Microbiome research reports最新文献

{"title":"The oncobiome; what, so what, now what?","authors":"Munawar Abbas, Mark Tangney","doi":"10.20517/mrr.2024.89","DOIUrl":"https://doi.org/10.20517/mrr.2024.89","url":null,"abstract":"<p><p>Microbial communities inhabiting various body sites play critical roles in the initiation, progression, and treatment of cancer. The gut microbiota, a highly diverse microbial ecosystem, interacts with immune cells to modulate inflammation and immune surveillance, influencing cancer risk and therapeutic outcomes. Local tissue microbiota may impact the transition from premalignant states to malignancy. Characterization of the intratumoral microbiota increasingly reveals distinct microbiomes that may influence tumor growth, immune responses, and treatment efficacy. Various bacteria species have been reported to modulate cancer therapies through mechanisms such as altering drug metabolism and shaping the tumor microenvironment (TME). For instance, gut or intratumoral bacterial enzymatic activity can convert prodrugs into active forms, enhancing therapeutic effects or, conversely, inactivating small-molecule chemotherapeutics. Specific bacterial species have also been linked to improved responses to immunotherapy, underscoring the microbiome's role in treatment outcomes. Furthermore, unique microbial signatures in cancer patients, compared with healthy individuals, demonstrate the diagnostic potential of microbiota. Beyond the gut, tumor-associated and local microbiomes also affect therapy by influencing inflammation, tumor progression, and drug resistance. This review explores the multifaceted relationships between microbiomes and cancer, focusing on their roles in modulating the TME, immune activation, and treatment efficacy. The diagnostic and therapeutic potential of bacterial members of microbiota represents a promising avenue for advancing precision oncology and improving patient outcomes. By leveraging microbial biomarkers and interventions, new strategies can be developed to optimize cancer diagnosis and treatment.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"4 1","pages":"16"},"PeriodicalIF":0.0,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11977386/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144040551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Host-dependent alteration of the gut microbiota: the role of luminal microRNAs.","authors":"Céline Cuinat, Jiali Pan, Elena M Comelli","doi":"10.20517/mrr.2024.46","DOIUrl":"https://doi.org/10.20517/mrr.2024.46","url":null,"abstract":"<p><p>MicroRNAs (miRNAs) are short, non-coding RNAs that play gene expression regulatory roles in eukaryotes. MiRNAs are also released in body fluids, and in the intestine, they are found in the lumen and feces. Here, together with exogenous dietary-derived miRNAs, they constitute the fecal miRNome. Several miRNAs were identified in the feces of healthy adults, including, as shown here, core miRNAs hsa-miR-21-5p and hsa-miR-1246. These miRNAs are important for intestinal homeostasis. Recent evidence suggests that miRNAs may interact with gut bacteria. This represents a new avenue to understand host-bacteria crosstalk in the gut and its role in health and disease. This review provides a comprehensive overview of current knowledge on fecal miRNAs, their representation across individuals, and their effects on the gut microbiota. It also discusses existing evidence on potential mechanisms of uptake and interaction with bacterial genomes, drawing from knowledge of prokaryotic small RNAs (sRNAs) regulation of gene expression. Finally, we review <i>in silico</i> and experimental approaches for profiling miRNA-mRNA interactions in bacterial species, highlighting challenges in target validation. This work emphasizes the need for further research into host miRNA-bacterial interactions to better understand their regulatory roles in the gut ecosystem and support their exploitation for disease prevention and treatment.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"4 1","pages":"15"},"PeriodicalIF":0.0,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11977366/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144060917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advances in engineered bacteria vaccines for enhancing anti-cancer immunity.","authors":"Wu Liu, Wenjing Chen, Yujie Cai, Yanhua Tang, Tingtao Chen","doi":"10.20517/mrr.2024.75","DOIUrl":"https://doi.org/10.20517/mrr.2024.75","url":null,"abstract":"<p><p>Advances in synthetic biology have enabled the development of tumor-targeted live bacterial therapeutics. In a recent study published in <i>Nature</i>, Redenti <i>et al.</i> engineered <i>Escherichia coli</i> Nissle 1917(EcNc^{Δlon/ΔompT/LLO+} nAg), which exploits the advantages of living medicines to deliver arrays of tumor-specific neoantigenic epitope in optimal environments, thereby providing a novel strategy for developing effective and durable cancer immunotherapies.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"4 1","pages":"14"},"PeriodicalIF":0.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11977376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144036811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Host-microbiota interactions in the infant gut revealed by daily faecal sample time series.","authors":"Nienke van Beek, Iiris Katavisto, Markku Lehto, Kaija-Leena Kolho, Willem M de Vos, Anne Salonen, Katri Korpela","doi":"10.20517/mrr.2024.45","DOIUrl":"https://doi.org/10.20517/mrr.2024.45","url":null,"abstract":"<p><p><b>Aim:</b> This study aims to explore the interplay between host immune factors and gut microbiota in human infants <i>in vivo</i> using time-series daily stool samples and identify biomarkers of host-microbe interactions. <b>Methods:</b> 216 faecal samples collected from infants aged 5-6 or 11-12 months were analysed for gut microbiota composition, total bacterial load, and biomarkers of immune function. <b>Results:</b> We identified indications of microbial stimulation of eosinophil cationic protein (ECP), IgA, calprotectin (Cal), intestinal alkaline phosphatase (IAP), and Bactericidal/permeability-increasing protein (BPI) at 6 and 12 months, as well as stimulation of lipocalin 2 (LCN2), lactoferrin (LTF), and alpha-defensin-5 only at 6 months. The associations between biomarker concentrations and bacterial population growth were primarily positive at 6 months and mostly negative at 12 months, suggesting increasing host regulation of the microbiota with age. The exceptions were IAP, which was predictive of declining bacterial populations at both time points, and Cal, whose associations changed from negative at 6 months to positive at 12 months. <b>Conclusion:</b> There is an age-associated development in the correlation pattern between bacterial population growth and the biomarker concentrations, suggesting that host-microbe interactions change during early development. Albumin appeared as a potential marker of gut permeability, while LCN2 seemed to correlate with gut transit time. Mucin degradation appeared to decrease with age. Mucin2 and IAP emerged as potentially important regulators of the bacterial populations in the infant gut. The study demonstrates the utility of biomarker and bacteria profiling from daily stool samples for analysing <i>in vivo</i> associations between the immune system and the gut microbiota and provides evidence of host regulation of the microbiota in infants.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"4 1","pages":"13"},"PeriodicalIF":0.0,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11977378/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144055928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How human milk shapes the gut microbiota in preterm infants: potential for optimizing early-life microbial development.","authors":"Pamela Thomson, Daniel Garrido","doi":"10.20517/mrr.2024.86","DOIUrl":"https://doi.org/10.20517/mrr.2024.86","url":null,"abstract":"<p><p>Breast milk plays a crucial role in shaping the gut microbiota of preterm infants, with significant microbial sharing influenced by feeding practices and antibiotics, highlighting the benefits of direct breastfeeding for gut health.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"4 1","pages":"12"},"PeriodicalIF":0.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11977357/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144049303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Potential effects of probiotics on atherosclerosis.","authors":"Gerrit A Stuivenberg, Annabel Poon, Jeremy P Burton, J David Spence","doi":"10.20517/mrr.2024.22","DOIUrl":"https://doi.org/10.20517/mrr.2024.22","url":null,"abstract":"<p><p>The rising global incidence of atherosclerosis highlights the inadequacies in our understanding of the pathophysiology and treatment of the disease. Increasing evidence outlines the importance of the intestinal microbiome in atherosclerosis, wherein gut-derived uremic toxins (GDUTs) may be of concern. Plasma levels of the GDUTs trimethylamine n-oxide (TMAO), <i>p</i>-cresyl sulfate, and indoxyl sulfate are associated with accelerated renal function decline and increased cardiovascular risk. Thus, reducing the amount of GDUTs in circulation is expected to benefit patients with atherosclerosis. Because some beneficial bacteria can clear GDUTs <i>in vitro</i> and <i>in vivo</i>, orally administered probiotics targeting the intestinal tract represent a promising way to bring about these changes. Atherosclerosis such, this perspective reviews the potential use of probiotics to treat atherosclerosis, particularly in patients with non-traditional risk factors and/or impaired renal function.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"4 1","pages":"11"},"PeriodicalIF":0.0,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11977382/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144035447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Galacto-oligosaccharides alone and combined with lactoferrin impact the Kenyan infant gut microbiota and epithelial barrier integrity during iron supplementation <i>in vitro</i>.","authors":"Carole Rachmühl, Christophe Lacroix, Adele Ferragamo, Ambra Giorgetti, Nicole U Stoffel, Michael B Zimmermann, Gary M Brittenham, Annelies Geirnaert","doi":"10.20517/mrr.2024.34","DOIUrl":"https://doi.org/10.20517/mrr.2024.34","url":null,"abstract":"<p><p><b>Aim:</b> Iron supplementation to African weaning infants was associated with increased enteropathogen levels. While cohort studies demonstrated that specific prebiotics inhibit enteropathogens during iron supplementation, their mechanisms remain elusive. Here, we investigated the <i>in vitro</i> impact of galacto-oligosaccharides (GOS) and iron-sequestering bovine lactoferrin (bLF) alone and combined on the gut microbiota of Kenyan infants during low-dose iron supplementation. <b>Methods:</b> Different doses of iron, GOS, and bLF were first screened during batch fermentations (<i>n</i> = 3), and the effect of these factors was studied on microbiota community structure and activity in the new Kenyan infant continuous intestinal PolyFermS model. The impact of different fermentation treatments on barrier integrity, enterotoxigenic <i>Escherichia coli</i> (ETEC) infection, and inflammatory response was assessed using a transwell co-culture of epithelial and immune cells. <b>Results:</b> A dose-dependent increase in short-chain fatty acid (SCFA) production, <i>Bifidobacterium</i> and <i>Lactobacillus</i>/<i>Leuconostoc</i>/<i>Pediococcus</i> (LLP) growth was detected with GOS alone and combined with bLF during iron supplementation in batches. This was confirmed in the continuous PolyFermS model, which also showed a treatment-induced inhibition of opportunistic pathogens <i>C. difficile</i> and <i>C. perfringens</i>. In all tests, supplementation of iron alone and combined with bLF did not have a significant effect on microbiota composition and activity. We observed a strengthening of the epithelial barrier and a decrease in cell death and pro-inflammatory response during ETEC infection with microbiota fermentation supernatants from iron + GOS, iron + bLF, and iron + GOS + bLF treatments compared to iron alone. <b>Conclusion:</b> Overall, beneficial effects on infant gut microbiota were shown using advanced <i>in vitro</i> models for GOS alone and combined with bLF during low-dose iron supplementation.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"4 1","pages":"9"},"PeriodicalIF":0.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11978484/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144061162","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Potential applications of engineered bacteria in disease diagnosis and treatment.","authors":"Zhaowei Luo, Zhanghua Qi, Jie Luo, Tingtao Chen","doi":"10.20517/mrr.2024.57","DOIUrl":"https://doi.org/10.20517/mrr.2024.57","url":null,"abstract":"<p><p>Probiotics are live microorganisms that confer health benefits to the host when administered in appropriate quantities. This beneficial effect has spurred extensive research in the medical and health fields. With rapid advancements in synthetic biology, the genetic and biological characteristics of a broad array of probiotics have been elucidated. Utilizing these insights, genetic editing technologies now enable the precise modification of probiotics, leading to the development of engineered bacteria. Emerging evidence underscores the significant potential of these engineered bacteria in disease management. This review explores the methodologies for creating engineered bacteria, their preliminary applications in healthcare, and the mechanisms underlying their functions. Engineered bacteria are being developed for roles such as <i>in vivo</i> drug delivery systems, biosensors, and mucosal vaccines, thereby contributing to the treatment, diagnosis, and prevention of conditions including inflammatory bowel disease (IBD), metabolic disorders, cancer, and neurodegenerative diseases. The review concludes by assessing the advantages and limitations of engineered bacteria in the context of disease management.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"4 1","pages":"10"},"PeriodicalIF":0.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11977365/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144059418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of mother's own milk <i>vs.</i> donor human milk on gut microbiota colonization in preterm infants: a systematic review.","authors":"Jing Chen, Aranka J van Wesemael, Nerissa P Denswil, Hendrik J Niemarkt, Johannes B van Goudoever, Vanesa Muncan, Tim G J de Meij, Chris H P van den Akker","doi":"10.20517/mrr.2024.44","DOIUrl":"https://doi.org/10.20517/mrr.2024.44","url":null,"abstract":"<p><p><b>Background:</b> Nutritional intake in preterm infants is associated with short- and long-term outcomes. The favorable outcomes of preterm infants who predominantly receive their mother's own milk (MOM) are thought to be mediated partly through beneficial effects on the gut microbiome. When MOM is not available, donor human milk (DHM) is recommended as the best alternative. However, DHM is less effective in preventing adverse outcomes, which may be explained by compositional differences between MOM and DHM, resulting in different microbiome development. This systematic review focuses on the effects of predominant DHM <i>vs.</i> MOM feeding on the gut microbiota composition in preterm infants. <b>Methods:</b> A comprehensive search was conducted across MEDLINE, Embase, and Cochrane databases. Eight out of the 717 publications identified were included. Data on gut microbiota composition, alpha diversity, and taxonomic differences between DHM- and MOM-fed preterm infants were extracted and analyzed. <b>Results:</b> The microbiome composition was distinct between the two feeding groups. Alpha diversity measures were lower in DHM-fed infants, particularly when preterm formula (PF) was also provided. DHM-fed infants showed higher abundances of <i>Staphylococcaceae</i> and <i>Clostridiaceae</i>, and lower abundances of Bacteroidetes and <i>Bifidobacterium</i>. <b>Conclusion:</b> The observed gut microbiome differences in DHM-fed preterm infants have previously been linked to adverse health outcomes. This underlines the importance of increasing the awareness of MOM intake in preterm infants. Further studies should explore the mechanisms through which human milk affects health outcomes.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"4 1","pages":"8"},"PeriodicalIF":0.0,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11977380/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144033496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mobile genetic elements: the hidden puppet masters underlying infant gut microbiome assembly?","authors":"Kim Kreuze, Ville-Petri Friman, Tommi Vatanen","doi":"10.20517/mrr.2024.51","DOIUrl":"https://doi.org/10.20517/mrr.2024.51","url":null,"abstract":"<p><p>The gut microbiota is important for healthy infant development. Part of the initial colonizing microbial strains originate from the maternal gut, and undergo a selective event, termed the \"colonization bottleneck\". While vertical mother-to-infant inheritance and subsequent colonization of bacteria have previously been studied, the role of mobile genetic elements (MGEs) in the infant gut microbiota assembly is unclear. In this perspective article, we discuss how horizontally and vertically transmitted phages and conjugative elements potentially have important roles in infant gut microbiota assembly and colonization through parasitic and mutualistic interactions with their bacterial hosts. While some of these MGEs are likely to be detrimental to their host survival, in other contexts, they may help bacteria colonize new niches, antagonize other bacteria, or protect themselves from other parasitic MGEs in the infant gut. As a result, the horizontal transfer of MGEs likely occurs at high rates in the infant gut, contributing to gene transfer between bacteria and affecting which bacteria can pass the colonization bottleneck. We conclude by highlighting the potential <i>in silico</i>, <i>in vitro</i>, and <i>in vivo</i> methodological approaches that could be employed to study the transmission and colonization dynamics of MGEs and bacteria in the infant gut.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"4 1","pages":"7"},"PeriodicalIF":0.0,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11977359/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144047292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}