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A special issue of Nutrients (ISSN 2072-6643).

Deadline for manuscript submissions: closed (31 August 2018) | Viewed by 116036

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Special Issue Editors

Dr. Michael Conlon

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Guest Editor

CSIRO Health & Biosecurity, Adelaide, SA 5000, Australia
Interests: diet; nutraceuticals; gut; health; microbiome; polysaccharides; prebiotics; probiotics; polyphenols; immune function

Dr. Cuong Tran

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Guest Editor

CSIRO Health & Biosecurity, Adelaide, Australia
Interests: diet and health; probiotics; micronutrients; gut barrier function; gut microbiota; gastrointestinal health and disease

Special Issue Information

Dear Colleagues,

A growing body of scientific evidence supports an important, if not critical, role for gut microbes in the maintenance of gastrointestinal and general health. Despite this awareness, there are still significant gaps in our knowledge relating to the impacts of diet, lifestyle, genes and the environment on the gut microbiome, and how this translates to beneficial or detrimental health outcomes. Influences on gut microbes during establishment of microbial population profiles during early infancy, and potentially any time thereafter, could lead to susceptibilities to some diseases through development of less than ideal microbial populations. Microbial dysbioses have not only been linked to gastrointestinal diseases such as inflammatory bowel disease but also to a wide range of conditions affecting other parts of the body, and could contribute to obesity and associated metabolic complications, mental health and behavioural problems, and allergies, to name some examples. Understanding what represents a normal or optimal gut microbial profile is challenging given the significant inter-individual variation in these populations but currently available methods such as next generation sequencing, metagenomics, transcriptomics and metabolomics are beginning to shed new light on the composition, activities and products of our complex human microbial populations. We invite submissions to this Special Issue, which use these and other methods to extend our understanding of the role of the gut microbiome and/or their products in human health, and especially submissions which also examine the influence of nutrition. Studies using in vitro systems, animal experimentation and human analysis or intervention are welcome, as are submissions describing the effects of probiotics, prebiotics and other treatments, which modulate gut microbial populations.

Dr. Michael Conlon
Dr. Cuong Tran
Guest Editors

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Keywords

Gut
Microbes
Diet
Health
Dysbiosis
Gastrointestinal Disease
Prebiotics
Probiotics
Fermentation
Metagenomics
Metabolomics

Published Papers (12 papers)

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Research

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18 pages, 1388 KiB

Open AccessArticle

Associations of Probiotic Fermented Milk (PFM) and Yogurt Consumption with Bifidobacterium and Lactobacillus Components of the Gut Microbiota in Healthy Adults

by Noemí Redondo-Useros, Alina Gheorghe, Ligia E. Díaz-Prieto, Brenda Villavisencio, Ascensión Marcos and Esther Nova

Nutrients 2019, 11(3), 651; https://doi.org/10.3390/nu11030651 - 18 Mar 2019

Cited by 33 | Viewed by 7353

Abstract

The current study investigates whether probiotic fermented milk (PFM) and yogurt consumption (YC) are related to both the ingested bacteria taxa and the overall gut microbiota (GM) composition in healthy adults. PFM and YC habits were analyzed in 260 subjects (51% male) by specific questionnaires, and the following groups were considered: (1) PFM groups: nonconsumers (PFM-NC, n = 175) and consumers (PFM, n = 85), divided as follows: Bifidobacterium-containing PFM (Bif-PFM; n = 33), Lactobacillus-containing PFM (Lb-PFM; n = 14), and mixed Bifidobacterium and Lactobacillus-containing PFM (Mixed-PFM; n = 38); (2) PFM-NC were classified as: yogurt nonconsumers (Y-NC; n = 40) and yogurt consumers (n = 135). GM was analyzed through 16S rRNA sequencing. PFM consumers showed higher Bifidobacteria taxa levels compared to NC, from phylum through to species. Specifically, Bif-PFM consumption was related to higher B. animalis levels (p < 0.001), whereas Lb-PFM consumption was associated to higher levels of Bifidobacterium (p < 0.045) and B. longum (p = 0.011). YC was related to higher levels of the yogurt starter Streptococcus thermophilus (p < 0.001). Lactobacilli and the overall GM were not related either to YC or PFM consumption. According to these results, healthy adults might benefit from PFM intake by increasing Bifidobacterium levels. Full article

(This article belongs to the Special Issue Gut Microbiome and Human Health)

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21 pages, 3750 KiB

Open AccessArticle

Isolation and Characterization of Potentially Probiotic Bacterial Strains from Mice: Proof of Concept for Personalized Probiotics

by Larissa S. Celiberto, Roseli Aparecida Pinto, Elizeu Antonio Rossi, Bruce A. Vallance and Daniela C. U. Cavallini

Nutrients 2018, 10(11), 1684; https://doi.org/10.3390/nu10111684 - 05 Nov 2018

Cited by 22 | Viewed by 8207

Abstract

Modulation of the gut microbiota through the use of probiotics has been widely used to treat or prevent several intestinal diseases. However, inconsistent results have compromised the efficacy of this approach, especially in severe conditions such as inflammatory bowel disease (IBD). The purpose of our study was to develop a personalized probiotic strategy and assess its efficacy in a murine model of intestinal inflammation. Commensal bacterial strains were isolated from the feces of healthy mice and then administered back to the host as a personalized treatment in dextran sodium sulfate (DSS)-induced colitis. Colonic tissues were collected for histological analysis and to investigate inflammatory markers such as Il-1β, Il-6, TGF-β, and Il-10, and the enzyme myeloperoxidase as a neutrophil marker. The group that received the personalized probiotic showed reduced susceptibility to DSS-colitis as compared to a commercial probiotic. This protection was characterized by a lower disease activity index and reduced histopathological damage in the colon. Moreover, the personalized probiotic was more effective in modulating the host immune response, leading to decreased Il-1β and Il-6 and increased TGF-β and Il-10 expression. In conclusion, our study suggests that personalized probiotics may possess an advantage over commercial probiotics in treating dysbiotic-related conditions, possibly because they are derived directly from the host’s own microbiota. Full article

(This article belongs to the Special Issue Gut Microbiome and Human Health)

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16 pages, 666 KiB

Open AccessArticle

Impact of Agaricus bisporus Mushroom Consumption on Gut Health Markers in Healthy Adults

by Julie Hess, Qi Wang, Trevor Gould and Joanne Slavin

Nutrients 2018, 10(10), 1402; https://doi.org/10.3390/nu10101402 - 02 Oct 2018

Cited by 43 | Viewed by 13746

Abstract

Eating Agaricus bisporus mushrooms may impact gut health, because they contain known prebiotics. This study assessed mushroom consumption compared to meat on gastrointestinal tolerance, short chain fatty acid (SCFA) production, laxation, and fecal microbiota. A randomized open-label crossover study was conducted in healthy adults (n = 32) consuming protein-matched amounts of mushrooms or meat twice daily for ten days. Breath hydrogen measures were taken on day one, and gastrointestinal tolerance was evaluated throughout treatments. Fecal sample collection was completed days 6–10, and samples were assessed for bacterial composition, SCFA concentrations, weight, pH, and consistency. There were no differences in breath hydrogen, stool frequency, consistency, fecal pH, or SCFA concentrations between the two diets. The mushroom diet led to greater overall gastrointestinal symptoms than the meat diet on days one and two. The mushroom-rich diet resulted in higher average stool weight (p = 0.002) and a different fecal microbiota composition compared to the meat diet, with greater abundance of Bacteroidetes (p = 0.0002) and lower abundance of Firmicutes (p = 0.0009). The increase in stool weight and presence of undigested mushrooms in stool suggests that mushroom consumption may impact laxation in healthy adults. Additional research is needed to interpret the health implications of fecal microbiota shifts with mushroom feeding. Full article

(This article belongs to the Special Issue Gut Microbiome and Human Health)

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13 pages, 2220 KiB

Open AccessArticle

Maternal Administration of Probiotic or Prebiotic Prevents Male Adult Rat Offspring against Developmental Programming of Hypertension Induced by High Fructose Consumption in Pregnancy and Lactation

by Chien-Ning Hsu, Yu-Ju Lin, Chih-Yao Hou and You-Lin Tain

Nutrients 2018, 10(9), 1229; https://doi.org/10.3390/nu10091229 - 04 Sep 2018

Cited by 79 | Viewed by 5786

Abstract

Excessive intake of fructose is associated with hypertension. Gut microbiota and their metabolites are thought to be associated with the development of hypertension. We examined whether maternal high-fructose (HF) diet-induced programmed hypertension via altering gut microbiota, regulating short-chain fatty acids (SCFAs) and their receptors, and mediating nutrient-sensing signals in adult male offspring. Next, we aimed to determine whether early gut microbiota-targeted therapies with probiotic Lactobacillus casei and prebiotic inulin can prevent maternal HF-induced programmed hypertension. Pregnant rats received 60% high-fructose (HF) diet, with 2 × 10⁸ CFU/day Lactobacillus casei via oral gavage (HF+Probiotic), or with 5% w/w long chain inulin (HF+prebiotic) during pregnancy and lactation. Male offspring (n = 7–8/group) were assigned to four groups: control, HF, HF+Probiotic, and HF+Prebiotic. Rats were sacrificed at 12 weeks of age. Maternal probiotic Lactobacillus casei and prebiotic inulin therapies protect against hypertension in male adult offspring born to fructose-fed mothers. Probiotic treatment prevents HF-induced hypertension is associated with reduced plasma acetate level and decreased renal mRNA expression of Olfr78. While prebiotic treatment increased plasma propionate level and restored HF-induced reduction of Frar2 expression. Maternal HF diet has long-term programming effects on the adult offspring’s gut microbiota. Probiotic and prebiotic therapies exerted similar protective effects on blood pressure but they showed different mechanisms on modulation of gut microbiota. Maternal HF diet induced developmental programming of hypertension, which probiotic Lactobacillus casei or prebiotic inulin therapy prevented. Maternal gut microbiota-targeted therapies could be reprogramming strategies to prevent the development of hypertension caused by maternal consumption of fructose-rich diet. Full article

(This article belongs to the Special Issue Gut Microbiome and Human Health)

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10 pages, 1869 KiB

Open AccessArticle

A High Salt Diet Modulates the Gut Microbiota and Short Chain Fatty Acids Production in a Salt-Sensitive Hypertension Rat Model

by Ariel Bier, Tzipi Braun, Rawan Khasbab, Ayelet Di Segni, Ehud Grossman, Yael Haberman and Avshalom Leibowitz

Nutrients 2018, 10(9), 1154; https://doi.org/10.3390/nu10091154 - 23 Aug 2018

Cited by 139 | Viewed by 10899

Abstract

Emerging data indicate a correlation between gut microbial composition and cardiovascular disease including hypertension. The host’s diet greatly affects microbial composition and metabolite production. Short chain fatty acids (SCFAs) are products of microbial fermentation, which can be utilized by the host. It has been suggested that SCFAs play a pivotal role as mediators in a microbiome host: microbial interactions occur in health and disease. The aim of this study was to evaluate the effect of a high salt diet (HSD) on microbial variation and to determine whether this effect is accompanied by an alteration in fecal SCFAs. To this end, Dahl salt-sensitive rats were divided into two groups (n = 10 each): (A) Control: fed regular chow; and (B) Fed HSD. High-throughput pyrosequencing of the 16S rRNA amplicon sequencing was used for microbiome characterizing. Chromatography-mass spectrometry was used to measure the levels of SCFAs: acetic acid, propionic acid, butyric acid, and isobutyric acid in fecal samples. Differences in microbial composition were noted between groups. Principal Coordinate Analysis (PCoA) principal coordinate 1 (PC1) primarily separated controls from the HSD. Four taxa displayed significant differences between HSD and controls. Taxa from the Erwinia genus, the Christensenellaceae and Corynebacteriaceae families, displayed an increased abundance in HSD versus control. In contrast, taxa from the Anaerostipes genus displayed a decreased abundance in HSD. We were able to identify seven unique taxa that were significantly associated with blood pressure. There was a significant difference in fecal acetic acid, as well as propionic and isobutyric acid, but not in the butyric acid composition between groups. Adding salt to a diet impacts the gut’s microbial composition, which may alter fecal SCFA production. Full article

(This article belongs to the Special Issue Gut Microbiome and Human Health)

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10 pages, 1302 KiB

Open AccessArticle

Inulin Supplementation Does Not Reduce Plasma Trimethylamine N-Oxide Concentrations in Individuals at Risk for Type 2 Diabetes

by Mary Elizabeth Baugh, Cortney N. Steele, Christopher J. Angiletta, Cassie M. Mitchell, Andrew P. Neilson, Brenda M. Davy, Matthew W. Hulver and Kevin P. Davy

Nutrients 2018, 10(6), 793; https://doi.org/10.3390/nu10060793 - 20 Jun 2018

Cited by 26 | Viewed by 6973

Abstract

Trimethylamine N-oxide (TMAO) is associated with type 2 diabetes (T2DM) and increased risk of adverse cardiovascular events. Prebiotic supplementation has been purported to reduce TMAO production, but whether prebiotics reduce fasting or postprandial TMAO levels is unclear. Sedentary, overweight/obese adults at risk for T2DM (n = 18) were randomized to consume a standardized diet (55% carbohydrate, 30% fat) with 10 g/day of either an inulin supplement or maltodextrin placebo for 6 weeks. Blood samples were obtained in the fasting state and hourly during a 4-h high-fat challenge meal (820 kcal; 25% carbohydrate, 63% fat; 317.4 mg choline, 62.5 mg betaine, 8.1 mg l-carnitine) before and after the diet. Plasma TMAO and trimethylamine (TMA) moieties (choline, l-carnitine, betaine, and γ-butyrobetaine) were measured using isocratic ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). There were no differences in fasting or postprandial TMAO or TMA moieties between the inulin and placebo groups at baseline (all p > 0.05). There were no significant changes in fasting or postprandial plasma TMAO or TMA moiety concentrations following inulin or placebo. These findings suggest that inulin supplementation for 6 weeks did not reduce fasting or postprandial TMAO in individuals at risk for T2DM. Future studies are needed to identify efficacious interventions that reduce plasma TMAO concentrations. Full article

(This article belongs to the Special Issue Gut Microbiome and Human Health)

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12 pages, 1950 KiB

Open AccessArticle

Protective Effects of Salvianolic Acid A against Dextran Sodium Sulfate-Induced Acute Colitis in Rats

by Kai Wang, Qinqin Yang, Quanxin Ma, Bei Wang, Zhengrui Wan, Minli Chen and Liming Wu

Nutrients 2018, 10(6), 791; https://doi.org/10.3390/nu10060791 - 19 Jun 2018

Cited by 51 | Viewed by 6159

Abstract

Salvianolic acid A (SAA) is an active phenolic acid derived from Salvia miltiorrhiza Bunge (Danshen). To explore whether SAA has a therapeutic effect against inflammatory bowel disease (IBD), an acute colitis model was induced in rats by administering 3% dextran sodium sulphate (DSS) for one week. SAA in doses of 4 and 8 mg/kg/day was given by tail vein injection during DSS administration. Both dosages of SAA ameliorated the colitis symptoms, with decreases observed in the disease activity index. A high dosage of SAA (8 mg/kg/day) promoted a longer colon length and an improved colonic tissue structure, compared with the DSS-treated rats not receiving SAA. SAA dose-dependently decreased colonic gene expression of pro-inflammatory cytokines (IL-1β, MCP-1 and IL-6). Moreover, a high dosage of SAA protected against DSS-induced damage to tight junctions (TJ) in the rats’ colons, by increasing TJ-related gene expression (ZO-1 and occuldin). Finally, using 16S rRNA phylogenetic sequencing, we found that SAA modulated gut microbiota imbalance during colitis by increasing the gut microbial diversity as well as selectively promoting some probiotic populations, including Akkermansia spp. Our study suggests that SAA is a promising candidate for the treatment of IBD. Full article

(This article belongs to the Special Issue Gut Microbiome and Human Health)

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18 pages, 3359 KiB

Open AccessArticle

Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project

by Natalia S. Klimenko, Alexander V. Tyakht, Anna S. Popenko, Anatoly S. Vasiliev, Ilya A. Altukhov, Dmitry S. Ischenko, Tatiana I. Shashkova, Daria A. Efimova, Dmitri A. Nikogosov, Dmitrii A. Osipenko, Sergey V. Musienko, Kseniya S. Selezneva, Ancha Baranova, Alexander M. Kurilshikov, Stepan M. Toshchakov, Aleksei A. Korzhenkov, Nazar I. Samarov, Margarita A. Shevchenko, Alina V. Tepliuk and Dmitry G. Alexeev

Nutrients 2018, 10(5), 576; https://doi.org/10.3390/nu10050576 - 08 May 2018

Cited by 91 | Viewed by 20907

Abstract

Personalized nutrition is of increasing interest to individuals actively monitoring their health. The relations between the duration of diet intervention and the effects on gut microbiota have yet to be elucidated. Here we examined the associations of short-term dietary changes, long-term dietary habits and lifestyle with gut microbiota. Stool samples from 248 citizen-science volunteers were collected before and after a self-reported 2-week personalized diet intervention, then analyzed using 16S rRNA sequencing. Considerable correlations between long-term dietary habits and gut community structure were detected. A higher intake of vegetables and fruits was associated with increased levels of butyrate-producing Clostridiales and higher community richness. A paired comparison of the metagenomes before and after the 2-week intervention showed that even a brief, uncontrolled intervention produced profound changes in community structure: resulting in decreased levels of Bacteroidaceae, Porphyromonadaceae and Rikenellaceae families and decreased alpha-diversity coupled with an increase of Methanobrevibacter, Bifidobacterium, Clostridium and butyrate-producing Lachnospiraceae- as well as the prevalence of a permatype (a bootstrapping-based variation of enterotype) associated with a higher diversity of diet. The response of microbiota to the intervention was dependent on the initial microbiota state. These findings pave the way for the development of an individualized diet. Full article

(This article belongs to the Special Issue Gut Microbiome and Human Health)

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11 pages, 390 KiB

Open AccessArticle

The Effect of Oligofructose-Enriched Inulin on Faecal Bacterial Counts and Microbiota-Associated Characteristics in Celiac Disease Children Following a Gluten-Free Diet: Results of a Randomized, Placebo-Controlled Trial

by Natalia Drabińska, Elżbieta Jarocka-Cyrta, Lidia Hanna Markiewicz and Urszula Krupa-Kozak

Nutrients 2018, 10(2), 201; https://doi.org/10.3390/nu10020201 - 12 Feb 2018

Cited by 53 | Viewed by 10218

Abstract

Celiac disease (CD) is associated with intestinal microbiota alterations. The administration of prebiotics could be a promising method of restoring gut homeostasis in CD. The aim of this study was to evaluate the effect of prolonged oligofructose-enriched inulin (Synergy 1) administration on the characteristics and metabolism of intestinal microbiota in CD children following a gluten-free diet (GFD). Thirty-four paediatric CD patients (mean age 10 years; 62% females) on a GFD were randomized into two experimental groups receiving Synergy 1 (10 g/day) or placebo (maltodextrin; 7 g/day) for 3 months. The quantitative gut microbiota characteristics and short-chain fatty acids (SCFAs) concentration were analysed. In addition, side effects were monitored. Generally, the administration of Synergy 1 in a GFD did not cause any side effects. After the intervention period, Bifidobacterium count increased significantly (p < 0.05) in the Synergy 1 group. Moreover, an increase in faecal acetate and butyrate levels was observed in the prebiotic group. Consequently, total SCFA levels were 31% higher than at the baseline. The presented trial shows that Synergy 1 applied as a supplement of a GFD had a moderate effect on the qualitative characteristics of faecal microbiota, whereas it stimulated the bacterial metabolite production in CD children. Full article

(This article belongs to the Special Issue Gut Microbiome and Human Health)

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Review

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21 pages, 1243 KiB

Open AccessReview

Gut Microbiota’s Relationship with Liver Disease and Role in Hepatoprotection by Dietary Natural Products and Probiotics

by Xiao Meng, Sha Li, Ya Li, Ren-You Gan and Hua-Bin Li

Nutrients 2018, 10(10), 1457; https://doi.org/10.3390/nu10101457 - 08 Oct 2018

Cited by 77 | Viewed by 9431

Abstract

A variety of dietary natural products have shown hepatoprotective effects. Increasing evidence has also demonstrated that gut microorganisms play an important role in the hepatoprotection contributed by natural products. Gut dysbiosis could increase permeability of the gut barrier, resulting in translocated bacteria and leaked gut-derived products, which can reach the liver through the portal vein and might lead to increased oxidative stress and inflammation, thereby threatening liver health. Targeting gut microbiota modulation represents a promising strategy for hepatoprotection. Many natural products could protect the liver from various injuries or mitigate hepatic disorders by reverting gut dysbiosis, improving intestinal permeability, altering the primary bile acid, and inhibiting hepatic fatty acid accumulation. The mechanisms underlying their beneficial effects also include reducing oxidative stress, suppressing inflammation, attenuating fibrosis, and decreasing apoptosis. This review discusses the hepatoprotective effects of dietary natural products via modulating the gut microbiota, mainly focusing on the mechanisms of action. Full article

(This article belongs to the Special Issue Gut Microbiome and Human Health)

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16 pages, 1136 KiB

Open AccessReview

The Microbiome and Radiation Induced-Bowel Injury: Evidence for Potential Mechanistic Role in Disease Pathogenesis

by Tomoko Kumagai, Farooq Rahman and Andrew M. Smith

Nutrients 2018, 10(10), 1405; https://doi.org/10.3390/nu10101405 - 02 Oct 2018

Cited by 99 | Viewed by 8007

Abstract

Radiotherapy has played a major role in both the curative and palliative treatment of cancer patients for decades. However, its toxic effect to the surrounding normal healthy tissue remains a major drawback. In cases of intra-abdominal and/or pelvic malignancy, healthy bowel is inevitably included in the radiation field, causing undesirable consequences that subsequently manifest as radiation-induced bowel injury, which is associated with significant morbidity and mortality. The pathophysiology of radiation-induced bowel injury is poorly understood, although we now know that it derives from a complex interplay of epithelial injury and alterations in the enteric immune, nervous, and vascular systems in genetically predisposed individuals. Furthermore, evidence supporting a pivotal role for the gut microbiota in the development of radiation-induced bowel injury has been growing. In this review, we aim to appraise our current understanding of radiation-induced bowel injury and the role of the microbiome in its pathogenesis as well as prevention and treatment. Greater understanding of the relationship between the disease mechanism of radiation-induced bowel injury and gut microbiome might shed light on potential future prevention and treatment strategies through the modification of a patient’s gut microbiome. Full article

(This article belongs to the Special Issue Gut Microbiome and Human Health)

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10 pages, 1457 KiB

Open AccessFeature PaperReview

Interactions between Bitter Taste, Diet and Dysbiosis: Consequences for Appetite and Obesity

by Alexandria Turner, Martin Veysey, Simon Keely, Christopher Scarlett, Mark Lucock and Emma L. Beckett

Nutrients 2018, 10(10), 1336; https://doi.org/10.3390/nu10101336 - 20 Sep 2018

Cited by 26 | Viewed by 6715

Abstract

The type 2 family of taste receptors (T2Rs) detect and respond to bitter tastants. These receptors are expressed throughout the gastrointestinal (GI) tract, with location dependant roles. In the oral cavity, T2Rs are involved in the conscious perception of bitter tastants, while in the lower GI tract they have roles in chemoreception and regulation of GI function. Through these diverse roles, these receptors may be involved in modulating appetite and diet, with consequences for weight regulation and obesity. Interestingly, the concentration of T2Rs in the GI tract is greatest in the large intestine, the organ with the densest colonisation of bacteria. The gut microbiome has been the subject of intense research, as a plethora of roles linking microbiota to human health continue to be uncovered. Of particular interest is the microbial signature associated with obesity. Obesity is a leading health concern, and advances in our understanding of this disease are needed. Diet is a known modifiable factor in the development of obesity. However, diet only partially explains disease risk. Changes in microbial energy harvesting by the microbiota plays a role in obesity, and the composition of these energy harvesting populations may be controlled by taste receptors. This review explores T2Rs as a potential link between obesity and the human GI microbiome. Full article

(This article belongs to the Special Issue Gut Microbiome and Human Health)

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