Fruit and Vegetable Supplemented Diet Modulates the Pig Transcriptome and Microbiome after a Two-Week Feeding Intervention

A study was conducted to determine the effects of a diet supplemented with fruits and vegetables (FV) on the host whole blood cell (WBC) transcriptome and the composition and function of the intestinal microbiome. Nine six-week-old pigs were fed a pig grower diet alone or supplemented with lyophilized FV equivalent to half the daily recommended amount prescribed for humans by the Dietary Guideline for Americans (DGA) for two weeks. Host transcriptome changes in the WBC were evaluated by RNA sequencing. Isolated DNA from the fecal microbiome was used for 16S rDNA taxonomic analysis and prediction of metabolomic function. Feeding an FV-supplemented diet to pigs induced differential expression of several genes associated with an increase in B-cell development and differentiation and the regulation of cellular movement, inflammatory response, and cell-to-cell signaling. Linear discriminant analysis effect size (LEfSe) in fecal microbiome samples showed differential increases in genera from Lachnospiraceae and Ruminococcaceae families within the order Clostridiales and Erysipelotrichaceae family with a predicted reduction in rgpE-glucosyltransferase protein associated with lipopolysaccharide biosynthesis in pigs fed the FV-supplemented diet. These results suggest that feeding an FV-supplemented diet for two weeks modulated markers of cellular inflammatory and immune function in the WBC transcriptome and the composition of the intestinal microbiome by increasing the abundance of bacterial taxa that have been associated with improved intestinal health.

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A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function

Microorganisms ◽

10.3390/microorganisms8121887 ◽

2020 ◽

Vol 8 (12) ◽

pp. 1887

Author(s):

Laurin Gierse ◽

Alexander Meene ◽

Daniel Schultz ◽

Theresa Schwaiger ◽

Claudia Karte ◽

...

Keyword(s):

16S Rrna ◽

Short Chain Fatty Acids ◽

Minimal Invasive ◽

Intestinal Microbiome ◽

Rrna Gene ◽

Fecal Microbiome ◽

Longitudinal Dynamics ◽

Microbiome Composition ◽

Swine Feces ◽

And Function

Swine are regarded as promising biomedical models, but the dynamics of their gastrointestinal microbiome have been much less investigated than that of humans or mice. The aim of this study was to establish an integrated multi-omics protocol to investigate the fecal microbiome of healthy swine. To this end, a preparation and analysis protocol including integrated sample preparation for meta-omics analyses of deep-frozen feces was developed. Subsequent data integration linked microbiome composition with function, and metabolic activity with protein inventories, i.e., 16S rRNA data and expressed proteins, and identified proteins with corresponding metabolites. 16S rRNA gene amplicon and metaproteomics analyses revealed a fecal microbiome dominated by Prevotellaceae, Lactobacillaceae, Lachnospiraceae, Ruminococcaceae and Clostridiaceae. Similar microbiome compositions in feces and colon, but not ileum samples, were observed, showing that feces can serve as minimal-invasive proxy for porcine colon microbiomes. Longitudinal dynamics in composition, e.g., temporal decreased abundance of Lactobacillaceae and Streptococcaceae during the experiment, were not reflected in microbiome function. Instead, metaproteomics and metabolomics showed a rather stable functional state, as evident from short-chain fatty acids (SCFA) profiles and associated metaproteome functions, pointing towards functional redundancy among microbiome constituents. In conclusion, our pipeline generates congruent data from different omics approaches on the taxonomy and functionality of the intestinal microbiome of swine.

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Production, Storage Stability, and Susceptibility Testing of Reuterin and Its Impact on the Murine Fecal Microbiome and Volatile Organic Compound Profile

Frontiers in Microbiology ◽

10.3389/fmicb.2021.699858 ◽

2021 ◽

Vol 12 ◽

Author(s):

Christoph Castellani ◽

Beate Obermüller ◽

Bernhard Kienesberger ◽

Georg Singer ◽

Clemens Peterbauer ◽

...

Keyword(s):

Antimicrobial Activity ◽

Storage Stability ◽

Antimicrobial Effect ◽

Intestinal Microbiome ◽

Rrna Gene ◽

Linear Discriminant ◽

Fecal Microbiome ◽

Alpha And Beta Diversity ◽

Volatile Organic

Background: Probiotics are generally considered as safe, but infections may rarely occur in vulnerable patients. Alternatives to live microorganisms to manage dysbiosis may be of interest in these patients. Reuterin is a complex component system exhibiting broad spectrum antimicrobial activity and a possible candidate substance in these cases.Methods: Reuterin supernatant was cultured from Lentilactobacillus diolivorans in a bioreactor in a two-step process. Storage stability at −20°C and effect of repeated freeze-thaw cycles were assessed by high performance liquid chromatography (HPLC). Antimicrobial activity was tested against Clostridium difficile, Listeria monocytogenes, Escherichia coli, Enterococcus faecium, Staphylococcus (S.) aureus, Staphylococcus epidermidis, Streptococcus (S.) agalactiae, Propionibacterium acnes, and Pseudomonas aeruginosae. Male BALBc mice were gavage fed with reuterin supernatant (n = 10) or culture medium (n = 10). Fecal volatile organic compounds (VOC) were assessed by gas chromatography mass spectroscopy; the microbiome was examined by 16S rRNA gene sequencing.Results: The supernatant contained 13.4 g/L reuterin (3-hydroxypropionaldehyde; 3-HPA). 3-HPA content remained stable at −20°C for 35 days followed by a slow decrease of its concentration. Repeated freezing/thawing caused a slow 3-HPA decrease. Antimicrobial activity was encountered against S. aureus, S. epidermidis, and S. agalactiae. Microbiome analysis showed no differences in alpha and beta diversity markers. Linear discriminant effect size (LEfSe) analysis identified Lachnospiraceae_bacterium_COE1 and Ruminoclostridium_5_uncultured_Clostridiales_ bacterium (in the reuterin medium group) and Desulfovibrio_uncultured_ bacterium, Candidatus Arthromitus, Ruminococcae_NK4A214_group, and Eubacterium_xylanophilum_group (in the reuterin group) as markers for group differentiation. VOC analysis showed a significant decrease of heptane and increase of 3-methylbutanal in the reuterin group.Conclusion: The supernatant produced in this study contained acceptable amounts of 3-HPA remaining stable for 35 days at −20°C and exhibiting an antimicrobial effect against S. aureus, S. agalactiae, and S. epidermidis. Under in vivo conditions, the reuterin supernatant caused alterations of the fecal microbiome. In the fecal, VOC analysis decreased heptane and increased 3-methylbutanal were encountered. These findings suggest the high potential of the reuterin system to influence the intestinal microbiome in health and disease, which needs to be examined in detail in future projects.

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The equine intestinal microbiome

Animal Health Research Reviews ◽

10.1017/s1466252312000035 ◽

2012 ◽

Vol 13 (1) ◽

pp. 121-128 ◽

Cited By ~ 43

Author(s):

Marcio C. Costa ◽

J. Scott Weese

Keyword(s):

Intestinal Microbiome ◽

Fecal Microbiome ◽

Disease States ◽

Normal Microbiota ◽

Health And Disease ◽

Therapeutic Measures ◽

And Function ◽

Relationship Of ◽

Near Future ◽

The Relationship

AbstractThe equine intestinal tract contains a complex microbial population (microbiota) that plays an important role in health and disease. Despite the undeniable importance of a ‘normal’ microbiota, understanding of the composition and function of this population is currently limited. As methods to characterize the microbiota and its genetic makeup (the microbiome) have evolved, the composition and complexity of this population are starting to be revealed. As is befitting a hindgut fermenter, members of the Firmicutes phylum appear to predominate, yet there are significant populations of numerous other phyla. The microbiome appears to be profoundly altered in certain disease states, and better understanding of these alterations may offer hope for novel preventive and therapeutic measures. The development and increasing availability of next generation sequencing and bioinformatics methods offer a revolution in microbiome evaluation and it is likely that significant advances will be made in the near future. Yet, proper use of these methods requires further study of basic aspects such as optimal testing protocols, the relationship of the fecal microbiome to more proximal locations where disease occurs, normal intra- and inter-horse variation, seasonal variation, and similar factors.

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Alterations in intestinal microbiota diversity, composition, and function in patients with sarcopenia

Scientific Reports ◽

10.1038/s41598-021-84031-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Lin Kang ◽

Pengtao Li ◽

Danyang Wang ◽

Taihao Wang ◽

Dong Hao ◽

...

Keyword(s):

Skeletal Muscle ◽

16S Rrna ◽

Intestinal Microbiota ◽

Muscle Growth ◽

Growth Function ◽

16S Rrna Sequencing ◽

Fecal Samples ◽

Lipopolysaccharide Biosynthesis ◽

Rrna Sequencing ◽

And Function

Abstract16S rRNA sequencing of human fecal samples has been tremendously successful in identifying microbiome changes associated with both aging and disease. A number of studies have described microbial alterations corresponding to physical frailty and nursing home residence among aging individuals. A gut-muscle axis through which the microbiome influences skeletal muscle growth/function has been hypothesized. However, the microbiome has yet to be examined in sarcopenia. Here, we collected fecal samples of 60 healthy controls (CON) and 27 sarcopenic (Case)/possibly sarcopenic (preCase) individuals and analyzed the intestinal microbiota using 16S rRNA sequencing. We observed an overall reduction in microbial diversity in Case and preCase samples. The genera Lachnospira, Fusicantenibacter, Roseburia, Eubacterium, and Lachnoclostridium—known butyrate producers—were significantly less abundant in Case and preCase subjects while Lactobacillus was more abundant. Functional pathways underrepresented in Case subjects included numerous transporters and phenylalanine, tyrosine, and tryptophan biosynthesis suggesting that protein processing and nutrient transport may be impaired. In contrast, lipopolysaccharide biosynthesis was overrepresented in Case and PreCase subjects suggesting that sarcopenia is associated with a pro-inflammatory metagenome. These analyses demonstrate structural and functional alterations in the intestinal microbiota that may contribute to loss of skeletal muscle mass and function in sarcopenia.

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Impact of Dietary Flavanols on Microbiota, Immunity and Inflammation in Metabolic Diseases

Nutrients ◽

10.3390/nu13030850 ◽

2021 ◽

Vol 13 (3) ◽

pp. 850

Author(s):

María Ángeles Martín ◽

Sonia Ramos

Keyword(s):

Immune System ◽

Fruits And Vegetables ◽

Metabolic Diseases ◽

Nuclear Factor Κb ◽

Low Grade ◽

Beneficial Effects ◽

Health And Disease ◽

Immunological Reactions ◽

And Function ◽

Positive Properties

Flavanols are natural occurring polyphenols abundant in fruits and vegetables to which have been attributed to beneficial effects on health, and also against metabolic diseases, such as diabetes, obesity and metabolic syndrome. These positive properties have been associated to the modulation of different molecular pathways, and importantly, to the regulation of immunological reactions (pro-inflammatory cytokines, chemokines, adhesion molecules, nuclear factor-κB [NF-κB], inducible enzymes), and the activity of cells of the immune system. In addition, flavanols can modulate the composition and function of gut microbiome in a prebiotic-like manner, resulting in the positive regulation of metabolic pathways and immune responses, and reduction of low-grade chronic inflammation. Moreover, the biotransformation of flavanols by gut bacteria increases their bioavailability generating a number of metabolites with potential to affect human metabolism, including during metabolic diseases. However, the exact mechanisms by which flavanols act on the microbiota and immune system to influence health and disease remain unclear, especially in humans where these connections have been scarcely explored. This review seeks to summarize recent advances on the complex interaction of flavanols with gut microbiota, immunity and inflammation focus on metabolic diseases.

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The Recent Understanding of the Neurotrophin's Role in Skeletal Muscle Adaptation

Journal of Biomedicine and Biotechnology ◽

10.1155/2011/201696 ◽

2011 ◽

Vol 2011 ◽

pp. 1-12 ◽

Cited By ~ 51

Author(s):

Kunihiro Sakuma ◽

Akihiko Yamaguchi

Keyword(s):

Skeletal Muscle ◽

Neuromuscular Disorders ◽

Muscle Fibers ◽

Brain Disorders ◽

Muscle Adaptation ◽

Bdnf Mrna ◽

Pathological Conditions ◽

Development And Differentiation ◽

And Function

This paper summarizes the various effects of neurotrophins in skeletal muscle and how these proteins act as potential regulators of the maintenance, function, and regeneration of skeletal muscle fibers. Increasing evidence suggests that this family of neurotrophic factors influence not only the survival and function of innervating motoneurons but also the development and differentiation of myoblasts and muscle fibers. Muscle contractions (e.g., exercise) produce BDNF mRNA and protein in skeletal muscle, and the BDNF seems to play a role in enhancing glucose metabolism and may act for myokine to improve various brain disorders (e.g., Alzheimer's disease and major depression). In adults with neuromuscular disorders, variations in neurotrophin expression are found, and the role of neurotrophins under such conditions is beginning to be elucidated. This paper provides a basis for a better understanding of the role of these factors under such pathological conditions and for treatment of human neuromuscular disease.

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PSIX-5 Diet is more powerful than age in shaping the rumen bacterial community and function of dairy cattle

Journal of Animal Science ◽

10.1093/jas/skab235.792 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 444-444

Author(s):

YangYi Hao ◽

Shuai Huang ◽

Shengli Li

Keyword(s):

Bacterial Community ◽

Dairy Cattle ◽

Rumen Fluid ◽

Rumen Bacteria ◽

Great Ability ◽

Linear Discriminant ◽

High Fiber ◽

Fiber Diet ◽

High Fiber Diet ◽

And Function

Abstract The objective was to understand the effects of diet and age on the rumen bacterial community and function, 48 dairy cattle were selected. Rumen fluid samples were collected from each animal at 1.5 (1.5M, milk and starter diet, n=8), 6 (6M, starter and oat grass, n=8), 9 (9M, high fiber diet, n=8), 18 (18M, high fiber diet, n=8), 23 (23M, high fiber diet, n=8) and 27 (27M, high grain diet, n=8) months old. The acetate/propionate ratio (A/P) at M9, M18, and M23 were significantly higher than M27 and M1.5 (P < 0.05), while the A/P at M6 was lower than others (P < 0.05). The total volatile fatty acid at M23 and M27 was higher than others (P < 0.05). The urease at M18 was significantly lower than M1.5, M6, and M9 (P < 0.05), and the xylanase at M18 was significantly higher than M1.5, M23, and M27 (P < 0.05). 16S rRNA sequencing data and the Linear discriminant analysis showed that thirty-three bacteria were identified as biomarkers among ages and diets. The age and diet contributed 7.98% and 32.49% to the rumen bacteria community using the variation partitioning approach analysis. The norank_f_p-251-o5 was significantly and positively correlated with age (r = 0.83, P < 0.01), while Eubacterium was significantly and negatively correlated with age (r = -0.84, P < 0.01). Dietary fiber showed a strong correlation (r > 0.80, P < 0.01) with Lachnospiraceae, NK4A214_group, Saccharofermentans, Clostridia, Pseudobutyrivibrio Bacteroidales_UCG-001. These genera also negatively correlated with dietary crude protein and starch (r < - 0.80, P < 0.01). All these bacteria were significantly correlated with A/P, acetate, and urease (r > 0.5, P < 0.05). These findings collectively indicated that diet drives the great ability to shape the rumen bacteria community and function than age.

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Deep Illumina-Based Shotgun Sequencing Reveals Dietary Effects on the Structure and Function of the Fecal Microbiome of Growing Kittens

PLoS ONE ◽

10.1371/journal.pone.0101021 ◽

2014 ◽

Vol 9 (7) ◽

pp. e101021 ◽

Cited By ~ 23

Author(s):

Oliver Deusch ◽

Ciaran O’Flynn ◽

Alison Colyer ◽

Penelope Morris ◽

David Allaway ◽

...

Keyword(s):

Structure And Function ◽

Shotgun Sequencing ◽

Dietary Effects ◽

Fecal Microbiome ◽

And Function

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Basal Diet Determined Long-Term Composition of the Gut Microbiome and Mouse Phenotype to a Greater Extent than Fecal Microbiome Transfer from Lean or Obese Human Donors

Nutrients ◽

10.3390/nu11071630 ◽

2019 ◽

Vol 11 (7) ◽

pp. 1630 ◽

Cited By ~ 6

Author(s):

Daphne M. Rodriguez ◽

Abby D. Benninghoff ◽

Niklas D.J. Aardema ◽

Sumira Phatak ◽

Korry J. Hintze

Keyword(s):

Gut Microbiome ◽

Basal Diet ◽

Body Type ◽

Human Donor ◽

Final Body Weight ◽

Linear Discriminant ◽

Fecal Microbiome ◽

Microbiome Composition ◽

Diet Induced Obesity ◽

Obese Human

The Western dietary pattern can alter the gut microbiome and cause obesity and metabolic disorders. To examine the interactions between diet, the microbiome, and obesity, we transplanted gut microbiota from lean or obese human donors into mice fed one of three diets for 22 weeks: (1) a control AIN93G diet; (2) the total Western diet (TWD), which mimics the American diet; or (3) a 45% high-fat diet-induced obesity (DIO) diet. We hypothesized that a fecal microbiome transfer (FMT) from obese donors would lead to an obese phenotype and aberrant glucose metabolism in recipient mice that would be exacerbated by consumption of the TWD or DIO diets. Prior to the FMT, the native microbiome was depleted using an established broad-spectrum antibiotic protocol. Interestingly, the human donor body type microbiome did not significantly affect final body weight or body composition in mice fed any of the experimental diets. Beta diversity analysis and linear discriminant analysis with effect size (LEfSe) showed that mice that received an FMT from obese donors had a significantly different microbiome compared to mice that received an FMT from lean donors. However, after 22 weeks, diet influenced the microbiome composition irrespective of donor body type, suggesting that diet is a key variable in the shaping of the gut microbiome after FMT.

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Dietary Patterns Differentially Affect Microbiome Composition and Function in a Porcine Model of Obesity-related Metabolic Disorder (OR23-04-19)

Current Developments in Nutrition ◽

10.1093/cdn/nzz040.or23-04-19 ◽

2019 ◽

Vol 3 (Supplement_1) ◽

Author(s):

Gloria Solano-Aguilar ◽

Jonathan Shao ◽

Joseph Urban ◽

Sukla Lakshman ◽

Saebyeol Jang ◽

...

Keyword(s):

Dietary Patterns ◽

Dietary Intervention ◽

Diversity Index ◽

Early Stage ◽

Saturated Fat ◽

Post Intervention ◽

Fecal Microbiome ◽

Microbiome Composition ◽

And Function ◽

The Impact

Abstract Objectives To determine the impact of two isocaloric diets containing (38% ,15% and 47% energy from fat, protein and carbohydrate, respectively): Western diet (WD) rich in saturated fat, refined carbohydrate, low in fiber and high in cholesterol, and a heart healthy diet (HHD) rich in unsaturated fat, unrefined carbohydrate, fruits/vegetables, high in fiber and low in cholesterol, on the composition and function of the gut microbiome Methods Thirty-Ossabaw pigs were fed WD or HHD diets with half within each group therapeutically treated with statin (atorvastatin [Lipitor]). The fecal microbiome was analyzed one and six months after dietary intervention by 16S rRNA sequencing and metagenomic function was empirically inferred Results Genus diversity was transiently affected with a reduced Shannon Diversity index one month after feeding the WD or HHD (FDR P < 0.05) with no change between groups at 6 months. Bacterial communities were clustered and separated by diet independent of gender and separated by treatment with statin in the HHD only. Verrucomicrobiaceae (Akkermansia) and Methanobacteriales (Methanobrevibacter) were increased in pigs as early as one month after feeding the HHD, as was Clostridiales and Bifidobacterium (associated with optimal intestinal health). There was an enrichment of Proteobacteria (Succinivibrionaceae, Desulfovibrionaceae) in pigs fed the WD. Additional members of the Firmicutes phylum were detected. Diet-dependent associations (all P < 0.05) were identified between Lachnospiraceae members and early host dyslipidemia, inflammation, and atheromatous lesions in the left anterior descending proximal (LAD) and LAD/Left circumflex (LCX) bifurcation six months post-intervention. Conclusions These data document for the first time a distinctive bacterial profile in Ossabaw pigs with a diet-induced dyslipidemia and early stage atherosclerosis. Taken together these results represent a new model to examine mechanistic pathways of dietary patterns and/or drug interactions and its effect on modulating microbiome in developing atherosclerosis. Funding Sources USDA project 8040-51530-056-00 and Inter Agency USDA Agreement 588-1950-9-001 between BHNRC and Jean Mayer USDA-HNRCA

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