Gut microbiota composition and variation in Baduy infants living traditional lifestyles in Banten, Indonesia

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.

The colonization characteristics of infant gut microbiota are influenced by many factors at various stages, but few studies have explored the longitudinal effects of environmental tobacco smoke exposure and quantitative breastfeeding duration on young children' gut microbiota. We explored the effects of smoke exposure and breastfeeding duration on gut microbiota by following 37 maternal and children pairs in China for 2 years. We collected the demographic information, frequency of smoke exposure, breastfeeding duration, and fecal samples (mothers in the late pregnancy and infants at 6, 12, and 24 months), and analyzed the microbiota results using the V3-V4 gene sequence of 16S rRNA. The diversity of gut microbiota in children was the highest at 24 months and most similar to that in mothers. Breastfeeding duration was positively correlated with Lactobacillus and negatively correlated with Clostridium_sensu_stricto_1. The α diversity of microbiota and the relative abundance of [Ruminococcus]_gnavus_group was higher in the non-smoke exposed group. The higher the smoke exposure, the higher the relative abundance of Megasphaera. Prolonged breastfeeding and reduced smoke exposure are beneficial to the diversity and composition of gut microbiota in young children.

Natural environments in the urban context and gut microbiota in infants

Background Literature has highlighted the gut microbiota’s role in metabolic functions, suggesting a potential link between gut microbiota composition and T2DM. The purpose of the study was to identify microbial signatures unique to T2DM patients and non-diabetic individuals, to compare microbial profiles between the two groups and to investigate how gut microbiota may be related to inflammation associated with T2DM. Methods A cross-sectional study was conducted involving 51 T2DM patients and 99 non-diabetic South African individuals. Faecal samples were collected and analysed using 16S rRNA gene sequencing to characterize the gut microbiota. Blood samples were obtained to perform HbA1c, CRP and ferritin tests. Bioinformatic and statistical analyses were performed to identify differences in microbial composition and diversity between the two groups. Results The gut microbiota in T2DM patients was predominantly composed of Firmicutes (47.7%), Bacteroidota (37.5%), and Proteobacteria (11.4%), while the non-diabetic group showed a slightly different microbial profile with higher Bacteroidota (41.9%) and a notable presence of Actinobacteriota (4.5%). Abundant families in the T2DM group included Bacteroidaceae (22.8%), Prevotellaceae (7.4%), Enterobacteriaceae (7.4%), Erysipelotrichaceae (6.0%) and Lachnospiraceae (5.2%). The non-diabetic group exhibited dominant families such as Lachnospiraceae 26.7%, Prevotellaceae (25.3%), Bacteroidaceae (12.7%), Ruminococcaceae (9.5%) and Oscillospiraceae (3.8%). At the genus level, Bacteroides (22.8%), Escherichia-Shigella (5.0%), Holdemanella (4.8%), Phascolarctobacterium (3.2%) and Blautia (2.8%) were prevalent in the T2DM group, while Prevotella_9 (22.1%), Bacteroides (12.7%), Agathobacter (6.7%), Blautia (6.3%) and Faecalibacterium (5.1%) were dominant in the non-diabetic group. Differential abundance testing revealed 5 phyla, 16 families, and 25 genera that were either enriched/depleted in T2DM patients relative to non-diabetic individuals. The comparison of alpha diversity metrics between the two groups revealed significant differences across all four measures (P < 0.001), with non-diabetic individuals showing higher values than T2DM patients. HbA1c and CRP levels showed correlations with the relative abundance of various gut microbes at various phyla, family, and genus levels, as well as with all alpha diversity metrics. Conclusion The study revealed distinct differences in gut microbiota composition between T2DM patients and non-diabetic individuals, with T2DM patients showing a higher prevalence of certain phyla, families, and genera linked to metabolic dysregulation. Non-diabetic individuals exhibited greater microbial diversity and beneficial taxa, highlighting a potential protective microbial profile.

Gut microbiota play a role in certain pain states. Hence, these microbiota also influence somatic pain. We aimed to determine if there was an association between gut microbiota (composition and diversity) and postoperative pain. Patients (n = 20) undergoing surgical fixation of distal radius fracture under axillary brachial plexus block were studied. Gut microbiota diversity and abundance were analysed for association with: (i) a verbal pain rating scale of < 4/10 throughout the first 24 h after surgery (ii) a level of pain deemed “acceptable” by the patient during the first 24 h following surgery (iii) a maximum self-reported pain score during the first 24 h postoperatively and (iv) analgesic consumption during the first postoperative week. Analgesic consumption was inversely correlated with the Shannon index of alpha diversity. There were also significant differences, at the genus level (including Lachnospira), with respect to pain being “not acceptable” at 24 h postoperatively. Porphyromonas was more abundant in the group reporting an acceptable pain level at 24 h. An inverse correlation was noted between abundance of Collinsella and maximum self-reported pain score with movement. We have demonstrated for the first time that postoperative pain is associated with gut microbiota composition and diversity. Further work on the relationship between the gut microbiome and somatic pain may offer new therapeutic targets.

Investigate the diversity of the gut microbiota in children with peanut allergies and assess its association with allergic reactions. Identify potential gut microbial biomarkers for the diagnosis and treatment of peanut allergies. Twenty-nine children with peanut allergy who visited the hospital from December 2020 to December 2022 were selected as the test group (PA), and twenty-seven healthy children who underwent physical examination during the same period and tested negative for peanut IgE were selected as the control group (Ctl). The differences in gut microbiota between the two groups were compared. The study enrolled 29 children with peanut allergy (PA group) and 27 healthy children (Ctl group) from December 2020 to December 2022. The PA group was defined by a positive reaction to peanut-specific IgE tests, while the Ctl group tested negative for peanut IgE and had no history of allergies. Fecal samples were collected and genomic DNA was extracted for 16S rRNA gene sequencing to assess gut microbiota composition. Alpha diversity indices, including the sob, ace, chao, shannon, and simpson indices, were calculated to assess microbial community richness and diversity. Beta diversity was analyzed using Principal Coordinate Analysis (PCoA) and Partial Least Squares Discriminant Analysis (PLS-DA) to compare microbial community structures between the PA and Ctl groups. The study identified significant differences in gut microbiota diversity between children with peanut allergy (PA group) and healthy controls (Ctl group). The PA group exhibited reduced alpha diversity, indicated by lower sob, ace, and chao indices (FDR ≤ 0.05), and a significantly lower Shannon index (FDR ≤ 0.01). Beta diversity analysis revealed distinct microbial community structures between the two groups. Notably, the PA group showed an increase in Proteobacteria and a decrease in Firmicutes and Bacteroidetes, with significant changes at the genus level, including lower relative abundance of Bacteroides and Faecalibacterium, and higher relative abundance of Bifidobacterium and Lactobacillus (FDR ≤ 0.05 or FDR ≤ 0.01). Correlation analysis highlighted a strong negative correlation between IgE levels and specific microbial groups, such as Alistipes and CAG-352 (FDR ≤ 0.001), and a positive correlation with Veillonella. Blood routine indicators were also found to be correlated with gut microbiota composition. The findings of this study provide compelling evidence that gut microbiota diversity and composition are significantly altered in children with peanut allergy. The observed shifts in microbial communities, particularly the increase in Proteobacteria and the decrease in beneficial bacteria such as Firmicutes and Bacteroidetes, underscore the potential role of the gut microbiome in the pathogenesis of peanut allergy. These results suggest that modulating the gut microbiota may be a viable therapeutic strategy for managing peanut allergy and highlight the need for further research to explore the clinical implications of these microbial changes.

Growing evidence has suggested a strong link between gut microbiota and host fitness, yet our understanding of the assembly mechanisms governing gut microbiota remains limited. Here, we collected invasive and native freshwater snails coexisting at four independent sites in Guangdong, China. We used high-throughput sequencing to study the assembly processes of their gut microbiota. Our results revealed significant differences in the diversity and composition of gut microbiota between invasive and native snails. Specifically, the gut microbiota of invasive snails exhibited lower alpha diversity and fewer enriched bacteria, with a significant phylogenetic signal identified in the microbes that were enriched or depleted. Both the phylogenetic normalized stochasticity ratio (pNST) and the phylogenetic-bin-based null model analysis (iCAMP) showed that the assembly process of gut microbiota in invasive snails was more deterministic compared with that in native snails, primarily driven by homogeneous selection. The linear mixed-effects model revealed a significant negative correlation between deterministic processes (homogeneous selection) and alpha diversity of snail gut microbiota, especially where phylogenetic diversity explained the most variance. This indicates that homogeneous selection acts as a filter by the host for specific microbial lineages, constraining the diversity of gut microbiota in invasive freshwater snails. Overall, our study suggests that deterministic assembly-mediated lineage filtering is a potential mechanism for maintaining the diversity of gut microbiota in freshwater snails.

The use of tacrolimus (TAC), a critical immunosuppressant post transplantation, is complicated by its high pharmacokinetic variability. While the gut microbiota has gained attention as a potential contributor, few studies have assessed its role in TAC metabolism variability. This study investigated the associations between the gut microbiota and TAC metabolism rates in kidney transplant recipients during the first month post transplantation-a crucial period for adjusting TAC to achieve therapeutic levels. We recruited 20 kidney transplant recipients and profiled their gut microbiota diversity and composition from stool samples collected before transplantation and at weeks 1 and 4 post transplantation via 16S rRNA sequencing. The TAC pharmacokinetic parameters were also collected. Associations between TAC metabolism status or pharmacokinetic parameters and gut microbiota diversity and composition were evaluated. Recipients with a fast TAC metabolism rate (C0/D ratio < 1.05ng/mL × 1/mg) presented significantly greater changes in both bacterial alpha and beta diversity metrics at 1week post transplantation than did those with a slow metabolism rate (C0/D ratio ≥ 1.05ng/mL × 1/mg). Compared with slow metabolizers, fast metabolizers were associated with a significant increase in the abundance of three bacterial genera (Faecalibacterium, Clostridia vadinBB60, and Ruminococcus) and a significant decrease in the abundance of two bacterial species (Bacteroides plebeius and Parabacteroides goldsteinii). This study revealed links between gut microbiota diversity and composition and TAC metabolism rates in kidney transplant recipients during the early posttransplant period, underscoring the importance of investigating the gut microbiota as a contributor to TAC pharmacokinetic variability. Clarifying this causal relationship could better predict inter- and intraindividual TAC pharmacokinetic variability.

Negative emotions and gut microbiota during pregnancy both bear significant public health implications. However, the relationship between them has not been fully elucidated. This study, utilizing data from a pregnancy cohort, employed metagenomic sequencing to elucidate the relationship between anxiety, depression, and gut microbiota's diversity, composition, species, and functional pathways. Data from 87 subjects, spanning 225 time points across early, mid, and late pregnancy, were analyzed. The results revealed that anxiety and depression significantly corresponded to lower alpha diversity (including the Shannon entropy and the Simpson index). Anxiety and depression scores, along with categorical distinctions of anxiety/non-anxiety and depression/non-depression, were found to account for 0.723%, 0.731%, 0.651%, and 0.810% of the variance in gut-microbiota composition (p = 0.001), respectively. Increased anxiety was significantly positively associated with the abundance of Oscillibacter sp. KLE 1745, Oscillibacter sp. PEA192, Oscillibacter sp. KLE 1728, Oscillospiraceae bacterium VE202 24, and Treponema socranskii. A similar association was significantly noted for Oscillibacter sp. KLE 1745 with elevated depression scores. While EC.3.5.3.1: arginase appeared to be higher in the anxious group than in the non-anxious group, vitamin B12-related enzymes appeared to be lower in the depression group than in the non-depression group. The changes were found to be not statistically significant after post-multiple comparison adjustment.

Background : Previous small–scale studies have suggested that dog ownership may beneficially influence the human gut microbiota, primarily through interspecies microbial exchange. However, these findings require validation in larger populations. Objectives : This study aimed to assess the association between dog ownership and gut microbiota composition and diversity using data from a large cohort. Methods : An independent analysis was conducted using data from a databank comprising 11,439 sequenced human gut microbiota species. Participants were categorized based on dog ownership or frequent interaction. Potential confounding factors, including gender, place of residence, diet, leisure activities, and medication, were identified and adjusted for in the analyses. Alpha and beta diversity metrics, as well as taxonomic and functional profiles, were compared between groups. Results : Samples from 2,761 dog-owning individuals showed no significant increase in alpha diversity. However, beta diversity analyses revealed significant differences in gut microbiota composition. Dog ownership was associated with higher relative abundances of the phylum Desulfobacterota and the genera Negativibacillus , Ruminococcus torques , and Oscillobacter , alongside a lower abundance of Lachnospiraceae UCG-001 . No significant differences were detected in metabolic pathways or functional modules. Conclusion : Dog ownership was associated with alterations in gut microbiota composition but not functionality. Given the presence of multiple confounding factors, generalization of these findings is limited. The study did not confirm previously reported beneficial effects of dog ownership on the human gut microbiota.

Context The continuous rise in urbanisation and its associated factors has been reflected in the structure of the human gut ecosystem. Objective The main focus of this review is to discuss and summarise the major risk factors associated with urbanisation that affect human gut microbiota thus affecting human health. Methods Multiple medical literature databases, namely PubMed, Google, Google Scholar, and Web of Science were used to find relevant materials for urbanisation and its major factors affecting human gut microbiota/microbiome. Both layman and Medical Subject Headings (MeSH) terms were used in the search. Due to the scarcity of the data, no limitation was set on the publication date. Relevant materials in the English language which include case reports, chapters of books, journal articles, online news reports and medical records were included in this review. Results Based on the data discussed in the review, it is quite clear that urbanisation and its associated factors have long-standing effects on the human gut microbiota that result in alterations of gut microbial diversity and composition. This is a matter of serious concern as chronic inflammatory diseases are on the rise in urbanised societies. Conclusion A better understanding of the factors associated with urbanisation will help us to identify and implement new biological and social approaches to prevent and treat diseases and improve health globally by deepening our understanding of these relationships and increasing studies across urbanisation gradients. HIGHLIGHTS Human gut microbiota have been linked to almost every important function, including metabolism, intestinal homeostasis, immune system, biosynthesis of vitamins, brain processes, and behaviour. However, dysbiosis i.e., alteration in the composition and diversity of gut microbiota is associated with the pathogenesis of many chronic conditions. In the 21st century, urbanisation represents a major demographic shift in developed and developing countries. During this period of urbanisation, humans have been exposed to many environmental exposures, all of which have led to the dysbiosis of human gut microbiota. The main focus of the review is to discuss and summarise the major risk factors associated with urbanisation and how it affects the diversity and composition of gut microbiota which ultimately affects human health.

Irritable bowel syndrome (IBS) is a prevalent functional gastrointestinal disorder characterized by abdominal pain, bloating, diarrhea, and constipation. Recent studies have underscored the significant role of the gut microbiota in the pathogenesis of IBS. Physical exercise, as a non-pharmacological intervention, has been proposed to alleviate IBS symptoms by modulating the gut microbiota. Aerobic exercise, such as running, swimming, and cycling, has been shown to enhance the diversity and abundance of beneficial gut bacteria, including Lactobacillus and Bifidobacterium. These bacteria produce short-chain fatty acids that possess anti-inflammatory properties and support gut barrier integrity. Studies involving IBS patients participating in structured aerobic exercise programs have reported significant improvements in their gut microbiota's composition and diversity, alongside an alleviation of symptoms like abdominal pain and bloating. Additionally, exercise positively influences mental health by reducing stress and improving mood, which can further relieve IBS symptoms via the gut-brain axis. Long-term exercise interventions provide sustained benefits, maintaining the gut microbiota's diversity and stability, supporting immune functions, and reducing systemic inflammation. However, exercise programs must be tailored to individual needs to avoid exacerbating IBS symptoms. Personalized exercise plans starting with low-to-moderate intensity and gradually increasing in intensity can maximize the benefits and minimize risks. This review examines the impact of various types and intensities of physical exercise on the gut microbiota in IBS patients, highlighting the need for further studies to explore optimal exercise protocols. Future research should include larger sample sizes, longer follow-up periods, and examine the synergistic effects of exercise and other lifestyle modifications. Integrating physical exercise into comprehensive IBS management plans can enhance symptom control and improve patients' quality of life.

Perturbations in early life gut microbiota can have long-term impacts on host health. In this study, we investigated antimicrobial-induced temporal changes in diversity, stability, and compositions of gut microbiota in neonatal veal calves, with the objective of identifying microbial markers that predict diarrhea. A total of 220 samples from 63 calves in first 8 weeks of life were used in this study. The results suggest that increase in diversity and stability of gut microbiota over time was a feature of “healthy” (non-diarrheic) calves during early life. Therapeutic antimicrobials delayed the temporal development of diversity and taxa–function robustness (a measure of microbial stability). In addition, predicted genes associated with beta lactam and cationic antimicrobial peptide resistance were more abundant in gut microbiota of calves treated with therapeutic antimicrobials. Random forest machine learning algorithm revealed that Trueperella, Streptococcus, Dorea, uncultured Lachnospiraceae, Ruminococcus 2, and Erysipelatoclostridium may be key microbial markers that can differentiate “healthy” and “unhealthy” (diarrheic) gut microbiota, as they predicted early life diarrhea with an accuracy of 84.3%. Our findings suggest that diarrhea in veal calves may be predicted by the shift in early life gut microbiota, which may provide an opportunity for early intervention (e.g., prebiotics or probiotics) to improve calf health with reduced usage of antimicrobials.

Introduction. The human body is home to a diverse community of microorganisms known as the microbiota. These microorganisms, including bacteria, fungi, and viruses, play crucial roles in maintaining overall health. They colonize the digestive tract shortly after birth, and the composition of the gut microbiota changes throughout an individual's life, largely influenced by diet and physical activity. Breastfeeding has long-term beneficial effects on the gut microbiota and gene expression in intestinal cells. Regular exercise not only improves cardiovascular and respiratory health but also affects metabolic, immunological, neural, and microbial pathways. This review explores how diet and physical activity impact the composition and diversity of gut microbiota, highlighting important findings and their implications for health. Aim of study. This study aims to review how physical activity influences gut microbiota, investigating the effects of different types and intensities of exercise on microbial composition and diversity, and their implications for overall health. Materials and methods. A non-systematic examination of the scientific literature was conducted using specific keywords such as gut microbiota, physical activity, sport, and microbiome. The examination took place on PubMed, with scrutiny of a total of 31 references published up to 2023. Conclusions. This review highlights the crucial role of gut microbiota in maintaining good health and its complex interaction with diet and physical activity. Regular exercise has a positive impact on the diversity of microbiota, especially when started at a young age. Imbalance in gut bacteria is linked to various diseases, underscoring the significance of a healthy microbiome. Encouraging physical activity and a nutritious diet can improve gut health, and more research is needed to understand the mechanisms and potential health indicators involved.

The gut microbiota is integral to the health and adaptability of wild herbivores. Interactions with soil microbiota can shape the composition and function of the gut microbiota, thereby influencing the hosts' adaptive strategies. As a result, soil microbiota plays a pivotal role in enabling wild herbivores to thrive in extreme environments. However, the influence of soil microbiota from distinct regions on host's gut microbiota has often been overlooked. We conducted the first comprehensive analysis of the composition and diversity of gut and soil microbiota in goitered gazelles across six regions in the Qaidam Basin, utilizing source tracking and ecological assembly process analyses. Significant differences were observed in the composition and diversity of soil and gut microbiota among the six groups. Source tracking analysis revealed that soil microbiota in the GangciGC (GC) group contributed the highest proportion to fecal microbiota (8.94%), while the Huaitoutala (HTTL) group contributed the lowest proportion (1.80%). The GC group also exhibited the lowest α-diversity in gut microbiota. The observed differences in gut microbial composition and diversity among goitered gazelles from six regions in the Qaidam Basin were closely tied to their adaptive strategies. Ecological assembly process analysis indicated that the gut microbiota were primarily influenced by stochastic processes, whereas deterministic processes dominated most soil microbial groups. Both the differences and commonalities in gut and soil microbiota play essential roles in enabling these gazelles to adapt to diverse environments. Notably, the utilization pattern of soil microbiota by gut microbiota did not align with regional trends in gut microbial α-diversity. This discrepancy may be attributed to variations in environmental pressures and the gut's filtering capacity, allowing gazelles to selectively acquire microbiota from soil to maintain homeostasis. This study highlights the significant regional variation in gut and soil microbiota diversity among goitered gazelle populations in the Qaidam Basin and underscores the critical role of soil-derived microbiota in their environmental adaptation.