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Microorganisms May 2024Latent tuberculosis infection (LTBI) is common in people living with HIV (PLHIV) in high-TB-burden settings. Active TB is associated with specific stool taxa; however,...
Latent tuberculosis infection (LTBI) is common in people living with HIV (PLHIV) in high-TB-burden settings. Active TB is associated with specific stool taxa; however, little is known about the stool microbiota and LTBI in PLHIV. We characterised the stool microbiota of PLHIV with [interferon- release assay (IGRA)- and tuberculin skin test (TST)-positive] or without (IGRA- and TST-negative) LTBI ( = 25 per group). The 16S rRNA DNA sequences were analysed using QIIME2, Dirichlet-Multinomial Mixtures, DESeq2, and PICRUSt2. No α- or β-diversity differences occurred by LTBI status; however, LTBI-positive people were -, -, -, and -enriched and -, -, -, and -depleted. Inferred metagenome data showed that LTBI-negative-enriched pathways included several metabolite degradation pathways. Stool from LTBI-positive people demonstrated differential taxa abundance based on a quantitative response to antigen stimulation. In LTBI-positive people, older people had different β-diversities than younger people, whereas in LTBI-negative people, no differences occurred across age groups. Amongst female PLHIV, those with LTBI were, vs. those without LTBI, -, -, -, and -enriched, which are producers of short-chain fatty acids. Taxonomic differences amongst people with LTBI occurred according to quantitative response to antigen stimulation and age. These data enhance our understanding of the microbiome's potential role in LTBI.
PubMed: 38930430
DOI: 10.3390/microorganisms12061048 -
Microorganisms May 2024Compared to commercial breeds, Chinese local pig breeds have a greater ability to digest dietary fiber, which may be due to differences in intestinal microbiota. In this...
Compared to commercial breeds, Chinese local pig breeds have a greater ability to digest dietary fiber, which may be due to differences in intestinal microbiota. In this study, we fed Ding'an and DLY pigs high and low levels of dietary fiber, respectively, to investigate factors contributing to high dietary fiber adaption in Ding'an pigs. Twelve Ding'an pigs and DLY pigs were randomly divided into a 2 (diet) × 2 (breed) factorial experiment ( = 3). Compared with commercial pigs, Ding'an pigs have a stronger ability to digest dietary fiber. was more prevalent in Ding'an pigs than in DLY pigs, which may be an important reason for the stronger ability of fiber degradation in Ding'an pigs. When the effects of feed and breed factors are considered, differences in abundance of 31 species and 14 species, respectively, may result in a greater ability of fiber degradation in Ding'an pigs. Among them, sp. may be a newly discovered bacterium related to fiber degradation, which positively correlated with many fiber-degrading bacteria (r > 0.7). We also found that the concentration of plant metabolites with anti-inflammatory and antioxidant effects was higher in the colonic chyme of Ding'an pigs after increasing the fiber content, which resulted in the downregulated expression of inflammatory factors in colonic mucosa. Spearman's correlation coefficient revealed a strong correlation between microbiota and the apparent digestibility of dietary fiber (r > 0.7). The mRNA expressions of , , and were significantly increased in the colonic mucosa of Ding'an pigs fed on high-fiber diets, which indicates that Ding'an pigs have an enhanced absorption of SCFAs. Our results suggested that an appropriate increase in dietary fiber content can reduce the inflammatory response and improve feed efficiency in Ding'an pigs, and differences in the intestinal microbial composition may be an important reason for the difference in the fiber degradation capacity between the two breeds of pigs.
PubMed: 38930415
DOI: 10.3390/microorganisms12061033 -
Journal of Clinical Medicine Jun 2024This study aims to assess the presence of pathogenic microorganisms in the corneal epithelial layer of keratoconus patients. DNA was extracted from corneal epithelial...
This study aims to assess the presence of pathogenic microorganisms in the corneal epithelial layer of keratoconus patients. DNA was extracted from corneal epithelial samples procured from ten individual keratoconus eyes and three healthy controls. Metagenomic next-generation sequencing (mNGS) was performed to detect ocular microbiota using an agnostic approach. Metagenomic sequencing revealed a low microbial read count in corneal epithelial samples derived from both keratoconus eyes (average: 530) and controls (average: 622) without a statistically significant difference ( = 0.29). Proteobacteria were the predominant phylum in both keratoconus and control samples (relative abundance: 72% versus 79%, respectively). The overall low microbial read count and the lack of difference in the relative abundance of different microbial species between keratoconus and control samples do not support the hypothesis that a chronic corneal infection is implicated in the pathogenesis of keratoconus. These findings do not rule out the possibility that an acute infection may be involved in the disease process as an initiating event.
PubMed: 38929928
DOI: 10.3390/jcm13123399 -
Life (Basel, Switzerland) May 2024Cholangiocarcinoma (CCC) still has a high mortality rate despite improvements in diagnostic and therapeutic techniques. The role of the human microbiome in CCC is poorly...
INTRODUCTION
Cholangiocarcinoma (CCC) still has a high mortality rate despite improvements in diagnostic and therapeutic techniques. The role of the human microbiome in CCC is poorly understood, and a recent metagenomic analysis demonstrated a significant correlation between microbiome-associated carcinogenesis and CCC. This study aimed to investigate changes in microbiome composition associated with CCC and its metabolic signature by integrating taxonomic and functional information with metabolomics data and in vitro experimental results.
METHODS
From February 2019 to January 2021, this study included patients who underwent endoscopic retrograde cholangiopancreatography (ERCP), both with and without a diagnosis of CCC. Bile samples were collected via endoscopic nasobiliary drainages (ENBD) and subjected to DNA extraction, PCR amplification of the bacterial 16S rRNA gene V3-V4 region, and data analysis using QIIME2. In vitro Carboxyfluorescein succinimidyl ester (CFSE) proliferation and Annexin V/PI apoptosis assays were performed to investigate the effects of metabolites on CCC cells.
RESULTS
A total of 24 patients were included in the study. Bile fluid analysis revealed a significantly higher abundance of in the CCC group. Alpha diversity analyses exhibited significant differences between the CCC and non-CCC groups, and Nuclear Magnetic Resonance (NMR) spectroscopy metabolic profiling identified 15 metabolites with significant concentration differences; isoleucine showed the most notable difference. In vitro experiments demonstrated that isoleucine suppressed CCC cell proliferation but did not induce apoptosis.
CONCLUSIONS
This research underlines the significance of biliary dysbiosis and specific bile metabolites, such as isoleucine, in influencing the development and progression of CCC.
PubMed: 38929681
DOI: 10.3390/life14060698 -
Life (Basel, Switzerland) May 2024The imbalance of skin microbiota in acne can induce changes leading to induction or to aggravation of chronic inflammatory lesions; complex mechanisms are involved. (...
BACKGROUND
The imbalance of skin microbiota in acne can induce changes leading to induction or to aggravation of chronic inflammatory lesions; complex mechanisms are involved. ( ribotypes RT4 and RT5 express more biofilm and are associated with inflammatory acne lesions. RT6 is a non-acne ribotype, beneficial for the skin.
OBJECTIVES
In an open clinical trial, acne adults were included and assessed clinically at baseline and at month 2 using the Investigator Global Assessment of Acne (IGA) score. A topical emulsion was applied twice daily for 2 months (M2) in each included patient. In the same series of acne patients, skin swab samples were collected from acne patients at baseline and M2 from lesional and non-lesional skin; skin swabs were collected for the metagenomic long-read analysis of microbiota.
MATERIALS AND METHODS
Acne patients with a gravity score IGA of >1<3 were included in this pilot study. An emulsion of O/W formulated with vegetal extract of associated with a polysaccharide at 1% was applied twice daily for 2 months. At baseline and M2 clinical assessments were made; skin swab samples were also taken for microbiota analysis from lesional and non-lesional skin in each included patient. Extractions of genomic DNA (gDNA) from swab samples from baseline and from M2 were made, followed by full-length (V1-V9) amplification of the 16S rDNA and sequencing of amplicon libraries for strain-level bacterial community profiling.
RESULTS
In a series of 32 adult acne patients, the mean initial IGA scale was 3.1; at M2 the IGA scale was 1.5 ( < 0.001). The mean decrease in acne lesions was by 63%. Microbiome metagenomic long-read analysis in these series was mainly dominated by followed by (. The density of ribotypes RT6 (non-acne strain) was increased at M2 compared to baseline and the density of ribotypes RT1 to RT5 was decreased at M2, compared to baseline ( < 0.0001). ribotypes (1 to 36) were non significantly increased at M2, compared to baseline ( < 0.1).
CONCLUSIONS
In a series of 32 acne patients that applied an emulsion based on vegetal extract of and a polysaccharide at 1% twice daily, a significant clinical improvement in IGA scale for acne lesions was seen at M2, compared to baseline ( < 0.0001). The clinical improvement was correlated with an improvement in skin microbiome at M2 compared to baseline, indicated by the increase in the relative abundance of non-acne strain of ribotype 6 and of the decrease in the relative abundance of acne strains ribotypes RT1 to RT5.
PubMed: 38929671
DOI: 10.3390/life14060688 -
Animals : An Open Access Journal From... Jun 2024The intestine of living organisms harbors different microbiota associated with the biological functioning and health of the host and influences the process of ecological...
The intestine of living organisms harbors different microbiota associated with the biological functioning and health of the host and influences the process of ecological adaptation. Here, we studied the intestinal microbiota's composition and functional differences using 16S rRNA and metagenomic analysis in the wild, farm, and released Chinese three-keeled pond turtle (). At the phylum level, Bacteroidota dominated, followed by Firmicutes, Fusobacteriota, and Actinobacteriota in the wild group, but Chloroflexi was more abundant in the farm and released groups. Moreover, , , , , and were abundant in the released and farm cohorts, respectively. , , , and showed an abundance in the wild group. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed that the relative abundance of most pathways was significantly higher in the wild turtles (carbohydrate metabolism, lipid metabolism, metabolism of cofactors, and vitamins). The comprehensive antibiotic resistance database (CARD) showed that the antibiotic resistance gene (ARG) subtype was the most abundant in the farm turtle group, while was higher in the wild turtles, and was higher in the released group. Our findings shed light on the association between the intestinal microbiota of and its habitats and could be useful for tracking habitats to protect and conserve this endangered species.
PubMed: 38929370
DOI: 10.3390/ani14121750 -
Foods (Basel, Switzerland) Jun 2024Kombucha is a trending tea fermented via a complex microflora of yeasts and acetic acid bacteria. It can be a valid low-calorie substitute for soft drinks due to its...
Kombucha is a trending tea fermented via a complex microflora of yeasts and acetic acid bacteria. It can be a valid low-calorie substitute for soft drinks due to its sour, naturally carbonated, and sweet taste. Despite increased interest, the microflora and functional properties of kombucha have not yet been fully understood. The aim of this work was to characterize, from a microbiological, chemico-physical, and functional point of view, three types of artisanal kombucha obtained by fermenting green tea containing sugar by means of different starter cultures. Metagenomic analysis revealed a predominance of yeasts compared to bacteria, regardless of the sample. In particular, spp. was found to be the dominant yeast. Moreover, the different types of kombucha had different microbial patterns in terms of acetic acid bacteria and yeasts. Ethanol and acetic acid were the dominant volatile molecules of the kombucha volatilome; the samples differed from each other in terms of their content of alcohols, esters, and acids. All the samples showed a high antioxidant potential linked to the high content of phenols. This study confirmed the positive chemico-physical and functional properties of kombucha and indicated that the microflora responsible for the fermentation process can significantly affect the characteristics of the final product.
PubMed: 38928888
DOI: 10.3390/foods13121947 -
International Journal of Molecular... Jun 2024This study aimed to investigate the gut microbiota composition in children with autism spectrum disorder (ASD) compared to neurotypical (NT) children, with a focus on...
Comprehensive Analysis of Gut Microbiota Composition and Functional Metabolism in Children with Autism Spectrum Disorder and Neurotypical Children: Implications for Sex-Based Differences and Metabolic Dysregulation.
This study aimed to investigate the gut microbiota composition in children with autism spectrum disorder (ASD) compared to neurotypical (NT) children, with a focus on identifying potential differences in gut bacteria between these groups. The microbiota was analyzed through the massive sequencing of region V3-V4 of the 16S RNA gene, utilizing DNA extracted from stool samples of participants. Our findings revealed no significant differences in the dominant bacterial phyla (Firmicutes, Bacteroidota, Actinobacteria, Proteobacteria, Verrucomicrobiota) between the ASD and NT groups. However, at the genus level, notable disparities were observed in the abundance of , , , and , all of which have been previously associated with ASD. Furthermore, a sex-based analysis unveiled additional discrepancies in gut microbiota composition. Specifically, three genera (, , ) exhibited variations between male and female groups in both ASD and NT cohorts. Particularly noteworthy was the exclusive presence of in females with ASD. Analysis of predicted metabolic pathways suggested an enrichment of pathways related to amine and polyamine degradation, as well as amino acid degradation in the ASD group. Conversely, pathways implicated in carbohydrate biosynthesis, degradation, and fermentation were found to be underrepresented. Despite the limitations of our study, including a relatively small sample size (30 ASD and 31 NT children) and the utilization of predicted metabolic pathways derived from 16S RNA gene analysis rather than metagenome sequencing, our findings contribute to the growing body of evidence suggesting a potential association between gut microbiota composition and ASD. Future research endeavors should focus on validating these findings with larger sample sizes and exploring the functional significance of these microbial differences in ASD. Additionally, there is a critical need for further investigations to elucidate sex differences in gut microbiota composition and their potential implications for ASD pathology and treatment.
Topics: Humans; Gastrointestinal Microbiome; Autism Spectrum Disorder; Female; Male; Child; RNA, Ribosomal, 16S; Bacteria; Feces; Child, Preschool; Sex Factors; Sex Characteristics; Metabolic Networks and Pathways
PubMed: 38928411
DOI: 10.3390/ijms25126701 -
Antibiotics (Basel, Switzerland) Jun 2024Freshwater environments are primary receiving systems of wastewater and effluents, which carry low concentrations of antibiotics and antimicrobial-resistant (AMR)...
Freshwater environments are primary receiving systems of wastewater and effluents, which carry low concentrations of antibiotics and antimicrobial-resistant (AMR) bacteria and genes. Aquatic microbial communities are thus exposed to environmentally relevant concentrations of antibiotics (ERCA) that presumably influence the acquisition and spread of environmental AMR. Here, we analyzed ERCA exposure with and without the additional presence of municipal wastewater treatment plant effluent (W) and swine manure run-off (M) on aquatic biofilm resistomes. Microscopic analyses revealed decreased taxonomic diversity and biofilm structural integrity, while metagenomic analysis revealed an increased abundance of resistance, virulence, and mobile element-related genes at the highest ERCA exposure levels, with less notable impacts observed when solely exposed to W or M effluents. Microbial function predictions indicated increased gene abundance associated with energy and cell membrane metabolism and heavy metal resistance under ERCA conditions. In silico predictions of increased resistance mechanisms did not correlate with observed phenotypic resistance patterns when whole communities were exposed to antimicrobial susceptibility testing. This reveals important insight into the complexity of whole-community coordination of physical and genetic responses to selective pressures. Lastly, the environmental AMR risk assessment of metagenomic data revealed a higher risk score for biofilms grown at sub-MIC antibiotic conditions.
PubMed: 38927205
DOI: 10.3390/antibiotics13060539 -
Biomolecules Jun 2024A notable shift in understanding the human microbiome's influence on cardiovascular disease (CVD) is underway, although the causal association remains elusive. A... (Meta-Analysis)
Meta-Analysis Review
A notable shift in understanding the human microbiome's influence on cardiovascular disease (CVD) is underway, although the causal association remains elusive. A systematic review and meta-analysis were conducted to synthesise current knowledge on microbial taxonomy and metabolite variations between healthy controls (HCs) and those with CVD. An extensive search encompassing three databases identified 67 relevant studies (2012-2023) covering CVD pathologies from 4707 reports. Metagenomic and metabolomic data, both qualitative and quantitative, were obtained. Analysis revealed substantial variability in microbial alpha and beta diversities. Moreover, specific changes in bacterial populations were shown, including increased and and decreased in patients with CVD compared with HC. Additionally, elevated trimethylamine N-oxide levels were reported in CVD cases. Biochemical parameter analysis indicated increased fasting glucose and triglycerides and decreased total cholesterol and low- and high-density lipoprotein cholesterol levels in diseased individuals. This study revealed a significant relationship between certain bacterial species and CVD. Additionally, it has become clear that there are substantial inconsistencies in the methodologies employed and the reporting standards adhered to in various studies. Undoubtedly, standardising research methodologies and developing extensive guidelines for microbiome studies are crucial for advancing the field.
Topics: Gastrointestinal Microbiome; Humans; Cardiovascular Diseases; Bacteria; Methylamines
PubMed: 38927134
DOI: 10.3390/biom14060731