picture
RJR-logo

About | BLOGS | Portfolio | Misc | Recommended | What's New | What's Hot

About | BLOGS | Portfolio | Misc | Recommended | What's New | What's Hot

icon

Bibliography Options Menu

icon
QUERY RUN:
08 Nov 2024 at 01:51
HITS:
70612
PAGE OPTIONS:
Hide Abstracts   |   Hide Additional Links
NOTE:
Long bibliographies are displayed in blocks of 100 citations at a time. At the end of each block there is an option to load the next block.

Bibliography on: Microbiome

RJR-3x

Robert J. Robbins is a biologist, an educator, a science administrator, a publisher, an information technologist, and an IT leader and manager who specializes in advancing biomedical knowledge and supporting education through the application of information technology. More About:  RJR | OUR TEAM | OUR SERVICES | THIS WEBSITE

RJR: Recommended Bibliography 08 Nov 2024 at 01:51 Created: 

Microbiome

It has long been known that every multicellular organism coexists with large prokaryotic ecosystems — microbiomes — that completely cover its surfaces, external and internal. Recent studies have shown that these associated microbiomes are not mere contamination, but instead have profound effects upon the function and fitness of the multicellular organism. We now know that all MCEs are actually functional composites, holobionts, composed of more prokaryotic cells than eukaryotic cells and expressing more prokaryotic genes than eukaryotic genes. A full understanding of the biology of "individual" eukaryotes will now depend on an understanding of their associated microbiomes.

Created with PubMed® Query: microbiome[tiab] NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

-->

RevDate: 2024-11-04

Zhang H, Zhou W, Gao P, et al (2024)

Ellagic Acid Protects against Alcohol-Related Liver Disease by Modulating the Hepatic Circadian Rhythm Signaling through the Gut Microbiota-NPAS2 Axis.

Journal of agricultural and food chemistry [Epub ahead of print].

Alcohol-related liver disease (ALD) encompasses a spectrum of hepatic disorders resulting from alcohol abuse, which constitutes the predominant etiology of morbidity and mortality associated with hepatic pathologies globally. Excessive alcohol consumption disrupts the integrity of the intestinal barrier and perturbs the balance of gut microbiota, thereby facilitating the progression of ALD. Ellagic acid (EA) has been extensively reported to be an effective intervention for alleviating liver symptoms. However, the target molecules of EA in improving ALD and its underlying mechanism remain elusive. First, our study indicates that EA ameliorated ALD through the hepatic circadian rhythm signaling by up-regulating neuronal PAS domain protein 2 (NPAS2). Furthermore, analysis of the intestinal microbiome showed that EA significantly enhanced the abundance of beneficial bacteria, which was positively correlated with NPAS2 expression and negatively correlated with liver injury. Finally, antibiotic treatment and fecal microbiota transplantation (FMT) experiments established a causal relationship between the reshaped microbiota and NPAS2 in the amelioration of ALD. In summary, our study demonstrates novel evidence that EA attenuated ALD by modulating the hepatic circadian rhythm signaling pathway via the gut microbiota-NPAS2 axis, providing valuable insights for EA and microbiome-targeted interventions against ALD.

RevDate: 2024-11-04

Muralitharan RR, Buikema JW, FZ Marques (2024)

Minimizing gut microbiome confounding factors in cardiovascular research.

Cardiovascular research pii:7874985 [Epub ahead of print].

RevDate: 2024-11-04

Fitz Axen AJ, Kim M-S, Klopfenstein NB, et al (2024)

Fire-associated microbial shifts in soils of western conifer forests with Armillaria root disease.

Applied and environmental microbiology [Epub ahead of print].

UNLABELLED: Fires in coniferous forests throughout the northern United States alter ecosystem processes and ecological communities, including the diversity and composition of microbial communities living in the soil. In addition to its influence on ecosystem processes and functions, the soil microbiome can interact with soilborne pathogens to facilitate or suppress plant disease development. Altering the microbiome composition to promote taxa that inhibit pathogenic activity has been suggested as a management strategy for forest diseases, including Armillaria root disease caused by Armillaria solidipes, which causes growth loss and mortality of conifers. These forest ecosystems are experiencing increased wildfire burn severity that could influence A. solidipes activity and interactions of the soil microbiome with Armillaria root disease. In this research, we examine changes to the soil microbiome following three levels of burn severity in a coniferous forest in northern Idaho, United States, where Armillaria root disease is prevalent. We further determine how these changes correspond to the soil microbiomes associated with the pathogen A. solidipes, and a putatively beneficial species, A. altimontana. At 15-months post-fire, we found significant differences in richness and diversity between bacterial communities associated with unburned and burned areas, yet no significant changes to these metrics were found in fungal communities following fire. However, both bacterial and fungal communities showed compositional changes associated with burn severity, including microbial taxa with altered relative abundance. Further, significant differences in the relative abundance of certain microbial taxa in communities associated with the three burn severity levels overlapped with taxa associated with various Armillaria spp. Following severe burn, we observed a decreased relative abundance of beneficial ectomycorrhizal fungi associated with the microbial communities of A. altimontana, which may contribute to the antagonistic activity of this soil microbial community. Additionally, A. solidipes and associated microbial taxa were found to dominate following high-severity burns, suggesting that severe fires provide suitable environmental conditions for these species. Overall, our results suggest that shifts in the soil microbiome and an associated increase in the activity of A. solidipes following high-severity burns in similar conifer forests may result in priority areas for monitoring and proactive management of Armillaria root disease.

IMPORTANCE: With its influence on ecosystem processes and functions, the soil microbiome can interact with soilborne pathogens to facilitate or suppress plant disease development. These forest ecosystems are experiencing increased wildfire frequency and burn severity that could influence the fungal root pathogen, Armillaria solidipes, and interactions with the soil microbiome. We examined changes to the soil microbiome following three levels of burn severity, and examined how these changes correspond with A. solidipes, and a putatively beneficial species, A. altimontana. Following severe burn, there was a decreased relative abundance of ectomycorrhizal fungi associated A. altimontana. A. solidipes and associated microbial taxa dominated following high-severity burns, suggesting that severe fires provide suitable environmental conditions for these species. Our results suggest that shifts in the soil microbiome and an associated increase in the activity of A. solidipes following high-severity burns in conifer forests may result in priority areas for monitoring and proactive management of Armillaria root disease.

RevDate: 2024-11-04

Lin Z, Liang Z, He S, et al (2024)

Salmonella dry surface biofilm: morphology, single-cell landscape, and sanitization.

Applied and environmental microbiology [Epub ahead of print].

In this study, Salmonella Typhimurium dry surface biofilm (DSB) formation was investigated in comparison with wet surface biofilm (WSB) development. Confocal laser scanning microscopic analysis revealed a prominent green cell signal during WSB formation, whereas a red signal predominated during DSB formation. Electron microscopy was also used to compare the features of DSB and WSB. Overall, WSB was unevenly scattered over the surface, whereas DSB was evenly dispersed. In contrast to WSB cells, which have a distinct plasma membrane and outer membrane layer, DSB cells are contained in large capsules and compressed. Next, microbiome single-cell transcriptomics was used to investigate the functional heterogeneity of the Salmonella DSB microbiome, with nine clusters successfully identified. Although over 60% of the dried cells were metabolically inactive, the rest of the Salmonella cells still demonstrated specific antioxidative and virulence capabilities, suggesting a possible concern for low-moisture food (LMF) safety. Finally, because sanitization in LMF industries must be conducted without water, a list of 39 flavonoids was tested for their combined effect with 70% isopropyl alcohol (IPA) against DSB, and morin induced the greatest reduction in the green:red ratio from 3.67 to 0.43. Significantly higher reductions of Salmonella viability in DSB were achieved by 10-, 100-, 1,000-, and 10,000-µg/mL morin (1.69 ± 0.25, 3.21 ± 0.23, 4.32 ± 0.24, and 5.18 ± 0.16 log CFU/sample reductions) than 70% IPA alone (1.55 ± 0.20 log CFU/sample reduction) (P < 0.05), indicating the potential to be formulated as a dry sanitizer for the LMF industry.IMPORTANCEDSB growth of foodborne pathogens in LMF processing environments is associated with food safety, financial loss, and compromised consumer trust. This work is the first comprehensive examination of the characteristics of Salmonella DSB while exploring its underlying survival mechanisms. Furthermore, morin dissolved in 70% IPA was proposed as an efficient dry sanitizer against DSB to provide insights into biofilm control during LMF processing.

RevDate: 2024-11-04

Fernandez-Materan FV, Olivos-Caicedo KY, Daniel SL, et al (2024)

Genome sequences of nine Clostridium scindens strains isolated from human feces.

Microbiology resource announcements [Epub ahead of print].

Clostridium scindens is an important member of the gut microbiome. Strains of C. scindens are model organisms for bile acid and steroid metabolism studies. The genome sequences for nine C. scindens strains isolated from human feces are reported. Genomes ranged from 3,403,497 to 4,318,168 bp, 46.5% to 48% G+C content, and 3,386 to 4,137 protein-coding total genes.

RevDate: 2024-11-04

Malcomson FC, Louca P, Nelson A, et al (2024)

Effects of non-digestible carbohydrates on gut microbiota and microbial metabolites: a randomised, controlled dietary intervention in healthy individuals.

The British journal of nutrition pii:S000711452400271X [Epub ahead of print].

The gut microbiome is impacted by certain types of dietary fibre. However, the type, duration, and dose needed to elicit gut microbial changes, and whether these changes also influence microbial metabolites, remains unclear. This study investigated the effects of supplementing healthy participants with two types of non-digestible carbohydrates (resistant starch (RS) and polydextrose (PD)), on the stool microbiota and microbial metabolite concentrations in plasma, stool, and urine, as secondary outcomes in the Dietary Intervention Stem Cells and Colorectal Cancer (DISC) Study.The DISC Study was a double-blind, randomised controlled trial that supplemented healthy participants with RS and/or PD or placebo for 50 days in a 2*2 factorial design. DNA was extracted from stool samples collected pre- and post-intervention, and V4 16S rRNA gene sequencing was used to profile the gut microbiota. Metabolite concentrations were measured in stool, plasma, and urine by high-performance liquid chromatography.A total of 58 participants with paired samples available were included. After 50 days, no effects of RS or PD were detected on composition of the gut microbiota diversity (alpha- and beta-diversity), on genus relative abundance, or on metabolite concentrations. However, Drichlet's multinomial mixture clustering-based approach suggests that some participants changed microbial enterotype post-intervention.The gut microbiome and faecal, plasma, and urinary microbial metabolites were stable in response to a 50-day fibre intervention in middle aged adults. Larger and longer studies, including those which explore the effects of specific fibre sub-types, may be required to determine the relationships between fibre intake, the gut microbiome, and host-health.

RevDate: 2024-11-05
CmpDate: 2024-11-05

Mansell T, Nuotio J, Vuillermin P, et al (2024)

Tracking of Vascular Measures From Infancy to Early Childhood: A Cohort Study.

Journal of the American Heart Association, 13(21):e036611.

BACKGROUND: Atherosclerosis develops across the life course, and variation in aortic intima-media thickness (IMT) is evident from infancy onward, although most early-life data are cross-sectional. We investigated whether abdominal aortic IMT at age 6 weeks is associated with vascular measures at 4 years and the relationship of prenatal and perinatal exposures with these measures in early childhood.

METHODS AND RESULTS: We analyzed data from 518 participants with 6-week and 4-year vascular measures from the Barwon Infant Study. Aortic IMT was measured at 6 weeks (mean, 6.1±SD 1.5 weeks) and aortic and carotid IMT, carotid-femoral pulse wave velocity, and blood pressure at 4 years of age (4.3±0.3 years). Associations of early-life exposures-maternal enteric microbiome, smoking and low-density lipoprotein cholesterol during pregnancy, birth weight, and gestational age-were also investigated. In the primary model, 6-week aortic IMT (649±66 μm) was associated with small differences in 4-year carotid IMT (453±45 μm) (mean difference in carotid IMT per 100 μm higher 6-week aortic IMT=7.0 μm [95% CI, 0.7-13.3]; P=0.03), with no evidence for associations with 4-year aortic IMT, pulse wave velocity, or blood pressure. Higher birth weight was associated with greater 4-year aortic IMT, and maternal smoking with higher systolic blood pressure.

CONCLUSIONS: Vascular measures do not show strong evidence of tracking between infancy and early childhood. Longitudinal studies with repeated assessment beyond age 4 years would inform optimal timing of early prevention and targets for primordial prevention.

RevDate: 2024-11-05

Wang L, Ma M, Li Y, et al (2024)

Effect of supplementation with lutein, zeaxanthin, and omega-3 fatty acids on macular pigment and visual function in young adults with long-term use of digital devices: study protocol for a randomized double-blind placebo-controlled study.

Frontiers in nutrition, 11:1422468.

BACKGROUND: Growing evidence emphasizes the importance of xanthophyll carotenoids and omega-3 fatty acids in eye health. However, the beneficial effects of such supplementation have not been thoroughly discussed among adults with high screen exposure. Current trial evidence on lutein bioavailability is contradictory, and the interactions of dietary intervention with host-related factors remain elusive. This study aims to investigate the comparative effectiveness of supplementation with macular xanthophylls and omega-3 fatty acids on macular pigment optical density (MPOD) and visual function, access the bioavailability of free lutein and lutein ester, and explore the complex interplay between genetic variations, intestinal microbiota, and the dietary intervention in Chinese adults with long-term exposure to digital devices.

METHODS: The Lutein, Zeaxanthin, and Omega-3 (LZO) clinical trial is a 24-week multicenter, randomized, double-blind, placebo-controlled trial of 600 participants recruited from research centers, universities, and communities. Individuals are eligible to participate if they are aged over 18 years and use digital devices for over 8 h daily in the last 2 years, and will be randomized to six arms. A total of three visits will be scheduled at baseline, 12 and 24 weeks. The primary outcome is the change in MPOD over the 24-week intervention. The secondary outcomes are changes in visual function (visual acuity, best-corrected visual acuity, contrast and glare sensitivity, critical flicker fusion, reaction time, visuognosis persistence, symptoms and signs of dry eye, retinal thickness, and optical quality), and changes in serum lutein and zeaxanthin concentrations, and erythrocyte membrane omega-3 fatty acids. Genetic variations will be determined using genome-wide genotyping at baseline. 16S rRNA gene sequencing will be utilized to assess microbiome compositional changes before and after intervention.

DISCUSSION: The trial is anticipated to establish early interventions to prevent photochemical ocular damage and delay the onset of vision impairment in young adults with long-term repeated exposure to screen-based electronic devices, and provide valuable insights for the development of precision nutrition strategies for maintaining eye health.

CLINICAL TRIAL REGISTRATION: www.clinicaltrials.in.th, Identifier, TCTR20220904002.

RevDate: 2024-11-05
CmpDate: 2024-11-04

Rueangmongkolrat N, Uthaipaisanwong P, Kusonmano K, et al (2024)

The role of microbiomes in cooperative detoxification mechanisms of arsenate reduction and arsenic methylation in surface agricultural soil.

PeerJ, 12:e18383.

Microbial arsenic (As) transformations play a vital role in both driving the global arsenic biogeochemical cycle and determining the mobility and toxicity of arsenic in soils. Due to the complexity of soils, variations in soil characteristics, and the presence and condition of overlying vegetation, soil microbiomes and their functional pathways vary from site to site. Consequently, key arsenic-transforming mechanisms in soil are not well characterized. This study utilized a combination of high-throughput amplicon sequencing and shotgun metagenomics to identify arsenic-transforming pathways in surface agricultural soils. The temporal and successional variations of the soil microbiome and arsenic-transforming bacteria in agricultural soils were examined during tropical monsoonal dry and wet seasons, with a six-month interval. Soil microbiomes of both dry and wet seasons were relatively consistent, particularly the relative abundance of Chloroflexi, Gemmatimonadota, and Bacteroidota. Common bacterial taxa present at high abundance, and potentially capable of arsenic transformations, were Bacillus, Streptomyces, and Microvirga. The resulting shotgun metagenome indicated that among the four key arsenic-functional genes, the arsC gene exhibited the highest relative abundance, followed by the arsM, aioA, and arrA genes, in declining sequence. Gene sequencing data based on 16S rRNA predicted only the arsC and aioA genes. Overall, this study proposed that a cooperative mechanism involving detoxification through arsenate reduction and arsenic methylation was a key arsenic transformation in surface agricultural soils with low arsenic concentration (7.60 to 10.28 mg/kg). This study significantly advances our knowledge of arsenic-transforming mechanisms interconnected with microbial communities in agricultural soil, enhancing pollution control measures, mitigating risks, and promoting sustainable soil management practices.

RevDate: 2024-11-05
CmpDate: 2024-11-04

Singh AK, Durairajan SSK, Iyaswamy A, et al (2024)

Elucidating the role of gut microbiota dysbiosis in hyperuricemia and gout: Insights and therapeutic strategies.

World journal of gastroenterology, 30(40):4404-4410.

Hyperuricemia (HUA) is a condition associated with a high concentration of uric acid (UA) in the bloodstream and can cause gout and chronic kidney disease. The gut microbiota of patients with gout and HUA is significantly altered compared to that of healthy people. This article focused on the complex interconnection between alterations in the gut microbiota and the development of this disorder. Some studies have suggested that changes in the composition, diversity, and activity of microbes play a key role in establishing and progressing HUA and gout pathogenesis. Therefore, we discussed how the gut microbiota contributes to HUA through purine metabolism, UA excretion, and intestinal inflammatory responses. We examined specific changes in the composition of the gut microbiota associated with gout and HUA, highlighting key bacterial taxa and the metabolic pathways involved. Additionally, we discussed the effect of conventional gout treatments on the gut microbiota composition, along with emerging therapeutic approaches that target the gut microbiome, such as the use of probiotics and prebiotics. We also provided insights into a study regarding the gut microbiota as a possible novel therapeutic intervention for gout treatment and dysbiosis-related diagnosis.

RevDate: 2024-11-05

Xie L, Zhuang Z, Guo B, et al (2024)

Ketamine induced gut microbiota dysbiosis and barrier and hippocampal dysfunction in rats.

iScience, 27(11):111089.

The microbiota-gut-brain axis (MGBA) plays a pivotal role in drug addiction. However, the pathophysiological mechanism of MGBA in ketamine addiction remains elusive. The present study investigated the ketamine-induced gut microbiota disorders, intestinal barrier dysfunction, and the alterations in brain function, using a conditioned place preference (CPP) model of ketamine addiction in rats. Compared with the control group, ketamine induced decreased amplitude of low-frequency fluctuation (ALFF) values in the hippocampus, and pyknotic nuclei and concentrated cytoplasm in hippocampal neurons, as well as alterations in gut microbiota composition, shortened ileum villi, and thinner colonic mucosa. We also found that the abundance of gut microbiota exhibited correlations with CPP score, hippocampal ALFF value, length of ileum villi, and thickness of colonic mucosa. Our findings provide evidence for abnormal alterations in the MGBA of ketamine-addicted rats, which improves our understating of the mechanism of ketamine addiction and the potential for developing new therapeutic strategies.

RevDate: 2024-11-05

Yang X, Liu W, Zhang X, et al (2024)

Glycerol-derived reuterin regulates human intestinal microbiota and metabolites.

Frontiers in microbiology, 15:1454408.

Reuterin, a mixture of different forms of 3-hydroxypropanal (3-HPA), including HPA hydrate and HPA dimer, is an antimicrobial compound converted from glycerol by Lactobacillus reuteri and other strains. Although its antimicrobial function may be related to its interaction with thiol groups, its temperature stability and effect on the gut environment remain unclear. The present study evaluated the antimicrobial effects and activity of reuterin against Escherichia coli and Salmonella typhimurium. Utilization of a reliable in vitro gut microbiome fermentation system revealed that reuterin has a modulatory effect on the gut microbial community. Reuterin treatment completely inhibited H2 and NH3 production in the gut and significantly enhanced the synthesis of branched short-chain fatty acids. 16s rRNA sequencing indicated that reuterin promoted the growth of Proteobacteria and Bacteroidetes in the in vitro system and significantly modulated gut microbiota composition.

RevDate: 2024-11-05

Duan X, Nie Y, Xie X, et al (2024)

Sex differences and testosterone interfere with the structure of the gut microbiota through the bile acid signaling pathway.

Frontiers in microbiology, 15:1421608.

BACKGROUND: The gut microbiome has a significant impact on human wellness, contributing to the emergence and progression of a range of health issues including inflammatory and autoimmune conditions, metabolic disorders, cardiovascular problems, and psychiatric disorders. Notably, clinical observations have revealed that these illnesses can display differences in incidence and presentation between genders. The present study aimed to evaluate whether the composition of gut microbiota is associated with sex-specific differences and to elucidate the mechanism.

METHODS: 16S-rRNA-sequencing technology, hormone analysis, gut microbiota transplantation, gonadectomy, and hormone treatment were employed to investigate the correlation between the gut microbiome and sex or sex hormones. Meanwhile, genes and proteins involved bile acid signaling pathway were analyzed both in the liver and ileum tissues.

RESULTS: The composition and diversity of the microbiota from the jejunum and feces and the level of sex hormones in the serum differed between the sexes in young and middle-aged Sprague Dawley (SD) rats. However, no similar phenomenon was found in geriatric rats. Interestingly, whether in young, middle-aged, or old rats, the composition of the microbiota and bacterial diversity differed between the jejunum and feces in rats. Gut microbiota transplantation, gonadectomy, and hormone replacement also suggested that hormones, particularly testosterone (T), influenced the composition of the gut microbiota in rats. Meanwhile, the mRNA and protein level of genes involved bile acid signaling pathway (specifically SHP, FXR, CYP7A1, and ASBT) exhibited gender-specific differences, and T may play a significant role in mediating the expression of this pathway.

CONCLUSION: Sex-specific differences in the structure of the gut microbiota are mediated by T through the bile acid signaling pathway, pointing to potential targets for disease prevention and management techniques by indicating that sex differences and T levels may alter the composition of the gut microbiota via the bile acid signaling pathway.

RevDate: 2024-11-05

Götz L, Ansafi T, Gerken M, et al (2024)

Effect of antibiotic drug use on outcome and therapy-related toxicity in patients with glioblastoma-A retrospective cohort study.

Neuro-oncology advances, 6(1):vdae170.

BACKGROUND: Glioblastoma (GB) is the most frequent malignant brain tumor and has a dismal prognosis. In other cancers, antibiotic use has been associated with severity of chemotherapy-induced toxicity and outcome. We investigated if these mechanisms are also involved in GB.

METHODS: We selected a cohort of 78 GB patients who received combined radiochemotherapy. We investigated if exposure to prediagnostic antibiotic use is associated with clinical side effects and laboratory changes during adjuvant therapy as well as overall survival (OS) and progression-free survival (PFS) using chi-square test, binary logistic regression, Kaplan-Meyer analysis, and multivariable Cox regression.

RESULTS: Seventeen patients (21.8%) received at least one course of prediagnostic antibiotics and 61 (78.2%) received no antibiotics. We found a higher incidence of loss of appetite (23.5% vs. 4.9%; P = .018) and myelosuppression (41.2% vs. 18.0%; P = .045) in the antibiotic group. Multivariable logistic regression analysis revealed antibiotics to be a predictor for nausea (OR = 6.94, 95% CI: 1.09-44.30; P = .041) and myelosuppression (OR = 9.75, 95% CI: 1.55-61.18; P = .015). Furthermore, lymphocytopenia was more frequent in the antibiotic group (90.0% vs. 56.1%, P = .033). There were no significant differences in OS (P = .404) and PFS (P = .844). Multivariable Cox regression showed a trend toward shorter survival time (P = .089) in the antibiotic group.

CONCLUSIONS: Our study suggests that antibiotic use affects symptoms and lab values in GB patients. Larger prospective studies are required to investigate if prediagnostic antibiotic use could be a prognostic factor in GB patients.

RevDate: 2024-11-05

Mulavu M, Khumalo CS, Moonga L, et al (2024)

Defining the bacterial microbiome of ticks in Chongwe and Chisamba Districts of Zambia.

Infectious medicine, 3(4):100131.

BACKGROUND: The microbiome composition of an arthropod vector may impede the growth of some pathogens, aid colonisation by pathogens or affect vector behaviour in ways that impact the transmission of pathogens. In Zambia, little is known of the microbial communities hosted by ticks and how pathogens like Rickettsia play a role in the microbiome composition.

OBJECTIVE: This study sought to determine the microbiome of Rickettsia-negative and Rickettsia-positive ticks in selected districts of Zambia.

METHODS: This was a cross-sectional study carried out on 94 ticks collected from cattle in Chongwe and Chisamba districts. The overall prevalence of Rickettsia spp. was detected using PCR amplification of the ompB gene. Thereafter, both Rickettsia-negative and positive ticks underwent 16S rRNA gene amplification and Illumina high-throughput sequencing. Data was analysed using QIIME2 analysis pipeline.

RESULTS: The prevalence of Rickettsia was found to be 47.9% (45/94) with prevalence in Amblyomma at 78.5% (22/28), Hyalomma at 68.9% (20/29) and Rhipicephalus having the lowest at 8.1% (3/37). Proteobacteria, Firmicutes, Actinobacteriota and Euryachaeota were the most common phyla, while endosymbionts were uncommonly detected in the ticks. Further analysis showed significant differences in microbiome composition based on Rickettsia detection status (p=0.001) and location (p=0.001), based on the alpha diversity Shannon index, Bray Curtis beta diversity and PERMANOVA, whilst differences according to life stage, tick species and genus was only shown based on the Bray Curtis beta diversity and PERMANOVA analysis.

CONCLUSION: Ultimately, this study provides valuable insights into the structure of the tick microbiome in parts of Zambia and how it is affected by the presence of Rickettsia.

RevDate: 2024-11-05

Lee HW, Bak JJ, SC Min (2024)

Effects of ultrasound-assisted plasma-activated water washing on the inhibition of natural microorganisms on fresh-cut celery and celery quality properties.

Food science and biotechnology, 33(15):3639-3650.

The effects of ultrasound (US)-assisted plasma-activated water (PAW) washing (UP) on the growth of indigenous bacteria, quality properties, and microbiome of fresh-cut Apium graveolens (celery) were investigated. Among the tested treatments (UP, NaClO solution, US alone, and PAW alone), UP was the most effective in decontaminating fresh-cut celery and inhibiting the growth of natural bacteria in the celery during storage at 4 and 10 °C. No significant differences were observed in the firmness, color, or sensory properties between untreated and UP-treated fresh-cut celery during storage. The proportion of Proteobacteria and Actinobacteria on UP-treated fresh-cut celery decreased after storage at 4 °C for 3 days, confirming the influence of UP treatment on the celery microbiome. The UP treatment induced alterations in the microbial composition of celery. These results demonstrate the potential utility of UP treatment as a novel microbial decontamination process for the preparation of fresh-cut celery products.

RevDate: 2024-11-05

Zaheer J, Khan MN, Rahman AU, et al (2024)

Identification and Epidemiological Analysis of Antibiotic-Resistant Bacteria in the Oral Microbiome of the Population in Pakistan.

Cureus, 16(10):e70666.

Background Antibiotic resistance in the oral microbiome poses serious health risks worldwide, particularly in developing countries like Pakistan. Public health efforts are challenged by the potential of the oral cavity to serve as a reservoir for resistant bacteria due to its frequent exposure to antibiotics. Objective This study aimed to identify and analyze the prevalence and epidemiology of antibiotic-resistant bacteria within the oral microbiome of the Pakistani population. Methodology A cross-sectional study was conducted at Akhtar Saeed Medical and Dental College, Lahore, and Gomal Medical College, Dera Ismail Khan, from January 2023 to December 2023. A total of 290 participants, aged 18 years or older, were recruited based on specific inclusion and exclusion criteria. Oral swabs were collected and analyzed using conventional culture methods. All descriptive and inferential statistical analyses were performed using SPSS version 25 (IBM Corp., Armonk, NY), with a significance level set at p <0.05. Results The most common antibiotic-resistant bacteria identified were Enterococcus faecalis (24.48%, n = 71), Staphylococcus aureus (27.24%, n = 79), and Streptococcus mutans (35.86%, n = 104). The most frequent resistances were to penicillin (32.14%, n = 93), tetracycline (23.45%, n = 68), and erythromycin (22.07%, n = 64). Recent antibiotic use was significantly associated with higher rates of resistance (p = 0.01), with 75.19% of individuals (n = 97) who had used antibiotics within the past three to six months showing resistance. Conclusion The study reveals a high prevalence of antibiotic-resistant bacteria, particularly to penicillin and tetracycline, in the oral microbiome of the Pakistani population.

RevDate: 2024-11-05

Liu M, Li M, Jin S, et al (2024)

Differential intestinal microbes and metabolites between Behcet's uveitis and Fuchs syndrome.

Heliyon, 10(20):e39393.

OBJECTIVE: Behcet's uveitis (BU) is a type of uveitis with a high rate of blindness, characterized by anterior segment inflammation, vitreous opacity, and retinal vasculitis. Its pathogenesis is still unclear. Fuchs syndrome (Fuchs) is another common type of uveitis, which clinically presents with anterior segment inflammation and vitreous opacity, but rarely causes blindness. This study aims to compare the gut microbiota and metabolites of two different types of uveitis to clarify whether the differences in clinical manifestations are relevant to the alterations in gut microbiota.

METHODS: Faecal samples were collected from new-onset BU (n = 11) patients without systemic treatment and other diseases. 16S rRNA and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were performed to analyze gut microbes and metabolites. Fuchs (n = 15) was used as the disease control, and healthy controls (n = 18) without autoimmune diseases and systemic medication were included.

RESULTS: Microbial composition and metabolite profiles differed significantly among the three groups. Compared to controls, Fusicatenibacter and eight metabolites were specifically altered in BU patients, and Pantoea and five metabolites in Fuchs. Pathways involving delta-tocopherol, palmitic acid, and serotonin are significantly disrupted in BU patients. Pathways involving linoleic acid are dysregulated considerably in Fuchs. Microbial markers consisting of 4 genera and 7 metabolites can respectively distinguish BU patients from controls. AUC values of metabolite markers were greater than those of microbial markers. Furthermore, serum zonulin levels were significantly elevated in both types of uveitis, with no difference between them. Correlation analysis revealed correlations between zonulin levels and multiple microbes.

CONCLUSIONS: Patients with BU and Fuchs syndrome showed significant differences in gut microbiota and metabolites. Disruption of the intestinal mucosal barrier was observed in both types of uveitis. However, the mechanism of different intestinal microbiota causing different clinical manifestations needs to be studied in the future.

RevDate: 2024-11-05
CmpDate: 2024-11-04

Jiang L, JG Fan (2024)

Gut microbiota in gastrointestinal diseases: Insights and therapeutic strategies.

World journal of gastroenterology, 30(39):4329-4332.

Considering the bidirectional crosstalk along the gut-liver axis, gut-derived microorganisms and metabolites can be released into the liver, potentially leading to liver injury. In this editorial, we comment on several studies published in the recent issue of the World Journal of Gastroenterology. We focus specifically on the roles of gut microbiota in selected gastrointestinal (GI) diseases that are prevalent, such as inflammatory bowel disease, metabolic dysfunction-associated steatotic liver disease, and hepatitis B virus-related portal hypertension. Over the past few decades, findings from both preclinical and clinical studies have indicated an association between compositional and metabolic changes in the gut microbiota and the pathogenesis of the aforementioned GI disorders. However, studies elucidating the mechanisms underlying the host-microbiota interactions remain limited. The purpose of this editorial is to summarize current findings and provide insights regarding the context-specific roles of gut microbiota. Ultimately, the discovery of microbiome-based biomarkers may facilitate disease diagnosis and the development of personalized medicine.

RevDate: 2024-11-04

Liu X, Feng Z, Zhang F, et al (2024)

Causal Effects of Gut Microbiota on Gout and Hyperuricemia: Insights from Genome-Wide Mendelian Randomization, RNA-Sequencing, 16S rRNA Sequencing, and Metabolomes.

Bioscience reports pii:235204 [Epub ahead of print].

This study investigated the causal relationship between gut microbiota (GM), serum metabolome, and host transcriptome in the development of gout and hyperuricemia (HUA) using genome-wide association studies (GWAS) data and HUA mouse model experiments. Methods: Mendelian randomization (MR) analysis of GWAS summary statistics was performed using an inverse variance weighted (IVW) approach to determine predict the causal role of the gut microbiota on gout. The HUA mouse model was used to characterize changes in the gut microbiome, host metabolome, and host kidney transcriptome by integrating cecal 16S rRNA sequencing, untargeted serum metabolomics, and host mRNA sequencing.

Results: Our analysis demonstrated causal effects of seven gut microbiota taxa on gout, including genera of Ruminococcus, Odoribacter, and Bacteroides. Thirty-eight, immune cell traits were associated with gout. Dysbiosis of Dubosiella, Lactobacillus,Bacteroides, Alloprevotella, and Lachnospiraceae_NK4A136_group genera were associated with changes in the serum metabolites and kidney transcriptome of the HUA model mice. The changes in the gut microbiome of the HUA model mice correlated significantly with alterations in the levels of serum metabolites such as taurodeoxycholic acid, phenylacetylglycine, vanylglycol, methyl hexadecanoic acid, carnosol, 6-aminopenicillanic acid, sphinganine, p-hydroxyphenylacetic acid, pyridoxamine, and de-o-methylsterigmatocystin, and expression of kidney genes such as CNDP2, SELENOP, TTR, CAR3, SLC12A3, SCD1, PIGR, CD74, MFSD4B5, and NAPSA.

Conclusion: Our study demonstrated a causal relationship between GM, immune cells, and gout. HUA development involved alterations in the vitamin B6 metabolism because of gut microbiota dysbiosis that resulted in altered pyridoxamine and pyridoxal levels, dysregulated sphingolipid metabolism, and excessive inflammation.

.

RevDate: 2024-11-04

Shijimaya T, Tahara T, Shimogama T, et al (2024)

Gastric microbiome composition accompanied with the Helicobacter pylori related DNA methylation anomaly.

Epigenomics [Epub ahead of print].

Aim: DNA methylation is associated with gastric cancer and Helicobacter pylori (H. pylori) infection, while increasing evidence indicated involvement of other microbes reside in gastric mucosa during gastric tumorigenesis. We investigated bacterial communities in the gastric mucosa accompanied with H. pylori related methylation anomaly.Materials & methods: Gastric mucosa samples from antrum were obtained from 182 cancer-free patients. Bacterial communities were evaluated using 16S rRNA sequencing. The result was correlated with H. pylori related promoter CpG island (CGI) methylation of five genes (IGF2, SLC16A12, SOX11, P2RX7 and MYOD1), LINE1 hypomethylation and telomere length.Results & conclusion: We showed correlation between lower bacterial alpha diversity and higher CGI methylation. Multivariate analysis demonstrated older age (t = 3.46, p = 0.0007), H. pylori infection (t = 9.99, p < 0.0001) and lower bacterial alfa diversity (Shannon index: t = -2.34, p = 0.02) were significantly associated with CGI hypermethylation. In genus or family levels, increased abundance of Helicobacter was associated with hyper CGI methylation with strongest correlation, while decreased abundance of four bacteria (Intrasporangiaceae family, Macellibacteroides, Peptostreptococcus and Dietziaceae family) was also associated with hyper CGI methylation. Our findings suggest the potential correlation between CGI methylation induction and lower bacterial alpha diversity in the gastric mucosa accompanied by H. pylori infection.

RevDate: 2024-11-04

Narayana JK, Mac Aogáin M, Hansbro PM, et al (2024)

The bronchiectasis microbiome: current understanding and treatment implications.

Current opinion in pulmonary medicine pii:00063198-990000000-00206 [Epub ahead of print].

PURPOSE OF REVIEW: Advances in DNA sequencing and analysis of the respiratory microbiome highlight its close association with bronchiectasis phenotypes, revealing fresh opportunities for diagnosis, stratification, and personalized clinical intervention. An under-recognized condition, bronchiectasis is increasingly the subject of recent large-scale, multicentre, and longitudinal clinical studies including detailed analysis of the microbiome. In this review, we summarize recent progress in our understanding of the bronchiectasis microbiome within the context of its potential use in treatment decisions.

RECENT FINDINGS: Diverse microbiome profiles exist in bronchiectasis, in line with the established disease heterogeneity including treatment response. Classical microbiology has established Pseudomonas aeruginosa and Haemophilus influenza as two microbial markers of disease, while holistic microbiome analysis has uncovered important associations with less common bacterial taxa including commensal an/or pathobiont species, including the emerging role of the fungal mycobiome, virome, and interactome. Integration of airway microbiomes with other high-dimensional biological and clinical datasets holds significant promise to determining treatable traits and mechanisms of disease related to the microbiome.

SUMMARY: The bronchiectasis microbiome is an emerging and key area of study with significant implications for understanding bronchiectasis, influencing treatment decisions and ultimately improving patient outcomes.

RevDate: 2024-11-04

Aslam S, Arslan M, KM Nowak (2023)

Microbial activity, community composition and degraders in the glyphosate-spiked soil are driven by glycine formation.

The Science of the total environment pii:S0048-9697(23)06833-X [Epub ahead of print].

Widely-used glyphosate may produce aminomethylphosphonic acid (AMPA), glycine and sarcosine. To date, little is known about effects of these degradation products on soil microorganisms and their potential degraders. Here, we incubated a soil spiked either with 2-[13]C-glyphosate, [13]C-AMPA, [13]C3-sarcosine or [13]C2-glycine for 75 days. Respiration (CO2 tot) and mineralization rates of the compound ([13]CO2) were estimated in addition to phospholipid fatty acids (PLFAstot and [13]C-PLFAs) as biomarkers to identify four groups of microorganisms (Gram-negative & Gram-positive bacteria, actinobacteria, fungi). 16S/ITS rRNA amplicon sequencing was also conducted to identify the microbial community at the phylum and genus level. The CO2 tot and [13]CO2 rates were highest on day 2 in all treatments, as follows: glycine (CO2 tot: 1.09 μmol g[-1]; [13]CO2: 18 %) > sarcosine (CO2 tot: 0.89 μmol g[-1]; [13]CO2: 8.5 %) > glyphosate (CO2 tot: 0.67 μmol g[-1]; [13]CO2: 2.2 %) > AMPA (CO2 tot: 0.53 μmol g[-1]; [13]CO2: 0.3 %). Both the PLFAstot and [13]C-PLFAs were highest in glycine (PLFAstot: 0.054-0.047 μmol g[-1]; [13]C-PLFAs: 0.2-0.4 %) and glyphosate (PLFAstot: 0.049-0.047 μmol g[-1]; [13]C-PLFAs: 0.1-0.3 %) treatments compared to sarcosine and AMPA treatments. Gram negative bacteria were major microbial group of soil microbiome as well as primary degraders of all compounds. In contrast, Gram-positive bacteria, actinobacteria and fungi could have been consumers of primary degraders. Certain genera e.g. Gemmatimonas, Arenimonas and Massilia showed increased abundance in certain treatments indicating their potential involvement in biodegradation. Based on similar time-dependent microbial activity and shifts in abundances of ([13]C-)PLFAs and 16S rRNA genera, we deduced that glyphosate was mainly degraded to glycine, and presumably at elevated amounts. We reported for the first time that the glycine presumably altered microbial activity and community composition rather than glyphosate directly. Future studies should thus also consider the potential impacts of degradation products of the parent compound on soil microbiomes.

RevDate: 2024-11-04

Adams M (2024)

Ammonia-stressed anaerobic digestion: Sensitivity dynamics of key syntrophic interactions and methanogenic pathways-A review.

Journal of environmental management, 371:123183 pii:S0301-4797(24)03169-4 [Epub ahead of print].

The problematic anaerobic digestion (AD) of protein-rich substrates owing to their high ammonia content continues to hinder optimum methanation despite their high potential for offsetting greenhouse gas (GHG) emissions. This review focuses on the analyses of the sensitivity dynamics of key AD processes as well as the microbial interactions and exchanges that occur with them. Aside from the apparent increased risk associated with thermophilic ammonia-rich substrate AD, the marginally higher energy generation compared to mesophilic systems is not commensurate to the energy requirement. Moreover, while comparable FAN thresholds have been confirmed, TAN thresholds are susceptible to physical chemistry and so vary greatly. Profiling of the metabolic capability of front-end AD microbiome revealed Bacteroidetes, Firmicutes, and Synergistetes as some of the ammonia-resilient bacteria groups while Proteobacteria and Actinobacteria were the most fragile taxa. Besides the predominance of incomplete propionate oxidizing bacteria under ammonia stress conditions, syntrophic propionate oxidation (SPO) is usually shifted from the methylmalonyl CoA to the dismutation pathway. Furthermore, besides their different recoverability potentials, distinct methanogenic groups are differentially impacted by different ammonia species. Prevailing literature evidence suggests that conductive material assisted bioaugmentation with SAO-HM consortia, and in-situ H2 supplementation are the most effective for expediting electron transfer and relieving ammonia stress. These valuable insights should inform the design of targeted ammonia inhibition mitigation strategies.

RevDate: 2024-11-04

Qiu M, Wu Z, Song J, et al (2023)

Chlorothalonil drives the antibiotic resistome in earthworm guts.

Journal of hazardous materials, 463:132831 pii:S0304-3894(23)02115-5 [Epub ahead of print].

Earthworms are recognized as carriers of pollutants; however, how fungicide residues affect microbiota and antibiotic resistance genes (ARGs) in earthworm guts has remained unclear. In this work, changes in the earthworm gut microbiome and resistome were investigated after chlorothalonil (CTL) application. Earthworm activity accelerated the dissipation of CTL in soil, while metagenomic analysis revealed that CTL altered the ARG profile, leading to an increased abundance of ARGs in earthworm guts, particularly with respect to ARG subtypes CRP and OXA-427. CTL also reduced bacterial diversity and elevated the relative abundance of the phylum Proteobacteria, including a potential ARG host, Aeromonas, which is a known pathogen. Various bacterial genera from the Actinobacteria and Proteobacteria phyla were identified as broad-spectrum hosts for ARGs in earthworm guts. CTL could increase the abundance of multidrug efflux pump genes and enhance the abundance of mobile genetic elements, especially plasmids. Various co-occurrence patterns between plasmids and ARGs were also found after CTL treatments. It is concluded that CTL may act as a selective stress for ARGs and lead to an increase in their abundance by facilitating the proliferation of potential ARG hosts and enhancing plasmid-mediated horizontal transfer frequency of ARGs in earthworm guts.

RevDate: 2024-11-04

Wu R, Cheng J, Qi Y, et al (2024)

Genetic link between gut microbiota, immune cells, and rheumatoid arthritis: Mechanism of action of CD28 proteins.

International journal of biological macromolecules pii:S0141-8130(24)08021-8 [Epub ahead of print].

The gut microbiota serves a crucial function in modulating the immune responses of the host, as well as in managing inflammation within the body. In this particular study, the researchers sought to delve deeper into the specific mechanisms through which CD28 interacts with the gut microbiota and influences the functionality of immune cells. The study collected intestinal microbial samples from RA patients and healthy controls, analyzed microbial composition by high-throughput sequencing, and detected CD28 expression in T cells in combination with cellular immunology methods. At the same time, the effects of CD28 deletion on intestinal microbiota changes and inflammatory responses were evaluated using animal models. The findings from this study revealed a notable distinction in the gut microbiota profiles of individuals diagnosed with rheumatoid arthritis (RA) when compared to those of healthy control subjects. Specifically, the abundance of certain microbial species was observed to have a negative correlation with the expression levels of CD28, highlighting a complex interaction between the gut microbiome and the immune regulatory mechanisms involved in RA. Furthermore, experiments conducted on mice lacking CD28 demonstrated considerable alterations in their gut microbiota composition. These Cd28-deficient mice exhibited elevated levels of inflammatory markers, indicating an interplay between CD28 and the regulation of both the microbiota and the immune response.

RevDate: 2024-11-05

Shimokawa C (2024)

The gut microbiome-helminth-immune axis in autoimmune diseases.

Parasitology international, 104:102985 pii:S1383-5769(24)00136-3 [Epub ahead of print].

The global prevalence of autoimmune diseases has surged in recent decades. Consequently, environmental triggers have emerged as crucial contributors to autoimmune diseases, equally relevant to classical risk factors, such as genetic polymorphisms, infections, and smoking. Sequencing-based approaches have demonstrated distinct gut microbiota compositions in individuals with autoimmune diseases, including multiple sclerosis, rheumatoid arthritis, type 1 diabetes mellitus (T1D), and systemic lupus erythematosus, compared to healthy controls. Furthermore, fecal microbiota transplantation and microbial inoculation experiments have supported the hypothesis that alterations in the gut microbiota can influence autoimmune responses and disease outcomes. Herein, we propose that intestinal helminths may serve as a critical factor in inducing alterations in the gut microbiota. The concept of helminth-mediated suppression of autoimmune diseases in humans is supported by substantial evidence, aligning with the long-standing "hygiene hypothesis." This review focused on T1D to explore the interactions between parasites, gut microbiota, and the immune system-a topic that remains a black box within this intricate triangular relationship.

RevDate: 2024-11-04

Li Y, Han Q, Liu Y, et al (2024)

Role of the Histone Deacetylase Family in Lipid Metabolism: Structural Specificity and Functional Diversity.

Pharmacological research pii:S1043-6618(24)00438-9 [Epub ahead of print].

Lipids play crucial roles in signal transduction. Lipid metabolism is associated with several transcriptional regulators, including peroxisome proliferator activated receptor γ, sterol regulatory element-binding protein 1, and acetyl-CoA carboxylase. In recent years, increasing evidence has suggested that members of the histone deacetylase (HDAC) family play key roles in lipid metabolism. However, the mechanisms by which each member of this family regulates lipid metabolism remain unclear. This review discusses the latest research on the roles played by HDACs in fat metabolism. The role of HDACs in obesity, diabetes, and atherosclerosis has also been discussed. In addition, the interaction of HDACs with the gut microbiome and circadian rhythm has been reviewed, and the future development trend in HDACs has been predicted, which may potentiate therapeutic application of targeted HDACs in related metabolic diseases.

RevDate: 2024-11-05

Iuffrida L, Spezzano R, Trapella G, et al (2024)

Physiological plasticity and life history traits affect Chamelea gallina acclimatory responses during a marine heatwave.

Environmental research, 263(Pt 3):120287 pii:S0013-9351(24)02194-7 [Epub ahead of print].

The striped venus clam (Chamelea gallina) is a relevant economic resource in the Adriatic Sea. This study explored the physiological status of C. gallina at four sites selected along a gradient from high to low incidence of recorded historical mortality events and low to high productivity in the Northwestern Adriatic Sea. Investigations were performed during the marine heatwave in 2022 (from July to November). The optimal temperature range for C. gallina was exceeded in July and September, exacerbating stress conditions and a poor nutritional status, particularly at the low productivity sites. Transcriptional profiles assessed in digestive glands showed that clams from the low productivity sites up-regulated transcripts related to feeding/digestive functions as a possible compensatory mechanism to withstand adverse environmental conditions. Clams from the high productivity sites, that in a previous study showed enrichment of health-promoting microbiome components, displayed a healthier metabolic makeup (IDH up-regulation) and induction of protective antioxidant and immune responses. These features are hallmarks of putative enhanced resilience of the species towards environmental stress. Despite the well-known high sensitivity of C. gallina to environmental variations and its narrow window of acclimatory potential, results highlight that local conditions may influence physiological plasticity of this clam species and shape either positively or negatively its response capabilities to environmental changes. The identification of health-promoting endogenous mechanisms both from the animal (this study) and from its associated microbiome may provide the foundation for developing novel tools and strategies to improve clam health and production in low productivity areas or under adverse environmental conditions.

RevDate: 2024-11-04

Larsen S, Coleine C, Albanese D, et al (2023)

Geology and elevation shape bacterial assembly in Antarctic endolithic communities.

The Science of the total environment pii:S0048-9697(23)06677-9 [Epub ahead of print].

Ice free areas of continental Antarctica are among the coldest and driest environments on Earth, and yet, they support surprisingly diverse and highly adapted microbial communities. Endolithic growth is one of the key adaptations to such extreme environments and often represents the dominant life-form. Despite growing scientific interest, little is known of the mechanisms that influence the assembly of endolithic microbiomes across these harsh environments. Here, we used metagenomics to examine the diversity and assembly of endolithic bacterial communities across Antarctica within different rock types and over a large elevation range. While granite supported richer and more heterogeneous communities than sandstone, elevation had no apparent effect on taxonomic richness, regardless of rock type. Conversely, elevation was clearly associated with turnover in community composition, with the deterministic process of variable selection driving microbial assembly along the elevation gradient. The turnover associated with elevation was modulated by geology, whereby for a given elevation difference, turnover was consistently larger between communities inhabiting different rock types. Overall, selection imposed by elevation and geology appeared stronger than turnover related to other spatially-structured environmental drivers. Our findings indicate that at the cold-arid limit of life on Earth, geology and elevation are key determinants of endolithic bacterial heterogeneity. This also suggests that warming temperatures may threaten the persistence of such extreme-adapted organisms.

RevDate: 2024-11-04

Huang S, Du J, Li Y, et al (2023)

LiaSR two-component system modulates the oxidative stress response in Streptococcusmutans.

Microbial pathogenesis pii:S0882-4010(23)00437-0 [Epub ahead of print].

Many commensal bacteria of the human oral microbiome can produce reactive oxygen species (ROS). ROS will inhibit the colonization of Streptococcusmutans (S.mutans), a major pathogenic bacteria in dental caries. The LiaSR two-component system in S.mutans can sense and respond to environmental oxidative stress. However, the molecular details of the LiaSR two-component system and oxidative stress response have been unclear. In this study, we aimed to elucidate the underlying mechanisms of the LiaSR two-component system and the mediated oxidative stress response in S.mutans. We performed the H2O2 killing assay, Confocal laser scanning microscopy, and 2,7-Dichlorofluoresce diacetate staining assay to evaluate the sensitivity of S.mutans to H2O2. The propidium iodide probe and TUNEL kit were used to detect the membrane permeability and DNA fragmentation. Quantitative real-time PCR was conducted to analyze the expression level of underlying regulated genes. The liaS and liaR deficient mutants were particularly sensitive to H2O2 compared to their wild strain S.mutans 593, which was previously isolated from a caries-active patient. The intracellular levels of ROS and membrane permeability increased in the mutants. The TUNEL assay showed that the rate of DNA fragmentation in the liaR mutant was higher compared to the wild strain and liaS mutant. Relative expression of the spxA2 gene in the mutants was lower than in the wild strain. The dpr and dinB genes were downregulated in the liaR mutant. These results indicated that the LiaSR two-component system mediated influence on spxA2 expression in S.mutans and contributed to membrane homeostasis, which was involved in the oxidative response process. S.mutans could also elevate the dpr and the dinB genes, which depend on the liaR component in the LiaSR system, may help reduce the DNA damage caused by ROS. This study provides valuable insights into the mechanisms of the LiaSR two-component system in the oxidative stress response of S.mutans.

RevDate: 2024-11-04

Zhao T, Lv J, Peng M, et al (2023)

Fecal microbiota transplantation and short-chain fatty acids improve learning and memory in fluorosis mice by BDNF-PI3K/AKT pathway.

Chemico-biological interactions pii:S0009-2797(23)00453-2 [Epub ahead of print].

Fluoride, an environmental toxicant, not only arouses intestinal microbiota dysbiosis, but also causes neuronal apoptosis and a decline in learning and memory ability. The purpose of this study was to explore whether fecal microbiota transplantation (FMT) from healthy mice and bacteria-derived metabolites short-chain fatty acids (SCFAs) supplement protect against fluoride-induced learning and memory impairment. Results showed that FMT reversed the elevated percentage of working memory errors (WME) and reference memory errors (RME) in fluorosis mice during the eight-arm maze test. Nissl and TUNEL staining presented that fluoride led to a decreased proportion of Nissl bodies area in the hippocampal CA3 region and an increased apoptotic ratio of nerve cells in CA1, CA3 and DG areas, whereas FMT alleviated those pathological damages. Moreover, the expressions of mRNA in hippocampal BDNF, PDK1, AKT, Bcl-2, and Bcl-xL were downregulated in mice exposed to fluoride, but the levels of PI3K, Bax, Bak, and Caspase-7 mRNA were upregulated. NaF treatment had an increase in PI3K and Caspase-3 protein levels and reduced the expressions of these four proteins, including BDNF, p-PI3K, AKT and p-AKT. By contrast, FMT enhanced the expression of BDNF and thus activated the PI3K/AKT pathway. Besides, the 16S rRNA sequencing revealed that fluoride caused a reduction in certain SCFA producers in the colon as evidenced by a decline in Erysipelatoclostridiaceae, and a downward trend in Akkermansia, Blautia and Alistipes. However, the disordered gut microbiome was restored via frequent FMT. Of note, SCFAs administration also increased BDNF levels and regulated its downstream pathways, which contributed to cell survival and learning and memory function recovery. In conclusion, FMT and SCFAs may activate the BDNF-PI3K/AKT pathway to play an anti-apoptotic role and ultimately improve learning and memory deficits in fluorosis mice.

RevDate: 2024-11-04

Yang J, Yang Z, Wu Y, et al (2023)

Identifying and ranking causal association between gut microbiota and neuroticism.

Progress in neuro-psychopharmacology & biological psychiatry pii:S0278-5846(23)00172-0 [Epub ahead of print].

BACKGROUND: Recent studies had explored that gut microbiota was associated with personality traits through the gut-brain axis. Nevertheless, the fundamental causality remained obscure.

METHODS: Mendelian randomization (MR) was used to investigate the causal relationship between gut microbiota, metabolites and neuroticism-related traits. Summary data-based Mendelian randomization (SMR) was utilized to identify genes associated pleiotropically with microbial taxa.

RESULTS: MR analyses identified reliable causal evidence of 20 bacterial taxa related to neuroticism and its worry or depressed affect sub-cluster. A higher relative abundance of the Ruminococcus gauvreauii genus was associated with a higher risk of neuroticism [odds ratio (OR) = 1.04, 95% CI: 1.02-1.06, P = 2.85 × 10-3], depressed affect [OR = 1.04, 95% CI: 1.02-1.06, P = 5.50 × 10-3] and worry (OR = 1.04, 95% CI: 1.02-1.06, P = 7.81 × 10-4), respectively. We identified the probes tagging CPSF1, that showed pleiotropic association with Ruminococcus gauvreauii in brain or colon tissues. Finally, we provided evidence that Ruminococcus gauvreauii present causal association with the neurotransmitter such as glutamine and glutamate.

CONCLUSIONS: This study implied a causal relationship between the gut microbiome composition, metabolites and neuroticism, thus providing novel insights into the gut microbiota-mediated development mechanism of neuroticism.

RevDate: 2024-11-04

Tziatzios G, Stylianakis E, Damoraki G, et al (2024)

Third generation sequencing analysis detects significant differences in duodenal microbiome composition between functional dyspepsia patients and control subjects.

Neurogastroenterology and motility [Epub ahead of print].

BACKGROUND: Functional dyspepsia (FD) is a multifactorial disorder as its development may be based on several different pathophysiological mechanisms. Interaction of gut microbiome with the host has been proposed as a potential mechanism involved in the disease's pathogenesis.

AIM/METHODS: We aimed to characterize microbiome profiling on duodenal luminal content (DLC) of FD patients and compare it to that of controls (CG) and patients with irritable bowel syndrome (IBS). Outpatients fulfilling Rome IV criteria for FD, IBS, and control group (CG) underwent upper gastrointestinal endoscopy and 2 cc of duodenal aspirate (3rd - 4th part) was aspirated in sterile traps. Duodenal microbiome was assessed after DNA extraction and 16S gene-based sequencing on Oxford Nanopore MinION followed by EPI2ME analysis (ONT/Metrich-ore Ltd). Bioanalysis of the microbiome (alpha-, beta-diversity, comparisons of relative abundances for all taxonomic ranks) was implemented in Python. Multiple group means comparisons were performed with one-way Analysis of Variance (ANOVA) and Kruskal-Wallis test with Tuckey's and Dunn's post hoc tests respectively, in case of significance (P-value <0.05).

RESULTS: 20 subjects with FD (8 females; age 49.9 ± 13.5 yrs.), 20 with IBS (14 females; age 57.6 ± 14.8 yrs.) and 10 CG (6 females; age 49.2 ± 13.8 yrs.) had their DLC analyzed. The α-diversity index of subjects with FD was significantly lower compared to controls (Shannon's index, p = 0.0218) and similar to that of patients with IBS. Principal Coordinate Analysis (PCoA) generated from species relative abundances (beta-diversity) showed no difference in the DLC profile of subjects with FD and IBS when compared to controls (p = 0.513). Compared to controls, the relative abundance (RA) of Chloroflexota phylum was lower in subjects with FD (p = 0.017) and IBS (p = 0.026), respectively. Additionally, the RA of the Rhodothermota and Thermotogota phyla was lower in FD (p = 0.017 and p = 0.018, respectively) but not in IBS patients (p = 0.15 and p = 0.06, respectively) compared to controls. Interestingly, the RA of specific taxa from Chloroflexota, Rhodothermota and Thermotogota phyla were consistently lower in subjects with FD when compared to CG but similar to IBS, during analysis of all the subsequent major ranks of taxonomy. At the class level, there were significant differences in Syntrophobacteria, Acidithiobacillia, Cytophagia and Flavobacteriia between the FD and CG groups (p < 0.05), but no such difference between FD and IBS was found. Finally, multiple significant differences at the order, family, genus and species level between the FD and CG groups were also detected. A positive relationship between the RA of Streptococcus and those from genus Granulicatella was observed both in FD (p = 0.014) and IBS (p = 0.014) patients.

CONCLUSION & INFERENCES: The microbiome profiling from duodenal luminal content of FD patients is significantly different to that of controls, including lower microflora diversity, different microflora structure/composition and specific taxa. Similar differences in the DLC between FD and IBS patients were not evident.

RevDate: 2024-11-06
CmpDate: 2024-11-04

Cansdale A, JPJ Chong (2024)

MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes.

Microbiome, 12(1):226.

BACKGROUND: Metagenomics, the whole genome sequencing of microbial communities, has provided insight into complex ecosystems. It has facilitated the discovery of novel microorganisms, explained community interactions and found applications in various fields. Advances in high-throughput and third-generation sequencing technologies have further fuelled its popularity. Nevertheless, managing the vast data produced and addressing variable dataset quality remain ongoing challenges. Another challenge arises from the number of assembly and binning strategies used across studies. Comparing datasets and analysis tools is complex as it requires the quantitative assessment of metagenome quality. The inherent limitations of metagenomic sequencing, which often involves sequencing complex communities, mean community members are challenging to interrogate with traditional culturing methods leading to many lacking reference sequences. MIMAG standards aim to provide a method to assess metagenome quality for comparison but have not been widely adopted.

RESULTS: To address the need for simple and quick metagenome quality assignation, here we introduce the pipeline MAGqual (Metagenome-Assembled Genome qualifier) and demonstrate its effectiveness at determining metagenomic dataset quality in the context of the MIMAG standards.

CONCLUSIONS: The MAGqual pipeline offers an accessible way to evaluate metagenome quality and generate metadata on a large scale. MAGqual is built in Snakemake to ensure readability and scalability, and its open-source nature promotes accessibility, community development, and ease of updates. MAGqual is built in Snakemake, R, and Python and is available under the MIT license on GitHub at https://github.com/ac1513/MAGqual . Video Abstract.

RevDate: 2024-11-03

Ren X, Wang M, Du J, et al (2024)

Glycans in the oral bacteria and fungi: Shaping host-microbe interactions and human health.

International journal of biological macromolecules pii:S0141-8130(24)07741-9 [Epub ahead of print].

The human oral cavity serves as the natural entry port to both the gastrointestinal and respiratory tracts, and hosts a diverse microbial community essential for maintaining health. Dysbiosis of this microbiome can lead to various diseases. Glycans, as vital carriers of biological information, are indispensable structural components of living organisms and play key roles in numerous biological processes. In the oral microbiome, glycans influence microbial binding to host receptors, promote colonization, and mediate communication among microbial communities, as well as between microbes and the host immune system. Targeting glycans may provide innovative strategies for modulating the composition of the oral microbiome, with broader implications for human health. Additionally, exogenous glycans regulate the oral microbiome by serving as carbon and energy sources for microbes, while certain specific glycans can inhibit microbial growth and activity. This review summarizes glycosylation pathways in oral bacteria and fungi, explores the regulation of host-microbiota interactions by glycans, and discusses the effects of exogenous glycans on oral microbiome. The review aims to highlight the multifaceted role of glycans in shaping the oral microbiome and its impact on the host, while also indicates potential future applications.

RevDate: 2024-11-03

Li T, Coker OO, Sun Y, et al (2024)

Multi-cohort analysis reveals altered archaea in colorectal cancer fecal samples across populations.

Gastroenterology pii:S0016-5085(24)05596-3 [Epub ahead of print].

BACKGROUND AND AIM: Archaea are important components of the host microbiome, but their roles in colorectal cancer (CRC) remain largely unclear. We aimed to elucidate the contribution of gut archaea to CRC across multiple populations.

METHODS: This study incorporated fecal metagenomic data from 10 independent cohorts from 7 countries and an additional in-house cohort, totaling 2101 metagenomes (748 CRC, 471 adenoma, and 882 healthy controls (HC)). Taxonomic profiling was performed using Kraken2 against the Genome Taxonomy Database. Alterations of archaeal communities and their interactions with bacteria and methanogenic functions were analyzed. Random Forest model was used to identify multicohort diagnostic microbial biomarkers in CRC.

RESULTS: The overall archaeal alpha diversity shifted from HC, adenoma patients to CRC patients with Methanobacteriota phylum enriched while order Methanomassiliicoccales depleted. At the species level, Methanobrevibacter_A smithii and Methanobrevibacter_A sp002496065 were enriched, while 8 species, including Methanosphaera stadtmanae and Methanomassiliicoccus_A intestinalis, were depleted in CRC patients across multiple cohorts. Among them, M. stadmanae, Methanobrevibacter_A sp900314695 and Methanocorpusculum sp001940805 exhibited a progressive decrease in the HC-adenoma-CRC sequence. CRC-depleted methanogenic archaea exhibited enhanced co-occurring interactions with butyrate-producing bacteria. Consistently, methanogenesis-related genes and pathways were enriched in CRC patients. A model incorporating archaeal and bacterial biomarkers outperformed single-kingdom models in discriminating CRC patients from healthy individuals with AUC ranging from 0.744 to 0.931 in leave-one-cohort-out analysis.

CONCLUSIONS: This multicohort analysis uncovered significant alterations in gut archaea and their interactions with bacteria in healthy individuals, adenoma patients and CRC patients. Archaeal biomarkers, combined with bacterial features, have potential as non-invasive diagnostic biomarkers for CRC.

RevDate: 2024-11-03

Sun Z, K Song (2024)

GEMimp: An accurate and robust imputation method for microbiome data using graph embedding neural network.

Journal of molecular biology pii:S0022-2836(24)00470-4 [Epub ahead of print].

Microbiome research has increasingly underscored the profound link between microbial compositions and human health, with numerous studies establishing a strong correlation between microbiome characteristics and various diseases. However, the analysis of microbiome data is frequently compromised by inherent sparsity issues, characterized by a substantial presence of observed zeros. These zeros not only skew the abundance distribution of microbial species but also undermine the reliability of scientific conclusions drawn from such data. Addressing this challenge, we introduce GEMimp, an innovative imputation method designed to infuse robustness into microbiome data analysis. GEMimp leverages the node2vec algorithm, which incorporates both Breadth-First Search (BFS) and Depth-First Search (DFS) strategies in its random walks sampling process. This approach enables GEMimp to learn nuanced, low-dimensional representations of each taxonomic unit, facilitating the reconstruction of their similarity networks with unprecedented accuracy. Our comparative analysis pits GEMimp against state-of-the-art imputation methods including SAVER, MAGIC and mbImpute. The results unequivocally demonstrate that GEMimp outperforms its counterparts by achieving the highest Pearson correlation coefficient when compared to the original raw dataset. Furthermore, GEMimp shows notable proficiency in identifying significant taxa, enhancing the detection of disease-related taxa and effectively mitigating the impact of sparsity on both simulated and real-world datasets, such as those pertaining to Type 2 Diabetes (T2D) and Colorectal Cancer (CRC). These findings collectively highlight the strong effectiveness of GEMimp, allowing for better analysis on microbial data. With alleviation of sparsity issues, it could be greatly facilitated in downstream analyses and even in the field of microbiology.

RevDate: 2024-11-03

Marangi M, Boughattas S, F Benslimane (2024)

Gut microbiome profile to the level species in diarrheic protozoan-carrier patients in Italy.

Life sciences pii:S0024-3205(24)00772-0 [Epub ahead of print].

The human gastrointestinal microbiota contains a diverse consortium of microbes, including bacteria, protozoa, viruses, and fungi that are involved in many physiological and metabolic as well pathogenetic processes. However, microbiological research is dominated by studies describing the impact of prokaryotic bacteria on gut microbiome with a limited understanding of their relationship with other integral microbiota constituents as protozoa. Here, we investigated the gut microbiome composition using Oxford Nanopore Technology approach in relation to protozoan colonization of Giardia duodenalis, Cryptosporidium parvum, Blastocystis sp. and Dientamoeba fragilis in patients with diarrheal diseases in Italy, taking into consideration different risk factors as protozoan coinfection, Blastocystis-subtypes, gender, age classes, origin, eosinophilia level and positivity to SARS-CoV-2 infection. Overall, out of 1413 investigated patients, 123 (8.7 %) have found positive to one or more protozoa microorganisms with a prevalence statistically significant in individuals from Northern Africa (p < 0.0001) and in the age classes 40-59 years-old (p < 0.0022). Within the 57 individuals eligible for gut microbiome analysis, diverse profiles are observed but interestingly, a predominance of the emergent Escherichia fergusonii ATCC 35469, was found across the different risk factors. Our results emphasize the importance of studies to investigate these aspects of protozoa colonization that will undoubtedly increase our understanding of complex interactions between intestinal protozoa, other microbiota organisms, and the human host.

RevDate: 2024-11-03

Gregoris K, WH Pope (2024)

Extraction of high-quality metagenomic DNA from the lichens Flavoparmelia caperata and Peltigera membranacea.

Journal of microbiological methods pii:S0167-7012(24)00177-5 [Epub ahead of print].

Lichens are composite organisms found throughout temperate terrestrial forests, with species-specific associations with industrial air pollution. Metagenomic analysis of lichen samples requires robust nucleic acid extraction methodology, a process that is challenging due to the protective cortex layers, high polysaccharide content, and the vast diversity of the internal microbiome. Our method includes physical lysis through garnet bead beating, chemical lysis using a sodium dodecyl sulfate buffer, phenol:chloroform:isoamyl alcohol extraction, and ethanol precipitation. The method was tested on three different lichen samples from two distinct species and yielded metagenomic DNA suitable for sequencing and PCR amplification. This procedure addresses the issues associated with DNA extraction from lichen using common laboratory equipment and reagents without the utilization of liquid nitrogen. This paper presents a cost-effective and accessible DNA extraction method for obtaining high-quality genetic material from dried and preserved lichen specimens.

RevDate: 2024-11-03

Li L, Lei B, Zhang W, et al (2024)

The disturbance of intestinal microbiome caused by the novel duck reovirus infection in Cherry Valley ducklings can induce intestinal damage.

Poultry science, 103(12):104428 pii:S0032-5791(24)01006-X [Epub ahead of print].

Novel duck reovirus disease is an infectious disease mainly caused by novel duck reovirus (NDRV), which is characterized by spleen necrosis and persistent diarrhea in ducks. However, the pathogenic mechanism of NDRV infection in Cherry Valley ducks remains unclear. To investigate the distribution of NDRV in the intestines of Cherry Valley ducks, intestinal morphogenesis, intestinal permeability, inflammatory cytokines, and the expression of tight junction proteins (TJPs), we introduced NDRV via intramuscular infection. The diversity and composition of ileum flora and content of short-chain fatty acids (SCFAs) were analyzed using Illumina MiSeq sequencing. The relationship between changes in the intestinal microbial community and intestinal damage in Cherry Valley ducks infected with NDRV was also assessed to offer new insights into the pathogenesis of NDRV and intestinal flora composition. The results showed that intestinal inflammation and barrier dysfunction occurred following NDRV infection. Additionally, a significant reduction in dominant bacterial species and a decrease in SCFA content within the intestinal microbiota led to weakened colonization resistance and the enrichment of opportunistic pathogens, exacerbating intestinal damage post-NDRV infection. Notably, TJPs and inflammatory cytokine disruptions were linked to a decline in SCFA-producing bacteria and an accumulation of pathogenic bacteria. In summary, changes in the ileum intestinal flora and disruptions to the intestinal barrier were associated with NDRV infection. Consequently, disturbances in intestinal flora caused by NDRV infection can lead to intestinal damage. These findings may offer us a new perspective, targeting the gut microbiota to better understand the progression of NDRV disease and investigate its underlying pathogenesis.

RevDate: 2024-11-06
CmpDate: 2024-11-03

Paz HA, Buddha L, Zhong Y, et al (2024)

Impact of maternal high-fat diet on offspring gut microbiota during short-term high-fat diet exposure in mice.

Physiological reports, 12(21):e70111.

Alterations in the gut microbiome have been linked to obesity, with maternal high-fat diet (HF) playing a role in shaping offspring microbiome composition. However, the sex-specific responses to maternal HF diet and the impact of subsequent dietary challenges remain unclear. This study investigated the effects of maternal HF diet on offspring gut microbiota structure and predicted functional profile in response to short-term postnatal HF diet exposure with a focus on sex-specific responses. Female and male offspring of maternal control (C) diet or maternal HF diet were weaned onto C diet or HF diet. Offspring were euthanized at 13 weeks of age and cecal contents were collected for bacterial taxonomic profiling. Maternal HF diet reduced α-diversity, notably in male offspring weaned onto HF diet. Sex-specific differences were observed in the gut microbial composition and predicted functional potential. Furthermore, the influence of maternal diet on bacterial community structure and functional potential varied depending on postnatal diet. Maternal HF diet led to increased relative abundance of Corynebacterium in female offspring and decreased abundance of Akkermansia and Roseburia in male offspring. These findings underscore the sexually dimorphic nature of maternal HF diet effects on gut microbiota composition and function, with implications for developmental programming and metabolic health.

RevDate: 2024-11-03

Heo SH, Choi BY, Kang J, et al (2024)

Dynamics of the airway microbiome in response to exposure to particulate matter 2.5 in patients with chronic obstructive pulmonary disease.

The Science of the total environment pii:S0048-9697(24)07471-0 [Epub ahead of print].

BACKGROUND: Particulate matter (PM) and air pollution have been suggested to be associated with chronic obstructive pulmonary disease (COPD), contributing significantly to global respiratory disease-related mortality. This study aimed to investigate whether seasonal exposure to PM influences dysbiosis in the respiratory microbiota of patients with COPD.

METHODS: Sputum samples were collected four times over 1 year from 102 patients with COPD, and 16S rRNA sequencing was performed. The dynamics of the airway microbiota were analyzed depending on PM exposure levels and season.

RESULTS: The PM-low exposure group had higher α-diversity compared to the PM-high exposure group, particularly noted in spring. Some bacterial groups, including seven species such as Treponema socranskii, were more abundant in the low exposure group. Additionally, the bacterial community structure in summer significantly differed from that in other seasons, with significantly increased α-diversity in this season. The difference in the airway microbiome due to PM exposure was prominent in patients with moderate COPD.

CONCLUSIONS: PM exposure may influence changes in the sputum microbiome depending on exposure levels and seasonal variations. Our results suggest that airway microbiomes could vary with PM exposure according to seasonal trends.

RevDate: 2024-11-03

Jo J, Jeon MJ, Park SK, et al (2024)

Anti-cariogenic effect of experimental resin cement containing ursolic acid using dental microcosm biofilm.

Journal of dentistry pii:S0300-5712(24)00617-1 [Epub ahead of print].

OBJECTIVE: This study aimed to assess the anticariogenic effects of resin cement containing varying ursolic acid (UA) concentrations and to determine the optimal UA concentrations in the microcosm biofilm model.

MATERIALS AND METHODS: Experimental resin cements with UA concentrations of 0, 0.1, 0.5, 1.0, and 2.0 wt% were prepared. Class I cavities were prepared on 50 extracted human molars and restored with composite inlays and experimental resin cements. Tooth samples were subjected to artificial caries induction for 10 days in a microcosm biofilm model using human saliva as an inoculum, and then mineral changes were evaluated using quantitative light-induced fluorescence (ΔF and ΔQ) and micro-computed tomography (CT). The bacterial composition of the human saliva was analyzed by 16s RNA microbiome profiling. One-way analysis of variance with Tukey and Duncan post-hoc tests was employed for statistical analysis (p < 0.05).

RESULTS: As the UA concentration increased, resin cement decreased ΔF and ΔQ before and after caries induction but showed a significant difference only in ΔQ at UA concentration ≥ 1.0% (p < 0.05). The gray value analysis result of micro CT also showed a significant difference at UA concentration ≥ 1.0% (p < 0.05). In the human saliva analysis, bacterial composition remained within normal oral microbiota ranges.

CONCLUSION: Resin cements containing at least 1.0% of UA exhibited an anticariogenic effect on dental microcosm biofilms.

CLINICAL RELEVANCE: To reduce the failure of restorations, it is essential to prevent the occurrence of secondary caries. The application of UA in resin cement can be utilized to prevent the formation of secondary caries due to the anticariogenic effect of UA.

RevDate: 2024-11-03

Felicianna , Kwan Lo EK, Chen C, et al (2024)

Low-dose Valine Attenuates Diet-induced Metabolic Dysfunction-associated Steatotic Liver Disease (MASLD) in Mice by Enhancing Leptin Sensitivity and Modulating the Gut Microbiome.

Molecular metabolism pii:S2212-8778(24)00190-X [Epub ahead of print].

Elevated circulating branched-chain amino acids (BCAAs) have been associated with obesity, insulin resistance, and MASLD, yet BCAA supplementation has been shown to provide protective outcomes towards the intervention of MASLD. Currently, there is a lack of study towards the contribution of the BCAA: valine on MASLD. This study investigates the effects of low-dose valine supplementation on MASLD in a high-fat/high-cholesterol diet (HFD) model. Low-dose valine was found to attenuate the progression of MASLD, significantly reducing body weight, liver weight, and eWAT weight, attenuating hyperglycemia and improving serum lipid profiles. It also decreased hyperleptinemia and enhanced hypothalamic leptin sensitivity, leading to reduced food intake. In the eWAT, metabolic flexibility was improved, as indicated by upregulated adipogenesis-related gene expressions and suppressed leptin expression. In the liver, valine improved hepatic leptin sensitivity, alleviated hepatic steatosis, and reduced triglycerides, cholesterol, TNFα, and IL-6 levels. Mechanistically, valine increased hepatic antioxidant capacity and modulated lipid metabolism and antioxidant pathways, downregulating de novo lipogenesis and cholesterol synthesis while increasing fatty acid oxidation, autophagy-related gene expressions. Moreover, hepatic AMPK pathway activity was enhanced, contributing to improved leptin sensitivity and signalling. Additionally, low-dose valine supplementation also modulated the gut microbiome, suggesting a multifaceted approach to managing MASLD.

RevDate: 2024-11-03

Wang Z, Wu G, Niu T, et al (2024)

Polysaccharide isolated from Dioscorea septemloba improves hyperuricemia and alleviates renal fibrosis through gut-kidney axis in mice.

International journal of biological macromolecules pii:S0141-8130(24)07921-2 [Epub ahead of print].

Hyperuricemia (HUA) is a common metabolic disorder that often accompanies kidney diseases such as tubule damage and renal interstitial fibrosis. The preventive and therapeutic effects of Dioscorea septemloba, an anti-HUA herb, polysaccharide of which was considered as the main active ingredient on HUA, need to be explored. The major polysaccharide component, BXP, was purified from Dioscorea septemloba, with an average molecular weight of 10.432 kDa. Structural analysis inferred that BXP backbone was composed of t-β-D-Glcp-(1 → 4)-α-D-Glcp-(1 → 4)-α-D-Glcp-(1 → 4, 3)-β-D-Glcp-(1→, along with the side chain of →1)-α-D-Glcp-(6, 4 → 3, 4)-β-D-Glcp-(1→. The HUA mouse model was further established to clarify the underlying effect of BXP on HUA alleviation. As results shown, BXP decreased serum uric acid by inhibiting XOD and regulating urate transporter expression (GLUT9, OAT3, OAT1, URAT1 and ABCG2) in HUA mice, as well as relieving kidney and liver damage. Moreover, results of microbiome and metabolomics indicated that BXP improved the abundance of gut bacteria and reversed the Lipids-related metabolism disorder caused by HUA. This study indicated that BXP had potential to alleviate HUA and kidney disease through the gut-kidney axis in mice.

RevDate: 2024-11-03

Hussain M, Aizpurua O, Pérez de Rozas A, et al (2024)

Positive impact of early-probiotic administration on performance parameters, intestinal health and microbiota populations in broiler chickens.

Poultry science, 103(12):104401 pii:S0032-5791(24)00980-5 [Epub ahead of print].

Minimizing the utilization of antibiotics in animal production is crucial to prevent the emergence of antimicrobial resistances. Thus, research on alternatives is needed to maintain productivity, sustainability, and animal health. To gain a comprehensive understanding of probiotics' modes of action on performance, intestinal microbiota, and gut health in poultry, 3 probiotic strains (Enterococcus faecalis CV1028 [EntF], Bacteroides fragilis GP1764 [BacF], and Ligilactobacillus salivarius CTC2197 [LacS]) were tested in 2 in vivo trials. Trial 1 comprised of a negative control group fed basal diet (BD) and 3 treatment groups that received BD with EntF, BacF and LacS. Trial 2 included a negative control group, a positive control group with Zinc-Bacitracin as antibiotic growth promoter (AGP), and 2 groups treated with a blend of probiotics (EntF+BacF+LacS) during 0 to 10 or 0 to 35 d, respectively. Wheat-soybean-rye based diets without exogenous enzymes were used as a challenge model to induce intestinal mild- or moderate-inflammatory process in the gut. In Trial 1, individually administered probiotics improved FCR at 8 d compared to Control, but these positive effects were lost in the following growing periods probably due to the high grade of challenging diet and a too low dose of probiotics. In Trial 2, both Probiotic treatments, administered only 10 or 35 d, significantly improved FCR to the same extent as of the Antibiotic group at the end of the trial. Although the performance between antibiotic and probiotic mixture showed similar values, microbiota analysis revealed different microbial composition at 7 d, but not at 21 d. This suggests that modes of action of the AGP and the tested probiotic blend differ on their effects on microbiome, and that the changes observed during the first days' posthatch are relevant on performance at the end of the study. Therefore, the probiotics administration only during the first 10 d posthatch was proven sufficient to induce similar performance improvements to those observed in birds fed antibiotic growth promoters throughout the whole experimental trial.

RevDate: 2024-11-04

Noguchi M, H Toju (2024)

Mycorrhizal and endophytic fungi structure forest below-ground symbiosis through contrasting but interdependent assembly processes.

Environmental microbiome, 19(1):84.

BACKGROUND: Interactions between plants and diverse root-associated fungi are essential drivers of forest ecosystem dynamics. The symbiosis is potentially dependent on multiple ecological factors/processes such as host/symbiont specificity, background soil microbiome, inter-root dispersal of symbionts, and fungus-fungus interactions within roots. Nonetheless, it has remained a major challenge to reveal the mechanisms by which those multiple factors/processes determine the assembly of root-associated fungal communities. Based on the framework of joint species distribution modeling, we examined 1,615 root-tips samples collected in a cool-temperate forest to reveal how root-associated fungal community structure was collectively formed through filtering by host plants, associations with background soil fungi, spatial autocorrelation, and symbiont-symbiont interactions. In addition, to detect fungi that drive the assembly of the entire root-associated fungal community, we inferred networks of direct fungus-fungus associations by a statistical modeling that could account for implicit environmental effects.

RESULTS: The fine-scale community structure of root-associated fungi were best explained by the statistical model including the four ecological factors/processes. Meanwhile, among partial models, those including background soil fungal community structure and within-root fungus-fungus interactions showed the highest performance. When fine-root distributions were examined, ectomycorrhizal fungi tended to show stronger associations with background soil community structure and spatially autocorrelated patterns than other fungal guilds. In contrast, the distributions of root-endophytic fungi were inferred to depend greatly on fungus-fungus interactions. An additional statistical analysis further suggested that some endophytic fungi, such as Phialocephala and Leptodontidium, were placed at the core positions within the web of direct associations with other root-associated fungi.

CONCLUSION: By applying emerging statistical frameworks to intensive datasets of root-associated fungal communities, we demonstrated background soil fungal community structure and fungus-fungus associations within roots, as well as filtering by host plants and spatial autocorrelation in ecological processes, could collectively drive the assembly of root-associated fungi. We also found that basic assembly rules could differ between mycorrhizal and endophytic fungi, both of which were major components of forest ecosystems. Consequently, knowledge of how multiple ecological factors/processes differentially drive the assembly of multiple fungal guilds is indispensable for comprehensively understanding the mechanisms by which terrestrial ecosystem dynamics are organized by plant-fungal symbiosis.

RevDate: 2024-11-04
CmpDate: 2024-11-02

Gulliver EL, Di Simone SK, Chonwerawong M, et al (2024)

Unlocking the potential for microbiome-based therapeutics to address the sustainable development goal of good health and wellbeing.

Microbial biotechnology, 17(11):e70041.

Recent years have witnessed major advances and an ever-growing list of healthcare applications for microbiome-based therapeutics. However, these advances have disproportionately targeted diseases common in high-income countries (HICs). Within low- to middle-income countries (LMIC), opportunities for microbiome-based therapeutics include sexual health epidemics, maternal health, early life mortality, malnutrition, vaccine response and infectious diseases. In this review we detail the advances that have been achieved in microbiome-based therapeutics for these areas of healthcare and identify where further work is required. Current efforts to characterise microbiomes from LMICs will aid in targeting and optimisation of therapeutics and preventative strategies specifically suited to the unmet needs within these populations. Once achieved, opportunities from disease treatment and improved treatment efficacy through to disease prevention and vector control can be effectively addressed using probiotics and live biotherapeutics. Together these strategies have the potential to increase individual health, overcome logistical challenges and reduce overall medical, individual, societal and economic costs.

RevDate: 2024-11-05
CmpDate: 2024-11-02

Probul N, Huang Z, Saak CC, et al (2024)

AI in microbiome-related healthcare.

Microbial biotechnology, 17(11):e70027.

Artificial intelligence (AI) has the potential to transform clinical practice and healthcare. Following impressive advancements in fields such as computer vision and medical imaging, AI is poised to drive changes in microbiome-based healthcare while facing challenges specific to the field. This review describes the state-of-the-art use of AI in microbiome-related healthcare. It points out limitations across topics such as data handling, AI modelling and safeguarding patient privacy. Furthermore, we indicate how these current shortcomings could be overcome in the future and discuss the influence and opportunities of increasingly complex data on microbiome-based healthcare.

RevDate: 2024-11-04

Shi M, Hao S, Wang Y, et al (2024)

Plant growth-promoting fungi improve tobacco yield and chemical components by reassembling rhizosphere fungal microbiome and recruiting probiotic taxa.

Environmental microbiome, 19(1):83.

BACKGROUND: Tobacco production faces ongoing challenges due to soil degradation, leading to a persistent decline in yield. Plant growth-promoting fungi (PGPF) have been recognized as an environmentally friendly agricultural strategy. However, many commercial PGPF products exhibit instability due to insufficient environmental compatibility.

RESULTS: In this study, Penicillium sp. PQxj3 was isolated and assessed for its potential to enhance tobacco productivity under field conditions. The results demonstrated that Penicillium sp. PQxj3 treatment significantly promoted the tobacco growth and improved the crop yield. The height of tobacco in Penicillium sp. PQxj3 treatment group significantly increased by 50.19% and 24.05% compared with CK at exuberant and maturity period (P < 0.05). The average yield of tobacco significantly increased by 36.16% compared to CK (P < 0.05). Fungal microbiome analysis revealed that phylogenetically similar probiotic taxa were recruited by Penicillium sp. PQxj3 and reassembled tobacco rhizosphere fungal microbiome. The key chemical indicators of tobacco such as alkaloid, total sugar, and phosphorus were significantly enhanced in Penicillium sp. PQxj3 treatment. The recruited probiotic taxa (Penicillium brasilianum, Penicillium simplicissimum, Penicillium macrosclerotiorum and Penicillium senticosum) were significantly associated with alkaloid, total sugar etc. (P < 0.05), which were identified as the key drivers for improving the chemical components of tobacco. Transcriptome analysis indicated that Penicillium sp. PQxj3 promoted up-regulation of key functional genes involved in alkaloid, indoleacetic, and gibberellin biosynthesis pathways.

CONCLUSION: In summary, this study assessed the biopromotion mechanism of PGPF Penicillium sp. PQxj3 linking chemical traits, rhizosphere fungal microbiome, and transcriptome profiling. The findings provide a fundamental basis and a sustainable solution for developing fungal fertilizers to enhance agricultural sustainability.

RevDate: 2024-11-04

Hou M, Leng C, Zhu J, et al (2024)

Alpine and subalpine plant microbiome mediated plants adapt to the cold environment: A systematic review.

Environmental microbiome, 19(1):82.

With global climate change, ecosystems are affected, some of which are more vulnerable than others, such as alpine ecosystems. Microbes play an important role in environmental change in global ecosystems. Plants and microbes are tightly associated, and symbiotic or commensal microorganisms are crucial for plants to respond to stress, particularly for alpine plants. The current study of alpine and subalpine plant microbiome only stays at the community structure scale, but its ecological function and mechanism to help plants to adapt to the harsh environments have not received enough attention. Therefore, it is essential to systematically understand the structure, functions and mechanisms of the microbial community of alpine and subalpine plants, which will be helpful for the conservation of alpine and subalpine plants using synthetic microbial communities in the future. This review mainly summarizes the research progress of the alpine plant microbiome and its mediating mechanism of plant cold adaptation from the following three perspectives: (1) Microbiome community structure and their unique taxa of alpine and subalpine plants; (2) The role of alpine and subalpine plant microbiome in plant adaptation to cold stress; (3) Mechanisms by which the microbiome of alpine and subalpine plants promotes plant adaptation to low-temperature environments. Finally, we also discussed the future application of high-throughput technologies in the development of microbial communities for alpine and subalpine plants. The existing knowledge could improve our understanding of the important role of microbes in plant adaptation to harsh environments. In addition, perspective further studies on microbes' function confirmation and microbial manipulations in microbiome engineering were also discussed.

RevDate: 2024-11-04
CmpDate: 2024-11-02

Chatthanathon P, Leelahavanichkul A, Cheibchalard T, et al (2024)

Comparative time-series analyses of gut microbiome profiles in genetically and chemically induced lupus-prone mice and the impacts of fecal transplantation.

Scientific reports, 14(1):26371.

Although the association between gut dysbiosis (imbalance of the microbiota) in systemic lupus erythematosus (SLE) is well-known, the simultaneous exploration in gut dysbiosis in fecal and different intestinal sections before and after lupus onset (at 2, 4, 6, 8, and 10 months old) resulting from the loss of inhibitory Fc gamma receptor IIb (FcGIIb) and pristane induction have never been conducted. Anti-dsDNA (an important lupus autoantibody) and proteinuria developed as early as 6 months old in both models, with higher levels in FcGRIIb deficient (FcGRIIb-/-) mice. Compared to the healthy control at 2 and 4 months, the lupus mice (both FcGRRIIb-/- and pristane) and healthy mice at 6 months old demonstrated an alteration as indicated by the Shannon alpha diversity index, highlighting influences of lupus- and age-induced dysbiosis, respectively. Non-metric multidimensional scaling (NMDS) revealed that the fecal microbiota of FcGRIIb-/- mice were distinct from the age-matched healthy control at all timepoints (at 6 month, p < 0.05), while pristane mice showed divergence at only some timepoints. Analyses of different intestinal sections revealed similarity among microbiota in the cecum, colon, and feces, contrasting with those in the small intestines (duodenum, jejunum, and ileum). Subtle differences were found between FcGRIIb-/- and pristane mice in feces and the intestinal sections as assessed by several analyses, for examples, the similar or dissimilar distances (NMDS), the neighbor-joining clustering, and the potential metabolisms (KEGG pathway analysis). Due to the differences between the gut microbiota (feces and intestinal sections) in the lupus mice and the healthy control, rebalancing of the microbiota using rectal administration of feces from the healthy control (fecal transplantation; FMT) to 7-month-old FcGIIb-/- mice (the established lupus; positive anti-dsDNA and proteinuria) was performed. In comparison to FcGRIIb-/- mice without FMT, FMT mice (more effect on the female than the male mice) showed the lower anti-dsDNA levels with similar fecal microbiome diversity (16s DNA gene copy number) and microbiota patterns to the healthy control. In conclusion, gut microbiota (feces and intestinal sections) of lupus mice (FcGRIIb-/- and pristane) diverged from the control as early as 4-6 months old, correlating with lupus characteristics (anti-dsDNA and proteinuria). The different gut microbiota in FcGRIIb-/- and pristane suggested a possible different gut microbiota in lupus with various molecular causes. Furthermore, FMT appeared to mitigate gut dysbiosis and reduce anti-dsDNA, supporting the benefit of the rebalancing gut microbiota in lupus, with more studies are warranted.

RevDate: 2024-11-04
CmpDate: 2024-11-02

Wardi M, Lemkhente Z, Alla AA, et al (2024)

Resistome analysis of wastewater treatment plants in Agadir city, Morocco, using a metagenomics approach.

Scientific reports, 14(1):26328.

Water scarcity has evolved into a pressing global issue, significantly impacting numerous regions worldwide. The use of treated wastewater stands out as a promising solution to this problem. However, the proliferation of various contaminants, primarily Antimicrobial Resistance Genes (ARGs), poses a significant challenge to its safe and sustainable use. In this study, we assessed the composition and abundance of 373 ARGs, corresponding to 31 different classes of antibiotics, in six wastewater treatment plants (WWTP) in Agadir city of Morocco. Influent and effluent samples were collected during the months of February and July in 2020, in addition to samples from the Atlantic Ocean. In total, 223 ARGs were uncovered, highlighting in particular resistance to aminoglycoside, macrolide lincosamide, beta-lactamase, chloramphenicol, sulfonamide, tetracycline, and other antibiotics. The mechanisms of action of these ARGs were mainly antibiotic inactivation, antibiotic target alteration, efflux pump and cellular protection. Mobile genetic elements (MGEs) were detected at high levels their co-occurrence with ARGs highlights their involvement in the acquisition and transmission of ARGs in microbial communities through horizontal gene transfer. While many wastewater treatment methods effectively reduce a large proportion of gene material and pathogens, a substantial fraction of ARGs and other contaminants persist in treated wastewater. This persistence poses potential risks to both human health and the environment, warranting the need of more effective treatment strategies.

RevDate: 2024-11-01

McGivern BB, Ellenbogen JB, Hoyt DW, et al (2024)

Polyphenol rewiring of the microbiome reduces methane emissions.

bioRxiv : the preprint server for biology pii:2024.10.22.619724.

Methane mitigation is regarded as a critical strategy to combat the scale of global warming. Currently, about 40% of methane emissions originate from microbial sources, which is causing strategies to suppress methanogens, either through direct toxic effects or by diverting their substrates and energy, to gain traction. Problematically, current microbial methane mitigation knowledge derives from rumen studies and lacks detailed microbiome-centered insights, limiting translation across ecosystems. Here we utilize genome-resolved metatranscriptomes and metabolomes to assess the impact of a proposed methane inhibitor, catechin, on greenhouse gas emissions for high-methane-emitting peatlands. In microcosms, catechin drastically reduced methane emissions by 72-84% compared to controls. Longitudinal sampling allowed for reconstruction of a novel catechin degradation pathway involving Actinomycetota and Clostridium, which break down catechin into smaller phenolic compounds within the first 21 days, followed by degradation of phenolic compounds by Pseudomonas_E from days 21 to 35. These genomes also co-expressed hydrogen-uptake genes, suggesting that hydrogenases may act as a hydrogen sink during catechin degradation, depriving methanogens of substrates. This was supported by decreased gene expression in hydrogenotrophic and hydrogen-dependent methylotrophic methanogens under catechin treatment. We also saw reduced gene expression from genomes inferred to be functioning syntrophically with hydrogen-utilizing methanogens. We propose that catechin metabolic redirection effectively starves hydrogen-utilizing methanogens, offering a potent avenue for curbing methane emissions across diverse environments including ruminants, landfills, and constructed or managed wetlands.

RevDate: 2024-11-05

Gustafson KL, Busi SB, McAdams ZL, et al (2024)

Fetal programming by the parental microbiome of offspring behavior, and DNA methylation and gene expression within the hippocampus.

bioRxiv : the preprint server for biology.

BACKGROUND: The microorganisms colonizing the gastrointestinal tract of animals, collectively referred to as the gut microbiome, affect numerous host behaviors dependent on the central nervous system (CNS). Studies comparing germ-free mice to normally colonized mice have demonstrated influences of the microbiome on anxiety-related behaviors, voluntary activity, and gene expression in the CNS. Additionally, there is epidemiologic evidence supporting an intergenerational influence of the maternal microbiome on neurodevelopment of offspring and behavior later in life. There is limited experimental evidence however directly linking the maternal microbiome to long-term neurodevelopmental outcomes, or knowledge regarding mechanisms responsible for such effects.

RESULTS: Here we show that that the maternal microbiome has a dominant influence on several offspring phenotypes including anxiety-related behavior, voluntary activity, and body weight. Adverse outcomes in offspring were associated with features of the maternal microbiome including bile salt hydrolase activity gene expression (bsh), abundance of certain bile acids, and hepatic expression of Slc10a1. In cross-foster experiments, offspring resembled their birth dam phenotypically, despite faithful colonization in the postnatal period with the surrogate dam microbiome. Genome-wide methylation analysis of hippocampal DNA identified microbiome-associated differences in methylation of 196 loci in total, 176 of which show conserved profiles between mother and offspring. Further, single-cell transcriptional analysis revealed accompanying differences in expression of several differentially methylated genes within certain hippocampal cell clusters, and vascular expression of genes associated with bile acid transport. Inferred cell-to-cell communication in the hippocampus based on coordinated ligand-receptor expression revealed differences in expression of neuropeptides associated with satiety.

CONCLUSIONS: Collectively, these data provide proof-of-principle that the maternal gut microbiome has a dominant influence on the neurodevelopment underlying certain offspring behaviors and activities, and selectively affects genome methylation and gene expression in the offspring CNS in conjunction with that neurodevelopment.

RevDate: 2024-11-01

Jiang B, Quinn-Bohmann N, Diener C, et al (2024)

Understanding disease-associated metabolic changes in human colon epithelial cells using i ColonEpithelium metabolic reconstruction.

bioRxiv : the preprint server for biology pii:2024.10.22.619644.

The colon epithelium plays a key role in the host-microbiome interactions, allowing uptake of various nutrients and driving important metabolic processes. To unravel detailed metabolic activities in the human colon epithelium, our present study focuses on the generation of the first cell-type specific genome-scale metabolic model (GEM) of human colonic epithelial cells, named iColonEpithelium. GEMs are powerful tools for exploring reactions and metabolites at systems level and predicting the flux distributions at steady state. Our cell-type-specific iColonEpithelium metabolic reconstruction captures genes specifically expressed in the human colonic epithelial cells. The iColonEpithelium is also capable of performing metabolic tasks specific to the cell type. A unique transport reaction compartment has been included to allow simulation of metabolic interactions with the gut microbiome. We used iColonEpithelium to identify metabolic signatures associated with inflammatory bowel disease. We integrated single-cell RNA sequencing data from Crohn's Diseases (CD) and ulcerative colitis (UC) samples with the iColonEpithelium metabolic network to predict metabolic signatures of colonocytes between CD and UC compared to healthy samples. We identified reactions in nucleotide interconversion, fatty acid synthesis and tryptophan metabolism were differentially regulated in CD and UC conditions, which were in accordance with experimental results. The iColonEpithelium metabolic network can be used to identify mechanisms at the cellular level, and our network has the potential to be integrated with gut microbiome models to explore the metabolic interactions between host and gut microbiota under various conditions.

RevDate: 2024-11-01

Mitra D, Armijo GK, Ober EH, et al (2024)

MIIST305 mitigates gastrointestinal acute radiation syndrome injury and ameliorates radiation-induced gut microbiome dysbiosis.

bioRxiv : the preprint server for biology pii:2024.10.22.619652.

High-dose radiation exposure results in gastrointestinal (GI) acute radiation syndrome identified by the destruction of mucosal layer, intestinal epithelial barrier dysfunction, and aberrant inflammatory responses. In addition, radiation causes gut microbiome dysbiosis characterized by diminished microbial diversity, reduction in the abundance of beneficial commensal bacteria, and the spread of bacterial pathogens that trigger the recruitment of immune cells and the production of pro-inflammatory factors that lead to further GI tissue damage. Currently, there are no FDA- approved countermeasures that can treat radiation-induced GI injury. To meet this critical need, Synedgen Inc ., has developed a glycopolymer radiomitigator (MIIST305) that is specifically targeted to the GI tract which acts by intercalating into the mucus layer and the glycocalyx of intestinal epithelial cells that could potentially ameliorate the deleterious effects of radiation. Male C57BL/6J adult mice were exposed to 13 Gy total body X-irradiation with 5% bone marrow shielding and MIIST305 was administered on days 1, 3, and 5 post-irradiation. Approximately 85% of the animals survived the irradiation exposure and were apparently healthy until the end of the 30-day study period. In contrast, no control, vehicle-treated animals survived past day 10 at this radiation dose. We show that MIIST305 improved intestinal epithelial barrier function and suppressed systemic inflammatory response mediated by radiation-induced pro-inflammatory cytokines. Taxonomic profiling and community structure of the fecal and colonic mucosa microbiota demonstrated that MIIST305 treatment increased microbial diversity and restored abundance of beneficial commensal bacteria, including Lactobacillus and Bifidobacterium genera, while suppressing potentially pathogenic bacteria compared with vehicle-treated animals. In summary, MIIST305 is a novel GI-targeted therapeutic that greatly enhances survival in mice exposed to lethal radiation and protects the GI tract from injury by restoring a balanced gut microbiota and effectively reducing proinflammatory responses. Further development of this drug as an FDA-approved medical countermeasure will be of critical importance in the event of a radiation public health emergency.

RevDate: 2024-11-01

Neugent ML, Hulyalkar NV, Ghosh D, et al (2024)

Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection.

bioRxiv : the preprint server for biology pii:2024.10.22.619727.

Recurrent urinary tract infections (rUTIs) are a major clinical challenge in postmenopausal women and their increasing prevalence underscores the need to define interactions between the host and the urinary microbiome that may underlie rUTI susceptibility. A body of work has identified the taxonomic profile of the female urinary microbiome associate with aging, menopause, and urinay disease. However, how this microbial community engages with the host niche, including the local biochemical environment of the urogenital tract, in health and disease is yet to be fully defined. This study directly assesses differences in the biochemical environment of the urine, or biochemical ecology, associated with recurrent urinary tract infection (UTI) and defines a microbe-metabolite association network of the female urinary microbiome. By integrating metagenomic and metabolomic data collected from a controlled cohort of women with rUTI, we find that distinct metabolites, such as methionine sulfoxide (Met-SO) and trimethylamine oxide (TMAO), are associated with differences in urinary microbiome diversity. We observe associations between microbial and biochemical beta diversity and unique metabolic networks of uropathogenic Escherichia coli and uroprotective Lactobacillus species, highlighting potential metabolite-driven ecological shifts that may influence UTI susceptibility. We identify a urinary lipid signature of active rUTI that can accurately distinguish (AUC = 0.987) cases controls. Finally, using time-to-relapse data we identify deoxycholic acid (DCA) as a new prognostic indicator for rUTI recurrence. Together these findings suggest that systemic metabolic processes may influence susceptibility, opening new avenues for therapeutic intervention and the development of more accurate diagnostic and prognostic to improve patient outcomes.

RevDate: 2024-11-01

Older EA, Mitchell MK, Campbell A, et al (2024)

Human gut commensal Alistipes timonensis modulates the host lipidome and delivers anti-inflammatory outer membrane vesicles to suppress colitis in an Il10 -deficient mouse model.

bioRxiv : the preprint server for biology pii:2024.10.23.619966.

Correlative studies have linked human gut microbes to specific health conditions. Alistipes is one such microbial genus negatively linked to inflammatory bowel disease (IBD). However, the protective role of Alistipes in IBD has not been studied and the underlying molecular mechanisms also remain unknown. In this study, colonization of Il10 -deficient mice with Alistipes timonensis DSM 27924 delays the development of colitis. Colonization with Alistipes does not significantly alter the gut microbiome composition during colitis development, but instead shifts the host plasma lipidome, increasing phosphatidic acids while decreasing triglycerides. Outer membrane vesicles (OMVs) derived from Alistipes are also detected in the plasma of colonized mice, which carry metabolites with immunomodulatory potential into the host circulatory system. We further demonstrate that fractions of A. timonensis OMVs suppress LPS-induced Il6 , Il1b , and Tnfa expression in vitro in murine macrophages. We detect immunomodulatory sulfonolipids (SoLs) in the active fraction, which are also increased in the blood of A. timonensis -colonized mice; and we identify other putative bioactive lipids in the A. timonensis OMVs. Thus, A. timonensis OMVs represent a potential mechanism for Alistipes -mediated delay of colitis progression in Il10 -deficient mice through the delivery of immunomodulatory lipids, including SoLs, and modulation of the host plasma lipidome.

RevDate: 2024-11-01

Hillege LE, Trepka KR, Ziemons J, et al (2024)

Metagenomic analysis during capecitabine therapy reveals microbial chemoprotective mechanisms and predicts drug toxicity in colorectal cancer patients.

medRxiv : the preprint server for health sciences pii:2024.10.11.24315249.

PURPOSE: Unpredictable chemotherapy side effects are a major barrier to successful treatment. Cell culture and mouse experiments indicate that the gut microbiota is influenced by and influences anti-cancer drugs. However, metagenomic data from patients paired to careful side effect monitoring remains limited. Herein, we focus on the oral fluoropyrimidine capecitabine (CAP). We investigate CAP-microbiome interactions through metagenomic sequencing of longitudinal stool sampling from a cohort of advanced colorectal cancer (CRC) patients.

METHODS: We established a prospective cohort study including 56 patients with advanced CRC treated with CAP monotherapy across 4 centers in the Netherlands. Stool samples and clinical questionnaires were collected at baseline, during cycle 3, and post-treatment. Metagenomic sequencing to assess microbial community structure and gene abundance was paired with transposon mutagenesis, targeted gene deletion, and media supplementation experiments. An independent US cohort was used for model validation.

RESULTS: CAP treatment significantly altered gut microbial composition and pathway abundance, enriching for menaquinol (vitamin K2) biosynthesis genes. Transposon library screens, targeted gene deletions, and media supplementation confirmed that menaquinol biosynthesis protects Escherichia coli from drug toxicity. Microbial menaquinol biosynthesis genes were associated with decreased peripheral sensory neuropathy. Machine learning models trained in this cohort predicted hand-foot syndrome and dose reductions in an independent cohort.

CONCLUSION: These results suggest treatment-associated increases in microbial vitamin biosynthesis serve a chemoprotective role for bacterial and host cells, with implications for toxicities outside the gastrointestinal tract. We provide a proof-of-concept for the use of microbiome profiling and machine learning to predict drug toxicities across independent cohorts. These observations provide a foundation for future human intervention studies, more in-depth mechanistic dissection in preclinical models, and extension to other cancer treatments.

RevDate: 2024-11-03
CmpDate: 2024-11-03

Geat N, Singh D, Saha P, et al (2024)

Deciphering Phyllomicrobiome of Cauliflower Leaf: Revelation by Metagenomic and Microbiological Analysis of Tolerant and Susceptible Genotypes Against Black Rot Disease.

Current microbiology, 81(12):439.

Understanding the phyllomicrobiome dynamics in cauliflower plants holds significant promise for enhancing crop resilience against black rot disease, caused by Xanthomonas campestris pv. campestris. In this study, the culturable microbiome and metagenomic profile of tolerant (BR-161) and susceptible (Pusa Sharad) cauliflower genotypes were investigated to elucidate microbial interactions associated with disease tolerance. Isolation of phyllospheric bacteria from asymptomatic and black rot disease symptomatic leaves of tolerant and susceptible cultivars yielded 46 diverse bacterial isolates. Molecular identification via 16S rRNA sequencing revealed differences in the diversity of microbial taxa between genotypes and health conditions. Metagenomic profiling using next-generation sequencing elucidated distinct microbial communities, with higher diversity observed in black rot disease symptomatic leaf of BR-161. Alpha and beta diversity indices highlighted differences in microbial community structure and composition between genotypes and health conditions. Taxonomic analysis revealed a core microbiome consisting of genera such as Xanthomonas, Psychrobacillus, Lactobacillus, and Pseudomonas across all the samples. Validation through microbiological methods confirmed the presence of these key genera. The findings provide novel insights into the phyllomicrobiome of black rot-tolerant and susceptible genotypes of cauliflower. Harnessing beneficial microbial communities identified in this study offers promising avenues for developing sustainable strategies to manage black rot disease and enhance cauliflower crop health and productivity.

RevDate: 2024-11-03

Anwar F, Al-Abbasi FA, Al-Bar OA, et al (2024)

Gut microbiome and inflammation in cardiovascular drug response: trends in therapeutic success and commercial focus.

Inflammopharmacology [Epub ahead of print].

The intricate Gut microbiome is evolving as an important system and is hypothesized to be a "metabolic organ" within the host. Alterations in Gut microbiota and inflammation associated with several diseases play a crucial role in drug transformation through microbiota-host co-metabolism, modified pharmacokinetic and pharmacodynamics profiles, and may result in the formation of toxic metabolites with interference in drug response. In recent studies, a large number of drugs are reported that are co-metabolized by the host and the Gut microbial enzymes. we summarize the direct and indirect involvement of Gut microbiome promotion or inhibition of cardiovascular diseases, mechanisms on bioavailability, and therapeutic outcomes of cardiovascular drugs, particularly pharmacokinetics and pharmacodynamics profiles in light of AUC, Tmax, Cmax, and bioavailability and drug transportation via immune cells, inter-individual variations in intestinal microbial taxonomy, influence of drugs on diversity and richness of microflora, high lightening limitations and significance of in personalized medicine. Recent advances in target-drug delivery by nanoparticles with limitations and challenges in application are discussed. The cross-talk between Gut microbiota and cardiovascular drugs signifies a better understanding and rationale for targeting the Gut microbiota to improve the therapeutic outcome for cardiovascular diseases, with present-day limitations.

RevDate: 2024-11-05
CmpDate: 2024-11-03

Zhou Z, Wang C, Cha X, et al (2024)

The biogeography of soil microbiome potential growth rates.

Nature communications, 15(1):9472.

Soil microbial growth, a vital biogeochemical process, governs both the accrual and loss of soil carbon. Here, we investigate the biogeography of soil microbiome potential growth rates and show that microbiomes in resource-rich (high organic matter and nutrients) and acid-neutral soils from cold and humid regions exhibit high potential growth. Conversely, in resource-poor, dry, hot, and hypersaline soils, soil microbiomes display lower potential growth rates, suggesting trade-offs between growth and resource acquisition or stress tolerance. In addition, the potential growth rates of soil microbiomes positively correlates with genome size and the number of ribosomal RNA operons but negatively correlates with optimum temperature, biomass carbon-to-phosphorus and nitrogen-to-phosphorus ratios. The spatial variation of microbial potential growth rates aligns with several macroecological theories. These findings not only enhance our understanding of microbial adaptation to diverse environments but also aid in realistically parameterizing microbial physiology in soil carbon cycling models.

RevDate: 2024-11-02

Nikola L, L Iva (2024)

Gut microbiota as a modulator of type 1 diabetes: A molecular perspective.

Life sciences pii:S0024-3205(24)00777-X [Epub ahead of print].

Type 1 diabetes (T1D) is defined as an autoimmune metabolic disorder, characterized by destruction of pancreatic β-cells and high blood sugar levels. If left untreated, T1D results in severe health complications, including cardiovascular and kidney disease, as well as nerve damage, with ultimately grave consequences. Besides the role of genetic and certain environmental factors in T1D development, in the last decade, one new player emerged to affect T1D pathology as well, and that is a gut microbiota. Dysbiosis of gut bacteria can contribute to T1D by gut barrier disruption and the activation of autoimmune response, leading to the destruction of insulin producing cells, causing the development and aggravation of T1D symptoms. The relationship between gut microbiota and diabetes is complex and varies between individuals and additional research is needed to fully understand the effects of gut microbiome alternations in T1D pathogenesis. Therefore, the goal of this review is to understand the current knowledge in underlying molecular mechanism of gut microbiota effects, which leads to the new approaches for further studies in the prevention and treatment of T1D.

RevDate: 2024-11-02

Li K, Wei W, Xu C, et al (2024)

Prebiotic inulin alleviates anxiety and depression-like behavior in alcohol withdrawal mice by modulating the gut microbiota and 5-HT metabolism.

Phytomedicine : international journal of phytotherapy and phytopharmacology, 135:156181 pii:S0944-7113(24)00838-9 [Epub ahead of print].

BACKGROUND: Alcohol dependence (AD) is a common psychiatric disorder, often accompanied by anxiety and depression. These comorbidities are linked to disturbances in serotonin (5-HT) metabolism and gut microbiota dysbiosis. Clinical studies suggest that inulin, a prebiotic, can alleviate anxiety and depression in AD patients by affecting the gut microbiota, although the mechanisms remain unclear.

PURPOSE: The purpose of this study is to investigate the potential mechanisms by which inulin, a prebiotic, improves anxiety and depression-like behaviors in AD withdrawal mice. This research is based on the drug and food homology and intestinal treatment of encephalopathy, with the goal of developing new clinical strategies for AD treatment.

STUDY DESIGN: For this purpose, fecal samples from AD patients were analyzed to identify microorganisms associated with AD. An AD withdrawal mouse model was created, with inulin as the intervention and fluvoxamine maleate as the control. Techniques such as 16S microbiome sequencing and UPLC-TQMS-targeted metabolomics were used to assess gut microbiota, short-chain fatty acids (SCFAs) levels, and 5-HT metabolism.

METHODS: The AD withdrawal model was built using the "Drinking-in-the-dark" protocol over 6 weeks. Inulin (2 g/kg/day) and fluvoxamine maleate (30 mg/kg/day) were administered for 4 weeks. The open field test, forced swim test, and tail suspension test were used to evaluate anxiety and depression-like behaviors in mice. ELISA and qRT-PCR assessed 5-HT metabolism in the colon, blood, and prefrontal cortex, while 16S microbiome sequencing analyzed changes in gut microbiota and UPLC-TQMS examined SCFAs levels. Immunohistochemistry was used to study intestinal barrier integrity.

RESULTS: AD patients showed reduced SCFA-producing bacteria such as Faecalibacterium and Roseburia. In mice, AD withdrawal led to anxiety and depression-like behaviors, disrupted 5-HT metabolism, and gut microbiota dysbiosis. Inulin supplementation alleviated these behaviors, increased 5-HT and 5-hydroxytryptophan (5-HTP) levels, upregulated colonic tryptophan hydroxylase 1 (TPH1) expression, and promoted the growth of beneficial bacteria such as Faecalibacterium and Roseburia, while also increasing SCFAs levels.

CONCLUSION: Inulin increases the abundance of Faecalibacterium and Roseburia, enhances SCFAs production, and regulates 5-HT metabolism, improving anxiety and depression-like behaviors in AD withdrawal mice. These findings suggest that inulin may serve as a nutritional intervention for mental health in AD patients by targeting the microbiome-gut-brain axis.

RevDate: 2024-11-02

Vecere G, Malka S, Sands N, et al (2024)

Assessment of the fecal microbiome of healthy rabbits (Oryctolagus cuniculus domesticus) compared with rabbits with gastrointestinal disease using next-generation DNA sequencing.

American journal of veterinary research [Epub ahead of print].

OBJECTIVE: To determine the normal fecal microbiome of healthy rabbits in comparison to rabbits with gastrointestinal (GI) disease. Next-generation DNA sequencing was used to identify the primary bacteria and fungi in the microbiome.

METHODS: Fecal pellets from 25 clinically healthy rabbits and 25 rabbits experiencing GI disease were collected. Next-generation DNA sequencing was performed targeting the ITS-2 region for mycobiome, and the V1-V3 region of the 16S rRNA for bacteriome analysis. ITS-2 stands for internal transcribed spacer 2, a region of DNA in fungi that is used to identify and classify species.

RESULTS: In healthy rabbit feces, Bacteroidales sp, Odoribacter sp, Paraprevotella xylaniphila, Lachnospiraceae sp, Papillibacter sp, Akkermansia sp, and Ruminococcus sp were noted to be more prevalent. Comparatively, Lachnoclostridium sp, Anaerotruncus sp, Subdoligranulum sp, and B uniformis were found in greater abundance in rabbits with GI disease. Only 1 fungal species, Malassezia restricta, was significantly enriched in the GI disease group.

CONCLUSIONS: Next-generation DNA sequencing technology can be used to evaluate the microbiome of the rabbit GI tract through fecal material and can provide a clinically accessible testing method for veterinarians.

CLINICAL RELEVANCE: Numerous bacteria and fungi in the fecal samples of healthy rabbits were identified that could be considered markers of gastrointestinal health; similarly, specific bacteria and fungi were noted in greater abundance in rabbits with GI disease, which should be further investigated for their importance in causing, contributing to, or as the result of clinical disease. These findings support the use of next-generation DNA sequencing in order to diversify our understanding of the microbiome of rabbit feces, aid in clinical diagnosis, and provide support for the need for more specific probiotic supplements for rabbits.

RevDate: 2024-11-02

Olasunkanmi OI, Aremu J, Wong ML, et al (2024)

Maternal gut-microbiota impacts the influence of intrauterine environmental stressors on the modulation of human cognitive development and behavior.

Journal of psychiatric research, 180:307-326 pii:S0022-3956(24)00613-7 [Epub ahead of print].

This review examines the longstanding debate of nature and intrauterine environmental challenges that shapes human development and behavior, with a special focus on the influence of maternal prenatal gut microbes. Recent research has revealed the critical role of the gut microbiome in human neurodevelopment, and evidence suggest that maternal microbiota can impact fetal gene and microenvironment composition, as well as immunophysiology and neurochemical responses. Furthermore, intrauterine neuroepigenetic regulation may be influenced by maternal microbiota, capable of having long-lasting effects on offspring behavior and cognition. By examining the complex relationship between maternal prenatal gut microbes and human development, this review highlights the importance of early-life environmental factors in shaping neurodevelopment and cognition.

RevDate: 2024-11-02

Garbayo-Salmons P, Saus E, Exposito-Serrano V, et al (2024)

Hidradenitis Suppurativa from a Multi-Omic Scope.

Journal of cutaneous medicine and surgery [Epub ahead of print].

Hidradenitis suppurativa (HS) is recognized as a systemic immune-mediated disease (IMID), sharing genetic and environmental risk factors with other IMIDs such as inflammatory bowel disease and psoriasis. Over time, correlating clinical findings with genetic, proteomic, and metabolomic results has been challenging due to diverse sampling methods, analysis techniques, and the use of variable clinical phenotype descriptions across studies. This review aims to summarize the results from various omics fields to explore the etiopathology of HS. Genetic studies highlight defects in Notch and γ-secretase signaling and inflammasome function. Syndromic HS involves specific mutations in autoinflammatory syndromes such as pyogenic sterile arthritis, pyoderma gangrenosum, and acne (PAPA) and pyoderma gangrenosum, acne, and HS (PASH). Proteomic analyses reveal key inflammatory pathways indicating activation of both innate and adaptive immunity. Additionally, microbiome studies show an increased presence of anaerobes like Prevotella in HS lesions and a decreased presence of commensals such as Staphylococcus epidermidis. Gut microbiota dysbiosis, particularly involving Ruminococcus gnavus and Clostridium ramosum, is associated with HS. Moreover, metabolomic profiling indicates dysregulated tryptophan catabolism and lipid metabolism, with increased 5-lipoxygenase-derived metabolites and odd-chain fatty acids suggesting bacterial involvement. In summary, despite advances, robust associations between genetics, proteomics, microbiome, and metabolomics in HS are still lacking. Integrating these datasets could identify new clinical phenotypes, genetic predispositions, microbial signatures, and therapeutic targets, enhancing personalized treatment strategies and biomarker discovery for HS classification, prognosis, and treatment response.

RevDate: 2024-11-02

Park J, Lee G, JK Park (2024)

Functional Assessment of a Bioprinted Immuno-Mimetic Peyer's Patch Recapitulating Gut-Associated Lymphoid Tissue.

Advanced healthcare materials [Epub ahead of print].

Gut immune models have attracted much interest in better understanding the microbiome in the human gastrointestinal tract. The gut-associated lymphoid tissue (GALT) has complex structures that interact with microorganisms, including the intestinal monolayer as a physiological barrier and the Peyer's patch (PP) involved in the immune system. Although essential for studying GALT and microbiome interactions, current research often uses simplified models that only recapitulate some components. In this study, GALT is recapitulated to consider the morphology and function of lymphocyte-containing PP beneath the intestinal monolayer and to analyze microbiome interaction. Using the bioprinting technique, a dome-shaped structure array for the PP is fabricated, and epithelial cells are cocultured to form the intestinal monolayer. The developed GALT model shows stable cell differentiation on the hydrogel while exhibiting durability against lipopolysaccharides. It also exhibits increased responsiveness to Escherichia coli, as indicated by elevated nitric oxide levels. In addition, the model underscores the critical role of GALT in maintaining bacterial coexistence and in facilitating immune defense against foreign antigens through the secretion of immunoglobulin A by lymphocyte spheroids. The proposed GALT model is expected to provide significant insights into studying the gut-immune system complexity and microbiome.

RevDate: 2024-11-05
CmpDate: 2024-11-02

Lu S, Wu Q, He W, et al (2024)

Vaginal microbiota in term pregnant women with differences in cervical ripeness revealed by 2bRAD-M.

BMC microbiology, 24(1):444.

BACKGROUND: Cervical ripening is a multifactorial outcome, and the association between cervical ripening and vaginal microbiota remains unexplored in term primiparous women. A new sequencing technology, microbiome 2bRAD sequencing (2bRAD-M) that provides a higher level of species discrimination compared to amplicon sequencing. We applied 2bRAD-M to analyze the vaginal microbiota in a population with variations in cervical ripeness and to explore potential microbiota factors influencing cervical ripening.

METHODS: A total of 30 full-term primigravid women participated in this study, with 15 belonging to the low scoring group of cervical ripeness and 15 to the high scoring group. Clinical information was collected from the participants, and the vaginal microbiota and community structure of both groups were analyzed using 2bRAD-M sequencing. Microbiota diversity and differential analyses were conducted to explore potential factors influencing cervical ripening.

RESULTS: A total of 605 species were detected. There was no difference in vaginal microbiota diversity between the two groups, and the vaginal microbial composition was structurally similar. In the two groups, Lactobacillus crispatus and Lactobacillus iners were identified as the two pivotal species through random forest analysis. Concurrent, extensive and close connections between species within the two groups were observed in the correlation analysis, influencing the aforementioned two species. Pairwise comparisons showed that Sphingomonas (P = 0.0017) and three others were abundant in high scoring group, while Alloprevotella (P = 0.0014), Tannerella (P = 0.0033), Bacteroides (P = 0.0132), Malassezia (P = 0.0296), Catonella (P = 0.0353) and Pseudomonas (P = 0.0353) and so on showed higher abundance in low scoring group. Linear discriminant analysis effect size identified 29 discriminative feature taxa.

CONCLUSION: For the first time, vaginal microbiota was sequenced using 2bRAD-M. With a relatively simple structure, a more stable vaginal microbiota is associated with higher cervical ripeness, and certain microorganisms, such as Sphingomonas, may play a beneficial role in cervical ripening.

RevDate: 2024-11-01
CmpDate: 2024-11-01

Xu M, Xiao H, Zou X, et al (2025)

Mechanisms of levan in ameliorating hyperuricemia: Insight into levan on serum metabolites, gut microbiota, and function in hyperuricemia rats.

Carbohydrate polymers, 347:122665.

This study aims to investigate the effects of levan on the progression of hyperuricemia (HUA) rats and elucidate its underlying mechanisms. After levan intervention, both low and high-dose groups exhibited a significant decrease in serum uric acid (UA) levels, reaching 71.0 % and 77.5 %, respectively, compared to the model group. Furthermore, levan could alleviate renal pathological damage caused by glomerular cell vacuolation, inflammatory infiltration and collagen deposition. The results of enzyme activity assay and real-time fluorescence quantitative PCR showed that levan decreased UA production by inhibiting adenosine deaminase (ADA) activity and gene expression in liver; it upregulated ATP-binding cassette subfamily G member 2 protein (ABCG2) and organic anion transporter 1 (OAT1) transporter gene expression in the kidney, promoting UA excretion. Gut microbiome analysis indicated that levan regulated gut flora dysbiosis induced by HUA, resulting in up-regulated the abundance of beneficial bacteria (Muribaculaceae, Faecalibaculum, Bifidobacterium, and Lactobacillus) and decreased conditioned pathogenic bacteria (Escherichia_Shigella and Proteus). Non-targeted metabolomics showed changes in various serum metabolites associated with glycerophospholipid metabolism, lipid metabolism, and inflammation following oral administration of levan. Therefore, levan may be a promising functional dietary supplement for regulating the gut flora and remodeling of metabolic disorders in individuals with HUA.

RevDate: 2024-11-01

Fayet-Moore F, SR Robinson (2024)

A breath of fresh air: Perspectives on inhaled nutrients and bacteria to improve human health.

Advances in nutrition (Bethesda, Md.) pii:S2161-8313(24)00167-4 [Epub ahead of print].

We propose that the human respiratory system and olfactory pathways sequester airborne nutrients (vitamins, fatty acids and trace minerals) that are beneficial for health, which we term 'aeronutrients'. In addition, airborne bacteria, termed 'aeromicrobes', have the potential for positive health effects by improving species diversity in the microbiotas of the respiratory and gastrointestinal tracts. These concepts have implications for people living in urban areas or those who have limited access to nature, such as astronauts exposed for long periods to highly filtered air which may be depleted of aeronutrients and aeromicrobes. The possibility that fresh air contributes to human nutrition and health may stimulate a re-evaluation of guidelines pertaining to nutrition and access to natural environments, and will open new avenues of scientific enquiry.

RevDate: 2024-11-01

Kattner AA (2024)

Divine life force: the fragile power of blood.

Issue 46-7 of the Biomedical Journal explores the delicate boundaries of human blood. It examines the relationship between anemia and the gut microbiome, as well as the modified activation patterns in compensatory blood oxygenation observed in COVID-19, and lastly a series of experiments investigates the effects of SARS-CoV-2 variant spike proteins on the biology and morphology of red blood cells. Additionally, a fungus endemic to Taiwan shows potential as a treatment for pulmonary fibrosis, while relevant co-infections in schistosomiasis appear to be benefitting from altered receptor signaling in macrophages. A genomic study identifies an important locus in Taiwanese patients with Tourette syndrome, and a retrospective evaluation is conducted on the incidental detection of common bile duct dilatation in pediatric patients.

RevDate: 2024-11-01

Kapoor B, Biswas P, Gulati M, et al (2024)

Gut microbiome and Alzheimer's disease: what we know and what remains to be explored.

Ageing research reviews pii:S1568-1637(24)00388-X [Epub ahead of print].

With advancement in human microbiome research, an increasing number of scientific evidences have endorsed the key role of gut microbiota in the pathogenesis of Alzheimer disease. Microbiome dysbiosis, characterized by altered diversity and composition, as well as rise of pathobionts influence not only various gut disorder but also central nervous system disorders such as AD. On the basis of accumulated evidences of past few years now it is quite clear that the gut microbiota can control the functions of the central nervous system (CNS) through the gut-brain axis, which provides a new prospective into the interactions between the gut and brain. The main focus of this review is on the molecular mechanism of the crosstalk between the gut microbiota and the brain through the gut-brain axis, and on the onset and development of neurological disorders triggered by the dysbiosis of gut microbiota. Due to microbiota dysbiosis the permeability of the gut and blood brain barrier is increased which may mediate or affect AD. Along with this, bacterial population of the gut microbiota can secrete amyloid proteins and lipopolysaccharides in a large quantity which may create a disturbance in the signaling pathways and the formation of proinflammatory cytokines associated with the pathogenesis of AD. These topics are followed by a critical analysis of potential intervention strategies targeting gut microbiota dysbiosis, including the use of probiotics, prebiotics, metabolites, diets and fecal microbiota transplantation. The main purpose of this review includes the summarization and discussion on the recent finding that may explain the role of the gut microbiota in the development of AD. Understanding of these fundamental mechanisms may provide a new insight into the novel therapeutic strategies for AD.

RevDate: 2024-11-01

Chen Y, Sun C, Yan Y, et al (2024)

Impact of arbuscular mycorrhizal fungi on maize rhizosphere microbiome stability under moderate drought conditions.

Microbiological research, 290:127957 pii:S0944-5013(24)00358-6 [Epub ahead of print].

With an alarming increase in global greenhouse gas emissions, unstable weather conditions are significantly impacting agricultural production. Drought stress is one of the frequent consequences of climate change that affects crop growth and yield. Addressing this issue is critical to ensure stable crop productivity under drought conditions. Arbuscular mycorrhizal fungi (AMF) establish symbiotic relationships with plants and enhance their resistance to adverse conditions. Effects of arbuscular mycorrhizal associations on the rhizosphere microbiome and root transcriptome under drought conditions have not been explored. Here, we investigated the effects of AMF and drought stress on rhizosphere microorganisms and root transcriptome of maize plants grown in chernozem soil. We used high-throughput sequencing data of bacterial 16S rRNA and fungal internal transcribed spacer regions (ITS) to identify rhizosphere microorganisms. Transcriptomic data were used to assess gene expression in maize plants under different treatments. Our results show that AMF maintains the composition of maize rhizosphere microorganisms under drought stress. In particular, the bacterial and fungal phyla maintained were Actinomycetes and Ascomycota, respectively. Transcriptomic data indicated that AMF influenced gene expression in maize plants under drought stress. Under drought stress, the expression of SWEET13, CHIT3, and RPL23A was significantly higher in the presence of AMF than it was without AMF inoculation, indicating better sugar transport, reduced malondialdehyde accumulation, and improved water use efficiency in AMF-inoculated maize plants. These findings suggest that AMF can enhance the resistance of maize to moderate drought stress by stabilising plant physical traits, which may help maintain the structure of the rhizosphere microbial community. This study provides valuable theoretical insights that should aid the utilization of AMF in sustainable agricultural practices.

RevDate: 2024-11-01

Singh R, Panganiban K, Au E, et al (2024)

Human-fecal microbiota transplantation in relation to gut microbiome signatures in animal models for schizophrenia: A scoping review.

Asian journal of psychiatry, 102:104285 pii:S1876-2018(24)00378-2 [Epub ahead of print].

More recently, attention has turned to the putative role of gut microbiome (GMB) in pathogenesis, symptomatology, treatment response and/or resistance in schizophrenia (SCZ). It is foreseeable that fecal microbiota transplantation (FMT) from SCZ patients (SCZ-FMT) to germ-free mice could represent a suitable experimental framework for a better understanding of the relationship between GMB and SCZ. Thus, we set out to identify literature (i) characterizing the GMB in animal models of SCZ, and (ii) employing SCZ-FMT into rodents to model SCZ in relation to behavioral and molecular phenotypes. Five studies examining animal models of SCZ suggest distinct GMB composition compared to respective control groups, which was correlated with SCZ-like behavioral phenotypes. Four additional studies investigated SCZ-FMT into rodents in relation to behavioral phenotypes, including spontaneous hyperlocomotion, social deficits, exaggerated startle response, and cognitive impairments, resembling those observed in SCZ patients. Mice receiving SCZ-FMT showed altered neurochemical and metabolic pathways in the brain. Animal models of SCZ have shown altered GMB composition, whereas reported behavioral and neurochemical alterations following FMT from patients into rodents suggest early face and construct validity for SCZ-FMT animal models. However, the predictive validity of these models remains to be validated.

RevDate: 2024-11-01

Wang L, Wang Z, Zhao Y, et al (2024)

Gut microbiota-mediated bile acid metabolism aggravates biliary injury after liver transplantation through mitochondrial apoptosis.

International immunopharmacology, 143(Pt 3):113413 pii:S1567-5769(24)01935-0 [Epub ahead of print].

Ischemic-type biliary lesions (ITBL) are a major cause of graft loss and even mortality after liver transplantation (LT). The underlying cellular mechanisms for ITBL remain unclear. Gut microbiota has been found to be closely related to complications after LT. Here, using gut microbiome compositions, we found patients with ITBL had a higher abundance of bacteria associated with bile salt metabolism. These bacteria are reported to convert cholic acid (CA) into deoxycholic acid (DCA), consistent with our data that there were higher DCA concentrations and DCA/CA ratio in patients with ITBL than patients without ITBL. Using an in vitro model, human intrahepatic biliary epithelial cells (HIBEC) subjected to DCA showed a higher apoptosis rate, lower viability, and higher levels of cleaved-caspase3 than CA at the same concentration. DCA also changed the morphology of mitochondria and farnesoid X receptor (FXR) expression. Interestingly, DCA-induced apoptosis rate was significantly reduced in HIBEC when the FXR or BAX gene was knocked down, suggesting that DCA-induced apoptosis was dependent on FXR-mitochondrial pathway. Furthermore, increasing DCA/CA ratio in a bile acid-feeding mouse model resulted in cholangiocyte apoptosis and impaired liver function. The patients with ITBL also showed an increased proportion of TUNEL-positive biliary epithelial cells than those without ITBL. These suggest that changes in the gut microbiota following LT may enhance the conversion of CA to DCA, and may contribute to biliary damage via FXR-mitochondrial apoptosis pathway, providing new ideas for the early monitoring and treatment of ITBL.

RevDate: 2024-11-01

Campbell R, Kyei L, Piedl K, et al (2024)

Bokeelamides: Lipopeptides from Bacteria Associated with Marine Egg Masses.

Organic letters [Epub ahead of print].

Moon snails (family: Naticidae) lay egg masses that are rich in bacterial species distinct from the surrounding environment. We hypothesized that this microbiome chemically defends the moon snail eggs from predation and pathogens. Herein, we report the discovery of bokeelamides, new lipopeptides from the egg mass-associated bacterium, Ectopseudomonas khazarica, which were discovered using mass spectrometry (MS)-based metabolomics. The structures of the bokeelamides were elucidated using two-dimensional (2D) nuclear magnetic resonance (NMR), tandem MS, Marfey's, and genomic analyses.

RevDate: 2024-11-01
CmpDate: 2024-11-01

Araujo David B, Atif J, Vargas E Silva Castanheira F, et al (2024)

Kupffer cell reverse migration into the liver sinusoids mitigates neonatal sepsis and meningitis.

Science immunology, 9(101):eadq9704.

In adults, liver-resident macrophages, or Kupffer cells (KCs), reside in the sinusoids and sterilize circulating blood by capturing rapidly flowing microbes. We developed quantitative intravital imaging of 1-day-old mice combined with transcriptomics, genetic manipulation, and in vivo infection assays to interrogate increased susceptibility of newborns to bloodstream infections. Whereas 1-day-old KCs were better at catching Escherichia coli in vitro, we uncovered a critical 1-week window postpartum when KCs have limited access to blood and must translocate from liver parenchyma into the sinusoids. KC migration was independent of the microbiome but depended on macrophage migration inhibitory factor, its receptor CD74, and the adhesion molecule CD44. On the basis of our findings, we propose a model of progenitor macrophage seeding of the liver sinusoids via a reverse transmigration process from liver parenchyma. These results also illustrate the importance of developing newborn mouse models to understand newborn immunity and disease.

RevDate: 2024-11-01
CmpDate: 2024-11-01

Achudhan AB, LM Saleena (2024)

Comparative genomic analysis and characterization of novel high-quality draft genomes from the coal metagenome.

World journal of microbiology & biotechnology, 40(12):370.

Coal, a sedimentary rock harbours a complex microbial community that plays a significant role in its formation and characteristics. However, coal metagenome sequencing and studies were less, limiting our understanding of this complex ecosystem. This study aimed to reconstruct high-quality metagenome-assembled genomes (MAGs) from the coal sample collected in the Neyveli mine to explore the unrevealed diversity of the coal microbiome. Using Illumina sequencing, we obtained high-quality raw reads in FASTQ format. Subsequently, de novo assembly and binning with metaWRAP software facilitated the reconstruction of coal MAGs. Quality assessment using CheckM identified 10 High-Quality MAGs (HQ MAGs), 7 medium-quality MAGs (MQ MAGs), and 6 low-quality MAGs (LQ MAGs). Further analysis using GTDB-Tk revealed four HQ MAGs as known species like Dermacoccus abyssi, Sphingomonas aquatilis, Acinetobacter baumannii, and Burkholderia cenocepacia. The remaining six HQ MAGs were classified as Comamonas, Arthrobacter, Noviherbaspirillum, Acidovorax, Oxalicibacterium, and Bordetella and designated as novel genomes by the validation of digital DNA-DNA hybridization (dDDH). Phylogenetic analysis and further pangenome analysis across the phylogenetic groups revealed a similar pattern with a high proportion of cloud genes. We further analysed the functional potential of these MAGs and closely related genomes using COG. The comparative functional genomics revealed that novel genomes are highly versatile, potentially reflecting adaptations to the coal environment. BlastKOALA was used to conduct a detailed analysis of the metabolic pathways associated with the MAGs. This study highlights the comparative genomic analysis of novel coal genomes with their closely related genomes to understand the evolutionary relationships and functional properties.

RevDate: 2024-11-05
CmpDate: 2024-11-01

Minaya DM, Kim JS, Kirkland R, et al (2024)

Transfer of microbiota from lean donors in combination with prebiotics prevents excessive weight gain and improves gut-brain vagal signaling in obese rats.

Gut microbes, 16(1):2421581.

Gastrointestinal (GI) microbiota plays an active role in regulating the host's immune system and metabolism, as well as certain pathophysiological processes. Diet is the main factor modulating GI microbiota composition and studies have shown that high fat (HF) diets induce detrimental changes (dysbiosis) in the GI bacterial makeup. HF diet induced dysbiosis has been associated with structural and functional changes in gut-brain vagally mediated signaling system, associated with overeating and obesity. Although HF-driven changes in microbiota composition are sufficient to alter vagal signaling, it is unknown if improving microbiota composition after diet-induced obesity has been established can ameliorate gut-brain signaling and metabolic outcomes. In this study, we evaluated the effect of lean gut microbiota transfer in obese, vagally compromised, rats on gut-brain communication, food intake, and body weight. Male rats were maintained on regular chow or 45% HF diet for nine weeks followed by three weeks of microbiota depletion using antibiotics. The animals were then divided into four groups (n = 10 each): LF - control fed regular chow, LF-LF - chow fed animals that received microbiota from chow fed donors, HF-LF - HF fed animals that received microbiota from chow fed donors, and HF-HF - HF fed animals that received microbiota from HF fed donors. HF-LF animals received inulin as a prebiotic to aid the establishment of the lean microbiome. We found that transferring a LF microbiota to HF fed animals (HF-LF) reduced caloric intake during the light phase when compared with HF-HF rats and prevented additional excessive weight gain. HF-LF animals displayed an increase in postprandial activation of both primary sensory neurons innervating the GI tract and brainstem secondary neurons. We concluded from these data that improving microbiota composition in obese rats is sufficient to ameliorate gut-brain communication and restore normal feeding patterns which was associated with a reduction in weight gain.

RevDate: 2024-11-01

Jimenez NR, Mancilla V, Łaniewski P, et al (2024)

Immunometabolic Contributions of Atopobiaceae Family Members in Human Papillomavirus Infection, Cervical Dysplasia and Cancer.

The Journal of infectious diseases pii:7863217 [Epub ahead of print].

BACKGROUND: In the cervicovaginal environment, HPV acquisition and cervical cancer progression are linked to non-Lactobacillus dominance, of which Atopobiaceae are key taxa. We hypothesize that Atopobiaceae modulates the cervicovaginal microenvironment to promote HPV persistence and progression to cancer. However, the extent to which Atopobiaceae impact the immunometabolic microenvironment is poorly understood.

METHODS: We investigated Atopobiaceae in a cohort of primarily Hispanic and non-Hispanic White women who were HPV-negative (n=20), HPV-positive (n=31) without dysplasia, diagnosed with cervical dysplasia (n=38), or newly diagnosed with invasive cervical carcinoma (n=9). Microbiome data was integrated with clinical and demographic surveys, immunoproteomics, and metabolomics data.

RESULTS: Atopobiaceae identified were Fannyhessea vaginae, Fannyhessea massiliense, Fannyhessea species type 2, Lancefieldella deltae, and an unclassified species. A higher prevalence of Atopobiaceae was observed in women who were Hispanic and had higher gravidity and parity. F. species type 2 and F. vaginae were observed with infections of high-risk HPV genotypes 31 and 52. Atopobiacaeae were negatively correlated with Lactobacillus and positively correlated to Sneathia, Dialister, Anaerococcus, Prevotella, and Bifidobacterium/Gardnerella. Proinflammatory cytokines (IL-1α, IL-1β, IL-12, TNFα), immune checkpoint proteins (PD-L1, LAG3), and cancer biomarkers (CEA, MIF, TRAIL) were positively associated with Atopobiaceae-rich profiles. Pro-oncogenic metabolites, including 4-hydroxybutyrate and sphingosine, were also elevated in women colonized by Atopobiaceae.

CONCLUSIONS: Our data implicate Atopobiaceae in lipid modulation, oxidative stress, inflammatory responses, and immune evasion, which may contribute to cancer. This study highlights a key family of pathogenic cervicovaginal bacteria that could be exploited to monitor HPV persistence and/or targeted to prevent HPV-mediated cancer.

RevDate: 2024-11-01
CmpDate: 2024-11-01

Wong CC, J Yu (2024)

Redefining the Gastric Microbes in Promoting Gastric Tumorigenesis: The Rise of the Non-H. pylori Microbiome.

Cancer discovery, 14(11):2051-2054.

Gastric cancer remains one of the top cancers in China compared with Western countries, mainly attributed to the high rates of Helicobacter pylori infection. However, recent discoveries on the non-H. pylori gastric microbiome have led to a paradigm shift in our understanding of microbial risk factors driving gastric cancer, which will impact future screening and prevention strategies.

RevDate: 2024-11-01

Kortekaas Krohn I, Callewaert C, Belasri H, et al (2024)

The influence of lifestyle and environmental factors on host resilience through a homeostatic skin microbiota: An EAACI Task Force Report.

Allergy [Epub ahead of print].

Human skin is colonized with skin microbiota that includes commensal bacteria, fungi, arthropods, archaea and viruses. The composition of the microbiota varies at different anatomical locations according to changes in body temperature, pH, humidity/hydration or sebum content. A homeostatic skin microbiota is crucial to maintain epithelial barrier functions, to protect from invading pathogens and to interact with the immune system. Therefore, maintaining homeostasis holds promise to be an achievable goal for microbiome-directed treatment strategies as well as a prophylactic strategy to prevent the development of skin diseases, as dysbiosis or disruption of homeostatic skin microbiota is associated with skin inflammation. A healthy skin microbiome is likely modulated by genetic as well as environmental and lifestyle factors. In this review, we aim to provide a complete overview of the lifestyle and environmental factors that can contribute to maintaining the skin microbiome healthy. Awareness of these factors could be the basis for a prophylactic strategy to prevent the development of skin diseases or to be used as a therapeutic approach.

RevDate: 2024-11-01

Shi F, Peng J, Li H, et al (2024)

Probiotics as a targeted intervention in anti-aging: A review.

Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals [Epub ahead of print].

The age-induced disruption of gut flora, termed gut dysbiosis, is intimately tied to compromised immune function, augmented oxidative stress, and a spectrum of age-linked disorders. This review examines the fundamental mechanisms employed by probiotic strains to modulate gut microbiota composition and metabolic profiles, mitigate cognitive decline via the gut-brain axis, modulate gene transcription, and alleviate inflammatory responses and oxidative stress. We elucidate the capacity of probiotics as a precision intervention to restore gut microbiome homeostasis and alleviate age-related conditions, thereby offering a theoretical framework for probiotics to decelerate aging, manage age-related diseases, and elevate quality of life.

RevDate: 2024-11-01

Doster RS (2024)

The vaginal microbiome, setting the stage for cancer?.

The Journal of infectious diseases pii:7861054 [Epub ahead of print].

RevDate: 2024-11-02
CmpDate: 2024-11-01

Worasilchai J, Thongchaichayakon P, Chansri K, et al (2024)

Fluconazole worsened lung inflammation, partly through lung microbiome dysbiosis in mice with ovalbumin-induced asthma.

PeerJ, 12:e18421.

Innate immunity in asthma may be influenced by alterations in lung microbiota, potentially affecting disease severity. This study investigates the differences in lung inflammation and microbiome between asthma-ovalbumin (OVA) administered with and without fluconazole treatment in C57BL/6 mice. Additionally, the role of inflammation was examined in an in vitro study using a pulmonary cell line. At 30 days post-OVA administration, allergic asthma mice exhibited increased levels of IgE and IL-4 in serum and lung tissue, higher pathological scores, and elevated eosinophils in bronchoalveolar lavage fluid (BALF) compared to control mice. Asthma inflammation was characterized by elevated serum IL-6, increased lung cytokines (TNF-α, IL-6, IL-10), and higher fungal abundance confirmed by polymerase chain reaction (PCR). Fluconazole-treated asthma mice displayed higher levels of cytokines in serum and lung tissue (TNF-α and IL-6), increased pathological scores, and a higher number of mononuclear cells in BALF, with undetectable fungal levels compared to untreated mice. Lung microbiome analysis revealed similarities between control and asthma mice; however, fluconazole-treated asthma mice exhibited higher Bacteroidota levels, lower Firmicutes, and reduced bacterial abundance. Pro-inflammatory cytokine production was increased in supernatants of the pulmonary cell line (NCI-H292) after co-stimulation with LPS and beta-glucan (BG) compared to LPS alone. Fluconazole treatment in OVA-induced asthma mice exacerbated inflammation, partially due to fungi and Gram-negative bacteria, as demonstrated by LPS+BG-activated pulmonary cells. Therefore, fluconazole should be reserved for treating fungal asthma rather than asthma caused by other etiologies.

RevDate: 2024-11-02

Cheng X, Ren C, Mei X, et al (2024)

Gut microbiota and irritable bowel syndrome: status and prospect.

Frontiers in medicine, 11:1429133.

Irritable bowel syndrome (IBS) is a very common gastrointestinal disease that, although not as aggressive as tumors, affects patients' quality of life in different ways. The cause of IBS is still unclear, but more and more studies have shown that the characteristics of the gut microbiota, such as diversity, abundance, and composition, are altered in patients with IBS, compared to the healthy population, which confirms that the gut microbiota plays a crucial role in the development of IBS. This paper aims to identify the commonalities by reviewing a large body of literature. Changes in the characteristics of gut microbiota in patients with different types of IBS are discussed, relevant mechanisms are described, and the treatment modalities of gut microbiota in IBS are summarized. Although there are more clinical trials that have made good progress, more standardized, more generalized, larger-scale, multi-omics clinical studies are what is missing. Overall, gut microbiota plays a crucial role in the development of IBS, and there is even more potential for treating IBS by modulating gut microbiota.

RevDate: 2024-11-02

Nurkolis F, Utami TW, Alatas AI, et al (2024)

Can salivary and skin microbiome become a biodetector for aging-associated diseases? Current insights and future perspectives.

Frontiers in aging, 5:1462569.

Growth and aging are fundamental elements of human development. Aging is defined by a decrease in physiological activities and higher illness vulnerability. Affected by lifestyle, environmental, and hereditary elements, aging results in disorders including cardiovascular, musculoskeletal, and neurological diseases, which accounted for 16.1 million worldwide deaths in 2019. Stress-induced cellular senescence, caused by DNA damage, can reduce tissue regeneration and repair, promoting aging. The root cause of many age-related disorders is inflammation, encouraged by the senescence-associated secretory phenotype (SASP). Aging's metabolic changes and declining immune systems raise illness risk via promoting microbiome diversity. Stable, individual-specific skin and oral microbiomes are essential for both health and disease since dysbiosis is linked with periodontitis and eczema. Present from birth to death, the human microbiome, under the influence of diet and lifestyle, interacts symbiotically with the body. Poor dental health has been linked to Alzheimer's and Parkinson's diseases since oral microorganisms and systemic diseases have important interactions. Emphasizing the importance of microbiome health across the lifetime, this study reviews the understanding of the microbiome's role in aging-related diseases that can direct novel diagnosis and treatment approaches.

RevDate: 2024-11-01

Camacho E, Dong Y, Chrissian C, et al (2024)

Dietary L-3,4-dihydroxyphenylalanine (L-DOPA) augments cuticular melanization in Anopheles mosquitos while reducing their lifespan and malaria parasite burden.

Research square pii:rs.3.rs-5167892.

L-3,4-dihydroxyphenylalanine (L-DOPA), a naturally occurring tyrosine derivative, is prevalent in environments that include mosquito habitats, potentially serving as part of their diet. Given its role as a precursor for melanin synthesis we investigated the effect of dietary L-DOPA on mosquito physiology and immunity to Plasmodium falciparum and Cryptococcus neoformans infection. Dietary L-DOPA was incorporated into mosquito melanin via a non-canonical pathway and had profound transcriptional effects that were associated with enhanced immunity, increased pigmentation, and reduced lifespan. Increased melanization resulted in an enhanced capacity to absorb electromagnetic radiation that affected mosquito temperatures. Bacteria in the mosquito microbiome were sources of dopamine, which is a substrate for melanization. Our results illustrate how an environmentally abundant amino acid analogue can affect mosquito physiology and suggest its potential usefulness as an environmentally friendly vector control agent to reduce malaria transmission, warranting further research and field studies.

RevDate: 2024-11-01

Goodman A, Kumar A, Sun R, et al (2024)

Impacts of Medications on Microbiome-mediated Protection against Enteric Pathogens.

Research square pii:rs.3.rs-5199936.

The majority of people in the U.S. manage health through at least one prescription drug. Drugs classified as non-antibiotics can adversely affect the gut microbiome and disrupt intestinal homeostasis. Here, we identified medications associated with an increased risk of GI infections across a population cohort of more than 1 million individuals monitored over 15 years. Notably, the cardiac glycoside digoxin and other drugs identified in this epidemiological study are sufficient to alter microbiome composition and risk of Salmonella enterica subsp. Typhimurium (S. Tm) infection in mice. The impact of digoxin treatment on S. Tm infection is transmissible via the microbiome, and characterization of this interaction highlights a digoxin-responsive β defensin that alters microbiome composition and consequent immune surveillance of the invading pathogen. Combining epidemiological and experimental approaches thus provides an opportunity to uncover drug-host-microbiome-pathogen interactions that increase infection risk in humans.

RevDate: 2024-11-02

Li Z, Li A, Liu P, et al (2024)

Mapping the evolution and impact of ketogenic diet research on diabetes management: a comprehensive bibliometric analysis from 2005 to 2024.

Frontiers in nutrition, 11:1485642.

OBJECTIVE: The ketogenic diet (KD) has been explored for diabetes management; however, a quantitative synthesis of its specific effects on diabetes has not yet been conducted. This study aims to examine the current status and research hotspots of KD in diabetes management from 2005 to 2024, providing a reference for future research.

METHODS: We retrieved articles published between 2005 and 2024 from the Web of Science database and analyzed them using R software, VOSviewer, and CiteSpace.

RESULTS: This study includes 432 relevant publications. From 2005 to 2024, the volume of literature in this field has shown a steady upward trend, with a notable increase from 2017 to 2021, and a slight decline observed from 2021 to 2023. The United States is the leading country in terms of the number of publications, followed by China, Australia, and Canada. The United States not only leads in publication volume but also maintains a broader international collaboration network. Nutrients and the American Journal of Clinical Nutrition are the most frequently published and cited journals. Current research hotspots primarily focus on the impact of KD on blood glucose control, insulin resistance, and lipid metabolism in diabetic patients. Mechanistic studies on KD in diabetes management concentrate on aspects such as the "regulation of genes by β-hydroxybutyrate," "anti-inflammatory effects," and "oxidative stress." The role of the gut microbiome is also emerging as an important research area. Currently, exploring the application of KD in managing different age groups and types of diabetes has become a significant research trend.

CONCLUSION: As an emerging dietary intervention, KD is gradually attracting widespread attention from researchers around the world and is expected to become a major research focus in the future for diabetes management and control. This paper provides a systematic review and analysis of the current research status and hotspots of KD in diabetes management, offering important references and insights for future research in related fields.

RevDate: 2024-11-02

Pita S, Myers PN, Johansen J, et al (2024)

CHAMP delivers accurate taxonomic profiles of the prokaryotes, eukaryotes, and bacteriophages in the human microbiome.

Frontiers in microbiology, 15:1425489.

INTRODUCTION: Accurate taxonomic profiling of the human microbiome composition is crucial for linking microbial species to health outcomes. Therefore, we created the Clinical Microbiomics Human Microbiome Profiler (CHAMP), a comprehensive tool designed for the profiling of prokaryotes, eukaryotes, and viruses across all body sites.

METHODS: CHAMP uses a reference database derived from 30,382 human microbiome samples, covering 6,567 prokaryotic and 244 eukaryotic species, as well as 64,003 viruses. We benchmarked CHAMP against established profiling tools (MetaPhlAn 4, Bracken 2, mOTUs 3, and Phanta) using a diverse set of in silico metagenomes and DNA mock communities.

RESULTS: CHAMP demonstrated unparalleled species recall, F1 score, and significantly reduced false positives compared to all other tools benchmarked. The false positive relative abundance (FPRA) for CHAMP was, on average, 50-fold lower than the second-best performing profiler. CHAMP also proved to be more robust than other tools at low sequencing depths, highlighting its application for low biomass samples.

DISCUSSION: Taken together, this establishes CHAMP as a best-in-class human microbiome profiler of prokaryotes, eukaryotes, and viruses in diverse and complex communities across low and high biomass samples. CHAMP profiling is offered as a service by Clinical Microbiomics A/S and is available for a fee at https://cosmosidhub.com.

RevDate: 2024-11-02
CmpDate: 2024-11-01

Chen G, Ren Q, Zhong Z, et al (2024)

Exploring the gut microbiome's role in colorectal cancer: diagnostic and prognostic implications.

Frontiers in immunology, 15:1431747.

The intricate interplay between the gut microbiome and colorectal cancer (CRC) presents novel avenues for early diagnosis and prognosis, crucial for improving patient outcomes. This comprehensive review synthesizes current findings on the gut microbiome's contribution to CRC pathogenesis, highlighting its potential as a biomarker for non-invasive CRC screening strategies. We explore the mechanisms through which the microbiome influences CRC, including its roles in inflammation, metabolism, and immune response modulation. Furthermore, we assess the viability of microbial signatures as predictive tools for CRC prognosis, offering insights into personalized treatment approaches. Our analysis underscores the necessity for advanced metagenomic studies to elucidate the complex microbiome-CRC nexus, aiming to refine diagnostic accuracy and prognostic assessment in clinical settings. This review propels forward the understanding of the microbiome's diagnostic and prognostic capabilities, paving the way for microbiome-based interventions in CRC management.

RevDate: 2024-11-02

Wei X, Xi P, Chen M, et al (2024)

Capsule robots for the monitoring, diagnosis, and treatment of intestinal diseases.

Materials today. Bio, 29:101294.

Current evidence suggests that the intestine as the new frontier for human health directly impacts both our physical and mental health. Therefore, it is highly desirable to develop the intelligent tool for the enhanced diagnosis and treatment of intestinal diseases. During the past 20 years, capsule robots have opened new avenues for research and clinical applications, potentially revolutionizing human health monitor, disease diagnosis and treatment. In this review, we summarize the research progress of edible multifunctional capsule robots in intestinal diseases. To begin, we introduce the correlation between the intestinal microbiome, intestinal gas and human diseases. After that, we focus on the technical structure of edible multifunctional robots. Subsequently, the biomedical applications in the monitoring, diagnosis and treatment of intestinal diseases are discussed in detail. Last but not least, the main challenges of multifunctional capsule robots during the development process are summarized, followed by a vision for future development opportunities.

RevDate: 2024-11-02

Cannon M, Toma R, Ganeshan S, et al (2024)

Salivary Transcriptome and Mitochondrial Analysis of Autism Spectrum Disorder Children Compared to Healthy Controls.

NeuroSci, 5(3):276-290.

Autism rates have been reported to be increasing rapidly in industrialized societies. The pathology most often combines neurological symptoms associated with language and social impairments with gastrointestinal symptoms. This study aimed to measure differences in oral metatranscriptome and mitochondrial health between ASD children and neurotypical USA and Colombia ("Blue Zone") children. In addition, this study aimed to determine whether using prebiotics and probiotics would change the oral microbiome and mitochondrial health of ASD children. Buccal swabs and saliva samples were obtained from 30 autistic individuals (USA) at three intervals: prior to intervention, post-prebiotic, and post-probiotic. In addition, a subject component who were neurotypical, which included individuals from the USA (30) and Colombia (30), had buccal swabbing and salivary sampling performed for metatranscriptomic and mitochondrial comparison. Significant differences were observed in the temporal data, demonstrating shifts that interventions with probiotics and polyols may have precipitated. Particular bacterial strains were significantly more prevalent in the autism group, including a strain that reduced neurotransmitter levels via enzymatic degradation. This supports the hypothesis that the microbiome may influence the occurrence and degree of autism. Verbal skills increased in six of the 30 ASD subjects following xylitol and three more after probiotic supplementation, according to both parental reports and the subjects' healthcare providers.

RevDate: 2024-11-02

Prescott SL, Holton KF, Lowry CA, et al (2024)

The Intersection of Ultra-Processed Foods, Neuropsychiatric Disorders, and Neurolaw: Implications for Criminal Justice.

NeuroSci, 5(3):354-377.

Over the last decade there has been increasing interest in the links between the consumption of ultra-processed foods and various neuropsychiatric disorders, aggression, and antisocial behavior. Neurolaw is an interdisciplinary field that seeks to translate the rapid and voluminous advances in brain science into legal decisions and policy. An enhanced understanding of biophysiological mechanisms by which ultra-processed foods influence brain and behavior allows for a historical reexamination of one of forensic neuropsychiatry's most famous cases-The People v. White and its associated 'Twinkie Defense'. Here in this Viewpoint article, we pair original court transcripts with emergent research in neurolaw, including nutritional neuroscience, microbiome sciences (legalome), pre-clinical mechanistic research, and clinical intervention trials. Advances in neuroscience, and related fields such as the microbiome, are challenging basic assumptions in the criminal justice system, including notions of universal free will. Recent dismissals of criminal charges related to auto-brewery syndrome demonstrate that courts are open to advances at the intersection of neuromicrobiology and nutritional neuroscience, including those that relate to criminal intent and diminished capacity. As such, it is our contention that experts in the neurosciences will play an increasing role in shaping research that underpins 21st-century courtroom discourse, policy, and decision-making.

RevDate: 2024-11-02
CmpDate: 2024-11-01

Gong M, Yu H, Qu H, et al (2024)

Global research trends and hotspots on human intestinal fungi and health: a bibliometric visualization study.

Frontiers in cellular and infection microbiology, 14:1460570.

BACKGROUND: This article employs bibliometric methods and visual maps to delineate the research background, collaborative relationships, hotspots, and trends in the study of gut fungi in human diseases and health.

METHODS: Publications related to human gut fungi were retrieved from the Web of Science Core Collection. VOSviewer, CiteSpace, R software and Microsoft Excel were employed to generate visual representations illustrating the contributions made by countries/regions, authors, organizations, and journals. Employing VOSviewer and CiteSpace, we conducted a comprehensive analysis of the retrieved publications, revealing underlying tendencies, research hotspots, and intricate knowledge networks.

RESULTS: This study analyzed a total of 3,954 publications. The United States ranks first in the number of published papers and has the highest number of citations and h-index. Mostafa S Elshahed is the most prolific author. The University of California System is the institution that published the most papers. Frontiers In Microbiology is the journal with the largest number of publications. Three frequently co-cited references have experienced a citation burst lasting until 2024.

CONCLUSION: Advancements in sequencing technologies have intensified research into human gut fungi and their health implications, shifting the research focus from gut fungal infections towards microbiome science. Inflammatory bowel diseases and Candida albicans have emerged as pivotal areas of interest in this endeavor. Through this study, we have gained a deeper insight into global trends and frontier hotspots within this field, thereby enhancing our understanding of the intricate relationship between gut fungi and human health.

RevDate: 2024-11-03
CmpDate: 2024-11-01

Nie D, Wang D, Wang Z, et al (2024)

The gut microbiome in patients with Cushing's disease affects depression- and anxiety-like behavior in mice.

Microbiome, 12(1):225.

BACKGROUND: Depression and anxiety significantly impact the quality of life in individuals with Cushing's disease (CD), which originates from pituitary neuroendocrine tumors (PitNETs), yet our understanding of the underlying mechanisms is limited. There is substantial evidence linking gut microbes to depression, anxiety, and endocrinology.

RESULTS: The gut bacterial phenotype of patients with Cushing's disease was significantly different from that of the control group, and when the mice were treated with fecal bacteria from these patients, both anxiety- and depression-like behavior were significantly increased. However, this effect can be alleviated by supplementing with 2-(14, 15-epoxyeicosatrienoyl) glycerol (2-14,15-EG) which was found at reduced levels in the peripheral blood of mice treated with coprofecal bacteria from Cushing's disease. In this process, the effects of hormone levels and immune factors were not significant. In addition, in an animal model, corticosterone has been observed to affect behavioral changes in mice through gut microbiota composition, clarifying the cause-and-effect relationship between hormones, microbiota, and behavior. Finally, there was no significant difference in gut microbiome composition and its effects on mouse behavior in patients with Cushing's disease with different levels of depression and anxiety.

CONCLUSIONS: In summary, this research enhances our current understanding of how gut microbes in patients with Cushing's disease contribute to depression and anxiety, offering novel insights for clinical treatment approaches. Video Abstract.

LOAD NEXT 100 CITATIONS

RJR Experience and Expertise

Researcher

Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.

Educator

Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.

Administrator

Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.

Technologist

Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.

Publisher

While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.

Speaker

Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.

Facilitator

Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.

Designer

Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

963 Red Tail Lane
Bellingham, WA 98226

206-300-3443

E-mail: RJR8222@gmail.com

Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

short personal version

Curriculum Vitae for R J Robbins

long standard version

RJR Picks from Around the Web (updated 11 MAY 2018 )