Microbiome最新文献

{"title":"Microbial diurnal rhythmicity in the rumen fluid impacted by feeding regimes and exogenous microbiome providing novel mechanisms regulating dynamics of the rumen microbiome.","authors":"Yangyi Hao, Wei Wang, Mengmeng Li, Youyoung Choi, Mi Zhou, Yixin Wang, Zhijun Cao, Ya Jing Wang, Hongjian Yang, Linshu Jiang, Le Luo Guan, Shengli Li","doi":"10.1186/s40168-025-02134-6","DOIUrl":"10.1186/s40168-025-02134-6","url":null,"abstract":"<p><strong>Background: </strong>Diurnal oscillations have been reported on ruminal prokaryotes, but the daily rhythmicity of eukaryotes remains unknown. This study investigated diurnal oscillations of ruminal prokaryotes and eukaryotes under three different feeding managements and rumen fluid transplantation conditions, aiming to elucidate the regulatory mechanisms influencing the dynamic shifts of rumen microbiome through the daily feeding cycle.</p><p><strong>Results: </strong>Quantification and profiling of the microbiota of 288 rumen samples collected from lactating dairy cows (n = 12) every 6-h over 48-h feeding cycles under ad libitum, restricted feeding at daytime and nighttime, respectively, revealed the rhythmicity in the population and abundance of ruminal bacteria, archaea, and protozoa. Under restricted-feeding regimes, 61.99% bacterial genera including Prevotella and Ruminococcus, and 7.19% archaeal species including Methanosphaera sp. ISO3-F5, and 66.93% protozoa genera including Entodinium and Isotricha showed feeding-time-influenced changes in circadian rhythms. However, 4.76% bacterial genera such as Prevotellaceae_UCG-001, and 0.29% archaeal species such as group 12 sp. ISO4-H5 exhibited non-feeding-time affected circadian rhythm pattern shifts. Further analysis of 176 rumen fluid samples collected after rumen fluid transplantation showed the proportion of bacterial, archaeal, and protozoal taxa displayed consistent (including Anaeroplasma and Fibrobacter), inconsistent (including Bacteroidales_UCG-001 and NK4A214_group), gain (including Prevotella and Succinivibrio), and loss (including Butyrivibrio and Mycoplasma) of circadian rhythms over the 48-h to 7-day period after transplantation. Similar circadian patterns were found among feed intake, ruminal volatile fatty acid concentrations, bacterial functions such as glycolysis/gluconeogenesis, and deterministic assembly processes of bacterial communities. However, different circadian patterns (12-h shifts) were observed for rumination time, ruminal pH, ammonia nitrogen concentration, and bacterial functions such as chemotaxis, nitrogen metabolism, and deterministic assembly processes of archaeal communities. Additionally, cross-lagged effects were observed between the relative abundance of microbial taxa and rumen fermentation parameters, which could affect feed intake, rumination time, microbial population/diversity, and microbial interactions. Video Abstract CONCLUSIONS: The classified feeding-time responsive, multi-factor responsive, consistent, and inconsistent circadian rhythm of microbial taxa underscore the driven factors behind the daily dynamics of rumen microbes, which also filled the gaps for targeting specific microbial taxa for better animal production.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"142"},"PeriodicalIF":13.8,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12168421/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144310191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HIV infection and exposure is associated with increased cariogenic taxa, reduced taxonomic turnover, and homogenized spatial differentiation for the supragingival microbiome.","authors":"Allison E Mann, Ciara Aumend, Suzanne Crull, Lauren M O'Connell, Esosa Osagie, Paul Akhigbe, Ozoemene Obuekwe, Augustine Omoigberale, Matthew Rowe, Thomas Blouin, Ashlyn Soule, Colton Kelly, Robert A Burne, Modupe O Coker, Vincent P Richards","doi":"10.1186/s40168-025-02123-9","DOIUrl":"10.1186/s40168-025-02123-9","url":null,"abstract":"<p><strong>Background: </strong>The oral microbiome consists of distinct microbial communities that colonize various ecological niches within the oral cavity, the composition of which are influenced by nutrient and substrate availability, host genetics, diet, behavior, age, and other diverse host and environmental factors. Unlike other densely populated human-associated microbial ecosystems (e.g., gut, urogenital), the oral microbiome is directly and frequently exposed to external influences, contributing to its relatively lower stability over time. In individuals with compromised immunity, such as those living with HIV, the composition and stability of the oral microbiome may be especially vulnerable to disruption. Cross-sectional studies of the oral microbiome in children living with HIV capture a glimpse of this temporal dynamism, yet a full appreciation of the relative stability, robusticity, and spatial structure of the oral environment is necessary to understand the role of microbial communities in promoting health or disease in the context of HIV. Here, we investigate the spatial and temporal stability of the oral microbiome over three sampling time points in the context of HIV infection and exposure. Individual teeth were sampled from a cohort of 565 Nigerian children with varying levels of tooth decay severity (i.e., caries disease). We collected 1960 supragingival plaque samples and characterized the oral microbiome using a metataxonomic approach targeting an approximately 478 bp region of the bacterial rpoC gene.</p><p><strong>Results: </strong>Both HIV infection and exposure have significant, if subtle, effects on the stability of the supragingival plaque microbiome. Specifically, we observed (1) a slight but significant reduction in taxonomic turnover among HIV-exposed and infected children; (2) an association between HIV infection and a more homogenized oral community across the anterior and posterior dentition in children living with HIV; and (3) a relationship between impaired immunity, lower taxonomic turnover over time, and an elevated frequency of cariogenic taxa, including Streptococcus mutans, in children living with HIV.</p><p><strong>Conclusions: </strong>Despite the influence of various contributing factors, we observe an effect of HIV status on both the temporal and spatial stability of the oral microbiome. Specifically, the results presented here indicate that the oral microbiome shows less community change over time in children living with or exposed to HIV, which we hypothesize may be linked to a reduced capacity to adapt to environmental changes. The observed taxonomic rigidity among children living with HIV may signal community dysfunction, potentially leading to a higher incidence of oral diseases, including caries, in this cohort. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"144"},"PeriodicalIF":13.8,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12168284/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144310190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Underground guardians: how collagen and chitin amendments shape soil microbiome structure and function for Meloidogyne enterolobii control.","authors":"Josephine M Pasche, Roshni Sawlani, Victor Hugo Buttrós, Johan Desaeger, Karen A Garrett, Samuel J Martins","doi":"10.1186/s40168-025-02132-8","DOIUrl":"10.1186/s40168-025-02132-8","url":null,"abstract":"<p><strong>Background: </strong>The 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.</p><p><strong>Results: </strong>Both 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.</p><p><strong>Conclusions: </strong>The findings highlight the potential of collagen and chitin to mitigate M. enterolobii infection by fostering beneficial soil microbial communities. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"141"},"PeriodicalIF":13.8,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12160343/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144285410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut bacterium Acinetobacter sp. assists Camellia weevil with host plant adaptation by degrading tea saponin via the benzoate pathway.","authors":"Feng Song, Jinping Shu, Shouke Zhang","doi":"10.1186/s40168-025-02131-9","DOIUrl":"10.1186/s40168-025-02131-9","url":null,"abstract":"<p><strong>Background: </strong>The 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.</p><p><strong>Methods: </strong>We 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.</p><p><strong>Results: </strong>Toxicity 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.</p><p><strong>Conclusion: </strong>Our 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.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"139"},"PeriodicalIF":13.8,"publicationDate":"2025-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12144740/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144248628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Species turnover within cystic fibrosis lung microbiota is indicative of acute pulmonary exacerbation onset.","authors":"Leah Cuthbertson, Lauren Hatfield, Helen Gavillet, Michelle Hardman, Ryan Marsh, Damian W Rivett, Christopher van der Gast","doi":"10.1186/s40168-025-02143-5","DOIUrl":"10.1186/s40168-025-02143-5","url":null,"abstract":"<p><strong>Background: </strong>Acute pulmonary exacerbations (PEx) are associated with increased morbidity and earlier mortality for people living with cystic fibrosis (pwCF). The most common causes of PEx in CF are by bacterial infection and concomitant inflammation leading to progressive airway damage. To draw attention to the seriousness of PEx they have been labelled as 'lung attacks', much like a 'heart attack' for acute myocardial infarction. Treatment typically starts when a pwCF presents with worsening respiratory symptoms. Hence, there is a pressing need to identify indicative biomarkers of PEx onset to allow more timely intervention. Set within an ecological framework, we investigated temporal microbiota dynamics to connect changes in the lung microbiota of pwCF to changes in disease states across a PEx event.</p><p><strong>Results: </strong>Species-time relationships (STR) describe how the richness of a community changes with time, here STRs were used to assess temporal turnover (w) within the lung microbiota of each pwCF (n = 12, mean sample duration 315.9 ± 42.7 days). STRs were characterised by high interpatient variability, indicating that turnover and hence temporal organization are a personalized feature of the CF lung microbiota. Greater turnover was found to be significantly associated with greater change in lung function with time. When microbiota turnover was examined at a finer scale across each pwCF time series, w-values could clearly be observed to increase in the exacerbation period, then peaking within the treatment period, demonstrating that increases in turnover were not solely a result of perturbations caused by PEx antibiotic interventions. STR w-values have been found to have a remarkable degree of similarity for different organisms, in a variety of habitats and ecosystems, and time lengths (typically not exceeding w = 0.5). Here, we found w-values soon increased beyond that. It was therefore possible to use the departure from that expected norm up to start of treatment to approximate onset of PEx in days (21.2 ± 8.9 days across the study participants).</p><p><strong>Conclusions: </strong>Here, we illustrate that changes in turnover of the lung microbiota of pwCF can be indicative of PEx onset in considerable advance of when treatment would normally be initiated. This offers translational potential to enable early detection of PEx and consequent timely intervention. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"140"},"PeriodicalIF":13.8,"publicationDate":"2025-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12144788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144248629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Effect of inulin supplementation in maternal fecal microbiota transplantation on the early growth of chicks.","authors":"Mengxian Chen, Junxing Pan, Yang Song, Shenao Liu, Peng Sun, Xin Zheng","doi":"10.1186/s40168-025-02135-5","DOIUrl":"10.1186/s40168-025-02135-5","url":null,"abstract":"","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"138"},"PeriodicalIF":13.8,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12131747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Feeding probiotics-fermented distiller's grains diets increases rumen enzyme activities and glycerophospholipid levels in finishing cattle by modulating rumen microbiota.","authors":"Rong Zhang, Shihui Mei, Guangxia He, Miaozhan Wei, Lan Chen, Ze Chen, Yuanqi Zhong, Bijun Zhou, Kaigong Wang, Zhentao Cheng, Chunmei Wang, Erpeng Zhu, Chao Chen","doi":"10.1186/s40168-025-02138-2","DOIUrl":"10.1186/s40168-025-02138-2","url":null,"abstract":"<p><strong>Background: </strong>Distiller's grains (DG), a major by-product of the Chinese Baijiu industry, represent an inexpensive yet high-quality protein raw material. Previous studies have shown that probiotics-fermented distiller's grains (FDG) hold the potential to serve as an effective livestock feed resource. However, the impacts of feeding FDG-based diets on rumen enzyme activities, rumen microbial communities and metabolism in finishing cattle, along with their underlying regulatory mechanisms, remain poorly understood.</p><p><strong>Results: </strong>After 45 days of feeding FDG diets, rumen enzyme activities increased significantly. Feeding 10% FDG diets increased the relative abundance of the bacterial genus Prevotella_1 and the fungal genera Candida, Mucor, and Scedosporium in the rumen. Conversely, the relative abundances of bacterial genera Veillonellaceae UCG-001 and Candidatus Saccharimonas, as well as fungal genus Talaromyces, were reduced notably in the rumen following FDG diet supplementation. Compared to the FDG-10% group, the FDG-20% group exhibited a higher relative abundance of the beneficial bacterial genus Bifidobacterium and the fungal genus Plectosphaerella. Non-targeted metabolomic analysis indicated that the differential metabolites were primarily categorized as benzenoids, lipids and lipid-like molecules, and organic acids and derivatives, which were significantly enriched in the neuroactive ligand-receptor interaction and taste transduction metabolic pathways. Untargeted lipidomic analysis further demonstrated that feeding 20% FDG diets elevated the levels of glycerophospholipids in the rumen. Spearman analysis identified the correlations between specific bacterial and fungal genera and rumen enzyme activities, differential metabolites, and lipids.</p><p><strong>Conclusions: </strong>These results suggest that feeding FDG diets potentially improves rumen enzyme activities and up-regulates the levels of glycerophospholipids in the rumen, which may be associated with the alterations in specific rumen microbiota involved in degrading cellulose. Of these, 20% FDG replacement emerges as a better dose within the range of FDG additions in this study. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"137"},"PeriodicalIF":13.8,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12131443/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144208943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ACE2 shedding exacerbates sepsis-induced gut leak via loss of microbial metabolite 5-methoxytryptophan.","authors":"Jiacheng Gong, Haoyang Lu, Yuhan Li, Qihan Xu, Yuanyuan Ma, Anni Lou, Wanfu Cui, Weihua Song, Peng Qu, Zhuoer Chen, Linghao Quan, Xi Liu, Ying Meng, Xu Li","doi":"10.1186/s40168-025-02128-4","DOIUrl":"10.1186/s40168-025-02128-4","url":null,"abstract":"<p><strong>Background: </strong>Sepsis, a critical organ dysfunction resulting from an aberrant host response to infection, remains a leading cause of mortality in ICU patients. Recent evidence suggests that angiotensin-converting enzyme 2 (ACE2) contributes to intestinal barrier function, the mechanism of which is yet to be explored. Additionally, alterations in intestinal microbiota and microbial metabolites could affect gut homeostasis, thus playing a potential role in modulating sepsis progression.</p><p><strong>Results: </strong>ACE2 shedding weakens the integrity of the intestinal barrier in sepsis. Mice deficient in ACE2 exhibited increased intestinal permeability and higher mortality rates post-operation compared to their wild-type counterparts. Notably, ACE2 deficiency was associated with distinct alterations in gut microbiota composition and reductions in protective metabolites, such as 5-methoxytryptophan (5-MTP). Supplementing septic mice with 5-MTP ameliorated gut leak through enhanced epithelial cell proliferation and repair. The PI3K-AKT-WEE1 signaling pathway was identified as a key mediator of the beneficial effects of 5-MTP administration.</p><p><strong>Conclusion: </strong>ACE2 plays a protective role in maintaining intestinal barrier function during sepsis, potentially through modulation of the gut microbiota and the production of key metabolite 5-MTP. Our study enriched the mechanisms by which ACE2 regulates gut homeostasis and shed light on further applications. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"136"},"PeriodicalIF":13.8,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12123736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144179996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A consortium of seven commensal bacteria promotes gut microbiota recovery and strengthens ecological barrier against vancomycin-resistant enterococci.","authors":"Alan Jan, Perrine Bayle, Nacer Mohellibi, Clara Lemoine, Frédéric Pepke, Fabienne Béguet-Crespel, Isabelle Jouanin, Marie Tremblay-Franco, Béatrice Laroche, Pascale Serror, Lionel Rigottier-Gois","doi":"10.1186/s40168-025-02127-5","DOIUrl":"10.1186/s40168-025-02127-5","url":null,"abstract":"<p><strong>Background: </strong>Vancomycin-resistant enterococci (VRE) often originate from the gastrointestinal tract, where their proliferation precedes dissemination into the bloodstream, and can lead to systemic infection. Uncovering the actors and mechanisms reducing the intestinal colonisation by VRE is essential to control infection. We aimed to identify commensal bacteria that interfere with VRE gut colonisation or act as an ecological barrier.</p><p><strong>Results: </strong>We performed a 3-week longitudinal analysis of the gut microbiota composition and VRE carriage levels during microbiota recovery in mice colonised with VRE after antibiotic-induced dysbiosis. By combining biological data and mathematical modelling, we identified 15 molecular species (OTUs) that negatively correlated with VRE overgrowth. Six strains representative of these OTUs were collected, cultivated and used in mixture with a seventh strain (Mix7) in two different mouse lines challenged with VRE. Of the seven strains, three belonged to Lachnospiraceae, one to Muribaculaceae, one to Ruminococcaceae and two to Lactobacillaceae. We found that Mix7 led to a better recovery of the gut microbiota composition and reduced VRE carriage. Differences in the effect of Mix7 were observed between responder and non-responder mice. These differences were associated with variations in the composition of the initial microbiota and during recovery and represent potential biomarkers for predicting response to Mix7. In a mouse model of alternative stable state of dysbiosis, response to Mix7 was associated with higher concentrations of short-chain fatty acids (acetate, propionate, butyrate) and a range of metabolites including bile acids, reflecting the recovery of the microbiota back to initial state. Furthermore, Muribaculum intestinale strain was required to obtain the Mix7 effect on VRE reduction in vivo, but the presence of at least one of the other six strains was needed. None of the supernatant of the seven strains, alone or in combination, inhibited VRE growth in vitro. Interestingly, five strains belong to species shared among humans and mice, and the other two have human functional equivalents.</p><p><strong>Conclusions: </strong>An innovative approach based on mathematical modelling of the microbiota composition permitted to identify a mixture of commensal bacterial strains, which improves the ecological barrier effect against VRE. The mechanisms are dependent on the recovery and initial composition of the microbiota. Ultimately, this work will enable a move towards a personalised medicine by targeting predisposed patients presenting a risk of infection, such as neutropenic or bone-marrow transplant patients, and likely to respond to supplementation with commensal strains, providing new live biotherapeutic products and biomarkers to predict response to supplementation. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"129"},"PeriodicalIF":13.8,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12105331/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144142918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Milk sialyl-oligosaccharides mediate the early colonization of gut commensal microbes in piglets.","authors":"Ryoga Hashimoto, Keita Nishiyama, Fu Namai, Kasumi Suzuki, Taiga Sakuma, Itsuko Fukuda, Yuta Sugiyama, Kenji Okano, Takafumi Shanoh, Eita Toyoshi, Ryusuke Ohgi, Sudeb Saha, Sae Tsuchida, Eri Nishiyama, Takao Mukai, Mutsumi Furukawa, Tomonori Nochi, Julio Villena, Wakako Ikeda-Ohtsubo, Gou Yoshioka, Eri Nakazaki, Yoshihito Suda, Haruki Kitazawa","doi":"10.1186/s40168-025-02129-3","DOIUrl":"10.1186/s40168-025-02129-3","url":null,"abstract":"<p><strong>Background: </strong>The suckling period in pigs is a key phase in development for shaping the gut microbiota, which is essential for maintaining biological homeostasis in neonates. In piglets fed sow milk, the gut microbiota comprises predominantly lactobacilli, indicating a host-gut microbiota symbiosis that is influenced by sow milk components. In this study, we sought to elucidate the mechanisms underlying the establishment and maintenance of the gut microbiome in suckling piglets, with a specific focus on the metabolism of sialyl-oligosaccharides by lactobacilli.</p><p><strong>Results: </strong>Based on liquid chromatography-mass spectrometry analysis, we identified 3'-sialyl-lactose (3'SL) as the major oligosaccharide in porcine milk, and microbiome profiling revealed the predominance of Ligilactobacillus salivarius during the suckling period, with a subsequent transition to Limosilactobacillus reuteri dominance post-weaning. Notably, sialic acid metabolism was established to be exclusively attributable to L. salivarius, thereby highlighting the pivotal role of 3'SL in determining species-specific bacterial segregation. L. salivarius was found to metabolize 3'SL when co-cultured with Bacteroides thetaiotaomicron, resulting in a shift in the predominant short-chain fatty acid produced, from lactate to acetate. This metabolic shift, in turn, inhibits the growth of enterotoxigenic Escherichia coli. Furthermore, the comparison of the gut microbiota between suckling piglets and those fed a low-3'SL formula revealed distinct diversity profiles. We accordingly speculate that an absence of sialyl-oligosaccharides in the formula-fed piglets may have restricted the growth of sialic acid-utilizing bacteria such as L. salivarius, thereby leading to a higher abundance of Enterobacteriaceae.</p><p><strong>Conclusions: </strong>Our findings reveal the influence of sialyl-oligosaccharides in promoting microbial diversity and gut homeostasis, thereby highlighting the importance of sialic acid as a key factor in shaping milk-driven microbial colonization during the early stages of piglet development. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"135"},"PeriodicalIF":13.8,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12103040/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144142920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}