effect on the intestinal microflora most similar to that of antibiotics, indicating its potential to promote the growth and development of finishing pigs. We also found the 1.5% bamboo vinegar powder group to have an increased abundance of Firmicutes/Bacteroidetes compared with the other bamboo vinegar powder groups, which may enhance the ability of the host to absorb food energy and store more body fat. Additionally, the effects of bamboo vinegar powder on promoting the abundances of Lactobacillus and Thalassospira and on inhibiting Streptococcus and Prevotella growth revealed it may play an important role in animal production. Moreover, functional predictions of microbes via PICRUSt indicated that feed supplemented with 1.5% bamboo vinegar powder could promote many vital metabolic pathways.

scholarly journals Soybean Oil Modulates the Gut Microbiota Associated with Atherogenic Biomarkers

2020 ◽  
Vol 8 (4) ◽  
pp. 486
Author(s):  
Hila Korach-Rechtman ◽  
Oren Rom ◽  
Lirane Mazouz ◽  
Shay Freilich ◽  
Helana Jeries ◽  
...  
Keyword(s):  
Soybean Oil ◽  
Metabolic Pathways ◽  
16S Rrna Gene Sequencing ◽  
Diagnostic Tools ◽  
Human Consumption ◽  
Rrna Gene ◽  
Non Invasive ◽  
Compositional Changes ◽  
Rrna Gene Sequencing ◽  
Fat Diets

During the last few decades there has been a staggering rise in human consumption of soybean-oil (SO). The microbiome and specific taxa composing it are dramatically affected by diet; specifically, by high-fat diets. Increasing evidence indicates the association between dysbiosis and health or disease state, including cardiovascular diseases (CVD) and atherosclerosis pathogenesis in human and animal models. To investigate the effects of high SO intake, C57BL/6 mice were orally supplemented with SO-based emulsion (SOE) for one month, followed by analyses of atherosclerosis-related biomarkers and microbiota profiling by 16S rRNA gene sequencing of fecal DNA. SOE-supplementation caused compositional changes to 64 taxa, including enrichment in Bacteroidetes, Mucispirillum, Prevotella and Ruminococcus, and decreased Firmicutes. These changes were previously associated with atherosclerosis in numerous studies. Among the shifted taxa, 40 significantly correlated with at least one atherosclerosis-related biomarker (FDR < 0.05), while 13 taxa positively correlated with the average of all biomarkers. These microbial alterations also caused a microbial-derived metabolic-pathways shift, including enrichment in different amino-acid metabolic-pathways known to be implicated in CVD. In conclusion, our results demonstrate dysbiosis following SOE supplementation associated with atherosclerosis-related biomarkers. These findings point to the microbiome as a possible mediator to CVD, and it may be implemented into non-invasive diagnostic tools or as potential therapeutic strategies.

scholarly journals Correction: 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome

PLoS ONE ◽  
2019 ◽  
Vol 14 (2) ◽  
pp. e0212474 ◽  
Author(s):  
Daniel E. Almonacid ◽  
Laurens Kraal ◽  
Francisco J. Ossandon ◽  
Yelena V. Budovskaya ◽  
Juan Pablo Cardenas ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gut Microbiome ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Reference Ranges ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Rrna Gene Sequencing

scholarly journals The Effect of Xuebijing on the Gut Microbiota and Metabolic of Heat 1 Stroke Rat 2

2021 ◽  
Author(s):  
Qiang wen ◽  
Xuan He ◽  
Yu Shao ◽  
Lun Peng ◽  
Li Zhao ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gut Microbiome ◽  
Heat Stroke ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Control Group ◽  
Rrna Gene ◽  
Metabolism Pathway ◽  
Rrna Gene Sequencing

Abstract The goal of the present study was to evaluate the fecal microbiome and serum metabolites in 16 Xuebijing (XBJ)-injected rats after heat stroke using 16S rRNA gene sequencing and gas chromatography-mass spectrometry (GC-MS) metabolomics. Eighteen rats were divided into the control group (CON), heat stroke group (HS), and XBJ group. The 16S rRNA gene sequencing results revealed that the abundance of Bacteroidetes was overrepresented in the XBJ group compared to the HS group, while Actinobacteria was underrepresented. Metabolomic profiling showed that the pyrimidine metabolism pathway, pentose phosphate pathway, and glycerophospholipid metabolism pathway were upregulated in the XBJ group compared to the HS group. Taken together, these results demonstrated that heat stroke not only altered the gut microbiome community structure of rats but also greatly affected metabolic functions, leading to gut microbiome toxicity.

scholarly journals Dietary sphinganine is selectively assimilated by members of the gut microbiome

2020 ◽  
Author(s):  
Min-Ting Lee ◽  
Henry H. Le ◽  
Elizabeth L. Johnson
Keyword(s):  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Dietary Lipids ◽  
Rrna Gene ◽  
Bioactive Components ◽  
Microbiome Composition ◽  
Metabolic Products ◽  
Comparative Metabolomics ◽  
Rrna Gene Sequencing ◽  
Gut Microbial Community

AbstractFunctions of the gut microbiome have a growing number of implications for host metabolic health, with diet being one of the most significant influences on microbiome composition. Compelling links between diet and the gut microbiome suggest key roles for various macronutrients, including lipids, yet how individual classes of dietary lipids interact with the microbiome remain largely unknown. A class of lipids known as sphingolipids are bioactive components of most foods and are produced by prominent gut microbes. This makes sphingolipids intriguing candidates for shaping diet-microbiome interactions. Here, we use a click-chemistry based approach to track the incorporation of bioorthogonal dietary omega-alkynyl sphinganine (sphinganine alkyne – SAA) into the gut microbial community (Click). Identification of microbe and SAA-specific metabolic products was achieved by fluorescence-based sorting of SAA containing microbes (Sort), 16S rRNA gene sequencing to identify the sphingolipid-interacting microbes (Seq), and comparative metabolomics to identify products of SAA assimilation by the microbiome (Spec). Together this approach, Click-Sort-Seq-Spec (ClickSSS), revealed that SAA-assimilation was nearly exclusively performed by gut Bacteroides, indicating that sphingolipid-producing bacteria play a major role in processing dietary sphinganine. Comparative metabolomics of cecal microbiota from SAA-treated mice showed conversion of SAA to a suite of dihydroceramides, consistent with metabolic activity via Bacteroides and Bifidobacterium. Additionally, other sphingolipid-interacting microbes were identified with a focus on an uncharacterized ability of Bacteroides and Bifidobacterium to metabolize dietary sphingolipids. Therefore, ClickSSS provides a platform to study the flux of virtually any alkyne-labeled metabolite in diet-microbiome interactions.

scholarly journals Commensal Bifidobacterium Strains Enhance the Efficacy of Neo-Epitope Based Cancer Vaccines

Vaccines ◽  
2021 ◽  
Vol 9 (11) ◽  
pp. 1356
Author(s):  
Michele Tomasi ◽  
Mattia Dalsass ◽  
Francesco Beghini ◽  
Ilaria Zanella ◽  
Elena Caproni ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Cancer Vaccines ◽  
Molecular Mimicry ◽  
Large Body ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Shotgun Metagenomics ◽  
Cancer Immunity ◽  
Rrna Gene Sequencing

A large body of data both in animals and humans demonstrates that the gut microbiome plays a fundamental role in cancer immunity and in determining the efficacy of cancer immunotherapy. In this work, we have investigated whether and to what extent the gut microbiome can influence the antitumor activity of neo-epitope-based cancer vaccines in a BALB/c-CT26 cancer mouse model. Similarly to that observed in the C57BL/6-B16 model, Bifidobacterium administration per se has a beneficial effect on CT26 tumor inhibition. Furthermore, the combination of Bifidobacterium administration and vaccination resulted in a protection which was superior to vaccination alone and to Bifidobacterium administration alone, and correlated with an increase in the frequency of vaccine-specific T cells. The gut microbiome analysis by 16S rRNA gene sequencing and shotgun metagenomics showed that tumor challenge rapidly altered the microbiome population, with Muribaculaceae being enriched and Lachnospiraceae being reduced. Over time, the population of Muribaculaceae progressively reduced while the Lachnospiraceae population increased—a trend that appeared to be retarded by the oral administration of Bifidobacterium. Interestingly, in some Bacteroidales, Prevotella and Muribaculacee species we identified sequences highly homologous to immunogenic neo-epitopes of CT26 cells, supporting the possible role of “molecular mimicry” in anticancer immunity. Our data strengthen the importance of the microbiome in cancer immunity and suggests a microbiome-based strategy to potentiate neo-epitope-based cancer vaccines.

scholarly journals Molecular and Microbial Signatures Predictive of Prebiotic Action of Neoagarotetraose in a Dextran Sulfate Sodium-Induced Murine Colitis Model

2020 ◽  
Vol 8 (7) ◽  
pp. 995
Author(s):  
Fang Liu ◽  
Jianan Liu ◽  
Thomas T.Y. Wang ◽  
Zhen Liu ◽  
Changhu Xue ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Dextran Sulfate ◽  
Dextran Sulfate Sodium ◽  
Intestinal Inflammation ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Murine Colitis ◽  
Bioactive Properties ◽  
Rrna Gene Sequencing ◽  
Colitis Model

Neoagarotetraose (NT), a hydrolytic product of agar by β-agarase, is known to possess bioactive properties. However, the mechanisms via which NT alleviates intestinal inflammation remain unknown. In this study, a dextran sulfate sodium (DSS)-induced murine model was developed to evaluate the effect of NT on gut microbiome and microbial metabolism using 16S rRNA gene sequencing and untargeted metabolomics. Our data demonstrate that NT ingestion improved gut integrity and inflammation scores. NT reversed the abundance of Proteobacteria from an elevated level induced by DSS and significantly increased the abundance of Verrucomicrobia. Further, NT significantly increased the abundance of Akkermansia and Lactobacillus and concomitantly decreased that of Sutterella, which were among the important features identified by random forests analysis contributing to classification accuracy for NT supplementation. A microbial signature consisting of Adlercreutzia (denominator) and Turicibacter (numerator) predicted the NT supplementation status. Moreover, NT significantly modulated multiple gut metabolites, particularly those related to histidine, polyamine and tocopherol metabolism. Together, our findings provided novel insights into the mechanisms by which NT modulated the gut microbiome and metabolome and should facilitate the development of NT as a potent prebiotic for colitis management.

scholarly journals Digestive gland microbiome of Pleurobema cordatum: mesocosms induce dysbiosis

2020 ◽  
Vol 86 (4) ◽  
pp. 280-289
Author(s):  
Alison K Aceves ◽  
Paul D Johnson ◽  
Carla L Atkinson ◽  
Brian C van Ee ◽  
Stephen A Bullard ◽  
...  
Keyword(s):  
Digestive Gland ◽  
Gut Microbiome ◽  
Bacterial Communities ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Artificial Rearing ◽  
Tennessee River ◽  
Wasting Syndrome ◽  
Water And Sediment ◽  
Rrna Gene Sequencing

ABSTRACT Herein, we characterized the digestive gland (‘gut’) bacterial community (microbiome) of the Ohio pigtoe, Pleurobema cordatum (Rafinesque, 1820), using 16S rRNA gene sequencing. Two populations were compared: wild P. cordatum (n = 5) from the Tennessee River and P. cordatum (n = 9) relocated to artificial mesocosms and exposed to various thermal regimes for 2 weeks. We also characterized the bacterial communities from the habitat (water and sediment) of these wild and mesocosm-held populations. The gut microbiome of wild P. cordatum was dominated by members of the bacterial phylum Tenericutes (72%). By contrast, the gut microbiome of mesocosm-held P. cordatum was dominated by members of the bacterial phylum Proteobacteria (64%). We found no temperature-associated difference in the gut microbiome of mesocosm-held P. cordatum. The bacterial communities of water and sediment from the Tennessee River were diverse and distinct from those of the studied mussels. By contrast, the bacterial communities of water and sediment in the mesocosms were dominated by Proteobacteria. These results suggest that when the studied mussels were moved into artificial rearing environments, their gut microbiome shifted to reflect that of their habitat (i.e. an increase in Proteobacteria). Moreover, the abundance of Tenericutes (also previously reported in other unionids) was reduced from 72% in wild mussels to 3% in mesocosm-held mussels. As a result, we think that mesocosm-held P. cordatum became dysbiotic, which could explain the observed wasting syndrome and associated trickling mortalities in captive P. cordatum.

scholarly journals Dietary sphinganine is selectively assimilated by members of the mammalian gut microbiome

2020 ◽  
pp. jlr.RA120000950 ◽  
Author(s):  
Min-Ting Lee ◽  
Henry H Le ◽  
Elizabeth L Johnson
Keyword(s):  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Dietary Lipids ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
Bioorthogonal Labeling ◽  
Comparative Metabolomics ◽  
Metabolic Activities ◽  
Rrna Gene Sequencing ◽  
Gut Microbial Community

Functions of the gut microbiome have a growing number of implications for host metabolic health, with diet being one of the most significant influences on microbiome composition. Compelling links between diet and the gut microbiome suggest key roles for various macronutrients, including lipids, yet how individual classes of dietary lipids interact with the microbiome remains largely unknown. Sphingolipids are bioactive components of most foods and are also produced by prominent gut microbes. This makes sphingolipids intriguing candidates for shaping diet–microbiome interactions. Here, we used a click chemistry–based approach to track the incorporation of bioorthogonal dietary omega-alkynyl sphinganine (sphinganine alkyne [SAA]) into the murine gut microbial community (Bioorthogonal labeling). We identified microbial and SAA-specific metabolic products through fluorescence-based sorting of SAA-containing microbes (Sort), 16S rRNA gene sequencing to identify the sphingolipid-interacting microbes (Seq), and comparative metabolomics to identify products of SAA assimilation by the microbiome (Spec). Together, this approach, termed Bioorthogonal labeling-Sort-Seq-Spec (BOSSS), revealed that SAA assimilation is nearly exclusively performed by gut Bacteroides, indicating that sphingolipid-producing bacteria play a major role in processing dietary sphinganine. Comparative metabolomics of cecal microbiota from SAA-treated mice revealed conversion of SAA to a suite of dihydroceramides, consistent with metabolic activities of Bacteroides and Bifidobacterium. Additionally, other sphingolipid-interacting microbes were identified with a focus on an uncharacterized ability of Bacteroides and Bifidobacterium to metabolize dietary sphingolipids. We conclude that BOSSS provides a platform to study the flux of virtually any alkyne-labeled metabolite in diet–microbiome interactions.

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