Fermented dairy foods offer potential to improve gastrointestinal symptoms due to their functional characteristics (e.g., presence of potentially health-promoting microorganisms, and/or bioactives), which may improve quality of life (QoL). This study examined the effect of a Lactobacillus delbrueckii subsp. bulgaricus fermented skimmed milk powder (FSMP) on gastrointestinal health in healthy individuals with mild-to-moderate gastrointestinal symptoms. Subjects received 20 g/day of either the FSMP, skimmed milk powder (SMP), or maltodextrin for 8 weeks. QoL, faecal calprotectin, gut transit time, gas evacuations, stool consistency, dietary intake, and anthropometry were all assessed. Eighty-four participants (62% female, 34.9 ± 5.9 years) completed the trial. SMP improved anxiety (P = 0.015), discomfort (P = 0.002), and global (P = 0.010) domain scores vs. maltodextrin. Similarly, SMP improved discomfort (P = 0.007) and global (P = 0.023) domain score relative to FSMP. No other differences between groups post-intervention were observed (P > 0.05). Sub-analyses indicated those with more severe symptoms at baseline had more normal stool consistency (P = 0.016) and fewer gas evacuations (P = 0.008) in response to FSMP relative to maltodextrin. Overall, this exploratory analysis found an L. delbrueckii subsp. bulgaricus FSMP had limited effects on gastrointestinal health in this cohort.
Cellobiose, a β-(1 → 4)-linked disaccharide indigestible by humans, is a novel candidate prebiotic. Evidence from controlled human trials on its effects on the gut microbiota and metabolites remains limited. We conducted an exploratory randomised, double-blind, placebo-controlled trial in 37 healthy adults. Participants were allocated to three arms for 4 weeks, received 5 g/day and 10 g/day for cellobiose, oligofructose P95, or maltodextrin placebo. The primary endpoint was change in absolute abundance of Bifidobacterium and Lactobacillus (measured by 16S rRNA gene sequencing). Secondary endpoints included other taxa, diversity, faecal short-chain fatty acids (SCFAs) measured by gas chromatography-mass spectrometry and gastrointestinal (GI) tolerability. Cellobiose did not significantly change Bifidobacterium or Lactobacillus versus baseline or placebo (P > 0.05). Oligofructose P95 induced a borderline increase in Bifidobacterium (P = 0.049). Overall community composition remained unchanged. However, network analyses under cellobiose revealed tighter positive correlations among key genera. Faecal SCFA levels were not altered. GI symptom rates were low and similar across all arms. Cellobiose, at doses up to 10 g/day, is safe and well tolerated but did not enrich classic beneficial taxa. The findings suggest cellobiose drives subtle community shifts towards butyrate-producing bacteria.
Studies characterising the immunoglobulin (Ig)-bound microbiota apply varying methodologies, making comparisons difficult. This scoping review synthesised evidence on Ig-microbiota binding patterns in maternal and infant contexts, identified recurrent Ig-bound and -unbound bacteria across studies, and highlighted knowledge gaps for further study. Nine articles investigating Ig-microbiota binding patterns in stool or breastmilk samples in mothers or infants were included. Ig-microbiota associations were influenced by sample type, Ig-subclass, genetics, and diet. The most important antibody was IgA, with partial functional redundancy with IgM, while IgG appeared more selective for pathobionts. Ig-bound taxa in early life included important commensals and pathobionts, with high levels of individuality. Ig-microbiota associations shifted with microbiome maturation, environmental and host factors, resembling adults at around 2 years of age. Transfer of Ig-bound Bifidobacterium through breastmilk may contribute to vertical transmission from mother to infant. Ig-microbiota associations also differed between health and disease states, beyond the overall microbiota. Results were limited by study numbers and a lack of methodological consistency. We propose the standardised term "Ig-Seq" in referring to the technique to study Ig-microbiota binding patterns, and suggest standardisation of laboratory protocols, bioinformatic pipelines, and statistical analyses to improve consistency in Ig-Seq.
The aim of this study is to describe the development and implementation of a novel Readiness to Change Nutritional Habits (RCNH) survey for use along with dietary assessment and gut microbiome profiling in a proof-of-concept study in individuals with early Alzheimer's disease dementia (eAD), mild cognitive impairment (MCI), and healthy controls (HC). Overall, this methods paper contributes to emerging research examining how behavioural readiness for change can be integrated with dietary assessment and gut microbiome profiling to better understand the microbiome's influence on the nervous system. This is a sub-study embedded within a multi-prong proof-of-concept, observational study mapping the gut microbiome in 45 participants (15 HC, 15 MCI, 15 eAD) at baseline, 3 months, and 6 months. The parent study collects gut microbiome profiles, dietary patterns, and cognitive assessments. The sub-study develops and administers the 32-item RCNH survey to characterize participants' readiness to adopt nutritional change. This manuscript reports the RCNH survey, its development process, the sub-study protocol including data collection procedures, and planned exploratory analyses. This protocol presents a novel intervention to assess the gut microbiome, individual dietary patterns, and readiness to make lifestyle changes related to diet.
Effective strategies are needed to increase the healthy lifespan and prevent age-related diseases in aging populations. Using senescence marker protein 30 knockout (SMP30 KO) mice-models that mimic human vitamin C (vitC) deficiency and exhibit accelerated aging-we investigated the effects of bioactive ceramic processed water (BCP) compared to natural mineral water (MW) and MW supplemented with vitamin C (MW-vitC) on gut microbial communities and hepatic metabolism. Due to pooled fecal sampling (n=1 composite library per group), microbiome results represent descriptive trends in diversity and composition. BCP was associated with discernible shifts in gut microbiota, including increased abundances of beneficial genera, such as Akkermansia, Lactobacillus, and Allobaculum, and the Muribaculaceae family. PICRUSt2 functional analysis suggested an enrichment in secondary metabolite biosynthesis, vitamin (e.g., retinol) metabolism, and xenobiotic biodegradation pathways. Furthermore, BCP was associated with significantly higher levels of activated hepatic AMP-activated protein kinase (AMPK), a key energy metabolism regulator, compared to control groups. Although microbiome findings are descriptive due to the study design, these results suggest BCP as a potential dietary intervention to help mitigate age-related metabolic decline and promote healthy ageing.
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.
Blood pressure (BP) variability is an independent risk factor for cardiovascular disease. Gut microbiome (GM) regulates BP, but its association with BP variability remains unclear. We examined the association of GM, determined by stool shotgun metagenomic sequencing, with 24-hour BP average real variability (ARV) assessed by ambulatory BP monitoring in 235 community-dwelling adults from Hong Kong (111 men and 124 women, mean age 54 ± 6 years) using covariate-adjusted statistical models. The GM alpha diversity was negatively associated with systolic BP (SBP) ARV in the full cohort, driven by women. In men, beta diversity of both GM species and function was associated with SBP ARV, while Bacteroides nordii and the steroid hormone biosynthesis pathway had a positive association with SBP ARV. Bacteroides nordii emerged as the key species driving the significant positive association of steroid hormone biosynthesis and other pro-pathogenic pathways with SBP ARV, including lipopolysaccharide biosynthesis, phenylalanine, and sulfur metabolism in men, warranting further investigation for its causal role. We demonstrated distinct signatures of GM dysbiosis, composition, and function with minimal overlap between men and women with increased 24-hour SBP variability. Our work suggests that sex differences should be an important consideration in mechanistic and therapeutic investigations of GM-mediated BP variability.
B. infantis abundance in the infant gut may be associated with growth and health outcomes. However, these relationships have not been widely studied in settings where B. infantis is a dominant early-life commensal and growth faltering is prevalent. Here, we estimated associations between neonatal B. infantis abundance and anthropometric outcomes up to 6 months of age in generally healthy infants in Dhaka, Bangladesh; diarrhoea and hospitalizations (at 1-2 and 6 months) were secondary morbidity outcomes. B. infantis stool absolute abundance was quantified by qPCR; for each infant, the primary exposure was mean abundance (0-28 days). Length-for-age, weight-for-age, and weight-for-length z-scores were derived at birth, 2, 3, and 6 months. Neonatal B. infantis abundance had a bimodal distribution, with 63% of infants having detectable B. infantis by 28 days of age. Anthropometric z-score distributions were shifted down, with means below zero. Neonatal B. infantis abundance was not associated with any anthropometric outcome at 2, 3, or 6 months of age (n = 830), or with the risks of diarrhoea or hospitalizations. The lack of association of neonatal B. infantis abundance with growth outcomes suggests that promoting early B. infantis colonization is unlikely to improve growth in populations with postnatal faltering.
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.
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.
