Gut Microbiota and Metabolism in Different Stages of Life and Health

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Gut Microbiota".

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 34394

Special Issue Editors

The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 11600, Palmerston North 4442, New Zealand
Interests: gut microbiome and metagenome; plant-based foods; prebiotics; host-gut microbiome–diet interactions; circadian rhythm
1. The New Zealand Institute for Plant and Food Research Limited (PFR), Private Bag 11600, Palmerston North 4442, New Zealand
2. Riddet Institute, Massey University, Palmerston North 4442, New Zealand
Interests: human gastrointestinal microbiota; food-microbiota; health and disease
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Special Issue Information

Dear Colleagues, 

Human gastrointestinal microbiota can be considered as postnatally acquired organ that performs important functions. The complex and diverse microbial community has been shown to be intimately associated with beneficial effects on its host. From the promotion of gut maturation and the development of the immune system to the maintenance of metabolic health and the prevention of inflammation, it plays a key role in conferring a number of health benefits throughout different stages of life. Gut microbial dysbiosis is linked to diseases such as obesity, diabetes, inflammatory conditions including irritable bowel syndrome, as well as inflammatory bowel disease and sleep disorders. Healthy development of the gut microbiome within the first 1000 days of life is believed to be important for protection against many diseases later in life. A diet, incorporating plant-based foods rich in fiber and polyphenols, and supplementation with probiotics, has been shown to modulate microbial structure and function, with enhanced benefits to the host.

This Special Issue of Microorganisms invites studies and reviews on the following themes: changes in gut microbiota at different stages of life, and health related to metabolic health and host well-being; in vitro and in vivo studies examining the role of diet in influencing gut microbial ecology, with a special emphasis on the microbiome of infants, and those affected by metabolic disease, sleep disorders, and gut disorders.

Dr. Shanthi G. Parkar
Dr. Pramod Gopal
Guest Editor

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Keywords

  • gut microbiome
  • infant gut
  • plant food
  • metabolic health
  • sleep disorders
  • prebiotics and probiotics

Published Papers (10 papers)

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Editorial

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4 pages, 215 KiB  
Editorial
Gut Microbiota and Metabolism in Different Stages of Life and Health
by Shanthi G. Parkar and Pramod K. Gopal
Microorganisms 2022, 10(2), 474; https://doi.org/10.3390/microorganisms10020474 - 21 Feb 2022
Viewed by 1652
Abstract
In a very fascinating read, John Goodsir, a Scottish surgeon, describes how he isolated “vegetable organisms” from the “ejected fluid” from the stomach of his 19-year-old patient [...] Full article
(This article belongs to the Special Issue Gut Microbiota and Metabolism in Different Stages of Life and Health)

Research

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14 pages, 9124 KiB  
Article
Subgingival Microbiota and Cytokines Profile Changes in Patients with Periodontitis: A Pilot Study Comparing Healthy and Diseased Sites in the Same Oral Cavities
by Pauline Esparbès, Arnaud Legrand, Octave Nadile Bandiaky, Marjorie Chéraud-Carpentier, Hamida Martin, Emmanuel Montassier and Assem Soueidan
Microorganisms 2021, 9(11), 2364; https://doi.org/10.3390/microorganisms9112364 - 16 Nov 2021
Cited by 6 | Viewed by 2000
Abstract
Periodontitis is a common condition characterized by an exacerbated pro-inflammatory response, which leads to tissue destruction and, ultimately, alveolar bone loss. In this pilot study, we assess the microbiota composition and cytokine profile changes in patients with stage III/IV, grade B/C periodontitis, specifically [...] Read more.
Periodontitis is a common condition characterized by an exacerbated pro-inflammatory response, which leads to tissue destruction and, ultimately, alveolar bone loss. In this pilot study, we assess the microbiota composition and cytokine profile changes in patients with stage III/IV, grade B/C periodontitis, specifically by comparing healthy and diseased sites in the same oral cavity. Overall, we found that microbiota architecture was significantly disrupted between diseased and healthy sites, and that the clustering was driven, in part, by the increased relative abundances of Synergistetes in diseased sites, as well as the increased abundances of Firmicutes in healthy sites. We also observed that diseased sites were enriched in Synergistetes, TM7, SR1, Spirochaetes, Bacteroidetes and Fusobacteria, and depleted in Firmicutes, Proteobacteria, Tenericutes and Actinobacteria compared to healthy sites. We found that Interleukin-1b, Interleukin-4, Interleukin-10, and Interleukin-17A were significantly overexpressed in diseased sites, whereas Interleukin-6 and TNF-alpha do not differ significantly between healthy and diseased sites. Here, we observed concomitant changes in the subgingival plaque microbiota and cytokines profile, suggesting that this combined alteration could contribute to the pathobiology of periodontitis. Full article
(This article belongs to the Special Issue Gut Microbiota and Metabolism in Different Stages of Life and Health)
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17 pages, 1529 KiB  
Article
Complementary Food Ingredients Alter Infant Gut Microbiome Composition and Metabolism In Vitro
by Shanthi G. Parkar, Doug I. Rosendale, Halina M. Stoklosinski, Carel M. H. Jobsis, Duncan I. Hedderley and Pramod Gopal
Microorganisms 2021, 9(10), 2089; https://doi.org/10.3390/microorganisms9102089 - 03 Oct 2021
Cited by 6 | Viewed by 2671
Abstract
We examined the prebiotic potential of 32 food ingredients on the developing infant microbiome using an in vitro gastroileal digestion and colonic fermentation model. There were significant changes in the concentrations of short-chain fatty-acid metabolites, confirming the potential of the tested ingredients to [...] Read more.
We examined the prebiotic potential of 32 food ingredients on the developing infant microbiome using an in vitro gastroileal digestion and colonic fermentation model. There were significant changes in the concentrations of short-chain fatty-acid metabolites, confirming the potential of the tested ingredients to stimulate bacterial metabolism. The 16S rRNA gene sequencing for a subset of the ingredients revealed significant increases in the relative abundances of the lactate- and acetate-producing Bifidobacteriaceae, Enterococcaceae, and Lactobacillaceae, and lactate- and acetate-utilizing Prevotellaceae, Lachnospiraceae, and Veillonellaceae. Selective changes in specific bacterial groups were observed. Infant whole-milk powder and an oat flour enhanced Bifidobacteriaceae and lactic acid bacteria. A New Zealand-origin spinach powder enhanced Prevotellaceae and Lachnospiraceae, while fruit and vegetable powders increased a mixed consortium of beneficial gut microbiota. All food ingredients demonstrated a consistent decrease in Clostridium perfringens, with this organism being increased in the carbohydrate-free water control. While further studies are required, this study demonstrates that the selected food ingredients can modulate the infant gut microbiome composition and metabolism in vitro. This approach provides an opportunity to design nutrient-rich complementary foods that fulfil infants’ growth needs and support the maturation of the infant gut microbiome. Full article
(This article belongs to the Special Issue Gut Microbiota and Metabolism in Different Stages of Life and Health)
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18 pages, 2791 KiB  
Article
The Species-Level Composition of the Fecal Bifidobacterium and Lactobacillus Genera in Indonesian Children Differs from That of Their Mothers
by Mengfan Ding, Bo Yang, Wei Wei Thwe Khine, Yuan-Kun Lee, Endang Sutriswati Rahayu, R. Paul Ross, Catherine Stanton, Jianxin Zhao, Hao Zhang and Wei Chen
Microorganisms 2021, 9(9), 1995; https://doi.org/10.3390/microorganisms9091995 - 21 Sep 2021
Cited by 8 | Viewed by 2569
Abstract
The infant gut microbiota plays a critical role in early life growth and derives mainly from maternal gut and breast milk. This study aimed to analyze the differences in the gut microbiota, namely Bifidobacterium and Lactobacillus communities at species level among breast milk [...] Read more.
The infant gut microbiota plays a critical role in early life growth and derives mainly from maternal gut and breast milk. This study aimed to analyze the differences in the gut microbiota, namely Bifidobacterium and Lactobacillus communities at species level among breast milk as well as maternal and infant feces at different time points after delivery. Fifty-one mother–infant pairs from Indonesia were recruited, and the breast milk and maternal and infant feces were collected and analyzed by high throughput sequencing (16S rRNA, Bifidobacterium groEL and Lactobacillus groEL genes). PCoA results showed bacterial composition was different among breast milk and maternal and infant feces within the first two years. The abundance of Bifidobacterium and Bacteroides were significantly higher in infant feces compared to their maternal feces from birth to two years of age, and maternal breast milk within six months after birth (p < 0.05), whereas the abundance of Blautia, Prevotella, and Faecalibacterium was higher in maternal feces compared to that in breast milk within six months and infant feces within one year after birth, respectively (p < 0.05). The relative abundances of Bacteroides and Lactobacillus was higher and lower in infant feces compared to that in maternal feces only between one and two years of age, respectively (p < 0.05). For Bifidobacterium community at species level, B. adolescentis, B. ruminantium, B. longum subsp. infantis, B. bifidum, and B. pseudolongum were identified in all samples. However, the profile of Bifidobacterium was different between maternal and infant feces at different ages. The relative abundances of B. adolescentis and B. ruminantium were higher in maternal feces compared to those in infant feces from birth to one year of age (p < 0.05), while the relative abundances of B. longum subsp. infantis and B. bifidum were higher in infant feces compared to those in maternal feces beyond three months, and the relative abundance of B. pseudolongum was only higher in infant feces between three and six months (p < 0.05). For Lactobacillus community, L. paragasseri showed higher relative abundance in infant feces when the infant was younger than one year of age (p < 0.05). This study showed bacterial composition at the genus level and Bifidobacterium and Lactobacillus communities at the species level were stage specific in maternal breast milk as well as and maternal and infant feces. Full article
(This article belongs to the Special Issue Gut Microbiota and Metabolism in Different Stages of Life and Health)
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11 pages, 456 KiB  
Article
Are Faecal Microbiota Analyses on Species-Level Suitable Clinical Biomarkers? A Pilot Study in Subjects with Morbid Obesity
by Per G. Farup and Maria G. Maseng
Microorganisms 2021, 9(3), 664; https://doi.org/10.3390/microorganisms9030664 - 23 Mar 2021
Cited by 4 | Viewed by 2152
Abstract
Background: An abnormal faecal microbiota could be a causal factor for disease. This study evaluated a new method for faecal microbiota analysis in subjects with obesity and irritable bowel syndrome. Methods: The study had a matched case-control design. Forty-six subjects with morbid obesity [...] Read more.
Background: An abnormal faecal microbiota could be a causal factor for disease. This study evaluated a new method for faecal microbiota analysis in subjects with obesity and irritable bowel syndrome. Methods: The study had a matched case-control design. Forty-six subjects with morbid obesity (defined as BMI > 40 or >35 kg/m2 with obesity-related complications) of whom 23 had irritable bowel syndrome (IBS), were compared with 46 healthy volunteers. The faecal microbiota was analysed with Precision Microbiome Profiling (PMP™) which quantified 104 bacteria species. The primary aim was comparisons between the cases and controls. Results: Two men and 44 women with a mean age of 43.6 years were included in each of the groups; BMI in the groups was (mean and SD) 41.9 (3.5) and 22.5 (1.5) kg/m2, respectively. Seventeen bacterial species showed statistically significant differences between the groups after adjusting for multiple testing. In a post hoc analysis, the sensitivity and specificity were 78%. Alpha diversity was lower in the group with obesity. In subjects with morbid obesity, no clinically significant differences were seen between subjects with and without IBS or from before to six months after bariatric surgery. Conclusions: The results encourage further evaluation of the new microbiome profiling tool. Full article
(This article belongs to the Special Issue Gut Microbiota and Metabolism in Different Stages of Life and Health)
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13 pages, 2385 KiB  
Article
The Adult Phenylketonuria (PKU) Gut Microbiome
by Viviana J. Mancilla, Allison E. Mann, Yan Zhang and Michael S. Allen
Microorganisms 2021, 9(3), 530; https://doi.org/10.3390/microorganisms9030530 - 04 Mar 2021
Cited by 20 | Viewed by 4796
Abstract
Phenylketonuria (PKU) is an inborn error of phenylalanine metabolism primarily treated through a phenylalanine-restrictive diet that is frequently supplemented with an amino acid formula to maintain proper nutrition. Little is known of the effects of these dietary interventions on the gut microbiome of [...] Read more.
Phenylketonuria (PKU) is an inborn error of phenylalanine metabolism primarily treated through a phenylalanine-restrictive diet that is frequently supplemented with an amino acid formula to maintain proper nutrition. Little is known of the effects of these dietary interventions on the gut microbiome of PKU patients, particularly in adults. In this study, we sequenced the V4 region of the 16S rRNA gene from stool samples collected from adults with PKU (n = 11) and non-PKU controls (n = 21). Gut bacterial communities were characterized through measurements of diversity and taxa abundance. Additionally, metabolic imputation was performed based on detected bacteria. Gut community diversity was lower in PKU individuals, though this effect was only statistically suggestive. A total of 65 genera across 5 phyla were statistically differentially abundant between PKU and control samples (p < 0.001). Additionally, we identified six metabolic pathways that differed between groups (p < 0.05), with four enriched in PKU samples and two in controls. While the child PKU gut microbiome has been previously investigated, this is the first study to explore the gut microbiome of adult PKU patients. We find that microbial diversity in PKU children differs from PKU adults and highlights the need for further studies to understand the effects of dietary restrictions. Full article
(This article belongs to the Special Issue Gut Microbiota and Metabolism in Different Stages of Life and Health)
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18 pages, 2115 KiB  
Article
Bioaminergic Responses in an In Vitro System Studying Human Gut Microbiota–Kiwifruit Interactions
by Shanthi G. Parkar, Carel M. H. Jobsis, Tania M. Trower, Janine M. Cooney, Duncan I. Hedderley and Kerry L. Bentley-Hewitt
Microorganisms 2020, 8(10), 1582; https://doi.org/10.3390/microorganisms8101582 - 14 Oct 2020
Cited by 4 | Viewed by 3763
Abstract
Whole kiwifruit (‘Hayward’ and ‘Zesy002’) were examined for their bioaminergic potential after being subjected to in vitro gastrointestinal digestion and colonic fermentation. Controls included the prebiotic inulin and water, a carbohydrate-free vehicle. The dopamine precursor l-dihydroxyphenylalanine (L-DOPA) and the serotonin precursor 5-hydroxytryptophan [...] Read more.
Whole kiwifruit (‘Hayward’ and ‘Zesy002’) were examined for their bioaminergic potential after being subjected to in vitro gastrointestinal digestion and colonic fermentation. Controls included the prebiotic inulin and water, a carbohydrate-free vehicle. The dopamine precursor l-dihydroxyphenylalanine (L-DOPA) and the serotonin precursor 5-hydroxytryptophan were increased in the kiwifruit gastrointestinal digesta (‘Hayward’ > ‘Zesy002’) in comparison to the water digesta. Fermentation of the digesta with human fecal bacteria for 18 h modulated the concentrations of bioamine metabolites. The most notable were the significant increases in L-DOPA (‘Zesy002’ > ‘Hayward’) and γ-aminobutyric acid (GABA) (‘Hayward’ > ‘Zesy002’). Kiwifruit increased Bifidobacterium spp. and Veillonellaceae (correlating with L-DOPA increase), and Lachnospira spp. (correlating with GABA). The digesta and fermenta were incubated with Caco-2 cells for 3 h followed by gene expression analysis. Effects were seen on genes related to serotonin synthesis/re-uptake/conversion to melatonin, gut tight junction, inflammation and circadian rhythm with different digesta and fermenta from the four treatments. These indicate potential effects of the substrates and the microbially generated organic acid and bioamine metabolites on intestinal functions that have physiological relevance. Further studies are required to confirm the potential bioaminergic effects of gut microbiota–kiwifruit interactions. Full article
(This article belongs to the Special Issue Gut Microbiota and Metabolism in Different Stages of Life and Health)
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Review

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18 pages, 868 KiB  
Review
Therapeutic Properties of Edible Mushrooms and Herbal Teas in Gut Microbiota Modulation
by Emanuel Vamanu, Laura Dorina Dinu, Diana Roxana Pelinescu and Florentina Gatea
Microorganisms 2021, 9(6), 1262; https://doi.org/10.3390/microorganisms9061262 - 10 Jun 2021
Cited by 11 | Viewed by 3738
Abstract
Edible mushrooms are functional foods and valuable but less exploited sources of biologically active compounds. Herbal teas are a range of products widely used due to the therapeutic properties that have been demonstrated by traditional medicine and a supplement in conventional therapies. Their [...] Read more.
Edible mushrooms are functional foods and valuable but less exploited sources of biologically active compounds. Herbal teas are a range of products widely used due to the therapeutic properties that have been demonstrated by traditional medicine and a supplement in conventional therapies. Their interaction with the human microbiota is an aspect that must be researched, the therapeutic properties depending on the interaction with the microbiota and the consequent fermentative activity. Modulation processes result from the activity of, for example, phenolic acids, which are a major component and which have already demonstrated activity in combating oxidative stress. The aim of this mini-review is to highlight the essential aspects of modulating the microbiota using edible mushrooms and herbal teas. Although the phenolic pattern is different for edible mushrooms and herbal teas, certain non-phenolic compounds (polysaccharides and/or caffeine) are important in alleviating chronic diseases. These specific functional compounds have modulatory properties against oxidative stress, demonstrating health-beneficial effects in vitro and/or In vivo. Moreover, recent advances in improving human health via gut microbiota are presented. Plant-derived miRNAs from mushrooms and herbal teas were highlighted as a potential strategy for new therapeutic effects. Full article
(This article belongs to the Special Issue Gut Microbiota and Metabolism in Different Stages of Life and Health)
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14 pages, 1035 KiB  
Review
Contribution of Inhibitory Metabolites and Competition for Nutrients to Colonization Resistance against Clostridioides difficile by Commensal Clostridium
by Amber D. Reed and Casey M. Theriot
Microorganisms 2021, 9(2), 371; https://doi.org/10.3390/microorganisms9020371 - 12 Feb 2021
Cited by 13 | Viewed by 3613
Abstract
Clostridioides difficile is an anaerobic pathogen that causes significant morbidity and mortality. Understanding the mechanisms of colonization resistance against C. difficile is important for elucidating the mechanisms by which C. difficile is able to colonize the gut after antibiotics. Commensal Clostridium play a [...] Read more.
Clostridioides difficile is an anaerobic pathogen that causes significant morbidity and mortality. Understanding the mechanisms of colonization resistance against C. difficile is important for elucidating the mechanisms by which C. difficile is able to colonize the gut after antibiotics. Commensal Clostridium play a key role in colonization resistance. They are able to modify bile acids which alter the C. difficile life cycle. Commensal Clostridium also produce other inhibitory metabolites including antimicrobials and short chain fatty acids. They also compete with C. difficile for vital nutrients such as proline. Understanding the mechanistic effects that these metabolites have on C. difficile and other gut pathogens is important for the development of new therapeutics against C. difficile infection (CDI), which are urgently needed. Full article
(This article belongs to the Special Issue Gut Microbiota and Metabolism in Different Stages of Life and Health)
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21 pages, 776 KiB  
Review
Maternal Microbiome and Infections in Pregnancy
by Mohammed Amir, Julia A. Brown, Stephanie L. Rager, Katherine Z. Sanidad, Aparna Ananthanarayanan and Melody Y. Zeng
Microorganisms 2020, 8(12), 1996; https://doi.org/10.3390/microorganisms8121996 - 15 Dec 2020
Cited by 36 | Viewed by 6328
Abstract
Pregnancy induces unique changes in maternal immune responses and metabolism. Drastic physiologic adaptations, in an intricately coordinated fashion, allow the maternal body to support the healthy growth of the fetus. The gut microbiome plays a central role in the regulation of the immune [...] Read more.
Pregnancy induces unique changes in maternal immune responses and metabolism. Drastic physiologic adaptations, in an intricately coordinated fashion, allow the maternal body to support the healthy growth of the fetus. The gut microbiome plays a central role in the regulation of the immune system, metabolism, and resistance to infections. Studies have reported changes in the maternal microbiome in the gut, vagina, and oral cavity during pregnancy; it remains unclear whether/how these changes might be related to maternal immune responses, metabolism, and susceptibility to infections during pregnancy. Our understanding of the concerted adaption of these different aspects of the human physiology to promote a successful pregnant remains limited. Here, we provide a comprehensive documentation and discussion of changes in the maternal microbiome in the gut, oral cavity, and vagina during pregnancy, metabolic changes and complications in the mother and newborn that may be, in part, driven by maternal gut dysbiosis, and, lastly, common infections in pregnancy. This review aims to shed light on how dysregulation of the maternal microbiome may underlie obstetrical metabolic complications and infections. Full article
(This article belongs to the Special Issue Gut Microbiota and Metabolism in Different Stages of Life and Health)
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