Life | Special Issue : Microbiota in Health and Disease

Research

15 pages, 3560 KiB

Open AccessArticle

Gut Microbiota Regulates the Homeostasis of Dendritic Epidermal T Cells

by Jinwoo Chung, Joo-Chan Lee, Hanna Oh, Yesung Kim, Suin Lim, Chanu Lee, Yoon-Gyu Shim, Eun-Chong Bang and Jea-Hyun Baek

Life 2024, 14(12), 1695; https://doi.org/10.3390/life14121695 - 21 Dec 2024

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Abstract

Dendritic epidermal T cells (DETCs) are a γδ T cell subset residing in the skin epidermis. Although they have been known for decades, the fate of DETCs has largely remained enigmatic. Recent studies have highlighted the relationship between the gut microbiome and γδ [...] Read more.

Dendritic epidermal T cells (DETCs) are a γδ T cell subset residing in the skin epidermis. Although they have been known for decades, the fate of DETCs has largely remained enigmatic. Recent studies have highlighted the relationship between the gut microbiome and γδ T cells in various epithelial and non-epithelial tissues, such as the small intestine, lung, liver, gingiva, and testis. While the skin microbiota has been shown to impact skin γδ T cells, a direct relationship between the gut microbiota and DETCs remains unexplored. In this study, we investigated whether DETCs are regulated by the gut microbiota in the steady-state skin epidermis. We examined the occurrence of DETCs in Balb/c mice, which have a skin epidermis barely populated with DETCs, compared to C57BL/6 mice, under different housing conditions. Our findings reveal that local skin inflammation markedly increases DETC numbers in the ear epidermis of Balb/c mice and that DETCs are activated by environmental factors. Furthermore, an investigation of the gut microbiota under different housing conditions revealed distinct microbial compositions and functional profiles. Taken together, these results suggest a strong connection between DETCs and gut microbiota. Full article

(This article belongs to the Special Issue Microbiota in Health and Disease)

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18 pages, 3851 KiB

Open AccessArticle

Enterotype-Specific Effects of Red Beetroot (Beta vulgaris L.) Powder and Betanin on Human Gut Microbiota: A Preliminary Study Based on In Vitro Fecal Fermentation Model

by Gwang-Pyo Ko, Hyejun Jo, Jungman Kim, Jeong Seon Kim, Kyung-Hwan Boo and Chang Sook Kim

Life 2024, 14(11), 1391; https://doi.org/10.3390/life14111391 - 29 Oct 2024

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Abstract

Red beetroots, rich in betanin, may act as prebiotics and impact gut microbiota. Because the human gut microbiota is unique to each person, the effectiveness of prebiotics varies with the enterotype. In this study, we hypothesized that the effects of red beetroot powder [...] Read more.

Red beetroots, rich in betanin, may act as prebiotics and impact gut microbiota. Because the human gut microbiota is unique to each person, the effectiveness of prebiotics varies with the enterotype. In this study, we hypothesized that the effects of red beetroot powder (RP) and betanin pigment (BP) would differ depending on the enterotype. Fecal samples from 30 subjects were analyzed and categorized into three enterotypes: Phocaeicola, Prevotella, and Bifidobacterium. Feces were collected from one representative subject from each enterotype cluster for fermentation. Results showed that RP and BP affected microbiota composition and short-chain fatty acid (SCFA) production differently across enterotypes. The Bifidobacterium cluster showed significantly reduced alpha diversity, with the direction of change in the gut microbiota composition being different from that of other subjects. Additionally, SCFAs significantly increased, with the highest increase in the Bifidobacterium cluster. In this cluster, metabolic pathways related to SCFAs (i.e., starch and sucrose metabolism and glycolysis/gluconeogenesis) were altered. Conversely, Prevotella-dominant feces exhibited fewer changes in SCFAs and a lower increase in Bifidobacterium abundance than the others. These findings highlight that RP and BP elicit enterotype-specific responses in the gut microbiota composition and SCFA production, emphasizing the importance of enterotypes in personalized nutrition. Full article

(This article belongs to the Special Issue Microbiota in Health and Disease)

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11 pages, 7781 KiB

Open AccessArticle

Anticancer Effects of Weizmannia coagulans MZY531 Postbiotics in CT26 Colorectal Tumor-Bearing Mice by Regulating Apoptosis and Autophagy

by Bao Zhong, Yujuan Zhao, Lei Gao, Ge Yang, Yansong Gao, Fenglin Li and Shengyu Li

Life 2024, 14(10), 1334; https://doi.org/10.3390/life14101334 - 19 Oct 2024

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Abstract

Weizmannia coagulans has been shown to have anticancer properties. However, there is limited research on the effects of postbiotic W. coagulans on colorectal cancer cell proliferation. Additionally, the exact mechanisms through which it influences apoptosis- and autophagy-related signaling pathways are yet to be [...] Read more.

Weizmannia coagulans has been shown to have anticancer properties. However, there is limited research on the effects of postbiotic W. coagulans on colorectal cancer cell proliferation. Additionally, the exact mechanisms through which it influences apoptosis- and autophagy-related signaling pathways are yet to be thoroughly elucidated. This study explored the role of W. coagulans MZY531 as a postbiotic in inhibiting tumor growth by modulating apoptosis and autophagy in tumor cells. During the experimental period in the model group, tumors proliferated, tumor markers increased significantly, and immunofluorescence results showed that caspase-3 and terminal deoxynucleotidyl transferase dUTP nick-end labeling were significantly decreased. Conversely, supplementation with W. coagulans MZY531 postbiotics significantly reduced the levels of tumor markers carcinoembryonic antigen, colon cancer antigen, and extracellular protein kinase A and promoted cell apoptosis by increasing the caspase-3-positive count and terminal deoxynucleotidyl transferase dUTP nick-end labeling-positive cells in tumor tissue. Mechanistically, W. coagulans MZY531 postbiotics inhibit tumor growth through the modulation of the Bax/Bcl-2/caspase-3 and JAK2/STAT3 apoptosis pathways and PI3K/AKT/mTOR and TGF-β/SMAD4 cell autophagy pathways. W. coagulans MZY531 postbiotics had a more significant effect than that of W. coagulans MZY531 alone. Probiotics are expected to become effective natural functional foods for the treatment of colorectal cancer. Full article

(This article belongs to the Special Issue Microbiota in Health and Disease)

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22 pages, 3832 KiB

Open AccessArticle

Comparison of the Skin Microbiota in the Periocular Region between Patients with Inflammatory Skin Diseases and Healthy Participants: A Preliminary Study

by Iva Ferček, Petar Ozretić, Arjana Tambić-Andrašević, Slave Trajanoski, Diana Ćesić, Marko Jelić, Goran Geber, Orjena Žaja, Josipa Paić, Liborija Lugović-Mihić and Rok Čivljak

Life 2024, 14(9), 1091; https://doi.org/10.3390/life14091091 - 30 Aug 2024

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Abstract

(1) Background: Periocular or periorbital dermatitis is a common term for all inflammatory skin diseases affecting the area of skin around the eyes. The clear etiopathogenesis of periocular dermatitis is still not fully understood. Advances in molecular techniques for studying microorganisms living in [...] Read more.

(1) Background: Periocular or periorbital dermatitis is a common term for all inflammatory skin diseases affecting the area of skin around the eyes. The clear etiopathogenesis of periocular dermatitis is still not fully understood. Advances in molecular techniques for studying microorganisms living in and on our bodies have highlighted the microbiome as a possible contributor to disease, as well as a promising diagnostic marker and target for innovative treatments. The aim of this study was to compare the composition and diversity of the skin microbiota in the periocular region between healthy individuals and individuals affected by the specific entity of periocular dermatitis. (2) Methods: A total of 35 patients with periocular dermatitis and 39 healthy controls were enrolled in the study. After a skin swab from the periocular region was taken from all participants, DNA extraction and 16S rRNA gene amplicon sequencing using Illumina NovaSeq technology were performed. (3) Results: Staphylococcus and Corynebacterium were the most abundant bacterial genera in the microbiota of healthy skin. Analysis of alpha diversity revealed a statistically significant change (p < 0.05) in biodiversity based on the Faith’s PD index between patients and healthy individuals. We did not observe changes in beta diversity. The linear discriminant analysis effect size (LEfSe) revealed that Rothia, Corynebacterium, Bartonella, and Paracoccus were enriched in patients, and Anaerococcus, Bacteroides, Porphyromonas, and Enhydrobacter were enriched in healthy controls. (4) Conclusions: According to the results obtained, we assume that the observed changes in the bacterial microbiota on the skin, particularly Gram-positive anaerobic cocci and skin commensals of the genus Corynebacterium, could be one of the factors in the pathogenesis of the investigated inflammatory diseases. The identified differences in the microbiota between healthy individuals and patients with periocular dermatitis should be further investigated. Full article

(This article belongs to the Special Issue Microbiota in Health and Disease)

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13 pages, 1631 KiB

Open AccessArticle

A Probiotic Amylase Blend Positively Impacts Gut Microbiota Modulation in a Randomized, Placebo-Controlled, Double-Blind Study

by Mahmoud A. Ghannoum, Mohammed Elshaer, Hilmi Al-Shakhshir, Mauricio Retuerto and Thomas S. McCormick

Life 2024, 14(7), 824; https://doi.org/10.3390/life14070824 - 28 Jun 2024

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Abstract

The present study was performed to determine if ingesting a blend of probiotics plus amylase would alter the abundance and diversity of gut microbiota in subjects consuming the blend over a 6-week period. 16S and ITS ribosomal RNA (rRNA) sequencing was performed on [...] Read more.

The present study was performed to determine if ingesting a blend of probiotics plus amylase would alter the abundance and diversity of gut microbiota in subjects consuming the blend over a 6-week period. 16S and ITS ribosomal RNA (rRNA) sequencing was performed on fecal samples provided by subjects who participated in a clinical study where they consumed either a probiotic amylase blend (Bifidobacterium breve 19bx, Lactobacillus acidophilus 16axg, Lacticaseibacillus rhamnosus 18fx, and Saccharomyces boulardii 16mxg, alpha amylase (500 SKB (Alpha-amylase-Dextrinizing Units)) or a placebo consisting of rice oligodextrin. The abundance and diversity of both bacterial and fungal organisms was assessed at baseline and following 6 weeks of probiotic amylase blend or placebo consumption. In the subjects consuming the probiotic blend, the abundance of Saccharomyces cerevisiae increased 200-fold, and its prevalence increased (~20% to ~60%) (p ≤ 0.05), whereas the potential pathogens Bacillus thuringiensis and Macrococcus caseolyticus decreased more than 150- and 175-fold, respectively, after probiotic-amylase blend consumption. We also evaluated the correlation between change in microbiota and clinical features reported following probiotic amylase consumption. Nine (9) species (seven bacterial and two fungal) were significantly (negatively or positively) associated with the change in 32 clinical features that were originally evaluated in the clinical study. Oral supplementation with the probiotic-amylase blend caused a marked increase in abundance of the beneficial yeast S. cerevisiae and concomitant modulation of gut-dwelling commensal bacterial organisms, providing the proof of concept that a beneficial commensal organism can re-align the gut microbiota. Full article

(This article belongs to the Special Issue Microbiota in Health and Disease)

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11 pages, 3217 KiB

Open AccessEditor’s ChoiceArticle

Beyond the Bile: Exploring the Microbiome and Metabolites in Cholangiocarcinoma

by Jungnam Lee, Hanul Kim and Jin-Seok Park

Life 2024, 14(6), 698; https://doi.org/10.3390/life14060698 - 29 May 2024

Cited by 1 | Viewed by 1260

Abstract

Introduction: Cholangiocarcinoma (CCC) still has a high mortality rate despite improvements in diagnostic and therapeutic techniques. The role of the human microbiome in CCC is poorly understood, and a recent metagenomic analysis demonstrated a significant correlation between microbiome-associated carcinogenesis and CCC. This study [...] Read more.

Introduction: Cholangiocarcinoma (CCC) still has a high mortality rate despite improvements in diagnostic and therapeutic techniques. The role of the human microbiome in CCC is poorly understood, and a recent metagenomic analysis demonstrated a significant correlation between microbiome-associated carcinogenesis and CCC. This study aimed to investigate changes in microbiome composition associated with CCC and its metabolic signature by integrating taxonomic and functional information with metabolomics data and in vitro experimental results. Methods: From February 2019 to January 2021, this study included patients who underwent endoscopic retrograde cholangiopancreatography (ERCP), both with and without a diagnosis of CCC. Bile samples were collected via endoscopic nasobiliary drainages (ENBD) and subjected to DNA extraction, PCR amplification of the bacterial 16S rRNA gene V3-V4 region, and data analysis using QIIME2. In vitro Carboxyfluorescein succinimidyl ester (CFSE) proliferation and Annexin V/PI apoptosis assays were performed to investigate the effects of metabolites on CCC cells. Results: A total of 24 patients were included in the study. Bile fluid analysis revealed a significantly higher abundance of Escherichia coli in the CCC group. Alpha diversity analyses exhibited significant differences between the CCC and non-CCC groups, and Nuclear Magnetic Resonance (NMR) spectroscopy metabolic profiling identified 15 metabolites with significant concentration differences; isoleucine showed the most notable difference. In vitro experiments demonstrated that isoleucine suppressed CCC cell proliferation but did not induce apoptosis. Conclusions: This research underlines the significance of biliary dysbiosis and specific bile metabolites, such as isoleucine, in influencing the development and progression of CCC. Full article

(This article belongs to the Special Issue Microbiota in Health and Disease)

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10 pages, 3011 KiB

Open AccessArticle

Bacteroidales-Specific Antimicrobial Genes Can Influence the Selection of the Dominant Fecal Strain of Bacteroides vulgatus and Bacteroides uniformis from the Gastrointestinal Tract Microbial Community

by Hyunmin Koo and Casey D. Morrow

Life 2024, 14(5), 555; https://doi.org/10.3390/life14050555 - 26 Apr 2024

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Abstract

Bacteroides vulgatus and Bacteroides uniformis are known to be abundant in the human fecal microbial community. Although these strains typically remain stable over time in humans, disruption of this microbial community following antibiotics resulted in the transient change to new strains suggesting that [...] Read more.

Bacteroides vulgatus and Bacteroides uniformis are known to be abundant in the human fecal microbial community. Although these strains typically remain stable over time in humans, disruption of this microbial community following antibiotics resulted in the transient change to new strains suggesting that a complex, dynamic strain community exists in humans. To further study the selection of dominant fecal microbial strains from the gastrointestinal tract (GIT) community, we analyzed three longitudinal metagenomic sequencing data sets using BLAST+ to identify genes encoding Bacteroidales-specific antimicrobial proteins (BSAP) that have known functions to restrict species-specific replication of B. uniformis (BSAP-2) or B. vulgatus (BSAP-3) and have been postulated to provide a competitive advantage in microbial communities. In the HMP (Human Microbiome Project) data set, we found fecal samples from individuals had B. vulgatus or B. uniformis with either complete or deleted BSAP genes that did not change over time. We also examined fecal samples from two separate longitudinal data sets of individuals who had been given either single or multiple antibiotics. The BSAP gene pattern from most individuals given either single or multiple antibiotics recovered to be the same as the pre-antibiotic strain. However, in a few individuals, we found incomplete BSAP-3 genes at early times during the recovery that were replaced by B. vulgatus with the complete BSAP-3 gene, consistent with the function of the BSAP to specifically restrict Bacteroides spp. The results of these studies provide insights into the fluxes that occur in the Bacteroides spp. GIT community following perturbation and the dynamics of the selection of a dominant fecal strain of Bacteroides spp. Full article

(This article belongs to the Special Issue Microbiota in Health and Disease)

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Review

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28 pages, 2501 KiB

Open AccessReview

The Microbiota–Gut–Brain Axis: Key Mechanisms Driving Glymphopathy and Cerebral Small Vessel Disease

by Che Mohd Nasril Che Mohd Nassir, Muhammad Danial Che Ramli, Mazira Mohamad Ghazali, Usman Jaffer, Hafizah Abdul Hamid, Muhammad Zulfadli Mehat and Zaw Myo Hein

Life 2025, 15(1), 3; https://doi.org/10.3390/life15010003 - 24 Dec 2024

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Abstract

The human microbiota constitute a very complex ecosystem of microorganisms inhabiting both the inside and outside of our bodies, in which health maintenance and disease modification are the main regulatory features. The recent explosion of microbiome research has begun to detail its important [...] Read more.

The human microbiota constitute a very complex ecosystem of microorganisms inhabiting both the inside and outside of our bodies, in which health maintenance and disease modification are the main regulatory features. The recent explosion of microbiome research has begun to detail its important role in neurological health, particularly concerning cerebral small vessel disease (CSVD), a disorder associated with cognitive decline and vascular dementia. This narrative review represents state-of-the-art knowledge of the intimate, complex interplay between microbiota and brain health through the gut–brain axis (GBA) and the emerging role of glymphatic system dysfunction (glymphopathy) and circulating cell-derived microparticles (MPs) as mediators of these interactions. We discuss how microbial dysbiosis promotes neuroinflammation, vascular dysfunction, and impaired waste clearance in the brain, which are critical factors in the pathogenesis of CSVD. Further, we discuss lifestyle factors that shape the composition and functionality of the microbiota, focusing on sleep as a modifiable risk factor in neurological disorders. This narrative review presents recent microbiome research from a neuroscientific and vascular perspective to establish future therapeutic avenues in targeting the microbiota to improve brain health and reduce the burden of CSVD. Full article

(This article belongs to the Special Issue Microbiota in Health and Disease)

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19 pages, 862 KiB

Open AccessReview

The Influence of the Gut Microbiota on Host Health: A Focus on the Gut–Lung Axis and Therapeutic Approaches

by Amal S. Alswat

Life 2024, 14(10), 1279; https://doi.org/10.3390/life14101279 - 9 Oct 2024

Cited by 3 | Viewed by 3696

Abstract

The human gut microbiota is a complex ecosystem harboring thousands of microbial strains that play a crucial role in maintaining the overall well-being of its host. The composition of the gut microbiota varies with age from infancy to adulthood and is influenced by [...] Read more.

The human gut microbiota is a complex ecosystem harboring thousands of microbial strains that play a crucial role in maintaining the overall well-being of its host. The composition of the gut microbiota varies with age from infancy to adulthood and is influenced by dietary habits, environment, and genetic disposition. Recent advances in culture-independent techniques and nucleic acid sequencing have improved our understanding of the diversity of the gut microbiota. The microbial species present in the gut release short-chain fatty acids (SCFAs), which have anti-inflammatory properties. The gut microbiota also plays a substantial role in modulating the host′s immune system, promoting immune tolerance, and maintaining homeostasis. The impact of the gut microbiota on the health of the host is quite evident, as gut dysbiosis has been linked to various diseases, including metabolic disorders, autoimmune diseases, allergies, and inflammatory bowel diseases. The gut microbiota has bidirectional communication with the respiratory system, creating the gut–lung axis, which has been associated with different respiratory diseases. Therapeutic approaches targeting the gut microbiota, such as probiotics, prebiotics, dietary interventions, and fecal microbiota transplantation (FMT), aim to restore microbial balance and promote the growth of beneficial strains in the gut. Nonetheless, gaining knowledge of the complex interactions between the gut microbiota and the host is necessary to develop personalized medicine approaches and microbiota-based therapies for various conditions. This review summarizes studies related to the gut–lung axis with particular emphasis on the role of the microbiota. Future research directions are also discussed. Full article

(This article belongs to the Special Issue Microbiota in Health and Disease)

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67 pages, 12154 KiB

Open AccessReview

The Microbiota–Gut–Brain Axis and Neurological Disorders: A Comprehensive Review

by Mohammed M. Nakhal, Lidya K. Yassin, Rana Alyaqoubi, Sara Saeed, Alreem Alderei, Alya Alhammadi, Mirah Alshehhi, Afra Almehairbi, Shaikha Al Houqani, Shamsa BaniYas, Haia Qanadilo, Bassam R. Ali, Safa Shehab, Yauhen Statsenko, Sarah Meribout, Bassem Sadek, Amal Akour and Mohammad I. K. Hamad

Life 2024, 14(10), 1234; https://doi.org/10.3390/life14101234 - 26 Sep 2024

Cited by 3 | Viewed by 8843

Abstract

Microbes have inhabited the earth for hundreds of millions of years longer than humans. The microbiota–gut–brain axis (MGBA) represents a bidirectional communication pathway. These communications occur between the central nervous system (CNS), the enteric nervous system (ENS), and the emotional and cognitive centres [...] Read more.

Microbes have inhabited the earth for hundreds of millions of years longer than humans. The microbiota–gut–brain axis (MGBA) represents a bidirectional communication pathway. These communications occur between the central nervous system (CNS), the enteric nervous system (ENS), and the emotional and cognitive centres of the brain. The field of research on the gut–brain axis has grown significantly during the past two decades. Signalling occurs between the gut microbiota and the brain through the neural, endocrine, immune, and humoral pathways. A substantial body of evidence indicates that the MGBA plays a pivotal role in various neurological diseases. These include Alzheimer’s disease (AD), autism spectrum disorder (ASD), Rett syndrome, attention deficit hyperactivity disorder (ADHD), non-Alzheimer’s neurodegeneration and dementias, fronto-temporal lobe dementia (FTLD), Wilson–Konovalov disease (WD), multisystem atrophy (MSA), Huntington’s chorea (HC), Parkinson’s disease (PD), multiple sclerosis (MS), amyotrophic lateral sclerosis (ALS), temporal lobe epilepsy (TLE), depression, and schizophrenia (SCZ). Furthermore, the bidirectional correlation between therapeutics and the gut–brain axis will be discussed. Conversely, the mood of delivery, exercise, psychotropic agents, stress, and neurologic drugs can influence the MGBA. By understanding the MGBA, it may be possible to facilitate research into microbial-based interventions and therapeutic strategies for neurological diseases. Full article

(This article belongs to the Special Issue Microbiota in Health and Disease)

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Other

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17 pages, 2040 KiB

Open AccessSystematic Review

The Impact of Probiotic Bifidobacterium on Liver Diseases and the Microbiota

by Gabriel Henrique Hizo and Pabulo Henrique Rampelotto

Life 2024, 14(2), 239; https://doi.org/10.3390/life14020239 - 8 Feb 2024

Cited by 8 | Viewed by 2654

Abstract

Recent studies have shown the promising potential of probiotics, especially the bacterial genus Bifidobacterium, in the treatment of liver diseases. In this work, a systematic review was conducted, with a focus on studies that employed advanced Next Generation Sequencing (NGS) technologies to [...] Read more.

Recent studies have shown the promising potential of probiotics, especially the bacterial genus Bifidobacterium, in the treatment of liver diseases. In this work, a systematic review was conducted, with a focus on studies that employed advanced Next Generation Sequencing (NGS) technologies to explore the potential of Bifidobacterium as a probiotic for treating liver pathologies such as Non-Alcoholic Fatty Liver Disease (NAFLD), Non-Alcoholic Steatohepatitis (NASH), Alcoholic Liver Disease (ALD), Cirrhosis, and Hepatocelullar Carcinoma (HCC) and its impact on the microbiota. Our results indicate that Bifidobacterium is a safe and effective probiotic for treating liver lesions. It successfully restored balance to the intestinal microbiota and improved biochemical and clinical parameters in NAFLD, ALD, and Cirrhosis. No significant adverse effects were identified. While more research is needed to establish its efficacy in treating NASH and HCC, the evidence suggests that Bifidobacterium is a promising probiotic for managing liver lesions. Full article

(This article belongs to the Special Issue Microbiota in Health and Disease)

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