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Advances in Probiotic: Interaction with the Gut Microbiota and the Molecular Mechanisms of the Beneficial Effects

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (31 May 2023) | Viewed by 21852

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Special Issue Editors

Prof. Dr. Xuewu Zhang

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Guest Editor

College of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
Interests: food nutrition and health
Special Issues, Collections and Topics in MDPI journals

Dr. Leilei Yu

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Guest Editor

1. State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
2. School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
3. International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi 214122, China
Interests: probiotics; prebiotics; dietary polysaccharide; functional food; gut microbiota and metabolites; gut health; food microbiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The diverse microbial species in the gastrointestinal tract (gut microbiota) are considered a ‘superorganism’ with important roles in the human physiology and metabolism. Their dysbiosis is associated with various diseases and some taxa can even serve as biomarkers or carry out the therapeutic targeting of specific diseases. The dietary intake appears to be a major regulator of the structure and function of gut microbiota. Specific dietary components, including probiotics, prebiotics, polysaccharides, polyphenols, and polypeptides, improve health status or reduce disease risk via the regulation of the gut microbiota. Although the importance of gut microbiota and diet on health and disease has attracted increasing attention, the complexity and variability of this relationship have not been fully recognized. New insights and technologies will help decipher the intricacies of microbiota–diet–health relationships.

Thus, a Special Issue entitled “Advances in Gut Microbiome in Health and Disease” is being released, welcoming all research and review articles that will improve our understanding of the molecular basis of host, diet, and gut microbiota interaction and create opportunities for breakthroughs in precise dietary interventions for personal health management.

Prof. Dr. Xuewu Zhang
Dr. Leilei Yu
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

gut microbiota
gut barrier
gut health
immune
inflammatory
dietary components
polysaccharide
probiotics

Published Papers (10 papers)

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Research

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14 pages, 5932 KiB

Open AccessArticle

Unique Gut Microbiome Signatures among Adult Patients with Moderate to Severe Atopic Dermatitis in Southern Chinese

by Yiwei Wang, Jinpao Hou, Joseph Chi-Ching Tsui, Lin Wang, Junwei Zhou, Un Kei Chan, Claudia Jun Yi Lo, Pui Ling Kella Siu, Steven King Fan Loo and Stephen Kwok Wing Tsui

Int. J. Mol. Sci. 2023, 24(16), 12856; https://doi.org/10.3390/ijms241612856 - 16 Aug 2023

Cited by 7 | Viewed by 1628

Abstract

Imbalance of the immune system caused by alterations of the gut microbiome is considered to be a critical factor in the pathogenesis of infant eczema, but the exact role of the gut microbiome in adult atopic dermatitis (AD) patients remains to be clarified. To investigate the differences of the gut microbiome between adult AD patients and healthy individuals, stool samples of 234 adults, containing 104 AD patients and 130 healthy subjects, were collected for 16S rRNA gene amplicon. Altered structure and metabolic dysfunctions of the gut microbiome were identified in adult AD patients. Our results illustrated that the adult AD patients were more likely to have allergies, particularly non-food allergies. In addition, the gut microbiome composition of the AD and normal groups were considerably different. Moreover, Romboutsia and Clostridi-um_sensu_stricto_1 was enriched in the normal group, whereas Blautia, Butyricicoccus, Lachnoclostridium, Eubacterium_hallii_group, Erysi-pelatoclostridium, Megasphaera, Oscillibacter, and Flavonifractor dominated in the AD group. Additionally, purine nucleotide degradation pathways were significantly enriched in the AD group, and the enrichment of proteinogenic amino acid biosynthesis pathways was found in the normal group. This study provides insights into new therapeutic strategies targeting the gut microbiome for AD and evidence for the involvement of the gut–skin axis in AD patients. Full article

(This article belongs to the Special Issue Advances in Probiotic: Interaction with the Gut Microbiota and the Molecular Mechanisms of the Beneficial Effects)

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15 pages, 3652 KiB

Open AccessArticle

Investigation into the Potential Role of Propionibacterium freudenreichii in Prevention of Colorectal Cancer and Its Effects on the Diversity of Gut Microbiota in Rats

by Ifeoma Julieth Dikeocha, Abdelkodose Mohammed Al-Kabsi, Ahmad Faheem Ahmeda, Michael Mathai and Mohammed Abdullah Alshawsh

Int. J. Mol. Sci. 2023, 24(9), 8080; https://doi.org/10.3390/ijms24098080 - 29 Apr 2023

Cited by 3 | Viewed by 2475

Abstract

Colorectal cancer (CRC) accounts for 10% of all cancer diagnoses and cancer-related deaths worldwide. Over the past two decades, several studies have demonstrated the clinical benefits of probiotic supplementation and some studies have shown that certain probiotics can modulate immunity and strengthen gut microbiota diversity. This study aims to assess the impact of the Propionibacterium freudenreichii (PF) probiotic against CRC induced by azoxymethane (AOM), and to investigate its effects on gut microbiota diversity in rats, as well as to evaluate the anti-proliferative activities of PF in HCT116 CRC cells. This experiment was performed using four groups of SD rats: normal control, AOM group, PF group (1 × 10⁹ CFU/mL), and standard drug control (5-fluorouracil, 35 mg/kg). Methylene blue staining of colon tissues showed that the administration of PF significantly reduced the formation of colonic aberrant crypt foci (ACF) compared to the AOM control group. In addition, treated rats had lower levels of malondialdehyde in their colon tissue homogenates, indicating that lipid peroxidation was suppressed by PF supplementation. Furthermore, 16S rRNA gene analysis revealed that probiotic treatment enhanced the diversity of gut microbiota in rats. In vitro study showed that the viability of HCT116 cells was inhibited by the probiotic cell-free supernatant with an IC₅₀ value of 13.3 ± 0.133. In conclusion, these results reveal that consuming PF as probiotic supplements modulates gut microbiota, inhibits the carcinogenic effects of AOM, and exerts anti-proliferative activity against CRC cells. Further studies are required to elucidate the role of PF on the immune response during the development and growth of CRC. Full article

(This article belongs to the Special Issue Advances in Probiotic: Interaction with the Gut Microbiota and the Molecular Mechanisms of the Beneficial Effects)

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17 pages, 2947 KiB

Open AccessArticle

Gut Microbiome and Small RNA Integrative-Omic Perspective of Meconium and Milk-FED Infant Stool Samples

by Polina Kazakova, Nerea Abasolo, Sara Martinez de Cripan, Emili Marquès, Adrià Cereto-Massagué, Lorena Garcia, Núria Canela, Ramón Tormo and Helena Torrell

Int. J. Mol. Sci. 2023, 24(9), 8069; https://doi.org/10.3390/ijms24098069 - 29 Apr 2023

Viewed by 1662

Abstract

The human gut microbiome plays an important role in health, and its initial development is conditioned by many factors, such as feeding. It has also been claimed that this colonization is guided by bacterial populations, the dynamic virome, and transkingdom interactions between host and microbial cells, partially mediated by epigenetic signaling. In this article, we characterized the bacteriome, virome, and smallRNome and their interaction in the meconium and stool samples from infants. Bacterial and viral DNA and RNA were extracted from the meconium and stool samples of 2- to 4-month-old milk-fed infants. The bacteriome, DNA and RNA virome, and smallRNome were assessed using 16S rRNA V4 sequencing, viral enrichment sequencing, and small RNA sequencing protocols, respectively. Data pathway analysis and integration were performed using the R package mixOmics. Our findings showed that the bacteriome differed among the three groups, while the virome and smallRNome presented significant differences, mainly between the meconium and stool of milk-fed infants. The gut environment is rapidly acquired after birth, and it is highly adaptable due to the interaction of environmental factors. Additionally, transkingdom interactions between viruses and bacteria can influence host and smallRNome profiles. However, virome characterization has several protocol limitations that must be considered. Full article

(This article belongs to the Special Issue Advances in Probiotic: Interaction with the Gut Microbiota and the Molecular Mechanisms of the Beneficial Effects)

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21 pages, 4521 KiB

Open AccessArticle

Anti-Inflammatory, Barrier Maintenance, and Gut Microbiome Modulation Effects of Saccharomyces cerevisiae QHNLD8L1 on DSS-Induced Ulcerative Colitis in Mice

by Qianjue Hu, Leilei Yu, Qixiao Zhai, Jianxin Zhao and Fengwei Tian

Int. J. Mol. Sci. 2023, 24(7), 6721; https://doi.org/10.3390/ijms24076721 - 04 Apr 2023

Cited by 5 | Viewed by 2160

Abstract

The use of probiotics has been considered as a new therapy option for ulcerative colitis (UC), and yeast has recently received widespread recommendation for human health. In this study, the probiotic characteristics of four yeast strains, Saccharomyces boulardii CNCMI-745, Kluyveromyces marxianus QHBYC4L2, Saccharomyces cerevisiae QHNLD8L1, and Debaryomyces hansenii QSCLS6L3, were evaluated in vitro; their ability to ameliorate dextran sulfate sodium (DSS)-induced colitis was investigated. Among these, S. cerevisiae QHNLD8L1 protected against colitis, which was reflected by increased body weight, colon length, histological injury relief, decreased gut inflammation markers, and intestinal barrier restoration. The abundance of the pathogenic bacteria Escherichia–Shigella and Enterococcaceae in mice with colitis decreased after S. cerevisiae QHNLD8L1 treatment. Moreover, S. cerevisiae QHNLD8L1 enriched beneficial bacteria Lactobacillus, Faecalibaculum, and Butyricimonas, enhanced carbon metabolism and fatty acid biosynthesis function, and increased short chain fatty acid (SCFAs) production. Taken together, our results indicate the great potential of S. cerevisiae QHNLD8L1 supplementation for the prevention and alleviation of UC. Full article

(This article belongs to the Special Issue Advances in Probiotic: Interaction with the Gut Microbiota and the Molecular Mechanisms of the Beneficial Effects)

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17 pages, 4543 KiB

Open AccessArticle

Exploring the Dose–Effect Relationship of Bifidobacterium longum in Relieving Loperamide Hydrochloride-Induced Constipation in Rats through Colon-Released Capsules

by Xin Zhou, Bingyong Mao, Xin Tang, Qiuxiang Zhang, Jianxin Zhao, Hao Zhang and Shumao Cui

Int. J. Mol. Sci. 2023, 24(7), 6585; https://doi.org/10.3390/ijms24076585 - 01 Apr 2023

Cited by 3 | Viewed by 1786

Abstract

Constipation is a common disease affecting humans. Bifidobacterium longum is reportedly effective in relieving constipation. Current studies generally focus on the dose–response relationship of oral doses; however, the dose–effect relationship of B. longum in the colon, which is the primary site where B. longum exerts constipation-relieving effects, to treat constipation has not been studied. Herein, three strains of B. longum (FGSZY6M4, FJSWXJ10M2, and FSDJN6M3) were packaged in colon-released capsules to explore the dose–effect relationship in the colon. For each strain, three groups of capsules (10⁴, 10⁶, and 10⁸ CFU/capsule, respectively) and one group of free probiotics (10⁸ CFU/mL) were used to explore the colonic dose effect of B. longum. The results showed that the three strains of B. longum improved fecal water content and promoted intestinal motility by regulating gastrointestinal peptide (MTL, GAS, and VIP), aquaporin-3, and 5-hydroxytryptamine levels while promoting gastrointestinal motility and relieving constipation by regulating the intestinal flora composition of constipated rats and changing their metabolite content (short-chain fatty acids). Among the three free bacterial solution groups (10⁸ CFU/mL), FGSZY6M4 was the most effective in relieving constipation caused by loperamide hydrochloride in rats. The optimal effective dose of each strain was 6M4 (10⁴ CFU/day), 10M2 (10⁶ CFU/day), and S3 (10⁸ CFU/day) of the colon-released capsules. Therefore, for some effective strains, the dose of oral probiotics can be reduced by colon-released capsules, and constipation can be relieved without administering a great number of bacterial solutions. Therefore, investigating the most effective dose of B. longum at the colon site can help to improve the efficiency of relieving constipation. Full article

(This article belongs to the Special Issue Advances in Probiotic: Interaction with the Gut Microbiota and the Molecular Mechanisms of the Beneficial Effects)

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17 pages, 4265 KiB

Open AccessArticle

Release of HMGB1 and Toll-like Receptors 2, 4, and 9 Signaling Are Modulated by Bifidobacterium animalis subsp. lactis BB-12 and Salmonella Typhimurium in a Gnotobiotic Piglet Model of Preterm Infants

by Igor Splichal, Sharon M. Donovan, Zdislava Kindlova, Zbynek Stranak, Vera Neuzil Bunesova, Marek Sinkora, Katerina Polakova, Barbora Valaskova and Alla Splichalova

Int. J. Mol. Sci. 2023, 24(3), 2329; https://doi.org/10.3390/ijms24032329 - 24 Jan 2023

Cited by 2 | Viewed by 1834

Abstract

Gnotobiotic (GN) animals with defined microbiota allow us to study host–microbiota and microbiota–microbiota interferences. Preterm germ-free (GF) piglets were mono-associated with probiotic Bifidobacterium animalis subsp. lactis BB-12 (BB12) to ameliorate/prevent the consequences of infection with the Salmonella Typhimurium strain LT2 (LT2). Goblet cell density; expression of Toll-like receptors (TLRs) 2, 4, and 9; high mobility group box 1 (HMGB1); interleukin (IL)-6; and IL-12/23p40 were analyzed to evaluate the possible modulatory effect of BB12. BB12 prevented an LT2-induced decrease of goblet cell density in the colon. TLRs signaling modified by LT2 was not influenced by the previous association with BB12. The expression of HMGB1, IL-6, and IL12/23p40 in the jejunum, ileum, and colon and their levels in plasma were all decreased by BB12, but these changes were not statistically significant. In the colon, differences in HMGB1 distribution between the GF and LT2 piglet groups were observed. In conclusion, the mono-association of GF piglets with BB12 prior to LT2 infection partially ameliorated the inflammatory response to LT2 infection. Full article

(This article belongs to the Special Issue Advances in Probiotic: Interaction with the Gut Microbiota and the Molecular Mechanisms of the Beneficial Effects)

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23 pages, 14258 KiB

Open AccessArticle

Postbiotics Prepared Using Lactobacillus paracasei CCFM1224 Prevent Nonalcoholic Fatty Liver Disease by Modulating the Gut Microbiota and Liver Metabolism

by Zhenghao Pan, Bingyong Mao, Qiuxiang Zhang, Xin Tang, Bo Yang, Jianxin Zhao, Shumao Cui and Hao Zhang

Int. J. Mol. Sci. 2022, 23(21), 13522; https://doi.org/10.3390/ijms232113522 - 04 Nov 2022

Cited by 14 | Viewed by 2371

Abstract

Postbiotics are rich in a variety of bioactive components, which may have beneficial effects in inhibiting hepatic lipid accumulation. In this study, we investigated the preventive effects of postbiotics (POST) prepared from Lactobacillus paracasei on non-alcoholic fatty liver disease (NAFLD). Our results showed that when mice ingested a high-fat diet (HFD) and POST simultaneously, weight gain was slowed, epididymal white fat hypertrophy and insulin resistance were suppressed, serum biochemical indicators related to blood lipid metabolism were improved, and hepatic steatosis and liver inflammation decreased. Bacterial sequencing showed that POST modulated the gut microbiota in HFD mice, increasing the relative abundance of Akkermansia and reducing the relative abundance of Lachnospiraceae NK4A136 group, Ruminiclostridium and Bilophila. Spearman’s correlation analysis revealed significant correlations between lipid metabolism parameters and gut microbes. Functional prediction results showed that the regulation of gut microbiota was associated with the improvement of metabolic status. The metabolomic analysis of the liver revealed that POST-regulated liver metabolic pathways, such as glycerophospholipid and ether lipid metabolism, pantothenate and CoA biosynthesis, some parts of amino acid metabolism, and other metabolic pathways. In addition, POST regulated the gene expression in hepatocytes at the mRNA level, thereby regulating lipid metabolism. These findings suggest that POST plays a protective role against NAFLD and may exert its efficacy by modulating the gut microbiota and liver metabolism, and these findings may be applied to related functional foods. Full article

(This article belongs to the Special Issue Advances in Probiotic: Interaction with the Gut Microbiota and the Molecular Mechanisms of the Beneficial Effects)

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22 pages, 3041 KiB

Open AccessArticle

Lactobacillus sakei MJM60958 as a Potential Probiotic Alleviated Non-Alcoholic Fatty Liver Disease in Mice Fed a High-Fat Diet by Modulating Lipid Metabolism, Inflammation, and Gut Microbiota

by Huong Thi Nguyen, Mingkun Gu, Pia Werlinger, Joo-Hyung Cho, Jinhua Cheng and Joo-Won Suh

Int. J. Mol. Sci. 2022, 23(21), 13436; https://doi.org/10.3390/ijms232113436 - 03 Nov 2022

Cited by 17 | Viewed by 2892

Abstract

Non-alcoholic fatty liver disease (NAFLD) is a common liver disease with a rapidly increasing number of cases worldwide. This study aimed to evaluate the effects of Lactobacillus sakei MJM60958 (MJM60958) on NAFLD in vitro and in vivo. In in vitro tests, MJM60958 significantly inhibited lipid accumulation by 46.79% in HepG2 cells stimulated with oleic acid and cholesterol (OA-C). Moreover, MJM60958 showed safe and probiotic characteristics in vitro. In the animal study, MJM60958 administration in a high-fat diet-induced NAFLD mouse model significantly reduced body weight and liver weight, and controlled aspartate aminotransferase (ALT), aspartate transaminase (AST), triglyceride (TG), urea nitrogen (BUN), and uric acid (UA) levels in the blood, which are features of NAFLD. Further, treatment with MJM60958 also reduced steatosis scores in liver tissues, serum leptin and interleukin, and increased serum adiponectin content. Moreover, administration of MJM60958 resulted in a significantly decreased expression of some genes and proteins which are related to lipid accumulation, such as fatty acid synthase (FAS), acetyl-CoA carboxylase (ACC), and sterol regulatory element-binding protein 1 (SREBP-1), and also upregulated genes and protein expression of lipid oxidation such as peroxisome proliferator-activated receptor alpha (PPARα) and carnitine palmitoyltransferase 1a (CPT1A). Administration of MJM60958 increased the relative abundance of specific microbial taxa such as Verrucomicrobia, which are abundant in non-NAFLD mice, and reduced Firmicutes, which are a major group in NAFLD mice. MJM60958 affected the modulation of gut microbiota and altered the strain profile of short-chain fatty acids (SCFAs) production in the cecum by reduced lactic acid and enhanced acetic acid production. Overall, MJM60958 showed potential as a probiotic that can prevent and treat NAFLD. Full article

(This article belongs to the Special Issue Advances in Probiotic: Interaction with the Gut Microbiota and the Molecular Mechanisms of the Beneficial Effects)

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Review

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26 pages, 1062 KiB

Open AccessReview

Direct and Indirect Evidence of Effects of Bacteroides spp. on Obesity and Inflammation

by Liangliang Wu, Seo-Hyun Park and Hojun Kim

Int. J. Mol. Sci. 2024, 25(1), 438; https://doi.org/10.3390/ijms25010438 - 28 Dec 2023

Cited by 1 | Viewed by 769

Abstract

Metabolic disorders present a significant public health challenge globally. The intricate relationship between the gut microbiome, particularly Bacteroides spp. (BAC), and obesity, including their specific metabolic functions, remains partly unresolved. This review consolidates current research on BAC’s role in obesity and lipid metabolism, with three objectives: (1) To summarize the gut microbiota’s impact on obesity; (2) To assess BAC’s efficacy in obesity intervention; (3) To explore BAC’s mechanisms in obesity and lipid metabolism management. This review critically examines the role of BAC in obesity, integrating findings from clinical and preclinical studies. We highlight the changes in BAC diversity and concentration following successful obesity treatment and discuss the notable differences in BAC characteristics among individuals with varying obesity levels. Furthermore, we review recent preclinical studies demonstrating the potential of BAC in ameliorating obesity and related inflammatory conditions, providing detailed insights into the methodologies of these in vivo experiments. Additionally, certain BAC-derived metabolites have been shown to be involved in the regulation of host lipid metabolism-related pathways. The enhanced TNF production by dendritic cells following BAC administration, in response to LPS, also positions BAC as a potential adjunctive therapy in obesity management. Full article

(This article belongs to the Special Issue Advances in Probiotic: Interaction with the Gut Microbiota and the Molecular Mechanisms of the Beneficial Effects)

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13 pages, 951 KiB

Open AccessReview

Does the Composition of Gut Microbiota Affect Hypertension? Molecular Mechanisms Involved in Increasing Blood Pressure

by Julita Tokarek, Emilian Budny, Maciej Saar, Joanna Kućmierz, Ewelina Młynarska, Jacek Rysz and Beata Franczyk

Int. J. Mol. Sci. 2023, 24(2), 1377; https://doi.org/10.3390/ijms24021377 - 10 Jan 2023

Cited by 9 | Viewed by 3430

Abstract

Arterial hypertension is a chronic disease which is very prevalent contemporarily. The aim of this review was to investigate the impact of gut microbiota on the development and potential treatment of hypertension, taking into consideration underlying molecular mechanisms. The bacteria present in the intestines have the ability to secrete different metabolites, which might play a significant role in the regulation of blood pressure. The most important include short-chain fatty acids (SCFAs), vasoactive hormones, trimethylamine (TMA) and trimethylamine N-oxide (TMAO) and uremic toxins, such as indoxyl sulfate (IS) and p-cresyl sulfate (PCS). Their action in regulating blood pressure is mainly based on their pro- or anti-inflammatory function. The use of specifically formulated probiotics to modify the composition of gut microbiota might be a beneficial way of supportive treatment of hypertension; however, further research on this topic is needed to choose the species of bacteria that could induce the hypotensive pattern. Full article

(This article belongs to the Special Issue Advances in Probiotic: Interaction with the Gut Microbiota and the Molecular Mechanisms of the Beneficial Effects)

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