Sampling frequency matters: mapping of the healthy infants' gut microbiome during the first year of life

Time-varying ambient air pollution exposure is associated with gut microbiome variation in the first 2 years of life

Effects of diet on the childhood gut microbiome and its implications for atopic dermatitis

ANALYZING OR EXPLAINING BETA DIVERSITY? COMMENT.

Effect of ultra-processed food consumption on the gut microbiota in the first year of life: Findings from the MINA-Brazil birth cohort study.

Objective. To describe the features of the taxonomic composition and alpha diversity of the gut microbiota in children and adolescents suffering from exogenous constitutional obesity and to establish the effect of the feeding type in the first year of life on these parameters. Patients and methods. This prospective single-stage study enrolled 188 children and adolescents aged 13.1 ± 4.1 (10–18) years, including healthy volunteers (n = 96) and patients with exogenous obesity (n = 92). A metagenomic analysis of gut microbial communities depending on the type of feeding in the first year of life was performed. The study of DNA extracted from stool samples was carried out by 16S rRNA gene sequencing (V3–V4 regions). Results. In the gut microbiome of obese children as compared with healthy ones, there was a statistically significant decrease in the content of Bacteroidetes phylum (35.36% vs 39.44%) and Proteobacteria (1.99% vs 2.53%) and an increase in the Firmicutes phylum (53.95% vs 49.29%) and alpha diversity indices (p < 0,05 for Chao1, Shannon, Simpson indices, number of OTUs). Healthy children who were fed artificially during their first year of life showed a statistically significant decrease in diversity indices of the gut microbiota in comparison with breastfed children. Conclusion. The results obtained indicate the importance of the feeding type over the first year of life in the development of the gut microbial diversity and indicate the long-term maintenance of the effect of this factor up to adolescence. Key words: obesity, gut microbiota, Bacteroidetes, Firmicutes, breastfeeding, 16S rRNA

Newborn screening for cystic fibrosis (CF) can identify affected but asymptomatic infants. The selection of omic technique for gut microbiota study is crucial due to both the small amount of feces available and the low microorganism load. Our aims were to compare the agreement between 16S rRNA amplicon sequencing and metaproteomics by a robust statistical analysis, including both presence and abundance of taxa, to describe the sequential establishment of the gut microbiota during the first year of life in a small size sample (8 infants and 28 fecal samples). The taxonomic assignations by the two techniques were similar, whereas certain discrepancies were observed in the abundance detection, mostly the lower predicted relative abundance of Bifidobacterium and the higher predicted relative abundance of certain Firmicutes and Proteobacteria by amplicon sequencing. During the first months of life, the CF gut microbiota is characterized by a significant enrichment of Ruminococcus gnavus, the expression of certain virulent bacterial traits, and the detection of human inflammation-related proteins. Metaproteomics provides information on composition and functionality, as well as data on host-microbiome interactions. Its strength is the identification and quantification of Actinobacteria and certain classes of Firmicutes, but alpha diversity indices are not comparable to those of amplicon sequencing. Both techniques detected an aberrant microbiota in our small cohort of infants with CF during their first year of life, dominated by the enrichment of R. gnavus within a human inflammatory environment. IMPORTANCE In recent years, some techniques have been incorporated for the study of microbial ecosystems, being 16S rRNA gene sequencing being the most widely used. Metaproteomics provides the advantage of identifying the interaction between microorganisms and human cells, but the available databases are less extensive as well as imprecise. Few studies compare the statistical differences between the two techniques to define the composition of an ecosystem. Our work shows that the two methods are comparable in terms of microorganism identification but provide different results in alpha diversity analysis. On the other hand, we have studied newborns with cystic fibrosis, for whom we have described the establishment of an intestinal ecosystem marked by the inflammatory response of the host and the enrichment of Ruminococcus gnavus.

Functional Abdominal Pain disorders (FAPDs) are a group of heterogeneous gastrointestinal disorders with unclear pathophysiology. In children, FAPDs are more common in the winter months than summer months. The possible influence of school stressors has been proposed. Previously, our group showed differences in bacterial relative abundances and alpha diversity in the gut microbiome and its relationship with stressors in a cross-sectional evaluation of children suffering from FAPDs compared to a healthy control group. We present longitudinal data to assess whether the gut microbiome changes over school terms in the control and FAPDs groups. The longitudinal study included children with FAPDs (n = 28) and healthy controls (n = 54). Gastrointestinal symptoms, as well as stool microbiome, were assessed in both groups. Stool samples were serially collected from all participants during both the school term and summer vacation. The stool samples were subjected to total genomic extraction, 16S rRNA amplicon sequencing, and bioinformatics analysis. The gut microbiome was compared at school and during vacation. Other metrics, alpha diversity, and beta diversity, were also compared between the two school terms in every group. In the healthy group, there were differences in microbiome composition between school terms and summer vacation. Conversely, we found no differences in the FAPDs group between the two terms. The healthy control group revealed differences (p-value < 0.05) in 55 bacterial species between the school term and vacation. Several of the differentially abundant identified bacteria were involved in short-chain fatty acids production (SCFAs), inflammation reduction, and gut homeostasis. Alpha diversity metrics, such as the Shannon index, were different in the control group and remained unchanged in the FAPDs group. Although preliminary, our findings suggest that the gut microbiome is static in FAPDs. This compares with a more dynamic healthy gut microbiome. Further studies are warranted to corroborate this and understand the interplay between stress, symptoms, and a less diverse and static microbiome. Future studies will also account for different variables such as diet and other patient demographic criteria that were missing in the current study.

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.

Severe injuries are frequently accompanied by hemorrhagic shock and harbor an increased risk for complications. Local or systemic inflammation after trauma/hemorrhage may lead to a leaky intestinal epithelial barrier and subsequent translocation of gut microbiota, potentially worsening outcomes. To evaluate the extent with which trauma affects the gut microbiota composition, we performed a post hoc analysis of a murine model of polytrauma and hemorrhage. Four hours after injury, organs and plasma samples were collected, and the diversity and composition of the cecal microbiome were evaluated using 16S rRNA gene sequencing. Although cecal microbial alpha diversity and microbial community composition were not found to be different between experimental groups, norepinephrine support in shock animals resulted in increased alpha diversity, as indicated by higher numbers of distinct microbial features. We observed that the concentrations of proinflammatory mediators in plasma and intestinal tissue were associated with measures of microbial alpha and beta diversity and the presence of specific microbial drivers of inflammation, suggesting that the composition of the gut microbiome at the time of trauma, or shortly after trauma exposure, may play an important role in determining physiological outcomes. In conclusion, we found associations between measures of gut microbial alpha and beta diversity and the severity of systemic and local gut inflammation. Furthermore, our data suggest that four hours following injury is too early for development of global changes in the alpha diversity or community composition of the intestinal microbiome. Future investigations with increased temporal-spatial resolution are needed in order to fully elucidate the effects of trauma and shock on the gut microbiome, biological signatures of inflammation, and proximal and distal outcomes.

Background: Many studies have explored changes in the gut microbiome associated with HIV infection, but the consistent pattern of changes has not been clarified. Men who have sex with men (MSM) are very likely to be an independent influencing factor of the gut microbiome, but relevant research is still lacking.Methods: We conducted a meta-analysis by screening 12 published studies of 16S rRNA gene amplicon sequencing of gut microbiomes related to HIV/AIDS (six of these studies contain data that is relevant and available to MSM) from NCBI and EBI databases. The analysis of gut microbiomes related to HIV infection status and MSM status included 1,288 samples (HIV-positive (HIV+) individuals, n = 744; HIV-negative (HIV–) individuals, n = 544) and 632 samples (MSM, n = 328; non-MSM, n = 304), respectively. The alpha diversity indexes, beta diversity indexes, differentially enriched genera, differentially enriched species, and differentially enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways related to gut microbiomes were calculated. Finally, the overall trend of the above indicators was evaluated.Results: Our results indicate that HIV+ status is associated with decreased alpha diversity of the gut microbiome. MSM status is an important factor that affects the study of HIV-related gut microbiomes; that is, MSM are associated with alpha diversity changes in the gut microbiome regardless of HIV infection, and the changes in the gut microbiome composition of MSM are more significant than those of HIV+ individuals. A consistent change in Bacteroides caccae, Bacteroides ovatus, Bacteroides uniformis, and Prevotella stercorea was found in HIV+ individuals and MSM. The differential expression of the gut microbiome may be accompanied by changes in functional pathways of carbohydrate metabolism, amino acid metabolism, and lipid Metabolism.Conclusions: This study shows that the changes in the gut microbiome are related to HIV and MSM status. Importantly, MSM status may have a far greater impact on the gut microbiome than HIV status.

Background:Patients diagnosed with spondyloarthritis (SpA) and dysbiosis or an alteration of the microbiota are linked to an inflammatory state with increased resistance to immunomodulatory treatments.Objectives:To describe and compare the composition...

Background: The gut microbiome may be linked to colorectal cancer (CRC) prognosis. Few studies characterized the gut microbiome longitudinally across CRC treatment. Herein, we investigated the gut microbiome dynamics before and up to two years after surgery among newly diagnosed CRC patients. Methods: We extracted DNA from stool collected longitudinally at baseline (pre-surgery) and at 6, 12, and 24-months after in the ColoCare Study. We characterized fecal bacteria using 16S rRNA gene sequencing (16S; N=133; baseline and 6 months only) and whole-genome shotgun sequencing (WGS; N=41; all timepoints). We estimated rarefied alpha diversity (richness and Shannon index) and beta diversity (Bray Curtis). We calculated centered-log ratio transformed relative abundances of a priori-selected taxa and functional genes (WGS only). We used permutational multivariate analysis of variance to estimate the percentage explained in variability of the Bray Curtis distance matrix. We estimated average differences in the microbiome metrics across time using linear mixed effects models adjusted for study center and treatment. Results: In total, 43% of the cohort received adjuvant therapy and 24% received neoadjuvant therapy. On average, from baseline to 6 months, alpha diversity decreased, with statistically significant declines in the Shannon index for 16S (β = -0.32, 95% CI = -0.47, -0.17; P <0.001) and WGS (β = -0.38, 95% CI = -0.56, -0.20; P <0.001). WGS alpha diversity tended to somewhat recover at 12 and 24 months. Bray Curtis distance variation was primarily explained by subject (e.g., for 16S: 75%, P=0.03); whereas timepoint explained about 3% of variation in 16S and WGS Bray Curtis distance (all P < 0.05). Among 16S genera (presented per 1-unit increase in log ratio), there was an average 0.33-unit increase in Fusobacterium (95% CI = 0.05, 0.62; P= 0.02) and a -0.98-unit decrease in Prevotella (95% CI = -1.41, -0.56; P <0.001) abundance over 6 months. At the species-level (WGS), there were progressively stronger decreases from baseline up to 24 months in multiple potentially pathogenic a priori bacteria. For example, the changes β’s (95% CIs) in Porphyromonas asaccharolytica were -1.33 (-2.11, -0.57; P<0.001) at 6 months, -1.53 (-2.33, -0.74; P<0.001) at 12 months, and -1.18 (-2.05, -0.31; P=0.01) at 24 months. Acetolactate synthase gene abundance, involved in branch chain amino acid synthesis, increased on average from baseline to 6 and 12 months. Conclusion: We found that microbial diversity tended to decrease over time, recovering somewhat around a year. We found that the abundance of multiple oral-originating species previously associated with CRC presence and prognosis tended to decrease over time (except Fusobacterium in the less detailed 16S data). Overall, our intriguing findings highlight that the microbiome may shift after tumor removal. Next steps will interrogate these shifts as they relate to clinical outcomes. Citation Format: Maria F. Gomez, Stephanie R. Hogue, Jessica R. Burns, Seth I. Felder, Esther Jean-Baptiste, Adetunji T. Toriola, Jane C. Figueiredo, Christopher I. Li, David Shibata, Victoria Damerell, Christoph Kahlert, Erin M. Siegel, Rashmi Sinha, Emily Vogtmann, Sheetal Hardikar, Mary Playdon, Leigh Greathouse, Biljana Gigic, Cornelia M. Ulrich, Doratha A. Byrd. Longitudinal changes in the gut microbiome among newly diagnosed colorectal cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 7391.

The appropriate sample handling for human fecal microbiota studies is essential to prevent changes in bacterial composition and quantities that could lead to misinterpretation of the data. This study firstly identified the potential effect of aerobic and anaerobic fecal sample collection and transport materials on microbiota and quantitative microbiota in healthy and fat-metabolic disorder Thai adults aged 23-43 years. We employed metagenomics followed by 16S rRNA gene sequencing and 16S rRNA gene qPCR, to analyze taxonomic composition, alpha diversity, beta diversity, bacterial quantification, Pearson's correlation with clinical factors for fat-metabolic disorder, and the microbial community and species potential metabolic functions. Our study successfully obtained microbiota results in percent and quantitative compositions. Each sample exhibited quality sequences with a >99% Good's coverage index, and a relatively plateau rarefaction curve. Alpha diversity indices showed no statistical difference in percent and quantitative microbiota OTU richness and evenness, between aerobic and anaerobic sample transport materials. Obligate and facultative anaerobic species were analyzed and no statistical difference was observed. Supportively, the beta diversity analysis by non-metric multidimensional scale (NMDS) constructed using various beta diversity coefficients showed resembling microbiota community structures between aerobic and anaerobic sample transport groups (P = 0.86). On the other hand, the beta diversity could distinguish microbiota community structures between healthy and fat-metabolic disorder groups (P = 0.02), along with Pearson's correlated clinical parameters (i.e., age, liver stiffness, GGT, BMI, and TC), the significantly associated bacterial species and their microbial metabolic functions. For example, genera such as Ruminococcus and Bifidobacterium in healthy human gut provide functions in metabolisms of cofactors and vitamins, biosynthesis of secondary metabolites against gut pathogens, energy metabolisms, digestive system, and carbohydrate metabolism. These microbial functional characteristics were also predicted as healthy individual biomarkers by LEfSe scores. In conclusion, this study demonstrated that aerobic sample collection and transport (<48 h) did not statistically affect the microbiota and quantitative microbiota analyses in alpha and beta diversity measurements. The study also showed that the short-term aerobic sample collection and transport still allowed fecal microbiota differentiation between healthy and fat-metabolic disorder subjects, similar to anaerobic sample collection and transport. The core microbiota were analyzed, and the findings were consistent. Moreover, the microbiota-related metabolic potentials and bacterial species biomarkers in healthy and fat-metabolic disorder were suggested with statistical bioinformatics (i.e., Bacteroides plebeius).

TRE is an emerging approach in obesity treatment, yet there is limited data on how it influences gut microbiome composition in humans. Our objective was to characterize the gut microbiome of human participants before and after a TRE intervention. This is a secondary analysis of a previously published clinical trial examining the effects of time-restricted eating (TRE). In a previously published, 12-week randomized controlled trial, Chow et al. evaluated the effects of an 8-h TRE intervention on body composition in human participants. Chow et al. demonstrated significant reductions in weight, lean mass, and visceral fat in the TRE group compared to those following time-unrestricted eating (non-TRE). Stool samples were collected by a subset of those participants using home kits at both baseline and post-intervention for shotgun metagenomic sequencing for this secondary analysis. Microbiome community composition was compared before and after intervention as alpha and beta diversity. Sixteen participants provided stool samples (eight in the TRE group and eight in the non-TRE group). Stool samples were collected from all participants at at least one time point, but both pre- and post-treatment samples were available from only five participants who completed both baseline and post-treatment collections. In alignment with the findings of Chow et al., the participants in the TRE group of the secondary analysis who collected microbiome sample(s) successfully reduced their eating window from an average of 15.3 ± 0.8 h at baseline to 9.3 ± 1.7 h during the intervention (mean ± SD, p < 0.001) and the non-TRE group's eating window remained unchanged. While the TRE group lost weight and visceral fat mass, no effect of the TRE intervention was observed on alpha diversity (Shannon index, Simpson index, and number of taxa, linear mixed models), beta diversity (Bray-Curtis, PERMANOVA), even after controlling for weight and visceral fat changes. Our analysis did not detect any significant differences in gut microbiome composition or diversity indices between participants undergoing a TRE intervention and those in the control group. The study's findings are limited by a small sample size, short duration, and the collection of stool samples at only two time points. Future studies with larger sample sizes, longer durations, and more frequent sampling, and collection of detailed dietary data are needed to better understand the relationship between TRE and gut microbiome dynamics.

Twenty two H. pylori-positive patients, aged 19 to 64 years, were enrolled in the study and randomized into two treatment groups, as follows: (1) ECAB-14 (n = 11), with esomeprazole 20 mg, clarithromycin 500 mg, amoxicillin 1000 mg, and bismuthate tripotassium dicitrate 240 mg, twice daily, per os, for 14 days, and (2), ECAB-Z-14 (n = 11), with esomeprazole 20 mg, clarithromycin 500 mg, amoxicillin 1000 mg, and bismuthate tripotassium dicitrate 240 mg, twice daily, along with butyric acid+inulin (Zacofalk), two tablets daily, each containing 250 mg of butyric acid, and 250 mg of inulin, per os, for 14 days. Fecal samples were collected from each subject prior to eradication therapy (time point I), after the end of eradication therapy (time point II), and a month after the end of eradication therapy (time point III). The total DNA from the fecal samples was isolated for whole genome sequencing using the Illumina NextSeq 500 platform. Qualitative and quantitative changes in gut microbiota were assessed, including alpha and beta diversity, functional potential and antibiotic resistance gene profiling. Gut microbiota alpha diversity significantly decreased compared with the baseline immediately after eradication therapy in both treatment groups (ECAB-14 and ECAB-Z-14). This diversity reached its baseline in the ECAB-Z-14 treatment group a month after the end of eradication therapy. However, in the ECAB-14 treatment arm, a reduction in the Shannon index was observed up to a month after the end of H. pylori eradication therapy. Fewer alterations in the gut microbiota functional potential were observed in the ECAB-Z-14 treatment group. The abundance of genes responsible for the metabolic pathway associated with butyrate production decreased only in the ECAB-14 treatment group. The prevalence of antibiotic-resistant genes in the gut microbiota increased significantly in both treatment groups by the end of treatment. However, more severe alterations were noted in the ECAB-14 treatment group. H. pylori eradication therapy leads to taxonomic changes, a reduction in the alpha diversity index, and alterations in the functional potential of the gut microbiota and gut resistome. Taking butyric acid+inulin supplements during H. pylori eradication therapy could help maintain the gut microbiota in its initial state and facilitate its recovery after H. pylori eradication.