Gut microbiome (Cambridge, England)最新文献

Researchers have studied gut microbiota changes following bariatric surgery (BS), but not gut diversity and function in patients who fail to reduce weight. Stool samples were collected from three groups of women: 15 women who did not lose weight after BS ("Yes" group), 9 overweight women without surgery, and 8 slim women ("No" group). 16S ribosomal RNA gene sequencing and PICRUSt2 were used for the analysis. The surgery and control groups had equal alpha and beta diversity, perhaps due to the high proportion of overweight participants (n = 24). All groupings were dominated by Bacteroidota and Bacillota. Barnesiellaceae decreased with BS, although Streptococcaceae remained frequent in overweight people. The iron supplementation group had High abundance of Atopobiaceae and Prevotellaceae. Barnesiellaceae abundance was considerably lower in both surgical groups (with and without iron supplementation) than in the no-iron and no-surgery groups. The ornithine degradation and haem biosynthesis routes use different metabolites than the glycine super system. Finally, the "Yes" group significantly upregulated PWY0-1241, PWY-5177, and PWY-5855 signaling pathways. In conclusion, gut bacteria and metabolic functions may predict weight loss after surgery better than diversity markers. The requirement for orthogonal validation assays is suggested by pathway analysis outperforming diversity metrics.

Oral administration of omega-3 polyunsaturated fatty acids (PUFAs) to rodents and humans is associated with an increase in gut bacteria that are predicted to synthesise short-chain fatty acids (SCFAs). We tested the hypothesis that physiological levels of omega-3 PUFAs in the distal intestinal lumen (1-50 μg/mL) are associated with increased SCFA synthesis in an in vitro fermentation model using faecal slurry from 10 healthy participants (mean age 30 years), with and without exogenous dietary fibres. SCFAs were measured by gas chromatography-flame ionisation detection (n = 10), and changes in bacterial composition were analysed by shotgun metagenomic sequencing (n = 6). In the presence of omega-3 PUFAs, there was a mean 9.3% (no inulin; P = 0.03) and 19.3% (+ 0.01 mg/mL inulin; P = 0.01) increase in total SCFA concentration at 24 h compared with paired control fermentations. Omega-3 PUFAs had a limited effect on the fermentation model microbiome in the absence of inulin. However, omega-3 PUFAs (50 μg/mL) were associated with increased abundance of Bifidobacteriaceae compared with paired control fermentations, if inulin (0.01 mg/mL) was present. Prebiotic activity of omega-3 PUFAs drives SCFA synthesis in an in vitro colonic fermentation model and is augmented by the soluble fibre inulin.

Lacticaseibacillus rhamnosus may modulate stress-induced anxiety, yet animal evidence has not been systematically evaluated. Following PRISMA guidelines, PubMed, Embase, and Scopus were searched (2011-2024) for animal studies evaluating the role of L. rhamnosus in stress-induced anxiety. Primary outcomes were behavioural anxiety measures; secondary outcomes included neuroendocrine, immune, epithelial, and microbiota changes. Fifteen studies met the inclusion criteria. Species included mice (n=7), rats (n=5), and hens (n=3). Stress models comprised chronic unpredictable mild stress (n=8), social defeat (n=2), maternal separation (n=1), restraint stress (n=1), and severe feather-pecking (n=3). Common strains were JB-1 (n=8), HN001 (n=2), LGG (n=2), LR-32 (n=1), 4B15 (n=1), and LR3201 (n=1). Of the 15 studies, 12 reported significant anxiolytic effects, most frequently in the elevated plus maze (7/10) and open-field test (6/9). JB-1 showed the most consistent behavioural improvement (7/8 studies). Mechanistic findings were reported in subsets of studies: HPA axis modulation in 4/15, monoamine changes in 4/15, GABAergic effects in 4/15, immune/anti-inflammatory changes in 4/15, tight junction restoration in 2/15, and gut microbiota or SCFA-related changes in 7/15. L. rhamnosus, particularly strain JB-1, shows consistent anxiolytic effects and multiple putative mechanistic pathways, though more rigorous and standardised preclinical designs are needed.

Current efforts to reduce the incidence of non-communicable disease (NCD) are slow, but increasing evidence highlights the microbiome as a potential target for prevention. The majority of microbial development occurs in the first 1,000 days of life, presenting opportunities for strategic intervention to reduce the prevalence of future NCDs. In this review, we explore the social, structural, and political barriers that may hinder physiological gut microbial development in the first 1,000 days in the context of current scientific knowledge, focusing on nutritional factors in pregnancy, and during the exclusive breastfeeding and complementary feeding periods. We summarise emerging evidence and explore obstacles to nutritional choices affecting microbial development, and unpack the rhetoric that healthy eating to develop a microbiome that supports optimum health is an individual choice. As evidence on the role of the microbiome in health and disease grows, specific attention must be applied to existing social, structural, and political barriers that may hinder optimal microbial development. Addressing the role of corporate actors and social determinants influencing dietary choices and barriers surrounding breastfeeding must be prioritised, alongside efforts to advance basic scientific research. Until a wider public health perspective is taken, the success of interventions and recommendations will be limited.

[This corrects the article DOI: 10.1017/gmb.2025.10008.].

Microbial dysbiosis has been linked to environmental enteropathy (EE) and alterations in nutrient absorption; however, compositional modifications following exposure to supplementary nutrients are poorly understood. Here, we report the effect of amino acid and micronutrient supplementation on the gut microbiome of adults with EE. In the AMAZE trial, adults with EE were randomized to amino acids (AA) and/or micronutrients (MM) for 16 weeks in a 2 × 2 factorial design against placebo. Endoscopy was performed before and after intervention, during which duodenal aspirates were collected as well as fecal samples. 16S rRNA amplicon sequencing was performed on both these samples, and differences in bacterial community composition before and after interventions were investigated using differential abundance analysis, corrected using false discovery rate, plus alpha and beta diversity measurements. HIV seropositive participants exhibited lower alpha and beta diversity at baseline. AA and/or MM supplementation did not show significant changes in abundance or diversity of genera post-intervention compared to placebo. Micronutrient supplementation resulted in an increase in the pyruvate fermentation to acetone MetaCyc pathways compared to the placebo arm. This study provides insights into the responsiveness of the gut microbiome to micronutrient and amino acid supplementation in adults with EE.

Non-nutritive sweeteners (NNSs) are popular sugar substitutes, valued for their potential to reduce caloric intake and associated health risks. However, their long-term effects on the human gut microbiome remain debatable. This study investigates the impact of tagatose, allulose, Rebaudioside-A (Reb-A), and saccharin on quorum-sensing (QS)-regulated phenotypes and gene expression in QS biosensor model bacteria. It sheds light on their potential influence on the gut microbiome. Our study revealed diverse effects among the NNSs. Tagatose and allulose demonstrated QS phenotypic inhibition in Chromobacterium violaceum (≈50%) and Pseudomonas aeruginosa (20-50%) in a concentration-dependent manner. Additionally, tagatose and allulose decreased the P. aeruginosa lasI gene expression. Reb-A and saccharin presented a significant, however less prominent, phenotypic inhibition on C. violaceum (25-30%) and P. aeruginosa swarming motility (≈20%). Both NNSs decreased the expression of the lasI gene of P. aeruginosa. Molecular docking of QS regulatory proteins showed that saccharin and Reb-A have significantly higher binding affinity compared to allulose and tagatose, relative to native inducers. These results suggest the complex interactions mediated by NNSs in QS regulatory pathways. These findings provide valuable insights into the varied, species and dose-dependent effects of NNS on microbial communication, suggesting potential implications for the gut microbiome.

Decreased gut microbial diversity is associated with greater depression symptoms in adults. Findings on the relationship between the gut microbiome and depression or anxiety in children and adolescents are mixed, and evidence syntheses are needed. Seven databases were searched for peer-reviewed studies on the gut microbiome and internalizing symptoms, depression, or anxiety, in children and adolescents (<19 years). Random-effects meta-analyses of alpha diversity indices were performed. Youth advisors validated the research findings' relevance to their experiences and contributed to dissemination planning. Eight studies were included, representing 2,865 participants (mean age = 11.4 years, SD = 4.3). Study designs were cross-sectional (n = 5), longitudinal (n = 2), and interventional (n = 1). No association was found between alpha or beta diversity and internalizing problems, depression, or anxiety. Increased abundance of genera within phyla Bacillota (e.g., Fusicatenibacter) and Pseudomonadota (e.g., Escherichia), along with decreased abundance of other Bacillota genera (e.g., Faecalibacterium), were associated with depression and anxiety symptoms. This review identified preliminary associations between specific bacterial taxa and depression and anxiety in children and adolescents. Larger studies using comprehensive analytical approaches are needed to explore the role of the gut microbiome in the genesis and treatment of internalizing disorders.

The efficiency of polymerase chain reaction (PCR) decreases under suboptimal conditions, such as low template concentration combined with high concentrations of similar sequences. Under these circumstances, mis-priming can occur, leading to the generation of erroneous copies. Specifically, in 16S amplicon sequencing of human intestinal biopsy samples, host off-target sequences are frequently generated and subsequently sequenced, particularly when the commonly used V3-V4 primers are employed. This issue not only introduces errors in data interpretation but also results in the unnecessary consumption of sequencing depth. In response to this challenge, we analysed over 1,300 publicly available V3-V4 amplicon sequences related to the human colon, profiling the colon microbiota while elucidating the biases introduced by host off-targets. Briefly, our findings reveal that unaddressed host DNA contamination can lead to false bacterial identifications and obscure significant differences in microbiota composition. Furthermore, we identified human sequences on chromosomes 5, 11, and 17 as the main contributors to the majority of off-target sequences. Finally, we suggest practical approaches to mitigate this issue without altering the original protocol design, retaining the widely used V3-V4 primers. In particular, using a C3 spacer-modified nucleotide targeting the off-target sequence is here proposed as a promising strategy acting upstream of the off-target generation.

Dietary patterns enriched in fermentable fibre (such as inulin) and inorganic nitrate are linked to cardiovascular benefits, possibly mediated by gut microbiota-derived bioactive compounds including short-chain fatty acids (SCFAs) and nitric oxide (NO). However, the potential synergistic effects remain unclear. We conducted a randomised, double-blind, crossover study to investigate the acute effects of inulin (15 g; INU), nitrate (400 mg; NO₃ ^-), and their combination (INU + NO₃ ^-) on plasma nitrate and nitrite levels, SCFAs, and blood pressure (BP) in 20 adults. Plasma nitrate and nitrite were significantly elevated following INU + NO₃ ^- and NO₃ ^- compared to INU (p < 0.001). Plasma SCFAs were increased after INU + NO₃ ^- and INU, but the incremental AUC was not statistically significant, likely due to large inter-individual variability. No significant main effects were observed on BP; however, inverse correlations were identified between peak plasma nitrite and diastolic BP (r_s = -0.61, p = 0.004) and mean arterial pressure (MAP) (r_s = -0.59, p = 0.005) following INU + NO₃ ^-. Peak nitrate concentrations were inversely correlated with diastolic BP following NO₃ ^- (r_s = -0.47, p = 0.004). Co-supplementation with inulin and nitrate did not enhance plasma nitrate/nitrite or BP beyond nitrate alone but modulated SCFA profiles, suggesting potential interactions between fibre fermentation and nitrate metabolism for cardiovascular health.