Characterising the gut microbiome of stranded harbour seals (Phoca vitulina) in rehabilitation

Animal rehabilitation centres provide a unique opportunity to study the microbiome of wild animals because subjects will be handled for their treatment and can therefore be sampled longitudinally. However, rehabilitation may have unintended consequences on the animals' microbiome because of a less varied and suboptimal diet, possible medical treatment and exposure to a different environment and human handlers. Our study describes the gut microbiome of two large seal cohorts, 50 pups (0-30 days old at arrival) and 23 weaners (more than 60 days old at arrival) of stranded harbour seals admitted for rehabilitation at the Sealcentre Pieterburen in the Netherlands, and the effect of rehabilitation on it. Faecal samples were collected from all seals at arrival, two times during rehabilitation and before release. Only seals that did not receive antimicrobial treatment were included in the study. The average time in rehabilitation was 95 days for the pups and 63 days for the weaners. We observed that during rehabilitation, there was an increase in the relative abundance of some of the Campylobacterota spp and Actinobacteriota spp. The alpha diversity of the pups' microbiome increased significantly during their rehabilitation (p-value <0.05), while there were no significant changes in alpha diversity over time for weaners. We hypothesize that aging is the main reason for the observed changes in the pups' microbiome. At release, the sex of a seal pup was significantly associated with the microbiome's alpha (i.e., Shannon diversity was higher for male pups, p-value <0.001) and beta diversity (p-value 0.001). For weaners, variation in the microbiome composition (beta diversity) at release was partly explained by sex and age of the seal (p-values 0.002 and 0.003 respectively). We mainly observed variables known to change the gut microbiome composition (e.g., age and sex) and conclude that rehabilitation in itself had only minor effects on the gut microbiome of seal pups and seal weaners.

Recent human and animal studies have found associations between gut microbiota composition and serum levels of sex hormones, indicating that they could be an important factor in shaping the microbiota. However, little is known about the effect of regular hormonal fluctuations over the menstrual cycle or CHC-related changes of hormone levels on gut microbiota structure, diversity and dynamics. The aim of this study was to investigate the effect of CHCs on human gut microbiota composition. The effect of CHC pill intake on gut microbiota composition was studied in a group of 7 healthy pre-menopausal women using the CHC pill, compared to the control group of 9 age-matched healthy women that have not used hormonal contraceptives in the six months prior the start of the study. By analyzing the gut microbiota composition in both groups during one menstrual cycle, we found that CHC usage is associated with a minor decrease in gut microbiota diversity and differences in the abundance of several bacterial taxa. These results call for further investigation of the mechanisms underlying hormonal and hormonal contraceptive-related changes of the gut microbiota and the potential implications of these changes for women's health. This article is protected by copyright. All rights reserved.

Simple SummaryVegetation composition and plant diversity of mixed deciduous forests in Europe is strongly linked with the dynamics of the forest stand and/or the regimes of forest management. In this work, we showed the influence of temporal interactions among the changes in the management system—the dominant development stage—the intensity of forest treatments, and herbaceous plant diversity. We argued that different arrangements of these interactions will result in different patterns of change in herbaceous plant diversity. We emphasized the need for careful interpretation of the levels of diversity (α, β) to evaluate the conservation status of forests.In recent years, there has been a growing awareness of the complex dependence of herbaceous plant diversity on forest structure and management. However, among the studies presented so far, those in which the chronosequence (approach based on the assumption of space-for-time substitution) was used, dominate. On the other hand, it is rare to find results based on long-term research on permanent or semi-permanent sampling plots. The aim of this study was to recognize the changes in the vegetation composition and dynamics of various indices of herbaceous plant diversity over 40 years of forest development, and their dependence on forest structure and management. Here we analyzed the temporal dynamics of herbaceous plant diversity in Carpathian fertile beech forests, based on datasets recorded on semi-permanent plots in three censuses (the 1970s, 2000s and 2010s). We checked the temporal changes in alpha, beta, and gamma diversity. Analyses of the plant diversity were performed on the background of changes in forest structure and management systems. We found that the within-plot (alfa diversity) and between-plot (beta diversity) herbaceous plant diversity metrics showed inconsistent patterns along with changes in the forest structure, management systems, and intensity of forest management, during the last 40 years. Temporal changes in the gamma diversity followed the changes in alpha diversity. Although the beta diversity after 40 years is greater than in the past, we argue that the conservation status of habitats typical for well-preserved fertile mountain beech forests has deteriorated due to a decline in the sharing of the diagnostic species of these forests. We showed the importance of the different temporal interactions between the forest structure and management for herbaceous plant diversity. We argue that, in view of the complexity of these processes, it would be a mistake to reject or prioritize alpha or beta diversity measurements to determine the real course of long-term changes in herbaceous plant diversity and to properly assess the state of the forest biodiversity, their conservation status, or conservation action plans. In addition, we need far more data from long-term observations to fully understand the possible relationship patterns between the factors controlling the forest structure and plant diversity.

To prospectively explore the association of maternal serum 25(OH)D levels with the infant's gut microbiota in Chinese populations, and to evaluate its potential influence on the dynamic change patterns of offspring's gut microbiota from 1 to 6 months old. Eighty-seven mother-infant dyads (vitamin D insufficient group vs. normal group = 59 vs. 28) were included in this longitudinal study. Two fecal samples were collected for the included infant at home by the parents at 1 month of age ("M1 phase") and 6 months of age ("M6 phase"). Gut microbiota were profiled by 16S rRNA gene sequencing. We performed mixed effects models on alpha diversity metrics, PERMANOVA tests on beta diversity distances, and linear discriminant analysis (LDA) to identify differently abundant taxa. We observed significantly lower Pielou's evenness and Shannon diversity in the vitamin D insufficient group in the M6 phase (p = 0.049 and 0.015, respectively), but not in the M1 phase (p > 0.05), and the dynamic changes in alpha diversity from 1 to 6 months old were significantly different according to maternal vitamin D status (p < 0.05). There were also significant differences in gut microbiota composition between the vitamin D insufficient group and normal group, both in the M1 and M6 phases (LDA score > 2.0, p < 0.05). Moreover, among the predicted metagenome functions, pathways related to amino acid biosynthesis, starch degradation, and purine nucleotides biosynthesis were enriched in the vitamin D insufficient group. Our findings highlight that maternal vitamin D status plays a pivotal role in shaping the early-life gut microbiota of the next generation.

The combination of meglumine antimoniate and allopurinol is considered one of the most effective treatments for canine leishmaniosis caused by Leishmania infantum. This study investigated the effects of this treatment on the gut microbiome of 10 dogs from Spain, Portugal, and Italy via fecal shotgun metagenomic sequencing over six months. Dogs were sampled at baseline (BL), after one month of combined treatment with meglumine antimoniate and allopurinol (M1) and after six months of allopurinol treatment (M6). Fecal samples had their total DNA extracted and sequenced by Illumina sequencing. Posteriorly, a microbiome analysis was conducted to analyze bacterial abundance, diversity and enrichment. The gut microbiome of Leishmania-infected dogs (BL) is dominated by Prevotella, Collinsella, Bacteroides, and Blautia, with individual variability being the primary determinant of microbiome composition. No significant changes in alpha diversity (Shannon index, gene number) or beta diversity (Bray-Curtis dissimilarity, UniFrac distance) were detected between pre- and post-treatment time points, suggesting that treatment with meglumine antimoniate and allopurinol does not disrupt the gut microbiota. Minor trends in taxonomic shifts were noted, with slight increases in Bifidobacterium pseudocantenulatum, Collinsella tanakaei, and Slackia piriformis after treatment, but these changes were not statistically significant after correction for multiple testing. Linear discriminant analysis and multivariable modeling confirmed that the microbial community structure was resilient to treatment effects. Individual-specific microbiome differences in diversity accounted for 52% of the observed variability, underscoring the personalized nature of the gut microbiota in dogs. Importantly, no adverse microbiome disruptions were detected, even with prolonged allopurinol use. This study highlights the robustness of the canine gut microbiome during antileishmanial therapy and highlights the use of meglumine antimoniate and allopurinol without compromising gut microbial diversity or health. Further studies with larger cohorts are recommended to confirm these findings and explore the functional roles of the gut microbiota in modulating immune responses in Leishmania-infected dogs.

Cystic fibrosis (CF) is frequently associated with gastrointestinal problems, including intestinal microbiota dysbiosis. Cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies, such as elexacaftor-tezacaftor-ivacaftor (ELX/TEZ/IVA), have demonstrated improvements in lung function, abdominal symptoms, and quality of life in patients with CF. However, the impact of these modulators on the intestinal microbiota in the pediatric population remains incompletely understood. The objective of this study was to characterize the changes in the intestinal microbiota of pediatric patients with CF after 6 months of treatment with ELX/TEZ/IVA. Thirty-one patients with CF, aged 6-18 years, were recruited. Stool samples were collected before the initiation of treatment and approximately 6 months thereafter. Microbiota analysis was performed using 16S rRNA gene amplicon sequencing. Statistical analyses were employed to evaluate changes in alpha and beta diversity and variations in the relative abundance of different bacterial taxa. Clinical variables such as concomitant use of azithromycin and probiotics were considered. After 6 months of treatment, no significant changes in the alpha diversity were observed. However, alterations in bacterial composition were detected. A decrease in the abundance of potentially pathogenic bacteria, such as Enterobacteriaceae members (Escherichia/Shigella) was observed. The abundance of genus Blautia increased. Differential analysis according to antibiotic and probiotic consumption revealed specific changes in microbiota composition. ELX/TEZ/IVA therapy for 6 months induces changes in the intestinal microbiota composition of pediatric patients with CF, characterized by a reduction in potentially harmful bacteria and an increase in potentially beneficial bacteria. These findings suggest a modulation towards a healthier intestinal microbiota profile.

Background: Autism Spectrum Disorder (ASD) is increasingly associated with alterations in gut microbiota, intestinal permeability, and immune dysregulation. However, integrative studies exploring these mechanisms in Latin American populations are lacking. Objective: To characterize gut microbiota profiles in Colombian children with ASD and evaluate the effects of two microbiota-targeted interventions, an anti-inflammatory diet and a probiotic formulation, on microbial diversity and taxonomic composition. Methods: In a two-phase study, shotgun metagenomic sequencing was performed on fecal samples from 23 children with ASD and 7 typically developing (TD) controls. In the second phase, 17 children with ASD were randomized to receive a 12-week intervention (anti-inflammatory diet, probiotics, or no intervention). Alpha diversity indices (Shannon, Pielou, and Chao1) and differential abundance analyses were conducted. Results: Compared to TD children, those with ASD showed a higher Firmicutes/Bacteroidetes ratio and a significantly increased abundance of genera such as Clostridioides, Thomasclavelia, Alistipes, and Coprococcus. The presence of functional gastrointestinal disorders (FGIDs) in ASD patients is associated with reduced microbial richness. POST-intervention, the anti-inflammatory diet group showed that no statistically significant changes in alpha diversity were observed, although a slight upward trend was noted and significant enrichment of six bacterial genera, including Moraxella and Eubacterium. The probiotic group exhibited a significant increase in Romboutsia and a decrease in Lachnospira. Cytokine–microbiota networks in ASD were fragmented and dominated by IFN-γ and MCP-1 hubs, indicating systemic immune activation. Interventions induced functional remodeling: The anti-inflammatory diet increased the number of beneficial genera (Eubacterium, Adlercreutzia) and shifted networks toward positive correlations involving IL-8 and MIP-1β. Probiotics increased Romboutsia, reduced Lachnospira, and restructured networks with regulatory cytokines (SDF-1α, Eotaxin) and SCFA-producing taxa (Blautia, Roseburia). Conclusions: Children with ASD in Colombia displayed distinct microbial profiles characterized by pro-inflammatory taxa and altered richness. Both the anti-inflammatory diet and probiotics produced compositional shifts in the gut microbiota, although global changes in diversity were limited. These findings support the potential of microbiota-targeted nutritional strategies for ASD and underscore the need for precision interventions tailored to specific clinical and microbial phenotypes.

Introduction. Many studies have evaluated the relationship between diabetes and microbiota. In animal models, the dipeptidyl peptidase-4 inhibitors altered the gut microbiota. We investigated whether linagliptin alters the gastrointestinal flora in humans. Materials and methods. This prospective cohort study enrolled 24 patients: 5 patients with maturity onset diabetes of the young associated with HNF1A mutation and 19 patients with type 2 diabetes mellitus. Stool samples were collected at baseline and 4 weeks after treatment intensification with either linagliptin or a sulphonylurea alongside current treatment. Faecal 16S rRNA was analysed by next-generation sequencing. Results. Nine patients initiated linagliptin whereas 15 patients initiated or increased the dose of a sulphonylurea. After linagliptin treatment, we did not observe changes in taxa in L2–L7 based on analysis of composition of microbiomes (ANCOM). The same held true for pairwise alpha diversity (Shannon diversity, p = 0.59; Pielou’s measure of evenness, p = 0.68; and observed operational taxonomic units [OTUs], p = 0.77) and beta diversity distances (unweighted UniFrac, p = 0.99; weighted UniFrac, p = 0.93; Bray-Curtis, p = 0.98; and Jaccard, p = 0.99). Similarly, after sulphonylurea intensification, we did not observe changes in taxa in L2–L7 in ANCOM, nor were there changes in alpha diversity (Shannon diversity, p = 0.19; Pielou’s measure of evenness, p = 0.21; and observed OTUs, p = 0.42) or beta diversity distances (unweighted UniFrac, p = 0.99; weighted UniFrac, p = 0.99; Bray-Curtis, p = 1; and Jaccard, p = 0.99). Conclusion. We did not observe changes in colonic microbiota 4 weeks after addition of linagliptin to current diabetes treatment. Further studies are required to determine whether linagliptin influences the colonic microbiota in humans.

ObjectivesAnkylosing Spondylitis (AS) is a chronic inflammatory disorder that primarily affects the spine and pelvis. Here, we aim to explore the Gut-Joint Axis in AS with a focus on changes in alpha diversity (diversity within a single sample) and beta diversity (differences in microbiota composition between samples) following Anti-TNF treatment.MethodsA comprehensive search of PubMed, Web of Science, Scopus, Embase, and Cochrane databases was conducted up to May 2024. Studies comparing fecal microbiota composition in AS patients before and after Anti-TNF therapy were identified and selected based on PRISMA guidelines. From an initial pool of 1,163 studies, 5 met inclusion criteria, involving 230 AS patients and 209 healthy controls (HC). We excluded duplicates, animal studies, case reports, conference abstracts, non-English articles, irrelevant studies, non-full-text manuscripts, and Mendelian randomization studies, as these do not provide direct observational data on microbiota composition and could introduce methodological heterogeneity.ResultsAfter manually screening 197 studies, 5 manuscripts were included, comprising 4 prospective cohorts and 1 case-control study. All the studies were conducted in China, with 16S rRNA sequencing used in 3 studies and Shotgun sequencing in 2 studies. None of the patients or controls in the included studies received antibiotics within the 3 months prior to enrollment. Across multiple studies, Anti-TNF therapy significantly impacts gut microbiota composition in AS patients, often shifting it toward a pattern more similar to healthy controls. Both alpha and beta diversity metrics show that AS patients have distinct gut microbiota compositions compared to healthy individuals, but Anti-TNF therapy appears to reduce these differences, suggesting a restorative effect on the microbiome (Table 1).ConclusionOur analysis underscores the potential role of gut microbiota as a target in AS treatment. The effect of Anti-TNF therapy on gut microbiota could potentially contribute to its therapeutic efficacy in managing Ankylosing Spondylitis.

Changes in Gut Microbial Diversity and Correlations with Clinical Outcomes in Patients with Newly Diagnosed Acute Myeloid Leukemia (AML) Receiving Intensive Chemotherapy

Background: It has been shown that gut microbiota dysbiosis may induce intestinal permeability, and systemic inflammation, leading to metabolic dysregulation. Furthermore, it has been implicated in the etiology of obesity. Dietary intake is known to affect the gut microbiota. These RCTs suggested that different dietary interventions may exhibit different effects on the composition of gut microbiota in overweight or obese individuals.Objectives: This systematic review aimed to determine the effect of dietary intervention on the gut microbiota profiles in overweight or obese adults. The primary outcome of this systematic review is alpha-beta diversity and its changes at the species level.Materials and Methods: This systematic review followed the PRISMA guidelines and was registered in the PROSPERO database with registration number CRD42022298891. A systematic search was conducted through the databases PubMed, MEDLINE, CINAHL, and Scopus literature using the terms: “gut microbiota”,“microbiome”,“overweight”,“obesity”, “insulin sensitivity”,“insulin resistance”,“blood glucose”,“randomized controlled trial”. After screening abstracts and full texts, 18 articles were extracted by two authors.Results: Among the 18 RCT studies, dietary intervention gave an impact on gut microbiota alpha diversity changes in four studies. However, 7 studies showed no significant changes or differences compared to the placebo group. Beta diversity analysis was reported in 7 among 11 studies that performed alpha diversity analysis. Significant changes were found in food nutrients group (fiber supplementation) studies conducted over 8-12 weeks period. Seven more studies did not report any analysis of variance in either alpha or beta diversity. Changes in the composition of gut microbiota could be observed in dietary pattern interventions and resulting in improved metabolic status, except in the fried meat group diet. Interventions with food groups, food nutrients, and probiotics did not change the composition of gut microbiota.Conclusion: The effects of dietary interventions on alpha-beta diversity are inconsistent, but rather showed more consistent effects on the changes in microbiota composition, especially in dietary pattern interventions.

The gut microbiota plays a crucial role in host physiology and the disruption of host–microbiota relationships caused by environmental stressors can impact host growth and survival. In this study, we used Daphnia galeata as a model organism to investigate the interactive effects of fish kairomones on the life-history traits and gut microbiota alterations of D. galeata, as well as the relationship between life-history traits and gut microbiota composition. The presence of fish kairomones enhanced fecundity, decreased growth, and altered gut microbiota, with significant changes in alpha diversity but not in beta diversity in the genotype KB5 of D. galeata. Statistical analysis revealed that the relative abundance of the Pseudomonadaceae family significantly increased upon exposure to fish kairomone, while the relative abundance of the Comamonadaceae family significantly decreased. The decreased growth in genotype KB5 may be associated with a significant increase in Pseudomonas, a member of the family Pseudomonadaceae, which is generally deficient in essential fatty acids, potentially negatively impacting growth. Meanwhile, it is speculated that the significant decrease in Limnohabitans belonging to the Comamonadaceae family is associated with the reduction of body size and increased fecundity of KB5 when exposed to fish kairomones. Furthermore, the genus Candidatus Protochlamydia was observed only under the fish kairomones-treated condition. These data suggest that variations in host life-history traits related to reproduction and growth are potentially associated with the relative abundance or presence of these microbial genera. Our research findings provide valuable insights into understanding the impact of biotic stress on the interaction between hosts and microbiota.

Changes in diet and lifestyle factors are frequently recommended for persons with irritable bowel syndrome (IBS). It is unknown whether these recommendations alter the gut microbiome and/or whether baseline microbiome predicts improvement in symptoms and quality of life following treatment. Therefore, the purpose of this study was to explore if baseline gut microbiome composition predicted response to a Comprehensive Self-Management (CSM) intervention and if the intervention resulted in a different gut microbiome composition compared to usual care. Individuals aged 18-70 years with IBS symptoms ≥6 months were recruited using convenience sampling. Individuals were excluded if medication use or comorbidities would influence symptoms or microbiome. Participants completed a baseline assessment and were randomized into the eight-session CSM intervention which included dietary education and cognitive behavioral therapy versus usual care. Questionnaires included demographics, quality of life, and symptom diaries. Fecal samples were collected at baseline and 3-month post-randomization for 16S rRNA-based microbiome analysis. Within the CSM intervention group (n = 30), Shannon diversity, richness, and beta diversity measures at baseline did not predict benefit from the CSM intervention at 3 months, as measured by change in abdominal pain and quality of life. Based on both alpha and beta diversity, the change from baseline to follow-up microbiome bacterial taxa did not differ between CSM (n = 25) and usual care (n = 25). Baseline microbiome does not predict symptom improvement with CSM intervention. We do not find evidence that the CSM intervention influences gut microbiome diversity or composition over the course of 3 months.

Background: Early time-restricted eating combined with energy restriction (eTRE + ER) has been shown to reduce fat mass, diastolic blood pressure (DBP) and fasting glucose more effectively than late TRE with energy restriction (lTRE + ER) or energy restriction (ER) alone. Given the gut microbiome’s sensitivity to circadian rhythms, we examined whether adding TRE, particularly eTRE, to ER alters gut microbiota composition beyond ER alone, and whether such effects persist during follow-up. Methods: We analysed anthropometric, biochemical and gut microbiome data from 76 participants at baseline and after a 3-month intervention (eTRE + ER: n = 33; lTRE + ER: n = 23; ER: n = 20). Follow-up microbiome data 6-months after the end of intervention were available for 43 participants. Gut microbiota composition was assessed via 16S rRNA gene sequencing of stool samples. Results: No significant between-group differences in beta diversity were observed over time. However, changes in alpha diversity differed significantly across groups at the end of the intervention (Shannon: F = 5.72, p < 0.001; Simpson: F = 6.72, p < 0.001; Richness: F = 3.99, p = 0.01) and at follow-up (Richness: F = 3.77, p = 0.02). lTRE + ER led to the greatest reductions in diversity post intervention, while ER was least favourable during follow-up. Although no significant between-group differences were observed at the phylum level either at the end of the intervention or during follow-up, only the eTRE + ER group exhibited a significant decrease in Bacillota and an increase in Bacteroidota during follow-up. At the genus level, differential abundance analysis revealed significant shifts in taxa such as Faecalibacterium, Subdoligranulum, and other genera within the Ruminococcaceae and Oscillospiraceae families. In the eTRE + ER, Faecalibacterium and Subdoligranulum increased, while in other groups decreased. Notably, the changes in Faecalibacterium were negatively correlated with fasting glucose, while the increase in Subdoligranulum was inversely associated with DBP; however, both associations were weak in strength. Conclusions: eTRE + ER may promote beneficial, lasting shifts in the gut microbiome associated with improved metabolic outcomes. These results support further research into personalized TRE strategies for treatment of obesity.

This study aimed to evaluate whether postpartum maternal stress is associated with infant gastrointestinal microbiome composition and diversity, and whether this relationship may be mediated by maternal caregiving and breastfeeding behaviors and human milk microbiome (HMM) composition. Infant fecal and human milk samples were collected from 51 exclusively breastfeeding mother-infant dyads in the Pacific Northwest between 1 and 6 months postpartum. Infant fecal samples with sequencing read counts > 773 (n = 48) and milk samples with read counts > 200 (n = 46) were analyzed for bacterial alpha diversity (richness, Shannon diversity), beta diversity (Bray-Curtis dissimilarity), and genera differential abundances. Infant fecal microbiome (IFM) measures were tested for associations with mothers' self-reported Parenting Stress Index total and subscale scores in regression (richness, Shannon diversity), envfit (beta diversity), and MaAsLin2 (genera abundance) models. Potential mediators of the relationship between maternal stress and IFM were explored (observed total time breastfeeding; maternal-infant physical contact frequency; and HMM alpha diversity, beta diversity, and genera abundance). Maternal stress was not associated with IFM alpha or beta diversities. Two maternal stress subscales were associated with differential abundances of Erysipelotrichaceae UCG-003 (positively) and Eggerthella (negatively) in infant feces. Maternal total stress and two stress subscales (Role Restriction, Attachment) were associated positively with HMM beta diversity (qattachment = 0.07) and negatively with HMM richness (qtotal = 0.08, qrole = 0.03). Postpartum stress is not consistently associated with IFM composition during exclusive breastfeeding. However, postpartum maternal stress is associated with HMM diversity, suggesting that maternal stress might influence other developmental pathways in the breastfeeding infant.