Important roles of Ruminococcaceae in the human intestine for resistant starch utilization

Potential role of key rumen microbes in regulating host health and growth performance in Hu sheep

BACKGROUND

Average daily gain (ADG) is an important component affecting the profitability of sheep. However, research on the relationship between rumen microbes and sheep growth phenotype is still very lacking. Therefore, in this study, 16 Hu sheep were selected from a cohort of 318 sheep assigned to the same feeding and management conditions, and divided into high growth rate (HADG, n = 8) group and low growth rate (LADG, n = 8) group according to the extreme ADG value. Then, the differences in rumen microbes, rumen fermentation and animal immune parameters were further compared between groups to explore the potential role of rumen key microbes in regulating the health and growth performance of Hu sheep hosts.

RESULTS

The results showed that specific pathogenic bacteria associated with ADG, including Anaerotruncus, Sediminibacterium and Glaesserella, exhibited significant correlations with interleukin-6 (IL-6) and immunoglobulin G (IgG). These interactions disrupt immune homeostasis in the host, leading to a metabolic prioritization of energy resources toward immune responses, thereby impairing growth and development. Succinivibrio_dextrinosolvens was enriched in HADG sheep and exhibited a significant positive correlation with propionate levels. This promoted propionate production in the rumen, enhancing the metabolic activity of carbohydrate, amino acid and energy metabolism, ultimately contributing to higher ADG in sheep. Importantly, random forest analysis results showed that Succinivibrio_dextrinosolvens could classify sheep into HADG and LADG with a prediction accuracy of 81.2%. Additionally, we identified 34 bacteria belonged to connectors in the HADG co-occurrence network, including Alloprevotella, Phascolarctobacterium, Anaerovibrio, Butyricicoccus, Ruminococcaceae_noname, and Roseburia, etc., which play an important role in the degradation of carbohydrates and convert them into short-chain fatty acids (SCFAs), maintaining rumen health, and modulating inflammation.

CONCLUSIONS

In summary, key microbes in the rumen affect the overall healthy homeostasis and rumen fermentation of the host, leading to changes in energy utilization, which in turn affects the average daily gain of Hu sheep. Succinivibrio_dextrinosolvens is a promising biomarker for selecting high growth rate sheep in the future. This study provides a new method to manipulate rumen bacteria to improve growth performance in sheep.

Sialic Acid (Neu5Ac)-Driven Modulation of Intestinal Sialylation as a Novel Approach to Mitigating Allergic Reactions to Shrimp Tropomyosin

Sialic acids are crucial for maintaining intestinal homeostasis, but their role in food allergies remains poorly understood. This study investigates the regulatory function of sialic acid (Neu5Ac) in tropomyosin-induced allergic responses, with the aim of identifying potential therapeutic targets. In a C57BL/6N mouse model sensitized with shrimp tropomyosin, Neu5Ac treatment alleviated allergic symptoms, as evidenced by reduced anaphylaxis scores, lower levels of allergen-specific antibodies and Th2 cytokines, enhanced gut microbiota composition, and increased short-chain fatty acid production. To validate these findings, we used the sialyltransferase inhibitor 3Fax-Peracetyl Neu5Ac to inhibit sialylation in both the mouse and CMT93 cell models. Mice with reduced sialylation displayed more severe allergic symptoms, including diarrhea, elevated anaphylaxis scores, increased antibody levels, a Th2-skewed immune response, compromised intestinal barriers, and higher mortality rates. Similarly, in CMT93 cells, sialylation inhibition led to increased secretion of inflammatory markers and greater cellular permeability. These findings underscore the protective effects of Neu5Ac in alleviating food allergies and suggest that enhancing sialylation could provide a novel therapeutic strategy for managing allergic responses.

Polyphenol metabolism, short-chain fatty acids production, and microbiota changes during in vitro digestion and fermentation of Chilean beans (Phaseolus vulgaris L.)

This study examines the effects of three Chilean boiled bean (Phaseolus vulgaris L.) landraces 'Negro', 'Peumo', and 'Tórtola' and their polyphenol-enriched extracts (PEE) on polyphenol release, gut microbiota, and short-chain fatty acid (SCFA) production after simulated digestion and colonic fermentation. Negro beans exhibited greater phenolic acid diversity post-digestion, while catechin bio accessibility increased in all landraces. PEE showed significant transformation, with oligomers degrading into flavan-3-ol monomers during digestion. Colonic fermentation of boiled beans produced SCFAs, confirming their prebiotic potential. Negro beans promoted beneficial bacteria, including Catenibacterium, Lachnospira, and Bifidobacterium, associated with fiber and polyphenol metabolism, while Tórtola beans favored Roseburia, an SCFA producer. These findings highlight the potential of Chilean beans and their bioactive compounds to enhance gut health.

Specific dietary fibers steer toward distal colonic saccharolytic fermentation using the microbiota of individuals with overweight/obesity

BACKGROUND

Evidence suggests that increased distal short-chain fatty acid (SCFA) production beneficially impacts metabolic health. However, indigestible carbohydrate availability is limited in the distal colon; consequently, microbes shift toward protein fermentation, often linked to adverse metabolic health effects. We aimed to identify specific fiber(s) that promote saccharolytic fermentation in the distal colon and thereby may (partially) inhibit proteolytic fermentation.

METHODS

Potato-fiber, pectin, and inulin were studied individually and in combination against a high (predigested) protein background using an in vitro model of the colon (TIM-2) inoculated with pooled, standardized fecal microbiota from individuals with overweight/obesity. Microbiota composition and activity were assessed at different timepoints to simulate the travel throughout the colon (proximal: 0-8 h, distal: 8-24 h) and compared to a high protein (HP)_control, receiving only proteins.

RESULTS

Fiber addition increased total SCFA production compared to HP_control (52.11 ± 1.49 vs 27.07 ± 0.26 mmol) whereas total branched-chain fatty acids (BCFA; a marker for protein fermentation) production only slightly decreased (3.31 ± 0.10 vs 4.18 ± 0.40 mmol). Combining potato-fiber and pectin led to the highest total and distal SCFA production and distal SCFA:BCFA. Fiber addition attenuated HP-induced increases in several bacterial taxa including Mogibacterium and Coprococcus, independent of fiber type. Additionally, time- and fiber-specific microbial signatures were identified: inulin increased Bifidobacterium (proximal) relative abundance and pectin and/or potato-fiber increased Prevotella 9 (distal) relative abundance.

CONCLUSION

The most marked increase in distal colonic SCFA production was induced by combining potato-fiber and pectin. Further research should elucidate whether this switch toward saccharolytic fermentation translates into beneficial metabolic health effects in humans.

Microbial Contamination in Urban Marine Sediments: Source Identification Using Microbial Community Analysis and Fecal Indicator Bacteria

We investigated the presence of the fecal indicator bacteria Escherichia coli, and other taxa associated with sewage communities in coastal sediments, near beaches with reported poor bathing water quality, focusing on the influence of effluent from a local wastewater treatment plant (WWTP) and combined sewer overflows (CSO). Using a three-year dataset, we found that treated wastewater effluent is a significant source of sewage-associated taxa and viable E. coli in the sediments and that no seasonal differences were observed between spring and summer samples. CSO events have a local and temporary effect on the microbial community of sediments, distinct from that of treated wastewater effluent. Sediments affected by CSO had higher abundances of families Lachnospiraceae, Ruminococcaceae, and Bacteroidaceae. Sewage releases may also impact the natural community of the sediments, as higher abundances of marine sulfur-cycling bacteria were noticed in locations where sewage taxa were also abundant. Microbial contamination at locations distant from known CSO and treatment plant outlets suggests additional sources, such as stormwater. This study highlights that while coastal sediments can be a reservoir of E. coli and contain sewage-associated taxa, their distribution and potential origins are complex and are likely not linked to a single source.

Understanding the role of Hedgehog signaling pathway and gut dysbiosis in fueling liver cancer

Liver cancer is one of the most prevalent types of cancer worldwide with less than 20% of patients surviving in the past half a decade. Several molecular pathways have been uncovered that may lead to the development of liver cancer but more recently the Hedgehog pathway (HH) and its interactions with the gut microbiota has emerged as an underlying cause of the development of liver cancer. Gut-liver axis is vital to maintaining homeostasis. The HH pathway controls cellular differentiation, proliferation, and apoptosis evasions, its abnormal activation can lead to uncontrolled proliferation of liver cancer stem cells. Additionally, the intricate interplay between HH signaling and the gut microbiota introduces a novel dimension. Recent investigations suggest that potential modulation of HH activity by gut microbiota influence HCC progression. This review explores a crosstalk between HH signaling and the gut microbiota, uncovering intricate mechanisms by which it fuels liver cancer development. This interplay provides insights into gut dysbiosis, HCC etiology and potential therapeutic avenues, highlighting the cooperative role of HH signaling and gut microbiota in shaping the overall HCC landscape.

The link between ultra-processed food consumption, fecal microbiota, and metabolomic profiles in older mediterranean adults at high cardiovascular risk

BACKGROUND

Ultra-processed food (UPF) consumption has been linked to adverse metabolic outcomes, potentially mediated by alterations in gut microbiota and metabolite production.

OBJECTIVE

This study aims to explore the cross-sectional and longitudinal associations between NOVA-classified UPF consumption, fecal microbiota, and fecal metabolome in a population of Mediterranean older adults at high cardiovascular risk.

METHODS

A total of 385 individuals, aged between 55 and 75 years, were included in the study. Dietary and lifestyle information, anthropometric measurements, and stool samples were collected at baseline and after 1-year follow-up. Fecal microbiota and metabolome were assessed using 16 S rRNA sequencing and liquid chromatography-tandem mass spectrometry, respectively.

RESULTS

At baseline, higher UPF consumption was associated with lower abundance of Ruminococcaceae incertae sedis (β = - 0.275, P = 0.047) and lower concentrations of the metabolites propionylcarnitine (β = - 0.0003, P = 0.013) and pipecolic acid (β = - 0.0003, P = 0.040) in feces. Longitudinally, increased UPF consumption was linked to reduced abundance of Parabacteroides spp. after a 1-year follow-up (β = - 0.278, P = 0.002).

CONCLUSIONS

High UPF consumption was associated with less favorable gut microbiota and metabolite profiles, suggesting a possible link to reduced short-chain fatty acid (SCFA) production, altered mitochondrial energy metabolism, and impaired amino acid metabolism. These findings support the reduction of UPF consumption and the promotion of dietary patterns rich in fiber for better gut health. Further research is needed to confirm these associations and clarify the underlying mechanisms.

TRIAL REGISTRATION

ISRCTN89898870 ( https://doi.org/10.1186/ISRCTN89898870 ).

Ruminococcus bromii-generated acetate alleviated Clonorchis sinensis-induced liver fibrosis in mice

Introduction

Infection with Clonorchis sinensis (C. sinensis) has the potential to induce liver fibrosis and significantly alter the gut microbiota. However, it remains unclear how these changes in the gut microbiota, through the gut-liver axis, influence the progression of liver fibrosis. Furthermore, it is uncertain whether targeting the gut microbiota, based on the concept of the gut-liver axis, could be a potential therapeutic strategy for alleviating liver fibrosis.

Methods

The gut microbiota alterations in C. sinensis-infected mice at multiple time points were analyzed through 16S rDNA high-throughput sequencing. Ruminococcus bromii (R.bromii) therapeutic effect on C. sinensis infected mice was evaluated. Metabolic changes following produced by R. bromii were analyzed using short-chain fatty acids (SCFAs) metabolomics. Additionally, R. bromii conditioned medium (R.b CM) or its metabolites were co-cultured with two hepatic stellate cell lines (LX2 and JS1) in vitro to assess their anti-fibrotic effects. Finally, RNA sequencing was employed to investigate the specific mechanism by which acetate inhibits hepatic stellate cells (HSCs) activation.

Results

The abundance of R. bromii increased during the inflammatory stage of C. sinensis infection and decreased significantly during the fibrosis stage. Oral gavage of R. bromii significantly inhibited C. sinensis-induced liver fibrosis while restoring the intestinal barrier. The activation of HSCs was significantly inhibited in vitro upon incubation with R.b CM. Acetate was identified as a key metabolite generated from R. bromii in R.b CM, and acetate attenuated C. sinensis-induced liver fibrosis in vitro and in vivo. Mechanistically, acetate inhibited the activation of HSCs by activating the PI3K/AKT signaling pathway to prevent the progression of liver fibrosis in mice infected with C. sinensis.

Discussion

R. bromii exerted a protective effect on hepatic fibrosis by delivering acetate via the gut-liver axis to active the PI3K/AKT signaling pathway in HSCs. Furthermore, R. bromii can be used as a probiotic therapy to alleviate hepatic fibrosis.

Study the effect of Lactobacillus plantarum ATCC 14917 for caries prevention and anti-obesity

Introduction

A complicated scenario where "multiple disease threats coexist and multiple health influencing factors are intertwined" is demonstrated by the fact that dental caries, obesity myopia and scoliosis have emerged as global public health issues. The problem of diseases co-existing in living things can be resolved by using probiotics. Lactobacillus plantarum, has gained attention recently due to its probiotic properties, useful traits, and potential medical applications.

Objective

Examining the anti-obesity and anti-caries effects of L. plantarum ATCC 14917 on dental caries and obese rat models caused by a high-fat and high-sugar diet is the aim of this study.

Method

In vitro, we assessed the L. plantarum strain's probiotic properties, such as its antibacterial activity and ability to build biofilms, to determine its ability to inhibit Streptococcus mutans. Prior to the in vivo experiment, the subsist test for L. plantarum ATCC 14917 was carried out by mimicking its capacity to lower blood sugar and blood lipid levels as well as its tolerance to gastrointestinal disorders. In order to assess the health promotion effect of L. plantarum in vivo. Three-week-old rats were fed a high-sugar, high-fat diet for 8 weeks. They were split into three groups: the control group (Control), the caries and obesity group (CA _OB) and the caries and obesity treated with L. plantarum ATCC14917 group (LP). L. plantarum ATCC 14917 was applied during the experiment, and the associated indices were then thoroughly assessed. These included the use of Mirco-CT to calculate the enamel volume, the staining of liver and fat cell sections, serological analysis, and 16S rRNA sequencing of feces.

Results

It was proved that the L. plantarum could inhibit the proliferation of S. mutans and remove dental plaque biofilm in time, which showed the remarkable effects of anti-caries in vitro. The demineralization rate of enamel decreased by 44.10% due to the inhibition of acid production by pathogenic bacteria. Moreover, In intestinal and stomach juice simulations, L. plantarum has a high survival rate. The characteristics of bacterial activity in a wide range of pH could degrade triglycerides and glucose in vitro smoothly. The LP group demonstrated it by reducing animal weight, serum biochemical indices, and HE-stained adipocytes as compared to the CA_OB group. 16S rRNA sequencing data showed that a high-fat and high-sugar diet induced the imbalance of intestinal flora, which showed an increase in microbial abundance, including unclassified_o__Clostridia_UCG-014, unclassified_f__Oscillospiraceae, Turicibacter, unclassified_f__Lachnospiraceae, Clostridium_sensu_stricto_1. After the intervention of L. plantarum, the number of Lactobacillus, Limosilactobacillus, unclassified_f__Muribaculaceae, Blautia, Faecalibaculum increased significantly.

Conclusion

Therefore, L. plantarum ATCC 14917 performed the potential of reducing tooth decay and controlling weight gain by a single strain. Support the management of dental caries and obesity, and establish a foundation for future functional food research and development.

Intermittent fasting reduces inflammation and joint damage in a murine model of rheumatoid arthritis: insights from transcriptomic and metagenomic analyses

BACKGROUND

Intermittent fasting (IF) has shown benefits in various pathological conditions. Although its anti-inflammatory potential has been recognized, its effects on the mechanism underlying rheumatoid arthritis (RA) remain insufficiently characterized. This study aimed to investigate the effects of IF in a murine model of RA.

METHODS

Collagen-induced arthritis (CIA) was developed in sixteen male DBA/1 mice, randomly assigned to two groups, with one undergoing IF every other day for four weeks. The effects of IF on joint inflammation and remodeling were evaluated clinically, histologically, and through tomography. Transcriptomic changes were characterized using expression microarrays, validated by RT-qPCR, and confirmed by immunohistochemistry. Additionally, modifications in gut microbiota were assessed through 16 S sequencing.

RESULTS

Mice subjected to IF significantly reduced the incidence and severity of clinical arthritis. Histological and radiographic assessments confirmed a decrease in inflammation and joint damage. Transcriptomic analysis revealed that IF led to the upregulation of 364 genes and the downregulation of 543 genes, with notable reductions in inflammatory signaling pathways associated with RA-related genes, including Cd72, Cd79a, Ifna, Il33, and Bglap 2. Notably, IL33 emerged as a pivotal mediator in the inflammatory processes mitigated by fasting. Key regulators associated with IF effects, such as CEBPA, FOXO1, HIF1A, PPARG, and PPARA, were identified, indicating a complex interplay between metabolic and inflammatory pathways. Furthermore, differential expression of microRNAs and lncRNAs, including miR-15b, miR-103-2, miR-302a, miR-6985, and miR- 5624, was observed. Metagenomic analysis indicated that IF enhanced the abundance and diversity of the gut microbiome, explicitly promoting anti-inflammatory bacterial populations, notably within the genus Ruminococcaceae.

CONCLUSION

Our findings suggest that IF exerts significant anti-inflammatory and immunoregulatory effects in the context of CIA. Given its non-risky nature, further investigation into the potential benefits of IF in patients with RA is warranted.

CLINICAL TRIAL NUMBER

Not applicable.

A One-Week Elderberry Juice Intervention Augments the Fecal Microbiota and Suggests Improvement in Glucose Tolerance and Fat Oxidation in a Randomized Controlled Trial

Obesity is a costly and ongoing health complication in the United States and globally. Bioactive-rich foods, especially those providing polyphenols, represent an emerging and attractive strategy to address this issue. Berry-derived anthocyanins and their metabolites are of particular interest for their bioactive effects, including weight maintenance and protection from metabolic aberrations. Earlier findings from small clinical trials suggest modulation of substrate oxidation and glucose tolerance with mediation of prospective benefits attributable to the gut microbiota, but mixed results suggest appropriate anthocyanin dosing poses a challenge. The objective of this randomized, placebo-controlled study was to determine if anthocyanin-dense elderberry juice (EBJ) reproduces glucoregulatory and substrate oxidation effects observed with other berries and if this is mediated by the gut microbiota. Overweight or obese adults (BMI > 25 kg/m2) without chronic illnesses were randomized to a 5-week crossover study protocol with two 1-week periods of twice-daily EBJ or placebo (PL) separated by a washout period. Each treatment period included 4 days of controlled feeding with a 40% fat diet to allow for comparison of measurements in fecal microbiota, meal tolerance testing (MTT), and indirect calorimetry between test beverages. Eighteen study volunteers completed the study. At the phylum level, EBJ significantly increased Firmicutes and Actinobacteria, and decreased Bacteroidetes. At the genus level, EBJ increased Faecalibacterium, Ruminococcaceae, and Bifidobacterium and decreased Bacteroides and lactic acid-producing bacteria, indicating a positive response to EBJ. Supporting the changes to the microbiota, the EBJ treatment significantly reduced blood glucose following the MTT. Fat oxidation also increased significantly both during the MTT and 30 min of moderate physical activity with the EBJ treatment. Our findings confirm the bioactivity of EBJ-sourced anthocyanins on outcomes related to gut health and obesity. Follow-up investigation is needed to confirm our findings and to test for longer durations.

mbDriver: identifying driver microbes in microbial communities based on time-series microbiome data

Alterations in human microbial communities are intricately linked to the onset and progression of diseases. Identifying the key microbes driving these community changes is crucial, as they may serve as valuable biomarkers for disease prevention, diagnosis, and treatment. However, there remains a need for further research to develop effective methods for addressing this critical task. This is primarily because defining the driver microbe requires consideration not only of each microbe's individual contributions but also their interactions. This paper introduces a novel framework, called mbDriver, for identifying driver microbes based on microbiome abundance data collected at discrete time points. mbDriver comprises three main components: (i) data preprocessing of time-series abundance data using smoothing splines based on the negative binomial distribution, (ii) parameter estimation for the generalized Lotka-Volterra (gLV) model using regularized least squares, and (iii) quantification of each microbe's contribution to the community's steady state by manipulating the causal graph implied by gLV equations. The performance of nonparametric spline-based denoising and regularized least squares estimation is comprehensively evaluated on simulated datasets, demonstrating superiority over existing methods. Furthermore, the practical applicability and effectiveness of mbDriver are showcased using a dietary fiber intervention dataset and an ulcerative colitis dataset. Notably, driver microbes identified in the dietary fiber intervention dataset exhibit significant effects on the abundances of short-chain fatty acids, while those identified in the ulcerative colitis dataset show a significant correlation with metabolism-related pathways.