@article {pmid39797472,
year = {2025},
author = {Chong-Nguyen, C and Yilmaz, B and Coles, B and Sokol, H and MacPherson, A and Siepe, M and Reineke, D and Mosbahi, S and Tomii, D and Nakase, M and Atighetchi, S and Ferro, C and Wingert, C and Gräni, C and Pilgrim, T and Windecker, S and Blasco, H and Dupuy, C and Emond, P and Banz, Y and Losmanovà, T and Döring, Y and Siontis, GCM},
title = {A scoping review evaluating the current state of gut microbiota and its metabolites in valvular heart disease physiopathology.},
journal = {European journal of clinical investigation},
volume = {},
number = {},
pages = {e14381},
doi = {10.1111/eci.14381},
pmid = {39797472},
issn = {1365-2362},
abstract = {BACKGROUND: The human microbiome is crucial in regulating intestinal and systemic functions. While its role in cardiovascular disease is better understood, the link between intestinal microbiota and valvular heart diseases (VHD) remains largely unexplored.

METHODS: Peer-reviewed studies on human, animal or cell models analysing gut microbiota profiles published up to April 2024 were included. Eligible studies used 16S rRNA or shotgun sequencing, metabolite profiling by mass spectrometry, and examined osteogenesis or fibrosis signalling in valve cells. Methods and findings were qualitatively analysed, with data charted to summarize study design, materials and outcomes.

RESULTS: Thirteen studies were included in the review: five human, three animal and five in vitro. Of the nine studies on calcific aortic stenosis (CAS), elevated trimethylamine N-oxide (TMAO) levels were linked to an increased risk of cardiovascular events in cohort studies, with CAS patients showing higher levels of Bacteroides plebeius, Enterobacteriaceae, Veillonella dispar and Prevotella copri. In vivo, TMAO promoted aortic valve fibrosis, while tryptophan derivatives stimulated osteogenic differentiation and interleukin-6 secretion in valvular interstitial cells. Two studies on rheumatic mitral valve disease found altered microbiota profiles and lower short-chain fatty acid levels, suggesting potential impacts on immune regulation. Two studies on Barlow's mitral valve disease in animal models revealed elevated TMAO levels in dogs with congestive heart failure, reduced Paraprevotellaceae, increased Actinomycetaceae and dysbiosis involving Turicibacter and E. coli.

CONCLUSIONS: TMAO has been mainly identified as a prognostic marker in VHD. Gut microbiota dysbiosis has been observed in various forms of VHD and deserve further study.},
}

@article {pmid39796469,
year = {2024},
author = {Wu, F and Guo, Y and Wang, Y and Sui, X and Wang, H and Zhang, H and Xin, B and Yang, C and Zhang, C and Jiang, S and Qu, L and Feng, Q and Dai, Z and Shi, C and Li, Y},
title = {Effects of Long-Term Fasting on Gut Microbiota, Serum Metabolome, and Their Association in Male Adults.},
journal = {Nutrients},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/nu17010035},
pmid = {39796469},
issn = {2072-6643},
support = {2022SY54B0506, BJH22WS1J002, 18035020103//the Advanced Space Medico-Engineering Research Project of China/ ; SMFA22Q03, SMFA22B04//The State Key Laboratory of Space Medicine, China Astronaut Research and Training Center/ ; HYZHXM01002//the Space Medical Experiment Project of China Manned Space Program/ ; JCYJ20200109110630285//he Shenzhen Science and Technology Innovation Commission 2020 Basic Research Project/ ; 2022YFA1604504//National Key R&D Program of China/ ; },
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/physiology ; *Fasting/blood ; *Metabolome ; Pilot Projects ; Adult ; Animals ; Obesity/microbiology/blood ; Bacteria/classification ; Diet, High-Fat ; },
abstract = {BACKGROUND: Long-term fasting demonstrates greater therapeutic potential and broader application prospects in extreme environments than intermittent fasting.

METHOD: This pilot study of 10-day complete fasting (CF), with a small sample size of 13 volunteers, aimed to investigate the time-series impacts on gut microbiome, serum metabolome, and their interrelationships with biochemical indices.

RESULTS: The results show CF significantly affected gut microbiota diversity, composition, and interspecies interactions, characterized by an expansion of the Proteobacteria phylum (about six-fold) and a decrease in Bacteroidetes (about 50%) and Firmicutes (about 34%) populations. Notably, certain bacteria taxa exhibited complex interactions and strong correlations with serum metabolites implicated in energy and amino acid metabolism, with a particular focus on fatty acylcarnitines and tryptophan derivatives. A key focus of our study was the effect of Ruthenibacterium lactatiformans, which was highly increased during CF and exhibited a strong correlation with fat metabolic indicators. This bacterium was found to mitigate high-fat diet-induced obesity, glucose intolerance, dyslipidemia, and intestinal barrier dysfunction in animal experiments. These effects suggest its potential as a probiotic candidate for the amelioration of dyslipidemia and for mediating the benefits of fasting on fat metabolism.

CONCLUSIONS: Our pilot study suggests that alterations in gut microbiota during CF contribute to the shift of energy metabolic substrate and the establishment of a novel homeostatic state during prolonged fasting.},
}

Humans
Male
*Gastrointestinal Microbiome/physiology
*Fasting/blood
*Metabolome
Pilot Projects
Adult
Animals
Obesity/microbiology/blood
Bacteria/classification
Diet, High-Fat

@article {pmid39796301,
year = {2024},
author = {Galazka, S and Vigl, V and Kuffner, M and Dielacher, I and Spettel, K and Kriz, R and Kreuzinger, N and Vierheilig, J and Woegerbauer, M},
title = {Prevalence of Antibiotic Resistance Genes in Differently Processed Smoothies and Fresh Produce from Austria.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/foods14010011},
pmid = {39796301},
issn = {2304-8158},
support = {BMASGK-74602/0005-IX/B/15/2019//Austrian Federal Ministry of Social Affairs, Health, Care and Consumer Protection (BMASGK)/ ; },
abstract = {Plant-derived foods are potential vehicles for microbial antibiotic resistance genes (ARGs), which can be transferred to the human microbiome if consumed raw or minimally processed. The aim of this study was to determine the prevalence and the amount of clinically relevant ARGs and mobile genetic elements (MGEs) in differently processed smoothies (freshly prepared, cold-pressed, pasteurized and high-pressure processed) and fresh produce samples (organically and conventionally cultivated) to assess potential health hazards associated with their consumption. The MGE ISPps and the class 1 integron-integrase gene intI1 were detected by probe-based qPCR in concentrations up to 10[4] copies/mL in all smoothies, lettuce, carrots and a single tomato sample. The highest total (2.2 × 10[5] copies/mL) and the most diverse ARG and MGE loads (16/26 targets) were observed in freshly prepared and the lowest prevalences (5/26) and concentrations (4.1 × 10[3] copies/mL) in high-pressure-processed (HPP) smoothies. BlaCTX-M-1-15 (1.2 × 10[5] c/mL) and strB (6.3 × 10[4] c/mL) were the most abundant, and qacEΔ1 (95%), blaTEM1 (85%), ermB and sul1 (75%, each) were the most prevalent ARGs. QnrS, vanA, sat-4, blaKPC, blaNDM-1 and blaOXA-10 were never detected. HPP treatment reduced the microbial loads by ca. 5 logs, also destroying extracellular DNA potentially encoding ARGs that could otherwise be transferred by bacterial transformation. The bacterial microbiome, potential pathogens, bacterial ARG carriers and competent bacteria able to take up ARGs were identified by Illumina 16S rRNA gene sequencing. To reduce the risk of AMR spread from smoothies, our data endorse the application of DNA-disintegrating processing techniques such as HPP.},
}

@article {pmid39794144,
year = {2025},
author = {Lan, P and Zhang, ZJ and He, Z},
title = {[Progress in the study of the surgical management of Crohn disease based on the mesenteric concept].},
journal = {Zhonghua wai ke za zhi [Chinese journal of surgery]},
volume = {63},
number = {2},
pages = {107-113},
doi = {10.3760/cma.j.cn112139-20240331-00155},
pmid = {39794144},
issn = {0529-5815},
support = {2022YFA1304000//National Key R&D Program of China/ ; U21A20344//Key Joint Project of National Natural Science Foundation of China/ ; },
abstract = {In recent years, with the deepening of mesentery research, it is found that its blood vessels, nerves, lymphoid tissue, adipose tissue and other structures play an important role in the occurrence and development of Crohn disease, and the degree of lesion is related with the disease process, surgical difficulty, the occurrence of intraoperative complications and postoperative recurrence. The optimal surgical strategy of Crohn disease based on mesenteric involvement has received great attention. Multiple retrospective studies found that extended mesenteric resection and Kono-S anastomosis potentially could reduce the rate of postoperative recurrence. However, the latest prospective randomized controlled studies did not achieve the expected results, and the evidence for the surgical strategy based on mesentery is still weak. This review summarises the findings of basic and clinical investigations of the mesentery in Crohn disease so far and explores its role in surgical treatment optimization, and provides new thinking and insights for the further research and surgical options for Crohn disease.},
}

@article {pmid39793044,
year = {2025},
author = {Putumbaka, S and Schut, GJ and Thorgersen, MP and Poole, FL and Shao, N and Rodionov, DA and Adams, MWW},
title = {Tungsten is utilized for lactate consumption and SCFA production by a dominant human gut microbe Eubacterium limosum.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {1},
pages = {e2411809121},
doi = {10.1073/pnas.2411809121},
pmid = {39793044},
issn = {1091-6490},
support = {R01 GM136885/GM/NIGMS NIH HHS/United States ; },
mesh = {*Eubacterium/metabolism/genetics ; Humans ; *Gastrointestinal Microbiome/physiology ; *Lactic Acid/metabolism ; *Tungsten/metabolism ; *Fatty Acids, Volatile/metabolism ; Bacterial Proteins/metabolism/genetics ; Gene Expression Regulation, Bacterial ; },
abstract = {Eubacterium limosum is a dominant member of the human gut microbiome and produces short-chain fatty acids (SCFAs). These promote immune system function and inhibit inflammation, making this microbe important for human health. Lactate is a primary source of gut SCFAs but its utilization by E. limosum has not been explored. We show that E. limosum growing on lactate takes up added tungstate rather than molybdate and produces the SCFAs acetate and butyrate, but not propionate. The genes encoding an electron bifurcating, tungsten-containing oxidoreductase (WOR1) and a tungsten-containing formate dehydrogenase (FDH), along with an electron bifurcating lactate dehydrogenase (LCT), lactate permease, and enzymes of the propanediol pathway, are all up-regulated on lactate compared to growth on glucose. Lactate metabolism is controlled by a GntR-family repressor (LctR) and two global regulators, Rex and CcpA, where Rex in part controls W storage and tungstopyranopterin (Tuco) biosynthesis. Tuco-dependent riboswitches, along with CcpA, also control two iron transporters, consistent with the increased iron demand for many iron-containing enzymes, including WOR1 and FDH, involved in SCFA production. From intracellular aldehyde concentrations and the substrate specificity of WOR1, we propose that WOR1 is involved in detoxifying acetaldehyde produced during lactate degradation. Lactate to SCFA conversion by E. limosum is clearly highly tungstocentric and tungsten might be an overlooked micronutrient in the human microbiome and in overall human health.},
}

*Eubacterium/metabolism/genetics
Humans
*Gastrointestinal Microbiome/physiology
*Lactic Acid/metabolism
*Tungsten/metabolism
*Fatty Acids, Volatile/metabolism
Bacterial Proteins/metabolism/genetics
Gene Expression Regulation, Bacterial

@article {pmid39792309,
year = {2025},
author = {Wang, P and Xia, P and Gao, S and Shi, W and Zhang, X},
title = {Critical Structures of Bisphenol Analogues on Embryonic Toxicity Identified by a Computational Approach.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c10012},
pmid = {39792309},
issn = {1520-5851},
abstract = {Safer chemical alternatives to bisphenol (BP) have been a major pursuit of modern green chemistry and toxicology. Using a chemical similarity-based approach, it is difficult to identify minor structural differences that contribute to the significant changes of toxicity. Here, we used omics and computational toxicology to identify chemical features associated with BP analogue-induced embryonic toxicity, offering valuable insights to inform the design of safer chemical alternatives. The zebrafish embryonic acute toxicity, behavioral effects, and concentration-dependent transcriptome analysis of 17 BP analogues were tested, and the chemical structure characteristics and key biological activities-induced embryonic toxicity were explored. BPE, BPF, BPP, BPBP, and BPS induced lower embryonic lethality than BPA. And, 8 BP analogues triggered hyperactive behavior at environmentally and human relevant concentrations. BP analogues with phenol rings linked via hydrophobic segments ("chain:alkaneBranch_neopentyl_C5") disturbed stress response, leading to embryonic lethality, and introducing hydrophobic groups on the meta position of bisphenol structure augmented their embryonic lethality effects. "3DACorr_TotChg_3" of BP analogues is a key physicochemical feature for behavioral disorders, and BP analogues with 3DACorr_TotChg_3 value < 0.11 could induce hyperactive behavior by perturbing neurodevelopment relevant biological pathways. This study provides an integrated strategy, combining data-driven profiling and mechanism-based analysis for safer chemical alternatives.},
}

@article {pmid39791890,
year = {2025},
author = {Soborowski, AL and Hackley, RK and Hwang, S and Zhou, G and Dulmage, KA and Schönheit, P and Daniels, C and Bisson-Filho, AW and Marchfelder, A and Maupin-Furlow, JA and Allers, T and Schmid, AK},
title = {Genomic re-sequencing reveals mutational divergence across genetically engineered strains of model archaea.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0108424},
doi = {10.1128/msystems.01084-24},
pmid = {39791890},
issn = {2379-5077},
abstract = {UNLABELLED: Archaeal molecular biology has been a topic of intense research in recent decades as their role in global ecosystems, nutrient cycles, and eukaryotic evolution comes to light. The hypersaline-adapted archaeal species Halobacterium salinarum and Haloferax volcanii serve as important model organisms for understanding archaeal genomics, genetics, and biochemistry, in part because efficient tools enable genetic manipulation. As a result, the number of strains in circulation among the haloarchaeal research community has increased in recent decades. However, the degree of genetic divergence and effects on genetic integrity resulting from the creation and inter-lab transfer of novel lab stock strains remain unclear. To address this, we performed whole-genome re-sequencing on a cross-section of wild-type, parental, and knockout strains in both model species. Integrating these data with existing repositories of re-sequencing data, we identify mutations that have arisen in a collection of 60 strains, sampled from two species across eight different labs. Independent of sequencing, we construct strain lineages, identifying branch points and significant genetic events in strain history. Combining this with our sequencing data, we identify small clusters of mutations that definitively separate lab strains. Additionally, an analysis of gene knockout strains suggests that roughly one in three strains currently in use harbors second-site mutations of potential phenotypic impact. Overall, we find that divergence among lab strains is thus far minimal, though as the archaeal research community continues to grow, careful strain provenance and genomic re-sequencing are required to keep inter-lab divergence to a minimum, prevent the compounding of mutations into fully independent lineages, and maintain the current high degree of reproducible research between lab groups.

IMPORTANCE: Archaea are a domain of microbial life whose member species play a critical role in the global carbon cycle, climate regulation, the human microbiome, and persistence in extreme habitats. In particular, hypersaline-adapted archaea are important, genetically tractable model organisms for studying archaeal genetics, genomics, and biochemistry. As the archaeal research community grows, keeping track of the genetic integrity of strains of interest is necessary. In particular, routine genetic manipulations and the common practice of sharing strains between labs allow mutations to arise in lab stocks. If these mutations affect cellular processes, they may jeopardize the reproducibility of work between research groups and confound the results of future studies. In this work, we examine DNA sequences from 60 strains across two species of archaea. We identify shared and unique mutations occurring between and within strains. Independently, we trace the lineage of each strain, identifying which genetic manipulations lead to observed off-target mutations. While overall divergence across labs is minimal so far, our work highlights the need for labs to continue proper strain husbandry.},
}

@article {pmid39789171,
year = {2025},
author = {Barman, I and Seo, H and Kim, S and Rahim, MA and Yoon, Y and Hossain, MS and Shuvo, MSH and Song, HY},
title = {Isolation of New Strains of Lactic Acid Bacteria from the Vaginal Microbiome of Postmenopausal Women and their Probiotic Characteristics.},
journal = {Current microbiology},
volume = {82},
number = {2},
pages = {76},
pmid = {39789171},
issn = {1432-0991},
support = {20018499//Ministry of Trade, Industry and Energy/ ; RS-2023-00219563//Ministry of Science and ICT, South Korea/ ; Soon Chun Hyang University Research Fund//Soon Chun Hyang University/ ; },
mesh = {Female ; *Probiotics ; Humans ; *Vagina/microbiology ; *Lactobacillales/genetics/isolation & purification/classification/metabolism ; *Postmenopause ; Bacterial Adhesion ; Microbial Sensitivity Tests ; Microbiota ; Anti-Bacterial Agents/pharmacology ; Cytokines/metabolism ; Macrophages/microbiology ; },
abstract = {Lactic acid bacteria (LAB), traditionally consumed as fermented foods, are now being applied to the medical field beyond health-functional food as probiotics. Therefore, it is necessary to continuously discover and evaluate new strains with suitable probiotic characteristics, mainly focusing on safety. In this study, we isolated eight new strains from postmenopausal vaginal fluid using culturomics approaches, an emerging area of interest. Data showed that most strains possessed significant cell surface hydrophobicity (≥ 76%), auto-aggregation capacity (17 to 61%), strong adhesion activity (8 to 34%), and excellent resistance to gastric acid, bile salt, and digestive enzyme, enhancing their survival in the gastrointestinal tract. Moreover, the strains exhibited functional characteristics, including substantial antibacterial activity with a minimal inhibitory concentration (MIC) ranging from 12.5 to 50%. They also harbored bacteriocins genes, produced short-chain fatty acids (acetate and propionate), exhibited significant phagocytic activity, possessed high antioxidative properties, rapidly depleted sodium nitrite, and exhibited proteolysis and β-glucosidase activity. In addition, heat-killed LAB strains significantly reduced the gene expressions of proinflammatory cytokines such as IL-β, IL-6, and iNOS in macrophages. Safety assessment revealed no cytotoxicity in macrophage cell lines. All strains tested negative for biogenic amine or H2O2 production, displayed no gelatinase or hemolytic activity, lacked virulence genes or detrimental enzymes, and displayed antibiotic susceptibility. In summary, these newly isolated strains demonstrate excellent probiotic functionality with a strong focus on safety, making them promising candidates for future drug development in the relevant fields.},
}

Female
*Probiotics
Humans
*Vagina/microbiology
*Lactobacillales/genetics/isolation & purification/classification/metabolism
*Postmenopause
Bacterial Adhesion
Microbial Sensitivity Tests
Microbiota
Anti-Bacterial Agents/pharmacology
Cytokines/metabolism
Macrophages/microbiology

@article {pmid39788169,
year = {2025},
author = {Xu, B and Luo, Z and Niu, X and Li, Z and Lu, Y and Li, J},
title = {Fungi, immunosenescence and cancer.},
journal = {Seminars in cancer biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semcancer.2025.01.002},
pmid = {39788169},
issn = {1096-3650},
abstract = {Fungal microbes are a small but immunoreactive component of the human microbiome, which may influence cancer development, progression and therapeutic response. Immunosenescence is a process of immune dysfunction that occurs with aging, including lymphoid organ remodeling, contributing to alterations in the immune system in the elderly, which plays a critical role in many aspects of cancer. There is evidence for the interactions between fungi and immunosenescence in potentially regulating cancer progression and remodeling the tumor microenvironment (TME). In this review, we summarize potential roles of commensal and pathogenic fungi in modulating cancer-associated processes and provide more-detailed discussions on the mechanisms of which fungi affect tumor biology, including local and distant regulation of the TME, modulating antitumor immune responses and interactions with neighboring bacterial commensals. We also delineate the features of immunosenescence and its influence on cancer development and treatment, and highlight the interactions between fungi and immunosenescence in cancer. We discuss the prospects and challenges for harnessing fungi and immunosenescence in cancer diagnosis and/or treatment. Considering the limited understanding and techniques in conducting such research, we also provide our view on how to overcome challenges faced by the exploration of fungi, immunosenescence and their interactions on tumor biology.},
}

@article {pmid39788158,
year = {2025},
author = {Theodosiou, AA and Fady, PE and Bennett, N and Read, RC and Bogaert, D and Jones, CE},
title = {Microbiotoxicity: a call to arms for cross-sector protection of the human microbiome.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106408},
doi = {10.1016/j.jinf.2025.106408},
pmid = {39788158},
issn = {1532-2742},
}

@article {pmid39775305,
year = {2025},
author = {Xu, Y and Wang, Z and Li, C and Tian, S and Du, W},
title = {Droplet microfluidics: unveiling the hidden complexity of the human microbiome.},
journal = {Lab on a chip},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4lc00877d},
pmid = {39775305},
issn = {1473-0189},
abstract = {The human body harbors diverse microbial communities essential for maintaining health and influencing disease processes. Droplet microfluidics, a precise and high-throughput platform for manipulating microscale droplets, has become vital in advancing microbiome research. This review introduces the foundational principles of droplet microfluidics, its operational capabilities, and wide-ranging applications. We emphasize its role in enhancing single-cell sequencing technologies, particularly genome and RNA sequencing, transforming our understanding of microbial diversity, gene expression, and community dynamics. We explore its critical function in isolating and cultivating traditionally unculturable microbes and investigating microbial activity and interactions, facilitating deeper insight into community behavior and metabolic functions. Lastly, we highlight its broader applications in microbial analysis and its potential to revolutionize human health research by driving innovations in diagnostics, therapeutic development, and personalized medicine. This review provides a comprehensive overview of droplet microfluidics' impact on microbiome research, underscoring its potential to transform our understanding of microbial dynamics and their relevance to health and disease.},
}

@article {pmid39770796,
year = {2024},
author = {Enderlin, D and Bieri, U and Gadient, J and Morsy, Y and Scharl, M and Rüschoff, JH and Hefermehl, LJ and Nikitin, A and Langenauer, J and Engeler, DS and Förster, B and Obrecht, F and Surber, J and Scherer, TP and Eberli, D and Poyet, C},
title = {Towards Reliable Methodology: Microbiome Analysis of Fresh Frozen vs. Formalin-Fixed Paraffin-Embedded Bladder Tissue Samples: A Feasibility Study.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122594},
pmid = {39770796},
issn = {2076-2607},
support = {KFS-5308-02-2021-R//the Swiss Cancer Research foundation/ ; },
abstract = {Studies have shown that the human microbiome influences the response to systemic immunotherapy. However, only scarce data exist on the impact of the urinary microbiome on the response rates of bladder cancer (BC) to local Bacillus Calmette-Guérin instillation therapy. We launched the prospective SILENT-EMPIRE study in 2022 to address this question. We report the results of the pilot study of SILENT-EMPIRE, which aimed to compare the microbiome between fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) samples in the cancerous tissue and adjacent healthy tissue of BC patients. Our results show that alpha diversity is increased in FF samples compared to FFPE (coverage index p = 0.041, core abundance index p = 0.008). No significant differences concerning alpha diversity could be detected between cancerous and non-cancerous tissue in the same BC patients. This study demonstrates that microbiome analysis from both FF and FFPE samples is feasible. Implementing this finding could aid in the translation of research findings into clinical practice.},
}

@article {pmid39770627,
year = {2024},
author = {Ricchezze, G and Buratti, E and De Micco, F and Cingolani, M and Scendoni, R},
title = {Medico-Legal Applications of the Human Microbiome and Critical Issues Due to Environmental Transfer: A Review.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122424},
pmid = {39770627},
issn = {2076-2607},
support = {ECS00000041 - VITALITY - CUP n° D83C22000710005//European Union - NextGenerationEU under the Italian Ministry of University and Research (MUR) National Innovation Ecosystem/ ; },
abstract = {Microbiome has recently seen an increase in its forensic applications. It could be employed to identify a suspect when DNA is not available; it can be used to establish postmortem interval (PMI). Furthermore, it could prove to be fundamental in cases of sexual assault. One of the most interesting aspects to study is how microbiomes are transferred. The aim of this review is to analyze the existing literature focusing on the potential transfer of microbiome from humans to environment. Searches on PubMed, Scopus, and Web of Science identified a total of 348 articles. Furthermore, from the bibliographies of the included articles, an additional publication was selected, in accordance with the established inclusion and exclusion criteria. This study has shown the potential of utilizing microbiomes as trace evidence, particularly in connecting individuals to specific environments or objects. However, the variability and dynamics of microbial transfer and persistence need to be carefully addressed.},
}

@article {pmid39763928,
year = {2024},
author = {Glowacki, RWP and Engelhart, MJ and Till, JM and Kadam, A and Nemet, I and Sangwan, N and Ahern, PP},
title = {Identification of strain-specific cues that regulate biofilm formation in Bacteroides thetaiotaomicron.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.20.629428},
pmid = {39763928},
issn = {2692-8205},
abstract = {UNLABELLED: Members of the gut microbiome encounter a barrage of host- and microbe-derived microbiocidal factors that must be overcome to maintain fitness in the intestine. The long-term stability of many gut microbiome strains within the microbiome suggests the existence of strain-specific strategies that have evolved to foster resilience to such insults. Despite this, little is known about the mechanisms that mediate this resistance. Biofilm formation represents one commonly employed defense strategy against stressors like those found in the intestine. Here, we demonstrate strain-level variation in the capacity of the gut symbiont Bacteroides thetaiotaomicron to form biofilms. Despite the potent induction of biofilm formation by purified bile in most strains, we show that the specific bile acid species driving biofilm formation differ among strains, and uncover that a secondary bile-acid, lithocholic acid, and its conjugated forms, potently induce biofilm formation in a strain-specific manner. Additionally, we found that the short-chain fatty acid, acetic acid, could suppress biofilm formation. Thus, our data defines the molecular components of bile that promote biofilm formation in B. thetaiotaomicron and reveals that distinct molecular cues trigger the induction or inhibition of this process. Moreover, we uncover strain-level variation in these responses, thus identifying that both shared and strain-specific determinants govern biofilm formation in this species.

IMPORTANCE: In order to thrive within the intestine, it is imperative that gut microbes resist the multitude of insults derived from the host immune system and other microbiome members. As such, they have evolved strategies that ensure their survival within the intestine. We investigated one such strategy, biofilm formation, in Bacteroides thetaiotaomicron , a common member of the human microbiome. We uncovered significant variation in natural biofilm formation in the absence of an overt stimulus among different Bacteroides thetaiotaomicron strains, and revealed that different strains adopted a biofilm lifestyle in response to distinct molecular stimuli. Thus our studies provide novel insights into factors mediating gut symbiont resiliency, revealing strain-specific and shared strategies in these responses. Collectively, our findings underscore the prevalence of strain-level differences that should be factored into our understanding of gut microbiome functions.},
}

@article {pmid39757039,
year = {2025},
author = {Cruz-Lebrón, A and Faiez, TS and Hess, MM and Sfanos, KS},
title = {Diet and the microbiome as mediators of prostate cancer risk, progression, and therapy response.},
journal = {Urologic oncology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.urolonc.2024.12.001},
pmid = {39757039},
issn = {1873-2496},
abstract = {Complex relationships between the human microbiome and cancer are increasingly recognized for cancer sites that harbor commensal microbial communities such as the gut, genitourinary tract, and skin. For organ sites that likely do not contain commensal microbiota, there is still a substantial capacity for the human-associated microbiota to influence disease etiology across the cancer spectrum. We propose such a relationship for prostate cancer, the most commonly diagnosed cancer in males in the United States. This review explores the current evidence for a role for the urinary and gut microbiota in prostate cancer risk, via both direct interactions (prostate infections) and long-distance interactions such as via the metabolism of procarcinogenic or anticarcinogenic dietary metabolites. We further explore a newly recognized role of the gut microbiota in mediating cancer treatment response or resistance either via production of androgens and/or procarcinogenic metabolites or via direct metabolism of anticancer drugs that are used to treat advanced disease. Overall, we present the current state of knowledge relating to how the human microbiome mediates prostate cancer risk, progression, and therapy response, as well as suggest future research directions for the field.},
}

@article {pmid39754316,
year = {2025},
author = {Peng, S and Wu, M and Yan, Q and Xu, G and Xie, Y and Tang, G and Lin, J and Yuan, Z and Liang, X and Yuan, Z and Weng, J and Bai, L and Wang, X and Yu, H and Huang, M and Luo, Y and Liu, X},
title = {Disrupting EDEM3-induced M2-like macrophage trafficking by glucose restriction overcomes resistance to PD-1/PD-L1 blockade.},
journal = {Clinical and translational medicine},
volume = {15},
number = {1},
pages = {e70161},
doi = {10.1002/ctm2.70161},
pmid = {39754316},
issn = {2001-1326},
support = {82372715//National Natural Science Foundation of China/ ; 82173067//National Natural Science Foundation of China/ ; 82272965//National Natural Science Foundation of China/ ; 2024A1515030054//Natural Science Foundation of Guangdong Province/ ; 2022A1515012656//Natural Science Foundation of Guangdong Province/ ; 2018026//Project 5010 of Clinical Medical Research of Sun Yat-sen University-5010 Cultivation Foundation/ ; 2025A04J4447//Science and Technology Program of Guangzhou/ ; 202201011004//Science and Technology Program of Guangzhou/ ; 2022JBGS07//Scientific Research Project of the Sixth Affiliated Hospital of Sun Yat-Sen University/ ; P20150227202010251//Talent Project of the Sixth Affiliated Hospital of Sun Yat-sen University/ ; R2021217202512965//Excellent Talent Training Project of the Sixth Affiliated Hospital of Sun Yat-sen University/ ; 1010CG(2022)-02//Sixth Affiliated Hospital of Sun Yat-sen University Clinical Research-'1010' Program/ ; 1010CG(2022)-03//Sixth Affiliated Hospital of Sun Yat-sen University Clinical Research-'1010' Program/ ; 1010PY(2022)-10)//Sixth Affiliated Hospital of Sun Yat-sen University Clinical Research-'1010' Program/ ; 23ykbj007//Fundamental Research Funds for the Central Universities, Sun Yat-sen University/ ; //Program of Introducing Talents of Discipline to Universities/ ; //National Key Clinical Discipline/ ; },
abstract = {BACKGROUND: Immunotherapy is beneficial for some colorectal cancer (CRC) patients, but immunosuppressive networks limit its effectiveness. Cancer-associatedfibroblasts (CAFs) are significant in immune escape and resistance toimmunotherapy, emphasizing the urgent need for new treatment strategies.

METHODS: Flow cytometric, Western blotting, proteomics analysis, analysis of public database data, genetically modified cell line models, T cell coculture, crystal violetstaining, ELISA, metabonomic and clinical tumour samples were conducted to assess the role of EDEM3 in immune escape and itsmolecular mechanisms. We evaluated theeffects of FMD plus 2-DG on antitumour immunity using multipleximmunofluorescence, flow cytometry, cytokine profiling, TUNEL assays, xenografttumours, and in vivo studies.

RESULTS: We show thatCAFs upregulate PD-L1 glycosylation and contribute to immune evasion byglycosyltransferase EDEM3. Additionally, EDEM3 plays a role in tumour immunityduring tumour progression. However, the EDEM3-mediated upregulation of PD-L1 expression underpins PD-1/PD-L1 blockade resistance in vivo. This finding contradictsthe previous trend that positive PD-L1 expression indicates a strong responseto PD-1/PD-L1 blockade. Mechanistically, high-EDEM3 expression facilitates M2-like This finding contradictsthe previous trend that positive PD-L1 expression indicates a strong responseto PD-1/PD-L1 blockade.Mechanistically, polarizationand chemotactic migration of macrophages, which are enriched in theperipheral region of tumours compared to thecore region, precluding access of CD8+ T cells to tumourfoci. Furthermore, we EDEM3 predominantly activates the recruited M2-like macrophagesvia a glucose metabolism-dependent mechanism. Manipulationof glucose utilization by a fasting-mimicking diet(FMD) plus 2-DG treatmentsynergistically with PD-1 antibody elicits potent antitumour activity byeffectively decreasing tumour glycosylated PD-L1 expression, augmenting the CD8+effector T cell infiltration and activation while concurrently reducing the infiltration.TheCAFs-EDEM3-M2-like macrophage axis plays a critical role in promotingimmunotherapy resistance. infiltration.TheCAFs-EDEM3-M2-like macrophage axis plays a critical role in promotingimmunotherapy resistance.

CONCLUSIONS: Our study suggests that blocking EDEM3-induced M2-like macro phage trafficking by FMD plus 2-DG is a promising and effective strategy to overcomeresistance to checkpoint blockade therapy offeringhope for improved treatment outcomes.

KEY POINTS: Cancer-associated fibroblasts (CAFs) can enhance PD-L1 glycosylation through the glycosyltransferase EDEM3, contributing to immune evasion during tumour progression. EDEM3 predominantly activates the recruit M2-like macrophages via a glucose metabolism-dependent mechanism. Blocking glucose utilization antagonizes recruiting and polarizing M2-like macrophages synergistically with PD-1 antibody to improve anticancer immunity.},
}

@article {pmid39747869,
year = {2025},
author = {Wu, W and Zhao, Y and Cheng, X and Xie, X and Zeng, Y and Tao, Q and Yang, Y and Xiao, C and Zhang, Z and Pang, J and Jin, J and He, H and Lin, Y and Li, B and Ma, J and Ye, X and Lin, WJ},
title = {Modulation of glymphatic system by visual circuit activation alleviates memory impairment and apathy in a mouse model of Alzheimer's disease.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {63},
pmid = {39747869},
issn = {2041-1723},
support = {81972967//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82172526//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82272586//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32271068//National Natural Science Foundation of China (National Science Foundation of China)/ ; 202007030001//Guangzhou Science and Technology Program key projects/ ; 202007030001//Guangzhou Science and Technology Program key projects/ ; 202007030001//Guangzhou Science and Technology Program key projects/ ; },
mesh = {Animals ; *Alzheimer Disease/therapy/metabolism ; *Disease Models, Animal ; Mice ; *Mice, Transgenic ; *Aquaporin 4/metabolism/genetics ; *Memory Disorders/therapy/metabolism ; *Amyloid beta-Peptides/metabolism ; *Glymphatic System/metabolism ; Apathy ; Hippocampus/metabolism ; Male ; Light ; Humans ; },
abstract = {Alzheimer's disease is characterized by progressive amyloid deposition and cognitive decline, yet the pathological mechanisms and treatments remain elusive. Here we report the therapeutic potential of low-intensity 40 hertz blue light exposure in a 5xFAD mouse model of Alzheimer's disease. Our findings reveal that light treatment prevents memory decline in 4-month-old 5xFAD mice and motivation loss in 14-month-old 5xFAD mice, accompanied by restoration of glial water channel aquaporin-4 polarity, improved brain drainage efficiency, and a reduction in hippocampal lipid accumulation. We further demonstrate the beneficial effects of 40 hertz blue light are mediated through the activation of the vLGN/IGL-Re visual circuit. Notably, concomitant use of anti-Aβ antibody with 40 hertz blue light demonstrates improved soluble Aβ clearance and cognitive performance in 5xFAD mice. These findings offer functional evidence on the therapeutic effects of 40 hertz blue light in Aβ-related pathologies and suggest its potential as a supplementary strategy to augment the efficacy of antibody-based therapy.},
}

Animals
*Alzheimer Disease/therapy/metabolism
*Disease Models, Animal
Mice
*Mice, Transgenic
*Aquaporin 4/metabolism/genetics
*Memory Disorders/therapy/metabolism
*Amyloid beta-Peptides/metabolism
*Glymphatic System/metabolism
Apathy
Hippocampus/metabolism
Male
Light
Humans

@article {pmid39747694,
year = {2025},
author = {Hsu, TY and Nzabarushimana, E and Wong, D and Luo, C and Beiko, RG and Langille, M and Huttenhower, C and Nguyen, LH and Franzosa, EA},
title = {Profiling lateral gene transfer events in the human microbiome using WAAFLE.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39747694},
issn = {2058-5276},
support = {K23DK125838//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R24DK110499//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; Research Scholars Award//American Gastroenterological Association (AGA)/ ; Career Development Award//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; T32CA009001//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; U54DE023798//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; },
abstract = {Lateral gene transfer (LGT), also known as horizontal gene transfer, facilitates genomic diversification in microbial populations. While previous work has surveyed LGT in human-associated microbial isolate genomes, the landscape of LGT arising in personal microbiomes is not well understood, as there are no widely adopted methods to characterize LGT from complex communities. Here we developed, benchmarked and validated a computational algorithm (WAAFLE or Workflow to Annotate Assemblies and Find LGT Events) to profile LGT from assembled metagenomes. WAAFLE prioritizes specificity while maintaining high sensitivity for intergenus LGT. Applying WAAFLE to >2,000 human metagenomes from diverse body sites, we identified >100,000 high-confidence previously uncharacterized LGT (~2 per microbial genome-equivalent). These were enriched for mobile elements, as well as restriction-modification functions associated with the destruction of foreign DNA. LGT frequency was influenced by biogeography, phylogenetic similarity of involved pairs (for example, Fusobacterium periodonticum and F. nucleatum) and donor abundance. These forces manifest as networks in which hub taxa donate unequally with phylogenetic neighbours. Our findings suggest that human microbiome LGT may be more ubiquitous than previously described.},
}

@article {pmid39747692,
year = {2025},
author = {Olm, MR and Spencer, SP and Takeuchi, T and Silva, EL and Sonnenburg, JL},
title = {Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39747692},
issn = {2058-5276},
support = {DP1AT009892//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; T32DK007056//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; F32DK128865//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; K08DK134856//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {IgA, the primary human antibody secreted from the gut mucosa, shapes the intestinal microbiota. Methodological limitations have hindered defining which microbial strains are targeted by IgA and the implications of binding. Here we develop a technique, metagenomic immunoglobulin sequencing (MIg-seq), that provides strain-level resolution of microbes coated by IgA and use it to determine IgA coating levels for 3,520 gut microbiome strains in healthy human faeces. We find that both health and disease-associated bacteria are targeted by IgA. Microbial genes are highly predictive of IgA binding levels; in particular, mucus degradation genes are correlated with high binding, and replication rates are significantly reduced for microbes bound by IgA. We demonstrate that IgA binding is more correlated with host immune status than traditional relative abundance measures of microbial community composition. This study introduces a powerful technique for assessing strain-level IgA binding in human stool, paving the way for deeper understanding of IgA-based host-microbe interactions.},
}

@article {pmid39746827,
year = {2025},
author = {Goldhawk, DE and Al, KF and Donnelly, SC and Varela-Mattatall, GE and Dassanayake, P and Gelman, N and Prato, FS and Burton, JP},
title = {Assessing microbiota in vivo: debugging with medical imaging.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2024.12.001},
pmid = {39746827},
issn = {1878-4380},
abstract = {The microbiota is integral to human health and has been mostly characterized through various ex vivo 'omic'-based approaches. To better understand the real-time function and impact of the microbiota, in vivo molecular imaging is required. With technologies such as positron emission tomography (PET), magnetic resonance imaging (MRI), and computed tomography (CT), insight into microbiological processes may be coupled to in vivo information. Noninvasive imaging enables longitudinal tracking of microbes and their components in real time; mapping of microbiota biodistribution, persistence and migration; and simultaneous monitoring of host physiological responses. The development of molecular imaging for clinical translation is an interdisciplinary science, with broad implications for deeper understanding of host-microbe interactions and the role(s) of the microbiome in health and disease.},
}

@article {pmid39740900,
year = {2025},
author = {Palkovsky, M and Modrackova, N and Neuzil-Bunesova, V and Liberko, M and Soumarova, R},
title = {The Bidirectional Impact of Cancer Radiotherapy and Human Microbiome: Microbiome as Potential Anti-tumor Treatment Efficacy and Toxicity Modulator.},
journal = {In vivo (Athens, Greece)},
volume = {39},
number = {1},
pages = {37-54},
doi = {10.21873/invivo.13803},
pmid = {39740900},
issn = {1791-7549},
mesh = {Humans ; *Neoplasms/radiotherapy/microbiology ; *Gastrointestinal Microbiome/radiation effects/drug effects ; *Microbiota/radiation effects ; Radiotherapy/adverse effects/methods ; Treatment Outcome ; },
abstract = {Microbiome and radiotherapy represent bidirectionally interacting entities. The human microbiome has emerged as a pivotal modulator of the efficacy and toxicity of radiotherapy; however, a reciprocal effect of radiotherapy on microbiome composition alterations has also been observed. This review explores the relationship between the microbiome and extracranial solid tumors, particularly focusing on the bidirectional impact of radiotherapy on organ-specific microbiome. This article aims to provide a systematic review on the radiotherapy-induced microbial alteration in-field as well as in distant microbiomes. In this review, particular focus is directed to the oral and gut microbiome, its role in the development and progression of cancer, and how it is altered throughout radiotherapy. This review concludes with recommendations for future research, such as exploring microbiome modification to optimize radiotherapy-induced toxicities or enhance its anti-cancer effects.},
}

Humans
*Neoplasms/radiotherapy/microbiology
*Gastrointestinal Microbiome/radiation effects/drug effects
*Microbiota/radiation effects
Radiotherapy/adverse effects/methods
Treatment Outcome

@article {pmid39738315,
year = {2024},
author = {Ecklu-Mensah, G and Miller, R and Maseng, MG and Hawes, V and Hinz, D and Kim, C and Gilbert, JA},
title = {Modulating the human gut microbiome and health markers through kombucha consumption: a controlled clinical study.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {31647},
pmid = {39738315},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Adult ; *Biomarkers ; Middle Aged ; Probiotics/administration & dosage ; Feces/microbiology ; Diet, Western/adverse effects ; },
abstract = {Fermented foods are becoming more popular due to their purported links to metabolic health and the gut microbiome. However, direct clinical evidence for the health claims is lacking. Here, we describe an eight-week clinical trial that explored the effects of a four-week kombucha supplement in healthy individuals consuming a Western diet, randomized into the kombucha (n = 16) or control (n = 8) group. We collected longitudinal stool and blood samples to profile the human microbiome and inflammation markers. We did not observe significant changes in either biochemical parameters or levels of circulating markers of inflammation across the entire cohort. However, paired analysis between baseline and end of intervention time points within kombucha or control groups revealed increases in fasting insulin and in HOMA-IR in the kombucha group whereas reductions in HDL cholesterol were associated with the control group. Shotgun metagenomic analysis revealed the relative abundance of Weizmannia, a kombucha-enriched probiotic and several SCFA producing taxa to be overrepresented in consumers at the end of the intervention. Collectively, in our healthy cohort consuming a Western diet, a short-term kombucha intervention induced modest impacts on human gut microbiome composition and biochemical parameters, which may be attributed to relatively small number of participants and the extensive inter-participant variability.},
}

Humans
*Gastrointestinal Microbiome
Male
Female
Adult
*Biomarkers
Middle Aged
Probiotics/administration & dosage
Feces/microbiology
Diet, Western/adverse effects

@article {pmid39737808,
year = {2024},
author = {Fagnano, A and Capocasa, G and Frateloreto, F and Latini, L and Mortera, SL and Lanzalunga, O and Di Stefano, S and Olivo, G},
title = {Deciphering the Role of Crown-ether Receptor Orientation in C-H Oxidation Catalyzed by Supramolecular Nonheme FeIV(O) Complexes.},
journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e202404041},
doi = {10.1002/chem.202404041},
pmid = {39737808},
issn = {1521-3765},
abstract = {The outstanding efficiency and selectivity of enzymatic reactions, such as C-H oxidation by nonheme iron oxygenases, stems from a precise control of substrate positioning inside the active site. The resulting proximity between a specific moiety (a certain C-H bond) to the reactant (a FeIV(O) active species) translates into higher rates and selectivity, that can be in part replicated also with artificial supramolecular catalysts. However, structural modification of the position and orientation of the binding site both in enzymes and in artificial catalysts often leads to significant variations in reactivity that can be difficult to rationalize due to the system's complexity. Herein, we quantitatively analyzed the impact of such a structural modification (namely receptor orientation) on the C-H oxidation reactivity (kinetics, Effective Molarity) and selectivity by comparing simple supramolecular FeIV(O) models. Overall, we did not observe significant differences in reaction rates, but we noticed slight changes in the selectivity profile. These results indicate that, when a crown-ether is employed as a recognition site, the key ingredient for enhanced reactivity is the presence of the supramolecular receptor itself rather than its exact orientation, providing a guide for the rational design of supramolecular catalysts.},
}

@article {pmid39735577,
year = {2025},
author = {Monshizadeh, M and Hong, Y and Ye, Y},
title = {Multitask knowledge-primed neural network for predicting missing metadata and host phenotype based on human microbiome.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbae203},
pmid = {39735577},
issn = {2635-0041},
abstract = {MOTIVATION: Microbial signatures in the human microbiome are closely associated with various human diseases, driving the development of machine learning models for microbiome-based disease prediction. Despite progress, challenges remain in enhancing prediction accuracy, generalizability, and interpretability. Confounding factors, such as host's gender, age, and body mass index, significantly influence the human microbiome, complicating microbiome-based predictions.

RESULTS: To address these challenges, we developed MicroKPNN-MT, a unified model for predicting human phenotype based on microbiome data, as well as additional metadata like age and gender. This model builds on our earlier MicroKPNN framework, which incorporates prior knowledge of microbial species into neural networks to enhance prediction accuracy and interpretability. In MicroKPNN-MT, metadata, when available, serves as additional input features for prediction. Otherwise, the model predicts metadata from microbiome data using additional decoders. We applied MicroKPNN-MT to microbiome data collected in mBodyMap, covering healthy individuals and 25 different diseases, and demonstrated its potential as a predictive tool for multiple diseases, which at the same time provided predictions for the missing metadata. Our results showed that incorporating real or predicted metadata helped improve the accuracy of disease predictions, and more importantly, helped improve the generalizability of the predictive models.

https://github.com/mgtools/MicroKPNN-MT.},
}

@article {pmid39732609,
year = {2024},
author = {Tegegne, HA and Savidge, TC},
title = {Leveraging human microbiomes for disease prediction and treatment.},
journal = {Trends in pharmacological sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tips.2024.11.007},
pmid = {39732609},
issn = {1873-3735},
abstract = {The human microbiome consists of diverse microorganisms that inhabit various body sites. As these microbes are increasingly recognized as key determinants of health, there is significant interest in leveraging individual microbiome profiles for early disease detection, prevention, and drug efficacy prediction. However, the complexity of microbiome data, coupled with conflicting study outcomes, has hindered its integration into clinical practice. This challenge is partially due to demographic and technological biases that impede the development of reliable disease classifiers. Here, we examine recent advances in 16S rRNA and shotgun-metagenomics sequencing, along with bioinformatics tools designed to enhance microbiome data integration for precision diagnostics and personalized treatments. We also highlight progress in microbiome-based therapies and address the challenges of establishing causality to ensure robust diagnostics and effective treatments for complex diseases.},
}

@article {pmid39731160,
year = {2024},
author = {Virtanen, S and Saqib, S and Kanerva, T and Ventin-Holmberg, R and Nieminen, P and Holster, T and Kalliala, I and Salonen, A},
title = {Metagenome-validated combined amplicon sequencing and text mining-based annotations for simultaneous profiling of bacteria and fungi: vaginal microbiota and mycobiota in healthy women.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {273},
pmid = {39731160},
issn = {2049-2618},
mesh = {Humans ; *Vagina/microbiology ; Female ; *RNA, Ribosomal, 16S/genetics ; *Fungi/genetics/classification/isolation & purification ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota/genetics ; *Metagenome ; *Data Mining ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Mycobiome ; Healthy Volunteers ; DNA, Bacterial/genetics ; },
abstract = {BACKGROUND: Amplicon sequencing of kingdom-specific tags such as 16S rRNA gene for bacteria and internal transcribed spacer (ITS) region for fungi are widely used for investigating microbial communities. So far most human studies have focused on bacteria while studies on host-associated fungi in health and disease have only recently started to accumulate. To enable cost-effective parallel analysis of bacterial and fungal communities in human and environmental samples, we developed a method where 16S rRNA gene and ITS1 amplicons were pooled together for a single Illumina MiSeq or HiSeq run and analysed after primer-based segregation. Taxonomic assignments were performed with Blast in combination with an iterative text-extraction-based filtration approach, which uses extensive literature records from public databases to select the most probable hits that were further validated by shotgun metagenomic sequencing.

RESULTS: Using 50 vaginal samples, we show that the combined run provides comparable results on bacterial composition and diversity to conventional 16S rRNA gene amplicon sequencing. The text-extraction-based taxonomic assignment-guided tool provided ecosystem-specific bacterial annotations that were confirmed by shotgun metagenomic sequencing (VIRGO, MetaPhlAn, Kraken2). Fungi were identified in 39/50 samples with ITS sequencing while in the metagenome data fungi largely remained undetected due to their low abundance and database issues. Co-abundance analysis of bacteria and fungi did not show strong between-kingdom correlations within the vaginal ecosystem of healthy women.

CONCLUSION: Combined amplicon sequencing for bacteria and fungi provides a simple and cost-effective method for simultaneous analysis of microbiota and mycobiota within the same samples. Conventional metagenomic sequencing does not provide sufficient fungal genome coverage for their reliable detection in vaginal samples. Text extraction-based annotation tool facilitates ecosystem-specific characterization and interpretation of microbial communities by coupling sequence homology to microbe metadata readily available through public databases. Video Abstract.},
}

Humans
*Vagina/microbiology
Female
*RNA, Ribosomal, 16S/genetics
*Fungi/genetics/classification/isolation & purification
*Bacteria/genetics/classification/isolation & purification
*Microbiota/genetics
*Metagenome
*Data Mining
Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
Mycobiome
Healthy Volunteers
DNA, Bacterial/genetics

@article {pmid39724786,
year = {2024},
author = {Ma, X and Zhang, J and Jiang, Q and Li, YX and Yang, G},
title = {Human microbiome-derived peptide affects the development of experimental autoimmune encephalomyelitis via molecular mimicry.},
journal = {EBioMedicine},
volume = {111},
number = {},
pages = {105516},
doi = {10.1016/j.ebiom.2024.105516},
pmid = {39724786},
issn = {2352-3964},
abstract = {BACKGROUND: Gut commensal microbiota has been identified as a potential environmental risk factor for multiple sclerosis (MS), and numerous studies have linked the commensal microorganism with the onset of MS. However, little is known about the mechanisms underlying the gut microbiome and host-immune system interaction.

METHODS: We employed bioinformatics methodologies to identify human microbial-derived peptides by analyzing their similarity to the MHC II-TCR binding patterns of self-antigens. Subsequently, we conducted a range of in vitro and in vivo assays to assess the encephalitogenic potential of these microbial-derived peptides.

FINDINGS: We analyzed 304,246 human microbiome genomes and 103 metagenomes collected from the MS cohort and identified 731 nonredundant analogs of myelin oligodendrocyte glycoprotein peptide 35-55 (MOG35-55). Of note, half of these analogs could bind to MHC II and interact with TCR through structural modeling of the interaction using fine-tuned AlphaFold. Among the 8 selected peptides, the peptide (P3) shows the ability to activate MOG35-55-specific CD4[+] T cells in vitro. Furthermore, P3 shows encephalitogenic capacity and has the potential to induce EAE in some animals. Notably, mice immunized with a combination of P3 and MOG35-55 develop severe EAE. Additionally, dendritic cells could process and present P3 to MOG35-55-specific CD4[+] T cells and activate these cells.

INTERPRETATION: Our data suggests the potential involvement of a MOG35-55-mimic peptide derived from the gut microbiota as a molecular trigger of EAE pathogenesis. Our findings offer direct evidence of how microbes can initiate the development of EAE, suggesting a potential explanation for the correlation between certain gut microorganisms and MS prevalence.

FUNDING: National Natural Science Foundation of China (82371350 to GY).},
}

@article {pmid39723602,
year = {2024},
author = {Ma, J and Palmer, DJ and Geddes, D and Lai, CT and Rea, A and Prescott, SL and D'Vaz, N and Stinson, LF},
title = {Maternal Allergic Disease Phenotype and Infant Birth Season Influence the Human Milk Microbiome.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16442},
pmid = {39723602},
issn = {1398-9995},
support = {//Medela/ ; //National Health and Medical Research Council/ ; //University of Western Australia/ ; //Telethon Kids Institute Ascend Fellowship/ ; },
abstract = {Early infancy is a critical period for immune development. In addition to being the primary food source during early infancy, human milk also provides multiple bioactive components that shape the infant gut microbiome and immune system and provides a constant source of exposure to maternal microbiota. Given the potential interplay between allergic diseases and the human microbiome, this study aimed to characterise the milk microbiome of allergic mothers. Full-length 16S rRNA gene sequencing was performed on milk samples collected at 3 and 6 months postpartum from 196 women with allergic disease. Multivariate linear mixed models were constructed to identify the maternal, infant, and environmental determinants of the milk microbiome. Human milk microbiome composition and beta diversity varied over time (PERMANOVA R[2] = 0.011, p = 0.011). The season of infant birth emerged as the strongest determinant of the microbiome community structure (PERMANOVA R[2] = 0.014, p = 0.011) with impacts on five of the most abundant taxa. The milk microbiome also varied according to the type of maternal allergic disease (allergic rhinitis, asthma, atopic dermatitis, and food allergy). Additionally, infant formula exposure reduced the relative abundance of several typical oral taxa in milk. In conclusion, the milk microbiome of allergic mothers was strongly shaped by the season of infant birth, maternal allergic disease phenotype, and infant feeding mode. Maternal allergic disease history and infant season of birth should therefore be considered in future studies of infant and maternal microbiota. Trial Registration: ClinicalTrials.gov identifier: ACTRN12606000281594.},
}

@article {pmid39720963,
year = {2024},
author = {Guha, SK and Niyogi, S},
title = {Microbial Dynamics in COVID-19: Unraveling the Impact of Human Microbiome on Disease Susceptibility and Therapeutic Strategies.},
journal = {Current microbiology},
volume = {82},
number = {1},
pages = {59},
pmid = {39720963},
issn = {1432-0991},
mesh = {Humans ; *COVID-19/microbiology/virology ; *SARS-CoV-2 ; *Microbiota ; *Dysbiosis/microbiology ; Disease Susceptibility ; Probiotics/therapeutic use ; Gastrointestinal Microbiome ; },
abstract = {This review explores the bidirectional relationship between the human microbiome and SARS-CoV-2 infection, elucidating its implications for COVID-19 susceptibility, severity, and therapeutic strategies. Metagenomic analyses reveal notable alterations in microbiome composition associated with SARS-CoV-2 infection, impacting disease severity and clinical outcomes. Dysbiosis within the respiratory, gastrointestinal, oral, and skin microbiomes exacerbates COVID-19 pathology through immune dysregulation and inflammatory pathways. Understanding these microbial shifts is pivotal for devising targeted therapeutic interventions. Notably, co-infection of oral pathogens with SARS-CoV-2 worsens lung pathology, while gut microbiome dysbiosis influences viral susceptibility and severity. Potential therapeutic approaches targeting the microbiome include probiotics, antimicrobial agents, and immunomodulatory strategies. This review underscores the importance of elucidating host-microbiota interactions to advance precision medicine and public health initiatives in combating COVID-19 and other infectious diseases.},
}

Humans
*COVID-19/microbiology/virology
*SARS-CoV-2
*Microbiota
*Dysbiosis/microbiology
Disease Susceptibility
Probiotics/therapeutic use
Gastrointestinal Microbiome

@article {pmid39717276,
year = {2024},
author = {Zhou, Y and Jiang, M and Li, X and Shen, K and Zong, H and Lv, Q and Shen, B},
title = {Bibliometric and visual analysis of human microbiome-breast cancer interactions: current insights and future directions.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1490007},
pmid = {39717276},
issn = {1664-302X},
abstract = {The composition of the gut microbiome differs from that of healthy individuals and is closely linked to the progression and development of breast cancer. Recent studies have increasingly examined the relationship between microbial communities and breast cancer. This study analyzed the research landscape of microbiome and breast cancer, focusing on 736 qualified publications from the Web of Science Core Collection (WoSCC). Publications in this field are on the rise, with the United States leading in contributions, followed by China and Italy. Despite this strong output, the centrality value of China in this field is comparatively low at ninth, highlighting a gap between the quantity of research and its global impact. This pattern is repetitively observed in institutional contributions, with a predominance of Western institutes among the top contributors, underscoring a potential research quality gap in China. Keyword analysis reveals that research hotspots are focused on the effect of microbiome on breast cancer pathogenesis and tumor metabolism, with risk factors and metabolic pathways being the most interesting areas. Publications point to a shift toward anti-tumor therapies and personalized medicine, with clusters such as "anti-tumor" and "potential regulatory agent" gaining prominence. Additionally, intratumor bacteria studies have emerged as a new area of significant interest, reflecting a new direction in research. The University of Helsinki and Adlercreutz H are influential institutions and researchers in this field. Current trends in microbiome and breast cancer research indicate a significant shift toward therapeutic applications and personalized medicine. Strengthening international collaborations and focusing on research quality is crucial for advancing microbiome and breast cancer research.},
}

@article {pmid39717208,
year = {2025},
author = {Fallah, A and Sedighian, H and Kachuei, R and Fooladi, AAI},
title = {Human microbiome in post-acute COVID-19 syndrome (PACS).},
journal = {Current research in microbial sciences},
volume = {8},
number = {},
pages = {100324},
pmid = {39717208},
issn = {2666-5174},
abstract = {The global COVID-19 pandemic, which began in 2019, is still ongoing. SARS-CoV-2, also known as the severe acute respiratory syndrome coronavirus 2, is the causative agent. Diarrhea, nausea, and vomiting are common GI symptoms observed in a significant number of COVID-19 patients. Additionally, the respiratory and GI tracts express high level of transmembrane protease serine 2 (TMPRSS2) and angiotensin-converting enzyme-2 (ACE2), making them primary sites for human microbiota and targets for SARS-CoV-2 infection. A growing body of research indicates that individuals with COVID-19 and post-acute COVID-19 syndrome (PACS) exhibit considerable alterations in their microbiome. In various human disorders, including diabetes, obesity, cancer, ulcerative colitis, Crohn's disease, and several viral infections, the microbiota play a significant immunomodulatory role. In this review, we investigate the potential therapeutic implications of the interactions between host microbiota and COVID-19. Microbiota-derived metabolites and components serve as primary mediators of microbiota-host interactions, influencing host immunity. We discuss the various mechanisms through which these metabolites or components produced by the microbiota impact the host's immune response to SARS-CoV-2 infection. Additionally, we address confounding factors in microbiome studies. Finally, we examine and discuss about a range of potential microbiota-based prophylactic measures and treatments for COVID-19 and PACS, as well as their effects on clinical outcomes and disease severity.},
}

@article {pmid39714161,
year = {2024},
author = {Neumann, CJ and Mohammadzadeh, R and Woh, PY and Kobal, T and Pausan, M-R and Shinde, T and Haid, V and Mertelj, P and Weiss, E-C and Kolovetsiou-Kreiner, V and Mahnert, A and Kumpitsch, C and Jantscher-Krenn, E and Moissl-Eichinger, C},
title = {First-year dynamics of the anaerobic microbiome and archaeome in infants' oral and gastrointestinal systems.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0107124},
doi = {10.1128/msystems.01071-24},
pmid = {39714161},
issn = {2379-5077},
abstract = {UNLABELLED: Recent research provides new insights into the early establishment of the infant gut microbiome, emphasizing the influence of breastfeeding on the development of gastrointestinal microbiomes. In our study, we longitudinally examined the taxonomic and functional dynamics of the oral and gastrointestinal tract (GIT) microbiomes of healthy infants (n = 30) in their first year, focusing on the often-over-looked aspects, the development of archaeal and anaerobic microbiomes. Breastfed (BF) infants exhibit a more defined transitional phase in their oral microbiome compared to non-breastfed (NBF) infants, marked by a decrease in Streptococcus and the emergence of anaerobic genera such as Granulicatella. This phase, characterized by increased alpha-diversity and significant changes in beta-diversity, occurs earlier in NBF infants (months 1-3) than in BF infants (months 4-6), suggesting that breastfeeding supports later, more defined microbiome maturation. We demonstrated the presence of archaea in the infant oral cavity and GIT microbiome from early infancy, with Methanobrevibacter being the predominant genus. Still, transient patterns show that no stable archaeome is formed. The GIT microbiome exhibited gradual development, with BF infants showing increased diversity and complexity between the third and eighth months, marked by anaerobic microbial networks. NBF infants showed complex microbial co-occurrence patterns from the start. These strong differences between BF and NBF infants' GIT microbiomes are less pronounced on functional levels than on taxonomic levels. Overall, the infant microbiome differentiates and stabilizes over the first year, with breastfeeding playing a crucial role in shaping anaerobic microbial networks and overall microbiome maturation.

IMPORTANCE: The first year of life is a crucial period for establishing a healthy human microbiome. Our study analyses the role of archaea and obligate anaerobes in the development of the human oral and gut microbiome, with a specific focus on the impact of breastfeeding in this process. Our findings demonstrated that the oral and gut microbiomes of breastfed infants undergo distinct phases of increased dynamics within the first year of life. In contrast, the microbiomes of non-breastfed infants are more mature from the first month, leading to a steadier development without distinct transitional phases in the first year. Additionally, we found that archaeal signatures are present in infants under 1 year of age, but they do not form a stable archaeome. In contrast to this, we could track specific bacterial strains transitioning from oral to gut or persisting in the gut over time.},
}

@article {pmid39702789,
year = {2024},
author = {Kaur, S and Patel, BCK and Collen, A and Malhotra, R},
title = {The microbiome and the eye: a new era in ophthalmology.},
journal = {Eye (London, England)},
volume = {},
number = {},
pages = {},
pmid = {39702789},
issn = {1476-5454},
abstract = {The human microbiome has progressively been recognised for its role in various disease processes. In ophthalmology, complex interactions between the gut and distinct ocular microbiota within each structure and microenvironment of the eye has advanced our knowledge on the multi-directional relationships of these ecosystems. Increasingly, studies have shown that modulation of the microbiome can be achieved through faecal microbiota transplantation and synbiotics producing favourable outcomes for ophthalmic diseases. As ophthalmologists, we are obliged to educate our patients on measures to cultivate a healthy gut microbiome through a range of holistic measures. Further integrative studies combining microbial metagenomics, metatranscriptomics and metabolomics are necessary to fully characterise the human microbiome and enable targeted therapeutic interventions.},
}

@article {pmid39701818,
year = {2024},
author = {Evans, SE and Valentine, ME and Gallimore, F and Meka, Y and Koehler, SI and Yu, HD and Valentovic, MA and Long, TE},
title = {Perturbations in the Gut Microbiome of C57BL/6J Mice by the Sobriety Aid Antabuse® (Disulfiram).},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxae305},
pmid = {39701818},
issn = {1365-2672},
abstract = {AIMS: Disulfiram (Antabuse®) is an oral alcohol sobriety medication that exhibits antimicrobial activity against Gram-positive facultative anaerobes. The aims of this study were to measure the antimicrobial activity against anaerobic bacteria of the gut human microbiome and establish the extent that disulfiram alters the microbial composition of the ileum, cecum, and feces using C57BL/6 mice.

METHODS AND RESULTS: Antimicrobial susceptibility testing by the microdilution method revealed that disulfiram inhibits the in vitro growth of gut anaerobic species of Bacteroides, Clostridium, Peptostreptococcus, and Porphyromonas. Differential sequencing of 16S rRNA isolated from the ileum, cecum, and feces contents of treated vs. untreated mice showed disulfiram enriches the Gram-negative enteric population. In female mice, the enrichment was greatest in the ileum whereas the feces composition in male mice was the most heavily altered.

CONCLUSIONS: Daily administration of oral disulfiram depletes the enteric Gram-positive anaerobe population as predicted by the MIC data for isolates from the human gut microbiota.},
}

@article {pmid39699186,
year = {2024},
author = {Lei, Y and Li, M and Zhang, H and Deng, Y and Dong, X and Chen, P and Li, Y and Zhang, S and Li, C and Wang, S and Tao, R},
title = {Comparative analysis of the human microbiome from four different regions of China and machine learning-based geographical inference.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0067224},
doi = {10.1128/msphere.00672-24},
pmid = {39699186},
issn = {2379-5042},
abstract = {The human microbiome, the community of microorganisms that reside on and inside the human body, is critically important for health and disease. However, it is influenced by various factors and may vary among individuals residing in distinct geographic regions. In this study, 220 samples, consisting of sterile swabs from palmar skin and oral and nasal cavities were collected from Chinese Han individuals living in Shanghai, Chifeng, Kunming, and Urumqi, representing the geographic regions of east, northeast, southwest, and northwest China. The full-length 16S rRNA gene of the microbiota in each sample was sequenced using the PacBio single-molecule real-time sequencing platform, followed by clustering the sequences into operational taxonomic units (OTUs). The analysis revealed significant differences in microbial communities among the four regions. Cutibacterium was the most abundant bacterium in palmar samples from Shanghai and Kunming, Psychrobacter in Chifeng samples, and Psychrobacillus in Urumqi samples. Additionally, Streptococcus and Staphylococcus were the dominant bacteria in the oral and nasal cavities. Individuals from the four regions could be distinguished and predicted based on a model constructed using the random forest algorithm, with the predictive effect of palmar microbiota being better than that of oral and nasal cavities. The prediction accuracy using hypervariable regions (V3-V4 and V4-V5) was comparable with that of using the entire 16S rRNA. Overall, our study highlights the distinctiveness of the human microbiome in individuals living in these four regions. Furthermore, the microbiome can serve as a biomarker for geographic origin inference, which has immense application value in forensic science.IMPORTANCEMicrobial communities in human hosts play a significant role in health and disease, varying in species, quantity, and composition due to factors such as gender, ethnicity, health status, lifestyle, and living environment. The characteristics of microbial composition at various body sites of individuals from different regions remain largely unexplored. This study utilized single-molecule real-time sequencing technology to detect the entire 16S rRNA gene of bacteria residing in the palmar skin, oral, and nasal cavities of Han individuals from four regions in China. The composition and structure of the bacteria at these three body sites were well characterized and found to differ regionally. The results elucidate the differences in bacterial communities colonizing these body sites across different regions and reveal the influence of geographical factors on human bacteria. These findings not only contribute to a deeper understanding of the diversity and geographical distribution of human bacteria but also enrich the microbiome data of the Asian population for further studies.},
}

@article {pmid39697649,
year = {2024},
author = {Aluthge, N and Adams, S and Davila, CA and Gocchi Carrasco, NR and Chiou, KS and Abadie, R and Bennett, SJ and Dombrowski, K and Major, AM and Valentín-Acevedo, A and West, JT and Wood, C and Fernando, SC},
title = {Gut microbiota profiling in injection drug users with and without HIV-1 infection in Puerto Rico.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1470037},
pmid = {39697649},
issn = {1664-302X},
abstract = {INTRODUCTION: The full extent of interactions between human immunodeficiency virus (HIV) infection, injection drug use, and the human microbiome is unclear. In this study, we examined the microbiomes of HIV-positive and HIV-negative individuals, both drug-injecting and non-injecting, to identify bacterial community changes in response to HIV and drug use. We utilized a well-established cohort of people who inject drugs in Puerto Rico, a region with historically high levels of injection drug use and an HIV incidence rate disproportionately associated with drug use.

METHODS: Using amplicon-based 16S rDNA sequencing, we identified amplicon sequence variants (ASVs) that demonstrated significant variations in the composition of microbial communities based on HIV status and drug use.

RESULTS AND DISCUSSION: Our findings indicate that the HIV-positive group exhibited a higher abundance of ASVs belonging to the genera Prevotella, Alloprevotella, Sutterella, Megasphaera, Fusobacterium, and Mitsuokella. However, Bifidobacteria and Lactobacillus ASVs were more abundant in injectors than in non-injectors. We examined the effect of drug use on the gut microbiome in both HIV-infected and non-infected patients, and found that multiple drug use significantly affected the microbial community composition. Analysis of differential of bacterial taxa revealed an enrichment of Bifidobacterium spp., Faecalibacterium spp., and Lactobacillus spp. in the multiple drug-injecting group. However, in the non-injecting group, Parabacteroides spp., Prevotella spp., Paraprevotella spp., Sutterella spp., and Lachnoclostridium spp. The presence of multiple drug-injecting groups was observed to be more prevalent. Our findings provide detailed insight into ASV-level changes in the microbiome in response to HIV and drug use, suggesting that the effect of HIV status and drug injection may have different effects on microbiome composition and in modulating gut bacterial populations.},
}

@article {pmid39695869,
year = {2024},
author = {Rodriguez, J and Cordaillat-Simmons, M and Badalato, N and Berger, B and Breton, H and de Lahondès, R and Deschasaux-Tanguy, M and Desvignes, C and D'Humières, C and Kampshoff, S and Lavelle, A and Metwaly, A and Quijada, NM and Seegers, JFML and Udocor, A and Zwart, H and , and Maguin, E and Doré, J and Druart, C},
title = {Microbiome testing in Europe: navigating analytical, ethical and regulatory challenges.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {258},
pmid = {39695869},
issn = {2049-2618},
mesh = {Humans ; Europe ; *Feces/microbiology ; Microbiota ; Reproducibility of Results ; },
abstract = {BACKGROUND: In recent years, human microbiome research has flourished and has drawn attention from both healthcare professionals and general consumers as the human microbiome is now recognized as having a significant influence on human health. This has led to the emergence of companies offering microbiome testing services. Some of these services are sold directly to the consumer via companies' websites or via medical laboratory websites.

METHODOLOGY: In order to provide an overview of the consumer experience proposed by these microbiome testing services, one single faecal sample was sent to six different companies (five based in Europe and one based in the USA). Two out of the six testing kits were commercialized by medical laboratories, but without any requirement for a medical prescription. The analyses and reports received were discussed with a panel of experts (21 experts from 8 countries) during an online workshop.

RESULTS: This workshop led to the identification of several limitations and challenges related to these kits, including over-promising messages from the companies, a lack of transparency in the methodology used for the analysis and a lack of reliability of the results. The experts considered the interpretations and recommendations provided in the different reports to be premature due to the lack of robust scientific evidence and the analyses associated with the reports to be of limited clinical utility. The experts also discussed the grey areas surrounding the regulatory status of these test kits, including their positioning in the European market. The experts recommended a distinction between regulatory requirements based on the intended use or purpose of the kit: on the one hand, test kits developed to satisfy consumer curiosity, with a clear mention of this objective, and no mention of any disease or risk of disease, and on the other hand, in vitro diagnostic (IVD) CE-marked test kits, which could go deeper into the analysis and interpretation of samples, as such a report would be intended for trained healthcare professionals.

CONCLUSIONS: Recommendations or actions, specific to the context of use of microbiome testing kits, are listed to improve the quality and the robustness of these test kits to meet expectations of end users (consumers, patients and healthcare professionals). The need for standardization, robust scientific evidence, qualification of microbiome-based biomarkers and a clear regulatory status in Europe are the main issues that will require attention in the near future to align laboratory development with societal needs and thus foster translation into daily health practice.},
}

Humans
Europe
*Feces/microbiology
Microbiota
Reproducibility of Results

@article {pmid39695352,
year = {2025},
author = {Moore, M and Whittington, HD and Knickmeyer, R and Azcarate-Peril, MA and Bruno-Bárcena, JM},
title = {Non-stochastic reassembly of a metabolically cohesive gut consortium shaped by N-acetyl-lactosamine-enriched fibers.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2440120},
doi = {10.1080/19490976.2024.2440120},
pmid = {39695352},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Bacteria/metabolism/classification/isolation & purification/genetics ; Feces/microbiology ; Lactose/metabolism ; Dietary Fiber/metabolism ; Oligosaccharides/metabolism ; Amino Sugars ; },
abstract = {Diet is one of the main factors shaping the human microbiome, yet our understanding of how specific dietary components influence microbial consortia assembly and subsequent stability in response to press disturbances - such as increasing resource availability (feeding rate) - is still incomplete. This study explores the reproducible re-assembly, metabolic interplay, and compositional stability within microbial consortia derived from pooled stool samples of three healthy infants. Using a single-step packed-bed reactor (PBR) system, we assessed the reassembly and metabolic output of consortia exposed to lactose, glucose, galacto-oligosaccharides (GOS), and humanized GOS (hGOS). Our findings reveal that complex carbohydrates, especially those containing low inclusion (~1.25 gL[-1]) components present in human milk, such as N-acetyl-lactosamine (LacNAc), promote taxonomic, and metabolic stability under varying feeding rates, as shown by diversity metrics and network analysis. Targeted metabolomics highlighted distinct metabolic responses to different carbohydrates: GOS was linked to increased lactate, lactose to propionate, sucrose to butyrate, and CO2, and the introduction of bile salts with GOS or hGOS resulted in butyrate reduction and increased hydrogen production. This study validates the use of single-step PBRs for reliably studying microbial consortium stability and functionality in response to nutritional press disturbances, offering insights into the dietary modulation of microbial consortia and their ecological dynamics.},
}

Humans
*Gastrointestinal Microbiome
Infant
*Bacteria/metabolism/classification/isolation & purification/genetics
Feces/microbiology
Lactose/metabolism
Dietary Fiber/metabolism
Oligosaccharides/metabolism
Amino Sugars

@article {pmid39690351,
year = {2024},
author = {Ullah, H and Hassan, SHA and Yang, Q and Salama, ES and Liu, P and Li, X},
title = {Dynamic interaction of antibiotic resistance between plant microbiome and organic fertilizers: sources, dissemination, and health risks.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {1},
pages = {4},
pmid = {39690351},
issn = {1573-0972},
support = {lzujbky-2024-ey12//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Microbiota/drug effects ; *Fertilizers/analysis ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Plants/microbiology ; *Soil Microbiology ; *Bacteria/drug effects/genetics/classification ; *Manure/microbiology ; Gene Transfer, Horizontal ; Agriculture/methods ; Drug Resistance, Bacterial ; Sewage/microbiology ; Drug Resistance, Microbial/genetics ; Wastewater/microbiology ; Animals ; Soil/chemistry ; },
abstract = {Antibiotic resistance is a global health problem driven by the irrational use of antibiotics in different areas (such as agriculture, animal farming, and human healthcare). Sub-lethal concentrations of antibiotic residues impose selective pressure on environmental, plant-associated, and human microbiome leading to the emergence of antibiotic-resistant bacteria (ARB). This review summarizes all sources of antibiotic resistance in agricultural soils (including manure, sewage sludge, wastewater, hospitals/pharmaceutical industry, and bioinoculants). The factors (such as the physicochemical properties of soil, root exudates, concentration of antibiotic exposure, and heavy metals) that facilitate the transmission of resistance in plant microbiomes are discussed. Potential solutions for effective measures and control of antibiotic resistance in the environment are also hypothesized. Manure exhibits the highest antibiotics load, followed by hospital and municipal WW. Chlortetracycline, tetracycline, and sulfadiazine have the highest concentrations in the manure. Antibiotic resistance from organic fertilizers is transmitted to the plant microbiome via horizontal gene transfer (HGT). Plant microbiomes serve as transmission routes of ARB and ARGS to humans. The ingestion of ARB leads to human health risks (such as ineffectiveness of medication, increased morbidity, and mortality).},
}

*Microbiota/drug effects
*Fertilizers/analysis
Humans
*Anti-Bacterial Agents/pharmacology
*Plants/microbiology
*Soil Microbiology
*Bacteria/drug effects/genetics/classification
*Manure/microbiology
Gene Transfer, Horizontal
Agriculture/methods
Drug Resistance, Bacterial
Sewage/microbiology
Drug Resistance, Microbial/genetics
Wastewater/microbiology
Animals
Soil/chemistry

@article {pmid39690257,
year = {2024},
author = {Tsuchida, S and Umemura, H and Iizuka, K and Yamamoto, H and Shimazaki, I and Shikata, E and Nakayama, T},
title = {Recent findings on metabolomics and the microbiome of oral bacteria involved in dental caries and periodontal disease.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {1},
pages = {11},
pmid = {39690257},
issn = {1573-0972},
mesh = {*Dental Caries/microbiology ; Humans ; *Microbiota ; *Mouth/microbiology ; *Metabolomics/methods ; *Periodontal Diseases/microbiology ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Biofilms/growth & development ; Animals ; },
abstract = {Periodontal disease is characterized by bacterial toxins within the oral biofilm surrounding the teeth, leading to gingivitis and the gradual dissolution of the alveolar bone, which supports the teeth. Notably, symptoms in the early stages of the disease are often absent. Similarly, dental caries occurs when oral bacteria metabolize dietary sugars, producing acids that dissolve tooth enamel and dentin. These bacteria are commonly present in the oral cavity of most individuals. Metabolomics, a relatively recent addition to the "omics" research landscape, involves the comprehensive analysis of metabolites in vivo to elucidate pathological mechanisms and accelerate drug discovery. Meanwhile, the term "microbiome" refers to the collection of microorganisms within a specific environmental niche or their collective genomes. The human microbiome plays a critical role in health and disease, influencing a wide array of physiological and pathological processes. Recent advances in microbiome research have identified numerous bacteria implicated in dental caries and periodontal disease. Additionally, studies have uncovered various pathogenic factors associated with these microorganisms. This review focuses on recent findings in metabolomics and the microbiome, specifically targeting oral bacteria linked to dental caries and periodontal disease. We acknowledge the limitation of relying exclusively on the MEDLINE database via PubMed, while excluding other sources such as gray literature, conference proceedings, and clinical practice guidelines.},
}

*Dental Caries/microbiology
Humans
*Microbiota
*Mouth/microbiology
*Metabolomics/methods
*Periodontal Diseases/microbiology
*Bacteria/classification/metabolism/genetics/isolation & purification
Biofilms/growth & development
Animals

@article {pmid39689342,
year = {2024},
author = {Chircop, O and Jaggers, C and Spiteri, M and Schembri, A and Padovese, V},
title = {DOXY do, or DOXY Don't? Syphilis and doxycycline post-exposure prophylaxis: A case report.},
journal = {International journal of STD & AIDS},
volume = {},
number = {},
pages = {9564624241308026},
doi = {10.1177/09564624241308026},
pmid = {39689342},
issn = {1758-1052},
abstract = {The resurgence of syphilis across Europe has led to a growing number of atypical cases, often characterised by varied symptoms that can delay diagnosis. We report the case of a young man who has sex with men (MSM), presenting with persistent headaches and swelling of the forehead suggestive of giant cell arteritis (GCA). Despite a recent negative syphilis test, further investigations confirmed the diagnosis of neurosyphilis. The patient had been using doxycycline post-exposure prophylaxis (DoxyPEP), which is suspected to have delayed the diagnosis by masking the typical antibody response. This case highlights concerns about DoxyPEP's impact on syphilis detection and disease progression. Further research is warranted to explore its effects on antimicrobial resistance, the human microbiome, and clinical outcomes.},
}

@article {pmid39688588,
year = {2024},
author = {Jiang, H and Miao, X and Thairu, MW and Beebe, M and Grupe, DW and Davidson, RJ and Handelsman, J and Sankaran, K},
title = {Multimedia: multimodal mediation analysis of microbiome data.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0113124},
doi = {10.1128/spectrum.01131-24},
pmid = {39688588},
issn = {2165-0497},
abstract = {UNLABELLED: Mediation analysis has emerged as a versatile tool for answering mechanistic questions in microbiome research because it provides a statistical framework for attributing treatment effects to alternative causal pathways. Using a series of linked regressions, this analysis quantifies how complementary data relate to one another and respond to treatments. Despite these advances, existing software's rigid assumptions often result in users viewing mediation analysis as a black box. We designed the multimedia R package to make advanced mediation analysis techniques accessible, ensuring that statistical components are interpretable and adaptable. The package provides a uniform interface to direct and indirect effect estimation, synthetic null hypothesis testing, bootstrap confidence interval construction, and sensitivity analysis, enabling experimentation with various mediator and outcome models while maintaining a simple overall workflow. The software includes modules for regularized linear, compositional, random forest, hierarchical, and hurdle modeling, making it well-suited to microbiome data. We illustrate the package through two case studies. The first re-analyzes a study of the microbiome and metabolome of Inflammatory Bowel Disease patients, uncovering potential mechanistic interactions between the microbiome and disease-associated metabolites, not found in the original study. The second analyzes new data about the influence of mindfulness practice on the microbiome. The mediation analysis highlights shifts in taxa previously associated with depression that cannot be explained indirectly by diet or sleep behaviors alone. A gallery of examples and further documentation can be found at https://go.wisc.edu/830110.

IMPORTANCE: Microbiome studies routinely gather complementary data to capture different aspects of a microbiome's response to a change, such as the introduction of a therapeutic. Mediation analysis clarifies the extent to which responses occur sequentially via mediators, thereby supporting causal, rather than purely descriptive, interpretation. Multimedia is a modular R package with close ties to the wider microbiome software ecosystem that makes statistically rigorous, flexible mediation analysis easily accessible, setting the stage for precise and causally informed microbiome engineering.},
}

@article {pmid39684937,
year = {2024},
author = {Balla, B and Illés, A and Tobiás, B and Pikó, H and Beke, A and Sipos, M and Lakatos, P and Kósa, JP},
title = {The Role of the Vaginal and Endometrial Microbiomes in Infertility and Their Impact on Pregnancy Outcomes in Light of Recent Literature.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
doi = {10.3390/ijms252313227},
pmid = {39684937},
issn = {1422-0067},
support = {2020-4.1.1.-TKP2020-MOLORKIV//Hungarian Ministry of Innovation and Technology/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; Pregnancy ; *Microbiota ; *Endometrium/microbiology/metabolism ; *Pregnancy Outcome ; Dysbiosis/microbiology ; Infertility, Female/microbiology ; Infertility/microbiology ; },
abstract = {The Human Microbiome Project (HMP), initiated in 2007, aimed to gather comprehensive knowledge to create a genetic and metabolic map of human-associated microorganisms and their contribution to physiological states and predisposition to certain diseases. Research has revealed that the human microbiome is highly diverse and exhibits significant interpersonal variability; consequently, its exact impact on health remains unclear. With the development of next-generation sequencing (NGS) technologies, the broad spectrum of microbial communities has been better characterized. The lower female genital tract, particularly the vagina, is colonized by various bacterial species, with Lactobacillus spp. predominating. The upper female genital tract, especially the uterus, was long considered sterile. However, recent studies have identified a distinct endometrial microbiome. A Lactobacillus-dominated microbiome of the female genital tract is associated with favorable reproductive outcomes, including higher success rates in natural conception and assisted reproductive technologies (ART). Conversely, microbial imbalances, or dysbiosis, marked by reduced Lactobacilli as well as an increased diversity and abundance of pathogenic species (e.g., Gardnerella vaginalis or Prevotella spp.), are linked to infertility, implantation failure, and pregnancy complications such as miscarriage and preterm birth. Dysbiosis can impair the vaginal or endometrial mucosal barrier and also trigger pro-inflammatory responses, disrupting essential reproductive processes like implantation. Despite growing evidence supporting the associations between the microbiome of the female genital tract and certain gynecological and obstetric conditions, clear microbial biomarkers have yet to be identified, and there is no consensus on the precise composition of a normal or healthy microbiome. The lack of standardized protocols and biomarkers limits the routine use of microbiome screening tests. Therefore, larger patient cohorts are needed to facilitate comparative studies and improve our understanding of the physiological microbiome profiles of the uterus and vagina, as well as how dysbiosis may influence clinical outcomes. Further research is required to refine diagnostic tools and develop personalized therapeutic strategies to improve fertility and pregnancy outcomes.},
}

Humans
Female
*Vagina/microbiology
Pregnancy
*Microbiota
*Endometrium/microbiology/metabolism
*Pregnancy Outcome
Dysbiosis/microbiology
Infertility, Female/microbiology
Infertility/microbiology

@article {pmid39684310,
year = {2024},
author = {Cominelli, G and Lonati, C and Pinto, D and Rinaldi, F and Franco, C and Favero, G and Rezzani, R},
title = {Melatonin Attenuates Ferritinophagy/Ferroptosis by Acting on Autophagy in the Liver of an Autistic Mouse Model BTBR T[+]Itpr3[tf]/J.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
doi = {10.3390/ijms252312598},
pmid = {39684310},
issn = {1422-0067},
support = {grants ex 60%//University of Brescia - Italy/ ; grant donation//FLAMMA S.p.A.- Italy/ ; },
mesh = {Animals ; *Melatonin/pharmacology ; Mice ; *Disease Models, Animal ; *Liver/metabolism/drug effects/pathology ; *Autophagy/drug effects ; *Ferroptosis/drug effects ; *Ferritins/metabolism ; Male ; Nuclear Receptor Coactivators/metabolism/genetics ; Microtubule-Associated Proteins/metabolism/genetics ; Autistic Disorder/metabolism/drug therapy/pathology ; Autism Spectrum Disorder/metabolism/drug therapy ; },
abstract = {Autism spectrum disorders (ASDs) are a pool of neurodevelopment disorders in which social impairment is the main symptom. Presently, there are no definitive medications to cure the symptoms but the therapeutic strategies that are taken ameliorate them. The purpose of this study was to investigate the effects of melatonin (MLT) in treating ASDs using an autistic mouse model BTBR T[+]Itpr3[tf]/J (BTBR). We evaluated the hepatic cytoarchitecture and some markers of autophagy, ferritinophagy/ferroptosis, in BTBR mice treated and not-treated with MLT. The hepatic morphology and the autophagy and ferritinophagy/ferroptosis pathways were analyzed by histological, immunohistochemical, and Western blotting techniques. We studied p62 and microtubule-associated protein 1 light chain 3 B (LC3B) for evaluating the autophagy; nuclear receptor co-activator 4 (NCOA4) and long-chain-coenzyme synthase (ACSL4) for monitoring ferritinophagy/ferroptosis. The liver of BTBR mice revealed that the hepatocytes showed many cytoplasmic inclusions recognized as Mallory-Denk bodies (MDBs); the expression and levels of p62 and LC3B were downregulated, whereas ACSL4 and NCOA4 were upregulated, as compared to control animals. MLT administration to BTBR mice ameliorated liver damage and reduced the impairment of autophagy and ferritinophagy/ferroptosis. In conclusion, we observed that MLT alleviates liver damage in BTBR mice by improving the degradation of intracellular MDBs, promoting autophagy, and suppressing ferritinophagy/ferroptosis.},
}

Animals
*Melatonin/pharmacology
Mice
*Disease Models, Animal
*Liver/metabolism/drug effects/pathology
*Autophagy/drug effects
*Ferroptosis/drug effects
*Ferritins/metabolism
Male
Nuclear Receptor Coactivators/metabolism/genetics
Microtubule-Associated Proteins/metabolism/genetics
Autistic Disorder/metabolism/drug therapy/pathology
Autism Spectrum Disorder/metabolism/drug therapy

@article {pmid39683635,
year = {2024},
author = {Ouédraogo, LO and Deng, L and Ouattara, CA and Compaoré, A and Ouédraogo, M and Argaw, A and Lachat, C and Houpt, ER and Saidi, Q and Haerynck, F and Sonnenburg, J and Azad, MB and Tavernier, SJ and Bastos-Moreira, Y and Toe, LC and Dailey-Chwalibóg, T},
title = {Describing Biological Vulnerability in Small, Vulnerable Newborns in Urban Burkina Faso (DenBalo): Gut Microbiota, Immune System, and Breastmilk Assembly.},
journal = {Nutrients},
volume = {16},
number = {23},
pages = {},
doi = {10.3390/nu16234242},
pmid = {39683635},
issn = {2072-6643},
support = {INV-035474 & INV-036154/GATES/Bill & Melinda Gates Foundation/United States ; },
mesh = {Humans ; Burkina Faso ; Female ; Infant, Newborn ; *Gastrointestinal Microbiome ; *Milk, Human/immunology ; Prospective Studies ; *Vagina/microbiology/immunology ; *Immune System ; Pregnancy ; Breast Feeding ; Infant, Small for Gestational Age ; Adult ; },
abstract = {Background: Small vulnerable newborns (SVNs), including those born preterm, small for gestational age, or with low birth weight, are at higher risk of neonatal mortality and long-term health complications. Early exposure to maternal vaginal microbiota and breastfeeding plays a critical role in the development of the neonatal microbiota and immune system, especially in low-resource settings like Burkina Faso, where neonatal mortality rates remain high. Objectives: The DenBalo study aims to investigate the role of maternal and neonatal factors, such as vaginal and gut microbiota, immune development, and early nutrition, in shaping health outcomes in SVNs and healthy infants. Methods: This prospective cohort observational study will recruit 141 mother-infant pairs (70 SVNs and 71 healthy controls) from four health centers in Bobo-Dioulasso, Burkina Faso. The mother-infant pairs will be followed for six months with anthropometric measurements and biospecimen collections, including blood, breast milk, saliva, stool, vaginal swabs, and placental biopsies. Multi-omics approaches, encompassing metagenomics, metabolomics, proteomics, and immune profiling, will be used to assess vaginal and gut microbiota composition and functionality, immune cell maturation, and cytokine levels at critical developmental stages. Conclusions: This study will generate comprehensive data on how microbiota, metabolomic, and proteomic profiles, along with immune system development, differ between SVNs and healthy infants. These findings will guide targeted interventions to improve neonatal health outcomes and reduce mortality, particularly in vulnerable populations.},
}

Humans
Burkina Faso
Female
Infant, Newborn
*Gastrointestinal Microbiome
*Milk, Human/immunology
Prospective Studies
*Vagina/microbiology/immunology
*Immune System
Pregnancy
Breast Feeding
Infant, Small for Gestational Age
Adult

@article {pmid39682776,
year = {2024},
author = {Kim, S and Rahim, MA and Tajdozian, H and Barman, I and Park, HA and Yoon, Y and Jo, S and Lee, S and Shuvo, MSH and Bae, SH and Lee, H and Ju, S and Park, CE and Kim, HK and Han, JH and Kim, JW and Yoon, SG and Kim, JH and Choi, YG and Lee, S and Seo, H and Song, HY},
title = {Clinical Potential of Novel Microbial Therapeutic LP51 Based on Xerosis-Microbiome Index.},
journal = {Cells},
volume = {13},
number = {23},
pages = {},
doi = {10.3390/cells13232029},
pmid = {39682776},
issn = {2073-4409},
support = {RS-2023-00219563//National Research Foundation of Korea/ ; P248400003//Korea Institute for Advancement of Technology/ ; },
mesh = {Humans ; Female ; *Microbiota/drug effects ; Double-Blind Method ; Adult ; Skin/microbiology/pathology ; Middle Aged ; },
abstract = {Xerosis, characterized by dry, rough skin, causes discomfort and aesthetic concerns, necessitating effective treatment. Traditional treatments often show limited efficacy, prompting the need for innovative therapies. This study highlights the efficacy of microbiome therapeutic LP51, derived from a healthy vaginal microbiome, in improving xerosis. A double-blind clinical trial involving 43 subjects with dry inner arm skin compared the effects of a 2.9% LP51 extract formulation to a placebo over 4 weeks. The LP51 group exhibited a significant increase in stratum corneum hydration (10.0 A.U.) compared to the placebo group (4.8 A.U.) and a 21.4% decrease in transepidermal water loss (TEWL), whereas the placebo group showed no significant change. LP51 also demonstrated benefits in enhancing skin hydration, improving the skin barrier, and exhibited anti-atopic, anti-inflammatory, and antioxidant properties. Safety was confirmed through in vitro cytotoxicity tests. These effects are attributed to the microbiome-safe component in LP51 and its role in improving xerosis, reflected by an increase in the xerosis-microbiome index, defined by the Firmicutes/Actinobacteria ratio. These findings position microbiome therapeutic LP51 as a promising novel treatment for xerosis.},
}

Humans
Female
*Microbiota/drug effects
Double-Blind Method
Adult
Skin/microbiology/pathology
Middle Aged

@article {pmid39682751,
year = {2024},
author = {Seo, H and Kim, S and Beck, S and Song, HY},
title = {Perspectives on Microbiome Therapeutics in Infectious Diseases: A Comprehensive Approach Beyond Immunology and Microbiology.},
journal = {Cells},
volume = {13},
number = {23},
pages = {},
doi = {10.3390/cells13232003},
pmid = {39682751},
issn = {2073-4409},
support = {RS-2023-00219563//Ministry of Science and ICT/ ; P248400003//Korea Institute for Advancement of Technology/ ; Soonchunhyang University Research Fund//Soonchunhyang University Research Fund/ ; },
mesh = {Humans ; *Microbiota/immunology ; *Probiotics/therapeutic use ; *COVID-19/immunology/virology/therapy ; Communicable Diseases/microbiology/therapy/immunology ; SARS-CoV-2/immunology ; },
abstract = {Although global life expectancy has increased over the past 20 years due to advancements in managing infectious diseases, one-fifth of people still die from infections. In response to this ongoing threat, significant efforts are underway to develop vaccines and antimicrobial agents. However, pathogens evolve resistance mechanisms, complicating their control. The COVID-19 pandemic has underscored the limitations of focusing solely on the pathogen-killing strategies of immunology and microbiology to address complex, multisystemic infectious diseases. This highlights the urgent need for practical advancements, such as microbiome therapeutics, that address these limitations while complementing traditional approaches. Our review emphasizes key outcomes in the field, including evidence of probiotics reducing disease severity and insights into host-microbiome crosstalk that have informed novel therapeutic strategies. These findings underscore the potential of microbiome-based interventions to promote physiological function alongside existing strategies aimed at enhancing host immune responses and pathogen destruction. This narrative review explores microbiome therapeutics as next-generation treatments for infectious diseases, focusing on the application of probiotics and their role in host-microbiome interactions. While offering a novel perspective grounded in a cooperative defense system, this review also addresses the practical challenges and limitations in translating these advancements into clinical settings.},
}

Humans
*Microbiota/immunology
*Probiotics/therapeutic use
*COVID-19/immunology/virology/therapy
Communicable Diseases/microbiology/therapy/immunology
SARS-CoV-2/immunology

@article {pmid39682542,
year = {2024},
author = {Morales, C and Ballestero, L and Del Río, P and Barbero-Herranz, R and Olavarrieta, L and Gómez-Artíguez, L and Galeano, J and Avendaño-Ortiz, J and Basterra, J and Del Campo, R},
title = {Should the Faecal Microbiota Composition Be Determined to Certify a Faecal Donor?.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {14},
number = {23},
pages = {},
doi = {10.3390/diagnostics14232635},
pmid = {39682542},
issn = {2075-4418},
support = {XX//Mikrobiomik/ ; },
abstract = {BACKGROUND/OBJECTIVES: Faecal microbiota transplantation (FMT) is considered a safe and effective therapy for recurrent Clostridioides difficile infection. It is the only current clinical indication for this technique, although numerous clinical research studies and trials propose its potential usefulness for treating other pathologies. Donor selection is a very rigorous process, based on a personal lifestyle interview and the absence of known pathogens in faeces and serum, leading to only a few volunteers finally achieving the corresponding certification. However, despite the high amount of data generated from the ongoing research studies relating microbiota and health, there is not yet a consensus defining what is a "healthy" microbiota. To date, knowledge of the composition of the microbiota is not a requirement to be a faecal donor. The aim of this work was to evaluate whether the analysis of the composition of the microbiota by massive sequencing of 16S rDNA could be useful in the selection of the faecal donors.

METHODS: Samples from 10 certified donors from Mikrobiomik Healthcare Company were collected and sequenced using 16S rDNA in a MiSeq (Illumina) platform. Alpha (Chao1 and Shannon indices) and beta diversity (Bray-Curtis) were performed using the bioinformatic web server Microbiome Analyst. The differences in microbial composition at the genera and phyla levels among the donors were evaluated.

RESULTS: The microbial diversity metric by alpha diversity indexes showed that most donors exhibited a similar microbial diversity and richness, whereas beta diversity by 16S rDNA sequencing revealed significant inter-donor differences, with a more stable microbial composition over time in some donors. The phyla Bacillota and Bacteroidota were predominant in all donors, while the density of other phyla, such as Actinomycota and Pseudomonota, varied among individuals. Each donor exhibited a characteristic genera distribution pattern; however, it was possible to define a microbiome core consisting of the genera Agathobacter, Eubacterium, Bacteroides, Clostridia UCG-014 and Akkermansia. Conclusions: The results suggest that donor certification does not need to rely exclusively on their microbiota composition, as it is unique to each donor. While one donor showed greater microbial diversity and richness, clear criteria for microbial normality and health have yet to be established. Therefore, donor certification should focus more on clinical and lifestyle aspects.},
}

@article {pmid39681696,
year = {2024},
author = {Joos, R and Boucher, K and Lavelle, A and Arumugam, M and Blaser, MJ and Claesson, MJ and Clarke, G and Cotter, PD and De Sordi, L and Dominguez-Bello, MG and Dutilh, BE and Ehrlich, SD and Ghosh, TS and Hill, C and Junot, C and Lahti, L and Lawley, TD and Licht, TR and Maguin, E and Makhalanyane, TP and Marchesi, JR and Matthijnssens, J and Raes, J and Ravel, J and Salonen, A and Scanlan, PD and Shkoporov, A and Stanton, C and Thiele, I and Tolstoy, I and Walter, J and Yang, B and Yutin, N and Zhernakova, A and Zwart, H and , and Doré, J and Ross, RP},
title = {Author Correction: Examining the healthy human microbiome concept.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41579-024-01145-8},
pmid = {39681696},
issn = {1740-1534},
}

@article {pmid39676876,
year = {2024},
author = {Bhatnagar, K and Jha, K and Dalal, N and Patki, N and Gupta, G and Kumar, A and Kumar, A and Chaudhary, S},
title = {Exploring micronutrients and microbiome synergy: pioneering new paths in cancer therapy.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1442788},
pmid = {39676876},
issn = {1664-3224},
mesh = {Humans ; *Micronutrients/therapeutic use ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/immunology/therapy/microbiology ; Animals ; Probiotics/therapeutic use ; Prebiotics/administration & dosage ; Dysbiosis/therapy ; },
abstract = {The human microbiome is the complex ecosystem consisting of trillions of microorganisms that play a key role in developing the immune system and nutrient metabolism. Alterations in the gut microbiome have been linked to cancer initiation, progression, metastasis, and response to treatment. Accumulating evidence suggests that levels of vitamins and minerals influence the gut environment and may have implications for cancer risk and progression. Bifidobacterium has been reported to reduce the colorectal cancer risk by binding to free iron. Additionally, zinc ions have been shown to activate the immune cells and enhance the effectiveness of immunotherapy. Higher selenium levels have been associated with a reduced risk of several cancers, including colorectal cancer. In contrast, enhanced copper uptake has been implicated in promoting cancer progression, including colon cancer. The interaction between cancer and gut bacteria, as well as dysbiosis impact has been studied in animal models. The interplay between prebiotics, probiotics, synbiotics, postbiotics and gut bacteria in cancer offers the diverse physiological benefits. We also explored the particular probiotic formulations like VSL#3, Prohep, Lactobacillus rhamnosus GG (LGG), etc., for their ability to modulate immune responses and reduce tumor burden in preclinical models. Targeting the gut microbiome through antibiotics, bacteriophage, microbiome transplantation-based therapies will offer a new perspective in cancer research. Hence, to understand this interplay, we outline the importance of micronutrients with an emphasis on the immunomodulatory function of the microbiome and highlight the microbiome's potential as a target for precision medicine in cancer treatment.},
}

Humans
*Micronutrients/therapeutic use
*Gastrointestinal Microbiome/immunology
*Neoplasms/immunology/therapy/microbiology
Animals
Probiotics/therapeutic use
Prebiotics/administration & dosage
Dysbiosis/therapy

@article {pmid39675162,
year = {2024},
author = {Skurnik, M},
title = {Scholarly discussion on the classification and electron microscopy analysis of lytic phage EC BD.},
journal = {International journal of food microbiology},
volume = {429},
number = {},
pages = {111012},
doi = {10.1016/j.ijfoodmicro.2024.111012},
pmid = {39675162},
issn = {1879-3460},
}

@article {pmid39662756,
year = {2024},
author = {Hodgkiss, R and Acharjee, A},
title = {Unravelling metabolite-microbiome interactions in inflammatory bowel disease through AI and interaction-based modelling.},
journal = {Biochimica et biophysica acta. Molecular basis of disease},
volume = {},
number = {},
pages = {167618},
doi = {10.1016/j.bbadis.2024.167618},
pmid = {39662756},
issn = {1879-260X},
abstract = {Inflammatory Bowel Diseases (IBDs) are chronic inflammatory disorders of the gastrointestinal tract and colon affecting approximately 7 million individuals worldwide. The knowledge of specific pathology and aetiological mechanisms leading to IBD is limited, however a reduced immune system, antibiotic use and reserved diet may initiate symptoms. Dysbiosis of the gut microbiome, and consequently a varied composition of the metabolome, has been extensively linked to these risk factors and IBD. Metagenomic sequencing and liquid-chromatography mass spectrometry (LC-MS) of N = 220 fecal samples by Fransoza et al., provided abundance data on microbial genera and metabolites for use in this study. Identification of differentially abundant microbes and metabolites was performed using a Wilcoxon test, followed by feature selection of random forest (RF), gradient-boosting (XGBoost) and least absolute shrinkage operator (LASSO) models. The performance of these features was then validated using RF models on the Human Microbiome Project 2 (HMP2) dataset and a microbial community (MICOM) model was utilised to predict and interpret the interactions between key microbes and metabolites. The Flavronifractor genus and microbes of the families Lachnospiraceae and Oscillospiraceae were found differential by all models. Metabolic pathways commonly influenced by such microbes in IBD were CoA biosynthesis, bile acid metabolism and amino acid production and degradation. This study highlights distinct interactive microbiome and metabolome profiles within IBD and the highly potential pathways causing disease pathology. It therefore paves way for future investigation into new therapeutic targets and non-invasive diagnostic tools for IBD.},
}

@article {pmid39657723,
year = {2024},
author = {Sinkko, H and Olah, P and Yang, Y and Maia, G and Barrientos-Somarribas, M and Rádai, Z and Mäenpää, K and Sorratto, T and Salava, A and Lauerma, A and Barker, J and Ranki, A and Homey, B and Andersson, B and Fyhrquist, N and Alenius, H and , },
title = {Taxonomic and functional profiling of skin microbiome in psoriasis.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljae471},
pmid = {39657723},
issn = {1365-2133},
}

@article {pmid39657633,
year = {2024},
author = {Yang, W and Wu, K and Chen, H and Huang, J and Yu, Z},
title = {Emerging role of rare earth elements in biomolecular functions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae241},
pmid = {39657633},
issn = {1751-7370},
abstract = {The importance of rare earth elements is increasingly recognized due to the increased demand for their mining and separation. This demand is driving research on the biology of rare earth elements. Biomolecules associated with rare earth elements include rare earth element-dependent enzymes (methanol dehydrogenase XoxF, ethanol dehydrogenase ExaF/PedH), rare earth element-binding proteins, and the relevant metallophores. Traditional (chemical) separation methods for rare earth elements harvesting and separation are typically inefficient, while causing environmental problems, whereas bioharvesting, potentially, offers more efficient, more green platforms. Here, we review the current state of research on the biological functions of rare earth element-dependent biomolecules, and the characteristics of the relevant proteins, including the specific amino acids involved in rare earth metal binding. We also provide an outlook at strategies for further understanding of biological processes and the potential applications of rare earth element-dependent enzymes and other biomolecules.},
}

@article {pmid39654676,
year = {2024},
author = {Han, H and Choi, YH and Kim, SY and Park, JH and Chung, J and Na, HS},
title = {Optimizing microbiome reference databases with PacBio full-length 16S rRNA sequencing for enhanced taxonomic classification and biomarker discovery.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1485073},
pmid = {39654676},
issn = {1664-302X},
abstract = {BACKGROUND: The study of the human microbiome is crucial for understanding disease mechanisms, identifying biomarkers, and guiding preventive measures. Advances in sequencing platforms, particularly 16S rRNA sequencing, have revolutionized microbiome research. Despite the benefits, large microbiome reference databases (DBs) pose challenges, including computational demands and potential inaccuracies. This study aimed to determine if full-length 16S rRNA sequencing data produced by PacBio could be used to optimize reference DBs and be applied to Illumina V3-V4 targeted sequencing data for microbial study.

METHODS: Oral and gut microbiome data (PRJNA1049979) were retrieved from NCBI. DADA2 was applied to full-length 16S rRNA PacBio data to obtain amplicon sequencing variants (ASVs). The RDP reference DB was used to assign the ASVs, which were then used as a reference DB to train the classifier. QIIME2 was used for V3-V4 targeted Illumina data analysis. BLAST was used to analyze alignment statistics. Linear discriminant analysis Effect Size (LEfSe) was employed for discriminant analysis.

RESULTS: ASVs produced by PacBio showed coverage of the oral microbiome similar to the Human Oral Microbiome Database. A phylogenetic tree was trimmed at various thresholds to obtain an optimized reference DB. This established method was then applied to gut microbiome data, and the optimized gut microbiome reference DB provided improved taxa classification and biomarker discovery efficiency.

CONCLUSION: Full-length 16S rRNA sequencing data produced by PacBio can be used to construct a microbiome reference DB. Utilizing an optimized reference DB can increase the accuracy of microbiome classification and enhance biomarker discovery.},
}

@article {pmid39651993,
year = {2024},
author = {Poncet, R and Gargominy, O},
title = {In the Shadow of Medicine: The Glaring Absence of Occurrence Records of Human-Hosted Biodiversity.},
journal = {Online journal of public health informatics},
volume = {16},
number = {},
pages = {e60140},
doi = {10.2196/60140},
pmid = {39651993},
issn = {1947-2579},
abstract = {Microbial diversity is vast, with bacteria playing a crucial role in human health. However, occurrence records (location, date, observer, and host interaction of human-associated bacteria) remain scarce. This lack of information hinders our understanding of human-microbe relationships and disease prevention. In this study, we show that existing solutions such as France's Système d'Information sur le Patrimoine Naturel framework, can be used to efficiently collect and manage occurrence data on human-associated bacteria. This user-friendly system allows medical personnel to easily share and access data on bacterial pathogens. By adopting similar national infrastructures and treating human-associated bacteria as biodiversity data, we can significantly improve public health management and research, and our understanding of the One Health concept, which emphasizes the interconnectedness of human, animal, and environmental health.},
}

@article {pmid39648582,
year = {2024},
author = {Burton, JP and Kofoed, RH and Rust, R},
title = {Science around the world.},
journal = {Trends in molecular medicine},
volume = {30},
number = {3},
pages = {197-199},
doi = {10.1016/j.molmed.2024.01.008},
pmid = {39648582},
issn = {1471-499X},
}

@article {pmid39647502,
year = {2024},
author = {Porcari, S and Mullish, BH and Asnicar, F and Ng, SC and Zhao, L and Hansen, R and O'Toole, PW and Raes, J and Hold, G and Putignani, L and Hvas, CL and Zeller, G and Koren, O and Tun, H and Valles-Colomer, M and Collado, MC and Fischer, M and Allegretti, J and Iqbal, T and Chassaing, B and Keller, J and Baunwall, SM and Abreu, M and Barbara, G and Zhang, F and Ponziani, FR and Costello, SP and Paramsothy, S and Kao, D and Kelly, C and Kupcinskas, J and Youngster, I and Franceschi, F and Khanna, S and Vehreschild, M and Link, A and De Maio, F and Pasolli, E and Miguez, AB and Brigidi, P and Posteraro, B and Scaldaferri, F and Stojanovic, MR and Megraud, F and Malfertheiner, P and Masucci, L and Arumugam, M and Kaakoush, N and Segal, E and Bajaj, J and Leong, R and Cryan, J and Weersma, RK and Knight, R and Guarner, F and Shanahan, F and Cani, PD and Elinav, E and Sanguinetti, M and de Vos, WM and El-Omar, E and Dorè, J and Marchesi, J and Tilg, H and Sokol, H and Segata, N and Cammarota, G and Gasbarrini, A and Ianiro, G},
title = {International consensus statement on microbiome testing in clinical practice.},
journal = {The lancet. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2468-1253(24)00311-X},
pmid = {39647502},
issn = {2468-1253},
abstract = {There is growing interest in the potential exploitation of the gut microbiome as a diagnostic tool in medicine, but evidence supporting its clinical usefulness is scarce. An increasing number of commercial providers offer direct-to-consumer microbiome diagnostic tests without any consensus on their regulation or any proven value in clinical practice, which could result in considerable waste of individual and health-care resources and potential drawbacks in the clinical management of patients. We convened an international multidisciplinary expert panel to standardise best practices of microbiome testing for clinical implementation, including recommendations on general principles and minimum requirements for their provision, indications, pre-testing protocols, method of analyses, reporting of results, and potential clinical value. We also evaluated current knowledge gaps and future directions in this field. We aimed to establish a framework to regulate the provision of microbiome testing and minimise the use of inappropriate tests and pave the way for the evidence-based development and use of human microbiome diagnostics in clinical medicine.},
}

@article {pmid39639265,
year = {2024},
author = {Ma, ZS},
title = {Revisiting microgenderome: detecting and cataloguing sexually unique and enriched species in human microbiomes.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {284},
pmid = {39639265},
issn = {1741-7007},
mesh = {Humans ; Female ; Male ; *Microbiota ; *Sex Characteristics ; Species Specificity ; },
abstract = {BACKGROUND: Microgenderome or arguably more accurately microsexome refers to studies on sexual dimorphism of human microbiomes aimed at investigating bidirectional interactions between human microbiomes, sex hormones, and immune systems. It is important because of its implications to disease susceptibility and therapy, in which men and women demonstrate divergence in many diseases especially autoimmune diseases. In a previous report [1], we presented analyses of several key ecological aspects of microgenderome by leveraging the large datasets of the HMP (human microbiome project) but failed to offer species-level composition differences such as sexually unique species (US) and enriched species (ES). Existing approaches, for such tasks, including differential species relative abundance analysis and differential network analysis, possess certain limitations given that virtually all rely on species abundance alone or are univariate, while ignoring species distribution information across samples. Obviously, it is both species abundance and distribution that shape/drive the structure and dynamics of human microbiomes, and both should be equally responsible for the universal heterogeneity of microbiomes including the sexual dimorphism.

RESULTS: Here, we fill the gap by taking advantages of a recently developed computational algorithm, species specificity, and specificity diversity (SSD) framework (refer to the companion article) to reanalyze the HMP and complementary seminovaginal microbiome datasets. The SSD framework can randomly search and catalogue the sexually specific unique/enriched species with statistical rigor, guided by species specificity (a synthetic metric of abundance and distribution) and specificity diversity (SD). The SSD framework reveals that men seem to have more unique species than women in their gut and reproductive system microbiomes, but women seem to have more unique species than men in the airway, oral, and skin microbiomes, which is likely due to sexual dimorphism in the hormone and immune systems. We further investigate co-dependency and heterogeneity of those sexually unique/enriched species across 15 body sites, with core/periphery network analyses.

CONCLUSIONS: This study not only produced sexually unique/enriched species in the human microbiomes and analyzed their codependency and heterogeneity but also further validated the robustness of the SSD framework presented in the companion article, by performing all negative control tests based on the HMP gut microbiome samples.},
}

Humans
Female
Male
*Microbiota
*Sex Characteristics
Species Specificity

@article {pmid39628703,
year = {2022},
author = {Liu, D and Siguenza, NE and Zarrinpar, A and Ding, Y},
title = {Methods of DNA introduction for the engineering of commensal microbes.},
journal = {Engineering microbiology},
volume = {2},
number = {4},
pages = {100048},
pmid = {39628703},
issn = {2667-3703},
abstract = {The microbiome is an essential component of ecological systems and is comprised of a diverse array of microbes. Over the past decades, the accumulated observational evidence reveals a close correlation between the microbiome and human health and disease. Many groups are now manipulating individual microbial strains, species and the community as a whole to gain a mechanistic understanding of the functions of the microbiome. Here, we discuss three major approaches for introducing DNA to engineer model bacteria and isolated undomesticated bacteria, including transformation, transduction, and conjugation. We provide an overview of these approaches and describe the advantages and limitations of each method. In addition, we highlight examples of human microbiome engineering using these approaches. Finally, we provide perspectives for the future of microbiome engineering.},
}

@article {pmid39626677,
year = {2024},
author = {He, Z and Yu, J and Gong, J and Wu, J and Zong, X and Luo, Z and He, X and Cheng, WM and Liu, Y and Liu, C and Zhang, Q and Dai, L and Ding, T and Gao, B and Gharaibeh, RZ and Huang, J and Jobin, C and Lan, P},
title = {Campylobacterjejuni-derived cytolethal distending toxin promotes colorectal cancer metastasis.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2024.11.006},
pmid = {39626677},
issn = {1934-6069},
abstract = {Various forms of solid tumors harbor intracellular bacteria, but the physiological consequences of these microorganisms are poorly understood. We show that Campylobacter is significantly enriched in primary colorectal cancer (CRC) lesions from patients with metastasis. Campylobacterjejuni-derived cytolethal distending toxin (CDT) promotes CRC metastasis through JAK2-STAT3-MMP9 signaling in liver or pulmonary metastatic mice models, as confirmed in C. jejuni-infected human colonic tissue and CDT-treated colonic tumoroids from patients. Genetic deletion of cdtB (ΔcdtB) or purified CdtB protein demonstrates that the genotoxin is essential for C. jejuni's pro-metastatic property. In C.-jejuni-colonized mice, increased translocation of CDT-producing C. jejuni to extraintestinal implanted tumors potentially leads to accelerated metastasis of these tumors. Overall, these findings demonstrate that an intratumor-bacteria-derived genotoxin accelerates tumor metastasis, potentially opening a new diagnostic and therapeutic avenue for cancer management.},
}

@article {pmid39624165,
year = {2024},
author = {Zhang, Y and Schluter, J and Zhang, L and Cao, X and Jenq, RR and Feng, H and Haines, J and Zhang, L},
title = {Review and revamp of compositional data transformation: A new framework combining proportion conversion and contrast transformation.},
journal = {Computational and structural biotechnology journal},
volume = {23},
number = {},
pages = {4088-4107},
pmid = {39624165},
issn = {2001-0370},
abstract = {Due to the development of next-generation sequencing technology and an increased appreciation of their role in modulating host immunity and their potential as therapeutic agents, the human microbiome has emerged as a key area of interest in various biological investigations of human health and disease. However, microbiome data present a number of statistical challenges not addressed by existing methods, such as the varying sequencing depth, the compositionality, and zero inflation. Solutions like scaling and transformation methods help to mitigate heterogeneity and release constraints, but often introduce biases and yield inconsistent results on the same data. To address these issues, we conduct a systematic review of compositional data transformation, with a particular focus on the connection and distinction of existing techniques. Additionally, we create a new framework that enables the development of new transformations by combining proportion conversion with contrast transformations. This framework includes well-known methods such as Additive Log Ratio (ALR) and Centered Log Ratio (CLR) as special cases. Using this framework, we develop two novel transformations-Centered Arcsine Contrast (CAC) and Additive Arcsine Contrast (AAC)-which show enhanced performance in scenarios with high zero-inflation. Moreover, our findings suggest that ALR and CLR transformations are more effective when zero values are less prevalent. This comprehensive review and the innovative framework provide microbiome researchers with a significant direction to enhance data transformation procedures and improve analytical outcomes.},
}

@article {pmid39621633,
year = {2024},
author = {Martins, FP and Andrade-Silva, J and Teixeira, BL and Ferrari, A and Christoff, AP and Cruz, GNF and Paladino, FV and de Oliveira, LFV and Hernandes, C},
title = {Oral microbiome test as an alternative diagnostic tool for gastric alterations: A prospective, bicentric cross-sectional study.},
journal = {PloS one},
volume = {19},
number = {12},
pages = {e0314660},
doi = {10.1371/journal.pone.0314660},
pmid = {39621633},
issn = {1932-6203},
mesh = {Humans ; Cross-Sectional Studies ; Female ; Male ; Middle Aged ; *Mouth/microbiology ; Prospective Studies ; Adult ; *Microbiota ; Brazil ; Aged ; Stomach/microbiology ; Bacteria/genetics/isolation & purification/classification ; Stomach Diseases/microbiology/diagnosis ; },
abstract = {The human microbiome plays a pivotal role in influencing various physiological processes and maintaining overall well-being, including the gastric system. Current diagnostic tests for gastric diseases often involve invasive procedures, sampling limitations, and medication effects, leading to potential diagnostic errors and discomfort to patients. Considering the connection between oral and gastric microbiomes, this cross-sectional study aimed to assess the diagnostic potential of the oral bacterial profile in patients undergoing upper digestive endoscopy. Oral samples from 266 participants across two Brazilian sites (Belterra and Sao Paulo) were sequenced and subjected to bioinformatic analysis to identify microbiome composition across endoscopy outcome groups, exploring alpha and beta-diversity, richness, and differential abundance and prevalence. Prevotella, Haemophilus, Fusobacterium, Neisseria, and Streptococcus were the most abundant genera observed. No significant associations were found between alpha diversity profiles and endoscopy outcomes; beta diversity analyses similarly showed no correlations. Overall, the study did not establish the oral microbiome as a reliable marker for gastric health, underscoring the necessity for broader studies in the development of non-invasive diagnostic tests.},
}

Humans
Cross-Sectional Studies
Female
Male
Middle Aged
*Mouth/microbiology
Prospective Studies
Adult
*Microbiota
Brazil
Aged
Stomach/microbiology
Bacteria/genetics/isolation & purification/classification
Stomach Diseases/microbiology/diagnosis

@article {pmid39619727,
year = {2024},
author = {Sawan, HM and Shroukh, W and Abutaima, R and Al Omari, SM and Abdel-Qader, DH and Binsuwaidan, R},
title = {Impact of Jordanian Pharmacists' Knowledge of the Human Microbiome: Has the Practice of Antibiotics and Probiotics Dispensing Been Affected? A Cross-Sectional Study.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {5203-5214},
pmid = {39619727},
issn = {1178-6973},
abstract = {OBJECTIVE: This study aimed to assess Jordanian pharmacists' knowledge of the human microbiome and the impact of their knowledge on their attitudes and practices toward antibiotics and probiotics.

METHODS: A self-administered survey was designed after reviewing the literature. Participants' demographics were collected, and questions to evaluate pharmacists' knowledge, attitudes, and practices toward antibiotic and probiotic dispensing were asked. The data were analyzed using the Statistical Package for the Social Sciences V.26. Pearson correlations and one-way ANOVA were employed to calculate the significance of knowledge, attitudes, and practices. Statistical significance was considered at p < 0.05.

RESULTS: Of the 333 respondents, around 75% (n=250) had a high level of general knowledge regarding the human gut microbiome. Almost equal proportions of participants had either intermediate or high levels of knowledge about the role of gut bacteria in health (n=164, 49.2%) (n=166, 49.8%), respectively, while almost two-thirds had an intermediate level of knowledge of the role of gut bacteria in disease (n=197, 59.2%). More than half of the participants had a positive attitude toward antibiotics, probiotics, and the human microbiome (n=179, 53.8%), and the majority (n=239, 71.8%) had an intermediate level of practice with them. There was a significant positive correlation between pharmacists' general knowledge of the human microbiome and their positive attitudes (r=0.306, p < 0.01) and practices (r=0.331, p < 0.01) toward antibiotics and probiotics.

CONCLUSION: Study results raise the importance of interventional educational measures to promote healthcare professionals' knowledge of the human microbiome and their potential beneficence on pharmacists' attitudes and practices regarding antibiotics and probiotics dispensing. The results also denote the urgent need for probiotics' clinical guidelines to ensure practice uniformity.},
}

@article {pmid39614169,
year = {2024},
author = {Tang, H and Du, S and Niu, Z and Zhang, D and Tang, Z and Chen, H and Chen, Z and Zhang, M and Xu, Y and Sun, Y and Fu, X and Norback, D and Shao, J and Zhao, Z},
title = {Nasal, dermal, oral and indoor dust microbe and their interrelationship in children with allergic rhinitis.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {505},
pmid = {39614169},
issn = {1471-2180},
mesh = {Humans ; *Dust/analysis ; Male ; Child ; Female ; *Rhinitis, Allergic/microbiology ; Case-Control Studies ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/isolation & purification/genetics ; *Skin/microbiology ; *Mouth/microbiology ; *Microbiota ; Nasal Cavity/microbiology ; Air Pollution, Indoor/analysis ; Child, Preschool ; Metagenomics/methods ; Nose/microbiology ; },
abstract = {BACKGROUND: Allergic rhinitis (AR) subjects might have their microenvironment changed due to pathogenesis and living environment. Whether the nasal microbe in AR children differs from healthy subjects and how it interplays with dermal, oral and indoor dust microbe needs to be elucidated.

METHODS: In this case-control study, we analyzed and compared the bacterial characterization and associations in nasal, dermal, oral swab samples and dust samples in 62 children with physician-diagnosed AR(cases) and 51 age- and gender-matched healthy ones with no history of allergic diseases(controls). Full-length 16S rRNA sequencing(swabs) and shotgun metagenomics(dust) were applied. Bacterial diversity, composition, abundance difference characteristics and fast expectation-maximization for microbial source tracking(FEAST) analysis were performed and compared between cases and controls.

RESULTS: The α-diversity of dust microorganisms in AR was lower than that in control group (P = 0.034), and the β-diversity indices of microorganisms in nasal cavity (P = 0.020), skin (P = 0.001) and dust (P = 0.004) were significantly different from those in control group. At species levels, a total of 10, 15, 12, and 15 bacterial species were differentially enriched in either cases or controls in nasal, dermal, oral, and dust samples, respectively(Linear Discriminant Analysis(LDA) score > 2, P < 0.05). Staphylococcus epidermidis was the single species simultaneously more abundant in nasal, dermal and dust samples in AR children. By FEAST analysis, 8.85% and 10.11% of S. epidermidis in AR dermal and dust samples came from nasal cavity. These proportions were significantly higher than those in controls (2.70% and 3.86%) (P < 0.05). The same significantly higher transfer proportions(P < 0.05) were observed for Staphylococcus aureus enriched in the nasal cavity in AR children. Classification models by random forest regression at species levels showed, bacterial species enriched in indoor dust, nasal and dermal samples had substantial power in distinguishing AR children from healthy ones, with the highest power in the dust samples (AUC = 0.88) followed by nasal(AUC = 0.81) and dermal ones(AUC = 0.80).

CONCLUSIONS: Our study presented the microbial enrichment characteristics in AR children both in the living environment(dust) and body sites exposed to environment through inhalation(nasal cavity), contact(skin) and ingestion(oral cavity) pathways, respectively. Nasal S.epidermidis and S.aureus had dominant influences on dust and other body sites in AR children.},
}

Humans
*Dust/analysis
Male
Child
Female
*Rhinitis, Allergic/microbiology
Case-Control Studies
*RNA, Ribosomal, 16S/genetics
*Bacteria/classification/isolation & purification/genetics
*Skin/microbiology
*Mouth/microbiology
*Microbiota
Nasal Cavity/microbiology
Air Pollution, Indoor/analysis
Child, Preschool
Metagenomics/methods
Nose/microbiology

@article {pmid39614246,
year = {2024},
author = {Marín-Sánchez, N and Paredes, R and Borgognone, A},
title = {Exploring potential associations between the human microbiota and reservoir of latent HIV.},
journal = {Retrovirology},
volume = {21},
number = {1},
pages = {21},
pmid = {39614246},
issn = {1742-4690},
support = {847943//European Union's Horizon 2020 Research and Innovation/ ; },
mesh = {Humans ; *HIV Infections/virology/microbiology/immunology ; *Virus Latency ; *HIV-1/physiology ; *Microbiota ; *Gastrointestinal Microbiome ; Virus Replication ; Disease Reservoirs/virology/microbiology ; },
abstract = {BACKGROUND: The rapid establishment and persistence of latent HIV-1 reservoirs is one of the main obstacles towards an HIV cure. While antiretroviral therapy supresses viral replication, it does not eradicate the latent reservoir of HIV-1-infected cells. Recent evidence suggests that the human microbiome, particularly the gut microbiome, may have the potential to modulate the HIV-1 reservoir. However, literature is limited and the exact mechanisms underlying the role of the microbiome in HIV immunity and potential regulation of the viral reservoir remain poorly understood.

RESULTS: Here, we review updated knowledge on the associations between the human microbiome and HIV reservoir across different anatomical sites, including the gut, the lungs and blood. We provide an overview of the predominant taxa associated with prominent microbiome changes in the context of HIV infection. Based on the current evidence, we summarize the main study findings, with specific focus on consistent bacterial and related byproduct associations. Specifically, we address the contribution of immune activation and inflammatory signatures on HIV-1 persistence. Furthermore, we discuss possible scenarios by which bacterial-associated inflammatory mediators, related metabolites and host immune signatures may modulate the HIV reservoir size. Finally, we speculate on potential implications of microbiome-based therapeutics for future HIV-1 cure strategies, highlighting challenges and limitations inherent in this research field.

CONCLUSIONS: Despite recent advances, this review underscores the need for further research to deepen the understanding of the complex interplay between the human microbiome and HIV reservoir. Further integrative multi-omics assessments and functional studies are crucial to test the outlined hypothesis and to identify potential therapeutic targets ultimately able to achieve an effective cure for HIV.},
}

Humans
*HIV Infections/virology/microbiology/immunology
*Virus Latency
*HIV-1/physiology
*Microbiota
*Gastrointestinal Microbiome
Virus Replication
Disease Reservoirs/virology/microbiology

@article {pmid39607341,
year = {2024},
author = {Merk, LN and Shur, AS and Jena, S and Munoz, J and Brubaker, DK and Murray, RM and Green, LN},
title = {Diagnostic and Therapeutic Microbial Circuit with Application to Intestinal Inflammation.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.3c00668},
pmid = {39607341},
issn = {2161-5063},
abstract = {Bacteria genetically engineered to execute defined therapeutic and diagnostic functions in physiological settings can be applied to colonize the human microbiome, providing in situ surveillance and conditional disease modulation. However, many engineered microbes can only respond to single-input environmental factors, limiting their tunability, precision, and effectiveness as living diagnostic and therapeutic systems. For engineering microbes to improve complex chronic disorders such as inflammatory bowel disease, the bacteria must respond to combinations of stimuli in the proper context and time. This work implements a previously characterized split activator AND logic gate in the probiotic Escherichia coli strain Nissle 1917 (EcN). Our system can respond to two input signals: the inflammatory biomarker tetrathionate and a second input signal, anhydrotetracycline (aTc), for manual control. We report 4-6 fold induction with a minimal leak when the two chemical signals are present. We model the AND gate dynamics using chemical reaction networks and tune parameters in silico to identify critical perturbations that affect our circuit's selectivity. Finally, we engineer the optimized AND gate to secrete a therapeutic anti-inflammatory cytokine IL-22 using the hemolysin secretion pathway in the probiotic E. coli strain. We used a germ-free transwell model of the human gut epithelium to show that our engineering bacteria produce similar host cytokine responses compared to recombinant cytokine. Our study presents a scalable workflow to engineer cytokine-secreting microbes driven by logical signal processing. It demonstrates the feasibility of IL-22 derived from probiotic EcN with minimal off-target effects in a gut epithelial context.},
}

@article {pmid39602306,
year = {2024},
author = {Pasolli, E and Mauriello, IE and Avagliano, M and Cavaliere, S and De Filippis, F and Ercolini, D},
title = {Bifidobacteriaceae diversity in the human microbiome from a large-scale genome-wide analysis.},
journal = {Cell reports},
volume = {43},
number = {12},
pages = {115027},
doi = {10.1016/j.celrep.2024.115027},
pmid = {39602306},
issn = {2211-1247},
abstract = {We performed a large-scale genome-wide analysis aiming to investigate the prevalence and strain-level diversity of Bifidobacteriaceae species in the human microbiome. We considered 9,528 publicly available human metagenomes and integrated them with 1,192 isolate genomes from different sources. The prevalence and abundance of Bifidobacteriaceae species in humans was linked to multiple host characteristics: they were reduced in older people and enriched in populations characterized by Westernized lifestyles with geography-specific patterns. Phylogenetic analysis highlighted 110 Bifidobacteriaceae species-level genome bins (SGBs), with 32 found in humans and 8 in food and probiotic sources. Functional annotation revealed a great diversity in carbohydrate-active enzyme families across these SGBs. We found potential subspecies for most of the SGBs prevalent in humans and identified patterns driven by age and geography. We provided evidence that strains used in probiotics were rarely identified in humans, with the only exception represented by Bifidobacterium animalis. We finally evaluated that the abundance of Bifidobacteriaceae species exhibited moderate and variable capabilities to predict health status in case-control studies.},
}

@article {pmid39600874,
year = {2024},
author = {Patjas, A and Jokiranta, TS and Kantele, A},
title = {Urinary tract infections: a retrospective cohort study of (mis)matching antimicrobial therapy and clinical outcome among Finnish adults.},
journal = {JAC-antimicrobial resistance},
volume = {6},
number = {6},
pages = {dlae188},
pmid = {39600874},
issn = {2632-1823},
abstract = {OBJECTIVES: With the global spread of antimicrobial resistance, treating urinary tract infections (UTIs) is becoming more challenging. Clinical data on UTI outcomes are scarce in cases with antimicrobial treatment mismatching the uropathogens' in vitro susceptibility profiles. We explored the association of (mis)matching antimicrobial treatment and clinical outcomes among patients with either ESBL-producing Enterobacterales (ESBL-PE) or non-ESBL-PE identified in urine samples.

PATIENTS AND METHODS: In 2015-2019, we recruited 18-65-year-old patients with laboratory-confirmed, community-acquired ESBL-PE (n = 130) or non-ESBL-PE (n = 187) UTI. Our study involved collecting data on in vitro susceptibility profiles, antimicrobial therapy (microbiological match/mismatch) and clinical outcomes, and a follow-up of relapses/reinfections.

RESULTS: Non-beta-lactam co-resistance was found more frequent among ESBL-PE than non-ESBL-PE isolates. The initial antimicrobial matched the in vitro susceptibility for 91.6% (164/179) of those with non-ESBL-PE and 46.9% (38/81) with ESBL-PE UTI (P < 0.001). The clinical cure rates in the non-ESBL-PE and ESBL-PE UTI groups were 82.6% (142/172) and 62.2% (74/119) (P < 0.001) for all, 87.3% (131/150) and 83.3% (30/36) for those treated with matching antimicrobials, and 33.3% (5/15) and 41.9% (18/43) for those given mismatching antimicrobials, respectively. Mismatching antimicrobial therapy was not associated with relapse/reinfection over the 3-month follow-up (P = 0.943).

CONCLUSIONS: In our data, (mis)matching microbiological susceptibility is only partially associated with the clinical outcome of UTI: microbiological matching appears to predict clinical cure better than mismatching predicts clinical failure.},
}

@article {pmid39600755,
year = {2024},
author = {Castro-Vidal, ZA and Mathew, F and Ibrahim, AA and Shubhangi, F and Cherian, RR and Choi, HK and Begum, A and Ravula, HK and Giri, H},
title = {The Role of Gastrointestinal Dysbiosis and Fecal Transplantation in Various Neurocognitive Disorders.},
journal = {Cureus},
volume = {16},
number = {10},
pages = {e72451},
pmid = {39600755},
issn = {2168-8184},
abstract = {This review explores the critical role of the human microbiome in neurological and neurodegenerative disorders, focusing on gut-brain axis dysfunction caused by dysbiosis, an imbalance in gut bacteria. Dysbiosis has been linked to diseases such as Alzheimer's disease, Parkinson's disease (PD), multiple sclerosis (MS), and stroke. The gut microbiome influences the central nervous system (CNS) through signaling molecules, including short-chain fatty acids, neurotransmitters, and metabolites, impacting brain health and disease progression. Emerging therapies, such as fecal microbiota transplantation (FMT), have shown promise in restoring microbial balance and alleviating neurological symptoms, especially in Alzheimer's and PD. Additionally, nutritional interventions such as probiotics, prebiotics, and specialized diets are being investigated for their ability to modify gut microbiota and improve patient outcomes. This review highlights the therapeutic potential of gut microbiota modulation but emphasizes the need for further clinical trials to establish the safety and efficacy of these interventions in neurological and mental health disorders.},
}

@article {pmid39596404,
year = {2024},
author = {Wang, Z and Kaplan, RC and Burk, RD and Qi, Q},
title = {The Oral Microbiota, Microbial Metabolites, and Immuno-Inflammatory Mechanisms in Cardiovascular Disease.},
journal = {International journal of molecular sciences},
volume = {25},
number = {22},
pages = {},
doi = {10.3390/ijms252212337},
pmid = {39596404},
issn = {1422-0067},
support = {K01 HL169019/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Cardiovascular Diseases/microbiology/immunology/metabolism ; *Mouth/microbiology ; Inflammation/microbiology/metabolism/immunology ; Gastrointestinal Microbiome ; Microbiota ; Animals ; },
abstract = {Cardiovascular diseases (CVDs) remain a leading cause of global morbidity and mortality. Recent advancements in high-throughput omics techniques have enhanced our understanding of the human microbiome's role in the development of CVDs. Although the relationship between the gut microbiome and CVDs has attracted considerable research attention and has been rapidly evolving in recent years, the role of the oral microbiome remains less understood, with most prior studies focusing on periodontitis-related pathogens. In this review, we summarized previously reported associations between the oral microbiome and CVD, highlighting known CVD-associated taxa such as Porphyromonas gingivalis, Fusobacterium nucleatum, and Aggregatibacter actinomycetemcomitans. We also discussed the interactions between the oral and gut microbes. The potential mechanisms by which the oral microbiota can influence CVD development include oral and systemic inflammation, immune responses, cytokine release, translocation of oral bacteria into the bloodstream, and the impact of microbial-related products such as microbial metabolites (e.g., short-chain fatty acids [SCFAs], trimethylamine oxide [TMAO], hydrogen sulfide [H2S], nitric oxide [NO]) and specific toxins (e.g., lipopolysaccharide [LPS], leukotoxin [LtxA]). The processes driven by these mechanisms may contribute to atherosclerosis, endothelial dysfunction, and other cardiovascular pathologies. Integrated multi-omics methodologies, along with large-scale longitudinal population studies and intervention studies, will facilitate a deeper understanding of the metabolic and functional roles of the oral microbiome in cardiovascular health. This fundamental knowledge will support the development of targeted interventions and effective therapies to prevent or reduce the progression from cardiovascular risk to clinical CVD events.},
}

Humans
*Cardiovascular Diseases/microbiology/immunology/metabolism
*Mouth/microbiology
Inflammation/microbiology/metabolism/immunology
Gastrointestinal Microbiome
Microbiota
Animals

@article {pmid39595814,
year = {2024},
author = {Belnap, N and Ramsey, K and Carvalho, ST and Nearman, L and Haas, H and Huentelman, M and Lee, K},
title = {Exploring the Frontier: The Human Microbiome's Role in Rare Childhood Neurological Diseases and Epilepsy.},
journal = {Brain sciences},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/brainsci14111051},
pmid = {39595814},
issn = {2076-3425},
abstract = {Emerging research into the human microbiome, an intricate ecosystem of microorganisms residing in and on our bodies, reveals that it plays a pivotal role in maintaining our health, highlighting the potential for microbiome-based interventions to prevent, diagnose, treat, and manage a myriad of diseases. The objective of this review is to highlight the importance of microbiome studies in enhancing our understanding of rare genetic epilepsy and related neurological disorders. Studies suggest that the gut microbiome, acting through the gut-brain axis, impacts the development and severity of epileptic conditions in children. Disruptions in microbial composition can affect neurotransmitter systems, inflammatory responses, and immune regulation, which are all critical factors in the pathogenesis of epilepsy. This growing body of evidence points to the potential of microbiome-targeted therapies, such as probiotics or dietary modifications, as innovative approaches to managing epilepsy. By harnessing the power of the microbiome, we stand to develop more effective and personalized treatment strategies for children affected by this disease and other rare neurological diseases.},
}

@article {pmid39595625,
year = {2024},
author = {Reshetova, M and Markin, P and Appolonova, S and Yunusov, I and Zolnikova, O and Bueverova, E and Dzhakhaya, N and Zharkova, M and Poluektova, E and Maslennikov, R and Ivashkin, V},
title = {Tryptophan Metabolites in the Progression of Liver Diseases.},
journal = {Biomolecules},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/biom14111449},
pmid = {39595625},
issn = {2218-273X},
mesh = {Humans ; *Tryptophan/metabolism/blood ; Male ; Female ; Middle Aged ; Adult ; Kynurenine/analogs & derivatives/metabolism/blood ; Disease Progression ; Liver Diseases, Alcoholic/metabolism/blood ; Serotonin/metabolism/blood ; Aged ; Fatty Liver/metabolism/blood ; Liver Cirrhosis/metabolism/blood ; },
abstract = {The aim of this study was to investigate the levels of various tryptophan metabolites in patients with alcoholic liver disease (ALD) and metabolic-associated fatty liver disease (MAFLD) at different stages of the disease. The present study included 44 patients diagnosed with MAFLD, 40 patients diagnosed with ALD, and 14 healthy individuals in the control group. The levels of tryptophan and its 16 metabolites (3-OH anthranilic acid, 5-hydroxytryptophan, 5-methoxytryptamine, 6-hydroxymelatonin, indole-3-acetic acid, indole-3-butyric, indole-3-carboxaldehyde, indole-3-lactic acid, indole-3-propionic acid, kynurenic acid, kynurenine, melatonin, quinolinic acid, serotonin, tryptamine, and xanthurenic acid) in the serum were determined via high-performance liquid chromatography and tandem mass spectrometry. In patients with cirrhosis resulting from MAFLD and ALD, there are significant divergent changes in the serotonin and kynurenine pathways of tryptophan catabolism as the disease progresses. All patients with cirrhosis showed a decrease in serotonin levels ([MAFLD]p = 0.038; [ALD]p < 0.001) and an increase in kynurenine levels ([MAFLD]p = 0.032; [ALD]p = 0.010). A negative correlation has been established between serotonin levels and the FIB-4 index (p < 0.001). The decrease in serotonin pathway metabolites was associated with manifestations of portal hypertension (p = 0.026), the development of hepatocellular insufficiency (p = 0.008) (hypoalbuminemia; hypocoagulation), and jaundice (p < 0.001), while changes in the kynurenine pathway metabolite xanthurenic acid were associated with the development of hepatic encephalopathy (p = 0.044). Depending on the etiological factors of cirrhosis, disturbances in the metabolic profile may be involved in various pathogenetic pathways.},
}

Humans
*Tryptophan/metabolism/blood
Male
Female
Middle Aged
Adult
Kynurenine/analogs & derivatives/metabolism/blood
Disease Progression
Liver Diseases, Alcoholic/metabolism/blood
Serotonin/metabolism/blood
Aged
Fatty Liver/metabolism/blood
Liver Cirrhosis/metabolism/blood

@article {pmid39589128,
year = {2024},
author = {Agnew, A and Humm, E and Zhou, K and Gunsalus, RP and Zhou, ZH},
title = {Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate.},
journal = {mBio},
volume = {},
number = {},
pages = {e0309024},
doi = {10.1128/mbio.03090-24},
pmid = {39589128},
issn = {2150-7511},
abstract = {Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID, toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5'-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.IMPORTANCEArchaea are one of the three domains of life, classified as a phylogenetically distinct lineage. There is a paucity of known enzyme structures from organisms of this domain, and this is often exacerbated by characteristically difficult growth conditions and a lack of readily available molecular biology toolkits to study proteins in archaeal cells. As a result, there is a gap in knowledge concerning the mechanisms governing archaeal protein behavior and their impacts on both the environment and human health; case in point, the synthesis of the widely utilized cofactor pyridoxal 5'-phosphate (PLP; a vitamer of vitamin B6, which humans cannot produce). By leveraging the power of single-particle cryo-EM and map-to-primary sequence identification, we determine the native structure of PLP synthase from cellular lysate. Our workflow allows the (i) rapid examination of new or less characterized systems with minimal sample requirements and (ii) discovery of structural states inaccessible by recombinant expression.},
}

@article {pmid39584055,
year = {2024},
author = {Kajova, M and Khawaja, T and Levonen, I and Pietilä, JP and Virtanen, J and Pakkanen, SH and Välimaa, H and Nousiainen, A and Hepojoki, J and Sironen, T and Vierikko, A and Ihalainen, J and Vapalahti, O and Kantele, A},
title = {Convalescent plasma therapy for COVID-19 - Donor selection strategies and establishment of a plasma bank.},
journal = {New microbes and new infections},
volume = {62},
number = {},
pages = {101525},
pmid = {39584055},
issn = {2052-2975},
abstract = {BACKGROUND: Early in the COVID-19 pandemic, convalescent plasma (CP) emerged as a potentially effective treatment neutralising SARS-CoV-2. Early CP therapy with high neutralising antibody (NAb) titre may benefit COVID-19 outpatients and, in sufficient quantities even some hospitalised patients. This study details the process of setting up a CP bank, containing high- and low-titre CP for a clinical trial.

STUDY DESIGN AND METHODS: We identified 18-65-year-old convalescents with SARS-CoV-2 NAb titres of ≥1:40 in microneutralisation test (MNT). Following eligibility pre-screening, the Finnish Red Cross Blood Service (FRCBS) determined suitability as CP donors.

RESULTS: Of the 6466 COVID-19 convalescents contacted, 1481 provided serum, with 851 (57.5 %) exhibiting NAb titres ≥1:40. Participation barriers included reluctance, advanced age and, for women, insufficient body size. Of the volunteers, 125 were evaluated at FRCBS, with major exclusions for HLA antibodies (42 women), interferon antibodies (five men), and NAb titres waning below 1:20 (16 participants). Finally, 70 underwent plasmapheresis, resulting in 50 suitable CP donors (0.8 % of initial contacts and 3.4 % of those tested for NAb).

DISCUSSION: The process of setting up a CP bank proved challenging. Excessive laboratory workloads during a pandemic hamper their ability to conduct MNT, underscoring the need for rapid screening tests. Only a small proportion of our convalescents exhibited high-titre CP, this fraction declining over time because of waning immunity. Strict plasmapheresis criteria further constrained donor eligibility. Establishing a plasma bank requires meticulous planning to maximize efficiency. Detailed insights from current experiences may prove critical in future pandemics before other remedies and vaccines become available.},
}

@article {pmid39582897,
year = {2024},
author = {Wang, Z and Wu, X and Wang, Y and Wen, Q and Cui, B and Zhang, F},
title = {Colonic transendoscopic enteral tubing is revolutionizing intestinal therapeutics, diagnosis, and microbiome research.},
journal = {Therapeutic advances in gastroenterology},
volume = {17},
number = {},
pages = {17562848241301574},
pmid = {39582897},
issn = {1756-283X},
abstract = {The intestine, as a crucial organ of the human body, has remained enigmatic despite the remarkable advancements in modern medical technology. Over the past decades, the invention of endoscopic technology has made the noninvasive intervention of the intestine a reality, expanding diagnostic and therapeutic options for diseases. However, due to the single-treatment feature of endoscopic procedures, continuous or repeated medication administration, sampling, and decompression drainage within the intestine have yet to be fulfilled. These limitations persisted until the invention of colonic transendoscopic enteral tubing (TET) in 2014, which realized repeated fecal microbiota transplantation, medication administration, and decompression drainage for the treatment of colon perforation and intestinal obstruction, as well as in situ dynamic sampling. These breakthroughs have not gone unnoticed, gaining global attention and recommendations from guidelines and consensuses. TET has emerged as a novel microbial research tool that offers new paradigms for human microbiome research. This review aims to update the research progress based on TET.},
}

@article {pmid39581825,
year = {2024},
author = {Isali, I and Almassi, N and Nizam, A and Campbell, R and Weight, C and Gupta, S and Pooja, G and Fulmes, A and Mishra, K and Abbosh, P and Bukavina, L},
title = {State of the Art: The Microbiome in Bladder Cancer.},
journal = {Urologic oncology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.urolonc.2024.11.008},
pmid = {39581825},
issn = {1873-2496},
abstract = {This review assesses the current understanding of the relationship between the human microbiome and BCa. Recognizing how the microbiome affects the tumor microenvironment provides valuable insights into cancer biology, potentially uncovering interactions that could be leveraged to develop innovative therapeutic approaches. By clarifying these intricate microbial-tumor dynamics, novel targets for microbiome-based interventions can be identified, ultimately improving treatment effectiveness and patient outcomes. Current literature lacks comprehensive insights into the effects of BCa treatment on the microbiome and the prevalence of immunotherapy-related toxicities. Further research into the microbiome's role in BCa development could bridge the gap between fundamental research and therapeutic applications. Implementing microbiome surveillance, metagenomic sequencing, and metabolomics in clinical trials could deepen our understanding of BCa and its treatment. This review explores the existing understanding of the urine, tissue, and gut microbiomes and their connections to BCa. Enhanced knowledge of these relationships can pave the way for future research to identify reliable disease predictors, prognostic markers, and novel therapeutic targets.},
}

@article {pmid39575247,
year = {2024},
author = {Zhu, Y and Liang, X and Zhi, M and Li, L and Zhang, G and Chen, C and Wang, L and Wang, P and Zhong, N and Feng, Q and Li, Z},
title = {Succession of the multi-site microbiome along pancreatic ductal adenocarcinoma tumorigenesis.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1487242},
pmid = {39575247},
issn = {1664-3224},
mesh = {Humans ; *Carcinoma, Pancreatic Ductal/microbiology/pathology ; *Pancreatic Neoplasms/microbiology/pathology ; Male ; Female ; Microbiota ; Middle Aged ; Saliva/microbiology ; Aged ; Carcinogenesis ; Bacteria/classification/genetics ; Pancreatitis, Chronic/microbiology ; RNA, Ribosomal, 16S/genetics ; Adult ; },
abstract = {BACKGROUND: To investigate microbial characteristics across multibody sites from chronic pancreatitis (CP), through pancreatic benign tumors, to pancreatic ductal adenocarcinoma (PDAC) at different stages.

METHODS: 16S ribosomal RNA (rRNA) amplicon sequencing was conducted on saliva, duodenal fluid, and pancreatic tissue obtained via endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) of patients with CP, pancreatic benign tumors, PDAC in stage I/II, III, and IV. The neutral community model (NCM) assessed the microbial assembly contribution and MaAslin2 identified the differential microbes.

RESULTS: From CP to stage IV PDAC patients, there was a marked surge in influence of salivary and duodenal microbiota on constitution of pancreatic microbial communities. Our observations revealed a successive alteration in microbial species across various bodily sites during PDAC tumorigenesis. Notably, Porphyromonas gingivalis, Treponema denticola, Peptoanaerobacter stomatis, Propionibacterium acidifaciens, Porphyromonas endodontalis, Filifactor alocis, etc., sequentially increased along PDAC progression in pancreatic tissue, whereas bacteria commonly used as probiotics Bifidobacterium breve, Lactiplantibacillus plantarum, etc., declined. Furthermore, the sequentially escalating trends of Peptoanaerobacter stomatis and Propionibacterium acidifaciens during PDAC tumorigenesis were mirrored in duodenal fluid and saliva. Porphyromonas gingivalis, Porphyromonas endodontalis, and Filifactor alocis, which intensified from CP to stage IV PDAC in pancreatic tissue, were also found to be enriched in saliva of patients with short-term survival (STS) compared with those with long-term survival (LTS).

CONCLUSIONS: Salivary and duodenal microorganisms were prominent factors in shaping pancreatic microbial landscape in PDAC context. Further exploration of these microbial entities is imperative to unravel their specific roles in PDAC pathogenesis, potentially yielding insights for future therapeutic strategies.},
}

Humans
*Carcinoma, Pancreatic Ductal/microbiology/pathology
*Pancreatic Neoplasms/microbiology/pathology
Male
Female
Microbiota
Middle Aged
Saliva/microbiology
Aged
Carcinogenesis
Bacteria/classification/genetics
Pancreatitis, Chronic/microbiology
RNA, Ribosomal, 16S/genetics
Adult

@article {pmid39575165,
year = {2024},
author = {Teng, Z and Li, Q and Shen, XF},
title = {Correlations of Nasal Microbiome with Allergic Rhinitis and Its Symptoms Severity in Children Progression.},
journal = {Journal of asthma and allergy},
volume = {17},
number = {},
pages = {1187-1196},
pmid = {39575165},
issn = {1178-6965},
abstract = {OBJECTIVE: Human microbiome is involved in the pathogenesis of allergic diseases, but the impact of nasal microbiota on allergic rhinitis (AR) symptoms severity has not been evaluated. This study aimed to characterize nasal microbiome in AR children and its correlations with AR symptoms.

METHODS: According to diagnostic guidelines for AR, 45 AR children and 40 healthy subjects were recruited from July to August in 2023. Based on the total score of nasal symptoms (TNSS), the 45 AR patients were divided into a mild AR group (MAR) (n = 16) and a moderate or severe AR group (MSAR) (n = 29). Nasal swabs were collected for microbiome analysis using 16S-rDNA sequencing.

RESULTS: The Simpson and Shannon indices were significantly higher in the AR group compared to the health control group, indicating an increase of nasal microbiota at the species evenness level in AR children. Moreover, the species evenness was significantly increased in the MSAR group compared to the MAR group. Staphylococcus (member of the Firmicutes phylum) was significantly dominant in the AR group, but Moraxella (member of the Proteobacteria phylum) was significantly dominant in the CG group. The LEfSe analysis showed that the mean relative abundances of Ralstonia in the MSAR group was higher than that in the MAR group. Meanwhile, the abundance divided by Ralstonia of Spearman correlation coefficients was positively correlated with the TNSS of AR symptoms (r = 0.4, P = 0.009).

CONCLUSION: The elevation of species evenness in nasal microbiome was likely related to the aggravation of AR symptoms. The Ralstonia may play a pro-inflammatory role in AR.},
}

@article {pmid39574598,
year = {2024},
author = {Nguyen, UT and Salamzade, R and Sandstrom, S and Swaney, MH and Townsend, EC and Wu, S and Cheong, JZA and Sardina, JA and Ludwikoski, I and Rybolt, M and Wan, H and Carlson, CM and Zaronowaki, R and Andes, DR and Currie, C and Kalan, L},
title = {Large-scale investigation for antimicrobial activity reveals novel defensive species across the healthy skin microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.04.621544},
pmid = {39574598},
issn = {2692-8205},
abstract = {The human skin microbiome constitutes a dynamic barrier that can impede pathogen invasion by producing antimicrobial natural products. Gene clusters encoding for production of secondary metabolites, biosynthetic gene clusters (BGCs), that are enriched in the human skin microbiome relative to other ecological settings, position this niche as a promising source for new natural product mining. Here, we introduce a new human microbiome isolate collection, the EPithelial Isolate Collection (EPIC). It includes a large phylogenetically diverse set of human skin-derived bacterial strains from eight body sites. This skin collection, consisting of 980 strains is larger and more diverse than existing resources, includes hundreds of rare and low-abundance species, and hundreds of unique BGCs. Using a large-scale co-culture screen to assess 8,756 pairwise interactions between skin-associated bacteria and potential pathogens, we reveal broad antifungal activity by skin microbiome members. Integrating 287 whole isolate genomes and 268 metagenomes from sampling sites demonstrates that while the distribution of BGC types is stable across body sites, specific gene cluster families (GCFs), each predicted to encode for a distinct secondary metabolite, can substantially vary. Sites that are dry or rarely moist harbor the greatest potential for discovery of novel bioactive metabolites. Among our discoveries are four novel bacterial species, three of which exert significant and broad-spectrum antifungal activity. This comprehensive isolate collection advances our understanding of the skin microbiomes biosynthetic capabilities and pathogen-fighting mechanisms, opening new avenues towards antimicrobial drug discovery and microbiome engineering.},
}

@article {pmid39571733,
year = {2024},
author = {Yu, J and Feng, L and Luo, Z and Yang, J and Zhang, Q and Liu, C and Liang, D and Xie, Y and Li, H and Gong, J and He, Z and Lan, P},
title = {Interleukin-10 deficiency suppresses colorectal cancer metastasis by enriching gut Parabacteroides distasonis.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2024.11.024},
pmid = {39571733},
issn = {2090-1224},
abstract = {INTRODUCTION: The intricate interplay of interleukin-10 (IL-10) and gut microbiota influences tumor development and progression, yet the impacts on colorectal cancer (CRC) metastasis remain incompletely understood.

METHODS: The impact of Il10 deficiency on CRC metastasis was first evaluated in CRC metastasis tumor samples and mouse model. Antibiotic sterilization and fecal microbiota transplantation (FMT) experiment were used to assess the role of gut microbiota in IL-10 mediated CRC metastasis, and full-length 16S rDNA sequencing analysis further identified the potential target bacteria influencing CRC metastasis. The inhibitory effect of Parabacteroides distasonis (P. distasonis) on CRC metastasis was evaluated by oral administration in mice. Key metabolites involved in P. distasonis inhibition of CRC metastasis was identified by widely-targeted metabolome analysis and validated both in vivo and in vitro. The underlying mechanisms of P-hydroxyphenyl acetic acid (4-HPAA) inhibiting CRC metastasis was investigated via RNA-sequencing and validated in cellular experiments.

RESULTS: We revealed that serum IL-10 levels were markedly elevated in metastatic CRC patients compared to non-metastatic cases. In parallel, Il10-deficiency (Il10[-/]) in mice resulted in decreased CRC metastasis in a gut microbiota-dependent manner. Mechanistically, Il10[-/-] mice reshaped gut microbiota composition, notably enriching P. distasonis. The enriched P. distasonis produced 4-HPAA, which activated the aryl hydrocarbon receptor (AHR) and subsequently inhibited the expression of VEGFA, a typical oncogene, thereby sequentially suppressing CRC metastasis. Importantly, engineered bacteria capable of producing 4-HPAA effectively hindered CRC metastasis. Furthermore, AHR depletion significantly disrupted the 4-HPAA-induced reduction in CRC cell migration and the inhibition of metastasis in both in vitro and in vivo lung metastasis mouse models.

CONCLUSIONS: These findings demonstrate the significance of IL-10 deficiency in suppressing CRC metastasis through the 4-HPPA-AHR-VEGFA axis mediated by gut P. distasonis, suggesting that P. distasonis or 4-HPAA supplementation could offer a promising therapeutic strategy for CRC metastasis prevention.},
}

@article {pmid39569373,
year = {2024},
author = {Talukdar, D and Sarkar, M and Ahrodia, T and Kumar, S and De, D and Nath, S and Jana, P and Verma, J and Mehta, O and Kothidar, A and Yodhaanjali, JR and Sharma, K and Bakshi, S and Singh, U and Kshetrapal, P and Wadhwa, N and Thiruvengadam, R and , and Nair, GB and Bhatnagar, S and Mukherjee, S and Das, B},
title = {Previse preterm birth in early pregnancy through vaginal microbiome signatures using metagenomics and dipstick assays.},
journal = {iScience},
volume = {27},
number = {11},
pages = {111238},
pmid = {39569373},
issn = {2589-0042},
abstract = {Annually, in India, 13% of all newborns are preterm, accounting for 23.4% of preterm birth (PTB) globally. The composition and diversity of the vaginal microbiome have a notable degree of ethnic inequality. For understanding differences in vaginal microbiome composition and functions between adverse and normal pregnancy, we have collected, processed and sequenced 600 high vaginal swab (HVS) samples across the three trimesters of pregnancy from 140 women who delivered at term and 60 women who delivered PTB, adopting a targeted metagenomics approach. The microbial signatures in HVS samples showed Lactobacillus genera to be highly abundant in term birth (TB), while in early pregnancy the abundances of Gardnerella, Atopobium, and Sneathia were found to be high in PTB. We further extended our analysis, identified specific microbial genomic signatures, and developed a dipstick assay for rapid identification of PTB-associated microbiota in HVS samples in low-resource settings.},
}

@article {pmid39565565,
year = {2024},
author = {Pino, A and Hiippala, K and Ronkainen, A and Vaccalluzzo, A and Caggia, C and Satokari, R and Randazzo, CL},
title = {Adhesion Properties and Pathogen Inhibition of Vaginal-Derived Lactobacilli.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {39565565},
issn = {1867-1314},
abstract = {In the present study, twenty-seven (27) lactobacilli strains, isolated from the vagina of healthy Italian women of reproductive age, were screened for probiotic properties. The strains were evaluated for antagonistic activity against pathogens, adhesion abilities, and potential to displace and/or inhibit the adhesion of previously adhered pathogens as a primary strain selection criterion. Overall, all the tested lactobacilli inhibited at least three pathogens, and the majority of them exhibited antimicrobial activity against Enterobacter cloacae DSM 30054, Pseudomonas aeruginosa DSM 3227, and Pseudomonas aeruginosa DSM 1117. The complete neutralization of antimicrobial activity after cell-free supernatant (CFS) neutralization suggested a pivotal role for lactic acid or other organic acids secreted by the lactobacilli. The strains showed variability in their adhesion levels, but all tested strains adhered to both human colonic epithelial cells (HT-29) and vaginal cells (VK2/E6E7) with adhesion percentages exceeding 1%. The ability to displace or inhibit pathogens was dependent on the pathogen and the lactobacilli strain; the pathogen displacement levels ranged from 9 to 82%, while pathogen exclusion levels varied from 1 to 99%. In conclusion, this study demonstrates the protective effect of vaginal lactobacilli against pathogens and confirms the suitability of the vaginal microbiota as a source of potential probiotic strains. The selected lactobacilli hold promise for the formulation of supplements to enhance genitourinary tract health.},
}

@article {pmid39565308,
year = {2024},
author = {Dong, PT and Shi, W and He, X and Borisy, GG},
title = {Adhesive interactions within microbial consortia can be differentiated at the single-cell level through expansion microscopy.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {48},
pages = {e2411617121},
doi = {10.1073/pnas.2411617121},
pmid = {39565308},
issn = {1091-6490},
support = {DE022586//HHS | NIH (NIH)/ ; DE023810//HHS | NIH (NIH)/ ; DE030943//HHS | NIH (NIH)/ ; K99DE033794//HHS | NIH (NIH)/ ; },
mesh = {*Biofilms/growth & development ; *Microbial Consortia/physiology ; *Bacterial Adhesion/physiology ; Single-Cell Analysis/methods ; Microscopy/methods ; Streptococcus/physiology ; Streptococcus mutans/physiology ; Fusobacterium nucleatum/physiology ; },
abstract = {Investigating microbe-microbe interactions at the single-cell level is critical to unraveling the ecology and dynamics of microbial communities. In many situations, microbes assemble themselves into densely packed multispecies biofilms. The density and complexity pose acute difficulties for visualizing individual cells and analyzing their interactions. Here, we address this problem through an unconventional application of expansion microscopy, which allows for the "decrowding" of individual bacterial cells within a multispecies community. Expansion microscopy generally has been carried out under isotropic expansion conditions and used as a resolution-enhancing method. In our variation of expansion microscopy, we carry out expansion under heterotropic conditions; that is, we expand the space between bacterial cells but not the space within individual cells. The separation of individual bacterial cells from each other reflects the competition between the expansion force pulling them apart and the adhesion force holding them together. We employed heterotropic expansion microscopy to study the relative strength of adhesion in model biofilm communities. These included mono- and dual-species Streptococcus biofilms and a three-species synthetic community (Fusobacterium nucleatum, Streptococcus mutans, and Streptococcus sanguinis) under conditions that facilitated interspecies coaggregation. Using adhesion mutants, we investigated the interplay between F. nucleatum outer membrane protein RadD and different Streptococcus species. We also examined the Schaalia-TM7 epibiont association. Quantitative proximity analysis was used to evaluate the separation of individual microbial members. Our study demonstrates that heterotropic expansion microscopy can "decrowd" dense biofilm communities, improve visualization of individual bacterial members, and enable analysis of microbe-microbe adhesive interactions at the single-cell level.},
}

*Biofilms/growth & development
*Microbial Consortia/physiology
*Bacterial Adhesion/physiology
Single-Cell Analysis/methods
Microscopy/methods
Streptococcus/physiology
Streptococcus mutans/physiology
Fusobacterium nucleatum/physiology

@article {pmid39563467,
year = {2024},
author = {Liu, R and Wang, Y and Cheng, D},
title = {Micro-DeMix: a mixture beta-multinomial model for investigating the heterogeneity of the stool microbiome compositions.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btae667},
pmid = {39563467},
issn = {1367-4811},
abstract = {MOTIVATION: Extensive research has uncovered the critical role of the human gut microbiome in various aspects of health, including metabolism, nutrition, physiology, and immune function. Fecal microbiota is often used as a proxy for understanding the gut microbiome, but it represents an aggregate view, overlooking spatial variations across different gastrointestinal (GI) locations. Emerging studies with spatial microbiome data collected from specific GI regions offer a unique opportunity to better understand the spatial composition of the stool microbiome.

RESULTS: We introduce Micro-DeMix, a mixture beta-multinomial model that deconvolutes the fecal microbiome at the compositional level by integrating stool samples with spatial microbiome data. Micro-DeMix facilitates the comparison of microbial compositions across different GI regions within the stool microbiome through a hypothesis-testing framework. We demonstrate the effectiveness and efficiency of Micro-DeMix using multiple simulated data sets and the Inflammatory Bowel Disease (IBD) data from the NIH Integrative Human Microbiome Project.

The R package is available at https://github.com/liuruoqian/MicroDemix.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid39562050,
year = {2024},
author = {Li, N and Li, Y and Huang, Z and Cao, Z and Cao, C and Gao, X and Zuo, T},
title = {Faecal phageome transplantation alleviates intermittent intestinal inflammation in IBD and the timing of transplantation matters: a preclinical proof-of-concept study in mice.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-333598},
pmid = {39562050},
issn = {1468-3288},
}

@article {pmid39561848,
year = {2024},
author = {Yang, J and Sun, S and Sun, N and Lu, L and Zhang, C and Shi, W and Zhao, Y and Jia, S},
title = {HMMER-extractor: An auxiliary toolkit for identifying genomic macromolecular metabolites based on hidden Markov models.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {137666},
doi = {10.1016/j.ijbiomac.2024.137666},
pmid = {39561848},
issn = {1879-0003},
abstract = {Human microbiome contains various microbial macromolecules with important biological functions. The Hidden Markov Models (HMMs) can overcome the problem of low similarity sequences with distant relationships and are widely implemented within various sequence alignment softwares. However, the HMM-based sequence alignments can generate a large number of results, how to quickly screen and batch extract target homologs from microbiomes is the major sticking points. It is necessary to develop an integrated gene filter and extraction pipeline to quickly and accurately screen homologs. Here, we introduced the HMMER-Extractor for amino acids or nucleotide sequences extraction, which was a supporting toolkit through provided filtering scores and an iterative keyword matching (IKM) logic. To make it more user-friendly and accessible, we further presented a visualized web server platform. An interactive HTML output provided a user-friendly way to browse homologous annotations and sequence extraction. The web server provided the community with a streamlined and user-friendly interface to analyze microbiomes. Through the HMMER-Extractor, we constructed a cardiovascular disease related gene dataset of the macromolecular metabolite trimethylamine (TMA) and lipopolysaccharide (LPS) based on 46,699 bacterial genomes from human gut. Approximately 21,014 and 1961 bacterial strains were identified to contain the cnt or cut operon of TMA, and the waa gene cluster of LPS, respectively. The Escherichia coli occupied the largest proportion among all the bacterial species, which belonged to the phyla Firmicutes. The HMMER-Extractor toolkit is an integrated pipeline and has been proven to be accurate and fast in extracting target macromolecular encoding genes from microbial genomes.},
}

@article {pmid39556491,
year = {2024},
author = {Shete, O and Ghosh, TS},
title = {Normal Gut Microbiomes in Diverse Populations: Clinical Implications.},
journal = {Annual review of medicine},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-med-051223-031809},
pmid = {39556491},
issn = {1545-326X},
abstract = {The human microbiome is a sensor and modulator of physiology and homeostasis. Remarkable tractability underpins the promise of therapeutic manipulation of the microbiome. However, the definition of a normal or healthy microbiome has been elusive. This is in part due to the underrepresentation of minority groups and major global regions in microbiome studies to date. We review studies of the microbiome in different populations and highlight a commonality among health-associated microbiome signatures along with major drivers of variation. We also provide an overview of microbiome-associated therapeutic interventions for some widespread, widely studied diseases. We discuss sources of bias and the challenges associated with defining population-specific microbiome reference bases. We propose a roadmap for defining normal microbiome references that can be used for population-customized microbiome therapeutics and diagnostics.},
}

@article {pmid39555415,
year = {2024},
author = {Chen, XY and Liu, Y and Zhu, WB and Li, SH and Wei, S and Cai, J and Lin, Y and Liang, JK and Yan, GM and Guo, L and Hu, C},
title = {Arming oncolytic M1 virus with gasdermin E enhances antitumor efficacy in breast cancer.},
journal = {iScience},
volume = {27},
number = {11},
pages = {111148},
pmid = {39555415},
issn = {2589-0042},
abstract = {Pyroptosis, driven by the N-terminal domain of gasdermin proteins (GSDM), promotes antitumor immunity by attracting lymphocytes to the tumor microenvironment (TME). However, current pyroptosis-inducing therapies like drug injections and phototherapy are limited to localized treatments, making them unsuitable for widespread or microscopic metastatic lesions. This study engineered oncolytic M1 viruses (rM1-mGSDME_FL and rM1-mGSDME_NT) to selectively deliver GSDME to tumor cells. These modified viruses enhanced tumor cell death in breast cancer models, suppressed tumor growth, extended survival in mice, and boosted immune cell infiltration, demonstrating significant anticancer potential through pyroptosis induction.},
}

@article {pmid39547283,
year = {2024},
author = {Zelasko, S and Swaney, MH and Sandstrom, S and Lee, KE and Dixon, J and Riley, C and Watson, L and Godfrey, JJ and Ledrowski, N and Rey, F and Safdar, N and Seroogy, CM and Gern, JE and Kalan, L and Currie, C},
title = {Early-life Upper Airway Microbiota are Associated with Decreased Lower Respiratory Tract Infections.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2024.11.008},
pmid = {39547283},
issn = {1097-6825},
abstract = {Microbial interactions mediating colonization resistance play key roles within the human microbiome, shaping susceptibility to infection from birth. To gain insight into microbiome-mediated defenses and respiratory pathogen colonization dynamics, we sequenced and analyzed nasal (n=229) and oral (n=210) microbiomes with associated health/environmental data from our Wisconsin Infant Study Cohort at age 24-months. Participants with early-life lower respiratory tract infection (LRTI) were more likely to be formula-fed, attend daycare, and experience wheezing. Shotgun metagenomic sequencing with detection of viral and bacterial respiratory pathogens revealed nasal microbiome composition to associate with prior LRTI - namely lower alpha diversity, depletion of Prevotella, and enrichment of Moraxella catarrhalis including drug-resistant strains. Prevotella originating from healthy microbiomes had higher biosynthetic gene cluster abundance and exhibited contact-independent inhibition of M. catarrhalis, suggesting interbacterial competition impacts nasal pathogen colonization. This work advances understanding of protective host-microbial interactions occurring in airway microbiomes that alter infection susceptibility in early-life.},
}

@article {pmid39545965,
year = {2024},
author = {Pawlik, MT and Rinneberg, G and Koch, A and Meyringer, H and Loew, TH and Kjellberg, A},
title = {Is there a rationale for hyperbaric oxygen therapy in the patients with Post COVID syndrome? : A critical review.},
journal = {European archives of psychiatry and clinical neuroscience},
volume = {},
number = {},
pages = {},
pmid = {39545965},
issn = {1433-8491},
abstract = {The SARS-CoV-2 pandemic has resulted in 762 million infections worldwide from 2020 to date, of which approximately ten percent are suffering from the effects after infection in 2019 (COVID-19) [1, 40]. In Germany, it is now assumed that at least one million people suffer from post-COVID condition with long-term consequences. These have been previously reported in diseases like Myalgic Encephalomyelitis (ME) and Chronic Fatigue Syndrome (CFS). Symptoms show a changing variability and recent surveys in the COVID context indicate that 10-30 % of outpatients, 50 to 70% of hospitalised patients suffer from sequelae. Recent data suggest that only 13% of all ill people were completely free of symptoms after recovery [3, 9]. Current hypotheses consider chronic inflammation, mitochondrial dysfunction, latent viral persistence, autoimmunity, changes of the human microbiome or multilocular sequelae in various organ system after infection. Hyperbaric oxygen therapy (HBOT) is applied since 1957 for heart surgery, scuba dive accidents, CO intoxication, air embolisms and infections with anaerobic pathogens. Under hyperbaric pressure, oxygen is physically dissolved in the blood in higher concentrations and reaches levels four times higher than under normobaric oxygen application. Moreover, the alternation of hyperoxia and normoxia induces a variety of processes at the cellular level, which improves oxygen supply in areas of locoregional hypoxia. Numerous target gene effects on new vessel formation, anti-inflammatory and anti-oedematous effects have been demonstrated [74]. The provision of intermittently high, local oxygen concentrations increases repair and regeneration processes and normalises the predominance of hyperinflammation. At present time only one prospective, randomized and placebo-controlled study exists with positive effects on global cognitive function, attention and executive function, psychiatric symptoms and pain interference. In conclusion, up to this date HBO is the only scientifically proven treatment in a prospective randomized controlled trial to be effective for cognitive improvement, regeneration of brain network and improvement of cardiac function. HBOT may have not only theoretical but also potential impact on targets of current pathophysiology of Post COVID condition, which warrants further scientific studies in patients.},
}

@article {pmid39545326,
year = {2024},
author = {Shah, AB and Shim, SH},
title = {Human microbiota peptides: important roles in human health.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4np00042k},
pmid = {39545326},
issn = {1460-4752},
abstract = {Covering: 1974 to 2024Human microbiota consist of a diverse array of microorganisms, such as bacteria, Eukarya, archaea, and viruses, which populate various parts of the human body and live in a cooperatively beneficial relationship with the host. They play a crucial role in supporting the functional balance of the microbiome. The coevolutionary progression has led to the development of specialized metabolites that have the potential to substitute traditional antibiotics in combating global health challenges. Although there has been a lot of research on the human microbiota, there is a considerable lack of understanding regarding the wide range of peptides that these microbial populations produce. Particularly noteworthy are the antibiotics that are uniquely produced by the human microbiome, especially by bacteria, to protect against invasive infections. This review seeks to fill this knowledge gap by providing a thorough understanding of various peptides, along with their in-depth biological importance in terms of human disorders. Advancements in genomics and the understanding of molecular mechanisms that control the interactions between microbiota and hosts have made it easier to find peptides that come from the human microbiome. We hope that this review will serve as a basis for developing new therapeutic approaches and personalized healthcare strategies. Additionally, it emphasizes the significance of these microbiota in the field of natural product discovery and development.},
}

@article {pmid39543873,
year = {2024},
author = {Saraswat, I and Goel, A},
title = {Therapeutic Modulation of the Microbiome in Oncology: Current Trends and Future Directions.},
journal = {Current pharmaceutical biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113892010353600241109132441},
pmid = {39543873},
issn = {1873-4316},
abstract = {Cancer is a predominant cause of mortality worldwide, necessitating the development of innovative therapeutic techniques. The human microbiome, particularly the gut microbiota, has become a significant element in cancer research owing to its essential role in sustaining health and influencing disease progression. This review examines the microbiome's makeup and essential functions, including immunological modulation and metabolic regulation, which may be evaluated using sophisticated methodologies such as metagenomics and 16S rRNA sequencing. The microbiome influences cancer development by promoting inflammation, modulating the immune system, and producing carcinogenic compounds. Dysbiosis, or microbial imbalance, can undermine the epithelial barrier and facilitate cancer. The microbiome influences chemotherapy and radiation results by modifying drug metabolism, either enhancing or reducing therapeutic efficacy and contributing to side effects and toxicity. Comprehending these intricate relationships emphasises the microbiome's significance in oncology and accentuates the possibility for microbiome-targeted therapeutics. Contemporary therapeutic approaches encompass the utilisation of probiotics and dietary components to regulate the microbiome, enhance treatment efficacy, and minimise unwanted effects. Advancements in research indicate that personalised microbiome-based interventions, have the potential to transform cancer therapy, by providing more effective and customised treatment alternatives. This study aims to provide a comprehensive analysis of the microbiome's influence on the onset and treatment of cancer, while emphasising current trends and future possibilities for therapeutic intervention.},
}

@article {pmid39541945,
year = {2024},
author = {Wu, J and Zeng, W and Xie, H and Cao, M and Yang, J and Xie, Y and Luo, Z and Zhang, Z and Xu, H and Huang, W and Zhou, T and Tan, J and Wu, X and Yang, Z and Zhu, S and Mao, R and He, Z and Lan, P},
title = {Microbiota-induced alteration of kynurenine metabolism in macrophages drives formation of creeping fat in Crohn's disease.},
journal = {Cell host & microbe},
volume = {32},
number = {11},
pages = {1927-1943.e9},
doi = {10.1016/j.chom.2024.10.008},
pmid = {39541945},
issn = {1934-6069},
abstract = {Hyperplasia of mesenteric tissues in Crohn's disease, called creeping fat (CrF), is associated with surgical recurrence. Although microbiota translocation and colonization have been found in CrF, convincing mouse phenotypes and the underlying mechanisms of CrF formation remain unclear. Utilizing single-nucleus RNA (snRNA) sequencing of CrF and different mouse models, we demonstrate that the commensal Achromobacter pulmonis induces mesenteric adipogenesis through macrophage alteration. Targeted metabolome analysis reveals that L-kynurenine is the most enriched metabolite in CrF. Upregulation of indoleamine 2,3-dioxygenase 1 (IDO1) enhances kynurenine metabolism and drives mesenteric adipogenesis. Leveraging single-cell RNA (scRNA) sequencing of mouse mesenteric tissues and macrophage-specific IDO1 knockout mice, we verify the role of macrophage-sourced L-kynurenine in mesenteric adipogenesis. Mechanistically, L-kynurenine-induced adipogenesis is mediated by the aryl hydrocarbon receptors in adipocytes. Administration of an IDO1 inhibitor or bacteria engineered to degrade L-kynurenine alleviates mesenteric adipogenesis in mice. Collectively, our study demonstrates that microbiota-induced modulation of macrophage metabolism potentiates CrF formation.},
}

@article {pmid39541940,
year = {2024},
author = {Monzel, E and Desai, MS},
title = {Bacterial small RNA makes a big impact for gut colonization.},
journal = {Cell host & microbe},
volume = {32},
number = {11},
pages = {1875-1877},
doi = {10.1016/j.chom.2024.10.010},
pmid = {39541940},
issn = {1934-6069},
abstract = {The functions of non-coding small RNAs (sRNAs) within the human microbiome remain largely unexplored. In this Cell Host & Microbe issue, El Mouali et al. identify Segatella RNA colonization factor (SrcF), a sRNA from a prevalent gut bacterium Segatella copri. SrcF promotes colonization of S. copri by regulating bacterial degradation of complex dietary carbohydrates.},
}

@article {pmid39540274,
year = {2024},
author = {Arcimowicz, M},
title = {Rational treatment of acute rhinosinusitis in the context of increasing antibiotic resistance.},
journal = {Otolaryngologia polska = The Polish otolaryngology},
volume = {78},
number = {6},
pages = {1-11},
doi = {10.5604/01.3001.0054.7506},
pmid = {39540274},
issn = {2300-8423},
mesh = {Humans ; *Sinusitis/drug therapy/microbiology ; *Rhinitis/drug therapy/microbiology ; *Anti-Bacterial Agents/therapeutic use ; Acute Disease ; Drug Resistance, Microbial ; Adult ; COVID-19 ; Drug Resistance, Bacterial ; Rhinosinusitis ; },
abstract = {Acute rhinosinusitis is one of the most common diseases in the population, both in primary and specialist otolaryngological care. It is also responsible for a disturbingly high percentage of prescribed antibiotic therapy, regardless of the etiology of the disease. Despite the fact that acute viral and acute postviral rhinosinusitis dominate among the phenotypes of acute rhinosinusitis, and the development of acute bacterial rhinosinusitis occurs in only 0.5-2% of all cases in adults and 5-10% in children, antibiotics still remain an important element of treatment, despite alarming data on the growing antibiotic resistance and the adverse effect of antibiotics on the human microbiome, leading to dysbiosis. The discovery of antibiotics was one of the greatest achievements of modern medicine, but their inappropriate use leads to the gradual increase in the phenomenon of antibiotic resistance, considered one of the most serious public health problems, recognized by the WHO as one of the 10 greatest threats to human health in the 21[st] century. The unjustified use of antibiotics in outpatient care is the key to the growth of this problem, in parallel with the lack of patient compliance. The COVID pandemic has intensified this unfavourable trend. That is why the knowledge of antibiotic stewardship is so important. According to the guidelines, in the therapy of acute rhinosinusitis, symptomatic and anti-inflammatory treatment dominates, and antibiotic therapy has very strictly defined and limited indications. The latest guidelines also recommend herbal medicines, including BNO 1016, in the treatment of acute viral and postviral rhinosinusitis. Available studies indicate that it has a beneficial effect not only on shortening the duration of the disease and reducing symptoms, but also reduces the need for antibiotic treatment in acute rhinosinusitis. Complications of acute rhinosinusitis are relatively rare and are not related to taking antibiotics.},
}

Humans
*Sinusitis/drug therapy/microbiology
*Rhinitis/drug therapy/microbiology
*Anti-Bacterial Agents/therapeutic use
Acute Disease
Drug Resistance, Microbial
Adult
COVID-19
Drug Resistance, Bacterial
Rhinosinusitis

@article {pmid39539377,
year = {2024},
author = {Efremova, I and Alieva, A and Maslennikov, R and Poluektova, E and Zharkova, M and Kudryavtseva, A and Krasnov, G and Zharikov, Y and Nerestyuk, Y and Karchevskaya, A and Ivashkin, V},
title = {Akkermansia muciniphila is associated with normal muscle mass and Eggerthella is related with sarcopenia in cirrhosis.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1438897},
doi = {10.3389/fnut.2024.1438897},
pmid = {39539377},
issn = {2296-861X},
abstract = {BACKGROUND: Sarcopenia and gut dysbiosis are common in cirrhosis. The aim is to study the correlations between the gut microbiota taxa and muscle mass level in cirrhosis.

METHODS: The study included 40 cirrhosis patients including 18 patients with sarcopenia. The gut microbiota composition was assessed using amplicon sequencing of the hypervariable V3-V4 regions of the 16S rRNA gene. The skeletal muscle mass, subcutaneous and visceral fat levels were assessed with abdominal computed tomography as skeletal muscle, subcutaneous and visceral fat indices (SMI, SFI and VFI).

RESULTS: Patients with sarcopenia had more relative abundance (RA) of Agathobacter, Anaerostipes, Butyricicoccus, Dorea, Eggerthella, Microbacteriaceae, Veillonella and less RA of Akkermansiaceae, Akkermansia muciniphila, Verrucomicrobiae and Bilophila compared to patients with normal muscle mass. SMI directly correlated with RA of Akkermansia, Alistipes indistinctus, Anaerotruncus, Atopobiaceae, Bacteroides clarus, Bacteroides salyersiae, Barnesiellaceae, Bilophila wadsworthia, Pseudomonadota, Olsenella, and Parabacteroides distasonis, and negatively correlated with RA of Anaerostipes and Eggerthella. Sarcopenia was detected in 20.0% patients whose gut microbiota had Akkermansia but not Eggerthella, and in all the patients, whose gut microbiota had Eggerthella but not Akkermansia. The Akkermansia and Eggerthella abundances were independent determinants of SMI. RA of Akkermansia, Akkermansia muciniphila, Akkermansiaceae, Bacteroides salyersiae, Barnesiella, Bilophila, Desulfobacterota, Verrucomicrobiota and other taxa correlated positively and RA of Anaerovoracaceae, Elusimicrobiaceae, Elusimicrobium, Kiritimatiellae, Spirochaetota, and other taxa correlated negatively with the SFI. RA of Alistripes, Romboutsia, Succinivibrio, and Succinivibrionaceae correlated positively and RA of Bacteroides thetaiotaomicron correlated negatively with VFI.

CONCLUSION: The muscle mass level in cirrhosis correlates with the abundance of several gut microbiota taxa, of which Akkermansia and Eggerthella seems to be the most important.},
}

@article {pmid39534501,
year = {2024},
author = {Koh, H},
title = {A general kernel machine regression framework using principal component analysis for jointly testing main and interaction effects: Applications to human microbiome studies.},
journal = {NAR genomics and bioinformatics},
volume = {6},
number = {4},
pages = {lqae148},
pmid = {39534501},
issn = {2631-9268},
abstract = {The effect of a treatment on a health or disease response can be modified by genetic or microbial variants. It is the matter of interaction effects between genetic or microbial variants and a treatment. To powerfully discover genetic or microbial biomarkers, it is crucial to incorporate such interaction effects in addition to the main effects. However, in the context of kernel machine regression analysis of its kind, existing methods cannot be utilized in a situation, where a kernel is available but its underlying real variants are unknown. To address such limitations, I introduce a general kernel machine regression framework using principal component analysis for jointly testing main and interaction effects. It begins with extracting principal components from an input kernel through the singular value decomposition. Then, it employs the principal components as surrogate variants to construct three endogenous kernels for the main effects, interaction effects, and both of them, respectively. Hence, it works with a kernel as an input without knowing its underlying real variants, and also detects either the main effects, interaction effects, or both of them robustly. I also introduce its omnibus testing extension to multiple input kernels, named OmniK. I demonstrate its use for human microbiome studies.},
}

@article {pmid39512939,
year = {2024},
author = {Costa, CFFA and Correia-de-Sá, T and Araujo, R and Barbosa, F and Burnet, PWJ and Ferreira-Gomes, J and Sampaio-Maia, B},
title = {The oral-gut microbiota relationship in healthy humans: identifying shared bacteria between environments and age groups.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1475159},
pmid = {39512939},
issn = {1664-302X},
abstract = {INTRODUCTION: Although the oral cavity and the gut are anatomically continuous regions of the gastrointestinal tract, research on the relationship between oral and gut microbiota remains sparse. Oral-gut bacterial translocation is mostly studied in pathological contexts, thus evidence of translocation in healthy conditions is still scarce. Studying the oral-gut microbiota relationship in humans in different life stages is necessary in order to understand how these microbial communities might relate throughout life.

METHODS: In this study, saliva and fecal samples were collected from healthy participants (39 children, 97 adults). Microbiota analysis was carried out by sequencing the V4 region of the 16S ribosomal RNA gene, followed by amplicon sequence variant (ASV) analysis.

RESULTS AND DISCUSSION: Although the oral and gut microbiota are vastly different, a subset of 61 ASVs were present in both the oral cavity and gut of the same individual, and represented 1.6% of all ASVs detected. From these, 26 ASVs (classified into 18 genera: Actinomyces, Rothia, Bacteroides, Porphyromonas, Prevotella, Alistipes, Fusobacterium, Neisseria, Haemophilus, Akkermansia, Solobacterium, Granulicatella, Streptococcus, Gemella, Mogibacterium, Dialister, Veillonella, Christensenellaceae R-7 group) were present in both children and adults, suggesting the possibility of persistent colonization of both habitats by these microorganisms, initiating in childhood. Additionally, 62% of shared ASVs were more abundant in the oral cavity, indicating that oral-to-gut translocation may be the main route of translocation between environments, and highlighting that this phenomenon might be more common than previously thought in healthy individuals of all ages.},
}

@article {pmid39531852,
year = {2024},
author = {Simbirtseva, KY and O'Toole, PW},
title = {Healthy and Unhealthy Aging and the Human Microbiome.},
journal = {Annual review of medicine},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-med-042423-042542},
pmid = {39531852},
issn = {1545-326X},
abstract = {An altered gut microbiome is a feature of many multifactorial diseases, and microbiome effects on host metabolism, immune function, and possibly neurological function are implicated. Increased biological age is accompanied by a change in the gut microbiome. However, age-related health loss does not occur uniformly across all subjects but rather depends on differential loss of gut commensals and gain of pathobionts. In this article, we summarize the known and possible effects of the gut microbiome on the hallmarks of aging and describe the most plausible mechanisms. Understanding and targeting these factors could lead to prolonging health span by rationally maintaining the gut microbiome.},
}