Microbial Metabolite Profiles Research Articles

A traditional fermented bamboo shoot reduces intracellular fat accumulation and promotes fat browning in differentiated 3T3‐L1 adipocyte cells through the activation of the AMPK signaling pathway

AbstractFunctional foods, such as fermented bamboo shoots, have a long history of consumption among the ethnic communities in northeast India. These locally fermented bamboo shoots contain a wealth of beneficial microbes and metabolites that can help combat metabolic syndromes like obesity. However, the precise effects and mechanism behind fermented bamboo shoot products and their anti‐obesity properties remain unknown. This study aims to explore the different types of fermented bamboo shoot products to determine their potential anti‐obesity effects as well as to analyze their microbial diversity and metabolite profiles. Using both culture‐dependent and culture‐independent methods, we found a high abundance of lactic acid bacteria from the Firmicutes and Proteobacteria phyla in the sample. Gas chromatography–mass spectrometry (GC–MS) based untargeted metabolite profiling detected several aroma‐active compounds, bioactive metabolites, short‐chain fatty acids, and essential amino acids in the samples. The water extract derived from a particular type of fermented bamboo shoot, Melye‐amiley, was found to significantly reduce intracellular lipid accumulation in cultured 3T3‐L1 cells. In addition, this extract increased the expression of lipolytic (hormone‐sensitive lipase, lipoprotein lipase, and adipose triglyceride lipase) and browning regulator genes (uncoupling protein [UCP1], PRDM16, and PGC1‐alpha). By activating the AMPK signaling pathway, the water extract from Melye‐amiley also upregulated thermogenic protein expression and promoted mitochondrial biogenesis and fatty acid β‐oxidation. These findings suggest that fermented bamboo shoot extract has promising anti‐obesity effects by boosting energy expenditure in white adipocytes. Future research is necessary to identify the active ingredient(s) that may lead to new therapies to treat obesity.

Effect of phenolics on soil microbe distribution, plant growth, and gall formation

Phenolic compounds, abundant secondary metabolites in plants, profoundly influence soil ecosystems, plant growth, and interactions with herbivores. In this study, we explore the intricate relationships between phenolics, soil microbes, and gall formation in Ageratina adenophora (A. adenophora), an invasive plant species in China known for its allelopathic traits. Using metabolomic and microbial profiling, significant differences in soil microbial composition and metabolite profiles were observed between bulk and rhizosphere soil samples. Phenolics influenced bacterial communities, with distinct microbial populations enriched in each soil type. Additionally, phenolics impacted soil metabolic processes, with variations observed in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis between different soil treatments. Analysis of phenolic content in plant and soil samples revealed considerable variations, with higher concentrations observed in certain plant tissues and soil types. Bioactive phenols extracted from plant and soil samples were identified using gas chromatography/mass spectrometry (GC–MS), providing insights into the diverse chemical composition of these compounds. Furthermore, the effects of phenolics on plant growth and gall formation were investigated. Phenols exhibited both stimulatory and inhibitory effects on plant growth, with optimal concentrations promoting emergence but higher concentrations hindering growth. Gall formation was influenced by phenolic concentrations, leading to structural alterations in stem tissue and gall morphology. Histochemical analysis revealed starch and lipid accumulation in gall tissues, indicating metabolic changes induced by phenolics. The presence of phenolics disrupted tissue structures and influenced vascular bundle orientation in gall tissues. Overall, our study highlights the multifaceted roles of phenolic compounds in soil ecosystems, plant development, and gall formation, facilitating the utilization of secondary metabolites in agriculture.

Changes in seminal plasma microecological dynamics and the mechanistic impact of core metabolite hexadecanamide in asthenozoospermia patients.

Asthenozoospermia (AZS) is a prevalent contributor to male infertility, characterized by a substantial decline in sperm motility. In recent years, large-scale studies have explored the interplay between the male reproductive system's microecology and its implications for reproductive health. Nevertheless, the direct association between seminal microecology and male infertility pathogenesis remains inconclusive. This study used 16S rDNA sequencing and multi-omics analysis to conduct a comprehensive investigation of the seminal microbial community and metabolites in AZS patients. Patients were categorized into four distinct groups: Normal, mild AZS (AZS-I), moderate AZS (AZS-II), and severe AZS (AZS-III). Microbiome differential abundance analysis revealed significant differences in microbial composition and metabolite profiles within the seminal plasma of these groups. Subsequently, patients were classified into a control group (Normal and AZS-I) and an AZS group (AZS-II and AZS-III). Correlation and cross-reference analyses identified distinct microbial genera and metabolites. Notably, the AZS group exhibited a reduced abundance of bacterial genera such as Pseudomonas, Serratia, and Methylobacterium-Methylorubrum in seminal plasma, positively correlating with core differential metabolite (hexadecanamide). Conversely, the AZS group displayed an increased abundance of bacterial genera such as Uruburuella, Vibrio, and Pseudoalteromonas, with a negative correlation with core differential metabolite (hexadecanamide). In vitro and in vivo experiments validated that hexadecanamide significantly enhanced sperm motility. Using predictive metabolite-targeting gene analysis and single-cell transcriptome sequencing, we profiled the gene expression of candidate target genes PAOX and CA2. Protein immunoblotting techniques validated the upregulation protein levels of PAOX and CA2 in sperm samples after hexadecanamide treatment, enhancing sperm motility. In conclusion, this study uncovered a significant correlation between six microbial genera in seminal plasma and the content of the metabolite hexadecanamide, which is related to AZS. Hexadecanamide notably enhances sperm motility, suggesting its potential integration into clinical strategies for managing AZS, providing a foundational framework for diagnostic and therapeutic advancements.

Effects of polyethylene, polylactic acid, and tire particles on the sediment microbiome and metabolome at high and low temperatures.

Global warming has led to a high incidence of extreme heat events, and the frequent occurrence of extreme heat events has had extensive and far-reaching impacts on wetland ecosystems. The widespread distribution of plastics in the environment, including polyethylene (PE), polylactic acid (PLA), and tire particles (TPs), has caused various environmental problems. Here, high-throughput sequencing techniques and metabolomics were used for the first time to investigate the effects of three popular microplastic types: PE, PLA, and TP, on the sediment microbiome and the metabolome at both temperatures. The microplastics were incorporated into the sediment at a concentration of 3% by weight of the dry sediment (wt/wt), to reflect environmentally relevant conditions. Sediment enzymatic activity and physicochemical properties were co-regulated by both temperatures and microplastics producing significant differences compared to controls. PE and PLA particles inhibited bacterial diversity at low temperatures and promoted bacterial diversity at high temperatures, and TP particles promoted both at both temperatures. For bacterial richness, only PLA showed inhibition at low temperature; all other treatments showed promotion. PE, PLA, and TP microplastics changed the community structure of sediment bacteria, forming two clusters at low and high temperatures. Furthermore, PE, PLA, and TP changed the sediment metabolic profiles, producing differential metabolites such as lipids and molecules, organic heterocyclic compounds, and organic acids and their derivatives, especially TP had the most significant effect. These findings contribute to a more comprehensive understanding of the potential impact of microplastic contamination.IMPORTANCEIn this study, we added 3% (wt/wt) microplastic particles, including polyethylene, polylactic acid, and tire particles, to natural sediments under simulated laboratory conditions. Subsequently, we simulated the sediment microbial and ecosystem responses under different temperature conditions by incubating them for 60 days at 15°C and 35°C, respectively. After synthesizing these results, our study strongly suggests that the presence of microplastics in sediment ecosystems and exposure under different temperature conditions may have profound effects on soil microbial communities, enzyme activities, and metabolite profiles. This is important for understanding the potential hazards of microplastic contamination on terrestrial ecosystems and for developing relevant environmental management strategies.

Changes in bacterial composition and metabolite profiles during kimchi fermentation with different garlic varieties

Garlic, a key ingredient in kimchi, is an indispensable source of lactic acid bacteria, which are essential for fermentation. This study explored the effects of various garlic varieties on kimchi fermentation, focusing on changes in microbial communities and metabolite profiles. We observed that the type of garlic used did not significantly alter the microbial community. However, the presence of garlic itself made a significant difference. Specifically, kimchi with garlic showed higher abundance of Leuconostoc and Weissella, which are bacteria primarily responsible for kimchi fermentation. Additionally, kimchi containing garlic had increased levels of mannitol and fructose, which significantly influence taste; however, lactic acid and putrescine levels were decreased. Therefore, the addition of garlic directly contributes to the flavor profile of kimchi. Sixty-two metabolites were identified using gas chromatography and mass spectrometry. The variety of garlic added influenced the metabolite profiles of kimchi, particularly in the later stages of fermentation. These profiles were categorized based on the garlic's origin, whether from southern or northern ecotypes (R2X = 0.933, R2Y = 0.986, Q2 = 0.878). These findings confirm that both the presence and the variety of garlic significantly impact the microbial ecology and metabolites during kimchi fermentation, underscoring its essential role in the process.

Wheat-origin Bacillus community drives the formation of characteristic metabolic profile in high-temperature Daqu

The wheat-origin microbiota plays a crucial role in the microbiome assembly of high-temperature Daqu (HTD), particularly during the early incubation stage. In this study, we compared the succession of microbiota and accumulation of metabolites in two groups: one with inactivated wheat-origin microbiotas and the other with non-inactivated microbiotas, under simulated incubation conditions. The results showed that the wheat-origin Bacillus improved the microbial diversity and metabolite profiles by regulating sugar and amino acid metabolisms. Furthermore, four Bacillus strains with excellent fermentation capabilities were specifically isolated and screened from wheat. Bioaugmentation test on HTD further validated that these wheat-origin Bacillus strains enhanced the accumulation of functional enzymes during the early incubation stage. Amylase activity in HTD significantly increased after inoculation with Priestia megaterium, while protease activity saw a significant boost after Bacillus aerophilus inoculation. Additionally, the introduction of wheat-origin Bacillus strains into the HTD microbiome exogenously caused structural changes in the microbial community, heightened the metabolic activity of the microbiota, and led to elevated levels of amino acids and sugars. The collective findings underscore the pivotal role of the wheat-origin Bacillus community in shaping the distinctive metabolic profile of high-temperature Daqu.

Dynamic Changes in the Microbial Community and Metabolite Profile during the Pile Fermentation Process of Fuzhuan Brick Tea.

The pile fermentation process of Fuzhuan brick tea is unique in that it involves preheating without the use of starter cultures. The detailed metabolite changes and their drivers during this procedure are not known. Characterizing these unknown changes that occur in the metabolites and microbes during pile fermentation of Fuzhuan brick tea is important for industrial modernization of this traditional fermented food. Using microbial DNA amplicon sequencing, mass spectrometry-based untargeted metabolomics, and feature-based molecular networking, we herein reveal that significant changes in the microbial community occur before changes in the metabolite profile. These changes were characterized by a decrease in Klebsiella and Aspergillus, alongside an increase in Bacillus and Eurotium. The decrease in lysophosphatidylcholines, unsaturated fatty acids, and some astringent flavan-3-ols and bitter amino acids, as well as the increase in some less astringent flavan-3-ols and sweet or umami amino acids, contributed importantly to the overall changes observed in the metabolite profile. The majority of these changes was caused by bacterial metabolism and the corresponding heat generated by it.

Plastic residues alter soil microbial community compositions and metabolite profiles under realistic conditions

Wide usage of plastic coupled with mismanagement has created a humongous environmental hazard threatening entire ecosystems. To date, the potential effects of plastic debris-induced soil nutrition substance changes and the relevant microbial metabolic behavior remain unclear. Here, we studied the effect of plastic films polyethylene and polylactic acid in differential soil environments (farmland, woodland, and wetland) for 120 days. Soil enzyme activities (urease, neutral phosphatase, and catalase) and nutrition substance (NH4+-N, available P, available K, and soil organic matter) present obvious variations in polylactic acid groups compared to polyethylene-treated samples. 16S rRNA gene sequencing indicates that several bacteria abundance such as Bacteroidales, Actinobacteriota, Nitrososphaeraceae, Pyrinomonadalcs, Muribaculaceae, exhibited obvious up-regulation or down-regulation, and simultaneously, the carbon, nitrogen, and phosphorus cycling relevant species Bryobacter, Bradyrhizobium, and Sphingomonas, expressed wider margin of down-regulation in abundance in plastic treatment soil samples. As a result, the abundance of metabolites including sugar, amino acid, and fatty acids, which may associated with nutrition substance metabolic pathways, were significantly altered in the stress of plastic. These findings provide valuable information on the environmental effects of plastics, and the relationships of subsequent nutrition substance changes and microbial metabolic behavior.

Alterations of the rhizosphere soil microbial community composition and metabolite profiles of Angelica sinensis seedlings by co-application of Nitrogen fixing bacteria and amino acids

Alterations of the rhizosphere soil microbial community composition and metabolite profiles of Angelica sinensis seedlings by co-application of Nitrogen fixing bacteria and amino acids

Milk oligosaccharide-driven persistence of Bifidobacterium pseudocatenulatum modulates local and systemic microbial metabolites upon synbiotic treatment in conventionally colonized mice

BackgroundBifidobacteria represent an important gut commensal in humans, particularly during initial microbiome assembly in the first year of life. Enrichment of Bifidobacterium is mediated though the utilization of human milk oligosaccharides (HMOs), as several human-adapted species have dedicated genomic loci for transport and metabolism of these glycans. This results in the release of fermentation products into the gut lumen which may offer physiological benefits to the host. Synbiotic pairing of probiotic species with a cognate prebiotic delivers a competitive advantage, as the prebiotic provides a nutrient niche.MethodsTo determine the fitness advantage and metabolic characteristics of an HMO-catabolizing Bifidobacterium strain in the presence or absence of 2′-fucosyllactose (2′-FL), conventionally colonized mice were gavaged with either Bifidobacterium pseudocatenulatum MP80 (B.p. MP80) (as the probiotic) or saline during the first 3 days of the experiment and received water or water containing 2′-FL (as the prebiotic) throughout the study.Results16S rRNA gene sequencing revealed that mice provided only B.p. MP80 were observed to have a similar microbiota composition as control mice throughout the experiment with a consistently low proportion of Bifidobacteriaceae present. Using 1H NMR spectroscopy, similar metabolic profiles of gut luminal contents and serum were observed between the control and B.p. MP80 group. Conversely, synbiotic supplemented mice exhibited dramatic shifts in their community structure across time with an overall increased, yet variable, proportion of Bifidobacteriaceae following oral inoculation. Parsing the synbiotic group into high and moderate bifidobacterial persistence based on the median proportion of Bifidobacteriaceae, significant differences in gut microbial diversity and metabolite profiles were observed. Notably, metabolites associated with the fermentation of 2′-FL by bifidobacteria were significantly greater in mice with a high proportion of Bifidobacteriaceae in the gut suggesting metabolite production scales with population density. Moreover, 1,2-propanediol, a fucose fermentation product, was only observed in the liver and brain of mice harboring high proportions of Bifidobacteriaceae.ConclusionsThis study reinforces that the colonization of the gut with a commensal microorganism does not guarantee a specific functional output.3PG9EvfQrbeVULfWFqBZHnVideo

Soil microbial community compositions and metabolite profiles of Achnatherum inebrians affect phytoremediation potential in Cd contaminated soil

Cadmium (Cd) contamination poses serious risks to soil ecosystems and human health. Herein, the effect of two drunken horse grasses (Achnatherum inebrians) including endophytes Epichloë gansuensis infected (E+ ) and uninfected (E-) on the phytoremediation of Cd-contaminated soils were analyzed by coupling high-throughput sequencing and soil metabolomics. The results showed that the high-risk soil Cd decreased and the medium- and low-risk Cd fraction increased to varying degrees after planting E+ and E- plants in the soil. Meanwhile, total Cd content decreased by 19.7 % and 35.1 % in E+ and E- A. inebrians-planted soils, respectively. Principal coordinate analysis revealed a significant impact of E+ and E- plants on the soil microbial community. Most stress-tolerant and gram-positive functional bacterial taxa were enriched to stabilize Cd(II) in E+ planted soil. Several beneficial fungal groups related to saprotroph and symbiotroph were enriched to absorb Cd(II) in E- soil. Soil metabolomic analysis showed that the introduction of A. inebrians could weaken the threat of CdCl2 to soil microbe metabolism and improve soil quality, which in turn promoted plant growth and improved phytoremediation efficiency in Cd-contaminated soil. In conclusion, A. inebrians plants alleviate soil Cd pollution by regulating soil microbial metabolism and microbial community structure. These results provide valuable information for an in-depth understanding of the phytoremediation mechanisms of A. inebrians.

Effect of salt concentration on Chinese soy sauce fermentation and characteristics

The effect of salt concentration on soy sauce fermentation was studied. Four groups of soy sauce samples with 8%, 12%, 16%, and 20% salt concentrations were prepared and their physicochemical parameters, non-volatile metabolites (organic acids, free amino acids, and biogenic amines), volatile metabolites, and microbial abundance were analyzed during the whole fermentation. The sensory characteristics of the final products were also assessed. Salt concentration significantly affected the microbial abundance and metabolite profiles during soy sauce fermentation, resulting in different characteristics among samples. The RT-qPCR analysis showed that the microbial abundance in lower salted soy sauce was higher. Correspondingly, the accumulation of total acid and the decrease of reducing sugar were observed in lower salted soy sauce, aggravating the sourness of soy sauce. The levels of free amino acids and biogenic amines (detected by HPLC) in lower salted soy sauce were higher, resulting in a taste of umami but making unsafe soy sauce. Additionally, HS-SPME/GC-MS analysis showed that several distinctive volatile compounds were absent in lower salted soy sauce. Sensory evaluation revealed that the highest total score for the quality of soy sauce was obtained through fermentation under 16% salt concentration. This study helped deepen our understanding of the effect of salt on soy sauce fermentation and provide a theoretical data reference for low salt soy sauce development.

Microbial Metabolism of the Soy Isoflavones Daidzein and Genistein in Postmenopausal Women: Human Intervention Study Reveals New Metabotypes.

Soy isoflavones belong to the group of phytoestrogens and are associated with beneficial health effects but are also discussed to have adverse effects. Isoflavones are intensively metabolized by the gut microbiota leading to metabolites with altered estrogenic potency. The population is classified into different isoflavone metabotypes based on individual metabolite profiles. So far, this classification was based on the capacity to metabolize daidzein and did not reflect genistein metabolism. We investigated the microbial metabolite profile of isoflavones considering daidzein and genistein. Isoflavones and metabolites were quantified in the urine of postmenopausal women receiving a soy isoflavone extract for 12 weeks. Based on these data, women were clustered in different isoflavone metabotypes. Further, the estrogenic potency of these metabotypes was estimated. Based on the excreted urinary amounts of isoflavones and metabolites, the metabolite profiles could be calculated, resulting in 5 metabotypes applying a hierarchical cluster analysis. The metabotypes differed in part strongly regarding their metabolite profile and their estimated estrogenic potency.

18 Fecal microbial metabolite profiles are unaltered by laminitis history

Microbial metabolites of the equine gastrointestinal tract may confer information about health and susceptibility to disease. Laminitis is often associated with metabolic disturbances, but little is known of its impact on functional microbial metabolism. A pilot study compared metabolomic profiles of feces collected from 55 native ponies, comprising n = 15 pairs of previously laminitic (PL) and non-laminitic (NL) ponies matched for location, diet, and management, and n = 25 ponies suspected of having an active episode of laminitis (SL) but without clinical diagnosis. Targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis was used. Univariate analyses (ANOVA with Fisher's least significant difference comparisons of PL, NL and SL groups) was performed with significance set at P < 0.05 following Benjamini-Hochberg correction. Principal component analysis (PCA) wasapplied to visualize clustering of individuals. Analysis was performed using the MetaboAnalyst 5.0 web-based interface. Of a panel of 167 metabolites, 104 were identified in the feces, however, none were significantly different between the laminitis status groups. Assessment of the PCA scores plot revealed no clustering of individuals by metabolic profile based on laminitis status. The similar fecal metabolite profile of previously laminitic and non-laminitic ponies indicates that laminitis may not result in significant long-term, alteration of microbial metabolism. Future work to combine these data with that of microbial abundance and species diversity in the feces may reveal further insights into the functional microbial metabolism in laminitic and healthy animals.

Effects of dietary crude protein level and sodium butyrate protected by medium-chain fatty acid salts on performance and gut health in weaned piglets.

To reduce the use of antibiotics, research into nutritional strategies designed to improve the gut health of weaned pigs is underway. This study sought to examine the effects of reducing dietary crude protein (CP) and/or supplementing the feed with sodium butyrate protected by the sodium salts of medium-chain fatty acids on the growth performance and gut health of weaned piglets. Ninety-six weaned piglets (Landrace × large white, 21 days of age) were allotted to four experimental treatments for 14 d. The experimental design was factorial with 2 CP levels and 2 feed-additive doses (0 vs. 1 kg/t). Results showed that reducing CP from 22.2% to 18.8% diet had no effect on piglet growth performance parameters during the first post-weaning week (P > 0.05), but did compromise growth in the second week (P = 0.011), impacting overall growth performance results (P = 0.019). Nonetheless, dietary CP level reduction led reducing crypt depth (P = 0.03657). In addition, Lactobacillus counts that were increased in the ileum (P = 0.032) and reduced in the colon (P = 0.032). Furthermore, apparent ileal digestibility of organic matter (P = 0.026) and fecal consistency (P < 0.05) were improved throughout the experiment. Moreover, in piglets fed diets containing 22.2% CP, the use of the feed-additive tended to improve the gain-to-feed ratio (P = 0.091) compared to those fed supplemented diets containing 18.8% CP. In addition, feed supplementation increased ileal numbers of goblet cells (P = 0.036), as well as apparent ileal digestibility of dry matter (P = 0.057) and organic matter (P = 0.003). Supplementation also had beneficial effects on the microbiota of the colon, increasing Lactobacillus counts (P = 0.006) and diminishing Enterobacteriaceae counts (P = 0.003), as well as affecting microbial metabolite profiles in that acetic acid concentrations tended to be increased (P = 0.088) and valeric acid concentrations were reduced (P = 0.002). These findings support the use of both strategies can improve the gut health of weaned piglets and prompt further research into the possible benefits of combining these two nutritional strategies on gut health and growth performance.

Microbial communities and metabolite profiles during the fermentation of Chinese Dongbei suancai with Chinese baijiu as supplementary material.

In industrial production of suancai, baijiu is commonly used to inhibit the spoilage bacteria and enhance the flavor. However, the effects of baijiu on the microbial diversity and metabolic pathways of suancai are rarely reported in the literature. This study aimed to explore the microbial community, its predicted functional roles, and the metabolites formed during fermentation of Chinese Dongbei suancai fermented using a mixed starter with Chinese baijiu as supplementary material. Results showed that Lactobacillus, Enterobacter, and Leuconostoc were the major bacterial genera in the Dongbei suancai fermented by adding baijiu. Linear discriminant analysis effect size indicated that Leuconostoc was the major biomarker in the early stage of fermentation, whereas Lactococcus, Weissella, and Lactobacillus plantarum were biomarkers in the middle and later stages of fermentation. A total of 638 metabolites were detected in suancai fermented by adding baijiu. However, the principal component analysis showed that baijiu significantly affected the metabolites of suancai in the early and later stages of fermentation. Furthermore, 58, 22, and 26 significantly differential metabolites (P < 0.01) were found on day0, day2, and day 30 of fermentation respectively. Moreover, Lactobacillus, Lactococcus, and Enterobacter had positive correlations with amino acids, nucleotides, organic acids, alcohols, and esters. Functional analysis implied that carbohydrate, amino acid, energy, and nucleotide metabolism were the major determinants of the characteristics of suancai fermented with baijiu as supplementary material. Baijiu changed the metabolites of inoculated fermented Dongbei suancai. © 2023 Society of Chemical Industry.

Lactate and buyrate proportions, methanogen growth and gas production during in vitro dietary fibre fermentation all depend on fibre concentration

Dietary fibre (DF) concentration plays a critical role in the gas kinetics and short-chain fatty acid production profiles during in vitro human faecal fermentation. However, the mechanisms leading to concentration-dependent fermentation outcomes are unknown. In this study, fructo-oligosaccharides and pectin at three concentrations (0.2, 0.4 and 0.6g/44mL), were selected to investigate the effect of DF type and concentration on human gut microbiota. An absolute quantification method was applied to determine the microbial biomass and load for each genus. Additionally, the gas kinetics and fermentation metabolites (acetate, propionate, butyrate, i-butyrate, valerate, i-valerate, formate, succinate, methanol, ethanol and lactate) were measured. Results showed that DF type and concentration affected the microbial diversity, microbial loads and metabolite profiles to different extents. At high DF concentrations Methanobrevibacter , a genus of Archaea, was found to increase by ∼28 fold for FOS, and ∼93 fold for pectin. We propose three main pathways, dictated by DF type and concentration, driving the observed alterations in microbial loads and metabolite profiles. Firstly, the lactate cross-feeding pathway could lead to increased butyrate production. Secondly, methanogenesis from H 2 and CO 2 , and thirdly, reductive acetyl-CoA pathways resulted in the conversion of gases to increase microbial biomass. Understanding these underlying mechanisms allows for tailoring DF fermentation by varying their concentrations to control SCFA and gas production. • Higher DF concentration led to increased butyrate proportion via lactate cross-feeding. • Higher DF concentration led to more gas production, triggering gas cross-feeding. • Absolute quantification of microbiota revealed concentration-dependent biomass shifts. • Methanogenesis and reductive acetyl-CoA pathways led to biomass growth. • Cross-feeding of lactate and gases also depended on DF type.

Periodontitis-induced oral microbiome alterations provide clues on how periodontitis exacerbates colitis.

To evaluate whether and how microbiota-derived metabolites associated with periodontitis aggravate colitis in mice. A mouse model of periodontitis and colitis was constructed. Unbiased transcriptomic analyses of the colon were performed to explore important pathways through which periodontitis exacerbated colitis. Oral and gut bacteria were analysed using 16S rRNA sequencing. Gas chromatography-mass spectrometry was used to observe the alterations of oral and gut metabolites. Isolated intestinal lamina propria lymphocytes were analysed by flow cytometry. Inflammasome pathway was detected using qRT-PCR, Western blotting or ELISA. Periodontitis activated the colonic inflammasome pathway and altered the gut microbial composition and metabolite profiles in mice with colitis. Notably, periodontitis induced increase of the faecal metabolite isoleucine (Ile) which was synthesized by microbiota and plants. Moreover, periodontitis upregulated the Ile levels in saliva, but not in serum, indicating that Ile might be an oral pathobiont-synthesizing metabolite that transited from the oral cavity to the gut. Ile triggered the inflammasome pathway, upregulated the number of inflammatory IL-1βhigh MHCIIhigh Ly6Chigh monocytes in colonic lamina propria, and exacerbated colitis. Further studies found that the Ile metabolite acetyl-coenzyme A positively regulated NLRP3 inflammasome by KAT5-mediated acetylation of NLRP3. Our study revealed that alteration in periodontitis-induced microbial metabolites deteriorated colitis in a mouse model and that this was associated with Ile production.

Molecular characterization of gut microbiome in weaning pigs supplemented with multi-strain probiotics using metagenomic, culturomic, and metabolomic approaches

BackgroundProbiotics have been reported to exhibit positive effects on host health, including improved intestinal barrier function, preventing pathogenic infection, and promoting nutrient digestion efficiency. These internal changes are reflected to the fecal microbiota composition and, bacterial metabolites production. In accordance, the application of probiotics has been broadened to industrial animals, including swine, which makes people to pursue better knowledge of the correlation between changes in the fecal microbiota and metabolites. Therefore, this study evaluated the effect of multi-strain probiotics (MSP) supplementation to piglets utilizing multiomics analytical approaches including metagenomics, culturomics, and metabolomics.ResultsSix-week-old piglets were supplemented with MSP composed of Lactobacillus isolated from the feces of healthy piglets. To examine the effect of MSP supplement, piglets of the same age were selected and divided into two groups; one with MSP supplement (MSP group) and the other one without MSP supplement (Control group). MSP feeding altered the composition of the fecal microbiota, as demonstrated by metagenomics analysis. The abundance of commensal Lactobacillus was increased by 2.39%, while Clostridium was decreased, which revealed the similar pattern to the culturomic approach. Next, we investigated the microbial metabolite profiles, specifically SCFAs using HPLC–MS/MS and others using GC–MS, respectively. MSP supplement elevated the abundance of amino acids, including valine, isoleucine and proline as well as the concentration of acetic acid. According to the correlation analyses, these alterations were found out to be crucial in energy synthesizing metabolism, such as branched-chain amino acid (BCAA) metabolism and coenzyme A biosynthesis. Furthermore, we isolated commensal Lactobacillus strains enriched by MSP supplement, and analyzed the metabolites and evaluated the functional improvement, related to tight junction from intestinal porcine enterocyte cell line (IPEC-J2).ConclusionsIn conclusion, MSP administration to piglets altered their fecal microbiota, by enriching commensal Lactobacillus strains. This change contributed amino acid, acetic acid, and BCAA concentrations to be increased, and energy metabolism pathway was also increased at in vivo and in vitro. These changes produced by MSP supplement suggests the correlation between the various physiological energy metabolism functions induced by health-promoting Lactobacillus and the growth performance of piglets.

Seasonal variations in microbial diversity and metabolite profiles of the gut of sea cucumber (Apostichopus japonicus)

The sea cucumber (Apostichopus japonicus) is the main economic species in China and has a significant role in aquaculture. Gut microbiome composition is closely related to external environments. In this study, we identified the effects of seasonal changes on the composition and main metabolites of symbiotic microorganisms in the intestine of A. japonicus. We used 16S rRNA sequencing to identify the composition of symbiotic microorganisms in different seasons. Intestinal metabolites were determined using liquid chromatography with tandem mass spectrometry, which linked symbiotic microorganisms to intestinal metabolites. Analyzing changes in intestinal microbial composition across different seasons. The results showed that seasonal changes of intestinal microorganisms were significant, A. japonicus were infected by Vibrio easily in summer, Stigmasterol and sitosterol could affect the growth of body wall of A. japonicus. It is vital importance for A. japonicus that the results benefit for the growth, immunity and aquaculture.