Comparative analysis of gut microbiota in children with obstructive sleep apnea: assessing the efficacy of 16S rRNA gene sequencing in metabolic function prediction based on weight status.

Background: Analyzing bacterial microbiomes consistently using next-generation sequencing (NGS) is challenging due to the diversity of synthetic platforms for 16S rRNA genes and their analytical pipelines. This study compares the efficacy of full-length (V1-V9 hypervariable regions) and partial-length (V3-V4 hypervariable regions) sequencing of synthetic 16S rRNA genes from human gut microbiomes, with a focus on childhood obesity. Methods: In this observational and comparative study, we explored the differences between these two sequencing methods in taxonomic categorization and weight status prediction among twelve children with obstructive sleep apnea. Results: The full-length NGS method by Pacbio® identified 118 genera and 248 species in the V1-V9 regions, all with a 0% unclassified rate. In contrast, the partial-length NGS method by Illumina® detected 142 genera (with a 39% unclassified rate) and 6 species (with a 99% unclassified rate) in the V3-V4 regions. These approaches showed marked differences in gut microbiome composition and functional predictions. The full-length method distinguished between obese and non-obese children using the Firmicutes/Bacteroidetes ratio, a known obesity marker (p = 0.046), whereas the partial-length method was less conclusive (p = 0.075). Additionally, out of 73 metabolic pathways identified through full-length sequencing, 35 (48%) were associated with level 1 metabolism, compared to 28 of 61 pathways (46%) identified through the partial-length method. The full-length NGS also highlighted complex associations between body mass index z-score, three bacterial species (Bacteroides ovatus, Bifidobacterium pseudocatenulatum, and Streptococcus parasanguinis ATCC 15912), and 17 metabolic pathways. Both sequencing techniques revealed relationships between gut microbiota composition and OSA-related parameters, with full-length sequencing offering more comprehensive insights into associated metabolic pathways than the V3-V4 technique. Conclusion: These findings highlight disparities in NGS-based assessments, emphasizing the value of full-length NGS with amplicon sequence variant analysis for clinical gut microbiome research. They underscore the importance of considering methodological differences in future meta-analyses.

In vitro ruminal fermentation and cow-to-mouse fecal transplantations verify the inter-relationship of microbiome and metabolome biomarkers: potential to promote health in dairy cows.

Introduction: There are differences in the gut microbiome and metabolome when the host undergoes different physical or pathological conditions. However, the inter-relationship of microbiome and metabolome biomarkers to potentially promote the health of dairy cows needs to be studied. Further, the development of next-generation probiotics for dairy cattle health promotion has not been demonstrated. Objective: In the present study, we identified the microbiome and metabolome biomarkers associated with healthy cows. Methods: We analyzed the relationships of the ruminal microorganism profile and metabolites between healthy and mastitis lactating dairy cows. The roles of bacterial biomarker were further verified by in vitro fermentation and cow-to-mouse fecal microbiota transplantation (FMT). Results: Two species, Ruminococcus flavefaciens and Bifidobacterium longum subsp. longum, and six rumen metabolites were positively correlated with healthy cows by Spearman's correlation analysis. Through in vitro ruminal fermentation, inoculating R. flavefaciens and B. longum subsp. longum showed the upregulation of the levels of putrescine, xanthurenic acid, and pyridoxal in the mastitis ruminal fluid, which confirmed the inter-relationships between these microbiota and metabolites associated with healthy cows. Further, we verified the role of R. flavefaciens and B. longum subsp. longum in promoting health by FMT. The administration of R. flavefaciens and B. longum subsp. longum reduced the death rate and recovered the bodyweight loss of germ-free mice caused by FMT mastitis feces. Discussion: We provided evidence that the bacterial biomarkers alter downstream metabolites. This could indirectly indicate that the two bacterial biomarkers have the potential to be used as next-generation probiotics for dairy cattle, although it needs more evidence to support our hypothesis. Two species, R. flavefaciens and B. longum subsp. longum, with three metabolites, putrescine, xanthurenic acid, and pyridoxal, identified in the ruminal fluid, may point to a new health-promoting and disease-preventing approach for dairy cattle.

Microbial metabolites regulate social novelty via CaMKII neurons in the BNST.

Social novelty is a cognitive process that is essential for animals to interact strategically with conspecifics based on their prior experiences. The commensal microbiome in the gut modulates social behavior through various routes, including microbe-derived metabolite signaling. Short-chain fatty acids (SCFAs), metabolites derived from bacterial fermentation in the gastrointestinal tract, have been previously shown to impact host behavior. Herein, we demonstrate that the delivery of SCFAs directly into the brain disrupts social novelty through distinct neuronal populations. We are the first to observe that infusion of SCFAs into the lateral ventricle disrupted social novelty in microbiome-depleted mice without affecting brain inflammatory responses. The deficit in social novelty can be recapitulated by activating calcium/calmodulin-dependent protein kinase II (CaMKII)-labeled neurons in the bed nucleus of the stria terminalis (BNST). Conversely, chemogenetic silencing of the CaMKII-labeled neurons and pharmacological inhibition of fatty acid oxidation in the BNST reversed the SCFAs-induced deficit in social novelty. Our findings suggest that microbial metabolites impact social novelty through a distinct neuron population in the BNST.

Sarcopenia-related gut microbial changes are associated with the risk of complications in people with cirrhosis.

Background & Aims: Sarcopenia and gut dysbiosis are common in individuals with cirrhosis. However, the association between sarcopenia and microbial alterations, and the subsequent impact on cirrhotic outcomes are poorly understood. This study aimed to identify muscle-dependent microbial changes and related risks of cirrhotic complications. Methods: From September 2018 to December 2020, 89 individuals with cirrhosis and 16 healthy volunteers were prospectively enrolled. Muscle and nutritional status, serum amino acids, and fecal microbiota were analyzed. The association between microbial signatures of sarcopenia and cirrhotic complications was investigated. Results: A decline in muscle mass and strength were associated with gut microbial alterations in individuals with cirrhosis. The greatest microbial dissimilarity was observed between those with sarcopenia (both decline in muscle mass and strength) and those with normal-muscle status (p = 0.035). Individuals with sarcopenia had lower serum levels of alanine, valine, leucine, isoleucine, proline, tryptophan and ornithine. Besides, gut microbial functions associated with amino acid biosynthesis were significantly reduced in individuals with sarcopenia and cirrhosis. Depletion of Dialister, Ruminococcus 2, and Anaerostipes were associated with cirrhotic sarcopenia, and significantly correlated with the serum levels of amino acids. Individuals with coexistent depletion of Ruminococcus 2 and Anaerostipes developed more infectious (44.4% vs. 3.0%) and non-infectious (74.1% vs. 3.0%) complications, and more hospitalizations (54 vs. 3) than those with cirrhosis with good microbial signatures (all p <0.001). In contrast, fecal enrichment of Ruminococcus 2 and Anaerostipes independently decreased the risk of 1-year complications. Conclusions: Sarcopenia-related fecal microbial alterations are associated with cirrhotic complications. These findings may facilitate measures to improve the outcomes of individuals with cirrhosis and sarcopenia by modifying gut microbiota. Impact and implications: The composition and biosynthetic functions of gut microbiota are significantly changed in individuals with sarcopenic cirrhosis. Those with a sarcopenia-related poor microbial signature, in which Ruminococcus 2 and Anaerostipes were both depleted, had significantly more infectious and non-infectious complications, as well as more hospitalizations. These findings highlight the therapeutic potential of modifying the gut microbiota of individuals with sarcopenic cirrhosis to improve their clinical outcomes.

Gut microbiota and metabolites associate with outcomes of immune checkpoint inhibitor-treated unresectable hepatocellular carcinoma.

BACKGROUND: Immune checkpoint inhibitors (ICIs) are promising agents for unresectable hepatocellular carcinoma (uHCC), but lack effective biomarker to predict outcomes. The gut microbiome can modulate tumor response to immunotherapy, but its effect on HCC remains unclear. METHODS: From May 2018 to February 2020, patients receiving ICI treatment for uHCC were prospectively enrolled; their fecal samples were collected before treatment. The fecal microbiota and metabolites were analyzed from 20 patients with radiology-proven objective responses (OR) and 21 randomly selected patients with progressive disease (PD). After March 2020, 33 consecutive Child-Pugh-A patients were recruited as a validation cohort. Additionally, feces from 17 healthy volunteers were collected for comparison of background microbes. RESULTS: A significant dissimilarity was observed in fecal bacteria between patients with OR and patients with PD before immunotherapy. Prevotella 9 was enriched in patients with PD, whereas Lachnoclostridium, Lachnospiraceae, and Veillonella were predominant in patients with OR. Ursodeoxycholic acid and ursocholic acid were significantly enriched in the feces of patients with OR and strongly correlated with the abundance of Lachnoclostridium. The coexistence of Lachnoclostridium enrichment and Prevotella 9 depletion significantly predicted better overall survival (OS). In the validation cohort, better progression-free survival (PFS) and OS were noted in patients who had a preferable microbial signature in comparison with counter-group (PFS: 8.8 months vs 1.8 months; OS: not reached vs 6.5 months, both p<0.001). CONCLUSIONS: Fecal microbiota and bile acids were associated with outcomes of immunotherapy for uHCC. These findings highlight the potential role of gut microbiota and metabolites as biomarkers to predict outcomes of ICI-treated HCC.

Visualization and (Semi-)quantification of submicrometer plastics through scanning electron microscopy and time-of-flight secondary ion mass spectrometry.

Increasing numbers of studies have demonstrated the existence of nanoplastics (1-999 nm) in the environment and commercial products, but the current technologies for detecting and quantifying nanoplastics are still developing. Herein, we present a combination of two techniques, e.g., scanning electron microscopy (SEM) and time-of-flight secondary ion mass spectrometry (ToF-SIMS), to analyze submicron-sized plastics. A drop-casting of a 20-nL particle suspension on a Piranha solution-cleaned silicon wafer with dry ice incubation and subsequent freeze-drying was used to suppress the coffee-ring effect. SEM images were used to quantify particles, and this technique is applicable for 0.195-1.04-µm polystyrene (PS), 0.311-µm polyethylene terephthalate (PET), and 0.344-µm polyethylene (PE) at a minimum concentration of 2.49 × 109 particles/mL. ToF-SIMS could not quantify the particle number, while it could semi-quantitatively estimate number ratios of submicron PE, PET, polyvinyl chloride (PVC), and PS particles in the mixture. Analysis of submicron plastics released from three hot water-steeped teabags (respectively made of PET/PE, polylactic acid (PLA), and PET) was revisited. The SEM-derived sizes and particle numbers were comparable to those measured by a nanoparticle tracking analysis (NTA) regardless of whether or not the hydro-soluble oligomers were removed. ToF-SIMS further confirmed the number ratios of different particles from a PET/PE composite teabag leachate. This method shows potential for application in analyzing more-complex plastic particles released from food contact materials.

Extraction method development for nanoplastics from oyster and fish tissues.

Nanoplastics are now found in some environmental media and consumer products. However, very limited data on nanoplastics are available for one of the main human consumption sources of microplastics: seafood. Unlike microplastics, a method for extracting nanoplastics from seafood is still lacking. Herein, a combination of common extraction techniques including enzymatic digestion, sequential membrane filtration, centrifugal concentration, and purification (dialysis and sodium dodecylsulfate (SDS) incubation), was developed to extract nanoplastics from oyster and fish tissues. Corolase with subsequent lipase treatment achieved the highest digestion efficiencies (88- 89%) for non-homogenized tissues compared to other proteases and additional cellulase or H2O2 treatment. With the exception of polyethylene terephthalate (PET), enzymatic digestion did not change the morphology or structure of polyvinyl chloride (PVC), polyethylene (PE), or polystyrene (PS) nanoplastic particles, and the subsequent extraction procedures had good recoveries of 71- 110% for fluorescence-labeled 76-nm PVC and 100- and 750-nm PS, as validated by a Nanoparticle Tracking Analysis (NTA). Few of the 1011 digested residual particles of 150- 300 nm in diameter per oyster or per serving of fish tissue were left in the method blank. Consequently, this efficient approach could be used as a pretreatment protocol for current potential nanoplastic detection methods.

Two-dimensional intact mitochondrial DNA agarose electrophoresis reveals the structural complexity of the mammalian mitochondrial genome.

The mitochondrial genome exists in numerous structural conformations, complicating the study of mitochondrial DNA (mtDNA) metabolism. Here, we describe the development of 2D intact mtDNA agarose gel electrophoresis (2D-IMAGE) for the separation and detection of approximately two-dozen distinct topoisomers. Although the major topoisomers were well conserved across many cell and tissue types, unique differences in certain cells and tissues were also observed. RNase treatment revealed that partially hybridized RNAs associated primarily with covalently closed circular DNA, consistent with this structure being the template for transcription. Circular structures composed of RNA:DNA hybrids contained only heavy-strand DNA sequences, implicating them as lagging-strand replication intermediates. During recovery from replicative arrest, 2D-IMAGE showed changes in both template selection and replication products. These studies suggest that discrete topoisomers are associated with specific mtDNA-directed processes. Because of the increased resolution, 2D-IMAGE has the potential to identify novel mtDNA intermediates involved in replication or transcription, or pathology including oxidative linearization, deletions or depletion.

Gender-specific effects of caloric restriction on the balance of vascular nitric oxide and superoxide radical.

AIMS: Caloric restriction (CR) and female gender attenuate oxidative damage and improve vascular endothelium-dependent relaxation (EDR). Multiple mechanisms that ameliorate vascular O(2)(*-) could enhance the NO(*)/O(2)(*-) balance and thus improve EDR. The aim of this study is to compare the effects of short-term (2 weeks) CR and gender on molecular mechanisms involved in NO(*)/O(2)(*-) balance and EDR. METHODS AND RESULTS: Wistar rats (8 weeks old) of both genders were fed ad libitum (control) or were subjected to CR (60% of food intake of controls) for 2 weeks. Plasma levels of NO(*), insulin, and ghrelin, EDR, vascular NO(*) and O(2)(*-) production, as well as endothelial NO(*) synthase (eNOS) and NADPH oxidase (Nox) expression were examined and analysed. CR improved EDR and vascular NO(*) levels and ameliorated NADPH-sensitive O(2)(*-) production in male rats more than in females. Both CR and female gender reduced mRNA expression of Nox1 and Nox p22phox (p22phox); however, CR reduced Nox4 and p47phox only in males. Protein expression studies showed that CR enhanced eNOS and reduced Nox4 only in males. CONCLUSION: Short-term CR improved the NO(*)/O(2)(*-) balance by lowering vascular O(2)(*-) production through decreased expression of Nox in males, thus enhancing bioactive NO(*) levels and EDR. In this regard, CR shifted the state of vascular NO(*)/O(2)(*-) balance in males to a state similar to that in females.

Propylthiouracil, independent of its antithyroid effect, produces endothelium-dependent vasodilatation through induction of nitric oxide bioactivity.

OBJECTIVE: Propylthiouracil (PTU), independent of its antithyroid effect, is recently found to have a potent antiatherosclerotic effect. The aim of this study is to investigate whether PTU has a beneficial effect on endothelial function. METHODS AND RESULTS: Ninety patients with a history of hyperthyroidism receiving either PTU (n=45) or methimazole (MMI) (n=45) during the euthyroid status were enrolled in this study. Brachial artery endothelium-dependent (flow-mediated dilatation [FMD]) and endothelium-independent (nitroglycerin-mediated dilatation) responses were assessed by high-resolution ultrasound image. Data for these two groups were compared with those of 41 healthy control subjects. The FMD values were significantly increased in patients maintained on PTU versus those in the MMI and control groups (9.3+/-4.4%, 3.4+/-2.5%, and 3.6+/-3.4%, respectively; P<0.01). Nitroglycerin-mediated dilatation had no significant difference between the PTU, MMI, and control groups (17.4+/-7.5%, 15.9+/-6.1%, and 17.5+/-6.8%, respectively; P=0.455). On multivariate analysis, no significant relationship was found between the FMD and thyroid hormone index levels. To further elucidate whether PTU has a direct effect on endothelial function, the effect of PTU on isolated segments of Sprague-Dawley rat aorta was studied. Vasodilatation induced by PTU was endothelium-dependent and could be blocked by pretreatment with nitric oxide (NO) inhibitors. PTU also increased NO formation in aortic segments. CONCLUSIONS: This study demonstrated that PTU produced endothelium-dependent vasodilatation through thyroid-independent and NO-mediated mechanisms that may contribute to its beneficial effect on atherosclerosis.

Paraquat-induced lipid peroxidation: effects of ovariectomy and estrogen receptor antagonist.

Estrogen protects females against cardiovascular diseases in both receptor-dependent, genomic or non-genomic manner. Although part of the protective effects is attributed to its enhancement of nitric oxide (NO) production and antioxidant properties, in vivo evidence is difficult to establish. We thus employed paraquat (PQ)-treated rats as a model for oxidative stress and to compare oxidative damage determined by malondialdehyde (MDA) contents as index for lipid peroxidation of various tissues. Samples from aorta, lung, and liver exhibited low but detectable MDA level in intact control rats; sham operation did not but PQ-treatment significantly enhanced the MDA levels of all tissues. Different hormonal status were achieved by comparing sham-operated (sham), sham treated with estrogen receptor antagonist ICI182,780 (ICI), and ovariectomized (OVX) rats. OVX significantly reduced plasma estrogen level, ICI effectively blocked estrous cycle without reducing estrogen level. Derived from rats subjected to identical PQ treatment, MDA level was significantly higher in OVX rats than that of sham in isolated aortic rings. In lung tissues, MDA level were similar in all groups. In liver tissues, ICI rats exhibited higher level of MDA than both sham and OVX rats. These data indicated that hormonal status could affect the degree of lipid peroxidation under similar oxidative stress induced by PQ, and that not all tissues responded identically.