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Keywords = fecal Clostridia

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17 pages, 855 KiB  
Article
Gut Microbiome Correlations in Hidradenitis Suppurativa Patients
by Edyta Lelonek, Piotr K. Krajewski and Jacek C. Szepietowski
J. Clin. Med. 2025, 14(14), 5074; https://doi.org/10.3390/jcm14145074 - 17 Jul 2025
Viewed by 243
Abstract
Background/Objectives: Hidradenitis suppurativa (HS) is a chronic autoinflammatory skin disease characterized by recurrent, painful, and persistently draining purulent lesions. Alterations in the composition of the microbiome may be associated with immune dysregulation and HS progression. The objective of this study was to [...] Read more.
Background/Objectives: Hidradenitis suppurativa (HS) is a chronic autoinflammatory skin disease characterized by recurrent, painful, and persistently draining purulent lesions. Alterations in the composition of the microbiome may be associated with immune dysregulation and HS progression. The objective of this study was to investigate the correlations between the gut microbiome and HS. Methods: A total of 80 participants (40 HS patients and 40 healthy controls [HCs]) were included in this study. Each participant filled out a specially designed questionnaire, which included demographics, HS severity, physical characteristics, dietary habits, and gastrointestinal disorders. DNA isolation and sequencing of microbiota were performed from fecal samples collected from each participant. Results: No statistically significant difference was observed in the alpha diversity between the microbiota of HS and HC. Nevertheless, HS was found to significantly decrease the chances of, among others, Collinsella, Izemoplasmatales, Clostridia, Lachnospiraceae, eligens group, xylanophilum group, and Pseudoflavonifractor occurrence. Conversely, HS significantly increased the chances of Enterorhabdus, Senegalimassilia, Gastranaerophilales, Candidatus Stoquefichus, Erysipelatoclostridiaceae, Holdemanella, Solobacterium, Ruminiclostridium, [Eubacterium] fissicatena group, Angelakisella, Comamonas, and Enterobacter occurrence. The logistic regression analysis, performed separately for each genus, showed a significant influence of disease severity (based on the Hurley scale) on the chances of occurrence for the following genera: Chloroplast (OR = 5.778), Dielma (OR = 5.75), Eisenbergiella (OR = 5.75) and Paludicola (OR = 5.778). Conclusions: In conclusion, our study adds to the growing body of literature on the gut microbiome in HS and provides valuable insights into the specific alterations in microbial occurrence and abundance associated with the disease. Full article
(This article belongs to the Special Issue Recent Advances in Acne, Rosacea and Hidradenitis Suppurativa)
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18 pages, 1903 KiB  
Article
Effects of Dietary Ratio of Insoluble Fiber to Soluble Fiber on Reproductive Performance, Biochemical Parameters, and Fecal Microbial Composition of Gestating Sows
by Xiaolu Wen, Qiwen Wu, Kaiguo Gao, Xuefen Yang, Hao Xiao, Zongyong Jiang and Li Wang
Animals 2025, 15(13), 1850; https://doi.org/10.3390/ani15131850 - 23 Jun 2025
Viewed by 392
Abstract
This study aimed to investigate the effects of dietary ISF:SF ratio on reproductive performance, biochemical parameters, colostrum composition, and fecal microbial composition in gestating sows. A total of 30 multiparous sows were randomly allocated to three dietary treatment groups: 8% inulin diet (ISF:SF [...] Read more.
This study aimed to investigate the effects of dietary ISF:SF ratio on reproductive performance, biochemical parameters, colostrum composition, and fecal microbial composition in gestating sows. A total of 30 multiparous sows were randomly allocated to three dietary treatment groups: 8% inulin diet (ISF:SF 1.14, Inulin group), 8% cotton fiber diet (ISF:SF 6.61, Cotton group), and 4% inulin + 4% cotton fiber diet (ISF:SF 2.37, Inulin + Cotton group). The results showed that, compared to the other groups, the Inulin group had a significantly higher number of piglets born alive, as well as increased plasma concentrations of acetic acid, butyric acid, hexanoic acid, and total short-chain fatty acids (SCFAs) (p < 0.05). Sows in the Inulin group had significantly lower fecal scores than those in the other groups from days 81 to 85 and from days 106 to 110 of gestation (p < 0.05). On day 90 of gestation, the serum levels of albumin, urea, uric acid, calcium, and phosphorus in the Inulin group were significantly lower than those in the other groups (p < 0.05). Additionally, the serum levels of triacylglycerol in the Inulin + Cotton Fiber group were significantly higher than those in the other groups (p < 0.05). However, there were no significant differences in serum concentrations of total protein, creatinine, glucose, cholesterol, HDL-cholesterol, or LDL-cholesterol among the treatments (p > 0.05). On day 110 of gestation, the serum content of urea, uric acid, calcium, and phosphorus in the Inulin group was significantly lower than those in the other groups (p < 0.05). Furthermore, the plasma levels of uric acid, triacylglycerol, and HDL-cholesterol in the Inulin + Cotton Fiber group were significantly higher than those in the Cotton Fiber group (p < 0.05), while the creatinine levels in the Inulin group were higher than those in the other groups (p < 0.05). No differences were observed in the composition and immune performance of colostrum (p > 0.05). Microbial sequencing analysis showed that dietary inulin supplementation to increase the proportion of soluble fiber significantly decreased the abundance of Firmicutes, Clostridia, Clostridiales, Lachnospiraceae, Streptococcaceae, and Streptococcus (p < 0.05). The abundance of short-chain fatty acid-producing microorganisms—Bacteroidetes, Bacteroidia, Bacteroidales, and Muribaculaceae—was significantly increased (p < 0.05). The results indicated that inulin supplementation decreased the dietary ISF:SF ratio, significantly alleviated constipation in sows, increased the number of piglets born alive, regulated intestinal microecology, and increased the plasma concentrations of short-chain fatty acids (SCFAs), including acetic, propionic, and butyric acids. Full article
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19 pages, 4217 KiB  
Article
Characterization of Gut Microbiome Composition in Depression and Completed Suicide
by Samat Kozhakhmetov, Alibek Kossumov, Tolkyn Zhakupova, Tatyana Polyakova, Nazgul Imambayeva, Bagyzhan Syzdykova, Aidana Rakhmankulova, Gulshat Dalibayeva, Artur Kovenskiy, Zharkyn Jarmukhanov, Argul Issilbayeva, Elizaveta Vinogradova and Almagul Kushugulova
Int. J. Mol. Sci. 2025, 26(10), 4880; https://doi.org/10.3390/ijms26104880 - 19 May 2025
Viewed by 876
Abstract
Growing evidence supports a bidirectional relationship between the gut microbiome and mental health. This study investigated the association between gut microbiota, depression, and suicidal behavior by analyzing fecal samples from 35 individuals with varying depression levels and 36 completed suicide cases. Standardized psychometric [...] Read more.
Growing evidence supports a bidirectional relationship between the gut microbiome and mental health. This study investigated the association between gut microbiota, depression, and suicidal behavior by analyzing fecal samples from 35 individuals with varying depression levels and 36 completed suicide cases. Standardized psychometric assessments were used for depression evaluation. Analysis revealed significant taxonomic differences between groups, with increased abundance of Firmicutes, Clostridia, Lachnospiraceae, Blautia, and Dorea in suicide cases, which also positively correlated with depression severity. Metabolic pathway analysis demonstrated a notable dichotomy: suicide cases showed elevated pathways related to infection processes, inflammation, and antibiotic resistance, while the control group exhibited higher energy metabolism and vitamin synthesis pathways. The findings establish specific microbiome profiles associated with both depression symptoms and suicidal behavior, suggesting that gut dysbiosis may influence mental health through altered energy metabolism and inflammatory processes, potentially offering new perspectives for diagnostic and therapeutic approaches. Full article
(This article belongs to the Special Issue Recent Research in Gut Microbiota–Gut–Brain Axis)
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26 pages, 10860 KiB  
Article
Glutamate Supplementation Regulates Nitrogen Metabolism in the Colon and Liver of Weaned Rats Fed a Low-Protein Diet
by Da Jiang, Jing Zhang, Yun Ji, Zhaolai Dai, Ying Yang and Zhenlong Wu
Nutrients 2025, 17(9), 1465; https://doi.org/10.3390/nu17091465 - 26 Apr 2025
Viewed by 654
Abstract
Background: Glutamate, a nutritionally non-essential amino acid, is a key intermediate in nitrogen metabolism. Despite more studies on its functional role in intestine health, it remains unknown how glutamate regulates nitrogen metabolism in animals fed a low-protein diet. Methods: Herein, we [...] Read more.
Background: Glutamate, a nutritionally non-essential amino acid, is a key intermediate in nitrogen metabolism. Despite more studies on its functional role in intestine health, it remains unknown how glutamate regulates nitrogen metabolism in animals fed a low-protein diet. Methods: Herein, we investigated the effects of glutamate supplementation on colonic amino acid transport, barrier protein expression, microbiota alterations, fecal nitrogen emissions, hepatic amino acid transport, and protein synthesis in weaned rats. Results: We found that protein restriction diminished the mucus thickness, reduced goblet cell numbers, and the expression of EAAT3, y+LAT2 in the colon. In contrast, glutamate supplementation reversed these effects, increasing the colon length and enhancing the expression of ZO-1, Occludin, and Claudin-1 in the colon. At the genus level, glutamate increased the abundance of Lactococcus and Clostridia_sensu_stricto_18. Additionally, glutamate supplementation resulted in an increased apparent nitrogen digestibility, reduced the ratio of fecal nitrogen to total nitrogen intake, and increased the ratio of fecal microbial nitrogen to total nitrogen intake. Protein restriction decreased the mRNA level of ATP1A1, EAAT3, SNAT9/2, and ASCT2, and the protein level of p-mTOR, mTOR, p-mTOR/mTOR, and p-p70S6K/p70S6K as well as p-4EBP1/4EBP1 in the liver. These effects were reversed by glutamate supplementation. Conclusions: In conclusion, glutamate supplementation upregulates amino acid transporters and barrier protein expression in the colon, modulates microbiota composition to reduce fecal nitrogen excretion, and enhances amino acid transport and protein synthesis in the liver by activating the mTOR/p70S6K/4EBP1 pathway, which influences nitrogen metabolism in weaned rats fed a low-protein diet. Full article
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16 pages, 2829 KiB  
Article
Analysis of Fecal Microbiome and Metabolome Changes in Goats When Consuming a Lower-Protein Diet with Varying Energy Levels
by Hu Liu, Anmiao Chen, Wenji Wang, Weishi Peng, Kaiyu Mao, Yuanting Yang, Qun Wu, Meng Zeng, Ke Wang, Jiancheng Han and Hanlin Zhou
Microorganisms 2025, 13(4), 941; https://doi.org/10.3390/microorganisms13040941 - 18 Apr 2025
Viewed by 560
Abstract
The objective of this study was to evaluate the effect of fecal bacterial community and metabolomics in goats when consuming a lower-protein diet with different energy levels. Eight healthy Leizhou goats, with 11 ± 0.78 kg of body weight, were selected and housed [...] Read more.
The objective of this study was to evaluate the effect of fecal bacterial community and metabolomics in goats when consuming a lower-protein diet with different energy levels. Eight healthy Leizhou goats, with 11 ± 0.78 kg of body weight, were selected and housed individually in cages. The animals were randomly allocated to a lower-protein diet that varied with four metabolites energy levels (7.01, 8.33, 9.66, and 10.98 MJ/kg DM) in a replicated 4 × 4 Latin square design. Notably, energy-dependent microbial restructuring was observed at both phylum and genus levels. At the phylum level, the relative abundances of Firmicutes and Spirochaetote increased linearly, whereas the Bacteroidota and Patescibacteria decreased linearly with increasing dietary energy levels (p < 0.05). The relative abundances of Verrucomicrobiota increased quadratically, whereas others decreased quadratically with increasing dietary energy levels (p < 0.05). At the genus level, a total of 316 bacteria were identified in the 32 fecal samples. The relative abundances of Christensenellaceae_R-7_group, unclassified_f__Lachnospiraceae, Ruminococcus, norank_o__Clostridia_UCG-014, Treponema, [Eubacterium]_siraeum_group, and [Eubacterium]_ruminantium_group increased linearly, whereas the Oscillospiraceae_UCG-005, norank_f__[Eubacterium]_coprostanoligenes_group, Prevotellaceae_UCG-004, unclassified_c__Clostridia, norank_f__Ruminococcaceae, unclassified_f__ Oscillospiraceae, and others decreased linearly with an increasing dietary energy levels (p < 0.05). In addition, the metabolomic analysis of feces showed that there are many differential metabolites in goats when consuming a lower-protein diet with different energy levels; for example, lipid metabolism and amino acid metabolic pathways were increased in MLE, MHE, and HE groups compared to the LE group. In conclusion, this study provides further information regarding the effects on fecal bacterial community composition and metabolites in goats when consuming a lower-protein diet with different energy levels. Full article
(This article belongs to the Section Gut Microbiota)
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18 pages, 2555 KiB  
Article
Unraveling the Metabolic and Microbiome Signatures in Fecal Samples of Pregnant Women with Prenatal Depression
by Jia Li, Peng-Cheng Mei, Na An, Xiao-Xiao Fan, Yan-Qun Liu, Quan-Fei Zhu and Yu-Qi Feng
Metabolites 2025, 15(3), 179; https://doi.org/10.3390/metabo15030179 - 6 Mar 2025
Cited by 1 | Viewed by 962
Abstract
Background/Objectives: Prenatal depression (PND) poses a significant threat to the health of both the mother and the developing fetus. Despite its increasing prevalence, the pathophysiology of PND is not yet fully elucidated. Methods: In this study, we aimed to investigate the [...] Read more.
Background/Objectives: Prenatal depression (PND) poses a significant threat to the health of both the mother and the developing fetus. Despite its increasing prevalence, the pathophysiology of PND is not yet fully elucidated. Methods: In this study, we aimed to investigate the fecal metabolites and gut microbiota in PND patients compared to healthy controls and to explore potential correlations between these factors. Results: Through untargeted metabolomics analysis, we identified 75 significantly altered metabolites in PND patients, of which 27 were structurally annotated and implicated key pathways, such as linoleic acid metabolism and phenylalanine, tyrosine, and tryptophan biosynthesis. Notably, two Clostridia-associated enterobacteria, unclassified_c_Clostridia and unclassified_f_Lachnospiraceae, which were enriched in the PND group, were significantly positively correlated with tyrosine and negatively correlated with multiple sulfated neurosteroids. Conclusions: Our findings underscore a robust association between gut microbiota dysbiosis and metabolic disturbances in PND, with specific alterations noted in tyrosine metabolism, sulfated neurosteroid homeostasis, and linoleic acid pathways. These dysregulated metabolites—tyrosine, sulfated neurosteroids, and linoleic acid—may serve as potential diagnostic biomarkers and therapeutic targets. Moreover, their interplay provides new insights into the pathophysiological mechanisms of PND, particularly highlighting the role of gut-brain axis signaling in neuroendocrine dysregulation and inflammatory responses. However, further large-scale studies and animal models are required to validate these findings and explore detailed mechanistic pathways. Full article
(This article belongs to the Section Endocrinology and Clinical Metabolic Research)
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22 pages, 6439 KiB  
Article
Role of Increasing Body Mass Index in Gut Barrier Dysfunction, Systemic Inflammation, and Metabolic Dysregulation in Obesity
by Fatima Maqoud, Francesco Maria Calabrese, Giuseppe Celano, Domenica Mallardi, Francesco Goscilo, Benedetta D’Attoma, Antonia Ignazzi, Michele Linsalata, Gabriele Bitetto, Martina Di Chito, Pasqua Letizia Pesole, Arianna Diciolla, Carmen Aurora Apa, Giovanni De Pergola, Gianluigi Giannelli, Maria De Angelis and Francesco Russo
Nutrients 2025, 17(1), 72; https://doi.org/10.3390/nu17010072 - 28 Dec 2024
Cited by 3 | Viewed by 1998
Abstract
Aims: This study explores the link between body mass index (BMI), intestinal permeability, and associated changes in anthropometric and impedance parameters, lipid profiles, inflammatory markers, fecal metabolites, and gut microbiota taxa composition in participants having excessive body mass. Methods: A cohort of 58 [...] Read more.
Aims: This study explores the link between body mass index (BMI), intestinal permeability, and associated changes in anthropometric and impedance parameters, lipid profiles, inflammatory markers, fecal metabolites, and gut microbiota taxa composition in participants having excessive body mass. Methods: A cohort of 58 obese individuals with comparable diet, age, and height was divided into three groups based on a priori clustering analyses that fit with BMI class ranges: Group I (25–29.9), Group II (30–39.9), and Group III (>40). Anthropometric and clinical parameters were assessed, including plasma C-reactive protein and cytokine profiles as inflammation markers. Intestinal permeability was measured using a multisaccharide assay, with fecal/serum zonulin and serum claudin-5 and claudin-15 levels. Fecal microbiota composition and metabolomic profiles were analyzed using a phylogenetic microarray and GC-MS techniques. Results: The statistical analyses of the clinical parameters were based on the full sample set, whereas a subset composed of 37 randomized patients was inspected for the GC/MS metabolite profiling of fecal specimens. An increase in potentially pro-inflammatory bacterial genera (e.g., Slackia, Dorea, Granulicatella) and a reduction in beneficial genera (e.g., Adlercreutzia, Clostridia UCG-014, Roseburia) were measured. The gas chromatography/mass spectrometry analysis of urine samples evidenced a statistically significant increase in m-cymen-8-ol, 1,3,5-Undecatriene, (E, Z) and a decreased concentration of p-cresol, carvone, p-cresol, and nonane. Conclusions: Together, these data demonstrated how an increased BMI led to significant changes in inflammatory markers, intestinal barrier metabolites, glucose metabolism, endocrine indicators, and fecal metabolomic profiles that can indicate a different metabolite production from gut microbiota. Our findings suggest that targeting intestinal permeability may offer a therapeutic approach to prevent and manage obesity and related metabolic complications, reinforcing the link between gut barrier function and obesity. Full article
(This article belongs to the Section Nutrition and Obesity)
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16 pages, 1617 KiB  
Article
Nano-Selenium Reduces Concentrations of Fecal Minerals by Altering Bacteria Composition in Feedlot Goats
by Hu Liu, Kaiyu Mao, Weishi Peng, Allan Degen, Gang Zuo, Yuanting Yang, Jiancheng Han, Qun Wu, Ke Wang, Qinyang Jiang and Hanlin Zhou
Agriculture 2024, 14(12), 2233; https://doi.org/10.3390/agriculture14122233 - 6 Dec 2024
Cited by 1 | Viewed by 847
Abstract
This study examined the effect of dietary supplementation of nano-selenium (nano-Se) on the average daily gain (ADG), fecal bacteria community, and concentrations of fecal minerals and volatile fatty acids in feedlot Hainan black goats. Eighteen goats (18.6 ± 0.69 kg) were divided randomly [...] Read more.
This study examined the effect of dietary supplementation of nano-selenium (nano-Se) on the average daily gain (ADG), fecal bacteria community, and concentrations of fecal minerals and volatile fatty acids in feedlot Hainan black goats. Eighteen goats (18.6 ± 0.69 kg) were divided randomly into three groups, with each group receiving a different level of supplementary nano-Se (n = six goats per treatment) as follows: (1) 0.0 mg (CON); (2) 0.2 mg; and (3) 0.4 mg nano-Se/kg dry matter intake (DMI). The final body weight (p = 0.012) and ADG increased linearly (p < 0.01), whereas the ratio of DMI to ADG decreased linearly (p < 0.01) with increasing dietary nano-Se levels. Fecal concentrations of Se increased linearly (p < 0.001), whereas Cu (p < 0.01), Zn (p = 0.020), and Fe (p = 0.010) decreased linearly with increasing dietary nano-Se levels. The relative abundances of Treponema (p = 0.046), norank_f__norank_o__Clostridia_UCG-014 (p < 0.01), norank_ f_norank_o__RF39 (p < 0.01), Eubacterium_siraeum_group (p < 0.001), and Family_XIII_AD3011_group (p = 0.040) increased linearly, and unclassified_f__Lachnospiraceae (p < 0.001), Rikenellaceae_RC9_gut_group (p < 0.01), Eubacterium_ruminantium_group (p = 0.021), and Prevotella (p < 0.001) decreased linearly with increasing dietary nano-Se levels. It was concluded that supplementary nano-Se could improve ADG and reduce the DMI to ADG ratio and fecal heavy metals by altering the bacterial community in feedlot goats. We recommend a dietary supplementation of approximately 0.4 mg nano-Se/kg DM for feedlot Hainan black goats, but further research is warranted to determine the precise dose and the possible contamination risks of Se. Full article
(This article belongs to the Section Farm Animal Production)
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12 pages, 537 KiB  
Article
Impacts of Nano-Composite of Copper and Carbon on Intestinal Luminal Micro-Ecosystem and Mucosal Homeostasis of Yellow-Feather Broilers
by Xianglin Wang, Chunlong Xiao, Shuqing Wu, Qingjie Lin, Shiying Lin, Jing Liu, Dingcheng Ye, Changkang Wang and Pingting Guo
Microorganisms 2024, 12(11), 2247; https://doi.org/10.3390/microorganisms12112247 - 6 Nov 2024
Viewed by 1181
Abstract
The present study was undertaken to evaluate the impacts of nano-composites of copper and carbon (NCCC) on the intestinal luminal micro-ecosystem and mucosal homeostasis of yellow-feather broilers. A total of two-hundred and forty 1-day-old male yellow-feather broilers were randomly allocated into four groups, [...] Read more.
The present study was undertaken to evaluate the impacts of nano-composites of copper and carbon (NCCC) on the intestinal luminal micro-ecosystem and mucosal homeostasis of yellow-feather broilers. A total of two-hundred and forty 1-day-old male yellow-feather broilers were randomly allocated into four groups, each with five replications of twelve birds. The control (CON) group received a corn-soybean basal diet, while the N50, N100, and N200 groups were supplemented with 50, 100, and 200 mg/kg of NCCC in basal diets, respectively. The trial duration was 63 days. The findings demonstrated that there were slight impacts of NCCC addition on the intestinal luminal micro-ecosystem of broilers, with the fecal moisture content in the N100 group being slightly higher on Day 3 in the starter phase (p < 0.05). The cecal microbiota structure also did not obviously change (p > 0.05), in spite of the fall in the relative abundance of the Ruminococcus torques group in the N50 group and norank Clostridia UCG-014 in N200 group (p < 0.05). But for intestinal mucosal homeostasis, NCCC played a crucial part in jejunal morphology, tight junction, immunologic status, and antioxidant capacity. There was linear growth in villus height and a quadratic increase in villus height, crypt depth and their ratio with the increase in NCCC dosage (p < 0.05), and 100 mg/kg NCCC supplementation could intensify the expression of CLDN-3 genes (p < 0.05). In addition, IL-4 and IL-10 linearly increased after NCCC treatment (p < 0.05), along with some irregular changes in sIgA (p < 0.05). In addition, higher jejunal mucosal total antioxidant capacities in N50 and N200 groups were also observed (p < 0.05). Overall, NCCC treatment optimized the intestinal mucosa function of broilers in terms of physical barrier and immune and antioxidant capacities, but exerted subtle influence in the luminal environment of yellow-feather broilers. More precisely, dietary supplementation with 50 mg/kg NCCC is recommended for intestinal homeostasis of broilers. Full article
(This article belongs to the Special Issue Dietary and Animal Gut Microbiota)
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13 pages, 1439 KiB  
Article
Shotgun Analysis of Gut Microbiota with Body Composition and Lipid Characteristics in Crohn’s Disease
by Péter Bacsur, Tamás Resál, Bernadett Farkas, Boldizsár Jójárt, Zoltán Gyuris, Gábor Jaksa, Lajos Pintér, Bertalan Takács, Sára Pál, Attila Gácser, Kata Judit Szántó, Mariann Rutka, Renáta Bor, Anna Fábián, Klaudia Farkas, József Maléth, Zoltán Szepes, Tamás Molnár and Anita Bálint
Biomedicines 2024, 12(9), 2100; https://doi.org/10.3390/biomedicines12092100 - 14 Sep 2024
Cited by 1 | Viewed by 1316
Abstract
Alterations to intestinal microbiota are assumed to occur in the pathogenesis of inflammatory bowel disease (IBD). This study aims to analyze the association of fecal microbiota composition, body composition, and lipid characteristics in patients with Crohn’s disease (CD). In our cross-sectional study, patients [...] Read more.
Alterations to intestinal microbiota are assumed to occur in the pathogenesis of inflammatory bowel disease (IBD). This study aims to analyze the association of fecal microbiota composition, body composition, and lipid characteristics in patients with Crohn’s disease (CD). In our cross-sectional study, patients with CD were enrolled and blood and fecal samples were collected. Clinical and endoscopic disease activity and body composition were assessed and laboratory tests were made. Fecal bacterial composition was analyzed using the shotgun method. Microbiota alterations based on obesity, lipid parameters, and disease characteristics were analyzed. In this study, 27 patients with CD were analyzed, of which 37.0% were obese based on visceral fat area (VFA). Beta diversities were higher in non-obese patients (p < 0.001), but relative abundances did not differ. C. innocuum had a higher abundance at a high cholesterol level than Bacillota (p = 0.001, p = 0.0034). Adlercreutzia, B. longum, and Blautia alterations were correlated with triglyceride levels. Higher Clostridia (p = 0.009) and B. schinkii (p = 0.032) and lower Lactobacillus (p = 0.035) were connected to high VFA. Disease activity was coupled with dysbiotic elements. Microbiota alterations in obesity highlight the importance of gut microbiota in diseases with a similar inflammatory background and project therapeutic options. Full article
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15 pages, 2571 KiB  
Article
Sequential Sampling of the Gastrointestinal Tract to Characterize the Entire Digestive Microbiome in Japanese Subjects
by Kota Ishizawa, Toru Tamahara, Suguo Suzuki, Yutaka Hatayama, Bin Li, Michiaki Abe, Yuichi Aoki, Ryutaro Arita, Natsumi Saito, Minoru Ohsawa, Soichiro Kaneko, Rie Ono, Shin Takayama, Muneaki Shimada, Kazuki Kumada, Tomoyuki Koike, Atsushi Masamune, Ko Onodera, Tadashi Ishii, Ritsuko Shimizu and Takeshi Kannoadd Show full author list remove Hide full author list
Microorganisms 2024, 12(7), 1324; https://doi.org/10.3390/microorganisms12071324 - 28 Jun 2024
Viewed by 2280
Abstract
The gastrointestinal (GI) tract harbors trillions of microorganisms known to influence human health and disease, and next-generation sequencing (NGS) now enables the in-depth analysis of their diversity and functions. Although a significant amount of research has been conducted on the GI microbiome, comprehensive [...] Read more.
The gastrointestinal (GI) tract harbors trillions of microorganisms known to influence human health and disease, and next-generation sequencing (NGS) now enables the in-depth analysis of their diversity and functions. Although a significant amount of research has been conducted on the GI microbiome, comprehensive metagenomic datasets covering the entire tract are scarce due to cost and technical challenges. Despite the widespread use of fecal samples, integrated datasets encompassing the entire digestive process, beginning at the mouth and ending with feces, are lacking. With this study, we aimed to fill this gap by analyzing the complete metagenome of the GI tract, providing insights into the dynamics of the microbiota and potential therapeutic avenues. In this study, we delved into the complex world of the GI microbiota, which we examined in five healthy Japanese subjects. While samples from the whole GI flora and fecal samples provided sufficient bacteria, samples obtained from the stomach and duodenum posed a challenge. Using a principal coordinate analysis (PCoA), clear clustering patterns were identified; these revealed significant diversity in the duodenum. Although this study was limited by its small sample size, the flora in the overall GI tract showed unwavering consistency, while the duodenum exhibited unprecedented phylogenetic diversity. A visual heat map illustrates the discrepancy in abundance, with Fusobacteria and Bacilli dominating the upper GI tract and Clostridia and Bacteroidia dominating the fecal samples. Negativicutes and Actinobacteria were found throughout the digestive tract. This study demonstrates that it is possible to continuously collect microbiome samples throughout the human digestive tract. These findings not only shed light on the complexity of GI microbiota but also provide a basis for future research. Full article
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22 pages, 2138 KiB  
Article
Idiosyncratic Drug-Induced Liver Injury and Amoxicillin–Clavulanate: Spotlight on Gut Microbiota, Fecal Metabolome and Bile Acid Profile in Patients
by Sara Román-Sagüillo, Raisa Quiñones Castro, María Juárez-Fernández, Polina Soluyanova, Camilla Stephens, Mercedes Robles-Díaz, Francisco Jorquera Plaza, Javier González-Gallego, Susana Martínez-Flórez, María Victoria García-Mediavilla, Esther Nistal, Ramiro Jover and Sonia Sánchez-Campos
Int. J. Mol. Sci. 2024, 25(13), 6863; https://doi.org/10.3390/ijms25136863 - 22 Jun 2024
Cited by 3 | Viewed by 2109
Abstract
Several hepatic disorders are influenced by gut microbiota, but its role in idiosyncratic drug-induced liver injury (iDILI), whose main causative agent is amoxicillin–clavulanate, remains unknown. This pioneering study aims to unravel particular patterns of gut microbiota composition and associated metabolites in iDILI and [...] Read more.
Several hepatic disorders are influenced by gut microbiota, but its role in idiosyncratic drug-induced liver injury (iDILI), whose main causative agent is amoxicillin–clavulanate, remains unknown. This pioneering study aims to unravel particular patterns of gut microbiota composition and associated metabolites in iDILI and iDILI patients by amoxicillin–clavulanate (iDILI-AC). Thus, serum and fecal samples from 46 patients were divided into three study groups: healthy controls (n = 10), non-iDILI acute hepatitis (n = 12) and iDILI patients (n = 24). To evaluate the amoxicillin–clavulanate effect, iDILI patients were separated into two subgroups: iDILI non-caused by amoxicillin–clavulanate (iDILI-nonAC) (n = 18) and iDILI-AC patients (n = 6). Gut microbiota composition and fecal metabolome plus serum and fecal bile acid (BA) analyses were performed, along with correlation analyses. iDILI patients presented a particular microbiome profile associated with reduced fecal secondary BAs and fecal metabolites linked to lower inflammation, such as dodecanedioic acid and pyridoxamine. Moreover, certain taxa like Barnesiella, Clostridia UCG-014 and Eubacterium spp. correlated with significant metabolites and BAs. Additionally, comparisons between iDILI-nonAC and iDILI-AC groups unraveled unique features associated with iDILI when caused by amoxicillin–clavulanate. In conclusion, specific gut microbiota profiles in iDILI and iDILI-AC patients were associated with particular metabolic and BA status, which could affect disease onset and progression. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Human Liver Diseases 2.0)
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16 pages, 4160 KiB  
Article
Lacticaseibacillus paracasei JS-3 Isolated from “Jiangshui” Ameliorates Hyperuricemia by Regulating Gut Microbiota and iTS Metabolism
by Jiahui Wu, Lvbu Aga, Leimengyuan Tang, Houxier Li, Nan Wang, Li Yang, Nan Zhang, Xiang Wang and Xueyong Wang
Foods 2024, 13(9), 1371; https://doi.org/10.3390/foods13091371 - 29 Apr 2024
Cited by 13 | Viewed by 2762
Abstract
Background: A diet high in purines can impair the function of the gut microbiota and disrupt purine metabolism, which is closely associated with the onset of hyperuricemia. Dietary regulation and intestinal health maintenance are key approaches for controlling uric acid (UA) levels. Investigating [...] Read more.
Background: A diet high in purines can impair the function of the gut microbiota and disrupt purine metabolism, which is closely associated with the onset of hyperuricemia. Dietary regulation and intestinal health maintenance are key approaches for controlling uric acid (UA) levels. Investigating the impacts of fermented foods offers potential dietary interventions for managing hyperuricemia. Methods: In this study, we isolated a strain with potent UA-degrading capabilities from “Jiangshui”, a fermented food product from Gansu, China. We performed strain identification and assessed its probiotic potential. Hyperuricemic quails, induced by a high-purine diet, were used to assess the UA degradation capability of strain JS-3 by measuring UA levels in serum and feces. Additionally, the UA degradation pathways were elucidated through analyses of the gut microbiome and fecal metabolomics. Results: JS-3, identified as Lacticaseibacillus paracasei, was capable of eliminating 16.11% of uric acid (UA) within 72 h, rapidly proliferating and producing acid within 12 h, and surviving in the gastrointestinal tract. Using hyperuricemic quail models, we assessed JS-3’s UA degradation capacity. Two weeks after the administration of JS-3 (2 × 108 cfu/d per quail), serum uric acid (SUA) levels significantly decreased to normal levels, and renal damage in quails was markedly improved. Concurrently, feces from the JS-3 group demonstrated a significant degradation of UA, achieving up to 49% within 24 h. 16S rRNA sequencing revealed JS-3’s role in gut microbiota restoration by augmenting the probiotic community (Bifidobacterium, Bacteroides unclassified_f-Lachnospiraceae, and norank_fynorank_o-Clostridia_UCG-014) and diminishing the pathogenic bacteria (Macrococus and Lactococcus). Corresponding with the rise in short-chain fatty acid (SCFA)-producing bacteria, JS-3 significantly increased SCFA levels (p < 0.05, 0.01). Additionally, JS-3 ameliorated metabolic disturbances in hyperuricemic quails, influencing 26 abnormal metabolites predominantly linked to purine, tryptophan, and bile acid metabolism, thereby enhancing UA degradation and renal protection. Conclusions: For the first time, we isolated and identified an active probiotic strain, JS-3, from the “Jiangshui” in Gansu, used for the treatment of hyperuricemia. It modulates host–microbiome interactions, impacts the metabolome, enhances intestinal UA degradation, reduces levels of SUA and fecal UA, alleviates renal damage, and effectively treats hyperuricemia without causing gastrointestinal damage. In summary, JS-3 can serve as a probiotic with potential therapeutic value for the treatment of hyperuricemia. Full article
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13 pages, 2040 KiB  
Article
The Changes in Fecal Bacterial Communities in Goats Offered Rumen-Protected Fat
by Hu Liu, Weishi Peng, Kaiyu Mao, Yuanting Yang, Qun Wu, Ke Wang, Meng Zeng, Xiaotao Han, Jiancheng Han and Hanlin Zhou
Microorganisms 2024, 12(4), 822; https://doi.org/10.3390/microorganisms12040822 - 19 Apr 2024
Cited by 9 | Viewed by 1961
Abstract
Leizhou goats are famous for their delicious meat but have inferior growth performance. There is little information on rumen-protected fat (RPF) from the Leizhou goat. Hence, we observed the effects of RPF on growth, fecal short-chain fatty acids, and bacteria community with respect [...] Read more.
Leizhou goats are famous for their delicious meat but have inferior growth performance. There is little information on rumen-protected fat (RPF) from the Leizhou goat. Hence, we observed the effects of RPF on growth, fecal short-chain fatty acids, and bacteria community with respect to Leizhou goats. Twelve goats (13.34 ± 0.024 kg) were selected and assigned randomly to one of two treatments: (1) a control diet (CON) and (2) 2.4% RPF with a control diet (RPF). The final body weight and average daily gain (ADG) were greater (p < 0.05), and the dry matter intake (DMI): ADG was lower (p < 0.05) in the RPF group than in the CON group. There were no differences in DMI between the CON and RPF groups. The concentrations of total short-chain fatty acids, acetate, propionate, and butyrate were lower (p < 0.05) in the RPF group than in the CON group. The relative abundances of Ruminococcus, Rikenellaceae_RC9_gut_group, Treponema, norank_f__norank_o__RF39, Eubacterium_siraeum_group, and Ruminococcus_torques_group were lower (p < 0.05) in the RPF group than in the CON group. The relative abundances of Bacteroides, norank_f__norank_o__Clostridia_UCG-014, norank_f__Eubacterium_coprostanoligenes_group, Eubacterium_ruminantium_group, norank_f__Oscillospirale-UCG-010, Oscillospiraceae_UCG-002, and Family_XIII_AD3011_group were greater (p < 0.05) in the RPF group than in the CON group. It was concluded that RPF could improve the goats’ growth performance by regulating their fecal bacteria communities. Full article
(This article belongs to the Section Veterinary Microbiology)
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16 pages, 2812 KiB  
Article
Marine Bacterial Community Structures of Selected Coastal Seawater and Sediment Sites in Qatar
by Shimaa S. El-Malah, Kashif Rasool, Khadeeja Abdul Jabbar, Muhammad Umar Sohail, Husam Musa Baalousha and Khaled A. Mahmoud
Microorganisms 2023, 11(12), 2827; https://doi.org/10.3390/microorganisms11122827 - 21 Nov 2023
Cited by 2 | Viewed by 2482
Abstract
Severe environmental conditions can have a diverse impact on marine microorganisms, including bacteria. This can have an inevitable impact on the biofouling of membrane-based desalination plants. In this work, we have utilized indicator bacteria such as total coliform, fecal coliform, and Pseudomonas aeruginosa [...] Read more.
Severe environmental conditions can have a diverse impact on marine microorganisms, including bacteria. This can have an inevitable impact on the biofouling of membrane-based desalination plants. In this work, we have utilized indicator bacteria such as total coliform, fecal coliform, and Pseudomonas aeruginosa, as well as 16S rRNA sequencing, to investigate the impact of environmental conditions and spatial variations on the diversity of bacterial communities in the coastal waters and sediments from selected sites in Qatar. The concentration levels of indicator bacteria were affected by increasing temperatures and pH, and by decreasing salinity of seawater samples. Diversity indices and the molecular phylogeny demonstrated that Proteobacteria, Bacteroidetes, and Cyanobacteria were the dominant phyla in all locations. The most abundant operational taxonomic units (OTUs) at the family level were from Flavobacteriaceae (27.07%, 4.31%) and Rhodobacteraceae (22.51%, 9.86%) in seawater and sediment, respectively. Alphaproteobacteria (33.87%, 16.82%), Flavobacteria (30.68%, 5.84%), and Gammaproteobacteria (20.35%, 12.45%) were abundant at the species level in both seawater and sediment, while Clostridia (13.72%) was abundant in sediment only. The results suggest that sediment can act as a reservoir for indicator bacteria, with higher diversity and lower abundance compared to seawater. Full article
(This article belongs to the Special Issue Marine Microorganisms and Ecology)
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