BackgroundThe human gut microbiota produces short-chain carboxylic acids (SCCA) through fermentation of undigested carbohydrates, and through chain elongation, a process that can be modulated through diet. Valerate is frequently recovered from human fecal samples, but little is known about dietary components, microbial contributors, and cross-feeding interactions that drive human intestinal valerate formation. We combined co-culture studies and in vitro human fecal microbiota batch fermentations (n = 20) with the analysis of a free-living cohort of obese and overweight women (n = 49) that monitored and modified (fermented) dairy consumption, to study the role of dairy-derived lactose and lactate in intestinal microbial formation of valerate.ResultsWhile the valerate producer Megasphaera elsdenii was not able to use lactose in single culture, valerate was formed (6.2 ± 1.3 mM) in co-culture with the lactose-utilizing and lactate-producing food microbe Streptococcus thermophilus. In vitro, valerate was produced by fecal microbiota of most donors (15/20) in control medium. Lactose addition significantly (p < 0.05) increased valerate formation of fecal microbiota that harbored Megasphaera at levels ≥ 5 log cells/mL (n = 4), while valerate formation was lower when Megasphaera was less abundant or not detected (n = 15). The addition of M. elsdenii to batch fermentations increased valerate production in 80% of samples and correlation analysis showed a positive correlation (p < 0.001) between relative abundance of Megasphaera and valerate levels. In vivo, 30% of study participants harbored Megasphaera based on 16S rRNA gene amplicon sequencing and species-specific qPCR. Diet supplementation with drained yogurt (skyr) led to higher fecal microbial diversity (p < 0.05) and relative abundance of Streptococcaceae. Participants that harbored Megasphaera and consumed skyr daily had significantly (p < 0.05) higher fecal valerate levels at week 6 compared to controls. In addition, fecal levels of lactate were higher in the skyr compared to the control group at 12 weeks. Linear discriminant analysis suggested co-occurrence of Megasphaera with the lactate-producer Lactobacillus and competition with other lactate utilizers such as the Anaerobutyricum hallii group.ConclusionThis study brings forward new mechanistic understanding on the intestinal microbial formation of the SCCA valerate. Our findings identified Megasphaera as an infrequently occurring and low abundant keystone taxon contributing to lactose/lactate-driven valerate production in overweight/obese women. Our results highlight that the presence of Megasphaera affects the fermentative response to daily consumption of fermented dairy.Video Supplementary InformationThe online version contains supplementary material available at 10.1186/s40168-025-02207-6.

The incidence of atopic dermatitis (AD) has increased globally in recent decades. A recent study identified enrichment of Faecalibacterium subspecies in young AD patients, implicating these gut bacteria in disease pathogenesis. This was unexpected, as Faecalibacterium is widely recognized as one of the most beneficial bacteria in the human gut. We tested the bacteria in female mice and observed their effect on the gut microbiome and overall health, which subsequently influenced the health of their offspring. These effects were markedly exacerbated when female mice were fed a low-fiber diet, leading to heightened systemic inflammation, skin damage, and hair loss in their offspring. Offspring of female mice receiving a low-fiber diet without pathobiont administration exhibited reduced symptom severity, which was further mitigated bythe administration of the beneficial strain A2-165. These findings provide compelling evidence that maternalFaecalibacterium pathobionts play a critical role in the development of systemic conditions in offspring, offering valuable insights into the etiology of AD. Furthermore, the synergistic effect of gut microbiota dysbiosis and low fiber intake highlights the potential impact of modern dietary trends on the rising prevalence of AD and other chronic conditions. Video Abstract.

BackgroundRecent studies suggest a role of gut microbiota in the development of neonatal hyperbilirubinemia, with bifidobacteria showing promise in alleviating symptoms. However, uncertainties persist regarding gut bifidobacterial species composition and their effects on bilirubin metabolism. Therefore, the study investigated the association between the gut microbiota and neonatal hyperbilirubinemia, assessing the potential and underlying mechanisms of Bifidobacterium in managing the condition.ResultsCompared to the high-risk group (requiring clinical intervention), low-risk neonates (designated as controls without therapeutic needed) demonstrated a higher abundance of breastfeeding-associated Bifidobacterium species, including Bifidobacterium longum subsp. infantis, B. bifidum, and B. breve. In an experimental neonatal hyperbilirubinemia rat model, these Bifidobacterium species’ protective effects were demonstrated by reducing serum bilirubin levels, maintaining growth and development, and improving neurobehavioral reflexes. These benefits are associated with improved liver and intestinal barrier functions and reduced enterohepatic circulation of bilirubin. Among the various treatment groups, B. longum subsp. infantis exhibited the most potent effect, followed by B. bifidum and B. breve. Intestinal metabolism analysis revealed that the levels of arachidonic acid and docosahexaenoic acid were increased and negatively correlated with bilirubin levels. These findings were further confirmed in the neonatal cohort study. Direct supplementation of these metabolites into the colon of neonatal rats improved disease phenotypes. In addition, both in vitro and in vivo experiments demonstrated the specific inhibitory effect of arachidonic acid and docosahexaenoic acid on β-glucuronidase enzyme activity. Notably, both in vitro intestinal fermentation models and genomic analyses demonstrated that the three Bifidobacterium species cannot synthesize these unsaturated fatty acids due to the lack of related genes. However, data suggested that these species might promote the accumulation of arachidonic acid and docosahexaenoic acid by regulating the gut microbiota’s structure and function. Moreover, these species show species-specific genomic distribution patterns, which might influence the gut microbiota's α-linolenic and linoleic acid metabolism pathways, thereby affecting bilirubin levels.ConclusionsThe results indicate that Bifidobacterium species associated with breastfeeding can prevent neonatal hyperbilirubinemia by regulating the gut microbiota–α-linolenic and linoleic acid metabolism–enterohepatic circulation axis, increasing gut metabolites arachidonic acid and docosahexaenoic acid, and reducing the enterohepatic circulation of bilirubin.Video Supplementary InformationThe online version contains supplementary material available at 10.1186/s40168-025-02190-y.

BackgroundSulfoquinovose (SQ) is a green-diet-derived sulfonated glucose and a selective substrate for a limited number of human gut bacteria. Complete anaerobic SQ degradation via interspecies metabolite transfer to sulfonate-respiring bacteria produces hydrogen sulfide, which has dose- and context-dependent health effects. Here, we studied potential SQ degradation by the mammalian host and the impact of SQ supplementation on human and murine gut microbiota diversity and metabolism.Results13CO2 breath tests with germ-free C57BL/6 mice gavaged with 13C-SQ were negative. Also, SQ was not degraded by human intestinal cells in vitro, indicating that SQ is not directly metabolized by mice and humans. Addition of increasing SQ concentrations to human fecal microcosms revealed dose-dependent responses of the microbiota and corroborated the relevance of Agathobacter rectalis and Bilophila wadsworthia in cooperative degradation of SQ to hydrogen sulfide via interspecies transfer of 2,3-dihydroxy-1-propanesulfonate (DHPS). Similar to the human gut microbiome, the genetic capacity for SQ or DHPS degradation is sparsely distributed among bacterial species in the gut of conventional laboratory mice. Escherichia coli and Enterocloster clostridioformis were identified as primary SQ degraders in the mouse gut. SQ and DHPS supplementation experiments with conventional laboratory mice and their intestinal contents showed that SQ was incompletely catabolized to DHPS. Although some E. clostridioformis genomes encode an extended sulfoglycolytic pathway for both SQ and DHPS fermentation, SQ was only degraded to DHPS by a mouse-derived E. clostridioformis strain.ConclusionsOur findings suggest that SQ is solely a nutrient for the gut microbiota and not for mice and humans, emphasizing its potential as a prebiotic. SQ degradation by the microbiota of conventional laboratory mice differs from the human gut microbiota by absence of DHPS degradation activity. Hence, the microbiota of conventional laboratory mice does not fully represent the SQ metabolism in humans, indicating the need for alternative model systems to assess the impact of SQ on human health. This study advances our understanding of how individual dietary compounds shape the microbial community structure and metabolism in the gut and thereby potentially influence host health.Video Supplementary InformationThe online version contains supplementary material available at 10.1186/s40168-025-02175-x.

BackgroundMangrove wetlands are critical hotspots of methane emissions, yet the role of naturally occurring minerals in shaping their microbial communities and methanogenic processes is poorly understood. Magnetite, a common iron mineral in soils and sediments, has been reported to enhance aceticlastic methanogenesis and facilitate syntrophic methanogenesis. In this study, we integrated multi-omic profiling with cultivation-based approaches to investigate the impact of magnetite on methanogenesis of microbial consortia derived from mangrove sediments, using lactate as a substrate.ResultsAcross five serial transfers, mangrove microbial consortia converted lactate to propionate and acetate, which were subsequently degraded into methane. Magnetite addition significantly stimulated methane production, leading to notable changes in community structure, particularly for aceticlastic methanogens, with Methanosarcina predominating in the magnetite-amended cultures and Methanothrix in controls. Four Methanosarcina strains T3, T4, T13, and MeOH were subsequently isolated from magnetite-amended cultures. Combined analyses of metagenome-assembled genomes and the genomes of these isolates revealed that the enriched Methanosarcina in magnetite-amended cultures belonged to type II deficient in hydrogenotrophic methanogenesis pathway. Metatranscriptomic analyses suggested that magnetite addition stimulated aceticlastic methanogenesis of type II Methanosarcina and hydrogenotrophic methanogenesis of Methanomicrobiales in the consortia. Furthermore, pure culture experiments confirmed that magnetite stimulated aceticlastic methanogenesis by Methanosarcina sp. T3, although its gene expression patterns differed from those observed in the microbial consortia. Additionally, Methanofastidiosales, an uncultured archaeal lineage possessing H2-dependent methylotrophic methanogenesis, was detected in all transfers.ConclusionsOur findings demonstrate that magnetite alters methanogenic consortia in mangrove sediments, selectively stimulating aceticlastic methanogenesis of type II Methanosarcina and modulating hydrogenotrophic activity in Methanomicrobiales. By integrating multi-omics analyses with pure culture validation, we demonstrate, for the first time, that magnetite directly enhances the aceticlastic methanogenesis of type II non-hydrogenotrophic Methanosarcina. This study provides new insights into the influence of magnetite on complex microbial consortia, offers a deeper understanding of the physiology of type II non-hydrogenotrophic Methanosarcina, and advances knowledge of mineral-mediated regulation of methanogenic networks in anoxic environments.Video Supplementary InformationThe online version contains supplementary material available at 10.1186/s40168-025-02157-z.

BackgroundPlant-microbe interactions are essential for mitigating abiotic and biotic stressors by shaping the rhizosphere environment. However, how rhizosphere beneficial bacteria and plant metabolites respond to glufosinate (GLU)-induced toxicity remains largely unknown.ResultsOur study investigates the impact of GLU on chili plant growth and rhizosphere microbiome, emphasizing GLU-induced alterations in amino acid profiles, secondary metabolites, and microbial community composition, with notable enrichment of the Rhodococcus genus. To uncover the underlying mechanisms of Rhodococcus genus-root exudate interactions under GLU stress, we successfully isolated an efficient Rhodococcus gordoniae strain TR-5 from soil samples contaminated with GLU. This strain, isolated from GLU-contaminated soil, demonstrates potential for bioremediation and achieved over 95% GLU degradation efficiency at 35 °C, pH 6.38, and 1% inoculation rate. Through growth analysis, chemotaxis analysis, and molecular docking, caffeic acid disrupts the bacterial strain’s metabolic pathways and impedes TR-5 development. In contrast, jasmonic acid (JA) acts as a chemoattractant, promoting bacterial growth and metabolic activity to degrade GLU residues, thereby effectively degrading GLU residues in the soil.ConclusionsThis research indicates that GLU significantly influences the metabolic mechanisms of pepper plants. The optimization of microbial remediation strategies may improve soil remediation efficiency and reduce environmental impacts, highlighting opportunities for integrating microbial remediation into sustainable agricultural practices. Our findings provide insights into the role of JA in attracting and promoting the growth and metabolic activities of the Rhodococcus genus, which could be harnessed to improve soil remediation and plant health under GLU stress.Bpan91VuLfcPc8VpwQR5MeVideo Graphical

BackgroundFecal microbiota transplantation (FMT) is widely used to treat severe infections and investigated for the treatment of complex diseases. The therapeutic efficacy of FMT is related to the successful engraftment of bacteriophages from healthy donors to recipients. However, gut bacteriophage contributions to FMT engraftment and treatment outcomes remain unclear.MethodsThe gut phageome from previously published metagenomes of donors and recipients across 23 FMT studies was assembled and functionally annotated for a meta-analysis.ResultsGut phageome profiles of FMT recipients, especially those with recurrent Clostridioides difficile infection (rCDI), shifted toward donor phageomes, accompanied by increased phageome alpha diversity. Engraftment of donor phages varied between recipient conditions with the highest engraftment rate, overrepresented by putative temperate phage, in patients with rCDI. Consistently, a higher proportion of auxiliary metabolic genes (AMGs), with the potential to support and modulate bacterial metabolism, were annotated on putative temperate phages.ConclusionsFMT leads to significant taxonomic, functional, and lifestyle shifts in recipient phageome composition. Future FMT studies should include gut phageome characterization and consider it as a potential factor in microbial community shifts and treatment outcomes.-G1oHZCF2wv-7sDo5fAhHeVideo

BackgroundThe emergence of the guava root-knot nematode (Meloidogyne enterolobii) poses a significant threat to tomato yields globally. This study evaluated the impact of collagen and chitin soil amendments on soil microbial composition and function (fungal and bacterial communities) and their effects on tomato plant health and M. enterolobii infection under standard (5000 eggs plant−1) and high (50,000 eggs plant−1) inoculum pressure. Conducted in a greenhouse setting, the study investigated the effectiveness of these amendments in nurturing beneficial microbial communities across both native and agricultural soils.ResultsBoth collagen and chitin were effective in reducing nematode egg counts by up to 66% and 84% under standard and high inoculum pressure, respectively, and enhanced plant health parameters (biomass and chlorophyll content). Moreover, a microbiome shift led to an increase in bacterial (Kitasatospora, Bacillus, and Streptomyces) and fungal (Phialemonium) genera, known for their chitinase, collagenase, and plant-parasitic nematode control. Among the microbes, Streptomyces spp. were found among the core microbiome and associated with a lower disease incidence assessed through a phenotype-OTU network analysis (PhONA). Under standard inoculum, higher metabolite expression was observed with amino acids representing a majority among the metabolite groups.ConclusionsThe findings highlight the potential of collagen and chitin to mitigate M. enterolobii infection by fostering beneficial soil microbial communities.3MP_RGo-aN6Gq_K2eAsUB4Video

BackgroundThe extent to which herbivorous insects depend on gut bacteria and the molecular mechanisms by which these microbes help overcome host plant chemical defenses remain controversial. This study explored how the gut symbiont Acinetobacter sp. AS23 of a Camellia weevil (Curculio chinensis) (CW) enhances the weevil’s tolerance to toxic tea saponins in host plants.MethodsWe first conducted toxicity assays in which third-instar CW larvae were exposed to fermentation filtrates containing tea saponin degradation products from the weevil’s gut bacterium, the AS23 strain. A combination of metabolomic and transcriptomic analyses was used to investigate the degradation pathway and key genes used by the AS23 strain in tea saponin metabolism. We then re-inoculated axenic larvae with bacterial mutants generated through CRISPR-Cas9 and verified gene functions in tea saponin degradation.ResultsToxicity assays demonstrated that the AS23 strain exhibited time-dependent tea saponin degradation capabilities. The benzoate degradation pathway emerged as a core metabolic pathway enriched during tea saponin degradation, with the involvement of four key enzyme genes confirmed through qPCR and functional studies. Knockout strains exhibited a significantly reduced detoxification capacity and increased larval mortality when reintroduced into CWs’ gut.ConclusionOur findings elucidated the key role of the AS23 strain in mediating CW larvae tolerance to tea saponins through the benzoate degradation pathway. This study highlights the potential of leveraging microbial saponin degradation pathways for developing environmentally friendly pest control strategies.