scholarly journals Dietary Bovine Milk Exosomes Elicit Changes in Microbial Communities in C57BL/6 Mice

2018 ◽  
Author(s):  
Fang Zhou ◽  
Henry A. Paz ◽  
Jiang Shu ◽  
Mahrou Sadri ◽  
Juan Cui ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Gut Microbiome ◽  
Bovine Milk ◽  
Cell Communication ◽  
Intestinal Microbiome ◽  
Operational Taxonomic Units ◽  
Health And Disease ◽  
Cecum Content ◽  
First Time ◽  
Bovine Species

ABSTRACTExosomes and exosome-like vesicles participate in cell-to-cell communication in animals, plant and bacteria. Dietary exosomes in bovine milk are bioavailable in non-bovine species, but a fraction of milk exosomes reaches the large intestine. We hypothesized that milk exosomes alter the composition of the gut microbiome in mice. C57BL/6 mice were fed AIN-93G diets, defined by their content of bovine milk exosomes and RNA cargos: exosome/RNA depleted (ERD) versus exosome/RNA-sufficient (ERS) diets. Feeding was initiated at age three weeks and cecum content was collected at ages 7, 15 and 47 weeks. Microbial communities were identified by 16S rRNA gene sequencing. The dietary intake of exosomes and age had significant effects on the microbial communities in the cecum. At the phylum level, the abundance of Verrucomicrobia was greater in mice fed ERD compared to ERS, and the abundance of both Firmicutes and Tenericutes was smaller in mice fed ERD compared to ERS at age 47 weeks. At the family level, the abundance of Anaeroplasmataceae was greater in mice fed ERD compared to ERS, and the abundance of Bifidobacteriaceae, Lachnospiraceae, and Dehalobacteriaceae was significantly greater in mice fed ERS than mice fed ERD at age 15 weeks. Exosome feeding significantly altered the abundance of 52 operational taxonomic units; diet effects were particularly strong in the Lachnospiraceae, Ruminococcaceae and the Verrucomicrobiaceae families. We conclude that exosomes in bovine milk alter microbial communities in non-bovine species, suggesting that exosomes and their cargos participate in the crosstalk between bacterial and animal kingdoms.IMPORTANCEVirtually all living cells, including bacteria communicate through exosomes, which can be found in all body fluids. Exosomes and the RNA cargos have been implicated in all aspects of health and disease, e.g., metastasis of cancer, neuronal signaling and embryonic development. Previously, we reported that exosomes and their microRNA cargos are not solely derived from endogenous synthesis, but may also be obtained from dietary sources such as bovine milk in non-bovine mammals. Here, we report for the first time that bovine milk exosomes communicate with the intestinal microbiome and alters microbial communities in mice. This is the first report suggesting that the gut microbiome facilitates the signaling by dietary exosomes across kingdoms: animal (cow) → bacteria → animal (mouse).

scholarly journals Dietary bovine milk exosomes elicit changes in bacterial communities in C57BL/6 mice

2019 ◽  
Vol 317 (5) ◽  
pp. G618-G624 ◽  
Author(s):  
Fang Zhou ◽  
Henry A. Paz ◽  
Mahrou Sadri ◽  
Juan Cui ◽  
Stephen D. Kachman ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Gut Microbiome ◽  
Bacterial Communities ◽  
Bovine Milk ◽  
Cell Communication ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
The Family ◽  
Rrna Gene Sequencing

Exosomes and exosome-like vesicles participate in cell-to-cell communication in animals, plant, and bacteria. Dietary exosomes in bovine milk are bioavailable in nonbovine species, but a fraction of milk exosomes reaches the large intestine. We hypothesized that milk exosomes alter the composition of the gut microbiome in mice. C57BL/6 mice were fed AIN-93G diets, defined by their content of bovine milk exosomes and RNA cargos: exosome/RNA-depleted (ERD) versus exosome/RNA-sufficient (ERS) diets. Feeding was initiated at age 3 wk, and cecum content was collected at ages 7, 15, and 47 wk. Microbial communities were identified by 16S rRNA gene sequencing. Milk exosomes altered bacterial communities in the murine cecum. The abundance of three phyla, seven families, and 52 operational taxonomic units (OTUs) was different in the ceca from mice fed ERD and ERS ( P < 0.05). For example, at the phylum level, Tenericutes had more than threefold abundance in ERS mice at ages 15 and 47 wk compared with ERD mice ( P < 0.05). At the family level, Verrucomicrobiaceae were much less abundant in ERS mice compared with ERD mice age 47 wk ( P < 0.05). At the OTU level, four OTUs from the family of Lachnospiraceae were more than two times more abundant in ERS mice compared with ERD at age 7 and 47 wk ( P < 0.05). We conclude that exosomes in bovine milk alter microbial communities in nonbovine species, suggesting that exosomes and their cargos participate in the crosstalk between bacterial and animal kingdoms. NEW & NOTEWORTHY This is the first report that exosomes from bovine milk alter microbial communities in mice. This report suggests that the gut microbiome facilitates cell-to-cell communication by milk exosomes across species boundaries, and milk exosomes facilitate communication across animal and bacteria kingdoms.

scholarly journals Estimating molecular preservation of the intestinal microbiome via metagenomic analyses of latrine sediments from two medieval cities

2020 ◽  
Vol 375 (1812) ◽  
pp. 20190576 ◽  
Author(s):  
Susanna Sabin ◽  
Hui-Yuan Yeh ◽  
Aleks Pluskowski ◽  
Christa Clamer ◽  
Piers D. Mitchell ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Intestinal Flora ◽  
Population Level ◽  
Intestinal Microbiome ◽  
Bulk Sediment ◽  
Theme Issue ◽  
Gastrointestinal Health ◽  
Health And Disease ◽  
The Rich ◽  
Microbial Dna

Ancient latrine sediments, which contain the concentrated collective biological waste of past whole human communities, have the potential to be excellent proxies for human gastrointestinal health on the population level. A rich body of literature explores their use to detect the presence of gut-associated eukaryotic parasites through microscopy, immunoassays and genetics. Despite this interest, a lack of studies have explored the whole genetic content of ancient latrine sediments through consideration not only of gut-associated parasites, but also of core community gut microbiome signals that remain from the group that used the latrine. Here, we present a metagenomic analysis of bulk sediment from medieval latrines in Riga (Latvia) and Jerusalem. Our analyses reveal survival of microbial DNA representative of intestinal flora as well as numerous parasites. These data are compared against parasite taxon identifications obtained via microscopy and ELISA techniques. Together, these findings provide a first glimpse into the rich prokaryotic and eukaryotic intestinal flora of pre-industrial agricultural populations, which may give a better context for interpreting the health of modern microbiomes. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.

scholarly journals Comparison of microbiome and culture techniques for determination of gastrointestinal microbial communities in ceca of chickens

2018 ◽  
Author(s):  
Kimberly Wilson ◽  
Whitney Briggs ◽  
Audrey Duff ◽  
Chasser Kaylin ◽  
Xialoun Sun ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Illumina Miseq ◽  
Intestinal Microbiome ◽  
P Value ◽  
Culture Techniques ◽  
Operational Taxonomic Units ◽  
Colony Forming Units ◽  
Miseq Platform ◽  
Next Generation Sequencing Ngs

The use of 16S next generation sequencing (NGS) technology to identify the relative abundance of microbial communities have become the standard when studying the intestinal microbiome. The increased use is due to the ability to identify a proportion of bacteria that cannot be observed with culture-based methods. However, culture-based techniques are acceptable to identify key bacterial groups, yet may grossly underestimate the microbial community in question. Since there is limited research comparing NGS results to colony forming units (CFU), the objective of this study was to compare total Enterobacteriaceae and lactic acid bacteria (LAB) recovery with culture techniques (CFU/g ceca) to total number of reads from operational taxonomic units (OTU) categorized as Enterobacteriaceae or LAB from Illumina MiSeq platform from matched chick cecal samples at three and 10 days of age. Both CFU recovery (1.09x109 ± 2.42x108; 1.37x108 ± 5.57x107) and reads (5460 ± 1164 ; 282 ± 163) belonging to Enterobacteriaceae decreased by 10 days of age (p < 0.001). Similarly, LAB reads decreased over time (21,128 ± 2262; 6220 ± 817, respectively p < 0.0001). However, LAB CFU recovery increased by 10 days (1.18x108 ± 1.91x107; 1.62x109 ± 5.00x108, respectively p < 0.01). At three days the Pearson’s correlation was -0.082 between CFU of culturable Enterobacteriaceae to reads and culturable LAB CFU to reads at 0.097, showing no correlation (p = 0.606, 0.551; respectively). By 10 days, no correlation of reads and CFU occurred with Enterobacteriaceae (r=-0.049; p-value = 0.769) while with LAB the correlation was 0.290 (p = 0.066) at 10 days. The CFU may be appropriate to identify a few families that change due to treatment or product. Without identifying viable cells to DNA recovered from NGS, there will always be the question whether the reads within the binned OTU in the intestinal tract is accurate.

scholarly journals A novel Microproteomic Approach Using Laser Capture Microdissection to Study Cellular Protrusions

2019 ◽  
Vol 20 (5) ◽  
pp. 1172 ◽  
Author(s):  
Karine Gousset ◽  
Ana Gordon ◽  
Shravan Kumar Kannan ◽  
Joey Tovar
Keyword(s):  
Laser Capture Microdissection ◽  
Protein Extraction ◽  
Cell Communication ◽  
Protein Composition ◽  
Fluorescent Markers ◽  
Different Types ◽  
Health And Disease ◽  
Multicellular Organisms ◽  
First Time ◽  
Laser Capture

Cell–cell communication is vital to multicellular organisms, and distinct types of cellular protrusions play critical roles during development, cell signaling, and the spreading of pathogens and cancer. The differences in the structure and protein composition of these different types of protrusions and their specific functions have not been elucidated due to the lack of a method for their specific isolation and analysis. In this paper, we described, for the first time, a method to specifically isolate distinct protrusion subtypes, based on their morphological structures or fluorescent markers, using laser capture microdissection (LCM). Combined with a unique fixation and protein extraction protocol, we pushed the limits of microproteomics and demonstrate that proteins from LCM-isolated protrusions can successfully and reproducibly be identified by mass spectrometry using ultra-high field Orbitrap technologies. Our method confirmed that different types of protrusions have distinct proteomes and it promises to advance the characterization and the understanding of these unique structures to shed light on their possible role in health and disease.

scholarly journals 368 Protein and amino acid effects on pig microbial ecology, health and nutrition

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 112-112
Author(s):  
Thomas Burkey
Keyword(s):  
Amino Acid ◽  
Microbial Ecology ◽  
Gut Microbiome ◽  
Genetic Background ◽  
Animal Health ◽  
Intestinal Microbiome ◽  
Specific Interactions ◽  
Protein Amino Acid ◽  
Health And Nutrition ◽  
Health And Disease

Abstract The gut microbiome is essential to animal health. Many factors, including both environmental (e.g. diet) and host-related (e.g. genetic background, sex, age), shape the intestinal microbiome. Pioneers in gut microbiology have stressed the critical importance of interactions among the diet, the gut microbiota, and the host on animal health and disease. Different protein types (e.g. plant-based vs. animal-based) have been shown to have differential effects on the gut microbiome. In addition, there is evidence of compartment-specific and amino acid-specific interactions that occur within the gastrointestinal tract. The result of these interactions must be considered to be essential as a variety of metabolites are produced and, for example, act as nutrients and modulators of physiologic processes. Our overarching goal is to discuss protein/amino acid effects on pig microbial ecology, health, and nutrition.

scholarly journals MetFish: A Metabolomics Platform for Studying Microbial Communities in Chemically Extreme Environments

2019 ◽  
Author(s):  
Chengdong Xu ◽  
Sneha P. Couvillion ◽  
Ryan L. Sontag ◽  
Nancy G. Isern ◽  
Yukari Maezato ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Mineral Content ◽  
Extreme Environments ◽  
Cell Communication ◽  
Microbial Consortia ◽  
Native Prairie ◽  
Prairie Soil ◽  
Fractured Well ◽  
First Time

Metabolites have essential roles in microbial communities, including as mediators of nutrient and energy exchange, cell-to-cell communication, and antibiosis. However, detecting and quantifying metabolites and other chemicals in samples having extremes in salt or mineral content using liquid chromatography-mass spectrometry (LC-MS)-based methods remains a significant challenge. Here we report a facile method based on in situ chemical derivatization followed by extraction for analysis of metabolites and other chemicals in hypersaline samples, enabling for the first time direct LC-MS-based exo-metabolomics analysis in sample matrices containing up to 2 molar total dissolved salts. The method, MetFish, is applicable to molecules containing amine, carboxylic acid, carbonyl, or hydroxyl functional groups, and can be integrated into either targeted or untargeted analysis pipelines. In targeted analyses, MetFish provided limits of quantification as low as 1 nM, broad linear dynamic ranges (up to 5-6 orders of magnitude) with excellent linearity, and low median inter-day reproducibility (e.g. 2.6%). MetFish was successfully applied in targeted and untargeted exo-metabolomics analyses of microbial consortia, quantifying amino acid dynamics in the exo-metabolome during community succession; in situ in a native prairie soil, whose exo-metabolome was isolated using a hypersaline extraction; and in input and produced fluids from a hydraulically fractured well, identifying dramatic changes in the exo-metabolome over time in the well.

scholarly journals Metabolic Disturbances and the Intestinal Microbiome

2015 ◽  
Vol 11 (01) ◽  
pp. 34
Author(s):  
Luigi F Meneghini ◽  
Keyword(s):  
Chronic Disease ◽  
Environmental Conditions ◽  
Gut Microbiome ◽  
Intestinal Microbiome ◽  
Gut Microflora ◽  
Therapeutic Approaches ◽  
Metabolic Disturbances ◽  
Health And Disease ◽  
The Impact

The gut microbiome, which can be affected by dietary and other “environmental” conditions, appears to have an important role in health and disease. A better understanding of the impact of changes in our gut microflora, as well as the determinants of these changes, represents an opportunity to address a number of acute and chronic disease conditions through novel mechanisms and therapeutic approaches.

scholarly journals Rhizosphere Microbiome of Arid Land Medicinal Plants and Extra Cellular Enzymes Contribute to Their Abundance

2020 ◽  
Vol 8 (2) ◽  
pp. 213 ◽  
Author(s):  
Abdul Latif Khan ◽  
Sajjad Asaf ◽  
Raeid M. M. Abed ◽  
Yen Ning Chai ◽  
Ahmed N. Al-Rawahi ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Extracellular Enzymes ◽  
Growth Conditions ◽  
Soil Conditions ◽  
Arid Environments ◽  
Operational Taxonomic Units ◽  
Rhizosphere Microbiome ◽  
First Time ◽  
Generation Sequencing

Revealing the unexplored rhizosphere microbiome of plants in arid environments can help in understanding their interactions between microbial communities and plants during harsh growth conditions. Here, we report the first investigation of rhizospheric fungal and bacterial communities of Adenium obesum, Aloe dhufarensis and Cleome austroarabica using next-generation sequencing approaches. A. obesum and A. dhufarensis grows in dry tropical and C. austroarabica in arid conditions of Arabian Peninsula. The results indicated the presence of 121 fungal and 3662 bacterial operational taxonomic units (OTUs) whilst microbial diversity was significantly high in the rhizosphere of A. obesum and A. dhufarensis and low in C. austroarabica. Among fungal phyla, Ascomycota and Basidiomycota were abundantly associated within rhizospheres of all three plants. However, Mucoromycota was only present in the rhizospheres of A. obesum and A. dhufarensis, suggesting a variation in fungal niche on the basis of host and soil types. In case of bacterial communities, Actinobacteria, Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, and Verrucomicrobia were predominant microbial phyla. These results demonstrated varying abundances of microbial structure across different hosts and locations in arid environments. Rhizosphere’s extracellular enzymes analysis revealed varying quantities, where, glucosidase, cellulase, esterase, and 1-aminocyclopropane-1-carboxylate deaminase were significantly higher in the rhizosphere of A. dhufarensis, while phosphatase and indole-acetic acid were highest in the rhizosphere of A. obesum. In conclusion, current findings usher for the first time the core microbial communities in the rhizospheric regions of three arid plants that vary greatly with location, host and soil conditions, and suggest the presence of extracellular enzymes could help in maintaining plant growth during the harsh environmental conditions.

scholarly journals Sulpiride Serves, a Substrate for the Gut Microbiome

Dose-Response ◽  
2021 ◽  
Vol 19 (1) ◽  
pp. 155932582098794
Author(s):  
Imran Mukhtar ◽  
Haseeb Anwar ◽  
Osman Asghar Mirza ◽  
Qasim Ali ◽  
Muhammad Umar Ijaz ◽  
...  
Keyword(s):  
Oral Administration ◽  
Gut Microbiome ◽  
Drug Target ◽  
Membrane Transporters ◽  
Intestinal Microbiome ◽  
Albino Rats ◽  
Body Organ ◽  
Total Absorbance ◽  
Research World

In the contemporary research world, the intestinal microbiome is now envisioned as a new body organ. Recently, the gut microbiome represents a new drug target in the gut, since various orthologues of intestinal drug transporters are also found present in the microbiome that lines the small intestine of the host. Owing to this, absorbance of sulpiride by the gut microbiome in an in vivo albino rats model was assessed after the oral administration with a single dose of 20mg/kg b.w. The rats were subsequently sacrificed at 2, 3, 4, 5 and 6 hours post oral administration to collect the gut microbial mass pellet. The drug absorbance by the gut microbiome was determined by pursuing the microbial lysate through RP-HPLC-UV. Total absorbance of sulpiride by the whole gut microbiome and drug absorbance per milligram of microbial pellet were found significantly higher at 4 hours post-administration as compared to all other groups. These results affirm the hypothesis that the structural homology between membrane transporters of the gut microbiome and intestinal epithelium of the host might play an important role in drug absorbance by gut microbes in an in vivo condition.

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