Microorganisms

Research

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11 pages, 1211 KiB

Open AccessArticle

Abnormal Development of Microbiota May Be a Risk Factor for Febrile Urinary Tract Infection in Infancy

by Chika Urakami, Sohsaku Yamanouchi, Takahisa Kimata, Shoji Tsuji, Shohei Akagawa, Jiro Kino, Yuko Akagawa, Shogo Kato, Atsushi Araki and Kazunari Kaneko

Microorganisms 2023, 11(10), 2574; https://doi.org/10.3390/microorganisms11102574 - 16 Oct 2023

Cited by 4 | Viewed by 1460

Abstract

Febrile urinary tract infection (fUTI) is common in infants, but specific risk factors for developing it remain unclear. As most fUTIs are caused by ascending infections of intestinal bacteria, dysbiosis—an imbalance in gut microbial communities—may increase fUTI risk. This study was conducted to [...] Read more.

Febrile urinary tract infection (fUTI) is common in infants, but specific risk factors for developing it remain unclear. As most fUTIs are caused by ascending infections of intestinal bacteria, dysbiosis—an imbalance in gut microbial communities—may increase fUTI risk. This study was conducted to test the hypothesis that abnormal development of gut microbiota during infancy increases the risk of developing fUTI. Stool samples were collected from 28 infants aged 3–11 months with first-onset fUTI (fUTI group) and 51 healthy infants of the same age (HC group). After bacterial DNA extraction, 16S rRNA expression was measured and the diversity of gut microbiota and constituent bacteria were compared between the two groups. The alpha diversity of gut microbiota (median Shannon index and Chao index) was significantly lower in the fUTI group (3.0 and 42.5) than in the HC group (3.7 and 97.0; p < 0.001). The beta diversity also formed different clusters between the two groups (p < 0.001), suggesting differences in their microbial composition. The linear discriminant analysis effect size showed that the fUTI group proportionally featured significantly more Escherichia-Shigella in the gut microbiota (9.5%) than the HC group (3.1%; p < 0.001). In summary, abnormal gut microbiota development during infancy may increase the risk of fUTI. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

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19 pages, 4064 KiB

Open AccessArticle

Impact of Sleeve Gastrectomy on Fecal Microbiota in Individuals with Morbid Obesity

by Danyta I. Tedjo, Jennifer A. Wilbrink, Jos Boekhorst, Harro M. Timmerman, Simon W. Nienhuijs, Arnold Stronkhorst, Paul H. M. Savelkoul, Ad A. M. Masclee, John Penders and Daisy M. A. E. Jonkers

Microorganisms 2023, 11(9), 2353; https://doi.org/10.3390/microorganisms11092353 - 20 Sep 2023

Cited by 2 | Viewed by 1681

Abstract

Background: The intestinal microbiota plays an important role in the etiology of obesity. Sleeve gastrectomy (SG) is a frequently performed and effective therapy for morbid obesity. Objective: To investigate the effect of sleeve gastrectomy on the fecal microbiota of individuals with morbid obesity [...] Read more.

Background: The intestinal microbiota plays an important role in the etiology of obesity. Sleeve gastrectomy (SG) is a frequently performed and effective therapy for morbid obesity. Objective: To investigate the effect of sleeve gastrectomy on the fecal microbiota of individuals with morbid obesity and to examine whether shifts in microbiota composition are associated with markers of inflammation and intestinal barrier function. Methods: Fecal and blood samples of healthy individuals (n = 27) and morbidly obese individuals pre-SG (n = 24), and at 2 months (n = 13) and 6 months post-SG (n = 9) were collected. The 16SrRNA gene was sequenced to assess microbiota composition. Fecal calprotectin, plasma inflammatory markers and intestinal permeability markers (multi-sugar test) were determined. Results: Fecal microbiota composition between morbidly obese and lean individuals was significantly different. The fecal microbiota composition changed significantly 2 and 6 months post-SG (p = 0.008) compared to pre-SG but not towards a more lean profile. The post-SG microbiota profile was characterized by an increase in facultative anaerobic bacteria, characteristic for the upper gastrointestinal tract. No correlations were found between inflammatory markers, intestinal permeability and microbial profile changes. Conclusions: Fecal microbiota composition in morbidly obese individuals changed significantly following SG. This change might be explained by functional changes induced by the SG procedure. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

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12 pages, 312 KiB

Open AccessArticle

The Association between Gut Microbiota and Depression in the Japanese Population

by Yichi Yang, Mone Mori, Kyi Mar Wai, Tao Jiang, Yoshikuni Sugimura, Wataru Munakata, Tatsuya Mikami, Koichi Murashita, Shigeyuki Nakaji and Kazushige Ihara

Microorganisms 2023, 11(9), 2286; https://doi.org/10.3390/microorganisms11092286 - 11 Sep 2023

Cited by 2 | Viewed by 1672

Abstract

Depression is a leading cause of disease worldwide. The association between gut microbiota and depression has barely been investigated in the Japanese population. We analyzed Iwaki health check-up data collected from 2017 to 2019 and constructed generalized linear mixed models. The independent variable [...] Read more.

Depression is a leading cause of disease worldwide. The association between gut microbiota and depression has barely been investigated in the Japanese population. We analyzed Iwaki health check-up data collected from 2017 to 2019 and constructed generalized linear mixed models. The independent variable was the relative abundance of each of the 37 gut microbiota genera that were reported to be associated with depression. The dependent variable was the presence of depression assessed by the Center for Epidemiologic Studies Depression Scale. Potential confounders, including grip strength, gender, height, weight, smoking, and drinking habits, were adjusted in the regression models. Nine genera’s regression coefficients (Alistipes, Blautia, Coprococcus, Dorea, Faecalibacterium, Holdemania, Lactobacillus, Mitsuokella, and Oscillibacter) showed statistical significance after multiple comparisons adjustment. Among these nine gut bacteria genera, Alistipes, Blautia, Coprococcus, Dorea, Faecalibacterium, and Oscillibacter were reported to be associated with butyrate production in the intestine. Our results indicate that gut microbiotas may influence the depression condition of the host via the butyrate-producing process. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

10 pages, 1258 KiB

Open AccessArticle

Infant Saliva Microbiome Activity Modulates Nutritional Impacts on Neurodevelopment

by Terrah Keck-Kester and Steven D. Hicks

Microorganisms 2023, 11(8), 2111; https://doi.org/10.3390/microorganisms11082111 - 18 Aug 2023

Cited by 1 | Viewed by 3125

Abstract

Neurodevelopment is influenced by complex interactions between environmental factors, including social determinants of health (SDOH), nutrition, and even the microbiome. This longitudinal cohort study of 142 infants tested the hypothesis that microbial activity modulates the effects of nutrition on neurodevelopment. Salivary microbiome activity [...] Read more.

Neurodevelopment is influenced by complex interactions between environmental factors, including social determinants of health (SDOH), nutrition, and even the microbiome. This longitudinal cohort study of 142 infants tested the hypothesis that microbial activity modulates the effects of nutrition on neurodevelopment. Salivary microbiome activity was measured at 6 months using RNA sequencing. Infant nutrition was assessed longitudinally with the Infant Feeding Practices survey. The primary outcome was presence/absence of neurodevelopmental delay (NDD) at 18 months on the Survey of Wellbeing in Young Children. A logistic regression model employing two microbial factors, one nutritional factor, and two SDOH accounted for 33.3% of the variance between neurodevelopmental groups (p < 0.001, AIC = 77.7). NDD was associated with Hispanic ethnicity (OR 18.1, 2.36–139.3; p = 0.003), no fish consumption (OR 10.6, 2.0–54.1; p = 0.003), and increased Candidatus Gracilibacteria activity (OR 1.43, 1.00–2.07; p = 0.007). Home built after 1977 (OR 0.02, 0.001–0.53; p = 0.004) and Chlorobi activity (OR 0.76, 0.62–0.93, p = 0.001) were associated with reduced risk of NDD. Microbial alpha diversity modulated the effect of fish consumption on NDD (X² = 5.7, p = 0.017). These data suggest the benefits of fish consumption for neurodevelopment may be mediated by microbial diversity. Confirmation in a larger, randomized trial is required. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

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15 pages, 2086 KiB

Open AccessArticle

Gut Microbiota and Respiratory Infections: Insights from Mendelian Randomization

by Shengyu Huang, Jiaqi Li, Zhihao Zhu, Xiaobin Liu, Tuo Shen, Yusong Wang, Qimin Ma, Xin Wang, Guangping Yang, Guanghua Guo and Feng Zhu

Microorganisms 2023, 11(8), 2108; https://doi.org/10.3390/microorganisms11082108 - 18 Aug 2023

Cited by 5 | Viewed by 2974

Abstract

The role of the gut microbiota in modulating the risk of respiratory infections has garnered increasing attention. However, conventional clinical trials have faced challenges in establishing the precise relationship between the two. In this study, we conducted a Mendelian randomization analysis with single [...] Read more.

The role of the gut microbiota in modulating the risk of respiratory infections has garnered increasing attention. However, conventional clinical trials have faced challenges in establishing the precise relationship between the two. In this study, we conducted a Mendelian randomization analysis with single nucleotide polymorphisms employed as instrumental variables to assess the causal links between the gut microbiota and respiratory infections. Two categories of bacteria, family Lactobacillaceae and genus Family XIII AD3011, were causally associated with the occurrence of upper respiratory tract infections (URTIs). Four categories of gut microbiota existed that were causally associated with lower respiratory tract infections (LRTIs), with order Bacillales and genus Paraprevotella showing a positive association and genus Alistipes and genus Ruminococcaceae UCG009 showing a negative association. The metabolites and metabolic pathways only played a role in the development of LRTIs, with the metabolite deoxycholine acting negatively and menaquinol 8 biosynthesis acting positively. The identification of specific bacterial populations, metabolites, and pathways may provide new clues for mechanism research concerning therapeutic interventions for respiratory infections. Future research should focus on elucidating the potential mechanisms regulating the gut microbiota and developing effective strategies to reduce the incidence of respiratory infections. These findings have the potential to significantly improve global respiratory health. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

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11 pages, 273 KiB

Open AccessCommunication

Correlating the Gut Microbiota and Circulating Hormones with Acne Lesion Counts and Skin Biophysical Features

by Raja K. Sivamani, Jessica Maloh and Yvonne Nong

Microorganisms 2023, 11(8), 2049; https://doi.org/10.3390/microorganisms11082049 - 9 Aug 2023

Cited by 2 | Viewed by 2526

Abstract

Acne vulgaris is a common inflammatory condition that is multi-factorial and impacted by both intrinsic and extrinsic features. Several previous studies have assessed for correlations between factors such as circulating hormones, stress, or the microbiome. However, there have not been any correlations specifically [...] Read more.

Acne vulgaris is a common inflammatory condition that is multi-factorial and impacted by both intrinsic and extrinsic features. Several previous studies have assessed for correlations between factors such as circulating hormones, stress, or the microbiome. However, there have not been any correlations specifically against lesion counts or differentiating correlations between inflammatory and non-inflammatory lesion counts. Here, we correlate several factors against acne lesions. Twenty men and women with mild to moderate acne were recruited, and their hormonal levels and their gut microbiome were collected and correlated against their inflammatory and non-inflammatory lesions of acne. Facial non-inflammatory lesions were weakly correlated to sebum excretion rate and weakly inversely correlated to forehead and cheek hydration. We examined stress through the use of a normalized peak-to-trough ratio (higher numbers indicated less stress), which correlated with skin hydration and inversely correlated with sebum excretion rate. Sebum excretion rate was weakly correlated to testosterone levels, and facial hydration correlated with estradiol levels. Correlations with the gut microbiome showed differential correlations with inflammatory and non-inflammatory lesions, with Clostridium sp AF 23-8 correlating to inflammatory lesion counts, while Actinomyces naeslundii str Howell 279 correlated to non-inflammatory lesions. Overall, measures of stress and circulating hormones correlate to skin biophysical properties and acne lesion counts. Also, different gut bacteria correlate with either inflammatory or non-inflammatory lesion counts. We hope that our findings stimulate further work on the gut–mind–stress–skin axis within acne. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

16 pages, 1270 KiB

Open AccessArticle

Personalized Response of Parkinson’s Disease Gut Microbiota to Nootropic Medicinal Herbs In Vitro: A Proof of Concept

by Christine Tara Peterson, Stanislav N. Iablokov, Dmitry A. Rodionov and Scott N. Peterson

Microorganisms 2023, 11(8), 1979; https://doi.org/10.3390/microorganisms11081979 - 1 Aug 2023

Cited by 1 | Viewed by 2105

Abstract

Parkinson’s disease (PD) is a neurodegenerative disease characterized by the loss of dopaminergic neurons. Although the etiology of PD remains elusive, it has been hypothesized that initial dysregulation may occur in the gastrointestinal tract and may be accompanied by gut barrier defects. A [...] Read more.

Parkinson’s disease (PD) is a neurodegenerative disease characterized by the loss of dopaminergic neurons. Although the etiology of PD remains elusive, it has been hypothesized that initial dysregulation may occur in the gastrointestinal tract and may be accompanied by gut barrier defects. A strong clinical interest in developing therapeutics exists, including for the treatment of gut microbiota and physiology. We previously reported the impact of healthy fecal microbiota anaerobic cultures supplemented with nootropic herbs. Here, we evaluated the effect of nootropic Ayurvedic herbs on fecal microbiota derived from subjects with PD in vitro using 16S rRNA sequencing. The microbiota underwent substantial change in response to each treatment, comparable in magnitude to that observed from healthy subjects. However, the fecal samples derived from each participant displayed unique changes, consistent with a personalized response. We used genome-wide metabolic reconstruction to predict the community’s metabolic potential to produce products relevant to PD pathology, including SCFAs, vitamins and amino acid degradation products. These results suggest the potential value of conducting in vitro cultivation and analyses of PD stool samples as a means of prescreening patients to select the medicinal herbs for which that individual is most likely to respond and derive benefit. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

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13 pages, 2111 KiB

Open AccessArticle

Effect of Oral Administration of Polyethylene Glycol 400 on Gut Microbiota Composition and Diet-Induced Obesity in Mice

by Riko Ishibashi, Rio Matsuhisa, Mio Nomoto, Seita Chudan, Miyu Nishikawa, Yoshiaki Tabuchi, Shinichi Ikushiro, Yoshinori Nagai and Yukihiro Furusawa

Microorganisms 2023, 11(8), 1882; https://doi.org/10.3390/microorganisms11081882 - 26 Jul 2023

Cited by 1 | Viewed by 2582

Abstract

Polyethylene glycol (PEG) is a commonly used dispersant for oral administration of hydrophobic agents. PEG is partly absorbed in the small intestine, and the unabsorbed fraction reaches the large intestine; thus, oral administration of PEG may impact the gut microbial community. However, to [...] Read more.

Polyethylene glycol (PEG) is a commonly used dispersant for oral administration of hydrophobic agents. PEG is partly absorbed in the small intestine, and the unabsorbed fraction reaches the large intestine; thus, oral administration of PEG may impact the gut microbial community. However, to the best of our knowledge, no study evaluated the effects of PEG on gut commensal bacteria. Herein, we aimed to determine whether oral administration of PEG modifies the gut microbiota. Administration of PEG400 and PEG4000 altered gut microbial diversity in a concentration-dependent manner. Taxonomic analysis revealed that Akkermansia muciniphila and particularly Parabacteroides goldsteinii were overrepresented in mice administered with 40% PEG. PEG400 administration ameliorated the high-fat diet (HFD)-induced obesity and adipose tissue inflammation. Fecal microbiome transplantation from PEG400-administered donors counteracted the HFD-induced body and epididymal adipose tissue weight gain, indicating that PEG400-associated bacteria are responsible for the anti-obesity effect. Conversely, carboxymethyl cellulose, also used as a dispersant, did not affect the abundance of these two bacterial species or HFD-induced obesity. In conclusion, we demonstrated that oral administration of a high concentration of PEG400 (40%) alters the gut microbiota composition and ameliorates HFD-induced obesity. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

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15 pages, 2099 KiB

Open AccessArticle

Gut Microbiome in Post-COVID-19 Patients Is Linked to Immune and Cardiovascular Health Status but Not COVID-19 Severity

by Olga N. Tkacheva, Natalia S. Klimenko, Daria A. Kashtanova, Alexander V. Tyakht, Lilit V. Maytesyan, Anna A. Akopyan, Stanislav I. Koshechkin and Irina D. Strazhesko

Microorganisms 2023, 11(4), 1036; https://doi.org/10.3390/microorganisms11041036 - 15 Apr 2023

Cited by 1 | Viewed by 2206

Abstract

The composition of the gut microbiome stores the imprints of prior infections and other impacts. COVID-19 can cause changes in inflammatory status that persist for a considerable time after infection ends. As the gut microbiome is closely associated with immunity and inflammation, the [...] Read more.

The composition of the gut microbiome stores the imprints of prior infections and other impacts. COVID-19 can cause changes in inflammatory status that persist for a considerable time after infection ends. As the gut microbiome is closely associated with immunity and inflammation, the infection severity might be linked to its community structure dynamics. Using 16S rRNA sequencing of stool samples, we investigated the microbiome three months after the end of the disease/infection or SARS-CoV-2 contact in 178 post-COVID-19 patients and those who contacted SARS-CoV-2 but were not infected. The cohort included 3 groups: asymptomatic subjects (n = 48), subjects who contacted COVID-19 patients with no further infection (n = 46), and severe patients (n = 86). Using a novel compositional statistical algorithm (nearest balance) and the concept of bacterial co-occurrence clusters (coops), we compared microbiome compositions between the groups as well as with multiple categories of clinical parameters including: immunity, cardiovascular parameters and markers of endothelial dysfunction, and blood metabolites. Although a number of clinical indicators varied drastically across the three groups, no differences in microbiome features were identified between them at this follow-up point. However, there were multiple associations between the microbiome features and clinical data. Among the immunity parameters, the relative lymphocyte number was linked to a balance including 14 genera. Cardiovascular parameters were associated with up to four bacterial cooperatives. Intercellular adhesion molecule 1 was linked to a balance including ten genera and one cooperative. Among the blood biochemistry parameters, calcium was the only parameter associated with the microbiome via a balance of 16 genera. Our results suggest comparable recovery of the gut community structure in the post-COVID-19 period, independently of severity or infection status. The multiple identified associations of clinical analysis data with the microbiome provide hypotheses about the participation of specific taxa in regulating immunity and homeostasis of cardiovascular and other body systems in health, as well as their disruption in SARS-CoV-2 infections and other diseases. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

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20 pages, 30790 KiB

Open AccessArticle

Microbiota Phenotype Promotes Anastomotic Leakage in a Model of Rats with Ischemic Colon Resection

by Diego Zamorano, Dinka Ivulic, Tomeu Viver, Felipe Morales, Francisco López-Kostner and Roberto M. Vidal

Microorganisms 2023, 11(3), 680; https://doi.org/10.3390/microorganisms11030680 - 7 Mar 2023

Cited by 5 | Viewed by 2091

Abstract

Anastomotic leakage (AL) is a major cause of morbidity and mortality after colorectal surgery, but the mechanism behind this complication is still not fully understood. Despite the advances in surgical techniques and perioperative care, the complication rates have remained steady. Recently, it has [...] Read more.

Anastomotic leakage (AL) is a major cause of morbidity and mortality after colorectal surgery, but the mechanism behind this complication is still not fully understood. Despite the advances in surgical techniques and perioperative care, the complication rates have remained steady. Recently, it has been suggested that colon microbiota may be involved in the development of complications after colorectal surgery. The aim of this study was to evaluate the association of gut microbiota in the development of colorectal AL and their possible virulence strategies to better understand the phenomenon. Using 16S rRNA sequencing of samples collected on the day of surgery and the sixth day following surgery, we analyzed the changes in tissue-associated microbiota at anastomotic sites created in a model of rats with ischemic colon resection. We discovered a trend for lower microbial diversity in the AL group compared to non-leak anastomosis (NLA). There were no differences in relative abundance in the different types of microbial respiration between these groups and the high abundance of the facultative anaerobic Gemella palaticanis is a marker species that stands out as a distinctive feature. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

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16 pages, 2078 KiB

Open AccessArticle

The Microbiota-Dependent Worsening Effects of Melatonin on Gut Inflammation

by Jefferson Luiz da Silva, Lia Vezenfard Barbosa, Camila Figueiredo Pinzan, Viviani Nardini, Irislene Simões Brigo, Cássia Aparecida Sebastião, Jefferson Elias-Oliveira, Vânia Brazão, José Clóvis do Prado Júnior, Daniela Carlos and Cristina Ribeiro de Barros Cardoso

Microorganisms 2023, 11(2), 460; https://doi.org/10.3390/microorganisms11020460 - 11 Feb 2023

Cited by 4 | Viewed by 9831

Abstract

Dysbiosis and disturbances in gut homeostasis may result in dysregulated responses, which are common in inflammatory bowel diseases (IBD). These conditions may be refractory to the usual treatments and novel therapies are still necessary to reach a more successful regulation of intestinal immunity. [...] Read more.

Dysbiosis and disturbances in gut homeostasis may result in dysregulated responses, which are common in inflammatory bowel diseases (IBD). These conditions may be refractory to the usual treatments and novel therapies are still necessary to reach a more successful regulation of intestinal immunity. The hormone melatonin (MLT) has been raised as a therapeutic alternative because of its known interactions with immune responses and gut microbiota. Hence, we evaluated the effects of MLT in experimental colitis that evolves with intestinal dysbiosis, inflammation and bacterial translocation. C57BL/6 mice were exposed to dextran sulfate sodium and treated with MLT. In acute colitis, the hormone led to increased clinical, systemic and intestinal inflammatory parameters. During remission, continued MLT administration delayed recovery, increased TNF, memory effector lymphocytes and diminished spleen regulatory cells. MLT treatment reduced Bacteroidetes and augmented Actinobacteria and Verrucomicrobia phyla in mice feces. Microbiota depletion resulted in a remarkable reversion of the colitis phenotype after MLT administration, including a counter-regulatory immune response, reduction in TNF and colon macrophages. There was a decrease in Actinobacteria, Firmicutes and, most strikingly, Verrucomicrobia phylum in recovering mice. Finally, these results pointed to a gut-microbiota-dependent effect of MLT in the potentiation of intestinal inflammation. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

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Review

Jump to: Research

24 pages, 474 KiB

Open AccessReview

Factors Influencing Neonatal Gut Microbiome and Health with a Focus on Necrotizing Enterocolitis

by Kay D. Beharry, Magdalena Latkowska, Arwin M. Valencia, Ahreen Allana, Jatnna Soto, Charles L. Cai, Sergio Golombek, Ivan Hand and Jacob V. Aranda

Microorganisms 2023, 11(10), 2528; https://doi.org/10.3390/microorganisms11102528 - 10 Oct 2023

Cited by 8 | Viewed by 3837

Abstract

Maturational changes in the gut start in utero and rapidly progress after birth, with some functions becoming fully developed several months or years post birth including the acquisition of a full gut microbiome, which is made up of trillions of bacteria of thousands [...] Read more.

Maturational changes in the gut start in utero and rapidly progress after birth, with some functions becoming fully developed several months or years post birth including the acquisition of a full gut microbiome, which is made up of trillions of bacteria of thousands of species. Many factors influence the normal development of the neonatal and infantile microbiome, resulting in dysbiosis, which is associated with various interventions used for neonatal morbidities and survival. Extremely low gestational age neonates (<28 weeks’ gestation) frequently experience recurring arterial oxygen desaturations, or apneas, during the first few weeks of life. Apnea, or the cessation of breathing lasting 15–20 s or more, occurs due to immature respiratory control and is commonly associated with intermittent hypoxia (IH). Chronic IH induces oxygen radical diseases of the neonate, including necrotizing enterocolitis (NEC), the most common and devastating gastrointestinal disease in preterm infants. NEC is associated with an immature intestinal structure and function and involves dysbiosis of the gut microbiome, inflammation, and necrosis of the intestinal mucosal layer. This review describes the factors that influence the neonatal gut microbiome and dysbiosis, which predispose preterm infants to NEC. Current and future management and therapies, including the avoidance of dysbiosis, the use of a human milk diet, probiotics, prebiotics, synbiotics, restricted antibiotics, and fecal transplantation, for the prevention of NEC and the promotion of a healthy gut microbiome are also reviewed. Interventions directed at boosting endogenous and/or exogenous antioxidant supplementation may not only help with prevention, but may also lessen the severity or shorten the course of the disease. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

21 pages, 3913 KiB

Open AccessReview

Gut Phageome—An Insight into the Role and Impact of Gut Microbiome and Their Correlation with Mammal Health and Diseases

by Yujie Zhang, Somanshu Sharma, Logan Tom, Yen-Te Liao and Vivian C. H. Wu

Microorganisms 2023, 11(10), 2454; https://doi.org/10.3390/microorganisms11102454 - 29 Sep 2023

Cited by 7 | Viewed by 3305

Abstract

The gut microbiota, including bacteria, archaea, fungi, and viruses, compose a diverse mammalian gut environment and are highly associated with host health. Bacteriophages, the viruses that infect bacteria, are the primary members of the gastrointestinal virome, known as the phageome. However, our knowledge [...] Read more.

The gut microbiota, including bacteria, archaea, fungi, and viruses, compose a diverse mammalian gut environment and are highly associated with host health. Bacteriophages, the viruses that infect bacteria, are the primary members of the gastrointestinal virome, known as the phageome. However, our knowledge regarding the gut phageome remains poorly understood. In this review, the critical role of the gut phageome and its correlation with mammalian health were summarized. First, an overall profile of phages across the gastrointestinal tract and their dynamic roles in shaping the surrounding microorganisms was elucidated. Further, the impacts of the gut phageome on gastrointestinal fitness and the bacterial community were highlighted, together with the influence of diets on the gut phageome composition. Additionally, new reports on the role of the gut phageome in the association of mammalian health and diseases were reviewed. Finally, a comprehensive update regarding the advanced phage benchwork and contributions of phage-based therapy to prevent/treat mammalian diseases was provided. This study provides insights into the role and impact of the gut phagenome in gut environments closely related to mammal health and diseases. The findings provoke the potential applications of phage-based diagnosis and therapy in clinical and agricultural fields. Future research is needed to uncover the underlying mechanism of phage–bacterial interactions in gut environments and explore the maintenance of mammalian health via phage-regulated gut microbiota. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

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21 pages, 1025 KiB

Open AccessReview

The Intestinal Microbiome after Traumatic Injury

by Jennifer A. Munley, Stacey L. Kirkpatrick, Gwendolyn S. Gillies, Letitia E. Bible, Philip A. Efron, Ravinder Nagpal and Alicia M. Mohr

Microorganisms 2023, 11(8), 1990; https://doi.org/10.3390/microorganisms11081990 - 2 Aug 2023

Cited by 8 | Viewed by 2630

Abstract

The intestinal microbiome plays a critical role in host immune function and homeostasis. Patients suffering from—as well as models representing—multiple traumatic injuries, isolated organ system trauma, and various severities of traumatic injury have been studied as an area of interest in the dysregulation [...] Read more.

The intestinal microbiome plays a critical role in host immune function and homeostasis. Patients suffering from—as well as models representing—multiple traumatic injuries, isolated organ system trauma, and various severities of traumatic injury have been studied as an area of interest in the dysregulation of immune function and systemic inflammation which occur after trauma. These studies also demonstrate changes in gut microbiome diversity and even microbial composition, with a transition to a pathobiome state. In addition, sex has been identified as a biological variable influencing alterations in the microbiome after trauma. Therapeutics such as fecal transplantation have been utilized to ameliorate not only these microbiome changes but may also play a role in recovery postinjury. This review summarizes the alterations in the gut microbiome that occur postinjury, either in isolated injury or multiple injuries, along with proposed mechanisms for these changes and future directions for the field. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

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25 pages, 1961 KiB

Open AccessReview

The Potential Value of Probiotics after Dental Implant Placement

by Jia Xu, Chenfeng Chen, Shuaiqi Gan, Yihan Liao, Ruijie Fu, Chuping Hou, Shuhan Yang, Zheng Zheng and Wenchuan Chen

Microorganisms 2023, 11(7), 1845; https://doi.org/10.3390/microorganisms11071845 - 20 Jul 2023

Cited by 6 | Viewed by 3035

Abstract

Dental implantation is currently the optimal solution for tooth loss. However, the health and stability of dental implants have emerged as global public health concerns. Dental implant placement, healing of the surgical site, osseointegration, stability of bone tissues, and prevention of peri-implant diseases [...] Read more.

Dental implantation is currently the optimal solution for tooth loss. However, the health and stability of dental implants have emerged as global public health concerns. Dental implant placement, healing of the surgical site, osseointegration, stability of bone tissues, and prevention of peri-implant diseases are challenges faced in achieving the long-term health and stability of implants. These have been ongoing concerns in the field of oral implantation. Probiotics, as beneficial microorganisms, play a significant role in the body by inhibiting pathogens, promoting bone tissue homeostasis, and facilitating tissue regeneration, modulating immune-inflammatory levels. This review explores the potential of probiotics in addressing post-implantation challenges. We summarize the existing research regarding the importance of probiotics in managing dental implant health and advocate for further research into their potential applications. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

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15 pages, 1608 KiB

Open AccessReview

Therapeutic Prospect of New Probiotics in Neurodegenerative Diseases

by Mingxia Bi, Chang Liu, Yulin Wang and Shuang-Jiang Liu

Microorganisms 2023, 11(6), 1527; https://doi.org/10.3390/microorganisms11061527 - 8 Jun 2023

Cited by 7 | Viewed by 3530

Abstract

Increasing clinical and preclinical evidence implicates gut microbiome (GM) dysbiosis as a key susceptibility factor for neurodegenerative disorders, including Alzheimer’s disease (AD) and Parkinson’s disease (PD). In recent years, neurodegenerative diseases have been viewed as being driven not solely by defects in the [...] Read more.

Increasing clinical and preclinical evidence implicates gut microbiome (GM) dysbiosis as a key susceptibility factor for neurodegenerative disorders, including Alzheimer’s disease (AD) and Parkinson’s disease (PD). In recent years, neurodegenerative diseases have been viewed as being driven not solely by defects in the brain, and the role of GM in modulating central nervous system function via the gut–brain axis has attracted considerable interest. Encouraged by current GM research, the development of new probiotics may lead to tangible impacts on the treatment of neurodegenerative disorders. This review summarizes current understandings of GM composition and characteristics associated with neurodegenerative diseases and research demonstrations of key molecules from the GM that affect neurodegeneration. Furthermore, applications of new probiotics, such as Clostridium butyricum, Akkermansia muciniphila, Faecalibacterium prausnitzii, and Bacteroides fragilis, for the remediation of neurodegenerative diseases are discussed. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

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19 pages, 1225 KiB

Open AccessReview

Homeostasis and Dysbiosis of the Intestinal Microbiota: Comparing Hallmarks of a Healthy State with Changes in Inflammatory Bowel Disease

by Jasminka Talapko, Aleksandar Včev, Tomislav Meštrović, Emina Pustijanac, Melita Jukić and Ivana Škrlec

Microorganisms 2022, 10(12), 2405; https://doi.org/10.3390/microorganisms10122405 - 5 Dec 2022

Cited by 17 | Viewed by 5084

Abstract

The gut microbiota, which represent a community of different microorganisms in the human intestinal tract, are crucial to preserving human health by participating in various physiological functions and acting as a metabolic organ. In physiological conditions, microbiota–host partnership exerts homeostatic stability; however, changes [...] Read more.

The gut microbiota, which represent a community of different microorganisms in the human intestinal tract, are crucial to preserving human health by participating in various physiological functions and acting as a metabolic organ. In physiological conditions, microbiota–host partnership exerts homeostatic stability; however, changes in intestinal microbiota composition (dysbiosis) are an important factor in the pathogenesis of inflammatory bowel disease and its two main disease entities: ulcerative colitis and Crohn’s disease. The incidence and prevalence of these inflammatory conditions have increased rapidly in the last decade, becoming a significant problem for the healthcare system and a true challenge in finding novel therapeutic solutions. The issue is that, despite numerous studies, the etiopathogenesis of inflammatory bowel disease is not completely clear. Based on current knowledge, chronic intestinal inflammation occurs due to altered intestinal microbiota and environmental factors, as well as a complex interplay between the genetic predisposition of the host and an inappropriate innate and acquired immune response. It is important to note that the development of biological and immunomodulatory therapy has led to significant progress in treating inflammatory bowel disease. Certain lifestyle changes and novel approaches—including fecal microbiota transplantation and nutritional supplementation with probiotics, prebiotics, and synbiotics—have offered solutions for dysbiosis management and paved the way towards restoring a healthy microbiome, with only minimal long-term unfavorable effects. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

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16 pages, 2988 KiB

Open AccessReview

Microbiome-Driven Proline Biogenesis in Plants under Stress: Perspectives for Balanced Diet to Minimize Depression Disorders in Humans

by Silva Vujanovic, Josko Vujanovic and Vladimir Vujanovic

Microorganisms 2022, 10(11), 2264; https://doi.org/10.3390/microorganisms10112264 - 15 Nov 2022

Cited by 7 | Viewed by 3388

Abstract

According to the World Health Organization (WHO), depression is a leading cause of disability worldwide and a major contributor to the overall global burden of mental disorders. An increasing number of studies have revealed that among 20 different amino acids, high proline consumption [...] Read more.

According to the World Health Organization (WHO), depression is a leading cause of disability worldwide and a major contributor to the overall global burden of mental disorders. An increasing number of studies have revealed that among 20 different amino acids, high proline consumption is a dietary factor with the strongest impact on depression in humans and animals, including insects. Recent studies acknowledged that gut microbiota play a key role in proline-related pathophysiology of depression. In addition, the multi-omics approach has alleged that a high level of metabolite proline is directly linked to depression severity, while variations in levels of circulating proline are dependent on microbiome composition. The gut–brain axis proline analysis is a gut microbiome model of studying depression, highlighting the critical importance of diet, but nothing is known about the role of the plant microbiome–food axis in determining proline concentration in the diet and thus about preventing excessive proline intake through food consumption. In this paper, we discuss the protocooperative potential of a holistic study approach combining the microbiota–gut–brain axis with the microbiota–plant–food–diet axis, as both are involved in proline biogenesis and metabolism and thus on in its effect on mood and cognitive function. In preharvest agriculture, the main scientific focus must be directed towards plant symbiotic endophytes, as scavengers of abiotic stresses in plants and modulators of high proline concentration in crops/legumes/vegetables under climate change. It is also implied that postharvest agriculture—including industrial food processing—may be critical in designing a proline-balanced diet, especially if corroborated with microbiome-based preharvest agriculture, within a circular agrifood system. The microbiome is suggested as a target for selecting beneficial plant endophytes in aiming for a balanced dietary proline content, as it is involved in the physiology and energy metabolism of eukaryotic plant/human/animal/insect hosts, i.e., in core aspects of this amino acid network, while opening new venues for an efficient treatment of depression that can be adapted to vast groups of consumers and patients. In that regard, the use of artificial intelligence (AI) and molecular biomarkers combined with rapid and non-destructive imaging technologies were also discussed in the scope of enhancing integrative science outcomes, agricultural efficiencies, and diagnostic medical precisions. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

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12 pages, 763 KiB

Open AccessReview

Psycho-Microbiology, a New Frontier for Probiotics: An Exploratory Overview

by Alessandra Accettulli, Maria Rosaria Corbo, Milena Sinigaglia, Barbara Speranza, Daniela Campaniello, Angela Racioppo, Clelia Altieri and Antonio Bevilacqua

Microorganisms 2022, 10(11), 2141; https://doi.org/10.3390/microorganisms10112141 - 29 Oct 2022

Cited by 9 | Viewed by 3469

Abstract

Probiotics are gradually gaining importance in the field of psychiatry in the form of psychobiotics. Psychobiotics’ studies examine the existing relationship between gut microbiota and mental phenomena; the intake of certain strains of probiotics, such as Bifidobacterium and Lactobacillus, for example, allow [...] Read more.

Probiotics are gradually gaining importance in the field of psychiatry in the form of psychobiotics. Psychobiotics’ studies examine the existing relationship between gut microbiota and mental phenomena; the intake of certain strains of probiotics, such as Bifidobacterium and Lactobacillus, for example, allow the gut microbial system to be modified in order to provide benefits at the psychic, immune, hormonal, and mental levels. Those who suffer from forms of depression, anxiety disorders, chronic stress, low mood, but also people who do not suffer from such disorders, can therefore benefit from the use of psychobiotics. Thanks to probiotics, neurochemicals can in fact be produced within the gut microbiota and interact with receptors of the enteric nervous system that innervate the entire gastrointestinal tract. Once they enter the portal circulation, these substances go on to influence components of the nervous system and ultimately the brain, through what is called the gut–brain axis. This article proposes an exploratory overview of the proven effects of probiotics on brain activity and psycho-related diseases, focusing on clinical studies and measurable outcomes. The search was conducted using two different online tools: ClinicalTrials.gov and PubMed. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

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25 pages, 2136 KiB

Open AccessReview

Gut Microbiota-Derived Short-Chain Fatty Acids: Impact on Cancer Treatment Response and Toxicities

by Ghanyah H. Al-Qadami, Kate R. Secombe, Courtney B. Subramaniam, Hannah R. Wardill and Joanne M. Bowen

Microorganisms 2022, 10(10), 2048; https://doi.org/10.3390/microorganisms10102048 - 17 Oct 2022

Cited by 51 | Viewed by 7989

Abstract

The gut microbiota has emerged as a key modulator of cancer treatment responses in terms of both efficacy and toxicity. This effect is clearly mediated by processes impacting the activation and modulation of immune responses. More recently, the ability to regulate chemotherapeutic drug [...] Read more.

The gut microbiota has emerged as a key modulator of cancer treatment responses in terms of both efficacy and toxicity. This effect is clearly mediated by processes impacting the activation and modulation of immune responses. More recently, the ability to regulate chemotherapeutic drug metabolism has also emerged as a key driver of response, although the direct mechanisms have yet to be fully elucidated. Through fermentation, the gut microbiota can produce several types of metabolites, including short-chain fatty acids (SCFAs). SCFAs play an important role in maintaining epithelial barrier functions and intestinal homeostasis, with recent work suggesting that SCFAs can modulate response to cancer treatments and influence both anti-tumor immune response and inflammatory-related side effects. In this review, we will discuss the importance of SCFAs and their implications for cancer treatment response and toxicities. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

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