Spatial Characteristics of Colonic Mucosa-Associated Gut Microbiota in Humans

Bacterial association with metals enables in vivo monitoring of urogenital microbiota using magnetic resonance imaging

Bacteria constitute a significant part of the biomass of the human microbiota, but their interactions are complex and difficult to replicate outside the host. Exploiting the superior resolution of magnetic resonance imaging (MRI) to examine signal parameters of selected human isolates may allow tracking of their dispersion throughout the body. Here we investigate longitudinal and transverse MRI relaxation rates and found significant differences between several bacterial strains. Common commensal strains of lactobacilli display notably high MRI relaxation rates, partially explained by elevated cellular manganese content, while other species contain more iron than manganese. Lactobacillus crispatus show particularly high values, 4-fold greater than any other species; up to 60-fold greater signal than relevant tissue background; and a linear relationship between relaxation rate and fraction of live cells. Different bacterial strains have detectable, repeatable MRI relaxation rates that in the future may enable monitoring of their persistence in the human body for enhanced molecular imaging.

The microbiome compositional and functional differences between rectal mucosa and feces

In recent years, most studies on the gut microbiome have primarily focused on feces samples, leaving the microbial communities in the intestinal mucosa relatively unexplored. To address this gap, our study employed shotgun metagenomics to analyze the microbial compositions in normal rectal mucosa and matched feces from 20 patients with colonic polyps. Our findings revealed a pronounced distinction of the microbial communities between these two sample sets. Compared with feces, the mucosal microbiome contains fewer genera, with Burkholderia being the most discriminating genus between feces and mucosa, highlighting its significant influence on the mucosa. Furthermore, based on the microbial classification and KEGG Orthology (KO) annotation results, we explored the association between rectal mucosal microbiota and factors such as age, gender, BMI, and polyp risk level. Notably, we identified novel biomarkers for these phenotypes, such as Clostridium ramosum and Enterobacter cloacae in age. The mucosal microbiota showed an enrichment of KO pathways related to sugar transport and short chain fatty acid metabolism. Our comprehensive approach not only bridges the knowledge gap regarding the microbial community in the rectal mucosa but also underscores the complexity and specificity of microbial interactions within the human gut, particularly in the Chinese population.

IMPORTANCE

This study presents a system-level map of the differences between feces and rectal mucosal microbial communities in samples with colorectal cancer risk. It reveals the unique microecological characteristics of rectal mucosa and its potential influence on health. Additionally, it provides novel insights into the role of the gut microbiome in the pathogenesis of colorectal cancer and paves the way for the development of new prevention and treatment strategies.

Mapping the geographical distribution of the mucosa-associated gut microbiome in GI-symptomatic children with autism spectrum disorder

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by cognitive, behavioral, and communication impairments. In the past few years, it has been proposed that alterations in the gut microbiota may contribute to an aberrant communication between the gut and brain in children with ASD. Consistent with this notion, several studies have demonstrated that children with ASD have an altered fecal microbiota compared with typically developing (TD) children. However, it is unclear where along the length of the gastrointestinal (GI) tract these alterations in microbial communities occur. In addition, the variation between specific mucosa-associated communities remains unknown. To address this gap in knowledge of the microbiome associated with ASD, biopsies from the antrum, duodenum, ileum, right colon, and rectum of children with ASD and age- and sex-matched TD children were examined by 16S rRNA sequencing. We observed an overall elevated abundance of Bacillota and Bacteroidota and a decreased abundance of Pseudomonadota in all GI tract regions of both male and female children with ASD compared with TD children. Further analysis at the genera level revealed unique differences in the microbiome in the different regions of the GI tract in children with ASD compared with TD children. We also observed sex-specific differences in the gut microbiota composition in children with ASD. These data indicate that the microbiota of children with ASD is altered in multiple regions of the GI tract and that different anatomic locations have unique alterations in mucosa-associated bacterial genera.NEW & NOTEWORTHY Analysis in stool samples has shown gut microbiota alterations in children with autism spectrum disorder (ASD) compared with typically developing (TD) children. However, it is unclear which segment(s) of the gut exhibit alterations in microbiome composition. In this study, we examined microbiota composition along the gastrointestinal (GI) tract in the stomach, duodenum, ileum, right colon, and rectum. We found site-specific and sex-specific differences in the gut microbiota of children with ASD, compared with controls.

Multivariate Analysis and Correlation Study Shows the Impact of Anthropometric and Demographic Variables on Gut Microbiota in Obese Egyptian Children

Deciphering the gut microbiome's link to obesity is crucial. Our study characterized the gut microbial community in Egyptian children and investigated the effect of covariates on the gut microbiome, body mass index (BMI), geographical location, gender, and age. We used 16S rRNA sequencing to characterize the gut microbial communities of 49 children. We then evaluated these communities for diversity, potential biomarkers, and functional capacity. Alpha diversity of the non-obese group was higher than that of the obese group (Chao1, P = 0.006 and observed species, P = 0.003). Beta diversity analysis revealed significant variations in the gut microbiome between the two geographical locations, Cairo and Ismailia (unweighted UniFrac, P = 0.03) and between obesity statuses, obese and non-obese (weighted UniFrac, P = 0.034; unweighted UniFrac, P = 0.015). We observed a significantly higher Firmicutes/Bacteroidetes ratio in obese males than in non-obese males (P = 0.004). Interestingly, this difference was not seen in females (P = 0.77). Multivariable association with linear models (MaAsLin2) identified 8 microbial features associated with obesity, 12 associated with non-obesity, and found 29 and 13 features specific to Cairo and Ismailia patients, respectively. It has also shown one microbial feature associated with patients under five years old. MaAsLin2, however, failed to recognize any association between gender and the gut microbiome. Moreover, it could find the most predominant features in groups 2-9 but not in group 1. Another method used in the analysis is the Linear discriminant analysis Effect Size (LEfSe) approach, which effectively identified 19 biomarkers linked to obesity, 9 linked non-obesity, 20 linked to patients residing in Cairo, 14 linked to patients in Ismailia, one linked to males, and 12 linked to females. LEfSe could not, however, detect any prevalent bacteria among children younger or older than five. Future studies should take advantage of such correlations, specifically BMI, to determine the interventions needed for obesity management.

Role of sulfidogenic members of the gut microbiota in human disease

The human gut flora comprises a dynamic network of bacterial species that coexist in a finely tuned equilibrium. The interaction with intestinal bacteria profoundly influences the host's development, metabolism, immunity, and overall health. Furthermore, dysbiosis, a disruption of the gut microbiota, can induce a variety of diseases, not exclusively associated with the intestinal tract. The increased consumption of animal protein, high-fat and high-sugar diets in Western countries has been implicated in the rise of chronic and inflammatory illnesses associated with dysbiosis. In particular, this diet leads to the overgrowth of sulfide-producing bacteria, known as sulfidogenic bacteria, which has been linked to inflammatory bowel diseases and colorectal cancer, among other disorders. Sulfidogenic bacteria include sulfate-reducing bacteria (Desulfovibrio spp.) and Bilophila wadsworthia among others, which convert organic and inorganic sulfur compounds to sulfide through the dissimilatory sulfite reduction pathway. At high concentrations, sulfide is cytotoxic and disrupts the integrity of the intestinal epithelium and mucus barrier, triggering inflammation. Besides producing sulfide, B. wadsworthia has revealed significant pathogenic potential, demonstrated in the ability to cause infection, adhere to intestinal cells, promote inflammation, and compromise the integrity of the colonic mucus layer. This review delves into the mechanisms by which taurine and sulfide-driven gut dysbiosis contribute to the pathogenesis of sulfidogenic bacteria, and discusses the role of these gut microbes, particularly B. wadsworthia, in human diseases.

Polyphenolic Compounds: Orchestrating Intestinal Microbiota Harmony during Aging

In the aging process, physiological decline occurs, posing a substantial threat to the physical and mental well-being of the elderly and contributing to the onset of age-related diseases. While traditional perspectives considered the maintenance of life as influenced by a myriad of factors, including environmental, genetic, epigenetic, and lifestyle elements such as exercise and diet, the pivotal role of symbiotic microorganisms had been understated. Presently, it is acknowledged that the intestinal microbiota plays a profound role in overall health by signaling to both the central and peripheral nervous systems, as well as other distant organs. Disruption in this bidirectional communication between bacteria and the host results in dysbiosis, fostering the development of various diseases, including neurological disorders, cardiovascular diseases, and cancer. This review aims to delve into the intricate biological mechanisms underpinning dysbiosis associated with aging and the clinical ramifications of such dysregulation. Furthermore, we aspire to explore bioactive compounds endowed with functional properties capable of modulating and restoring balance in this aging-related dysbiotic process through epigenetics alterations.

Comparison of gut microbiome composition in colonic biopsies, endoscopically-collected and at-home-collected stool samples

Aim

The goal of this study is to compare microbiome composition in three different sample types in women, namely stool brought from home vs. solid stool samples obtained at the time of an unprepped sigmoidoscopy vs. biopsies of the colonic mucosa at the time of an unprepped sigmoidoscopy, using alpha- and beta-diversity metrics following bacterial 16S rRNA sequencing. The findings may have relevance to health and disease states in which bacterial metabolism has a significant impact on molecules/metabolites that are recirculated between the gut lumen and mucosa and systemic circulation, such as estrogens (as in breast cancer) or bile acids.

Methods

Concomitant at-home-collected stool, endoscopically-collected stool, and colonic biopsy samples were collected from 48 subjects (24 breast cancer, 24 control.) After 16S rRNA sequencing, an amplicon sequence variant (ASV) based approach was used to analyze the data. Alpha diversity metrics (Chao1, Pielou's Evenness, Faith PD, Shannon, and Simpson) and beta diversity metrics (Bray-Curtis, Weighted and Unweighted Unifrac) were calculated. LEfSe was used to analyze differences in the abundance of various taxa between sample types.

Results

Alpha and beta diversity metrics were significantly different between the three sample types. Biopsy samples were different than stool samples in all metrics. The highest variation in microbiome diversity was noted in the colonic biopsy samples. At-home and endoscopically-collected stool showed more similarities in count-based and weighted beta diversity metrics. There were significant differences in rare taxa and phylogenetically-diverse taxa between the two types of stool samples. Generally, there were higher levels of Proteobacteria in biopsy samples, with significantly more Actinobacteria and Firmicutes in stool (all p < 0.001, q-value < 0.05). Overall, there was a significantly higher relative abundance of Lachnospiraceae and Ruminococcaceae in stool samples (at-home collected and endoscopically-collected) and higher abundances of Tisserellaceae in biopsy samples (all p < 0.001, q-value < 0.05).

Conclusion

Our data shows that different sampling methods can impact results when looking at the composition of the gut microbiome using ASV-based approaches.

Toddalia asiatica extract attenuates adjuvant-induced arthritis by modulating colon Th17/Treg balance and colony homeostasis

ETHNOPHARMACOLOGICAL RELEVANCE

Given the adverse effects of the current principal treatments, there is still a great need for effective cures for rheumatoid arthritis (RA), an immune-mediated disease. Toddalia asiatica (L.) Lam is a traditional medicinal herb that can be used for RA treatment because of its anti-inflammatory and analgesic properties.

AIM OF THE STUDY

To investigate the possible effects of Toddalia asiatica extract (TAE) on intestinal immunity and the intestinal bacterial flora in a rat model of RA.

MATERIALS AND METHODS

The anti-arthritis effect of TAE was evaluated in arthritis rats induced by complete Freund's adjuvant-induced arthritis (AIA). Arthritis index (AI) scores, systemic inflammation scores, histopathologic changes in the colon and ankle were detected by hematoxylin and eosin staining. Western blot analysis was performed to assess the protein expression of IL-17A, RORC, IL-1β, IL-6, FOXP3, IL-10 in the colon. RT-PCR was performed to assess the expression of the colon's mRNA. Finally, changes to the gut microbiome by sequencing 16S rDNA. Microbial function prediction was performed using PICRUSt with the KEGG databases and correlation analysis was carried out by computing Spearman's rank correlations.

RESULTS

demonstrated that TAE administration at a dose of 3 g/kg dramatically decreased AI scores, systemic inflammation scores, and histopathologic lesions of the ankle and colon in AIA rats. TAE was found to significantly reduce the expression levels of Th17-related proteins and mRNAs (IL-17A, RORC, IL-1β and IL-6) in the colon, while increasing the expression levels of Treg-related proteins and mRNA (IL-10 and FOXP3), which helped restore the balance of Th17/Treg immune cells in the colon. Meanwhile, TAE was also found to be capable of remodeling the gut microbiota in AIA rats. Depleting RA-associated genera and thereby increasing α-diversity enriched the gut microbiota's diversity and shifted the community composition dramatically, leading to the increase of Firmicutes_unclassified, Ruminococcaceae_unclassified, Muribaculum, Subdoligranulum, Lachnospira, Marvinbryantia, and the reduction of RA-related bacteria Ligilactobacillus, Streptococcus and Eubacterium-eligens-group. Furthermore, PICRUSt analysis revealed that metabolic pathways were associated with TAE treatment, with metabolic pathways dominating. Among them, metabolic pathways were predominant. Correlation studies showed that a total of 9 microorganisms, including Ligilactobacillus, Eubacterium-eligens-group and Subdoligranulum, were significantly associated with Th17/Treg expression.

CONCLUSIONS

This study demonstrates that TAE is a low-toxicity poly alkaline drug that can rapidly and effectively improve joint symptoms in RA rats and increases beneficial intestinal bacteria and decreases harmful ones, which is associated with modulating Th17/Treg interactions in intestinal T cells and reversing microbial disorders.

Sugar intake and colorectal cancer risk: A prospective Japanese cohort study

The influence of sugar consumption on the risk of colorectal cancer (CRC) remains controversial. Prospective cohort studies focusing on total and specific types of sugar intake among the Asian population who have different patterns of sugar intake sources than American and European populations are scarce. We intended to examine the association of sugar intake with CRC risk among middle-aged adults in a Japanese large-scale population-based cohort study. The participants (42,405 men and 48,600 women) who were 45-74 years old and answered the questionnaire in 1995-1999 in the Japan Public Health Center-based Prospective Study were followed up until December 2013. Total sugars, total fructose, and specific types of sugar intake were estimated using a validated 147-item food frequency questionnaire and divided into quintiles (Q1-Q5). We used Cox proportional hazard regression models adjusted for potential confounders to estimate hazard ratios (HRs) and 95% confidence intervals (CIs). During the follow-up, 2118 CRC cases (1226 men and 892 women) were identified. We did not observe any clear association between all types of sugar intake and an increased risk of CRC. Analyses by tumor sites yielded a positive association of total sugar consumption with rectal cancer in women (1.75 [1.07-2.87] for Q1 vs. Q5; p _{linear trend}  = 0.03), but no statistically significant trend was detected among men. Sugar intake was not associated with CRC risk in middle-aged Japanese adults. However, for rectal cancer, the probability of an increased risk among women with a higher total sugar intake cannot be excluded.

Relationship between mucosa-associated gut microbiota and human diseases

The mucus layer covering the gastrointestinal (GI) tract plays a critical role in maintaining gut homeostasis. In the colon, the inner mucus layer ensures commensal microbes are kept at a safe distance from the epithelium while mucin glycans in the outer mucus layer provide microbes with nutrients and binding sites. Microbes residing in the mucus form part of the so-called 'mucosa-associated microbiota' (MAM), a microbial community which, due to its close proximity to the epithelium, has a profound impact on immune and metabolic health by directly impacting gut barrier function and the immune system. Alterations in GI microbial communities have been linked to human diseases. Although most of this knowledge is based on analysis of the faecal microbiota, a growing number of studies show that the MAM signature differs from faecal or luminal microbiota and has the potential to be used to distinguish between diseased and healthy status in well-studied conditions such as IBD, IBS and CRC. However, our knowledge about spatial microbial alterations in pathogenesis remains severely hampered by issues surrounding access to microbial communities in the human gut. In this review, we provide state-of-the-art information on how to access MAM in humans, the composition of MAM, and how changes in MAM relate to changes in human health and disease. A better understanding of interactions occurring at the mucosal surface is essential to advance our understanding of diseases affecting the GI tract and beyond.

Effects of Poncirin, a Citrus Flavonoid and Its Aglycone, Isosakuranetin, on the Gut Microbial Diversity and Metabolomics in Mice

Poncirin (PC) and its aglycone, isosakuranetin (IR), occur naturally in citrus fruits. This study aimed to explore the pathways behind the different health benefits of PC and IR by evaluating the effect of these two bioactive flavonoids on the gut microbial diversity and metabolomics of mice. The 16S rRNA gene sequencing was used to analyze the alteration of gut microbiota in mice after PC and IR intervention. The metabolic impact of PC and IR in mice were studied using a metabolomics approach based on LC-MS analysis. Results showed that, after 7 days intervention, PC and IR multiplied the abundance of Parabacteroides in mice’s intestinal tracts by 1.2 and 1.0 times, respectively. PC increased the abundance of Bacteroides by 2.4 times. IR reduced the Allobaculum abundance by 1.0 time and increased Alloprevotella abundance by 1.5 times. When mice were given PC, their fecal acetic acid level increased by 1.8 times, while their isobutyric and isovaleric acid content increased by 1.2 and 1.3 times, respectively. Supplementation with IR had no significant effect on the content of short-chain fatty acids (SCFAs) in the feces of mice. The potential urine biomarkers of mice in the PC group were involved in the digestion and absorption of protein and carbohydrate, as well as the metabolism of amino acids, such as glycine, serine, threonine, tryptophan, D-arginine, D-ornithine, etc. IR mainly affected the amino acid metabolic pathways in mice, including taurine and hypotaurine metabolism, glutathione metabolism, histidine metabolism, D-glutamate metabolism, etc. This study provided valuable clues for future research on the health promoting mechanisms of PC and IR.